From Sumei.Wang at uphs.upenn.edu Wed Jan 7 16:39:57 2009 From: Sumei.Wang at uphs.upenn.edu (Wang, Sumei) Date: Wed, 07 Jan 2009 16:39:57 -0500 Subject: [Mristudio-users] 16 direction Philips gradient tables In-Reply-To: <73alti$34bjq7@ipex2.johnshopkins.edu> Message-ID: <4BFD060857263F43AEA4C10586DDE44603C80471@uphsmbx8.UPHS.PENNHEALTH.PRV> Hi all, Does anybody have 16 direction gradient table (medium) for Philips system? I searched the forum and just got 15 dir gradient table as follows. Thanks for your help. Sumei -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org]On Behalf Of susumu Sent: Friday, July 25, 2008 7:13 AM To: 'DTI Studio, ROI Editor, Landmarker Questions/Support' Subject: Re: [Mristudio-users] Philips gradient tables Seongjin, In Philips, there are 3 types (low: 6, medium: 15, high: 32) x 2 (overplus on/off) = 6 gradient tables. The "gradient overplus = on" always use at least two gradients to enhance b efficiency and therefore gaining several millisecond of echo time. In your example, the low and high is "overplus = off" and the medium is "overplus = on". You can see "1, 0, 0" in the first two but not in the medium. The medium with "overplus = off" should look like; 0: 0, 0, 0 1: 1, 0, 0 2: 0, 1, 0 3: 0, 0, 1 4: -0.0424,-0.1146,-0.9925 5: 0.1749,-0.2005,-0.9639 6: 0.2323,-0.1626,-0.9590 7: 0.3675,0.0261,-0.9296 8: 0.1902,0.3744,-0.9076 9: -0.1168,0.8334,-0.5402 10: -0.2005,0.2527,-0.9466 11: -0.4958,0.1345,-0.8580 12: -0.0141,-0.6281,-0.7780 13: -0.7445,-0.1477,-0.6511 14: -0.7609,0.3204,-0.5643 15: -0.1809,0.9247,-0.33510 16: -0.6796,-0.4224,-0.5997 17: 0.7771,0.4707,-0.4178 18: 0.9242,-0.1036,-0.3677 19: 0.4685,-0.7674,-0.4378 20: 0.8817,-0.1893,-0.4322 21: 0.6904,0.7062,-0.1569 22: 0.2391,0.7571,-0.6080 23: -0.0578,0.9837,0.1703 24: -0.5368,0.8361,-0.1135 25: -0.9918,-0.1207,-0.0423 26: -0.9968,0.0709,-0.0379 27: -0.8724,0.4781,-0.1014 28: -0.2487,0.9335,0.2581 29: 0.1183,0.9919,-0.0471 30: 0.3376,0.8415,0.4218 31: 0.5286,0.8409,0.1163 32: 0.9969,0.0550,-0.0571 In general, I do not recommend to user "overplus = on", because tensor calculation get complicated when oblique planes are used. You have to recalculate the table based on the image angles. Also, please note that the "0, 0, 0" could be the first or the last image depending on how you specify the output files. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of [Seongjin] Sent: Wednesday, July 23, 2008 3:47 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] Philips gradient tables Dear DTIstudio users, I wonder if you have gradient tables for Philips Achieva system. >From a source I have a gradient table for low resolution as follows: 0:1.0000, 0.0000, 0.0000 1:0.0000, 1.0000, 0.0000 2:0.0000, 0.0000, 1.0000 3:-0.7044, -0.0881, -0.7044 4:0.7044, 0.7044, 0.0881 5:0.0881, 0.7044, 0.7044 6:0.0000, 0.0000, 0.0000 For medium, 0: 0.7071 -0.7071 1.00 1: 0.7071 -0.7071 -1.00 2: 1.0000 1.0000 0.0000 3: 0.9999 -0.1561 0.9879 4: 0.9894 0.4091 0.9240 5: 0.4674 0.8874 0.9970 6: 0.3866 0.9297 0.9930 7: 0.7667 -0.9511 0.7124 8: 0.6945 0.9954 -0.7295 9: 0.3580 -0.9800 -0.9547 10: 1.0000 -0.9992 -0.0392 11: 0.9999 -0.3989 -0.9171 12: 0.9923 0.4082 -0.9213 13: 0.9989 0.9982 -0.0759 14: 0.2899 0.9919 -0.9655 15: 0.0000 0.0000 0.0000 For high, 0: 1.000, 0.000, 0.000 1: 0.000, 1.000, 0.000 2: 0.000, 0.000, 1.000 3: -0.042, -0.115, -0.993 4: 0.175, -0.200, -0.964 5: 0.232, -0.163, -0.959 6: 0.368, 0.026, -0.930 7: 0.190, 0.374, -0.908 8: -0.117, 0.833, -0.540 9: -0.200, 0.253, -0.947 10: -0.496, 0.134, -0.858 11: -0.014, -0.628, -0.778 12: -0.744, -0.148, -0.651 13: -0.761, 0.320, -0.564 14: -0.181, 0.925, -0.335 15: -0.680, -0.422, -0.600 16: 0.777, 0.471, -0.418 17: 0.924, -0.104, -0.368 18: 0.468, -0.767, -0.438 19: 0.882, -0.189, -0.432 20: 0.690, 0.706, -0.157 21: 0.239, 0.757, -0.608 22: -0.058, 0.984, 0.170 23: -0.537, 0.836, -0.113 24: -0.992, -0.121, -0.042 25: -0.997, 0.071, -0.038 26: -0.872, 0.478, -0.101 27: -0.249, 0.933, 0.258 28: 0.118, 0.992, -0.047 29: 0.338, 0.841, 0.422 30: 0.529, 0.841, 0.116 31: 0.997, 0.055, -0.057 32: 0.000, 0.000, 0.000 I wonder if the tables above are correct or not. Is there anything incorrect or partially incomplete, please let me know. Thanks in advance. Sincerely, Seongjin The information contained in this e-mail message is intended only for the personal and confidential use of the recipient(s) named above. If the reader of this message is not the intended recipient or an agent responsible for delivering it to the intended recipient, you are hereby notified that you have received this document in error and that any review, dissemination, distribution, or copying of this message is strictly prohibited. If you have received this communication in error, please notify us immediately by e-mail, and delete the original message. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090107/f18d5438/attachment-0001.html From choisj70 at gmail.com Wed Jan 7 19:27:12 2009 From: choisj70 at gmail.com (Seongjin) Date: Wed, 07 Jan 2009 19:27:12 -0500 Subject: [Mristudio-users] 16 direction Philips gradient tables In-Reply-To: <4BFD060857263F43AEA4C10586DDE44603C80471@uphsmbx8.UPHS.PENNHEALTH.PRV> References: <73alti$34bjq7@ipex2.johnshopkins.edu> <4BFD060857263F43AEA4C10586DDE44603C80471@uphsmbx8.UPHS.PENNHEALTH.PRV> Message-ID: Sumei, The number starts from 0 and ends as 15. So the total number of gradients is 16. I recommend you following link for the gradient table of Philips system. http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html To use the JAVA applet, you should have a JAVA run time environment (JRE) installed on your computer. Good luck. SC On Wed, Jan 7, 2009 at 4:39 PM, Wang, Sumei wrote: > Hi all, > > Does anybody have 16 direction gradient table (medium) for Philips system? > I searched the forum and just got 15 dir gradient table as follows. > > Thanks for your help. > > Sumei > > -----Original Message----- > *From:* mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org]*On Behalf Of *susumu > *Sent:* Friday, July 25, 2008 7:13 AM > *To:* 'DTI Studio, ROI Editor, Landmarker Questions/Support' > *Subject:* Re: [Mristudio-users] Philips gradient tables > > Seongjin, > > > > In Philips, there are 3 types (low: 6, medium: 15, high: 32) x 2 (overplus > on/off) = 6 gradient tables. > > > > The "gradient overplus = on" always use at least two gradients to enhance b > efficiency and therefore gaining several millisecond of echo time. In your > example, the low and high is "overplus = off" and the medium is "overplus = > on". You can see "1, 0, 0" in the first two but not in the medium. > > > > The medium with "overplus = off" should look like; > > > > 0: 0, 0, 0 > > 1: 1, 0, 0 > > 2: 0, 1, 0 > > 3: 0, 0, 1 > > 4: -0.0424,-0.1146,-0.9925 > > 5: 0.1749,-0.2005,-0.9639 > > 6: 0.2323,-0.1626,-0.9590 > > 7: 0.3675,0.0261,-0.9296 > > 8: 0.1902,0.3744,-0.9076 > > 9: -0.1168,0.8334,-0.5402 > > 10: -0.2005,0.2527,-0.9466 > > 11: -0.4958,0.1345,-0.8580 > > 12: -0.0141,-0.6281,-0.7780 > > 13: -0.7445,-0.1477,-0.6511 > > 14: -0.7609,0.3204,-0.5643 > > 15: -0.1809,0.9247,-0.33510 > > 16: -0.6796,-0.4224,-0.5997 > > 17: 0.7771,0.4707,-0.4178 > > 18: 0.9242,-0.1036,-0.3677 > > 19: 0.4685,-0.7674,-0.4378 > > 20: 0.8817,-0.1893,-0.4322 > > 21: 0.6904,0.7062,-0.1569 > > 22: 0.2391,0.7571,-0.6080 > > 23: -0.0578,0.9837,0.1703 > > 24: -0.5368,0.8361,-0.1135 > > 25: -0.9918,-0.1207,-0.0423 > > 26: -0.9968,0.0709,-0.0379 > > 27: -0.8724,0.4781,-0.1014 > > 28: -0.2487,0.9335,0.2581 > > 29: 0.1183,0.9919,-0.0471 > > 30: 0.3376,0.8415,0.4218 > > 31: 0.5286,0.8409,0.1163 > > 32: 0.9969,0.0550,-0.0571 > > > > In general, I do not recommend to user "overplus = on", because tensor > calculation get complicated when oblique planes are used. You have to > recalculate the table based on the image angles. > > > > Also, please note that the "0, 0, 0" could be the first or the last image > depending on how you specify the output files. > > > > Susumu > > > ------------------------------ > > *From:* mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org] *On Behalf Of *[Seongjin] > *Sent:* Wednesday, July 23, 2008 3:47 PM > *To:* DTI Studio, ROI Editor, Landmarker Questions/Support > *Subject:* [Mristudio-users] Philips gradient tables > > > > Dear DTIstudio users, > > I wonder if you have gradient tables for Philips Achieva system. > > >From a source I have a gradient table for low resolution as follows: > > 0:1.0000, 0.0000, 0.0000 > 1:0.0000, 1.0000, 0.0000 > 2:0.0000, 0.0000, 1.0000 > 3:-0.7044, -0.0881, -0.7044 > 4:0.7044, 0.7044, 0.0881 > 5:0.0881, 0.7044, 0.7044 > 6:0.0000, 0.0000, 0.0000 > > > For medium, > > 0: 0.7071 -0.7071 1.00 > 1: 0.7071 -0.7071 -1.00 > 2: 1.0000 1.0000 0.0000 > 3: 0.9999 -0.1561 0.9879 > 4: 0.9894 0.4091 0.9240 > 5: 0.4674 0.8874 0.9970 > 6: 0.3866 0.9297 0.9930 > 7: 0.7667 -0.9511 0.7124 > 8: 0.6945 0.9954 -0.7295 > 9: 0.3580 -0.9800 -0.9547 > 10: 1.0000 -0.9992 -0.0392 > 11: 0.9999 -0.3989 -0.9171 > 12: 0.9923 0.4082 -0.9213 > 13: 0.9989 0.9982 -0.0759 > 14: 0.2899 0.9919 -0.9655 > 15: 0.0000 0.0000 0.0000 > > > For high, > > 0: 1.000, 0.000, 0.000 > 1: 0.000, 1.000, 0.000 > 2: 0.000, 0.000, 1.000 > 3: -0.042, -0.115, -0.993 > 4: 0.175, -0.200, -0.964 > 5: 0.232, -0.163, -0.959 > 6: 0.368, 0.026, -0.930 > 7: 0.190, 0.374, -0.908 > 8: -0.117, 0.833, -0.540 > 9: -0.200, 0.253, -0.947 > 10: -0.496, 0.134, -0.858 > 11: -0.014, -0.628, -0.778 > 12: -0.744, -0.148, -0.651 > 13: -0.761, 0.320, -0.564 > 14: -0.181, 0.925, -0.335 > 15: -0.680, -0.422, -0.600 > 16: 0.777, 0.471, -0.418 > 17: 0.924, -0.104, -0.368 > 18: 0.468, -0.767, -0.438 > 19: 0.882, -0.189, -0.432 > 20: 0.690, 0.706, -0.157 > 21: 0.239, 0.757, -0.608 > 22: -0.058, 0.984, 0.170 > 23: -0.537, 0.836, -0.113 > 24: -0.992, -0.121, -0.042 > 25: -0.997, 0.071, -0.038 > 26: -0.872, 0.478, -0.101 > 27: -0.249, 0.933, 0.258 > 28: 0.118, 0.992, -0.047 > 29: 0.338, 0.841, 0.422 > 30: 0.529, 0.841, 0.116 > 31: 0.997, 0.055, -0.057 > 32: 0.000, 0.000, 0.000 > > > I wonder if the tables above are correct or not. Is there anything > incorrect or partially incomplete, please let me know. > Thanks in advance. > > Sincerely, > Seongjin > > > The information contained in this e-mail message is intended only for the > personal and confidential use of the recipient(s) named above. If the reader > of this message is not the intended recipient or an agent responsible for > delivering it to the intended recipient, you are hereby notified that you > have received this document in error and that any review, dissemination, > distribution, or copying of this message is strictly prohibited. If you have > received this communication in error, please notify us immediately by > e-mail, and delete the original message. > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090107/e73ea14b/attachment.html From Sumei.Wang at uphs.upenn.edu Thu Jan 8 10:41:33 2009 From: Sumei.Wang at uphs.upenn.edu (Wang, Sumei) Date: Thu, 08 Jan 2009 10:41:33 -0500 Subject: [Mristudio-users] 16 direction Philips gradient tables In-Reply-To: Message-ID: <4BFD060857263F43AEA4C10586DDE44603C80474@uphsmbx8.UPHS.PENNHEALTH.PRV> Hi Seongjin, Thank you so much for the help. It works. Sumei -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org]On Behalf Of [Seongjin] Sent: Wednesday, January 07, 2009 7:27 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] 16 direction Philips gradient tables Sumei, The number starts from 0 and ends as 15. So the total number of gradients is 16. I recommend you following link for the gradient table of Philips system. http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html To use the JAVA applet, you should have a JAVA run time environment (JRE) installed on your computer. Good luck. SC On Wed, Jan 7, 2009 at 4:39 PM, Wang, Sumei < Sumei.Wang at uphs.upenn.edu> wrote: Hi all, Does anybody have 16 direction gradient table (medium) for Philips system? I searched the forum and just got 15 dir gradient table as follows. Thanks for your help. Sumei -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto: mristudio-users-bounces at mristudio.org]On Behalf Of susumu Sent: Friday, July 25, 2008 7:13 AM To: 'DTI Studio, ROI Editor, Landmarker Questions/Support' Subject: Re: [Mristudio-users] Philips gradient tables Seongjin, In Philips, there are 3 types (low: 6, medium: 15, high: 32) x 2 (overplus on/off) = 6 gradient tables. The "gradient overplus = on" always use at least two gradients to enhance b efficiency and therefore gaining several millisecond of echo time. In your example, the low and high is "overplus = off" and the medium is "overplus = on". You can see "1, 0, 0" in the first two but not in the medium. The medium with "overplus = off" should look like; 0: 0, 0, 0 1: 1, 0, 0 2: 0, 1, 0 3: 0, 0, 1 4: -0.0424,-0.1146,-0.9925 5: 0.1749,-0.2005,-0.9639 6: 0.2323,-0.1626,-0.9590 7: 0.3675,0.0261,-0.9296 8: 0.1902,0.3744,-0.9076 9: -0.1168,0.8334,-0.5402 10: -0.2005,0.2527,-0.9466 11: -0.4958,0.1345,-0.8580 12: -0.0141,-0.6281,-0.7780 13: -0.7445,-0.1477,-0.6511 14: -0.7609,0.3204,-0.5643 15: -0.1809,0.9247,-0.33510 16: -0.6796,-0.4224,-0.5997 17: 0.7771,0.4707,-0.4178 18: 0.9242,-0.1036,-0.3677 19: 0.4685,-0.7674,-0.4378 20: 0.8817,-0.1893,-0.4322 21: 0.6904,0.7062,-0.1569 22: 0.2391,0.7571,-0.6080 23: -0.0578,0.9837,0.1703 24: -0.5368,0.8361,-0.1135 25: -0.9918,-0.1207,-0.0423 26: -0.9968,0.0709,-0.0379 27: -0.8724,0.4781,-0.1014 28: -0.2487,0.9335,0.2581 29: 0.1183,0.9919,-0.0471 30: 0.3376,0.8415,0.4218 31: 0.5286,0.8409,0.1163 32: 0.9969,0.0550,-0.0571 In general, I do not recommend to user "overplus = on", because tensor calculation get complicated when oblique planes are used. You have to recalculate the table based on the image angles. Also, please note that the "0, 0, 0" could be the first or the last image depending on how you specify the output files. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto: mristudio-users-bounces at mristudio.org] On Behalf Of [Seongjin] Sent: Wednesday, July 23, 2008 3:47 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] Philips gradient tables Dear DTIstudio users, I wonder if you have gradient tables for Philips Achieva system. >From a source I have a gradient table for low resolution as follows: 0:1.0000, 0.0000, 0.0000 1:0.0000, 1.0000, 0.0000 2:0.0000, 0.0000, 1.0000 3:-0.7044, -0.0881, -0.7044 4:0.7044, 0.7044, 0.0881 5:0.0881, 0.7044, 0.7044 6:0.0000, 0.0000, 0.0000 For medium, 0: 0.7071 -0.7071 1.00 1: 0.7071 -0.7071 -1.00 2: 1.0000 1.0000 0.0000 3: 0.9999 -0.1561 0.9879 4: 0.9894 0.4091 0.9240 5: 0.4674 0.8874 0.9970 6: 0.3866 0.9297 0.9930 7: 0.7667 -0.9511 0.7124 8: 0.6945 0.9954 -0.7295 9: 0.3580 -0.9800 -0.9547 10: 1.0000 -0.9992 -0.0392 11: 0.9999 -0.3989 -0.9171 12: 0.9923 0.4082 -0.9213 13: 0.9989 0.9982 -0.0759 14: 0.2899 0.9919 -0.9655 15: 0.0000 0.0000 0.0000 For high, 0: 1.000, 0.000, 0.000 1: 0.000, 1.000, 0.000 2: 0.000, 0.000, 1.000 3: -0.042, -0.115, -0.993 4: 0.175, -0.200, -0.964 5: 0.232, -0.163, -0.959 6: 0.368, 0.026, -0.930 7: 0.190, 0.374, -0.908 8: -0.117, 0.833, -0.540 9: -0.200, 0.253, -0.947 10: -0.496, 0.134, -0.858 11: -0.014, -0.628, -0.778 12: -0.744, -0.148, -0.651 13: -0.761, 0.320, -0.564 14: -0.181, 0.925, -0.335 15: -0.680, -0.422, -0.600 16: 0.777, 0.471, -0.418 17: 0.924, -0.104, -0.368 18: 0.468, -0.767, -0.438 19: 0.882, -0.189, -0.432 20: 0.690, 0.706, -0.157 21: 0.239, 0.757, -0.608 22: -0.058, 0.984, 0.170 23: -0.537, 0.836, -0.113 24: -0.992, -0.121, -0.042 25: -0.997, 0.071, -0.038 26: -0.872, 0.478, -0.101 27: -0.249, 0.933, 0.258 28: 0.118, 0.992, -0.047 29: 0.338, 0.841, 0.422 30: 0.529, 0.841, 0.116 31: 0.997, 0.055, -0.057 32: 0.000, 0.000, 0.000 I wonder if the tables above are correct or not. Is there anything incorrect or partially incomplete, please let me know. Thanks in advance. Sincerely, Seongjin The information contained in this e-mail message is intended only for the personal and confidential use of the recipient(s) named above. If the reader of this message is not the intended recipient or an agent responsible for delivering it to the intended recipient, you are hereby notified that you have received this document in error and that any review, dissemination, distribution, or copying of this message is strictly prohibited. If you have received this communication in error, please notify us immediately by e-mail, and delete the original message. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users The information contained in this e-mail message is intended only for the personal and confidential use of the recipient(s) named above. If the reader of this message is not the intended recipient or an agent responsible for delivering it to the intended recipient, you are hereby notified that you have received this document in error and that any review, dissemination, distribution, or copying of this message is strictly prohibited. If you have received this communication in error, please notify us immediately by e-mail, and delete the original message. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090108/813b8dae/attachment-0001.html From jsadino at hotmail.com Mon Jan 12 18:13:13 2009 From: jsadino at hotmail.com (Jeff Sadino) Date: Mon, 12 Jan 2009 16:13:13 -0700 Subject: [Mristudio-users] Values in ROI Default format Message-ID: Hello everybody, I am trying to decode the ROI files from DTI Studio. I loaded them into matlab so that there is one number on each of the 173 lines. I understand the first few numbers "translate" into ImageROI, then the header gives x resolution, y resolution, x fov, y fov, and so on, then there are a bunch of zeroes, then the ROI coordinates and shape are given. I have gone through guess and check to narrow down what all of these values represent, but still have much more to go. Does anybody know what each of these values represent? This is what I have so far (with my notes added in): 73 - I 109 - m 97 - a 103 - g 101 - e 82 - R 79 - O 73 - I 1 0 0 0 128 - x resolution 0 0 0 128 - y resolution 0 0 0 1 - image slices 0 0 0 0 0 220 - x fov 63 - ? 0 0 220 - y fov 63 - ? 0 0 128 64 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 2 :1 means circle :2 means rectangle 0 0 0 0 0 0 0 0 0 0 0 10 2 0 0 0 3-x corodinate tl 0 0 0 1-y coordinate tl 0 0 0 0 : image slice 0 0 0 11-x coordinate -1 br 0 0 0 5-y corodinate -1 br 0 0 0 0 0 0 0 Thanks, Jeff Sadino _________________________________________________________________ Windows Live?: Keep your life in sync. http://windowslive.com/explore?ocid=TXT_TAGLM_WL_t1_allup_explore_012009 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090112/509b6f0c/attachment.html From rajagov2 at ccf.org Tue Jan 13 12:42:40 2009 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Tue, 13 Jan 2009 12:42:40 -0500 Subject: [Mristudio-users] Files from FSL to DTI studio Message-ID: <77A88E90A851594AAEF830450587C39D01EDA97F@CCHSCLEXMB56.cc.ad.cchs.net> Dear All, I did field map correction of my DTI images using FSL's FUGUE for which i have to convert the dicom files into NIFTI format to use it in FSL. I am done with field map correction now i want to bring the undistorted images back to DTIstudio and do processing. FSL allows me to save my files only in analyze or nifti format,so i saved them in analyze format which i am not able to open in DTI studio which is one problem the other problem is for tensor calculation and other paramater estimation i don't have analyze option in DTI studio i have options to feed them only in DICOM format, so how to open these images in DTI studio is there any software that can convert back NIFTI into DICOM. Kindly help me with this. Thanks in advance. Regards venkateswaran P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S. News & World Report (2008). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090113/264e75bd/attachment.html From y-wu7 at northwestern.edu Tue Jan 13 14:01:59 2009 From: y-wu7 at northwestern.edu (Ying Wu) Date: Tue, 13 Jan 2009 13:01:59 -0600 Subject: [Mristudio-users] Files from FSL to DTI studio Message-ID: <20090113190159.8330974C3@merle.it.northwestern.edu> An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090113/ff32369a/attachment.html From aimanba1 at jhu.edu Thu Jan 15 14:08:07 2009 From: aimanba1 at jhu.edu (Anuar Imanbayev) Date: Thu, 15 Jan 2009 14:08:07 -0500 Subject: [Mristudio-users] How to Process Siemens Mosaic files in DTIStudio? Message-ID: Hello everyone, I usually deal with .par and .rec files. However, my PI's collaborator works with Siemens Mosaic files and needs help in being able to perform tensor calculations on them. I'm working out the kinks so then I can report sometime next week with my findings. At first, the collaborating doctor informed me that the files were .IMA files. Indeed they did masquerade as those, but in reality responded only to Siemens Mosaic filetype under DTIStudio. Dr. Hangyi Jiang identified the data files not as ima but as mosaic files for me and helped me around in general. Still, I'm at a loss with which gradient files to treat these Siemens Mosaic files and how to perform Tensor calculations that produce credible color maps (mine so far were just red dots all around) I'll keep experimenting and poking around in the meantime. Please help me understand and deal with this new file type. Also, apparently there were no b0 or standard data files associated with the data set that the collaborator sent - just a bunch of image files. Would that be a problem in the long run? How to handle the situation when those are provided? With just image files, how do I go about creating an image quality file, then saving it after my scanning for bad quality images? Thank you for your time and assistance in advance, Sincerely yours, Anuar Imanbayev Undergraduate Neuroscience 2010 From susumu at mri.jhu.edu Thu Jan 15 16:00:32 2009 From: susumu at mri.jhu.edu (susumu) Date: Thu, 15 Jan 2009 16:00:32 -0500 Subject: [Mristudio-users] How to Process Siemens Mosaic files in DTIStudio? In-Reply-To: References: Message-ID: <63D2EBDD01C74E49BC619E7F9C1CA9D1@SusumuThinkPad> Hi Anuar, 1) Could you read the IMA (mosaic format data)? If so, make sure how many images are loaded. You can use "MRIView3D -> Siemens Mosaic" and load the data. If successful, you should see a list of loaded images in the pull-down menu in the right column of the viewing window. For example, if you used typical Siemens 12-orientation scheme, you should find 1 b0 + 12 DWI (total 13 images). 2) Then you need to find a correct gradient table. If you are using an off-the-shelf Siemens DTI method, there are Siemens-supplied gradient tables for that. If you don't know the table, please let us know, together with the number of images you get in the step #1. If you are using a user-specified table, you need to find the table. 3) Final thing you have to check is the version of your operating system and oblique plane angle. If you are using the latest operating system or your imaging plane is not oblique, you are fine. If you are using an old operating system AND an oblique plane, than, you have to check "Rotate gradients if applicable" box. Susumu -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Anuar Imanbayev Sent: Thursday, January 15, 2009 2:08 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] How to Process Siemens Mosaic files in DTIStudio? Hello everyone, I usually deal with .par and .rec files. However, my PI's collaborator works with Siemens Mosaic files and needs help in being able to perform tensor calculations on them. I'm working out the kinks so then I can report sometime next week with my findings. At first, the collaborating doctor informed me that the files were .IMA files. Indeed they did masquerade as those, but in reality responded only to Siemens Mosaic filetype under DTIStudio. Dr. Hangyi Jiang identified the data files not as ima but as mosaic files for me and helped me around in general. Still, I'm at a loss with which gradient files to treat these Siemens Mosaic files and how to perform Tensor calculations that produce credible color maps (mine so far were just red dots all around) I'll keep experimenting and poking around in the meantime. Please help me understand and deal with this new file type. Also, apparently there were no b0 or standard data files associated with the data set that the collaborator sent - just a bunch of image files. Would that be a problem in the long run? How to handle the situation when those are provided? With just image files, how do I go about creating an image quality file, then saving it after my scanning for bad quality images? Thank you for your time and assistance in advance, Sincerely yours, Anuar Imanbayev Undergraduate Neuroscience 2010 _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From sreading at jhmi.edu Fri Jan 16 10:34:23 2009 From: sreading at jhmi.edu (Sarah Reading) Date: Fri, 16 Jan 2009 10:34:23 -0500 Subject: [Mristudio-users] Super computer processing time? In-Reply-To: <63D2EBDD01C74E49BC619E7F9C1CA9D1@SusumuThinkPad> Message-ID: <73ap56$5df358@ipex1.johnshopkins.edu> Hi, Just wondering what kind of turn around time I can expect for the LDDMM analysis from the supercomputer. I understand I will get an email reporting when the analysis began - it's been almost 48 hrs since I successfully transferred data and I haven't gotten any notice. No complaints just trying to know if I should be concerned. Thanks, Sarah. From hjyu at ic.sunysb.edu Fri Jan 16 13:10:46 2009 From: hjyu at ic.sunysb.edu (hjyu) Date: Fri, 16 Jan 2009 13:10:46 -0500 Subject: [Mristudio-users] Fiber Tracking Message-ID: <4970cda6.272.6916.12805@ic.sunysb.edu> Dear DTIStudio users, I am interested in doing fiber statistics in DTI studio on a portion of a selected fiber. Briefly, I used the OR/AND function and selected a fiber track of interest, now I want to look at the statistics on different portions of that fiber. The cut function didn?t seem to work. So my questions are the following: 1. How do I select a portion of a selected fiber in DTI studio? 2. How do I modify the fiber-data file within DTI studio or using other softwares such as MATLAB? 3. How can I read fiber-tracking results saved in Analyze format back into DTI studio (it only seems to work for dat format)? 4. Where can I access information such as #fibers for a particular voxel? 5. Are the statistical calculations given by the Statistics Profile weighted by fibers/voxel? Thank you in advance for your responses. HJ From hui.jing.yu at gmail.com Fri Jan 16 13:05:24 2009 From: hui.jing.yu at gmail.com (Hui Jing Yu) Date: Fri, 16 Jan 2009 13:05:24 -0500 Subject: [Mristudio-users] Fiber Tracking Message-ID: <4970cc63.6105be0a.5cae.6fb3@mx.google.com> Dear DTIStudio users, I am interested in doing fiber statistics in DTI studio on a portion of a selected fiber. Briefly, I used the OR/AND function and selected a fiber track of interest, now I want to look at the statistics on different portions of that fiber. The cut function didn't seem to work. So my questions are the following: 1. How do I select a portion of a selected fiber in DTI studio? 2. How do I modify the fiber-data file within DTI studio or using other softwares such as MATLAB? 3. How can I read fiber-tracking results saved in Analyze format back into DTI studio (it only seems to work for dat format)? 4. Where can I access information such as #fibers for a particular voxel? 5. Are the statistical calculations given by the Statistics Profile weighted by fibers/voxel? Thank you in advance for your responses. HJ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090116/05373ca2/attachment.html From tmsusmaras at suffolk.edu Fri Jan 16 14:01:47 2009 From: tmsusmaras at suffolk.edu (Teresa Susmaras) Date: Fri, 16 Jan 2009 14:01:47 -0500 (EST) Subject: [Mristudio-users] Normalization Message-ID: <20090116140147.BGA56305@mp1.suffolk.edu> Hi, When I put read that has been normalized in SPM back into DTI studio, how do those coordinates in DTI Studio convert from the MNI coordinates output by SPM? Thank you, Teresa -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090116/da0d7327/attachment.html From sreading at jhmi.edu Sun Jan 18 10:47:24 2009 From: sreading at jhmi.edu (Sarah A Reading) Date: Sun, 18 Jan 2009 10:47:24 -0500 Subject: [Mristudio-users] Question Message-ID: Hi, I have now successfully downloaded my resultant LDDMM data and have applied the new matrix to the "target.img" data - subsequently resampled the data back to ICBM space and saved as float then evaluated in ROI editor - all looks good. My "target" data was only my .b0 and .fa so now I have those transformed and saved. I know I know the answer to this but I cannot figure it out. How do I apply the transformation matrix to the rest of the registered data - specifically to the .d? I know that I save the matrix (as .dat??) - which I have done - but what is next? Thanks! Sarah. From susumu at mri.jhu.edu Mon Jan 19 12:32:55 2009 From: susumu at mri.jhu.edu (susumu) Date: Mon, 19 Jan 2009 12:32:55 -0500 Subject: [Mristudio-users] Question In-Reply-To: Message-ID: <6u9vds$64l8kc@ipex3.johnshopkins.edu> Hi Sarah, The registration results of LDDMM you want to use is "kmap" and "hmap", which are transformation matrix. The "target" and "template" images are what you submitted and came back just for record. Most likely you don't use them. Once you got the transformation matrices, you want to apply them to your co-registered DTI (or other co-registered MRI) images such as fa and b0. The target and template images are converted to binary images and could be intensity normalized and size adjusted. You don't want to use them. You want to apply the matrices to your MRI/DTI data after affine transformation but before LDDMM submission, which are still floating point and, if you use our template, have the 181x217x181 matrix size. -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Sarah A Reading Sent: Sunday, January 18, 2009 10:47 AM To: lddmmproc at mristudio.org; mristudio-users at mristudio.org Subject: [Mristudio-users] Question Hi, I have now successfully downloaded my resultant LDDMM data and have applied the new matrix to the "target.img" data - subsequently resampled the data back to ICBM space and saved as float then evaluated in ROI editor - all looks good. My "target" data was only my .b0 and .fa so now I have those transformed and saved. I know I know the answer to this but I cannot figure it out. How do I apply the transformation matrix to the rest of the registered data - specifically to the .d? I know that I save the matrix (as .dat??) - which I have done - but what is next? Thanks! Sarah. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From susumu at mri.jhu.edu Mon Jan 19 15:48:58 2009 From: susumu at mri.jhu.edu (susumu) Date: Mon, 19 Jan 2009 15:48:58 -0500 Subject: [Mristudio-users] Fiber Tracking In-Reply-To: <4970cc63.6105be0a.5cae.6fb3@mx.google.com> Message-ID: <6u9vds$64mo6t@ipex3.johnshopkins.edu> 1. How do I select a portion of a selected fiber in DTI studio? > Use the Cut operation. After you click CUT, it waits for two inputs. The first ROI will be treated as "OR" and the result looks like "OR". Proceed for the second ROI. After the input of the second ROI, only the projection between the two ROIs are constructed. > Use the "Statistics -> Profile" function. If the trajectory of the reconstructed fiber is rather straight (not U-shape), you can use this function. It generates a table in which you can see pixel values averaged over axial, coronal, and sagittal slices. In this way, you can retrieve values at each slice level. > Use RoiEditor: Save the result as a "binary" format and read it to RoiEditor together with the image you want to quantify (e.g. FA map). With some creative mind, you can do several interesting things using functions in RoiEditor. For example, with a region growing tool, you can re-define the fiber coordinates within RoiEditor (called "object") and apply it as an ROI to any co-registered images such as FA. You can manually modify the object. You can also manually remove the fiber coordinate in the binary map at one slice level. Then you can do region growing to define a new object and the region growing will stop at the slice level you modified. 2. How do I modify the fiber-data file within DTI studio or using other softwares such as MATLAB? > In the FAQ section of www.mristudio.org, there is a section explaining the format of the DtiStudio fiber files. If you saved your fiber in this format, you can reload and re-edit them in DtiStudio. Once you convert the data into the binary format (1/0 for each pixel), RoiEditor is the way to go to modify them. 3. How can I read fiber-tracking results saved in Analyze format back into DTI studio (it only seems to work for dat format)? > If I'm not mistaken, fiber-tracking results in Analyze format is pixel-by-pixel "image data" (for example, 256x256x50 matrix data). For example, a binary image in which pixels that contain the fiber is 1 and everything else is 0. The original "loss-less" fiber-tracking file should be streamline information, not the pixel-by-pixel information. For exmaple, such file should contain information about how many fibers are reconstructed and then coordinate information of each line. Once this type of streamline information is converted to an image format, the tracking information is degenerated and streamline can not be reconstructed (and further editing is impossible). So, yes, you need the dat format to prevent any information loss. 4. Where can I access information such as #fibers for a particular voxel? > That's a good question. I believe that there is a version that can save an image for "the number of fibers at each pixel". > Hangyi, the version with this function is ready? 5. Are the statistical calculations given by the Statistics Profile weighted by fibers/voxel? > Yes, the current version is weighted by the fibers/voxel, but we have a newer version in which you can choose weighting / not weighting. > I'll check the status of the latest version. I think we will release Version 3, non-beta very soon. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090119/617cc7f0/attachment-0001.html From susumu at mri.jhu.edu Mon Jan 19 15:51:11 2009 From: susumu at mri.jhu.edu (susumu) Date: Mon, 19 Jan 2009 15:51:11 -0500 Subject: [Mristudio-users] Super computer processing time? In-Reply-To: <73ap56$5df358@ipex1.johnshopkins.edu> Message-ID: <6u9vds$64mokg@ipex3.johnshopkins.edu> It should be about 6 hours, but during the heavy usage, you may see some degerioration of computation time. We are investing on our computation resource now and you should be seeing improvement in recent days. -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Sarah Reading Sent: Friday, January 16, 2009 10:34 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] Super computer processing time? Hi, Just wondering what kind of turn around time I can expect for the LDDMM analysis from the supercomputer. I understand I will get an email reporting when the analysis began - it's been almost 48 hrs since I successfully transferred data and I haven't gotten any notice. No complaints just trying to know if I should be concerned. Thanks, Sarah. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From aimanba1 at jhu.edu Mon Jan 19 17:03:57 2009 From: aimanba1 at jhu.edu (Anuar Imanbayev) Date: Mon, 19 Jan 2009 17:03:57 -0500 Subject: [Mristudio-users] How to Process Siemens Mosaic files in DTIStudio? In-Reply-To: <63D2EBDD01C74E49BC619E7F9C1CA9D1@SusumuThinkPad> References: <63D2EBDD01C74E49BC619E7F9C1CA9D1@SusumuThinkPad> Message-ID: Hello Dr. Mori, I'm very glad to hear from you. 1.) I loaded the data fine. However, in the pull-down menu in the right column of the view window, it only displays [IMA\ - 15] thru [IMA\ - 30] and [IMA\ - 46] to [IMA\ - 52], which are just the raw data images that I've been provided with. There is a catch yet. I've only received parts 2 and 4 of this data set. I'm awaiting parts 1 and 3 and hopefully those will have the b0 and standard images. At the same time, they may be just more raw data files. So far I've got: [IMA\ - 15] to [IMA\ - 30] which comprises part 2 [IMA\ - 46] to [IMA\ - 52] which comprises part 4. I'm missing: [IMA\ - 1] to [IMA\ - 14] which should comprise part 1 [IMA\ - 31] to [IMA\ - 45] which should comprise part 3 2.) I do know of the gradient table. I have contacted the collaborating doctor asking him to provide the gradient table his technicians used for image acquisition. Hopefully, as you've said, the image numbers provide a clue. To me they don't because they just look like raw single-type image files. 3.) My operating system is a Dell Inspiron 9400 32-bit Interl(R) Core(TM) Duo CPU T2350 @1.86GHz 1.87 GHz, so it's up to date. Now, I'm not sure about this imaging plane being oblique. I don't think it is because I can view the images fine and dandy on DTIStudio. Thank you very much for your time and assistance, In the meantime, I'll try and circumvent the problem by utilizing MRIConvert to get these .ima mosaic files into .pars and .recs somehow, if possible. Sincerely yours, Anuar Imanbayev ----- Original Message ----- From: susumu Date: Thursday, January 15, 2009 4:00 pm Subject: Re: [Mristudio-users] How to Process Siemens Mosaic files in DTIStudio? To: "'DTI Studio, ROI Editor, Landmarker Questions/Support'" > Hi Anuar, > > 1) Could you read the IMA (mosaic format data)? If so, make sure how > many > images are loaded. You can use "MRIView3D -> Siemens Mosaic" and load > the > data. If successful, you should see a list of loaded images in the pull-down > menu in the right column of the viewing window. For example, if you used > typical Siemens 12-orientation scheme, you should find 1 b0 + 12 DWI > (total > 13 images). > 2) Then you need to find a correct gradient table. If you are using an > off-the-shelf Siemens DTI method, there are Siemens-supplied gradient > tables > for that. If you don't know the table, please let us know, together > with the > number of images you get in the step #1. If you are using a user-specified > table, you need to find the table. > 3) Final thing you have to check is the version of your operating > system and > oblique plane angle. If you are using the latest operating system or > your > imaging plane is not oblique, you are fine. If you are using an old > operating system AND an oblique plane, than, you have to check "Rotate > gradients if applicable" box. > > Susumu > > -----Original Message----- > From: mristudio-users-bounces at mristudio.org > [ On Behalf Of Anuar Imanbayev > Sent: Thursday, January 15, 2009 2:08 PM > To: mristudio-users at mristudio.org > Subject: [Mristudio-users] How to Process Siemens Mosaic files in DTIStudio? > > Hello everyone, > > I usually deal with .par and .rec files. However, my PI's > collaborator works > with Siemens Mosaic files and needs help in being able to perform tensor > calculations on them. I'm working out the kinks so then I can report > sometime next week with my findings. > > > At first, the collaborating doctor informed me that the files were .IMA > files. Indeed they did masquerade as those, but in reality responded > only to > Siemens Mosaic filetype under DTIStudio. > > Dr. Hangyi Jiang identified the data files not as ima but as mosaic files > for me and helped me around in general. Still, I'm at a loss with which > gradient files to treat these Siemens Mosaic files and how to perform > Tensor > calculations that produce credible color maps (mine so far were just > red > dots all around) I'll keep experimenting and poking around in the meantime. > > Please help me understand and deal with this new file type. Also, apparently > there were no b0 or standard data files associated with the data set > that > the collaborator sent - just a bunch of image files. Would that be a > problem in the long run? How to handle the situation when those are > provided? With just image files, how do I go about creating an image > quality > file, then saving it after my scanning for bad quality images? > > Thank you for your time and assistance in advance, > Sincerely yours, > Anuar Imanbayev > Undergraduate Neuroscience 2010 > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > From aimanba1 at jhu.edu Mon Jan 19 17:05:58 2009 From: aimanba1 at jhu.edu (Anuar Imanbayev) Date: Mon, 19 Jan 2009 17:05:58 -0500 Subject: [Mristudio-users] How to Process Siemens Mosaic files in DTIStudio? In-Reply-To: References: <63D2EBDD01C74E49BC619E7F9C1CA9D1@SusumuThinkPad> Message-ID: Correction 2.) I do NOT know what gradient table to use at this time. ----- Original Message ----- From: Anuar Imanbayev Date: Monday, January 19, 2009 5:04 pm Subject: Re: [Mristudio-users] How to Process Siemens Mosaic files in DTIStudio? To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > Hello Dr. Mori, > > I'm very glad to hear from you. > > 1.) I loaded the data fine. However, in the pull-down menu in the > right column of the view window, it only displays [IMA\ - 15] thru > [IMA\ - 30] and [IMA\ - 46] to [IMA\ - 52], which are just the raw > data images that I've been provided with. There is a catch yet. I've > only received parts 2 and 4 of this data set. I'm awaiting parts 1 and > 3 and hopefully those will have the b0 and standard images. At the > same time, they may be just more raw data files. > > So far I've got: > [IMA\ - 15] to [IMA\ - 30] which comprises part 2 > [IMA\ - 46] to [IMA\ - 52] which comprises part 4. > I'm missing: > [IMA\ - 1] to [IMA\ - 14] which should comprise part 1 > [IMA\ - 31] to [IMA\ - 45] which should comprise part 3 > > 2.) I do know of the gradient table. I have contacted the > collaborating doctor asking him to provide the gradient table his > technicians used for image acquisition. Hopefully, as you've said, the > image numbers provide a clue. To me they don't because they just look > like raw single-type image files. > > 3.) My operating system is a Dell Inspiron 9400 32-bit Interl(R) > Core(TM) Duo CPU T2350 @1.86GHz 1.87 GHz, so it's up to date. Now, I'm > not sure about this imaging plane being oblique. I don't think it is > because I can view the images fine and dandy on DTIStudio. > > Thank you very much for your time and assistance, > In the meantime, I'll try and circumvent the problem by utilizing > MRIConvert to get these .ima mosaic files into .pars and .recs > somehow, if possible. > > Sincerely yours, > Anuar Imanbayev > > ----- Original Message ----- > From: susumu > Date: Thursday, January 15, 2009 4:00 pm > Subject: Re: [Mristudio-users] How to Process Siemens Mosaic files in DTIStudio? > To: "'DTI Studio, ROI Editor, Landmarker Questions/Support'" > > > > Hi Anuar, > > > > 1) Could you read the IMA (mosaic format data)? If so, make sure > how > > many > > images are loaded. You can use "MRIView3D -> Siemens Mosaic" and > load > > the > > data. If successful, you should see a list of loaded images in the > pull-down > > menu in the right column of the viewing window. For example, if > you used > > typical Siemens 12-orientation scheme, you should find 1 b0 + 12 > DWI > > (total > > 13 images). > > 2) Then you need to find a correct gradient table. If you are > using an > > off-the-shelf Siemens DTI method, there are Siemens-supplied > gradient > > tables > > for that. If you don't know the table, please let us know, > together > > with the > > number of images you get in the step #1. If you are using a user-specified > > table, you need to find the table. > > 3) Final thing you have to check is the version of your operating > > > system and > > oblique plane angle. If you are using the latest operating system > or > > your > > imaging plane is not oblique, you are fine. If you are using an old > > operating system AND an oblique plane, than, you have to check "Rotate > > gradients if applicable" box. > > > > Susumu > > > > -----Original Message----- > > From: mristudio-users-bounces at mristudio.org > > [ On Behalf Of Anuar Imanbayev > > Sent: Thursday, January 15, 2009 2:08 PM > > To: mristudio-users at mristudio.org > > Subject: [Mristudio-users] How to Process Siemens Mosaic files in > DTIStudio? > > > > Hello everyone, > > > > I usually deal with .par and .rec files. However, my PI's > > collaborator works > > with Siemens Mosaic files and needs help in being able to perform > tensor > > calculations on them. I'm working out the kinks so then I can report > > sometime next week with my findings. > > > > > > At first, the collaborating doctor informed me that the files were > .IMA > > files. Indeed they did masquerade as those, but in reality > responded > > only to > > Siemens Mosaic filetype under DTIStudio. > > > > Dr. Hangyi Jiang identified the data files not as ima but as > mosaic files > > for me and helped me around in general. Still, I'm at a loss with > which > > gradient files to treat these Siemens Mosaic files and how to > perform > > Tensor > > calculations that produce credible color maps (mine so far were > just > > red > > dots all around) I'll keep experimenting and poking around in the > meantime. > > > > Please help me understand and deal with this new file type. Also, > apparently > > there were no b0 or standard data files associated with the data > set > > that > > the collaborator sent - just a bunch of image files. Would that > be a > > problem in the long run? How to handle the situation when those are > > provided? With just image files, how do I go about creating an > image > > quality > > file, then saving it after my scanning for bad quality images? > > > > Thank you for your time and assistance in advance, > > Sincerely yours, > > Anuar Imanbayev > > Undergraduate Neuroscience 2010 > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > From korolevi at msu.edu Wed Jan 21 07:05:14 2009 From: korolevi at msu.edu (Igor Korolev) Date: Wed, 21 Jan 2009 07:05:14 -0500 Subject: [Mristudio-users] Re-orienting DTI data Message-ID: Hi Everyone, While in the scanner, some of our subjects had their heads tilted, resulting in DTI volumes that are out of standard orientation. We want to rotate the DTI volumes into standard orientation (i.e. with AC-PC line as the horizontal). I understand this can be done by co-registering the data to a template in Landmarker, but this requires normalization of the original data. Is there a way to re-orient the data in MRI Studio, for instance relative to a user-defined AC-PC line, without normalizing data (as we want to preserve original dimensions in the data)? Thank you for your help! Best, Igor -- ------------------------------------------------------------------ Igor O. Korolev Physician-Scientist Student (Year 3) D.O./Ph.D. Training Program College of Osteopathic Medicine Neuroscience Program Michigan State University E-mail: korolevi at msu.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090121/7b4a74c4/attachment.html From susumu at mri.jhu.edu Wed Jan 21 09:50:40 2009 From: susumu at mri.jhu.edu (susumu) Date: Wed, 21 Jan 2009 09:50:40 -0500 Subject: [Mristudio-users] Re-orienting DTI data In-Reply-To: Message-ID: <6u9vds$65b6rk@ipex3.johnshopkins.edu> Hi Igor, I think the easiest way is to use "rigid" transformation in Landmarker. Whatever the method you choose, you have to do at least the rigid transformation (just rotation and translation) of your data to realign your data to AC-PC. Because your data is a tensor data, you have to be careful and use a tool that can re-orient each tensor in each pixel. Of course, if you first calculate FA map and then do AC-PC alignment, you don't have to worry about it. Using Landmarker, there are two ways; 1) Use the rigid transformation option in AIR. By using this option, it will re-sample your original data to the template of your choice. For example, if you choose our ICBM-DTI-MNI, the output will be 181x217x181 with 1mm resolution. The brain position and orientation should be aligned to those of the ICBM-DTI-MNI image. As long as you are using rigid, it doesn't touch the size of your data. If you don't want the resampling to the atlas dimensions, you can use one of your good data, say, 256x256x50, as your template. Then you can keep the original dimensions. 2) Use the landmarking functions. Again, you can choose one of our atlases or one of your good data as a template. Pick AC and PC in the template data and also in the data you want to re-align. Because your data could have an olbique angle, you have to be precise and careful to define the AC and the PC. Then use the landmark-driven rigid alignment, which are provided as one of the buttons in the top menu bar. Hope this will work. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Igor Korolev Sent: Wednesday, January 21, 2009 7:05 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] Re-orienting DTI data Hi Everyone, While in the scanner, some of our subjects had their heads tilted, resulting in DTI volumes that are out of standard orientation. We want to rotate the DTI volumes into standard orientation (i.e. with AC-PC line as the horizontal). I understand this can be done by co-registering the data to a template in Landmarker, but this requires normalization of the original data. Is there a way to re-orient the data in MRI Studio, for instance relative to a user-defined AC-PC line, without normalizing data (as we want to preserve original dimensions in the data)? Thank you for your help! Best, Igor -- ------------------------------------------------------------------ Igor O. Korolev Physician-Scientist Student (Year 3) D.O./Ph.D. Training Program College of Osteopathic Medicine Neuroscience Program Michigan State University E-mail: korolevi at msu.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090121/d086c6a3/attachment-0001.html From dea.dundara at ts.infn.it Thu Jan 22 05:51:06 2009 From: dea.dundara at ts.infn.it (dea.dundara at ts.infn.it) Date: Thu, 22 Jan 2009 11:51:06 +0100 (CET) Subject: [Mristudio-users] Fiber Tracking - FA along the selected fibers Message-ID: <2542.140.105.7.137.1232621466.squirrel@webmail.ts.infn.it> Dear, I'm a new MRIstudio-user. Please sorry if I will repeat a question that maybe has been asked before. When I start to do Fiber Tracking, it appears a window where the fiber-tracking parameters have to be defined,in particular I have to specify the FA value at which the tracking will start and stop. I use the default value of 0.25. After this I select fibers using a specific ROI. But there is a problem. If I go to see the statistics, and I'm interested in the FA along the selected fibers, I realize that the FA Min of ImgVal is smaller than the threshold of 0.25 that I have set before. Please explain me what is this minimum value refered to. Thanks Dea Dundara From susumu at mri.jhu.edu Sat Jan 24 18:49:42 2009 From: susumu at mri.jhu.edu (susumu) Date: Sat, 24 Jan 2009 18:49:42 -0500 Subject: [Mristudio-users] Fiber Tracking - FA along the selected fibers In-Reply-To: <2542.140.105.7.137.1232621466.squirrel@webmail.ts.infn.it> References: <2542.140.105.7.137.1232621466.squirrel@webmail.ts.infn.it> Message-ID: <23662A15E1724B94AC3B54E4E93A905D@SusumuThinkPad> Hangyi, correct me if it's wrong, but I believe that is because the tracking terminates when the leading tip enters a pixel with FA lower than the threshold. So, for each streamline, the two endpoints could have FA lower than the threshold. -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of dea.dundara at ts.infn.it Sent: Thursday, January 22, 2009 5:51 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] Fiber Tracking - FA along the selected fibers Dear, I'm a new MRIstudio-user. Please sorry if I will repeat a question that maybe has been asked before. When I start to do Fiber Tracking, it appears a window where the fiber-tracking parameters have to be defined,in particular I have to specify the FA value at which the tracking will start and stop. I use the default value of 0.25. After this I select fibers using a specific ROI. But there is a problem. If I go to see the statistics, and I'm interested in the FA along the selected fibers, I realize that the FA Min of ImgVal is smaller than the threshold of 0.25 that I have set before. Please explain me what is this minimum value refered to. Thanks Dea Dundara _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From pwang_xjtu at hotmail.com Sat Jan 24 23:53:00 2009 From: pwang_xjtu at hotmail.com (WangPing) Date: Sun, 25 Jan 2009 12:53:00 +0800 Subject: [Mristudio-users] human brain atlas In-Reply-To: <23662A15E1724B94AC3B54E4E93A905D@SusumuThinkPad> References: <2542.140.105.7.137.1232621466.squirrel@webmail.ts.infn.it> <23662A15E1724B94AC3B54E4E93A905D@SusumuThinkPad> Message-ID: Dear Dr. Mori and the List: Could anyone recommend a brain atlas (label atlas) that covers the main white matters? It will be great if this atlas is easy to register to MNI template. Thanks a lot!Ping _________________________________________________________________ ?????????????????????????????? http://piao.live.com/?form=PANER01 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090125/741cfb89/attachment.html From susumu at mri.jhu.edu Sun Jan 25 08:38:18 2009 From: susumu at mri.jhu.edu (susumu) Date: Sun, 25 Jan 2009 08:38:18 -0500 Subject: [Mristudio-users] human brain atlas In-Reply-To: References: <2542.140.105.7.137.1232621466.squirrel@webmail.ts.infn.it> <23662A15E1724B94AC3B54E4E93A905D@SusumuThinkPad> Message-ID: Hi Ping, We have several white matter atlases in lbam.med.jhmi.edu, but the easiest way is to download Landmarker/RoiEditor from www.mristudio.org , which come with different types of electronic atlases. One of them is population-averaged atlas in the MNI coordinates. If you use linear normalization, I recommend using this atlas (named ICBM_DTI-81 for GE/Siemens and JHU-MNI-GA for Philips). If you use highly non-linear normalization, I recommend the single-subject atlas (named JHU-MNI-SS). Both atlases come with a hand-segmented white matter parcellation map (WMPM). If you download RoiEditor, this software can apply the WMPM for various types of image quantification. Please refer to www.mristudio.org for more info. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of WangPing Sent: Saturday, January 24, 2009 11:53 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] human brain atlas Importance: High Dear Dr. Mori and the List: Could anyone recommend a brain atlas (label atlas) that covers the main white matters? It will be great if this atlas is easy to register to MNI template. Thanks a lot! Ping _____ ???? MSN ?????? MSN ????? ???? ?? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090125/043d51cb/attachment.html From pwang_xjtu at hotmail.com Sun Jan 25 12:00:06 2009 From: pwang_xjtu at hotmail.com (WangPing) Date: Mon, 26 Jan 2009 01:00:06 +0800 Subject: [Mristudio-users] human brain atlas In-Reply-To: References: <2542.140.105.7.137.1232621466.squirrel@webmail.ts.infn.it> <23662A15E1724B94AC3B54E4E93A905D@SusumuThinkPad> Message-ID: I understand, many thanks Susumu! Have a great weekend, ping Date: Sun, 25 Jan 2009 08:38:18 -0500From: susumu at mri.jhu.eduTo: mristudio-users at mristudio.orgSubject: Re: [Mristudio-users] human brain atlas Hi Ping, We have several white matter atlases in lbam.med.jhmi.edu, but the easiest way is to download Landmarker/RoiEditor from www.mristudio.org, which come with different types of electronic atlases. One of them is population-averaged atlas in the MNI coordinates. If you use linear normalization, I recommend using this atlas (named ICBM_DTI-81 for GE/Siemens and JHU-MNI-GA for Philips). If you use highly non-linear normalization, I recommend the single-subject atlas (named JHU-MNI-SS). Both atlases come with a hand-segmented white matter parcellation map (WMPM). If you download RoiEditor, this software can apply the WMPM for various types of image quantification. Please refer to www.mristudio.org for more info. Susumu From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of WangPingSent: Saturday, January 24, 2009 11:53 PMTo: mristudio-users at mristudio.orgSubject: [Mristudio-users] human brain atlasImportance: High Dear Dr. Mori and the List: Could anyone recommend a brain atlas (label atlas) that covers the main white matters? It will be great if this atlas is easy to register to MNI template. Thanks a lot!Ping ???? MSN ?????? MSN ????? ?????? _________________________________________________________________ ?Windows Live ?????????? MSN? http://im.live.cn/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090126/d9ef91e7/attachment-0001.html From naamab at stanford.edu Sun Jan 25 13:28:32 2009 From: naamab at stanford.edu (Naama Barnea-Goraly) Date: Sun, 25 Jan 2009 10:28:32 -0800 Subject: [Mristudio-users] roieditor colormap generated rois on an FA map References: <5310C336-2EE4-4859-A294-406D8A9519EC@stanford.edu> Message-ID: <928158CE-6BBF-4141-A5E1-B266820C1B83@stanford.edu> Dear mristudio team, I created an ROI on a colormap using roieditor and then opened in on my FA map. On the color map it looks fine, but on the FA map it has a "hole" in the middle (see pic). Please advise. Thanks, Naama > > > -------------- next part -------------- A non-text attachment was scrubbed... Name: roi.tiff Type: image/tiff Size: 24242 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090125/599d9769/attachment-0001.tiff -------------- next part -------------- > > Naama Barnea-Goraly M.D. Instructor Center for Interdisciplinary Brain Sciences Research Stanford University Division of Child and Adolescent Psychiatry 401 Quarry Rd. MC 5795 Stanford University School of Medicine Stanford, CA 94305-5795 Phone: (650) 736-1874, fax: (650) 724-4794 CONFIDENTIALITY NOTICE: This e-mail communication and any attachments may contain confidential information for the use of the designated recipients named above. If you are not the intended recipient, you are hereby notified that you have received this communication in error and that any review, disclosure, dissemination, distribution or copying of it or its contents is prohibited. If you have received this communication in error, please notify Stanford Medical Center immediately by telephone at (650) 725-5722 and destroy all copies of this communication and any attachments. Thank you. From susumu at mri.jhu.edu Sun Jan 25 14:21:13 2009 From: susumu at mri.jhu.edu (susumu) Date: Sun, 25 Jan 2009 14:21:13 -0500 Subject: [Mristudio-users] roieditor colormap generated rois on an FA map In-Reply-To: <928158CE-6BBF-4141-A5E1-B266820C1B83@stanford.edu> References: <5310C336-2EE4-4859-A294-406D8A9519EC@stanford.edu> <928158CE-6BBF-4141-A5E1-B266820C1B83@stanford.edu> Message-ID: Hi Naama, I think this is correct. In RoiEditor, once an ROI is registered as an "object", it shows only the boundary of the object and the inside is not filled. -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Naama Barnea-Goraly Sent: Sunday, January 25, 2009 1:29 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] roieditor colormap generated rois on an FA map Dear mristudio team, I created an ROI on a colormap using roieditor and then opened in on my FA map. On the color map it looks fine, but on the FA map it has a "hole" in the middle (see pic). Please advise. Thanks, Naama > > > From pwang_xjtu at hotmail.com Mon Jan 26 11:31:58 2009 From: pwang_xjtu at hotmail.com (WangPing) Date: Tue, 27 Jan 2009 00:31:58 +0800 Subject: [Mristudio-users] human brain atlas In-Reply-To: References: <2542.140.105.7.137.1232621466.squirrel@webmail.ts.infn.it> <23662A15E1724B94AC3B54E4E93A905D@SusumuThinkPad> Message-ID: Susumu, I just played with RoiEditor for a while, and found the atlas with the software. I am wondering if the tool (or you may recommend other tool) can use the atlas to label my subjects. Right now my subjects have been normalized to MNI152 space (non-linear registration), there are white matter lesions on some subjects, I want to calculate the lesion volume on the white matter regions. IF I can label my subjects, I will know the lesion volume on each parcellation. I do not have to need a very detailed label atlas at this point, maybe a atlas that can divide a brain into a few parcellations will be okay. Thanks, any suggestion is high appreciated. Best Regards, Ping Date: Sun, 25 Jan 2009 08:38:18 -0500 From: susumu at mri.jhu.edu To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] human brain atlas Hi Ping, We have several white matter atlases in lbam.med.jhmi.edu, but the easiest way is to download Landmarker/RoiEditor from www.mristudio.org, which come with different types of electronic atlases. One of them is population-averaged atlas in the MNI coordinates. If you use linear normalization, I recommend using this atlas (named ICBM_DTI-81 for GE/Siemens and JHU-MNI-GA for Philips). If you use highly non-linear normalization, I recommend the single-subject atlas (named JHU-MNI-SS). Both atlases come with a hand-segmented white matter parcellation map (WMPM). If you download RoiEditor, this software can apply the WMPM for various types of image quantification. Please refer to www.mristudio.org for more info. Susumu From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of WangPing Sent: Saturday, January 24, 2009 11:53 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] human brain atlas Importance: High Dear Dr. Mori and the List: Could anyone recommend a brain atlas (label atlas) that covers the main white matters? It will be great if this atlas is easy to register to MNI template. Thanks a lot! Ping ???? MSN ?????? MSN ????? ?????? _________________________________________________________________ ?????????????????????????????? http://cnweb.search.live.com/xrank/results.aspx?q=%e5%91%a8%e6%9d%b0%e4%bc%a6&FORM=MSNH -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090127/adb7dc51/attachment.html From susumu at mri.jhu.edu Mon Jan 26 12:50:23 2009 From: susumu at mri.jhu.edu (susumu) Date: Mon, 26 Jan 2009 12:50:23 -0500 Subject: [Mristudio-users] human brain atlas In-Reply-To: Message-ID: <6u9vds$671qf0@ipex3.johnshopkins.edu> 1) Landmarker can normalize your data to ICBM-152. It comes with the ICBM (including our ICBM-DTI contrasts) and you can doa linear or non-linear method. 2) If you already normalized to the ICBM-152, the first step can be skipped. Just make sure the following; > our ICBM-152 has 181x217x181 matrix with 1 mm resolution > You can load our ICBM-152 and your normalized images to Landmarker (or any other software) to make sure that the compatibility of two ICBM-152 (one you used and the other one implemented in Landmarker and RoiEditor). > Also, all of our software follows the Radiology convention (right is left). If you find your image is loaded upside down, that is because of the brain orientation issue. It is a good practice to make sure right-left is correct in your entire procedure using a subject with some characteristic asymmetry 3) Once you confirm that your ICBM atlas was compatible with the one implemented in our software, do the following; > Load your normalized data. If you have lesion volume data (I assume it is 1/0 binary data), load it with some anatomical image such as T2. > Make sure that the image dimension is 181x217x181 / 1mm > Then, choose "ICBM" as an atlas in the right column > There is a button looks like the lung. Click it. This automatically segment your data into many white matter and gray matter regions and give you a report. For your lesion image, you can get how many "1 = lesion pixel" are in each segmented white matter area. > If you want to see the segmentation visually, use the "load" button in the "atlas" section and load one of the "WMPM". You can visually see the superimiposition of the segmentation on the loaded images. Try _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of WangPing Sent: Monday, January 26, 2009 11:32 AM To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] human brain atlas Importance: High Susumu, I just played with RoiEditor for a while, and found the atlas with the software. I am wondering if the tool (or you may recommend other tool) can use the atlas to label my subjects. Right now my subjects have been normalized to MNI152 space (non-linear registration), there are white matter lesions on some subjects, I want to calculate the lesion volume on the white matter regions. IF I can label my subjects, I will know the lesion volume on each parcellation. I do not have to need a very detailed label atlas at this point, maybe a atlas that can divide a brain into a few parcellations will be okay. Thanks, any suggestion is high appreciated. Best Regards, Ping Date: Sun, 25 Jan 2009 08:38:18 -0500 From: susumu at mri.jhu.edu To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] human brain atlas Hi Ping, We have several white matter atlases in lbam.med.jhmi.edu, but the easiest way is to download Landmarker/RoiEditor from www.mristudio.org , which come with different types of electronic atlases. One of them is population-averaged atlas in the MNI coordinates. If you use linear normalization, I recommend using this atlas (named ICBM_DTI-81 for GE/Siemens and JHU-MNI-GA for Philips). If you use highly non-linear normalization, I recommend the single-subject atlas (named JHU-MNI-SS). Both atlases come with a hand-segmented white matter parcellation map (WMPM). If you download RoiEditor, this software can apply the WMPM for various types of image quantification. Please refer to www.mristudio.org for more info. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of WangPing Sent: Saturday, January 24, 2009 11:53 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] human brain atlas Importance: High Dear Dr. Mori and the List: Could anyone recommend a brain atlas (label atlas) that covers the main white matters? It will be great if this atlas is easy to register to MNI template. Thanks a lot! Ping _____ ???? MSN ?????? MSN ????? ???? ?? _____ ??????????MSN??? ????? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090126/81475b51/attachment-0001.html From pwang_xjtu at hotmail.com Mon Jan 26 15:16:56 2009 From: pwang_xjtu at hotmail.com (WangPing) Date: Tue, 27 Jan 2009 04:16:56 +0800 Subject: [Mristudio-users] human brain atlas In-Reply-To: <6u9vds$671qf0@ipex3.johnshopkins.edu> References: <6u9vds$671qf0@ipex3.johnshopkins.edu> Message-ID: Susumu, thank you very much. Ping Date: Mon, 26 Jan 2009 12:50:23 -0500 From: susumu at mri.jhu.edu To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] human brain atlas 1) Landmarker can normalize your data to ICBM-152. It comes with the ICBM (including our ICBM-DTI contrasts) and you can doa linear or non-linear method. 2) If you already normalized to the ICBM-152, the first step can be skipped. Just make sure the following; > our ICBM-152 has 181x217x181 matrix with 1 mm resolution > You can load our ICBM-152 and your normalized images to Landmarker (or any other software) to make sure that the compatibility of two ICBM-152 (one you used and the other one implemented in Landmarker and RoiEditor). > Also, all of our software follows the Radiology convention (right is left). If you find your image is loaded upside down, that is because of the brain orientation issue. It is a good practice to make sure right-left is correct in your entire procedure using a subject with some characteristic asymmetry 3) Once you confirm that your ICBM atlas was compatible with the one implemented in our software, do the following; > Load your normalized data. If you have lesion volume data (I assume it is 1/0 binary data), load it with some anatomical image such as T2. > Make sure that the image dimension is 181x217x181 / 1mm > Then, choose "ICBM" as an atlas in the right column > There is a button looks like the lung. Click it. This automatically segment your data into many white matter and gray matter regions and give you a report. For your lesion image, you can get how many "1 = lesion pixel" are in each segmented white matter area. > If you want to see the segmentation visually, use the "load" button in the "atlas" section and load one of the "WMPM". You can visually see the superimiposition of the segmentation on the loaded images. Try From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of WangPing Sent: Monday, January 26, 2009 11:32 AM To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] human brain atlas Importance: High Susumu, I just played with RoiEditor for a while, and found the atlas with the software. I am wondering if the tool (or you may recommend other tool) can use the atlas to label my subjects. Right now my subjects have been normalized to MNI152 space (non-linear registration), there are white matter lesions on some subjects, I want to calculate the lesion volume on the white matter regions. IF I can label my subjects, I will know the lesion volume on each parcellation. I do not have to need a very detailed label atlas at this point, maybe a atlas that can divide a brain into a few parcellations will be okay. Thanks, any suggestion is high appreciated. Best Regards, Ping Date: Sun, 25 Jan 2009 08:38:18 -0500 From: susumu at mri.jhu.edu To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] human brain atlas Hi Ping, We have several white matter atlases in lbam.med.jhmi.edu, but the easiest way is to download Landmarker/RoiEditor from www.mristudio.org, which come with different types of electronic atlases. One of them is population-averaged atlas in the MNI coordinates. If you use linear normalization, I recommend using this atlas (named ICBM_DTI-81 for GE/Siemens and JHU-MNI-GA for Philips). If you use highly non-linear normalization, I recommend the single-subject atlas (named JHU-MNI-SS). Both atlases come with a hand-segmented white matter parcellation map (WMPM). If you download RoiEditor, this software can apply the WMPM for various types of image quantification. Please refer to www.mristudio.org for more info. Susumu From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of WangPing Sent: Saturday, January 24, 2009 11:53 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] human brain atlas Importance: High Dear Dr. Mori and the List: Could anyone recommend a brain atlas (label atlas) that covers the main white matters? It will be great if this atlas is easy to register to MNI template. Thanks a lot! Ping ???? MSN ?????? MSN ????? ?????? ??????????MSN??? ????? _________________________________________________________________ ?Windows Live ?????????? MSN? http://im.live.cn/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090127/9623cbf1/attachment.html From gifforda at kennedykrieger.org Tue Jan 27 14:48:17 2009 From: gifforda at kennedykrieger.org (Aliya Gifford) Date: Tue, 27 Jan 2009 14:48:17 -0500 Subject: [Mristudio-users] Problem loading fiber tracks Message-ID: <497F25A30200003900012DF6@KKI-GSPGWIA.KKI.ORG> Hi - I have a question about loading previously created fiber tracks in DTIStudio that I'm hoping someone can help me with. I have used DTIStudio to create fiber tracks by selecting "File -> Fiber Tracking" and opening the desired *.fa and *.vec files and inputting the parameters and creating the fiber tracts from the images. This was no problem. The problem comes in trying to re-load the fiber tracts back onto the original image. What I want to do is have the image from which I created the tracts and open all the fiber tracts at the same time so I can see them on the image. I have tried doing this in two methods. 1) Re-open the .fa and .vec files as if I will re-track the files. Then click on the "Fiber" tab and open the fiber file. When I do this I get an error saying the image parameters do not match. When the fiber is then displayed on the image it is in the wrong place. 2) Open the image file from going to "File - > MRI View3D" and inputting the correct image parameters. Then going to "File -> Load Fiber-Data" and opening the fiber tract file. But the same error appears saying the image parameters do not match. Any help with this issue would be greatly appreciated! ~Aliya Please consider the environment before printing this E-Mail. Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. From hjiang at jhmi.edu Tue Jan 27 17:02:26 2009 From: hjiang at jhmi.edu (Hangyi Jiang) Date: Tue, 27 Jan 2009 17:02:26 -0500 Subject: [Mristudio-users] Problem loading fiber tracks Message-ID: <497F3E21020000630001BB35@cis27.hosts.jhmi.edu> hi, Aliya, the method 2) you had tried is the right way to load pre-saved fibers and superimpose them on to the images. in the fiber data file, the image parameters from fiber tracking are being saved. when you re-load the fiber data, these parameters must be same as that of the image you want to superimpose on. otherwise, the fibers will not be displayed correctly. these parameters include image dimensions, pixel slze and image orientation, slicing sequence etc. please double check the parameters when you load the images, they must be same as that of the fiber tracking was carried on. if you have only few pre-saved fiber data files, you may do fiber tracking again using "corrected" image parameters. fiber tracking does not take long time. :) if you have many files, and really cannot retrieve the parameters back, you can sent me a fiber data file, I can take a look. regards, hangyi >>> Aliya Gifford 01/27/09 2:48 PM >>> Hi - I have a question about loading previously created fiber tracks in DTIStudio that I'm hoping someone can help me with. I have used DTIStudio to create fiber tracks by selecting "File -> Fiber Tracking" and opening the desired *.fa and *.vec files and inputting the parameters and creating the fiber tracts from the images. This was no problem. The problem comes in trying to re-load the fiber tracts back onto the original image. What I want to do is have the image from which I created the tracts and open all the fiber tracts at the same time so I can see them on the image. I have tried doing this in two methods. 1) Re-open the .fa and .vec files as if I will re-track the files. Then click on the "Fiber" tab and open the fiber file. When I do this I get an error saying the image parameters do not match. When the fiber is then displayed on the image it is in the wrong place. 2) Open the image file from going to "File - > MRI View3D" and inputting the correct image parameters. Then going to "File -> Load Fiber-Data" and opening the fiber tract file. But the same error appears saying the image parameters do not match. Any help with this issue would be greatly appreciated! ~Aliya Please consider the environment before printing this E-Mail. Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From naamab at stanford.edu Tue Jan 27 17:32:22 2009 From: naamab at stanford.edu (Naama Barnea-Goraly) Date: Tue, 27 Jan 2009 14:32:22 -0800 Subject: [Mristudio-users] roieditor colormap generated rois on an FA map In-Reply-To: References: <5310C336-2EE4-4859-A294-406D8A9519EC@stanford.edu> <928158CE-6BBF-4141-A5E1-B266820C1B83@stanford.edu> Message-ID: <774AF029-0DB0-45C2-B1E1-3105454791D4@stanford.edu> Thanks. But it will still use the whole ROI to generate stats? Thanks, Naama On Jan 25, 2009, at 11:21 AM, susumu wrote: > Hi Naama, > > I think this is correct. In RoiEditor, once an ROI is registered as an > "object", it shows only the boundary of the object and the inside is > not > filled. > > -----Original Message----- > From: mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Naama > Barnea-Goraly > Sent: Sunday, January 25, 2009 1:29 PM > To: mristudio-users at mristudio.org > Subject: [Mristudio-users] roieditor colormap generated rois on an > FA map > > > Dear mristudio team, > > I created an ROI on a colormap using roieditor and then opened in on > my FA map. On the color map it looks fine, but on the FA map it has a > "hole" in the middle (see pic). > Please advise. > > Thanks, > > Naama > > >> >> >> > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users Naama Barnea-Goraly M.D. Instructor Center for Interdisciplinary Brain Sciences Research Stanford University Division of Child and Adolescent Psychiatry 401 Quarry Rd. MC 5795 Stanford University School of Medicine Stanford, CA 94305-5795 Phone: (650) 736-1874, fax: (650) 724-4794 CONFIDENTIALITY NOTICE: This e-mail communication and any attachments may contain confidential information for the use of the designated recipients named above. If you are not the intended recipient, you are hereby notified that you have received this communication in error and that any review, disclosure, dissemination, distribution or copying of it or its contents is prohibited. If you have received this communication in error, please notify Stanford Medical Center immediately by telephone at (650) 725-5722 and destroy all copies of this communication and any attachments. Thank you. From susumu at mri.jhu.edu Tue Jan 27 19:17:54 2009 From: susumu at mri.jhu.edu (susumu at mri.jhu.edu) Date: Wed, 28 Jan 2009 00:17:54 +0000 Subject: [Mristudio-users] roieditor colormap generated rois on an FA map In-Reply-To: <774AF029-0DB0-45C2-B1E1-3105454791D4@stanford.edu> References: <5310C336-2EE4-4859-A294-406D8A9519EC@stanford.edu> <928158CE-6BBF-4141-A5E1-B266820C1B83@stanford.edu> <774AF029-0DB0-45C2-B1E1-3105454791D4@stanford.edu> Message-ID: <2132861523-1233101879-cardhu_decombobulator_blackberry.rim.net-221217102-@bxe032.bisx.prod.on.blackberry> I'm not sure if I understood your question, but yes, if you define an object (ROI), all the pixels inside it are grouped to generate statistics. That's the point of drawing ROIs, right? You also have an option to export the pixel values to generate a histogram. Sent via BlackBerry by AT&T -----Original Message----- From: Naama Barnea-Goraly Date: Tue, 27 Jan 2009 14:32:22 To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] roieditor colormap generated rois on an FA map Thanks. But it will still use the whole ROI to generate stats? Thanks, Naama On Jan 25, 2009, at 11:21 AM, susumu wrote: > Hi Naama, > > I think this is correct. In RoiEditor, once an ROI is registered as an > "object", it shows only the boundary of the object and the inside is > not > filled. > > -----Original Message----- > From: mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Naama > Barnea-Goraly > Sent: Sunday, January 25, 2009 1:29 PM > To: mristudio-users at mristudio.org > Subject: [Mristudio-users] roieditor colormap generated rois on an > FA map > > > Dear mristudio team, > > I created an ROI on a colormap using roieditor and then opened in on > my FA map. On the color map it looks fine, but on the FA map it has a > "hole" in the middle (see pic). > Please advise. > > Thanks, > > Naama > > >> >> >> > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users Naama Barnea-Goraly M.D. Instructor Center for Interdisciplinary Brain Sciences Research Stanford University Division of Child and Adolescent Psychiatry 401 Quarry Rd. MC 5795 Stanford University School of Medicine Stanford, CA 94305-5795 Phone: (650) 736-1874, fax: (650) 724-4794 CONFIDENTIALITY NOTICE: This e-mail communication and any attachments may contain confidential information for the use of the designated recipients named above. If you are not the intended recipient, you are hereby notified that you have received this communication in error and that any review, disclosure, dissemination, distribution or copying of it or its contents is prohibited. If you have received this communication in error, please notify Stanford Medical Center immediately by telephone at (650) 725-5722 and destroy all copies of this communication and any attachments. Thank you. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From varangovind at gmail.com Wed Feb 4 13:47:27 2009 From: varangovind at gmail.com (Varan Govind) Date: Wed, 04 Feb 2009 13:47:27 -0500 Subject: [Mristudio-users] LDDMM in LandMarker Message-ID: <25a47ed60902041047m361906b2y77af012c27a32261@mail.gmail.com> Dear LandMarker Developers and Users, I've been trying to use the LDDMM option in LandMarker to perform intra-subject registration of T2-weighted images with b=0 images following the procedure detailed in Dr. Mori's paper,entitled, 'Correction of B0 susceptibility induced distortion in diffusion-weighted images using large-deformation diffeomorphic metric mapping', Magn. Reson. Imaging 26:1294-302 (2008). Briefly, the following were performed: Step 1: In DtiStudio (version 3.0 Beta), to correct eddy current distorion, all DWI were registered to b=0 images using AIR and selecting 'Affine' for the 'Linear Transformation Approach'. Step 2: T2-weighted and mean b=0 images were skull stripped using MRICro. Step 3: Skull-stripped T2 (target) and b=0 images (subject) were loaded to LandMarker. Both the images were resampled so that they have the same spatial resolution using 'Resample Image', prior to which, data format of both were changed to using 'Change Image Data Format' option (both the files have the same spatial resolutions, i.e., 128x128x2 mm3 resolution). Step 4: Intensity of both the images (T2 and b=0) were adjusted using 'Intensity Correction' option in the Volume LDDMM. Step 5: 'Single channel' option under Volume LDDMM was selected to set parameters for this registration process and provided my email address and submitted the data for remote processing. After a few minutes, I have got an email from lddmmproc at cis.jhu.edu with an Md5 String and an ftp link for downloading the processed data. Step 6: To view the registered data, I copied the Md5 string from the email message and pasted it at 'Retrieve Results From Remote Volume LDDMM' in LandMarker. A little while later, I've got a message that said 'The Kimap file cannot be found in the resultant data'. I extracted the files from the Results.zip file and found a non-zero size Kimap file, named as Kimap000.vtk. If anybody got the same message in LandMarker, 'The Kimap file cannot be found in the resultant data', could you please let me know how I can see the results? Thank you very much in advance, govind University of Miami, Miami, Florida -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090204/53ec5a84/attachment.html From xli16 at jhmi.edu Wed Feb 4 15:23:57 2009 From: xli16 at jhmi.edu (XIN LI) Date: Wed, 04 Feb 2009 15:23:57 -0500 Subject: [Mristudio-users] LDDMM in LandMarker In-Reply-To: <25a47ed60902041047m361906b2y77af012c27a32261@mail.gmail.com> References: <25a47ed60902041047m361906b2y77af012c27a32261@mail.gmail.com> Message-ID: Govind, I am going to fix this problem. Please ignore the message. Kimap000.vtk is the Kimap you need to transform your image. Xin ----- Original Message ----- From: Varan Govind Date: Wednesday, February 4, 2009 1:47 pm Subject: [Mristudio-users] LDDMM in LandMarker To: mristudio-users at mristudio.org > Dear LandMarker Developers and Users, > > I've been trying to use the LDDMM option in LandMarker to perform > intra-subject registration of T2-weighted images with b=0 images following > the procedure detailed in Dr. Mori's paper,entitled, 'Correction of B0 > susceptibility induced distortion in diffusion-weighted images using > large-deformation diffeomorphic metric mapping', Magn. Reson. Imaging > 26:1294-302 (2008). Briefly, the following were performed: > > Step 1: In DtiStudio (version 3.0 Beta), to correct eddy current distorion, > all DWI were registered to b=0 images using AIR and selecting > 'Affine' for > the 'Linear Transformation Approach'. > > Step 2: T2-weighted and mean b=0 images were skull stripped using MRICro. > > Step 3: Skull-stripped T2 (target) and b=0 images (subject) were > loaded to > LandMarker. Both the images were resampled so that they have the same > spatial resolution using 'Resample Image', prior to which, data > format of > both were changed to using 'Change Image Data Format' option (both > the > files have the same spatial resolutions, i.e., 128x128x2 mm3 resolution). > > Step 4: Intensity of both the images (T2 and b=0) were adjusted using > 'Intensity Correction' option in the Volume LDDMM. > > Step 5: 'Single channel' option under Volume LDDMM was selected to set > parameters for this registration process and provided my email > address and > submitted the data for remote processing. > > After a few minutes, I have got an email from lddmmproc at cis.jhu.edu > with an > Md5 String and an ftp link for downloading the processed data. > > Step 6: To view the registered data, I copied the Md5 string from the > email > message and pasted it at 'Retrieve Results From Remote Volume LDDMM' > in > LandMarker. A little while later, I've got a message that said 'The Kimap > file cannot be found in the resultant data'. I extracted the files > from the > Results.zip file and found a non-zero size Kimap file, named as > Kimap000.vtk. > > If anybody got the same message in LandMarker, 'The Kimap file cannot > be > found in the resultant data', could you please let me know how I can > see the > results? > > Thank you very much in advance, > > govind > University of Miami, Miami, Florida > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > From Ihssan.Abdulkareem at liverpool.ac.uk Fri Feb 6 04:52:42 2009 From: Ihssan.Abdulkareem at liverpool.ac.uk (Abdul-Kareem, Ihssan) Date: Fri, 06 Feb 2009 09:52:42 +0000 Subject: [Mristudio-users] roieditor colormap generated rois on an FA map In-Reply-To: <2132861523-1233101879-cardhu_decombobulator_blackberry.rim.net-221217102-@bxe032.bisx.prod.on.blackberry> References: <5310C336-2EE4-4859-A294-406D8A9519EC@stanford.edu> <928158CE-6BBF-4141-A5E1-B266820C1B83@stanford.edu> <774AF029-0DB0-45C2-B1E1-3105454791D4@stanford.edu> <2132861523-1233101879-cardhu_decombobulator_blackberry.rim.net-221217102-@bxe032.bisx.prod.on.blackberry> Message-ID: Hi Can any body give me an optimum DTI 3T Siemens sequence sothat I can implement in our scanner in Liverpool University. ________________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of susumu at mri.jhu.edu [susumu at mri.jhu.edu] Sent: 28 January 2009 00:17 To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] roieditor colormap generated rois on an FA map I'm not sure if I understood your question, but yes, if you define an object (ROI), all the pixels inside it are grouped to generate statistics. That's the point of drawing ROIs, right? You also have an option to export the pixel values to generate a histogram. Sent via BlackBerry by AT&T -----Original Message----- From: Naama Barnea-Goraly Date: Tue, 27 Jan 2009 14:32:22 To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] roieditor colormap generated rois on an FA map Thanks. But it will still use the whole ROI to generate stats? Thanks, Naama On Jan 25, 2009, at 11:21 AM, susumu wrote: > Hi Naama, > > I think this is correct. In RoiEditor, once an ROI is registered as an > "object", it shows only the boundary of the object and the inside is > not > filled. > > -----Original Message----- > From: mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Naama > Barnea-Goraly > Sent: Sunday, January 25, 2009 1:29 PM > To: mristudio-users at mristudio.org > Subject: [Mristudio-users] roieditor colormap generated rois on an > FA map > > > Dear mristudio team, > > I created an ROI on a colormap using roieditor and then opened in on > my FA map. On the color map it looks fine, but on the FA map it has a > "hole" in the middle (see pic). > Please advise. > > Thanks, > > Naama > > >> >> >> > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users Naama Barnea-Goraly M.D. Instructor Center for Interdisciplinary Brain Sciences Research Stanford University Division of Child and Adolescent Psychiatry 401 Quarry Rd. MC 5795 Stanford University School of Medicine Stanford, CA 94305-5795 Phone: (650) 736-1874, fax: (650) 724-4794 CONFIDENTIALITY NOTICE: This e-mail communication and any attachments may contain confidential information for the use of the designated recipients named above. If you are not the intended recipient, you are hereby notified that you have received this communication in error and that any review, disclosure, dissemination, distribution or copying of it or its contents is prohibited. If you have received this communication in error, please notify Stanford Medical Center immediately by telephone at (650) 725-5722 and destroy all copies of this communication and any attachments. Thank you. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From susumu at mri.jhu.edu Sun Feb 8 11:06:26 2009 From: susumu at mri.jhu.edu (susumu) Date: Sun, 08 Feb 2009 11:06:26 -0500 Subject: [Mristudio-users] Problem loading fiber tracks In-Reply-To: <497F25A30200003900012DF6@KKI-GSPGWIA.KKI.ORG> Message-ID: <7iunte$6c0ngr@ipex3.johnshopkins.edu> Hi Aliya, Usually this message happens when the image matrix or pixel size doesn't match with the fiber file. Could you do a simple test? Do a fiber tracking, save a result, close the program, restart it, load the FA map you used, and load the tract using the #2 method. If DtiStudio failed this simple test, please send us your FA image and the tract file. We will look into the issue. Pleas make sure that all image parameters are identical in the first and the second image loading. Susumu -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Aliya Gifford Sent: Tuesday, January 27, 2009 2:48 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] Problem loading fiber tracks Hi - I have a question about loading previously created fiber tracks in DTIStudio that I'm hoping someone can help me with. I have used DTIStudio to create fiber tracks by selecting "File -> Fiber Tracking" and opening the desired *.fa and *.vec files and inputting the parameters and creating the fiber tracts from the images. This was no problem. The problem comes in trying to re-load the fiber tracts back onto the original image. What I want to do is have the image from which I created the tracts and open all the fiber tracts at the same time so I can see them on the image. I have tried doing this in two methods. 1) Re-open the .fa and .vec files as if I will re-track the files. Then click on the "Fiber" tab and open the fiber file. When I do this I get an error saying the image parameters do not match. When the fiber is then displayed on the image it is in the wrong place. 2) Open the image file from going to "File - > MRI View3D" and inputting the correct image parameters. Then going to "File -> Load Fiber-Data" and opening the fiber tract file. But the same error appears saying the image parameters do not match. Any help with this issue would be greatly appreciated! ~Aliya Please consider the environment before printing this E-Mail. Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From varangovind at gmail.com Mon Feb 9 17:13:49 2009 From: varangovind at gmail.com (Varan Govind) Date: Mon, 09 Feb 2009 17:13:49 -0500 Subject: [Mristudio-users] LDDMM in LandMarker In-Reply-To: References: <25a47ed60902041047m361906b2y77af012c27a32261@mail.gmail.com> Message-ID: <25a47ed60902091413g1d16fbdby9792ad3ff61c146b@mail.gmail.com> Dr. Xin, Thank you for your reply. Could you please let me know after fixing this problem? govind On Wed, Feb 4, 2009 at 3:23 PM, XIN LI wrote: > Govind, > > I am going to fix this problem. Please ignore the message. Kimap000.vtk is > the Kimap you need to transform your image. > > > Xin > > > > > > ----- Original Message ----- > From: Varan Govind > Date: Wednesday, February 4, 2009 1:47 pm > Subject: [Mristudio-users] LDDMM in LandMarker > To: mristudio-users at mristudio.org > > > > Dear LandMarker Developers and Users, > > > > I've been trying to use the LDDMM option in LandMarker to perform > > intra-subject registration of T2-weighted images with b=0 images > following > > the procedure detailed in Dr. Mori's paper,entitled, 'Correction of B0 > > susceptibility induced distortion in diffusion-weighted images using > > large-deformation diffeomorphic metric mapping', Magn. Reson. Imaging > > 26:1294-302 (2008). Briefly, the following were performed: > > > > Step 1: In DtiStudio (version 3.0 Beta), to correct eddy current > distorion, > > all DWI were registered to b=0 images using AIR and selecting > > 'Affine' for > > the 'Linear Transformation Approach'. > > > > Step 2: T2-weighted and mean b=0 images were skull stripped using > MRICro. > > > > Step 3: Skull-stripped T2 (target) and b=0 images (subject) were > > loaded to > > LandMarker. Both the images were resampled so that they have the same > > spatial resolution using 'Resample Image', prior to which, data > > format of > > both were changed to using 'Change Image Data Format' option (both > > the > > files have the same spatial resolutions, i.e., 128x128x2 mm3 > resolution). > > > > Step 4: Intensity of both the images (T2 and b=0) were adjusted using > > 'Intensity Correction' option in the Volume LDDMM. > > > > Step 5: 'Single channel' option under Volume LDDMM was selected to set > > parameters for this registration process and provided my email > > address and > > submitted the data for remote processing. > > > > After a few minutes, I have got an email from lddmmproc at cis.jhu.edu > > with an > > Md5 String and an ftp link for downloading the processed data. > > > > Step 6: To view the registered data, I copied the Md5 string from the > > email > > message and pasted it at 'Retrieve Results From Remote Volume LDDMM' > > in > > LandMarker. A little while later, I've got a message that said 'The > Kimap > > file cannot be found in the resultant data'. I extracted the files > > from the > > Results.zip file and found a non-zero size Kimap file, named as > > Kimap000.vtk. > > > > If anybody got the same message in LandMarker, 'The Kimap file cannot > > be > > found in the resultant data', could you please let me know how I can > > see the > > results? > > > > Thank you very much in advance, > > > > govind > > University of Miami, Miami, Florida > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090209/e650d46f/attachment-0001.html From usinhaster at gmail.com Mon Feb 9 14:38:18 2009 From: usinhaster at gmail.com (Usha Sinha) Date: Mon, 09 Feb 2009 11:38:18 -0800 Subject: [Mristudio-users] fiber tracking capillary phantom Message-ID: Hi I have been using DTIStudio for a while for tracking fibers in muscle. Muscle fiber FA values are lower than white matter ( in the range 0.2-0.4). I am currently evaluating with a capillary phantom with an FA of 0.20. This is a straight 5 cm capillary imaged with the capillary axis along the z-axis. I am trying to check the SNR conditions, as well geometry parameters that provide an accurate estimate of the capillary length. Slice by slice evaluation of the capillary region clearly gives a value of +_2 degrees to the z-axis for the leading eigenvector. So our SNR is sufficient to give the correct lead eigenvector orientation but the tracking results are surprising: A: Tracking condition: FA threshold: 0.15, angle threshold: 10 degree 1) if a seed point of 1 voxel is used, the fibers are either short or there are often no fibers tracked from the seed point (even though seed point and neighbor voxels have values of FA above threshold) 2) if the entire capillary array is selected, then there are some fibers yet average length of fibers is 2 cm (and not 5 cm as expected). I guess the difference between 1 and 2 is that in (2) several multiple connections are found by the 'brute force' methods. B: Tracking condition: FA threshold: 0.15, angle threshold: 70 degree The number of fibers are many more for this condition still fiber length does not reach 5 cm average (more like 3 cm)! My questions:: 1) Why are the fibers not tracked for 10 degree angle threshold? These are straight capillaries with angle differences only arising from noise (which our measurements show are within 2-3 degrees) 2) Examining fibers from a single seed point, we see that fibers are not entirely parallel to the capillary axis; rather short segments and curvature of fiber is seen. 3) Is there a restriction on how anisotropic the slice voxel can be: we have in-plane of 0.3125x0.3125 and thickness of 5mm--- however capillary axis is along the slice axis. I wonder of this affects the interpolation needed for FACT This has been of great concern-- please do send me some feedback usha sinha usinha at sciences.sdsu.edu usinhaster at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090209/b3f326b5/attachment.html From yapengw at u.washington.edu Mon Feb 9 20:12:23 2009 From: yapengw at u.washington.edu (yapengw at u.washington.edu) Date: Mon, 09 Feb 2009 17:12:23 -0800 (PST) Subject: [Mristudio-users] fiber tracking and DTI map between two groups Message-ID: Hi studio users, I'm ready to compare whether the FA, RA values and the fibers going through Frontal, ACC and Parietal lobes are different for two groups(A and B). Right now, I know how to calculate the FA and RA, and to do fiber tracking at the whole brain for single subject, but I do now know how to get the FA and RA values, and fiber tracking resluts at a specific area for single subject and two groups. It seems that for FA and RA analysis, and fiber tracking, to attain my research purpose, I have to do ROI analysis. Should I draw ROI and do ROI analysis subject by subject, or there is other method to do ROI analysis in an easier way? When I finish ROI analysis for FA, RA and fiber tracking. How can I know FA and RA values and fiber tracking resluts at a specific ROI? Thank you very much! Yapeng Yapeng Wang, ph.D. Institute for Learning and Brain Sciences Mailstop 357988 University of Washington Seattle, WA 98195 From xli16 at jhmi.edu Tue Feb 10 10:08:21 2009 From: xli16 at jhmi.edu (XIN LI) Date: Tue, 10 Feb 2009 10:08:21 -0500 Subject: [Mristudio-users] LDDMM in LandMarker In-Reply-To: <25a47ed60902091413g1d16fbdby9792ad3ff61c146b@mail.gmail.com> References: <25a47ed60902041047m361906b2y77af012c27a32261@mail.gmail.com> <25a47ed60902091413g1d16fbdby9792ad3ff61c146b@mail.gmail.com> Message-ID: Govind, We have fixed the problem. You wouldn't get the warning message any more. Xin ----- Original Message ----- From: Varan Govind Date: Monday, February 9, 2009 5:14 pm Subject: Re: [Mristudio-users] LDDMM in LandMarker To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > Dr. Xin, > > Thank you for your reply. Could you please let me know after fixing this > problem? > > govind > > On Wed, Feb 4, 2009 at 3:23 PM, XIN LI wrote: > > > Govind, > > > > I am going to fix this problem. Please ignore the message. > Kimap000.vtk is > > the Kimap you need to transform your image. > > > > > > Xin > > > > > > > > > > > > ----- Original Message ----- > > From: Varan Govind > > Date: Wednesday, February 4, 2009 1:47 pm > > Subject: [Mristudio-users] LDDMM in LandMarker > > To: mristudio-users at mristudio.org > > > > > > > Dear LandMarker Developers and Users, > > > > > > I've been trying to use the LDDMM option in LandMarker to perform > > > intra-subject registration of T2-weighted images with b=0 images > > following > > > the procedure detailed in Dr. Mori's paper,entitled, 'Correction > of B0 > > > susceptibility induced distortion in diffusion-weighted images using > > > large-deformation diffeomorphic metric mapping', Magn. Reson. Imaging > > > 26:1294-302 (2008). Briefly, the following were performed: > > > > > > Step 1: In DtiStudio (version 3.0 Beta), to correct eddy current > > distorion, > > > all DWI were registered to b=0 images using AIR and selecting > > > 'Affine' for > > > the 'Linear Transformation Approach'. > > > > > > Step 2: T2-weighted and mean b=0 images were skull stripped using > > MRICro. > > > > > > Step 3: Skull-stripped T2 (target) and b=0 images (subject) were > > > loaded to > > > LandMarker. Both the images were resampled so that they have the > same > > > spatial resolution using 'Resample Image', prior to which, data > > > format of > > > both were changed to using 'Change Image Data Format' option (both > > > the > > > files have the same spatial resolutions, i.e., 128x128x2 mm3 > > resolution). > > > > > > Step 4: Intensity of both the images (T2 and b=0) were adjusted > using > > > 'Intensity Correction' option in the Volume LDDMM. > > > > > > Step 5: 'Single channel' option under Volume LDDMM was selected > to set > > > parameters for this registration process and provided my email > > > address and > > > submitted the data for remote processing. > > > > > > After a few minutes, I have got an email from lddmmproc at cis.jhu.edu > > > with an > > > Md5 String and an ftp link for downloading the processed data. > > > > > > Step 6: To view the registered data, I copied the Md5 string > from the > > > email > > > message and pasted it at 'Retrieve Results From Remote Volume LDDMM' > > > in > > > LandMarker. A little while later, I've got a message that said 'The > > Kimap > > > file cannot be found in the resultant data'. I extracted the files > > > from the > > > Results.zip file and found a non-zero size Kimap file, named as > > > Kimap000.vtk. > > > > > > If anybody got the same message in LandMarker, 'The Kimap file cannot > > > be > > > found in the resultant data', could you please let me know how I > can > > > see the > > > results? > > > > > > Thank you very much in advance, > > > > > > govind > > > University of Miami, Miami, Florida > > > _______________________________________________ > > > Mristudio-users mailing list > > > Mristudio-users at mristudio.org > > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > From SCopeland at mednet.ucla.edu Tue Feb 10 12:49:08 2009 From: SCopeland at mednet.ucla.edu (Copeland, Sarah A.) Date: Tue, 10 Feb 2009 09:49:08 -0800 Subject: [Mristudio-users] saving files Message-ID: Hello, I am having a problem when trying to save processed files and reopen them later. I am able to load DTI data and process it to the point where I have FA, mean of B0, etc. I click the "save" button, and get the window which allows me to choose files to save (with the arrow pointing to the right hand box) and I do so. When I try to open them, though, the program essentially starts me over by asking me to load file parameters and then reprocessing the data. So for example if I try to save colormap 0 just as a test, when I try to reopen I'm back to the point where I would have to start calculating tensors, etc. over again. I am trying to save mean of B0s to bring it into Landmarker and use AIR to coregister MPRAGE images to the DTI data. I thought of doing this in DTI studio, but cannot open the MPRAGE image in DTI studio (it won't recognize anything except the raw data files in the pull-down menu). I know people are able to save and reopen files all the time. Am I missing an obvious step? Thank you! IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. From varangovind at gmail.com Thu Feb 12 08:58:12 2009 From: varangovind at gmail.com (Varan Govind) Date: Thu, 12 Feb 2009 08:58:12 -0500 Subject: [Mristudio-users] LDDMM in LandMarker In-Reply-To: References: <25a47ed60902041047m361906b2y77af012c27a32261@mail.gmail.com> <25a47ed60902091413g1d16fbdby9792ad3ff61c146b@mail.gmail.com> Message-ID: <25a47ed60902120558j9176915ue2e41419968cdc82@mail.gmail.com> Dr. Xin, Thank you for your quick response. govind On Tue, Feb 10, 2009 at 10:08 AM, XIN LI wrote: > Govind, > > We have fixed the problem. You wouldn't get the warning message any more. > > > Xin > > ----- Original Message ----- > From: Varan Govind > Date: Monday, February 9, 2009 5:14 pm > Subject: Re: [Mristudio-users] LDDMM in LandMarker > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" < > mristudio-users at mristudio.org> > > > > Dr. Xin, > > > > Thank you for your reply. Could you please let me know after fixing this > > problem? > > > > govind > > > > On Wed, Feb 4, 2009 at 3:23 PM, XIN LI wrote: > > > > > Govind, > > > > > > I am going to fix this problem. Please ignore the message. > > Kimap000.vtk is > > > the Kimap you need to transform your image. > > > > > > > > > Xin > > > > > > > > > > > > > > > > > > ----- Original Message ----- > > > From: Varan Govind > > > Date: Wednesday, February 4, 2009 1:47 pm > > > Subject: [Mristudio-users] LDDMM in LandMarker > > > To: mristudio-users at mristudio.org > > > > > > > > > > Dear LandMarker Developers and Users, > > > > > > > > I've been trying to use the LDDMM option in LandMarker to perform > > > > intra-subject registration of T2-weighted images with b=0 images > > > following > > > > the procedure detailed in Dr. Mori's paper,entitled, 'Correction > > of B0 > > > > susceptibility induced distortion in diffusion-weighted images > using > > > > large-deformation diffeomorphic metric mapping', Magn. Reson. > Imaging > > > > 26:1294-302 (2008). Briefly, the following were performed: > > > > > > > > Step 1: In DtiStudio (version 3.0 Beta), to correct eddy current > > > distorion, > > > > all DWI were registered to b=0 images using AIR and selecting > > > > 'Affine' for > > > > the 'Linear Transformation Approach'. > > > > > > > > Step 2: T2-weighted and mean b=0 images were skull stripped using > > > MRICro. > > > > > > > > Step 3: Skull-stripped T2 (target) and b=0 images (subject) were > > > > loaded to > > > > LandMarker. Both the images were resampled so that they have the > > same > > > > spatial resolution using 'Resample Image', prior to which, data > > > > format of > > > > both were changed to using 'Change Image Data Format' option > (both > > > > the > > > > files have the same spatial resolutions, i.e., 128x128x2 mm3 > > > resolution). > > > > > > > > Step 4: Intensity of both the images (T2 and b=0) were adjusted > > using > > > > 'Intensity Correction' option in the Volume LDDMM. > > > > > > > > Step 5: 'Single channel' option under Volume LDDMM was selected > > to set > > > > parameters for this registration process and provided my email > > > > address and > > > > submitted the data for remote processing. > > > > > > > > After a few minutes, I have got an email from > lddmmproc at cis.jhu.edu > > > > with an > > > > Md5 String and an ftp link for downloading the processed data. > > > > > > > > Step 6: To view the registered data, I copied the Md5 string > > from the > > > > email > > > > message and pasted it at 'Retrieve Results From Remote Volume > LDDMM' > > > > in > > > > LandMarker. A little while later, I've got a message that said 'The > > > Kimap > > > > file cannot be found in the resultant data'. I extracted the files > > > > from the > > > > Results.zip file and found a non-zero size Kimap file, named as > > > > Kimap000.vtk. > > > > > > > > If anybody got the same message in LandMarker, 'The Kimap file > cannot > > > > be > > > > found in the resultant data', could you please let me know how I > > can > > > > see the > > > > results? > > > > > > > > Thank you very much in advance, > > > > > > > > govind > > > > University of Miami, Miami, Florida > > > > _______________________________________________ > > > > Mristudio-users mailing list > > > > Mristudio-users at mristudio.org > > > > > > > _______________________________________________ > > > Mristudio-users mailing list > > > Mristudio-users at mristudio.org > > > > > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090212/1bf06ed7/attachment-0001.html From 2mijung.kim at gmail.com Thu Feb 12 15:11:32 2009 From: 2mijung.kim at gmail.com (Mi Jung Kim) Date: Thu, 12 Feb 2009 12:11:32 -0800 Subject: [Mristudio-users] fiber tracking Message-ID: <53bb0fa40902121211k7edf8b6cs2c81f2be1757cac3@mail.gmail.com> Hi, I have been using Dtistudio with my phantom DTI data. Each slice seems to be fine, but I do not see any good result of fiber tracking, which means that I expect that fiber length is our phantom length, but it is not like that. Is anybody out there having similar problem? Thanks, Mi Jung -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090212/ae64a2e8/attachment.html From susumu at mri.jhu.edu Thu Feb 12 15:29:18 2009 From: susumu at mri.jhu.edu (susumu) Date: Thu, 12 Feb 2009 15:29:18 -0500 Subject: [Mristudio-users] fiber tracking In-Reply-To: <53bb0fa40902121211k7edf8b6cs2c81f2be1757cac3@mail.gmail.com> Message-ID: <7k7ed7$6dledh@ipex3.johnshopkins.edu> please make sure that the +/- sign and x, y, z order of your gradient table is correct. For example, typical gradient table supplied by Siemens and Philips need to have the +/- signs of x (siemens) or z (philips) components flipped when subjects are scanned in axial places with face up in the bore. This is explained in detail in the DtiStudio manual in www.mristudio.org. susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Mi Jung Kim Sent: Thursday, February 12, 2009 3:12 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] fiber tracking Hi, I have been using Dtistudio with my phantom DTI data. Each slice seems to be fine, but I do not see any good result of fiber tracking, which means that I expect that fiber length is our phantom length, but it is not like that. Is anybody out there having similar problem? Thanks, Mi Jung -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090212/8d715022/attachment.html From susumu at mri.jhu.edu Mon Feb 16 18:26:05 2009 From: susumu at mri.jhu.edu (susumu) Date: Mon, 16 Feb 2009 18:26:05 -0500 Subject: [Mristudio-users] fiber tracking capillary phantom In-Reply-To: Message-ID: <7k7ed7$6euu6g@ipex3.johnshopkins.edu> Hi Usha, Because we have been using DtiStudio for many fixed mouse brains and fiber tracking results can correctly follow the small convoluted paths of their white matter tracts, I think the algorithm should be working without, at least, a large amount of inaccuracy. DtiStudio does not keep tracking results if they are only few pixel long. That is why you sometimes don't see tracking results. For your data, the first thing you want to check is the SNR. Please look at the color map of your capilary phantom. Because the capilary is aligned along Z, they should look blue. If they look noisy and not pure blue, then SNR could be the culprit. Please also look at your vector image. You can place your cursor in the capilary, right click, and see pixel values of neiboring pixels. In this way, you can see FA values and vector values and understand which threshold came in to prevent you from seeing long fibers. With FA around 0.2, you need to have very high SNR to perform long-distance tracking. Regards, Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Usha Sinha Sent: Monday, February 09, 2009 2:38 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] fiber tracking capillary phantom Hi I have been using DTIStudio for a while for tracking fibers in muscle. Muscle fiber FA values are lower than white matter ( in the range 0.2-0.4). I am currently evaluating with a capillary phantom with an FA of 0.20. This is a straight 5 cm capillary imaged with the capillary axis along the z-axis. I am trying to check the SNR conditions, as well geometry parameters that provide an accurate estimate of the capillary length. Slice by slice evaluation of the capillary region clearly gives a value of +_2 degrees to the z-axis for the leading eigenvector. So our SNR is sufficient to give the correct lead eigenvector orientation but the tracking results are surprising: A: Tracking condition: FA threshold: 0.15, angle threshold: 10 degree 1) if a seed point of 1 voxel is used, the fibers are either short or there are often no fibers tracked from the seed point (even though seed point and neighbor voxels have values of FA above threshold) 2) if the entire capillary array is selected, then there are some fibers yet average length of fibers is 2 cm (and not 5 cm as expected). I guess the difference between 1 and 2 is that in (2) several multiple connections are found by the 'brute force' methods. B: Tracking condition: FA threshold: 0.15, angle threshold: 70 degree The number of fibers are many more for this condition still fiber length does not reach 5 cm average (more like 3 cm)! My questions:: 1) Why are the fibers not tracked for 10 degree angle threshold? These are straight capillaries with angle differences only arising from noise (which our measurements show are within 2-3 degrees) 2) Examining fibers from a single seed point, we see that fibers are not entirely parallel to the capillary axis; rather short segments and curvature of fiber is seen. 3) Is there a restriction on how anisotropic the slice voxel can be: we have in-plane of 0.3125x0.3125 and thickness of 5mm--- however capillary axis is along the slice axis. I wonder of this affects the interpolation needed for FACT This has been of great concern-- please do send me some feedback usha sinha usinha at sciences.sdsu.edu usinhaster at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090216/a022202f/attachment.html From SCopeland at mednet.ucla.edu Wed Feb 18 01:26:51 2009 From: SCopeland at mednet.ucla.edu (Copeland, Sarah A.) Date: Tue, 17 Feb 2009 22:26:51 -0800 Subject: [Mristudio-users] saving files Message-ID: Thanks, Hangyi - I have tried to do this before when loading data files, and tried it again as you suggested. I get the message "please enter an integer between 1 and 4096". I don't know where to enter an integer, or which to enter, but I've tried all options and still get the same error message. Can you help? Thanks again - Sarah hi, after saving, you can re-load the image by "File->MRI View 3D->..-> File_Format=RAW, Data_Type="Color" (for color map), or Data_Type="float" (for FA etc..)...-> OK" regards, hangyi > Hello, > > I am having a problem when trying to save processed files and reopen them later. > I am able to load DTI data and process it to the point where I have FA, mean of > B0, etc. I click the "save" button, and get the window which allows me to choose > files to save (with the arrow pointing to the right hand box) and I do so. When > I try to open them, though, the program essentially starts me over by asking me > to load file parameters and then reprocessing the data. So for example if I try > to save colormap 0 just as a test, when I try to reopen I'm back to the point > where I would have to start calculating tensors, etc. over again. > > I am trying to save mean of B0s to bring it into Landmarker and use AIR to > coregister MPRAGE images to the DTI data. I thought of doing this in DTI studio, > but cannot open the MPRAGE image in DTI studio (it won't recognize anything > except the raw data files in the pull-down menu). I know people are able to save > and reopen files all the time. Am I missing an obvious step? > > Thank you! IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. From SCopeland at mednet.ucla.edu Wed Feb 18 01:26:56 2009 From: SCopeland at mednet.ucla.edu (Copeland, Sarah A.) Date: Tue, 17 Feb 2009 22:26:56 -0800 Subject: [Mristudio-users] saving files Message-ID: Thanks, Hangyi - I have tried to do this before when loading data files, and tried it again as you suggested. I get the message "please enter an integer between 1 and 4096". I don't know where to enter an integer, or which to enter, but I've tried all options and still get the same error message. Can you help? Thanks again - Sarah hi, after saving, you can re-load the image by "File->MRI View 3D->..-> File_Format=RAW, Data_Type="Color" (for color map), or Data_Type="float" (for FA etc..)...-> OK" regards, hangyi > Hello, > > I am having a problem when trying to save processed files and reopen them later. > I am able to load DTI data and process it to the point where I have FA, mean of > B0, etc. I click the "save" button, and get the window which allows me to choose > files to save (with the arrow pointing to the right hand box) and I do so. When > I try to open them, though, the program essentially starts me over by asking me > to load file parameters and then reprocessing the data. So for example if I try > to save colormap 0 just as a test, when I try to reopen I'm back to the point > where I would have to start calculating tensors, etc. over again. > > I am trying to save mean of B0s to bring it into Landmarker and use AIR to > coregister MPRAGE images to the DTI data. I thought of doing this in DTI studio, > but cannot open the MPRAGE image in DTI studio (it won't recognize anything > except the raw data files in the pull-down menu). I know people are able to save > and reopen files all the time. Am I missing an obvious step? > > Thank you! IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. From SCopeland at mednet.ucla.edu Wed Feb 18 01:27:04 2009 From: SCopeland at mednet.ucla.edu (Copeland, Sarah A.) Date: Tue, 17 Feb 2009 22:27:04 -0800 Subject: [Mristudio-users] saving files Message-ID: Thanks, Hangyi - I have tried to do this before when loading data files, and tried it again as you suggested. I get the message "please enter an integer between 1 and 4096". I don't know where to enter an integer, or which to enter, but I've tried all options and still get the same error message. Can you help? Thanks again - Sarah hi, after saving, you can re-load the image by "File->MRI View 3D->..-> File_Format=RAW, Data_Type="Color" (for color map), or Data_Type="float" (for FA etc..)...-> OK" regards, hangyi > Hello, > > I am having a problem when trying to save processed files and reopen them later. > I am able to load DTI data and process it to the point where I have FA, mean of > B0, etc. I click the "save" button, and get the window which allows me to choose > files to save (with the arrow pointing to the right hand box) and I do so. When > I try to open them, though, the program essentially starts me over by asking me > to load file parameters and then reprocessing the data. So for example if I try > to save colormap 0 just as a test, when I try to reopen I'm back to the point > where I would have to start calculating tensors, etc. over again. > > I am trying to save mean of B0s to bring it into Landmarker and use AIR to > coregister MPRAGE images to the DTI data. I thought of doing this in DTI studio, > but cannot open the MPRAGE image in DTI studio (it won't recognize anything > except the raw data files in the pull-down menu). I know people are able to save > and reopen files all the time. Am I missing an obvious step? > > Thank you! IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. From susumu at mri.jhu.edu Wed Feb 18 13:30:22 2009 From: susumu at mri.jhu.edu (susumu) Date: Wed, 18 Feb 2009 13:30:22 -0500 Subject: [Mristudio-users] saving files In-Reply-To: Message-ID: <7k7ed7$6fksp2@ipex3.johnshopkins.edu> Hi Sarah, This happens when one of the boxes in "Image Dimension" and "Voxel Size" is "0". Please check. When you are reading "Raw" data, you need to know the matrix and pixel sizes and provide these numbers in these boxes. When you are reading "DICOM" or "Analyze", the information is provided from their header files. So, these boxes are inactivated. There is one silly issue of DtiStudio, which is that it doesn't like "0" in any of these boxes even if DICOM or Analyze data are used. Please input non-0 number in these boxed before you choose "DICOM" or "Analyze" and the boxes are inactivated. Susumu -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Copeland, Sarah A. Sent: Wednesday, February 18, 2009 1:27 AM To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] saving files Thanks, Hangyi - I have tried to do this before when loading data files, and tried it again as you suggested. I get the message "please enter an integer between 1 and 4096". I don't know where to enter an integer, or which to enter, but I've tried all options and still get the same error message. Can you help? Thanks again - Sarah hi, after saving, you can re-load the image by "File->MRI View 3D->..-> File_Format=RAW, Data_Type="Color" (for color map), or Data_Type="float" (for FA etc..)...-> OK" regards, hangyi > Hello, > > I am having a problem when trying to save processed files and reopen them later. > I am able to load DTI data and process it to the point where I have > FA, mean of B0, etc. I click the "save" button, and get the window > which allows me to choose files to save (with the arrow pointing to > the right hand box) and I do so. When I try to open them, though, the > program essentially starts me over by asking me to load file > parameters and then reprocessing the data. So for example if I try to > save colormap 0 just as a test, when I try to reopen I'm back to the point where I would have to start calculating tensors, etc. over again. > > I am trying to save mean of B0s to bring it into Landmarker and use > AIR to coregister MPRAGE images to the DTI data. I thought of doing > this in DTI studio, but cannot open the MPRAGE image in DTI studio (it > won't recognize anything except the raw data files in the pull-down > menu). I know people are able to save and reopen files all the time. Am I missing an obvious step? > > Thank you! IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From igor.yakushev at uni-mainz.de Fri Feb 20 11:33:35 2009 From: igor.yakushev at uni-mainz.de (Yakushev, Igor) Date: Fri, 20 Feb 2009 17:33:35 +0100 Subject: [Mristudio-users] DTI-Studio crashes without any specific error message Message-ID: <7D7FACBADC09BE44B8617B9467285B53D6B0827552@EXCHANGE-02.zdv.uni-mainz.de> Dear Colleagues, I?m new to DtiStudio and am trying to get this nice program running. We use data from a 1.5 T Siemens Magnetom Sonata; each dataset contains 280 DICOM files (6-orientation DTI, 7x256x256x40). I can load the data, but after initiating further steps within the DtiMap tab (both display images and calculation), the program crashes without any specific error message. What might be the reason? I?m quite sure that the gradient combination is listed in the same order as their corresponding volumes: 0: 0.000, 0.000, 0.000 1: -1.000, 0.000, -1.000 2: 1.000, 0.000, -1.000 3: 0.000, 1.000, -1.000 4: 0.000, 1.000, 1.000 5: -1.000, 1.000, 0.000 6: 1.000, 1.000, 0.000 I assume that the combination of gradients is the same for all datasets, i.e. volunteers imaged with the above mentioned scanner. Is it right? Best wishes, Igor Yakushev From susumu at mri.jhu.edu Fri Feb 20 11:43:00 2009 From: susumu at mri.jhu.edu (susumu) Date: Fri, 20 Feb 2009 11:43:00 -0500 Subject: [Mristudio-users] DTI-Studio crashes without any specific error message In-Reply-To: <7D7FACBADC09BE44B8617B9467285B53D6B0827552@EXCHANGE-02.zdv.uni-mainz.de> Message-ID: <7k7ed7$6gdd8k@ipex3.johnshopkins.edu> The most likely cause of the crush is memory shortage, although your data set is not that big. What is the amount of RAM? Please try to limit the number of slices you load at the initial data input window (like loading only slice 0-4). If it works, you definitly have memory shortage. -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Yakushev, Igor Sent: Friday, February 20, 2009 11:34 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] DTI-Studio crashes without any specific error message Dear Colleagues, I'm new to DtiStudio and am trying to get this nice program running. We use data from a 1.5 T Siemens Magnetom Sonata; each dataset contains 280 DICOM files (6-orientation DTI, 7x256x256x40). I can load the data, but after initiating further steps within the DtiMap tab (both display images and calculation), the program crashes without any specific error message. What might be the reason? I'm quite sure that the gradient combination is listed in the same order as their corresponding volumes: 0: 0.000, 0.000, 0.000 1: -1.000, 0.000, -1.000 2: 1.000, 0.000, -1.000 3: 0.000, 1.000, -1.000 4: 0.000, 1.000, 1.000 5: -1.000, 1.000, 0.000 6: 1.000, 1.000, 0.000 I assume that the combination of gradients is the same for all datasets, i.e. volunteers imaged with the above mentioned scanner. Is it right? Best wishes, Igor Yakushev _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From choisj70 at gmail.com Fri Feb 20 14:42:26 2009 From: choisj70 at gmail.com (Seongjin) Date: Fri, 20 Feb 2009 14:42:26 -0500 Subject: [Mristudio-users] Manual or Instructions Message-ID: Dear DTIstudio users, Is there any instructions and manuals on how to use LANDMARKER and ROIEDITOR? I would like to know data normalization on DTI studio. Thanks in advance. -SC -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090220/49d4158c/attachment.html From susumu at mri.jhu.edu Fri Feb 20 14:47:42 2009 From: susumu at mri.jhu.edu (susumu) Date: Fri, 20 Feb 2009 14:47:42 -0500 Subject: [Mristudio-users] Manual or Instructions In-Reply-To: Message-ID: <7k7ed7$6gfnkt@ipex3.johnshopkins.edu> I must admit that the manual of these two programs are meager. We are working on "Get Started", which will hopefully be distributed within a month or so. We are also planning to have a tutorial on 18th or 19th in Hawaii/ISMRM. The announcement should follow shortly. Meanwhile, the only instruction available is in www.mristudio.org. _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of [Seongjin] Sent: Friday, February 20, 2009 2:42 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] Manual or Instructions Dear DTIstudio users, Is there any instructions and manuals on how to use LANDMARKER and ROIEDITOR? I would like to know data normalization on DTI studio. Thanks in advance. -SC -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090220/166d393f/attachment.html From zhou1 at jhmi.edu Fri Feb 20 15:02:41 2009 From: zhou1 at jhmi.edu (Zhipeng Hou) Date: Fri, 20 Feb 2009 15:02:41 -0500 Subject: [Mristudio-users] Manual or Instructions In-Reply-To: <7k7ed7$6gfnkt@ipex3.johnshopkins.edu> References: <7k7ed7$6gfnkt@ipex3.johnshopkins.edu> Message-ID: <568cc7760902201202r7526a14aj6a69629c65b4879d@mail.gmail.com> SC, Click following link you can see "Normalization" present by Dr. Susumu Mori: http://162.129.247.245/Software/other/Protocol/DTS/Tutorial/htm/Landmarker.htm Zhipeng On Fri, Feb 20, 2009 at 2:47 PM, susumu wrote: > I must admit that the manual of these two programs are meager. We are > working on "Get Started", which will hopefully be distributed within a month > or so. > > We are also planning to have a tutorial on 18th or 19th in Hawaii/ISMRM. The > announcement should follow shortly. > > Meanwhile, the only instruction available is in www.mristudio.org. > ________________________________ > From: mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of [Seongjin] > Sent: Friday, February 20, 2009 2:42 PM > To: DTI Studio, ROI Editor, Landmarker Questions/Support > Subject: [Mristudio-users] Manual or Instructions > > Dear DTIstudio users, > > Is there any instructions and manuals on how to use LANDMARKER and > ROIEDITOR? > I would like to know data normalization on DTI studio. > Thanks in advance. > > -SC > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090220/c3f001de/attachment-0001.html From choisj70 at gmail.com Fri Feb 20 15:51:59 2009 From: choisj70 at gmail.com (Seongjin) Date: Fri, 20 Feb 2009 15:51:59 -0500 Subject: [Mristudio-users] Manual or Instructions In-Reply-To: <568cc7760902201202r7526a14aj6a69629c65b4879d@mail.gmail.com> References: <7k7ed7$6gfnkt@ipex3.johnshopkins.edu> <568cc7760902201202r7526a14aj6a69629c65b4879d@mail.gmail.com> Message-ID: Thanks a lot! Zhipeng. Seongjin On Fri, Feb 20, 2009 at 3:02 PM, Zhipeng Hou wrote: > SC, > > Click following link you can see "Normalization" present by Dr. Susumu > Mori: > > > http://162.129.247.245/Software/other/Protocol/DTS/Tutorial/htm/Landmarker.htm > > Zhipeng > > > > > On Fri, Feb 20, 2009 at 2:47 PM, susumu wrote: > > I must admit that the manual of these two programs are meager. We are > > working on "Get Started", which will hopefully be distributed within a > month > > or so. > > > > We are also planning to have a tutorial on 18th or 19th in Hawaii/ISMRM. > The > > announcement should follow shortly. > > > > Meanwhile, the only instruction available is in www.mristudio.org. > > ________________________________ > > From: mristudio-users-bounces at mristudio.org > > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of [Seongjin] > > Sent: Friday, February 20, 2009 2:42 PM > > To: DTI Studio, ROI Editor, Landmarker Questions/Support > > Subject: [Mristudio-users] Manual or Instructions > > > > Dear DTIstudio users, > > > > Is there any instructions and manuals on how to use LANDMARKER and > > ROIEDITOR? > > I would like to know data normalization on DTI studio. > > Thanks in advance. > > > > -SC > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090220/c8b7ef33/attachment.html From siewmin.gan at gmail.com Sat Feb 21 08:23:20 2009 From: siewmin.gan at gmail.com (Siewmin Gan) Date: Sun, 22 Feb 2009 00:23:20 +1100 Subject: [Mristudio-users] temporal lobe tracts Message-ID: Dear all, I am trying to reproduce some tracts associated with the temporal lobe using the ROI drawing protocols from the paper "Reproducibility of Quantitative Tractography Methods Applied to Cerebral White Matter". The acquisitions of the DTI are similiar to the paper. I had good results with the ILF, but couldn't get the uncinate fasciculus and cingulum in controls and patients data. For these tracts, after I draw the 1st ROI with the "Or" function, I couldn't see tracts in the specified area/slice mentioned in the protocol to place the 2nd ROI. I wonder if I have misinterpreted the protocols. Secondly, the dti slices were acquired parallel to the AC-PC line in the paper and the protocols are based on anatomical landmarks. If the dti data I tried on are not acquired exactly parallel to the AC-PC line, would it make a difference in the reproducibility using the protocol? Much appreciated if any of you have tried and could derive these two tracts. Many Thanks Siewmin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090222/094af698/attachment.html From yi.jiang at duke.edu Sat Feb 21 12:23:23 2009 From: yi.jiang at duke.edu (Yi Jiang) Date: Sat, 21 Feb 2009 12:23:23 -0500 Subject: [Mristudio-users] DTIstudio reference In-Reply-To: References: Message-ID: <8A4E52C245174EDEBE743EB6717D20FD@YiDell2> Hello, if I'd like to refer to DTIstudio in my paper. Which reference should I use? Thank you! Yi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090221/0ee52468/attachment.html From susumu at mri.jhu.edu Sat Feb 21 12:46:13 2009 From: susumu at mri.jhu.edu (susumu) Date: Sat, 21 Feb 2009 12:46:13 -0500 Subject: [Mristudio-users] DTIstudio reference In-Reply-To: <8A4E52C245174EDEBE743EB6717D20FD@YiDell2> References: <8A4E52C245174EDEBE743EB6717D20FD@YiDell2> Message-ID: Jiang, H., et al., DtiStudio: resource program for diffusion tensor computation and fiber bundle tracking. Comput Methods Programs Biomed, 2006. 81: p. 106-116. Thanks! _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Yi Jiang Sent: Saturday, February 21, 2009 12:23 PM To: 'DTI Studio, ROI Editor, Landmarker Questions/Support' Subject: [Mristudio-users] DTIstudio reference Hello, if I'd like to refer to DTIstudio in my paper. Which reference should I use? Thank you! Yi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090221/30b47b1d/attachment.html From neuroscience at rambler.ru Mon Feb 23 11:22:45 2009 From: neuroscience at rambler.ru (Igor Yakushev) Date: Mon, 23 Feb 2009 19:22:45 +0300 Subject: [Mristudio-users] DTI-Studio crashes without any specific error message In-Reply-To: <7k7ed7$6gdd8k@ipex3.johnshopkins.edu> References: <7D7FACBADC09BE44B8617B9467285B53D6B0827552@EXCHANGE-02.zdv.uni-mainz.de> <7k7ed7$6gdd8k@ipex3.johnshopkins.edu> Message-ID: <934160802.1235406165.162694628.36064@mcgi55.rambler.ru> Dear Susumu Mori, thank you for your response. The amount of RAM is 2Gb. I've tryed loading only 5 slices (0-5), but the program crashed unfortunately again. Could you suggest other reasons? * susumu [Fri, 20 Feb 2009 11:43:00 -0500]: > The most likely cause of the crush is memory shortage, although your > data > set is not that big. What is the amount of RAM? > > Please try to limit the number of slices you load at the initial data > input > window (like loading only slice 0-4). If it works, you definitly have > memory > shortage. > > -----Original Message----- > From: mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Yakushev, > Igor > Sent: Friday, February 20, 2009 11:34 AM > To: mristudio-users at mristudio.org > Subject: [Mristudio-users] DTI-Studio crashes without any specific error > message > > Dear Colleagues, > > I'm new to DtiStudio and am trying to get this nice program running. > We use data from a 1.5 T Siemens Magnetom Sonata; each dataset contains > 280 > DICOM files (6-orientation DTI, 7x256x256x40). > I can load the data, but after initiating further steps within the > DtiMap > tab (both display images and calculation), the program crashes without > any > specific error message. What might be the reason? I'm quite sure that > the > gradient combination is listed in the same order as their corresponding > volumes: > 0: 0.000, 0.000, 0.000 > 1: -1.000, 0.000, -1.000 > 2: 1.000, 0.000, -1.000 > 3: 0.000, 1.000, -1.000 > 4: 0.000, 1.000, 1.000 > 5: -1.000, 1.000, 0.000 > 6: 1.000, 1.000, 0.000 > > I assume that the combination of gradients is the same for all datasets, > i.e. volunteers imaged with the above mentioned scanner. Is it right? > > Best wishes, > Igor Yakushev > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users -- Igor Yakushev. From susumu at mri.jhu.edu Mon Feb 23 11:30:08 2009 From: susumu at mri.jhu.edu (susumu) Date: Mon, 23 Feb 2009 11:30:08 -0500 Subject: [Mristudio-users] DTI-Studio crashes without any specific errormessage In-Reply-To: <934160802.1235406165.162694628.36064@mcgi55.rambler.ru> Message-ID: <7k7ed7$6h5qsd@ipex3.johnshopkins.edu> Ok, then I think we should have closer look at your data. It is possible to send it to us? -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Igor Yakushev Sent: Monday, February 23, 2009 11:23 AM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] DTI-Studio crashes without any specific errormessage Dear Susumu Mori, thank you for your response. The amount of RAM is 2Gb. I've tryed loading only 5 slices (0-5), but the program crashed unfortunately again. Could you suggest other reasons? * susumu [Fri, 20 Feb 2009 11:43:00 -0500]: > The most likely cause of the crush is memory shortage, although your > data > set is not that big. What is the amount of RAM? > > Please try to limit the number of slices you load at the initial data > input > window (like loading only slice 0-4). If it works, you definitly have > memory > shortage. > > -----Original Message----- > From: mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Yakushev, > Igor > Sent: Friday, February 20, 2009 11:34 AM > To: mristudio-users at mristudio.org > Subject: [Mristudio-users] DTI-Studio crashes without any specific error > message > > Dear Colleagues, > > I'm new to DtiStudio and am trying to get this nice program running. > We use data from a 1.5 T Siemens Magnetom Sonata; each dataset contains > 280 > DICOM files (6-orientation DTI, 7x256x256x40). > I can load the data, but after initiating further steps within the > DtiMap > tab (both display images and calculation), the program crashes without > any > specific error message. What might be the reason? I'm quite sure that > the > gradient combination is listed in the same order as their corresponding > volumes: > 0: 0.000, 0.000, 0.000 > 1: -1.000, 0.000, -1.000 > 2: 1.000, 0.000, -1.000 > 3: 0.000, 1.000, -1.000 > 4: 0.000, 1.000, 1.000 > 5: -1.000, 1.000, 0.000 > 6: 1.000, 1.000, 0.000 > > I assume that the combination of gradients is the same for all datasets, > i.e. volunteers imaged with the above mentioned scanner. Is it right? > > Best wishes, > Igor Yakushev > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users -- Igor Yakushev. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From susumu at mri.jhu.edu Mon Feb 23 14:37:43 2009 From: susumu at mri.jhu.edu (susumu) Date: Mon, 23 Feb 2009 14:37:43 -0500 Subject: [Mristudio-users] temporal lobe tracts In-Reply-To: Message-ID: <7k7ed7$6h8lth@ipex3.johnshopkins.edu> Hi Siewmin, Please make sure that you correctly set the "flip" options. If you are using Siemens and the manufacturer-provided gradient table, the chance is high that you have to "X-flip" before fiber tracking. If you are using Philips, then "Z-flip". Please place an ROI in the mid-sagittal corpus callosum and make sure that you get the correct shape of the corpus callosum. If not, you could be setting the "flip" in a wrong way. There is a detailed description about the "flip" function in the DtiStudio manual. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Siewmin Gan Sent: Saturday, February 21, 2009 8:23 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] temporal lobe tracts Dear all, I am trying to reproduce some tracts associated with the temporal lobe using the ROI drawing protocols from the paper "Reproducibility of Quantitative Tractography Methods Applied to Cerebral White Matter". The acquisitions of the DTI are similiar to the paper. I had good results with the ILF, but couldn't get the uncinate fasciculus and cingulum in controls and patients data. For these tracts, after I draw the 1st ROI with the "Or" function, I couldn't see tracts in the specified area/slice mentioned in the protocol to place the 2nd ROI. I wonder if I have misinterpreted the protocols. Secondly, the dti slices were acquired parallel to the AC-PC line in the paper and the protocols are based on anatomical landmarks. If the dti data I tried on are not acquired exactly parallel to the AC-PC line, would it make a difference in the reproducibility using the protocol? Much appreciated if any of you have tried and could derive these two tracts. Many Thanks Siewmin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090223/f8adb5ea/attachment.html From varangovind at gmail.com Mon Feb 23 15:53:28 2009 From: varangovind at gmail.com (Varan Govind) Date: Mon, 23 Feb 2009 15:53:28 -0500 Subject: [Mristudio-users] Landmarker Load Command File option Message-ID: <25a47ed60902231253g66585edbj3da8cb3d4f087755@mail.gmail.com> ** Dear all, In Landmarker, does anybody know how to use the Load Command File option to resample multiple images, etc, i.e., how to create a command file (what are the commands available for use) and load it into Landmarker to perform the resampling functions, etc? Thanks, govind -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090223/ccef9ad3/attachment.html From xli16 at jhmi.edu Mon Feb 23 16:57:05 2009 From: xli16 at jhmi.edu (XIN LI) Date: Mon, 23 Feb 2009 16:57:05 -0500 Subject: [Mristudio-users] Landmarker Load Command File option In-Reply-To: <25a47ed60902231253g66585edbj3da8cb3d4f087755@mail.gmail.com> References: <25a47ed60902231253g66585edbj3da8cb3d4f087755@mail.gmail.com> Message-ID: Govind, You need to create a command txt file named as "xx.cf" first. The attached is an example. It decribes the syntax of the commands. The Load Command File option process all the loaded subject images based on these commands. Hope this will help you. Xin ----- Original Message ----- From: Varan Govind Date: Monday, February 23, 2009 3:53 pm Subject: [Mristudio-users] Landmarker Load Command File option To: mristudio-users at mristudio.org > ** > > Dear all, > > In Landmarker, does anybody know how to use the Load Command File > option to > resample multiple images, etc, i.e., how to create a command file > (what are > the commands available for use) and load it into Landmarker to > perform the > resampling functions, etc? > > > Thanks, > govind > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > -------------- next part -------------- A non-text attachment was scrubbed... Name: ResampleFileFormat.cf Type: application/octet-stream Size: 960 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090223/452c0cb4/attachment.obj From siewmin.gan at gmail.com Mon Feb 23 21:36:18 2009 From: siewmin.gan at gmail.com (Siewmin Gan) Date: Tue, 24 Feb 2009 13:36:18 +1100 Subject: [Mristudio-users] temporal lobe tracts In-Reply-To: <7k7ed7$6h8lth@ipex3.johnshopkins.edu> References: <7k7ed7$6h8lth@ipex3.johnshopkins.edu> Message-ID: Thanks Susumu. I'll try that. Siewmin On Tue, Feb 24, 2009 at 6:37 AM, susumu wrote: > Hi Siewmin, > > Please make sure that you correctly set the "flip" options. If you are > using Siemens and the manufacturer-provided gradient table, the chance is > high that you have to "X-flip" before fiber tracking. If you are using > Philips, then "Z-flip". > > Please place an ROI in the mid-sagittal corpus callosum and make sure that > you get the correct shape of the corpus callosum. If not, you could be > setting the "flip" in a wrong way. > > There is a detailed description about the "flip" function in the DtiStudio > manual. > > Susumu > > ------------------------------ > *From:* mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org] *On Behalf Of *Siewmin Gan > *Sent:* Saturday, February 21, 2009 8:23 AM > *To:* mristudio-users at mristudio.org > *Subject:* [Mristudio-users] temporal lobe tracts > > Dear all, I am trying to reproduce some tracts associated with > the temporal lobe using the ROI drawing protocols from the paper > "Reproducibility of Quantitative Tractography Methods Applied to Cerebral > White Matter". The acquisitions of the DTI are similiar to the paper. I had > good results with the ILF, but couldn't get the uncinate fasciculus and > cingulum in controls and patients data. For these tracts, after I draw the > 1st ROI with the "Or" function, I couldn't see tracts in the specified > area/slice mentioned in the protocol to place the 2nd ROI. > > I wonder if I have misinterpreted the protocols. Secondly, the dti slices > were acquired parallel to the AC-PC line in the paper and the protocols are > based on anatomical landmarks. If the dti data I tried on are not acquired > exactly parallel to the AC-PC line, would it make a difference in the > reproducibility using the protocol? Much appreciated if any of you have > tried and could derive these two tracts. > > Many Thanks > > Siewmin > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090224/dec10e22/attachment.html From varangovind at gmail.com Tue Feb 24 08:57:29 2009 From: varangovind at gmail.com (Varan Govind) Date: Tue, 24 Feb 2009 08:57:29 -0500 Subject: [Mristudio-users] Landmarker Load Command File option In-Reply-To: References: <25a47ed60902231253g66585edbj3da8cb3d4f087755@mail.gmail.com> Message-ID: <25a47ed60902240557u21fc03b9wadcec61d3e14a5f3@mail.gmail.com> Dear Dr. Li, Thank you very much for your quick response. govind On Mon, Feb 23, 2009 at 4:57 PM, XIN LI wrote: > Govind, > > You need to create a command txt file named as "xx.cf" first. The attached > is an example. It decribes the syntax of the commands. The Load Command File > option process all the loaded subject images based on these commands. > > Hope this will help you. > > Xin > > > > ----- Original Message ----- > From: Varan Govind > Date: Monday, February 23, 2009 3:53 pm > Subject: [Mristudio-users] Landmarker Load Command File option > To: mristudio-users at mristudio.org > > > > ** > > > > Dear all, > > > > In Landmarker, does anybody know how to use the Load Command File > > option to > > resample multiple images, etc, i.e., how to create a command file > > (what are > > the commands available for use) and load it into Landmarker to > > perform the > > resampling functions, etc? > > > > > > Thanks, > > govind > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090224/9acb7dba/attachment-0001.html From Andreas.Buchmann at kispi.uzh.ch Thu Feb 26 07:57:38 2009 From: Andreas.Buchmann at kispi.uzh.ch (Buchmann Andreas) Date: Thu, 26 Feb 2009 13:57:38 +0100 Subject: [Mristudio-users] 2D/3D view Message-ID: Dear List, I'm using DTI images stored as GE Dicom files. from the list archive I learned that DTI studio shows the images in radiologic convention. However, the 3D-view seems flipped in x-axis. Am I right that -2D views are radiologic -3D view is neurologic (left=left)? Many thanks for confirmation/correction! Andreas -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090226/0ea11474/attachment.html -------------- next part -------------- A non-text attachment was scrubbed... Name: PGP.sig Type: application/pgp-signature Size: 488 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090226/0ea11474/attachment.bin From susumu at mri.jhu.edu Thu Feb 26 09:39:40 2009 From: susumu at mri.jhu.edu (susumu) Date: Thu, 26 Feb 2009 09:39:40 -0500 Subject: [Mristudio-users] 2D/3D view In-Reply-To: Message-ID: <7k7ed7$6ib54s@ipex3.johnshopkins.edu> Hi Andreas, Yes, 3D reflects the physical entity. So, right is right and left is left. There is no freedom or ambiguity there. When we visualize 2D there is always two degrees of freedom; whether we are looking at the slice from the front or behind (or from upside or downside), which is related to the Neurology and Radiology conventions. susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Buchmann Andreas Sent: Thursday, February 26, 2009 7:58 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] 2D/3D view Dear List, I'm using DTI images stored as GE Dicom files. from the list archive I learned that DTI studio shows the images in radiologic convention. However, the 3D-view seems flipped in x-axis. Am I right that -2D views are radiologic -3D view is neurologic (left=left)? Many thanks for confirmation/correction! Andreas -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090226/2521de22/attachment.html From thomas.thesen at med.nyu.edu Thu Feb 26 09:44:09 2009 From: thomas.thesen at med.nyu.edu (Thesen, Thomas) Date: Thu, 26 Feb 2009 09:44:09 -0500 Subject: [Mristudio-users] 2D/3D view In-Reply-To: <7k7ed7$6ib54s@ipex3.johnshopkins.edu> References: <7k7ed7$6ib54s@ipex3.johnshopkins.edu> Message-ID: Please unsubscribe me from this list On Feb 26, 2009, at 9:40 AM, "susumu" wrote: > Hi Andreas, > > Yes, 3D reflects the physical entity. So, right is right and left is > left. There is no freedom or ambiguity there. > When we visualize 2D there is always two degrees of freedom; whether > we are looking at the slice from the front or behind (or from upside > or downside), which is related to the Neurology and Radiology > conventions. > > susumu > From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org > ] On Behalf Of Buchmann Andreas > Sent: Thursday, February 26, 2009 7:58 AM > To: mristudio-users at mristudio.org > Subject: [Mristudio-users] 2D/3D view > > Dear List, > > I'm using DTI images stored as GE Dicom files. > from the list archive I learned that DTI studio shows the images in > radiologic convention. > However, the 3D-view seems flipped in x-axis. > > Am I right that > -2D views are radiologic > -3D view is neurologic (left=left)? > > Many thanks for confirmation/correction! > > Andreas > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. 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URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090226/f57b2f41/attachment.html From evangelouI at ninds.nih.gov Thu Feb 26 10:26:48 2009 From: evangelouI at ninds.nih.gov (Evangelou, Iordanis (NIH/NINDS) [E]) Date: Thu, 26 Feb 2009 10:26:48 -0500 Subject: [Mristudio-users] DTIStudio NIFTI Files References: <7k7ed7$6ib54s@ipex3.johnshopkins.edu> Message-ID: <9A3BEE43EE449840B003538CCC889030886635@nihcesmlbx2.nih.gov> is it possible for DTI Studio to include support for NIFTI files? thanks Iordanis ------------------------------------------------------------------- Iordanis E. Evangelou, DPhil, Eur Ing, MIET Research Fellow Neuroimaging Section Neuroimmunology Branch National Institute of Neurological Disorders and Stroke National Institutes of Health Building 10, Room 5C203B Bethesda, MD 20892 USA ------------------------------------------------------------------- -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 2526 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090226/bb368bba/attachment-0001.bin From susumu at mri.jhu.edu Thu Feb 26 10:38:36 2009 From: susumu at mri.jhu.edu (susumu) Date: Thu, 26 Feb 2009 10:38:36 -0500 Subject: [Mristudio-users] DTIStudio NIFTI Files In-Reply-To: <9A3BEE43EE449840B003538CCC889030886635@nihcesmlbx2.nih.gov> Message-ID: <7k7ed7$6icde7@ipex3.johnshopkins.edu> Hi Hangyi, What is the status of NIFTI in DtiStudio? Susumu ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ To unsubscribe this mailing list, please go to www.mristudio.org / Mailing List / Mristudio-users. There you can find the unsubscribe option. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Evangelou, Iordanis (NIH/NINDS) [E] Sent: Thursday, February 26, 2009 10:27 AM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] DTIStudio NIFTI Files is it possible for DTI Studio to include support for NIFTI files? thanks Iordanis ------------------------------------------------------------------- Iordanis E. Evangelou, DPhil, Eur Ing, MIET Research Fellow Neuroimaging Section Neuroimmunology Branch National Institute of Neurological Disorders and Stroke National Institutes of Health Building 10, Room 5C203B Bethesda, MD 20892 USA ------------------------------------------------------------------- From evangelouI at ninds.nih.gov Thu Feb 26 11:52:23 2009 From: evangelouI at ninds.nih.gov (Evangelou, Iordanis (NIH/NINDS) [E]) Date: Thu, 26 Feb 2009 11:52:23 -0500 Subject: [Mristudio-users] DTIStudio NIFTI Files References: <7k7ed7$6icde7@ipex3.johnshopkins.edu> Message-ID: <9A3BEE43EE449840B003538CCC889030886637@nihcesmlbx2.nih.gov> we have at NIH a C library for NIFTI i/o and documentation at http://nifti.nimh.nih.gov/nifti-1/ thanks ------------------------------------------------------------------- Iordanis E. Evangelou, DPhil, Eur Ing, MIET Research Fellow Neuroimaging Section Neuroimmunology Branch National Institute of Neurological Disorders and Stroke National Institutes of Health Building 10, Room 5C203B Bethesda, MD 20892 USA ------------------------------------------------------------------- -----Original Message----- From: Mori, Susumu (NIH/NIMH) Sent: Thu 2/26/2009 10:38 AM To: 'DTI Studio, ROI Editor, Landmarker Questions/Support' Subject: Re: [Mristudio-users] DTIStudio NIFTI Files Hi Hangyi, What is the status of NIFTI in DtiStudio? Susumu ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ To unsubscribe this mailing list, please go to www.mristudio.org / Mailing List / Mristudio-users. There you can find the unsubscribe option. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Evangelou, Iordanis (NIH/NINDS) [E] Sent: Thursday, February 26, 2009 10:27 AM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] DTIStudio NIFTI Files is it possible for DTI Studio to include support for NIFTI files? thanks Iordanis ------------------------------------------------------------------- Iordanis E. Evangelou, DPhil, Eur Ing, MIET Research Fellow Neuroimaging Section Neuroimmunology Branch National Institute of Neurological Disorders and Stroke National Institutes of Health Building 10, Room 5C203B Bethesda, MD 20892 USA ------------------------------------------------------------------- _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From neuroscience at rambler.ru Thu Feb 26 12:12:36 2009 From: neuroscience at rambler.ru (Igor Yakushev) Date: Thu, 26 Feb 2009 20:12:36 +0300 Subject: [Mristudio-users] Scanner-specific gradients? In-Reply-To: <7k7ed7$6icde7@ipex3.johnshopkins.edu> References: <9A3BEE43EE449840B003538CCC889030886635@nihcesmlbx2.nih.gov> <7k7ed7$6icde7@ipex3.johnshopkins.edu> Message-ID: <330120587.1235668356.66828136.3147@mcgi70.rambler.ru> Dear Susumu, dear Users, I have a beginners question: Should be the combination of gradients the same for all subjects imaged with the same scanner (i.e. scanner-specific gradients)? Or the gradients may be different for different scans/subjects (i.e. scan-specific gradients)? Such ?individual? gradients (bvec) can be calculated using e.g. MRIcron. For example, gradient table (as provided by radiologists) in the first case looks like: 0: 0, 0, 0 1: -0.7, 0, -0.7 2: 0.7, 0, -0.7 3: 0, 0.7, -0.7 4: 0, 0.7, 0.7 5: -0.7, 0.7, 0 6: 0.7, 0.7, 0 in the second case (calculated with MRIcron) completely different: 0: 0.000, 0.000, 0.000 1: 0.704, -0.146, -0.695 2: -0.710, -0.146, -0.689 3: 0.004, 0.546, -0.838 4: 0.003, 0.838, 0.546 5: 0.706, 0.692, -0.149 6: -0.708, 0.692, -0.142 Accordingly, results (tracks originated from the same ROI) are very different. Thanks, Igor From susumu at mri.jhu.edu Thu Feb 26 20:04:51 2009 From: susumu at mri.jhu.edu (susumu) Date: Thu, 26 Feb 2009 20:04:51 -0500 Subject: [Mristudio-users] Scanner-specific gradients? In-Reply-To: <330120587.1235668356.66828136.3147@mcgi70.rambler.ru> Message-ID: <7k7ed7$6ijitj@ipex3.johnshopkins.edu> Hi Igor, Unless you explicity change the gradient table, the same imaging protocol should use the same gradient table. However, there are several things that make the matter complicated; 1) The manufacturers provide gradient tables. For example, Siemens has 6- and 12-orientation tables. While they provide only one kind of the 12-orientation Siemens table, when actual scan happens, they dynamically change the table. 2) For example, you may use axial, coronal, or sagital scans. The patient may go in the scanner head-first or leg-first. Or they could be face up, face down, or facing to the side. There are so many possibilities related to the relative relationship between the subject, the physical gradients, and the imaging parameters. Apparently, one gradient table can not be applied to all these setttings. 3) One of the issues due to this type of degrees of freedom is that the +/- sign of the gradient table may not represent what the scanner actually did. As a matter of fact, the +/- sign is arbitrary defined. What is most important is the relationship between the diffusion gradients and imaging gradients, which are changed dynamically depending on your protocol. Usually, for siemens, axial, head-first, face-up, the sign of the X gradient has to be flipped. 4) If you look the two tables you got carefully, you notice that the x components have opposite signs. I suspect the first one is the one provided by Siemens and the second one is read from DICOM header. The latter one reflects what was actually done by the scanner, I believe. 5) If you use the one provided by the manufacturer (the first one) for tensor calculation, it won't affect your FA, ADC, and diffusivity, but it affects vector angles (and thus fiber tracking). This is why DtiStudio has a function of "flip" before fiber tracking. Of course, it is much better approach to use the second table with the correct +/- sign. 5) The second thing you notice is that there is a small differences in each component. I suspect this is because you used oblique imaging. Please check if this is actually the case. This is a very tricky issue and you have to make sure that you are doing a right thing. Not using oblique makes situation much simpler, but if you want to use oblique, you have to consider the following; 6) If you are using older operating system of Siemens, you HAVE TO recalculate your gradient table based on oblique angles. You can do it automatically if you are using DICOM or Mosaic. You have to check "rotate gradient if applicable" box. Then DtiStudio read the oblique information and reorient the table for you. 7) If you are using the latest operating system, you don't have to recalculate the table. So you don't want to check the "rotate gradient if appliable" box. Either way, it is advised to image one person with a severe oblique plane, process the data, and perform tracking. This immediately tells if things are correctly working. Vendors change things without notice. You'd better learn how to protect yourself. 8) If you are not sure, you can send the tracking results to us. Susumu -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Igor Yakushev Sent: Thursday, February 26, 2009 12:13 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] Scanner-specific gradients? Dear Susumu, dear Users, I have a beginners question:Should be the combination of gradients the same for all subjects imaged with the same scanner (i.e. scanner-specific gradients)? Or the gradients may be different for different scans/subjects (i.e. scan-specific gradients)? Such "individual" gradients (bvec) can be calculated using e.g. MRIcron. For example, gradient table (as provided by radiologists) in the first case looks like: 0: 0, 0, 0 1: -0.7, 0, -0.7 2: 0.7, 0, -0.7 3: 0, 0.7, -0.7 4: 0, 0.7, 0.7 5: -0.7, 0.7, 0 6: 0.7, 0.7, 0 in the second case (calculated with MRIcron) completely different: 0: 0.000, 0.000, 0.000 1: 0.704, -0.146, -0.695 2: -0.710, -0.146, -0.689 3: 0.004, 0.546, -0.838 4: 0.003, 0.838, 0.546 5: 0.706, 0.692, -0.149 6: -0.708, 0.692, -0.142 Accordingly, results (tracks originated from the same ROI) are very different. Thanks,Igor_______________________________________________Mristudio-users mailing listMristudio-users at mristudio.orghttp://lists.mristudio.org/mailman/listinfo /mristudio-users From artzimy at gmail.com Wed Mar 4 14:34:31 2009 From: artzimy at gmail.com (Moran Artzi) Date: Wed, 04 Mar 2009 21:34:31 +0200 Subject: [Mristudio-users] Mean_ADC units Message-ID: <9220666f0903041134r59c44a35m16be35d36c31613a@mail.gmail.com> Hi what units are used when reporting the ADC Map - Mean value on the DTI-Studio Fiber Statistic option? ADC Map - Mean Max. of ImgVal: 4.2198 Min. of ImgVal: 0.1643 Mean of ImgVal: 0.9090 Std. of ImgVal: 0.3467 Many thanks Moran -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090304/589c2729/attachment.html From james.neeley at duke.edu Wed Mar 4 14:51:36 2009 From: james.neeley at duke.edu (Jim Neeley) Date: Wed, 04 Mar 2009 14:51:36 -0500 Subject: [Mristudio-users] Scanner-specific gradients? In-Reply-To: <330120587.1235668356.66828136.3147@mcgi70.rambler.ru> References: <9A3BEE43EE449840B003538CCC889030886635@nihcesmlbx2.nih.gov> <7k7ed7$6icde7@ipex3.johnshopkins.edu> <330120587.1235668356.66828136.3147@mcgi70.rambler.ru> Message-ID: An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090304/8b29648a/attachment.html From james.neeley at duke.edu Wed Mar 4 15:46:43 2009 From: james.neeley at duke.edu (Jim Neeley) Date: Wed, 04 Mar 2009 15:46:43 -0500 Subject: [Mristudio-users] Mean_ADC units In-Reply-To: <9220666f0903041134r59c44a35m16be35d36c31613a@mail.gmail.com> References: <9220666f0903041134r59c44a35m16be35d36c31613a@mail.gmail.com> Message-ID: An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090304/6ba5fb13/attachment-0001.html From hjiang at jhmi.edu Wed Mar 4 15:55:29 2009 From: hjiang at jhmi.edu (Hangyi Jiang) Date: Wed, 04 Mar 2009 15:55:29 -0500 Subject: [Mristudio-users] Mean_ADC units Message-ID: <49AEA471020000630001D2AA@cis27.hosts.jhmi.edu> its unit is (mm^2/s) when you consider the b-value during the calculation. hangyi >>> Moran Artzi 03/04/09 2:34 PM >>> Hi what units are used when reporting the ADC Map - Mean value on the DTI-Studio Fiber Statistic option? ADC Map - Mean Max. of ImgVal: 4.2198 Min. of ImgVal: 0.1643 Mean of ImgVal: 0.9090 Std. of ImgVal: 0.3467 Many thanks Moran From superjx2318 at hotmail.com Wed Mar 4 23:21:11 2009 From: superjx2318 at hotmail.com (jiangxi) Date: Thu, 05 Mar 2009 04:21:11 +0000 Subject: [Mristudio-users] Mean_ADC units In-Reply-To: <49AEA471020000630001D2AA@cis27.hosts.jhmi.edu> References: <49AEA471020000630001D2AA@cis27.hosts.jhmi.edu> Message-ID: Hi, I'am wondering that how to use DTI data to reconstruct the cerebral cortex surface or WM surface. The DTIStudio seems that can only carriy out to the fiber-tracking step. Thanks! > Date: Wed, 4 Mar 2009 15:55:29 -0500 > From: hjiang at jhmi.edu > To: mristudio-users at mristudio.org > Subject: Re: [Mristudio-users] Mean_ADC units > > its unit is (mm^2/s) when you consider the b-value during the calculation. > > hangyi > > > > >>> Moran Artzi 03/04/09 2:34 PM >>> > Hi > what units are used when reporting the ADC Map - Mean value on the > DTI-Studio Fiber Statistic option? > ADC Map - Mean > Max. of ImgVal: 4.2198 > Min. of ImgVal: 0.1643 > Mean of ImgVal: 0.9090 > Std. of ImgVal: 0.3467 > > Many thanks > > Moran > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users _________________________________________________________________ ??K???????????????????MClub???? http://club.msn.cn/?form=3 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090305/c9d7d6f0/attachment.html From neuroscience at rambler.ru Thu Mar 5 07:45:04 2009 From: neuroscience at rambler.ru (Igor Yakushev) Date: Thu, 05 Mar 2009 15:45:04 +0300 Subject: [Mristudio-users] Scanner-specific gradients? Message-ID: <115228089.1236257104.228548748.33148@mcgi35.rambler.ru> Dear Susumu, Thanks again for your careful answer! We have ascertained that the scan-specific (extracted from individual DICOM headers) gradients were the right ones. I have one more practical question: Our individual gradients have values of 14-15 digits following zero, e.g. -0.145791634917259. To what decimal digit should/may one round these values? It's important to know, as we're going to analyse large amount of data and, as i wrote, we have to introduce a different gradient table for each individual case. Of note, there is a rather small difference between the values, please see an example of a gradient table in my previous mail and one more below (rounded to 3 decimal digits): 0: 0.000, 0.000, 0.000 1: 0.696, -0.157, -0.701 2: -0.718, -0.157, -0.678 3: -0.014, 0.533, -0.846 4: 0.009, 0.846, 0.533 5: 0.704, 0.690, -0.168 6: -0.710, 0.690, -0.145 Thank you! Igor * susumu [Thu, 26 Feb 2009 20:04:51 -0500]: > Hi Igor, > > Unless you explicity change the gradient table, the same imaging > protocol > should use the same gradient table. > However, there are several things that make the matter complicated; > > 1) The manufacturers provide gradient tables. For example, Siemens has > 6- > and 12-orientation tables. While they provide only one kind of the > 12-orientation Siemens table, when actual scan happens, they dynamically > change the table. > 2) For example, you may use axial, coronal, or sagital scans. The > patient > may go in the scanner head-first or leg-first. Or they could be face up, > face down, or facing to the side. There are so many possibilities > related to > the relative relationship between the subject, the physical gradients, > and > the imaging parameters. Apparently, one gradient table can not be > applied to > all these setttings. > 3) One of the issues due to this type of degrees of freedom is that the > +/- > sign of the gradient table may not represent what the scanner actually > did. > As a matter of fact, the +/- sign is arbitrary defined. What is most > important is the relationship between the diffusion gradients and > imaging > gradients, which are changed dynamically depending on your protocol. > Usually, for siemens, axial, head-first, face-up, the sign of the X > gradient > has to be flipped. > 4) If you look the two tables you got carefully, you notice that the x > components have opposite signs. I suspect the first one is the one > provided > by Siemens and the second one is read from DICOM header. The latter one > reflects what was actually done by the scanner, I believe. > 5) If you use the one provided by the manufacturer (the first one) for > tensor calculation, it won't affect your FA, ADC, and diffusivity, but > it > affects vector angles (and thus fiber tracking). This is why DtiStudio > has a > function of "flip" before fiber tracking. Of course, it is much better > approach to use the second table with the correct +/- sign. > 5) The second thing you notice is that there is a small differences in > each > component. I suspect this is because you used oblique imaging. Please > check > if this is actually the case. This is a very tricky issue and you have > to > make sure that you are doing a right thing. Not using oblique makes > situation much simpler, but if you want to use oblique, you have to > consider > the following; > 6) If you are using older operating system of Siemens, you HAVE TO > recalculate your gradient table based on oblique angles. You can do it > automatically if you are using DICOM or Mosaic. You have to check > "rotate > gradient if applicable" box. Then DtiStudio read the oblique information > and > reorient the table for you. > 7) If you are using the latest operating system, you don't have to > recalculate the table. So you don't want to check the "rotate gradient > if > appliable" box. Either way, it is advised to image one person with a > severe > oblique plane, process the data, and perform tracking. This immediately > tells if things are correctly working. Vendors change things without > notice. > You'd better learn how to protect yourself. > 8) If you are not sure, you can send the tracking results to us. > > Susumu > > > > > > -----Original Message----- > From: mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Igor > Yakushev > Sent: Thursday, February 26, 2009 12:13 PM > To: DTI Studio, ROI Editor, Landmarker Questions/Support > Subject: [Mristudio-users] Scanner-specific gradients? > > Dear Susumu, dear Users, > I have a beginners question:Should be the combination of gradients the > same > for all subjects imaged with the same scanner (i.e. scanner-specific > gradients)? Or the gradients may be different for different > scans/subjects > (i.e. scan-specific gradients)? Such "individual" gradients (bvec) can > be > calculated using e.g. MRIcron. > For example, gradient table (as provided by radiologists) in the first > case > looks like: > 0: 0, 0, 0 1: -0.7, 0, -0.7 2: 0.7, 0, -0.7 3: 0, 0.7, -0.7 4: 0, 0.7, > 0.7 > 5: -0.7, 0.7, 0 6: 0.7, 0.7, 0 in the second case (calculated with > MRIcron) > completely different: > 0: 0.000, 0.000, 0.000 1: 0.704, -0.146, -0.695 2: -0.710, -0.146, > -0.689 3: > 0.004, 0.546, -0.838 4: 0.003, 0.838, 0.546 5: 0.706, 0.692, -0.149 6: > -0.708, 0.692, -0.142 Accordingly, results (tracks originated from the > same > ROI) are very different. > Thanks,Igor_______________________________________________Mristudio-users > mailing > listMristudio-users at mristudio.orghttp://lists.mristudio.org/mailman/listinfo > /mristudio-users > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users From yj3 at duke.edu Thu Mar 5 10:29:16 2009 From: yj3 at duke.edu (Yi Jiang) Date: Thu, 05 Mar 2009 10:29:16 -0500 Subject: [Mristudio-users] gradient table normalization? b0 image b-value? References: <49AEA471020000630001D2AA@cis27.hosts.jhmi.edu> Message-ID: <2F83066B198C48F8AC26ADA7DCB8693B@panpan> Hello, when I use a .dpf file to calculate diffusion tensor, should I normalize the gradient table? For example, can I use the following lines in the .dpf file or do I have to normalize the gradient table? Will the normalization or non-normalization affect the calculated diffusivity values? --------------------------- B-Value: 1000 Begin_Of_Gradient_Table 0: 0,0,0 1: 45.3060, 15.6000, 36.1080 2: 1.4340, -20.4720, 56.3820 3: 12.6960, 50.9160, 29.0880 4: -28.7580, 42.6360, 30.9000 5: -23.6280, -37.8120, 40.1460 6: -36.9540, 15.6900, 44.5860 7: 33.4800, -44.4300, 22.4760 8: -57.2400, -4.0020, 17.5440 9: 51.7140, -24.1140, 18.5400 10: 13.7760, 12.4080, 57.0660 11: -47.2500, -36.9180, 2.0940 12: -2.0760, -59.3820, 8.3520 End_Of_Gradient_Table --------------------------- Moreover, if my b0 file has some small value (not exactly 0), such as b0 has b-value of 10 and other DWIs has b-value of 1000, how can I indicate that in the .dpf file? Thank you very much! Best, Yi From hjiang at jhmi.edu Thu Mar 5 10:41:38 2009 From: hjiang at jhmi.edu (Hangyi Jiang) Date: Thu, 05 Mar 2009 10:41:38 -0500 Subject: [Mristudio-users] Scanner-specific gradients? Message-ID: <49AFAC62020000630001D304@cis27.hosts.jhmi.edu> hi, Igor, 4 decimal digits are good enough. Why? as we known, the original DWIs' intensity is usually a 4 digits integer (actually, the maximum is 2^12 = 4096, less than 5000). because the number of significant digits depends on the data underlying the calcuations, it will have no extra benifit to round a number more than 4 digits. BTW: the significant digit of a float data is less than 8 (or 7.2, more precisely). any numbers more than 8 digits are not accuracy. regards, hangyi >>> Igor Yakushev 03/05/09 7:45 AM >>> Dear Susumu, Thanks again for your careful answer! We have ascertained that the scan-specific (extracted from individual DICOM headers) gradients were the right ones. I have one more practical question: Our individual gradients have values of 14-15 digits following zero, e.g. -0.145791634917259. To what decimal digit should/may one round these values? It's important to know, as we're going to analyse large amount of data and, as i wrote, we have to introduce a different gradient table for each individual case. Of note, there is a rather small difference between the values, please see an example of a gradient table in my previous mail and one more below (rounded to 3 decimal digits): 0: 0.000, 0.000, 0.000 1: 0.696, -0.157, -0.701 2: -0.718, -0.157, -0.678 3: -0.014, 0.533, -0.846 4: 0.009, 0.846, 0.533 5: 0.704, 0.690, -0.168 6: -0.710, 0.690, -0.145 Thank you! Igor * susumu [Thu, 26 Feb 2009 20:04:51 -0500]: > Hi Igor, > > Unless you explicity change the gradient table, the same imaging > protocol > should use the same gradient table. > However, there are several things that make the matter complicated; > > 1) The manufacturers provide gradient tables. For example, Siemens has > 6- > and 12-orientation tables. While they provide only one kind of the > 12-orientation Siemens table, when actual scan happens, they dynamically > change the table. > 2) For example, you may use axial, coronal, or sagital scans. The > patient > may go in the scanner head-first or leg-first. Or they could be face up, > face down, or facing to the side. There are so many possibilities > related to > the relative relationship between the subject, the physical gradients, > and > the imaging parameters. Apparently, one gradient table can not be > applied to > all these setttings. > 3) One of the issues due to this type of degrees of freedom is that the > +/- > sign of the gradient table may not represent what the scanner actually > did. > As a matter of fact, the +/- sign is arbitrary defined. What is most > important is the relationship between the diffusion gradients and > imaging > gradients, which are changed dynamically depending on your protocol. > Usually, for siemens, axial, head-first, face-up, the sign of the X > gradient > has to be flipped. > 4) If you look the two tables you got carefully, you notice that the x > components have opposite signs. I suspect the first one is the one > provided > by Siemens and the second one is read from DICOM header. The latter one > reflects what was actually done by the scanner, I believe. > 5) If you use the one provided by the manufacturer (the first one) for > tensor calculation, it won't affect your FA, ADC, and diffusivity, but > it > affects vector angles (and thus fiber tracking). This is why DtiStudio > has a > function of "flip" before fiber tracking. Of course, it is much better > approach to use the second table with the correct +/- sign. > 5) The second thing you notice is that there is a small differences in > each > component. I suspect this is because you used oblique imaging. Please > check > if this is actually the case. This is a very tricky issue and you have > to > make sure that you are doing a right thing. Not using oblique makes > situation much simpler, but if you want to use oblique, you have to > consider > the following; > 6) If you are using older operating system of Siemens, you HAVE TO > recalculate your gradient table based on oblique angles. You can do it > automatically if you are using DICOM or Mosaic. You have to check > "rotate > gradient if applicable" box. Then DtiStudio read the oblique information > and > reorient the table for you. > 7) If you are using the latest operating system, you don't have to > recalculate the table. So you don't want to check the "rotate gradient > if > appliable" box. Either way, it is advised to image one person with a > severe > oblique plane, process the data, and perform tracking. This immediately > tells if things are correctly working. Vendors change things without > notice. > You'd better learn how to protect yourself. > 8) If you are not sure, you can send the tracking results to us. > > Susumu > > > > > > -----Original Message----- > From: mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Igor > Yakushev > Sent: Thursday, February 26, 2009 12:13 PM > To: DTI Studio, ROI Editor, Landmarker Questions/Support > Subject: [Mristudio-users] Scanner-specific gradients? > > Dear Susumu, dear Users, > I have a beginners question:Should be the combination of gradients the > same > for all subjects imaged with the same scanner (i.e. scanner-specific > gradients)? Or the gradients may be different for different > scans/subjects > (i.e. scan-specific gradients)? Such "individual" gradients (bvec) can > be > calculated using e.g. MRIcron. > For example, gradient table (as provided by radiologists) in the first > case > looks like: > 0: 0, 0, 0 1: -0.7, 0, -0.7 2: 0.7, 0, -0.7 3: 0, 0.7, -0.7 4: 0, 0.7, > 0.7 > 5: -0.7, 0.7, 0 6: 0.7, 0.7, 0 in the second case (calculated with > MRIcron) > completely different: > 0: 0.000, 0.000, 0.000 1: 0.704, -0.146, -0.695 2: -0.710, -0.146, > -0.689 3: > 0.004, 0.546, -0.838 4: 0.003, 0.838, 0.546 5: 0.706, 0.692, -0.149 6: > -0.708, 0.692, -0.142 Accordingly, results (tracks originated from the > same > ROI) are very different. > Thanks,Igor_______________________________________________Mristudio-users > mailing > listMristudio-users at mristudio.orghttp://lists.mristudio.org/mailman/listinfo > /mristudio-users > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From pabeach1 at gmail.com Thu Mar 5 10:51:50 2009 From: pabeach1 at gmail.com (Paul Beach) Date: Thu, 05 Mar 2009 10:51:50 -0500 Subject: [Mristudio-users] Landmarker - Reorientation questions Message-ID: <8874e3900903050751l68574c16i5188ffb91cb6381b@mail.gmail.com> Greetings everyone, I have been attempting to use Landmarker to re-orient subject brains to a template provided by the developers (we successfully changed the template to our dimensions), and I have several questions regarding rigid transformations. I have successfully transformed subjects using several anatomical landmarks (AC/PC, 1st and 2nd mid sagital, most anterior/posterior/superior/inferior/left/right). However, subject brains are still usually a bit slanted in certain views, post-transformation. Is there any advice as to how to correct for this occuring? Is it likely a landmark placement issue? Also, once the transformations are made, I have been attempting to apply the saved landmarks for the subjects to the fiber tracking data (say for a bilateral cingulum) that we have already produced for that subject using MRI studio. However, we are a bit stumped in attempting to find a way to take that reoriented fiber tract data and view it 3D on MRI studio without having to redo all the ROI placement, etc. Any advice for this? I have also been experimenting with using the rotation/shift image buttons to change subject images (I actually used this to fix a problem with the template, as when we re-sliced it to our dimensions it was shifted off-center axially/coronally to the user-right). Would using these buttons affect the results of a rigid transformation? Also, I was curious regarding the general algorithm for the rigid transformation. Is it a similar one to AFNI's manual Talairaching(?) or does Landmarker simply re-orient the brain in a way such as to minimize the variance in distance between all the placed landmarks? Many thanks for your assistance, Paul -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090305/d8067aa9/attachment-0001.html From xli16 at jhmi.edu Thu Mar 5 11:37:44 2009 From: xli16 at jhmi.edu (XIN LI) Date: Thu, 05 Mar 2009 11:37:44 -0500 Subject: [Mristudio-users] Landmarker - Reorientation questions In-Reply-To: <8874e3900903050751l68574c16i5188ffb91cb6381b@mail.gmail.com> References: <8874e3900903050751l68574c16i5188ffb91cb6381b@mail.gmail.com> Message-ID: Dr. Beach, You are right about the algorithm for the rigid transformation. Landmarker re-orients the brain in a way to minimize the variance in distance between all the placed landmarks. Xin ----- Original Message ----- From: Paul Beach Date: Thursday, March 5, 2009 10:51 am Subject: [Mristudio-users] Landmarker - Reorientation questions To: mristudio-users at mristudio.org > Greetings everyone, > > I have been attempting to use Landmarker to re-orient subject brains > to a > template provided by the developers (we successfully changed the > template to > our dimensions), and I have several questions regarding rigid > transformations. > > I have successfully transformed subjects using several anatomical landmarks > (AC/PC, 1st and 2nd mid sagital, most > anterior/posterior/superior/inferior/left/right). > However, subject brains are still usually a bit slanted in certain views, > post-transformation. Is there any advice as to how to correct for this > occuring? Is it likely a landmark placement issue? > > Also, once the transformations are made, I have been attempting to > apply the > saved landmarks for the subjects to the fiber tracking data (say for > a > bilateral cingulum) that we have already produced for that subject > using MRI > studio. However, we are a bit stumped in attempting to find a way to > take > that reoriented fiber tract data and view it 3D on MRI studio without > having > to redo all the ROI placement, etc. Any advice for this? > > I have also been experimenting with using the rotation/shift image buttons > to change subject images (I actually used this to fix a problem with > the > template, as when we re-sliced it to our dimensions it was shifted > off-center axially/coronally to the user-right). Would using these buttons > affect the results of a rigid transformation? > > Also, I was curious regarding the general algorithm for the rigid > transformation. Is it a similar one to AFNI's manual Talairaching(?) > or > does Landmarker simply re-orient the brain in a way such as to > minimize the > variance in distance between all the placed landmarks? > > Many thanks for your assistance, > > Paul > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > From naamab at stanford.edu Thu Mar 5 11:50:33 2009 From: naamab at stanford.edu (Naama Barnea-Goraly) Date: Thu, 05 Mar 2009 08:50:33 -0800 Subject: [Mristudio-users] Importing analyze format ROIs to dtistudio Message-ID: <5A6535AE-5B36-441A-B193-0AEFC495B28E@stanford.edu> This was brought up in the past but I cannot find a clear answer in the archives - Is there an easy way to import analyze format ROIs into dtistudio? Thanks, Naama Naama Barnea-Goraly M.D. Instructor Center for Interdisciplinary Brain Sciences Research Stanford University Division of Child and Adolescent Psychiatry 401 Quarry Rd. MC 5795 Stanford University School of Medicine Stanford, CA 94305-5795 Phone: (650) 736-1874, fax: (650) 724-4794 CONFIDENTIALITY NOTICE: This e-mail communication and any attachments may contain confidential information for the use of the designated recipients named above. If you are not the intended recipient, you are hereby notified that you have received this communication in error and that any review, disclosure, dissemination, distribution or copying of it or its contents is prohibited. If you have received this communication in error, please notify Stanford Medical Center immediately by telephone at (650) 725-5722 and destroy all copies of this communication and any attachments. Thank you. From susumu at mri.jhu.edu Thu Mar 5 11:56:53 2009 From: susumu at mri.jhu.edu (susumu) Date: Thu, 05 Mar 2009 11:56:53 -0500 Subject: [Mristudio-users] Scanner-specific gradients? In-Reply-To: <115228089.1236257104.228548748.33148@mcgi35.rambler.ru> Message-ID: <7k7ed7$6l0md7@ipex3.johnshopkins.edu> Hi Igor, It depend on the precision of your measurement. With typical 1.5T, 2.5 mm resolution, and 5-10 min scan, the SNR is such that we have about +/- 4 degree of measurement variability (see Fig. 8 of the attached manuscript). In this case, it doesn't matter if you specify the gradient table with the accuracy of 0.1 degree. I'm not sure how this is translated into the decimal points (I think it's not difficult to calculate the actual angle difference by rounding the numbers), but would be surprised if you need the 4th digit. Susumu -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Igor Yakushev Sent: Thursday, March 05, 2009 7:45 AM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] Scanner-specific gradients? Dear Susumu, Thanks again for your careful answer! We have ascertained that the scan-specific (extracted from individual DICOM headers) gradients were the right ones. I have one more practical question: Our individual gradients have values of 14-15 digits following zero, e.g. -0.145791634917259. To what decimal digit should/may one round these values? It's important to know, as we're going to analyse large amount of data and, as i wrote, we have to introduce a different gradient table for each individual case. Of note, there is a rather small difference between the values, please see an example of a gradient table in my previous mail and one more below (rounded to 3 decimal digits): 0: 0.000, 0.000, 0.000 1: 0.696, -0.157, -0.701 2: -0.718, -0.157, -0.678 3: -0.014, 0.533, -0.846 4: 0.009, 0.846, 0.533 5: 0.704, 0.690, -0.168 6: -0.710, 0.690, -0.145 Thank you! Igor * susumu [Thu, 26 Feb 2009 20:04:51 -0500]: > Hi Igor, > > Unless you explicity change the gradient table, the same imaging > protocol > should use the same gradient table. > However, there are several things that make the matter complicated; > > 1) The manufacturers provide gradient tables. For example, Siemens has > 6- > and 12-orientation tables. While they provide only one kind of the > 12-orientation Siemens table, when actual scan happens, they dynamically > change the table. > 2) For example, you may use axial, coronal, or sagital scans. The > patient > may go in the scanner head-first or leg-first. Or they could be face up, > face down, or facing to the side. There are so many possibilities > related to > the relative relationship between the subject, the physical gradients, > and > the imaging parameters. Apparently, one gradient table can not be > applied to > all these setttings. > 3) One of the issues due to this type of degrees of freedom is that the > +/- > sign of the gradient table may not represent what the scanner actually > did. > As a matter of fact, the +/- sign is arbitrary defined. What is most > important is the relationship between the diffusion gradients and > imaging > gradients, which are changed dynamically depending on your protocol. > Usually, for siemens, axial, head-first, face-up, the sign of the X > gradient > has to be flipped. > 4) If you look the two tables you got carefully, you notice that the x > components have opposite signs. I suspect the first one is the one > provided > by Siemens and the second one is read from DICOM header. The latter one > reflects what was actually done by the scanner, I believe. > 5) If you use the one provided by the manufacturer (the first one) for > tensor calculation, it won't affect your FA, ADC, and diffusivity, but > it > affects vector angles (and thus fiber tracking). This is why DtiStudio > has a > function of "flip" before fiber tracking. Of course, it is much better > approach to use the second table with the correct +/- sign. > 5) The second thing you notice is that there is a small differences in > each > component. I suspect this is because you used oblique imaging. Please > check > if this is actually the case. This is a very tricky issue and you have > to > make sure that you are doing a right thing. Not using oblique makes > situation much simpler, but if you want to use oblique, you have to > consider > the following; > 6) If you are using older operating system of Siemens, you HAVE TO > recalculate your gradient table based on oblique angles. You can do it > automatically if you are using DICOM or Mosaic. You have to check > "rotate > gradient if applicable" box. Then DtiStudio read the oblique information > and > reorient the table for you. > 7) If you are using the latest operating system, you don't have to > recalculate the table. So you don't want to check the "rotate gradient > if > appliable" box. Either way, it is advised to image one person with a > severe > oblique plane, process the data, and perform tracking. This immediately > tells if things are correctly working. Vendors change things without > notice. > You'd better learn how to protect yourself. > 8) If you are not sure, you can send the tracking results to us. > > Susumu > > > > > > -----Original Message----- > From: mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Igor > Yakushev > Sent: Thursday, February 26, 2009 12:13 PM > To: DTI Studio, ROI Editor, Landmarker Questions/Support > Subject: [Mristudio-users] Scanner-specific gradients? > > Dear Susumu, dear Users, > I have a beginners question:Should be the combination of gradients the > same > for all subjects imaged with the same scanner (i.e. scanner-specific > gradients)? Or the gradients may be different for different > scans/subjects > (i.e. scan-specific gradients)? Such "individual" gradients (bvec) can > be > calculated using e.g. MRIcron. > For example, gradient table (as provided by radiologists) in the first > case > looks like: > 0: 0, 0, 0 1: -0.7, 0, -0.7 2: 0.7, 0, -0.7 3: 0, 0.7, -0.7 4: 0, 0.7, > 0.7 > 5: -0.7, 0.7, 0 6: 0.7, 0.7, 0 in the second case (calculated with > MRIcron) > completely different: > 0: 0.000, 0.000, 0.000 1: 0.704, -0.146, -0.695 2: -0.710, -0.146, > -0.689 3: > 0.004, 0.546, -0.838 4: 0.003, 0.838, 0.546 5: 0.706, 0.692, -0.149 6: > -0.708, 0.692, -0.142 Accordingly, results (tracks originated from the > same > ROI) are very different. > Thanks,Igor_______________________________________________Mristudio-users > mailing > listMristudio-users at mristudio.orghttp://lists.mristudio.org/mailman/listinfo > /mristudio-users > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------- next part -------------- A non-text attachment was scrubbed... Name: fulltext.pdf Type: application/pdf Size: 2138102 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090305/ba6ae682/attachment-0001.pdf From neuroscience at rambler.ru Thu Mar 5 12:13:42 2009 From: neuroscience at rambler.ru (Igor Yakushev) Date: Thu, 05 Mar 2009 20:13:42 +0300 Subject: [Mristudio-users] a tricky option "AND" Message-ID: <1043033703.1236273222.77778824.36232@mcgi67.rambler.ru> Dear DTI-Studio Experts, 1) i choose the option "AND" and draw 2 ROIs along the length of a track of interest -> i get no track between the ROIs 2) i choose the option "OR" and draw one ROI -> i get multiple tracks; A. then i choose "AND" and draw one ROI within the mixture of tracks -> the number of tracks becomes reduced. B. then i choose "AND" and draw one ROI beyond the mixture of tracks -> all tracks disappear. Is it the expected sequence of phenomena? If yes, I conclude that the option "AND" works only for 2 ROIs, which are drawn within the already defined (visualized) mixture of tracks (obtained using e.g. the option "OR") to separate the track of interest. Is it right? Thanks, Igor From susumu at mri.jhu.edu Thu Mar 5 13:58:46 2009 From: susumu at mri.jhu.edu (susumu) Date: Thu, 05 Mar 2009 13:58:46 -0500 Subject: [Mristudio-users] Importing analyze format ROIs to dtistudio In-Reply-To: <5A6535AE-5B36-441A-B193-0AEFC495B28E@stanford.edu> Message-ID: <7k7ed7$6l2qla@ipex3.johnshopkins.edu> Hi Naama, I don't think you can directly import Analyze ROI to DtiStudio. However, Analyze consists of *.hdr and *.img. The *.img file is a raw data. If the *.img is a binary data, I believe that you can load it as an ROI through the ROI/ "raw" format. One thing you have to know is that the default Analyze format follows Neurology convention. Because DtiStudio follows Radiology convention, reaing the *.img directly as a raw data may lead to upside-down location. I would recommend you to read your Analyze ROI file as Analyze image by DtiStudio or RoiEditor first (maybe RoiEditor is better). Then save the data as binary raw data or "binary map" format. I believe the "binary map" format is one of the most powerful format to communicate with DtiStudio fiber tracking function. The easiest way to learn the "binary map" format is to draw ROIs for fiber tracking in DtiStudio and save the ROI as the "binary map" format. You will find binary ROI files and one text file, which is a kind of a header file. You can open and read the text file to understand the file format. Please let us know if you can follow my suggestion. Susumu -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Naama Barnea-Goraly Sent: Thursday, March 05, 2009 11:51 AM To: Landmarker Questions/Support DTI Studio ROI Editor Subject: [Mristudio-users] Importing analyze format ROIs to dtistudio This was brought up in the past but I cannot find a clear answer in the archives - Is there an easy way to import analyze format ROIs into dtistudio? Thanks, Naama Naama Barnea-Goraly M.D. Instructor Center for Interdisciplinary Brain Sciences Research Stanford University Division of Child and Adolescent Psychiatry 401 Quarry Rd. MC 5795 Stanford University School of Medicine Stanford, CA 94305-5795 Phone: (650) 736-1874, fax: (650) 724-4794 CONFIDENTIALITY NOTICE: This e-mail communication and any attachments may contain confidential information for the use of the designated recipients named above. If you are not the intended recipient, you are hereby notified that you have received this communication in error and that any review, disclosure, dissemination, distribution or copying of it or its contents is prohibited. If you have received this communication in error, please notify Stanford Medical Center immediately by telephone at (650) 725-5722 and destroy all copies of this communication and any attachments. Thank you. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From susumu at mri.jhu.edu Thu Mar 5 14:17:31 2009 From: susumu at mri.jhu.edu (susumu) Date: Thu, 05 Mar 2009 14:17:31 -0500 Subject: [Mristudio-users] Landmarker - Reorientation questions In-Reply-To: <8874e3900903050751l68574c16i5188ffb91cb6381b@mail.gmail.com> Message-ID: <7k7ed7$6l3156@ipex3.johnshopkins.edu> Hi Paul, The landmark-based registration simply follows your landmarks. So, if you want to modify the outcome, you need to modify (or add more) landmarks. You can also test automated volume registration by AIR. Either way, you can save the transformation matrix and apply it to fiber tracking results. There is one important limitation in our current software when you normalize the tracking results. For the normalization, you have to convert the streamline information (DtiStudio-specific fiber data format) into pixel-by-pixel image format. For example, suppose your tracking generated 10 fibers with average 50-pixel long. Then your native streamline information contains [x,y,z] information for the 10 streamlines saved sequentially. This streamline information is not easy to transform. I believe Luke in my lab has an IDL code to do this, but our MriStudio family can not do it. Please contact khua at jhu.edu if you want the IDL code. You can convert this streamline information to 1/0 pixel-by-pixel image format. For example, if your data is 256x256x50, the pixels that contain the tracking result are 1 and do not contain are 0. You can save and load this info as an image file. Then you can transform (normalize) this file as if one of your MRI contrasts. The problem of this approach is, you can not retrieve streamline info once it was converted to the 1/0 binary image. You should think why you need to retain the streamline information after brain registration (normalization). For example, you can create all necessary information in a native space such as connectivity maps and transform the resultant map. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Paul Beach Sent: Thursday, March 05, 2009 10:52 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] Landmarker - Reorientation questions Greetings everyone, I have been attempting to use Landmarker to re-orient subject brains to a template provided by the developers (we successfully changed the template to our dimensions), and I have several questions regarding rigid transformations. I have successfully transformed subjects using several anatomical landmarks (AC/PC, 1st and 2nd mid sagital, most anterior/posterior/superior/ inferior/left/right). However, subject brains are still usually a bit slanted in certain views, post-transformation. Is there any advice as to how to correct for this occuring? Is it likely a landmark placement issue? Also, once the transformations are made, I have been attempting to apply the saved landmarks for the subjects to the fiber tracking data (say for a bilateral cingulum) that we have already produced for that subject using MRI studio. However, we are a bit stumped in attempting to find a way to take that reoriented fiber tract data and view it 3D on MRI studio without having to redo all the ROI placement, etc. Any advice for this? I have also been experimenting with using the rotation/shift image buttons to change subject images (I actually used this to fix a problem with the template, as when we re-sliced it to our dimensions it was shifted off-center axially/coronally to the user-right). Would using these buttons affect the results of a rigid transformation? Also, I was curious regarding the general algorithm for the rigid transformation. Is it a similar one to AFNI's manual Talairaching(?) or does Landmarker simply re-orient the brain in a way such as to minimize the variance in distance between all the placed landmarks? Many thanks for your assistance, Paul -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090305/eb3bf535/attachment.html From susumu at mri.jhu.edu Thu Mar 5 14:21:46 2009 From: susumu at mri.jhu.edu (susumu) Date: Thu, 05 Mar 2009 14:21:46 -0500 Subject: [Mristudio-users] gradient table normalization? b0 image b-value? In-Reply-To: <2F83066B198C48F8AC26ADA7DCB8693B@panpan> Message-ID: <7k7ed7$6l32ie@ipex3.johnshopkins.edu> Hi Yi, I think you don't have to. The only number you have to be careful is [100, 100, 100]. You can't use this combination because this is set aside to instruct DtiStudio to "Ignore the image". -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Yi Jiang Sent: Thursday, March 05, 2009 10:29 AM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] gradient table normalization? b0 image b-value? Hello, when I use a .dpf file to calculate diffusion tensor, should I normalize the gradient table? For example, can I use the following lines in the .dpf file or do I have to normalize the gradient table? Will the normalization or non-normalization affect the calculated diffusivity values? --------------------------- B-Value: 1000 Begin_Of_Gradient_Table 0: 0,0,0 1: 45.3060, 15.6000, 36.1080 2: 1.4340, -20.4720, 56.3820 3: 12.6960, 50.9160, 29.0880 4: -28.7580, 42.6360, 30.9000 5: -23.6280, -37.8120, 40.1460 6: -36.9540, 15.6900, 44.5860 7: 33.4800, -44.4300, 22.4760 8: -57.2400, -4.0020, 17.5440 9: 51.7140, -24.1140, 18.5400 10: 13.7760, 12.4080, 57.0660 11: -47.2500, -36.9180, 2.0940 12: -2.0760, -59.3820, 8.3520 End_Of_Gradient_Table --------------------------- Moreover, if my b0 file has some small value (not exactly 0), such as b0 has b-value of 10 and other DWIs has b-value of 1000, how can I indicate that in the .dpf file? Thank you very much! Best, Yi _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From susumu at mri.jhu.edu Thu Mar 5 14:28:52 2009 From: susumu at mri.jhu.edu (susumu) Date: Thu, 05 Mar 2009 14:28:52 -0500 Subject: [Mristudio-users] Mean_ADC units In-Reply-To: Message-ID: <7k7ed7$6l34lr@ipex3.johnshopkins.edu> I suggest to use RoiEditor. Load your FA map and use the "thresholding" or "region growing" tool to define the white matter - cortex boundary with FA = 0.15-0.25. This usually gives the good white matter surface. If you need skullstip, load b0 or mean(DWI) image (you can create it by DtiStudio) and use the thresholding or region growing tool to define the brain outline. Register it as one object and use "+-/x" button to use the object as "masking". This usually can clean up all the extra-cranial junks. _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of jiangxi Sent: Wednesday, March 04, 2009 11:21 PM To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] Mean_ADC units Hi, I'am wondering that how to use DTI data to reconstruct the cerebral cortex surface or WM surface. The DTIStudio seems that can only carriy out to the fiber-tracking step. Thanks! > Date: Wed, 4 Mar 2009 15:55:29 -0500 > From: hjiang at jhmi.edu > To: mristudio-users at mristudio.org > Subject: Re: [Mristudio-users] Mean_ADC units > > its unit is (mm^2/s) when you consider the b-value during the calculation. > > hangyi > > > > >>> Moran Artzi 03/04/09 2:34 PM >>> > Hi > what units are used when reporting the ADC Map - Mean value on the > DTI-Studio Fiber Statistic option? > ADC Map - Mean > Max. of ImgVal: 4.2198 > Min. of ImgVal: 0.1643 > Mean of ImgVal: 0.9090 > Std. of ImgVal: 0.3467 > > Many thanks > > Moran > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users _____ ?MSN???????????????? ??? ?? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090305/d068fbd0/attachment-0001.html From susumu at mri.jhu.edu Thu Mar 5 14:57:08 2009 From: susumu at mri.jhu.edu (susumu) Date: Thu, 05 Mar 2009 14:57:08 -0500 Subject: [Mristudio-users] Mean_ADC units In-Reply-To: <49AEA471020000630001D2AA@cis27.hosts.jhmi.edu> Message-ID: <7k7ed7$6l3e7q@ipex3.johnshopkins.edu> The ADC value you are reporting seems too high. Please make sure that you specify the correct b-value (in the first data input window) and the check box of "consider b-value" in clicked (after you click "tensor calculation" button). If you didn't specify one of these, the calculation is based on b = 1. If you use b=1,000, you have to divide the value by 1,000 to get the correct unit (mm^2/s). -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hangyi Jiang Sent: Wednesday, March 04, 2009 3:55 PM To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] Mean_ADC units its unit is (mm^2/s) when you consider the b-value during the calculation. hangyi >>> Moran Artzi 03/04/09 2:34 PM >>> Hi what units are used when reporting the ADC Map - Mean value on the DTI-Studio Fiber Statistic option? ADC Map - Mean Max. of ImgVal: 4.2198 Min. of ImgVal: 0.1643 Mean of ImgVal: 0.9090 Std. of ImgVal: 0.3467 Many thanks Moran _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From jyw.chen at utoronto.ca Thu Mar 5 15:58:39 2009 From: jyw.chen at utoronto.ca (Jerry Yeou-Wei Chen) Date: Thu, 05 Mar 2009 15:58:39 -0500 Subject: [Mristudio-users] Importing analyze format ROIs to dtistudio In-Reply-To: <7k7ed7$6l2qla@ipex3.johnshopkins.edu> References: <5A6535AE-5B36-441A-B193-0AEFC495B28E@stanford.edu> <7k7ed7$6l2qla@ipex3.johnshopkins.edu> Message-ID: <3050363f0903051258j782b290fle8594ccb7e1dddfe@mail.gmail.com> Hi Naama, Here's a method I used that worked for me (roughly what Susumu recommended below) I had created masks in FSL that I wanted to use in DTIStudio to seed tracts, and here's what worked: Here are steps in FSL ?Use fslview to draw mask ?Convert to 8-bit > fslmaths input -add 0 output -odt char ?Convert to Analyze > fslchfiletype ANALYZE output Here are steps in DTIstudio ?Load as Analyze in DTIstudio (MRI View3D)? ?Save as raw ?Load Fiber Tracking ?Load ROI as binary image (raw)? Good luck! - Jerry On Thu, Mar 5, 2009 at 1:58 PM, susumu wrote: > Hi Naama, > > I don't think you can directly import Analyze ROI to DtiStudio. > However, Analyze consists of *.hdr and *.img. The *.img file is a raw data. > If the *.img is a binary data, I believe that you can load it as an ROI > through the ROI/ "raw" format. > > One thing you have to know is that the default Analyze format follows > Neurology convention. Because DtiStudio follows Radiology convention, > reaing > the *.img directly as a raw data may lead to upside-down location. > > I would recommend you to read your Analyze ROI file as Analyze image by > DtiStudio or RoiEditor first (maybe RoiEditor is better). Then save the > data > as binary raw data or "binary map" format. I believe the "binary map" > format > is one of the most powerful format to communicate with DtiStudio fiber > tracking function. > > The easiest way to learn the "binary map" format is to draw ROIs for fiber > tracking in DtiStudio and save the ROI as the "binary map" format. You will > find binary ROI files and one text file, which is a kind of a header file. > You can open and read the text file to understand the file format. > > Please let us know if you can follow my suggestion. > > Susumu > > -----Original Message----- > From: mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Naama > Barnea-Goraly > Sent: Thursday, March 05, 2009 11:51 AM > To: Landmarker Questions/Support DTI Studio ROI Editor > Subject: [Mristudio-users] Importing analyze format ROIs to dtistudio > > > This was brought up in the past but I cannot find a clear answer in > the archives - Is there an easy way to import analyze format ROIs into > dtistudio? > > Thanks, > > Naama > > > > Naama Barnea-Goraly M.D. > Instructor > Center for Interdisciplinary Brain Sciences Research > Stanford University Division of Child and Adolescent Psychiatry > 401 Quarry Rd. MC 5795 > Stanford University School of Medicine > Stanford, CA 94305-5795 > Phone: (650) 736-1874, fax: (650) 724-4794 > > > CONFIDENTIALITY NOTICE: This e-mail communication and any attachments > may contain confidential information for the use of the designated > recipients named above. If you are not the intended recipient, you > are hereby notified that you have received this communication in error > and that any review, disclosure, dissemination, distribution or > copying of it or its contents is prohibited. If you have received > this communication in error, please notify Stanford Medical Center > immediately by telephone at (650) 725-5722 and destroy all copies of > this communication and any attachments. Thank you. > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090305/202de3f2/attachment.html From superjx2318 at hotmail.com Fri Mar 6 01:19:53 2009 From: superjx2318 at hotmail.com (jiangxi) Date: Fri, 06 Mar 2009 06:19:53 +0000 Subject: [Mristudio-users] Mean_ADC units In-Reply-To: <7k7ed7$6l34lr@ipex3.johnshopkins.edu> References: <7k7ed7$6l34lr@ipex3.johnshopkins.edu> Message-ID: Hi,susumu Thanks for your advice. When I use the "thresholding" tool to define WM cortex boundary with ranging from 0.15-0.25, it appears many red points in the FA map to express the WM cortex. But I'm still confused with the sequence steps: 1.How to save the red point- labeled FA map? 2.how can I use the map to reconstruct the WM surface? 3.How can the reconstructed the WM surface be visualized? Many thanks! Date: Thu, 5 Mar 2009 14:28:52 -0500 From: susumu at mri.jhu.edu To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] Mean_ADC units I suggest to use RoiEditor. Load your FA map and use the "thresholding" or "region growing" tool to define the white matter - cortex boundary with FA = 0.15-0.25. This usually gives the good white matter surface. If you need skullstip, load b0 or mean(DWI) image (you can create it by DtiStudio) and use the thresholding or region growing tool to define the brain outline. Register it as one object and use "+-/x" button to use the object as "masking". This usually can clean up all the extra-cranial junks. From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of jiangxi Sent: Wednesday, March 04, 2009 11:21 PM To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] Mean_ADC units Hi, I'am wondering that how to use DTI data to reconstruct the cerebral cortex surface or WM surface. The DTIStudio seems that can only carriy out to the fiber-tracking step. Thanks! > Date: Wed, 4 Mar 2009 15:55:29 -0500 > From: hjiang at jhmi.edu > To: mristudio-users at mristudio.org > Subject: Re: [Mristudio-users] Mean_ADC units > > its unit is (mm^2/s) when you consider the b-value during the calculation. > > hangyi > > > > >>> Moran Artzi 03/04/09 2:34 PM >>> > Hi > what units are used when reporting the ADC Map - Mean value on the > DTI-Studio Fiber Statistic option? > ADC Map - Mean > Max. of ImgVal: 4.2198 > Min. of ImgVal: 0.1643 > Mean of ImgVal: 0.9090 > Std. of ImgVal: 0.3467 > > Many thanks > > Moran > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users ?MSN???????????????? ????? _________________________________________________________________ MSN??????????????????MSN??? http://im.live.cn/safe/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090306/6ef6982d/attachment.html From susumu at mri.jhu.edu Fri Mar 6 15:16:32 2009 From: susumu at mri.jhu.edu (susumu) Date: Fri, 06 Mar 2009 15:16:32 -0500 Subject: [Mristudio-users] Mean_ADC units In-Reply-To: Message-ID: <7k7ed7$6leou5@ipex3.johnshopkins.edu> OK, here is the procedure; 1) Please prepare one FA map and one b0 (or meanDWI) 2) Load the FA map to RoiEditor using the left upper "open" icon 3) Load the b0 (or meanDWI) using the "open" icon in the right column, "Image" section. 4) Make sure that you have FA and b0 both loaded into one window using the pull-down menu in the "image" section ------ Skull-stripping Using b0 (or meanDWI) -------- 5) Choose the b0 image as the active image. 6) Choose the "Seeded Region Growing" tool in the "Tool" section 7) Choose "absolute" and "3D" radio buttons. 8) Change the minimum value (for example "10") and click apply. Click an arbitrary pixel within the brain. See how the brain is defined by red color 9) Keep changing the minimum value until you are satisfied with the way the brain is defined by the red color. 10) Once you are satisfied, look at the "ROI Object" section and make sure that "Object 1" is there. If not, right click the mouse buttons within the square space below "ROI Objects" and define a new object 11) Click the "add" button in the "Selection" section. The red selected area disappeared and defined by the "Object 1" color now. 12) Click the "+-/x" button in the "ROI" section. Choose the FA map in the left and Object 1 in the right. In the middle box, choose "masking" and click "OK". You should get a skull-stripped FA map. ------ Define the white matter --------- 13) Right click on the "Object 1" in the "ROI Objects" section and choose "delete object". 14) Right click the empty square below the "ROI Objects" and choose "new object". You redefined Object 1. 15) Choose the skull-stripped FA as the active image. 16) Choose "Seeded Region Growing". Choose "Absolute" and "3D" radio buttons. Input 0.2 for the minimum and 1.0 for the maximum. Click on an arbitrary pixel within the bright white matter area. 17) Click "Add" button. The red area turns into Object 1. If you find junk pixels outside the white matter and want to manually touch up the result, choose the "pencil" in the "Selection" section, write on the junk pixels (red color appears), and click "Subtract" button. 18) Click the "save" icon in the "ROI" section. You can save the Object 1 that defines the white matter as Analyze or Binary. Let me know if you are stuck or this doesn't work. _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of jiangxi Sent: Friday, March 06, 2009 1:20 AM To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] Mean_ADC units Hi,susumu Thanks for your advice. When I use the "thresholding" tool to define WM cortex boundary with ranging from 0.15-0.25, it appears many red points in the FA map to express the WM cortex. But I'm still confused with the sequence steps: 1.How to save the red point- labeled FA map? 2.how can I use the map to reconstruct the WM surface? 3.How can the reconstructed the WM surface be visualized? Many thanks! _____ Date: Thu, 5 Mar 2009 14:28:52 -0500 From: susumu at mri.jhu.edu To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] Mean_ADC units I suggest to use RoiEditor. Load your FA map and use the "thresholding" or "region growing" tool to define the white matter - cortex boundary with FA = 0.15-0.25. This usually gives the good white matter surface. If you need skullstip, load b0 or mean(DWI) image (you can create it by DtiStudio) and use the thresholding or region growing tool to define the brain outline. Register it as one object and use "+-/x" button to use the object as "masking". This usually can clean up all the extra-cranial junks. _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of jiangxi Sent: Wednesday, March 04, 2009 11:21 PM To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] Mean_ADC units Hi, I'am wondering that how to use DTI data to reconstruct the cerebral cortex surface or WM surface. The DTIStudio seems that can only carriy out to the fiber-tracking step. Thanks! > Date: Wed, 4 Mar 2009 15:55:29 -0500 > From: hjiang at jhmi.edu > To: mristudio-users at mristudio.org > Subject: Re: [Mristudio-users] Mean_ADC units > > its unit is (mm^2/s) when you consider the b-value during the calculation. > > hangyi > > > > >>> Moran Artzi 03/04/09 2:34 PM >>> > Hi > what units are used when reporting the ADC Map - Mean value on the > DTI-Studio Fiber Statistic option? > ADC Map - Mean > Max. of ImgVal: 4.2198 > Min. of ImgVal: 0.1643 > Mean of ImgVal: 0.9090 > Std. of ImgVal: 0.3467 > > Many thanks > > Moran > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users _____ ?MSN???????????????? ? ???? _____ ????? Windows Live Messenger ???????? ????? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090306/14f8a61c/attachment-0001.html From huyuzheng at gmail.com Sun Mar 8 07:14:18 2009 From: huyuzheng at gmail.com (=?GB2312?B?uvrT8dX9?=) Date: Sun, 08 Mar 2009 19:14:18 +0800 Subject: [Mristudio-users] read 4D DWI Philips Achieva 3T DICOM files Message-ID: <39c428d80903080414p110fe556l2f76dd7d153c6ea6@mail.gmail.com> Hi: I have DWI DICOM files from a Philips Achieva 3T scanner. They are 4D DICOM file with all the slices and directions in one file, e.g. 'IM_001' without any extensions. It could be converted to NIFTI or ANALYZE format with dcm2niigui.exe. However, DTIStudio was failed to open my data with neither NIFTI nor Analyze format. How can I read with DTIStudio, or convert it to 3D DICOM files ? The same question has been posted before, here it is: http://lists.mristudio.org/pipermail/mristudio-users/2008/000229.html. Is it solved now? Sincerely, Hu Y.Z. Zhejiang University, Hangzhou, China. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090308/3b70c2fd/attachment.html From susumu at mri.jhu.edu Mon Mar 9 10:08:44 2009 From: susumu at mri.jhu.edu (susumu) Date: Mon, 09 Mar 2009 10:08:44 -0400 Subject: [Mristudio-users] read 4D DWI Philips Achieva 3T DICOM files In-Reply-To: <39c428d80903080414p110fe556l2f76dd7d153c6ea6@mail.gmail.com> Message-ID: <7k7ed7$6m1aq5@ipex3.johnshopkins.edu> This must be the new "extended DICOM" format. I wonder if it is possible to send our your original DICOM and converted NIFTI and Analyze so that we can find out why you are having the I/O error. _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of ??? Sent: Sunday, March 08, 2009 7:14 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] read 4D DWI Philips Achieva 3T DICOM files Hi: I have DWI DICOM files from a Philips Achieva 3T scanner. They are 4D DICOM file with all the slices and directions in one file, e.g. 'IM_001' without any extensions. It could be converted to NIFTI or ANALYZE format with dcm2niigui.exe. However, DTIStudio was failed to open my data with neither NIFTI nor Analyze format. How can I read with DTIStudio, or convert it to 3D DICOM files ? The same question has been posted before, here it is: http://lists.mristudio.org/pipermail/mristudio-users/2008/000229.html. Is it solved now? Sincerely, Hu Y.Z. Zhejiang University, Hangzhou, China. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090309/9514f74e/attachment.html From c.bieck at T-Online.de Mon Mar 9 15:10:00 2009 From: c.bieck at T-Online.de (Christian Bieck) Date: Mon, 09 Mar 2009 19:10 +0000 (GMT) Subject: [Mristudio-users] How to do a Tailarach transformation? Message-ID: <1LgkrK-14QxaC0@fwd04.aul.t-online.de> Hello, I'm still working on analyzing the optic radiation via DTI and would like to transform the subjects' data into Talairach space via Landmarker so as to then position the relevant ROIs in a more objective manner. I am still unsure about the whole process, though. I watched all five videos of the DTIStudio tutorial which Landmarker was only a small part of and then tried to follow the Landmarker manual, but I still don't know how to proceed exactly. The best I could come up with is to use Landmarks on the AC, PC and most superior, inferior, anterior, posterior, left and right parts of the Talairach DWI template brain and the individual subject's DWI data, which resulted in a slightly rotated transformed brain, however, and didn't look quite right to me. Now my main question is if I am somehow on the right path or if I forgot some vital steps in all of this. In the case of using a Landmark-based transformation, would it be a problem if, for example, the most anterior part of the template brain and hence the Landmark would be on the right hemisphere while the subject's most anterior part would be on the left hemisphere? Should I include an AIR transformation before that? As you can see, I'm somewhat lost in all of this and so would very much appreciate any input you could give me on how to do a proper Talairach transformation via Landmarker. Thank you very much for your time and effort. Sincerely, Christian Bieck From huyuzheng at gmail.com Mon Mar 9 21:21:42 2009 From: huyuzheng at gmail.com (=?GB2312?B?uvrT8dX9?=) Date: Tue, 10 Mar 2009 09:21:42 +0800 Subject: [Mristudio-users] read 4D DWI Philips Achieva 3T DICOM files In-Reply-To: <7k7ed7$6m1aq5@ipex3.johnshopkins.edu> References: <39c428d80903080414p110fe556l2f76dd7d153c6ea6@mail.gmail.com> <7k7ed7$6m1aq5@ipex3.johnshopkins.edu> Message-ID: <39c428d80903091821p71a71548h584e5b8f9a496742@mail.gmail.com> Hi, Thanks for your reply. I want to sen you a copy of my raw data, but it is too big to email. I upload it to here : http://hyz123.vdisk.cn/VDISK2009/web2/index.html?tab=corpshare&act=linkcode&lc_code=3511366A7136. I have tested it. Any one should get it by this link. But this is a chinese website, I am not sure if everyone can access it. I have ever used dcm2niigui.exe to convert it to ANALYZE or NIFTI format, and I obtained one .bval and one .bvec file exept the img file(s). All thanks. Yuzheng 2009/3/9 susumu > This must be the new "extended DICOM" format. > > > > I wonder if it is possible to send our your original DICOM and converted > NIFTI and Analyze so that we can find out why you are having the I/O error. > > > ------------------------------ > > *From:* mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org] *On Behalf Of *??? > *Sent:* Sunday, March 08, 2009 7:14 AM > *To:* mristudio-users at mristudio.org > *Subject:* [Mristudio-users] read 4D DWI Philips Achieva 3T DICOM files > > > > Hi: > > I have DWI DICOM files from a Philips Achieva 3T scanner. They are 4D > DICOM file with all the slices and directions in one file, e.g. > 'IM_001' without any extensions. > > It could be converted to NIFTI or ANALYZE format with dcm2niigui.exe. > However, DTIStudio was failed to open my data with neither NIFTI nor Analyze > format. > > How can I read with DTIStudio, or convert it to 3D DICOM files ? > > The same question has been posted before, here it is: > http://lists.mristudio.org/pipermail/mristudio-users/2008/000229.html. Is > it solved now? > > > > Sincerely, > > > > > > Hu Y.Z. > > > > Zhejiang University, Hangzhou, China. > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090310/864099b2/attachment.html From superjx2318 at hotmail.com Tue Mar 10 05:57:33 2009 From: superjx2318 at hotmail.com (jiangxi) Date: Tue, 10 Mar 2009 09:57:33 +0000 Subject: [Mristudio-users] reconstruct WM surface In-Reply-To: <7k7ed7$6m1aq5@ipex3.johnshopkins.edu> References: <39c428d80903080414p110fe556l2f76dd7d153c6ea6@mail.gmail.com> <7k7ed7$6m1aq5@ipex3.johnshopkins.edu> Message-ID: Hi,susumu I wonder if I've got an ideal segmentation of WM based on DTI data, how can I use it to reconstruct the WM surface? Many thanks! Xi Jiang Date: Mon, 9 Mar 2009 10:08:44 -0400 From: susumu at mri.jhu.edu To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] read 4D DWI Philips Achieva 3T DICOM files This must be the new "extended DICOM" format. I wonder if it is possible to send our your original DICOM and converted NIFTI and Analyze so that we can find out why you are having the I/O error. From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of ??? Sent: Sunday, March 08, 2009 7:14 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] read 4D DWI Philips Achieva 3T DICOM files Hi: I have DWI DICOM files from a Philips Achieva 3T scanner. They are 4D DICOM file with all the slices and directions in one file, e.g. 'IM_001' without any extensions. It could be converted to NIFTI or ANALYZE format with dcm2niigui.exe. However, DTIStudio was failed to open my data with neither NIFTI nor Analyze format. How can I read with DTIStudio, or convert it to 3D DICOM files ? The same question has been posted before, here it is: http://lists.mristudio.org/pipermail/mristudio-users/2008/000229.html. Is it solved now? Sincerely, Hu Y.Z. Zhejiang University, Hangzhou, China. _________________________________________________________________ ??K???????????????????MClub???? http://club.msn.cn/?form=3 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090310/0f4f2ffa/attachment-0001.html From mallarc at alleninstitute.org Tue Mar 10 10:57:37 2009 From: mallarc at alleninstitute.org (Mallar Chakravarty) Date: Tue, 10 Mar 2009 07:57:37 -0700 Subject: [Mristudio-users] read 4D DWI Philips Achieva 3T DICOM files References: <39c428d80903080414p110fe556l2f76dd7d153c6ea6@mail.gmail.com> <7k7ed7$6m1aq5@ipex3.johnshopkins.edu> <39c428d80903091821p71a71548h584e5b8f9a496742@mail.gmail.com> Message-ID: Great that makes sense. Thanks for the reply! mallar -----Original Message----- From: mristudio-users-bounces at mristudio.org on behalf of ??? Sent: Mon 3/9/2009 6:21 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] read 4D DWI Philips Achieva 3T DICOM files Hi, Thanks for your reply. I want to sen you a copy of my raw data, but it is too big to email. I upload it to here : http://hyz123.vdisk.cn/VDISK2009/web2/index.html?tab=corpshare&act=linkcode&lc_code=3511366A7136. I have tested it. Any one should get it by this link. But this is a chinese website, I am not sure if everyone can access it. I have ever used dcm2niigui.exe to convert it to ANALYZE or NIFTI format, and I obtained one .bval and one .bvec file exept the img file(s). All thanks. Yuzheng 2009/3/9 susumu > This must be the new "extended DICOM" format. > > > > I wonder if it is possible to send our your original DICOM and converted > NIFTI and Analyze so that we can find out why you are having the I/O error. > > > ------------------------------ > > *From:* mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org] *On Behalf Of *??? > *Sent:* Sunday, March 08, 2009 7:14 AM > *To:* mristudio-users at mristudio.org > *Subject:* [Mristudio-users] read 4D DWI Philips Achieva 3T DICOM files > > > > Hi: > > I have DWI DICOM files from a Philips Achieva 3T scanner. They are 4D > DICOM file with all the slices and directions in one file, e.g. > 'IM_001' without any extensions. > > It could be converted to NIFTI or ANALYZE format with dcm2niigui.exe. > However, DTIStudio was failed to open my data with neither NIFTI nor Analyze > format. > > How can I read with DTIStudio, or convert it to 3D DICOM files ? > > The same question has been posted before, here it is: > http://lists.mristudio.org/pipermail/mristudio-users/2008/000229.html. Is > it solved now? > > > > Sincerely, > > > > > > Hu Y.Z. > > > > Zhejiang University, Hangzhou, China. > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 4069 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090310/52d338c3/attachment.bin From susumu at mri.jhu.edu Tue Mar 10 21:56:47 2009 From: susumu at mri.jhu.edu (susumu) Date: Tue, 10 Mar 2009 21:56:47 -0400 Subject: [Mristudio-users] reconstruct WM surface In-Reply-To: References: <39c428d80903080414p110fe556l2f76dd7d153c6ea6@mail.gmail.com> <7k7ed7$6m1aq5@ipex3.johnshopkins.edu> Message-ID: <1E6021BF1E3741F5AB9590813ABAF093@SusumuThinkPad> Hi Xi, We have very basic software for 3D visualization. Please contact Luke (khua1 at jhu.edu) if you want to try it. 3D visualization usually doesn?t have much scientific value for daily image evaluation. We use it only for publication and for that purpose we use a commercial program called Amira. _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of jiangxi Sent: Tuesday, March 10, 2009 5:58 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] reconstruct WM surface Hi,susumu I wonder if I've got an ideal segmentation of WM based on DTI data, how can I use it to reconstruct the WM surface? Many thanks! Xi Jiang _____ Date: Mon, 9 Mar 2009 10:08:44 -0400 From: susumu at mri.jhu.edu To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] read 4D DWI Philips Achieva 3T DICOM files This must be the new "extended DICOM" format. I wonder if it is possible to send our your original DICOM and converted NIFTI and Analyze so that we can find out why you are having the I/O error. _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of ??? Sent: Sunday, March 08, 2009 7:14 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] read 4D DWI Philips Achieva 3T DICOM files Hi: I have DWI DICOM files from a Philips Achieva 3T scanner. They are 4D DICOM file with all the slices and directions in one file, e.g. 'IM_001' without any extensions. It could be converted to NIFTI or ANALYZE format with dcm2niigui.exe. However, DTIStudio was failed to open my data with neither NIFTI nor Analyze format. How can I read with DTIStudio, or convert it to 3D DICOM files ? The same question has been posted before, here it is: http://lists.mristudio.org/pipermail/mristudio-users/2008/000229.html. Is it solved now? Sincerely, Hu Y.Z. Zhejiang University, Hangzhou, China. _____ ?MSN???????????????? ??? ?? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090310/db56f400/attachment.html From neuroscience at rambler.ru Wed Mar 11 04:38:33 2009 From: neuroscience at rambler.ru (Igor Yakushev) Date: Wed, 11 Mar 2009 11:38:33 +0300 Subject: [Mristudio-users] Tracking of the cingulum bundle In-Reply-To: <1E6021BF1E3741F5AB9590813ABAF093@SusumuThinkPad> References: <39c428d80903080414p110fe556l2f76dd7d153c6ea6@mail.gmail.com> <7k7ed7$6m1aq5@ipex3.johnshopkins.edu> <1E6021BF1E3741F5AB9590813ABAF093@SusumuThinkPad> Message-ID: <544786854.1236760713.87694392.41512@mcgi61.rambler.ru> Dear Susumu, dear Experts, I?m trying to establish an algorithm, which would allow tracking of the cingulum bundle (CB) with a good reproducibility. I have started with the superior part of CB. First, I place two ROIs (2 x option OR): one at the level of the splenium of the corpus callosum (CC) (Wakana et al., 2007 NI) and one at the border between the anterior 1/3 and posterior 2/3 of the CC body, please see ppt slides. According to Wakana et al. the second ROI should be placed at the level of the genu, but in this case no tracks are found between the ROIs. Relatively large ROIs are used in order to ensure initial inclusion of all voxels related to CB according to a color-coded map. Then, I place two smaller ROIs (2 x option AND) at the same locations. Fibers, whose direction roughly deviates from the direction of the CB, are excluded with the option NOT. 1) Any critique, improvements to this schema, please? Finally, I get a fiber track, which is substantially smaller than the extension of (green) voxels related to CC, please see the slides. 2) How should/may this be interpreted? Is this related to the procedure of the ROI placement? Back to tracking.. I?d like to continue tracking of CB going to its anterior or descending part. I start again with the option OR. Then one needs AND, but AND refers to all ROIs within the image, right? Accordingly, placement of one more ROI (option AND) e.g. at the level of the pons results in disappearance of the previously reconstructed portion of CB. 3) Possible solutions? Should one just save the previously reconstructed track? When all portions are tracked, it must be possible to save all portions as one track, isn?t it? The aim is to get statistics from the whole CB, not only from its portions. Many thanks! Igor P.S. Actually, i wrote and tryed to post this message for the first time 2 days ago, but it hasn't reached the list probably because of a relative large size of the attached file (1 MB power point presentation). Therefore, i don't attache the file to the present message, but would be happy to send it separately. Unfortunately, a person (akolasny at mristudio.org), who should approve the message, seems to be out of the office. How can i send the file to the list? From fjnavas2 at gmail.com Wed Mar 11 08:14:58 2009 From: fjnavas2 at gmail.com (Javier Navas) Date: Wed, 11 Mar 2009 13:14:58 +0100 Subject: [Mristudio-users] Extract values of the Fiber tract ROI Message-ID: <6fd5e4b20903110514p3a01448du1d89e25e0645014e@mail.gmail.com> Dear all, I`m working in Fiber Tracking of the corpus callosum with DTIstudio, I want to extract the values of my ROI (the statistics with the number of fibers selected, length of fibers, FA values...) to a text file or SPSS archive, but I don`t know how can I do it. Thank you for help me, Javier -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090311/0c466edc/attachment.html From neuroscience at rambler.ru Mon Mar 9 14:52:31 2009 From: neuroscience at rambler.ru (Igor Yakushev) Date: Mon, 09 Mar 2009 21:52:31 +0300 Subject: [Mristudio-users] Tracking of the cingulum bundle Message-ID: <928711110.1236624751.161529108.21225@mcgi48.rambler.ru> Dear Susumu, dear Experts, I?m trying to establish an algorithm, which would allow tracking of the cingulum bundle (CB) with a good reproducibility. I have started with the superior part of CB. First, I place two ROIs (2 x option OR): one at the level of the splenium of the corpus callosum (CC) (Wakana et al., 2007 NI) and one at the border between the anterior 1/3 and posterior 2/3 of the CC body, please see ppt slides. According to Wakana et al. the second ROI should be placed at the level of the genu, but in this case no tracks are found between the ROIs. Relatively large ROIs are used in order to ensure initial inclusion of all voxels related to CC according to a color-coded map. Then, I place two smaller ROIs (2 x option AND) at the same locations. Fibers, whose direction roughly deviates from the direction of the CB, are excluded with the option NOT. 1) Any critique, improvements to this schema, please? Finally, I get a fiber track, which is substantially smaller than the extension of (green) voxels related to CC, please see the slides. 2) How should/may this be interpreted? Is this related to the procedure of the ROI placement? Back to tracking.. I?d like to continue tracking of CB going to its anterior or descending part. I start again with the option OR. Then one needs AND, but AND refers to all ROIs within the image, right? Accordingly, placement of one more ROI (option AND) e.g. at the level of the pons results in disappearance of the previously reconstructed portion of CB. 3) Possible solutions? Should one just save the previously reconstructed track? When all portions are tracked, it must be possible to save all portions as one track, isn?t it? The aim is to get statistics from the whole CB, not only from its portions. Many thanks! Igor -------------- next part -------------- A non-text attachment was scrubbed... Name: CB_superior_part_IY.ppt Type: application/vnd.ms-powerpoint Size: 1093120 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090309/f2a4cc6b/attachment-0001.ppt From 2mijung.kim at gmail.com Tue Mar 10 00:39:07 2009 From: 2mijung.kim at gmail.com (Mi Jung Kim) Date: Mon, 09 Mar 2009 21:39:07 -0700 Subject: [Mristudio-users] LDDMM Message-ID: <53bb0fa40903092139k6ceb89adt8bfe826bbd9b309c@mail.gmail.com> Hi, I would like to submit my phantom data. Could you let me know how to do it? Sincerely, Mi Jung -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090309/f0634e30/attachment-0001.html From neuroscience at rambler.ru Tue Mar 10 07:58:58 2009 From: neuroscience at rambler.ru (Igor Yakushev) Date: Tue, 10 Mar 2009 14:58:58 +0300 Subject: [Mristudio-users] Fwd: Tracking of the cingulum bundle Message-ID: <740344210.1236686338.163883820.34776@mcgi39.rambler.ru> It seems that my mail from yesterday hasn't reached the list. Please see this mail below. Thanks! -------------- next part -------------- An embedded message was scrubbed... From: Igor Yakushev Subject: Tracking of the cingulum bundle Date: Mon, 09 Mar 2009 21:52:31 +0300 Size: 1479537 Url: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090310/2f4e98af/attachment-0001.mht From choisj70 at gmail.com Thu Mar 12 10:07:30 2009 From: choisj70 at gmail.com (Seongjin) Date: Thu, 12 Mar 2009 10:07:30 -0400 Subject: [Mristudio-users] 3D ROI Message-ID: Is there anyone who know how to make 3D ROI in DTI Studio? Seongjin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090312/bedfc8ab/attachment.html From hjiang at jhmi.edu Thu Mar 12 10:13:29 2009 From: hjiang at jhmi.edu (Hangyi Jiang) Date: Thu, 12 Mar 2009 10:13:29 -0400 Subject: [Mristudio-users] 3D ROI Message-ID: <49B8E049020000630001D817@cis27.hosts.jhmi.edu> you can do it by: 1. using 3D-regional growing tool, which is labled as "3D Wand." in the "ROI" tab. or 2. draw 2D ROIs slice by slice using "OR" operation. hangyi >>> "[Seongjin]" 03/12/09 10:07 AM >>> Is there anyone who know how to make 3D ROI in DTI Studio? Seongjin From susumu at mri.jhu.edu Thu Mar 12 11:26:24 2009 From: susumu at mri.jhu.edu (susumu) Date: Thu, 12 Mar 2009 11:26:24 -0400 Subject: [Mristudio-users] 3D ROI In-Reply-To: <49B8E049020000630001D817@cis27.hosts.jhmi.edu> Message-ID: <7k7ed7$6n97pp@ipex3.johnshopkins.edu> Or use RoiEditor and export the ROI file to DtiStudio. If you need ROIs for fiber tracking, use the "BinaryMap" format. -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hangyi Jiang Sent: Thursday, March 12, 2009 10:13 AM To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] 3D ROI you can do it by: 1. using 3D-regional growing tool, which is labled as "3D Wand." in the "ROI" tab. or 2. draw 2D ROIs slice by slice using "OR" operation. hangyi >>> "[Seongjin]" 03/12/09 10:07 AM >>> Is there anyone who know how to make 3D ROI in DTI Studio? Seongjin _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From huyuzheng at gmail.com Thu Mar 12 11:55:21 2009 From: huyuzheng at gmail.com (=?GB2312?B?uvrT8dX9?=) Date: Thu, 12 Mar 2009 23:55:21 +0800 Subject: [Mristudio-users] LDDMM In-Reply-To: <53bb0fa40903092139k6ceb89adt8bfe826bbd9b309c@mail.gmail.com> References: <53bb0fa40903092139k6ceb89adt8bfe826bbd9b309c@mail.gmail.com> Message-ID: <39c428d80903120855v394c9946q9babe2da019f605a@mail.gmail.com> Hi, Maybe ... You can register an account on www.vdisk.cn and upload dataset there, then offer a download link. Hope it help! Yuzheng 2009/3/10 Mi Jung Kim <2mijung.kim at gmail.com> > Hi, > > I would like to submit my phantom data. Could you let me know how to do it? > > Sincerely, > > Mi Jung > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090312/9058e60d/attachment.html From coniglio.fbf.isola at gmail.com Thu Mar 12 12:38:33 2009 From: coniglio.fbf.isola at gmail.com (Angela Coniglio) Date: Thu, 12 Mar 2009 17:38:33 +0100 Subject: [Mristudio-users] 3D ROI In-Reply-To: <7k7ed7$6n97pp@ipex3.johnshopkins.edu> References: <49B8E049020000630001D817@cis27.hosts.jhmi.edu> <7k7ed7$6n97pp@ipex3.johnshopkins.edu> Message-ID: Dear Susumu, dear all, I'm a medical physicist and I was involved in clinical studies of cardiac MRI applications. I was wondering if DTI-Studio could be the right software to analyze DTI acquisitions, supposing they could be feasible. Do you think the fiber tracking algorithms could be applicable for this purpose? Thanks in advance AC -- dott.ssa Angela Coniglio Esperto Qualificato III grado n. 496 Dirigente Fisico Osp. S. Giovanni Calibita Fatebenefratelli via Ponte 4 Capi n. 39 00186 Roma tel. 06 6837419/282 cell. 3496357344 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090312/2fa477d4/attachment.html From support at mristudio.org Thu Mar 12 15:24:35 2009 From: support at mristudio.org (support at mristudio.org) Date: Thu, 12 Mar 2009 15:24:35 -0400 (EDT) Subject: [Mristudio-users] Extract values of the Fiber tract ROI In-Reply-To: <6fd5e4b20903110514p3a01448du1d89e25e0645014e@mail.gmail.com> References: <6fd5e4b20903110514p3a01448du1d89e25e0645014e@mail.gmail.com> Message-ID: <4281.10.16.57.13.1236885875.squirrel@webmail.mristudio.org> hi, Javier, you can get the statistics by "Fiber Statistics" button in the "fiber" tab, just try it. hangyi > Dear all, > > I`m working in Fiber Tracking of the corpus callosum with DTIstudio, > > I want to extract the values of my ROI (the statistics with the number of > fibers selected, length of fibers, FA values...) to a text file or SPSS > archive, but I don`t know how can I do it. > > > Thank you for help me, > > Javier > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > From susumu at mri.jhu.edu Thu Mar 12 18:47:43 2009 From: susumu at mri.jhu.edu (susumu) Date: Thu, 12 Mar 2009 18:47:43 -0400 Subject: [Mristudio-users] Tracking of the cingulum bundle In-Reply-To: <928711110.1236624751.161529108.21225@mcgi48.rambler.ru> Message-ID: <7k7ed7$6nefr8@ipex3.johnshopkins.edu> I suspect that your gradient table is not correct. I'm not sure but you may want to check your "flip x/y/z". To test this, choose the entire corpus callosum at the midsagittal. If it doesn't look right, you can send the screenshot to susumu at mri.jhu.edu. If you are using Siemens, usually you have to do 'flip-x' and for Philips, 'flip-z' for axial DTI with head-first, face-up. -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Igor Yakushev Sent: Monday, March 09, 2009 2:53 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] Tracking of the cingulum bundle Dear Susumu, dear Experts, I'm trying to establish an algorithm, which would allow tracking of the cingulum bundle (CB) with a good reproducibility. I have started with the superior part of CB. First, I place two ROIs (2 x option OR): one at the level of the splenium of the corpus callosum (CC) (Wakana et al., 2007 NI) and one at the border between the anterior 1/3 and posterior 2/3 of the CC body, please see ppt slides. According to Wakana et al. the second ROI should be placed at the level of the genu, but in this case no tracks are found between the ROIs. Relatively large ROIs are used in order to ensure initial inclusion of all voxels related to CC according to a color-coded map. Then, I place two smaller ROIs (2 x option AND) at the same locations. Fibers, whose direction roughly deviates from the direction of the CB, are excluded with the option NOT. 1) Any critique, improvements to this schema, please? Finally, I get a fiber track, which is substantially smaller than the extension of (green) voxels related to CC, please see the slides. 2) How should/may this be interpreted? Is this related to the procedure of the ROI placement? Back to tracking.. I'd like to continue tracking of CB going to its anterior or descending part. I start again with the option OR. Then one needs AND, but AND refers to all ROIs within the image, right? Accordingly, placement of one more ROI (option AND) e.g. at the level of the pons results in disappearance of the previously reconstructed portion of CB. 3) Possible solutions? Should one just save the previously reconstructed track? When all portions are tracked, it must be possible to save all portions as one track, isn't it? The aim is to get statistics from the whole CB, not only from its portions. Many thanks! Igor From susumu at mri.jhu.edu Thu Mar 12 19:30:11 2009 From: susumu at mri.jhu.edu (susumu) Date: Thu, 12 Mar 2009 19:30:11 -0400 Subject: [Mristudio-users] Extract values of the Fiber tract ROI In-Reply-To: <6fd5e4b20903110514p3a01448du1d89e25e0645014e@mail.gmail.com> Message-ID: <7k7ed7$6nep95@ipex3.johnshopkins.edu> Hi Javier, Are you talking about the statistics of the ROI you drew or using the fiber tracking results as an ROI? Susumu ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ To unsubscribe this mailing list, please go to www.mristudio.org / Mailing List / Mristudio-users. There you can find the unsubscribe option. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Javier Navas Sent: Wednesday, March 11, 2009 8:15 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] Extract values of the Fiber tract ROI Dear all, I`m working in Fiber Tracking of the corpus callosum with DTIstudio, I want to extract the values of my ROI (the statistics with the number of fibers selected, length of fibers, FA values...) to a text file or SPSS archive, but I don`t know how can I do it. Thank you for help me, Javier -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090312/b60ad2af/attachment-0001.html From choisj70 at gmail.com Thu Mar 12 19:51:54 2009 From: choisj70 at gmail.com (Seongjin) Date: Thu, 12 Mar 2009 19:51:54 -0400 Subject: [Mristudio-users] 3D ROI In-Reply-To: <49B8E049020000630001D817@cis27.hosts.jhmi.edu> References: <49B8E049020000630001D817@cis27.hosts.jhmi.edu> Message-ID: Thanks a lot! I will try it. On Thu, Mar 12, 2009 at 10:13 AM, Hangyi Jiang wrote: > you can do it by: > > 1. using 3D-regional growing tool, which is labled as "3D Wand." in the > "ROI" tab. > or > 2. draw 2D ROIs slice by slice using "OR" operation. > > > hangyi > > > > > > >>> "[Seongjin]" 03/12/09 10:07 AM >>> > Is there anyone who know how to make 3D ROI in DTI Studio? > Seongjin > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090312/d639af98/attachment.html From choisj70 at gmail.com Thu Mar 12 19:52:16 2009 From: choisj70 at gmail.com (Seongjin) Date: Thu, 12 Mar 2009 19:52:16 -0400 Subject: [Mristudio-users] 3D ROI In-Reply-To: <7k7ed7$6n97pp@ipex3.johnshopkins.edu> References: <49B8E049020000630001D817@cis27.hosts.jhmi.edu> <7k7ed7$6n97pp@ipex3.johnshopkins.edu> Message-ID: I appreciate it. On Thu, Mar 12, 2009 at 11:26 AM, susumu wrote: > Or use RoiEditor and export the ROI file to DtiStudio. > If you need ROIs for fiber tracking, use the "BinaryMap" format. > > -----Original Message----- > From: mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hangyi Jiang > Sent: Thursday, March 12, 2009 10:13 AM > To: mristudio-users at mristudio.org > Subject: Re: [Mristudio-users] 3D ROI > > you can do it by: > > 1. using 3D-regional growing tool, which is labled as "3D Wand." in the > "ROI" tab. > or > 2. draw 2D ROIs slice by slice using "OR" operation. > > > hangyi > > > > > > >>> "[Seongjin]" 03/12/09 10:07 AM >>> > Is there anyone who know how to make 3D ROI in DTI Studio? > Seongjin > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090312/05195bcf/attachment.html From fjnavas2 at gmail.com Thu Mar 12 20:33:13 2009 From: fjnavas2 at gmail.com (Javier Navas) Date: Fri, 13 Mar 2009 01:33:13 +0100 Subject: [Mristudio-users] Extract values of the Fiber tract ROI In-Reply-To: <7k7ed7$6nep95@ipex3.johnshopkins.edu> References: <6fd5e4b20903110514p3a01448du1d89e25e0645014e@mail.gmail.com> <7k7ed7$6nep95@ipex3.johnshopkins.edu> Message-ID: <6fd5e4b20903121733h16ddbb21yb9d640fba98c18de@mail.gmail.com> Hi Susumu, I`m talking about the statistics of the fiber tracking results as an ROI. I want to extract all the voxels values in the FA map that are included in the corpus callusum tract to a text file. I don`t want only the mean or the max/minimum value. Becouse I want to do a parcellation of the corpus callosum and do a correlation of this values with the age or the IQ of the pacients. I?m working with the software some months ago, and I`m new in the list. This is my first message. Thank you for your answer. 2009/3/13 susumu > Hi Javier, > > > > Are you talking about the statistics of the ROI you drew or using the fiber > tracking results as an ROI? > > > > Susumu > > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > To unsubscribe this mailing list, please go to www.mristudio.org / Mailing > List / Mristudio-users. There you can find the unsubscribe option. > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > > > ------------------------------ > > *From:* mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org] *On Behalf Of *Javier Navas > *Sent:* Wednesday, March 11, 2009 8:15 AM > *To:* mristudio-users at mristudio.org > *Subject:* [Mristudio-users] Extract values of the Fiber tract ROI > > > > Dear all, > > I`m working in Fiber Tracking of the corpus callosum with DTIstudio, > > I want to extract the values of my ROI (the statistics with the number of > fibers selected, length of fibers, FA values...) to a text file or SPSS > archive, but I don`t know how can I do it. > > > Thank you for help me, > > Javier > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090313/625193a7/attachment.html From evanfletcher at gmail.com Thu Mar 12 20:46:00 2009 From: evanfletcher at gmail.com (Evan Fletcher) Date: Thu, 12 Mar 2009 17:46:00 -0700 Subject: [Mristudio-users] Extract values of the Fiber tract ROI In-Reply-To: <7k7ed7$6nep95@ipex3.johnshopkins.edu> References: <6fd5e4b20903110514p3a01448du1d89e25e0645014e@mail.gmail.com> <7k7ed7$6nep95@ipex3.johnshopkins.edu> Message-ID: <62b297960903121746q58b22a06ia0858770240de95d@mail.gmail.com> Please unsubscribe me!! I cannot find the option to do so as printed in your list: To unsubscribe this mailing list, please go to www.mristudio.org / Mailing List / Mristudio-users. There you can find the unsubscribe option. This looks like an invalid URL! And I can't find the option to unsubscribe at your home page. Thank you. Evan Fletcher On Thu, Mar 12, 2009 at 4:30 PM, susumu wrote: > Hi Javier, > > > > Are you talking about the statistics of the ROI you drew or using the fiber > tracking results as an ROI? > > > > Susumu > > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > To unsubscribe this mailing list, please go to www.mristudio.org / Mailing > List / Mristudio-users. There you can find the unsubscribe option. > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > > > ------------------------------ > > *From:* mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org] *On Behalf Of *Javier Navas > *Sent:* Wednesday, March 11, 2009 8:15 AM > *To:* mristudio-users at mristudio.org > *Subject:* [Mristudio-users] Extract values of the Fiber tract ROI > > > > Dear all, > > I`m working in Fiber Tracking of the corpus callosum with DTIstudio, > > I want to extract the values of my ROI (the statistics with the number of > fibers selected, length of fibers, FA values...) to a text file or SPSS > archive, but I don`t know how can I do it. > > > Thank you for help me, > > Javier > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -- Evan Fletcher, PhD Project Scientist IDeA Lab Department of Neurology, UCDMC and Lecturer Integrated Studies Program, UC Davis -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090312/1a6a483b/attachment.html From evanfletcher at gmail.com Thu Mar 12 20:47:25 2009 From: evanfletcher at gmail.com (Evan Fletcher) Date: Thu, 12 Mar 2009 17:47:25 -0700 Subject: [Mristudio-users] Extract values of the Fiber tract ROI In-Reply-To: <6fd5e4b20903121733h16ddbb21yb9d640fba98c18de@mail.gmail.com> References: <6fd5e4b20903110514p3a01448du1d89e25e0645014e@mail.gmail.com> <7k7ed7$6nep95@ipex3.johnshopkins.edu> <6fd5e4b20903121733h16ddbb21yb9d640fba98c18de@mail.gmail.com> Message-ID: <62b297960903121747w5fa75e30s5cdea3861e6b6d09@mail.gmail.com> Please unsubscribe me!! I tried to do it myself, following your instructions: >>> To unsubscribe this mailing list, please go to www.mristudio.org / Mailing List / Mristudio-users. There you can find the unsubscribe option. <<< But this appears to be an invalid URL address, and I cannot find the unsubscribe option. Thank you Evan Fletcher On Thu, Mar 12, 2009 at 5:33 PM, Javier Navas wrote: > Hi Susumu, > > I`m talking about the statistics of the fiber tracking results as an ROI. I > want to extract all the voxels values in the FA map that are included in the > corpus callusum tract to a text file. I don`t want only the mean or the > max/minimum value. Becouse I want to do a parcellation of the corpus > callosum and do a correlation of this values with the age or the IQ of the > pacients. > > I?m working with the software some months ago, and I`m new in the list. > This is my first message. Thank you for your answer. > > > 2009/3/13 susumu > >> Hi Javier, >> >> >> >> Are you talking about the statistics of the ROI you drew or using the >> fiber tracking results as an ROI? >> >> >> >> Susumu >> >> >> >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >> >> To unsubscribe this mailing list, please go to www.mristudio.org / >> Mailing List / Mristudio-users. There you can find the unsubscribe option. >> >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >> >> >> >> >> ------------------------------ >> >> *From:* mristudio-users-bounces at mristudio.org [mailto: >> mristudio-users-bounces at mristudio.org] *On Behalf Of *Javier Navas >> *Sent:* Wednesday, March 11, 2009 8:15 AM >> *To:* mristudio-users at mristudio.org >> *Subject:* [Mristudio-users] Extract values of the Fiber tract ROI >> >> >> >> Dear all, >> >> I`m working in Fiber Tracking of the corpus callosum with DTIstudio, >> >> I want to extract the values of my ROI (the statistics with the number of >> fibers selected, length of fibers, FA values...) to a text file or SPSS >> archive, but I don`t know how can I do it. >> >> >> Thank you for help me, >> >> Javier >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/mristudio-users >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -- Evan Fletcher, PhD Project Scientist IDeA Lab Department of Neurology, UCDMC and Lecturer Integrated Studies Program, UC Davis -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090312/108b8382/attachment-0001.html From Kenneth.Hisley at dmu.edu Thu Mar 12 22:59:57 2009 From: Kenneth.Hisley at dmu.edu (Hisley, Kenneth) Date: Thu, 12 Mar 2009 21:59:57 -0500 Subject: [Mristudio-users] request for information Message-ID: Hello, Can someone please direct me to the site where I can download the DTI Studio and additional functional documentation suitable for printing. I checked on one of the web sites that was supposed to have it but failed to find it. Thanks, Cal Kenneth Hisley, Ph.D. Assistant Professor Department of Anatomy 3200 Grand Avenue 152 Ryan Hall Des Moines University Des Moines, Iowa 50312 office: 515-271-1577 cellular: 410-458-6892 From hjiang at jhmi.edu Fri Mar 13 09:56:03 2009 From: hjiang at jhmi.edu (Hangyi Jiang) Date: Fri, 13 Mar 2009 09:56:03 -0400 Subject: [Mristudio-users] Extract values of the Fiber tract ROI Message-ID: <49BA2DB3020000630001D925@cis27.hosts.jhmi.edu> you can do it by yourself goto: http://lists.mristudio.org/mailman/listinfo/mristudio-users, the "unsubscribe" buttion is on the bottom. thanks, >>> Evan Fletcher 03/12/09 8:47 PM >>> Please unsubscribe me!! I tried to do it myself, following your instructions: >>> To unsubscribe this mailing list, please go to www.mristudio.org / Mailing List / Mristudio-users. There you can find the unsubscribe option. <<< But this appears to be an invalid URL address, and I cannot find the unsubscribe option. Thank you Evan Fletcher On Thu, Mar 12, 2009 at 5:33 PM, Javier Navas wrote: > Hi Susumu, > > I`m talking about the statistics of the fiber tracking results as an ROI. I > want to extract all the voxels values in the FA map that are included in the > corpus callusum tract to a text file. I don`t want only the mean or the > max/minimum value. Becouse I want to do a parcellation of the corpus > callosum and do a correlation of this values with the age or the IQ of the > pacients. > > I?m working with the software some months ago, and I`m new in the list. > This is my first message. Thank you for your answer. > > > 2009/3/13 susumu > >> Hi Javier, >> >> >> >> Are you talking about the statistics of the ROI you drew or using the >> fiber tracking results as an ROI? >> >> >> >> Susumu >> >> >> >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >> >> To unsubscribe this mailing list, please go to www.mristudio.org / >> Mailing List / Mristudio-users. There you can find the unsubscribe option. >> >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >> >> >> >> >> ------------------------------ >> >> *From:* mristudio-users-bounces at mristudio.org [mailto: >> mristudio-users-bounces at mristudio.org] *On Behalf Of *Javier Navas >> *Sent:* Wednesday, March 11, 2009 8:15 AM >> *To:* mristudio-users at mristudio.org >> *Subject:* [Mristudio-users] Extract values of the Fiber tract ROI >> >> >> >> Dear all, >> >> I`m working in Fiber Tracking of the corpus callosum with DTIstudio, >> >> I want to extract the values of my ROI (the statistics with the number of >> fibers selected, length of fibers, FA values...) to a text file or SPSS >> archive, but I don`t know how can I do it. >> >> >> Thank you for help me, >> >> Javier >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/mristudio-users >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -- Evan Fletcher, PhD Project Scientist IDeA Lab Department of Neurology, UCDMC and Lecturer Integrated Studies Program, UC Davis From hjiang at jhmi.edu Fri Mar 13 09:58:04 2009 From: hjiang at jhmi.edu (Hangyi Jiang) Date: Fri, 13 Mar 2009 09:58:04 -0400 Subject: [Mristudio-users] request for information Message-ID: <49BA2E2D020000630001D929@cis27.hosts.jhmi.edu> goto: https://www.mristudio.org/, clicking "download" link on the right thank you. >>> "Hisley, Kenneth" 03/12/09 10:59 PM >>> Hello, Can someone please direct me to the site where I can download the DTI Studio and additional functional documentation suitable for printing. I checked on one of the web sites that was supposed to have it but failed to find it. Thanks, Cal Kenneth Hisley, Ph.D. Assistant Professor Department of Anatomy 3200 Grand Avenue 152 Ryan Hall Des Moines University Des Moines, Iowa 50312 office: 515-271-1577 cellular: 410-458-6892 _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From susumu at mri.jhu.edu Fri Mar 13 19:48:51 2009 From: susumu at mri.jhu.edu (susumu) Date: Fri, 13 Mar 2009 19:48:51 -0400 Subject: [Mristudio-users] Extract values of the Fiber tract ROI In-Reply-To: <6fd5e4b20903121733h16ddbb21yb9d640fba98c18de@mail.gmail.com> Message-ID: <7k7ed7$6npt7r@ipex3.johnshopkins.edu> Hi Javier, I'm not sure if I'm answering your question, but here I listed what you can do after you get a tractgraphy result; 1) Click the "statistics" button and specify an MRI image (e.g. FA map) you want to quantify. This gives you the average and standard deviation of all pixels included in the tract (this is not what you want). 2) Then click "profile" button. This give you pixel values within each slice in axial, coronal, and sagittal orientations. This works nicely if the tract of your interest has a linear shape. For tracts like the corpus callosum (U-shape), this approach has some issue. 3) Save the tract as a binary image (1/0 map). Load this binary image as an image to RoiEditor as well as a map you want to quantify (e.g. FA map). Using the binary image and the thresholding tool, define an object that identify pixels with value "1"; namely, redefine the tract as an object. Bring the FA map as an active image and right-click the object you defined in the "object list". This allows export (text file) of FA values of all pixels that belong to the tract you defined. You can read this text file into Excel and create a histogram 4) You can normalize the binary image to one of the atlas provided in Landmarker. By normalize population data, you can create probabilistic tract maps. Using RoiEditor, you can mask FA maps by tractography results and then normalize. This may allow you to do pixel-based analysis in an atlas space. After normalization, you can also "segment" the tracking result into the corpus callosum region and corona radiata region by combining your binary tracking image and "white matter parcellation map (WMPM)" provided in RoiEditor. I must admit that currently manuals of RoiEditor and Landmarker are very limited. We are working on it and it may take some time. If you think one of the above 4 methods can provide what you want, you can contact us for more specific instruction. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Javier Navas Sent: Thursday, March 12, 2009 8:33 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] Extract values of the Fiber tract ROI Hi Susumu, I`m talking about the statistics of the fiber tracking results as an ROI. I want to extract all the voxels values in the FA map that are included in the corpus callusum tract to a text file. I don`t want only the mean or the max/minimum value. Becouse I want to do a parcellation of the corpus callosum and do a correlation of this values with the age or the IQ of the pacients. I?m working with the software some months ago, and I`m new in the list. This is my first message. Thank you for your answer. 2009/3/13 susumu Hi Javier, Are you talking about the statistics of the ROI you drew or using the fiber tracking results as an ROI? Susumu ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ To unsubscribe this mailing list, please go to www.mristudio.org / Mailing List / Mristudio-users. There you can find the unsubscribe option. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Javier Navas Sent: Wednesday, March 11, 2009 8:15 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] Extract values of the Fiber tract ROI Dear all, I`m working in Fiber Tracking of the corpus callosum with DTIstudio, I want to extract the values of my ROI (the statistics with the number of fibers selected, length of fibers, FA values...) to a text file or SPSS archive, but I don`t know how can I do it. Thank you for help me, Javier _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090313/6cd10fc6/attachment.html From susumu at mri.jhu.edu Fri Mar 13 21:23:27 2009 From: susumu at mri.jhu.edu (susumu) Date: Fri, 13 Mar 2009 21:23:27 -0400 Subject: [Mristudio-users] How to do a Tailarach transformation? In-Reply-To: <1LgkrK-14QxaC0@fwd04.aul.t-online.de> Message-ID: <7k7ed7$6nq8ls@ipex3.johnshopkins.edu> Hi Christian, Sorry that the manuals for Landmarker and RoiEditor are still quite behind. This year, we will most likely provide 2-day tutorial in Hawaii ISMRM (Sat and Sun). Announcement will be sent next week. Join one of these tutorials is the best way at this point. We are working on manuals and hopefully can provide "Getting Started" soon. As for your question, there are several points I want to make; 1) There are three ways to do normalization: manual landmark-based (rigid, affine, and LDDMM), automated linear & low-order non-linear (AIR), and automated high-order non-linear (LDDMM). 2) Usually, automated AIR (rigid or affine) + automated LDDMM is the easiest way. 3) Talairach brain is VERY different from normal subjects. To accurately transform your data to Talairach, AIR is not enough. You need extensive landmarking or AIR+LDDMM. 4) Manual landmark-based normalization has a great flexibility but it's time consuming and require some experience. I recommend you to start with #2. If you don't come to ISMRM, please wait for the Getting Started or you are welcome to visit my lab. Susumu ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ To unsubscribe this mailing list, please go to http://lists.mristudio.org/mailman/listinfo/mristudio-users. There you can find the unsubscribe option. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Christian Bieck Sent: Monday, March 09, 2009 3:10 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] How to do a Tailarach transformation? Hello, I'm still working on analyzing the optic radiation via DTI and would like to transform the subjects' data into Talairach space via Landmarker so as to then position the relevant ROIs in a more objective manner. I am still unsure about the whole process, though. I watched all five videos of the DTIStudio tutorial which Landmarker was only a small part of and then tried to follow the Landmarker manual, but I still don't know how to proceed exactly. The best I could come up with is to use Landmarks on the AC, PC and most superior, inferior, anterior, posterior, left and right parts of the Talairach DWI template brain and the individual subject's DWI data, which resulted in a slightly rotated transformed brain, however, and didn't look quite right to me. Now my main question is if I am somehow on the right path or if I forgot some vital steps in all of this. In the case of using a Landmark-based transformation, would it be a problem if, for example, the most anterior part of the template brain and hence the Landmark would be on the right hemisphere while the subject's most anterior part would be on the left hemisphere? Should I include an AIR transformation before that? As you can see, I'm somewhat lost in all of this and so would very much appreciate any input you could give me on how to do a proper Talairach transformation via Landmarker. Thank you very much for your time and effort. Sincerely, Christian Bieck _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From drajaygarg at gmail.com Fri Mar 13 21:35:58 2009 From: drajaygarg at gmail.com (Ajay Garg) Date: Sat, 14 Mar 2009 07:05:58 +0530 Subject: [Mristudio-users] Gradient Table 64 dir Siemens Message-ID: <31e5fd2f0903131835u60d1cd54v4e140cbe2ab315c1@mail.gmail.com> Dear DTIStudio users, Does anybody have 64 direction gradient table for Siemens Avonto system? Thanks for your help. Ajay -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090314/d4116e7c/attachment.html From jayashreemenon at gmail.com Sat Mar 14 00:13:04 2009 From: jayashreemenon at gmail.com (Jayasree) Date: Sat, 14 Mar 2009 09:43:04 +0530 Subject: [Mristudio-users] Gradient Table 64 dir Siemens In-Reply-To: <31e5fd2f0903131835u60d1cd54v4e140cbe2ab315c1@mail.gmail.com> References: <31e5fd2f0903131835u60d1cd54v4e140cbe2ab315c1@mail.gmail.com> Message-ID: Dear Dr.Ajay Garg, Here is the 64 direction gradient table for Siemens Avanto System Vector table for 64 directions: Vector_0 =[ 1.000000, 0.000000, 0.000000 ] Vector_1 =[ 0.000000, 1.000000, 0.000000 ] Vector_2 =[ -0.026007, 0.649170, 0.760199 ] Vector_3 =[ 0.591136, -0.766176, 0.252058 ] Vector_4 =[ -0.236071, -0.524158, 0.818247 ] Vector_5 =[ -0.893021, -0.259006, 0.368008 ] Vector_6 =[ 0.796184, 0.129030, 0.591137 ] Vector_7 =[ 0.233964, 0.929855, 0.283956 ] Vector_8 =[ 0.935686, 0.139953, 0.323891 ] Vector_9 =[ 0.505827, -0.844710, -0.174940 ] Vector_10 =[ 0.346220, -0.847539, -0.402256 ] Vector_11 =[ 0.456968, -0.630956, -0.626956 ] Vector_12 =[ -0.486997, -0.388997, 0.781995 ] Vector_13 =[ -0.617845, 0.672831, 0.406898 ] Vector_14 =[ -0.576984, -0.104997, -0.809978 ] Vector_15 =[ -0.826695, -0.520808, 0.212921 ] Vector_16 =[ 0.893712, -0.039987, -0.446856 ] Vector_17 =[ 0.290101, -0.541189, -0.789276 ] Vector_18 =[ 0.115951, -0.962591, -0.244896 ] Vector_19 =[ -0.800182, 0.403092, -0.444101 ] Vector_20 =[ 0.513981, 0.839970, 0.173994 ] Vector_21 =[ -0.788548, 0.152912, -0.595659 ] Vector_22 =[ 0.949280, -0.233069, 0.211062 ] Vector_23 =[ 0.232964, 0.782880, 0.576911 ] Vector_24 =[ -0.020999, -0.187990, -0.981946 ] Vector_25 =[ 0.216932, -0.955701, 0.198938 ] Vector_26 =[ 0.774003, -0.604002, 0.190001 ] Vector_27 =[ -0.160928, 0.355840, 0.920587 ] Vector_28 =[ -0.147035, 0.731173, -0.666158 ] Vector_29 =[ 0.888141, 0.417066, 0.193031 ] Vector_30 =[ -0.561971, 0.231988, -0.793959 ] Vector_31 =[ -0.380809, 0.142928, 0.913541 ] Vector_32 =[ -0.306000, -0.199000, -0.931001 ] Vector_33 =[ -0.332086, -0.130034, 0.934243 ] Vector_34 =[ -0.963226, -0.265062, 0.044010 ] Vector_35 =[ -0.959501, 0.205107, 0.193101 ] Vector_36 =[ 0.452965, -0.888932, 0.067995 ] Vector_37 =[ -0.773133, 0.628108, 0.088015 ] Vector_38 =[ 0.709082, 0.408047, 0.575066 ] Vector_39 =[ -0.692769, 0.023992, 0.720760 ] Vector_40 =[ 0.681659, 0.528735, -0.505747 ] Vector_41 =[ -0.141995, -0.724976, 0.673978 ] Vector_42 =[ -0.740168, 0.388088, 0.549125 ] Vector_43 =[ -0.103006, 0.822044, 0.560030 ] Vector_44 =[ 0.584037, -0.596038, 0.551035 ] Vector_45 =[ -0.088008, -0.335031, 0.938088 ] Vector_46 =[ -0.552263, -0.792377, 0.259123 ] Vector_47 =[ 0.838158, -0.458086, -0.296056 ] Vector_48 =[ 0.362995, -0.560993, 0.743990 ] Vector_49 =[ -0.184062, 0.392133, -0.901306 ] Vector_50 =[ -0.720938, -0.692941, 0.008999 ] Vector_51 =[ 0.433101, 0.682159, -0.589137 ] Vector_52 =[ 0.502114, 0.690157, 0.521119 ] Vector_53 =[ -0.170944, -0.508833, -0.843722 ] Vector_54 =[ 0.462968, 0.422971, 0.778946 ] Vector_55 =[ 0.385030, -0.809064, 0.444035 ] Vector_56 =[ -0.713102, -0.247035, 0.656094 ] Vector_57 =[ 0.259923, 0.884737, -0.386885 ] Vector_58 =[ 0.001000, 0.077002, -0.997030 ] Vector_59 =[ 0.037002, -0.902057, 0.430027 ] Vector_60 =[ 0.570320, -0.303170, -0.763428 ] Vector_61 =[ -0.282105, 0.145054, -0.948354 ] Vector_62 =[ 0.721098, 0.608082, 0.332045 ] Vector_63 =[ 0.266985, 0.959945, -0.084995 ] Best wishes Jayasree.R.S -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090314/eaee55a8/attachment-0001.html From drajaygarg at gmail.com Sat Mar 14 03:39:54 2009 From: drajaygarg at gmail.com (Ajay Garg) Date: Sat, 14 Mar 2009 13:09:54 +0530 Subject: [Mristudio-users] Gradient Table 64 dir Siemens In-Reply-To: References: <31e5fd2f0903131835u60d1cd54v4e140cbe2ab315c1@mail.gmail.com> Message-ID: <1AC94F62-F218-4B14-8EEF-AB4FAAD9AFEA@gmail.com> Thanks a lot. Ajay On 14-Mar-09, at 9:43 AM, Jayasree wrote: > Dear Dr.Ajay Garg, > Here is the 64 direction gradient table for Siemens Avanto System > > Vector table for 64 directions: > > Vector_0 =[ 1.000000, 0.000000, 0.000000 ] > > Vector_1 =[ 0.000000, 1.000000, 0.000000 ] > > Vector_2 =[ -0.026007, 0.649170, 0.760199 ] > > Vector_3 =[ 0.591136, -0.766176, 0.252058 ] > > Vector_4 =[ -0.236071, -0.524158, 0.818247 ] > > Vector_5 =[ -0.893021, -0.259006, 0.368008 ] > > Vector_6 =[ 0.796184, 0.129030, 0.591137 ] > > Vector_7 =[ 0.233964, 0.929855, 0.283956 ] > > Vector_8 =[ 0.935686, 0.139953, 0.323891 ] > > Vector_9 =[ 0.505827, -0.844710, -0.174940 ] > > Vector_10 =[ 0.346220, -0.847539, -0.402256 ] > > Vector_11 =[ 0.456968, -0.630956, -0.626956 ] > > Vector_12 =[ -0.486997, -0.388997, 0.781995 ] > > Vector_13 =[ -0.617845, 0.672831, 0.406898 ] > > Vector_14 =[ -0.576984, -0.104997, -0.809978 ] > > Vector_15 =[ -0.826695, -0.520808, 0.212921 ] > > Vector_16 =[ 0.893712, -0.039987, -0.446856 ] > > Vector_17 =[ 0.290101, -0.541189, -0.789276 ] > > Vector_18 =[ 0.115951, -0.962591, -0.244896 ] > > Vector_19 =[ -0.800182, 0.403092, -0.444101 ] > > Vector_20 =[ 0.513981, 0.839970, 0.173994 ] > > Vector_21 =[ -0.788548, 0.152912, -0.595659 ] > > Vector_22 =[ 0.949280, -0.233069, 0.211062 ] > > Vector_23 =[ 0.232964, 0.782880, 0.576911 ] > > Vector_24 =[ -0.020999, -0.187990, -0.981946 ] > > Vector_25 =[ 0.216932, -0.955701, 0.198938 ] > > Vector_26 =[ 0.774003, -0.604002, 0.190001 ] > > Vector_27 =[ -0.160928, 0.355840, 0.920587 ] > > Vector_28 =[ -0.147035, 0.731173, -0.666158 ] > > Vector_29 =[ 0.888141, 0.417066, 0.193031 ] > > Vector_30 =[ -0.561971, 0.231988, -0.793959 ] > > Vector_31 =[ -0.380809, 0.142928, 0.913541 ] > > Vector_32 =[ -0.306000, -0.199000, -0.931001 ] > > Vector_33 =[ -0.332086, -0.130034, 0.934243 ] > > Vector_34 =[ -0.963226, -0.265062, 0.044010 ] > > Vector_35 =[ -0.959501, 0.205107, 0.193101 ] > > Vector_36 =[ 0.452965, -0.888932, 0.067995 ] > > Vector_37 =[ -0.773133, 0.628108, 0.088015 ] > > Vector_38 =[ 0.709082, 0.408047, 0.575066 ] > > Vector_39 =[ -0.692769, 0.023992, 0.720760 ] > > Vector_40 =[ 0.681659, 0.528735, -0.505747 ] > > Vector_41 =[ -0.141995, -0.724976, 0.673978 ] > > Vector_42 =[ -0.740168, 0.388088, 0.549125 ] > > Vector_43 =[ -0.103006, 0.822044, 0.560030 ] > > Vector_44 =[ 0.584037, -0.596038, 0.551035 ] > > Vector_45 =[ -0.088008, -0.335031, 0.938088 ] > > Vector_46 =[ -0.552263, -0.792377, 0.259123 ] > > Vector_47 =[ 0.838158, -0.458086, -0.296056 ] > > Vector_48 =[ 0.362995, -0.560993, 0.743990 ] > > Vector_49 =[ -0.184062, 0.392133, -0.901306 ] > > Vector_50 =[ -0.720938, -0.692941, 0.008999 ] > > Vector_51 =[ 0.433101, 0.682159, -0.589137 ] > > Vector_52 =[ 0.502114, 0.690157, 0.521119 ] > > Vector_53 =[ -0.170944, -0.508833, -0.843722 ] > > Vector_54 =[ 0.462968, 0.422971, 0.778946 ] > > Vector_55 =[ 0.385030, -0.809064, 0.444035 ] > > Vector_56 =[ -0.713102, -0.247035, 0.656094 ] > > Vector_57 =[ 0.259923, 0.884737, -0.386885 ] > > Vector_58 =[ 0.001000, 0.077002, -0.997030 ] > > Vector_59 =[ 0.037002, -0.902057, 0.430027 ] > > Vector_60 =[ 0.570320, -0.303170, -0.763428 ] > > Vector_61 =[ -0.282105, 0.145054, -0.948354 ] > > Vector_62 =[ 0.721098, 0.608082, 0.332045 ] > > Vector_63 =[ 0.266985, 0.959945, -0.084995 ] > > Best wishes > Jayasree.R.S > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users From evanfletcher at gmail.com Sat Mar 14 13:00:29 2009 From: evanfletcher at gmail.com (Evan Fletcher) Date: Sat, 14 Mar 2009 10:00:29 -0700 Subject: [Mristudio-users] Tracking of the cingulum bundle In-Reply-To: <7k7ed7$6nefr8@ipex3.johnshopkins.edu> References: <928711110.1236624751.161529108.21225@mcgi48.rambler.ru> <7k7ed7$6nefr8@ipex3.johnshopkins.edu> Message-ID: <62b297960903141000y64d48cc1v1ffc0d0c04ab48b9@mail.gmail.com> Dear Dr. Susumu, I signed up as a member so I could have access to your DTI data. But I did not realize that this would automatically put me on your mailing list. Now I am being spammed by every question and "thank you" from every user. I cannot find a place on the web site to unsubscribe, even though your emails say there is such an option. Sorry, could you please just unsubscribe me? Thank you, Evan Fletcher On Thu, Mar 12, 2009 at 3:47 PM, susumu wrote: > I suspect that your gradient table is not correct. I'm not sure but you may > want to check your "flip x/y/z". To test this, choose the entire corpus > callosum at the midsagittal. If it doesn't look right, you can send the > screenshot to susumu at mri.jhu.edu. > > If you are using Siemens, usually you have to do 'flip-x' and for Philips, > 'flip-z' for axial DTI with head-first, face-up. > > -----Original Message----- > From: mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Igor Yakushev > Sent: Monday, March 09, 2009 2:53 PM > To: DTI Studio, ROI Editor, Landmarker Questions/Support > Subject: [Mristudio-users] Tracking of the cingulum bundle > > Dear Susumu, dear Experts, > > I'm trying to establish an algorithm, which would allow tracking of the > cingulum bundle (CB) with a good reproducibility. > I have started with the superior part of CB. First, I place two ROIs (2 > x option OR): one at the level of the splenium of the corpus callosum > (CC) (Wakana et al., 2007 NI) and one at the border between the anterior > 1/3 and posterior 2/3 of the CC body, please see ppt slides. According > to Wakana et al. the second ROI should be placed at the level of the > genu, but in this case no tracks are found between the ROIs. Relatively > large ROIs are used in order to ensure > initial inclusion of all voxels related to CC according to a color-coded > map. Then, I place two smaller ROIs (2 x option AND) at the same > locations. Fibers, whose direction roughly deviates from the direction > of the CB, are excluded with the option NOT. > 1) Any critique, improvements to this schema, please? > Finally, I get a fiber track, which is substantially smaller than the > extension of (green) voxels related to CC, please see the slides. 2) How > should/may this be interpreted? Is this related to the procedure of the > ROI placement? > > Back to tracking.. I'd like to continue tracking of CB going to its > anterior or descending part. I start again with the option OR. Then one > needs AND, but AND refers to all ROIs within the image, right? > Accordingly, placement of one more ROI (option AND) e.g. at the level of > the pons results in disappearance of the previously reconstructed > portion of CB. 3) Possible solutions? Should one just save the > previously reconstructed track? When all portions are tracked, it must > be possible to save all portions as one track, isn't it? The aim is to > get statistics from the whole CB, not only from its portions. > > Many thanks! > Igor > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > -- Evan Fletcher, PhD Project Scientist IDeA Lab Department of Neurology, UCDMC and Lecturer Integrated Studies Program, UC Davis -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090314/993932c2/attachment.html From fjnavas2 at gmail.com Tue Mar 17 06:55:18 2009 From: fjnavas2 at gmail.com (Javier Navas) Date: Tue, 17 Mar 2009 11:55:18 +0100 Subject: [Mristudio-users] Extract values of the Fiber tract ROI In-Reply-To: <6fd5e4b20903170332w749e774ek6c3434d80ba1fc5f@mail.gmail.com> References: <6fd5e4b20903121733h16ddbb21yb9d640fba98c18de@mail.gmail.com> <7k7ed7$6npt7r@ipex3.johnshopkins.edu> <6fd5e4b20903170332w749e774ek6c3434d80ba1fc5f@mail.gmail.com> Message-ID: <6fd5e4b20903170355y5f517992kb3a96ba4ddbb901b@mail.gmail.com> Thank you very much Mr. Susumu, with ROI editor I can extract the pixel values in a txt file, that is what I want, thank you. But I have a problem. The FA mean value that results in DTI Studio is different that the FA mean value that results in ROI editor, with the same binary image, why occur this?. For example, with the same mask of the genu of corpus callosum, I have the same number of pixels (2835 pixels) but the FA statistics is different. DTI studio: FA Max. of ImgVal: 0.9690 Min. of ImgVal: 0.0591 * Mean of ImgVal: 0.5385* Std. of ImgVal: 0.1689 ROI editor: Min: 0.06 Max: 0.97 *Mean: 0.45* Std: 0.17 Could you explain me why the FA mean values are different? THANK YOU Javier 2009/3/14 susumu Hi Javier, > > > > I'm not sure if I'm answering your question, but here I listed what you can > do after you get a tractgraphy result; > > > > 1) Click the "statistics" button and specify an MRI image (e.g. FA map) you > want to quantify. This gives you the average and standard deviation of all > pixels included in the tract (this is not what you want). > > 2) Then click "profile" button. This give you pixel values within each > slice in axial, coronal, and sagittal orientations. This works nicely if the > tract of your interest has a linear shape. For tracts like the corpus > callosum (U-shape), this approach has some issue. > > 3) Save the tract as a binary image (1/0 map). Load this binary image as an > image to RoiEditor as well as a map you want to quantify (e.g. FA map). > Using the binary image and the thresholding tool, define an object that > identify pixels with value "1"; namely, redefine the tract as an object. > Bring the FA map as an active image and right-click the object you defined > in the "object list". This allows export (text file) of FA values of all > pixels that belong to the tract you defined. You can read this text file > into Excel and create a histogram > > 4) You can normalize the binary image to one of the atlas provided in > Landmarker. By normalize population data, you can create probabilistic tract > maps. Using RoiEditor, you can mask FA maps by tractography results and then > normalize. This may allow you to do pixel-based analysis in an atlas space. > After normalization, you can also "segment" the tracking result into the > corpus callosum region and corona radiata region by combining your binary > tracking image and "white matter parcellation map (WMPM)" provided in > RoiEditor. > > > > I must admit that currently manuals of RoiEditor and Landmarker are very > limited. We are working on it and it may take some time. If you think one of > the above 4 methods can provide what you want, you can contact us for more > specific instruction. > > > > Susumu > > > ------------------------------ > > *From:* mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org] *On Behalf Of *Javier Navas > *Sent:* Thursday, March 12, 2009 8:33 PM > *To:* DTI Studio, ROI Editor, Landmarker Questions/Support > *Subject:* Re: [Mristudio-users] Extract values of the Fiber tract ROI > > > > Hi Susumu, > > I`m talking about the statistics of the fiber tracking results as an ROI. I > want to extract all the voxels values in the FA map that are included in the > corpus callusum tract to a text file. I don`t want only the mean or the > max/minimum value. Becouse I want to do a parcellation of the corpus > callosum and do a correlation of this values with the age or the IQ of the > pacients. > > I?m working with the software some months ago, and I`m new in the list. > This is my first message. Thank you for your answer. > > 2009/3/13 susumu > > Hi Javier, > > > > Are you talking about the statistics of the ROI you drew or using the fiber > tracking results as an ROI? > > > > Susumu > > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > To unsubscribe this mailing list, please go to www.mristudio.org / Mailing > List / Mristudio-users. There you can find the unsubscribe option. > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > > > ------------------------------ > > *From:* mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org] *On Behalf Of *Javier Navas > *Sent:* Wednesday, March 11, 2009 8:15 AM > *To:* mristudio-users at mristudio.org > *Subject:* [Mristudio-users] Extract values of the Fiber tract ROI > > > > Dear all, > > I`m working in Fiber Tracking of the corpus callosum with DTIstudio, > > I want to extract the values of my ROI (the statistics with the number of > fibers selected, length of fibers, FA values...) to a text file or SPSS > archive, but I don`t know how can I do it. > > > Thank you for help me, > > Javier > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090317/bfc78acf/attachment-0001.html From susumu at mri.jhu.edu Tue Mar 17 11:37:26 2009 From: susumu at mri.jhu.edu (susumu) Date: Tue, 17 Mar 2009 11:37:26 -0400 Subject: [Mristudio-users] Extract values of the Fiber tract ROI In-Reply-To: <6fd5e4b20903121733h16ddbb21yb9d640fba98c18de@mail.gmail.com> Message-ID: <7k7ed7$6on869@ipex3.johnshopkins.edu> Dear Users, Javier raised an important issue and I want to share his results with all of you. Here is what he did; 1) Did fiber tracking using DtiStudio, use the "statistics" button, and get an FA value of the entire reconstructed fiber. 2) Save the fiber tracking results as 1/0 binary image, load the file to RoiEditor, superimpose the binary masking on the FA map, and get an FA value of the entire reconstructed fiber The results were different as indicated in his email. This is because the ways FA is measured for the reconstructed tracts are fundamentally different between the two programs. DtiStudio: Suppose you have two fibers. One is 10-pixel long and the other is 5-pixel long. Also suppose that the second 5-pixel fiber shares the same 5 pixels within the first 10-pixel fiber. This means, the second fiber is completely contained within the first fiber. In DtiStudio, FA is measured along the first fiber. It also measures FA along the second fiber. The end result is, for example; First fiber [0.2, 0.25, 0.3, 0.35, 0.4, 0.45, 0.5, 0.55, 0.6, 0.65] Second [0.2, 0.25, 0.3, 0.35, 0.4] As you can see, the first 5 pixels are identical. Then DtiStudio calculates the average of the 15 pixels. This means, the first 5 pixels are "double-counted". In this way, DtiStudio provides natural weighting for pixels that contain more fibers. In reality, some pixels may contains 10s of fibers (reconstructed streamlines) while some pixels may contain only one fiber. The more fibers a pixel contains, more weighting it receives, because it would be counted many more times. RoiEditor: Once you save the fiber tracking result into 1/0 binary information, all the streamline information is lost, so as the number of fibers each pixel contains. In RoiEditor, the binary image can be read and applied to an FA map as a non-weighted binary masking. I hope this explains the difference among the two methods. Because DtiStudio counts the core white matter regions many more times than peripheral areas, the average FA values tend to be higher. There is nothing like one is better than the other. They are just two different approaches. Maybe the natural weighting may sound more reasonable but the non-weighting 1/0 masking should also be a valid approach. You just need to apply the same method (or both methods) to all data. Please let us know if you have any questions regarding this issue. Thanks, Susumu ________________________________________ From: Javier Navas [mailto:fjnavas2 at gmail.com] Sent: Tuesday, March 17, 2009 6:55 AM To: susumu at mri.jhu.edu; DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] Extract values of the Fiber tract ROI Thank you very much Mr. Susumu, with ROI editor I can extract the pixel values in a txt file, that is what I want, thank you. But I have a problem. The FA mean value that results in DTI Studio is different that the FA mean value that results in ROI editor, with the same binary image, why occur this?. For example, with the same mask of the genu of corpus callosum, I have the same number of pixels (2835 pixels) but the FA statistics is different. DTI studio: ????? FA ??????? Max. of ImgVal:?? 0.9690 ??????? Min. of ImgVal:?? 0.0591 ??????? Mean of ImgVal:?? 0.5385 ??????? Std. of ImgVal:?? 0.1689 ROI editor: ???????? Min:??? 0.06 ???????? Max:??? 0.97 ???????? Mean:??? 0.45 ???????? Std:??? 0.17 ________________________________________ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Javier Navas Sent: Thursday, March 12, 2009 8:33 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] Extract values of the Fiber tract ROI Hi Susumu, I`m talking about the statistics of the fiber tracking results as an ROI. I want to extract all the voxels values in the FA map that are included in the corpus callusum tract to a text file. I don`t want only the mean or the max/minimum value. Becouse I want to do a parcellation of the corpus callosum and do a correlation of this values with the age or the IQ of the pacients. I?m working with the software some months ago, and I`m new in the list. This is my first message. Thank you for your answer. 2009/3/13 susumu Hi Javier, ? Are you talking about the statistics of the ROI you drew or using the fiber tracking results as an ROI? ? Susumu ? ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ To unsubscribe this mailing list, please go to www.mristudio.org / Mailing List / Mristudio-users. There you can find the unsubscribe option. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ? ? ________________________________________ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Javier Navas Sent: Wednesday, March 11, 2009 8:15 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] Extract values of the Fiber tract ROI ? Dear all, I`m working in Fiber Tracking of the corpus callosum with DTIstudio, I want to extract the values of my ROI (the statistics with the number of fibers selected, length of fibers, FA values...) to a text file or SPSS archive, but I don`t know how can I do it. Thank you for help me, Javier _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From yingding at hku.hk Thu Mar 19 05:50:30 2009 From: yingding at hku.hk (Abby Ding) Date: Thu, 19 Mar 2009 17:50:30 +0800 Subject: [Mristudio-users] Multiple b-value gradient table & how to save the post-cross-out raw images Message-ID: <0951E3AA34604ED8889722BBA3AE387A@ABBY> Dear Susumu, dear all, I have two questions when using the DTIstudio for DTI mapping as bellow. Q1.I'm doing some DKI experiments which have 4 b-value (500,1000,1500,2000) and 30 directions for each b-value on a Bruker 7T scanner. I tried to define the multiple b-value gradient table (which was editted from the 30-direction DTI gradient table I used to define and opened the dataset successfully) for screening the DWI images for further calculation. But every time it kept saying that "file size is bigger than DW-image size" and failed to open the dataset correctly. I wonder if there is any mistake in my gradient table? Here it is (5 b0 images).... Furthermore, what should I put in the "b-value" option in this multiple b-value case? Would it affect the tensor calculation? -------------------------------------------------------------------------- 0: 0.000, 0.000, 0.000 1: 0.000, 0.000, 0.000 2: 0.000, 0.000, 0.000 3: 0.000, 0.000, 0.000 4: 0.000, 0.000, 0.000 5: 0.000, 1.000, 0.000, 500 6: 0.986, 0.166, 0.000, 500 7: 0.664, -0.110, 0.740, 500 8: -0.419, 0.901, -0.110, 500 9: -0.601, -0.169, 0.781, 500 10: -0.386, -0.815, 0.433, 500 11: 0.366, 0.656, 0.660, 500 12: 0.800, 0.582, 0.143, 500 13: 0.259, 0.900, 0.350, 500 14: -0.698, 0.693, 0.178, 500 15: -0.924, 0.357, -0.140, 500 16: -0.488, 0.543, -0.683, 500 17: -0.396, -0.525, 0.753, 500 18: 0.689, -0.639, 0.341, 500 19: -0.013, -0.330, -0.944, 500 20: -0.783, -0.524, 0.335, 500 21: -0.065, 0.609, -0.791, 500 22: -0.233, 0.220, -0.947, 500 23: -0.910, -0.004, -0.415, 500 24: 0.627, -0.511, -0.589, 500 25: 0.737, 0.414, 0.535, 500 26: 0.139, -0.679, -0.721, 500 27: -0.296, 0.884, 0.362, 500 28: 0.432, 0.262, 0.863, 500 29: 0.185, 0.088, -0.979, 500 30: -0.907, 0.294, 0.302, 500 31: -0.089, 0.887, -0.453, 500 32: -0.443, 0.257, 0.859, 500 33: 0.867, 0.086, -0.491, 500 34: 0.504, 0.863, -0.025, 500 35: 0.000, 1.000, 0.000, 1000 36: 0.986, 0.166, 0.000, 1000 37: 0.664, -0.110, 0.740, 1000 38: -0.419, 0.901, -0.110, 1000 39: -0.601, -0.169, 0.781, 1000 40: -0.386, -0.815, 0.433, 1000 41: 0.366, 0.656, 0.660, 1000 42: 0.800, 0.582, 0.143, 1000 43: 0.259, 0.900, 0.350, 1000 44: -0.698, 0.693, 0.178, 1000 45: -0.924, 0.357, -0.140, 1000 46: -0.488, 0.543, -0.683, 1000 47: -0.396, -0.525, 0.753, 1000 48: 0.689, -0.639, 0.341, 1000 49: -0.013, -0.330, -0.944, 1000 50: -0.783, -0.524, 0.335, 1000 51: -0.065, 0.609, -0.791, 1000 52: -0.233, 0.220, -0.947, 1000 53: -0.910, -0.004, -0.415, 1000 54: 0.627, -0.511, -0.589, 1000 55: 0.737, 0.414, 0.535, 1000 56: 0.139, -0.679, -0.721, 1000 57: -0.296, 0.884, 0.362, 1000 58: 0.432, 0.262, 0.863, 1000 59: 0.185, 0.088, -0.979, 1000 60: -0.907, 0.294, 0.302, 1000 61: -0.089, 0.887, -0.453, 1000 62: -0.443, 0.257, 0.859, 1000 63: 0.867, 0.086, -0.491, 1000 64: 0.504, 0.863, -0.025, 1000 65: 0.000, 1.000, 0.000, 1500 66: 0.986, 0.166, 0.000, 1500 67: 0.664, -0.110, 0.740, 1500 68: -0.419, 0.901, -0.110, 1500 69: -0.601, -0.169, 0.781, 1500 70: -0.386, -0.815, 0.433, 1500 71: 0.366, 0.656, 0.660, 1500 72: 0.800, 0.582, 0.143, 1500 73: 0.259, 0.900, 0.350, 1500 74: -0.698, 0.693, 0.178, 1500 75: -0.924, 0.357, -0.140, 1500 76: -0.488, 0.543, -0.683, 1500 77: -0.396, -0.525, 0.753, 1500 78: 0.689, -0.639, 0.341, 1500 79: -0.013, -0.330, -0.944, 1500 80: -0.783, -0.524, 0.335, 1500 81: -0.065, 0.609, -0.791, 1500 82: -0.233, 0.220, -0.947, 1500 83: -0.910, -0.004, -0.415, 1500 84: 0.627, -0.511, -0.589, 1500 85: 0.737, 0.414, 0.535, 1500 86: 0.139, -0.679, -0.721, 1500 87: -0.296, 0.884, 0.362, 1500 88: 0.432, 0.262, 0.863, 1500 89: 0.185, 0.088, -0.979, 1500 90: -0.907, 0.294, 0.302, 1500 91: -0.089, 0.887, -0.453, 1500 92: -0.443, 0.257, 0.859, 1500 93: 0.867, 0.086, -0.491, 1500 94: 0.504, 0.863, -0.025, 1500 95: 0.000, 1.000, 0.000, 2000 96: 0.986, 0.166, 0.000, 2000 97: 0.664, -0.110, 0.740, 2000 98: -0.419, 0.901, -0.110, 2000 99: -0.601, -0.169, 0.781, 2000 100: -0.386, -0.815, 0.433, 2000 101: 0.366, 0.656, 0.660, 2000 102: 0.800, 0.582, 0.143, 2000 103: 0.259, 0.900, 0.350, 2000 104: -0.698, 0.693, 0.178, 2000 105: -0.924, 0.357, -0.140, 2000 106: -0.488, 0.543, -0.683, 2000 107: -0.396, -0.525, 0.753, 2000 108: 0.689, -0.639, 0.341, 2000 109: -0.013, -0.330, -0.944, 2000 110: -0.783, -0.524, 0.335, 2000 111: -0.065, 0.609, -0.791, 2000 112: -0.233, 0.220, -0.947, 2000 113: -0.910, -0.004, -0.415, 2000 114: 0.627, -0.511, -0.589, 2000 115: 0.737, 0.414, 0.535, 2000 116: 0.139, -0.679, -0.721, 2000 117: -0.296, 0.884, 0.362, 2000 118: 0.432, 0.262, 0.863, 2000 119: 0.185, 0.088, -0.979, 2000 120: -0.907, 0.294, 0.302, 2000 121: -0.089, 0.887, -0.453, 2000 122: -0.443, 0.257, 0.859, 2000 123: 0.867, 0.086, -0.491, 2000 124: 0.504, 0.863, -0.025, 2000 ------------------------------------------------------------------------------------------------- Q2. I'd like to save the post-cross-out raw images (Philips REC file format) in order to record the images I used to calculate the tensor, but I found no way to achieve that either by using "save" or "save as" function in DTIstudio. Is DTIstudio capable to save these data? I just want to achieve that every time when I open the same dataset, it will automatically show me where I've crossed out for tensor calculation last time. Thank you very much for your attention! Best Regards, Abby -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090319/93d308bf/attachment.html From vikey.han at 163.com Thu Mar 19 05:59:46 2009 From: vikey.han at 163.com (vikey.han) Date: Thu, 19 Mar 2009 17:59:46 +0800 (CST) Subject: [Mristudio-users] Extract values of the Fiber tract ROI In-Reply-To: <7k7ed7$6on869@ipex3.johnshopkins.edu> References: <7k7ed7$6on869@ipex3.johnshopkins.edu> Message-ID: <7669594.340781237456786669.JavaMail.coremail@bj163app64.163.com> Then I have a question, if the two or more fibers share the same sequence of pixels, how does DTIsutio represent the fibers tracked, for example, Fiber1={pixel1,pixel2,pixel3,pixel4,pixel5} Fiber2={pixel1,pixel2,pixel3,pixel6,pixel7} then whether the fiber1 and fiber1 have the same data structure as the above, or Fiber1={pixel1,pixel2,pixel3,pixel4,pixel5} Fiber2={pixel6,pixel7} or maybe DTIStudio generates three fibers: Fiber1={pixel1,pixel2,pixel3} Fiber2={pixel6,pixel7} Fiber3={pixel4,pixel5} Is it possible that the last two cases happening? 2009-03-17?susumu ? >Dear Users, > >Javier raised an important issue and I want to share his results with all of >you. > >Here is what he did; > >1) Did fiber tracking using DtiStudio, use the "statistics" button, and get >an FA value of the entire reconstructed fiber. >2) Save the fiber tracking results as 1/0 binary image, load the file to >RoiEditor, superimpose the binary masking on the FA map, and get an FA value >of the entire reconstructed fiber > >The results were different as indicated in his email. > >This is because the ways FA is measured for the reconstructed tracts are >fundamentally different between the two programs. > >DtiStudio: > >Suppose you have two fibers. One is 10-pixel long and the other is 5-pixel >long. Also suppose that the second 5-pixel fiber shares the same 5 pixels >within the first 10-pixel fiber. This means, the second fiber is completely >contained within the first fiber. > >In DtiStudio, FA is measured along the first fiber. It also measures FA >along the second fiber. The end result is, for example; > >First fiber [0.2, 0.25, 0.3, 0.35, 0.4, 0.45, 0.5, 0.55, 0.6, 0.65] >Second [0.2, 0.25, 0.3, 0.35, 0.4] > >As you can see, the first 5 pixels are identical. Then DtiStudio calculates >the average of the 15 pixels. This means, the first 5 pixels are >"double-counted". > >In this way, DtiStudio provides natural weighting for pixels that contain >more fibers. In reality, some pixels may contains 10s of fibers >(reconstructed streamlines) while some pixels may contain only one fiber. >The more fibers a pixel contains, more weighting it receives, because it >would be counted many more times. > >RoiEditor: > >Once you save the fiber tracking result into 1/0 binary information, all the >streamline information is lost, so as the number of fibers each pixel >contains. In RoiEditor, the binary image can be read and applied to an FA >map as a non-weighted binary masking. > >I hope this explains the difference among the two methods. Because DtiStudio >counts the core white matter regions many more times than peripheral areas, >the average FA values tend to be higher. > >There is nothing like one is better than the other. They are just two >different approaches. Maybe the natural weighting may sound more reasonable >but the non-weighting 1/0 masking should also be a valid approach. You just >need to apply the same method (or both methods) to all data. > >Please let us know if you have any questions regarding this issue. > >Thanks, > >Susumu > > > >________________________________________ >From: Javier Navas [mailto:fjnavas2 at gmail.com] >Sent: Tuesday, March 17, 2009 6:55 AM >To: susumu at mri.jhu.edu; DTI Studio, ROI Editor, Landmarker Questions/Support >Subject: [Mristudio-users] Extract values of the Fiber tract ROI > > >Thank you very much Mr. Susumu, > >with ROI editor I can extract the pixel values in a txt file, that is what I >want, thank you. > >But I have a problem. The FA mean value that results in DTI Studio is >different that the FA mean value that results in ROI editor, with the same >binary image, why occur this?. > >For example, with the same mask of the genu of corpus callosum, I have the >same number of pixels (2835 pixels) but the FA statistics is different. > >DTI studio: >????? FA >??????? Max. of ImgVal:?? 0.9690 >??????? Min. of ImgVal:?? 0.0591 >??????? Mean of ImgVal:?? 0.5385 >??????? Std. of ImgVal:?? 0.1689 > >ROI editor: >???????? Min:??? 0.06 >???????? Max:??? 0.97 >???????? Mean:??? 0.45 >???????? Std:??? 0.17 > >________________________________________ >From: mristudio-users-bounces at mristudio.org >[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Javier Navas >Sent: Thursday, March 12, 2009 8:33 PM >To: DTI Studio, ROI Editor, Landmarker Questions/Support >Subject: Re: [Mristudio-users] Extract values of the Fiber tract ROI > >Hi Susumu, > >I`m talking about the statistics of the fiber tracking results as an ROI. I >want to extract all the voxels values in the FA map that are included in the >corpus callusum tract to a text file. I don`t want only the mean or the >max/minimum value. Becouse I want to do a parcellation of the corpus >callosum and do a correlation of this values with the age or the IQ of the >pacients. > >I?m working with the software some months ago, and I`m new in the list. This >is my first message. Thank you for your answer. > >2009/3/13 susumu >Hi Javier, >? >Are you talking about the statistics of the ROI you drew or using the fiber >tracking results as an ROI? >? >Susumu >? >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >To unsubscribe this mailing list, please go to www.mristudio.org / Mailing >List / Mristudio-users. There you can find the unsubscribe option. >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >? >? >________________________________________ >From: mristudio-users-bounces at mristudio.org >[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Javier Navas >Sent: Wednesday, March 11, 2009 8:15 AM >To: mristudio-users at mristudio.org >Subject: [Mristudio-users] Extract values of the Fiber tract ROI >? >Dear all, > >I`m working in Fiber Tracking of the corpus callosum with DTIstudio, > >I want to extract the values of my ROI (the statistics with the number of >fibers selected, length of fibers, FA values...) to a text file or SPSS >archive, but I don`t know how can I do it. > > >Thank you for help me, > >Javier > >_______________________________________________ >Mristudio-users mailing list >Mristudio-users at mristudio.org >http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > >_______________________________________________ >Mristudio-users mailing list >Mristudio-users at mristudio.org >http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090319/0f5ef8b7/attachment-0001.html From yingding at hku.hk Thu Mar 19 06:01:22 2009 From: yingding at hku.hk (Abby Ding) Date: Thu, 19 Mar 2009 18:01:22 +0800 Subject: [Mristudio-users] 15-direction gradient table Message-ID: <4ED4B4AD0EB74C6D9EABCBD367536810@ABBY> Dear users, Does any one of you have a 15-direction gradient table to share with me? Thank you very much for your kindly help! Best Regards, Abby -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090319/8363e21f/attachment.html From fjnavas2 at gmail.com Tue Mar 17 06:32:31 2009 From: fjnavas2 at gmail.com (Javier Navas) Date: Tue, 17 Mar 2009 11:32:31 +0100 Subject: [Mristudio-users] Extract values of the Fiber tract ROI In-Reply-To: <7k7ed7$6npt7r@ipex3.johnshopkins.edu> References: <6fd5e4b20903121733h16ddbb21yb9d640fba98c18de@mail.gmail.com> <7k7ed7$6npt7r@ipex3.johnshopkins.edu> Message-ID: <6fd5e4b20903170332w749e774ek6c3434d80ba1fc5f@mail.gmail.com> Thank you very much Mr. Susumu, with ROI editor I can extract the pixel values in a txt file, that is what I want, thank you. But I have a problem. The FA mean value that results in DTI Studio is different that the FA mean value that results in ROI editor, with the same binary image, why occur this?. For example, with the same mask of the genu of corpus callosum, I have the same number of pixels (2835 pixels) but the FA statistics is different. DTI studio: FA Max. of ImgVal: 0.9690 Min. of ImgVal: 0.0591 * Mean of ImgVal: 0.5385* Std. of ImgVal: 0.1689 ROI editor: Min: 0.06 Max: 0.97 *Mean: 0.45* Std: 0.17 Could you explain me why the FA mean values are different? THANK YOU Javier 2009/3/14 susumu > Hi Javier, > > > > I'm not sure if I'm answering your question, but here I listed what you can > do after you get a tractgraphy result; > > > > 1) Click the "statistics" button and specify an MRI image (e.g. FA map) you > want to quantify. This gives you the average and standard deviation of all > pixels included in the tract (this is not what you want). > > 2) Then click "profile" button. This give you pixel values within each > slice in axial, coronal, and sagittal orientations. This works nicely if the > tract of your interest has a linear shape. For tracts like the corpus > callosum (U-shape), this approach has some issue. > > 3) Save the tract as a binary image (1/0 map). Load this binary image as an > image to RoiEditor as well as a map you want to quantify (e.g. FA map). > Using the binary image and the thresholding tool, define an object that > identify pixels with value "1"; namely, redefine the tract as an object. > Bring the FA map as an active image and right-click the object you defined > in the "object list". This allows export (text file) of FA values of all > pixels that belong to the tract you defined. You can read this text file > into Excel and create a histogram > > 4) You can normalize the binary image to one of the atlas provided in > Landmarker. By normalize population data, you can create probabilistic tract > maps. Using RoiEditor, you can mask FA maps by tractography results and then > normalize. This may allow you to do pixel-based analysis in an atlas space. > After normalization, you can also "segment" the tracking result into the > corpus callosum region and corona radiata region by combining your binary > tracking image and "white matter parcellation map (WMPM)" provided in > RoiEditor. > > > > I must admit that currently manuals of RoiEditor and Landmarker are very > limited. We are working on it and it may take some time. If you think one of > the above 4 methods can provide what you want, you can contact us for more > specific instruction. > > > > Susumu > > > ------------------------------ > > *From:* mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org] *On Behalf Of *Javier Navas > *Sent:* Thursday, March 12, 2009 8:33 PM > *To:* DTI Studio, ROI Editor, Landmarker Questions/Support > *Subject:* Re: [Mristudio-users] Extract values of the Fiber tract ROI > > > > Hi Susumu, > > I`m talking about the statistics of the fiber tracking results as an ROI. I > want to extract all the voxels values in the FA map that are included in the > corpus callusum tract to a text file. I don`t want only the mean or the > max/minimum value. Becouse I want to do a parcellation of the corpus > callosum and do a correlation of this values with the age or the IQ of the > pacients. > > I?m working with the software some months ago, and I`m new in the list. > This is my first message. Thank you for your answer. > > 2009/3/13 susumu > > Hi Javier, > > > > Are you talking about the statistics of the ROI you drew or using the fiber > tracking results as an ROI? > > > > Susumu > > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > To unsubscribe this mailing list, please go to www.mristudio.org / Mailing > List / Mristudio-users. There you can find the unsubscribe option. > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > > > ------------------------------ > > *From:* mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org] *On Behalf Of *Javier Navas > *Sent:* Wednesday, March 11, 2009 8:15 AM > *To:* mristudio-users at mristudio.org > *Subject:* [Mristudio-users] Extract values of the Fiber tract ROI > > > > Dear all, > > I`m working in Fiber Tracking of the corpus callosum with DTIstudio, > > I want to extract the values of my ROI (the statistics with the number of > fibers selected, length of fibers, FA values...) to a text file or SPSS > archive, but I don`t know how can I do it. > > > Thank you for help me, > > Javier > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090317/3fe0e7c8/attachment.html From susumu at mri.jhu.edu Thu Mar 19 07:37:42 2009 From: susumu at mri.jhu.edu (susumu) Date: Thu, 19 Mar 2009 07:37:42 -0400 Subject: [Mristudio-users] Multiple b-value gradient table & how to save the post-cross-out raw images In-Reply-To: <0951E3AA34604ED8889722BBA3AE387A@ABBY> References: <0951E3AA34604ED8889722BBA3AE387A@ABBY> Message-ID: <01F56F730E694A6BAC977D718239190E@SusumuThinkPad> Hi Abby, In general, when you get this message, please check the following; 1) Read the data by MRI3DView, not DtiMapping. Make sure that DtiStudio can correctly read the raw data. Make sure that the image dimensions (especially the numbe of the slices) are correct and there are 125 images. 2) If all the imaging parameters and the number of the images are correct, read the data by DtiMapping by ignoring the warning message. Again, make sure that the number of the images and image dimensions are correct and all 125 images are read. 3) Close the window and open the initial image parameter input window by choosing DtiMapping. There, the gradient table you specified in the last session is still remembered by DtiStudio. The difference is, if you made any mistake in the syntax of the gradient table (like colons and commas), you can see how DtiStudio interpreted the table wrongly, and therefore it is easier to detect errors. I believe that the "b-value" option is not used if you specify b-values in the table, but I'll confirm with Hangyi. _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Abby Ding Sent: Thursday, March 19, 2009 5:51 AM To: MRIstudio Subject: [Mristudio-users] Multiple b-value gradient table & how to save the post-cross-out raw images Dear Susumu, dear all, I have two questions when using the DTIstudio for DTI mapping as bellow. Q1.I'm doing some DKI experiments which have 4 b-value (500,1000,1500,2000) and 30 directions for each b-value on a Bruker 7T scanner. I tried to define the multiple b-value gradient table (which was editted from the 30-direction DTI gradient table I used to define and opened the dataset successfully) for screening the DWI images for further calculation. But every time it kept saying that "file size is bigger than DW-image size" and failed to open the dataset correctly. I wonder if there is any mistake in my gradient table? Here it is (5 b0 images).... Furthermore, what should I put in the "b-value" option in this multiple b-value case? Would it affect the tensor calculation? -------------------------------------------------------------------------- 0: 0.000, 0.000, 0.000 1: 0.000, 0.000, 0.000 2: 0.000, 0.000, 0.000 3: 0.000, 0.000, 0.000 4: 0.000, 0.000, 0.000 5: 0.000, 1.000, 0.000, 500 6: 0.986, 0.166, 0.000, 500 7: 0.664, -0.110, 0.740, 500 8: -0.419, 0.901, -0.110, 500 9: -0.601, -0.169, 0.781, 500 10: -0.386, -0.815, 0.433, 500 11: 0.366, 0.656, 0.660, 500 12: 0.800, 0.582, 0.143, 500 13: 0.259, 0.900, 0.350, 500 14: -0.698, 0.693, 0.178, 500 15: -0.924, 0.357, -0.140, 500 16: -0.488, 0.543, -0.683, 500 17: -0.396, -0.525, 0.753, 500 18: 0.689, -0.639, 0.341, 500 19: -0.013, -0.330, -0.944, 500 20: -0.783, -0.524, 0.335, 500 21: -0.065, 0.609, -0.791, 500 22: -0.233, 0.220, -0.947, 500 23: -0.910, -0.004, -0.415, 500 24: 0.627, -0.511, -0.589, 500 25: 0.737, 0.414, 0.535, 500 26: 0.139, -0.679, -0.721, 500 27: -0.296, 0.884, 0.362, 500 28: 0.432, 0.262, 0.863, 500 29: 0.185, 0.088, -0.979, 500 30: -0.907, 0.294, 0.302, 500 31: -0.089, 0.887, -0.453, 500 32: -0.443, 0.257, 0.859, 500 33: 0.867, 0.086, -0.491, 500 34: 0.504, 0.863, -0.025, 500 35: 0.000, 1.000, 0.000, 1000 36: 0.986, 0.166, 0.000, 1000 37: 0.664, -0.110, 0.740, 1000 38: -0.419, 0.901, -0.110, 1000 39: -0.601, -0.169, 0.781, 1000 40: -0.386, -0.815, 0.433, 1000 41: 0.366, 0.656, 0.660, 1000 42: 0.800, 0.582, 0.143, 1000 43: 0.259, 0.900, 0.350, 1000 44: -0.698, 0.693, 0.178, 1000 45: -0.924, 0.357, -0.140, 1000 46: -0.488, 0.543, -0.683, 1000 47: -0.396, -0.525, 0.753, 1000 48: 0.689, -0.639, 0.341, 1000 49: -0.013, -0.330, -0.944, 1000 50: -0.783, -0.524, 0.335, 1000 51: -0.065, 0.609, -0.791, 1000 52: -0.233, 0.220, -0.947, 1000 53: -0.910, -0.004, -0.415, 1000 54: 0.627, -0.511, -0.589, 1000 55: 0.737, 0.414, 0.535, 1000 56: 0.139, -0.679, -0.721, 1000 57: -0.296, 0.884, 0.362, 1000 58: 0.432, 0.262, 0.863, 1000 59: 0.185, 0.088, -0.979, 1000 60: -0.907, 0.294, 0.302, 1000 61: -0.089, 0.887, -0.453, 1000 62: -0.443, 0.257, 0.859, 1000 63: 0.867, 0.086, -0.491, 1000 64: 0.504, 0.863, -0.025, 1000 65: 0.000, 1.000, 0.000, 1500 66: 0.986, 0.166, 0.000, 1500 67: 0.664, -0.110, 0.740, 1500 68: -0.419, 0.901, -0.110, 1500 69: -0.601, -0.169, 0.781, 1500 70: -0.386, -0.815, 0.433, 1500 71: 0.366, 0.656, 0.660, 1500 72: 0.800, 0.582, 0.143, 1500 73: 0.259, 0.900, 0.350, 1500 74: -0.698, 0.693, 0.178, 1500 75: -0.924, 0.357, -0.140, 1500 76: -0.488, 0.543, -0.683, 1500 77: -0.396, -0.525, 0.753, 1500 78: 0.689, -0.639, 0.341, 1500 79: -0.013, -0.330, -0.944, 1500 80: -0.783, -0.524, 0.335, 1500 81: -0.065, 0.609, -0.791, 1500 82: -0.233, 0.220, -0.947, 1500 83: -0.910, -0.004, -0.415, 1500 84: 0.627, -0.511, -0.589, 1500 85: 0.737, 0.414, 0.535, 1500 86: 0.139, -0.679, -0.721, 1500 87: -0.296, 0.884, 0.362, 1500 88: 0.432, 0.262, 0.863, 1500 89: 0.185, 0.088, -0.979, 1500 90: -0.907, 0.294, 0.302, 1500 91: -0.089, 0.887, -0.453, 1500 92: -0.443, 0.257, 0.859, 1500 93: 0.867, 0.086, -0.491, 1500 94: 0.504, 0.863, -0.025, 1500 95: 0.000, 1.000, 0.000, 2000 96: 0.986, 0.166, 0.000, 2000 97: 0.664, -0.110, 0.740, 2000 98: -0.419, 0.901, -0.110, 2000 99: -0.601, -0.169, 0.781, 2000 100: -0.386, -0.815, 0.433, 2000 101: 0.366, 0.656, 0.660, 2000 102: 0.800, 0.582, 0.143, 2000 103: 0.259, 0.900, 0.350, 2000 104: -0.698, 0.693, 0.178, 2000 105: -0.924, 0.357, -0.140, 2000 106: -0.488, 0.543, -0.683, 2000 107: -0.396, -0.525, 0.753, 2000 108: 0.689, -0.639, 0.341, 2000 109: -0.013, -0.330, -0.944, 2000 110: -0.783, -0.524, 0.335, 2000 111: -0.065, 0.609, -0.791, 2000 112: -0.233, 0.220, -0.947, 2000 113: -0.910, -0.004, -0.415, 2000 114: 0.627, -0.511, -0.589, 2000 115: 0.737, 0.414, 0.535, 2000 116: 0.139, -0.679, -0.721, 2000 117: -0.296, 0.884, 0.362, 2000 118: 0.432, 0.262, 0.863, 2000 119: 0.185, 0.088, -0.979, 2000 120: -0.907, 0.294, 0.302, 2000 121: -0.089, 0.887, -0.453, 2000 122: -0.443, 0.257, 0.859, 2000 123: 0.867, 0.086, -0.491, 2000 124: 0.504, 0.863, -0.025, 2000 ---------------------------------------------------------------------------- --------------------- Q2. I'd like to save the post-cross-out raw images (Philips REC file format) in order to record the images I used to calculate the tensor, but I found no way to achieve that either by using "save" or "save as" function in DTIstudio. Is DTIstudio capable to save these data? I just want to achieve that every time when I open the same dataset, it will automatically show me where I've crossed out for tensor calculation last time. Thank you very much for your attention! Best Regards, Abby -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090319/e5312194/attachment-0001.html From susumu at mri.jhu.edu Thu Mar 19 07:52:37 2009 From: susumu at mri.jhu.edu (susumu) Date: Thu, 19 Mar 2009 07:52:37 -0400 Subject: [Mristudio-users] Extract values of the Fiber tract ROI In-Reply-To: <7669594.340781237456786669.JavaMail.coremail@bj163app64.163.com> References: <7k7ed7$6on869@ipex3.johnshopkins.edu> <7669594.340781237456786669.JavaMail.coremail@bj163app64.163.com> Message-ID: <190F47A30FBC4352BB0F3D73F7D25569@SusumuThinkPad> I?m not sure if I understood your question correctly, but let me try. In DtiStudio, fiber tracking is initiated from all pixels in the brain (more precisely pixels with FA above the threshold). Some may think that tracking is initiated from pixels in ROIs, but that is not the case. We draw ROIs just to retrieve fiber tracking results that penetrate the ROIs. For the first case of your fibers, ROI could be Pixel2 and for the Fiber #1, the seed pixel could be Pixel#5 and for the Fiber #2, the seed pixel could be Pixel#7. So, it?s possible. The Case 2 and Case 3 seem not possible because there is no common pixel as your ROI location. Also, suppose we have hypothetical ?real? tract with Fiber1={pixel1,pixel2,pixel3,pixel4,pixel5} Then we may get 5 streamlines after fiber tracking; one seeded from Pixel#1, one from Pixel#2,,,, one from Pixel#5. These 5 streamlines have slightly different coordinates because each tracking starts from the center of each pixel and tracking takes place in floating number coordinates. For quantification, the streamline information is often converted to pixel-by-pixel information. After this conversion, the 5 floating-point streamlines may converted to the identical string of pixels, which is in this case, Fiber1={pixel1,pixel2,pixel3,pixel4,pixel5}. In reality, these 5 streamlines often start to diverge at the peripheral regions while the core areas are likely to share many pixels. _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of vikey.han Sent: Thursday, March 19, 2009 6:00 AM To: DTI Studio ROI Editor Landmarker Questions/Support Subject: Re: [Mristudio-users] Extract values of the Fiber tract ROI Then I have a question, if the two or more fibers share the same sequence of pixels, how does DTIsutio represent the fibers tracked, for example, Fiber1={pixel1,pixel2,pixel3,pixel4,pixel5} Fiber2={pixel1,pixel2,pixel3,pixel6,pixel7} then whether the fiber1 and fiber1 have the same data structure as the above, or Fiber1={pixel1,pixel2,pixel3,pixel4,pixel5} Fiber2={pixel6,pixel7} or maybe DTIStudio generates three fibers: Fiber1={pixel1,pixel2,pixel3} Fiber2={pixel6,pixel7} Fiber3={pixel4,pixel5} Is it possible that the last two cases happening? 2009-03-17?susumu ? >Dear Users, > >Javier raised an important issue and I want to share his results with all of >you. > >Here is what he did; > >1) Did fiber tracking using DtiStudio, use the "statistics" button, and get >an FA value of the entire reconstructed fiber. >2) Save the fiber tracking results as 1/0 binary image, load the file to >RoiEditor, superimpose the binary masking on the FA map, and get an FA value >of the entire reconstructed fiber > >The results were different as indicated in his email. > >This is because the ways FA is measured for the reconstructed tracts are >fundamentally different between the two programs. > >DtiStudio: > >Suppose you have two fibers. One is 10-pixel long and the other is 5-pixel >long. Also suppose that the second 5-pixel fiber shares the same 5 pixels >within the first 10-pixel fiber. This means, the second fiber is completely >contained within the first fiber. > >In DtiStudio, FA is measured along the first fiber. It also measures FA >along the second fiber. The end result is, for example; > >First fiber [0.2, 0.25, 0.3, 0.35, 0.4, 0.45, 0.5, 0.55, 0.6, 0.65] >Second [0.2, 0.25, 0.3, 0.35, 0.4] > >As you can see, the first 5 pixels are identical. Then DtiStudio calculates >the average of the 15 pixels. This means, the first 5 pixels are >"double-counted". > >In this way, DtiStudio provides natural weighting for pixels that contain >more fibers. In reality, some pixels may contains 10s of fibers >(reconstructed streamlines) while some pixels may contain only one fiber. >The more fibers a pixel contains, more weighting it receives, because it >would be counted many more times. > >RoiEditor: > >Once you save the fiber tracking result into 1/0 binary information, all the >streamline information is lost, so as the number of fibers each pixel >contains. In RoiEditor, the binary image can be read and applied to an FA >map as a non-weighted binary masking. > >I hope this explains the difference among the two methods. Because DtiStudio >counts the core white matter regions many more times than peripheral areas, >the average FA values tend to be higher. > >There is nothing like one is better than the other. They are just two >different approaches. Maybe the natural weighting may sound more reasonable >but the non-weighting 1/0 masking should also be a valid approach. You just >need to apply the same method (or both methods) to all data. > >Please let us know if you have any questions regarding this issue. > >Thanks, > >Susumu > > > >________________________________________ >From: Javier Navas [mailto:fjnavas2 at gmail.com] >Sent: Tuesday, March 17, 2009 6:55 AM >To: susumu at mri.jhu.edu; DTI Studio, ROI Editor, Landmarker Questions/Support >Subject: [Mristudio-users] Extract values of the Fiber tract ROI > > >Thank you very much Mr. Susumu, > >with ROI editor I can extract the pixel values in a txt file, that is what I >want, thank you. > >But I have a problem. The FA mean value that results in DTI Studio is >different that the FA mean value that results in ROI editor, with the same >binary image, why occur this?. > >For example, with the same mask of the genu of corpus callosum, I have the >same number of pixels (2835 pixels) but the FA statistics is different. > >DTI studio: > FA > Max. of ImgVal: 0.9690 > Min. of ImgVal: 0.0591 > Mean of ImgVal: 0.5385 > Std. of ImgVal: 0.1689 > >ROI editor: > Min: 0.06 > Max: 0.97 > Mean: 0.45 > Std: 0.17 > >________________________________________ >From: mristudio-users-bounces at mristudio.org >[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Javier Navas >Sent: Thursday, March 12, 2009 8:33 PM >To: DTI Studio, ROI Editor, Landmarker Questions/Support >Subject: Re: [Mristudio-users] Extract values of the Fiber tract ROI > >Hi Susumu, > >I`m talking about the statistics of the fiber tracking results as an ROI. I >want to extract all the voxels values in the FA map that are included in the >corpus callusum tract to a text file. I don`t want only the mean or the >max/minimum value. Becouse I want to do a parcellation of the corpus >callosum and do a correlation of this values with the age or the IQ of the >pacients. > >I?m working with the software some months ago, and I`m new in the list. This >is my first message. Thank you for your answer. > >2009/3/13 susumu >Hi Javier, > >Are you talking about the statistics of the ROI you drew or using the fiber >tracking results as an ROI? > >Susumu > >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >To unsubscribe this mailing list, please go to www.mristudio.org / Mailing >List / Mristudio-users. There you can find the unsubscribe option. >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > >________________________________________ >From: mristudio-users-bounces at mristudio.org >[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Javier Navas >Sent: Wednesday, March 11, 2009 8:15 AM >To: mristudio-users at mristudio.org >Subject: [Mristudio-users] Extract values of the Fiber tract ROI > >Dear all, > >I`m working in Fiber Tracking of the corpus callosum with DTIstudio, > >I want to extract the values of my ROI (the statistics with the number of >fibers selected, length of fibers, FA values...) to a text file or SPSS >archive, but I don`t know how can I do it. > > >Thank you for help me, > >Javier > >_______________________________________________ >Mristudio-users mailing list >Mristudio-users at mristudio.org >http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > >_______________________________________________ >Mristudio-users mailing list >Mristudio-users at mristudio.org >http://lists.mristudio.org/mailman/listinfo/mristudio-users _____ ????????????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090319/b7c6ef36/attachment-0001.html From susumu at mri.jhu.edu Thu Mar 19 09:45:36 2009 From: susumu at mri.jhu.edu (susumu) Date: Thu, 19 Mar 2009 09:45:36 -0400 Subject: [Mristudio-users] 15-direction gradient table In-Reply-To: <4ED4B4AD0EB74C6D9EABCBD367536810@ABBY> Message-ID: <7k7ed7$6pdapu@ipex3.johnshopkins.edu> for which scanner? Or something you can implement in a scanner by yourself? Anyway, these are some options you can consider; Philips "Medium" 15-orientation: 0: 0, 0, 0 1: 1.0, 0.0, 0.0 2: 0.0, 1.0, 0.0 3: 0.0, 0.0, 1.0 4: -0.1789, -0.1113, -0.9776 5: -0.0635, 0.3767, -0.9242 6: 0.710, 0.0516, -0.7015 7: 0.6191, -0.4385, -0.6515 8: 0.2424, 0.7843, -0.5710 9: -0.2589, -0.6180, -0.7423 10: -0.8169, 0.1697, -0.5513 11: -0.8438, 0.5261, -0.1060 12: -0.2626, 0.9548, -0.1389 13: 0.0001, 0.9689, 0.2476 14: 0.7453, 0.6663, 0.0242 15: 0.9726, 0.2317, 0.0209 GE 15-orientation 0: 0.000, 0.000, 0.000 1: 0.216, -0.8986, 0.38188 2: -0.444, -0.4187, 0.7918 3: -0.6351, -0.7700, -0.05947 4: 0.500, -0.19253, 0.8440 5: -0.2212, 0.5311, -0.8178 6: -0.8919, 0.07914, -0.4451 7: -0.1693, 0.5134, 0.8412 8: -0.2639, -0.4402, -0.8581 9: 0.59852, 0.00692, -0.8010 10: -0.899, 0.2234, 0.3751 11: 0.9853, -0.1664, 0.0385 12: 0.6279, 0.6270, 0.46098 13: -0.3501, 0.9364, 0.02096 14: 0.5270, 0.7731, -0.3528 15: 0.4206, -0.8041, -0.4200 There are Jones10 and Jones20, but I am not sure if there is Jones15. _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Abby Ding Sent: Thursday, March 19, 2009 6:01 AM To: MRIstudio Subject: [Mristudio-users] 15-direction gradient table Dear users, Does any one of you have a 15-direction gradient table to share with me? Thank you very much for your kindly help! Best Regards, Abby -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090319/e3a7ead5/attachment.html From vikey.han at 163.com Thu Mar 19 10:23:58 2009 From: vikey.han at 163.com (vikey.han) Date: Thu, 19 Mar 2009 22:23:58 +0800 (CST) Subject: [Mristudio-users] Extract values of the Fiber tract ROI In-Reply-To: <190F47A30FBC4352BB0F3D73F7D25569@SusumuThinkPad> References: <190F47A30FBC4352BB0F3D73F7D25569@SusumuThinkPad> <7k7ed7$6on869@ipex3.johnshopkins.edu> <7669594.340781237456786669.JavaMail.coremail@bj163app64.163.com> Message-ID: <1839972.211651237472638496.JavaMail.coremail@bj163app171.163.com> Hi,Susumu, thank you, I learned more from you, then is my following description correct? if we have two hypothetical ?real? tracts with Fiber1={pixel1,pixel2,pixel3,pixel4,pixel5} Fiber2={pixel1,pixel2,pixel3,pixel6,pixel7} generally, the value of FA at pixel3 will be decreased because it is a cross point, so, it is possible that the value of FA at pixel3 is less than the threshold, in this case, we will not track to pixel 3 from the seed point, pixel5, thus will generate three parts: streamline1={pixel1,pixel2,pixel3} , seeding from pixel 1 or 2 or 3 streamline2={pixel4,pixel5} seeding from pixel 4 or 5 streamline3={pixel6,pixe7} seeding from pixel 6 or 7 furthermore, if we slelect seed, pixel 1, the principal diffusion direction at the pixel 1 maybe change too much so as to more than the threshold of angle. Is the above correct? 2009-03-19?susumu ? I?m not sure if I understood your question correctly, but let me try. In DtiStudio, fiber tracking is initiated from all pixels in the brain (more precisely pixels with FA above the threshold). Some may think that tracking is initiated from pixels in ROIs, but that is not the case. We draw ROIs just to retrieve fiber tracking results that penetrate the ROIs. For the first case of your fibers, ROI could be Pixel2 and for the Fiber #1, the seed pixel could be Pixel#5 and for the Fiber #2, the seed pixel could be Pixel#7. So, it?s possible. The Case 2 and Case 3 seem not possible because there is no common pixel as your ROI location. Also, suppose we have hypothetical ?real? tract with Fiber1={pixel1,pixel2,pixel3,pixel4,pixel5} Then we may get 5 streamlines after fiber tracking; one seeded from Pixel#1, one from Pixel#2,,,, one from Pixel#5. These 5 streamlines have slightly different coordinates because each tracking starts from the center of each pixel and tracking takes place in floating number coordinates. For quantification, the streamline information is often converted to pixel-by-pixel information. After this conversion, the 5 floating-point streamlines may converted to the identical string of pixels, which is in this case, Fiber1={pixel1,pixel2,pixel3,pixel4,pixel5}. In reality, these 5 streamlines often start to diverge at the peripheral regions while the core areas are likely to share many pixels. From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of vikey.han Sent: Thursday, March 19, 2009 6:00 AM To: DTI Studio ROI Editor Landmarker Questions/Support Subject: Re: [Mristudio-users] Extract values of the Fiber tract ROI Then I have a question, if the two or more fibers share the same sequence of pixels, how does DTIsutio represent the fibers tracked, for example, Fiber1={pixel1,pixel2,pixel3,pixel4,pixel5} Fiber2={pixel1,pixel2,pixel3,pixel6,pixel7} then whether the fiber1 and fiber1 have the same data structure as the above, or Fiber1={pixel1,pixel2,pixel3,pixel4,pixel5} Fiber2={pixel6,pixel7} or maybe DTIStudio generates three fibers: Fiber1={pixel1,pixel2,pixel3} Fiber2={pixel6,pixel7} Fiber3={pixel4,pixel5} Is it possible that the last two cases happening? 2009-03-17?susumu ? >Dear Users, > >Javier raised an important issue and I want to share his results with all of >you. > >Here is what he did; > >1) Did fiber tracking using DtiStudio, use the "statistics" button, and get >an FA value of the entire reconstructed fiber. >2) Save the fiber tracking results as 1/0 binary image, load the file to >RoiEditor, superimpose the binary masking on the FA map, and get an FA value >of the entire reconstructed fiber > >The results were different as indicated in his email. > >This is because the ways FA is measured for the reconstructed tracts are >fundamentally different between the two programs. > >DtiStudio: > >Suppose you have two fibers. One is 10-pixel long and the other is 5-pixel >long. Also suppose that the second 5-pixel fiber shares the same 5 pixels >within the first 10-pixel fiber. This means, the second fiber is completely >contained within the first fiber. > >In DtiStudio, FA is measured along the first fiber. It also measures FA >along the second fiber. The end result is, for example; > >First fiber [0.2, 0.25, 0.3, 0.35, 0.4, 0.45, 0.5, 0.55, 0.6, 0.65] >Second [0.2, 0.25, 0.3, 0.35, 0.4] > >As you can see, the first 5 pixels are identical. Then DtiStudio calculates >the average of the 15 pixels. This means, the first 5 pixels are >"double-counted". > >In this way, DtiStudio provides natural weighting for pixels that contain >more fibers. In reality, some pixels may contains 10s of fibers >(reconstructed streamlines) while some pixels may contain only one fiber. >The more fibers a pixel contains, more weighting it receives, because it >would be counted many more times. > >RoiEditor: > >Once you save the fiber tracking result into 1/0 binary information, all the >streamline information is lost, so as the number of fibers each pixel >contains. In RoiEditor, the binary image can be read and applied to an FA >map as a non-weighted binary masking. > >I hope this explains the difference among the two methods. Because DtiStudio >counts the core white matter regions many more times than peripheral areas, >the average FA values tend to be higher. > >There is nothing like one is better than the other. They are just two >different approaches. Maybe the natural weighting may sound more reasonable >but the non-weighting 1/0 masking should also be a valid approach. You just >need to apply the same method (or both methods) to all data. > >Please let us know if you have any questions regarding this issue. > >Thanks, > >Susumu > > > >________________________________________ >From: Javier Navas [mailto:fjnavas2 at gmail.com] >Sent: Tuesday, March 17, 2009 6:55 AM >To: susumu at mri.jhu.edu; DTI Studio, ROI Editor, Landmarker Questions/Support >Subject: [Mristudio-users] Extract values of the Fiber tract ROI > > >Thank you very much Mr. Susumu, > >with ROI editor I can extract the pixel values in a txt file, that is what I >want, thank you. > >But I have a problem. The FA mean value that results in DTI Studio is >different that the FA mean value that results in ROI editor, with the same >binary image, why occur this?. > >For example, with the same mask of the genu of corpus callosum, I have the >same number of pixels (2835 pixels) but the FA statistics is different. > >DTI studio: > FA > Max. of ImgVal: 0.9690 > Min. of ImgVal: 0.0591 > Mean of ImgVal: 0.5385 > Std. of ImgVal: 0.1689 > >ROI editor: > Min: 0.06 > Max: 0.97 > Mean: 0.45 > Std: 0.17 > >________________________________________ >From: mristudio-users-bounces at mristudio.org >[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Javier Navas >Sent: Thursday, March 12, 2009 8:33 PM >To: DTI Studio, ROI Editor, Landmarker Questions/Support >Subject: Re: [Mristudio-users] Extract values of the Fiber tract ROI > >Hi Susumu, > >I`m talking about the statistics of the fiber tracking results as an ROI. I >want to extract all the voxels values in the FA map that are included in the >corpus callusum tract to a text file. I don`t want only the mean or the >max/minimum value. Becouse I want to do a parcellation of the corpus >callosum and do a correlation of this values with the age or the IQ of the >pacients. > >I?m working with the software some months ago, and I`m new in the list. This >is my first message. Thank you for your answer. > >2009/3/13 susumu >Hi Javier, > >Are you talking about the statistics of the ROI you drew or using the fiber >tracking results as an ROI? > >Susumu > >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >To unsubscribe this mailing list, please go to www.mristudio.org / Mailing >List / Mristudio-users. There you can find the unsubscribe option. >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > >________________________________________ >From: mristudio-users-bounces at mristudio.org >[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Javier Navas >Sent: Wednesday, March 11, 2009 8:15 AM >To: mristudio-users at mristudio.org >Subject: [Mristudio-users] Extract values of the Fiber tract ROI > >Dear all, > >I`m working in Fiber Tracking of the corpus callosum with DTIstudio, > >I want to extract the values of my ROI (the statistics with the number of >fibers selected, length of fibers, FA values...) to a text file or SPSS >archive, but I don`t know how can I do it. > > >Thank you for help me, > >Javier > >_______________________________________________ >Mristudio-users mailing list >Mristudio-users at mristudio.org >http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > >_______________________________________________ >Mristudio-users mailing list >Mristudio-users at mristudio.org >http://lists.mristudio.org/mailman/listinfo/mristudio-users ????????????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090319/eb344b25/attachment-0001.html From jenabi at optonline.net Thu Mar 19 22:55:28 2009 From: jenabi at optonline.net (jenabi at optonline.net) Date: Fri, 20 Mar 2009 02:55:28 +0000 (GMT) Subject: [Mristudio-users] 15-direction gradient table In-Reply-To: <7k7ed7$6pdapu@ipex3.johnshopkins.edu> References: <4ED4B4AD0EB74C6D9EABCBD367536810@ABBY> <7k7ed7$6pdapu@ipex3.johnshopkins.edu> Message-ID: Could you please stop sending me e-mails? ----- Original Message ----- From: susumu Date: Thursday, March 19, 2009 9:46 am Subject: Re: [Mristudio-users] 15-direction gradient table To: "'DTI Studio, ROI Editor, Landmarker Questions/Support'" > > > for which scanner? Or something you can implement in a scanner > by yourself? > Anyway, these are some options you can consider; > > > > Philips "Medium" 15-orientation: > > > > 0: 0, 0, 0 > > 1: 1.0, 0.0, 0.0 > > 2: 0.0, 1.0, 0.0 > > 3: 0.0, 0.0, 1.0 > > 4: -0.1789, -0.1113, -0.9776 > > 5: -0.0635, 0.3767, -0.9242 > > 6: 0.710, 0.0516, -0.7015 > > 7: 0.6191, -0.4385, -0.6515 > > 8: 0.2424, 0.7843, -0.5710 > > 9: -0.2589, -0.6180, -0.7423 > > 10: -0.8169, 0.1697, -0.5513 > > 11: -0.8438, 0.5261, -0.1060 > > 12: -0.2626, 0.9548, -0.1389 > > 13: 0.0001, 0.9689, 0.2476 > > 14: 0.7453, 0.6663, 0.0242 > > 15: 0.9726, 0.2317, 0.0209 > > > > > > GE 15-orientation > > > > 0: 0.000, 0.000, 0.000 > > 1: 0.216, -0.8986, 0.38188 > > 2: -0.444, -0.4187, 0.7918 > > 3: -0.6351, -0.7700, -0.05947 > > 4: 0.500, -0.19253, 0.8440 > > 5: -0.2212, 0.5311, -0.8178 > > 6: -0.8919, 0.07914, -0.4451 > > 7: -0.1693, 0.5134, 0.8412 > > 8: -0.2639, -0.4402, -0.8581 > > 9: 0.59852, 0.00692, -0.8010 > > 10: -0.899, 0.2234, 0.3751 > > 11: 0.9853, -0.1664, 0.0385 > > 12: 0.6279, 0.6270, 0.46098 > > 13: -0.3501, 0.9364, 0.02096 > > 14: 0.5270, 0.7731, -0.3528 > > 15: 0.4206, -0.8041, -0.4200 > > > > There are Jones10 and Jones20, but I am not sure if there is > Jones15. > > > > _____ > > From: mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Abby Ding > Sent: Thursday, March 19, 2009 6:01 AM > To: MRIstudio > Subject: [Mristudio-users] 15-direction gradient table > > > > Dear users, > > > > Does any one of you have a 15-direction gradient table to share > with me? > > > > Thank you very much for your kindly help! > > > > Best Regards, > > Abby > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090320/40fb8c69/attachment.html From jnavarro at bcm.tmc.edu Fri Mar 20 10:32:19 2009 From: jnavarro at bcm.tmc.edu (Cruz Navarro, Jovany) Date: Fri, 20 Mar 2009 09:32:19 -0500 Subject: [Mristudio-users] 15-direction gradient table References: <4ED4B4AD0EB74C6D9EABCBD367536810@ABBY> <7k7ed7$6pdapu@ipex3.johnshopkins.edu> Message-ID: <5F4CE8876744A34C8B58096BCD979F6734EF2B@BCMEVS15.ad.bcm.edu> Could you please stop sending me e-mails? ________________________________ From: mristudio-users-bounces at mristudio.org on behalf of jenabi at optonline.net Sent: Thu 3/19/2009 9:55 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] 15-direction gradient table Could you please stop sending me e-mails? ----- Original Message ----- From: susumu Date: Thursday, March 19, 2009 9:46 am Subject: Re: [Mristudio-users] 15-direction gradient table To: "'DTI Studio, ROI Editor, Landmarker Questions/Support'" > > > for which scanner? Or something you can implement in a scanner > by yourself? > Anyway, these are some options you can consider; > > > > Philips "Medium" 15-orientation: > > > > 0: 0, 0, 0 > > 1: 1.0, 0.0, 0.0 > > 2: 0.0, 1.0, 0.0 > > 3: 0.0, 0.0, 1.0 > > 4: -0.1789, -0.1113, -0.9776 > > 5: -0.0635, 0.3767, -0.9242 > > 6: 0.710, 0.0516, -0.7015 > > 7: 0.6191, -0.4385, -0.6515 > > 8: 0.2424, 0.7843, -0.5710 > > 9: -0.2589, -0.6180, -0.7423 > > 10: -0.8169, 0.1697, -0.5513 > > 11: -0.8438, 0.5261, -0.1060 > > 12: -0.2626, 0.9548, -0.1389 > > 13: 0.0001, 0.9689, 0.2476 > > 14: 0.7453, 0.6663, 0.0242 > > 15: 0.9726, 0.2317, 0.0209 > > > > > > GE 15-orientation > > > > 0: 0.000, 0.000, 0.000 > > 1: 0.216, -0.8986, 0.38188 > > 2: -0.444, -0.4187, 0.7918 > > 3: -0.6351, -0.7700, -0.05947 > > 4: 0.500, -0.19253, 0.8440 > > 5: -0.2212, 0.5311, -0.8178 > > 6: -0.8919, 0.07914, -0.4451 > > 7: -0.1693, 0.5134, 0.8412 > > 8: -0.2639, -0.4402, -0.8581 > > 9: 0.59852, 0.00692, -0.8010 > > 10: -0.899, 0.2234, 0.3751 > > 11: 0.9853, -0.1664, 0.0385 > > 12: 0.6279, 0.6270, 0.46098 > > 13: -0.3501, 0.9364, 0.02096 > > 14: 0.5270, 0.7731, -0.3528 > > 15: 0.4206, -0.8041, -0.4200 > > > > There are Jones10 and Jones20, but I am not sure if there is > Jones15. > > > > _____ > > From: mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Abby Ding > Sent: Thursday, March 19, 2009 6:01 AM > To: MRIstudio > Subject: [Mristudio-users] 15-direction gradient table > > > > Dear users, > > > > Does any one of you have a 15-direction gradient table to share > with me? > > > > Thank you very much for your kindly help! > > > > Best Regards, > > Abby > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090320/3deba1bf/attachment.html From zhongsuyu123 at 163.com Mon Mar 23 00:14:02 2009 From: zhongsuyu123 at 163.com (zhongsuyu123) Date: Mon, 23 Mar 2009 12:14:02 +0800 (CST) Subject: [Mristudio-users] About the registration of the rat brain Message-ID: <27953703.177261237781642887.JavaMail.coremail@bj163app98.163.com> Hi, I want to kown where I can get the template of the rat brain.In the Landermarker,I can only load the Human's template.Are there any templates for registration of the rat brain? If not, how can I do the registration of the rat brain. Thank you. Suyu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090323/27ab6618/attachment.html From pabeach1 at gmail.com Wed Mar 25 13:55:51 2009 From: pabeach1 at gmail.com (Paul Beach) Date: Wed, 25 Mar 2009 13:55:51 -0400 Subject: [Mristudio-users] Problem with Landmarker not loading subjects Message-ID: <8874e3900903251055o49f6detf48792a6ff04fee1@mail.gmail.com> Hi everyone, So every once and a while I'll be on Landmarker and when I'm trying to load a subject I'll receive an error message saying "please enter a number between 0 and 4096." The first time this happened I just closed all my programs and reopened Landmarker and things worked again. Other times (such as the latest one) I went so far as to restart my computer, which lead to no effect. This is obviously a huge problem as I can't load subjects whatsoever. Any ideas? Thanks, Paul p.s. In case this is necessary information, I've been using landmarks to reorient subject brains and fiber tracts using affine/rigid transformations. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090325/e7780f9b/attachment.html From xli16 at jhmi.edu Wed Mar 25 15:02:36 2009 From: xli16 at jhmi.edu (XIN LI) Date: Wed, 25 Mar 2009 15:02:36 -0400 Subject: [Mristudio-users] Problem with Landmarker not loading subjects In-Reply-To: <8874e3900903251055o49f6detf48792a6ff04fee1@mail.gmail.com> References: <8874e3900903251055o49f6detf48792a6ff04fee1@mail.gmail.com> Message-ID: Paul, When you loaded the subject, if the subject is a raw image, did you input the corresponding parameters of the subject in the image parameters window? These parameters are Image Width, Image Height, Slice Orientation, Fov Width, Fov Height, Slice Thickness and Image Data Format. You need to make sure the values of these parameters are the right ones for the subject. Xin ----- Original Message ----- From: Paul Beach Date: Wednesday, March 25, 2009 1:56 pm Subject: [Mristudio-users] Problem with Landmarker not loading subjects To: Mristudio-users at mristudio.org > Hi everyone, > > So every once and a while I'll be on Landmarker and when I'm trying > to load > a subject I'll receive an error message saying "please enter a number > between 0 and 4096." The first time this happened I just closed all > my > programs and reopened Landmarker and things worked again. Other > times (such > as the latest one) I went so far as to restart my computer, which > lead to no > effect. > > This is obviously a huge problem as I can't load subjects whatsoever. > > Any ideas? > > Thanks, > > Paul > > p.s. In case this is necessary information, I've been using landmarks > to > reorient subject brains and fiber tracts using affine/rigid transformations. > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > From pabeach1 at gmail.com Wed Mar 25 15:23:39 2009 From: pabeach1 at gmail.com (Paul Beach) Date: Wed, 25 Mar 2009 15:23:39 -0400 Subject: [Mristudio-users] Mristudio-users Digest, Vol 14, Issue 19 In-Reply-To: References: Message-ID: <8874e3900903251223j5b13e077pc37a5308d3bd9149@mail.gmail.com> Xin, Thanks for the reply. The problem with your suggestion is the image files are in fact not raw, they're analyze (.img, or .hdr). Any other suggestions? On Wed, Mar 25, 2009 at 3:02 PM, wrote: > Send Mristudio-users mailing list submissions to > mristudio-users at mristudio.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.mristudio.org/mailman/listinfo/mristudio-users > or, via email, send a message with subject or body 'help' to > mristudio-users-request at mristudio.org > > You can reach the person managing the list at > mristudio-users-owner at mristudio.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Mristudio-users digest..." > > > Today's Topics: > > 1. Re: 15-direction gradient table (jenabi at optonline.net) > 2. Re: 15-direction gradient table (Cruz Navarro, Jovany) > 3. About the registration of the rat brain (zhongsuyu123) > 4. Problem with Landmarker not loading subjects (Paul Beach) > 5. Re: Problem with Landmarker not loading subjects (XIN LI) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 20 Mar 2009 02:55:28 +0000 (GMT) > From: jenabi at optonline.net > Subject: Re: [Mristudio-users] 15-direction gradient table > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > > Message-ID: > Content-Type: text/plain; charset="us-ascii" > > Could you please stop sending me e-mails? > > ----- Original Message ----- > From: susumu > Date: Thursday, March 19, 2009 9:46 am > Subject: Re: [Mristudio-users] 15-direction gradient table > To: "'DTI Studio, ROI Editor, Landmarker Questions/Support'" > > > > > > > for which scanner? Or something you can implement in a scanner > > by yourself? > > Anyway, these are some options you can consider; > > > > > > > > Philips "Medium" 15-orientation: > > > > > > > > 0: 0, 0, 0 > > > > 1: 1.0, 0.0, 0.0 > > > > 2: 0.0, 1.0, 0.0 > > > > 3: 0.0, 0.0, 1.0 > > > > 4: -0.1789, -0.1113, -0.9776 > > > > 5: -0.0635, 0.3767, -0.9242 > > > > 6: 0.710, 0.0516, -0.7015 > > > > 7: 0.6191, -0.4385, -0.6515 > > > > 8: 0.2424, 0.7843, -0.5710 > > > > 9: -0.2589, -0.6180, -0.7423 > > > > 10: -0.8169, 0.1697, -0.5513 > > > > 11: -0.8438, 0.5261, -0.1060 > > > > 12: -0.2626, 0.9548, -0.1389 > > > > 13: 0.0001, 0.9689, 0.2476 > > > > 14: 0.7453, 0.6663, 0.0242 > > > > 15: 0.9726, 0.2317, 0.0209 > > > > > > > > > > > > GE 15-orientation > > > > > > > > 0: 0.000, 0.000, 0.000 > > > > 1: 0.216, -0.8986, 0.38188 > > > > 2: -0.444, -0.4187, 0.7918 > > > > 3: -0.6351, -0.7700, -0.05947 > > > > 4: 0.500, -0.19253, 0.8440 > > > > 5: -0.2212, 0.5311, -0.8178 > > > > 6: -0.8919, 0.07914, -0.4451 > > > > 7: -0.1693, 0.5134, 0.8412 > > > > 8: -0.2639, -0.4402, -0.8581 > > > > 9: 0.59852, 0.00692, -0.8010 > > > > 10: -0.899, 0.2234, 0.3751 > > > > 11: 0.9853, -0.1664, 0.0385 > > > > 12: 0.6279, 0.6270, 0.46098 > > > > 13: -0.3501, 0.9364, 0.02096 > > > > 14: 0.5270, 0.7731, -0.3528 > > > > 15: 0.4206, -0.8041, -0.4200 > > > > > > > > There are Jones10 and Jones20, but I am not sure if there is > > Jones15. > > > > > > > > _____ > > > > From: mristudio-users-bounces at mristudio.org > > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Abby Ding > > Sent: Thursday, March 19, 2009 6:01 AM > > To: MRIstudio > > Subject: [Mristudio-users] 15-direction gradient table > > > > > > > > Dear users, > > > > > > > > Does any one of you have a 15-direction gradient table to share > > with me? > > > > > > > > Thank you very much for your kindly help! > > > > > > > > Best Regards, > > > > Abby > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090320/40fb8c69/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Fri, 20 Mar 2009 09:32:19 -0500 > From: "Cruz Navarro, Jovany" > Subject: Re: [Mristudio-users] 15-direction gradient table > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > > Message-ID: > <5F4CE8876744A34C8B58096BCD979F6734EF2B at BCMEVS15.ad.bcm.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Could you please stop sending me e-mails? > > ________________________________ > > From: mristudio-users-bounces at mristudio.org on behalf of > jenabi at optonline.net > Sent: Thu 3/19/2009 9:55 PM > To: DTI Studio, ROI Editor, Landmarker Questions/Support > Subject: Re: [Mristudio-users] 15-direction gradient table > > > Could you please stop sending me e-mails? > > ----- Original Message ----- > From: susumu > Date: Thursday, March 19, 2009 9:46 am > Subject: Re: [Mristudio-users] 15-direction gradient table > To: "'DTI Studio, ROI Editor, Landmarker Questions/Support'" > > > > > > > for which scanner? Or something you can implement in a scanner > > by yourself? > > Anyway, these are some options you can consider; > > > > > > > > Philips "Medium" 15-orientation: > > > > > > > > 0: 0, 0, 0 > > > > 1: 1.0, 0.0, 0.0 > > > > 2: 0.0, 1.0, 0.0 > > > > 3: 0.0, 0.0, 1.0 > > > > 4: -0.1789, -0.1113, -0.9776 > > > > 5: -0.0635, 0.3767, -0.9242 > > > > 6: 0.710, 0.0516, -0.7015 > > > > 7: 0.6191, -0.4385, -0.6515 > > > > 8: 0.2424, 0.7843, -0.5710 > > > > 9: -0.2589, -0.6180, -0.7423 > > > > 10: -0.8169, 0.1697, -0.5513 > > > > 11: -0.8438, 0.5261, -0.1060 > > > > 12: -0.2626, 0.9548, -0.1389 > > > > 13: 0.0001, 0.9689, 0.2476 > > > > 14: 0.7453, 0.6663, 0.0242 > > > > 15: 0.9726, 0.2317, 0.0209 > > > > > > > > > > > > GE 15-orientation > > > > > > > > 0: 0.000, 0.000, 0.000 > > > > 1: 0.216, -0.8986, 0.38188 > > > > 2: -0.444, -0.4187, 0.7918 > > > > 3: -0.6351, -0.7700, -0.05947 > > > > 4: 0.500, -0.19253, 0.8440 > > > > 5: -0.2212, 0.5311, -0.8178 > > > > 6: -0.8919, 0.07914, -0.4451 > > > > 7: -0.1693, 0.5134, 0.8412 > > > > 8: -0.2639, -0.4402, -0.8581 > > > > 9: 0.59852, 0.00692, -0.8010 > > > > 10: -0.899, 0.2234, 0.3751 > > > > 11: 0.9853, -0.1664, 0.0385 > > > > 12: 0.6279, 0.6270, 0.46098 > > > > 13: -0.3501, 0.9364, 0.02096 > > > > 14: 0.5270, 0.7731, -0.3528 > > > > 15: 0.4206, -0.8041, -0.4200 > > > > > > > > There are Jones10 and Jones20, but I am not sure if there is > > Jones15. > > > > > > > > _____ > > > > From: mristudio-users-bounces at mristudio.org > > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Abby Ding > > Sent: Thursday, March 19, 2009 6:01 AM > > To: MRIstudio > > Subject: [Mristudio-users] 15-direction gradient table > > > > > > > > Dear users, > > > > > > > > Does any one of you have a 15-direction gradient table to share > > with me? > > > > > > > > Thank you very much for your kindly help! > > > > > > > > Best Regards, > > > > Abby > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090320/3deba1bf/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: Mon, 23 Mar 2009 12:14:02 +0800 (CST) > From: zhongsuyu123 > Subject: [Mristudio-users] About the registration of the rat brain > To: mristudio-users at mristudio.org > Message-ID: > <27953703.177261237781642887.JavaMail.coremail at bj163app98.163.com> > Content-Type: text/plain; charset="gbk" > > Hi, > I want to kown where I can get the template of the rat brain.In the > Landermarker,I can only load the Human's template.Are there any templates > for registration of the rat brain? If not, how can I do the registration of > the rat brain. > Thank you. > Suyu > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090323/27ab6618/attachment-0001.html > > ------------------------------ > > Message: 4 > Date: Wed, 25 Mar 2009 13:55:51 -0400 > From: Paul Beach > Subject: [Mristudio-users] Problem with Landmarker not loading > subjects > To: Mristudio-users at mristudio.org > Message-ID: > <8874e3900903251055o49f6detf48792a6ff04fee1 at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi everyone, > > So every once and a while I'll be on Landmarker and when I'm trying to load > a subject I'll receive an error message saying "please enter a number > between 0 and 4096." The first time this happened I just closed all my > programs and reopened Landmarker and things worked again. Other times > (such > as the latest one) I went so far as to restart my computer, which lead to > no > effect. > > This is obviously a huge problem as I can't load subjects whatsoever. > > Any ideas? > > Thanks, > > Paul > > p.s. In case this is necessary information, I've been using landmarks to > reorient subject brains and fiber tracts using affine/rigid > transformations. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090325/e7780f9b/attachment-0001.html > > ------------------------------ > > Message: 5 > Date: Wed, 25 Mar 2009 15:02:36 -0400 > From: XIN LI > Subject: Re: [Mristudio-users] Problem with Landmarker not loading > subjects > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > > Message-ID: > Content-Type: text/plain; charset=us-ascii > > Paul, > > When you loaded the subject, if the subject is a raw image, did you input > the corresponding parameters of the subject in the image parameters window? > These parameters are Image Width, Image Height, Slice Orientation, Fov > Width, Fov Height, Slice Thickness and Image Data Format. You need to make > sure the values of these parameters are the right ones for the subject. > > > Xin > > > > > ----- Original Message ----- > From: Paul Beach > Date: Wednesday, March 25, 2009 1:56 pm > Subject: [Mristudio-users] Problem with Landmarker not loading subjects > To: Mristudio-users at mristudio.org > > > > Hi everyone, > > > > So every once and a while I'll be on Landmarker and when I'm trying > > to load > > a subject I'll receive an error message saying "please enter a number > > between 0 and 4096." The first time this happened I just closed all > > my > > programs and reopened Landmarker and things worked again. Other > > times (such > > as the latest one) I went so far as to restart my computer, which > > lead to no > > effect. > > > > This is obviously a huge problem as I can't load subjects whatsoever. > > > > Any ideas? > > > > Thanks, > > > > Paul > > > > p.s. In case this is necessary information, I've been using landmarks > > to > > reorient subject brains and fiber tracts using affine/rigid > transformations. > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > > ------------------------------ > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > End of Mristudio-users Digest, Vol 14, Issue 19 > *********************************************** > -- Paul Beach Michigan State University College of Osteopathic Medicine - Medical Scientist Training Program Neuroscience Program -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090325/49f28aa2/attachment-0001.html From kimdoyeon at gmail.com Wed Mar 25 15:25:37 2009 From: kimdoyeon at gmail.com (Doyeon Kim) Date: Wed, 25 Mar 2009 15:25:37 -0400 Subject: [Mristudio-users] Mristudio-users Digest, Vol 14, Issue 19 In-Reply-To: <8874e3900903251223j5b13e077pc37a5308d3bd9149@mail.gmail.com> References: <8874e3900903251223j5b13e077pc37a5308d3bd9149@mail.gmail.com> Message-ID: Please remove me from this list. 2009/3/25 Paul Beach > Xin, > > Thanks for the reply. The problem with your suggestion is the image files > are in fact not raw, they're analyze (.img, or .hdr). Any other > suggestions? > > > > > > On Wed, Mar 25, 2009 at 3:02 PM, wrote: > >> Send Mristudio-users mailing list submissions to >> mristudio-users at mristudio.org >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://lists.mristudio.org/mailman/listinfo/mristudio-users >> or, via email, send a message with subject or body 'help' to >> mristudio-users-request at mristudio.org >> >> You can reach the person managing the list at >> mristudio-users-owner at mristudio.org >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Mristudio-users digest..." >> >> >> Today's Topics: >> >> 1. Re: 15-direction gradient table (jenabi at optonline.net) >> 2. Re: 15-direction gradient table (Cruz Navarro, Jovany) >> 3. About the registration of the rat brain (zhongsuyu123) >> 4. Problem with Landmarker not loading subjects (Paul Beach) >> 5. Re: Problem with Landmarker not loading subjects (XIN LI) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Fri, 20 Mar 2009 02:55:28 +0000 (GMT) >> From: jenabi at optonline.net >> Subject: Re: [Mristudio-users] 15-direction gradient table >> To: "DTI Studio, ROI Editor, Landmarker Questions/Support" >> >> Message-ID: >> Content-Type: text/plain; charset="us-ascii" >> >> Could you please stop sending me e-mails? >> >> ----- Original Message ----- >> From: susumu >> Date: Thursday, March 19, 2009 9:46 am >> Subject: Re: [Mristudio-users] 15-direction gradient table >> To: "'DTI Studio, ROI Editor, Landmarker Questions/Support'" >> >> > >> > >> > for which scanner? Or something you can implement in a scanner >> > by yourself? >> > Anyway, these are some options you can consider; >> > >> > >> > >> > Philips "Medium" 15-orientation: >> > >> > >> > >> > 0: 0, 0, 0 >> > >> > 1: 1.0, 0.0, 0.0 >> > >> > 2: 0.0, 1.0, 0.0 >> > >> > 3: 0.0, 0.0, 1.0 >> > >> > 4: -0.1789, -0.1113, -0.9776 >> > >> > 5: -0.0635, 0.3767, -0.9242 >> > >> > 6: 0.710, 0.0516, -0.7015 >> > >> > 7: 0.6191, -0.4385, -0.6515 >> > >> > 8: 0.2424, 0.7843, -0.5710 >> > >> > 9: -0.2589, -0.6180, -0.7423 >> > >> > 10: -0.8169, 0.1697, -0.5513 >> > >> > 11: -0.8438, 0.5261, -0.1060 >> > >> > 12: -0.2626, 0.9548, -0.1389 >> > >> > 13: 0.0001, 0.9689, 0.2476 >> > >> > 14: 0.7453, 0.6663, 0.0242 >> > >> > 15: 0.9726, 0.2317, 0.0209 >> > >> > >> > >> > >> > >> > GE 15-orientation >> > >> > >> > >> > 0: 0.000, 0.000, 0.000 >> > >> > 1: 0.216, -0.8986, 0.38188 >> > >> > 2: -0.444, -0.4187, 0.7918 >> > >> > 3: -0.6351, -0.7700, -0.05947 >> > >> > 4: 0.500, -0.19253, 0.8440 >> > >> > 5: -0.2212, 0.5311, -0.8178 >> > >> > 6: -0.8919, 0.07914, -0.4451 >> > >> > 7: -0.1693, 0.5134, 0.8412 >> > >> > 8: -0.2639, -0.4402, -0.8581 >> > >> > 9: 0.59852, 0.00692, -0.8010 >> > >> > 10: -0.899, 0.2234, 0.3751 >> > >> > 11: 0.9853, -0.1664, 0.0385 >> > >> > 12: 0.6279, 0.6270, 0.46098 >> > >> > 13: -0.3501, 0.9364, 0.02096 >> > >> > 14: 0.5270, 0.7731, -0.3528 >> > >> > 15: 0.4206, -0.8041, -0.4200 >> > >> > >> > >> > There are Jones10 and Jones20, but I am not sure if there is >> > Jones15. >> > >> > >> > >> > _____ >> > >> > From: mristudio-users-bounces at mristudio.org >> > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Abby Ding >> > Sent: Thursday, March 19, 2009 6:01 AM >> > To: MRIstudio >> > Subject: [Mristudio-users] 15-direction gradient table >> > >> > >> > >> > Dear users, >> > >> > >> > >> > Does any one of you have a 15-direction gradient table to share >> > with me? >> > >> > >> > >> > Thank you very much for your kindly help! >> > >> > >> > >> > Best Regards, >> > >> > Abby >> > >> > >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090320/40fb8c69/attachment-0001.html >> >> ------------------------------ >> >> Message: 2 >> Date: Fri, 20 Mar 2009 09:32:19 -0500 >> From: "Cruz Navarro, Jovany" >> Subject: Re: [Mristudio-users] 15-direction gradient table >> To: "DTI Studio, ROI Editor, Landmarker Questions/Support" >> >> Message-ID: >> <5F4CE8876744A34C8B58096BCD979F6734EF2B at BCMEVS15.ad.bcm.edu> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Could you please stop sending me e-mails? >> >> ________________________________ >> >> From: mristudio-users-bounces at mristudio.org on behalf of >> jenabi at optonline.net >> Sent: Thu 3/19/2009 9:55 PM >> To: DTI Studio, ROI Editor, Landmarker Questions/Support >> Subject: Re: [Mristudio-users] 15-direction gradient table >> >> >> Could you please stop sending me e-mails? >> >> ----- Original Message ----- >> From: susumu >> Date: Thursday, March 19, 2009 9:46 am >> Subject: Re: [Mristudio-users] 15-direction gradient table >> To: "'DTI Studio, ROI Editor, Landmarker Questions/Support'" >> >> > >> > >> > for which scanner? Or something you can implement in a scanner >> > by yourself? >> > Anyway, these are some options you can consider; >> > >> > >> > >> > Philips "Medium" 15-orientation: >> > >> > >> > >> > 0: 0, 0, 0 >> > >> > 1: 1.0, 0.0, 0.0 >> > >> > 2: 0.0, 1.0, 0.0 >> > >> > 3: 0.0, 0.0, 1.0 >> > >> > 4: -0.1789, -0.1113, -0.9776 >> > >> > 5: -0.0635, 0.3767, -0.9242 >> > >> > 6: 0.710, 0.0516, -0.7015 >> > >> > 7: 0.6191, -0.4385, -0.6515 >> > >> > 8: 0.2424, 0.7843, -0.5710 >> > >> > 9: -0.2589, -0.6180, -0.7423 >> > >> > 10: -0.8169, 0.1697, -0.5513 >> > >> > 11: -0.8438, 0.5261, -0.1060 >> > >> > 12: -0.2626, 0.9548, -0.1389 >> > >> > 13: 0.0001, 0.9689, 0.2476 >> > >> > 14: 0.7453, 0.6663, 0.0242 >> > >> > 15: 0.9726, 0.2317, 0.0209 >> > >> > >> > >> > >> > >> > GE 15-orientation >> > >> > >> > >> > 0: 0.000, 0.000, 0.000 >> > >> > 1: 0.216, -0.8986, 0.38188 >> > >> > 2: -0.444, -0.4187, 0.7918 >> > >> > 3: -0.6351, -0.7700, -0.05947 >> > >> > 4: 0.500, -0.19253, 0.8440 >> > >> > 5: -0.2212, 0.5311, -0.8178 >> > >> > 6: -0.8919, 0.07914, -0.4451 >> > >> > 7: -0.1693, 0.5134, 0.8412 >> > >> > 8: -0.2639, -0.4402, -0.8581 >> > >> > 9: 0.59852, 0.00692, -0.8010 >> > >> > 10: -0.899, 0.2234, 0.3751 >> > >> > 11: 0.9853, -0.1664, 0.0385 >> > >> > 12: 0.6279, 0.6270, 0.46098 >> > >> > 13: -0.3501, 0.9364, 0.02096 >> > >> > 14: 0.5270, 0.7731, -0.3528 >> > >> > 15: 0.4206, -0.8041, -0.4200 >> > >> > >> > >> > There are Jones10 and Jones20, but I am not sure if there is >> > Jones15. >> > >> > >> > >> > _____ >> > >> > From: mristudio-users-bounces at mristudio.org >> > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Abby Ding >> > Sent: Thursday, March 19, 2009 6:01 AM >> > To: MRIstudio >> > Subject: [Mristudio-users] 15-direction gradient table >> > >> > >> > >> > Dear users, >> > >> > >> > >> > Does any one of you have a 15-direction gradient table to share >> > with me? >> > >> > >> > >> > Thank you very much for your kindly help! >> > >> > >> > >> > Best Regards, >> > >> > Abby >> > >> > >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090320/3deba1bf/attachment-0001.html >> >> ------------------------------ >> >> Message: 3 >> Date: Mon, 23 Mar 2009 12:14:02 +0800 (CST) >> From: zhongsuyu123 >> Subject: [Mristudio-users] About the registration of the rat brain >> To: mristudio-users at mristudio.org >> Message-ID: >> <27953703.177261237781642887.JavaMail.coremail at bj163app98.163.com> >> Content-Type: text/plain; charset="gbk" >> >> Hi, >> I want to kown where I can get the template of the rat brain.In the >> Landermarker,I can only load the Human's template.Are there any templates >> for registration of the rat brain? If not, how can I do the registration of >> the rat brain. >> Thank you. >> Suyu >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090323/27ab6618/attachment-0001.html >> >> ------------------------------ >> >> Message: 4 >> Date: Wed, 25 Mar 2009 13:55:51 -0400 >> From: Paul Beach >> Subject: [Mristudio-users] Problem with Landmarker not loading >> subjects >> To: Mristudio-users at mristudio.org >> Message-ID: >> <8874e3900903251055o49f6detf48792a6ff04fee1 at mail.gmail.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Hi everyone, >> >> So every once and a while I'll be on Landmarker and when I'm trying to >> load >> a subject I'll receive an error message saying "please enter a number >> between 0 and 4096." The first time this happened I just closed all my >> programs and reopened Landmarker and things worked again. Other times >> (such >> as the latest one) I went so far as to restart my computer, which lead to >> no >> effect. >> >> This is obviously a huge problem as I can't load subjects whatsoever. >> >> Any ideas? >> >> Thanks, >> >> Paul >> >> p.s. In case this is necessary information, I've been using landmarks to >> reorient subject brains and fiber tracts using affine/rigid >> transformations. >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090325/e7780f9b/attachment-0001.html >> >> ------------------------------ >> >> Message: 5 >> Date: Wed, 25 Mar 2009 15:02:36 -0400 >> From: XIN LI >> Subject: Re: [Mristudio-users] Problem with Landmarker not loading >> subjects >> To: "DTI Studio, ROI Editor, Landmarker Questions/Support" >> >> Message-ID: >> Content-Type: text/plain; charset=us-ascii >> >> Paul, >> >> When you loaded the subject, if the subject is a raw image, did you input >> the corresponding parameters of the subject in the image parameters window? >> These parameters are Image Width, Image Height, Slice Orientation, Fov >> Width, Fov Height, Slice Thickness and Image Data Format. You need to make >> sure the values of these parameters are the right ones for the subject. >> >> >> Xin >> >> >> >> >> ----- Original Message ----- >> From: Paul Beach >> Date: Wednesday, March 25, 2009 1:56 pm >> Subject: [Mristudio-users] Problem with Landmarker not loading subjects >> To: Mristudio-users at mristudio.org >> >> >> > Hi everyone, >> > >> > So every once and a while I'll be on Landmarker and when I'm trying >> > to load >> > a subject I'll receive an error message saying "please enter a number >> > between 0 and 4096." The first time this happened I just closed all >> > my >> > programs and reopened Landmarker and things worked again. Other >> > times (such >> > as the latest one) I went so far as to restart my computer, which >> > lead to no >> > effect. >> > >> > This is obviously a huge problem as I can't load subjects whatsoever. >> > >> > Any ideas? >> > >> > Thanks, >> > >> > Paul >> > >> > p.s. In case this is necessary information, I've been using landmarks >> > to >> > reorient subject brains and fiber tracts using affine/rigid >> transformations. >> > _______________________________________________ >> > Mristudio-users mailing list >> > Mristudio-users at mristudio.org >> > >> >> >> ------------------------------ >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/mristudio-users >> >> >> End of Mristudio-users Digest, Vol 14, Issue 19 >> *********************************************** >> > > > > -- > Paul Beach > Michigan State University > College of Osteopathic Medicine > - Medical Scientist Training Program > Neuroscience Program > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090325/f529276e/attachment-0001.html From darshanp20 at yahoo.com Wed Mar 25 16:39:02 2009 From: darshanp20 at yahoo.com (darshan pai) Date: Wed, 25 Mar 2009 13:39:02 -0700 (PDT) Subject: [Mristudio-users] Mristudio-users Digest, Vol 14, Issue 19 In-Reply-To: <8874e3900903251223j5b13e077pc37a5308d3bd9149@mail.gmail.com> References: <8874e3900903251223j5b13e077pc37a5308d3bd9149@mail.gmail.com> Message-ID: <314704.88159.qm@web30707.mail.mud.yahoo.com> Never really got that error . But DTI Studio has an option to convert from analyze to raw. I find it easier to work with raw in Landmarker, so I usually convert everything , and reconvert back after .. ________________________________ From: Paul Beach To: mristudio-users at mristudio.org Sent: Wednesday, March 25, 2009 3:23:39 PM Subject: Re: [Mristudio-users] Mristudio-users Digest, Vol 14, Issue 19 Xin, Thanks for the reply. The problem with your suggestion is the image files are in fact not raw, they're analyze (.img, or .hdr). Any other suggestions? On Wed, Mar 25, 2009 at 3:02 PM, wrote: Send Mristudio-users mailing list submissions to mristudio-users at mristudio.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.mristudio.org/mailman/listinfo/mristudio-users or, via email, send a message with subject or body 'help' to mristudio-users-request at mristudio.org You can reach the person managing the list at mristudio-users-owner at mristudio.org When replying, please edit your Subject line so it is more specific than "Re: Contents of Mristudio-users digest..." Today's Topics: 1. Re: 15-direction gradient table (jenabi at optonline.net) 2. Re: 15-direction gradient table (Cruz Navarro, Jovany) 3. About the registration of the rat brain (zhongsuyu123) 4. Problem with Landmarker not loading subjects (Paul Beach) 5. Re: Problem with Landmarker not loading subjects (XIN LI) ---------------------------------------------------------------------- Message: 1 Date: Fri, 20 Mar 2009 02:55:28 +0000 (GMT) From: jenabi at optonline.net Subject: Re: [Mristudio-users] 15-direction gradient table To: "DTI Studio, ROI Editor, Landmarker Questions/Support" Message-ID: Content-Type: text/plain; charset="us-ascii" Could you please stop sending me e-mails? ----- Original Message ----- From: susumu Date: Thursday, March 19, 2009 9:46 am Subject: Re: [Mristudio-users] 15-direction gradient table To: "'DTI Studio, ROI Editor, Landmarker Questions/Support'" > > > for which scanner? Or something you can implement in a scanner > by yourself? > Anyway, these are some options you can consider; > > > > Philips "Medium" 15-orientation: > > > > 0: 0, 0, 0 > > 1: 1.0, 0.0, 0.0 > > 2: 0.0, 1.0, 0.0 > > 3: 0.0, 0.0, 1.0 > > 4: -0.1789, -0.1113, -0.9776 > > 5: -0.0635, 0.3767, -0.9242 > > 6: 0.710, 0.0516, -0.7015 > > 7: 0.6191, -0.4385, -0.6515 > > 8: 0.2424, 0.7843, -0.5710 > > 9: -0.2589, -0.6180, -0.7423 > > 10: -0.8169, 0.1697, -0.5513 > > 11: -0.8438, 0.5261, -0.1060 > > 12: -0.2626, 0.9548, -0.1389 > > 13: 0.0001, 0.9689, 0.2476 > > 14: 0.7453, 0.6663, 0.0242 > > 15: 0.9726, 0.2317, 0.0209 > > > > > > GE 15-orientation > > > > 0: 0.000, 0.000, 0.000 > > 1: 0.216, -0.8986, 0.38188 > > 2: -0.444, -0.4187, 0.7918 > > 3: -0.6351, -0.7700, -0.05947 > > 4: 0.500, -0.19253, 0.8440 > > 5: -0.2212, 0.5311, -0.8178 > > 6: -0.8919, 0.07914, -0.4451 > > 7: -0.1693, 0.5134, 0.8412 > > 8: -0.2639, -0.4402, -0.8581 > > 9: 0.59852, 0.00692, -0.8010 > > 10: -0.899, 0.2234, 0.3751 > > 11: 0.9853, -0.1664, 0.0385 > > 12: 0.6279, 0.6270, 0.46098 > > 13: -0.3501, 0.9364, 0.02096 > > 14: 0.5270, 0.7731, -0.3528 > > 15: 0.4206, -0.8041, -0.4200 > > > > There are Jones10 and Jones20, but I am not sure if there is > Jones15. > > > > _____ > > From: mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Abby Ding > Sent: Thursday, March 19, 2009 6:01 AM > To: MRIstudio > Subject: [Mristudio-users] 15-direction gradient table > > > > Dear users, > > > > Does any one of you have a 15-direction gradient table to share > with me? > > > > Thank you very much for your kindly help! > > > > Best Regards, > > Abby > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090320/40fb8c69/attachment-0001.html ------------------------------ Message: 2 Date: Fri, 20 Mar 2009 09:32:19 -0500 From: "Cruz Navarro, Jovany" Subject: Re: [Mristudio-users] 15-direction gradient table To: "DTI Studio, ROI Editor, Landmarker Questions/Support" Message-ID: <5F4CE8876744A34C8B58096BCD979F6734EF2B at BCMEVS15.ad.bcm.edu> Content-Type: text/plain; charset="iso-8859-1" Could you please stop sending me e-mails? ________________________________ From: mristudio-users-bounces at mristudio.org on behalf of jenabi at optonline.net Sent: Thu 3/19/2009 9:55 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] 15-direction gradient table Could you please stop sending me e-mails? ----- Original Message ----- From: susumu Date: Thursday, March 19, 2009 9:46 am Subject: Re: [Mristudio-users] 15-direction gradient table To: "'DTI Studio, ROI Editor, Landmarker Questions/Support'" > > > for which scanner? Or something you can implement in a scanner > by yourself? > Anyway, these are some options you can consider; > > > > Philips "Medium" 15-orientation: > > > > 0: 0, 0, 0 > > 1: 1.0, 0.0, 0.0 > > 2: 0.0, 1.0, 0.0 > > 3: 0.0, 0.0, 1.0 > > 4: -0.1789, -0.1113, -0.9776 > > 5: -0.0635, 0.3767, -0.9242 > > 6: 0.710, 0.0516, -0.7015 > > 7: 0.6191, -0.4385, -0.6515 > > 8: 0.2424, 0.7843, -0.5710 > > 9: -0.2589, -0.6180, -0.7423 > > 10: -0.8169, 0.1697, -0.5513 > > 11: -0.8438, 0.5261, -0.1060 > > 12: -0.2626, 0.9548, -0.1389 > > 13: 0.0001, 0.9689, 0.2476 > > 14: 0.7453, 0.6663, 0.0242 > > 15: 0.9726, 0.2317, 0.0209 > > > > > > GE 15-orientation > > > > 0: 0.000, 0.000, 0.000 > > 1: 0.216, -0.8986, 0.38188 > > 2: -0.444, -0.4187, 0.7918 > > 3: -0.6351, -0.7700, -0.05947 > > 4: 0.500, -0.19253, 0.8440 > > 5: -0.2212, 0.5311, -0.8178 > > 6: -0.8919, 0.07914, -0.4451 > > 7: -0.1693, 0.5134, 0.8412 > > 8: -0.2639, -0.4402, -0.8581 > > 9: 0.59852, 0.00692, -0.8010 > > 10: -0.899, 0.2234, 0.3751 > > 11: 0.9853, -0.1664, 0.0385 > > 12: 0.6279, 0.6270, 0.46098 > > 13: -0.3501, 0.9364, 0.02096 > > 14: 0.5270, 0.7731, -0.3528 > > 15: 0.4206, -0.8041, -0.4200 > > > > There are Jones10 and Jones20, but I am not sure if there is > Jones15. > > > > _____ > > From: mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Abby Ding > Sent: Thursday, March 19, 2009 6:01 AM > To: MRIstudio > Subject: [Mristudio-users] 15-direction gradient table > > > > Dear users, > > > > Does any one of you have a 15-direction gradient table to share > with me? > > > > Thank you very much for your kindly help! > > > > Best Regards, > > Abby > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090320/3deba1bf/attachment-0001.html ------------------------------ Message: 3 Date: Mon, 23 Mar 2009 12:14:02 +0800 (CST) From: zhongsuyu123 Subject: [Mristudio-users] About the registration of the rat brain To: mristudio-users at mristudio.org Message-ID: <27953703.177261237781642887.JavaMail.coremail at bj163app98.163.com> Content-Type: text/plain; charset="gbk" Hi, I want to kown where I can get the template of the rat brain.In the Landermarker,I can only load the Human's template.Are there any templates for registration of the rat brain? If not, how can I do the registration of the rat brain. Thank you. Suyu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090323/27ab6618/attachment-0001.html ------------------------------ Message: 4 Date: Wed, 25 Mar 2009 13:55:51 -0400 From: Paul Beach Subject: [Mristudio-users] Problem with Landmarker not loading subjects To: Mristudio-users at mristudio.org Message-ID: <8874e3900903251055o49f6detf48792a6ff04fee1 at mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hi everyone, So every once and a while I'll be on Landmarker and when I'm trying to load a subject I'll receive an error message saying "please enter a number between 0 and 4096." The first time this happened I just closed all my programs and reopened Landmarker and things worked again. Other times (such as the latest one) I went so far as to restart my computer, which lead to no effect. This is obviously a huge problem as I can't load subjects whatsoever. Any ideas? Thanks, Paul p.s. In case this is necessary information, I've been using landmarks to reorient subject brains and fiber tracts using affine/rigid transformations. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090325/e7780f9b/attachment-0001.html ------------------------------ Message: 5 Date: Wed, 25 Mar 2009 15:02:36 -0400 From: XIN LI Subject: Re: [Mristudio-users] Problem with Landmarker not loading subjects To: "DTI Studio, ROI Editor, Landmarker Questions/Support" Message-ID: Content-Type: text/plain; charset=us-ascii Paul, When you loaded the subject, if the subject is a raw image, did you input the corresponding parameters of the subject in the image parameters window? These parameters are Image Width, Image Height, Slice Orientation, Fov Width, Fov Height, Slice Thickness and Image Data Format. You need to make sure the values of these parameters are the right ones for the subject. Xin ----- Original Message ----- From: Paul Beach Date: Wednesday, March 25, 2009 1:56 pm Subject: [Mristudio-users] Problem with Landmarker not loading subjects To: Mristudio-users at mristudio.org > Hi everyone, > > So every once and a while I'll be on Landmarker and when I'm trying > to load > a subject I'll receive an error message saying "please enter a number > between 0 and 4096." The first time this happened I just closed all > my > programs and reopened Landmarker and things worked again. Other > times (such > as the latest one) I went so far as to restart my computer, which > lead to no > effect. > > This is obviously a huge problem as I can't load subjects whatsoever. > > Any ideas? > > Thanks, > > Paul > > p.s. In case this is necessary information, I've been using landmarks > to > reorient subject brains and fiber tracts using affine/rigid transformations. > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > ------------------------------ _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users End of Mristudio-users Digest, Vol 14, Issue 19 *********************************************** -- Paul Beach Michigan State University College of Osteopathic Medicine - Medical Scientist Training Program Neuroscience Program -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090325/31620631/attachment-0001.html From darshanp20 at yahoo.com Wed Mar 25 16:43:15 2009 From: darshanp20 at yahoo.com (darshan pai) Date: Wed, 25 Mar 2009 13:43:15 -0700 (PDT) Subject: [Mristudio-users] To unsubscribe !!! In-Reply-To: References: <8874e3900903251223j5b13e077pc37a5308d3bd9149@mail.gmail.com> Message-ID: <998791.77248.qm@web30706.mail.mud.yahoo.com> http://lists.mristudio.org/mailman/listinfo/mristudio-users This is the link to unsubscribe . It is appended to all the messages that come through the list . Please do the needful Regards ________________________________ From: Doyeon Kim To: "DTI Studio, ROI Editor, Landmarker Questions/Support" Sent: Wednesday, March 25, 2009 3:25:37 PM Subject: Re: [Mristudio-users] Mristudio-users Digest, Vol 14, Issue 19 Please remove me from this list. 2009/3/25 Paul Beach Xin, Thanks for the reply. The problem with your suggestion is the image files are in fact not raw, they're analyze (.img, or .hdr). Any other suggestions? On Wed, Mar 25, 2009 at 3:02 PM, wrote: Send Mristudio-users mailing list submissions to mristudio-users at mristudio.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.mristudio.org/mailman/listinfo/mristudio-users or, via email, send a message with subject or body 'help' to mristudio-users-request at mristudio.org You can reach the person managing the list at mristudio-users-owner at mristudio.org When replying, please edit your Subject line so it is more specific than "Re: Contents of Mristudio-users digest..." Today's Topics: 1. Re: 15-direction gradient table (jenabi at optonline.net) 2. Re: 15-direction gradient table (Cruz Navarro, Jovany) 3. About the registration of the rat brain (zhongsuyu123) 4. Problem with Landmarker not loading subjects (Paul Beach) 5. Re: Problem with Landmarker not loading subjects (XIN LI) ---------------------------------------------------------------------- Message: 1 Date: Fri, 20 Mar 2009 02:55:28 +0000 (GMT) From: jenabi at optonline.net Subject: Re: [Mristudio-users] 15-direction gradient table To: "DTI Studio, ROI Editor, Landmarker Questions/Support" Message-ID: Content-Type: text/plain; charset="us-ascii" Could you please stop sending me e-mails? ----- Original Message ----- From: susumu Date: Thursday, March 19, 2009 9:46 am Subject: Re: [Mristudio-users] 15-direction gradient table To: "'DTI Studio, ROI Editor, Landmarker Questions/Support'" > > > for which scanner? Or something you can implement in a scanner > by yourself? > Anyway, these are some options you can consider; > > > > Philips "Medium" 15-orientation: > > > > 0: 0, 0, 0 > > 1: 1.0, 0.0, 0.0 > > 2: 0.0, 1.0, 0.0 > > 3: 0.0, 0.0, 1.0 > > 4: -0.1789, -0.1113, -0.9776 > > 5: -0.0635, 0.3767, -0.9242 > > 6: 0.710, 0.0516, -0.7015 > > 7: 0.6191, -0.4385, -0.6515 > > 8: 0.2424, 0.7843, -0.5710 > > 9: -0.2589, -0.6180, -0.7423 > > 10: -0.8169, 0.1697, -0.5513 > > 11: -0.8438, 0.5261, -0.1060 > > 12: -0.2626, 0.9548, -0.1389 > > 13: 0.0001, 0.9689, 0.2476 > > 14: 0.7453, 0.6663, 0.0242 > > 15: 0.9726, 0.2317, 0.0209 > > > > > > GE 15-orientation > > > > 0: 0.000, 0.000, 0.000 > > 1: 0.216, -0.8986, 0.38188 > > 2: -0.444, -0.4187, 0.7918 > > 3: -0.6351, -0.7700, -0.05947 > > 4: 0.500, -0.19253, 0.8440 > > 5: -0.2212, 0.5311, -0.8178 > > 6: -0.8919, 0.07914, -0.4451 > > 7: -0.1693, 0.5134, 0.8412 > > 8: -0.2639, -0.4402, -0.8581 > > 9: 0.59852, 0.00692, -0.8010 > > 10: -0.899, 0.2234, 0.3751 > > 11: 0.9853, -0.1664, 0.0385 > > 12: 0.6279, 0.6270, 0.46098 > > 13: -0.3501, 0.9364, 0.02096 > > 14: 0.5270, 0.7731, -0.3528 > > 15: 0.4206, -0.8041, -0.4200 > > > > There are Jones10 and Jones20, but I am not sure if there is > Jones15. > > > > _____ > > From: mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Abby Ding > Sent: Thursday, March 19, 2009 6:01 AM > To: MRIstudio > Subject: [Mristudio-users] 15-direction gradient table > > > > Dear users, > > > > Does any one of you have a 15-direction gradient table to share > with me? > > > > Thank you very much for your kindly help! > > > > Best Regards, > > Abby > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090320/40fb8c69/attachment-0001.html ------------------------------ Message: 2 Date: Fri, 20 Mar 2009 09:32:19 -0500 From: "Cruz Navarro, Jovany" Subject: Re: [Mristudio-users] 15-direction gradient table To: "DTI Studio, ROI Editor, Landmarker Questions/Support" Message-ID: <5F4CE8876744A34C8B58096BCD979F6734EF2B at BCMEVS15.ad.bcm.edu> Content-Type: text/plain; charset="iso-8859-1" Could you please stop sending me e-mails? ________________________________ From: mristudio-users-bounces at mristudio.org on behalf of jenabi at optonline.net Sent: Thu 3/19/2009 9:55 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] 15-direction gradient table Could you please stop sending me e-mails? ----- Original Message ----- From: susumu Date: Thursday, March 19, 2009 9:46 am Subject: Re: [Mristudio-users] 15-direction gradient table To: "'DTI Studio, ROI Editor, Landmarker Questions/Support'" > > > for which scanner? Or something you can implement in a scanner > by yourself? > Anyway, these are some options you can consider; > > > > Philips "Medium" 15-orientation: > > > > 0: 0, 0, 0 > > 1: 1.0, 0.0, 0.0 > > 2: 0.0, 1.0, 0.0 > > 3: 0.0, 0.0, 1.0 > > 4: -0.1789, -0.1113, -0.9776 > > 5: -0.0635, 0.3767, -0.9242 > > 6: 0.710, 0.0516, -0.7015 > > 7: 0.6191, -0.4385, -0.6515 > > 8: 0.2424, 0.7843, -0.5710 > > 9: -0.2589, -0.6180, -0.7423 > > 10: -0.8169, 0.1697, -0.5513 > > 11: -0.8438, 0.5261, -0.1060 > > 12: -0.2626, 0.9548, -0.1389 > > 13: 0.0001, 0.9689, 0.2476 > > 14: 0.7453, 0.6663, 0.0242 > > 15: 0.9726, 0.2317, 0.0209 > > > > > > GE 15-orientation > > > > 0: 0.000, 0.000, 0.000 > > 1: 0.216, -0.8986, 0.38188 > > 2: -0.444, -0.4187, 0.7918 > > 3: -0.6351, -0.7700, -0.05947 > > 4: 0.500, -0.19253, 0.8440 > > 5: -0.2212, 0.5311, -0.8178 > > 6: -0.8919, 0.07914, -0.4451 > > 7: -0.1693, 0.5134, 0.8412 > > 8: -0.2639, -0.4402, -0.8581 > > 9: 0.59852, 0.00692, -0.8010 > > 10: -0.899, 0.2234, 0.3751 > > 11: 0.9853, -0.1664, 0.0385 > > 12: 0.6279, 0.6270, 0.46098 > > 13: -0.3501, 0.9364, 0.02096 > > 14: 0.5270, 0.7731, -0.3528 > > 15: 0.4206, -0.8041, -0.4200 > > > > There are Jones10 and Jones20, but I am not sure if there is > Jones15. > > > > _____ > > From: mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Abby Ding > Sent: Thursday, March 19, 2009 6:01 AM > To: MRIstudio > Subject: [Mristudio-users] 15-direction gradient table > > > > Dear users, > > > > Does any one of you have a 15-direction gradient table to share > with me? > > > > Thank you very much for your kindly help! > > > > Best Regards, > > Abby > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090320/3deba1bf/attachment-0001.html ------------------------------ Message: 3 Date: Mon, 23 Mar 2009 12:14:02 +0800 (CST) From: zhongsuyu123 Subject: [Mristudio-users] About the registration of the rat brain To: mristudio-users at mristudio.org Message-ID: <27953703.177261237781642887.JavaMail.coremail at bj163app98.163.com> Content-Type: text/plain; charset="gbk" Hi, I want to kown where I can get the template of the rat brain.In the Landermarker,I can only load the Human's template.Are there any templates for registration of the rat brain? If not, how can I do the registration of the rat brain. Thank you. Suyu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090323/27ab6618/attachment-0001.html ------------------------------ Message: 4 Date: Wed, 25 Mar 2009 13:55:51 -0400 From: Paul Beach Subject: [Mristudio-users] Problem with Landmarker not loading subjects To: Mristudio-users at mristudio.org Message-ID: <8874e3900903251055o49f6detf48792a6ff04fee1 at mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hi everyone, So every once and a while I'll be on Landmarker and when I'm trying to load a subject I'll receive an error message saying "please enter a number between 0 and 4096." The first time this happened I just closed all my programs and reopened Landmarker and things worked again. Other times (such as the latest one) I went so far as to restart my computer, which lead to no effect. This is obviously a huge problem as I can't load subjects whatsoever. Any ideas? Thanks, Paul p.s. In case this is necessary information, I've been using landmarks to reorient subject brains and fiber tracts using affine/rigid transformations. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090325/e7780f9b/attachment-0001.html ------------------------------ Message: 5 Date: Wed, 25 Mar 2009 15:02:36 -0400 From: XIN LI Subject: Re: [Mristudio-users] Problem with Landmarker not loading subjects To: "DTI Studio, ROI Editor, Landmarker Questions/Support" Message-ID: Content-Type: text/plain; charset=us-ascii Paul, When you loaded the subject, if the subject is a raw image, did you input the corresponding parameters of the subject in the image parameters window? These parameters are Image Width, Image Height, Slice Orientation, Fov Width, Fov Height, Slice Thickness and Image Data Format. You need to make sure the values of these parameters are the right ones for the subject. Xin ----- Original Message ----- From: Paul Beach Date: Wednesday, March 25, 2009 1:56 pm Subject: [Mristudio-users] Problem with Landmarker not loading subjects To: Mristudio-users at mristudio.org > Hi everyone, > > So every once and a while I'll be on Landmarker and when I'm trying > to load > a subject I'll receive an error message saying "please enter a number > between 0 and 4096." The first time this happened I just closed all > my > programs and reopened Landmarker and things worked again. Other > times (such > as the latest one) I went so far as to restart my computer, which > lead to no > effect. > > This is obviously a huge problem as I can't load subjects whatsoever. > > Any ideas? > > Thanks, > > Paul > > p.s. In case this is necessary information, I've been using landmarks > to > reorient subject brains and fiber tracts using affine/rigid transformations. > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > ------------------------------ _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users End of Mristudio-users Digest, Vol 14, Issue 19 *********************************************** -- Paul Beach Michigan State University College of Osteopathic Medicine - Medical Scientist Training Program Neuroscience Program _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090325/d8bf65f0/attachment-0001.html From susumu at mri.jhu.edu Wed Mar 25 17:19:51 2009 From: susumu at mri.jhu.edu (susumu) Date: Wed, 25 Mar 2009 17:19:51 -0400 Subject: [Mristudio-users] About the registration of the rat brain In-Reply-To: <27953703.177261237781642887.JavaMail.coremail@bj163app98.163.com> Message-ID: <7k7ed7$6rnn4i@ipex3.johnshopkins.edu> Currently we are not providing rat atlases. We have mouse atlases, though. _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of zhongsuyu123 Sent: Monday, March 23, 2009 12:14 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] About the registration of the rat brain Hi, I want to kown where I can get the template of the rat brain.In the Landermarker,I can only load the Human's template.Are there any templates for registration of the rat brain? If not, how can I do the registration of the rat brain. Thank you. Suyu _____ ????????????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090325/0ffa6532/attachment.html From xli16 at jhmi.edu Wed Mar 25 17:24:16 2009 From: xli16 at jhmi.edu (XIN LI) Date: Wed, 25 Mar 2009 17:24:16 -0400 Subject: [Mristudio-users] Problem with Landmarker not loading subjects In-Reply-To: <8874e3900903251055o49f6detf48792a6ff04fee1@mail.gmail.com> References: <8874e3900903251055o49f6detf48792a6ff04fee1@mail.gmail.com> Message-ID: Paul, When you loaded the subject, did you select "Analyze" as the image file format in the image parameter window? Xin ----- Original Message ----- From: Paul Beach Date: Wednesday, March 25, 2009 1:56 pm Subject: [Mristudio-users] Problem with Landmarker not loading subjects To: Mristudio-users at mristudio.org > Hi everyone, > > So every once and a while I'll be on Landmarker and when I'm trying > to load > a subject I'll receive an error message saying "please enter a number > between 0 and 4096." The first time this happened I just closed all > my > programs and reopened Landmarker and things worked again. Other > times (such > as the latest one) I went so far as to restart my computer, which > lead to no > effect. > > This is obviously a huge problem as I can't load subjects whatsoever. > > Any ideas? > > Thanks, > > Paul > > p.s. In case this is necessary information, I've been using landmarks > to > reorient subject brains and fiber tracts using affine/rigid transformations. > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > From SCopeland at mednet.ucla.edu Fri Mar 27 13:09:27 2009 From: SCopeland at mednet.ucla.edu (Copeland, Sarah A.) Date: Fri, 27 Mar 2009 10:09:27 -0700 Subject: [Mristudio-users] loading AIR files Message-ID: Hello, I think that I may have managed to use AIR's linear registration to register my anatomic image to the mean B0 image in landmarker. The program asks you to supply a filename, and after the process is complete I can find a file of type "AIR" in the correct location, but can't open it. It's obviously not analyze format, but when I try to open as "raw" I get the error "please enter an integer between 1 and 4096" that pops up from time to time. However, the boxes which contain 0s are greyed out and can't be changed. Any suggestions as to how I can open and view the file? Also, the anatomic image filename in the open "subject" window now has the name "updated_filename". Is this still the original, or is the registered image? I can't open the original when this one is open, so I thought perhaps this is still the original file just with "updated" appended, but I'm not sure. If it's the registered image, the registration is not working very well, so I'm hoping it's not. Thanks so much - Sarah Copeland IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. From SCopeland at mednet.ucla.edu Fri Mar 27 13:09:32 2009 From: SCopeland at mednet.ucla.edu (Copeland, Sarah A.) Date: Fri, 27 Mar 2009 10:09:32 -0700 Subject: [Mristudio-users] loading AIR files Message-ID: Hello, I think that I may have managed to use AIR's linear registration to register my anatomic image to the mean B0 image in landmarker. The program asks you to supply a filename, and after the process is complete I can find a file of type "AIR" in the correct location, but can't open it. It's obviously not analyze format, but when I try to open as "raw" I get the error "please enter an integer between 1 and 4096" that pops up from time to time. However, the boxes which contain 0s are greyed out and can't be changed. Any suggestions as to how I can open and view the file? Also, the anatomic image filename in the open "subject" window now has the name "updated_filename". Is this still the original, or is the registered image? I can't open the original when this one is open, so I thought perhaps this is still the original file just with "updated" appended, but I'm not sure. If it's the registered image, the registration is not working very well, so I'm hoping it's not. Thanks so much - Sarah Copeland IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. From SCopeland at mednet.ucla.edu Fri Mar 27 13:09:37 2009 From: SCopeland at mednet.ucla.edu (Copeland, Sarah A.) Date: Fri, 27 Mar 2009 10:09:37 -0700 Subject: [Mristudio-users] loading AIR files Message-ID: Hello, I think that I may have managed to use AIR's linear registration to register my anatomic image to the mean B0 image in landmarker. The program asks you to supply a filename, and after the process is complete I can find a file of type "AIR" in the correct location, but can't open it. It's obviously not analyze format, but when I try to open as "raw" I get the error "please enter an integer between 1 and 4096" that pops up from time to time. However, the boxes which contain 0s are greyed out and can't be changed. Any suggestions as to how I can open and view the file? Also, the anatomic image filename in the open "subject" window now has the name "updated_filename". Is this still the original, or is the registered image? I can't open the original when this one is open, so I thought perhaps this is still the original file just with "updated" appended, but I'm not sure. If it's the registered image, the registration is not working very well, so I'm hoping it's not. Thanks so much - Sarah Copeland IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. From SCopeland at mednet.ucla.edu Fri Mar 27 13:09:42 2009 From: SCopeland at mednet.ucla.edu (Copeland, Sarah A.) Date: Fri, 27 Mar 2009 10:09:42 -0700 Subject: [Mristudio-users] loading AIR files Message-ID: Hello, I think that I may have managed to use AIR's linear registration to register my anatomic image to the mean B0 image in landmarker. The program asks you to supply a filename, and after the process is complete I can find a file of type "AIR" in the correct location, but can't open it. It's obviously not analyze format, but when I try to open as "raw" I get the error "please enter an integer between 1 and 4096" that pops up from time to time. However, the boxes which contain 0s are greyed out and can't be changed. Any suggestions as to how I can open and view the file? Also, the anatomic image filename in the open "subject" window now has the name "updated_filename". Is this still the original, or is the registered image? I can't open the original when this one is open, so I thought perhaps this is still the original file just with "updated" appended, but I'm not sure. If it's the registered image, the registration is not working very well, so I'm hoping it's not. Thanks so much - Sarah Copeland IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. From SCopeland at mednet.ucla.edu Fri Mar 27 13:22:06 2009 From: SCopeland at mednet.ucla.edu (Copeland, Sarah A.) Date: Fri, 27 Mar 2009 10:22:06 -0700 Subject: [Mristudio-users] loading AIR files Message-ID: Hello, I think that I may have managed to use AIR's linear registration to register my anatomic image to the mean B0 image in landmarker. The program asks you to supply a filename, and after the process is complete I can find a file of type "AIR" in the correct location, but can't open it. It's obviously not analyze format, but when I try to open as "raw" I get the error "please enter an integer between 1 and 4096" that pops up from time to time. However, the boxes which contain 0s are greyed out and can't be changed. Any suggestions as to how I can open and view the file? Also, the anatomic image filename in the open "subject" window now has the name "updated_filename". Is this still the original, or is the registered image? I can't open the original when this one is open, so I thought perhaps this is still the original file just with "updated" appended, but I'm not sure. If it's the registered image, the registration is not working very well, so I'm hoping it's not. Thanks so much - Sarah Copeland IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. From pabeach1 at gmail.com Fri Mar 27 13:30:05 2009 From: pabeach1 at gmail.com (Paul Beach) Date: Fri, 27 Mar 2009 13:30:05 -0400 Subject: [Mristudio-users] Mristudio-users Digest, Vol 14, Issue 24 In-Reply-To: References: Message-ID: <8874e3900903271030g4db90a80i7cb35acf9f4136cb@mail.gmail.com> Xin, Yes, they are analyze files. But I've actually figured out (and fixed) what happened. Apparently a (-) was being inserted into the "field of view width" input. I simply clicked on "raw image" and removed the (-) and everything worked! Thanks so much for your suggestions! Paul On Fri, Mar 27, 2009 at 1:22 PM, wrote: > Send Mristudio-users mailing list submissions to > mristudio-users at mristudio.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.mristudio.org/mailman/listinfo/mristudio-users > or, via email, send a message with subject or body 'help' to > mristudio-users-request at mristudio.org > > You can reach the person managing the list at > mristudio-users-owner at mristudio.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Mristudio-users digest..." > > > Today's Topics: > > 1. Re: About the registration of the rat brain (susumu) > 2. Re: Problem with Landmarker not loading subjects (XIN LI) > 3. loading AIR files (Copeland, Sarah A.) > 4. loading AIR files (Copeland, Sarah A.) > 5. loading AIR files (Copeland, Sarah A.) > 6. loading AIR files (Copeland, Sarah A.) > 7. loading AIR files (Copeland, Sarah A.) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 25 Mar 2009 17:19:51 -0400 > From: susumu > Subject: Re: [Mristudio-users] About the registration of the rat brain > To: "'DTI Studio, ROI Editor, Landmarker Questions/Support'" > > Message-ID: <7k7ed7$6rnn4i at ipex3.johnshopkins.edu> > Content-Type: text/plain; charset="gb2312" > > Currently we are not providing rat atlases. We have mouse atlases, though. > > > > _____ > > From: mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of zhongsuyu123 > Sent: Monday, March 23, 2009 12:14 AM > To: mristudio-users at mristudio.org > Subject: [Mristudio-users] About the registration of the rat brain > > > > Hi, > > I want to kown where I can get the template of the rat brain.In the > Landermarker,I can only load the Human's template.Are there any templates > for registration of the rat brain? If not, how can I do the registration of > the rat brain. > > Thank you. > > Suyu > > > > > > > _____ > > ????????????????? > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090325/0ffa6532/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Wed, 25 Mar 2009 17:24:16 -0400 > From: XIN LI > Subject: Re: [Mristudio-users] Problem with Landmarker not loading > subjects > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > > Message-ID: > Content-Type: text/plain; charset=us-ascii > > Paul, > > When you loaded the subject, did you select "Analyze" as the image file > format in the image parameter window? > > > Xin > > > ----- Original Message ----- > From: Paul Beach > Date: Wednesday, March 25, 2009 1:56 pm > Subject: [Mristudio-users] Problem with Landmarker not loading subjects > To: Mristudio-users at mristudio.org > > > > Hi everyone, > > > > So every once and a while I'll be on Landmarker and when I'm trying > > to load > > a subject I'll receive an error message saying "please enter a number > > between 0 and 4096." The first time this happened I just closed all > > my > > programs and reopened Landmarker and things worked again. Other > > times (such > > as the latest one) I went so far as to restart my computer, which > > lead to no > > effect. > > > > This is obviously a huge problem as I can't load subjects whatsoever. > > > > Any ideas? > > > > Thanks, > > > > Paul > > > > p.s. In case this is necessary information, I've been using landmarks > > to > > reorient subject brains and fiber tracts using affine/rigid > transformations. > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > > ------------------------------ > > Message: 3 > Date: Fri, 27 Mar 2009 10:09:27 -0700 > From: "Copeland, Sarah A." > Subject: [Mristudio-users] loading AIR files > To: "mristudio-users at mristudio.org" > Message-ID: > > > Content-Type: text/plain; charset=us-ascii > > Hello, > > I think that I may have managed to use AIR's linear registration to > register my anatomic image to the mean B0 image in landmarker. The program > asks you to supply a filename, and after the process is complete I can find > a file of type "AIR" in the correct location, but can't open it. It's > obviously not analyze format, but when I try to open as "raw" I get the > error "please enter an integer between 1 and 4096" that pops up from time to > time. However, the boxes which contain 0s are greyed out and can't be > changed. Any suggestions as to how I can open and view the file? > > Also, the anatomic image filename in the open "subject" window now has the > name "updated_filename". Is this still the original, or is the registered > image? I can't open the original when this one is open, so I thought perhaps > this is still the original file just with "updated" appended, but I'm not > sure. If it's the registered image, the registration is not working very > well, so I'm hoping it's not. > > Thanks so much - > > Sarah Copeland > > IMPORTANT WARNING: This email (and any attachments) is only intended for > the use of the person or entity to which it is addressed, and may contain > information that is privileged and confidential. You, the recipient, are > obligated to maintain it in a safe, secure and confidential manner. > Unauthorized redisclosure or failure to maintain confidentiality may > subject you to federal and state penalties. If you are not the intended > recipient, please immediately notify us by return email, and delete this > message from your computer. > > > > ------------------------------ > > Message: 4 > Date: Fri, 27 Mar 2009 10:09:32 -0700 > From: "Copeland, Sarah A." > Subject: [Mristudio-users] loading AIR files > To: "mristudio-users at mristudio.org" > Message-ID: > > > Content-Type: text/plain; charset=us-ascii > > Hello, > > I think that I may have managed to use AIR's linear registration to > register my anatomic image to the mean B0 image in landmarker. The program > asks you to supply a filename, and after the process is complete I can find > a file of type "AIR" in the correct location, but can't open it. It's > obviously not analyze format, but when I try to open as "raw" I get the > error "please enter an integer between 1 and 4096" that pops up from time to > time. However, the boxes which contain 0s are greyed out and can't be > changed. Any suggestions as to how I can open and view the file? > > Also, the anatomic image filename in the open "subject" window now has the > name "updated_filename". Is this still the original, or is the registered > image? I can't open the original when this one is open, so I thought perhaps > this is still the original file just with "updated" appended, but I'm not > sure. If it's the registered image, the registration is not working very > well, so I'm hoping it's not. > > Thanks so much - > > Sarah Copeland > > IMPORTANT WARNING: This email (and any attachments) is only intended for > the use of the person or entity to which it is addressed, and may contain > information that is privileged and confidential. You, the recipient, are > obligated to maintain it in a safe, secure and confidential manner. > Unauthorized redisclosure or failure to maintain confidentiality may > subject you to federal and state penalties. If you are not the intended > recipient, please immediately notify us by return email, and delete this > message from your computer. > > > > ------------------------------ > > Message: 5 > Date: Fri, 27 Mar 2009 10:09:37 -0700 > From: "Copeland, Sarah A." > Subject: [Mristudio-users] loading AIR files > To: "mristudio-users at mristudio.org" > Message-ID: > > > Content-Type: text/plain; charset=us-ascii > > Hello, > > I think that I may have managed to use AIR's linear registration to > register my anatomic image to the mean B0 image in landmarker. The program > asks you to supply a filename, and after the process is complete I can find > a file of type "AIR" in the correct location, but can't open it. It's > obviously not analyze format, but when I try to open as "raw" I get the > error "please enter an integer between 1 and 4096" that pops up from time to > time. However, the boxes which contain 0s are greyed out and can't be > changed. Any suggestions as to how I can open and view the file? > > Also, the anatomic image filename in the open "subject" window now has the > name "updated_filename". Is this still the original, or is the registered > image? I can't open the original when this one is open, so I thought perhaps > this is still the original file just with "updated" appended, but I'm not > sure. If it's the registered image, the registration is not working very > well, so I'm hoping it's not. > > Thanks so much - > > Sarah Copeland > > IMPORTANT WARNING: This email (and any attachments) is only intended for > the use of the person or entity to which it is addressed, and may contain > information that is privileged and confidential. You, the recipient, are > obligated to maintain it in a safe, secure and confidential manner. > Unauthorized redisclosure or failure to maintain confidentiality may > subject you to federal and state penalties. If you are not the intended > recipient, please immediately notify us by return email, and delete this > message from your computer. > > > > ------------------------------ > > Message: 6 > Date: Fri, 27 Mar 2009 10:09:42 -0700 > From: "Copeland, Sarah A." > Subject: [Mristudio-users] loading AIR files > To: "mristudio-users at mristudio.org" > Message-ID: > > > Content-Type: text/plain; charset=us-ascii > > Hello, > > I think that I may have managed to use AIR's linear registration to > register my anatomic image to the mean B0 image in landmarker. The program > asks you to supply a filename, and after the process is complete I can find > a file of type "AIR" in the correct location, but can't open it. It's > obviously not analyze format, but when I try to open as "raw" I get the > error "please enter an integer between 1 and 4096" that pops up from time to > time. However, the boxes which contain 0s are greyed out and can't be > changed. Any suggestions as to how I can open and view the file? > > Also, the anatomic image filename in the open "subject" window now has the > name "updated_filename". Is this still the original, or is the registered > image? I can't open the original when this one is open, so I thought perhaps > this is still the original file just with "updated" appended, but I'm not > sure. If it's the registered image, the registration is not working very > well, so I'm hoping it's not. > > Thanks so much - > > Sarah Copeland > > IMPORTANT WARNING: This email (and any attachments) is only intended for > the use of the person or entity to which it is addressed, and may contain > information that is privileged and confidential. You, the recipient, are > obligated to maintain it in a safe, secure and confidential manner. > Unauthorized redisclosure or failure to maintain confidentiality may > subject you to federal and state penalties. If you are not the intended > recipient, please immediately notify us by return email, and delete this > message from your computer. > > > > ------------------------------ > > Message: 7 > Date: Fri, 27 Mar 2009 10:22:06 -0700 > From: "Copeland, Sarah A." > Subject: [Mristudio-users] loading AIR files > To: "mristudio-users at mristudio.org" > Message-ID: > > > Content-Type: text/plain; charset=us-ascii > > Hello, > > I think that I may have managed to use AIR's linear registration to > register my anatomic image to the mean B0 image in landmarker. The program > asks you to supply a filename, and after the process is complete I can find > a file of type "AIR" in the correct location, but can't open it. It's > obviously not analyze format, but when I try to open as "raw" I get the > error "please enter an integer between 1 and 4096" that pops up from time to > time. However, the boxes which contain 0s are greyed out and can't be > changed. Any suggestions as to how I can open and view the file? > > Also, the anatomic image filename in the open "subject" window now has the > name "updated_filename". Is this still the original, or is the registered > image? I can't open the original when this one is open, so I thought perhaps > this is still the original file just with "updated" appended, but I'm not > sure. If it's the registered image, the registration is not working very > well, so I'm hoping it's not. > > Thanks so much - > > Sarah Copeland > > IMPORTANT WARNING: This email (and any attachments) is only intended for > the use of the person or entity to which it is addressed, and may contain > information that is privileged and confidential. You, the recipient, are > obligated to maintain it in a safe, secure and confidential manner. > Unauthorized redisclosure or failure to maintain confidentiality may > subject you to federal and state penalties. If you are not the intended > recipient, please immediately notify us by return email, and delete this > message from your computer. > > > > ------------------------------ > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > End of Mristudio-users Digest, Vol 14, Issue 24 > *********************************************** > -- Paul Beach Michigan State University College of Osteopathic Medicine - Medical Scientist Training Program Neuroscience Program -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090327/993d7c4c/attachment-0001.html From xli16 at jhmi.edu Fri Mar 27 14:34:17 2009 From: xli16 at jhmi.edu (XIN LI) Date: Fri, 27 Mar 2009 14:34:17 -0400 Subject: [Mristudio-users] Mristudio-users Digest, Vol 14, Issue 24 In-Reply-To: <8874e3900903271030g4db90a80i7cb35acf9f4136cb@mail.gmail.com> References: <8874e3900903271030g4db90a80i7cb35acf9f4136cb@mail.gmail.com> Message-ID: Paul, You're welcome! I am glad that you have solved the problem. Xin ----- Original Message ----- From: Paul Beach Date: Friday, March 27, 2009 1:30 pm Subject: Re: [Mristudio-users] Mristudio-users Digest, Vol 14, Issue 24 To: mristudio-users at mristudio.org > Xin, > > Yes, they are analyze files. But I've actually figured out (and > fixed) what > happened. Apparently a (-) was being inserted into the "field of view > width" input. I simply clicked on "raw image" and removed the (-) and > everything worked! > > Thanks so much for your suggestions! > > Paul > > > On Fri, Mar 27, 2009 at 1:22 PM, wrote: > > > Send Mristudio-users mailing list submissions to > > mristudio-users at mristudio.org > > > > To subscribe or unsubscribe via the World Wide Web, visit > > > > or, via email, send a message with subject or body 'help' to > > mristudio-users-request at mristudio.org > > > > You can reach the person managing the list at > > mristudio-users-owner at mristudio.org > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of Mristudio-users digest..." > > > > > > Today's Topics: > > > > 1. Re: About the registration of the rat brain (susumu) > > 2. Re: Problem with Landmarker not loading subjects (XIN LI) > > 3. loading AIR files (Copeland, Sarah A.) > > 4. loading AIR files (Copeland, Sarah A.) > > 5. loading AIR files (Copeland, Sarah A.) > > 6. loading AIR files (Copeland, Sarah A.) > > 7. loading AIR files (Copeland, Sarah A.) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Wed, 25 Mar 2009 17:19:51 -0400 > > From: susumu > > Subject: Re: [Mristudio-users] About the registration of the rat brain > > To: "'DTI Studio, ROI Editor, Landmarker Questions/Support'" > > > > Message-ID: <7k7ed7$6rnn4i at ipex3.johnshopkins.edu> > > Content-Type: text/plain; charset="gb2312" > > > > Currently we are not providing rat atlases. We have mouse atlases, > though. > > > > > > > > _____ > > > > From: mristudio-users-bounces at mristudio.org > > [ On Behalf Of zhongsuyu123 > > Sent: Monday, March 23, 2009 12:14 AM > > To: mristudio-users at mristudio.org > > Subject: [Mristudio-users] About the registration of the rat brain > > > > > > > > Hi, > > > > I want to kown where I can get the template of the rat brain.In the > > Landermarker,I can only load the Human's template.Are there any templates > > for registration of the rat brain? If not, how can I do the > registration of > > the rat brain. > > > > Thank you. > > > > Suyu > > > > > > > > > > > > > > _____ > > > > <> ????????????????? > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > > > ------------------------------ > > > > Message: 2 > > Date: Wed, 25 Mar 2009 17:24:16 -0400 > > From: XIN LI > > Subject: Re: [Mristudio-users] Problem with Landmarker not loading > > subjects > > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > > > > Message-ID: > > Content-Type: text/plain; charset=us-ascii > > > > Paul, > > > > When you loaded the subject, did you select "Analyze" as the image > file > > format in the image parameter window? > > > > > > Xin > > > > > > ----- Original Message ----- > > From: Paul Beach > > Date: Wednesday, March 25, 2009 1:56 pm > > Subject: [Mristudio-users] Problem with Landmarker not loading subjects > > To: Mristudio-users at mristudio.org > > > > > > > Hi everyone, > > > > > > So every once and a while I'll be on Landmarker and when I'm trying > > > to load > > > a subject I'll receive an error message saying "please enter a number > > > between 0 and 4096." The first time this happened I just closed > all > > > my > > > programs and reopened Landmarker and things worked again. Other > > > times (such > > > as the latest one) I went so far as to restart my computer, which > > > lead to no > > > effect. > > > > > > This is obviously a huge problem as I can't load subjects whatsoever. > > > > > > Any ideas? > > > > > > Thanks, > > > > > > Paul > > > > > > p.s. In case this is necessary information, I've been using landmarks > > > to > > > reorient subject brains and fiber tracts using affine/rigid > > transformations. > > > _______________________________________________ > > > Mristudio-users mailing list > > > Mristudio-users at mristudio.org > > > > > > > > > ------------------------------ > > > > Message: 3 > > Date: Fri, 27 Mar 2009 10:09:27 -0700 > > From: "Copeland, Sarah A." > > Subject: [Mristudio-users] loading AIR files > > To: "mristudio-users at mristudio.org" > > Message-ID: > > > > > > Content-Type: text/plain; charset=us-ascii > > > > Hello, > > > > I think that I may have managed to use AIR's linear registration to > > register my anatomic image to the mean B0 image in landmarker. The > program > > asks you to supply a filename, and after the process is complete I > can find > > a file of type "AIR" in the correct location, but can't open it. It's > > obviously not analyze format, but when I try to open as "raw" I get > the > > error "please enter an integer between 1 and 4096" that pops up > from time to > > time. However, the boxes which contain 0s are greyed out and can't > be > > changed. Any suggestions as to how I can open and view the file? > > > > Also, the anatomic image filename in the open "subject" window now > has the > > name "updated_filename". Is this still the original, or is the registered > > image? I can't open the original when this one is open, so I > thought perhaps > > this is still the original file just with "updated" appended, but > I'm not > > sure. If it's the registered image, the registration is not working > very > > well, so I'm hoping it's not. > > > > Thanks so much - > > > > Sarah Copeland > > > > IMPORTANT WARNING: This email (and any attachments) is only > intended for > > the use of the person or entity to which it is addressed, and may contain > > information that is privileged and confidential. You, the > recipient, are > > obligated to maintain it in a safe, secure and confidential manner. > > Unauthorized redisclosure or failure to maintain confidentiality may > > subject you to federal and state penalties. If you are not the intended > > recipient, please immediately notify us by return email, and delete > this > > message from your computer. > > > > > > > > ------------------------------ > > > > Message: 4 > > Date: Fri, 27 Mar 2009 10:09:32 -0700 > > From: "Copeland, Sarah A." > > Subject: [Mristudio-users] loading AIR files > > To: "mristudio-users at mristudio.org" > > Message-ID: > > > > > > Content-Type: text/plain; charset=us-ascii > > > > Hello, > > > > I think that I may have managed to use AIR's linear registration to > > register my anatomic image to the mean B0 image in landmarker. The > program > > asks you to supply a filename, and after the process is complete I > can find > > a file of type "AIR" in the correct location, but can't open it. It's > > obviously not analyze format, but when I try to open as "raw" I get > the > > error "please enter an integer between 1 and 4096" that pops up > from time to > > time. However, the boxes which contain 0s are greyed out and can't > be > > changed. Any suggestions as to how I can open and view the file? > > > > Also, the anatomic image filename in the open "subject" window now > has the > > name "updated_filename". Is this still the original, or is the registered > > image? I can't open the original when this one is open, so I > thought perhaps > > this is still the original file just with "updated" appended, but > I'm not > > sure. If it's the registered image, the registration is not working > very > > well, so I'm hoping it's not. > > > > Thanks so much - > > > > Sarah Copeland > > > > IMPORTANT WARNING: This email (and any attachments) is only > intended for > > the use of the person or entity to which it is addressed, and may contain > > information that is privileged and confidential. You, the > recipient, are > > obligated to maintain it in a safe, secure and confidential manner. > > Unauthorized redisclosure or failure to maintain confidentiality may > > subject you to federal and state penalties. If you are not the intended > > recipient, please immediately notify us by return email, and delete > this > > message from your computer. > > > > > > > > ------------------------------ > > > > Message: 5 > > Date: Fri, 27 Mar 2009 10:09:37 -0700 > > From: "Copeland, Sarah A." > > Subject: [Mristudio-users] loading AIR files > > To: "mristudio-users at mristudio.org" > > Message-ID: > > > > > > Content-Type: text/plain; charset=us-ascii > > > > Hello, > > > > I think that I may have managed to use AIR's linear registration to > > register my anatomic image to the mean B0 image in landmarker. The > program > > asks you to supply a filename, and after the process is complete I > can find > > a file of type "AIR" in the correct location, but can't open it. It's > > obviously not analyze format, but when I try to open as "raw" I get > the > > error "please enter an integer between 1 and 4096" that pops up > from time to > > time. However, the boxes which contain 0s are greyed out and can't > be > > changed. Any suggestions as to how I can open and view the file? > > > > Also, the anatomic image filename in the open "subject" window now > has the > > name "updated_filename". Is this still the original, or is the registered > > image? I can't open the original when this one is open, so I > thought perhaps > > this is still the original file just with "updated" appended, but > I'm not > > sure. If it's the registered image, the registration is not working > very > > well, so I'm hoping it's not. > > > > Thanks so much - > > > > Sarah Copeland > > > > IMPORTANT WARNING: This email (and any attachments) is only > intended for > > the use of the person or entity to which it is addressed, and may contain > > information that is privileged and confidential. You, the > recipient, are > > obligated to maintain it in a safe, secure and confidential manner. > > Unauthorized redisclosure or failure to maintain confidentiality may > > subject you to federal and state penalties. If you are not the intended > > recipient, please immediately notify us by return email, and delete > this > > message from your computer. > > > > > > > > ------------------------------ > > > > Message: 6 > > Date: Fri, 27 Mar 2009 10:09:42 -0700 > > From: "Copeland, Sarah A." > > Subject: [Mristudio-users] loading AIR files > > To: "mristudio-users at mristudio.org" > > Message-ID: > > > > > > Content-Type: text/plain; charset=us-ascii > > > > Hello, > > > > I think that I may have managed to use AIR's linear registration to > > register my anatomic image to the mean B0 image in landmarker. The > program > > asks you to supply a filename, and after the process is complete I > can find > > a file of type "AIR" in the correct location, but can't open it. It's > > obviously not analyze format, but when I try to open as "raw" I get > the > > error "please enter an integer between 1 and 4096" that pops up > from time to > > time. However, the boxes which contain 0s are greyed out and can't > be > > changed. Any suggestions as to how I can open and view the file? > > > > Also, the anatomic image filename in the open "subject" window now > has the > > name "updated_filename". Is this still the original, or is the registered > > image? I can't open the original when this one is open, so I > thought perhaps > > this is still the original file just with "updated" appended, but > I'm not > > sure. If it's the registered image, the registration is not working > very > > well, so I'm hoping it's not. > > > > Thanks so much - > > > > Sarah Copeland > > > > IMPORTANT WARNING: This email (and any attachments) is only > intended for > > the use of the person or entity to which it is addressed, and may contain > > information that is privileged and confidential. You, the > recipient, are > > obligated to maintain it in a safe, secure and confidential manner. > > Unauthorized redisclosure or failure to maintain confidentiality may > > subject you to federal and state penalties. If you are not the intended > > recipient, please immediately notify us by return email, and delete > this > > message from your computer. > > > > > > > > ------------------------------ > > > > Message: 7 > > Date: Fri, 27 Mar 2009 10:22:06 -0700 > > From: "Copeland, Sarah A." > > Subject: [Mristudio-users] loading AIR files > > To: "mristudio-users at mristudio.org" > > Message-ID: > > > > > > Content-Type: text/plain; charset=us-ascii > > > > Hello, > > > > I think that I may have managed to use AIR's linear registration to > > register my anatomic image to the mean B0 image in landmarker. The > program > > asks you to supply a filename, and after the process is complete I > can find > > a file of type "AIR" in the correct location, but can't open it. It's > > obviously not analyze format, but when I try to open as "raw" I get > the > > error "please enter an integer between 1 and 4096" that pops up > from time to > > time. However, the boxes which contain 0s are greyed out and can't > be > > changed. Any suggestions as to how I can open and view the file? > > > > Also, the anatomic image filename in the open "subject" window now > has the > > name "updated_filename". Is this still the original, or is the registered > > image? I can't open the original when this one is open, so I > thought perhaps > > this is still the original file just with "updated" appended, but > I'm not > > sure. If it's the registered image, the registration is not working > very > > well, so I'm hoping it's not. > > > > Thanks so much - > > > > Sarah Copeland > > > > IMPORTANT WARNING: This email (and any attachments) is only > intended for > > the use of the person or entity to which it is addressed, and may contain > > information that is privileged and confidential. You, the > recipient, are > > obligated to maintain it in a safe, secure and confidential manner. > > Unauthorized redisclosure or failure to maintain confidentiality may > > subject you to federal and state penalties. If you are not the intended > > recipient, please immediately notify us by return email, and delete > this > > message from your computer. > > > > > > > > ------------------------------ > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > > > > > End of Mristudio-users Digest, Vol 14, Issue 24 > > *********************************************** > > > > > > -- > Paul Beach > Michigan State University > College of Osteopathic Medicine > - Medical Scientist Training Program > Neuroscience Program > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > From xli16 at jhmi.edu Fri Mar 27 14:45:16 2009 From: xli16 at jhmi.edu (XIN LI) Date: Fri, 27 Mar 2009 14:45:16 -0400 Subject: [Mristudio-users] loading AIR files In-Reply-To: References: Message-ID: Sarah, The "AIR" file is not an image file. It has the transformation information and its format is special. You cannot open it using Landmarker but you can apply this AIR file to the loaded subject images and get updated images by clicking the button "load transformation matrix". The images that named "updated_filename" are the registerd images. The original image is still in the subject window. There is a image list in the right pannel. You can select the image that you want to display in the views. Hope this will give you some help. Xin ----- Original Message ----- From: "Copeland, Sarah A." Date: Friday, March 27, 2009 1:09 pm Subject: [Mristudio-users] loading AIR files To: "mristudio-users at mristudio.org" > Hello, > > I think that I may have managed to use AIR's linear registration to > register my anatomic image to the mean B0 image in landmarker. The > program asks you to supply a filename, and after the process is > complete I can find a file of type "AIR" in the correct location, but > can't open it. It's obviously not analyze format, but when I try to > open as "raw" I get the error "please enter an integer between 1 and > 4096" that pops up from time to time. However, the boxes which contain > 0s are greyed out and can't be changed. Any suggestions as to how I > can open and view the file? > > Also, the anatomic image filename in the open "subject" window now > has the name "updated_filename". Is this still the original, or is the > registered image? I can't open the original when this one is open, so > I thought perhaps this is still the original file just with "updated" > appended, but I'm not sure. If it's the registered image, the > registration is not working very well, so I'm hoping it's not. > > Thanks so much - > > Sarah Copeland > > IMPORTANT WARNING: This email (and any attachments) is only intended > for the use of the person or entity to which it is addressed, and may > contain information that is privileged and confidential. You, the > recipient, are obligated to maintain it in a safe, secure and > confidential manner. Unauthorized redisclosure or failure to maintain > confidentiality may subject you to federal and state penalties. If you > are not the intended recipient, please immediately notify us by return > email, and delete this message from your computer. > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > From susumu at mri.jhu.edu Fri Mar 27 21:09:44 2009 From: susumu at mri.jhu.edu (susumu) Date: Fri, 27 Mar 2009 21:09:44 -0400 Subject: [Mristudio-users] Problem with Landmarker not loading subjects In-Reply-To: <8874e3900903251055o49f6detf48792a6ff04fee1@mail.gmail.com> Message-ID: <7k7ed7$6sihma@ipex3.johnshopkins.edu> Hi Paul (and also one of the questions Sarah asked recently), What you experienced ("please enter a number between 0 and 4096") is a sort of a small bug. In the image parameter windows, you are not allowed to put 0 for image dimensions and pixel sizes. However, when you specify Analyze and Dicom, these sections are grayed out (because these parameters are obtained from the headers) and you can't change them even if one of the sections have 0. When you encounter this problem, please temporarily choose the "raw" format, activate the image parameter sections, input any numbers other than 0, and then choose Analyze or Dicom again. This should work, I hope. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Paul Beach Sent: Wednesday, March 25, 2009 1:56 PM To: Mristudio-users at mristudio.org Subject: [Mristudio-users] Problem with Landmarker not loading subjects Hi everyone, So every once and a while I'll be on Landmarker and when I'm trying to load a subject I'll receive an error message saying "please enter a number between 0 and 4096." The first time this happened I just closed all my programs and reopened Landmarker and things worked again. Other times (such as the latest one) I went so far as to restart my computer, which lead to no effect. This is obviously a huge problem as I can't load subjects whatsoever. Any ideas? Thanks, Paul p.s. In case this is necessary information, I've been using landmarks to reorient subject brains and fiber tracts using affine/rigid transformations. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090327/021c38d8/attachment-0001.html From SCopeland at mednet.ucla.edu Mon Mar 30 14:20:21 2009 From: SCopeland at mednet.ucla.edu (Copeland, Sarah A.) Date: Mon, 30 Mar 2009 11:20:21 -0700 Subject: [Mristudio-users] image quality flags Message-ID: Hello, I have a question about how to use the image quality flag feature in DTI studio. First, when you view the original images and choose the flagged ones, is there a particular button or appropriate way to save the .flg file, or do you just save it using the "save" icon and create a file with the .flg extension? Second, since the ability to view and flag the images isn't there until after you run DTI mapping, should you save the flag file and then re-run DTI mapping so that you can check the box which incorporates the information from the .flg file? Thanks for your help. Sarah Copeland IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. From SCopeland at mednet.ucla.edu Mon Mar 30 14:33:23 2009 From: SCopeland at mednet.ucla.edu (Copeland, Sarah A.) Date: Mon, 30 Mar 2009 11:33:23 -0700 Subject: [Mristudio-users] image quality flags Message-ID: Hello, I have a question about how to use the image quality flag feature in DTI studio. First, when you view the original images and choose the flagged ones, is there a particular button or appropriate way to save the .flg file, or do you just save it using the "save" icon and create a file with the .flg extension? Second, since the ability to view and flag the images isn't there until after you run DTI mapping, should you save the flag file and then re-run DTI mapping so that you can check the box which incorporates the information from the .flg file? Thanks for your help. Sarah Copeland IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. From SCopeland at mednet.ucla.edu Mon Mar 30 14:33:31 2009 From: SCopeland at mednet.ucla.edu (Copeland, Sarah A.) Date: Mon, 30 Mar 2009 11:33:31 -0700 Subject: [Mristudio-users] image quality flags Message-ID: Hello, I have a question about how to use the image quality flag feature in DTI studio. First, when you view the original images and choose the flagged ones, is there a particular button or appropriate way to save the .flg file, or do you just save it using the "save" icon and create a file with the .flg extension? Second, since the ability to view and flag the images isn't there until after you run DTI mapping, should you save the flag file and then re-run DTI mapping so that you can check the box which incorporates the information from the .flg file? Thanks for your help. Sarah Copeland IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. From pabeach1 at gmail.com Tue Mar 31 14:53:23 2009 From: pabeach1 at gmail.com (Paul Beach) Date: Tue, 31 Mar 2009 14:53:23 -0400 Subject: [Mristudio-users] problem with re-oriented fiber tracts Message-ID: <8874e3900903311153q388ca5ebode55e5fef272e53a@mail.gmail.com> Hi everyone, I'm in the process of reorienting subjects to a more standard space using 7 landmarks across subjects. For the most part the transformation matrix saved post rigid/affine transformation is reorienting fiber tracts perfectly (we're confirming this using FSL). However some subject's fiber tracts are going way off when we apply their respective transformation matrices. They'll be slanted in the axial view, etc. Something I've noticed is that the subjects whose tracts are mis-rotated are loading into landmarker upside down and require me to remove a (-) sign from their raw image information. However, not all subjects that load upside down are resulting in fiber tracts that are mis-oriented. Any suggestions as to why this might be occurring? Thanks, Paul -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090331/8f55cfcc/attachment.html From susumu at mri.jhu.edu Tue Mar 31 18:35:18 2009 From: susumu at mri.jhu.edu (susumu) Date: Tue, 31 Mar 2009 18:35:18 -0400 Subject: [Mristudio-users] problem with re-oriented fiber tracts In-Reply-To: <8874e3900903311153q388ca5ebode55e5fef272e53a@mail.gmail.com> Message-ID: <7k7ed7$6to5jl@ipex3.johnshopkins.edu> Hi Paul, Several questions: 1) Did you do tracking before the rotation, converted to 1/0 binary image, and rotate with the image? 2) Or did you rotate the image and then do the tracking? If so, did you rotate the tensor using the "Open *.d" button so that you can get correct tensor re-orientation? 3) You mentioned, "upside-down". Does it mean you did #1 above? If you did tracking after image rotation (#2 approach), I guess you won't get the fiber upside-down with respect to the image. 4) What do you mean by (-) sign of the raw image? In general, if you get your image upside-down, the culprit is the mixture of our raw format (Radiology convention) and the Analyze format (Neurology convention as the default). Please clarify. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Paul Beach Sent: Tuesday, March 31, 2009 2:53 PM To: Mristudio-users at mristudio.org Subject: [Mristudio-users] problem with re-oriented fiber tracts Hi everyone, I'm in the process of reorienting subjects to a more standard space using 7 landmarks across subjects. For the most part the transformation matrix saved post rigid/affine transformation is reorienting fiber tracts perfectly (we're confirming this using FSL). However some subject's fiber tracts are going way off when we apply their respective transformation matrices. They'll be slanted in the axial view, etc. Something I've noticed is that the subjects whose tracts are mis-rotated are loading into landmarker upside down and require me to remove a (-) sign from their raw image information. However, not all subjects that load upside down are resulting in fiber tracts that are mis-oriented. Any suggestions as to why this might be occurring? Thanks, Paul -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090331/846b644f/attachment.html From c.bieck at T-Online.de Wed Apr 1 06:08:00 2009 From: c.bieck at T-Online.de (Christian Bieck) Date: Wed, 01 Apr 2009 10:08 +0000 (GMT) Subject: [Mristudio-users] How to do a Tailarach transformation? Message-ID: <1LoxNJ-1tzuBE0@fwd05.aul.t-online.de> Hello, I made an attempt at 2) and did a rigid AIR transformation, followed by an LDDMM. As the grey scale images have to be in byte format, I transformed both the JHU_MNI_GA_DWI sample image and one of my test subject's DWI file to byte format via the BFW button. I then went on to do an automated single channel LDDMM, not changing the default parameters, and after a while Landmarker said that the files had been sent. Now while I typed in my registered email address, I didn't get a confirmation nor a Process Complete email, so I'm wondering how long such a remote LDDMM processing normally takes or if I made some mistake during the whole process. Are there any vital details during LDDMM that I may have overlooked? Any input would be greatly appreciated. Thanks for your time. Sincerely, Christian Bieck > > Hi Christian, > > Sorry that the manuals for Landmarker and RoiEditor are still quite behind. > This year, we will most likely provide 2-day tutorial in Hawaii ISMRM (Sat > and Sun). Announcement will be sent next week. Join one of these tutorials > is the best way at this point. We are working on manuals and hopefully can > provide "Getting Started" soon. > > As for your question, there are several points I want to make; > 1) There are three ways to do normalization: manual landmark-based (rigid, > affine, and LDDMM), automated linear & low-order non-linear (AIR), and > automated high-order non-linear (LDDMM). > 2) Usually, automated AIR (rigid or affine) + automated LDDMM is the easiest > way. > 3) Talairach brain is VERY different from normal subjects. To accurately > transform your data to Talairach, AIR is not enough. You need extensive > landmarking or AIR+LDDMM. > 4) Manual landmark-based normalization has a great flexibility but it's time > consuming and require some experience. > > I recommend you to start with #2. If you don't come to ISMRM, please wait > for the Getting Started or you are welcome to visit my lab. > > Susumu From vikey.han at 163.com Tue Mar 31 23:05:23 2009 From: vikey.han at 163.com (vikey.han) Date: Wed, 01 Apr 2009 11:05:23 +0800 (CST) Subject: [Mristudio-users] unable to generate FA image Message-ID: <23854935.129451238555123410.JavaMail.coremail@bj163app110.163.com> Hi everyone, I use DTIstudio to compute FA image, but find the result is not correct, the attachment is the snapshot of FA image, could you tell me what mistakes I make probably? thanks, vikey -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090401/3dda674d/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: 1.bmp Type: image/bmp Size: 1476006 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090401/3dda674d/attachment-0001.bmp From susumu at mri.jhu.edu Wed Apr 1 07:41:08 2009 From: susumu at mri.jhu.edu (susumu) Date: Wed, 01 Apr 2009 07:41:08 -0400 Subject: [Mristudio-users] unable to generate FA image In-Reply-To: <23854935.129451238555123410.JavaMail.coremail@bj163app110.163.com> References: <23854935.129451238555123410.JavaMail.coremail@bj163app110.163.com> Message-ID: <3E8E2E3E3E774A2EAC0E0F6C89A7B262@SusumuThinkPad> Hi Vikey, It seems the image looks fine. If you are concerning about the bright signals outside the brain, that?s because FA was calculated for the noise floor. To remove these signals from outside the brain, please raise the threshold value (the default is ?10?), which you can specify when you do the tensor calculation. _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of vikey.han Sent: Tuesday, March 31, 2009 11:05 PM To: Mristudio-users at mristudio.org Subject: [Mristudio-users] unable to generate FA image Hi everyone, I use DTIstudio to compute FA image, but find the result is not correct, the attachment is the snapshot of FA image, could you tell me what mistakes I make probably? thanks, vikey _____ ????????????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090401/822309ae/attachment.html From susumu at mri.jhu.edu Wed Apr 1 07:48:28 2009 From: susumu at mri.jhu.edu (susumu) Date: Wed, 01 Apr 2009 07:48:28 -0400 Subject: [Mristudio-users] How to do a Tailarach transformation? In-Reply-To: <1LoxNJ-1tzuBE0@fwd05.aul.t-online.de> References: <1LoxNJ-1tzuBE0@fwd05.aul.t-online.de> Message-ID: Once you get the confirmation email, you should receive the results. It usually takes about 2-6 hours depending on the length of the queue. If you don't receive the results within 24 hours, please let us know, by sending an email to xli at jhmi.edu with the identifier number. We will have substantial increase in our computational resource this year. I hope this will open up the throughput a lot. -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Christian Bieck Sent: Wednesday, April 01, 2009 6:08 AM To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] How to do a Tailarach transformation? Hello, I made an attempt at 2) and did a rigid AIR transformation, followed by an LDDMM. As the grey scale images have to be in byte format, I transformed both the JHU_MNI_GA_DWI sample image and one of my test subject's DWI file to byte format via the BFW button. I then went on to do an automated single channel LDDMM, not changing the default parameters, and after a while Landmarker said that the files had been sent. Now while I typed in my registered email address, I didn't get a confirmation nor a Process Complete email, so I'm wondering how long such a remote LDDMM processing normally takes or if I made some mistake during the whole process. Are there any vital details during LDDMM that I may have overlooked? Any input would be greatly appreciated. Thanks for your time. Sincerely, Christian Bieck > > Hi Christian, > > Sorry that the manuals for Landmarker and RoiEditor are still quite behind. > This year, we will most likely provide 2-day tutorial in Hawaii ISMRM (Sat > and Sun). Announcement will be sent next week. Join one of these tutorials > is the best way at this point. We are working on manuals and hopefully can > provide "Getting Started" soon. > > As for your question, there are several points I want to make; > 1) There are three ways to do normalization: manual landmark-based (rigid, > affine, and LDDMM), automated linear & low-order non-linear (AIR), and > automated high-order non-linear (LDDMM). > 2) Usually, automated AIR (rigid or affine) + automated LDDMM is the easiest > way. > 3) Talairach brain is VERY different from normal subjects. To accurately > transform your data to Talairach, AIR is not enough. You need extensive > landmarking or AIR+LDDMM. > 4) Manual landmark-based normalization has a great flexibility but it's time > consuming and require some experience. > > I recommend you to start with #2. If you don't come to ISMRM, please wait > for the Getting Started or you are welcome to visit my lab. > > Susumu _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From xli16 at jhmi.edu Wed Apr 1 09:58:48 2009 From: xli16 at jhmi.edu (Xin Li) Date: Wed, 01 Apr 2009 09:58:48 -0400 Subject: [Mristudio-users] How to do a Tailarach transformation? In-Reply-To: <1LoxNJ-1tzuBE0@fwd05.aul.t-online.de> References: <1LoxNJ-1tzuBE0@fwd05.aul.t-online.de> Message-ID: Christian, Do you mean that you didn't receive any confirmation or process complete emails from mristudio after you had sent the data to mristudio server? Xin ----- Original Message ----- From: Christian Bieck Date: Wednesday, April 1, 2009 6:09 am Subject: Re: [Mristudio-users] How to do a Tailarach transformation? To: mristudio-users at mristudio.org > Hello, > > I made an attempt at 2) and did a rigid AIR transformation, followed > by an LDDMM. As the grey scale images have to be in byte format, I > transformed both the JHU_MNI_GA_DWI sample image and one of my test > subject's DWI file to byte format via the BFW button. > I then went on to do an automated single channel LDDMM, not changing > the default parameters, and after a while Landmarker said that the > files had been sent. > Now while I typed in my registered email address, I didn't get a > confirmation nor a Process Complete email, so I'm wondering how long > such a remote LDDMM processing normally takes or if I made some > mistake during the whole process. > Are there any vital details during LDDMM that I may have overlooked? > Any input would be greatly appreciated. Thanks for your time. > > Sincerely, > Christian Bieck > > > > > Hi Christian, > > > > Sorry that the manuals for Landmarker and RoiEditor are still quite > behind. > > This year, we will most likely provide 2-day tutorial in Hawaii > ISMRM (Sat > > and Sun). Announcement will be sent next week. Join one of these tutorials > > is the best way at this point. We are working on manuals and > hopefully can > > provide "Getting Started" soon. > > > > As for your question, there are several points I want to make; > > 1) There are three ways to do normalization: manual landmark-based > (rigid, > > affine, and LDDMM), automated linear & low-order non-linear (AIR), > and > > automated high-order non-linear (LDDMM). > > 2) Usually, automated AIR (rigid or affine) + automated LDDMM is > the easiest > > way. > > 3) Talairach brain is VERY different from normal subjects. To accurately > > transform your data to Talairach, AIR is not enough. You need extensive > > landmarking or AIR+LDDMM. > > 4) Manual landmark-based normalization has a great flexibility but > it's time > > consuming and require some experience. > > > > I recommend you to start with #2. If you don't come to ISMRM, > please wait > > for the Getting Started or you are welcome to visit my lab. > > > > Susumu > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > From zhou1 at jhmi.edu Wed Apr 1 10:49:10 2009 From: zhou1 at jhmi.edu (Zhipeng Hou) Date: Wed, 01 Apr 2009 10:49:10 -0400 Subject: [Mristudio-users] How to do a Tailarach transformation? In-Reply-To: References: <1LoxNJ-1tzuBE0@fwd05.aul.t-online.de> Message-ID: <568cc7760904010749w3cb48398n6b4b70946694172b@mail.gmail.com> It will takes more than 24 hours if more people submit together. So please wait one more day. On Wed, Apr 1, 2009 at 7:48 AM, susumu wrote: > Once you get the confirmation email, you should receive the results. > It usually takes about 2-6 hours depending on the length of the queue. > > If you don't receive the results within 24 hours, please let us know, by > sending an email to xli at jhmi.edu with the identifier number. > > We will have substantial increase in our computational resource this year. > I > hope this will open up the throughput a lot. > > -----Original Message----- > From: mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Christian > Bieck > Sent: Wednesday, April 01, 2009 6:08 AM > To: mristudio-users at mristudio.org > Subject: Re: [Mristudio-users] How to do a Tailarach transformation? > > Hello, > > I made an attempt at 2) and did a rigid AIR transformation, followed by an > LDDMM. As the grey scale images have to be in byte format, I transformed > both the JHU_MNI_GA_DWI sample image and one of my test subject's DWI file > to byte format via the BFW button. > I then went on to do an automated single channel LDDMM, not changing the > default parameters, and after a while Landmarker said that the files had > been sent. > Now while I typed in my registered email address, I didn't get a > confirmation nor a Process Complete email, so I'm wondering how long such a > remote LDDMM processing normally takes or if I made some mistake during the > whole process. > Are there any vital details during LDDMM that I may have overlooked? > Any input would be greatly appreciated. Thanks for your time. > > Sincerely, > Christian Bieck > > > > > Hi Christian, > > > > Sorry that the manuals for Landmarker and RoiEditor are still quite > behind. > > This year, we will most likely provide 2-day tutorial in Hawaii ISMRM > (Sat > > and Sun). Announcement will be sent next week. Join one of these > tutorials > > is the best way at this point. We are working on manuals and hopefully > can > > provide "Getting Started" soon. > > > > As for your question, there are several points I want to make; > > 1) There are three ways to do normalization: manual landmark-based > (rigid, > > affine, and LDDMM), automated linear & low-order non-linear (AIR), and > > automated high-order non-linear (LDDMM). > > 2) Usually, automated AIR (rigid or affine) + automated LDDMM is the > easiest > > way. > > 3) Talairach brain is VERY different from normal subjects. To accurately > > transform your data to Talairach, AIR is not enough. You need extensive > > landmarking or AIR+LDDMM. > > 4) Manual landmark-based normalization has a great flexibility but it's > time > > consuming and require some experience. > > > > I recommend you to start with #2. If you don't come to ISMRM, please wait > > for the Getting Started or you are welcome to visit my lab. > > > > Susumu > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090401/0aa1195f/attachment.html From vikey.han at 163.com Wed Apr 1 10:29:47 2009 From: vikey.han at 163.com (vikey.han) Date: Wed, 01 Apr 2009 22:29:47 +0800 (CST) Subject: [Mristudio-users] unable to generate FA image In-Reply-To: <3E8E2E3E3E774A2EAC0E0F6C89A7B262@SusumuThinkPad> References: <3E8E2E3E3E774A2EAC0E0F6C89A7B262@SusumuThinkPad> <23854935.129451238555123410.JavaMail.coremail@bj163app110.163.com> Message-ID: <23914403.449651238596187372.JavaMail.coremail@bj163app64.163.com> Thanks, susumu, I doubt the FA image because I can't get the correct fiber streamlines, but I think I have selected the corrected parameters. Could you help me check it? the attachment includes the data and parameters. susumu wrote? Hi Vikey, It seems the image looks fine. If you are concerning about the bright signals outside the brain, that?s because FA was calculated for the noise floor. To remove these signals from outside the brain, please raise the threshold value (the default is ?10?), which you can specify when you do the tensor calculation. From:mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of vikey.han Sent: Tuesday, March 31, 2009 11:05 PM To:Mristudio-users at mristudio.org Subject: [Mristudio-users] unable to generate FA image Hi everyone, I use DTIstudio to compute FA image, but find the result is not correct, the attachment is the snapshot of FA image, could you tell me what mistakes I make probably? thanks, vikey ????????????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090401/f641f41d/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: para.rar Type: application/octet-stream Size: 214922 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090401/f641f41d/attachment-0002.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: 1.rar Type: application/octet-stream Size: 12670964 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090401/f641f41d/attachment-0003.obj From tangjinsonghn at yahoo.com.cn Tue Apr 7 12:51:58 2009 From: tangjinsonghn at yahoo.com.cn (jinsong tang) Date: Wed, 08 Apr 2009 00:51:58 +0800 (CST) Subject: [Mristudio-users] =?utf-8?q?_re=EF=BC=9A__How_to_do_a_Tailarach_t?= =?utf-8?q?ransformation=3F?= In-Reply-To: References: <1LoxNJ-1tzuBE0@fwd05.aul.t-online.de> Message-ID: <474451.99686.qm@web15608.mail.cnb.yahoo.com> Hello everyone, Now the Siemens? 3.0 T MRI?scanner can collect?30 ?non-collinear directions diffusion data. Does this?helpful for fiber tracking ? ? But I found most paper only use 12 directions. Does anybody know why? ? Best, ? Jinsong ___________________________________________________________ ????????????????? http://card.mail.cn.yahoo.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090408/94e9cade/attachment.html From susumu at mri.jhu.edu Tue Apr 7 13:36:27 2009 From: susumu at mri.jhu.edu (susumu) Date: Tue, 07 Apr 2009 13:36:27 -0400 Subject: [Mristudio-users] =?gb2312?b?cmWjuiAgSG93IHRvIGRvIGEgVGFpbGFyYWNo?= =?gb2312?b?IHRyYW5zZm9ybWF0aW9uPw==?= In-Reply-To: <474451.99686.qm@web15608.mail.cnb.yahoo.com> References: <1LoxNJ-1tzuBE0@fwd05.aul.t-online.de> <474451.99686.qm@web15608.mail.cnb.yahoo.com> Message-ID: <460AFE188A494F4CB51F30253AAB0F5D@SusumuThinkPad> Hi Jinsong, It depends on whom you ask the question, but here is my opinion. When you are using diffusion ??tensor?? imaging, all data will be fitted to obtain only the 6 tensor elements. Therefore, you need only 6 directions mathematically. However, such measurement takes only less than 1 min and do not have enough SNR (signal-to-noise ratio). To enhance the SNR, you need to acquire more data. Usually people spend 4-10 min of time for DTI, in which you can acquire about 30 ?C 100 images. Then you have several options. For example, you can repeat the 6-orientation measurement 5 times (total 30) or one 30-orientation measurement within the same amount of time (should be within 5 min). Purely from mathematical point of views, I don??t think 6-direction x 5 vs 30-orientation have that much difference in terms of overall SNR. However, it is true that the 6-orientation measurement has more orientation-dependent inhomogeneity in SNR. This means, certain orientations can be measured with higher SNR while some orientation has poorer SNR. By adopting more orientations, such orientation-dependent SNR profile becomes more homogeneous (less orientation dependent). In reality, within practical imaging time, I don??t think you can observe such effect clearly. Our past measurement (Landman et al, NeuroImage) suggests once you have 12-orientation or more, you don??t see much differences. Some researchers are seeking for diffusion ??more than one tensor?? imaging. If you want it, you may need more than 30 orientations and higher b-values. So, you may need to design very different protocols. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of jinsong tang Sent: Tuesday, April 07, 2009 12:52 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] re?? How to do a Tailarach transformation? Hello everyone, Now the Siemens 3.0 T MRI scanner can collect 30 non-collinear directions diffusion data. Does this helpful for fiber tracking ? But I found most paper only use 12 directions. Does anybody know why? Best, Jinsong _____ ?????????????????????????????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090407/43cf64e8/attachment.html From mithra at mail.utexas.edu Tue Apr 7 15:32:14 2009 From: mithra at mail.utexas.edu (Mithra) Date: Tue, 07 Apr 2009 14:32:14 -0500 Subject: [Mristudio-users] Load a nifti file Message-ID: <42fe38b80904071232p1285ddbeu6ddf9b6097975fde@mail.gmail.com> Hello, I was wondering if there is any way to load a nifti file in DTIStudio. I found the FA score and the eigen vectors using FDT tool in FSL. All the data I obtained are in Nifti format. Is there a way I can open them in DTI STudio or do I need to convert them to analyze format. Thank you. Regards, Mithra. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090407/696bcd31/attachment.html From jyw.chen at utoronto.ca Tue Apr 7 18:51:07 2009 From: jyw.chen at utoronto.ca (Jerry Yeou-Wei Chen) Date: Tue, 07 Apr 2009 18:51:07 -0400 Subject: [Mristudio-users] image quality flags In-Reply-To: References: Message-ID: <3050363f0904071551i758b369cve3b6c41a002473df@mail.gmail.com> Hi Sarah, I'm not sure if I understand your question correctly.... but my understanding is that this is the typical order of operations in using the flag file: 1) create the flag file: when loading a DTI series, you type in the name (and path) of the file you wish to create in the textbox under the "Image Quality Flag File (Optional)" section of the "DW-Image Parameters" window (e.g. F:\data\myflagfile.flg) 2) fill in the rest of the window to load your DTI series 3) calculate Mean, STD ... 4) display Original - ADC - Mean - STD 5) flag the bad slices at this point, you can re-calculate the Mean, STD ... and it will take into account the flags when you close the window, you'll be asked it you want to save the flg file - say yes next time when you open the series, load the flg file you saved, and you can re-calculate the Mean, STD ... Hope that helps, - Jerry Slide 2 ?Calculate Mean, STD ? ?Display Original ? ADC ? Mean - STD ?Filter out bad scans On Mon, Mar 30, 2009 at 2:20 PM, Copeland, Sarah A. < SCopeland at mednet.ucla.edu> wrote: > Hello, > > I have a question about how to use the image quality flag feature in DTI > studio. First, when you view the original images and choose the flagged > ones, is there a particular button or appropriate way to save the .flg file, > or do you just save it using the "save" icon and create a file with the .flg > extension? > > Second, since the ability to view and flag the images isn't there until > after you run DTI mapping, should you save the flag file and then re-run DTI > mapping so that you can check the box which incorporates the information > from the .flg file? > > Thanks for your help. > > Sarah Copeland > > IMPORTANT WARNING: This email (and any attachments) is only intended for > the use of the person or entity to which it is addressed, and may contain > information that is privileged and confidential. You, the recipient, are > obligated to maintain it in a safe, secure and confidential manner. > Unauthorized redisclosure or failure to maintain confidentiality may > subject you to federal and state penalties. If you are not the intended > recipient, please immediately notify us by return email, and delete this > message from your computer. > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090407/6484c3fb/attachment-0001.html From choisj70 at gmail.com Tue Apr 7 22:31:14 2009 From: choisj70 at gmail.com (Seongjin) Date: Tue, 07 Apr 2009 22:31:14 -0400 Subject: [Mristudio-users] =?gb2312?b?IFJlOiAgcmWjuiBIb3cgdG8gZG8gYSBUYWls?= =?gb2312?b?YXJhY2ggdHJhbnNmb3JtYXRpb24/?= In-Reply-To: <460AFE188A494F4CB51F30253AAB0F5D@SusumuThinkPad> References: <1LoxNJ-1tzuBE0@fwd05.aul.t-online.de> <474451.99686.qm@web15608.mail.cnb.yahoo.com> <460AFE188A494F4CB51F30253AAB0F5D@SusumuThinkPad> Message-ID: Dear Susumu, Do you have relevant literature on your opinion: "...In reality, within practical imaging time, I don??t think you can observe such effect clearly. Our past measurement (Landman et al, NeuroImage) suggests once you have 12-orientation or more, you don??t see much differences..." If you had, could you share the literature? Thanks. - SC 2009/4/7 susumu > Hi Jinsong, > > > > It depends on whom you ask the question, but here is my opinion. > > > > When you are using diffusion ??tensor?? imaging, all data will be fitted to > obtain only the 6 tensor elements. Therefore, you need only 6 directions > mathematically. However, such measurement takes only less than 1 min and do > not have enough SNR (signal-to-noise ratio). To enhance the SNR, you need to > acquire more data. > > > > Usually people spend 4-10 min of time for DTI, in which you can acquire > about 30 ?C 100 images. Then you have several options. For example, you can > repeat the 6-orientation measurement 5 times (total 30) or one > 30-orientation measurement within the same amount of time (should be within > 5 min). > > > > Purely from mathematical point of views, I don??t think 6-direction x 5 vs > 30-orientation have that much difference in terms of overall SNR. However, > it is true that the 6-orientation measurement has more orientation-dependent > inhomogeneity in SNR. This means, certain orientations can be measured with > higher SNR while some orientation has poorer SNR. By adopting more > orientations, such orientation-dependent SNR profile becomes more > homogeneous (less orientation dependent). > > > > In reality, within practical imaging time, I don??t think you can observe > such effect clearly. Our past measurement (Landman et al, NeuroImage) > suggests once you have 12-orientation or more, you don??t see much > differences. > > > > Some researchers are seeking for diffusion ??more than one tensor?? imaging. > If you want it, you may need more than 30 orientations and higher b-values. > So, you may need to design very different protocols. > > > > Susumu > > > > > > > ------------------------------ > > *From:* mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org] *On Behalf Of *jinsong tang > *Sent:* Tuesday, April 07, 2009 12:52 PM > *To:* DTI Studio, ROI Editor, Landmarker Questions/Support > *Subject:* [Mristudio-users] re?? How to do a Tailarach transformation? > > > > Hello everyone, > > > > Now the Siemens 3.0 T MRI scanner can collect 30 non-collinear > directions diffusion data. Does this helpful for fiber tracking ? > > > > But I found most paper only use 12 directions. Does anybody know why? > > > > Best, > > > > Jinsong > > > ------------------------------ > > ?????????????????????????????????? > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090407/6c1900e1/attachment.html From susumu at mri.jhu.edu Wed Apr 8 11:10:01 2009 From: susumu at mri.jhu.edu (susumu) Date: Wed, 08 Apr 2009 11:10:01 -0400 Subject: [Mristudio-users] =?gb2312?b?cmWjuiBIb3cgdG8gZG8gYSBUYWlsYXJhY2gg?= =?gb2312?b?dHJhbnNmb3JtYXRpb24/?= In-Reply-To: Message-ID: <7k7ed7$70cpil@ipex3.johnshopkins.edu> Here it is. _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of [Seongjin] Sent: Tuesday, April 07, 2009 10:31 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] Re: re?? How to do a Tailarach transformation? Dear Susumu, Do you have relevant literature on your opinion: "...In reality, within practical imaging time, I don??t think you can observe such effect clearly. Our past measurement (Landman et al, NeuroImage) suggests once you have 12-orientation or more, you don??t see much differences..." If you had, could you share the literature? Thanks. - SC 2009/4/7 susumu Hi Jinsong, It depends on whom you ask the question, but here is my opinion. When you are using diffusion ??tensor?? imaging, all data will be fitted to obtain only the 6 tensor elements. Therefore, you need only 6 directions mathematically. However, such measurement takes only less than 1 min and do not have enough SNR (signal-to-noise ratio). To enhance the SNR, you need to acquire more data. Usually people spend 4-10 min of time for DTI, in which you can acquire about 30 ?C 100 images. Then you have several options. For example, you can repeat the 6-orientation measurement 5 times (total 30) or one 30-orientation measurement within the same amount of time (should be within 5 min). Purely from mathematical point of views, I don??t think 6-direction x 5 vs 30-orientation have that much difference in terms of overall SNR. However, it is true that the 6-orientation measurement has more orientation-dependent inhomogeneity in SNR. This means, certain orientations can be measured with higher SNR while some orientation has poorer SNR. By adopting more orientations, such orientation-dependent SNR profile becomes more homogeneous (less orientation dependent). In reality, within practical imaging time, I don??t think you can observe such effect clearly. Our past measurement (Landman et al, NeuroImage) suggests once you have 12-orientation or more, you don??t see much differences. Some researchers are seeking for diffusion ??more than one tensor?? imaging. If you want it, you may need more than 30 orientations and higher b-values. So, you may need to design very different protocols. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of jinsong tang Sent: Tuesday, April 07, 2009 12:52 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] re?? How to do a Tailarach transformation? Hello everyone, Now the Siemens 3.0 T MRI scanner can collect 30 non-collinear directions diffusion data. Does this helpful for fiber tracking ? But I found most paper only use 12 directions. Does anybody know why? Best, Jinsong _____ ?????????????????????????????????? _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090408/7085e1e5/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: reprient.pdf Type: application/pdf Size: 3028073 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090408/7085e1e5/attachment-0001.pdf From mithra at mail.utexas.edu Wed Apr 8 12:31:20 2009 From: mithra at mail.utexas.edu (Mithra) Date: Wed, 08 Apr 2009 11:31:20 -0500 Subject: [Mristudio-users] Load a nifti file in DTIStudio Message-ID: <42fe38b80904080931q2c6177f6q6b11bc32bbc0174@mail.gmail.com> Hello, I was wondering if there is any way to load a nifti file in DTIStudio. I found the FA score and the eigen vectors using FDT tool in FSL. All the data I obtained are in Nifti format. Is there a way I can open them in DTI STudio or do I need to convert them to analyze format. Thank you. Regards, Mithra. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090408/292b0e6c/attachment.html From choisj70 at gmail.com Wed Apr 8 14:37:52 2009 From: choisj70 at gmail.com (Seongjin) Date: Wed, 08 Apr 2009 14:37:52 -0400 Subject: [Mristudio-users] =?gb2312?b?IFJlOiAgcmWjuiBIb3cgdG8gZG8gYSBUYWls?= =?gb2312?b?YXJhY2ggdHJhbnNmb3JtYXRpb24/?= In-Reply-To: <7k7ed7$70cpil@ipex3.johnshopkins.edu> References: <7k7ed7$70cpil@ipex3.johnshopkins.edu> Message-ID: Thanks a lot! SC 2009/4/8 susumu > Here it is. > > ------------------------------ > *From:* mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org] *On Behalf Of *[Seongjin] > *Sent:* Tuesday, April 07, 2009 10:31 PM > *To:* DTI Studio, ROI Editor, Landmarker Questions/Support > *Subject:* [Mristudio-users] Re: re?? How to do a Tailarach transformation? > > Dear Susumu, > > Do you have relevant literature on your opinion: > > "...In reality, within practical imaging time, I don??t think you can > observe such effect clearly. Our past measurement (Landman et al, > NeuroImage) suggests once you have 12-orientation or more, you don??t see > much differences..." > > If you had, could you share the literature? > > Thanks. > > - SC > > > 2009/4/7 susumu > >> Hi Jinsong, >> >> >> >> It depends on whom you ask the question, but here is my opinion. >> >> >> >> When you are using diffusion ??tensor?? imaging, all data will be fitted to >> obtain only the 6 tensor elements. Therefore, you need only 6 directions >> mathematically. However, such measurement takes only less than 1 min and do >> not have enough SNR (signal-to-noise ratio). To enhance the SNR, you need to >> acquire more data. >> >> >> >> Usually people spend 4-10 min of time for DTI, in which you can acquire >> about 30 ?C 100 images. Then you have several options. For example, you can >> repeat the 6-orientation measurement 5 times (total 30) or one >> 30-orientation measurement within the same amount of time (should be within >> 5 min). >> >> >> >> Purely from mathematical point of views, I don??t think 6-direction x 5 vs >> 30-orientation have that much difference in terms of overall SNR. However, >> it is true that the 6-orientation measurement has more orientation-dependent >> inhomogeneity in SNR. This means, certain orientations can be measured with >> higher SNR while some orientation has poorer SNR. By adopting more >> orientations, such orientation-dependent SNR profile becomes more >> homogeneous (less orientation dependent). >> >> >> >> In reality, within practical imaging time, I don??t think you can observe >> such effect clearly. Our past measurement (Landman et al, NeuroImage) >> suggests once you have 12-orientation or more, you don??t see much >> differences. >> >> >> >> Some researchers are seeking for diffusion ??more than one tensor?? imaging. >> If you want it, you may need more than 30 orientations and higher b-values. >> So, you may need to design very different protocols. >> >> >> >> Susumu >> >> >> >> >> >> >> ------------------------------ >> >> *From:* mristudio-users-bounces at mristudio.org [mailto: >> mristudio-users-bounces at mristudio.org] *On Behalf Of *jinsong tang >> *Sent:* Tuesday, April 07, 2009 12:52 PM >> *To:* DTI Studio, ROI Editor, Landmarker Questions/Support >> *Subject:* [Mristudio-users] re?? How to do a Tailarach transformation? >> >> >> >> Hello everyone, >> >> >> >> Now the Siemens 3.0 T MRI scanner can collect 30 non-collinear >> directions diffusion data. Does this helpful for fiber tracking ? >> >> >> >> But I found most paper only use 12 directions. Does anybody know why? >> >> >> >> Best, >> >> >> >> Jinsong >> >> >> ------------------------------ >> >> ?????????????????????????????????? >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/mristudio-users >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090408/c22787a5/attachment.html From james.neeley at duke.edu Wed Apr 8 17:33:54 2009 From: james.neeley at duke.edu (Jim Neeley) Date: Wed, 08 Apr 2009 17:33:54 -0400 Subject: [Mristudio-users] Siemens Mosaic with bad colors In-Reply-To: <42fe38b80904080931q2c6177f6q6b11bc32bbc0174@mail.gmail.com> References: <42fe38b80904080931q2c6177f6q6b11bc32bbc0174@mail.gmail.com> Message-ID: An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090408/f7b8bf79/attachment.html From wangxiuyuan85 at gmail.com Wed Apr 8 18:29:30 2009 From: wangxiuyuan85 at gmail.com (Hugh Wang) Date: Wed, 08 Apr 2009 18:29:30 -0400 Subject: [Mristudio-users] MriView3D application close Message-ID: Hi, I was using the dtistudio (ver. 2.4) to look at the Siemens DICOM diffusion images (1baseline,64 gradients). After successfully loading the images, I click the "dti map" option at lower right corner. Whatever calculation I choose, it always gives me an error: "MriView3D MFC Application has encountered a problem and needs to close. We are sorry for the inconvenience." I tried several PCs, and the problem keeped the same. I would appreciate that if there's anyone having any idea on how to solve it. Thanks. Best, Hugh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090408/174aa5a5/attachment.html From susumu at mri.jhu.edu Wed Apr 8 21:32:22 2009 From: susumu at mri.jhu.edu (susumu) Date: Wed, 08 Apr 2009 21:32:22 -0400 Subject: [Mristudio-users] Load a nifti file In-Reply-To: <42fe38b80904071232p1285ddbeu6ddf9b6097975fde@mail.gmail.com> Message-ID: <7k7ed7$70jdgm@ipex3.johnshopkins.edu> We have a new version not posted yet but can read Nifty. Please contact Hangyi if you want try one. _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Mithra Sent: Tuesday, April 07, 2009 3:32 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] Load a nifti file Hello, I was wondering if there is any way to load a nifti file in DTIStudio. I found the FA score and the eigen vectors using FDT tool in FSL. All the data I obtained are in Nifti format. Is there a way I can open them in DTI STudio or do I need to convert them to analyze format. Thank you. Regards, Mithra. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090408/0ed524ce/attachment-0001.html From tangjinsonghn at yahoo.com.cn Thu Apr 9 00:26:56 2009 From: tangjinsonghn at yahoo.com.cn (jinsong tang) Date: Thu, 09 Apr 2009 12:26:56 +0800 (CST) Subject: [Mristudio-users] =?utf-8?b?IHJl77yaICByZe+8miAgSG93IHRvIGRvIGEg?= =?utf-8?q?Tailarach_transformation=3F?= In-Reply-To: <460AFE188A494F4CB51F30253AAB0F5D@SusumuThinkPad> References: <1LoxNJ-1tzuBE0@fwd05.aul.t-online.de> <474451.99686.qm@web15608.mail.cnb.yahoo.com> <460AFE188A494F4CB51F30253AAB0F5D@SusumuThinkPad> Message-ID: <901519.89706.qm@web15605.mail.cnb.yahoo.com> Susumu, Thank you so much for your suggestions. Best, Jinsong ________________________________ ???? susumu ???? "DTI Studio, ROI Editor, Landmarker Questions/Support" ???? 2009/4/8(??), ??1:36:27 ??? Re: [Mristudio-users] re? How to do a Tailarach transformation? Hi Jinsong, ? It depends on whom you ask the question, but here is my opinion. ? When you are using diffusion ?tensor? imaging, all data will be fitted to obtain only the 6 tensor elements. Therefore, you need only 6 directions mathematically. However, such measurement takes only less than 1 min and do not have enough SNR (signal-to-noise ratio). To enhance the SNR, you need to acquire more data. ? Usually people spend 4-10 min of time for DTI, in which you can acquire about 30 ? 100 images. Then you have several options. For example, you can repeat the 6-orientation measurement 5 times (total 30) or one 30-orientation measurement within the same amount of time (should be within 5 min). ? Purely from mathematical point of views, I don?t think 6-direction x 5 vs 30-orientation have that much difference in terms of overall SNR. However, it is true that the 6-orientation measurement has more orientation-dependent inhomogeneity in SNR. This means, certain orientations can be measured with higher SNR while some orientation has poorer SNR. By adopting more orientations, such orientation-dependent SNR profile becomes more homogeneous (less orientation dependent). ? In reality, within practical imaging time, I don?t think you can observe such effect clearly. Our past measurement (Landman et al, NeuroImage) suggests once you have 12-orientation or more, you don?t see much differences. ? Some researchers are seeking for diffusion ?more than one tensor? imaging. If you want it, you may need more than 30 orientations and higher b-values. So, you may need to design very different protocols. ? Susumu ? ? ? ________________________________ From:mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of jinsong tang Sent: Tuesday, April 07, 2009 12:52 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] re?How to do a Tailarach transformation? ? Hello everyone, ? Now the Siemens? 3.0 T MRI?scanner can collect?30 ?non-collinear directions diffusion data. Does this?helpful for fiber tracking ? ? But I found most paper only use 12 directions. Does anybody know why? ? Best, ? Jinsong ? ________________________________ ????????????????? ___________________________________________________________ ????????????????? http://card.mail.cn.yahoo.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090409/3c2aecda/attachment.html From susumu at mri.jhu.edu Thu Apr 9 11:04:09 2009 From: susumu at mri.jhu.edu (susumu) Date: Thu, 09 Apr 2009 11:04:09 -0400 Subject: [Mristudio-users] MriView3D application close In-Reply-To: Message-ID: <7k7ed7$70pbun@ipex3.johnshopkins.edu> Hi Hugh, When you got this error, please suspect one of the following two reasons; 1) Memory shortage: Even if you have many GB of memories, 32-bit Windows system can allocate only 1 - 1.5 GB to each program. To check if you have the memory problem, please restrict the slices to be calculated. In the initial data parameter window, there is a section called "Slices to be processed". Here you can specify only a portion of slices to be processed. Please limit the slices to, for example, 0-9 and see how it goes. If you can calculate tensors without errors, then you have the memory problem. The solution is; a) upgrade to the 64-bit system or b) devide the calculation to 2 batches (e.g. slice 0-29 for the first batch and 30-59 for the second batch), calculate all maps (e.g. FA), and later combine them. 2) Mismatch between the gradient table and the number of images: For example, if you specify 12-orientation table and 30 volume images, then you get the error. After loading the data and before you go to the Dti Map tab, make sure that you have 1 b0 + 64 DWIs in the pull-down menu in the right column of the Image tab. If you have the correct number of the images, then you might have an error in your gradient table. Small mistakes such as missing "," are often difficult to detect. The best way is; a) load the data using DtiMapping under the "File" button on the top left, b) close the window, c) open the image paremater window again by clicking "DtiMapping" in the "File" button again, d) the window still remembers the gradient table you entered last time. This remembered window tells how DtiStudio interpreted your gradient table. If there is any syntax errors, you may find them much easier. For example, if you enter, "4: 1 0.5 0", instead of "4: 1, 0.5, 0", then you would find, "4: 1, 0, 0". If any of these do not solve the issue, please let us know. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hugh Wang Sent: Wednesday, April 08, 2009 6:30 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] MriView3D application close Hi, I was using the dtistudio (ver. 2.4) to look at the Siemens DICOM diffusion images (1baseline,64 gradients). After successfully loading the images, I click the "dti map" option at lower right corner. Whatever calculation I choose, it always gives me an error: "MriView3D MFC Application has encountered a problem and needs to close. We are sorry for the inconvenience." I tried several PCs, and the problem keeped the same. I would appreciate that if there's anyone having any idea on how to solve it. Thanks. Best, Hugh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090409/4fa0df17/attachment.html From wangxiuyuan85 at gmail.com Thu Apr 9 15:25:52 2009 From: wangxiuyuan85 at gmail.com (Hugh Wang) Date: Thu, 09 Apr 2009 15:25:52 -0400 Subject: [Mristudio-users] MriView3D application close In-Reply-To: <7k7ed7$70pbun@ipex3.johnshopkins.edu> References: <7k7ed7$70pbun@ipex3.johnshopkins.edu> Message-ID: Thank you very much, Dr. Mori Now I'm sure that the problem lies in the gradient table and the number of images. the original files are dicom files, which is 96*96 in size and 1662 slices. bvecs and bvals text files are within the folder when I got the images. After I loaded the image into dtistudio, the pull down menu in the right column of the image tab only showed one DWI (see attachment) Do I need to extract the bvec information from dicom files instead of using the existed one? Best, Hugh On Thu, Apr 9, 2009 at 11:04 AM, susumu wrote: > Hi Hugh, > > When you got this error, please suspect one of the following two reasons; > > 1) Memory shortage: > > Even if you have many GB of memories, 32-bit Windows system can allocate > only 1 - 1.5 GB to each program. To check if you have the memory problem, > please restrict the slices to be calculated. In the initial data parameter > window, there is a section called "Slices to be processed". Here you can > specify only a portion of slices to be processed. Please limit the slices > to, for example, 0-9 and see how it goes. If you can calculate tensors > without errors, then you have the memory problem. The solution is; a) > upgrade to the 64-bit system or b) devide the calculation to 2 batches (e.g. > slice 0-29 for the first batch and 30-59 for the second batch), calculate > all maps (e.g. FA), and later combine them. > > 2) Mismatch between the gradient table and the number of images: > > For example, if you specify 12-orientation table and 30 volume images, then > you get the error. After loading the data and before you go to the Dti Map > tab, make sure that you have 1 b0 + 64 DWIs in the pull-down menu in the > right column of the Image tab. If you have the correct number of the images, > then you might have an error in your gradient table. Small mistakes such as > missing "," are often difficult to detect. The best way is; a) load the data > using DtiMapping under the "File" button on the top left, b) close the > window, c) open the image paremater window again by clicking "DtiMapping" in > the "File" button again, d) the window still remembers the gradient table > you entered last time. This remembered window tells how DtiStudio > interpreted your gradient table. If there is any syntax errors, you may find > them much easier. For example, if you enter, "4: 1 0.5 0", instead of "4: 1, > 0.5, 0", then you would find, "4: 1, 0, 0". > > If any of these do not solve the issue, please let us know. > > Susumu > > ------------------------------ > *From:* mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org] *On Behalf Of *Hugh Wang > *Sent:* Wednesday, April 08, 2009 6:30 PM > *To:* mristudio-users at mristudio.org > *Subject:* [Mristudio-users] MriView3D application close > > Hi, > > I was using the dtistudio (ver. 2.4) to look at the Siemens DICOM > diffusion images (1baseline,64 gradients). After successfully loading the > images, I click the "dti map" option at lower right corner. Whatever > calculation I choose, it always gives me an error: > > "MriView3D MFC Application has encountered a problem and needs to close. > We are sorry for the inconvenience." > > I tried several PCs, and the problem keeped the same. I would appreciate > that if there's anyone having any idea on how to solve it. Thanks. > > Best, > Hugh > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090409/24c451da/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: dti.JPG Type: image/jpeg Size: 151196 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090409/24c451da/attachment-0001.jpe From mithra at mail.utexas.edu Thu Apr 9 16:20:13 2009 From: mithra at mail.utexas.edu (Mithra) Date: Thu, 09 Apr 2009 15:20:13 -0500 Subject: [Mristudio-users] Gradient information in DWI Mapping Message-ID: <42fe38b80904091320l2a08e9f3s6e6cc82a21492d6a@mail.gmail.com> Hello all, I would like to do DWI mapping on our image set. I was wondering how I should input the gradients. We have 25 gradients in the x directions. Is this the same as bvecs file? Thank you. - MIthra. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090409/a1d7f5b9/attachment.html From tangjinsonghn at yahoo.com.cn Wed Apr 15 00:05:58 2009 From: tangjinsonghn at yahoo.com.cn (jinsong tang) Date: Wed, 15 Apr 2009 12:05:58 +0800 (CST) Subject: [Mristudio-users] =?utf-8?q?_re=EF=BC=9A__MriView3D_application_c?= =?utf-8?q?lose?= In-Reply-To: <7k7ed7$70pbun@ipex3.johnshopkins.edu> References: <7k7ed7$70pbun@ipex3.johnshopkins.edu> Message-ID: <725142.5716.qm@web15605.mail.cnb.yahoo.com> Dear Susumu, This is my protocol of DTI? and 3D scaning at SIEMENS 3T,? Would you please review it and give me some suggestions. Thanks, Jinsong DTI: Axial FOV= 240?240mm Slice thickness= 3mm Slice number=45 Gap=0mm Matrix=128?128 NEX=5? or? 1 TR=6046ms? ? TE=93 Diffusion directiuon =12 b=1000, b0=0. 3D TR= 2000ms TE=2.6ms FOV=240?240mm Slice thickness=1mm Gap=0mm Slices=176 Matrix=256?256 Slice orientation= sagittal Flip angle=15? NEX=1 ________________________________ ???? susumu ???? "DTI Studio, ROI Editor, Landmarker Questions/Support" ???? 2009/4/9(??), ??11:04:09 ??? Re: [Mristudio-users] MriView3D application close Hi Hugh, ? When you got this error, please suspect one of the following two reasons; ? 1) Memory shortage: ? Even if you have many GB of memories, 32-bit Windows system can allocate only 1 - 1.5 GB to each program. To check if you have the memory problem, please?restrict the slices to be calculated. In the initial?data parameter window, there is a section called "Slices to be processed". Here you can specify only a portion of slices to be processed. Please limit the slices to, for example, 0-9 and see how it goes. If you can calculate tensors without errors, then you have the memory problem. The solution is; a) upgrade to the 64-bit system or b) devide the calculation to 2 batches (e.g. slice 0-29 for the first batch and 30-59 for the second batch), calculate all maps (e.g. FA), and later combine them. ? 2) Mismatch between the gradient table and the number of images: ? For example, if you specify 12-orientation table and 30 volume images, then you get the error. After loading the data and before you go to the Dti Map tab, make sure that you have 1 b0 + 64 DWIs in the pull-down menu in the right column of the Image tab. If you have the correct number of the images, then you might have an error in your gradient table. Small mistakes such as missing "," are often difficult to detect. The best way is; a) load the data using DtiMapping under the "File" button on the top left, b) close the window, c) open the image paremater window again by clicking "DtiMapping" in the "File" button again, d) the window still remembers the gradient table you entered last time. This remembered window tells how DtiStudio interpreted your gradient table. If there is any syntax errors, you may find them much easier. For example, if you enter, "4: 1 0.5 0", instead of "4: 1, 0.5, 0", then you would find, "4: 1, 0, 0". ? If any of these do not solve the issue, please let us know. ? Susumu ________________________________ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hugh Wang Sent: Wednesday, April 08, 2009 6:30 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] MriView3D application close Hi, I was using the dtistudio (ver. 2.4)? to look at the Siemens DICOM diffusion images (1baseline,64 gradients). After successfully loading the images, I click the "dti map" option at lower right corner. Whatever calculation I choose, it always gives me an error: "MriView3D MFC Application has encountered a problem and needs to close.? We are sorry for the inconvenience." I tried several PCs, and the problem keeped the same. I would appreciate that if there's anyone having any idea on how to solve it. Thanks. Best, Hugh ___________________________________________________________ ????????????????? http://card.mail.cn.yahoo.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090415/f68c0309/attachment.html From raj.jaswal at gmail.com Thu Apr 16 20:44:19 2009 From: raj.jaswal at gmail.com (Raj Jaswal) Date: Thu, 16 Apr 2009 20:44:19 -0400 Subject: [Mristudio-users] ROI Drawing - "Fixed Size" Message-ID: <32a27f2a0904161744m560c9cd7kf2ad3a7a58439906@mail.gmail.com> Hi all, Can anyone tell me about the "Fixed Size" option under "ROI Drawing - Shape" in the ROI/Fiber tab (also available in ROI Editor)? For example, would 10x10 equate to 10pixels x 10pixels? Thank you. - RJ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090416/c148dd1e/attachment.html From qcdunk at hotmail.com Thu Apr 16 21:43:51 2009 From: qcdunk at hotmail.com (eric Q) Date: Fri, 17 Apr 2009 11:43:51 +1000 Subject: [Mristudio-users] Gradient table In-Reply-To: <7k7ed7$70pbun@ipex3.johnshopkins.edu> References: <7k7ed7$70pbun@ipex3.johnshopkins.edu> Message-ID: Hello Dear DTIstudio users: I am new to DTIstudio, I was hoping someone could give me some much needed advises for beginners. I was trying to obtain the FA values for my brain phantom (PHILIP 3T scanner). When I clicked on "DTI mapping", it prompted me to enter the "gradient table", how do I calculate the "gradient table"? Thanks in advanced Best regards Eric Date: Thu, 9 Apr 2009 11:04:09 -0400 From: susumu at mri.jhu.edu To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] MriView3D application close Hi Hugh, When you got this error, please suspect one of the following two reasons; 1) Memory shortage: Even if you have many GB of memories, 32-bit Windows system can allocate only 1 - 1.5 GB to each program. To check if you have the memory problem, please restrict the slices to be calculated. In the initial data parameter window, there is a section called "Slices to be processed". Here you can specify only a portion of slices to be processed. Please limit the slices to, for example, 0-9 and see how it goes. If you can calculate tensors without errors, then you have the memory problem. The solution is; a) upgrade to the 64-bit system or b) devide the calculation to 2 batches (e.g. slice 0-29 for the first batch and 30-59 for the second batch), calculate all maps (e.g. FA), and later combine them. 2) Mismatch between the gradient table and the number of images: For example, if you specify 12-orientation table and 30 volume images, then you get the error. After loading the data and before you go to the Dti Map tab, make sure that you have 1 b0 + 64 DWIs in the pull-down menu in the right column of the Image tab. If you have the correct number of the images, then you might have an error in your gradient table. Small mistakes such as missing "," are often difficult to detect. The best way is; a) load the data using DtiMapping under the "File" button on the top left, b) close the window, c) open the image paremater window again by clicking "DtiMapping" in the "File" button again, d) the window still remembers the gradient table you entered last time. This remembered window tells how DtiStudio interpreted your gradient table. If there is any syntax errors, you may find them much easier. For example, if you enter, "4: 1 0.5 0", instead of "4: 1, 0.5, 0", then you would find, "4: 1, 0, 0". If any of these do not solve the issue, please let us know. Susumu From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hugh Wang Sent: Wednesday, April 08, 2009 6:30 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] MriView3D application close Hi, I was using the dtistudio (ver. 2.4) to look at the Siemens DICOM diffusion images (1baseline,64 gradients). After successfully loading the images, I click the "dti map" option at lower right corner. Whatever calculation I choose, it always gives me an error: "MriView3D MFC Application has encountered a problem and needs to close. We are sorry for the inconvenience." I tried several PCs, and the problem keeped the same. I would appreciate that if there's anyone having any idea on how to solve it. Thanks. Best, Hugh _________________________________________________________________ Looking to change your car this year? Find car news, reviews and more http://a.ninemsn.com.au/b.aspx?URL=http%3A%2F%2Fsecure%2Dau%2Eimrworldwide%2Ecom%2Fcgi%2Dbin%2Fa%2Fci%5F450304%2Fet%5F2%2Fcg%5F801459%2Fpi%5F1004813%2Fai%5F859641&_t=762955845&_r=tig_OCT07&_m=EXT -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090417/5edc5d52/attachment-0001.html From susumu at mri.jhu.edu Fri Apr 17 02:33:19 2009 From: susumu at mri.jhu.edu (susumu) Date: Fri, 17 Apr 2009 02:33:19 -0400 Subject: [Mristudio-users] Gradient table In-Reply-To: References: <7k7ed7$70pbun@ipex3.johnshopkins.edu> Message-ID: Hi Eric, For Philips scanner there are several types of gradient tables you can specify in the scanner. Please check your protocol for the following points; 1) Gradient table: High (32-orientation)/ Medium (15-orientation) / Low (6-orientation) 2) Overplus (ON / OFF) 3) Oblique plane (X/Y/Z angles) The first option has 3 choices and the second option has 2 choices. Therefore, there are 3 x 2 = 6 gradient tables. If the second option (Overplus) is NO, the third option has no effect. If the second option is YES, the gradient table has to be rotated based on the oblique angles. To simplify the DTI processing, we recommend Overplus = NO. We have the basic 6 tables, which can be used as is if you use Overplus = OFF or Oblique angles = 0/0/0 degree. Please let us know which options you are using. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of eric Q Sent: Thursday, April 16, 2009 9:44 PM To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] Gradient table Hello Dear DTIstudio users: I am new to DTIstudio, I was hoping someone could give me some much needed advises for beginners. I was trying to obtain the FA values for my brain phantom (PHILIP 3T scanner). When I clicked on "DTI mapping", it prompted me to enter the "gradient table", how do I calculate the "gradient table"? Thanks in advanced Best regards Eric _____ Date: Thu, 9 Apr 2009 11:04:09 -0400 From: susumu at mri.jhu.edu To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] MriView3D application close Hi Hugh, When you got this error, please suspect one of the following two reasons; 1) Memory shortage: Even if you have many GB of memories, 32-bit Windows system can allocate only 1 - 1.5 GB to each program. To check if you have the memory problem, please restrict the slices to be calculated. In the initial data parameter window, there is a section called "Slices to be processed". Here you can specify only a portion of slices to be processed. Please limit the slices to, for example, 0-9 and see how it goes. If you can calculate tensors without errors, then you have the memory problem. The solution is; a) upgrade to the 64-bit system or b) devide the calculation to 2 batches (e.g. slice 0-29 for the first batch and 30-59 for the second batch), calculate all maps (e.g. FA), and later combine them. 2) Mismatch between the gradient table and the number of images: For example, if you specify 12-orientation table and 30 volume images, then you get the error. After loading the data and before you go to the Dti Map tab, make sure that you have 1 b0 + 64 DWIs in the pull-down menu in the right column of the Image tab. If you have the correct number of the images, then you might have an error in your gradient table. Small mistakes such as missing "," are often difficult to detect. The best way is; a) load the data using DtiMapping under the "File" button on the top left, b) close the window, c) open the image paremater window again by clicking "DtiMapping" in the "File" button again, d) the window still remembers the gradient table you entered last time. This remembered window tells how DtiStudio interpreted your gradient table. If there is any syntax errors, you may find them much easier. For example, if you enter, "4: 1 0.5 0", instead of "4: 1, 0.5, 0", then you would find, "4: 1, 0, 0". If any of these do not solve the issue, please let us know. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hugh Wang Sent: Wednesday, April 08, 2009 6:30 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] MriView3D application close Hi, I was using the dtistudio (ver. 2.4) to look at the Siemens DICOM diffusion images (1baseline,64 gradients). After successfully loading the images, I click the "dti map" option at lower right corner. Whatever calculation I choose, it always gives me an error: "MriView3D MFC Application has encountered a problem and needs to close. We are sorry for the inconvenience." I tried several PCs, and the problem keeped the same. I would appreciate that if there's anyone having any idea on how to solve it. Thanks. Best, Hugh _____ Find car news, reviews and more Looking to change your car this year? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090417/8cf3201e/attachment.html From susumu at mri.jhu.edu Fri Apr 17 02:35:32 2009 From: susumu at mri.jhu.edu (susumu) Date: Fri, 17 Apr 2009 02:35:32 -0400 Subject: [Mristudio-users] ROI Drawing - "Fixed Size" In-Reply-To: <32a27f2a0904161744m560c9cd7kf2ad3a7a58439906@mail.gmail.com> References: <32a27f2a0904161744m560c9cd7kf2ad3a7a58439906@mail.gmail.com> Message-ID: Fixed size ROI options should be available for both DtiStudio and RoiEditor. For DtiStudio, you have to choose "Oval" or "Rectangular". Then "Fixed Size" option should be activated. _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Raj Jaswal Sent: Thursday, April 16, 2009 8:44 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] ROI Drawing - "Fixed Size" Hi all, Can anyone tell me about the "Fixed Size" option under "ROI Drawing - Shape" in the ROI/Fiber tab (also available in ROI Editor)? For example, would 10x10 equate to 10pixels x 10pixels? Thank you. - RJ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090417/a2d55c6d/attachment-0001.html From susumu at mri.jhu.edu Fri Apr 17 03:41:48 2009 From: susumu at mri.jhu.edu (susumu) Date: Fri, 17 Apr 2009 03:41:48 -0400 Subject: [Mristudio-users] =?utf-8?q?re=EF=BC=9A__MriView3D_application_cl?= =?utf-8?q?ose?= In-Reply-To: <725142.5716.qm@web15605.mail.cnb.yahoo.com> References: <7k7ed7$70pbun@ipex3.johnshopkins.edu> <725142.5716.qm@web15605.mail.cnb.yahoo.com> Message-ID: <05E52E6BD3A343618FBA608DEF333C89@SusumuThinkPad> Hi Jinsong, 1) I usually use 2.5 x 2.5 x 2.5 mm for 1.5 T. About 60 DWI (with 12-orientation, 5 repeated NEX=1 (preferable) or NEX=5) should give decent SNR, which should take about 7-8 min. With 3T, 30 DWI should look good (3.5-4 min). For this protocol, 240x240 mm / 96x96 will do. 2) We also use 2.2 x 2.2 x 2.2 mm for 3T with 60 DWI (8 min). 3) Your protocol is 240/128 = 1.9 x 1.9. With 3 mm slice, this is about the same as 2.2x2.2x2.2. So, I think 12-orientation x 5 (60DWI) should provide decent SNR. However, because you are using longer echo trains, you have longer echo time (= SNR loss), more distortion, and more blurring (less true resolution due to T2* decay during the long echo). I prefer 96x96 with that reason. 4) I prefer NEX = 1 x 5 repetition rather than NEX = 5, but I believe recent Siemens scanners have an option for ?no average? even if you use NEX = 5 (all 5 NEX data are saved separately). 5) I use shortest TR and your TR seems right. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of jinsong tang Sent: Wednesday, April 15, 2009 12:06 AM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] re? MriView3D application close Dear Susumu, This is my protocol of DTI and 3D scaning at SIEMENS 3T, Would you please review it and give me some suggestions. Thanks, Jinsong DTI: Axial FOV= 240?240mm Slice thickness= 3mm Slice number=45 Gap=0mm Matrix=128?128 NEX=5 or 1 TR=6046ms ? TE=93 Diffusion directiuon =12 b=1000, b0=0. 3D TR= 2000ms TE=2.6ms FOV=240?240mm Slice thickness=1mm Gap=0mm Slices=176 Matrix=256?256 Slice orientation= sagittal Flip angle=15? NEX=1 _____ ???? susumu ???? "DTI Studio, ROI Editor, Landmarker Questions/Support" ???? 2009/4/9(??), ??11:04:09 ??? Re: [Mristudio-users] MriView3D application close Hi Hugh, When you got this error, please suspect one of the following two reasons; 1) Memory shortage: Even if you have many GB of memories, 32-bit Windows system can allocate only 1 - 1.5 GB to each program. To check if you have the memory problem, please restrict the slices to be calculated. In the initial data parameter window, there is a section called "Slices to be processed". Here you can specify only a portion of slices to be processed. Please limit the slices to, for example, 0-9 and see how it goes. If you can calculate tensors without errors, then you have the memory problem. The solution is; a) upgrade to the 64-bit system or b) devide the calculation to 2 batches (e.g. slice 0-29 for the first batch and 30-59 for the second batch), calculate all maps (e.g. FA), and later combine them. 2) Mismatch between the gradient table and the number of images: For example, if you specify 12-orientation table and 30 volume images, then you get the error. After loading the data and before you go to the Dti Map tab, make sure that you have 1 b0 + 64 DWIs in the pull-down menu in the right column of the Image tab. If you have the correct number of the images, then you might have an error in your gradient table. Small mistakes such as missing "," are often difficult to detect. The best way is; a) load the data using DtiMapping under the "File" button on the top left, b) close the window, c) open the image paremater window again by clicking "DtiMapping" in the "File" button again, d) the window still remembers the gradient table you entered last time. This remembered window tells how DtiStudio interpreted your gradient table. If there is any syntax errors, you may find them much easier. For example, if you enter, "4: 1 0.5 0", instead of "4: 1, 0.5, 0", then you would find, "4: 1, 0, 0". If any of these do not solve the issue, please let us know. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hugh Wang Sent: Wednesday, April 08, 2009 6:30 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] MriView3D application close Hi, I was using the dtistudio (ver. 2.4) to look at the Siemens DICOM diffusion images (1baseline,64 gradients). After successfully loading the images, I click the "dti map" option at lower right corner. Whatever calculation I choose, it always gives me an error: "MriView3D MFC Application has encountered a problem and needs to close. We are sorry for the inconvenience." I tried several PCs, and the problem keeped the same. I would appreciate that if there's anyone having any idea on how to solve it. Thanks. Best, Hugh _____ ????????????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090417/6a7ba7f9/attachment.html From tangjinsonghn at yahoo.com.cn Sat Apr 18 08:04:57 2009 From: tangjinsonghn at yahoo.com.cn (jinsong tang) Date: Sat, 18 Apr 2009 20:04:57 +0800 (CST) Subject: [Mristudio-users] =?utf-8?b?IOWbnuWkje+8miAgcmXvvJogIE1yaVZpZXcz?= =?utf-8?q?D_application_close?= In-Reply-To: <05E52E6BD3A343618FBA608DEF333C89@SusumuThinkPad> References: <7k7ed7$70pbun@ipex3.johnshopkins.edu> <725142.5716.qm@web15605.mail.cnb.yahoo.com> <05E52E6BD3A343618FBA608DEF333C89@SusumuThinkPad> Message-ID: <82468.53032.qm@web15607.mail.cnb.yahoo.com> Dear Susumu, ? Thanks for your comments. another question.?How to use?DTIstudio deal with 3T seimens DTI data, they are saved in volumes by volumes, not slice by sclice Best, Jinsong ________________________________ ???? susumu ???? "DTI Studio, ROI Editor, Landmarker Questions/Support" ???? 2009/4/17(??), ??3:41:48 ??? Re: [Mristudio-users] re? MriView3D application close Hi Jinsong, ? 1) I usually use 2.5 x 2.5 x 2.5 mm for 1.5 T. About 60 DWI (with 12-orientation, 5 repeated NEX=1 (preferable) or NEX=5) should give decent SNR, which should take about 7-8 min. With 3T, 30 DWI should look good (3.5-4 min). ? For this protocol, 240x240 mm / 96x96 will do. ? 2) We also use 2.2 x 2.2 x 2.2 mm for 3T with 60 DWI (8 min). ? 3) Your protocol is 240/128 = 1.9 x 1.9. With 3 mm slice, this is about the same as 2.2x2.2x2.2. So, I think 12-orientation x 5 (60DWI) should provide decent SNR. However, because you are using longer echo trains, you have longer echo time (= SNR loss), more distortion, and more blurring (less true resolution due to T2* decay during the long echo). I prefer 96x96 with that reason. ? 4) I prefer NEX = 1 x 5 repetition rather than NEX = 5, but I believe recent Siemens scanners have an option for ?no average? even if you use NEX = 5 (all 5 NEX data are saved separately). ? 5) I use shortest TR and your TR seems right. ? Susumu ? ________________________________ From:mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of jinsong tang Sent: Wednesday, April 15, 2009 12:06 AM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] re?MriView3D application close ? Dear Susumu, This is my protocol of DTI? and 3D scaning at SIEMENS 3T,? Would you please review it and give me some suggestions. ? Thanks, ? Jinsong ? DTI: Axial FOV= 240?240mm Slice thickness= 3mm Slice number=45 Gap=0mm Matrix=128?128 NEX=5? or? 1 TR=6046ms? ? TE=93 Diffusion directiuon =12 b=1000, b0=0. ? 3D TR= 2000ms TE=2.6ms FOV=240?240mm Slice thickness=1mm Gap=0mm Slices=176 Matrix=256?256 Slice orientation= sagittal Flip angle=15? NEX=1 ? ________________________________ ????susumu ????"DTI Studio, ROI Editor, Landmarker Questions/Support" ????2009/4/9(??), ??11:04:09 ???Re: [Mristudio-users] MriView3D application close Hi Hugh, ? When you got this error, please suspect one of the following two reasons; ? 1) Memory shortage: ? Even if you have many GB of memories, 32-bit Windows system can allocate only 1 - 1.5 GB to each program. To check if you have the memory problem, please?restrict the slices to be calculated. In the initial?data parameter window, there is a section called "Slices to be processed". Here you can specify only a portion of slices to be processed. Please limit the slices to, for example, 0-9 and see how it goes. If you can calculate tensors without errors, then you have the memory problem. The solution is; a) upgrade to the 64-bit system or b) devide the calculation to 2 batches (e.g. slice 0-29 for the first batch and 30-59 for the second batch), calculate all maps (e.g. FA), and later combine them. ? 2) Mismatch between the gradient table and the number of images: ? For example, if you specify 12-orientation table and 30 volume images, then you get the error. After loading the data and before you go to the Dti Map tab, make sure that you have 1 b0 + 64 DWIs in the pull-down menu in the right column of the Image tab. If you have the correct number of the images, then you might have an error in your gradient table. Small mistakes such as missing "," are often difficult to detect. The best way is; a) load the data using DtiMapping under the "File" button on the top left, b) close the window, c) open the image paremater window again by clicking "DtiMapping" in the "File" button again, d) the window still remembers the gradient table you entered last time. This remembered window tells how DtiStudio interpreted your gradient table. If there is any syntax errors, you may find them much easier. For example, if you enter, "4: 1 0.5 0", instead of "4: 1, 0.5, 0", then you would find, "4: 1, 0, 0". ? If any of these do not solve the issue, please let us know. ? Susumu ? ________________________________ From:mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hugh Wang Sent: Wednesday, April 08, 2009 6:30 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] MriView3D application close Hi, I was using the dtistudio (ver. 2.4)? to look at the Siemens DICOM diffusion images (1baseline,64 gradients). After successfully loading the images, I click the "dti map" option at lower right corner. Whatever calculation I choose, it always gives me an error: "MriView3D MFC Application has encountered a problem and needs to close.? We are sorry for the inconvenience." I tried several PCs, and the problem keeped the same. I would appreciate that if there's anyone having any idea on how to solve it. Thanks. Best, Hugh ? ________________________________ ????????????????? ___________________________________________________________ ????????????????? http://card.mail.cn.yahoo.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090418/03394ae1/attachment-0001.html From susumu at mri.jhu.edu Sat Apr 18 11:28:48 2009 From: susumu at mri.jhu.edu (susumu) Date: Sat, 18 Apr 2009 11:28:48 -0400 Subject: [Mristudio-users] =?utf-8?b?5Zue5aSN77yaICByZe+8miAgTXJpVmlldzNE?= =?utf-8?q?_application_close?= In-Reply-To: <82468.53032.qm@web15607.mail.cnb.yahoo.com> References: <7k7ed7$70pbun@ipex3.johnshopkins.edu> <725142.5716.qm@web15605.mail.cnb.yahoo.com> <05E52E6BD3A343618FBA608DEF333C89@SusumuThinkPad> <82468.53032.qm@web15607.mail.cnb.yahoo.com> Message-ID: <3DE9AD1FBB9D45269D47FD41C2C57DFA@SusumuThinkPad> Please try Siemens ?Mosaic? format. _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of jinsong tang Sent: Saturday, April 18, 2009 8:05 AM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] ??? re? MriView3D application close Dear Susumu, Thanks for your comments. another question. How to use DTIstudio deal with 3T seimens DTI data, they are saved in volumes by volumes, not slice by sclice Best, Jinsong _____ ???? susumu ???? "DTI Studio, ROI Editor, Landmarker Questions/Support" ???? 2009/4/17(??), ??3:41:48 ??? Re: [Mristudio-users] re? MriView3D application close Hi Jinsong, 1) I usually use 2.5 x 2.5 x 2.5 mm for 1.5 T. About 60 DWI (with 12-orientation, 5 repeated NEX=1 (preferable) or NEX=5) should give decent SNR, which should take about 7-8 min. With 3T, 30 DWI should look good (3.5-4 min). For this protocol, 240x240 mm / 96x96 will do. 2) We also use 2.2 x 2.2 x 2.2 mm for 3T with 60 DWI (8 min). 3) Your protocol is 240/128 = 1.9 x 1.9. With 3 mm slice, this is about the same as 2.2x2.2x2.2. So, I think 12-orientation x 5 (60DWI) should provide decent SNR. However, because you are using longer echo trains, you have longer echo time (= SNR loss), more distortion, and more blurring (less true resolution due to T2* decay during the long echo). I prefer 96x96 with that reason. 4) I prefer NEX = 1 x 5 repetition rather than NEX = 5, but I believe recent Siemens scanners have an option for ?no average? even if you use NEX = 5 (all 5 NEX data are saved separately). 5) I use shortest TR and your TR seems right. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of jinsong tang Sent: Wednesday, April 15, 2009 12:06 AM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] re? MriView3D application close Dear Susumu, This is my protocol of DTI and 3D scaning at SIEMENS 3T, Would you please review it and give me some suggestions. Thanks, Jinsong DTI: Axial FOV= 240?240mm Slice thickness= 3mm Slice number=45 Gap=0mm Matrix=128?128 NEX=5 or 1 TR=6046ms ? TE=93 Diffusion directiuon =12 b=1000, b0=0. 3D TR= 2000ms TE=2.6ms FOV=240?240mm Slice thickness=1mm Gap=0mm Slices=176 Matrix=256?256 Slice orientation= sagittal Flip angle=15? NEX=1 _____ ???? susumu ???? "DTI Studio, ROI Editor, Landmarker Questions/Support" ???? 2009/4/9(??), ??11:04:09 ??? Re: [Mristudio-users] MriView3D application close Hi Hugh, When you got this error, please suspect one of the following two reasons; 1) Memory shortage: Even if you have many GB of memories, 32-bit Windows system can allocate only 1 - 1.5 GB to each program. To check if you have the memory problem, please restrict the slices to be calculated. In the initial data parameter window, there is a section called "Slices to be processed". Here you can specify only a portion of slices to be processed. Please limit the slices to, for example, 0-9 and see how it goes. If you can calculate tensors without errors, then you have the memory problem. The solution is; a) upgrade to the 64-bit system or b) devide the calculation to 2 batches (e.g. slice 0-29 for the first batch and 30-59 for the second batch), calculate all maps (e.g. FA), and later combine them. 2) Mismatch between the gradient table and the number of images: For example, if you specify 12-orientation table and 30 volume images, then you get the error. After loading the data and before you go to the Dti Map tab, make sure that you have 1 b0 + 64 DWIs in the pull-down menu in the right column of the Image tab. If you have the correct number of the images, then you might have an error in your gradient table. Small mistakes such as missing "," are often difficult to detect. The best way is; a) load the data using DtiMapping under the "File" button on the top left, b) close the window, c) open the image paremater window again by clicking "DtiMapping" in the "File" button again, d) the window still remembers the gradient table you entered last time. This remembered window tells how DtiStudio interpreted your gradient table. If there is any syntax errors, you may find them much easier. For example, if you enter, "4: 1 0.5 0", instead of "4: 1, 0.5, 0", then you would find, "4: 1, 0, 0". If any of these do not solve the issue, please let us know. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hugh Wang Sent: Wednesday, April 08, 2009 6:30 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] MriView3D application close Hi, I was using the dtistudio (ver. 2.4) to look at the Siemens DICOM diffusion images (1baseline,64 gradients). After successfully loading the images, I click the "dti map" option at lower right corner. Whatever calculation I choose, it always gives me an error: "MriView3D MFC Application has encountered a problem and needs to close. We are sorry for the inconvenience." I tried several PCs, and the problem keeped the same. I would appreciate that if there's anyone having any idea on how to solve it. Thanks. Best, Hugh _____ ????????????????? _____ ????????????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090418/eb500c00/attachment-0001.html From wanglbit at gmail.com Sat Apr 18 14:42:07 2009 From: wanglbit at gmail.com (liang wang) Date: Sat, 18 Apr 2009 11:42:07 -0700 Subject: [Mristudio-users] Gradient table In-Reply-To: References: <7k7ed7$70pbun@ipex3.johnshopkins.edu> Message-ID: Dear Susumu, I also have a similar question about gradient tables in Philips scanner. My data were collected using following protocols: 1) Gradient table: Medium 2) Gradient overplus: no 3) Oblique plane: yes, and different angles between subjects. Looking through your answer, I know that this set can result in the same gradient table input into DTIstudio for all subject. However, 1) I am not sure which coordinates (space) the ultimate gradient table was relative to, such as frequency- and phase-encoding of image, horizontal and vertical direction of image, or magnets' x/y/z coordinates. Based on your reply, I think that it might be the last one. 2) In my *.PAR file, there was last 3 columns representing diffusion directions but obviously different between subjects. I don't know what diffusion were recorded in this header file. Many thanks Liang 2009/4/16 susumu > Hi Eric, > > > > For Philips scanner there are several types of gradient tables you can > specify in the scanner. Please check your protocol for the following points; > > > > 1) Gradient table: High (32-orientation)/ Medium (15-orientation) / > Low (6-orientation) > > 2) Overplus (ON / OFF) > > 3) Oblique plane (X/Y/Z angles) > > > > The first option has 3 choices and the second option has 2 choices. > Therefore, there are 3 x 2 = 6 gradient tables. > > If the second option (Overplus) is NO, the third option has no effect. If > the second option is YES, the gradient table has to be rotated based on the > oblique angles. > > > > To simplify the DTI processing, we recommend Overplus = NO. > > > > We have the basic 6 tables, which can be used as is if you use Overplus = > OFF or Oblique angles = 0/0/0 degree. > > Please let us know which options you are using. > > > > Susumu > > > ------------------------------ > > *From:* mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org] *On Behalf Of *eric Q > *Sent:* Thursday, April 16, 2009 9:44 PM > *To:* mristudio-users at mristudio.org > *Subject:* Re: [Mristudio-users] Gradient table > > > > Hello Dear DTIstudio users: > > I am new to DTIstudio, I was hoping someone could give me some much needed > advises for beginners. > > > I was trying to obtain the FA values for my brain phantom (PHILIP 3T > scanner). When I clicked on "DTI mapping", it prompted me to enter the > "gradient table", how do I calculate the "gradient table"? > > Thanks in advanced > > Best regards > > Eric > > > ------------------------------ > > Date: Thu, 9 Apr 2009 11:04:09 -0400 > From: susumu at mri.jhu.edu > To: mristudio-users at mristudio.org > Subject: Re: [Mristudio-users] MriView3D application close > > Hi Hugh, > > > > When you got this error, please suspect one of the following two reasons; > > > > 1) Memory shortage: > > > > Even if you have many GB of memories, 32-bit Windows system can allocate > only 1 - 1.5 GB to each program. To check if you have the memory problem, > please restrict the slices to be calculated. In the initial data parameter > window, there is a section called "Slices to be processed". Here you can > specify only a portion of slices to be processed. Please limit the slices > to, for example, 0-9 and see how it goes. If you can calculate tensors > without errors, then you have the memory problem. The solution is; a) > upgrade to the 64-bit system or b) devide the calculation to 2 batches (e.g. > slice 0-29 for the first batch and 30-59 for the second batch), calculate > all maps (e.g. FA), and later combine them. > > > > 2) Mismatch between the gradient table and the number of images: > > > > For example, if you specify 12-orientation table and 30 volume images, then > you get the error. After loading the data and before you go to the Dti Map > tab, make sure that you have 1 b0 + 64 DWIs in the pull-down menu in the > right column of the Image tab. If you have the correct number of the images, > then you might have an error in your gradient table. Small mistakes such as > missing "," are often difficult to detect. The best way is; a) load the data > using DtiMapping under the "File" button on the top left, b) close the > window, c) open the image paremater window again by clicking "DtiMapping" in > the "File" button again, d) the window still remembers the gradient table > you entered last time. This remembered window tells how DtiStudio > interpreted your gradient table. If there is any syntax errors, you may find > them much easier. For example, if you enter, "4: 1 0.5 0", instead of "4: 1, > 0.5, 0", then you would find, "4: 1, 0, 0". > > > > If any of these do not solve the issue, please let us know. > > > > Susumu > > > ------------------------------ > > *From:* mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org] *On Behalf Of *Hugh Wang > *Sent:* Wednesday, April 08, 2009 6:30 PM > *To:* mristudio-users at mristudio.org > *Subject:* [Mristudio-users] MriView3D application close > > Hi, > > I was using the dtistudio (ver. 2.4) to look at the Siemens DICOM > diffusion images (1baseline,64 gradients). After successfully loading the > images, I click the "dti map" option at lower right corner. Whatever > calculation I choose, it always gives me an error: > > "MriView3D MFC Application has encountered a problem and needs to close. > We are sorry for the inconvenience." > > I tried several PCs, and the problem keeped the same. I would appreciate > that if there's anyone having any idea on how to solve it. Thanks. > > Best, > Hugh > ------------------------------ > > Find car news, reviews and more Looking to change your car this year? > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wanglbit at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090418/384af2aa/attachment.html From tangjinsonghn at yahoo.com.cn Sun Apr 19 12:02:24 2009 From: tangjinsonghn at yahoo.com.cn (jinsong tang) Date: Mon, 20 Apr 2009 00:02:24 +0800 (CST) Subject: [Mristudio-users] question about the data orientation In-Reply-To: References: <7k7ed7$70pbun@ipex3.johnshopkins.edu> Message-ID: <610762.94522.qm@web15601.mail.cnb.yahoo.com> Dear all, As I know the raw data is saved in DICOM formate, they are in radiological orientation ((with left on the right)?, is this right? When we use DTIstudio and SPM to deal with the DTI data: 1, use DTIstudio to ctreate the FA map, they will be saved in the same orientation of the raw data because DTIstudio don't flip the data. 2, then normalize and smooth FA? and do indepent t-test using SPM2, spm2 will not flip the data too. 3?using xjview to view the result, now what's the ?oreientation (radiological orientation? or? neurological orientation?) Best, Jinsong ___________________________________________________________ ????????????????? http://card.mail.cn.yahoo.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090420/96e1f196/attachment-0001.html From xli16 at jhmi.edu Mon Apr 20 02:20:00 2009 From: xli16 at jhmi.edu (Xin Li) Date: Mon, 20 Apr 2009 02:20:00 -0400 Subject: [Mristudio-users] ROI Drawing - "Fixed Size" In-Reply-To: <32a27f2a0904161744m560c9cd7kf2ad3a7a58439906@mail.gmail.com> References: <32a27f2a0904161744m560c9cd7kf2ad3a7a58439906@mail.gmail.com> Message-ID: Raj, You are right. For the "Fixed Size" option, 10x10 equates to 10pixels x 10pixels. Xin ----- Original Message ----- From: Raj Jaswal Date: Thursday, April 16, 2009 8:44 pm Subject: [Mristudio-users] ROI Drawing - "Fixed Size" To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > Hi all, > > Can anyone tell me about the "Fixed Size" option under "ROI Drawing > - > Shape" in the ROI/Fiber tab (also available in ROI Editor)? For example, > would 10x10 equate to 10pixels x 10pixels? > > Thank you. > > - RJ > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > From chuan800917 at tom.com Wed Apr 22 03:40:19 2009 From: chuan800917 at tom.com (=?gb2312?B?tKg=?=) Date: Wed, 22 Apr 2009 15:40:19 +0800 (CST) Subject: [Mristudio-users] =?gb2312?b?cXVlc3Rpb24gYWJvdXQgdGhlIGRhdGEgb3Jp?= =?gb2312?b?ZW50YXRpb24=?= Message-ID: <49EEC9E3.000046.06514@bjapp42> dear? thank you very much for your answering -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090422/dc3801e2/attachment.html From siewmin.gan at gmail.com Thu Apr 23 05:08:32 2009 From: siewmin.gan at gmail.com (Siewmin Gan) Date: Thu, 23 Apr 2009 17:08:32 +0800 Subject: [Mristudio-users] question using AIR in Landmarker Message-ID: Hi, I'm trying to do non-linear registration to normalise my resampled aDWI images to the ICBM_DTI_81 DWI template. When I clicked on the "align button", I recieved two error messages (below), and could not perform the registration step: "C:/Landmarker/align_warp.exe. The parameter is incorrect" followed by "cannot find warp file". I have placed the aligned_warp.exe file in the folder landmarker where software is located, and am not sure where the problem may be. Many Thanks Siewmin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090423/3d1a411c/attachment.html From arun.bokde at tcd.ie Tue Apr 28 06:48:44 2009 From: arun.bokde at tcd.ie (Arun Bokde, PhD) Date: Tue, 28 Apr 2009 12:48:44 +0200 Subject: [Mristudio-users] human brain atlas In-Reply-To: <6u9vds$671qf0@ipex3.johnshopkins.edu> References: <6u9vds$671qf0@ipex3.johnshopkins.edu> Message-ID: <5D55FC0A54F25C45B8757BE038B01D91708BEFF9D1@EXMB21.cortado.com> Hello, The ICBM-152 Atlas that comes from the UCLA web site has dimensions of 182 x 218 x 182 . Within DTI Studio it is 181 x 217 x 181. There seems to be a single slice difference between both templates? Where would the single slice need to be added for both templates to match? Regards, Arun From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu Sent: 26 January 2009 17:50 To: 'DTI Studio, ROI Editor, Landmarker Questions/Support' Subject: Re: [Mristudio-users] human brain atlas 1) Landmarker can normalize your data to ICBM-152. It comes with the ICBM (including our ICBM-DTI contrasts) and you can doa linear or non-linear method. 2) If you already normalized to the ICBM-152, the first step can be skipped. Just make sure the following; > our ICBM-152 has 181x217x181 matrix with 1 mm resolution > You can load our ICBM-152 and your normalized images to Landmarker (or any other software) to make sure that the compatibility of two ICBM-152 (one you used and the other one implemented in Landmarker and RoiEditor). > Also, all of our software follows the Radiology convention (right is left). If you find your image is loaded upside down, that is because of the brain orientation issue. It is a good practice to make sure right-left is correct in your entire procedure using a subject with some characteristic asymmetry 3) Once you confirm that your ICBM atlas was compatible with the one implemented in our software, do the following; > Load your normalized data. If you have lesion volume data (I assume it is 1/0 binary data), load it with some anatomical image such as T2. > Make sure that the image dimension is 181x217x181 / 1mm > Then, choose "ICBM" as an atlas in the right column > There is a button looks like the lung. Click it. This automatically segment your data into many white matter and gray matter regions and give you a report. For your lesion image, you can get how many "1 = lesion pixel" are in each segmented white matter area. > If you want to see the segmentation visually, use the "load" button in the "atlas" section and load one of the "WMPM". You can visually see the superimiposition of the segmentation on the loaded images. Try ________________________________ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of WangPing Sent: Monday, January 26, 2009 11:32 AM To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] human brain atlas Importance: High Susumu, I just played with RoiEditor for a while, and found the atlas with the software. I am wondering if the tool (or you may recommend other tool) can use the atlas to label my subjects. Right now my subjects have been normalized to MNI152 space (non-linear registration), there are white matter lesions on some subjects, I want to calculate the lesion volume on the white matter regions. IF I can label my subjects, I will know the lesion volume on each parcellation. I do not have to need a very detailed label atlas at this point, maybe a atlas that can divide a brain into a few parcellations will be okay. Thanks, any suggestion is high appreciated. Best Regards, Ping Date: Sun, 25 Jan 2009 08:38:18 -0500 From: susumu at mri.jhu.edu To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] human brain atlas Hi Ping, We have several white matter atlases in lbam.med.jhmi.edu, but the easiest way is to download Landmarker/RoiEditor from www.mristudio.org, which come with different types of electronic atlases. One of them is population-averaged atlas in the MNI coordinates. If you use linear normalization, I recommend using this atlas (named ICBM_DTI-81 for GE/Siemens and JHU-MNI-GA for Philips). If you use highly non-linear normalization, I recommend the single-subject atlas (named JHU-MNI-SS). Both atlases come with a hand-segmented white matter parcellation map (WMPM). If you download RoiEditor, this software can apply the WMPM for various types of image quantification. Please refer to www.mristudio.org for more info. Susumu ________________________________ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of WangPing Sent: Saturday, January 24, 2009 11:53 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] human brain atlas Importance: High Dear Dr. Mori and the List: Could anyone recommend a brain atlas (label atlas) that covers the main white matters? It will be great if this atlas is easy to register to MNI template. Thanks a lot! Ping ________________________________ ???? MSN ?????? MSN ????? ?????? ________________________________ ??????????MSN??? ????? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090428/3a4710c6/attachment-0001.html From susumu at mri.jhu.edu Tue Apr 28 09:28:52 2009 From: susumu at mri.jhu.edu (susumu) Date: Tue, 28 Apr 2009 09:28:52 -0400 Subject: [Mristudio-users] human brain atlas In-Reply-To: <5D55FC0A54F25C45B8757BE038B01D91708BEFF9D1@EXMB21.cortado.com> Message-ID: <7k7ed7$77llb6@ipex3.johnshopkins.edu> Hi Arun, It is likely that the difference is just 0 padding at the 182th, 218th, and 182th line. You can convert our 181x217x181 atlas to 182x218x182 using the "Crop" function in Landmarker. Another possibility is that it was interpolated, which can also be done by Landmarker. You may want to make sure by subtracting the images (you can do it in RoiEditor). We also got ICBM-152 from UCLA and don't know why there are two versions with different dimensions. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Arun Bokde, PhD Sent: Tuesday, April 28, 2009 6:49 AM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] human brain atlas Hello, The ICBM-152 Atlas that comes from the UCLA web site has dimensions of 182 x 218 x 182 . Within DTI Studio it is 181 x 217 x 181. There seems to be a single slice difference between both templates? Where would the single slice need to be added for both templates to match? Regards, Arun From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu Sent: 26 January 2009 17:50 To: 'DTI Studio, ROI Editor, Landmarker Questions/Support' Subject: Re: [Mristudio-users] human brain atlas 1) Landmarker can normalize your data to ICBM-152. It comes with the ICBM (including our ICBM-DTI contrasts) and you can doa linear or non-linear method. 2) If you already normalized to the ICBM-152, the first step can be skipped. Just make sure the following; > our ICBM-152 has 181x217x181 matrix with 1 mm resolution > You can load our ICBM-152 and your normalized images to Landmarker (or any other software) to make sure that the compatibility of two ICBM-152 (one you used and the other one implemented in Landmarker and RoiEditor). > Also, all of our software follows the Radiology convention (right is left). If you find your image is loaded upside down, that is because of the brain orientation issue. It is a good practice to make sure right-left is correct in your entire procedure using a subject with some characteristic asymmetry 3) Once you confirm that your ICBM atlas was compatible with the one implemented in our software, do the following; > Load your normalized data. If you have lesion volume data (I assume it is 1/0 binary data), load it with some anatomical image such as T2. > Make sure that the image dimension is 181x217x181 / 1mm > Then, choose "ICBM" as an atlas in the right column > There is a button looks like the lung. Click it. This automatically segment your data into many white matter and gray matter regions and give you a report. For your lesion image, you can get how many "1 = lesion pixel" are in each segmented white matter area. > If you want to see the segmentation visually, use the "load" button in the "atlas" section and load one of the "WMPM". You can visually see the superimiposition of the segmentation on the loaded images. Try _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of WangPing Sent: Monday, January 26, 2009 11:32 AM To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] human brain atlas Importance: High Susumu, I just played with RoiEditor for a while, and found the atlas with the software. I am wondering if the tool (or you may recommend other tool) can use the atlas to label my subjects. Right now my subjects have been normalized to MNI152 space (non-linear registration), there are white matter lesions on some subjects, I want to calculate the lesion volume on the white matter regions. IF I can label my subjects, I will know the lesion volume on each parcellation. I do not have to need a very detailed label atlas at this point, maybe a atlas that can divide a brain into a few parcellations will be okay. Thanks, any suggestion is high appreciated. Best Regards, Ping Date: Sun, 25 Jan 2009 08:38:18 -0500 From: susumu at mri.jhu.edu To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] human brain atlas Hi Ping, We have several white matter atlases in lbam.med.jhmi.edu, but the easiest way is to download Landmarker/RoiEditor from www.mristudio.org , which come with different types of electronic atlases. One of them is population-averaged atlas in the MNI coordinates. If you use linear normalization, I recommend using this atlas (named ICBM_DTI-81 for GE/Siemens and JHU-MNI-GA for Philips). If you use highly non-linear normalization, I recommend the single-subject atlas (named JHU-MNI-SS). Both atlases come with a hand-segmented white matter parcellation map (WMPM). If you download RoiEditor, this software can apply the WMPM for various types of image quantification. Please refer to www.mristudio.org for more info. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of WangPing Sent: Saturday, January 24, 2009 11:53 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] human brain atlas Importance: High Dear Dr. Mori and the List: Could anyone recommend a brain atlas (label atlas) that covers the main white matters? It will be great if this atlas is easy to register to MNI template. Thanks a lot! Ping _____ ???? MSN ?????? MSN ????? ???? ?? _____ ??????????MSN??? ????? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090428/12f556c3/attachment.html From SCopeland at mednet.ucla.edu Tue Apr 28 16:21:28 2009 From: SCopeland at mednet.ucla.edu (Copeland, Sarah A.) Date: Tue, 28 Apr 2009 13:21:28 -0700 Subject: [Mristudio-users] ROI editor Message-ID: Hello, I think I have managed to save a ROI in binary map format in ROI editor. However, when I try to open that same ROI in DTI studio, I get the message "Unrecognized image-ROI data file!" Is there anywhere in the documentation that gives some information on saving and reopening ROIs? I have tried searching, but haven't found anything about htis issue. I tried drawing an ROI in MRIcro as well, but wasn't able to open it in DTI studio or in ROIeditor. Thanks - Sarah IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. From susumu at mri.jhu.edu Tue Apr 28 16:48:21 2009 From: susumu at mri.jhu.edu (susumu) Date: Tue, 28 Apr 2009 16:48:21 -0400 Subject: [Mristudio-users] ROI editor In-Reply-To: Message-ID: <7k7ed7$77u68g@ipex3.johnshopkins.edu> If you save your ROI as a binary format, you have to open it as a binary format. Please make sure. Also, please don't be confused with "binary" and "binary map". They are different. I think it is worth mastering the "binary map" format if you want to export ROIs to DtiStudio for fiber tracking. Please go to "Mailing List" -> "MriStudio-Users" -> "Mristudio-users Archive" -> 2008 (or go to http://lists.mristudio.org/pipermail/mristudio-users/2008/thread.html). There search for "Load ROI's drawn in fMRI images on DTI image", answered by "support at mristudio.org". There, you can find a detailed description for "binary map" format. -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Copeland, Sarah A. Sent: Tuesday, April 28, 2009 4:21 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] ROI editor Hello, I think I have managed to save a ROI in binary map format in ROI editor. However, when I try to open that same ROI in DTI studio, I get the message "Unrecognized image-ROI data file!" Is there anywhere in the documentation that gives some information on saving and reopening ROIs? I have tried searching, but haven't found anything about htis issue. I tried drawing an ROI in MRIcro as well, but wasn't able to open it in DTI studio or in ROIeditor. Thanks - Sarah IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From xli16 at jhmi.edu Wed Apr 29 11:30:19 2009 From: xli16 at jhmi.edu (Xin Li) Date: Wed, 29 Apr 2009 11:30:19 -0400 Subject: [Mristudio-users] question using AIR in Landmarker In-Reply-To: References: Message-ID: Siewmin, Where did you see this error message "C:/Landmarker/align_warp.exe. The parameter is incorrect" ? Did you see it in the C command window or in a pop up warning window? Xin ----- Original Message ----- From: Siewmin Gan Date: Thursday, April 23, 2009 5:08 am Subject: [Mristudio-users] question using AIR in Landmarker To: mristudio-users at mristudio.org > Hi, I'm trying to do non-linear registration to normalise my resampled > aDWI images to the ICBM_DTI_81 DWI template. When I clicked on the "align > button", I recieved two error messages (below), and could not perform > the > registration step: > > "C:/Landmarker/align_warp.exe. The parameter is incorrect" followed by > "cannot find warp file". > > I have placed the aligned_warp.exe file in the folder landmarker where > software is located, and am not sure where the problem may be. > > Many Thanks > > Siewmin > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > From SCopeland at mednet.ucla.edu Thu Apr 30 02:57:48 2009 From: SCopeland at mednet.ucla.edu (Copeland, Sarah A.) Date: Wed, 29 Apr 2009 23:57:48 -0700 Subject: [Mristudio-users] [SPM] ROI drawing Message-ID: Hello Susumu - I have read the post you suggested about using binary map file format for my ROIs, but still have problems. My ROI is hand drawn, and when I save as binary map format, I get the two .dat files, but not the third file mentioned. When I try to open one of the dat files as binary format, I get the error message File size is less than expected: (Img Width*ImgHeight*2 bytes) + header Followed by the path name. I have drawn the ROI on a T1 image which has been coregistered in SPM to the mean b0 image, as the AIR coregistration I tried gave poor results. I appreciate any suggestions you can give me. Sarah IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. From siewmin.gan at gmail.com Thu Apr 30 11:31:00 2009 From: siewmin.gan at gmail.com (Siewmin Gan) Date: Thu, 30 Apr 2009 23:31:00 +0800 Subject: [Mristudio-users] question using AIR in Landmarker In-Reply-To: References: Message-ID: Hi Xin, the error message occurs in a pop up warning window on the DTIstudio GUI. thanks Siewmin On Wed, Apr 29, 2009 at 11:30 PM, Xin Li wrote: > Siewmin, > > Where did you see this error message "C:/Landmarker/align_warp.exe. The > parameter is incorrect" ? Did you see it in the C command window or in a pop > up warning window? > > > Xin > > > > ----- Original Message ----- > From: Siewmin Gan > Date: Thursday, April 23, 2009 5:08 am > Subject: [Mristudio-users] question using AIR in Landmarker > To: mristudio-users at mristudio.org > > > > Hi, I'm trying to do non-linear registration to normalise my resampled > > aDWI images to the ICBM_DTI_81 DWI template. When I clicked on the > "align > > button", I recieved two error messages (below), and could not perform > > the > > registration step: > > > > "C:/Landmarker/align_warp.exe. The parameter is incorrect" followed by > > "cannot find warp file". > > > > I have placed the aligned_warp.exe file in the folder landmarker where > > software is located, and am not sure where the problem may be. > > > > Many Thanks > > > > Siewmin > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090430/a7b4569b/attachment.html From xli16 at jhmi.edu Thu Apr 30 12:02:29 2009 From: xli16 at jhmi.edu (Xin Li) Date: Thu, 30 Apr 2009 12:02:29 -0400 Subject: [Mristudio-users] question using AIR in Landmarker In-Reply-To: References: Message-ID: Siewmin, Could you take snapshots of these two error messages? And please tell me the whole path of the warp file that you were going to save on your machine. The whole path of the warp file should not have any spaces. I am not sure if this is the reason. Xin ----- Original Message ----- From: Siewmin Gan Date: Thursday, April 30, 2009 11:31 am Subject: Re: [Mristudio-users] question using AIR in Landmarker To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > Hi Xin, the error message occurs in a pop up warning window on the DTIstudio > GUI. > thanks > > Siewmin > > On Wed, Apr 29, 2009 at 11:30 PM, Xin Li wrote: > > > Siewmin, > > > > Where did you see this error message "C:/Landmarker/align_warp.exe. > The > > parameter is incorrect" ? Did you see it in the C command window or > in a pop > > up warning window? > > > > > > Xin > > > > > > > > ----- Original Message ----- > > From: Siewmin Gan > > Date: Thursday, April 23, 2009 5:08 am > > Subject: [Mristudio-users] question using AIR in Landmarker > > To: mristudio-users at mristudio.org > > > > > > > Hi, I'm trying to do non-linear registration to normalise my resampled > > > aDWI images to the ICBM_DTI_81 DWI template. When I clicked on the > > "align > > > button", I recieved two error messages (below), and could not perform > > > the > > > registration step: > > > > > > "C:/Landmarker/align_warp.exe. The parameter is incorrect" > followed by > > > "cannot find warp file". > > > > > > I have placed the aligned_warp.exe file in the folder landmarker > where > > > software is located, and am not sure where the problem may be. > > > > > > Many Thanks > > > > > > Siewmin > > > _______________________________________________ > > > Mristudio-users mailing list > > > Mristudio-users at mristudio.org > > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > From choisj70 at gmail.com Thu Apr 30 12:28:18 2009 From: choisj70 at gmail.com (Seongjin) Date: Thu, 30 Apr 2009 12:28:18 -0400 Subject: [Mristudio-users] Gradient table Message-ID: I appreciate the tutorial session at Queen's Medical Center in Honolulu. I am using gradient table (for DTI studio ) generated at the following link: http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html I wonder if I can directly use the gradient table from this java applet without field flipping. Thanks in advance. -SC -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090430/5e726f9e/attachment.html From support at mristudio.org Thu Apr 30 12:59:29 2009 From: support at mristudio.org (support at mristudio.org) Date: Thu, 30 Apr 2009 12:59:29 -0400 (EDT) Subject: [Mristudio-users] [SPM] ROI drawing In-Reply-To: References: Message-ID: <4455.10.16.57.13.1241110769.squirrel@webmail.mristudio.org> hello, Sarah, the best way to learn how to use "Binary Maps" (for fiber selection) is letting DtiStudio to save a sample in following steps: 1. do fiber tracking...; 2. using tools in the "fiber" tab, draw two ROIs for fiber selection. using "OR" operation for the 1st ROI, "AND" operation for the second one; 3. clicking "Save" button in the "ROI-Operation" section, select "Binary Maps" option, clicking "OK", specify a file name (or use the default name (RoiMap.dat) and "Save" it; 4. then you will get 3 files: RoiMap_00.dat, RoiMap_01.dat and RoiMap_ROI.map. here, RoiMap_00.dat is a binary image for the 1st ROI you had drawn, RoiMap_01.dat is the binary image for the 2nd ROI. RoiMap_ROI.map is a plain-text file. you can open/view/edit it using any text-editor (like NotePad), it may looks like this: --------------------------------------------------- *** ROI Map *** Begin ImageWidth: 256 ImageHeight: 256 ImageSlices: 54 PixelSizeWidth: 0.937500 PixelSizeHeight: 0.937500 SliceThickness: 2.500000 SliceOrientation: 1 SliceSequencing: 0 BinaryFile: C:\Hangyi\Test\RoiMap_00.dat Operation: 0 FiberColor: (255,0,0) ColorMode: 0 BinaryFile: C:\Hangyi\Test\RoiMap_01.dat Operation: 1 FiberColor: (255,0,0) ColorMode: 0 End Note: Slice Orientation: 0=Coronal, 1=Axial, 2=Sagittal Slice Sequencing: 0=Positive, 1=Negative ROI Operation: 0=OR, 1=AND, 3=NOT, 4=Cut0, 5=Cut1, 6=AndClr, 7=NotClr, 8=CutClr0, 9=CutClr1 Fiber Color: (r,g,b) = (0..255, 0..255, 0..255) Color Mode: 0=random, 1=user-defined *** ROI Map *** --------------------------------------------------- the first part of this file is the image parameters, the second part (started from "BinaryFile:..") indicates the ROIs and operations that would be used for the fiber selection. and the third part is just a guide-line shows how to use this file. this file tells DtiStudio uses RoiMap_00.dat as the 1st ROI with "OR" operation (operation=0), and load the 2nd ROI (RoiMap_01.dat) with "AND" (operaion=1) sequentially for fiber selection. 5. Now, you can create your own ROI files using any tools (as long as the ROI is saved as binary image - 8 bits (or 1 byte) per pixel, and same dimension as that of the original images), and modify "RoiMap_ROI.map" to specify your ROI file locations and operations. then with DtiStudio, using ROI-"Load" button of the "fiber" tab, choose "Binary Map" option to load in your "RoiMap_ROI.map". you will get the fibers with your ROIs combination. regards, MriStudio Supporter > Hello Susumu - > > I have read the post you suggested about using binary map file format for my > ROIs, but still have problems. My ROI is hand drawn, and when I save as binary > map format, I get the two .dat files, but not the third file mentioned. When I > try to open one of the dat files as binary format, I get the error message > > File size is less than expected: (Img Width*ImgHeight*2 bytes) + header > > Followed by the path name. I have drawn the ROI on a T1 image which has been > coregistered in SPM to the mean b0 image, as the AIR coregistration I tried gave > poor results. > > I appreciate any suggestions you can give me. > > Sarah > > IMPORTANT WARNING: This email (and any attachments) is only intended for the > use of the person or entity to which it is addressed, and may contain > information that is privileged and confidential. You, the recipient, are > obligated to maintain it in a safe, secure and confidential manner. > Unauthorized redisclosure or failure to maintain confidentiality may subject you > to federal and state penalties. If you are not the intended recipient, please > immediately notify us by return email, and delete this message from your > computer. > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > From susumu at mri.jhu.edu Thu Apr 30 13:18:55 2009 From: susumu at mri.jhu.edu (susumu) Date: Thu, 30 Apr 2009 13:18:55 -0400 Subject: [Mristudio-users] Gradient table In-Reply-To: Message-ID: <7k7ed7$7948nt@ipex3.johnshopkins.edu> The gradient table for Philips scanner calculated by this program is "correct", meaning no flipping and other modifications are necessary. I strong encourage users to use this program if you are using the "overplus" option + oblique slice. You can type in the oblique angles and get a recalculated table. _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of [Seongjin] Sent: Thursday, April 30, 2009 12:28 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] Gradient table I appreciate the tutorial session at Queen's Medical Center in Honolulu. I am using gradient table (for DTI studio ) generated at the following link: http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html I wonder if I can directly use the gradient table from this java applet without field flipping. Thanks in advance. -SC -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090430/d63b653f/attachment.html From choisj70 at gmail.com Thu Apr 30 15:31:57 2009 From: choisj70 at gmail.com (Seongjin) Date: Thu, 30 Apr 2009 15:31:57 -0400 Subject: [Mristudio-users] Gradient table In-Reply-To: <7k7ed7$7948nt@ipex3.johnshopkins.edu> References: <7k7ed7$7948nt@ipex3.johnshopkins.edu> Message-ID: After AIR registration (with option modified gradient table if available...), I have a new gradient table in AirMatrix.txt file. Then I loaded AIR registered image and the new gradient table for tensor calculation and tractography. Am I doing right? Thanks in advance. -SC On Thu, Apr 30, 2009 at 1:18 PM, susumu wrote: > The gradient table for Philips scanner calculated by this program is > "correct", meaning no flipping and other modifications are necessary. > > > > I strong encourage users to use this program if you are using the > "overplus" option + oblique slice. You can type in the oblique angles and > get a recalculated table. > > > ------------------------------ > > *From:* mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org] *On Behalf Of *[Seongjin] > *Sent:* Thursday, April 30, 2009 12:28 PM > *To:* DTI Studio, ROI Editor, Landmarker Questions/Support > *Subject:* [Mristudio-users] Gradient table > > > > I appreciate the tutorial session at Queen's Medical Center in Honolulu. > > I am using gradient table (for DTI studio ) generated at the following > link: > http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html > > I wonder if I can directly use the gradient table from this java applet > without field flipping. > Thanks in advance. > > -SC > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090430/9d4b4dac/attachment.html From susumu at mri.jhu.edu Fri May 1 09:32:56 2009 From: susumu at mri.jhu.edu (susumu) Date: Fri, 01 May 2009 09:32:56 -0400 Subject: [Mristudio-users] Gradient table In-Reply-To: References: <7k7ed7$70pbun@ipex3.johnshopkins.edu> Message-ID: <983CB2E670554293BF6C85B3A59CD86B@SusumuThinkPad> Hi Liang, 1) I am not sure which coordinates (space) the ultimate gradient table was relative to, such as frequency- and phase-encoding of image, horizontal and vertical direction of image, or magnets' x/y/z coordinates. Based on your reply, I think that it might be the last one. When you present vectors, color maps, or performing fiber tracking, X, Y, and Z need to be defined by the image matrix. This is the most natural way. The frequency/phase/slice and image x/y/z have permutation relationship, like frequency - image x / phase - image y / slice - image z or frequency - image y / phase - image x / slice - image z. The relationship between magnet x / y / z and image x / y / z could have oblique relationship if oblique scan is used, and therefore could be very complicated. The gradient table, ultimately, needs to adopt the image x / y / z system. Now most vendor system is adopting a way to deliver gradient application in the frequency/phase/slice system, moving away from gradient x/y/z. This means, when oblique scan is employed, the scanner dynamically recalculates the gradient table in the f/p/s coordinates. If the scanner doesn't do this (like old Siemens system), we have to recalculate the table based on the oblique angles by ourselves. The former is more fool-proof. 2) In my *.PAR file, there was last 3 columns representing diffusion directions but obviously different between subjects. I don't know what diffusion were recorded in this header file. I don't have much experience with the new PAR file, but if you are using oblique scans, it is not surprising the each patient have different gradient table in the "magnet" coordinate. Suppose we want to apply [1, 0, 0] in the first line of the gradient table, which is the "X" orientation. If we use an oblique scan, magnet X and image X are no longer the same. As I mentioned above, in the end, what we want to know is gradient orientation in the image coordinate. So we have two choices. Choice 1: deliver magnet [1, 0, 0], meaning pure X gradient application. This X gradient could be something like [0.9, 0.15, 0] in the image coordinate. We need to do [1, 0, 0] x ImageRotation to get new gradient table to do tensor calculation. Choice 2: deliver magnet [0.9, -0.15, 0] (I just made up these numbers) so that the applied gradient aligns the image X axis. In this case, we can use gradient table [1, 0, 0] for tensor calculation. I hope this makes your questions answered. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of liang wang Sent: Saturday, April 18, 2009 2:42 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] Gradient table Dear Susumu, I also have a similar question about gradient tables in Philips scanner. My data were collected using following protocols: 1) Gradient table: Medium 2) Gradient overplus: no 3) Oblique plane: yes, and different angles between subjects. Looking through your answer, I know that this set can result in the same gradient table input into DTIstudio for all subject. However, 1) I am not sure which coordinates (space) the ultimate gradient table was relative to, such as frequency- and phase-encoding of image, horizontal and vertical direction of image, or magnets' x/y/z coordinates. Based on your reply, I think that it might be the last one. 2) In my *.PAR file, there was last 3 columns representing diffusion directions but obviously different between subjects. I don't know what diffusion were recorded in this header file. Many thanks Liang 2009/4/16 susumu Hi Eric, For Philips scanner there are several types of gradient tables you can specify in the scanner. Please check your protocol for the following points; 1) Gradient table: High (32-orientation)/ Medium (15-orientation) / Low (6-orientation) 2) Overplus (ON / OFF) 3) Oblique plane (X/Y/Z angles) The first option has 3 choices and the second option has 2 choices. Therefore, there are 3 x 2 = 6 gradient tables. If the second option (Overplus) is NO, the third option has no effect. If the second option is YES, the gradient table has to be rotated based on the oblique angles. To simplify the DTI processing, we recommend Overplus = NO. We have the basic 6 tables, which can be used as is if you use Overplus = OFF or Oblique angles = 0/0/0 degree. Please let us know which options you are using. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of eric Q Sent: Thursday, April 16, 2009 9:44 PM To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] Gradient table Hello Dear DTIstudio users: I am new to DTIstudio, I was hoping someone could give me some much needed advises for beginners. I was trying to obtain the FA values for my brain phantom (PHILIP 3T scanner). When I clicked on "DTI mapping", it prompted me to enter the "gradient table", how do I calculate the "gradient table"? Thanks in advanced Best regards Eric _____ Date: Thu, 9 Apr 2009 11:04:09 -0400 From: susumu at mri.jhu.edu To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] MriView3D application close Hi Hugh, When you got this error, please suspect one of the following two reasons; 1) Memory shortage: Even if you have many GB of memories, 32-bit Windows system can allocate only 1 - 1.5 GB to each program. To check if you have the memory problem, please restrict the slices to be calculated. In the initial data parameter window, there is a section called "Slices to be processed". Here you can specify only a portion of slices to be processed. Please limit the slices to, for example, 0-9 and see how it goes. If you can calculate tensors without errors, then you have the memory problem. The solution is; a) upgrade to the 64-bit system or b) devide the calculation to 2 batches (e.g. slice 0-29 for the first batch and 30-59 for the second batch), calculate all maps (e.g. FA), and later combine them. 2) Mismatch between the gradient table and the number of images: For example, if you specify 12-orientation table and 30 volume images, then you get the error. After loading the data and before you go to the Dti Map tab, make sure that you have 1 b0 + 64 DWIs in the pull-down menu in the right column of the Image tab. If you have the correct number of the images, then you might have an error in your gradient table. Small mistakes such as missing "," are often difficult to detect. The best way is; a) load the data using DtiMapping under the "File" button on the top left, b) close the window, c) open the image paremater window again by clicking "DtiMapping" in the "File" button again, d) the window still remembers the gradient table you entered last time. This remembered window tells how DtiStudio interpreted your gradient table. If there is any syntax errors, you may find them much easier. For example, if you enter, "4: 1 0.5 0", instead of "4: 1, 0.5, 0", then you would find, "4: 1, 0, 0". If any of these do not solve the issue, please let us know. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hugh Wang Sent: Wednesday, April 08, 2009 6:30 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] MriView3D application close Hi, I was using the dtistudio (ver. 2.4) to look at the Siemens DICOM diffusion images (1baseline,64 gradients). After successfully loading the images, I click the "dti map" option at lower right corner. Whatever calculation I choose, it always gives me an error: "MriView3D MFC Application has encountered a problem and needs to close. We are sorry for the inconvenience." I tried several PCs, and the problem keeped the same. I would appreciate that if there's anyone having any idea on how to solve it. Thanks. Best, Hugh _____ Find car news, reviews and more Looking to change your car this year? _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wanglbit at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090501/92ec1e8b/attachment-0001.html From siewmin.gan at gmail.com Fri May 1 01:34:51 2009 From: siewmin.gan at gmail.com (Siewmin Gan) Date: Fri, 01 May 2009 13:34:51 +0800 Subject: [Mristudio-users] question using AIR in Landmarker In-Reply-To: References: Message-ID: Hi Xin thanks. I have attached a few shots here with a brief description.1. the landmarker window where I clicked on the "align button" at the bottom left corner 2. The folder where I would save the output file (filename: AlignWarpOutput and filetype:(*.warp)). This folder is in my Computer/Local Disk/Landmarker (i.e C:/Landmarker) where I have placed the Landmarker software and the .exe files. 3. In snapshot 3, i change the save as type file to all files, so you can see that the align_warp.exe and other .exe files are also in this folder. 4. The snapshot of the 1st error msg. When I clicked "OK", the second error message occur as shown in shot 5. Initially, I did get a warning message that there should be no spaces in the whole path of the warp file etc, and have resolved that error message. Many Thanks Siewmin On Fri, May 1, 2009 at 12:02 AM, Xin Li wrote: > Siewmin, > > Could you take snapshots of these two error messages? And please tell me > the whole path of the warp file that you were going to save on your machine. > The whole path of the warp file should not have any spaces. I am not sure if > this is the reason. > > > Xin > > > > ----- Original Message ----- > From: Siewmin Gan > Date: Thursday, April 30, 2009 11:31 am > Subject: Re: [Mristudio-users] question using AIR in Landmarker > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" < > mristudio-users at mristudio.org> > > > > Hi Xin, the error message occurs in a pop up warning window on the > DTIstudio > > GUI. > > thanks > > > > Siewmin > > > > On Wed, Apr 29, 2009 at 11:30 PM, Xin Li wrote: > > > > > Siewmin, > > > > > > Where did you see this error message "C:/Landmarker/align_warp.exe. > > The > > > parameter is incorrect" ? Did you see it in the C command window or > > in a pop > > > up warning window? > > > > > > > > > Xin > > > > > > > > > > > > ----- Original Message ----- > > > From: Siewmin Gan > > > Date: Thursday, April 23, 2009 5:08 am > > > Subject: [Mristudio-users] question using AIR in Landmarker > > > To: mristudio-users at mristudio.org > > > > > > > > > > Hi, I'm trying to do non-linear registration to normalise my > resampled > > > > aDWI images to the ICBM_DTI_81 DWI template. When I clicked on the > > > "align > > > > button", I recieved two error messages (below), and could not > perform > > > > the > > > > registration step: > > > > > > > > "C:/Landmarker/align_warp.exe. The parameter is incorrect" > > followed by > > > > "cannot find warp file". > > > > > > > > I have placed the aligned_warp.exe file in the folder landmarker > > where > > > > software is located, and am not sure where the problem may be. > > > > > > > > Many Thanks > > > > > > > > Siewmin > > > > _______________________________________________ > > > > Mristudio-users mailing list > > > > Mristudio-users at mristudio.org > > > > > > > _______________________________________________ > > > Mristudio-users mailing list > > > Mristudio-users at mristudio.org > > > > > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > -------------- next part -------------- An HTML attachment was scrubbed... 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Name: screenshot4.png Type: image/png Size: 117551 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090501/9b8cfe74/attachment-0008.png -------------- next part -------------- A non-text attachment was scrubbed... Name: screenshot5.png Type: image/png Size: 114538 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090501/9b8cfe74/attachment-0009.png From choisj70 at gmail.com Fri May 1 10:39:11 2009 From: choisj70 at gmail.com (Seongjin) Date: Fri, 01 May 2009 10:39:11 -0400 Subject: [Mristudio-users] Gradient table In-Reply-To: References: <7k7ed7$70pbun@ipex3.johnshopkins.edu> Message-ID: Following link will be a bit of help. http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html You need to have JAVA runtime on your computer. Use your examcard when you filling the boxes provided in the link. You will have a gradient table. Overplus-On option will give you different gradient table for each different angulation info. Overplus-Off option will give you the same result no matter what angulation info. Only difference comes from directional resolution. -SC On Sat, Apr 18, 2009 at 2:42 PM, liang wang wrote: > Dear Susumu, > > I also have a similar question about gradient tables in Philips scanner. > > My data were collected using following protocols: > 1) Gradient table: Medium > 2) Gradient overplus: no > 3) Oblique plane: yes, and different angles between subjects. > > Looking through your answer, I know that this set can result in the same > gradient table input into DTIstudio for all subject. However, 1) I am not > sure which coordinates (space) the ultimate gradient table was relative to, > such as frequency- and phase-encoding of image, horizontal and vertical > direction of image, or magnets' x/y/z coordinates. Based on your reply, I > think that it might be the last one. > > 2) In my *.PAR file, there was last 3 columns representing diffusion > directions but obviously different between subjects. I don't know what > diffusion were recorded in this header file. > > Many thanks > > Liang > > 2009/4/16 susumu > >> Hi Eric, >> >> >> >> For Philips scanner there are several types of gradient tables you can >> specify in the scanner. Please check your protocol for the following points; >> >> >> >> 1) Gradient table: High (32-orientation)/ Medium (15-orientation) / >> Low (6-orientation) >> >> 2) Overplus (ON / OFF) >> >> 3) Oblique plane (X/Y/Z angles) >> >> >> >> The first option has 3 choices and the second option has 2 choices. >> Therefore, there are 3 x 2 = 6 gradient tables. >> >> If the second option (Overplus) is NO, the third option has no effect. If >> the second option is YES, the gradient table has to be rotated based on the >> oblique angles. >> >> >> >> To simplify the DTI processing, we recommend Overplus = NO. >> >> >> >> We have the basic 6 tables, which can be used as is if you use Overplus = >> OFF or Oblique angles = 0/0/0 degree. >> >> Please let us know which options you are using. >> >> >> >> Susumu >> >> >> ------------------------------ >> >> *From:* mristudio-users-bounces at mristudio.org [mailto: >> mristudio-users-bounces at mristudio.org] *On Behalf Of *eric Q >> *Sent:* Thursday, April 16, 2009 9:44 PM >> *To:* mristudio-users at mristudio.org >> *Subject:* Re: [Mristudio-users] Gradient table >> >> >> >> Hello Dear DTIstudio users: >> >> I am new to DTIstudio, I was hoping someone could give me some much needed >> advises for beginners. >> >> >> I was trying to obtain the FA values for my brain phantom (PHILIP 3T >> scanner). When I clicked on "DTI mapping", it prompted me to enter the >> "gradient table", how do I calculate the "gradient table"? >> >> Thanks in advanced >> >> Best regards >> >> Eric >> >> >> ------------------------------ >> >> Date: Thu, 9 Apr 2009 11:04:09 -0400 >> From: susumu at mri.jhu.edu >> To: mristudio-users at mristudio.org >> Subject: Re: [Mristudio-users] MriView3D application close >> >> Hi Hugh, >> >> >> >> When you got this error, please suspect one of the following two reasons; >> >> >> >> 1) Memory shortage: >> >> >> >> Even if you have many GB of memories, 32-bit Windows system can allocate >> only 1 - 1.5 GB to each program. To check if you have the memory problem, >> please restrict the slices to be calculated. In the initial data parameter >> window, there is a section called "Slices to be processed". Here you can >> specify only a portion of slices to be processed. Please limit the slices >> to, for example, 0-9 and see how it goes. If you can calculate tensors >> without errors, then you have the memory problem. The solution is; a) >> upgrade to the 64-bit system or b) devide the calculation to 2 batches (e.g. >> slice 0-29 for the first batch and 30-59 for the second batch), calculate >> all maps (e.g. FA), and later combine them. >> >> >> >> 2) Mismatch between the gradient table and the number of images: >> >> >> >> For example, if you specify 12-orientation table and 30 volume images, >> then you get the error. After loading the data and before you go to the Dti >> Map tab, make sure that you have 1 b0 + 64 DWIs in the pull-down menu in the >> right column of the Image tab. If you have the correct number of the images, >> then you might have an error in your gradient table. Small mistakes such as >> missing "," are often difficult to detect. The best way is; a) load the data >> using DtiMapping under the "File" button on the top left, b) close the >> window, c) open the image paremater window again by clicking "DtiMapping" in >> the "File" button again, d) the window still remembers the gradient table >> you entered last time. This remembered window tells how DtiStudio >> interpreted your gradient table. If there is any syntax errors, you may find >> them much easier. For example, if you enter, "4: 1 0.5 0", instead of "4: 1, >> 0.5, 0", then you would find, "4: 1, 0, 0". >> >> >> >> If any of these do not solve the issue, please let us know. >> >> >> >> Susumu >> >> >> ------------------------------ >> >> *From:* mristudio-users-bounces at mristudio.org [mailto: >> mristudio-users-bounces at mristudio.org] *On Behalf Of *Hugh Wang >> *Sent:* Wednesday, April 08, 2009 6:30 PM >> *To:* mristudio-users at mristudio.org >> *Subject:* [Mristudio-users] MriView3D application close >> >> Hi, >> >> I was using the dtistudio (ver. 2.4) to look at the Siemens DICOM >> diffusion images (1baseline,64 gradients). After successfully loading the >> images, I click the "dti map" option at lower right corner. Whatever >> calculation I choose, it always gives me an error: >> >> "MriView3D MFC Application has encountered a problem and needs to close. >> We are sorry for the inconvenience." >> >> I tried several PCs, and the problem keeped the same. I would appreciate >> that if there's anyone having any idea on how to solve it. Thanks. >> >> Best, >> Hugh >> ------------------------------ >> >> Find car news, reviews and more Looking to change your car this year? >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/mristudio-users >> >> > > > -- > Liang Wang, PhD > Postdoctoral Fellow > Woodward Lab > Department of Psychiatry > University of British Columbia > BC Mental Health & Addiction Services > 938 West 28th Avenue > Vancouver BC V5Z 4H4 > Telephone: 1-604-875-2000 (ext. 4735) > Fax: 1-604-875-3871 > Email: wanglbit at gmail.com > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090501/2f1522f4/attachment.html From choisj70 at gmail.com Fri May 1 12:01:05 2009 From: choisj70 at gmail.com (Seongjin) Date: Fri, 01 May 2009 12:01:05 -0400 Subject: [Mristudio-users] Questions regarding Transformation in Landmark Message-ID: I have data sets having reduced field of view compared to template in the Landmarker. I simply used linear AIR for space normalization. Translation and non-linear AIR seems not available for data of different dimensions from the template. Q1. I wonder what other restrictions in the space normalization or transformation by using Landmarker. Q2. After transformation, I would like to do fiber tracking in DTI Studio. What steps should I go through? I tried to use "Fiber Tracking" in DTI Studio main menu, however it asked to load "*.ani" file and "*.vec" file. Those files were not generated at all from the normalization. I have updated FA, eigenvalue, tensor and AlignlinearOuptut.air. Thanks in advance. -SC -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090501/047dfd1e/attachment-0001.html From susumu at mri.jhu.edu Fri May 1 13:10:50 2009 From: susumu at mri.jhu.edu (susumu) Date: Fri, 01 May 2009 13:10:50 -0400 Subject: [Mristudio-users] question using AIR in Landmarker In-Reply-To: Message-ID: <7k7ed7$79s3i3@ipex3.johnshopkins.edu> Hi Siewmin, I hope Xin is working on the error message you got. I just want to comment on your "Screenshot1". In this window, the template is T1 and your data to be normalized is FA. I recommend to use the same contrast. For example, you can use b0 (T2) or DWI for both template and your data. There are two ways to normalize FA; 1) you can load both DWI (or b0) and FA. Choose DWI in active window before you start AIR. After AIR all leaded images (in this case FA) will also be normalized based on the DWI-DWI (or b0-b0) intra-contrast AIR result. Avoid cross-contrast AIR as much as possible. 2) you can do DWI-DWI (or b0-b0) AIR and save the AIR output file (transformation matrix). Later, you can load FA, ADC, or whatever images you want to normalize. Then apply the AIR transformation matrix using the button with "M coming out of a folder" button in the "Volume LDDMM" section. _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Siewmin Gan Sent: Friday, May 01, 2009 1:35 AM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] question using AIR in Landmarker Hi Xin thanks. I have attached a few shots here with a brief description. 1. the landmarker window where I clicked on the "align button" at the bottom left corner 2. The folder where I would save the output file (filename: AlignWarpOutput and filetype:(*.warp)). This folder is in my Computer/Local Disk/Landmarker (i.e C:/Landmarker) where I have placed the Landmarker software and the .exe files. 3. In snapshot 3, i change the save as type file to all files, so you can see that the align_warp.exe and other .exe files are also in this folder. 4. The snapshot of the 1st error msg. When I clicked "OK", the second error message occur as shown in shot 5. Initially, I did get a warning message that there should be no spaces in the whole path of the warp file etc, and have resolved that error message. Many Thanks Siewmin On Fri, May 1, 2009 at 12:02 AM, Xin Li wrote: Siewmin, Could you take snapshots of these two error messages? And please tell me the whole path of the warp file that you were going to save on your machine. The whole path of the warp file should not have any spaces. I am not sure if this is the reason. Xin ----- Original Message ----- From: Siewmin Gan Date: Thursday, April 30, 2009 11:31 am Subject: Re: [Mristudio-users] question using AIR in Landmarker To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > Hi Xin, the error message occurs in a pop up warning window on the DTIstudio > GUI. > thanks > > Siewmin > > On Wed, Apr 29, 2009 at 11:30 PM, Xin Li wrote: > > > Siewmin, > > > > Where did you see this error message "C:/Landmarker/align_warp.exe. > The > > parameter is incorrect" ? Did you see it in the C command window or > in a pop > > up warning window? > > > > > > Xin > > > > > > > > ----- Original Message ----- > > From: Siewmin Gan > > Date: Thursday, April 23, 2009 5:08 am > > Subject: [Mristudio-users] question using AIR in Landmarker > > To: mristudio-users at mristudio.org > > > > > > > Hi, I'm trying to do non-linear registration to normalise my resampled > > > aDWI images to the ICBM_DTI_81 DWI template. When I clicked on the > > "align > > > button", I recieved two error messages (below), and could not perform > > > the > > > registration step: > > > > > > "C:/Landmarker/align_warp.exe. The parameter is incorrect" > followed by > > > "cannot find warp file". > > > > > > I have placed the aligned_warp.exe file in the folder landmarker > where > > > software is located, and am not sure where the problem may be. > > > > > > Many Thanks > > > > > > Siewmin > > > _______________________________________________ > > > Mristudio-users mailing list > > > Mristudio-users at mristudio.org > > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090501/c7d3f19c/attachment.html From darshanp20 at yahoo.com Fri May 1 15:18:01 2009 From: darshanp20 at yahoo.com (darshan pai) Date: Fri, 01 May 2009 12:18:01 -0700 (PDT) Subject: [Mristudio-users] Questions regarding Transformation in Landmark In-Reply-To: References: Message-ID: <104498.25444.qm@web30707.mail.mud.yahoo.com> *.ani is the updated_FA file and *.vec is the updated eigenvector0 file. I think the format for both is *.dat .. just different extensions to differentiate I guess .. ________________________________ From: [Seongjin] To: "DTI Studio, ROI Editor, Landmarker Questions/Support" Sent: Friday, May 1, 2009 12:01:05 PM Subject: [Mristudio-users] Questions regarding Transformation in Landmark I have data sets having reduced field of view compared to template in the Landmarker. I simply used linear AIR for space normalization. Translation and non-linear AIR seems not available for data of different dimensions from the template. Q1. I wonder what other restrictions in the space normalization or transformation by using Landmarker. Q2. After transformation, I would like to do fiber tracking in DTI Studio. What steps should I go through? I tried to use "Fiber Tracking" in DTI Studio main menu, however it asked to load "*.ani" file and "*.vec" file. Those files were not generated at all from the normalization. I have updated FA, eigenvalue, tensor and AlignlinearOuptut.air. Thanks in advance. -SC -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090501/20b13894/attachment.html From choisj70 at gmail.com Fri May 1 16:43:27 2009 From: choisj70 at gmail.com (Seongjin) Date: Fri, 01 May 2009 16:43:27 -0400 Subject: [Mristudio-users] Questions regarding Transformation in Landmark In-Reply-To: <104498.25444.qm@web30707.mail.mud.yahoo.com> References: <104498.25444.qm@web30707.mail.mud.yahoo.com> Message-ID: Thanks for you reply. I guessed *.ani file will be the same. However, regarding *.vec file, I were warned not to transform vector file. I have no idea on this. Anyone who knows the answer? -SC On Fri, May 1, 2009 at 3:18 PM, darshan pai wrote: > *.ani is the updated_FA file > and *.vec is the updated eigenvector0 file. > I think the format for both is *.dat .. just different extensions to > differentiate I guess .. > > ------------------------------ > *From:* [Seongjin] > *To:* "DTI Studio, ROI Editor, Landmarker Questions/Support" < > mristudio-users at mristudio.org> > *Sent:* Friday, May 1, 2009 12:01:05 PM > *Subject:* [Mristudio-users] Questions regarding Transformation in > Landmark > > I have data sets having reduced field of view compared to template in the > Landmarker. > I simply used linear AIR for space normalization. > > Translation and non-linear AIR seems not available for data of different > dimensions from the template. > > > Q1. I wonder what other restrictions in the space normalization or > transformation by using Landmarker. > > Q2. After transformation, I would like to do fiber tracking in DTI Studio. > What steps should I go through? > I tried to use "Fiber Tracking" in DTI Studio main menu, however it > asked to load "*.ani" file and "*.vec" file. > Those files were not generated at all from the normalization. > I have updated FA, eigenvalue, tensor and AlignlinearOuptut.air. > > Thanks in advance. > > -SC > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090501/152984e4/attachment-0001.html From darshanp20 at yahoo.com Fri May 1 19:08:24 2009 From: darshanp20 at yahoo.com (darshan pai) Date: Fri, 01 May 2009 16:08:24 -0700 (PDT) Subject: [Mristudio-users] Questions regarding Transformation in Landmark In-Reply-To: References: <104498.25444.qm@web30707.mail.mud.yahoo.com> Message-ID: <173442.34069.qm@web30704.mail.mud.yahoo.com> no you do not transform the vector file. you have the tensor right . You open the tensor in DTIStudio using the Open .d button, choose the tensor . It asks you for options regarding if you want to make eigen vectors FA , RA etc . Let it run, it will make all the files , just save what you need . HTH ________________________________ From: [Seongjin] To: "DTI Studio, ROI Editor, Landmarker Questions/Support" Sent: Friday, May 1, 2009 4:43:27 PM Subject: Re: [Mristudio-users] Questions regarding Transformation in Landmark Thanks for you reply. I guessed *.ani file will be the same. However, regarding *.vec file, I were warned not to transform vector file. I have no idea on this. Anyone who knows the answer? -SC On Fri, May 1, 2009 at 3:18 PM, darshan pai wrote: *.ani is the updated_FA file and *.vec is the updated eigenvector0 file. I think the format for both is *.dat .. just different extensions to differentiate I guess .. ________________________________ From: [Seongjin] To: "DTI Studio, ROI Editor, Landmarker Questions/Support" Sent: Friday, May 1, 2009 12:01:05 PM Subject: [Mristudio-users] Questions regarding Transformation in Landmark I have data sets having reduced field of view compared to template in the Landmarker. I simply used linear AIR for space normalization. Translation and non-linear AIR seems not available for data of different dimensions from the template. Q1. I wonder what other restrictions in the space normalization or transformation by using Landmarker. Q2. After transformation, I would like to do fiber tracking in DTI Studio. What steps should I go through? I tried to use "Fiber Tracking" in DTI Studio main menu, however it asked to load "*.ani" file and "*.vec" file. Those files were not generated at all from the normalization. I have updated FA, eigenvalue, tensor and AlignlinearOuptut.air. Thanks in advance. -SC _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090501/a1485c8f/attachment.html From rkumar at mednet.ucla.edu Fri May 1 19:40:39 2009 From: rkumar at mednet.ucla.edu (Rajesh Kumar) Date: Fri, 01 May 2009 16:40:39 -0700 Subject: [Mristudio-users] Questions regarding Transformation in Landmark In-Reply-To: <173442.34069.qm@web30704.mail.mud.yahoo.com> References: <104498.25444.qm@web30707.mail.mud.yahoo.com> <173442.34069.qm@web30704.mail.mud.yahoo.com> Message-ID: <49FB8877.6070403@mednet.ucla.edu> Hi List: I want to normalize tensor map to common space (MNI template) in DTI studio. Is there anybody who can suggest me how to proceed? I am not sure that i should use b0 or trace template (in MNI space) for the same. With regards Rajesh IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. From choisj70 at gmail.com Sat May 2 06:56:35 2009 From: choisj70 at gmail.com (Seongjin) Date: Sat, 02 May 2009 06:56:35 -0400 Subject: [Mristudio-users] Questions regarding Transformation in Landmark In-Reply-To: <173442.34069.qm@web30704.mail.mud.yahoo.com> References: <104498.25444.qm@web30707.mail.mud.yahoo.com> <173442.34069.qm@web30704.mail.mud.yahoo.com> Message-ID: Darshan, thanks a lot! -SC On Fri, May 1, 2009 at 7:08 PM, darshan pai wrote: > no you do not transform the vector file. you have the tensor right . You > open the tensor in DTIStudio using the Open .d button, choose the tensor . > It asks you for options regarding if you want to make eigen vectors FA , RA > etc . Let it run, it will make all the files , just save what you need . > > HTH > > ------------------------------ > *From:* [Seongjin] > *To:* "DTI Studio, ROI Editor, Landmarker Questions/Support" < > mristudio-users at mristudio.org> > *Sent:* Friday, May 1, 2009 4:43:27 PM > *Subject:* Re: [Mristudio-users] Questions regarding Transformation in > Landmark > > Thanks for you reply. > > I guessed *.ani file will be the same. However, regarding *.vec file, I > were warned not to transform vector file. I have no idea on this. Anyone who > knows the answer? > > -SC > > On Fri, May 1, 2009 at 3:18 PM, darshan pai wrote: > >> *.ani is the updated_FA file >> and *.vec is the updated eigenvector0 file. >> I think the format for both is *.dat .. just different extensions to >> differentiate I guess .. >> >> ------------------------------ >> *From:* [Seongjin] >> *To:* "DTI Studio, ROI Editor, Landmarker Questions/Support" < >> mristudio-users at mristudio.org> >> *Sent:* Friday, May 1, 2009 12:01:05 PM >> *Subject:* [Mristudio-users] Questions regarding Transformation in >> Landmark >> >> I have data sets having reduced field of view compared to template in the >> Landmarker. >> I simply used linear AIR for space normalization. >> >> Translation and non-linear AIR seems not available for data of different >> dimensions from the template. >> >> >> Q1. I wonder what other restrictions in the space normalization or >> transformation by using Landmarker. >> >> Q2. After transformation, I would like to do fiber tracking in DTI Studio. >> What steps should I go through? >> I tried to use "Fiber Tracking" in DTI Studio main menu, however it >> asked to load "*.ani" file and "*.vec" file. >> Those files were not generated at all from the normalization. >> I have updated FA, eigenvalue, tensor and AlignlinearOuptut.air. >> >> Thanks in advance. >> >> -SC >> >> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/mristudio-users >> >> > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090502/1dc2b9bf/attachment.html From siewmin.gan at gmail.com Mon May 4 12:35:09 2009 From: siewmin.gan at gmail.com (Siewmin Gan) Date: Tue, 05 May 2009 00:35:09 +0800 Subject: [Mristudio-users] question using AIR in Landmarker In-Reply-To: <7k7ed7$79s3i3@ipex3.johnshopkins.edu> References: <7k7ed7$79s3i3@ipex3.johnshopkins.edu> Message-ID: Hi Susumu and Xin, many thanks. It works great. Siewmin On Sat, May 2, 2009 at 1:10 AM, susumu wrote: > Hi Siewmin, > > > > I hope Xin is working on the error message you got. > > I just want to comment on your "Screenshot1". In this window, the template > is T1 and your data to be normalized is FA. > > I recommend to use the same contrast. For example, you can use b0 (T2) or > DWI for both template and your data. > > There are two ways to normalize FA; > > 1) you can load both DWI (or b0) and FA. Choose DWI in active window before > you start AIR. After AIR all leaded images (in this case FA) will also be > normalized based on the DWI-DWI (or b0-b0) intra-contrast AIR result. Avoid > cross-contrast AIR as much as possible. > > 2) you can do DWI-DWI (or b0-b0) AIR and save the AIR output file > (transformation matrix). Later, you can load FA, ADC, or whatever images you > want to normalize. Then apply the AIR transformation matrix using the button > with "M coming out of a folder" button in the "Volume LDDMM" section. > > > ------------------------------ > > *From:* mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org] *On Behalf Of *Siewmin Gan > *Sent:* Friday, May 01, 2009 1:35 AM > > *To:* DTI Studio, ROI Editor, Landmarker Questions/Support > *Subject:* Re: [Mristudio-users] question using AIR in Landmarker > > > > Hi Xin thanks. I have attached a few shots here with a brief description. > > 1. the landmarker window where I clicked on the "align button" at the > bottom left corner > > 2. The folder where I would save the output file (filename: AlignWarpOutput > and filetype:(*.warp)). This folder is in my Computer/Local Disk/Landmarker > (i.e C:/Landmarker) where I have placed the Landmarker software and the .exe > files. > > 3. In snapshot 3, i change the save as type file to all files, so you can > see that the align_warp.exe and other .exe files are also in this folder. > > 4. The snapshot of the 1st error msg. When I clicked "OK", the second error > message occur as shown in shot 5. > > > > Initially, I did get a warning message that there should be no spaces in > the whole path of the warp file etc, and have resolved that error message. > > > > Many Thanks > > > > Siewmin > > > > On Fri, May 1, 2009 at 12:02 AM, Xin Li wrote: > > Siewmin, > > Could you take snapshots of these two error messages? And please tell me > the whole path of the warp file that you were going to save on your machine. > The whole path of the warp file should not have any spaces. I am not sure if > this is the reason. > > > > Xin > > > > ----- Original Message ----- > From: Siewmin Gan > > Date: Thursday, April 30, 2009 11:31 am > Subject: Re: [Mristudio-users] question using AIR in Landmarker > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" < > mristudio-users at mristudio.org> > > > > Hi Xin, the error message occurs in a pop up warning window on the > DTIstudio > > GUI. > > thanks > > > > Siewmin > > > > On Wed, Apr 29, 2009 at 11:30 PM, Xin Li wrote: > > > > > Siewmin, > > > > > > Where did you see this error message "C:/Landmarker/align_warp.exe. > > The > > > parameter is incorrect" ? Did you see it in the C command window or > > in a pop > > > up warning window? > > > > > > > > > Xin > > > > > > > > > > > > ----- Original Message ----- > > > From: Siewmin Gan > > > Date: Thursday, April 23, 2009 5:08 am > > > Subject: [Mristudio-users] question using AIR in Landmarker > > > To: mristudio-users at mristudio.org > > > > > > > > > > Hi, I'm trying to do non-linear registration to normalise my > resampled > > > > aDWI images to the ICBM_DTI_81 DWI template. When I clicked on the > > > "align > > > > button", I recieved two error messages (below), and could not > perform > > > > the > > > > registration step: > > > > > > > > "C:/Landmarker/align_warp.exe. The parameter is incorrect" > > followed by > > > > "cannot find warp file". > > > > > > > > I have placed the aligned_warp.exe file in the folder landmarker > > where > > > > software is located, and am not sure where the problem may be. > > > > > > > > Many Thanks > > > > > > > > Siewmin > > > > _______________________________________________ > > > > Mristudio-users mailing list > > > > Mristudio-users at mristudio.org > > > > > > > _______________________________________________ > > > Mristudio-users mailing list > > > Mristudio-users at mristudio.org > > > > > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090505/b90b2278/attachment-0001.html From qcdunk at hotmail.com Tue May 5 02:05:13 2009 From: qcdunk at hotmail.com (eric Q) Date: Tue, 05 May 2009 16:05:13 +1000 Subject: [Mristudio-users] program crashes In-Reply-To: <983CB2E670554293BF6C85B3A59CD86B@SusumuThinkPad> References: <7k7ed7$70pbun@ipex3.johnshopkins.edu> <983CB2E670554293BF6C85B3A59CD86B@SusumuThinkPad> Message-ID: Hi Susumu: Thank you for answering my question regarding the gradient table. However the program crashes every time when I try to do a calculation (DTI mapping). I've tried to calculate Tensor, Color map, ADC map, Mean, but I always get this "The mriView3D MFC application has encountered a problem and needs to close". I am a new user to DTI studio, so there are probably a lot of mistakes I've made on my end, but could you please tell me what are the likely causes for the crash of my program? Your time and help is much appreciated. Regards Eric Q Date: Fri, 1 May 2009 09:32:56 -0400 From: susumu at mri.jhu.edu To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] Gradient table Hi Liang, 1) I am not sure which coordinates (space) the ultimate gradient table was relative to, such as frequency- and phase-encoding of image, horizontal and vertical direction of image, or magnets' x/y/z coordinates. Based on your reply, I think that it might be the last one. When you present vectors, color maps, or performing fiber tracking, X, Y, and Z need to be defined by the image matrix. This is the most natural way. The frequency/phase/slice and image x/y/z have permutation relationship, like frequency ? image x / phase ? image y / slice ? image z or frequency ? image y / phase ? image x / slice ? image z. The relationship between magnet x / y / z and image x / y / z could have oblique relationship if oblique scan is used, and therefore could be very complicated. The gradient table, ultimately, needs to adopt the image x / y / z system. Now most vendor system is adopting a way to deliver gradient application in the frequency/phase/slice system, moving away from gradient x/y/z. This means, when oblique scan is employed, the scanner dynamically recalculates the gradient table in the f/p/s coordinates. If the scanner doesn?t do this (like old Siemens system), we have to recalculate the table based on the oblique angles by ourselves. The former is more fool-proof. 2) In my *.PAR file, there was last 3 columns representing diffusion directions but obviously different between subjects. I don't know what diffusion were recorded in this header file. I don?t have much experience with the new PAR file, but if you are using oblique scans, it is not surprising the each patient have different gradient table in the ?magnet? coordinate. Suppose we want to apply [1, 0, 0] in the first line of the gradient table, which is the ?X? orientation. If we use an oblique scan, magnet X and image X are no longer the same. As I mentioned above, in the end, what we want to know is gradient orientation in the image coordinate. So we have two choices. Choice 1: deliver magnet [1, 0, 0], meaning pure X gradient application. This X gradient could be something like [0.9, 0.15, 0] in the image coordinate. We need to do [1, 0, 0] x ImageRotation to get new gradient table to do tensor calculation. Choice 2: deliver magnet [0.9, -0.15, 0] (I just made up these numbers) so that the applied gradient aligns the image X axis. In this case, we can use gradient table [1, 0, 0] for tensor calculation. I hope this makes your questions answered. Susumu From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of liang wang Sent: Saturday, April 18, 2009 2:42 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] Gradient table Dear Susumu, I also have a similar question about gradient tables in Philips scanner. My data were collected using following protocols: 1) Gradient table: Medium 2) Gradient overplus: no 3) Oblique plane: yes, and different angles between subjects. Looking through your answer, I know that this set can result in the same gradient table input into DTIstudio for all subject. However, 1) I am not sure which coordinates (space) the ultimate gradient table was relative to, such as frequency- and phase-encoding of image, horizontal and vertical direction of image, or magnets' x/y/z coordinates. Based on your reply, I think that it might be the last one. 2) In my *.PAR file, there was last 3 columns representing diffusion directions but obviously different between subjects. I don't know what diffusion were recorded in this header file. Many thanks Liang 2009/4/16 susumu Hi Eric, For Philips scanner there are several types of gradient tables you can specify in the scanner. Please check your protocol for the following points; 1) Gradient table: High (32-orientation)/ Medium (15-orientation) / Low (6-orientation) 2) Overplus (ON / OFF) 3) Oblique plane (X/Y/Z angles) The first option has 3 choices and the second option has 2 choices. Therefore, there are 3 x 2 = 6 gradient tables. If the second option (Overplus) is NO, the third option has no effect. If the second option is YES, the gradient table has to be rotated based on the oblique angles. To simplify the DTI processing, we recommend Overplus = NO. We have the basic 6 tables, which can be used as is if you use Overplus = OFF or Oblique angles = 0/0/0 degree. Please let us know which options you are using. Susumu From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of eric Q Sent: Thursday, April 16, 2009 9:44 PM To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] Gradient table Hello Dear DTIstudio users: I am new to DTIstudio, I was hoping someone could give me some much needed advises for beginners. I was trying to obtain the FA values for my brain phantom (PHILIP 3T scanner). When I clicked on "DTI mapping", it prompted me to enter the "gradient table", how do I calculate the "gradient table"? Thanks in advanced Best regards Eric Date: Thu, 9 Apr 2009 11:04:09 -0400 From: susumu at mri.jhu.edu To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] MriView3D application close Hi Hugh, When you got this error, please suspect one of the following two reasons; 1) Memory shortage: Even if you have many GB of memories, 32-bit Windows system can allocate only 1 - 1.5 GB to each program. To check if you have the memory problem, please restrict the slices to be calculated. In the initial data parameter window, there is a section called "Slices to be processed". Here you can specify only a portion of slices to be processed. Please limit the slices to, for example, 0-9 and see how it goes. If you can calculate tensors without errors, then you have the memory problem. The solution is; a) upgrade to the 64-bit system or b) devide the calculation to 2 batches (e.g. slice 0-29 for the first batch and 30-59 for the second batch), calculate all maps (e.g. FA), and later combine them. 2) Mismatch between the gradient table and the number of images: For example, if you specify 12-orientation table and 30 volume images, then you get the error. After loading the data and before you go to the Dti Map tab, make sure that you have 1 b0 + 64 DWIs in the pull-down menu in the right column of the Image tab. If you have the correct number of the images, then you might have an error in your gradient table. Small mistakes such as missing "," are often difficult to detect. The best way is; a) load the data using DtiMapping under the "File" button on the top left, b) close the window, c) open the image paremater window again by clicking "DtiMapping" in the "File" button again, d) the window still remembers the gradient table you entered last time. This remembered window tells how DtiStudio interpreted your gradient table. If there is any syntax errors, you may find them much easier. For example, if you enter, "4: 1 0.5 0", instead of "4: 1, 0.5, 0", then you would find, "4: 1, 0, 0". If any of these do not solve the issue, please let us know. Susumu From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hugh Wang Sent: Wednesday, April 08, 2009 6:30 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] MriView3D application close Hi, I was using the dtistudio (ver. 2.4) to look at the Siemens DICOM diffusion images (1baseline,64 gradients). After successfully loading the images, I click the "dti map" option at lower right corner. Whatever calculation I choose, it always gives me an error: "MriView3D MFC Application has encountered a problem and needs to close. We are sorry for the inconvenience." I tried several PCs, and the problem keeped the same. I would appreciate that if there's anyone having any idea on how to solve it. Thanks. Best, Hugh Find car news, reviews and more Looking to change your car this year? _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wanglbit at gmail.com _________________________________________________________________ Looking for a fresh way to share your photos? Check out the new Windows Live Messenger http://windowslive.ninemsn.com.au/article.aspx?id=792335 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090505/97a6dd37/attachment-0001.html From hjiang at jhmi.edu Tue May 5 11:03:35 2009 From: hjiang at jhmi.edu (Hangyi Jiang) Date: Tue, 05 May 2009 11:03:35 -0400 Subject: [Mristudio-users] program crashes Message-ID: <4A001D07020000630001FF08@cis27.hosts.jhmi.edu> mostly, this happens when the number of images doesn't match with that of gradients specified in the gradeint table. when the dataset was successfully being loaded in, the image volumes will be listed in the "Image List" of the "image" tab. please view these images, make sure the # of images are same as the # of items in the gradient table. another common mistake for Siemens dataset is that the images are Masaic format but they were loaded in as DICOM format. regards, hangyi >>> eric Q 05/05/09 2:05 AM >>> Hi Susumu: Thank you for answering my question regarding the gradient table. However the program crashes every time when I try to do a calculation (DTI mapping). I've tried to calculate Tensor, Color map, ADC map, Mean, but I always get this "The mriView3D MFC application has encountered a problem and needs to close". I am a new user to DTI studio, so there are probably a lot of mistakes I've made on my end, but could you please tell me what are the likely causes for the crash of my program? Your time and help is much appreciated. Regards Eric Q Date: Fri, 1 May 2009 09:32:56 -0400 From: susumu at mri.jhu.edu To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] Gradient table Hi Liang, 1) I am not sure which coordinates (space) the ultimate gradient table was relative to, such as frequency- and phase-encoding of image, horizontal and vertical direction of image, or magnets' x/y/z coordinates. Based on your reply, I think that it might be the last one. When you present vectors, color maps, or performing fiber tracking, X, Y, and Z need to be defined by the image matrix. This is the most natural way. The frequency/phase/slice and image x/y/z have permutation relationship, like frequency ? image x / phase ? image y / slice ? image z or frequency ? image y / phase ? image x / slice ? image z. The relationship between magnet x / y / z and image x / y / z could have oblique relationship if oblique scan is used, and therefore could be very complicated. The gradient table, ultimately, needs to adopt the image x / y / z system. Now most vendor system is adopting a way to deliver gradient application in the frequency/phase/slice system, moving away from gradient x/y/z. This means, when oblique scan is employed, the scanner dynamically recalculates the gradient table in the f/p/s coordinates. If the scanner doesn?t do this (like old Siemens system), we have to recalculate the table based on the oblique angles by ourselves. The former is more fool-proof. 2) In my *.PAR file, there was last 3 columns representing diffusion directions but obviously different between subjects. I don't know what diffusion were recorded in this header file. I don?t have much experience with the new PAR file, but if you are using oblique scans, it is not surprising the each patient have different gradient table in the ?magnet? coordinate. Suppose we want to apply [1, 0, 0] in the first line of the gradient table, which is the ?X? orientation. If we use an oblique scan, magnet X and image X are no longer the same. As I mentioned above, in the end, what we want to know is gradient orientation in the image coordinate. So we have two choices. Choice 1: deliver magnet [1, 0, 0], meaning pure X gradient application. This X gradient could be something like [0.9, 0.15, 0] in the image coordinate. We need to do [1, 0, 0] x ImageRotation to get new gradient table to do tensor calculation. Choice 2: deliver magnet [0.9, -0.15, 0] (I just made up these numbers) so that the applied gradient aligns the image X axis. In this case, we can use gradient table [1, 0, 0] for tensor calculation. I hope this makes your questions answered. Susumu From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of liang wang Sent: Saturday, AprI also have a similar question about gradient tables in Philips scanner. My data were collected using following protocols: 1) Gradient table: Medium 2) Gradient overplus: no 3) Oblique plane: yes, and different angles between subjects. Looking through your answer, I know that this set can result in the same gradient table input into DTIstudio for all subject. However, 1) I am not sure which coordinates (space) the ultimate gradient table was relative to, such as frequency- and phase-encoding of image, horizontal and vertical direction of image, or magnets' x/y/z coordinates. Based on your reply, I think that it might be the last one. 2) In my *.PAR file, there was last 3 columns representing diffusion directions but obviously different between subjects. I don't know what diffusion were recorded in this header file. Many thanks Liang 2009/4/16 susumu Hi Eric, For Philips scanner there are several types of gradient tables you can specify in the scanner. Please check your protocol for the following points; 1) Gradient table: High (32-orientation)/ Medium (15-orientation) / Low (6-orientation) 2) Overplus (ON / OFF) 3) Oblique plane (X/Y/Z angles) The first option has 3 choices and the second option has 2 choices. Therefore, there are 3 x 2 = 6 gradient tables. If the second option (Overplus) is NO, the third option has no effect. If the second option is YES, the gradient table has to be rotated based on the oblique angles. To simplify the DTI processing, we recommend Overplus = NO. We have the basic 6 tables, which can be used as is if you use Overplus = OFF or Oblique angles = 0/0/0 degree. Please let us know which options you are using. Susumu From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of eric Q Sent: Thursday, April 16, 2009 9:44 PM To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] Gradient table Hello Dear DTIstudio users: I am new to DTIstudio, I was hoping someone could give me some much needed advises for beginners. I was trying to obtain the FA values for my brain phantom (PHILIP 3T scanner). When I clicked on "DTI mapping", it prompted me to enter the "gradient table", how do I calculate the "gradient table"? Thanks in advanced Best regards Eric Date: Thu, 9 Apr 2009 11:04:09 -0400 From: susumu at mri.jhu.edu To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] MriView3D application close Hi Hugh, When you got this error, please suspect one of the following two reasons; 1) Memory shortage: Even if you have many GB of memories, 32-bit Windows system can allocate only 1 - 1.5 GB to each program. To check if you have the memory problem, please restrict the slices to be calculated. In the initial data parameter window, there is a section called "Slices to be processed". Here you can specify only a portion of slices to be processed. Please limit the slices to, for example, 0-9 and see how it goes. If you can calculate tensors without errors, then you have the memory problem. The solution is; a) upgrade to the 64-bit system or b) devide the calculation to 2 batches (e.g. slice 0-29 for the first batch and 30-59 for the second batch), calculate all maps (e.g. FA), and later combine them. 2) Mismatch between the gradient table and the number of images: For example, if you specify 12-orientation table and 30 volume images, then you get the error. After loading the data and before you go to the Dti Map tab, make sure that you have 1 b0 + 64 DWIs in the pull-down menu in the right column of the Image tab. If you have the correct number of the images, then you might have an error in your gradient tab"DtiMapping" in the "File" button again, d) the window still remembers the gradient table you entered last time. This remembered window tells how DtiStudio interpreted your gradient table. If there is any syntax errors, you may find them much easier. For example, if you enter, "4: 1 0.5 0", instead of "4: 1, 0.5, 0", then you would find, "4: 1, 0, 0". If any of these do not solve the issue, please let us know. Susumu From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hugh Wang Sent: Wednesday, April 08, 2009 6:30 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] MriView3D application close Hi, I was using the dtistudio (ver. 2.4) to look at the Siemens DICOM diffusion images (1baseline,64 gradients). After successfully loading the images, I click the "dti map" option at lower right corner. Whatever calculation I choose, it always gives me an error: "MriView3D MFC Application has encountered a problem and needs to close. We are sorry for the inconvenience." I tried several PCs, and the problem keeped the same. I would appreciate that if there's anyone having any idea on how to solve it. Thanks. Best, Hugh Find car news, reviews and more Looking to change your car this year? _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wanglbit at gmail.com _________________________________________________________________ Looking for a fresh way to share your photos? Check out the new Windows Live Messenger http://windowslive.ninemsn.com.au/article.aspx?id=792335 From susumu at mri.jhu.edu Tue May 5 18:04:07 2009 From: susumu at mri.jhu.edu (susumu) Date: Tue, 05 May 2009 18:04:07 -0400 Subject: [Mristudio-users] Questions regarding Transformation in Landmark In-Reply-To: <49FB8877.6070403@mednet.ucla.edu> Message-ID: <7k7ed7$7c2r5k@ipex3.johnshopkins.edu> Hi Rajesh, Currently, our program can not register a tensor to another tensor file. For linear transformation, most of the information to judge the good registration comes from brain boundary. Therefore, as long as the brain boundary is well defined, you can use any images and the results won't be that much different. In our templates, you can find T1 / B0 / DWI images and you can choose any of them. Suppose you chose DWI from our atlas, then you want to use DWI of your data to perform the linear transformation. Once DWI-to-DWI transformation is done, the resultant transformation is applied to all loaded images. If FA and ADC maps are loaded, they are transformed too. In this case, you are not using FA and ADC to drive the registration. The registration was done between the two DWI and only the resultant transformation information is applied to loaded FA and ADC. If you save the transformation matrix, you can later apply it to any co-registered images. When you transform the tensor field, care must be taken because you have to instruct Landmarker that it is a tensor file, not an ordinary scalar image, because tensor requires re-orientations based on the transformation. That is because there is an dedicated "open *.d" button in Landmarker. Once a tensor file is loaded through this button, you can find 6 scalar maps for Dxx, Dyy, Dzz, Dxy, Dxz, and Dyz. If these images are loaded when the DWI-to-DWI transformation is performed, these 6 tensor element images are automatically transformed. After the transformation, you can save all 6 images into one file to recreate a "registered tensor file". You can also apply the transformation to a tensor file if you already finished the transformation and save the transformation matrix. The basic flow of the procedure is very similar for the LDDMM-based non-linear transformation, although for the LDDMM, you get only a transformation matrix. So, you have to load FA, ADC, tensor (via "open *.d"), and other co-registered images and apply the transformation matrix. -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Rajesh Kumar Sent: Friday, May 01, 2009 7:41 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] Questions regarding Transformation in Landmark Hi List: I want to normalize tensor map to common space (MNI template) in DTI studio. Is there anybody who can suggest me how to proceed? I am not sure that i should use b0 or trace template (in MNI space) for the same. With regards Rajesh IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From pabeach1 at gmail.com Thu May 7 15:26:06 2009 From: pabeach1 at gmail.com (Paul Beach) Date: Thu, 07 May 2009 15:26:06 -0400 Subject: [Mristudio-users] overlaying analyze anatomical and fiber tract data in DTI studio Message-ID: <8874e3900905071226v46585229g20cb9454f2e270f3@mail.gmail.com> To Whom It May Concern: We were hoping for some input regarding viewing Fiber tracts and DTI images concurrently. Due to limitations in our data, we have been forced to reorient our DTI images and our Fiber tracks accordingly using the Landmarker program. Unfortunately we have not been able to decipher a way to view these two images overlayed simultaneously which is needed as part of our delimitation methods. We previously have done this by saving our Fiber ROI?s, then placing them on a DTI (through DTIstudio) when needed. Since this step is not a part of the reorientation process we do not have this data to use. Essentially we are limited to trying to work with ANALYZE files and were wondering if DTIstudio or its sister programs had the ability to load these in to be viewed simultaneously. The work we?re currently attempting to do is to list certain boundaries based on anatomical and select fiber tract data (for example the coronal boundary of the crura/fornical junction) and this requires having the fiber tract data mapped onto the anatomical DTIs. Thanks, Paul -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090507/a5a85a63/attachment.html From choisj70 at gmail.com Thu May 7 15:39:51 2009 From: choisj70 at gmail.com (Seongjin) Date: Thu, 07 May 2009 15:39:51 -0400 Subject: [Mristudio-users] Noise level for mask image during tensor calculation Message-ID: I wonder if any standard number for the noise level of the mask image for tensor calculation. -SC -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090507/76407025/attachment.html From hjiang at jhmi.edu Thu May 7 15:56:30 2009 From: hjiang at jhmi.edu (Hangyi Jiang) Date: Thu, 07 May 2009 15:56:30 -0400 Subject: [Mristudio-users] overlaying analyze anatomical and fiber tract data in DTI studio Message-ID: <4A0304AE020000630002016F@cis27.hosts.jhmi.edu> hi,Paul if you saved your fiber data in default "DTI studio" format, you can overlay the tracts using "File->Load Fiber data" command after your Analyze images are loaded in. as long as your Analyze images (or any other kind of images) have same parameters as that of original images (from where the fiber-tracking was done), the fibers can be overlaid on the images without any problem. regards, hangyi >>> Paul Beach 05/07/09 3:26 PM >>> To Whom It May Concern: We were hoping for some input regarding viewing Fiber tracts and DTI images concurrently. Due to limitations in our data, we have been forced to reorient our DTI images and our Fiber tracks accordingly using the Landmarker program. Unfortunately we have not been able to decipher a way to view these two images overlayed simultaneously which is needed as part of our delimitation methods. We previously have done this by saving our Fiber ROI?s, then placing them on a DTI (through DTIstudio) when needed. Since this step is not a part of the reorientation process we do not have this data to use. Essentially we are limited to trying to work with ANALYZE files and were wondering if DTIstudio or its sister programs had the ability to load these in to be viewed simultaneously. The work we?re currently attempting to do is to list certain boundaries based on anatomical and select fiber tract data (for example the coronal boundary of the crura/fornical junction) and this requires having the fiber tract data mapped onto the anatomical DTIs. Thanks, Paul From hjiang at jhmi.edu Thu May 7 16:17:03 2009 From: hjiang at jhmi.edu (Hangyi Jiang) Date: Thu, 07 May 2009 16:17:03 -0400 Subject: [Mristudio-users] Noise level for mask image during tensor calculation Message-ID: <4A03097F0200006300020189@cis27.hosts.jhmi.edu> no. you can estimate this value by moving the cursor around non-brain area of DWIs (e.g. B0 image), read the image values on the bottom-left of the window (status bar area), then you will get an idea about the background noise level of your dataset. >>> "[Seongjin]" 05/07/09 3:39 PM >>> I wonder if any standard number for the noise level of the mask image for tensor calculation. -SC From smnewlander at yahoo.com Thu May 7 16:37:49 2009 From: smnewlander at yahoo.com (Shawn Newlander) Date: Thu, 07 May 2009 13:37:49 -0700 (PDT) Subject: [Mristudio-users] Image formats Message-ID: <445679.54336.qm@web32807.mail.mud.yahoo.com> I have images in Siemens dicom mosaic format , which I saved in analyze format in DTI studios to do the brain extraction. In order to do DTI mapping, I tried to import the raw images; however, I am getting this error: "Number of files in this folder is less than expected (Img_Slices*Img_Blocks)" I have 35 slices for 26 gradient directions. Is there a way to import this images without having to break apart each volume? Shawn smnewlander at yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090507/d768631f/attachment.html From choisj70 at gmail.com Thu May 7 17:04:08 2009 From: choisj70 at gmail.com (Seongjin) Date: Thu, 07 May 2009 17:04:08 -0400 Subject: [Mristudio-users] AIR and tensor data Message-ID: DTI studio developers and users, After AIR I did tensor calculation and saved tensor data. In the image part, original image set and AIRed image set are sitting together. I wonder if the tensor data reflected the adjusted by AIR or not. Or should I reload AIRed image set and use the gradient table in the airmatrix.txt? Thanks in advance. -SC -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090507/214a61a4/attachment.html From choisj70 at gmail.com Thu May 7 17:05:08 2009 From: choisj70 at gmail.com (Seongjin) Date: Thu, 07 May 2009 17:05:08 -0400 Subject: [Mristudio-users] Noise level for mask image during tensor calculation In-Reply-To: <4A03097F0200006300020189@cis27.hosts.jhmi.edu> References: <4A03097F0200006300020189@cis27.hosts.jhmi.edu> Message-ID: Thanks a lot! -SC On Thu, May 7, 2009 at 4:17 PM, Hangyi Jiang wrote: > no. > > you can estimate this value by moving the cursor around non-brain area of > DWIs (e.g. B0 image), read the image values on the bottom-left of the window > (status bar area), then you will get an idea about the background noise > level of your dataset. > > > > > > > >>> "[Seongjin]" 05/07/09 3:39 PM >>> > I wonder if any standard number for the noise level of the mask image for > tensor calculation. > > -SC > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090507/d804b018/attachment.html From hjiang at jhmi.edu Fri May 8 10:42:22 2009 From: hjiang at jhmi.edu (Hangyi Jiang) Date: Fri, 08 May 2009 10:42:22 -0400 Subject: [Mristudio-users] AIR and tensor data Message-ID: <4A040C8E020000630002022A@cis27.hosts.jhmi.edu> when you do AIR, you can disable "Create new images after AIR" option, then the AIRed images will replace the original DWIs and tensor calculation will be carried on the ARIed images. if the option "Create new images after AIR" is enaabled, then a new set of images will be created (as the case you mentioned), the original DWIs will not being touched. then tensor calculation will be still on the original images. while, you can save the the AIRed images as a new dataset, and use the new gradeint tables (if applicable, in the "airmatrix.txt") for later on calculation. regards, hangyi >>> "[Seongjin]" 05/07/09 5:04 PM >>> DTI studio developers and users, After AIR I did tensor calculation and saved tensor data. In the image part, original image set and AIRed image set are sitting together. I wonder if the tensor data reflected the adjusted by AIR or not. Or should I reload AIRed image set and use the gradient table in the airmatrix.txt? Thanks in advance. -SC From susumu at mri.jhu.edu Fri May 8 10:54:34 2009 From: susumu at mri.jhu.edu (susumu) Date: Fri, 08 May 2009 10:54:34 -0400 Subject: [Mristudio-users] Gradient table In-Reply-To: Message-ID: <7k7ed7$7dk111@ipex3.johnshopkins.edu> Yes. That's the idea. One thing you have to be careful is, if you have repeated dataset, like 3 sets of 12-orientation measurements. After AIR, each DWI could be rotated in a different way and therefore obtain a new gradient orientation. That means, the 3 repeated measurements may no longer have the same 12-orientation gradient table. Instead, you will get 36 orientations. Therefore, you have to combine all 3 sets to create one measurement with 36 orientations and your gradient table also has to be one 36-orientation table. Is this correct, Hangyi? In DtiStudio, you can create average and subtracted images of repeated measurements using the "mean, STD" button. From these images, you can get idea about how much translation and rotation occurred during the scans. Usually, the rotation is very tiny, like within 1 degree. In this case, you don't have to use gradient table rotation, in my opinion. Unless you have a bad data in which subject was moving more than few degrees, this rotation correction may not have much importance. On the other hand, if the subject is moving around, you may have other issues like image corruptions and motion within one image (odd and even slices are not registered), which can not be solved by AIR. So, I guess what I'm saying is you should carefully inspect your data, instead of just throwing your data into AIR, do gradient table rotation, and forget about it. _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of [Seongjin] Sent: Thursday, April 30, 2009 3:32 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] Gradient table After AIR registration (with option modified gradient table if available...), I have a new gradient table in AirMatrix.txt file. Then I loaded AIR registered image and the new gradient table for tensor calculation and tractography. Am I doing right? Thanks in advance. -SC On Thu, Apr 30, 2009 at 1:18 PM, susumu wrote: The gradient table for Philips scanner calculated by this program is "correct", meaning no flipping and other modifications are necessary. I strong encourage users to use this program if you are using the "overplus" option + oblique slice. You can type in the oblique angles and get a recalculated table. _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of [Seongjin] Sent: Thursday, April 30, 2009 12:28 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] Gradient table I appreciate the tutorial session at Queen's Medical Center in Honolulu. I am using gradient table (for DTI studio ) generated at the following link: http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html I wonder if I can directly use the gradient table from this java applet without field flipping. Thanks in advance. -SC _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090508/5b96a009/attachment-0001.html From choisj70 at gmail.com Fri May 8 11:02:57 2009 From: choisj70 at gmail.com (Seongjin) Date: Fri, 08 May 2009 11:02:57 -0400 Subject: [Mristudio-users] AIR and tensor data In-Reply-To: <4A040C8E020000630002022A@cis27.hosts.jhmi.edu> References: <4A040C8E020000630002022A@cis27.hosts.jhmi.edu> Message-ID: Thanks a lot. -SC On Fri, May 8, 2009 at 10:42 AM, Hangyi Jiang wrote: > when you do AIR, you can disable "Create new images after AIR" option, then > the AIRed images will replace the original DWIs and tensor calculation will > be carried on the ARIed images. > > if the option "Create new images after AIR" is enaabled, then a new set of > images will be created (as the case you mentioned), the original DWIs will > not being touched. then tensor calculation will be still on the original > images. while, you can save the the AIRed images as a new dataset, and use > the new gradeint tables (if applicable, in the "airmatrix.txt") for later on > calculation. > > regards, > > hangyi > > > > > >>> "[Seongjin]" 05/07/09 5:04 PM >>> > DTI studio developers and users, > > > > After AIR I did tensor calculation and saved tensor data. > > In the image part, original image set and AIRed image set are sitting > together. > > I wonder if the tensor data reflected the adjusted by AIR or not. > > Or should I reload AIRed image set and use the gradient table in the > airmatrix.txt? > > Thanks in advance. > > > > -SC > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090508/53333e1a/attachment.html From choisj70 at gmail.com Fri May 8 11:24:09 2009 From: choisj70 at gmail.com (Seongjin) Date: Fri, 08 May 2009 11:24:09 -0400 Subject: [Mristudio-users] Gradient table In-Reply-To: <7k7ed7$7dk111@ipex3.johnshopkins.edu> References: <7k7ed7$7dk111@ipex3.johnshopkins.edu> Message-ID: Thanks for your comment. -SC On Fri, May 8, 2009 at 10:54 AM, susumu wrote: > Yes. That's the idea. > > One thing you have to be careful is, if you have repeated dataset, like 3 > sets of 12-orientation measurements. > > After AIR, each DWI could be rotated in a different way and therefore > obtain a new gradient orientation. > > That means, the 3 repeated measurements may no longer have the same > 12-orientation gradient table. Instead, you will get 36 orientations. > Therefore, you have to combine all 3 sets to create one measurement with 36 > orientations and your gradient table also has to be one 36-orientation > table. > > > > Is this correct, Hangyi? > > > > In DtiStudio, you can create average and subtracted images of repeated > measurements using the "mean, STD" button. From these images, you can get > idea about how much translation and rotation occurred during the scans. > Usually, the rotation is very tiny, like within 1 degree. In this case, you > don't have to use gradient table rotation, in my opinion. Unless you have a > bad data in which subject was moving more than few degrees, this rotation > correction may not have much importance. On the other hand, if the subject > is moving around, you may have other issues like image corruptions and > motion within one image (odd and even slices are not registered), which can > not be solved by AIR. > > > > So, I guess what I'm saying is you should carefully inspect your data, > instead of just throwing your data into AIR, do gradient table rotation, and > forget about it. > > > ------------------------------ > > *From:* mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org] *On Behalf Of *[Seongjin] > *Sent:* Thursday, April 30, 2009 3:32 PM > *To:* DTI Studio, ROI Editor, Landmarker Questions/Support > *Subject:* Re: [Mristudio-users] Gradient table > > > > After AIR registration (with option modified gradient table if > available...), I have a new gradient table in AirMatrix.txt file. > Then I loaded AIR registered image and the new gradient table for tensor > calculation and tractography. > Am I doing right? > Thanks in advance. > > -SC > > On Thu, Apr 30, 2009 at 1:18 PM, susumu wrote: > > The gradient table for Philips scanner calculated by this program is > "correct", meaning no flipping and other modifications are necessary. > > > > I strong encourage users to use this program if you are using the > "overplus" option + oblique slice. You can type in the oblique angles and > get a recalculated table. > > > ------------------------------ > > *From:* mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org] *On Behalf Of *[Seongjin] > *Sent:* Thursday, April 30, 2009 12:28 PM > *To:* DTI Studio, ROI Editor, Landmarker Questions/Support > *Subject:* [Mristudio-users] Gradient table > > > > I appreciate the tutorial session at Queen's Medical Center in Honolulu. > > I am using gradient table (for DTI studio ) generated at the following > link: > http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html > > I wonder if I can directly use the gradient table from this java applet > without field flipping. > Thanks in advance. > > -SC > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090508/5b9fc008/attachment.html From siewmin.gan at gmail.com Fri May 8 18:22:39 2009 From: siewmin.gan at gmail.com (Siewmin Gan) Date: Sat, 09 May 2009 06:22:39 +0800 Subject: [Mristudio-users] transformations with AIR in Landmarker Message-ID: Hi, I am trying to perform tractography analysis on AC-PC aligned data with and without rotating the tensor, and came across some questions on the way, mainly with regards to the transformation steps. First, I tried rotating the tensor but had problems with the results. When I look at the colour map from the resulting tensor, it looks ok generally, but there are certain areas of blotchiness and some mixing of colours especially in the sidelines of white matter regions (i.e there can be a striking red line or a blotch of redness in the middle of a green regions within the saggital stratum). These are the steps I took, and would like to check if it is done correctly. 1. resample mean DWI of subject data (together with the 4D DTI data and the tensor) to DWI of ICBM 81 template. Non-linear transform (2nd order trilinear) the resampled meandwi of subject to dwi of template, and used that to drive the transformation of the resampled 4D DTI and the resampled tensor simultaneously. (The resampled tensor was loaded with the .dat button.) I used MRIview 3D to load the normalised 4D DTI, followed by the normalised tensor with the .dat button, and calculate the fa, colour etc maps from the normalised tensor. I tried various thresholding with AIR but the colour maps problem remains. Second, I tried without rotating the tensor. I calculate the scalar and colour maps from the original 4D DTI data, aligned the maps to AC-PC line, draw rois on them and invert transform the rois back to native dti space to extract the relevant white matter tracts. I had two problems here. 1) with orienting the subjects scalar DWI to another particular subject's DWI with rigid transformation in AIR and 2) Invert transform ROIs drawn on the registered colour map back to the original DTI space. These are the steps I took: 1. A subject's data which is acquired // to AC-PC is chosen and other subjects not acquired //to AC are registered to this. Again the meanDWI is used for source and target images, this time using rigid transformation in AIR in Landmarker. However, there is no difference detected after the transformation has taken place. However, if I change the target image from a subject's DWI to the mean DWI of the ICBM 81 template, it works but the source data would be subsampled to that of the ICBM template. I'm not sure why it didn't work in the 1st case? Additionally, using either another subject or the template DWI as target image, would yield the an output file (AlignlinearOutput.air) when the transformation has been performed, which I saved the invert_AlignlinearOutput.air. However, when I clicked on these .air files in the folder it is saved as an installer package, I get the following error message " An error has occurred.The application could not be installed because the AIR file is damaged. Try obtaining a new AIR file from the application author." I have installed the air application and placed it in the same folder, together with the alignlinear.exe file. Is it possible to view the transformation matrix files saved or did I not installed the air application appropriately? 2. ROIs are drawn on the transformed AC-PC aligned colour maps with ROI-editor. I would like to check if it's OK to draw rois on the transformed colour map? These ROIs would later be used as the start ROI and stop ROI to extract the corresponding white matter tract with DTI studio) 3. I tried to invert-transform these ROIs back to the original DTI space with the previously saved invert_matrix.air file. How is that done in Landmarker and if the previous error message needs to be resolved before I can used the matrix files? Many thanks Siewmin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090509/a855c40a/attachment-0001.html From susumu at mri.jhu.edu Fri May 8 19:44:42 2009 From: susumu at mri.jhu.edu (susumu) Date: Fri, 08 May 2009 19:44:42 -0400 Subject: [Mristudio-users] transformations with AIR in Landmarker In-Reply-To: Message-ID: <7k7ed7$7dst7f@ipex3.johnshopkins.edu> First, I tried rotating the tensor but had problems with the results. When I look at the colour map from the resulting tensor, it looks ok generally, but there are certain areas of blotchiness and some mixing of colours especially in the sidelines of white matter regions (i.e there can be a striking red line or a blotch of redness in the middle of a green regions within the saggital stratum). These are the steps I took, and would like to check if it is done correctly. 1. resample mean DWI of subject data (together with the 4D DTI data and the tensor) to DWI of ICBM 81 template. Non-linear transform (2nd order trilinear) the resampled meandwi of subject to dwi of template, and used that to drive the transformation of the resampled 4D DTI and the resampled tensor simultaneously. (The resampled tensor was loaded with the .dat button.) I used MRIview 3D to load the normalised 4D DTI, followed by the normalised tensor with the .dat button, and calculate the fa, colour etc maps from the normalised tensor. I tried various thresholding with AIR but the colour maps problem remains. > First of all, I think you don't have to resample DTI images before AIR. AIR can take data with different matrix and pixel sizes and the output images have the same matrix/pixel dimensions as the template (in your case, 181x217x181 of ICBM81). > By saying "4D DTI", do you mean raw 4D DWI before tensor calculation? if so, I don't think you want transform raw DWIs. If you want to do anything to raw DTI, you also want to transform the corresponding gradient table, which could be messy. Our tools do not provide methods to transform raw DWIs. > When you say, "tensor" data, I assume you are talking about 4D file that contains "Dxx, Dyy, Dzz, Dxy, Dxz, Dyz" images in one file. If so, please make sure that you load this 4D tensor file by the "open .d" button in Landmarker. Once read in Landmarker, the 4D tensor file is disassembled to 6 3D data for Dxx, Dyy, Dzz, Dxy, Dxz, Dyz. > Once the AIR is done using mean DWI (your data) - mean DWI (template), the 6 3D tensor element data should be stored all together into one file as a "transformed 4D tensor file". > This transformed 4D tensor file needs to be read into DtiStudio to re-calculate new transformed FA, color, vec, etc. > The blotch-looking colormap could happen by; 1) transform the color map directly (you should recreate color maps using the recalcuated FA and vector files from the transformed tensor file or 2) you transformed a vector file (transformed vector files should be obtained from the transformed tensor file. Vector can not be directly transformed). Second, I tried without rotating the tensor. I calculate the scalar and colour maps from the original 4D DTI data, aligned the maps to AC-PC line, draw rois on them and invert transform the rois back to native dti space to extract the relevant white matter tracts. I had two problems here. 1) with orienting the subjects scalar DWI to another particular subject's DWI with rigid transformation in AIR and 2) Invert transform ROIs drawn on the registered colour map back to the original DTI space. These are the steps I took: > Maybe you are transforming raw DWI data? Again, you should not transform raw DWI and recalcuate tensor. You have to first calculate tensor (throw away the raw DWIs) and transform the tensor. 1. A subject's data which is acquired // to AC-PC is chosen and other subjects not acquired //to AC are registered to this. Again the meanDWI is used for source and target images, this time using rigid transformation in AIR in Landmarker. However, there is no difference detected after the transformation has taken place. However, if I change the target image from a subject's DWI to the mean DWI of the ICBM 81 template, it works but the source data would be subsampled to that of the ICBM template. I'm not sure why it didn't work in the 1st case? > As mentioned above, AIR not only adjust the image orientation and translation, but also the matrix / pixel size.. > Rigid transformation of AIR is sometimes very cranky. We are working on alternative methods now. please try different threshold or affine. Additionally, using either another subject or the template DWI as target image, would yield the an output file (AlignlinearOutput.air) when the transformation has been performed, which I saved the invert_AlignlinearOutput.air. However, when I clicked on these .air files in the folder it is saved as an installer package, I get the following error message " An error has occurred.The application could not be installed because the AIR file is damaged. Try obtaining a new AIR file from the application author." I have installed the air application and placed it in the same folder, together with the alignlinear.exe file. Is it possible to view the transformation matrix files saved or did I not installed the air application appropriately? > Maybe Xin can answer this question better, but I'm not sure why you want to open *.air?? > Once you save the *.air, you can load it back to Landmarker and apply to images by using the "open M" button in the LDDMM section. 2. ROIs are drawn on the transformed AC-PC aligned colour maps with ROI-editor. I would like to check if it's OK to draw rois on the transformed colour map? These ROIs would later be used as the start ROI and stop ROI to extract the corresponding white matter tract with DTI studio) > Drawing ROIs on color maps is fine. ROI is simply 1/0 information about which pixels you chose and the color maps are simply what is displayed to aid your ROI drawing. > If you draw ROI in the atlas space and have a plan to back-transform your ROI files to the native space, there are several things you have to know; 1) Atlas space is 1x1x1 and your native space could be 2-3 mm. The ROI defined in the thin 1 mm slice could be lost after transformation to the thick 2-3mm slice. Therefore, you have to create 3D ROIs in the atlas space with at least 3mm thick 2) Use nearest neighbor interpolation when you back-transfer. You don't want to get a pixel with 0.3 or 0.4 after transformation. You want 1/0 3. I tried to invert-transform these ROIs back to the original DTI space with the previously saved invert_matrix.air file. How is that done in Landmarker and if the previous error message needs to be resolved before I can used the matrix files? > Xin, how to do the invert-transformation of *.air? Susumu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090508/e257679d/attachment.html From siewmin.gan at gmail.com Sun May 10 07:01:35 2009 From: siewmin.gan at gmail.com (Siewmin Gan) Date: Sun, 10 May 2009 19:01:35 +0800 Subject: [Mristudio-users] transformations with AIR in Landmarker In-Reply-To: <7k7ed7$7dst7f@ipex3.johnshopkins.edu> References: <7k7ed7$7dst7f@ipex3.johnshopkins.edu> Message-ID: Hi Susumu, Thanks. I got the mean DWI and tensor file from the original 4D DWI. The tensor file is as you've said, which contains "Dxx, Dyy, Dzz, Dxy, Dxz Dyz" in one file. In Landmarker, I loaded only the mean DWI of the subject and then the tensor file with the "open .d" button. The 4D raw DWI is not used in Landmarker or later. With the "linear" option in AIR, I could rotate the tensor and the mean DWI to the template DWI without having to subsample the input data first. The "nonlinear" option requires the subject data (mean DWI and the tensor file) to be of the same dimension as the template (i.e 181, 217, 181 if ICBM81 DWI is used as template). This is noted in the pop up message, and it would only continue once the input files are resampled to the template. Additionally, I tried affine in the linear registration option. The output DWI of the registration is identical to the input of the DWIs if I used one of my subject's DWI as the template. Using the 2nd order polynomial in nonlinear option, an error message occurs "registration terminated due to a calculation problem, please try a lower order model". It seems to only work if the template is one of those provided in Landmarker. I then saved the rotated tensor file as one file in the .dat format and the linearly registered 3D meanDWI. In MRIview3D, I loaded this new 3D DWI and open this new tensor.dat file with the open.dat button to re-calculates the fa, colour map etc. I viewed the colour map output from this and it looks pretty good, and as described previously. I saved the fa and principal eigenvector file and used them to perform fiber-tracking. The tracts that are manually extracted obtained looks similiar to the fiber tracts from the original raw 4D DWI. The FA values of these tracts are smaller uniformly in comparison, and the assymetry preserved (i.e the left tract FA is smaller than the right tract FA using the maps calculated from the original and rotated tensor). If the non-linear option is used, is there a problem that the tensor is subsampled first before it is re-oriented, as described above? Do you suggest using the affine or non-linear transformation of the DWIs and the corresponding transformation of the tensor? Lastly, I'm not sure if the colour map display is of an issue? It occurs both using the linear affine option and the non-linear option. Thanks Siewmin On Sat, May 9, 2009 at 7:44 AM, susumu wrote: > First, I tried rotating the tensor but had problems with the results. > When I look at the colour map from the resulting tensor, it looks ok > generally, but there are certain areas of blotchiness and some mixing of > colours especially in the sidelines of white matter regions (i.e there can > be a striking red line or a blotch of redness in the middle of a green > regions within the saggital stratum). These are the steps I took, and would > like to check if it is done correctly. > > 1. resample mean DWI of subject data (together with the 4D DTI data and the > tensor) to DWI of ICBM 81 template. Non-linear transform (2nd order > trilinear) the resampled meandwi of subject to dwi of template, and used > that to drive the transformation of the resampled 4D DTI and the resampled > tensor simultaneously. (The resampled tensor was loaded with the .dat > button.) I used MRIview 3D to load the normalised 4D DTI, followed by the > normalised tensor with the .dat button, and calculate the fa, colour etc > maps from the normalised tensor. I tried various thresholding with AIR but > the colour maps problem remains. > > > > > First of all, I think you don't have to resample DTI images before AIR. > AIR can take data with different matrix and pixel sizes and the output > images have the same matrix/pixel dimensions as the template (in your case, > 181x217x181 of ICBM81). > > > By saying "4D DTI", do you mean raw 4D DWI before tensor calculation? if > so, I don't think you want transform raw DWIs. If you want to do anything to > raw DTI, you also want to transform the corresponding gradient table, which > could be messy. Our tools do not provide methods to transform raw DWIs. > > > When you say, "tensor" data, I assume you are talking about 4D file that > contains "Dxx, Dyy, Dzz, Dxy, Dxz, Dyz" images in one file. If so, please > make sure that you load this 4D tensor file by the "open .d" button in > Landmarker. Once read in Landmarker, the 4D tensor file is disassembled to 6 > 3D data for Dxx, Dyy, Dzz, Dxy, Dxz, Dyz. > > > Once the AIR is done using mean DWI (your data) - mean DWI (template), > the 6 3D tensor element data should be stored all together into one file as > a "transformed 4D tensor file". > > > This transformed 4D tensor file needs to be read into DtiStudio to > re-calculate new transformed FA, color, vec, etc. > > > The blotch-looking colormap could happen by; 1) transform the color map > directly (you should recreate color maps using the recalcuated FA and vector > files from the transformed tensor file or 2) you transformed a vector file > (transformed vector files should be obtained from the transformed tensor > file. Vector can not be directly transformed). > > > > Second, I tried without rotating the tensor. I calculate the scalar and > colour maps from the original 4D DTI data, aligned the maps to AC-PC line, > draw rois on them and invert transform the rois back to native dti space to > extract the relevant white matter tracts. I had two problems here. 1) with > orienting the subjects scalar DWI to another particular subject's DWI with > rigid transformation in AIR and 2) Invert transform ROIs drawn on the > registered colour map back to the original DTI space. These are the steps I > took: > > > > > Maybe you are transforming raw DWI data? Again, you should not transform > raw DWI and recalcuate tensor. You have to first calculate tensor (throw > away the raw DWIs) and transform the tensor. > > > > 1. A subject's data which is acquired // to AC-PC is chosen and other > subjects not acquired //to AC are registered to this. Again the meanDWI is > used for source and target images, this time using rigid transformation in > AIR in Landmarker. However, there is no difference detected after the > transformation has taken place. However, if I change the target image from a > subject's DWI to the mean DWI of the ICBM 81 template, it works but the > source data would be subsampled to that of the ICBM template. I'm not sure > why it didn't work in the 1st case? > > > > > As mentioned above, AIR not only adjust the image orientation and > translation, but also the matrix / pixel size.. > > > Rigid transformation of AIR is sometimes very cranky. We are working on > alternative methods now. please try different threshold or affine. > > > > Additionally, using either another subject or the template DWI as target > image, would yield the an output file (AlignlinearOutput.air) when the > transformation has been performed, which I saved the > invert_AlignlinearOutput.air. However, when I clicked on these .air files in > the folder it is saved as an installer package, I get the following error > message " An error has occurred.The application could not be installed > because the AIR file is damaged. Try obtaining a new AIR file from the > application author." I have installed the air application and placed it in > the same folder, together with the alignlinear.exe file. Is it possible to > view the transformation matrix files saved or did I not installed the air > application appropriately? > > > > > Maybe Xin can answer this question better, but I'm not sure why you want > to open *.air?? > > > Once you save the *.air, you can load it back to Landmarker and apply to > images by using the "open M" button in the LDDMM section. > > > > 2. ROIs are drawn on the transformed AC-PC aligned colour maps with > ROI-editor. I would like to check if it's OK to draw rois on the transformed > colour map? These ROIs would later be used as the start ROI and stop ROI to > extract the corresponding white matter tract with DTI studio) > > > > > Drawing ROIs on color maps is fine. ROI is simply 1/0 information about > which pixels you chose and the color maps are simply what is displayed to > aid your ROI drawing. > > > If you draw ROI in the atlas space and have a plan to back-transform your > ROI files to the native space, there are several things you have to know; > > 1) Atlas space is 1x1x1 and your native space could be 2-3 mm. The ROI > defined in the thin 1 mm slice could be lost after transformation to the > thick 2-3mm slice. Therefore, you have to create 3D ROIs in the atlas space > with at least 3mm thick > > 2) Use nearest neighbor interpolation when you back-transfer. You don't > want to get a pixel with 0.3 or 0.4 after transformation. You want 1/0 > > > > 3. I tried to invert-transform these ROIs back to the original DTI space > with the previously saved invert_matrix.air file. How is that done in > Landmarker and if the previous error message needs to be resolved before I > can used the matrix files? > > > > > Xin, how to do the invert-transformation of *.air? > > > > Susumu > > > > > > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090510/8f5c30ea/attachment-0001.html From susumu at mri.jhu.edu Sun May 10 09:39:22 2009 From: susumu at mri.jhu.edu (susumu) Date: Sun, 10 May 2009 09:39:22 -0400 Subject: [Mristudio-users] transformations with AIR in Landmarker In-Reply-To: References: <7k7ed7$7dst7f@ipex3.johnshopkins.edu> Message-ID: Siewmin raised some important points and I hope other users could gain some important information from this thread. I got the mean DWI and tensor file from the original 4D DWI. The tensor file is as you've said, which contains "Dxx, Dyy, Dzz, Dxy, Dxz Dyz" in one file. In Landmarker, I loaded only the mean DWI of the subject and then the tensor file with the "open .d" button. The 4D raw DWI is not used in Landmarker or later. With the "linear" option in AIR, I could rotate the tensor and the mean DWI to the template DWI without having to subsample the input data first. The "nonlinear" option requires the subject data (mean DWI and the tensor file) to be of the same dimension as the template (i.e 181, 217, 181 if ICBM81 DWI is used as template). This is noted in the pop up message, and it would only continue once the input files are resampled to the template. >It is always advised to do linear transformation first. To start non-linear, you have to make sure that the brain locations and shapes are as similar as possible. This is similar to non-linear fitting. You always have to provide "initial" values close to the real solutions. Otherwise, non-linear fitting could converge to a wrong solution (trapped by "local minima"). Additionally, I tried affine in the linear registration option. The output DWI of the registration is identical to the input of the DWIs if I used one of my subject's DWI as the template. Using the 2nd order polynomial in nonlinear option, an error message occurs "registration terminated due to a calculation problem, please try a lower order model". It seems to only work if the template is one of those provided in Landmarker. > If you can send us two images you are having the problem, we can take a look at why AIR doesn't work. I then saved the rotated tensor file as one file in the .dat format and the linearly registered 3D meanDWI. In MRIview3D, I loaded this new 3D DWI and open this new tensor.dat file with the open.dat button to re-calculates the fa, colour map etc. I viewed the colour map output from this and it looks pretty good, and as described previously. > This is the correct procedure. I saved the fa and principal eigenvector file and used them to perform fiber-tracking. The tracts that are manually extracted obtained looks similiar to the fiber tracts from the original raw 4D DWI. > That is a good sign. The FA values of these tracts are smaller uniformly in comparison, and the assymetry preserved (i.e the left tract FA is smaller than the right tract FA using the maps calculated from the original and rotated tensor). > Normalization requires pixel interpolation, which leads to decreased FA. So you can not compare FA values with and without normalization. If the non-linear option is used, is there a problem that the tensor is subsampled first before it is re-oriented, as described above? > As I mentioned above, nonlinear should be AFTER linear transformation. This means, the data are transformed multiple times and pixels are interpolated multiple times. To avoid this, once you did linear (save transformation matrix: T-linear) and nonlinear (save transformation matrix: T-nonlinear), you can combine the T-linear x T-nonlinear using one of the buttons in the LDDMM section. Once you combined all transformation matrices, you can apply it only once to the original image in the native space. > Another interesting thing is, there are two ways to transform images; transform your image to an atlas or transform atlas (usually, binary segmentation map) to your original data for automated segmentation. For the latter approach, you don't have to transform (therefore interpolate) your original data. When you transform the atlas (segmentation map), make sure to use "nearest neighbor" (no interpolation), not the tri-linear interpolation. The segmentation map consists of arbitrary numbers assigned to each segment (e.g. the internal capsule is "1" and the corona radiata is "3"). If you interpolate these two segments and obtain "2" in between these two segments and if "2" means pons, you would get the pons in between the internal capsule and the corona radiata. On the other hand, when you are transforming your data to an atlas space, use the tri-linear interpolation. Otherwise, you could get strange discontinuity artifacts. Do you suggest using the affine or non-linear transformation of the DWIs and the corresponding transformation of the tensor? Lastly, I'm not sure if the colour map display is of an issue? It occurs both using the linear affine option and the non-linear option. > When everything is working right, the color map should look smooth and clean. Maybe you are using "nearest neighbor" for the tensor transformation? Thanks Siewmin On Sat, May 9, 2009 at 7:44 AM, susumu wrote: First, I tried rotating the tensor but had problems with the results. When I look at the colour map from the resulting tensor, it looks ok generally, but there are certain areas of blotchiness and some mixing of colours especially in the sidelines of white matter regions (i.e there can be a striking red line or a blotch of redness in the middle of a green regions within the saggital stratum). These are the steps I took, and would like to check if it is done correctly. 1. resample mean DWI of subject data (together with the 4D DTI data and the tensor) to DWI of ICBM 81 template. Non-linear transform (2nd order trilinear) the resampled meandwi of subject to dwi of template, and used that to drive the transformation of the resampled 4D DTI and the resampled tensor simultaneously. (The resampled tensor was loaded with the .dat button.) I used MRIview 3D to load the normalised 4D DTI, followed by the normalised tensor with the .dat button, and calculate the fa, colour etc maps from the normalised tensor. I tried various thresholding with AIR but the colour maps problem remains. > First of all, I think you don't have to resample DTI images before AIR. AIR can take data with different matrix and pixel sizes and the output images have the same matrix/pixel dimensions as the template (in your case, 181x217x181 of ICBM81). > By saying "4D DTI", do you mean raw 4D DWI before tensor calculation? if so, I don't think you want transform raw DWIs. If you want to do anything to raw DTI, you also want to transform the corresponding gradient table, which could be messy. Our tools do not provide methods to transform raw DWIs. > When you say, "tensor" data, I assume you are talking about 4D file that contains "Dxx, Dyy, Dzz, Dxy, Dxz, Dyz" images in one file. If so, please make sure that you load this 4D tensor file by the "open .d" button in Landmarker. Once read in Landmarker, the 4D tensor file is disassembled to 6 3D data for Dxx, Dyy, Dzz, Dxy, Dxz, Dyz. > Once the AIR is done using mean DWI (your data) - mean DWI (template), the 6 3D tensor element data should be stored all together into one file as a "transformed 4D tensor file". > This transformed 4D tensor file needs to be read into DtiStudio to re-calculate new transformed FA, color, vec, etc. > The blotch-looking colormap could happen by; 1) transform the color map directly (you should recreate color maps using the recalcuated FA and vector files from the transformed tensor file or 2) you transformed a vector file (transformed vector files should be obtained from the transformed tensor file. Vector can not be directly transformed). Second, I tried without rotating the tensor. I calculate the scalar and colour maps from the original 4D DTI data, aligned the maps to AC-PC line, draw rois on them and invert transform the rois back to native dti space to extract the relevant white matter tracts. I had two problems here. 1) with orienting the subjects scalar DWI to another particular subject's DWI with rigid transformation in AIR and 2) Invert transform ROIs drawn on the registered colour map back to the original DTI space. These are the steps I took: > Maybe you are transforming raw DWI data? Again, you should not transform raw DWI and recalcuate tensor. You have to first calculate tensor (throw away the raw DWIs) and transform the tensor. 1. A subject's data which is acquired // to AC-PC is chosen and other subjects not acquired //to AC are registered to this. Again the meanDWI is used for source and target images, this time using rigid transformation in AIR in Landmarker. However, there is no difference detected after the transformation has taken place. However, if I change the target image from a subject's DWI to the mean DWI of the ICBM 81 template, it works but the source data would be subsampled to that of the ICBM template. I'm not sure why it didn't work in the 1st case? > As mentioned above, AIR not only adjust the image orientation and translation, but also the matrix / pixel size.. > Rigid transformation of AIR is sometimes very cranky. We are working on alternative methods now. please try different threshold or affine. Additionally, using either another subject or the template DWI as target image, would yield the an output file (AlignlinearOutput.air) when the transformation has been performed, which I saved the invert_AlignlinearOutput.air. However, when I clicked on these .air files in the folder it is saved as an installer package, I get the following error message " An error has occurred.The application could not be installed because the AIR file is damaged. Try obtaining a new AIR file from the application author." I have installed the air application and placed it in the same folder, together with the alignlinear.exe file. Is it possible to view the transformation matrix files saved or did I not installed the air application appropriately? > Maybe Xin can answer this question better, but I'm not sure why you want to open *.air?? > Once you save the *.air, you can load it back to Landmarker and apply to images by using the "open M" button in the LDDMM section. 2. ROIs are drawn on the transformed AC-PC aligned colour maps with ROI-editor. I would like to check if it's OK to draw rois on the transformed colour map? These ROIs would later be used as the start ROI and stop ROI to extract the corresponding white matter tract with DTI studio) > Drawing ROIs on color maps is fine. ROI is simply 1/0 information about which pixels you chose and the color maps are simply what is displayed to aid your ROI drawing. > If you draw ROI in the atlas space and have a plan to back-transform your ROI files to the native space, there are several things you have to know; 1) Atlas space is 1x1x1 and your native space could be 2-3 mm. The ROI defined in the thin 1 mm slice could be lost after transformation to the thick 2-3mm slice. Therefore, you have to create 3D ROIs in the atlas space with at least 3mm thick 2) Use nearest neighbor interpolation when you back-transfer. You don't want to get a pixel with 0.3 or 0.4 after transformation. You want 1/0 3. I tried to invert-transform these ROIs back to the original DTI space with the previously saved invert_matrix.air file. How is that done in Landmarker and if the previous error message needs to be resolved before I can used the matrix files? > Xin, how to do the invert-transformation of *.air? Susumu _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090510/2b26ed7d/attachment-0001.html From nbulak at gata.edu.tr Mon May 11 07:44:44 2009 From: nbulak at gata.edu.tr (=?iso-8859-9?Q?Nail_Bulakba=FE=FD?=) Date: Mon, 11 May 2009 14:44:44 +0300 Subject: [Mristudio-users] please remove me from mailing list Message-ID: <63AC31CBD23078449BC254FB828951AD17706C@GATAMAIL.gatadomain.com.tr> please remove me from mailing list Nail Bulakbasi M.D. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090511/c569ec8c/attachment.html From GJEYARA at emory.edu Mon May 11 11:49:38 2009 From: GJEYARA at emory.edu (Jeyaraj, Gunasingh) Date: Mon, 11 May 2009 11:49:38 -0400 Subject: [Mristudio-users] transformations with AIR in Landmarker In-Reply-To: References: <7k7ed7$7dst7f@ipex3.johnshopkins.edu> Message-ID: <328ADA5CC29C8D4CADC8D72650E5533C011FDE0659DF@EXCHANGE11.Enterprise.emory.net> Could you kindly remove my name from your mailing list. Thanks Gunasingh ________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of susumu [susumu at mri.jhu.edu] Sent: Sunday, May 10, 2009 9:39 AM To: 'DTI Studio, ROI Editor, Landmarker Questions/Support' Subject: Re: [Mristudio-users] transformations with AIR in Landmarker Siewmin raised some important points and I hope other users could gain some important information from this thread. I got the mean DWI and tensor file from the original 4D DWI. The tensor file is as you've said, which contains "Dxx, Dyy, Dzz, Dxy, Dxz Dyz" in one file. In Landmarker, I loaded only the mean DWI of the subject and then the tensor file with the "open .d" button. The 4D raw DWI is not used in Landmarker or later. With the "linear" option in AIR, I could rotate the tensor and the mean DWI to the template DWI without having to subsample the input data first. The "nonlinear" option requires the subject data (mean DWI and the tensor file) to be of the same dimension as the template (i.e 181, 217, 181 if ICBM81 DWI is used as template). This is noted in the pop up message, and it would only continue once the input files are resampled to the template. >It is always advised to do linear transformation first. To start non-linear, you have to make sure that the brain locations and shapes are as similar as possible. This is similar to non-linear fitting. You always have to provide ?initial? values close to the real solutions. Otherwise, non-linear fitting could converge to a wrong solution (trapped by ?local minima?). Additionally, I tried affine in the linear registration option. The output DWI of the registration is identical to the input of the DWIs if I used one of my subject's DWI as the template. Using the 2nd order polynomial in nonlinear option, an error message occurs "registration terminated due to a calculation problem, please try a lower order model". It seems to only work if the template is one of those provided in Landmarker. > If you can send us two images you are having the problem, we can take a look at why AIR doesn?t work. I then saved the rotated tensor file as one file in the .dat format and the linearly registered 3D meanDWI. In MRIview3D, I loaded this new 3D DWI and open this new tensor.dat file with the open.dat button to re-calculates the fa, colour map etc. I viewed the colour map output from this and it looks pretty good, and as described previously. > This is the correct procedure. I saved the fa and principal eigenvector file and used them to perform fiber-tracking. The tracts that are manually extracted obtained looks similiar to the fiber tracts from the original raw 4D DWI. > That is a good sign. The FA values of these tracts are smaller uniformly in comparison, and the assymetry preserved (i.e the left tract FA is smaller than the right tract FA using the maps calculated from the original and rotated tensor). > Normalization requires pixel interpolation, which leads to decreased FA. So you can not compare FA values with and without normalization. If the non-linear option is used, is there a problem that the tensor is subsampled first before it is re-oriented, as described above? > As I mentioned above, nonlinear should be AFTER linear transformation. This means, the data are transformed multiple times and pixels are interpolated multiple times. To avoid this, once you did linear (save transformation matrix: T-linear) and nonlinear (save transformation matrix: T-nonlinear), you can combine the T-linear x T-nonlinear using one of the buttons in the LDDMM section. Once you combined all transformation matrices, you can apply it only once to the original image in the native space. > Another interesting thing is, there are two ways to transform images; transform your image to an atlas or transform atlas (usually, binary segmentation map) to your original data for automated segmentation. For the latter approach, you don?t have to transform (therefore interpolate) your original data. When you transform the atlas (segmentation map), make sure to use ?nearest neighbor? (no interpolation), not the tri-linear interpolation. The segmentation map consists of arbitrary numbers assigned to each segment (e.g. the internal capsule is ?1? and the corona radiata is ?3?). If you interpolate these two segments and obtain ?2? in between these two segments and if ?2? means pons, you would get the pons in between the internal capsule and the corona radiata. On the other hand, when you are transforming your data to an atlas space, use the tri-linear interpolation. Otherwise, you could get strange discontinuity artifacts. Do you suggest using the affine or non-linear transformation of the DWIs and the corresponding transformation of the tensor? Lastly, I'm not sure if the colour map display is of an issue? It occurs both using the linear affine option and the non-linear option. > When everything is working right, the color map should look smooth and clean. Maybe you are using ?nearest neighbor? for the tensor transformation? Thanks Siewmin On Sat, May 9, 2009 at 7:44 AM, susumu > wrote: First, I tried rotating the tensor but had problems with the results. When I look at the colour map from the resulting tensor, it looks ok generally, but there are certain areas of blotchiness and some mixing of colours especially in the sidelines of white matter regions (i.e there can be a striking red line or a blotch of redness in the middle of a green regions within the saggital stratum). These are the steps I took, and would like to check if it is done correctly. 1. resample mean DWI of subject data (together with the 4D DTI data and the tensor) to DWI of ICBM 81 template. Non-linear transform (2nd order trilinear) the resampled meandwi of subject to dwi of template, and used that to drive the transformation of the resampled 4D DTI and the resampled tensor simultaneously. (The resampled tensor was loaded with the .dat button.) I used MRIview 3D to load the normalised 4D DTI, followed by the normalised tensor with the .dat button, and calculate the fa, colour etc maps from the normalised tensor. I tried various thresholding with AIR but the colour maps problem remains. > First of all, I think you don't have to resample DTI images before AIR. AIR can take data with different matrix and pixel sizes and the output images have the same matrix/pixel dimensions as the template (in your case, 181x217x181 of ICBM81). > By saying "4D DTI", do you mean raw 4D DWI before tensor calculation? if so, I don't think you want transform raw DWIs. If you want to do anything to raw DTI, you also want to transform the corresponding gradient table, which could be messy. Our tools do not provide methods to transform raw DWIs. > When you say, "tensor" data, I assume you are talking about 4D file that contains "Dxx, Dyy, Dzz, Dxy, Dxz, Dyz" images in one file. If so, please make sure that you load this 4D tensor file by the "open .d" button in Landmarker. Once read in Landmarker, the 4D tensor file is disassembled to 6 3D data for Dxx, Dyy, Dzz, Dxy, Dxz, Dyz. > Once the AIR is done using mean DWI (your data) - mean DWI (template), the 6 3D tensor element data should be stored all together into one file as a "transformed 4D tensor file". > This transformed 4D tensor file needs to be read into DtiStudio to re-calculate new transformed FA, color, vec, etc. > The blotch-looking colormap could happen by; 1) transform the color map directly (you should recreate color maps using the recalcuated FA and vector files from the transformed tensor file or 2) you transformed a vector file (transformed vector files should be obtained from the transformed tensor file. Vector can not be directly transformed). Second, I tried without rotating the tensor. I calculate the scalar and colour maps from the original 4D DTI data, aligned the maps to AC-PC line, draw rois on them and invert transform the rois back to native dti space to extract the relevant white matter tracts. I had two problems here. 1) with orienting the subjects scalar DWI to another particular subject's DWI with rigid transformation in AIR and 2) Invert transform ROIs drawn on the registered colour map back to the original DTI space. These are the steps I took: > Maybe you are transforming raw DWI data? Again, you should not transform raw DWI and recalcuate tensor. You have to first calculate tensor (throw away the raw DWIs) and transform the tensor. 1. A subject's data which is acquired // to AC-PC is chosen and other subjects not acquired //to AC are registered to this. Again the meanDWI is used for source and target images, this time using rigid transformation in AIR in Landmarker. However, there is no difference detected after the transformation has taken place. However, if I change the target image from a subject's DWI to the mean DWI of the ICBM 81 template, it works but the source data would be subsampled to that of the ICBM template. I'm not sure why it didn't work in the 1st case? > As mentioned above, AIR not only adjust the image orientation and translation, but also the matrix / pixel size.. > Rigid transformation of AIR is sometimes very cranky. We are working on alternative methods now. please try different threshold or affine. Additionally, using either another subject or the template DWI as target image, would yield the an output file (AlignlinearOutput.air) when the transformation has been performed, which I saved the invert_AlignlinearOutput.air. However, when I clicked on these .air files in the folder it is saved as an installer package, I get the following error message " An error has occurred.The application could not be installed because the AIR file is damaged. Try obtaining a new AIR file from the application author." I have installed the air application and placed it in the same folder, together with the alignlinear.exe file. Is it possible to view the transformation matrix files saved or did I not installed the air application appropriately? > Maybe Xin can answer this question better, but I'm not sure why you want to open *.air?? > Once you save the *.air, you can load it back to Landmarker and apply to images by using the "open M" button in the LDDMM section. 2. ROIs are drawn on the transformed AC-PC aligned colour maps with ROI-editor. I would like to check if it's OK to draw rois on the transformed colour map? These ROIs would later be used as the start ROI and stop ROI to extract the corresponding white matter tract with DTI studio) > Drawing ROIs on color maps is fine. ROI is simply 1/0 information about which pixels you chose and the color maps are simply what is displayed to aid your ROI drawing. > If you draw ROI in the atlas space and have a plan to back-transform your ROI files to the native space, there are several things you have to know; 1) Atlas space is 1x1x1 and your native space could be 2-3 mm. The ROI defined in the thin 1 mm slice could be lost after transformation to the thick 2-3mm slice. Therefore, you have to create 3D ROIs in the atlas space with at least 3mm thick 2) Use nearest neighbor interpolation when you back-transfer. You don't want to get a pixel with 0.3 or 0.4 after transformation. You want 1/0 3. I tried to invert-transform these ROIs back to the original DTI space with the previously saved invert_matrix.air file. How is that done in Landmarker and if the previous error message needs to be resolved before I can used the matrix files? > Xin, how to do the invert-transformation of *.air? Susumu _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090511/60772123/attachment-0001.html From siewmin.gan at gmail.com Mon May 11 12:20:42 2009 From: siewmin.gan at gmail.com (Siewmin Gan) Date: Tue, 12 May 2009 00:20:42 +0800 Subject: [Mristudio-users] transformations with AIR in Landmarker In-Reply-To: <328ADA5CC29C8D4CADC8D72650E5533C011FDE0659DF@EXCHANGE11.Enterprise.emory.net> References: <7k7ed7$7dst7f@ipex3.johnshopkins.edu> <328ADA5CC29C8D4CADC8D72650E5533C011FDE0659DF@EXCHANGE11.Enterprise.emory.net> Message-ID: Hi Susumu, I have learnt a lot from your correspondence, as usual. Will try as you've suggested. Thanks Siewmin ------------------------------ > *From:* mristudio-users-bounces at mristudio.org [ > mristudio-users-bounces at mristudio.org] On Behalf Of susumu [ > susumu at mri.jhu.edu] > *Sent:* Sunday, May 10, 2009 9:39 AM > *To:* 'DTI Studio, ROI Editor, Landmarker Questions/Support' > *Subject:* Re: [Mristudio-users] transformations with AIR in Landmarker > > Siewmin raised some important points and I hope other users could gain > some important information from this thread. > > > > I got the mean DWI and tensor file from the original 4D DWI. The tensor > file is as you've said, which contains "Dxx, Dyy, Dzz, Dxy, Dxz Dyz" in one > file. In Landmarker, I loaded only the mean DWI of the subject and then the > tensor file with the "open .d" button. The 4D raw DWI is not used in > Landmarker or later. With the "linear" option in AIR, I could rotate the > tensor and the mean DWI to the template DWI without having to subsample the > input data first. The "nonlinear" option requires the subject data (mean DWI > and the tensor file) to be of the same dimension as the template (i.e 181, > 217, 181 if ICBM81 DWI is used as template). This is noted in the pop up > message, and it would only continue once the input files are resampled to > the template. > > > > >It is always advised to do linear transformation first. To start > non-linear, you have to make sure that the brain locations and shapes are as > similar as possible. This is similar to non-linear fitting. You always have > to provide ?initial? values close to the real solutions. Otherwise, > non-linear fitting could converge to a wrong solution (trapped by ?local > minima?). > > > > Additionally, I tried affine in the linear registration option. The output > DWI of the registration is identical to the input of the DWIs if I used one > of my subject's DWI as the template. Using the 2nd order polynomial in > nonlinear option, an error message occurs "registration terminated due to a > calculation problem, please try a lower order model". It seems to only work > if the template is one of those provided in Landmarker. > > > > > If you can send us two images you are having the problem, we can take a > look at why AIR doesn?t work. > > > > I then saved the rotated tensor file as one file in the .dat format and the > linearly registered 3D meanDWI. In MRIview3D, I loaded this new 3D DWI and > open this new tensor.dat file with the open.dat button to re-calculates the > fa, colour map etc. I viewed the colour map output from this and it looks > pretty good, and as described previously. > > > > > This is the correct procedure. > > > > I saved the fa and principal eigenvector file and used them to perform > fiber-tracking. The tracts that are manually extracted obtained looks > similiar to the fiber tracts from the original raw 4D DWI. > > > > > That is a good sign. > > > > The FA values of these tracts are smaller uniformly in comparison, and the > assymetry preserved (i.e the left tract FA is smaller than the right tract > FA using the maps calculated from the original and rotated tensor). > > > > > Normalization requires pixel interpolation, which leads to decreased FA. > So you can not compare FA values with and without normalization. > > > > If the non-linear option is used, is there a problem that the tensor is > subsampled first before it is re-oriented, as described above? > > > > > As I mentioned above, nonlinear should be AFTER linear transformation. > This means, the data are transformed multiple times and pixels are > interpolated multiple times. To avoid this, once you did linear (save > transformation matrix: T-linear) and nonlinear (save transformation matrix: > T-nonlinear), you can combine the T-linear x T-nonlinear using one of the > buttons in the LDDMM section. Once you combined all transformation matrices, > you can apply it only once to the original image in the native space. > > > > > Another interesting thing is, there are two ways to transform images; > transform your image to an atlas or transform atlas (usually, binary > segmentation map) to your original data for automated segmentation. For the > latter approach, you don?t have to transform (therefore interpolate) your > original data. When you transform the atlas (segmentation map), make sure to > use ?nearest neighbor? (no interpolation), not the tri-linear interpolation. > The segmentation map consists of arbitrary numbers assigned to each segment > (e.g. the internal capsule is ?1? and the corona radiata is ?3?). If you > interpolate these two segments and obtain ?2? in between these two segments > and if ?2? means pons, you would get the pons in between the internal > capsule and the corona radiata. On the other hand, when you are transforming > your data to an atlas space, use the tri-linear interpolation. Otherwise, > you could get strange discontinuity artifacts. > > > > Do you suggest using the affine or non-linear transformation of the DWIs > and the corresponding transformation of the tensor? Lastly, I'm not sure if > the colour map display is of an issue? It occurs both using the linear > affine option and the non-linear option. > > > > > When everything is working right, the color map should look smooth and > clean. Maybe you are using ?nearest neighbor? for the tensor transformation? > > > > Thanks > > > > Siewmin > > > > > > > > > > On Sat, May 9, 2009 at 7:44 AM, susumu wrote: > > First, I tried rotating the tensor but had problems with the results. When > I look at the colour map from the resulting tensor, it looks ok generally, > but there are certain areas of blotchiness and some mixing of colours > especially in the sidelines of white matter regions (i.e there can be a > striking red line or a blotch of redness in the middle of a green regions > within the saggital stratum). These are the steps I took, and would like to > check if it is done correctly. > > 1. resample mean DWI of subject data (together with the 4D DTI data and the > tensor) to DWI of ICBM 81 template. Non-linear transform (2nd order > trilinear) the resampled meandwi of subject to dwi of template, and used > that to drive the transformation of the resampled 4D DTI and the resampled > tensor simultaneously. (The resampled tensor was loaded with the .dat > button.) I used MRIview 3D to load the normalised 4D DTI, followed by the > normalised tensor with the .dat button, and calculate the fa, colour etc > maps from the normalised tensor. I tried various thresholding with AIR but > the colour maps problem remains. > > > > > First of all, I think you don't have to resample DTI images before AIR. > AIR can take data with different matrix and pixel sizes and the output > images have the same matrix/pixel dimensions as the template (in your case, > 181x217x181 of ICBM81). > > > By saying "4D DTI", do you mean raw 4D DWI before tensor calculation? if > so, I don't think you want transform raw DWIs. If you want to do anything to > raw DTI, you also want to transform the corresponding gradient table, which > could be messy. Our tools do not provide methods to transform raw DWIs. > > > When you say, "tensor" data, I assume you are talking about 4D file that > contains "Dxx, Dyy, Dzz, Dxy, Dxz, Dyz" images in one file. If so, please > make sure that you load this 4D tensor file by the "open .d" button in > Landmarker. Once read in Landmarker, the 4D tensor file is disassembled to 6 > 3D data for Dxx, Dyy, Dzz, Dxy, Dxz, Dyz. > > > Once the AIR is done using mean DWI (your data) - mean DWI (template), > the 6 3D tensor element data should be stored all together into one file as > a "transformed 4D tensor file". > > > This transformed 4D tensor file needs to be read into DtiStudio to > re-calculate new transformed FA, color, vec, etc. > > > The blotch-looking colormap could happen by; 1) transform the color map > directly (you should recreate color maps using the recalcuated FA and vector > files from the transformed tensor file or 2) you transformed a vector file > (transformed vector files should be obtained from the transformed tensor > file. Vector can not be directly transformed). > > > > Second, I tried without rotating the tensor. I calculate the scalar and > colour maps from the original 4D DTI data, aligned the maps to AC-PC line, > draw rois on them and invert transform the rois back to native dti space to > extract the relevant white matter tracts. I had two problems here. 1) with > orienting the subjects scalar DWI to another particular subject's DWI with > rigid transformation in AIR and 2) Invert transform ROIs drawn on the > registered colour map back to the original DTI space. These are the steps I > took: > > > > > Maybe you are transforming raw DWI data? Again, you should not transform > raw DWI and recalcuate tensor. You have to first calculate tensor (throw > away the raw DWIs) and transform the tensor. > > > > 1. A subject's data which is acquired // to AC-PC is chosen and other > subjects not acquired //to AC are registered to this. Again the meanDWI is > used for source and target images, this time using rigid transformation in > AIR in Landmarker. However, there is no difference detected after the > transformation has taken place. However, if I change the target image from a > subject's DWI to the mean DWI of the ICBM 81 template, it works but the > source data would be subsampled to that of the ICBM template. I'm not sure > why it didn't work in the 1st case? > > > > > As mentioned above, AIR not only adjust the image orientation and > translation, but also the matrix / pixel size.. > > > Rigid transformation of AIR is sometimes very cranky. We are working on > alternative methods now. please try different threshold or affine. > > > > Additionally, using either another subject or the template DWI as target > image, would yield the an output file (AlignlinearOutput.air) when the > transformation has been performed, which I saved the > invert_AlignlinearOutput.air. However, when I clicked on these .air files in > the folder it is saved as an installer package, I get the following error > message " An error has occurred.The application could not be installed > because the AIR file is damaged. Try obtaining a new AIR file from the > application author." I have installed the air application and placed it in > the same folder, together with the alignlinear.exe file. Is it possible to > view the transformation matrix files saved or did I not installed the air > application appropriately? > > > > > Maybe Xin can answer this question better, but I'm not sure why you want > to open *.air?? > > > Once you save the *.air, you can load it back to Landmarker and apply to > images by using the "open M" button in the LDDMM section. > > > > 2. ROIs are drawn on the transformed AC-PC aligned colour maps with > ROI-editor. I would like to check if it's OK to draw rois on the transformed > colour map? These ROIs would later be used as the start ROI and stop ROI to > extract the corresponding white matter tract with DTI studio) > > > > > Drawing ROIs on color maps is fine. ROI is simply 1/0 information about > which pixels you chose and the color maps are simply what is displayed to > aid your ROI drawing. > > > If you draw ROI in the atlas space and have a plan to back-transform your > ROI files to the native space, there are several things you have to know; > > 1) Atlas space is 1x1x1 and your native space could be 2-3 mm. The ROI > defined in the thin 1 mm slice could be lost after transformation to the > thick 2-3mm slice. Therefore, you have to create 3D ROIs in the atlas space > with at least 3mm thick > > 2) Use nearest neighbor interpolation when you back-transfer. You don't > want to get a pixel with 0.3 or 0.4 after transformation. You want 1/0 > > > > 3. I tried to invert-transform these ROIs back to the original DTI space > with the previously saved invert_matrix.air file. How is that done in > Landmarker and if the previous error message needs to be resolved before I > can used the matrix files? > > > > > Xin, how to do the invert-transformation of *.air? > > > > Susumu > > > > > > > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > > ------------------------------ > This e-mail message (including any attachments) is for the sole use of > the intended recipient(s) and may contain confidential and privileged > information. If the reader of this message is not the intended > recipient, you are hereby notified that any dissemination, distribution > or copying of this message (including any attachments) is strictly > prohibited. > > If you have received this message in error, please contact > the sender by reply e-mail message and destroy all copies of the > original message (including attachments). > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090512/cac99a9c/attachment-0001.html From xli16 at jhmi.edu Mon May 11 12:27:30 2009 From: xli16 at jhmi.edu (Xin Li) Date: Mon, 11 May 2009 12:27:30 -0400 Subject: [Mristudio-users] transformations with AIR in Landmarker In-Reply-To: <7k7ed7$7dst7f@ipex3.johnshopkins.edu> References: <7k7ed7$7dst7f@ipex3.johnshopkins.edu> Message-ID: Siewmin, > Maybe Xin can answer this question better, but I'm not sure why you want to open *.air?? *.air is not a text file. If you want to view the transformation matrix in the file, you have to run a AIR application "scanair.exe" in C command window. Please go to AIR's website to check the information about this function. > Xin, how to do the invert-transformation of *.air? Landmarker has the function to invert *.air. There is a "Invert" button beside the AIR linear button. Hope this will give you some help. Xin From ltao97 at 163.com Mon May 11 14:58:08 2009 From: ltao97 at 163.com (ltao97) Date: Tue, 12 May 2009 02:58:08 +0800 (CST) Subject: [Mristudio-users] thank you Message-ID: <9375544.555981242068288595.JavaMail.coremail@bj163app132.163.com> Dear sir Don't send these e-mails to the mailbox. Please send the e-mails to another mailbox which is ltao97 at 126.com Thank you! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090512/ee1daad8/attachment.html From susumu at mri.jhu.edu Mon May 11 14:25:29 2009 From: susumu at mri.jhu.edu (susumu) Date: Mon, 11 May 2009 14:25:29 -0400 Subject: [Mristudio-users] transformations with AIR in Landmarker In-Reply-To: Message-ID: <7k7ed7$7f10r2@ipex3.johnshopkins.edu> For those who are interested in image normalization by Landmarker, here I attached a step-by-step instruction. Siewmin, I could transform your data with the default setup using this procedure. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Siewmin Gan Sent: Monday, May 11, 2009 12:21 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] transformations with AIR in Landmarker Hi Susumu, I have learnt a lot from your correspondence, as usual. Will try as you've suggested. Thanks Siewmin _____ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of susumu [susumu at mri.jhu.edu] Sent: Sunday, May 10, 2009 9:39 AM To: 'DTI Studio, ROI Editor, Landmarker Questions/Support' Subject: Re: [Mristudio-users] transformations with AIR in Landmarker Siewmin raised some important points and I hope other users could gain some important information from this thread. I got the mean DWI and tensor file from the original 4D DWI. The tensor file is as you've said, which contains "Dxx, Dyy, Dzz, Dxy, Dxz Dyz" in one file. In Landmarker, I loaded only the mean DWI of the subject and then the tensor file with the "open .d" button. The 4D raw DWI is not used in Landmarker or later. With the "linear" option in AIR, I could rotate the tensor and the mean DWI to the template DWI without having to subsample the input data first. The "nonlinear" option requires the subject data (mean DWI and the tensor file) to be of the same dimension as the template (i.e 181, 217, 181 if ICBM81 DWI is used as template). This is noted in the pop up message, and it would only continue once the input files are resampled to the template. >It is always advised to do linear transformation first. To start non-linear, you have to make sure that the brain locations and shapes are as similar as possible. This is similar to non-linear fitting. You always have to provide "initial" values close to the real solutions. Otherwise, non-linear fitting could converge to a wrong solution (trapped by "local minima"). Additionally, I tried affine in the linear registration option. The output DWI of the registration is identical to the input of the DWIs if I used one of my subject's DWI as the template. Using the 2nd order polynomial in nonlinear option, an error message occurs "registration terminated due to a calculation problem, please try a lower order model". It seems to only work if the template is one of those provided in Landmarker. > If you can send us two images you are having the problem, we can take a look at why AIR doesn't work. I then saved the rotated tensor file as one file in the .dat format and the linearly registered 3D meanDWI. In MRIview3D, I loaded this new 3D DWI and open this new tensor.dat file with the open.dat button to re-calculates the fa, colour map etc. I viewed the colour map output from this and it looks pretty good, and as described previously. > This is the correct procedure. I saved the fa and principal eigenvector file and used them to perform fiber-tracking. The tracts that are manually extracted obtained looks similiar to the fiber tracts from the original raw 4D DWI. > That is a good sign. The FA values of these tracts are smaller uniformly in comparison, and the assymetry preserved (i.e the left tract FA is smaller than the right tract FA using the maps calculated from the original and rotated tensor). > Normalization requires pixel interpolation, which leads to decreased FA. So you can not compare FA values with and without normalization. If the non-linear option is used, is there a problem that the tensor is subsampled first before it is re-oriented, as described above? > As I mentioned above, nonlinear should be AFTER linear transformation. This means, the data are transformed multiple times and pixels are interpolated multiple times. To avoid this, once you did linear (save transformation matrix: T-linear) and nonlinear (save transformation matrix: T-nonlinear), you can combine the T-linear x T-nonlinear using one of the buttons in the LDDMM section. Once you combined all transformation matrices, you can apply it only once to the original image in the native space. > Another interesting thing is, there are two ways to transform images; transform your image to an atlas or transform atlas (usually, binary segmentation map) to your original data for automated segmentation. For the latter approach, you don't have to transform (therefore interpolate) your original data. When you transform the atlas (segmentation map), make sure to use "nearest neighbor" (no interpolation), not the tri-linear interpolation. The segmentation map consists of arbitrary numbers assigned to each segment (e.g. the internal capsule is "1" and the corona radiata is "3"). If you interpolate these two segments and obtain "2" in between these two segments and if "2" means pons, you would get the pons in between the internal capsule and the corona radiata. On the other hand, when you are transforming your data to an atlas space, use the tri-linear interpolation. Otherwise, you could get strange discontinuity artifacts. Do you suggest using the affine or non-linear transformation of the DWIs and the corresponding transformation of the tensor? Lastly, I'm not sure if the colour map display is of an issue? It occurs both using the linear affine option and the non-linear option. > When everything is working right, the color map should look smooth and clean. Maybe you are using "nearest neighbor" for the tensor transformation? Thanks Siewmin On Sat, May 9, 2009 at 7:44 AM, susumu wrote: First, I tried rotating the tensor but had problems with the results. When I look at the colour map from the resulting tensor, it looks ok generally, but there are certain areas of blotchiness and some mixing of colours especially in the sidelines of white matter regions (i.e there can be a striking red line or a blotch of redness in the middle of a green regions within the saggital stratum). These are the steps I took, and would like to check if it is done correctly. 1. resample mean DWI of subject data (together with the 4D DTI data and the tensor) to DWI of ICBM 81 template. Non-linear transform (2nd order trilinear) the resampled meandwi of subject to dwi of template, and used that to drive the transformation of the resampled 4D DTI and the resampled tensor simultaneously. (The resampled tensor was loaded with the .dat button.) I used MRIview 3D to load the normalised 4D DTI, followed by the normalised tensor with the .dat button, and calculate the fa, colour etc maps from the normalised tensor. I tried various thresholding with AIR but the colour maps problem remains. > First of all, I think you don't have to resample DTI images before AIR. AIR can take data with different matrix and pixel sizes and the output images have the same matrix/pixel dimensions as the template (in your case, 181x217x181 of ICBM81). > By saying "4D DTI", do you mean raw 4D DWI before tensor calculation? if so, I don't think you want transform raw DWIs. If you want to do anything to raw DTI, you also want to transform the corresponding gradient table, which could be messy. Our tools do not provide methods to transform raw DWIs. > When you say, "tensor" data, I assume you are talking about 4D file that contains "Dxx, Dyy, Dzz, Dxy, Dxz, Dyz" images in one file. If so, please make sure that you load this 4D tensor file by the "open .d" button in Landmarker. Once read in Landmarker, the 4D tensor file is disassembled to 6 3D data for Dxx, Dyy, Dzz, Dxy, Dxz, Dyz. > Once the AIR is done using mean DWI (your data) - mean DWI (template), the 6 3D tensor element data should be stored all together into one file as a "transformed 4D tensor file". > This transformed 4D tensor file needs to be read into DtiStudio to re-calculate new transformed FA, color, vec, etc. > The blotch-looking colormap could happen by; 1) transform the color map directly (you should recreate color maps using the recalcuated FA and vector files from the transformed tensor file or 2) you transformed a vector file (transformed vector files should be obtained from the transformed tensor file. Vector can not be directly transformed). Second, I tried without rotating the tensor. I calculate the scalar and colour maps from the original 4D DTI data, aligned the maps to AC-PC line, draw rois on them and invert transform the rois back to native dti space to extract the relevant white matter tracts. I had two problems here. 1) with orienting the subjects scalar DWI to another particular subject's DWI with rigid transformation in AIR and 2) Invert transform ROIs drawn on the registered colour map back to the original DTI space. These are the steps I took: > Maybe you are transforming raw DWI data? Again, you should not transform raw DWI and recalcuate tensor. You have to first calculate tensor (throw away the raw DWIs) and transform the tensor. 1. A subject's data which is acquired // to AC-PC is chosen and other subjects not acquired //to AC are registered to this. Again the meanDWI is used for source and target images, this time using rigid transformation in AIR in Landmarker. However, there is no difference detected after the transformation has taken place. However, if I change the target image from a subject's DWI to the mean DWI of the ICBM 81 template, it works but the source data would be subsampled to that of the ICBM template. I'm not sure why it didn't work in the 1st case? > As mentioned above, AIR not only adjust the image orientation and translation, but also the matrix / pixel size.. > Rigid transformation of AIR is sometimes very cranky. We are working on alternative methods now. please try different threshold or affine. Additionally, using either another subject or the template DWI as target image, would yield the an output file (AlignlinearOutput.air) when the transformation has been performed, which I saved the invert_AlignlinearOutput.air. However, when I clicked on these .air files in the folder it is saved as an installer package, I get the following error message " An error has occurred.The application could not be installed because the AIR file is damaged. Try obtaining a new AIR file from the application author." I have installed the air application and placed it in the same folder, together with the alignlinear.exe file. Is it possible to view the transformation matrix files saved or did I not installed the air application appropriately? > Maybe Xin can answer this question better, but I'm not sure why you want to open *.air?? > Once you save the *.air, you can load it back to Landmarker and apply to images by using the "open M" button in the LDDMM section. 2. ROIs are drawn on the transformed AC-PC aligned colour maps with ROI-editor. I would like to check if it's OK to draw rois on the transformed colour map? These ROIs would later be used as the start ROI and stop ROI to extract the corresponding white matter tract with DTI studio) > Drawing ROIs on color maps is fine. ROI is simply 1/0 information about which pixels you chose and the color maps are simply what is displayed to aid your ROI drawing. > If you draw ROI in the atlas space and have a plan to back-transform your ROI files to the native space, there are several things you have to know; 1) Atlas space is 1x1x1 and your native space could be 2-3 mm. The ROI defined in the thin 1 mm slice could be lost after transformation to the thick 2-3mm slice. Therefore, you have to create 3D ROIs in the atlas space with at least 3mm thick 2) Use nearest neighbor interpolation when you back-transfer. You don't want to get a pixel with 0.3 or 0.4 after transformation. You want 1/0 3. I tried to invert-transform these ROIs back to the original DTI space with the previously saved invert_matrix.air file. How is that done in Landmarker and if the previous error message needs to be resolved before I can used the matrix files? > Xin, how to do the invert-transformation of *.air? Susumu _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users _____ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090511/78e53993/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: siewmin.ppt Type: application/vnd.ms-powerpoint Size: 2935296 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090511/78e53993/attachment-0001.ppt From yj3 at duke.edu Mon May 11 16:52:49 2009 From: yj3 at duke.edu (Yi Jiang) Date: Mon, 11 May 2009 16:52:49 -0400 Subject: [Mristudio-users] save and read fiber in Amira format References: <7k7ed7$7f10r2@ipex3.johnshopkins.edu> Message-ID: <2593DC540EEE4FF49F04CAB92AAC2023@panpan> Hello, dear all, I tried to select multiple fiber tracts in multiple colors (say, the final selected fibers are from 20 ROIs and in 8 colors). I saved the "selected fibers" in amira format. I tried to load the fiber file in Amira. It was loaded in with no complaint. I then displayed the fibers as lineSetView in Amira. But all the lines displayed with the same color, instead of the 8 colors I would hope. My questions are: are the fiber color (labels or indices) saved in the amira format? If yes, how can I display them in different colors as in DTIstudio? Thank you very much! Best, Yi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090511/a07adc9d/attachment.html From hjyu at ic.sunysb.edu Mon May 11 17:40:59 2009 From: hjyu at ic.sunysb.edu (Hui J Yu) Date: Mon, 11 May 2009 17:40:59 -0400 Subject: [Mristudio-users] transformations with AIR in Landmarker In-Reply-To: <7k7ed7$7f10r2@ipex3.johnshopkins.edu> References: <7k7ed7$7f10r2@ipex3.johnshopkins.edu> Message-ID: <73a0fe2b315e.4a08632b@ic.sunysb.edu> Hi, I have a follow-up question regarding calculations using DTIstudio after AIR transformation in Landmarker.? I noticed that you can only load the normalized image (B0, DWI, etc.) in MRI view3D, then extract other parameters such as EigenVal, EigenVec, FA etc. through loading the corresponding tensor (.d).? However, when this option is used, we lost the ability to get more results (such as Trace, Geometrical index, or radial diffusivity) or save results (semi-automatically through simiply checking) that we would get in DTI-Map options.? Although it is true that those measurements can be simply calculated using ROIeditor or offline programs, it would be nice to know if there is a way to load the normalized images (in raw format saved by Landmarker) using DTI-mapping or somehow being able to access DtiMap calculation options.? Right now if I go to DTI Mapping >> Raw files >>enter the correct parameters (for example, for the 181x217x181), it would give me an error saying "Number of files in this fold is less than expected: (Img_slices*Img_blocks). Thank you very much for your response. HJ ----- Original Message ----- From: susumu Date: Monday, May 11, 2009 4:45 pm Subject: Re: [Mristudio-users] transformations with AIR in Landmarker To: "'DTI Studio, ROI Editor, Landmarker Questions/Support'" > For those who are interested in image normalization by Landmarker, here I attached a step-by-step instruction. > Siewmin, I could transform your data with the default setup using this procedure. > ? > Susumu > ? ----------------------------------------------------------- ? > From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Siewmin Gan > Sent: Monday, May 11, 2009 12:21 PM > To: DTI Studio, ROI Editor, Landmarker Questions/Support > Subject: Re: [Mristudio-users] transformations with AIR in Landmarker ? > ? > Hi Susumu, I have learnt a lot from your correspondence, as usual. Will try as you've suggested. > ? ? > Thanks ? > ? ? > Siewmin > ? ----------------------------------------------------------- ? > From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of susumu [susumu at mri.jhu.edu] > Sent: Sunday, May 10, 2009 9:39 AM > To: 'DTI Studio, ROI Editor, Landmarker Questions/Support' > Subject: Re: [Mristudio-users] transformations with AIR in Landmarker ? > Siewmin raised some important points and I hope other users could gain some important information from this thread. > ? ? > ?I got the mean DWI and tensor file from the original 4D DWI. The tensor file is as you've said, which contains ?"Dxx, Dyy, Dzz, Dxy, Dxz Dyz" in one file. In Landmarker, I loaded only the mean DWI of the subject and then the tensor file with the "open .d" button. The 4D raw DWI is not used in Landmarker or later. With the "linear" option in AIR, I could rotate the tensor and the mean DWI to the template DWI without having to subsample the input data first. The "nonlinear" option requires the subject data (mean DWI and the tensor file) to be of the same dimension as the template (i.e 181, 217, 181 if ICBM81 DWI is used as template). This is noted in the pop up message, and it would only continue once the input files are resampled to the template.? > ? > >It is always advised to do linear transformation first. To start non-linear, you have to make sure that the brain locations and shapes are as similar as possible. This is similar to non-linear fitting. You always have to provide ?initial? values close to the real solutions. Otherwise, non-linear fitting could converge to a wrong solution (trapped by ?local minima?). ? > ? ? > Additionally, I tried affine in the linear registration option. The output DWI of the registration is identical to the input of the DWIs if I used one of my subject's DWI as the template. Using the 2nd order polynomial in nonlinear option, an error message occurs "registration terminated due to a calculation problem, please try a lower order model". It seems to only work if the template is one of those provided in Landmarker. > ? > > If you can send us two images you are having the problem, we can take a look at why AIR doesn?t work. > ? ? > I then saved the rotated tensor file as one file in the .dat format and the linearly registered 3D ?meanDWI. In MRIview3D, I loaded this new 3D DWI and open this new tensor.dat file with the open.dat button to re-calculates the fa, colour map etc. I viewed the colour map output from this and it looks pretty good, and as described previously. > ? > > This is the correct procedure. > ? > I saved the fa and principal eigenvector file and used them to perform fiber-tracking. The tracts that are manually extracted obtained looks similiar to the fiber tracts from the original raw 4D DWI. > ? > > That is a good sign. > ? > The FA values of these tracts are smaller uniformly in comparison, and the assymetry preserved (i.e the left tract FA is smaller than the right tract FA using the maps calculated from the original and rotated tensor). > ? > > Normalization requires pixel interpolation, which leads to decreased FA. So you can not compare FA values with and without normalization. > ? > If the non-linear option is used, is there a problem that the tensor is subsampled first before it is re-oriented, as described above? > ? > > As I mentioned above, nonlinear should be AFTER linear transformation. This means, the data are transformed multiple times and pixels are interpolated multiple times. To avoid this, once you did linear (save transformation matrix: T-linear) and nonlinear (save transformation matrix: T-nonlinear), you can combine the T-linear x T-nonlinear using one of the buttons in the LDDMM section. Once you combined all transformation matrices, you can apply it only once to the original image in the native space. > ? > > Another interesting thing is, there are two ways to transform images; transform your image to an atlas or transform atlas (usually, binary segmentation map) to your original data for automated segmentation. For the latter approach, you don?t have to transform (therefore interpolate) your original data. When you transform the atlas (segmentation map), make sure to use ?nearest neighbor? (no interpolation), not the tri-linear interpolation. The segmentation map consists of arbitrary numbers assigned to each segment (e.g. the internal capsule is ?1? and the corona radiata is ?3?). If you interpolate these two segments and obtain ?2? in between these two segments and if ?2? means pons, you would get the pons in between the internal capsule and the corona radiata. On the other hand, when you are transforming your data to an atlas space, use the tri-linear interpolation. Otherwise, you could get strange discontinuity artifacts. > ? > Do you suggest?using the affine or non-linear transformation of the DWIs and the corresponding transformation of the tensor? Lastly, I'm?not sure if the colour map display is of an issue? It occurs both using the linear affine option and the non-linear option. > ? > > When everything is working right, the color map should look smooth and clean. Maybe you are using ?nearest neighbor? for the tensor transformation? ? > ? ? > Thanks ? > ? ? > Siewmin > ? > ? ? > ? ? > ? ? > On Sat, May 9, 2009 at 7:44 AM, susumu wrote: > First, I tried rotating the tensor but had problems with the results. When I look at the colour map from the resulting tensor, it looks ok generally, but there are certain areas of blotchiness and some mixing of colours especially in the sidelines of white matter regions (i.e there can be a striking red line or a blotch of redness in the middle of a green regions within the saggital stratum). These are the steps I took, and would like to check if it is done correctly. ? ? > 1. resample mean DWI of subject data (together with the 4D DTI data and the tensor) to DWI of ICBM 81 template. Non-linear transform (2nd order trilinear) the resampled meandwi of subject to dwi of template, and used that to drive the transformation of the resampled 4D DTI and the resampled tensor simultaneously. (The resampled tensor was loaded with the .dat button.) I used MRIview 3D to load the normalised 4D DTI, followed by the normalised tensor with the .dat button, and calculate the fa, colour etc maps from the normalised tensor. I ?tried various thresholding with AIR but the colour maps problem remains. > ? ? > > First of all, I think you don't have to resample DTI images before AIR. AIR can take data with different matrix and pixel sizes and the output images have the same matrix/pixel dimensions as the template (in your case, 181x217x181 of ICBM81). > > By saying "4D DTI", do you mean raw 4D DWI before tensor calculation? if so, I don't think you want transform raw DWIs. If you want to do anything to raw DTI, you also want to transform the corresponding gradient table, which could be messy. Our tools do not provide methods to transform raw DWIs. > > When you say, "tensor" data, I assume you are talking about 4D file that contains "Dxx, Dyy, Dzz, Dxy, Dxz, Dyz" images in one file. If so, please make sure that you load this 4D tensor file by the "open .d" button in Landmarker. Once read in Landmarker, the 4D tensor file is disassembled to 6 3D data for Dxx, Dyy, Dzz, Dxy, Dxz, Dyz. > > Once the AIR is done using mean DWI (your data) - mean DWI (template), the 6 3D tensor element data should be stored all together into one file as a "transformed 4D tensor file". > > This transformed 4D tensor file needs to be read into DtiStudio to re-calculate new transformed FA, color, vec, etc. > > The blotch-looking colormap could happen by; 1) transform the color map directly (you should recreate color maps using the recalcuated FA and vector files from the transformed tensor file or 2) you transformed a vector file (transformed vector files should be obtained from the transformed tensor file. Vector can not be directly transformed). ? > ? ? > Second, I tried without rotating the tensor. I calculate the scalar and colour maps from the original 4D DTI data, aligned the maps to AC-PC line, draw rois on them and invert transform the rois back to native dti space to extract the relevant white matter tracts. I had two problems here. 1) ?with orienting the subjects scalar DWI to ?another particular subject's DWI with rigid transformation in AIR and 2) Invert transform ROIs drawn on the registered colour map back to the original DTI space. These are the steps I took: > ? ? > > Maybe you are transforming raw DWI data? Again, you should not transform raw DWI and recalcuate tensor. You have to first calculate tensor (throw away the raw DWIs) and transform the tensor. ? > ? ? > 1. A subject's data which is acquired // to AC-PC is chosen and other subjects not acquired //to AC are registered to this. Again the meanDWI is used for source and target images, this time using rigid transformation in AIR in Landmarker. However, there is no difference detected after the transformation has taken place. However, if I change the target image from a subject's DWI to the mean DWI of the ICBM 81 template, it works but the source data would be subsampled to that of the ICBM template. I'm not sure why it didn't work in the 1st case?? > ? ? > > As mentioned above, AIR not only adjust the image orientation and translation, but also the matrix / pixel size.. > > Rigid transformation of AIR is sometimes very cranky. We are working on alternative methods now. please try different threshold or affine. ? > ? ? > Additionally, using either another subject or the template DWI as target image, would yield the an output file (AlignlinearOutput.air) when the transformation has been performed, which I saved the invert_AlignlinearOutput.air. However, when I clicked on these .air files in the folder it is saved as an installer package, I get the following error message?"?An error has occurred.The application could not be installed because the AIR file is damaged. Try obtaining a new AIR file from the application author." I have installed the air application and placed it in the same folder, together with the alignlinear.exe file. Is it possible to view the transformation matrix files saved or did I not installed the air application appropriately? > ? ? > > Maybe Xin can answer this question better, but I'm not sure why you want to open *.air?? > > Once you save the *.air, you can load it back to Landmarker and apply to images by using the "open M" button in the LDDMM section. ? > ? ? > 2. ROIs are drawn on the transformed AC-PC aligned?colour maps with ROI-editor.?I would like to check if it's OK to draw rois on the transformed colour map??These ROIs would later be used as the start ROI and stop ROI to extract the corresponding white matter tract with DTI studio)? > ? ? > > Drawing ROIs on color maps is fine. ROI is simply 1/0 information about which pixels you chose and the color maps are simply what is displayed to aid your ROI drawing. > > If you draw ROI in the atlas space and have a plan to back-transform your ROI files to the native space, there are several things you have to know; > 1) Atlas space is 1x1x1 and your native space could be 2-3 mm. The ROI defined in the thin 1 mm slice could be lost after transformation to the thick 2-3mm slice. Therefore, you have to create 3D ROIs in the atlas space with at least 3mm thick > 2) Use nearest neighbor interpolation when you back-transfer. You don't want to get a pixel with 0.3 or 0.4 after transformation. You want 1/0 ? > ? ? > 3. I ?tried to invert-transform these ROIs back to the original DTI space with the previously saved invert_matrix.air file. How is that done in Landmarker and if the previous error message needs to be resolved before I can used the matrix files?? > ? ? > > Xin, how to do the invert-transformation of *.air? ? > ? ? > Susumu ? > ? ? > ? ? > ? ? > ? ? ? ? > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users ? > ? ? ? ? ? ? ? ? ? > ? ? ? ----------------------------------------------------------- ? > This e-mail message (including any attachments) is for the sole use of > the intended recipient(s) and may contain confidential and privileged > information. If the reader of this message is not the intended > recipient, you are hereby notified that any dissemination, distribution > or copying of this message (including any attachments) is strictly > prohibited. > > If you have received this message in error, please contact > the sender by reply e-mail message and destroy all copies of the > original message (including attachments). ? > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users ? > ? ? ? > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090511/d8f34917/attachment-0001.html From fijoy at jhu.edu Mon May 11 19:50:41 2009 From: fijoy at jhu.edu (Fijoy Vadakkumpadan) Date: Mon, 11 May 2009 19:50:41 -0400 Subject: [Mristudio-users] Landmarker LDDMM error Message-ID: Hi all, I am trying to run single channel remote volume LDDMM using the Landmarker 1.4. The Landmarker is installed on a 64-bit Windows Vista virtual machine (VMware Player). In addition to the intensity information, I am using landmarks also for the LDDMM registration. However, I am receiving the following pop-up error message: "Cannot upload this file: d39d65436099132a2a82efb0dfc8810a.zip" Could anyone please help me with resolving this problem? Thank you, Fijoy From wangchuns at 126.com Mon May 11 21:23:28 2009 From: wangchuns at 126.com (wangchuns) Date: Tue, 12 May 2009 09:23:28 +0800 (CST) Subject: [Mristudio-users] Reply: please remove me from mailing list In-Reply-To: <63AC31CBD23078449BC254FB828951AD17706C@GATAMAIL.gatadomain.com.tr> References: <63AC31CBD23078449BC254FB828951AD17706C@GATAMAIL.gatadomain.com.tr> Message-ID: <32204533.675161242091408906.JavaMail.coremail@bj126app70.126.com> please remove me from mailing list -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090512/86fec0f8/attachment.html From wangchuns at qq.com Mon May 11 21:28:08 2009 From: wangchuns at qq.com (=?gbk?B?tLrT6g==?=) Date: Tue, 12 May 2009 09:28:08 +0800 Subject: [Mristudio-users] =?gbk?b?u9i4tDogUmVwbHk6IHBsZWFzZSByZW1vdmUg?= =?gbk?q?me_from_mailing_list?= Message-ID: please remove me from mailing list -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090512/747f2608/attachment.html From poiuy9 at qq.com Mon May 11 21:29:18 2009 From: poiuy9 at qq.com (=?gbk?B?cG9pdXk5?=) Date: Tue, 12 May 2009 09:29:18 +0800 Subject: [Mristudio-users] =?gbk?b?u9i4tDogUmVwbHk6IHBsZWFzZSByZW1vdmUg?= =?gbk?q?me_from_mailing_list?= Message-ID: please remove me from mailing list ????? ????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090512/fad957b1/attachment.html From lvyating198247 at gmail.com Mon May 11 21:28:12 2009 From: lvyating198247 at gmail.com (yating lv) Date: Tue, 12 May 2009 09:28:12 +0800 Subject: [Mristudio-users] please remove me from mailing list Message-ID: <8d3e08d60905111828w261936cal2782e6a24b582096@mail.gmail.com> Please remove me from mailing list Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090512/33cfd8ac/attachment.html From ahn-kj at catholic.ac.kr Tue May 12 00:39:04 2009 From: ahn-kj at catholic.ac.kr (=?EUC-KR?B?vsixucH4?=) Date: Tue, 12 May 2009 13:39:04 +0900 (KST) Subject: [Mristudio-users] Hi. This is Ahn. Message-ID: <4559472.1242103144448.JavaMail.root@mail2> .Bold { font-weight: bold; } .Title { font-weight: bold; font-size: 18px; color: #cc3300; } .Code { border: #8b4513 1px solid; padding-right: 5px; padding-left: 5px;color: #000066; font-family: 'Courier New' , Monospace;background-color: #ff9933; } please remove me from mailing list BODY{FONT-SIZE: 10pt;} DIV, P {FONT-SIZE: 10pt;margin-top:2px;margin-bottom:2px;} TD {FONT-SIZE: 10pt} Ahn, Kook-Jin MD PhD Department of Radiology, College of Medicine, The Catholic University of Korea 505 Kangnam St. Mary's Hospital, Banpo-dong, Seocho-gu, Seoul 137-701 Korea Tel: 82-2-2142-7492 Fax: 82-2-599-6771 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090512/936aa444/attachment.html From zpmatrix at gmail.com Tue May 12 00:44:58 2009 From: zpmatrix at gmail.com (zp zhang) Date: Tue, 12 May 2009 12:44:58 +0800 Subject: [Mristudio-users] pls remove me from the mailing list Message-ID: <4a352ba80905112144r5d277287le0fa57af1f1d6669@mail.gmail.com> Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090512/72e4b74d/attachment.html From darshanp20 at yahoo.com Tue May 12 00:47:10 2009 From: darshanp20 at yahoo.com (darshan pai) Date: Mon, 11 May 2009 21:47:10 -0700 (PDT) Subject: [Mristudio-users] pls remove me from the mailing list In-Reply-To: <4a352ba80905112144r5d277287le0fa57af1f1d6669@mail.gmail.com> References: <4a352ba80905112144r5d277287le0fa57af1f1d6669@mail.gmail.com> Message-ID: <716826.79432.qm@web30704.mail.mud.yahoo.com> Come on guys . The instructions to remove yourself from the list is appended with each email sent through listserv .. Please do it yourself . ________________________________ From: zp zhang To: Mristudio-users at mristudio.org Sent: Tuesday, May 12, 2009 12:44:58 AM Subject: [Mristudio-users] pls remove me from the mailing list Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090511/ad000cec/attachment.html From siewmin.gan at gmail.com Tue May 12 07:40:38 2009 From: siewmin.gan at gmail.com (Siewmin Gan) Date: Tue, 12 May 2009 19:40:38 +0800 Subject: [Mristudio-users] transformations with AIR in Landmarker In-Reply-To: <7k7ed7$7f10r2@ipex3.johnshopkins.edu> References: <7k7ed7$7f10r2@ipex3.johnshopkins.edu> Message-ID: Thanks Susumu and Xin, I'll download the air files and try again. Siewmin On Tue, May 12, 2009 at 2:25 AM, susumu wrote: > For those who are interested in image normalization by Landmarker, here I > attached a step-by-step instruction. > > Siewmin, I could transform your data with the default setup using this > procedure. > > > > Susumu > > > ------------------------------ > > *From:* mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org] *On Behalf Of *Siewmin Gan > *Sent:* Monday, May 11, 2009 12:21 PM > > *To:* DTI Studio, ROI Editor, Landmarker Questions/Support > *Subject:* Re: [Mristudio-users] transformations with AIR in Landmarker > > > > Hi Susumu, I have learnt a lot from your correspondence, as usual. Will try > as you've suggested. > > > > Thanks > > > > Siewmin > > > ------------------------------ > > *From:* mristudio-users-bounces at mristudio.org [ > mristudio-users-bounces at mristudio.org] On Behalf Of susumu [ > susumu at mri.jhu.edu] > *Sent:* Sunday, May 10, 2009 9:39 AM > *To:* 'DTI Studio, ROI Editor, Landmarker Questions/Support' > *Subject:* Re: [Mristudio-users] transformations with AIR in Landmarker > > Siewmin raised some important points and I hope other users could gain some > important information from this thread. > > > > I got the mean DWI and tensor file from the original 4D DWI. The tensor > file is as you've said, which contains "Dxx, Dyy, Dzz, Dxy, Dxz Dyz" in one > file. In Landmarker, I loaded only the mean DWI of the subject and then the > tensor file with the "open .d" button. The 4D raw DWI is not used in > Landmarker or later. With the "linear" option in AIR, I could rotate the > tensor and the mean DWI to the template DWI without having to subsample the > input data first. The "nonlinear" option requires the subject data (mean DWI > and the tensor file) to be of the same dimension as the template (i.e 181, > 217, 181 if ICBM81 DWI is used as template). This is noted in the pop up > message, and it would only continue once the input files are resampled to > the template. > > > > >It is always advised to do linear transformation first. To start > non-linear, you have to make sure that the brain locations and shapes are as > similar as possible. This is similar to non-linear fitting. You always have > to provide ?initial? values close to the real solutions. Otherwise, > non-linear fitting could converge to a wrong solution (trapped by ?local > minima?). > > > > Additionally, I tried affine in the linear registration option. The output > DWI of the registration is identical to the input of the DWIs if I used one > of my subject's DWI as the template. Using the 2nd order polynomial in > nonlinear option, an error message occurs "registration terminated due to a > calculation problem, please try a lower order model". It seems to only work > if the template is one of those provided in Landmarker. > > > > > If you can send us two images you are having the problem, we can take a > look at why AIR doesn?t work. > > > > I then saved the rotated tensor file as one file in the .dat format and the > linearly registered 3D meanDWI. In MRIview3D, I loaded this new 3D DWI and > open this new tensor.dat file with the open.dat button to re-calculates the > fa, colour map etc. I viewed the colour map output from this and it looks > pretty good, and as described previously. > > > > > This is the correct procedure. > > > > I saved the fa and principal eigenvector file and used them to perform > fiber-tracking. The tracts that are manually extracted obtained looks > similiar to the fiber tracts from the original raw 4D DWI. > > > > > That is a good sign. > > > > The FA values of these tracts are smaller uniformly in comparison, and the > assymetry preserved (i.e the left tract FA is smaller than the right tract > FA using the maps calculated from the original and rotated tensor). > > > > > Normalization requires pixel interpolation, which leads to decreased FA. > So you can not compare FA values with and without normalization. > > > > If the non-linear option is used, is there a problem that the tensor is > subsampled first before it is re-oriented, as described above? > > > > > As I mentioned above, nonlinear should be AFTER linear transformation. > This means, the data are transformed multiple times and pixels are > interpolated multiple times. To avoid this, once you did linear (save > transformation matrix: T-linear) and nonlinear (save transformation matrix: > T-nonlinear), you can combine the T-linear x T-nonlinear using one of the > buttons in the LDDMM section. Once you combined all transformation matrices, > you can apply it only once to the original image in the native space. > > > > > Another interesting thing is, there are two ways to transform images; > transform your image to an atlas or transform atlas (usually, binary > segmentation map) to your original data for automated segmentation. For the > latter approach, you don?t have to transform (therefore interpolate) your > original data. When you transform the atlas (segmentation map), make sure to > use ?nearest neighbor? (no interpolation), not the tri-linear interpolation. > The segmentation map consists of arbitrary numbers assigned to each segment > (e.g. the internal capsule is ?1? and the corona radiata is ?3?). If you > interpolate these two segments and obtain ?2? in between these two segments > and if ?2? means pons, you would get the pons in between the internal > capsule and the corona radiata. On the other hand, when you are transforming > your data to an atlas space, use the tri-linear interpolation. Otherwise, > you could get strange discontinuity artifacts. > > > > Do you suggest using the affine or non-linear transformation of the DWIs > and the corresponding transformation of the tensor? Lastly, I'm not sure if > the colour map display is of an issue? It occurs both using the linear > affine option and the non-linear option. > > > > > When everything is working right, the color map should look smooth and > clean. Maybe you are using ?nearest neighbor? for the tensor transformation? > > > > Thanks > > > > Siewmin > > > > > > > > > > On Sat, May 9, 2009 at 7:44 AM, susumu wrote: > > First, I tried rotating the tensor but had problems with the results. When > I look at the colour map from the resulting tensor, it looks ok generally, > but there are certain areas of blotchiness and some mixing of colours > especially in the sidelines of white matter regions (i.e there can be a > striking red line or a blotch of redness in the middle of a green regions > within the saggital stratum). These are the steps I took, and would like to > check if it is done correctly. > > 1. resample mean DWI of subject data (together with the 4D DTI data and the > tensor) to DWI of ICBM 81 template. Non-linear transform (2nd order > trilinear) the resampled meandwi of subject to dwi of template, and used > that to drive the transformation of the resampled 4D DTI and the resampled > tensor simultaneously. (The resampled tensor was loaded with the .dat > button.) I used MRIview 3D to load the normalised 4D DTI, followed by the > normalised tensor with the .dat button, and calculate the fa, colour etc > maps from the normalised tensor. I tried various thresholding with AIR but > the colour maps problem remains. > > > > > First of all, I think you don't have to resample DTI images before AIR. > AIR can take data with different matrix and pixel sizes and the output > images have the same matrix/pixel dimensions as the template (in your case, > 181x217x181 of ICBM81). > > > By saying "4D DTI", do you mean raw 4D DWI before tensor calculation? if > so, I don't think you want transform raw DWIs. If you want to do anything to > raw DTI, you also want to transform the corresponding gradient table, which > could be messy. Our tools do not provide methods to transform raw DWIs. > > > When you say, "tensor" data, I assume you are talking about 4D file that > contains "Dxx, Dyy, Dzz, Dxy, Dxz, Dyz" images in one file. If so, please > make sure that you load this 4D tensor file by the "open .d" button in > Landmarker. Once read in Landmarker, the 4D tensor file is disassembled to 6 > 3D data for Dxx, Dyy, Dzz, Dxy, Dxz, Dyz. > > > Once the AIR is done using mean DWI (your data) - mean DWI (template), > the 6 3D tensor element data should be stored all together into one file as > a "transformed 4D tensor file". > > > This transformed 4D tensor file needs to be read into DtiStudio to > re-calculate new transformed FA, color, vec, etc. > > > The blotch-looking colormap could happen by; 1) transform the color map > directly (you should recreate color maps using the recalcuated FA and vector > files from the transformed tensor file or 2) you transformed a vector file > (transformed vector files should be obtained from the transformed tensor > file. Vector can not be directly transformed). > > > > Second, I tried without rotating the tensor. I calculate the scalar and > colour maps from the original 4D DTI data, aligned the maps to AC-PC line, > draw rois on them and invert transform the rois back to native dti space to > extract the relevant white matter tracts. I had two problems here. 1) with > orienting the subjects scalar DWI to another particular subject's DWI with > rigid transformation in AIR and 2) Invert transform ROIs drawn on the > registered colour map back to the original DTI space. These are the steps I > took: > > > > > Maybe you are transforming raw DWI data? Again, you should not transform > raw DWI and recalcuate tensor. You have to first calculate tensor (throw > away the raw DWIs) and transform the tensor. > > > > 1. A subject's data which is acquired // to AC-PC is chosen and other > subjects not acquired //to AC are registered to this. Again the meanDWI is > used for source and target images, this time using rigid transformation in > AIR in Landmarker. However, there is no difference detected after the > transformation has taken place. However, if I change the target image from a > subject's DWI to the mean DWI of the ICBM 81 template, it works but the > source data would be subsampled to that of the ICBM template. I'm not sure > why it didn't work in the 1st case? > > > > > As mentioned above, AIR not only adjust the image orientation and > translation, but also the matrix / pixel size.. > > > Rigid transformation of AIR is sometimes very cranky. We are working on > alternative methods now. please try different threshold or affine. > > > > Additionally, using either another subject or the template DWI as target > image, would yield the an output file (AlignlinearOutput.air) when the > transformation has been performed, which I saved the > invert_AlignlinearOutput.air. However, when I clicked on these .air files in > the folder it is saved as an installer package, I get the following error > message " An error has occurred.The application could not be installed > because the AIR file is damaged. Try obtaining a new AIR file from the > application author." I have installed the air application and placed it in > the same folder, together with the alignlinear.exe file. Is it possible to > view the transformation matrix files saved or did I not installed the air > application appropriately? > > > > > Maybe Xin can answer this question better, but I'm not sure why you want > to open *.air?? > > > Once you save the *.air, you can load it back to Landmarker and apply to > images by using the "open M" button in the LDDMM section. > > > > 2. ROIs are drawn on the transformed AC-PC aligned colour maps with > ROI-editor. I would like to check if it's OK to draw rois on the transformed > colour map? These ROIs would later be used as the start ROI and stop ROI to > extract the corresponding white matter tract with DTI studio) > > > > > Drawing ROIs on color maps is fine. ROI is simply 1/0 information about > which pixels you chose and the color maps are simply what is displayed to > aid your ROI drawing. > > > If you draw ROI in the atlas space and have a plan to back-transform your > ROI files to the native space, there are several things you have to know; > > 1) Atlas space is 1x1x1 and your native space could be 2-3 mm. The ROI > defined in the thin 1 mm slice could be lost after transformation to the > thick 2-3mm slice. Therefore, you have to create 3D ROIs in the atlas space > with at least 3mm thick > > 2) Use nearest neighbor interpolation when you back-transfer. You don't > want to get a pixel with 0.3 or 0.4 after transformation. You want 1/0 > > > > 3. I tried to invert-transform these ROIs back to the original DTI space > with the previously saved invert_matrix.air file. How is that done in > Landmarker and if the previous error message needs to be resolved before I > can used the matrix files? > > > > > Xin, how to do the invert-transformation of *.air? > > > > Susumu > > > > > > > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > > > ------------------------------ > > This e-mail message (including any attachments) is for the sole use of > the intended recipient(s) and may contain confidential and privileged > information. If the reader of this message is not the intended > recipient, you are hereby notified that any dissemination, distribution > or copying of this message (including any attachments) is strictly > prohibited. > > If you have received this message in error, please contact > the sender by reply e-mail message and destroy all copies of the > original message (including attachments). > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090512/5c287725/attachment-0001.html From herrera.diego at gmail.com Tue May 12 08:39:49 2009 From: herrera.diego at gmail.com (Diego Herrera) Date: Tue, 12 May 2009 07:39:49 -0500 Subject: [Mristudio-users] transformations with AIR in Landmarker In-Reply-To: References: <7k7ed7$7f10r2@ipex3.johnshopkins.edu> Message-ID: please remove me from mailing list -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090512/dd3c29d2/attachment.html From carly at ualberta.ca Tue May 12 09:01:26 2009 From: carly at ualberta.ca (carly at ualberta.ca) Date: Tue, 12 May 2009 07:01:26 -0600 Subject: [Mristudio-users] pls remove me from the mailing list In-Reply-To: <4a352ba80905112144r5d277287le0fa57af1f1d6669@mail.gmail.com> References: <4a352ba80905112144r5d277287le0fa57af1f1d6669@mail.gmail.com> Message-ID: <20090512070126.98401tn6o7gi2gqs@webmail.ualberta.ca> > Thank you From menglu1982 at gmail.com Tue May 12 09:31:53 2009 From: menglu1982 at gmail.com (lu meng) Date: Tue, 12 May 2009 09:31:53 -0400 Subject: [Mristudio-users] Remove me from list,plz Message-ID: please remove me from mailing list _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090512/991117f1/attachment.html From mohitindelhi at yahoo.com Tue May 12 09:50:44 2009 From: mohitindelhi at yahoo.com (mohit saxena) Date: Tue, 12 May 2009 19:20:44 +0530 (IST) Subject: [Mristudio-users] please remove me from mailing list Message-ID: <594980.70929.qm@web95210.mail.in2.yahoo.com> Mohit Saxena Ph.D Student Department of Neurology All India Institute of Medical sciences Asari Nagar New Delhi India +919968569874 Now surf faster and smarter ! Check out the new Firefox 3 - Yahoo! Edition http://downloads.yahoo.com/in/firefox/?fr=om_email_firefox -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090512/694731eb/attachment.html From benoburt at gmail.com Tue May 12 10:56:38 2009 From: benoburt at gmail.com (benoburt at gmail.com) Date: Tue, 12 May 2009 14:56:38 +0000 Subject: [Mristudio-users] Pls remove me from list Message-ID: <1323957827-1242136627-cardhu_decombobulator_blackberry.rim.net-1396668963-@bxe1229.bisx.prod.on.blackberry> Sent via BlackBerry from T-Mobile From xli16 at jhmi.edu Tue May 12 10:41:27 2009 From: xli16 at jhmi.edu (Xin Li) Date: Tue, 12 May 2009 10:41:27 -0400 Subject: [Mristudio-users] Landmarker LDDMM error In-Reply-To: References: Message-ID: Fijoy, Please test if your computer can access our ftp server. In Command Prompt Window, please try the ftp program. It should look like: C:\Documents and Setting\Administrator>ftp ftp.mristudio.org Connected to ftp.mristudio.org. 220 Welcome to MRI STudio FTP service. -- Turn off Passive Mode. User (ftp.mristudio.org:(none)): anonymous 331 Please specify the password. Password: 230 Login successful. ftp> dir Please let me the test result. Xin ----- Original Message ----- From: Fijoy Vadakkumpadan Date: Monday, May 11, 2009 7:50 pm Subject: [Mristudio-users] Landmarker LDDMM error To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > Hi all, > > I am trying to run single channel remote volume LDDMM using the > Landmarker 1.4. The Landmarker is installed on a 64-bit Windows Vista > virtual machine (VMware Player). In addition to the intensity > information, I am using landmarks also for the LDDMM registration. > However, I am receiving the following pop-up error message: > > "Cannot upload this file: d39d65436099132a2a82efb0dfc8810a.zip" > > Could anyone please help me with resolving this problem? > > Thank you, > Fijoy > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > From n.langer at psychologie.uzh.ch Tue May 12 11:03:33 2009 From: n.langer at psychologie.uzh.ch (Nicki Langer) Date: Tue, 12 May 2009 17:03:33 +0200 Subject: [Mristudio-users] please remove me from mailing list In-Reply-To: <63AC31CBD23078449BC254FB828951AD17706C@GATAMAIL.gatadomain.com.tr> References: <63AC31CBD23078449BC254FB828951AD17706C@GATAMAIL.gatadomain.com.tr> Message-ID: <4A098FC5.9090800@psychologie.uzh.ch> Please remove me from the mailing list. Thanks -- Nicolas Langer MSc. UZH (lic. phil.) Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, 8050 Zurich, Switzerland 0041 44 635 73 96 (phone office) 0041 76 422 46 45 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) n.langer[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) From alandarkenergy at gmail.com Tue May 12 11:19:24 2009 From: alandarkenergy at gmail.com (Alan Francis) Date: Tue, 12 May 2009 11:19:24 -0400 Subject: [Mristudio-users] please remove me from mailing list In-Reply-To: <4A098FC5.9090800@psychologie.uzh.ch> References: <63AC31CBD23078449BC254FB828951AD17706C@GATAMAIL.gatadomain.com.tr> <4A098FC5.9090800@psychologie.uzh.ch> Message-ID: Dear Susumu: Please remove me from the mailing list. Thanks Alan Francis PhD Harvard Med School On 5/12/09, Nicki Langer wrote: > > Please remove me from the mailing list. Thanks > > -- > > Nicolas Langer > > MSc. UZH (lic. phil.) > > Division Neuropsychology > > Institute of Psychology > > University of Zurich > > Binzmuehlestrasse 14, > > 8050 Zurich, Switzerland > > 0041 44 635 73 96 (phone office) > > 0041 76 422 46 45 (phone mobile) > > 0041 44 635 74 09 (fax office) > > BIN 4.D.04 (office room number) > > n.langer[at]psychologie.uzh.ch (email) > > http://www.psychologie.uzh.ch/neuropsy/ (website) > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090512/f1dfa1cb/attachment.html From wangxyz007 at hotmail.com Tue May 12 11:49:29 2009 From: wangxyz007 at hotmail.com (wangxiaoyu) Date: Tue, 12 May 2009 23:49:29 +0800 Subject: [Mristudio-users] please remove me from the mailing list In-Reply-To: <716826.79432.qm@web30704.mail.mud.yahoo.com> References: <4a352ba80905112144r5d277287le0fa57af1f1d6669@mail.gmail.com> <716826.79432.qm@web30704.mail.mud.yahoo.com> Message-ID: Thanks ? _________________________________________________________________ MSN ??????????????? http://im.live.cn/emoticons/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090512/c892f202/attachment-0001.html From darshanp20 at yahoo.com Tue May 12 12:14:32 2009 From: darshanp20 at yahoo.com (darshan pai) Date: Tue, 12 May 2009 09:14:32 -0700 (PDT) Subject: [Mristudio-users] Since noone reads email I put as subject. Instruction to unsubscribe is added to every email sent thru list serv!!!!! In-Reply-To: References: <63AC31CBD23078449BC254FB828951AD17706C@GATAMAIL.gatadomain.com.tr> <4A098FC5.9090800@psychologie.uzh.ch> Message-ID: <313059.84117.qm@web30708.mail.mud.yahoo.com> ________________________________ From: Alan Francis To: "DTI Studio, ROI Editor, Landmarker Questions/Support" Sent: Tuesday, May 12, 2009 11:19:24 AM Subject: Re: [Mristudio-users] please remove me from mailing list Dear Susumu: Please remove me from the mailing list. Thanks Alan Francis PhD Harvard Med School On 5/12/09, Nicki Langer wrote: Please remove me from the mailing list. Thanks -- Nicolas Langer MSc. UZH (lic. phil.) Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, 8050 Zurich, Switzerland 0041 44 635 73 96 (phone office) 0041 76 422 46 45 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) n.langer[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090512/fdffeb03/attachment.html From choisj70 at gmail.com Tue May 12 12:30:16 2009 From: choisj70 at gmail.com (Seongjin) Date: Tue, 12 May 2009 12:30:16 -0400 Subject: [Mristudio-users] save and read fiber in Amira format In-Reply-To: <2593DC540EEE4FF49F04CAB92AAC2023@panpan> References: <7k7ed7$7f10r2@ipex3.johnshopkins.edu> <2593DC540EEE4FF49F04CAB92AAC2023@panpan> Message-ID: Dear users using Amira, Is there any other way to see Amira format without purchase of Amira SW? For example, free viewer for Amira formatted file. Thanks in advance. -SC On Mon, May 11, 2009 at 4:52 PM, Yi Jiang wrote: > Hello, dear all, > > I tried to select multiple fiber tracts in multiple colors (say, the final > selected fibers are from 20 ROIs and in 8 colors). I saved the "selected > fibers" in amira format. I tried to load the fiber file in Amira. It was > loaded in with no complaint. I then displayed the fibers as lineSetView in > Amira. But all the lines displayed with the same color, instead of the 8 > colors I would hope. > > My questions are: are the fiber color (labels or indices) saved in the > amira format? If yes, how can I display them in different colors as in > DTIstudio? > > Thank you very much! > > Best, > Yi > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090512/35394e87/attachment.html From okyuan2008 at gmail.com Tue May 12 12:33:59 2009 From: okyuan2008 at gmail.com (Kai Yuan) Date: Wed, 13 May 2009 00:33:59 +0800 Subject: [Mristudio-users] Please remove me from this maillist Message-ID: Thanks. -- Best wishes. Kai Yuan, Life Science Research Center, School of Electronic Engineering P.O.Box 97,Xidian University No.2 TaiBai South Rd, Xi'an Shaanxi 710071, China Tel: 86 029 88201842 Fax: 86 029 88201842 Email: kyuan at fingerpass.net.cn yuankai at life.xidian.edu.cn okyuan2008 at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090513/e058784f/attachment.html From susumu at mri.jhu.edu Tue May 12 13:01:14 2009 From: susumu at mri.jhu.edu (susumu) Date: Tue, 12 May 2009 13:01:14 -0400 Subject: [Mristudio-users] how to unsubscribe In-Reply-To: Message-ID: <7k7ed7$7fiq2r@ipex3.johnshopkins.edu> Hi all, Due to recent increase in the volume of activities in the Mailing List, there were a series of unsubscribe requests. If you want to unsubscribe, please do one of the following steps rather than mailing the request to all subscribing users; 1) Go to http://lists.mristudio.org/mailman/listinfo/mristudio-users. At the bottom of the page, there is a section for unsubscribe. 2) If, for some reason, you could not unsubscribe, please send an email to xin_xu at mri.jhu.edu and request unsubscribe. We are currently testing a forum. I hope this will reduce the volume of mailing related to MriStudio. Once it's ready, I'll circulate the notice. Thanks, Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Kai Yuan Sent: Tuesday, May 12, 2009 12:34 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] Please remove me from this maillist Thanks. -- Best wishes. Kai Yuan, Life Science Research Center, School of Electronic Engineering P.O.Box 97,Xidian University No.2 TaiBai South Rd, Xi'an Shaanxi 710071, China Tel: 86 029 88201842 Fax: 86 029 88201842 Email: kyuan at fingerpass.net.cn yuankai at life.xidian.edu.cn okyuan2008 at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090512/e5ff7b52/attachment.html From irit.weissmanfogel at uhnresearch.ca Tue May 12 13:33:44 2009 From: irit.weissmanfogel at uhnresearch.ca (Irit Weissman-Fogel) Date: Tue, 12 May 2009 13:33:44 -0400 Subject: [Mristudio-users] Please remove me from mailing list Message-ID: <4A09B2F8.6030202@uhnresearch.ca> Dear Susumu: Please remove me from the mailing list. Thanks, Irit Weissman Fogel PhD Toronto Western Research Institute From susumu at mri.jhu.edu Tue May 12 17:10:10 2009 From: susumu at mri.jhu.edu (susumu) Date: Tue, 12 May 2009 17:10:10 -0400 Subject: [Mristudio-users] save and read fiber in Amira format In-Reply-To: Message-ID: <7k7ed7$7fmd31@ipex3.johnshopkins.edu> You can try our 3D viewer. It has only limited functions but it works. You can get it from Kegang Hua. Xin, is it possible to post this handy 3D visualization software in the MriStudio.org website? _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of [Seongjin] Sent: Tuesday, May 12, 2009 12:30 PM To: Yi Jiang; DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] save and read fiber in Amira format Dear users using Amira, Is there any other way to see Amira format without purchase of Amira SW? For example, free viewer for Amira formatted file. Thanks in advance. -SC On Mon, May 11, 2009 at 4:52 PM, Yi Jiang wrote: Hello, dear all, I tried to select multiple fiber tracts in multiple colors (say, the final selected fibers are from 20 ROIs and in 8 colors). I saved the "selected fibers" in amira format. I tried to load the fiber file in Amira. It was loaded in with no complaint. I then displayed the fibers as lineSetView in Amira. But all the lines displayed with the same color, instead of the 8 colors I would hope. My questions are: are the fiber color (labels or indices) saved in the amira format? If yes, how can I display them in different colors as in DTIstudio? Thank you very much! Best, Yi _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090512/1f6e6dc6/attachment.html From yj3 at duke.edu Tue May 12 17:53:58 2009 From: yj3 at duke.edu (Yi Jiang) Date: Tue, 12 May 2009 17:53:58 -0400 Subject: [Mristudio-users] save and read fiber in Amira format References: <7k7ed7$7fmd31@ipex3.johnshopkins.edu> Message-ID: <831497880E484D7990FCF2C16132CD74@panpan> Thank you very much. How can I contact Kegang Hua to get 3DViewer? Thank you! Yi ----- Original Message ----- From: susumu To: 'DTI Studio, ROI Editor, Landmarker Questions/Support' Sent: Tuesday, May 12, 2009 5:10 PM Subject: Re: [Mristudio-users] save and read fiber in Amira format You can try our 3D viewer. It has only limited functions but it works. You can get it from Kegang Hua. Xin, is it possible to post this handy 3D visualization software in the MriStudio.org website? ------------------------------------------------------------------------------ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of [Seongjin] Sent: Tuesday, May 12, 2009 12:30 PM To: Yi Jiang; DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] save and read fiber in Amira format Dear users using Amira, Is there any other way to see Amira format without purchase of Amira SW? For example, free viewer for Amira formatted file. Thanks in advance. -SC On Mon, May 11, 2009 at 4:52 PM, Yi Jiang wrote: Hello, dear all, I tried to select multiple fiber tracts in multiple colors (say, the final selected fibers are from 20 ROIs and in 8 colors). I saved the "selected fibers" in amira format. I tried to load the fiber file in Amira. It was loaded in with no complaint. I then displayed the fibers as lineSetView in Amira. But all the lines displayed with the same color, instead of the 8 colors I would hope. My questions are: are the fiber color (labels or indices) saved in the amira format? If yes, how can I display them in different colors as in DTIstudio? Thank you very much! Best, Yi _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users ------------------------------------------------------------------------------ _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090512/845f0804/attachment.html From susumu at mri.jhu.edu Tue May 12 18:10:50 2009 From: susumu at mri.jhu.edu (susumu) Date: Tue, 12 May 2009 18:10:50 -0400 Subject: [Mristudio-users] Landmarker LDDMM error In-Reply-To: Message-ID: <7k7ed7$7fn0ps@ipex3.johnshopkins.edu> Hi Xin and Anthony, This should get some attention of yours. If I'm not mistaken, this is often caused by user's fire wall? Susumu -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Fijoy Vadakkumpadan Sent: Monday, May 11, 2009 7:51 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] Landmarker LDDMM error Hi all, I am trying to run single channel remote volume LDDMM using the Landmarker 1.4. The Landmarker is installed on a 64-bit Windows Vista virtual machine (VMware Player). In addition to the intensity information, I am using landmarks also for the LDDMM registration. However, I am receiving the following pop-up error message: "Cannot upload this file: d39d65436099132a2a82efb0dfc8810a.zip" Could anyone please help me with resolving this problem? Thank you, Fijoy _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From susumu at mri.jhu.edu Tue May 12 18:20:14 2009 From: susumu at mri.jhu.edu (susumu) Date: Tue, 12 May 2009 18:20:14 -0400 Subject: [Mristudio-users] save and read fiber in Amira format In-Reply-To: <2593DC540EEE4FF49F04CAB92AAC2023@panpan> Message-ID: <7k7ed7$7fn3di@ipex3.johnshopkins.edu> You can't pass the color information from DtiStudio to Amira, unfortunately. You have to use the color function of Amira to paint the fibers in different colors. _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Yi Jiang Sent: Monday, May 11, 2009 4:53 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] save and read fiber in Amira format Hello, dear all, I tried to select multiple fiber tracts in multiple colors (say, the final selected fibers are from 20 ROIs and in 8 colors). I saved the "selected fibers" in amira format. I tried to load the fiber file in Amira. It was loaded in with no complaint. I then displayed the fibers as lineSetView in Amira. But all the lines displayed with the same color, instead of the 8 colors I would hope. My questions are: are the fiber color (labels or indices) saved in the amira format? If yes, how can I display them in different colors as in DTIstudio? Thank you very much! Best, Yi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090512/2ddcd4e1/attachment-0001.html From susumu at mri.jhu.edu Tue May 12 19:01:40 2009 From: susumu at mri.jhu.edu (susumu) Date: Tue, 12 May 2009 19:01:40 -0400 Subject: [Mristudio-users] Image formats In-Reply-To: <445679.54336.qm@web32807.mail.mud.yahoo.com> Message-ID: <7k7ed7$7fnhc4@ipex3.johnshopkins.edu> Hi Shawn, 1) Why you don't read the Siemens DICOM directly to DtiStudio? 2) There is one thing you want to know when you are processing Siemens data. When you are using a) oblique slices AND b) your operating system is older than the latest one, then you have to re-calculate your gradient table based on the oblique angle. This can be done by simply clicking the "rotate gradient table if applicable" in the data parameter window in the beginning. However, this works only when you are using DICOM. Once you convert it to Analyze or Raw, the oblique information is removed and you can't use this function. 3) If you get that message, that mean your image file size is not; file size = X resolution x Y resolution x the number of slices x the number of orientation + the number of b0. You can read you DICOM and click the "hummer and scissors" button to check X resolution, Y resolution, and the number of slices. You can also check the pull-down menu to find how many 3D images are loaded. The number of 3D images has to match your gradient table. In your case, 26 direction + 1 b0 should be 27 3D images. Use "MriView3D" to read the DICOM or Analyze and check all the dimensions and the number of 3D images. _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Shawn Newlander Sent: Thursday, May 07, 2009 4:38 PM To: Mristudio-users at mristudio.org Subject: [Mristudio-users] Image formats I have images in Siemens dicom mosaic format , which I saved in analyze format in DTI studios to do the brain extraction. In order to do DTI mapping, I tried to import the raw images; however, I am getting this error: "Number of files in this folder is less than expected (Img_Slices*Img_Blocks)" I have 35 slices for 26 gradient directions. Is there a way to import this images without having to break apart each volume? Shawn smnewlander at yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090512/8610306f/attachment.html From sbh1010 at chonbuk.ac.kr Tue May 12 22:52:27 2009 From: sbh1010 at chonbuk.ac.kr (=?EUC-KR?B?IsiyvcK56CI=?=) Date: Wed, 13 May 2009 11:52:27 +0900 Subject: [Mristudio-users] =?euc-kr?q?Please_remove_me_from_the_mailing_li?= =?euc-kr?q?st?= Message-ID: <1242183147300246.755680268@mail.chonbuk.ac.kr> Please remove me from the mailing list !! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090513/3fb155b2/attachment.html From ltao97 at 163.com Tue May 12 23:15:23 2009 From: ltao97 at 163.com (ltao97) Date: Wed, 13 May 2009 11:15:23 +0800 (CST) Subject: [Mristudio-users] please remove me from mailing list Message-ID: <14705304.157271242184523545.JavaMail.coremail@app142.163.com> please remove me from mailing list thanks If possible? you can add the e-mail which is ltao97 at 126.com to the mailing list! Thank you! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090513/80e9cdc2/attachment.html From siewmin.gan at gmail.com Wed May 13 07:16:19 2009 From: siewmin.gan at gmail.com (Siewmin Gan) Date: Wed, 13 May 2009 19:16:19 +0800 Subject: [Mristudio-users] datatype Message-ID: Hi, I have a 4D DWI of float 32 datatype in Analyze format. Currently, I have to convert it to integer 16 for DTI mapping to read it and calculate the tensor and other maps. There may be some data loss during the conversion of datatype. Is there any way I can input the float 32 file into DTI mapping to perform this function? Thanks Siewmin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090513/88247a94/attachment.html From xin_xu at mri.jhu.edu Wed May 13 09:50:17 2009 From: xin_xu at mri.jhu.edu (Xin Xu) Date: Wed, 13 May 2009 09:50:17 -0400 Subject: [Mristudio-users] save and read fiber in Amira format In-Reply-To: <831497880E484D7990FCF2C16132CD74@panpan> Message-ID: <8EB377A29F4B4F0B93383C27791FC512@HMRI12> Hi Yi, The email of Kegang Hua is khua1 at jhu.edu . Thanks, Xin -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Yi Jiang Sent: Tuesday, May 12, 2009 5:54 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] save and read fiber in Amira format Thank you very much. How can I contact Kegang Hua to get 3DViewer? Thank you! Yi ----- Original Message ----- From: susumu To: 'DTI Studio, ROI Editor, Landmarker Questions/Support' Sent: Tuesday, May 12, 2009 5:10 PM Subject: Re: [Mristudio-users] save and read fiber in Amira format You can try our 3D viewer. It has only limited functions but it works. You can get it from Kegang Hua. Xin, is it possible to post this handy 3D visualization software in the MriStudio.org website? _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of [Seongjin] Sent: Tuesday, May 12, 2009 12:30 PM To: Yi Jiang; DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] save and read fiber in Amira format Dear users using Amira, Is there any other way to see Amira format without purchase of Amira SW? For example, free viewer for Amira formatted file. Thanks in advance. -SC On Mon, May 11, 2009 at 4:52 PM, Yi Jiang wrote: Hello, dear all, I tried to select multiple fiber tracts in multiple colors (say, the final selected fibers are from 20 ROIs and in 8 colors). I saved the "selected fibers" in amira format. I tried to load the fiber file in Amira. It was loaded in with no complaint. I then displayed the fibers as lineSetView in Amira. But all the lines displayed with the same color, instead of the 8 colors I would hope. My questions are: are the fiber color (labels or indices) saved in the amira format? If yes, how can I display them in different colors as in DTIstudio? Thank you very much! Best, Yi _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users _____ _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090513/09f04e6e/attachment-0001.html From sitaram.ranganatha at uni-tuebingen.de Wed May 13 10:05:31 2009 From: sitaram.ranganatha at uni-tuebingen.de (Sitaram Ranganatha) Date: Wed, 13 May 2009 16:05:31 +0200 Subject: [Mristudio-users] PLEASE REMOVE ME FROM THIS LIST ASAP. THANKS. Message-ID: <20090513160531.69511iuftqg3c14b@webmail.uni-tuebingen.de> From dea.dundara at ts.infn.it Wed May 13 11:32:11 2009 From: dea.dundara at ts.infn.it (dea.dundara at ts.infn.it) Date: Wed, 13 May 2009 17:32:11 +0200 (CEST) Subject: [Mristudio-users] minimum fiber length Message-ID: <2325.140.105.7.137.1242228731.squirrel@webmail.ts.infn.it> Hi all! On the article of Jiang at all, 2006(DtiStudio:Resource program for diffusion tensor computation and fiber bundle tracking) is written that there is a minimum fiber length testing that is performed on the fiber chain to remove tracts shorter than a user-defined threshold. But I haven't seen where the user have to specify this value. Can someone explain me this thing? Using my DTI sequences always happens that the minimum length is 7 pixels. Why? Thanks Dea Dundara From choisj70 at gmail.com Wed May 13 11:33:44 2009 From: choisj70 at gmail.com (Seongjin) Date: Wed, 13 May 2009 11:33:44 -0400 Subject: [Mristudio-users] Image algebra on DTI Studio Message-ID: I would like to some image algebra on registered imaged using AIR included in DTI Studio. I wonder if we can do image algebra on DTI Studio without exporting data from DTI studio to other tool, e.g. IDL or MatLab. -SC -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090513/19366ba4/attachment.html From james.neeley at duke.edu Wed May 13 14:26:57 2009 From: james.neeley at duke.edu (Jim Neeley) Date: Wed, 13 May 2009 14:26:57 -0400 Subject: [Mristudio-users] how to unsubscribe In-Reply-To: <7k7ed7$7fiq2r@ipex3.johnshopkins.edu> References: <7k7ed7$7fiq2r@ipex3.johnshopkins.edu> Message-ID: An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090513/3ddbde02/attachment.html From noreply at ci.faniq.com Thu May 14 06:48:53 2009 From: noreply at ci.faniq.com (Jameen ARM) Date: Thu, 14 May 2009 06:48:53 -0400 (EDT) Subject: [Mristudio-users] Jameen A has sent you a private message Message-ID: <0KJM005X2RDHTX00@jhuin3.jhu.edu> An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090514/6911f621/attachment.html From xli16 at jhmi.edu Thu May 14 10:41:04 2009 From: xli16 at jhmi.edu (Xin Li) Date: Thu, 14 May 2009 10:41:04 -0400 Subject: [Mristudio-users] [developers] Landmarker -Transformation matrix -normalization issues In-Reply-To: <2802e1eb0806181316t63adb2a3hbe64cc61f08025cc@mail.gmail.com> References: <2802e1eb0806141311x7dd0020cp2492e6ac7fcdfeb3@mail.gmail.com> <2802e1eb0806181316t63adb2a3hbe64cc61f08025cc@mail.gmail.com> Message-ID: Tilak, Landmarker is a user-interacted software. If you want to do the batch work of AIR transformation, you can run AIR applications in the command prompt window. Please check the website of AIR http://bishopw.loni.ucla.edu/AIR5/programs.html. Xin ----- Original Message ----- From: ramtilak gattu Date: Thursday, May 14, 2009 7:52 am Subject: Re: [developers] Landmarker -Transformation matrix -normalization issues To: mristudio-users at mristudio.org, susumu , developers at mristudio.org Cc: "Benson, Randall" > Hello mristudio Users, > > I have two questions regarding Normalization using Landmarker > > 1) I normalized one subject' FA brain to the Icbm Mni space FA template > using Landmarker using linear algorithm. The issue is - I am trying > to use > the transformation matrix (Alignlinearoutput.air) file to batch up "n" > number of subjects at a time to save time and to avoid some tedious > work in > loading up all the images and doing them individually. The output > image is > very very bad and it doesn't show up clearly while normalizing using > this > transformation matrix ( with a single subject or 'n' subjects). My question > is ' Am I missing some step' to get a proper result? > In simple words , We have 50 brains which are in our template > space. We > would like to apply the same transformation matrix to all 50 brains > to get > them into your template space so we can do the regional analysis. We > have > found that all we need is a simple linear normalization to get there. > So > how to apply the Alignlinearoutput.air transform to all 50 brains. > > 2) I even tried loading up "n" images and tried linear normalization > it > gives updated images-"n".img but some look good some look translated > and > some look rotated. Doesn't landmarker normalize ' n' images at a time > as SPM > does? > > One last question, Couple of weeks back I loaded up one FA image > for non > linear processing using the option of remote processing in > Landmarker. I > still didnt get any reply from the remote site, normally how long > does it > take for us to see the results (retrieve the results)? FYI , My user > name is > ao3080 at wayne.edu. > > Thanks for your time and help. > > Regards > Tilak > > On Sat, Jun 14, 2008 at 4:11 PM, ramtilak gattu > wrote: > > > Hello Dr Susumu Mori, > > > > I have two questions regarding Normalization using Landmarker > > 1) I normalized one subject' FA brain to the Icbm Mni space FA template > > using Landmarker using linear algorithm. The issue is - I am trying > to use > > the transformation matrix (AIRlinearoutput.air) file to batch up > "n" number > > of subjects at a time to save time and to avoid some tedious work > in loading > > up all the images and doing them individually. The output image is > very very > > bad and it doesn't show up clearly while normalizing using this > > transformation matrix ( with a single subject or 'n' subjects). My > question > > is ' Am I missing some step' to get a proper result? > > > > 2) I even tried loading up "n" images and tried linear > normalization it > > gives updated images-"n".img but some look good some look > translated and > > some look rotated. Doesn't landmarker normalize ' n' images at a > time as SPM > > does? > > > > One last question, Couple of weeks back I loaded up one FA image > for non > > linear processing using the option of remote processing in > Landmarker. I > > still didnt get any reply from the remote site, normally how long > does it > > take for us to see the results (retrieve the results)? FYI , My > user name is > > ao3080 at wayne.edu. > > > > Thanks for your time and help. > > > > Regards > > Tilak > > -- > > Ramtilak Gattu > > 21530 Green Hill Rd > > #127 > > Farmington Hills > > Michigan-48335 > > ph: 313-887-1766 > > 313-820-8862 > > 313-745-1388 > > > > > > -- > Ramtilak Gattu > 21530 Green Hill Rd > #127 > Farmington Hills > Michigan-48335 > ph: 313-887-1766 > 313-820-8862 > 313-745-1388 > _______________________________________________ > Developers mailing list > Developers at mristudio.org > > Unsubscribe, send a blank email to: > Developers-unsubscribe at mristudio.org developers From fijoy at jhu.edu Thu May 14 13:09:17 2009 From: fijoy at jhu.edu (Fijoy Vadakkumpadan) Date: Thu, 14 May 2009 13:09:17 -0400 Subject: [Mristudio-users] Landmarker resampling Message-ID: Hi all, I am planning to use Landmarker 1.5 to resample tensor images. What method does the Landmarker use to resample tensor images? Is it Log-Euclidian? Thank you. Fijoy From susumu at mri.jhu.edu Thu May 14 15:33:33 2009 From: susumu at mri.jhu.edu (susumu) Date: Thu, 14 May 2009 15:33:33 -0400 Subject: [Mristudio-users] overlaying analyze anatomical and fiber tract data in DTI studio In-Reply-To: <8874e3900905071226v46585229g20cb9454f2e270f3@mail.gmail.com> Message-ID: <7k7ed7$7gh5nc@ipex3.johnshopkins.edu> Hi Paul, I'm not sure if I understood your question correctly, but let me try. There are two types of file formats to save tracking results; one is streamline and the other is binary image. The streamline contains the most information. You can superimpose on images and edit (add more ROIs to choose a part of it) them using DtiStudio. The downside of the streamline information is that now we don't provide a way to transform the coordinate such as reorientation. You need to do fiber tracking again after you reorient your tensor. The binary image contain 1/0 information; pixels with "1" contain the tract. This contains less information (some information is degenerated) because you don't know which pixels are connected to which pixels. This you can consider as a binary mask. This one can be easily transformed, just like an image. To superimpose the transformed fiber coordinates, you can use RoiEditor. For example, you can load transformed (and coregistered) FA map to RoiEditor and also the transformed binary map. Make sure that the 1/0 binary map was transformed by nearest neighbor (1/0 is preserved and you don't get pixels with "0.5"). Then you can define pixels with "1" using a threshold tool and register these pixels as an Object. Then change the active image from the binary map to the FA map. You can see the outline for Object is superimposed on the FA map. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Paul Beach Sent: Thursday, May 07, 2009 3:26 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] overlaying analyze anatomical and fiber tract data in DTI studio To Whom It May Concern: We were hoping for some input regarding viewing Fiber tracts and DTI images concurrently. Due to limitations in our data, we have been forced to reorient our DTI images and our Fiber tracks accordingly using the Landmarker program. Unfortunately we have not been able to decipher a way to view these two images overlayed simultaneously which is needed as part of our delimitation methods. We previously have done this by saving our Fiber ROI's, then placing them on a DTI (through DTIstudio) when needed. Since this step is not a part of the reorientation process we do not have this data to use. Essentially we are limited to trying to work with ANALYZE files and were wondering if DTIstudio or its sister programs had the ability to load these in to be viewed simultaneously. The work we're currently attempting to do is to list certain boundaries based on anatomical and select fiber tract data (for example the coronal boundary of the crura/fornical junction) and this requires having the fiber tract data mapped onto the anatomical DTIs. Thanks, Paul -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090514/d413922e/attachment-0001.html From jeongwon at pet.wayne.edu Thu May 14 15:36:13 2009 From: jeongwon at pet.wayne.edu (Jeong-Won Jeong) Date: Thu, 14 May 2009 15:36:13 -0400 Subject: [Mristudio-users] Display binary ROI map Message-ID: <005f01c9d4cb$41731340$c45939c0$@wayne.edu> Hello, I have a set of ROI binary map for fiber selection (i.e., ROIMap.dat and RoiMap_01.dat) and could filter the fibers in the "fiber" tab. Anybody knows how to overlap the ROI region with filtered tracts? When I load the map in the "ROI" tab (i.e. ROI-Files), following message's coming up. "unrecognized image-ROI data file". Thank you, Jeong-Won -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090514/efadaa9b/attachment.html From rajagov2 at ccf.org Thu May 14 15:49:40 2009 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Thu, 14 May 2009 15:49:40 -0400 Subject: [Mristudio-users] motion ocrrection of DTI gradient table Message-ID: <77A88E90A851594AAEF830450587C39D01EDAA4F@CCHSCLEXMB56.cc.ad.cchs.net> Dear MRI studio Users, I recently came across the following article "DTI Fiber Tracking: The Importance of Adjusting DTI Gradient Tables for Motion Correction. CATNAP - A Tool to Simplify and Accelerate DTI Analysis". The results in this paper suggested the need for motion correction of gradient tables. I am wondering do i need to carry out this preprocessing step of motion correction of gradient table in CATNAP before supplying the gradient table values in DTI studio for calculation of DTI metrics and tractography or the recent versions of DTI studio takes care of this problem. This being a short article i am not able to understand much about the importance of motion correction of b-tables could anyone please suggest me some additional references to understand the need for this b-table correction. Thanks Regards venkateswaran =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S. News & World Report (2008). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090514/457b0718/attachment.html From susumu at mri.jhu.edu Thu May 14 16:25:15 2009 From: susumu at mri.jhu.edu (susumu) Date: Thu, 14 May 2009 16:25:15 -0400 Subject: [Mristudio-users] motion ocrrection of DTI gradient table In-Reply-To: <77A88E90A851594AAEF830450587C39D01EDAA4F@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: <7k7ed7$7ghukf@ipex3.johnshopkins.edu> Hi Venkateswaran, When you run AIR, you can find an option toward the bottom of the window, called "Adjusting the gradients for the diffuion-weighted images if applicable". By activating this function, the gradient table is rotated if AIR does any rotation. In regular DTI, you should expect only less than 1-2 degree of rotation in average. If so, the table rotation is not so important. If subject moves much more than that, the table rotation becomes important but there would be many other more problematic artifacts like mis-registration between the odd and even numbered slices within a 3D data and image corruption, which can not be fixed. So, this is a bit "looking at leaves without looking at the tree'. I believe what the paper stressed, if I'm not mistaken, is when you want to combine data scanned at two different time points, then the position and orientation of the brain could be very different. If you want to co-register raw DWI images between the two separate scans, you have to rotate the gradient table. This is very true, but you don't have many occasions when you want to combine two separate scans with different head positions. If you have two separate scans, you can calculate tensor first, and then coregister with a proper tensor-reorientation method. Then you don't have to worry about the gradient table rotation. Hope these help. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Rajagopalan, Venkateswaran Sent: Thursday, May 14, 2009 3:50 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] motion ocrrection of DTI gradient table Dear MRI studio Users, I recently came across the following article "DTI Fiber Tracking: The Importance of Adjusting DTI Gradient Tables for Motion Correction. CATNAP - A Tool to Simplify and Accelerate DTI Analysis". The results in this paper suggested the need for motion correction of gradient tables. I am wondering do i need to carry out this preprocessing step of motion correction of gradient table in CATNAP before supplying the gradient table values in DTI studio for calculation of DTI metrics and tractography or the recent versions of DTI studio takes care of this problem. This being a short article i am not able to understand much about the importance of motion correction of b-tables could anyone please suggest me some additional references to understand the need for this b-table correction. Thanks Regards venkateswaran =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S. News & World Report (2008). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090514/f1651bb2/attachment-0001.html From rajagov2 at ccf.org Thu May 14 16:31:51 2009 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Thu, 14 May 2009 16:31:51 -0400 Subject: [Mristudio-users] motion ocrrection of DTI gradient table References: <7k7ed7$7ghukf@ipex3.johnshopkins.edu> Message-ID: <77A88E90A851594AAEF830450587C39D01EDAA50@CCHSCLEXMB56.cc.ad.cchs.net> Dear Dr. Susumu, Thank you very much for your kind clarification. Regards venkateswaran ________________________________ From: mristudio-users-bounces at mristudio.org on behalf of susumu Sent: Thu 5/14/2009 4:25 PM To: 'DTI Studio, ROI Editor, Landmarker Questions/Support' Subject: Re: [Mristudio-users] motion ocrrection of DTI gradient table Hi Venkateswaran, When you run AIR, you can find an option toward the bottom of the window, called "Adjusting the gradients for the diffuion-weighted images if applicable". By activating this function, the gradient table is rotated if AIR does any rotation. In regular DTI, you should expect only less than 1-2 degree of rotation in average. If so, the table rotation is not so important. If subject moves much more than that, the table rotation becomes important but there would be many other more problematic artifacts like mis-registration between the odd and even numbered slices within a 3D data and image corruption, which can not be fixed. So, this is a bit "looking at leaves without looking at the tree'. I believe what the paper stressed, if I'm not mistaken, is when you want to combine data scanned at two different time points, then the position and orientation of the brain could be very different. If you want to co-register raw DWI images between the two separate scans, you have to rotate the gradient table. This is very true, but you don't have many occasions when you want to combine two separate scans with different head positions. If you have two separate scans, you can calculate tensor first, and then coregister with a proper tensor-reorientation method. Then you don't have to worry about the gradient table rotation. Hope these help. Susumu ________________________________ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Rajagopalan, Venkateswaran Sent: Thursday, May 14, 2009 3:50 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] motion ocrrection of DTI gradient table Dear MRI studio Users, I recently came across the following article "DTI Fiber Tracking: The Importance of Adjusting DTI Gradient Tables for Motion Correction. CATNAP - A Tool to Simplify and Accelerate DTI Analysis". The results in this paper suggested the need for motion correction of gradient tables. I am wondering do i need to carry out this preprocessing step of motion correction of gradient table in CATNAP before supplying the gradient table values in DTI studio for calculation of DTI metrics and tractography or the recent versions of DTI studio takes care of this problem. This being a short article i am not able to understand much about the importance of motion correction of b-tables could anyone please suggest me some additional references to understand the need for this b-table correction. Thanks Regards venkateswaran =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S. News & World Report (2008). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S. News & World Report (2008). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 10022 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090514/695db2ff/attachment.bin From choisj70 at gmail.com Fri May 15 16:16:39 2009 From: choisj70 at gmail.com (Seongjin) Date: Fri, 15 May 2009 16:16:39 -0400 Subject: [Mristudio-users] save and read fiber in Amira format In-Reply-To: <7k7ed7$7fmd31@ipex3.johnshopkins.edu> References: <7k7ed7$7fmd31@ipex3.johnshopkins.edu> Message-ID: I could not find the 3D viewer for Amira format in the MRI studio.org. Is there anyone who already received reply from Kegang with the 3D viewer? I am waiting for reply from Kegang Hua. -SC On Tue, May 12, 2009 at 5:10 PM, susumu wrote: > You can try our 3D viewer. It has only limited functions but it works. > > > > You can get it from Kegang Hua. > > > > Xin, is it possible to post this handy 3D visualization software in the > MriStudio.org website? > > > ------------------------------ > > *From:* mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org] *On Behalf Of *[Seongjin] > *Sent:* Tuesday, May 12, 2009 12:30 PM > *To:* Yi Jiang; DTI Studio, ROI Editor, Landmarker Questions/Support > *Subject:* Re: [Mristudio-users] save and read fiber in Amira format > > > > Dear users using Amira, > > Is there any other way to see Amira format without purchase of Amira SW? > For example, free viewer for Amira formatted file. > Thanks in advance. > > -SC > > On Mon, May 11, 2009 at 4:52 PM, Yi Jiang wrote: > > Hello, dear all, > > > > I tried to select multiple fiber tracts in multiple colors (say, the final > selected fibers are from 20 ROIs and in 8 colors). I saved the "selected > fibers" in amira format. I tried to load the fiber file in Amira. It was > loaded in with no complaint. I then displayed the fibers as lineSetView in > Amira. But all the lines displayed with the same color, instead of the 8 > colors I would hope. > > > > My questions are: are the fiber color (labels or indices) saved in the > amira format? If yes, how can I display them in different colors as in > DTIstudio? > > > > Thank you very much! > > > > Best, > > Yi > > > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090515/6211b9c5/attachment-0001.html From luessi at neurologie.klinik.uni-mainz.de Sat May 16 12:07:28 2009 From: luessi at neurologie.klinik.uni-mainz.de (Dr. Felix =?iso-8859-1?b?TPxzc2k=?=) Date: Sat, 16 May 2009 18:07:28 +0200 Subject: [Mristudio-users] Please remove me from this maillist In-Reply-To: References: Message-ID: <20090516180728.nkx6j0e10ks4ss4w@imp2.klinik.uni-mainz.de> Thanks. Best wishes. F. Luessi, MD Department of Neurology University Mainz Germany From xnbn at sohu.com Sun May 17 11:30:40 2009 From: xnbn at sohu.com (xnbn) Date: Sun, 17 May 2009 23:30:40 +0800 Subject: [Mristudio-users] (no subject) Message-ID: <200905172330380836866@sohu.com> hello,I can not online the website to download landmarker.Every time I went to the site,it showed "The requested URL /AIR5/programs.html. was not found on this server".How did I do? 2009-05-17 xnbn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090517/d0d75f2a/attachment.html From xli16 at jhmi.edu Mon May 18 10:14:29 2009 From: xli16 at jhmi.edu (Xin Li) Date: Mon, 18 May 2009 10:14:29 -0400 Subject: [Mristudio-users] (no subject) In-Reply-To: <200905172330380836866@sohu.com> References: <200905172330380836866@sohu.com> Message-ID: xnbn, Please try again at this webpage https://www.mristudio.org/wiki/installation. Xin ----- Original Message ----- From: xnbn Date: Sunday, May 17, 2009 11:31 am Subject: [Mristudio-users] (no subject) To: mristudio-users > hello,I can not online the website to download landmarker.Every time I > went to the site,it showed "The requested URL /AIR5/programs.html. was > not found on this server".How did I do? > 2009-05-17 > > > > xnbn > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org mristudio-users From khua1 at jhu.edu Mon May 18 14:17:17 2009 From: khua1 at jhu.edu (Hua KG) Date: Mon, 18 May 2009 18:17:17 +0000 Subject: [Mristudio-users] save and read fiber in Amira format In-Reply-To: References: <7k7ed7$7fmd31@ipex3.johnshopkins.edu> Message-ID: Hi, SC I was trying to write a manual for the program. Once, I wrote it up, I'll give to Xin and she can put it online. Thank for your interests! Date: Fri, 15 May 2009 16:16:39 -0400 From: choisj70 at gmail.com Subject: Re: [Mristudio-users] save and read fiber in Amira format To: mristudio-users at mristudio.org I could not find the 3D viewer for Amira format in the MRI studio.org. Is there anyone who already received reply from Kegang with the 3D viewer? I am waiting for reply from Kegang Hua. -SC On Tue, May 12, 2009 at 5:10 PM, susumu wrote: You can try our 3D viewer. It has only limited functions but it works. You can get it from Kegang Hua. Xin, is it possible to post this handy 3D visualization software in the MriStudio.org website? From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of [Seongjin] Sent: Tuesday, May 12, 2009 12:30 PM To: Yi Jiang; DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] save and read fiber in Amira format Dear users using Amira, Is there any other way to see Amira format without purchase of Amira SW? For example, free viewer for Amira formatted file. Thanks in advance. -SC On Mon, May 11, 2009 at 4:52 PM, Yi Jiang wrote: Hello, dear all, I tried to select multiple fiber tracts in multiple colors (say, the final selected fibers are from 20 ROIs and in 8 colors). I saved the "selected fibers" in amira format. I tried to load the fiber file in Amira. It was loaded in with no complaint. I then displayed the fibers as lineSetView in Amira. But all the lines displayed with the same color, instead of the 8 colors I would hope. My questions are: are the fiber color (labels or indices) saved in the amira format? If yes, how can I display them in different colors as in DTIstudio? Thank you very much! Best, Yi _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users _________________________________________________________________ More than messages?check out the rest of the Windows Live?. http://www.microsoft.com/windows/windowslive/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090518/15fe529d/attachment.html From fijoy at jhu.edu Mon May 18 18:20:27 2009 From: fijoy at jhu.edu (Fijoy Vadakkumpadan) Date: Mon, 18 May 2009 18:20:27 -0400 Subject: [Mristudio-users] LDDMM in Landmarker Message-ID: Hi all, I am trying to use landmarks to perform LDDMM registration in Landmarker. It seems to me that there are two possible choices to do this in Landmarker: 1) The first choice is to load all the landmarks and use "Landmark-Based LDDMM" option under the "Transformation" pull-down menu in the top left. 2) The second choice is to load all the landmarks and use the "Single Channel" button under "Remote Volume LDDMM" in the subject panel. Could anyone please tell me if both the above two choices will incorporate landmark information in LDDMM registration? If yes, what is the difference between the two choices? Thank you. -Fijoy From choisj70 at gmail.com Tue May 19 00:07:06 2009 From: choisj70 at gmail.com (Seongjin) Date: Tue, 19 May 2009 00:07:06 -0400 Subject: [Mristudio-users] save and read fiber in Amira format In-Reply-To: References: <7k7ed7$7fmd31@ipex3.johnshopkins.edu> Message-ID: I appreciate all your efforts on this. -SC On Mon, May 18, 2009 at 2:17 PM, Hua KG wrote: > Hi, SC > > I was trying to write a manual for the program. Once, I wrote it up, I'll > give to Xin and she can put it online. > > Thank for your interests! > > > ------------------------------ > Date: Fri, 15 May 2009 16:16:39 -0400 > From: choisj70 at gmail.com > Subject: Re: [Mristudio-users] save and read fiber in Amira format > To: mristudio-users at mristudio.org > > > I could not find the 3D viewer for Amira format in the MRI studio.org. > Is there anyone who already received reply from Kegang with the 3D viewer? > I am waiting for reply from Kegang Hua. > > -SC > > On Tue, May 12, 2009 at 5:10 PM, susumu wrote: > > You can try our 3D viewer. It has only limited functions but it works. > > You can get it from Kegang Hua. > > Xin, is it possible to post this handy 3D visualization software in the > MriStudio.org website? > > ------------------------------ > *From:* mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org] *On Behalf Of *[Seongjin] > *Sent:* Tuesday, May 12, 2009 12:30 PM > *To:* Yi Jiang; DTI Studio, ROI Editor, Landmarker Questions/Support > *Subject:* Re: [Mristudio-users] save and read fiber in Amira format > > > Dear users using Amira, > > Is there any other way to see Amira format without purchase of Amira SW? > For example, free viewer for Amira formatted file. > Thanks in advance. > > -SC > > On Mon, May 11, 2009 at 4:52 PM, Yi Jiang wrote: > Hello, dear all, > > I tried to select multiple fiber tracts in multiple colors (say, the > final selected fibers are from 20 ROIs and in 8 colors). I saved the > "selected fibers" in amira format. I tried to load the fiber file in Amira. > It was loaded in with no complaint. I then displayed the fibers as > lineSetView in Amira. But all the lines displayed with the same color, > instead of the 8 colors I would hope. > > My questions are: are the fiber color (labels or indices) saved in the > amira format? If yes, how can I display them in different colors as in > DTIstudio? > > Thank you very much! > > Best, > Yi > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > > ------------------------------ > check out the rest of the Windows Live?. More than mail?Windows Live? goes > way beyond your inbox. More than messages > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org mristudio-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090519/326d2ef6/attachment-0001.html From vrao at jhmi.edu Tue May 19 07:20:54 2009 From: vrao at jhmi.edu (Vani Rao) Date: Tue, 19 May 2009 07:20:54 -0400 Subject: [Mristudio-users] PLEASE DELETE MY NAME FROM LIST Message-ID: <4A125DDC020000C100047B0C@cis27.hosts.jhmi.edu> THANKS! >>> "[Seongjin]" 05/19/09 12:07 AM >>> I appreciate all your efforts on this. -SC On Mon, May 18, 2009 at 2:17 PM, Hua KG wrote: > Hi, SC > > I was trying to write a manual for the program. Once, I wrote it up, I'll > give to Xin and she can put it online. > > Thank for your interests! > > > ------------------------------ > Date: Fri, 15 May 2009 16:16:39 -0400 > From: choisj70 at gmail.com > Subject: Re: [Mristudio-users] save and read fiber in Amira format > To: mristudio-users at mristudio.org > > > I could not find the 3D viewer for Amira format in the MRI studio.org. > Is there anyone who already received reply from Kegang with the 3D viewer? > I am waiting for reply from Kegang Hua. > > -SC > > On Tue, May 12, 2009 at 5:10 PM, susumu wrote: > > You can try our 3D viewer. It has only limited functions but it works. > > You can get it from Kegang Hua. > > Xin, is it possible to post this handy 3D visualization software in the > MriStudio.org website? > > ------------------------------ > *From:* mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org] *On Behalf Of *[Seongjin] > *Sent:* Tuesday, May 12, 2009 12:30 PM > *To:* Yi Jiang; DTI Studio, ROI Editor, Landmarker Questions/Support > *Subject:* Re: [Mristudio-users] save and read fiber in Amira format > > > Dear users using Amira, > > Is there any other way to see Amira format without purchase of Amira SW? > For example, free viewer for Amira formatted file. > Thanks in advance. > > -SC > > On Mon, May 11, 2009 at 4:52 PM, Yi Jiang wrote: > Hello, dear all, > > I tried to select multiple fiber tracts in multiple colors (say, the > final selected fibers are from 20 ROIs and in 8 colors). I saved the > "selected fibers" in amira format. I tried to load the fiber file in Amira. > It was loaded in with no complaint. I then displayed the fibers as > lineSetView in Amira. But all the lines displayed with the same color, > instead of the 8 colors I would hope. > > My questions are: are the fiber color (labels or indices) saved in the > amira format? If yes, how can I display them in different colors as in > DTIstudio? > > Thank you very much! > > Best, > Yi > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > > ------------------------------ > check out the rest of the Windows Live?. More than mail?Windows Live? goes > way beyond your inbox. More than messages > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org mristudio-users > > From aimanba1 at jhu.edu Tue May 19 12:20:29 2009 From: aimanba1 at jhu.edu (Anuar Imanbayev) Date: Tue, 19 May 2009 12:20:29 -0400 Subject: [Mristudio-users] program crashes In-Reply-To: <4A001D07020000630001FF08@cis27.hosts.jhmi.edu> References: <4A001D07020000630001FF08@cis27.hosts.jhmi.edu> Message-ID: Eric, If you're still having trouble with these Siemens files and they happen to be Mosaic files, I created a handy protocol on how to deal with these Siemens Mosaic files in DTI. There are just some adjustments to be made, that's all. Good luck, Anuar ----- Original Message ----- From: Hangyi Jiang Date: Tuesday, May 5, 2009 11:04 am Subject: Re: [Mristudio-users] program crashes To: mristudio-users at mristudio.org > mostly, this happens when the number of images doesn't match with that > of gradients specified in the gradeint table. > when the dataset was successfully being loaded in, the image volumes > will be listed in the "Image List" of the "image" tab. please view > these images, make sure the # of images are same as the # of items in > the gradient table. > > another common mistake for Siemens dataset is that the images are Masaic > format but they were loaded in as DICOM format. > > regards, > > hangyi > > > > >>> eric Q 05/05/09 2:05 AM >>> > > Hi Susumu: > > Thank you for answering my question regarding the gradient table. > However the program crashes every time when I try to do a calculation > (DTI mapping). I've tried to calculate Tensor, Color map, ADC map, Mean, > but I always get this "The mriView3D MFC application has encountered > a > problem and needs to close". > > > I am a new user to DTI studio, so there are probably a lot of mistakes > I've made on my end, but could you please tell me what are the likely > causes for the crash of my program? Your time and help is much > appreciated. > > Regards > > Eric Q > > Date: Fri, 1 May 2009 09:32:56 -0400 > From: susumu at mri.jhu.edu > To: mristudio-users at mristudio.org > Subject: Re: [Mristudio-users] Gradient table > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Hi Liang, > > > > 1) I > am not sure which coordinates (space) the ultimate gradient table was > relative > to, such as frequency- and phase-encoding of image, horizontal and > vertical > direction of image, or magnets' x/y/z coordinates. Based on your reply, > I think > that it might be the last one. > > When you present vectors, color maps, or performing > fiber tracking, X, Y, and Z need to be defined by the image matrix. This > is the > most natural way. The frequency/phase/slice and image x/y/z have > permutation > relationship, like frequency ? image x / phase ? image y / slice ? > image z or frequency ? image y / phase ? image x / slice ? image > z. > > The relationship between magnet x / y / z and image x > / y / z could have oblique relationship if oblique scan is used, and > therefore > could be very complicated. > > The gradient table, ultimately, needs to adopt the > image x / y / z system. Now most vendor system is adopting a way to > deliver > gradient application in the frequency/phase/slice system, moving away > from > gradient x/y/z. This means, when oblique scan is employed, the scanner > dynamically recalculates the gradient table in the f/p/s coordinates. > If > the > scanner doesn?t do this (like old Siemens system), we have to > recalculate > the table based on the oblique angles by ourselves. The former is more > fool-proof. > > > > 2) In my *.PAR file, there was last 3 columns representing diffusion > directions > but obviously different between subjects. I don't know what diffusion > were > recorded in this header file. > > I don?t have much experience with the new PAR > file, but if you are using oblique scans, it is not surprising the each > patient > have different gradient table in the ?magnet? coordinate. Suppose > we want to apply [1, 0, 0] in the first line of the gradient table, > which is the > ?X? orientation. If we use an oblique scan, magnet X and image X > are no longer the same. As I mentioned above, in the end, what we want > to know > is gradient orientation in the image coordinate. So we have two choices. > > > Choice 1: deliver magnet [1, 0, 0], meaning pure X > gradient application. This X gradient could be something like [0.9, > 0.15, 0] in > the image coordinate. We need to do [1, 0, 0] x ImageRotation to get > new > gradient table to do tensor calculation. > > Choice 2: deliver magnet [0.9, -0.15, 0] (I just made > up these numbers) so that the applied gradient aligns the image X axis. > In this > case, we can use gradient table [1, 0, 0] for tensor calculation. > > > > I hope this makes your questions answered. > > Susumu > > > > > > > > > > > > > > From: > mristudio-users-bounces at mristudio.org > [ On Behalf Of liang wang > > Sent: Saturday, AprI also have a similar question about gradient > tables in Philips scanner. > > > > > My data were collected using following protocols: > > 1) Gradient table: Medium > > 2) Gradient overplus: no > > 3) Oblique plane: yes, and different angles between subjects. > > > > Looking through your answer, I know that this set can result in the same > gradient table input into DTIstudio for all subject. However, 1) I am > not sure > which coordinates (space) the ultimate gradient table was relative to, > such as > frequency- and phase-encoding of image, horizontal and vertical > direction of > image, or magnets' x/y/z coordinates. Based on your reply, I think that > it > might be the last one. > > > > 2) In my *.PAR file, there was last 3 columns representing diffusion > directions > but obviously different between subjects. I don't know what diffusion > were > recorded in this header file. > > > > Many thanks > > > > Liang > > > > 2009/4/16 susumu > > > > > > Hi Eric, > > > > > > For Philips scanner there are several types of gradient > tables you can specify in the scanner. Please check your protocol for > the > following points; > > > > > > 1) Gradient table: High (32-orientation)/ Medium (15-orientation) > / > Low (6-orientation) > > 2) Overplus (ON / OFF) > > 3) Oblique plane (X/Y/Z angles) > > > > > The first option has 3 choices and the second option has 2 > choices. Therefore, there are 3 x 2 = 6 gradient tables. > > > If the second option (Overplus) is NO, the third option has > no effect. If the second option is YES, the gradient table has to be > rotated > based on the oblique angles. > > > > > > To simplify the DTI processing, we recommend Overplus = NO. > > > > > > We have the basic 6 tables, which can be used as is if you > use Overplus = OFF or Oblique angles = 0/0/0 degree. > > > Please let us know which options you are using. > > > > > > Susumu > > > > > > > > > > > > > > From: mristudio-users-bounces at mristudio.org > [ > On Behalf Of eric Q > > Sent: Thursday, April 16, 2009 > 9:44 PM > > > > > > > To: mristudio-users at mristudio.org > > > > Subject: Re: > [Mristudio-users] Gradient table > > > > > > > > > > > Hello Dear DTIstudio users: > > > > I am new to DTIstudio, I was hoping someone could give me some much > needed > advises for beginners. > > > > > > I was trying to obtain the FA values for my brain phantom (PHILIP 3T > scanner). > When I clicked on "DTI mapping", it prompted me to enter the > "gradient table", how do I calculate the "gradient table"? > > > > Thanks in advanced > > > > Best regards > > > > Eric > > > > > > > > > > > > Date: Thu, 9 Apr 2009 11:04:09 > -0400 > > From: susumu at mri.jhu.edu > > To: mristudio-users at mristudio.org > > Subject: Re: [Mristudio-users] MriView3D application close > > Hi Hugh, > > > > > > When you got this error, please suspect one of the following > two reasons; > > > > > > 1) Memory shortage: > > > > > > Even if you have many GB of memories, 32-bit Windows system > can allocate only 1 - 1.5 GB to each program. To check if you have the > memory > problem, please restrict the slices to be calculated. In the > initial data parameter window, there is a section called "Slices to > be processed". Here you can specify only a portion of slices to be > processed. Please limit the slices to, for example, 0-9 and see how it > goes. If > you can calculate tensors without errors, then you have the memory > problem. The > solution is; a) upgrade to the 64-bit system or b) devide the > calculation to 2 > batches (e.g. slice 0-29 for the first batch and 30-59 for the second > batch), > calculate all maps (e.g. FA), and later combine them. > > > > > > 2) Mismatch between the gradient table and the number of > images: > > > > > > For example, if you specify 12-orientation table and 30 > volume images, then you get the error. After loading the data and before > you go > to the Dti Map tab, make sure that you have 1 b0 + 64 DWIs in the > pull-down > menu in the right column of the Image tab. If you have the correct > number of > the images, then you might have an error in your gradient > tab"DtiMapping" in the "File" button again, d) the window still > remembers the gradient table you entered last time. This remembered > window > tells how DtiStudio interpreted your gradient table. If there is any > syntax > errors, you may find them much easier. For example, if you enter, "4: > 1 > 0.5 0", instead of "4: 1, 0.5, 0", then you would find, "4: > 1, 0, 0". > > > > > > If any of these do not solve the issue, please let us know. > > > > > > Susumu > > > > > > > > > > > > From: mristudio-users-bounces at mristudio.org > [ > On Behalf Of Hugh Wang > > Sent: Wednesday, April 08, 2009 > 6:30 PM > > To: mristudio-users at mristudio.org > > Subject: [Mristudio-users] > MriView3D application close > > Hi, > > > > I was using the dtistudio (ver. 2.4) to look at the Siemens DICOM > diffusion images (1baseline,64 gradients). After successfully loading > the > images, I click the "dti map" option at lower right corner. Whatever > calculation I choose, it always gives me an error: > > > > "MriView3D MFC Application has encountered a problem and needs to > close. We are sorry for the inconvenience." > > > > I tried several PCs, and the problem keeped the same. I would appreciate > that > if there's anyone having any idea on how to solve it. Thanks. > > > Best, > > Hugh > > > > > > > > Find > car news, reviews and more Looking to change your car this year? > > > > > > > > > > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > > > > > > > > -- > > Liang Wang, PhD > > Postdoctoral Fellow > > Woodward Lab > > Department of Psychiatry > > University of British Columbia > > BC Mental Health & Addiction Services > > 938 West 28th Avenue > > Vancouver BC > V5Z 4H4 > > Telephone: 1-604-875-2000 (ext. 4735) > > Fax: 1-604-875-3871 > > Email: wanglbit at gmail.com > > > _________________________________________________________________ > Looking for a fresh way to share your photos? Check out the new Windows > Live Messenger > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > From reza77p at yahoo.com Tue May 19 16:55:15 2009 From: reza77p at yahoo.com (reza p) Date: Tue, 19 May 2009 13:55:15 -0700 (PDT) Subject: [Mristudio-users] (no subject) Message-ID: <798012.94699.qm@web32801.mail.mud.yahoo.com> -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090519/ddc25578/attachment.html From fijoy at jhu.edu Wed May 20 12:50:29 2009 From: fijoy at jhu.edu (Fijoy Vadakkumpadan) Date: Wed, 20 May 2009 12:50:29 -0400 Subject: [Mristudio-users] Landmarker 1.5 transformation matrix Message-ID: Hi all, I am trying to save the transformation matrix after an affine transformation in Landmarker 1.5. It seems to me that the button for saving the matrix is disabled in Landmarker 1.5. Is it possible to save the transformation matrix in Landmarker 1.5? Thank you. Fijoy From xli16 at jhmi.edu Wed May 20 14:20:15 2009 From: xli16 at jhmi.edu (Xin Li) Date: Wed, 20 May 2009 14:20:15 -0400 Subject: [Mristudio-users] Landmarker 1.5 transformation matrix In-Reply-To: References: Message-ID: Fijoy, Thanks for your message. I have fixed this problem. Please download Landmarker 1.5.1 at the website of Mristudio. Xin ----- Original Message ----- From: Fijoy Vadakkumpadan Date: Wednesday, May 20, 2009 12:51 pm Subject: [Mristudio-users] Landmarker 1.5 transformation matrix To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > Hi all, > > I am trying to save the transformation matrix after an affine > transformation in Landmarker 1.5. It seems to me that the button for > saving the matrix is disabled in Landmarker 1.5. Is it possible to > save the transformation matrix in Landmarker 1.5? Thank you. > > Fijoy > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org mristudio-users From xli16 at jhmi.edu Wed May 20 14:35:10 2009 From: xli16 at jhmi.edu (Xin Li) Date: Wed, 20 May 2009 14:35:10 -0400 Subject: [Mristudio-users] 3DMRI Viewer Message-ID: Hello,There is a software "DTI3DMRI" at Mristudio. A ppt manual is included in the package. You are welcome to try it. Xin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090520/071a2132/attachment-0001.html From Roderick.McColl at utsouthwestern.edu Wed May 20 18:03:07 2009 From: Roderick.McColl at utsouthwestern.edu (Roderick McColl) Date: Wed, 20 May 2009 17:03:07 -0500 Subject: [Mristudio-users] tips for compiling AIR 5.2.6 under Windows with VisualStudio Message-ID: <4A1437E6.765D.00C3.0@UTSouthwestern.edu> I am trying to understand using Landmarker and today I found I need AIR to do registration to a template. I have Windows 2K and VisualStudio v6. Does anyone have any tips or, ideally, a VS-firendly Makefile to compile AIR on a Windows box? Alternatively anyone have a way to do this with e.g. GCC? Thanks -roddy From choisj70 at gmail.com Wed May 20 22:36:57 2009 From: choisj70 at gmail.com (Seongjin) Date: Wed, 20 May 2009 22:36:57 -0400 Subject: [Mristudio-users] 3DMRI Viewer In-Reply-To: References: Message-ID: Xin, I appreciate your efforts on this. -SC On Wed, May 20, 2009 at 2:35 PM, Xin Li wrote: > Hello, > > There is a software "DTI3DMRI" at Mristudio. A ppt manual is included in > the package. You are welcome to try it. > > > > Xin > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org mristudio-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090520/c94c7b0f/attachment.html From choisj70 at gmail.com Thu May 21 01:56:55 2009 From: choisj70 at gmail.com (Seongjin) Date: Thu, 21 May 2009 01:56:55 -0400 Subject: [Mristudio-users] 3DMRI Viewer In-Reply-To: References: Message-ID: Whatever the number for thresholds I type in, I got a consistent error message: "The threshold has been set to high, please reset it." I tried numbers between 0 - 100. But it did not work. Any solution to this? Thanks in advance. -SC On Wed, May 20, 2009 at 10:36 PM, [Seongjin] wrote: > Xin, > > I appreciate your efforts on this. > > -SC > > On Wed, May 20, 2009 at 2:35 PM, Xin Li wrote: > >> Hello, >> >> There is a software "DTI3DMRI" at Mristudio. A ppt manual is included in >> the package. You are welcome to try it. >> >> >> >> Xin >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org mristudio-users >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090521/0da2ddff/attachment.html From khua1 at jhu.edu Fri May 22 06:22:59 2009 From: khua1 at jhu.edu (Hua KG) Date: Fri, 22 May 2009 10:22:59 +0000 Subject: [Mristudio-users] FW: 3DMRI Viewer In-Reply-To: References: Message-ID: Hi, SC The problem you described normally results from too low or too high threshold. The intensity of ISO image could run from 0 to couple of thousands. You could change the threshold higher to see if it solve the problem. And then, you can slide the threshold bar to try out couple of threshold values(remember to click on the render window to update the render scene). Attached is a small program I use to convert iso(float) to rec(unsigned short). This program will normalize the iso intensity to 0-255. (The output is "Output.rec"). Also, you can try to toggle on/off the byte order check box to see if the data is big endian or little endian. Data from some Unix machine could use big endian. Hope it helps! Kegang(Luke) Hua Date: Thu, 21 May 2009 01:56:55 -0400 From: choisj70 at gmail.com Subject: Re: [Mristudio-users] 3DMRI Viewer To: mristudio-users at mristudio.org Whatever the number for thresholds I type in, I got a consistent error message: "The threshold has been set to high, please reset it." I tried numbers between 0 - 100. But it did not work. Any solution to this? Thanks in advance. -SC On Wed, May 20, 2009 at 10:36 PM, [Seongjin] wrote: Xin, I appreciate your efforts on this. -SC On Wed, May 20, 2009 at 2:35 PM, Xin Li wrote: Hello, There is a software "DTI3DMRI" at Mristudio. A ppt manual is included in the package. You are welcome to try it. Xin _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org mristudio-users Windows Live?: Keep your life in sync. Check it out! _________________________________________________________________ Drag n? drop?Get easy photo sharing with Windows Live? Photos. http://www.microsoft.com/windows/windowslive/products/photos.aspx -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090522/e933b004/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: iso2rec.zip Type: application/x-zip-compressed Size: 38450 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090522/e933b004/attachment-0001.bin From c.bieck at T-Online.de Mon May 25 16:32:00 2009 From: c.bieck at T-Online.de (Christian Bieck) Date: Mon, 25 May 2009 20:32 +0000 (GMT) Subject: [Mristudio-users] Handling of post-LDDMM tensor files Message-ID: <1M8gq7-0VPQMS0@fwd10.aul.t-online.de> Salutations, I finally managed to do a proper and repeatable LDDMM processing, thanks to the exceptionally helpful Anthony Kolasny, but have encountered further problems along the way, about which I'd be very grateful to get some input for. My main goal is to transform tensor information to MNI space so that I may do a fiber tracking for all subjects using the same ROI. Here's what I did so far: 1. In DTI Studio: Calculated the DWI image and the 6 tensor files. 2. In Landmarker: a.) Opened the JHU-MNI_DWI Template b.) Loaded the DWI file (Image Size 96x96; Image Slices 60; Slice Orientation Axial; Slice Sequencing Inferior-Superior; FOV 192x192; Slice Thickness 2; Pixel Size 2x2) as the subject c.) Loaded the six tensor files (Image Size 96x96; Image Slices 60; Slice Orientation Axial; Slice Sequencing Inferior-Superior; FOV 192x192; Slice Thickness 2; Pixel Size 2x2) via the "Open .d file", selecting the "X-component for the "Flip Eigen Vector" d.) Did a Linear AIR Transform with default values and Affine/Trilinear selected, leaving the parameters of the Image and tensor files equal to the parameters of the Template file (Image Size 181x217; Image Slices 181; FOV 181x217; Slice Thickness 1; Pixel Size 1x1) e.) Converted all images (Template, DWI and tensors) to byte file format with the "BFW" button f.) Chose a Single channel Volume LDDMM, where the images were first automatically changed to 182*218*182. I then left all the default parameters and sent the files (Template, subject DWI and tensors) to the server. 3. Shortly thereafter, the processing was finished, but instead of a transformed subject DWI and transformed tensors, the zip file contained only a template.img, target.img,the transformation matrixes hmap.vtk and kimap.vtk and some text files. 4. In Landmarker: a.) Opened the template.img as the template (Image Size 182x218; Image Slices 182; Slice Orientation Axial; Slice Sequencing Inferior-Superior; FOV 182x218; Slice Thickness 1; Pixel Size 1x1) b.) Opened the target.img as the subject (Image Size 182x218; Image Slices 182; Slice Orientation Axial; Slice Sequencing Inferior-Superior; FOV 182x218; Slice Thickness 1; Pixel Size 1x1) c.) As there were no LDDMM processed tensor files, I resampled the original tensor files (that were not Linearly AIR'd, maybe that might be a problem) to the parameters of the target.img/template.img d.) I opened said resampled tensor files via the "Open .d file" button, with Flip Eigen Vector X-component selected e. I loaded the LDDMM Matrix (VTK Format) via the Load Transformation Matrix button (Is it important whether the Hmap.vtk or Kimap.vtk gets chosen?) f.) Saved the Updated_Target.img and the Updated Tensor files 5. In DTISTudio: a.) Opened the Updated_Target.img b.) Opened the Updated Tensor files via the "Open .d" button,, selecting the "Get eigen-values/etc." option and specifiying the "DTISTudio" format c.) Saved the resulting Eigenvector0 and FA images for the Fiber Tracking d.) As my computer had severe problems handling any ROI operations for the original Image size 182x218; Image Slices 182 files, I resampled the Eigenvector0 and FA files to Image Size 96x96; Image Slices 60 with Landmarker and then did the Fiber Tracking (again, with Flip Eigenvector X-component selected) and ROI operations Now, my questions are: 1. Is the general procedure sound so far or do any of the steps lead to the important tensor information getting distorted to the point of unusability? I still want to track the optic radiation and want to compare FA values (which might have only slight differences between patients and normals), after all. 2. The LDDMM target.img looks very different from the sent subject DWI image even before applying the LDDMM transformation matrix, leading to the Upated Tensor files looking very different from the Updated_target.img. Is that a problem? Do the Tensor files still get properly transformed to MNI space? Thank you very much for your time and effort, Christian Bieck From carly at ualberta.ca Mon May 25 16:36:03 2009 From: carly at ualberta.ca (carly at ualberta.ca) Date: Mon, 25 May 2009 14:36:03 -0600 Subject: [Mristudio-users] please remove me from mailing list Message-ID: <20090525143603.18492qur6g77m7ac@webmail.ualberta.ca> From afzaliesfahan at yahoo.com Tue May 26 07:26:09 2009 From: afzaliesfahan at yahoo.com (maryam afzali) Date: Tue, 26 May 2009 04:26:09 -0700 (PDT) Subject: [Mristudio-users] changing .dat file to Analyze file Message-ID: <344254.50458.qm@web57903.mail.re3.yahoo.com> Hi, I extracted eigenvalues from DTI data and the results are saved in .dat format. I want to open them in Matlab. But the figure in Matlab is not true. I don?t know what is the problem. Is the problem due to data or due to Matlab codes? How can I change the format from .dat to Analyze? ?Can you help me please? I use this commands to open the .dat file. Is it true? ?? >>fid = fopen(' EigenVal_0.dat','r'); >> x = fread(fid, 'uint32'); >> B=reshape(x,256,256,41); Thank you very much. Afzali. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090526/466607cb/attachment.html From darshanp20 at yahoo.com Tue May 26 11:33:35 2009 From: darshanp20 at yahoo.com (darshan pai) Date: Tue, 26 May 2009 08:33:35 -0700 (PDT) Subject: [Mristudio-users] changing .dat file to Analyze file In-Reply-To: <344254.50458.qm@web57903.mail.re3.yahoo.com> References: <344254.50458.qm@web57903.mail.re3.yahoo.com> Message-ID: <385475.86615.qm@web30704.mail.mud.yahoo.com> You have an option to save as Analyze in DTI-studio the same way you saved the dat file. ________________________________ From: maryam afzali To: mristudio-users at mristudio.org Sent: Tuesday, May 26, 2009 7:26:09 AM Subject: [Mristudio-users] changing .dat file to Analyze file Hi, I extracted eigenvalues from DTI data and the results are saved in .dat format. I want to open them in Matlab. But the figure in Matlab is not true. I don?t know what is the problem. Is the problem due to data or due to Matlab codes? How can I change the format from .dat to Analyze? Can you help me please? I use this commands to open the .dat file. Is it true? >>fid = fopen(' EigenVal_0.dat','r'); >> x = fread(fid, 'uint32'); >> B=reshape(x,256,256,41); Thank you very much. Afzali. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090526/7e81107c/attachment.html From susumu at mri.jhu.edu Tue May 26 16:02:38 2009 From: susumu at mri.jhu.edu (susumu) Date: Tue, 26 May 2009 16:02:38 -0400 Subject: [Mristudio-users] changing .dat file to Analyze file In-Reply-To: <385475.86615.qm@web30704.mail.mud.yahoo.com> Message-ID: <7k7ed7$7l6e56@ipex3.johnshopkins.edu> Hi Afzali, The default format of DtiStudio is "raw", meaning unformatted data without header. Just a simple string of numbers. If your data is 256x256x41, your data size must be 4 (float) x 256x256x41. As Darshan already pointed out, maybe you can try Analyze format. When you save data by DtiStudio, you can choose the Analyze format. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of darshan pai Sent: Tuesday, May 26, 2009 11:34 AM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] changing .dat file to Analyze file You have an option to save as Analyze in DTI-studio the same way you saved the dat file. _____ From: maryam afzali To: mristudio-users at mristudio.org Sent: Tuesday, May 26, 2009 7:26:09 AM Subject: [Mristudio-users] changing .dat file to Analyze file Hi, I extracted eigenvalues from DTI data and the results are saved in .dat format. I want to open them in Matlab. But the figure in Matlab is not true. I don't know what is the problem. Is the problem due to data or due to Matlab codes? How can I change the format from .dat to Analyze? Can you help me please? I use this commands to open the .dat file. Is it true? >>fid = fopen(' EigenVal_0.dat','r'); >> x = fread(fid, 'uint32'); >> B=reshape(x,256,256,41); Thank you very much. Afzali. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090526/e1e1b959/attachment-0001.html From susumu at mri.jhu.edu Tue May 26 17:01:02 2009 From: susumu at mri.jhu.edu (susumu) Date: Tue, 26 May 2009 17:01:02 -0400 Subject: [Mristudio-users] Handling of post-LDDMM tensor files In-Reply-To: <1M8gq7-0VPQMS0@fwd10.aul.t-online.de> Message-ID: <7k7ed7$7l73qk@ipex3.johnshopkins.edu> Sorry for the poor instructions about Landmarker and RoiEditor. We are working on "getting started" currently. Your procedure is correct up to #3, but from #4, it's not the right way. Please give us few days. We will put up step-by-step screen shot for LDDMM. I'll let you know once they are up. -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Christian Bieck Sent: Monday, May 25, 2009 4:32 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] Handling of post-LDDMM tensor files Salutations, I finally managed to do a proper and repeatable LDDMM processing, thanks to the exceptionally helpful Anthony Kolasny, but have encountered further problems along the way, about which I'd be very grateful to get some input for. My main goal is to transform tensor information to MNI space so that I may do a fiber tracking for all subjects using the same ROI. Here's what I did so far: 1. In DTI Studio: Calculated the DWI image and the 6 tensor files. 2. In Landmarker: a.) Opened the JHU-MNI_DWI Template b.) Loaded the DWI file (Image Size 96x96; Image Slices 60; Slice Orientation Axial; Slice Sequencing Inferior-Superior; FOV 192x192; Slice Thickness 2; Pixel Size 2x2) as the subject c.) Loaded the six tensor files (Image Size 96x96; Image Slices 60; Slice Orientation Axial; Slice Sequencing Inferior-Superior; FOV 192x192; Slice Thickness 2; Pixel Size 2x2) via the "Open .d file", selecting the "X-component for the "Flip Eigen Vector" d.) Did a Linear AIR Transform with default values and Affine/Trilinear selected, leaving the parameters of the Image and tensor files equal to the parameters of the Template file (Image Size 181x217; Image Slices 181; FOV 181x217; Slice Thickness 1; Pixel Size 1x1) e.) Converted all images (Template, DWI and tensors) to byte file format with the "BFW" button f.) Chose a Single channel Volume LDDMM, where the images were first automatically changed to 182*218*182. I then left all the default parameters and sent the files (Template, subject DWI and tensors) to the server. 3. Shortly thereafter, the processing was finished, but instead of a transformed subject DWI and transformed tensors, the zip file contained only a template.img, target.img,the transformation matrixes hmap.vtk and kimap.vtk and some text files. 4. In Landmarker: a.) Opened the template.img as the template (Image Size 182x218; Image Slices 182; Slice Orientation Axial; Slice Sequencing Inferior-Superior; FOV 182x218; Slice Thickness 1; Pixel Size 1x1) b.) Opened the target.img as the subject (Image Size 182x218; Image Slices 182; Slice Orientation Axial; Slice Sequencing Inferior-Superior; FOV 182x218; Slice Thickness 1; Pixel Size 1x1) c.) As there were no LDDMM processed tensor files, I resampled the original tensor files (that were not Linearly AIR'd, maybe that might be a problem) to the parameters of the target.img/template.img d.) I opened said resampled tensor files via the "Open .d file" button, with Flip Eigen Vector X-component selected e. I loaded the LDDMM Matrix (VTK Format) via the Load Transformation Matrix button (Is it important whether the Hmap.vtk or Kimap.vtk gets chosen?) f.) Saved the Updated_Target.img and the Updated Tensor files 5. In DTISTudio: a.) Opened the Updated_Target.img b.) Opened the Updated Tensor files via the "Open .d" button,, selecting the "Get eigen-values/etc." option and specifiying the "DTISTudio" format c.) Saved the resulting Eigenvector0 and FA images for the Fiber Tracking d.) As my computer had severe problems handling any ROI operations for the original Image size 182x218; Image Slices 182 files, I resampled the Eigenvector0 and FA files to Image Size 96x96; Image Slices 60 with Landmarker and then did the Fiber Tracking (again, with Flip Eigenvector X-component selected) and ROI operations Now, my questions are: 1. Is the general procedure sound so far or do any of the steps lead to the important tensor information getting distorted to the point of unusability? I still want to track the optic radiation and want to compare FA values (which might have only slight differences between patients and normals), after all. 2. The LDDMM target.img looks very different from the sent subject DWI image even before applying the LDDMM transformation matrix, leading to the Upated Tensor files looking very different from the Updated_target.img. Is that a problem? Do the Tensor files still get properly transformed to MNI space? Thank you very much for your time and effort, Christian Bieck _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org mristudio-users From dylan.alegria at gmail.com Thu May 28 15:17:31 2009 From: dylan.alegria at gmail.com (Dylan Alegria) Date: Thu, 28 May 2009 12:17:31 -0700 Subject: [Mristudio-users] Late Stage AIR? Message-ID: Hi, I'm still a novice with DTIStudio, and I've run into a concerning issue during fiber-tracking. We collected a 30 direction DTI sequence with 2 repetitions on 25 subjects and have run it through DTI Studio to do fiber tracking. We did not initially register with AIR because we believed that our subjects were reasonably aligned and we didn't want to add artifacts from registration if we didn't have to. While drawing ROIs for fiber tracking some differences in tilting are obvious. We are considering running AIR on the processed data to remedy this problem. This brings me to 3 questions. 1) Given that fiber tracking operates in a 3D space, how important is it to have subjects in exactly the same alignment for drawing the seed ROIs? 2) Is it possible to register the FA/Eigenvector/etc. images without recalculating them, or going back and re-flagging bad slices? 3) Is it of vital importance to run AIR before doing the quality checks for some other reason than having similarly aligned subjects? Any help would be greatly appreciated. Thank you very much in advance! Dylan Dylan Alegria CIBSR Imaging RA Stanford University dalegria at stanford.edu (650) 736 0732 From tigerzjs at msn.com Thu May 28 19:15:57 2009 From: tigerzjs at msn.com (Jingsheng zhou) Date: Thu, 28 May 2009 23:15:57 +0000 Subject: [Mristudio-users] how to cancel the email list In-Reply-To: References: Message-ID: Dear, I don't want to receive this email. How to cancel it? thanks Jingshng > Date: Thu, 28 May 2009 12:17:31 -0700 > From: dylan.alegria at gmail.com > To: mristudio-users at mristudio.org > Subject: [Mristudio-users] Late Stage AIR? > > Hi, > I'm still a novice with DTIStudio, and I've run into a concerning > issue during fiber-tracking. We collected a 30 direction DTI sequence > with 2 repetitions on 25 subjects and have run it through DTI Studio > to do fiber tracking. We did not initially register with AIR because > we believed that our subjects were reasonably aligned and we didn't > want to add artifacts from registration if we didn't have to. > > While drawing ROIs for fiber tracking some differences in tilting are > obvious. We are considering running AIR on the processed data to > remedy this problem. This brings me to 3 questions. > > 1) Given that fiber tracking operates in a 3D space, how important is > it to have subjects in exactly the same alignment for drawing the seed > ROIs? > 2) Is it possible to register the FA/Eigenvector/etc. images without > recalculating them, or going back and re-flagging bad slices? > 3) Is it of vital importance to run AIR before doing the quality > checks for some other reason than having similarly aligned subjects? > > Any help would be greatly appreciated. Thank you very much in advance! > > Dylan > > > Dylan Alegria > CIBSR Imaging RA > Stanford University > dalegria at stanford.edu > (650) 736 0732 > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org mristudio-users _________________________________________________________________ Invite your mail contacts to join your friends list with Windows Live Spaces. It's easy! http://spaces.live.com/spacesapi.aspx?wx_action=create&wx_url=/friends.aspx&mkt=en-us -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090528/244d4706/attachment.html From Volker.Baur at puk.zh.ch Fri May 29 10:02:55 2009 From: Volker.Baur at puk.zh.ch (Baur Volker) Date: Fri, 29 May 2009 16:02:55 +0200 Subject: [Mristudio-users] Image Quality Check in DTIStudio Message-ID: <7349D26C85C75B408639D98E70F9C01D55436CBBD8@PUKMBX.puknet.local> Dear colleagues, I have a question concerning the image quality check in DTIStudio. I've heard that DTIStudio can automatically exclude bad images from the data set, but I can't find this feature. Moreover, of I want to do the check manually, how can I save the flg-file? When I close the window after removing one picture, for example, there is no prompt appearing that asks me to save a flg-file. I would be very glad about your answer! With kind regards Volker -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090529/807627a8/attachment.html From evangelouI at ninds.nih.gov Fri May 29 11:02:23 2009 From: evangelouI at ninds.nih.gov (Evangelou, Iordanis (NIH/NINDS) [E]) Date: Fri, 29 May 2009 11:02:23 -0400 Subject: [Mristudio-users] tips for compiling AIR 5.2.6 under Windows withVisualStudio In-Reply-To: <4A1437E6.765D.00C3.0@UTSouthwestern.edu> References: <4A1437E6.765D.00C3.0@UTSouthwestern.edu> Message-ID: <9A3BEE43EE449840B003538CCC88903001235312@nihcesmlbx2.nih.gov> I have compiled it using gcc under cygwin and Vista/XP Let me know if you need a copy, not sure it will work on Win 2K ------------------------------------------------------------------- Iordanis E. Evangelou, DPhil, Eur Ing, MIET Research Fellow Neuroimaging Section Neuroimmunology Branch National Institute of Neurological Disorders and Stroke National Institutes of Health Building 10, Room 5C203B Bethesda, MD 20892 USA ------------------------------------------------------------------- " If we knew what it was we were doing, it would not be called research, would it? " Albert Einstein -----Original Message----- From: Roderick McColl [mailto:Roderick.McColl at utsouthwestern.edu] Sent: Wednesday, May 20, 2009 6:03 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] tips for compiling AIR 5.2.6 under Windows withVisualStudio I am trying to understand using Landmarker and today I found I need AIR to do registration to a template. I have Windows 2K and VisualStudio v6. Does anyone have any tips or, ideally, a VS-firendly Makefile to compile AIR on a Windows box? Alternatively anyone have a way to do this with e.g. GCC? Thanks -roddy _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org mristudio-users From xli16 at jhmi.edu Fri May 29 11:33:36 2009 From: xli16 at jhmi.edu (Xin Li) Date: Fri, 29 May 2009 11:33:36 -0400 Subject: [Mristudio-users] how to cancel the email list In-Reply-To: References: Message-ID: Please send a black email to Mristudio-users-unsubscribe at mristudio.org Xin ----- Original Message ----- From: Jingsheng zhou Date: Thursday, May 28, 2009 7:16 pm Subject: [Mristudio-users] how to cancel the email list To: mristudio-users at mristudio.org > Dear, > > I don't want to receive this email. How to cancel it? > > > > thanks > > > > Jingshng > > > Date: Thu, 28 May 2009 12:17:31 -0700 > > From: dylan.alegria at gmail.com > > To: mristudio-users at mristudio.org > > Subject: [Mristudio-users] Late Stage AIR? > > > > Hi, > > I'm still a novice with DTIStudio, and I've run into a concerning > > issue during fiber-tracking. We collected a 30 direction DTI > sequence > > with 2 repetitions on 25 subjects and have run it through DTI > Studio > > to do fiber tracking. We did not initially register with AIR > because > > we believed that our subjects were reasonably aligned and we didn't > > > want to add artifacts from registration if we didn't have to. > > > > While drawing ROIs for fiber tracking some differences in tilting > are > > obvious. We are considering running AIR on the processed data to > > remedy this problem. This brings me to 3 questions. > > > > 1) Given that fiber tracking operates in a 3D space, how important > is > > it to have subjects in exactly the same alignment for drawing the > seed > > ROIs? > > 2) Is it possible to register the FA/Eigenvector/etc. images > without > > recalculating them, or going back and re-flagging bad slices? > > 3) Is it of vital importance to run AIR before doing the quality > > checks for some other reason than having similarly aligned subjects? > > > > Any help would be greatly appreciated. Thank you very much in advance! > > > > Dylan > > > > > > Dylan Alegria > > CIBSR Imaging RA > > Stanford University > > dalegria at stanford.edu > > (650) 736 0732 > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org mristudio-users > > _________________________________________________________________ > Invite your mail contacts to join your friends list with Windows Live > Spaces. It's easy! > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org mristudio-users From xli16 at jhmi.edu Fri May 29 11:35:14 2009 From: xli16 at jhmi.edu (Xin Li) Date: Fri, 29 May 2009 11:35:14 -0400 Subject: [Mristudio-users] how to cancel the email list In-Reply-To: References: Message-ID: Please send a blank email to Mristudio-users-unsubscribe at mristudio.org Xin ----- Original Message ----- From: Jingsheng zhou Date: Thursday, May 28, 2009 7:16 pm Subject: [Mristudio-users] how to cancel the email list To: mristudio-users at mristudio.org > Dear, > > I don't want to receive this email. How to cancel it? > > > > thanks > > > > Jingshng > > > Date: Thu, 28 May 2009 12:17:31 -0700 > > From: dylan.alegria at gmail.com > > To: mristudio-users at mristudio.org > > Subject: [Mristudio-users] Late Stage AIR? > > > > Hi, > > I'm still a novice with DTIStudio, and I've run into a concerning > > issue during fiber-tracking. We collected a 30 direction DTI > sequence > > with 2 repetitions on 25 subjects and have run it through DTI > Studio > > to do fiber tracking. We did not initially register with AIR > because > > we believed that our subjects were reasonably aligned and we didn't > > > want to add artifacts from registration if we didn't have to. > > > > While drawing ROIs for fiber tracking some differences in tilting > are > > obvious. We are considering running AIR on the processed data to > > remedy this problem. This brings me to 3 questions. > > > > 1) Given that fiber tracking operates in a 3D space, how important > is > > it to have subjects in exactly the same alignment for drawing the > seed > > ROIs? > > 2) Is it possible to register the FA/Eigenvector/etc. images > without > > recalculating them, or going back and re-flagging bad slices? > > 3) Is it of vital importance to run AIR before doing the quality > > checks for some other reason than having similarly aligned subjects? > > > > Any help would be greatly appreciated. Thank you very much in advance! > > > > Dylan > > > > > > Dylan Alegria > > CIBSR Imaging RA > > Stanford University > > dalegria at stanford.edu > > (650) 736 0732 > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org mristudio-users > > _________________________________________________________________ > Invite your mail contacts to join your friends list with Windows Live > Spaces. It's easy! > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org mristudio-users From jnavarro at bcm.tmc.edu Fri May 29 16:07:19 2009 From: jnavarro at bcm.tmc.edu (Cruz Navarro, Jovany) Date: Fri, 29 May 2009 15:07:19 -0500 Subject: [Mristudio-users] (no subject) Message-ID: <5F4CE8876744A34C8B58096BCD979F6734EF75@BCMEVS15.ad.bcm.edu> -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090529/67104f34/attachment.html From j_grynspan at hotmail.com Fri May 29 21:29:07 2009 From: j_grynspan at hotmail.com (jonathan grynspan) Date: Sat, 30 May 2009 01:29:07 +0000 Subject: [Mristudio-users] Late Stage AIR? In-Reply-To: References: Message-ID: please remove me from msiling list > Date: Thu, 28 May 2009 12:17:31 -0700 > From: dylan.alegria at gmail.com > To: mristudio-users at mristudio.org > Subject: [Mristudio-users] Late Stage AIR? > > Hi, > I'm still a novice with DTIStudio, and I've run into a concerning > issue during fiber-tracking. We collected a 30 direction DTI sequence > with 2 repetitions on 25 subjects and have run it through DTI Studio > to do fiber tracking. We did not initially register with AIR because > we believed that our subjects were reasonably aligned and we didn't > want to add artifacts from registration if we didn't have to. > > While drawing ROIs for fiber tracking some differences in tilting are > obvious. We are considering running AIR on the processed data to > remedy this problem. This brings me to 3 questions. > > 1) Given that fiber tracking operates in a 3D space, how important is > it to have subjects in exactly the same alignment for drawing the seed > ROIs? > 2) Is it possible to register the FA/Eigenvector/etc. images without > recalculating them, or going back and re-flagging bad slices? > 3) Is it of vital importance to run AIR before doing the quality > checks for some other reason than having similarly aligned subjects? > > Any help would be greatly appreciated. Thank you very much in advance! > > Dylan > > > Dylan Alegria > CIBSR Imaging RA > Stanford University > dalegria at stanford.edu > (650) 736 0732 > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org mristudio-users _________________________________________________________________ Windows Live helps you keep up with all your friends, in one place. http://go.microsoft.com/?linkid=9660826 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090530/22d31703/attachment.html From jeongwon at pet.wayne.edu Sun May 31 18:19:03 2009 From: jeongwon at pet.wayne.edu (Jeong-Won Jeong) Date: Sun, 31 May 2009 18:19:03 -0400 Subject: [Mristudio-users] tips for compiling AIR 5.2.6 under Windows withVisualStudio In-Reply-To: <9A3BEE43EE449840B003538CCC88903001235312@nihcesmlbx2.nih.gov> References: <4A1437E6.765D.00C3.0@UTSouthwestern.edu> <9A3BEE43EE449840B003538CCC88903001235312@nihcesmlbx2.nih.gov> Message-ID: <000601c9e23d$d0bf2500$723d6f00$@wayne.edu> Hi, Iordanis. Can you get your copy of AIR compiled for Window XP? Many thanks, Jeong-Won Jeong Email: jeongwon.jeong at gmail.com. -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Evangelou, Iordanis (NIH/NINDS) [E] Sent: Friday, May 29, 2009 11:02 AM To: DTI Studio, ROI Editor,Landmarker Questions/Support Subject: Re: [Mristudio-users] tips for compiling AIR 5.2.6 under Windows withVisualStudio I have compiled it using gcc under cygwin and Vista/XP Let me know if you need a copy, not sure it will work on Win 2K ------------------------------------------------------------------- Iordanis E. Evangelou, DPhil, Eur Ing, MIET Research Fellow Neuroimaging Section Neuroimmunology Branch National Institute of Neurological Disorders and Stroke National Institutes of Health Building 10, Room 5C203B Bethesda, MD 20892 USA ------------------------------------------------------------------- " If we knew what it was we were doing, it would not be called research, would it? " Albert Einstein -----Original Message----- From: Roderick McColl [mailto:Roderick.McColl at utsouthwestern.edu] Sent: Wednesday, May 20, 2009 6:03 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] tips for compiling AIR 5.2.6 under Windows withVisualStudio I am trying to understand using Landmarker and today I found I need AIR to do registration to a template. I have Windows 2K and VisualStudio v6. Does anyone have any tips or, ideally, a VS-firendly Makefile to compile AIR on a Windows box? Alternatively anyone have a way to do this with e.g. GCC? Thanks -roddy _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org mristudio-users _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org mristudio-users From susumu at mri.jhu.edu Mon Jun 1 10:54:53 2009 From: susumu at mri.jhu.edu (susumu) Date: Mon, 01 Jun 2009 10:54:53 -0400 Subject: [Mristudio-users] Late Stage AIR? In-Reply-To: Message-ID: <7k7ed7$7n5og3@ipex3.johnshopkins.edu> Hi Dylan, We use AIR-based image co-registration for two purposes; 1) Within one DTI dataset, the images (e.g. b0 and 30 diffusion-weighted images) may not be perfectly registered because of subject motion. We do this type of "intra-DTI data" registration to improve the accuracy of tensor calculation. This has nothing to do with the orientation of the brain such as AC-PC alignment. 2) If you get DTI data from multiple subjects, their brain orientations may not be well aligned. In this case, if you try to extract a "corresponding axial slice" from all subjects, you may have a hard time. This may affect reproducible fiber tracking because it relies on visually finding equivalent 2D slices to draw ROIs. Because you mentioned "Our subjects were reasonably aligned", I assume that you are talking about #2. Question 1) It is preferable that the brain orientations are aligned to define seed ROIs reproducibly. We usually scan subjects in AC-PC aligned. On the other hand, reconstruction of some tracts is relatively insensitive to the exact locations of see ROIs if multiple ROIs are used to impose anatomical constraints. So, it depends, but it doesn't hurt to align the brain at scanning. Question 2) Landmarker can re-orient the brains. There are, theoretically, several ways to do this. For example, you can re-orient raw DWIs and then do tensor calculation. Alternatively, you can finish tensor calculation and then re-orient the tensor. If you are using Landmarker, it is much easier to do the second way. Once the tensor is re-oriented, you can recalculate FA and eigenvectors. In this way, because you already finished tensor calculation once, you don't have to do re-flagging. Question 3) there is no good answer to it. We usually do AIR for intra-DTI alignment and then do quality check. Again, once you get a tensor file in the original space, you can re-orient the tensor to the standard AC-PC orientation using Landmarker. Susumu -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Dylan Alegria Sent: Thursday, May 28, 2009 3:18 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] Late Stage AIR? Hi, I'm still a novice with DTIStudio, and I've run into a concerning issue during fiber-tracking. We collected a 30 direction DTI sequence with 2 repetitions on 25 subjects and have run it through DTI Studio to do fiber tracking. We did not initially register with AIR because we believed that our subjects were reasonably aligned and we didn't want to add artifacts from registration if we didn't have to. While drawing ROIs for fiber tracking some differences in tilting are obvious. We are considering running AIR on the processed data to remedy this problem. This brings me to 3 questions. 1) Given that fiber tracking operates in a 3D space, how important is it to have subjects in exactly the same alignment for drawing the seed ROIs? 2) Is it possible to register the FA/Eigenvector/etc. images without recalculating them, or going back and re-flagging bad slices? 3) Is it of vital importance to run AIR before doing the quality checks for some other reason than having similarly aligned subjects? Any help would be greatly appreciated. Thank you very much in advance! Dylan Dylan Alegria CIBSR Imaging RA Stanford University dalegria at stanford.edu (650) 736 0732 _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org mristudio-users From john.migliozzi at gmail.com Wed Jun 3 12:56:28 2009 From: john.migliozzi at gmail.com (John Migliozzi) Date: Wed, 03 Jun 2009 12:56:28 -0400 Subject: [Mristudio-users] ROI Editor Questions Message-ID: Hi everyone, I'm working with ROI Editor, and I have a few questions regarding some features of the program. 1. Operations. I understand how mask works, but cannot figure out the add, subtract, multiply, divide, and T2 2. Change ROI File Header. 3. Threshold. 4. Skull Stripping. I cannot figure out how to appropriately adjust these parameters. 5. Export Pixel Value option when you right-click on an object. What do the numbers in the text file mean? Also, I am having a problem when I try to import ROIs from ROI Editor back into DTI Studio. Regardless of what format in which I export the data, DTI Studio tells me it is an "unrecognized Image-ROI data file." If anyone can answer any of these questions, I would be really appreciative. Thanks, John Migliozzi john.migliozzi at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090603/39f99f41/attachment-0001.html From susumu at mri.jhu.edu Wed Jun 3 19:07:14 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 03 Jun 2009 19:07:14 -0400 Subject: [Mristudio-users] ROI Editor Questions In-Reply-To: References: Message-ID: Hi John, Xin can answer some questions better than me, but let me answer some questions; 1: Add / Subtract / Multiply / Divide: you need to load at least two images into one window. The first image needs to be loaded using the "open" icon in the upper menu bar and the second from the "open" icon in the right column of the viewing window. Once two images are loaded, you should see them listed in the pull-down menu in the right column. If you have more than 2 images, you can use this function for addition / subtraction / multiplication / division. The T2 option can calculate a T2 map from multiple T2-weighted images. For example, if you have two images with TE = 40 and 100 ms, you can load them into one window. If you choose the T2 option, another window pops up for you to specify the echo times. Then, you can calculate a T2 map. 3: You can select pixels based on thresholding. For example, you can load an FA map and specify pixels between 0.3 and 0.8 using this button. Then you can register such pixels as an ROI. 4: Skull stripping: I agree that there are too many parameters. There are single and multi-contrast options. For the single-image option, it is basically a automate region-growing. It is like you start to blow a balloon from the center of the image. The balloon stops expanding when it hits the brain boundary (large intensity change between the brain and skull). Then the balloon stops growing when it becomes the shape of the brain. In this way, it can automatically define the boundary of the brain and thus can remove the skull. Some of the parameters can control the softness of the balloon. If the balloon is too stiff, it can not accurately trace the brain shape. If it's too soft, it can leak to connected structures such as the skull and eyeballs. You can use aDWI (average of all DWIs) or b0 with the single-image skull stripping. With the default values, it should work. These images usually has very faint skull intensity and skull removal should be straightforward. For the dual-image option, you can specify b0 or aDWI (with which the skull strip is easy) and T1 or T2 anatomical images (with which the skull strip is difficult). It first does the single-image skull strip using b0 or aDWI. Then the defined brain boundary is transferred to T1 or T2 anatomical images. Here, the T1 and T2 must be coregistered with b0 (or aDWI) and has the same dimension by going through our registration software (Landmarker). Because b0/aDWI often has image distortion (and also registration errors), the simple transfer of the brain boundary defined by b0 (or aDWI) is not accurate. This software then searched the nearest brain boundary by massaging the initial shape. We had some success to skull-strip co-registered T2-weighted anatomical images using this function, but it is still work-in-progress. That's why all the parameters are available for us to do parameter setup. 5: Export Pixel value: This is to create a histogram. Once you define an object (ROI), you can get a report of pixel intensity averaged over all pixels inside the ROI. However, you may not want such average and want to know the distribution of values of all pixels in the ROI. In this case, you can export the pixel values as a text file, read by Exel, and create a histogram. Susumu On Wed, Jun 3, 2009 at 12:56 PM, John Migliozzi wrote: > Hi everyone, > > I'm working with ROI Editor, and I have a few questions regarding some > features of the program. > > 1. Operations. I understand how mask works, but cannot figure out the > add, subtract, multiply, divide, and T2 > 2. Change ROI File Header. > 3. Threshold. > 4. Skull Stripping. I cannot figure out how to appropriately adjust these > parameters. > 5. Export Pixel Value option when you right-click on an object. What do > the numbers in the text file mean? > > Also, I am having a problem when I try to import ROIs from ROI Editor back > into DTI Studio. Regardless of what format in which I export the data, DTI > Studio tells me it is an "unrecognized Image-ROI data file." > > If anyone can answer any of these questions, I would be really > appreciative. > > Thanks, > > John Migliozzi > john.migliozzi at gmail.com > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090603/88d016bf/attachment.html From john.migliozzi at gmail.com Thu Jun 4 10:47:48 2009 From: john.migliozzi at gmail.com (John Migliozzi) Date: Thu, 04 Jun 2009 10:47:48 -0400 Subject: [Mristudio-users] ROI Editor Questions In-Reply-To: References: Message-ID: Thank you. I have another question as well: In Landmarker, I would like to preform multichannel LDDMM, between my data and some of the Atlas Sample Data, but none of the Atlas Sample Data has parameters that match my data. Is there a way that I can adjust the sample data (or my data) so that they both have the same paramters? Thanks, John On Wed, Jun 3, 2009 at 7:07 PM, susumu mori wrote: > Hi John, > > Xin can answer some questions better than me, but let me answer some > questions; > > 1: Add / Subtract / Multiply / Divide: you need to load at least two images > into one window. The first image needs to be loaded using the "open" icon in > the upper menu bar and the second from the "open" icon in the right column > of the viewing window. Once two images are loaded, you should see them > listed in the pull-down menu in the right column. If you have more than 2 > images, you can use this function for addition / subtraction / > multiplication / division. The T2 option can calculate a T2 map from > multiple T2-weighted images. For example, if you have two images with TE = > 40 and 100 ms, you can load them into one window. If you choose the T2 > option, another window pops up for you to specify the echo times. Then, you > can calculate a T2 map. > > 3: You can select pixels based on thresholding. For example, you can load > an FA map and specify pixels between 0.3 and 0.8 using this button. Then you > can register such pixels as an ROI. > > 4: Skull stripping: I agree that there are too many parameters. There are > single and multi-contrast options. For the single-image option, it is > basically a automate region-growing. It is like you start to blow a balloon > from the center of the image. The balloon stops expanding when it hits the > brain boundary (large intensity change between the brain and skull). Then > the balloon stops growing when it becomes the shape of the brain. In this > way, it can automatically define the boundary of the brain and thus can > remove the skull. Some of the parameters can control the softness of the > balloon. If the balloon is too stiff, it can not accurately trace the brain > shape. If it's too soft, it can leak to connected structures such as the > skull and eyeballs. You can use aDWI (average of all DWIs) or b0 with the > single-image skull stripping. With the default values, it should work. These > images usually has very faint skull intensity and skull removal should be > straightforward. > > For the dual-image option, you can specify b0 or aDWI (with which the skull > strip is easy) and T1 or T2 anatomical images (with which the skull strip is > difficult). It first does the single-image skull strip using b0 or aDWI. > Then the defined brain boundary is transferred to T1 or T2 anatomical > images. Here, the T1 and T2 must be coregistered with b0 (or aDWI) and has > the same dimension by going through our registration software (Landmarker). > Because b0/aDWI often has image distortion (and also registration errors), > the simple transfer of the brain boundary defined by b0 (or aDWI) is not > accurate. This software then searched the nearest brain boundary by > massaging the initial shape. We had some success to skull-strip > co-registered T2-weighted anatomical images using this function, but it is > still work-in-progress. That's why all the parameters are available for us > to do parameter setup. > > 5: Export Pixel value: This is to create a histogram. Once you define an > object (ROI), you can get a report of pixel intensity averaged over all > pixels inside the ROI. However, you may not want such average and want to > know the distribution of values of all pixels in the ROI. In this case, you > can export the pixel values as a text file, read by Exel, and create a > histogram. > > Susumu > > On Wed, Jun 3, 2009 at 12:56 PM, John Migliozzi wrote: > >> Hi everyone, >> >> I'm working with ROI Editor, and I have a few questions regarding some >> features of the program. >> >> 1. Operations. I understand how mask works, but cannot figure out the >> add, subtract, multiply, divide, and T2 >> 2. Change ROI File Header. >> 3. Threshold. >> 4. Skull Stripping. I cannot figure out how to appropriately adjust >> these parameters. >> 5. Export Pixel Value option when you right-click on an object. What do >> the numbers in the text file mean? >> >> Also, I am having a problem when I try to import ROIs from ROI Editor back >> into DTI Studio. Regardless of what format in which I export the data, DTI >> Studio tells me it is an "unrecognized Image-ROI data file." >> >> If anyone can answer any of these questions, I would be really >> appreciative. >> >> Thanks, >> >> John Migliozzi >> john.migliozzi at gmail.com >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090604/1736c0fb/attachment.html From susumu at mri.jhu.edu Thu Jun 4 20:13:29 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Thu, 04 Jun 2009 20:13:29 -0400 Subject: [Mristudio-users] ROI Editor Questions In-Reply-To: References: Message-ID: please go over https://www.mristudio.org/wiki/user_manual/landmarker and follow Step one-two-three. For the first step, you can choose any ICBM-152 based atlas (JHN-MNI-GA, JHU-MNI-SS, ICBM-DTI-81). After Step 1, not only the brain location and orientation become similar to the atlas, but also he matrix and pixel size become the same; 181x217x181 / 1x1x1 mm. This pre-conditioning is necessary to do LDMM (Step 2). On Thu, Jun 4, 2009 at 10:47 AM, John Migliozzi wrote: > Thank you. I have another question as well: In Landmarker, I would like > to preform multichannel LDDMM, between my data and some of the Atlas Sample > Data, but none of the Atlas Sample Data has parameters that match my data. > Is there a way that I can adjust the sample data (or my data) so that they > both have the same paramters? > > Thanks, > John > > On Wed, Jun 3, 2009 at 7:07 PM, susumu mori wrote: > >> Hi John, >> >> Xin can answer some questions better than me, but let me answer some >> questions; >> >> 1: Add / Subtract / Multiply / Divide: you need to load at least two >> images into one window. The first image needs to be loaded using the "open" >> icon in the upper menu bar and the second from the "open" icon in the right >> column of the viewing window. Once two images are loaded, you should see >> them listed in the pull-down menu in the right column. If you have more than >> 2 images, you can use this function for addition / subtraction / >> multiplication / division. The T2 option can calculate a T2 map from >> multiple T2-weighted images. For example, if you have two images with TE = >> 40 and 100 ms, you can load them into one window. If you choose the T2 >> option, another window pops up for you to specify the echo times. Then, you >> can calculate a T2 map. >> >> 3: You can select pixels based on thresholding. For example, you can load >> an FA map and specify pixels between 0.3 and 0.8 using this button. Then you >> can register such pixels as an ROI. >> >> 4: Skull stripping: I agree that there are too many parameters. There are >> single and multi-contrast options. For the single-image option, it is >> basically a automate region-growing. It is like you start to blow a balloon >> from the center of the image. The balloon stops expanding when it hits the >> brain boundary (large intensity change between the brain and skull). Then >> the balloon stops growing when it becomes the shape of the brain. In this >> way, it can automatically define the boundary of the brain and thus can >> remove the skull. Some of the parameters can control the softness of the >> balloon. If the balloon is too stiff, it can not accurately trace the brain >> shape. If it's too soft, it can leak to connected structures such as the >> skull and eyeballs. You can use aDWI (average of all DWIs) or b0 with the >> single-image skull stripping. With the default values, it should work. These >> images usually has very faint skull intensity and skull removal should be >> straightforward. >> >> For the dual-image option, you can specify b0 or aDWI (with which the >> skull strip is easy) and T1 or T2 anatomical images (with which the skull >> strip is difficult). It first does the single-image skull strip using b0 or >> aDWI. Then the defined brain boundary is transferred to T1 or T2 anatomical >> images. Here, the T1 and T2 must be coregistered with b0 (or aDWI) and has >> the same dimension by going through our registration software (Landmarker). >> Because b0/aDWI often has image distortion (and also registration errors), >> the simple transfer of the brain boundary defined by b0 (or aDWI) is not >> accurate. This software then searched the nearest brain boundary by >> massaging the initial shape. We had some success to skull-strip >> co-registered T2-weighted anatomical images using this function, but it is >> still work-in-progress. That's why all the parameters are available for us >> to do parameter setup. >> >> 5: Export Pixel value: This is to create a histogram. Once you define an >> object (ROI), you can get a report of pixel intensity averaged over all >> pixels inside the ROI. However, you may not want such average and want to >> know the distribution of values of all pixels in the ROI. In this case, you >> can export the pixel values as a text file, read by Exel, and create a >> histogram. >> >> Susumu >> >> On Wed, Jun 3, 2009 at 12:56 PM, John Migliozzi > > wrote: >> >>> Hi everyone, >>> >>> I'm working with ROI Editor, and I have a few questions regarding some >>> features of the program. >>> >>> 1. Operations. I understand how mask works, but cannot figure out the >>> add, subtract, multiply, divide, and T2 >>> 2. Change ROI File Header. >>> 3. Threshold. >>> 4. Skull Stripping. I cannot figure out how to appropriately adjust >>> these parameters. >>> 5. Export Pixel Value option when you right-click on an object. What do >>> the numbers in the text file mean? >>> >>> Also, I am having a problem when I try to import ROIs from ROI Editor >>> back into DTI Studio. Regardless of what format in which I export the data, >>> DTI Studio tells me it is an "unrecognized Image-ROI data file." >>> >>> If anyone can answer any of these questions, I would be really >>> appreciative. >>> >>> Thanks, >>> >>> John Migliozzi >>> john.migliozzi at gmail.com >>> >>> _______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: >>> Mristudio-users-unsubscribe at mristudio.org >>> >>> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090604/3937f1ef/attachment-0001.html From svazirian at ucla.edu Fri Jun 5 14:44:13 2009 From: svazirian at ucla.edu (Samra Vazirian) Date: Fri, 05 Jun 2009 11:44:13 -0700 Subject: [Mristudio-users] HOW TO RUN DTI STUDIO-latest-x86.exe. ON MAC Message-ID: <20090605114413.st7mfruzcccg8gkw@mail.ucla.edu> Hi, I tried to download DTI studio, version: DtiStudio-latest-x86.exe. on MAC, but it is not running. Could you please guide me how to run DTI studio on MAC?. Many thanks, Samra ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Samra Vazirian, M.D. Postdoctoral Scholar UCLA Center for Autism Research and Treatment Semel Institute for Neuroscience and Human Behavior 760 Westwood Plaza, Suite 68-217 Los Angeles, CA 90024-1759 TEL: 310.794-9330 e-mail: svazirian at ucla.edu From siewmin.gan at gmail.com Fri Jun 5 16:50:47 2009 From: siewmin.gan at gmail.com (Siewmin Gan) Date: Sat, 06 Jun 2009 06:50:47 +1000 Subject: [Mristudio-users] HOW TO RUN DTI STUDIO-latest-x86.exe. ON MAC In-Reply-To: <20090605114413.st7mfruzcccg8gkw@mail.ucla.edu> References: <20090605114413.st7mfruzcccg8gkw@mail.ucla.edu> Message-ID: Hi Samra, you can install a VMware fusion and Windows (XP) on it. You can then work on the DTI studio on your additional windows platform. cheers Siewmin On Sat, Jun 6, 2009 at 4:44 AM, Samra Vazirian wrote: > Hi, > > I tried to download DTI studio, version: DtiStudio-latest-x86.exe. on > MAC, but it is not running. Could you please guide me how to run DTI > studio on MAC?. > > Many thanks, > Samra > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > Samra Vazirian, M.D. > > Postdoctoral Scholar > UCLA Center for Autism Research and Treatment > Semel Institute for Neuroscience and Human Behavior > 760 Westwood Plaza, Suite 68-217 > Los Angeles, CA 90024-1759 > TEL: 310.794-9330 > e-mail: svazirian at ucla.edu > > > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090606/2b44c5ab/attachment.html From naamab at stanford.edu Fri Jun 5 17:27:50 2009 From: naamab at stanford.edu (Naama Barnea-Goraly) Date: Fri, 05 Jun 2009 14:27:50 -0700 Subject: [Mristudio-users] Is there a way to see the ROIs we imported for fibertracking ? Message-ID: <85D04FA7-E983-43C1-A960-09BF34A6E062@stanford.edu> Dear MRIstudio list, We are importing ROIs generated in FSL into DTIstudio for fibertracking (thanks to support we got on the list). I am using roieditor to save the rois as a raw image and then open it in DTIstudio. It works for fibertracking but I cannot see the actual ROI I am using, so I can't tell what is the original ROI and what was "tracked" from it. Is there a way to make the ROI visible? Thanks, Naama Naama Barnea-Goraly M.D. Instructor Center for Interdisciplinary Brain Sciences Research Stanford University Division of Child and Adolescent Psychiatry 401 Quarry Rd. MC 5795 Stanford University School of Medicine Stanford, CA 94305-5795 Phone: (650) 736-1874, fax: (650) 724-4794 CONFIDENTIALITY NOTICE: This e-mail communication and any attachments may contain confidential information for the use of the designated recipients named above. If you are not the intended recipient, you are hereby notified that you have received this communication in error and that any review, disclosure, dissemination, distribution or copying of it or its contents is prohibited. If you have received this communication in error, please notify Stanford Medical Center immediately by telephone at (650) 725-5722 and destroy all copies of this communication and any attachments. Thank you. From susumu at mri.jhu.edu Sat Jun 6 10:00:07 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Sat, 06 Jun 2009 10:00:07 -0400 Subject: [Mristudio-users] HOW TO RUN DTI STUDIO-latest-x86.exe. ON MAC In-Reply-To: References: <20090605114413.st7mfruzcccg8gkw@mail.ucla.edu> Message-ID: Hi Samra, Siewmin is right. Our program doesn't run on Mac OS. You need emulation software. On Fri, Jun 5, 2009 at 4:50 PM, Siewmin Gan wrote: > Hi Samra, you can install a VMware fusion and Windows (XP) on it. You can > then work on the DTI studio on your additional windows platform. > cheers > Siewmin > > > On Sat, Jun 6, 2009 at 4:44 AM, Samra Vazirian wrote: > >> Hi, >> >> I tried to download DTI studio, version: DtiStudio-latest-x86.exe. on >> MAC, but it is not running. Could you please guide me how to run DTI >> studio on MAC?. >> >> Many thanks, >> Samra >> >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >> >> Samra Vazirian, M.D. >> >> Postdoctoral Scholar >> UCLA Center for Autism Research and Treatment >> Semel Institute for Neuroscience and Human Behavior >> 760 Westwood Plaza, Suite 68-217 >> Los Angeles, CA 90024-1759 >> TEL: 310.794-9330 >> e-mail: svazirian at ucla.edu >> >> >> >> >> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090606/04782206/attachment.html From xli16 at jhmi.edu Mon Jun 8 15:28:12 2009 From: xli16 at jhmi.edu (Xin Li) Date: Mon, 08 Jun 2009 15:28:12 -0400 Subject: [Mristudio-users] ROI Editor Questions In-Reply-To: References: Message-ID: Hi John, I am not quite sure about what you exactly mean by "Change ROI header file, but I can give several general information. For ROI, you have options for RoiEditor format, Analyze format or Binary Map. The last format won't save some information such as names of the ROIs. We recommend to use the RoiEditor format, as much as possible. The RoiEditor format consists of two files; one integer file that stores the coordinates of the ROIs and one header file. You can not open and edit this header file. If you have a situation in which you want to copy a header file to another integer ROI file with different image dimensions, please try the "Change ROI File Header" function in RoiEditor. Hope this will give you some help. Xin ----- Original Message ----- From: John Migliozzi Date: Wednesday, June 3, 2009 12:57 pm Subject: [Mristudio-users] ROI Editor Questions To: mristudio-users at mristudio.org > Hi everyone, > > I'm working with ROI Editor, and I have a few questions regarding some > features of the program. > > 1. Operations. I understand how mask works, but cannot figure out > the add, > subtract, multiply, divide, and T2 > 2. Change ROI File Header. > 3. Threshold. > 4. Skull Stripping. I cannot figure out how to appropriately adjust > these > parameters. > 5. Export Pixel Value option when you right-click on an object. > What do > the numbers in the text file mean? > > Also, I am having a problem when I try to import ROIs from ROI Editor > back > into DTI Studio. Regardless of what format in which I export the > data, DTI > Studio tells me it is an "unrecognized Image-ROI data file." > > If anyone can answer any of these questions, I would be really > appreciative. > > Thanks, > > John Migliozzi > john.migliozzi at gmail.com > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From fcanturk at erciyes.edu.tr Tue Jun 9 02:51:08 2009 From: fcanturk at erciyes.edu.tr (fcanturk at erciyes.edu.tr) Date: Tue, 09 Jun 2009 06:51:08 +0000 Subject: [Mristudio-users] Diffusion calculated Message-ID: Hello Dr. Susumu and mristudio users I have got a few questions. 1- I want to calculate the diffusion. Are there diffrerent between MRI view 3D and DTI mapping in the DTI Studio? Which can calculate the most accurate diffusion ? Can I calculate the diffusion in the DTI Studio? 2-This warning "File size is smaller than DW-image size, continue anyway" in the DTI mapping. From fcanturk at erciyes.edu.tr Tue Jun 9 03:35:01 2009 From: fcanturk at erciyes.edu.tr (fcanturk at erciyes.edu.tr) Date: Tue, 09 Jun 2009 07:35:01 +0000 Subject: [Mristudio-users] Diffusion calculated In-Reply-To: Message-ID: Hello Dr. Susumu and mristudio users I have got a few questions. 1- I want to calculate the diffusion. Are there diffrerent between MRI view 3D and DTI mapping in the DTI Studio? Which can calculate the most accurate diffusion ? Can I calculate the diffusion in the DTI Studio? 2-This warning "File size is smaller than DW-image size, continue anyway" in the DTI mapping. FAZ?LE CANTURK From shivangi.lohia at gmail.com Tue Jun 9 09:34:23 2009 From: shivangi.lohia at gmail.com (Shivangi Lohia) Date: Tue, 09 Jun 2009 09:34:23 -0400 Subject: [Mristudio-users] DTIstudtio Message-ID: <350167f10906090634g8c50ec6ob48715b5051fb32f@mail.gmail.com> Hi Dr. Susumu, I am a research intern at Children's National Medical Center. We've been working to download the latest versions of DTIstudio and ROIeditor, however, we are unable to do so because the website requires a username and password. I know in the past this was not an issue and we are wondering how to get around that. Please let me know when you have a chance. Thank you. Shivangi Lohia Children's National Medical Center Children's Research Institute 111 Michigan Avenue, NW Washington, D.C. 20010 From raj.jaswal at gmail.com Tue Jun 9 14:08:33 2009 From: raj.jaswal at gmail.com (Raj Jaswal) Date: Tue, 09 Jun 2009 14:08:33 -0400 Subject: [Mristudio-users] DTIstudtio In-Reply-To: <350167f10906090634g8c50ec6ob48715b5051fb32f@mail.gmail.com> References: <350167f10906090634g8c50ec6ob48715b5051fb32f@mail.gmail.com> Message-ID: <32a27f2a0906091108q50448b3ama3183f2c60a20d1c@mail.gmail.com> Hi Shivangi, You can click on "Register New Account" on the front page and create a username/password in order to download the s/w you need. That should work. - RJ On Tue, Jun 9, 2009 at 9:34 AM, Shivangi Lohia wrote: > Hi Dr. Susumu, > > I am a research intern at Children's National Medical Center. We've > been working to download the latest versions of DTIstudio and > ROIeditor, however, we are unable to do so because the website > requires a username and password. I know in the past this was not an > issue and we are wondering how to get around that. Please let me know > when you have a chance. Thank you. > > > > Shivangi Lohia > > Children's National Medical Center > > Children's Research Institute > > 111 Michigan Avenue, NW > > Washington, D.C. 20010 > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090609/466f30d3/attachment.html From dylan.alegria at gmail.com Thu Jun 11 15:32:22 2009 From: dylan.alegria at gmail.com (Dylan Alegria) Date: Thu, 11 Jun 2009 12:32:22 -0700 Subject: [Mristudio-users] transformations with AIR in Landmarker In-Reply-To: <7k7ed7$7f10r2@ipex3.johnshopkins.edu> References: <7k7ed7$7f10r2@ipex3.johnshopkins.edu> Message-ID: Hi Susumu, The protocol listed here and online have been very useful to me as I attempt to normalize my data. However, even while following these procedures I suffer from the same problems. Namely, when I attempt to register to another subject in my group no changes are made. As Siewmin said: "It seems to only work if the template is one of those provided in Landmarker." Any suggestions would be greatly appreciated. Additionally, when I use one of the provided templates and save them, I find that they cannot be opened by DTIStudio. The number of slices in the newly created image does not match what is displayed in Landmarker. I understand that it should be resampled to the resolution of the template, but even using these dimensions does not allow for correct display of the images. I have found this to be true for FA images as well as EigenVectors and Tensor images. It is possible that I don't have the correct dimensions for importing, but I have tried all that seem logical (given the dimensions of the template and original image). Again, any comments would be very helpful. Best, Dylan Dylan Alegria CIBSR Imaging RA Stanford University dalegria at stanford.edu (650) 736 0732 On May 11, 2009, at 11:25 AM, susumu wrote: > For those who are interested in image normalization by Landmarker, > here I attached a step-by-step instruction. > Siewmin, I could transform your data with the default setup using > this procedure. > > Susumu > > From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org > ] On Behalf Of Siewmin Gan > Sent: Monday, May 11, 2009 12:21 PM > To: DTI Studio, ROI Editor, Landmarker Questions/Support > Subject: Re: [Mristudio-users] transformations with AIR in Landmarker > > Hi Susumu, I have learnt a lot from your correspondence, as usual. > Will try as you've suggested. > > Thanks > > Siewmin > > From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org > ] On Behalf Of susumu [susumu at mri.jhu.edu] > Sent: Sunday, May 10, 2009 9:39 AM > To: 'DTI Studio, ROI Editor, Landmarker Questions/Support' > Subject: Re: [Mristudio-users] transformations with AIR in Landmarker > Siewmin raised some important points and I hope other users could > gain some important information from this thread. > > > > I got the mean DWI and tensor file from the original 4D DWI. The > tensor file is as you've said, which contains "Dxx, Dyy, Dzz, Dxy, > Dxz Dyz" in one file. In Landmarker, I loaded only the mean DWI of > the subject and then the tensor file with the "open .d" button. The > 4D raw DWI is not used in Landmarker or later. With the "linear" > option in AIR, I could rotate the tensor and the mean DWI to the > template DWI without having to subsample the input data first. The > "nonlinear" option requires the subject data (mean DWI and the > tensor file) to be of the same dimension as the template (i.e 181, > 217, 181 if ICBM81 DWI is used as template). This is noted in the > pop up message, and it would only continue once the input files are > resampled to the template. > > > > >It is always advised to do linear transformation first. To start > non-linear, you have to make sure that the brain locations and > shapes are as similar as possible. This is similar to non-linear > fitting. You always have to provide ?initial? values close to the > real solutions. Otherwise, non-linear fitting could converge to a > wrong solution (trapped by ?local minima?). > > > > Additionally, I tried affine in the linear registration option. The > output DWI of the registration is identical to the input of the DWIs > if I used one of my subject's DWI as the template. Using the 2nd > order polynomial in nonlinear option, an error message occurs > "registration terminated due to a calculation problem, please try a > lower order model". It seems to only work if the template is one of > those provided in Landmarker. > > > > > If you can send us two images you are having the problem, we can > take a look at why AIR doesn?t work. > > > > I then saved the rotated tensor file as one file in the .dat format > and the linearly registered 3D meanDWI. In MRIview3D, I loaded this > new 3D DWI and open this new tensor.dat file with the open.dat > button to re-calculates the fa, colour map etc. I viewed the colour > map output from this and it looks pretty good, and as described > previously. > > > > > This is the correct procedure. > > > > I saved the fa and principal eigenvector file and used them to > perform fiber-tracking. The tracts that are manually extracted > obtained looks similiar to the fiber tracts from the original raw 4D > DWI. > > > > > That is a good sign. > > > > The FA values of these tracts are smaller uniformly in comparison, > and the assymetry preserved (i.e the left tract FA is smaller than > the right tract FA using the maps calculated from the original and > rotated tensor). > > > > > Normalization requires pixel interpolation, which leads to > decreased FA. So you can not compare FA values with and without > normalization. > > > > If the non-linear option is used, is there a problem that the tensor > is subsampled first before it is re-oriented, as described above? > > > > > As I mentioned above, nonlinear should be AFTER linear > transformation. This means, the data are transformed multiple times > and pixels are interpolated multiple times. To avoid this, once you > did linear (save transformation matrix: T-linear) and nonlinear > (save transformation matrix: T-nonlinear), you can combine the T- > linear x T-nonlinear using one of the buttons in the LDDMM section. > Once you combined all transformation matrices, you can apply it only > once to the original image in the native space. > > > > > Another interesting thing is, there are two ways to transform > images; transform your image to an atlas or transform atlas > (usually, binary segmentation map) to your original data for > automated segmentation. For the latter approach, you don?t have to > transform (therefore interpolate) your original data. When you > transform the atlas (segmentation map), make sure to use ?nearest > neighbor? (no interpolation), not the tri-linear interpolation. The > segmentation map consists of arbitrary numbers assigned to each > segment (e.g. the internal capsule is ?1? and the corona radiata is > ?3?). If you interpolate these two segments and obtain ?2? in > between these two segments and if ?2? means pons, you would get the > pons in between the internal capsule and the corona radiata. On the > other hand, when you are transforming your data to an atlas space, > use the tri-linear interpolation. Otherwise, you could get strange > discontinuity artifacts. > > > > Do you suggest using the affine or non-linear transformation of the > DWIs and the corresponding transformation of the tensor? Lastly, I'm > not sure if the colour map display is of an issue? It occurs both > using the linear affine option and the non-linear option. > > > > > When everything is working right, the color map should look smooth > and clean. Maybe you are using ?nearest neighbor? for the tensor > transformation? > > > > Thanks > > > > Siewmin > > > > > > > > > > On Sat, May 9, 2009 at 7:44 AM, susumu wrote: > > First, I tried rotating the tensor but had problems with the > results. When I look at the colour map from the resulting tensor, it > looks ok generally, but there are certain areas of blotchiness and > some mixing of colours especially in the sidelines of white matter > regions (i.e there can be a striking red line or a blotch of redness > in the middle of a green regions within the saggital stratum). These > are the steps I took, and would like to check if it is done correctly. > > 1. resample mean DWI of subject data (together with the 4D DTI data > and the tensor) to DWI of ICBM 81 template. Non-linear transform > (2nd order trilinear) the resampled meandwi of subject to dwi of > template, and used that to drive the transformation of the resampled > 4D DTI and the resampled tensor simultaneously. (The resampled > tensor was loaded with the .dat button.) I used MRIview 3D to load > the normalised 4D DTI, followed by the normalised tensor with > the .dat button, and calculate the fa, colour etc maps from the > normalised tensor. I tried various thresholding with AIR but the > colour maps problem remains. > > > > > First of all, I think you don't have to resample DTI images before > AIR. AIR can take data with different matrix and pixel sizes and the > output images have the same matrix/pixel dimensions as the template > (in your case, 181x217x181 of ICBM81). > > > By saying "4D DTI", do you mean raw 4D DWI before tensor > calculation? if so, I don't think you want transform raw DWIs. If > you want to do anything to raw DTI, you also want to transform the > corresponding gradient table, which could be messy. Our tools do not > provide methods to transform raw DWIs. > > > When you say, "tensor" data, I assume you are talking about 4D > file that contains "Dxx, Dyy, Dzz, Dxy, Dxz, Dyz" images in one > file. If so, please make sure that you load this 4D tensor file by > the "open .d" button in Landmarker. Once read in Landmarker, the 4D > tensor file is disassembled to 6 3D data for Dxx, Dyy, Dzz, Dxy, > Dxz, Dyz. > > > Once the AIR is done using mean DWI (your data) - mean DWI > (template), the 6 3D tensor element data should be stored all > together into one file as a "transformed 4D tensor file". > > > This transformed 4D tensor file needs to be read into DtiStudio to > re-calculate new transformed FA, color, vec, etc. > > > The blotch-looking colormap could happen by; 1) transform the > color map directly (you should recreate color maps using the > recalcuated FA and vector files from the transformed tensor file or > 2) you transformed a vector file (transformed vector files should be > obtained from the transformed tensor file. Vector can not be > directly transformed). > > > > Second, I tried without rotating the tensor. I calculate the scalar > and colour maps from the original 4D DTI data, aligned the maps to > AC-PC line, draw rois on them and invert transform the rois back to > native dti space to extract the relevant white matter tracts. I had > two problems here. 1) with orienting the subjects scalar DWI to > another particular subject's DWI with rigid transformation in AIR > and 2) Invert transform ROIs drawn on the registered colour map back > to the original DTI space. These are the steps I took: > > > > > Maybe you are transforming raw DWI data? Again, you should not > transform raw DWI and recalcuate tensor. You have to first calculate > tensor (throw away the raw DWIs) and transform the tensor. > > > > 1. A subject's data which is acquired // to AC-PC is chosen and > other subjects not acquired //to AC are registered to this. Again > the meanDWI is used for source and target images, this time using > rigid transformation in AIR in Landmarker. However, there is no > difference detected after the transformation has taken place. > However, if I change the target image from a subject's DWI to the > mean DWI of the ICBM 81 template, it works but the source data would > be subsampled to that of the ICBM template. I'm not sure why it > didn't work in the 1st case? > > > > > As mentioned above, AIR not only adjust the image orientation and > translation, but also the matrix / pixel size.. > > > Rigid transformation of AIR is sometimes very cranky. We are > working on alternative methods now. please try different threshold > or affine. > > > > Additionally, using either another subject or the template DWI as > target image, would yield the an output file (AlignlinearOutput.air) > when the transformation has been performed, which I saved the > invert_AlignlinearOutput.air. However, when I clicked on these .air > files in the folder it is saved as an installer package, I get the > following error message " An error has occurred.The application > could not be installed because the AIR file is damaged. Try > obtaining a new AIR file from the application author." I have > installed the air application and placed it in the same folder, > together with the alignlinear.exe file. Is it possible to view the > transformation matrix files saved or did I not installed the air > application appropriately? > > > > > Maybe Xin can answer this question better, but I'm not sure why > you want to open *.air?? > > > Once you save the *.air, you can load it back to Landmarker and > apply to images by using the "open M" button in the LDDMM section. > > > > 2. ROIs are drawn on the transformed AC-PC aligned colour maps with > ROI-editor. I would like to check if it's OK to draw rois on the > transformed colour map? These ROIs would later be used as the start > ROI and stop ROI to extract the corresponding white matter tract > with DTI studio) > > > > > Drawing ROIs on color maps is fine. ROI is simply 1/0 information > about which pixels you chose and the color maps are simply what is > displayed to aid your ROI drawing. > > > If you draw ROI in the atlas space and have a plan to back- > transform your ROI files to the native space, there are several > things you have to know; > > 1) Atlas space is 1x1x1 and your native space could be 2-3 mm. The > ROI defined in the thin 1 mm slice could be lost after > transformation to the thick 2-3mm slice. Therefore, you have to > create 3D ROIs in the atlas space with at least 3mm thick > > 2) Use nearest neighbor interpolation when you back-transfer. You > don't want to get a pixel with 0.3 or 0.4 after transformation. You > want 1/0 > > > > 3. I tried to invert-transform these ROIs back to the original DTI > space with the previously saved invert_matrix.air file. How is that > done in Landmarker and if the previous error message needs to be > resolved before I can used the matrix files? > > > > > Xin, how to do the invert-transformation of *.air? > > > > Susumu > > > > > > > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > > > This e-mail message (including any attachments) is for the sole use of > the intended recipient(s) and may contain confidential and privileged > information. If the reader of this message is not the intended > recipient, you are hereby notified that any dissemination, > distribution > or copying of this message (including any attachments) is strictly > prohibited. > > If you have received this message in error, please contact > the sender by reply e-mail message and destroy all copies of the > original message (including attachments). > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090611/1e903de5/attachment-0001.html From Kavindra.Nath at moffitt.org Fri Jun 12 09:21:48 2009 From: Kavindra.Nath at moffitt.org (Nath, Kavindra) Date: Fri, 12 Jun 2009 09:21:48 -0400 Subject: [Mristudio-users] About DTI Message-ID: Hi I have DTI data from GE 1.5 scanner, 408 images, 34 slices, dodeca. How can I use the DTI studio software to open this file for processing and quantitation. There are 408 MRGE images and software takes only one image. Please suggest. Thanks Kavindra Nath Moffitt Cancer Center Tampa Florida This transmission may be confidential or protected from disclosure and is only for review and use by the intended recipient. Access by anyone else is unauthorized. Any unauthorized reader is hereby notified that any review, use, dissemination, disclosure or copying of this information, or any act or omission taken in reliance on it, is prohibited and may be unlawful. If you received this transmission in error, please notify the sender immediately. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090612/1b108524/attachment.html From rajagov2 at ccf.org Tue Jun 16 15:25:03 2009 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Tue, 16 Jun 2009 15:25:03 -0400 Subject: [Mristudio-users] Color map image References: <7k7ed7$7ghukf@ipex3.johnshopkins.edu> Message-ID: <77A88E90A851594AAEF830450587C39D01EDAA88@CCHSCLEXMB56.cc.ad.cchs.net> Dear DTI studio Users, I am having difficulty in loading "color map 0" (color coded FA map created in DTI studio) in FSL (where i am doing some analysis of DTI images processed using DTI studio) . When i try to load it even for viewing purpose FSL rejects by saying that "data format 128 not supported". Could anyone please help me with this. Is it possible to convert this image "data 128" to "data 16" (i mean interger 16 format). Thanks in advance, venkateswaran =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S. News & World Report (2008). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 3452 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090616/51010a90/attachment.bin From susumu at mri.jhu.edu Mon Jun 22 09:55:19 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Mon, 22 Jun 2009 09:55:19 -0400 Subject: [Mristudio-users] Color map image In-Reply-To: <77A88E90A851594AAEF830450587C39D01EDAA88@CCHSCLEXMB56.cc.ad.cchs.net> References: <7k7ed7$7ghukf@ipex3.johnshopkins.edu> <77A88E90A851594AAEF830450587C39D01EDAA88@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: I'm not sure what is the file format of FLS needs to be for color maps, but you may try the Analyze format. On Tue, Jun 16, 2009 at 3:25 PM, Rajagopalan, Venkateswaran < rajagov2 at ccf.org> wrote: > Dear DTI studio Users, > > I am having difficulty in loading "color map 0" (color coded FA map created > in DTI studio) in FSL (where i am doing some analysis of DTI images > processed using DTI studio) . When i try to load it even for viewing purpose > FSL rejects by saying that "data format 128 not supported". Could anyone > please help me with this. Is it possible to convert this image "data 128" to > "data 16" (i mean interger 16 format). > > Thanks in advance, > > venkateswaran > > > > > > > > > =================================== > > P Please consider the environment before printing this e-mail > > Cleveland Clinic is ranked one of the top hospitals > in America by U.S. News & World Report (2008). > Visit us online at http://www.clevelandclinic.org for > a complete listing of our services, staff and > locations. > > > Confidentiality Note: This message is intended for use > only by the individual or entity to which it is addressed > and may contain information that is privileged, > confidential, and exempt from disclosure under applicable > law. If the reader of this message is not the intended > recipient or the employee or agent responsible for > delivering the message to the intended recipient, you are > hereby notified that any dissemination, distribution or > copying of this communication is strictly prohibited. If > you have received this communication in error, please > contact the sender immediately and destroy the material in > its entirety, whether electronic or hard copy. Thank you. > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090622/87983546/attachment.html From rajagov2 at ccf.org Tue Jun 23 09:48:19 2009 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Tue, 23 Jun 2009 09:48:19 -0400 Subject: [Mristudio-users] Color map image References: <7k7ed7$7ghukf@ipex3.johnshopkins.edu> <77A88E90A851594AAEF830450587C39D01EDAA88@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: <77A88E90A851594AAEF830450587C39D01EDAA94@CCHSCLEXMB56.cc.ad.cchs.net> Thanks Dr.Mori, i tried using analyze format but it says "data format 128 not supported". When i looked at what is data format 128 by looking at the header information by comparing the header files (analyze format) of this colormap with the regular dti image (i.e the EPI image) in the data format for EPI image it says "16" (i think this is number of bits) whereas for the color map this data format value is "128". Thanks again for your kind help. Regards venkateswaran ________________________________ From: mristudio-users-bounces at mristudio.org on behalf of susumu mori Sent: Mon 6/22/2009 9:55 AM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] Color map image I'm not sure what is the file format of FLS needs to be for color maps, but you may try the Analyze format. On Tue, Jun 16, 2009 at 3:25 PM, Rajagopalan, Venkateswaran wrote: Dear DTI studio Users, I am having difficulty in loading "color map 0" (color coded FA map created in DTI studio) in FSL (where i am doing some analysis of DTI images processed using DTI studio) . When i try to load it even for viewing purpose FSL rejects by saying that "data format 128 not supported". Could anyone please help me with this. Is it possible to convert this image "data 128" to "data 16" (i mean interger 16 format). Thanks in advance, venkateswaran =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S. News & World Report (2008). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S. News & World Report (2008). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 5910 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090623/6f6a61f1/attachment-0001.bin From choisj70 at gmail.com Tue Jun 23 22:15:57 2009 From: choisj70 at gmail.com (Seongjin) Date: Tue, 23 Jun 2009 22:15:57 -0400 Subject: [Mristudio-users] Fiber tracking after normalization Message-ID: I have normalized FA data and tensor data. I would like to fiber tracking with the normalized data. However, vector normalization is not recommended on Landmarker and fiber tracking needs FA data and vector data. Anybody know what I should do at this stage? Thanks in advance. -SC -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090623/22ae7593/attachment.html From choisj70 at gmail.com Wed Jun 24 08:12:12 2009 From: choisj70 at gmail.com (Seongjin) Date: Wed, 24 Jun 2009 08:12:12 -0400 Subject: [Mristudio-users] Questions regarding Transformation in Landmark In-Reply-To: <173442.34069.qm@web30704.mail.mud.yahoo.com> References: <104498.25444.qm@web30707.mail.mud.yahoo.com> <173442.34069.qm@web30704.mail.mud.yahoo.com> Message-ID: Hi HTH, When I tried to read normalized tensor.d file, I need to load DTI data with gradient table, but these are not generated from Landmark. As far as I get, all of them are updated FA, ADC, tensor file etc. When I start with data before normalization read and I can open the tensor file. Otherwise there is no way to read tensor file. I wonder if I am doing correctly. Do you know other way to read tensor file only? Thanks in advance. -SC On Fri, May 1, 2009 at 7:08 PM, darshan pai wrote: > no you do not transform the vector file. you have the tensor right . You > open the tensor in DTIStudio using the Open .d button, choose the tensor . > It asks you for options regarding if you want to make eigen vectors FA , RA > etc . Let it run, it will make all the files , just save what you need . > > HTH > > ------------------------------ > *From:* [Seongjin] > *To:* "DTI Studio, ROI Editor, Landmarker Questions/Support" < > mristudio-users at mristudio.org> > *Sent:* Friday, May 1, 2009 4:43:27 PM > *Subject:* Re: [Mristudio-users] Questions regarding Transformation in > Landmark > > Thanks for you reply. > > I guessed *.ani file will be the same. However, regarding *.vec file, I > were warned not to transform vector file. I have no idea on this. Anyone who > knows the answer? > > -SC > > On Fri, May 1, 2009 at 3:18 PM, darshan pai wrote: > >> *.ani is the updated_FA file >> and *.vec is the updated eigenvector0 file. >> I think the format for both is *.dat .. just different extensions to >> differentiate I guess .. >> >> ------------------------------ >> *From:* [Seongjin] >> *To:* "DTI Studio, ROI Editor, Landmarker Questions/Support" < >> mristudio-users at mristudio.org> >> *Sent:* Friday, May 1, 2009 12:01:05 PM >> *Subject:* [Mristudio-users] Questions regarding Transformation in >> Landmark >> >> I have data sets having reduced field of view compared to template in the >> Landmarker. >> I simply used linear AIR for space normalization. >> >> Translation and non-linear AIR seems not available for data of different >> dimensions from the template. >> >> >> Q1. I wonder what other restrictions in the space normalization or >> transformation by using Landmarker. >> >> Q2. After transformation, I would like to do fiber tracking in DTI Studio. >> What steps should I go through? >> I tried to use "Fiber Tracking" in DTI Studio main menu, however it >> asked to load "*.ani" file and "*.vec" file. >> Those files were not generated at all from the normalization. >> I have updated FA, eigenvalue, tensor and AlignlinearOuptut.air. >> >> Thanks in advance. >> >> -SC >> >> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/mristudio-users >> >> > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090624/30e492b2/attachment.html From susumu at mri.jhu.edu Wed Jun 24 11:11:10 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 24 Jun 2009 11:11:10 -0400 Subject: [Mristudio-users] Questions regarding Transformation in Landmark In-Reply-To: References: <104498.25444.qm@web30707.mail.mud.yahoo.com> <173442.34069.qm@web30704.mail.mud.yahoo.com> Message-ID: Hi all, I made a PPT presentation showing how you can recalculate normalized maps based on a normalized tensor file. Please go to, https://www.mristudio.org/wiki/user_manual/landmarker and see "Step one: Recalculation of DTI Maps from a Normalized Tensor File" To obtain the normalized tensor file, you can follow other "Step One" sections of "Getting Started". Hope this will help. Susumu On Wed, Jun 24, 2009 at 8:12 AM, [Seongjin] wrote: > Hi HTH, > > When I tried to read normalized tensor.d file, I need to load DTI data with > gradient table, but these are not generated from Landmark. As far as I get, > all of them are updated FA, ADC, tensor file etc. > > When I start with data before normalization read and I can open the tensor > file. Otherwise there is no way to read tensor file. I wonder if I am doing > correctly. Do you know other way to read tensor file only? > > Thanks in advance. > > -SC > > On Fri, May 1, 2009 at 7:08 PM, darshan pai wrote: > >> no you do not transform the vector file. you have the tensor right . You >> open the tensor in DTIStudio using the Open .d button, choose the tensor . >> It asks you for options regarding if you want to make eigen vectors FA , RA >> etc . Let it run, it will make all the files , just save what you need . >> >> HTH >> >> ------------------------------ >> *From:* [Seongjin] >> *To:* "DTI Studio, ROI Editor, Landmarker Questions/Support" < >> mristudio-users at mristudio.org> >> *Sent:* Friday, May 1, 2009 4:43:27 PM >> *Subject:* Re: [Mristudio-users] Questions regarding Transformation in >> Landmark >> >> Thanks for you reply. >> >> I guessed *.ani file will be the same. However, regarding *.vec file, I >> were warned not to transform vector file. I have no idea on this. Anyone who >> knows the answer? >> >> -SC >> >> On Fri, May 1, 2009 at 3:18 PM, darshan pai wrote: >> >>> *.ani is the updated_FA file >>> and *.vec is the updated eigenvector0 file. >>> I think the format for both is *.dat .. just different extensions to >>> differentiate I guess .. >>> >>> ------------------------------ >>> *From:* [Seongjin] >>> *To:* "DTI Studio, ROI Editor, Landmarker Questions/Support" < >>> mristudio-users at mristudio.org> >>> *Sent:* Friday, May 1, 2009 12:01:05 PM >>> *Subject:* [Mristudio-users] Questions regarding Transformation in >>> Landmark >>> >>> I have data sets having reduced field of view compared to template in the >>> Landmarker. >>> I simply used linear AIR for space normalization. >>> >>> Translation and non-linear AIR seems not available for data of different >>> dimensions from the template. >>> >>> >>> Q1. I wonder what other restrictions in the space normalization or >>> transformation by using Landmarker. >>> >>> Q2. After transformation, I would like to do fiber tracking in DTI >>> Studio. What steps should I go through? >>> I tried to use "Fiber Tracking" in DTI Studio main menu, however it >>> asked to load "*.ani" file and "*.vec" file. >>> Those files were not generated at all from the normalization. >>> I have updated FA, eigenvalue, tensor and AlignlinearOuptut.air. >>> >>> Thanks in advance. >>> >>> -SC >>> >>> >>> >>> _______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/mristudio-users >>> >>> >> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/mristudio-users >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090624/6c6a03ec/attachment.html From choisj70 at gmail.com Wed Jun 24 13:29:38 2009 From: choisj70 at gmail.com (Seongjin) Date: Wed, 24 Jun 2009 13:29:38 -0400 Subject: [Mristudio-users] Questions regarding Transformation in Landmark In-Reply-To: References: <104498.25444.qm@web30707.mail.mud.yahoo.com> <173442.34069.qm@web30704.mail.mud.yahoo.com> Message-ID: Thanks a lot! All my questions are cleared now. -SC On Wed, Jun 24, 2009 at 11:11 AM, susumu mori wrote: > Hi all, > > I made a PPT presentation showing how you can recalculate normalized maps > based on a normalized tensor file. > > Please go to, https://www.mristudio.org/wiki/user_manual/landmarker and > see "Step one: Recalculation of DTI Maps from a Normalized Tensor File" > > To obtain the normalized tensor file, you can follow other "Step One" > sections of "Getting Started". > > Hope this will help. > > Susumu > > On Wed, Jun 24, 2009 at 8:12 AM, [Seongjin] wrote: > >> Hi HTH, >> >> When I tried to read normalized tensor.d file, I need to load DTI data >> with gradient table, but these are not generated from Landmark. As far as I >> get, all of them are updated FA, ADC, tensor file etc. >> >> When I start with data before normalization read and I can open the tensor >> file. Otherwise there is no way to read tensor file. I wonder if I am doing >> correctly. Do you know other way to read tensor file only? >> >> Thanks in advance. >> >> -SC >> >> On Fri, May 1, 2009 at 7:08 PM, darshan pai wrote: >> >>> no you do not transform the vector file. you have the tensor right . You >>> open the tensor in DTIStudio using the Open .d button, choose the tensor . >>> It asks you for options regarding if you want to make eigen vectors FA , RA >>> etc . Let it run, it will make all the files , just save what you need . >>> >>> HTH >>> >>> ------------------------------ >>> *From:* [Seongjin] >>> *To:* "DTI Studio, ROI Editor, Landmarker Questions/Support" < >>> mristudio-users at mristudio.org> >>> *Sent:* Friday, May 1, 2009 4:43:27 PM >>> *Subject:* Re: [Mristudio-users] Questions regarding Transformation in >>> Landmark >>> >>> Thanks for you reply. >>> >>> I guessed *.ani file will be the same. However, regarding *.vec file, I >>> were warned not to transform vector file. I have no idea on this. Anyone who >>> knows the answer? >>> >>> -SC >>> >>> On Fri, May 1, 2009 at 3:18 PM, darshan pai wrote: >>> >>>> *.ani is the updated_FA file >>>> and *.vec is the updated eigenvector0 file. >>>> I think the format for both is *.dat .. just different extensions to >>>> differentiate I guess .. >>>> >>>> ------------------------------ >>>> *From:* [Seongjin] >>>> *To:* "DTI Studio, ROI Editor, Landmarker Questions/Support" < >>>> mristudio-users at mristudio.org> >>>> *Sent:* Friday, May 1, 2009 12:01:05 PM >>>> *Subject:* [Mristudio-users] Questions regarding Transformation in >>>> Landmark >>>> >>>> I have data sets having reduced field of view compared to template in >>>> the Landmarker. >>>> I simply used linear AIR for space normalization. >>>> >>>> Translation and non-linear AIR seems not available for data of different >>>> dimensions from the template. >>>> >>>> >>>> Q1. I wonder what other restrictions in the space normalization or >>>> transformation by using Landmarker. >>>> >>>> Q2. After transformation, I would like to do fiber tracking in DTI >>>> Studio. What steps should I go through? >>>> I tried to use "Fiber Tracking" in DTI Studio main menu, however >>>> it asked to load "*.ani" file and "*.vec" file. >>>> Those files were not generated at all from the normalization. >>>> I have updated FA, eigenvalue, tensor and AlignlinearOuptut.air. >>>> >>>> Thanks in advance. >>>> >>>> -SC >>>> >>>> >>>> >>>> _______________________________________________ >>>> Mristudio-users mailing list >>>> Mristudio-users at mristudio.org >>>> http://lists.mristudio.org/mailman/listinfo/mristudio-users >>>> >>>> >>> >>> >>> _______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/mristudio-users >>> >>> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090624/c785fb1f/attachment-0001.html From fijoy at jhu.edu Tue Jun 30 11:49:23 2009 From: fijoy at jhu.edu (Fijoy Vadakkumpadan) Date: Tue, 30 Jun 2009 10:49:23 -0500 Subject: [Mristudio-users] Landmarker: Multichannel Volume LDDMM Message-ID: Hi all, I have a template image and a subject image, each containing 5 intensities, including the 0 intensity for the background. I would like to use the Landmarker to perform multichannel LDDMM to register the two images. I looked at the window that pops up after I press the "Multichannel" button in the Landmarker, and I was wondering if someone could please clarify the following: 1. How many channels should I use? Should I use 4 channels, one for each nonzero intensity that the images have? 2. The pop up window asks for a list of template images and a list of subject images. How many template and subject images should I create? How do I create them? 3. If I should have more than 1 template image, how do I load multiple template images into the Landmarker? Thank you very much for your help. Fijoy From bbb at medicine.wisc.edu Tue Jun 30 12:33:36 2009 From: bbb at medicine.wisc.edu (Barbara Bendlin) Date: Tue, 30 Jun 2009 11:33:36 -0500 Subject: [Mristudio-users] Load ROIs in fibre tracking In-Reply-To: References: <49F2A9E7CD49B24AAC16C3C5D38CFD0B0F6AD8@EVS-EC1-NODE1.surrey.ac.uk> Message-ID: <4A49F8100200004F0000BA3E@gwmail.medicine.wisc.edu> Hello all, I am having a problem loading an ROI for fiber tracking. What happens is this: After fiber tracking I draw the ROI in DTI Studio (genu of the corpus callosum for example). The fibers are displayed. I then save the ROI as "binary map" format. When I attempt to load the ROI again (using the load tab under "ROI operation"), I choose the RoiMap_ROI.map file and get this error message: "file OPEN error: C:\Documents" I get the same error message when the ROI is created in ROI Editor. Is this a problem with the location of my files? DTI studio .exe is located on C:\Program Files\dtistudio My ROI files are located in C:\Documents and Settings\dom-user\My Documents\Studies\ Or maybe I am missing something else? Thanks for your help. Barb >>> susumu 9/5/2008 11:40 AM >>> Hi Shan, Hangyi may have a more "official" answer to your question, but I want to introduce you to the "Binary Map" option. When you store your ROI, there are several options for the format and one of them is the "Binary Map". If you click it, you get 3 files. Two 3D binary files (your ROI pixels are 1 and all other pixels are 0) and one text file. You get the two binary files because you drew 2 ROIs. If you drew 3 ROIs, you get 3 binary files. Please open the text file and study what's inside. It is like a header file containing information about the ROI binary file paths and image dimensions. There you can also find "operation" fields, in which you can specify how to use each ROI files. If one ROI have operation "0", then it is used as "OR". "1" is for "AND". There is an explanation at the end of the file. You can specify the two ROI files for CUT#1 and CUT#2 too. This format is much more powerful because you can import any 1/0 binary maps, such as fMRI activation maps, and combine them with different operators (OR, AND, NOT, CUT etc). Also in this way, you should not have the problem you reported. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Shan.Shen at surrey.ac.uk Sent: Thursday, August 28, 2008 6:32 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] Save ROIs in fibre tracking Hi, I would like to use the 'cut' operation to track fibres between two ROIs. I did the fibre tracking first, then drew the two ROIs, the fibres displayed were those between the two ROIs. However, if I save the ROIs and load them again, this time the fibres displayed are not the ones between the ROIs anymore, but are fibres passing through one of the ROIs. Could anyone tell me what the possible problem is? I tried saving the ROIs as different formats, but the problem is the same. Many thanks shan From susumu at mri.jhu.edu Tue Jun 30 12:43:36 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Tue, 30 Jun 2009 12:43:36 -0400 Subject: [Mristudio-users] Load ROIs in fibre tracking In-Reply-To: <4A49F8100200004F0000BA3E@gwmail.medicine.wisc.edu> References: <49F2A9E7CD49B24AAC16C3C5D38CFD0B0F6AD8@EVS-EC1-NODE1.surrey.ac.uk> <4A49F8100200004F0000BA3E@gwmail.medicine.wisc.edu> Message-ID: Hi Barb, I think the problem is caused by the space in the file path. For example, your directory path contains "Document[space]and[space]Settings". Our code is based on MS-DOS, which interprets such a space as the end of each attribute. So, in your case, the code thought the directory information ended after "Documents". I know that it's a silly problem. The code was written using the compiler provided by Microsoft but it doesn't work for some directory names used in Windows..... Anyway, please move all your data to another directory without "space" in your file path and try again. In general, it is a good idea to avoid any directories with "space" in the file path when you use our programs. Susumu On Tue, Jun 30, 2009 at 12:33 PM, Barbara Bendlin wrote: > Hello all, > I am having a problem loading an ROI for fiber tracking. What happens is > this: > After fiber tracking I draw the ROI in DTI Studio (genu of the corpus > callosum for example). > The fibers are displayed. > I then save the ROI as "binary map" format. > When I attempt to load the ROI again (using the load tab under "ROI > operation"), I choose the RoiMap_ROI.map file and get this error message: > "file OPEN error: C:\Documents" > I get the same error message when the ROI is created in ROI Editor. > Is this a problem with the location of my files? DTI studio .exe is located > on C:\Program Files\dtistudio > My ROI files are located in C:\Documents and Settings\dom-user\My > Documents\Studies\ > Or maybe I am missing something else? > Thanks for your help. > Barb > > > >>> susumu 9/5/2008 11:40 AM >>> > > > Hi Shan, > > > > Hangyi may have a more "official" answer to your question, but I want to > introduce you to the "Binary Map" option. > > > > When you store your ROI, there are several options for the format and one > of > them is the "Binary Map". If you click it, you get 3 files. Two 3D binary > files (your ROI pixels are 1 and all other pixels are 0) and one text file. > You get the two binary files because you drew 2 ROIs. If you drew 3 ROIs, > you get 3 binary files. Please open the text file and study what's inside. > It is like a header file containing information about the ROI binary file > paths and image dimensions. There you can also find "operation" fields, in > which you can specify how to use each ROI files. If one ROI have operation > "0", then it is used as "OR". "1" is for "AND". There is an explanation at > the end of the file. You can specify the two ROI files for CUT#1 and CUT#2 > too. > > > > This format is much more powerful because you can import any 1/0 binary > maps, such as fMRI activation maps, and combine them with different > operators (OR, AND, NOT, CUT etc). Also in this way, you should not have > the > problem you reported. > > > > Susumu > > > > _____ > > From: mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of > Shan.Shen at surrey.ac.uk > Sent: Thursday, August 28, 2008 6:32 AM > To: mristudio-users at mristudio.org > Subject: [Mristudio-users] Save ROIs in fibre tracking > > > > Hi, > > > > I would like to use the 'cut' operation to track fibres between two ROIs. I > did the fibre tracking first, then drew the two ROIs, the fibres displayed > were those between the two ROIs. However, if I save the ROIs and load them > again, this time the fibres displayed are not the ones between the ROIs > anymore, but are fibres passing through one of the ROIs. Could anyone tell > me what the possible problem is? I tried saving the ROIs as different > formats, but the problem is the same. > > > > Many thanks > > > > > > shan > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090630/a57016d9/attachment.html From bbb at medicine.wisc.edu Tue Jun 30 12:50:35 2009 From: bbb at medicine.wisc.edu (Barbara Bendlin) Date: Tue, 30 Jun 2009 11:50:35 -0500 Subject: [Mristudio-users] Load ROIs in fibre tracking In-Reply-To: References: <49F2A9E7CD49B24AAC16C3C5D38CFD0B0F6AD8@EVS-EC1-NODE1.surrey.ac.uk> <4A49F8100200004F0000BA3E@gwmail.medicine.wisc.edu> Message-ID: <4A49FC0B0200004F0000BA5B@gwmail.medicine.wisc.edu> That worked, thanks. >>> susumu mori 6/30/2009 11:43 AM >>> Hi Barb, I think the problem is caused by the space in the file path. For example, your directory path contains "Document[space]and[space]Settings". Our code is based on MS-DOS, which interprets such a space as the end of each attribute. So, in your case, the code thought the directory information ended after "Documents". I know that it's a silly problem. The code was written using the compiler provided by Microsoft but it doesn't work for some directory names used in Windows..... Anyway, please move all your data to another directory without "space" in your file path and try again. In general, it is a good idea to avoid any directories with "space" in the file path when you use our programs. Susumu On Tue, Jun 30, 2009 at 12:33 PM, Barbara Bendlin wrote: > Hello all, > I am having a problem loading an ROI for fiber tracking. What happens is > this: > After fiber tracking I draw the ROI in DTI Studio (genu of the corpus > callosum for example). > The fibers are displayed. > I then save the ROI as "binary map" format. > When I attempt to load the ROI again (using the load tab under "ROI > operation"), I choose the RoiMap_ROI.map file and get this error message: > "file OPEN error: C:\Documents" > I get the same error message when the ROI is created in ROI Editor. > Is this a problem with the location of my files? DTI studio .exe is located > on C:\Program Files\dtistudio > My ROI files are located in C:\Documents and Settings\dom-user\My > Documents\Studies\ > Or maybe I am missing something else? > Thanks for your help. > Barb > > > >>> susumu 9/5/2008 11:40 AM >>> > > > Hi Shan, > > > > Hangyi may have a more "official" answer to your question, but I want to > introduce you to the "Binary Map" option. > > > > When you store your ROI, there are several options for the format and one > of > them is the "Binary Map". If you click it, you get 3 files. Two 3D binary > files (your ROI pixels are 1 and all other pixels are 0) and one text file. > You get the two binary files because you drew 2 ROIs. If you drew 3 ROIs, > you get 3 binary files. Please open the text file and study what's inside. > It is like a header file containing information about the ROI binary file > paths and image dimensions. There you can also find "operation" fields, in > which you can specify how to use each ROI files. If one ROI have operation > "0", then it is used as "OR". "1" is for "AND". There is an explanation at > the end of the file. You can specify the two ROI files for CUT#1 and CUT#2 > too. > > > > This format is much more powerful because you can import any 1/0 binary > maps, such as fMRI activation maps, and combine them with different > operators (OR, AND, NOT, CUT etc). Also in this way, you should not have > the > problem you reported. > > > > Susumu > > > > _____ > > From: mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of > Shan.Shen at surrey.ac.uk > Sent: Thursday, August 28, 2008 6:32 AM > To: mristudio-users at mristudio.org > Subject: [Mristudio-users] Save ROIs in fibre tracking > > > > Hi, > > > > I would like to use the 'cut' operation to track fibres between two ROIs. I > did the fibre tracking first, then drew the two ROIs, the fibres displayed > were those between the two ROIs. However, if I save the ROIs and load them > again, this time the fibres displayed are not the ones between the ROIs > anymore, but are fibres passing through one of the ROIs. Could anyone tell > me what the possible problem is? I tried saving the ROIs as different > formats, but the problem is the same. > > > > Many thanks > > > > > > shan > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > From aimanba1 at jhu.edu Tue Jun 30 14:30:57 2009 From: aimanba1 at jhu.edu (Anuar Imanbayev) Date: Tue, 30 Jun 2009 14:30:57 -0400 Subject: [Mristudio-users] Gradient Table for Siemens Sensation 16 CT Scanner Message-ID: Greetings all, I have DICOM files taken from Siemens Sensation 16 CT Scanner. I can load them up fine directly from the DICOM files through MRI View3D with the option [Siemens DICOM (1.00)]. The option [Siemens, GE, or Philips DICOM] produces a full even image but is otherwise barren. I can arrive at the same destination by converting to .RAWs and .MHDs or NIfTI .HDRs and .IMGs. Analyze .HDRs and .IMGs invert the image. There are certain issues however. Each file folder has a varied number of image files (51, 72, 66, 160, 54, etc). What kind of gradient tables handle such variety? I did notice that DTI did turn these different size folders into 17, 19, or 33 slice in the program. I reckon that there might be 17, 19, and 33 slice Siemens gradient tables for these? I do not possess such Siemens gradient table(s). I will try calling the manufacturer but if Dr. Mori or Dr. Jiang have a compatible gradient table. I'm currently working with three folders to develop a processing pipeline from these DICOM files into DtiStudio and then manual ROI and Landmarker. The three file folders are 100-318, 134-104, and 152-302 They are up on Godzilla fileserver: /kki/g2/aimanba1 I'll give a call to Dr. Mori about this and other matters this week. Thank you for your time and consideration, Sincerely yours, Anuar Imanbayev From susumu at mri.jhu.edu Tue Jun 30 21:17:26 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Tue, 30 Jun 2009 21:17:26 -0400 Subject: [Mristudio-users] Landmarker: Multichannel Volume LDDMM In-Reply-To: References: Message-ID: Please see below; On Tue, Jun 30, 2009 at 11:49 AM, Fijoy Vadakkumpadan wrote: > Hi all, > > I have a template image and a subject image, each containing 5 > intensities, including the 0 intensity for the background. I would > like to use the Landmarker to perform multichannel LDDMM to register > the two images. I looked at the window that pops up after I press the > "Multichannel" button in the Landmarker, and I was wondering if > someone could please clarify the following: > > 1. How many channels should I use? Should I use 4 channels, one for > each nonzero intensity that the images have? > If I understand it correctly, you have segmented data. For example, if we do gray matter - white matter segmentation, you may get ONE IMAGE in which outside is 0, gray matter is 1, white matter is 2, and ventricle 3. For a template and a subject, you have two of these images. You can submit these two images to the "single-channel" LDDMM. > > > 2. The pop up window asks for a list of template images and a list of > subject images. How many template and subject images should I create? > How do I create them? > You can use the multi-channel if you have the following situation; > Suppose you have the above segmented image based on T1-weighted image. > Then you create SECOND segmentation map using a FA map. For example, use FA>0.25 and create another map in which white matter is 1 and outside is 0. > Now you have TWO segmentation maps for the template and for the subject (total 4 images). > In this case, you use the "multi-channel" LDDMM. For the template, you choose T1-based and FA-based segmentation maps and for the subject, you choose T1-based and FA-based segmentation maps. > Then LDDMM will do; Template T1 - Subject T1 mapping as well as Template FA - Subject FA to get one solution that satisfies the two matching simultaneously. > > > 3. If I should have more than 1 template image, how do I load multiple > template images into the Landmarker? > First, open the template T1 using the Open icon in the top menu. > Once you get a viewing window, use the Open icon in the right column of the viewing window to open template FA. > Go back to the Open icon in the top menu and open the subject T1 > Once you get another viewing window for the subject, use the Open icon in the right column of the subject viewing window to open subject FA. > Go to "multi-channel" LDDMM. You can find T1 and FA are listed for Template and also for the subject. Hope this clarifies your question. Susumu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090630/e0b2af5b/attachment.html From kevinspitler at ucla.edu Wed Jul 1 09:23:54 2009 From: kevinspitler at ucla.edu (Kevin Spitler) Date: Wed, 01 Jul 2009 06:23:54 -0700 Subject: [Mristudio-users] tractography of CST Message-ID: <9770ef210907010623i1f645fe3n6f96b4d8f8f80572@mail.gmail.com> Hello, I am trying to trace the corticospinal tract using DTI Studio and the tractography algorithm proposed by Wakana et al 2007 NeuroImage. After making the 2 ROIs at the cerebral peduncle and then at the precentral gryus, I find the majority of remaining fibers enter the cerebellum. After removing these with the "NOT" ROIs, I find the remaining fibers are very lateral in the cerebral peduncle which is not the typical position of the corticospinal tract. Is there a mistake I am making or is there another algorithm for ROI placement that may be better in my situation? Thank you for your help Best, Kevin From susumu at mri.jhu.edu Wed Jul 1 09:52:20 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 01 Jul 2009 09:52:20 -0400 Subject: [Mristudio-users] tractography of CST In-Reply-To: <9770ef210907010623i1f645fe3n6f96b4d8f8f80572@mail.gmail.com> References: <9770ef210907010623i1f645fe3n6f96b4d8f8f80572@mail.gmail.com> Message-ID: Hi Kevin; 1) What we call, "CST" is actually the mixture of the CST and cortico-pontine-cerebellar pathways. 2) once the CST tract leaches pons, the CST branches to the real CST that penetrate the pons toward the spinal cord and the cortico-pontine-cerebellar pathways. 3) The latter pathways outnumber the real CST by far. 4) Of course, DTI, which is pixel-by-pixel imaging, can not distingish these two pathways when they bifurcate at the pons. 5) Anatomically, the best ROI positoins for the CST would be one at the motor cortex and the other at the medula or spinal cord, which can eliminate all cortico-pontine-cerebellar pathways effectively. 6) However, if you use this combination (similar to what you did: use NOT to remove that latter pathways), the tractography results become unstable because so many exit to the cerebellum (which is anatomically correct) and subtle differences in pixel locations and partial voluming could afect the outcome. 7) That is the reason we reconstructed only up to the cerebral peduncle, avoiding the complex pons area. 8) Some more elaborated tractography methods, either deterministic approaches with some kinds of regularization or probabilistic methods may provide more stable results, less affected by a small number of pixels that would wobble due to mixed fibers, but what these provide is mathematically more stable solution, not necessarily anatomically more correct solution. Nonetheless, they could be usefull tools as long as you know the nature of the tool well. If your finiding, the CST is located too lateral, is a reproducible finding among different subjects, you may want to check your DTI processing pipeline. One of the most common mistakes is how oblique angles are handled. GE, Philips (non-overplus), and Siemens (the latest version VB15?) do not require any procedure to incorporate the oblique information, but Philips (overplus) and Siemens (previous version) require recalculation of gradient table based on the oblique angles. If you are using DICOM or Mosaic, this can be easily done by check a box beneath the gradient table window. Susumu On Wed, Jul 1, 2009 at 9:23 AM, Kevin Spitler wrote: > Hello, > > I am trying to trace the corticospinal tract using DTI Studio and the > tractography algorithm proposed by Wakana et al 2007 NeuroImage. > After making the 2 ROIs at the cerebral peduncle and then at the > precentral gryus, I find the majority of remaining fibers enter the > cerebellum. After removing these with the "NOT" ROIs, I find the > remaining fibers are very lateral in the cerebral peduncle which is > not the typical position of the corticospinal tract. Is there a > mistake I am making or is there another algorithm for ROI placement > that may be better in my situation? > Thank you for your help > > Best, > Kevin > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090701/b8c8285a/attachment.html From jiangz at ccf.org Thu Jul 2 11:48:05 2009 From: jiangz at ccf.org (Jiang, Zhiguo) Date: Thu, 02 Jul 2009 11:48:05 -0400 Subject: [Mristudio-users] 12 direction Siemens Trio 3T gradient table Message-ID: Hi, Does anyone have a standard 12 direction Siemens gradient table to share with me? Thanks a lot. Best, Tony =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S. News & World Report (2008). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090702/a6d56d43/attachment.html From fijoy at jhu.edu Thu Jul 2 12:09:51 2009 From: fijoy at jhu.edu (Fijoy Vadakkumpadan) Date: Thu, 02 Jul 2009 12:09:51 -0400 Subject: [Mristudio-users] Landmarker: Multichannel Volume LDDMM In-Reply-To: References: Message-ID: Hi Dr. Mori, Thank you so much for your prompt reply. It clarifies my questions. I was thinking of generating multiple (four in my case) binary images from my segmented template image, by creating one binary image for each tissue type. Similarly, I create multiple binary images from the segmented subject image as well. Then, I wanted to use multichannel LDDMM to register the subject binary images with template binary images, all at once. I felt that I might obtain better registration by using the multichannel LDDMM on these binary images, rather than using the single channel LDDMM on the segmented images. Fijoy On Tue, Jun 30, 2009 at 9:17 PM, susumu mori wrote: > Please see below; > > On Tue, Jun 30, 2009 at 11:49 AM, Fijoy Vadakkumpadan wrote: >> >> Hi all, >> >> I have a template image and a subject image, each containing 5 >> intensities, including the 0 intensity for the background. I would >> like to use the Landmarker to perform multichannel LDDMM to register >> the two images. I looked at the window that pops up after I press the >> "Multichannel" button in the Landmarker, and I was wondering if >> someone could please clarify the following: >> >> 1. How many channels should I use? Should I use 4 channels, one for >> each nonzero intensity that the images have? > >> If I understand it correctly, you have segmented data. For example, if we >> do gray matter - white matter segmentation, you may get ONE IMAGE in which >> outside is 0, gray matter is 1, white matter is 2, and ventricle 3. For a >> template and a subject, you have two of these images. You can submit these >> two images to the "single-channel" LDDMM. >> >> >> 2. The pop up window asks for a list of template images and a list of >> subject images. How many template and subject images should I create? >> How do I create them? > >> You can use the multi-channel if you have the following situation; >> Suppose you have the above segmented image based on T1-weighted image. >> Then you create SECOND segmentation map using a FA map. For example, use >> FA>0.25 and create another map in which white matter is 1 and outside is 0. >> Now you have TWO segmentation maps for the template and for the subject >> (total 4 images). >> In this case, you use the "multi-channel" LDDMM. For the template, you >> choose T1-based and FA-based segmentation maps and for the subject, you >> choose T1-based and FA-based segmentation maps. >> Then LDDMM will do; Template T1 - Subject T1 mapping as well as Template >> FA - Subject FA to get one solution that satisfies the two matching >> simultaneously. >> >> >> 3. If I should have more than 1 template image, how do I load multiple >> template images into the Landmarker? > >> First, open the template T1 using the Open icon in the top menu. >> Once you get a viewing window, use the Open icon in the right column of >> the viewing window to open template FA. >> Go back to the Open icon in the top menu and open the subject T1 >> Once you get another viewing window for the subject, use the Open icon in >> the right column of the subject viewing window to open subject FA. >> Go to "multi-channel" LDDMM. You can find T1 and FA are listed for >> Template and also for the subject. > > Hope this clarifies your question. > > Susumu > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > From susumu at mri.jhu.edu Thu Jul 2 12:25:06 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Thu, 02 Jul 2009 12:25:06 -0400 Subject: [Mristudio-users] 12 direction Siemens Trio 3T gradient table In-Reply-To: References: Message-ID: Please let me know if this doesn't work. Also, Siemens users should be very careful about how to deal with oblique angles. Unless you are using the latest operating system, you have to use the "Rotate gradients if applicable" option to recalculate the table. You can find this option in the initial data input window just beneath the section for gradient table. I strongly suggest to do one quick test by scanning a person with severe oblique angle. If you are using DICOM or Mosaic, the oblique information is automatically read and table is recalculated once this option is activated. 0: 0, 0, 0 1: 1.000000, 0.414250, -0.414250 2: 1.000000, -0.414250, -0.414250 3: 1.000000, -0.414250, 0.414250 4: 1.000000, 0.414250, 0.414250 5: 0.414250, 0.414250, 1.000000 6: 0.414250, 1.000000, 0.414250 7: 0.414250, 1.000000, -0.414250 8: 0.414250, 0.414250, -1.000000 9: 0.414250, -0.414250, -1.000000 10: 0.414250, -1.000000, -0.414250 11: 0.414250, -1.000000, 0.414250 12: 0.414250, -0.414250, 1.000000 On Thu, Jul 2, 2009 at 11:48 AM, Jiang, Zhiguo wrote: > Hi, > > > > Does anyone have a standard 12 direction Siemens gradient table to share > with me? Thanks a lot. > > > > > > Best, > > > > Tony > > =================================== > > P Please consider the environment before printing this e-mail > > > Cleveland Clinic is ranked one of the top hospitals > in America by U.S. News & World Report (2008). > Visit us online at http://www.clevelandclinic.org for > a complete listing of our services, staff and > locations. > > > Confidentiality Note: This message is intended for use > only by the individual or entity to which it is addressed > and may contain information that is privileged, > confidential, and exempt from disclosure under applicable > law. If the reader of this message is not the intended > recipient or the employee or agent responsible for > delivering the message to the intended recipient, you are > hereby notified that any dissemination, distribution or > copying of this communication is strictly prohibited. If > you have received this communication in error, please > contact the sender immediately and destroy the material in > its entirety, whether electronic or hard copy. Thank you. > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090702/7964b163/attachment.html From hkim at peds.uab.edu Thu Jul 2 12:29:32 2009 From: hkim at peds.uab.edu (Hyunmi Kim, M.D.) Date: Thu, 02 Jul 2009 11:29:32 -0500 Subject: [Mristudio-users] (no subject) Message-ID: <66073DDBA72FF542AAA13469EF91E79E04D54163@ex1-777peds.peds.uab.edu> Dear all; Do you have a standard 25 direction GE gradient table? Please share with me. Thank you, Hyunmi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090702/5a310258/attachment.html From JLaMarche at tams.com Thu Jul 2 13:01:24 2009 From: JLaMarche at tams.com (John LaMarche) Date: Thu, 02 Jul 2009 10:01:24 -0700 Subject: [Mristudio-users] John LaMarche is out of the office. Message-ID: I will be out of the office starting 07/01/2009 and will not return until 07/15/2009. I will respond to your message when I return. From yj3 at duke.edu Tue Jul 7 15:40:27 2009 From: yj3 at duke.edu (Yi Jiang) Date: Tue, 07 Jul 2009 15:40:27 -0400 Subject: [Mristudio-users] build AIR executable for landmarker References: Message-ID: <90CD86EA788D4AAABA07983557BA77BC@panpan> Hello, dear all, I am trying to use Landmarker with the AIR functions. I am using a 64bit windows XP. According to the instruction, I should build the relevant AIR functions myself: "If you would like to use the functions "Automatic Image Linear Registration", "Automatic Image Nonlinear Registration" and "Invert AIR Linear Matrix", you need to build makeaheader.exe, alignlinear.exe, align_warp.exe and invert_air.exe by yourself." However, after some efforts, I was not able to build those executable files. I am wondering if anyone has those makeaheader.exe, alignlinear.exe, align_warp.exe and invert_air.exe files for a 64bits windows XP, and could share them with me. Thank you very much for your help! Best, Yi From yj3 at duke.edu Wed Jul 8 17:29:39 2009 From: yj3 at duke.edu (Yi Jiang) Date: Wed, 08 Jul 2009 17:29:39 -0400 Subject: [Mristudio-users] AIR files References: Message-ID: <3C147873216E4E6ABC5683FA6BFA15FF@panpan> Hello Xin, The AIR files work well. Thank you so much for your help! When I tried to do single channel LDDMM, however, I kept getting an error message: Cannot upload this file: 50e2d839a4e9cba6a1d6ce400313c689.zip My image size is 512x256x256 for template or subject image. I have transferred them into byte format and I kept all the default settings of LDDMM. Is that because my image is too big? Or a firewall? I have not tried the multi-channel LDDMM, though. I have another two questions: 1. if I have a template image and a subject image and I want to register these two by LDDMM eventually, 1. should I use LDDMM to register these two directly or 2. should I use AIR linear to affine transform them first, and then LDDMM the updated subject image? In the 2nd case, I need to reorient tensors twice, once by the AIR transformation matrix and once by the LDDMM transformation matrix, right? I am asking this question because for some other registration software I have used, it seems the elastic transformation works better after affine registering the images first. Or maybe LDDMM covers rigid and affine transformation well already so we can do #1? 2. There is no online manual for the nonlinear AIR. Do you usually use that? Can Landmarker load in the resulted non-linear AIR transformation and reorient tensors accordingly? How does the nonlinear AIR compensate/compare with LDDMM? Thank you very much! Best, Yi ----- Original Message ----- From: Xin Li To: Yi Jiang Cc: Susumu Mori Sent: Tuesday, July 07, 2009 5:00 PM Subject: AIR files Yi, The attachment includes all the AIR files required by Landmarker. Regards, Xin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090708/4426e22f/attachment-0001.html From luca.binotto at unipd.it Sun Jul 12 04:12:03 2009 From: luca.binotto at unipd.it (luca.binotto at unipd.it) Date: Sun, 12 Jul 2009 10:12:03 +0200 (CEST) Subject: [Mristudio-users] gradient table update Message-ID: <9b2fc529d0344dcc5e40aa4d37aa3a5e.squirrel@webmail.unipd.it> Hello I am a beginner and I'm in doubt about the gradient table upgrade after AIR coregistration. If I decide to rewrite the dataset and I select the radiobutton "Adjusting the gradient table if applicable" and then I interrupt the current work session (i.e. I close DtiStudio), after reloading the same dataset in a successive DtiStudio session, should I copy and paste the new gradient table written in the last part of the AirMatrix file text in order to compute again the diffusion tensor from the coregistered volumes? (And so, in every case have I to select "Save transformation matrices as file" in order to know the new gradient table to use when reloading? ). thank in advance, Luca From susumu at mri.jhu.edu Sun Jul 12 19:20:25 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Mon, 13 Jul 2009 08:20:25 +0900 Subject: [Mristudio-users] gradient table update In-Reply-To: <9b2fc529d0344dcc5e40aa4d37aa3a5e.squirrel@webmail.unipd.it> References: <9b2fc529d0344dcc5e40aa4d37aa3a5e.squirrel@webmail.unipd.it> Message-ID: Hi Luca, If you copy the gradient table supplied from a manufacturer into Dtitudio, check the "adjust .." box, and read DICOM files, the table is recalculated based on the oblique information in the DICOM. Note that this recalculation is necessary for old SIEMENS system. If you close DtiStudio and reopen the data, DtiStudio remembers the previous table. Importantly, it remembes the table AFTER the recalculation. This means, if you used oblique imaging, the table is differen from the one you copied originally. So you have to either re-enter the original table (and check the "adjust" button) or keep the recalculatd table and uncheck the "adjust" button. I hope this clears your question. Susumu On Sun, Jul 12, 2009 at 5:12 PM, wrote: > Hello > I am a beginner and I'm in doubt about the gradient table upgrade after > AIR coregistration. > If I decide to rewrite the dataset and I select the radiobutton "Adjusting > the gradient table if applicable" > and then I interrupt the current work session (i.e. I close DtiStudio), > after reloading the same dataset in a successive DtiStudio session, > should I copy and paste the new gradient > table written in the last part of the AirMatrix file text in order to > compute again the diffusion tensor from the coregistered volumes? > (And so, in every case have I to select "Save transformation matrices as > file" in order to know the new gradient table to use when reloading? ). > > thank in advance, > > Luca > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090713/e0d7aa20/attachment.html From gjmuro at optonline.net Sun Jul 12 20:26:55 2009 From: gjmuro at optonline.net (gjmuro at optonline.net) Date: Mon, 13 Jul 2009 00:26:55 +0000 Subject: [Mristudio-users] gradient table update In-Reply-To: References: <9b2fc529d0344dcc5e40aa4d37aa3a5e.squirrel@webmail.unipd.it> Message-ID: <1786367948-1247444713-cardhu_decombobulator_blackberry.rim.net-1274096709-@bxe1235.bisx.prod.on.blackberry> Ff Sent from my Verizon Wireless BlackBerry -----Original Message----- From: susumu mori Date: Mon, 13 Jul 2009 08:20:25 To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] gradient table update _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From gjmuro at optonline.net Sun Jul 12 20:27:03 2009 From: gjmuro at optonline.net (gjmuro at optonline.net) Date: Mon, 13 Jul 2009 00:27:03 +0000 Subject: [Mristudio-users] gradient table update In-Reply-To: References: <9b2fc529d0344dcc5e40aa4d37aa3a5e.squirrel@webmail.unipd.it> Message-ID: <543321176-1247444723-cardhu_decombobulator_blackberry.rim.net-1858079505-@bxe1235.bisx.prod.on.blackberry> Gvvv Sent from my Verizon Wireless BlackBerry -----Original Message----- From: susumu mori Date: Mon, 13 Jul 2009 08:20:25 To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] gradient table update _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From gjmuro at optonline.net Sun Jul 12 20:27:12 2009 From: gjmuro at optonline.net (gjmuro at optonline.net) Date: Mon, 13 Jul 2009 00:27:12 +0000 Subject: [Mristudio-users] gradient table update In-Reply-To: References: <9b2fc529d0344dcc5e40aa4d37aa3a5e.squirrel@webmail.unipd.it> Message-ID: <1906022595-1247444730-cardhu_decombobulator_blackberry.rim.net-125657041-@bxe1235.bisx.prod.on.blackberry> Gvvgvg Sent from my Verizon Wireless BlackBerry -----Original Message----- From: susumu mori Date: Mon, 13 Jul 2009 08:20:25 To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] gradient table update _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From gjmuro at optonline.net Sun Jul 12 20:27:21 2009 From: gjmuro at optonline.net (gjmuro at optonline.net) Date: Mon, 13 Jul 2009 00:27:21 +0000 Subject: [Mristudio-users] gradient table update In-Reply-To: References: <9b2fc529d0344dcc5e40aa4d37aa3a5e.squirrel@webmail.unipd.it> Message-ID: <1729361619-1247444739-cardhu_decombobulator_blackberry.rim.net-2476978-@bxe1235.bisx.prod.on.blackberry> Bgvyuuy Sent from my Verizon Wireless BlackBerry -----Original Message----- From: susumu mori Date: Mon, 13 Jul 2009 08:20:25 To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] gradient table update _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From sung.h.bae at vanderbilt.edu Sun Jul 12 22:11:11 2009 From: sung.h.bae at vanderbilt.edu (Sung Hoon Bae) Date: Sun, 12 Jul 2009 21:11:11 -0500 Subject: [Mristudio-users] Using fiber tracking data from DTIstudio in MATLAB Message-ID: Hello everyone, Is it possible to use the fiber tracking data from DTIstudio in MATLAB? If so, would someone briefly explain how? I really appreciate your help/time! Sincerely, -- Sung -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090712/a7dbcf86/attachment.html From luca.binotto at unipd.it Mon Jul 13 05:51:51 2009 From: luca.binotto at unipd.it (luca.binotto at unipd.it) Date: Mon, 13 Jul 2009 11:51:51 +0200 (CEST) Subject: [Mristudio-users] gradient table update Message-ID: <1df644805e20822bc507ffb6fea5411e.squirrel@webmail.unipd.it> Hello to everibody, many thanks for your replies. As I said I unchecked ?create new image after registration? and so, as was written in an older post as reply, I?m working on a .rec dataset downloaded from your website. After closing the current session (with Air coregistration process completed ) and loading again the same dataset I noted the gradient table was still the original one and not the one in the AirMatrix.txt. Of course, after copying the updated one this time I can say it remembers the table created after the recalculation. In every case, this is not a problem stated that the dataset was overwritten with the coregistered DWIs because I don't need anymore to pass through Air processing and can continue directly with diffusion tensor computation. Many thanks again. Luca From yj3 at duke.edu Mon Jul 13 16:12:27 2009 From: yj3 at duke.edu (Yi Jiang) Date: Mon, 13 Jul 2009 16:12:27 -0400 Subject: [Mristudio-users] LDDMM questions Message-ID: <8690084356BB4B1EA98ED947765A29A3@panpan> Dear All, I have two questions about LDDMM: 1. if I have a template image and a subject image and I want to register these two by LDDMM eventually, 1). should I use LDDMM to register these two directly or 2). should I use AIR linear to affine transform them first, and then LDDMM the updated subject image? In the 2nd case, I need to reorient tensors twice, once by the AIR transformation matrix and once by the LDDMM transformation matrix, right? I am asking this question because for some other registration software I have used, it seems the elastic transformation works better after affine registering the images first. Or maybe LDDMM covers rigid and affine transformation well already so we can do #1? 2. How does the nonlinear AIR compensate/compare with LDDMM? Can the nonlinear AIR transformation be applied to reorient tensors? Thank you very much! Best, Yi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090713/eff7ac1d/attachment-0001.html From susumu at mri.jhu.edu Tue Jul 14 02:21:04 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Tue, 14 Jul 2009 02:21:04 -0400 Subject: [Mristudio-users] LDDMM questions In-Reply-To: <8690084356BB4B1EA98ED947765A29A3@panpan> References: <8690084356BB4B1EA98ED947765A29A3@panpan> Message-ID: Hi Yi, 1) I recommend you to do AIR first from two reasons. First one is a practical reason. Our LDDMM requires that the matrix and pixel sizes of the two images are identical. After AIR, even if the input images have different dimensions, the output will have the same dimension. This is handy. Second one is more important. Let me use fitting of a X-Y plot for analogy. When you use linear fitting, no matter which software you use, the results are almost identical. This is because the energy landscape of linear fitting usually has a very simple "one-valley" shape, meaning the results always converge at the same solution. On the other hand, when you are using non-linear fitting, you are required to provide initial values, which are close to the real solution. Usually you first do linear solution and then use the result as the initial value for the subsequent non-linear fitting. This is because the energy landscape of non-linear fitting has a complicated "multi-valley" shape. If your initial values are far away from the real solution, the fitting is trapped by a local minima. Non-linear warping is very similar. You are required to bring two brains as close as possible before you start non-linear warping. When you adopt AIR+LDDMM, you have to transform the image twice, including tensor reorientation. Landmarker can combine transformation matrices so that you can do multiple transformation at once to avoid multiple interpolation. Xin, can we combine AIR matrix and LDDMM matrix? 2) We usually don't use non-linear AIR. So we don't have much experience with it. Yes, it should do tensor reorientation if you apply the transformation to a tensor file. On Mon, Jul 13, 2009 at 4:12 PM, Yi Jiang wrote: > Dear All, > > I have two questions about LDDMM: > > > > 1. if I have a template image and a subject image and I want to register > these two by LDDMM eventually, 1). should I use LDDMM to register these two > directly or 2). should I use AIR linear to affine transform them first, and > then LDDMM the updated subject image? In the 2nd case, I need to reorient > tensors twice, once by the AIR transformation matrix and once by the LDDMM > transformation matrix, right? > > > > I am asking this question because for some other registration software I > have used, it seems the elastic transformation works better after affine > registering the images first. > > > > Or maybe LDDMM covers rigid and affine transformation well already so we > can do #1? > > > > 2. How does the nonlinear AIR compensate/compare with LDDMM? Can the > nonlinear AIR transformation be applied to reorient tensors? > > > > Thank you very much! > > > > Best, > > Yi > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090714/1a5a2cd6/attachment.html From xli16 at jhmi.edu Tue Jul 14 10:10:47 2009 From: xli16 at jhmi.edu (Xin Li) Date: Tue, 14 Jul 2009 10:10:47 -0400 Subject: [Mristudio-users] LDDMM questions In-Reply-To: References: <8690084356BB4B1EA98ED947765A29A3@panpan> Message-ID: Yi, Landmarker can combine AIR matrix and LDDMM matrix. The button for this function is right below the button for multichannel remote LDDMM. Xin ----- Original Message ----- From: susumu mori Date: Tuesday, July 14, 2009 2:21 am Subject: Re: [Mristudio-users] LDDMM questions To: Yi Jiang , "DTI Studio, ROI Editor, Landmarker Questions/Support" , Xin Li > Hi Yi, > > 1) I recommend you to do AIR first from two reasons. First one is a > practical reason. Our LDDMM requires that the matrix and pixel sizes > of the > two images are identical. After AIR, even if the input images have different > dimensions, the output will have the same dimension. This is handy. Second > one is more important. Let me use fitting of a X-Y plot for analogy. > When > you use linear fitting, no matter which software you use, the results > are > almost identical. This is because the energy landscape of linear fitting > usually has a very simple "one-valley" shape, meaning the results always > converge at the same solution. On the other hand, when you are using > non-linear fitting, you are required to provide initial values, which > are > close to the real solution. Usually you first do linear solution and > then > use the result as the initial value for the subsequent non-linear fitting. > This is because the energy landscape of non-linear fitting has a complicated > "multi-valley" shape. If your initial values are far away from the real > solution, the fitting is trapped by a local minima. > > Non-linear warping is very similar. You are required to bring two > brains as > close as possible before you start non-linear warping. > > When you adopt AIR+LDDMM, you have to transform the image twice, including > tensor reorientation. Landmarker can combine transformation matrices > so that > you can do multiple transformation at once to avoid multiple interpolation. > > Xin, can we combine AIR matrix and LDDMM matrix? > > 2) We usually don't use non-linear AIR. So we don't have much experience > with it. Yes, it should do tensor reorientation if you apply the > transformation to a tensor file. > > > > On Mon, Jul 13, 2009 at 4:12 PM, Yi Jiang wrote: > > > Dear All, > > > > I have two questions about LDDMM: > > > > > > > > 1. if I have a template image and a subject image and I want to register > > these two by LDDMM eventually, 1). should I use LDDMM to register > these two > > directly or 2). should I use AIR linear to affine transform them > first, and > > then LDDMM the updated subject image? In the 2nd case, I need to reorient > > tensors twice, once by the AIR transformation matrix and once by > the LDDMM > > transformation matrix, right? > > > > > > > > I am asking this question because for some other registration > software I > > have used, it seems the elastic transformation works better after affine > > registering the images first. > > > > > > > > Or maybe LDDMM covers rigid and affine transformation well already > so we > > can do #1? > > > > > > > > 2. How does the nonlinear AIR compensate/compare with LDDMM? Can the > > nonlinear AIR transformation be applied to reorient tensors? > > > > > > > > Thank you very much! > > > > > > > > Best, > > > > Yi > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > > Mristudio-users-unsubscribe at mristudio.org > > > > From rajagov2 at ccf.org Tue Jul 14 10:23:08 2009 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Tue, 14 Jul 2009 10:23:08 -0400 Subject: [Mristudio-users] measureing Volume of CST Message-ID: <77A88E90A851594AAEF830450587C39D01EDAAB9@CCHSCLEXMB56.cc.ad.cchs.net> Dear MRI studio Users, I am wondering is there a way to measure quantitatively the volume of CST. If so can anyone please tell me how to do it using DTI studio. In essence we are interested in seeing whether CST tract volume is reduced in our ALS patients when compared to controls. Thanks Regards venkateswaran =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S. News & World Report (2008). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090714/4d7489f8/attachment.html From tangjinsonghn at yahoo.com.cn Tue Jul 14 10:30:55 2009 From: tangjinsonghn at yahoo.com.cn (jinsong tang) Date: Tue, 14 Jul 2009 22:30:55 +0800 (CST) Subject: [Mristudio-users] =?utf-8?q?Re=EF=BC=9A__LDDMM_questions?= In-Reply-To: References: <8690084356BB4B1EA98ED947765A29A3@panpan> Message-ID: <977947.96698.qm@web15608.mail.cnb.yahoo.com> Hello, Dear all, I am trying to use Landmarker with the AIR functions. I am using a 32bit windows XP. According to the instruction, I?need to compile the AIR functions myself. However,? I was not able to build those executable files. Are there anyone has those .exe files,and could share them with us. Best regars, Jinsong ________________________________ ???? Xin Li ???? Yi Jiang ??? "DTI Studio, ROI Editor, Landmarker Questions/Support" ???? 2009/7/14(??), ??10:10:47 ??? Re: [Mristudio-users] LDDMM questions Yi, Landmarker can combine AIR matrix and LDDMM matrix. The button for this function is right below the button for multichannel remote LDDMM. Xin ----- Original Message ----- From: susumu mori Date: Tuesday, July 14, 2009 2:21 am Subject: Re: [Mristudio-users] LDDMM questions To: Yi Jiang , "DTI Studio, ROI Editor, Landmarker Questions/Support" , Xin Li > Hi Yi, >? >? 1) I recommend you to do AIR first from two reasons. First one is a >? practical reason. Our LDDMM requires that the matrix and pixel sizes > of the >? two images are identical. After AIR, even if the input images have different >? dimensions, the output will have the same dimension. This is handy. Second >? one is more important. Let me use fitting of a X-Y plot for analogy. > When >? you use linear fitting, no matter which software you use, the results > are >? almost identical. This is because the energy landscape of linear fitting >? usually has a very simple "one-valley" shape, meaning the results always >? converge at the same solution. On the other hand, when you are using >? non-linear fitting, you are required to provide initial values, which > are >? close to the real solution. Usually you first do linear solution and > then >? use the result as the initial value for the subsequent non-linear fitting. >? This is because the energy landscape of non-linear fitting has a complicated >? "multi-valley" shape. If your initial values are far away from the real >? solution, the fitting is trapped by a local minima. >? >? Non-linear warping is very similar. You are required to bring two > brains as >? close as possible before you start non-linear warping. >? >? When you adopt AIR+LDDMM, you have to transform the image twice, including >? tensor reorientation. Landmarker can combine transformation matrices > so that >? you can do multiple transformation at once to avoid multiple interpolation. >? >? Xin, can we combine AIR matrix and LDDMM matrix? >? >? 2) We usually don't use non-linear AIR. So we don't have much experience >? with it. Yes, it should do tensor reorientation if you apply the >? transformation to a tensor file. >? >? >? >? On Mon, Jul 13, 2009 at 4:12 PM, Yi Jiang wrote: >? >? >? Dear All, >? > >? > I have two questions about LDDMM: >? > >? > >? > >? > 1. if I have a template image and a subject image and I want to register >? > these two by LDDMM eventually, 1). should I use LDDMM to register > these two >? > directly or 2). should I use AIR linear to affine transform them > first, and >? > then LDDMM the updated subject image? In the 2nd case, I need to reorient >? > tensors twice, once by the AIR transformation matrix and once by > the LDDMM >? > transformation matrix, right? >? > >? > >? > >? > I am asking this question because for some other registration > software I >? > have used, it seems the elastic transformation works better after affine >? > registering the images first. >? > >? > >? > >? > Or maybe LDDMM covers rigid and affine transformation well already > so we >? > can do #1? >? > >? > >? > >? > 2. How does the nonlinear AIR compensate/compare with LDDMM? Can the >? > nonlinear AIR transformation be applied to reorient tensors? >? > >? > >? > >? > Thank you very much! >? > >? > >? > >? > Best, >? > >? > Yi >? > >? > _______________________________________________ >? > Mristudio-users mailing list >? > Mristudio-users at mristudio.org >? > >? > Unsubscribe, send a blank email to: >? > Mristudio-users-unsubscribe at mristudio.org >? > >? > _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org ___________________________________________________________ ????????????????? http://card.mail.cn.yahoo.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090714/6b1dc8a6/attachment-0001.html From siewmin.gan at gmail.com Tue Jul 14 10:35:12 2009 From: siewmin.gan at gmail.com (Siewmin Gan) Date: Wed, 15 Jul 2009 00:35:12 +1000 Subject: [Mristudio-users] =?gb2312?b?UmWjuiBMRERNTSBxdWVzdGlvbnM=?= In-Reply-To: <977947.96698.qm@web15608.mail.cnb.yahoo.com> References: <8690084356BB4B1EA98ED947765A29A3@panpan> <977947.96698.qm@web15608.mail.cnb.yahoo.com> Message-ID: Hi, This is from Xin. It works. https://www.yousendit.com/download/cmcyWUhwMGtxRTJGa1E9PQ. Siewmin On Wed, Jul 15, 2009 at 12:30 AM, jinsong tang wrote: > Hello, Dear all, > > I am trying to use Landmarker with the AIR functions. I am using a 32bit > windows XP. According to the instruction, I need to compile the AIR > functions myself. However, I was not able to build those executable files. > Are there anyone has those .exe files,and could share them with us. > > Best regars, > > Jinsong > ------------------------------ > *????* Xin Li > *????* Yi Jiang > *???* "DTI Studio, ROI Editor, Landmarker Questions/Support" < > mristudio-users at mristudio.org> > *????* 2009/7/14(??), ??10:10:47 > *???* Re: [Mristudio-users] LDDMM questions > > Yi, > > Landmarker can combine AIR matrix and LDDMM matrix. The button for this > function is right below the button for multichannel remote LDDMM. > > > Xin > > > > ----- Original Message ----- > From: susumu mori > Date: Tuesday, July 14, 2009 2:21 am > Subject: Re: [Mristudio-users] LDDMM questions > To: Yi Jiang , "DTI Studio, ROI Editor, Landmarker > Questions/Support" , Xin Li > > > > > Hi Yi, > > > > 1) I recommend you to do AIR first from two reasons. First one is a > > practical reason. Our LDDMM requires that the matrix and pixel sizes > > of the > > two images are identical. After AIR, even if the input images have > different > > dimensions, the output will have the same dimension. This is handy. > Second > > one is more important. Let me use fitting of a X-Y plot for analogy. > > When > > you use linear fitting, no matter which software you use, the results > > are > > almost identical. This is because the energy landscape of linear fitting > > usually has a very simple "one-valley" shape, meaning the results always > > converge at the same solution. On the other hand, when you are using > > non-linear fitting, you are required to provide initial values, which > > are > > close to the real solution. Usually you first do linear solution and > > then > > use the result as the initial value for the subsequent non-linear > fitting. > > This is because the energy landscape of non-linear fitting has a > complicated > > "multi-valley" shape. If your initial values are far away from the real > > solution, the fitting is trapped by a local minima. > > > > Non-linear warping is very similar. You are required to bring two > > brains as > > close as possible before you start non-linear warping. > > > > When you adopt AIR+LDDMM, you have to transform the image twice, > including > > tensor reorientation. Landmarker can combine transformation matrices > > so that > > you can do multiple transformation at once to avoid multiple > interpolation. > > > > Xin, can we combine AIR matrix and LDDMM matrix? > > > > 2) We usually don't use non-linear AIR. So we don't have much experience > > with it. Yes, it should do tensor reorientation if you apply the > > transformation to a tensor file. > > > > > > > > On Mon, Jul 13, 2009 at 4:12 PM, Yi Jiang wrote: > > > > > Dear All, > > > > > > I have two questions about LDDMM: > > > > > > > > > > > > 1. if I have a template image and a subject image and I want to > register > > > these two by LDDMM eventually, 1). should I use LDDMM to register > > these two > > > directly or 2). should I use AIR linear to affine transform them > > first, and > > > then LDDMM the updated subject image? In the 2nd case, I need to > reorient > > > tensors twice, once by the AIR transformation matrix and once by > > the LDDMM > > > transformation matrix, right? > > > > > > > > > > > > I am asking this question because for some other registration > > software I > > > have used, it seems the elastic transformation works better after > affine > > > registering the images first. > > > > > > > > > > > > Or maybe LDDMM covers rigid and affine transformation well already > > so we > > > can do #1? > > > > > > > > > > > > 2. How does the nonlinear AIR compensate/compare with LDDMM? Can the > > > nonlinear AIR transformation be applied to reorient tensors? > > > > > > > > > > > > Thank you very much! > > > > > > > > > > > > Best, > > > > > > Yi > > > > > > _______________________________________________ > > > Mristudio-users mailing list > > > Mristudio-users at mristudio.org > > > > > > Unsubscribe, send a blank email to: > > > Mristudio-users-unsubscribe at mristudio.org > > > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > ------------------------------ > ????????????????? > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090715/be2a5e92/attachment.html From rajagov2 at ccf.org Tue Jul 14 10:44:49 2009 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Tue, 14 Jul 2009 10:44:49 -0400 Subject: [Mristudio-users] LDDMM questions References: <8690084356BB4B1EA98ED947765A29A3@panpan> <977947.96698.qm@web15608.mail.cnb.yahoo.com> Message-ID: <77A88E90A851594AAEF830450587C39D01EDAABA@CCHSCLEXMB56.cc.ad.cchs.net> Hi Jinsong, I am attaching the executable AIR files which i obtained form Xin Li longtime ago. venkateswaran ________________________________ From: mristudio-users-bounces at mristudio.org on behalf of jinsong tang Sent: Tue 7/14/2009 10:30 AM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] Re: LDDMM questions Hello, Dear all, I am trying to use Landmarker with the AIR functions. I am using a 32bit windows XP. According to the instruction, I need to compile the AIR functions myself. However, I was not able to build those executable files. Are there anyone has those .exe files,and could share them with us. Best regars, Jinsong ________________________________ ???: Xin Li ???: Yi Jiang ??: "DTI Studio, ROI Editor, Landmarker Questions/Support" ???: 2009/7/14(??), ??10:10:47 ??: Re: [Mristudio-users] LDDMM questions Yi, Landmarker can combine AIR matrix and LDDMM matrix. The button for this function is right below the button for multichannel remote LDDMM. Xin ----- Original Message ----- From: susumu mori Date: Tuesday, July 14, 2009 2:21 am Subject: Re: [Mristudio-users] LDDMM questions To: Yi Jiang , "DTI Studio, ROI Editor, Landmarker Questions/Support" , Xin Li > Hi Yi, > > 1) I recommend you to do AIR first from two reasons. First one is a > practical reason. Our LDDMM requires that the matrix and pixel sizes > of the > two images are identical. After AIR, even if the input images have different > dimensions, the output will have the same dimension. This is handy. Second > one is more important. Let me use fitting of a X-Y plot for analogy. > When > you use linear fitting, no matter which software you use, the results > are > almost identical. This is because the energy landscape of linear fitting > usually has a very simple "one-valley" shape, meaning the results always > converge at the same solution. On the other hand, when you are using > non-linear fitting, you are required to provide initial values, which > are > close to the real solution. Usually you first do linear solution and > then > use the result as the initial value for the subsequent non-linear fitting. > This is because the energy landscape of non-linear fitting has a complicated > "multi-valley" shape. If your initial values are far away from the real > solution, the fitting is trapped by a local minima. > > Non-linear warping is very similar. You are required to bring two > brains as > close as possible before you start non-linear warping. > > When you adopt AIR+LDDMM, you have to transform the image twice, including > tensor reorientation. Landmarker can combine transformation matrices > so that > you can do multiple transformation at once to avoid multiple interpolation. > > Xin, can we combine AIR matrix and LDDMM matrix? > > 2) We usually don't use non-linear AIR. So we don't have much experience > with it. Yes, it should do tensor reorientation if you apply the > transformation to a tensor file. > > > > On Mon, Jul 13, 2009 at 4:12 PM, Yi Jiang wrote: > > > Dear All, > > > > I have two questions about LDDMM: > > > > > > > > 1. if I have a template image and a subject image and I want to register > > these two by LDDMM eventually, 1). should I use LDDMM to register > these two > > directly or 2). should I use AIR linear to affine transform them > first, and > > then LDDMM the updated subject image? In the 2nd case, I need to reorient > > tensors twice, once by the AIR transformation matrix and once by > the LDDMM > > transformation matrix, right? > > > > > > > > I am asking this question because for some other registration > software I > > have used, it seems the elastic transformation works better after affine > > registering the images first. > > > > > > > > Or maybe LDDMM covers rigid and affine transformation well already > so we > > can do #1? > > > > > > > > 2. How does the nonlinear AIR compensate/compare with LDDMM? Can the > > nonlinear AIR transformation be applied to reorient tensors? > > > > > > > > Thank you very much! > > > > > > > > Best, > > > > Yi > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > > Mristudio-users-unsubscribe at mristudio.org > > > > _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org ________________________________ ???????,????????! =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S. News & World Report (2008). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 9863 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090714/931b4acf/attachment-0001.bin From siewmin.gan at gmail.com Tue Jul 14 12:15:44 2009 From: siewmin.gan at gmail.com (Siewmin Gan) Date: Wed, 15 Jul 2009 02:15:44 +1000 Subject: [Mristudio-users] fa intensity range post linear registration Message-ID: Hi, After linear registration, the aligned FA max range value becomes around 0.96-0.98 for some subjects (the original FA range prior to registration is 0-1). May I ask why the the max intensity or range would decrease, after linear registration with AIR? Hence when I change this post-aligned FA image format to byte before feeding it to multichannel processing, the max intensity would be shown as the previous altered max value (i.e 0.96). Would it be fine to leave it as that when the max value of the atlas FA is 1? Thanks Siewmin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090715/8da711f7/attachment.html From tangjinsonghn at yahoo.com.cn Wed Jul 15 09:32:43 2009 From: tangjinsonghn at yahoo.com.cn (jinsong tang) Date: Wed, 15 Jul 2009 21:32:43 +0800 (CST) Subject: [Mristudio-users] =?utf-8?b?IOWbnuWkje+8miAgUmXvvJogTERETU0gcXVl?= =?utf-8?q?stions?= In-Reply-To: References: <8690084356BB4B1EA98ED947765A29A3@panpan> <977947.96698.qm@web15608.mail.cnb.yahoo.com> Message-ID: <653054.78413.qm@web15608.mail.cnb.yahoo.com> Dear Siewmin and venkateswaran, Thank you for your kindly help.? But I cannot download the attachments. Would you please sent it again. Best, Jinsong ? ________________________________ ???? Siewmin Gan ???? "DTI Studio, ROI Editor, Landmarker Questions/Support" ???? 2009/7/14(??), ??10:35:12 ??? Re: [Mristudio-users] Re? LDDMM questions Hi, This is from Xin. It works. ?https://www.yousendit.com/download/cmcyWUhwMGtxRTJGa1E9PQ. Siewmin On Wed, Jul 15, 2009 at 12:30 AM, jinsong tang wrote: Hello, Dear all, I am trying to use Landmarker with the AIR functions. I am using a 32bit windows XP. According to the instruction, I?need to compile the AIR functions myself. However,? I was not able to build those executable files. Are there anyone has those .exe files,and could share them with us. Best regars, Jinsong ________________________________ ???? Xin Li ???? Yi Jiang ??? "DTI Studio, ROI Editor, Landmarker Questions/Support" ???? 2009/7/14(??), ??10:10:47 ??? Re: [Mristudio-users] LDDMM questions Yi, Landmarker can combine AIR matrix and LDDMM matrix. The button for this function is right below the button for multichannel remote LDDMM. Xin ----- Original Message ----- From: susumu mori Date: Tuesday, July 14, 2009 2:21 am Subject: Re: [Mristudio-users] LDDMM questions To: Yi Jiang , "DTI Studio, ROI Editor, Landmarker Questions/Support" , Xin Li > Hi Yi, >? >? 1) I recommend you to do AIR first from two reasons. First one is a >? practical reason. Our LDDMM requires that the matrix and pixel sizes > of the >? two images are identical. After AIR, even if the input images have different >? dimensions, the output will have the same dimension. This is handy. Second >? one is more important. Let me use fitting of a X-Y plot for analogy. > When >? you use linear fitting, no matter which software you use, the results > are >? almost identical. This is because the energy landscape of linear fitting >? usually has a very simple "one-valley" shape, meaning the results always >? converge at the same solution. On the other hand, when you are using >? non-linear fitting, you are required to provide initial values, which > are >? close to the real solution. Usually you first do linear solution and > then >? use the result as the initial value for the subsequent non-linear fitting. >? This is because the energy landscape of non-linear fitting has a complicated >? "multi-valley" shape. If your initial values are far away from the real >? solution, the fitting is trapped by a local minima. >? >? Non-linear warping is very similar. You are required to bring two > brains as >? close as possible before you start non-linear warping. >? >? When you adopt AIR+LDDMM, you have to transform the image twice, including >? tensor reorientation. Landmarker can combine transformation matrices > so that >? you can do multiple transformation at once to avoid multiple interpolation. >? >? Xin, can we combine AIR matrix and LDDMM matrix? >? >? 2) We usually don't use non-linear AIR. So we don't have much experience >? with it. Yes, it should do tensor reorientation if you apply the >? transformation to a tensor file. >? >? >? >? On Mon, Jul 13, 2009 at 4:12 PM, Yi Jiang wrote: >? >? >? Dear All, >? > >? > I have two questions about LDDMM: >? > >? > >? > >? > 1. if I have a template image and a subject image and I want to register >? > these two by LDDMM eventually, 1). should I use LDDMM to register > these two >? > directly or 2). should I use AIR linear to affine transform them > first, and >? > then LDDMM the updated subject image? In the 2nd case, I need to reorient >? > tensors twice, once by the AIR transformation matrix and once by > the LDDMM >? > transformation matrix, right? >? > >? > >? > >? > I am asking this question because for some other registration > software I >? > have used, it seems the elastic transformation works better after affine >? > registering the images first. >? > >? > >? > >? > Or maybe LDDMM covers rigid and affine transformation well already > so we >? > can do #1? >? > >? > >? > >? > 2. How does the nonlinear AIR compensate/compare with LDDMM? Can the >? > nonlinear AIR transformation be applied to reorient tensors? >? > >? > >? > >? > Thank you very much! >? > >? > >? > >? > Best, >? > >? > Yi >? > >? > _______________________________________________ >? > Mristudio-users mailing list >? > Mristudio-users at mristudio.org >? > >? > Unsubscribe, send a blank email to: >? > Mristudio-users-unsubscribe at mristudio.org >? > >? > _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org ________________________________ ????????????????? _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org ___________________________________________________________ ????????????????? http://card.mail.cn.yahoo.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090715/f744f364/attachment.html From siewmin.gan at gmail.com Wed Jul 15 10:07:32 2009 From: siewmin.gan at gmail.com (Siewmin Gan) Date: Wed, 15 Jul 2009 10:07:32 -0400 Subject: [Mristudio-users] =?gb2312?b?IFJlOiAgu9i4tKO6IFJlo7ogTERETU0gcXVl?= =?gb2312?b?c3Rpb25z?= In-Reply-To: <653054.78413.qm@web15608.mail.cnb.yahoo.com> References: <8690084356BB4B1EA98ED947765A29A3@panpan> <977947.96698.qm@web15608.mail.cnb.yahoo.com> <653054.78413.qm@web15608.mail.cnb.yahoo.com> Message-ID: Hi Jinsong, click on the link I sent you. I just downloaded it and it's fine. Siewmin On Wed, Jul 15, 2009 at 9:32 AM, jinsong tang wrote: > Dear Siewmin and venkateswaran, > > Thank you for your kindly help. But I cannot download the attachments. > Would you please sent it again. > > Best, > > Jinsong > > > ------------------------------ > *????* Siewmin Gan > *????* "DTI Studio, ROI Editor, Landmarker Questions/Support" < > mristudio-users at mristudio.org> > *????* 2009/7/14(??), ??10:35:12 > *???* Re: [Mristudio-users] Re? LDDMM questions > > Hi, This is from Xin. It works. > https://www.yousendit.com/download/cmcyWUhwMGtxRTJGa1E9PQ. > > Siewmin > > On Wed, Jul 15, 2009 at 12:30 AM, jinsong tang > wrote: > >> Hello, Dear all, >> >> I am trying to use Landmarker with the AIR functions. I am using a 32bit >> windows XP. According to the instruction, I need to compile the AIR >> functions myself. However, I was not able to build those executable >> files. Are there anyone has those .exe files,and could share them with us. >> >> Best regars, >> >> Jinsong >> ------------------------------ >> *????* Xin Li >> *????* Yi Jiang >> *???* "DTI Studio, ROI Editor, Landmarker Questions/Support" < >> mristudio-users at mristudio.org> >> *????* 2009/7/14(??), ??10:10:47 >> *???* Re: [Mristudio-users] LDDMM questions >> >> Yi, >> >> Landmarker can combine AIR matrix and LDDMM matrix. The button for this >> function is right below the button for multichannel remote LDDMM. >> >> >> Xin >> >> >> >> ----- Original Message ----- >> From: susumu mori >> Date: Tuesday, July 14, 2009 2:21 am >> Subject: Re: [Mristudio-users] LDDMM questions >> To: Yi Jiang , "DTI Studio, ROI Editor, Landmarker >> Questions/Support" , Xin Li < >> xli16 at jhmi.edu> >> >> >> > Hi Yi, >> > >> > 1) I recommend you to do AIR first from two reasons. First one is a >> > practical reason. Our LDDMM requires that the matrix and pixel sizes >> > of the >> > two images are identical. After AIR, even if the input images have >> different >> > dimensions, the output will have the same dimension. This is handy. >> Second >> > one is more important. Let me use fitting of a X-Y plot for analogy. >> > When >> > you use linear fitting, no matter which software you use, the results >> > are >> > almost identical. This is because the energy landscape of linear >> fitting >> > usually has a very simple "one-valley" shape, meaning the results >> always >> > converge at the same solution. On the other hand, when you are using >> > non-linear fitting, you are required to provide initial values, which >> > are >> > close to the real solution. Usually you first do linear solution and >> > then >> > use the result as the initial value for the subsequent non-linear >> fitting. >> > This is because the energy landscape of non-linear fitting has a >> complicated >> > "multi-valley" shape. If your initial values are far away from the real >> > solution, the fitting is trapped by a local minima. >> > >> > Non-linear warping is very similar. You are required to bring two >> > brains as >> > close as possible before you start non-linear warping. >> > >> > When you adopt AIR+LDDMM, you have to transform the image twice, >> including >> > tensor reorientation. Landmarker can combine transformation matrices >> > so that >> > you can do multiple transformation at once to avoid multiple >> interpolation. >> > >> > Xin, can we combine AIR matrix and LDDMM matrix? >> > >> > 2) We usually don't use non-linear AIR. So we don't have much >> experience >> > with it. Yes, it should do tensor reorientation if you apply the >> > transformation to a tensor file. >> > >> > >> > >> > On Mon, Jul 13, 2009 at 4:12 PM, Yi Jiang wrote: >> > >> > > Dear All, >> > > >> > > I have two questions about LDDMM: >> > > >> > > >> > > >> > > 1. if I have a template image and a subject image and I want to >> register >> > > these two by LDDMM eventually, 1). should I use LDDMM to register >> > these two >> > > directly or 2). should I use AIR linear to affine transform them >> > first, and >> > > then LDDMM the updated subject image? In the 2nd case, I need to >> reorient >> > > tensors twice, once by the AIR transformation matrix and once by >> > the LDDMM >> > > transformation matrix, right? >> > > >> > > >> > > >> > > I am asking this question because for some other registration >> > software I >> > > have used, it seems the elastic transformation works better after >> affine >> > > registering the images first. >> > > >> > > >> > > >> > > Or maybe LDDMM covers rigid and affine transformation well already >> > so we >> > > can do #1? >> > > >> > > >> > > >> > > 2. How does the nonlinear AIR compensate/compare with LDDMM? Can the >> > > nonlinear AIR transformation be applied to reorient tensors? >> > > >> > > >> > > >> > > Thank you very much! >> > > >> > > >> > > >> > > Best, >> > > >> > > Yi >> > > >> > > _______________________________________________ >> > > Mristudio-users mailing list >> > > Mristudio-users at mristudio.org >> > > >> > > Unsubscribe, send a blank email to: >> > > Mristudio-users-unsubscribe at mristudio.org >> > > >> > > >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> ------------------------------ >> ????????????????? >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > ------------------------------ > ????????????????? > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090715/8d4d9f14/attachment-0001.html From tangjinsonghn at yahoo.com.cn Wed Jul 15 10:36:52 2009 From: tangjinsonghn at yahoo.com.cn (jinsong tang) Date: Wed, 15 Jul 2009 22:36:52 +0800 (CST) Subject: [Mristudio-users] =?utf-8?b?IFJF77yaICAgUmU6ICDlm57lpI3vvJogUmU=?= =?utf-8?q?=EF=BC=9A_LDDMM_questions?= In-Reply-To: References: <8690084356BB4B1EA98ED947765A29A3@panpan> <977947.96698.qm@web15608.mail.cnb.yahoo.com> <653054.78413.qm@web15608.mail.cnb.yahoo.com> Message-ID: <70839.72449.qm@web15601.mail.cnb.yahoo.com> I will try it again.?The internet explorer cannot display the webpage in the office. I will try it at home. Thanks, Jinsong ________________________________ ???? Siewmin Gan ???? "DTI Studio, ROI Editor, Landmarker Questions/Support" ???? 2009/7/15(??), ??10:07:32 ??? [Mristudio-users] Re: ??? Re? LDDMM questions Hi Jinsong, click on the link I sent you. I just?downloaded it?and it's fine. Siewmin On Wed, Jul 15, 2009 at 9:32 AM, jinsong tang wrote: Dear Siewmin and venkateswaran, Thank you for your kindly help.? But I cannot download the attachments. Would you please sent it again. Best, Jinsong ? ________________________________ ???? Siewmin Gan ???? "DTI Studio, ROI Editor, Landmarker Questions/Support" ???? 2009/7/14(??), ??10:35:12 ??? Re: [Mristudio-users] Re? LDDMM questions Hi, This is from Xin. It works. ?https://www.yousendit.com/download/cmcyWUhwMGtxRTJGa1E9PQ. Siewmin On Wed, Jul 15, 2009 at 12:30 AM, jinsong tang wrote: Hello, Dear all, I am trying to use Landmarker with the AIR functions. I am using a 32bit windows XP. According to the instruction, I?need to compile the AIR functions myself. However,? I was not able to build those executable files. Are there anyone has those .exe files,and could share them with us. Best regars, Jinsong ________________________________ ???? Xin Li ???? Yi Jiang ??? "DTI Studio, ROI Editor, Landmarker Questions/Support" ???? 2009/7/14(??), ??10:10:47 ??? Re: [Mristudio-users] LDDMM questions Yi, Landmarker can combine AIR matrix and LDDMM matrix. The button for this function is right below the button for multichannel remote LDDMM. Xin ----- Original Message ----- From: susumu mori Date: Tuesday, July 14, 2009 2:21 am Subject: Re: [Mristudio-users] LDDMM questions To: Yi Jiang , "DTI Studio, ROI Editor, Landmarker Questions/Support" , Xin Li > Hi Yi, >? >? 1) I recommend you to do AIR first from two reasons. First one is a >? practical reason. Our LDDMM requires that the matrix and pixel sizes > of the >? two images are identical. After AIR, even if the input images have different >? dimensions, the output will have the same dimension. This is handy. Second >? one is more important. Let me use fitting of a X-Y plot for analogy. > When >? you use linear fitting, no matter which software you use, the results > are >? almost identical. This is because the energy landscape of linear fitting >? usually has a very simple "one-valley" shape, meaning the results always >? converge at the same solution. On the other hand, when you are using >? non-linear fitting, you are required to provide initial values, which > are >? close to the real solution. Usually you first do linear solution and > then >? use the result as the initial value for the subsequent non-linear fitting. >? This is because the energy landscape of non-linear fitting has a complicated >? "multi-valley" shape. If your initial values are far away from the real >? solution, the fitting is trapped by a local minima. >? >? Non-linear warping is very similar. You are required to bring two > brains as >? close as possible before you start non-linear warping. >? >? When you adopt AIR+LDDMM, you have to transform the image twice, including >? tensor reorientation. Landmarker can combine transformation matrices > so that >? you can do multiple transformation at once to avoid multiple interpolation. >? >? Xin, can we combine AIR matrix and LDDMM matrix? >? >? 2) We usually don't use non-linear AIR. So we don't have much experience >? with it. Yes, it should do tensor reorientation if you apply the >? transformation to a tensor file. >? >? >? >? On Mon, Jul 13, 2009 at 4:12 PM, Yi Jiang wrote: >? >? >? Dear All, >? > >? > I have two questions about LDDMM: >? > >? > >? > >? > 1. if I have a template image and a subject image and I want to register >? > these two by LDDMM eventually, 1). should I use LDDMM to register > these two >? > directly or 2). should I use AIR linear to affine transform them > first, and >? > then LDDMM the updated subject image? In the 2nd case, I need to reorient >? > tensors twice, once by the AIR transformation matrix and once by > the LDDMM >? > transformation matrix, right? >? > >? > >? > >? > I am asking this question because for some other registration > software I >? > have used, it seems the elastic transformation works better after affine >? > registering the images first. >? > >? > >? > >? > Or maybe LDDMM covers rigid and affine transformation well already > so we >? > can do #1? >? > >? > >? > >? > 2. How does the nonlinear AIR compensate/compare with LDDMM? Can the >? > nonlinear AIR transformation be applied to reorient tensors? >? > >? > >? > >? > Thank you very much! >? > >? > >? > >? > Best, >? > >? > Yi >? > >? > _______________________________________________ >? > Mristudio-users mailing list >? > Mristudio-users at mristudio.org >? > >? > Unsubscribe, send a blank email to: >? > Mristudio-users-unsubscribe at mristudio.org >? > >? > _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org ________________________________ ????????????????? _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org ________________________________ ????????????????? _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org ___________________________________________________________ ????????????????? http://card.mail.cn.yahoo.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090715/5f80f28b/attachment.html From siewmin.gan at gmail.com Wed Jul 15 10:45:23 2009 From: siewmin.gan at gmail.com (Siewmin Gan) Date: Wed, 15 Jul 2009 10:45:23 -0400 Subject: [Mristudio-users] =?gb2312?b?IFJlOiAgUkWjuiBSZTogu9i4tKO6IFJlo7og?= =?gb2312?b?TERETU0gcXVlc3Rpb25z?= In-Reply-To: <70839.72449.qm@web15601.mail.cnb.yahoo.com> References: <8690084356BB4B1EA98ED947765A29A3@panpan> <977947.96698.qm@web15608.mail.cnb.yahoo.com> <653054.78413.qm@web15608.mail.cnb.yahoo.com> <70839.72449.qm@web15601.mail.cnb.yahoo.com> Message-ID: sorry about that. the zip and unzip files are executable and gmail doesn't allow me send it, for security reason Siewmin On Wed, Jul 15, 2009 at 10:36 AM, jinsong tang wrote: > I will try it again. The internet explorer cannot display the webpage in > the office. I will try it at home. > > Thanks, > > Jinsong > ------------------------------ > *????* Siewmin Gan > *????* "DTI Studio, ROI Editor, Landmarker Questions/Support" < > mristudio-users at mristudio.org> > *????* 2009/7/15(??), ??10:07:32 > *???* [Mristudio-users] Re: ??? Re? LDDMM questions > > Hi Jinsong, click on the link I sent you. I just downloaded it and it's > fine. > > Siewmin > > On Wed, Jul 15, 2009 at 9:32 AM, jinsong tang wrote: > >> Dear Siewmin and venkateswaran, >> >> Thank you for your kindly help. But I cannot download the attachments. >> Would you please sent it again. >> >> Best, >> >> Jinsong >> >> >> ------------------------------ >> *????* Siewmin Gan >> *????* "DTI Studio, ROI Editor, Landmarker Questions/Support" < >> mristudio-users at mristudio.org> >> *????* 2009/7/14(??), ??10:35:12 >> *???* Re: [Mristudio-users] Re? LDDMM questions >> >> Hi, This is from Xin. It works. >> https://www.yousendit.com/download/cmcyWUhwMGtxRTJGa1E9PQ. >> >> Siewmin >> >> On Wed, Jul 15, 2009 at 12:30 AM, jinsong tang < >> tangjinsonghn at yahoo.com.cn> wrote: >> >>> Hello, Dear all, >>> >>> I am trying to use Landmarker with the AIR functions. I am using a 32bit >>> windows XP. According to the instruction, I need to compile the AIR >>> functions myself. However, I was not able to build those executable >>> files. Are there anyone has those .exe files,and could share them with us. >>> >>> Best regars, >>> >>> Jinsong >>> ------------------------------ >>> *????* Xin Li >>> *????* Yi Jiang >>> *???* "DTI Studio, ROI Editor, Landmarker Questions/Support" < >>> mristudio-users at mristudio.org> >>> *????* 2009/7/14(??), ??10:10:47 >>> *???* Re: [Mristudio-users] LDDMM questions >>> >>> Yi, >>> >>> Landmarker can combine AIR matrix and LDDMM matrix. The button for this >>> function is right below the button for multichannel remote LDDMM. >>> >>> >>> Xin >>> >>> >>> >>> ----- Original Message ----- >>> From: susumu mori >>> Date: Tuesday, July 14, 2009 2:21 am >>> Subject: Re: [Mristudio-users] LDDMM questions >>> To: Yi Jiang , "DTI Studio, ROI Editor, Landmarker >>> Questions/Support" , Xin Li < >>> xli16 at jhmi.edu> >>> >>> >>> > Hi Yi, >>> > >>> > 1) I recommend you to do AIR first from two reasons. First one is a >>> > practical reason. Our LDDMM requires that the matrix and pixel sizes >>> > of the >>> > two images are identical. After AIR, even if the input images have >>> different >>> > dimensions, the output will have the same dimension. This is handy. >>> Second >>> > one is more important. Let me use fitting of a X-Y plot for analogy. >>> > When >>> > you use linear fitting, no matter which software you use, the results >>> > are >>> > almost identical. This is because the energy landscape of linear >>> fitting >>> > usually has a very simple "one-valley" shape, meaning the results >>> always >>> > converge at the same solution. On the other hand, when you are using >>> > non-linear fitting, you are required to provide initial values, which >>> > are >>> > close to the real solution. Usually you first do linear solution and >>> > then >>> > use the result as the initial value for the subsequent non-linear >>> fitting. >>> > This is because the energy landscape of non-linear fitting has a >>> complicated >>> > "multi-valley" shape. If your initial values are far away from the >>> real >>> > solution, the fitting is trapped by a local minima. >>> > >>> > Non-linear warping is very similar. You are required to bring two >>> > brains as >>> > close as possible before you start non-linear warping. >>> > >>> > When you adopt AIR+LDDMM, you have to transform the image twice, >>> including >>> > tensor reorientation. Landmarker can combine transformation matrices >>> > so that >>> > you can do multiple transformation at once to avoid multiple >>> interpolation. >>> > >>> > Xin, can we combine AIR matrix and LDDMM matrix? >>> > >>> > 2) We usually don't use non-linear AIR. So we don't have much >>> experience >>> > with it. Yes, it should do tensor reorientation if you apply the >>> > transformation to a tensor file. >>> > >>> > >>> > >>> > On Mon, Jul 13, 2009 at 4:12 PM, Yi Jiang wrote: >>> > >>> > > Dear All, >>> > > >>> > > I have two questions about LDDMM: >>> > > >>> > > >>> > > >>> > > 1. if I have a template image and a subject image and I want to >>> register >>> > > these two by LDDMM eventually, 1). should I use LDDMM to register >>> > these two >>> > > directly or 2). should I use AIR linear to affine transform them >>> > first, and >>> > > then LDDMM the updated subject image? In the 2nd case, I need to >>> reorient >>> > > tensors twice, once by the AIR transformation matrix and once by >>> > the LDDMM >>> > > transformation matrix, right? >>> > > >>> > > >>> > > >>> > > I am asking this question because for some other registration >>> > software I >>> > > have used, it seems the elastic transformation works better after >>> affine >>> > > registering the images first. >>> > > >>> > > >>> > > >>> > > Or maybe LDDMM covers rigid and affine transformation well already >>> > so we >>> > > can do #1? >>> > > >>> > > >>> > > >>> > > 2. How does the nonlinear AIR compensate/compare with LDDMM? Can the >>> > > nonlinear AIR transformation be applied to reorient tensors? >>> > > >>> > > >>> > > >>> > > Thank you very much! >>> > > >>> > > >>> > > >>> > > Best, >>> > > >>> > > Yi >>> > > >>> > > _______________________________________________ >>> > > Mristudio-users mailing list >>> > > Mristudio-users at mristudio.org >>> > > >>> > > Unsubscribe, send a blank email to: >>> > > Mristudio-users-unsubscribe at mristudio.org >>> > > >>> > > >>> _______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: >>> Mristudio-users-unsubscribe at mristudio.org >>> >>> ------------------------------ >>> ????????????????? >>> >>> _______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: >>> Mristudio-users-unsubscribe at mristudio.org >>> >>> >> >> ------------------------------ >> ????????????????? >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > ------------------------------ > ????????????????? > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090715/e83aaf6d/attachment-0001.html From xli16 at jhmi.edu Wed Jul 15 11:17:27 2009 From: xli16 at jhmi.edu (Xin Li) Date: Wed, 15 Jul 2009 11:17:27 -0400 Subject: [Mristudio-users] fa intensity range post linear registration In-Reply-To: References: Message-ID: Siewmin, Sorry, I misunderstood your words. You said the FA max is 0.96 not the byte max. I think it is fine to leave it that way. After Andreai comes back, I will ask her if it would affect the lddmm result. Xin ----- Original Message ----- From: Siewmin Gan Date: Tuesday, July 14, 2009 12:16 pm Subject: [Mristudio-users] fa intensity range post linear registration To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > Hi, > After linear registration, the aligned FA max range value becomes > around > 0.96-0.98 for some subjects (the original FA range prior to > registration is > 0-1). May I ask why the the max intensity or range would decrease, after > linear registration with AIR? > > Hence when I change this post-aligned FA image format to byte before > feeding > it to multichannel processing, the max intensity would be shown as the > previous altered max value (i.e 0.96). Would it be fine to leave it > as that > when the max value of the atlas FA is 1? > > Thanks > > Siewmin > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From yj3 at duke.edu Wed Jul 15 14:30:27 2009 From: yj3 at duke.edu (Yi Jiang) Date: Wed, 15 Jul 2009 14:30:27 -0400 Subject: [Mristudio-users] LDDMM questions References: <8690084356BB4B1EA98ED947765A29A3@panpan> Message-ID: <8DCCDAAEA9D84D65BDD16E0CAB2322F9@panpan> Hello, Dr Mori, Thank you very much for your reply. It's very clear. Also, I really appreciate all the help from Xin and Anthony. They are really quick and helpful, and they have solved all my problems so far. I have one more question: It seems there is no manual or instruction about using LDDMM with manually placed landmarkers. Is there such a function? Or is the current LDDMM only working without landmarker? If yes, how do we do that? Just add some landmarkers and then start a LDDMM job? Thank you! Best, Yi ----- Original Message ----- From: susumu mori To: Yi Jiang ; DTI Studio, ROI Editor, Landmarker Questions/Support ; Xin Li Sent: Tuesday, July 14, 2009 2:21 AM Subject: Re: [Mristudio-users] LDDMM questions Hi Yi, 1) I recommend you to do AIR first from two reasons. First one is a practical reason. Our LDDMM requires that the matrix and pixel sizes of the two images are identical. After AIR, even if the input images have different dimensions, the output will have the same dimension. This is handy. Second one is more important. Let me use fitting of a X-Y plot for analogy. When you use linear fitting, no matter which software you use, the results are almost identical. This is because the energy landscape of linear fitting usually has a very simple "one-valley" shape, meaning the results always converge at the same solution. On the other hand, when you are using non-linear fitting, you are required to provide initial values, which are close to the real solution. Usually you first do linear solution and then use the result as the initial value for the subsequent non-linear fitting. This is because the energy landscape of non-linear fitting has a complicated "multi-valley" shape. If your initial values are far away from the real solution, the fitting is trapped by a local minima. Non-linear warping is very similar. You are required to bring two brains as close as possible before you start non-linear warping. When you adopt AIR+LDDMM, you have to transform the image twice, including tensor reorientation. Landmarker can combine transformation matrices so that you can do multiple transformation at once to avoid multiple interpolation. Xin, can we combine AIR matrix and LDDMM matrix? 2) We usually don't use non-linear AIR. So we don't have much experience with it. Yes, it should do tensor reorientation if you apply the transformation to a tensor file. On Mon, Jul 13, 2009 at 4:12 PM, Yi Jiang wrote: Dear All, I have two questions about LDDMM: 1. if I have a template image and a subject image and I want to register these two by LDDMM eventually, 1). should I use LDDMM to register these two directly or 2). should I use AIR linear to affine transform them first, and then LDDMM the updated subject image? In the 2nd case, I need to reorient tensors twice, once by the AIR transformation matrix and once by the LDDMM transformation matrix, right? I am asking this question because for some other registration software I have used, it seems the elastic transformation works better after affine registering the images first. Or maybe LDDMM covers rigid and affine transformation well already so we can do #1? 2. How does the nonlinear AIR compensate/compare with LDDMM? Can the nonlinear AIR transformation be applied to reorient tensors? Thank you very much! Best, Yi _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org ------------------------------------------------------------------------------ _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090715/eeb6fb3d/attachment.html From kevinspitler at ucla.edu Fri Jul 17 12:54:05 2009 From: kevinspitler at ucla.edu (Kevin Spitler) Date: Fri, 17 Jul 2009 09:54:05 -0700 Subject: [Mristudio-users] DICOM files error: "no DICOM files found" Message-ID: <9770ef210907170954m1a69cb95r55a000ffcfa7446e@mail.gmail.com> Hello, I am working with DICOM files and am having problems grouping them into different volumes (associated with gradient directions). The data is from a Siemens MRI. I am wondering what DCM header information DTI Studio uses to group images as on most of my patient data sets I receive the error "no dcm files found." Thank you very much, Kevin From susumu at mri.jhu.edu Fri Jul 17 20:08:34 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Fri, 17 Jul 2009 20:08:34 -0400 Subject: [Mristudio-users] DICOM files error: "no DICOM files found" In-Reply-To: <9770ef210907170954m1a69cb95r55a000ffcfa7446e@mail.gmail.com> References: <9770ef210907170954m1a69cb95r55a000ffcfa7446e@mail.gmail.com> Message-ID: Hi Kevin, I have several questions; 1) When you mentioned "grouping them", do you mean using DtiStudio for the grouping or is it a general question like, "how can I separate DICOM files into different directories?" 2) Could you read the DICOM files into DtiStudio successfully and your question is about how to save these files in a different format? 3) The "no dcm files found" happens when DtiStudio looks for *.dcm files (the default extension for the DICOM formant), while your DICOM files have different extensions. In this case, you choose "all files" in the file open window. Susumu On Fri, Jul 17, 2009 at 12:54 PM, Kevin Spitler wrote: > Hello, > > I am working with DICOM files and am having problems grouping them > into different volumes (associated with gradient directions). The data > is from a Siemens MRI. I am wondering what DCM header information DTI > Studio uses to group images as on most of my patient data sets I > receive the error "no dcm files found." > > Thank you very much, > Kevin > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090717/9a040469/attachment.html From susumu at mri.jhu.edu Fri Jul 17 21:14:29 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Fri, 17 Jul 2009 21:14:29 -0400 Subject: [Mristudio-users] LDDMM questions In-Reply-To: <8DCCDAAEA9D84D65BDD16E0CAB2322F9@panpan> References: <8690084356BB4B1EA98ED947765A29A3@panpan> <8DCCDAAEA9D84D65BDD16E0CAB2322F9@panpan> Message-ID: Hi Yi, Landmarker has very strong functionality in landmark-based transformation, but as you noticed, we haven't made a manual yet. We use landmarks when; 1) Initial linear transformation failed with some reasons (brain locations, orientations, and FOV coverages are too different). 2) Two images have so much different contrasts (e.g. normalizing 0 year to 1 year old neonates) 3) When the patient has strong anatomical deformation such as tumor and chronic stroke and want to ignore some regions of the brain. We'll do our best to make a PPT "getting started" shortly. Susumu On Wed, Jul 15, 2009 at 2:30 PM, Yi Jiang wrote: > Hello, Dr Mori, > > > > Thank you very much for your reply. It's very clear. Also, I really > appreciate all the help from Xin and Anthony. They are really quick and > helpful, and they have solved all my problems so far. > > > > I have one more question: > > > > It seems there is no manual or instruction about using LDDMM with manually > placed landmarkers. Is there such a function? Or is the current LDDMM only > working without landmarker? If yes, how do we do that? Just add some > landmarkers and then start a LDDMM job? > > > > Thank you! > > > > Best, > > Yi > > > > > ----- Original Message ----- > > *From:* susumu mori > *To:* Yi Jiang ; DTI Studio, ROI Editor, Landmarker > Questions/Support ; Xin Li > *Sent:* Tuesday, July 14, 2009 2:21 AM > *Subject:* Re: [Mristudio-users] LDDMM questions > > Hi Yi, > > 1) I recommend you to do AIR first from two reasons. First one is a > practical reason. Our LDDMM requires that the matrix and pixel sizes of the > two images are identical. After AIR, even if the input images have different > dimensions, the output will have the same dimension. This is handy. Second > one is more important. Let me use fitting of a X-Y plot for analogy. When > you use linear fitting, no matter which software you use, the results are > almost identical. This is because the energy landscape of linear fitting > usually has a very simple "one-valley" shape, meaning the results always > converge at the same solution. On the other hand, when you are using > non-linear fitting, you are required to provide initial values, which are > close to the real solution. Usually you first do linear solution and then > use the result as the initial value for the subsequent non-linear fitting. > This is because the energy landscape of non-linear fitting has a complicated > "multi-valley" shape. If your initial values are far away from the real > solution, the fitting is trapped by a local minima. > > Non-linear warping is very similar. You are required to bring two brains as > close as possible before you start non-linear warping. > > When you adopt AIR+LDDMM, you have to transform the image twice, including > tensor reorientation. Landmarker can combine transformation matrices so that > you can do multiple transformation at once to avoid multiple interpolation. > > Xin, can we combine AIR matrix and LDDMM matrix? > > 2) We usually don't use non-linear AIR. So we don't have much experience > with it. Yes, it should do tensor reorientation if you apply the > transformation to a tensor file. > > > > On Mon, Jul 13, 2009 at 4:12 PM, Yi Jiang wrote: > >> Dear All, >> >> I have two questions about LDDMM: >> >> >> >> 1. if I have a template image and a subject image and I want to register >> these two by LDDMM eventually, 1). should I use LDDMM to register these two >> directly or 2). should I use AIR linear to affine transform them first, and >> then LDDMM the updated subject image? In the 2nd case, I need to reorient >> tensors twice, once by the AIR transformation matrix and once by the LDDMM >> transformation matrix, right? >> >> >> >> I am asking this question because for some other registration software I >> have used, it seems the elastic transformation works better after affine >> registering the images first. >> >> >> >> Or maybe LDDMM covers rigid and affine transformation well already so we >> can do #1? >> >> >> >> 2. How does the nonlinear AIR compensate/compare with LDDMM? Can the >> nonlinear AIR transformation be applied to reorient tensors? >> >> >> >> Thank you very much! >> >> >> >> Best, >> >> Yi >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > ------------------------------ > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090717/d98ccd08/attachment-0001.html From susumu at mri.jhu.edu Sat Jul 18 09:01:52 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Sat, 18 Jul 2009 09:01:52 -0400 Subject: [Mristudio-users] measureing Volume of CST In-Reply-To: <77A88E90A851594AAEF830450587C39D01EDAAB9@CCHSCLEXMB56.cc.ad.cchs.net> References: <77A88E90A851594AAEF830450587C39D01EDAAB9@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: Hi Venkateswaran, There are several ways; 1) Manual delineation: CST goes through the corona radiata, internal capsule, cerebral peduncle, pons, and medulla. As it descends, the size seems to reduce but this is because there are so many fibers running parallel; some go to the thalamus, midbrain, pons, and cerebellum. So, it would be difficult to manually define the pure CST at the higher slices at the level of the corona radiata, internal capsule, and cerebral peduncle. You can manually define it at the pons where you can find much purer CST. For the manual delineation, you can use DtiStudio but I suggest RoiEditor which has better interface for ROI drawing. 2) Tractography: You can use multiple ROIs to extract a trajectory that mimics the known CST trajectory. Once you reconstruct it, you can count the number of the pixels occupied by the reconstructed CST. You can use "Fiber Tracking" function in DtiStudio and the "Statistics" button to get the number of pixels. This may sound better method, but you may find a large amount of variability among individuals. Susumu On Tue, Jul 14, 2009 at 10:23 AM, Rajagopalan, Venkateswaran < rajagov2 at ccf.org> wrote: > Dear MRI studio Users, > > I am wondering is there a way to measure quantitatively the volume of CST. > If so can anyone please tell me how to do it using DTI studio. In essence > we are interested in seeing whether CST tract volume is reduced in our ALS > patients when compared to controls. > > Thanks > > Regards > venkateswaran > > =================================== > > P Please consider the environment before printing this e-mail > > > Cleveland Clinic is ranked one of the top hospitals > in America by U.S. News & World Report (2008). > Visit us online at http://www.clevelandclinic.org for > a complete listing of our services, staff and > locations. > > > Confidentiality Note: This message is intended for use > only by the individual or entity to which it is addressed > and may contain information that is privileged, > confidential, and exempt from disclosure under applicable > law. If the reader of this message is not the intended > recipient or the employee or agent responsible for > delivering the message to the intended recipient, you are > hereby notified that any dissemination, distribution or > copying of this communication is strictly prohibited. If > you have received this communication in error, please > contact the sender immediately and destroy the material in > its entirety, whether electronic or hard copy. Thank you. > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090718/5454f6eb/attachment.html From susumu at mri.jhu.edu Sat Jul 18 19:42:29 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Sat, 18 Jul 2009 19:42:29 -0400 Subject: [Mristudio-users] Using fiber tracking data from DTIstudio in MATLAB In-Reply-To: References: Message-ID: Hi Sung, In the FAQ section, there is an explanation for the format of the tract file stored by DtiStudio. It should be straightforward to write a MATLAB code to read it. Susumu On Sun, Jul 12, 2009 at 10:11 PM, Sung Hoon Bae wrote: > Hello everyone, > > Is it possible to use the fiber tracking data from DTIstudio in MATLAB? > If so, would someone briefly explain how? > > I really appreciate your help/time! > > Sincerely, > > -- > Sung > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090718/fd3dda4b/attachment.html From rajagov2 at ccf.org Mon Jul 20 09:40:20 2009 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Mon, 20 Jul 2009 09:40:20 -0400 Subject: [Mristudio-users] measureing Volume of CST References: <77A88E90A851594AAEF830450587C39D01EDAAB9@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: <77A88E90A851594AAEF830450587C39D01EDAABF@CCHSCLEXMB56.cc.ad.cchs.net> Dear Dr.Mori, Thank you very much for your kind information. I will adopt your second approach as we need to measure FA and other DTI metrics also along the CST. Thanks again for your kind help. Regards venkateswaran ________________________________ From: mristudio-users-bounces at mristudio.org on behalf of susumu mori Sent: Sat 7/18/2009 9:01 AM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] measureing Volume of CST Hi Venkateswaran, There are several ways; 1) Manual delineation: CST goes through the corona radiata, internal capsule, cerebral peduncle, pons, and medulla. As it descends, the size seems to reduce but this is because there are so many fibers running parallel; some go to the thalamus, midbrain, pons, and cerebellum. So, it would be difficult to manually define the pure CST at the higher slices at the level of the corona radiata, internal capsule, and cerebral peduncle. You can manually define it at the pons where you can find much purer CST. For the manual delineation, you can use DtiStudio but I suggest RoiEditor which has better interface for ROI drawing. 2) Tractography: You can use multiple ROIs to extract a trajectory that mimics the known CST trajectory. Once you reconstruct it, you can count the number of the pixels occupied by the reconstructed CST. You can use "Fiber Tracking" function in DtiStudio and the "Statistics" button to get the number of pixels. This may sound better method, but you may find a large amount of variability among individuals. Susumu On Tue, Jul 14, 2009 at 10:23 AM, Rajagopalan, Venkateswaran wrote: Dear MRI studio Users, I am wondering is there a way to measure quantitatively the volume of CST. If so can anyone please tell me how to do it using DTI studio. In essence we are interested in seeing whether CST tract volume is reduced in our ALS patients when compared to controls. Thanks Regards venkateswaran =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S. News & World Report (2008). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S. News & World Report (2008). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 7103 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090720/abe33d8a/attachment-0001.bin From shereeda at email.uc.edu Tue Jul 21 16:19:39 2009 From: shereeda at email.uc.edu (Duke Shereen) Date: Tue, 21 Jul 2009 16:19:39 -0400 (EDT) Subject: [Mristudio-users] sending questions via email address not on mailing list Message-ID: <20090721161939.DFG32869@mirapoint.uc.edu> Hello All, I just sent a question via email through an email account different from that on the mailing list. This is because of file size limitations. The email account I used was: ahmed.shereen at cchmc.org. Hope this doesn't cause too much confusion. From Helen.Carlson at albertahealthservices.ca Wed Jul 22 16:40:26 2009 From: Helen.Carlson at albertahealthservices.ca (Helen Carlson) Date: Wed, 22 Jul 2009 14:40:26 -0600 Subject: [Mristudio-users] How to Process Siemens Mosaic files in DTIStudio? Message-ID: Hi all, I am trying to create a tensor image from a 6 direction DTI scan and am having trouble. I can load my 42 IMA images successfully into DTI Studio (they are in mosaic format). However I would expect to see 7 options in the drop down list on the right side of the Image tab. These options should be composed of a b0 and the 6 DWI directions. However, I see 42 options in the drop down list. As I scroll through these options I see 7 b0 images interleaved with 6 diffusion weighted images between them giving me the 42 images in the list. The resulting FA and Color maps are of poor resolution. I suspect this is because the wrong b0 is used in the noise calculations. So my question is, what am I doing wrong while loading the data that causes this? I searched the archives and found an email (below) addressing this issue. It was helpful though I still cannot resolve my problem. Thank-you in advance for your help. Regards, Helen. ~~~~~~~~ Orginal message: Hi Anuar, 1) Could you read the IMA (mosaic format data)? If so, make sure how many images are loaded. You can use "MRIView3D -> Siemens Mosaic" and load the data. If successful, you should see a list of loaded images in the pull-down menu in the right column of the viewing window. For example, if you used typical Siemens 12-orientation scheme, you should find 1 b0 + 12 DWI (total 13 images). 2) Then you need to find a correct gradient table. If you are using an off-the-shelf Siemens DTI method, there are Siemens-supplied gradient tables for that. If you don't know the table, please let us know, together with the number of images you get in the step #1. If you are using a user-specified table, you need to find the table. 3) Final thing you have to check is the version of your operating system and oblique plane angle. If you are using the latest operating system or your imaging plane is not oblique, you are fine. If you are using an old operating system AND an oblique plane, than, you have to check "Rotate gradients if applicable" box. Susumu -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Anuar Imanbayev Sent: Thursday, January 15, 2009 2:08 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] How to Process Siemens Mosaic files in DTIStudio? Hello everyone, I usually deal with .par and .rec files. However, my PI's collaborator works with Siemens Mosaic files and needs help in being able to perform tensor calculations on them. I'm working out the kinks so then I can report sometime next week with my findings. At first, the collaborating doctor informed me that the files were .IMA files. Indeed they did masquerade as those, but in reality responded only to Siemens Mosaic filetype under DTIStudio. Dr. Hangyi Jiang identified the data files not as ima but as mosaic files for me and helped me around in general. Still, I'm at a loss with which gradient files to treat these Siemens Mosaic files and how to perform Tensor calculations that produce credible color maps (mine so far were just red dots all around) I'll keep experimenting and poking around in the meantime. Please help me understand and deal with this new file type. Also, apparently there were no b0 or standard data files associated with the data set that the collaborator sent - just a bunch of image files. Would that be a problem in the long run? How to handle the situation when those are provided? With just image files, how do I go about creating an image quality file, then saving it after my scanning for bad quality images? Thank you for your time and assistance in advance, Sincerely yours, Anuar Imanbayev Undergraduate Neuroscience 2010 _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users ________________________________ This message and any attached documents are only for the use of the intended recipient(s), are confidential and may contain privileged information. Any unauthorized review, use, retransmission, or other disclosure is strictly prohibited. If you have received this message in error, please notify the sender immediately, and then delete the original message. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090722/74d166f9/attachment.html From susumu at mri.jhu.edu Wed Jul 22 22:01:24 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 22 Jul 2009 22:01:24 -0400 Subject: [Mristudio-users] How to Process Siemens Mosaic files in DTIStudio? In-Reply-To: References: Message-ID: Hi Helen, 1) You have 42 mosaic files. This means, you did (1 b0 + 6 DWI) x 6 repetitions, I think. 2) In recent Siemens system, if you do signal averaging, the scanners save the repeated measurements separately instead of averaging them. This enables you to do image co-registration to minimize motion-related problems. Please note that if the scanners average multiple acquisitions, you can not do co-registration anymore. 3) There are two ways to load the 42 images; a) load all of them as one sequential data, b) load the data as 6 independent (1 b0 + 6 DWI) data. 4) You loaded the data as #a method. In this case, you have to modify your b-table. For example, if your b-table is; 0: 0, 0, 0 1: 1, 1, 0 2: 1, 0, 1 3: 0, 1, 1 4: -1, 1, 0 5: -1,0, 1 6: 0, -1,1 you have to repeat this 6 times like; 0: 0, 0, 0 1: 1, 1, 0 2: 1, 0, 1 3: 0, 1, 1 4: -1, 1, 0 5: -1,0, 1 6: 0, -1,1 7: 0, 0, 0 8: 1, 1, 0 9: 1, 0, 1 10: 0, 1, 1 11: -1, 1, 0 12: -1,0, 1 13: 0, -1,1 . . and so on. 5) Method #a should work fine, but Method #b has several advantages. For example, you can calculate standard deviations and subtraction images for the 6 repeated measurements. These repeated measurements should look identical. You can easily see if the subject moves and if co-registration works fine. Corrupted images can be detected much easiler too. There are two ways to convert the 42 sequential data to 6 repeated parallel data; 5-1) Separate the 42 IMA files into 6 different directories (1 b0 + 6 DWIs in each directory) and list the 6 directories in the DtiStudio data input window. This can be most easily done if you can specify the scanner to save the data in this way (I thought it's possible). Otherwise, you may find it difficult to figure out how to divide the 42 files into the 6 repeated data. 5-2) Once you read the 42 IMA data, you can save them as 6 raw files; each raw file contains 7 images. You can do it by using the "save" icon in the right column. Close the window and load the raw data as the "REC" format. Load the all 6 raw files at once. One problem is, during the conversion of Mosaic -> Raw, you loose information about oblique imaging (see #6), which means you should not use this method if you used oblique angles. In both cases, the b-table will be; 0: 0, 0, 0 1: 1, 1, 0 2: 1, 0, 1 3: 0, 1, 1 4: -1, 1, 0 5: -1,0, 1 6: 0, -1,1 6) As I mentioned multiple times in the previous communications, Siemens users have to be very careful when oblique imaging is used. Unless you are using the latest VB15 operating system, the gradient table has to be recalculated based on the oblique angles. This can be done by checking the box ("rotate if applicable") beneath the b-table window. DtiStudio automatically reads the angle information from Dicom/Mosaic headers and rotate the b-table. If you are using VB15, this is already taken care of at the time of data acquisition and therefore you don't check this box. If you convert the Dicom/Mosaic to a raw data format (REC format), the oblique information is lost and you can not use this function. Therefore the approach #5-2 can not be used unless you are not using oblique imaging. Susumu On Wed, Jul 22, 2009 at 4:40 PM, Helen Carlson < Helen.Carlson at albertahealthservices.ca> wrote: > Hi all, > I am trying to create a tensor image from a 6 direction DTI scan and am > having trouble. I can load my 42 IMA images successfully into DTI Studio > (they are in mosaic format). However I would expect to see 7 options in the > drop down list on the right side of the Image tab. These options should be > composed of a b0 and the 6 DWI directions. > > However, I see 42 options in the drop down list. As I scroll through these > options I see 7 b0 images interleaved with 6 diffusion weighted images > between them giving me the 42 images in the list. > > The resulting FA and Color maps are of poor resolution. I suspect this is > because the wrong b0 is used in the noise calculations. > > So my question is, what am I doing wrong while loading the data that causes > this? I searched the archives and found an email (below) addressing this > issue. It was helpful though I still cannot resolve my problem. > > Thank-you in advance for your help. > Regards, > Helen. > > ~~~~~~~~ > > > > > Orginal message: > > Hi Anuar, > > 1) Could you read the IMA (mosaic format data)? If so, make sure how many > images are loaded. You can use "MRIView3D -> Siemens Mosaic" and load the > data. If successful, you should see a list of loaded images in the pull-down > menu in the right column of the viewing window. For example, if you used > typical Siemens 12-orientation scheme, you should find 1 b0 + 12 DWI (total > 13 images). > 2) Then you need to find a correct gradient table. If you are using an > off-the-shelf Siemens DTI method, there are Siemens-supplied gradient tables > for that. If you don't know the table, please let us know, together with the > number of images you get in the step #1. If you are using a user-specified > table, you need to find the table. > 3) Final thing you have to check is the version of your operating system and > oblique plane angle. If you are using the latest operating system or your > imaging plane is not oblique, you are fine. If you are using an old > operating system AND an oblique plane, than, you have to check "Rotate > gradients if applicable" box. > > Susumu > > -----Original Message----- > From: mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org ] On Behalf Of Anuar Imanbayev > Sent: Thursday, January 15, 2009 2:08 PM > To: mristudio-users at mristudio.org > Subject: [Mristudio-users] How to Process Siemens Mosaic files in DTIStudio? > > Hello everyone, > > I usually deal with .par and .rec files. However, my PI's collaborator works > with Siemens Mosaic files and needs help in being able to perform tensor > calculations on them. I'm working out the kinks so then I can report > sometime next week with my findings. > > > At first, the collaborating doctor informed me that the files were .IMA > files. Indeed they did masquerade as those, but in reality responded only to > Siemens Mosaic filetype under DTIStudio. > > Dr. Hangyi Jiang identified the data files not as ima but as mosaic files > for me and helped me around in general. Still, I'm at a loss with which > gradient files to treat these Siemens Mosaic files and how to perform Tensor > calculations that produce credible color maps (mine so far were just red > dots all around) I'll keep experimenting and poking around in the meantime. > > Please help me understand and deal with this new file type. Also, apparently > there were no b0 or standard data files associated with the data set that > the collaborator sent - just a bunch of image files. Would that be a > problem in the long run? How to handle the situation when those are > provided? With just image files, how do I go about creating an image quality > file, then saving it after my scanning for bad quality images? > > Thank you for your time and assistance in advance, > Sincerely yours, > Anuar Imanbayev > Undergraduate Neuroscience 2010 > _______________________________________________ > Mristudio-users mailing listMristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > ------------------------------ > This message and any attached documents are only for the use of the > intended recipient(s), are confidential and may contain privileged > information. Any unauthorized review, use, retransmission, or other > disclosure is strictly prohibited. If you have received this message in > error, please notify the sender immediately, and then delete the original > message. Thank you. > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090722/daa787f4/attachment-0001.html From Helen.Carlson at albertahealthservices.ca Thu Jul 23 15:49:41 2009 From: Helen.Carlson at albertahealthservices.ca (Helen Carlson) Date: Thu, 23 Jul 2009 13:49:41 -0600 Subject: [Mristudio-users] How to Process Siemens Mosaic files in DTIStudio? Message-ID: Hi Susumu, Thank you very much for all your help. Since we do use oblique angles I am currently exploring option 5-1 below. My question is: Is there a way I can manually determine which file is which for putting them in six different directories? Is there something in the header that would allow me to write a script to do this automatically? At the moment there does not seem to be a logical naming sequence that I can use to seperate them out. Thank-you again. Helen. Helen Carlson, Ph.D. Neuropsychology Department of Neurosciences Alberta Children's Hospital ________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori [susumu at mri.jhu.edu] Sent: July 22, 2009 8:01 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] How to Process Siemens Mosaic files in DTIStudio? Hi Helen, 1) You have 42 mosaic files. This means, you did (1 b0 + 6 DWI) x 6 repetitions, I think. 2) In recent Siemens system, if you do signal averaging, the scanners save the repeated measurements separately instead of averaging them. This enables you to do image co-registration to minimize motion-related problems. Please note that if the scanners average multiple acquisitions, you can not do co-registration anymore. 3) There are two ways to load the 42 images; a) load all of them as one sequential data, b) load the data as 6 independent (1 b0 + 6 DWI) data. 4) You loaded the data as #a method. In this case, you have to modify your b-table. For example, if your b-table is; 0: 0, 0, 0 1: 1, 1, 0 2: 1, 0, 1 3: 0, 1, 1 4: -1, 1, 0 5: -1,0, 1 6: 0, -1,1 you have to repeat this 6 times like; 0: 0, 0, 0 1: 1, 1, 0 2: 1, 0, 1 3: 0, 1, 1 4: -1, 1, 0 5: -1,0, 1 6: 0, -1,1 7: 0, 0, 0 8: 1, 1, 0 9: 1, 0, 1 10: 0, 1, 1 11: -1, 1, 0 12: -1,0, 1 13: 0, -1,1 . . and so on. 5) Method #a should work fine, but Method #b has several advantages. For example, you can calculate standard deviations and subtraction images for the 6 repeated measurements. These repeated measurements should look identical. You can easily see if the subject moves and if co-registration works fine. Corrupted images can be detected much easiler too. There are two ways to convert the 42 sequential data to 6 repeated parallel data; 5-1) Separate the 42 IMA files into 6 different directories (1 b0 + 6 DWIs in each directory) and list the 6 directories in the DtiStudio data input window. This can be most easily done if you can specify the scanner to save the data in this way (I thought it's possible). Otherwise, you may find it difficult to figure out how to divide the 42 files into the 6 repeated data. 5-2) Once you read the 42 IMA data, you can save them as 6 raw files; each raw file contains 7 images. You can do it by using the "save" icon in the right column. Close the window and load the raw data as the "REC" format. Load the all 6 raw files at once. One problem is, during the conversion of Mosaic -> Raw, you loose information about oblique imaging (see #6), which means you should not use this method if you used oblique angles. In both cases, the b-table will be; 0: 0, 0, 0 1: 1, 1, 0 2: 1, 0, 1 3: 0, 1, 1 4: -1, 1, 0 5: -1,0, 1 6: 0, -1,1 6) As I mentioned multiple times in the previous communications, Siemens users have to be very careful when oblique imaging is used. Unless you are using the latest VB15 operating system, the gradient table has to be recalculated based on the oblique angles. This can be done by checking the box ("rotate if applicable") beneath the b-table window. DtiStudio automatically reads the angle information from Dicom/Mosaic headers and rotate the b-table. If you are using VB15, this is already taken care of at the time of data acquisition and therefore you don't check this box. If you convert the Dicom/Mosaic to a raw data format (REC format), the oblique information is lost and you can not use this function. Therefore the approach #5-2 can not be used unless you are not using oblique imaging. Susumu On Wed, Jul 22, 2009 at 4:40 PM, Helen Carlson > wrote: Hi all, I am trying to create a tensor image from a 6 direction DTI scan and am having trouble. I can load my 42 IMA images successfully into DTI Studio (they are in mosaic format). However I would expect to see 7 options in the drop down list on the right side of the Image tab. These options should be composed of a b0 and the 6 DWI directions. However, I see 42 options in the drop down list. As I scroll through these options I see 7 b0 images interleaved with 6 diffusion weighted images between them giving me the 42 images in the list. The resulting FA and Color maps are of poor resolution. I suspect this is because the wrong b0 is used in the noise calculations. So my question is, what am I doing wrong while loading the data that causes this? I searched the archives and found an email (below) addressing this issue. It was helpful though I still cannot resolve my problem. Thank-you in advance for your help. Regards, Helen. ~~~~~~~~ Orginal message: Hi Anuar, 1) Could you read the IMA (mosaic format data)? If so, make sure how many images are loaded. You can use "MRIView3D -> Siemens Mosaic" and load the data. If successful, you should see a list of loaded images in the pull-down menu in the right column of the viewing window. For example, if you used typical Siemens 12-orientation scheme, you should find 1 b0 + 12 DWI (total 13 images). 2) Then you need to find a correct gradient table. If you are using an off-the-shelf Siemens DTI method, there are Siemens-supplied gradient tables for that. If you don't know the table, please let us know, together with the number of images you get in the step #1. If you are using a user-specified table, you need to find the table. 3) Final thing you have to check is the version of your operating system and oblique plane angle. If you are using the latest operating system or your imaging plane is not oblique, you are fine. If you are using an old operating system AND an oblique plane, than, you have to check "Rotate gradients if applicable" box. Susumu -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Anuar Imanbayev Sent: Thursday, January 15, 2009 2:08 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] How to Process Siemens Mosaic files in DTIStudio? Hello everyone, I usually deal with .par and .rec files. However, my PI's collaborator works with Siemens Mosaic files and needs help in being able to perform tensor calculations on them. I'm working out the kinks so then I can report sometime next week with my findings. At first, the collaborating doctor informed me that the files were .IMA files. Indeed they did masquerade as those, but in reality responded only to Siemens Mosaic filetype under DTIStudio. Dr. Hangyi Jiang identified the data files not as ima but as mosaic files for me and helped me around in general. Still, I'm at a loss with which gradient files to treat these Siemens Mosaic files and how to perform Tensor calculations that produce credible color maps (mine so far were just red dots all around) I'll keep experimenting and poking around in the meantime. Please help me understand and deal with this new file type. Also, apparently there were no b0 or standard data files associated with the data set that the collaborator sent - just a bunch of image files. Would that be a problem in the long run? How to handle the situation when those are provided? With just image files, how do I go about creating an image quality file, then saving it after my scanning for bad quality images? Thank you for your time and assistance in advance, Sincerely yours, Anuar Imanbayev Undergraduate Neuroscience 2010 _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users ________________________________ This message and any attached documents are only for the use of the intended recipient(s), are confidential and may contain privileged information. Any unauthorized review, use, retransmission, or other disclosure is strictly prohibited. If you have received this message in error, please notify the sender immediately, and then delete the original message. Thank you. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org ________________________________ This message and any attached documents are only for the use of the intended recipient(s), are confidential and may contain privileged information. Any unauthorized review, use, retransmission, or other disclosure is strictly prohibited. If you have received this message in error, please notify the sender immediately, and then delete the original message. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090723/6672c401/attachment.html From susumu at mri.jhu.edu Thu Jul 23 19:21:22 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Thu, 23 Jul 2009 19:21:22 -0400 Subject: [Mristudio-users] How to Process Siemens Mosaic files in DTIStudio? In-Reply-To: References: Message-ID: That's a good question. I remember that I tried to divide them simply based on the file name but it didn't work. If you could ftp the data to us, we can take a look at the data to see if we can easily write a code to separate them. Susumu On Thu, Jul 23, 2009 at 3:49 PM, Helen Carlson < Helen.Carlson at albertahealthservices.ca> wrote: > Hi Susumu, > Thank you very much for all your help. > > Since we do use oblique angles I am currently exploring option 5-1 below. > My question is: Is there a way I can manually determine which file is > which for putting them in six different directories? Is there something in > the header that would allow me to write a script to do this automatically? > At the moment there does not seem to be a logical naming sequence that I can > use to seperate them out. > > Thank-you again. > Helen. > > > *Helen Carlson*, Ph.D. > Neuropsychology > Department of Neurosciences > Alberta Children's Hospital > > ------------------------------ > *From:* mristudio-users-bounces at mristudio.org [ > mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori [ > susumu at mri.jhu.edu] > *Sent:* July 22, 2009 8:01 PM > *To:* DTI Studio, ROI Editor, Landmarker Questions/Support > *Subject:* Re: [Mristudio-users] How to Process Siemens Mosaic files in > DTIStudio? > > Hi Helen, > > 1) You have 42 mosaic files. This means, you did (1 b0 + 6 DWI) x 6 > repetitions, I think. > 2) In recent Siemens system, if you do signal averaging, the scanners save > the repeated measurements separately instead of averaging them. This enables > you to do image co-registration to minimize motion-related problems. Please > note that if the scanners average multiple acquisitions, you can not do > co-registration anymore. > 3) There are two ways to load the 42 images; a) load all of them as one > sequential data, b) load the data as 6 independent (1 b0 + 6 DWI) data. > 4) You loaded the data as #a method. In this case, you have to modify your > b-table. For example, if your b-table is; > > 0: 0, 0, 0 > 1: 1, 1, 0 > 2: 1, 0, 1 > 3: 0, 1, 1 > 4: -1, 1, 0 > 5: -1,0, 1 > 6: 0, -1,1 > > you have to repeat this 6 times like; > > 0: 0, 0, 0 > 1: 1, 1, 0 > 2: 1, 0, 1 > 3: 0, 1, 1 > 4: -1, 1, 0 > 5: -1,0, 1 > 6: 0, -1,1 > 7: 0, 0, 0 > 8: 1, 1, 0 > 9: 1, 0, 1 > 10: 0, 1, 1 > 11: -1, 1, 0 > 12: -1,0, 1 > 13: 0, -1,1 > . > . > and so on. > > 5) Method #a should work fine, but Method #b has several advantages. For > example, you can calculate standard deviations and subtraction images for > the 6 repeated measurements. These repeated measurements should look > identical. You can easily see if the subject moves and if co-registration > works fine. Corrupted images can be detected much easiler too. There are two > ways to convert the 42 sequential data to 6 repeated parallel data; > 5-1) Separate the 42 IMA files into 6 different directories (1 b0 + 6 DWIs > in each directory) and list the 6 directories in the DtiStudio data input > window. This can be most easily done if you can specify the scanner to save > the data in this way (I thought it's possible). Otherwise, you may find it > difficult to figure out how to divide the 42 files into the 6 repeated data. > 5-2) Once you read the 42 IMA data, you can save them as 6 raw files; each > raw file contains 7 images. You can do it by using the "save" icon in the > right column. Close the window and load the raw data as the "REC" format. > Load the all 6 raw files at once. One problem is, during the conversion of > Mosaic -> Raw, you loose information about oblique imaging (see #6), which > means you should not use this method if you used oblique angles. > > In both cases, the b-table will be; > > 0: 0, 0, 0 > 1: 1, 1, 0 > 2: 1, 0, 1 > 3: 0, 1, 1 > 4: -1, 1, 0 > 5: -1,0, 1 > 6: 0, -1,1 > > 6) As I mentioned multiple times in the previous communications, Siemens > users have to be very careful when oblique imaging is used. Unless you are > using the latest VB15 operating system, the gradient table has to be > recalculated based on the oblique angles. This can be done by checking the > box ("rotate if applicable") beneath the b-table window. DtiStudio > automatically reads the angle information from Dicom/Mosaic headers and > rotate the b-table. If you are using VB15, this is already taken care of at > the time of data acquisition and therefore you don't check this box. If you > convert the Dicom/Mosaic to a raw data format (REC format), the oblique > information is lost and you can not use this function. Therefore the > approach #5-2 can not be used unless you are not using oblique imaging. > > Susumu > > On Wed, Jul 22, 2009 at 4:40 PM, Helen Carlson < > Helen.Carlson at albertahealthservices.ca> wrote: > >> Hi all, >> I am trying to create a tensor image from a 6 direction DTI scan and am >> having trouble. I can load my 42 IMA images successfully into DTI Studio >> (they are in mosaic format). However I would expect to see 7 options in the >> drop down list on the right side of the Image tab. These options should be >> composed of a b0 and the 6 DWI directions. >> >> However, I see 42 options in the drop down list. As I scroll through these >> options I see 7 b0 images interleaved with 6 diffusion weighted images >> between them giving me the 42 images in the list. >> >> The resulting FA and Color maps are of poor resolution. I suspect this is >> because the wrong b0 is used in the noise calculations. >> >> So my question is, what am I doing wrong while loading the data that >> causes this? I searched the archives and found an email (below) addressing >> this issue. It was helpful though I still cannot resolve my problem. >> >> Thank-you in advance for your help. >> Regards, >> Helen. >> >> ~~~~~~~~ >> >> >> >> >> Orginal message: >> >> Hi Anuar, >> >> 1) Could you read the IMA (mosaic format data)? If so, make sure how many >> images are loaded. You can use "MRIView3D -> Siemens Mosaic" and load the >> data. If successful, you should see a list of loaded images in the pull-down >> menu in the right column of the viewing window. For example, if you used >> typical Siemens 12-orientation scheme, you should find 1 b0 + 12 DWI (total >> 13 images). >> 2) Then you need to find a correct gradient table. If you are using an >> off-the-shelf Siemens DTI method, there are Siemens-supplied gradient tables >> for that. If you don't know the table, please let us know, together with the >> number of images you get in the step #1. If you are using a user-specified >> table, you need to find the table. >> 3) Final thing you have to check is the version of your operating system and >> oblique plane angle. If you are using the latest operating system or your >> imaging plane is not oblique, you are fine. If you are using an old >> operating system AND an oblique plane, than, you have to check "Rotate >> gradients if applicable" box. >> >> Susumu >> >> -----Original Message----- >> From: mristudio-users-bounces at mristudio.org >> [mailto:mristudio-users-bounces at mristudio.org ] On Behalf Of Anuar Imanbayev >> Sent: Thursday, January 15, 2009 2:08 PM >> To: mristudio-users at mristudio.org >> Subject: [Mristudio-users] How to Process Siemens Mosaic files in DTIStudio? >> >> Hello everyone, >> >> I usually deal with .par and .rec files. However, my PI's collaborator works >> with Siemens Mosaic files and needs help in being able to perform tensor >> calculations on them. I'm working out the kinks so then I can report >> sometime next week with my findings. >> >> >> At first, the collaborating doctor informed me that the files were .IMA >> files. Indeed they did masquerade as those, but in reality responded only to >> Siemens Mosaic filetype under DTIStudio. >> >> Dr. Hangyi Jiang identified the data files not as ima but as mosaic files >> for me and helped me around in general. Still, I'm at a loss with which >> gradient files to treat these Siemens Mosaic files and how to perform Tensor >> calculations that produce credible color maps (mine so far were just red >> dots all around) I'll keep experimenting and poking around in the meantime. >> >> Please help me understand and deal with this new file type. Also, apparently >> there were no b0 or standard data files associated with the data set that >> the collaborator sent - just a bunch of image files. Would that be a >> problem in the long run? How to handle the situation when those are >> provided? With just image files, how do I go about creating an image quality >> file, then saving it after my scanning for bad quality images? >> >> Thank you for your time and assistance in advance, >> Sincerely yours, >> Anuar Imanbayev >> Undergraduate Neuroscience 2010 >> _______________________________________________ >> Mristudio-users mailing listMristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users >> >> >> ------------------------------ >> This message and any attached documents are only for the use of the >> intended recipient(s), are confidential and may contain privileged >> information. Any unauthorized review, use, retransmission, or other >> disclosure is strictly prohibited. If you have received this message in >> error, please notify the sender immediately, and then delete the original >> message. Thank you. >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > ------------------------------ > This message and any attached documents are only for the use of the > intended recipient(s), are confidential and may contain privileged > information. Any unauthorized review, use, retransmission, or other > disclosure is strictly prohibited. If you have received this message in > error, please notify the sender immediately, and then delete the original > message. Thank you. > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090723/178a7c0a/attachment-0001.html From dr.fellgiebel at t-online.de Fri Jul 24 01:33:24 2009 From: dr.fellgiebel at t-online.de (Fellgiebel) Date: Fri, 24 Jul 2009 05:33:24 +0000 Subject: [Mristudio-users] How to Process Siemens Mosaic filesin DTIStudio? In-Reply-To: References: Message-ID: <1940574156-1248413696-cardhu_decombobulator_blackberry.rim.net-176933797-@bxe1070.bisx.produk.on.blackberry> Dear Susumu, please unsubscibe! (I tried several times the unsubscribe E-Mail unsucessfully). Thanks in advance! Andreas ------------------------ -----Original Message----- From: susumu mori Date: Thu, 23 Jul 2009 19:21:22 To: DTI Studio, ROI Editor, Landmarker Questions/Support; Hangyi Jiang; Zhipeng Hou Subject: Re: [Mristudio-users] How to Process Siemens Mosaic files in DTIStudio? _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From JJames2 at radiology.umsmed.edu Fri Jul 24 15:33:01 2009 From: JJames2 at radiology.umsmed.edu (Judy James) Date: Fri, 24 Jul 2009 14:33:01 -0500 Subject: [Mristudio-users] 3D volume of the whole brain Message-ID: <4A69C61D0200002A00027083@GWIA1.umsmed.edu> Hello all, I would like to know if there is a way to create or display the fibres chosen on a 3D volume of the whole brain instead of just the 3 orthogonal planes in the left upper corner. If not, what are other programs that would allow for this feature? Thank you Judy ***************************************************** Dr. Judy Rose James MR Physicist/Assistant Professor Department of Radiology University of Mississippi Medical Centre Jackson, MS Ph: 601-984-2585 Pager: 601-929-2442 email: jjames2 at radiology.umsmed.edu ***************************************************** Individuals who have received this information in error or are not authorized to receive it must promptly return or dispose of the information and notify the sender. Those individuals are hereby notified that they are strictly prohibited from reviewing, forwarding, printing, copying, distributing or using this information in any way. From susumu at mri.jhu.edu Mon Jul 27 12:42:08 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Mon, 27 Jul 2009 12:42:08 -0400 Subject: [Mristudio-users] 3D volume of the whole brain In-Reply-To: <4A69C61D0200002A00027083@GWIA1.umsmed.edu> References: <4A69C61D0200002A00027083@GWIA1.umsmed.edu> Message-ID: Hi Judy, I believe DTI3DMRI is the program you want to try. You can find this program in https://www.mristudio.org/wiki/installation. This has basic functions for 3D rendering. For serious presentations, we use Amira and DtiStudio can save data in Amira format for seamless communication, but it costs $4,000. Susumu On Fri, Jul 24, 2009 at 3:33 PM, Judy James wrote: > Hello all, > I would like to know if there is a way to create or display the fibres > chosen on a 3D volume of the whole brain instead of just the 3 orthogonal > planes in the left upper corner. > > If not, what are other programs that would allow for this feature? > > Thank you > Judy > > ***************************************************** > Dr. Judy Rose James > MR Physicist/Assistant Professor > Department of Radiology > University of Mississippi Medical Centre > Jackson, MS > Ph: 601-984-2585 > Pager: 601-929-2442 > email: jjames2 at radiology.umsmed.edu > ***************************************************** > > Individuals who have received this information in error or are not > authorized to receive it must promptly return or dispose of the information > and notify the sender. Those individuals are hereby notified that they are > strictly prohibited from reviewing, forwarding, printing, copying, > distributing or using this information in any way. > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090727/e0598db3/attachment.html From JJames2 at radiology.umsmed.edu Tue Jul 28 14:20:56 2009 From: JJames2 at radiology.umsmed.edu (Judy James) Date: Tue, 28 Jul 2009 13:20:56 -0500 Subject: [Mristudio-users] 3D volume of the whole brain Message-ID: <4A6EFB390200002A000272DC@GWIA1.umsmed.edu> Thank you Susumu. I downloaded the s/w and tried to load a mean DWI (Bo) image that is generated from DTIstudio. It did not work. In the VTK output, it is giving errors in reading the file. I tried saving the mean DW images in all the 3 formats mentioned: raw, analyze and NRD. But the DTI3DMRI was not able to take any. Also there was an error message that popped mentioning about the threshold being set high. 30 was the default, but I set it to '0'. But it still kept taking 30. Could you please advise me the loading of the data into DTI3DMRI so that I can visualize the fibers on the brain volume in 3D format? Thank you Judy ***************************************************** Dr. Judy Rose James MR Physicist/Assistant Professor Department of Radiology University of Mississippi Medical Centre Jackson, MS Ph: 601-984-2585 Pager: 601-929-2442 email: jjames2 at radiology.umsmed.edu ***************************************************** >>> susumu mori 07/27/09 11:42 AM >>> Hi Judy, I believe DTI3DMRI is the program you want to try. You can find this program in https://www.mristudio.org/wiki/installation. This has basic functions for 3D rendering. For serious presentations, we use Amira and DtiStudio can save data in Amira format for seamless communication, but it costs $4,000. Susumu On Fri, Jul 24, 2009 at 3:33 PM, Judy James wrote: > Hello all, > I would like to know if there is a way to create or display the fibres > chosen on a 3D volume of the whole brain instead of just the 3 orthogonal > planes in the left upper corner. > > If not, what are other programs that would allow for this feature? > > Thank you > Judy > > ***************************************************** > Dr. Judy Rose James > MR Physicist/Assistant Professor > Department of Radiology > University of Mississippi Medical Centre > Jackson, MS > Ph: 601-984-2585 > Pager: 601-929-2442 > email: jjames2 at radiology.umsmed.edu > ***************************************************** > > Individuals who have received this information in error or are not > authorized to receive it must promptly return or dispose of the information > and notify the sender. Those individuals are hereby notified that they are > strictly prohibited from reviewing, forwarding, printing, copying, > distributing or using this information in any way. > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > Individuals who have received this information in error or are not authorized to receive it must promptly return or dispose of the information and notify the sender. Those individuals are hereby notified that they are strictly prohibited from reviewing, forwarding, printing, copying, distributing or using this information in any way. From mverber at mcw.edu Tue Jul 28 14:26:27 2009 From: mverber at mcw.edu (Verber, Matthew) Date: Tue, 28 Jul 2009 13:26:27 -0500 Subject: [Mristudio-users] 3D volume of the whole brain In-Reply-To: <4A6EFB390200002A000272DC@GWIA1.umsmed.edu> Message-ID: They are good. On 7/28/09 1:20 PM, "Judy James" wrote: Thank you Susumu. I downloaded the s/w and tried to load a mean DWI (Bo) image that is generated from DTIstudio. It did not work. In the VTK output, it is giving errors in reading the file. I tried saving the mean DW images in all the 3 formats mentioned: raw, analyze and NRD. But the DTI3DMRI was not able to take any. Also there was an error message that popped mentioning about the threshold being set high. 30 was the default, but I set it to '0'. But it still kept taking 30. Could you please advise me the loading of the data into DTI3DMRI so that I can visualize the fibers on the brain volume in 3D format? Thank you Judy ***************************************************** Dr. Judy Rose James MR Physicist/Assistant Professor Department of Radiology University of Mississippi Medical Centre Jackson, MS Ph: 601-984-2585 Pager: 601-929-2442 email: jjames2 at radiology.umsmed.edu ***************************************************** >>> susumu mori 07/27/09 11:42 AM >>> Hi Judy, I believe DTI3DMRI is the program you want to try. You can find this program in https://www.mristudio.org/wiki/installation. This has basic functions for 3D rendering. For serious presentations, we use Amira and DtiStudio can save data in Amira format for seamless communication, but it costs $4,000. Susumu On Fri, Jul 24, 2009 at 3:33 PM, Judy James wrote: > Hello all, > I would like to know if there is a way to create or display the fibres > chosen on a 3D volume of the whole brain instead of just the 3 orthogonal > planes in the left upper corner. > > If not, what are other programs that would allow for this feature? > > Thank you > Judy > > ***************************************************** > Dr. Judy Rose James > MR Physicist/Assistant Professor > Department of Radiology > University of Mississippi Medical Centre > Jackson, MS > Ph: 601-984-2585 > Pager: 601-929-2442 > email: jjames2 at radiology.umsmed.edu > ***************************************************** > > Individuals who have received this information in error or are not > authorized to receive it must promptly return or dispose of the information > and notify the sender. Those individuals are hereby notified that they are > strictly prohibited from reviewing, forwarding, printing, copying, > distributing or using this information in any way. > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > Individuals who have received this information in error or are not authorized to receive it must promptly return or dispose of the information and notify the sender. Those individuals are hereby notified that they are strictly prohibited from reviewing, forwarding, printing, copying, distributing or using this information in any way. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From khua1 at jhu.edu Wed Jul 29 12:41:00 2009 From: khua1 at jhu.edu (Hua KG) Date: Wed, 29 Jul 2009 16:41:00 +0000 Subject: [Mristudio-users] 3D volume of the whole brain In-Reply-To: <4A6EFB390200002A000272DC@GWIA1.umsmed.edu> References: <4A6EFB390200002A000272DC@GWIA1.umsmed.edu> Message-ID: Hi, Judy You may try to use mean DWI image generated from DTIStudio. B0 image is not exactly mean DWI image. If you still can't find appropriate threshold, you may try to toggle on/off the byte order. The s/w only works with raw images so far. Thanks! Let me know if you have further questions! Kegang(Luke) Hua > Date: Tue, 28 Jul 2009 13:20:56 -0500 > From: JJames2 at radiology.umsmed.edu > Subject: Re: [Mristudio-users] 3D volume of the whole brain > To: mristudio-users at mristudio.org > > Thank you Susumu. > I downloaded the s/w and tried to load a mean DWI (Bo) image that is generated from DTIstudio. It did not work. In the VTK output, it is giving errors in reading the file. I tried saving the mean DW images in all the 3 formats mentioned: raw, analyze and NRD. But the DTI3DMRI was not able to take any. Also there was an error message that popped mentioning about the threshold being set high. 30 was the default, but I set it to '0'. But it still kept taking 30. > > Could you please advise me the loading of the data into DTI3DMRI so that I can visualize the fibers on the brain volume in 3D format? > > Thank you > Judy > > > ***************************************************** > Dr. Judy Rose James > MR Physicist/Assistant Professor > Department of Radiology > University of Mississippi Medical Centre > Jackson, MS > Ph: 601-984-2585 > Pager: 601-929-2442 > email: jjames2 at radiology.umsmed.edu > ***************************************************** > >>> susumu mori 07/27/09 11:42 AM >>> > Hi Judy, > > I believe DTI3DMRI is the program you want to try. You can find this program > in https://www.mristudio.org/wiki/installation. > This has basic functions for 3D rendering. For serious presentations, we use > Amira and DtiStudio can save data in Amira format for seamless > communication, but it costs $4,000. > > Susumu > > On Fri, Jul 24, 2009 at 3:33 PM, Judy James wrote: > > > Hello all, > > I would like to know if there is a way to create or display the fibres > > chosen on a 3D volume of the whole brain instead of just the 3 orthogonal > > planes in the left upper corner. > > > > If not, what are other programs that would allow for this feature? > > > > Thank you > > Judy > > > > ***************************************************** > > Dr. Judy Rose James > > MR Physicist/Assistant Professor > > Department of Radiology > > University of Mississippi Medical Centre > > Jackson, MS > > Ph: 601-984-2585 > > Pager: 601-929-2442 > > email: jjames2 at radiology.umsmed.edu > > ***************************************************** > > > > Individuals who have received this information in error or are not > > authorized to receive it must promptly return or dispose of the information > > and notify the sender. Those individuals are hereby notified that they are > > strictly prohibited from reviewing, forwarding, printing, copying, > > distributing or using this information in any way. > > > > > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > http://lists.mristudio.org/mailman/listinfo/ > > Unsubscribe, send a blank email to: > > Mristudio-users-unsubscribe at mristudio.org > > > > > Individuals who have received this information in error or are not authorized to receive it must promptly return or dispose of the information and notify the sender. Those individuals are hereby notified that they are strictly prohibited from reviewing, forwarding, printing, copying, distributing or using this information in any way. > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org _________________________________________________________________ Share your memories online with anyone you want. http://www.microsoft.com/middleeast/windows/windowslive/products/photos-share.aspx?tab=1 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090729/8bd24721/attachment-0001.html From yj3 at duke.edu Tue Aug 4 16:31:25 2009 From: yj3 at duke.edu (Yi Jiang) Date: Tue, 04 Aug 2009 16:31:25 -0400 Subject: [Mristudio-users] how to save the transformation matrix from a landmarker based transformation References: <77A88E90A851594AAEF830450587C39D01EDAAB9@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: <25DDB702A1EF4743801941995A57E192@panpan> Dear All, I have tried to look through the online manual, but could not find the answer. I tried to use the landmark based transformation (translation) from the main menu of the Landmarker window. The result is pretty good. However, I do not know how to save the transformation matrix. I tried to click the "save transformation matrix" button in the subject window. It seems two files was saved (.hdr? and .dat), but the file sizes were very small. I also want to combine the transformation matrix from the landmark based translation with a AIR linear rigid, a AIR linear affine transformation, and a LDDMM matrix. Can I do that? I do not know if the transformation matrix from landmark based translation is a AIR format, or LDDMM raw format, or a LDDMM vtk format, which was asked in the combine matrix window. The last question may be stupid: if there are defined landmarks in the memory, when I click on AIR linear or multichannel LDDMM (not from the main menu, but the buttons in the subject window), those landmarks were not used in transformation, right? Thank you very much! Best, Yi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090804/1cf4f2ea/attachment.html From susumu at mri.jhu.edu Tue Aug 4 21:59:54 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Tue, 04 Aug 2009 21:59:54 -0400 Subject: [Mristudio-users] how to save the transformation matrix from a landmarker based transformation In-Reply-To: <25DDB702A1EF4743801941995A57E192@panpan> References: <77A88E90A851594AAEF830450587C39D01EDAAB9@CCHSCLEXMB56.cc.ad.cchs.net> <25DDB702A1EF4743801941995A57E192@panpan> Message-ID: Hi Yi, I believe you can save the matrix. Xin should know how to do it. As for the matrix combination, I remember that we discussed about exactly the same topic in my lab. I thought that answer was Yes, but don't exactly remember how to do it. Andreia and Xin, do you know how to do it? On Tue, Aug 4, 2009 at 4:31 PM, Yi Jiang wrote: > Dear All, > > I have tried to look through the online manual, but could not find the > answer. > > I tried to use the landmark based transformation (translation) from the > main menu of the Landmarker window. The result is pretty good. However, I do > not know how to save the transformation matrix. I tried to click the "save > transformation matrix" button in the subject window. It seems two files was > saved (.hdr? and .dat), but the file sizes were very small. > > I also want to combine the transformation matrix from the landmark based > translation with a AIR linear rigid, a AIR linear affine transformation, and > a LDDMM matrix. Can I do that? I do not know if the transformation matrix > from landmark based translation is a AIR format, or LDDMM raw format, or a > LDDMM vtk format, which was asked in the combine matrix window. > > The last question may be stupid: if there are defined landmarks in the > memory, when I click on AIR linear or multichannel LDDMM (not from the main > menu, but the buttons in the subject window), those landmarks were not used > in transformation, right? > > Thank you very much! > > Best, > Yi > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090804/130d143c/attachment.html From afaria1 at jhmi.edu Tue Aug 4 23:43:08 2009 From: afaria1 at jhmi.edu (Andreia Faria) Date: Tue, 04 Aug 2009 23:43:08 -0400 Subject: [Mristudio-users] how to save the transformation matrix from a landmarker based transformation In-Reply-To: References: <77A88E90A851594AAEF830450587C39D01EDAAB9@CCHSCLEXMB56.cc.ad.cchs.net> <25DDB702A1EF4743801941995A57E192@panpan> Message-ID: Hi Yi, 1. Your procedure to save the matrix is correct. The file (.dat) is small because it is just a 3x4 matrix. 2. In the current Landmarker version you can combine LDDMM and .air matrix but not .dat matrix (Xin, please correct me if I am wrong). But you can apply the .dat matrix you saved using the 'load transformation matrix' button, choosing the option 'translation, affine or rigid. 3. Yes, the landmarks are not used, the linear transformation (in the subject window) and LDDMM are based on the image intensity. Please let me know if it is not clear. Best regards, Andreia. ----- Original Message ----- From: susumu mori Date: Tuesday, August 4, 2009 9:59 pm Subject: Re: [Mristudio-users] how to save the transformation matrix from a landmarker based transformation To: Yi Jiang , "DTI Studio, ROI Editor, Landmarker Questions/Support" , Xin Li , ANDREIA FARIA > Hi Yi, > > I believe you can save the matrix. Xin should know how to do it. > As for the matrix combination, I remember that we discussed about exactly > the same topic in my lab. I thought that answer was Yes, but don't exactly > remember how to do it. Andreia and Xin, do you know how to do it? > > On Tue, Aug 4, 2009 at 4:31 PM, Yi Jiang wrote: > > > Dear All, > > > > I have tried to look through the online manual, but could not find > the > > answer. > > > > I tried to use the landmark based transformation (translation) from > the > > main menu of the Landmarker window. The result is pretty good. > However, I do > > not know how to save the transformation matrix. I tried to click > the "save > > transformation matrix" button in the subject window. It seems two > files was > > saved (.hdr? and .dat), but the file sizes were very small. > > > > I also want to combine the transformation matrix from the landmark > based > > translation with a AIR linear rigid, a AIR linear affine > transformation, and > > a LDDMM matrix. Can I do that? I do not know if the transformation > matrix > > from landmark based translation is a AIR format, or LDDMM raw > format, or a > > LDDMM vtk format, which was asked in the combine matrix window. > > > > The last question may be stupid: if there are defined landmarks in > the > > memory, when I click on AIR linear or multichannel LDDMM (not from > the main > > menu, but the buttons in the subject window), those landmarks were > not used > > in transformation, right? > > > > Thank you very much! > > > > Best, > > Yi > > > > > > > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > > Mristudio-users-unsubscribe at mristudio.org > > > > From xli16 at jhmi.edu Wed Aug 5 10:09:35 2009 From: xli16 at jhmi.edu (Xin Li) Date: Wed, 05 Aug 2009 10:09:35 -0400 Subject: [Mristudio-users] how to save the transformation matrix from a landmarker based transformation In-Reply-To: References: <77A88E90A851594AAEF830450587C39D01EDAAB9@CCHSCLEXMB56.cc.ad.cchs.net> <25DDB702A1EF4743801941995A57E192@panpan> Message-ID: Yi, You can take a look at the .dat file by opening it using notepad. Just as Andreia said, it is a 3x4 matrix. As Andreia said, the "combine matrix" function combines LDDMM map and .air file but not .dat matrix. Xin ----- Original Message ----- From: Andreia Faria Date: Tuesday, August 4, 2009 11:43 pm Subject: Re: [Mristudio-users] how to save the transformation matrix from a landmarker based transformation To: susumu mori Cc: Yi Jiang , "DTI Studio, ROI Editor, Landmarker Questions/Support" , Xin Li > Hi Yi, > > 1. Your procedure to save the matrix is correct. The file (.dat) is > small because it is just a 3x4 matrix. > > 2. In the current Landmarker version you can combine LDDMM and .air > matrix but not .dat matrix (Xin, please correct me if I am wrong). But > you can apply the .dat matrix you saved using the 'load transformation > matrix' button, choosing the option 'translation, affine or rigid. > > 3. Yes, the landmarks are not used, the linear transformation (in the > subject window) and LDDMM are based on the image intensity. > > Please let me know if it is not clear. > > Best regards, > > Andreia. > > > > ----- Original Message ----- > From: susumu mori > Date: Tuesday, August 4, 2009 9:59 pm > Subject: Re: [Mristudio-users] how to save the transformation matrix > from a landmarker based transformation > To: Yi Jiang , "DTI Studio, ROI Editor, Landmarker > Questions/Support" , Xin Li > , ANDREIA FARIA > > > > Hi Yi, > > > > I believe you can save the matrix. Xin should know how to do it. > > As for the matrix combination, I remember that we discussed about > exactly > > the same topic in my lab. I thought that answer was Yes, but don't > exactly > > remember how to do it. Andreia and Xin, do you know how to do it? > > > > On Tue, Aug 4, 2009 at 4:31 PM, Yi Jiang wrote: > > > > > Dear All, > > > > > > I have tried to look through the online manual, but could not > find > > the > > > answer. > > > > > > I tried to use the landmark based transformation (translation) > from > > the > > > main menu of the Landmarker window. The result is pretty good. > > However, I do > > > not know how to save the transformation matrix. I tried to click > > > the "save > > > transformation matrix" button in the subject window. It seems > two > > files was > > > saved (.hdr? and .dat), but the file sizes were very small. > > > > > > I also want to combine the transformation matrix from the > landmark > > based > > > translation with a AIR linear rigid, a AIR linear affine > > transformation, and > > > a LDDMM matrix. Can I do that? I do not know if the > transformation > > matrix > > > from landmark based translation is a AIR format, or LDDMM raw > > format, or a > > > LDDMM vtk format, which was asked in the combine matrix window. > > > > > > The last question may be stupid: if there are defined landmarks > in > > the > > > memory, when I click on AIR linear or multichannel LDDMM (not > from > > the main > > > menu, but the buttons in the subject window), those landmarks > were > > not used > > > in transformation, right? > > > > > > Thank you very much! > > > > > > Best, > > > Yi > > > > > > > > > > > > > > > _______________________________________________ > > > Mristudio-users mailing list > > > Mristudio-users at mristudio.org > > > > > > Unsubscribe, send a blank email to: > > > Mristudio-users-unsubscribe at mristudio.org > > > > > > From yj3 at duke.edu Thu Aug 6 14:32:39 2009 From: yj3 at duke.edu (Yi Jiang) Date: Thu, 06 Aug 2009 14:32:39 -0400 Subject: [Mristudio-users] how to save the transformation matrix from alandmarker based transformation References: <77A88E90A851594AAEF830450587C39D01EDAAB9@CCHSCLEXMB56.cc.ad.cchs.net> <25DDB702A1EF4743801941995A57E192@panpan> Message-ID: <1D8D0348817A418FAF125362146C779C@panpan> Hi Dr Mori, Thank you very much. Andreia and Xin have helped me to make it work. I have another question. I am wondering if you have suggestion or software about averaging eigenvectors or tensors. In other words, if we have, say, DTI dataset of 10 brains, all registered together, how can we calculate the mean (and variation) of the 10 primary eigenvector field or calculate the mean (and variation) of the 10 tensor field? Any suggestion is highly appreciated! Yi ----- Original Message ----- From: susumu mori To: Yi Jiang ; DTI Studio, ROI Editor, Landmarker Questions/Support ; Xin Li ; ANDREIA FARIA Sent: Tuesday, August 04, 2009 9:59 PM Subject: Re: [Mristudio-users] how to save the transformation matrix from alandmarker based transformation Hi Yi, I believe you can save the matrix. Xin should know how to do it. As for the matrix combination, I remember that we discussed about exactly the same topic in my lab. I thought that answer was Yes, but don't exactly remember how to do it. Andreia and Xin, do you know how to do it? On Tue, Aug 4, 2009 at 4:31 PM, Yi Jiang wrote: Dear All, I have tried to look through the online manual, but could not find the answer. I tried to use the landmark based transformation (translation) from the main menu of the Landmarker window. The result is pretty good. However, I do not know how to save the transformation matrix. I tried to click the "save transformation matrix" button in the subject window. It seems two files was saved (.hdr? and .dat), but the file sizes were very small. I also want to combine the transformation matrix from the landmark based translation with a AIR linear rigid, a AIR linear affine transformation, and a LDDMM matrix. Can I do that? I do not know if the transformation matrix from landmark based translation is a AIR format, or LDDMM raw format, or a LDDMM vtk format, which was asked in the combine matrix window. The last question may be stupid: if there are defined landmarks in the memory, when I click on AIR linear or multichannel LDDMM (not from the main menu, but the buttons in the subject window), those landmarks were not used in transformation, right? Thank you very much! Best, Yi _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090806/4a3414bc/attachment-0001.html From susumu at mri.jhu.edu Fri Aug 7 09:10:44 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Fri, 07 Aug 2009 09:10:44 -0400 Subject: [Mristudio-users] how to save the transformation matrix from alandmarker based transformation In-Reply-To: <1D8D0348817A418FAF125362146C779C@panpan> References: <77A88E90A851594AAEF830450587C39D01EDAAB9@CCHSCLEXMB56.cc.ad.cchs.net> <25DDB702A1EF4743801941995A57E192@panpan> <1D8D0348817A418FAF125362146C779C@panpan> Message-ID: Hi Yi, Currently we don't have a program for what you need. We use our own codes in IDL or SPM (MatLab). Ken and Andreia are doing it routinely. Please ask them if you have specific questions. There are a couple of points I want to make; 1) If you normalize your data to an atlas, all your data will have similar shape. Then, you can perform pixel-by-pixel statistics. This is voxel-based analysis. I believe SPM has an array of tools for this. 2) If you transform an atlas (especially our white matter parcellation map (WMPM)) to the shape of your data, you will get numbers (such as volume, FA, MD, etc) from 100-176 regions of each brain (automated segmentation). This process converts image data to a string of numbers. Then the data can be analyzed by Excel for statistical analyses. The approach #1 is ideal for strong abnorality in a small region. The approach can theoretically detect abnormality as small as one pixel but each pixel has low statistical power. The approach #2 is ideal for diffuse abnormality. It groups all pixels that belong to one of the 100-176 regions, which increases the statistical power but if the abnormal region is only a small portion of one segment, the pixel grouping reduces the sensitivity. So, the two approaches are complementary. We have been working on a statistical tool for approach #1 but it'll take some time. Susumu On Thu, Aug 6, 2009 at 2:32 PM, Yi Jiang wrote: > Hi Dr Mori, > > Thank you very much. Andreia and Xin have helped me to make it work. > > I have another question. I am wondering if you have suggestion or software > about averaging eigenvectors or tensors. In other words, if we have, say, > DTI dataset of 10 brains, all registered together, how can we calculate the > mean (and variation) of the 10 primary eigenvector field or calculate the > mean (and variation) of the 10 tensor field? > > Any suggestion is highly appreciated! > > Yi > > > ----- Original Message ----- > *From:* susumu mori > *To:* Yi Jiang ; DTI Studio, ROI Editor, Landmarker > Questions/Support ; Xin Li; ANDREIA > FARIA > *Sent:* Tuesday, August 04, 2009 9:59 PM > *Subject:* Re: [Mristudio-users] how to save the transformation matrix > from alandmarker based transformation > > Hi Yi, > > I believe you can save the matrix. Xin should know how to do it. > As for the matrix combination, I remember that we discussed about exactly > the same topic in my lab. I thought that answer was Yes, but don't exactly > remember how to do it. Andreia and Xin, do you know how to do it? > > On Tue, Aug 4, 2009 at 4:31 PM, Yi Jiang wrote: > >> Dear All, >> >> I have tried to look through the online manual, but could not find the >> answer. >> >> I tried to use the landmark based transformation (translation) from the >> main menu of the Landmarker window. The result is pretty good. However, I do >> not know how to save the transformation matrix. I tried to click the "save >> transformation matrix" button in the subject window. It seems two files was >> saved (.hdr? and .dat), but the file sizes were very small. >> >> I also want to combine the transformation matrix from the landmark based >> translation with a AIR linear rigid, a AIR linear affine transformation, and >> a LDDMM matrix. Can I do that? I do not know if the transformation matrix >> from landmark based translation is a AIR format, or LDDMM raw format, or a >> LDDMM vtk format, which was asked in the combine matrix window. >> >> The last question may be stupid: if there are defined landmarks in the >> memory, when I click on AIR linear or multichannel LDDMM (not from the main >> menu, but the buttons in the subject window), those landmarks were not used >> in transformation, right? >> >> Thank you very much! >> >> Best, >> Yi >> >> >> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090807/422e51a5/attachment.html From mmoayedi at uhnres.utoronto.ca Sun Aug 9 16:59:03 2009 From: mmoayedi at uhnres.utoronto.ca (Massieh Moayedi) Date: Sun, 09 Aug 2009 16:59:03 -0400 Subject: [Mristudio-users] L and R in files Message-ID: <4A7F3897.5090601@uhnres.utoronto.ca> Hello MriStudio experts, I am currently importing GE dicoms to DTiStudio and (after AIR and removing corrupted images) saving the images as ANALYZE files. I just want to check and see if the orientation of the images changes at any point. In other words, what orientation are the images imported and then later saved in? Thanks, Massih -- Massieh Moayedi B.Sc. (Hons) Graduate Student Institute of Medical Science University of Toronto Brain, Imaging and Behaviour- Systems Neuroscience MP 14-301 Toronto Western Research Institute University Health Network 399 Bathurst Street Toronto, Ontario Canada M5T 2S8 Tel: 416-603-5882 massih.moayedi at utoronto.ca mmoayedi at uhnres.utoronto.ca From rajagov2 at ccf.org Thu Aug 13 12:17:35 2009 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Thu, 13 Aug 2009 12:17:35 -0400 Subject: [Mristudio-users] Seimens Gradient table Message-ID: <77A88E90A851594AAEF830450587C39D01EDAADE@CCHSCLEXMB56.cc.ad.cchs.net> Dear DTI Studio Users, I am looking specifically for seimens 1.5 T, Avanto machine, software version VB11, 12 directional gradient table. If anyone has it can you please share with me. Thanks in advance. Regards venkateswaran =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S. News & World Report (2008). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090813/9ac05e62/attachment.html From susumu at mri.jhu.edu Thu Aug 13 14:51:02 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Thu, 13 Aug 2009 14:51:02 -0400 Subject: [Mristudio-users] Seimens Gradient table In-Reply-To: <77A88E90A851594AAEF830450587C39D01EDAADE@CCHSCLEXMB56.cc.ad.cchs.net> References: <77A88E90A851594AAEF830450587C39D01EDAADE@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: I noticed that Siemens changed their tables and not sure which one is for VB11, but one of these should work. Old table: 0: 0.000, 0.000, 0.000 1: 1.000, 0.000, 0.500 2: 0.000, 0.500, 1.000 3: 0.500, 1.000, 0.000 4: 1.000, 0.500, 0.000 5: 0.000, 1.000, 0.500 6: 0.500, 0.000, 1.000 7: 1.000, 0.000, -0.500 8: 0.000, -0.500, 1.000 9: -0.500, 1.000, 0.000 10: 1.000, -0.500, 0.000 11: 0.000, 1.000, -0.500 12: -0.500, 0.000, 1.000 New table: 0: 0, 0, 0 1: 1.000000, 0.414250, -0.414250 2: 1.000000, -0.414250, -0.414250 3: 1.000000, -0.414250, 0.414250 4: 1.000000, 0.414250, 0.414250 5: 0.414250, 0.414250, 1.000000 6: 0.414250, 1.000000, 0.414250 7: 0.414250, 1.000000, -0.414250 8: 0.414250, 0.414250, -1.000000 9: 0.414250, -0.414250, -1.000000 10: 0.414250, -1.000000, -0.414250 11: 0.414250, -1.000000, 0.414250 12: 0.414250, -0.414250, 1.000000 On Thu, Aug 13, 2009 at 12:17 PM, Rajagopalan, Venkateswaran < rajagov2 at ccf.org> wrote: > Dear DTI Studio Users, > > I am looking specifically for seimens 1.5 T, Avanto machine, software > version VB11, 12 directional gradient table. If anyone has it can you > please share with me. > > Thanks in advance. > > Regards > venkateswaran > > > > =================================== > > P Please consider the environment before printing this e-mail > > > Cleveland Clinic is ranked one of the top hospitals > in America by U.S. News & World Report (2008). > Visit us online at http://www.clevelandclinic.org for > a complete listing of our services, staff and > locations. > > > Confidentiality Note: This message is intended for use > only by the individual or entity to which it is addressed > and may contain information that is privileged, > confidential, and exempt from disclosure under applicable > law. If the reader of this message is not the intended > recipient or the employee or agent responsible for > delivering the message to the intended recipient, you are > hereby notified that any dissemination, distribution or > copying of this communication is strictly prohibited. If > you have received this communication in error, please > contact the sender immediately and destroy the material in > its entirety, whether electronic or hard copy. Thank you. > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090813/741884c1/attachment-0001.html From rajagov2 at ccf.org Thu Aug 13 14:58:19 2009 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Thu, 13 Aug 2009 14:58:19 -0400 Subject: [Mristudio-users] Seimens Gradient table References: <77A88E90A851594AAEF830450587C39D01EDAADE@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: <77A88E90A851594AAEF830450587C39D01EDAAE1@CCHSCLEXMB56.cc.ad.cchs.net> Thanks very much Dr.Mori the table named as "Old table" works thanks a lot for your kind help. venkateswaran ________________________________ From: mristudio-users-bounces at mristudio.org on behalf of susumu mori Sent: Thu 8/13/2009 2:51 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] Seimens Gradient table I noticed that Siemens changed their tables and not sure which one is for VB11, but one of these should work. Old table: 0: 0.000, 0.000, 0.000 1: 1.000, 0.000, 0.500 2: 0.000, 0.500, 1.000 3: 0.500, 1.000, 0.000 4: 1.000, 0.500, 0.000 5: 0.000, 1.000, 0.500 6: 0.500, 0.000, 1.000 7: 1.000, 0.000, -0.500 8: 0.000, -0.500, 1.000 9: -0.500, 1.000, 0.000 10: 1.000, -0.500, 0.000 11: 0.000, 1.000, -0.500 12: -0.500, 0.000, 1.000 New table: 0: 0, 0, 0 1: 1.000000, 0.414250, -0.414250 2: 1.000000, -0.414250, -0.414250 3: 1.000000, -0.414250, 0.414250 4: 1.000000, 0.414250, 0.414250 5: 0.414250, 0.414250, 1.000000 6: 0.414250, 1.000000, 0.414250 7: 0.414250, 1.000000, -0.414250 8: 0.414250, 0.414250, -1.000000 9: 0.414250, -0.414250, -1.000000 10: 0.414250, -1.000000, -0.414250 11: 0.414250, -1.000000, 0.414250 12: 0.414250, -0.414250, 1.000000 On Thu, Aug 13, 2009 at 12:17 PM, Rajagopalan, Venkateswaran wrote: Dear DTI Studio Users, I am looking specifically for seimens 1.5 T, Avanto machine, software version VB11, 12 directional gradient table. If anyone has it can you please share with me. Thanks in advance. Regards venkateswaran =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S. News & World Report (2008). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S. News & World Report (2008). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 6765 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090813/10df4e51/attachment.bin From susumu at mri.jhu.edu Thu Aug 13 16:41:39 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Thu, 13 Aug 2009 16:41:39 -0400 Subject: [Mristudio-users] L and R in files In-Reply-To: <4A7F3897.5090601@uhnres.utoronto.ca> References: <4A7F3897.5090601@uhnres.utoronto.ca> Message-ID: Hi Massieh, Please refer to FAQ 15 at https://www.mristudio.org/wiki/faq. Hope this will answer your question. Susumu On Sun, Aug 9, 2009 at 4:59 PM, Massieh Moayedi wrote: > Hello MriStudio experts, > > I am currently importing GE dicoms to DTiStudio and (after AIR and > removing corrupted images) saving the images as ANALYZE files. I just > want to check and see if the orientation of the images changes at any > point. In other words, what orientation are the images imported and > then later saved in? > > Thanks, > > Massih > > -- > Massieh Moayedi B.Sc. (Hons) > Graduate Student > Institute of Medical Science > University of Toronto > > Brain, Imaging and Behaviour- Systems Neuroscience > MP 14-301 > Toronto Western Research Institute > University Health Network > 399 Bathurst Street > Toronto, Ontario > Canada M5T 2S8 > Tel: 416-603-5882 > > massih.moayedi at utoronto.ca > mmoayedi at uhnres.utoronto.ca > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090813/73f507a5/attachment.html From choisj70 at gmail.com Sat Aug 15 02:46:32 2009 From: choisj70 at gmail.com (Seongjin) Date: Sat, 15 Aug 2009 02:46:32 -0400 Subject: [Mristudio-users] ROI editor and DTI Studio Message-ID: Dear Susumu, I created an ROI using ROI Editor with save-option 'Binary maps' as well as 'ROI editor defined' . However I could not load the saved ROI in DTI studio. Do you have any solution to this problem? Sincerely, -SC -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090815/e767556c/attachment.html From xli16 at jhmi.edu Wed Aug 19 10:16:01 2009 From: xli16 at jhmi.edu (Xin Li) Date: Wed, 19 Aug 2009 10:16:01 -0400 Subject: [Mristudio-users] ROI editor and DTI Studio In-Reply-To: References: Message-ID: Please take a look at this post. http://lists.mristudio.org/pipermail/mristudio-users/2008/000315.html Xin ----- Original Message ----- From: "[Seongjin]" Date: Saturday, August 15, 2009 2:46 am Subject: [Mristudio-users] ROI editor and DTI Studio To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > Dear Susumu, > > I created an ROI using ROI Editor with save-option 'Binary maps' as > well as > 'ROI editor defined' . > However I could not load the saved ROI in DTI studio. Do you have any > solution to this problem? > > Sincerely, > > -SC > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From choisj70 at gmail.com Wed Aug 19 15:48:11 2009 From: choisj70 at gmail.com (Seongjin) Date: Wed, 19 Aug 2009 15:48:11 -0400 Subject: [Mristudio-users] ROI editor and DTI Studio In-Reply-To: References: Message-ID: I figured out how to do it. Some how the ROIs drawn in ROI Editor are invisible. However, loading the ROI produces fiber bundles selected by the created ROIs. Thanks! The link you sent to me contains helpful tips for me. -SC On Wed, Aug 19, 2009 at 10:16 AM, Xin Li wrote: > Please take a look at this post. > > http://lists.mristudio.org/pipermail/mristudio-users/2008/000315.html > > > Xin > > > > ----- Original Message ----- > From: "[Seongjin]" > Date: Saturday, August 15, 2009 2:46 am > Subject: [Mristudio-users] ROI editor and DTI Studio > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" < > mristudio-users at mristudio.org> > > > > Dear Susumu, > > > > I created an ROI using ROI Editor with save-option 'Binary maps' as > > well as > > 'ROI editor defined' . > > However I could not load the saved ROI in DTI studio. Do you have any > > solution to this problem? > > > > Sincerely, > > > > -SC > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090819/1fdb3296/attachment-0001.html From qianwenshu at gmail.com Wed Aug 19 22:04:34 2009 From: qianwenshu at gmail.com (=?GB2312?B?x67OxMrg?=) Date: Thu, 20 Aug 2009 10:04:34 +0800 Subject: [Mristudio-users] ROI editor and DTI Studio In-Reply-To: References: Message-ID: <2404f5960908191904tb93ac3do4760368f2969aa9c@mail.gmail.com> Hi, Xin, First of all, thank you for your reply! But I can not open the website, and the email you replied is not mine, I think~ 2009-08-19 ------------------------------ ?X???? Qian Wenshu ???????W?????\?t?W???????\???W Department of Diagnostic Radiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, HK ???M????Contact: Mobile:852-95191930 MSN: qianws-acc at hotmail.com E-mail: qianwenshu at gmail.com h0994136 at hku.hk 2009/8/19 Xin Li > Please take a look at this post. > > http://lists.mristudio.org/pipermail/mristudio-users/2008/000315.html > > > Xin > > > > ----- Original Message ----- > From: "[Seongjin]" > Date: Saturday, August 15, 2009 2:46 am > Subject: [Mristudio-users] ROI editor and DTI Studio > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" < > mristudio-users at mristudio.org> > > > > Dear Susumu, > > > > I created an ROI using ROI Editor with save-option 'Binary maps' as > > well as > > 'ROI editor defined' . > > However I could not load the saved ROI in DTI studio. Do you have any > > solution to this problem? > > > > Sincerely, > > > > -SC > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090820/c1035bd9/attachment.html From prizzut2 at jhu.edu Thu Aug 20 13:43:36 2009 From: prizzut2 at jhu.edu (Patrick Rizzuto) Date: Thu, 20 Aug 2009 13:43:36 -0400 Subject: [Mristudio-users] DTIStudio crashing during tensor calculations Message-ID: Hi all, I am attempting to use the DTIStudio component of MRIStudio in order to perform the standard tensor calculations on a .dpf file (post image-registration); however, about a second or so after it asks me about automatic outlier rejection, the program (in particular, the MFC application, according to the popup) invariably crashes, citing an exception at location "0x73ed2659". I have used this same procedure successfully on four other similar AIR-.dpf files, and yet I cannot avoid this problem on this particular .dpf file, even after restarting the computer. This same .dpf file is unusual in another way. When first loading it in, it gives me warnings that the (three) .rec file sizes are smaller than the DW-image size. I occasionally received similar warnings for the other .dpf files, but these were easily resolved by tinkering with the number of slices specified in the .dpf file. In this case, though, there does not appear to be a correct number of slices - while it gives me a message that the .rec files are small with 52 slices, it also warns me that the .rec files are too BIG with 51 slices. Let me emphasize that in both cases, the .dpf file successfully loads if the warnings are dismissed, and the brain images look normal - a problem is only revealed once I attempt to perform the calculations. The .par files for these .rec files are also different - a few of the parameters that were mentioned in the other .par files are not specified in these 3. In particular, there is no mention of the recon. scan resolution or of the slice thickness. If anyone has any tips on how to resolve this, I would greatly appreciate it. Thanks! Pat Rizzuto Johns Hopkins Center for Imaging Science From choisj70 at gmail.com Wed Aug 26 08:37:58 2009 From: choisj70 at gmail.com (Seongjin) Date: Wed, 26 Aug 2009 08:37:58 -0400 Subject: [Mristudio-users] NifTi and DTI Studio Message-ID: Dear all, Is there anybody know how to import NifTi format data into DTI Studio? -SC -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090826/dacda1f6/attachment.html From junyiwang2002 at yahoo.com Wed Aug 26 12:11:00 2009 From: junyiwang2002 at yahoo.com (Jun Yi Wang) Date: Wed, 26 Aug 2009 09:11:00 -0700 (PDT) Subject: [Mristudio-users] NifTi and DTI Studio In-Reply-To: References: Message-ID: <772396.37050.qm@web50512.mail.re2.yahoo.com> I use FSL to change nifti format to analyze and then use DTI Studio to change analyze to dat format. JY ________________________________ From: [Seongjin] To: "DTI Studio, ROI Editor, Landmarker Questions/Support" Sent: Wednesday, August 26, 2009 5:37:58 AM Subject: [Mristudio-users] NifTi and DTI Studio Dear all, Is there anybody know how to import NifTi format data into DTI Studio? -SC -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090826/de2d146f/attachment.html From huyuzheng at gmail.com Wed Aug 26 12:22:42 2009 From: huyuzheng at gmail.com (=?GB2312?B?uvrT8dX9?=) Date: Thu, 27 Aug 2009 00:22:42 +0800 Subject: [Mristudio-users] NifTi and DTI Studio In-Reply-To: <772396.37050.qm@web50512.mail.re2.yahoo.com> References: <772396.37050.qm@web50512.mail.re2.yahoo.com> Message-ID: <39c428d80908260922p6e857432k4f1d6a52311eda65@mail.gmail.com> > I use FSL to change nifti format to analyze and then use DTI Studio to > change analyze to dat format. > Did you realy make it? I have used the same way but failed... If NIFITI files could be imported directly into the DTIStudio, it will be wonderful. Hope some make it. Yuzheng > > JY > > ------------------------------ > *From:* [Seongjin] > *To:* "DTI Studio, ROI Editor, Landmarker Questions/Support" < > mristudio-users at mristudio.org> > *Sent:* Wednesday, August 26, 2009 5:37:58 AM > *Subject:* [Mristudio-users] NifTi and DTI Studio > > Dear all, > Is there anybody know how to import NifTi format data into DTI Studio? > > -SC > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090827/92037aac/attachment.html From shereeda at mail.uc.edu Fri Aug 28 13:22:45 2009 From: shereeda at mail.uc.edu (Shereen, Ahmed (shereeda)) Date: Fri, 28 Aug 2009 17:22:45 +0000 Subject: [Mristudio-users] units? Message-ID: <73AB8D89B9AABB4FBF603FCC7F345620A3EF@BL2PRD0102MB008.prod.exchangelabs.com> Hello, I have a problem which I think has to do with the units for the eigenvalues calculated in ROIEditor. Basically, when I draw ROIs, save them, and then load them into the FA image, everything works fine. When I then load the eigenvalue images, the ROIs that gave me good FA values give me the same eigenvalues for all ROIs. I'm attaching the ROI data file. Has anybody seen anything like this? Thank you, Duke -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090828/8df7c0b7/attachment-0001.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: ROIStatistics_L1.txt Url: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090828/8df7c0b7/attachment-0001.txt From rodd at cis.jhu.edu Fri Aug 28 14:16:36 2009 From: rodd at cis.jhu.edu (Rodd Pribik) Date: Fri, 28 Aug 2009 14:16:36 -0400 Subject: [Mristudio-users] units? In-Reply-To: <73AB8D89B9AABB4FBF603FCC7F345620A3EF@BL2PRD0102MB008.prod.exchangelabs.com> References: <73AB8D89B9AABB4FBF603FCC7F345620A3EF@BL2PRD0102MB008.prod.exchangelabs.com> Message-ID: <4A981F04.7050403@cis.jhu.edu> Hi Kate, Another question... I'm having that problem where I'm using the -o tag, but the _surf_cut.byu is given the long name, and not the -o name. Do you remember the fix? Here is the version. Shereen, Ahmed (shereeda) wrote: > Hello, > I have a problem which I think has to do with the units for the > eigenvalues calculated in ROIEditor. Basically, when I draw ROIs, > save them, and then load them into the FA image, everything works > fine. When I then load the eigenvalue images, the ROIs that gave me > good FA values give me the same eigenvalues for all ROIs. I'm > attaching the ROI data file. Has anybody seen anything like this? > Thank you, > Duke > ------------------------------------------------------------------------ > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- A non-text attachment was scrubbed... Name: LCDM_pipeline.sh Type: application/x-sh Size: 13059 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090828/ffd46c1a/attachment.sh From rodd at cis.jhu.edu Fri Aug 28 14:18:57 2009 From: rodd at cis.jhu.edu (Rodd Pribik) Date: Fri, 28 Aug 2009 14:18:57 -0400 Subject: [Mristudio-users] units? In-Reply-To: <4A981F04.7050403@cis.jhu.edu> References: <73AB8D89B9AABB4FBF603FCC7F345620A3EF@BL2PRD0102MB008.prod.exchangelabs.com> <4A981F04.7050403@cis.jhu.edu> Message-ID: <4A981F91.6010508@cis.jhu.edu> Sorry, that was not meant for this mailing list. Rodd Pribik wrote: > Hi Kate, > > Another question... I'm having that problem where I'm using the -o > tag, but the _surf_cut.byu is given the long name, and not the -o > name. Do you remember the fix? Here is the version. > > Shereen, Ahmed (shereeda) wrote: >> Hello, >> I have a problem which I think has to do with the units for the >> eigenvalues calculated in ROIEditor. Basically, when I draw ROIs, >> save them, and then load them into the FA image, everything works >> fine. When I then load the eigenvalue images, the ROIs that gave me >> good FA values give me the same eigenvalues for all ROIs. I'm >> attaching the ROI data file. Has anybody seen anything like this? >> Thank you, >> Duke >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org > ------------------------------------------------------------------------ > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > From xli16 at jhmi.edu Fri Aug 28 16:14:01 2009 From: xli16 at jhmi.edu (Xin Li) Date: Fri, 28 Aug 2009 16:14:01 -0400 Subject: [Mristudio-users] units? In-Reply-To: <73AB8D89B9AABB4FBF603FCC7F345620A3EF@BL2PRD0102MB008.prod.exchangelabs.com> References: <73AB8D89B9AABB4FBF603FCC7F345620A3EF@BL2PRD0102MB008.prod.exchangelabs.com> Message-ID: Hello, The current version of ROIEditor reports the statistical result as four decimal precision. When your eigenvalue data are very small, this problem happens. You may scale the eigenvalue data before the statistical caculation. Xin ----- Original Message ----- From: "Shereen, Ahmed (shereeda)" Date: Friday, August 28, 2009 1:26 pm Subject: [Mristudio-users] units? To: "mristudio-users at mristudio.org" > Hello, > I have a problem which I think has to do with the units for the > eigenvalues calculated in ROIEditor. Basically, when I draw ROIs, > save them, and then load them into the FA image, everything works > fine. When I then load the eigenvalue images, the ROIs that gave me > good FA values give me the same eigenvalues for all ROIs. I'm > attaching the ROI data file. Has anybody seen anything like this? > Thank you, > Duke > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From yj3 at duke.edu Fri Aug 28 16:20:58 2009 From: yj3 at duke.edu (Yi Jiang) Date: Fri, 28 Aug 2009 16:20:58 -0400 Subject: [Mristudio-users] fiber tracking and tensor transformation algorithms References: <73AB8D89B9AABB4FBF603FCC7F345620A3EF@BL2PRD0102MB008.prod.exchangelabs.com> <4A981F04.7050403@cis.jhu.edu> Message-ID: <3CF7456181A346AD85B984F03662DF73@panpan> Hello, I am using DTIstudio to track fibers and using LandMarker to register the brains and transform (reorient) tensors in each brain by the overall matrix combining AIR linear affine and LDDMM. May I have a simple description about the fiber tracking algorithm (FACT or other?) in DTIstudio, and the tensor transformation (reorienting )algorithm (preserve the principal direction? or other?) in LandMarker? And I would like to have the references to the above algorithms (tracking, registration, and tensor transformation) so I can cite in my paper. Another two small questions about LandMarker: 1. Is the overall matrix combining AIR transformation and LDDMM in the same format as LDDMM raw? 2. I found two channel LDDMM finished much faster than single channel LDDMM (2 channels in about 2 hours, and single channel ain bout 48 hours). Is that normal? I am just curious. Thank you very much for your help! Best, Yi From xli16 at jhmi.edu Fri Aug 28 16:36:26 2009 From: xli16 at jhmi.edu (Xin Li) Date: Fri, 28 Aug 2009 16:36:26 -0400 Subject: [Mristudio-users] fiber tracking and tensor transformation algorithms In-Reply-To: <3CF7456181A346AD85B984F03662DF73@panpan> References: <73AB8D89B9AABB4FBF603FCC7F345620A3EF@BL2PRD0102MB008.prod.exchangelabs.com> <4A981F04.7050403@cis.jhu.edu> <3CF7456181A346AD85B984F03662DF73@panpan> Message-ID: Hello, To understand the tensor transformation algorithm, please refer to this paper. Spatial Normalization of Diffusion Tensor Fields by Dongrong Xu, Susumu Mori Magnetic Resonance in Medicine 50:175-182 (2003) > Another two small questions about LandMarker: > 1. Is the overall matrix combining AIR transformation and LDDMM in > the same > format as LDDMM raw? Yes. > 2. I found two channel LDDMM finished much faster than single channel > LDDMM > (2 channels in about 2 hours, and single channel ain bout 48 hours). > Is that > normal? I am just curious. It is not normal. It shouldn't take 48 hours to process any data. Please try again. If you still have the same problem, please let me know. Xin ----- Original Message ----- From: Yi Jiang Date: Friday, August 28, 2009 4:21 pm Subject: [Mristudio-users] fiber tracking and tensor transformation algorithms To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > Hello, > > I am using DTIstudio to track fibers and using LandMarker to register > the > brains and transform (reorient) tensors in each brain by the overall > matrix > combining AIR linear affine and LDDMM. > > May I have a simple description about the fiber tracking algorithm > (FACT or > other?) in DTIstudio, and the tensor transformation (reorienting > )algorithm > (preserve the principal direction? or other?) in LandMarker? And I > would > like to have the references to the above algorithms (tracking, > registration, > and tensor transformation) so I can cite in my paper. > > Another two small questions about LandMarker: > 1. Is the overall matrix combining AIR transformation and LDDMM in > the same > format as LDDMM raw? > 2. I found two channel LDDMM finished much faster than single channel > LDDMM > (2 channels in about 2 hours, and single channel ain bout 48 hours). > Is that > normal? I am just curious. > > Thank you very much for your help! > > Best, > Yi > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From shereeda at mail.uc.edu Fri Aug 28 18:49:49 2009 From: shereeda at mail.uc.edu (Shereen, Ahmed (shereeda)) Date: Fri, 28 Aug 2009 22:49:49 +0000 Subject: [Mristudio-users] units? In-Reply-To: References: <73AB8D89B9AABB4FBF603FCC7F345620A3EF@BL2PRD0102MB008.prod.exchangelabs.com> Message-ID: <73AB8D89B9AABB4FBF603FCC7F345620A7A6@BL2PRD0102MB008.prod.exchangelabs.com> Thank you, I have another question. Sometimes when I draw ROIs not all of the pink pixels become part of the ROI object when I push the (Add(a)) button. I check the statistics box to double check that it is not just a visual misplacement. The number of pixels also does not increase from the statistics gui, although extra pixels were selected prior to pushing Add(a). Any ideas? Again, thank you, Duke ________________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] on behalf of Xin Li [xli16 at jhmi.edu] Sent: Friday, August 28, 2009 4:14 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] units? Hello, The current version of ROIEditor reports the statistical result as four decimal precision. When your eigenvalue data are very small, this problem happens. You may scale the eigenvalue data before the statistical caculation. Xin ----- Original Message ----- From: "Shereen, Ahmed (shereeda)" Date: Friday, August 28, 2009 1:26 pm Subject: [Mristudio-users] units? To: "mristudio-users at mristudio.org" > Hello, > I have a problem which I think has to do with the units for the > eigenvalues calculated in ROIEditor. Basically, when I draw ROIs, > save them, and then load them into the FA image, everything works > fine. When I then load the eigenvalue images, the ROIs that gave me > good FA values give me the same eigenvalues for all ROIs. I'm > attaching the ROI data file. Has anybody seen anything like this? > Thank you, > Duke > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From susumu at mri.jhu.edu Sat Aug 29 18:27:18 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Sat, 29 Aug 2009 18:27:18 -0400 Subject: [Mristudio-users] NifTi and DTI Studio In-Reply-To: <39c428d80908260922p6e857432k4f1d6a52311eda65@mail.gmail.com> References: <772396.37050.qm@web50512.mail.re2.yahoo.com> <39c428d80908260922p6e857432k4f1d6a52311eda65@mail.gmail.com> Message-ID: There is a newer version of DtiStudio that can read Nifty. Hangyi and Xin, please work on posting the latest version with updated features. We'll notify users once a newer version is available on the web. On Wed, Aug 26, 2009 at 12:22 PM, ??? wrote: > > I use FSL to change nifti format to analyze and then use DTI Studio to >> change analyze to dat format. >> > > Did you realy make it? I have used the same way but failed... > If NIFITI files could be imported directly into the DTIStudio, it will be > wonderful. Hope some make it. > > Yuzheng > >> >> JY >> >> ------------------------------ >> *From:* [Seongjin] >> *To:* "DTI Studio, ROI Editor, Landmarker Questions/Support" < >> mristudio-users at mristudio.org> >> *Sent:* Wednesday, August 26, 2009 5:37:58 AM >> *Subject:* [Mristudio-users] NifTi and DTI Studio >> >> Dear all, >> Is there anybody know how to import NifTi format data into DTI Studio? >> >> -SC >> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090829/45f98173/attachment.html From yj3 at duke.edu Sun Aug 30 15:45:11 2009 From: yj3 at duke.edu (Yi Jiang) Date: Sun, 30 Aug 2009 15:45:11 -0400 Subject: [Mristudio-users] fiber tracking and tensor transformationalgorithms References: <73AB8D89B9AABB4FBF603FCC7F345620A3EF@BL2PRD0102MB008.prod.exchangelabs.com> <4A981F04.7050403@cis.jhu.edu> <3CF7456181A346AD85B984F03662DF73@panpan> Message-ID: <3D33B3729F8B40AA8C32014D1F9AFF52@panpan> Thank you very much, Xin. May I also have the reference to the fiber tracking algorithm (FACT or other?) used in DTIstudio? Thank you! Yi ----- Original Message ----- From: "Xin Li" To: "Yi Jiang" ; "DTI Studio, ROI Editor, Landmarker Questions/Support" Sent: Friday, August 28, 2009 4:36 PM Subject: Re: [Mristudio-users] fiber tracking and tensor transformationalgorithms > Hello, > > To understand the tensor transformation algorithm, please refer to this > paper. > > Spatial Normalization of Diffusion Tensor Fields > by Dongrong Xu, Susumu Mori > Magnetic Resonance in Medicine 50:175-182 (2003) > > >> Another two small questions about LandMarker: >> 1. Is the overall matrix combining AIR transformation and LDDMM in >> the same >> format as LDDMM raw? > > Yes. > > >> 2. I found two channel LDDMM finished much faster than single channel >> LDDMM >> (2 channels in about 2 hours, and single channel ain bout 48 hours). >> Is that >> normal? I am just curious. > > It is not normal. It shouldn't take 48 hours to process any data. Please > try again. If you still have the same problem, please let me know. > > > Xin > > > ----- Original Message ----- > From: Yi Jiang > Date: Friday, August 28, 2009 4:21 pm > Subject: [Mristudio-users] fiber tracking and tensor transformation > algorithms > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > > > >> Hello, >> >> I am using DTIstudio to track fibers and using LandMarker to register >> the >> brains and transform (reorient) tensors in each brain by the overall >> matrix >> combining AIR linear affine and LDDMM. >> >> May I have a simple description about the fiber tracking algorithm >> (FACT or >> other?) in DTIstudio, and the tensor transformation (reorienting >> )algorithm >> (preserve the principal direction? or other?) in LandMarker? And I >> would >> like to have the references to the above algorithms (tracking, >> registration, >> and tensor transformation) so I can cite in my paper. >> >> Another two small questions about LandMarker: >> 1. Is the overall matrix combining AIR transformation and LDDMM in >> the same >> format as LDDMM raw? >> 2. I found two channel LDDMM finished much faster than single channel >> LDDMM >> (2 channels in about 2 hours, and single channel ain bout 48 hours). >> Is that >> normal? I am just curious. >> >> Thank you very much for your help! >> >> Best, >> Yi >> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org > From xli16 at jhmi.edu Mon Aug 31 09:47:56 2009 From: xli16 at jhmi.edu (Xin Li) Date: Mon, 31 Aug 2009 09:47:56 -0400 Subject: [Mristudio-users] units? In-Reply-To: <73AB8D89B9AABB4FBF603FCC7F345620A7A6@BL2PRD0102MB008.prod.exchangelabs.com> References: <73AB8D89B9AABB4FBF603FCC7F345620A3EF@BL2PRD0102MB008.prod.exchangelabs.com> <73AB8D89B9AABB4FBF603FCC7F345620A7A6@BL2PRD0102MB008.prod.exchangelabs.com> Message-ID: Hello, After you push the Add button, only the contour of the ROI displays. But you said that the number of pixels does not increase from the statistics gui. Could you give me some details about this problem, for example some screenshots and the statitics file? Xin ----- Original Message ----- From: "Shereen, Ahmed (shereeda)" Date: Friday, August 28, 2009 6:52 pm Subject: Re: [Mristudio-users] units? To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > Thank you, > > I have another question. Sometimes when I draw ROIs not all of the > pink pixels become part of the ROI object when I push the (Add(a)) > button. I check the statistics box to double check that it is not > just a visual misplacement. The number of pixels also does not > increase from the statistics gui, although extra pixels were selected > prior to pushing Add(a). > > Any ideas? > Again, thank you, > Duke > ________________________________________ > From: mristudio-users-bounces at mristudio.org > [mristudio-users-bounces at mristudio.org] on behalf of Xin Li [xli16 at jhmi.edu] > Sent: Friday, August 28, 2009 4:14 PM > To: DTI Studio, ROI Editor, Landmarker Questions/Support > Subject: Re: [Mristudio-users] units? > > Hello, > > The current version of ROIEditor reports the statistical result as > four decimal precision. When your eigenvalue data are very small, this > problem happens. You may scale the eigenvalue data before the > statistical caculation. > > Xin > > ----- Original Message ----- > From: "Shereen, Ahmed (shereeda)" > Date: Friday, August 28, 2009 1:26 pm > Subject: [Mristudio-users] units? > To: "mristudio-users at mristudio.org" > > > > Hello, > > I have a problem which I think has to do with the units for the > > eigenvalues calculated in ROIEditor. Basically, when I draw ROIs, > > save them, and then load them into the FA image, everything works > > fine. When I then load the eigenvalue images, the ROIs that gave me > > good FA values give me the same eigenvalues for all ROIs. I'm > > attaching the ROI data file. Has anybody seen anything like this? > > Thank you, > > Duke > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From rajagov2 at ccf.org Mon Aug 31 11:49:21 2009 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Mon, 31 Aug 2009 11:49:21 -0400 Subject: [Mristudio-users] NifTi and DTI Studio References: <772396.37050.qm@web50512.mail.re2.yahoo.com> <39c428d80908260922p6e857432k4f1d6a52311eda65@mail.gmail.com> Message-ID: <77A88E90A851594AAEF830450587C39D01EDAAF7@CCHSCLEXMB56.cc.ad.cchs.net> Dr.Mori, Sorry to intrude in Yuzheng's question section. I have the following question, i am using FSL to perform distortion correction of DTI images, after this i convert them into analyze format and open them in DTI studio and save them as RAW format and then run "DTI mapping" to calculate FA and other metrics, in answersing to a question in the forum on b-matrix rotation you have indicated that with "RAW" format we cannot actually perform b-matrix rotation option. Now the only way for me to bring the distortion corrected images from FSL is by analyze format and save as RAW format so in this case i am not able to do this b-matrix rotation, in some of my data i observed that b-matrix is significantly rotated so i prefer to check the b-matrix rotation option in my data sets. Any suggestion on this. Thanks in advance, Regards venkateswaran ________________________________ From: mristudio-users-bounces at mristudio.org on behalf of susumu mori Sent: Sat 8/29/2009 6:27 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support; Hangyi Jiang; Xin Li Subject: Re: [Mristudio-users] NifTi and DTI Studio There is a newer version of DtiStudio that can read Nifty. Hangyi and Xin, please work on posting the latest version with updated features. We'll notify users once a newer version is available on the web. On Wed, Aug 26, 2009 at 12:22 PM, ??? wrote: I use FSL to change nifti format to analyze and then use DTI Studio to change analyze to dat format. Did you realy make it? I have used the same way but failed... If NIFITI files could be imported directly into the DTIStudio, it will be wonderful. Hope some make it. Yuzheng JY ________________________________ From: [Seongjin] To: "DTI Studio, ROI Editor, Landmarker Questions/Support" Sent: Wednesday, August 26, 2009 5:37:58 AM Subject: [Mristudio-users] NifTi and DTI Studio Dear all, Is there anybody know how to import NifTi format data into DTI Studio? -SC _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S. News & World Report (2008). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 6943 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090831/89965b06/attachment-0001.bin From susumu at mri.jhu.edu Mon Aug 31 12:20:29 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Mon, 31 Aug 2009 12:20:29 -0400 Subject: [Mristudio-users] NifTi and DTI Studio In-Reply-To: <77A88E90A851594AAEF830450587C39D01EDAAF7@CCHSCLEXMB56.cc.ad.cchs.net> References: <772396.37050.qm@web50512.mail.re2.yahoo.com> <39c428d80908260922p6e857432k4f1d6a52311eda65@mail.gmail.com> <77A88E90A851594AAEF830450587C39D01EDAAF7@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: Hi venkateswaran 1) It seems the DtiStudio version currently posted in www.mristudio.orgalready has the function to read/write Nifty. Please check and send me feedbacks if you encounter and problems. 2) As for the "distortion correction", do you mean Eddy current distortion correction or B0 susceptibility correction? If the former is the case, you can use the Affine tool in DtiStudio. 3) As for the b-matrix rotation, do you mean the rotation for oblique-angle imaging that affect older Siemens system? If that is the case, it would be a complicated issue. The easiest way is, to read the Dicom/Mosaic directly to DtiStudio, which can automatically recalculate the b-table based on the oblique information in the header. Once you go through FLS and data is converted to Nifty/Analyze/Raw, the oblique information is lost. You can still trick DtiStudio in the following way, but it is a bit cumbersome. > Read Mosaic/Dicom directly to DtiStudio, provide the Siemens-provide original b-table, click the "rotation if applicable", and load the data. > Close the window and re-open the data input window. There you can find that b-table of the previous session still remembered by DtiStudio. This table is already rotated (not the original b-table anymore). You can use this table for the Raw data. 4) The b-table rotation option for oblique imaging doesn't work for Raw/Analyze/Nifty in DtiStudio. Do Analyze and Nifty have a field for oblique angles? If so, maybe Hangyi wants to see if we can make the option available for Analyze and Nifty. On Mon, Aug 31, 2009 at 11:49 AM, Rajagopalan, Venkateswaran < rajagov2 at ccf.org> wrote: > Dr.Mori, > > Sorry to intrude in Yuzheng's question section. I have the following > question, i am using FSL to perform distortion correction of DTI images, > after this i convert them into analyze format and open them in DTI studio > and save them as RAW format and then run "DTI mapping" to calculate FA and > other metrics, in answersing to a question in the forum on b-matrix rotation > you have indicated that with "RAW" format we cannot actually perform > b-matrix rotation option. Now the only way for me to bring the distortion > corrected images from FSL is by analyze format and save as RAW format so in > this case i am not able to do this b-matrix rotation, in some of my data i > observed that b-matrix is significantly rotated so i prefer to check the > b-matrix rotation option in my data sets. Any suggestion on this. > > Thanks in advance, > > Regards > venkateswaran > > ________________________________ > > From: mristudio-users-bounces at mristudio.org on behalf of susumu mori > Sent: Sat 8/29/2009 6:27 PM > To: DTI Studio, ROI Editor, Landmarker Questions/Support; Hangyi Jiang; Xin > Li > Subject: Re: [Mristudio-users] NifTi and DTI Studio > > > There is a newer version of DtiStudio that can read Nifty. > Hangyi and Xin, please work on posting the latest version with updated > features. > We'll notify users once a newer version is available on the web. > > > On Wed, Aug 26, 2009 at 12:22 PM, ??? wrote: > > > > I use FSL to change nifti format to analyze and then use DTI > Studio to change analyze to dat format. > > > Did you realy make it? I have used the same way but failed... > If NIFITI files could be imported directly into the DTIStudio, it > will be wonderful. Hope some make it. > > Yuzheng > > > > JY > > > ________________________________ > > From: [Seongjin] > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" < > mristudio-users at mristudio.org> > Sent: Wednesday, August 26, 2009 5:37:58 AM > Subject: [Mristudio-users] NifTi and DTI Studio > > > Dear all, > > Is there anybody know how to import NifTi format data into > DTI Studio? > > -SC > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > > > > > =================================== > > P Please consider the environment before printing this e-mail > > Cleveland Clinic is ranked one of the top hospitals > in America by U.S. News & World Report (2008). > Visit us online at http://www.clevelandclinic.org for > a complete listing of our services, staff and > locations. > > > Confidentiality Note: This message is intended for use > only by the individual or entity to which it is addressed > and may contain information that is privileged, > confidential, and exempt from disclosure under applicable > law. If the reader of this message is not the intended > recipient or the employee or agent responsible for > delivering the message to the intended recipient, you are > hereby notified that any dissemination, distribution or > copying of this communication is strictly prohibited. If > you have received this communication in error, please > contact the sender immediately and destroy the material in > its entirety, whether electronic or hard copy. Thank you. > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090831/456805e2/attachment.html From rajagov2 at ccf.org Mon Aug 31 12:52:40 2009 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Mon, 31 Aug 2009 12:52:40 -0400 Subject: [Mristudio-users] NifTi and DTI Studio References: <772396.37050.qm@web50512.mail.re2.yahoo.com> <39c428d80908260922p6e857432k4f1d6a52311eda65@mail.gmail.com> <77A88E90A851594AAEF830450587C39D01EDAAF7@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: <77A88E90A851594AAEF830450587C39D01EDAAF8@CCHSCLEXMB56.cc.ad.cchs.net> Dear Dr.Mori, Thanks for your kind information. As for the "distortion correction", do you mean Eddy current distortion correction or B0 susceptibility correction? If the former is the case, you can use the Affine tool in DtiStudio. Sorry i was not clear earlier, it is B0 suspectibily artifacts correction. As for the b-matrix rotation, do you mean the rotation for oblique-angle imaging that affect older Siemens system? Yes, our scanners are seimens scanners. Read Mosaic/Dicom directly to DtiStudio, provide the Siemens-provide original b-table, click the "rotation if applicable", and load the data. Close the window and re-open the data input window. There you can find that b-table of the previous session still remembered by DtiStudio. This table is already rotated (not the original b-table anymore). You can use this table for the Raw data. Thanks for this information i also thought about this, but one question prevented me from doing this, i would like to clarify that with you, after distortion correction especially the voxels in frontal regions of the brain like corpus callosum ( i am not good in anatomy sorry apologize me if i am wrong) are streched or in other words restored to their original positions, so i am wondering whether this kind of voxel stretching and squeezing (undistorted) will contribute to any additional changes in b-matrix when compared to the changes in b-mtarix contributed by the original i.e distorted images. I understand that b-matrix rotation i calculated from the rotation matrix of the main affine matrix, i don't know whether the affine matrix will be different between before and after distortion correction images. I am sorry if i am not clear. The b-table rotation option for oblique imaging doesn't work for Raw/Analyze/Nifty in DtiStudio. Do Analyze and Nifty have a field for oblique angles? I am sorry Dr.Mori i don't whether Analyze and Nifti has fields for oblique angles. Thanks again for your help. Regards venkateswaran ________________________________ From: mristudio-users-bounces at mristudio.org on behalf of susumu mori Sent: Mon 8/31/2009 12:20 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support; Hangyi Jiang Subject: Re: [Mristudio-users] NifTi and DTI Studio Hi venkateswaran 1) It seems the DtiStudio version currently posted in www.mristudio.org already has the function to read/write Nifty. Please check and send me feedbacks if you encounter and problems. 2) As for the "distortion correction", do you mean Eddy current distortion correction or B0 susceptibility correction? If the former is the case, you can use the Affine tool in DtiStudio. 3) As for the b-matrix rotation, do you mean the rotation for oblique-angle imaging that affect older Siemens system? If that is the case, it would be a complicated issue. The easiest way is, to read the Dicom/Mosaic directly to DtiStudio, which can automatically recalculate the b-table based on the oblique information in the header. Once you go through FLS and data is converted to Nifty/Analyze/Raw, the oblique information is lost. You can still trick DtiStudio in the following way, but it is a bit cumbersome. > Read Mosaic/Dicom directly to DtiStudio, provide the Siemens-provide original b-table, click the "rotation if applicable", and load the data. > Close the window and re-open the data input window. There you can find that b-table of the previous session still remembered by DtiStudio. This table is already rotated (not the original b-table anymore). You can use this table for the Raw data. 4) The b-table rotation option for oblique imaging doesn't work for Raw/Analyze/Nifty in DtiStudio. Do Analyze and Nifty have a field for oblique angles? If so, maybe Hangyi wants to see if we can make the option available for Analyze and Nifty. On Mon, Aug 31, 2009 at 11:49 AM, Rajagopalan, Venkateswaran wrote: Dr.Mori, Sorry to intrude in Yuzheng's question section. I have the following question, i am using FSL to perform distortion correction of DTI images, after this i convert them into analyze format and open them in DTI studio and save them as RAW format and then run "DTI mapping" to calculate FA and other metrics, in answersing to a question in the forum on b-matrix rotation you have indicated that with "RAW" format we cannot actually perform b-matrix rotation option. Now the only way for me to bring the distortion corrected images from FSL is by analyze format and save as RAW format so in this case i am not able to do this b-matrix rotation, in some of my data i observed that b-matrix is significantly rotated so i prefer to check the b-matrix rotation option in my data sets. Any suggestion on this. Thanks in advance, Regards venkateswaran ________________________________ From: mristudio-users-bounces at mristudio.org on behalf of susumu mori Sent: Sat 8/29/2009 6:27 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support; Hangyi Jiang; Xin Li Subject: Re: [Mristudio-users] NifTi and DTI Studio There is a newer version of DtiStudio that can read Nifty. Hangyi and Xin, please work on posting the latest version with updated features. We'll notify users once a newer version is available on the web. On Wed, Aug 26, 2009 at 12:22 PM, ??? wrote: I use FSL to change nifti format to analyze and then use DTI Studio to change analyze to dat format. Did you realy make it? I have used the same way but failed... If NIFITI files could be imported directly into the DTIStudio, it will be wonderful. Hope some make it. Yuzheng JY ________________________________ From: [Seongjin] To: "DTI Studio, ROI Editor, Landmarker Questions/Support" Sent: Wednesday, August 26, 2009 5:37:58 AM Subject: [Mristudio-users] NifTi and DTI Studio Dear all, Is there anybody know how to import NifTi format data into DTI Studio? -SC _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S. News & World Report (2008). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S. News & World Report (2008). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 11563 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090831/44709fb6/attachment-0001.bin From susumu at mri.jhu.edu Mon Aug 31 18:17:45 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Mon, 31 Aug 2009 18:17:45 -0400 Subject: [Mristudio-users] DTIStudio crashing during tensor calculations In-Reply-To: References: Message-ID: Hi Pat, Usually, the most like cause of crash is memory shortage. The second cause is the mismatch between the number of images and the supplied b-table. You should avoid receiving the warning of the size mismatch. If you could load the data, please go over all the loaded images listed in the pull-down menu and make sure that the image size is right (for example, if you read 50-slice images as 49-slice image, you can see that the last slice of the first slice is included in the second image and last two slices of the second images are included in the third image, and so on). Also the total number of 3D images should match the number of b-orientations. For example, if you do 1 b0 + 12 DWIs, you should see 13 image listed. If these are not correctly read, it could crash the program. If you are not sure about your data, you can always send us the data so that we can take a look. Please contact Zhipeng if you want to do so. Susumu On Thu, Aug 20, 2009 at 1:43 PM, Patrick Rizzuto wrote: > Hi all, > > I am attempting to use the DTIStudio component of MRIStudio in order to > perform the standard tensor calculations on a .dpf file (post > image-registration); however, about a second or so after it asks me about > automatic outlier rejection, the program (in particular, the MFC > application, according to the popup) invariably crashes, citing an exception > at location "0x73ed2659". I have used this same procedure successfully on > four other similar AIR-.dpf files, and yet I cannot avoid this problem on > this particular .dpf file, even after restarting the computer. > > This same .dpf file is unusual in another way. When first loading it in, > it gives me warnings that the (three) .rec file sizes are smaller than the > DW-image size. I occasionally received similar warnings for the other .dpf > files, but these were easily resolved by tinkering with the number of slices > specified in the .dpf file. In this case, though, there does not appear to > be a correct number of slices - while it gives me a message that the .rec > files are small with 52 slices, it also warns me that the .rec files are too > BIG with 51 slices. Let me emphasize that in both cases, the .dpf file > successfully loads if the warnings are dismissed, and the brain images look > normal - a problem is only revealed once I attempt to perform the > calculations. > > The .par files for these .rec files are also different - a few of the > parameters that were mentioned in the other .par files are not specified in > these 3. In particular, there is no mention of the recon. scan resolution > or of the slice thickness. If anyone has any tips on how to resolve this, I > would greatly appreciate it. > > Thanks! > Pat Rizzuto > Johns Hopkins Center for Imaging Science > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090831/ba2974c8/attachment.html From john.migliozzi at gmail.com Mon Aug 31 19:38:43 2009 From: john.migliozzi at gmail.com (John Migliozzi) Date: Mon, 31 Aug 2009 19:38:43 -0400 Subject: [Mristudio-users] Please remove me from the email list In-Reply-To: References: Message-ID: <28A8ED74-3780-49EB-A28A-BC4066D5E5C0@gmail.com> Thanks, John Migliozzi From choisj70 at gmail.com Mon Aug 31 22:24:41 2009 From: choisj70 at gmail.com (Seongjin) Date: Mon, 31 Aug 2009 22:24:41 -0400 Subject: [Mristudio-users] Save after Oblique operation Message-ID: Dear all, I tried to save images after tilted angle correction using Oblique operation. However, after save all the image files, when I read the saved files into ROI Editor or DTI Studio it is remained tilted before oblique operation applied. How I can save the image with tilt correction using oblique operation. Thanks in advance. -SC -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090831/1aa2496c/attachment.html From hjiang at jhmi.edu Tue Sep 1 08:41:58 2009 From: hjiang at jhmi.edu (Hangyi Jiang) Date: Tue, 01 Sep 2009 08:41:58 -0400 Subject: [Mristudio-users] Save after Oblique operation Message-ID: <4A9CDE560200006300024CE4@cis27.hosts.jhmi.edu> after oblique rotation, right-clicking on the 2D view panes, and select "save this image as" command... you can save the image after rotation. if the original image's orientation is in axial, you'd better to right-clicking on the Axial-pane to do so. please beware that the rotated image's dimension is usually different with that of the original. you may need to write down the image parameters after rotation by right-clicking ->"information of this image".... regards, hangyi >>> "[Seongjin]" 08/31/09 10:24 PM >>> Dear all, I tried to save images after tilted angle correction using Oblique operation. However, after save all the image files, when I read the saved files into ROI Editor or DTI Studio it is remained tilted before oblique operation applied. How I can save the image with tilt correction using oblique operation. Thanks in advance. -SC From xli16 at jhmi.edu Tue Sep 1 09:57:01 2009 From: xli16 at jhmi.edu (Xin Li) Date: Tue, 01 Sep 2009 09:57:01 -0400 Subject: [Mristudio-users] Please remove me from the email list In-Reply-To: <28A8ED74-3780-49EB-A28A-BC4066D5E5C0@gmail.com> References: <28A8ED74-3780-49EB-A28A-BC4066D5E5C0@gmail.com> Message-ID: To unsubscribe, please send a blank email to: Mristudio-users-unsubscribe at mristudio.org Xin ----- Original Message ----- From: John Migliozzi Date: Monday, August 31, 2009 7:39 pm Subject: [Mristudio-users] Please remove me from the email list To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > Thanks, > > John Migliozzi > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From shereeda at mail.uc.edu Tue Sep 1 12:20:47 2009 From: shereeda at mail.uc.edu (Shereen, Ahmed (shereeda)) Date: Tue, 01 Sep 2009 16:20:47 +0000 Subject: [Mristudio-users] units? In-Reply-To: References: <73AB8D89B9AABB4FBF603FCC7F345620A3EF@BL2PRD0102MB008.prod.exchangelabs.com> <73AB8D89B9AABB4FBF603FCC7F345620A7A6@BL2PRD0102MB008.prod.exchangelabs.com> Message-ID: <73AB8D89B9AABB4FBF603FCC7F345620A814@BL2PRD0102MB008.prod.exchangelabs.com> Hello, Thank you for your reply. I think I found a quick workaround. The pixels that weren't included belonged to other ROIs. So, I deleted them and when I tried again the original ROI was able to include the pixels that previously overlapped with the ROI I had deleted. However, am I missing something here? I would imagine that I should be able to have multiple ROIs with some overlap? thanks again, Duke ________________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] on behalf of Xin Li [xli16 at jhmi.edu] Sent: Monday, August 31, 2009 9:47 AM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] units? Hello, After you push the Add button, only the contour of the ROI displays. But you said that the number of pixels does not increase from the statistics gui. Could you give me some details about this problem, for example some screenshots and the statitics file? Xin ----- Original Message ----- From: "Shereen, Ahmed (shereeda)" Date: Friday, August 28, 2009 6:52 pm Subject: Re: [Mristudio-users] units? To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > Thank you, > > I have another question. Sometimes when I draw ROIs not all of the > pink pixels become part of the ROI object when I push the (Add(a)) > button. I check the statistics box to double check that it is not > just a visual misplacement. The number of pixels also does not > increase from the statistics gui, although extra pixels were selected > prior to pushing Add(a). > > Any ideas? > Again, thank you, > Duke > ________________________________________ > From: mristudio-users-bounces at mristudio.org > [mristudio-users-bounces at mristudio.org] on behalf of Xin Li [xli16 at jhmi.edu] > Sent: Friday, August 28, 2009 4:14 PM > To: DTI Studio, ROI Editor, Landmarker Questions/Support > Subject: Re: [Mristudio-users] units? > > Hello, > > The current version of ROIEditor reports the statistical result as > four decimal precision. When your eigenvalue data are very small, this > problem happens. You may scale the eigenvalue data before the > statistical caculation. > > Xin > > ----- Original Message ----- > From: "Shereen, Ahmed (shereeda)" > Date: Friday, August 28, 2009 1:26 pm > Subject: [Mristudio-users] units? > To: "mristudio-users at mristudio.org" > > > > Hello, > > I have a problem which I think has to do with the units for the > > eigenvalues calculated in ROIEditor. Basically, when I draw ROIs, > > save them, and then load them into the FA image, everything works > > fine. When I then load the eigenvalue images, the ROIs that gave me > > good FA values give me the same eigenvalues for all ROIs. I'm > > attaching the ROI data file. Has anybody seen anything like this? > > Thank you, > > Duke > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From susumu at mri.jhu.edu Tue Sep 1 13:10:35 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Tue, 01 Sep 2009 13:10:35 -0400 Subject: [Mristudio-users] units? In-Reply-To: <73AB8D89B9AABB4FBF603FCC7F345620A814@BL2PRD0102MB008.prod.exchangelabs.com> References: <73AB8D89B9AABB4FBF603FCC7F345620A3EF@BL2PRD0102MB008.prod.exchangelabs.com> <73AB8D89B9AABB4FBF603FCC7F345620A7A6@BL2PRD0102MB008.prod.exchangelabs.com> <73AB8D89B9AABB4FBF603FCC7F345620A814@BL2PRD0102MB008.prod.exchangelabs.com> Message-ID: Hi Duke, I'm not sure if this answers your question, but there is an interpolation issue. When a line is drawn for manual ROI, the line could be narrower or larger than a pixel, depending on the choice of "pen width". When the software convert it to the pixel-by-pixel binary information, it has to judge which pixel to include. For example, if the center of the line is at a pixel coordinate 1.5, it has to judge if ROI is only up to pixel 1 or 2. If 1 is chosen, the selected pixels always look shifted to the left. Do you think your issue is related to this? On Tue, Sep 1, 2009 at 12:20 PM, Shereen, Ahmed (shereeda) < shereeda at mail.uc.edu> wrote: > Hello, > Thank you for your reply. I think I found a quick workaround. The pixels > that weren't included belonged to other ROIs. So, I deleted them and when I > tried again the original ROI was able to include the pixels that previously > overlapped with the ROI I had deleted. However, am I missing something > here? I would imagine that I should be able to have multiple ROIs with some > overlap? > thanks again, > Duke > ________________________________________ > From: mristudio-users-bounces at mristudio.org [ > mristudio-users-bounces at mristudio.org] on behalf of Xin Li [xli16 at jhmi.edu > ] > Sent: Monday, August 31, 2009 9:47 AM > To: DTI Studio, ROI Editor, Landmarker Questions/Support > Subject: Re: [Mristudio-users] units? > > Hello, > > After you push the Add button, only the contour of the ROI displays. > > But you said that the number of pixels does not increase from the > statistics gui. Could you give me some details about this problem, for > example some screenshots and the statitics file? > > > Xin > > > ----- Original Message ----- > From: "Shereen, Ahmed (shereeda)" > Date: Friday, August 28, 2009 6:52 pm > Subject: Re: [Mristudio-users] units? > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" < > mristudio-users at mristudio.org> > > > > Thank you, > > > > I have another question. Sometimes when I draw ROIs not all of the > > pink pixels become part of the ROI object when I push the (Add(a)) > > button. I check the statistics box to double check that it is not > > just a visual misplacement. The number of pixels also does not > > increase from the statistics gui, although extra pixels were selected > > prior to pushing Add(a). > > > > Any ideas? > > Again, thank you, > > Duke > > ________________________________________ > > From: mristudio-users-bounces at mristudio.org > > [mristudio-users-bounces at mristudio.org] on behalf of Xin Li [ > xli16 at jhmi.edu] > > Sent: Friday, August 28, 2009 4:14 PM > > To: DTI Studio, ROI Editor, Landmarker Questions/Support > > Subject: Re: [Mristudio-users] units? > > > > Hello, > > > > The current version of ROIEditor reports the statistical result as > > four decimal precision. When your eigenvalue data are very small, this > > problem happens. You may scale the eigenvalue data before the > > statistical caculation. > > > > Xin > > > > ----- Original Message ----- > > From: "Shereen, Ahmed (shereeda)" > > Date: Friday, August 28, 2009 1:26 pm > > Subject: [Mristudio-users] units? > > To: "mristudio-users at mristudio.org" > > > > > > > Hello, > > > I have a problem which I think has to do with the units for the > > > eigenvalues calculated in ROIEditor. Basically, when I draw ROIs, > > > save them, and then load them into the FA image, everything works > > > fine. When I then load the eigenvalue images, the ROIs that gave me > > > good FA values give me the same eigenvalues for all ROIs. I'm > > > attaching the ROI data file. Has anybody seen anything like this? > > > Thank you, > > > Duke > > > _______________________________________________ > > > Mristudio-users mailing list > > > Mristudio-users at mristudio.org > > > > > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090901/6cce2bac/attachment-0001.html From xli16 at jhmi.edu Tue Sep 1 13:59:26 2009 From: xli16 at jhmi.edu (Xin Li) Date: Tue, 01 Sep 2009 13:59:26 -0400 Subject: [Mristudio-users] units? In-Reply-To: <73AB8D89B9AABB4FBF603FCC7F345620A814@BL2PRD0102MB008.prod.exchangelabs.com> References: <73AB8D89B9AABB4FBF603FCC7F345620A3EF@BL2PRD0102MB008.prod.exchangelabs.com> <73AB8D89B9AABB4FBF603FCC7F345620A7A6@BL2PRD0102MB008.prod.exchangelabs.com> <73AB8D89B9AABB4FBF603FCC7F345620A814@BL2PRD0102MB008.prod.exchangelabs.com> Message-ID: Hello Duke, In ROIEditor, one voxel can only belong to one ROI object. Any overlaps are not allowed in ROIEditor. So you have to delete the previous ROI objects if you want to add some pixels in them to another ROI object. Xin ----- Original Message ----- From: "Shereen, Ahmed (shereeda)" Date: Tuesday, September 1, 2009 12:23 pm Subject: Re: [Mristudio-users] units? To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > Hello, > Thank you for your reply. I think I found a quick workaround. The > pixels that weren't included belonged to other ROIs. So, I deleted > them and when I tried again the original ROI was able to include the > pixels that previously overlapped with the ROI I had deleted. > However, am I missing something here? I would imagine that I should > be able to have multiple ROIs with some overlap? > thanks again, > Duke > ________________________________________ > From: mristudio-users-bounces at mristudio.org > [mristudio-users-bounces at mristudio.org] on behalf of Xin Li [xli16 at jhmi.edu] > Sent: Monday, August 31, 2009 9:47 AM > To: DTI Studio, ROI Editor, Landmarker Questions/Support > Subject: Re: [Mristudio-users] units? > > Hello, > > After you push the Add button, only the contour of the ROI displays. > > But you said that the number of pixels does not increase from the > statistics gui. Could you give me some details about this problem, for > example some screenshots and the statitics file? > > > Xin > > > ----- Original Message ----- > From: "Shereen, Ahmed (shereeda)" > Date: Friday, August 28, 2009 6:52 pm > Subject: Re: [Mristudio-users] units? > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > > > > Thank you, > > > > I have another question. Sometimes when I draw ROIs not all of the > > pink pixels become part of the ROI object when I push the (Add(a)) > > button. I check the statistics box to double check that it is not > > just a visual misplacement. The number of pixels also does not > > increase from the statistics gui, although extra pixels were selected > > prior to pushing Add(a). > > > > Any ideas? > > Again, thank you, > > Duke > > ________________________________________ > > From: mristudio-users-bounces at mristudio.org > > [mristudio-users-bounces at mristudio.org] on behalf of Xin Li [xli16 at jhmi.edu] > > Sent: Friday, August 28, 2009 4:14 PM > > To: DTI Studio, ROI Editor, Landmarker Questions/Support > > Subject: Re: [Mristudio-users] units? > > > > Hello, > > > > The current version of ROIEditor reports the statistical result as > > four decimal precision. When your eigenvalue data are very small, this > > problem happens. You may scale the eigenvalue data before the > > statistical caculation. > > > > Xin > > > > ----- Original Message ----- > > From: "Shereen, Ahmed (shereeda)" > > Date: Friday, August 28, 2009 1:26 pm > > Subject: [Mristudio-users] units? > > To: "mristudio-users at mristudio.org" > > > > > > > Hello, > > > I have a problem which I think has to do with the units for the > > > eigenvalues calculated in ROIEditor. Basically, when I draw ROIs, > > > save them, and then load them into the FA image, everything works > > > fine. When I then load the eigenvalue images, the ROIs that > gave me > > > good FA values give me the same eigenvalues for all ROIs. I'm > > > attaching the ROI data file. Has anybody seen anything like this? > > > Thank you, > > > Duke > > > _______________________________________________ > > > Mristudio-users mailing list > > > Mristudio-users at mristudio.org > > > > > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From xli16 at jhmi.edu Tue Sep 1 14:19:26 2009 From: xli16 at jhmi.edu (Xin Li) Date: Tue, 01 Sep 2009 14:19:26 -0400 Subject: [Mristudio-users] units? In-Reply-To: References: <73AB8D89B9AABB4FBF603FCC7F345620A3EF@BL2PRD0102MB008.prod.exchangelabs.com> <73AB8D89B9AABB4FBF603FCC7F345620A7A6@BL2PRD0102MB008.prod.exchangelabs.com> <73AB8D89B9AABB4FBF603FCC7F345620A814@BL2PRD0102MB008.prod.exchangelabs.com> Message-ID: Sorry, what I said in the previous email, "So you have to delete the previous ROI objects if you want to add some pixels in them to another ROI object.", actually is not right. When you push the "Add" button, the pixels always belong to the hightlighted ROI object no matter if they already belong to some ROI object. If you don't want to change a ROI object, you can fix it by righ clicking the ROI object and selecting "Fix". Xin ----- Original Message ----- From: Xin Li Date: Tuesday, September 1, 2009 1:59 pm Subject: Re: [Mristudio-users] units? To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > Hello Duke, > > In ROIEditor, one voxel can only belong to one ROI object. Any > overlaps are not allowed in ROIEditor. So you have to delete the > previous ROI objects if you want to add some pixels in them to another > ROI object. > > > Xin > > > > ----- Original Message ----- > From: "Shereen, Ahmed (shereeda)" > Date: Tuesday, September 1, 2009 12:23 pm > Subject: Re: [Mristudio-users] units? > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > > > > Hello, > > Thank you for your reply. I think I found a quick workaround. > The > > pixels that weren't included belonged to other ROIs. So, I deleted > > > them and when I tried again the original ROI was able to include > the > > pixels that previously overlapped with the ROI I had deleted. > > However, am I missing something here? I would imagine that I > should > > be able to have multiple ROIs with some overlap? > > thanks again, > > Duke > > ________________________________________ > > From: mristudio-users-bounces at mristudio.org > > [mristudio-users-bounces at mristudio.org] on behalf of Xin Li [xli16 at jhmi.edu] > > Sent: Monday, August 31, 2009 9:47 AM > > To: DTI Studio, ROI Editor, Landmarker Questions/Support > > Subject: Re: [Mristudio-users] units? > > > > Hello, > > > > After you push the Add button, only the contour of the ROI displays. > > > > But you said that the number of pixels does not increase from the > > > statistics gui. Could you give me some details about this problem, > for > > example some screenshots and the statitics file? > > > > > > Xin > > > > > > ----- Original Message ----- > > From: "Shereen, Ahmed (shereeda)" > > Date: Friday, August 28, 2009 6:52 pm > > Subject: Re: [Mristudio-users] units? > > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > > > > > > > Thank you, > > > > > > I have another question. Sometimes when I draw ROIs not all of > the > > > pink pixels become part of the ROI object when I push the (Add(a)) > > > button. I check the statistics box to double check that it is not > > > just a visual misplacement. The number of pixels also does not > > > increase from the statistics gui, although extra pixels were selected > > > prior to pushing Add(a). > > > > > > Any ideas? > > > Again, thank you, > > > Duke > > > ________________________________________ > > > From: mristudio-users-bounces at mristudio.org > > > [mristudio-users-bounces at mristudio.org] on behalf of Xin Li [xli16 at jhmi.edu] > > > Sent: Friday, August 28, 2009 4:14 PM > > > To: DTI Studio, ROI Editor, Landmarker Questions/Support > > > Subject: Re: [Mristudio-users] units? > > > > > > Hello, > > > > > > The current version of ROIEditor reports the statistical result > as > > > four decimal precision. When your eigenvalue data are very > small, this > > > problem happens. You may scale the eigenvalue data before the > > > statistical caculation. > > > > > > Xin > > > > > > ----- Original Message ----- > > > From: "Shereen, Ahmed (shereeda)" > > > Date: Friday, August 28, 2009 1:26 pm > > > Subject: [Mristudio-users] units? > > > To: "mristudio-users at mristudio.org" > > > > > > > > > > Hello, > > > > I have a problem which I think has to do with the units for > the > > > > eigenvalues calculated in ROIEditor. Basically, when I draw > ROIs, > > > > save them, and then load them into the FA image, everything works > > > > fine. When I then load the eigenvalue images, the ROIs that > > > gave me > > > > good FA values give me the same eigenvalues for all ROIs. I'm > > > > attaching the ROI data file. Has anybody seen anything like > this? > > > > Thank you, > > > > Duke > > > > _______________________________________________ > > > > Mristudio-users mailing list > > > > Mristudio-users at mristudio.org > > > > > > > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > > > _______________________________________________ > > > Mristudio-users mailing list > > > Mristudio-users at mristudio.org > > > > > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > > > > > > _______________________________________________ > > > Mristudio-users mailing list > > > Mristudio-users at mristudio.org > > > > > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From shereeda at mail.uc.edu Tue Sep 1 14:49:04 2009 From: shereeda at mail.uc.edu (Shereen, Ahmed (shereeda)) Date: Tue, 01 Sep 2009 18:49:04 +0000 Subject: [Mristudio-users] units? In-Reply-To: References: <73AB8D89B9AABB4FBF603FCC7F345620A3EF@BL2PRD0102MB008.prod.exchangelabs.com> <73AB8D89B9AABB4FBF603FCC7F345620A7A6@BL2PRD0102MB008.prod.exchangelabs.com> <73AB8D89B9AABB4FBF603FCC7F345620A814@BL2PRD0102MB008.prod.exchangelabs.com> Message-ID: <73AB8D89B9AABB4FBF603FCC7F345620ABA6@BL2PRD0102MB008.prod.exchangelabs.com> Hi, I'm familiar with the interpolation issue. I think this is a separate problem. It occurs despite which ROI drawing tool I use (I tried all of them to see if it makes a difference). Essentially, with two or more ROIs, if an attempt is made to draw an ROI that overlaps with a previous one, then those pixels that overlap are excluded from the newest ROI. I imagine the problem lay with me, since this would be obvous to most users? Please let me know if I should send some data to demonstrate what I mean. Thank you, Duke ________________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] on behalf of susumu mori [susumu at mri.jhu.edu] Sent: Tuesday, September 01, 2009 1:10 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] units? Hi Duke, I'm not sure if this answers your question, but there is an interpolation issue. When a line is drawn for manual ROI, the line could be narrower or larger than a pixel, depending on the choice of "pen width". When the software convert it to the pixel-by-pixel binary information, it has to judge which pixel to include. For example, if the center of the line is at a pixel coordinate 1.5, it has to judge if ROI is only up to pixel 1 or 2. If 1 is chosen, the selected pixels always look shifted to the left. Do you think your issue is related to this? On Tue, Sep 1, 2009 at 12:20 PM, Shereen, Ahmed (shereeda) > wrote: Hello, Thank you for your reply. I think I found a quick workaround. The pixels that weren't included belonged to other ROIs. So, I deleted them and when I tried again the original ROI was able to include the pixels that previously overlapped with the ROI I had deleted. However, am I missing something here? I would imagine that I should be able to have multiple ROIs with some overlap? thanks again, Duke ________________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] on behalf of Xin Li [xli16 at jhmi.edu] Sent: Monday, August 31, 2009 9:47 AM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] units? Hello, After you push the Add button, only the contour of the ROI displays. But you said that the number of pixels does not increase from the statistics gui. Could you give me some details about this problem, for example some screenshots and the statitics file? Xin ----- Original Message ----- From: "Shereen, Ahmed (shereeda)" > Date: Friday, August 28, 2009 6:52 pm Subject: Re: [Mristudio-users] units? To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > > Thank you, > > I have another question. Sometimes when I draw ROIs not all of the > pink pixels become part of the ROI object when I push the (Add(a)) > button. I check the statistics box to double check that it is not > just a visual misplacement. The number of pixels also does not > increase from the statistics gui, although extra pixels were selected > prior to pushing Add(a). > > Any ideas? > Again, thank you, > Duke > ________________________________________ > From: mristudio-users-bounces at mristudio.org > [mristudio-users-bounces at mristudio.org] on behalf of Xin Li [xli16 at jhmi.edu] > Sent: Friday, August 28, 2009 4:14 PM > To: DTI Studio, ROI Editor, Landmarker Questions/Support > Subject: Re: [Mristudio-users] units? > > Hello, > > The current version of ROIEditor reports the statistical result as > four decimal precision. When your eigenvalue data are very small, this > problem happens. You may scale the eigenvalue data before the > statistical caculation. > > Xin > > ----- Original Message ----- > From: "Shereen, Ahmed (shereeda)" > > Date: Friday, August 28, 2009 1:26 pm > Subject: [Mristudio-users] units? > To: "mristudio-users at mristudio.org" > > > > > Hello, > > I have a problem which I think has to do with the units for the > > eigenvalues calculated in ROIEditor. Basically, when I draw ROIs, > > save them, and then load them into the FA image, everything works > > fine. When I then load the eigenvalue images, the ROIs that gave me > > good FA values give me the same eigenvalues for all ROIs. I'm > > attaching the ROI data file. Has anybody seen anything like this? > > Thank you, > > Duke > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From shereeda at mail.uc.edu Tue Sep 1 14:54:38 2009 From: shereeda at mail.uc.edu (Shereen, Ahmed (shereeda)) Date: Tue, 01 Sep 2009 18:54:38 +0000 Subject: [Mristudio-users] units? In-Reply-To: References: <73AB8D89B9AABB4FBF603FCC7F345620A3EF@BL2PRD0102MB008.prod.exchangelabs.com> <73AB8D89B9AABB4FBF603FCC7F345620A7A6@BL2PRD0102MB008.prod.exchangelabs.com> <73AB8D89B9AABB4FBF603FCC7F345620A814@BL2PRD0102MB008.prod.exchangelabs.com> Message-ID: <73AB8D89B9AABB4FBF603FCC7F345620ABB9@BL2PRD0102MB008.prod.exchangelabs.com> I'm not sure what you mean. So, if I don't have "Fix" selected and "Add" pixels that belonged to previous ROI object to a new ROI object, then those pixels will belong to the new ROI object but not the previous? Unless of course "Fix" is selected for all ROIs in which case the pixels won't transfer to the newer ROI? ________________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] on behalf of Xin Li [xli16 at jhmi.edu] Sent: Tuesday, September 01, 2009 2:19 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] units? Sorry, what I said in the previous email, "So you have to delete the previous ROI objects if you want to add some pixels in them to another ROI object.", actually is not right. When you push the "Add" button, the pixels always belong to the hightlighted ROI object no matter if they already belong to some ROI object. If you don't want to change a ROI object, you can fix it by righ clicking the ROI object and selecting "Fix". Xin ----- Original Message ----- From: Xin Li Date: Tuesday, September 1, 2009 1:59 pm Subject: Re: [Mristudio-users] units? To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > Hello Duke, > > In ROIEditor, one voxel can only belong to one ROI object. Any > overlaps are not allowed in ROIEditor. So you have to delete the > previous ROI objects if you want to add some pixels in them to another > ROI object. > > > Xin > > > > ----- Original Message ----- > From: "Shereen, Ahmed (shereeda)" > Date: Tuesday, September 1, 2009 12:23 pm > Subject: Re: [Mristudio-users] units? > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > > > > Hello, > > Thank you for your reply. I think I found a quick workaround. > The > > pixels that weren't included belonged to other ROIs. So, I deleted > > > them and when I tried again the original ROI was able to include > the > > pixels that previously overlapped with the ROI I had deleted. > > However, am I missing something here? I would imagine that I > should > > be able to have multiple ROIs with some overlap? > > thanks again, > > Duke > > ________________________________________ > > From: mristudio-users-bounces at mristudio.org > > [mristudio-users-bounces at mristudio.org] on behalf of Xin Li [xli16 at jhmi.edu] > > Sent: Monday, August 31, 2009 9:47 AM > > To: DTI Studio, ROI Editor, Landmarker Questions/Support > > Subject: Re: [Mristudio-users] units? > > > > Hello, > > > > After you push the Add button, only the contour of the ROI displays. > > > > But you said that the number of pixels does not increase from the > > > statistics gui. Could you give me some details about this problem, > for > > example some screenshots and the statitics file? > > > > > > Xin > > > > > > ----- Original Message ----- > > From: "Shereen, Ahmed (shereeda)" > > Date: Friday, August 28, 2009 6:52 pm > > Subject: Re: [Mristudio-users] units? > > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > > > > > > > Thank you, > > > > > > I have another question. Sometimes when I draw ROIs not all of > the > > > pink pixels become part of the ROI object when I push the (Add(a)) > > > button. I check the statistics box to double check that it is not > > > just a visual misplacement. The number of pixels also does not > > > increase from the statistics gui, although extra pixels were selected > > > prior to pushing Add(a). > > > > > > Any ideas? > > > Again, thank you, > > > Duke > > > ________________________________________ > > > From: mristudio-users-bounces at mristudio.org > > > [mristudio-users-bounces at mristudio.org] on behalf of Xin Li [xli16 at jhmi.edu] > > > Sent: Friday, August 28, 2009 4:14 PM > > > To: DTI Studio, ROI Editor, Landmarker Questions/Support > > > Subject: Re: [Mristudio-users] units? > > > > > > Hello, > > > > > > The current version of ROIEditor reports the statistical result > as > > > four decimal precision. When your eigenvalue data are very > small, this > > > problem happens. You may scale the eigenvalue data before the > > > statistical caculation. > > > > > > Xin > > > > > > ----- Original Message ----- > > > From: "Shereen, Ahmed (shereeda)" > > > Date: Friday, August 28, 2009 1:26 pm > > > Subject: [Mristudio-users] units? > > > To: "mristudio-users at mristudio.org" > > > > > > > > > > Hello, > > > > I have a problem which I think has to do with the units for > the > > > > eigenvalues calculated in ROIEditor. Basically, when I draw > ROIs, > > > > save them, and then load them into the FA image, everything works > > > > fine. When I then load the eigenvalue images, the ROIs that > > > gave me > > > > good FA values give me the same eigenvalues for all ROIs. I'm > > > > attaching the ROI data file. Has anybody seen anything like > this? > > > > Thank you, > > > > Duke > > > > _______________________________________________ > > > > Mristudio-users mailing list > > > > Mristudio-users at mristudio.org > > > > > > > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > > > _______________________________________________ > > > Mristudio-users mailing list > > > Mristudio-users at mristudio.org > > > > > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > > > > > > _______________________________________________ > > > Mristudio-users mailing list > > > Mristudio-users at mristudio.org > > > > > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From susumu at mri.jhu.edu Tue Sep 1 15:01:43 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Tue, 01 Sep 2009 15:01:43 -0400 Subject: [Mristudio-users] units? In-Reply-To: <73AB8D89B9AABB4FBF603FCC7F345620ABA6@BL2PRD0102MB008.prod.exchangelabs.com> References: <73AB8D89B9AABB4FBF603FCC7F345620A3EF@BL2PRD0102MB008.prod.exchangelabs.com> <73AB8D89B9AABB4FBF603FCC7F345620A7A6@BL2PRD0102MB008.prod.exchangelabs.com> <73AB8D89B9AABB4FBF603FCC7F345620A814@BL2PRD0102MB008.prod.exchangelabs.com> <73AB8D89B9AABB4FBF603FCC7F345620ABA6@BL2PRD0102MB008.prod.exchangelabs.com> Message-ID: As Xin mentioned, RoiEditor doesn't allow "double labeling". If you define a first ROI. Then if you draw a second ROI that contains a part of the first ROI, the second ROI "eats" that portion of the first ROI. If you choose the "fix" option of the first ROI, then the first ROI pixels are protected and the overlapped portion of your second ROI will be ignored. Does it explain? On Tue, Sep 1, 2009 at 2:49 PM, Shereen, Ahmed (shereeda) < shereeda at mail.uc.edu> wrote: > Hi, > I'm familiar with the interpolation issue. I think this is a separate > problem. It occurs despite which ROI drawing tool I use (I tried all of > them to see if it makes a difference). Essentially, with two or more ROIs, > if an attempt is made to draw an ROI that overlaps with a previous one, then > those pixels that overlap are excluded from the newest ROI. I imagine the > problem lay with me, since this would be obvous to most users? > Please let me know if I should send some data to demonstrate what I mean. > Thank you, > Duke > ________________________________________ > From: mristudio-users-bounces at mristudio.org [ > mristudio-users-bounces at mristudio.org] on behalf of susumu mori [ > susumu at mri.jhu.edu] > Sent: Tuesday, September 01, 2009 1:10 PM > To: DTI Studio, ROI Editor, Landmarker Questions/Support > Subject: Re: [Mristudio-users] units? > > Hi Duke, > > I'm not sure if this answers your question, but there is an interpolation > issue. When a line is drawn for manual ROI, the line could be narrower or > larger than a pixel, depending on the choice of "pen width". When the > software convert it to the pixel-by-pixel binary information, it has to > judge which pixel to include. For example, if the center of the line is at a > pixel coordinate 1.5, it has to judge if ROI is only up to pixel 1 or 2. If > 1 is chosen, the selected pixels always look shifted to the left. Do you > think your issue is related to this? > > On Tue, Sep 1, 2009 at 12:20 PM, Shereen, Ahmed (shereeda) < > shereeda at mail.uc.edu> wrote: > Hello, > Thank you for your reply. I think I found a quick workaround. The pixels > that weren't included belonged to other ROIs. So, I deleted them and when I > tried again the original ROI was able to include the pixels that previously > overlapped with the ROI I had deleted. However, am I missing something > here? I would imagine that I should be able to have multiple ROIs with some > overlap? > thanks again, > Duke > ________________________________________ > From: mristudio-users-bounces at mristudio.org mristudio-users-bounces at mristudio.org> [ > mristudio-users-bounces at mristudio.org mristudio-users-bounces at mristudio.org>] on behalf of Xin Li [ > xli16 at jhmi.edu] > Sent: Monday, August 31, 2009 9:47 AM > To: DTI Studio, ROI Editor, Landmarker Questions/Support > Subject: Re: [Mristudio-users] units? > > Hello, > > After you push the Add button, only the contour of the ROI displays. > > But you said that the number of pixels does not increase from the > statistics gui. Could you give me some details about this problem, for > example some screenshots and the statitics file? > > > Xin > > > ----- Original Message ----- > From: "Shereen, Ahmed (shereeda)" shereeda at mail.uc.edu>> > Date: Friday, August 28, 2009 6:52 pm > Subject: Re: [Mristudio-users] units? > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" < > mristudio-users at mristudio.org> > > > > Thank you, > > > > I have another question. Sometimes when I draw ROIs not all of the > > pink pixels become part of the ROI object when I push the (Add(a)) > > button. I check the statistics box to double check that it is not > > just a visual misplacement. The number of pixels also does not > > increase from the statistics gui, although extra pixels were selected > > prior to pushing Add(a). > > > > Any ideas? > > Again, thank you, > > Duke > > ________________________________________ > > From: mristudio-users-bounces at mristudio.org mristudio-users-bounces at mristudio.org> > > [mristudio-users-bounces at mristudio.org mristudio-users-bounces at mristudio.org>] on behalf of Xin Li [ > xli16 at jhmi.edu] > > Sent: Friday, August 28, 2009 4:14 PM > > To: DTI Studio, ROI Editor, Landmarker Questions/Support > > Subject: Re: [Mristudio-users] units? > > > > Hello, > > > > The current version of ROIEditor reports the statistical result as > > four decimal precision. When your eigenvalue data are very small, this > > problem happens. You may scale the eigenvalue data before the > > statistical caculation. > > > > Xin > > > > ----- Original Message ----- > > From: "Shereen, Ahmed (shereeda)" shereeda at mail.uc.edu>> > > Date: Friday, August 28, 2009 1:26 pm > > Subject: [Mristudio-users] units? > > To: "mristudio-users at mristudio.org" > > > > > > > > > Hello, > > > I have a problem which I think has to do with the units for the > > > eigenvalues calculated in ROIEditor. Basically, when I draw ROIs, > > > save them, and then load them into the FA image, everything works > > > fine. When I then load the eigenvalue images, the ROIs that gave me > > > good FA values give me the same eigenvalues for all ROIs. I'm > > > attaching the ROI data file. Has anybody seen anything like this? > > > Thank you, > > > Duke > > > _______________________________________________ > > > Mristudio-users mailing list > > > Mristudio-users at mristudio.org > > > > > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org Mristudio-users-unsubscribe at mristudio.org> > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org Mristudio-users-unsubscribe at mristudio.org> > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org Mristudio-users-unsubscribe at mristudio.org> > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org Mristudio-users-unsubscribe at mristudio.org> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org Mristudio-users-unsubscribe at mristudio.org> > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090901/33370c37/attachment.html From susumu at mri.jhu.edu Tue Sep 1 20:52:31 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Tue, 01 Sep 2009 20:52:31 -0400 Subject: [Mristudio-users] NifTi and DTI Studio In-Reply-To: <77A88E90A851594AAEF830450587C39D01EDAAF8@CCHSCLEXMB56.cc.ad.cchs.net> References: <772396.37050.qm@web50512.mail.re2.yahoo.com> <39c428d80908260922p6e857432k4f1d6a52311eda65@mail.gmail.com> <77A88E90A851594AAEF830450587C39D01EDAAF7@CCHSCLEXMB56.cc.ad.cchs.net> <77A88E90A851594AAEF830450587C39D01EDAAF8@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: > > > > Thanks for this information i also thought about this, but one question > prevented me from doing this, i would like to clarify that with you, after > distortion correction especially the voxels in frontal regions of the brain > like corpus callosum ( i am not good in anatomy sorry apologize me if i am > wrong) are streched or in other words restored to their original positions, > so i am wondering whether this kind of voxel stretching and squeezing > (undistorted) will contribute to any additional changes in b-matrix when > compared to the changes in b-mtarix contributed by the original i.e > distorted images. I understand that b-matrix rotation i calculated from the > rotation matrix of the main affine matrix, i don't know whether the affine > matrix will be different between before and after distortion correction > images. I am sorry if i am not clear. > > > This is a good point. In a short answer, I believe that you don't have to worry about b-table or tensor reorientation for B0 distortion correction. Here is why; > For DWI, we first apply diffusion weighting along one axis, for example, along X axis (b = [1, 0, 0]). Then we apply imaging gradient to obtain an image; a circle object should look circle. During the data acquisition, B0 susceptibility influences the acquisition and brain signal intensity is "mislocated"; the circle object may look oval now.Important thing is, the diffusion weighting scheme and the imaging scheme are two separate process. B0 correction simply correct this mis-registered signal to the right place; the oval is corrected to a circle. For example, suppose you have two pixels side-by-side and a fiber is running along the right-left connecting the two pixels. If you apply [1, 0, 0] gradient (=x axis), both pixels look dark. If gradient is [0, 1, 0], they look bright. Tensor calculation tells that the fibers are running horizontally connecting the two pixels. Then if B0 distortion misplaces the right pixel shifted upward and now they are located at 45 degree each other. The tensor calculation still tells that the fiber is running holizontally. In this case, we want to move the right pixel shifted downward without touching the tensor calculation; now they are side-by-side and connected by the fiber. If you apply b-table rotation or tensor re-orientation, by the time the two pixels are aligned side-by-side, the fiber angles are rotated 45 degree running diagonally, which you don't want. I hope this makes sense. > When you are dealing with mis-registration by patient motion, it is a very different story. Suppose we run two DTI set. In the first set, the brain is upright when [1,0,0] gradient is applied and in the second set, the brain is 5 degree tilted and the same [1, 0, 0] is applied. Then we co-register these two images by rotating the second set by -5 degree. In this case, you have to rotate the second [1, 0, 0] b weighting by -5 degree to keep the consistency between the two sets. I think this is understandable. > Like wise, if you are trying to normalize two brains; say one is circle and the other is oval. In this case, when pixels are shifted to make the oval to the circle, you have to re-orient the b-table > When an object shape is transformed, you can either reorient the b-table before the tensor calculation or do the tensor calculation first and then rotate the tensor. They may provide slightly different results. Therefore, you'd better pick one of the methods and stick to it. I hope this helps. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090901/dc9ae589/attachment-0001.html From choisj70 at gmail.com Tue Sep 1 20:56:38 2009 From: choisj70 at gmail.com (Seongjin) Date: Tue, 01 Sep 2009 20:56:38 -0400 Subject: [Mristudio-users] Save after Oblique operation In-Reply-To: <4A9CDE560200006300024CE4@cis27.hosts.jhmi.edu> References: <4A9CDE560200006300024CE4@cis27.hosts.jhmi.edu> Message-ID: Thanks a lot! -SC On Tue, Sep 1, 2009 at 8:41 AM, Hangyi Jiang wrote: > after oblique rotation, right-clicking on the 2D view panes, and select > "save this image as" command... you can save the image after rotation. if > the original image's orientation is in axial, you'd better to right-clicking > on the Axial-pane to do so. > > please beware that the rotated image's dimension is usually different with > that of the original. you may need to write down the image parameters after > rotation by right-clicking ->"information of this image".... > > regards, > > hangyi > > > > > >>> "[Seongjin]" 08/31/09 10:24 PM >>> > Dear all, > > I tried to save images after tilted angle correction using Oblique > operation. > However, after save all the image files, when I read the saved files into > ROI Editor or DTI Studio it is remained tilted before oblique operation > applied. > How I can save the image with tilt correction using oblique operation. > > Thanks in advance. > > -SC > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090901/1bfca003/attachment.html From rajagov2 at ccf.org Wed Sep 2 10:46:17 2009 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Wed, 02 Sep 2009 10:46:17 -0400 Subject: [Mristudio-users] NifTi and DTI Studio References: <772396.37050.qm@web50512.mail.re2.yahoo.com> <39c428d80908260922p6e857432k4f1d6a52311eda65@mail.gmail.com> <77A88E90A851594AAEF830450587C39D01EDAAF7@CCHSCLEXMB56.cc.ad.cchs.net> <77A88E90A851594AAEF830450587C39D01EDAAF8@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: <77A88E90A851594AAEF830450587C39D01EDAB0A@CCHSCLEXMB56.cc.ad.cchs.net> Thanks very much Dr.Mori, beautiful explanation. Thanks again, venkateswaran ________________________________ From: mristudio-users-bounces at mristudio.org on behalf of susumu mori Sent: Tue 9/1/2009 8:52 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] NifTi and DTI Studio Thanks for this information i also thought about this, but one question prevented me from doing this, i would like to clarify that with you, after distortion correction especially the voxels in frontal regions of the brain like corpus callosum ( i am not good in anatomy sorry apologize me if i am wrong) are streched or in other words restored to their original positions, so i am wondering whether this kind of voxel stretching and squeezing (undistorted) will contribute to any additional changes in b-matrix when compared to the changes in b-mtarix contributed by the original i.e distorted images. I understand that b-matrix rotation i calculated from the rotation matrix of the main affine matrix, i don't know whether the affine matrix will be different between before and after distortion correction images. I am sorry if i am not clear. This is a good point. In a short answer, I believe that you don't have to worry about b-table or tensor reorientation for B0 distortion correction. Here is why; > For DWI, we first apply diffusion weighting along one axis, for example, along X axis (b = [1, 0, 0]). Then we apply imaging gradient to obtain an image; a circle object should look circle. During the data acquisition, B0 susceptibility influences the acquisition and brain signal intensity is "mislocated"; the circle object may look oval now.Important thing is, the diffusion weighting scheme and the imaging scheme are two separate process. B0 correction simply correct this mis-registered signal to the right place; the oval is corrected to a circle. For example, suppose you have two pixels side-by-side and a fiber is running along the right-left connecting the two pixels. If you apply [1, 0, 0] gradient (=x axis), both pixels look dark. If gradient is [0, 1, 0], they look bright. Tensor calculation tells that the fibers are running horizontally connecting the two pixels. Then if B0 distortion misplaces the right pixel shifted upward and now they are located at 45 degree each other. The tensor calculation still tells that the fiber is running holizontally. In this case, we want to move the right pixel shifted downward without touching the tensor calculation; now they are side-by-side and connected by the fiber. If you apply b-table rotation or tensor re-orientation, by the time the two pixels are aligned side-by-side, the fiber angles are rotated 45 degree running diagonally, which you don't want. I hope this makes sense. > When you are dealing with mis-registration by patient motion, it is a very different story. Suppose we run two DTI set. In the first set, the brain is upright when [1,0,0] gradient is applied and in the second set, the brain is 5 degree tilted and the same [1, 0, 0] is applied. Then we co-register these two images by rotating the second set by -5 degree. In this case, you have to rotate the second [1, 0, 0] b weighting by -5 degree to keep the consistency between the two sets. I think this is understandable. > Like wise, if you are trying to normalize two brains; say one is circle and the other is oval. In this case, when pixels are shifted to make the oval to the circle, you have to re-orient the b-table > When an object shape is transformed, you can either reorient the b-table before the tensor calculation or do the tensor calculation first and then rotate the tensor. They may provide slightly different results. Therefore, you'd better pick one of the methods and stick to it. I hope this helps. =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S. News & World Report (2008). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 6299 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090902/b4d484b1/attachment.bin From susumu at mri.jhu.edu Wed Sep 9 11:26:29 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 09 Sep 2009 11:26:29 -0400 Subject: [Mristudio-users] (no subject) In-Reply-To: <66073DDBA72FF542AAA13469EF91E79E04D54163@ex1-777peds.peds.uab.edu> References: <66073DDBA72FF542AAA13469EF91E79E04D54163@ex1-777peds.peds.uab.edu> Message-ID: Hi Hyumi, Sorry if I haven't responded to your question. Here I attached a GE table. I hope GE hasn't changed their tables recently. If it doesn't work, please let us know. For some orientations, including the 25, I changed the format to that of DtiStudio, so that you can directly cut & paste to DtiStudio. Susumu On Thu, Jul 2, 2009 at 12:29 PM, Hyunmi Kim, M.D. wrote: > Dear all; > > > > Do you have a standard 25 direction GE gradient table? > > Please share with me. > > Thank you, > > Hyunmi > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090909/097cc853/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: Diffusion_directions_VB15.doc Type: application/msword Size: 73216 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090909/097cc853/attachment-0001.doc From choisj70 at gmail.com Wed Sep 9 12:59:43 2009 From: choisj70 at gmail.com (Seongjin) Date: Wed, 09 Sep 2009 12:59:43 -0400 Subject: [Mristudio-users] Noise level setting for AIR in DTI Studio Message-ID: Dear all, I heard of that empirical noise level is 40 for AIR in DTI Studio and AIR is sensitive to the noise level.What kind of differences we should know about AIR between using higher noise level and lower noise level? -SC -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090909/1e64ab5e/attachment.html From susumu at mri.jhu.edu Wed Sep 9 15:22:18 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 09 Sep 2009 15:22:18 -0400 Subject: [Mristudio-users] Noise level setting for AIR in DTI Studio In-Reply-To: References: Message-ID: If you have two repeated sets of DTI, yu can easily see the degree of motion by showing substraction images. When AIR is working, you can see that the subtraction images become just noises. The subtraction images can be created by the "mean, STD" button. The threshold for AIR is empirical. When it's too low, AIR trys to match noises and motion may not be corrected. When it's too high, the brains are not well defined and the results deteriorates. In between these is a range of values AIR works. You have to figure it out although once you find it you can keep using the same value for other data from the same scanner. On 9/9/09, [Seongjin] wrote: > Dear all, > > I heard of that empirical noise level is 40 for AIR in DTI Studio and AIR > is > sensitive to the noise level.What kind of differences we should know about > AIR between using higher noise level and lower noise level? > > -SC > -- Sent from my mobile device From choisj70 at gmail.com Wed Sep 9 22:48:23 2009 From: choisj70 at gmail.com (Seongjin) Date: Wed, 09 Sep 2009 22:48:23 -0400 Subject: [Mristudio-users] Noise level setting for AIR in DTI Studio In-Reply-To: References: Message-ID: Thanks for your kind explanation. -SC On Wed, Sep 9, 2009 at 3:22 PM, susumu mori wrote: > If you have two repeated sets of DTI, yu can easily see the degree of > motion by showing substraction images. When AIR is working, you can > see that the subtraction images become just noises. The subtraction > images can be created by the "mean, STD" button. > > The threshold for AIR is empirical. When it's too low, AIR trys to > match noises and motion may not be corrected. When it's too high, the > brains are not well defined and the results deteriorates. In between > these is a range of values AIR works. You have to figure it out > although once you find it you can keep using the same value for other > data from the same scanner. > > On 9/9/09, [Seongjin] wrote: > > Dear all, > > > > I heard of that empirical noise level is 40 for AIR in DTI Studio and AIR > > is > > sensitive to the noise level.What kind of differences we should know > about > > AIR between using higher noise level and lower noise level? > > > > -SC > > > > -- > Sent from my mobile device > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090909/97e8dabc/attachment.html From faridisme at gmail.com Thu Sep 10 04:49:48 2009 From: faridisme at gmail.com (mdfarid a r) Date: Thu, 10 Sep 2009 16:49:48 +0800 Subject: [Mristudio-users] DTI studio Fibertracking Message-ID: <7e403aa50909100149y5a1eaa86l7f9d1e075741dfe1@mail.gmail.com> Dear all, Is it possible in DTI studio to carry out ROI operators on prepared ROI 3D masks? Hence, use the 3D masks as a target region instead of just a seed region. I vaguely remember reading either from emails or the faq (in both case, sorry for repeating this question), that DTI studio only allows these ROI 3D masks to be defined as the seed region. Was wondering if there is any reasoning for this? Thanks and Regards, Muhammad Farid -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090910/e6310e57/attachment.html From prizzut2 at jhu.edu Mon Sep 14 10:44:43 2009 From: prizzut2 at jhu.edu (Patrick Rizzuto) Date: Mon, 14 Sep 2009 10:44:43 -0400 Subject: [Mristudio-users] Noise level setting for AIR in DTI Studio In-Reply-To: References: Message-ID: My colleague and I are also experiencing a problem that I suspect may be related to this. While preparing a B0 file for distortion correction LDDMM, I attempt to normalize the intensities of the B0 file as well as a related T2 file. In another step, I also strip the skull from the T2 image. I have found, however, that while intensity normalization appears to work normally BEFORE stripping the T2-skull, attempting to do so AFTER skull-stripping results in a halo appearing on the updated image, radiating out a little ways from the brain. My colleague and I also experienced this last week, while attempting to prepare a separate set of images for nonlinear LDDMM. The reason why I ask this as a reply to this particular thread, however, is because I am now concerned that this halo-generation may be in part due to the noise threshold I set previously being too low - the value I have been working with is 20. While the problem appears to be solved simply by reordering the relevant steps, I want to make sure this is not symptomatic of a noise threshold problem. Are the two at all related? Thank you, Pat Rizzuto - JHU Center for Imaging Science ----- Original Message ----- From: susumu mori Date: Wednesday, September 9, 2009 3:22 pm Subject: Re: [Mristudio-users] Noise level setting for AIR in DTI Studio To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > If you have two repeated sets of DTI, yu can easily see the degree of > motion by showing substraction images. When AIR is working, you can > see that the subtraction images become just noises. The subtraction > images can be created by the "mean, STD" button. > > The threshold for AIR is empirical. When it's too low, AIR trys to > match noises and motion may not be corrected. When it's too high, the > brains are not well defined and the results deteriorates. In between > these is a range of values AIR works. You have to figure it out > although once you find it you can keep using the same value for other > data from the same scanner. > > On 9/9/09, [Seongjin] wrote: > > Dear all, > > > > I heard of that empirical noise level is 40 for AIR in DTI Studio > and AIR > > is > > sensitive to the noise level.What kind of differences we should > know about > > AIR between using higher noise level and lower noise level? > > > > -SC > > > > -- > Sent from my mobile device > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From susumu at mri.jhu.edu Mon Sep 14 18:49:24 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Mon, 14 Sep 2009 18:49:24 -0400 Subject: [Mristudio-users] DTI studio Fibertracking In-Reply-To: <7e403aa50909100149y5a1eaa86l7f9d1e075741dfe1@mail.gmail.com> References: <7e403aa50909100149y5a1eaa86l7f9d1e075741dfe1@mail.gmail.com> Message-ID: Hi Muhammad, Sorry that it took so long to answer your question. We dug up the past question related to yours and put it in the FAQ section of www.mristudio.org. Please look at the last one (Q16). Susumu On Thu, Sep 10, 2009 at 4:49 AM, mdfarid a r wrote: > > > Dear all, > > Is it possible in DTI studio to carry out ROI operators on prepared ROI 3D > masks? Hence, use the 3D masks as a target region instead of just a seed > region. > > I vaguely remember reading either from emails or the faq (in both case, > sorry for repeating this question), that DTI studio only allows these ROI 3D > masks to be defined as the seed region. Was wondering if there is any > reasoning for this? > > Thanks and Regards, > Muhammad Farid > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090914/aedcd8a6/attachment.html From faridisme at gmail.com Tue Sep 15 22:02:28 2009 From: faridisme at gmail.com (mdfarid a r) Date: Wed, 16 Sep 2009 10:02:28 +0800 Subject: [Mristudio-users] DTI studio Fibertracking In-Reply-To: References: <7e403aa50909100149y5a1eaa86l7f9d1e075741dfe1@mail.gmail.com> Message-ID: <7e403aa50909151902o8e633e5ge425ae27f6356871@mail.gmail.com> Thank you Dr Mori. That FAQ was exactly what I was looking for. Farid On Tue, Sep 15, 2009 at 6:49 AM, susumu mori wrote: > Hi Muhammad, > > Sorry that it took so long to answer your question. We dug up the past > question related to yours and put it in the FAQ section of > www.mristudio.org. Please look at the last one (Q16). > > Susumu > > On Thu, Sep 10, 2009 at 4:49 AM, mdfarid a r wrote: > >> >> >> Dear all, >> >> Is it possible in DTI studio to carry out ROI operators on prepared ROI 3D >> masks? Hence, use the 3D masks as a target region instead of just a seed >> region. >> >> I vaguely remember reading either from emails or the faq (in both case, >> sorry for repeating this question), that DTI studio only allows these ROI 3D >> masks to be defined as the seed region. Was wondering if there is any >> reasoning for this? >> >> Thanks and Regards, >> Muhammad Farid >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090916/bb39308e/attachment-0001.html From thewcheung at gmail.com Thu Sep 17 04:10:42 2009 From: thewcheung at gmail.com (Matthew Cheung) Date: Thu, 17 Sep 2009 16:10:42 +0800 Subject: [Mristudio-users] registration of fixed samples In-Reply-To: <3050363f0904071551i758b369cve3b6c41a002473df@mail.gmail.com> References: <3050363f0904071551i758b369cve3b6c41a002473df@mail.gmail.com> Message-ID: <4AB1EF02.4020201@gmail.com> Dear all, I find it quite difficult to register B0 and DW images of fixed samples. Has anyone faced the same problem as well? I'm using Air5.25 to perform rigid transformation. Thanks, Matthew From susumu at mri.jhu.edu Thu Sep 17 08:26:45 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Thu, 17 Sep 2009 08:26:45 -0400 Subject: [Mristudio-users] registration of fixed samples In-Reply-To: <4AB1EF02.4020201@gmail.com> References: <3050363f0904071551i758b369cve3b6c41a002473df@mail.gmail.com> <4AB1EF02.4020201@gmail.com> Message-ID: do you mean formaline-fixed ex vivo samples? There should not be any difference between in vivo and ex vivo data. How did you confirm the registration accuracy? AIR is very sensitive to the image threshold, which you need to specify. Have you tried with different threshold values? On Thu, Sep 17, 2009 at 4:10 AM, Matthew Cheung wrote: > Dear all, > > I find it quite difficult to register B0 and DW images of fixed > samples. Has anyone faced the same problem as well? > I'm using Air5.25 to perform rigid transformation. > > Thanks, > Matthew > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090917/9e8145e8/attachment.html From raj.jaswal at gmail.com Thu Sep 17 14:37:45 2009 From: raj.jaswal at gmail.com (Raj Jaswal) Date: Thu, 17 Sep 2009 14:37:45 -0400 Subject: [Mristudio-users] NifTi and DTI Studio In-Reply-To: References: <772396.37050.qm@web50512.mail.re2.yahoo.com> <39c428d80908260922p6e857432k4f1d6a52311eda65@mail.gmail.com> <77A88E90A851594AAEF830450587C39D01EDAAF7@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: <32a27f2a0909171137h4b6044a1n5e08847a5a73d3eb@mail.gmail.com> Hi all, In relation to what was mentioned a few weeks ago about a newer version of DTI Studio that can read/write NIFTI ... I'm not able to see that functionality. I downloaded the "DtiStudio-latest-x86.exe" file but did not see an option to load NIFTI files. Should I have downloaded the beta "DtiStudio-3.0.1beta-x86.exe" file instead? When clicking on the file for download, I get a 404 page error. If anyone can let me know where to get the updated s/w or if I'm making a simple mistake I would appreciate it. Thanks. - RJ On Mon, Aug 31, 2009 at 12:20 PM, susumu mori wrote: > Hi venkateswaran > > 1) It seems the DtiStudio version currently posted in www.mristudio.orgalready has the function to read/write Nifty. Please check and send me > feedbacks if you encounter and problems. > 2) As for the "distortion correction", do you mean Eddy current distortion > correction or B0 susceptibility correction? If the former is the case, you > can use the Affine tool in DtiStudio. > 3) As for the b-matrix rotation, do you mean the rotation for oblique-angle > imaging that affect older Siemens system? If that is the case, it would be a > complicated issue. The easiest way is, to read the Dicom/Mosaic directly to > DtiStudio, which can automatically recalculate the b-table based on the > oblique information in the header. Once you go through FLS and data is > converted to Nifty/Analyze/Raw, the oblique information is lost. You can > still trick DtiStudio in the following way, but it is a bit cumbersome. > > > Read Mosaic/Dicom directly to DtiStudio, provide the Siemens-provide > original b-table, click the "rotation if applicable", and load the data. > > Close the window and re-open the data input window. There you can find > that b-table of the previous session still remembered by DtiStudio. This > table is already rotated (not the original b-table anymore). You can use > this table for the Raw data. > > 4) The b-table rotation option for oblique imaging doesn't work for > Raw/Analyze/Nifty in DtiStudio. Do Analyze and Nifty have a field for > oblique angles? If so, maybe Hangyi wants to see if we can make the option > available for Analyze and Nifty. > > > > On Mon, Aug 31, 2009 at 11:49 AM, Rajagopalan, Venkateswaran < > rajagov2 at ccf.org> wrote: > >> Dr.Mori, >> >> Sorry to intrude in Yuzheng's question section. I have the following >> question, i am using FSL to perform distortion correction of DTI images, >> after this i convert them into analyze format and open them in DTI studio >> and save them as RAW format and then run "DTI mapping" to calculate FA and >> other metrics, in answersing to a question in the forum on b-matrix rotation >> you have indicated that with "RAW" format we cannot actually perform >> b-matrix rotation option. Now the only way for me to bring the distortion >> corrected images from FSL is by analyze format and save as RAW format so in >> this case i am not able to do this b-matrix rotation, in some of my data i >> observed that b-matrix is significantly rotated so i prefer to check the >> b-matrix rotation option in my data sets. Any suggestion on this. >> >> Thanks in advance, >> >> Regards >> venkateswaran >> >> ________________________________ >> >> From: mristudio-users-bounces at mristudio.org on behalf of susumu mori >> Sent: Sat 8/29/2009 6:27 PM >> To: DTI Studio, ROI Editor, Landmarker Questions/Support; Hangyi Jiang; >> Xin Li >> Subject: Re: [Mristudio-users] NifTi and DTI Studio >> >> >> There is a newer version of DtiStudio that can read Nifty. >> Hangyi and Xin, please work on posting the latest version with updated >> features. >> We'll notify users once a newer version is available on the web. >> >> >> On Wed, Aug 26, 2009 at 12:22 PM, ??? wrote: >> >> >> >> I use FSL to change nifti format to analyze and then use >> DTI Studio to change analyze to dat format. >> >> >> Did you realy make it? I have used the same way but failed... >> If NIFITI files could be imported directly into the DTIStudio, it >> will be wonderful. Hope some make it. >> >> Yuzheng >> >> >> >> JY >> >> >> ________________________________ >> >> From: [Seongjin] >> To: "DTI Studio, ROI Editor, Landmarker Questions/Support" >> >> Sent: Wednesday, August 26, 2009 5:37:58 AM >> Subject: [Mristudio-users] NifTi and DTI Studio >> >> >> Dear all, >> >> Is there anybody know how to import NifTi format data into >> DTI Studio? >> >> -SC >> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> >> >> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> >> >> >> >> =================================== >> >> P Please consider the environment before printing this e-mail >> >> Cleveland Clinic is ranked one of the top hospitals >> in America by U.S. News & World Report (2008). >> Visit us online at http://www.clevelandclinic.org for >> a complete listing of our services, staff and >> locations. >> >> >> Confidentiality Note: This message is intended for use >> only by the individual or entity to which it is addressed >> and may contain information that is privileged, >> confidential, and exempt from disclosure under applicable >> law. If the reader of this message is not the intended >> recipient or the employee or agent responsible for >> delivering the message to the intended recipient, you are >> hereby notified that any dissemination, distribution or >> copying of this communication is strictly prohibited. If >> you have received this communication in error, please >> contact the sender immediately and destroy the material in >> its entirety, whether electronic or hard copy. Thank you. >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090917/ba965208/attachment.html From choisj70 at gmail.com Wed Sep 23 00:06:38 2009 From: choisj70 at gmail.com (Seongjin) Date: Wed, 23 Sep 2009 00:06:38 -0400 Subject: [Mristudio-users] Fiber branching Message-ID: Dear all, This might be a very naive question. But I need to know.Do the fibers tracked by FACT algorithm in DTIStudio contain branched fibers? As an example, let's consider some fibers passing through an ROI drawn in the mid-sagittal plane. In this case, the number of fiber passing through the ROI and the number of all fibers tracked are the same? If they are the same, it would be simply fiber panning. If the number of fibers tracked is more than the fibers passing through the ROI, then, it might be the case of branched fibers. Is there any opinion on this? Thanks. -SC -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090923/9d3c4450/attachment-0001.html From susumu at mri.jhu.edu Wed Sep 23 07:28:32 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 23 Sep 2009 07:28:32 -0400 Subject: [Mristudio-users] Fiber branching In-Reply-To: References: Message-ID: FACT algorithm never branches. From one seed, only one unbranched line propagates. However, there is a very important thing you need to know. If you draw an ROI with 10 pixels and start FACT from these 10 pixels, you get 10 unbranched lines passing through the ROI. Alternatively, you can do a brute-force approach, in which you start FACT from every single pixels inside the brain (above FA threshold). Maybe you can find 10s of thousands of seed pixels and the equal number of propagated lines in this way. Then you can retain all tracking results that go through the 10-pixel ROI. In this case, you likely to find more than 100 lines going into the ROI. This is because many FACT reconstructed lines merge. So, even if FACT can not branch, it can merge if you are using a brute-force method. The' speed and simplicity of FACT algorithm allows us to use this "reverse" approach within a short time (and this is what DtiStudio is using). This aspect of FACT is often overlooked when it is compared to other more sophisticated (but complex) methods. On Wed, Sep 23, 2009 at 12:06 AM, [Seongjin] wrote: > Dear all, > > This might be a very naive question. But I need to know. Do the fibers > tracked by FACT algorithm in DTIStudio contain branched fibers? > > As an example, let's consider some fibers passing through an ROI drawn in > the mid-sagittal plane. > In this case, the number of fiber passing through the ROI and the number of > all fibers tracked are the same? > If they are the same, it would be simply fiber panning. If the number of > fibers tracked is more than the fibers passing through the ROI, then, it > might be the case of branched fibers. > > Is there any opinion on this? > > Thanks. > > -SC > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090923/1c56c427/attachment.html From choisj70 at gmail.com Wed Sep 23 11:58:47 2009 From: choisj70 at gmail.com (Seongjin) Date: Wed, 23 Sep 2009 11:58:47 -0400 Subject: [Mristudio-users] Fiber branching In-Reply-To: References: Message-ID: I appreciate your kind explanation. -SC On Wed, Sep 23, 2009 at 7:28 AM, susumu mori wrote: > FACT algorithm never branches. From one seed, only one unbranched line > propagates. However, there is a very important thing you need to know. > > If you draw an ROI with 10 pixels and start FACT from these 10 pixels, you > get 10 unbranched lines passing through the ROI. > > Alternatively, you can do a brute-force approach, in which you start FACT > from every single pixels inside the brain (above FA threshold). Maybe you > can find 10s of thousands of seed pixels and the equal number of propagated > lines in this way. Then you can retain all tracking results that go through > the 10-pixel ROI. > > In this case, you likely to find more than 100 lines going into the ROI. > This is because many FACT reconstructed lines merge. So, even if FACT can > not branch, it can merge if you are using a brute-force method. The' speed > and simplicity of FACT algorithm allows us to use this "reverse" approach > within a short time (and this is what DtiStudio is using). > > This aspect of FACT is often overlooked when it is compared to other more > sophisticated (but complex) methods. > > On Wed, Sep 23, 2009 at 12:06 AM, [Seongjin] wrote: > >> Dear all, >> >> This might be a very naive question. But I need to know. Do the fibers >> tracked by FACT algorithm in DTIStudio contain branched fibers? >> >> As an example, let's consider some fibers passing through an ROI drawn in >> the mid-sagittal plane. >> In this case, the number of fiber passing through the ROI and the number >> of all fibers tracked are the same? >> If they are the same, it would be simply fiber panning. If the number of >> fibers tracked is more than the fibers passing through the ROI, then, it >> might be the case of branched fibers. >> >> Is there any opinion on this? >> >> Thanks. >> >> -SC >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090923/9c86680a/attachment.html From miguel.burgaleta at uam.es Fri Sep 25 19:07:28 2009 From: miguel.burgaleta at uam.es (miguel.burgaleta at uam.es) Date: Sat, 26 Sep 2009 01:07:28 +0200 Subject: [Mristudio-users] GE 15 gradient table Message-ID: <20090926010728.41642b3gpxzrci1w@webmail.uam.es> Dear DTIStudio group, I have a beginner's question regarding the gradient table that I should use with my DTI. The scanner is a GE and I already have the standard medium table from the manufacturer, but I get weird FA colormaps when using it (non-symmetric, corpus callosum not red). However, if I use a gradient table made by reading the DICOM headers with dcm2nii, I get a gradient table that leads to symmetric, solid red CC FA colormaps. I have read in this list before that this is a good criterion to make sure that the gradient table is the right one, but also heard that it could be incorrect too! So the question is how to make sure that the gradient table is the right one? I appreciate your help. Miguel From susumu at mri.jhu.edu Sun Sep 27 08:55:52 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Sun, 27 Sep 2009 08:55:52 -0400 Subject: [Mristudio-users] GE 15 gradient table In-Reply-To: <20090926010728.41642b3gpxzrci1w@webmail.uam.es> References: <20090926010728.41642b3gpxzrci1w@webmail.uam.es> Message-ID: Hi Miguel, There are two possibilities; 1) your table is wrong. 2) your table format is wrong. I suspect #2. The table has to be rewritten to DtiStudio format, which is; 0: x, y, z 1: x, y, z Common mistakes are; 0; x, y, z (";" instead of ":") 1: x y z (missing ",") . . (there is no [0, 0, 0] in the table) When you have a long table, it is sometimes difficult to catch one mistake. In this case, please do the following; >Use your current table and load the images. You will get the problem you reported. >Close the window and choose "DtiMapping" again. >You will get the initial data input window, which still remembers all the parameters you specified last time, including the gradient table. >Closely inspect the gradient table. This time it contains the table which is NOT the one you typed in but the version interpreted by the software. If you made a mistake in the syntax, it is much easier to catch it in this version. I hope this will help. Susumu On Fri, Sep 25, 2009 at 7:07 PM, wrote: > > Dear DTIStudio group, > > I have a beginner's question regarding the gradient table that I > should use with my DTI. The scanner is a GE and I already have the > standard medium table from the manufacturer, but I get weird FA > colormaps when using it (non-symmetric, corpus callosum not red). > However, if I use a gradient table made by reading the DICOM headers > with dcm2nii, I get a gradient table that leads to symmetric, solid > red CC FA colormaps. > > I have read in this list before that this is a good criterion to make > sure that the gradient table is the right one, but also heard that it > could be incorrect too! So the question is how to make sure that the > gradient table is the right one? > > I appreciate your help. > > Miguel > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090927/cb5a2433/attachment.html From miguel.burgaleta at uam.es Sun Sep 27 13:31:02 2009 From: miguel.burgaleta at uam.es (miguel.burgaleta at uam.es) Date: Sun, 27 Sep 2009 19:31:02 +0200 Subject: [Mristudio-users] GE 15 gradient table In-Reply-To: References: <20090926010728.41642b3gpxzrci1w@webmail.uam.es> Message-ID: <20090927193102.17066t5oy5sz448w@webmail.uam.es> Hi Susumu, I'm sorry but what I was trying to mean is if I can trust the gradient table whose values come from the DICOM headers. I have 2 gradient tables: one from the manufacturer (medium GE) and one from the DICOM headers. When I use the former I get wrong colormaps (I have validated this with other software), but when I use the latter, the colormaps *seem* to be OK (red corpus callosum, symmetric colors). So the question is: even if the CC is solid red and the colormap is symmetric, is it still possible that the gradient table is wrong? Since I am a beginner I am not able to see it just by looking at the colormap. I know this is a basic question, perhaps beyond the scope of this list. So any help will be highly appreciated. Thanks, Miguel Quoting susumu mori : > Hi Miguel, > > There are two possibilities; > > 1) your table is wrong. > 2) your table format is wrong. > > I suspect #2. The table has to be rewritten to DtiStudio format, which is; > > 0: x, y, z > 1: x, y, z > > Common mistakes are; > > 0; x, y, z (";" instead of ":") > 1: x y z (missing ",") > . > . > (there is no [0, 0, 0] in the table) > > When you have a long table, it is sometimes difficult to catch one mistake. > In this case, please do the following; > >> Use your current table and load the images. You will get the problem you > reported. >> Close the window and choose "DtiMapping" again. >> You will get the initial data input window, which still remembers all the > parameters you specified last time, including the gradient table. >> Closely inspect the gradient table. This time it contains the table which > is NOT the one you typed in but the version interpreted by the software. If > you made a mistake in the syntax, it is much easier to catch it in this > version. > > I hope this will help. > > Susumu > > On Fri, Sep 25, 2009 at 7:07 PM, wrote: > >> >> Dear DTIStudio group, >> >> I have a beginner's question regarding the gradient table that I >> should use with my DTI. The scanner is a GE and I already have the >> standard medium table from the manufacturer, but I get weird FA >> colormaps when using it (non-symmetric, corpus callosum not red). >> However, if I use a gradient table made by reading the DICOM headers >> with dcm2nii, I get a gradient table that leads to symmetric, solid >> red CC FA colormaps. >> >> I have read in this list before that this is a good criterion to make >> sure that the gradient table is the right one, but also heard that it >> could be incorrect too! So the question is how to make sure that the >> gradient table is the right one? >> >> I appreciate your help. >> >> Miguel >> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> > From bender at wayne.edu Tue Sep 29 13:01:09 2009 From: bender at wayne.edu (Andrew Bender) Date: Tue, 29 Sep 2009 13:01:09 -0400 Subject: [Mristudio-users] Eddy current correction on Siemens 3T console Message-ID: <02F03D0A-040D-4E23-9AB7-5C8F449AD888@wayne.edu> Hello all, This is less of a DTIstudio question than a practical consideration for DTI processing. Specifically, our institution has a newly installed Siemens 3T Magnetom Verio scanner and the console has the option of outputting computed DTI maps for FA, ADC, radial and axial diffusivities, and eigenvalues. However, nobody I've asked is clear as to whether these have been corrected for eddy current distortion when the console generates them. Does anybody know whether these console-generated DTI maps have been corrected or otherwise AIR registered? I've read recently that some newer consoles incorporate such correction algorithms, but our MR techs do not know and emails to Siemens have not been returned. Obviously, corrected DTI maps that don't require the same degree of pre-processing are preferable for workflow considerations. I'm planning on doing some comparisons for purposes of further validation using the AIRtool affine registration on the raw dicom images before generating the DTI maps in DTIstudion and Analyze, and comparing ROIs between those and the Siemens console generated maps to see if there are differences in output quality. Thanks in advance for your help. -Andrew ************************************************ Andrew R. Bender, M.A. Graduate Research Assistant Cognitive Neuroscience of Aging Lab Department of Psychology Institute of Gerontology Wayne State University 87 E. Ferry Street Detroit, Michigan 48202 bender at wayne.edu (313) 871-0710 From choisj70 at gmail.com Wed Sep 30 09:07:11 2009 From: choisj70 at gmail.com (Seongjin) Date: Wed, 30 Sep 2009 09:07:11 -0400 Subject: [Mristudio-users] Intra-individual Registration question Message-ID: Dear all, I am testing intra-individual registration in DTI studio. What is the best strategy for intra-individual registration? Currently I register each DW images (of a DTI data) to averaged DWIs (of the DTI data). This approach is based on registration to a data of the same contrast. Is there anyone who found potential drawback in this approach? Best, -SC -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090930/0d401986/attachment.html From choisj70 at gmail.com Wed Sep 30 11:50:08 2009 From: choisj70 at gmail.com (Seongjin) Date: Wed, 30 Sep 2009 11:50:08 -0400 Subject: [Mristudio-users] To Philips Users Message-ID: Dear Philips users among DTI studio users, DTI data (from a scanner) consists of b=0 image, other DWIs corresponding to the number of gradients and one more extra image. Anyone knows the details of the extra image from the scanner? In DTI studio, it's gradient table is 100, 100, 100. Typically it comes last in the data set. It looks like a averaged image of all other DWIs. However, it looks different from the mean of all DWIs generated from DTI Studio. Thanks in advance. -SC -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090930/b442a679/attachment.html From susumu at mri.jhu.edu Fri Oct 2 15:55:43 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Fri, 02 Oct 2009 15:55:43 -0400 Subject: [Mristudio-users] To Philips Users In-Reply-To: References: Message-ID: Here are important facts about Philips data; 1) You can control the number of b0 images (say 5 b0). However, no matter how many b0 you take, you get only 1 b0 image in the file (they are already averaged). 2) The final appended image is a calculated "isotropically diffusion-weighted image" (I believe). I'm not sure exactly how it is created. Maybe simply a sum of all DWIs. You don't use this image for tensor calculation. As you mentioned, in DtiStudio, you remove it by using [100, 100, 100]. 3) The order of b0, DWI, and the appended iso-DWI can be specified in the console. In the past, the default order was b0 - DWIs - iso, but in newer versions of operating system, you may get a file with DWIs-b0-iso order. Hope it helps. Susumu On Wed, Sep 30, 2009 at 11:50 AM, [Seongjin] wrote: > Dear Philips users among DTI studio users, > DTI data (from a scanner) consists of b=0 image, other DWIs corresponding > to the number of gradients and one more extra image. > Anyone knows the details of the extra image from the scanner? In DTI > studio, it's gradient table is 100, 100, 100. Typically it comes last in the > data set. > It looks like a averaged image of all other DWIs. However, it looks > different from the mean of all DWIs generated from DTI Studio. > > Thanks in advance. > > -SC > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091002/977fc657/attachment.html From susumu at mri.jhu.edu Fri Oct 2 18:57:24 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Fri, 02 Oct 2009 18:57:24 -0400 Subject: [Mristudio-users] Eddy current correction on Siemens 3T console In-Reply-To: <02F03D0A-040D-4E23-9AB7-5C8F449AD888@wayne.edu> References: <02F03D0A-040D-4E23-9AB7-5C8F449AD888@wayne.edu> Message-ID: Andrew, This seems a question you'd better ask to Siemens, but I have several general comments; 1) If your Siemens scanners are well calibrated, you should not see that much eddy current, which manifests as a bright high-FA ring especially at the front and back of the brain. If you don't see it, eddy current-corrected or not, you don't have to worry about it. 2) You want to do affine registration to correct both eddy current-distortion and motion-caused misregistration. No matter what algorithms you use, the solution is only approximation and you get different solutions depending on which algorithm you use (or even by using different parameters using the same algorithm). Therefore, you won't get a clear answer by comparing your Siemens results with other software such as DtiStudio. 3) Probably the best way to tell if the Siemens console does affine registration is; > the first and the last slice often become partial because of X or Y rotation. > Compare to images without registration (you can create this by processing DICOM using DtiStudio without AIR registration), registered images seem blur and higher SNR because of pixel interpolation necessary for registration. I hope this helps. On Tue, Sep 29, 2009 at 1:01 PM, Andrew Bender wrote: > Hello all, > > This is less of a DTIstudio question than a practical consideration > for DTI processing. Specifically, our institution has a newly > installed Siemens 3T Magnetom Verio scanner and the console has the > option of outputting computed DTI maps for FA, ADC, radial and axial > diffusivities, and eigenvalues. However, nobody I've asked is clear > as to whether these have been corrected for eddy current distortion > when the console generates them. Does anybody know whether these > console-generated DTI maps have been corrected or otherwise AIR > registered? I've read recently that some newer consoles incorporate > such correction algorithms, but our MR techs do not know and emails to > Siemens have not been returned. > > Obviously, corrected DTI maps that don't require the same degree of > pre-processing are preferable for workflow considerations. I'm > planning on doing some comparisons for purposes of further validation > using the AIRtool affine registration on the raw dicom images before > generating the DTI maps in DTIstudion and Analyze, and comparing ROIs > between those and the Siemens console generated maps to see if there > are differences in output quality. > > Thanks in advance for your help. > > -Andrew > > > ************************************************ > Andrew R. Bender, M.A. > Graduate Research Assistant > Cognitive Neuroscience of Aging Lab > Department of Psychology > Institute of Gerontology > Wayne State University > 87 E. Ferry Street > Detroit, Michigan 48202 > bender at wayne.edu > (313) 871-0710 > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091002/081825ee/attachment.html From susumu at mri.jhu.edu Fri Oct 2 21:43:48 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Fri, 02 Oct 2009 21:43:48 -0400 Subject: [Mristudio-users] GE 15 gradient table In-Reply-To: <20090927193102.17066t5oy5sz448w@webmail.uam.es> References: <20090926010728.41642b3gpxzrci1w@webmail.uam.es> <20090927193102.17066t5oy5sz448w@webmail.uam.es> Message-ID: Yes, There are three cases when things can go wrong even if the colormaps look fine. 1) Simple mistake in the gradient table (e.g. [1, -1, 0] instead of [1, 1, 0] in one of the tables). Here I assume you made a mistake in one or several lines of the gradient table by typos. This is the most difficult kind of problems to catch. When you do tensor calculation, it asks "Automated Rejection?". This function is not working well in the current implementation. We are about to release a much better version soon, but there is one handy function, called "Create images of the DWI-Fitting" and "Create images of the difference between ....". Click these two check boxes. For outlier rejection threshold, put a large number to effectively turn off this function. After calculation, click "Original-Mean-ADC-STD" button. Here, you can find raw DWI, theoretical DWI back-calculated from fitting results, and difference of the two. Think these results in this way; suppose you have 4 points in a X-Y plot and did a linear fitting. After fitting, you can measure error between the fitting results and each measured point. The bottom row of the inspection window shows the difference (error) maps. These error maps should look random noise. If there is any mistake in the gradient table, you can immediately tell because you can clearly see anatomical structures in this error map. Also, these error maps are handy to visually see the amount of eddy current and subject motion. 2) Oblique angle When you are using oblique angle axial imaging AND > you are using Philips scanner AND using the "gradient overplus" option. > you are using Siemens scanner AND the operating system prior to VB15 Then you need to re-calculate your gradient table based on the oblique angles. If you are a Philips scanner user, you can get a handy software from mri.kennedykrieger.org that can do the calculation. If you are using DICOM, you can simply click "rotate gradient if applicable" beneath the gradient table input section. Then the software can read the oblique info from the header and do the recalculation 3) +/- sign If +/- sign is wrong for only one of the table lines, it is the case described in #1. If +/- sign of, for example, all X components of all lines are flipped, that's a totally different story. There is a detailed description of this issue in the manual of DtiStudio. Basically, +/- definition of any given gradient table is arbitrary, and dynamically changed depending on imaging protocol. If +/- signs of one of the X, Y, Z components are flipped, you won't notice by looking at eigenvalue-based maps such as MD and FA. The color map also looks correct. You notice the problem only when you start fiber tracking. Please refer to the manual for detail. Susumu On Sun, Sep 27, 2009 at 1:31 PM, wrote: > > > Hi Susumu, > > I'm sorry but what I was trying to mean is if I can trust the gradient > table whose values come from the DICOM headers. > > I have 2 gradient tables: one from the manufacturer (medium GE) and one > from the DICOM headers. When I use the former I get wrong colormaps (I have > validated this with other software), but when I use > the latter, the colormaps *seem* to be OK (red corpus callosum, symmetric > colors). > > So the question is: even if the CC is solid red and the colormap is > symmetric, is it still possible that the gradient table is wrong? Since I am > a beginner I am not able to see it just by looking at the colormap. > > I know this is a basic question, perhaps beyond the scope of this list. So > any help will be highly appreciated. > > Thanks, > Miguel > > > > Quoting susumu mori : > > Hi Miguel, >> >> There are two possibilities; >> >> 1) your table is wrong. >> 2) your table format is wrong. >> >> I suspect #2. The table has to be rewritten to DtiStudio format, which is; >> >> 0: x, y, z >> 1: x, y, z >> >> Common mistakes are; >> >> 0; x, y, z (";" instead of ":") >> 1: x y z (missing ",") >> . >> . >> (there is no [0, 0, 0] in the table) >> >> When you have a long table, it is sometimes difficult to catch one >> mistake. >> In this case, please do the following; >> >> Use your current table and load the images. You will get the problem you >>> >> reported. >> >>> Close the window and choose "DtiMapping" again. >>> You will get the initial data input window, which still remembers all the >>> >> parameters you specified last time, including the gradient table. >> >>> Closely inspect the gradient table. This time it contains the table which >>> >> is NOT the one you typed in but the version interpreted by the software. >> If >> you made a mistake in the syntax, it is much easier to catch it in this >> version. >> >> I hope this will help. >> >> Susumu >> >> On Fri, Sep 25, 2009 at 7:07 PM, wrote: >> >> >>> Dear DTIStudio group, >>> >>> I have a beginner's question regarding the gradient table that I >>> should use with my DTI. The scanner is a GE and I already have the >>> standard medium table from the manufacturer, but I get weird FA >>> colormaps when using it (non-symmetric, corpus callosum not red). >>> However, if I use a gradient table made by reading the DICOM headers >>> with dcm2nii, I get a gradient table that leads to symmetric, solid >>> red CC FA colormaps. >>> >>> I have read in this list before that this is a good criterion to make >>> sure that the gradient table is the right one, but also heard that it >>> could be incorrect too! So the question is how to make sure that the >>> gradient table is the right one? >>> >>> I appreciate your help. >>> >>> Miguel >>> >>> >>> _______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: >>> Mristudio-users-unsubscribe at mristudio.org >>> >>> >> > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091002/ad034eef/attachment-0001.html From choisj70 at gmail.com Sun Oct 4 15:28:06 2009 From: choisj70 at gmail.com (Seongjin) Date: Sun, 04 Oct 2009 15:28:06 -0400 Subject: [Mristudio-users] To Philips Users In-Reply-To: References: Message-ID: Susumu, Thanks for your answer to my question.To me the appended image in the last place looks like an averaged image, but it look different from the mean of all DWIs generated by DTI Studio. So the origin or feature of the appended image is still not clear. Based on this, using the mean of all DWIs generated by DTI Studio would be better for intra-individual registration (built-in AIR) template, I guess. Do you have any opinion to this intra-individual registration approach? -SC On Fri, Oct 2, 2009 at 3:55 PM, susumu mori wrote: > Here are important facts about Philips data; > > 1) You can control the number of b0 images (say 5 b0). However, no matter > how many b0 you take, you get only 1 b0 image in the file (they are already > averaged). > 2) The final appended image is a calculated "isotropically > diffusion-weighted image" (I believe). I'm not sure exactly how it is > created. Maybe simply a sum of all DWIs. You don't use this image for tensor > calculation. As you mentioned, in DtiStudio, you remove it by using [100, > 100, 100]. > 3) The order of b0, DWI, and the appended iso-DWI can be specified in the > console. In the past, the default order was b0 - DWIs - iso, but in newer > versions of operating system, you may get a file with DWIs-b0-iso order. > > Hope it helps. > > Susumu > > On Wed, Sep 30, 2009 at 11:50 AM, [Seongjin] wrote: > >> Dear Philips users among DTI studio users, >> DTI data (from a scanner) consists of b=0 image, other DWIs corresponding >> to the number of gradients and one more extra image. >> Anyone knows the details of the extra image from the scanner? In DTI >> studio, it's gradient table is 100, 100, 100. Typically it comes last in the >> data set. >> It looks like a averaged image of all other DWIs. However, it looks >> different from the mean of all DWIs generated from DTI Studio. >> >> Thanks in advance. >> >> -SC >> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091004/1a33cc9a/attachment.html From lkreber at cnsneuro.com Mon Oct 5 18:34:39 2009 From: lkreber at cnsneuro.com (lkreber at cnsneuro.com) Date: Mon, 05 Oct 2009 15:34:39 -0700 Subject: [Mristudio-users] bug in version 2.4.01 of DTI dti studio??? In-Reply-To: Message-ID: Hi, All: I just downloaded version 2.4.01 of DTI studio and everytime I try to create the DTI map and select "NO" to "automatically reject outliers", the program gets an error message and closes. What can I do to fix this issue? I have uninstalled and installed the version several times. Please help. Thanks, Lisa Lisa A. Kreber, Ph.D., CBIS Senior Neuroscientist/Research Coordinator Centre for Neuro Skills (CNS)? Clinical Research & Education Foundation (CREF) 2658 Mt. Vernon Avenue Bakersfield, CA 93306 (661) 872-3408 (661) 335-1458 Cell (661) 872-5150 Fax From susumu at mri.jhu.edu Mon Oct 5 19:15:32 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Mon, 05 Oct 2009 19:15:32 -0400 Subject: [Mristudio-users] bug in version 2.4.01 of DTI dti studio??? In-Reply-To: References: Message-ID: Are you using DICOM? If so, it is possible that your gradient table is not right. For example, if your table suggest there should be 13 images and if your data file contains 14 images, DtiStudio gets error. Please do the following: 1) Once data are read, please look at the pull-down menu in the "Image" tab, go over all images, and make sure how many images are loaded and all loaded images have the same number of slices. 2) Close the window before you move to the tensor calculation and open the same DTI set again. When you get the opening data input window, check carefully the gradient table, which DtiStudio remembers from the previous session. If you made any mistake in the table, here you should be able to find it. Please try. On Mon, Oct 5, 2009 at 6:34 PM, wrote: > Hi, All: > > I just downloaded version 2.4.01 of DTI studio and everytime I try to > create the DTI map and select "NO" to "automatically reject outliers", the > program gets an error message and closes. What can I do to fix this issue? > I have uninstalled and installed the version several times. > > Please help. > > Thanks, > > Lisa > > > > > Lisa A. Kreber, Ph.D., CBIS > Senior Neuroscientist/Research Coordinator > Centre for Neuro Skills (CNS)? > Clinical Research & Education Foundation (CREF) > 2658 Mt. Vernon Avenue > Bakersfield, CA 93306 > (661) 872-3408 > (661) 335-1458 Cell > (661) 872-5150 Fax > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091005/3dec21c1/attachment.html From lkreber at cnsneuro.com Tue Oct 6 11:35:06 2009 From: lkreber at cnsneuro.com (lkreber at cnsneuro.com) Date: Tue, 06 Oct 2009 08:35:06 -0700 Subject: [Mristudio-users] bug in version 2.4.01 of DTI dti studio??? In-Reply-To: Message-ID: This did not work. I have checked the gradient table and it is correct. I have the same number of gradient directions as I have images and the images are all being read into dti studio. The program always shuts down at "automatic outier rejection" when I select no. The message I get is: The instruction at "0x73dd11c7" referenced memory at "0x00000004" the memory could not be read" Any help would be greatly appreciated. Lisa A. Kreber, Ph.D., CBIS Senior Neuroscientist/Research Coordinator Centre for Neuro Skills (CNS)? Clinical Research & Education Foundation (CREF) 2658 Mt. Vernon Avenue Bakersfield, CA 93306 (661) 872-3408 (661) 335-1458 Cell (661) 872-5150 Fax susumu mori To Sent by: "DTI Studio, ROI Editor, Landmarker mristudio-users-b Questions/Support" ounces at mristudio. org cc Subject 10/05/2009 04:15 Re: [Mristudio-users] bug in PM version 2.4.01 of DTI dti studio??? Please respond to "DTI Studio, ROI Editor, Landmarker Questions/Support " Are you using DICOM? If so, it is possible that your gradient table is not right. For example, if your table suggest there should be 13 images and if your data file contains 14 images, DtiStudio gets error. Please do the following: 1) Once data are read, please look at the pull-down menu in the "Image" tab, go over all images, and make sure how many images are loaded and all loaded images have the same number of slices. 2) Close the window before you move to the tensor calculation and open the same DTI set again. When you get the opening data input window, check carefully the gradient table, which DtiStudio remembers from the previous session. If you made any mistake in the table, here you should be able to find it. Please try. On Mon, Oct 5, 2009 at 6:34 PM, wrote: Hi, All: I just downloaded version 2.4.01 of DTI studio and everytime I try to create the DTI map and select "NO" to "automatically reject outliers", the program gets an error message and closes. ?What can I do to fix this issue? I have uninstalled and installed the version several times. Please help. Thanks, Lisa Lisa A. Kreber, Ph.D., CBIS Senior Neuroscientist/Research Coordinator Centre for Neuro Skills (CNS)? Clinical Research & Education Foundation (CREF) 2658 Mt. Vernon Avenue Bakersfield, CA 93306 (661) 872-3408 (661) 335-1458 Cell (661) 872-5150 Fax _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From KBlackst at cnmc.org Mon Oct 12 09:10:29 2009 From: KBlackst at cnmc.org (Blackstone, Kaitlin) Date: Mon, 12 Oct 2009 09:10:29 -0400 Subject: [Mristudio-users] MRI studio software download username/password In-Reply-To: Message-ID: Good morning, I am trying to download the most updated software for DTI Studio and ROI editor but I cannot remember the username and password from our lab. Our PI information is below: William D. Gaillard, Children's National Medical Center, email: wgaillar at cnmc.org, phone: 202-476-8272 and Madison Berl, Children's National Medical Center, email: mberl at cnmc.org, phone: 202-476-2545 Would it be possible to send along the username and password that is connected with either/both of these PI's? Thank you very much!! Kaitlin Blackstone, B.A. Children's National Medical Center Children's Research Institute 111 Michigan Avenue, NW Washington, D.C. 20010 202-476-4755 Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091012/3f66eb2e/attachment-0001.html From xli16 at jhmi.edu Mon Oct 12 09:58:54 2009 From: xli16 at jhmi.edu (Xin Li) Date: Mon, 12 Oct 2009 09:58:54 -0400 Subject: [Mristudio-users] MRI studio software download username/password In-Reply-To: References: Message-ID: Kaitlin, Do you know which email address was used to register? As long as you have the email address, you can get the username and password back. At www.mristudio.org, you can find the links "Forget password" and "Forget username". Hope this can help you. Xin ----- Original Message ----- From: "Blackstone, Kaitlin" Date: Monday, October 12, 2009 9:10 am Subject: [Mristudio-users] MRI studio software download username/password To: "DTI Studio, ROI Editor,Landmarker Questions/Support" > Good morning, > > > > I am trying to download the most updated software for DTI Studio and > ROI > editor but I cannot remember the username and password from our lab. > Our > PI information is below: > > > > William D. Gaillard, Children's National Medical Center, email: > wgaillar at cnmc.org, phone: 202-476-8272 > > and > > Madison Berl, Children's National Medical Center, email: mberl at cnmc.org, > phone: 202-476-2545 > > > > Would it be possible to send along the username and password that is > connected with either/both of these PI's? > > > > > > Thank you very much!! > > > > Kaitlin Blackstone, B.A. > > Children's National Medical Center > > Children's Research Institute > > 111 Michigan Avenue, NW > > Washington, D.C. 20010 > > 202-476-4755 > > > > Confidentiality Notice: This e-mail message, including any > attachments, is for the sole use of the intended > recipient(s) and may contain confidential and privileged information. > Any unauthorized review, use, disclosure or distribution is > prohibited. > If you are not the intended recipient, please contact the sender by > reply e-mail and destroy all copies of the original message. > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From amangupta2005 at gmail.com Mon Oct 12 11:00:11 2009 From: amangupta2005 at gmail.com (aman gupta) Date: Mon, 12 Oct 2009 10:00:11 -0500 Subject: [Mristudio-users] bug in version 2.4.01 of DTI dti studio??? In-Reply-To: References: Message-ID: Hi All, I am also facing the same problem while using DTI studio. I am getting the same error message as mentioned in the email below. Any suggestions would be really helpful. Thanks, Aman Gupta PhD Candidate Department of Bioengineering, University of Ilinois at Chicago, Sports Biomechanics Research Lab, Department of Orthopedics, Rush University Medical Center, Chicago, IL-60612. On Tue, Oct 6, 2009 at 10:35 AM, wrote: > This did not work. ?I have checked the gradient table and it is correct. ?I > have the same number of gradient directions as I have images and the images > are all being read into dti studio. > > The program always shuts down at "automatic outier rejection" when I select > no. ?The message I get is: The instruction at "0x73dd11c7" referenced > memory at "0x00000004" the memory could not be read" > > Any help would be greatly appreciated. > > > > > > Lisa A. Kreber, Ph.D., CBIS > Senior Neuroscientist/Research Coordinator > Centre for Neuro Skills (CNS)? > Clinical Research & Education Foundation (CREF) > 2658 Mt. Vernon Avenue > Bakersfield, CA 93306 > (661) 872-3408 > (661) 335-1458 Cell > (661) 872-5150 Fax > > > > > ? ? ? ? ? ? susumu mori > ? ? ? ? ? ? ? ? ? ? ? ? du> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?To > ? ? ? ? ? ? Sent by: ? ? ? ? ? ? ? ? ?"DTI Studio, ROI Editor, Landmarker > ? ? ? ? ? ? mristudio-users-b ? ? ? ? Questions/Support" > ? ? ? ? ? ? ounces at mristudio. ? ? ? ? > ? ? ? ? ? ? org ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?cc > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Subject > ? ? ? ? ? ? 10/05/2009 04:15 ? ? ? ? ?Re: [Mristudio-users] bug in > ? ? ? ? ? ? PM ? ? ? ? ? ? ? ? ? ? ? ?version 2.4.01 of DTI dti studio??? > > > ? ? ? ? ? ? Please respond to > ? ? ? ? ? ? "DTI Studio, ROI > ? ? ? ? ? ? ? ? ?Editor, > ? ? ? ? ? ? ? ?Landmarker > ? ? ? ? ? ? Questions/Support > ? ? ? ? ? ? ? ? ? ? " > ? ? ? ? ? ? ? ? ? ? ? ? ?mristudio.org> > > > > > > > Are you using DICOM? If so, it is possible that your gradient table is not > right. For example, if your table suggest there should be 13 images and if > your data file contains 14 images, DtiStudio gets error. Please do the > following: > > 1) Once data are read, please look at the pull-down menu in the "Image" > tab, go over all images, and make sure how many images are loaded and all > loaded images have the same number of slices. > 2) Close the window before you move to the tensor calculation and open the > same DTI set again. When you get the opening data input window, check > carefully the gradient table, which DtiStudio remembers from the previous > session. If you made any mistake in the table, here you should be able to > find it. > > Please try. > > On Mon, Oct 5, 2009 at 6:34 PM, wrote: > ?Hi, All: > > ?I just downloaded version 2.4.01 of DTI studio and everytime I try to > ?create the DTI map and select "NO" to "automatically reject outliers", > ?the > ?program gets an error message and closes. ?What can I do to fix this > ?issue? > ?I have uninstalled and installed the version several times. > > ?Please help. > > ?Thanks, > > ?Lisa > > > > > ?Lisa A. Kreber, Ph.D., CBIS > ?Senior Neuroscientist/Research Coordinator > ?Centre for Neuro Skills (CNS)? > ?Clinical Research & Education Foundation (CREF) > ?2658 Mt. Vernon Avenue > ?Bakersfield, CA 93306 > ?(661) 872-3408 > ?(661) 335-1458 Cell > ?(661) 872-5150 Fax > > > ?_______________________________________________ > ?Mristudio-users mailing list > ?Mristudio-users at mristudio.org > ?http://lists.mristudio.org/mailman/listinfo/ > ?Unsubscribe, send a blank email to: > ?Mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > From ghariba1 at illinois.edu Tue Oct 13 13:30:12 2009 From: ghariba1 at illinois.edu (Armen Gharibans) Date: Tue, 13 Oct 2009 12:30:12 -0500 Subject: [Mristudio-users] File Type Question Message-ID: <6F3B49DE-435B-4B89-8B04-6BAE7C01710F@illinois.edu> I have Analyze data file that I can open and view in MRI View3D. It is 6 slices and 30 different directions in one analyze file and a separate header file. When I try to do DTI Mapping, it doesn't give the option for Analyze data, so I used MRI View3D to convert the Analyze data to Raw Data and also NRRD, and I get errors with both. My gradient table should be correct. When I try to use the raw data, which is just one .dat file, I get the message, "Number of files in this fold is less than expected." I am guessing that is because the raw data should be a bunch of .bin files. Why did it save it in one .dat file? Thank you. Armen Gharibans From susumu at mri.jhu.edu Wed Oct 14 11:13:43 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 14 Oct 2009 11:13:43 -0400 Subject: [Mristudio-users] File Type Question In-Reply-To: <6F3B49DE-435B-4B89-8B04-6BAE7C01710F@illinois.edu> References: <6F3B49DE-435B-4B89-8B04-6BAE7C01710F@illinois.edu> Message-ID: Hi Armen, That means, the gradient table and the file size didn't match. When you converted the analyze to raw, I assume that you saved all images in one file. Then, your file size should be; 192x192 (I assume that your in-plane resolution is 192x192) x 6 x (30+1 b0) x 2 (integer). Then your gradient table should have 31 (30 dwi +1 b0) lines. Ignore the error message and load the data. See if the dimension of your images are correct. Look at the pull-down menu to see you really have 31 images loaded. Close the window and choose "DtiMapping" again. In the opening window, it still remembers the gradient table you specified in the previous session. Inspect the table and make sure that you have 31 lines. Susumu On Tue, Oct 13, 2009 at 1:30 PM, Armen Gharibans wrote: > I have Analyze data file that I can open and view in MRI View3D. It > is 6 slices and 30 different directions in one analyze file and a > separate header file. When I try to do DTI Mapping, it doesn't give > the option for Analyze data, so I used MRI View3D to convert the > Analyze data to Raw Data and also NRRD, and I get errors with both. > My gradient table should be correct. > > When I try to use the raw data, which is just one .dat file, I get the > message, "Number of files in this fold is less than expected." I am > guessing that is because the raw data should be a bunch of .bin > files. Why did it save it in one .dat file? > > Thank you. > Armen Gharibans > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091014/b709376d/attachment.html From ghariba1 at illinois.edu Wed Oct 14 11:45:11 2009 From: ghariba1 at illinois.edu (Armen Gharibans) Date: Wed, 14 Oct 2009 10:45:11 -0500 Subject: [Mristudio-users] File Type Question In-Reply-To: References: <6F3B49DE-435B-4B89-8B04-6BAE7C01710F@illinois.edu> Message-ID: <44CF0BC6-D20E-4EC6-A0B7-0B1BCF5BCE87@illinois.edu> Susumu and Hangyi, Thanks for the replies. When I load the analyze date with MRI View3D, it shows all 31 images in the drop down menu. When I was saving it to raw data, I selected all the images and it saved it in one .dat file. When I want to load the .dat file in MRI View 3D, I have to click "Float" in the "Image Data Format" for it to give the right images. When it opens it up, there is only Image.dat in the drop down menu, but there are 31x6 images stacked on each other basically as if there were 186 slices. Is this correct? I can click through all of them. When I try to open up the .dat file in DTI Mapping, I choose Philips REC. I get the error message, "File size is smaller than DW-image size, continue anyway?" The scans are actually of the calf muscle, we are trying to track the fibers in the muscle. The Image Dimension is 64x64. The voxel size is 200x200mm and slice thickness 10mm. Armen On Oct 14, 2009, at 10:13 AM, susumu mori wrote: > Hi Armen, > > That means, the gradient table and the file size didn't match. > When you converted the analyze to raw, I assume that you saved all > images in one file. Then, your file size should be; > > 192x192 (I assume that your in-plane resolution is 192x192) x 6 x > (30+1 b0) x 2 (integer). > > Then your gradient table should have 31 (30 dwi +1 b0) lines. > > Ignore the error message and load the data. See if the dimension of > your images are correct. Look at the pull-down menu to see you > really have 31 images loaded. > > Close the window and choose "DtiMapping" again. In the opening > window, it still remembers the gradient table you specified in the > previous session. Inspect the table and make sure that you have 31 > lines. > > Susumu > On Oct 14, 2009, at 7:53 AM, Hangyi Jiang wrote: > hi, Armen, > > with "File->DTI Mapping" command, choose "Philips REC" for your > resaved .dat file, it should work if the .dat file contains all > directional images and if the image data type is in 16 bits unsigned > integer. > > regards, > > hangyi > On Tue, Oct 13, 2009 at 1:30 PM, Armen Gharibans > wrote: > I have Analyze data file that I can open and view in MRI View3D. It > is 6 slices and 30 different directions in one analyze file and a > separate header file. When I try to do DTI Mapping, it doesn't give > the option for Analyze data, so I used MRI View3D to convert the > Analyze data to Raw Data and also NRRD, and I get errors with both. > My gradient table should be correct. > > When I try to use the raw data, which is just one .dat file, I get the > message, "Number of files in this fold is less than expected." I am > guessing that is because the raw data should be a bunch of .bin > files. Why did it save it in one .dat file? > > Thank you. > Armen Gharibans > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091014/1847582b/attachment-0001.html From susumu at mri.jhu.edu Sun Oct 18 18:11:45 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Sun, 18 Oct 2009 18:11:45 -0400 Subject: [Mristudio-users] bug in version 2.4.01 of DTI dti studio??? In-Reply-To: References: Message-ID: Hi Hangyi, Could you follow up this error message? Do you think it's just caused by memory shortage? Aman and Lisa, how much RAM do you have and how large is your raw DWI data? Have you tried to limit the number of slices to be calculated? Susumu On Mon, Oct 12, 2009 at 11:00 AM, aman gupta wrote: > Hi All, > > I am also facing the same problem while using DTI studio. I am getting > the same error message as mentioned in the email below. Any > suggestions would be really helpful. > > Thanks, > Aman Gupta > PhD Candidate > Department of Bioengineering, > University of Ilinois at Chicago, > Sports Biomechanics Research Lab, > Department of Orthopedics, > Rush University Medical Center, > Chicago, IL-60612. > > > On Tue, Oct 6, 2009 at 10:35 AM, wrote: > > This did not work. I have checked the gradient table and it is correct. > I > > have the same number of gradient directions as I have images and the > images > > are all being read into dti studio. > > > > The program always shuts down at "automatic outier rejection" when I > select > > no. The message I get is: The instruction at "0x73dd11c7" referenced > > memory at "0x00000004" the memory could not be read" > > > > Any help would be greatly appreciated. > > > > > > > > > > > > Lisa A. Kreber, Ph.D., CBIS > > Senior Neuroscientist/Research Coordinator > > Centre for Neuro Skills (CNS)? > > Clinical Research & Education Foundation (CREF) > > 2658 Mt. Vernon Avenue > > Bakersfield, CA 93306 > > (661) 872-3408 > > (661) 335-1458 Cell > > (661) 872-5150 Fax > > > > > > > > > > susumu mori > > > du> To > > Sent by: "DTI Studio, ROI Editor, Landmarker > > mristudio-users-b Questions/Support" > > ounces at mristudio. > > org cc > > > > Subject > > 10/05/2009 04:15 Re: [Mristudio-users] bug in > > PM version 2.4.01 of DTI dti studio??? > > > > > > Please respond to > > "DTI Studio, ROI > > Editor, > > Landmarker > > Questions/Support > > " > > > mristudio.org> > > > > > > > > > > > > > > Are you using DICOM? If so, it is possible that your gradient table is > not > > right. For example, if your table suggest there should be 13 images and > if > > your data file contains 14 images, DtiStudio gets error. Please do the > > following: > > > > 1) Once data are read, please look at the pull-down menu in the "Image" > > tab, go over all images, and make sure how many images are loaded and all > > loaded images have the same number of slices. > > 2) Close the window before you move to the tensor calculation and open > the > > same DTI set again. When you get the opening data input window, check > > carefully the gradient table, which DtiStudio remembers from the previous > > session. If you made any mistake in the table, here you should be able to > > find it. > > > > Please try. > > > > On Mon, Oct 5, 2009 at 6:34 PM, wrote: > > Hi, All: > > > > I just downloaded version 2.4.01 of DTI studio and everytime I try to > > create the DTI map and select "NO" to "automatically reject outliers", > > the > > program gets an error message and closes. What can I do to fix this > > issue? > > I have uninstalled and installed the version several times. > > > > Please help. > > > > Thanks, > > > > Lisa > > > > > > > > > > Lisa A. Kreber, Ph.D., CBIS > > Senior Neuroscientist/Research Coordinator > > Centre for Neuro Skills (CNS)? > > Clinical Research & Education Foundation (CREF) > > 2658 Mt. Vernon Avenue > > Bakersfield, CA 93306 > > (661) 872-3408 > > (661) 335-1458 Cell > > (661) 872-5150 Fax > > > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > http://lists.mristudio.org/mailman/listinfo/ > > Unsubscribe, send a blank email to: > > Mristudio-users-unsubscribe at mristudio.org > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > http://lists.mristudio.org/mailman/listinfo/ > > Unsubscribe, send a blank email to: > > Mristudio-users-unsubscribe at mristudio.org > > > > > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > http://lists.mristudio.org/mailman/listinfo/ > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091018/9d639d03/attachment.html From Lisa_Kreber/CNSNEURO at cnsneuro.com Sun Oct 18 20:54:33 2009 From: Lisa_Kreber/CNSNEURO at cnsneuro.com (Lisa_Kreber/CNSNEURO at cnsneuro.com) Date: Sun, 18 Oct 2009 17:54:33 -0700 Subject: [Mristudio-users] bug in version 2.4.01 of DTI dti studio??? Message-ID: Hi, I have plenty of RAM and my dataset is only 64 slices. As soon as I removed this version of DTI studio and downloaded the newer version, I had no more issues and no longer received the error message. I made no changes to my gradient table and did the same procedure, just with the new version. My colleague (who has a different brand of computer and not as much RAM as I do, was doing the same thing that I was with the same dataset but she never encountered the problem that I did with the 2.4.01 version. Lisa ----- Original Message ----- From: susumu mori [susumu at mri.jhu.edu] Sent: 10/18/2009 06:11 PM AST To: "DTI Studio, ROI Editor, Landmarker Questions/Support" Subject: Re: [Mristudio-users] bug in version 2.4.01 of DTI dti studio??? Hi Hangyi, Could you follow up this error message? Do you think it's just caused by memory shortage? Aman and Lisa, how much RAM do you have and how large is your raw DWI data? Have you tried to limit the number of slices to be calculated? Susumu On Mon, Oct 12, 2009 at 11:00 AM, aman gupta wrote: > Hi All, > > I am also facing the same problem while using DTI studio. I am getting > the same error message as mentioned in the email below. Any > suggestions would be really helpful. > > Thanks, > Aman Gupta > PhD Candidate > Department of Bioengineering, > University of Ilinois at Chicago, > Sports Biomechanics Research Lab, > Department of Orthopedics, > Rush University Medical Center, > Chicago, IL-60612. > > > On Tue, Oct 6, 2009 at 10:35 AM, wrote: > > This did not work. I have checked the gradient table and it is correct. > I > > have the same number of gradient directions as I have images and the > images > > are all being read into dti studio. > > > > The program always shuts down at "automatic outier rejection" when I > select > > no. The message I get is: The instruction at "0x73dd11c7" referenced > > memory at "0x00000004" the memory could not be read" > > > > Any help would be greatly appreciated. > > > > > > > > > > > > Lisa A. Kreber, Ph.D., CBIS > > Senior Neuroscientist/Research Coordinator > > Centre for Neuro Skills (CNS)? > > Clinical Research & Education Foundation (CREF) > > 2658 Mt. Vernon Avenue > > Bakersfield, CA 93306 > > (661) 872-3408 > > (661) 335-1458 Cell > > (661) 872-5150 Fax > > > > > > > > > > susumu mori > > > du> To > > Sent by: "DTI Studio, ROI Editor, Landmarker > > mristudio-users-b Questions/Support" > > ounces at mristudio. > > org cc > > > > Subject > > 10/05/2009 04:15 Re: [Mristudio-users] bug in > > PM version 2.4.01 of DTI dti studio??? > > > > > > Please respond to > > "DTI Studio, ROI > > Editor, > > Landmarker > > Questions/Support > > " > > > mristudio.org> > > > > > > > > > > > > > > Are you using DICOM? If so, it is possible that your gradient table is > not > > right. For example, if your table suggest there should be 13 images and > if > > your data file contains 14 images, DtiStudio gets error. Please do the > > following: > > > > 1) Once data are read, please look at the pull-down menu in the "Image" > > tab, go over all images, and make sure how many images are loaded and all > > loaded images have the same number of slices. > > 2) Close the window before you move to the tensor calculation and open > the > > same DTI set again. When you get the opening data input window, check > > carefully the gradient table, which DtiStudio remembers from the previous > > session. If you made any mistake in the table, here you should be able to > > find it. > > > > Please try. > > > > On Mon, Oct 5, 2009 at 6:34 PM, wrote: > > Hi, All: > > > > I just downloaded version 2.4.01 of DTI studio and everytime I try to > > create the DTI map and select "NO" to "automatically reject outliers", > > the > > program gets an error message and closes. What can I do to fix this > > issue? > > I have uninstalled and installed the version several times. > > > > Please help. > > > > Thanks, > > > > Lisa > > > > > > > > > > Lisa A. Kreber, Ph.D., CBIS > > Senior Neuroscientist/Research Coordinator > > Centre for Neuro Skills (CNS)? > > Clinical Research & Education Foundation (CREF) > > 2658 Mt. Vernon Avenue > > Bakersfield, CA 93306 > > (661) 872-3408 > > (661) 335-1458 Cell > > (661) 872-5150 Fax > > > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > http://lists.mristudio.org/mailman/listinfo/ > > Unsubscribe, send a blank email to: > > Mristudio-users-unsubscribe at mristudio.org > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > http://lists.mristudio.org/mailman/listinfo/ > > Unsubscribe, send a blank email to: > > Mristudio-users-unsubscribe at mristudio.org > > > > > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > http://lists.mristudio.org/mailman/listinfo/ > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091018/a85b8c33/attachment-0001.html -------------- next part -------------- _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From support at mristudio.org Mon Oct 19 09:07:53 2009 From: support at mristudio.org (support at mristudio.org) Date: Mon, 19 Oct 2009 09:07:53 -0400 (EDT) Subject: [Mristudio-users] bug in version 2.4.01 of DTI dti studio??? In-Reply-To: References: Message-ID: <2213.10.16.57.13.1255957673.squirrel@webmail.mristudio.org> if the DICOM files are not in default format, the old version will not work with it. please use the new version. > Hi, > > I have plenty of RAM and my dataset is only 64 slices. As soon as I removed this > version of DTI studio and downloaded the newer version, I had no more issues and > no longer received the error message. I made no changes to my gradient table and > did the same procedure, just with the new version. My colleague (who has a > different brand of computer and not as much RAM as I do, was doing the same > thing that I was with the same dataset but she never encountered the problem > that I did with the 2.4.01 version. > > Lisa > > > ----- Original Message ----- > From: susumu mori [susumu at mri.jhu.edu] > Sent: 10/18/2009 06:11 PM AST > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > > Subject: Re: [Mristudio-users] bug in version 2.4.01 of DTI dti studio??? > > > > Hi Hangyi, > > Could you follow up this error message? Do you think it's just caused by > memory shortage? > Aman and Lisa, how much RAM do you have and how large is your raw DWI data? > Have you tried to limit the number of slices to be calculated? > > Susumu > > On Mon, Oct 12, 2009 at 11:00 AM, aman gupta wrote: > >> Hi All, >> >> I am also facing the same problem while using DTI studio. I am getting >> the same error message as mentioned in the email below. Any >> suggestions would be really helpful. >> >> Thanks, >> Aman Gupta >> PhD Candidate >> Department of Bioengineering, >> University of Ilinois at Chicago, >> Sports Biomechanics Research Lab, >> Department of Orthopedics, >> Rush University Medical Center, >> Chicago, IL-60612. >> >> >> On Tue, Oct 6, 2009 at 10:35 AM, wrote: >> > This did not work. I have checked the gradient table and it is correct. >> I >> > have the same number of gradient directions as I have images and the >> images >> > are all being read into dti studio. >> > >> > The program always shuts down at "automatic outier rejection" when I >> select >> > no. The message I get is: The instruction at "0x73dd11c7" referenced >> > memory at "0x00000004" the memory could not be read" >> > >> > Any help would be greatly appreciated. >> > >> > >> > >> > >> > >> > Lisa A. Kreber, Ph.D., CBIS >> > Senior Neuroscientist/Research Coordinator >> > Centre for Neuro Skills (CNS)?? >> > Clinical Research & Education Foundation (CREF) >> > 2658 Mt. Vernon Avenue >> > Bakersfield, CA 93306 >> > (661) 872-3408 >> > (661) 335-1458 Cell >> > (661) 872-5150 Fax >> > >> > >> > >> > >> > susumu mori >> > > > du> To >> > Sent by: "DTI Studio, ROI Editor, Landmarker >> > mristudio-users-b Questions/Support" >> > ounces at mristudio. >> > org cc >> > >> > Subject >> > 10/05/2009 04:15 Re: [Mristudio-users] bug in >> > PM version 2.4.01 of DTI dti studio??? >> > >> > >> > Please respond to >> > "DTI Studio, ROI >> > Editor, >> > Landmarker >> > Questions/Support >> > " >> > > > mristudio.org> >> > >> > >> > >> > >> > >> > >> > Are you using DICOM? If so, it is possible that your gradient table is >> not >> > right. For example, if your table suggest there should be 13 images and >> if >> > your data file contains 14 images, DtiStudio gets error. Please do the >> > following: >> > >> > 1) Once data are read, please look at the pull-down menu in the "Image" >> > tab, go over all images, and make sure how many images are loaded and all >> > loaded images have the same number of slices. >> > 2) Close the window before you move to the tensor calculation and open >> the >> > same DTI set again. When you get the opening data input window, check >> > carefully the gradient table, which DtiStudio remembers from the previous >> > session. If you made any mistake in the table, here you should be able to >> > find it. >> > >> > Please try. >> > >> > On Mon, Oct 5, 2009 at 6:34 PM, wrote: >> > Hi, All: >> > >> > I just downloaded version 2.4.01 of DTI studio and everytime I try to >> > create the DTI map and select "NO" to "automatically reject outliers", >> > the >> > program gets an error message and closes. What can I do to fix this >> > issue? >> > I have uninstalled and installed the version several times. >> > >> > Please help. >> > >> > Thanks, >> > >> > Lisa >> > >> > >> > >> > >> > Lisa A. Kreber, Ph.D., CBIS >> > Senior Neuroscientist/Research Coordinator >> > Centre for Neuro Skills (CNS)?? >> > Clinical Research & Education Foundation (CREF) >> > 2658 Mt. Vernon Avenue >> > Bakersfield, CA 93306 >> > (661) 872-3408 >> > (661) 335-1458 Cell >> > (661) 872-5150 Fax >> > >> > >> > _______________________________________________ >> > Mristudio-users mailing list >> > Mristudio-users at mristudio.org >> > http://lists.mristudio.org/mailman/listinfo/ >> > Unsubscribe, send a blank email to: >> > Mristudio-users-unsubscribe at mristudio.org >> > >> > _______________________________________________ >> > Mristudio-users mailing list >> > Mristudio-users at mristudio.org >> > http://lists.mristudio.org/mailman/listinfo/ >> > Unsubscribe, send a blank email to: >> > Mristudio-users-unsubscribe at mristudio.org >> > >> > >> > >> > _______________________________________________ >> > Mristudio-users mailing list >> > Mristudio-users at mristudio.org >> > http://lists.mristudio.org/mailman/listinfo/ >> > Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> > >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > From amangupta2005 at gmail.com Mon Oct 19 13:33:40 2009 From: amangupta2005 at gmail.com (aman gupta) Date: Mon, 19 Oct 2009 12:33:40 -0500 Subject: [Mristudio-users] bug in version 2.4.01 of DTI dti studio??? In-Reply-To: <2213.10.16.57.13.1255957673.squirrel@webmail.mristudio.org> References: <2213.10.16.57.13.1255957673.squirrel@webmail.mristudio.org> Message-ID: Hi, That's helpful to know. Thanks for sharing. I have 2 GB of RAM, but i haven't tried the newer version yet. Let me download and check if my dataset works on the new version. Thanks, Aman On Mon, Oct 19, 2009 at 8:07 AM, wrote: > > > if the DICOM files are not in default format, the old version will not work with > it. ?please use the new version. > > > > > > > > >> Hi, >> >> I have plenty of RAM and my dataset is only 64 slices. As soon as I removed this >> version of DTI studio and downloaded the newer version, I had no more issues and >> no longer received the error message. I made no changes to my gradient table and >> did the same procedure, just with the new version. My colleague (who has a >> different brand of computer and not as much RAM as I do, was doing the same >> thing that I was with the same dataset but she never encountered the problem >> that I did with the 2.4.01 version. >> >> Lisa >> >> >> ----- Original Message ----- >> From: susumu mori [susumu at mri.jhu.edu] >> Sent: 10/18/2009 06:11 PM AST >> To: "DTI Studio, ROI Editor, Landmarker Questions/Support" >> >> Subject: Re: [Mristudio-users] bug in version 2.4.01 of DTI dti studio??? >> >> >> >> Hi Hangyi, >> >> Could you follow up this error message? Do you think it's just caused by >> memory shortage? >> Aman and Lisa, how much RAM do you have and how large is your raw DWI data? >> Have you tried to limit the number of slices to be calculated? >> >> Susumu >> >> On Mon, Oct 12, 2009 at 11:00 AM, aman gupta wrote: >> >>> Hi All, >>> >>> I am also facing the same problem while using DTI studio. I am getting >>> the same error message as mentioned in the email below. Any >>> suggestions would be really helpful. >>> >>> Thanks, >>> Aman Gupta >>> PhD Candidate >>> Department of Bioengineering, >>> University of Ilinois at Chicago, >>> Sports Biomechanics Research Lab, >>> Department of Orthopedics, >>> Rush University Medical Center, >>> Chicago, IL-60612. >>> >>> >>> On Tue, Oct 6, 2009 at 10:35 AM, ? wrote: >>> > This did not work. ?I have checked the gradient table and it is correct. >>> ?I >>> > have the same number of gradient directions as I have images and the >>> images >>> > are all being read into dti studio. >>> > >>> > The program always shuts down at "automatic outier rejection" when I >>> select >>> > no. ?The message I get is: The instruction at "0x73dd11c7" referenced >>> > memory at "0x00000004" the memory could not be read" >>> > >>> > Any help would be greatly appreciated. >>> > >>> > >>> > >>> > >>> > >>> > Lisa A. Kreber, Ph.D., CBIS >>> > Senior Neuroscientist/Research Coordinator >>> > Centre for Neuro Skills (CNS)?? >>> > Clinical Research & Education Foundation (CREF) >>> > 2658 Mt. Vernon Avenue >>> > Bakersfield, CA 93306 >>> > (661) 872-3408 >>> > (661) 335-1458 Cell >>> > (661) 872-5150 Fax >>> > >>> > >>> > >>> > >>> > ? ? ? ? ? ? susumu mori >>> > ? ? ? ? ? ? >> > ? ? ? ? ? ? du> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?To >>> > ? ? ? ? ? ? Sent by: ? ? ? ? ? ? ? ? ?"DTI Studio, ROI Editor, Landmarker >>> > ? ? ? ? ? ? mristudio-users-b ? ? ? ? Questions/Support" >>> > ? ? ? ? ? ? ounces at mristudio. ? ? ? ? >>> > ? ? ? ? ? ? org ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?cc >>> > >>> > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Subject >>> > ? ? ? ? ? ? 10/05/2009 04:15 ? ? ? ? ?Re: [Mristudio-users] bug in >>> > ? ? ? ? ? ? PM ? ? ? ? ? ? ? ? ? ? ? ?version 2.4.01 of DTI dti studio??? >>> > >>> > >>> > ? ? ? ? ? ? Please respond to >>> > ? ? ? ? ? ? "DTI Studio, ROI >>> > ? ? ? ? ? ? ? ? ?Editor, >>> > ? ? ? ? ? ? ? ?Landmarker >>> > ? ? ? ? ? ? Questions/Support >>> > ? ? ? ? ? ? ? ? ? ? " >>> > ? ? ? ? ? ? >> > ? ? ? ? ? ? ?mristudio.org> >>> > >>> > >>> > >>> > >>> > >>> > >>> > Are you using DICOM? If so, it is possible that your gradient table is >>> not >>> > right. For example, if your table suggest there should be 13 images and >>> if >>> > your data file contains 14 images, DtiStudio gets error. Please do the >>> > following: >>> > >>> > 1) Once data are read, please look at the pull-down menu in the "Image" >>> > tab, go over all images, and make sure how many images are loaded and all >>> > loaded images have the same number of slices. >>> > 2) Close the window before you move to the tensor calculation and open >>> the >>> > same DTI set again. When you get the opening data input window, check >>> > carefully the gradient table, which DtiStudio remembers from the previous >>> > session. If you made any mistake in the table, here you should be able to >>> > find it. >>> > >>> > Please try. >>> > >>> > On Mon, Oct 5, 2009 at 6:34 PM, wrote: >>> > ?Hi, All: >>> > >>> > ?I just downloaded version 2.4.01 of DTI studio and everytime I try to >>> > ?create the DTI map and select "NO" to "automatically reject outliers", >>> > ?the >>> > ?program gets an error message and closes. ?What can I do to fix this >>> > ?issue? >>> > ?I have uninstalled and installed the version several times. >>> > >>> > ?Please help. >>> > >>> > ?Thanks, >>> > >>> > ?Lisa >>> > >>> > >>> > >>> > >>> > ?Lisa A. Kreber, Ph.D., CBIS >>> > ?Senior Neuroscientist/Research Coordinator >>> > ?Centre for Neuro Skills (CNS)?? >>> > ?Clinical Research & Education Foundation (CREF) >>> > ?2658 Mt. Vernon Avenue >>> > ?Bakersfield, CA 93306 >>> > ?(661) 872-3408 >>> > ?(661) 335-1458 Cell >>> > ?(661) 872-5150 Fax >>> > >>> > >>> > ?_______________________________________________ >>> > ?Mristudio-users mailing list >>> > ?Mristudio-users at mristudio.org >>> > ?http://lists.mristudio.org/mailman/listinfo/ >>> > ?Unsubscribe, send a blank email to: >>> > ?Mristudio-users-unsubscribe at mristudio.org >>> > >>> > _______________________________________________ >>> > Mristudio-users mailing list >>> > Mristudio-users at mristudio.org >>> > http://lists.mristudio.org/mailman/listinfo/ >>> > Unsubscribe, send a blank email to: >>> > Mristudio-users-unsubscribe at mristudio.org >>> > >>> > >>> > >>> > _______________________________________________ >>> > Mristudio-users mailing list >>> > Mristudio-users at mristudio.org >>> > http://lists.mristudio.org/mailman/listinfo/ >>> > Unsubscribe, send a blank email to: >>> Mristudio-users-unsubscribe at mristudio.org >>> > >>> >>> _______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: >>> Mristudio-users-unsubscribe at mristudio.org >>> >>> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org >> > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > From HuangS4 at uthscsa.edu Mon Nov 2 11:26:28 2009 From: HuangS4 at uthscsa.edu (Huang, Shiliang) Date: Mon, 02 Nov 2009 10:26:28 -0600 Subject: [Mristudio-users] What is the name of the image after AIR Registration Message-ID: <54BCF36E4FE44644A377261164E3104548CD1BCC5B@HSC-M2.win.uthscsa.edu> Hi every one I used automatic image registration in DTIStudio and select the option"creat new images after registration". It should creat a new file which is the registrated image. Where can I find this new file? What is the name of this file? Thanks, Shiliang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091102/8cf1882f/attachment.html From support at mristudio.org Mon Nov 2 11:49:05 2009 From: support at mristudio.org (support at mristudio.org) Date: Mon, 2 Nov 2009 11:49:05 -0500 (EST) Subject: [Mristudio-users] What is the name of the image after AIR Registration In-Reply-To: <54BCF36E4FE44644A377261164E3104548CD1BCC5B@HSC-M2.win.uthscsa.edu> References: <54BCF36E4FE44644A377261164E3104548CD1BCC5B@HSC-M2.win.uthscsa.edu> Message-ID: <1168.10.16.57.13.1257180545.squirrel@webmail.mristudio.org> the new images can be found in the drop-down image list; > Hi every one > I used automatic image registration in DTIStudio and select the option"creat new > images after registration". It should creat a new file which is the registrated > image. Where can I find this new file? What is the name of this file? > Thanks, > Shiliang > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > From HuangS4 at uthscsa.edu Mon Nov 2 11:55:30 2009 From: HuangS4 at uthscsa.edu (Huang, Shiliang) Date: Mon, 02 Nov 2009 10:55:30 -0600 Subject: [Mristudio-users] What is the name of the image after AIR Registration In-Reply-To: <1168.10.16.57.13.1257180545.squirrel@webmail.mristudio.org> References: <54BCF36E4FE44644A377261164E3104548CD1BCC5B@HSC-M2.win.uthscsa.edu> <1168.10.16.57.13.1257180545.squirrel@webmail.mristudio.org> Message-ID: <54BCF36E4FE44644A377261164E3104548CD1BCC64@HSC-M2.win.uthscsa.edu> Thank you. How to save them as a REC file? Thanks Shiliang -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of support at mristudio.org Sent: Monday, November 02, 2009 10:49 AM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] What is the name of the image after AIR Registration the new images can be found in the drop-down image list; > Hi every one > I used automatic image registration in DTIStudio and select the option"creat new > images after registration". It should creat a new file which is the registrated > image. Where can I find this new file? What is the name of this file? > Thanks, > Shiliang > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From Joseph.Helpern at nyumc.org Mon Nov 2 11:59:14 2009 From: Joseph.Helpern at nyumc.org (Helpern, Joseph) Date: Mon, 02 Nov 2009 11:59:14 -0500 Subject: [Mristudio-users] What is the name of the image after AIR Registration Message-ID: <56BD66F92D85B1438E3661D306508C2864610B9F@MSGWSDCPMB07.nyumc.org> Although I find this rivetting, would you be kind enough to take this conversation off line? Thanks. ----- Original Message ----- From: mristudio-users-bounces at mristudio.org To: DTI Studio, ROI Editor, Landmarker Questions/Support Sent: Mon Nov 02 11:55:30 2009 Subject: Re: [Mristudio-users] What is the name of the image after AIR Registration Thank you. How to save them as a REC file? Thanks Shiliang -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of support at mristudio.org Sent: Monday, November 02, 2009 10:49 AM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] What is the name of the image after AIR Registration the new images can be found in the drop-down image list; > Hi every one > I used automatic image registration in DTIStudio and select the option"creat new > images after registration". It should creat a new file which is the registrated > image. Where can I find this new file? What is the name of this file? > Thanks, > Shiliang > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. ================================= From ccapeland at anatomicaltravel.com Mon Nov 2 15:55:03 2009 From: ccapeland at anatomicaltravel.com (Chad Capeland) Date: Mon, 02 Nov 2009 15:55:03 -0500 Subject: [Mristudio-users] What is the name of the image after AIR Registration In-Reply-To: <56BD66F92D85B1438E3661D306508C2864610B9F@MSGWSDCPMB07.nyumc.org> References: <56BD66F92D85B1438E3661D306508C2864610B9F@MSGWSDCPMB07.nyumc.org> Message-ID: <4AEF4727.4080206@anatomicaltravel.com> Helpern, Joseph wrote: > Although I find this rivetting, would you be kind enough to take this conversation off line? Thanks. > You could unsubscribe from the support list, while staying subscribed to the announcement list. Will reduce volume for you. -- Chad Capeland Director R&D Anatomical Travelogue LLC ccapeland at anatomicaltravel.com 212-625-6665 www.thevisualmd.com www.anatomicaltravel.com/research -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. From Joseph.Helpern at nyumc.org Mon Nov 2 16:08:26 2009 From: Joseph.Helpern at nyumc.org (Helpern, Joseph) Date: Mon, 02 Nov 2009 16:08:26 -0500 Subject: [Mristudio-users] What is the name of the image after AIR Registration Message-ID: <56BD66F92D85B1438E3661D306508C2864610BA5@MSGWSDCPMB07.nyumc.org> Understood, but then why has this been the first barrage of emails I have received like this? ----- Original Message ----- From: mristudio-users-bounces at mristudio.org To: DTI Studio, ROI Editor, Landmarker Questions/Support Sent: Mon Nov 02 15:55:03 2009 Subject: Re: [Mristudio-users] What is the name of the image after AIR Registration Helpern, Joseph wrote: > Although I find this rivetting, would you be kind enough to take this conversation off line? Thanks. > You could unsubscribe from the support list, while staying subscribed to the announcement list. Will reduce volume for you. -- Chad Capeland Director R&D Anatomical Travelogue LLC ccapeland at anatomicaltravel.com 212-625-6665 www.thevisualmd.com www.anatomicaltravel.com/research -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. ================================= From Joseph.Helpern at nyumc.org Mon Nov 2 16:10:22 2009 From: Joseph.Helpern at nyumc.org (Helpern, Joseph) Date: Mon, 02 Nov 2009 16:10:22 -0500 Subject: [Mristudio-users] What is the name of the image after AIR Registration Message-ID: <56BD66F92D85B1438E3661D306508C2864610BA6@MSGWSDCPMB07.nyumc.org> Perhaps something is afoul with their server? ----- Original Message ----- From: mristudio-users-bounces at mristudio.org To: DTI Studio, ROI Editor, Landmarker Questions/Support Sent: Mon Nov 02 15:55:03 2009 Subject: Re: [Mristudio-users] What is the name of the image after AIR Registration Helpern, Joseph wrote: > Although I find this rivetting, would you be kind enough to take this conversation off line? Thanks. > You could unsubscribe from the support list, while staying subscribed to the announcement list. Will reduce volume for you. -- Chad Capeland Director R&D Anatomical Travelogue LLC ccapeland at anatomicaltravel.com 212-625-6665 www.thevisualmd.com www.anatomicaltravel.com/research -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. ================================= From ccapeland at anatomicaltravel.com Mon Nov 2 16:25:23 2009 From: ccapeland at anatomicaltravel.com (Chad Capeland) Date: Mon, 02 Nov 2009 16:25:23 -0500 Subject: [Mristudio-users] What is the name of the image after AIR Registration In-Reply-To: <56BD66F92D85B1438E3661D306508C2864610BA5@MSGWSDCPMB07.nyumc.org> References: <56BD66F92D85B1438E3661D306508C2864610BA5@MSGWSDCPMB07.nyumc.org> Message-ID: <4AEF4E43.9060904@anatomicaltravel.com> Helpern, Joseph wrote: > Understood, but then why has this been the first barrage of emails I have received like this? > Barrage? Maybe you see something I don't? I'm getting no more than 5-6 messages per day. -- Chad Capeland Director R&D Anatomical Travelogue LLC ccapeland at anatomicaltravel.com 212-625-6665 www.thevisualmd.com www.anatomicaltravel.com/research -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. From HuangS4 at uthscsa.edu Tue Nov 3 11:45:44 2009 From: HuangS4 at uthscsa.edu (Huang, Shiliang) Date: Tue, 03 Nov 2009 10:45:44 -0600 Subject: [Mristudio-users] How to finish drawing ROI In-Reply-To: <56BD66F92D85B1438E3661D306508C2864610BA6@MSGWSDCPMB07.nyumc.org> References: <56BD66F92D85B1438E3661D306508C2864610BA6@MSGWSDCPMB07.nyumc.org> Message-ID: <54BCF36E4FE44644A377261164E3104548CD1BCCF2@HSC-M2.win.uthscsa.edu> Hi everyone There is following message on the DTISudio manual " ROI drawing - shape This section is used to change ROI shapes. There are three kinds of ROI shapes available. They are: Poly: Draw a polygon with a series of mouse clicks. Finish drawing by double-clicking or cancel drawing by double-clicking while holding "ESC-key"." But I can not finish drawing ROI by double-clicking. The ROI will dispear after I double-clicking. It is the same result with double-clicking while holding "ESC-key. How can I finish drawing ROI? Thanks Shiliang -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Helpern, Joseph Sent: Monday, November 02, 2009 3:10 PM To: 'mristudio-users at mristudio.org' Subject: Re: [Mristudio-users] What is the name of the image after AIR Registration Perhaps something is afoul with their server? ----- Original Message ----- From: mristudio-users-bounces at mristudio.org To: DTI Studio, ROI Editor, Landmarker Questions/Support Sent: Mon Nov 02 15:55:03 2009 Subject: Re: [Mristudio-users] What is the name of the image after AIR Registration Helpern, Joseph wrote: > Although I find this rivetting, would you be kind enough to take this conversation off line? Thanks. > You could unsubscribe from the support list, while staying subscribed to the announcement list. Will reduce volume for you. -- Chad Capeland Director R&D Anatomical Travelogue LLC ccapeland at anatomicaltravel.com 212-625-6665 www.thevisualmd.com www.anatomicaltravel.com/research -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. ================================= _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From susumu at mri.jhu.edu Tue Nov 3 13:14:16 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Tue, 03 Nov 2009 13:14:16 -0500 Subject: [Mristudio-users] How to finish drawing ROI In-Reply-To: <54BCF36E4FE44644A377261164E3104548CD1BCCF2@HSC-M2.win.uthscsa.edu> References: <56BD66F92D85B1438E3661D306508C2864610BA6@MSGWSDCPMB07.nyumc.org> <54BCF36E4FE44644A377261164E3104548CD1BCCF2@HSC-M2.win.uthscsa.edu> Message-ID: Hi Shiliang, I believe Hangyi will follow up your question, but if you are using DtiStudio for ROI-based image analysis, not for fiber tracking, I suggest you to look at RoiEditor, which is much more powerful for image quantification. Susumu On Tue, Nov 3, 2009 at 11:45 AM, Huang, Shiliang wrote: > Hi everyone > There is following message on the DTISudio manual > " ROI drawing - shape > This section is used to change ROI shapes. There are three kinds of ROI > shapes available. They are: Poly: Draw a polygon with a series of mouse > clicks. Finish drawing by double-clicking or cancel drawing by > double-clicking while holding "ESC-key"." > > > But I can not finish drawing ROI by double-clicking. The ROI will dispear > after I double-clicking. It is the same result with double-clicking while > holding "ESC-key. > > How can I finish drawing ROI? > Thanks > Shiliang > > > > > > > > > > > > > > > > > -----Original Message----- > From: mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org] On Behalf Of Helpern, Joseph > Sent: Monday, November 02, 2009 3:10 PM > To: 'mristudio-users at mristudio.org' > Subject: Re: [Mristudio-users] What is the name of the image after AIR > Registration > > Perhaps something is afoul with their server? > > > ----- Original Message ----- > From: mristudio-users-bounces at mristudio.org < > mristudio-users-bounces at mristudio.org> > To: DTI Studio, ROI Editor, Landmarker Questions/Support < > mristudio-users at mristudio.org> > Sent: Mon Nov 02 15:55:03 2009 > Subject: Re: [Mristudio-users] What is the name of the image after AIR > Registration > > Helpern, Joseph wrote: > > Although I find this rivetting, would you be kind enough to take this > conversation off line? Thanks. > > > You could unsubscribe from the support list, while staying subscribed to > the announcement list. Will reduce volume for you. > > -- > Chad Capeland > Director R&D > Anatomical Travelogue LLC > ccapeland at anatomicaltravel.com > 212-625-6665 > > www.thevisualmd.com > www.anatomicaltravel.com/research > > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > ------------------------------------------------------------ > This email message, including any attachments, is for the sole use of the > intended recipient(s) and may contain information that is proprietary, > confidential, and exempt from disclosure under applicable law. Any > unauthorized review, use, disclosure, or distribution is prohibited. If you > have received this email in error please notify the sender by return email > and delete the original message. Please note, the recipient should check > this email and any attachments for the presence of viruses. The organization > accepts no liability for any damage caused by any virus transmitted by this > email. > ================================= > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091103/8861fde8/attachment-0001.html From Min.Xu at utsouthwestern.edu Tue Nov 3 13:47:09 2009 From: Min.Xu at utsouthwestern.edu (Min Xu) Date: Tue, 03 Nov 2009 12:47:09 -0600 Subject: [Mristudio-users] How to draw the ROI bilateral using ROIEditor Message-ID: <4AF0264F.0658.0056.0@UTSouthwestern.edu> Hi everyone I am a new player with ROIEditor. I am trying to draw the ROI bilateral. It is easy to draw ROI on the lesion side, but I find it is difficult to draw the same shape and size of ROI on the contralateral. How can I finish drawing ROI with same shape and size bilateral? Thanks a lot, Min From HuangS4 at uthscsa.edu Wed Nov 4 17:05:06 2009 From: HuangS4 at uthscsa.edu (Huang, Shiliang) Date: Wed, 04 Nov 2009 16:05:06 -0600 Subject: [Mristudio-users] How much are the ADC and FA of the white matter and grey matter of human brain Message-ID: <54BCF36E4FE44644A377261164E3104548CD1BCDBE@HSC-M2.win.uthscsa.edu> Hi every one I have got the results with DTIStudio. Thank you all very much. I got the mean value with ROI. My results are : White matter std Gray matter std ADC 8.48e-004 1.97e-004 1.01e-003 2.59e-004 FA 0.26 0.11 0.23 0.08 But I do not know if my results right or not. Can anyone tell me how much are the ADC and FA of the white matter and grey matter of human brain? Thanks Shiliang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091104/39b221e9/attachment.html From HuangS4 at uthscsa.edu Wed Nov 4 17:40:18 2009 From: HuangS4 at uthscsa.edu (Huang, Shiliang) Date: Wed, 04 Nov 2009 16:40:18 -0600 Subject: [Mristudio-users] Why some part of images dispeared after registed with AIR? Message-ID: <54BCF36E4FE44644A377261164E3104548CD1BCDC7@HSC-M2.win.uthscsa.edu> Hi everyone I found some of registed images have been cut away after register with AIR? What is the reason? Thanks, Shiliang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091104/e1a32f76/attachment.html From susumu at mri.jhu.edu Wed Nov 4 17:53:51 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 04 Nov 2009 17:53:51 -0500 Subject: [Mristudio-users] Why some part of images dispeared after registed with AIR? In-Reply-To: <54BCF36E4FE44644A377261164E3104548CD1BCDC7@HSC-M2.win.uthscsa.edu> References: <54BCF36E4FE44644A377261164E3104548CD1BCDC7@HSC-M2.win.uthscsa.edu> Message-ID: Hi Shiliang, If you see that the first and the last slices of images are cut away, that is the proof that the images went through image registration. If there is slight rotation involved in image registration, there is through-slice image interpolation. This works except for the first and the last slices, which do not have slices beneath or above it. Consequently, the part of the slice is occupied by empty pixels. Does it make sense? Once you use b0 - DWI image registration to reduce subjection motion, it is likely that you have to throw away these two slices. Susumu On Wed, Nov 4, 2009 at 5:40 PM, Huang, Shiliang wrote: > Hi everyone > > I found some of registed images have been cut away after register with AIR? > What is the reason? > > Thanks, > > Shiliang > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091104/aa7b1c70/attachment.html From grojasy at puc.cl Sun Nov 8 19:04:26 2009 From: grojasy at puc.cl (Gonzalo Rojas) Date: Sun, 08 Nov 2009 21:04:26 -0300 Subject: [Mristudio-users] gradient directions table... Message-ID: <4AF75C8A.409@puc.cl> Hi: Which are the gradient direction table (20 directions) for a Siemens Avanto (syngo MR B15) ? Sincerely, Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl From susumu at mri.jhu.edu Wed Nov 11 20:55:05 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 11 Nov 2009 20:55:05 -0500 Subject: [Mristudio-users] gradient directions table... In-Reply-To: <4AF75C8A.409@puc.cl> References: <4AF75C8A.409@puc.cl> Message-ID: Hi Gonzalo, Here I attached a list of VB13 gradient table. Please let us know if it doesn't work. Susumu On Sun, Nov 8, 2009 at 7:04 PM, Gonzalo Rojas wrote: > Hi: > > Which are the gradient direction table (20 directions) for a Siemens > Avanto (syngo MR B15) ? > > Sincerely, > > > Gonzalo Rojas Costa > Department of Radiology > Las Condes Clinic > Lo Fontecilla 441, Las Condes, Santiago, Chile. > Tel: 56-2-2105170 > Cel: 56-9-97771785 > www.clc.cl > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091111/fa641dd4/attachment-0001.html -------------- next part -------------- case 1: m_lDirections = lDirections ; delete [] m_sVector ; m_sVector = new VectorStruct [m_lDirections] ; m_eCoordinateSystem = PRS ; switch (cFlag) { case 'P': setVector (0, 1.0, 0, 0) ; break ; case 'R': setVector (0, 0, 1.0, 0) ; break ; case 'S': setVector (0, 0, 0, 1.0) ; break ; default: if ( ! isContextPrepForBinarySearch || (m_lDebugLevel & DEBUG_RETURN) ) TRACE_PUT2 (TC_INFO, TF_SEQ, "%s ERROR: Invalid control flag '%c' in sequence code.", ptModule, cFlag) ; return false ; } break ; case 3: m_lDirections = lDirections ; delete [] m_sVector ; m_sVector = new VectorStruct [m_lDirections] ; switch (cFlag) { case 'O': m_eCoordinateSystem = PRS ; setVector (0, 1.0, 0, 0) ; setVector (1, 0, 1.0, 0) ; setVector (2, 0, 0, 1.0) ; break ; case 'T': m_eCoordinateSystem = XYZ ; setVector (0, 1.0, 1.0, -0.5) ; setVector (1, 1.0, -0.5, 1.0) ; setVector (2, -0.5, 1.0, 1.0) ; break ; default: if ( ! isContextPrepForBinarySearch || (m_lDebugLevel & DEBUG_RETURN) ) TRACE_PUT2 (TC_INFO, TF_SEQ, "%s ERROR: Invalid control flag '%c' in sequence code.", ptModule, cFlag) ; return false ; } break ; case 6: m_lDirections = lDirections ; delete [] m_sVector ; m_sVector = new VectorStruct [m_lDirections] ; m_eCoordinateSystem = XYZ ; // (Note: do not modify the following comments - doxygen greps for them) // vector set for 6 directions (normalised to maximum) setVector (0, 1.0, 0.0, 1.0) ; setVector (1, -1.0, 0.0, 1.0) ; setVector (2, 0.0, 1.0, 1.0) ; setVector (3, 0.0, 1.0, -1.0) ; setVector (4, 1.0, 1.0, 0.0) ; setVector (5, -1.0, 1.0, 0.0) ; break ; case 10: m_lDirections = lDirections ; delete [] m_sVector ; m_sVector = new VectorStruct [m_lDirections] ; m_eCoordinateSystem = XYZ ; // vector set for 10 directions (normalised to maximum) setVector (0, 0.000000, 0.809017, 0.618034 ) ; setVector (1, 0.000000, 0.190983, 1.000000 ) ; setVector (2, -0.587785, 0.809017, 0.190983 ) ; setVector (3, -0.951057, 0.190983, 0.309017 ) ; setVector (4, -0.363271, 0.809017, -0.500000 ) ; setVector (5, -0.587785, 0.190983, -0.809017 ) ; setVector (6, 0.363271, 0.809017, -0.500000 ) ; setVector (7, 0.587785, 0.190983, -0.809017 ) ; setVector (8, 0.587785, 0.809017, 0.190983 ) ; setVector (9, 0.951057, 0.190983, 0.309017 ) ; break ; case 12: m_lDirections = lDirections ; delete [] m_sVector ; m_sVector = new VectorStruct [m_lDirections] ; m_eCoordinateSystem = XYZ ; // vector set for 12 directions (normalised to maximum) setVector (0, 1.000000, 0.414250, -0.414250 ); setVector (1, 1.000000, -0.414250, -0.414250 ); setVector (2, 1.000000, -0.414250, 0.414250 ); setVector (3, 1.000000, 0.414250, 0.414250 ); setVector (4, 0.414250, 0.414250, 1.000000 ); setVector (5, 0.414250, 1.000000, 0.414250 ); setVector (6, 0.414250, 1.000000, -0.414250 ); setVector (7, 0.414250, 0.414250, -1.000000 ); setVector (8, 0.414250, -0.414250, -1.000000 ); setVector (9, 0.414250, -1.000000, -0.414250 ); setVector (10, 0.414250, -1.000000, 0.414250 ); setVector (11, 0.414250, -0.414250, 1.000000 ); break ; case 20: m_lDirections = lDirections ; delete [] m_sVector ; m_sVector = new VectorStruct [m_lDirections] ; m_eCoordinateSystem = XYZ ; // vector set for 20 directions (normalised to maximum) setVector (0, 1.000000, 0.000000, 0.000000) ; setVector (1, 0.000000, 1.000000, 0.000000) ; setVector (2, -0.031984, 0.799591, 0.599693) ; setVector (3, 0.856706, 0.493831, -0.148949) ; setVector (4, 0.834429, 0.309159, 0.456234) ; setVector (5, 0.834429, -0.309159, 0.456234) ; setVector (6, 0.856706, -0.493831, -0.148949) ; setVector (7, 0.822228, 0.000000, -0.569158) ; setVector (8, 0.550834, 0.425872, -0.717784) ; setVector (9, 0.468173, 0.834308, -0.291108) ; setVector (10, 0.515933, 0.808894, 0.281963) ; setVector (11, 0.391890, 0.515855, 0.761785) ; setVector (12, 0.478151, 0.000000, 0.878278) ; setVector (13, 0.391890, -0.515855, 0.761785) ; setVector (14, 0.515933, -0.808894, 0.281963) ; setVector (15, 0.468173, -0.834308, -0.291108) ; setVector (16, 0.550834, -0.425872, -0.717784) ; setVector (17, 0.111012, -0.264029, -0.958105) ; setVector (18, 0.111012, 0.264029, -0.958105) ; setVector (19, 0.031984, 0.799591, -0.599693) ; break ; 0: 0, 0, 0 1: 1.000000, 0.000000, 0.000000; 2: 0.000000, 1.000000, 0.000000; 3: -0.031984, 0.799591, 0.599693; 4: 0.856706, 0.493831, -0.148949; 5: 0.834429, 0.309159, 0.456234; 6: 0.834429, -0.309159, 0.456234; 7: 0.856706, -0.493831, -0.148949; 8: 0.822228, 0.000000, -0.569158; 9: 0.550834, 0.425872, -0.717784 ; 10: 0.468173, 0.834308, -0.291108 ; 11: 0.515933, 0.808894, 0.281963 ; 12: 0.391890, 0.515855, 0.761785 ; 13: 0.478151, 0.000000, 0.878278 ; 14: 0.391890, -0.515855, 0.761785 ; 15: 0.515933, -0.808894, 0.281963 ; 16: 0.468173, -0.834308, -0.291108 ; 17: 0.550834, -0.425872, -0.717784 ; 18: 0.111012, -0.264029, -0.958105 ; 19: 0.111012, 0.264029, -0.958105 ; 20: 0.031984, 0.799591, -0.599693 ; case 30: m_lDirections = lDirections ; delete [] m_sVector ; m_sVector = new VectorStruct [m_lDirections] ; m_eCoordinateSystem = XYZ ; // vector set for 30 directions (normalised to maximum) setVector (0, -0.208098, 0.525514, 0.850005 ) ; setVector (1, 0.202387, 0.526131, 0.851002 ) ; setVector (2, 0.409956, 0.175267, 0.918257 ) ; setVector (3, -0.412630, 0.742620, 0.565889 ) ; setVector (4, -0.207127, 0.959492, 0.280092 ) ; setVector (5, -0.872713, 0.525505, 0.064764 ) ; setVector (6, -0.746815, 0.526129, 0.455449 ) ; setVector (7, -0.415238, 0.175473, 0.915841 ) ; setVector (8, -0.746636, 0.175268, 0.673642 ) ; setVector (9, -0.665701, 0.742619, -0.217574 ) ; setVector (10, -0.330391, 0.959489, -0.110458 ) ; setVector (11, -0.331275, 0.525513, -0.809983 ) ; setVector (12, -0.663936, 0.526130, -0.569521 ) ; setVector (13, -0.999332, 0.175474, -0.111904 ) ; setVector (14, -0.871398, 0.175267, -0.501922 ) ; setVector (15, 0.001214, 0.742616, -0.700356 ) ; setVector (16, 0.002949, 0.959483, -0.348370 ) ; setVector (17, 0.667975, 0.525509, -0.565356 ) ; setVector (18, 0.336490, 0.526126, -0.807431 ) ; setVector (19, 0.202383, -0.175470, 0.985002 ) ; setVector (20, 0.208094, 0.175265, -0.983848 ) ; setVector (21, 0.666452, 0.742619, -0.215262 ) ; setVector (22, 0.332212, 0.959489, -0.104850 ) ; setVector (23, 0.205064, 0.958364, 0.285421 ) ; setVector (24, 0.412630, 0.742620, 0.565889 ) ; setVector (25, 0.746093, 0.175315, 0.674232 ) ; setVector (26, 0.744110, 0.525505, 0.460568 ) ; setVector (27, 0.871894, 0.526125, 0.070507 ) ; setVector (28, 0.874264, 0.175471, -0.496841 ) ; setVector (29, 1.000000, 0.175267, -0.106112 ) ; break ; case 64: m_lDirections = lDirections ; delete [] m_sVector ; m_sVector = new VectorStruct [m_lDirections] ; m_eCoordinateSystem = XYZ ; // vector set for 64 directions (normalised to maximum) setVector (0, 1.000000, 0.000000, 0.000000); setVector (1, 0.000000, 1.000000, 0.000000); setVector (2, -0.026007, 0.649170, 0.760199); setVector (3, 0.591136, -0.766176, 0.252058); setVector (4, -0.236071, -0.524158, 0.818247); setVector (5, -0.893021, -0.259006, 0.368008); setVector (6, 0.796184, 0.129030, 0.591137); setVector (7, 0.233964, 0.929855, 0.283956); setVector (8, 0.935686, 0.139953, 0.323891); setVector (9, 0.505827, -0.844710, -0.174940); setVector (10, 0.346220, -0.847539, -0.402256); setVector (11, 0.456968, -0.630956, -0.626956); setVector (12, -0.486997, -0.388997, 0.781995); setVector (13, -0.617845, 0.672831, 0.406898); setVector (14, -0.576984, -0.104997, -0.809978); setVector (15, -0.826695, -0.520808, 0.212921); setVector (16, 0.893712, -0.039987, -0.446856); setVector (17, 0.290101, -0.541189, -0.789276); setVector (18, 0.115951, -0.962591, -0.244896); setVector (19, -0.800182, 0.403092, -0.444101); setVector (20, 0.513981, 0.839970, 0.173994); setVector (21, -0.788548, 0.152912, -0.595659); setVector (22, 0.949280, -0.233069, 0.211062); setVector (23, 0.232964, 0.782880, 0.576911); setVector (24, -0.020999, -0.187990, -0.981946); setVector (25, 0.216932, -0.955701, 0.198938); setVector (26, 0.774003, -0.604002, 0.190001); setVector (27, -0.160928, 0.355840, 0.920587); setVector (28, -0.147035, 0.731173, -0.666158); setVector (29, 0.888141, 0.417066, 0.193031); setVector (30, -0.561971, 0.231988, -0.793959); setVector (31, -0.380809, 0.142928, 0.913541); setVector (32, -0.306000, -0.199000, -0.931001); setVector (33, -0.332086, -0.130034, 0.934243); setVector (34, -0.963226, -0.265062, 0.044010); setVector (35, -0.959501, 0.205107, 0.193101); setVector (36, 0.452965, -0.888932, 0.067995); setVector (37, -0.773133, 0.628108, 0.088015); setVector (38, 0.709082, 0.408047, 0.575066); setVector (39, -0.692769, 0.023992, 0.720760); setVector (40, 0.681659, 0.528735, -0.505747); setVector (41, -0.141995, -0.724976, 0.673978); setVector (42, -0.740168, 0.388088, 0.549125); setVector (43, -0.103006, 0.822044, 0.560030); setVector (44, 0.584037, -0.596038, 0.551035); setVector (45, -0.088008, -0.335031, 0.938088); setVector (46, -0.552263, -0.792377, 0.259123); setVector (47, 0.838158, -0.458086, -0.296056); setVector (48, 0.362995, -0.560993, 0.743990); setVector (49, -0.184062, 0.392133, -0.901306); setVector (50, -0.720938, -0.692941, 0.008999); setVector (51, 0.433101, 0.682159, -0.589137); setVector (52, 0.502114, 0.690157, 0.521119); setVector (53, -0.170944, -0.508833, -0.843722); setVector (54, 0.462968, 0.422971, 0.778946); setVector (55, 0.385030, -0.809064, 0.444035); setVector (56, -0.713102, -0.247035, 0.656094); setVector (57, 0.259923, 0.884737, -0.386885); setVector (58, 0.001000, 0.077002, -0.997030); setVector (59, 0.037002, -0.902057, 0.430027); setVector (60, 0.570320, -0.303170, -0.763428); setVector (61, -0.282105, 0.145054, -0.948354); setVector (62, 0.721098, 0.608082, 0.332045); setVector (63, 0.266985, 0.959945, -0.084995); break ; case 256: m_lDirections = lDirections ; delete [] m_sVector ; m_sVector = new VectorStruct [m_lDirections] ; m_eCoordinateSystem = XYZ ; // vector set for 256 directions (normalised to maximum) setVector (0, 0.059010, -0.013002, 0.998173); setVector (1, 0.070008, 0.157018, 0.985111); setVector (2, -0.078038, 0.083041, 0.993486); setVector (3, -0.092987, -0.086988, 0.991860); setVector (4, 0.046987, -0.178952, 0.982735); setVector (5, 0.199944, -0.108970, 0.973729); setVector (6, 0.211021, 0.052005, 0.976097); setVector (7, 0.210999, 0.212999, 0.953997); setVector (8, -0.050982, 0.250913, 0.966666); setVector (9, -0.208056, 0.186050, 0.960259); setVector (10, -0.355044, 0.120015, 0.927114); setVector (11, -0.225050, 0.016004, 0.974216); setVector (12, -0.239998, -0.156999, 0.957994); setVector (13, -0.107055, -0.253129, 0.961491); setVector (14, 0.031988, -0.337873, 0.940648); setVector (15, 0.191053, -0.268075, 0.944264); setVector (16, 0.333011, -0.202007, 0.921030); setVector (17, 0.350043, -0.034004, 0.936116); setVector (18, 0.353962, 0.131986, 0.925900); setVector (19, 0.321087, 0.303082, 0.897243); setVector (20, 0.124035, 0.337095, 0.933264); setVector (21, -0.028007, 0.395092, 0.918214); setVector (22, -0.189921, 0.343856, 0.919616); setVector (23, -0.340929, 0.281942, 0.896814); setVector (24, -0.483028, 0.214012, 0.849048); setVector (25, -0.492017, 0.052002, 0.869031); setVector (26, -0.364886, -0.049984, 0.929710); setVector (27, -0.376988, -0.226993, 0.897972); setVector (28, -0.251019, -0.327024, 0.911068); setVector (29, -0.116041, -0.415148, 0.902323); setVector (30, 0.027007, -0.490130, 0.871231); setVector (31, 0.176089, -0.413208, 0.893450); setVector (32, 0.323985, -0.380982, 0.865960); setVector (33, 0.451026, -0.272016, 0.850049); setVector (34, 0.477203, -0.106045, 0.872371); setVector (35, 0.487906, 0.059988, 0.870832); setVector (36, 0.468001, 0.231001, 0.853003); setVector (37, 0.426147, 0.394136, 0.814282); setVector (38, 0.266963, 0.442939, 0.855883); setVector (39, 0.120952, 0.485807, 0.865657); setVector (40, -0.024989, 0.534766, 0.844631); setVector (41, -0.176029, 0.491082, 0.853142); setVector (42, -0.323126, 0.437171, 0.839328); setVector (43, -0.463978, 0.371982, 0.803961); setVector (44, -0.613900, 0.139977, 0.776874); setVector (45, -0.617975, -0.018999, 0.785968); setVector (46, -0.493054, -0.117013, 0.862094); setVector (47, -0.503790, -0.292878, 0.812661); setVector (48, -0.383865, -0.394861, 0.834705); setVector (49, -0.253926, -0.486859, 0.835757); setVector (50, -0.113952, -0.565762, 0.816657); setVector (51, 0.037997, -0.625950, 0.778937); setVector (52, 0.182983, -0.543949, 0.818924); setVector (53, 0.328974, -0.543956, 0.771938); setVector (54, 0.446988, -0.437988, 0.779979); setVector (55, 0.565718, -0.320840, 0.759621); setVector (56, 0.595011, -0.163003, 0.787015); setVector (57, 0.611304, -0.002001, 0.791393); setVector (58, 0.600103, 0.163028, 0.783134); setVector (59, 0.568061, 0.325035, 0.756081); setVector (60, 0.512003, 0.482003, 0.711004); setVector (61, 0.362192, 0.543287, 0.757401); setVector (62, 0.211049, 0.594139, 0.776181); setVector (63, 0.058967, 0.640642, 0.765572); setVector (64, -0.119057, 0.637302, 0.761361); setVector (65, -0.274102, 0.590219, 0.759282); setVector (66, -0.421992, 0.527990, 0.736986); setVector (67, -0.560010, 0.454008, 0.693012); setVector (68, -0.598017, 0.298008, 0.744021); setVector (69, -0.730015, 0.044001, 0.682014); setVector (70, -0.718931, -0.123988, 0.683934); setVector (71, -0.607904, -0.181971, 0.772878); setVector (72, -0.643781, -0.311894, 0.698762); setVector (73, -0.524667, -0.433725, 0.732535); setVector (74, -0.395115, -0.537156, 0.745217); setVector (75, -0.255897, -0.624749, 0.737703); setVector (76, -0.106010, -0.694064, 0.712066); setVector (77, 0.051982, -0.740746, 0.669771); setVector (78, 0.198017, -0.665057, 0.720062); setVector (79, 0.338997, -0.682994, 0.646994); setVector (80, 0.455869, -0.583832, 0.671807); setVector (81, 0.567210, -0.477177, 0.671249); setVector (82, 0.670100, -0.360054, 0.649097); setVector (83, 0.704211, -0.210063, 0.678203); setVector (84, 0.723245, -0.057019, 0.688233); setVector (85, 0.720289, 0.101041, 0.686276); setVector (86, 0.696042, 0.258015, 0.670040); setVector (87, 0.650084, 0.411053, 0.639082); setVector (88, 0.582844, 0.557851, 0.590842); setVector (89, 0.441061, 0.629087, 0.640089); setVector (90, 0.292091, 0.685213, 0.667208); setVector (91, 0.136935, 0.732653, 0.666684); setVector (92, -0.035006, 0.744130, 0.667117); setVector (93, -0.207001, 0.724004, 0.658004); setVector (94, -0.361776, 0.671585, 0.646600); setVector (95, -0.506971, 0.602966, 0.615965); setVector (96, -0.641109, 0.517088, 0.567097); setVector (97, -0.690897, 0.366945, 0.622907); setVector (98, -0.718746, 0.206927, 0.663766); setVector (99, -0.821800, 0.110973, 0.558864); setVector (100, -0.820917, -0.048995, 0.568942); setVector (101, -0.787722, -0.210926, 0.578796); setVector (102, -0.733198, -0.353096, 0.581157); setVector (103, -0.632761, -0.470822, 0.614768); setVector (104, -0.516033, -0.577036, 0.633040); setVector (105, -0.386042, -0.669073, 0.635069); setVector (106, -0.244127, -0.745387, 0.620322); setVector (107, -0.092982, -0.802848, 0.588888); setVector (108, 0.061971, -0.837608, 0.542746); setVector (109, 0.207049, -0.774182, 0.598141); setVector (110, 0.355042, -0.784093, 0.509061); setVector (111, 0.480125, -0.691179, 0.540140); setVector (112, 0.596018, -0.585017, 0.550016); setVector (113, 0.703421, -0.465279, 0.537322); setVector (114, 0.781234, -0.304091, 0.545163); setVector (115, 0.812165, -0.145029, 0.565115); setVector (116, 0.821641, 0.016993, 0.569751); setVector (117, 0.808928, 0.175984, 0.560950); setVector (118, 0.774726, 0.330883, 0.538810); setVector (119, 0.718831, 0.477888, 0.504881); setVector (120, 0.642730, 0.615741, 0.455808); setVector (121, 0.509022, 0.697030, 0.505021); setVector (122, 0.366176, 0.758364, 0.539259); setVector (123, 0.213039, 0.808148, 0.549100); setVector (124, 0.045984, 0.830708, 0.554805); setVector (125, -0.123006, 0.826039, 0.550026); setVector (126, -0.288131, 0.793361, 0.536244); setVector (127, -0.439982, 0.734970, 0.515979); setVector (128, -0.579687, 0.658644, 0.479741); setVector (129, -0.705004, 0.567003, 0.426002); setVector (130, -0.764589, 0.424772, 0.484740); setVector (131, -0.800709, 0.269902, 0.534806); setVector (132, -0.892958, 0.161992, 0.419980); setVector (133, -0.900927, 0.002000, 0.433965); setVector (134, -0.879831, -0.158969, 0.447914); setVector (135, -0.833019, -0.319007, 0.452010); setVector (136, -0.747071, -0.470045, 0.470045); setVector (137, -0.637748, -0.587767, 0.497803); setVector (138, -0.513898, -0.689863, 0.509899); setVector (139, -0.377037, -0.775076, 0.507050); setVector (140, -0.230976, -0.842913, 0.485950); setVector (141, -0.081983, -0.889811, 0.448905); setVector (142, 0.074014, -0.912169, 0.403075); setVector (143, 0.219092, -0.860361, 0.460193); setVector (144, 0.362034, -0.861080, 0.357033); setVector (145, 0.490041, -0.778065, 0.393033); setVector (146, 0.608025, -0.678028, 0.413017); setVector (147, 0.718996, -0.558997, 0.412998); setVector (148, 0.810079, -0.408040, 0.421041); setVector (149, 0.870877, -0.239966, 0.428940); setVector (150, 0.894955, -0.073996, 0.439978); setVector (151, 0.896096, 0.088009, 0.435047); setVector (152, 0.874684, 0.243912, 0.418849); setVector (153, 0.831860, 0.391934, 0.392934); setVector (154, 0.768978, 0.530985, 0.355990); setVector (155, 0.687097, 0.657093, 0.310044); setVector (156, 0.564702, 0.745606, 0.353813); setVector (157, 0.432080, 0.812149, 0.392072); setVector (158, 0.286963, 0.863887, 0.413946); setVector (159, 0.126973, 0.895811, 0.425910); setVector (160, -0.039977, 0.903483, 0.426756); setVector (161, -0.206046, 0.885199, 0.417094); setVector (162, -0.364892, 0.841750, 0.397882); setVector (163, -0.510950, 0.775924, 0.369964); setVector (164, -0.639907, 0.695898, 0.325952); setVector (165, -0.753755, 0.597806, 0.272911); setVector (166, -0.818055, 0.471032, 0.330022); setVector (167, -0.862916, 0.318969, 0.391962); setVector (168, -0.938282, 0.216065, 0.270081); setVector (169, -0.956045, 0.055003, 0.288014); setVector (170, -0.946681, -0.106964, 0.303898); setVector (171, -0.909812, -0.267945, 0.316935); setVector (172, -0.839417, -0.429702, 0.332769); setVector (173, -0.741292, -0.573226, 0.349138); setVector (174, -0.624959, -0.687955, 0.368976); setVector (175, -0.493966, -0.784946, 0.373974); setVector (176, -0.353977, -0.861944, 0.362977); setVector (177, -0.211958, -0.918819, 0.332934); setVector (178, -0.066965, -0.953504, 0.293847); setVector (179, 0.084956, -0.963501, 0.253868); setVector (180, 0.228069, -0.924279, 0.306092); setVector (181, 0.333060, -0.925167, 0.182033); setVector (182, 0.466929, -0.853870, 0.229965); setVector (183, 0.595385, -0.760492, 0.259168); setVector (184, 0.709740, -0.647763, 0.276899); setVector (185, 0.814356, -0.503220, 0.289126); setVector (186, 0.892778, -0.337916, 0.297926); setVector (187, 0.938954, -0.162992, 0.302985); setVector (188, 0.954223, 0.004001, 0.299070); setVector (189, 0.944039, 0.166007, 0.285012); setVector (190, 0.909805, 0.321931, 0.261944); setVector (191, 0.852595, 0.469777, 0.228891); setVector (192, 0.771212, 0.608168, 0.188052); setVector (193, 0.644272, 0.742313, 0.184078); setVector (194, 0.512029, 0.830048, 0.221013); setVector (195, 0.371982, 0.891957, 0.256988); setVector (196, 0.218003, 0.934014, 0.283004); setVector (197, 0.147000, 0.978001, 0.148000); setVector (198, 0.050005, 0.955101, 0.292031); setVector (199, -0.120044, 0.950347, 0.287105); setVector (200, -0.287133, 0.918424, 0.272126); setVector (201, -0.444757, 0.861529, 0.244866); setVector (202, -0.582982, 0.786976, 0.201994); setVector (203, -0.707118, 0.690116, 0.154026); setVector (204, -0.823874, 0.547916, 0.144978); setVector (205, -0.895869, 0.373945, 0.239965); setVector (206, -0.956936, 0.266982, 0.113992); setVector (207, -0.984969, 0.108997, 0.133996); setVector (208, -0.987109, -0.053006, 0.151017); setVector (209, -0.962464, -0.213103, 0.168081); setVector (210, -0.907966, -0.372986, 0.190993); setVector (211, -0.822992, -0.528995, 0.206998); setVector (212, -0.712235, -0.666220, 0.221073); setVector (213, -0.584746, -0.777662, 0.230900); setVector (214, -0.445210, -0.866409, 0.226107); setVector (215, -0.302832, -0.932484, 0.196891); setVector (216, -0.155030, -0.975188, 0.158031); setVector (217, 0.003001, -0.992396, 0.123049); setVector (218, -0.105043, 0.994407, 0.011005); setVector (219, 0.184970, -0.973842, 0.131979); setVector (220, 0.279071, -0.960245, 0.007002); setVector (221, 0.426883, -0.902753, 0.052986); setVector (222, 0.560256, -0.822376, 0.099045); setVector (223, 0.687169, -0.716176, 0.122030); setVector (224, 0.794057, -0.589042, 0.150011); setVector (225, 0.887491, -0.430238, 0.165091); setVector (226, 0.951729, -0.254927, 0.170951); setVector (227, 0.983436, -0.085038, 0.160071); setVector (228, 0.985899, 0.079992, 0.146985); setVector (229, 0.961934, 0.241983, 0.126991); setVector (230, 0.912643, 0.396845, 0.097962); setVector (231, 0.837257, 0.543167, 0.063019); setVector (232, 0.723919, 0.687923, 0.051994); setVector (233, 0.588089, 0.807122, 0.052008); setVector (234, 0.450862, 0.888729, 0.082975); setVector (235, 0.304931, 0.944787, 0.119973); setVector (236, -0.233066, -0.972275, 0.019005); setVector (237, 0.073019, 0.997258, 0.012003); setVector (238, -0.026001, 0.988038, 0.152006); setVector (239, -0.200088, 0.969424, 0.142062); setVector (240, -0.365992, 0.922979, 0.118997); setVector (241, -0.510695, 0.856488, 0.074955); setVector (242, -0.640958, 0.766950, 0.030998); setVector (243, -0.764977, 0.643980, 0.010000); setVector (244, 0.857996, -0.512998, 0.026000); setVector (245, -0.901024, 0.423011, 0.096003); setVector (246, 0.938499, -0.343182, 0.038020); setVector (247, 0.983769, -0.177958, 0.022995); setVector (248, 0.999898, -0.012999, 0.005999); setVector (249, -0.988633, -0.149944, 0.010996); setVector (250, -0.949788, -0.310931, 0.034992); setVector (251, -0.883406, -0.464213, 0.064029); setVector (252, -0.783923, -0.615940, 0.077992); setVector (253, -0.660104, -0.746118, 0.087014); setVector (254, -0.521822, -0.848711, 0.085971); setVector (255, -0.380935, -0.922844, 0.056990); break ; From xli16 at jhmi.edu Thu Nov 12 10:19:26 2009 From: xli16 at jhmi.edu (Xin Li) Date: Thu, 12 Nov 2009 10:19:26 -0500 Subject: [Mristudio-users] Please post questions to mristudio-users@mristudio.org Message-ID: Hello mristudio users,Please post your questions to mristudio-users at mristudio.org. The email address announcements at mristudio.org is used only when you want to send an announcement to every user. Thanks!Xin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091112/65be4783/attachment.html From lintian at hotmail.co.uk Thu Nov 12 21:11:16 2009 From: lintian at hotmail.co.uk (T lin) Date: Fri, 13 Nov 2009 02:11:16 +0000 Subject: [Mristudio-users] Please post questions to mristudio-users@mristudio.org In-Reply-To: References: Message-ID: ok thanks! lin Date: Thu, 12 Nov 2009 10:19:26 -0500 From: xli16 at jhmi.edu To: mristudio-users at mristudio.org Subject: [Mristudio-users] Please post questions to mristudio-users at mristudio.org Hello mristudio users, Please post your questions to mristudio-users at mristudio.org. The email address announcements at mristudio.org is used only when you want to send an announcement to every user. Thanks! Xin _________________________________________________________________ Hotmail: Trusted email with powerful SPAM protection. http://clk.atdmt.com/GBL/go/177141665/direct/01/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091113/e2dfb1d5/attachment.html From tdqiangqiang at foxmail.com Wed Nov 18 21:31:35 2009 From: tdqiangqiang at foxmail.com (=?gbk?B?zrHTsA==?=) Date: Thu, 19 Nov 2009 10:31:35 +0800 Subject: [Mristudio-users] Please post questionsto mristudio-users@mristudio.org Message-ID: Hi, I am not familiar with dtistudio.I wonder whether it can show the sagittal views of the image such as midsagittal view after process of axial data with dtistudio. Thanks. liq -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091119/eaa222b5/attachment.html From tdqiangqiang at foxmail.com Wed Nov 18 22:38:57 2009 From: tdqiangqiang at foxmail.com (=?gbk?B?zrHTsA==?=) Date: Thu, 19 Nov 2009 11:38:57 +0800 Subject: [Mristudio-users] =?gbk?b?u9i4tKO6ICBQbGVhc2UgcG9zdCBxdWVzdGlv?= =?gbk?q?nstomristudio-users=40mristudio=2Eorg?= Message-ID: Hi, Who can tell me how to display the midsagittal plane of the image after procession? Thanks. ------------------ ???? ------------------ ???: "??"; ????: 2009?11?19?(???) ??10:31 ???: "DTI Studio, ROI Editor,Landmarker Questions/Support"; ??: Re: [Mristudio-users] Please post questionstomristudio-users at mristudio.org Hi, I am not familiar with dtistudio.I wonder whether it can show the sagittal views of the image such as midsagittal view after process of axial data with dtistudio. Thanks. liq -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091119/7dc1d078/attachment.html From jhuang.neurology.umsmed.edu at umsmed.edu Wed Nov 4 17:27:02 2009 From: jhuang.neurology.umsmed.edu at umsmed.edu (Juebin Huang) Date: Wed, 04 Nov 2009 16:27:02 -0600 Subject: [Mristudio-users] How much are the ADC and FA of the white matter and grey matter of human brain Message-ID: <4AF1AB560200002700046A39@GWIA1.umsmed.edu> I think you can simply check some literatures to find the anwsers. Juebin Huang, MD,PhD Assistant Professor Department of Neurology The University of Mississippi Medical Center 2500 North State Street, Jackson, MS, 39216 Tel: (601) 984-5444 Fax: (601) 984-5503 Email: jhuang at neurology.umsmed.edu >>> "Huang, Shiliang" 11/04/09 4:05 PM >>> Hi every one I have got the results with DTIStudio. Thank you all very much. I got the mean value with ROI. My results are : White matter std Gray matter std ADC 8.48e-004 1.97e-004 1.01e-003 2.59e-004 FA 0.26 0.11 0.23 0.08 But I do not know if my results right or not. Can anyone tell me how much are the ADC and FA of the white matter and grey matter of human brain? Thanks Shiliang Individuals who have received this information in error or are not authorized to receive it must promptly return or dispose of the information and notify the sender. Those individuals are hereby notified that they are strictly prohibited from reviewing, forwarding, printing, copying, distributing or using this information in any way. From wmcgarry at gmu.edu Thu Nov 19 12:55:40 2009 From: wmcgarry at gmu.edu (Ryan) Date: Thu, 19 Nov 2009 12:55:40 -0500 Subject: [Mristudio-users] DTIStudio keeps crashing Message-ID: I have a problem similar to the individual below (reported by Hugh), where DTIStudio keeps getting an error and crashing. When I try to perform any calculations like ADC-Map, I get an error saying "The mriView3D MFC application has encountered a problem and needs to close." At this point the program crashes. I think the error is related to the fact that the gradient table doesn't match the number of images, I don't know how else to get them to match. I already went through the gradient table and made sure there weren't any errors like missing commas. I also tried reloading the data with the methods listed by Susumu below, but when I look at the gradient table that was reloaded, it's not the most recent information (but instead information from a previous example data set I used). Please let me know what I can do to prevent this error happening, thank you. -Ryan Hi Hugh, When you got this error, please suspect one of the following two reasons; 1) Memory shortage: Even if you have many GB of memories, 32-bit Windows system can allocate only 1 - 1.5 GB to each program. To check if you have the memory problem, please restrict the slices to be calculated. In the initial data parameter window, there is a section called "Slices to be processed". Here you can specify only a portion of slices to be processed. Please limit the slices to, for example, 0-9 and see how it goes. If you can calculate tensors without errors, then you have the memory problem. The solution is; a) upgrade to the 64-bit system or b) devide the calculation to 2 batches (e.g. slice 0-29 for the first batch and 30-59 for the second batch), calculate all maps (e.g. FA), and later combine them. 2) Mismatch between the gradient table and the number of images: For example, if you specify 12-orientation table and 30 volume images, then you get the error. After loading the data and before you go to the Dti Map tab, make sure that you have 1 b0 + 64 DWIs in the pull-down menu in the right column of the Image tab. If you have the correct number of the images, then you might have an error in your gradient table. Small mistakes such as missing "," are often difficult to detect. The best way is; a) load the data using DtiMapping under the "File" button on the top left, b) close the window, c) open the image paremater window again by clicking "DtiMapping" in the "File" button again, d) the window still remembers the gradient table you entered last time. This remembered window tells how DtiStudio interpreted your gradient table. If there is any syntax errors, you may find them much easier. For example, if you enter, "4: 1 0.5 0", instead of "4: 1, 0.5, 0", then you would find, "4: 1, 0, 0". If any of these do not solve the issue, please let us know. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hugh Wang Sent: Wednesday, April 08, 2009 6:30 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] MriView3D application close Hi, I was using the dtistudio (ver. 2.4) to look at the Siemens DICOM diffusion images (1baseline,64 gradients). After successfully loading the images, I click the "dti map" option at lower right corner. Whatever calculation I choose, it always gives me an error: "MriView3D MFC Application has encountered a problem and needs to close. We are sorry for the inconvenience." I tried several PCs, and the problem keeped the same. I would appreciate that if there's anyone having any idea on how to solve it. Thanks. Best, Hugh From Lisa_Kreber/CNSNEURO at cnsneuro.com Thu Nov 19 18:36:18 2009 From: Lisa_Kreber/CNSNEURO at cnsneuro.com (Lisa_Kreber/CNSNEURO at cnsneuro.com) Date: Thu, 19 Nov 2009 15:36:18 -0800 Subject: [Mristudio-users] DTIStudio keeps crashing Message-ID: Hi, Ryan: I was having the same problem that you were with DTI studio crashing. I uninstalled it and downloaded the latest version of dti studio (the beta version). This has fixed the problem and dti studio has not crashed since. Hope this helps you out. Lisa ----- Original Message ----- From: Ryan [wmcgarry at gmu.edu] Sent: 11/19/2009 12:55 PM EST To: mristudio-users at mristudio.org Subject: [Mristudio-users] DTIStudio keeps crashing I have a problem similar to the individual below (reported by Hugh), where DTIStudio keeps getting an error and crashing. When I try to perform any calculations like ADC-Map, I get an error saying "The mriView3D MFC application has encountered a problem and needs to close." At this point the program crashes. I think the error is related to the fact that the gradient table doesn't match the number of images, I don't know how else to get them to match. I already went through the gradient table and made sure there weren't any errors like missing commas. I also tried reloading the data with the methods listed by Susumu below, but when I look at the gradient table that was reloaded, it's not the most recent information (but instead information from a previous example data set I used). Please let me know what I can do to prevent this error happening, thank you. -Ryan Hi Hugh, When you got this error, please suspect one of the following two reasons; 1) Memory shortage: Even if you have many GB of memories, 32-bit Windows system can allocate only 1 - 1.5 GB to each program. To check if you have the memory problem, please restrict the slices to be calculated. In the initial data parameter window, there is a section called "Slices to be processed". Here you can specify only a portion of slices to be processed. Please limit the slices to, for example, 0-9 and see how it goes. If you can calculate tensors without errors, then you have the memory problem. The solution is; a) upgrade to the 64-bit system or b) devide the calculation to 2 batches (e.g. slice 0-29 for the first batch and 30-59 for the second batch), calculate all maps (e.g. FA), and later combine them. 2) Mismatch between the gradient table and the number of images: For example, if you specify 12-orientation table and 30 volume images, then you get the error. After loading the data and before you go to the Dti Map tab, make sure that you have 1 b0 + 64 DWIs in the pull-down menu in the right column of the Image tab. If you have the correct number of the images, then you might have an error in your gradient table. Small mistakes such as missing "," are often difficult to detect. The best way is; a) load the data using DtiMapping under the "File" button on the top left, b) close the window, c) open the image paremater window again by clicking "DtiMapping" in the "File" button again, d) the window still remembers the gradient table you entered last time. This remembered window tells how DtiStudio interpreted your gradient table. If there is any syntax errors, you may find them much easier. For example, if you enter, "4: 1 0.5 0", instead of "4: 1, 0.5, 0", then you would find, "4: 1, 0, 0". If any of these do not solve the issue, please let us know. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hugh Wang Sent: Wednesday, April 08, 2009 6:30 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] MriView3D application close Hi, I was using the dtistudio (ver. 2.4) to look at the Siemens DICOM diffusion images (1baseline,64 gradients). After successfully loading the images, I click the "dti map" option at lower right corner. Whatever calculation I choose, it always gives me an error: "MriView3D MFC Application has encountered a problem and needs to close. We are sorry for the inconvenience." I tried several PCs, and the problem keeped the same. I would appreciate that if there's anyone having any idea on how to solve it. Thanks. Best, Hugh _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From saksena.sona at gmail.com Fri Nov 20 08:33:04 2009 From: saksena.sona at gmail.com (Sona Saksena) Date: Fri, 20 Nov 2009 08:33:04 -0500 Subject: [Mristudio-users] registration Message-ID: <9018fecc0911200533o2e4582e1ya51a1991bd9aea94@mail.gmail.com> Hello, We have 2 set of images, Flair and DTI images. In Flair, slice thickness is 5mm and no spacing (image matrix 320x224) while DTI is 2.6mm slice thickness and no spacing (image matrix 96x96). The question is how can we register these images? Is there any option in DTI studio software of coregistering them by reslicing them. The idea is to draw ROI's on the gad images and superimpose them on the DTI images and get the values. Please do let me know. Thanks. regards Sona Saksena -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091120/54f6c6ae/attachment.html From susumu at mri.jhu.edu Fri Nov 20 08:43:38 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Fri, 20 Nov 2009 08:43:38 -0500 Subject: [Mristudio-users] DTIStudio keeps crashing In-Reply-To: References: Message-ID: Thanks Lisa. Ryan, please keep us posted if your problem persists with the newer version. Susumu On Thu, Nov 19, 2009 at 6:36 PM, wrote: > Hi, Ryan: > > I was having the same problem that you were with DTI studio crashing. I > uninstalled it and downloaded the latest version of dti studio (the beta > version). This has fixed the problem and dti studio has not crashed since. > Hope this helps you out. > > Lisa > > > > > ----- Original Message ----- > From: Ryan [wmcgarry at gmu.edu] > Sent: 11/19/2009 12:55 PM EST > To: mristudio-users at mristudio.org > Subject: [Mristudio-users] DTIStudio keeps crashing > > > > I have a problem similar to the individual below (reported by Hugh), > where DTIStudio keeps getting an error and crashing. When I try to > perform any > calculations like ADC-Map, I get an error saying "The mriView3D MFC > application has encountered a problem and needs to close." At this > point the program crashes. I think the error is related to the fact > that the gradient table doesn't match the number of images, I don't > know how else to get them to match. I already went through the > gradient table and made sure there weren't any errors like missing > commas. I also tried reloading the data with the methods listed by > Susumu below, but when I look at the gradient table that was reloaded, > it's not the most recent information (but instead information from a > previous example data set I used). Please > let me know what I can do to prevent this error happening, thank you. > -Ryan > > > Hi Hugh, > > When you got this error, please suspect one of the following two reasons; > > 1) Memory shortage: > > Even if you have many GB of memories, 32-bit Windows system can allocate > only 1 - 1.5 GB to each program. To check if you have the memory problem, > please restrict the slices to be calculated. In the initial data parameter > window, there is a section called "Slices to be processed". Here you can > specify only a portion of slices to be processed. Please limit the slices > to, for example, 0-9 and see how it goes. If you can calculate tensors > without errors, then you have the memory problem. The solution is; a) > upgrade to the 64-bit system or b) devide the calculation to 2 batches > (e.g. > slice 0-29 for the first batch and 30-59 for the second batch), calculate > all maps (e.g. FA), and later combine them. > > 2) Mismatch between the gradient table and the number of images: > > For example, if you specify 12-orientation table and 30 volume images, then > you get the error. After loading the data and before you go to the Dti Map > tab, make sure that you have 1 b0 + 64 DWIs in the pull-down menu in the > right column of the Image tab. If you have the correct number of the > images, > then you might have an error in your gradient table. Small mistakes such as > missing "," are often difficult to detect. The best way is; a) load the > data > using DtiMapping under the "File" button on the top left, b) close the > window, c) open the image paremater window again by clicking "DtiMapping" > in > the "File" button again, d) the window still remembers the gradient table > you entered last time. This remembered window tells how DtiStudio > interpreted your gradient table. If there is any syntax errors, you may > find > them much easier. For example, if you enter, "4: 1 0.5 0", instead of "4: > 1, > 0.5, 0", then you would find, "4: 1, 0, 0". > > If any of these do not solve the issue, please let us know. > > Susumu > > _____ > > From: mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hugh Wang > Sent: Wednesday, April 08, 2009 6:30 PM > To: mristudio-users at mristudio.org > Subject: [Mristudio-users] MriView3D application close > > > Hi, > > I was using the dtistudio (ver. 2.4) to look at the Siemens DICOM > diffusion > images (1baseline,64 gradients). After successfully loading the images, I > click the "dti map" option at lower right corner. Whatever calculation I > choose, it always gives me an error: > > "MriView3D MFC Application has encountered a problem and needs to close. > We > are sorry for the inconvenience." > > I tried several PCs, and the problem keeped the same. I would appreciate > that if there's anyone having any idea on how to solve it. Thanks. > > Best, > Hugh > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091120/0f66e6b1/attachment.html From susumu at mri.jhu.edu Fri Nov 20 10:10:56 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Fri, 20 Nov 2009 10:10:56 -0500 Subject: [Mristudio-users] registration In-Reply-To: <9018fecc0911200533o2e4582e1ya51a1991bd9aea94@mail.gmail.com> References: <9018fecc0911200533o2e4582e1ya51a1991bd9aea94@mail.gmail.com> Message-ID: Hi Sona, You need to use DiffeoMap (previously called Landmarker) for that. I would recommend to register Flair to DTI, not DTI to Flair because you have to register all DWIs independently to Flair. Alternatively, you can calculate the FA map (and other maps you want to create) first and then register to Flair. Anyway, when you use DiffeoMap, the first image you open will be the target (say, b0 image) and the second image (say, Flair) will be registered to the target. Once you open the two images, you can use AIR - rigid for the registration. At this time, any differences in matrix dimensions and FOV will be adjusted to those of the target. Because your DTI data are distorted due to B0 susceptibility, the rigid registration may not be perfect, but this is a problem hard to solve. Also, if one of your image has strong extra-cranial signals (like skull and face) and the other doesn't, the AIR registration algorithm may be confused. In this case, you may need to remove the skull (you can do it by a simple threshold or a skull strip tool in RoiEditor or other software). Susumu On Fri, Nov 20, 2009 at 8:33 AM, Sona Saksena wrote: > Hello, > We have 2 set of images, Flair and DTI images. In Flair, slice thickness is > 5mm and no spacing (image matrix 320x224) while DTI is 2.6mm slice thickness > and no spacing (image matrix 96x96). The question is how can we register > these images? Is there any option in DTI studio software of coregistering > them by reslicing them. The idea is to draw ROI's on the gad images and > superimpose them on the DTI images and get the values. > Please do let me know. > Thanks. > > regards > Sona Saksena > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091120/9ac51a69/attachment.html From wmcgarry at gmu.edu Tue Nov 24 15:42:52 2009 From: wmcgarry at gmu.edu (Ryan) Date: Tue, 24 Nov 2009 15:42:52 -0500 Subject: [Mristudio-users] DTIStudio isn't reading headers correctly Message-ID: I'm encountering some trouble where DTIStudio isn't reading my headers correctly. I have MRI data collected with an Allegra scanner. It contains a b0 with 12 directions, but 26 appear in the drop-down list on the "Image" tab. I would greatly appreciate any ideas people may have. Thanks. -Ryan From JJames2 at radiology.umsmed.edu Tue Nov 24 15:57:23 2009 From: JJames2 at radiology.umsmed.edu (Judy James) Date: Tue, 24 Nov 2009 14:57:23 -0600 Subject: [Mristudio-users] DTIStudio isn't reading headers correctly Message-ID: <4B0BF4540200002A0002BF03@GWIA1.umsmed.edu> How many averages have you collected your data with? Some scanners if the mosaic option is turned on, will collect images twice instead of averaging it into 1 data set and this can cause 12 directions x 2 avg. + 1(b0) x 2 avg. = 26 sets of images. Judy ***************************************************** Dr. Judy Rose James MR Physicist/Assistant Professor Department of Radiology University of Mississippi Medical Centre Jackson, MS 39216 Ph: 601-984-2585 Pager: 601-929-2442 email: jjames2 at radiology.umsmed.edu ***************************************************** >>> Ryan 11/24/09 2:42 PM >>> I'm encountering some trouble where DTIStudio isn't reading my headers correctly. I have MRI data collected with an Allegra scanner. It contains a b0 with 12 directions, but 26 appear in the drop-down list on the "Image" tab. I would greatly appreciate any ideas people may have. Thanks. -Ryan _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org Individuals who have received this information in error or are not authorized to receive it must promptly return or dispose of the information and notify the sender. Those individuals are hereby notified that they are strictly prohibited from reviewing, forwarding, printing, copying, distributing or using this information in any way. From susumu at mri.jhu.edu Tue Nov 24 17:26:55 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Tue, 24 Nov 2009 17:26:55 -0500 Subject: [Mristudio-users] DTIStudio isn't reading headers correctly In-Reply-To: <4B0BF4540200002A0002BF03@GWIA1.umsmed.edu> References: <4B0BF4540200002A0002BF03@GWIA1.umsmed.edu> Message-ID: Judy is right. I think you did two signal averaging. For DTI, Siemens scanners do not actually average data and save them into separate files. So if you do 2 signal averaging of 13 DWI+b0 scans, you get 26 Mosaic files. Below, I provide some related info you may be interested in. 1) In regular MR scans, such as T1 and T2, signal averaging is done in time-domain data (called k-space) with so-called phase-cycling. For example, if you do 2 averaging, the actual data in the time domain looks inverted. If one seems to have a positive k-space peak, the other has a negative peak. These two data are acquired in a way that they are completely opposite. When the actual averaging is done, they are subtracted, not added; a - (-a) = 2a, suppose "a" is the signal. They do this to remove consistent noise. Suppose the non-random consistent noise (such as leakage of certain radio signal into the scanner), the first scan signal becomes a+b (b = noise) and the second scan is -a+b. If you subtract these two (a+b) - (-a+b) = 2a; you can see that the consistent noise is canceled out. 2) In DTI, there is a reason that you can't do this "time domain (k-space) averaging". This is because of physiological motion such as pulsation. If you do two scans and one is denoted as "a", then the second scan becomes "a*", in which "*" means some phase inconsistency among the scans due to motion. Note that this motion-caused phase inconsistency is due to very tiny tissue motion. Much smaller than the pixel size, which can not be suppressed unless the subject is dead. Because of this issue, you can not use the phase-cycling approach; a - (-a*) is not equal to 2a. As a result, DTI scans do not do k-space (time-domain) averaging. They calculate image first; the time domain signal "a" is converted to image "A". Because after magnitude image calculation, phase information is discarded, the second scan "a*" also becomes "A". So, you can do simple signal averaging A + A = 2A, in the image domain. 3) Now, once the time domain data "a" or "a*" are converted to image "A", we may ask, "what the point of creating 2A by adding two images?". Please note that once you calculate the magnitude image "A", you can not expect to cancel out the consistent noise "b" like the time-domain averaging. Such noise just keeps adding up. Creating 2A images, on the other hand, have negative impacts. For example, if the subject moved between the two scans, you can not do image registration anymore once the two scans are added. If one of the images are corrupted and two images are added, both images get corrupted. Therefore, it is a good idea to keep the two images stored separately. 4) Going back to your problem, you need to create a new table like; 0: 0.000, 0.000, 0.000 1: 1.000, 0.414, -0.414 2: 1.000, -0.414, -0.414 3: 1.000, -0.414, 0.414 4: 1.000, 0.414, 0.414 5: 0.414, 0.414, 1.000 6: 0.414, 1.000, 0.414 7: 0.414, 1.000, -0.414 8: 0.414, 0.414, -1.000 9: 0.414, -0.414, -1.000 10: 0.414, -1.000, -0.414 11: 0.414, -1.000, 0.414 12: 0.414, -0.414, 1.000 13: 0.000, 0.000, 0.000 14: 1.000, 0.414, -0.414 15: 1.000, -0.414, -0.414 16: 1.000, -0.414, 0.414 17: 1.000, 0.414, 0.414 18: 0.414, 0.414, 1.000 19: 0.414, 1.000, 0.414 20: 0.414, 1.000, -0.414 21: 0.414, 0.414, -1.000 22: 0.414, -0.414, -1.000 23: 0.414, -1.000, -0.414 24: 0.414, -1.000, 0.414 25: 0.414, -0.414, 1.000 , which is a simple repeated copy of the 12-orientation table, or submit two separate scans rather than two signal averaging, from which you will get two separate directories, each contain 13 images. In this case, you can list the two directories as the sources of data and use 0: 0, 0, 0 1: 1.000000, 0.414250, -0.414250 2: 1.000000, -0.414250, -0.414250 3: 1.000000, -0.414250, 0.414250 4: 1.000000, 0.414250, 0.414250 5: 0.414250, 0.414250, 1.000000 6: 0.414250, 1.000000, 0.414250 7: 0.414250, 1.000000, -0.414250 8: 0.414250, 0.414250, -1.000000 9: 0.414250, -0.414250, -1.000000 10: 0.414250, -1.000000, -0.414250 11: 0.414250, -1.000000, 0.414250 12: 0.414250, -0.414250, 1.000000 The former dataset is considered as one set of 26 DWI+b0 data. The latter will be considered as (13 DWI+b0)x2 data. The advantage of the second approach is that DtiStudio can provide you subtracted images of the two sets, from which you can get idea about patient motion. I hope it helps. Susumu On Tue, Nov 24, 2009 at 3:57 PM, Judy James wrote: > How many averages have you collected your data with? > Some scanners if the mosaic option is turned on, will collect images twice > instead of averaging it into 1 data set and this can cause 12 directions x 2 > avg. + 1(b0) x 2 avg. = 26 sets of images. > > Judy > > > ***************************************************** > Dr. Judy Rose James > MR Physicist/Assistant Professor > Department of Radiology > University of Mississippi Medical Centre > Jackson, MS 39216 > Ph: 601-984-2585 > Pager: 601-929-2442 > email: jjames2 at radiology.umsmed.edu > ***************************************************** > >>> Ryan 11/24/09 2:42 PM >>> > I'm encountering some trouble where DTIStudio isn't reading my headers > correctly. I have MRI data collected with an Allegra scanner. It > contains a b0 with 12 directions, but 26 appear in the drop-down list > on the "Image" tab. I would greatly appreciate any ideas people may > have. Thanks. > -Ryan > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > > > Individuals who have received this information in error or are not > authorized to receive it must promptly return or dispose of the information > and notify the sender. Those individuals are hereby notified that they are > strictly prohibited from reviewing, forwarding, printing, copying, > distributing or using this information in any way. > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091124/92183793/attachment.html From appenzellersimone at yahoo.com Tue Nov 24 17:29:35 2009 From: appenzellersimone at yahoo.com (simone appenzeller) Date: Tue, 24 Nov 2009 14:29:35 -0800 (PST) Subject: [Mristudio-users] DTIStudio isn't reading headers correctly In-Reply-To: References: <4B0BF4540200002A0002BF03@GWIA1.umsmed.edu> Message-ID: <772826.62499.qm@web37308.mail.mud.yahoo.com> obrigada ________________________________ From: susumu mori To: "DTI Studio, ROI Editor, Landmarker Questions/Support" Cc: wmcgarry at gmu.edu Sent: Tue, November 24, 2009 8:26:55 PM Subject: Re: [Mristudio-users] DTIStudio isn't reading headers correctly Judy is right. I think you did two signal averaging. For DTI, Siemens scanners do not actually average data and save them into separate files. So if you do 2 signal averaging of 13 DWI+b0 scans, you get 26 Mosaic files. Below, I provide some related info you may be interested in. 1) In regular MR scans, such as T1 and T2, signal averaging is done in time-domain data (called k-space) with so-called phase-cycling. For example, if you do 2 averaging, the actual data in the time domain looks inverted. If one seems to have a positive k-space peak, the other has a negative peak. These two data are acquired in a way that they are completely opposite. When the actual averaging is done, they are subtracted, not added; a - (-a) = 2a, suppose "a" is the signal. They do this to remove consistent noise. Suppose the non-random consistent noise (such as leakage of certain radio signal into the scanner), the first scan signal becomes a+b (b = noise) and the second scan is -a+b. If you subtract these two (a+b) - (-a+b) = 2a; you can see that the consistent noise is canceled out. 2) In DTI, there is a reason that you can't do this "time domain (k-space) averaging". This is because of physiological motion such as pulsation. If you do two scans and one is denoted as "a", then the second scan becomes "a*", in which "*" means some phase inconsistency among the scans due to motion. Note that this motion-caused phase inconsistency is due to very tiny tissue motion. Much smaller than the pixel size, which can not be suppressed unless the subject is dead. Because of this issue, you can not use the phase-cycling approach; a - (-a*) is not equal to 2a. As a result, DTI scans do not do k-space (time-domain) averaging. They calculate image first; the time domain signal "a" is converted to image "A". Because after magnitude image calculation, phase information is discarded, the second scan "a*" also becomes "A". So, you can do simple signal averaging A + A = 2A, in the image domain. 3) Now, once the time domain data "a" or "a*" are converted to image "A", we may ask, "what the point of creating 2A by adding two images?". Please note that once you calculate the magnitude image "A", you can not expect to cancel out the consistent noise "b" like the time-domain averaging. Such noise just keeps adding up. Creating 2A images, on the other hand, have negative impacts. For example, if the subject moved between the two scans, you can not do image registration anymore once the two scans are added. If one of the images are corrupted and two images are added, both images get corrupted. Therefore, it is a good idea to keep the two images stored separately. 4) Going back to your problem, you need to create a new table like; 0: 0.000, 0.000, 0.000 1: 1.000, 0.414, -0.414 2: 1.000, -0.414, -0.414 3: 1.000, -0.414, 0.414 4: 1.000, 0.414, 0.414 5: 0.414, 0.414, 1.000 6: 0.414, 1.000, 0.414 7: 0.414, 1.000, -0.414 8: 0.414, 0.414, -1.000 9: 0.414, -0.414, -1.000 10: 0.414, -1.000, -0.414 11: 0.414, -1.000, 0.414 12: 0.414, -0.414, 1.000 13: 0.000, 0.000, 0.000 14: 1.000, 0.414, -0.414 15: 1.000, -0.414, -0.414 16: 1.000, -0.414, 0.414 17: 1.000, 0.414, 0.414 18: 0.414, 0.414, 1.000 19: 0.414, 1.000, 0.414 20: 0.414, 1.000, -0.414 21: 0.414, 0.414, -1.000 22: 0.414, -0.414, -1.000 23: 0.414, -1.000, -0.414 24: 0.414, -1.000, 0.414 25: 0.414, -0.414, 1.000 , which is a simple repeated copy of the 12-orientation table, or submit two separate scans rather than two signal averaging, from which you will get two separate directories, each contain 13 images. In this case, you can list the two directories as the sources of data and use 0: 0, 0, 0 1: 1.000000, 0.414250, -0.414250 2: 1.000000, -0.414250, -0.414250 3: 1.000000, -0.414250, 0.414250 4: 1.000000, 0.414250, 0.414250 5: 0.414250, 0.414250, 1.000000 6: 0.414250, 1.000000, 0.414250 7: 0.414250, 1.000000, -0.414250 8: 0.414250, 0.414250, -1.000000 9: 0.414250, -0.414250, -1.000000 10: 0.414250, -1.000000, -0.414250 11: 0.414250, -1.000000, 0.414250 12: 0.414250, -0.414250, 1.000000 The former dataset is considered as one set of 26 DWI+b0 data. The latter will be considered as (13 DWI+b0)x2 data. The advantage of the second approach is that DtiStudio can provide you subtracted images of the two sets, from which you can get idea about patient motion. I hope it helps. Susumu On Tue, Nov 24, 2009 at 3:57 PM, Judy James wrote: How many averages have you collected your data with? >>Some scanners if the mosaic option is turned on, will collect images twice instead of averaging it into 1 data set and this can cause 12 directions x 2 avg. + 1(b0) x 2 avg. = 26 sets of images. > >>Judy > > >>***************************************************** >>Dr. Judy Rose James >>MR Physicist/Assistant Professor >>Department of Radiology >>University of Mississippi Medical Centre >>Jackson, MS 39216 >>Ph: 601-984-2585 >>Pager: 601-929-2442 >>email: jjames2 at radiology.umsmed.edu >>***************************************************** >>>>> Ryan 11/24/09 2:42 PM >>> > >I'm encountering some trouble where DTIStudio isn't reading my headers >>correctly. I have MRI data collected with an Allegra scanner. It >>contains a b0 with 12 directions, but 26 appear in the drop-down list >>on the "Image" tab. I would greatly appreciate any ideas people may >>have. Thanks. >> -Ryan >>_______________________________________________ >>Mristudio-users mailing list >Mristudio-users at mristudio.org >http://lists.mristudio.org/mailman/listinfo/ >>Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > > > >Individuals who have received this information in error or are not authorized to receive it must promptly return or dispose of the information and notify the sender. Those individuals are hereby notified that they are strictly prohibited from reviewing, forwarding, printing, copying, distributing or using this information in any way. > > > > >>_______________________________________________ >>Mristudio-users mailing list >Mristudio-users at mristudio.org >http://lists.mristudio.org/mailman/listinfo/ >>Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091124/4c190f53/attachment-0001.html From rajagov2 at ccf.org Mon Nov 30 14:51:19 2009 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Mon, 30 Nov 2009 14:51:19 -0500 Subject: [Mristudio-users] Range of RA Message-ID: <77A88E90A851594AAEF830450587C39D01EDABB7@CCHSCLEXMB56.cc.ad.cchs.net> Dear MRI studio users, Just a clarification, the value of RA calculated in DTI studio ranges between 0 to 2 1/2 or 0 to 1. Thanks venkateswaran =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091130/8a951bb5/attachment.html From mksarma at gmail.com Thu Dec 3 18:57:56 2009 From: mksarma at gmail.com (manoj sarma) Date: Thu, 03 Dec 2009 17:57:56 -0600 Subject: [Mristudio-users] Reduce number of slices after generation of DTI-map Message-ID: <33c01b0b0912031557v389e5f1dob65890e1cb25bf69@mail.gmail.com> Hi, I am new to DTI-Studio. I am facing a problem regarding number of slices produced after I generate DTI-map. My raw DTI data have 76 slices and after processing with DTI-Studio I get the same. But when I generate DTI map it produces 50 slices only. I am confused where is the problem. How can I have same number of slices generate as the raw data? regards, Manoj -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091203/d1aa199e/attachment.html From susumu at mri.jhu.edu Thu Dec 3 21:57:19 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Thu, 03 Dec 2009 21:57:19 -0500 Subject: [Mristudio-users] Reduce number of slices after generation of DTI-map In-Reply-To: <33c01b0b0912031557v389e5f1dob65890e1cb25bf69@mail.gmail.com> References: <33c01b0b0912031557v389e5f1dob65890e1cb25bf69@mail.gmail.com> Message-ID: Hi Manoj, Please make sure that you chose "all slice" in the data input window in the beginning. There is a function to restrict the number of slices to process in case you run into memory shortage. Susumu On Thu, Dec 3, 2009 at 6:57 PM, manoj sarma wrote: > Hi, > > I am new to DTI-Studio. I am facing a problem regarding number of slices > produced after I generate DTI-map. My raw DTI data have 76 slices and after > processing with DTI-Studio I get the same. But when I generate DTI map it > produces 50 slices only. I am confused where is the problem. How can I have > same number of slices generate as the raw data? > > > regards, > Manoj > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091203/46203dc0/attachment.html From mksarma at gmail.com Thu Dec 3 23:05:35 2009 From: mksarma at gmail.com (manoj sarma) Date: Thu, 03 Dec 2009 20:05:35 -0800 Subject: [Mristudio-users] Reduce number of slices after generation of DTI-map In-Reply-To: References: <33c01b0b0912031557v389e5f1dob65890e1cb25bf69@mail.gmail.com> Message-ID: <33c01b0b0912032005v1e136f13x2e6913a0988eed54@mail.gmail.com> Hi Susumu, Thanks for your prompt reply. I have already chosen "all slice" in the data input window and that's why I am confused. When I process the raw data, there is no problem. I am facing problem when I try to use "DTI map " function to generate FA, MD map etc. regards, Manoj On Thu, Dec 3, 2009 at 6:57 PM, susumu mori wrote: > Hi Manoj, > > Please make sure that you chose "all slice" in the data input window in the > beginning. There is a function to restrict the number of slices to process > in case you run into memory shortage. > > Susumu > > On Thu, Dec 3, 2009 at 6:57 PM, manoj sarma wrote: > >> Hi, >> >> I am new to DTI-Studio. I am facing a problem regarding number of slices >> produced after I generate DTI-map. My raw DTI data have 76 slices and after >> processing with DTI-Studio I get the same. But when I generate DTI map it >> produces 50 slices only. I am confused where is the problem. How can I have >> same number of slices generate as the raw data? >> >> >> regards, >> Manoj >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091203/6beafc62/attachment.html From susumu at mri.jhu.edu Fri Dec 4 09:25:13 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Fri, 04 Dec 2009 09:25:13 -0500 Subject: [Mristudio-users] Reduce number of slices after generation of DTI-map In-Reply-To: <33c01b0b0912032005v1e136f13x2e6913a0988eed54@mail.gmail.com> References: <33c01b0b0912031557v389e5f1dob65890e1cb25bf69@mail.gmail.com> <33c01b0b0912032005v1e136f13x2e6913a0988eed54@mail.gmail.com> Message-ID: Hi Manoj, Please test the following. I also experienced some similar issues some time ago and I though this issue was solved since then, but may be still there. The issue is, DtiStudio remembers parameters in the previous session. When you choose "all slice", it may still take the slice number of the previous session. >In the opening data input window, choose "partial slice" and specify 0 - 75. >Load the data and close the DtiStudio. >Load the same data with "all slice" and close the window This may refresh the memory. Also please try the latest version posted in MriStudio.org. If nothing works, we'll look into the data. Susumu On Thu, Dec 3, 2009 at 11:05 PM, manoj sarma wrote: > Hi Susumu, > > Thanks for your prompt reply. I have already chosen "all slice" in the data > input window and that's why I am confused. When I process the raw data, > there is no problem. I am facing problem when I try to use "DTI map " > function to generate FA, MD map etc. > > regards, > Manoj > > > > > On Thu, Dec 3, 2009 at 6:57 PM, susumu mori wrote: > >> Hi Manoj, >> >> Please make sure that you chose "all slice" in the data input window in >> the beginning. There is a function to restrict the number of slices to >> process in case you run into memory shortage. >> >> Susumu >> >> On Thu, Dec 3, 2009 at 6:57 PM, manoj sarma wrote: >> >>> Hi, >>> >>> I am new to DTI-Studio. I am facing a problem regarding number of slices >>> produced after I generate DTI-map. My raw DTI data have 76 slices and after >>> processing with DTI-Studio I get the same. But when I generate DTI map it >>> produces 50 slices only. I am confused where is the problem. How can I have >>> same number of slices generate as the raw data? >>> >>> >>> regards, >>> Manoj >>> >>> _______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: >>> Mristudio-users-unsubscribe at mristudio.org >>> >>> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091204/11c1de49/attachment-0001.html From mksarma at gmail.com Fri Dec 4 21:30:20 2009 From: mksarma at gmail.com (manoj sarma) Date: Fri, 04 Dec 2009 20:30:20 -0600 Subject: [Mristudio-users] Reduce number of slices after generation of DTI-map In-Reply-To: References: <33c01b0b0912031557v389e5f1dob65890e1cb25bf69@mail.gmail.com> <33c01b0b0912032005v1e136f13x2e6913a0988eed54@mail.gmail.com> Message-ID: <33c01b0b0912041830q21d38751r8c0bb82da83c4474@mail.gmail.com> Hi Susumu, Thanks for the help. I tried as you told and its working now. regards, Manoj On Fri, Dec 4, 2009 at 8:25 AM, susumu mori wrote: > Hi Manoj, > > Please test the following. I also experienced some similar issues some time > ago and I though this issue was solved since then, but may be still there. > The issue is, DtiStudio remembers parameters in the previous session. When > you choose "all slice", it may still take the slice number of the previous > session. > > >In the opening data input window, choose "partial slice" and specify 0 - > 75. > >Load the data and close the DtiStudio. > >Load the same data with "all slice" and close the window > > This may refresh the memory. > > Also please try the latest version posted in MriStudio.org. > > If nothing works, we'll look into the data. > > Susumu > > > On Thu, Dec 3, 2009 at 11:05 PM, manoj sarma wrote: > >> Hi Susumu, >> >> Thanks for your prompt reply. I have already chosen "all slice" in the >> data input window and that's why I am confused. When I process the raw data, >> there is no problem. I am facing problem when I try to use "DTI map " >> function to generate FA, MD map etc. >> >> regards, >> Manoj >> >> >> >> >> On Thu, Dec 3, 2009 at 6:57 PM, susumu mori wrote: >> >>> Hi Manoj, >>> >>> Please make sure that you chose "all slice" in the data input window in >>> the beginning. There is a function to restrict the number of slices to >>> process in case you run into memory shortage. >>> >>> Susumu >>> >>> On Thu, Dec 3, 2009 at 6:57 PM, manoj sarma wrote: >>> >>>> Hi, >>>> >>>> I am new to DTI-Studio. I am facing a problem regarding number of slices >>>> produced after I generate DTI-map. My raw DTI data have 76 slices and after >>>> processing with DTI-Studio I get the same. But when I generate DTI map it >>>> produces 50 slices only. I am confused where is the problem. How can I have >>>> same number of slices generate as the raw data? >>>> >>>> >>>> regards, >>>> Manoj >>>> >>>> _______________________________________________ >>>> Mristudio-users mailing list >>>> Mristudio-users at mristudio.org >>>> http://lists.mristudio.org/mailman/listinfo/ >>>> Unsubscribe, send a blank email to: >>>> Mristudio-users-unsubscribe at mristudio.org >>>> >>>> >>> >>> _______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: >>> Mristudio-users-unsubscribe at mristudio.org >>> >>> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091204/db71525e/attachment.html From JJames2 at radiology.umsmed.edu Mon Dec 7 12:29:04 2009 From: JJames2 at radiology.umsmed.edu (Judy James) Date: Mon, 07 Dec 2009 11:29:04 -0600 Subject: [Mristudio-users] symmetrical ROI on the contra lateral side? Message-ID: <4B1CE7000200002A0002C728@GWIA1.umsmed.edu> Hello, I needed some help in ROI drawing. I would like to how to draw a symmetrical ROI on the contra lateral side of the brain given one ROI is drawn on one side? Is there any feature in DTI studio that will allow to do this in any shape (free, oval, polygon etc...). Any suggestions will be appreciated. Thanks Judy ***************************************************** Dr. Judy Rose James MR Physicist/Assistant Professor Department of Radiology University of Mississippi Medical Centre Jackson, MS 39216 Ph: 601-984-2585 Pager: 601-929-2442 email: jjames2 at radiology.umsmed.edu ***************************************************** Individuals who have received this information in error or are not authorized to receive it must promptly return or dispose of the information and notify the sender. Those individuals are hereby notified that they are strictly prohibited from reviewing, forwarding, printing, copying, distributing or using this information in any way. From susumu at mri.jhu.edu Wed Dec 9 11:30:50 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 09 Dec 2009 11:30:50 -0500 Subject: [Mristudio-users] symmetrical ROI on the contra lateral side? In-Reply-To: <4B1CE7000200002A0002C728@GWIA1.umsmed.edu> References: <4B1CE7000200002A0002C728@GWIA1.umsmed.edu> Message-ID: Hi Judy, There is no direct function that allows you to flip an ROI to the symmetric site. If you are using a symmetric ROI option (not the free-hand polygon) such as circle, oval, and rectangle, you can move the ROI by the arrow key manually to the contralateral side. Susumu On Mon, Dec 7, 2009 at 12:29 PM, Judy James wrote: > Hello, > > I needed some help in ROI drawing. I would like to how to draw a > symmetrical ROI on the contra lateral side of the brain given one ROI is > drawn on one side? > Is there any feature in DTI studio that will allow to do this in any shape > (free, oval, polygon etc...). Any suggestions will be appreciated. > > Thanks > Judy > > > ***************************************************** > Dr. Judy Rose James > MR Physicist/Assistant Professor > Department of Radiology > University of Mississippi Medical Centre > Jackson, MS 39216 > Ph: 601-984-2585 > Pager: 601-929-2442 > email: jjames2 at radiology.umsmed.edu > ***************************************************** > > Individuals who have received this information in error or are not > authorized to receive it must promptly return or dispose of the information > and notify the sender. Those individuals are hereby notified that they are > strictly prohibited from reviewing, forwarding, printing, copying, > distributing or using this information in any way. > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091209/87807bfd/attachment.html From sailasuta at hmri.org Wed Dec 9 13:37:04 2009 From: sailasuta at hmri.org (Pom Sailasuta) Date: Wed, 09 Dec 2009 10:37:04 -0800 Subject: [Mristudio-users] acquiring DTI images Message-ID: <9f9dcd90912091037u5de167c2i7540b5e683eca758@mail.gmail.com> Hello, Can you point to the location of the recommend data acqn protocol? Thank you very much, Pom ( a newbie in DTI world). -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091209/6972d6b9/attachment.html From lucas_lessa at yahoo.com.br Thu Dec 10 09:36:48 2009 From: lucas_lessa at yahoo.com.br (Lucas Lessa) Date: Thu, 10 Dec 2009 06:36:48 -0800 (PST) Subject: [Mristudio-users] Another way to use ROIeditor with different imagens (different matrix) Message-ID: <251299.84967.qm@web110206.mail.gq1.yahoo.com> Good Morning, I'm in the middle of a study that correlates the fractional anisotropy of corticospinal tract with transfer magnetization (MTR). But I can't correlate than in ROIeditor since the series had been done with different matrix. Is there another way to correlate this series with ROIs in the same place or I will have to do this manually? (the imagens have the same number os slices and same orientation, but with different FOV too). Thank you very much. Lucas Lessa S?o Paulo/Brazil ____________________________________________________________________________________ Veja quais s?o os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091210/2f9c6463/attachment-0001.html From lucas_lessa at yahoo.com.br Thu Dec 10 09:47:33 2009 From: lucas_lessa at yahoo.com.br (Lucas Lessa) Date: Thu, 10 Dec 2009 06:47:33 -0800 (PST) Subject: [Mristudio-users] Is better to do 3 DTI series or just one well done? Message-ID: <55145.37743.qm@web110203.mail.gq1.yahoo.com> Good morning, As I said in aonther post, I'm in the middle of a DTI study that, obsviously, uses DTI studio to process the data. The other researcher brought (a think from John Hopkins) a model that uses 3 DTI series, just to increase the ratio between sign/noise. The exams are taking so long and I would like to increase the resolution from 112x110 to 256x256, and maybe, 512x512. Is this a good idea? Or it's better to continue making the exams with the 3 DTI series? And wich is the bennefit of doing 3 DTI series (the vendor software only uses one at a time)? One more time thank you. Lucas Lessa S?o Paulo/Brazil ____________________________________________________________________________________ Veja quais s?o os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091210/221653bf/attachment.html From susumu at mri.jhu.edu Thu Dec 10 12:22:41 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Thu, 10 Dec 2009 12:22:41 -0500 Subject: [Mristudio-users] Is better to do 3 DTI series or just one well done? In-Reply-To: <55145.37743.qm@web110203.mail.gq1.yahoo.com> References: <55145.37743.qm@web110203.mail.gq1.yahoo.com> Message-ID: If you are using a 1.5 T scanner, I think 2.5 mm isotropic resolution is a good compromise between scanning time and SNR. With a 30-orientation scheme, you may want to do at least two repetition (total 60 DWIs) to get a decent SNR. If you want to increase the resolution, you need more dwis and a longer scanning time. What is important is the total number of images, in this case 60. So, if you are using a 15-orientation scheme, you need 4 repetitions. A 30-orientation scheme should take about 4-5min in Siemens and Philips. GE may take 7-8 min in some versions because of gradient overheating precaution (TR can't be too short). So, two repetitions (total 60 dwis) should take 8-10 min in Siemens/Philips. This is certainly a long scan, especially for clinical. If time is important, you can do one repetition (total 30 dwis), scarifying the SNR. In this case, you definitely don't want to increase the resolution, which would make the SNR worse. For 3T, 30 dwis can give you a decent SNR with 2.5mm resolution. Or if you stick with a 60 dwis protocol, you can use 2.2 mm resolution. I have seen nice 2.0 mm resolution with the latest head coils. For 2.2 mm, you need to use 112x112 matrix. Please note that larger matrix leads to more distortion. Because 3T has larger distortion than 1.5 T, using a larger matrix in 3T is not a good idea in general. Hope it helps. Susumu On Thu, Dec 10, 2009 at 9:47 AM, Lucas Lessa wrote: > Good morning, > > As I said in aonther post, I'm in the middle of a DTI study that, > obsviously, uses DTI studio to process the data. > The other researcher brought (a think from John Hopkins) a model that uses > 3 DTI series, just to increase the ratio between sign/noise. > The exams are taking so long and I would like to increase the resolution > from 112x110 to 256x256, and maybe, 512x512. > Is this a good idea? Or it's better to continue making the exams with the 3 > DTI series? > And wich is the bennefit of doing 3 DTI series (the vendor software only > uses one at a time)? > One more time thank you. > > Lucas Lessa > S?o Paulo/Brazil > > ------------------------------ > Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top 10- > Celebridades- > M?sica- > Esportes > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091210/09db23e4/attachment.html From susumu at mri.jhu.edu Thu Dec 10 12:37:36 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Thu, 10 Dec 2009 12:37:36 -0500 Subject: [Mristudio-users] Another way to use ROIeditor with different imagens (different matrix) In-Reply-To: <251299.84967.qm@web110206.mail.gq1.yahoo.com> References: <251299.84967.qm@web110206.mail.gq1.yahoo.com> Message-ID: 1) If multiple images are co-registered, meaning the patient was scanned in the same session and didn't move; 1-1) if all images, say T1, T2, DTI, MTR, share the same center of FOV and imaging angles; > you can use DiffeoMap (previously called Landmarker) to simply resize the matrix and FOV. Then they will be all co-registered (suppose the patient didn't move during the scan) 1-2) If different images did not share the same center of FOV and have different angles; > You can get the FOV locations and FOV angle information from the DICOM header and use the information to shift, rotate, resize, rematrix in DiffeoMap to co-register the images. 2) Or, if you find 1-2 is too much of work or if you suspect the patient moved, You can run AIR or MI in Diffeomap to coregister the two images (e.g. DTI and MTR). These two images can have different matrix size and FOV. The output of AIR or MI will have the same dimensions as the template you choose. So, I believe DiffeoMap can solve your problem in any cases. On Thu, Dec 10, 2009 at 9:36 AM, Lucas Lessa wrote: > Good Morning, > > I'm in the middle of a study that correlates the fractional anisotropy of > corticospinal tract with transfer magnetization (MTR). > But I can't correlate than in ROIeditor since the series had been done with > different matrix. > Is there another way to correlate this series with ROIs in the same place > or I will have to do this manually? (the imagens have the same number os > slices and same orientation, but with different FOV too). > Thank you very much. > > Lucas Lessa > S?o Paulo/Brazil > > ------------------------------ > Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top 10- > Celebridades- > M?sica- > Esportes > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091210/c67125d3/attachment.html From lucas_lessa at yahoo.com.br Thu Dec 10 13:25:25 2009 From: lucas_lessa at yahoo.com.br (Lucas Lessa) Date: Thu, 10 Dec 2009 10:25:25 -0800 (PST) Subject: [Mristudio-users] Enc: Another way to use ROIeditor with different imagens (different matrix) Message-ID: <653537.11916.qm@web110204.mail.gq1.yahoo.com> Good Morning, I'm in the middle of a study that correlates the fractional anisotropy of corticospinal tract with transfer magnetization (MTR). But I can't correlate than in ROIeditor since the series had been done with different matrix. Is there another way to correlate this series with ROIs in the same place or I will have to do this manually? (the imagens have the same number os slices and same orientation, but with different FOV too). Thank you very much. Lucas Lessa S?o Paulo/Brazil ____________________________________________________________________________________ Veja quais s?o os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091210/51449fd6/attachment.html From lucas_lessa at yahoo.com.br Thu Dec 10 13:33:39 2009 From: lucas_lessa at yahoo.com.br (Lucas Lessa) Date: Thu, 10 Dec 2009 10:33:39 -0800 (PST) Subject: [Mristudio-users] Is better to do 3 DTI series or just one well done? In-Reply-To: Message-ID: <200110.2554.qm@web110209.mail.gq1.yahoo.com> Dr. Susumu Mori you helped me a lot. I'm using 3 repetions of a 33 dir DTI in a Philips 1.5T (the voxel is about 2.2mm.) when I want to do an exam for a research, for the real life I use just one repetion. Indeed the SNR is much better with 3 repetions, but just in DTI Studio, because Philip's software don't handle the 3 series like one. What do you think in increase my resolution to 256x256 in this scanner? Will the exam take so long? Can I use just 2 repetitions? Thank you. ? Lucas Lessa. ? --- Em qui, 10/12/09, susumu mori escreveu: De: susumu mori Assunto: Re: [Mristudio-users] Is better to do 3 DTI series or just one well done? Para: "DTI Studio, ROI Editor, Landmarker Questions/Support" Data: Quinta-feira, 10 de Dezembro de 2009, 15:22 If you are using a 1.5 T scanner, I think 2.5 mm isotropic resolution is a good compromise between scanning time and SNR. With a 30-orientation scheme, you may want to do at least two repetition (total 60 DWIs) to get a decent SNR. If you want to increase the resolution, you need more dwis and a longer scanning time. What is important is the total number of images, in this case 60. So, if you are using a 15-orientation scheme, you need 4 repetitions. A 30-orientation scheme should take about 4-5min in Siemens and Philips. GE may take 7-8 min in some versions because of gradient overheating precaution (TR can't be too short). So, two repetitions (total 60 dwis) should take 8-10 min in Siemens/Philips. This is certainly a long scan, especially for clinical. If time is important, you can do one repetition (total 30 dwis), scarifying the SNR. In this case, you definitely don't want to increase the resolution, which would make the SNR worse. For 3T, 30 dwis can give you a decent SNR with 2.5mm resolution. Or if you stick with a 60 dwis protocol, you can use 2.2 mm resolution. I have seen nice 2.0 mm resolution with the latest head coils. For 2.2 mm, you need to use 112x112 matrix. Please note that larger matrix leads to more distortion. Because 3T has larger distortion than 1.5 T, using a larger matrix in 3T is not a good idea in general. Hope it helps. Susumu On Thu, Dec 10, 2009 at 9:47 AM, Lucas Lessa wrote: Good morning, As I said in aonther post, I'm in the middle of a DTI study that, obsviously, uses DTI studio to process the data. The other researcher brought (a think from John Hopkins) a model that uses 3 DTI series, just to increase the ratio between sign/noise. The exams are taking so long and I would like to increase the resolution from 112x110 to 256x256, and maybe, 512x512. Is this a good idea? Or it's better to continue making the exams with the 3 DTI series? And wich is the bennefit of doing 3 DTI series (the vendor software only uses one at a time)? One more time thank you. Lucas Lessa S?o Paulo/Brazil Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top 10 - Celebridades - M?sica - Esportes _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -----Anexo incorporado----- _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org ____________________________________________________________________________________ Veja quais s?o os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091210/1e0231f6/attachment-0001.html From susumu at mri.jhu.edu Thu Dec 10 13:59:59 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Thu, 10 Dec 2009 13:59:59 -0500 Subject: [Mristudio-users] Is better to do 3 DTI series or just one well done? In-Reply-To: <200110.2554.qm@web110209.mail.gq1.yahoo.com> References: <200110.2554.qm@web110209.mail.gq1.yahoo.com> Message-ID: I wouldn't push the resolution that much. I even hesitate to use 128x128, unless we can use SENSE factor of 4 so that the echotrain is 128/4 =32 On Thu, Dec 10, 2009 at 1:33 PM, Lucas Lessa wrote: > Dr. Susumu Mori you helped me a lot. > I'm using 3 repetions of a 33 dir DTI in a Philips 1.5T (the voxel is about > 2.2mm.) when I want to do an exam for a research, for the real life I use > just one repetion. > Indeed the SNR is much better with 3 repetions, but just in DTI Studio, > because Philip's software don't handle the 3 series like one. > What do you think in increase my resolution to 256x256 in this scanner? > Will the exam take so long? Can I use just 2 repetitions? > Thank you. > > Lucas Lessa. > > > > --- Em *qui, 10/12/09, susumu mori * escreveu: > > > De: susumu mori > Assunto: Re: [Mristudio-users] Is better to do 3 DTI series or just one > well done? > Para: "DTI Studio, ROI Editor, Landmarker Questions/Support" < > mristudio-users at mristudio.org> > Data: Quinta-feira, 10 de Dezembro de 2009, 15:22 > > > If you are using a 1.5 T scanner, I think 2.5 mm isotropic resolution is a > good compromise between scanning time and SNR. With a 30-orientation scheme, > you may want to do at least two repetition (total 60 DWIs) to get a decent > SNR. If you want to increase the resolution, you need more dwis and a longer > scanning time. > > What is important is the total number of images, in this case 60. So, if > you are using a 15-orientation scheme, you need 4 repetitions. A > 30-orientation scheme should take about 4-5min in Siemens and Philips. GE > may take 7-8 min in some versions because of gradient overheating precaution > (TR can't be too short). So, two repetitions (total 60 dwis) should take > 8-10 min in Siemens/Philips. This is certainly a long scan, especially for > clinical. If time is important, you can do one repetition (total 30 dwis), > scarifying the SNR. In this case, you definitely don't want to increase the > resolution, which would make the SNR worse. > > For 3T, 30 dwis can give you a decent SNR with 2.5mm resolution. Or if you > stick with a 60 dwis protocol, you can use 2.2 mm resolution. I have seen > nice 2.0 mm resolution with the latest head coils. For 2.2 mm, you need to > use 112x112 matrix. Please note that larger matrix leads to more distortion. > Because 3T has larger distortion than 1.5 T, using a larger matrix in 3T is > not a good idea in general. > > Hope it helps. > > Susumu > > On Thu, Dec 10, 2009 at 9:47 AM, Lucas Lessa > > wrote: > >> Good morning, >> >> As I said in aonther post, I'm in the middle of a DTI study that, >> obsviously, uses DTI studio to process the data. >> The other researcher brought (a think from John Hopkins) a model that uses >> 3 DTI series, just to increase the ratio between sign/noise. >> The exams are taking so long and I would like to increase the resolution >> from 112x110 to 256x256, and maybe, 512x512. >> Is this a good idea? Or it's better to continue making the exams with the >> 3 DTI series? >> And wich is the bennefit of doing 3 DTI series (the vendor software only >> uses one at a time)? >> One more time thank you. >> >> Lucas Lessa >> S?o Paulo/Brazil >> >> ------------------------------ >> Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top 10- >> Celebridades- >> M?sica- >> Esportes >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > -----Anexo incorporado----- > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > > ------------------------------ > Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top 10- > Celebridades- > M?sica- > Esportes > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091210/82b79a06/attachment.html From KBlackst at cnmc.org Fri Dec 11 09:30:31 2009 From: KBlackst at cnmc.org (Blackstone, Kaitlin) Date: Fri, 11 Dec 2009 09:30:31 -0500 Subject: [Mristudio-users] Diffeomap (Landmarker) software registration In-Reply-To: Message-ID: Good morning, I downloaded DiffeoMap (Landmarker) and I am unable to register the program on my computer so that I may use it. When I enter the registration key given to me (LMgQxVkI5tQEE NMM/A9dfefzK6), I get an error message saying "Error verifying license: key value not valid". My machine ID is -1123397049. Is there another way I can get this program or somehow register it properly? Thank you very much! Kaitlin Blackstone, B.A. Children's National Medical Center Children's Research Institute 111 Michigan Avenue, NW Washington, D.C. 20010 202-476-4755 Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091211/c86eff83/attachment.html From xli16 at jhmi.edu Fri Dec 11 10:02:14 2009 From: xli16 at jhmi.edu (Xin Li) Date: Fri, 11 Dec 2009 10:02:14 -0500 Subject: [Mristudio-users] Diffeomap (Landmarker) software registration In-Reply-To: References: Message-ID: Kaitlin, Is Diffeomap installed in your local computer? Xin ----- Original Message ----- From: "Blackstone, Kaitlin" Date: Friday, December 11, 2009 9:32 am Subject: [Mristudio-users] Diffeomap (Landmarker) software registration To: "DTI Studio, ROI Editor,Landmarker Questions/Support" > Good morning, > > > > I downloaded DiffeoMap (Landmarker) and I am unable to register the > program on my computer so that I may use it. When I enter the > registration key given to me (LMgQxVkI5tQEE NMM/A9dfefzK6), I get an > error message saying "Error verifying license: key value not valid". > My > machine ID is -1123397049. Is there another way I can get this program > or somehow register it properly? > > Thank you very much! > > > > > > Kaitlin Blackstone, B.A. > > Children's National Medical Center > > Children's Research Institute > > 111 Michigan Avenue, NW > > Washington, D.C. 20010 > > 202-476-4755 > > > > Confidentiality Notice: This e-mail message, including any > attachments, is for the sole use of the intended > recipient(s) and may contain confidential and privileged information. > Any unauthorized review, use, disclosure or distribution is > prohibited. > If you are not the intended recipient, please contact the sender by > reply e-mail and destroy all copies of the original message. > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From KBlackst at cnmc.org Fri Dec 11 10:05:55 2009 From: KBlackst at cnmc.org (Blackstone, Kaitlin) Date: Fri, 11 Dec 2009 10:05:55 -0500 Subject: [Mristudio-users] Diffeomap (Landmarker) software registration In-Reply-To: Message-ID: Yes, it is. Kaitlin Blackstone, B.A. Children's National Medical Center Children's Research Institute 111 Michigan Avenue, NW Washington, D.C. 20010 202-476-4755 -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Xin Li Sent: Friday, December 11, 2009 10:02 AM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] Diffeomap (Landmarker) software registration Kaitlin, Is Diffeomap installed in your local computer? Xin ----- Original Message ----- From: "Blackstone, Kaitlin" Date: Friday, December 11, 2009 9:32 am Subject: [Mristudio-users] Diffeomap (Landmarker) software registration To: "DTI Studio, ROI Editor,Landmarker Questions/Support" > Good morning, > > > > I downloaded DiffeoMap (Landmarker) and I am unable to register the > program on my computer so that I may use it. When I enter the > registration key given to me (LMgQxVkI5tQEE NMM/A9dfefzK6), I get an > error message saying "Error verifying license: key value not valid". > My > machine ID is -1123397049. Is there another way I can get this program > or somehow register it properly? > > Thank you very much! > > > > > > Kaitlin Blackstone, B.A. > > Children's National Medical Center > > Children's Research Institute > > 111 Michigan Avenue, NW > > Washington, D.C. 20010 > > 202-476-4755 > > > > Confidentiality Notice: This e-mail message, including any > attachments, is for the sole use of the intended > recipient(s) and may contain confidential and privileged information. > Any unauthorized review, use, disclosure or distribution is > prohibited. > If you are not the intended recipient, please contact the sender by > reply e-mail and destroy all copies of the original message. > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. From lucas_lessa at yahoo.com.br Fri Dec 11 11:05:30 2009 From: lucas_lessa at yahoo.com.br (Lucas Lessa) Date: Fri, 11 Dec 2009 08:05:30 -0800 (PST) Subject: [Mristudio-users] Is better to do 3 DTI series or just one well done? In-Reply-To: Message-ID: <662032.53943.qm@web110201.mail.gq1.yahoo.com> Once again thank you Dr Mori. and what do you think about increase the SNR in GE 1.5T scanners? We only do one serie with 33 directions, but we have to use slices with 5mm thickness, and NEX 3. Is it better to do 3 series like in Phillips or push the parameters? --- Em qui, 10/12/09, susumu mori escreveu: De: susumu mori Assunto: Re: [Mristudio-users] Is better to do 3 DTI series or just one well done? Para: "DTI Studio, ROI Editor, Landmarker Questions/Support" Data: Quinta-feira, 10 de Dezembro de 2009, 16:59 I wouldn't push the resolution that much. I even hesitate to use 128x128, unless we can use SENSE factor of 4 so that the echotrain is 128/4 =32 On Thu, Dec 10, 2009 at 1:33 PM, Lucas Lessa wrote: Dr. Susumu Mori you helped me a lot. I'm using 3 repetions of a 33 dir DTI in a Philips 1.5T (the voxel is about 2.2mm.) when I want to do an exam for a research, for the real life I use just one repetion. Indeed the SNR is much better with 3 repetions, but just in DTI Studio, because Philip's software don't handle the 3 series like one. What do you think in increase my resolution to 256x256 in this scanner? Will the exam take so long? Can I use just 2 repetitions? Thank you. ? Lucas Lessa. ? --- Em qui, 10/12/09, susumu mori escreveu: De: susumu mori Assunto: Re: [Mristudio-users] Is better to do 3 DTI series or just one well done? Para: "DTI Studio, ROI Editor, Landmarker Questions/Support" Data: Quinta-feira, 10 de Dezembro de 2009, 15:22 If you are using a 1.5 T scanner, I think 2.5 mm isotropic resolution is a good compromise between scanning time and SNR. With a 30-orientation scheme, you may want to do at least two repetition (total 60 DWIs) to get a decent SNR. If you want to increase the resolution, you need more dwis and a longer scanning time. What is important is the total number of images, in this case 60. So, if you are using a 15-orientation scheme, you need 4 repetitions. A 30-orientation scheme should take about 4-5min in Siemens and Philips. GE may take 7-8 min in some versions because of gradient overheating precaution (TR can't be too short). So, two repetitions (total 60 dwis) should take 8-10 min in Siemens/Philips. This is certainly a long scan, especially for clinical. If time is important, you can do one repetition (total 30 dwis), scarifying the SNR. In this case, you definitely don't want to increase the resolution, which would make the SNR worse. For 3T, 30 dwis can give you a decent SNR with 2.5mm resolution. Or if you stick with a 60 dwis protocol, you can use 2.2 mm resolution. I have seen nice 2.0 mm resolution with the latest head coils. For 2.2 mm, you need to use 112x112 matrix. Please note that larger matrix leads to more distortion. Because 3T has larger distortion than 1.5 T, using a larger matrix in 3T is not a good idea in general. Hope it helps. Susumu On Thu, Dec 10, 2009 at 9:47 AM, Lucas Lessa wrote: Good morning, As I said in aonther post, I'm in the middle of a DTI study that, obsviously, uses DTI studio to process the data. The other researcher brought (a think from John Hopkins) a model that uses 3 DTI series, just to increase the ratio between sign/noise. The exams are taking so long and I would like to increase the resolution from 112x110 to 256x256, and maybe, 512x512. Is this a good idea? Or it's better to continue making the exams with the 3 DTI series? And wich is the bennefit of doing 3 DTI series (the vendor software only uses one at a time)? One more time thank you. Lucas Lessa S?o Paulo/Brazil Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top 10 - Celebridades - M?sica - Esportes _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -----Anexo incorporado----- _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top 10 - Celebridades - M?sica - Esportes _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -----Anexo incorporado----- _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org ____________________________________________________________________________________ Veja quais s?o os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091211/ac66f179/attachment.html From dima_mk at hotmail.com Fri Dec 11 11:56:30 2009 From: dima_mk at hotmail.com (Demitry Kazlouski) Date: Fri, 11 Dec 2009 09:56:30 -0700 Subject: [Mristudio-users] ROI placement Message-ID: Hello, Can someone suggest me a better way to place ROI(s) within a white matter tract and get accurate FAs (fractional anisotropy values) for a group comparison? I see two ways by using ROI tab. One is to place ROI of a fixed shape for all subjects. The other way is to create manually drawn ROIs. If I use the first method, there would be some uncertainty because the fibers of other white matter tracts might be selected. If I use the second method, my ROIs would have different areas and, I assume, this would affect FA values. It seems like both methods have pros and cons. Please let me know your opinion. Thanks. Demitry Kazlouski, BS Research Assistant, Developmental Brain Research Program University of Colorado Denver The Children's Hospital, Gary Pavilion A036/B-130 13123 East 16th Avenue Aurora, CO 80045 dima_mk at hotmail.com -------------- next part -------------- A non-text attachment was scrubbed... Name: winmail.dat Type: application/ms-tnef Size: 4994 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091211/807f5d2a/attachment-0001.bin From domenico.zaca at gmail.com Fri Dec 4 11:10:12 2009 From: domenico.zaca at gmail.com (Domenico Zaca) Date: Fri, 04 Dec 2009 11:10:12 -0500 Subject: [Mristudio-users] B0 averages Message-ID: <54a7b29a0912040810u6cdc486anaed75a7979677757@mail.gmail.com> Hi, Does anyone know if there is a way to set up on a 3T Siemens Trio scanner a DTI sequence with a number of B0 acquisitions different than the number of acquisitions for each gradient direction (e.g 4 B0 averages and 2 averages for each of the other directions)? Thanks, Domenico -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091204/af5c4c06/attachment-0001.html From zhipenghou at gmail.com Fri Dec 11 10:13:51 2009 From: zhipenghou at gmail.com (Zhipeng Hou) Date: Fri, 11 Dec 2009 10:13:51 -0500 Subject: [Mristudio-users] Diffeomap (Landmarker) software registration In-Reply-To: <145933A2BE9E4F48AE079A201379BF2F1FC40FBE1E@RAD-EXCH1.win.ad.jhu.edu> References: <145933A2BE9E4F48AE079A201379BF2F1FC40FBE1E@RAD-EXCH1.win.ad.jhu.edu> Message-ID: <568cc7760912110713j18d6466k2c9423c6e9567b0d@mail.gmail.com> Right click DiffeoMap "Run as Administrator" On Fri, Dec 11, 2009 at 10:06 AM, Blackstone, Kaitlin wrote: > Yes, it is. > > Kaitlin Blackstone, B.A. > Children's National Medical Center > Children's Research Institute > 111 Michigan Avenue, NW > Washington, D.C. 20010 > 202-476-4755 > > > -----Original Message----- > From: mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Xin Li > Sent: Friday, December 11, 2009 10:02 AM > To: DTI Studio, ROI Editor, Landmarker Questions/Support > Subject: Re: [Mristudio-users] Diffeomap (Landmarker) software > registration > > Kaitlin, > > Is Diffeomap installed in your local computer? > > Xin > > > ----- Original Message ----- > From: "Blackstone, Kaitlin" > Date: Friday, December 11, 2009 9:32 am > Subject: [Mristudio-users] Diffeomap (Landmarker) software registration > To: "DTI Studio, ROI Editor,Landmarker Questions/Support" > > > > > Good morning, > > > > > > > > I downloaded DiffeoMap (Landmarker) and I am unable to register the > > program on my computer so that I may use it. When I enter the > > registration key given to me (LMgQxVkI5tQEE NMM/A9dfefzK6), I get an > > error message saying "Error verifying license: key value not valid". > > My > > machine ID is -1123397049. Is there another way I can get this > program > > or somehow register it properly? > > > > Thank you very much! > > > > > > > > > > > > Kaitlin Blackstone, B.A. > > > > Children's National Medical Center > > > > Children's Research Institute > > > > 111 Michigan Avenue, NW > > > > Washington, D.C. 20010 > > > > 202-476-4755 > > > > > > > > Confidentiality Notice: This e-mail message, including any > > attachments, is for the sole use of the intended > > recipient(s) and may contain confidential and privileged information. > > > Any unauthorized review, use, disclosure or distribution is > > prohibited. > > If you are not the intended recipient, please contact the sender by > > reply e-mail and destroy all copies of the original message. > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > Confidentiality Notice: This e-mail message, including any attachments, is > for the sole use of the intended > recipient(s) and may contain confidential and privileged information. Any > unauthorized review, use, disclosure or distribution is prohibited. > If you are not the intended recipient, please contact the sender by reply > e-mail and destroy all copies of the original message. > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091211/564241cd/attachment-0001.html From miguel.burgaleta at uam.es Fri Dec 11 13:48:02 2009 From: miguel.burgaleta at uam.es (Miguel Burgaleta) Date: Fri, 11 Dec 2009 19:48:02 +0100 Subject: [Mristudio-users] Flip eigen vector Message-ID: <164AFB34-6BF5-4310-8416-179393C747BA@uam.es> Dear DTIStudio experts, My question has to do with the flipping of the eigenvectors in fiber tracking. It looks like this is something very tricky, so I would like to make sure that I am choosing the right one. So I ran the fiber tracking ( starting and ending FA thresholds at .2 and angle at 40) and tried a single 'OR' ROI in the brainstem, capturing the corticospinal tract. I used this single ROI to track fibers in 4 conditions: no flipping of eigenvectors, flipping of X, flipping of Y and flipping of Z. Please see results in attachment (note that the acquisition is not a full brain coverage). I'm not very good at anatomy but would say that flipping the Y eigenvector leads to the best results - better than no flipping... What do you think? Thanks in advance for your time. Miguel -------------- next part -------------- A non-text attachment was scrubbed... Name: flipEigenvector.jpg Type: image/jpeg Size: 89242 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091211/b1745ca0/attachment-0001.jpg -------------- next part -------------- From susumu at mri.jhu.edu Fri Dec 11 16:14:26 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Fri, 11 Dec 2009 16:14:26 -0500 Subject: [Mristudio-users] ROI placement In-Reply-To: References: Message-ID: 1) If you do a lot of ROI drawing, I recommend you to move to RoiEditor you can download from www.mristudio.org. It has a seamless interface between DtiStudio and has much stronger functions for ROI drawing. 2) When you draw ROIs, there are two ways; a: draw ROIs in individual images such that you define the corresponding structures among different subjects b: draw the same ROI (the same size, shape, and location) and change the shapes of the subjects. If eveybody's shape becomes the same, you draw an ROI only once and can apply it to everybody else. The latter is, as you know, called brain normalization. DiffeoMap, which also can be downloaded from www.mristudio.org, provides several tools for the brain normalization. Once you normalize your images into the shape of our template (atlas), you can also use our pre-defined sets of ROIs, called White Matter Parcellation Maps (WMPM). In these maps, white matter and gray matter strucutres are pre-segmented (50-176 regions depending on the type of WMPM). You can apply these pre-defined ROIs to the normalized images. If you are interested in all these, I recoomend you to read; Mori S.,* *Oishi K., Jiang H, Jiang L., Li X., Akhter K., Hua K., Faria AV., Mahmod A., Woods R., Toga WA., Pike B, Rosa Neto P, Evans A, Zhang J, Huang H, Miller MI, van Zijl, PCM, Mazziotta, J, "Stereotaxic white matter atlas based on diffusion tensor imaging in an ICBM template", NeuroImage, 40, 570-582(2008) Oishi K, Zilles K, Amunts K, Faria A, Jiang H, Li X, Akhter K, Hua K, Woods R, Toga AW, Pike GB, Posa-Neto P, Evans A, Zhang J, Huang H, Mikker MI, van Zijl PCM, Mazziotta J, Mori S, "Human brain white matter atlas: identification and assignment of common anatomical structures in superficial white matter", Neuroimage, 43, 447-457 (2008) Oishi K, Faria A, Jiang H, Li X, Akhter K, Zhang J, Hsu J, Miller MI, van Zijl PCM, Albert M, Lyketsos CG, Woods R, Toga AW, Pike GB, Rosa-Neto P, Evans A, Mazziotta J, Mori S, "Atlas-based whole brain white matter analysis using large deformation diffeomorphic metric mapping: Application to normal elderly and Alzheimers' disease participants", Neuroimage, 46, 486-499 (2009) There are a nice "Getting Started" for the DiffeoMap section of www.mristudio.org, but our manuals are not ready yet. You can ask questions to the forum in www.mristudio.org. Susumu On Fri, Dec 11, 2009 at 11:56 AM, Demitry Kazlouski wrote: > Hello, > > > > Can someone suggest me a better way to place ROI(s) within a white matter > tract and get accurate FAs (fractional anisotropy values) for a group > comparison? > > I see two ways by using ROI tab. One is to place ROI of a fixed shape for > all subjects. The other way is to create manually drawn ROIs. If I use the > first method, there would be some uncertainty because the fibers of other > white matter tracts might be selected. If I use the second method, my ROIs > would have different areas and, I assume, this would affect FA values. It > seems like both methods have pros and cons. Please let me know your > opinion. > Thanks. > > > > > > Demitry Kazlouski, BS > > Research Assistant, Developmental Brain Research Program University of > Colorado Denver > > The Children's Hospital, Gary Pavilion A036/B-130 > > 13123 East 16th Avenue > > Aurora, CO 80045 > > dima_mk at hotmail.com > > > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091211/9478c1a3/attachment.html From vanerp at LifeSci.UCLA.EDU Fri Dec 11 18:14:51 2009 From: vanerp at LifeSci.UCLA.EDU (Theo van Erp) Date: Fri, 11 Dec 2009 15:14:51 -0800 Subject: [Mristudio-users] B0 averages In-Reply-To: <54a7b29a0912040810u6cdc486anaed75a7979677757@mail.gmail.com> Message-ID: Domenico, You should be able to fully customize your sequence by scanning in free mode, though I think this may require a research agreement. Here are some instructions that may be helpful (you need Advanced User access on your scanner for this): 1) Gain Advanced User access: To gain Advanced User access, press the [escape]+[control] keys simultaneously. If Windows Explorer is visible in the menu, then Advanced User is already on. If not, turn on Advanced User mode on by going to: [Programs]--->[Advanced User], then enter the Advanced User password. 2) Create DiffusionVectors.txt file: Go to: [Windows Explorer]--->[My Computer]--->[MedSystem C]--->[MedCom]--->[MriCustomer]--->[seq], and create a custom "DiffusionVectors.txt" (correct capitalization is important). 3) Verify the sequence parameters and copy sequence to scheduled scans: Go back to exam window and to verify that: * DiffusionMode=Free * b=1000, or what you plan to specify for you non b=0 weighed images If settings are correct, copy sequence to the list of scheduled scans. Once the scan is completed, rename the "DiffusionVectors.txt" file so other Users do not accidentally run your custom DTI sequence. Your DiffusionVectors.txt file should look something like this: --- # My custom diffusion vector set # 5 b=0 images # 4 diffusion weighted images [directions=9] CoordinateSystem = xyz vector[0] = ( 0.000000, 0.000000, 0.000000) vector[1] = ( 0.000000, 0.000000, 0.000000) vector[2] = ( 0.000000, 0.000000, 0.000000) vector[3] = ( 0.000000, 0.000000, 0.000000) vector[4] = ( 0.000000, 0.000000, 0.000000) vector[5] = ( -0.525731, -0.850651, 0.000000) vector[6] = ( -0.525731, 0.850651, 0.000000) vector[7] = ( 0.000000, 0.525731, 0.850651) vector[8] = ( 0.000000, -0.525731, 0.850651) --- Best, Theo On 12/4/09 8:10 AM, "Domenico Zaca" wrote: > Hi, > > Does anyone know if there is a way to set up on a 3T Siemens Trio scanner > a DTI sequence with a number of B0 acquisitions different than the number of > acquisitions for each gradient direction (e.g 4 B0 averages and 2 averages for > each of the other directions)? > > Thanks, > Domenico > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org Best, Theo _____________________________________________________________ Theo G.M. van Erp, Ph.D. Assistant Researcher Associate Director of the Clinical Neuroscience Lab NAPLS MRI Task Force Scientific Project Coordinator Clinical Neuroscience Lab Department of Psychology vanerp at psych.ucla.edu University of California Los Angeles voice (310) 206-4902 1285 Franz Hall, room 5562 fax (310) 794-9740 Los Angeles, California, 90095-1563 http://www.bol.ucla.edu/~vanerp http://napls.psych.ucla.edu _____________________________________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091211/f23c7010/attachment.html From susumu at mri.jhu.edu Fri Dec 11 20:20:01 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Fri, 11 Dec 2009 20:20:01 -0500 Subject: [Mristudio-users] Flip eigen vector In-Reply-To: <164AFB34-6BF5-4310-8416-179393C747BA@uam.es> References: <164AFB34-6BF5-4310-8416-179393C747BA@uam.es> Message-ID: Hi Miguel, It seems your Y-flip is right, although it's very rare that you have to flip Y. Usually X (Siemens) or Z (Philips). Please also do try genu, body, and splenium of the corpus callosum at the mid-sagittal level. I think it'll work but just to make sure. Also, if you are using Siemens (before VB15) or Philips (if you are using Gradient Overplus), make sure that you are taking care the oblique angles right. Susumu On Fri, Dec 11, 2009 at 1:48 PM, Miguel Burgaleta wrote: > > Dear DTIStudio experts, > > My question has to do with the flipping of the eigenvectors in fiber > tracking. It looks like this is something very tricky, so I would like to > make sure that I am choosing the right one. > > So I ran the fiber tracking ( starting and ending FA thresholds at .2 and > angle at 40) and tried a single 'OR' ROI in the brainstem, capturing the > corticospinal tract. I used this single ROI to track fibers in 4 conditions: > no flipping of eigenvectors, flipping of X, flipping of Y and flipping of Z. > > Please see results in attachment (note that the acquisition is not a full > brain coverage). I'm not very good at anatomy but would say that flipping > the Y eigenvector leads to the best results - better than no flipping... > What do you think? > > Thanks in advance for your time. > > Miguel > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091211/d05ac238/attachment-0001.html From susumu at mri.jhu.edu Fri Dec 11 21:14:01 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Fri, 11 Dec 2009 21:14:01 -0500 Subject: [Mristudio-users] Is better to do 3 DTI series or just one well done? In-Reply-To: <662032.53943.qm@web110201.mail.gq1.yahoo.com> References: <662032.53943.qm@web110201.mail.gq1.yahoo.com> Message-ID: Do you mean you are doing 33-orientation x 3 signal averaging for 5 mm slice? That is equivalent to 99 DWIs. With such as thick slice and the 99 DWI equivalent, you should have enough SNR even with 1.5T. 3 NEX and 3 series are equivalent in terms of SNR. The only difference is whether the scanner average the data for you or you get them saved separately. Usually, if you do 3 separate series, MR scanner can not combine them and does not offer an FA map based on the all 3 series. So, for clinical scans, you have no choice but using 3 NEX. If you are using Siemens, 3NEX and 3 series are completely identical because they actually save the 3 NEX scans separately and use all of them for tensor calculation. For example, if you do 3NEX of 33-orientaiton, you can find 99 Mosaic files. They don't actually average 3 scans. So it's the same as 3 series. I'm not sure how GE works. I believe if you do 3NEX of 33-orientaiton, you may get only 33 images, in which the 3 scans are already averaged. The disadvantage of this approach is, if the subject moved or one of the images are corrupted, you can not correct them once 3 images are averaged. These issues can be corrected to some degree if you are using off-line programs like DtiStudio or FSL. However, if you rely on FA map generation by the scanner, I guess you'd better use 3NEX. On Fri, Dec 11, 2009 at 11:05 AM, Lucas Lessa wrote: > Once again thank you Dr Mori. > and what do you think about increase the SNR in GE 1.5T scanners? > We only do one serie with 33 directions, but we have to use slices with 5mm > thickness, and NEX 3. Is it better to do 3 series like in Phillips or push > the parameters? > > > --- Em *qui, 10/12/09, susumu mori * escreveu: > > > De: susumu mori > Assunto: Re: [Mristudio-users] Is better to do 3 DTI series or just one > well done? > Para: "DTI Studio, ROI Editor, Landmarker Questions/Support" < > mristudio-users at mristudio.org> > Data: Quinta-feira, 10 de Dezembro de 2009, 16:59 > > I wouldn't push the resolution that much. I even hesitate to use 128x128, > unless we can use SENSE factor of 4 so that the echotrain is 128/4 =32 > > On Thu, Dec 10, 2009 at 1:33 PM, Lucas Lessa > > wrote: > >> Dr. Susumu Mori you helped me a lot. >> I'm using 3 repetions of a 33 dir DTI in a Philips 1.5T (the voxel is >> about 2.2mm.) when I want to do an exam for a research, for the real life I >> use just one repetion. >> Indeed the SNR is much better with 3 repetions, but just in DTI Studio, >> because Philip's software don't handle the 3 series like one. >> What do you think in increase my resolution to 256x256 in this scanner? >> Will the exam take so long? Can I use just 2 repetitions? >> Thank you. >> >> Lucas Lessa. >> >> >> >> --- Em *qui, 10/12/09, susumu mori >> >* escreveu: >> >> >> De: susumu mori >> > >> Assunto: Re: [Mristudio-users] Is better to do 3 DTI series or just one >> well done? >> Para: "DTI Studio, ROI Editor, Landmarker Questions/Support" < >> mristudio-users at mristudio.org >> > >> Data: Quinta-feira, 10 de Dezembro de 2009, 15:22 >> >> >> If you are using a 1.5 T scanner, I think 2.5 mm isotropic resolution is a >> good compromise between scanning time and SNR. With a 30-orientation scheme, >> you may want to do at least two repetition (total 60 DWIs) to get a decent >> SNR. If you want to increase the resolution, you need more dwis and a longer >> scanning time. >> >> What is important is the total number of images, in this case 60. So, if >> you are using a 15-orientation scheme, you need 4 repetitions. A >> 30-orientation scheme should take about 4-5min in Siemens and Philips. GE >> may take 7-8 min in some versions because of gradient overheating precaution >> (TR can't be too short). So, two repetitions (total 60 dwis) should take >> 8-10 min in Siemens/Philips. This is certainly a long scan, especially for >> clinical. If time is important, you can do one repetition (total 30 dwis), >> scarifying the SNR. In this case, you definitely don't want to increase the >> resolution, which would make the SNR worse. >> >> For 3T, 30 dwis can give you a decent SNR with 2.5mm resolution. Or if you >> stick with a 60 dwis protocol, you can use 2.2 mm resolution. I have seen >> nice 2.0 mm resolution with the latest head coils. For 2.2 mm, you need to >> use 112x112 matrix. Please note that larger matrix leads to more distortion. >> Because 3T has larger distortion than 1.5 T, using a larger matrix in 3T is >> not a good idea in general. >> >> Hope it helps. >> >> Susumu >> >> On Thu, Dec 10, 2009 at 9:47 AM, Lucas Lessa >> > wrote: >> >>> Good morning, >>> >>> As I said in aonther post, I'm in the middle of a DTI study that, >>> obsviously, uses DTI studio to process the data. >>> The other researcher brought (a think from John Hopkins) a model that >>> uses 3 DTI series, just to increase the ratio between sign/noise. >>> The exams are taking so long and I would like to increase the resolution >>> from 112x110 to 256x256, and maybe, 512x512. >>> Is this a good idea? Or it's better to continue making the exams with the >>> 3 DTI series? >>> And wich is the bennefit of doing 3 DTI series (the vendor software only >>> uses one at a time)? >>> One more time thank you. >>> >>> Lucas Lessa >>> S?o Paulo/Brazil >>> >>> ------------------------------ >>> Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top 10- >>> Celebridades- >>> M?sica- >>> Esportes >>> >>> _______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: >>> Mristudio-users-unsubscribe at mristudio.org >>> >>> >> >> -----Anexo incorporado----- >> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> >> ------------------------------ >> Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top 10- >> Celebridades- >> M?sica- >> Esportes >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > -----Anexo incorporado----- > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > > ------------------------------ > Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top 10- > Celebridades- > M?sica- > Esportes > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091211/678496ba/attachment.html From lucas_lessa at yahoo.com.br Sat Dec 12 12:21:40 2009 From: lucas_lessa at yahoo.com.br (Lucas Lessa) Date: Sat, 12 Dec 2009 09:21:40 -0800 (PST) Subject: [Mristudio-users] Is better to do 3 DTI series or just one well done? In-Reply-To: Message-ID: <839002.17516.qm@web110207.mail.gq1.yahoo.com> I'm using a GE too, and only 33 images (for the dirrections) are created. My doubt is wich one is better, use the 3NEX ou make 3 series, but as you said before, I will keep using the 3 NEX and hope for patients cooperation. Thank you very much. --- Em s?b, 12/12/09, susumu mori escreveu: De: susumu mori Assunto: Re: [Mristudio-users] Is better to do 3 DTI series or just one well done? Para: "DTI Studio, ROI Editor, Landmarker Questions/Support" Data: S?bado, 12 de Dezembro de 2009, 0:14 Do you mean you are doing 33-orientation x 3 signal averaging for 5 mm slice? That is equivalent to 99 DWIs. With such as thick slice and the 99 DWI equivalent, you should have enough SNR even with 1.5T. 3 NEX and 3 series are equivalent in terms of SNR. The only difference is whether the scanner average the data for you or you get them saved separately. Usually, if you do 3 separate series, MR scanner can not combine them and does not offer an FA map based on the all 3 series. So, for clinical scans, you have no choice but using 3 NEX. If you are using Siemens, 3NEX and 3 series are completely identical because they actually save the 3 NEX scans separately and use all of them for tensor calculation. For example, if you do 3NEX of 33-orientaiton, you can find 99 Mosaic files. They don't actually average 3 scans. So it's the same as 3 series. I'm not sure how GE works. I believe if you do 3NEX of 33-orientaiton, you may get only 33 images, in which the 3 scans are already averaged. The disadvantage of this approach is, if the subject moved or one of the images are corrupted, you can not correct them once 3 images are averaged. These issues can be corrected to some degree if you are using off-line programs like DtiStudio or FSL. However, if you rely on FA map generation by the scanner, I guess you'd better use 3NEX. On Fri, Dec 11, 2009 at 11:05 AM, Lucas Lessa wrote: Once again thank you Dr Mori. and what do you think about increase the SNR in GE 1.5T scanners? We only do one serie with 33 directions, but we have to use slices with 5mm thickness, and NEX 3. Is it better to do 3 series like in Phillips or push the parameters? --- Em qui, 10/12/09, susumu mori escreveu: De: susumu mori Assunto: Re: [Mristudio-users] Is better to do 3 DTI series or just one well done? Para: "DTI Studio, ROI Editor, Landmarker Questions/Support" Data: Quinta-feira, 10 de Dezembro de 2009, 16:59 I wouldn't push the resolution that much. I even hesitate to use 128x128, unless we can use SENSE factor of 4 so that the echotrain is 128/4 =32 On Thu, Dec 10, 2009 at 1:33 PM, Lucas Lessa wrote: Dr. Susumu Mori you helped me a lot. I'm using 3 repetions of a 33 dir DTI in a Philips 1.5T (the voxel is about 2.2mm.) when I want to do an exam for a research, for the real life I use just one repetion. Indeed the SNR is much better with 3 repetions, but just in DTI Studio, because Philip's software don't handle the 3 series like one. What do you think in increase my resolution to 256x256 in this scanner? Will the exam take so long? Can I use just 2 repetitions? Thank you. ? Lucas Lessa. ? --- Em qui, 10/12/09, susumu mori escreveu: De: susumu mori Assunto: Re: [Mristudio-users] Is better to do 3 DTI series or just one well done? Para: "DTI Studio, ROI Editor, Landmarker Questions/Support" Data: Quinta-feira, 10 de Dezembro de 2009, 15:22 If you are using a 1.5 T scanner, I think 2.5 mm isotropic resolution is a good compromise between scanning time and SNR. With a 30-orientation scheme, you may want to do at least two repetition (total 60 DWIs) to get a decent SNR. If you want to increase the resolution, you need more dwis and a longer scanning time. What is important is the total number of images, in this case 60. So, if you are using a 15-orientation scheme, you need 4 repetitions. A 30-orientation scheme should take about 4-5min in Siemens and Philips. GE may take 7-8 min in some versions because of gradient overheating precaution (TR can't be too short). So, two repetitions (total 60 dwis) should take 8-10 min in Siemens/Philips. This is certainly a long scan, especially for clinical. If time is important, you can do one repetition (total 30 dwis), scarifying the SNR. In this case, you definitely don't want to increase the resolution, which would make the SNR worse. For 3T, 30 dwis can give you a decent SNR with 2.5mm resolution. Or if you stick with a 60 dwis protocol, you can use 2.2 mm resolution. I have seen nice 2.0 mm resolution with the latest head coils. For 2.2 mm, you need to use 112x112 matrix. Please note that larger matrix leads to more distortion. Because 3T has larger distortion than 1.5 T, using a larger matrix in 3T is not a good idea in general. Hope it helps. Susumu On Thu, Dec 10, 2009 at 9:47 AM, Lucas Lessa wrote: Good morning, As I said in aonther post, I'm in the middle of a DTI study that, obsviously, uses DTI studio to process the data. The other researcher brought (a think from John Hopkins) a model that uses 3 DTI series, just to increase the ratio between sign/noise. The exams are taking so long and I would like to increase the resolution from 112x110 to 256x256, and maybe, 512x512. Is this a good idea? Or it's better to continue making the exams with the 3 DTI series? And wich is the bennefit of doing 3 DTI series (the vendor software only uses one at a time)? One more time thank you. Lucas Lessa S?o Paulo/Brazil Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top 10 - Celebridades - M?sica - Esportes _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -----Anexo incorporado----- _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top 10 - Celebridades - M?sica - Esportes _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -----Anexo incorporado----- _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top 10 - Celebridades - M?sica - Esportes _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -----Anexo incorporado----- _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org ____________________________________________________________________________________ Veja quais s?o os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... 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X-BeenThere: mristudio-users at mristudio.org X-Mailman-Version: 2.1.9 Precedence: list Reply-To: "DTI Studio, ROI Editor, Landmarker Questions/Support" List-Id: "DTI Studio, ROI Editor, Landmarker Questions/Support" List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Sender: mristudio-users-bounces at mristudio.org Errors-To: mristudio-users-bounces at mristudio.org Content-Length: 1209 From subarna29 at gmail.com Sun Dec 13 11:19:39 2009 From: subarna29 at gmail.com (Subarna Ghosh) Date: Sun, 13 Dec 2009 11:19:39 -0500 Subject: [Mristudio-users] reading nrrd images Message-ID: <64fe815c0912130819u13b7df97ub30b01b414f8c93d@mail.gmail.com> Hi all, I recently started using DTIstudio, and created some nrrd files of DTI tensor details(Dxx,Dyy etc.). I need to read the values through ITK but wasnt able to. Basically i need all the values in the form of matices for some processing and I am not sure how to do it. I used various examples given : itkNrrdVectorImageReadTest.cxx etc. Please let me know about how I could go about it. Thanks ! Regards, Subarna Ghosh. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091213/66e4cbe1/attachment.html From yj3 at duke.edu Mon Dec 14 16:25:41 2009 From: yj3 at duke.edu (Yi Jiang) Date: Mon, 14 Dec 2009 16:25:41 -0500 Subject: [Mristudio-users] a question about gradient table in dpf file References: <662032.53943.qm@web110201.mail.gq1.yahoo.com> Message-ID: Hello, I am wondering if it's fine to use two b0 images in the gradient table in the dpf file, such as following: Begin_Of_Gradient_Table 0: 0,0,0 1: 160, 160, 0 2: 0, -160, 160 3: -160, 0, -160 4: 160, -160, 0 5: 0, 160, 160 6: 160, 0, -160 7: 0,0,0 8: -160, -160, 0 9: 0, 160, -160 10: 160, 0, 160 11: -160, 160, 0 12: 0, -160, -160 13: -160, 0, 160 End_Of_Gradient_Table Is DTIStudio able to recoganize and use both b0 images? Moreover, is there a way to specify b-value for the b0 images (e.g., although very low, it may be 10 or 50, instead of 0)? Thank you very much! Best, Yi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091214/ecd259fc/attachment.html From hjiang at jhmi.edu Tue Dec 15 08:50:14 2009 From: hjiang at jhmi.edu (Hangyi Jiang) Date: Tue, 15 Dec 2009 08:50:14 -0500 Subject: [Mristudio-users] a question about gradient table in dpf file In-Reply-To: References: <662032.53943.qm@web110201.mail.gq1.yahoo.com> Message-ID: <145933A2BE9E4F48AE079A201379BF2F1FC4145DD5@RAD-EXCH1.win.ad.jhu.edu> Q: I am wondering if it's fine to use two b0 images in the gradient table in the dpf file, Is DTIStudio able to recoganize and use both b0 images? A: yes. multiple B0s are just fine. Q: is there a way to specify b-value for the b0 images (e.g., although very low, it may be 10 or 50, instead of 0)? A: yes, you can define the gradient table in this way: #: x, y, z, b-value. for example: 0: 0,0,0, 30 1: 160, 160, 0, 800 2: 0, -160, 160, 800 3: -160, 0, -160, 800 .... and more, you can use multiple b-values for your dataset, for example: 0: 0,0,0, 30 1: 160, 160, 0, 800 2: 0, -160, 160, 800 3: -160, 0, -160, 800 .... 7: 0,0,0, 30 8: 160, 160, 0, 1600 9: 0, -160, 160, 1600 regards, hangyi ________________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Yi Jiang [yj3 at duke.edu] Sent: Monday, December 14, 2009 4:25 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] a question about gradient table in dpf file Hello, I am wondering if it's fine to use two b0 images in the gradient table in the dpf file, such as following: Begin_Of_Gradient_Table 0: 0,0,0 1: 160, 160, 0 2: 0, -160, 160 3: -160, 0, -160 4: 160, -160, 0 5: 0, 160, 160 6: 160, 0, -160 7: 0,0,0 8: -160, -160, 0 9: 0, 160, -160 10: 160, 0, 160 11: -160, 160, 0 12: 0, -160, -160 13: -160, 0, 160 End_Of_Gradient_Table Is DTIStudio able to recoganize and use both b0 images? Moreover, is there a way to specify b-value for the b0 images (e.g., although very low, it may be 10 or 50, instead of 0)? Thank you very much! Best, Yi From susumu at mri.jhu.edu Tue Dec 15 16:20:37 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Tue, 15 Dec 2009 16:20:37 -0500 Subject: [Mristudio-users] reading nrrd images In-Reply-To: <64fe815c0912130819u13b7df97ub30b01b414f8c93d@mail.gmail.com> References: <64fe815c0912130819u13b7df97ub30b01b414f8c93d@mail.gmail.com> Message-ID: Hi Subarna, 1) Do you have to use the nrrd format? If you save the matrix as a "raw" file, the tensor elements will be stored as (dxx, dyy, dzz, dxy, dxz, dyz) x D1 x D2 x D3 where D1-3 are the dimensions of the image matrix. 2) Are you asking the exact format of the tensor-nrrd file created by DtiStudio? Susumu On Sun, Dec 13, 2009 at 11:19 AM, Subarna Ghosh wrote: > Hi all, > > I recently started using DTIstudio, and created some nrrd files of DTI > tensor details(Dxx,Dyy etc.). I need to read the values through ITK but > wasnt able to. > Basically i need all the values in the form of matices for some processing > and I am not sure how to do it. > I used various examples given : itkNrrdVectorImageReadTest.cxx etc. > Please let me know about how I could go about it. > > Thanks ! > > Regards, > Subarna Ghosh. > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091215/032b7bae/attachment-0001.html From mpinsk at gmail.com Tue Dec 15 21:37:11 2009 From: mpinsk at gmail.com (Mark A. Pinsk) Date: Tue, 15 Dec 2009 21:37:11 -0500 Subject: [Mristudio-users] Using processed data Message-ID: Hi, someone asked this a while ago in the archives but I didn't see a reply. Can I use data that I've processed in FSL (eddy current correction, motion correction, and field map-based undistortion) and bring it into dti-studio? The data is in one large 4D nifti file. I don't see where I can do this, is it not possible? thanks mark From grojasy at puc.cl Tue Dec 15 22:29:51 2009 From: grojasy at puc.cl (Gonzalo Rojas) Date: Wed, 16 Dec 2009 00:29:51 -0300 Subject: [Mristudio-users] Using processed data In-Reply-To: References: Message-ID: <4B28542F.5000803@puc.cl> Hi Mark: Yes... you could do all the processing that you mentioned (in FSL), and bring it to dti-studio... the FSL output file format is NIFTI.GZ... you must convert it to ANALYZE 4D, and then you must load that ANALYZE 4D file as a RAW data file format in DTI-STUDIO... Sincerely, Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl El 15-12-2009 23:37, Mark A. Pinsk escribi?: > Hi, someone asked this a while ago in the archives but I didn't see a > reply. Can I use data that I've processed in FSL (eddy current > correction, motion correction, and field map-based undistortion) and > bring it into dti-studio? The data is in one large 4D nifti file. I > don't see where I can do this, is it not possible? > > thanks > mark > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > From mpinsk at gmail.com Tue Dec 15 23:07:33 2009 From: mpinsk at gmail.com (Mark A. Pinsk) Date: Tue, 15 Dec 2009 23:07:33 -0500 Subject: [Mristudio-users] Using processed data In-Reply-To: <4B28542F.5000803@puc.cl> References: <4B28542F.5000803@puc.cl> Message-ID: Thanks ! I converted by 4D NIFTI file to a 4D ANALYZE file as you suggested. I attempt to read it in as RAW, but it seems to get stuck... I specify the file in the Raw-BIN Files Folder field, but I get this message: "Number of files in this fold is less than expected: (Img_Slices*Img_Blocks)." I only have a single .img/.hdr pair in my folder since it is a 4D file (i.e. it contains 65 volumes (5 b0 volumes + 60 directions)). Sorry, any help would be greatly appreciated. Thanks Mark On Tue, Dec 15, 2009 at 10:29 PM, Gonzalo Rojas wrote: > Hi Mark: > > ?Yes... you could do all the processing that you mentioned (in FSL), and > bring it to dti-studio... the FSL output file format is NIFTI.GZ... you must > convert it to ANALYZE 4D, and then you must load that ANALYZE 4D file as a > RAW data file format in DTI-STUDIO... > > ?Sincerely, > > > Gonzalo Rojas Costa > Department of Radiology > Las Condes Clinic > Lo Fontecilla 441, Las Condes, Santiago, Chile. > Tel: 56-2-2105170 > Cel: 56-9-97771785 > www.clc.cl > > El 15-12-2009 23:37, Mark A. Pinsk escribi?: >> >> Hi, someone asked this a while ago in the archives but I didn't see a >> reply. ? Can I use data that I've processed in FSL (eddy current >> correction, motion correction, and field map-based undistortion) and >> bring it into dti-studio? ? The data is in one large 4D nifti file. ?I >> don't see where I can do this, is it not possible? >> >> thanks >> mark >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> > From grojasy at puc.cl Tue Dec 15 23:42:02 2009 From: grojasy at puc.cl (Gonzalo Rojas) Date: Wed, 16 Dec 2009 01:42:02 -0300 Subject: [Mristudio-users] Using processed data In-Reply-To: References: <4B28542F.5000803@puc.cl> Message-ID: <4B28651A.4020202@puc.cl> Hi Mark: Many questions: i) do you specify correctly the "image slices" quantity in "iamge dimension" ?... that value is the quantitry of axial slices in each gradient direction... ii) and the "image width" and "image height" in "image dimension" ?... did you checked that values ?... ii) in "lice orientation" did you specify "axial" ?.. iii) and in "Voxel Size", "Field of View-width" and "Field of View-Heigth" did you specifiy the FOV value correctly ?... iv) you could check the previos values looking at "Pixel Size-Width" and "Pixel Size-Height"... v) in "Slices to be processed" it must appears 0-(image slices-1) vi) in gradient table you must put the 61 (0-60) directions... in your 4D analyze file is included the "mean" of all the 60 directions at the end of the file ?... if it is, you must put "100,100,100" as the last gradient direction to skip that image in the computation... vii) in "Image secuence" you must select "Gradient by Gradient" option... viii) in "Raw-BIN Files folder you must specify the IMG file of the Analyze pair... ix) why you have 5 b0 volumes ?... to compute tractography, you must have only one b0 volume... you must put "100,100,100" in "Gradient Table" for each of the 4 b0 slices to skipt them... Sincerely, Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl El 16-12-2009 1:07, Mark A. Pinsk escribi?: > Thanks ! > > I converted by 4D NIFTI file to a 4D ANALYZE file as you suggested. > > I attempt to read it in as RAW, but it seems to get stuck... > > I specify the file in the Raw-BIN Files Folder field, but I get this message: > "Number of files in this fold is less than expected: (Img_Slices*Img_Blocks)." > > I only have a single .img/.hdr pair in my folder since it is a 4D file > (i.e. it contains 65 volumes (5 b0 volumes + 60 directions)). > > Sorry, any help would be greatly appreciated. > Thanks > Mark > > > > > On Tue, Dec 15, 2009 at 10:29 PM, Gonzalo Rojas wrote: >> Hi Mark: >> >> Yes... you could do all the processing that you mentioned (in FSL), and >> bring it to dti-studio... the FSL output file format is NIFTI.GZ... you must >> convert it to ANALYZE 4D, and then you must load that ANALYZE 4D file as a >> RAW data file format in DTI-STUDIO... >> >> Sincerely, >> >> >> Gonzalo Rojas Costa >> Department of Radiology >> Las Condes Clinic >> Lo Fontecilla 441, Las Condes, Santiago, Chile. >> Tel: 56-2-2105170 >> Cel: 56-9-97771785 >> www.clc.cl >> >> El 15-12-2009 23:37, Mark A. Pinsk escribi?: >>> >>> Hi, someone asked this a while ago in the archives but I didn't see a >>> reply. Can I use data that I've processed in FSL (eddy current >>> correction, motion correction, and field map-based undistortion) and >>> bring it into dti-studio? The data is in one large 4D nifti file. I >>> don't see where I can do this, is it not possible? >>> >>> thanks >>> mark >>> _______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: >>> Mristudio-users-unsubscribe at mristudio.org >>> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > From mpinsk at gmail.com Wed Dec 16 00:09:19 2009 From: mpinsk at gmail.com (Mark A. Pinsk) Date: Wed, 16 Dec 2009 00:09:19 -0500 Subject: [Mristudio-users] Using processed data In-Reply-To: <4B28651A.4020202@puc.cl> References: <4B28542F.5000803@puc.cl> <4B28651A.4020202@puc.cl> Message-ID: Thanks for your help, I'll do my best to answer them... FYI: these are small volumes from animal scans ( 1 x 1 x 1.1 mm resolution): Image Dimensions: 96 Width, 128 Height, 47 slices Slice Orientation: Axial Slice Sequencing: Inferior-Superior FOV: 96 Width, 128 Height, 1.1 Slice Thickness Pixel Size: 1.000 Width, 1.000 Height Slices to be processed: 0 to 46, All Slices Image Sequence: Gradient By Gradient b_Value: 1000 My gradient table has 65 entries. The first 5 entries are B0 images, the remaining 60 are for the 60 directions. There is no mean image at the end of my data. I can discard 4 of the B0 images, but that does not seem to make a difference on my error message. I have several B0 images in accord with recent work that suggests having a ratio of 6:1 diffusion to non-diffusion weighted images (Zhu et al. NeuroImage 2008). On Tue, Dec 15, 2009 at 11:42 PM, Gonzalo Rojas wrote: > Hi Mark: > > ?Many questions: > > i) do you specify correctly the "image slices" quantity in "iamge dimension" > ?... that value is the quantitry of axial slices in each gradient > direction... > > ii) and the "image width" and "image height" in "image dimension" ?... did > you checked that values ?... > > ii) in "lice orientation" did you specify "axial" ?.. > > iii) and in "Voxel Size", "Field of View-width" and "Field of View-Heigth" > did you specifiy the FOV value correctly ?... > > iv) you could check the previos values looking at "Pixel Size-Width" and > "Pixel Size-Height"... > > v) in "Slices to be processed" it must appears 0-(image slices-1) > > vi) in gradient table you must put the 61 (0-60) directions... in your 4D > analyze file is included the "mean" of all the 60 directions at the end of > the file ?... if it is, you must put "100,100,100" as the last gradient > direction to skip that image in the computation... > > vii) in "Image secuence" you must select "Gradient by Gradient" option... > > viii) in "Raw-BIN Files folder you must specify the IMG file of the Analyze > pair... > > ix) why you have 5 b0 volumes ?... to compute tractography, you must have > only one b0 volume... you must put "100,100,100" in "Gradient Table" for > each of the 4 b0 slices to skipt them... > > ?Sincerely, > > > Gonzalo Rojas Costa > Department of Radiology > Las Condes Clinic > Lo Fontecilla 441, Las Condes, Santiago, Chile. > Tel: 56-2-2105170 > Cel: 56-9-97771785 > www.clc.cl > > El 16-12-2009 1:07, Mark A. Pinsk escribi?: >> >> Thanks ! >> >> I converted by 4D NIFTI file to a 4D ANALYZE file as you suggested. >> >> I attempt to read it in as RAW, but it seems to get stuck... >> >> I specify the file in the Raw-BIN Files Folder field, but I get this >> message: >> "Number of files in this fold is less than expected: >> (Img_Slices*Img_Blocks)." >> >> I only have a single .img/.hdr pair in my folder since it is a 4D file >> (i.e. it contains 65 volumes (5 b0 volumes + 60 directions)). >> >> Sorry, any help would be greatly appreciated. >> Thanks >> Mark >> >> >> >> >> On Tue, Dec 15, 2009 at 10:29 PM, Gonzalo Rojas ?wrote: >>> >>> Hi Mark: >>> >>> ?Yes... you could do all the processing that you mentioned (in FSL), and >>> bring it to dti-studio... the FSL output file format is NIFTI.GZ... you >>> must >>> convert it to ANALYZE 4D, and then you must load that ANALYZE 4D file as >>> a >>> RAW data file format in DTI-STUDIO... >>> >>> ?Sincerely, >>> >>> >>> Gonzalo Rojas Costa >>> Department of Radiology >>> Las Condes Clinic >>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >>> Tel: 56-2-2105170 >>> Cel: 56-9-97771785 >>> www.clc.cl >>> >>> El 15-12-2009 23:37, Mark A. Pinsk escribi?: >>>> >>>> Hi, someone asked this a while ago in the archives but I didn't see a >>>> reply. ? Can I use data that I've processed in FSL (eddy current >>>> correction, motion correction, and field map-based undistortion) and >>>> bring it into dti-studio? ? The data is in one large 4D nifti file. ?I >>>> don't see where I can do this, is it not possible? >>>> >>>> thanks >>>> mark >>>> _______________________________________________ >>>> Mristudio-users mailing list >>>> Mristudio-users at mristudio.org >>>> http://lists.mristudio.org/mailman/listinfo/ >>>> Unsubscribe, send a blank email to: >>>> Mristudio-users-unsubscribe at mristudio.org >>>> >>> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> > From mpinsk at gmail.com Wed Dec 16 00:13:42 2009 From: mpinsk at gmail.com (Mark A. Pinsk) Date: Wed, 16 Dec 2009 00:13:42 -0500 Subject: [Mristudio-users] Using processed data In-Reply-To: References: <4B28542F.5000803@puc.cl> <4B28651A.4020202@puc.cl> Message-ID: Also, I should mention that the Analyze file loads just fine using "MRI View3D" and "Analyze" file format. On Wed, Dec 16, 2009 at 12:09 AM, Mark A. Pinsk wrote: > Thanks for your help, I'll do my best to answer them... > > FYI: these are small volumes from animal scans ( 1 x 1 x 1.1 mm resolution): > > Image Dimensions: 96 Width, 128 Height, 47 slices > Slice Orientation: Axial > Slice Sequencing: Inferior-Superior > FOV: 96 Width, 128 Height, 1.1 Slice Thickness > Pixel Size: 1.000 Width, 1.000 Height > Slices to be processed: 0 to 46, All Slices > Image Sequence: Gradient By Gradient > b_Value: 1000 > > My gradient table has 65 entries. ?The first 5 entries are B0 images, > the remaining 60 are for the 60 directions. ?There is no mean image at > the end of my data. ? I can discard 4 of the B0 images, but that does > not seem to make a difference on my error message. ?I have several B0 > images in accord with recent work that suggests having a ratio of 6:1 > diffusion to non-diffusion weighted images (Zhu et al. NeuroImage > 2008). > > > > On Tue, Dec 15, 2009 at 11:42 PM, Gonzalo Rojas wrote: >> Hi Mark: >> >> ?Many questions: >> >> i) do you specify correctly the "image slices" quantity in "iamge dimension" >> ?... that value is the quantitry of axial slices in each gradient >> direction... >> >> ii) and the "image width" and "image height" in "image dimension" ?... did >> you checked that values ?... >> >> ii) in "lice orientation" did you specify "axial" ?.. >> >> iii) and in "Voxel Size", "Field of View-width" and "Field of View-Heigth" >> did you specifiy the FOV value correctly ?... >> >> iv) you could check the previos values looking at "Pixel Size-Width" and >> "Pixel Size-Height"... >> >> v) in "Slices to be processed" it must appears 0-(image slices-1) >> >> vi) in gradient table you must put the 61 (0-60) directions... in your 4D >> analyze file is included the "mean" of all the 60 directions at the end of >> the file ?... if it is, you must put "100,100,100" as the last gradient >> direction to skip that image in the computation... >> >> vii) in "Image secuence" you must select "Gradient by Gradient" option... >> >> viii) in "Raw-BIN Files folder you must specify the IMG file of the Analyze >> pair... >> >> ix) why you have 5 b0 volumes ?... to compute tractography, you must have >> only one b0 volume... you must put "100,100,100" in "Gradient Table" for >> each of the 4 b0 slices to skipt them... >> >> ?Sincerely, >> >> >> Gonzalo Rojas Costa >> Department of Radiology >> Las Condes Clinic >> Lo Fontecilla 441, Las Condes, Santiago, Chile. >> Tel: 56-2-2105170 >> Cel: 56-9-97771785 >> www.clc.cl >> >> El 16-12-2009 1:07, Mark A. Pinsk escribi?: >>> >>> Thanks ! >>> >>> I converted by 4D NIFTI file to a 4D ANALYZE file as you suggested. >>> >>> I attempt to read it in as RAW, but it seems to get stuck... >>> >>> I specify the file in the Raw-BIN Files Folder field, but I get this >>> message: >>> "Number of files in this fold is less than expected: >>> (Img_Slices*Img_Blocks)." >>> >>> I only have a single .img/.hdr pair in my folder since it is a 4D file >>> (i.e. it contains 65 volumes (5 b0 volumes + 60 directions)). >>> >>> Sorry, any help would be greatly appreciated. >>> Thanks >>> Mark >>> >>> >>> >>> >>> On Tue, Dec 15, 2009 at 10:29 PM, Gonzalo Rojas ?wrote: >>>> >>>> Hi Mark: >>>> >>>> ?Yes... you could do all the processing that you mentioned (in FSL), and >>>> bring it to dti-studio... the FSL output file format is NIFTI.GZ... you >>>> must >>>> convert it to ANALYZE 4D, and then you must load that ANALYZE 4D file as >>>> a >>>> RAW data file format in DTI-STUDIO... >>>> >>>> ?Sincerely, >>>> >>>> >>>> Gonzalo Rojas Costa >>>> Department of Radiology >>>> Las Condes Clinic >>>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >>>> Tel: 56-2-2105170 >>>> Cel: 56-9-97771785 >>>> www.clc.cl >>>> >>>> El 15-12-2009 23:37, Mark A. Pinsk escribi?: >>>>> >>>>> Hi, someone asked this a while ago in the archives but I didn't see a >>>>> reply. ? Can I use data that I've processed in FSL (eddy current >>>>> correction, motion correction, and field map-based undistortion) and >>>>> bring it into dti-studio? ? The data is in one large 4D nifti file. ?I >>>>> don't see where I can do this, is it not possible? >>>>> >>>>> thanks >>>>> mark >>>>> _______________________________________________ >>>>> Mristudio-users mailing list >>>>> Mristudio-users at mristudio.org >>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>> Unsubscribe, send a blank email to: >>>>> Mristudio-users-unsubscribe at mristudio.org >>>>> >>>> >>> >>> _______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: >>> Mristudio-users-unsubscribe at mristudio.org >>> >> > From subarna29 at gmail.com Wed Dec 16 00:48:17 2009 From: subarna29 at gmail.com (Subarna Ghosh) Date: Wed, 16 Dec 2009 00:48:17 -0500 Subject: [Mristudio-users] reading nrrd images In-Reply-To: References: <64fe815c0912130819u13b7df97ub30b01b414f8c93d@mail.gmail.com> Message-ID: <64fe815c0912152148g6bc847d4ve1bcea66044bc3f8@mail.gmail.com> Hi Susumu, I am interested in the tensor data (eigen vectors, eigenvalues etc.). I created the raw file, but not sure how to read the matrix data. Is it a Binary file? What is the format like? I will appreciate any help in this direction. Thanks and regards, Subarna Ghosh. On Tue, Dec 15, 2009 at 4:20 PM, susumu mori wrote: > Hi Subarna, > > 1) Do you have to use the nrrd format? If you save the matrix as a "raw" > file, the tensor elements will be stored as (dxx, dyy, dzz, dxy, dxz, dyz) x > D1 x D2 x D3 where D1-3 are the dimensions of the image matrix. > 2) Are you asking the exact format of the tensor-nrrd file created by > DtiStudio? > > Susumu > > On Sun, Dec 13, 2009 at 11:19 AM, Subarna Ghosh wrote: > >> Hi all, >> >> I recently started using DTIstudio, and created some nrrd files of DTI >> tensor details(Dxx,Dyy etc.). I need to read the values through ITK but >> wasnt able to. >> Basically i need all the values in the form of matices for some processing >> and I am not sure how to do it. >> I used various examples given : itkNrrdVectorImageReadTest.cxx etc. >> Please let me know about how I could go about it. >> >> Thanks ! >> >> Regards, >> Subarna Ghosh. >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091216/f5f2699d/attachment.html From gjmuro at optonline.net Wed Dec 16 06:41:12 2009 From: gjmuro at optonline.net (gjmuro at optonline.net) Date: Wed, 16 Dec 2009 11:41:12 +0000 Subject: [Mristudio-users] reading nrrd images In-Reply-To: <64fe815c0912152148g6bc847d4ve1bcea66044bc3f8@mail.gmail.com> References: <64fe815c0912130819u13b7df97ub30b01b414f8c93d@mail.gmail.com> <64fe815c0912152148g6bc847d4ve1bcea66044bc3f8@mail.gmail.com> Message-ID: <432523624-1260963614-cardhu_decombobulator_blackberry.rim.net-2057224172-@bda114.bisx.prod.on.blackberry> Gg Sent from my Verizon Wireless BlackBerry -----Original Message----- From: Subarna Ghosh Date: Wed, 16 Dec 2009 00:48:17 To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] reading nrrd images _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From gjmuro at optonline.net Wed Dec 16 06:41:20 2009 From: gjmuro at optonline.net (gjmuro at optonline.net) Date: Wed, 16 Dec 2009 11:41:20 +0000 Subject: [Mristudio-users] Using processed data In-Reply-To: References: <4B28542F.5000803@puc.cl> <4B28651A.4020202@puc.cl> Message-ID: <1345981269-1260963623-cardhu_decombobulator_blackberry.rim.net-412409679-@bda114.bisx.prod.on.blackberry> R Sent from my Verizon Wireless BlackBerry -----Original Message----- From: "Mark A. Pinsk" Date: Wed, 16 Dec 2009 00:13:42 To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] Using processed data Also, I should mention that the Analyze file loads just fine using "MRI View3D" and "Analyze" file format. On Wed, Dec 16, 2009 at 12:09 AM, Mark A. Pinsk wrote: > Thanks for your help, I'll do my best to answer them... > > FYI: these are small volumes from animal scans ( 1 x 1 x 1.1 mm resolution): > > Image Dimensions: 96 Width, 128 Height, 47 slices > Slice Orientation: Axial > Slice Sequencing: Inferior-Superior > FOV: 96 Width, 128 Height, 1.1 Slice Thickness > Pixel Size: 1.000 Width, 1.000 Height > Slices to be processed: 0 to 46, All Slices > Image Sequence: Gradient By Gradient > b_Value: 1000 > > My gradient table has 65 entries. ?The first 5 entries are B0 images, > the remaining 60 are for the 60 directions. ?There is no mean image at > the end of my data. ? I can discard 4 of the B0 images, but that does > not seem to make a difference on my error message. ?I have several B0 > images in accord with recent work that suggests having a ratio of 6:1 > diffusion to non-diffusion weighted images (Zhu et al. NeuroImage > 2008). > > > > On Tue, Dec 15, 2009 at 11:42 PM, Gonzalo Rojas wrote: >> Hi Mark: >> >> ?Many questions: >> >> i) do you specify correctly the "image slices" quantity in "iamge dimension" >> ?... that value is the quantitry of axial slices in each gradient >> direction... >> >> ii) and the "image width" and "image height" in "image dimension" ?... did >> you checked that values ?... >> >> ii) in "lice orientation" did you specify "axial" ?.. >> >> iii) and in "Voxel Size", "Field of View-width" and "Field of View-Heigth" >> did you specifiy the FOV value correctly ?... >> >> iv) you could check the previos values looking at "Pixel Size-Width" and >> "Pixel Size-Height"... >> >> v) in "Slices to be processed" it must appears 0-(image slices-1) >> >> vi) in gradient table you must put the 61 (0-60) directions... in your 4D >> analyze file is included the "mean" of all the 60 directions at the end of >> the file ?... if it is, you must put "100,100,100" as the last gradient >> direction to skip that image in the computation... >> >> vii) in "Image secuence" you must select "Gradient by Gradient" option... >> >> viii) in "Raw-BIN Files folder you must specify the IMG file of the Analyze >> pair... >> >> ix) why you have 5 b0 volumes ?... to compute tractography, you must have >> only one b0 volume... you must put "100,100,100" in "Gradient Table" for >> each of the 4 b0 slices to skipt them... >> >> ?Sincerely, >> >> >> Gonzalo Rojas Costa >> Department of Radiology >> Las Condes Clinic >> Lo Fontecilla 441, Las Condes, Santiago, Chile. >> Tel: 56-2-2105170 >> Cel: 56-9-97771785 >> www.clc.cl >> >> El 16-12-2009 1:07, Mark A. Pinsk escribi?: >>> >>> Thanks ! >>> >>> I converted by 4D NIFTI file to a 4D ANALYZE file as you suggested. >>> >>> I attempt to read it in as RAW, but it seems to get stuck... >>> >>> I specify the file in the Raw-BIN Files Folder field, but I get this >>> message: >>> "Number of files in this fold is less than expected: >>> (Img_Slices*Img_Blocks)." >>> >>> I only have a single .img/.hdr pair in my folder since it is a 4D file >>> (i.e. it contains 65 volumes (5 b0 volumes + 60 directions)). >>> >>> Sorry, any help would be greatly appreciated. >>> Thanks >>> Mark >>> >>> >>> >>> >>> On Tue, Dec 15, 2009 at 10:29 PM, Gonzalo Rojas ?wrote: >>>> >>>> Hi Mark: >>>> >>>> ?Yes... you could do all the processing that you mentioned (in FSL), and >>>> bring it to dti-studio... the FSL output file format is NIFTI.GZ... you >>>> must >>>> convert it to ANALYZE 4D, and then you must load that ANALYZE 4D file as >>>> a >>>> RAW data file format in DTI-STUDIO... >>>> >>>> ?Sincerely, >>>> >>>> >>>> Gonzalo Rojas Costa >>>> Department of Radiology >>>> Las Condes Clinic >>>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >>>> Tel: 56-2-2105170 >>>> Cel: 56-9-97771785 >>>> www.clc.cl >>>> >>>> El 15-12-2009 23:37, Mark A. Pinsk escribi?: >>>>> >>>>> Hi, someone asked this a while ago in the archives but I didn't see a >>>>> reply. ? Can I use data that I've processed in FSL (eddy current >>>>> correction, motion correction, and field map-based undistortion) and >>>>> bring it into dti-studio? ? The data is in one large 4D nifti file. ?I >>>>> don't see where I can do this, is it not possible? >>>>> >>>>> thanks >>>>> mark >>>>>_______________________________________________ >>>>> Mristudio-users mailing list >>>>> Mristudio-users at mristudio.org >>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>> Unsubscribe, send a blank email to: >>>>> Mristudio-users-unsubscribe at mristudio.org >>>>> >>>> >>> >>>_______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: >>> Mristudio-users-unsubscribe at mristudio.org >>> >> > _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From darshanp20 at yahoo.com Wed Dec 16 13:34:00 2009 From: darshanp20 at yahoo.com (darshan pai) Date: Wed, 16 Dec 2009 10:34:00 -0800 (PST) Subject: [Mristudio-users] Using processed data In-Reply-To: References: <4B28542F.5000803@puc.cl> <4B28651A.4020202@puc.cl> Message-ID: <274936.72080.qm@web30701.mail.mud.yahoo.com> when you say a 4D file I assume that you have a Analyze file with an entry on the number of volumes , Is it? . If it is then try to make it a 3D file with all the 65 slices added in the z direction and see if it helps.. Regards????? Dp??? ----- Original Message ---- From: Mark A. Pinsk To: "DTI Studio, ROI Editor, Landmarker Questions/Support" Sent: Wed, December 16, 2009 12:13:42 AM Subject: Re: [Mristudio-users] Using processed data Also, I should mention that the Analyze file loads just fine using "MRI View3D" and "Analyze" file format. On Wed, Dec 16, 2009 at 12:09 AM, Mark A. Pinsk wrote: > Thanks for your help, I'll do my best to answer them... > > FYI: these are small volumes from animal scans ( 1 x 1 x 1.1 mm resolution): > > Image Dimensions: 96 Width, 128 Height, 47 slices > Slice Orientation: Axial > Slice Sequencing: Inferior-Superior > FOV: 96 Width, 128 Height, 1.1 Slice Thickness > Pixel Size: 1.000 Width, 1.000 Height > Slices to be processed: 0 to 46, All Slices > Image Sequence: Gradient By Gradient > b_Value: 1000 > > My gradient table has 65 entries. ?The first 5 entries are B0 images, > the remaining 60 are for the 60 directions. ?There is no mean image at > the end of my data. ? I can discard 4 of the B0 images, but that does > not seem to make a difference on my error message. ?I have several B0 > images in accord with recent work that suggests having a ratio of 6:1 > diffusion to non-diffusion weighted images (Zhu et al. NeuroImage > 2008). > > > > On Tue, Dec 15, 2009 at 11:42 PM, Gonzalo Rojas wrote: >> Hi Mark: >> >> ?Many questions: >> >> i) do you specify correctly the "image slices" quantity in "iamge dimension" >> ?... that value is the quantitry of axial slices in each gradient >> direction... >> >> ii) and the "image width" and "image height" in "image dimension" ?... did >> you checked that values ?... >> >> ii) in "lice orientation" did you specify "axial" ?.. >> >> iii) and in "Voxel Size", "Field of View-width" and "Field of View-Heigth" >> did you specifiy the FOV value correctly ?... >> >> iv) you could check the previos values looking at "Pixel Size-Width" and >> "Pixel Size-Height"... >> >> v) in "Slices to be processed" it must appears 0-(image slices-1) >> >> vi) in gradient table you must put the 61 (0-60) directions... in your 4D >> analyze file is included the "mean" of all the 60 directions at the end of >> the file ?... if it is, you must put "100,100,100" as the last gradient >> direction to skip that image in the computation... >> >> vii) in "Image secuence" you must select "Gradient by Gradient" option... >> >> viii) in "Raw-BIN Files folder you must specify the IMG file of the Analyze >> pair... >> >> ix) why you have 5 b0 volumes ?... to compute tractography, you must have >> only one b0 volume... you must put "100,100,100" in "Gradient Table" for >> each of the 4 b0 slices to skipt them... >> >> ?Sincerely, >> >> >> Gonzalo Rojas Costa >> Department of Radiology >> Las Condes Clinic >> Lo Fontecilla 441, Las Condes, Santiago, Chile. >> Tel: 56-2-2105170 >> Cel: 56-9-97771785 >> www.clc.cl >> >> El 16-12-2009 1:07, Mark A. Pinsk escribi?: >>> >>> Thanks ! >>> >>> I converted by 4D NIFTI file to a 4D ANALYZE file as you suggested. >>> >>> I attempt to read it in as RAW, but it seems to get stuck... >>> >>> I specify the file in the Raw-BIN Files Folder field, but I get this >>> message: >>> "Number of files in this fold is less than expected: >>> (Img_Slices*Img_Blocks)." >>> >>> I only have a single .img/.hdr pair in my folder since it is a 4D file >>> (i.e. it contains 65 volumes (5 b0 volumes + 60 directions)). >>> >>> Sorry, any help would be greatly appreciated. >>> Thanks >>> Mark >>> >>> >>> >>> >>> On Tue, Dec 15, 2009 at 10:29 PM, Gonzalo Rojas ?wrote: >>>> >>>> Hi Mark: >>>> >>>> ?Yes... you could do all the processing that you mentioned (in FSL), and >>>> bring it to dti-studio... the FSL output file format is NIFTI.GZ... you >>>> must >>>> convert it to ANALYZE 4D, and then you must load that ANALYZE 4D file as >>>> a >>>> RAW data file format in DTI-STUDIO... >>>> >>>> ?Sincerely, >>>> >>>> >>>> Gonzalo Rojas Costa >>>> Department of Radiology >>>> Las Condes Clinic >>>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >>>> Tel: 56-2-2105170 >>>> Cel: 56-9-97771785 >>>> www.clc.cl >>>> >>>> El 15-12-2009 23:37, Mark A. Pinsk escribi?: >>>>> >>>>> Hi, someone asked this a while ago in the archives but I didn't see a >>>>> reply. ? Can I use data that I've processed in FSL (eddy current >>>>> correction, motion correction, and field map-based undistortion) and >>>>> bring it into dti-studio? ? The data is in one large 4D nifti file. ?I >>>>> don't see where I can do this, is it not possible? >>>>> >>>>> thanks >>>>> mark >>>>> _______________________________________________ >>>>> Mristudio-users mailing list >>>>> Mristudio-users at mristudio.org >>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>> Unsubscribe, send a blank email to: >>>>> Mristudio-users-unsubscribe at mristudio.org >>>>> >>>> >>> >>> _______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: >>> Mristudio-users-unsubscribe at mristudio.org >>> >> > _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From gjmuro at optonline.net Wed Dec 16 14:11:20 2009 From: gjmuro at optonline.net (gjmuro at optonline.net) Date: Wed, 16 Dec 2009 19:11:20 +0000 Subject: [Mristudio-users] Using processed data In-Reply-To: <274936.72080.qm@web30701.mail.mud.yahoo.com> References: <4B28542F.5000803@puc.cl> <4B28651A.4020202@puc.cl> <274936.72080.qm@web30701.mail.mud.yahoo.com> Message-ID: <247239735-1260990628-cardhu_decombobulator_blackberry.rim.net-1262061469-@bda114.bisx.prod.on.blackberry> F Sent from my Verizon Wireless BlackBerry -----Original Message----- From: darshan pai Date: Wed, 16 Dec 2009 10:34:00 To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] Using processed data when you say a 4D file I assume that you have a Analyze file with an entry on the number of volumes , Is it? . If it is then try to make it a 3D file with all the 65 slices added in the z direction and see if it helps.. Regards????? Dp??? ----- Original Message ---- From: Mark A. Pinsk To: "DTI Studio, ROI Editor, Landmarker Questions/Support" Sent: Wed, December 16, 2009 12:13:42 AM Subject: Re: [Mristudio-users] Using processed data Also, I should mention that the Analyze file loads just fine using "MRI View3D" and "Analyze" file format. On Wed, Dec 16, 2009 at 12:09 AM, Mark A. Pinsk wrote: > Thanks for your help, I'll do my best to answer them... > > FYI: these are small volumes from animal scans ( 1 x 1 x 1.1 mm resolution): > > Image Dimensions: 96 Width, 128 Height, 47 slices > Slice Orientation: Axial > Slice Sequencing: Inferior-Superior > FOV: 96 Width, 128 Height, 1.1 Slice Thickness > Pixel Size: 1.000 Width, 1.000 Height > Slices to be processed: 0 to 46, All Slices > Image Sequence: Gradient By Gradient > b_Value: 1000 > > My gradient table has 65 entries. ?The first 5 entries are B0 images, > the remaining 60 are for the 60 directions. ?There is no mean image at > the end of my data. ? I can discard 4 of the B0 images, but that does > not seem to make a difference on my error message. ?I have several B0 > images in accord with recent work that suggests having a ratio of 6:1 > diffusion to non-diffusion weighted images (Zhu et al. NeuroImage > 2008). > > > > On Tue, Dec 15, 2009 at 11:42 PM, Gonzalo Rojas wrote: >> Hi Mark: >> >> ?Many questions: >> >> i) do you specify correctly the "image slices" quantity in "iamge dimension" >> ?... that value is the quantitry of axial slices in each gradient >> direction... >> >> ii) and the "image width" and "image height" in "image dimension" ?... did >> you checked that values ?... >> >> ii) in "lice orientation" did you specify "axial" ?.. >> >> iii) and in "Voxel Size", "Field of View-width" and "Field of View-Heigth" >> did you specifiy the FOV value correctly ?... >> >> iv) you could check the previos values looking at "Pixel Size-Width" and >> "Pixel Size-Height"... >> >> v) in "Slices to be processed" it must appears 0-(image slices-1) >> >> vi) in gradient table you must put the 61 (0-60) directions... in your 4D >> analyze file is included the "mean" of all the 60 directions at the end of >> the file ?... if it is, you must put "100,100,100" as the last gradient >> direction to skip that image in the computation... >> >> vii) in "Image secuence" you must select "Gradient by Gradient" option... >> >> viii) in "Raw-BIN Files folder you must specify the IMG file of the Analyze >> pair... >> >> ix) why you have 5 b0 volumes ?... to compute tractography, you must have >> only one b0 volume... you must put "100,100,100" in "Gradient Table" for >> each of the 4 b0 slices to skipt them... >> >> ?Sincerely, >> >> >> Gonzalo Rojas Costa >> Department of Radiology >> Las Condes Clinic >> Lo Fontecilla 441, Las Condes, Santiago, Chile. >> Tel: 56-2-2105170 >> Cel: 56-9-97771785 >> www.clc.cl >> >> El 16-12-2009 1:07, Mark A. Pinsk escribi?: >>> >>> Thanks ! >>> >>> I converted by 4D NIFTI file to a 4D ANALYZE file as you suggested. >>> >>> I attempt to read it in as RAW, but it seems to get stuck... >>> >>> I specify the file in the Raw-BIN Files Folder field, but I get this >>> message: >>> "Number of files in this fold is less than expected: >>> (Img_Slices*Img_Blocks)." >>> >>> I only have a single .img/.hdr pair in my folder since it is a 4D file >>> (i.e. it contains 65 volumes (5 b0 volumes + 60 directions)). >>> >>> Sorry, any help would be greatly appreciated. >>> Thanks >>> Mark >>> >>> >>> >>> >>> On Tue, Dec 15, 2009 at 10:29 PM, Gonzalo Rojas ?wrote: >>>> >>>> Hi Mark: >>>> >>>> ?Yes... you could do all the processing that you mentioned (in FSL), and >>>> bring it to dti-studio... the FSL output file format is NIFTI.GZ... you >>>> must >>>> convert it to ANALYZE 4D, and then you must load that ANALYZE 4D file as >>>> a >>>> RAW data file format in DTI-STUDIO... >>>> >>>> ?Sincerely, >>>> >>>> >>>> Gonzalo Rojas Costa >>>> Department of Radiology >>>> Las Condes Clinic >>>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >>>> Tel: 56-2-2105170 >>>> Cel: 56-9-97771785 >>>> www.clc.cl >>>> >>>> El 15-12-2009 23:37, Mark A. Pinsk escribi?: >>>>> >>>>> Hi, someone asked this a while ago in the archives but I didn't see a >>>>> reply. ? Can I use data that I've processed in FSL (eddy current >>>>> correction, motion correction, and field map-based undistortion) and >>>>> bring it into dti-studio? ? The data is in one large 4D nifti file. ?I >>>>> don't see where I can do this, is it not possible? >>>>> >>>>> thanks >>>>> mark >>>>>_______________________________________________ >>>>> Mristudio-users mailing list >>>>> Mristudio-users at mristudio.org >>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>> Unsubscribe, send a blank email to: >>>>> Mristudio-users-unsubscribe at mristudio.org >>>>> >>>> >>> >>>_______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: >>> Mristudio-users-unsubscribe at mristudio.org >>> >> > _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From mpinsk at gmail.com Wed Dec 16 19:39:40 2009 From: mpinsk at gmail.com (Mark A. Pinsk) Date: Wed, 16 Dec 2009 19:39:40 -0500 Subject: [Mristudio-users] Using processed data In-Reply-To: <274936.72080.qm@web30701.mail.mud.yahoo.com> References: <4B28542F.5000803@puc.cl> <4B28651A.4020202@puc.cl> <274936.72080.qm@web30701.mail.mud.yahoo.com> Message-ID: No luck. Let me outline my steps here: 1. I start with a 4D NIFTI file that contains 65 volumes (60 DWI + 5 B0). The image dimensions are 96x128, 47 slices per volume. Slice orientation is Coronal. FOV is 96x128. Pixels are 1x1x1.1. 2. I split the 4D NIFTI file into 65 3D NIFTI files using this FSL command: fslsplit input.nii.gz 3. I convert each of the 65 3D NIFTI files to ANALYZE format: fslchfiletype ANALYZE vol0000.nii.gz [..] fslchfiletype ANALYZE vol0064.nii.gz 4. I am able to successfully import the ANALYZE files in MRIView3D by choosing Analyze format (but no luck with Raw format). 5. I have no luck importing the ANALYZE files in DTI Mapping choosing Raw format. I get this message: "Number of files in this fold is less than expected: (Img_Slices*Img_Blocks). Any suggestions? Thanks for all your help! Mark On Wed, Dec 16, 2009 at 1:34 PM, darshan pai wrote: > when you say a 4D file I assume that you have a Analyze file with an entry on the number of volumes , Is it? . If it is then try to make it a 3D file with all the 65 slices added in the z direction and see if it helps.. > > Regards > > Dp > > > > ----- Original Message ---- > From: Mark A. Pinsk > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > Sent: Wed, December 16, 2009 12:13:42 AM > Subject: Re: [Mristudio-users] Using processed data > > Also, I should mention that the Analyze file loads just fine using > "MRI View3D" and "Analyze" file format. > > > On Wed, Dec 16, 2009 at 12:09 AM, Mark A. Pinsk wrote: >> Thanks for your help, I'll do my best to answer them... >> >> FYI: these are small volumes from animal scans ( 1 x 1 x 1.1 mm resolution): >> >> Image Dimensions: 96 Width, 128 Height, 47 slices >> Slice Orientation: Axial >> Slice Sequencing: Inferior-Superior >> FOV: 96 Width, 128 Height, 1.1 Slice Thickness >> Pixel Size: 1.000 Width, 1.000 Height >> Slices to be processed: 0 to 46, All Slices >> Image Sequence: Gradient By Gradient >> b_Value: 1000 >> >> My gradient table has 65 entries. ?The first 5 entries are B0 images, >> the remaining 60 are for the 60 directions. ?There is no mean image at >> the end of my data. ? I can discard 4 of the B0 images, but that does >> not seem to make a difference on my error message. ?I have several B0 >> images in accord with recent work that suggests having a ratio of 6:1 >> diffusion to non-diffusion weighted images (Zhu et al. NeuroImage >> 2008). >> >> >> >> On Tue, Dec 15, 2009 at 11:42 PM, Gonzalo Rojas wrote: >>> Hi Mark: >>> >>> ?Many questions: >>> >>> i) do you specify correctly the "image slices" quantity in "iamge dimension" >>> ?... that value is the quantitry of axial slices in each gradient >>> direction... >>> >>> ii) and the "image width" and "image height" in "image dimension" ?... did >>> you checked that values ?... >>> >>> ii) in "lice orientation" did you specify "axial" ?.. >>> >>> iii) and in "Voxel Size", "Field of View-width" and "Field of View-Heigth" >>> did you specifiy the FOV value correctly ?... >>> >>> iv) you could check the previos values looking at "Pixel Size-Width" and >>> "Pixel Size-Height"... >>> >>> v) in "Slices to be processed" it must appears 0-(image slices-1) >>> >>> vi) in gradient table you must put the 61 (0-60) directions... in your 4D >>> analyze file is included the "mean" of all the 60 directions at the end of >>> the file ?... if it is, you must put "100,100,100" as the last gradient >>> direction to skip that image in the computation... >>> >>> vii) in "Image secuence" you must select "Gradient by Gradient" option... >>> >>> viii) in "Raw-BIN Files folder you must specify the IMG file of the Analyze >>> pair... >>> >>> ix) why you have 5 b0 volumes ?... to compute tractography, you must have >>> only one b0 volume... you must put "100,100,100" in "Gradient Table" for >>> each of the 4 b0 slices to skipt them... >>> >>> ?Sincerely, >>> >>> >>> Gonzalo Rojas Costa >>> Department of Radiology >>> Las Condes Clinic >>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >>> Tel: 56-2-2105170 >>> Cel: 56-9-97771785 >>> www.clc.cl >>> >>> El 16-12-2009 1:07, Mark A. Pinsk escribi?: >>>> >>>> Thanks ! >>>> >>>> I converted by 4D NIFTI file to a 4D ANALYZE file as you suggested. >>>> >>>> I attempt to read it in as RAW, but it seems to get stuck... >>>> >>>> I specify the file in the Raw-BIN Files Folder field, but I get this >>>> message: >>>> "Number of files in this fold is less than expected: >>>> (Img_Slices*Img_Blocks)." >>>> >>>> I only have a single .img/.hdr pair in my folder since it is a 4D file >>>> (i.e. it contains 65 volumes (5 b0 volumes + 60 directions)). >>>> >>>> Sorry, any help would be greatly appreciated. >>>> Thanks >>>> Mark >>>> >>>> >>>> >>>> >>>> On Tue, Dec 15, 2009 at 10:29 PM, Gonzalo Rojas ?wrote: >>>>> >>>>> Hi Mark: >>>>> >>>>> ?Yes... you could do all the processing that you mentioned (in FSL), and >>>>> bring it to dti-studio... the FSL output file format is NIFTI.GZ... you >>>>> must >>>>> convert it to ANALYZE 4D, and then you must load that ANALYZE 4D file as >>>>> a >>>>> RAW data file format in DTI-STUDIO... >>>>> >>>>> ?Sincerely, >>>>> >>>>> >>>>> Gonzalo Rojas Costa >>>>> Department of Radiology >>>>> Las Condes Clinic >>>>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >>>>> Tel: 56-2-2105170 >>>>> Cel: 56-9-97771785 >>>>> www.clc.cl >>>>> >>>>> El 15-12-2009 23:37, Mark A. Pinsk escribi?: >>>>>> >>>>>> Hi, someone asked this a while ago in the archives but I didn't see a >>>>>> reply. ? Can I use data that I've processed in FSL (eddy current >>>>>> correction, motion correction, and field map-based undistortion) and >>>>>> bring it into dti-studio? ? The data is in one large 4D nifti file. ?I >>>>>> don't see where I can do this, is it not possible? >>>>>> >>>>>> thanks >>>>>> mark >>>>>> _______________________________________________ >>>>>> Mristudio-users mailing list >>>>>> Mristudio-users at mristudio.org >>>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>>> Unsubscribe, send a blank email to: >>>>>> Mristudio-users-unsubscribe at mristudio.org >>>>>> >>>>> >>>> >>>> _______________________________________________ >>>> Mristudio-users mailing list >>>> Mristudio-users at mristudio.org >>>> http://lists.mristudio.org/mailman/listinfo/ >>>> Unsubscribe, send a blank email to: >>>> Mristudio-users-unsubscribe at mristudio.org >>>> >>> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > From mpinsk at gmail.com Wed Dec 16 19:43:53 2009 From: mpinsk at gmail.com (Mark A. Pinsk) Date: Wed, 16 Dec 2009 19:43:53 -0500 Subject: [Mristudio-users] Using processed data In-Reply-To: References: <4B28542F.5000803@puc.cl> <4B28651A.4020202@puc.cl> <274936.72080.qm@web30701.mail.mud.yahoo.com> Message-ID: When I read in a 3D ANALYZE file using MRIView3D + Analyze file format, all of the parameters are grayed out, and they read as follows. This reads in the file successfully as far as I can tell. Image Width: 96 Image Height: 128 Image Slices: 1 ?? Coronal / Ant-Pos FOV: 96 x 128 Slice thickness: 1.1 Pixel Size: 0 x 0 ?? # of Image-blocks: 1 Word (16 Bits). Image File Format: Analyze Image Sequence: in blocks. On Wed, Dec 16, 2009 at 7:39 PM, Mark A. Pinsk wrote: > No luck. ?Let me outline my steps here: > > 1. I start with a 4D NIFTI file that contains 65 volumes (60 DWI + 5 B0). > The image dimensions are 96x128, 47 slices per volume. > Slice orientation is Coronal. ?FOV is 96x128. ?Pixels are 1x1x1.1. > > 2. I split the 4D NIFTI file into 65 3D NIFTI files using this FSL command: > fslsplit input.nii.gz > > 3. I convert each of the 65 3D NIFTI files to ANALYZE format: > fslchfiletype ANALYZE vol0000.nii.gz > [..] > fslchfiletype ANALYZE vol0064.nii.gz > > 4. I am able to successfully import the ANALYZE files in MRIView3D by > choosing Analyze format (but no luck with Raw format). > > 5. I have no luck importing the ANALYZE files in DTI Mapping choosing > Raw format. ?I get this message: > "Number of files in this fold is less than expected: (Img_Slices*Img_Blocks). > > Any suggestions? ?Thanks for all your help! > Mark > > > > > On Wed, Dec 16, 2009 at 1:34 PM, darshan pai wrote: >> when you say a 4D file I assume that you have a Analyze file with an entry on the number of volumes , Is it? . If it is then try to make it a 3D file with all the 65 slices added in the z direction and see if it helps.. >> >> Regards >> >> Dp >> >> >> >> ----- Original Message ---- >> From: Mark A. Pinsk >> To: "DTI Studio, ROI Editor, Landmarker Questions/Support" >> Sent: Wed, December 16, 2009 12:13:42 AM >> Subject: Re: [Mristudio-users] Using processed data >> >> Also, I should mention that the Analyze file loads just fine using >> "MRI View3D" and "Analyze" file format. >> >> >> On Wed, Dec 16, 2009 at 12:09 AM, Mark A. Pinsk wrote: >>> Thanks for your help, I'll do my best to answer them... >>> >>> FYI: these are small volumes from animal scans ( 1 x 1 x 1.1 mm resolution): >>> >>> Image Dimensions: 96 Width, 128 Height, 47 slices >>> Slice Orientation: Axial >>> Slice Sequencing: Inferior-Superior >>> FOV: 96 Width, 128 Height, 1.1 Slice Thickness >>> Pixel Size: 1.000 Width, 1.000 Height >>> Slices to be processed: 0 to 46, All Slices >>> Image Sequence: Gradient By Gradient >>> b_Value: 1000 >>> >>> My gradient table has 65 entries. ?The first 5 entries are B0 images, >>> the remaining 60 are for the 60 directions. ?There is no mean image at >>> the end of my data. ? I can discard 4 of the B0 images, but that does >>> not seem to make a difference on my error message. ?I have several B0 >>> images in accord with recent work that suggests having a ratio of 6:1 >>> diffusion to non-diffusion weighted images (Zhu et al. NeuroImage >>> 2008). >>> >>> >>> >>> On Tue, Dec 15, 2009 at 11:42 PM, Gonzalo Rojas wrote: >>>> Hi Mark: >>>> >>>> ?Many questions: >>>> >>>> i) do you specify correctly the "image slices" quantity in "iamge dimension" >>>> ?... that value is the quantitry of axial slices in each gradient >>>> direction... >>>> >>>> ii) and the "image width" and "image height" in "image dimension" ?... did >>>> you checked that values ?... >>>> >>>> ii) in "lice orientation" did you specify "axial" ?.. >>>> >>>> iii) and in "Voxel Size", "Field of View-width" and "Field of View-Heigth" >>>> did you specifiy the FOV value correctly ?... >>>> >>>> iv) you could check the previos values looking at "Pixel Size-Width" and >>>> "Pixel Size-Height"... >>>> >>>> v) in "Slices to be processed" it must appears 0-(image slices-1) >>>> >>>> vi) in gradient table you must put the 61 (0-60) directions... in your 4D >>>> analyze file is included the "mean" of all the 60 directions at the end of >>>> the file ?... if it is, you must put "100,100,100" as the last gradient >>>> direction to skip that image in the computation... >>>> >>>> vii) in "Image secuence" you must select "Gradient by Gradient" option... >>>> >>>> viii) in "Raw-BIN Files folder you must specify the IMG file of the Analyze >>>> pair... >>>> >>>> ix) why you have 5 b0 volumes ?... to compute tractography, you must have >>>> only one b0 volume... you must put "100,100,100" in "Gradient Table" for >>>> each of the 4 b0 slices to skipt them... >>>> >>>> ?Sincerely, >>>> >>>> >>>> Gonzalo Rojas Costa >>>> Department of Radiology >>>> Las Condes Clinic >>>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >>>> Tel: 56-2-2105170 >>>> Cel: 56-9-97771785 >>>> www.clc.cl >>>> >>>> El 16-12-2009 1:07, Mark A. Pinsk escribi?: >>>>> >>>>> Thanks ! >>>>> >>>>> I converted by 4D NIFTI file to a 4D ANALYZE file as you suggested. >>>>> >>>>> I attempt to read it in as RAW, but it seems to get stuck... >>>>> >>>>> I specify the file in the Raw-BIN Files Folder field, but I get this >>>>> message: >>>>> "Number of files in this fold is less than expected: >>>>> (Img_Slices*Img_Blocks)." >>>>> >>>>> I only have a single .img/.hdr pair in my folder since it is a 4D file >>>>> (i.e. it contains 65 volumes (5 b0 volumes + 60 directions)). >>>>> >>>>> Sorry, any help would be greatly appreciated. >>>>> Thanks >>>>> Mark >>>>> >>>>> >>>>> >>>>> >>>>> On Tue, Dec 15, 2009 at 10:29 PM, Gonzalo Rojas ?wrote: >>>>>> >>>>>> Hi Mark: >>>>>> >>>>>> ?Yes... you could do all the processing that you mentioned (in FSL), and >>>>>> bring it to dti-studio... the FSL output file format is NIFTI.GZ... you >>>>>> must >>>>>> convert it to ANALYZE 4D, and then you must load that ANALYZE 4D file as >>>>>> a >>>>>> RAW data file format in DTI-STUDIO... >>>>>> >>>>>> ?Sincerely, >>>>>> >>>>>> >>>>>> Gonzalo Rojas Costa >>>>>> Department of Radiology >>>>>> Las Condes Clinic >>>>>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >>>>>> Tel: 56-2-2105170 >>>>>> Cel: 56-9-97771785 >>>>>> www.clc.cl >>>>>> >>>>>> El 15-12-2009 23:37, Mark A. Pinsk escribi?: >>>>>>> >>>>>>> Hi, someone asked this a while ago in the archives but I didn't see a >>>>>>> reply. ? Can I use data that I've processed in FSL (eddy current >>>>>>> correction, motion correction, and field map-based undistortion) and >>>>>>> bring it into dti-studio? ? The data is in one large 4D nifti file. ?I >>>>>>> don't see where I can do this, is it not possible? >>>>>>> >>>>>>> thanks >>>>>>> mark >>>>>>> _______________________________________________ >>>>>>> Mristudio-users mailing list >>>>>>> Mristudio-users at mristudio.org >>>>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>>>> Unsubscribe, send a blank email to: >>>>>>> Mristudio-users-unsubscribe at mristudio.org >>>>>>> >>>>>> >>>>> >>>>> _______________________________________________ >>>>> Mristudio-users mailing list >>>>> Mristudio-users at mristudio.org >>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>> Unsubscribe, send a blank email to: >>>>> Mristudio-users-unsubscribe at mristudio.org >>>>> >>>> >>> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org >> >> >> >> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org >> > From grojasy at puc.cl Wed Dec 16 19:51:42 2009 From: grojasy at puc.cl (Gonzalo Rojas) Date: Wed, 16 Dec 2009 21:51:42 -0300 Subject: [Mristudio-users] Using processed data In-Reply-To: References: <4B28542F.5000803@puc.cl> <4B28651A.4020202@puc.cl> <274936.72080.qm@web30701.mail.mud.yahoo.com> Message-ID: <4B29809E.50805@puc.cl> Hi Mark: I read your e-mail, but why you convert the 4D NIFTI to 3D NIFTI ?... you must convert the 4D NIFTI to 4D ANALYZE... no 3D... you must read the 4D ANLYZE in DTI mapping using RAW format, but you must specify coronal as the "slice orientation"... Sincerely, Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl El 16-12-2009 21:39, Mark A. Pinsk escribi?: > No luck. Let me outline my steps here: > > 1. I start with a 4D NIFTI file that contains 65 volumes (60 DWI + 5 B0). > The image dimensions are 96x128, 47 slices per volume. > Slice orientation is Coronal. FOV is 96x128. Pixels are 1x1x1.1. > > 2. I split the 4D NIFTI file into 65 3D NIFTI files using this FSL command: > fslsplit input.nii.gz > > 3. I convert each of the 65 3D NIFTI files to ANALYZE format: > fslchfiletype ANALYZE vol0000.nii.gz > [..] > fslchfiletype ANALYZE vol0064.nii.gz > > 4. I am able to successfully import the ANALYZE files in MRIView3D by > choosing Analyze format (but no luck with Raw format). > > 5. I have no luck importing the ANALYZE files in DTI Mapping choosing > Raw format. I get this message: > "Number of files in this fold is less than expected: (Img_Slices*Img_Blocks). > > Any suggestions? Thanks for all your help! > Mark > > > > > On Wed, Dec 16, 2009 at 1:34 PM, darshan pai wrote: >> when you say a 4D file I assume that you have a Analyze file with an entry on the number of volumes , Is it? . If it is then try to make it a 3D file with all the 65 slices added in the z direction and see if it helps.. >> >> Regards >> >> Dp >> >> >> >> ----- Original Message ---- >> From: Mark A. Pinsk >> To: "DTI Studio, ROI Editor, Landmarker Questions/Support" >> Sent: Wed, December 16, 2009 12:13:42 AM >> Subject: Re: [Mristudio-users] Using processed data >> >> Also, I should mention that the Analyze file loads just fine using >> "MRI View3D" and "Analyze" file format. >> >> >> On Wed, Dec 16, 2009 at 12:09 AM, Mark A. Pinsk wrote: >>> Thanks for your help, I'll do my best to answer them... >>> >>> FYI: these are small volumes from animal scans ( 1 x 1 x 1.1 mm resolution): >>> >>> Image Dimensions: 96 Width, 128 Height, 47 slices >>> Slice Orientation: Axial >>> Slice Sequencing: Inferior-Superior >>> FOV: 96 Width, 128 Height, 1.1 Slice Thickness >>> Pixel Size: 1.000 Width, 1.000 Height >>> Slices to be processed: 0 to 46, All Slices >>> Image Sequence: Gradient By Gradient >>> b_Value: 1000 >>> >>> My gradient table has 65 entries. The first 5 entries are B0 images, >>> the remaining 60 are for the 60 directions. There is no mean image at >>> the end of my data. I can discard 4 of the B0 images, but that does >>> not seem to make a difference on my error message. I have several B0 >>> images in accord with recent work that suggests having a ratio of 6:1 >>> diffusion to non-diffusion weighted images (Zhu et al. NeuroImage >>> 2008). >>> >>> >>> >>> On Tue, Dec 15, 2009 at 11:42 PM, Gonzalo Rojas wrote: >>>> Hi Mark: >>>> >>>> Many questions: >>>> >>>> i) do you specify correctly the "image slices" quantity in "iamge dimension" >>>> ?... that value is the quantitry of axial slices in each gradient >>>> direction... >>>> >>>> ii) and the "image width" and "image height" in "image dimension" ?... did >>>> you checked that values ?... >>>> >>>> ii) in "lice orientation" did you specify "axial" ?.. >>>> >>>> iii) and in "Voxel Size", "Field of View-width" and "Field of View-Heigth" >>>> did you specifiy the FOV value correctly ?... >>>> >>>> iv) you could check the previos values looking at "Pixel Size-Width" and >>>> "Pixel Size-Height"... >>>> >>>> v) in "Slices to be processed" it must appears 0-(image slices-1) >>>> >>>> vi) in gradient table you must put the 61 (0-60) directions... in your 4D >>>> analyze file is included the "mean" of all the 60 directions at the end of >>>> the file ?... if it is, you must put "100,100,100" as the last gradient >>>> direction to skip that image in the computation... >>>> >>>> vii) in "Image secuence" you must select "Gradient by Gradient" option... >>>> >>>> viii) in "Raw-BIN Files folder you must specify the IMG file of the Analyze >>>> pair... >>>> >>>> ix) why you have 5 b0 volumes ?... to compute tractography, you must have >>>> only one b0 volume... you must put "100,100,100" in "Gradient Table" for >>>> each of the 4 b0 slices to skipt them... >>>> >>>> Sincerely, >>>> >>>> >>>> Gonzalo Rojas Costa >>>> Department of Radiology >>>> Las Condes Clinic >>>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >>>> Tel: 56-2-2105170 >>>> Cel: 56-9-97771785 >>>> www.clc.cl >>>> >>>> El 16-12-2009 1:07, Mark A. Pinsk escribi?: >>>>> >>>>> Thanks ! >>>>> >>>>> I converted by 4D NIFTI file to a 4D ANALYZE file as you suggested. >>>>> >>>>> I attempt to read it in as RAW, but it seems to get stuck... >>>>> >>>>> I specify the file in the Raw-BIN Files Folder field, but I get this >>>>> message: >>>>> "Number of files in this fold is less than expected: >>>>> (Img_Slices*Img_Blocks)." >>>>> >>>>> I only have a single .img/.hdr pair in my folder since it is a 4D file >>>>> (i.e. it contains 65 volumes (5 b0 volumes + 60 directions)). >>>>> >>>>> Sorry, any help would be greatly appreciated. >>>>> Thanks >>>>> Mark >>>>> >>>>> >>>>> >>>>> >>>>> On Tue, Dec 15, 2009 at 10:29 PM, Gonzalo Rojas wrote: >>>>>> >>>>>> Hi Mark: >>>>>> >>>>>> Yes... you could do all the processing that you mentioned (in FSL), and >>>>>> bring it to dti-studio... the FSL output file format is NIFTI.GZ... you >>>>>> must >>>>>> convert it to ANALYZE 4D, and then you must load that ANALYZE 4D file as >>>>>> a >>>>>> RAW data file format in DTI-STUDIO... >>>>>> >>>>>> Sincerely, >>>>>> >>>>>> >>>>>> Gonzalo Rojas Costa >>>>>> Department of Radiology >>>>>> Las Condes Clinic >>>>>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >>>>>> Tel: 56-2-2105170 >>>>>> Cel: 56-9-97771785 >>>>>> www.clc.cl >>>>>> >>>>>> El 15-12-2009 23:37, Mark A. Pinsk escribi?: >>>>>>> >>>>>>> Hi, someone asked this a while ago in the archives but I didn't see a >>>>>>> reply. Can I use data that I've processed in FSL (eddy current >>>>>>> correction, motion correction, and field map-based undistortion) and >>>>>>> bring it into dti-studio? The data is in one large 4D nifti file. I >>>>>>> don't see where I can do this, is it not possible? >>>>>>> >>>>>>> thanks >>>>>>> mark >>>>>>> _______________________________________________ >>>>>>> Mristudio-users mailing list >>>>>>> Mristudio-users at mristudio.org >>>>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>>>> Unsubscribe, send a blank email to: >>>>>>> Mristudio-users-unsubscribe at mristudio.org >>>>>>> >>>>>> >>>>> >>>>> _______________________________________________ >>>>> Mristudio-users mailing list >>>>> Mristudio-users at mristudio.org >>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>> Unsubscribe, send a blank email to: >>>>> Mristudio-users-unsubscribe at mristudio.org >>>>> >>>> >>> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org >> >> >> >> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > From mpinsk at gmail.com Wed Dec 16 19:57:13 2009 From: mpinsk at gmail.com (Mark A. Pinsk) Date: Wed, 16 Dec 2009 19:57:13 -0500 Subject: [Mristudio-users] Using processed data In-Reply-To: <4B29809E.50805@puc.cl> References: <4B28542F.5000803@puc.cl> <4B28651A.4020202@puc.cl> <274936.72080.qm@web30701.mail.mud.yahoo.com> <4B29809E.50805@puc.cl> Message-ID: Hi Gonzalo, Yes, I tried that first after your suggestions yesterday: 4D NIFTI to 4D ANALYZE: fslchfiletype ANALYZE input.nii.gz And I get the same error about less than expected number of files, even though it's only one img/hdr pair in that folder. Somebody else next suggested going to 65 3D Analyze files instead of a single 4D Analyze file. That also did not work. Sorry this is turning out to be so difficult! I wonder where I went wrong.... On Wed, Dec 16, 2009 at 7:51 PM, Gonzalo Rojas wrote: > Hi Mark: > > ?I read your e-mail, but why you convert the 4D NIFTI to 3D NIFTI ?... you > must convert the 4D NIFTI to 4D ANALYZE... no 3D... you must read the 4D > ANLYZE in DTI mapping using RAW format, but you must specify coronal as the > "slice orientation"... > > ?Sincerely, > > > > Gonzalo Rojas Costa > Department of Radiology > Las Condes Clinic > Lo Fontecilla 441, Las Condes, Santiago, Chile. > Tel: 56-2-2105170 > Cel: 56-9-97771785 > www.clc.cl > > > El 16-12-2009 21:39, Mark A. Pinsk escribi?: >> >> No luck. ?Let me outline my steps here: >> >> 1. I start with a 4D NIFTI file that contains 65 volumes (60 DWI + 5 B0). >> The image dimensions are 96x128, 47 slices per volume. >> Slice orientation is Coronal. ?FOV is 96x128. ?Pixels are 1x1x1.1. >> >> 2. I split the 4D NIFTI file into 65 3D NIFTI files using this FSL >> command: >> fslsplit input.nii.gz >> >> 3. I convert each of the 65 3D NIFTI files to ANALYZE format: >> fslchfiletype ANALYZE vol0000.nii.gz >> [..] >> fslchfiletype ANALYZE vol0064.nii.gz >> >> 4. I am able to successfully import the ANALYZE files in MRIView3D by >> choosing Analyze format (but no luck with Raw format). >> >> 5. I have no luck importing the ANALYZE files in DTI Mapping choosing >> Raw format. ?I get this message: >> "Number of files in this fold is less than expected: >> (Img_Slices*Img_Blocks). >> >> Any suggestions? ?Thanks for all your help! >> Mark >> >> >> >> >> On Wed, Dec 16, 2009 at 1:34 PM, darshan pai ?wrote: >>> >>> when you say a 4D file I assume that you have a Analyze file with an >>> entry on the number of volumes , Is it? . If it is then try to make it a 3D >>> file with all the 65 slices added in the z direction and see if it helps.. >>> >>> Regards >>> >>> Dp >>> >>> >>> >>> ----- Original Message ---- >>> From: Mark A. Pinsk >>> To: "DTI Studio, ROI Editor, Landmarker >>> Questions/Support" >>> Sent: Wed, December 16, 2009 12:13:42 AM >>> Subject: Re: [Mristudio-users] Using processed data >>> >>> Also, I should mention that the Analyze file loads just fine using >>> "MRI View3D" and "Analyze" file format. >>> >>> >>> On Wed, Dec 16, 2009 at 12:09 AM, Mark A. Pinsk ?wrote: >>>> >>>> Thanks for your help, I'll do my best to answer them... >>>> >>>> FYI: these are small volumes from animal scans ( 1 x 1 x 1.1 mm >>>> resolution): >>>> >>>> Image Dimensions: 96 Width, 128 Height, 47 slices >>>> Slice Orientation: Axial >>>> Slice Sequencing: Inferior-Superior >>>> FOV: 96 Width, 128 Height, 1.1 Slice Thickness >>>> Pixel Size: 1.000 Width, 1.000 Height >>>> Slices to be processed: 0 to 46, All Slices >>>> Image Sequence: Gradient By Gradient >>>> b_Value: 1000 >>>> >>>> My gradient table has 65 entries. ?The first 5 entries are B0 images, >>>> the remaining 60 are for the 60 directions. ?There is no mean image at >>>> the end of my data. ? I can discard 4 of the B0 images, but that does >>>> not seem to make a difference on my error message. ?I have several B0 >>>> images in accord with recent work that suggests having a ratio of 6:1 >>>> diffusion to non-diffusion weighted images (Zhu et al. NeuroImage >>>> 2008). >>>> >>>> >>>> >>>> On Tue, Dec 15, 2009 at 11:42 PM, Gonzalo Rojas ?wrote: >>>>> >>>>> Hi Mark: >>>>> >>>>> ?Many questions: >>>>> >>>>> i) do you specify correctly the "image slices" quantity in "iamge >>>>> dimension" >>>>> ?... that value is the quantitry of axial slices in each gradient >>>>> direction... >>>>> >>>>> ii) and the "image width" and "image height" in "image dimension" ?... >>>>> did >>>>> you checked that values ?... >>>>> >>>>> ii) in "lice orientation" did you specify "axial" ?.. >>>>> >>>>> iii) and in "Voxel Size", "Field of View-width" and "Field of >>>>> View-Heigth" >>>>> did you specifiy the FOV value correctly ?... >>>>> >>>>> iv) you could check the previos values looking at "Pixel Size-Width" >>>>> and >>>>> "Pixel Size-Height"... >>>>> >>>>> v) in "Slices to be processed" it must appears 0-(image slices-1) >>>>> >>>>> vi) in gradient table you must put the 61 (0-60) directions... in your >>>>> 4D >>>>> analyze file is included the "mean" of all the 60 directions at the end >>>>> of >>>>> the file ?... if it is, you must put "100,100,100" as the last gradient >>>>> direction to skip that image in the computation... >>>>> >>>>> vii) in "Image secuence" you must select "Gradient by Gradient" >>>>> option... >>>>> >>>>> viii) in "Raw-BIN Files folder you must specify the IMG file of the >>>>> Analyze >>>>> pair... >>>>> >>>>> ix) why you have 5 b0 volumes ?... to compute tractography, you must >>>>> have >>>>> only one b0 volume... you must put "100,100,100" in "Gradient Table" >>>>> for >>>>> each of the 4 b0 slices to skipt them... >>>>> >>>>> ?Sincerely, >>>>> >>>>> >>>>> Gonzalo Rojas Costa >>>>> Department of Radiology >>>>> Las Condes Clinic >>>>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >>>>> Tel: 56-2-2105170 >>>>> Cel: 56-9-97771785 >>>>> www.clc.cl >>>>> >>>>> El 16-12-2009 1:07, Mark A. Pinsk escribi?: >>>>>> >>>>>> Thanks ! >>>>>> >>>>>> I converted by 4D NIFTI file to a 4D ANALYZE file as you suggested. >>>>>> >>>>>> I attempt to read it in as RAW, but it seems to get stuck... >>>>>> >>>>>> I specify the file in the Raw-BIN Files Folder field, but I get this >>>>>> message: >>>>>> "Number of files in this fold is less than expected: >>>>>> (Img_Slices*Img_Blocks)." >>>>>> >>>>>> I only have a single .img/.hdr pair in my folder since it is a 4D file >>>>>> (i.e. it contains 65 volumes (5 b0 volumes + 60 directions)). >>>>>> >>>>>> Sorry, any help would be greatly appreciated. >>>>>> Thanks >>>>>> Mark >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On Tue, Dec 15, 2009 at 10:29 PM, Gonzalo Rojas >>>>>> ?wrote: >>>>>>> >>>>>>> Hi Mark: >>>>>>> >>>>>>> ?Yes... you could do all the processing that you mentioned (in FSL), >>>>>>> and >>>>>>> bring it to dti-studio... the FSL output file format is NIFTI.GZ... >>>>>>> you >>>>>>> must >>>>>>> convert it to ANALYZE 4D, and then you must load that ANALYZE 4D file >>>>>>> as >>>>>>> a >>>>>>> RAW data file format in DTI-STUDIO... >>>>>>> >>>>>>> ?Sincerely, >>>>>>> >>>>>>> >>>>>>> Gonzalo Rojas Costa >>>>>>> Department of Radiology >>>>>>> Las Condes Clinic >>>>>>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >>>>>>> Tel: 56-2-2105170 >>>>>>> Cel: 56-9-97771785 >>>>>>> www.clc.cl >>>>>>> >>>>>>> El 15-12-2009 23:37, Mark A. Pinsk escribi?: >>>>>>>> >>>>>>>> Hi, someone asked this a while ago in the archives but I didn't see >>>>>>>> a >>>>>>>> reply. ? Can I use data that I've processed in FSL (eddy current >>>>>>>> correction, motion correction, and field map-based undistortion) and >>>>>>>> bring it into dti-studio? ? The data is in one large 4D nifti file. >>>>>>>> ?I >>>>>>>> don't see where I can do this, is it not possible? >>>>>>>> >>>>>>>> thanks >>>>>>>> mark >>>>>>>> _______________________________________________ >>>>>>>> Mristudio-users mailing list >>>>>>>> Mristudio-users at mristudio.org >>>>>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>>>>> Unsubscribe, send a blank email to: >>>>>>>> Mristudio-users-unsubscribe at mristudio.org >>>>>>>> >>>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Mristudio-users mailing list >>>>>> Mristudio-users at mristudio.org >>>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>>> Unsubscribe, send a blank email to: >>>>>> Mristudio-users-unsubscribe at mristudio.org >>>>>> >>>>> >>>> >>> >>> _______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: >>> Mristudio-users-unsubscribe at mristudio.org >>> >>> >>> >>> >>> >>> _______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: >>> Mristudio-users-unsubscribe at mristudio.org >>> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> > From mpinsk at gmail.com Wed Dec 16 20:00:13 2009 From: mpinsk at gmail.com (Mark A. Pinsk) Date: Wed, 16 Dec 2009 20:00:13 -0500 Subject: [Mristudio-users] Using processed data In-Reply-To: References: <4B28542F.5000803@puc.cl> <4B28651A.4020202@puc.cl> <274936.72080.qm@web30701.mail.mud.yahoo.com> <4B29809E.50805@puc.cl> Message-ID: A report of my 4D Analyze header reads as follows. Can anyone spot anything strange? fslinfo data.hdr data_type dim1 96 dim2 128 dim3 47 dim4 65 datatype 16 pixdim1 -1.0000000000 pixdim2 1.0000000000 pixdim3 1.1000000238 pixdim4 1.0000000000 cal_max 3154.5610 cal_min -1285.1160 glmax 0 glmin 0 origin1 51 origin2 66 origin3 9 file_type ANALYZE-7.5 On Wed, Dec 16, 2009 at 7:57 PM, Mark A. Pinsk wrote: > Hi Gonzalo, > > Yes, I tried that first after your suggestions yesterday: > 4D NIFTI to 4D ANALYZE: > fslchfiletype ANALYZE input.nii.gz > > And I get the same error about less than expected number of files, > even though it's only one img/hdr pair in that folder. > > Somebody else next suggested going to 65 3D Analyze files instead of a > single 4D Analyze file. ?That also did not work. > > Sorry this is turning out to be so difficult! ? I wonder where I went wrong.... > > > > On Wed, Dec 16, 2009 at 7:51 PM, Gonzalo Rojas wrote: >> Hi Mark: >> >> ?I read your e-mail, but why you convert the 4D NIFTI to 3D NIFTI ?... you >> must convert the 4D NIFTI to 4D ANALYZE... no 3D... you must read the 4D >> ANLYZE in DTI mapping using RAW format, but you must specify coronal as the >> "slice orientation"... >> >> ?Sincerely, >> >> >> >> Gonzalo Rojas Costa >> Department of Radiology >> Las Condes Clinic >> Lo Fontecilla 441, Las Condes, Santiago, Chile. >> Tel: 56-2-2105170 >> Cel: 56-9-97771785 >> www.clc.cl >> >> >> El 16-12-2009 21:39, Mark A. Pinsk escribi?: >>> >>> No luck. ?Let me outline my steps here: >>> >>> 1. I start with a 4D NIFTI file that contains 65 volumes (60 DWI + 5 B0). >>> The image dimensions are 96x128, 47 slices per volume. >>> Slice orientation is Coronal. ?FOV is 96x128. ?Pixels are 1x1x1.1. >>> >>> 2. I split the 4D NIFTI file into 65 3D NIFTI files using this FSL >>> command: >>> fslsplit input.nii.gz >>> >>> 3. I convert each of the 65 3D NIFTI files to ANALYZE format: >>> fslchfiletype ANALYZE vol0000.nii.gz >>> [..] >>> fslchfiletype ANALYZE vol0064.nii.gz >>> >>> 4. I am able to successfully import the ANALYZE files in MRIView3D by >>> choosing Analyze format (but no luck with Raw format). >>> >>> 5. I have no luck importing the ANALYZE files in DTI Mapping choosing >>> Raw format. ?I get this message: >>> "Number of files in this fold is less than expected: >>> (Img_Slices*Img_Blocks). >>> >>> Any suggestions? ?Thanks for all your help! >>> Mark >>> >>> >>> >>> >>> On Wed, Dec 16, 2009 at 1:34 PM, darshan pai ?wrote: >>>> >>>> when you say a 4D file I assume that you have a Analyze file with an >>>> entry on the number of volumes , Is it? . If it is then try to make it a 3D >>>> file with all the 65 slices added in the z direction and see if it helps.. >>>> >>>> Regards >>>> >>>> Dp >>>> >>>> >>>> >>>> ----- Original Message ---- >>>> From: Mark A. Pinsk >>>> To: "DTI Studio, ROI Editor, Landmarker >>>> Questions/Support" >>>> Sent: Wed, December 16, 2009 12:13:42 AM >>>> Subject: Re: [Mristudio-users] Using processed data >>>> >>>> Also, I should mention that the Analyze file loads just fine using >>>> "MRI View3D" and "Analyze" file format. >>>> >>>> >>>> On Wed, Dec 16, 2009 at 12:09 AM, Mark A. Pinsk ?wrote: >>>>> >>>>> Thanks for your help, I'll do my best to answer them... >>>>> >>>>> FYI: these are small volumes from animal scans ( 1 x 1 x 1.1 mm >>>>> resolution): >>>>> >>>>> Image Dimensions: 96 Width, 128 Height, 47 slices >>>>> Slice Orientation: Axial >>>>> Slice Sequencing: Inferior-Superior >>>>> FOV: 96 Width, 128 Height, 1.1 Slice Thickness >>>>> Pixel Size: 1.000 Width, 1.000 Height >>>>> Slices to be processed: 0 to 46, All Slices >>>>> Image Sequence: Gradient By Gradient >>>>> b_Value: 1000 >>>>> >>>>> My gradient table has 65 entries. ?The first 5 entries are B0 images, >>>>> the remaining 60 are for the 60 directions. ?There is no mean image at >>>>> the end of my data. ? I can discard 4 of the B0 images, but that does >>>>> not seem to make a difference on my error message. ?I have several B0 >>>>> images in accord with recent work that suggests having a ratio of 6:1 >>>>> diffusion to non-diffusion weighted images (Zhu et al. NeuroImage >>>>> 2008). >>>>> >>>>> >>>>> >>>>> On Tue, Dec 15, 2009 at 11:42 PM, Gonzalo Rojas ?wrote: >>>>>> >>>>>> Hi Mark: >>>>>> >>>>>> ?Many questions: >>>>>> >>>>>> i) do you specify correctly the "image slices" quantity in "iamge >>>>>> dimension" >>>>>> ?... that value is the quantitry of axial slices in each gradient >>>>>> direction... >>>>>> >>>>>> ii) and the "image width" and "image height" in "image dimension" ?... >>>>>> did >>>>>> you checked that values ?... >>>>>> >>>>>> ii) in "lice orientation" did you specify "axial" ?.. >>>>>> >>>>>> iii) and in "Voxel Size", "Field of View-width" and "Field of >>>>>> View-Heigth" >>>>>> did you specifiy the FOV value correctly ?... >>>>>> >>>>>> iv) you could check the previos values looking at "Pixel Size-Width" >>>>>> and >>>>>> "Pixel Size-Height"... >>>>>> >>>>>> v) in "Slices to be processed" it must appears 0-(image slices-1) >>>>>> >>>>>> vi) in gradient table you must put the 61 (0-60) directions... in your >>>>>> 4D >>>>>> analyze file is included the "mean" of all the 60 directions at the end >>>>>> of >>>>>> the file ?... if it is, you must put "100,100,100" as the last gradient >>>>>> direction to skip that image in the computation... >>>>>> >>>>>> vii) in "Image secuence" you must select "Gradient by Gradient" >>>>>> option... >>>>>> >>>>>> viii) in "Raw-BIN Files folder you must specify the IMG file of the >>>>>> Analyze >>>>>> pair... >>>>>> >>>>>> ix) why you have 5 b0 volumes ?... to compute tractography, you must >>>>>> have >>>>>> only one b0 volume... you must put "100,100,100" in "Gradient Table" >>>>>> for >>>>>> each of the 4 b0 slices to skipt them... >>>>>> >>>>>> ?Sincerely, >>>>>> >>>>>> >>>>>> Gonzalo Rojas Costa >>>>>> Department of Radiology >>>>>> Las Condes Clinic >>>>>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >>>>>> Tel: 56-2-2105170 >>>>>> Cel: 56-9-97771785 >>>>>> www.clc.cl >>>>>> >>>>>> El 16-12-2009 1:07, Mark A. Pinsk escribi?: >>>>>>> >>>>>>> Thanks ! >>>>>>> >>>>>>> I converted by 4D NIFTI file to a 4D ANALYZE file as you suggested. >>>>>>> >>>>>>> I attempt to read it in as RAW, but it seems to get stuck... >>>>>>> >>>>>>> I specify the file in the Raw-BIN Files Folder field, but I get this >>>>>>> message: >>>>>>> "Number of files in this fold is less than expected: >>>>>>> (Img_Slices*Img_Blocks)." >>>>>>> >>>>>>> I only have a single .img/.hdr pair in my folder since it is a 4D file >>>>>>> (i.e. it contains 65 volumes (5 b0 volumes + 60 directions)). >>>>>>> >>>>>>> Sorry, any help would be greatly appreciated. >>>>>>> Thanks >>>>>>> Mark >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Tue, Dec 15, 2009 at 10:29 PM, Gonzalo Rojas >>>>>>> ?wrote: >>>>>>>> >>>>>>>> Hi Mark: >>>>>>>> >>>>>>>> ?Yes... you could do all the processing that you mentioned (in FSL), >>>>>>>> and >>>>>>>> bring it to dti-studio... the FSL output file format is NIFTI.GZ... >>>>>>>> you >>>>>>>> must >>>>>>>> convert it to ANALYZE 4D, and then you must load that ANALYZE 4D file >>>>>>>> as >>>>>>>> a >>>>>>>> RAW data file format in DTI-STUDIO... >>>>>>>> >>>>>>>> ?Sincerely, >>>>>>>> >>>>>>>> >>>>>>>> Gonzalo Rojas Costa >>>>>>>> Department of Radiology >>>>>>>> Las Condes Clinic >>>>>>>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >>>>>>>> Tel: 56-2-2105170 >>>>>>>> Cel: 56-9-97771785 >>>>>>>> www.clc.cl >>>>>>>> >>>>>>>> El 15-12-2009 23:37, Mark A. Pinsk escribi?: >>>>>>>>> >>>>>>>>> Hi, someone asked this a while ago in the archives but I didn't see >>>>>>>>> a >>>>>>>>> reply. ? Can I use data that I've processed in FSL (eddy current >>>>>>>>> correction, motion correction, and field map-based undistortion) and >>>>>>>>> bring it into dti-studio? ? The data is in one large 4D nifti file. >>>>>>>>> ?I >>>>>>>>> don't see where I can do this, is it not possible? >>>>>>>>> >>>>>>>>> thanks >>>>>>>>> mark >>>>>>>>> _______________________________________________ >>>>>>>>> Mristudio-users mailing list >>>>>>>>> Mristudio-users at mristudio.org >>>>>>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>>>>>> Unsubscribe, send a blank email to: >>>>>>>>> Mristudio-users-unsubscribe at mristudio.org >>>>>>>>> >>>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Mristudio-users mailing list >>>>>>> Mristudio-users at mristudio.org >>>>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>>>> Unsubscribe, send a blank email to: >>>>>>> Mristudio-users-unsubscribe at mristudio.org >>>>>>> >>>>>> >>>>> >>>> >>>> _______________________________________________ >>>> Mristudio-users mailing list >>>> Mristudio-users at mristudio.org >>>> http://lists.mristudio.org/mailman/listinfo/ >>>> Unsubscribe, send a blank email to: >>>> Mristudio-users-unsubscribe at mristudio.org >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> Mristudio-users mailing list >>>> Mristudio-users at mristudio.org >>>> http://lists.mristudio.org/mailman/listinfo/ >>>> Unsubscribe, send a blank email to: >>>> Mristudio-users-unsubscribe at mristudio.org >>>> >>> >>> _______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: >>> Mristudio-users-unsubscribe at mristudio.org >>> >> > From grojasy at puc.cl Wed Dec 16 20:02:12 2009 From: grojasy at puc.cl (Gonzalo Rojas) Date: Wed, 16 Dec 2009 22:02:12 -0300 Subject: [Mristudio-users] Using processed data In-Reply-To: References: <4B28542F.5000803@puc.cl> <4B28651A.4020202@puc.cl> <274936.72080.qm@web30701.mail.mud.yahoo.com> <4B29809E.50805@puc.cl> Message-ID: <4B298314.10301@puc.cl> Hi Mark: And could you please send me the gradient direction table that you input in gradient table window ?... and could you please send me an screenshot of the "DW-image Parameters" window ?... But, you must use 4D files... not 3D ones... Sincerely, Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl El 16-12-2009 21:57, Mark A. Pinsk escribi?: > Hi Gonzalo, > > Yes, I tried that first after your suggestions yesterday: > 4D NIFTI to 4D ANALYZE: > fslchfiletype ANALYZE input.nii.gz > > And I get the same error about less than expected number of files, > even though it's only one img/hdr pair in that folder. > > Somebody else next suggested going to 65 3D Analyze files instead of a > single 4D Analyze file. That also did not work. > > Sorry this is turning out to be so difficult! I wonder where I went wrong.... > > > > On Wed, Dec 16, 2009 at 7:51 PM, Gonzalo Rojas wrote: >> Hi Mark: >> >> I read your e-mail, but why you convert the 4D NIFTI to 3D NIFTI ?... you >> must convert the 4D NIFTI to 4D ANALYZE... no 3D... you must read the 4D >> ANLYZE in DTI mapping using RAW format, but you must specify coronal as the >> "slice orientation"... >> >> Sincerely, >> >> >> >> Gonzalo Rojas Costa >> Department of Radiology >> Las Condes Clinic >> Lo Fontecilla 441, Las Condes, Santiago, Chile. >> Tel: 56-2-2105170 >> Cel: 56-9-97771785 >> www.clc.cl >> >> >> El 16-12-2009 21:39, Mark A. Pinsk escribi?: >>> >>> No luck. Let me outline my steps here: >>> >>> 1. I start with a 4D NIFTI file that contains 65 volumes (60 DWI + 5 B0). >>> The image dimensions are 96x128, 47 slices per volume. >>> Slice orientation is Coronal. FOV is 96x128. Pixels are 1x1x1.1. >>> >>> 2. I split the 4D NIFTI file into 65 3D NIFTI files using this FSL >>> command: >>> fslsplit input.nii.gz >>> >>> 3. I convert each of the 65 3D NIFTI files to ANALYZE format: >>> fslchfiletype ANALYZE vol0000.nii.gz >>> [..] >>> fslchfiletype ANALYZE vol0064.nii.gz >>> >>> 4. I am able to successfully import the ANALYZE files in MRIView3D by >>> choosing Analyze format (but no luck with Raw format). >>> >>> 5. I have no luck importing the ANALYZE files in DTI Mapping choosing >>> Raw format. I get this message: >>> "Number of files in this fold is less than expected: >>> (Img_Slices*Img_Blocks). >>> >>> Any suggestions? Thanks for all your help! >>> Mark >>> >>> >>> >>> >>> On Wed, Dec 16, 2009 at 1:34 PM, darshan pai wrote: >>>> >>>> when you say a 4D file I assume that you have a Analyze file with an >>>> entry on the number of volumes , Is it? . If it is then try to make it a 3D >>>> file with all the 65 slices added in the z direction and see if it helps.. >>>> >>>> Regards >>>> >>>> Dp >>>> >>>> >>>> >>>> ----- Original Message ---- >>>> From: Mark A. Pinsk >>>> To: "DTI Studio, ROI Editor, Landmarker >>>> Questions/Support" >>>> Sent: Wed, December 16, 2009 12:13:42 AM >>>> Subject: Re: [Mristudio-users] Using processed data >>>> >>>> Also, I should mention that the Analyze file loads just fine using >>>> "MRI View3D" and "Analyze" file format. >>>> >>>> >>>> On Wed, Dec 16, 2009 at 12:09 AM, Mark A. Pinsk wrote: >>>>> >>>>> Thanks for your help, I'll do my best to answer them... >>>>> >>>>> FYI: these are small volumes from animal scans ( 1 x 1 x 1.1 mm >>>>> resolution): >>>>> >>>>> Image Dimensions: 96 Width, 128 Height, 47 slices >>>>> Slice Orientation: Axial >>>>> Slice Sequencing: Inferior-Superior >>>>> FOV: 96 Width, 128 Height, 1.1 Slice Thickness >>>>> Pixel Size: 1.000 Width, 1.000 Height >>>>> Slices to be processed: 0 to 46, All Slices >>>>> Image Sequence: Gradient By Gradient >>>>> b_Value: 1000 >>>>> >>>>> My gradient table has 65 entries. The first 5 entries are B0 images, >>>>> the remaining 60 are for the 60 directions. There is no mean image at >>>>> the end of my data. I can discard 4 of the B0 images, but that does >>>>> not seem to make a difference on my error message. I have several B0 >>>>> images in accord with recent work that suggests having a ratio of 6:1 >>>>> diffusion to non-diffusion weighted images (Zhu et al. NeuroImage >>>>> 2008). >>>>> >>>>> >>>>> >>>>> On Tue, Dec 15, 2009 at 11:42 PM, Gonzalo Rojas wrote: >>>>>> >>>>>> Hi Mark: >>>>>> >>>>>> Many questions: >>>>>> >>>>>> i) do you specify correctly the "image slices" quantity in "iamge >>>>>> dimension" >>>>>> ?... that value is the quantitry of axial slices in each gradient >>>>>> direction... >>>>>> >>>>>> ii) and the "image width" and "image height" in "image dimension" ?... >>>>>> did >>>>>> you checked that values ?... >>>>>> >>>>>> ii) in "lice orientation" did you specify "axial" ?.. >>>>>> >>>>>> iii) and in "Voxel Size", "Field of View-width" and "Field of >>>>>> View-Heigth" >>>>>> did you specifiy the FOV value correctly ?... >>>>>> >>>>>> iv) you could check the previos values looking at "Pixel Size-Width" >>>>>> and >>>>>> "Pixel Size-Height"... >>>>>> >>>>>> v) in "Slices to be processed" it must appears 0-(image slices-1) >>>>>> >>>>>> vi) in gradient table you must put the 61 (0-60) directions... in your >>>>>> 4D >>>>>> analyze file is included the "mean" of all the 60 directions at the end >>>>>> of >>>>>> the file ?... if it is, you must put "100,100,100" as the last gradient >>>>>> direction to skip that image in the computation... >>>>>> >>>>>> vii) in "Image secuence" you must select "Gradient by Gradient" >>>>>> option... >>>>>> >>>>>> viii) in "Raw-BIN Files folder you must specify the IMG file of the >>>>>> Analyze >>>>>> pair... >>>>>> >>>>>> ix) why you have 5 b0 volumes ?... to compute tractography, you must >>>>>> have >>>>>> only one b0 volume... you must put "100,100,100" in "Gradient Table" >>>>>> for >>>>>> each of the 4 b0 slices to skipt them... >>>>>> >>>>>> Sincerely, >>>>>> >>>>>> >>>>>> Gonzalo Rojas Costa >>>>>> Department of Radiology >>>>>> Las Condes Clinic >>>>>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >>>>>> Tel: 56-2-2105170 >>>>>> Cel: 56-9-97771785 >>>>>> www.clc.cl >>>>>> >>>>>> El 16-12-2009 1:07, Mark A. Pinsk escribi?: >>>>>>> >>>>>>> Thanks ! >>>>>>> >>>>>>> I converted by 4D NIFTI file to a 4D ANALYZE file as you suggested. >>>>>>> >>>>>>> I attempt to read it in as RAW, but it seems to get stuck... >>>>>>> >>>>>>> I specify the file in the Raw-BIN Files Folder field, but I get this >>>>>>> message: >>>>>>> "Number of files in this fold is less than expected: >>>>>>> (Img_Slices*Img_Blocks)." >>>>>>> >>>>>>> I only have a single .img/.hdr pair in my folder since it is a 4D file >>>>>>> (i.e. it contains 65 volumes (5 b0 volumes + 60 directions)). >>>>>>> >>>>>>> Sorry, any help would be greatly appreciated. >>>>>>> Thanks >>>>>>> Mark >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Tue, Dec 15, 2009 at 10:29 PM, Gonzalo Rojas >>>>>>> wrote: >>>>>>>> >>>>>>>> Hi Mark: >>>>>>>> >>>>>>>> Yes... you could do all the processing that you mentioned (in FSL), >>>>>>>> and >>>>>>>> bring it to dti-studio... the FSL output file format is NIFTI.GZ... >>>>>>>> you >>>>>>>> must >>>>>>>> convert it to ANALYZE 4D, and then you must load that ANALYZE 4D file >>>>>>>> as >>>>>>>> a >>>>>>>> RAW data file format in DTI-STUDIO... >>>>>>>> >>>>>>>> Sincerely, >>>>>>>> >>>>>>>> >>>>>>>> Gonzalo Rojas Costa >>>>>>>> Department of Radiology >>>>>>>> Las Condes Clinic >>>>>>>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >>>>>>>> Tel: 56-2-2105170 >>>>>>>> Cel: 56-9-97771785 >>>>>>>> www.clc.cl >>>>>>>> >>>>>>>> El 15-12-2009 23:37, Mark A. Pinsk escribi?: >>>>>>>>> >>>>>>>>> Hi, someone asked this a while ago in the archives but I didn't see >>>>>>>>> a >>>>>>>>> reply. Can I use data that I've processed in FSL (eddy current >>>>>>>>> correction, motion correction, and field map-based undistortion) and >>>>>>>>> bring it into dti-studio? The data is in one large 4D nifti file. >>>>>>>>> I >>>>>>>>> don't see where I can do this, is it not possible? >>>>>>>>> >>>>>>>>> thanks >>>>>>>>> mark >>>>>>>>> _______________________________________________ >>>>>>>>> Mristudio-users mailing list >>>>>>>>> Mristudio-users at mristudio.org >>>>>>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>>>>>> Unsubscribe, send a blank email to: >>>>>>>>> Mristudio-users-unsubscribe at mristudio.org >>>>>>>>> >>>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Mristudio-users mailing list >>>>>>> Mristudio-users at mristudio.org >>>>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>>>> Unsubscribe, send a blank email to: >>>>>>> Mristudio-users-unsubscribe at mristudio.org >>>>>>> >>>>>> >>>>> >>>> >>>> _______________________________________________ >>>> Mristudio-users mailing list >>>> Mristudio-users at mristudio.org >>>> http://lists.mristudio.org/mailman/listinfo/ >>>> Unsubscribe, send a blank email to: >>>> Mristudio-users-unsubscribe at mristudio.org >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> Mristudio-users mailing list >>>> Mristudio-users at mristudio.org >>>> http://lists.mristudio.org/mailman/listinfo/ >>>> Unsubscribe, send a blank email to: >>>> Mristudio-users-unsubscribe at mristudio.org >>>> >>> >>> _______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: >>> Mristudio-users-unsubscribe at mristudio.org >>> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > From mpinsk at gmail.com Wed Dec 16 20:02:49 2009 From: mpinsk at gmail.com (Mark A. Pinsk) Date: Wed, 16 Dec 2009 20:02:49 -0500 Subject: [Mristudio-users] Using processed data In-Reply-To: References: <4B28651A.4020202@puc.cl> <274936.72080.qm@web30701.mail.mud.yahoo.com> <4B29809E.50805@puc.cl> Message-ID: And the original 4D Nifti follow reads as follows, in comparison: fslinfo data.nii data_type FLOAT32 dim1 96 dim2 128 dim3 47 dim4 65 datatype 16 pixdim1 1.0000000000 pixdim2 1.0000000000 pixdim3 1.1000000238 pixdim4 1.0000000000 cal_max 3154.5610 cal_min -1285.1160 file_type NIFTI-1+ On Wed, Dec 16, 2009 at 8:00 PM, Mark A. Pinsk wrote: > A report of my 4D Analyze header reads as follows. Can anyone spot > anything strange? > > fslinfo data.hdr > > data_type > dim1 ? ? ? ? ? 96 > dim2 ? ? ? ? ? 128 > dim3 ? ? ? ? ? 47 > dim4 ? ? ? ? ? 65 > datatype ? ? ? 16 > pixdim1 ? ? ? ?-1.0000000000 > pixdim2 ? ? ? ?1.0000000000 > pixdim3 ? ? ? ?1.1000000238 > pixdim4 ? ? ? ?1.0000000000 > cal_max ? ? ? ?3154.5610 > cal_min ? ? ? ?-1285.1160 > glmax ? ? ? ? ?0 > glmin ? ? ? ? ?0 > origin1 ? ? ? ?51 > origin2 ? ? ? ?66 > origin3 ? ? ? ?9 > file_type ? ? ?ANALYZE-7.5 > > > > On Wed, Dec 16, 2009 at 7:57 PM, Mark A. Pinsk wrote: >> Hi Gonzalo, >> >> Yes, I tried that first after your suggestions yesterday: >> 4D NIFTI to 4D ANALYZE: >> fslchfiletype ANALYZE input.nii.gz >> >> And I get the same error about less than expected number of files, >> even though it's only one img/hdr pair in that folder. >> >> Somebody else next suggested going to 65 3D Analyze files instead of a >> single 4D Analyze file. ?That also did not work. >> >> Sorry this is turning out to be so difficult! ? I wonder where I went wrong.... >> >> >> >> On Wed, Dec 16, 2009 at 7:51 PM, Gonzalo Rojas wrote: >>> Hi Mark: >>> >>> ?I read your e-mail, but why you convert the 4D NIFTI to 3D NIFTI ?... you >>> must convert the 4D NIFTI to 4D ANALYZE... no 3D... you must read the 4D >>> ANLYZE in DTI mapping using RAW format, but you must specify coronal as the >>> "slice orientation"... >>> >>> ?Sincerely, >>> >>> >>> >>> Gonzalo Rojas Costa >>> Department of Radiology >>> Las Condes Clinic >>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >>> Tel: 56-2-2105170 >>> Cel: 56-9-97771785 >>> www.clc.cl >>> >>> >>> El 16-12-2009 21:39, Mark A. Pinsk escribi?: >>>> >>>> No luck. ?Let me outline my steps here: >>>> >>>> 1. I start with a 4D NIFTI file that contains 65 volumes (60 DWI + 5 B0). >>>> The image dimensions are 96x128, 47 slices per volume. >>>> Slice orientation is Coronal. ?FOV is 96x128. ?Pixels are 1x1x1.1. >>>> >>>> 2. I split the 4D NIFTI file into 65 3D NIFTI files using this FSL >>>> command: >>>> fslsplit input.nii.gz >>>> >>>> 3. I convert each of the 65 3D NIFTI files to ANALYZE format: >>>> fslchfiletype ANALYZE vol0000.nii.gz >>>> [..] >>>> fslchfiletype ANALYZE vol0064.nii.gz >>>> >>>> 4. I am able to successfully import the ANALYZE files in MRIView3D by >>>> choosing Analyze format (but no luck with Raw format). >>>> >>>> 5. I have no luck importing the ANALYZE files in DTI Mapping choosing >>>> Raw format. ?I get this message: >>>> "Number of files in this fold is less than expected: >>>> (Img_Slices*Img_Blocks). >>>> >>>> Any suggestions? ?Thanks for all your help! >>>> Mark >>>> >>>> >>>> >>>> >>>> On Wed, Dec 16, 2009 at 1:34 PM, darshan pai ?wrote: >>>>> >>>>> when you say a 4D file I assume that you have a Analyze file with an >>>>> entry on the number of volumes , Is it? . If it is then try to make it a 3D >>>>> file with all the 65 slices added in the z direction and see if it helps.. >>>>> >>>>> Regards >>>>> >>>>> Dp >>>>> >>>>> >>>>> >>>>> ----- Original Message ---- >>>>> From: Mark A. Pinsk >>>>> To: "DTI Studio, ROI Editor, Landmarker >>>>> Questions/Support" >>>>> Sent: Wed, December 16, 2009 12:13:42 AM >>>>> Subject: Re: [Mristudio-users] Using processed data >>>>> >>>>> Also, I should mention that the Analyze file loads just fine using >>>>> "MRI View3D" and "Analyze" file format. >>>>> >>>>> >>>>> On Wed, Dec 16, 2009 at 12:09 AM, Mark A. Pinsk ?wrote: >>>>>> >>>>>> Thanks for your help, I'll do my best to answer them... >>>>>> >>>>>> FYI: these are small volumes from animal scans ( 1 x 1 x 1.1 mm >>>>>> resolution): >>>>>> >>>>>> Image Dimensions: 96 Width, 128 Height, 47 slices >>>>>> Slice Orientation: Axial >>>>>> Slice Sequencing: Inferior-Superior >>>>>> FOV: 96 Width, 128 Height, 1.1 Slice Thickness >>>>>> Pixel Size: 1.000 Width, 1.000 Height >>>>>> Slices to be processed: 0 to 46, All Slices >>>>>> Image Sequence: Gradient By Gradient >>>>>> b_Value: 1000 >>>>>> >>>>>> My gradient table has 65 entries. ?The first 5 entries are B0 images, >>>>>> the remaining 60 are for the 60 directions. ?There is no mean image at >>>>>> the end of my data. ? I can discard 4 of the B0 images, but that does >>>>>> not seem to make a difference on my error message. ?I have several B0 >>>>>> images in accord with recent work that suggests having a ratio of 6:1 >>>>>> diffusion to non-diffusion weighted images (Zhu et al. NeuroImage >>>>>> 2008). >>>>>> >>>>>> >>>>>> >>>>>> On Tue, Dec 15, 2009 at 11:42 PM, Gonzalo Rojas ?wrote: >>>>>>> >>>>>>> Hi Mark: >>>>>>> >>>>>>> ?Many questions: >>>>>>> >>>>>>> i) do you specify correctly the "image slices" quantity in "iamge >>>>>>> dimension" >>>>>>> ?... that value is the quantitry of axial slices in each gradient >>>>>>> direction... >>>>>>> >>>>>>> ii) and the "image width" and "image height" in "image dimension" ?... >>>>>>> did >>>>>>> you checked that values ?... >>>>>>> >>>>>>> ii) in "lice orientation" did you specify "axial" ?.. >>>>>>> >>>>>>> iii) and in "Voxel Size", "Field of View-width" and "Field of >>>>>>> View-Heigth" >>>>>>> did you specifiy the FOV value correctly ?... >>>>>>> >>>>>>> iv) you could check the previos values looking at "Pixel Size-Width" >>>>>>> and >>>>>>> "Pixel Size-Height"... >>>>>>> >>>>>>> v) in "Slices to be processed" it must appears 0-(image slices-1) >>>>>>> >>>>>>> vi) in gradient table you must put the 61 (0-60) directions... in your >>>>>>> 4D >>>>>>> analyze file is included the "mean" of all the 60 directions at the end >>>>>>> of >>>>>>> the file ?... if it is, you must put "100,100,100" as the last gradient >>>>>>> direction to skip that image in the computation... >>>>>>> >>>>>>> vii) in "Image secuence" you must select "Gradient by Gradient" >>>>>>> option... >>>>>>> >>>>>>> viii) in "Raw-BIN Files folder you must specify the IMG file of the >>>>>>> Analyze >>>>>>> pair... >>>>>>> >>>>>>> ix) why you have 5 b0 volumes ?... to compute tractography, you must >>>>>>> have >>>>>>> only one b0 volume... you must put "100,100,100" in "Gradient Table" >>>>>>> for >>>>>>> each of the 4 b0 slices to skipt them... >>>>>>> >>>>>>> ?Sincerely, >>>>>>> >>>>>>> >>>>>>> Gonzalo Rojas Costa >>>>>>> Department of Radiology >>>>>>> Las Condes Clinic >>>>>>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >>>>>>> Tel: 56-2-2105170 >>>>>>> Cel: 56-9-97771785 >>>>>>> www.clc.cl >>>>>>> >>>>>>> El 16-12-2009 1:07, Mark A. Pinsk escribi?: >>>>>>>> >>>>>>>> Thanks ! >>>>>>>> >>>>>>>> I converted by 4D NIFTI file to a 4D ANALYZE file as you suggested. >>>>>>>> >>>>>>>> I attempt to read it in as RAW, but it seems to get stuck... >>>>>>>> >>>>>>>> I specify the file in the Raw-BIN Files Folder field, but I get this >>>>>>>> message: >>>>>>>> "Number of files in this fold is less than expected: >>>>>>>> (Img_Slices*Img_Blocks)." >>>>>>>> >>>>>>>> I only have a single .img/.hdr pair in my folder since it is a 4D file >>>>>>>> (i.e. it contains 65 volumes (5 b0 volumes + 60 directions)). >>>>>>>> >>>>>>>> Sorry, any help would be greatly appreciated. >>>>>>>> Thanks >>>>>>>> Mark >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On Tue, Dec 15, 2009 at 10:29 PM, Gonzalo Rojas >>>>>>>> ?wrote: >>>>>>>>> >>>>>>>>> Hi Mark: >>>>>>>>> >>>>>>>>> ?Yes... you could do all the processing that you mentioned (in FSL), >>>>>>>>> and >>>>>>>>> bring it to dti-studio... the FSL output file format is NIFTI.GZ... >>>>>>>>> you >>>>>>>>> must >>>>>>>>> convert it to ANALYZE 4D, and then you must load that ANALYZE 4D file >>>>>>>>> as >>>>>>>>> a >>>>>>>>> RAW data file format in DTI-STUDIO... >>>>>>>>> >>>>>>>>> ?Sincerely, >>>>>>>>> >>>>>>>>> >>>>>>>>> Gonzalo Rojas Costa >>>>>>>>> Department of Radiology >>>>>>>>> Las Condes Clinic >>>>>>>>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >>>>>>>>> Tel: 56-2-2105170 >>>>>>>>> Cel: 56-9-97771785 >>>>>>>>> www.clc.cl >>>>>>>>> >>>>>>>>> El 15-12-2009 23:37, Mark A. Pinsk escribi?: >>>>>>>>>> >>>>>>>>>> Hi, someone asked this a while ago in the archives but I didn't see >>>>>>>>>> a >>>>>>>>>> reply. ? Can I use data that I've processed in FSL (eddy current >>>>>>>>>> correction, motion correction, and field map-based undistortion) and >>>>>>>>>> bring it into dti-studio? ? The data is in one large 4D nifti file. >>>>>>>>>> ?I >>>>>>>>>> don't see where I can do this, is it not possible? >>>>>>>>>> >>>>>>>>>> thanks >>>>>>>>>> mark >>>>>>>>>> _______________________________________________ >>>>>>>>>> Mristudio-users mailing list >>>>>>>>>> Mristudio-users at mristudio.org >>>>>>>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>>>>>>> Unsubscribe, send a blank email to: >>>>>>>>>> Mristudio-users-unsubscribe at mristudio.org >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Mristudio-users mailing list >>>>>>>> Mristudio-users at mristudio.org >>>>>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>>>>> Unsubscribe, send a blank email to: >>>>>>>> Mristudio-users-unsubscribe at mristudio.org >>>>>>>> >>>>>>> >>>>>> >>>>> >>>>> _______________________________________________ >>>>> Mristudio-users mailing list >>>>> Mristudio-users at mristudio.org >>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>> Unsubscribe, send a blank email to: >>>>> Mristudio-users-unsubscribe at mristudio.org >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Mristudio-users mailing list >>>>> Mristudio-users at mristudio.org >>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>> Unsubscribe, send a blank email to: >>>>> Mristudio-users-unsubscribe at mristudio.org >>>>> >>>> >>>> _______________________________________________ >>>> Mristudio-users mailing list >>>> Mristudio-users at mristudio.org >>>> http://lists.mristudio.org/mailman/listinfo/ >>>> Unsubscribe, send a blank email to: >>>> Mristudio-users-unsubscribe at mristudio.org >>>> >>> >> > From susumu at mri.jhu.edu Wed Dec 16 20:46:40 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 16 Dec 2009 20:46:40 -0500 Subject: [Mristudio-users] Using processed data In-Reply-To: References: <4B28542F.5000803@puc.cl> <4B28651A.4020202@puc.cl> <274936.72080.qm@web30701.mail.mud.yahoo.com> Message-ID: Hi Mark, Please try Philips REC format. This is a 4D raw format with integer. For both "raw" and "Philips REC", DtiStudio expect you to have 4D raw (no-header) file, not a bunch of 3D files. In your case, you need a single raw file that contains all 65 volume data (65 x 96 x 128 x 47) in one file. For this conversion, you can read 4D Nifty or 4D analyze (depending on the version of DtiStudio) by MriView3D and save all the images at once as a "raw" format. Then, the images are ready for DtiMapping. In DtiMapping, as I mentioned, open it as Philips REC. In the opening window, specify; 96x128x47 Then you should get "65" as the number of the 3D images correctly calculated from the file size at the left bottom of the window. Also choose gradient-by-gradient for the order of the file. If you have a correct table with 65 lines, you should not get the error message. If you have the 4D analyze file, the *.img file of the Analyze format can also be directly read as "Philips REC". However, you have to be careful because if the Analyze is in Neurology convention (default setup) and read the *.img as "Philips REC", the images may be inverted because DtiStudio uses Radiology convention. I hope it helps. Susumu On Wed, Dec 16, 2009 at 7:39 PM, Mark A. Pinsk wrote: > No luck. Let me outline my steps here: > > 1. I start with a 4D NIFTI file that contains 65 volumes (60 DWI + 5 B0). > The image dimensions are 96x128, 47 slices per volume. > Slice orientation is Coronal. FOV is 96x128. Pixels are 1x1x1.1. > > 2. I split the 4D NIFTI file into 65 3D NIFTI files using this FSL command: > fslsplit input.nii.gz > > 3. I convert each of the 65 3D NIFTI files to ANALYZE format: > fslchfiletype ANALYZE vol0000.nii.gz > [..] > fslchfiletype ANALYZE vol0064.nii.gz > > 4. I am able to successfully import the ANALYZE files in MRIView3D by > choosing Analyze format (but no luck with Raw format). > > 5. I have no luck importing the ANALYZE files in DTI Mapping choosing > Raw format. I get this message: > "Number of files in this fold is less than expected: > (Img_Slices*Img_Blocks). > > Any suggestions? Thanks for all your help! > Mark > > > > > On Wed, Dec 16, 2009 at 1:34 PM, darshan pai wrote: > > when you say a 4D file I assume that you have a Analyze file with an > entry on the number of volumes , Is it? . If it is then try to make it a 3D > file with all the 65 slices added in the z direction and see if it helps.. > > > > Regards > > > > Dp > > > > > > > > ----- Original Message ---- > > From: Mark A. Pinsk > > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" < > mristudio-users at mristudio.org> > > Sent: Wed, December 16, 2009 12:13:42 AM > > Subject: Re: [Mristudio-users] Using processed data > > > > Also, I should mention that the Analyze file loads just fine using > > "MRI View3D" and "Analyze" file format. > > > > > > On Wed, Dec 16, 2009 at 12:09 AM, Mark A. Pinsk > wrote: > >> Thanks for your help, I'll do my best to answer them... > >> > >> FYI: these are small volumes from animal scans ( 1 x 1 x 1.1 mm > resolution): > >> > >> Image Dimensions: 96 Width, 128 Height, 47 slices > >> Slice Orientation: Axial > >> Slice Sequencing: Inferior-Superior > >> FOV: 96 Width, 128 Height, 1.1 Slice Thickness > >> Pixel Size: 1.000 Width, 1.000 Height > >> Slices to be processed: 0 to 46, All Slices > >> Image Sequence: Gradient By Gradient > >> b_Value: 1000 > >> > >> My gradient table has 65 entries. The first 5 entries are B0 images, > >> the remaining 60 are for the 60 directions. There is no mean image at > >> the end of my data. I can discard 4 of the B0 images, but that does > >> not seem to make a difference on my error message. I have several B0 > >> images in accord with recent work that suggests having a ratio of 6:1 > >> diffusion to non-diffusion weighted images (Zhu et al. NeuroImage > >> 2008). > >> > >> > >> > >> On Tue, Dec 15, 2009 at 11:42 PM, Gonzalo Rojas wrote: > >>> Hi Mark: > >>> > >>> Many questions: > >>> > >>> i) do you specify correctly the "image slices" quantity in "iamge > dimension" > >>> ?... that value is the quantitry of axial slices in each gradient > >>> direction... > >>> > >>> ii) and the "image width" and "image height" in "image dimension" ?... > did > >>> you checked that values ?... > >>> > >>> ii) in "lice orientation" did you specify "axial" ?.. > >>> > >>> iii) and in "Voxel Size", "Field of View-width" and "Field of > View-Heigth" > >>> did you specifiy the FOV value correctly ?... > >>> > >>> iv) you could check the previos values looking at "Pixel Size-Width" > and > >>> "Pixel Size-Height"... > >>> > >>> v) in "Slices to be processed" it must appears 0-(image slices-1) > >>> > >>> vi) in gradient table you must put the 61 (0-60) directions... in your > 4D > >>> analyze file is included the "mean" of all the 60 directions at the end > of > >>> the file ?... if it is, you must put "100,100,100" as the last gradient > >>> direction to skip that image in the computation... > >>> > >>> vii) in "Image secuence" you must select "Gradient by Gradient" > option... > >>> > >>> viii) in "Raw-BIN Files folder you must specify the IMG file of the > Analyze > >>> pair... > >>> > >>> ix) why you have 5 b0 volumes ?... to compute tractography, you must > have > >>> only one b0 volume... you must put "100,100,100" in "Gradient Table" > for > >>> each of the 4 b0 slices to skipt them... > >>> > >>> Sincerely, > >>> > >>> > >>> Gonzalo Rojas Costa > >>> Department of Radiology > >>> Las Condes Clinic > >>> Lo Fontecilla 441, Las Condes, Santiago, Chile. > >>> Tel: 56-2-2105170 > >>> Cel: 56-9-97771785 > >>> www.clc.cl > >>> > >>> El 16-12-2009 1:07, Mark A. Pinsk escribi?: > >>>> > >>>> Thanks ! > >>>> > >>>> I converted by 4D NIFTI file to a 4D ANALYZE file as you suggested. > >>>> > >>>> I attempt to read it in as RAW, but it seems to get stuck... > >>>> > >>>> I specify the file in the Raw-BIN Files Folder field, but I get this > >>>> message: > >>>> "Number of files in this fold is less than expected: > >>>> (Img_Slices*Img_Blocks)." > >>>> > >>>> I only have a single .img/.hdr pair in my folder since it is a 4D file > >>>> (i.e. it contains 65 volumes (5 b0 volumes + 60 directions)). > >>>> > >>>> Sorry, any help would be greatly appreciated. > >>>> Thanks > >>>> Mark > >>>> > >>>> > >>>> > >>>> > >>>> On Tue, Dec 15, 2009 at 10:29 PM, Gonzalo Rojas > wrote: > >>>>> > >>>>> Hi Mark: > >>>>> > >>>>> Yes... you could do all the processing that you mentioned (in FSL), > and > >>>>> bring it to dti-studio... the FSL output file format is NIFTI.GZ... > you > >>>>> must > >>>>> convert it to ANALYZE 4D, and then you must load that ANALYZE 4D file > as > >>>>> a > >>>>> RAW data file format in DTI-STUDIO... > >>>>> > >>>>> Sincerely, > >>>>> > >>>>> > >>>>> Gonzalo Rojas Costa > >>>>> Department of Radiology > >>>>> Las Condes Clinic > >>>>> Lo Fontecilla 441, Las Condes, Santiago, Chile. > >>>>> Tel: 56-2-2105170 > >>>>> Cel: 56-9-97771785 > >>>>> www.clc.cl > >>>>> > >>>>> El 15-12-2009 23:37, Mark A. Pinsk escribi?: > >>>>>> > >>>>>> Hi, someone asked this a while ago in the archives but I didn't see > a > >>>>>> reply. Can I use data that I've processed in FSL (eddy current > >>>>>> correction, motion correction, and field map-based undistortion) and > >>>>>> bring it into dti-studio? The data is in one large 4D nifti file. > I > >>>>>> don't see where I can do this, is it not possible? > >>>>>> > >>>>>> thanks > >>>>>> mark > >>>>>> _______________________________________________ > >>>>>> Mristudio-users mailing list > >>>>>> Mristudio-users at mristudio.org > >>>>>> http://lists.mristudio.org/mailman/listinfo/ > >>>>>> Unsubscribe, send a blank email to: > >>>>>> Mristudio-users-unsubscribe at mristudio.org > >>>>>> > >>>>> > >>>> > >>>> _______________________________________________ > >>>> Mristudio-users mailing list > >>>> Mristudio-users at mristudio.org > >>>> http://lists.mristudio.org/mailman/listinfo/ > >>>> Unsubscribe, send a blank email to: > >>>> Mristudio-users-unsubscribe at mristudio.org > >>>> > >>> > >> > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > http://lists.mristudio.org/mailman/listinfo/ > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > > > > > > > > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > http://lists.mristudio.org/mailman/listinfo/ > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091216/985ac953/attachment-0001.html From grojasy at puc.cl Wed Dec 16 21:39:44 2009 From: grojasy at puc.cl (Gonzalo Rojas) Date: Wed, 16 Dec 2009 23:39:44 -0300 Subject: [Mristudio-users] Using processed data In-Reply-To: References: <4B28542F.5000803@puc.cl> <4B28651A.4020202@puc.cl> <274936.72080.qm@web30701.mail.mud.yahoo.com> <4B29809E.50805@puc.cl> Message-ID: <4B2999F0.8030804@puc.cl> Hi Mark: pixdim = -1 is strange... Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl El 16-12-2009 22:00, Mark A. Pinsk escribi?: > A report of my 4D Analyze header reads as follows. Can anyone spot > anything strange? > > fslinfo data.hdr > > data_type > dim1 96 > dim2 128 > dim3 47 > dim4 65 > datatype 16 > pixdim1 -1.0000000000 > pixdim2 1.0000000000 > pixdim3 1.1000000238 > pixdim4 1.0000000000 > cal_max 3154.5610 > cal_min -1285.1160 > glmax 0 > glmin 0 > origin1 51 > origin2 66 > origin3 9 > file_type ANALYZE-7.5 > > > > On Wed, Dec 16, 2009 at 7:57 PM, Mark A. Pinsk wrote: >> Hi Gonzalo, >> >> Yes, I tried that first after your suggestions yesterday: >> 4D NIFTI to 4D ANALYZE: >> fslchfiletype ANALYZE input.nii.gz >> >> And I get the same error about less than expected number of files, >> even though it's only one img/hdr pair in that folder. >> >> Somebody else next suggested going to 65 3D Analyze files instead of a >> single 4D Analyze file. That also did not work. >> >> Sorry this is turning out to be so difficult! I wonder where I went wrong.... >> >> >> >> On Wed, Dec 16, 2009 at 7:51 PM, Gonzalo Rojas wrote: >>> Hi Mark: >>> >>> I read your e-mail, but why you convert the 4D NIFTI to 3D NIFTI ?... you >>> must convert the 4D NIFTI to 4D ANALYZE... no 3D... you must read the 4D >>> ANLYZE in DTI mapping using RAW format, but you must specify coronal as the >>> "slice orientation"... >>> >>> Sincerely, >>> >>> >>> >>> Gonzalo Rojas Costa >>> Department of Radiology >>> Las Condes Clinic >>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >>> Tel: 56-2-2105170 >>> Cel: 56-9-97771785 >>> www.clc.cl >>> >>> >>> El 16-12-2009 21:39, Mark A. Pinsk escribi?: >>>> >>>> No luck. Let me outline my steps here: >>>> >>>> 1. I start with a 4D NIFTI file that contains 65 volumes (60 DWI + 5 B0). >>>> The image dimensions are 96x128, 47 slices per volume. >>>> Slice orientation is Coronal. FOV is 96x128. Pixels are 1x1x1.1. >>>> >>>> 2. I split the 4D NIFTI file into 65 3D NIFTI files using this FSL >>>> command: >>>> fslsplit input.nii.gz >>>> >>>> 3. I convert each of the 65 3D NIFTI files to ANALYZE format: >>>> fslchfiletype ANALYZE vol0000.nii.gz >>>> [..] >>>> fslchfiletype ANALYZE vol0064.nii.gz >>>> >>>> 4. I am able to successfully import the ANALYZE files in MRIView3D by >>>> choosing Analyze format (but no luck with Raw format). >>>> >>>> 5. I have no luck importing the ANALYZE files in DTI Mapping choosing >>>> Raw format. I get this message: >>>> "Number of files in this fold is less than expected: >>>> (Img_Slices*Img_Blocks). >>>> >>>> Any suggestions? Thanks for all your help! >>>> Mark >>>> >>>> >>>> >>>> >>>> On Wed, Dec 16, 2009 at 1:34 PM, darshan pai wrote: >>>>> >>>>> when you say a 4D file I assume that you have a Analyze file with an >>>>> entry on the number of volumes , Is it? . If it is then try to make it a 3D >>>>> file with all the 65 slices added in the z direction and see if it helps.. >>>>> >>>>> Regards >>>>> >>>>> Dp >>>>> >>>>> >>>>> >>>>> ----- Original Message ---- >>>>> From: Mark A. Pinsk >>>>> To: "DTI Studio, ROI Editor, Landmarker >>>>> Questions/Support" >>>>> Sent: Wed, December 16, 2009 12:13:42 AM >>>>> Subject: Re: [Mristudio-users] Using processed data >>>>> >>>>> Also, I should mention that the Analyze file loads just fine using >>>>> "MRI View3D" and "Analyze" file format. >>>>> >>>>> >>>>> On Wed, Dec 16, 2009 at 12:09 AM, Mark A. Pinsk wrote: >>>>>> >>>>>> Thanks for your help, I'll do my best to answer them... >>>>>> >>>>>> FYI: these are small volumes from animal scans ( 1 x 1 x 1.1 mm >>>>>> resolution): >>>>>> >>>>>> Image Dimensions: 96 Width, 128 Height, 47 slices >>>>>> Slice Orientation: Axial >>>>>> Slice Sequencing: Inferior-Superior >>>>>> FOV: 96 Width, 128 Height, 1.1 Slice Thickness >>>>>> Pixel Size: 1.000 Width, 1.000 Height >>>>>> Slices to be processed: 0 to 46, All Slices >>>>>> Image Sequence: Gradient By Gradient >>>>>> b_Value: 1000 >>>>>> >>>>>> My gradient table has 65 entries. The first 5 entries are B0 images, >>>>>> the remaining 60 are for the 60 directions. There is no mean image at >>>>>> the end of my data. I can discard 4 of the B0 images, but that does >>>>>> not seem to make a difference on my error message. I have several B0 >>>>>> images in accord with recent work that suggests having a ratio of 6:1 >>>>>> diffusion to non-diffusion weighted images (Zhu et al. NeuroImage >>>>>> 2008). >>>>>> >>>>>> >>>>>> >>>>>> On Tue, Dec 15, 2009 at 11:42 PM, Gonzalo Rojas wrote: >>>>>>> >>>>>>> Hi Mark: >>>>>>> >>>>>>> Many questions: >>>>>>> >>>>>>> i) do you specify correctly the "image slices" quantity in "iamge >>>>>>> dimension" >>>>>>> ?... that value is the quantitry of axial slices in each gradient >>>>>>> direction... >>>>>>> >>>>>>> ii) and the "image width" and "image height" in "image dimension" ?... >>>>>>> did >>>>>>> you checked that values ?... >>>>>>> >>>>>>> ii) in "lice orientation" did you specify "axial" ?.. >>>>>>> >>>>>>> iii) and in "Voxel Size", "Field of View-width" and "Field of >>>>>>> View-Heigth" >>>>>>> did you specifiy the FOV value correctly ?... >>>>>>> >>>>>>> iv) you could check the previos values looking at "Pixel Size-Width" >>>>>>> and >>>>>>> "Pixel Size-Height"... >>>>>>> >>>>>>> v) in "Slices to be processed" it must appears 0-(image slices-1) >>>>>>> >>>>>>> vi) in gradient table you must put the 61 (0-60) directions... in your >>>>>>> 4D >>>>>>> analyze file is included the "mean" of all the 60 directions at the end >>>>>>> of >>>>>>> the file ?... if it is, you must put "100,100,100" as the last gradient >>>>>>> direction to skip that image in the computation... >>>>>>> >>>>>>> vii) in "Image secuence" you must select "Gradient by Gradient" >>>>>>> option... >>>>>>> >>>>>>> viii) in "Raw-BIN Files folder you must specify the IMG file of the >>>>>>> Analyze >>>>>>> pair... >>>>>>> >>>>>>> ix) why you have 5 b0 volumes ?... to compute tractography, you must >>>>>>> have >>>>>>> only one b0 volume... you must put "100,100,100" in "Gradient Table" >>>>>>> for >>>>>>> each of the 4 b0 slices to skipt them... >>>>>>> >>>>>>> Sincerely, >>>>>>> >>>>>>> >>>>>>> Gonzalo Rojas Costa >>>>>>> Department of Radiology >>>>>>> Las Condes Clinic >>>>>>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >>>>>>> Tel: 56-2-2105170 >>>>>>> Cel: 56-9-97771785 >>>>>>> www.clc.cl >>>>>>> >>>>>>> El 16-12-2009 1:07, Mark A. Pinsk escribi?: >>>>>>>> >>>>>>>> Thanks ! >>>>>>>> >>>>>>>> I converted by 4D NIFTI file to a 4D ANALYZE file as you suggested. >>>>>>>> >>>>>>>> I attempt to read it in as RAW, but it seems to get stuck... >>>>>>>> >>>>>>>> I specify the file in the Raw-BIN Files Folder field, but I get this >>>>>>>> message: >>>>>>>> "Number of files in this fold is less than expected: >>>>>>>> (Img_Slices*Img_Blocks)." >>>>>>>> >>>>>>>> I only have a single .img/.hdr pair in my folder since it is a 4D file >>>>>>>> (i.e. it contains 65 volumes (5 b0 volumes + 60 directions)). >>>>>>>> >>>>>>>> Sorry, any help would be greatly appreciated. >>>>>>>> Thanks >>>>>>>> Mark >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On Tue, Dec 15, 2009 at 10:29 PM, Gonzalo Rojas >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> Hi Mark: >>>>>>>>> >>>>>>>>> Yes... you could do all the processing that you mentioned (in FSL), >>>>>>>>> and >>>>>>>>> bring it to dti-studio... the FSL output file format is NIFTI.GZ... >>>>>>>>> you >>>>>>>>> must >>>>>>>>> convert it to ANALYZE 4D, and then you must load that ANALYZE 4D file >>>>>>>>> as >>>>>>>>> a >>>>>>>>> RAW data file format in DTI-STUDIO... >>>>>>>>> >>>>>>>>> Sincerely, >>>>>>>>> >>>>>>>>> >>>>>>>>> Gonzalo Rojas Costa >>>>>>>>> Department of Radiology >>>>>>>>> Las Condes Clinic >>>>>>>>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >>>>>>>>> Tel: 56-2-2105170 >>>>>>>>> Cel: 56-9-97771785 >>>>>>>>> www.clc.cl >>>>>>>>> >>>>>>>>> El 15-12-2009 23:37, Mark A. Pinsk escribi?: >>>>>>>>>> >>>>>>>>>> Hi, someone asked this a while ago in the archives but I didn't see >>>>>>>>>> a >>>>>>>>>> reply. Can I use data that I've processed in FSL (eddy current >>>>>>>>>> correction, motion correction, and field map-based undistortion) and >>>>>>>>>> bring it into dti-studio? The data is in one large 4D nifti file. >>>>>>>>>> I >>>>>>>>>> don't see where I can do this, is it not possible? >>>>>>>>>> >>>>>>>>>> thanks >>>>>>>>>> mark >>>>>>>>>> _______________________________________________ >>>>>>>>>> Mristudio-users mailing list >>>>>>>>>> Mristudio-users at mristudio.org >>>>>>>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>>>>>>> Unsubscribe, send a blank email to: >>>>>>>>>> Mristudio-users-unsubscribe at mristudio.org >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Mristudio-users mailing list >>>>>>>> Mristudio-users at mristudio.org >>>>>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>>>>> Unsubscribe, send a blank email to: >>>>>>>> Mristudio-users-unsubscribe at mristudio.org >>>>>>>> >>>>>>> >>>>>> >>>>> >>>>> _______________________________________________ >>>>> Mristudio-users mailing list >>>>> Mristudio-users at mristudio.org >>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>> Unsubscribe, send a blank email to: >>>>> Mristudio-users-unsubscribe at mristudio.org >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Mristudio-users mailing list >>>>> Mristudio-users at mristudio.org >>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>> Unsubscribe, send a blank email to: >>>>> Mristudio-users-unsubscribe at mristudio.org >>>>> >>>> >>>> _______________________________________________ >>>> Mristudio-users mailing list >>>> Mristudio-users at mristudio.org >>>> http://lists.mristudio.org/mailman/listinfo/ >>>> Unsubscribe, send a blank email to: >>>> Mristudio-users-unsubscribe at mristudio.org >>>> >>> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > From grojasy at puc.cl Wed Dec 16 21:46:46 2009 From: grojasy at puc.cl (Gonzalo Rojas) Date: Wed, 16 Dec 2009 23:46:46 -0300 Subject: [Mristudio-users] Using processed data In-Reply-To: References: <4B28651A.4020202@puc.cl> <274936.72080.qm@web30701.mail.mud.yahoo.com> <4B29809E.50805@puc.cl> Message-ID: <4B299B96.6000301@puc.cl> Hi Mark: Are you sure that the Pixel Size is 1 mm in your DWI images ?... You entered that value in DTI-Studio, and you have that values in the Analyze and NIFTI files, but it is a uncomon pixel size for DWI... Sincerely, Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl El 16-12-2009 22:02, Mark A. Pinsk escribi?: > And the original 4D Nifti follow reads as follows, in comparison: > > fslinfo data.nii > > data_type FLOAT32 > dim1 96 > dim2 128 > dim3 47 > dim4 65 > datatype 16 > pixdim1 1.0000000000 > pixdim2 1.0000000000 > pixdim3 1.1000000238 > pixdim4 1.0000000000 > cal_max 3154.5610 > cal_min -1285.1160 > file_type NIFTI-1+ From mpinsk at gmail.com Wed Dec 16 22:07:58 2009 From: mpinsk at gmail.com (Mark A. Pinsk) Date: Wed, 16 Dec 2009 22:07:58 -0500 Subject: [Mristudio-users] Using processed data In-Reply-To: <4B299B96.6000301@puc.cl> References: <274936.72080.qm@web30701.mail.mud.yahoo.com> <4B29809E.50805@puc.cl> <4B299B96.6000301@puc.cl> Message-ID: Yes, these are small animal brains so I am scanning at high resolution (1x1x1.1). The change to -1 in one of the dimensions is indeed strange, as you noted. I will try going to rec format as suggested by Susumu in a recent reply, and post my outcome. On Wed, Dec 16, 2009 at 9:46 PM, Gonzalo Rojas wrote: > Hi Mark: > > ?Are you sure that the Pixel Size is 1 mm in your DWI images ?... ?You > entered that value in DTI-Studio, and you have that values in the Analyze > and NIFTI files, but it is a uncomon pixel size for DWI... > > ?Sincerely, > > Gonzalo Rojas Costa > Department of Radiology > Las Condes Clinic > Lo Fontecilla 441, Las Condes, Santiago, Chile. > Tel: 56-2-2105170 > Cel: 56-9-97771785 > www.clc.cl > > El 16-12-2009 22:02, Mark A. Pinsk escribi?: >> >> And the original 4D Nifti follow reads as follows, in comparison: >> >> fslinfo data.nii >> >> data_type ? ? ?FLOAT32 >> dim1 ? ? ? ? ? 96 >> dim2 ? ? ? ? ? 128 >> dim3 ? ? ? ? ? 47 >> dim4 ? ? ? ? ? 65 >> datatype ? ? ? 16 >> pixdim1 ? ? ? ?1.0000000000 >> pixdim2 ? ? ? ?1.0000000000 >> pixdim3 ? ? ? ?1.1000000238 >> pixdim4 ? ? ? ?1.0000000000 >> cal_max ? ? ? ?3154.5610 >> cal_min ? ? ? ?-1285.1160 >> file_type ? ? ?NIFTI-1+ > From grojasy at puc.cl Wed Dec 16 22:15:58 2009 From: grojasy at puc.cl (Gonzalo Rojas) Date: Thu, 17 Dec 2009 00:15:58 -0300 Subject: [Mristudio-users] Using processed data In-Reply-To: References: <274936.72080.qm@web30701.mail.mud.yahoo.com> <4B29809E.50805@puc.cl> <4B299B96.6000301@puc.cl> Message-ID: <4B29A26E.3090705@puc.cl> Hi Mark: Yes... you could use the instructions of Susumu... I always used REC format to load the RAW part of Analyze images, but which is the difference in DTI-Studio betwen the REC load option and RAW load option (question to Susumu) ?... Sincerely, Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl El 17-12-2009 0:07, Mark A. Pinsk escribi?: > Yes, these are small animal brains so I am scanning at high resolution > (1x1x1.1). > > The change to -1 in one of the dimensions is indeed strange, as you noted. > > I will try going to rec format as suggested by Susumu in a recent > reply, and post my outcome. > > > > On Wed, Dec 16, 2009 at 9:46 PM, Gonzalo Rojas wrote: >> Hi Mark: >> >> Are you sure that the Pixel Size is 1 mm in your DWI images ?... You >> entered that value in DTI-Studio, and you have that values in the Analyze >> and NIFTI files, but it is a uncomon pixel size for DWI... >> >> Sincerely, >> >> Gonzalo Rojas Costa >> Department of Radiology >> Las Condes Clinic >> Lo Fontecilla 441, Las Condes, Santiago, Chile. >> Tel: 56-2-2105170 >> Cel: 56-9-97771785 >> www.clc.cl >> >> El 16-12-2009 22:02, Mark A. Pinsk escribi?: >>> >>> And the original 4D Nifti follow reads as follows, in comparison: >>> >>> fslinfo data.nii >>> >>> data_type FLOAT32 >>> dim1 96 >>> dim2 128 >>> dim3 47 >>> dim4 65 >>> datatype 16 >>> pixdim1 1.0000000000 >>> pixdim2 1.0000000000 >>> pixdim3 1.1000000238 >>> pixdim4 1.0000000000 >>> cal_max 3154.5610 >>> cal_min -1285.1160 >>> file_type NIFTI-1+ >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > From gjmuro at optonline.net Wed Dec 16 22:31:01 2009 From: gjmuro at optonline.net (gjmuro at optonline.net) Date: Thu, 17 Dec 2009 03:31:01 +0000 Subject: [Mristudio-users] Using processed data In-Reply-To: <4B2999F0.8030804@puc.cl> References: <4B28542F.5000803@puc.cl> <4B28651A.4020202@puc.cl> <274936.72080.qm@web30701.mail.mud.yahoo.com> <4B29809E.50805@puc.cl> <4B2999F0.8030804@puc.cl> Message-ID: <1257706524-1261020649-cardhu_decombobulator_blackberry.rim.net-361651625-@bda114.bisx.prod.on.blackberry> Sent from my Verizon Wireless BlackBerry -----Original Message----- From: Gonzalo Rojas Date: Wed, 16 Dec 2009 23:39:44 To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] Using processed data Hi Mark: pixdim = -1 is strange... Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl El 16-12-2009 22:00, Mark A. Pinsk escribi?: > A report of my 4D Analyze header reads as follows. Can anyone spot > anything strange? > > fslinfo data.hdr > > data_type > dim1 96 > dim2 128 > dim3 47 > dim4 65 > datatype 16 > pixdim1 -1.0000000000 > pixdim2 1.0000000000 > pixdim3 1.1000000238 > pixdim4 1.0000000000 > cal_max 3154.5610 > cal_min -1285.1160 > glmax 0 > glmin 0 > origin1 51 > origin2 66 > origin3 9 > file_type ANALYZE-7.5 > > > > On Wed, Dec 16, 2009 at 7:57 PM, Mark A. Pinsk wrote: >> Hi Gonzalo, >> >> Yes, I tried that first after your suggestions yesterday: >> 4D NIFTI to 4D ANALYZE: >> fslchfiletype ANALYZE input.nii.gz >> >> And I get the same error about less than expected number of files, >> even though it's only one img/hdr pair in that folder. >> >> Somebody else next suggested going to 65 3D Analyze files instead of a >> single 4D Analyze file. That also did not work. >> >> Sorry this is turning out to be so difficult! I wonder where I went wrong.... >> >> >> >> On Wed, Dec 16, 2009 at 7:51 PM, Gonzalo Rojas wrote: >>> Hi Mark: >>> >>> I read your e-mail, but why you convert the 4D NIFTI to 3D NIFTI ?... you >>> must convert the 4D NIFTI to 4D ANALYZE... no 3D... you must read the 4D >>> ANLYZE in DTI mapping using RAW format, but you must specify coronal as the >>> "slice orientation"... >>> >>> Sincerely, >>> >>> >>> >>> Gonzalo Rojas Costa >>> Department of Radiology >>> Las Condes Clinic >>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >>> Tel: 56-2-2105170 >>> Cel: 56-9-97771785 >>> www.clc.cl >>> >>> >>> El 16-12-2009 21:39, Mark A. Pinsk escribi?: >>>> >>>> No luck. Let me outline my steps here: >>>> >>>> 1. I start with a 4D NIFTI file that contains 65 volumes (60 DWI + 5 B0). >>>> The image dimensions are 96x128, 47 slices per volume. >>>> Slice orientation is Coronal. FOV is 96x128. Pixels are 1x1x1.1. >>>> >>>> 2. I split the 4D NIFTI file into 65 3D NIFTI files using this FSL >>>> command: >>>> fslsplit input.nii.gz >>>> >>>> 3. I convert each of the 65 3D NIFTI files to ANALYZE format: >>>> fslchfiletype ANALYZE vol0000.nii.gz >>>> [..] >>>> fslchfiletype ANALYZE vol0064.nii.gz >>>> >>>> 4. I am able to successfully import the ANALYZE files in MRIView3D by >>>> choosing Analyze format (but no luck with Raw format). >>>> >>>> 5. I have no luck importing the ANALYZE files in DTI Mapping choosing >>>> Raw format. I get this message: >>>> "Number of files in this fold is less than expected: >>>> (Img_Slices*Img_Blocks). >>>> >>>> Any suggestions? Thanks for all your help! >>>> Mark >>>> >>>> >>>> >>>> >>>> On Wed, Dec 16, 2009 at 1:34 PM, darshan pai wrote: >>>>> >>>>> when you say a 4D file I assume that you have a Analyze file with an >>>>> entry on the number of volumes , Is it? . If it is then try to make it a 3D >>>>> file with all the 65 slices added in the z direction and see if it helps.. >>>>> >>>>> Regards >>>>> >>>>> Dp >>>>> >>>>> >>>>> >>>>> ----- Original Message ---- >>>>> From: Mark A. Pinsk >>>>> To: "DTI Studio, ROI Editor, Landmarker >>>>> Questions/Support" >>>>> Sent: Wed, December 16, 2009 12:13:42 AM >>>>> Subject: Re: [Mristudio-users] Using processed data >>>>> >>>>> Also, I should mention that the Analyze file loads just fine using >>>>> "MRI View3D" and "Analyze" file format. >>>>> >>>>> >>>>> On Wed, Dec 16, 2009 at 12:09 AM, Mark A. Pinsk wrote: >>>>>> >>>>>> Thanks for your help, I'll do my best to answer them... >>>>>> >>>>>> FYI: these are small volumes from animal scans ( 1 x 1 x 1.1 mm >>>>>> resolution): >>>>>> >>>>>> Image Dimensions: 96 Width, 128 Height, 47 slices >>>>>> Slice Orientation: Axial >>>>>> Slice Sequencing: Inferior-Superior >>>>>> FOV: 96 Width, 128 Height, 1.1 Slice Thickness >>>>>> Pixel Size: 1.000 Width, 1.000 Height >>>>>> Slices to be processed: 0 to 46, All Slices >>>>>> Image Sequence: Gradient By Gradient >>>>>> b_Value: 1000 >>>>>> >>>>>> My gradient table has 65 entries. The first 5 entries are B0 images, >>>>>> the remaining 60 are for the 60 directions. There is no mean image at >>>>>> the end of my data. I can discard 4 of the B0 images, but that does >>>>>> not seem to make a difference on my error message. I have several B0 >>>>>> images in accord with recent work that suggests having a ratio of 6:1 >>>>>> diffusion to non-diffusion weighted images (Zhu et al. NeuroImage >>>>>> 2008). >>>>>> >>>>>> >>>>>> >>>>>> On Tue, Dec 15, 2009 at 11:42 PM, Gonzalo Rojas wrote: >>>>>>> >>>>>>> Hi Mark: >>>>>>> >>>>>>> Many questions: >>>>>>> >>>>>>> i) do you specify correctly the "image slices" quantity in "iamge >>>>>>> dimension" >>>>>>> ?... that value is the quantitry of axial slices in each gradient >>>>>>> direction... >>>>>>> >>>>>>> ii) and the "image width" and "image height" in "image dimension" ?... >>>>>>> did >>>>>>> you checked that values ?... >>>>>>> >>>>>>> ii) in "lice orientation" did you specify "axial" ?.. >>>>>>> >>>>>>> iii) and in "Voxel Size", "Field of View-width" and "Field of >>>>>>> View-Heigth" >>>>>>> did you specifiy the FOV value correctly ?... >>>>>>> >>>>>>> iv) you could check the previos values looking at "Pixel Size-Width" >>>>>>> and >>>>>>> "Pixel Size-Height"... >>>>>>> >>>>>>> v) in "Slices to be processed" it must appears 0-(image slices-1) >>>>>>> >>>>>>> vi) in gradient table you must put the 61 (0-60) directions... in your >>>>>>> 4D >>>>>>> analyze file is included the "mean" of all the 60 directions at the end >>>>>>> of >>>>>>> the file ?... if it is, you must put "100,100,100" as the last gradient >>>>>>> direction to skip that image in the computation... >>>>>>> >>>>>>> vii) in "Image secuence" you must select "Gradient by Gradient" >>>>>>> option... >>>>>>> >>>>>>> viii) in "Raw-BIN Files folder you must specify the IMG file of the >>>>>>> Analyze >>>>>>> pair... >>>>>>> >>>>>>> ix) why you have 5 b0 volumes ?... to compute tractography, you must >>>>>>> have >>>>>>> only one b0 volume... you must put "100,100,100" in "Gradient Table" >>>>>>> for >>>>>>> each of the 4 b0 slices to skipt them... >>>>>>> >>>>>>> Sincerely, >>>>>>> >>>>>>> >>>>>>> Gonzalo Rojas Costa >>>>>>> Department of Radiology >>>>>>> Las Condes Clinic >>>>>>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >>>>>>> Tel: 56-2-2105170 >>>>>>> Cel: 56-9-97771785 >>>>>>> www.clc.cl >>>>>>> >>>>>>> El 16-12-2009 1:07, Mark A. Pinsk escribi?: >>>>>>>> >>>>>>>> Thanks ! >>>>>>>> >>>>>>>> I converted by 4D NIFTI file to a 4D ANALYZE file as you suggested. >>>>>>>> >>>>>>>> I attempt to read it in as RAW, but it seems to get stuck... >>>>>>>> >>>>>>>> I specify the file in the Raw-BIN Files Folder field, but I get this >>>>>>>> message: >>>>>>>> "Number of files in this fold is less than expected: >>>>>>>> (Img_Slices*Img_Blocks)." >>>>>>>> >>>>>>>> I only have a single .img/.hdr pair in my folder since it is a 4D file >>>>>>>> (i.e. it contains 65 volumes (5 b0 volumes + 60 directions)). >>>>>>>> >>>>>>>> Sorry, any help would be greatly appreciated. >>>>>>>> Thanks >>>>>>>> Mark >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On Tue, Dec 15, 2009 at 10:29 PM, Gonzalo Rojas >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> Hi Mark: >>>>>>>>> >>>>>>>>> Yes... you could do all the processing that you mentioned (in FSL), >>>>>>>>> and >>>>>>>>> bring it to dti-studio... the FSL output file format is NIFTI.GZ... >>>>>>>>> you >>>>>>>>> must >>>>>>>>> convert it to ANALYZE 4D, and then you must load that ANALYZE 4D file >>>>>>>>> as >>>>>>>>> a >>>>>>>>> RAW data file format in DTI-STUDIO... >>>>>>>>> >>>>>>>>> Sincerely, >>>>>>>>> >>>>>>>>> >>>>>>>>> Gonzalo Rojas Costa >>>>>>>>> Department of Radiology >>>>>>>>> Las Condes Clinic >>>>>>>>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >>>>>>>>> Tel: 56-2-2105170 >>>>>>>>> Cel: 56-9-97771785 >>>>>>>>> www.clc.cl >>>>>>>>> >>>>>>>>> El 15-12-2009 23:37, Mark A. Pinsk escribi?: >>>>>>>>>> >>>>>>>>>> Hi, someone asked this a while ago in the archives but I didn't see >>>>>>>>>> a >>>>>>>>>> reply. Can I use data that I've processed in FSL (eddy current >>>>>>>>>> correction, motion correction, and field map-based undistortion) and >>>>>>>>>> bring it into dti-studio? The data is in one large 4D nifti file. >>>>>>>>>> I >>>>>>>>>> don't see where I can do this, is it not possible? >>>>>>>>>> >>>>>>>>>> thanks >>>>>>>>>> mark >>>>>>>>>>_______________________________________________ >>>>>>>>>> Mristudio-users mailing list >>>>>>>>>> Mristudio-users at mristudio.org >>>>>>>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>>>>>>> Unsubscribe, send a blank email to: >>>>>>>>>> Mristudio-users-unsubscribe at mristudio.org >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>>_______________________________________________ >>>>>>>> Mristudio-users mailing list >>>>>>>> Mristudio-users at mristudio.org >>>>>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>>>>> Unsubscribe, send a blank email to: >>>>>>>> Mristudio-users-unsubscribe at mristudio.org >>>>>>>> >>>>>>> >>>>>> >>>>> >>>>>_______________________________________________ >>>>> Mristudio-users mailing list >>>>> Mristudio-users at mristudio.org >>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>> Unsubscribe, send a blank email to: >>>>> Mristudio-users-unsubscribe at mristudio.org >>>>> >>>>> >>>>> >>>>> >>>>> >>>>>_______________________________________________ >>>>> Mristudio-users mailing list >>>>> Mristudio-users at mristudio.org >>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>> Unsubscribe, send a blank email to: >>>>> Mristudio-users-unsubscribe at mristudio.org >>>>> >>>> >>>>_______________________________________________ >>>> Mristudio-users mailing list >>>> Mristudio-users at mristudio.org >>>> http://lists.mristudio.org/mailman/listinfo/ >>>> Unsubscribe, send a blank email to: >>>> Mristudio-users-unsubscribe at mristudio.org >>>> >>> >> > >_______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From gjmuro at optonline.net Wed Dec 16 22:31:25 2009 From: gjmuro at optonline.net (gjmuro at optonline.net) Date: Thu, 17 Dec 2009 03:31:25 +0000 Subject: [Mristudio-users] Using processed data In-Reply-To: <4B299B96.6000301@puc.cl> References: <4B28651A.4020202@puc.cl> <274936.72080.qm@web30701.mail.mud.yahoo.com> <4B29809E.50805@puc.cl> <4B299B96.6000301@puc.cl> Message-ID: <1454758758-1261020672-cardhu_decombobulator_blackberry.rim.net-1794452486-@bda114.bisx.prod.on.blackberry> Sent from my Verizon Wireless BlackBerry -----Original Message----- From: Gonzalo Rojas Date: Wed, 16 Dec 2009 23:46:46 To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] Using processed data Hi Mark: Are you sure that the Pixel Size is 1 mm in your DWI images ?... You entered that value in DTI-Studio, and you have that values in the Analyze and NIFTI files, but it is a uncomon pixel size for DWI... Sincerely, Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl El 16-12-2009 22:02, Mark A. Pinsk escribi?: > And the original 4D Nifti follow reads as follows, in comparison: > > fslinfo data.nii > > data_type FLOAT32 > dim1 96 > dim2 128 > dim3 47 > dim4 65 > datatype 16 > pixdim1 1.0000000000 > pixdim2 1.0000000000 > pixdim3 1.1000000238 > pixdim4 1.0000000000 > cal_max 3154.5610 > cal_min -1285.1160 > file_type NIFTI-1+ _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From gjmuro at optonline.net Wed Dec 16 22:31:36 2009 From: gjmuro at optonline.net (gjmuro at optonline.net) Date: Thu, 17 Dec 2009 03:31:36 +0000 Subject: [Mristudio-users] Using processed data In-Reply-To: <4B29A26E.3090705@puc.cl> References: <274936.72080.qm@web30701.mail.mud.yahoo.com> <4B29809E.50805@puc.cl> <4B299B96.6000301@puc.cl> <4B29A26E.3090705@puc.cl> Message-ID: <1037601931-1261020683-cardhu_decombobulator_blackberry.rim.net-674539142-@bda114.bisx.prod.on.blackberry> Sent from my Verizon Wireless BlackBerry -----Original Message----- From: Gonzalo Rojas Date: Thu, 17 Dec 2009 00:15:58 To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] Using processed data Hi Mark: Yes... you could use the instructions of Susumu... I always used REC format to load the RAW part of Analyze images, but which is the difference in DTI-Studio betwen the REC load option and RAW load option (question to Susumu) ?... Sincerely, Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl El 17-12-2009 0:07, Mark A. Pinsk escribi?: > Yes, these are small animal brains so I am scanning at high resolution > (1x1x1.1). > > The change to -1 in one of the dimensions is indeed strange, as you noted. > > I will try going to rec format as suggested by Susumu in a recent > reply, and post my outcome. > > > > On Wed, Dec 16, 2009 at 9:46 PM, Gonzalo Rojas wrote: >> Hi Mark: >> >> Are you sure that the Pixel Size is 1 mm in your DWI images ?... You >> entered that value in DTI-Studio, and you have that values in the Analyze >> and NIFTI files, but it is a uncomon pixel size for DWI... >> >> Sincerely, >> >> Gonzalo Rojas Costa >> Department of Radiology >> Las Condes Clinic >> Lo Fontecilla 441, Las Condes, Santiago, Chile. >> Tel: 56-2-2105170 >> Cel: 56-9-97771785 >> www.clc.cl >> >> El 16-12-2009 22:02, Mark A. Pinsk escribi?: >>> >>> And the original 4D Nifti follow reads as follows, in comparison: >>> >>> fslinfo data.nii >>> >>> data_type FLOAT32 >>> dim1 96 >>> dim2 128 >>> dim3 47 >>> dim4 65 >>> datatype 16 >>> pixdim1 1.0000000000 >>> pixdim2 1.0000000000 >>> pixdim3 1.1000000238 >>> pixdim4 1.0000000000 >>> cal_max 3154.5610 >>> cal_min -1285.1160 >>> file_type NIFTI-1+ >> > >_______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From mpinsk at gmail.com Wed Dec 16 22:40:25 2009 From: mpinsk at gmail.com (Mark A. Pinsk) Date: Wed, 16 Dec 2009 22:40:25 -0500 Subject: [Mristudio-users] Using processed data In-Reply-To: References: <4B28542F.5000803@puc.cl> <4B28651A.4020202@puc.cl> <274936.72080.qm@web30701.mail.mud.yahoo.com> Message-ID: Still no luck. In the DTI Mapping parameters window, there is no lower left field for the number "65" to appear. I only see that in the MRIView3D parameters window. I am beginning to wonder if I'm having a more low-level problem? I'm running the latest DTI-Studio 3.0.1 beta x64 on Windows 7 64bit. I also tried DTI-Studio 3.0.1 beta x86. Anyone interested in having a copy of my 4D Nifti file and seeing if they can import it? thanks Mark On Wed, Dec 16, 2009 at 8:46 PM, susumu mori wrote: > Hi Mark, > > Please try Philips REC format. This is a 4D raw format with integer. For > both "raw" and "Philips REC", DtiStudio expect you to have 4D raw > (no-header) file, not a bunch of 3D files. In your case, you need a single > raw file that contains all 65 volume data (65 x 96 x 128 x 47) in one file. > > For this conversion, you can read 4D Nifty or 4D analyze (depending on the > version of DtiStudio) by MriView3D and save all the images at once as a > "raw" format. Then, the images are ready for DtiMapping. In DtiMapping, as I > mentioned, open it as Philips REC. In the opening window, specify; > > 96x128x47 > > Then you should get "65" as the number of the 3D images correctly calculated > from the file size at the left bottom of the window. Also choose > gradient-by-gradient for the order of the file. If you have a correct table > with 65 lines, you should not get the error message. > > If you have the 4D analyze file, the *.img file of the Analyze format can > also be directly read as "Philips REC". However, you have to be careful > because if the Analyze is in Neurology convention (default setup) and read > the *.img as "Philips REC", the images may be inverted because DtiStudio > uses Radiology convention. > > I hope it helps. > > Susumu > > > > On Wed, Dec 16, 2009 at 7:39 PM, Mark A. Pinsk wrote: >> >> No luck. ?Let me outline my steps here: >> >> 1. I start with a 4D NIFTI file that contains 65 volumes (60 DWI + 5 B0). >> The image dimensions are 96x128, 47 slices per volume. >> Slice orientation is Coronal. ?FOV is 96x128. ?Pixels are 1x1x1.1. >> >> 2. I split the 4D NIFTI file into 65 3D NIFTI files using this FSL >> command: >> fslsplit input.nii.gz >> >> 3. I convert each of the 65 3D NIFTI files to ANALYZE format: >> fslchfiletype ANALYZE vol0000.nii.gz >> [..] >> fslchfiletype ANALYZE vol0064.nii.gz >> >> 4. I am able to successfully import the ANALYZE files in MRIView3D by >> choosing Analyze format (but no luck with Raw format). >> >> 5. I have no luck importing the ANALYZE files in DTI Mapping choosing >> Raw format. ?I get this message: >> "Number of files in this fold is less than expected: >> (Img_Slices*Img_Blocks). >> >> Any suggestions? ?Thanks for all your help! >> Mark >> >> >> >> >> On Wed, Dec 16, 2009 at 1:34 PM, darshan pai wrote: >> > when you say a 4D file I assume that you have a Analyze file with an >> > entry on the number of volumes , Is it? . If it is then try to make it a 3D >> > file with all the 65 slices added in the z direction and see if it helps.. >> > >> > Regards >> > >> > Dp >> > >> > >> > >> > ----- Original Message ---- >> > From: Mark A. Pinsk >> > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" >> > >> > Sent: Wed, December 16, 2009 12:13:42 AM >> > Subject: Re: [Mristudio-users] Using processed data >> > >> > Also, I should mention that the Analyze file loads just fine using >> > "MRI View3D" and "Analyze" file format. >> > >> > >> > On Wed, Dec 16, 2009 at 12:09 AM, Mark A. Pinsk >> > wrote: >> >> Thanks for your help, I'll do my best to answer them... >> >> >> >> FYI: these are small volumes from animal scans ( 1 x 1 x 1.1 mm >> >> resolution): >> >> >> >> Image Dimensions: 96 Width, 128 Height, 47 slices >> >> Slice Orientation: Axial >> >> Slice Sequencing: Inferior-Superior >> >> FOV: 96 Width, 128 Height, 1.1 Slice Thickness >> >> Pixel Size: 1.000 Width, 1.000 Height >> >> Slices to be processed: 0 to 46, All Slices >> >> Image Sequence: Gradient By Gradient >> >> b_Value: 1000 >> >> >> >> My gradient table has 65 entries. ?The first 5 entries are B0 images, >> >> the remaining 60 are for the 60 directions. ?There is no mean image at >> >> the end of my data. ? I can discard 4 of the B0 images, but that does >> >> not seem to make a difference on my error message. ?I have several B0 >> >> images in accord with recent work that suggests having a ratio of 6:1 >> >> diffusion to non-diffusion weighted images (Zhu et al. NeuroImage >> >> 2008). >> >> >> >> >> >> >> >> On Tue, Dec 15, 2009 at 11:42 PM, Gonzalo Rojas wrote: >> >>> Hi Mark: >> >>> >> >>> ?Many questions: >> >>> >> >>> i) do you specify correctly the "image slices" quantity in "iamge >> >>> dimension" >> >>> ?... that value is the quantitry of axial slices in each gradient >> >>> direction... >> >>> >> >>> ii) and the "image width" and "image height" in "image dimension" ?... >> >>> did >> >>> you checked that values ?... >> >>> >> >>> ii) in "lice orientation" did you specify "axial" ?.. >> >>> >> >>> iii) and in "Voxel Size", "Field of View-width" and "Field of >> >>> View-Heigth" >> >>> did you specifiy the FOV value correctly ?... >> >>> >> >>> iv) you could check the previos values looking at "Pixel Size-Width" >> >>> and >> >>> "Pixel Size-Height"... >> >>> >> >>> v) in "Slices to be processed" it must appears 0-(image slices-1) >> >>> >> >>> vi) in gradient table you must put the 61 (0-60) directions... in your >> >>> 4D >> >>> analyze file is included the "mean" of all the 60 directions at the >> >>> end of >> >>> the file ?... if it is, you must put "100,100,100" as the last >> >>> gradient >> >>> direction to skip that image in the computation... >> >>> >> >>> vii) in "Image secuence" you must select "Gradient by Gradient" >> >>> option... >> >>> >> >>> viii) in "Raw-BIN Files folder you must specify the IMG file of the >> >>> Analyze >> >>> pair... >> >>> >> >>> ix) why you have 5 b0 volumes ?... to compute tractography, you must >> >>> have >> >>> only one b0 volume... you must put "100,100,100" in "Gradient Table" >> >>> for >> >>> each of the 4 b0 slices to skipt them... >> >>> >> >>> ?Sincerely, >> >>> >> >>> >> >>> Gonzalo Rojas Costa >> >>> Department of Radiology >> >>> Las Condes Clinic >> >>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >> >>> Tel: 56-2-2105170 >> >>> Cel: 56-9-97771785 >> >>> www.clc.cl >> >>> >> >>> El 16-12-2009 1:07, Mark A. Pinsk escribi?: >> >>>> >> >>>> Thanks ! >> >>>> >> >>>> I converted by 4D NIFTI file to a 4D ANALYZE file as you suggested. >> >>>> >> >>>> I attempt to read it in as RAW, but it seems to get stuck... >> >>>> >> >>>> I specify the file in the Raw-BIN Files Folder field, but I get this >> >>>> message: >> >>>> "Number of files in this fold is less than expected: >> >>>> (Img_Slices*Img_Blocks)." >> >>>> >> >>>> I only have a single .img/.hdr pair in my folder since it is a 4D >> >>>> file >> >>>> (i.e. it contains 65 volumes (5 b0 volumes + 60 directions)). >> >>>> >> >>>> Sorry, any help would be greatly appreciated. >> >>>> Thanks >> >>>> Mark >> >>>> >> >>>> >> >>>> >> >>>> >> >>>> On Tue, Dec 15, 2009 at 10:29 PM, Gonzalo Rojas >> >>>> ?wrote: >> >>>>> >> >>>>> Hi Mark: >> >>>>> >> >>>>> ?Yes... you could do all the processing that you mentioned (in FSL), >> >>>>> and >> >>>>> bring it to dti-studio... the FSL output file format is NIFTI.GZ... >> >>>>> you >> >>>>> must >> >>>>> convert it to ANALYZE 4D, and then you must load that ANALYZE 4D >> >>>>> file as >> >>>>> a >> >>>>> RAW data file format in DTI-STUDIO... >> >>>>> >> >>>>> ?Sincerely, >> >>>>> >> >>>>> >> >>>>> Gonzalo Rojas Costa >> >>>>> Department of Radiology >> >>>>> Las Condes Clinic >> >>>>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >> >>>>> Tel: 56-2-2105170 >> >>>>> Cel: 56-9-97771785 >> >>>>> www.clc.cl >> >>>>> >> >>>>> El 15-12-2009 23:37, Mark A. Pinsk escribi?: >> >>>>>> >> >>>>>> Hi, someone asked this a while ago in the archives but I didn't see >> >>>>>> a >> >>>>>> reply. ? Can I use data that I've processed in FSL (eddy current >> >>>>>> correction, motion correction, and field map-based undistortion) >> >>>>>> and >> >>>>>> bring it into dti-studio? ? The data is in one large 4D nifti file. >> >>>>>> ?I >> >>>>>> don't see where I can do this, is it not possible? >> >>>>>> >> >>>>>> thanks >> >>>>>> mark >> >>>>>> _______________________________________________ >> >>>>>> Mristudio-users mailing list >> >>>>>> Mristudio-users at mristudio.org >> >>>>>> http://lists.mristudio.org/mailman/listinfo/ >> >>>>>> Unsubscribe, send a blank email to: >> >>>>>> Mristudio-users-unsubscribe at mristudio.org >> >>>>>> >> >>>>> >> >>>> >> >>>> _______________________________________________ >> >>>> Mristudio-users mailing list >> >>>> Mristudio-users at mristudio.org >> >>>> http://lists.mristudio.org/mailman/listinfo/ >> >>>> Unsubscribe, send a blank email to: >> >>>> Mristudio-users-unsubscribe at mristudio.org >> >>>> >> >>> >> >> >> > >> > _______________________________________________ >> > Mristudio-users mailing list >> > Mristudio-users at mristudio.org >> > http://lists.mristudio.org/mailman/listinfo/ >> > Unsubscribe, send a blank email to: >> > Mristudio-users-unsubscribe at mristudio.org >> > >> > >> > >> > >> > >> > _______________________________________________ >> > Mristudio-users mailing list >> > Mristudio-users at mristudio.org >> > http://lists.mristudio.org/mailman/listinfo/ >> > Unsubscribe, send a blank email to: >> > Mristudio-users-unsubscribe at mristudio.org >> > >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > From gjmuro at optonline.net Wed Dec 16 22:45:19 2009 From: gjmuro at optonline.net (gjmuro at optonline.net) Date: Thu, 17 Dec 2009 03:45:19 +0000 Subject: [Mristudio-users] Using processed data In-Reply-To: References: <4B28542F.5000803@puc.cl> <4B28651A.4020202@puc.cl> <274936.72080.qm@web30701.mail.mud.yahoo.com> Message-ID: <1590135565-1261021506-cardhu_decombobulator_blackberry.rim.net-1705826348-@bda114.bisx.prod.on.blackberry> T Sent from my Verizon Wireless BlackBerry -----Original Message----- From: "Mark A. Pinsk" Date: Wed, 16 Dec 2009 22:40:25 To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] Using processed data Still no luck. In the DTI Mapping parameters window, there is no lower left field for the number "65" to appear. I only see that in the MRIView3D parameters window. I am beginning to wonder if I'm having a more low-level problem? I'm running the latest DTI-Studio 3.0.1 beta x64 on Windows 7 64bit. I also tried DTI-Studio 3.0.1 beta x86. Anyone interested in having a copy of my 4D Nifti file and seeing if they can import it? thanks Mark On Wed, Dec 16, 2009 at 8:46 PM, susumu mori wrote: > Hi Mark, > > Please try Philips REC format. This is a 4D raw format with integer. For > both "raw" and "Philips REC", DtiStudio expect you to have 4D raw > (no-header) file, not a bunch of 3D files. In your case, you need a single > raw file that contains all 65 volume data (65 x 96 x 128 x 47) in one file. > > For this conversion, you can read 4D Nifty or 4D analyze (depending on the > version of DtiStudio) by MriView3D and save all the images at once as a > "raw" format. Then, the images are ready for DtiMapping. In DtiMapping, as I > mentioned, open it as Philips REC. In the opening window, specify; > > 96x128x47 > > Then you should get "65" as the number of the 3D images correctly calculated > from the file size at the left bottom of the window. Also choose > gradient-by-gradient for the order of the file. If you have a correct table > with 65 lines, you should not get the error message. > > If you have the 4D analyze file, the *.img file of the Analyze format can > also be directly read as "Philips REC". However, you have to be careful > because if the Analyze is in Neurology convention (default setup) and read > the *.img as "Philips REC", the images may be inverted because DtiStudio > uses Radiology convention. > > I hope it helps. > > Susumu > > > > On Wed, Dec 16, 2009 at 7:39 PM, Mark A. Pinsk wrote: >> >> No luck. ?Let me outline my steps here: >> >> 1. I start with a 4D NIFTI file that contains 65 volumes (60 DWI + 5 B0). >> The image dimensions are 96x128, 47 slices per volume. >> Slice orientation is Coronal. ?FOV is 96x128. ?Pixels are 1x1x1.1. >> >> 2. I split the 4D NIFTI file into 65 3D NIFTI files using this FSL >> command: >> fslsplit input.nii.gz >> >> 3. I convert each of the 65 3D NIFTI files to ANALYZE format: >> fslchfiletype ANALYZE vol0000.nii.gz >> [..] >> fslchfiletype ANALYZE vol0064.nii.gz >> >> 4. I am able to successfully import the ANALYZE files in MRIView3D by >> choosing Analyze format (but no luck with Raw format). >> >> 5. I have no luck importing the ANALYZE files in DTI Mapping choosing >> Raw format. ?I get this message: >> "Number of files in this fold is less than expected: >> (Img_Slices*Img_Blocks). >> >> Any suggestions? ?Thanks for all your help! >> Mark >> >> >> >> >> On Wed, Dec 16, 2009 at 1:34 PM, darshan pai wrote: >> > when you say a 4D file I assume that you have a Analyze file with an >> > entry on the number of volumes , Is it? . If it is then try to make it a 3D >> > file with all the 65 slices added in the z direction and see if it helps.. >> > >> > Regards >> > >> > Dp >> > >> > >> > >> > ----- Original Message ---- >> > From: Mark A. Pinsk >> > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" >> > >> > Sent: Wed, December 16, 2009 12:13:42 AM >> > Subject: Re: [Mristudio-users] Using processed data >> > >> > Also, I should mention that the Analyze file loads just fine using >> > "MRI View3D" and "Analyze" file format. >> > >> > >> > On Wed, Dec 16, 2009 at 12:09 AM, Mark A. Pinsk >> > wrote: >> >> Thanks for your help, I'll do my best to answer them... >> >> >> >> FYI: these are small volumes from animal scans ( 1 x 1 x 1.1 mm >> >> resolution): >> >> >> >> Image Dimensions: 96 Width, 128 Height, 47 slices >> >> Slice Orientation: Axial >> >> Slice Sequencing: Inferior-Superior >> >> FOV: 96 Width, 128 Height, 1.1 Slice Thickness >> >> Pixel Size: 1.000 Width, 1.000 Height >> >> Slices to be processed: 0 to 46, All Slices >> >> Image Sequence: Gradient By Gradient >> >> b_Value: 1000 >> >> >> >> My gradient table has 65 entries. ?The first 5 entries are B0 images, >> >> the remaining 60 are for the 60 directions. ?There is no mean image at >> >> the end of my data. ? I can discard 4 of the B0 images, but that does >> >> not seem to make a difference on my error message. ?I have several B0 >> >> images in accord with recent work that suggests having a ratio of 6:1 >> >> diffusion to non-diffusion weighted images (Zhu et al. NeuroImage >> >> 2008). >> >> >> >> >> >> >> >> On Tue, Dec 15, 2009 at 11:42 PM, Gonzalo Rojas wrote: >> >>> Hi Mark: >> >>> >> >>> ?Many questions: >> >>> >> >>> i) do you specify correctly the "image slices" quantity in "iamge >> >>> dimension" >> >>> ?... that value is the quantitry of axial slices in each gradient >> >>> direction... >> >>> >> >>> ii) and the "image width" and "image height" in "image dimension" ?... >> >>> did >> >>> you checked that values ?... >> >>> >> >>> ii) in "lice orientation" did you specify "axial" ?.. >> >>> >> >>> iii) and in "Voxel Size", "Field of View-width" and "Field of >> >>> View-Heigth" >> >>> did you specifiy the FOV value correctly ?... >> >>> >> >>> iv) you could check the previos values looking at "Pixel Size-Width" >> >>> and >> >>> "Pixel Size-Height"... >> >>> >> >>> v) in "Slices to be processed" it must appears 0-(image slices-1) >> >>> >> >>> vi) in gradient table you must put the 61 (0-60) directions... in your >> >>> 4D >> >>> analyze file is included the "mean" of all the 60 directions at the >> >>> end of >> >>> the file ?... if it is, you must put "100,100,100" as the last >> >>> gradient >> >>> direction to skip that image in the computation... >> >>> >> >>> vii) in "Image secuence" you must select "Gradient by Gradient" >> >>> option... >> >>> >> >>> viii) in "Raw-BIN Files folder you must specify the IMG file of the >> >>> Analyze >> >>> pair... >> >>> >> >>> ix) why you have 5 b0 volumes ?... to compute tractography, you must >> >>> have >> >>> only one b0 volume... you must put "100,100,100" in "Gradient Table" >> >>> for >> >>> each of the 4 b0 slices to skipt them... >> >>> >> >>> ?Sincerely, >> >>> >> >>> >> >>> Gonzalo Rojas Costa >> >>> Department of Radiology >> >>> Las Condes Clinic >> >>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >> >>> Tel: 56-2-2105170 >> >>> Cel: 56-9-97771785 >> >>> www.clc.cl >> >>> >> >>> El 16-12-2009 1:07, Mark A. Pinsk escribi?: >> >>>> >> >>>> Thanks ! >> >>>> >> >>>> I converted by 4D NIFTI file to a 4D ANALYZE file as you suggested. >> >>>> >> >>>> I attempt to read it in as RAW, but it seems to get stuck... >> >>>> >> >>>> I specify the file in the Raw-BIN Files Folder field, but I get this >> >>>> message: >> >>>> "Number of files in this fold is less than expected: >> >>>> (Img_Slices*Img_Blocks)." >> >>>> >> >>>> I only have a single .img/.hdr pair in my folder since it is a 4D >> >>>> file >> >>>> (i.e. it contains 65 volumes (5 b0 volumes + 60 directions)). >> >>>> >> >>>> Sorry, any help would be greatly appreciated. >> >>>> Thanks >> >>>> Mark >> >>>> >> >>>> >> >>>> >> >>>> >> >>>> On Tue, Dec 15, 2009 at 10:29 PM, Gonzalo Rojas >> >>>> ?wrote: >> >>>>> >> >>>>> Hi Mark: >> >>>>> >> >>>>> ?Yes... you could do all the processing that you mentioned (in FSL), >> >>>>> and >> >>>>> bring it to dti-studio... the FSL output file format is NIFTI.GZ... >> >>>>> you >> >>>>> must >> >>>>> convert it to ANALYZE 4D, and then you must load that ANALYZE 4D >> >>>>> file as >> >>>>> a >> >>>>> RAW data file format in DTI-STUDIO... >> >>>>> >> >>>>> ?Sincerely, >> >>>>> >> >>>>> >> >>>>> Gonzalo Rojas Costa >> >>>>> Department of Radiology >> >>>>> Las Condes Clinic >> >>>>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >> >>>>> Tel: 56-2-2105170 >> >>>>> Cel: 56-9-97771785 >> >>>>> www.clc.cl >> >>>>> >> >>>>> El 15-12-2009 23:37, Mark A. Pinsk escribi?: >> >>>>>> >> >>>>>> Hi, someone asked this a while ago in the archives but I didn't see >> >>>>>> a >> >>>>>> reply. ? Can I use data that I've processed in FSL (eddy current >> >>>>>> correction, motion correction, and field map-based undistortion) >> >>>>>> and >> >>>>>> bring it into dti-studio? ? The data is in one large 4D nifti file. >> >>>>>> ?I >> >>>>>> don't see where I can do this, is it not possible? >> >>>>>> >> >>>>>> thanks >> >>>>>> mark >> >>>>>>_______________________________________________ >> >>>>>> Mristudio-users mailing list >> >>>>>> Mristudio-users at mristudio.org >> >>>>>> http://lists.mristudio.org/mailman/listinfo/ >> >>>>>> Unsubscribe, send a blank email to: >> >>>>>> Mristudio-users-unsubscribe at mristudio.org >> >>>>>> >> >>>>> >> >>>> >> >>>>_______________________________________________ >> >>>> Mristudio-users mailing list >> >>>> Mristudio-users at mristudio.org >> >>>> http://lists.mristudio.org/mailman/listinfo/ >> >>>> Unsubscribe, send a blank email to: >> >>>> Mristudio-users-unsubscribe at mristudio.org >> >>>> >> >>> >> >> >> > >> >_______________________________________________ >> > Mristudio-users mailing list >> > Mristudio-users at mristudio.org >> > http://lists.mristudio.org/mailman/listinfo/ >> > Unsubscribe, send a blank email to: >> > Mristudio-users-unsubscribe at mristudio.org >> > >> > >> > >> > >> > >> >_______________________________________________ >> > Mristudio-users mailing list >> > Mristudio-users at mristudio.org >> > http://lists.mristudio.org/mailman/listinfo/ >> > Unsubscribe, send a blank email to: >> > Mristudio-users-unsubscribe at mristudio.org >> > >> >>_______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> > > >_______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From bender at wayne.edu Wed Dec 16 23:11:38 2009 From: bender at wayne.edu (Andrew) Date: Thu, 17 Dec 2009 04:11:38 +0000 Subject: [Mristudio-users] Using processed data In-Reply-To: <1590135565-1261021506-cardhu_decombobulator_blackberry.rim.net-1705826348-@bda114.bisx.prod.on.blackberry> References: <4B28542F.5000803@puc.cl> <4B28651A.4020202@puc.cl> <274936.72080.qm@web30701.mail.mud.yahoo.com> <1590135565-1261021506-cardhu_decombobulator_blackberry.rim.net-1705826348-@bda114.bisx.prod.on.blackberry> Message-ID: <475670525-1261023096-cardhu_decombobulator_blackberry.rim.net-769838405-@bda651.bisx.prod.on.blackberry> Pardon me, but you should know that it appears you have been inadvertantly emailing the dtistudio email list from your blackberry. Regards Sent from my Verizon Wireless BlackBerry -----Original Message----- From: gjmuro at optonline.net Date: Thu, 17 Dec 2009 03:45:19 To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] Using processed data T Sent from my Verizon Wireless BlackBerry -----Original Message----- From: "Mark A. Pinsk" Date: Wed, 16 Dec 2009 22:40:25 To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] Using processed data Still no luck. In the DTI Mapping parameters window, there is no lower left field for the number "65" to appear. I only see that in the MRIView3D parameters window. I am beginning to wonder if I'm having a more low-level problem? I'm running the latest DTI-Studio 3.0.1 beta x64 on Windows 7 64bit. I also tried DTI-Studio 3.0.1 beta x86. Anyone interested in having a copy of my 4D Nifti file and seeing if they can import it? thanks Mark On Wed, Dec 16, 2009 at 8:46 PM, susumu mori wrote: > Hi Mark, > > Please try Philips REC format. This is a 4D raw format with integer. For > both "raw" and "Philips REC", DtiStudio expect you to have 4D raw > (no-header) file, not a bunch of 3D files. In your case, you need a single > raw file that contains all 65 volume data (65 x 96 x 128 x 47) in one file. > > For this conversion, you can read 4D Nifty or 4D analyze (depending on the > version of DtiStudio) by MriView3D and save all the images at once as a > "raw" format. Then, the images are ready for DtiMapping. In DtiMapping, as I > mentioned, open it as Philips REC. In the opening window, specify; > > 96x128x47 > > Then you should get "65" as the number of the 3D images correctly calculated > from the file size at the left bottom of the window. Also choose > gradient-by-gradient for the order of the file. If you have a correct table > with 65 lines, you should not get the error message. > > If you have the 4D analyze file, the *.img file of the Analyze format can > also be directly read as "Philips REC". However, you have to be careful > because if the Analyze is in Neurology convention (default setup) and read > the *.img as "Philips REC", the images may be inverted because DtiStudio > uses Radiology convention. > > I hope it helps. > > Susumu > > > > On Wed, Dec 16, 2009 at 7:39 PM, Mark A. Pinsk wrote: >> >> No luck. ?Let me outline my steps here: >> >> 1. I start with a 4D NIFTI file that contains 65 volumes (60 DWI + 5 B0). >> The image dimensions are 96x128, 47 slices per volume. >> Slice orientation is Coronal. ?FOV is 96x128. ?Pixels are 1x1x1.1. >> >> 2. I split the 4D NIFTI file into 65 3D NIFTI files using this FSL >> command: >> fslsplit input.nii.gz >> >> 3. I convert each of the 65 3D NIFTI files to ANALYZE format: >> fslchfiletype ANALYZE vol0000.nii.gz >> [..] >> fslchfiletype ANALYZE vol0064.nii.gz >> >> 4. I am able to successfully import the ANALYZE files in MRIView3D by >> choosing Analyze format (but no luck with Raw format). >> >> 5. I have no luck importing the ANALYZE files in DTI Mapping choosing >> Raw format. ?I get this message: >> "Number of files in this fold is less than expected: >> (Img_Slices*Img_Blocks). >> >> Any suggestions? ?Thanks for all your help! >> Mark >> >> >> >> >> On Wed, Dec 16, 2009 at 1:34 PM, darshan pai wrote: >> > when you say a 4D file I assume that you have a Analyze file with an >> > entry on the number of volumes , Is it? . If it is then try to make it a 3D >> > file with all the 65 slices added in the z direction and see if it helps.. >> > >> > Regards >> > >> > Dp >> > >> > >> > >> > ----- Original Message ---- >> > From: Mark A. Pinsk >> > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" >> > >> > Sent: Wed, December 16, 2009 12:13:42 AM >> > Subject: Re: [Mristudio-users] Using processed data >> > >> > Also, I should mention that the Analyze file loads just fine using >> > "MRI View3D" and "Analyze" file format. >> > >> > >> > On Wed, Dec 16, 2009 at 12:09 AM, Mark A. Pinsk >> > wrote: >> >> Thanks for your help, I'll do my best to answer them... >> >> >> >> FYI: these are small volumes from animal scans ( 1 x 1 x 1.1 mm >> >> resolution): >> >> >> >> Image Dimensions: 96 Width, 128 Height, 47 slices >> >> Slice Orientation: Axial >> >> Slice Sequencing: Inferior-Superior >> >> FOV: 96 Width, 128 Height, 1.1 Slice Thickness >> >> Pixel Size: 1.000 Width, 1.000 Height >> >> Slices to be processed: 0 to 46, All Slices >> >> Image Sequence: Gradient By Gradient >> >> b_Value: 1000 >> >> >> >> My gradient table has 65 entries. ?The first 5 entries are B0 images, >> >> the remaining 60 are for the 60 directions. ?There is no mean image at >> >> the end of my data. ? I can discard 4 of the B0 images, but that does >> >> not seem to make a difference on my error message. ?I have several B0 >> >> images in accord with recent work that suggests having a ratio of 6:1 >> >> diffusion to non-diffusion weighted images (Zhu et al. NeuroImage >> >> 2008). >> >> >> >> >> >> >> >> On Tue, Dec 15, 2009 at 11:42 PM, Gonzalo Rojas wrote: >> >>> Hi Mark: >> >>> >> >>> ?Many questions: >> >>> >> >>> i) do you specify correctly the "image slices" quantity in "iamge >> >>> dimension" >> >>> ?... that value is the quantitry of axial slices in each gradient >> >>> direction... >> >>> >> >>> ii) and the "image width" and "image height" in "image dimension" ?... >> >>> did >> >>> you checked that values ?... >> >>> >> >>> ii) in "lice orientation" did you specify "axial" ?.. >> >>> >> >>> iii) and in "Voxel Size", "Field of View-width" and "Field of >> >>> View-Heigth" >> >>> did you specifiy the FOV value correctly ?... >> >>> >> >>> iv) you could check the previos values looking at "Pixel Size-Width" >> >>> and >> >>> "Pixel Size-Height"... >> >>> >> >>> v) in "Slices to be processed" it must appears 0-(image slices-1) >> >>> >> >>> vi) in gradient table you must put the 61 (0-60) directions... in your >> >>> 4D >> >>> analyze file is included the "mean" of all the 60 directions at the >> >>> end of >> >>> the file ?... if it is, you must put "100,100,100" as the last >> >>> gradient >> >>> direction to skip that image in the computation... >> >>> >> >>> vii) in "Image secuence" you must select "Gradient by Gradient" >> >>> option... >> >>> >> >>> viii) in "Raw-BIN Files folder you must specify the IMG file of the >> >>> Analyze >> >>> pair... >> >>> >> >>> ix) why you have 5 b0 volumes ?... to compute tractography, you must >> >>> have >> >>> only one b0 volume... you must put "100,100,100" in "Gradient Table" >> >>> for >> >>> each of the 4 b0 slices to skipt them... >> >>> >> >>> ?Sincerely, >> >>> >> >>> >> >>> Gonzalo Rojas Costa >> >>> Department of Radiology >> >>> Las Condes Clinic >> >>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >> >>> Tel: 56-2-2105170 >> >>> Cel: 56-9-97771785 >> >>> www.clc.cl >> >>> >> >>> El 16-12-2009 1:07, Mark A. Pinsk escribi?: >> >>>> >> >>>> Thanks ! >> >>>> >> >>>> I converted by 4D NIFTI file to a 4D ANALYZE file as you suggested. >> >>>> >> >>>> I attempt to read it in as RAW, but it seems to get stuck... >> >>>> >> >>>> I specify the file in the Raw-BIN Files Folder field, but I get this >> >>>> message: >> >>>> "Number of files in this fold is less than expected: >> >>>> (Img_Slices*Img_Blocks)." >> >>>> >> >>>> I only have a single .img/.hdr pair in my folder since it is a 4D >> >>>> file >> >>>> (i.e. it contains 65 volumes (5 b0 volumes + 60 directions)). >> >>>> >> >>>> Sorry, any help would be greatly appreciated. >> >>>> Thanks >> >>>> Mark >> >>>> >> >>>> >> >>>> >> >>>> >> >>>> On Tue, Dec 15, 2009 at 10:29 PM, Gonzalo Rojas >> >>>> ?wrote: >> >>>>> >> >>>>> Hi Mark: >> >>>>> >> >>>>> ?Yes... you could do all the processing that you mentioned (in FSL), >> >>>>> and >> >>>>> bring it to dti-studio... the FSL output file format is NIFTI.GZ... >> >>>>> you >> >>>>> must >> >>>>> convert it to ANALYZE 4D, and then you must load that ANALYZE 4D >> >>>>> file as >> >>>>> a >> >>>>> RAW data file format in DTI-STUDIO... >> >>>>> >> >>>>> ?Sincerely, >> >>>>> >> >>>>> >> >>>>> Gonzalo Rojas Costa >> >>>>> Department of Radiology >> >>>>> Las Condes Clinic >> >>>>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >> >>>>> Tel: 56-2-2105170 >> >>>>> Cel: 56-9-97771785 >> >>>>> www.clc.cl >> >>>>> >> >>>>> El 15-12-2009 23:37, Mark A. Pinsk escribi?: >> >>>>>> >> >>>>>> Hi, someone asked this a while ago in the archives but I didn't see >> >>>>>> a >> >>>>>> reply. ? Can I use data that I've processed in FSL (eddy current >> >>>>>> correction, motion correction, and field map-based undistortion) >> >>>>>> and >> >>>>>> bring it into dti-studio? ? The data is in one large 4D nifti file. >> >>>>>> ?I >> >>>>>> don't see where I can do this, is it not possible? >> >>>>>> >> >>>>>> thanks >> >>>>>> mark >> >>>>>>_______________________________________________ >> >>>>>> Mristudio-users mailing list >> >>>>>> Mristudio-users at mristudio.org >> >>>>>> http://lists.mristudio.org/mailman/listinfo/ >> >>>>>> Unsubscribe, send a blank email to: >> >>>>>> Mristudio-users-unsubscribe at mristudio.org >> >>>>>> >> >>>>> >> >>>> >> >>>>_______________________________________________ >> >>>> Mristudio-users mailing list >> >>>> Mristudio-users at mristudio.org >> >>>> http://lists.mristudio.org/mailman/listinfo/ >> >>>> Unsubscribe, send a blank email to: >> >>>> Mristudio-users-unsubscribe at mristudio.org >> >>>> >> >>> >> >> >> > >> >_______________________________________________ >> > Mristudio-users mailing list >> > Mristudio-users at mristudio.org >> > http://lists.mristudio.org/mailman/listinfo/ >> > Unsubscribe, send a blank email to: >> > Mristudio-users-unsubscribe at mristudio.org >> > >> > >> > >> > >> > >> >_______________________________________________ >> > Mristudio-users mailing list >> > Mristudio-users at mristudio.org >> > http://lists.mristudio.org/mailman/listinfo/ >> > Unsubscribe, send a blank email to: >> > Mristudio-users-unsubscribe at mristudio.org >> > >> >>_______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> > > >_______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From grojasy at puc.cl Thu Dec 17 10:13:07 2009 From: grojasy at puc.cl (Gonzalo Rojas) Date: Thu, 17 Dec 2009 12:13:07 -0300 Subject: [Mristudio-users] Using processed data In-Reply-To: References: <4B28542F.5000803@puc.cl> <4B28651A.4020202@puc.cl> <274936.72080.qm@web30701.mail.mud.yahoo.com> Message-ID: <4B2A4A83.4070506@puc.cl> Hi Mark: If you want, you could send me the images to test it with DTI-Studio... it is better to send me the 4D Nifti, and the DICOM original ones... you could use www.senduit.com... Sincerely, Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl El 17-12-2009 0:40, Mark A. Pinsk escribi?: > Still no luck. In the DTI Mapping parameters window, there is no > lower left field for the number "65" to appear. I only see that in > the MRIView3D parameters window. > > I am beginning to wonder if I'm having a more low-level problem? I'm > running the latest DTI-Studio 3.0.1 beta x64 on Windows 7 64bit. I > also tried DTI-Studio 3.0.1 beta x86. > > Anyone interested in having a copy of my 4D Nifti file and seeing if > they can import it? > > thanks > Mark > > > > On Wed, Dec 16, 2009 at 8:46 PM, susumu mori wrote: >> Hi Mark, >> >> Please try Philips REC format. This is a 4D raw format with integer. For >> both "raw" and "Philips REC", DtiStudio expect you to have 4D raw >> (no-header) file, not a bunch of 3D files. In your case, you need a single >> raw file that contains all 65 volume data (65 x 96 x 128 x 47) in one file. >> >> For this conversion, you can read 4D Nifty or 4D analyze (depending on the >> version of DtiStudio) by MriView3D and save all the images at once as a >> "raw" format. Then, the images are ready for DtiMapping. In DtiMapping, as I >> mentioned, open it as Philips REC. In the opening window, specify; >> >> 96x128x47 >> >> Then you should get "65" as the number of the 3D images correctly calculated >> from the file size at the left bottom of the window. Also choose >> gradient-by-gradient for the order of the file. If you have a correct table >> with 65 lines, you should not get the error message. >> >> If you have the 4D analyze file, the *.img file of the Analyze format can >> also be directly read as "Philips REC". However, you have to be careful >> because if the Analyze is in Neurology convention (default setup) and read >> the *.img as "Philips REC", the images may be inverted because DtiStudio >> uses Radiology convention. >> >> I hope it helps. >> >> Susumu >> >> >> >> On Wed, Dec 16, 2009 at 7:39 PM, Mark A. Pinsk wrote: >>> >>> No luck. Let me outline my steps here: >>> >>> 1. I start with a 4D NIFTI file that contains 65 volumes (60 DWI + 5 B0). >>> The image dimensions are 96x128, 47 slices per volume. >>> Slice orientation is Coronal. FOV is 96x128. Pixels are 1x1x1.1. >>> >>> 2. I split the 4D NIFTI file into 65 3D NIFTI files using this FSL >>> command: >>> fslsplit input.nii.gz >>> >>> 3. I convert each of the 65 3D NIFTI files to ANALYZE format: >>> fslchfiletype ANALYZE vol0000.nii.gz >>> [..] >>> fslchfiletype ANALYZE vol0064.nii.gz >>> >>> 4. I am able to successfully import the ANALYZE files in MRIView3D by >>> choosing Analyze format (but no luck with Raw format). >>> >>> 5. I have no luck importing the ANALYZE files in DTI Mapping choosing >>> Raw format. I get this message: >>> "Number of files in this fold is less than expected: >>> (Img_Slices*Img_Blocks). >>> >>> Any suggestions? Thanks for all your help! >>> Mark >>> >>> >>> >>> >>> On Wed, Dec 16, 2009 at 1:34 PM, darshan pai wrote: >>>> when you say a 4D file I assume that you have a Analyze file with an >>>> entry on the number of volumes , Is it? . If it is then try to make it a 3D >>>> file with all the 65 slices added in the z direction and see if it helps.. >>>> >>>> Regards >>>> >>>> Dp >>>> >>>> >>>> >>>> ----- Original Message ---- >>>> From: Mark A. Pinsk >>>> To: "DTI Studio, ROI Editor, Landmarker Questions/Support" >>>> >>>> Sent: Wed, December 16, 2009 12:13:42 AM >>>> Subject: Re: [Mristudio-users] Using processed data >>>> >>>> Also, I should mention that the Analyze file loads just fine using >>>> "MRI View3D" and "Analyze" file format. >>>> >>>> >>>> On Wed, Dec 16, 2009 at 12:09 AM, Mark A. Pinsk >>>> wrote: >>>>> Thanks for your help, I'll do my best to answer them... >>>>> >>>>> FYI: these are small volumes from animal scans ( 1 x 1 x 1.1 mm >>>>> resolution): >>>>> >>>>> Image Dimensions: 96 Width, 128 Height, 47 slices >>>>> Slice Orientation: Axial >>>>> Slice Sequencing: Inferior-Superior >>>>> FOV: 96 Width, 128 Height, 1.1 Slice Thickness >>>>> Pixel Size: 1.000 Width, 1.000 Height >>>>> Slices to be processed: 0 to 46, All Slices >>>>> Image Sequence: Gradient By Gradient >>>>> b_Value: 1000 >>>>> >>>>> My gradient table has 65 entries. The first 5 entries are B0 images, >>>>> the remaining 60 are for the 60 directions. There is no mean image at >>>>> the end of my data. I can discard 4 of the B0 images, but that does >>>>> not seem to make a difference on my error message. I have several B0 >>>>> images in accord with recent work that suggests having a ratio of 6:1 >>>>> diffusion to non-diffusion weighted images (Zhu et al. NeuroImage >>>>> 2008). >>>>> >>>>> >>>>> >>>>> On Tue, Dec 15, 2009 at 11:42 PM, Gonzalo Rojas wrote: >>>>>> Hi Mark: >>>>>> >>>>>> Many questions: >>>>>> >>>>>> i) do you specify correctly the "image slices" quantity in "iamge >>>>>> dimension" >>>>>> ?... that value is the quantitry of axial slices in each gradient >>>>>> direction... >>>>>> >>>>>> ii) and the "image width" and "image height" in "image dimension" ?... >>>>>> did >>>>>> you checked that values ?... >>>>>> >>>>>> ii) in "lice orientation" did you specify "axial" ?.. >>>>>> >>>>>> iii) and in "Voxel Size", "Field of View-width" and "Field of >>>>>> View-Heigth" >>>>>> did you specifiy the FOV value correctly ?... >>>>>> >>>>>> iv) you could check the previos values looking at "Pixel Size-Width" >>>>>> and >>>>>> "Pixel Size-Height"... >>>>>> >>>>>> v) in "Slices to be processed" it must appears 0-(image slices-1) >>>>>> >>>>>> vi) in gradient table you must put the 61 (0-60) directions... in your >>>>>> 4D >>>>>> analyze file is included the "mean" of all the 60 directions at the >>>>>> end of >>>>>> the file ?... if it is, you must put "100,100,100" as the last >>>>>> gradient >>>>>> direction to skip that image in the computation... >>>>>> >>>>>> vii) in "Image secuence" you must select "Gradient by Gradient" >>>>>> option... >>>>>> >>>>>> viii) in "Raw-BIN Files folder you must specify the IMG file of the >>>>>> Analyze >>>>>> pair... >>>>>> >>>>>> ix) why you have 5 b0 volumes ?... to compute tractography, you must >>>>>> have >>>>>> only one b0 volume... you must put "100,100,100" in "Gradient Table" >>>>>> for >>>>>> each of the 4 b0 slices to skipt them... >>>>>> >>>>>> Sincerely, >>>>>> >>>>>> >>>>>> Gonzalo Rojas Costa >>>>>> Department of Radiology >>>>>> Las Condes Clinic >>>>>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >>>>>> Tel: 56-2-2105170 >>>>>> Cel: 56-9-97771785 >>>>>> www.clc.cl >>>>>> >>>>>> El 16-12-2009 1:07, Mark A. Pinsk escribi?: >>>>>>> >>>>>>> Thanks ! >>>>>>> >>>>>>> I converted by 4D NIFTI file to a 4D ANALYZE file as you suggested. >>>>>>> >>>>>>> I attempt to read it in as RAW, but it seems to get stuck... >>>>>>> >>>>>>> I specify the file in the Raw-BIN Files Folder field, but I get this >>>>>>> message: >>>>>>> "Number of files in this fold is less than expected: >>>>>>> (Img_Slices*Img_Blocks)." >>>>>>> >>>>>>> I only have a single .img/.hdr pair in my folder since it is a 4D >>>>>>> file >>>>>>> (i.e. it contains 65 volumes (5 b0 volumes + 60 directions)). >>>>>>> >>>>>>> Sorry, any help would be greatly appreciated. >>>>>>> Thanks >>>>>>> Mark >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Tue, Dec 15, 2009 at 10:29 PM, Gonzalo Rojas >>>>>>> wrote: >>>>>>>> >>>>>>>> Hi Mark: >>>>>>>> >>>>>>>> Yes... you could do all the processing that you mentioned (in FSL), >>>>>>>> and >>>>>>>> bring it to dti-studio... the FSL output file format is NIFTI.GZ... >>>>>>>> you >>>>>>>> must >>>>>>>> convert it to ANALYZE 4D, and then you must load that ANALYZE 4D >>>>>>>> file as >>>>>>>> a >>>>>>>> RAW data file format in DTI-STUDIO... >>>>>>>> >>>>>>>> Sincerely, >>>>>>>> >>>>>>>> >>>>>>>> Gonzalo Rojas Costa >>>>>>>> Department of Radiology >>>>>>>> Las Condes Clinic >>>>>>>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >>>>>>>> Tel: 56-2-2105170 >>>>>>>> Cel: 56-9-97771785 >>>>>>>> www.clc.cl >>>>>>>> >>>>>>>> El 15-12-2009 23:37, Mark A. Pinsk escribi?: >>>>>>>>> >>>>>>>>> Hi, someone asked this a while ago in the archives but I didn't see >>>>>>>>> a >>>>>>>>> reply. Can I use data that I've processed in FSL (eddy current >>>>>>>>> correction, motion correction, and field map-based undistortion) >>>>>>>>> and >>>>>>>>> bring it into dti-studio? The data is in one large 4D nifti file. >>>>>>>>> I >>>>>>>>> don't see where I can do this, is it not possible? >>>>>>>>> >>>>>>>>> thanks >>>>>>>>> mark >>>>>>>>> _______________________________________________ >>>>>>>>> Mristudio-users mailing list >>>>>>>>> Mristudio-users at mristudio.org >>>>>>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>>>>>> Unsubscribe, send a blank email to: >>>>>>>>> Mristudio-users-unsubscribe at mristudio.org >>>>>>>>> >>>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Mristudio-users mailing list >>>>>>> Mristudio-users at mristudio.org >>>>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>>>> Unsubscribe, send a blank email to: >>>>>>> Mristudio-users-unsubscribe at mristudio.org >>>>>>> >>>>>> >>>>> >>>> >>>> _______________________________________________ >>>> Mristudio-users mailing list >>>> Mristudio-users at mristudio.org >>>> http://lists.mristudio.org/mailman/listinfo/ >>>> Unsubscribe, send a blank email to: >>>> Mristudio-users-unsubscribe at mristudio.org >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> Mristudio-users mailing list >>>> Mristudio-users at mristudio.org >>>> http://lists.mristudio.org/mailman/listinfo/ >>>> Unsubscribe, send a blank email to: >>>> Mristudio-users-unsubscribe at mristudio.org >>>> >>> >>> _______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: >>> Mristudio-users-unsubscribe at mristudio.org >>> >> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > From junyiwang2002 at yahoo.com Thu Dec 17 11:18:40 2009 From: junyiwang2002 at yahoo.com (Jun Yi Wang) Date: Thu, 17 Dec 2009 08:18:40 -0800 (PST) Subject: [Mristudio-users] Using processed data In-Reply-To: References: <4B28542F.5000803@puc.cl> <4B28651A.4020202@puc.cl> <274936.72080.qm@web30701.mail.mud.yahoo.com> Message-ID: <660377.54711.qm@web50504.mail.re2.yahoo.com> Hi Mark, You can load the 4D analyze file in 3D viewer and then save it in raw file format. Then you can load the raw file in DTI mapping. Jun Yi Wang ________________________________ From: Mark A. Pinsk To: "DTI Studio, ROI Editor, Landmarker Questions/Support" Sent: Wed, December 16, 2009 4:43:53 PM Subject: Re: [Mristudio-users] Using processed data When I read in a 3D ANALYZE file using MRIView3D + Analyze file format, all of the parameters are grayed out, and they read as follows. This reads in the file successfully as far as I can tell. Image Width: 96 Image Height: 128 Image Slices: 1 ?? Coronal / Ant-Pos FOV: 96 x 128 Slice thickness: 1.1 Pixel Size: 0 x 0 ?? # of Image-blocks: 1 Word (16 Bits). Image File Format: Analyze Image Sequence: in blocks. On Wed, Dec 16, 2009 at 7:39 PM, Mark A. Pinsk wrote: > No luck. Let me outline my steps here: > > 1. I start with a 4D NIFTI file that contains 65 volumes (60 DWI + 5 B0). > The image dimensions are 96x128, 47 slices per volume. > Slice orientation is Coronal. FOV is 96x128. Pixels are 1x1x1.1. > > 2. I split the 4D NIFTI file into 65 3D NIFTI files using this FSL command: > fslsplit input.nii.gz > > 3. I convert each of the 65 3D NIFTI files to ANALYZE format: > fslchfiletype ANALYZE vol0000.nii.gz > [..] > fslchfiletype ANALYZE vol0064.nii.gz > > 4. I am able to successfully import the ANALYZE files in MRIView3D by > choosing Analyze format (but no luck with Raw format). > > 5. I have no luck importing the ANALYZE files in DTI Mapping choosing > Raw format. I get this message: > "Number of files in this fold is less than expected: (Img_Slices*Img_Blocks). > > Any suggestions? Thanks for all your help! > Mark > > > > > On Wed, Dec 16, 2009 at 1:34 PM, darshan pai wrote: >> when you say a 4D file I assume that you have a Analyze file with an entry on the number of volumes , Is it? . If it is then try to make it a 3D file with all the 65 slices added in the z direction and see if it helps.. >> >> Regards >> >> Dp >> >> >> >> ----- Original Message ---- >> From: Mark A. Pinsk >> To: "DTI Studio, ROI Editor, Landmarker Questions/Support" >> Sent: Wed, December 16, 2009 12:13:42 AM >> Subject: Re: [Mristudio-users] Using processed data >> >> Also, I should mention that the Analyze file loads just fine using >> "MRI View3D" and "Analyze" file format. >> >> >> On Wed, Dec 16, 2009 at 12:09 AM, Mark A. Pinsk wrote: >>> Thanks for your help, I'll do my best to answer them... >>> >>> FYI: these are small volumes from animal scans ( 1 x 1 x 1.1 mm resolution): >>> >>> Image Dimensions: 96 Width, 128 Height, 47 slices >>> Slice Orientation: Axial >>> Slice Sequencing: Inferior-Superior >>> FOV: 96 Width, 128 Height, 1.1 Slice Thickness >>> Pixel Size: 1.000 Width, 1.000 Height >>> Slices to be processed: 0 to 46, All Slices >>> Image Sequence: Gradient By Gradient >>> b_Value: 1000 >>> >>> My gradient table has 65 entries. The first 5 entries are B0 images, >>> the remaining 60 are for the 60 directions. There is no mean image at >>> the end of my data. I can discard 4 of the B0 images, but that does >>> not seem to make a difference on my error message. I have several B0 >>> images in accord with recent work that suggests having a ratio of 6:1 >>> diffusion to non-diffusion weighted images (Zhu et al. NeuroImage >>> 2008). >>> >>> >>> >>> On Tue, Dec 15, 2009 at 11:42 PM, Gonzalo Rojas wrote: >>>> Hi Mark: >>>> >>>> Many questions: >>>> >>>> i) do you specify correctly the "image slices" quantity in "iamge dimension" >>>> ?... that value is the quantitry of axial slices in each gradient >>>> direction... >>>> >>>> ii) and the "image width" and "image height" in "image dimension" ?... did >>>> you checked that values ?... >>>> >>>> ii) in "lice orientation" did you specify "axial" ?.. >>>> >>>> iii) and in "Voxel Size", "Field of View-width" and "Field of View-Heigth" >>>> did you specifiy the FOV value correctly ?... >>>> >>>> iv) you could check the previos values looking at "Pixel Size-Width" and >>>> "Pixel Size-Height"... >>>> >>>> v) in "Slices to be processed" it must appears 0-(image slices-1) >>>> >>>> vi) in gradient table you must put the 61 (0-60) directions... in your 4D >>>> analyze file is included the "mean" of all the 60 directions at the end of >>>> the file ?... if it is, you must put "100,100,100" as the last gradient >>>> direction to skip that image in the computation... >>>> >>>> vii) in "Image secuence" you must select "Gradient by Gradient" option... >>>> >>>> viii) in "Raw-BIN Files folder you must specify the IMG file of the Analyze >>>> pair... >>>> >>>> ix) why you have 5 b0 volumes ?... to compute tractography, you must have >>>> only one b0 volume... you must put "100,100,100" in "Gradient Table" for >>>> each of the 4 b0 slices to skipt them... >>>> >>>> Sincerely, >>>> >>>> >>>> Gonzalo Rojas Costa >>>> Department of Radiology >>>> Las Condes Clinic >>>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >>>> Tel: 56-2-2105170 >>>> Cel: 56-9-97771785 >>>> www.clc.cl >>>> >>>> El 16-12-2009 1:07, Mark A. Pinsk escribi?: >>>>> >>>>> Thanks ! >>>>> >>>>> I converted by 4D NIFTI file to a 4D ANALYZE file as you suggested. >>>>> >>>>> I attempt to read it in as RAW, but it seems to get stuck... >>>>> >>>>> I specify the file in the Raw-BIN Files Folder field, but I get this >>>>> message: >>>>> "Number of files in this fold is less than expected: >>>>> (Img_Slices*Img_Blocks)." >>>>> >>>>> I only have a single .img/.hdr pair in my folder since it is a 4D file >>>>> (i.e. it contains 65 volumes (5 b0 volumes + 60 directions)). >>>>> >>>>> Sorry, any help would be greatly appreciated. >>>>> Thanks >>>>> Mark >>>>> >>>>> >>>>> >>>>> >>>>> On Tue, Dec 15, 2009 at 10:29 PM, Gonzalo Rojas wrote: >>>>>> >>>>>> Hi Mark: >>>>>> >>>>>> Yes... you could do all the processing that you mentioned (in FSL), and >>>>>> bring it to dti-studio... the FSL output file format is NIFTI.GZ... you >>>>>> must >>>>>> convert it to ANALYZE 4D, and then you must load that ANALYZE 4D file as >>>>>> a >>>>>> RAW data file format in DTI-STUDIO... >>>>>> >>>>>> Sincerely, >>>>>> >>>>>> >>>>>> Gonzalo Rojas Costa >>>>>> Department of Radiology >>>>>> Las Condes Clinic >>>>>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >>>>>> Tel: 56-2-2105170 >>>>>> Cel: 56-9-97771785 >>>>>> www.clc.cl >>>>>> >>>>>> El 15-12-2009 23:37, Mark A. Pinsk escribi?: >>>>>>> >>>>>>> Hi, someone asked this a while ago in the archives but I didn't see a >>>>>>> reply. Can I use data that I've processed in FSL (eddy current >>>>>>> correction, motion correction, and field map-based undistortion) and >>>>>>> bring it into dti-studio? The data is in one large 4D nifti file. I >>>>>>> don't see where I can do this, is it not possible? >>>>>>> >>>>>>> thanks >>>>>>> mark >>>>>>> _______________________________________________ >>>>>>> Mristudio-users mailing list >>>>>>> Mristudio-users at mristudio.org >>>>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>>>> Unsubscribe, send a blank email to: >>>>>>> Mristudio-users-unsubscribe at mristudio.org >>>>>>> >>>>>> >>>>> >>>>> _______________________________________________ >>>>> Mristudio-users mailing list >>>>> Mristudio-users at mristudio.org >>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>> Unsubscribe, send a blank email to: >>>>> Mristudio-users-unsubscribe at mristudio.org >>>>> >>>> >>> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org >> >> >> >> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org >> > _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091217/346c1ac3/attachment-0001.html From mpinsk at gmail.com Thu Dec 17 11:21:30 2009 From: mpinsk at gmail.com (Mark A. Pinsk) Date: Thu, 17 Dec 2009 11:21:30 -0500 Subject: [Mristudio-users] Using processed data In-Reply-To: <660377.54711.qm@web50504.mail.re2.yahoo.com> References: <4B28542F.5000803@puc.cl> <4B28651A.4020202@puc.cl> <274936.72080.qm@web30701.mail.mud.yahoo.com> <660377.54711.qm@web50504.mail.re2.yahoo.com> Message-ID: Thanks for all your help. It looks like the issue is my data is in 32bit Float, and DTI Mapping wants it in 16 bit unsigned integer. Once I convert to 16bit, all should be well ! On Thu, Dec 17, 2009 at 11:18 AM, Jun Yi Wang wrote: > Hi Mark, > > You can load the 4D analyze file in 3D viewer and then save it in raw file > format.? Then you can load the raw file in DTI mapping. > > Jun Yi Wang > > ________________________________ > From: Mark A. Pinsk > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > > Sent: Wed, December 16, 2009 4:43:53 PM > Subject: Re: [Mristudio-users] Using processed data > > When I read in a 3D ANALYZE file using MRIView3D + Analyze file > format, all of the parameters are grayed out, and they read as > follows.? This reads in the file successfully as far as I can tell. > > Image Width: 96 > Image Height: 128 > Image Slices: 1? ?? > Coronal / Ant-Pos > FOV: 96 x 128 > Slice thickness: 1.1 > Pixel Size: 0 x 0? ?? > # of Image-blocks: 1 > Word (16 Bits). > Image File Format: Analyze > Image Sequence: in blocks. > > > On Wed, Dec 16, 2009 at 7:39 PM, Mark A. Pinsk wrote: >> No luck. ?Let me outline my steps here: >> >> 1. I start with a 4D NIFTI file that contains 65 volumes (60 DWI + 5 B0). >> The image dimensions are 96x128, 47 slices per volume. >> Slice orientation is Coronal. ?FOV is 96x128. ?Pixels are 1x1x1.1. >> >> 2. I split the 4D NIFTI file into 65 3D NIFTI files using this FSL >> command: >> fslsplit input.nii.gz >> >> 3. I convert each of the 65 3D NIFTI files to ANALYZE format: >> fslchfiletype ANALYZE vol0000.nii.gz >> [..] >> fslchfiletype ANALYZE vol0064.nii.gz >> >> 4. I am able to successfully import the ANALYZE files in MRIView3D by >> choosing Analyze format (but no luck with Raw format). >> >> 5. I have no luck importing the ANALYZE files in DTI Mapping choosing >> Raw format. ?I get this message: >> "Number of files in this fold is less than expected: >> (Img_Slices*Img_Blocks). >> >> Any suggestions? ?Thanks for all your help! >> Mark >> >> >> >> >> On Wed, Dec 16, 2009 at 1:34 PM, darshan pai wrote: >>> when you say a 4D file I assume that you have a Analyze file with an >>> entry on the number of volumes , Is it? . If it is then try to make it a 3D >>> file with all the 65 slices added in the z direction and see if it helps.. >>> >>> Regards >>> >>> Dp >>> >>> >>> >>> ----- Original Message ---- >>> From: Mark A. Pinsk >>> To: "DTI Studio, ROI Editor, Landmarker Questions/Support" >>> >>> Sent: Wed, December 16, 2009 12:13:42 AM >>> Subject: Re: [Mristudio-users] Using processed data >>> >>> Also, I should mention that the Analyze file loads just fine using >>> "MRI View3D" and "Analyze" file format. >>> >>> >>> On Wed, Dec 16, 2009 at 12:09 AM, Mark A. Pinsk wrote: >>>> Thanks for your help, I'll do my best to answer them... >>>> >>>> FYI: these are small volumes from animal scans ( 1 x 1 x 1.1 mm >>>> resolution): >>>> >>>> Image Dimensions: 96 Width, 128 Height, 47 slices >>>> Slice Orientation: Axial >>>> Slice Sequencing: Inferior-Superior >>>> FOV: 96 Width, 128 Height, 1.1 Slice Thickness >>>> Pixel Size: 1.000 Width, 1.000 Height >>>> Slices to be processed: 0 to 46, All Slices >>>> Image Sequence: Gradient By Gradient >>>> b_Value: 1000 >>>> >>>> My gradient table has 65 entries. ?The first 5 entries are B0 images, >>>> the remaining 60 are for the 60 directions. ?There is no mean image at >>>> the end of my data. ? I can discard 4 of the B0 images, but that does >>>> not seem to make a difference on my error message. ?I have several B0 >>>> images in accord with recent work that suggests having a ratio of 6:1 >>>> diffusion to non-diffusion weighted images (Zhu et al. NeuroImage >>>> 2008). >>>> >>>> >>>> >>>> On Tue, Dec 15, 2009 at 11:42 PM, Gonzalo Rojas wrote: >>>>> Hi Mark: >>>>> >>>>> ?Many questions: >>>>> >>>>> i) do you specify correctly the "image slices" quantity in "iamge >>>>> dimension" >>>>> ?... that value is the quantitry of axial slices in each gradient >>>>> direction... >>>>> >>>>> ii) and the "image width" and "image height" in "image dimension" ?... >>>>> did >>>>> you checked that values ?... >>>>> >>>>> ii) in "lice orientation" did you specify "axial" ?.. >>>>> >>>>> iii) and in "Voxel Size", "Field of View-width" and "Field of >>>>> View-Heigth" >>>>> did you specifiy the FOV value correctly ?... >>>>> >>>>> iv) you could check the previos values looking at "Pixel Size-Width" >>>>> and >>>>> "Pixel Size-Height"... >>>>> >>>>> v) in "Slices to be processed" it must appears 0-(image slices-1) >>>>> >>>>> vi) in gradient table you must put the 61 (0-60) directions... in your >>>>> 4D >>>>> analyze file is included the "mean" of all the 60 directions at the end >>>>> of >>>>> the file ?... if it is, you must put "100,100,100" as the last gradient >>>>> direction to skip that image in the computation... >>>>> >>>>> vii) in "Image secuence" you must select "Gradient by Gradient" >>>>> option... >>>>> >>>>> viii) in "Raw-BIN Files folder you must specify the IMG file of the >>>>> Analyze >>>>> pair... >>>>> >>>>> ix) why you have 5 b0 volumes ?... to compute tractography, you must >>>>> have >>>>> only one b0 volume... you must put "100,100,100" in "Gradient Table" >>>>> for >>>>> each of the 4 b0 slices to skipt them... >>>>> >>>>> ?Sincerely, >>>>> >>>>> >>>>> Gonzalo Rojas Costa >>>>> Department of Radiology >>>>> Las Condes Clinic >>>>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >>>>> Tel: 56-2-2105170 >>>>> Cel: 56-9-97771785 >>>>> www.clc.cl >>>>> >>>>> El 16-12-2009 1:07, Mark A. Pinsk escribi?: >>>>>> >>>>>> Thanks ! >>>>>> >>>>>> I converted by 4D NIFTI file to a 4D ANALYZE file as you suggested. >>>>>> >>>>>> I attempt to read it in as RAW, but it seems to get stuck... >>>>>> >>>>>> I specify the file in the Raw-BIN Files Folder field, but I get this >>>>>> message: >>>>>> "Number of files in this fold is less than expected: >>>>>> (Img_Slices*Img_Blocks)." >>>>>> >>>>>> I only have a single .img/.hdr pair in my folder since it is a 4D file >>>>>> (i.e. it contains 65 volumes (5 b0 volumes + 60 directions)). >>>>>> >>>>>> Sorry, any help would be greatly appreciated. >>>>>> Thanks >>>>>> Mark >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On Tue, Dec 15, 2009 at 10:29 PM, Gonzalo Rojas >>>>>> ?wrote: >>>>>>> >>>>>>> Hi Mark: >>>>>>> >>>>>>> ?Yes... you could do all the processing that you mentioned (in FSL), >>>>>>> and >>>>>>> bring it to dti-studio... the FSL output file format is NIFTI.GZ... >>>>>>> you >>>>>>> must >>>>>>> convert it to ANALYZE 4D, and then you must load that ANALYZE 4D file >>>>>>> as >>>>>>> a >>>>>>> RAW data file format in DTI-STUDIO... >>>>>>> >>>>>>> ?Sincerely, >>>>>>> >>>>>>> >>>>>>> Gonzalo Rojas Costa >>>>>>> Department of Radiology >>>>>>> Las Condes Clinic >>>>>>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >>>>>>> Tel: 56-2-2105170 >>>>>>> Cel: 56-9-97771785 >>>>>>> www.clc.cl >>>>>>> >>>>>>> El 15-12-2009 23:37, Mark A. Pinsk escribi?: >>>>>>>> >>>>>>>> Hi, someone asked this a while ago in the archives but I didn't see >>>>>>>> a >>>>>>>> reply. ? Can I use data that I've processed in FSL (eddy current >>>>>>>> correction, motion correction, and field map-based undistortion) and >>>>>>>> bring it into dti-studio? ? The data is in one large 4D nifti file. >>>>>>>> ?I >>>>>>>> don't see where I can do this, is it not possible? >>>>>>>> >>>>>>>> thanks >>>>>>>> mark >>>>>>>> _______________________________________________ >>>>>>>> Mristudio-users mailing list >>>>>>>> Mristudio-users at mristudio.org >>>>>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>>>>> Unsubscribe, send a blank email to: >>>>>>>> Mristudio-users-unsubscribe at mristudio.org >>>>>>>> >>>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Mristudio-users mailing list >>>>>> Mristudio-users at mristudio.org >>>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>>> Unsubscribe, send a blank email to: >>>>>> Mristudio-users-unsubscribe at mristudio.org >>>>>> >>>>> >>>> >>> >>> _______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: >>> Mristudio-users-unsubscribe at mristudio.org >>> >>> >>> >>> >>> >>> _______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: >>> Mristudio-users-unsubscribe at mristudio.org >>> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > From zamyadim at sri.utoronto.ca Thu Dec 17 13:09:39 2009 From: zamyadim at sri.utoronto.ca (Mojdeh) Date: Thu, 17 Dec 2009 13:09:39 -0500 Subject: [Mristudio-users] all positive eigenvectors! Message-ID: <4B2A73E3.2030603@sri.utoronto.ca> Hi there, I have 49 slice DTI image of brain with 2 B0 + 23 gradient directions. I loaded the image and calculated the tensor, eigenvectors, ... for the image and then save the results in analyze format. However, when I load the eigenvectors into MATLAB and look at the x-y-z coordinates of eigenvectors they are all positive numbers which doesn't make any sense to me! Does anyone know what might be the problem? Thanks a lot in advance, Mojdeh From susumu at mri.jhu.edu Fri Dec 18 22:15:14 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Fri, 18 Dec 2009 22:15:14 -0500 Subject: [Mristudio-users] all positive eigenvectors! In-Reply-To: <4B2A73E3.2030603@sri.utoronto.ca> References: <4B2A73E3.2030603@sri.utoronto.ca> Message-ID: Hi Mojdeh, Please load the eigenvector file into DtiStudio as a "vector" file and read the pixel-by-pixel values at the bottom of the window by placing the cursor. If you find that the vector file does contain both positive and negative elements, then, the problem seems to be the file reading by MatLab. Susumu On Thu, Dec 17, 2009 at 1:09 PM, Mojdeh wrote: > Hi there, > > I have 49 slice DTI image of brain with 2 B0 + 23 gradient directions. > I loaded the image and calculated the tensor, eigenvectors, ... for the > image and then save the results in analyze format. However, when I load > the eigenvectors into MATLAB and look at the x-y-z coordinates of > eigenvectors they are all positive numbers which doesn't make any sense > to me! Does anyone know what might be the problem? > > Thanks a lot in advance, > Mojdeh > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... 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Follow instructions in above notice Status: 4.7.0 -------------- next part -------------- >From Lucas Lessa Thu Dec 10 18:33:39 2009 X-Apparently-To: sl0003 at yahoo.com via 68.180.197.175; Thu, 10 Dec 2009 10:34:28 -0800 Return-Path: X-YMailISG: uXqKW70WLDvO8zwiqtHc74fl1uezQhXB.0ng6.vLymWtigDQK08Xb6mnA2dAL1IWK3d8db0qe6.iZkGb74jX6akuGi60GQcNjIiZ3CGntmdp1JGL0KQLN4VcLMdQhHMCkyb2wazLcBGo3juUa7_UHSEezYhPfWDlOIM70dnEaoKyf92eHa7hpMENgOPL4HoaAkf6nbncryHRiyCjHd4_PHuWJsiAsBxD.sqg1YiteIYSL5zPMMoVEeJFHY50SqywrB3jrDafB0zwXqvRzw67nuD_nIXmca7ClQw78qQmjzsx0djaDCvykZ_FTGsO9VUS03Rv2mzLP0MXlY0w3YzRzco3vUheOsT0BDyK6lI.Qq0xKtPDVA1oOwfnoYVAmQBHLotSduwNvQh06Oj6HQlgQww2D4.XHRJptabfc_V0Py8GYFRsLCkLE5IB9aiL8JW.vkwzPhpjUmZq X-Originating-IP: [162.129.8.141] Authentication-Results: mta1015.mail.ac4.yahoo.com from=mristudio.org; domainkeys=neutral (no sig); from=mristudio.org; dkim=neutral (no sig) Received: from 127.0.0.1 (EHLO ipex1.johnshopkins.edu) (162.129.8.141) by mta1015.mail.ac4.yahoo.com with SMTP; Thu, 10 Dec 2009 10:34:27 -0800 X-IronPort-Anti-Spam-Filtered: true X-IronPort-Anti-Spam-Result: An0IACPOIEuA3OjrjGdsb2JhbACCVY1HB4FugQKHCYEYEwEBAQocrA2Gc4hwhCsEhHR1F4F1gmc X-IronPort-AV: E=Sophos;i="4.47,376,1257138000"; d="scan'208";a="277023208" Received: from smtp.mristudio.org (HELO io16.mristudio.org) ([128.220.232.235]) by ipex1.johnshopkins.edu with ESMTP/TLS/DHE-RSA-AES256-SHA; 10 Dec 2009 13:34:23 -0500 Received: from io16.mristudio.org (io16.mristudio.org [127.0.0.1]) by io16.mristudio.org (8.13.8/8.13.8) with ESMTP id nBAIXhte027124; Thu, 10 Dec 2009 13:34:19 -0500 Received: from jhuin3.jhu.edu (jhuin3.jhu.edu [10.181.31.167]) by io16.mristudio.org (8.13.8/8.13.8) with ESMTP id nBAIXg5P027121 for ; Thu, 10 Dec 2009 13:33:42 -0500 Received: from ipex2.johnshopkins.edu (ipex2.johnshopkins.edu [162.129.8.151]) by jhuin3.jhu.edu (Sun Java System Messaging Server 6.1 HotFix 0.02 (built Aug 25 2004)) with ESMTPS id <0KUG00IR78W68820 at jhuin3.jhu.edu> for mristudio-users at mristudio.org; Thu, 10 Dec 2009 13:33:42 -0500 (EST) Received: from web110209.mail.gq1.yahoo.com ([67.195.8.185]) by ipex2.johnshopkins.edu with SMTP; Thu, 10 Dec 2009 13:33:40 -0500 Received: (qmail 3641 invoked by uid 60001); Thu, 10 Dec 2009 18:33:40 +0000 Received: from [200.245.168.181] by web110209.mail.gq1.yahoo.com via HTTP; Thu, 10 Dec 2009 10:33:39 -0800 (PST) Date: Thu, 10 Dec 2009 10:33:39 -0800 (PST) From: Lucas Lessa In-reply-to: To: ROI Editor Landmarker Questions/SupportDTI Studio Message-id: <200110.2554.qm at web110209.mail.gq1.yahoo.com> MIME-version: 1.0 X-Mailer: YahooMailClassic/9.0.19 YahooMailWebService/0.8.100.260964 X-IronPort-Anti-Spam-Filtered: true X-IronPort-Anti-Spam-Result: AuEBACPOIEtDwwi5mWdsb2JhbACCVY1HgXWBAocJgSsBAQEBAQgLCgcTq3qBMYVCiGoBBQQBhCYEhHR1F4F1 X-IronPort-AV: E=Sophos;i="4.47,376,1257138000"; d="scan'208";a="278725189" X-YMail-OSG: GJTukmYVM1mg5MqkTIHG3JE2wcoV8vAO8_kmtmFlMBy0AuJA..gCkxCf Subject: Re: [Mristudio-users] Is better to do 3 DTI series or just one well done? X-BeenThere: mristudio-users at mristudio.org X-Mailman-Version: 2.1.9 Precedence: list Reply-To: "DTI Studio, ROI Editor, Landmarker Questions/Support" List-Id: "DTI Studio, ROI Editor, Landmarker Questions/Support" List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Content-Type: multipart/mixed; boundary="===============8005539807460804403==" Sender: mristudio-users-bounces at mristudio.org Errors-To: mristudio-users-bounces at mristudio.org Content-Length: 11439 From saksena.sona at gmail.com Tue Dec 22 10:39:37 2009 From: saksena.sona at gmail.com (Sona Saksena) Date: Tue, 22 Dec 2009 10:39:37 -0500 Subject: [Mristudio-users] a question about gradient table in dpf file In-Reply-To: References: <662032.53943.qm@web110201.mail.gq1.yahoo.com> Message-ID: <9018fecc0912220739w20330ca3nbcddcfcf97117d3f@mail.gmail.com> Hello, I have downloaded DtiStudio latest-x86.exe version. While I am processing the DTI data acquired in 26 non-collinear directions using DTI Mapping, an error occurs saying that MriView3D MFC Application has encountered a problem and needs to close. Please suggest what to do. Thanks Sona On Mon, Dec 14, 2009 at 4:25 PM, Yi Jiang wrote: > Hello, I am wondering if it's fine to use two b0 images in the gradient > table in the dpf file, such as following: > > Begin_Of_Gradient_Table > 0: 0,0,0 > 1: 160, 160, 0 > 2: 0, -160, 160 > 3: -160, 0, -160 > 4: 160, -160, 0 > 5: 0, 160, 160 > 6: 160, 0, -160 > 7: 0,0,0 > 8: -160, -160, 0 > 9: 0, 160, -160 > 10: 160, 0, 160 > 11: -160, 160, 0 > 12: 0, -160, -160 > 13: -160, 0, 160 > > End_Of_Gradient_Table > > > Is DTIStudio able to recoganize and use both b0 images? > > Moreover, is there a way to specify b-value for the b0 images (e.g., > although very low, it may be 10 or 50, instead of 0)? > > Thank you very much! > > Best, > Yi > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -- Sona Saksena Ph. D Scholar -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091222/b4dc14ef/attachment.html From zamyadim at sri.utoronto.ca Tue Dec 22 11:18:25 2009 From: zamyadim at sri.utoronto.ca (Mojdeh) Date: Tue, 22 Dec 2009 11:18:25 -0500 Subject: [Mristudio-users] all positive eigenvectors! In-Reply-To: <4B2A73E3.2030603@sri.utoronto.ca> References: <4B2A73E3.2030603@sri.utoronto.ca> Message-ID: <4B30F151.80101@sri.utoronto.ca> Thanks Susumu! I looked at the eigenvector file in the DTIstudio and it indeed has both + and - numbers! The problem is that when I save the file in the "Analyze" format and open it in MATLAB all the values are between 0-1! I was thinking this is because the real x-y-z coordinate values are converted into RGB values, is this right? how can I access the actual coordinate values in MATLAB? Thanks a lot, Mojdeh Mojdeh wrote: > Hi there, > > I have 49 slice DTI image of brain with 2 B0 + 23 gradient > directions. I loaded the image and calculated the tensor, > eigenvectors, ... for the image and then save the results in analyze > format. However, when I load the eigenvectors into MATLAB and look at > the x-y-z coordinates of eigenvectors they are all positive numbers > which doesn't make any sense to me! Does anyone know what might be the > problem? > > Thanks a lot in advance, > Mojdeh > From support at mristudio.org Tue Dec 22 11:18:25 2009 From: support at mristudio.org (support at mristudio.org) Date: Tue, 22 Dec 2009 11:18:25 -0500 (EST) Subject: [Mristudio-users] a question about gradient table in dpf file In-Reply-To: <9018fecc0912220739w20330ca3nbcddcfcf97117d3f@mail.gmail.com> References: <662032.53943.qm@web110201.mail.gq1.yahoo.com> <9018fecc0912220739w20330ca3nbcddcfcf97117d3f@mail.gmail.com> Message-ID: <4667.10.16.57.13.1261498705.squirrel@webmail.mristudio.org> at first, please check: 1. the # of gradients in the gradient table should match with that of the image volumes; 2. all images are been re-constructed correctly; the images have same image dimensions; regards, > Hello, > > I have downloaded DtiStudio latest-x86.exe version. While I am processing > the DTI data acquired in 26 non-collinear directions using DTI Mapping, an > error occurs saying that MriView3D MFC Application has encountered a problem > and needs to close. > > Please suggest what to do. > > Thanks > > Sona > > On Mon, Dec 14, 2009 at 4:25 PM, Yi Jiang wrote: > >> Hello, I am wondering if it's fine to use two b0 images in the gradient >> table in the dpf file, such as following: >> >> Begin_Of_Gradient_Table >> 0: 0,0,0 >> 1: 160, 160, 0 >> 2: 0, -160, 160 >> 3: -160, 0, -160 >> 4: 160, -160, 0 >> 5: 0, 160, 160 >> 6: 160, 0, -160 >> 7: 0,0,0 >> 8: -160, -160, 0 >> 9: 0, 160, -160 >> 10: 160, 0, 160 >> 11: -160, 160, 0 >> 12: 0, -160, -160 >> 13: -160, 0, 160 >> >> End_Of_Gradient_Table >> >> >> Is DTIStudio able to recoganize and use both b0 images? >> >> Moreover, is there a way to specify b-value for the b0 images (e.g., >> although very low, it may be 10 or 50, instead of 0)? >> >> Thank you very much! >> >> Best, >> Yi >> >> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > > -- > Sona Saksena > Ph. D Scholar > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > From grojasy at puc.cl Wed Dec 23 10:29:25 2009 From: grojasy at puc.cl (Gonzalo Rojas) Date: Wed, 23 Dec 2009 12:29:25 -0300 Subject: [Mristudio-users] DTI-Studio and tensor filtering... Message-ID: <4B323755.6020906@puc.cl> Hi: How can I do a tensor filtering (or smoothing) with DTI-Studio ?... Do you know any other tractography related software that have those option ?... Sincerely, Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl From susumu at mri.jhu.edu Wed Dec 23 10:56:23 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 23 Dec 2009 10:56:23 -0500 Subject: [Mristudio-users] DTI-Studio and tensor filtering... In-Reply-To: <4B323755.6020906@puc.cl> References: <4B323755.6020906@puc.cl> Message-ID: DtiStudio doesn't have functions for spatial filtering. DiffeoMap has some functions for resampling images for tensor data. On Wed, Dec 23, 2009 at 10:29 AM, Gonzalo Rojas wrote: > Hi: > > How can I do a tensor filtering (or smoothing) with DTI-Studio ?... > Do you know any other tractography related software that have those > option ?... > > Sincerely, > > > Gonzalo Rojas Costa > Department of Radiology > Las Condes Clinic > Lo Fontecilla 441, Las Condes, Santiago, Chile. > Tel: 56-2-2105170 > Cel: 56-9-97771785 > www.clc.cl > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091223/9eb32f4d/attachment.html From HuangS4 at uthscsa.edu Wed Dec 23 14:56:40 2009 From: HuangS4 at uthscsa.edu (Huang, Shiliang) Date: Wed, 23 Dec 2009 13:56:40 -0600 Subject: [Mristudio-users] How to do in plan fiber tracking with ROI in DTIStudio Message-ID: <54BCF36E4FE44644A377261164E3104548CF49FBB2@HSC-M2.win.uthscsa.edu> Hi I did fiber tracking with DTIStudio. But I want to get the statics of in-plan fiber tracking with ROI. I want to get only the in-plan fiber in a ROI (I do not want to include the fibers which cross this plan). Who can tell me how to do? Thanks, Shiliang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091223/b25dc316/attachment.html From susumu at mri.jhu.edu Wed Dec 23 15:05:00 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 23 Dec 2009 15:05:00 -0500 Subject: [Mristudio-users] How to do in plan fiber tracking with ROI in DTIStudio In-Reply-To: <54BCF36E4FE44644A377261164E3104548CF49FBB2@HSC-M2.win.uthscsa.edu> References: <54BCF36E4FE44644A377261164E3104548CF49FBB2@HSC-M2.win.uthscsa.edu> Message-ID: After you get, for example, FA of the entire fiber using the "statistics" button, a button called "profile" is available within the same window. This will give you a number for each slice in all three directions. On Wed, Dec 23, 2009 at 2:56 PM, Huang, Shiliang wrote: > Hi > > I did fiber tracking with DTIStudio. But I want to get the statics of > in-plan fiber tracking with ROI. I want to get only the in-plan fiber in a > ROI (I do not want to include the fibers which cross this plan). Who can > tell me how to do? > > Thanks, > > Shiliang > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091223/aba4d6ba/attachment-0001.html From faridisme at gmail.com Mon Dec 28 19:34:02 2009 From: faridisme at gmail.com (mdfarid a r) Date: Tue, 29 Dec 2009 08:34:02 +0800 Subject: [Mristudio-users] DTI-Studio ROI operations and saving tensor as .d file Message-ID: <7e403aa50912281634v6ba909ddj4b36a41500fa3e13@mail.gmail.com> Hi all, I am trying to revisualise the fibertracks after I process it in matlab. To be specific, I merely select a number of the fibers instead of all the fibers before I rewrite it into the file format. However, I realised that fibertracks which I obtained by using the ROI operation CUT will cause an error in DTIStudio causing it to close. The fibertracks which I obtained by using the ROI operation OR and AND did not have this problem and worked fine. Has anyone else encountered this situation? A second thing, how do I save the calculated tensors as .d file? I look forward to your kind assistance. Regards, Farid -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091229/e16106e0/attachment.html From HuangS4 at uthscsa.edu Tue Dec 29 14:37:22 2009 From: HuangS4 at uthscsa.edu (Huang, Shiliang) Date: Tue, 29 Dec 2009 13:37:22 -0600 Subject: [Mristudio-users] How to do in plan fiber tracking with ROI in DTIStudio In-Reply-To: References: <54BCF36E4FE44644A377261164E3104548CF49FBB2@HSC-M2.win.uthscsa.edu> Message-ID: <54BCF36E4FE44644A377261164E3104548CF49FBF3@HSC-M2.win.uthscsa.edu> Thank you Mor But it seems like there are no the value of the Maximum length ,Minimum length after I push the "profile".How can I get the Maximum length ,Minimum length of the in-plan fiber in a ROI? Thanks, Shiliang From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori Sent: Wednesday, December 23, 2009 2:05 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] How to do in plan fiber tracking with ROI in DTIStudio After you get, for example, FA of the entire fiber using the "statistics" button, a button called "profile" is available within the same window. This will give you a number for each slice in all three directions. On Wed, Dec 23, 2009 at 2:56 PM, Huang, Shiliang > wrote: Hi I did fiber tracking with DTIStudio. But I want to get the statics of in-plan fiber tracking with ROI. I want to get only the in-plan fiber in a ROI (I do not want to include the fibers which cross this plan). Who can tell me how to do? Thanks, Shiliang _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091229/8d6c1cb8/attachment.html From susumu at mri.jhu.edu Wed Dec 30 14:31:00 2009 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 30 Dec 2009 14:31:00 -0500 Subject: [Mristudio-users] DTI-Studio ROI operations and saving tensor as .d file In-Reply-To: <7e403aa50912281634v6ba909ddj4b36a41500fa3e13@mail.gmail.com> References: <7e403aa50912281634v6ba909ddj4b36a41500fa3e13@mail.gmail.com> Message-ID: Hi Farid, As for your first question, it is difficult to answer not exactly knowing what you did with matlab and possible errors. For the second question, after you finish tensor calculation, you can obtain dxx, dyy, dzz, dxy, dxz, dyz images. What we call *.d file is a 4D data that contains the all 6 3D tensor element images within one file. You can save these 6 images at once into one file using DtiStudio. Susumu On Mon, Dec 28, 2009 at 7:34 PM, mdfarid a r wrote: > > Hi all, > > I am trying to revisualise the fibertracks after I process it in matlab. To > be specific, I merely select a number of the fibers instead of all the > fibers before I rewrite it into the file format. However, I realised that > fibertracks which I obtained by using the ROI operation CUT will cause an > error in DTIStudio causing it to close. The fibertracks which I obtained by > using the ROI operation OR and AND did not have this problem and worked > fine. Has anyone else encountered this situation? > > A second thing, how do I save the calculated tensors as .d file? > > I look forward to your kind assistance. > > Regards, > Farid > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20091230/f9f868aa/attachment.html