From lianocd at gmail.com  Mon Jan  3 02:33:29 2011
From: lianocd at gmail.com (Qingwei Li)
Date: Mon, 03 Jan 2011 15:33:29 +0800
Subject: [Mristudio-users] Happy New Year!
In-Reply-To: <AANLkTik8TUGQHABZQNn+pNCt3J1NRrE4h7xNOCcH6g4B@mail.gmail.com>
References: <AANLkTik8TUGQHABZQNn+pNCt3J1NRrE4h7xNOCcH6g4B@mail.gmail.com>
Message-ID: <AANLkTimKiUtvmZRwn8WkahdNK0AJU+m27W0GQcYZekyL@mail.gmail.com>

??????

?????????????????????

On Sat, Jan 1, 2011 at 7:36 AM, Chunxiao Zhou <czhou4 at gmail.com> wrote:

> Dear MRIStudio Experts,
>
> I want to take the time to wish you and your family a VERY Happy New
> Year!  Thank you for your consistent help! I wanted you to know that
> all your efforts are appreciated.
>
> Have a wonderful 2011!
>
> Chunxiao(Andrew)
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>



-- 
Qingwei Li
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From zamyadim at sri.utoronto.ca  Thu Jan  6 10:16:34 2011
From: zamyadim at sri.utoronto.ca (Mojdeh)
Date: Thu, 06 Jan 2011 10:16:34 -0500
Subject: [Mristudio-users] DiffeoMap Remote Processing
Message-ID: <4D25DCD2.6010202@sri.utoronto.ca>

Hi there,
I submitted a job through DiffeoMap's LDDMM for remote processing last 
Friday (Dec 31) and have not yet received any emails ... could someone 
tell me how long does it usually take for a job to be complete or 
whether I need to resubmit?
thanks,
Mojdeh

From akolasny at jhu.edu  Thu Jan  6 10:20:36 2011
From: akolasny at jhu.edu (akolasny at jhu.edu)
Date: Thu, 06 Jan 2011 10:20:36 -0500 (EST)
Subject: [Mristudio-users] DiffeoMap Remote Processing
In-Reply-To: <4D25DCD2.6010202@sri.utoronto.ca>
References: <4D25DCD2.6010202@sri.utoronto.ca>
Message-ID: <47129.192.168.2.29.1294327236.squirrel@webmail.cis.jhu.edu>


Mojdeh,

Please check your spam filter. Maybe, the email messages got sent there.

I checked the logs. There was a job that completed with
your identity. I'll provide it in a followup email.

-Anthony


> Hi there,
> I submitted a job through DiffeoMap's LDDMM for remote processing last
> Friday (Dec 31) and have not yet received any emails ... could someone
> tell me how long does it usually take for a job to be complete or
> whether I need to resubmit?
> thanks,
> 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
>



From zamyadim at sri.utoronto.ca  Thu Jan  6 12:09:05 2011
From: zamyadim at sri.utoronto.ca (Mojdeh)
Date: Thu, 06 Jan 2011 12:09:05 -0500
Subject: [Mristudio-users] more DiffeoMap questions
Message-ID: <4D25F731.6070800@sri.utoronto.ca>

Hi all :)
I finally managed to successfully run and download the results of my 
first LDDMM job ... now I have a question about viewing the output 
transformations. In the manual located @ 
https://www.mristudio.org/wiki/user_manual/diffeomap/MultichannelVolumeLDDMM 
, it's mentioned that "output transformation matrix can be loaded by 
clicking the load button under the Volume LDDMM menu and can be saved 
Raw format. However, in my DiffeoMap there is only one "Retrieve Results 
>From Remote Volume LDDMM" which can only be used for retrieving the data 
and not loading them! Could you please advise me on how to access the 
raw transformations and also how to view the "transformed target" image?
Thanks for the help,
Mojdeh


From xli16 at jhmi.edu  Thu Jan  6 12:22:11 2011
From: xli16 at jhmi.edu (Xin Li)
Date: Thu, 06 Jan 2011 12:22:11 -0500
Subject: [Mristudio-users] more DiffeoMap questions
In-Reply-To: <4D25F731.6070800@sri.utoronto.ca>
References: <4D25F731.6070800@sri.utoronto.ca>
Message-ID: <7230e613c5aa.4d25b3f3@johnshopkins.edu>

Hello,

After you retrieve the resultant data, you can load the trasformation matrix Kimap by clicking the button "Load Transformation Matrix" in the tool panel in the subject window. The Kimap file is in VTK format.

The "Getting Started" section at https://www.mristudio.org/wiki/user_manual/diffeomap should be able to answer your questions.


Xin



----- Original Message -----
From: Mojdeh <zamyadim at sri.utoronto.ca>
Date: Thursday, January 6, 2011 12:09 pm
Subject: [Mristudio-users] more DiffeoMap questions
To: mristudio-users at mristudio.org


> Hi all :)
>  I finally managed to successfully run and download the results of my 
> 
>  first LDDMM job ... now I have a question about viewing the output 
>  transformations. In the manual located @ 
>   
>  , it's mentioned that "output transformation matrix can be loaded by 
> 
>  clicking the load button under the Volume LDDMM menu and can be saved 
> 
>  Raw format. However, in my DiffeoMap there is only one "Retrieve 
> Results 
>  >From Remote Volume LDDMM" which can only be used for retrieving the 
> data 
>  and not loading them! Could you please advise me on how to access the 
> 
>  raw transformations and also how to view the "transformed target" image?
>  Thanks for the help,
>  Mojdeh
>  
>  _______________________________________________
>  mristudio-users mailing list
>  mristudio-users at mristudio.org
>  
>  Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org 

From j.houenou at yahoo.fr  Sun Jan  9 15:29:28 2011
From: j.houenou at yahoo.fr (Josselin)
Date: Sun, 09 Jan 2011 20:29:28 +0000 (GMT)
Subject: [Mristudio-users] LDDMM Processing started once again
Message-ID: <94113.49839.qm@web25602.mail.ukl.yahoo.com>

Hello everyone,
I have just received several emails from <lddmmproc at cis.jhu.edu>noticing me ICM 
Multichannel Processings which have already been done around the 5th of 
January(e.g. eead2982115e7e90dff57a080ae665a3).
Has there been any issue with these processings ?
Thanks !
Best regards,
Josselin Houenou



      


From susumu at mri.jhu.edu  Sun Jan  9 18:06:05 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Sun, 09 Jan 2011 18:06:05 -0500
Subject: [Mristudio-users] LDDMM Processing started once again
In-Reply-To: <94113.49839.qm@web25602.mail.ukl.yahoo.com>
References: <94113.49839.qm@web25602.mail.ukl.yahoo.com>
Message-ID: <AANLkTi=-zNK4rT4RvBty3o4Pn3q6P9Ka1q0-4yjogVHn@mail.gmail.com>

Hi all,

Yes, there was a bug in the latest upgrade of the LDDMM pipeline and
everybody who received the faulty data are now getting emails. The data are
supposed to be reprocessed automatically and you need to reload the correct
data based on the information in the email. I believe the error started on
12/28. If you receive emails, please disregard the data you received
previously and download the new one.

This affects those who used the cascading (multiple) alpha method. If you
used the 3-alpha approach, you receive Kimap001, Kimap002, Kimap003, and
Kimap. The final "Kimap" is supposed to be the combination of the all other
3 Kimaps, but this combination routine was not working. You can still obtain
the correct overall Kimap by manually combining the previous three Kimap
(001,002,003), but soon you should receive the correct combined Kimap.

Sorry for this error and we hope that it didn't cost you much time.

Susumu

On Sun, Jan 9, 2011 at 3:29 PM, Josselin <j.houenou at yahoo.fr> wrote:

> Hello everyone,
> I have just received several emails from <lddmmproc at cis.jhu.edu>noticing
> me ICM
> Multichannel Processings which have already been done around the 5th of
> January(e.g. eead2982115e7e90dff57a080ae665a3).
> Has there been any issue with these processings ?
> Thanks !
> Best regards,
> Josselin Houenou
>
>
>
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
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From j.houenou at yahoo.fr  Sun Jan  9 18:14:41 2011
From: j.houenou at yahoo.fr (Josselin)
Date: Sun, 09 Jan 2011 23:14:41 +0000 (GMT)
Subject: [Mristudio-users] Re :  LDDMM Processing started once again
In-Reply-To: <AANLkTi=-zNK4rT4RvBty3o4Pn3q6P9Ka1q0-4yjogVHn@mail.gmail.com>
References: <94113.49839.qm@web25602.mail.ukl.yahoo.com>
	<AANLkTi=-zNK4rT4RvBty3o4Pn3q6P9Ka1q0-4yjogVHn@mail.gmail.com>
Message-ID: <530623.19059.qm@web25605.mail.ukl.yahoo.com>

Hi,

Thanks for the reply. 
Has the bug affected also Hmaps ?

Josselin




________________________________
De : susumu mori <susumu at mri.jhu.edu>
? : "DTI Studio, ROI Editor, DiffeoMap Questions/Support" 
<mristudio-users at mristudio.org>
Envoy? le : Lun 10 janvier 2011, 0h 06min 05s
Objet : Re: [Mristudio-users] LDDMM Processing started once again

Hi all,

Yes, there was a bug in the latest upgrade of the LDDMM pipeline and everybody 
who received the faulty data are now getting emails. The data are supposed to be 
reprocessed automatically and you need to reload the correct data based on the 
information in the email. I believe the error started on 12/28. If you receive 
emails, please disregard the data you received previously and download the new 
one.

This affects those who used the cascading (multiple) alpha method. If you used 
the 3-alpha approach, you receive Kimap001, Kimap002, Kimap003, and Kimap. The 
final "Kimap" is supposed to be the combination of the all other 3 Kimaps, but 
this combination routine was not working. You can still obtain the correct 
overall Kimap by manually combining the previous three Kimap (001,002,003), but 
soon you should receive the correct combined Kimap. 

Sorry for this error and we hope that it didn't cost you much time.

Susumu


On Sun, Jan 9, 2011 at 3:29 PM, Josselin <j.houenou at yahoo.fr> wrote:

Hello everyone,
>I have just received several emails from <lddmmproc at cis.jhu.edu>noticing me ICM
>Multichannel Processings which have already been done around the 5th of
>January(e.g. eead2982115e7e90dff57a080ae665a3).
>Has there been any issue with these processings ?
>Thanks !
>Best regards,
>Josselin Houenou
>
>
>
>
>
>_______________________________________________
>mristudio-users mailing list
>mristudio-users at mristudio.org
>http://lists.mristudio.org/mailman/listinfo/
>Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org
>



      
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From acy.chung at gmail.com  Sun Jan  9 18:36:47 2011
From: acy.chung at gmail.com (Alice)
Date: Mon, 10 Jan 2011 07:36:47 +0800
Subject: [Mristudio-users] LDDMM Processing started once again
In-Reply-To: <94113.49839.qm@web25602.mail.ukl.yahoo.com>
References: <94113.49839.qm@web25602.mail.ukl.yahoo.com>
Message-ID: <AANLkTikcr8+xN5MW_3-61d7rUbKXjbwS1Rc-kX_7ZA9w@mail.gmail.com>

Thanks
I will translate the information to my classmate.
Alice
????????,????,??????,
????????????,????????~112009~



2011/1/10 Josselin <j.houenou at yahoo.fr>

> Hello everyone,
> I have just received several emails from <lddmmproc at cis.jhu.edu>noticing
> me ICM
> Multichannel Processings which have already been done around the 5th of
> January(e.g. eead2982115e7e90dff57a080ae665a3).
> Has there been any issue with these processings ?
> Thanks !
> Best regards,
> Josselin Houenou
>
>
>
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
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From susumu at mri.jhu.edu  Sun Jan  9 20:39:56 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Sun, 09 Jan 2011 20:39:56 -0500
Subject: [Mristudio-users] Re : LDDMM Processing started once again
In-Reply-To: <530623.19059.qm@web25605.mail.ukl.yahoo.com>
References: <94113.49839.qm@web25602.mail.ukl.yahoo.com>
	<AANLkTi=-zNK4rT4RvBty3o4Pn3q6P9Ka1q0-4yjogVHn@mail.gmail.com>
	<530623.19059.qm@web25605.mail.ukl.yahoo.com>
Message-ID: <AANLkTi=h8s80bA9uE8nVwEqngOWdQ=x9-j6v6zVUW2FV@mail.gmail.com>

I believe so.

On Sun, Jan 9, 2011 at 6:14 PM, Josselin <j.houenou at yahoo.fr> wrote:

> Hi,
>
> Thanks for the reply.
> Has the bug affected also Hmaps ?
>
> Josselin
>
> ------------------------------
> *De :* susumu mori <susumu at mri.jhu.edu>
> *? :* "DTI Studio, ROI Editor, DiffeoMap Questions/Support" <
> mristudio-users at mristudio.org>
> *Envoy? le :* Lun 10 janvier 2011, 0h 06min 05s
> *Objet :* Re: [Mristudio-users] LDDMM Processing started once again
>
> Hi all,
>
> Yes, there was a bug in the latest upgrade of the LDDMM pipeline and
> everybody who received the faulty data are now getting emails. The data are
> supposed to be reprocessed automatically and you need to reload the correct
> data based on the information in the email. I believe the error started on
> 12/28. If you receive emails, please disregard the data you received
> previously and download the new one.
>
> This affects those who used the cascading (multiple) alpha method. If you
> used the 3-alpha approach, you receive Kimap001, Kimap002, Kimap003, and
> Kimap. The final "Kimap" is supposed to be the combination of the all other
> 3 Kimaps, but this combination routine was not working. You can still obtain
> the correct overall Kimap by manually combining the previous three Kimap
> (001,002,003), but soon you should receive the correct combined Kimap.
>
> Sorry for this error and we hope that it didn't cost you much time.
>
> Susumu
>
> On Sun, Jan 9, 2011 at 3:29 PM, Josselin <j.houenou at yahoo.fr> wrote:
>
>> Hello everyone,
>> I have just received several emails from <lddmmproc at cis.jhu.edu>noticing
>> me ICM
>> Multichannel Processings which have already been done around the 5th of
>> January(e.g. eead2982115e7e90dff57a080ae665a3).
>> Has there been any issue with these processings ?
>> Thanks !
>> Best regards,
>> Josselin Houenou
>>
>>
>>
>>
>>
>> _______________________________________________
>> mristudio-users mailing 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
>
>
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From j.houenou at yahoo.fr  Tue Jan 11 16:13:29 2011
From: j.houenou at yahoo.fr (Josselin)
Date: Tue, 11 Jan 2011 21:13:29 +0000 (GMT)
Subject: [Mristudio-users] a question about applying the AIR and LDDMM
	transformations
Message-ID: <202779.88698.qm@web25602.mail.ukl.yahoo.com>

Hello everyone,

When I apply an AIR transformation matrix or a LDDMM transformation matrix (e.g. 
a Hmap.vtk) on a "subject" image in diffeomap, what kind of information is used 
from the "template" image ? Is this only the size of the template image used ?

Thanks,

Josselin Houenou



      


From xli16 at jhmi.edu  Tue Jan 11 17:27:36 2011
From: xli16 at jhmi.edu (Xin Li)
Date: Tue, 11 Jan 2011 17:27:36 -0500
Subject: [Mristudio-users] a question about applying the AIR and LDDMM
 transformations
In-Reply-To: <202779.88698.qm@web25602.mail.ukl.yahoo.com>
References: <202779.88698.qm@web25602.mail.ukl.yahoo.com>
Message-ID: <7280a8a2112ed.4d2c9308@johnshopkins.edu>

Yes. Only the size of the template image is used. So you can load FA, DWI or any other image as the template as long as the size is the same.


xin

----- Original Message -----
From: Josselin <j.houenou at yahoo.fr>
Date: Tuesday, January 11, 2011 4:13 pm
Subject: [Mristudio-users] a question about applying the AIR and LDDMM transformations
To: mristudio-users at mristudio.org


> Hello everyone,
>  
>  When I apply an AIR transformation matrix or a LDDMM transformation 
> matrix (e.g. 
>  a Hmap.vtk) on a "subject" image in diffeomap, what kind of 
> information is used 
>  from the "template" image ? Is this only the size of the template 
> image used ?
>  
>  Thanks,
>  
>  Josselin Houenou
>  
>  
>  
>        
>  
>  _______________________________________________
>  mristudio-users mailing list
>  mristudio-users at mristudio.org
>  
>  Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org 

From sorento7 at gmail.com  Fri Jan 14 13:51:12 2011
From: sorento7 at gmail.com (Sourena Soheili)
Date: Fri, 14 Jan 2011 10:51:12 -0800
Subject: [Mristudio-users] more DiffeoMap questions
In-Reply-To: <4D25F731.6070800@sri.utoronto.ca>
References: <4D25F731.6070800@sri.utoronto.ca>
Message-ID: <AANLkTinJHOdKqfhm3q6L3+jy8MvSseiTyHncOvks1AWB@mail.gmail.com>

Dear Mojdeh
Are you iranian? Cuz I'd like to find someone with my nationality here
for consult.
Sourena

On Thursday, January 6, 2011, Mojdeh <zamyadim at sri.utoronto.ca> wrote:
> Hi all :)
> I finally managed to successfully run and download the results of my
> first LDDMM job ... now I have a question about viewing the output
> transformations. In the manual located @
> https://www.mristudio.org/wiki/user_manual/diffeomap/MultichannelVolumeLDDMM
> , it's mentioned that "output transformation matrix can be loaded by
> clicking the load button under the Volume LDDMM menu and can be saved
> Raw format. However, in my DiffeoMap there is only one "Retrieve Results
> >From Remote Volume LDDMM" which can only be used for retrieving the data
> and not loading them! Could you please advise me on how to access the
> raw transformations and also how to view the "transformed target" image?
> Thanks for the help,
> 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
>

From varintsai at gmail.com  Fri Jan 14 14:03:53 2011
From: varintsai at gmail.com (Varin Tsai)
Date: Fri, 14 Jan 2011 11:03:53 -0800
Subject: [Mristudio-users] more DiffeoMap questions
In-Reply-To: <AANLkTinJHOdKqfhm3q6L3+jy8MvSseiTyHncOvks1AWB@mail.gmail.com>
References: <4D25F731.6070800@sri.utoronto.ca>
	<AANLkTinJHOdKqfhm3q6L3+jy8MvSseiTyHncOvks1AWB@mail.gmail.com>
Message-ID: <4D309E19.8090004@gmail.com>

Hi,

I have a question on file conversion and Siemens Mosaic files.  I 
recently received a patient for processing whos files came in Siemens 
Mosaic.  After having ran through such protocols as DCM2NII.gui, I had a 
30 direction set of files that, when run through Diffusion 
Toolkit/Trackvis, yielded me a 6x6 matrix view of the transaxial cuts of 
the brain.  I ran this through DTI studios because of its actual Siemens 
Mosaic protocol and was able to (with the right gradient table) create a 
semi-usable FA map.  The problem is that while DTI studios gave me a 
representation of the brain, the coronal and sagittal views are 
upside-down and inverted.  I'd like to know if anybody had thoughts on 
reorienting those views of the brain.

I had tried going through Vinci 2.54.0 to use Magic Tool (for those not 
acquainted, Magic Tool allows you to tilt and rotate images how you 
please in order for them to fit your needs), however if I try to rotate 
the sagittal cut, the rest of the cuts are affected such that the 
transaxial cut will be flipped - they are, as expected, linked.

If anyone could provide any insight on either using DTI studios to 
correctly convert the Siemens Mosaic files into usable directions for 
tractography purposes (either in DTI studios or Diffusion 
Toolkit/Trackvis), I'd greatly appreciate it.  Thanks!

Varin Tsai

On 1/14/2011 10:51 AM, Sourena Soheili wrote:
> Dear Mojdeh
> Are you iranian? Cuz I'd like to find someone with my nationality here
> for consult.
> Sourena
>
> On Thursday, January 6, 2011, Mojdeh<zamyadim at sri.utoronto.ca>  wrote:
>> Hi all :)
>> I finally managed to successfully run and download the results of my
>> first LDDMM job ... now I have a question about viewing the output
>> transformations. In the manual located @
>> https://www.mristudio.org/wiki/user_manual/diffeomap/MultichannelVolumeLDDMM
>> , it's mentioned that "output transformation matrix can be loaded by
>> clicking the load button under the Volume LDDMM menu and can be saved
>> Raw format. However, in my DiffeoMap there is only one "Retrieve Results
>> > From Remote Volume LDDMM" which can only be used for retrieving the data
>> and not loading them! Could you please advise me on how to access the
>> raw transformations and also how to view the "transformed target" image?
>> Thanks for the help,
>> 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
>>
> _______________________________________________
> mristudio-users mailing 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  Fri Jan 14 14:23:31 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Fri, 14 Jan 2011 14:23:31 -0500
Subject: [Mristudio-users] more DiffeoMap questions
In-Reply-To: <4D309E19.8090004@gmail.com>
References: <4D25F731.6070800@sri.utoronto.ca>
	<AANLkTinJHOdKqfhm3q6L3+jy8MvSseiTyHncOvks1AWB@mail.gmail.com>
	<4D309E19.8090004@gmail.com>
Message-ID: <AANLkTimoRD8JcX88J7Ai5M7d0JbhDZSvbQx0WRdsHbUE@mail.gmail.com>

I hope FAQ15 in this page (https://www.mristudio.org/wiki/faq) will help.

On Fri, Jan 14, 2011 at 2:03 PM, Varin Tsai <varintsai at gmail.com> wrote:

> Hi,
>
> I have a question on file conversion and Siemens Mosaic files.  I
> recently received a patient for processing whos files came in Siemens
> Mosaic.  After having ran through such protocols as DCM2NII.gui, I had a
> 30 direction set of files that, when run through Diffusion
> Toolkit/Trackvis, yielded me a 6x6 matrix view of the transaxial cuts of
> the brain.  I ran this through DTI studios because of its actual Siemens
> Mosaic protocol and was able to (with the right gradient table) create a
> semi-usable FA map.  The problem is that while DTI studios gave me a
> representation of the brain, the coronal and sagittal views are
> upside-down and inverted.  I'd like to know if anybody had thoughts on
> reorienting those views of the brain.
>
> I had tried going through Vinci 2.54.0 to use Magic Tool (for those not
> acquainted, Magic Tool allows you to tilt and rotate images how you
> please in order for them to fit your needs), however if I try to rotate
> the sagittal cut, the rest of the cuts are affected such that the
> transaxial cut will be flipped - they are, as expected, linked.
>
> If anyone could provide any insight on either using DTI studios to
> correctly convert the Siemens Mosaic files into usable directions for
> tractography purposes (either in DTI studios or Diffusion
> Toolkit/Trackvis), I'd greatly appreciate it.  Thanks!
>
> Varin Tsai
>
> On 1/14/2011 10:51 AM, Sourena Soheili wrote:
> > Dear Mojdeh
> > Are you iranian? Cuz I'd like to find someone with my nationality here
> > for consult.
> > Sourena
> >
> > On Thursday, January 6, 2011, Mojdeh<zamyadim at sri.utoronto.ca>  wrote:
> >> Hi all :)
> >> I finally managed to successfully run and download the results of my
> >> first LDDMM job ... now I have a question about viewing the output
> >> transformations. In the manual located @
> >>
> https://www.mristudio.org/wiki/user_manual/diffeomap/MultichannelVolumeLDDMM
> >> , it's mentioned that "output transformation matrix can be loaded by
> >> clicking the load button under the Volume LDDMM menu and can be saved
> >> Raw format. However, in my DiffeoMap there is only one "Retrieve Results
> >> > From Remote Volume LDDMM" which can only be used for retrieving the
> data
> >> and not loading them! Could you please advise me on how to access the
> >> raw transformations and also how to view the "transformed target" image?
> >> Thanks for the help,
> >> 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
> >>
> > _______________________________________________
> > mristudio-users mailing 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
>
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From thomasballinger at gmail.com  Thu Jan 20 13:16:07 2011
From: thomasballinger at gmail.com (Thomas Ballinger)
Date: Thu, 20 Jan 2011 13:16:07 -0500
Subject: [Mristudio-users] Producing a nhdr format tensor file
Message-ID: <AANLkTi=4j71hyLSo4DPBCZXKK1K9aKuKuqaEAkSTcoJ+@mail.gmail.com>

I was given the following (MRI-Studio created) files by a collaborator:

U016_color_map_0.dat
U016_eigen_vector_0.dat
U016_FA.dat
U016_tensor.dat

Preprocessing:
ImgQltFlag.bin
U016_DTI1.PAR
U016_DTI1.REC
U016_DTI2.PAR
U016_DTI2.REC
U016_DTI3.PAR
U016_DTI3.REC
U016_DTI4.PAR
U016_DTI4.REC
U016_ImgQuality.flg
U016_LoadData.dpf.txt
U016_LoadData_MI.dpf.tx
U016_MI000.raw
U016_MI001.raw
U016_MI002.raw
U016_MI003.raw
U016_MI_Matrix.txt
U016_MI.nhdr

I'd like to get a tensor file in nhdr format for use with Slicer.  I can use
the .nhdr DWI file, but it includes some bad slices that are apparently
excluded in the DTI-Studio processing, which I'd also like to exclude.
Therefore I have three questions, only one of which needs to be answered for
me to obtain my desired nhdr format tensor file.

1) How do I load the tensor.dat file to be saved as a nhdr (if this is
possible) in DTI-Studio, or how do I use other data I have here with
DTI-Studio to create a nhdr tensor file that excludes the slices which were
found to be bad?

2) How do I read the tensor.dat file?  If I understand the data format I can
convert it to nrrd tensor file format

3) Where is this data quality flag information stored, and how do I read
it?  I could use the nhdr I have already and remove the offending bad
slices, then estimate tensors without these slices, producing a nrrd format
tensor file.

Thanks very much,

Thomas Ballinger
Research Assistant
Psychiatry Neuroimaging Laboratory
Brigham and Women's Hospital
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From jakaba at med.unideb.hu  Sun Jan 23 15:01:33 2011
From: jakaba at med.unideb.hu (=?ISO-8859-1?Q?Andr=E1s_Jakab_MD?=)
Date: Sun, 23 Jan 2011 21:01:33 +0100
Subject: [Mristudio-users] Pediatric DTI
Message-ID: <AANLkTimbYY2yhz3YUgnziqPaJ=CK4f0QgjMitU8FRBPf@mail.gmail.com>

Dear Prof. Mori and MRIstudio list members,

The link to the "Pediatric DTI" website seems to be broken on the
http://www.dtiatlas.org/ page. I'd like to inquire about the availability of
the abovementioned database.

Best regards,
Andr?s Jakab MD
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From blue.year at msa.hinet.net  Sun Jan 23 19:19:06 2011
From: blue.year at msa.hinet.net (Syu-JyunPeng)
Date: Mon, 24 Jan 2011 08:19:06 +0800 (CST)
Subject: [Mristudio-users] Thanks for helping
Message-ID: <1531005449.1295828346592.JavaMail.nobody@sg2000-ap-1>

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From blue.year at msa.hinet.net  Sun Jan 23 19:47:06 2011
From: blue.year at msa.hinet.net (Syu-JyunPeng)
Date: Mon, 24 Jan 2011 08:47:06 +0800 (CST)
Subject: [Mristudio-users] helping
Message-ID: <943335884.1295830030470.JavaMail.nobody@sg2000-ap-1>

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From alex.dresner at philips.com  Mon Jan 24 08:54:30 2011
From: alex.dresner at philips.com (Dresner, Alex)
Date: Mon, 24 Jan 2011 14:54:30 +0100
Subject: [Mristudio-users] DICOM name removal
In-Reply-To: <1531005449.1295828346592.JavaMail.nobody@sg2000-ap-1>
References: <1531005449.1295828346592.JavaMail.nobody@sg2000-ap-1>
Message-ID: <F47DF122278D44439E845976F7C266D742DBE6A2CD@NLCLUEXM04.connect1.local>

Dear Syu-Jyun,
There are DICOM anonymization services available online, such as Trial Wire by IXICO.  http://www.ixico.com/Products/TrialWire/
(Some of Ixico?s employees are friends of mine, but this is a free service with nothing to download.  You may have to sign up to get a site user name, but they do not abuse the e-mail address in any way.)

Regards,
Alex

____________________
M. Alex Dresner, Ph.D.
MR Clinical Scientist
alex.dresner at philips.com
____________________



From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Syu-JyunPeng
Sent: Sunday, January 23, 2011 7:19 PM
To: Andr?sJakabMD; mristudio-users at mristudio.org; susumu at mri.jhu.edu
Subject: [Mristudio-users] Thanks for helping


Dear ladies and gentlemans

How to remove patient informations and maintain other in the DICOM header?

Do you have related software or ideal?

Thank you very much for helping

Best regards,

Syu-Jyun

--- ?????HiNet WebMail ---

________________________________
The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message.
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From amirzolal at gmail.com  Sat Jan 29 12:43:09 2011
From: amirzolal at gmail.com (Amir Zolal)
Date: Sat, 29 Jan 2011 18:43:09 +0100
Subject: [Mristudio-users] question - changes of FA and eigenvalues after Gd
	contrast
Message-ID: <AANLkTinad47mj6TUa7t59ALOJarH0gWVo3TALaM7L5+1@mail.gmail.com>

Hi,

I have tried comparing DTI images before and after Gd contrast
administration, and I have found that the FA was increased after the
contrast agent (more in the ROIs where there was contrast
enhancement), I have also (among other things) seen a significant
decrease of all eigenvalues, however the third eigenvalue decreased
the most (the difference between the change of lambda1 and lambda3 was
also significant), causing the paradoxical increase in FA. This was
not observable in the normal white matter. Because I don't believe,
that the contrast agent would in any way influence water diffusion, my
theory is, that the addition of a paramagnetic contrast agent  could
cause more local noise and the small attenuation in the (lambda3)
direction would be even less discernible, in contrast to the strong
attenuation in the (lambda1) direction. My question is, to your
knowledge, would there be anything else in the processing of the DTI
datasets that could cause the above described effect?

Thanks in advance for your ideas,

Amir

From susumu at mri.jhu.edu  Sat Jan 29 17:57:03 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Sat, 29 Jan 2011 17:57:03 -0500
Subject: [Mristudio-users] question - changes of FA and eigenvalues
 after Gd contrast
In-Reply-To: <AANLkTinad47mj6TUa7t59ALOJarH0gWVo3TALaM7L5+1@mail.gmail.com>
References: <AANLkTinad47mj6TUa7t59ALOJarH0gWVo3TALaM7L5+1@mail.gmail.com>
Message-ID: <AANLkTikMPNwH20mdSpWjQyH2nHPV0jv3xjwo0fz0m9JL@mail.gmail.com>

Hi Amir, nice observation.

For NMR/MRI of living organs, we are dealing with a system with a huge
number of compartments. Waters inside cytoplasm, nucleus, golgi, mito,
extracelluar space, bound to macromolecules, inside an axonal process,
trapped between neurofilaments/microtubles, inside myeline, etc. These
microscopic environment varies within a scale of micrometer scale or less.
Then, there are larger scale structure units such as neurons, astrocytes,
then even larger such as WM and GM, from small (tens of microns) to large
(millimeter). These structural units with different scales coexist within
one pixel.

In this complicated multi-compartment systems, water molecules move around
about 10 micron, in average, experiencing different environments, some place
could be isotropic and some could be anisotropic. If we can assume that
during the 40-60ms of observation time (typical separation between two
gradient pulses, in which water moved 10micron), all water molecules
experience all compartments and effectively averaged out the existence of
different diffusion environments, we can assume that the system is
homogeneous (fast-exchange regime). Usually, we can's assume it; many water
molecules are trapped in one compartment or visiting only several
compartments. Then our pixels consist of multiple compartments with
different diffusion environment.

Now, it is not only diffusion properties that are different among these
compartment. Their relaxation properties are also very different. Suppose
one simple and extreme case in which we have only two compartments and there
is no exchange between them (like intra and extra-cellular spaces with very
slow membrane exchange). Also assume that intra cellular component is
dominant (90%) with high anisotropy and short T2 and extra cellular
component is minority (10%) with low anisotropy and long T2 (I just made up
all these numbers). If we use a short echo sequence, the signal from the
intracelluar compartment dominate the signal and the system looks very
anisotropy. If we use a long echo sequence, the signal from the
extracellular space becomes dominant and the same pixel now looks less
anisotropic.

So, as long as we are dealing with multiple compartment systems with slow
exchange regime, changing relaxation time (like altering T1 and T2) and
sequence (like long echo or rapid repetition), you can effectively change
the final contribution of of each compartment to the signal. Therefore, it
is likely that T1, T2, AND "measured" diffusion properties change by adding
Gd, even if Gd doesn't directly change water diffusion.



On Sat, Jan 29, 2011 at 12:43 PM, Amir Zolal <amirzolal at gmail.com> wrote:

> Hi,
>
> I have tried comparing DTI images before and after Gd contrast
> administration, and I have found that the FA was increased after the
> contrast agent (more in the ROIs where there was contrast
> enhancement), I have also (among other things) seen a significant
> decrease of all eigenvalues, however the third eigenvalue decreased
> the most (the difference between the change of lambda1 and lambda3 was
> also significant), causing the paradoxical increase in FA. This was
> not observable in the normal white matter. Because I don't believe,
> that the contrast agent would in any way influence water diffusion, my
> theory is, that the addition of a paramagnetic contrast agent  could
> cause more local noise and the small attenuation in the (lambda3)
> direction would be even less discernible, in contrast to the strong
> attenuation in the (lambda1) direction. My question is, to your
> knowledge, would there be anything else in the processing of the DTI
> datasets that could cause the above described effect?
>
> Thanks in advance for your ideas,
>
> Amir
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
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From SyedSalman.Shahid at usq.edu.au  Mon Jan 31 08:36:53 2011
From: SyedSalman.Shahid at usq.edu.au (Syed Salman Shahid)
Date: Mon, 31 Jan 2011 23:36:53 +1000
Subject: [Mristudio-users] extraction of Tensor values
In-Reply-To: <AANLkTikMPNwH20mdSpWjQyH2nHPV0jv3xjwo0fz0m9JL@mail.gmail.com>
References: <AANLkTinad47mj6TUa7t59ALOJarH0gWVo3TALaM7L5+1@mail.gmail.com>
	<AANLkTikMPNwH20mdSpWjQyH2nHPV0jv3xjwo0fz0m9JL@mail.gmail.com>
Message-ID: <3318FC529C6A6E448A90CB5AB5B1F56C2518406794@EXCHMB.usq.edu.au>

Hi,

I would like to extract the numerical values of diffusion tensor from the tensor.dat file using matlab. I got the Tensor.dat file from DTIStudio, however, the format is not compatible with either notepad or matlab importing tools. Is it possible to save this tensor file in some other text file format?

With regards
Salman


From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori
Sent: Sunday, 30 January 2011 8:57 AM
To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
Subject: Re: [Mristudio-users] question - changes of FA and eigenvalues after Gd contrast

Hi Amir, nice observation.

For NMR/MRI of living organs, we are dealing with a system with a huge number of compartments. Waters inside cytoplasm, nucleus, golgi, mito, extracelluar space, bound to macromolecules, inside an axonal process, trapped between neurofilaments/microtubles, inside myeline, etc. These microscopic environment varies within a scale of micrometer scale or less. Then, there are larger scale structure units such as neurons, astrocytes, then even larger such as WM and GM, from small (tens of microns) to large (millimeter). These structural units with different scales coexist within one pixel.

In this complicated multi-compartment systems, water molecules move around about 10 micron, in average, experiencing different environments, some place could be isotropic and some could be anisotropic. If we can assume that during the 40-60ms of observation time (typical separation between two gradient pulses, in which water moved 10micron), all water molecules experience all compartments and effectively averaged out the existence of different diffusion environments, we can assume that the system is homogeneous (fast-exchange regime). Usually, we can's assume it; many water molecules are trapped in one compartment or visiting only several compartments. Then our pixels consist of multiple compartments with different diffusion environment.

Now, it is not only diffusion properties that are different among these compartment. Their relaxation properties are also very different. Suppose one simple and extreme case in which we have only two compartments and there is no exchange between them (like intra and extra-cellular spaces with very slow membrane exchange). Also assume that intra cellular component is dominant (90%) with high anisotropy and short T2 and extra cellular component is minority (10%) with low anisotropy and long T2 (I just made up all these numbers). If we use a short echo sequence, the signal from the intracelluar compartment dominate the signal and the system looks very anisotropy. If we use a long echo sequence, the signal from the extracellular space becomes dominant and the same pixel now looks less anisotropic.

So, as long as we are dealing with multiple compartment systems with slow exchange regime, changing relaxation time (like altering T1 and T2) and sequence (like long echo or rapid repetition), you can effectively change the final contribution of of each compartment to the signal. Therefore, it is likely that T1, T2, AND "measured" diffusion properties change by adding Gd, even if Gd doesn't directly change water diffusion.



On Sat, Jan 29, 2011 at 12:43 PM, Amir Zolal <amirzolal at gmail.com<mailto:amirzolal at gmail.com>> wrote:
Hi,

I have tried comparing DTI images before and after Gd contrast
administration, and I have found that the FA was increased after the
contrast agent (more in the ROIs where there was contrast
enhancement), I have also (among other things) seen a significant
decrease of all eigenvalues, however the third eigenvalue decreased
the most (the difference between the change of lambda1 and lambda3 was
also significant), causing the paradoxical increase in FA. This was
not observable in the normal white matter. Because I don't believe,
that the contrast agent would in any way influence water diffusion, my
theory is, that the addition of a paramagnetic contrast agent  could
cause more local noise and the small attenuation in the (lambda3)
direction would be even less discernible, in contrast to the strong
attenuation in the (lambda1) direction. My question is, to your
knowledge, would there be anything else in the processing of the DTI
datasets that could cause the above described effect?

Thanks in advance for your ideas,

Amir
_______________________________________________
mristudio-users mailing list
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http://lists.mristudio.org/mailman/listinfo/
Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org<mailto:mristudio-users-unsubscribe at mristudio.org>


This email (including any attached files) is confidential and is for the
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please, as a courtesy, tell the sender, then delete this email.

The views and opinions are the originator's and do not necessarily
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From sabahihadi at yahoo.com  Mon Jan 31 09:20:49 2011
From: sabahihadi at yahoo.com (hadi sabahi)
Date: Mon, 31 Jan 2011 06:20:49 -0800 (PST)
Subject: [Mristudio-users] question about analyze format
Message-ID: <727705.53006.qm@web113309.mail.gq1.yahoo.com>

hello, first excuse me for my bad writing skill.
I have DTI data (dicom format)?that I convert them in analyze format (for register them with T1 modulite). now I want to call this registered?volumes in DtiStudio but?this software dosenot accept analyze format.
How can I cal this data in DtiStudio ?
?
Thanks in advance for your ideas,
Hadi Sabahi

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From afzaliesfahan at yahoo.com  Mon Jan 31 10:13:24 2011
From: afzaliesfahan at yahoo.com (maryam afzali)
Date: Mon, 31 Jan 2011 07:13:24 -0800 (PST)
Subject: [Mristudio-users] question about analyze format
In-Reply-To: <727705.53006.qm@web113309.mail.gq1.yahoo.com>
References: <727705.53006.qm@web113309.mail.gq1.yahoo.com>
Message-ID: <790937.60815.qm@web161716.mail.bf1.yahoo.com>

Hi,
DTI-Studio can read the analyze format. 
You can do the following:
File> MRI View3D?
And then choose the data. Also in the 'Image parameters', 'Image File Format' 
you should choose the Analyze format.




________________________________
From: hadi sabahi <sabahihadi at yahoo.com>
To: mristudio-users at mristudio.org
Sent: Mon, January 31, 2011 6:20:49 AM
Subject: [Mristudio-users] question about analyze format


hello, first excuse me for my bad writing skill.
I have DTI data (dicom format)?that I convert them in analyze format (for 
register them with T1 modulite). now I want to call this registered?volumes in 
DtiStudio but?this software dosenot accept analyze format.
How can I cal this data in DtiStudio ?

Thanks in advance for your ideas,
Hadi Sabahi 


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From thomasballinger at gmail.com  Mon Jan 31 10:57:48 2011
From: thomasballinger at gmail.com (Thomas Ballinger)
Date: Mon, 31 Jan 2011 10:57:48 -0500
Subject: [Mristudio-users] extraction of Tensor values
In-Reply-To: <3318FC529C6A6E448A90CB5AB5B1F56C2518406794@EXCHMB.usq.edu.au>
References: <AANLkTinad47mj6TUa7t59ALOJarH0gWVo3TALaM7L5+1@mail.gmail.com>
	<AANLkTikMPNwH20mdSpWjQyH2nHPV0jv3xjwo0fz0m9JL@mail.gmail.com>
	<3318FC529C6A6E448A90CB5AB5B1F56C2518406794@EXCHMB.usq.edu.au>
Message-ID: <AANLkTinRr0bmnpUmcBF8bwse_gDUMpzY4zpTet_uQZ=m@mail.gmail.com>

I don't know much about DTI studio, but I recently had to do this, and I did
it by extracting the diffusion tensor scalar directions (saving the xx xy xz
yy yz zz directions) as separate volumes.  I saved them as NRRD volumes
because that was what I needed, but analyze format was also an option.
There are several Matlab libraries for loading nifti files, though I don't
know much about them.  I bet other folks will have better suggestions.

Thomas Ballinger

On Mon, Jan 31, 2011 at 8:36 AM, Syed Salman Shahid <
SyedSalman.Shahid at usq.edu.au> wrote:

>  Hi,
>
>
>
> I would like to extract the numerical values of diffusion tensor from the
> tensor.dat file using matlab. I got the Tensor.dat file from DTIStudio,
> however, the format is not compatible with either notepad or matlab
> importing tools. Is it possible to save this tensor file in some other text
> file format?
>
>
>
> With regards
>
> Salman
>
>
>
>
>
> *From:* mristudio-users-bounces at mristudio.org [mailto:
> mristudio-users-bounces at mristudio.org] *On Behalf Of *susumu mori
> *Sent:* Sunday, 30 January 2011 8:57 AM
> *To:* DTI Studio, ROI Editor, DiffeoMap Questions/Support
> *Subject:* Re: [Mristudio-users] question - changes of FA and eigenvalues
> after Gd contrast
>
>
>
> Hi Amir, nice observation.
>
>
>
> For NMR/MRI of living organs, we are dealing with a system with a huge
> number of compartments. Waters inside cytoplasm, nucleus, golgi, mito,
> extracelluar space, bound to macromolecules, inside an axonal process,
> trapped between neurofilaments/microtubles, inside myeline, etc. These
> microscopic environment varies within a scale of micrometer scale or less.
> Then, there are larger scale structure units such as neurons, astrocytes,
> then even larger such as WM and GM, from small (tens of microns) to large
> (millimeter). These structural units with different scales coexist within
> one pixel.
>
>
>
> In this complicated multi-compartment systems, water molecules move around
> about 10 micron, in average, experiencing different environments, some place
> could be isotropic and some could be anisotropic. If we can assume that
> during the 40-60ms of observation time (typical separation between two
> gradient pulses, in which water moved 10micron), all water molecules
> experience all compartments and effectively averaged out the existence of
> different diffusion environments, we can assume that the system is
> homogeneous (fast-exchange regime). Usually, we can's assume it; many water
> molecules are trapped in one compartment or visiting only several
> compartments. Then our pixels consist of multiple compartments with
> different diffusion environment.
>
>
>
> Now, it is not only diffusion properties that are different among these
> compartment. Their relaxation properties are also very different. Suppose
> one simple and extreme case in which we have only two compartments and there
> is no exchange between them (like intra and extra-cellular spaces with very
> slow membrane exchange). Also assume that intra cellular component is
> dominant (90%) with high anisotropy and short T2 and extra cellular
> component is minority (10%) with low anisotropy and long T2 (I just made up
> all these numbers). If we use a short echo sequence, the signal from the
> intracelluar compartment dominate the signal and the system looks very
> anisotropy. If we use a long echo sequence, the signal from the
> extracellular space becomes dominant and the same pixel now looks less
> anisotropic.
>
>
>
> So, as long as we are dealing with multiple compartment systems with slow
> exchange regime, changing relaxation time (like altering T1 and T2) and
> sequence (like long echo or rapid repetition), you can effectively change
> the final contribution of of each compartment to the signal. Therefore, it
> is likely that T1, T2, AND "measured" diffusion properties change by adding
> Gd, even if Gd doesn't directly change water diffusion.
>
>
>
>
>
>
>
> On Sat, Jan 29, 2011 at 12:43 PM, Amir Zolal <amirzolal at gmail.com> wrote:
>
> Hi,
>
> I have tried comparing DTI images before and after Gd contrast
> administration, and I have found that the FA was increased after the
> contrast agent (more in the ROIs where there was contrast
> enhancement), I have also (among other things) seen a significant
> decrease of all eigenvalues, however the third eigenvalue decreased
> the most (the difference between the change of lambda1 and lambda3 was
> also significant), causing the paradoxical increase in FA. This was
> not observable in the normal white matter. Because I don't believe,
> that the contrast agent would in any way influence water diffusion, my
> theory is, that the addition of a paramagnetic contrast agent  could
> cause more local noise and the small attenuation in the (lambda3)
> direction would be even less discernible, in contrast to the strong
> attenuation in the (lambda1) direction. My question is, to your
> knowledge, would there be anything else in the processing of the DTI
> datasets that could cause the above described effect?
>
> Thanks in advance for your ideas,
>
> Amir
> _______________________________________________
> mristudio-users mailing 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 (including any attached files) is confidential and is for the
> intended recipient(s) only. If you received this email by mistake, please,
> as a courtesy, tell the sender, then delete this email.
>
> The views and opinions are the originator's and do not necessarily reflect
> those of the University of Southern Queensland. Although all reasonable
> precautions were taken to ensure that this email contained no viruses at the
> time it was sent we accept no liability for any losses arising from its
> receipt.
>
> The University of Southern Queensland is a registered provider of education
> with the Australian Government (CRICOS Institution Code No's. QLD 00244B /
> NSW 02225M)
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From susumu at mri.jhu.edu  Mon Jan 31 11:06:48 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Mon, 31 Jan 2011 11:06:48 -0500
Subject: [Mristudio-users] extraction of Tensor values
In-Reply-To: <3318FC529C6A6E448A90CB5AB5B1F56C2518406794@EXCHMB.usq.edu.au>
References: <AANLkTinad47mj6TUa7t59ALOJarH0gWVo3TALaM7L5+1@mail.gmail.com>
	<AANLkTikMPNwH20mdSpWjQyH2nHPV0jv3xjwo0fz0m9JL@mail.gmail.com>
	<3318FC529C6A6E448A90CB5AB5B1F56C2518406794@EXCHMB.usq.edu.au>
Message-ID: <AANLkTikvwV0rMvkBQkZNL7xxuAtB1gUJRtMhmRQ9GZ0b@mail.gmail.com>

You can load it back to DtiStudio. Then you will find 6 independent images;
dxx, dyy, dzz, dxy, dxz, dyz. You can save these into 6 different files.
These 6 images are simple 3D floating-point matrices, just like FA maps. I
guess Matlab can read them one-by-one.

On Mon, Jan 31, 2011 at 8:36 AM, Syed Salman Shahid <
SyedSalman.Shahid at usq.edu.au> wrote:

>  Hi,
>
>
>
> I would like to extract the numerical values of diffusion tensor from the
> tensor.dat file using matlab. I got the Tensor.dat file from DTIStudio,
> however, the format is not compatible with either notepad or matlab
> importing tools. Is it possible to save this tensor file in some other text
> file format?
>
>
>
> With regards
>
> Salman
>
>
>
>
>
> *From:* mristudio-users-bounces at mristudio.org [mailto:
> mristudio-users-bounces at mristudio.org] *On Behalf Of *susumu mori
> *Sent:* Sunday, 30 January 2011 8:57 AM
> *To:* DTI Studio, ROI Editor, DiffeoMap Questions/Support
> *Subject:* Re: [Mristudio-users] question - changes of FA and eigenvalues
> after Gd contrast
>
>
>
> Hi Amir, nice observation.
>
>
>
> For NMR/MRI of living organs, we are dealing with a system with a huge
> number of compartments. Waters inside cytoplasm, nucleus, golgi, mito,
> extracelluar space, bound to macromolecules, inside an axonal process,
> trapped between neurofilaments/microtubles, inside myeline, etc. These
> microscopic environment varies within a scale of micrometer scale or less.
> Then, there are larger scale structure units such as neurons, astrocytes,
> then even larger such as WM and GM, from small (tens of microns) to large
> (millimeter). These structural units with different scales coexist within
> one pixel.
>
>
>
> In this complicated multi-compartment systems, water molecules move around
> about 10 micron, in average, experiencing different environments, some place
> could be isotropic and some could be anisotropic. If we can assume that
> during the 40-60ms of observation time (typical separation between two
> gradient pulses, in which water moved 10micron), all water molecules
> experience all compartments and effectively averaged out the existence of
> different diffusion environments, we can assume that the system is
> homogeneous (fast-exchange regime). Usually, we can's assume it; many water
> molecules are trapped in one compartment or visiting only several
> compartments. Then our pixels consist of multiple compartments with
> different diffusion environment.
>
>
>
> Now, it is not only diffusion properties that are different among these
> compartment. Their relaxation properties are also very different. Suppose
> one simple and extreme case in which we have only two compartments and there
> is no exchange between them (like intra and extra-cellular spaces with very
> slow membrane exchange). Also assume that intra cellular component is
> dominant (90%) with high anisotropy and short T2 and extra cellular
> component is minority (10%) with low anisotropy and long T2 (I just made up
> all these numbers). If we use a short echo sequence, the signal from the
> intracelluar compartment dominate the signal and the system looks very
> anisotropy. If we use a long echo sequence, the signal from the
> extracellular space becomes dominant and the same pixel now looks less
> anisotropic.
>
>
>
> So, as long as we are dealing with multiple compartment systems with slow
> exchange regime, changing relaxation time (like altering T1 and T2) and
> sequence (like long echo or rapid repetition), you can effectively change
> the final contribution of of each compartment to the signal. Therefore, it
> is likely that T1, T2, AND "measured" diffusion properties change by adding
> Gd, even if Gd doesn't directly change water diffusion.
>
>
>
>
>
>
>
> On Sat, Jan 29, 2011 at 12:43 PM, Amir Zolal <amirzolal at gmail.com> wrote:
>
> Hi,
>
> I have tried comparing DTI images before and after Gd contrast
> administration, and I have found that the FA was increased after the
> contrast agent (more in the ROIs where there was contrast
> enhancement), I have also (among other things) seen a significant
> decrease of all eigenvalues, however the third eigenvalue decreased
> the most (the difference between the change of lambda1 and lambda3 was
> also significant), causing the paradoxical increase in FA. This was
> not observable in the normal white matter. Because I don't believe,
> that the contrast agent would in any way influence water diffusion, my
> theory is, that the addition of a paramagnetic contrast agent  could
> cause more local noise and the small attenuation in the (lambda3)
> direction would be even less discernible, in contrast to the strong
> attenuation in the (lambda1) direction. My question is, to your
> knowledge, would there be anything else in the processing of the DTI
> datasets that could cause the above described effect?
>
> Thanks in advance for your ideas,
>
> Amir
> _______________________________________________
> mristudio-users mailing 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 (including any attached files) is confidential and is for the
> intended recipient(s) only. If you received this email by mistake, please,
> as a courtesy, tell the sender, then delete this email.
>
> The views and opinions are the originator's and do not necessarily reflect
> those of the University of Southern Queensland. Although all reasonable
> precautions were taken to ensure that this email contained no viruses at the
> time it was sent we accept no liability for any losses arising from its
> receipt.
>
> The University of Southern Queensland is a registered provider of education
> with the Australian Government (CRICOS Institution Code No's. QLD 00244B /
> NSW 02225M)
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From amangupta2005 at gmail.com  Mon Jan 31 16:36:37 2011
From: amangupta2005 at gmail.com (aman gupta)
Date: Mon, 31 Jan 2011 15:36:37 -0600
Subject: [Mristudio-users] matrix size changes when i load Bruker's PV4
	images to DTIstudio?
Message-ID: <AANLkTikXaMozBakF8X9x=3Ygak+u-RWwwgEKc=jg7Z7Y@mail.gmail.com>

Hi Dr. Mori,

I am trying to run Tractography on DTI images obtained from Bruker's
paravision 4 using DTIstudio V3.0. The matrix size that i have from Bruker
is 192x64x16, but when i load the images in DTI studio, it changes the
matrix to 64x256x16? Why does it do that? I am using Siemens DICOM ( Ver.
1.00) as the file type to load bruker images because DTIstudio crashes if i
try to use any other file type. I will appreciate your input on this.

Thanks,
Aman
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From susumu at mri.jhu.edu  Mon Jan 31 19:41:15 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Mon, 31 Jan 2011 19:41:15 -0500
Subject: [Mristudio-users] matrix size changes when i load Bruker's PV4
 images to DTIstudio?
In-Reply-To: <AANLkTikXaMozBakF8X9x=3Ygak+u-RWwwgEKc=jg7Z7Y@mail.gmail.com>
References: <AANLkTikXaMozBakF8X9x=3Ygak+u-RWwwgEKc=jg7Z7Y@mail.gmail.com>
Message-ID: <AANLkTi=fuEUO0qUJ_VHdb3wbHgV0MbnooGowbhe2iFzw@mail.gmail.com>

We do not have PV4 yet, but I guess you mean Bruker now support DICOM?
If that is the case, we may need to look into the Bruker-DICOM format.

On Mon, Jan 31, 2011 at 4:36 PM, aman gupta <amangupta2005 at gmail.com> wrote:

> Hi Dr. Mori,
>
> I am trying to run Tractography on DTI images obtained from Bruker's
> paravision 4 using DTIstudio V3.0. The matrix size that i have from Bruker
> is 192x64x16, but when i load the images in DTI studio, it changes the
> matrix to 64x256x16? Why does it do that? I am using Siemens DICOM ( Ver.
> 1.00) as the file type to load bruker images because DTIstudio crashes if i
> try to use any other file type. I will appreciate your input on this.
>
> Thanks,
> Aman
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From Diana.Lindquist at cchmc.org  Tue Feb  1 06:49:38 2011
From: Diana.Lindquist at cchmc.org (Diana Lindquist)
Date: Tue, 01 Feb 2011 06:49:38 -0500
Subject: [Mristudio-users] matrix size changes when i load Bruker's PV4
 images to DTIstudio?
Message-ID: <4D47AD020200005A00098EEB@n6mcgw16.cchmc.org>

Have you tried just loading the 2dseq file?  You can do that if you choose the Philips *rec option.  I suspect that the DICOM conversion is zerofilling or otherwise padding your data up to the next power of 2, which won't happen if you tell DTIStudio to use the 2dseq data.


Regards,
Diana Lindquist

Diana M. Lindquist, PhD
Director, 7T facility
Imaging Research Center
Assistant Professor
Department of Radiology
Cincinnati Children's Hospital Medical Center
3333 Burnet Ave, ML 5033
Cincinnati, OH 45229-3039
Ph. 513-636-9268
Fax. 513-636-0434
>>> aman gupta  01/31/11 5:35 PM >>>
Hi Dr. Mori,

I am trying to run Tractography on DTI images obtained from Bruker's
paravision 4 using DTIstudio V3.0. The matrix size that i have from Bruker
is 192x64x16, but when i load the images in DTI studio, it changes the
matrix to 64x256x16? Why does it do that? I am using Siemens DICOM ( Ver.
1.00) as the file type to load bruker images because DTIstudio crashes if i
try to use any other file type. I will appreciate your input on this.

Thanks,
Aman




From felixbeacher at hotmail.co.uk  Tue Feb  1 17:42:27 2011
From: felixbeacher at hotmail.co.uk (Felix Beacher)
Date: Tue, 01 Feb 2011 17:42:27 -0500
Subject: [Mristudio-users] tensor calculation
In-Reply-To: <AANLkTi=fuEUO0qUJ_VHdb3wbHgV0MbnooGowbhe2iFzw@mail.gmail.com>
References: <AANLkTikXaMozBakF8X9x=3Ygak+u-RWwwgEKc=jg7Z7Y@mail.gmail.com>
	<AANLkTi=fuEUO0qUJ_VHdb3wbHgV0MbnooGowbhe2iFzw@mail.gmail.com>
Message-ID: <BLU159-w40837A5A63D4B2AC543D396E50@phx.gbl>


Hello!I am trying to get started with my first DTI analysis but have come across an early-stage problem with tensor calculation.  I have loaded my data (Siemens DICOM, FA) and I am in the DTI mapping tab. The data looks as if it has loaded OK. However, when I hit the 'Original-ADC-STD-Mean' button I get an error message saying 'an invalid argument was encountered' followed by a blank screen saying 'image not ready'.Can anyone help with this?Many thanksFelix



 		 	   		  
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From susumu at mri.jhu.edu  Tue Feb  1 18:00:22 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Tue, 01 Feb 2011 18:00:22 -0500
Subject: [Mristudio-users] tensor calculation
In-Reply-To: <BLU159-w40837A5A63D4B2AC543D396E50@phx.gbl>
References: <AANLkTikXaMozBakF8X9x=3Ygak+u-RWwwgEKc=jg7Z7Y@mail.gmail.com>
	<AANLkTi=fuEUO0qUJ_VHdb3wbHgV0MbnooGowbhe2iFzw@mail.gmail.com>
	<BLU159-w40837A5A63D4B2AC543D396E50@phx.gbl>
Message-ID: <AANLkTim0gjrCBF2qMwDiRdRXzOqGyhEhyzzCDXKOccjv@mail.gmail.com>

usually, that is caused by a mismatch between the number of images and the
gradient table you specified.

For example, if your gradient table consists of 6 orientations and your data
have 12 diffusion-weighted images, DtiStudio can't calculate a tensor.

If you are using the regular Siemens table, it should be a 12-orientation
scheme. After you load the image, find how many b0 and diffusion-weighted
images are loaded. Then confirm if it matches to the number of orientations
of the table you used.

The video tutorial in www.mristudo.org may help.

On Tue, Feb 1, 2011 at 5:42 PM, Felix Beacher <felixbeacher at hotmail.co.uk>wrote:

>  Hello!
>
> I am trying to get started with my first DTI analysis but have come across
> an early-stage problem with tensor calculation.
>
> I have loaded my data (Siemens DICOM, FA) and I am in the DTI mapping tab.
> The data looks as if it has loaded OK. However, when I hit the
> 'Original-ADC-STD-Mean' button I get an error message saying 'an invalid
> argument was encountered' followed by a blank screen saying 'image not
> ready'.
>
> Can anyone help with this?
>
> Many thanks
>
> Felix
>
>
>
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From felixbeacher at hotmail.co.uk  Wed Feb  2 18:17:18 2011
From: felixbeacher at hotmail.co.uk (Felix Beacher)
Date: Wed, 02 Feb 2011 18:17:18 -0500
Subject: [Mristudio-users] tensor calculation
Message-ID: <BLU159-w183F699F211062031828596E40@phx.gbl>


Hello!I am trying to get started with my first DTI analysis but have come across an early-stage problem with tensor calculation.  I have loaded my data (Siemens DICOM, FA) and I am in the DTI mapping tab. The data looks as if it has loaded OK. However, when I hit the 'Original-ADC-STD-Mean' button I get an error message saying 'an invalid argument was encountered' followed by a blank screen saying 'image not ready'.Can anyone help with this?Many thanksFelix

Felix Beacher, PhD
 
Dept of Biomedical EngineeringStony Brook University School of MedicineBioengineering Building, Room 117Stony Brook, NY  11794-5281
office:  631-632-1911fax:  631-632-3222
http://lsec.neuropraxia.webfactional.com/Welcome.html


 		 	   		  
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From susumu at mri.jhu.edu  Wed Feb  2 18:56:00 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Wed, 02 Feb 2011 18:56:00 -0500
Subject: [Mristudio-users] tensor calculation
In-Reply-To: <BLU159-w183F699F211062031828596E40@phx.gbl>
References: <BLU159-w183F699F211062031828596E40@phx.gbl>
Message-ID: <AANLkTimghRXVAZ9Tt_8_k-XNJE5vwWU7JewpyF3ojt2z@mail.gmail.com>

It seems like your gradient table is not right.
Please make sure that the number of images you loaded and the number of
gradient orientations in your gradient table are matching.

On Wed, Feb 2, 2011 at 6:17 PM, Felix Beacher <felixbeacher at hotmail.co.uk>wrote:

>  Hello!
>
> I am trying to get started with my first DTI analysis but have come across
> an early-stage problem with tensor calculation.
>
> I have loaded my data (Siemens DICOM, FA) and I am in the DTI mapping tab.
> The data looks as if it has loaded OK. However, when I hit the
> 'Original-ADC-STD-Mean' button I get an error message saying 'an invalid
> argument was encountered' followed by a blank screen saying 'image not
> ready'.
>
> Can anyone help with this?
>
> Many thanks
>
> Felix
>
>
> *Felix Beacher, PhD*
>
> Dept of Biomedical Engineering
> Stony Brook University School of Medicine
> Bioengineering Building, Room 117
> Stony Brook, NY  11794-5281
>
> office:  631-632-1911
> fax:  631-632-3222
>
> http://lsec.neuropraxia.webfactional.com/Welcome.html<http://lsec.neuropraxia.webfactional.com/Site/Welcome.html>
>
>
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From fventrice at fleni.org.ar  Thu Feb  3 08:52:27 2011
From: fventrice at fleni.org.ar (Fernando Ventrice)
Date: Thu, 03 Feb 2011 10:52:27 -0300
Subject: [Mristudio-users] data base age range
Message-ID: <DE398D66EF593547B29F6FEE84176B840569E05168@exchange.fleni.org.ar>

Hello mristudio users,
I would like to ask if it is possible to know which range of ages are included in the data base that your group share at https://www.mristudio.org/download/data/dti/
Thank you very much,
Fernando Ventrice

El contenido del presente mensaje y el de sus adjuntos, es confidencial, privado y de uso exclusivo de los destinatarios a los cuales est? dirigido, pudiendo contener informaci?n legalmente protegida. Queda prohibida la revisi?n, divulgaci?n, publicaci?n, modificaci?n, copia, distribuci?n o acci?n en relaci?n con esta informaci?n, por personas o entidades distintas al destinatario. Si usted, por alguna raz?n, lo ha recibido por error, por favor tenga la amabilidad de eliminarlo de su sistema. Las opiniones contenidas, son exclusivas de su autor, y no representa necesariamente, la opini?n de FLENI.
http://www.fleni.org.ar


From salvador.castaneda at med.uni-tuebingen.de  Thu Feb  3 10:09:24 2011
From: salvador.castaneda at med.uni-tuebingen.de (Castaneda, Salvador)
Date: Thu, 03 Feb 2011 16:09:24 +0100
Subject: [Mristudio-users] tensor calculation
In-Reply-To: <AANLkTimghRXVAZ9Tt_8_k-XNJE5vwWU7JewpyF3ojt2z@mail.gmail.com>
References: <BLU159-w183F699F211062031828596E40@phx.gbl>
	<AANLkTimghRXVAZ9Tt_8_k-XNJE5vwWU7JewpyF3ojt2z@mail.gmail.com>
Message-ID: <0AC64F4CB253074799B64FF8F0772D350126C675@azex2003.raddiag.med.uni-tuebingen.de>

Hello Mri studio users,
 
I am working with a MRI scanner with bruker hardware and siemens
software. I acquire mosaic files and have been able to work with the
mosaic in DTI studio to then do a AIR registration. I produce whatever
maps i need. It works great. I then, upload the maps created by DTI
studio to another imaging software called PMOD, as Analize files, for
coregistration with a T2W rat brain Anatomy image. I am able produce
good quality ROIs of the brain areas i need. Just recently i have
discovered, that the MR can also provide for me the FA, TRACE, DWI, and
ADC maps as DICOMs. These I can also upload to Pmod for coregistration
with the anatomy. So theoretically I can choose to do this, but i have
noticed that the quality of the maps produced by the MR software are
somehow "lacking". So my question is : Is the AIR and mutual image
registration in DTI studio crutial for the processing of the data from
the MR? I like the images produced by DTI studio better, but what is the
basis of the improvement? how is it different to the images calculated
by the MR? The MR software is Siemens Syngo. I know that DTI studio also
provides tractography which makes a better tool for this analisis, but
if i would be just interested inthe FA maps, are the images produced by
the scanner enough? (regarding affine coregistration)
thanks in advance for your responses. 
 
Salvador
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From susumu at mri.jhu.edu  Fri Feb  4 10:49:35 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Fri, 04 Feb 2011 10:49:35 -0500
Subject: [Mristudio-users] tensor calculation
In-Reply-To: <0AC64F4CB253074799B64FF8F0772D350126C675@azex2003.raddiag.med.uni-tuebingen.de>
References: <BLU159-w183F699F211062031828596E40@phx.gbl>
	<AANLkTimghRXVAZ9Tt_8_k-XNJE5vwWU7JewpyF3ojt2z@mail.gmail.com>
	<0AC64F4CB253074799B64FF8F0772D350126C675@azex2003.raddiag.med.uni-tuebingen.de>
Message-ID: <AANLkTi=uWO4qyUvrmbgKppFqTTpQcw7waU6WsqbSJ8LL@mail.gmail.com>

Hi Salvador,

AIR/MI registration is a common procedure for human MRI because of two
reasons. First, they tend to move (more than 1 pixel). Second, human
scanners have larger eddy current, which shifts and deforms the images. To
remove these registration errors, we use the co-registration tools. I
believe it is not necessary for animal studies because they are sedated and
heads are fixed.

After the co-registration process, we inevitably apply pixel interpolation,
which reduces resolution and enhances SNR. So, that could be one of the
reasons why the images look different. I guess if you skip the registration,
the images look much similar.

Just one note; we have DiffeoMap and RoiEditor you can download from
www.mristudio.org, which allows you to do cross-contrast and cross-animal
registration.

Susumu

On Thu, Feb 3, 2011 at 10:09 AM, Castaneda, Salvador <
salvador.castaneda at med.uni-tuebingen.de> wrote:

>  Hello Mri studio users,
>
> I am working with a MRI scanner with bruker hardware and siemens software.
> I acquire mosaic files and have been able to work with the mosaic in DTI
> studio to then do a AIR registration. I produce whatever maps i need. It
> works great. I then, upload the maps created by DTI studio to another
> imaging software called PMOD, as Analize files, for coregistration with
> a T2W rat brain Anatomy image. I am able produce good quality ROIs of the
> brain areas i need. Just recently i have discovered, that the MR can also
> provide for me the FA, TRACE, DWI, and ADC maps as DICOMs. These I can also
> upload to Pmod for coregistration with the anatomy. So theoretically I can
> choose to do this, but i have noticed that the quality of the maps produced
> by the MR software are somehow "lacking". So my question is : Is the AIR and
> mutual image registration in DTI studio crutial for the processing of the
> data from the MR? I like the images produced by DTI studio better, but what
> is the basis of the improvement? how is it different to the images
> calculated by the MR? The MR software is Siemens Syngo. I know that DTI
> studio also provides tractography which makes a better tool for this
> analisis, but if i would be just interested inthe FA maps, are the images
> produced by the scanner enough? (regarding affine coregistration)
> thanks in advance for your responses.
>
> Salvador
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From salvador.castaneda at med.uni-tuebingen.de  Mon Feb  7 12:54:37 2011
From: salvador.castaneda at med.uni-tuebingen.de (Castaneda, Salvador)
Date: Mon, 07 Feb 2011 18:54:37 +0100
Subject: [Mristudio-users] tensor calculation
In-Reply-To: <AANLkTi=uWO4qyUvrmbgKppFqTTpQcw7waU6WsqbSJ8LL@mail.gmail.com>
References: <BLU159-w183F699F211062031828596E40@phx.gbl>
	<AANLkTimghRXVAZ9Tt_8_k-XNJE5vwWU7JewpyF3ojt2z@mail.gmail.com>
	<0AC64F4CB253074799B64FF8F0772D350126C675@azex2003.raddiag.med.uni-tuebingen.de>
	<AANLkTi=uWO4qyUvrmbgKppFqTTpQcw7waU6WsqbSJ8LL@mail.gmail.com>
Message-ID: <0AC64F4CB253074799B64FF8F0772D350126C67C@azex2003.raddiag.med.uni-tuebingen.de>

Hello Susumu,
 
Thank you for your reply. Things are clearer now. I have run some
phantom measurements on the 7 tesla MR i'm using for these animal
measurements, and have also found this distortion from the eddy current,
I assume. So i think that the AIR somehow also helps correct that in
this case. I think that I will continue using the AIR...
I have used diffeomap and ROI editor but still am on a learning
process...
I had another question. Are you able to evaluate more than one 0 and
1000 b value. Are you able to analize multiple B values?
 
All the best to your and your group.
 
Salvador
________________________________

Von: mristudio-users-bounces at mristudio.org
[mailto:mristudio-users-bounces at mristudio.org] Im Auftrag von susumu
mori
Gesendet: Freitag, 4. Februar 2011 16:50
An: DTI Studio, ROI Editor, DiffeoMap Questions/Support
Betreff: Re: [Mristudio-users] tensor calculation


Hi Salvador, 

AIR/MI registration is a common procedure for human MRI because of two
reasons. First, they tend to move (more than 1 pixel). Second, human
scanners have larger eddy current, which shifts and deforms the images.
To remove these registration errors, we use the co-registration tools. I
believe it is not necessary for animal studies because they are sedated
and heads are fixed.

After the co-registration process, we inevitably apply pixel
interpolation, which reduces resolution and enhances SNR. So, that could
be one of the reasons why the images look different. I guess if you skip
the registration, the images look much similar.

Just one note; we have DiffeoMap and RoiEditor you can download from
www.mristudio.org, which allows you to do cross-contrast and
cross-animal registration.

Susumu


On Thu, Feb 3, 2011 at 10:09 AM, Castaneda, Salvador
<salvador.castaneda at med.uni-tuebingen.de> wrote:


	Hello Mri studio users,
	 
	I am working with a MRI scanner with bruker hardware and siemens
software. I acquire mosaic files and have been able to work with the
mosaic in DTI studio to then do a AIR registration. I produce whatever
maps i need. It works great. I then, upload the maps created by DTI
studio to another imaging software called PMOD, as Analize files, for
coregistration with a T2W rat brain Anatomy image. I am able produce
good quality ROIs of the brain areas i need. Just recently i have
discovered, that the MR can also provide for me the FA, TRACE, DWI, and
ADC maps as DICOMs. These I can also upload to Pmod for coregistration
with the anatomy. So theoretically I can choose to do this, but i have
noticed that the quality of the maps produced by the MR software are
somehow "lacking". So my question is : Is the AIR and mutual image
registration in DTI studio crutial for the processing of the data from
the MR? I like the images produced by DTI studio better, but what is the
basis of the improvement? how is it different to the images calculated
by the MR? The MR software is Siemens Syngo. I know that DTI studio also
provides tractography which makes a better tool for this analisis, but
if i would be just interested inthe FA maps, are the images produced by
the scanner enough? (regarding affine coregistration)
	thanks in advance for your responses. 
	 
	
	Salvador

	_______________________________________________
	mristudio-users mailing list
	mristudio-users at mristudio.org
	http://lists.mristudio.org/mailman/listinfo/
	Unsubscribe, send a blank email to:
mristudio-users-unsubscribe at mristudio.org
	
	


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From susumu at mri.jhu.edu  Mon Feb  7 13:16:11 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Mon, 07 Feb 2011 13:16:11 -0500
Subject: [Mristudio-users] tensor calculation
In-Reply-To: <0AC64F4CB253074799B64FF8F0772D350126C67C@azex2003.raddiag.med.uni-tuebingen.de>
References: <BLU159-w183F699F211062031828596E40@phx.gbl>
	<AANLkTimghRXVAZ9Tt_8_k-XNJE5vwWU7JewpyF3ojt2z@mail.gmail.com>
	<0AC64F4CB253074799B64FF8F0772D350126C675@azex2003.raddiag.med.uni-tuebingen.de>
	<AANLkTi=uWO4qyUvrmbgKppFqTTpQcw7waU6WsqbSJ8LL@mail.gmail.com>
	<0AC64F4CB253074799B64FF8F0772D350126C67C@azex2003.raddiag.med.uni-tuebingen.de>
Message-ID: <AANLkTim=LSMOHd5rtObbkryDh41yzFZa9ZEjp4E=SRHn@mail.gmail.com>

Yes. You can specify b-values in the gradient table of DtiStudio.
I believe you can just append the b-value, like 0: 1, 0, 0, 500

On Mon, Feb 7, 2011 at 12:54 PM, Castaneda, Salvador <
salvador.castaneda at med.uni-tuebingen.de> wrote:

>  Hello Susumu,
>
> Thank you for your reply. Things are clearer now. I have run some phantom
> measurements on the 7 tesla MR i'm using for these animal measurements, and
> have also found this distortion from the eddy current, I assume. So i think
> that the AIR somehow also helps correct that in this case. I think that I
> will continue using the AIR...
> I have used diffeomap and ROI editor but still am on a learning process...
> I had another question. Are you able to evaluate more than one 0 and 1000 b
> value. Are you able to analize multiple B values?
>
> All the best to your and your group.
>
> Salvador
>  ------------------------------
>  *Von:* mristudio-users-bounces at mristudio.org [mailto:
> mristudio-users-bounces at mristudio.org] *Im Auftrag von *susumu mori
> *Gesendet:* Freitag, 4. Februar 2011 16:50
> *An:* DTI Studio, ROI Editor, DiffeoMap Questions/Support
> *Betreff:* Re: [Mristudio-users] tensor calculation
>
> Hi Salvador,
>
> AIR/MI registration is a common procedure for human MRI because of two
> reasons. First, they tend to move (more than 1 pixel). Second, human
> scanners have larger eddy current, which shifts and deforms the images. To
> remove these registration errors, we use the co-registration tools. I
> believe it is not necessary for animal studies because they are sedated and
> heads are fixed.
>
> After the co-registration process, we inevitably apply pixel interpolation,
> which reduces resolution and enhances SNR. So, that could be one of the
> reasons why the images look different. I guess if you skip the registration,
> the images look much similar.
>
> Just one note; we have DiffeoMap and RoiEditor you can download from
> www.mristudio.org, which allows you to do cross-contrast and cross-animal
> registration.
>
> Susumu
>
> On Thu, Feb 3, 2011 at 10:09 AM, Castaneda, Salvador <
> salvador.castaneda at med.uni-tuebingen.de> wrote:
>
>>  Hello Mri studio users,
>>
>> I am working with a MRI scanner with bruker hardware and siemens software.
>> I acquire mosaic files and have been able to work with the mosaic in DTI
>> studio to then do a AIR registration. I produce whatever maps i need. It
>> works great. I then, upload the maps created by DTI studio to another
>> imaging software called PMOD, as Analize files, for coregistration with
>> a T2W rat brain Anatomy image. I am able produce good quality ROIs of the
>> brain areas i need. Just recently i have discovered, that the MR can also
>> provide for me the FA, TRACE, DWI, and ADC maps as DICOMs. These I can also
>> upload to Pmod for coregistration with the anatomy. So theoretically I can
>> choose to do this, but i have noticed that the quality of the maps produced
>> by the MR software are somehow "lacking". So my question is : Is the AIR and
>> mutual image registration in DTI studio crutial for the processing of the
>> data from the MR? I like the images produced by DTI studio better, but what
>> is the basis of the improvement? how is it different to the images
>> calculated by the MR? The MR software is Siemens Syngo. I know that DTI
>> studio also provides tractography which makes a better tool for this
>> analisis, but if i would be just interested inthe FA maps, are the images
>> produced by the scanner enough? (regarding affine coregistration)
>> thanks in advance for your responses.
>>
>> Salvador
>>
>> _______________________________________________
>> mristudio-users mailing 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
>
>
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From petya_dti at yahoo.com  Wed Feb  9 13:30:26 2011
From: petya_dti at yahoo.com (Petya R)
Date: Wed, 09 Feb 2011 10:30:26 -0800 (PST)
Subject: [Mristudio-users] Saving of ROIs in DTI studio
Message-ID: <965768.22706.qm@web121701.mail.ne1.yahoo.com>

Hello,

We are trying to save ROIs that we generate in DTI Studio (through the "Fiber" tab), and later be able to view the ROIs.? We have two non-overlapping ROIs: for the first ROI we select the "or" button (under "ROI-Operation"); and for the second ROI, we select the "and" button.? (Btw, after the second ROI is drawn, it disappears from the 2D view on which it is drawn).? So this method shows the fibers that go through both ROIs.? 

However, we're not able to save these two ROIs, and view them later.? At best, we could save the first ROI, immediately after drawing it.? If we use the "save" button (under "ROI-Operation") after drawing the second ROI, and try to load up the ROI file in DTI Studio or ROI editor, we either see only the first ROI, or get the error message "There is no ROI data.", depending on the file format...

Please let me/us know if you have any suggestions, as to how to save both ROIs and be able to view/load them later.

Thank you very much for your help!
Petya




      
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From choisj70 at gmail.com  Wed Feb  9 19:32:05 2011
From: choisj70 at gmail.com (Seongjin)
Date: Wed, 09 Feb 2011 19:32:05 -0500
Subject: [Mristudio-users] Saving of ROIs in DTI studio
In-Reply-To: <965768.22706.qm@web121701.mail.ne1.yahoo.com>
References: <965768.22706.qm@web121701.mail.ne1.yahoo.com>
Message-ID: <AANLkTimUwrCiFep94j7hpZtcMc1yXJjQVy7nk_5tZXuu@mail.gmail.com>

It might be better to use ROIeditor for ROI work.
You can use ROIs (saved using ROIeditor) in DTI Studio but you might be able
to see them. However it works exactly what you intended.

-SC

On Wed, Feb 9, 2011 at 1:30 PM, Petya R <petya_dti at yahoo.com> wrote:

> Hello,
>
> We are trying to save ROIs that we generate in DTI Studio (through the
> "Fiber" tab), and later be able to view the ROIs.  We have two
> non-overlapping ROIs: for the first ROI we select the "or" button (under
> "ROI-Operation"); and for the second ROI, we select the "and" button.  (Btw,
> after the second ROI is drawn, it disappears from the 2D view on which it is
> drawn).  So this method shows the fibers that go through both ROIs.
>
> However, we're not able to save these two ROIs, and view them later.  At
> best, we could save the first ROI, immediately after drawing it.  If we use
> the "save" button (under "ROI-Operation") after drawing the second ROI, and
> try to load up the ROI file in DTI Studio or ROI editor, we either see only
> the first ROI, or get the error message "There is no ROI data.", depending
> on the file format...
>
> Please let me/us know if you have any suggestions, as to how to save both
> ROIs and be able to view/load them later.
>
> Thank you very much for your help!
> Petya
>
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From salvador.castaneda at med.uni-tuebingen.de  Thu Feb 10 04:12:34 2011
From: salvador.castaneda at med.uni-tuebingen.de (Castaneda, Salvador)
Date: Thu, 10 Feb 2011 10:12:34 +0100
Subject: [Mristudio-users] Saving of ROIs in DTI studio
In-Reply-To: <AANLkTimUwrCiFep94j7hpZtcMc1yXJjQVy7nk_5tZXuu@mail.gmail.com>
References: <965768.22706.qm@web121701.mail.ne1.yahoo.com>
	<AANLkTimUwrCiFep94j7hpZtcMc1yXJjQVy7nk_5tZXuu@mail.gmail.com>
Message-ID: <0AC64F4CB253074799B64FF8F0772D350126C682@azex2003.raddiag.med.uni-tuebingen.de>

Yeah ROI editor is nice, but i don't believe it can do fiber ROI
tracking saving.or can it?
 
S Castaneda

________________________________

Von: mristudio-users-bounces at mristudio.org
[mailto:mristudio-users-bounces at mristudio.org] Im Auftrag von [Seongjin]
Gesendet: Donnerstag, 10. Februar 2011 01:32
An: DTI Studio, ROI Editor, DiffeoMap Questions/Support
Betreff: Re: [Mristudio-users] Saving of ROIs in DTI studio


It might be better to use ROIeditor for ROI work.  
You can use ROIs (saved using ROIeditor) in DTI Studio but you might be
able to see them. However it works exactly what you intended.

-SC 


On Wed, Feb 9, 2011 at 1:30 PM, Petya R <petya_dti at yahoo.com> wrote:


Hello,

We are trying to save ROIs that we generate in DTI Studio (through the
"Fiber" tab), and later be able to view the ROIs.  We have two
non-overlapping ROIs: for the first ROI we select the "or" button (under
"ROI-Operation"); and for the second ROI, we select the "and" button.
(Btw, after the second ROI is drawn, it disappears from the 2D view on
which it is drawn).  So this method shows the fibers that go through
both ROIs.  

However, we're not able to save these two ROIs, and view them later.  At
best, we could save the first ROI, immediately after drawing it.  If we
use the "save" button (under "ROI-Operation") after drawing the second
ROI, and try to load up the ROI file in DTI Studio or ROI editor, we
either see only the first ROI, or get the error message "There is no ROI
data.", depending on the file format...

Please let me/us know if you have any suggestions, as to how to save
both ROIs and be able to view/load them later.

Thank you very much for your help!
Petya

	


	_______________________________________________
	mristudio-users mailing list
	mristudio-users at mristudio.org
	http://lists.mristudio.org/mailman/listinfo/
	Unsubscribe, send a blank email to:
mristudio-users-unsubscribe at mristudio.org
	
	


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From susumu at mri.jhu.edu  Thu Feb 10 06:35:19 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Thu, 10 Feb 2011 06:35:19 -0500
Subject: [Mristudio-users] Saving of ROIs in DTI studio
In-Reply-To: <0AC64F4CB253074799B64FF8F0772D350126C682@azex2003.raddiag.med.uni-tuebingen.de>
References: <965768.22706.qm@web121701.mail.ne1.yahoo.com>
	<AANLkTimUwrCiFep94j7hpZtcMc1yXJjQVy7nk_5tZXuu@mail.gmail.com>
	<0AC64F4CB253074799B64FF8F0772D350126C682@azex2003.raddiag.med.uni-tuebingen.de>
Message-ID: <AANLkTi=Teo=k0_y5qy2Exq89vgVct8zdHR2rPuhhmM5n@mail.gmail.com>

Please refer to FAQ16 of https://www.mristudio.org/wiki/faq.
Using this function, you can manage ROI files better.
For the reconstructed fibers, you can use the function of DtiStudio to save
them.
I hope Hangyi can follow up about your question of displaying ROIs in
DtiStudio.

On Thu, Feb 10, 2011 at 4:12 AM, Castaneda, Salvador <
salvador.castaneda at med.uni-tuebingen.de> wrote:

>  Yeah ROI editor is nice, but i don't believe it can do fiber ROI tracking
> saving.or can it?
>
> S Castaneda
>
>  ------------------------------
> *Von:* mristudio-users-bounces at mristudio.org [mailto:
> mristudio-users-bounces at mristudio.org] *Im Auftrag von *[Seongjin]
> *Gesendet:* Donnerstag, 10. Februar 2011 01:32
> *An:* DTI Studio, ROI Editor, DiffeoMap Questions/Support
> *Betreff:* Re: [Mristudio-users] Saving of ROIs in DTI studio
>
> It might be better to use ROIeditor for ROI work.
> You can use ROIs (saved using ROIeditor) in DTI Studio but you might be
> able to see them. However it works exactly what you intended.
>
> -SC
>
> On Wed, Feb 9, 2011 at 1:30 PM, Petya R <petya_dti at yahoo.com> wrote:
>
>>   Hello,
>>
>> We are trying to save ROIs that we generate in DTI Studio (through the
>> "Fiber" tab), and later be able to view the ROIs.  We have two
>> non-overlapping ROIs: for the first ROI we select the "or" button (under
>> "ROI-Operation"); and for the second ROI, we select the "and" button.  (Btw,
>> after the second ROI is drawn, it disappears from the 2D view on which it is
>> drawn).  So this method shows the fibers that go through both ROIs.
>>
>> However, we're not able to save these two ROIs, and view them later.  At
>> best, we could save the first ROI, immediately after drawing it.  If we use
>> the "save" button (under "ROI-Operation") after drawing the second ROI, and
>> try to load up the ROI file in DTI Studio or ROI editor, we either see only
>> the first ROI, or get the error message "There is no ROI data.", depending
>> on the file format...
>>
>> Please let me/us know if you have any suggestions, as to how to save both
>> ROIs and be able to view/load them later.
>>
>> Thank you very much for your help!
>> Petya
>>
>>
>>
>> _______________________________________________
>> mristudio-users mailing 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
>
>
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From hjiang at jhmi.edu  Thu Feb 10 09:38:34 2011
From: hjiang at jhmi.edu (Hangyi Jiang)
Date: Thu, 10 Feb 2011 09:38:34 -0500
Subject: [Mristudio-users] Saving of ROIs in DTI studio
In-Reply-To: <965768.22706.qm@web121701.mail.ne1.yahoo.com>
References: <965768.22706.qm@web121701.mail.ne1.yahoo.com>
Message-ID: <145933A2BE9E4F48AE079A201379BF2F2448262A58@RAD-EXCH1.win.ad.jhu.edu>

hi,

seems that this question brings a discussion in this community,   I'd copy my reply to Petya here:

---
hi, Petya,

you can save them as "Binary Map", in this way, you will get two ROI-image files (.dat) and one plain-text file (.map).  the 1st_ROI file is the ROI with "OR" operation, the 2nd is the one with "AND" operation.  the ROI-image can be loaded in using "File->MriView3D" command -> file format = RAW; data type = Byte"...;   the ROI area is marked with non-zero value (you may need right clicking on 2D image area -> Image level ->..",  adjusting the image level to make ROI be visible.

when you draw ROIs for fiber selection,  the ROIs may disappear if the ROIs has no overlapped region when "AND" operation is being used, only the selected fibers are shown (if there are any).  Why?  because it is designed for "Fiber Selection", not ROI-Displaying  ;)

-------

in some cases, it would be helpful if individual ROIs are shown with selected fibers.   thank you all for this valuable comments.   we will consider this in the updated version.


regards,

hangyi




________________________________________
From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Petya R [petya_dti at yahoo.com]
Sent: Wednesday, February 09, 2011 1:30 PM
To: mristudio-users at mristudio.org
Subject: [Mristudio-users] Saving of ROIs in DTI studio

Hello,

We are trying to save ROIs that we generate in DTI Studio (through the "Fiber" tab), and later be able to view the ROIs.  We have two non-overlapping ROIs: for the first ROI we select the "or" button (under "ROI-Operation"); and for the second ROI, we select the "and" button.  (Btw, after the second ROI is drawn, it disappears from the 2D view on which it is drawn).  So this method shows the fibers that go through both ROIs.

However, we're not able to save these two ROIs, and view them later.  At best, we could save the first ROI, immediately after drawing it.  If we use the "save" button (under "ROI-Operation") after drawing the second ROI, and try to load up the ROI file in DTI Studio or ROI editor, we either see only the first ROI, or get the error message "There is no ROI data.", depending on the file format...

Please let me/us know if you have any suggestions, as to how to save both ROIs and be able to view/load them later.

Thank you very much for your help!
Petya





From choisj70 at gmail.com  Fri Feb 11 14:33:21 2011
From: choisj70 at gmail.com (Seongjin)
Date: Fri, 11 Feb 2011 14:33:21 -0500
Subject: [Mristudio-users] ROI editor and DTI studio
Message-ID: <AANLkTikDtSs1vn2nw-sMH_wCGfbr4s0475F-Yof1Mofu@mail.gmail.com>

Dear DTIstudio users and developers,

When I loaded the same images of DTI metrics using ROIeditor and DTIstudio,
I found images does not look the same way on both tools.

The data does not have isotropic voxel dimensions (acquired as 1x1x6 and
interpolated to 0.5x0.5x6).
This voxel dimension was not for brain but for other anatomical region. It
was determined intentionally.
DTI studio shows images reflecting actual FOV info not matrix dimension
only.
However, ROI editor shows similar images but not quite good as DTI studio.

If DTIstudio and ROIeditor show the same images in the same manner, that
would be great.

Thanks,
- SC
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From xli16 at jhmi.edu  Fri Feb 11 15:02:57 2011
From: xli16 at jhmi.edu (Xin Li)
Date: Fri, 11 Feb 2011 15:02:57 -0500
Subject: [Mristudio-users] ROI editor and DTI studio
In-Reply-To: <AANLkTikDtSs1vn2nw-sMH_wCGfbr4s0475F-Yof1Mofu@mail.gmail.com>
References: <AANLkTikDtSs1vn2nw-sMH_wCGfbr4s0475F-Yof1Mofu@mail.gmail.com>
Message-ID: <7220f7bbcd01.4d554fa1@johnshopkins.edu>

Hello,

I will look into it. Could you provide the screenshots to show this difference?


Xin

----- Original Message -----
From: "[Seongjin]" <choisj70 at gmail.com>
Date: Friday, February 11, 2011 2:33 pm
Subject: [Mristudio-users] ROI editor and DTI studio
To: "DTI Studio, ROI Editor, Landmarker Questions/Support" <mristudio-users at mristudio.org>


> Dear DTIstudio users and developers,
>  
>  When I loaded the same images of DTI metrics using ROIeditor and DTIstudio,
>  I found images does not look the same way on both tools.
>  
>  The data does not have isotropic voxel dimensions (acquired as 1x1x6 
> and
>  interpolated to 0.5x0.5x6).
>  This voxel dimension was not for brain but for other anatomical 
> region. It
>  was determined intentionally.
>  DTI studio shows images reflecting actual FOV info not matrix dimension
>  only.
>  However, ROI editor shows similar images but not quite good as DTI studio.
>  
>  If DTIstudio and ROIeditor show the same images in the same manner, that
>  would be great.
>  
>  Thanks,
>  - SC 
> _______________________________________________
>  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  Fri Feb 11 15:31:58 2011
From: xli16 at jhmi.edu (Xin Li)
Date: Fri, 11 Feb 2011 15:31:58 -0500
Subject: [Mristudio-users] ROI editor and DTI studio
In-Reply-To: <AANLkTikDtSs1vn2nw-sMH_wCGfbr4s0475F-Yof1Mofu@mail.gmail.com>
References: <AANLkTikDtSs1vn2nw-sMH_wCGfbr4s0475F-Yof1Mofu@mail.gmail.com>
Message-ID: <7230f7dd854d.4d55566e@johnshopkins.edu>

Hello,

You may not be allowed to send attach files to the mailing list. Please send the screenshots and the image you loaded directly to my email account (xli16 at jhmi.ed). ROIEditor uses the same way as DtiStudio to display images. I will check what causes this difference.



Xin



----- Original Message -----
From: "[Seongjin]" <choisj70 at gmail.com>
Date: Friday, February 11, 2011 2:33 pm
Subject: [Mristudio-users] ROI editor and DTI studio
To: "DTI Studio, ROI Editor, Landmarker Questions/Support" <mristudio-users at mristudio.org>


> Dear DTIstudio users and developers,
>  
>  When I loaded the same images of DTI metrics using ROIeditor and DTIstudio,
>  I found images does not look the same way on both tools.
>  
>  The data does not have isotropic voxel dimensions (acquired as 1x1x6 
> and
>  interpolated to 0.5x0.5x6).
>  This voxel dimension was not for brain but for other anatomical 
> region. It
>  was determined intentionally.
>  DTI studio shows images reflecting actual FOV info not matrix dimension
>  only.
>  However, ROI editor shows similar images but not quite good as DTI studio.
>  
>  If DTIstudio and ROIeditor show the same images in the same manner, that
>  would be great.
>  
>  Thanks,
>  - SC 
> _______________________________________________
>  mristudio-users mailing list
>  mristudio-users at mristudio.org
>  
>  Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org 

From dafnab at tasmc.health.gov.il  Mon Feb 14 03:15:16 2011
From: dafnab at tasmc.health.gov.il (Dafna Ben Bashat)
Date: Mon, 14 Feb 2011 10:15:16 +0200
Subject: [Mristudio-users] Increasing decimal numbers
In-Reply-To: <145933A2BE9E4F48AE079A201379BF2F2448262A58@RAD-EXCH1.win.ad.jhu.edu>
References: <965768.22706.qm@web121701.mail.ne1.yahoo.com>
	<145933A2BE9E4F48AE079A201379BF2F2448262A58@RAD-EXCH1.win.ad.jhu.edu>
Message-ID: <5EDAC8080B8BEF4E8F13D293108E5898143FC66F@EXCH-VS.tasmc.corp>

Dear users,
When we calculate average diffusivity values within a tract, we get only 4 decimal numbers.
How can we increase sensitivity (especially for the eigen values and ADC) and get more decimal numbers? We are using b=700 so we can't use -1 for the b value?

Thanks
Dafna


Dafna Ben Bashat Ph.D. 

Senior Investigator
In charge?of MR systems
The Wohl institute for Advanced Imaging
Brain Imaging Center
Tel Aviv Sourasky Medical Center

Phone: 972-3-6973953 (o)          Fax: 972-3-6973080

       972-52-4262515 (m)        Mail: dafnab at tasmc.health.gov.il

blank email to: mristudio-users-unsubscribe at mristudio.org


From susumu at mri.jhu.edu  Fri Feb 18 19:59:19 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Fri, 18 Feb 2011 19:59:19 -0500
Subject: [Mristudio-users] Does the inferior fronto-occipital fasciculus
	exists?
In-Reply-To: <87D3B497-D79E-4EF4-A452-B4E4F9784268@stanford.edu>
References: <87D3B497-D79E-4EF4-A452-B4E4F9784268@stanford.edu>
Message-ID: <AANLkTinRfZa58CXeTyMANASfXP=Goi2fYCz6kGXtPs=Q@mail.gmail.com>

Hi Naama,

This is a good question and please allow me to share my though with people
in the MriStudio mailing list.

When we describe white matter, there are two ways. Let me use the analogy of
geological maps. If I see a map of Baltimore, there are essentially two
types of information; boundaries that define boarders of locations like
city, county, and state. The other is road information like route 95 that
travels from Washingon DC to NY. The former defines locations and the latter
doesn't belong to any single location.

Likewise, WM map has two ways to define. Many WM names define locations,
like the internal capsule, which is a WM location between the basal ganglia.
There are many "roads" that penetrate the internal capsule like
cortico-thalamic, thalamo-cortical, cortico-spinal, cortico-pontine, to name
few, but they are all intermingled and it's not possible to completely
decipher them, at least by DTI/MRI. There are also names of WM that imply
something similar to the road names. For example, the corticospinal tract
and IFO defines two destinations.

Our atlas obviously defines locations; all segments are defined by boarders.
Some of the defined locations have names that implies roads (e.g. IFO, SFO,
CST, ets), but they actually define locations. This is one source of
confusion.

Now, there are some more confusing things. I believe many macroscopic
anatomical nomenclature is based on classic histology observations. The SFO
and IFO are assigned to large white matter bundles that sweep from front to
back, which look like connecting the frontal and occipital lobes, but I
don't think it was confirmed that there are actually axons connecting the
frontal and occipital lobes. Therefore, the foundation of the assigned names
are not as sound as the corticospinal tracts, which are confirmed in many
animals and human.

Now, we assigned some locations of the brain "SFO" and "IFO". There is not
doubt that there are large axonal bundles travelling front to back (or back
to front) in the designated locations. However, if one asks, "do you know if
these locations really contain axons connecting the frontal and occipital
lobes?", well, I must say, "not sure". To me, it seems like an issue of
nomenclature.

In any case, assignments of "road-type" names to the WM is a tricky effort
because even for the "corticospinal tract", the designated locations may
contain many other axons like cortico-pontine and cortico-bulbar axons. As
long as they are mixed in a microscopic level, we can only say, "this region
has high concentration of the corticospinal tract" and, to be strict, we can
always argue that it is not correct to give a binary definition to a place
like, "this is the corticospinal tract", because the "real" corticospinal
tract refers to axons that connect the cortex and the spinal cord, not to
many millimeters of anatomical locations visualized by MRI/DTI.

So, going back to your original question, there were controversy over the
existence of SFO and now IFO . In these cases what is discussed is "is there
really a large concentration of axons that connect the frontal and occipital
lobes in the WM locations called SFO/IFO?" How does it affect our study?
Well, for the IFO, maybe we should change the name of the location to "a
large WM bundle running front-back (green color) at the junction of the
frontal lobe and the temporal lobe". To me, the source of the problem is the
adoption of road names to refer to locations. As long as we use our atlas to
define locations and do quantitative measurements such as volumes and FAs,
how we call each location is not really a critical issue. Of course, it
could profoundly affect the interpretation. If the FA of "IFO" is low, we
should not immediately conclude connectivity problems between the frontal
and occipital lobes, simply based on the name of the location. In this
sense, you raised an important issue. On the other hand, IFO/SFO have been
widely used to refer some specific locations and we can communicate about
anatomical locations through these terms. So, even if they
are mis-nomenclature, we may need to keep using them unless the anatomist
society comes up with a new set of anatomical languages to refer these
anatomical locations.

Susumu

On Fri, Feb 18, 2011 at 5:07 PM, Naama Barnea-Goraly <naamab at stanford.edu>wrote:

>
> Dear Susumu,
>
> A recent analysis we are running yielded some significant results in the
> IFOF (according to the JHU White matter tractography atlas) which lead me to
> some investigation on this pathway. I was very surprised to read in " White
> matter of the Brain" ( a book by Schmahmann and Pandya), that in fact the
> IFOF does not exist (page 445). They think the IFOF is in fact the ILF
> /uncinate/extreme capsule mistaken by early anatomists as a separate tract.
> What do you think?
>
> 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.
>
>
>
>
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From susumu at mri.jhu.edu  Sat Feb 19 12:04:25 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Sat, 19 Feb 2011 12:04:25 -0500
Subject: [Mristudio-users] Fibrebundle - help
In-Reply-To: <4A662A1A3737D3418374FA089F6E2E213834428EFE@MAPI.ad.kent.ac.uk>
References: <4A662A1A3737D3418374FA089F6E2E213834428EFE@MAPI.ad.kent.ac.uk>
Message-ID: <AANLkTikV7wUhrwaKQUUnzpaUQkfhtMem4pEAbvz-5UeG@mail.gmail.com>

Hi Nagulan,

-------------------------------------------------------------------------------------------------

>Considering a deterministic tracking method and one seed point,

>Is it really natural to represent a whole bundle by a single line? is this
representation not at risk of being misinterpreted clinically? What is the
exact interpretation of these lines?

>Please can you suugest some idas or references about these questions.

------------------------------------------------------------------------------------------------

It's an important and fundamental question and please allow me to share my
though with other users in the mailing list. What I'm going to describe
below is mostly my opinion and I'll try to make clear which is fact and
which is my opinion.

First of all, when we talk about tracts and fibers and bundles and
connections, we are talking about axons. There are 100 billion neurons in
the brain and each neuron has one axon to communicate with other regions of
the brain. The axon branches at its terminal but also along the trajectory.
Combined with the dendrite network, the notion of fibers and connections
could be very complicated; even if we can reconstruct a complete picture of
one neuron, its anatomy and connection are far from simple one-to-one
communication. If one neuron communicate with 10 neurons in average, it is a
question of the size of 100 billion x 10 (or maybe 100 billion^10?).

Apparently, this is way beyond our ability for complete delineation of the
system. Therefore, we need to resort to some kind of methods to reduce the
dimension of the information. During this process, it is inevitable that
much information is degenerated. For example, if we obtain 10GB worth of
anatomical information from one brain, we still loose an astronomical amount
of information. So in general, when we talk about axonal anatomy and
connectivity, we need to accept whatever the technique we use gives only
approximation with HUGELY degenerated information.

The above argument started from a microscopic cellular level point of view.
When we do MRI, we usually approach from the other end of the spectrum. We
observe properties of water molecules (which is a very indirect indicator of
any cellular entity) with 1-3 mm spatial resolution, acquired within 10 min,
and has merely 10 MB of data. We can understand that a huge amount of
anatomical information is already lost at the point of data acquisition,
which is impossible to recover using any sophisticated mathematical tools.
We can say any biological statement from this kind of measurements can only
be an approximation. On the other hand, we can also argue that it is an
excellent method to systematically, consistently, and quantitatively reduce
the unmanageably large system to 10 MB within 10 min so that we can
investigate and compare the status of the anatomy, which can't be done by
any microscopic (histological) methods.

There is a very common issue that arises in this kind of situations; between
the microscopic cellular studies and macroscopic imaging methods, there is a
gap  so large that we often (well, I would say usually) can't connect these
two sides of information; e.g. if we find one line generated by a
deterministic tracking, we don't know what it exactly means in terms of a
cellular level entity.

In my opinion, there are two types of approaches we usually take to deal
with this "information gap". First, we often use EMPIRICAL RELATIONSHIP. I
believe many radiological diagnosis is based on this. Certain appearance in
brain MRI suggests brain tumor even if it doesn't necessary tell where
exactly is the tumor. Decrease in diffusion constant suggest stroke
infarction.  These are the examples of useful empirical relationship we use
every day. Second is GROUP DIFFERENCE. T1-weighted images of AD patients may
suggest cortical thinning. This could be real thinning or maybe due to
contrast change. Even if we don't know the real cellular event, if MRI can
reproducibly detect differences, it is very useful information. As for fiber
tracking, one may find that a particular tract in a disease group is
smaller. This could be due to FA decrease or size reduction of the tract. We
can't immediately tell what is really happening, but the fact the
DTI/tractography can detect such changes non-invasive and reproducibly may
prove very useful.

Now let's go back to the question of "what does the line mean". There are
also related questions like, "is the line really true (validation)" or "does
it really represent connection". Before answering this question, we first
have to define what is exactly the anatomical entity we are going after.
Without defining the target, we can't do validation studies. First of all,
it is obvious that we are not talking about a single axon which is only few
micron in diameter. Nobody would argue that DTI-based tractography
represents a single axon and I'm sure nobody wants to study 100 billion
axons either. Then what is exactly we want to study? Suppose we have a dream
imaging method that can give complete pictures of whatever we want to image.
Then what is the exact anatomical entity we want to study? Well, as long as
we are talking about the white matter, it must be "a bundle of axons". One
may argue, "we know that the corticospinal tract does exist and this is what
we want to know". There are many bundles of axons that were described for
many years such as SLF, cingulum, thalamic radiation, etc. These structures
have been described using histology samples and visual inspection of the
macroscopic configuration of the white matter. Those named fibers are mostly
"anatomical features", with loose definitions about the boarders; many axons
may merge and exit along the tract. Because they are merely features without
clear definition, it becomes a very difficult to task to use them as the
target of the study; if the anatomical target is vague, how can we validate
our DTI-tractography results against it? For example, the CST is one of the
most well-characterized tracts. We know that it exists and also know the
location quite well. However, there are so many other fibers running
parallel to it that it is very difficult to define it in the cerebral
hemisphere. At the pons level, it has much more compacted shape with much
less contaminating axons, although there still contain a lot of
corticopontine and corticobulbar axons. Even at the pons level, histology
reveals that the CST axons are interdigitated with a significant number of
pontine crossing fibers and the CST axons are distributed from the high
concentration at the center to gradual reduction of the concentration toward
the edge. So, even if we have histology, it is very difficult to define
boundary and the clear entity of the CST. So, if we can obtain line (or
lines) seemingly representing the CST, it is hard to tell the validity or
what it exactly represents.

So, in summary, the problem we are facing is, the DTI-tractography only
gives macroscopic and indirect (water property) measure of white matter
features, while the anatomy we are interested in is also vaguely defined.
Therefore any efforts that try to attach true (whatever the "true" means)
anatomical meaning to DTI results often hit a big wall. There are other
similar situations when we ask, "what is the meaning of decreased FA" and
"can we study brain connectivity"; in both cases, the measurements and
targets are not well defined. In this kind of situation, in my opinion, I
feel that we have to resort to "empirical relationship" and "group
differences" to extract some PRACTICAL conclusions. This  may be enough if
one wants to contribute to clinical diagnosis. If one is interested in
neuroscience (or ground truth), DTI/MRI may give a good indication about
what could be wrong in which area so that we can direct subsequent analyses
using, for example, histology or other modalities.

Another common and specific question about tractography is, "then how we can
believe tractography results when we do tumor surgery". If we have to take
"real or not" approach, it should be not too difficult to come up with many
cases showing how tractography fails, and thus dismiss tractography. In this
kind of questions, I think it's very important to define practical goals
rather than asking a simple deterministic question like "is it real or not".
For example, the usefulness or accuracy of tractography can be judged
differently depending on whether we are asking 5 mm accuracy or merely
asking "is the CST left or right side of the tumor". This is a good example
that our answer requires clear statement about the end goal. Without
defining the goal and a required accuracy level, it is sometimes sterile to
discuss about the validity of tools. In this case, we are actually asking
"does the availability of tractography results on the CST improve the
outcome of the tumor surgery?". When we ask this kind of questions, we
rarely expect improvement in 100% cases. Just like drug trials, we should
talk about statistically significant improvement and evaluate cost/benefit
functions including the rate of adverse impacts. In this situation, I think
a simple question like "does tractography give real CST" is a too naive
question.

I guess I'm not giving you a straight answer, but hope this would give you a
good background about DTI/Tractography research.

Susumu


On Mon, Feb 14, 2011 at 5:52 AM, N.Ratnarajah <rn54 at kent.ac.uk> wrote:

> Dear Susumu
>
> Considering a deterministic tracking method and one seed point,
>
> Is it really natural to represent a whole bundle by a single line? is this
> representation not at risk of being misinterpreted clinically? What is the
> exact interpretation of these lines?
>
> Please can you suugest some idas or references about these questions..
>
> Sincerely
> Nagulan
>
>
>
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From dc02hana at m6.gyao.ne.jp  Mon Feb 21 08:45:42 2011
From: dc02hana at m6.gyao.ne.jp (hanaie)
Date: Mon, 21 Feb 2011 22:45:42 +0900
Subject: [Mristudio-users] radial diffusivity,  mean diffusivity
Message-ID: <003001cbd1cd$a1befba0$e53cf2e0$@gyao.ne.jp>

Dear DTI experts

 

How can I do to obtain the radial diffusivity and mean diffusivity in DTI
studio?

 

1.     In the " Dti Map" tab, clicking "Tensor, color Map etc" button, and
checking the checkboxes "Radial", "Trace"

 

2.     After tensor calculation and fiber tracking, if I click "statistics"
button in the "Fiber" tab and 

 I choose the each image and click "go" button in the another window, can I
obtain radial and mean diffusivity?

 

 

Please give me any suggestion.

 

Many thanks.

 

Ryuzo

 

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From buchmann2 at wisc.edu  Mon Feb 21 09:02:32 2011
From: buchmann2 at wisc.edu (Andreas Buchmann)
Date: Mon, 21 Feb 2011 08:02:32 -0600
Subject: [Mristudio-users] radial diffusivity,  mean diffusivity
In-Reply-To: <003001cbd1cd$a1befba0$e53cf2e0$@gyao.ne.jp>
Message-ID: <0LGZ009NT0CPOU00@smtpauth1.wiscmail.wisc.edu>

Dear Ryuzo,

 

yes, you're on the right track with (1). After the estimation, DTI-Studio
appends the images to the list of images you have, and you can see them
under the 'Image'-tab and save them with right-click on the image.

 

Good luck

Andreas

 

  _____  

From: mristudio-users-bounces at mristudio.org
[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of hanaie
Sent: Montag, 21. Februar 2011 07:46
To: mristudio-users at mristudio.org
Subject: [Mristudio-users] radial diffusivity, mean diffusivity

 

Dear DTI experts

 

How can I do to obtain the radial diffusivity and mean diffusivity in DTI
studio?

 

1.       In the " Dti Map" tab, clicking "Tensor, color Map etc" button, and
checking the checkboxes "Radial", "Trace"

 

2.       After tensor calculation and fiber tracking, if I click
"statistics" button in the "Fiber" tab and 

 I choose the each image and click "go" button in the another window, can I
obtain radial and mean diffusivity?

 

 

Please give me any suggestion.

 

Many thanks.

 

Ryuzo

 

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From dc02hana at m6.gyao.ne.jp  Tue Feb 22 09:54:25 2011
From: dc02hana at m6.gyao.ne.jp (hanaie)
Date: Tue, 22 Feb 2011 23:54:25 +0900
Subject: [Mristudio-users] radial diffusivity,  mean diffusivity
In-Reply-To: <0LGZ009NT0CPOU00@smtpauth1.wiscmail.wisc.edu>
References: <003001cbd1cd$a1befba0$e53cf2e0$@gyao.ne.jp>
	<0LGZ009NT0CPOU00@smtpauth1.wiscmail.wisc.edu>
Message-ID: <002c01cbd2a0$662a7550$327f5ff0$@gyao.ne.jp>

Dear Andreas

 

Thank you very much for your suggestion.  I will try.

 

Ryuzo

 

From: mristudio-users-bounces at mristudio.org
[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Andreas Buchmann
Sent: Monday, February 21, 2011 11:03 PM
To: 'DTI Studio, ROI Editor, DiffeoMap Questions/Support'
Subject: Re: [Mristudio-users] radial diffusivity, mean diffusivity

 

Dear Ryuzo,

 

yes, you're on the right track with (1). After the estimation, DTI-Studio
appends the images to the list of images you have, and you can see them
under the 'Image'-tab and save them with right-click on the image.

 

Good luck

Andreas

 

  _____  

From: mristudio-users-bounces at mristudio.org
[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of hanaie
Sent: Montag, 21. Februar 2011 07:46
To: mristudio-users at mristudio.org
Subject: [Mristudio-users] radial diffusivity, mean diffusivity

 

Dear DTI experts

 

How can I do to obtain the radial diffusivity and mean diffusivity in DTI
studio?

 

1.     In the " Dti Map" tab, clicking "Tensor, color Map etc" button, and
checking the checkboxes "Radial", "Trace"

 

2.     After tensor calculation and fiber tracking, if I click "statistics"
button in the "Fiber" tab and 

 I choose the each image and click "go" button in the another window, can I
obtain radial and mean diffusivity?

 

 

Please give me any suggestion.

 

Many thanks.

 

Ryuzo

 

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From 107310 at ib.k.u-tokyo.ac.jp  Tue Feb 22 20:36:20 2011
From: 107310 at ib.k.u-tokyo.ac.jp (107310 at ib.k.u-tokyo.ac.jp)
Date: Wed, 23 Feb 2011 10:36:20 +0900
Subject: [Mristudio-users] radial diffusivity,  mean diffusivity
In-Reply-To: <002c01cbd2a0$662a7550$327f5ff0$@gyao.ne.jp>
References: <003001cbd1cd$a1befba0$e53cf2e0$@gyao.ne.jp>
	<0LGZ009NT0CPOU00@smtpauth1.wiscmail.wisc.edu>
	<002c01cbd2a0$662a7550$327f5ff0$@gyao.ne.jp>
Message-ID: <20110223013620.000068D1.0399@ib.k.u-tokyo.ac.jp>

Dear Andreas, Ryuzo and DTI experts


I also try to calculate mean diffusivity.
But in DTI studio, only the radial diffusivity and ADCs can calculate at 
the 'Image'-tab with ROI.

Is there any function to measure mean diffusivity?
Please give me any suggestion.
 
Many thanks.


YO


> Dear Andreas
> 
>  
> 
> Thank you very much for your suggestion.  I will try.
> 
>  
> 
> Ryuzo
> 
>  
> 
> From: mristudio-users-bounces at mristudio.org
> [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Andreas 
Buchmann
> Sent: Monday, February 21, 2011 11:03 PM
> To: 'DTI Studio, ROI Editor, DiffeoMap Questions/Support'
> Subject: Re: [Mristudio-users] radial diffusivity, mean diffusivity
> 
>  
> 
> Dear Ryuzo,
> 
>  
> 
> yes, you're on the right track with (1). After the estimation, DTI-
Studio
> appends the images to the list of images you have, and you can see 
them
> under the 'Image'-tab and save them with right-click on the image.
> 
>  
> 
> Good luck
> 
> Andreas
> 
>  
> 
>   _____  
> 
> From: mristudio-users-bounces at mristudio.org
> [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of hanaie
> Sent: Montag, 21. Februar 2011 07:46
> To: mristudio-users at mristudio.org
> Subject: [Mristudio-users] radial diffusivity, mean diffusivity
> 
>  
> 
> Dear DTI experts
> 
>  
> 
> How can I do to obtain the radial diffusivity and mean diffusivity in 
DTI
> studio?
> 
>  
> 
> 1.     In the " Dti Map" tab, clicking "Tensor, color Map etc" button, 
and
> checking the checkboxes "Radial", "Trace"
> 
>  
> 
> 2.     After tensor calculation and fiber tracking, if I click "
statistics"
> button in the "Fiber" tab and 
> 
>  I choose the each image and click "go" button in the another window, 
can I
> obtain radial and mean diffusivity?
> 
>  
> 
>  
> 
> Please give me any suggestion.
> 
>  
> 
> Many thanks.
> 
>  
> 
> Ryuzo
> 
>  
> 
>  
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to: mristudio-users-unsubscribe@
mristudio.org
> 



From buchmann2 at wisc.edu  Wed Feb 23 08:31:17 2011
From: buchmann2 at wisc.edu (Andreas Buchmann)
Date: Wed, 23 Feb 2011 07:31:17 -0600
Subject: [Mristudio-users] radial diffusivity,  mean diffusivity
In-Reply-To: <20110223013620.000068D1.0399@ib.k.u-tokyo.ac.jp>
Message-ID: <0LH20086JO891D30@smtpauth1.wiscmail.wisc.edu>

Dear Yo,

I'm using trace diffusivity, which is strongly related to mean diffusivity
(I think, just multiplied with a constant factor, experts correct me if I'm
wrong).

Andreas



-----Original Message-----
From: mristudio-users-bounces at mristudio.org
[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of
107310 at ib.k.u-tokyo.ac.jp
Sent: Dienstag, 22. Februar 2011 19:36
To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
Subject: Re: [Mristudio-users] radial diffusivity, mean diffusivity

Dear Andreas, Ryuzo and DTI experts


I also try to calculate mean diffusivity.
But in DTI studio, only the radial diffusivity and ADCs can calculate at 
the 'Image'-tab with ROI.

Is there any function to measure mean diffusivity?
Please give me any suggestion.
 
Many thanks.


YO


> Dear Andreas
> 
>  
> 
> Thank you very much for your suggestion.  I will try.
> 
>  
> 
> Ryuzo
> 
>  
> 
> From: mristudio-users-bounces at mristudio.org
> [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Andreas 
Buchmann
> Sent: Monday, February 21, 2011 11:03 PM
> To: 'DTI Studio, ROI Editor, DiffeoMap Questions/Support'
> Subject: Re: [Mristudio-users] radial diffusivity, mean diffusivity
> 
>  
> 
> Dear Ryuzo,
> 
>  
> 
> yes, you're on the right track with (1). After the estimation, DTI-
Studio
> appends the images to the list of images you have, and you can see 
them
> under the 'Image'-tab and save them with right-click on the image.
> 
>  
> 
> Good luck
> 
> Andreas
> 
>  
> 
>   _____  
> 
> From: mristudio-users-bounces at mristudio.org
> [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of hanaie
> Sent: Montag, 21. Februar 2011 07:46
> To: mristudio-users at mristudio.org
> Subject: [Mristudio-users] radial diffusivity, mean diffusivity
> 
>  
> 
> Dear DTI experts
> 
>  
> 
> How can I do to obtain the radial diffusivity and mean diffusivity in 
DTI
> studio?
> 
>  
> 
> 1.     In the " Dti Map" tab, clicking "Tensor, color Map etc" button, 
and
> checking the checkboxes "Radial", "Trace"
> 
>  
> 
> 2.     After tensor calculation and fiber tracking, if I click "
statistics"
> button in the "Fiber" tab and 
> 
>  I choose the each image and click "go" button in the another window, 
can I
> obtain radial and mean diffusivity?
> 
>  
> 
>  
> 
> Please give me any suggestion.
> 
>  
> 
> Many thanks.
> 
>  
> 
> Ryuzo
> 
>  
> 
>  
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to: mristudio-users-unsubscribe@
mristudio.org
> 


_______________________________________________
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mristudio-users at mristudio.org
http://lists.mristudio.org/mailman/listinfo/
Unsubscribe, send a blank email to:
mristudio-users-unsubscribe at mristudio.org


From hjiang at jhmi.edu  Wed Feb 23 09:23:21 2011
From: hjiang at jhmi.edu (Hangyi Jiang)
Date: Wed, 23 Feb 2011 09:23:21 -0500
Subject: [Mristudio-users] radial diffusivity,  mean diffusivity
In-Reply-To: <20110223013620.000068D1.0399@ib.k.u-tokyo.ac.jp>
References: <003001cbd1cd$a1befba0$e53cf2e0$@gyao.ne.jp>
	<0LGZ009NT0CPOU00@smtpauth1.wiscmail.wisc.edu>
	<002c01cbd2a0$662a7550$327f5ff0$@gyao.ne.jp>
	<20110223013620.000068D1.0399@ib.k.u-tokyo.ac.jp>
Message-ID: <145933A2BE9E4F48AE079A201379BF2F2448262A6D@RAD-EXCH1.win.ad.jhu.edu>

hi, Yo,

when you do Tensor calculation, you can get mean diffusivity by enable "TRACE (Dxx+Dyy+Dzz)" option:
   
mean diffusivity = TRACE / 3;

regards,



________________________________________
From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of 107310 at ib.k.u-tokyo.ac.jp [107310 at ib.k.u-tokyo.ac.jp]
Sent: Tuesday, February 22, 2011 8:36 PM
To: DTI Studio, ROI Editor,   DiffeoMap Questions/Support
Subject: Re: [Mristudio-users] radial diffusivity,  mean diffusivity

Dear Andreas, Ryuzo and DTI experts


I also try to calculate mean diffusivity.
But in DTI studio, only the radial diffusivity and ADCs can calculate at
the 'Image'-tab with ROI.

Is there any function to measure mean diffusivity?
Please give me any suggestion.

Many thanks.


YO


> Dear Andreas
>
>
>
> Thank you very much for your suggestion.  I will try.
>
>
>
> Ryuzo
>
>
>
> From: mristudio-users-bounces at mristudio.org
> [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Andreas
Buchmann
> Sent: Monday, February 21, 2011 11:03 PM
> To: 'DTI Studio, ROI Editor, DiffeoMap Questions/Support'
> Subject: Re: [Mristudio-users] radial diffusivity, mean diffusivity
>
>
>
> Dear Ryuzo,
>
>
>
> yes, you're on the right track with (1). After the estimation, DTI-
Studio
> appends the images to the list of images you have, and you can see
them
> under the 'Image'-tab and save them with right-click on the image.
>
>
>
> Good luck
>
> Andreas
>
>
>
>   _____
>
> From: mristudio-users-bounces at mristudio.org
> [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of hanaie
> Sent: Montag, 21. Februar 2011 07:46
> To: mristudio-users at mristudio.org
> Subject: [Mristudio-users] radial diffusivity, mean diffusivity
>
>
>
> Dear DTI experts
>
>
>
> How can I do to obtain the radial diffusivity and mean diffusivity in
DTI
> studio?
>
>
>
> 1.     In the " Dti Map" tab, clicking "Tensor, color Map etc" button,
and
> checking the checkboxes "Radial", "Trace"
>
>
>
> 2.     After tensor calculation and fiber tracking, if I click "
statistics"
> button in the "Fiber" tab and
>
>  I choose the each image and click "go" button in the another window,
can I
> obtain radial and mean diffusivity?
>
>
>
>
>
> Please give me any suggestion.
>
>
>
> Many thanks.
>
>
>
> Ryuzo
>
>
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to: mristudio-users-unsubscribe@
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 Feb 23 09:35:03 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Wed, 23 Feb 2011 09:35:03 -0500
Subject: [Mristudio-users] radial diffusivity, mean diffusivity
In-Reply-To: <0LH20086JO891D30@smtpauth1.wiscmail.wisc.edu>
References: <20110223013620.000068D1.0399@ib.k.u-tokyo.ac.jp>
	<0LH20086JO891D30@smtpauth1.wiscmail.wisc.edu>
Message-ID: <AANLkTikZMJqg2fPA61UnxvPcewTNoT2PA5TOCyKL1A5z@mail.gmail.com>

Andreas is right.
So called ADC (average diffusion constant, apparent diffusion constant) and
MD (mean diffusivity) are obtained by trace/3 (trace divided by 3), while
the trace is (eigenvalue0+eigenvalue1+eigenvalue2).

also, axial diffusivity is same as eigenvalue0 and radial diffusivity is the
average of eigenvalue1 and 2 [ (eigenvalue1+eigenvalue2)/2].

On Wed, Feb 23, 2011 at 8:31 AM, Andreas Buchmann <buchmann2 at wisc.edu>wrote:

> Dear Yo,
>
> I'm using trace diffusivity, which is strongly related to mean diffusivity
> (I think, just multiplied with a constant factor, experts correct me if I'm
> wrong).
>
> Andreas
>
>
>
> -----Original Message-----
> From: mristudio-users-bounces at mristudio.org
> [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of
> 107310 at ib.k.u-tokyo.ac.jp
> Sent: Dienstag, 22. Februar 2011 19:36
> To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
> Subject: Re: [Mristudio-users] radial diffusivity, mean diffusivity
>
> Dear Andreas, Ryuzo and DTI experts
>
>
> I also try to calculate mean diffusivity.
> But in DTI studio, only the radial diffusivity and ADCs can calculate at
> the 'Image'-tab with ROI.
>
> Is there any function to measure mean diffusivity?
> Please give me any suggestion.
>
> Many thanks.
>
>
> YO
>
>
> > Dear Andreas
> >
> >
> >
> > Thank you very much for your suggestion.  I will try.
> >
> >
> >
> > Ryuzo
> >
> >
> >
> > From: mristudio-users-bounces at mristudio.org
> > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Andreas
> Buchmann
> > Sent: Monday, February 21, 2011 11:03 PM
> > To: 'DTI Studio, ROI Editor, DiffeoMap Questions/Support'
> > Subject: Re: [Mristudio-users] radial diffusivity, mean diffusivity
> >
> >
> >
> > Dear Ryuzo,
> >
> >
> >
> > yes, you're on the right track with (1). After the estimation, DTI-
> Studio
> > appends the images to the list of images you have, and you can see
> them
> > under the 'Image'-tab and save them with right-click on the image.
> >
> >
> >
> > Good luck
> >
> > Andreas
> >
> >
> >
> >   _____
> >
> > From: mristudio-users-bounces at mristudio.org
> > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of hanaie
> > Sent: Montag, 21. Februar 2011 07:46
> > To: mristudio-users at mristudio.org
> > Subject: [Mristudio-users] radial diffusivity, mean diffusivity
> >
> >
> >
> > Dear DTI experts
> >
> >
> >
> > How can I do to obtain the radial diffusivity and mean diffusivity in
> DTI
> > studio?
> >
> >
> >
> > 1.     In the " Dti Map" tab, clicking "Tensor, color Map etc" button,
> and
> > checking the checkboxes "Radial", "Trace"
> >
> >
> >
> > 2.     After tensor calculation and fiber tracking, if I click "
> statistics"
> > button in the "Fiber" tab and
> >
> >  I choose the each image and click "go" button in the another window,
> can I
> > obtain radial and mean diffusivity?
> >
> >
> >
> >
> >
> > Please give me any suggestion.
> >
> >
> >
> > Many thanks.
> >
> >
> >
> > Ryuzo
> >
> >
> >
> >
> > _______________________________________________
> > mristudio-users mailing list
> > mristudio-users at mristudio.org
> > http://lists.mristudio.org/mailman/listinfo/
> > Unsubscribe, send a blank email to: mristudio-users-unsubscribe@
> 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
>
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From dc02hana at m6.gyao.ne.jp  Wed Feb 23 09:36:36 2011
From: dc02hana at m6.gyao.ne.jp (hanaie)
Date: Wed, 23 Feb 2011 23:36:36 +0900
Subject: [Mristudio-users] radial diffusivity,  mean diffusivity
In-Reply-To: <20110223013620.000068D1.0399@ib.k.u-tokyo.ac.jp>
References: <003001cbd1cd$a1befba0$e53cf2e0$@gyao.ne.jp>
	<0LGZ009NT0CPOU00@smtpauth1.wiscmail.wisc.edu>
	<002c01cbd2a0$662a7550$327f5ff0$@gyao.ne.jp>
	<20110223013620.000068D1.0399@ib.k.u-tokyo.ac.jp>
Message-ID: <002201cbd367$13009a90$3901cfb0$@gyao.ne.jp>

Dear Yo

Sorry, I can not help you.
I am new user for DTI studio.
Also, I want to know about how to calculate mean diffusivity of
reconstructed fiber.

Mean diffusivity=trace(Dxx+Dyy+Dzz)/3 ?

Ryuzo

-----Original Message-----
From: mristudio-users-bounces at mristudio.org
[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of
107310 at ib.k.u-tokyo.ac.jp
Sent: Wednesday, February 23, 2011 10:36 AM
To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
Subject: Re: [Mristudio-users] radial diffusivity, mean diffusivity

Dear Andreas, Ryuzo and DTI experts


I also try to calculate mean diffusivity.
But in DTI studio, only the radial diffusivity and ADCs can calculate at 
the 'Image'-tab with ROI.

Is there any function to measure mean diffusivity?
Please give me any suggestion.
 
Many thanks.


YO


> Dear Andreas
> 
>  
> 
> Thank you very much for your suggestion.  I will try.
> 
>  
> 
> Ryuzo
> 
>  
> 
> From: mristudio-users-bounces at mristudio.org
> [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Andreas 
Buchmann
> Sent: Monday, February 21, 2011 11:03 PM
> To: 'DTI Studio, ROI Editor, DiffeoMap Questions/Support'
> Subject: Re: [Mristudio-users] radial diffusivity, mean diffusivity
> 
>  
> 
> Dear Ryuzo,
> 
>  
> 
> yes, you're on the right track with (1). After the estimation, DTI-
Studio
> appends the images to the list of images you have, and you can see 
them
> under the 'Image'-tab and save them with right-click on the image.
> 
>  
> 
> Good luck
> 
> Andreas
> 
>  
> 
>   _____  
> 
> From: mristudio-users-bounces at mristudio.org
> [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of hanaie
> Sent: Montag, 21. Februar 2011 07:46
> To: mristudio-users at mristudio.org
> Subject: [Mristudio-users] radial diffusivity, mean diffusivity
> 
>  
> 
> Dear DTI experts
> 
>  
> 
> How can I do to obtain the radial diffusivity and mean diffusivity in 
DTI
> studio?
> 
>  
> 
> 1.     In the " Dti Map" tab, clicking "Tensor, color Map etc" button, 
and
> checking the checkboxes "Radial", "Trace"
> 
>  
> 
> 2.     After tensor calculation and fiber tracking, if I click "
statistics"
> button in the "Fiber" tab and 
> 
>  I choose the each image and click "go" button in the another window, 
can I
> obtain radial and mean diffusivity?
> 
>  
> 
>  
> 
> Please give me any suggestion.
> 
>  
> 
> Many thanks.
> 
>  
> 
> Ryuzo
> 
>  
> 
>  
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to: mristudio-users-unsubscribe@
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 Feb 23 14:30:11 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Wed, 23 Feb 2011 14:30:11 -0500
Subject: [Mristudio-users] Fwd: Does the inferior fronto-occipital
	fasciculus exists?
In-Reply-To: <AANLkTik8z=bm+w2=SsTpgtA9x_OVKBs8MByW=XCwrreh@mail.gmail.com>
References: <87D3B497-D79E-4EF4-A452-B4E4F9784268@stanford.edu>
	<AANLkTinRfZa58CXeTyMANASfXP=Goi2fYCz6kGXtPs=Q@mail.gmail.com>
	<A0963F36-DCA9-4FBC-B5EC-989F0DA120BC@stanford.edu>
	<AANLkTik8z=bm+w2=SsTpgtA9x_OVKBs8MByW=XCwrreh@mail.gmail.com>
Message-ID: <AANLkTim20BhiPj=hwAjvLtWeWLV8CRYHUdZUu=Ue2s7h@mail.gmail.com>

"Atlantis" is a good one.

Just want to add a couple of things.

First of all, pixel-by-pixel evaluation of DTI, like define ROIs on FA maps
or inspect color maps, and tractography results are very different things.

As for the pixel-by-pixel evaluation, there are a cluster of pixels
currently named as IFO in our atlas. So, it is a real entity (not Atlantis).
Then the issue here is whether it is appropriate to call this location IFO.
This is an issue of nomenclature as well as interpretation.

As for the tractography, the reconstructed trajectory convincingly shows
that so-called "IFO" travels between the frontal and occipital lobes, just
like past histology sections have shown. However, it is a very valid
argument that there is actually not axons that travel the entire length of
the "IFO". In this case, the connection called IFO is "Atlantis". It seems
there, reported numerous times, but actually doesn't exist.

s


On Wed, Feb 23, 2011 at 2:30 AM, Naama Barnea-Goraly <naamab at stanford.edu>wrote:

>
> Dear Susumu,
>
> Thank for the informative response. In this case, Schmahmann and Pandya
> would argue (I think) that it is not about a "road description" or a "map
> description". To use your "Baltimore" analogy they might say the IFOF is
> "Atlantis": We don't know where it is, and it probably doesn't exist,
> although it has been described in ancient times.
> In their book section about the IFOF (labeled "Identification of the
> apparently non-existent IFOF") they say there are no "substantial direct
> anatomical connections between the inferior occipital lobes and the ventral
> prefrontal cortex" and that fibers referred to as the IFOF are in fact
> either the uncinate or the extreme capsule. They base their claims
> on isotope anterograde tract tracers.
>
> Attached are the relevant pages from their book and a paper they wrote a
> year later talking about the FOF (they say SFOF and IFOF should not be
> used). On the other hand, the IFOF is often mentioned and demonstrated in
> DTI and dissection studies so it does seem like a controversial topic. I
> agree with you that it is a nomenclature issue as there are fibers there.
>
> As you suggested, neuroanatomists should consider a meeting to discuss
> current knowledge of white matter brain pathways and naming conventions for
> white matter tracts.
>
> Thanks,
>
> Naama
>
>
>
>
>
>
> On Feb 18, 2011, at 4:59 PM, susumu mori wrote:
>
> Hi Naama,
>
> This is a good question and please allow me to share my though with people
> in the MriStudio mailing list.
>
> When we describe white matter, there are two ways. Let me use the analogy
> of geological maps. If I see a map of Baltimore, there are essentially two
> types of information; boundaries that define boarders of locations like
> city, county, and state. The other is road information like route 95 that
> travels from Washingon DC to NY. The former defines locations and the latter
> doesn't belong to any single location.
>
> Likewise, WM map has two ways to define. Many WM names define locations,
> like the internal capsule, which is a WM location between the basal ganglia.
> There are many "roads" that penetrate the internal capsule like
> cortico-thalamic, thalamo-cortical, cortico-spinal, cortico-pontine, to name
> few, but they are all intermingled and it's not possible to completely
> decipher them, at least by DTI/MRI. There are also names of WM that imply
> something similar to the road names. For example, the corticospinal tract
> and IFO defines two destinations.
>
> Our atlas obviously defines locations; all segments are defined by
> boarders. Some of the defined locations have names that implies roads (e.g.
> IFO, SFO, CST, ets), but they actually define locations. This is one source
> of confusion.
>
> Now, there are some more confusing things. I believe many macroscopic
> anatomical nomenclature is based on classic histology observations. The SFO
> and IFO are assigned to large white matter bundles that sweep from front to
> back, which look like connecting the frontal and occipital lobes, but I
> don't think it was confirmed that there are actually axons connecting the
> frontal and occipital lobes. Therefore, the foundation of the assigned names
> are not as sound as the corticospinal tracts, which are confirmed in many
> animals and human.
>
> Now, we assigned some locations of the brain "SFO" and "IFO". There is not
> doubt that there are large axonal bundles travelling front to back (or back
> to front) in the designated locations. However, if one asks, "do you know if
> these locations really contain axons connecting the frontal and occipital
> lobes?", well, I must say, "not sure". To me, it seems like an issue of
> nomenclature.
>
> In any case, assignments of "road-type" names to the WM is a tricky effort
> because even for the "corticospinal tract", the designated locations may
> contain many other axons like cortico-pontine and cortico-bulbar axons. As
> long as they are mixed in a microscopic level, we can only say, "this region
> has high concentration of the corticospinal tract" and, to be strict, we can
> always argue that it is not correct to give a binary definition to a place
> like, "this is the corticospinal tract", because the "real" corticospinal
> tract refers to axons that connect the cortex and the spinal cord, not to
> many millimeters of anatomical locations visualized by MRI/DTI.
>
> So, going back to your original question, there were controversy over the
> existence of SFO and now IFO . In these cases what is discussed is "is there
> really a large concentration of axons that connect the frontal and occipital
> lobes in the WM locations called SFO/IFO?" How does it affect our study?
> Well, for the IFO, maybe we should change the name of the location to "a
> large WM bundle running front-back (green color) at the junction of the
> frontal lobe and the temporal lobe". To me, the source of the problem is the
> adoption of road names to refer to locations. As long as we use our atlas to
> define locations and do quantitative measurements such as volumes and FAs,
> how we call each location is not really a critical issue. Of course, it
> could profoundly affect the interpretation. If the FA of "IFO" is low, we
> should not immediately conclude connectivity problems between the frontal
> and occipital lobes, simply based on the name of the location. In this
> sense, you raised an important issue. On the other hand, IFO/SFO have been
> widely used to refer some specific locations and we can communicate about
> anatomical locations through these terms. So, even if they
> are mis-nomenclature, we may need to keep using them unless the anatomist
> society comes up with a new set of anatomical languages to refer these
> anatomical locations.
>
> Susumu
>
> On Fri, Feb 18, 2011 at 5:07 PM, Naama Barnea-Goraly <naamab at stanford.edu>wrote:
>
>>
>> Dear Susumu,
>>
>> A recent analysis we are running yielded some significant results in the
>> IFOF (according to the JHU White matter tractography atlas) which lead me to
>> some investigation on this pathway. I was very surprised to read in " White
>> matter of the Brain" ( a book by Schmahmann and Pandya), that in fact the
>> IFOF does not exist (page 445). They think the IFOF is in fact the ILF
>> /uncinate/extreme capsule mistaken by early anatomists as a separate tract.
>> What do you think?
>>
>> 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.
>>
>>
>>
>>
>
> 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.
>
>
>
>
>
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From 107310 at ib.k.u-tokyo.ac.jp  Wed Feb 23 20:51:39 2011
From: 107310 at ib.k.u-tokyo.ac.jp (107310 at ib.k.u-tokyo.ac.jp)
Date: Thu, 24 Feb 2011 10:51:39 +0900
Subject: [Mristudio-users] radial diffusivity, mean diffusivity
In-Reply-To: <AANLkTikZMJqg2fPA61UnxvPcewTNoT2PA5TOCyKL1A5z@mail.gmail.com>
References: <20110223013620.000068D1.0399@ib.k.u-tokyo.ac.jp>
	<0LH20086JO891D30@smtpauth1.wiscmail.wisc.edu>
	<AANLkTikZMJqg2fPA61UnxvPcewTNoT2PA5TOCyKL1A5z@mail.gmail.com>
Message-ID: <20110224015139.00004CDA.0747@ib.k.u-tokyo.ac.jp>

Dear all

Thanks for many helps.
I'll try to measure Trace.


Regards
YO


> Andreas is right.
> So called ADC (average diffusion constant, apparent diffusion constant)
 and
> MD (mean diffusivity) are obtained by trace/3 (trace divided by 3), 
while
> the trace is (eigenvalue0+eigenvalue1+eigenvalue2).
> 
> also, axial diffusivity is same as eigenvalue0 and radial diffusivity 
is the
> average of eigenvalue1 and 2 [ (eigenvalue1+eigenvalue2)/2].
> 
> On Wed, Feb 23, 2011 at 8:31 AM, Andreas Buchmann <buchmann2 at wisc.edu>
wrote:
> 
> > Dear Yo,
> >
> > I'm using trace diffusivity, which is strongly related to mean 
diffusivity
> > (I think, just multiplied with a constant factor, experts correct me 
if I'm
> > wrong).
> >
> > Andreas
> >
> >
> >
> > -----Original Message-----
> > From: mristudio-users-bounces at mristudio.org
> > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of
> > 107310 at ib.k.u-tokyo.ac.jp
> > Sent: Dienstag, 22. Februar 2011 19:36
> > To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
> > Subject: Re: [Mristudio-users] radial diffusivity, mean diffusivity
> >
> > Dear Andreas, Ryuzo and DTI experts
> >
> >
> > I also try to calculate mean diffusivity.
> > But in DTI studio, only the radial diffusivity and ADCs can 
calculate at
> > the 'Image'-tab with ROI.
> >
> > Is there any function to measure mean diffusivity?
> > Please give me any suggestion.
> >
> > Many thanks.
> >
> >
> > YO
> >
> >
> > > Dear Andreas
> > >
> > >
> > >
> > > Thank you very much for your suggestion.  I will try.
> > >
> > >
> > >
> > > Ryuzo
> > >
> > >
> > >
> > > From: mristudio-users-bounces at mristudio.org
> > > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of 
Andreas
> > Buchmann
> > > Sent: Monday, February 21, 2011 11:03 PM
> > > To: 'DTI Studio, ROI Editor, DiffeoMap Questions/Support'
> > > Subject: Re: [Mristudio-users] radial diffusivity, mean 
diffusivity
> > >
> > >
> > >
> > > Dear Ryuzo,
> > >
> > >
> > >
> > > yes, you're on the right track with (1). After the estimation, DTI
-
> > Studio
> > > appends the images to the list of images you have, and you can see
> > them
> > > under the 'Image'-tab and save them with right-click on the image.
> > >
> > >
> > >
> > > Good luck
> > >
> > > Andreas
> > >
> > >
> > >
> > >   _____
> > >
> > > From: mristudio-users-bounces at mristudio.org
> > > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of hanaie
> > > Sent: Montag, 21. Februar 2011 07:46
> > > To: mristudio-users at mristudio.org
> > > Subject: [Mristudio-users] radial diffusivity, mean diffusivity
> > >
> > >
> > >
> > > Dear DTI experts
> > >
> > >
> > >
> > > How can I do to obtain the radial diffusivity and mean diffusivity 
in
> > DTI
> > > studio?
> > >
> > >
> > >
> > > 1.     In the " Dti Map" tab, clicking "Tensor, color Map etc" 
button,
> > and
> > > checking the checkboxes "Radial", "Trace"
> > >
> > >
> > >
> > > 2.     After tensor calculation and fiber tracking, if I click "
> > statistics"
> > > button in the "Fiber" tab and
> > >
> > >  I choose the each image and click "go" button in the another 
window,
> > can I
> > > obtain radial and mean diffusivity?
> > >
> > >
> > >
> > >
> > >
> > > Please give me any suggestion.
> > >
> > >
> > >
> > > Many thanks.
> > >
> > >
> > >
> > > Ryuzo
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > mristudio-users mailing list
> > > mristudio-users at mristudio.org
> > > http://lists.mristudio.org/mailman/listinfo/
> > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe@
> > 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@
mristudio.org
> 



From susumu at mri.jhu.edu  Fri Feb 25 15:07:39 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Fri, 25 Feb 2011 15:07:39 -0500
Subject: [Mristudio-users] data base age range
In-Reply-To: <DE398D66EF593547B29F6FEE84176B840569E05168@exchange.fleni.org.ar>
References: <AQHLw6mXdWGueeCTokOysGtauXmoIg==@jhuin3.jhu.edu>
	<DE398D66EF593547B29F6FEE84176B840569E05168@exchange.fleni.org.ar>
Message-ID: <AANLkTimSLXLu1XCMsrFPYNLqr49JeJ_zRYMwDG93hFcJ@mail.gmail.com>

Hi Fernando,

Sorry for my slow reply. We compiled the demographic data of the subjects in
the shared data. We'll try to post this information in the web. Let me know
if you can't find this info in the same site shortly.

Susumu

2011/2/3 Fernando Ventrice <fventrice at fleni.org.ar>

> Hello mristudio users,
> I would like to ask if it is possible to know which range of ages are
> included in the data base that your group share at
> https://www.mristudio.org/download/data/dti/
> Thank you very much,
> Fernando Ventrice
>
> El contenido del presente mensaje y el de sus adjuntos, es confidencial,
> privado y de uso exclusivo de los destinatarios a los cuales est? dirigido,
> pudiendo contener informaci?n legalmente protegida. Queda prohibida la
> revisi?n, divulgaci?n, publicaci?n, modificaci?n, copia, distribuci?n o
> acci?n en relaci?n con esta informaci?n, por personas o entidades distintas
> al destinatario. Si usted, por alguna raz?n, lo ha recibido por error, por
> favor tenga la amabilidad de eliminarlo de su sistema. Las opiniones
> contenidas, son exclusivas de su autor, y no representa necesariamente, la
> opini?n de FLENI.
> http://www.fleni.org.ar
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
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From binwang87828 at gmail.com  Sat Feb 26 08:48:25 2011
From: binwang87828 at gmail.com (bin wang)
Date: Sat, 26 Feb 2011 21:48:25 +0800
Subject: [Mristudio-users] 3D ROI
Message-ID: <AANLkTi=3_FH0nsPq5EB5=DXzc6UxUScL=5SjFXD5Uwgd@mail.gmail.com>

Hello DTIstudio user:
I am a new DTIStudio user, I want to know if the ROIEditor can drawing a 3D
ROI, and how to operation?
bin

-- 
++++++++++++++++++++++++++++++
Bin Wang
major?apply psychology
South China Normal University
Zhongshan Avenue West 55, Tianhe District
Guangzhou 510631
P. R. China
Tel: 13416157706
++++++++++++++++++++++++++++++
??
??????
??????
* ???
*??? ??? ??? ???? ?55?
???510631
??? 13416157706 (??, ??)
+++++++++++++++++++++++++
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From susumu at mri.jhu.edu  Sat Feb 26 11:10:54 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Sat, 26 Feb 2011 11:10:54 -0500
Subject: [Mristudio-users] 3D ROI
In-Reply-To: <AANLkTi=3_FH0nsPq5EB5=DXzc6UxUScL=5SjFXD5Uwgd@mail.gmail.com>
References: <AANLkTi=3_FH0nsPq5EB5=DXzc6UxUScL=5SjFXD5Uwgd@mail.gmail.com>
Message-ID: <AANLkTi=Rf3TbSbDoOgjv19Z8cg2exvny_dZ6Kv4MifWB@mail.gmail.com>

Yes, RoiEditor can draw 3D ROIs. Because the ROI drawing capability of
DtiStudio is limited, I recommend to use RoiEditor. It is possible to create
multiple 3D ROIs in RoiEditor and pass them DtiStudio for fiber tracking.
Please refer to FAQ16 in https://www.mristudio.org/wiki/faq.

2011/2/26 bin wang <binwang87828 at gmail.com>

> Hello DTIstudio user:
> I am a new DTIStudio user, I want to know if the ROIEditor can drawing a 3D
> ROI, and how to operation?
> bin
>
> --
> ++++++++++++++++++++++++++++++
> Bin Wang
> major?apply psychology
> South China Normal University
> Zhongshan Avenue West 55, Tianhe District
> Guangzhou 510631
> P. R. China
> Tel: 13416157706
> ++++++++++++++++++++++++++++++
> ??
> ??????
> ??????
> * ???
> *??? ??? ??? ???? ?55?
> ???510631
> ??? 13416157706 (??, ??)
> +++++++++++++++++++++++++
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From choisj70 at gmail.com  Sun Feb 27 00:22:10 2011
From: choisj70 at gmail.com (Seongjin)
Date: Sun, 27 Feb 2011 00:22:10 -0500
Subject: [Mristudio-users] Question about Coregistration between
 high-resolution anatomy and DTI data
Message-ID: <AANLkTi=ko2-0iJOQz7cSyRTLxhRXM-QhkkkCAbefCQjD@mail.gmail.com>

I know DTI studio supports only intra-subject/intra-DTI registration.
I tried to use Diffeomap, but it complained about images are not of the same
image parameters.
If you have a complete guide about how to coregistration of DTI (e.g.
256x256) to High-resolution anatomy (e.g. 512x512), could you share it with
me and whole community?

I appreciate that in advance.

SC
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From binwang87828 at gmail.com  Sun Feb 27 03:27:33 2011
From: binwang87828 at gmail.com (bin wang)
Date: Sun, 27 Feb 2011 16:27:33 +0800
Subject: [Mristudio-users] 3D ROI
In-Reply-To: <AANLkTi=Rf3TbSbDoOgjv19Z8cg2exvny_dZ6Kv4MifWB@mail.gmail.com>
References: <AANLkTi=3_FH0nsPq5EB5=DXzc6UxUScL=5SjFXD5Uwgd@mail.gmail.com>
	<AANLkTi=Rf3TbSbDoOgjv19Z8cg2exvny_dZ6Kv4MifWB@mail.gmail.com>
Message-ID: <AANLkTi=O1-Yb5LOqhKx_QPo0df6HvmZaN8T5RJsuNbJB@mail.gmail.com>

Dr Mori:
I have two questions:
(1). If I want to create a 3D ROI, Must I draw the ROI in every slice in
ROIEditor manually?
(2). I have a binary mask image(img/hdr), it is the calcarine regions of the
brain, I want to make a ROI of the region to track the fiber in this region,
and how can I do in ROIEditor or DTIstudio.
Thanks in advance
Bin

? 2011?2?27? ??12:10?susumu mori <susumu at mri.jhu.edu>???

> Yes, RoiEditor can draw 3D ROIs. Because the ROI drawing capability of
> DtiStudio is limited, I recommend to use RoiEditor. It is possible to create
> multiple 3D ROIs in RoiEditor and pass them DtiStudio for fiber tracking.
> Please refer to FAQ16 in https://www.mristudio.org/wiki/faq.
>
> 2011/2/26 bin wang <binwang87828 at gmail.com>
>
>> Hello DTIstudio user:
>> I am a new DTIStudio user, I want to know if the ROIEditor can drawing a
>> 3D ROI, and how to operation?
>> bin
>>
>> --
>> ++++++++++++++++++++++++++++++
>> Bin Wang
>> major?apply psychology
>> South China Normal University
>> Zhongshan Avenue West 55, Tianhe District
>> Guangzhou 510631
>> P. R. China
>> Tel: 13416157706
>> ++++++++++++++++++++++++++++++
>> ??
>> ??????
>> ??????
>> * ???
>> *??? ??? ??? ???? ?55?
>> ???510631
>> ??? 13416157706 (??, ??)
>> +++++++++++++++++++++++++
>>
>>
>> _______________________________________________
>> mristudio-users mailing 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
>
>


-- 
++++++++++++++++++++++++++++++
Bin Wang
major?apply psychology
South China Normal University
Zhongshan Avenue West 55, Tianhe District
Guangzhou 510631
P. R. China
Tel: 13416157706
++++++++++++++++++++++++++++++
??
??????
??????
* ???
*??? ??? ??? ???? ?55?
???510631
??? 13416157706 (??, ??)
+++++++++++++++++++++++++
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From susumu at mri.jhu.edu  Sun Feb 27 06:31:08 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Sun, 27 Feb 2011 06:31:08 -0500
Subject: [Mristudio-users] 3D ROI
In-Reply-To: <AANLkTi=O1-Yb5LOqhKx_QPo0df6HvmZaN8T5RJsuNbJB@mail.gmail.com>
References: <AANLkTi=3_FH0nsPq5EB5=DXzc6UxUScL=5SjFXD5Uwgd@mail.gmail.com>
	<AANLkTi=Rf3TbSbDoOgjv19Z8cg2exvny_dZ6Kv4MifWB@mail.gmail.com>
	<AANLkTi=O1-Yb5LOqhKx_QPo0df6HvmZaN8T5RJsuNbJB@mail.gmail.com>
Message-ID: <AANLkTimAvM=p4_Ui8-3Sov=x++P1A-AsXUvSJZY0WJ1V@mail.gmail.com>

2011/2/27 bin wang <binwang87828 at gmail.com>

> Dr Mori:
> I have two questions:
> (1). If I want to create a 3D ROI, Must I draw the ROI in every slice in
> ROIEditor manually?
>

If the structure of interest has clear contrast, you can use a region
growing tool. For example the caudate in T1 has a good contrast. You can use
3D or slice-by-slice region growing tool to define it much easier than
manual. When you are using DTI colormap, there is a color region growing
tool to specify a region with the same color.

If does not have clear contrast, you can first use the global threshold or
region growing to define a tissue of interest. For example, if you are
interested in a white matter structure, you can use FA>0.25. If you are
interested in the cortex, you can use a threshold tool with T1. Please note
that white matter structures and the cortex do not have clear contrast
boundary from adjacent structures. Therefore the region growing or
thresholding almost always leak to adjacent structures. After you do the
global tissue segmentation, you can visit each slice and use manual ROI +
AND operation to define the structure.

If you get tired of defining a lot of ROIs without clear boundaries, please
try our automated full-brain segmentation tools. You need to learn how to
use DiffeoMap and RoiEditor. You can find manuals and videos in
www.mristudio.org.



> (2). I have a binary mask image(img/hdr), it is the calcarine regions of
> the brain, I want to make a ROI of the region to track the fiber in this
> region, and how can I do in ROIEditor or DTIstudio.
>

You can load it to RoiEditor as an ROI file and save as "Binary Map". Please
refer to FAQ16 about Binary Map format.


> Thanks in advance
> Bin
>
> ? 2011?2?27? ??12:10?susumu mori <susumu at mri.jhu.edu>???
>
> Yes, RoiEditor can draw 3D ROIs. Because the ROI drawing capability of
>> DtiStudio is limited, I recommend to use RoiEditor. It is possible to create
>> multiple 3D ROIs in RoiEditor and pass them DtiStudio for fiber tracking.
>> Please refer to FAQ16 in https://www.mristudio.org/wiki/faq.
>>
>> 2011/2/26 bin wang <binwang87828 at gmail.com>
>>
>>>  Hello DTIstudio user:
>>> I am a new DTIStudio user, I want to know if the ROIEditor can drawing a
>>> 3D ROI, and how to operation?
>>> bin
>>>
>>> --
>>> ++++++++++++++++++++++++++++++
>>> Bin Wang
>>> major?apply psychology
>>> South China Normal University
>>> Zhongshan Avenue West 55, Tianhe District
>>> Guangzhou 510631
>>> P. R. China
>>> Tel: 13416157706
>>> ++++++++++++++++++++++++++++++
>>> ??
>>> ??????
>>> ??????
>>> * ???
>>> *??? ??? ??? ???? ?55?
>>> ???510631
>>> ??? 13416157706 (??, ??)
>>> +++++++++++++++++++++++++
>>>
>>>
>>> _______________________________________________
>>> mristudio-users mailing 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
>>
>>
>
>
> --
> ++++++++++++++++++++++++++++++
> Bin Wang
> major?apply psychology
> South China Normal University
> Zhongshan Avenue West 55, Tianhe District
> Guangzhou 510631
> P. R. China
> Tel: 13416157706
> ++++++++++++++++++++++++++++++
> ??
> ??????
> ??????
> * ???
> *??? ??? ??? ???? ?55?
> ???510631
> ??? 13416157706 (??, ??)
> +++++++++++++++++++++++++
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From susumu at mri.jhu.edu  Sun Feb 27 06:35:04 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Sun, 27 Feb 2011 06:35:04 -0500
Subject: [Mristudio-users] Question about Coregistration between
 high-resolution anatomy and DTI data
In-Reply-To: <AANLkTi=ko2-0iJOQz7cSyRTLxhRXM-QhkkkCAbefCQjD@mail.gmail.com>
References: <AANLkTi=ko2-0iJOQz7cSyRTLxhRXM-QhkkkCAbefCQjD@mail.gmail.com>
Message-ID: <AANLkTimphT9VWB56COFrUVqVZPZAB42CXji=skZBrK=D@mail.gmail.com>

Hi SC,

In the upper left, there is a series of buttons for pre-processing including
matrix size/pixel size conversion, translation, rotation, data format
conversion, etc. You can use these buttons to adjust the parameters of the
images. This is the best way if the two images share the same center of FOV
and image orientation (co-registered already)

If the two images are not coregistered, the easiest way is, to go straight
into a linear registration, which can take images with different dimensions
and spits out co-registered images in the same image parameters as the
template image.

s

On Sun, Feb 27, 2011 at 12:22 AM, [Seongjin] <choisj70 at gmail.com> wrote:

> I know DTI studio supports only intra-subject/intra-DTI registration.
> I tried to use Diffeomap, but it complained about images are not of the
> same image parameters.
> If you have a complete guide about how to coregistration of DTI (e.g.
> 256x256) to High-resolution anatomy (e.g. 512x512), could you share it with
> me and whole community?
>
> I appreciate that 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
>
>
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From salvador.castaneda at med.uni-tuebingen.de  Mon Feb 28 03:04:34 2011
From: salvador.castaneda at med.uni-tuebingen.de (Castaneda, Salvador)
Date: Mon, 28 Feb 2011 09:04:34 +0100
Subject: [Mristudio-users] Question about Coregistration between
 high-resolution anatomy and DTI data
In-Reply-To: <AANLkTi=ko2-0iJOQz7cSyRTLxhRXM-QhkkkCAbefCQjD@mail.gmail.com>
References: <AANLkTi=ko2-0iJOQz7cSyRTLxhRXM-QhkkkCAbefCQjD@mail.gmail.com>
Message-ID: <0AC64F4CB253074799B64FF8F0772D350126C692@azex2003.raddiag.med.uni-tuebingen.de>

Hello SC,
 
I think i have already had this question and there is a way to
coregister with an anatomical reference. you can probably read Dr.
Mori's answers in earlier threads if you keep the emails.
What i have done but didn't continue to use it, was to reduce the size
of the anatomical image to the size of the DT image using diffeomap.
Later did AIR in DTIstudio using the anatomy as a reference to the
Mosaic DTI images i had, which were cut in the same size as my anatomy.
After this coregistration there was a nice mixed image of anatomy with
the DTI. So then i saved this as separate analize file and proceeded to
the DTI analysis as usual. When it came time to draw my ROIs, I would
open the coregistered anatomy with DTI analize file, which know was
exactly the same position and size, and then i would have nice clear
ROIs. The ROIs i would draw either with ROI editor or DTIstudio.
I didn't continue to do this, because it is obviously tedious method. So
i proceeded to do all the DTI analysis in DTi studio, export the files
as Analize, and then coregister my anatomy images with another program.
It was hard for me to work with ROI editor because the resolution of my
DTI is relatively bad. So i had to use a different program. 
Any way i hope this helps,
 
cheers
Salvador C

________________________________

Von: mristudio-users-bounces at mristudio.org
[mailto:mristudio-users-bounces at mristudio.org] Im Auftrag von [Seongjin]
Gesendet: Sonntag, 27. Februar 2011 06:22
An: DTI Studio, ROI Editor, Landmarker Questions/Support
Betreff: [Mristudio-users] Question about Coregistration between
high-resolution anatomy and DTI data


I know DTI studio supports only intra-subject/intra-DTI registration.
I tried to use Diffeomap, but it complained about images are not of the
same image parameters.
If you have a complete guide about how to coregistration of DTI (e.g.
256x256) to High-resolution anatomy (e.g. 512x512), could you share it
with me and whole community?

I appreciate that in advance.

SC

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From cmuwyb at gmail.com  Mon Feb 28 08:15:49 2011
From: cmuwyb at gmail.com (Yibao Wang)
Date: Mon, 28 Feb 2011 08:15:49 -0500
Subject: [Mristudio-users] About loaded ROI into my Anatomy Image
In-Reply-To: <AANLkTi=ko2-0iJOQz7cSyRTLxhRXM-QhkkkCAbefCQjD@mail.gmail.com>
References: <AANLkTi=ko2-0iJOQz7cSyRTLxhRXM-QhkkkCAbefCQjD@mail.gmail.com>
Message-ID: <966C380A532C40B488F9A9AB1A5E678D@VAIO>

Is there a method to load the well-known ROI into my Anatomy Image?
I explain my question in detail,
for example, the are lots of well-known ROI such as insular, hippocampus,
it was diffcult to draw it in the anatomy image, sometimes because its poor resoultion.
Could we loaded those ROI into my Image? 
I wonder is there any software could analysize the well-konwn interested ROI from the poor resolution anatomy image.
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From choisj70 at gmail.com  Mon Feb 28 08:47:36 2011
From: choisj70 at gmail.com (Seongjin)
Date: Mon, 28 Feb 2011 08:47:36 -0500
Subject: [Mristudio-users] Question about Coregistration between
 high-resolution anatomy and DTI data
In-Reply-To: <AANLkTimphT9VWB56COFrUVqVZPZAB42CXji=skZBrK=D@mail.gmail.com>
References: <AANLkTi=ko2-0iJOQz7cSyRTLxhRXM-QhkkkCAbefCQjD@mail.gmail.com>
	<AANLkTimphT9VWB56COFrUVqVZPZAB42CXji=skZBrK=D@mail.gmail.com>
Message-ID: <AANLkTim7hns7Tz4UHaNzp0E8jHk6V-QpWd0Ax74GtQ2p@mail.gmail.com>

I appreciate your reply to my question.

SC

On Sun, Feb 27, 2011 at 6:35 AM, susumu mori <susumu at mri.jhu.edu> wrote:

> Hi SC,
>
> In the upper left, there is a series of buttons for pre-processing
> including matrix size/pixel size conversion, translation, rotation, data
> format conversion, etc. You can use these buttons to adjust the parameters
> of the images. This is the best way if the two images share the same center
> of FOV and image orientation (co-registered already)
>
> If the two images are not coregistered, the easiest way is, to go straight
> into a linear registration, which can take images with different dimensions
> and spits out co-registered images in the same image parameters as the
> template image.
>
> s
>
> On Sun, Feb 27, 2011 at 12:22 AM, [Seongjin] <choisj70 at gmail.com> wrote:
>
>> I know DTI studio supports only intra-subject/intra-DTI registration.
>> I tried to use Diffeomap, but it complained about images are not of the
>> same image parameters.
>> If you have a complete guide about how to coregistration of DTI (e.g.
>> 256x256) to High-resolution anatomy (e.g. 512x512), could you share it with
>> me and whole community?
>>
>> I appreciate that 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
>
>
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From choisj70 at gmail.com  Mon Feb 28 08:48:08 2011
From: choisj70 at gmail.com (Seongjin)
Date: Mon, 28 Feb 2011 08:48:08 -0500
Subject: [Mristudio-users] Question about Coregistration between
 high-resolution anatomy and DTI data
In-Reply-To: <0AC64F4CB253074799B64FF8F0772D350126C692@azex2003.raddiag.med.uni-tuebingen.de>
References: <AANLkTi=ko2-0iJOQz7cSyRTLxhRXM-QhkkkCAbefCQjD@mail.gmail.com>
	<0AC64F4CB253074799B64FF8F0772D350126C692@azex2003.raddiag.med.uni-tuebingen.de>
Message-ID: <AANLkTik-VhSvxXEHhdVwAUCyOsjs=xnxGO9g9x6nHPvf@mail.gmail.com>

I appreciate your answer to my question.

SC

On Mon, Feb 28, 2011 at 3:04 AM, Castaneda, Salvador <
salvador.castaneda at med.uni-tuebingen.de> wrote:

>  Hello SC,
>
> I think i have already had this question and there is a way to coregister
> with an anatomical reference. you can probably read Dr. Mori's answers in
> earlier threads if you keep the emails.
> What i have done but didn't continue to use it, was to reduce the size of
> the anatomical image to the size of the DT image using diffeomap. Later did
> AIR in DTIstudio using the anatomy as a reference to the Mosaic DTI images i
> had, which were cut in the same size as my anatomy. After this
> coregistration there was a nice mixed image of anatomy with the DTI. So then
> i saved this as separate analize file and proceeded to the DTI analysis as
> usual. When it came time to draw my ROIs, I would open the coregistered
> anatomy with DTI analize file, which know was exactly the same position and
> size, and then i would have nice clear ROIs. The ROIs i would draw either
> with ROI editor or DTIstudio.
> I didn't continue to do this, because it is obviously tedious method. So i
> proceeded to do all the DTI analysis in DTi studio, export the files as
> Analize, and then coregister my anatomy images with another program. It was
> hard for me to work with ROI editor because the resolution of my DTI is
> relatively bad. So i had to use a different program.
> Any way i hope this helps,
>
> cheers
> Salvador C
>
>  ------------------------------
> *Von:* mristudio-users-bounces at mristudio.org [mailto:
> mristudio-users-bounces at mristudio.org] *Im Auftrag von *[Seongjin]
> *Gesendet:* Sonntag, 27. Februar 2011 06:22
> *An:* DTI Studio, ROI Editor, Landmarker Questions/Support
> *Betreff:* [Mristudio-users] Question about Coregistration between
> high-resolution anatomy and DTI data
>
> I know DTI studio supports only intra-subject/intra-DTI registration.
> I tried to use Diffeomap, but it complained about images are not of the
> same image parameters.
> If you have a complete guide about how to coregistration of DTI (e.g.
> 256x256) to High-resolution anatomy (e.g. 512x512), could you share it with
> me and whole community?
>
> I appreciate that 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
>
>
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From choisj70 at gmail.com  Mon Feb 28 12:15:30 2011
From: choisj70 at gmail.com (Seongjin)
Date: Mon, 28 Feb 2011 12:15:30 -0500
Subject: [Mristudio-users] About loaded ROI into my Anatomy Image
In-Reply-To: <966C380A532C40B488F9A9AB1A5E678D@VAIO>
References: <AANLkTi=ko2-0iJOQz7cSyRTLxhRXM-QhkkkCAbefCQjD@mail.gmail.com>
	<966C380A532C40B488F9A9AB1A5E678D@VAIO>
Message-ID: <AANLkTi=C70rB2eiNKeCnvYYkE=5xf3-CE9L71P-=6=Lb@mail.gmail.com>

I believe that you should do spatial normalization of your data to a well
known ATLAS first.

SC


On Mon, Feb 28, 2011 at 8:15 AM, Yibao Wang <cmuwyb at gmail.com> wrote:

>   Is there a method to load the well-known ROI into my Anatomy Image?
>  I explain my question in detail,
>  for example, the are lots of well-known ROI such as insular, hippocampus,
>  it was diffcult to draw it in the anatomy image, sometimes because its
> poor resoultion.
>  Could we loaded those ROI into my Image?
>  I wonder is there any software could analysize the well-konwn interested
> ROI from the poor resolution anatomy image.
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From susumu at mri.jhu.edu  Mon Feb 28 12:44:05 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Mon, 28 Feb 2011 12:44:05 -0500
Subject: [Mristudio-users] About loaded ROI into my Anatomy Image
In-Reply-To: <AANLkTi=C70rB2eiNKeCnvYYkE=5xf3-CE9L71P-=6=Lb@mail.gmail.com>
References: <AANLkTi=ko2-0iJOQz7cSyRTLxhRXM-QhkkkCAbefCQjD@mail.gmail.com>
	<966C380A532C40B488F9A9AB1A5E678D@VAIO>
	<AANLkTi=C70rB2eiNKeCnvYYkE=5xf3-CE9L71P-=6=Lb@mail.gmail.com>
Message-ID: <AANLkTiku6=LpPbbJ+ppzVPjoEex+ov48e6qO3LgpEJzL@mail.gmail.com>

As SC suggested, I would recommend to look into the Atlas-based
segmentation.
We have some papers by Oishi et al (for anatomical study) and Zhang Y et al
(for tractography). Using DiffeoMap and RoiEditor, you can do the
atlas-driven automated brain segmentation.

On Mon, Feb 28, 2011 at 12:15 PM, [Seongjin] <choisj70 at gmail.com> wrote:

> I believe that you should do spatial normalization of your data to a well
> known ATLAS first.
>
> SC
>
>
> On Mon, Feb 28, 2011 at 8:15 AM, Yibao Wang <cmuwyb at gmail.com> wrote:
>
>>   Is there a method to load the well-known ROI into my Anatomy Image?
>>  I explain my question in detail,
>>  for example, the are lots of well-known ROI such as insular,
>> hippocampus,
>>  it was diffcult to draw it in the anatomy image, sometimes because its
>> poor resoultion.
>>  Could we loaded those ROI into my Image?
>>  I wonder is there any software could analysize the well-konwn interested
>> ROI from the poor resolution anatomy image.
>>
>>
>> _______________________________________________
>> mristudio-users mailing 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
>
>
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From binwang87828 at gmail.com  Mon Feb 28 20:54:10 2011
From: binwang87828 at gmail.com (bin wang)
Date: Tue, 01 Mar 2011 09:54:10 +0800
Subject: [Mristudio-users] 3D ROI
In-Reply-To: <AANLkTimAvM=p4_Ui8-3Sov=x++P1A-AsXUvSJZY0WJ1V@mail.gmail.com>
References: <AANLkTi=3_FH0nsPq5EB5=DXzc6UxUScL=5SjFXD5Uwgd@mail.gmail.com>
	<AANLkTi=Rf3TbSbDoOgjv19Z8cg2exvny_dZ6Kv4MifWB@mail.gmail.com>
	<AANLkTi=O1-Yb5LOqhKx_QPo0df6HvmZaN8T5RJsuNbJB@mail.gmail.com>
	<AANLkTimAvM=p4_Ui8-3Sov=x++P1A-AsXUvSJZY0WJ1V@mail.gmail.com>
Message-ID: <AANLkTinYYxYceDF6TXFCk8pzhZ7B-6Grt=3oLKOVHk-z@mail.gmail.com>

Dr Mori:
Thank you for the patience to answer, I will try as you say.
But there is still a question that I can't save it as "Binary Map" after
loading the mask image to RoiEditor, I must draw a ROI manually or using
other ways. I want to know that can I make the mask as a ROI directly, so
the ROIEditor can save it.
Best
bin

? 2011?2?27? ??7:31?susumu mori <susumu at mri.jhu.edu>???

>
>
> 2011/2/27 bin wang <binwang87828 at gmail.com>
>
> Dr Mori:
>> I have two questions:
>> (1). If I want to create a 3D ROI, Must I draw the ROI in every slice in
>> ROIEditor manually?
>>
>
> If the structure of interest has clear contrast, you can use a region
> growing tool. For example the caudate in T1 has a good contrast. You can use
> 3D or slice-by-slice region growing tool to define it much easier than
> manual. When you are using DTI colormap, there is a color region growing
> tool to specify a region with the same color.
>
> If does not have clear contrast, you can first use the global threshold or
> region growing to define a tissue of interest. For example, if you are
> interested in a white matter structure, you can use FA>0.25. If you are
> interested in the cortex, you can use a threshold tool with T1. Please note
> that white matter structures and the cortex do not have clear contrast
> boundary from adjacent structures. Therefore the region growing or
> thresholding almost always leak to adjacent structures. After you do the
> global tissue segmentation, you can visit each slice and use manual ROI +
> AND operation to define the structure.
>
> If you get tired of defining a lot of ROIs without clear boundaries, please
> try our automated full-brain segmentation tools. You need to learn how to
> use DiffeoMap and RoiEditor. You can find manuals and videos in
> www.mristudio.org.
>
>
>
>> (2). I have a binary mask image(img/hdr), it is the calcarine regions of
>> the brain, I want to make a ROI of the region to track the fiber in this
>> region, and how can I do in ROIEditor or DTIstudio.
>>
>
> You can load it to RoiEditor as an ROI file and save as "Binary Map".
> Please refer to FAQ16 about Binary Map format.
>
>
>> Thanks in advance
>> Bin
>>
>> ? 2011?2?27? ??12:10?susumu mori <susumu at mri.jhu.edu>???
>>
>> Yes, RoiEditor can draw 3D ROIs. Because the ROI drawing capability of
>>> DtiStudio is limited, I recommend to use RoiEditor. It is possible to create
>>> multiple 3D ROIs in RoiEditor and pass them DtiStudio for fiber tracking.
>>> Please refer to FAQ16 in https://www.mristudio.org/wiki/faq.
>>>
>>> 2011/2/26 bin wang <binwang87828 at gmail.com>
>>>
>>>>  Hello DTIstudio user:
>>>> I am a new DTIStudio user, I want to know if the ROIEditor can drawing a
>>>> 3D ROI, and how to operation?
>>>> bin
>>>>
>>>> --
>>>> ++++++++++++++++++++++++++++++
>>>> Bin Wang
>>>> major?apply psychology
>>>> South China Normal University
>>>> Zhongshan Avenue West 55, Tianhe District
>>>> Guangzhou 510631
>>>> P. R. China
>>>> Tel: 13416157706
>>>> ++++++++++++++++++++++++++++++
>>>> ??
>>>> ??????
>>>> ??????
>>>> * ???
>>>> *??? ??? ??? ???? ?55?
>>>> ???510631
>>>> ??? 13416157706 (??, ??)
>>>> +++++++++++++++++++++++++
>>>>
>>>>
>>>> _______________________________________________
>>>> mristudio-users mailing 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
>>>
>>>
>>
>>
>> --
>> ++++++++++++++++++++++++++++++
>> Bin Wang
>> major?apply psychology
>> South China Normal University
>> Zhongshan Avenue West 55, Tianhe District
>> Guangzhou 510631
>> P. R. China
>> Tel: 13416157706
>> ++++++++++++++++++++++++++++++
>> ??
>> ??????
>> ??????
>> * ???
>> *??? ??? ??? ???? ?55?
>> ???510631
>> ??? 13416157706 (??, ??)
>> +++++++++++++++++++++++++
>>
>>
>> _______________________________________________
>> mristudio-users mailing 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
>
>


-- 
++++++++++++++++++++++++++++++
Bin Wang
major?apply psychology
South China Normal University
Zhongshan Avenue West 55, Tianhe District
Guangzhou 510631
P. R. China
Tel: 13416157706
++++++++++++++++++++++++++++++
??
??????
??????
* ???
*??? ??? ??? ???? ?55?
???510631
??? 13416157706 (??, ??)
+++++++++++++++++++++++++
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From susumu at mri.jhu.edu  Mon Feb 28 21:19:02 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Mon, 28 Feb 2011 21:19:02 -0500
Subject: [Mristudio-users] 3D ROI
In-Reply-To: <AANLkTinYYxYceDF6TXFCk8pzhZ7B-6Grt=3oLKOVHk-z@mail.gmail.com>
References: <AANLkTi=3_FH0nsPq5EB5=DXzc6UxUScL=5SjFXD5Uwgd@mail.gmail.com>
	<AANLkTi=Rf3TbSbDoOgjv19Z8cg2exvny_dZ6Kv4MifWB@mail.gmail.com>
	<AANLkTi=O1-Yb5LOqhKx_QPo0df6HvmZaN8T5RJsuNbJB@mail.gmail.com>
	<AANLkTimAvM=p4_Ui8-3Sov=x++P1A-AsXUvSJZY0WJ1V@mail.gmail.com>
	<AANLkTinYYxYceDF6TXFCk8pzhZ7B-6Grt=3oLKOVHk-z@mail.gmail.com>
Message-ID: <AANLkTi=E5vmhLBgqofqKFzn=D8HD48jLBe3HOj5KkVsJ@mail.gmail.com>

Hi Bin,

To save a file as "Binary Map", you have to open it as ROI, not as an image.
There are two "open" icons in the right column of RoiEditor; one for image
and the other for ROI.

To access to these icons, you first have to open an image. The image can be
anything as long as it has the same image dimension. For example, you can
open the ROI file as an image, get the viewing window, and then open the
same file as an ROI file.

Then you can save the ROI as "Binary Map".

Susumu



2011/2/28 bin wang <binwang87828 at gmail.com>

> Dr Mori:
> Thank you for the patience to answer, I will try as you say.
> But there is still a question that I can't save it as "Binary Map" after
> loading the mask image to RoiEditor, I must draw a ROI manually or using
> other ways. I want to know that can I make the mask as a ROI directly, so
> the ROIEditor can save it.
> Best
> bin
>
> ? 2011?2?27? ??7:31?susumu mori <susumu at mri.jhu.edu>???
>
>
>>
>> 2011/2/27 bin wang <binwang87828 at gmail.com>
>>
>> Dr Mori:
>>> I have two questions:
>>> (1). If I want to create a 3D ROI, Must I draw the ROI in every slice in
>>> ROIEditor manually?
>>>
>>
>> If the structure of interest has clear contrast, you can use a region
>> growing tool. For example the caudate in T1 has a good contrast. You can use
>> 3D or slice-by-slice region growing tool to define it much easier than
>> manual. When you are using DTI colormap, there is a color region growing
>> tool to specify a region with the same color.
>>
>> If does not have clear contrast, you can first use the global threshold or
>> region growing to define a tissue of interest. For example, if you are
>> interested in a white matter structure, you can use FA>0.25. If you are
>> interested in the cortex, you can use a threshold tool with T1. Please note
>> that white matter structures and the cortex do not have clear contrast
>> boundary from adjacent structures. Therefore the region growing or
>> thresholding almost always leak to adjacent structures. After you do the
>> global tissue segmentation, you can visit each slice and use manual ROI +
>> AND operation to define the structure.
>>
>> If you get tired of defining a lot of ROIs without clear boundaries,
>> please try our automated full-brain segmentation tools. You need to learn
>> how to use DiffeoMap and RoiEditor. You can find manuals and videos in
>> www.mristudio.org.
>>
>>
>>
>>> (2). I have a binary mask image(img/hdr), it is the calcarine regions of
>>> the brain, I want to make a ROI of the region to track the fiber in this
>>> region, and how can I do in ROIEditor or DTIstudio.
>>>
>>
>> You can load it to RoiEditor as an ROI file and save as "Binary Map".
>> Please refer to FAQ16 about Binary Map format.
>>
>>
>>> Thanks in advance
>>> Bin
>>>
>>> ? 2011?2?27? ??12:10?susumu mori <susumu at mri.jhu.edu>???
>>>
>>> Yes, RoiEditor can draw 3D ROIs. Because the ROI drawing capability of
>>>> DtiStudio is limited, I recommend to use RoiEditor. It is possible to create
>>>> multiple 3D ROIs in RoiEditor and pass them DtiStudio for fiber tracking.
>>>> Please refer to FAQ16 in https://www.mristudio.org/wiki/faq.
>>>>
>>>> 2011/2/26 bin wang <binwang87828 at gmail.com>
>>>>
>>>>>  Hello DTIstudio user:
>>>>> I am a new DTIStudio user, I want to know if the ROIEditor can drawing
>>>>> a 3D ROI, and how to operation?
>>>>> bin
>>>>>
>>>>> --
>>>>> ++++++++++++++++++++++++++++++
>>>>> Bin Wang
>>>>> major?apply psychology
>>>>> South China Normal University
>>>>> Zhongshan Avenue West 55, Tianhe District
>>>>> Guangzhou 510631
>>>>> P. R. China
>>>>> Tel: 13416157706
>>>>> ++++++++++++++++++++++++++++++
>>>>> ??
>>>>> ??????
>>>>> ??????
>>>>> * ???
>>>>> *??? ??? ??? ???? ?55?
>>>>> ???510631
>>>>> ??? 13416157706 (??, ??)
>>>>> +++++++++++++++++++++++++
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> mristudio-users mailing 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
>>>>
>>>>
>>>
>>>
>>> --
>>> ++++++++++++++++++++++++++++++
>>> Bin Wang
>>> major?apply psychology
>>> South China Normal University
>>> Zhongshan Avenue West 55, Tianhe District
>>> Guangzhou 510631
>>> P. R. China
>>> Tel: 13416157706
>>> ++++++++++++++++++++++++++++++
>>> ??
>>> ??????
>>> ??????
>>> * ???
>>> *??? ??? ??? ???? ?55?
>>> ???510631
>>> ??? 13416157706 (??, ??)
>>> +++++++++++++++++++++++++
>>>
>>>
>>> _______________________________________________
>>> mristudio-users mailing 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
>>
>>
>
>
> --
> ++++++++++++++++++++++++++++++
> Bin Wang
> major?apply psychology
> South China Normal University
> Zhongshan Avenue West 55, Tianhe District
> Guangzhou 510631
> P. R. China
> Tel: 13416157706
> ++++++++++++++++++++++++++++++
> ??
> ??????
> ??????
> * ???
> *??? ??? ??? ???? ?55?
> ???510631
> ??? 13416157706 (??, ??)
> +++++++++++++++++++++++++
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From 107310 at ib.k.u-tokyo.ac.jp  Mon Feb 28 21:24:53 2011
From: 107310 at ib.k.u-tokyo.ac.jp (107310 at ib.k.u-tokyo.ac.jp)
Date: Tue, 01 Mar 2011 11:24:53 +0900
Subject: [Mristudio-users] =?utf-8?q?How_to_pass_the_ROI_data=3F?=
Message-ID: <20110301022453.0000597C.0997@ib.k.u-tokyo.ac.jp>

Dear DTI experts

I can't pass the ROI data saved in ROIEditor to DTI-studio.
(I use the same subject.)

In ROI editor, I drew the ROI and saved in specified format(ROI editor 
defined, Analyse, Binary map).

Then go to DTI-studio, and open the ROI files in ROI tab.

The erroe message is
unrecognized image-ROI data file!
(I tried 3 formats.)

If there is a problem, please let me know.
Many thanks!

YO




From susumu at mri.jhu.edu  Mon Feb 28 21:53:07 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Mon, 28 Feb 2011 21:53:07 -0500
Subject: [Mristudio-users] How to pass the ROI data?
In-Reply-To: <20110301022453.0000597C.0997@ib.k.u-tokyo.ac.jp>
References: <20110301022453.0000597C.0997@ib.k.u-tokyo.ac.jp>
Message-ID: <AANLkTikVfuJbjaHG7mNsZTtQ+nQi-autj3btgm8hHBGQ@mail.gmail.com>

Hi YO,

RoiEditor communicate with DtiStudio by Binary Map.

Please refer to FAQ16 at https://www.mristudio.org/wiki/faq.

On Mon, Feb 28, 2011 at 9:24 PM, <107310 at ib.k.u-tokyo.ac.jp> wrote:

> Dear DTI experts
>
> I can't pass the ROI data saved in ROIEditor to DTI-studio.
> (I use the same subject.)
>
> In ROI editor, I drew the ROI and saved in specified format(ROI editor
> defined, Analyse, Binary map).
>
> Then go to DTI-studio, and open the ROI files in ROI tab.
>
> The erroe message is
> unrecognized image-ROI data file!
> (I tried 3 formats.)
>
> If there is a problem, please let me know.
> Many thanks!
>
> YO
>
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
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From 107310 at ib.k.u-tokyo.ac.jp  Wed Mar  2 00:30:21 2011
From: 107310 at ib.k.u-tokyo.ac.jp (107310 at ib.k.u-tokyo.ac.jp)
Date: Wed, 02 Mar 2011 14:30:21 +0900
Subject: [Mristudio-users] =?utf-8?q?How_to_pass_the_ROI_data=3F?=
In-Reply-To: <AANLkTikVfuJbjaHG7mNsZTtQ+nQi-autj3btgm8hHBGQ@mail.gmail.com>
References: <20110301022453.0000597C.0997@ib.k.u-tokyo.ac.jp>
	<AANLkTikVfuJbjaHG7mNsZTtQ+nQi-autj3btgm8hHBGQ@mail.gmail.com>
Message-ID: <20110302053021.000027C3.0831@ib.k.u-tokyo.ac.jp>

Dr. Mori

Thanks for the rapid reply.

I missed to pass the ROI Map file, though I did according to the manual 
and FAQ16.

I drew one object in ROIEditor.
Saved the ROI data in Binary maps.
ROIMap_00_00.dat(160KB) and ROIMap_00_map.dat(1KB) were generated.
Passed them to DTI studio, the error message was "Unrecognized image-ROI 
data file!"

I wonder if I didnt definite or save the ROI correctly.

If there is a problem, please let me know.
Thanks.


YO

 






> Hi YO,
> 
> RoiEditor communicate with DtiStudio by Binary Map.
> 
> Please refer to FAQ16 at https://www.mristudio.org/wiki/faq.
> 
> On Mon, Feb 28, 2011 at 9:24 PM, <107310 at ib.k.u-tokyo.ac.jp> wrote:
> 
> > Dear DTI experts
> >
> > I can't pass the ROI data saved in ROIEditor to DTI-studio.
> > (I use the same subject.)
> >
> > In ROI editor, I drew the ROI and saved in specified format(ROI 
editor
> > defined, Analyse, Binary map).
> >
> > Then go to DTI-studio, and open the ROI files in ROI tab.
> >
> > The erroe message is
> > unrecognized image-ROI data file!
> > (I tried 3 formats.)
> >
> > If there is a problem, please let me know.
> > Many thanks!
> >
> > YO
> >
> >
> >
> > _______________________________________________
> > mristudio-users mailing 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@
mristudio.org
> 




From susumu at mri.jhu.edu  Wed Mar  2 06:44:36 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Wed, 02 Mar 2011 06:44:36 -0500
Subject: [Mristudio-users] How to pass the ROI data?
In-Reply-To: <20110302053021.000027C3.0831@ib.k.u-tokyo.ac.jp>
References: <20110301022453.0000597C.0997@ib.k.u-tokyo.ac.jp>
	<AANLkTikVfuJbjaHG7mNsZTtQ+nQi-autj3btgm8hHBGQ@mail.gmail.com>
	<20110302053021.000027C3.0831@ib.k.u-tokyo.ac.jp>
Message-ID: <AANLkTikBAE2CjDQ_r3pOdeUH3OS9QdTANP5_YNi_kE7X@mail.gmail.com>

Are you trying to open the ROI from the "ROI" tab to do ROI-based
measurement or in the "Fiber" tab to do fiber tracking?

The communication between the DtiStudio and RoiEditor through the Binary Map
format is for fiber tracking. If so, you have to read the Binary Map file
inside the "Fiber" tab. I believe that the ROI tab deals only with the
DtiStudio format. If you want to do ROI-based measurement, you should read
images in to RoiEditor rather than read ROI to DtiStudio.

On Wed, Mar 2, 2011 at 12:30 AM, <107310 at ib.k.u-tokyo.ac.jp> wrote:

> Dr. Mori
>
> Thanks for the rapid reply.
>
> I missed to pass the ROI Map file, though I did according to the manual
> and FAQ16.
>
> I drew one object in ROIEditor.
> Saved the ROI data in Binary maps.
> ROIMap_00_00.dat(160KB) and ROIMap_00_map.dat(1KB) were generated.
> Passed them to DTI studio, the error message was "Unrecognized image-ROI
> data file!"
>
> I wonder if I didnt definite or save the ROI correctly.
>
> If there is a problem, please let me know.
> Thanks.
>
>
> YO
>
>
>
>
>
>
>
>
> > Hi YO,
> >
> > RoiEditor communicate with DtiStudio by Binary Map.
> >
> > Please refer to FAQ16 at https://www.mristudio.org/wiki/faq.
> >
> > On Mon, Feb 28, 2011 at 9:24 PM, <107310 at ib.k.u-tokyo.ac.jp> wrote:
> >
> > > Dear DTI experts
> > >
> > > I can't pass the ROI data saved in ROIEditor to DTI-studio.
> > > (I use the same subject.)
> > >
> > > In ROI editor, I drew the ROI and saved in specified format(ROI
> editor
> > > defined, Analyse, Binary map).
> > >
> > > Then go to DTI-studio, and open the ROI files in ROI tab.
> > >
> > > The erroe message is
> > > unrecognized image-ROI data file!
> > > (I tried 3 formats.)
> > >
> > > If there is a problem, please let me know.
> > > Many thanks!
> > >
> > > YO
> > >
> > >
> > >
> > > _______________________________________________
> > > mristudio-users mailing 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@
> 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
>
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From 107310 at ib.k.u-tokyo.ac.jp  Fri Mar  4 00:02:30 2011
From: 107310 at ib.k.u-tokyo.ac.jp (107310 at ib.k.u-tokyo.ac.jp)
Date: Fri, 04 Mar 2011 14:02:30 +0900
Subject: [Mristudio-users] =?utf-8?q?How_to_pass_the_ROI_data=3F?=
In-Reply-To: <AANLkTikBAE2CjDQ_r3pOdeUH3OS9QdTANP5_YNi_kE7X@mail.gmail.com>
References: <20110301022453.0000597C.0997@ib.k.u-tokyo.ac.jp>
	<AANLkTikVfuJbjaHG7mNsZTtQ+nQi-autj3btgm8hHBGQ@mail.gmail.com>
	<20110302053021.000027C3.0831@ib.k.u-tokyo.ac.jp>
	<AANLkTikBAE2CjDQ_r3pOdeUH3OS9QdTANP5_YNi_kE7X@mail.gmail.com>
Message-ID: <20110304050230.000067DE.0596@ib.k.u-tokyo.ac.jp>

Dear Dr Mori

I understand what you say.
Only the fiber tracking can communicate in this case.

I'd like to measure MD of the 2D slice image by using ROI, so I do my 
mesurement in the ROIEditor from now on.

Thank you.

YO


> Are you trying to open the ROI from the "ROI" tab to do ROI-based
> measurement or in the "Fiber" tab to do fiber tracking?
> 
> The communication between the DtiStudio and RoiEditor through the 
Binary Map
> format is for fiber tracking. If so, you have to read the Binary Map 
file
> inside the "Fiber" tab. I believe that the ROI tab deals only with the
> DtiStudio format. If you want to do ROI-based measurement, you should 
read
> images in to RoiEditor rather than read ROI to DtiStudio.
> 
> On Wed, Mar 2, 2011 at 12:30 AM, <107310 at ib.k.u-tokyo.ac.jp> wrote:
> 
> > Dr. Mori
> >
> > Thanks for the rapid reply.
> >
> > I missed to pass the ROI Map file, though I did according to the 
manual
> > and FAQ16.
> >
> > I drew one object in ROIEditor.
> > Saved the ROI data in Binary maps.
> > ROIMap_00_00.dat(160KB) and ROIMap_00_map.dat(1KB) were generated.
> > Passed them to DTI studio, the error message was "Unrecognized image
-ROI
> > data file!"
> >
> > I wonder if I didnt definite or save the ROI correctly.
> >
> > If there is a problem, please let me know.
> > Thanks.
> >
> >
> > YO
> >
> >
> >
> >
> >
> >
> >
> >
> > > Hi YO,
> > >
> > > RoiEditor communicate with DtiStudio by Binary Map.
> > >
> > > Please refer to FAQ16 at https://www.mristudio.org/wiki/faq.
> > >
> > > On Mon, Feb 28, 2011 at 9:24 PM, <107310 at ib.k.u-tokyo.ac.jp> wrote:
> > >
> > > > Dear DTI experts
> > > >
> > > > I can't pass the ROI data saved in ROIEditor to DTI-studio.
> > > > (I use the same subject.)
> > > >
> > > > In ROI editor, I drew the ROI and saved in specified format(ROI
> > editor
> > > > defined, Analyse, Binary map).
> > > >
> > > > Then go to DTI-studio, and open the ROI files in ROI tab.
> > > >
> > > > The erroe message is
> > > > unrecognized image-ROI data file!
> > > > (I tried 3 formats.)
> > > >
> > > > If there is a problem, please let me know.
> > > > Many thanks!
> > > >
> > > > YO
> > > >
> > > >
> > > >
> > > > _______________________________________________
> > > > mristudio-users mailing 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@
> > 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@
mristudio.org
> 




From dc02hana at m6.gyao.ne.jp  Sun Mar  6 09:10:26 2011
From: dc02hana at m6.gyao.ne.jp (hanaie)
Date: Sun, 06 Mar 2011 23:10:26 +0900
Subject: [Mristudio-users] high Rd value
Message-ID: <000901cbdc08$3db12620$b9137260$@gyao.ne.jp>

Dear DTI experts,

 

After fiber tracking, I obtained FA, trace , Rd, Ad value.

 

Eigen Value - 0

        Max. of ImgVal:   4.647e-003  Min. of ImgVal:   0.000e+000

        Mean of ImgVal:   2.179e-003  Std. of ImgVal:   5.147e-004

Radial Diffusivity

        Max. of ImgVal:   1.998e-003   Min. of ImgVal:   0.000e+000

        Mean of ImgVal:   6.584e-004? Std. of ImgVal:   3.607e-004

Tensor - Trace

        Max. of ImgVal:   8.643e-003   Min. of ImgVal:   0.000e+000

        Mean of ImgVal:   3.496e-003  Std. of ImgVal:   1.130e-003

Anisotropy - FA

        Max. of ImgVal:   0.8998    Min. of ImgVal:   0.000e+000

        Mean of ImgVal:   0.6589   Std. of ImgVal:   0.1486

 

And , I have questions.

 

Q1. When I report these values, which number must I report? Mean of Imgval?

Q2. When I report MD value, Can I divide trace value by 3?

Q3. I guess that these values obtained are too high, especially Ad and Rd.

   Why happen like this? Values are for superior cerebellar peduncle.

 

Please give me any suggestion.

 

Many thanks.

 

Ryuzo

 

 

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From susumu at mri.jhu.edu  Sun Mar  6 10:00:29 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Sun, 06 Mar 2011 10:00:29 -0500
Subject: [Mristudio-users] high Rd value
In-Reply-To: <000901cbdc08$3db12620$b9137260$@gyao.ne.jp>
References: <000901cbdc08$3db12620$b9137260$@gyao.ne.jp>
Message-ID: <AANLkTinTuLGkvRyn6y+TiT-EeAWGbYvNwKLoTEogZmd9@mail.gmail.com>

2011/3/6 hanaie <dc02hana at m6.gyao.ne.jp>:
> Dear DTI experts,
>
>
>
> After fiber tracking, I obtained FA, trace , Rd, Ad value.
>
>
>
> Eigen Value - 0
>
> ??????? Max. of ImgVal:?? 4.647e-003? Min. of ImgVal:?? 0.000e+000
>
> ??????? Mean of ImgVal:?? 2.179e-003? Std. of ImgVal:?? 5.147e-004
>
> Radial Diffusivity
>
> ??????? Max. of ImgVal:?? 1.998e-003?? Min. of ImgVal:?? 0.000e+000
>
> ??????? Mean of ImgVal:?? 6.584e-004? Std. of ImgVal:?? 3.607e-004
>
> Tensor - Trace
>
> ??????? Max. of ImgVal:?? 8.643e-003?? Min. of ImgVal:?? 0.000e+000
>
> ??????? Mean of ImgVal:?? 3.496e-003? Std. of ImgVal:?? 1.130e-003
>
> Anisotropy - FA
>
> ??????? Max. of ImgVal:?? 0.8998??? Min. of ImgVal:?? 0.000e+000
>
> ??????? Mean of ImgVal:?? 0.6589?? Std. of ImgVal:?? 0.1486
>
>
>
> And , I have questions.
>
>
>
> Q1. When I report these values, which number must I report? Mean of Imgval?

that's correct.

>
> Q2. When I report MD value, Can I divide trace value by 3?

that's correct.

>
> Q3. I guess that these values obtained are too high, especially Ad and Rd.

I believe that MD should be about 0.9-1.0. So your reported value is a
bit high.
Please make sure that you used correct b-values. For example, if you
used b=1,000 for data acquisition and used b=800 for processing, MD
becomes higher.
Also, smaller b-value tends to give higher MD. Many labs use b=1,000.
If you are using b=700, then your MD becomes a bit higher even if you
used the correct b-value for processing. This is because diffusion
signal decay is not mono-exponential and decays faster in low b-value
range than high b-value range.
>
> ?? Why happen like this? Values are for superior cerebellar peduncle.
>
>
>
> Please give me any suggestion.
>
>
>
> Many thanks.
>
>
>
> Ryuzo
>
>
>
>
>
> _______________________________________________
> mristudio-users mailing 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 dc02hana at m6.gyao.ne.jp  Mon Mar  7 10:41:15 2011
From: dc02hana at m6.gyao.ne.jp (hanaie)
Date: Tue, 08 Mar 2011 00:41:15 +0900
Subject: [Mristudio-users] high Rd value
In-Reply-To: <AANLkTinTuLGkvRyn6y+TiT-EeAWGbYvNwKLoTEogZmd9@mail.gmail.com>
References: <000901cbdc08$3db12620$b9137260$@gyao.ne.jp>
	<AANLkTinTuLGkvRyn6y+TiT-EeAWGbYvNwKLoTEogZmd9@mail.gmail.com>
Message-ID: <003301cbdcde$182e0270$488a0750$@gyao.ne.jp>

Dear Dr Mori

In my labs, we use both b=800 and b=1000 for data acquisition.
I am sure that I used correct b-values for data processing.
But I can find high Ad value and Rd value in both date(b=800, b=1000).

In literature, I saw that Rd is about 0.4-0.6 and Ad is about1.2-1.6.
I believe that usually Ad is higher than Rd.
Comparing with these values in the literature, values I obtained are too much high.

Is there any other causes?

Many thanks,

Ryuzo



-----Original Message-----
From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori
Sent: Monday, March 07, 2011 12:00 AM
To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
Subject: Re: [Mristudio-users] high Rd value

2011/3/6 hanaie <dc02hana at m6.gyao.ne.jp>:
> Dear DTI experts,
>
>
>
> After fiber tracking, I obtained FA, trace , Rd, Ad value.
>
>
>
> Eigen Value - 0
>
>         Max. of ImgVal:   4.647e-003  Min. of ImgVal:   0.000e+000
>
>         Mean of ImgVal:   2.179e-003  Std. of ImgVal:   5.147e-004
>
> Radial Diffusivity
>
>         Max. of ImgVal:   1.998e-003   Min. of ImgVal:   0.000e+000
>
>         Mean of ImgVal:   6.584e-004? Std. of ImgVal:   3.607e-004
>
> Tensor - Trace
>
>         Max. of ImgVal:   8.643e-003   Min. of ImgVal:   0.000e+000
>
>         Mean of ImgVal:   3.496e-003  Std. of ImgVal:   1.130e-003
>
> Anisotropy - FA
>
>         Max. of ImgVal:   0.8998    Min. of ImgVal:   0.000e+000
>
>         Mean of ImgVal:   0.6589   Std. of ImgVal:   0.1486
>
>
>
> And , I have questions.
>
>
>
> Q1. When I report these values, which number must I report? Mean of Imgval?

that's correct.

>
> Q2. When I report MD value, Can I divide trace value by 3?

that's correct.

>
> Q3. I guess that these values obtained are too high, especially Ad and Rd.

I believe that MD should be about 0.9-1.0. So your reported value is a
bit high.
Please make sure that you used correct b-values. For example, if you
used b=1,000 for data acquisition and used b=800 for processing, MD
becomes higher.
Also, smaller b-value tends to give higher MD. Many labs use b=1,000.
If you are using b=700, then your MD becomes a bit higher even if you
used the correct b-value for processing. This is because diffusion
signal decay is not mono-exponential and decays faster in low b-value
range than high b-value range.
>
>    Why happen like this? Values are for superior cerebellar peduncle.
>
>
>
> Please give me any suggestion.
>
>
>
> Many thanks.
>
>
>
> Ryuzo
>
>
>
>
>
> _______________________________________________
> mristudio-users mailing 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 cmuwyb at gmail.com  Tue Mar  8 19:46:09 2011
From: cmuwyb at gmail.com (Yibao Wang)
Date: Tue, 08 Mar 2011 19:46:09 -0500
Subject: [Mristudio-users] Question about Artifact and Mix with the
	adajacent bundle.
In-Reply-To: <AANLkTik-VhSvxXEHhdVwAUCyOsjs=xnxGO9g9x6nHPvf@mail.gmail.com>
References: <AANLkTi=ko2-0iJOQz7cSyRTLxhRXM-QhkkkCAbefCQjD@mail.gmail.com>
	<0AC64F4CB253074799B64FF8F0772D350126C692@azex2003.raddiag.med.uni-tuebingen.de>
	<AANLkTik-VhSvxXEHhdVwAUCyOsjs=xnxGO9g9x6nHPvf@mail.gmail.com>
Message-ID: <D9CB68B54C1448929CF1A2C1F442D017@VAIO>

When we doing the tractography, sometimes artifact occurred and easily mixed with the adjacent bundles.
For example, I reconstructed a fiber bundle which shape is similar to fornix, but its ROI is above the fornix,
But location of reconstructed fibers bundle is different from the reconstruction of fornix when we put them together,
In this condition, could we tell that it is not mixed with fornix?
Thanks for your help.
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From susumu at mri.jhu.edu  Tue Mar  8 20:18:34 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Tue, 08 Mar 2011 20:18:34 -0500
Subject: [Mristudio-users] Question about Artifact and Mix with the
 adajacent bundle.
In-Reply-To: <D9CB68B54C1448929CF1A2C1F442D017@VAIO>
References: <AANLkTi=ko2-0iJOQz7cSyRTLxhRXM-QhkkkCAbefCQjD@mail.gmail.com>
	<0AC64F4CB253074799B64FF8F0772D350126C692@azex2003.raddiag.med.uni-tuebingen.de>
	<AANLkTik-VhSvxXEHhdVwAUCyOsjs=xnxGO9g9x6nHPvf@mail.gmail.com>
	<D9CB68B54C1448929CF1A2C1F442D017@VAIO>
Message-ID: <AANLkTik-7pBr=ye8R=A9iDxj4SgD3+ReZkSmZ9sJR4M3@mail.gmail.com>

Hi Yibao,

I'm not sure which tract you referring to without images, but in
general, it is common that tractography contains contamination, such
as tracts running parallel at some points. It is always advisable to
use multiple ROIs to obtain cleaner results. For example, if you are
interested in the fornix, one ROI could define the column of the
fornix and the other defining its projection along the hippocampus.
Then you can ask tractography to retrieve trajectories that penetrate
the two ROIs.

Susumu

On Tue, Mar 8, 2011 at 7:46 PM, Yibao Wang <cmuwyb at gmail.com> wrote:
> When we doing the tractography, sometimes artifact occurred and easily mixed
> with the adjacent bundles.
> For example, I reconstructed a fiber bundle which shape is similar to
> fornix, but its ROI is above the fornix,
> But location of reconstructed fibers bundle is different from the
> reconstruction of fornix when we put them together,
> In this condition, could we tell that it is not mixed with fornix?
>
> Thanks for your help.
> _______________________________________________
> mristudio-users mailing 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 krithika982 at gmail.com  Wed Mar  9 09:36:42 2011
From: krithika982 at gmail.com (krithika balasubramanian)
Date: Wed, 09 Mar 2011 20:06:42 +0530
Subject: [Mristudio-users] query regarding fibre tracking in rat brain
Message-ID: <AANLkTikx3gE4pLbbprwc79m90hFG+RUycn5HmqW9qUSf@mail.gmail.com>

Dear Dr. Mori:
I am working on rat model of MS using Bruker 4.7 T animal MR scanner to
obtain rat brain images. For DTI I use the following parameters:
no of directions = 30, b values = 3 (0, 250, 855 s/mm2) (in addition to 5 A0
images), no. of slices = 7, slice thickness=  2 mm with no interslice gap.
 I recently started using DTI studio to carry out fibre tracking. I have few
queries related to fibre tracking for which i need clarification:

I am able to open my bruker raw data as philips 2dseq, and i had modified
the gradient table such that it consists of 95 directions ((30 dir x 3
b-values) + 5 A0 images). So i get a total of 95 images on which i carry out
tensor calculation and fiber tracking. However when i draw ROI after
clicking fibre tracking, it gives more of a colour coding within the ROI
instead of fibre tracts.
I tried opening the file in 3DMRI. In 3DMRI, the fibres are single coloured
and the colours need to be changed manually. Also, i do not get the brain
anatomical structure on which the fibres are visualized. Rather i get a
rectangular plane containing the fibres when i change the threshold value.
 In addition, i am unable to use the ROIeditor as i assume it does not
contain any atlas for rat brain. Also i am unable to use the Diifeomap.exe
(for 32 bit OS) that i downloaded from your website as it gives
error message that the file is corrupt (I use a 32-bit system).
So here are my questions:
1. Is there any atlas available for rat brain that can be used in ROI editor
and 3DMRI
2. How can i use the diffeomap?
3. How can we see the entire colour coded fibre tracts of rat brain (in the
RGB format indicating the Superior-inferior, right-left, up-down directions)
in 3DMRI/DTI studio
4. In fibre tracking, after increasing the tract-turning angle (say 70 deg)
 will the number of fibres (or colur codes) not decrease when compared with
lower angle (say 40 deg). But we observe more colour codes when the
tract-turning angle is increased. Can you kindly explain the reason for
this? Consequently, are the statistical details of fibres within an ROI in
DTI STUDIO correct and can they be reported?

Thanks in advance
Regards,

Krithika Balasubramanian
Ph.D student
Department of NMR & MRI facility,
All India Institute of Medical Sciences
Ansari Nagar
New Delhi 110029
India
email: krithika982 at gmail.com
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From davidprakash at gmail.com  Thu Mar 10 03:14:25 2011
From: davidprakash at gmail.com (David Prakash)
Date: Thu, 10 Mar 2011 16:14:25 +0800
Subject: [Mristudio-users] Fiber Data Reading
In-Reply-To: <AANLkTik7cYHc8hHED=5=H9-RewJHJEtDK3abstkcEon5@mail.gmail.com>
References: <AANLkTik7cYHc8hHED=5=H9-RewJHJEtDK3abstkcEon5@mail.gmail.com>
Message-ID: <AANLkTi=Ww0UHr=kX2ZCu-nYn3EBtXR20PXxs-x5uJYVj@mail.gmail.com>

Dear all

I am trying to read the fiber data file using my own java code.
In the header I am able to get the sFiberFileTag as "FiberDat".

Assuming fiber is stored as follows after the 128 bytes header:
int nFiberLength; // fiber length
unsigned char cReserved;
RGB_TRIPLE rgbFiberColor; // R-G-B, 3 bytes totally
int nSelectFiberStartPoint;
int nSelectFiberEndPoint;
XYZ_TRIPLE xyzFiberCoordinate[nFiberLength]; //x-y-z

Can I say that there are nFiberNr fibers?
For the first fiber data, I tried to read XYZ_TRIPLE data nFiberLength times
but some how get EOF exception half way.

I got a value of 704643132 for nFiberNr.
These are the values for the first fiber:

nFiberLength: 922746880
cReserved: 1
RGB_TRIPLE.r: 221
RGB_TRIPLE.g: 138
RGB_TRIPLE.b: 9
nSelectFiberStartPoint: 0
nSelectFiberEndPoint: 922746880

I got the EOF while reading the 721879 th XYZ_TRIPLE data. Should
there be 922746880 XYZ_TRIPLE data in the first fiber?

Please advice.
--
Regards,
David

From dmccoy at temple.edu  Thu Mar 10 10:54:23 2011
From: dmccoy at temple.edu (David McCoy)
Date: Thu, 10 Mar 2011 10:54:23 -0500
Subject: [Mristudio-users] Fiber Data Reading
In-Reply-To: <AANLkTi=Ww0UHr=kX2ZCu-nYn3EBtXR20PXxs-x5uJYVj@mail.gmail.com>
References: <AANLkTik7cYHc8hHED=5=H9-RewJHJEtDK3abstkcEon5@mail.gmail.com>
	<AANLkTi=Ww0UHr=kX2ZCu-nYn3EBtXR20PXxs-x5uJYVj@mail.gmail.com>
Message-ID: <AANLkTim7CZqATcVNCyzTnTdXxdOq0c+7ZvEZRcqhwHtk@mail.gmail.com>

Hello All,

Does anyone know who I need to get in contact with to register for the March
workshop?

On Thu, Mar 10, 2011 at 3:14 AM, David Prakash <davidprakash at gmail.com>wrote:

> Dear all
>
> I am trying to read the fiber data file using my own java code.
> In the header I am able to get the sFiberFileTag as "FiberDat".
>
> Assuming fiber is stored as follows after the 128 bytes header:
> int nFiberLength; // fiber length
> unsigned char cReserved;
> RGB_TRIPLE rgbFiberColor; // R-G-B, 3 bytes totally
> int nSelectFiberStartPoint;
> int nSelectFiberEndPoint;
> XYZ_TRIPLE xyzFiberCoordinate[nFiberLength]; //x-y-z
>
> Can I say that there are nFiberNr fibers?
> For the first fiber data, I tried to read XYZ_TRIPLE data nFiberLength
> times
> but some how get EOF exception half way.
>
> I got a value of 704643132 for nFiberNr.
> These are the values for the first fiber:
>
> nFiberLength: 922746880
> cReserved: 1
> RGB_TRIPLE.r: 221
> RGB_TRIPLE.g: 138
> RGB_TRIPLE.b: 9
> nSelectFiberStartPoint: 0
> nSelectFiberEndPoint: 922746880
>
> I got the EOF while reading the 721879 th XYZ_TRIPLE data. Should
> there be 922746880 XYZ_TRIPLE data in the first fiber?
>
> Please advice.
> --
> Regards,
> David
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>



-- 
David B. McCoy
Research Specialist - Olson Lab
Department of Psychology
Temple University - College of Liberal Arts
dmccoy at temple.edu
215-204-1708


Center for Cognitive Neuroscience
Department of Psychology
University of Pennsylvania
dmccoy at psych.upenn.edu
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From xli16 at jhmi.edu  Thu Mar 10 11:59:41 2011
From: xli16 at jhmi.edu (Xin Li)
Date: Thu, 10 Mar 2011 11:59:41 -0500
Subject: [Mristudio-users] Fiber Data Reading
In-Reply-To: <AANLkTim7CZqATcVNCyzTnTdXxdOq0c+7ZvEZRcqhwHtk@mail.gmail.com>
References: <AANLkTik7cYHc8hHED=5=H9-RewJHJEtDK3abstkcEon5@mail.gmail.com>
	<AANLkTi=Ww0UHr=kX2ZCu-nYn3EBtXR20PXxs-x5uJYVj@mail.gmail.com>
	<AANLkTim7CZqATcVNCyzTnTdXxdOq0c+7ZvEZRcqhwHtk@mail.gmail.com>
Message-ID: <73008e4a24ee4.4d78bd2d@johnshopkins.edu>

hello,

You can send me emails about the registration of the tutorials.


Xin

----- Original Message -----
From: David McCoy <dmccoy at temple.edu>
Date: Thursday, March 10, 2011 10:57 am
Subject: Re: [Mristudio-users] Fiber Data Reading
To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" <mristudio-users at mristudio.org>


> Hello All,
>  
>  Does anyone know who I need to get in contact with to register for 
> the March
>  workshop?
>  
>  On Thu, Mar 10, 2011 at 3:14 AM, David Prakash <davidprakash at gmail.com>wrote:
>  
>  > Dear all
>  >
>  > I am trying to read the fiber data file using my own java code.
>  > In the header I am able to get the sFiberFileTag as "FiberDat".
>  >
>  > Assuming fiber is stored as follows after the 128 bytes header:
>  > int nFiberLength; // fiber length
>  > unsigned char cReserved;
>  > RGB_TRIPLE rgbFiberColor; // R-G-B, 3 bytes totally
>  > int nSelectFiberStartPoint;
>  > int nSelectFiberEndPoint;
>  > XYZ_TRIPLE xyzFiberCoordinate[nFiberLength]; //x-y-z
>  >
>  > Can I say that there are nFiberNr fibers?
>  > For the first fiber data, I tried to read XYZ_TRIPLE data nFiberLength
>  > times
>  > but some how get EOF exception half way.
>  >
>  > I got a value of 704643132 for nFiberNr.
>  > These are the values for the first fiber:
>  >
>  > nFiberLength: 922746880
>  > cReserved: 1
>  > RGB_TRIPLE.r: 221
>  > RGB_TRIPLE.g: 138
>  > RGB_TRIPLE.b: 9
>  > nSelectFiberStartPoint: 0
>  > nSelectFiberEndPoint: 922746880
>  >
>  > I got the EOF while reading the 721879 th XYZ_TRIPLE data. Should
>  > there be 922746880 XYZ_TRIPLE data in the first fiber?
>  >
>  > Please advice.
>  > --
>  > Regards,
>  > David
>  > _______________________________________________
>  > mristudio-users mailing list
>  > mristudio-users at mristudio.org
>  > 
>  > Unsubscribe, send a blank email to:
>  > mristudio-users-unsubscribe at mristudio.org
>  >
>  
>  
>  
>  -- 
>  David B. McCoy
>  Research Specialist - Olson Lab
>  Department of Psychology
>  Temple University - College of Liberal Arts
>  dmccoy at temple.edu
>  215-204-1708
>  
>  
>  Center for Cognitive Neuroscience
>  Department of Psychology
>  University of Pennsylvania
>  dmccoy at psych.upenn.edu 
> _______________________________________________
>  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  Sat Mar 12 03:24:24 2011
From: choisj70 at gmail.com (Seongjin)
Date: Sat, 12 Mar 2011 03:24:24 -0500
Subject: [Mristudio-users] Registration to BETed b=0 image
Message-ID: <AANLkTi=ik1nGom2YBmB3LqOtAxsMDBE-5ajck+p6o4qw@mail.gmail.com>

Dear DTI studio developer and users:

I tried registration of DTI data to brain extracted (using FSL) b=0 image.
I expected registered DWI images with brain only. But it did not come out
that way.

Is there anyone who knows the trick using DTI studio?

Thanks in advance.
-SC
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From choisj70 at gmail.com  Sat Mar 12 10:30:58 2011
From: choisj70 at gmail.com (Seongjin)
Date: Sat, 12 Mar 2011 10:30:58 -0500
Subject: [Mristudio-users] [Re] Registration to BETed b=0 image
Message-ID: <AANLkTinwRjs3E4MJbqXpUBCMBt+L9CBLJhbBwekhEkTi@mail.gmail.com>

I solved my question.

Please ignore previous question to you.

Thanks,
-SC
-------------------------------------------------------------------------------------------------------------------------------


Dear DTI studio developer and users:

I tried registration of DTI data to brain extracted (using FSL) b=0 image.
I expected registered DWI images with brain only. But it did not come out
that way.

Is there anyone who knows the trick using DTI studio?

Thanks in advance.
-SC
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From jmcentee at jhmi.edu  Wed Mar 16 12:13:59 2011
From: jmcentee at jhmi.edu (Julie E McEntee)
Date: Wed, 16 Mar 2011 12:13:59 -0400
Subject: [Mristudio-users] handling of multiple b values
Message-ID: <7120f1658844.4d80a987@johnshopkins.edu>

Hello,

I am attempting to process some DTI data in Siemens Mosaic format that have multiple b values; that is, in addition to the volumes obtained with b = 0, DWI images with b = 300 and b = 1100 were obtained (please see attached gradient table and associated b values; obtained using DTIStudio "get gradient table" button).

Does DTIStudio properly handle such data correctly, that is, are tensor calculation and other calculations/images derived from DWIs with different b values performed appropriately? For example, I tried using the pixel rejection method for outlier rejection and many of pixels within b = 300 DWIs were rejected.

Thank you for your time,

-Julie

Julie E. McEntee, M.A., C.C.R.P.
Consultant
Department of Psychiatry- Neuroimaging
Department of Medical Psychology
Johns Hopkins University School of Medicine
600 N. Wolfe St./ Phipps 300
Baltimore, MD 21287

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From lucas_lessa at yahoo.com.br  Sat Mar 19 19:00:50 2011
From: lucas_lessa at yahoo.com.br (Lucas Lessa)
Date: Sat, 19 Mar 2011 16:00:50 -0700 (PDT)
Subject: [Mristudio-users] Problem with Philips TRACE Images in DTI
	calculation
Message-ID: <384418.97266.qm@web121210.mail.ne1.yahoo.com>

Dear friends,
Good evening,
I have some data made with the Achieva 1,5 T that produced just one DICOM Enhanced file.In this file I have the B0 the different gradients and the trace file at the end.The problem ins that I can't take off these trace images for the DTI calculation.I tryed to subtract the last volume using the MRISTUDIO but whenever file that I save before isn't recognize nby the DTISTUDIO (I tryed all of them - NRRD, RAW and analyse).Is there a way in DTISTUDIO to tell the program ignore the last volume, like in the gradient table?
Thank you very much.
Lucas Lessa.


      
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From susumu at mri.jhu.edu  Sun Mar 20 07:52:18 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Sun, 20 Mar 2011 07:52:18 -0400
Subject: [Mristudio-users] Problem with Philips TRACE Images in DTI
 calculation
In-Reply-To: <384418.97266.qm@web121210.mail.ne1.yahoo.com>
References: <384418.97266.qm@web121210.mail.ne1.yahoo.com>
Message-ID: <AANLkTimFQyQxSOQaqp7-Ynpgt2LjEXx81bpFfaZu81GO@mail.gmail.com>

Hi Lucus,

You can use x: 100, 100, 100 in the table to remove the image from the
subsequent calculation.

Susumu

On Sat, Mar 19, 2011 at 7:00 PM, Lucas Lessa <lucas_lessa at yahoo.com.br>wrote:

> Dear friends,
>
> Good evening,
>
> I have some data made with the Achieva 1,5 T that produced just one DICOM
> Enhanced file.
> In this file I have the B0 the different gradients and the trace file at
> the end.
> The problem ins that I can't take off these trace images for the DTI
> calculation.
> I tryed to subtract the last volume using the MRISTUDIO but whenever file
> that I save before isn't recognize nby the DTISTUDIO (I tryed all of them -
> NRRD, RAW and analyse).
> Is there a way in DTISTUDIO to tell the program ignore the last volume,
> like in the gradient table?
>
> Thank you very much.
>
> Lucas Lessa.
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From tejasviramanand at gmail.com  Thu Mar 24 22:21:47 2011
From: tejasviramanand at gmail.com (Tejasvi Ramanand)
Date: Thu, 24 Mar 2011 21:21:47 -0500
Subject: [Mristudio-users] Probability atlas ?
Message-ID: <AANLkTim0t55kDFEo1gwHhjsg7cJywwPsnjg3yEHEpxpB@mail.gmail.com>

Hi,

 I am new to the field of DTI. I am trying to use probability atlas for some
data analysis.
 I downloaded the JHU atlas from the FSL website.
 There are 2 JHU White matter atlases.
 1)JHU ICBM-DTI-81 White-Matter Labels
 2) JHU White-Matter Tractography Atlas

 From what I understand JHU White-Matter Tractography Atlas, is a
probability atlas.
 So, for every voxel in each tract (20 tracts) specified  there should be a
0 to 1 probability value.
 This probability will determine the probability of that voxel belonging to
that particular tract.
 But, where could I find the probability values?
 When I use DTIStudio to open the atlas, all I could see as the intensity
are the indexes that are given for each tract.


   -  Please let me know if I am using the wrong atlas?

           (or) How I could find the probability values of the tracts?


   -  What is the difference between these files
   JHU-ICBM-tracts-maxprob-thr50-2mm.nii.gz  and

           JHU-ICBM-tracts-maxprob-thr25-2mm.nii.gz

Thanks in advance.
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From jsadino.queens at gmail.com  Fri Mar 25 13:47:48 2011
From: jsadino.queens at gmail.com (Jeff Sadino)
Date: Fri, 25 Mar 2011 07:47:48 -1000
Subject: [Mristudio-users] DiffeoMap Interpolation Accuracy
Message-ID: <AANLkTi=DhZJf+ObpDPVv5fT15afwN086kT+EVtNfEzkG@mail.gmail.com>

Hello,

I am wondering about how DiffeoMap upsamples the slice number when
performing linear registration to the JHU template.  After doing the LDDMM
process, I have some ROIs that look interesting.  However, these ROIs are
smaller than my slice thickness.  I am wondering how valid it is to draw
conclusions about an ROI that exists entirely at sub-native voxel
resolution.

Thank you,
Jeff Sadino
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From susumu at mri.jhu.edu  Fri Mar 25 15:20:19 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Fri, 25 Mar 2011 15:20:19 -0400
Subject: [Mristudio-users] DiffeoMap Interpolation Accuracy
In-Reply-To: <AANLkTi=DhZJf+ObpDPVv5fT15afwN086kT+EVtNfEzkG@mail.gmail.com>
References: <AANLkTi=DhZJf+ObpDPVv5fT15afwN086kT+EVtNfEzkG@mail.gmail.com>
Message-ID: <AANLkTinFQD-VVevvR7Pv0_svEznvpEmrLgNG3rye0qLJ@mail.gmail.com>

Hi Jeff,

Maybe I didn't quite understand your question, but if you are talking
about the LDDMM-based image segmentation, each ROI is 3D. So, I'm not
sure if you encounter a situation where you deal with a ROI in one
slice, although maybe this is not relevant to your question.

Suppose your original image is 3mm and you resample it to 1mm. Then if
you draw one 2D ROI, you have a choice of 3 slices within the native
3mm slice. The center slice could be identical to the original image
but the edge two slices may be interpolated if you used trilinear
interpolation option. If you use the nearest neighbor, you simply get
3 1mm copies of the original 3mm slice.

I believe your question can be generalized as "what is the effect of
interpolation". Interpolation is a difficult issue. If you have an FA
map and interpolate it, you get a different result from interpolating
a tensor map and re-calculate a FA map from the interpolated tensor
map. There are also multiple options for interpolation. I would
recommend you to stick with one method and I don't think that we can
conclude one is better than the other.

You can also bring the pre-segmented atlas map all the way to your
original image space. In this way, you can at least forget about the
interpolation issue.

Susumu

On Fri, Mar 25, 2011 at 1:47 PM, Jeff Sadino <jsadino.queens at gmail.com> wrote:
> Hello,
> I am wondering about how DiffeoMap upsamples the slice number when
> performing linear registration to the JHU template. ?After doing the LDDMM
> process, I have some ROIs that look interesting. ?However, these ROIs are
> smaller than my slice thickness. ?I am wondering how valid it is to draw
> conclusions about an ROI that exists entirely at sub-native voxel
> resolution.
> Thank you,
> Jeff Sadino
> _______________________________________________
> mristudio-users mailing 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  Fri Mar 25 21:32:44 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Fri, 25 Mar 2011 21:32:44 -0400
Subject: [Mristudio-users] Probability atlas ?
In-Reply-To: <AANLkTim0t55kDFEo1gwHhjsg7cJywwPsnjg3yEHEpxpB@mail.gmail.com>
References: <AANLkTim0t55kDFEo1gwHhjsg7cJywwPsnjg3yEHEpxpB@mail.gmail.com>
Message-ID: <AANLkTinpktWCm9_f1=GSWZesWgGKmguvwfPK7jLAW43K@mail.gmail.com>

Hi Tejasvi,

I must admit that I'm not familiar with the exact data format you can
download from the FSL website. I thought the tractography atlases are
scaled 0-1....

>From www.mristudio.org, you can download RoiEditor, which comes with 4
different types of atlases. Three of them, ICBM-DTI-81, JHU-GA, and
JHU-SS, also have probabilistic tract maps. For the JHU-SS atlas,
there is also a comprehensive set of tract probabilistic maps for more
than 40 tracts, which you can download from our website. Please
contact Yajing for the location

On Thu, Mar 24, 2011 at 10:21 PM, Tejasvi Ramanand
<tejasviramanand at gmail.com> wrote:
> Hi,
>
> ?I am new to the field of DTI. I am trying to use probability atlas for some
> data analysis.
> ?I downloaded the JHU atlas from the FSL website.
> ?There are 2 JHU White matter atlases.
> ?1)JHU ICBM-DTI-81 White-Matter Labels
> ?2) JHU White-Matter Tractography Atlas
>
> ?From what I understand JHU White-Matter Tractography Atlas, is a
> probability atlas.
> ?So, for every voxel in each tract (20 tracts) specified? there should be a
> 0 to 1 probability value.
> ?This probability will determine the probability of that voxel belonging to
> that particular tract.
> ?But, where could I find the probability values?
> ?When I use DTIStudio to open the atlas, all I could see as the intensity
> are the indexes that are given for each tract.
>
> ?Please let me know if I am using the wrong atlas?
>
> ?????????? (or) How I could find the probability values of the tracts?
>
>
> ?What is the difference between these files
> JHU-ICBM-tracts-maxprob-thr50-2mm.nii.gz? and
>
> ?????????? JHU-ICBM-tracts-maxprob-thr25-2mm.nii.gz
>
> Thanks in advance.
>
>
>
>
>
> _______________________________________________
> mristudio-users mailing 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 jsadino.queens at gmail.com  Sat Mar 26 00:26:03 2011
From: jsadino.queens at gmail.com (Jeff Sadino)
Date: Fri, 25 Mar 2011 18:26:03 -1000
Subject: [Mristudio-users] DiffeoMap Interpolation Accuracy
In-Reply-To: <AANLkTinFQD-VVevvR7Pv0_svEznvpEmrLgNG3rye0qLJ@mail.gmail.com>
References: <AANLkTi=DhZJf+ObpDPVv5fT15afwN086kT+EVtNfEzkG@mail.gmail.com>
	<AANLkTinFQD-VVevvR7Pv0_svEznvpEmrLgNG3rye0qLJ@mail.gmail.com>
Message-ID: <BANLkTi=FNDJVMb6LnmmYKfBe8M_yiiRFnA@mail.gmail.com>

Thank you Hangyi and Susumu for your quick and, as always, detailed replies,
and my apologies for the unclear question.  Please let me give some more
details.

Our current workflow is as follows:
DTI Studio: to create FA, ADC, etc. maps.
DiffeoMap: AIR registration of FA, ADC, etc., to JHU templates (which
resamples), then LDDMM registration to JHU templates.  Apply Kimap.
ROIEditor: Extract FA, ADC, etc on the subject image (now in template space)
using the Type II WMPM atlas.

One of the ROIs we found significiant was the Nigra.  Our original image
slice was 4.6mm thick with a .4mm gap.  The Nigra from the Type II WMPM is
only 6mm thick.  After reading your comments, I would generalize my question
as: is there a minimum ROI threshold size that I should be using, relative
to the size of my acquisition voxels?  If we can throw some of the smaller
ROIs out, it would also help with multiple comparisons.  If it was your
paper, would you include the Nigra, considering the original slice
dimensions?  Perhaps this is one area where manual ROI placement would be
superior to autamated placement.

Thank you very much,
Jeff Sadino

On Fri, Mar 25, 2011 at 9:20 AM, susumu mori <susumu at mri.jhu.edu> wrote:

> Hi Jeff,
>
> Maybe I didn't quite understand your question, but if you are talking
> about the LDDMM-based image segmentation, each ROI is 3D. So, I'm not
> sure if you encounter a situation where you deal with a ROI in one
> slice, although maybe this is not relevant to your question.
>
> Suppose your original image is 3mm and you resample it to 1mm. Then if
> you draw one 2D ROI, you have a choice of 3 slices within the native
> 3mm slice. The center slice could be identical to the original image
> but the edge two slices may be interpolated if you used trilinear
> interpolation option. If you use the nearest neighbor, you simply get
> 3 1mm copies of the original 3mm slice.
>
> I believe your question can be generalized as "what is the effect of
> interpolation". Interpolation is a difficult issue. If you have an FA
> map and interpolate it, you get a different result from interpolating
> a tensor map and re-calculate a FA map from the interpolated tensor
> map. There are also multiple options for interpolation. I would
> recommend you to stick with one method and I don't think that we can
> conclude one is better than the other.
>
> You can also bring the pre-segmented atlas map all the way to your
> original image space. In this way, you can at least forget about the
> interpolation issue.
>
> Susumu
>
> On Fri, Mar 25, 2011 at 1:47 PM, Jeff Sadino <jsadino.queens at gmail.com>
> wrote:
> > Hello,
> > I am wondering about how DiffeoMap upsamples the slice number when
> > performing linear registration to the JHU template.  After doing the
> LDDMM
> > process, I have some ROIs that look interesting.  However, these ROIs are
> > smaller than my slice thickness.  I am wondering how valid it is to draw
> > conclusions about an ROI that exists entirely at sub-native voxel
> > resolution.
> > Thank you,
> > Jeff Sadino
> > _______________________________________________
> > mristudio-users mailing 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
>
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From susumu at mri.jhu.edu  Sat Mar 26 08:39:00 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Sat, 26 Mar 2011 08:39:00 -0400
Subject: [Mristudio-users] DiffeoMap Interpolation Accuracy
In-Reply-To: <BANLkTi=FNDJVMb6LnmmYKfBe8M_yiiRFnA@mail.gmail.com>
References: <AANLkTi=DhZJf+ObpDPVv5fT15afwN086kT+EVtNfEzkG@mail.gmail.com>
	<AANLkTinFQD-VVevvR7Pv0_svEznvpEmrLgNG3rye0qLJ@mail.gmail.com>
	<BANLkTi=FNDJVMb6LnmmYKfBe8M_yiiRFnA@mail.gmail.com>
Message-ID: <AANLkTim9RUnxxYMDtQMXJX96w2dyve4VVQSiQufbimL_@mail.gmail.com>

Hi Jeff,

First of all, if the structure of your interest (in this case SN) is
not well defined (too small or no contrast) in your original image,
computer algorithm cannot define it reliably. Also, the small size
(with respect to pixel size) of the structure would lead to partial
volume effect in raw data (thus poor reproducibility) and, again,
computer algorithm cannot get the reliable information even after
upsampling or normalization. So, everything is in your raw image. I
guess we all agree on it.

To answer your question, maybe a good approach is to use Hmap and warp
the WMPM to your raw image without interpolation. In this way, you may
get better idea about what the automated method is doing more
intuitively. Suppose a ROI is only 10 pixel large in the 1mm WMPM
which is warp to a raw image with 10 times lower resolution. Then, you
will find a ROI with only 1 pixel. This should give you some idea to
judge if the operation is reliable or not. The best way is to scan the
same person multiple times and measure the SN to find the reliability
range.

On Sat, Mar 26, 2011 at 12:26 AM, Jeff Sadino <jsadino.queens at gmail.com> wrote:
> Thank you Hangyi and Susumu for your quick and, as always, detailed replies,
> and my apologies for the unclear question. ?Please let me give some more
> details.
>
> Our current workflow is as follows:
> DTI Studio: to create FA, ADC, etc. maps.
> DiffeoMap:?AIR registration of FA, ADC, etc.,?to JHU templates (which
> resamples), then?LDDMM registration to JHU templates.? Apply Kimap.
> ROIEditor: Extract FA, ADC, etc on the subject image (now in template space)
> using the Type II WMPM atlas.
>
> One of the ROIs we found significiant was the Nigra.? Our original image
> slice was 4.6mm thick with a .4mm gap.? The Nigra from the Type II WMPM is
> only 6mm thick.? After reading your comments, I would generalize my question
> as: is there a minimum ROI threshold size that I should be using, relative
> to the size of my acquisition voxels?? If we can throw some of the smaller
> ROIs out, it would also help with multiple comparisons.? If it was your
> paper, would you include the Nigra, considering the original slice
> dimensions?? Perhaps this is one area where manual ROI placement would be
> superior to autamated placement.
>
> Thank you very much,
> Jeff Sadino
>
> On Fri, Mar 25, 2011 at 9:20 AM, susumu mori <susumu at mri.jhu.edu> wrote:
>>
>> Hi Jeff,
>>
>> Maybe I didn't quite understand your question, but if you are talking
>> about the LDDMM-based image segmentation, each ROI is 3D. So, I'm not
>> sure if you encounter a situation where you deal with a ROI in one
>> slice, although maybe this is not relevant to your question.
>>
>> Suppose your original image is 3mm and you resample it to 1mm. Then if
>> you draw one 2D ROI, you have a choice of 3 slices within the native
>> 3mm slice. The center slice could be identical to the original image
>> but the edge two slices may be interpolated if you used trilinear
>> interpolation option. If you use the nearest neighbor, you simply get
>> 3 1mm copies of the original 3mm slice.
>>
>> I believe your question can be generalized as "what is the effect of
>> interpolation". Interpolation is a difficult issue. If you have an FA
>> map and interpolate it, you get a different result from interpolating
>> a tensor map and re-calculate a FA map from the interpolated tensor
>> map. There are also multiple options for interpolation. I would
>> recommend you to stick with one method and I don't think that we can
>> conclude one is better than the other.
>>
>> You can also bring the pre-segmented atlas map all the way to your
>> original image space. In this way, you can at least forget about the
>> interpolation issue.
>>
>> Susumu
>>
>> On Fri, Mar 25, 2011 at 1:47 PM, Jeff Sadino <jsadino.queens at gmail.com>
>> wrote:
>> > Hello,
>> > I am wondering about how DiffeoMap upsamples the slice number when
>> > performing linear registration to the JHU template. ?After doing the
>> > LDDMM
>> > process, I have some ROIs that look interesting. ?However, these ROIs
>> > are
>> > smaller than my slice thickness. ?I am wondering how valid it is to draw
>> > conclusions about an ROI that exists entirely at sub-native voxel
>> > resolution.
>> > Thank you,
>> > Jeff Sadino
>> > _______________________________________________
>> > mristudio-users mailing 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 zhangyajing9996 at gmail.com  Sat Mar 26 15:14:49 2011
From: zhangyajing9996 at gmail.com (Yajing Zhang)
Date: Sat, 26 Mar 2011 15:14:49 -0400
Subject: [Mristudio-users] Probability atlas ?
In-Reply-To: <AANLkTinpktWCm9_f1=GSWZesWgGKmguvwfPK7jLAW43K@mail.gmail.com>
References: <AANLkTim0t55kDFEo1gwHhjsg7cJywwPsnjg3yEHEpxpB@mail.gmail.com>
	<AANLkTinpktWCm9_f1=GSWZesWgGKmguvwfPK7jLAW43K@mail.gmail.com>
Message-ID: <AANLkTi=Dzx+_Vq44yuR_aR9kFkeZfkKTXhAFA1nkOb04@mail.gmail.com>

Hi, Tejasvi,

As for the probabilistic tract maps, you can download from the following
website, and follow the instructions on the page to use these data.
http://lbam.med.jhmi.edu/cmrm/Data_Yajing/fiberMenu.htm .

Best regards,
Yajing



On Fri, Mar 25, 2011 at 9:32 PM, susumu mori <susumu at mri.jhu.edu> wrote:

> Hi Tejasvi,
>
> I must admit that I'm not familiar with the exact data format you can
> download from the FSL website. I thought the tractography atlases are
> scaled 0-1....
>
> From www.mristudio.org, you can download RoiEditor, which comes with 4
> different types of atlases. Three of them, ICBM-DTI-81, JHU-GA, and
> JHU-SS, also have probabilistic tract maps. For the JHU-SS atlas,
> there is also a comprehensive set of tract probabilistic maps for more
> than 40 tracts, which you can download from our website. Please
> contact Yajing for the location
>
> On Thu, Mar 24, 2011 at 10:21 PM, Tejasvi Ramanand
> <tejasviramanand at gmail.com> wrote:
> > Hi,
> >
> >  I am new to the field of DTI. I am trying to use probability atlas for
> some
> > data analysis.
> >  I downloaded the JHU atlas from the FSL website.
> >  There are 2 JHU White matter atlases.
> >  1)JHU ICBM-DTI-81 White-Matter Labels
> >  2) JHU White-Matter Tractography Atlas
> >
> >  From what I understand JHU White-Matter Tractography Atlas, is a
> > probability atlas.
> >  So, for every voxel in each tract (20 tracts) specified  there should be
> a
> > 0 to 1 probability value.
> >  This probability will determine the probability of that voxel belonging
> to
> > that particular tract.
> >  But, where could I find the probability values?
> >  When I use DTIStudio to open the atlas, all I could see as the intensity
> > are the indexes that are given for each tract.
> >
> >  Please let me know if I am using the wrong atlas?
> >
> >            (or) How I could find the probability values of the tracts?
> >
> >
> >  What is the difference between these files
> > JHU-ICBM-tracts-maxprob-thr50-2mm.nii.gz  and
> >
> >            JHU-ICBM-tracts-maxprob-thr25-2mm.nii.gz
> >
> > Thanks in advance.
> >
> >
> >
> >
> >
> > _______________________________________________
> > mristudio-users mailing list
> > mristudio-users at mristudio.org
> > http://lists.mristudio.org/mailman/listinfo/
> > Unsubscribe, send a blank email to:
> > mristudio-users-unsubscribe at mristudio.org
> >
>
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From yj3 at duke.edu  Mon Mar 28 10:32:51 2011
From: yj3 at duke.edu (Yi Jiang)
Date: Mon, 28 Mar 2011 10:32:51 -0400
Subject: [Mristudio-users] a paper of Dr Mori
References: <AANLkTi=DhZJf+ObpDPVv5fT15afwN086kT+EVtNfEzkG@mail.gmail.com>
	<AANLkTinFQD-VVevvR7Pv0_svEznvpEmrLgNG3rye0qLJ@mail.gmail.com>
	<BANLkTi=FNDJVMb6LnmmYKfBe8M_yiiRFnA@mail.gmail.com>
	<AANLkTim9RUnxxYMDtQMXJX96w2dyve4VVQSiQufbimL_@mail.gmail.com>
Message-ID: <2EE008FA847449EB9D2EE3207E727E66@panpan>

Dear Dr Mori,

I am looking for one of your papers:

DIFFUSION WEIGHTING BY THE TRACE OF THE DIFFUSION TENSOR WITHIN A SINGLE
SCAN
Author(s): MORI S, VANZIJL PCM Source: MAGNETIC RESONANCE IN MEDICINE
Volume: 33    Issue: 1    Pages: 41-52    Published: JAN 1995

But I could not find it. Could you please send a copy to me if you have one?

Thank you very much!

Best,
Yi



From miguel.burgaleta at uam.es  Wed Mar 30 12:56:41 2011
From: miguel.burgaleta at uam.es (Miguel Burgaleta)
Date: Wed, 30 Mar 2011 18:56:41 +0200
Subject: [Mristudio-users] test-retest
Message-ID: <F4175545-99B9-4BB8-B295-9C8B3AFD3916@uam.es>


Hi,

We have a sample of DWI acquired twice for each subject, 1 month in  
between, and would like to analyze the test-retest reproducibility of  
a selection of tracts with DTIStudio. We would also like to see the  
effect of outlier pixel rejection on the reproducibility. However, we  
are not sure of how to proceed so that we control for the intra-rater  
reliability.

One option we thought of is to perform tractography at time 1, save  
both binary tracts and ROIs, and then register each FA image in time 1  
to its corresponding FA image in time 2, apply that transformation to  
the ROIs and get the tract for time 2. Is this feasible with DTIStudio?

If you know a better way to do this, please let me know.

Best,
Miguel




From susumu at mri.jhu.edu  Thu Mar 31 18:15:56 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Thu, 31 Mar 2011 18:15:56 -0400
Subject: [Mristudio-users] test-retest
In-Reply-To: <F4175545-99B9-4BB8-B295-9C8B3AFD3916@uam.es>
References: <F4175545-99B9-4BB8-B295-9C8B3AFD3916@uam.es>
Message-ID: <AANLkTi=Bnn_jp44vr1X4j-Y4aAwR_YW_RW7McxxUcHza@mail.gmail.com>

Hi Miguel,

You can do it using Diffeomap (or FSL or SPM). First do tractography
in image 1 and 2 independently. Save the results as a 3D 1/0 mask in
DtiStudio.
Then run a rigid transformation between the image 1 and 2. You can do
FA vs FA but b0 vs b0 could be easier because FA maps could have some
random intense pixels outside the brain that may interfere with the
rigid alignment. Save the transformation matrix and apply it to your
1/0 binary fiber mask image. Then you can superimpose the aligned #1
and original #2 see the reproducibility. You can do all these very
easily by DiffeoMap.

Susumu

On Wed, Mar 30, 2011 at 12:56 PM, Miguel Burgaleta
<miguel.burgaleta at uam.es> wrote:
>
> Hi,
>
> We have a sample of DWI acquired twice for each subject, 1 month in
> between, and would like to analyze the test-retest reproducibility of
> a selection of tracts with DTIStudio. We would also like to see the
> effect of outlier pixel rejection on the reproducibility. However, we
> are not sure of how to proceed so that we control for the intra-rater
> reliability.
>
> One option we thought of is to perform tractography at time 1, save
> both binary tracts and ROIs, and then register each FA image in time 1
> to its corresponding FA image in time 2, apply that transformation to
> the ROIs and get the tract for time 2. Is this feasible with DTIStudio?
>
> If you know a better way to do this, please let me know.
>
> Best,
> 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 miguel.burgaleta at uam.es  Fri Apr  1 04:39:48 2011
From: miguel.burgaleta at uam.es (Miguel Burgaleta)
Date: Fri, 01 Apr 2011 10:39:48 +0200
Subject: [Mristudio-users] test-retest
In-Reply-To: <AANLkTi=Bnn_jp44vr1X4j-Y4aAwR_YW_RW7McxxUcHza@mail.gmail.com>
References: <F4175545-99B9-4BB8-B295-9C8B3AFD3916@uam.es>
	<AANLkTi=Bnn_jp44vr1X4j-Y4aAwR_YW_RW7McxxUcHza@mail.gmail.com>
Message-ID: <BA5FFAD6-3C1B-4603-8C28-15939FAA7CB7@uam.es>


Hi Susumu,

Thanks for your reply.

I find your suggestion very helpful! However, with that method I don't  
see how to separate the reproducibility of the tract from the rater  
reliability. If the tract in time 1 is different from that in time 2,  
we don't really know to what extent it is caused by small errors in  
the ROI placement, or by problems of reproducibility...

Another possibility would be to do tractography in time 1 twice, and  
once in time 2, so that we can look at the time1-time2 reproducibility  
relative to the time1-time1 reliability.

Also, can ROIs be transformed with Diffeomap as well (just like I  
suggested in my previous email)? That would help ensure that  
differences are due to reproducibility only.

Thanks,
Miguel


On Apr 1, 2011, at 12:15 AM, susumu mori wrote:

> Hi Miguel,
>
> You can do it using Diffeomap (or FSL or SPM). First do tractography
> in image 1 and 2 independently. Save the results as a 3D 1/0 mask in
> DtiStudio.
> Then run a rigid transformation between the image 1 and 2. You can do
> FA vs FA but b0 vs b0 could be easier because FA maps could have some
> random intense pixels outside the brain that may interfere with the
> rigid alignment. Save the transformation matrix and apply it to your
> 1/0 binary fiber mask image. Then you can superimpose the aligned #1
> and original #2 see the reproducibility. You can do all these very
> easily by DiffeoMap.
>
> Susumu
>
> On Wed, Mar 30, 2011 at 12:56 PM, Miguel Burgaleta
> <miguel.burgaleta at uam.es> wrote:
>>
>> Hi,
>>
>> We have a sample of DWI acquired twice for each subject, 1 month in
>> between, and would like to analyze the test-retest reproducibility of
>> a selection of tracts with DTIStudio. We would also like to see the
>> effect of outlier pixel rejection on the reproducibility. However, we
>> are not sure of how to proceed so that we control for the intra-rater
>> reliability.
>>
>> One option we thought of is to perform tractography at time 1, save
>> both binary tracts and ROIs, and then register each FA image in  
>> time 1
>> to its corresponding FA image in time 2, apply that transformation to
>> the ROIs and get the tract for time 2. Is this feasible with  
>> DTIStudio?
>>
>> If you know a better way to do this, please let me know.
>>
>> Best,
>> 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
>>
> _______________________________________________
> mristudio-users mailing 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 Apr  2 14:54:29 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Sat, 02 Apr 2011 14:54:29 -0400
Subject: [Mristudio-users] test-retest
In-Reply-To: <BA5FFAD6-3C1B-4603-8C28-15939FAA7CB7@uam.es>
References: <F4175545-99B9-4BB8-B295-9C8B3AFD3916@uam.es>
	<AANLkTi=Bnn_jp44vr1X4j-Y4aAwR_YW_RW7McxxUcHza@mail.gmail.com>
	<BA5FFAD6-3C1B-4603-8C28-15939FAA7CB7@uam.es>
Message-ID: <AANLkTimedB4K8xDt4FLSxsWPTU3yJGqOHBF4t6dyx6sK@mail.gmail.com>

Please see below;

On Fri, Apr 1, 2011 at 4:39 AM, Miguel Burgaleta
<miguel.burgaleta at uam.es> wrote:
>
> Hi Susumu,
>
> Thanks for your reply.
>
> I find your suggestion very helpful! However, with that method I don't
> see how to separate the reproducibility of the tract from the rater
> reliability. If the tract in time 1 is different from that in time 2,
> we don't really know to what extent it is caused by small errors in
> the ROI placement, or by problems of reproducibility...
>
> Another possibility would be to do tractography in time 1 twice, and
> once in time 2, so that we can look at the time1-time2 reproducibility
> relative to the time1-time1 reliability.

Yes, for intra/inter-operator reproducibility, you have to pick one
data (e.g. Time 1) and perform ROI drawing multiple times by the same
and different operators.

For inter-measurement reproducibility, you have to have Time 1 and
Time 2 data. In this case, if you draw ROI independently on Time 1 and
2, you have both inter-measurement and intra-operator reproducibility
mixed.

>
> Also, can ROIs be transformed with Diffeomap as well (just like I
> suggested in my previous email)? That would help ensure that
> differences are due to reproducibility only.
>

To remove the intra-operator factor from the inter-measurement
reproducibility, you can transform the ROI used for Time 1 to Time 2.
In this case, I suggest you to save the ROIs as the "Binary Map"
format. For example, suppose you drew 3 ROIs for tractography on Time
1. If you save the ROIs as the Binary Map, you'll get 4 files. Three
files are 1/0 binary mask files for 3 ROIs. The final one is a header
file in a text format. You can read and study the header. There is an
explanation section at the bottom of the header file.

Then you can apply the transformation matrix to the 3 ROI files in
DiffeoMap. As mentioned in the earlier email, you can use, for
example, b0 (Time1) to b0 (Time2) linear transformation and save the
transformation matrix. This matrix can be applied to the 3 ROI files.
Save these 3 new transformed ROI files. Then, rewrite the text header
files and specify the filenames of the 3 new ROI files.

You can load all necessary files (vector and FA files) for Time 2 for
tractography in DtiStudio. Then, you can load the revised Binary Map,
which will load the 3 new ROI files and apply the ROIs.

Hope this will do.

Susumu


> Thanks,
> Miguel
>
>
> On Apr 1, 2011, at 12:15 AM, susumu mori wrote:
>
>> Hi Miguel,
>>
>> You can do it using Diffeomap (or FSL or SPM). First do tractography
>> in image 1 and 2 independently. Save the results as a 3D 1/0 mask in
>> DtiStudio.
>> Then run a rigid transformation between the image 1 and 2. You can do
>> FA vs FA but b0 vs b0 could be easier because FA maps could have some
>> random intense pixels outside the brain that may interfere with the
>> rigid alignment. Save the transformation matrix and apply it to your
>> 1/0 binary fiber mask image. Then you can superimpose the aligned #1
>> and original #2 see the reproducibility. You can do all these very
>> easily by DiffeoMap.
>>
>> Susumu
>>
>> On Wed, Mar 30, 2011 at 12:56 PM, Miguel Burgaleta
>> <miguel.burgaleta at uam.es> wrote:
>>>
>>> Hi,
>>>
>>> We have a sample of DWI acquired twice for each subject, 1 month in
>>> between, and would like to analyze the test-retest reproducibility of
>>> a selection of tracts with DTIStudio. We would also like to see the
>>> effect of outlier pixel rejection on the reproducibility. However, we
>>> are not sure of how to proceed so that we control for the intra-rater
>>> reliability.
>>>
>>> One option we thought of is to perform tractography at time 1, save
>>> both binary tracts and ROIs, and then register each FA image in
>>> time 1
>>> to its corresponding FA image in time 2, apply that transformation to
>>> the ROIs and get the tract for time 2. Is this feasible with
>>> DTIStudio?
>>>
>>> If you know a better way to do this, please let me know.
>>>
>>> Best,
>>> 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
>>>
>> _______________________________________________
>> mristudio-users mailing 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 miguel.burgaleta at uam.es  Sun Apr  3 07:23:52 2011
From: miguel.burgaleta at uam.es (Miguel Burgaleta)
Date: Sun, 03 Apr 2011 13:23:52 +0200
Subject: [Mristudio-users] test-retest
In-Reply-To: <AANLkTimedB4K8xDt4FLSxsWPTU3yJGqOHBF4t6dyx6sK@mail.gmail.com>
References: <F4175545-99B9-4BB8-B295-9C8B3AFD3916@uam.es>
	<AANLkTi=Bnn_jp44vr1X4j-Y4aAwR_YW_RW7McxxUcHza@mail.gmail.com>
	<BA5FFAD6-3C1B-4603-8C28-15939FAA7CB7@uam.es>
	<AANLkTimedB4K8xDt4FLSxsWPTU3yJGqOHBF4t6dyx6sK@mail.gmail.com>
Message-ID: <53914923-E755-4C49-995D-BF1FF42F173C@uam.es>


Thanks a lot, Susumu. It is very clear now.

Miguel


On Apr 2, 2011, at 8:54 PM, susumu mori wrote:

> Please see below;
>
> On Fri, Apr 1, 2011 at 4:39 AM, Miguel Burgaleta
> <miguel.burgaleta at uam.es> wrote:
>>
>> Hi Susumu,
>>
>> Thanks for your reply.
>>
>> I find your suggestion very helpful! However, with that method I  
>> don't
>> see how to separate the reproducibility of the tract from the rater
>> reliability. If the tract in time 1 is different from that in time 2,
>> we don't really know to what extent it is caused by small errors in
>> the ROI placement, or by problems of reproducibility...
>>
>> Another possibility would be to do tractography in time 1 twice, and
>> once in time 2, so that we can look at the time1-time2  
>> reproducibility
>> relative to the time1-time1 reliability.
>
> Yes, for intra/inter-operator reproducibility, you have to pick one
> data (e.g. Time 1) and perform ROI drawing multiple times by the same
> and different operators.
>
> For inter-measurement reproducibility, you have to have Time 1 and
> Time 2 data. In this case, if you draw ROI independently on Time 1 and
> 2, you have both inter-measurement and intra-operator reproducibility
> mixed.
>
>>
>> Also, can ROIs be transformed with Diffeomap as well (just like I
>> suggested in my previous email)? That would help ensure that
>> differences are due to reproducibility only.
>>
>
> To remove the intra-operator factor from the inter-measurement
> reproducibility, you can transform the ROI used for Time 1 to Time 2.
> In this case, I suggest you to save the ROIs as the "Binary Map"
> format. For example, suppose you drew 3 ROIs for tractography on Time
> 1. If you save the ROIs as the Binary Map, you'll get 4 files. Three
> files are 1/0 binary mask files for 3 ROIs. The final one is a header
> file in a text format. You can read and study the header. There is an
> explanation section at the bottom of the header file.
>
> Then you can apply the transformation matrix to the 3 ROI files in
> DiffeoMap. As mentioned in the earlier email, you can use, for
> example, b0 (Time1) to b0 (Time2) linear transformation and save the
> transformation matrix. This matrix can be applied to the 3 ROI files.
> Save these 3 new transformed ROI files. Then, rewrite the text header
> files and specify the filenames of the 3 new ROI files.
>
> You can load all necessary files (vector and FA files) for Time 2 for
> tractography in DtiStudio. Then, you can load the revised Binary Map,
> which will load the 3 new ROI files and apply the ROIs.
>
> Hope this will do.
>
> Susumu
>
>
>> Thanks,
>> Miguel
>>
>>
>> On Apr 1, 2011, at 12:15 AM, susumu mori wrote:
>>
>>> Hi Miguel,
>>>
>>> You can do it using Diffeomap (or FSL or SPM). First do tractography
>>> in image 1 and 2 independently. Save the results as a 3D 1/0 mask in
>>> DtiStudio.
>>> Then run a rigid transformation between the image 1 and 2. You can  
>>> do
>>> FA vs FA but b0 vs b0 could be easier because FA maps could have  
>>> some
>>> random intense pixels outside the brain that may interfere with the
>>> rigid alignment. Save the transformation matrix and apply it to your
>>> 1/0 binary fiber mask image. Then you can superimpose the aligned #1
>>> and original #2 see the reproducibility. You can do all these very
>>> easily by DiffeoMap.
>>>
>>> Susumu
>>>
>>> On Wed, Mar 30, 2011 at 12:56 PM, Miguel Burgaleta
>>> <miguel.burgaleta at uam.es> wrote:
>>>>
>>>> Hi,
>>>>
>>>> We have a sample of DWI acquired twice for each subject, 1 month in
>>>> between, and would like to analyze the test-retest  
>>>> reproducibility of
>>>> a selection of tracts with DTIStudio. We would also like to see the
>>>> effect of outlier pixel rejection on the reproducibility.  
>>>> However, we
>>>> are not sure of how to proceed so that we control for the intra- 
>>>> rater
>>>> reliability.
>>>>
>>>> One option we thought of is to perform tractography at time 1, save
>>>> both binary tracts and ROIs, and then register each FA image in
>>>> time 1
>>>> to its corresponding FA image in time 2, apply that  
>>>> transformation to
>>>> the ROIs and get the tract for time 2. Is this feasible with
>>>> DTIStudio?
>>>>
>>>> If you know a better way to do this, please let me know.
>>>>
>>>> Best,
>>>> 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
>>>>
>>> _______________________________________________
>>> mristudio-users mailing 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 jsadino.queens at gmail.com  Tue Apr  5 22:02:21 2011
From: jsadino.queens at gmail.com (Jeff Sadino)
Date: Tue, 05 Apr 2011 16:02:21 -1000
Subject: [Mristudio-users] Applying Hmap and Kimap
Message-ID: <BANLkTinM3b6BBLzjcTYftz-5D9Hz=X_JGA@mail.gmail.com>

Hello,

I was reading a post from February 2010 titled "apply transformation to
landmarkers & command file" and wanted to ask one more question about it.
 The poster is asking how to apply the Kimap outside of DiffeoMap, mainly
Matlab.  Can someone please explain to me the format of the Kimap and Hmap
Transformations?  What do you guys mean when you say Vector (x, y, z)
x X-dimension
x Y-dimension x Z-dimension?  When I loaded up my Kimap into matlab as a
binary file, the first six values after the header were:

  1.0e+031 *

   7.800029524490799
   0.000000000022612
   0.000001498922010
   0.000000000000000
   0.000001839432419
   0.000000000000000

My image was 181 x 217 x 181.  Thank you very much,
Jeff Sadino

The original post is below:

1. One thing I need to note is that the transformation matrix I have is
a "final" combined matrix of AIR rigid, AIR affine, and LDDMM K map (so it
should be in the raw data format). Can I extract the "vector" information at
the specified location in this transformation matrix? And how?

Hello Yi,

As Susumu said, transformation matrices contain vectors at each coordinate,
indicating where is the new location. The structure is Vector (x, y, z) x
X-dimension x Y-dimension x Z-dimension. You may write matlab code to
extract the vector information.
-------------- next part --------------
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From xli16 at jhmi.edu  Wed Apr  6 10:52:14 2011
From: xli16 at jhmi.edu (Xin Li)
Date: Wed, 06 Apr 2011 10:52:14 -0400
Subject: [Mristudio-users] Applying Hmap and Kimap
In-Reply-To: <BANLkTinM3b6BBLzjcTYftz-5D9Hz=X_JGA@mail.gmail.com>
References: <BANLkTinM3b6BBLzjcTYftz-5D9Hz=X_JGA@mail.gmail.com>
Message-ID: <7270ec7e206b1.4d9c45de@johnshopkins.edu>

Kimap and Hmap gives the changes of the coordinates after transformation. Hmap is reciprocal to Kimap. For example, the first three values of your Kimap tells that the coordinate(0,0,0) in the transformed subject image corresponds to the coordinate(7.800029524490799, 0.000000000022612, 0.000001498922010) in the original subject image. The second three values tells that the coordinate(1.0,0,0) in the transformed subject image corresponds to the coordinate(0.000000000000000, 0.000001839432419, 0.000000000000000) in the original subject image.



Xin



----- Original Message -----
From: Jeff Sadino <jsadino.queens at gmail.com>
Date: Tuesday, April 5, 2011 10:03 pm
Subject: [Mristudio-users] Applying Hmap and Kimap
To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" <mristudio-users at mristudio.org>


> Hello,
>  
>  I was reading a post from February 2010 titled "apply transformation 
> to
>  landmarkers & command file" and wanted to ask one more question about 
> it.
>   The poster is asking how to apply the Kimap outside of DiffeoMap, mainly
>  Matlab.  Can someone please explain to me the format of the Kimap and 
> Hmap
>  Transformations?  What do you guys mean when you say Vector (x, y, z)
>  x X-dimension
>  x Y-dimension x Z-dimension?  When I loaded up my Kimap into matlab 
> as a
>  binary file, the first six values after the header were:
>  
>    1.0e+031 *
>  
>     7.800029524490799
>     0.000000000022612
>     0.000001498922010
>     0.000000000000000
>     0.000001839432419
>     0.000000000000000
>  
>  My image was 181 x 217 x 181.  Thank you very much,
>  Jeff Sadino
>  
>  The original post is below:
>  
>  1. One thing I need to note is that the transformation matrix I have 
> is
>  a "final" combined matrix of AIR rigid, AIR affine, and LDDMM K map 
> (so it
>  should be in the raw data format). Can I extract the "vector" 
> information at
>  the specified location in this transformation matrix? And how?
>  
>  Hello Yi,
>  
>  As Susumu said, transformation matrices contain vectors at each coordinate,
>  indicating where is the new location. The structure is Vector (x, y, 
> z) x
>  X-dimension x Y-dimension x Z-dimension. You may write matlab code to
>  extract the vector information. 
> _______________________________________________
>  mristudio-users mailing list
>  mristudio-users at mristudio.org
>  
>  Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org 

From moldmari at gmail.com  Wed Apr  6 10:55:14 2011
From: moldmari at gmail.com (Maria Moldoveanu)
Date: Wed, 06 Apr 2011 17:55:14 +0300
Subject: [Mristudio-users] Applying Hmap and Kimap
In-Reply-To: <BANLkTinM3b6BBLzjcTYftz-5D9Hz=X_JGA@mail.gmail.com>
References: <BANLkTinM3b6BBLzjcTYftz-5D9Hz=X_JGA@mail.gmail.com>
Message-ID: <BANLkTi=jHFM+Duqjx+2vtW0H5Sv9grxHSA@mail.gmail.com>

Hi,
 I'm a radiologyst .I work at 1,5T .Actualy we use neuro3D aplication for DTI.
But I want  to transfer  it on PC.

How can I transform DICOM -format of scans in DTI tool?
thank you!!!!

2011/4/6, Jeff Sadino <jsadino.queens at gmail.com>:
> Hello,
>
> I was reading a post from February 2010 titled "apply transformation to
> landmarkers & command file" and wanted to ask one more question about it.
>  The poster is asking how to apply the Kimap outside of DiffeoMap, mainly
> Matlab.  Can someone please explain to me the format of the Kimap and Hmap
> Transformations?  What do you guys mean when you say Vector (x, y, z)
> x X-dimension
> x Y-dimension x Z-dimension?  When I loaded up my Kimap into matlab as a
> binary file, the first six values after the header were:
>
>   1.0e+031 *
>
>    7.800029524490799
>    0.000000000022612
>    0.000001498922010
>    0.000000000000000
>    0.000001839432419
>    0.000000000000000
>
> My image was 181 x 217 x 181.  Thank you very much,
> Jeff Sadino
>
> The original post is below:
>
> 1. One thing I need to note is that the transformation matrix I have is
> a "final" combined matrix of AIR rigid, AIR affine, and LDDMM K map (so it
> should be in the raw data format). Can I extract the "vector" information at
> the specified location in this transformation matrix? And how?
>
> Hello Yi,
>
> As Susumu said, transformation matrices contain vectors at each coordinate,
> indicating where is the new location. The structure is Vector (x, y, z) x
> X-dimension x Y-dimension x Z-dimension. You may write matlab code to
> extract the vector information.
>


-- 
marisa

From xli16 at jhmi.edu  Wed Apr  6 10:59:11 2011
From: xli16 at jhmi.edu (Xin Li)
Date: Wed, 06 Apr 2011 10:59:11 -0400
Subject: [Mristudio-users] Applying Hmap and Kimap
In-Reply-To: <BANLkTi=jHFM+Duqjx+2vtW0H5Sv9grxHSA@mail.gmail.com>
References: <BANLkTinM3b6BBLzjcTYftz-5D9Hz=X_JGA@mail.gmail.com>
	<BANLkTi=jHFM+Duqjx+2vtW0H5Sv9grxHSA@mail.gmail.com>
Message-ID: <7310db18205df.4d9c477f@johnshopkins.edu>

You can use DtiStudio to upload DICOM format images.

There is an online manual at https://www.mristudio.org/wiki/user_manual/DTI_Studio_User_Manual

Xin

----- Original Message -----
From: Maria Moldoveanu <moldmari at gmail.com>
Date: Wednesday, April 6, 2011 10:55 am
Subject: Re: [Mristudio-users] Applying Hmap and Kimap
To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" <mristudio-users at mristudio.org>


> Hi,
>   I'm a radiologyst .I work at 1,5T .Actualy we use neuro3D aplication 
> for DTI.
>  But I want  to transfer  it on PC.
>  
>  How can I transform DICOM -format of scans in DTI tool?
>  thank you!!!!
>  
>  2011/4/6, Jeff Sadino <jsadino.queens at gmail.com>:
>  > Hello,
>  >
>  > I was reading a post from February 2010 titled "apply 
> transformation to
>  > landmarkers & command file" and wanted to ask one more question 
> about it.
>  >  The poster is asking how to apply the Kimap outside of DiffeoMap, 
> mainly
>  > Matlab.  Can someone please explain to me the format of the Kimap 
> and Hmap
>  > Transformations?  What do you guys mean when you say Vector (x, y, 
> z)
>  > x X-dimension
>  > x Y-dimension x Z-dimension?  When I loaded up my Kimap into matlab 
> as a
>  > binary file, the first six values after the header were:
>  >
>  >   1.0e+031 *
>  >
>  >    7.800029524490799
>  >    0.000000000022612
>  >    0.000001498922010
>  >    0.000000000000000
>  >    0.000001839432419
>  >    0.000000000000000
>  >
>  > My image was 181 x 217 x 181.  Thank you very much,
>  > Jeff Sadino
>  >
>  > The original post is below:
>  >
>  > 1. One thing I need to note is that the transformation matrix I 
> have is
>  > a "final" combined matrix of AIR rigid, AIR affine, and LDDMM K map 
> (so it
>  > should be in the raw data format). Can I extract the "vector" 
> information at
>  > the specified location in this transformation matrix? And how?
>  >
>  > Hello Yi,
>  >
>  > As Susumu said, transformation matrices contain vectors at each coordinate,
>  > indicating where is the new location. The structure is Vector (x, 
> y, z) x
>  > X-dimension x Y-dimension x Z-dimension. You may write matlab code 
> to
>  > extract the vector information.
>  >
>  
>  
>  -- 
>  marisa
>  _______________________________________________
>  mristudio-users mailing list
>  mristudio-users at mristudio.org
>  
>  Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org 

From moldmari at gmail.com  Wed Apr  6 14:44:24 2011
From: moldmari at gmail.com (Maria Moldoveanu)
Date: Wed, 06 Apr 2011 21:44:24 +0300
Subject: [Mristudio-users] Applying Hmap and Kimap
In-Reply-To: <7310db18205df.4d9c477f@johnshopkins.edu>
References: <BANLkTinM3b6BBLzjcTYftz-5D9Hz=X_JGA@mail.gmail.com>
	<BANLkTi=jHFM+Duqjx+2vtW0H5Sv9grxHSA@mail.gmail.com>
	<7310db18205df.4d9c477f@johnshopkins.edu>
Message-ID: <BANLkTinP+E7hjSpfbDusmzWNft9anyafFg@mail.gmail.com>

Thank you a lot!!!!

2011/4/6, Xin Li <xli16 at jhmi.edu>:
> You can use DtiStudio to upload DICOM format images.
>
> There is an online manual at
> https://www.mristudio.org/wiki/user_manual/DTI_Studio_User_Manual
>
> Xin
>
> ----- Original Message -----
> From: Maria Moldoveanu <moldmari at gmail.com>
> Date: Wednesday, April 6, 2011 10:55 am
> Subject: Re: [Mristudio-users] Applying Hmap and Kimap
> To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support"
> <mristudio-users at mristudio.org>
>
>
>> Hi,
>>   I'm a radiologyst .I work at 1,5T .Actualy we use neuro3D aplication
>> for DTI.
>>  But I want  to transfer  it on PC.
>>
>>  How can I transform DICOM -format of scans in DTI tool?
>>  thank you!!!!
>>
>>  2011/4/6, Jeff Sadino <jsadino.queens at gmail.com>:
>>  > Hello,
>>  >
>>  > I was reading a post from February 2010 titled "apply
>> transformation to
>>  > landmarkers & command file" and wanted to ask one more question
>> about it.
>>  >  The poster is asking how to apply the Kimap outside of DiffeoMap,
>> mainly
>>  > Matlab.  Can someone please explain to me the format of the Kimap
>> and Hmap
>>  > Transformations?  What do you guys mean when you say Vector (x, y,
>> z)
>>  > x X-dimension
>>  > x Y-dimension x Z-dimension?  When I loaded up my Kimap into matlab
>> as a
>>  > binary file, the first six values after the header were:
>>  >
>>  >   1.0e+031 *
>>  >
>>  >    7.800029524490799
>>  >    0.000000000022612
>>  >    0.000001498922010
>>  >    0.000000000000000
>>  >    0.000001839432419
>>  >    0.000000000000000
>>  >
>>  > My image was 181 x 217 x 181.  Thank you very much,
>>  > Jeff Sadino
>>  >
>>  > The original post is below:
>>  >
>>  > 1. One thing I need to note is that the transformation matrix I
>> have is
>>  > a "final" combined matrix of AIR rigid, AIR affine, and LDDMM K map
>> (so it
>>  > should be in the raw data format). Can I extract the "vector"
>> information at
>>  > the specified location in this transformation matrix? And how?
>>  >
>>  > Hello Yi,
>>  >
>>  > As Susumu said, transformation matrices contain vectors at each
>> coordinate,
>>  > indicating where is the new location. The structure is Vector (x,
>> y, z) x
>>  > X-dimension x Y-dimension x Z-dimension. You may write matlab code
>> to
>>  > extract the vector information.
>>  >
>>
>>
>>  --
>>  marisa
>>  _______________________________________________
>>  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
>


-- 
marisa

From haitao.ge at hotmail.com  Wed Apr  6 22:21:57 2011
From: haitao.ge at hotmail.com (Haitao Ge)
Date: Thu, 07 Apr 2011 10:21:57 +0800
Subject: [Mristudio-users] How to do tractography using FA map?
Message-ID: <SNT111-DS47B60D8483AE2AD639F1EF9A40@phx.gbl>

Hi,

I have created FA-map via FSL and I wanna do fiber tracking. What i should do to do tractography based the FA map via DtiStudio.

Thanks in advance,

Haitao
-------------------------------------------------------

Haitao Ge, Ph.D.

Center for Sectional and Imaging Anatomy
Shandong University School of Medicine
44#, West Wenhua Rd.
Jinan 250012, Shandong
P.R.China

Tel: +86-15965644699
Email: haitao.ge at homail.com
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From miguel.burgaleta at uam.es  Thu Apr  7 07:56:37 2011
From: miguel.burgaleta at uam.es (Miguel Burgaleta)
Date: Thu, 07 Apr 2011 13:56:37 +0200
Subject: [Mristudio-users] test-retest
In-Reply-To: <AANLkTimedB4K8xDt4FLSxsWPTU3yJGqOHBF4t6dyx6sK@mail.gmail.com>
References: <F4175545-99B9-4BB8-B295-9C8B3AFD3916@uam.es>
	<AANLkTi=Bnn_jp44vr1X4j-Y4aAwR_YW_RW7McxxUcHza@mail.gmail.com>
	<BA5FFAD6-3C1B-4603-8C28-15939FAA7CB7@uam.es>
	<AANLkTimedB4K8xDt4FLSxsWPTU3yJGqOHBF4t6dyx6sK@mail.gmail.com>
Message-ID: <E0B4E28E-A7B8-4617-BB4C-FC79D046CF91@uam.es>


Hi Susumu,

Is there any way to save ROIs in analyze format? If not, can we  
somehow convert dat files into analyze or nifti images within DTIStudio?

Thanks
Miguel



On Apr 2, 2011, at 8:54 PM, susumu mori wrote:

> Please see below;
>
> On Fri, Apr 1, 2011 at 4:39 AM, Miguel Burgaleta
> <miguel.burgaleta at uam.es> wrote:
>>
>> Hi Susumu,
>>
>> Thanks for your reply.
>>
>> I find your suggestion very helpful! However, with that method I  
>> don't
>> see how to separate the reproducibility of the tract from the rater
>> reliability. If the tract in time 1 is different from that in time 2,
>> we don't really know to what extent it is caused by small errors in
>> the ROI placement, or by problems of reproducibility...
>>
>> Another possibility would be to do tractography in time 1 twice, and
>> once in time 2, so that we can look at the time1-time2  
>> reproducibility
>> relative to the time1-time1 reliability.
>
> Yes, for intra/inter-operator reproducibility, you have to pick one
> data (e.g. Time 1) and perform ROI drawing multiple times by the same
> and different operators.
>
> For inter-measurement reproducibility, you have to have Time 1 and
> Time 2 data. In this case, if you draw ROI independently on Time 1 and
> 2, you have both inter-measurement and intra-operator reproducibility
> mixed.
>
>>
>> Also, can ROIs be transformed with Diffeomap as well (just like I
>> suggested in my previous email)? That would help ensure that
>> differences are due to reproducibility only.
>>
>
> To remove the intra-operator factor from the inter-measurement
> reproducibility, you can transform the ROI used for Time 1 to Time 2.
> In this case, I suggest you to save the ROIs as the "Binary Map"
> format. For example, suppose you drew 3 ROIs for tractography on Time
> 1. If you save the ROIs as the Binary Map, you'll get 4 files. Three
> files are 1/0 binary mask files for 3 ROIs. The final one is a header
> file in a text format. You can read and study the header. There is an
> explanation section at the bottom of the header file.
>
> Then you can apply the transformation matrix to the 3 ROI files in
> DiffeoMap. As mentioned in the earlier email, you can use, for
> example, b0 (Time1) to b0 (Time2) linear transformation and save the
> transformation matrix. This matrix can be applied to the 3 ROI files.
> Save these 3 new transformed ROI files. Then, rewrite the text header
> files and specify the filenames of the 3 new ROI files.
>
> You can load all necessary files (vector and FA files) for Time 2 for
> tractography in DtiStudio. Then, you can load the revised Binary Map,
> which will load the 3 new ROI files and apply the ROIs.
>
> Hope this will do.
>
> Susumu
>
>
>> Thanks,
>> Miguel
>>
>>
>> On Apr 1, 2011, at 12:15 AM, susumu mori wrote:
>>
>>> Hi Miguel,
>>>
>>> You can do it using Diffeomap (or FSL or SPM). First do tractography
>>> in image 1 and 2 independently. Save the results as a 3D 1/0 mask in
>>> DtiStudio.
>>> Then run a rigid transformation between the image 1 and 2. You can  
>>> do
>>> FA vs FA but b0 vs b0 could be easier because FA maps could have  
>>> some
>>> random intense pixels outside the brain that may interfere with the
>>> rigid alignment. Save the transformation matrix and apply it to your
>>> 1/0 binary fiber mask image. Then you can superimpose the aligned #1
>>> and original #2 see the reproducibility. You can do all these very
>>> easily by DiffeoMap.
>>>
>>> Susumu
>>>
>>> On Wed, Mar 30, 2011 at 12:56 PM, Miguel Burgaleta
>>> <miguel.burgaleta at uam.es> wrote:
>>>>
>>>> Hi,
>>>>
>>>> We have a sample of DWI acquired twice for each subject, 1 month in
>>>> between, and would like to analyze the test-retest  
>>>> reproducibility of
>>>> a selection of tracts with DTIStudio. We would also like to see the
>>>> effect of outlier pixel rejection on the reproducibility.  
>>>> However, we
>>>> are not sure of how to proceed so that we control for the intra- 
>>>> rater
>>>> reliability.
>>>>
>>>> One option we thought of is to perform tractography at time 1, save
>>>> both binary tracts and ROIs, and then register each FA image in
>>>> time 1
>>>> to its corresponding FA image in time 2, apply that  
>>>> transformation to
>>>> the ROIs and get the tract for time 2. Is this feasible with
>>>> DTIStudio?
>>>>
>>>> If you know a better way to do this, please let me know.
>>>>
>>>> Best,
>>>> 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
>>>>
>>> _______________________________________________
>>> mristudio-users mailing 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  Thu Apr  7 11:19:10 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Thu, 07 Apr 2011 11:19:10 -0400
Subject: [Mristudio-users] test-retest
In-Reply-To: <E0B4E28E-A7B8-4617-BB4C-FC79D046CF91@uam.es>
References: <F4175545-99B9-4BB8-B295-9C8B3AFD3916@uam.es>
	<AANLkTi=Bnn_jp44vr1X4j-Y4aAwR_YW_RW7McxxUcHza@mail.gmail.com>
	<BA5FFAD6-3C1B-4603-8C28-15939FAA7CB7@uam.es>
	<AANLkTimedB4K8xDt4FLSxsWPTU3yJGqOHBF4t6dyx6sK@mail.gmail.com>
	<E0B4E28E-A7B8-4617-BB4C-FC79D046CF91@uam.es>
Message-ID: <BANLkTikOtH8QDZMj3E1-ftXqa4hwaP1cKA@mail.gmail.com>

If you are using RoiEditor to define ROIs, you can directly save them
as the Analyze format.
If you are using DtiStudio, you can save the ROI as a binary or binary
map format. You can read them as image files and save them as Analyze.

On Thu, Apr 7, 2011 at 7:56 AM, Miguel Burgaleta
<miguel.burgaleta at uam.es> wrote:
>
> Hi Susumu,
>
> Is there any way to save ROIs in analyze format? If not, can we
> somehow convert dat files into analyze or nifti images within DTIStudio?
>
> Thanks
> Miguel
>
>
>
> On Apr 2, 2011, at 8:54 PM, susumu mori wrote:
>
>> Please see below;
>>
>> On Fri, Apr 1, 2011 at 4:39 AM, Miguel Burgaleta
>> <miguel.burgaleta at uam.es> wrote:
>>>
>>> Hi Susumu,
>>>
>>> Thanks for your reply.
>>>
>>> I find your suggestion very helpful! However, with that method I
>>> don't
>>> see how to separate the reproducibility of the tract from the rater
>>> reliability. If the tract in time 1 is different from that in time 2,
>>> we don't really know to what extent it is caused by small errors in
>>> the ROI placement, or by problems of reproducibility...
>>>
>>> Another possibility would be to do tractography in time 1 twice, and
>>> once in time 2, so that we can look at the time1-time2
>>> reproducibility
>>> relative to the time1-time1 reliability.
>>
>> Yes, for intra/inter-operator reproducibility, you have to pick one
>> data (e.g. Time 1) and perform ROI drawing multiple times by the same
>> and different operators.
>>
>> For inter-measurement reproducibility, you have to have Time 1 and
>> Time 2 data. In this case, if you draw ROI independently on Time 1 and
>> 2, you have both inter-measurement and intra-operator reproducibility
>> mixed.
>>
>>>
>>> Also, can ROIs be transformed with Diffeomap as well (just like I
>>> suggested in my previous email)? That would help ensure that
>>> differences are due to reproducibility only.
>>>
>>
>> To remove the intra-operator factor from the inter-measurement
>> reproducibility, you can transform the ROI used for Time 1 to Time 2.
>> In this case, I suggest you to save the ROIs as the "Binary Map"
>> format. For example, suppose you drew 3 ROIs for tractography on Time
>> 1. If you save the ROIs as the Binary Map, you'll get 4 files. Three
>> files are 1/0 binary mask files for 3 ROIs. The final one is a header
>> file in a text format. You can read and study the header. There is an
>> explanation section at the bottom of the header file.
>>
>> Then you can apply the transformation matrix to the 3 ROI files in
>> DiffeoMap. As mentioned in the earlier email, you can use, for
>> example, b0 (Time1) to b0 (Time2) linear transformation and save the
>> transformation matrix. This matrix can be applied to the 3 ROI files.
>> Save these 3 new transformed ROI files. Then, rewrite the text header
>> files and specify the filenames of the 3 new ROI files.
>>
>> You can load all necessary files (vector and FA files) for Time 2 for
>> tractography in DtiStudio. Then, you can load the revised Binary Map,
>> which will load the 3 new ROI files and apply the ROIs.
>>
>> Hope this will do.
>>
>> Susumu
>>
>>
>>> Thanks,
>>> Miguel
>>>
>>>
>>> On Apr 1, 2011, at 12:15 AM, susumu mori wrote:
>>>
>>>> Hi Miguel,
>>>>
>>>> You can do it using Diffeomap (or FSL or SPM). First do tractography
>>>> in image 1 and 2 independently. Save the results as a 3D 1/0 mask in
>>>> DtiStudio.
>>>> Then run a rigid transformation between the image 1 and 2. You can
>>>> do
>>>> FA vs FA but b0 vs b0 could be easier because FA maps could have
>>>> some
>>>> random intense pixels outside the brain that may interfere with the
>>>> rigid alignment. Save the transformation matrix and apply it to your
>>>> 1/0 binary fiber mask image. Then you can superimpose the aligned #1
>>>> and original #2 see the reproducibility. You can do all these very
>>>> easily by DiffeoMap.
>>>>
>>>> Susumu
>>>>
>>>> On Wed, Mar 30, 2011 at 12:56 PM, Miguel Burgaleta
>>>> <miguel.burgaleta at uam.es> wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>> We have a sample of DWI acquired twice for each subject, 1 month in
>>>>> between, and would like to analyze the test-retest
>>>>> reproducibility of
>>>>> a selection of tracts with DTIStudio. We would also like to see the
>>>>> effect of outlier pixel rejection on the reproducibility.
>>>>> However, we
>>>>> are not sure of how to proceed so that we control for the intra-
>>>>> rater
>>>>> reliability.
>>>>>
>>>>> One option we thought of is to perform tractography at time 1, save
>>>>> both binary tracts and ROIs, and then register each FA image in
>>>>> time 1
>>>>> to its corresponding FA image in time 2, apply that
>>>>> transformation to
>>>>> the ROIs and get the tract for time 2. Is this feasible with
>>>>> DTIStudio?
>>>>>
>>>>> If you know a better way to do this, please let me know.
>>>>>
>>>>> Best,
>>>>> 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
>>>>>
>>>> _______________________________________________
>>>> mristudio-users mailing 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 miguel.burgaleta at uam.es  Fri Apr  8 12:34:34 2011
From: miguel.burgaleta at uam.es (miguel.burgaleta at uam.es)
Date: Fri, 08 Apr 2011 18:34:34 +0200
Subject: [Mristudio-users] save tensor
In-Reply-To: <BANLkTikOtH8QDZMj3E1-ftXqa4hwaP1cKA@mail.gmail.com>
References: <F4175545-99B9-4BB8-B295-9C8B3AFD3916@uam.es>
	<AANLkTi=Bnn_jp44vr1X4j-Y4aAwR_YW_RW7McxxUcHza@mail.gmail.com>
	<BA5FFAD6-3C1B-4603-8C28-15939FAA7CB7@uam.es>
	<AANLkTimedB4K8xDt4FLSxsWPTU3yJGqOHBF4t6dyx6sK@mail.gmail.com>
	<E0B4E28E-A7B8-4617-BB4C-FC79D046CF91@uam.es>
	<BANLkTikOtH8QDZMj3E1-ftXqa4hwaP1cKA@mail.gmail.com>
Message-ID: <20110408183434.9803748gai6sfx0c@webmail.uam.es>



Hi all,

I would like to apply outlier pixel rejection, save the tensor and  
load it in a later session. Could you please say how to do this in  
DTIStudio?

Thanks in advance,
Miguel



From Jacquie.Hodge at albertahealthservices.ca  Fri Apr  8 12:56:55 2011
From: Jacquie.Hodge at albertahealthservices.ca (Jacquie Hodge)
Date: Fri, 08 Apr 2011 10:56:55 -0600
Subject: [Mristudio-users] Fa values
Message-ID: <1DC4211314F7D9458B66A28F947F60B99C45CED3DF@EXMBX4C.crha.bewell.ca>

Good morning everyone,

I am using DTI studio for my project where I am interested in comparing the left and right CST's in children who have suffereed injury in that area and after reading many studies on DTI decided to compare average FA values of the tracts as one of my variables. However, I have come across this questino from one of my supervisors and cannot really answer it and am hoping for your help/expertise.
Here is goes:
Is the FA value still a viable measure to look at and use to make a correlation if you are using FA values to pull the white matter tract? It seems like if the tract is made from FA values then you should not be able to use the FA as an outcome variable. This question has come up as I presented my research idea and I'm not sure how to answer it. Most studies that use DTI use FA thresholds to pull the tracts and then also the FA values (eg. mean FA) to make comparisons between the tracts.

I really hope that my question makes sense as I have found it very hard to word properly.

Thank you very much,
Jacquie

Jacquie Hodge MSc candidate in Neuroscience, BSc
Neuroscience, University of Calgary
Research Assistant, Calgary Pediatric Stroke Program
Alberta Children's Hospital
2888 Shaganappi Trail NW, Calgary, AB, Canada T3B 6A8
Phone: 403-955-7733 Fax: 403-955-2922
jacquie.hodge at albertahealthservices.ca
Program website: http://www.calgaryhealthregion.ca/programs/stroke/pediatric.htm

________________________________
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From susumu at mri.jhu.edu  Fri Apr  8 14:51:44 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Fri, 08 Apr 2011 14:51:44 -0400
Subject: [Mristudio-users] Fa values
In-Reply-To: <1DC4211314F7D9458B66A28F947F60B99C45CED3DF@EXMBX4C.crha.bewell.ca>
References: <1DC4211314F7D9458B66A28F947F60B99C45CED3DF@EXMBX4C.crha.bewell.ca>
Message-ID: <BANLkTik-hHetYx57X1J-6UXfEgRszG+g2g@mail.gmail.com>

Hi Jacqui,

This is a typical question of a coupling between morphology and pixel
intensity (contrast) measurements. The notion of "morphology" is based
on a cluster of pixel. There is no concept of morphology if you pick
one pixel. If you define a group of pixels, then you ask morphological
questions such as shapes and volumes. For pixel intensity, you can
measure it for single pixel as well as a cluster of pixels.

For example, you extract one axial slice at the pons where you can
identify the CST clearly. When somebody ask you to measure FA, you
need to define a boundary. If you define only the core of the CST, the
FA goes up and the size goes down. If your definition includes the
boarder of the CST, the FA goes down and the size goes up. The same
image, two different results; the former method may tell you "this
patient has smaller CST but FA is preserved" and the latter method
tells you "this patient has lower FA but the size was preserved".

So, the question is which is correct? Unfortunately, MRI/DTI can't
answer the question. You are asking a question such as "what is the
status of the CST", which calls for cellular-level information, while
we have merely 20MB of data for the entire brain based on water
diffusion property. Information is already degenerated too much to
answer your specific questions about neuroanatomy.

On top of it, even if we have a histology slice of the patient, it is
very difficult to define the CST because many brain structures do not
have a sharp boundary. The axons comprises the CST is very dense at
the core but toward the edge there are many pontine crossing fibers
interdigitating the CST axons. Even with histology, we can't clearly
define the boarder of the CST, while any image-based quantification
methods require us to define a boarder. So our effort for image-based
quantification is in some sense an atrifactual effort.

Then, the question is, why we do image-based quantification if it
gives results that can only be remotely connected to actual cellular
entities. Well, using MRI/DTI, you can systematically contract the
astronomical entity to a mere 10-20MB matrix, with which you can
readily quantify values and compare subjects and groups. In addition,
it takes only 5 min and non-invasive. While we are enjoying all these,
we really can't complain that it doesn't give us a straight answer
about what is the real cellular events happening in a patient.

Now, going back to the two different results from the same image, all
you can do is to apply the same criteria when you define a structure.
When we draw ROIs to define a boundary, we should try to be
consistent. Using FA threshold is one good way to remove
inter/intra-rater variability. As long as we apply consistent and
reproducible quantification approach, the data are good. However, if
we make mistake, that is when we interpret the data. Even if the
results scream that "No size change, FA goes down!", maybe what is
happening is the reduced size without FA change. Or histologically,
the former would suggest myelination loss or axonal loss, but in
reality it could be the reduced number of axons. So, we just have to
be careful when we interpret the data. Again, in MRI/DTI, the
anatomical data is astronomically degenerated. It is not always
possible to conclude what is happening in cellular levels.

So, to answer your question, yes, measure FA of the CST which is
defined by FA threshold is a tricky approach. Because if there is FA
loss, you may end up in a smaller CST with unchanged FA value simply
because you extracted only high FA portion of the CST. In this case,
you detected FA change by changes in size; a good example of
morphology-contrast coupling. If you find a consistent differences
between the control and patient groups, it's a good start. You just
don't wan to immediately conclude like "therefore, the CST atrophy" or
"therefore FA changed".

>From purely methodological point of view, you can also warp our
probabilistic CST location and measure FA values along the CST. In
this way, you don't perform tractography in each subject. You transfer
the population-based CST definition to each subject. In this way, you
can "freeze" the morphological information and perform pure contrast
detection. However, the downside is, you invite a nuisance factor,
called registration accuracy.

There is no perfect quantification method for image analysis. We just
have to know pros&cons and it is advisable to use multiple approaches.

Susumu



On Fri, Apr 8, 2011 at 12:56 PM, Jacquie Hodge
<Jacquie.Hodge at albertahealthservices.ca> wrote:
> Good morning everyone,
>
> I am using DTI studio for my project where I am interested in comparing the
> left and right CST's in children who have suffereed injury in that area and
> after reading many studies on DTI decided to compare average FA values of
> the tracts as one of my variables. However, I have come across this questino
> from one of my supervisors and cannot really answer it and am hoping for
> your help/expertise.
> Here is goes:
> Is the FA value still a viable measure to look at and use to make a
> correlation if you are using FA values to pull the white matter tract? It
> seems like if the tract is made from FA values then you should not be able
> to use the FA as an outcome variable. This question has come up as I
> presented my research idea and I'm not sure how to answer it. Most studies
> that use DTI use FA thresholds to pull the tracts and then also the FA
> values (eg. mean FA) to make comparisons between the tracts.
>
> I really hope that my question makes sense as I have found it very hard to
> word properly.
>
> Thank you very much,
> Jacquie
>
> Jacquie Hodge MSc candidate in Neuroscience, BSc
> Neuroscience, University of Calgary
> Research Assistant, Calgary Pediatric Stroke Program
> Alberta Children's Hospital
> 2888 Shaganappi Trail NW, Calgary, AB, Canada T3B 6A8
> Phone: 403-955-7733 Fax: 403-955-2922
> jacquie.hodge at albertahealthservices.ca
> Program website:
> http://www.calgaryhealthregion.ca/programs/stroke/pediatric.htm
> ________________________________
> 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
>
>

From deborahmlittle at gmail.com  Sun Apr 10 16:05:12 2011
From: deborahmlittle at gmail.com (Deborah Little)
Date: Sun, 10 Apr 2011 15:05:12 -0500
Subject: [Mristudio-users] 4d nii file into dti mapping
Message-ID: <4da20c92.8b3b2b0a.2c18.fffff2a7@mx.google.com>

Has anyone found a solution for reading in a 4D DTI file into DTI studio
(Achieva 2.6.3.4)? I've tried to do it as a rec format which does not help
as it either gives me an error with the number of files and/or only
reconstructs the one slice across all grad directions. I tried it as dicom
which does the same thing. Reading it in as a raw file also produces similar
problems. 

 

Thanks

 

Deborah M. Little PhD

Associate Professor of Neurology

The University of Illinois College of Medicine

 

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From jjames2 at umc.edu  Mon Apr 11 11:58:03 2011
From: jjames2 at umc.edu (Judy James)
Date: Mon, 11 Apr 2011 10:58:03 -0500
Subject: [Mristudio-users] ADC map from DWI
Message-ID: <2AA97D653978D24B85A02663FCC3916118EE578ED0@EXMBX3.ntummc.umsmed.edu>

Is any one in this group aware of how to calculate ADC maps from the original DWI images in DTI studio - not DTI images, like how to set the gradient table in such a case?

Any input/help will be highly appreciated.

Thank you,
Judy James "



*********************************************************************
Judy Rose James, Ph.D.
Clinical Physicist, MR Imaging Division
Assistant Professor, Department of Radiology
University of Mississippi Medical Center
Jackson, MS - 39216
Ph: (601) 984-2585; Pager: (601) 929-2442
Email: jjames2 at umc.edu<mailto:jjames2 at umc.edu>
*********************************************************************


________________________________
From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Jacquie Hodge [Jacquie.Hodge at albertahealthservices.ca]
Sent: Friday, April 08, 2011 11:56 AM
To: mristudio-users at mristudio.org
Subject: [Mristudio-users] Fa values

Good morning everyone,

I am using DTI studio for my project where I am interested in comparing the left and right CST's in children who have suffereed injury in that area and after reading many studies on DTI decided to compare average FA values of the tracts as one of my variables. However, I have come across this questino from one of my supervisors and cannot really answer it and am hoping for your help/expertise.
Here is goes:
Is the FA value still a viable measure to look at and use to make a correlation if you are using FA values to pull the white matter tract? It seems like if the tract is made from FA values then you should not be able to use the FA as an outcome variable. This question has come up as I presented my research idea and I'm not sure how to answer it. Most studies that use DTI use FA thresholds to pull the tracts and then also the FA values (eg. mean FA) to make comparisons between the tracts.

I really hope that my question makes sense as I have found it very hard to word properly.

Thank you very much,
Jacquie

Jacquie Hodge MSc candidate in Neuroscience, BSc
Neuroscience, University of Calgary
Research Assistant, Calgary Pediatric Stroke Program
Alberta Children's Hospital
2888 Shaganappi Trail NW, Calgary, AB, Canada T3B 6A8
Phone: 403-955-7733 Fax: 403-955-2922
jacquie.hodge at albertahealthservices.ca
Program website: http://www.calgaryhealthregion.ca/programs/stroke/pediatric.htm

________________________________
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.


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.

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From susumu at mri.jhu.edu  Mon Apr 11 13:15:29 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Mon, 11 Apr 2011 13:15:29 -0400
Subject: [Mristudio-users] ADC map from DWI
In-Reply-To: <2AA97D653978D24B85A02663FCC3916118EE578ED0@EXMBX3.ntummc.umsmed.edu>
References: <2AA97D653978D24B85A02663FCC3916118EE578ED0@EXMBX3.ntummc.umsmed.edu>
Message-ID: <BANLkTikzMDeBqEcjHGKN0hy27eWLZwV4jg@mail.gmail.com>

Judy, in DtiStudio, ADC (or also called MD) should be obtained from "Trace".

Trace is defined as Dxx+Dyy+Dzz. If you divide it by 3, it becomes
"Average diffusion constant (ADC)" or "Mean diffusivity (MD)". We like
to use the term "trace" because it has clear mathematical definition
while ADC is also used for "Apparent diffusion constant", which has a
different meaning from "average diffusion constant".

On Mon, Apr 11, 2011 at 11:58 AM, Judy James <jjames2 at umc.edu> wrote:
> Is any one in this group aware of?how to?calculate ADC maps from the
> original DWI images in DTI studio?- not DTI images, like how to set the
> gradient table in such a case?
> Any input/help will be highly appreciated.
>
> Thank you,
> Judy James "
>
>
>
> *********************************************************************
> Judy Rose James, Ph.D.
> Clinical?Physicist, MR Imaging Division
> Assistant Professor, Department of Radiology
> University of Mississippi Medical Center
> Jackson, MS - 39216
> Ph:?(601) 984-2585; Pager:?(601) 929-2442
> Email: jjames2 at umc.edu
> *********************************************************************
>
>
> ________________________________
> From: mristudio-users-bounces at mristudio.org
> [mristudio-users-bounces at mristudio.org] On Behalf Of Jacquie Hodge
> [Jacquie.Hodge at albertahealthservices.ca]
> Sent: Friday, April 08, 2011 11:56 AM
> To: mristudio-users at mristudio.org
> Subject: [Mristudio-users] Fa values
>
> Good morning everyone,
>
> I am using DTI studio for my project where I am interested in comparing the
> left and right CST's in children who have suffereed injury in that area and
> after reading many studies on DTI decided to compare average FA values of
> the tracts as one of my variables. However, I have come across this questino
> from one of my supervisors and cannot really answer it and am hoping for
> your help/expertise.
> Here is goes:
> Is the FA value still a viable measure to look at and use to make a
> correlation if you are using FA values to pull the white matter tract? It
> seems like if the tract is made from FA values then you should not be able
> to use the FA as an outcome variable. This question has come up as I
> presented my research idea and I'm not sure how to answer it. Most studies
> that use DTI use FA thresholds to pull the tracts and then also the FA
> values (eg. mean FA) to make comparisons between the tracts.
>
> I really hope that my question makes sense as I have found it very hard to
> word properly.
>
> Thank you very much,
> Jacquie
>
> Jacquie Hodge MSc candidate in Neuroscience, BSc
> Neuroscience, University of Calgary
> Research Assistant, Calgary Pediatric Stroke Program
> Alberta Children's Hospital
> 2888 Shaganappi Trail NW, Calgary, AB, Canada T3B 6A8
> Phone: 403-955-7733 Fax: 403-955-2922
> jacquie.hodge at albertahealthservices.ca
> Program website:
> http://www.calgaryhealthregion.ca/programs/stroke/pediatric.htm
> ________________________________
> 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.
>
> 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 alex.dresner at philips.com  Mon Apr 11 13:39:08 2011
From: alex.dresner at philips.com (Dresner, Alex)
Date: Mon, 11 Apr 2011 19:39:08 +0200
Subject: [Mristudio-users] 4d nii file into dti mapping
In-Reply-To: <4da20c92.8b3b2b0a.2c18.fffff2a7@mx.google.com>
References: <4da20c92.8b3b2b0a.2c18.fffff2a7@mx.google.com>
Message-ID: <F47DF122278D44439E845976F7C266D742E7E64B6A@NLCLUEXM04.connect1.local>

Hi Deborah,
The Rec file import should work, but you might have to switch between slice-by-slice and gradient-by-gradient (top right of the import window after you select Rec file import) depending on which Par/Rec version you are using.   Also, the gradient table may need adjustment because the Philips scanner exports the isotropically weighted image which DTI Studio does not need.  It also matters if the acquisition protocol uses the 'overplus' gradients, though you can tell from the gradients in the Par file too.

Hope this is helpful,
Alex

____________________
M. Alex Dresner, Ph.D.
MR Clinical Scientist
alex.dresner at philips.com
___________________


From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Deborah Little
Sent: Sunday, April 10, 2011 4:05 PM
To: mristudio-users at mristudio.org
Subject: [Mristudio-users] 4d nii file into dti mapping

Has anyone found a solution for reading in a 4D DTI file into DTI studio (Achieva 2.6.3.4)? I've tried to do it as a rec format which does not help as it either gives me an error with the number of files and/or only reconstructs the one slice across all grad directions. I tried it as dicom which does the same thing. Reading it in as a raw file also produces similar problems.

Thanks

Deborah M. Little PhD
Associate Professor of Neurology
The University of Illinois College of Medicine


________________________________
The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message.
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From Jacquie.Hodge at albertahealthservices.ca  Mon Apr 11 14:24:09 2011
From: Jacquie.Hodge at albertahealthservices.ca (Jacquie Hodge)
Date: Mon, 11 Apr 2011 12:24:09 -0600
Subject: [Mristudio-users] Fa values
In-Reply-To: <BANLkTik-hHetYx57X1J-6UXfEgRszG+g2g@mail.gmail.com>
References: <1DC4211314F7D9458B66A28F947F60B99C45CED3DF@EXMBX4C.crha.bewell.ca>
	<BANLkTik-hHetYx57X1J-6UXfEgRszG+g2g@mail.gmail.com>
Message-ID: <1DC4211314F7D9458B66A28F947F60B99C45CED3F1@EXMBX4C.crha.bewell.ca>

Thank you for that explanation Susumu.

Jacquie

Jacquie Hodge MSc candidate in Neuroscience, BSc
Neuroscience, University of Calgary
Research Assistant, Calgary Pediatric Stroke Program
Alberta Children's Hospital
2888 Shaganappi Trail NW, Calgary, AB, Canada T3B 6A8
Phone: 403-955-7733 Fax: 403-955-2922
jacquie.hodge at albertahealthservices.ca
Program website: http://www.calgaryhealthregion.ca/programs/stroke/pediatric.htm
________________________________________
From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori [susumu at mri.jhu.edu]
Sent: April 8, 2011 12:51 PM
To: DTI Studio, ROI Editor, DiffeoMap Questions/Support; Xin Li
Subject: Re: [Mristudio-users] Fa values

Hi Jacqui,

This is a typical question of a coupling between morphology and pixel
intensity (contrast) measurements. The notion of "morphology" is based
on a cluster of pixel. There is no concept of morphology if you pick
one pixel. If you define a group of pixels, then you ask morphological
questions such as shapes and volumes. For pixel intensity, you can
measure it for single pixel as well as a cluster of pixels.

For example, you extract one axial slice at the pons where you can
identify the CST clearly. When somebody ask you to measure FA, you
need to define a boundary. If you define only the core of the CST, the
FA goes up and the size goes down. If your definition includes the
boarder of the CST, the FA goes down and the size goes up. The same
image, two different results; the former method may tell you "this
patient has smaller CST but FA is preserved" and the latter method
tells you "this patient has lower FA but the size was preserved".

So, the question is which is correct? Unfortunately, MRI/DTI can't
answer the question. You are asking a question such as "what is the
status of the CST", which calls for cellular-level information, while
we have merely 20MB of data for the entire brain based on water
diffusion property. Information is already degenerated too much to
answer your specific questions about neuroanatomy.

On top of it, even if we have a histology slice of the patient, it is
very difficult to define the CST because many brain structures do not
have a sharp boundary. The axons comprises the CST is very dense at
the core but toward the edge there are many pontine crossing fibers
interdigitating the CST axons. Even with histology, we can't clearly
define the boarder of the CST, while any image-based quantification
methods require us to define a boarder. So our effort for image-based
quantification is in some sense an atrifactual effort.

Then, the question is, why we do image-based quantification if it
gives results that can only be remotely connected to actual cellular
entities. Well, using MRI/DTI, you can systematically contract the
astronomical entity to a mere 10-20MB matrix, with which you can
readily quantify values and compare subjects and groups. In addition,
it takes only 5 min and non-invasive. While we are enjoying all these,
we really can't complain that it doesn't give us a straight answer
about what is the real cellular events happening in a patient.

Now, going back to the two different results from the same image, all
you can do is to apply the same criteria when you define a structure.
When we draw ROIs to define a boundary, we should try to be
consistent. Using FA threshold is one good way to remove
inter/intra-rater variability. As long as we apply consistent and
reproducible quantification approach, the data are good. However, if
we make mistake, that is when we interpret the data. Even if the
results scream that "No size change, FA goes down!", maybe what is
happening is the reduced size without FA change. Or histologically,
the former would suggest myelination loss or axonal loss, but in
reality it could be the reduced number of axons. So, we just have to
be careful when we interpret the data. Again, in MRI/DTI, the
anatomical data is astronomically degenerated. It is not always
possible to conclude what is happening in cellular levels.

So, to answer your question, yes, measure FA of the CST which is
defined by FA threshold is a tricky approach. Because if there is FA
loss, you may end up in a smaller CST with unchanged FA value simply
because you extracted only high FA portion of the CST. In this case,
you detected FA change by changes in size; a good example of
morphology-contrast coupling. If you find a consistent differences
between the control and patient groups, it's a good start. You just
don't wan to immediately conclude like "therefore, the CST atrophy" or
"therefore FA changed".

>From purely methodological point of view, you can also warp our
probabilistic CST location and measure FA values along the CST. In
this way, you don't perform tractography in each subject. You transfer
the population-based CST definition to each subject. In this way, you
can "freeze" the morphological information and perform pure contrast
detection. However, the downside is, you invite a nuisance factor,
called registration accuracy.

There is no perfect quantification method for image analysis. We just
have to know pros&cons and it is advisable to use multiple approaches.

Susumu



On Fri, Apr 8, 2011 at 12:56 PM, Jacquie Hodge
<Jacquie.Hodge at albertahealthservices.ca> wrote:
> Good morning everyone,
>
> I am using DTI studio for my project where I am interested in comparing the
> left and right CST's in children who have suffereed injury in that area and
> after reading many studies on DTI decided to compare average FA values of
> the tracts as one of my variables. However, I have come across this questino
> from one of my supervisors and cannot really answer it and am hoping for
> your help/expertise.
> Here is goes:
> Is the FA value still a viable measure to look at and use to make a
> correlation if you are using FA values to pull the white matter tract? It
> seems like if the tract is made from FA values then you should not be able
> to use the FA as an outcome variable. This question has come up as I
> presented my research idea and I'm not sure how to answer it. Most studies
> that use DTI use FA thresholds to pull the tracts and then also the FA
> values (eg. mean FA) to make comparisons between the tracts.
>
> I really hope that my question makes sense as I have found it very hard to
> word properly.
>
> Thank you very much,
> Jacquie
>
> Jacquie Hodge MSc candidate in Neuroscience, BSc
> Neuroscience, University of Calgary
> Research Assistant, Calgary Pediatric Stroke Program
> Alberta Children's Hospital
> 2888 Shaganappi Trail NW, Calgary, AB, Canada T3B 6A8
> Phone: 403-955-7733 Fax: 403-955-2922
> jacquie.hodge at albertahealthservices.ca
> Program website:
> http://www.calgaryhealthregion.ca/programs/stroke/pediatric.htm
> ________________________________
> 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
>
>
_______________________________________________
mristudio-users mailing 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.


From Jacquie.Hodge at albertahealthservices.ca  Mon Apr 11 19:59:26 2011
From: Jacquie.Hodge at albertahealthservices.ca (Jacquie Hodge)
Date: Mon, 11 Apr 2011 17:59:26 -0600
Subject: [Mristudio-users] disappearing ROI
Message-ID: <1DC4211314F7D9458B66A28F947F60B99C45CED3F8@EXMBX4C.crha.bewell.ca>

Hello everyone,

When I load my second ROI after successfully loading the first ROI all of my fibers disappear. This does not happen all the time and I save my ROI's in the same way everytime. I'm wondering if someone can tell me why this is happening or maybe what I am doing wrong?

Thank you,

Jacquie

Jacquie Hodge MSc candidate in Neuroscience, BSc
Neuroscience, University of Calgary
Research Assistant, Calgary Pediatric Stroke Program
Alberta Children's Hospital
2888 Shaganappi Trail NW, Calgary, AB, Canada T3B 6A8
Phone: 403-955-7733 Fax: 403-955-2922
jacquie.hodge at albertahealthservices.ca
Program website: http://www.calgaryhealthregion.ca/programs/stroke/pediatric.htm

________________________________
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.
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From joanne.lin at auckland.ac.nz  Wed Apr 13 23:40:50 2011
From: joanne.lin at auckland.ac.nz (Joanne Lin)
Date: Thu, 14 Apr 2011 15:40:50 +1200
Subject: [Mristudio-users] AIR error in DiffeoMap
Message-ID: <924B2B288B4D9B47B764BA944068BDB905975818@fmhsx2.fmhs.auckland.ac.nz>

Hi all,

 

I'm new to MRI Studio and all its related tools, so I apologise for the
simplicity of this question.

 

>From ready previous posts on the mailing list and looking at respective
user manuals, I am trying to perform a linear transformation but when I
click the 'AIR Linear' button in the 'Transformation' section, an error
message comes up, saying -

 

"Cannot find makeaheader.exe.

Please go to http://air.bmap.ucla.edu:16080/AIR5/ to get AIR.

Then please build  makeaheader.exe and put it in the folder DiffeoMap."

 

However, when I follow the above instructions, the web page does not
work.  Is there something I'm missing/doing wrong?

 

Any advice would be greatly appreciated!

 

 

Cheers,

 

Joanne Lin

BPharm (Hons), RegPharmNZ

 

Pharmacist/PhD Candidate
School of Pharmacy

Faculty of Medical & Health Sciences

The University of Auckland

Private Bag 92019

Auckland, New Zealand

+64 9 373 7599 Ext 88468

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From yitaotome at yahoo.com.cn  Thu Apr 14 08:30:23 2011
From: yitaotome at yahoo.com.cn (tome ffffffffffd2 ffffffffffc1)
Date: Thu, 14 Apr 2011 20:30:23 +0800 (CST)
Subject: [Mristudio-users] =?utf-8?b?IOWbnuWkje+8miAgZGlzYXBwZWFyaW5nIFJP?=
 =?utf-8?q?I?=
In-Reply-To: <1DC4211314F7D9458B66A28F947F60B99C45CED3F8@EXMBX4C.crha.bewell.ca>
Message-ID: <978926.14577.qm@web15601.mail.cnb.yahoo.com>



--- 11?4?12????, Jacquie Hodge <Jacquie.Hodge at albertahealthservices.ca> ???


???: Jacquie Hodge <Jacquie.Hodge at albertahealthservices.ca>
??: [Mristudio-users] disappearing ROI
???: "mristudio-users at mristudio.org" <mristudio-users at mristudio.org>
??: 2011?4?12?,??,??7:59









Hello everyone, 
?
When I load my second ROI after successfully loading the first ROI all of my fibers disappear. This does not happen all the time and I save my ROI's in the same way everytime. I'm wondering if someone can tell me why this is happening or maybe what I am doing wrong?
?
Thank you, 
?
Jacquie
?

Jacquie Hodge MSc candidate in Neuroscience, BSc
Neuroscience, University of Calgary
Research Assistant, Calgary Pediatric Stroke Program
Alberta Children's Hospital
2888 Shaganappi Trail NW, Calgary, AB, Canada T3B 6A8
Phone: 403-955-7733 Fax: 403-955-2922
jacquie.hodge at albertahealthservices.ca
Program website: http://www.calgaryhealthregion.ca/programs/stroke/pediatric.htm


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.

-----???????-----


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From kevinspitler at ucla.edu  Tue Apr 19 17:42:57 2011
From: kevinspitler at ucla.edu (Kevin Spitler)
Date: Tue, 19 Apr 2011 14:42:57 -0700
Subject: [Mristudio-users] Error #_of_Images != (#_of_gradients) x
	(#_of_repetitions)
Message-ID: <BANLkTikeiiVKKmdYTVeS+gUBY9Qh0Hjpug@mail.gmail.com>

Hello,

I have several Siemens datasets with the Error that the number of
Images does not equal the product of the number of gradients and
repetitions.

What is the recommended way to debug this problem?  Is this a problem
with the gradient that I am using?

My gradient is:
0: 0.000, 0.000, 0.000
 1: 0.500, 0.000, 0.500
 2: -0.500, 0.000, 0.500
 3: 0.000, 0.500, 0.500
 4: 0.000, 0.500, -0.500
 5: 0.500, 0.500, 0.000
 6: -0.500, 0.500, 0.000
 7: 1.000, 0.000, 1.000
 8: -1.000, 0.000, 1.000
 9: 0.000, 1.000, 1.000
 10: 0.000, 1.000, -1.000
 11: 1.000, 1.000, 0.000
 12: -1.000, 1.000, 0.000

After I click "OK" on the error message, DTI Studio does not crash.
Typically, only a portion of the brain is displayed (e.g., the
inferior portion).

B values used are 0,600,1200.  I have tried the following gradient
with similar results:
 0: 0.000, 0.000, 0.000,600
 1: 0.500, 0.000, 0.500,600
 2: -0.500, 0.000, 0.500,600
 3: 0.000, 0.500, 0.500,600
 4: 0.000, 0.500, -0.500,600
 5: 0.500, 0.500, 0.000,600
 6: -0.500, 0.500, 0.000,600
 7: 1.000, 0.000, 1.000,600
 8: -1.000, 0.000, 1.000,600
 9: 0.000, 1.000, 1.000,600
 10: 0.000, 1.000, -1.000,600
 11: 1.000, 1.000, 0.000,600
 12: -1.000, 1.000, 0.000,600
13: 0.500, 0.000, 0.500,1200
14: -0.500, 0.000, 0.500,1200
15: 0.000, 0.500, 0.500,1200
16: 0.000, 0.500, -0.500,1200
17: 0.500, 0.500, 0.000,1200
18: -0.500, 0.500, 0.000,1200
19: 1.000, 0.000, 1.000,1200
20: -1.000, 0.000, 1.000,1200
21: 0.000, 1.000, 1.000,1200
22: 0.000, 1.000, -1.000,1200
23: 1.000, 1.000, 0.000,1200
24: -1.000, 1.000, 0.000,1200

The error message then has the number of gradients =25, with the same
number of repetitions and images.

Thank you for helping me use these datasets.

Best,
Kevin

From susumu at mri.jhu.edu  Tue Apr 19 18:46:45 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Tue, 19 Apr 2011 18:46:45 -0400
Subject: [Mristudio-users] Error #_of_Images != (#_of_gradients) x
 (#_of_repetitions)
In-Reply-To: <BANLkTikeiiVKKmdYTVeS+gUBY9Qh0Hjpug@mail.gmail.com>
References: <BANLkTikeiiVKKmdYTVeS+gUBY9Qh0Hjpug@mail.gmail.com>
Message-ID: <BANLkTinxymo7yHQyyCcTm5FgkvgQSshJUA@mail.gmail.com>

Hi Kevin,

1) First, load the images using Mri3DView. It should load all images,
which are listed in the pull-down menu.
2) Check the number of 3D images and also the image dimensions. Make
sure that all 3D images look fine. For example, if you did the
12-orientation Siemens DTI, you should find 13 3D volumes.
3) Then load the same data by DtiMapping. In the initial data input
window, the number of gradient orientations need to match what you saw
in Mri3DView.
4) In the initial data input window, there is also a section to
specify if all slices need to be read. Here you need to say "all
slices"

susumu

On Tue, Apr 19, 2011 at 5:42 PM, Kevin Spitler <kevinspitler at ucla.edu> wrote:
> Hello,
>
> I have several Siemens datasets with the Error that the number of
> Images does not equal the product of the number of gradients and
> repetitions.
>
> What is the recommended way to debug this problem? ?Is this a problem
> with the gradient that I am using?
>
> My gradient is:
> 0: 0.000, 0.000, 0.000
> ?1: 0.500, 0.000, 0.500
> ?2: -0.500, 0.000, 0.500
> ?3: 0.000, 0.500, 0.500
> ?4: 0.000, 0.500, -0.500
> ?5: 0.500, 0.500, 0.000
> ?6: -0.500, 0.500, 0.000
> ?7: 1.000, 0.000, 1.000
> ?8: -1.000, 0.000, 1.000
> ?9: 0.000, 1.000, 1.000
> ?10: 0.000, 1.000, -1.000
> ?11: 1.000, 1.000, 0.000
> ?12: -1.000, 1.000, 0.000
>
> After I click "OK" on the error message, DTI Studio does not crash.
> Typically, only a portion of the brain is displayed (e.g., the
> inferior portion).
>
> B values used are 0,600,1200. ?I have tried the following gradient
> with similar results:
> ?0: 0.000, 0.000, 0.000,600
> ?1: 0.500, 0.000, 0.500,600
> ?2: -0.500, 0.000, 0.500,600
> ?3: 0.000, 0.500, 0.500,600
> ?4: 0.000, 0.500, -0.500,600
> ?5: 0.500, 0.500, 0.000,600
> ?6: -0.500, 0.500, 0.000,600
> ?7: 1.000, 0.000, 1.000,600
> ?8: -1.000, 0.000, 1.000,600
> ?9: 0.000, 1.000, 1.000,600
> ?10: 0.000, 1.000, -1.000,600
> ?11: 1.000, 1.000, 0.000,600
> ?12: -1.000, 1.000, 0.000,600
> 13: 0.500, 0.000, 0.500,1200
> 14: -0.500, 0.000, 0.500,1200
> 15: 0.000, 0.500, 0.500,1200
> 16: 0.000, 0.500, -0.500,1200
> 17: 0.500, 0.500, 0.000,1200
> 18: -0.500, 0.500, 0.000,1200
> 19: 1.000, 0.000, 1.000,1200
> 20: -1.000, 0.000, 1.000,1200
> 21: 0.000, 1.000, 1.000,1200
> 22: 0.000, 1.000, -1.000,1200
> 23: 1.000, 1.000, 0.000,1200
> 24: -1.000, 1.000, 0.000,1200
>
> The error message then has the number of gradients =25, with the same
> number of repetitions and images.
>
> Thank you for helping me use these datasets.
>
> 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
>


From kevinspitler at ucla.edu  Wed Apr 20 07:31:20 2011
From: kevinspitler at ucla.edu (Kevin Spitler)
Date: Wed, 20 Apr 2011 04:31:20 -0700
Subject: [Mristudio-users] gradient for GE Signa HDx
Message-ID: <BANLkTimU9LNj_NDum5M3Xr2CZ8zG_bkWeA@mail.gmail.com>

Hello,

What gradient is used for DTIStudio for a GE Signa HDx?  The parameters are
12 directions
2 b values, including 1000

Thank you for your help

Best,
Kevin

From Malek.Makki at kispi.uzh.ch  Wed Apr 20 08:46:09 2011
From: Malek.Makki at kispi.uzh.ch (Makki Malek)
Date: Wed, 20 Apr 2011 14:46:09 +0200
Subject: [Mristudio-users] gradient for GE Signa HDx
In-Reply-To: <BANLkTimU9LNj_NDum5M3Xr2CZ8zG_bkWeA@mail.gmail.com>
Message-ID: <FD1E6887BC99C341800CBFD7ABC2F9C2029769C7@exzh1.kispi.int>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256


Hi Kevin

 Below the 12D scheme on our HDxt. Unless you modified the sequence,
your 2 b0 set of data are acquired first in  a GE system.


1.000000 0.000000 0.000000
0.726000 0.688000 0.000000
0.167000 -0.199000 0.966000
0.732000 -0.619000 -0.284000
- -0.239000 -0.710000 0.662000
- -0.759000 -0.223000 0.612000
0.544000 0.480000 0.688000
0.079000 0.997000 -0.005000
0.773000 -0.183000 0.608000
0.485000 -0.782000 0.392000
0.081000 -0.788000 -0.611000
0.363000 -0.245000 -0.899000


~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Malek I. Makki, PhD
Diagnostic Imaging Department
MRI Center
Kinderspital Zurich
 
Phone. +41(0)44 266 3130
Fax:      +41(0)44 266 7153
malek.makki at kispi.uzh.ch
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~



- -----Original Message-----
From: mristudio-users-bounces at mristudio.org
[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Kevin
Spitler
Sent: Wednesday, April 20, 2011 1:31 PM
To: Mristudio-users at mristudio.org
Subject: [Mristudio-users] gradient for GE Signa HDx

Hello,

What gradient is used for DTIStudio for a GE Signa HDx?  The parameters
are
12 directions
2 b values, including 1000

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

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From choisj70 at gmail.com  Fri Apr 22 16:05:22 2011
From: choisj70 at gmail.com (Seongjin)
Date: Fri, 22 Apr 2011 16:05:22 -0400
Subject: [Mristudio-users] gradient table
Message-ID: <BANLkTimncRg9hy+mbPxNsTKH9JGpYx7_fg@mail.gmail.com>

Dear DTI studio users,

I am working with Philips Scanner.
I use the web link for gradient table (
http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html) for
typical Philips gradient table (low, medium, high).
Recently I am using the customized gradient table.
I wonder if I need to perform the gradient flip or not when the customized
gradient table is used in DTI studio.

Thanks in advance,
SC
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From susumu at mri.jhu.edu  Fri Apr 22 18:12:02 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Fri, 22 Apr 2011 18:12:02 -0400
Subject: [Mristudio-users] gradient table
In-Reply-To: <BANLkTimncRg9hy+mbPxNsTKH9JGpYx7_fg@mail.gmail.com>
References: <BANLkTimncRg9hy+mbPxNsTKH9JGpYx7_fg@mail.gmail.com>
Message-ID: <BANLkTikd=d_Fn61tcrFH262UPU6RqFnmMA@mail.gmail.com>

Hi SC,

I believe you need to, but I recommend you to check it.
After calculating a tensor field, perform some fiber tracking like
corpus callosum and fornix. If there is any error in "flip", you can
immediately tell.

Also, I would suggest you to calculate "theory" image and "fitting
error" images. If you make any mistake in gradient table (not the
consistent sign flip but typo in a single (or multiple) table row),
you can find it due to a consistent fitting error in one of the DWIs
throughout the all slices.

Susumu

On Fri, Apr 22, 2011 at 4:05 PM, [Seongjin] <choisj70 at gmail.com> wrote:
> Dear DTI studio users,
>
> I am working with Philips Scanner.
> I use the web link for gradient table
> (http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html) for
> typical Philips gradient table (low, medium, high).
> Recently I am using the customized gradient table.
> I wonder if I need to perform the gradient flip or not when the customized
> gradient table is used in 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
>
>

From choisj70 at gmail.com  Fri Apr 22 21:12:55 2011
From: choisj70 at gmail.com (Seongjin)
Date: Fri, 22 Apr 2011 21:12:55 -0400
Subject: [Mristudio-users] gradient table
In-Reply-To: <BANLkTikd=d_Fn61tcrFH262UPU6RqFnmMA@mail.gmail.com>
References: <BANLkTimncRg9hy+mbPxNsTKH9JGpYx7_fg@mail.gmail.com>
	<BANLkTikd=d_Fn61tcrFH262UPU6RqFnmMA@mail.gmail.com>
Message-ID: <BANLkTimO965QM89Bg2qAuAWasX8a_nCpgw@mail.gmail.com>

I appreciate your reply to my query.

best,
SC

On Fri, Apr 22, 2011 at 6:12 PM, susumu mori <susumu at mri.jhu.edu> wrote:

> Hi SC,
>
> I believe you need to, but I recommend you to check it.
> After calculating a tensor field, perform some fiber tracking like
> corpus callosum and fornix. If there is any error in "flip", you can
> immediately tell.
>
> Also, I would suggest you to calculate "theory" image and "fitting
> error" images. If you make any mistake in gradient table (not the
> consistent sign flip but typo in a single (or multiple) table row),
> you can find it due to a consistent fitting error in one of the DWIs
> throughout the all slices.
>
> Susumu
>
> On Fri, Apr 22, 2011 at 4:05 PM, [Seongjin] <choisj70 at gmail.com> wrote:
> > Dear DTI studio users,
> >
> > I am working with Philips Scanner.
> > I use the web link for gradient table
> > (http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html) for
> > typical Philips gradient table (low, medium, high).
> > Recently I am using the customized gradient table.
> > I wonder if I need to perform the gradient flip or not when the
> customized
> > gradient table is used in 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
>
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From zimer at post.tau.ac.il  Sun Apr 24 05:24:26 2011
From: zimer at post.tau.ac.il (Gali)
Date: Sun, 24 Apr 2011 12:24:26 +0300
Subject: [Mristudio-users] performing fiber tracking on a nifti file
Message-ID: <E9B6ED49A31C43CCA769B3109B85A4C7@galipc>

Hello all

How can I perform fiber tracking in DTIstudio on a brain data saved in a
nifti format?

(I am trying to use "DTI mapping" but not one of the format options seem to
match NIFTI)

Thanks!

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From Manuel.Kager.RAD08 at fh-joanneum.at  Sun Apr 24 07:16:05 2011
From: Manuel.Kager.RAD08 at fh-joanneum.at (Kager Manuel)
Date: Sun, 24 Apr 2011 13:16:05 +0200
Subject: [Mristudio-users] performing fiber tracking on a nifti file
References: <E9B6ED49A31C43CCA769B3109B85A4C7@galipc>
Message-ID: <111D34A74180884EA7AA4A564EBBF08D16299040@OLYMPIA.technikum.fh-joanneum.local>




-----Urspr?ngliche Nachricht-----
Von: mristudio-users-bounces at mristudio.org im Auftrag von Gali
Gesendet: So 24.04.2011 11:24
An: mristudio-users at mristudio.org
Betreff: [Mristudio-users] performing fiber tracking on a nifti file
 
Hello all

How can I perform fiber tracking in DTIstudio on a brain data saved in a
nifti format?

(I am trying to use "DTI mapping" but not one of the format options seem to
match NIFTI)

Thanks!


MR Icron is a good software where you can convert Dicom files (an example) to NIfti files. 




FH JOANNEUM Gesellschaft mbH
Rechtsform/Legal form: GmbH
Firmenbuchgericht/Court of registry: Landesgericht f?r ZRS Graz
Firmenbuchnummer/Company registration: FN 125888 f
DVR: 0813559
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From susumu at mri.jhu.edu  Sun Apr 24 07:35:41 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Sun, 24 Apr 2011 07:35:41 -0400
Subject: [Mristudio-users] performing fiber tracking on a nifti file
In-Reply-To: <E9B6ED49A31C43CCA769B3109B85A4C7@galipc>
References: <E9B6ED49A31C43CCA769B3109B85A4C7@galipc>
Message-ID: <BANLkTim-i-7=H5RS_EeTMJVTwteSnS8bsQ@mail.gmail.com>

You can open Nifti by Mri3DView and save it as "REC" format by saving
all images into one file. This is a raw format without a header. So,
you have to remember image dimensions. DtiMapping, then, can read it.
You may be able to save the loaded Nifti images as a 4D Analyze too,
but I'm not sure, if DtiMapping can properly read it.

On Sun, Apr 24, 2011 at 5:24 AM, Gali <zimer at post.tau.ac.il> wrote:
> Hello all
>
> How can I perform fiber tracking in DTIstudio on a brain data saved in a
> nifti format?
>
> (I am trying to use "DTI mapping" but not one of the format options seem to
> match NIFTI)
>
> Thanks!
>
> _______________________________________________
> mristudio-users mailing 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 zhongchongguang at msn.com  Sun Apr 24 11:28:30 2011
From: zhongchongguang at msn.com (zhongchongguang)
Date: Sun, 24 Apr 2011 23:28:30 +0800
Subject: [Mristudio-users] How to perform fiber tracking from a struct ROI
Message-ID: <BLU0-SMTP50BA77521DF3754C6C550AA6970@phx.gbl>


Dear DTI studio users,

I want to perform fiber tracking from a struct ROI, rather than drawing ROI on a slice with mouse. Could someone can tell me how to do this? And I want to know that whether the DTI studio can perform tracking from ROI A to ROI B, from ROI B to ROI A and between ROI A and ROI B, like Brain Voyager software.


Thanks?
Best regards

Chongguang Zhong
Intelligent Medical Research Center
Institute of Automation, Chinese Academy of Sciences


2011-03-08 
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From kevinspitler at ucla.edu  Sun Apr 24 16:43:50 2011
From: kevinspitler at ucla.edu (Kevin Spitler)
Date: Sun, 24 Apr 2011 13:43:50 -0700
Subject: [Mristudio-users] gradient for GE Signa HDx
In-Reply-To: <FD1E6887BC99C341800CBFD7ABC2F9C2029769C7@exzh1.kispi.int>
References: <BANLkTimU9LNj_NDum5M3Xr2CZ8zG_bkWeA@mail.gmail.com>
	<FD1E6887BC99C341800CBFD7ABC2F9C2029769C7@exzh1.kispi.int>
Message-ID: <BANLkTimM6jmuP=p_Z9Az0BnJz6kn_ApXxg@mail.gmail.com>

Thank you Dr. Makki.  The datasets load in DTIStudio now with a good
color map 0.

I have a problem with tractography, when I attempt to do pathways
thattravel in the rostral-caudal plane.  For example, in attempts of
the
Inferior longitudinal fasciculus and the anterior thalamic radiation,
using the Wakana et al., 2007 methods, the resultant tractography only
travels in the Superior-Inferior plane, and these tracts have
signifcant rostro-caudal projection.  Would this hint at a specific
problem in the way I load of the data?  (images of the tractography
are too large to send to the group)

I am using the gradient from Dr. Makki with format modification with
gradient line number and a colon:
0: 0,0,0
1: 1.000000 0.000000 0.000000
2: 0.726000 0.688000 0.000000
3: 0.167000 -0.199000 0.966000
4: 0.732000 -0.619000 -0.284000
5: -0.239000 -0.710000 0.662000
6: -0.759000 -0.223000 0.612000
7:  0.544000 0.480000 0.688000
8:  0.079000 0.997000 -0.005000
9:  0.773000 -0.183000 0.608000
10: 0.485000 -0.782000 0.392000
11: 0.081000 -0.788000 -0.611000
12: 0.363000 -0.245000 -0.899000

For Fiber Tracing, I click the "X-component" on the Flip Eigen Vector.

I typically analyze data from a Siemens machine, so I am having
trouble with this data and appreciate your help.

Best,
Kevin

On Wed, Apr 20, 2011 at 5:46 AM, Makki Malek <Malek.Makki at kispi.uzh.ch> wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA256
>
>
> Hi Kevin
>
> ?Below the 12D scheme on our HDxt. Unless you modified the sequence,
> your 2 b0 set of data are acquired first in ?a GE system.
>
>
> 1.000000 0.000000 0.000000
> 0.726000 0.688000 0.000000
> 0.167000 -0.199000 0.966000
> 0.732000 -0.619000 -0.284000
> - -0.239000 -0.710000 0.662000
> - -0.759000 -0.223000 0.612000
> 0.544000 0.480000 0.688000
> 0.079000 0.997000 -0.005000
> 0.773000 -0.183000 0.608000
> 0.485000 -0.782000 0.392000
> 0.081000 -0.788000 -0.611000
> 0.363000 -0.245000 -0.899000
>
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Malek I. Makki, PhD
> Diagnostic Imaging Department
> MRI Center
> Kinderspital Zurich
>
> Phone. +41(0)44 266 3130
> Fax: ? ? ?+41(0)44 266 7153
> malek.makki at kispi.uzh.ch
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
>
>
> - -----Original Message-----
> From: mristudio-users-bounces at mristudio.org
> [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Kevin
> Spitler
> Sent: Wednesday, April 20, 2011 1:31 PM
> To: Mristudio-users at mristudio.org
> Subject: [Mristudio-users] gradient for GE Signa HDx
>
> Hello,
>
> What gradient is used for DTIStudio for a GE Signa HDx? ?The parameters
> are
> 12 directions
> 2 b values, including 1000
>
> 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
>
> -----BEGIN PGP SIGNATURE-----
> Version: PGP Universal 3.1.0 (Build 860)
> Charset: us-ascii
>
> wsBVAwUBTa7VkUf0hhcdLXEYAQi4+QgAtBqC+4hwhla9syA97C/gWeaCMnmWn43u
> up0lpnntg2cRr755ibvdlRDu9Qd1l83o14OkyeWB5fZ7Rxb3WIC/V0iF0ffo5sSK
> UXDFIn1DKBx17gXYiDCS52JJ48Qu3uAALNImwLFGNnMhIT3YAH/5f2rTFpZnss8k
> 1VnvKvwL47Eek1SSMPc6AoVD+7KIicgJwGvR0/4Y1TrVGuMjdXnCyTQoc1j3QK2y
> k3htT6c70Hv+9jDjmd45GKG8AuKK6mO7j8b3wEIcY7mGEB8rX7Omn4DhXA/N/Syt
> iAg4fK5MgDNREyZpjNaPpbOnkFJqzYOEPot9lWvH398cUvwLYDGXVw==
> =O8Dg
> -----END PGP SIGNATURE-----
> _______________________________________________
> mristudio-users mailing 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  Sun Apr 24 22:40:21 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Sun, 24 Apr 2011 22:40:21 -0400
Subject: [Mristudio-users] gradient for GE Signa HDx
In-Reply-To: <BANLkTimM6jmuP=p_Z9Az0BnJz6kn_ApXxg@mail.gmail.com>
References: <BANLkTimU9LNj_NDum5M3Xr2CZ8zG_bkWeA@mail.gmail.com>
	<FD1E6887BC99C341800CBFD7ABC2F9C2029769C7@exzh1.kispi.int>
	<BANLkTimM6jmuP=p_Z9Az0BnJz6kn_ApXxg@mail.gmail.com>
Message-ID: <BANLkTik5ZF9fRpyc4OG0CTjn1KqxV5S5Pg@mail.gmail.com>

Hi Kevin,

sometimes, gradient table signs are already corrected. Have you tried
Makki's table without X-flip?

Susumu

On Sun, Apr 24, 2011 at 4:43 PM, Kevin Spitler <kevinspitler at ucla.edu> wrote:
> Thank you Dr. Makki. ?The datasets load in DTIStudio now with a good
> color map 0.
>
> I have a problem with tractography, when I attempt to do pathways
> thattravel in the rostral-caudal plane. ?For example, in attempts of
> the
> Inferior longitudinal fasciculus and the anterior thalamic radiation,
> using the Wakana et al., 2007 methods, the resultant tractography only
> travels in the Superior-Inferior plane, and these tracts have
> signifcant rostro-caudal projection. ?Would this hint at a specific
> problem in the way I load of the data? ?(images of the tractography
> are too large to send to the group)
>
> I am using the gradient from Dr. Makki with format modification with
> gradient line number and a colon:
> 0: 0,0,0
> 1: 1.000000 0.000000 0.000000
> 2: 0.726000 0.688000 0.000000
> 3: 0.167000 -0.199000 0.966000
> 4: 0.732000 -0.619000 -0.284000
> 5: -0.239000 -0.710000 0.662000
> 6: -0.759000 -0.223000 0.612000
> 7: ?0.544000 0.480000 0.688000
> 8: ?0.079000 0.997000 -0.005000
> 9: ?0.773000 -0.183000 0.608000
> 10: 0.485000 -0.782000 0.392000
> 11: 0.081000 -0.788000 -0.611000
> 12: 0.363000 -0.245000 -0.899000
>
> For Fiber Tracing, I click the "X-component" on the Flip Eigen Vector.
>
> I typically analyze data from a Siemens machine, so I am having
> trouble with this data and appreciate your help.
>
> Best,
> Kevin
>
> On Wed, Apr 20, 2011 at 5:46 AM, Makki Malek <Malek.Makki at kispi.uzh.ch> wrote:
>> -----BEGIN PGP SIGNED MESSAGE-----
>> Hash: SHA256
>>
>>
>> Hi Kevin
>>
>> ?Below the 12D scheme on our HDxt. Unless you modified the sequence,
>> your 2 b0 set of data are acquired first in ?a GE system.
>>
>>
>> 1.000000 0.000000 0.000000
>> 0.726000 0.688000 0.000000
>> 0.167000 -0.199000 0.966000
>> 0.732000 -0.619000 -0.284000
>> - -0.239000 -0.710000 0.662000
>> - -0.759000 -0.223000 0.612000
>> 0.544000 0.480000 0.688000
>> 0.079000 0.997000 -0.005000
>> 0.773000 -0.183000 0.608000
>> 0.485000 -0.782000 0.392000
>> 0.081000 -0.788000 -0.611000
>> 0.363000 -0.245000 -0.899000
>>
>>
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> Malek I. Makki, PhD
>> Diagnostic Imaging Department
>> MRI Center
>> Kinderspital Zurich
>>
>> Phone. +41(0)44 266 3130
>> Fax: ? ? ?+41(0)44 266 7153
>> malek.makki at kispi.uzh.ch
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>
>>
>>
>> - -----Original Message-----
>> From: mristudio-users-bounces at mristudio.org
>> [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Kevin
>> Spitler
>> Sent: Wednesday, April 20, 2011 1:31 PM
>> To: Mristudio-users at mristudio.org
>> Subject: [Mristudio-users] gradient for GE Signa HDx
>>
>> Hello,
>>
>> What gradient is used for DTIStudio for a GE Signa HDx? ?The parameters
>> are
>> 12 directions
>> 2 b values, including 1000
>>
>> 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
>>
>> -----BEGIN PGP SIGNATURE-----
>> Version: PGP Universal 3.1.0 (Build 860)
>> Charset: us-ascii
>>
>> wsBVAwUBTa7VkUf0hhcdLXEYAQi4+QgAtBqC+4hwhla9syA97C/gWeaCMnmWn43u
>> up0lpnntg2cRr755ibvdlRDu9Qd1l83o14OkyeWB5fZ7Rxb3WIC/V0iF0ffo5sSK
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>> 1VnvKvwL47Eek1SSMPc6AoVD+7KIicgJwGvR0/4Y1TrVGuMjdXnCyTQoc1j3QK2y
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>> iAg4fK5MgDNREyZpjNaPpbOnkFJqzYOEPot9lWvH398cUvwLYDGXVw==
>> =O8Dg
>> -----END PGP SIGNATURE-----
>> _______________________________________________
>> mristudio-users mailing 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 Malek.Makki at kispi.uzh.ch  Mon Apr 25 01:57:51 2011
From: Malek.Makki at kispi.uzh.ch (Makki Malek)
Date: Mon, 25 Apr 2011 07:57:51 +0200
Subject: [Mristudio-users] gradient for GE Signa HDx
References: <BANLkTimU9LNj_NDum5M3Xr2CZ8zG_bkWeA@mail.gmail.com>
	<FD1E6887BC99C341800CBFD7ABC2F9C2029769C7@exzh1.kispi.int>
	<BANLkTimM6jmuP=p_Z9Az0BnJz6kn_ApXxg@mail.gmail.com>
	<BANLkTik5ZF9fRpyc4OG0CTjn1KqxV5S5Pg@mail.gmail.com>
Message-ID: <FD1E6887BC99C341800CBFD7ABC2F9C20267FCDC@exzh1.kispi.int>

Hi Susumo
Hi Kevin
 
The table is used wthout any flip. For fiber-tracking, I apply  z-flip (not x-sflip), and perfom this on well known tract.
 
Regards
 

________________________________

From: mristudio-users-bounces at mristudio.org on behalf of susumu mori
Sent: Mon 4/25/2011 4:40 AM
To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
Subject: Re: [Mristudio-users] gradient for GE Signa HDx



Hi Kevin,

sometimes, gradient table signs are already corrected. Have you tried
Makki's table without X-flip?

Susumu

On Sun, Apr 24, 2011 at 4:43 PM, Kevin Spitler <kevinspitler at ucla.edu> wrote:
> Thank you Dr. Makki.  The datasets load in DTIStudio now with a good
> color map 0.
>
> I have a problem with tractography, when I attempt to do pathways
> thattravel in the rostral-caudal plane.  For example, in attempts of
> the
> Inferior longitudinal fasciculus and the anterior thalamic radiation,
> using the Wakana et al., 2007 methods, the resultant tractography only
> travels in the Superior-Inferior plane, and these tracts have
> signifcant rostro-caudal projection.  Would this hint at a specific
> problem in the way I load of the data?  (images of the tractography
> are too large to send to the group)
>
> I am using the gradient from Dr. Makki with format modification with
> gradient line number and a colon:
> 0: 0,0,0
> 1: 1.000000 0.000000 0.000000
> 2: 0.726000 0.688000 0.000000
> 3: 0.167000 -0.199000 0.966000
> 4: 0.732000 -0.619000 -0.284000
> 5: -0.239000 -0.710000 0.662000
> 6: -0.759000 -0.223000 0.612000
> 7:  0.544000 0.480000 0.688000
> 8:  0.079000 0.997000 -0.005000
> 9:  0.773000 -0.183000 0.608000
> 10: 0.485000 -0.782000 0.392000
> 11: 0.081000 -0.788000 -0.611000
> 12: 0.363000 -0.245000 -0.899000
>
> For Fiber Tracing, I click the "X-component" on the Flip Eigen Vector.
>
> I typically analyze data from a Siemens machine, so I am having
> trouble with this data and appreciate your help.
>
> Best,
> Kevin
>
> On Wed, Apr 20, 2011 at 5:46 AM, Makki Malek <Malek.Makki at kispi.uzh.ch> wrote:
>> -----BEGIN PGP SIGNED MESSAGE-----
>> Hash: SHA256
>>
>>
>> Hi Kevin
>>
>>  Below the 12D scheme on our HDxt. Unless you modified the sequence,
>> your 2 b0 set of data are acquired first in  a GE system.
>>
>>
>> 1.000000 0.000000 0.000000
>> 0.726000 0.688000 0.000000
>> 0.167000 -0.199000 0.966000
>> 0.732000 -0.619000 -0.284000
>> - -0.239000 -0.710000 0.662000
>> - -0.759000 -0.223000 0.612000
>> 0.544000 0.480000 0.688000
>> 0.079000 0.997000 -0.005000
>> 0.773000 -0.183000 0.608000
>> 0.485000 -0.782000 0.392000
>> 0.081000 -0.788000 -0.611000
>> 0.363000 -0.245000 -0.899000
>>
>>
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> Malek I. Makki, PhD
>> Diagnostic Imaging Department
>> MRI Center
>> Kinderspital Zurich
>>
>> Phone. +41(0)44 266 3130
>> Fax:      +41(0)44 266 7153
>> malek.makki at kispi.uzh.ch
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>
>>
>>
>> - -----Original Message-----
>> From: mristudio-users-bounces at mristudio.org
>> [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Kevin
>> Spitler
>> Sent: Wednesday, April 20, 2011 1:31 PM
>> To: Mristudio-users at mristudio.org
>> Subject: [Mristudio-users] gradient for GE Signa HDx
>>
>> Hello,
>>
>> What gradient is used for DTIStudio for a GE Signa HDx?  The parameters
>> are
>> 12 directions
>> 2 b values, including 1000
>>
>> 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
>>
>> -----BEGIN PGP SIGNATURE-----
>> Version: PGP Universal 3.1.0 (Build 860)
>> Charset: us-ascii
>>
>> wsBVAwUBTa7VkUf0hhcdLXEYAQi4+QgAtBqC+4hwhla9syA97C/gWeaCMnmWn43u
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>> UXDFIn1DKBx17gXYiDCS52JJ48Qu3uAALNImwLFGNnMhIT3YAH/5f2rTFpZnss8k
>> 1VnvKvwL47Eek1SSMPc6AoVD+7KIicgJwGvR0/4Y1TrVGuMjdXnCyTQoc1j3QK2y
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>> iAg4fK5MgDNREyZpjNaPpbOnkFJqzYOEPot9lWvH398cUvwLYDGXVw==
>> =O8Dg
>> -----END PGP SIGNATURE-----
>> _______________________________________________
>> mristudio-users mailing 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



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From hjiang at jhmi.edu  Mon Apr 25 09:49:00 2011
From: hjiang at jhmi.edu (Hangyi Jiang)
Date: Mon, 25 Apr 2011 09:49:00 -0400
Subject: [Mristudio-users] How to perform fiber tracking from a struct
	ROI
In-Reply-To: <BLU0-SMTP50BA77521DF3754C6C550AA6970@phx.gbl>
References: <BLU0-SMTP50BA77521DF3754C6C550AA6970@phx.gbl>
Message-ID: <145933A2BE9E4F48AE079A201379BF2F24498EB037@RAD-EXCH1.win.ad.jhu.edu>

hi Chongguand,

I supposed that you want to use your ROIs (which are created outside of DtiStudio) for fiber tracking (actually, fiber selection).  if so,  you can do it by loading the ROIs as "binary map" when you clicking the ROI-load button of the "ROI-Operation" section in the "fiber" tab.  to learn how does "binary image map" works, you can draw some ROIs and save them as "binary map" using "ROI-Save" button. you will get a .map file, which is a text file.  read it and get some ideas, then edit it for your purpose.  you can also find dome info. about it in our old emailing list.

anyway, let me know if you need more help.

thand you,

hangyi


________________________________
From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of zhongchongguang [zhongchongguang at msn.com]
Sent: Sunday, April 24, 2011 11:28 AM
To: mristudio-users
Subject: [Mristudio-users] How to perform fiber tracking from a struct ROI


Dear DTI studio users,

I want to perform fiber tracking from a struct ROI, rather than drawing ROI on a slice with mouse. Could someone can tell me how to do this? And I want to know that whether the DTI studio can perform tracking from ROI A to ROI B, from ROI B to ROI A and between ROI A and ROI B, like Brain Voyager software.

Thanks?
Best regards

Chongguang Zhong
Intelligent Medical Research Center
Institute of Automation, Chinese Academy of Sciences


2011-03-08
________________________________


From kevinspitler at ucla.edu  Mon Apr 25 14:05:55 2011
From: kevinspitler at ucla.edu (Kevin Spitler)
Date: Mon, 25 Apr 2011 11:05:55 -0700
Subject: [Mristudio-users] gradient for GE Signa HDx
In-Reply-To: <FD1E6887BC99C341800CBFD7ABC2F9C20267FCDC@exzh1.kispi.int>
References: <BANLkTimU9LNj_NDum5M3Xr2CZ8zG_bkWeA@mail.gmail.com>
	<FD1E6887BC99C341800CBFD7ABC2F9C2029769C7@exzh1.kispi.int>
	<BANLkTimM6jmuP=p_Z9Az0BnJz6kn_ApXxg@mail.gmail.com>
	<BANLkTik5ZF9fRpyc4OG0CTjn1KqxV5S5Pg@mail.gmail.com>
	<FD1E6887BC99C341800CBFD7ABC2F9C20267FCDC@exzh1.kispi.int>
Message-ID: <BANLkTin7Ufc0CkKffo1dGThif=KXPBNhuA@mail.gmail.com>

Thank you Drs Makki and Mori and all the forum very much.

I am able to do fiber tracking with a Z flip.

Best,
Kevin

On Sun, Apr 24, 2011 at 10:57 PM, Makki Malek <Malek.Makki at kispi.uzh.ch> wrote:
> Hi Susumo
> Hi Kevin
>
> The table is used wthout any flip. For fiber-tracking,?I apply? z-flip (not
> x-sflip), and perfom?this on well known?tract.
>
> Regards
>
> ________________________________
> From: mristudio-users-bounces at mristudio.org on behalf of susumu mori
> Sent: Mon 4/25/2011 4:40 AM
> To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
> Subject: Re: [Mristudio-users] gradient for GE Signa HDx
>
> Hi Kevin,
>
> sometimes, gradient table signs are already corrected. Have you tried
> Makki's table without X-flip?
>
> Susumu
>
> On Sun, Apr 24, 2011 at 4:43 PM, Kevin Spitler <kevinspitler at ucla.edu>
> wrote:
>> Thank you Dr. Makki. ?The datasets load in DTIStudio now with a good
>> color map 0.
>>
>> I have a problem with tractography, when I attempt to do pathways
>> thattravel in the rostral-caudal plane. ?For example, in attempts of
>> the
>> Inferior longitudinal fasciculus and the anterior thalamic radiation,
>> using the Wakana et al., 2007 methods, the resultant tractography only
>> travels in the Superior-Inferior plane, and these tracts have
>> signifcant rostro-caudal projection. ?Would this hint at a specific
>> problem in the way I load of the data? ?(images of the tractography
>> are too large to send to the group)
>>
>> I am using the gradient from Dr. Makki with format modification with
>> gradient line number and a colon:
>> 0: 0,0,0
>> 1: 1.000000 0.000000 0.000000
>> 2: 0.726000 0.688000 0.000000
>> 3: 0.167000 -0.199000 0.966000
>> 4: 0.732000 -0.619000 -0.284000
>> 5: -0.239000 -0.710000 0.662000
>> 6: -0.759000 -0.223000 0.612000
>> 7: ?0.544000 0.480000 0.688000
>> 8: ?0.079000 0.997000 -0.005000
>> 9: ?0.773000 -0.183000 0.608000
>> 10: 0.485000 -0.782000 0.392000
>> 11: 0.081000 -0.788000 -0.611000
>> 12: 0.363000 -0.245000 -0.899000
>>
>> For Fiber Tracing, I click the "X-component" on the Flip Eigen Vector.
>>
>> I typically analyze data from a Siemens machine, so I am having
>> trouble with this data and appreciate your help.
>>
>> Best,
>> Kevin
>>
>> On Wed, Apr 20, 2011 at 5:46 AM, Makki Malek <Malek.Makki at kispi.uzh.ch>
>> wrote:
>>> -----BEGIN PGP SIGNED MESSAGE-----
>>> Hash: SHA256
>>>
>>>
>>> Hi Kevin
>>>
>>> ?Below the 12D scheme on our HDxt. Unless you modified the sequence,
>>> your 2 b0 set of data are acquired first in ?a GE system.
>>>
>>>
>>> 1.000000 0.000000 0.000000
>>> 0.726000 0.688000 0.000000
>>> 0.167000 -0.199000 0.966000
>>> 0.732000 -0.619000 -0.284000
>>> - -0.239000 -0.710000 0.662000
>>> - -0.759000 -0.223000 0.612000
>>> 0.544000 0.480000 0.688000
>>> 0.079000 0.997000 -0.005000
>>> 0.773000 -0.183000 0.608000
>>> 0.485000 -0.782000 0.392000
>>> 0.081000 -0.788000 -0.611000
>>> 0.363000 -0.245000 -0.899000
>>>
>>>
>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>> Malek I. Makki, PhD
>>> Diagnostic Imaging Department
>>> MRI Center
>>> Kinderspital Zurich
>>>
>>> Phone. +41(0)44 266 3130
>>> Fax: ? ? ?+41(0)44 266 7153
>>> malek.makki at kispi.uzh.ch
>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>>
>>>
>>>
>>> - -----Original Message-----
>>> From: mristudio-users-bounces at mristudio.org
>>> [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Kevin
>>> Spitler
>>> Sent: Wednesday, April 20, 2011 1:31 PM
>>> To: Mristudio-users at mristudio.org
>>> Subject: [Mristudio-users] gradient for GE Signa HDx
>>>
>>> Hello,
>>>
>>> What gradient is used for DTIStudio for a GE Signa HDx? ?The parameters
>>> are
>>> 12 directions
>>> 2 b values, including 1000
>>>
>>> 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
>>>
>>> -----BEGIN PGP SIGNATURE-----
>>> Version: PGP Universal 3.1.0 (Build 860)
>>> Charset: us-ascii
>>>
>>> wsBVAwUBTa7VkUf0hhcdLXEYAQi4+QgAtBqC+4hwhla9syA97C/gWeaCMnmWn43u
>>> up0lpnntg2cRr755ibvdlRDu9Qd1l83o14OkyeWB5fZ7Rxb3WIC/V0iF0ffo5sSK
>>> UXDFIn1DKBx17gXYiDCS52JJ48Qu3uAALNImwLFGNnMhIT3YAH/5f2rTFpZnss8k
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>>> =O8Dg
>>> -----END PGP SIGNATURE-----
>>> _______________________________________________
>>> mristudio-users mailing 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  Mon Apr 25 14:32:57 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Mon, 25 Apr 2011 14:32:57 -0400
Subject: [Mristudio-users] How to perform fiber tracking from a struct
	ROI
In-Reply-To: <145933A2BE9E4F48AE079A201379BF2F24498EB037@RAD-EXCH1.win.ad.jhu.edu>
References: <BLU0-SMTP50BA77521DF3754C6C550AA6970@phx.gbl>
	<145933A2BE9E4F48AE079A201379BF2F24498EB037@RAD-EXCH1.win.ad.jhu.edu>
Message-ID: <BANLkTikFf4gx0-EMcA9=oq2zU+=eXy3YCw@mail.gmail.com>

also, please check Q16 at https://www.mristudio.org/wiki/faq

2011/4/25 Hangyi Jiang <hjiang at jhmi.edu>:
> hi Chongguand,
>
> I supposed that you want to use your ROIs (which are created outside of DtiStudio) for fiber tracking (actually, fiber selection). ?if so, ?you can do it by loading the ROIs as "binary map" when you clicking the ROI-load button of the "ROI-Operation" section in the "fiber" tab. ?to learn how does "binary image map" works, you can draw some ROIs and save them as "binary map" using "ROI-Save" button. you will get a .map file, which is a text file. ?read it and get some ideas, then edit it for your purpose. ?you can also find dome info. about it in our old emailing list.
>
> anyway, let me know if you need more help.
>
> thand you,
>
> hangyi
>
>
> ________________________________
> From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of zhongchongguang [zhongchongguang at msn.com]
> Sent: Sunday, April 24, 2011 11:28 AM
> To: mristudio-users
> Subject: [Mristudio-users] How to perform fiber tracking from a struct ROI
>
>
> Dear DTI studio users,
>
> I want to perform fiber tracking from a struct ROI, rather than drawing ROI on a slice with mouse. Could someone can tell me how to do this? And I want to know that whether the DTI studio can perform tracking from ROI A to ROI B, from ROI B to ROI A and between ROI A and ROI B, like Brain Voyager software.
>
> Thanks?
> Best regards
>
> Chongguang Zhong
> Intelligent Medical Research Center
> Institute of Automation, Chinese Academy of Sciences
>
>
> 2011-03-08
> ________________________________
>
> _______________________________________________
> mristudio-users mailing 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 Karan.Shukla at uth.tmc.edu  Mon Apr 25 14:34:18 2011
From: Karan.Shukla at uth.tmc.edu (Shukla, Karan)
Date: Mon, 25 Apr 2011 13:34:18 -0500
Subject: [Mristudio-users] "Out of memory"
Message-ID: <440E0EC90CCF104283C8BF9A9BEE111E06C786E675@UTHCMS2.uthouston.edu>

Hello,

I am working with DTI Studio on windows 7 XP mode and I am receiving an "Out of Memory" pop up when I am trying to calculate the tensor, color map, etc. Are there any settings to be be adjusted so that my memory space may be increased or cleared?

Thanks

Karan
UT Houston


From susumu at mri.jhu.edu  Mon Apr 25 14:45:34 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Mon, 25 Apr 2011 14:45:34 -0400
Subject: [Mristudio-users] "Out of memory"
In-Reply-To: <440E0EC90CCF104283C8BF9A9BEE111E06C786E675@UTHCMS2.uthouston.edu>
References: <440E0EC90CCF104283C8BF9A9BEE111E06C786E675@UTHCMS2.uthouston.edu>
Message-ID: <BANLkTi=iSOf02DR52QjdJEqhrgYqemnPAg@mail.gmail.com>

Hi Karen,

I encourage you to use the 64-bit version of Windows. The 32-bit
version can allocate 1-1.5 GB memory to a single program no matter how
much memory you have.

With the 64-bit, you'd better have more than 4 GB of memory. If you
are processing images with large matrices, you may need more.

Susumu

On Mon, Apr 25, 2011 at 2:34 PM, Shukla, Karan <Karan.Shukla at uth.tmc.edu> wrote:
> Hello,
>
> I am working with DTI Studio on windows 7 XP mode and I am receiving an "Out of Memory" pop up when I am trying to calculate the tensor, color map, etc. Are there any settings to be be adjusted so that my memory space may be increased or cleared?
>
> Thanks
>
> Karan
> UT Houston
>
> _______________________________________________
> mristudio-users mailing 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 zimer at post.tau.ac.il  Tue Apr 26 00:58:34 2011
From: zimer at post.tau.ac.il (Gali)
Date: Tue, 26 Apr 2011 07:58:34 +0300
Subject: [Mristudio-users] performing fiber tracking on a nifti file
In-Reply-To: <BANLkTim-i-7=H5RS_EeTMJVTwteSnS8bsQ@mail.gmail.com>
References: <E9B6ED49A31C43CCA769B3109B85A4C7@galipc>
	<BANLkTim-i-7=H5RS_EeTMJVTwteSnS8bsQ@mail.gmail.com>
Message-ID: <377AF1B694E24CDBA05FDC4D74791CEE@galipc>

Thanks for the answer. It worked!

Gali Zimmerman-Moreno
Biomedical Engineering dept., TAU
03-6405839

-----Original Message-----
From: mristudio-users-bounces at mristudio.org
[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori
Sent: Sunday, April 24, 2011 2:36 PM
To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
Subject: Re: [Mristudio-users] performing fiber tracking on a nifti file

You can open Nifti by Mri3DView and save it as "REC" format by saving
all images into one file. This is a raw format without a header. So,
you have to remember image dimensions. DtiMapping, then, can read it.
You may be able to save the loaded Nifti images as a 4D Analyze too,
but I'm not sure, if DtiMapping can properly read it.

On Sun, Apr 24, 2011 at 5:24 AM, Gali <zimer at post.tau.ac.il> wrote:
> Hello all
>
> How can I perform fiber tracking in DTIstudio on a brain data saved in a
> nifti format?
>
> (I am trying to use "DTI mapping" but not one of the format options seem
to
> match NIFTI)
>
> Thanks!
>
> _______________________________________________
> mristudio-users mailing 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 houhong2009 at hotmail.com  Tue Apr 26 01:17:54 2011
From: houhong2009 at hotmail.com (=?gb2312?B?wO7Wx8bm?=)
Date: Tue, 26 Apr 2011 05:17:54 +0000
Subject: [Mristudio-users] fiber tracking
Message-ID: <BAY151-w51097EED7650E55CE14CEFB8990@phx.gbl>


Hello all,
      
I have  problems when I attempt to perform fiber tracking using DTI Studio. For exemple,  when I pressed the fiber tracking button in the DtiMap tab or  chose fiber tracking in the File menu, the  fiber imaging could not be displayed correctly. I wonder if the resultant tractography may be influenced by the parameters of fiber tracking? (My DT-MRI data was acquired from Siemens 3.0T magnet, data format is Siemens DICOM.TR8400,TE82,FOV230*230,Matrix128,slice thickness3.5, slice number=38, 13 directions(12Ds + a b0))
Thanks!

Zhiqi Li
Shanghai Medical School, Fudan University

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From susumu at mri.jhu.edu  Tue Apr 26 07:59:21 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Tue, 26 Apr 2011 07:59:21 -0400
Subject: [Mristudio-users] fiber tracking
In-Reply-To: <BAY151-w51097EED7650E55CE14CEFB8990@phx.gbl>
References: <BAY151-w51097EED7650E55CE14CEFB8990@phx.gbl>
Message-ID: <BANLkTinov4SqzR=02k9ZiOp5QcHuQqOiSg@mail.gmail.com>

Hi Zhiqi,

In DtiStudio, fiber tracking is performed from all pixels (above the
FA threshold) at the beginning and the results are stored. These
fibers are visualized only after you draw ROIs, which select fibers to
be visualized.

Susumu

2011/4/26 ??? <houhong2009 at hotmail.com>:
> Hello all,
>
> I have  problems when I attempt to perform fiber tracking using DTI Studio.
> For exemple,  when I pressed the fiber tracking button in the DtiMap tab or
> chose fiber tracking in the File menu, the  fiber imaging could not be
> displayed correctly. I wonder if the resultant tractography may be
> influenced by the parameters of fiber tracking? (My DT-MRI data was
> acquired from Siemens 3.0T magnet, data format is Siemens
> DICOM.TR8400,TE82,FOV230*230,Matrix128,slice thickness3.5, slice number=38,
> 13 directions(12Ds + a b0))
> Thanks!
>
> Zhiqi Li
> Shanghai Medical School, Fudan University
>
>
>
> _______________________________________________
> mristudio-users mailing 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 houhong2009 at hotmail.com  Wed Apr 27 07:09:12 2011
From: houhong2009 at hotmail.com (=?gb2312?B?wO7Wx8bm?=)
Date: Wed, 27 Apr 2011 11:09:12 +0000
Subject: [Mristudio-users] fiber tracking
In-Reply-To: <BANLkTinov4SqzR=02k9ZiOp5QcHuQqOiSg@mail.gmail.com>
References: <BAY151-w51097EED7650E55CE14CEFB8990@phx.gbl>
	<BANLkTinov4SqzR=02k9ZiOp5QcHuQqOiSg@mail.gmail.com>
Message-ID: <BAY151-w652512972486479428BE3BB8980@phx.gbl>



 I tried, but a dialog box which said invalid parameter after I pressed the button of fiber tracking in the DtiMap tab 

> Date: Tue, 26 Apr 2011 07:59:21 -0400
> From: susumu at mri.jhu.edu
> To: mristudio-users at mristudio.org
> Subject: Re: [Mristudio-users] fiber tracking
> 
> Hi Zhiqi,
> 
> In DtiStudio, fiber tracking is performed from all pixels (above the
> FA threshold) at the beginning and the results are stored. These
> fibers are visualized only after you draw ROIs, which select fibers to
> be visualized.
> 
> Susumu
> 
> 2011/4/26 ??? <houhong2009 at hotmail.com>:
> > Hello all,
> >
> > I have problems when I attempt to perform fiber tracking using DTI Studio.
> > For exemple, when I pressed the fiber tracking button in the DtiMap tab or
> > chose fiber tracking in the File menu, the fiber imaging could not be
> > displayed correctly. I wonder if the resultant tractography may be
> > influenced by the parameters of fiber tracking? (My DT-MRI data was
> > acquired from Siemens 3.0T magnet, data format is Siemens
> > DICOM.TR8400,TE82,FOV230*230,Matrix128,slice thickness3.5, slice number=38,
> > 13 directions(12Ds + a b0))
> > Thanks!
> >
> > Zhiqi Li
> > Shanghai Medical School, Fudan University
> >
> >
> >
> > _______________________________________________
> > mristudio-users mailing 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
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From weinmaya at gmail.com  Sun May  1 02:50:58 2011
From: weinmaya at gmail.com (maya weinstein)
Date: Sun, 01 May 2011 08:50:58 +0200
Subject: [Mristudio-users] Question regarding integers
Message-ID: <BANLkTinsGtp7waQdNdCu3nPoMfJLT0FSaA@mail.gmail.com>

Hello,

I'm working on data of babies scanned at a term and I used b0=700.

When looking at the statistics from some ROIs or tracts I get values of
0.00xx.

for example:

*ADC* 0.0017, *Eig0* 0.0021, *Eig1* 0.0017, *Eig2* 0.0013, *FA* 0.2424

Is there a way that I can get more integers in order to increase the
sensitivity?

Thank you,

Maya
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From xiajgky at 163.com  Mon May  2 00:52:41 2011
From: xiajgky at 163.com (=?GBK?B?z8S9qLn6?=)
Date: Mon, 02 May 2011 12:52:41 +0800 (CST)
Subject: [Mristudio-users] Question regarding integers
In-Reply-To: <BANLkTinsGtp7waQdNdCu3nPoMfJLT0FSaA@mail.gmail.com>
References: <BANLkTinsGtp7waQdNdCu3nPoMfJLT0FSaA@mail.gmail.com>
Message-ID: <3427fd16.5680.12faf0d1648.Coremail.xiajgky@163.com>

I am sorry, I am not know it you say. Please ask someone else. Sorry!


At 2011-05-01 14:50:58?"maya weinstein" <weinmaya at gmail.com> wrote:

Hello,
 
I'm working on data of babies scanned at a term and I used b0=700.
 
When looking at the statistics from some ROIs or tracts I get values of 0.00xx. 
 
for example:

ADC 0.0017,Eig0 0.0021,Eig1 0.0017,Eig2 0.0013,FA0.2424

Is there a way that I can get more integers in order to increase the sensitivity?

Thank you,

Maya

 

 

 
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From Malek.Makki at kispi.uzh.ch  Mon May  2 02:17:04 2011
From: Malek.Makki at kispi.uzh.ch (Makki Malek)
Date: Mon, 02 May 2011 08:17:04 +0200
Subject: [Mristudio-users] Question regarding integers
In-Reply-To: <BANLkTinsGtp7waQdNdCu3nPoMfJLT0FSaA@mail.gmail.com>
Message-ID: <FD1E6887BC99C341800CBFD7ABC2F9C2029769E1@exzh1.kispi.int>

Hi 

Have you tried something like b=70 instead of 700 ? than you multiply
your result by 10

In theory it works since this is a factor that divide your gradient
matrix  (or table) 

 

 

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Malek I. Makki, PhD

Diagnostic Imaging Department

MRI Center

Kinderspital Zurich

 

Phone. +41(0)44 266 3130

Fax:      +41(0)44 266 7153

malek.makki at kispi.uzh.ch <mailto:malek.makki at kispi.uzh.ch> 

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

 

 

________________________________

From: mristudio-users-bounces at mristudio.org
[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of maya
weinstein
Sent: Sunday, May 01, 2011 8:51 AM
To: mristudio-users at mristudio.org
Subject: [Mristudio-users] Question regarding integers

 

Hello,

 

I'm working on data of babies scanned at a term and I used b0=700.

 

When looking at the statistics from some ROIs or tracts I get values of
0.00xx. 

 

for example: 

ADC 0.0017, Eig0 0.0021, Eig1 0.0017, Eig2 0.0013, FA 0.2424

Is there a way that I can get more integers in order to increase the
sensitivity?

Thank you,

Maya

 

 

 

 

 

 

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From weinmaya at gmail.com  Mon May  2 02:31:33 2011
From: weinmaya at gmail.com (maya weinstein)
Date: Mon, 02 May 2011 08:31:33 +0200
Subject: [Mristudio-users] Question regarding integers
In-Reply-To: <FD1E6887BC99C341800CBFD7ABC2F9C2029769E1@exzh1.kispi.int>
References: <BANLkTinsGtp7waQdNdCu3nPoMfJLT0FSaA@mail.gmail.com>
	<FD1E6887BC99C341800CBFD7ABC2F9C2029769E1@exzh1.kispi.int>
Message-ID: <BANLkTimB1-0yuE04bsanM6Pkwuus8o6VEA@mail.gmail.com>

Hi Malek,
Thanks for your advice- it worked!
Have a great week,
Maya

On Mon, May 2, 2011 at 8:17 AM, Makki Malek <Malek.Makki at kispi.uzh.ch>wrote:

>  Hi
>
> Have you tried something like b=70 instead of 700 ? than you multiply your
> result by 10
>
> In theory it works since this is a factor that divide your gradient matrix
>  (or table)
>
>
>
>
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
> Malek I. Makki, PhD
>
> Diagnostic Imaging Department
>
> MRI Center
>
> Kinderspital Zurich
>
>
>
> Phone. +41(0)44 266 3130
>
> Fax:      +41(0)44 266 7153
>
> malek.makki at kispi.uzh.ch
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
>
>
>
>  ------------------------------
>
> *From:* mristudio-users-bounces at mristudio.org [mailto:
> mristudio-users-bounces at mristudio.org] *On Behalf Of *maya weinstein
> *Sent:* Sunday, May 01, 2011 8:51 AM
> *To:* mristudio-users at mristudio.org
> *Subject:* [Mristudio-users] Question regarding integers
>
>
>
> Hello,
>
>
>
> I'm working on data of babies scanned at a term and I used b0=700.
>
>
>
> When looking at the statistics from some ROIs or tracts I get values of
> 0.00xx.
>
>
>
> for example:
>
> *ADC* 0.0017, *Eig0* 0.0021, *Eig1* 0.0017, *Eig2* 0.0013, *FA* 0.2424
>
> Is there a way that I can get more integers in order to increase the
> sensitivity?
>
> Thank you,
>
> Maya
>
>
>
>
>
>
>
>
>
>
>
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From susumu at mri.jhu.edu  Mon May  2 17:29:46 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Mon, 02 May 2011 17:29:46 -0400
Subject: [Mristudio-users] Question regarding integers
In-Reply-To: <BANLkTimB1-0yuE04bsanM6Pkwuus8o6VEA@mail.gmail.com>
References: <BANLkTinsGtp7waQdNdCu3nPoMfJLT0FSaA@mail.gmail.com>
	<FD1E6887BC99C341800CBFD7ABC2F9C2029769E1@exzh1.kispi.int>
	<BANLkTimB1-0yuE04bsanM6Pkwuus8o6VEA@mail.gmail.com>
Message-ID: <BANLkTi=o=hzSVX6hj=QsObcuSxYzgmh_Og@mail.gmail.com>

Thanks Makki,

Maya, the latest version of DtiStudio should provide the scientific format.
Please check.

Susumu

On Mon, May 2, 2011 at 2:31 AM, maya weinstein <weinmaya at gmail.com> wrote:

> Hi Malek,
> Thanks for your advice- it worked!
> Have a great week,
> Maya
>
> On Mon, May 2, 2011 at 8:17 AM, Makki Malek <Malek.Makki at kispi.uzh.ch>wrote:
>
>>  Hi
>>
>> Have you tried something like b=70 instead of 700 ? than you multiply your
>> result by 10
>>
>> In theory it works since this is a factor that divide your gradient matrix
>>  (or table)
>>
>>
>>
>>
>>
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>
>> Malek I. Makki, PhD
>>
>> Diagnostic Imaging Department
>>
>> MRI Center
>>
>> Kinderspital Zurich
>>
>>
>>
>> Phone. +41(0)44 266 3130
>>
>> Fax:      +41(0)44 266 7153
>>
>> malek.makki at kispi.uzh.ch
>>
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>
>>
>>
>>
>>  ------------------------------
>>
>> *From:* mristudio-users-bounces at mristudio.org [mailto:
>> mristudio-users-bounces at mristudio.org] *On Behalf Of *maya weinstein
>> *Sent:* Sunday, May 01, 2011 8:51 AM
>> *To:* mristudio-users at mristudio.org
>> *Subject:* [Mristudio-users] Question regarding integers
>>
>>
>>
>> Hello,
>>
>>
>>
>> I'm working on data of babies scanned at a term and I used b0=700.
>>
>>
>>
>> When looking at the statistics from some ROIs or tracts I get values of
>> 0.00xx.
>>
>>
>>
>> for example:
>>
>> *ADC* 0.0017, *Eig0* 0.0021, *Eig1* 0.0017, *Eig2* 0.0013, *FA* 0.2424
>>
>> Is there a way that I can get more integers in order to increase the
>> sensitivity?
>>
>> Thank you,
>>
>> Maya
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> mristudio-users mailing 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
>
>
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From weinmaya at gmail.com  Wed May 11 03:56:34 2011
From: weinmaya at gmail.com (maya weinstein)
Date: Wed, 11 May 2011 09:56:34 +0200
Subject: [Mristudio-users] error in uploading ANALYZE format to dtistudio
Message-ID: <BANLkTikiFM1u9=UxzkP3DkettMFmhmnnNQ@mail.gmail.com>

Hello users,

I did bet and eddy current correction to my data and saved it in ANALYZE
format.
When I tried to load it to dtistudio the message "file size is bigger than
DW image size- continue anyway?" appeared.
I double-checked and all the DTI parameters were entered correctly (slice
thickness, matrix, FOV etc.)
Should I continue and disregard the message, or is there a way to fix it?
(When I load the raw dicoms- the message doesn't appear).

Thank You,
Maya

-- 
Maya Weinstein
Department of Psychology, Bar-Ilan University
Functional Brain Imaging Unit, Wohl Institute for Advanced Imaging, Tel-Aviv
Sourasky Medical Center
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From susumu at mri.jhu.edu  Wed May 11 06:36:47 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Wed, 11 May 2011 06:36:47 -0400
Subject: [Mristudio-users] error in uploading ANALYZE format to dtistudio
In-Reply-To: <BANLkTikiFM1u9=UxzkP3DkettMFmhmnnNQ@mail.gmail.com>
References: <BANLkTikiFM1u9=UxzkP3DkettMFmhmnnNQ@mail.gmail.com>
Message-ID: <BANLkTinYmkshp2j9ikzBDBjj8H3uFc4cgQ@mail.gmail.com>

Please read the data by Mri3DView first and see how many 3D images are
loaded. You can count the number of images in the pull-down menu of
the right column.

Then start DtiMapping and fill in the gradient table information.
Here, please make sure that the number of the table rows agrees with
the number of the 3D images.

For example, if you load Philips 32-orientation data, there are 33
rows in the table for one b0 and 32 diffusion orientations. Then you
may find there are 34 3D volumes in your data, which would give the
error message you got. This is because Philips added 34th calculated
DWI in the end of the data. If so, you have to add 34th row in the
table (33: 100, 100, 100), in which [100, 100, 100] means "don't use
this data".



On Wed, May 11, 2011 at 3:56 AM, maya weinstein <weinmaya at gmail.com> wrote:
> Hello users,
>
> I did bet and eddy current correction to my data and saved it in ANALYZE
> format.
> When I tried to load it to dtistudio the message "file size is bigger than
> DW image size- continue anyway?" appeared.
> I double-checked and all the DTI parameters were entered correctly (slice
> thickness, matrix, FOV etc.)
> Should I continue and disregard the message, or is there a way to fix it?
> (When I load the raw dicoms- the message doesn't appear).
>
> Thank You,
> Maya
> --
> Maya Weinstein
> Department of Psychology,?Bar-Ilan University
> Functional Brain Imaging Unit, Wohl Institute for Advanced Imaging, Tel-Aviv
> Sourasky Medical Center
>
> _______________________________________________
> mristudio-users mailing 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 weinmaya at gmail.com  Sat May 14 14:11:04 2011
From: weinmaya at gmail.com (maya weinstein)
Date: Sat, 14 May 2011 20:11:04 +0200
Subject: [Mristudio-users] error in uploading ANALYZE format to dtistudio
In-Reply-To: <BANLkTinYmkshp2j9ikzBDBjj8H3uFc4cgQ@mail.gmail.com>
References: <BANLkTikiFM1u9=UxzkP3DkettMFmhmnnNQ@mail.gmail.com>
	<BANLkTinYmkshp2j9ikzBDBjj8H3uFc4cgQ@mail.gmail.com>
Message-ID: <BANLkTin3EGykEO7gxjoeZ_=KkoiqLd=jiQ@mail.gmail.com>

Thank you very much, indeed that was the problem.
Maya

On Wed, May 11, 2011 at 12:36 PM, susumu mori <susumu at mri.jhu.edu> wrote:

> Please read the data by Mri3DView first and see how many 3D images are
> loaded. You can count the number of images in the pull-down menu of
> the right column.
>
> Then start DtiMapping and fill in the gradient table information.
> Here, please make sure that the number of the table rows agrees with
> the number of the 3D images.
>
> For example, if you load Philips 32-orientation data, there are 33
> rows in the table for one b0 and 32 diffusion orientations. Then you
> may find there are 34 3D volumes in your data, which would give the
> error message you got. This is because Philips added 34th calculated
> DWI in the end of the data. If so, you have to add 34th row in the
> table (33: 100, 100, 100), in which [100, 100, 100] means "don't use
> this data".
>
>
>
> On Wed, May 11, 2011 at 3:56 AM, maya weinstein <weinmaya at gmail.com>
> wrote:
> > Hello users,
> >
> > I did bet and eddy current correction to my data and saved it in ANALYZE
> > format.
> > When I tried to load it to dtistudio the message "file size is bigger
> than
> > DW image size- continue anyway?" appeared.
> > I double-checked and all the DTI parameters were entered correctly (slice
> > thickness, matrix, FOV etc.)
> > Should I continue and disregard the message, or is there a way to fix it?
> > (When I load the raw dicoms- the message doesn't appear).
> >
> > Thank You,
> > Maya
> > --
> > Maya Weinstein
> > Department of Psychology, Bar-Ilan University
> > Functional Brain Imaging Unit, Wohl Institute for Advanced Imaging,
> Tel-Aviv
> > Sourasky Medical Center
> >
> > _______________________________________________
> > mristudio-users mailing 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
>



-- 
Maya Weinstein
Department of Psychology, Bar-Ilan University
Functional Brain Imaging Unit, Wohl Institute for Advanced Imaging, Tel-Aviv
Sourasky Medical Center
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From faridisme at gmail.com  Sun May 15 22:34:08 2011
From: faridisme at gmail.com (mdfarid a r)
Date: Mon, 16 May 2011 10:34:08 +0800
Subject: [Mristudio-users] Pediatric DTI
In-Reply-To: <AANLkTimbYY2yhz3YUgnziqPaJ=CK4f0QgjMitU8FRBPf@mail.gmail.com>
References: <AANLkTimbYY2yhz3YUgnziqPaJ=CK4f0QgjMitU8FRBPf@mail.gmail.com>
Message-ID: <BANLkTikuZcYNfUTJjuTgVcBAT8xgnr6ErQ@mail.gmail.com>

Hello all,

I also visited the site and the link to http://www.pediatricdti.org/. I
would like to know if the database for pediatric brain, in particular 6
months, is available.

Thank you and Regards,
Farid

2011/1/24 Andr?s Jakab MD <jakaba at med.unideb.hu>

> Dear Prof. Mori and MRIstudio list members,
>
> The link to the "Pediatric DTI" website seems to be broken on the
> http://www.dtiatlas.org/ page. I'd like to inquire about the availability
> of the abovementioned database.
>
> Best regards,
> Andr?s Jakab MD
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From wang052235 at hotmail.com  Mon May 16 04:37:13 2011
From: wang052235 at hotmail.com (=?gb2312?B?zfXPo7qj?=)
Date: Mon, 16 May 2011 08:37:13 +0000
Subject: [Mristudio-users] Pediatric DTI
In-Reply-To: <BANLkTikuZcYNfUTJjuTgVcBAT8xgnr6ErQ@mail.gmail.com>
References: <AANLkTimbYY2yhz3YUgnziqPaJ=CK4f0QgjMitU8FRBPf@mail.gmail.com>
	<BANLkTikuZcYNfUTJjuTgVcBAT8xgnr6ErQ@mail.gmail.com>
Message-ID: <COL112-W47AE81930815CCE58BC976D38D0@phx.gbl>


Hello,Idon't have DTI database.but I have conservationg MR images ,such as T1W?T2W?DWI?


Thank you and Regards
Date: Mon, 16 May 2011 10:34:08 +0800
From: faridisme at gmail.com
To: mristudio-users at mristudio.org
Subject: Re: [Mristudio-users] Pediatric DTI
Hello all,

I also visited the site and the link to http://www.pediatricdti.org/. I would like to know if the database for pediatric brain, in particular 6 months, is available.


Thank you and Regards,
Farid

2011/1/24 Andr?s Jakab MD <jakaba at med.unideb.hu>

Dear Prof. Mori and MRIstudio list members,

The link to the "Pediatric DTI" website seems to be broken on the http://www.dtiatlas.org/ page. I'd like to inquire about the availability of the abovementioned database.



Best regards,
Andr?s Jakab MD



_______________________________________________

mristudio-users mailing 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 		 	   		  
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From ycheng30 at jhmi.edu  Mon May 16 11:08:48 2011
From: ycheng30 at jhmi.edu (Ying Cheng)
Date: Mon, 16 May 2011 11:08:48 -0400
Subject: [Mristudio-users] Loading in ROI images into DTIStudio to view the
	fiber
Message-ID: <71908c368d49.4dd105c0@johnshopkins.edu>

Hello DTIStudio users,

I am a PhD student currently working on a DTI visualization course project. The data I have are FA images and corresponding principle eigenvector images, as well as a T1-MR images. They are all raw file. I did the tractography based on these two files using DTIStudio, and then I want to visualize the fibers that passing through a certain ROI. I know this can be accomplished by manually drawing the ROI, however I have several ROI images as the mask (which have the same dimension, data format with the FA images), and these mask images are binary in which pixel inside the ROI are 1 and 0 elsewhere. When I load into a ROI image under the Fiber panel, ROI operation -> load -> binary image, it pops out a window saying 'image parameters in this file are not consistent with the current ones'. And I clicked on 'yes' to continue, but there was no fibers shown corresponding to this ROI. So is it because DTIStudio has its own definition of ROI images? Do I need to change my ROI mask ima
ge format/header format then? 


Thanks!!

Best,

Ying Cheng

-

From susumu at mri.jhu.edu  Mon May 16 20:17:28 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Mon, 16 May 2011 20:17:28 -0400
Subject: [Mristudio-users] Loading in ROI images into DTIStudio to view
 the fiber
In-Reply-To: <71908c368d49.4dd105c0@johnshopkins.edu>
References: <71908c368d49.4dd105c0@johnshopkins.edu>
Message-ID: <BANLkTi=tgssb-0uEhJ_goHEXzNgejiAB-A@mail.gmail.com>

Hi Ying,

This usually means the file size of your binary mask file is not
right. For example, DtiStudio is waiting for a binary data while you
fed integer data. Or the matrix size is not right. There must be
something not consistent.

Also, FAQ16 at https://www.mristudio.org/wiki/faq may be helpful.

Susumu

On Mon, May 16, 2011 at 11:08 AM, Ying Cheng <ycheng30 at jhmi.edu> wrote:
> Hello DTIStudio users,
>
> I am a PhD student currently working on a DTI visualization course project. The data I have are FA images and corresponding principle eigenvector images, as well as a T1-MR images. They are all raw file. I did the tractography based on these two files using DTIStudio, and then I want to visualize the fibers that passing through a certain ROI. I know this can be accomplished by manually drawing the ROI, however I have several ROI images as the mask (which have the same dimension, data format with the FA images), and these mask images are binary in which pixel inside the ROI are 1 and 0 elsewhere. When I load into a ROI image under the Fiber panel, ROI operation -> load -> binary image, it pops out a window saying 'image parameters in this file are not consistent with the current ones'. And I clicked on 'yes' to continue, but there was no fibers shown corresponding to this ROI. So is it because DTIStudio has its own definition of ROI images? Do I need to change my ROI mask ima
> ge format/header format then?
>
>
> Thanks!!
>
> Best,
>
> Ying Cheng
>
> -
> _______________________________________________
> mristudio-users mailing 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  Mon May 16 20:23:02 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Mon, 16 May 2011 20:23:02 -0400
Subject: [Mristudio-users] Pediatric DTI
In-Reply-To: <BANLkTikuZcYNfUTJjuTgVcBAT8xgnr6ErQ@mail.gmail.com>
References: <AANLkTimbYY2yhz3YUgnziqPaJ=CK4f0QgjMitU8FRBPf@mail.gmail.com>
	<BANLkTikuZcYNfUTJjuTgVcBAT8xgnr6ErQ@mail.gmail.com>
Message-ID: <BANLkTin+rZxya+de39BiE2YTex48BUPLPw@mail.gmail.com>

Hi Farid,

The database is now moved to our website, lbam.med.jhmi.edu. Please
contact Xin Xu if you have any issues in downloading the data.

thanks,

susumu

On Sun, May 15, 2011 at 10:34 PM, mdfarid a r <faridisme at gmail.com> wrote:
> Hello all,
>
> I also visited the site and the link to http://www.pediatricdti.org/. I
> would like to know if the database for pediatric brain, in particular 6
> months, is available.
>
> Thank you and Regards,
> Farid
>
> 2011/1/24 Andr?s Jakab MD <jakaba at med.unideb.hu>
>>
>> Dear Prof. Mori and MRIstudio list members,
>>
>> The link to the "Pediatric DTI" website seems to be broken on the
>> http://www.dtiatlas.org/ page. I'd like to inquire about the availability of
>> the abovementioned database.
>>
>> Best regards,
>> Andr?s Jakab MD
>>
>>
>> _______________________________________________
>> mristudio-users mailing 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 melcarr at umich.edu  Tue May 17 21:11:05 2011
From: melcarr at umich.edu (Melisa Carrasco)
Date: Tue, 17 May 2011 21:11:05 -0400
Subject: [Mristudio-users] Question about importing fiber tracking findings
 from DTI Studio to MATLAB for group statistics
Message-ID: <BANLkTimA+MLkgDBS6znoCyOG-QQ7XHqtRA@mail.gmail.com>

Hello,

We're relatively new to DTI-Studio and were wondering: Would anyone happen
to have a protocol to be able to do the following?

We'd like, using DTI-Studio, to:

1. Define two ROIs in each individual subject's FA map
2. Run fiber tracking / tractography so we can find the fiber tracts that
intersect both ROIs
3. Extract these fibers for each individual, then load these into MATLAB for
group statistics...

Just wondering if this is even feasible to do.

Thank you,

-Melisa Carrasco

--

Melisa Carrasco, M.S.
MD/PhD Student, Year Grad-4 (Ph.D. Candidate)

University of Michigan, Neuroscience Graduate Program, Class of 2012
University of Rochester School of Medicine and Dentistry, Class of 2014

About me: http://sitemaker.umich.edu/melisa.carrasco/home
GO BLUE!
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From susumu at mri.jhu.edu  Tue May 17 21:22:29 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Tue, 17 May 2011 21:22:29 -0400
Subject: [Mristudio-users] Question about importing fiber tracking
 findings from DTI Studio to MATLAB for group statistics
In-Reply-To: <BANLkTimA+MLkgDBS6znoCyOG-QQ7XHqtRA@mail.gmail.com>
References: <BANLkTimA+MLkgDBS6znoCyOG-QQ7XHqtRA@mail.gmail.com>
Message-ID: <BANLkTikBRR1aUhua=bLxEyFamamNjSUCLA@mail.gmail.com>

That should be feasible, although we don't have experiences in the
Step #3 with a MatLab code. We do Step #3 using our programs in
MriStudio family, DiffoeMap and RoiEditor. These programs can be
downloaded from www.mristudio.org and you can also find some tutorial
materials there.

On Tue, May 17, 2011 at 9:11 PM, Melisa Carrasco <melcarr at umich.edu> wrote:
> Hello,
>
> We're relatively new to DTI-Studio and were wondering: Would anyone happen
> to have a protocol to be able to do the following?
>
> We'd like, using DTI-Studio, to:
>
> 1. Define two ROIs in each individual subject's FA map
> 2. Run fiber tracking / tractography so we can find the fiber tracts that
> intersect both ROIs
> 3. Extract these fibers for each individual, then load these into MATLAB for
> group statistics...
>
> Just wondering if this is even feasible to do.
>
> Thank you,
>
> -Melisa Carrasco
>
> --
>
> Melisa Carrasco, M.S.
> MD/PhD Student, Year Grad-4 (Ph.D. Candidate)
>
> University of Michigan, Neuroscience Graduate Program, Class of 2012
> University of Rochester School of Medicine and Dentistry, Class of 2014
>
> About me: http://sitemaker.umich.edu/melisa.carrasco/home
> GO BLUE!
>
>
> _______________________________________________
> mristudio-users mailing 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 melcarr at umich.edu  Tue May 17 21:24:39 2011
From: melcarr at umich.edu (melcarr at umich.edu)
Date: Tue, 17 May 2011 21:24:39 -0400
Subject: [Mristudio-users] Question about importing fiber tracking
 findings from DTI Studio to MATLAB for group statistics
In-Reply-To: <BANLkTikBRR1aUhua=bLxEyFamamNjSUCLA@mail.gmail.com>
References: <BANLkTimA+MLkgDBS6znoCyOG-QQ7XHqtRA@mail.gmail.com>
	<BANLkTikBRR1aUhua=bLxEyFamamNjSUCLA@mail.gmail.com>
Message-ID: <20110517212439.140935x1mxxyemkg@web.mail.umich.edu>

Dr. Mori,

Thank you for your immediate response! If not MATLAB, what software  
packages would you recommend for pursuing the group statistics /  
analysis?

Thank you,

-Melisa Carrasco

--

Melisa Carrasco, M.S.
MD/PhD Student, Year Grad-4 (Ph.D. Candidate)

University of Michigan, Neuroscience Graduate Program, Class of 2012
University of Rochester School of Medicine and Dentistry, Class of 2014

About me: http://sitemaker.umich.edu/melisa.carrasco/home
GO BLUE!


Quoting susumu mori <susumu at mri.jhu.edu>:

> That should be feasible, although we don't have experiences in the
> Step #3 with a MatLab code. We do Step #3 using our programs in
> MriStudio family, DiffoeMap and RoiEditor. These programs can be
> downloaded from www.mristudio.org and you can also find some tutorial
> materials there.
>
> On Tue, May 17, 2011 at 9:11 PM, Melisa Carrasco <melcarr at umich.edu> wrote:
>> Hello,
>>
>> We're relatively new to DTI-Studio and were wondering: Would anyone happen
>> to have a protocol to be able to do the following?
>>
>> We'd like, using DTI-Studio, to:
>>
>> 1. Define two ROIs in each individual subject's FA map
>> 2. Run fiber tracking / tractography so we can find the fiber tracts that
>> intersect both ROIs
>> 3. Extract these fibers for each individual, then load these into MATLAB for
>> group statistics...
>>
>> Just wondering if this is even feasible to do.
>>
>> Thank you,
>>
>> -Melisa Carrasco
>>
>> --
>>
>> Melisa Carrasco, M.S.
>> MD/PhD Student, Year Grad-4 (Ph.D. Candidate)
>>
>> University of Michigan, Neuroscience Graduate Program, Class of 2012
>> University of Rochester School of Medicine and Dentistry, Class of 2014
>>
>> About me: http://sitemaker.umich.edu/melisa.carrasco/home
>> GO BLUE!
>>
>>
>> _______________________________________________
>> mristudio-users mailing 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  Tue May 17 21:30:49 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Tue, 17 May 2011 21:30:49 -0400
Subject: [Mristudio-users] Question about importing fiber tracking
 findings from DTI Studio to MATLAB for group statistics
In-Reply-To: <20110517212439.140935x1mxxyemkg@web.mail.umich.edu>
References: <BANLkTimA+MLkgDBS6znoCyOG-QQ7XHqtRA@mail.gmail.com>
	<BANLkTikBRR1aUhua=bLxEyFamamNjSUCLA@mail.gmail.com>
	<20110517212439.140935x1mxxyemkg@web.mail.umich.edu>
Message-ID: <BANLkTikFMCU7C1aQuT2kR440UySH_WJ6DA@mail.gmail.com>

yes, we use our own programs (DiffeoMap and RoiEditor) for image
registration and analysis.

The "Getting Started" section of
https://www.mristudio.org/wiki/user_manual/diffeomap should give you
some idea about how to do group analysis using these programs.

There is also a video tutorial here
(https://www.mristudio.org/wiki/user_manual).

On Tue, May 17, 2011 at 9:24 PM,  <melcarr at umich.edu> wrote:
> Dr. Mori,
>
> Thank you for your immediate response! If not MATLAB, what software
> packages would you recommend for pursuing the group statistics /
> analysis?
>
> Thank you,
>
> -Melisa Carrasco
>
> --
>
> Melisa Carrasco, M.S.
> MD/PhD Student, Year Grad-4 (Ph.D. Candidate)
>
> University of Michigan, Neuroscience Graduate Program, Class of 2012
> University of Rochester School of Medicine and Dentistry, Class of 2014
>
> About me: http://sitemaker.umich.edu/melisa.carrasco/home
> GO BLUE!
>
>
> Quoting susumu mori <susumu at mri.jhu.edu>:
>
>> That should be feasible, although we don't have experiences in the
>> Step #3 with a MatLab code. We do Step #3 using our programs in
>> MriStudio family, DiffoeMap and RoiEditor. These programs can be
>> downloaded from www.mristudio.org and you can also find some tutorial
>> materials there.
>>
>> On Tue, May 17, 2011 at 9:11 PM, Melisa Carrasco <melcarr at umich.edu> wrote:
>>> Hello,
>>>
>>> We're relatively new to DTI-Studio and were wondering: Would anyone happen
>>> to have a protocol to be able to do the following?
>>>
>>> We'd like, using DTI-Studio, to:
>>>
>>> 1. Define two ROIs in each individual subject's FA map
>>> 2. Run fiber tracking / tractography so we can find the fiber tracts that
>>> intersect both ROIs
>>> 3. Extract these fibers for each individual, then load these into MATLAB for
>>> group statistics...
>>>
>>> Just wondering if this is even feasible to do.
>>>
>>> Thank you,
>>>
>>> -Melisa Carrasco
>>>
>>> --
>>>
>>> Melisa Carrasco, M.S.
>>> MD/PhD Student, Year Grad-4 (Ph.D. Candidate)
>>>
>>> University of Michigan, Neuroscience Graduate Program, Class of 2012
>>> University of Rochester School of Medicine and Dentistry, Class of 2014
>>>
>>> About me: http://sitemaker.umich.edu/melisa.carrasco/home
>>> GO BLUE!
>>>
>>>
>>> _______________________________________________
>>> mristudio-users mailing 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 melcarr at umich.edu  Tue May 17 21:55:38 2011
From: melcarr at umich.edu (melcarr at umich.edu)
Date: Tue, 17 May 2011 21:55:38 -0400
Subject: [Mristudio-users] Question about importing fiber tracking
 findings from DTI Studio to MATLAB for group statistics
In-Reply-To: <BANLkTikFMCU7C1aQuT2kR440UySH_WJ6DA@mail.gmail.com>
References: <BANLkTimA+MLkgDBS6znoCyOG-QQ7XHqtRA@mail.gmail.com>
	<BANLkTikBRR1aUhua=bLxEyFamamNjSUCLA@mail.gmail.com>
	<20110517212439.140935x1mxxyemkg@web.mail.umich.edu>
	<BANLkTikFMCU7C1aQuT2kR440UySH_WJ6DA@mail.gmail.com>
Message-ID: <20110517215538.75931in2bsmjq1wk@web.mail.umich.edu>

Dr. Mori,

Sounds great, thank you!

-Melisa Carrasco

--

Melisa Carrasco, M.S.
MD/PhD Student, Year Grad-4 (Ph.D. Candidate)

University of Michigan, Neuroscience Graduate Program, Class of 2012
University of Rochester School of Medicine and Dentistry, Class of 2014

About me: http://sitemaker.umich.edu/melisa.carrasco/home
GO BLUE!


Quoting susumu mori <susumu at mri.jhu.edu>:

> yes, we use our own programs (DiffeoMap and RoiEditor) for image
> registration and analysis.
>
> The "Getting Started" section of
> https://www.mristudio.org/wiki/user_manual/diffeomap should give you
> some idea about how to do group analysis using these programs.
>
> There is also a video tutorial here
> (https://www.mristudio.org/wiki/user_manual).
>
> On Tue, May 17, 2011 at 9:24 PM,  <melcarr at umich.edu> wrote:
>> Dr. Mori,
>>
>> Thank you for your immediate response! If not MATLAB, what software
>> packages would you recommend for pursuing the group statistics /
>> analysis?
>>
>> Thank you,
>>
>> -Melisa Carrasco
>>
>> --
>>
>> Melisa Carrasco, M.S.
>> MD/PhD Student, Year Grad-4 (Ph.D. Candidate)
>>
>> University of Michigan, Neuroscience Graduate Program, Class of 2012
>> University of Rochester School of Medicine and Dentistry, Class of 2014
>>
>> About me: http://sitemaker.umich.edu/melisa.carrasco/home
>> GO BLUE!
>>
>>
>> Quoting susumu mori <susumu at mri.jhu.edu>:
>>
>>> That should be feasible, although we don't have experiences in the
>>> Step #3 with a MatLab code. We do Step #3 using our programs in
>>> MriStudio family, DiffoeMap and RoiEditor. These programs can be
>>> downloaded from www.mristudio.org and you can also find some tutorial
>>> materials there.
>>>
>>> On Tue, May 17, 2011 at 9:11 PM, Melisa Carrasco <melcarr at umich.edu> wrote:
>>>> Hello,
>>>>
>>>> We're relatively new to DTI-Studio and were wondering: Would anyone happen
>>>> to have a protocol to be able to do the following?
>>>>
>>>> We'd like, using DTI-Studio, to:
>>>>
>>>> 1. Define two ROIs in each individual subject's FA map
>>>> 2. Run fiber tracking / tractography so we can find the fiber tracts that
>>>> intersect both ROIs
>>>> 3. Extract these fibers for each individual, then load these into  
>>>> MATLAB for
>>>> group statistics...
>>>>
>>>> Just wondering if this is even feasible to do.
>>>>
>>>> Thank you,
>>>>
>>>> -Melisa Carrasco
>>>>
>>>> --
>>>>
>>>> Melisa Carrasco, M.S.
>>>> MD/PhD Student, Year Grad-4 (Ph.D. Candidate)
>>>>
>>>> University of Michigan, Neuroscience Graduate Program, Class of 2012
>>>> University of Rochester School of Medicine and Dentistry, Class of 2014
>>>>
>>>> About me: http://sitemaker.umich.edu/melisa.carrasco/home
>>>> GO BLUE!
>>>>
>>>>
>>>> _______________________________________________
>>>> mristudio-users mailing 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 Weihong.Yuan at cchmc.org  Tue May 17 22:35:07 2011
From: Weihong.Yuan at cchmc.org (Weihong Yuan)
Date: Tue, 17 May 2011 22:35:07 -0400
Subject: [Mristudio-users]  Question about automatic bad slice rejection
In-Reply-To: <BANLkTimB1-0yuE04bsanM6Pkwuus8o6VEA@mail.gmail.com>
References: <BANLkTinsGtp7waQdNdCu3nPoMfJLT0FSaA@mail.gmail.com>
	<FD1E6887BC99C341800CBFD7ABC2F9C2029769E1@exzh1.kispi.int>
	<BANLkTimB1-0yuE04bsanM6Pkwuus8o6VEA@mail.gmail.com>
Message-ID: <4DD2F81C.42F5.004B.1@cchmc.org>

Dear all,
 
I have some questions regarding the automatic bad slice detection/rejection step.
 
1. When I select  the option for Automatic Image_Slice rejection, what is the definition of the relative_error? Is it some form of difference between the slice and the Theory Image? Can you give me the definition, please? The default is set to 3%. Is there anything we need to be careful about when selecting this number?  
 
2. Is there a way to "read out" the flag file generated after the automatic bad slice rejection? I am trying to compare the DTI studio method and another software. If would be great if the flag file can be turned in to a text file or a spreadsheet so I can have a list with the volume number and slide number for all the rejected slices.
 
Thanks
Weihong
 
 
Weihong Yuan, Ph.D.
Research Assistant Professor
Pediatric Neuroimaging Research Consortium
Imaging Research Center, Dept. of Radiology
Children's Hospital Research Foundation
3333  Burnet Ave. 
Cincinnati, OH 45229
Phone: 513-636-2862
FAX: 513-636-0434

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From sljzzw at gmail.com  Tue May 17 22:57:20 2011
From: sljzzw at gmail.com (Zhang Zhongwei)
Date: Tue, 17 May 2011 22:57:20 -0400
Subject: [Mristudio-users] Question about automatic bad slice rejection
In-Reply-To: <4DD2F81C.42F5.004B.1@cchmc.org>
References: <BANLkTinsGtp7waQdNdCu3nPoMfJLT0FSaA@mail.gmail.com>
	<FD1E6887BC99C341800CBFD7ABC2F9C2029769E1@exzh1.kispi.int>
	<BANLkTimB1-0yuE04bsanM6Pkwuus8o6VEA@mail.gmail.com>
	<4DD2F81C.42F5.004B.1@cchmc.org>
Message-ID: <BANLkTim4bgOAz5-mnx=fyDHPXEjNgSBvjQ@mail.gmail.com>


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From melcarr at umich.edu  Wed May 18 00:12:39 2011
From: melcarr at umich.edu (melcarr at umich.edu)
Date: Wed, 18 May 2011 00:12:39 -0400
Subject: [Mristudio-users] Obtaining tract volume data
Message-ID: <20110518001239.12783v9a9a6brbqc@web.mail.umich.edu>

Hello,

I'm attempting to calculate mean tract volume for a tract spanning  
between two ROIs in a subject's FA map.

Is it safe to define tract volume as: the number of voxels between  
both ROIs multiplied by the size of an individual voxel?

Does the first measure above ("the number of voxels between both  
ROIs") correspond to the measure "Average Length, mm" in the Fiber  
Statistics window (an example of this window is shown in the User  
Manual, page 26, Figure 19. Fiber-statistics)?

Just wondering, thank you.

-Melisa Carrasco

--

Melisa Carrasco, M.S.
MD/PhD Student, Year Grad-4 (Ph.D. Candidate)

University of Michigan, Neuroscience Graduate Program, Class of 2012
University of Rochester School of Medicine and Dentistry, Class of 2014

About me: http://sitemaker.umich.edu/melisa.carrasco/home
GO BLUE!





From susumu at mri.jhu.edu  Wed May 18 12:09:31 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Wed, 18 May 2011 12:09:31 -0400
Subject: [Mristudio-users] Question about automatic bad slice rejection
In-Reply-To: <4DD2F81C.42F5.004B.1@cchmc.org>
References: <BANLkTinsGtp7waQdNdCu3nPoMfJLT0FSaA@mail.gmail.com>
	<FD1E6887BC99C341800CBFD7ABC2F9C2029769E1@exzh1.kispi.int>
	<BANLkTimB1-0yuE04bsanM6Pkwuus8o6VEA@mail.gmail.com>
	<4DD2F81C.42F5.004B.1@cchmc.org>
Message-ID: <BANLkTikj1-pSTg2iktm4NdDyEJ65wQQJiQ@mail.gmail.com>

Hi Weihong,

I think Hangyi can give you detailed answer, but I would suggest you
to look into "pixel rejection" option rather than "slice rejection".
In many cases, image corruption is confined in a small area, unless
the subject had bulk motion during a scan. The pixel rejection seems
to work nicely for most of these cases. Please try.

The detailed description can be found here;
https://www.mristudio.org/wiki/changelog/dtistudio-3.0.2

On Tue, May 17, 2011 at 10:35 PM, Weihong Yuan <Weihong.Yuan at cchmc.org> wrote:
> Dear all,
>
> I have?some questions regarding the automatic bad slice detection/rejection
> step.
>
> 1.?When I select ?the option for Automatic Image_Slice rejection, what is
> the definition of the relative_error? Is it some form of difference?between
> the slice?and the Theory Image? Can you give me the definition, please? The
> default is set to 3%.?Is there anything we need to?be careful about?when
> selecting this number?
>
> 2. Is there a way to "read out" the flag file generated after the automatic
> bad slice rejection? I am trying to compare the DTI studio method and
> another software. If would be great if the flag file can be turned in to a
> text file or a spreadsheet so I can have a list with the volume number and
> slide number?for all the rejected slices.
>
> Thanks
> Weihong
>
>
> Weihong Yuan, Ph.D.
> Research Assistant Professor
> Pediatric Neuroimaging Research Consortium
> Imaging Research Center, Dept. of Radiology
> Children's Hospital Research Foundation
> 3333? Burnet Ave.
> Cincinnati, OH 45229
> Phone: 513-636-2862
> FAX: 513-636-0434
>
>
> _______________________________________________
> mristudio-users mailing 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 Malek.Makki at kispi.uzh.ch  Thu May 19 10:58:23 2011
From: Malek.Makki at kispi.uzh.ch (Makki Malek)
Date: Thu, 19 May 2011 16:58:23 +0200
Subject: [Mristudio-users] image-registration
Message-ID: <FD1E6887BC99C341800CBFD7ABC2F9C2029769FE@exzh1.kispi.int>

Dear Users

 I am acquiring DTI (35 directions) with interleaved T2w (1 every 7
DWI).

  What is the best strategy to perform AIR in DTIStudio

 

            1) Register all the DW images to the averaged T2W

            2)  Register each set of DTI to the closer T2W

            3) Register all DTI + T2W to the 1st acquired T2W

 

Is there a quantitative technique to compare each of these methods

 

Thanks

 

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Malek I. Makki, PhD

Diagnostic Imaging Department

MRI Center

Kinderspital Zurich

 

Phone. +41(0)44 266 3130

Fax:      +41(0)44 266 7153

malek.makki at kispi.uzh.ch <mailto:malek.makki at kispi.uzh.ch> 

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

 

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From susumu at mri.jhu.edu  Thu May 19 11:33:21 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Thu, 19 May 2011 11:33:21 -0400
Subject: [Mristudio-users] image-registration
In-Reply-To: <FD1E6887BC99C341800CBFD7ABC2F9C2029769FE@exzh1.kispi.int>
References: <FD1E6887BC99C341800CBFD7ABC2F9C2029769FE@exzh1.kispi.int>
Message-ID: <BANLkTi=Yz=2dczor959Szve9s6GF=hsR_Q@mail.gmail.com>

Hi Malek,

I think it depends on how and when the subject moves. Maybe choosing
one b0 (T2w) in the middle of the scan is the most reasonable way, I
think.

If you have two repeated scans, subtracted images of the two sets
would give you a nice clue about the amount of the motion and efficacy
of the motion correction.

Susumu

On Thu, May 19, 2011 at 10:58 AM, Makki Malek <Malek.Makki at kispi.uzh.ch> wrote:
> Dear Users
>
> ?I am acquiring DTI (35 directions) with interleaved T2w (1 every 7 DWI).
>
> ? What is the best strategy to perform AIR in DTIStudio
>
>
>
> ??????????? 1) Register all the DW images to the averaged T2W
>
> ??????????? 2) ?Register each set of DTI to the closer T2W
>
> ??????????? 3) Register all DTI + T2W to the 1st acquired T2W
>
>
>
> Is there a quantitative technique to compare each of these methods
>
>
>
> Thanks
>
>
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
> Malek I. Makki, PhD
>
> Diagnostic Imaging Department
>
> MRI Center
>
> Kinderspital Zurich
>
>
>
> Phone. +41(0)44 266 3130
>
> Fax:????? +41(0)44 266 7153
>
> malek.makki at kispi.uzh.ch
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
>
>
> _______________________________________________
> mristudio-users mailing 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 May 19 11:48:00 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Thu, 19 May 2011 11:48:00 -0400
Subject: [Mristudio-users] Obtaining tract volume data
In-Reply-To: <20110518001239.12783v9a9a6brbqc@web.mail.umich.edu>
References: <20110518001239.12783v9a9a6brbqc@web.mail.umich.edu>
Message-ID: <BANLkTinNU-VuqABS-gfwUH5_E5aBT0Ug4g@mail.gmail.com>

Hi Melisa,

On Wed, May 18, 2011 at 12:12 AM,  <melcarr at umich.edu> wrote:
> Hello,
>
> I'm attempting to calculate mean tract volume for a tract spanning
> between two ROIs in a subject's FA map.
>
> Is it safe to define tract volume as: the number of voxels between
> both ROIs multiplied by the size of an individual voxel?

This is what we do too.

>
> Does the first measure above ("the number of voxels between both
> ROIs") correspond to the measure "Average Length, mm" in the Fiber
> Statistics window (an example of this window is shown in the User
> Manual, page 26, Figure 19. Fiber-statistics)?

I think the number of voxels occupied by fibers and the average length
of the fibers are very different. The former has unit of mm^3 and the
latter is mm. I don't use the length of fibers for quantification.


>
> Just wondering, thank you.
>
> -Melisa Carrasco
>
> --
>
> Melisa Carrasco, M.S.
> MD/PhD Student, Year Grad-4 (Ph.D. Candidate)
>
> University of Michigan, Neuroscience Graduate Program, Class of 2012
> University of Rochester School of Medicine and Dentistry, Class of 2014
>
> About me: http://sitemaker.umich.edu/melisa.carrasco/home
> GO BLUE!
>
>
>
>
> _______________________________________________
> mristudio-users mailing 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 salvador.castaneda at med.uni-tuebingen.de  Thu May 19 11:56:55 2011
From: salvador.castaneda at med.uni-tuebingen.de (Castaneda, Salvador)
Date: Thu, 19 May 2011 17:56:55 +0200
Subject: [Mristudio-users] Obtaining tract volume data
In-Reply-To: <BANLkTinNU-VuqABS-gfwUH5_E5aBT0Ug4g@mail.gmail.com>
References: <20110518001239.12783v9a9a6brbqc@web.mail.umich.edu>
	<BANLkTinNU-VuqABS-gfwUH5_E5aBT0Ug4g@mail.gmail.com>
Message-ID: <0AC64F4CB253074799B64FF8F0772D350126C6F4@azex2003.raddiag.med.uni-tuebingen.de>

Hello Susumu,

I've been using DTIstudio for over a year... It works good. But i just started running a tensor calculation with 4 b values and 256 directions. But it is crashing in the process of the calculation. I'm not requesting any other commands, just the tensor... Do you have any idea what i could do to calculate it... Do i have to analize with less bvalues?
Thanks
salvador 

-----Urspr?ngliche Nachricht-----
Von: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] Im Auftrag von susumu mori
Gesendet: Donnerstag, 19. Mai 2011 17:48
An: DTI Studio, ROI Editor, DiffeoMap Questions/Support
Betreff: Re: [Mristudio-users] Obtaining tract volume data

Hi Melisa,

On Wed, May 18, 2011 at 12:12 AM,  <melcarr at umich.edu> wrote:
> Hello,
>
> I'm attempting to calculate mean tract volume for a tract spanning
> between two ROIs in a subject's FA map.
>
> Is it safe to define tract volume as: the number of voxels between
> both ROIs multiplied by the size of an individual voxel?

This is what we do too.

>
> Does the first measure above ("the number of voxels between both
> ROIs") correspond to the measure "Average Length, mm" in the Fiber
> Statistics window (an example of this window is shown in the User
> Manual, page 26, Figure 19. Fiber-statistics)?

I think the number of voxels occupied by fibers and the average length
of the fibers are very different. The former has unit of mm^3 and the
latter is mm. I don't use the length of fibers for quantification.


>
> Just wondering, thank you.
>
> -Melisa Carrasco
>
> --
>
> Melisa Carrasco, M.S.
> MD/PhD Student, Year Grad-4 (Ph.D. Candidate)
>
> University of Michigan, Neuroscience Graduate Program, Class of 2012
> University of Rochester School of Medicine and Dentistry, Class of 2014
>
> About me: http://sitemaker.umich.edu/melisa.carrasco/home
> GO BLUE!
>
>
>
>
> _______________________________________________
> mristudio-users mailing 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 salvador.castaneda at med.uni-tuebingen.de  Thu May 19 14:34:52 2011
From: salvador.castaneda at med.uni-tuebingen.de (Castaneda, Salvador)
Date: Thu, 19 May 2011 20:34:52 +0200
Subject: [Mristudio-users] Obtaining tract volume data
In-Reply-To: <145933A2BE9E4F48AE079A201379BF2F244D9670CB@RAD-EXCH1.win.ad.jhu.edu>
References: <20110518001239.12783v9a9a6brbqc@web.mail.umich.edu>
	<BANLkTinNU-VuqABS-gfwUH5_E5aBT0Ug4g@mail.gmail.com>
	<0AC64F4CB253074799B64FF8F0772D350126C6F4@azex2003.raddiag.med.uni-tuebingen.de>
	<145933A2BE9E4F48AE079A201379BF2F244D9670CB@RAD-EXCH1.win.ad.jhu.edu>
Message-ID: <0AC64F4CB253074799B64FF8F0772D350126C6F5@azex2003.raddiag.med.uni-tuebingen.de>

Hey,

I did this already. The gradient table was acquired from the header file of the mosaic. The B values were copied in there automatically. I also have placed te b values separated by a comma on the Bvalues, optional Box. I don't understand what the problem is. Thanks
Any other ideas????
Best,

salvador 

-----Urspr?ngliche Nachricht-----
Von: Hangyi Jiang [mailto:hjiang at jhmi.edu] 
Gesendet: Donnerstag, 19. Mai 2011 20:07
An: Castaneda, Salvador
Betreff: RE: [Mristudio-users] Obtaining tract volume data

hi,

for multiple b-value dataset, you can define the gradeint table as:  #: x, y, z, b-value
e.g.

0: 1, 0, 0, 600
1: 0,1,0, 600
....
32: 1,0,0, 1000
33: 0,1,0, 1000
...

regards,

hangyi



________________________________________
From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Castaneda, Salvador [salvador.castaneda at med.uni-tuebingen.de]
Sent: Thursday, May 19, 2011 11:56 AM
To: DTI Studio, ROI Editor,DiffeoMap Questions/Support
Subject: Re: [Mristudio-users] Obtaining tract volume data

Hello Susumu,

I've been using DTIstudio for over a year... It works good. But i just started running a tensor calculation with 4 b values and 256 directions. But it is crashing in the process of the calculation. I'm not requesting any other commands, just the tensor... Do you have any idea what i could do to calculate it... Do i have to analize with less bvalues?
Thanks
salvador

-----Urspr?ngliche Nachricht-----
Von: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] Im Auftrag von susumu mori
Gesendet: Donnerstag, 19. Mai 2011 17:48
An: DTI Studio, ROI Editor, DiffeoMap Questions/Support
Betreff: Re: [Mristudio-users] Obtaining tract volume data

Hi Melisa,

On Wed, May 18, 2011 at 12:12 AM,  <melcarr at umich.edu> wrote:
> Hello,
>
> I'm attempting to calculate mean tract volume for a tract spanning
> between two ROIs in a subject's FA map.
>
> Is it safe to define tract volume as: the number of voxels between
> both ROIs multiplied by the size of an individual voxel?

This is what we do too.

>
> Does the first measure above ("the number of voxels between both
> ROIs") correspond to the measure "Average Length, mm" in the Fiber
> Statistics window (an example of this window is shown in the User
> Manual, page 26, Figure 19. Fiber-statistics)?

I think the number of voxels occupied by fibers and the average length
of the fibers are very different. The former has unit of mm^3 and the
latter is mm. I don't use the length of fibers for quantification.


>
> Just wondering, thank you.
>
> -Melisa Carrasco
>
> --
>
> Melisa Carrasco, M.S.
> MD/PhD Student, Year Grad-4 (Ph.D. Candidate)
>
> University of Michigan, Neuroscience Graduate Program, Class of 2012
> University of Rochester School of Medicine and Dentistry, Class of 2014
>
> About me: http://sitemaker.umich.edu/melisa.carrasco/home
> GO BLUE!
>
>
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org
>
_______________________________________________
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mristudio-users at mristudio.org
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From susumu at mri.jhu.edu  Thu May 19 14:56:02 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Thu, 19 May 2011 14:56:02 -0400
Subject: [Mristudio-users] Obtaining tract volume data
In-Reply-To: <0AC64F4CB253074799B64FF8F0772D350126C6F4@azex2003.raddiag.med.uni-tuebingen.de>
References: <20110518001239.12783v9a9a6brbqc@web.mail.umich.edu>
	<BANLkTinNU-VuqABS-gfwUH5_E5aBT0Ug4g@mail.gmail.com>
	<0AC64F4CB253074799B64FF8F0772D350126C6F4@azex2003.raddiag.med.uni-tuebingen.de>
Message-ID: <BANLkTimpVO3ng4_gH6Y1ZDHhpEmmribeNQ@mail.gmail.com>

If you are using DICOM, one of the common culprits is the mismatch
between your gradient table and the number of of the images.

Please read the images first by Mri3DView. Check the image dimensions
and the number of 3D volumes.

Then make sure the number of the 3D volumes exactly match the row of
your gradient table. in your case, there should be 260 3D images to
load and 260 rows in the table.

Another common issue is the shortage of RAM. If you are using a 32-bit
operating system, it may not be able to process your large data, no
matter how much RAM you have. To check it, limit the number of the
slices to process in the opening data input window of DtiMapping (e.g.
slice 0-4). If your calculation runs through with this limited number
of slices, then it is the RAM shortage. Then the only solution is to
migrate to a 64-bit operating system.

On Thu, May 19, 2011 at 11:56 AM, Castaneda, Salvador
<salvador.castaneda at med.uni-tuebingen.de> wrote:
> Hello Susumu,
>
> I've been using DTIstudio for over a year... It works good. But i just started running a tensor calculation with 4 b values and 256 directions. But it is crashing in the process of the calculation. I'm not requesting any other commands, just the tensor... Do you have any idea what i could do to calculate it... Do i have to analize with less bvalues?
> Thanks
> salvador
>
> -----Urspr?ngliche Nachricht-----
> Von: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] Im Auftrag von susumu mori
> Gesendet: Donnerstag, 19. Mai 2011 17:48
> An: DTI Studio, ROI Editor, DiffeoMap Questions/Support
> Betreff: Re: [Mristudio-users] Obtaining tract volume data
>
> Hi Melisa,
>
> On Wed, May 18, 2011 at 12:12 AM, ?<melcarr at umich.edu> wrote:
>> Hello,
>>
>> I'm attempting to calculate mean tract volume for a tract spanning
>> between two ROIs in a subject's FA map.
>>
>> Is it safe to define tract volume as: the number of voxels between
>> both ROIs multiplied by the size of an individual voxel?
>
> This is what we do too.
>
>>
>> Does the first measure above ("the number of voxels between both
>> ROIs") correspond to the measure "Average Length, mm" in the Fiber
>> Statistics window (an example of this window is shown in the User
>> Manual, page 26, Figure 19. Fiber-statistics)?
>
> I think the number of voxels occupied by fibers and the average length
> of the fibers are very different. The former has unit of mm^3 and the
> latter is mm. I don't use the length of fibers for quantification.
>
>
>>
>> Just wondering, thank you.
>>
>> -Melisa Carrasco
>>
>> --
>>
>> Melisa Carrasco, M.S.
>> MD/PhD Student, Year Grad-4 (Ph.D. Candidate)
>>
>> University of Michigan, Neuroscience Graduate Program, Class of 2012
>> University of Rochester School of Medicine and Dentistry, Class of 2014
>>
>> About me: http://sitemaker.umich.edu/melisa.carrasco/home
>> GO BLUE!
>>
>>
>>
>>
>> _______________________________________________
>> mristudio-users mailing 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 salvador.castaneda at med.uni-tuebingen.de  Thu May 19 15:59:54 2011
From: salvador.castaneda at med.uni-tuebingen.de (Castaneda, Salvador)
Date: Thu, 19 May 2011 21:59:54 +0200
Subject: [Mristudio-users] Obtaining tract volume data
In-Reply-To: <BANLkTimpVO3ng4_gH6Y1ZDHhpEmmribeNQ@mail.gmail.com>
References: <20110518001239.12783v9a9a6brbqc@web.mail.umich.edu>
	<BANLkTinNU-VuqABS-gfwUH5_E5aBT0Ug4g@mail.gmail.com>
	<0AC64F4CB253074799B64FF8F0772D350126C6F4@azex2003.raddiag.med.uni-tuebingen.de>
	<BANLkTimpVO3ng4_gH6Y1ZDHhpEmmribeNQ@mail.gmail.com>
Message-ID: <0AC64F4CB253074799B64FF8F0772D350126C6F6@azex2003.raddiag.med.uni-tuebingen.de>

 
I tried running on a 64bit system  but it didn't work.
I opened the files in Mri3DView and the number of total volumes was 769. I saved this as image.dat and opened it in DTI mapping. The gradient table, when you acquire it from the image.dat image and folder is this:
0: 0, 0, 0, 0
1: 0.036259, 0.056137, 0.997764, 200
2: 0.013466, 0.095094, 0.995377, 200
3: -0.009638, 0.015681, 0.999831, 200
4: 0.001832, -0.022235, 0.999751, 200
5: 0.033903, -0.116385, 0.992625, 200
6: -0.120536, -0.052798, 0.991304, 200
7: 0.125837, 0.004680, -0.992040, 200
8: 0.149493, -0.174174, -0.973301, 200
9: -0.026872, 0.198141, 0.979805, 200
10: -0.139299, -0.140766, -0.980194, 200
11: -0.300591, -0.086983, -0.949778, 200
12: -0.139099, 0.042379, -0.989371, 200
13: 0.172552, -0.113993, 0.978382, 200
14: 0.038590, -0.207922, 0.977384, 200
15: 0.033657, -0.297325, 0.954183, 200
16: -0.134182, -0.236161, 0.962405, 200
17: -0.287050, -0.175442, 0.941713, 200
18: -0.284042, 0.009099, 0.958769, 200
19: 0.301289, -0.098527, -0.948429, 200
20: 0.287165, -0.298248, -0.910266, 200
21: -0.063655, 0.305652, 0.950013, 200
22: -0.034158, 0.363119, 0.931117, 200
23: -0.143075, -0.322678, -0.935633, 200
24: -0.309259, -0.273854, -0.910694, 200
25: 0.470230, 0.217485, 0.855327, 200
26: 0.456033, 0.029969, 0.889458, 200
27: 0.303741, -0.011250, 0.952688, 200
28: 0.342908, -0.216865, 0.913993, 200
29: 0.209809, -0.313582, 0.926092, 200
30: 0.065844, -0.397050, 0.915432, 200
31: 0.021398, -0.480248, 0.876871, 200
32: -0.133124, -0.404479, 0.904807, 200
33: -0.304717, -0.392947, 0.867606, 200
34: 0.440864, 0.284286, -0.851364, 200
35: 0.448379, 0.089940, -0.889307, 200
36: -0.452391, 0.037178, 0.891044, 200
37: -0.455053, 0.235011, 0.858892, 200
38: -0.428186, 0.422193, 0.799006, 200
39: 0.246323, -0.456900, -0.854732, 200
40: -0.082416, 0.489028, 0.868366, 200
41: -0.019594, 0.535460, 0.844333, 200
42: 0.148339, 0.504380, 0.850645, 200
43: -0.310554, -0.456845, -0.833576, 200
44: 0.467890, 0.401117, 0.787517, 200
45: 0.619277, 0.159392, 0.768824, 200
46: -0.607824, 0.020036, -0.793818, 200
47: -0.467757, 0.109019, -0.877108, 200
48: -0.505282, 0.318847, -0.801889, 200
49: 0.377350, -0.416435, 0.827157, 200
50: 0.238544, -0.507810, 0.827784, 200
51: 0.088776, -0.584904, 0.806229, 200
52: -0.011200, -0.648146, 0.761433, 200
53: -0.163437, -0.567064, 0.807296, 200
54: -0.333650, -0.586528, 0.738012, 200
55: 0.456124, 0.477580, -0.750911, 200
56: 0.582984, 0.358747, -0.728993, 200
57: 0.600321, 0.178753, -0.779527, 200
58: 0.595215, -0.006598, -0.803539, 200
59: -0.605081, 0.179819, 0.775591, 200
60: -0.584334, 0.366385, 0.724097, 200
61: -0.533540, 0.537917, 0.652671, 200
62: 0.372150, -0.589462, -0.716966, 200
63: 0.203971, -0.631619, -0.747966, 200
64: -0.038081, 0.668874, 0.742400, 200
65: 0.107427, 0.671267, 0.733390, 200
66: -0.276565, -0.634833, -0.721456, 200
67: 0.436423, 0.579837, 0.687985, 200
68: 0.586746, 0.509690, 0.629242, 200
69: 0.614617, 0.337766, 0.712854, 200
70: -0.747235, -0.070408, -0.660820, 200
71: -0.740225, 0.157686, -0.653607, 200
72: -0.616376, 0.204745, -0.760369, 200
73: -0.668941, 0.363307, -0.648480, 200
74: -0.545117, 0.483429, -0.684940, 200
75: 0.409217, -0.587629, 0.698021, 200
76: 0.261085, -0.672117, 0.692888, 200
77: 0.100259, -0.737787, 0.667547, 200
78: -0.051884, -0.786250, 0.615727, 200
79: -0.199352, -0.713602, 0.671588, 200
80: -0.360512, -0.742101, 0.565081, 200
81: 0.479984, 0.645347, -0.594257, 200
82: 0.595629, 0.537963, -0.596509, 200
83: 0.699846, 0.419151, -0.578384, 200
84: 0.730334, 0.252692, -0.634633, 200
85: -0.739374, -0.085351, 0.667863, 200
86: -0.740223, 0.132217, 0.659233, 200
87: -0.724162, 0.307746, 0.617157, 200
88: -0.680016, 0.472366, 0.560757, 200
89: -0.610808, 0.624622, 0.486581, 200
90: -0.465596, 0.690863, 0.553108, 200
91: 0.307912, -0.743415, -0.593738, 200
92: -0.139608, 0.784653, 0.604011, 200
93: 0.029068, 0.789075, 0.613609, 200
94: -0.221269, -0.779100, -0.586552, 200
95: -0.382101, -0.732934, -0.562855, 200
96: 0.533331, 0.667426, 0.519712, 200
97: 0.669254, 0.581598, 0.462431, 200
98: 0.721238, 0.432058, 0.541425, 200
99: -0.747263, -0.257056, -0.612797, 200
100: -0.853109, -0.166885, -0.494323, 200
101: -0.852107, 0.098101, -0.514091, 200
102: -0.818856, 0.275502, -0.503561, 200
103: -0.763785, 0.420091, -0.490057, 200
104: -0.663240, 0.534602, -0.523750, 200
105: -0.544408, 0.639635, -0.542667, 200
106: -0.411817, 0.730946, -0.544175, 200
107: 0.262892, -0.801784, 0.536686, 200
108: 0.106747, -0.854417, 0.508504, 200
109: -0.077662, -0.887958, 0.453321, 200
110: -0.228520, -0.828921, 0.510558, 200
111: 0.380882, 0.839144, -0.388285, 200
112: 0.508757, 0.751237, -0.420487, 200
113: 0.622958, 0.649506, -0.435965, 200
114: 0.730241, 0.534516, -0.425489, 200
115: -0.811787, -0.371994, 0.450136, 200
116: -0.843916, -0.202772, 0.496678, 200
117: -0.852167, 0.061240, 0.519674, 200
118: -0.839753, 0.236280, 0.488863, 200
119: -0.802252, 0.401396, 0.441898, 200
120: -0.743628, 0.546715, 0.384864, 200
121: -0.662088, 0.676900, 0.321630, 200
122: -0.535336, 0.754382, 0.379900, 200
123: -0.393464, 0.815384, 0.424659, 200
124: 0.234683, -0.863471, -0.446477, 200
125: -0.057531, 0.881194, 0.469241, 200
126: -0.139792, -0.879196, -0.455491, 200
127: -0.313907, -0.849048, -0.424947, 200
128: 0.468076, 0.791046, 0.393892, 200
129: 0.601712, 0.718179, 0.349516, 200
130: 0.720257, 0.630979, 0.288263, 200
131: 0.787196, 0.494988, 0.367843, 200
132: -0.830365, -0.337456, -0.443416, 200
133: -0.917761, -0.238002, -0.317914, 200
134: -0.931300, -0.067505, -0.357944, 200
135: -0.906488, 0.233102, -0.352056, 200
136: -0.853547, 0.393741, -0.341210, 200
137: -0.767201, 0.540351, -0.345578, 200
138: -0.660922, 0.651784, -0.371967, 200
139: -0.537754, 0.750412, -0.384321, 200
140: -0.402768, 0.829810, -0.386255, 200
141: 0.258431, -0.892706, 0.369174, 200
142: 0.108288, -0.934897, 0.337996, 200
143: -0.103269, -0.952927, 0.285073, 200
144: -0.247919, -0.908086, 0.337514, 200
145: 0.387189, 0.896444, -0.215576, 200
146: 0.510010, 0.822590, -0.251468, 200
147: 0.625713, 0.731902, -0.269819, 200
148: 0.732591, 0.622074, -0.276286, 200
149: -0.825719, -0.481523, 0.293810, 200
150: -0.893115, -0.315207, 0.320922, 200
151: -0.923078, -0.146442, 0.355642, 200
152: -0.924562, 0.159829, 0.345890, 200
153: -0.896124, 0.321247, 0.306207, 200
154: -0.844171, 0.465941, 0.265093, 200
155: -0.776249, 0.592099, 0.216462, 200
156: -0.689929, 0.706497, 0.157671, 200
157: -0.580942, 0.787897, 0.204269, 200
158: -0.456911, 0.853319, 0.251158, 200
159: 0.315677, -0.906537, -0.280246, 200
160: 0.154045, -0.938848, -0.307953, 200
161: 0.063748, 0.946176, 0.317313, 200
162: -0.238359, -0.926232, -0.292026, 200
163: 0.394160, 0.881346, 0.260514, 200
164: 0.529382, 0.817229, 0.227796, 200
165: 0.646506, 0.741844, 0.178037, 200
166: 0.749878, 0.649193, 0.127401, 200
167: -0.821144, -0.538063, -0.190293, 200
168: -0.877963, -0.395612, -0.269578, 200
169: -0.941734, -0.303674, -0.144638, 200
170: -0.972785, -0.145023, -0.180713, 200
171: -0.961602, 0.192841, -0.195279, 200
172: -0.917628, 0.348329, -0.191377, 200
173: -0.842874, 0.500918, -0.196582, 200
174: -0.747422, 0.632324, -0.203780, 200
175: -0.638449, 0.736433, -0.223716, 200
176: -0.515717, 0.825565, -0.229083, 200
177: -0.380807, 0.897996, -0.220429, 200
178: 0.244375, -0.949683, 0.195917, 200
179: 0.103556, -0.980520, 0.166900, 200
180: -0.125358, -0.984739, 0.120724, 200
181: -0.259814, -0.950502, 0.170420, 200
182: 0.357112, 0.933268, -0.038492, 200
183: 0.481864, 0.872611, -0.079739, 200
184: 0.601163, 0.791669, -0.108920, 200
185: 0.709697, 0.693312, -0.125097, 200
186: -0.810680, -0.567100, 0.145587, 200
187: -0.892786, -0.418678, 0.166258, 200
188: -0.950524, -0.249310, 0.185335, 200
189: -0.976052, 0.088129, 0.198885, 200
190: -0.953022, 0.253569, 0.165687, 200
191: -0.906853, 0.402109, 0.126201, 200
192: -0.841703, 0.533089, 0.085741, 200
193: -0.755320, 0.654095, 0.040644, 200
194: -0.638760, 0.768644, 0.034221, 200
195: -0.521779, 0.850032, 0.072063, 200
196: -0.395071, 0.911888, 0.111266, 200
197: 0.251893, -0.956855, -0.144842, 200
198: 0.184927, -0.982654, -0.013881, 200
199: 0.088490, -0.982747, -0.162414, 200
200: -0.155487, -0.975737, -0.154148, 200
201: 0.315590, 0.939987, 0.129722, 200
202: 0.462076, 0.881832, 0.094115, 200
203: 0.583808, 0.810153, 0.053107, 200
204: 0.692813, 0.721088, 0.006538, 200
205: -0.800257, -0.599653, -0.001963, 200
206: -0.888084, -0.448046, -0.102767, 200
207: -0.935797, -0.352209, 0.015301, 200
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209: -0.987553, 0.152445, -0.038740, 200
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560: -0.501645, 0.306783, -0.808849, 1000
561: -0.379304, 0.409519, -0.829712, 1000
562: -0.247407, 0.500752, -0.829480, 1000
563: 0.104053, -0.578799, 0.808805, 1000
564: -0.028231, -0.639010, 0.768681, 1000
565: -0.175010, -0.557730, 0.811362, 1000
566: 0.325600, 0.560910, -0.761160, 1000
567: 0.445480, 0.454533, -0.771329, 1000
568: 0.566756, 0.337330, -0.751662, 1000
569: 0.594966, 0.175303, -0.784400, 1000
570: 0.609819, 0.008937, -0.792490, 1000
571: -0.600377, 0.174624, 0.780419, 1000
572: -0.569310, 0.341613, 0.747788, 1000
573: -0.512791, 0.501512, 0.696801, 1000
574: -0.359595, 0.561008, 0.745628, 1000
575: -0.205299, 0.610194, 0.765190, 1000
576: 0.049791, -0.654468, -0.754448, 1000
577: -0.111126, -0.652431, -0.749657, 1000
578: 0.269680, 0.607320, 0.747285, 1000
579: 0.420692, 0.546811, 0.723890, 1000
580: 0.561943, 0.473525, 0.678229, 1000
581: 0.599757, 0.313970, 0.736013, 1000
582: -0.734356, -0.056962, -0.676370, 1000
583: -0.723205, 0.139017, -0.676497, 1000
584: -0.608944, 0.195192, -0.768822, 1000
585: -0.647046, 0.329806, -0.687430, 1000
586: -0.525154, 0.452431, -0.720777, 1000
587: -0.392998, 0.555618, -0.732694, 1000
588: -0.251231, 0.642522, -0.723912, 1000
589: 0.099525, -0.709824, 0.697312, 1000
590: -0.045764, -0.756215, 0.652721, 1000
591: 0.192566, 0.682159, -0.705392, 1000
592: 0.337121, 0.702424, -0.626858, 1000
593: 0.456227, 0.603521, -0.653926, 1000
594: 0.569184, 0.497459, -0.654648, 1000
595: 0.673988, 0.379755, -0.633661, 1000
596: 0.708832, 0.226551, -0.668006, 1000
597: -0.727056, -0.070200, 0.682980, 1000
598: -0.724523, 0.115344, 0.679531, 1000
599: -0.700185, 0.275500, 0.658667, 1000
600: -0.653672, 0.431311, 0.621839, 1000
601: -0.584690, 0.578880, 0.568362, 1000
602: -0.441607, 0.648799, 0.619712, 1000
603: -0.289338, 0.704023, 0.648564, 1000
604: 0.132577, -0.749508, -0.648584, 1000
605: -0.028352, -0.759171, -0.650274, 1000
606: 0.203212, 0.741735, 0.639167, 1000
607: 0.360594, 0.690981, 0.626512, 1000
608: 0.508297, 0.623593, 0.593941, 1000
609: 0.643445, 0.538847, 0.543712, 1000
610: 0.694774, 0.388107, 0.605526, 1000
611: -0.723271, -0.224011, -0.653222, 1000
612: -0.828465, -0.128797, -0.545029, 1000
613: -0.827678, 0.065262, -0.557395, 1000
614: -0.793611, 0.230556, -0.563050, 1000
615: -0.737448, 0.374246, -0.562238, 1000
616: -0.635428, 0.491993, -0.595125, 1000
617: -0.517249, 0.597243, -0.612988, 1000
618: -0.385235, 0.689099, -0.613789, 1000
619: -0.241441, 0.763690, -0.598736, 1000
620: 0.089324, -0.819036, 0.566747, 1000
621: -0.058642, -0.852924, 0.518731, 1000
622: 0.204797, 0.791619, -0.575672, 1000
623: 0.354476, 0.801967, -0.480828, 1000
624: 0.480850, 0.710966, -0.513139, 1000
625: 0.597954, 0.606419, -0.524125, 1000
626: 0.706443, 0.487213, -0.513383, 1000
627: -0.786393, -0.325775, 0.524839, 1000
628: -0.818400, -0.163241, 0.550976, 1000
629: -0.828413, 0.031900, 0.559208, 1000
630: -0.815187, 0.194585, 0.545533, 1000
631: -0.779341, 0.352646, 0.517947, 1000
632: -0.721596, 0.500270, 0.478570, 1000
633: -0.643242, 0.636382, 0.425745, 1000
634: -0.509621, 0.716640, 0.476145, 1000
635: -0.365972, 0.777153, 0.511955, 1000
636: -0.211500, 0.825382, 0.523461, 1000
637: 0.041986, -0.845925, -0.531646, 1000
638: -0.120079, -0.842240, -0.525559, 1000
639: 0.287018, 0.811380, 0.509199, 1000
640: 0.439958, 0.754134, 0.487564, 1000
641: 0.580237, 0.678886, 0.449932, 1000
642: 0.705634, 0.588036, 0.395341, 1000
643: -0.767944, -0.447186, -0.458571, 1000
644: -0.805982, -0.291401, -0.515246, 1000
645: -0.898855, -0.183987, -0.397756, 1000
646: -0.908614, -0.021367, -0.417090, 1000
647: -0.886023, 0.180486, -0.427070, 1000
648: -0.837066, 0.341814, -0.427181, 1000
649: -0.749364, 0.492488, -0.442616, 1000
650: -0.638972, 0.609036, -0.469884, 1000
651: -0.514534, 0.710047, -0.480716, 1000
652: -0.376562, 0.793216, -0.478550, 1000
653: -0.230254, 0.859197, -0.456907, 1000
654: 0.080083, -0.903775, 0.420449, 1000
655: -0.073695, -0.924985, 0.372788, 1000
656: 0.218060, 0.875839, -0.430530, 1000
657: 0.361601, 0.874720, -0.322660, 1000
658: 0.488936, 0.794834, -0.359416, 1000
659: 0.607745, 0.697276, -0.380070, 1000
660: 0.719365, 0.580648, -0.381263, 1000
661: -0.812366, -0.430465, 0.393397, 1000
662: -0.875771, -0.262762, 0.404945, 1000
663: -0.901930, -0.094216, 0.421480, 1000
664: -0.902884, 0.108479, 0.415973, 1000
665: -0.879255, 0.266666, 0.394715, 1000
666: -0.833726, 0.414667, 0.364628, 1000
667: -0.767968, 0.552814, 0.323452, 1000
668: -0.684293, 0.675622, 0.274370, 1000
669: -0.562940, 0.762612, 0.318623, 1000
670: -0.431563, 0.827743, 0.358600, 1000
671: -0.286417, 0.878821, 0.381626, 1000
672: 0.126563, -0.909451, -0.396081, 1000
673: -0.038396, -0.916559, -0.398053, 1000
674: 0.205757, 0.899308, 0.385887, 1000
675: 0.364028, 0.857116, 0.364466, 1000
676: 0.510145, 0.792068, 0.335233, 1000
677: 0.637908, 0.713455, 0.289923, 1000
678: -0.750152, -0.617267, -0.237180, 1000
679: -0.817365, -0.493105, -0.297928, 1000
680: -0.865987, -0.342479, -0.364383, 1000
681: -0.940108, -0.240872, -0.241199, 1000
682: -0.961326, -0.077974, -0.264146, 1000
683: -0.951365, 0.130514, -0.279052, 1000
684: -0.911826, 0.292310, -0.288319, 1000
685: -0.839240, 0.452669, -0.301276, 1000
686: -0.739910, 0.593881, -0.315972, 1000
687: -0.623542, 0.706521, -0.334698, 1000
688: -0.493315, 0.800941, -0.339314, 1000
689: -0.353179, 0.876044, -0.328347, 1000
690: -0.212080, 0.930384, -0.299011, 1000
691: 0.068280, -0.962961, 0.260852, 1000
692: -0.086752, -0.971645, 0.219957, 1000
693: 0.228125, 0.934952, -0.271706, 1000
694: 0.331727, 0.932186, -0.144865, 1000
695: 0.464547, 0.864362, -0.192548, 1000
696: 0.592015, 0.774852, -0.221636, 1000
697: 0.706303, 0.665637, -0.240964, 1000
698: -0.812137, -0.524604, 0.255390, 1000
699: -0.892934, -0.362352, 0.267151, 1000
700: -0.942543, -0.187154, 0.276743, 1000
701: -0.960644, 0.025934, 0.276570, 1000
702: -0.946973, 0.190853, 0.258491, 1000
703: -0.909306, 0.346127, 0.230996, 1000
704: -0.848766, 0.491647, 0.194628, 1000
705: -0.765063, 0.626049, 0.150801, 1000
706: -0.638361, 0.755751, 0.146064, 1000
707: -0.509087, 0.841033, 0.183014, 1000
708: -0.371041, 0.902182, 0.219990, 1000
709: -0.218379, 0.943779, 0.248179, 1000
710: -0.148830, 0.982349, 0.113313, 1000
711: 0.050605, -0.964402, -0.259554, 1000
712: -0.120659, -0.959790, -0.253464, 1000
713: 0.287293, 0.928169, 0.236569, 1000
714: 0.442854, 0.872256, 0.207482, 1000
715: 0.578614, 0.798948, 0.163972, 1000
716: 0.700182, 0.704443, 0.116210, 1000
717: -0.816248, -0.567298, -0.109143, 1000
718: -0.893896, -0.397413, -0.207395, 1000
719: -0.952698, -0.292700, -0.081818, 1000
720: -0.985161, -0.135864, -0.104881, 1000
721: -0.989230, 0.078420, -0.123587, 1000
722: -0.961154, 0.239283, -0.137571, 1000
723: -0.904292, 0.396723, -0.157692, 1000
724: -0.817946, 0.549242, -0.171164, 1000
725: -0.707258, 0.682772, -0.183328, 1000
726: -0.581027, 0.790599, -0.193292, 1000
727: -0.442805, 0.876473, -0.188994, 1000
728: -0.302387, 0.939693, -0.159809, 1000
729: -0.156226, 0.980071, -0.122695, 1000
730: -0.006613, -0.995882, 0.090414, 1000
731: -0.108285, -0.993878, 0.021917, 1000
732: 0.186635, 0.977716, -0.096123, 1000
733: 0.278492, 0.960043, 0.027559, 1000
734: 0.422906, 0.906026, -0.016389, 1000
735: 0.554093, 0.830209, -0.061099, 1000
736: 0.679276, 0.729046, -0.084125, 1000
737: -0.786555, -0.607012, 0.113441, 1000
738: -0.881890, -0.452949, 0.130793, 1000
739: -0.949828, -0.279886, 0.139608, 1000
740: -0.985050, -0.110787, 0.131923, 1000
741: -0.987169, 0.106528, 0.118951, 1000
742: -0.958650, 0.268097, 0.095472, 1000
743: -0.905410, 0.419730, 0.063714, 1000
744: -0.826951, 0.561609, 0.027343, 1000
745: -0.713594, 0.700390, 0.015442, 1000
746: -0.580134, 0.814383, 0.015011, 1000
747: -0.446592, 0.893582, 0.045466, 1000
748: -0.304272, 0.948966, 0.082954, 1000
749: -0.234079, 0.972085, 0.016056, 1000
750: 0.076706, -0.996842, 0.020570, 1000
751: -0.029110, -0.992515, -0.118604, 1000
752: 0.201452, 0.973671, 0.106686, 1000
753: 0.364186, 0.927727, 0.081803, 1000
754: 0.505145, 0.862223, 0.037419, 1000
755: 0.631614, 0.775262, -0.005682, 1000
756: -0.753175, -0.657324, 0.025551, 1000
757: -0.846858, -0.531745, -0.008881, 1000
758: -0.893156, -0.445599, -0.060936, 1000
759: -0.930099, -0.367278, 0.004724, 1000
760: -0.978723, -0.205012, -0.008492, 1000
761: -0.998900, -0.041282, -0.022248, 1000
762: -0.983881, 0.177767, 0.019400, 1000
763: -0.941919, 0.335835, -0.001633, 1000
764: -0.873761, 0.485508, -0.028716, 1000
765: -0.773893, 0.631986, -0.041033, 1000
766: -0.651986, 0.756588, -0.049881, 1000
767: -0.516083, 0.855183, -0.048171, 1000
768: -0.378344, 0.925432, -0.020770, 1000

I dont understand why you mention it should be 260 rows and 260 volumes? I have 256 directions and 4 B values... I dont understand where the error is...
Best,
salvador

-----Urspr?ngliche Nachricht-----
Von: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] Im Auftrag von susumu mori
Gesendet: Donnerstag, 19. Mai 2011 20:56
An: DTI Studio, ROI Editor, DiffeoMap Questions/Support
Betreff: Re: [Mristudio-users] Obtaining tract volume data

If you are using DICOM, one of the common culprits is the mismatch
between your gradient table and the number of of the images.

Please read the images first by Mri3DView. Check the image dimensions
and the number of 3D volumes.

Then make sure the number of the 3D volumes exactly match the row of
your gradient table. in your case, there should be 260 3D images to
load and 260 rows in the table.

Another common issue is the shortage of RAM. If you are using a 32-bit
operating system, it may not be able to process your large data, no
matter how much RAM you have. To check it, limit the number of the
slices to process in the opening data input window of DtiMapping (e.g.
slice 0-4). If your calculation runs through with this limited number
of slices, then it is the RAM shortage. Then the only solution is to
migrate to a 64-bit operating system.

On Thu, May 19, 2011 at 11:56 AM, Castaneda, Salvador
<salvador.castaneda at med.uni-tuebingen.de> wrote:
> Hello Susumu,
>
> I've been using DTIstudio for over a year... It works good. But i just started running a tensor calculation with 4 b values and 256 directions. But it is crashing in the process of the calculation. I'm not requesting any other commands, just the tensor... Do you have any idea what i could do to calculate it... Do i have to analize with less bvalues?
> Thanks
> salvador
>
> -----Urspr?ngliche Nachricht-----
> Von: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] Im Auftrag von susumu mori
> Gesendet: Donnerstag, 19. Mai 2011 17:48
> An: DTI Studio, ROI Editor, DiffeoMap Questions/Support
> Betreff: Re: [Mristudio-users] Obtaining tract volume data
>
> Hi Melisa,
>
> On Wed, May 18, 2011 at 12:12 AM, ?<melcarr at umich.edu> wrote:
>> Hello,
>>
>> I'm attempting to calculate mean tract volume for a tract spanning
>> between two ROIs in a subject's FA map.
>>
>> Is it safe to define tract volume as: the number of voxels between
>> both ROIs multiplied by the size of an individual voxel?
>
> This is what we do too.
>
>>
>> Does the first measure above ("the number of voxels between both
>> ROIs") correspond to the measure "Average Length, mm" in the Fiber
>> Statistics window (an example of this window is shown in the User
>> Manual, page 26, Figure 19. Fiber-statistics)?
>
> I think the number of voxels occupied by fibers and the average length
> of the fibers are very different. The former has unit of mm^3 and the
> latter is mm. I don't use the length of fibers for quantification.
>
>
>>
>> Just wondering, thank you.
>>
>> -Melisa Carrasco
>>
>> --
>>
>> Melisa Carrasco, M.S.
>> MD/PhD Student, Year Grad-4 (Ph.D. Candidate)
>>
>> University of Michigan, Neuroscience Graduate Program, Class of 2012
>> University of Rochester School of Medicine and Dentistry, Class of 2014
>>
>> About me: http://sitemaker.umich.edu/melisa.carrasco/home
>> GO BLUE!
>>
>>
>>
>>
>> _______________________________________________
>> mristudio-users mailing list
>> mristudio-users at mristudio.org
>> http://lists.mristudio.org/mailman/listinfo/
>> Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org
>>
> _______________________________________________
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>
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>
>

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From susumu at mri.jhu.edu  Thu May 19 16:07:27 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Thu, 19 May 2011 16:07:27 -0400
Subject: [Mristudio-users] Obtaining tract volume data
In-Reply-To: <0AC64F4CB253074799B64FF8F0772D350126C6F6@azex2003.raddiag.med.uni-tuebingen.de>
References: <20110518001239.12783v9a9a6brbqc@web.mail.umich.edu>
	<BANLkTinNU-VuqABS-gfwUH5_E5aBT0Ug4g@mail.gmail.com>
	<0AC64F4CB253074799B64FF8F0772D350126C6F4@azex2003.raddiag.med.uni-tuebingen.de>
	<BANLkTimpVO3ng4_gH6Y1ZDHhpEmmribeNQ@mail.gmail.com>
	<0AC64F4CB253074799B64FF8F0772D350126C6F6@azex2003.raddiag.med.uni-tuebingen.de>
Message-ID: <BANLkTineGW_dfV197byd_7SoR1iy31vUog@mail.gmail.com>

sorry I thought you did 256 orientations + 4 b0.

With 769 3D volumes, you might have run into memory problem even with
the 64-bit system.
Please try to limit the number of the slices for testing.

On Thu, May 19, 2011 at 3:59 PM, Castaneda, Salvador
<salvador.castaneda at med.uni-tuebingen.de> wrote:
>
> I tried running on a 64bit system ?but it didn't work.
> I opened the files in Mri3DView and the number of total volumes was 769. I saved this as image.dat and opened it in DTI mapping. The gradient table, when you acquire it from the image.dat image and folder is this:
> 0: 0, 0, 0, 0
> 1: 0.036259, 0.056137, 0.997764, 200
> 2: 0.013466, 0.095094, 0.995377, 200
> 3: -0.009638, 0.015681, 0.999831, 200
> 4: 0.001832, -0.022235, 0.999751, 200
> 5: 0.033903, -0.116385, 0.992625, 200
> 6: -0.120536, -0.052798, 0.991304, 200
> 7: 0.125837, 0.004680, -0.992040, 200
> 8: 0.149493, -0.174174, -0.973301, 200
> 9: -0.026872, 0.198141, 0.979805, 200
> 10: -0.139299, -0.140766, -0.980194, 200
> 11: -0.300591, -0.086983, -0.949778, 200
> 12: -0.139099, 0.042379, -0.989371, 200
> 13: 0.172552, -0.113993, 0.978382, 200
> 14: 0.038590, -0.207922, 0.977384, 200
> 15: 0.033657, -0.297325, 0.954183, 200
> 16: -0.134182, -0.236161, 0.962405, 200
> 17: -0.287050, -0.175442, 0.941713, 200
> 18: -0.284042, 0.009099, 0.958769, 200
> 19: 0.301289, -0.098527, -0.948429, 200
> 20: 0.287165, -0.298248, -0.910266, 200
> 21: -0.063655, 0.305652, 0.950013, 200
> 22: -0.034158, 0.363119, 0.931117, 200
> 23: -0.143075, -0.322678, -0.935633, 200
> 24: -0.309259, -0.273854, -0.910694, 200
> 25: 0.470230, 0.217485, 0.855327, 200
> 26: 0.456033, 0.029969, 0.889458, 200
> 27: 0.303741, -0.011250, 0.952688, 200
> 28: 0.342908, -0.216865, 0.913993, 200
> 29: 0.209809, -0.313582, 0.926092, 200
> 30: 0.065844, -0.397050, 0.915432, 200
> 31: 0.021398, -0.480248, 0.876871, 200
> 32: -0.133124, -0.404479, 0.904807, 200
> 33: -0.304717, -0.392947, 0.867606, 200
> 34: 0.440864, 0.284286, -0.851364, 200
> 35: 0.448379, 0.089940, -0.889307, 200
> 36: -0.452391, 0.037178, 0.891044, 200
> 37: -0.455053, 0.235011, 0.858892, 200
> 38: -0.428186, 0.422193, 0.799006, 200
> 39: 0.246323, -0.456900, -0.854732, 200
> 40: -0.082416, 0.489028, 0.868366, 200
> 41: -0.019594, 0.535460, 0.844333, 200
> 42: 0.148339, 0.504380, 0.850645, 200
> 43: -0.310554, -0.456845, -0.833576, 200
> 44: 0.467890, 0.401117, 0.787517, 200
> 45: 0.619277, 0.159392, 0.768824, 200
> 46: -0.607824, 0.020036, -0.793818, 200
> 47: -0.467757, 0.109019, -0.877108, 200
> 48: -0.505282, 0.318847, -0.801889, 200
> 49: 0.377350, -0.416435, 0.827157, 200
> 50: 0.238544, -0.507810, 0.827784, 200
> 51: 0.088776, -0.584904, 0.806229, 200
> 52: -0.011200, -0.648146, 0.761433, 200
> 53: -0.163437, -0.567064, 0.807296, 200
> 54: -0.333650, -0.586528, 0.738012, 200
> 55: 0.456124, 0.477580, -0.750911, 200
> 56: 0.582984, 0.358747, -0.728993, 200
> 57: 0.600321, 0.178753, -0.779527, 200
> 58: 0.595215, -0.006598, -0.803539, 200
> 59: -0.605081, 0.179819, 0.775591, 200
> 60: -0.584334, 0.366385, 0.724097, 200
> 61: -0.533540, 0.537917, 0.652671, 200
> 62: 0.372150, -0.589462, -0.716966, 200
> 63: 0.203971, -0.631619, -0.747966, 200
> 64: -0.038081, 0.668874, 0.742400, 200
> 65: 0.107427, 0.671267, 0.733390, 200
> 66: -0.276565, -0.634833, -0.721456, 200
> 67: 0.436423, 0.579837, 0.687985, 200
> 68: 0.586746, 0.509690, 0.629242, 200
> 69: 0.614617, 0.337766, 0.712854, 200
> 70: -0.747235, -0.070408, -0.660820, 200
> 71: -0.740225, 0.157686, -0.653607, 200
> 72: -0.616376, 0.204745, -0.760369, 200
> 73: -0.668941, 0.363307, -0.648480, 200
> 74: -0.545117, 0.483429, -0.684940, 200
> 75: 0.409217, -0.587629, 0.698021, 200
> 76: 0.261085, -0.672117, 0.692888, 200
> 77: 0.100259, -0.737787, 0.667547, 200
> 78: -0.051884, -0.786250, 0.615727, 200
> 79: -0.199352, -0.713602, 0.671588, 200
> 80: -0.360512, -0.742101, 0.565081, 200
> 81: 0.479984, 0.645347, -0.594257, 200
> 82: 0.595629, 0.537963, -0.596509, 200
> 83: 0.699846, 0.419151, -0.578384, 200
> 84: 0.730334, 0.252692, -0.634633, 200
> 85: -0.739374, -0.085351, 0.667863, 200
> 86: -0.740223, 0.132217, 0.659233, 200
> 87: -0.724162, 0.307746, 0.617157, 200
> 88: -0.680016, 0.472366, 0.560757, 200
> 89: -0.610808, 0.624622, 0.486581, 200
> 90: -0.465596, 0.690863, 0.553108, 200
> 91: 0.307912, -0.743415, -0.593738, 200
> 92: -0.139608, 0.784653, 0.604011, 200
> 93: 0.029068, 0.789075, 0.613609, 200
> 94: -0.221269, -0.779100, -0.586552, 200
> 95: -0.382101, -0.732934, -0.562855, 200
> 96: 0.533331, 0.667426, 0.519712, 200
> 97: 0.669254, 0.581598, 0.462431, 200
> 98: 0.721238, 0.432058, 0.541425, 200
> 99: -0.747263, -0.257056, -0.612797, 200
> 100: -0.853109, -0.166885, -0.494323, 200
> 101: -0.852107, 0.098101, -0.514091, 200
> 102: -0.818856, 0.275502, -0.503561, 200
> 103: -0.763785, 0.420091, -0.490057, 200
> 104: -0.663240, 0.534602, -0.523750, 200
> 105: -0.544408, 0.639635, -0.542667, 200
> 106: -0.411817, 0.730946, -0.544175, 200
> 107: 0.262892, -0.801784, 0.536686, 200
> 108: 0.106747, -0.854417, 0.508504, 200
> 109: -0.077662, -0.887958, 0.453321, 200
> 110: -0.228520, -0.828921, 0.510558, 200
> 111: 0.380882, 0.839144, -0.388285, 200
> 112: 0.508757, 0.751237, -0.420487, 200
> 113: 0.622958, 0.649506, -0.435965, 200
> 114: 0.730241, 0.534516, -0.425489, 200
> 115: -0.811787, -0.371994, 0.450136, 200
> 116: -0.843916, -0.202772, 0.496678, 200
> 117: -0.852167, 0.061240, 0.519674, 200
> 118: -0.839753, 0.236280, 0.488863, 200
> 119: -0.802252, 0.401396, 0.441898, 200
> 120: -0.743628, 0.546715, 0.384864, 200
> 121: -0.662088, 0.676900, 0.321630, 200
> 122: -0.535336, 0.754382, 0.379900, 200
> 123: -0.393464, 0.815384, 0.424659, 200
> 124: 0.234683, -0.863471, -0.446477, 200
> 125: -0.057531, 0.881194, 0.469241, 200
> 126: -0.139792, -0.879196, -0.455491, 200
> 127: -0.313907, -0.849048, -0.424947, 200
> 128: 0.468076, 0.791046, 0.393892, 200
> 129: 0.601712, 0.718179, 0.349516, 200
> 130: 0.720257, 0.630979, 0.288263, 200
> 131: 0.787196, 0.494988, 0.367843, 200
> 132: -0.830365, -0.337456, -0.443416, 200
> 133: -0.917761, -0.238002, -0.317914, 200
> 134: -0.931300, -0.067505, -0.357944, 200
> 135: -0.906488, 0.233102, -0.352056, 200
> 136: -0.853547, 0.393741, -0.341210, 200
> 137: -0.767201, 0.540351, -0.345578, 200
> 138: -0.660922, 0.651784, -0.371967, 200
> 139: -0.537754, 0.750412, -0.384321, 200
> 140: -0.402768, 0.829810, -0.386255, 200
> 141: 0.258431, -0.892706, 0.369174, 200
> 142: 0.108288, -0.934897, 0.337996, 200
> 143: -0.103269, -0.952927, 0.285073, 200
> 144: -0.247919, -0.908086, 0.337514, 200
> 145: 0.387189, 0.896444, -0.215576, 200
> 146: 0.510010, 0.822590, -0.251468, 200
> 147: 0.625713, 0.731902, -0.269819, 200
> 148: 0.732591, 0.622074, -0.276286, 200
> 149: -0.825719, -0.481523, 0.293810, 200
> 150: -0.893115, -0.315207, 0.320922, 200
> 151: -0.923078, -0.146442, 0.355642, 200
> 152: -0.924562, 0.159829, 0.345890, 200
> 153: -0.896124, 0.321247, 0.306207, 200
> 154: -0.844171, 0.465941, 0.265093, 200
> 155: -0.776249, 0.592099, 0.216462, 200
> 156: -0.689929, 0.706497, 0.157671, 200
> 157: -0.580942, 0.787897, 0.204269, 200
> 158: -0.456911, 0.853319, 0.251158, 200
> 159: 0.315677, -0.906537, -0.280246, 200
> 160: 0.154045, -0.938848, -0.307953, 200
> 161: 0.063748, 0.946176, 0.317313, 200
> 162: -0.238359, -0.926232, -0.292026, 200
> 163: 0.394160, 0.881346, 0.260514, 200
> 164: 0.529382, 0.817229, 0.227796, 200
> 165: 0.646506, 0.741844, 0.178037, 200
> 166: 0.749878, 0.649193, 0.127401, 200
> 167: -0.821144, -0.538063, -0.190293, 200
> 168: -0.877963, -0.395612, -0.269578, 200
> 169: -0.941734, -0.303674, -0.144638, 200
> 170: -0.972785, -0.145023, -0.180713, 200
> 171: -0.961602, 0.192841, -0.195279, 200
> 172: -0.917628, 0.348329, -0.191377, 200
> 173: -0.842874, 0.500918, -0.196582, 200
> 174: -0.747422, 0.632324, -0.203780, 200
> 175: -0.638449, 0.736433, -0.223716, 200
> 176: -0.515717, 0.825565, -0.229083, 200
> 177: -0.380807, 0.897996, -0.220429, 200
> 178: 0.244375, -0.949683, 0.195917, 200
> 179: 0.103556, -0.980520, 0.166900, 200
> 180: -0.125358, -0.984739, 0.120724, 200
> 181: -0.259814, -0.950502, 0.170420, 200
> 182: 0.357112, 0.933268, -0.038492, 200
> 183: 0.481864, 0.872611, -0.079739, 200
> 184: 0.601163, 0.791669, -0.108920, 200
> 185: 0.709697, 0.693312, -0.125097, 200
> 186: -0.810680, -0.567100, 0.145587, 200
> 187: -0.892786, -0.418678, 0.166258, 200
> 188: -0.950524, -0.249310, 0.185335, 200
> 189: -0.976052, 0.088129, 0.198885, 200
> 190: -0.953022, 0.253569, 0.165687, 200
> 191: -0.906853, 0.402109, 0.126201, 200
> 192: -0.841703, 0.533089, 0.085741, 200
> 193: -0.755320, 0.654095, 0.040644, 200
> 194: -0.638760, 0.768644, 0.034221, 200
> 195: -0.521779, 0.850032, 0.072063, 200
> 196: -0.395071, 0.911888, 0.111266, 200
> 197: 0.251893, -0.956855, -0.144842, 200
> 198: 0.184927, -0.982654, -0.013881, 200
> 199: 0.088490, -0.982747, -0.162414, 200
> 200: -0.155487, -0.975737, -0.154148, 200
> 201: 0.315590, 0.939987, 0.129722, 200
> 202: 0.462076, 0.881832, 0.094115, 200
> 203: 0.583808, 0.810153, 0.053107, 200
> 204: 0.692813, 0.721088, 0.006538, 200
> 205: -0.800257, -0.599653, -0.001963, 200
> 206: -0.888084, -0.448046, -0.102767, 200
> 207: -0.935797, -0.352209, 0.015301, 200
> 208: -0.978576, -0.205441, -0.013497, 200
> 209: -0.987553, 0.152445, -0.038740, 200
> 210: -0.952344, 0.302345, -0.040364, 200
> 211: -0.892373, 0.447973, -0.054695, 200
> 212: -0.807542, 0.586311, -0.064147, 200
> 213: -0.704403, 0.705915, -0.074169, 200
> 214: -0.586852, 0.805813, -0.079175, 200
> 215: -0.462264, 0.883390, -0.077031, 200
> 216: -0.331361, 0.941979, -0.053620, 200
> 217: 0.194660, -0.980581, 0.023835, 200
> 218: -0.048128, -0.998836, -0.003247, 200
> 219: -0.148802, -0.982269, 0.114045, 200
> 220: -0.222975, -0.974806, -0.006012, 200
> 221: 0.306629, 0.944216, 0.120147, 200
> 222: 0.436739, 0.895495, 0.085720, 200
> 223: 0.556895, 0.829481, 0.042775, 200
> 224: 0.670037, 0.742041, 0.020645, 200
> 225: -0.772601, -0.634859, 0.006437, 200
> 226: -0.866962, -0.497569, 0.028322, 200
> 227: -0.938482, -0.343166, 0.038594, 200
> 228: -0.982328, -0.182467, 0.041692, 200
> 229: -0.983536, 0.177944, 0.031501, 200
> 230: -0.943267, 0.332006, -0.004445, 200
> 231: -0.881950, 0.469778, -0.038390, 200
> 232: -0.803617, 0.590776, -0.071997, 200
> 233: -0.698778, 0.709894, -0.088089, 200
> 234: -0.577622, 0.811842, -0.085235, 200
> 235: -0.458400, 0.886979, -0.056028, 200
> 236: -0.330928, 0.943475, -0.018480, 200
> 237: -0.264276, 0.958227, 0.109358, 200
> 238: 0.121618, -0.986120, 0.113033, 200
> 239: -0.070631, -0.997194, -0.024803, 200
> 240: -0.237666, -0.971344, -0.002581, 200
> 241: 0.386158, 0.922139, -0.023257, 200
> 242: 0.511709, 0.856713, -0.064782, 200
> 243: 0.623042, 0.774808, -0.107201, 200
> 244: 0.730440, 0.672019, -0.121854, 200
> 245: -0.820148, -0.562614, -0.104035, 200
> 246: -0.869952, -0.491549, 0.039536, 200
> 247: -0.903303, -0.419725, -0.088743, 200
> 248: -0.956380, -0.275585, -0.096901, 200
> 249: -0.987328, -0.121038, -0.102632, 200
> 250: -0.963306, 0.247122, 0.104749, 200
> 251: -0.914874, 0.393140, 0.091911, 200
> 252: -0.848217, 0.525025, 0.069836, 200
> 253: -0.754436, 0.653534, 0.060994, 200
> 254: -0.642941, 0.764060, 0.053286, 200
> 255: -0.522020, 0.851164, 0.054920, 200
> 256: -0.397642, 0.913960, 0.080986, 200
> 257: -0.032715, -0.004544, 0.999454, 800
> 258: 0.047086, -0.152807, -0.987134, 800
> 259: -0.054139, -0.077361, -0.995532, 800
> 260: 0.068734, -0.081769, 0.994278, 800
> 261: -0.023602, -0.175383, 0.984217, 800
> 262: 0.179363, 0.106709, -0.977979, 800
> 263: -0.189737, 0.048653, 0.980629, 800
> 264: -0.194347, 0.215235, 0.957028, 800
> 265: -0.029929, -0.250069, -0.967765, 800
> 266: 0.189677, 0.187433, 0.963790, 800
> 267: 0.342613, 0.122463, 0.931461, 800
> 268: 0.204033, 0.011518, 0.978896, 800
> 269: -0.222678, 0.157042, -0.962160, 800
> 270: 0.087670, -0.253369, 0.963389, 800
> 271: -0.012534, -0.339640, 0.940472, 800
> 272: 0.174037, 0.272060, -0.946411, 800
> 273: 0.320618, 0.207318, -0.924242, 800
> 274: 0.334791, 0.033111, -0.941711, 800
> 275: -0.341380, 0.135265, 0.930142, 800
> 276: -0.311459, 0.311507, 0.897751, 800
> 277: 0.107508, -0.341141, -0.933844, 800
> 278: 0.010395, 0.399292, 0.916765, 800
> 279: -0.175680, -0.349953, -0.920147, 800
> 280: 0.330990, 0.291617, 0.897444, 800
> 281: 0.478885, 0.224959, 0.848565, 800
> 282: 0.484644, 0.056469, 0.872887, 800
> 283: -0.350883, 0.050820, -0.935039, 800
> 284: -0.367580, 0.234252, -0.900006, 800
> 285: -0.238430, 0.335176, -0.911487, 800
> 286: 0.100548, -0.422975, 0.900546, 800
> 287: -0.011358, -0.498363, 0.866894, 800
> 288: -0.163499, -0.422184, 0.891644, 800
> 289: 0.316355, 0.393764, -0.863058, 800
> 290: 0.446193, 0.283949, -0.848695, 800
> 291: 0.470139, 0.112431, -0.875402, 800
> 292: -0.480890, 0.064159, 0.874430, 800
> 293: -0.463936, 0.241674, 0.852266, 800
> 294: -0.423483, 0.410365, 0.807628, 800
> 295: -0.258010, 0.456530, 0.851476, 800
> 296: 0.108666, -0.496721, -0.861081, 800
> 297: 0.010895, 0.544991, 0.838371, 800
> 298: -0.165249, -0.504283, -0.847580, 800
> 299: 0.316953, 0.452232, 0.833683, 800
> 300: 0.462024, 0.388678, 0.797160, 800
> 301: 0.614514, 0.152311, 0.774064, 800
> 302: -0.616603, 0.026677, -0.786822, 800
> 303: -0.487208, 0.123605, -0.864494, 800
> 304: -0.502458, 0.308158, -0.807821, 800
> 305: -0.379413, 0.409891, -0.829479, 800
> 306: -0.246105, 0.501677, -0.829308, 800
> 307: 0.103582, -0.579646, 0.808258, 800
> 308: -0.027209, -0.640306, 0.767638, 800
> 309: -0.174332, -0.558793, 0.810777, 800
> 310: 0.325195, 0.563212, -0.759632, 800
> 311: 0.445708, 0.457066, -0.769698, 800
> 312: 0.567345, 0.339057, -0.750440, 800
> 313: 0.595056, 0.176715, -0.784015, 800
> 314: 0.609916, 0.009395, -0.792410, 800
> 315: -0.600879, 0.175813, 0.779766, 800
> 316: -0.569723, 0.343934, 0.746408, 800
> 317: -0.513605, 0.503860, 0.694504, 800
> 318: -0.359612, 0.563753, 0.743547, 800
> 319: -0.204106, 0.611897, 0.764149, 800
> 320: 0.048874, -0.655985, -0.753190, 800
> 321: -0.110166, -0.653926, -0.748495, 800
> 322: 0.269810, 0.609066, 0.745816, 800
> 323: 0.421500, 0.548774, 0.721931, 800
> 324: 0.562965, 0.476211, 0.675495, 800
> 325: 0.600260, 0.316595, 0.734477, 800
> 326: -0.734784, -0.058640, -0.675761, 800
> 327: -0.724427, 0.140041, -0.674977, 800
> 328: -0.608972, 0.195791, -0.768648, 800
> 329: -0.647820, 0.332688, -0.685309, 800
> 330: -0.526194, 0.454056, -0.718995, 800
> 331: -0.393825, 0.557790, -0.730597, 800
> 332: -0.251971, 0.644496, -0.721898, 800
> 333: 0.099282, -0.711920, 0.695207, 800
> 334: -0.044768, -0.758360, 0.650297, 800
> 335: -0.193594, -0.684784, 0.702561, 800
> 336: 0.338197, 0.704857, -0.623538, 800
> 337: 0.456758, 0.606921, -0.650399, 800
> 338: 0.570137, 0.500429, -0.651548, 800
> 339: 0.675496, 0.382811, -0.630207, 800
> 340: 0.709523, 0.229130, -0.666391, 800
> 341: -0.728027, -0.071471, 0.681813, 800
> 342: -0.725140, 0.116025, 0.678756, 800
> 343: -0.701377, 0.278905, 0.655959, 800
> 344: -0.654706, 0.434674, 0.618400, 800
> 345: -0.586358, 0.582064, 0.563370, 800
> 346: -0.442713, 0.652143, 0.615397, 800
> 347: -0.290611, 0.706930, 0.644822, 800
> 348: 0.131586, -0.751705, -0.646239, 800
> 349: 0.028385, 0.761487, 0.647558, 800
> 350: 0.204071, 0.744401, 0.635784, 800
> 351: 0.361425, 0.694342, 0.622303, 800
> 352: 0.509209, 0.627018, 0.589537, 800
> 353: 0.644825, 0.542064, 0.538858, 800
> 354: 0.696392, 0.390904, 0.601858, 800
> 355: -0.724756, -0.226528, -0.650703, 800
> 356: -0.829780, -0.131606, -0.542352, 800
> 357: -0.829252, 0.067851, -0.554741, 800
> 358: -0.794886, 0.233825, -0.559894, 800
> 359: -0.739030, 0.377851, -0.557731, 800
> 360: -0.636594, 0.495465, -0.590985, 800
> 361: -0.518437, 0.600862, -0.608431, 800
> 362: -0.386178, 0.691696, -0.610266, 800
> 363: -0.242004, 0.766460, -0.594957, 800
> 364: 0.089327, -0.821803, 0.562726, 800
> 365: -0.058762, -0.855377, 0.514663, 800
> 366: 0.205768, 0.794375, -0.571514, 800
> 367: 0.355830, 0.805073, -0.474597, 800
> 368: 0.482171, 0.713678, -0.508109, 800
> 369: 0.599105, 0.609057, -0.519733, 800
> 370: 0.707577, 0.491006, -0.508182, 800
> 371: -0.787516, -0.329378, 0.520892, 800
> 372: -0.820197, -0.166203, 0.547406, 800
> 373: -0.829829, 0.034406, 0.556955, 800
> 374: -0.816922, 0.197884, 0.541739, 800
> 375: -0.780719, 0.355437, 0.513948, 800
> 376: -0.723022, 0.503556, 0.472937, 800
> 377: -0.644353, 0.639579, 0.419224, 800
> 378: -0.510392, 0.719697, 0.470677, 800
> 379: -0.367116, 0.780114, 0.506604, 800
> 380: -0.212477, 0.828034, 0.518858, 800
> 381: 0.042492, -0.848576, -0.527364, 800
> 382: -0.120697, -0.844623, -0.521580, 800
> 383: 0.288447, 0.814173, 0.503907, 800
> 384: 0.441193, 0.756780, 0.482320, 800
> 385: 0.581362, 0.681990, 0.443743, 800
> 386: 0.706552, 0.591429, 0.388582, 800
> 387: -0.768979, -0.450839, -0.453228, 800
> 388: -0.807521, -0.294319, -0.511162, 800
> 389: -0.900199, -0.187641, -0.392980, 800
> 390: -0.909995, -0.024038, -0.413922, 800
> 391: -0.887401, 0.183622, -0.422851, 800
> 392: -0.838515, 0.345084, -0.421675, 800
> 393: -0.750339, 0.495870, -0.437156, 800
> 394: -0.639804, 0.612668, -0.463993, 800
> 395: -0.515861, 0.712619, -0.475460, 800
> 396: -0.377700, 0.796069, -0.472881, 800
> 397: -0.231539, 0.861660, -0.451588, 800
> 398: 0.081783, -0.906184, 0.414901, 800
> 399: -0.074304, -0.927049, 0.367504, 800
> 400: 0.218918, 0.878352, -0.424938, 800
> 401: 0.362923, 0.876793, -0.315472, 800
> 402: 0.490736, 0.797104, -0.351858, 800
> 403: 0.608472, 0.700207, -0.373461, 800
> 404: 0.720212, 0.583363, -0.375478, 800
> 405: -0.813198, -0.434737, 0.386928, 800
> 406: -0.876647, -0.266010, 0.400909, 800
> 407: -0.903616, -0.096815, 0.417260, 800
> 408: -0.904267, 0.111715, 0.412093, 800
> 409: -0.880571, 0.270306, 0.389267, 800
> 410: -0.834232, 0.419383, 0.358015, 800
> 411: -0.768787, 0.555718, 0.316456, 800
> 412: -0.684935, 0.677889, 0.267076, 800
> 413: -0.564047, 0.764635, 0.311746, 800
> 414: -0.432450, 0.830245, 0.351680, 800
> 415: -0.287377, 0.881068, 0.375678, 800
> 416: 0.127833, -0.911654, -0.390572, 800
> 417: -0.039771, -0.918750, -0.392832, 800
> 418: 0.206722, 0.901556, 0.380083, 800
> 419: 0.365617, 0.859326, 0.357607, 800
> 420: 0.511371, 0.794224, 0.328189, 800
> 421: 0.638317, 0.715934, 0.282825, 800
> 422: -0.750035, -0.620089, -0.230081, 800
> 423: -0.817450, -0.497009, -0.291131, 800
> 424: -0.867016, -0.345766, -0.358788, 800
> 425: -0.940674, -0.244663, -0.235099, 800
> 426: -0.962412, -0.083265, -0.258514, 800
> 427: -0.952368, 0.135065, -0.273408, 800
> 428: -0.912533, 0.296032, -0.282221, 800
> 429: -0.839496, 0.456208, -0.295163, 800
> 430: -0.740572, 0.597338, -0.307799, 800
> 431: -0.624541, 0.709217, -0.327048, 800
> 432: -0.493987, 0.803725, -0.331667, 800
> 433: -0.355109, 0.877487, -0.322357, 800
> 434: -0.213515, 0.932137, -0.292457, 800
> 435: 0.069602, -0.964432, 0.255002, 800
> 436: -0.087797, -0.972858, 0.214100, 800
> 437: 0.230248, 0.936513, -0.264442, 800
> 438: 0.332863, 0.932853, -0.137797, 800
> 439: 0.465378, 0.865562, -0.185004, 800
> 440: 0.592504, 0.776453, -0.214614, 800
> 441: 0.706228, 0.668501, -0.233127, 800
> 442: -0.812510, -0.527821, 0.247451, 800
> 443: -0.893163, -0.366205, 0.261064, 800
> 444: -0.943374, -0.190961, 0.271255, 800
> 445: -0.961826, 0.030181, 0.271993, 800
> 446: -0.947798, 0.194236, 0.252886, 800
> 447: -0.909443, 0.350167, 0.224267, 800
> 448: -0.848262, 0.495526, 0.186830, 800
> 449: -0.764301, 0.628628, 0.143772, 800
> 450: -0.638422, 0.757187, 0.138148, 800
> 451: -0.509053, 0.842668, 0.175434, 800
> 452: -0.371941, 0.903398, 0.213383, 800
> 453: -0.220047, 0.945206, 0.241172, 800
> 454: -0.150592, 0.982884, 0.106117, 800
> 455: 0.052692, -0.965795, -0.253897, 800
> 456: -0.122026, -0.961291, -0.247042, 800
> 457: 0.288627, 0.929600, 0.229212, 800
> 458: 0.443517, 0.873661, 0.200022, 800
> 459: 0.578673, 0.800536, 0.155821, 800
> 460: 0.699760, 0.706094, 0.108478, 800
> 461: -0.815510, -0.569897, -0.100802, 800
> 462: -0.893432, -0.401677, -0.201085, 800
> 463: -0.951918, -0.296914, -0.075458, 800
> 464: -0.985176, -0.140301, -0.098716, 800
> 465: -0.989411, 0.084107, -0.118290, 800
> 466: -0.960886, 0.243954, -0.131092, 800
> 467: -0.903590, 0.401028, -0.150672, 800
> 468: -0.817342, 0.552482, -0.163449, 800
> 469: -0.706662, 0.685232, -0.176312, 800
> 470: -0.580978, 0.792497, -0.185508, 800
> 471: -0.443816, 0.877681, -0.180838, 800
> 472: -0.304106, 0.940283, -0.152928, 800
> 473: -0.158339, 0.980499, -0.116409, 800
> 474: -0.008358, -0.996418, 0.084148, 800
> 475: -0.110385, -0.993480, 0.028517, 800
> 476: 0.187618, 0.978131, -0.089771, 800
> 477: 0.280605, 0.959211, 0.034288, 800
> 478: 0.423249, 0.905965, -0.009454, 800
> 479: 0.554131, 0.830688, -0.053820, 800
> 480: 0.678889, 0.730234, -0.076606, 800
> 481: -0.785803, -0.609407, 0.105533, 800
> 482: -0.880805, -0.457114, 0.123411, 800
> 483: -0.949199, -0.285032, 0.133332, 800
> 484: -0.985318, -0.115427, 0.125797, 800
> 485: -0.987230, 0.111468, 0.113811, 800
> 486: -0.958227, 0.271806, 0.089006, 800
> 487: -0.904087, 0.423546, 0.056885, 800
> 488: -0.825209, 0.564477, 0.019902, 800
> 489: -0.712225, 0.701907, 0.007878, 800
> 490: -0.580199, 0.814444, 0.007130, 800
> 491: -0.447777, 0.893318, 0.038462, 800
> 492: -0.305659, 0.949102, 0.076015, 800
> 493: -0.235455, 0.971621, 0.022659, 800
> 494: 0.079664, -0.996460, 0.026854, 800
> 495: -0.031413, -0.993231, -0.111828, 800
> 496: 0.203253, 0.974129, 0.098798, 800
> 497: 0.364655, 0.928106, 0.075140, 800
> 498: 0.505025, 0.862562, 0.030607, 800
> 499: 0.630899, 0.775752, -0.013190, 800
> 500: -0.751395, -0.658998, 0.033567, 800
> 501: -0.844665, -0.535068, -0.015572, 800
> 502: -0.891891, -0.448934, -0.054666, 800
> 503: -0.928495, -0.371340, -0.002096, 800
> 504: -0.977595, -0.209980, -0.014700, 800
> 505: -0.998518, -0.046691, -0.027975, 800
> 506: -0.982889, 0.182413, 0.025577, 800
> 507: -0.940396, 0.340048, 0.004806, 800
> 508: -0.872088, 0.488863, -0.021802, 800
> 509: -0.772738, 0.633798, -0.034283, 800
> 510: -0.650707, 0.758167, -0.041996, 800
> 511: -0.515929, 0.855639, -0.041218, 800
> 512: -0.379415, 0.925134, -0.013116, 800
> 513: -0.037501, -0.007836, 0.999266, 1000
> 514: 0.051244, -0.155618, -0.986487, 1000
> 515: -0.057807, -0.079520, -0.995156, 1000
> 516: 0.072727, -0.084178, 0.993793, 1000
> 517: -0.027377, -0.177862, 0.983675, 1000
> 518: 0.183512, 0.108772, -0.976981, 1000
> 519: -0.193829, 0.050678, 0.979726, 1000
> 520: -0.196508, 0.216369, 0.956331, 1000
> 521: -0.032710, -0.251835, -0.967217, 1000
> 522: 0.193186, 0.188233, 0.962937, 1000
> 523: 0.344332, 0.124325, 0.930580, 1000
> 524: 0.207518, 0.014571, 0.978123, 1000
> 525: -0.225208, 0.158937, -0.961260, 1000
> 526: 0.090584, -0.255673, 0.962510, 1000
> 527: -0.015590, -0.341293, 0.939828, 1000
> 528: 0.177433, 0.273114, -0.945477, 1000
> 529: 0.322894, 0.208183, -0.923255, 1000
> 530: 0.337272, 0.035365, -0.940743, 1000
> 531: -0.343220, 0.136245, 0.929321, 1000
> 532: -0.313153, 0.311948, 0.897008, 1000
> 533: 0.109976, -0.342616, -0.933016, 1000
> 534: 0.012503, 0.400302, 0.916298, 1000
> 535: 0.178132, 0.351126, 0.919228, 1000
> 536: 0.332790, 0.291131, 0.896936, 1000
> 537: 0.479200, 0.224325, 0.848555, 1000
> 538: 0.485609, 0.057191, 0.872303, 1000
> 539: -0.353537, 0.051801, -0.933985, 1000
> 540: -0.369240, 0.235221, -0.899073, 1000
> 541: -0.240189, 0.335278, -0.910987, 1000
> 542: 0.102877, -0.423048, 0.900248, 1000
> 543: -0.013663, -0.498841, 0.866586, 1000
> 544: -0.165444, -0.422285, 0.891237, 1000
> 545: 0.317123, 0.392995, -0.863127, 1000
> 546: 0.446736, 0.283771, -0.848470, 1000
> 547: 0.471416, 0.112239, -0.874740, 1000
> 548: -0.481790, 0.065592, 0.873829, 1000
> 549: -0.463849, 0.241219, 0.852442, 1000
> 550: -0.423104, 0.409694, 0.808167, 1000
> 551: -0.260014, 0.455538, 0.851398, 1000
> 552: 0.109237, -0.496373, -0.861209, 1000
> 553: 0.012942, 0.544595, 0.838599, 1000
> 554: -0.166952, -0.503002, -0.848007, 1000
> 555: 0.317331, 0.451266, 0.834063, 1000
> 556: 0.462216, 0.387337, 0.797701, 1000
> 557: 0.614638, 0.152010, 0.774024, 1000
> 558: -0.617326, 0.026475, -0.786262, 1000
> 559: -0.488276, 0.124362, -0.863783, 1000
> 560: -0.501645, 0.306783, -0.808849, 1000
> 561: -0.379304, 0.409519, -0.829712, 1000
> 562: -0.247407, 0.500752, -0.829480, 1000
> 563: 0.104053, -0.578799, 0.808805, 1000
> 564: -0.028231, -0.639010, 0.768681, 1000
> 565: -0.175010, -0.557730, 0.811362, 1000
> 566: 0.325600, 0.560910, -0.761160, 1000
> 567: 0.445480, 0.454533, -0.771329, 1000
> 568: 0.566756, 0.337330, -0.751662, 1000
> 569: 0.594966, 0.175303, -0.784400, 1000
> 570: 0.609819, 0.008937, -0.792490, 1000
> 571: -0.600377, 0.174624, 0.780419, 1000
> 572: -0.569310, 0.341613, 0.747788, 1000
> 573: -0.512791, 0.501512, 0.696801, 1000
> 574: -0.359595, 0.561008, 0.745628, 1000
> 575: -0.205299, 0.610194, 0.765190, 1000
> 576: 0.049791, -0.654468, -0.754448, 1000
> 577: -0.111126, -0.652431, -0.749657, 1000
> 578: 0.269680, 0.607320, 0.747285, 1000
> 579: 0.420692, 0.546811, 0.723890, 1000
> 580: 0.561943, 0.473525, 0.678229, 1000
> 581: 0.599757, 0.313970, 0.736013, 1000
> 582: -0.734356, -0.056962, -0.676370, 1000
> 583: -0.723205, 0.139017, -0.676497, 1000
> 584: -0.608944, 0.195192, -0.768822, 1000
> 585: -0.647046, 0.329806, -0.687430, 1000
> 586: -0.525154, 0.452431, -0.720777, 1000
> 587: -0.392998, 0.555618, -0.732694, 1000
> 588: -0.251231, 0.642522, -0.723912, 1000
> 589: 0.099525, -0.709824, 0.697312, 1000
> 590: -0.045764, -0.756215, 0.652721, 1000
> 591: 0.192566, 0.682159, -0.705392, 1000
> 592: 0.337121, 0.702424, -0.626858, 1000
> 593: 0.456227, 0.603521, -0.653926, 1000
> 594: 0.569184, 0.497459, -0.654648, 1000
> 595: 0.673988, 0.379755, -0.633661, 1000
> 596: 0.708832, 0.226551, -0.668006, 1000
> 597: -0.727056, -0.070200, 0.682980, 1000
> 598: -0.724523, 0.115344, 0.679531, 1000
> 599: -0.700185, 0.275500, 0.658667, 1000
> 600: -0.653672, 0.431311, 0.621839, 1000
> 601: -0.584690, 0.578880, 0.568362, 1000
> 602: -0.441607, 0.648799, 0.619712, 1000
> 603: -0.289338, 0.704023, 0.648564, 1000
> 604: 0.132577, -0.749508, -0.648584, 1000
> 605: -0.028352, -0.759171, -0.650274, 1000
> 606: 0.203212, 0.741735, 0.639167, 1000
> 607: 0.360594, 0.690981, 0.626512, 1000
> 608: 0.508297, 0.623593, 0.593941, 1000
> 609: 0.643445, 0.538847, 0.543712, 1000
> 610: 0.694774, 0.388107, 0.605526, 1000
> 611: -0.723271, -0.224011, -0.653222, 1000
> 612: -0.828465, -0.128797, -0.545029, 1000
> 613: -0.827678, 0.065262, -0.557395, 1000
> 614: -0.793611, 0.230556, -0.563050, 1000
> 615: -0.737448, 0.374246, -0.562238, 1000
> 616: -0.635428, 0.491993, -0.595125, 1000
> 617: -0.517249, 0.597243, -0.612988, 1000
> 618: -0.385235, 0.689099, -0.613789, 1000
> 619: -0.241441, 0.763690, -0.598736, 1000
> 620: 0.089324, -0.819036, 0.566747, 1000
> 621: -0.058642, -0.852924, 0.518731, 1000
> 622: 0.204797, 0.791619, -0.575672, 1000
> 623: 0.354476, 0.801967, -0.480828, 1000
> 624: 0.480850, 0.710966, -0.513139, 1000
> 625: 0.597954, 0.606419, -0.524125, 1000
> 626: 0.706443, 0.487213, -0.513383, 1000
> 627: -0.786393, -0.325775, 0.524839, 1000
> 628: -0.818400, -0.163241, 0.550976, 1000
> 629: -0.828413, 0.031900, 0.559208, 1000
> 630: -0.815187, 0.194585, 0.545533, 1000
> 631: -0.779341, 0.352646, 0.517947, 1000
> 632: -0.721596, 0.500270, 0.478570, 1000
> 633: -0.643242, 0.636382, 0.425745, 1000
> 634: -0.509621, 0.716640, 0.476145, 1000
> 635: -0.365972, 0.777153, 0.511955, 1000
> 636: -0.211500, 0.825382, 0.523461, 1000
> 637: 0.041986, -0.845925, -0.531646, 1000
> 638: -0.120079, -0.842240, -0.525559, 1000
> 639: 0.287018, 0.811380, 0.509199, 1000
> 640: 0.439958, 0.754134, 0.487564, 1000
> 641: 0.580237, 0.678886, 0.449932, 1000
> 642: 0.705634, 0.588036, 0.395341, 1000
> 643: -0.767944, -0.447186, -0.458571, 1000
> 644: -0.805982, -0.291401, -0.515246, 1000
> 645: -0.898855, -0.183987, -0.397756, 1000
> 646: -0.908614, -0.021367, -0.417090, 1000
> 647: -0.886023, 0.180486, -0.427070, 1000
> 648: -0.837066, 0.341814, -0.427181, 1000
> 649: -0.749364, 0.492488, -0.442616, 1000
> 650: -0.638972, 0.609036, -0.469884, 1000
> 651: -0.514534, 0.710047, -0.480716, 1000
> 652: -0.376562, 0.793216, -0.478550, 1000
> 653: -0.230254, 0.859197, -0.456907, 1000
> 654: 0.080083, -0.903775, 0.420449, 1000
> 655: -0.073695, -0.924985, 0.372788, 1000
> 656: 0.218060, 0.875839, -0.430530, 1000
> 657: 0.361601, 0.874720, -0.322660, 1000
> 658: 0.488936, 0.794834, -0.359416, 1000
> 659: 0.607745, 0.697276, -0.380070, 1000
> 660: 0.719365, 0.580648, -0.381263, 1000
> 661: -0.812366, -0.430465, 0.393397, 1000
> 662: -0.875771, -0.262762, 0.404945, 1000
> 663: -0.901930, -0.094216, 0.421480, 1000
> 664: -0.902884, 0.108479, 0.415973, 1000
> 665: -0.879255, 0.266666, 0.394715, 1000
> 666: -0.833726, 0.414667, 0.364628, 1000
> 667: -0.767968, 0.552814, 0.323452, 1000
> 668: -0.684293, 0.675622, 0.274370, 1000
> 669: -0.562940, 0.762612, 0.318623, 1000
> 670: -0.431563, 0.827743, 0.358600, 1000
> 671: -0.286417, 0.878821, 0.381626, 1000
> 672: 0.126563, -0.909451, -0.396081, 1000
> 673: -0.038396, -0.916559, -0.398053, 1000
> 674: 0.205757, 0.899308, 0.385887, 1000
> 675: 0.364028, 0.857116, 0.364466, 1000
> 676: 0.510145, 0.792068, 0.335233, 1000
> 677: 0.637908, 0.713455, 0.289923, 1000
> 678: -0.750152, -0.617267, -0.237180, 1000
> 679: -0.817365, -0.493105, -0.297928, 1000
> 680: -0.865987, -0.342479, -0.364383, 1000
> 681: -0.940108, -0.240872, -0.241199, 1000
> 682: -0.961326, -0.077974, -0.264146, 1000
> 683: -0.951365, 0.130514, -0.279052, 1000
> 684: -0.911826, 0.292310, -0.288319, 1000
> 685: -0.839240, 0.452669, -0.301276, 1000
> 686: -0.739910, 0.593881, -0.315972, 1000
> 687: -0.623542, 0.706521, -0.334698, 1000
> 688: -0.493315, 0.800941, -0.339314, 1000
> 689: -0.353179, 0.876044, -0.328347, 1000
> 690: -0.212080, 0.930384, -0.299011, 1000
> 691: 0.068280, -0.962961, 0.260852, 1000
> 692: -0.086752, -0.971645, 0.219957, 1000
> 693: 0.228125, 0.934952, -0.271706, 1000
> 694: 0.331727, 0.932186, -0.144865, 1000
> 695: 0.464547, 0.864362, -0.192548, 1000
> 696: 0.592015, 0.774852, -0.221636, 1000
> 697: 0.706303, 0.665637, -0.240964, 1000
> 698: -0.812137, -0.524604, 0.255390, 1000
> 699: -0.892934, -0.362352, 0.267151, 1000
> 700: -0.942543, -0.187154, 0.276743, 1000
> 701: -0.960644, 0.025934, 0.276570, 1000
> 702: -0.946973, 0.190853, 0.258491, 1000
> 703: -0.909306, 0.346127, 0.230996, 1000
> 704: -0.848766, 0.491647, 0.194628, 1000
> 705: -0.765063, 0.626049, 0.150801, 1000
> 706: -0.638361, 0.755751, 0.146064, 1000
> 707: -0.509087, 0.841033, 0.183014, 1000
> 708: -0.371041, 0.902182, 0.219990, 1000
> 709: -0.218379, 0.943779, 0.248179, 1000
> 710: -0.148830, 0.982349, 0.113313, 1000
> 711: 0.050605, -0.964402, -0.259554, 1000
> 712: -0.120659, -0.959790, -0.253464, 1000
> 713: 0.287293, 0.928169, 0.236569, 1000
> 714: 0.442854, 0.872256, 0.207482, 1000
> 715: 0.578614, 0.798948, 0.163972, 1000
> 716: 0.700182, 0.704443, 0.116210, 1000
> 717: -0.816248, -0.567298, -0.109143, 1000
> 718: -0.893896, -0.397413, -0.207395, 1000
> 719: -0.952698, -0.292700, -0.081818, 1000
> 720: -0.985161, -0.135864, -0.104881, 1000
> 721: -0.989230, 0.078420, -0.123587, 1000
> 722: -0.961154, 0.239283, -0.137571, 1000
> 723: -0.904292, 0.396723, -0.157692, 1000
> 724: -0.817946, 0.549242, -0.171164, 1000
> 725: -0.707258, 0.682772, -0.183328, 1000
> 726: -0.581027, 0.790599, -0.193292, 1000
> 727: -0.442805, 0.876473, -0.188994, 1000
> 728: -0.302387, 0.939693, -0.159809, 1000
> 729: -0.156226, 0.980071, -0.122695, 1000
> 730: -0.006613, -0.995882, 0.090414, 1000
> 731: -0.108285, -0.993878, 0.021917, 1000
> 732: 0.186635, 0.977716, -0.096123, 1000
> 733: 0.278492, 0.960043, 0.027559, 1000
> 734: 0.422906, 0.906026, -0.016389, 1000
> 735: 0.554093, 0.830209, -0.061099, 1000
> 736: 0.679276, 0.729046, -0.084125, 1000
> 737: -0.786555, -0.607012, 0.113441, 1000
> 738: -0.881890, -0.452949, 0.130793, 1000
> 739: -0.949828, -0.279886, 0.139608, 1000
> 740: -0.985050, -0.110787, 0.131923, 1000
> 741: -0.987169, 0.106528, 0.118951, 1000
> 742: -0.958650, 0.268097, 0.095472, 1000
> 743: -0.905410, 0.419730, 0.063714, 1000
> 744: -0.826951, 0.561609, 0.027343, 1000
> 745: -0.713594, 0.700390, 0.015442, 1000
> 746: -0.580134, 0.814383, 0.015011, 1000
> 747: -0.446592, 0.893582, 0.045466, 1000
> 748: -0.304272, 0.948966, 0.082954, 1000
> 749: -0.234079, 0.972085, 0.016056, 1000
> 750: 0.076706, -0.996842, 0.020570, 1000
> 751: -0.029110, -0.992515, -0.118604, 1000
> 752: 0.201452, 0.973671, 0.106686, 1000
> 753: 0.364186, 0.927727, 0.081803, 1000
> 754: 0.505145, 0.862223, 0.037419, 1000
> 755: 0.631614, 0.775262, -0.005682, 1000
> 756: -0.753175, -0.657324, 0.025551, 1000
> 757: -0.846858, -0.531745, -0.008881, 1000
> 758: -0.893156, -0.445599, -0.060936, 1000
> 759: -0.930099, -0.367278, 0.004724, 1000
> 760: -0.978723, -0.205012, -0.008492, 1000
> 761: -0.998900, -0.041282, -0.022248, 1000
> 762: -0.983881, 0.177767, 0.019400, 1000
> 763: -0.941919, 0.335835, -0.001633, 1000
> 764: -0.873761, 0.485508, -0.028716, 1000
> 765: -0.773893, 0.631986, -0.041033, 1000
> 766: -0.651986, 0.756588, -0.049881, 1000
> 767: -0.516083, 0.855183, -0.048171, 1000
> 768: -0.378344, 0.925432, -0.020770, 1000
>
> I dont understand why you mention it should be 260 rows and 260 volumes? I have 256 directions and 4 B values... I dont understand where the error is...
> Best,
> salvador
>
> -----Urspr?ngliche Nachricht-----
> Von: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] Im Auftrag von susumu mori
> Gesendet: Donnerstag, 19. Mai 2011 20:56
> An: DTI Studio, ROI Editor, DiffeoMap Questions/Support
> Betreff: Re: [Mristudio-users] Obtaining tract volume data
>
> If you are using DICOM, one of the common culprits is the mismatch
> between your gradient table and the number of of the images.
>
> Please read the images first by Mri3DView. Check the image dimensions
> and the number of 3D volumes.
>
> Then make sure the number of the 3D volumes exactly match the row of
> your gradient table. in your case, there should be 260 3D images to
> load and 260 rows in the table.
>
> Another common issue is the shortage of RAM. If you are using a 32-bit
> operating system, it may not be able to process your large data, no
> matter how much RAM you have. To check it, limit the number of the
> slices to process in the opening data input window of DtiMapping (e.g.
> slice 0-4). If your calculation runs through with this limited number
> of slices, then it is the RAM shortage. Then the only solution is to
> migrate to a 64-bit operating system.
>
> On Thu, May 19, 2011 at 11:56 AM, Castaneda, Salvador
> <salvador.castaneda at med.uni-tuebingen.de> wrote:
>> Hello Susumu,
>>
>> I've been using DTIstudio for over a year... It works good. But i just started running a tensor calculation with 4 b values and 256 directions. But it is crashing in the process of the calculation. I'm not requesting any other commands, just the tensor... Do you have any idea what i could do to calculate it... Do i have to analize with less bvalues?
>> Thanks
>> salvador
>>
>> -----Urspr?ngliche Nachricht-----
>> Von: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] Im Auftrag von susumu mori
>> Gesendet: Donnerstag, 19. Mai 2011 17:48
>> An: DTI Studio, ROI Editor, DiffeoMap Questions/Support
>> Betreff: Re: [Mristudio-users] Obtaining tract volume data
>>
>> Hi Melisa,
>>
>> On Wed, May 18, 2011 at 12:12 AM, ?<melcarr at umich.edu> wrote:
>>> Hello,
>>>
>>> I'm attempting to calculate mean tract volume for a tract spanning
>>> between two ROIs in a subject's FA map.
>>>
>>> Is it safe to define tract volume as: the number of voxels between
>>> both ROIs multiplied by the size of an individual voxel?
>>
>> This is what we do too.
>>
>>>
>>> Does the first measure above ("the number of voxels between both
>>> ROIs") correspond to the measure "Average Length, mm" in the Fiber
>>> Statistics window (an example of this window is shown in the User
>>> Manual, page 26, Figure 19. Fiber-statistics)?
>>
>> I think the number of voxels occupied by fibers and the average length
>> of the fibers are very different. The former has unit of mm^3 and the
>> latter is mm. I don't use the length of fibers for quantification.
>>
>>
>>>
>>> Just wondering, thank you.
>>>
>>> -Melisa Carrasco
>>>
>>> --
>>>
>>> Melisa Carrasco, M.S.
>>> MD/PhD Student, Year Grad-4 (Ph.D. Candidate)
>>>
>>> University of Michigan, Neuroscience Graduate Program, Class of 2012
>>> University of Rochester School of Medicine and Dentistry, Class of 2014
>>>
>>> About me: http://sitemaker.umich.edu/melisa.carrasco/home
>>> GO BLUE!
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> mristudio-users mailing 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 liyiou at gmail.com  Thu May 19 18:48:39 2011
From: liyiou at gmail.com (Yiou Li)
Date: Thu, 19 May 2011 15:48:39 -0700
Subject: [Mristudio-users] Problem uploading files for LDDMM registration
Message-ID: <BANLkTi=jckh3Lp2Y3vjwLXEjPTMXy33G3w@mail.gmail.com>

Dear MRIStudio,

I am newly registered user and want to try the LDDMM for image
registration.

I prepared my files as instructed by
http://www.slicer.org/slicerWiki/index.php/Slicer3:LDDMM

Is this the right instruction to follow?

And when I ftp to mristudio.org using username: anonymous and my registered
email as password (actually, any password works here), I was successfully
logged in. But I can only "cd" into the "pub" directory and I found no
"INCOMING" directory where we supposed to upload the files...

Could you please kindly advise if there is anything wrong in my procedure?

Best regards and many thanks!

Yiou (Leo) Li

University of California San Francisco
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From jarxico at hotmail.com  Fri May 20 12:47:58 2011
From: jarxico at hotmail.com (Jairo Hidalgo)
Date: Fri, 20 May 2011 16:47:58 +0000
Subject: [Mristudio-users] Help with modules DTI Fiber Tracking in MeVisLab
Message-ID: <COL104-W58ED77233DDC234123F4F9AB710@phx.gbl>


Hi all ...
 I'm doing a little research, in terms of diffusion tensor imaging DTI, would that I could help implement this type of processing MeVisLab because there is not much documentation for this software.

 In particular I wish to know how to use modules of DTI Fiber Tracking in MeVisLab.

 Please, your answers would be of great help ...





--
Jairo Hidalgo
Estudiante de Electronica y Telecomunicaciones
Universidad T?cnica Particular de Loja
Loja - Ecuador

 		 	   		  
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From jorgepm69 at hotmail.com  Fri May 20 12:48:35 2011
From: jorgepm69 at hotmail.com (=?iso-8859-1?B?Sm9yZ2UgSXNyYWVsIFBhZGlsbGEgTXXxb3o=?=)
Date: Fri, 20 May 2011 11:48:35 -0500
Subject: [Mristudio-users] Help with DTI (diffusion tensor imaging) in MIPAV
Message-ID: <SNT102-W13D2D56387E21747F5C96DA8710@phx.gbl>



Hi all ...
I am conducting research using in MIPAV program.
I would like information in order to make the program MIPAV DTI.

I wish I could help in the processing of medical images using MIPAV specifically withDTI (diffusion tensor imaging).
and in turn would like to know what kind of medical image format is the most optimalfor the development of DTI.

I appreciate your help.


-------------Jorge PadillaEstudianteElectr?nica y Telecomunicaciones Universidad T?cnica Particular Loja Loja - Ecuador 		 	   		  
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From jarxico at hotmail.com  Mon May 23 23:23:24 2011
From: jarxico at hotmail.com (Jairo Hidalgo)
Date: Tue, 24 May 2011 03:23:24 +0000
Subject: [Mristudio-users] Help with modules DTI Fiber Tracking in MeVisLab
In-Reply-To: <COL104-W58ED77233DDC234123F4F9AB710@phx.gbl>
References: <COL104-W58ED77233DDC234123F4F9AB710@phx.gbl>
Message-ID: <COL104-W584A4998965E25035E4086AB750@phx.gbl>










Hi all ...
 I'm doing a little research, in terms of diffusion tensor imaging DTI, would that I could help implement this type of processing MeVisLab because there is not much documentation for this software.

 In particular I wish to know how to use modules of DTI Fiber Tracking in MeVisLab.

 Please, your answers would be of great help ...





--
Jairo Hidalgo
Estudiante de Electronica y Telecomunicaciones
Universidad T?cnica Particular de Loja
Loja - Ecuador

 		 	   		  
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From Jacquie.Hodge at albertahealthservices.ca  Wed May 25 16:20:59 2011
From: Jacquie.Hodge at albertahealthservices.ca (Jacquie Hodge)
Date: Wed, 25 May 2011 14:20:59 -0600
Subject: [Mristudio-users] Theory_Air
Message-ID: <1DC4211314F7D9458B66A28F947F60B99C48B6D20D@EXMBX4C.crha.bewell.ca>

Hi everyone,

I receive my DTI images as 6 directions with 6 repeats. Today I tried the Theory_Air registration on a set that I have already done many analysis on and I found that although the fiber statistics stayed generally similar when doing tractography, the FA values were quite different for the tracts.. From an average of 0.55 to 0.41 when I did the Theory_Air.
Can someone explain why for me? Should I not be using this with 6 repeats?
What I really would like to do is co-register one of my nice anatomical images with the FA or color FA for more accurate placement of my ROI's.

Thanks,

Jacquie

Jacquie Hodge MSc candidate in Neuroscience, BSc
Neuroscience, University of Calgary
Research Assistant, Calgary Pediatric Stroke Program
Alberta Children's Hospital
2888 Shaganappi Trail NW, Calgary, AB, Canada T3B 6A8
Phone: 403-955-7733 Fax: 403-955-2922
jacquie.hodge at albertahealthservices.ca
Program website: www.perinatalstroke.com

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.


From salvador.castaneda at med.uni-tuebingen.de  Thu May 26 04:57:26 2011
From: salvador.castaneda at med.uni-tuebingen.de (Castaneda, Salvador)
Date: Thu, 26 May 2011 10:57:26 +0200
Subject: [Mristudio-users] Theory_Air
In-Reply-To: <1DC4211314F7D9458B66A28F947F60B99C48B6D20D@EXMBX4C.crha.bewell.ca>
References: <1DC4211314F7D9458B66A28F947F60B99C48B6D20D@EXMBX4C.crha.bewell.ca>
Message-ID: <0AC64F4CB253074799B64FF8F0772D350126C700@azex2003.raddiag.med.uni-tuebingen.de>

Hey jacquie,

I had the exact same issue when i started using it. What i did was export the all the maps i was measuring (FA, RD, ADC..) as analyze files. Then i used another software, in my case Pmod, and then uploaded all the files. The files have the same header and so they are already coregistered, you only have to ( i prefer) manually coregister them to an anatomy. Then i drew the rois there. ROI editor from the dti studio software is also good, but i found it hard to coregister the anatomy there. I think i'm not properly qualified to give you an answer about the tracts, so i leave it to someone else to answer that, but i would first look at the shimming you are performing on the region you are studying, and then i would guess there is going to be variability in the tracts that should average out with many samples, i think the averages should only help... Maybe the seeding of the tracts?
Best,

Salvador
----------------------------------------------------------------------------------- 
Salvador Castaneda, MD.
University of T?bingen - Department of Radiology
R?ntgenweg 13
72076 T?bingen
Germany
 
Office:      +49 (7071) 29-82977
Fax:          +49 (7071) 29-4451
E-mail:     Salvador.Castaneda at med.uni.tuebingen.de
Web:         www.preclinicalimaging.org 


-----Urspr?ngliche Nachricht-----
Von: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] Im Auftrag von Jacquie Hodge
Gesendet: Mittwoch, 25. Mai 2011 22:21
An: mristudio-users at mristudio.org
Betreff: [Mristudio-users] Theory_Air

Hi everyone,

I receive my DTI images as 6 directions with 6 repeats. Today I tried the Theory_Air registration on a set that I have already done many analysis on and I found that although the fiber statistics stayed generally similar when doing tractography, the FA values were quite different for the tracts.. From an average of 0.55 to 0.41 when I did the Theory_Air.
Can someone explain why for me? Should I not be using this with 6 repeats?
What I really would like to do is co-register one of my nice anatomical images with the FA or color FA for more accurate placement of my ROI's.

Thanks,

Jacquie

Jacquie Hodge MSc candidate in Neuroscience, BSc
Neuroscience, University of Calgary
Research Assistant, Calgary Pediatric Stroke Program
Alberta Children's Hospital
2888 Shaganappi Trail NW, Calgary, AB, Canada T3B 6A8
Phone: 403-955-7733 Fax: 403-955-2922
jacquie.hodge at albertahealthservices.ca
Program website: www.perinatalstroke.com

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


From taohaojuan at 163.com  Thu May 26 05:20:25 2011
From: taohaojuan at 163.com (taohaojuan)
Date: Thu, 26 May 2011 17:20:25 +0800 (CST)
Subject: [Mristudio-users] Theory_Air
In-Reply-To: <0AC64F4CB253074799B64FF8F0772D350126C700@azex2003.raddiag.med.uni-tuebingen.de>
References: <0AC64F4CB253074799B64FF8F0772D350126C700@azex2003.raddiag.med.uni-tuebingen.de>
	<1DC4211314F7D9458B66A28F947F60B99C48B6D20D@EXMBX4C.crha.bewell.ca>
Message-ID: <128113bf.1a2ef.1302b9ad53d.Coremail.taohaojuan@163.com>






At 2011-05-26 16:57:26?"Castaneda, Salvador" <salvador.castaneda at med.uni-tuebingen.de> wrote:

>Hey jacquie,
>
>I had the exact same issue when i started using it. What i did was export the all the maps i was measuring (FA, RD, ADC..) as analyze files. Then i used another software, in my case Pmod, and then uploaded all the files. The files have the same header and so they are already coregistered, you only have to ( i prefer) manually coregister them to an anatomy. Then i drew the rois there. ROI editor from the dti studio software is also good, but i found it hard to coregister the anatomy there. I think i'm not properly qualified to give you an answer about the tracts, so i leave it to someone else to answer that, but i would first look at the shimming you are performing on the region you are studying, and then i would guess there is going to be variability in the tracts that should average out with many samples, i think the averages should only help... Maybe the seeding of the tracts?
>Best,
>
>Salvador
>----------------------------------------------------------------------------------- 
>Salvador Castaneda, MD.
>University of T?bingen - Department of Radiology
>R?ntgenweg 13
>72076 T?bingen
>Germany
> 
>Office:      +49 (7071) 29-82977
>Fax:          +49 (7071) 29-4451
>E-mail:     Salvador.Castaneda at med.uni.tuebingen.de
>Web:         www.preclinicalimaging.org 
>
>
>-----Urspr?ngliche Nachricht-----
>Von: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] Im Auftrag von Jacquie Hodge
>Gesendet: Mittwoch, 25. Mai 2011 22:21
>An: mristudio-users at mristudio.org
>Betreff: [Mristudio-users] Theory_Air
>
>Hi everyone,
>
>I receive my DTI images as 6 directions with 6 repeats. Today I tried the Theory_Air registration on a set that I have already done many analysis on and I found that although the fiber statistics stayed generally similar when doing tractography, the FA values were quite different for the tracts.. From an average of 0.55 to 0.41 when I did the Theory_Air.
>Can someone explain why for me? Should I not be using this with 6 repeats?
>What I really would like to do is co-register one of my nice anatomical images with the FA or color FA for more accurate placement of my ROI's.
>
>Thanks,
>
>Jacquie
>
>Jacquie Hodge MSc candidate in Neuroscience, BSc
>Neuroscience, University of Calgary
>Research Assistant, Calgary Pediatric Stroke Program
>Alberta Children's Hospital
>2888 Shaganappi Trail NW, Calgary, AB, Canada T3B 6A8
>Phone: 403-955-7733 Fax: 403-955-2922
>jacquie.hodge at albertahealthservices.ca
>Program website: www.perinatalstroke.com
>
>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
>
>_______________________________________________
>mristudio-users mailing list
>mristudio-users at mristudio.org
>http://lists.mristudio.org/mailman/listinfo/
>Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org
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From susumu at mri.jhu.edu  Thu May 26 10:29:55 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Thu, 26 May 2011 10:29:55 -0400
Subject: [Mristudio-users] Theory_Air
In-Reply-To: <0AC64F4CB253074799B64FF8F0772D350126C700@azex2003.raddiag.med.uni-tuebingen.de>
References: <1DC4211314F7D9458B66A28F947F60B99C48B6D20D@EXMBX4C.crha.bewell.ca>
	<0AC64F4CB253074799B64FF8F0772D350126C700@azex2003.raddiag.med.uni-tuebingen.de>
Message-ID: <BANLkTimYRxh3a0gGxrpbs=3zTU3ytBz7aw@mail.gmail.com>

Thank you for the report. We'll look into the issue.

On Thu, May 26, 2011 at 4:57 AM, Castaneda, Salvador
<salvador.castaneda at med.uni-tuebingen.de> wrote:
> Hey jacquie,
>
> I had the exact same issue when i started using it. What i did was export the all the maps i was measuring (FA, RD, ADC..) as analyze files. Then i used another software, in my case Pmod, and then uploaded all the files. The files have the same header and so they are already coregistered, you only have to ( i prefer) manually coregister them to an anatomy. Then i drew the rois there. ROI editor from the dti studio software is also good, but i found it hard to coregister the anatomy there. I think i'm not properly qualified to give you an answer about the tracts, so i leave it to someone else to answer that, but i would first look at the shimming you are performing on the region you are studying, and then i would guess there is going to be variability in the tracts that should average out with many samples, i think the averages should only help... Maybe the seeding of the tracts?
> Best,
>
> Salvador
> -----------------------------------------------------------------------------------
> Salvador Castaneda, MD.
> University of T?bingen - Department of Radiology
> R?ntgenweg 13
> 72076 T?bingen
> Germany
>
> Office: ? ? ?+49 (7071) 29-82977
> Fax: ? ? ? ? ?+49 (7071) 29-4451
> E-mail: ? ? Salvador.Castaneda at med.uni.tuebingen.de
> Web: ? ? ? ? www.preclinicalimaging.org
>
>
> -----Urspr?ngliche Nachricht-----
> Von: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] Im Auftrag von Jacquie Hodge
> Gesendet: Mittwoch, 25. Mai 2011 22:21
> An: mristudio-users at mristudio.org
> Betreff: [Mristudio-users] Theory_Air
>
> Hi everyone,
>
> I receive my DTI images as 6 directions with 6 repeats. Today I tried the Theory_Air registration on a set that I have already done many analysis on and I found that although the fiber statistics stayed generally similar when doing tractography, the FA values were quite different for the tracts.. From an average of 0.55 to 0.41 when I did the Theory_Air.
> Can someone explain why for me? Should I not be using this with 6 repeats?
> What I really would like to do is co-register one of my nice anatomical images with the FA or color FA for more accurate placement of my ROI's.
>
> Thanks,
>
> Jacquie
>
> Jacquie Hodge MSc candidate in Neuroscience, BSc
> Neuroscience, University of Calgary
> Research Assistant, Calgary Pediatric Stroke Program
> Alberta Children's Hospital
> 2888 Shaganappi Trail NW, Calgary, AB, Canada T3B 6A8
> Phone: 403-955-7733 Fax: 403-955-2922
> jacquie.hodge at albertahealthservices.ca
> Program website: www.perinatalstroke.com
>
> 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
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> http://lists.mristudio.org/mailman/listinfo/
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>
>


From jjames2 at umc.edu  Fri May 27 16:42:34 2011
From: jjames2 at umc.edu (Judy James)
Date: Fri, 27 May 2011 15:42:34 -0500
Subject: [Mristudio-users] Problemin loading Phrama Scan 7T DTI data set
In-Reply-To: <2AA97D653978D24B85A02663FCC3916118F094631C@EXMBX3.ntummc.umsmed.edu>
References: <2AA97D653978D24B85A02663FCC3916118F094631C@EXMBX3.ntummc.umsmed.edu>
Message-ID: <2AA97D653978D24B85A02663FCC3916118F094631D@EXMBX3.ntummc.umsmed.edu>

Hello users,

I have some DTI data set from Phrama Scan 7T collected with 35 gradient directions, the 1st 5 being collected at b= 0. There are 20 data sets for each gradient with total 700 images. When I load them in DTI studio, all the 700 images appear as coming from 1 gradient dircetion; instead of breaking the images into 20 each for ecah gradient set,
Due to this reason, I am not able to do any further DTI calculations as it gives error and crashes the program.

I used the "Siemens, GE, Philips dicom" option to load the data. Can any one help me to decode this problem?

Thanks in advance.
Judy James,
UMC




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.

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From mborich at umn.edu  Mon May 30 20:50:41 2011
From: mborich at umn.edu (Michael Borich)
Date: Mon, 30 May 2011 19:50:41 -0500
Subject: [Mristudio-users] Calculate gradient table using HARDI dataset on
	Philips 3T
Message-ID: <Gophermail.2.0.1105301950410.18144@vs-w.tc.umn.edu>

Hello,

Does anyone know how to calculate 60 orientation gradient table for data 
collected on a Philips 3T? I tried using the Kennedy Krieger DTI Gradient 
Table creator but without success. Thanks in advance!

Best,
Michael

-- 
Michael Borich, DPT, PhD
Postdoctoral Research Fellow
University of British Columbia
604-827-3369

From susumu at mri.jhu.edu  Mon May 30 21:33:08 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Mon, 30 May 2011 21:33:08 -0400
Subject: [Mristudio-users] Calculate gradient table using HARDI dataset
 on Philips 3T
In-Reply-To: <Gophermail.2.0.1105301950410.18144@vs-w.tc.umn.edu>
References: <Gophermail.2.0.1105301950410.18144@vs-w.tc.umn.edu>
Message-ID: <BANLkTimutzWafDbyzn=LCA-GUFj68JBZzw@mail.gmail.com>

Hi Mike,

Philips' built-in gradient has only 6, 15, or 32 orientations, unless
there is something new in the latest operating system.

Where did you get the 60-orientation scheme?

Susumu

On Mon, May 30, 2011 at 8:50 PM, Michael Borich <mborich at umn.edu> wrote:
> Hello,
>
> Does anyone know how to calculate 60 orientation gradient table for data
> collected on a Philips 3T? I tried using the Kennedy Krieger DTI Gradient
> Table creator but without success. Thanks in advance!
>
> Best,
> Michael
>
> --
> Michael Borich, DPT, PhD
> Postdoctoral Research Fellow
> University of British Columbia
> 604-827-3369
> _______________________________________________
> mristudio-users mailing 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 mborich14 at gmail.com  Mon May 30 22:21:38 2011
From: mborich14 at gmail.com (Michael Borich)
Date: Mon, 30 May 2011 19:21:38 -0700
Subject: [Mristudio-users] Calculate gradient table using HARDI dataset
 on Philips 3T
In-Reply-To: <BANLkTimutzWafDbyzn=LCA-GUFj68JBZzw@mail.gmail.com>
References: <Gophermail.2.0.1105301950410.18144@vs-w.tc.umn.edu>
	<BANLkTimutzWafDbyzn=LCA-GUFj68JBZzw@mail.gmail.com>
Message-ID: <1930D6F5-FD58-4653-9725-95013156117A@umn.edu>

Hi Susumu, 

That is what I thought re: number of orientations. I tried using the matlab script from Kennedy Krieger with user defined gradient directions without success. It is a new sequence that our MR physicist wants to get up and running. That being said, I am not certain if the scanner has recently been updated. Will check on this issue. Will this type of scanning protocol be compatible with DTI studio? Thanks again for the prompt reply.

Best,
Michael


Michael Borich, DPT, PhD
Postdoctoral Research Fellow
University of British Columbia


On 2011-05-30, at 6:33 PM, susumu mori <susumu at mri.jhu.edu> wrote:

> Hi Mike,
> 
> Philips' built-in gradient has only 6, 15, or 32 orientations, unless
> there is something new in the latest operating system.
> 
> Where did you get the 60-orientation scheme?
> 
> Susumu
> 
> On Mon, May 30, 2011 at 8:50 PM, Michael Borich <mborich at umn.edu> wrote:
>> Hello,
>> 
>> Does anyone know how to calculate 60 orientation gradient table for data
>> collected on a Philips 3T? I tried using the Kennedy Krieger DTI Gradient
>> Table creator but without success. Thanks in advance!
>> 
>> Best,
>> Michael
>> 
>> --
>> Michael Borich, DPT, PhD
>> Postdoctoral Research Fellow
>> University of British Columbia
>> 604-827-3369
>> _______________________________________________
>> mristudio-users mailing 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 Malek.Makki at kispi.uzh.ch  Tue May 31 08:16:24 2011
From: Malek.Makki at kispi.uzh.ch (Makki Malek)
Date: Tue, 31 May 2011 14:16:24 +0200
Subject: [Mristudio-users] Calculate gradient table using HARDI dataset
 on Philips 3T
In-Reply-To: <1930D6F5-FD58-4653-9725-95013156117A@umn.edu>
Message-ID: <FD1E6887BC99C341800CBFD7ABC2F9C202976A1D@exzh1.kispi.int>


Hi Susumu and Michael

Philips has a 60 directions scheme which is implemented under research
mode. I've got the following one (attached file) for Achieva system. I
don't know if this table changes between 2 versions ..

It is also a good idea to check whether flipping X-Y, or Y-Z etc...
provides expecting results

I hops this helps.

Regards

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Malek I. Makki, PhD
Diagnostic Imaging Department
MRI Center
Kinderspital Zurich
 
Phone. +41(0)44 266 3130
Fax:      +41(0)44 266 7153
malek.makki at kispi.uzh.ch
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


-----Original Message-----
From: mristudio-users-bounces at mristudio.org
[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Michael
Borich
Sent: Tuesday, May 31, 2011 4:22 AM
To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
Subject: Re: [Mristudio-users] Calculate gradient table using HARDI
dataset on Philips 3T

Hi Susumu, 

That is what I thought re: number of orientations. I tried using the
matlab script from Kennedy Krieger with user defined gradient directions
without success. It is a new sequence that our MR physicist wants to get
up and running. That being said, I am not certain if the scanner has
recently been updated. Will check on this issue. Will this type of
scanning protocol be compatible with DTI studio? Thanks again for the
prompt reply.

Best,
Michael


Michael Borich, DPT, PhD
Postdoctoral Research Fellow
University of British Columbia


On 2011-05-30, at 6:33 PM, susumu mori <susumu at mri.jhu.edu> wrote:

> Hi Mike,
> 
> Philips' built-in gradient has only 6, 15, or 32 orientations, unless
> there is something new in the latest operating system.
> 
> Where did you get the 60-orientation scheme?
> 
> Susumu
> 
> On Mon, May 30, 2011 at 8:50 PM, Michael Borich <mborich at umn.edu>
wrote:
>> Hello,
>> 
>> Does anyone know how to calculate 60 orientation gradient table for
data
>> collected on a Philips 3T? I tried using the Kennedy Krieger DTI
Gradient
>> Table creator but without success. Thanks in advance!
>> 
>> Best,
>> Michael
>> 
>> --
>> Michael Borich, DPT, PhD
>> Postdoctoral Research Fellow
>> University of British Columbia
>> 604-827-3369
>> _______________________________________________
>> mristudio-users mailing 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

_______________________________________________
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mristudio-users at mristudio.org
http://lists.mristudio.org/mailman/listinfo/
Unsubscribe, send a blank email to:
mristudio-users-unsubscribe at mristudio.org
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From SyedSalman.Shahid at usq.edu.au  Wed Jun  1 13:46:35 2011
From: SyedSalman.Shahid at usq.edu.au (Syed Salman Shahid)
Date: Thu, 02 Jun 2011 03:46:35 +1000
Subject: [Mristudio-users] Co-registeration of DTI data with T1 or T2 data
In-Reply-To: <FD1E6887BC99C341800CBFD7ABC2F9C202976A1D@exzh1.kispi.int>
References: <1930D6F5-FD58-4653-9725-95013156117A@umn.edu>
	<FD1E6887BC99C341800CBFD7ABC2F9C202976A1D@exzh1.kispi.int>
Message-ID: <3318FC529C6A6E448A90CB5AB5B1F56C2D92938E34@EXCHMB.usq.edu.au>

Hi,
Just wondering if it is possible in DTI studio environment to co-register DTI data set with T1 or T2 data set before the DTI processing without losing any tensor information.

With regards
Salman


This email (including any attached files) is confidential and is for the
intended recipient(s) only.  If you received this email by mistake,
please, as a courtesy, tell the sender, then delete this email.

The views and opinions are the originator's and do not necessarily
reflect those of the University of Southern Queensland.  Although all
reasonable precautions were taken to ensure that this email contained no
viruses at the time it was sent we accept no liability for any losses
arising from its receipt.

The University of Southern Queensland is a registered provider of
education with the Australian Government (CRICOS Institution Code No's.
QLD 00244B / NSW 02225M)




From susumu at mri.jhu.edu  Wed Jun  1 16:26:19 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Wed, 01 Jun 2011 16:26:19 -0400
Subject: [Mristudio-users] Co-registeration of DTI data with T1 or T2
	data
In-Reply-To: <3318FC529C6A6E448A90CB5AB5B1F56C2D92938E34@EXCHMB.usq.edu.au>
References: <1930D6F5-FD58-4653-9725-95013156117A@umn.edu>
	<FD1E6887BC99C341800CBFD7ABC2F9C202976A1D@exzh1.kispi.int>
	<3318FC529C6A6E448A90CB5AB5B1F56C2D92938E34@EXCHMB.usq.edu.au>
Message-ID: <BANLkTi=7qink5iGJMxuCrckE_ugZo6GmbA@mail.gmail.com>

You can do that using DiffeoMap.

If you assume that the subject didn't move, you can use a tool to
change the location, rotation, FOV, and matrix size to theoretically
align the images. Otherwise, you can use a rigid transformation using
AIR or MI in DiffeoMap. You can submit two images with different
FOV/matrix and the resultant image will have exactly the same
dimensions as the template image. If the initial location of the brain
within the FOVs are too different, you may need some pre-adjustment to
bring the brain positions to a similar location within the FOVs.

I recommend you to do the registration of DTI data after tensor
calculation. If you move raw DWIs, you need to reorient the gradient
table too. Once you calculate scalar maps like FA, MD, EVs, then you
can register them to T1/T2 just like a regular image. If you want to
register a tensor map, you have to load it through the "Open *.d"
button so that DiffeoMap knows that it has to do tensor reorientation
procedure.

Because b0 and T2 have very similar contrast, you can do registration
between T2 and b0, save the transformation matrix and later you can
apply the matrix to any DTI-derived maps like FA, MD, EV, tensor, etc.
Avoid transforming vector maps. Instead, transform the tensor and then
calculate vector maps.

You can also do non-linear warping using LDDMM between b0 and T2 to
minimize B0-susceptibility distortion.

On Wed, Jun 1, 2011 at 1:46 PM, Syed Salman Shahid
<SyedSalman.Shahid at usq.edu.au> wrote:
> Hi,
> Just wondering if it is possible in DTI studio environment to co-register DTI data set with T1 or T2 data set before the DTI processing without losing any tensor information.
>
> With regards
> Salman
>
>
> This email (including any attached files) is confidential and is for the
> intended recipient(s) only. ?If you received this email by mistake,
> please, as a courtesy, tell the sender, then delete this email.
>
> The views and opinions are the originator's and do not necessarily
> reflect those of the University of Southern Queensland. ?Although all
> reasonable precautions were taken to ensure that this email contained no
> viruses at the time it was sent we accept no liability for any losses
> arising from its receipt.
>
> The University of Southern Queensland is a registered provider of
> education with the Australian Government (CRICOS Institution Code No's.
> QLD 00244B / NSW 02225M)
>
>
>
> _______________________________________________
> mristudio-users mailing 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  Thu Jun  2 09:25:54 2011
From: HuangS4 at uthscsa.edu (Huang, Shiliang)
Date: Thu, 02 Jun 2011 13:25:54 +0000
Subject: [Mristudio-users] Where can I get the DiffeoMap software?
In-Reply-To: <BANLkTi=7qink5iGJMxuCrckE_ugZo6GmbA@mail.gmail.com>
References: <1930D6F5-FD58-4653-9725-95013156117A@umn.edu>
	<FD1E6887BC99C341800CBFD7ABC2F9C202976A1D@exzh1.kispi.int>
	<3318FC529C6A6E448A90CB5AB5B1F56C2D92938E34@EXCHMB.usq.edu.au>
	<BANLkTi=7qink5iGJMxuCrckE_ugZo6GmbA@mail.gmail.com>
Message-ID: <5C82391AE0431149A408CE6D90F56C80050137@EX-CCF-MBX1.win.uthscsa.edu>

Hi  All
Where can I get the DiffeoMap software?

Thanks

Shiliang

-----Original Message-----
From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori
Sent: Wednesday, June 01, 2011 3:26 PM
To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
Subject: Re: [Mristudio-users] Co-registeration of DTI data with T1 or T2 data

You can do that using DiffeoMap.

If you assume that the subject didn't move, you can use a tool to
change the location, rotation, FOV, and matrix size to theoretically
align the images. Otherwise, you can use a rigid transformation using
AIR or MI in DiffeoMap. You can submit two images with different
FOV/matrix and the resultant image will have exactly the same
dimensions as the template image. If the initial location of the brain
within the FOVs are too different, you may need some pre-adjustment to
bring the brain positions to a similar location within the FOVs.

I recommend you to do the registration of DTI data after tensor
calculation. If you move raw DWIs, you need to reorient the gradient
table too. Once you calculate scalar maps like FA, MD, EVs, then you
can register them to T1/T2 just like a regular image. If you want to
register a tensor map, you have to load it through the "Open *.d"
button so that DiffeoMap knows that it has to do tensor reorientation
procedure.

Because b0 and T2 have very similar contrast, you can do registration
between T2 and b0, save the transformation matrix and later you can
apply the matrix to any DTI-derived maps like FA, MD, EV, tensor, etc.
Avoid transforming vector maps. Instead, transform the tensor and then
calculate vector maps.

You can also do non-linear warping using LDDMM between b0 and T2 to
minimize B0-susceptibility distortion.

On Wed, Jun 1, 2011 at 1:46 PM, Syed Salman Shahid
<SyedSalman.Shahid at usq.edu.au> wrote:
> Hi,
> Just wondering if it is possible in DTI studio environment to co-register DTI data set with T1 or T2 data set before the DTI processing without losing any tensor information.
>
> With regards
> Salman
>
>
> This email (including any attached files) is confidential and is for the
> intended recipient(s) only. ?If you received this email by mistake,
> please, as a courtesy, tell the sender, then delete this email.
>
> The views and opinions are the originator's and do not necessarily
> reflect those of the University of Southern Queensland. ?Although all
> reasonable precautions were taken to ensure that this email contained no
> viruses at the time it was sent we accept no liability for any losses
> arising from its receipt.
>
> The University of Southern Queensland is a registered provider of
> education with the Australian Government (CRICOS Institution Code No's.
> QLD 00244B / NSW 02225M)
>
>
>
> _______________________________________________
> mristudio-users mailing 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 choisj70 at gmail.com  Mon Jun  6 17:54:06 2011
From: choisj70 at gmail.com (Seongjin)
Date: Mon, 06 Jun 2011 17:54:06 -0400
Subject: [Mristudio-users] Q on DifferoMap
Message-ID: <BANLkTikvqzvBWUQWBPPuWK5U3h80oGMJdw@mail.gmail.com>

Dear DTI studio users,

Is there any manual on options on Mutual information registration in
DiffeoMap (not DTI studio).
There are Optimization Tolerance (1 field) and Ininital Optimization Vetors
(12 fields).

I searched through DTIstudio website, but I could not find manual or guide
on that options at all.

Thanks in advance,
SC
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From khua1 at jhu.edu  Mon Jun  6 18:25:22 2011
From: khua1 at jhu.edu (HUA KEGANG)
Date: Mon, 06 Jun 2011 22:25:22 +0000
Subject: [Mristudio-users] Q on DifferoMap
In-Reply-To: <BANLkTikvqzvBWUQWBPPuWK5U3h80oGMJdw@mail.gmail.com>
References: <BANLkTikvqzvBWUQWBPPuWK5U3h80oGMJdw@mail.gmail.com>
Message-ID: <BLU164-w26398D80C5EF0F4BD89F20B2600@phx.gbl>


Hi, 
 
There are some information about mutual info registration on the faq www.mristudio.org/wiki/faq. The mutual info algorithm is implemented using powell optimization method. For more detailed description of Powell method, please refer to "Numerical Recipes in C" by Press.
 
The following classical paper about mutual information registration also discussed about Powell method.
"Multimodality Image Registration by Maximization of Mutual Information" Meas IEEE TMI 1997
 
Thanks!

KEGANG(LUKE) HUA
Department of Radiology
Johns Hopkins University School of Medicine
720 Rutland Ave Traylor217
Baltimore, MD, 21205



 



Date: Mon, 6 Jun 2011 17:54:06 -0400
From: choisj70 at gmail.com
Subject: [Mristudio-users] Q on DifferoMap
To: mristudio-users at mristudio.org

Dear DTI studio users,

Is there any manual on options on Mutual information registration in DiffeoMap (not DTI studio).
There are Optimization Tolerance (1 field) and Ininital Optimization Vetors (12 fields).

I searched through DTIstudio website, but I could not find manual or guide on that options at all.

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  		 	   		  
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From ksupreet6 at gmail.com  Tue Jun  7 13:48:07 2011
From: ksupreet6 at gmail.com (Supreet kaur)
Date: Tue, 07 Jun 2011 13:48:07 -0400
Subject: [Mristudio-users] problem processing the NIFTI file
Message-ID: <BANLkTin6fsgCRS=-3-p=hdRSOusBWvB71g@mail.gmail.com>

hi
          I have a problem processing the NIFTI file. I save the images in
the files in the .REC format,
the problem comes when I try to process those raw files to DTI mapping, it
gives me an error file.
PLease help me on this.
I'll appreciate your reply.

Thanks,

-- 
Sincerely,

Supreet kaur
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From gsalves123 at hotmail.com  Tue Jun  7 15:41:06 2011
From: gsalves123 at hotmail.com (Gilberto Alves)
Date: Tue, 07 Jun 2011 22:41:06 +0300
Subject: [Mristudio-users] problem processing the NIFTI file
In-Reply-To: <BANLkTin6fsgCRS=-3-p=hdRSOusBWvB71g@mail.gmail.com>
References: <BANLkTin6fsgCRS=-3-p=hdRSOusBWvB71g@mail.gmail.com>
Message-ID: <COL106-W565BAAE05A9E0BB90F997886630@phx.gbl>


HI Supreet, 
 
If you say your data is in REC format, you need to convert these files to the Nifti format (.nii.gz). 
This can be easily done with some softwares. 
I recommend MRI cron. You can download it for free. Drag all files to the directory dcm2niigui and you will have the conversion. 
 
Cheers,
 
Gilberto Sousa Alves 
 


Date: Tue, 7 Jun 2011 13:48:07 -0400
From: ksupreet6 at gmail.com
To: mristudio-users at mristudio.org
Subject: [Mristudio-users] problem processing the NIFTI file


hi
          I have a problem processing the NIFTI file. I save the images in the files in the .REC format, 
the problem comes when I try to process those raw files to DTI mapping, it gives me an error file.
PLease help me on this.
I'll appreciate your reply.
 
Thanks,
-- 
Sincerely,

Supreet kaur


_______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org 		 	   		  
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From ksupreet6 at gmail.com  Tue Jun  7 15:46:54 2011
From: ksupreet6 at gmail.com (Supreet kaur)
Date: Tue, 07 Jun 2011 15:46:54 -0400
Subject: [Mristudio-users] need help
Message-ID: <BANLkTimZkk_tFe4OJLsATDC3J7R0ybYh+g@mail.gmail.com>

hello,
             The problem is that in our lab, we are provided with the motion
corrected NITFI files (.ni files). so when we view them in the DTI studio,
they can be veiwed in 3D View. Then the next step, i did the AIR regeration
and
saved the files in the RAW (.rec) format. I am not able to view them ok in
the 3D MRI view in the DTI studio; it gives me strange images.
 I am also providing you with the image parameter, look in the word file..
so I am stuck at this step..and not able to do DTI mapping..
I wanted to covert it into the REC format. I am providing you the details of
the image parameters in the attached word format. please help me..with this
as this is urgent..I have to do the manual segmentaiton for the tracks and
its due on Thursday...
I'll appreciate your help.

Thanks,
Supreet.
-- 
Sincerely,

Supreet kaur
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From rajagov2 at ccf.org  Tue Jun  7 16:24:33 2011
From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran)
Date: Tue, 07 Jun 2011 16:24:33 -0400
Subject: [Mristudio-users] need help
References: <BANLkTimZkk_tFe4OJLsATDC3J7R0ybYh+g@mail.gmail.com>
Message-ID: <77A88E90A851594AAEF830450587C39D04183589@CCHSCLEXMB56.cc.ad.cchs.net>

Hi Supreet,
 
I don't know whether I understood you correctly.
 
"Then the next step, i did the AIR regeration and saved the files in the RAW (.rec) format. I am not able to view them ok in the 3D MRI view in the DTI studio; it gives me strange images."
 
You also say "I wanted to covert it into the REC format."
 
I am a bit confused here.
 
 I have experienced problems with opening files in DTI studio. I think it kind of has memory of previous settings and won't let to open a new file. What I do normally is uninstall DTI studio and reinstall or log off and log in. It works for me sometimes like that. Another thing is if it is just for viewing i.e. cheking your results what you can do is save them in Analyse format (I haven't used AIR registration in DTI studio so I don't know whether you have this option while saving your images) and open in 3Dview by checking Analyse format option.
I am sorry I am not of much help here.
 
Venkat

________________________________

From: mristudio-users-bounces at mristudio.org on behalf of Supreet kaur
Sent: Tue 6/7/2011 3:46 PM
To: mristudio-users at mristudio.org
Subject: [Mristudio-users] need help



hello, 
             The problem is that in our lab, we are provided with the motion corrected NITFI files (.ni files). so when we view them in the DTI studio,
they can be veiwed in 3D View. Then the next step, i did the AIR regeration and 
saved the files in the RAW (.rec) format. I am not able to view them ok in the 3D MRI view in the DTI studio; it gives me strange images. 
 I am also providing you with the image parameter, look in the word file.. so I am stuck at this step..and not able to do DTI mapping..

I wanted to covert it into the REC format. I am providing you the details of the image parameters in the attached word format. please help me..with this as this is urgent..I have to do the manual segmentaiton for the tracks and its due on Thursday...
I'll appreciate your help.
 
Thanks,
Supreet.
-- 
Sincerely,

Supreet kaur



===================================

 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 (2010).  
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
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From ksupreet6 at gmail.com  Tue Jun  7 16:41:52 2011
From: ksupreet6 at gmail.com (Supreet kaur)
Date: Tue, 07 Jun 2011 16:41:52 -0400
Subject: [Mristudio-users] problem processing the NIFTI file
In-Reply-To: <COL106-W565BAAE05A9E0BB90F997886630@phx.gbl>
References: <BANLkTin6fsgCRS=-3-p=hdRSOusBWvB71g@mail.gmail.com>
	<COL106-W565BAAE05A9E0BB90F997886630@phx.gbl>
Message-ID: <BANLkTimkJy6rQWPGoUVTEsg5SC==vs5cTQ@mail.gmail.com>

hello all,
               My data is already in NIFTI format (.nii.gz); since I want to
process the data for the fiber segmentation using fiber tracking in the
DTI studio. I converted the data into the analyze format and REC format. But
I need to do DTI mapping, I am not able to load either of these two
file formats for DTI mapping.
Could you guys provide your useful feedback and help on this. I'll
appreciate your help as this  is urgent.
Thanks
Supreet


On Tue, Jun 7, 2011 at 3:41 PM, Gilberto Alves <gsalves123 at hotmail.com>wrote:

> HI Supreet,
>
> If you say your data is in REC format, you need to convert these files to
> the Nifti format (.nii.gz).
> This can be easily done with some softwares.
> I recommend MRI cron. You can download it for free. Drag all files to the
> directory dcm2niigui and you will have the conversion.
>
> Cheers,
>
> Gilberto Sousa Alves
>
> ------------------------------
> Date: Tue, 7 Jun 2011 13:48:07 -0400
> From: ksupreet6 at gmail.com
>
> To: mristudio-users at mristudio.org
> Subject: [Mristudio-users] problem processing the NIFTI file
>
>
> hi
>           I have a problem processing the NIFTI file. I save the images in
> the files in the .REC format,
> the problem comes when I try to process those raw files to DTI mapping, it
> gives me an error file.
> PLease help me on this.
> I'll appreciate your reply.
>
> Thanks,
>
> --
> Sincerely,
>
> Supreet kaur
>
>
> _______________________________________________ mristudio-users mailing
> 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
>
>


-- 
Sincerely,

Supreet kaur
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From rajagov2 at ccf.org  Tue Jun  7 17:08:49 2011
From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran)
Date: Tue, 07 Jun 2011 17:08:49 -0400
Subject: [Mristudio-users] problem processing the NIFTI file
References: <BANLkTin6fsgCRS=-3-p=hdRSOusBWvB71g@mail.gmail.com>
	<COL106-W565BAAE05A9E0BB90F997886630@phx.gbl>
	<BANLkTimkJy6rQWPGoUVTEsg5SC==vs5cTQ@mail.gmail.com>
Message-ID: <77A88E90A851594AAEF830450587C39D0418358A@CCHSCLEXMB56.cc.ad.cchs.net>

Hi Supreet,
 
When you load raw format for DTI mapping try choosing Phillips scanner option for REC format.
 
Venkat

________________________________

From: mristudio-users-bounces at mristudio.org on behalf of Supreet kaur
Sent: Tue 6/7/2011 4:41 PM
To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
Subject: Re: [Mristudio-users] problem processing the NIFTI file


hello all,
               My data is already in NIFTI format (.nii.gz); since I want to process the data for the fiber segmentation using fiber tracking in the
DTI studio. I converted the data into the analyze format and REC format. But I need to do DTI mapping, I am not able to load either of these two 
file formats for DTI mapping. 
Could you guys provide your useful feedback and help on this. I'll appreciate your help as this  is urgent.
Thanks
Supreet



On Tue, Jun 7, 2011 at 3:41 PM, Gilberto Alves <gsalves123 at hotmail.com> wrote:


	HI Supreet, 
	 
	If you say your data is in REC format, you need to convert these files to the Nifti format (.nii.gz). 
	This can be easily done with some softwares. 
	I recommend MRI cron. You can download it for free. Drag all files to the directory dcm2niigui and you will have the conversion. 
	 
	Cheers,
	 
	Gilberto Sousa Alves 
	 
	
________________________________

	Date: Tue, 7 Jun 2011 13:48:07 -0400
	From: ksupreet6 at gmail.com 

	To: mristudio-users at mristudio.org
	
	Subject: [Mristudio-users] problem processing the NIFTI file 


	hi
	          I have a problem processing the NIFTI file. I save the images in the files in the .REC format, 
	the problem comes when I try to process those raw files to DTI mapping, it gives me an error file.
	PLease help me on this.
	I'll appreciate your reply.
	 
	Thanks,
	
	-- 
	Sincerely,
	
	Supreet kaur
	
	

	_______________________________________________ mristudio-users mailing 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
	
	




-- 
Sincerely,

Supreet kaur



===================================

 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 (2010).  
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
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From choisj70 at gmail.com  Tue Jun  7 19:03:09 2011
From: choisj70 at gmail.com (Seongjin)
Date: Tue, 07 Jun 2011 19:03:09 -0400
Subject: [Mristudio-users] problem processing the NIFTI file
In-Reply-To: <BANLkTimkJy6rQWPGoUVTEsg5SC==vs5cTQ@mail.gmail.com>
References: <BANLkTin6fsgCRS=-3-p=hdRSOusBWvB71g@mail.gmail.com>
	<COL106-W565BAAE05A9E0BB90F997886630@phx.gbl>
	<BANLkTimkJy6rQWPGoUVTEsg5SC==vs5cTQ@mail.gmail.com>
Message-ID: <BANLkTiknjC3Huze8TpcOM5ivy06w21FdsA@mail.gmail.com>

If your Nifty format was compressed (filename.nii.gz), DTI studio will
complain.
Try to use uncompressed version. It will work. If not, your file might be
corrupted.

Good luck!
SC

On Tue, Jun 7, 2011 at 4:41 PM, Supreet kaur <ksupreet6 at gmail.com> wrote:

> hello all,
>                My data is already in NIFTI format (.nii.gz); since I want
> to process the data for the fiber segmentation using fiber tracking in the
> DTI studio. I converted the data into the analyze format and REC format.
> But I need to do DTI mapping, I am not able to load either of these two
> file formats for DTI mapping.
> Could you guys provide your useful feedback and help on this. I'll
> appreciate your help as this  is urgent.
> Thanks
> Supreet
>
>
> On Tue, Jun 7, 2011 at 3:41 PM, Gilberto Alves <gsalves123 at hotmail.com>wrote:
>
>> HI Supreet,
>>
>> If you say your data is in REC format, you need to convert these files to
>> the Nifti format (.nii.gz).
>> This can be easily done with some softwares.
>> I recommend MRI cron. You can download it for free. Drag all files to the
>> directory dcm2niigui and you will have the conversion.
>>
>> Cheers,
>>
>> Gilberto Sousa Alves
>>
>> ------------------------------
>> Date: Tue, 7 Jun 2011 13:48:07 -0400
>> From: ksupreet6 at gmail.com
>>
>> To: mristudio-users at mristudio.org
>> Subject: [Mristudio-users] problem processing the NIFTI file
>>
>>
>> hi
>>           I have a problem processing the NIFTI file. I save the images in
>> the files in the .REC format,
>> the problem comes when I try to process those raw files to DTI mapping, it
>> gives me an error file.
>> PLease help me on this.
>> I'll appreciate your reply.
>>
>> Thanks,
>>
>> --
>> Sincerely,
>>
>> Supreet kaur
>>
>>
>> _______________________________________________ mristudio-users mailing
>> 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
>>
>>
>
>
> --
> Sincerely,
>
> Supreet kaur
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From issel at jhu.edu  Thu Jun  2 11:50:26 2011
From: issel at jhu.edu (Issel Anne Lim)
Date: Thu, 02 Jun 2011 11:50:26 -0400
Subject: [Mristudio-users] Where can I get the DiffeoMap software?
In-Reply-To: <5C82391AE0431149A408CE6D90F56C80050137@EX-CCF-MBX1.win.uthscsa.edu>
References: <1930D6F5-FD58-4653-9725-95013156117A@umn.edu>
	<FD1E6887BC99C341800CBFD7ABC2F9C202976A1D@exzh1.kispi.int>
	<3318FC529C6A6E448A90CB5AB5B1F56C2D92938E34@EXCHMB.usq.edu.au>
	<BANLkTi=7qink5iGJMxuCrckE_ugZo6GmbA@mail.gmail.com>
	<5C82391AE0431149A408CE6D90F56C80050137@EX-CCF-MBX1.win.uthscsa.edu>
Message-ID: <BANLkTikQCtt1oNZz+gvqDVtNzGYh9NQXSw@mail.gmail.com>

Hello --
The entire MRIStudio suite is available on the MRIStudio website:
https://www.mristudio.org/wiki/installation
~~
Issel Anne L. Lim
PhD Candidate
Biomedical Engineering
Johns Hopkins University
http://alum.mit.edu/www/issel
issel at jhu.edu


On Thu, Jun 2, 2011 at 9:25 AM, Huang, Shiliang <HuangS4 at uthscsa.edu> wrote:

> Hi  All
> Where can I get the DiffeoMap software?
>
> Thanks
>
> Shiliang
>
> -----Original Message-----
> From: mristudio-users-bounces at mristudio.org [mailto:
> mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori
> Sent: Wednesday, June 01, 2011 3:26 PM
> To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
> Subject: Re: [Mristudio-users] Co-registeration of DTI data with T1 or T2
> data
>
> You can do that using DiffeoMap.
>
> If you assume that the subject didn't move, you can use a tool to
> change the location, rotation, FOV, and matrix size to theoretically
> align the images. Otherwise, you can use a rigid transformation using
> AIR or MI in DiffeoMap. You can submit two images with different
> FOV/matrix and the resultant image will have exactly the same
> dimensions as the template image. If the initial location of the brain
> within the FOVs are too different, you may need some pre-adjustment to
> bring the brain positions to a similar location within the FOVs.
>
> I recommend you to do the registration of DTI data after tensor
> calculation. If you move raw DWIs, you need to reorient the gradient
> table too. Once you calculate scalar maps like FA, MD, EVs, then you
> can register them to T1/T2 just like a regular image. If you want to
> register a tensor map, you have to load it through the "Open *.d"
> button so that DiffeoMap knows that it has to do tensor reorientation
> procedure.
>
> Because b0 and T2 have very similar contrast, you can do registration
> between T2 and b0, save the transformation matrix and later you can
> apply the matrix to any DTI-derived maps like FA, MD, EV, tensor, etc.
> Avoid transforming vector maps. Instead, transform the tensor and then
> calculate vector maps.
>
> You can also do non-linear warping using LDDMM between b0 and T2 to
> minimize B0-susceptibility distortion.
>
> On Wed, Jun 1, 2011 at 1:46 PM, Syed Salman Shahid
> <SyedSalman.Shahid at usq.edu.au> wrote:
> > Hi,
> > Just wondering if it is possible in DTI studio environment to co-register
> DTI data set with T1 or T2 data set before the DTI processing without losing
> any tensor information.
> >
> > With regards
> > Salman
> >
> >
> > This email (including any attached files) is confidential and is for the
> > intended recipient(s) only.  If you received this email by mistake,
> > please, as a courtesy, tell the sender, then delete this email.
> >
> > The views and opinions are the originator's and do not necessarily
> > reflect those of the University of Southern Queensland.  Although all
> > reasonable precautions were taken to ensure that this email contained no
> > viruses at the time it was sent we accept no liability for any losses
> > arising from its receipt.
> >
> > The University of Southern Queensland is a registered provider of
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> > QLD 00244B / NSW 02225M)
> >
> >
> >
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> >
>
> _______________________________________________
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> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
> _______________________________________________
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From ksupreet6 at gmail.com  Thu Jun  9 11:04:53 2011
From: ksupreet6 at gmail.com (Supreet kaur)
Date: Thu, 09 Jun 2011 11:04:53 -0400
Subject: [Mristudio-users] need urgent help!!!!!!!!
Message-ID: <BANLkTimcvCgfzn9rmbW27U8aOd8nC6+3JQ@mail.gmail.com>

hello Hanygi,

            I am working on the fiber tracking in DTI studio. I am facing a
color map problem.
The data was initially provided in the (brain_data_1.iso.ni) NIFTI format, I
converted it into the (.REC format). Then I loaded
it in the DTI studio and did the DTI mapping and calculated the Tensor,
color map, etc.
The color map images are coming out to be terrible...as you know that the
color map images are imporant in fiber
tracking;
Could you please provide your valuble feedback on this..I am attacking a
word file as I took some shots if those images
and also providing you with the image parameters.
I'll appreciate your help.

Sincerely,

Supreet kaur
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From ksupreet6 at gmail.com  Thu Jun  9 11:13:22 2011
From: ksupreet6 at gmail.com (Supreet kaur)
Date: Thu, 09 Jun 2011 11:13:22 -0400
Subject: [Mristudio-users] need help
Message-ID: <BANLkTinvQD5SWvX5aiqLi_pLTHKvLVcoXg@mail.gmail.com>

hello Hanygi,

            I am working on the fiber tracking in DTI studio. I am facing a
color map problem.
The data was initially provided in the (brain_data_1.iso.ni) NIFTI format, I
converted it into the (.REC format). Then I loaded
it in the DTI studio and did the DTI mapping and calculated the Tensor,
color map, etc.
The color map images are coming out to be terrible...as you know that the
color map images are imporant in fiber
tracking;
Could you please provide your valuble feedback on this..I'll appreciate your
help.

Sincerely,

Supreet kaur
-------------- next part --------------
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From alex.dresner at philips.com  Thu Jun  9 11:49:23 2011
From: alex.dresner at philips.com (Dresner, Alex)
Date: Thu, 09 Jun 2011 17:49:23 +0200
Subject: [Mristudio-users] urgent help
In-Reply-To: <BANLkTimcvCgfzn9rmbW27U8aOd8nC6+3JQ@mail.gmail.com>
References: <BANLkTimcvCgfzn9rmbW27U8aOd8nC6+3JQ@mail.gmail.com>
Message-ID: <F47DF122278D44439E845976F7C266D7431706D235@NLCLUEXM04.connect1.local>

Dear Supreet Kaur,
Most often a color map problem indicates something is wrong with the gradient table that was entered.  Two easy problems to fix are that your DTI data may not be in Slice-By-Slice rather than Gradient By Gradient (button, top right of DWI Parameters window) or that your gradient table may be rotated or flipped, so that the columns do not represent the right x, y, and z directions.
Good luck,
Alex

____________________
M. Alex Dresner, Ph.D.
MR Clinical Scientist
alex.dresner at philips.com<mailto:alex.dresner at philips.com>
____________________



From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Supreet kaur
Sent: Thursday, June 09, 2011 11:05 AM
To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
Subject: [Mristudio-users] need urgent help!!!!!!!!

hello Hanygi,

            I am working on the fiber tracking in DTI studio. I am facing a color map problem.
The data was initially provided in the (brain_data_1.iso.ni<http://brain_data_1.iso.ni>) NIFTI format, I converted it into the (.REC format). Then I loaded
it in the DTI studio and did the DTI mapping and calculated the Tensor, color map, etc.
The color map images are coming out to be terrible...as you know that the color map images are imporant in fiber
tracking;
Could you please provide your valuble feedback on this..I am attacking a word file as I took some shots if those images
and also providing you with the image parameters.
I'll appreciate your help.

Sincerely,

Supreet kaur

________________________________
The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message.
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From alex.dresner at philips.com  Mon Jun 13 23:49:16 2011
From: alex.dresner at philips.com (Dresner, Alex)
Date: Tue, 14 Jun 2011 05:49:16 +0200
Subject: [Mristudio-users] help for DTI FA map
In-Reply-To: <BANLkTinSrwdYM3iJYzXouVXAaZcLvhdzqA@mail.gmail.com>
References: <BANLkTinSrwdYM3iJYzXouVXAaZcLvhdzqA@mail.gmail.com>
Message-ID: <F47DF122278D44439E845976F7C266D743170ED888@NLCLUEXM04.connect1.local>

Dear Chunxiang,
Your email was probably bounced because of the size of the attachment.  (You can try just sending the text as an e-mail to find out.)

Your steps sound correct.  It's possible that the AIR is taking out the first slice because of motions or misregistration between volumes, and this could be a problem with your last slice as well.  I don't have much experience with AIR myself yet, but is there a step to apply the AIR registration to the gradient table?  Your FA images certainly look 'cleaner' after the AIR process, so it definitely seems worthwhile.  As far as the correctness of the gradients, are the colors in the color FA map correct (Color Map 0: red corpus callosum, green optic radiations)?

Regards,
Alex

From: me [mailto:favusome at gmail.com]
Sent: Monday, June 13, 2011 10:29 PM
To: Dresner, Alex
Subject: help for DTI FA map

Dear Alex,

I am a newbie for dtistudio who had encountered big problem as described in the attached. My email to the DTIstudion forum was bounced back, luckily that I saw that you are helping people with all these questions. Please help me since I have been tangled there and can't move forward...Thank you very much for your time.


Best Regards,
Chunxiang

________________________________
The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message.
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From favusome at gmail.com  Tue Jun 14 02:26:40 2011
From: favusome at gmail.com (me)
Date: Tue, 14 Jun 2011 14:26:40 +0800
Subject: [Mristudio-users] FA=1 and more strange Dtistudio problems,
	please help
Message-ID: <BANLkTikLPgQEb_cE0iZLq0nMwh1j3F7p2g@mail.gmail.com>

Dear Dtistudio experts,

I am a newbie user of this software who have encountered very confusing
problems that I don't understand how to solve. Please see the description
below. I keenly look forward to your help! Thank you very much for tutoring.



Detailed data processing procedure:
1. Acquisition: Siemens Trio 3.0T with Mosaic format
Parameters: diffusion directions=20, slices=25, average=2, number of b-value
is 6 plus b0.
2. Extract different b-value subfiles using matlab
3. Raw data converted from DICOM to NIfTI using dcm2niigui.exe, resulting in
four sets of files: **.img,  **.hdr,  **.bvec,  **.bval.
3. Adjust **.bval file to the right format suitable for DTIstudio
4. Load **.img file to DTIstudio ? MRI View 3D, choose ?image file format?
as ?Analyze?, then automatic image registration (AIR), the data saved as
**.dat
5. Opening DTI mapping, select Philips REC format, add the **.dat file
generated in Step 4. Copy the gradient table generated in Step 3
6. Calculate the tensor, color map, etc

Question1:
Is my data processing procedure correct?

Question2:
Under AIR condition, after sensor calculation and checking ?Anisotropy-FA?,
I found that slice0 shows nothing, as if the information in slice0 is
lost.The last slice shows apparently wrong FA because many pixels value
FA=1. But the slices between these two slices seem to be normal. If I don?t
do the AIR, slice0 information is not lost , and slice24 shows normal FA
values.


Sincerely,
Chunxiang
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From kevinspitler at ucla.edu  Wed Jun 15 17:46:21 2011
From: kevinspitler at ucla.edu (Kevin Spitler)
Date: Wed, 15 Jun 2011 14:46:21 -0700
Subject: [Mristudio-users] dtistudio failure on Fiber tracking
Message-ID: <BANLkTikVpZ8+cw0==NV-RVBkqNi831oing@mail.gmail.com>

Hello,

I have one dataset collected on a Siemens machine that loads, and I am
able to calculate "Tensor, Color Map", "ADC-Map", "Mean (DWIs, B0s)",
but DtiStudio crashes on Fiber Tracking on slice 26 (consistently).
This occurs on DtiStudio version 2.40.

In DtiStudio version 3.0.3, fiber tracking is successful.  I was
wondering what could cause this fiber tracking problem in the older
DtiStudio version?

Thanks for your help

Best,
Kevin

From choisj70 at gmail.com  Wed Jun 22 16:26:40 2011
From: choisj70 at gmail.com (Seongjin)
Date: Wed, 22 Jun 2011 16:26:40 -0400
Subject: [Mristudio-users] gradient table java applet question
Message-ID: <BANLkTinjDtU+Q1MKVu09nRe4owXm7M1tsg@mail.gmail.com>

Dear DTI studio users,

I wonder if you have any issue with the JAVA applet for gradient table for
Philips Scanner available in the following link:
http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html.

Whenever I generated gradient table using that applet, it allowed me to cut
and paste the gradient table.
Somehow it does not work anymore in that way.

Anyone know how to make it work?

Regards,
SC
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From susumu at mri.jhu.edu  Wed Jun 22 16:49:54 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Wed, 22 Jun 2011 16:49:54 -0400
Subject: [Mristudio-users] gradient table java applet question
In-Reply-To: <BANLkTinjDtU+Q1MKVu09nRe4owXm7M1tsg@mail.gmail.com>
References: <BANLkTinjDtU+Q1MKVu09nRe4owXm7M1tsg@mail.gmail.com>
Message-ID: <BANLkTinpeXLGvzKEKLaAyfHbQ3Bac_x6zQ@mail.gmail.com>

I'm using Chrome and I get a message to upgrade Java but if I ignore
it, I could still use it as usual.

On Wed, Jun 22, 2011 at 4:26 PM, [Seongjin] <choisj70 at gmail.com> wrote:
> Dear DTI studio users,
>
> I wonder if you have any issue with the JAVA applet for gradient table for
> Philips Scanner available in the following link:
> http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html.
>
> Whenever I generated gradient table using that applet, it allowed me to cut
> and paste the gradient table.
> Somehow it does not work anymore in that way.
>
> Anyone know how to make it work?
>
> Regards,
> 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
>
>

From choisj70 at gmail.com  Thu Jun 23 00:14:26 2011
From: choisj70 at gmail.com (Seongjin)
Date: Thu, 23 Jun 2011 00:14:26 -0400
Subject: [Mristudio-users] gradient table java applet question
In-Reply-To: <BANLkTinpeXLGvzKEKLaAyfHbQ3Bac_x6zQ@mail.gmail.com>
References: <BANLkTinjDtU+Q1MKVu09nRe4owXm7M1tsg@mail.gmail.com>
	<BANLkTinpeXLGvzKEKLaAyfHbQ3Bac_x6zQ@mail.gmail.com>
Message-ID: <BANLkTikpdhDdiQnmK0PhAVfCeLLBeknLhQ@mail.gmail.com>

Dear Susumu,

Thanks for your replay and advice.

Sincerely,
SC

On Wed, Jun 22, 2011 at 4:49 PM, susumu mori <susumu at mri.jhu.edu> wrote:

> I'm using Chrome and I get a message to upgrade Java but if I ignore
> it, I could still use it as usual.
>
> On Wed, Jun 22, 2011 at 4:26 PM, [Seongjin] <choisj70 at gmail.com> wrote:
> > Dear DTI studio users,
> >
> > I wonder if you have any issue with the JAVA applet for gradient table
> for
> > Philips Scanner available in the following link:
> > http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html.
> >
> > Whenever I generated gradient table using that applet, it allowed me to
> cut
> > and paste the gradient table.
> > Somehow it does not work anymore in that way.
> >
> > Anyone know how to make it work?
> >
> > Regards,
> > 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
>
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From siddharthray at ufl.edu  Fri Jun 24 14:20:37 2011
From: siddharthray at ufl.edu (Ray,Siddharth)
Date: Fri, 24 Jun 2011 14:20:37 -0400
Subject: [Mristudio-users] unzip .img files
Message-ID: <1ee16c43ad40c00e711d0c7d4e63ea0e@ufl.edu>

Hello,

I have rat brain DTI(2nd order) data with .img extension. I am not able 
to open and unzip it. can somebody help me out.

Regards
Siddharth Ray

From bkatsaros at otenet.gr  Fri Jun 24 16:04:04 2011
From: bkatsaros at otenet.gr (Vasilis Katsaros)
Date: Fri, 24 Jun 2011 23:04:04 +0300
Subject: [Mristudio-users] Siemens version
Message-ID: <000601cc32a9$e0362b50$a0a281f0$@gr>

Hello there,

 

I am using a Magnetom Symphony 1.5 T and acquire data of DTI by a sequence
called mddw in 12 directions b1000#0.

 

I asked my vendor application specialist about the DICOM version I should
use in MRI studio (low angle v.1, v.2 or high angle) and he could not answer
my question.

 

Can you help me please ?

 

Vasilis

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From siddharthray at ufl.edu  Tue Jun 28 16:27:52 2011
From: siddharthray at ufl.edu (Ray,Siddharth)
Date: Tue, 28 Jun 2011 16:27:52 -0400
Subject: [Mristudio-users] Rat Brain Data.
Message-ID: <a137b095440e18f546e9e8126a275006@ufl.edu>

Hello All,

Does anyone have a rat brain DTI data(for 2nd or 4th order)? I have one 
in DTI studio but i am not able to access the gradient vector, tensor 
coefficients. :( Or Does anyone know how can i see them?

Best Regards
Siddharth Ray

From jsadino.queens at gmail.com  Thu Jun 30 17:39:47 2011
From: jsadino.queens at gmail.com (Jeff Sadino)
Date: Thu, 30 Jun 2011 11:39:47 -1000
Subject: [Mristudio-users] MultiChannel Process Does Not Complete
Message-ID: <BANLkTimSQ4P5H2s413s9R4QBaiwMpLUfOw@mail.gmail.com>

Hello,

I am having a problem with some of my LDDMM submissions not being returned
from the server.  This happens about 15% percent of the time for the past
two weeks.  A couple recent ones are hash
numbers f48bb8d2b94679a1009249000cabe267 and
752303b61ba1fb71898fb03c634d930e.  I am sending them from user account
jchung (jinac1224 at gmail.com).  I sent them last Friday.  I receive emails
saying that my subject was received and has started processing, but then I
do not get the final email saying it is complete.  However, if I resubmit
them later, they do complete.  Can anyone suggest something that I can do
differently so that more of my subjects come back?

Thank you,
Jeff
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From susumu at mri.jhu.edu  Thu Jun 30 19:28:02 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Thu, 30 Jun 2011 19:28:02 -0400
Subject: [Mristudio-users] MultiChannel Process Does Not Complete
In-Reply-To: <BANLkTimSQ4P5H2s413s9R4QBaiwMpLUfOw@mail.gmail.com>
References: <BANLkTimSQ4P5H2s413s9R4QBaiwMpLUfOw@mail.gmail.com>
Message-ID: <BANLkTin3vDv9E5s9t4S4DTEGpiCfDk=4jA@mail.gmail.com>

Hi Jeff,

Sorry for the inconvenience you are experiencing.
We will look into the issues asap.

Susumu

On Thu, Jun 30, 2011 at 5:39 PM, Jeff Sadino <jsadino.queens at gmail.com>wrote:

> Hello,
>
> I am having a problem with some of my LDDMM submissions not being returned
> from the server.  This happens about 15% percent of the time for the past
> two weeks.  A couple recent ones are hash
> numbers f48bb8d2b94679a1009249000cabe267 and
> 752303b61ba1fb71898fb03c634d930e.  I am sending them from user account
> jchung (jinac1224 at gmail.com).  I sent them last Friday.  I receive emails
> saying that my subject was received and has started processing, but then I
> do not get the final email saying it is complete.  However, if I resubmit
> them later, they do complete.  Can anyone suggest something that I can do
> differently so that more of my subjects come back?
>
> Thank you,
> Jeff
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From akolasny at jhu.edu  Fri Jul  1 07:57:52 2011
From: akolasny at jhu.edu (akolasny at jhu.edu)
Date: Fri, 01 Jul 2011 07:57:52 -0400 (EDT)
Subject: [Mristudio-users] MultiChannel Process Does Not Complete
In-Reply-To: <BANLkTin3vDv9E5s9t4S4DTEGpiCfDk=4jA@mail.gmail.com>
References: <BANLkTimSQ4P5H2s413s9R4QBaiwMpLUfOw@mail.gmail.com>
	<BANLkTin3vDv9E5s9t4S4DTEGpiCfDk=4jA@mail.gmail.com>
Message-ID: <38213.192.168.2.29.1309521472.squirrel@webmail.cis.jhu.edu>

Jeff,

I'm manually running 752303b61ba1fb71898fb03c634d930e to see what happens.

The cluster that we were using has gone offline this morning due to
a campus wide power outage. When it comes back online, I'll check to
see if there are error messages there.

To be continued ...
Anthony

> Hi Jeff,
>
> Sorry for the inconvenience you are experiencing.
> We will look into the issues asap.
>
> Susumu
>
> On Thu, Jun 30, 2011 at 5:39 PM, Jeff Sadino
> <jsadino.queens at gmail.com>wrote:
>
>> Hello,
>>
>> I am having a problem with some of my LDDMM submissions not being
>> returned
>> from the server.  This happens about 15% percent of the time for the
>> past
>> two weeks.  A couple recent ones are hash
>> numbers f48bb8d2b94679a1009249000cabe267 and
>> 752303b61ba1fb71898fb03c634d930e.  I am sending them from user account
>> jchung (jinac1224 at gmail.com).  I sent them last Friday.  I receive
>> emails
>> saying that my subject was received and has started processing, but then
>> I
>> do not get the final email saying it is complete.  However, if I
>> resubmit
>> them later, they do complete.  Can anyone suggest something that I can
>> do
>> differently so that more of my subjects come back?
>>
>> Thank you,
>> Jeff
>>
>> _______________________________________________
>> mristudio-users mailing 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 jsadino.queens at gmail.com  Fri Jul  1 14:30:46 2011
From: jsadino.queens at gmail.com (Jeff Sadino)
Date: Fri, 01 Jul 2011 08:30:46 -1000
Subject: [Mristudio-users] MultiChannel Process Does Not Complete
In-Reply-To: <38213.192.168.2.29.1309521472.squirrel@webmail.cis.jhu.edu>
References: <BANLkTimSQ4P5H2s413s9R4QBaiwMpLUfOw@mail.gmail.com>
	<BANLkTin3vDv9E5s9t4S4DTEGpiCfDk=4jA@mail.gmail.com>
	<38213.192.168.2.29.1309521472.squirrel@webmail.cis.jhu.edu>
Message-ID: <BANLkTinOJ8mO9L2N0UVmGO9n0Ru+Ehc7Ew@mail.gmail.com>

Thank you very much everybody for your toubleshooting!  Anything you can
find will be helpful.  We noticed that the ICM last night (Hawaii time) was
giving this message: CANNOT ACCESS ICM CLUSTER.  Must have been because of
the power outage.  Hope you guys get back up and running soon!

Thank you,
Jeff

On Fri, Jul 1, 2011 at 1:57 AM, <akolasny at jhu.edu> wrote:

> Jeff,
>
> I'm manually running 752303b61ba1fb71898fb03c634d930e to see what happens.
>
> The cluster that we were using has gone offline this morning due to
> a campus wide power outage. When it comes back online, I'll check to
> see if there are error messages there.
>
> To be continued ...
> Anthony
>
> > Hi Jeff,
> >
> > Sorry for the inconvenience you are experiencing.
> > We will look into the issues asap.
> >
> > Susumu
> >
> > On Thu, Jun 30, 2011 at 5:39 PM, Jeff Sadino
> > <jsadino.queens at gmail.com>wrote:
> >
> >> Hello,
> >>
> >> I am having a problem with some of my LDDMM submissions not being
> >> returned
> >> from the server.  This happens about 15% percent of the time for the
> >> past
> >> two weeks.  A couple recent ones are hash
> >> numbers f48bb8d2b94679a1009249000cabe267 and
> >> 752303b61ba1fb71898fb03c634d930e.  I am sending them from user account
> >> jchung (jinac1224 at gmail.com).  I sent them last Friday.  I receive
> >> emails
> >> saying that my subject was received and has started processing, but then
> >> I
> >> do not get the final email saying it is complete.  However, if I
> >> resubmit
> >> them later, they do complete.  Can anyone suggest something that I can
> >> do
> >> differently so that more of my subjects come back?
> >>
> >> Thank you,
> >> Jeff
> >>
> >> _______________________________________________
> >> mristudio-users mailing 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
>
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From akolasny at jhu.edu  Fri Jul  1 18:12:41 2011
From: akolasny at jhu.edu (akolasny at jhu.edu)
Date: Fri, 01 Jul 2011 18:12:41 -0400 (EDT)
Subject: [Mristudio-users] MultiChannel Process Does Not Complete
In-Reply-To: <BANLkTinOJ8mO9L2N0UVmGO9n0Ru+Ehc7Ew@mail.gmail.com>
References: <BANLkTimSQ4P5H2s413s9R4QBaiwMpLUfOw@mail.gmail.com>
	<BANLkTin3vDv9E5s9t4S4DTEGpiCfDk=4jA@mail.gmail.com>
	<38213.192.168.2.29.1309521472.squirrel@webmail.cis.jhu.edu>
	<BANLkTinOJ8mO9L2N0UVmGO9n0Ru+Ehc7Ew@mail.gmail.com>
Message-ID: <59840.68.50.209.72.1309558361.squirrel@webmail.cis.jhu.edu>

The ICM cluster is back online. Queued jobs have been restarted. -Anthony


> Thank you very much everybody for your toubleshooting!  Anything you can
> find will be helpful.  We noticed that the ICM last night (Hawaii time)
> was
> giving this message: CANNOT ACCESS ICM CLUSTER.  Must have been because of
> the power outage.  Hope you guys get back up and running soon!
>
> Thank you,
> Jeff
>
> On Fri, Jul 1, 2011 at 1:57 AM, <akolasny at jhu.edu> wrote:
>
>> Jeff,
>>
>> I'm manually running 752303b61ba1fb71898fb03c634d930e to see what
>> happens.
>>
>> The cluster that we were using has gone offline this morning due to
>> a campus wide power outage. When it comes back online, I'll check to
>> see if there are error messages there.
>>
>> To be continued ...
>> Anthony
>>
>> > Hi Jeff,
>> >
>> > Sorry for the inconvenience you are experiencing.
>> > We will look into the issues asap.
>> >
>> > Susumu
>> >
>> > On Thu, Jun 30, 2011 at 5:39 PM, Jeff Sadino
>> > <jsadino.queens at gmail.com>wrote:
>> >
>> >> Hello,
>> >>
>> >> I am having a problem with some of my LDDMM submissions not being
>> >> returned
>> >> from the server.  This happens about 15% percent of the time for the
>> >> past
>> >> two weeks.  A couple recent ones are hash
>> >> numbers f48bb8d2b94679a1009249000cabe267 and
>> >> 752303b61ba1fb71898fb03c634d930e.  I am sending them from user
>> account
>> >> jchung (jinac1224 at gmail.com).  I sent them last Friday.  I receive
>> >> emails
>> >> saying that my subject was received and has started processing, but
>> then
>> >> I
>> >> do not get the final email saying it is complete.  However, if I
>> >> resubmit
>> >> them later, they do complete.  Can anyone suggest something that I
>> can
>> >> do
>> >> differently so that more of my subjects come back?
>> >>
>> >> Thank you,
>> >> Jeff
>> >>
>> >> _______________________________________________
>> >> mristudio-users mailing 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 Madhura.Ingalhalikar at uphs.upenn.edu  Thu Jul 14 12:14:29 2011
From: Madhura.Ingalhalikar at uphs.upenn.edu (Ingalhalikar, Madhura)
Date: Thu, 14 Jul 2011 12:14:29 -0400
Subject: [Mristudio-users] Fiber parametrization
Message-ID: <AEF9AAC7275B204982BD541763D9A8643A73F4@uphmasphi008.UPHS.PENNHEALTH.PRV>


Hi,
I need to compute the mean fiber:

1. Is there a way to do that using Dtistudio fiber tracking.
2. If not is there a way to get the points on the fibers (parametrization) in a certain format so that I can attempt to compute the mean from that.

Thanks,

Madhura



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From dzaca2 at jhmi.edu  Fri Jul 15 10:06:25 2011
From: dzaca2 at jhmi.edu (Domenico Zaca)
Date: Fri, 15 Jul 2011 10:06:25 -0400
Subject: [Mristudio-users] installation issue
Message-ID: <CA+sDYtd4X6KLeriGnvo2FMuAPuUfcuVMWJBnT5jAws=o=g9MPw@mail.gmail.com>

Hi,

I downloaded the latest edition of DTI studio on a Windows XP 64 desktop (
DtiStudio_latest-x64.exe<https://www.mristudio.org/download/binaries/DtiStudio-latest-x64.exe>)
and when I launch it I get this error message
*
The application has failed to start because the application configuration is
incorrect*

Any suggestion?

Thanks

-- 
Domenico Zaca', PhD
PostDoc Fellow
The Russell H. Morgan Department of
Radiology and Radiological Science
Johns Hopkins Univ. School of Medicine
Telephone: (410) 502-2408
Email:dzaca2 at jhmi.edu
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From dzaca2 at jhmi.edu  Fri Jul 15 10:41:54 2011
From: dzaca2 at jhmi.edu (Domenico Zaca)
Date: Fri, 15 Jul 2011 10:41:54 -0400
Subject: [Mristudio-users] installation issue
In-Reply-To: <CA+sDYtd4X6KLeriGnvo2FMuAPuUfcuVMWJBnT5jAws=o=g9MPw@mail.gmail.com>
References: <CA+sDYtd4X6KLeriGnvo2FMuAPuUfcuVMWJBnT5jAws=o=g9MPw@mail.gmail.com>
Message-ID: <CA+sDYtfGar=pV_PsyvdxHqHj3B3_0c2BFV3CY92WrYLJogVUng@mail.gmail.com>

Fixed it!


Thanks

On Fri, Jul 15, 2011 at 10:06 AM, Domenico Zaca <dzaca2 at jhmi.edu> wrote:

> Hi,
>
> I downloaded the latest edition of DTI studio on a Windows XP 64 desktop (
> DtiStudio_latest-x64.exe<https://www.mristudio.org/download/binaries/DtiStudio-latest-x64.exe>)
> and when I launch it I get this error message
> *
> The application has failed to start because the application configuration
> is incorrect*
>
> Any suggestion?
>
> Thanks
>
> --
> Domenico Zaca', PhD
> PostDoc Fellow
> The Russell H. Morgan Department of
> Radiology and Radiological Science
> Johns Hopkins Univ. School of Medicine
> Telephone: (410) 502-2408
> Email:dzaca2 at jhmi.edu
>



--
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From sjarso at mri.jhu.edu  Fri Jul 15 13:00:06 2011
From: sjarso at mri.jhu.edu (samson jarso)
Date: Fri, 15 Jul 2011 13:00:06 -0400
Subject: [Mristudio-users] installation issue
In-Reply-To: <CA+sDYtd4X6KLeriGnvo2FMuAPuUfcuVMWJBnT5jAws=o=g9MPw@mail.gmail.com>
References: <CA+sDYtd4X6KLeriGnvo2FMuAPuUfcuVMWJBnT5jAws=o=g9MPw@mail.gmail.com>
Message-ID: <4E207216.1070702@mri.jhu.edu>

Yes, domenico.  It's much easier to load this from a disk.  I have the 
disk at home.
I can bring it in on Tuesday.  I'll be at NIH on Monday.

One issue is that there can not be any spaces in the words in the pathway.

for example if you load the program in Start Menu
ie.     C:\Documents and Settings\Administrator\Start Menu

DTI studio will not work because it doesn't like "Documents and 
Settings" - There is a space here.
You have to install the software at C:\  level.

If that doesn't help I'll just bring my disk, it should take 5mins.

Samson



Domenico Zaca wrote:
> Hi,
>
> I downloaded the latest edition of DTI studio on a Windows XP 64 
> desktop (DtiStudio_latest-x64.exe 
> <https://www.mristudio.org/download/binaries/DtiStudio-latest-x64.exe>) and 
> when I launch it I get this error message
> /
> The application has failed to start because the application 
> configuration is incorrect/
>
> Any suggestion?
>
> Thanks
>
> -- 
> Domenico Zaca', PhD
> PostDoc Fellow
> The Russell H. Morgan Department of
> Radiology and Radiological Science
> Johns Hopkins Univ. School of Medicine
> Telephone: (410) 502-2408
> Email:dzaca2 at jhmi.edu <mailto:Email%3Adzaca2 at jhmi.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
>    


From llanyon at eyecarecentre.org  Fri Jul 15 18:14:22 2011
From: llanyon at eyecarecentre.org (Linda Lanyon)
Date: Fri, 15 Jul 2011 15:14:22 -0700
Subject: [Mristudio-users] Mean FA
Message-ID: <7EFE6518F6AAEE40989E649BBF66418F01095BF64D33@srv1.eyecarecentre.org>

Is there a way in DTI Studio (or MRI Studio) to find a mean tract position for a bundle of fibers along the same pathway, and then to calculate mean FA along that tract (preferably divided into segments along the tract)?

The only method I can find in DTI Studio is to reduce the tracts down to a selected few and then perform statistics, which gives mean FA. - just wondering if there is a way to get the mean tract as I've seen this published with other software.

Thanks!
Linda

------------------------------------------------------------------------------------------------
Linda Lanyon PhD BSc(Hons) CEng CITP MBCS
Michael Smith Foundation for Health Research Post Doctoral Research Fellow
University of British Columbia, Human Vision & Eye Movement Laboratory
VGH Eye Care Centre, 3rd Floor Research Labs
2550 Willow St, Vancouver
Phone: +1-604-675-8865
Cell: +1-778-378-5545
Fax: +1 604-875-4663
email: llanyon at eyecarecentre.org
web: http://www.neuroophthalmology.ca/UBCNeuroOp/JBarton/labstaff/Linda.htm

Director, Society for Canadian Women in Science and Technology: www.scwist.ca
SCWIST is a non-profit association that promotes, encourages and empowers women
and girls in science, engineering and technology.
------------------------------------------------------------------------------------------------

"If we knew what it was we were doing, it would not be called research, would it?"
Albert Einstein
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From buchmann2 at wisc.edu  Fri Jul 15 19:35:45 2011
From: buchmann2 at wisc.edu (Andreas Buchmann)
Date: Fri, 15 Jul 2011 17:35:45 -0600
Subject: [Mristudio-users] switching between images of different voxel sizes
Message-ID: <0LOE009NGEVBO710@smtpauth2.wiscmail.wisc.edu>

Dear MRI-Studio experts,

 

I'm using DTI Studio version 3.0.2.

When I open images with a certain voxel size and later swap to images with a
different voxel size, DTI Studio still uses the old voxel size.

For example, analyze images correctly shown in 0.86mm in-plane resolution
were saved as 1x1mm voxels in rec format (but with correct slice thickness,
which changed too), so the images were blurred in xy-plane.

 

Earlier, I observed a similar problem with defining image parameters in the
'DTI mapping' tab: for example, the program switched some parameters
automatically to the new image type, leaving others according to the old
images, which lead to inconsistencies (for example, 39 slices, but the slice
number went from 0 to 54).

 

I solved the problem by reading in the new image type several times. Is
there a less cumbersome procedure?

 

Many thanks

Andreas

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From susumu at mri.jhu.edu  Fri Jul 15 23:15:20 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Fri, 15 Jul 2011 23:15:20 -0400
Subject: [Mristudio-users] switching between images of different voxel
	sizes
In-Reply-To: <0LOE009NGEVBO710@smtpauth2.wiscmail.wisc.edu>
References: <0LOE009NGEVBO710@smtpauth2.wiscmail.wisc.edu>
Message-ID: <CAEq9apK1d0AcRo=sM-7e8LE9zywfAo=XDQnZfQv1rc0Lt1DxWw@mail.gmail.com>

Hi Andreas,

There are basically two types of files; those with and without header
information. Raw and Rec files are raw formats without header. So, every
time you open them, you have to tell DtiStudio about their image dimensions.
If you find anything wrong about image dimensions, it is either you
specified the wrong parameters or you didn't specify and DtiStudio simply
used parameters of the previous data (DtiStudio assumes the parameter of the
new data are the same as the previous ones if you don't specify).

Because RAW and Rec files do not contain image dimension information, the
dimension information you had in Analyze (i.e. 0.86mm) is lost. If you find
the image resolution is 1mm later when you load Rec, that means you
specified so when you load the Rec (e.g. matrix size is 256x256 and FOV is
256x256 in the data loading window). In this case, you simply had to type in
correct FOV (e.g. 240x240).

DtiStudio doesn't have functions to change dimensions. So before and after
data processing, the dimensions should remain the same. If your image looks
blurrier, the only reason I can think of is due to image co-registration.

The same goes for the number slices. Analyze format contains this
information but Rec/RAW don't. There is a field to specify the number of the
slices in the initial data loading window. If you don't specify this field,
it keeps the information from the previous session. If the number of the
slices are 55, then you have to explicitly type "55" or choose "All slices".

On Fri, Jul 15, 2011 at 7:35 PM, Andreas Buchmann <buchmann2 at wisc.edu>wrote:

>  Dear MRI-Studio experts,****
>
> ** **
>
> I'm using DTI Studio version 3.0.2.****
>
> When I open images with a certain voxel size and later swap to images with
> a different voxel size, DTI Studio still uses the old voxel size.****
>
> For example, analyze images correctly shown in 0.86mm in-plane resolution
> were saved as 1x1mm voxels in rec format (but with correct slice thickness,
> which changed too), so the images were blurred in xy-plane.****
>
> ** **
>
> Earlier, I observed a similar problem with defining image parameters in the
> 'DTI mapping' tab: for example, the program switched some parameters
> automatically to the new image type, leaving others according to the old
> images, which lead to inconsistencies (for example, 39 slices, but the slice
> number went from 0 to 54).****
>
> ** **
>
> I solved the problem by reading in the new image type several times. Is
> there a less cumbersome procedure?****
>
> ** **
>
> Many thanks****
>
> Andreas****
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From susumu at mri.jhu.edu  Sat Jul 16 00:09:07 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Sat, 16 Jul 2011 00:09:07 -0400
Subject: [Mristudio-users] Mean FA
In-Reply-To: <7EFE6518F6AAEE40989E649BBF66418F01095BF64D33@srv1.eyecarecentre.org>
References: <7EFE6518F6AAEE40989E649BBF66418F01095BF64D33@srv1.eyecarecentre.org>
Message-ID: <CAEq9apJLXYBhGzZ_yGUU25q_BnLuAfy8E49GAttkcY9_vAP7iw@mail.gmail.com>

Hi Linda,

I'm not sure what you exactly mean by "mean tract position". To calculate a
mean, you need a population. The "population" could be across 10 different
individuals, 10 repeated scans, 10 voxels within the same individual, etc.

I assume that you meant; "after tractography, it is common to obtain 10s of
streamlines that belong to the same pathway and can we calculate a "mean
streamline"  of the 10s of streamlines?"

If so, DtiStudio doesn't have such a function explicitly, but has the
following functions;

1) After tractography (and thus obtained 10s of streamlines), this
information is converted to 1/0 binary masking, in which voxels that contain
the streamline are assigned "1". Then it reports mean FA of the masked
voxels.
2) In the above method, a voxel that contains 1 streamline and 10
streamlines are both equally weighted (they are both assigned "1"). I
believe that there is a function to perform "weighted FA calculation".
Please ask Hangyi about the detail of this function. This may provide a
similar result to calculating a mean tract and measuring FA.

To divide the tractography results, DtiStudio can report FA of a tract at
each slice level. For example, if you have 50 axial slices, you can get a
report of FA at 50 axial levels.  Then the problem is, you have to identify
corresponding axial levels when you compare the reported slice-specific
numbers across individuals. For example, the FA of the CST at axial slice
#24 may correspond to slice #26 of another subject. When you get FA of the
entire CST from the pons to the motor cortex, you don't have this problem.
As soon as dividing the CST into "regions", you need spatial normalization
across individuals to make sure you are comparing the same "regions" across
individuals.

There are several ways to do this normalization. Probably the easiest way is
to normalize the orientation and the size of the brains across the
population using a linear transformation such that each axial level is more
or less consistent and thus the slice-by-slice reporting can be population
averaged. Or you can use our full brain segmentation using the
DiffeoMap/RoiEditor pipeline such that the CST pathway can be divided into
anatomical segments such as "pons", "midbrain", "internal capusule", "corona
radiata".

Hope this helps.

On Fri, Jul 15, 2011 at 6:14 PM, Linda Lanyon <llanyon at eyecarecentre.org>wrote:

>  Is there a way in DTI Studio (or MRI Studio) to find a mean tract
> position for a bundle of fibers along the same pathway, and then to
> calculate mean FA along that tract (preferably divided into segments along
> the tract)?
>
> The only method I can find in DTI Studio is to reduce the tracts down to a
> selected few and then perform statistics, which gives mean FA. - just
> wondering if there is a way to get the mean tract as I've seen this
> published with other software.
>
> Thanks!
> Linda
>
>
> ------------------------------------------------------------------------------------------------
> Linda Lanyon PhD BSc(Hons) CEng CITP MBCS
> Michael Smith Foundation for Health Research Post Doctoral Research Fellow
> University of British Columbia, Human Vision & Eye Movement Laboratory
> VGH Eye Care Centre, 3rd Floor Research Labs
> 2550 Willow St, Vancouver
> Phone: +1-604-675-8865
> Cell: +1-778-378-5545
> Fax: +1 604-875-4663
> email: llanyon at eyecarecentre.org
> web:
> http://www.neuroophthalmology.ca/UBCNeuroOp/JBarton/labstaff/Linda.htm
>
> Director, Society for Canadian Women in Science and Technology:
> www.scwist.ca
> *SCWIST is a non-profit association that promotes, encourages and empowers
> women
> and girls in science, engineering and technology.
> *
> ------------------------------------------------------------------------------------------------
>
>  "If we knew what it was we were doing, it would not be called research,
> would it?"
> Albert Einstein
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From susumu at mri.jhu.edu  Sat Jul 16 00:38:53 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Sat, 16 Jul 2011 00:38:53 -0400
Subject: [Mristudio-users] Fiber parametrization
In-Reply-To: <AEF9AAC7275B204982BD541763D9A8643A73F4@uphmasphi008.UPHS.PENNHEALTH.PRV>
References: <AEF9AAC7275B204982BD541763D9A8643A73F4@uphmasphi008.UPHS.PENNHEALTH.PRV>
Message-ID: <CAEq9ap+KXbW5NyUHmQvewsfGmYma0oo0jCQTpgzFVnfticBtmg@mail.gmail.com>

Hi Madhura,

The actual information of reconstructed fibers are fiber coordinates. By
saying "mean", do you mean population-averaged fiber coordinates? Or means
of pixel properties (e.g. FA, MD, etc) of the fibers?

Susumu

On Thu, Jul 14, 2011 at 12:14 PM, Ingalhalikar, Madhura <
Madhura.Ingalhalikar at uphs.upenn.edu> wrote:

>
> Hi,
> I need to compute the mean fiber:
>
> 1. Is there a way to do that using Dtistudio fiber tracking.
> 2. If not is there a way to get the points on the fibers (parametrization)
> in a certain format so that I can attempt to compute the mean from that.
>
> Thanks,
>
> Madhura
>
>
>
> 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/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
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From llanyon at eyecarecentre.org  Sat Jul 16 12:50:49 2011
From: llanyon at eyecarecentre.org (Linda Lanyon)
Date: Sat, 16 Jul 2011 09:50:49 -0700
Subject: [Mristudio-users] Mean FA
In-Reply-To: <CAEq9apJLXYBhGzZ_yGUU25q_BnLuAfy8E49GAttkcY9_vAP7iw@mail.gmail.com>
References: <7EFE6518F6AAEE40989E649BBF66418F01095BF64D33@srv1.eyecarecentre.org>
	<CAEq9apJLXYBhGzZ_yGUU25q_BnLuAfy8E49GAttkcY9_vAP7iw@mail.gmail.com>
Message-ID: <7EFE6518F6AAEE40989E649BBF66418F01095BF64D35@srv1.eyecarecentre.org>

Thanks for the comprehensive reply.
Yes, your assumption of what I meant - the mean streamline - is correct.
The weighted FA calculation would be useful, thanks Hangyi.

many thanks
Linda

________________________________
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 15, 2011 9:09 PM
To: DTI Studio, ROI Editor, DiffeoMap Questions/Support; Hangyi Jiang
Subject: Re: [Mristudio-users] Mean FA

Hi Linda,

I'm not sure what you exactly mean by "mean tract position". To calculate a mean, you need a population. The "population" could be across 10 different individuals, 10 repeated scans, 10 voxels within the same individual, etc.

I assume that you meant; "after tractography, it is common to obtain 10s of streamlines that belong to the same pathway and can we calculate a "mean streamline"  of the 10s of streamlines?"

If so, DtiStudio doesn't have such a function explicitly, but has the following functions;

1) After tractography (and thus obtained 10s of streamlines), this information is converted to 1/0 binary masking, in which voxels that contain the streamline are assigned "1". Then it reports mean FA of the masked voxels.
2) In the above method, a voxel that contains 1 streamline and 10 streamlines are both equally weighted (they are both assigned "1"). I believe that there is a function to perform "weighted FA calculation". Please ask Hangyi about the detail of this function. This may provide a similar result to calculating a mean tract and measuring FA.

To divide the tractography results, DtiStudio can report FA of a tract at each slice level. For example, if you have 50 axial slices, you can get a report of FA at 50 axial levels.  Then the problem is, you have to identify corresponding axial levels when you compare the reported slice-specific numbers across individuals. For example, the FA of the CST at axial slice #24 may correspond to slice #26 of another subject. When you get FA of the entire CST from the pons to the motor cortex, you don't have this problem. As soon as dividing the CST into "regions", you need spatial normalization across individuals to make sure you are comparing the same "regions" across individuals.

There are several ways to do this normalization. Probably the easiest way is to normalize the orientation and the size of the brains across the population using a linear transformation such that each axial level is more or less consistent and thus the slice-by-slice reporting can be population averaged. Or you can use our full brain segmentation using the DiffeoMap/RoiEditor pipeline such that the CST pathway can be divided into anatomical segments such as "pons", "midbrain", "internal capusule", "corona radiata".

Hope this helps.

On Fri, Jul 15, 2011 at 6:14 PM, Linda Lanyon <llanyon at eyecarecentre.org<mailto:llanyon at eyecarecentre.org>> wrote:
Is there a way in DTI Studio (or MRI Studio) to find a mean tract position for a bundle of fibers along the same pathway, and then to calculate mean FA along that tract (preferably divided into segments along the tract)?

The only method I can find in DTI Studio is to reduce the tracts down to a selected few and then perform statistics, which gives mean FA. - just wondering if there is a way to get the mean tract as I've seen this published with other software.

Thanks!
Linda

------------------------------------------------------------------------------------------------
Linda Lanyon PhD BSc(Hons) CEng CITP MBCS
Michael Smith Foundation for Health Research Post Doctoral Research Fellow
University of British Columbia, Human Vision & Eye Movement Laboratory
VGH Eye Care Centre, 3rd Floor Research Labs
2550 Willow St, Vancouver
Phone: +1-604-675-8865<tel:%2B1-604-675-8865>
Cell: +1-778-378-5545<tel:%2B1-778-378-5545>
Fax: +1 604-875-4663<tel:%2B1%20604-875-4663>
email: llanyon at eyecarecentre.org<mailto:llanyon at eyecarecentre.org>
web: http://www.neuroophthalmology.ca/UBCNeuroOp/JBarton/labstaff/Linda.htm

Director, Society for Canadian Women in Science and Technology: www.scwist.ca<http://www.scwist.ca>
SCWIST is a non-profit association that promotes, encourages and empowers women
and girls in science, engineering and technology.
------------------------------------------------------------------------------------------------

"If we knew what it was we were doing, it would not be called research, would it?"
Albert Einstein

_______________________________________________
mristudio-users mailing list
mristudio-users at mristudio.org<mailto:mristudio-users at mristudio.org>
http://lists.mristudio.org/mailman/listinfo/
Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org<mailto:mristudio-users-unsubscribe at mristudio.org>


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From Madhura.Ingalhalikar at uphs.upenn.edu  Mon Jul 18 09:28:04 2011
From: Madhura.Ingalhalikar at uphs.upenn.edu (Ingalhalikar, Madhura)
Date: Mon, 18 Jul 2011 09:28:04 -0400
Subject: [Mristudio-users] Fiber parametrization
References: <AEF9AAC7275B204982BD541763D9A8643A73F4@uphmasphi008.UPHS.PENNHEALTH.PRV>
	<CAEq9ap+KXbW5NyUHmQvewsfGmYma0oo0jCQTpgzFVnfticBtmg@mail.gmail.com>
Message-ID: <AEF9AAC7275B204982BD541763D9A8643A73F9@uphmasphi008.UPHS.PENNHEALTH.PRV>

Susumu, 

Thanks for your reply. 
I mean the mean fiber ( mean of all the fibers, something similar to the skeleton in TBSS ). 

Madhura

-----Original Message-----
From: mristudio-users-bounces at mristudio.org on behalf of susumu mori
Sent: Sat 7/16/2011 12:38 AM
To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
Subject: Re: [Mristudio-users] Fiber parametrization
 
Hi Madhura,

The actual information of reconstructed fibers are fiber coordinates. By
saying "mean", do you mean population-averaged fiber coordinates? Or means
of pixel properties (e.g. FA, MD, etc) of the fibers?

Susumu

On Thu, Jul 14, 2011 at 12:14 PM, Ingalhalikar, Madhura <
Madhura.Ingalhalikar at uphs.upenn.edu> wrote:

>
> Hi,
> I need to compute the mean fiber:
>
> 1. Is there a way to do that using Dtistudio fiber tracking.
> 2. If not is there a way to get the points on the fibers (parametrization)
> in a certain format so that I can attempt to compute the mean from that.
>
> Thanks,
>
> Madhura
>
>
>
> 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/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>



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.


From jsaygbe at masonlive.gmu.edu  Mon Jul 18 21:50:22 2011
From: jsaygbe at masonlive.gmu.edu (jsaygbe)
Date: Tue, 19 Jul 2011 01:50:22 +0000
Subject: [Mristudio-users] Fiber parametrization
In-Reply-To: <AEF9AAC7275B204982BD541763D9A8643A73F4@uphmasphi008.UPHS.PENNHEALTH.PRV>
References: <AEF9AAC7275B204982BD541763D9A8643A73F4@uphmasphi008.UPHS.PENNHEALTH.PRV>
Message-ID: <6784089528212D44921B9D823A279E400B21B5@CH1PRD0102MB098.prod.exchangelabs.com>

Hi All,

Does anyone know if DTI Studio accepts Nifty Files?

Also, does anyone have any tutorials on gradient/corrected files, as it relates DTI Studio. How do the two relate? What is the importance of said files when using DTI?

Any and all help (before 2PM, July 19th) would be much appreciated, as I have a meeting at 4PM tomorrow, July 19th, in which I have to briefly present on said topics.

Thank you in advance.

Warmest Regards,

Johnetta Saygbe

George Mason University (GMU)
2013
B.S. Neuroscience
Minor in African and African American Studies

Alpha Epsilon Delta Health Preprofessional Honor Society Honorary Member
Early Identification Program Alumna, GMU
Louis Strokes Alliance for Minority Participation (LSAMP) Member
Pre-College Initiative (PCI) Co-Chairperson, National Society of Black Engineers, GMU

"Commit to the Lord whatever you do, and your plans will succeed."
Proverbs 16:3

________________________________________
From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] on behalf of Ingalhalikar, Madhura [Madhura.Ingalhalikar at uphs.upenn.edu]
Sent: Thursday, July 14, 2011 12:14 PM
To: mristudio-users at mristudio.org
Subject: [Mristudio-users] Fiber parametrization

Hi,
I need to compute the mean fiber:

1. Is there a way to do that using Dtistudio fiber tracking.
2. If not is there a way to get the points on the fibers (parametrization) in a certain format so that I can attempt to compute the mean from that.

Thanks,

Madhura



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.

_______________________________________________
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Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org

From jsaygbe at masonlive.gmu.edu  Tue Jul 19 09:54:32 2011
From: jsaygbe at masonlive.gmu.edu (jsaygbe)
Date: Tue, 19 Jul 2011 13:54:32 +0000
Subject: [Mristudio-users] DTI Studio and Nifty Files
Message-ID: <6784089528212D44921B9D823A279E400B382C@CH1PRD0102MB098.prod.exchangelabs.com>

Hi All,

Does anyone know if DTI Studio accepts Nifty Files?

Also, does anyone have any tutorials on gradient/corrected files, as it relates DTI Studio. How do the two relate? What is the importance of said files when using DTI?

Any and all help (before 2PM, July 19th) would be much appreciated, as I have a meeting at 4PM today, July 19th, in which I have to briefly present on said topics.

Thank you in advance.

Warmest Regards,

Johnetta Saygbe

George Mason University (GMU)
2013
B.S. Neuroscience
Minor in African and African American Studies

Alpha Epsilon Delta Health Preprofessional Honor Society Honorary Member
Early Identification Program Alumna, GMU
Louis Strokes Alliance for Minority Participation (LSAMP) Member
Pre-College Initiative (PCI) Co-Chairperson, National Society of Black Engineers, GMU

"Commit to the Lord whatever you do, and your plans will succeed."
Proverbs 16:3

________________________________________
From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] on behalf of Ingalhalikar, Madhura [Madhura.Ingalhalikar at uphs.upenn.edu]
Sent: Thursday, July 14, 2011 12:14 PM
To: mristudio-users at mristudio.org
Subject: [Mristudio-users] Fiber parametrization

Hi,
I need to compute the mean fiber:

1. Is there a way to do that using Dtistudio fiber tracking.
2. If not is there a way to get the points on the fibers (parametrization) in a certain format so that I can attempt to compute the mean from that.

Thanks,

Madhura



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.

_______________________________________________
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mristudio-users at mristudio.org
http://lists.mristudio.org/mailman/listinfo/
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From jsaygbe at masonlive.gmu.edu  Tue Jul 19 09:56:26 2011
From: jsaygbe at masonlive.gmu.edu (jsaygbe)
Date: Tue, 19 Jul 2011 13:56:26 +0000
Subject: [Mristudio-users] DTI Studio tutorial
Message-ID: <6784089528212D44921B9D823A279E400B3A42@CH1PRD0102MB098.prod.exchangelabs.com>

Hi All,

Anyone have a link for an online tutorial that provides a visual tour of  DTI-studio?

Warmest Regards,

Johnetta Saygbe

George Mason University (GMU)
2013
B.S. Neuroscience
Minor in African and African American Studies and Performance Theatre

Alpha Epsilon Delta Health Preprofessional Honor Society Honorary Member
Early Identification Program Alumna, GMU
Louis Strokes Alliance for Minority Participation (LSAMP) Member
Pre-College Initiative (PCI) Co-Chairperson, National Society of Black Engineers, GMU

"Commit to the Lord whatever you do, and your plans will succeed."
Proverbs 16:3

________________________________________
From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] on behalf of jsaygbe [jsaygbe at masonlive.gmu.edu]
Sent: Tuesday, July 19, 2011 9:54 AM
To: DTI Studio, ROI Editor,     DiffeoMap Questions/Support
Subject: [Mristudio-users] DTI Studio and Nifty Files

Hi All,

Does anyone know if DTI Studio accepts Nifty Files?

Also, does anyone have any tutorials on gradient/corrected files, as it relates DTI Studio. How do the two relate? What is the importance of said files when using DTI?

Any and all help (before 2PM, July 19th) would be much appreciated, as I have a meeting at 4PM today, July 19th, in which I have to briefly present on said topics.

Thank you in advance.

Warmest Regards,

Johnetta Saygbe

George Mason University (GMU)
2013
B.S. Neuroscience
Minor in African and African American Studies

Alpha Epsilon Delta Health Preprofessional Honor Society Honorary Member
Early Identification Program Alumna, GMU
Louis Strokes Alliance for Minority Participation (LSAMP) Member
Pre-College Initiative (PCI) Co-Chairperson, National Society of Black Engineers, GMU

"Commit to the Lord whatever you do, and your plans will succeed."
Proverbs 16:3

________________________________________
From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] on behalf of Ingalhalikar, Madhura [Madhura.Ingalhalikar at uphs.upenn.edu]
Sent: Thursday, July 14, 2011 12:14 PM
To: mristudio-users at mristudio.org
Subject: [Mristudio-users] Fiber parametrization

Hi,
I need to compute the mean fiber:

1. Is there a way to do that using Dtistudio fiber tracking.
2. If not is there a way to get the points on the fibers (parametrization) in a certain format so that I can attempt to compute the mean from that.

Thanks,

Madhura



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.

_______________________________________________
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mristudio-users at mristudio.org
http://lists.mristudio.org/mailman/listinfo/
Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org
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Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org
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From buchmann2 at wisc.edu  Tue Jul 19 10:01:16 2011
From: buchmann2 at wisc.edu (Andreas Buchmann)
Date: Tue, 19 Jul 2011 08:01:16 -0600
Subject: [Mristudio-users] DTI Studio and Nifty Files
In-Reply-To: <6784089528212D44921B9D823A279E400B382C@CH1PRD0102MB098.prod.exchangelabs.com>
Message-ID: <0LOL00GNZ2YANR00@smtpauth2.wiscmail.wisc.edu>

Dear Johnetta,

MriStudio can read Nifti files.

I don't know exactly what you mean with 'gradient/corrected files'.

There is a short tutorial on the DTI Studio Website.
https://www.mristudio.org/wiki/user_manual

Good luck!
Andreas

-----Original Message-----
From: mristudio-users-bounces at mristudio.org
[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of jsaygbe
Sent: Dienstag, 19. Juli 2011 07:55
To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
Subject: [Mristudio-users] DTI Studio and Nifty Files
Importance: High

Hi All,

Does anyone know if DTI Studio accepts Nifty Files?

Also, does anyone have any tutorials on gradient/corrected files, as it
relates DTI Studio. How do the two relate? What is the importance of said
files when using DTI?

Any and all help (before 2PM, July 19th) would be much appreciated, as I
have a meeting at 4PM today, July 19th, in which I have to briefly present
on said topics.

Thank you in advance.

Warmest Regards,

Johnetta Saygbe

George Mason University (GMU)
2013
B.S. Neuroscience
Minor in African and African American Studies

Alpha Epsilon Delta Health Preprofessional Honor Society Honorary Member
Early Identification Program Alumna, GMU
Louis Strokes Alliance for Minority Participation (LSAMP) Member
Pre-College Initiative (PCI) Co-Chairperson, National Society of Black
Engineers, GMU

"Commit to the Lord whatever you do, and your plans will succeed."
Proverbs 16:3

________________________________________
From: mristudio-users-bounces at mristudio.org
[mristudio-users-bounces at mristudio.org] on behalf of Ingalhalikar, Madhura
[Madhura.Ingalhalikar at uphs.upenn.edu]
Sent: Thursday, July 14, 2011 12:14 PM
To: mristudio-users at mristudio.org
Subject: [Mristudio-users] Fiber parametrization

Hi,
I need to compute the mean fiber:

1. Is there a way to do that using Dtistudio fiber tracking.
2. If not is there a way to get the points on the fibers (parametrization)
in a certain format so that I can attempt to compute the mean from that.

Thanks,

Madhura



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/
Unsubscribe, send a blank email to:
mristudio-users-unsubscribe at mristudio.org
_______________________________________________
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mristudio-users at mristudio.org
http://lists.mristudio.org/mailman/listinfo/
Unsubscribe, send a blank email to:
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From zhou1 at jhmi.edu  Tue Jul 19 10:01:37 2011
From: zhou1 at jhmi.edu (Zhipeng Hou)
Date: Tue, 19 Jul 2011 10:01:37 -0400
Subject: [Mristudio-users] DTI Studio tutorial
In-Reply-To: <145933A2BE9E4F48AE079A201379BF2F2470CD1BE7@RAD-EXCH1.win.ad.jhu.edu>
References: <145933A2BE9E4F48AE079A201379BF2F2470CD1BE7@RAD-EXCH1.win.ad.jhu.edu>
Message-ID: <CACeZz4gvB_Oxfq5GkkNjbx69gJUjEKo7tWmYLj7FPr7jhJo1ng@mail.gmail.com>

 link:

https://www.mristudio.org/documentation/video/MristudioTutorialVideo/index.htm



On Tue, Jul 19, 2011 at 9:57 AM, jsaygbe <jsaygbe at masonlive.gmu.edu> wrote:

> Hi All,
>
> Anyone have a link for an online tutorial that provides a visual tour of
>  DTI-studio?
>
> Warmest Regards,
>
> Johnetta Saygbe
>
> George Mason University (GMU)
> 2013
> B.S. Neuroscience
> Minor in African and African American Studies and Performance Theatre
-------------- next part --------------
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From jsaygbe at masonlive.gmu.edu  Tue Jul 19 13:27:19 2011
From: jsaygbe at masonlive.gmu.edu (jsaygbe)
Date: Tue, 19 Jul 2011 17:27:19 +0000
Subject: [Mristudio-users] DTI Studio and Nifty Files
In-Reply-To: <0LOL00GNZ2YANR00@smtpauth2.wiscmail.wisc.edu>
References: <6784089528212D44921B9D823A279E400B382C@CH1PRD0102MB098.prod.exchangelabs.com>
	<0LOL00GNZ2YANR00@smtpauth2.wiscmail.wisc.edu>
Message-ID: <6784089528212D44921B9D823A279E400B3A88@CH1PRD0102MB098.prod.exchangelabs.com>

Thank you, Andreas!

Warmest Regards,

Johnetta Saygbe

George Mason University (GMU)
2013
B.S. Neuroscience
Minor in African and African American Studies and Performance Theatre

Alpha Epsilon Delta Health Preprofessional Honor Society Honorary Member
Early Identification Program Alumna, GMU
Louis Strokes Alliance for Minority Participation (LSAMP) Member
Pre-College Initiative (PCI) Co-Chairperson, National Society of Black Engineers, GMU

"Commit to the Lord whatever you do, and your plans will succeed."
Proverbs 16:3

________________________________________
From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] on behalf of Andreas Buchmann [buchmann2 at wisc.edu]
Sent: Tuesday, July 19, 2011 10:01 AM
To: 'DTI Studio, ROI Editor,    DiffeoMap Questions/Support'
Subject: Re: [Mristudio-users] DTI Studio and Nifty Files

Dear Johnetta,

MriStudio can read Nifti files.

I don't know exactly what you mean with 'gradient/corrected files'.

There is a short tutorial on the DTI Studio Website.
https://www.mristudio.org/wiki/user_manual

Good luck!
Andreas

-----Original Message-----
From: mristudio-users-bounces at mristudio.org
[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of jsaygbe
Sent: Dienstag, 19. Juli 2011 07:55
To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
Subject: [Mristudio-users] DTI Studio and Nifty Files
Importance: High

Hi All,

Does anyone know if DTI Studio accepts Nifty Files?

Also, does anyone have any tutorials on gradient/corrected files, as it
relates DTI Studio. How do the two relate? What is the importance of said
files when using DTI?

Any and all help (before 2PM, July 19th) would be much appreciated, as I
have a meeting at 4PM today, July 19th, in which I have to briefly present
on said topics.

Thank you in advance.

Warmest Regards,

Johnetta Saygbe

George Mason University (GMU)
2013
B.S. Neuroscience
Minor in African and African American Studies

Alpha Epsilon Delta Health Preprofessional Honor Society Honorary Member
Early Identification Program Alumna, GMU
Louis Strokes Alliance for Minority Participation (LSAMP) Member
Pre-College Initiative (PCI) Co-Chairperson, National Society of Black
Engineers, GMU

"Commit to the Lord whatever you do, and your plans will succeed."
Proverbs 16:3

________________________________________
From: mristudio-users-bounces at mristudio.org
[mristudio-users-bounces at mristudio.org] on behalf of Ingalhalikar, Madhura
[Madhura.Ingalhalikar at uphs.upenn.edu]
Sent: Thursday, July 14, 2011 12:14 PM
To: mristudio-users at mristudio.org
Subject: [Mristudio-users] Fiber parametrization

Hi,
I need to compute the mean fiber:

1. Is there a way to do that using Dtistudio fiber tracking.
2. If not is there a way to get the points on the fibers (parametrization)
in a certain format so that I can attempt to compute the mean from that.

Thanks,

Madhura



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/
Unsubscribe, send a blank email to:
mristudio-users-unsubscribe at mristudio.org
_______________________________________________
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Unsubscribe, send a blank email to:
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From kajal5888 at yahoo.co.in  Tue Jul 19 14:55:01 2011
From: kajal5888 at yahoo.co.in (diljit singh)
Date: Wed, 20 Jul 2011 00:25:01 +0530 (IST)
Subject: [Mristudio-users] DTI Studio and Nifty Files
In-Reply-To: <6784089528212D44921B9D823A279E400B3A88@CH1PRD0102MB098.prod.exchangelabs.com>
References: <6784089528212D44921B9D823A279E400B382C@CH1PRD0102MB098.prod.exchangelabs.com>
	<0LOL00GNZ2YANR00@smtpauth2.wiscmail.wisc.edu>
	<6784089528212D44921B9D823A279E400B3A88@CH1PRD0102MB098.prod.exchangelabs.com>
Message-ID: <1311101701.17438.YahooMailNeo@web95509.mail.in.yahoo.com>

hello everyone, 

does anyone have gradient table for Siemens 1.5T Syngo scanner, 30 Direction DTI??

thank & regards

?
Diljit Singh Kajal
M.Tech (Clinical Engineering)
Indian Institute Of Technology Madras,
Christian Medical College- Vellore,
SCTIMST-Thiruvananthpuram,
INDIA



________________________________
From: jsaygbe <jsaygbe at masonlive.gmu.edu>
To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" <mristudio-users at mristudio.org>
Sent: Tuesday, 19 July 2011 10:27 AM
Subject: Re: [Mristudio-users] DTI Studio and Nifty Files

Thank you, Andreas!

Warmest Regards,

Johnetta Saygbe

George Mason University (GMU)
2013
B.S. Neuroscience
Minor in African and African American Studies and Performance Theatre

Alpha Epsilon Delta Health Preprofessional Honor Society Honorary Member
Early Identification Program Alumna, GMU
Louis Strokes Alliance for Minority Participation (LSAMP) Member
Pre-College Initiative (PCI) Co-Chairperson, National Society of Black Engineers, GMU

"Commit to the Lord whatever you do, and your plans will succeed."
Proverbs 16:3

________________________________________
From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] on behalf of Andreas Buchmann [buchmann2 at wisc.edu]
Sent: Tuesday, July 19, 2011 10:01 AM
To: 'DTI Studio, ROI Editor,? ? DiffeoMap Questions/Support'
Subject: Re: [Mristudio-users] DTI Studio and Nifty Files

Dear Johnetta,

MriStudio can read Nifti files.

I don't know exactly what you mean with 'gradient/corrected files'.

There is a short tutorial on the DTI Studio Website.
https://www.mristudio.org/wiki/user_manual

Good luck!
Andreas

-----Original Message-----
From: mristudio-users-bounces at mristudio.org
[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of jsaygbe
Sent: Dienstag, 19. Juli 2011 07:55
To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
Subject: [Mristudio-users] DTI Studio and Nifty Files
Importance: High

Hi All,

Does anyone know if DTI Studio accepts Nifty Files?

Also, does anyone have any tutorials on gradient/corrected files, as it
relates DTI Studio. How do the two relate? What is the importance of said
files when using DTI?

Any and all help (before 2PM, July 19th) would be much appreciated, as I
have a meeting at 4PM today, July 19th, in which I have to briefly present
on said topics.

Thank you in advance.

Warmest Regards,

Johnetta Saygbe

George Mason University (GMU)
2013
B.S. Neuroscience
Minor in African and African American Studies

Alpha Epsilon Delta Health Preprofessional Honor Society Honorary Member
Early Identification Program Alumna, GMU
Louis Strokes Alliance for Minority Participation (LSAMP) Member
Pre-College Initiative (PCI) Co-Chairperson, National Society of Black
Engineers, GMU

"Commit to the Lord whatever you do, and your plans will succeed."
Proverbs 16:3

________________________________________
From: mristudio-users-bounces at mristudio.org
[mristudio-users-bounces at mristudio.org] on behalf of Ingalhalikar, Madhura
[Madhura.Ingalhalikar at uphs.upenn.edu]
Sent: Thursday, July 14, 2011 12:14 PM
To: mristudio-users at mristudio.org
Subject: [Mristudio-users] Fiber parametrization

Hi,
I need to compute the mean fiber:

1. Is there a way to do that using Dtistudio fiber tracking.
2. If not is there a way to get the points on the fibers (parametrization)
in a certain format so that I can attempt to compute the mean from that.

Thanks,

Madhura



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/
Unsubscribe, send a blank email to:
mristudio-users-unsubscribe at mristudio.org
_______________________________________________
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mristudio-users at mristudio.org
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Unsubscribe, send a blank email to:
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Unsubscribe, send a blank email to:
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From siddharthray at ufl.edu  Tue Jul 19 17:23:26 2011
From: siddharthray at ufl.edu (Ray,Siddharth)
Date: Tue, 19 Jul 2011 17:23:26 -0400
Subject: [Mristudio-users] HARDI Dataset
Message-ID: <713bbf0a6616e8605caa48e64b8e1c0e@ufl.edu>

Hello Everyone,

Do anybody have Human or Rat brain HARDI dataset?

Best Regards
Siddharth Ray

From Jacquie.Hodge at albertahealthservices.ca  Wed Jul 20 16:33:02 2011
From: Jacquie.Hodge at albertahealthservices.ca (Jacquie Hodge)
Date: Wed, 20 Jul 2011 14:33:02 -0600
Subject: [Mristudio-users] About loaded ROI into my Anatomy Image
In-Reply-To: <AANLkTi=C70rB2eiNKeCnvYYkE=5xf3-CE9L71P-=6=Lb@mail.gmail.com>
References: <AANLkTi=C70rB2eiNKeCnvYYkE=5xf3-CE9L71P-=6=Lb@mail.gmail.com>
Message-ID: <1DC4211314F7D9458B66A28F947F60B9AF055C1504@EXMBX4C.crha.bewell.ca>

Hello All,

I have been going through older emails to try and answer my own questions and came across this email. Can someone please share with me a "well known Atlas" and maybe elaborate a bit on the uses for these, how it would help me and what I do with it?

Thank you in advance :)

Jacquie

Jacquie Hodge MSc candidate in Neuroscience, BSc
Neuroscience, University of Calgary
Research Assistant, Calgary Pediatric Stroke Program
Alberta Children's Hospital
2888 Shaganappi Trail NW, Calgary, AB, Canada T3B 6A8
Phone: 403-955-7733 Fax: 403-955-2922
jacquie.hodge at albertahealthservices.ca
Program website: www.perinatalstroke.com
________________________________________
From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of [Seongjin] [choisj70 at gmail.com]
Sent: February 28, 2011 10:15 AM
To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
Subject: Re: [Mristudio-users] About loaded ROI into my Anatomy Image

I believe that you should do spatial normalization of your data to a well known ATLAS first.

SC



On Mon, Feb 28, 2011 at 8:15 AM, Yibao Wang <cmuwyb at gmail.com<mailto:cmuwyb at gmail.com>> wrote:


Is there a method to load the well-known ROI into my Anatomy Image?
I explain my question in detail,
for example, the are lots of well-known ROI such as insular, hippocampus,
it was diffcult to draw it in the anatomy image, sometimes because its poor resoultion.
Could we loaded those ROI into my Image?
I wonder is there any software could analysize the well-konwn interested ROI from the poor resolution anatomy image.


_______________________________________________
mristudio-users mailing list
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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.


From jangouk at kennedykrieger.org  Fri Jul 22 10:34:22 2011
From: jangouk at kennedykrieger.org (Jangouk, Parastoo)
Date: Fri, 22 Jul 2011 14:34:22 +0000
Subject: [Mristudio-users] About loaded ROI into my Anatomy Image
In-Reply-To: <1DC4211314F7D9458B66A28F947F60B9AF055C1504@EXMBX4C.crha.bewell.ca>
References: <AANLkTi=C70rB2eiNKeCnvYYkE=5xf3-CE9L71P-=6=Lb@mail.gmail.com>
	<1DC4211314F7D9458B66A28F947F60B9AF055C1504@EXMBX4C.crha.bewell.ca>
Message-ID: <16C42831A84D3A4C9C4E7D16083952188DE99D@kki-gsp-mail2.kki.org>


Hello everybody,

I want to work with DTIstudio in Mac environment using VWware. And as I have to do a whole lot of data analysis, I would like to know if this is comparable to the original windows environment or there is a preference to go for the traditional Windows on a PC?

Thanks
Parastoo



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 mail at andreas-horn.de  Fri Jul 22 10:58:46 2011
From: mail at andreas-horn.de (Andreas Horn)
Date: Fri, 22 Jul 2011 16:58:46 +0200 (MEST)
Subject: [Mristudio-users] IFO, MdLF and EmC
Message-ID: <201107221458.p6MEwkUv016490@post.webmailer.de>

Hello everybody, dear Susumu,

I have read your response about IFO and SFO (http://lists.mristudio.org/pipermail/mristudio-users/2011/001928.html).

Now I still wonder what anatomical structures are most likely included (or with which ones the cut-set is biggest) in IFO.
When I look at the tract, it seems that the extreme capsule is definitely included, most likely also parts of external capsule, possibly uncinatus. Is this correct?

I would also be very glad about three-dimensional data of the MdLF as delineated in Makris 2009 and/or the partialized SLF (I-III plus AF) but can't seem to find them anywhere. Do you have any ideas how to get access to these files?

All I want to do is to assign our tracts to anatomical structures.

Thank you so much for your help!

Yours, sincerely, Andreas Horn


From cfigley at gmail.com  Fri Jul 22 15:11:04 2011
From: cfigley at gmail.com (Chase Figley)
Date: Fri, 22 Jul 2011 15:11:04 -0400
Subject: [Mristudio-users] About loaded ROI into my Anatomy Image
In-Reply-To: <16C42831A84D3A4C9C4E7D16083952188DE99D@kki-gsp-mail2.kki.org>
References: <AANLkTi=C70rB2eiNKeCnvYYkE=5xf3-CE9L71P-=6=Lb@mail.gmail.com>
	<1DC4211314F7D9458B66A28F947F60B9AF055C1504@EXMBX4C.crha.bewell.ca>
	<16C42831A84D3A4C9C4E7D16083952188DE99D@kki-gsp-mail2.kki.org>
Message-ID: <CAFn7RgO-=-osG_Wk9GdN77be5ShkQ9XxR_uAcoztPL_gvddVWA@mail.gmail.com>

Hi Parastoo,

I *have* run DTIstudio on a virtual machine before, but I used Parallels
instead of VMware, so I am not familiar with the exact nuances of VMware.
However, what I can tell you is that while DTIstudio *will *run on a virtual
machine, it is less than ideal if you're going to be doing "a whole lot of
data analysis".  In the best case, it will probably be very slow, and in the
worst case, you may simply run out of memory (depending on how much RAM you
had to begin with, and how much you have chosen to allocate to VMware).

Anyway, if you are using a newer Mac with an Intel chip, you should probably
just install and run DTIstudio through a Bootcamp partition.  This is what I
finally settled on, and it works extremely well :)

Hope that helps,

Chase


On Fri, Jul 22, 2011 at 10:34 AM, Jangouk, Parastoo <
jangouk at kennedykrieger.org> wrote:

>
> Hello everybody,
>
> I want to work with DTIstudio in Mac environment using VWware. And as I
> have to do a whole lot of data analysis, I would like to know if this is
> comparable to the original windows environment or there is a preference to
> go for the traditional Windows on a PC?
>
> Thanks
> Parastoo
>
>
>
> 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/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>



-- 
Chase Figley, PhD
Johns Hopkins University
Department of Neuroscience
Department of Psychological and Brain Sciences
F.M. Kirby Research Center for Functional Brain Imaging
http://sites.google.com/site/cfigley/
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From susumu at mri.jhu.edu  Fri Jul 22 18:06:31 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Fri, 22 Jul 2011 18:06:31 -0400
Subject: [Mristudio-users] About loaded ROI into my Anatomy Image
In-Reply-To: <16C42831A84D3A4C9C4E7D16083952188DE99D@kki-gsp-mail2.kki.org>
References: <AANLkTi=C70rB2eiNKeCnvYYkE=5xf3-CE9L71P-=6=Lb@mail.gmail.com>
	<1DC4211314F7D9458B66A28F947F60B9AF055C1504@EXMBX4C.crha.bewell.ca>
	<16C42831A84D3A4C9C4E7D16083952188DE99D@kki-gsp-mail2.kki.org>
Message-ID: <CAEq9apJFnJe6MTL1S9oyJaNmBPvNvmLX1FDUiWiQM_FEM9f6DA@mail.gmail.com>

Hi Parastoo,

I don't have any experience with VWware, but I assume it'll work. Of course,
native Windows should be a better solution.

Susumu

On Fri, Jul 22, 2011 at 10:34 AM, Jangouk, Parastoo <
jangouk at kennedykrieger.org> wrote:

>
> Hello everybody,
>
> I want to work with DTIstudio in Mac environment using VWware. And as I
> have to do a whole lot of data analysis, I would like to know if this is
> comparable to the original windows environment or there is a preference to
> go for the traditional Windows on a PC?
>
> Thanks
> Parastoo
>
>
>
> 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/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
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From madamson at stanford.edu  Fri Jul 22 18:11:52 2011
From: madamson at stanford.edu (Maheen M. Adamson)
Date: Fri, 22 Jul 2011 15:11:52 -0700
Subject: [Mristudio-users] About loaded ROI into my Anatomy Image
In-Reply-To: <CAEq9apJFnJe6MTL1S9oyJaNmBPvNvmLX1FDUiWiQM_FEM9f6DA@mail.gmail.com>
References: <AANLkTi=C70rB2eiNKeCnvYYkE=5xf3-CE9L71P-=6=Lb@mail.gmail.com>
	<1DC4211314F7D9458B66A28F947F60B9AF055C1504@EXMBX4C.crha.bewell.ca>
	<16C42831A84D3A4C9C4E7D16083952188DE99D@kki-gsp-mail2.kki.org>
	<CAEq9apJFnJe6MTL1S9oyJaNmBPvNvmLX1FDUiWiQM_FEM9f6DA@mail.gmail.com>
Message-ID: <001501cc48bc$5e7243a0$1b56cae0$@edu>

Dear Parastoo,

VM Ware works fine with a native Mac environment running Windows. I run
Windows and Linux. However if you want to run DTI-studio and are running a
lot of analyses, you need to allocate a lot of memory to VM ware as it can
run very slow. You will need a powerful machine.

Thank you

Maheen

 

 

 

From: mristudio-users-bounces at mristudio.org
[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori
Sent: Friday, July 22, 2011 3:07 PM
To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
Subject: Re: [Mristudio-users] About loaded ROI into my Anatomy Image

 

Hi Parastoo,

 

I don't have any experience with VWware, but I assume it'll work. Of course,
native Windows should be a better solution.

 

Susumu

On Fri, Jul 22, 2011 at 10:34 AM, Jangouk, Parastoo
<jangouk at kennedykrieger.org> wrote:


Hello everybody,

I want to work with DTIstudio in Mac environment using VWware. And as I have
to do a whole lot of data analysis, I would like to know if this is
comparable to the original windows environment or there is a preference to
go for the traditional Windows on a PC?

Thanks
Parastoo



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/
Unsubscribe, send a blank email to:
mristudio-users-unsubscribe at mristudio.org

 

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From susumu at mri.jhu.edu  Fri Jul 22 19:08:24 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Fri, 22 Jul 2011 19:08:24 -0400
Subject: [Mristudio-users] About loaded ROI into my Anatomy Image
In-Reply-To: <1DC4211314F7D9458B66A28F947F60B9AF055C1504@EXMBX4C.crha.bewell.ca>
References: <AANLkTi=C70rB2eiNKeCnvYYkE=5xf3-CE9L71P-=6=Lb@mail.gmail.com>
	<1DC4211314F7D9458B66A28F947F60B9AF055C1504@EXMBX4C.crha.bewell.ca>
Message-ID: <CAEq9apJMpE4X+YgrMGie7nqqq8g+D1Js8SX=pA=auitVfvwngw@mail.gmail.com>

Hi Jacquie,

Defining a brain structure or ROI is usually performed by manual drawing.
The manual definition is usually treated as a gold standard (if it is done
by an experienced person). However, as you pointed out, it has several
problems; it requires training, time consuming, poor reproducibility, etc.
Therefore, more automated approaches are much needed.  The issue you raised,
low resolution or poor contrast, is a more fundamental issue, because it
affects both manual and automated approaches. For example, if the resolution
is poor to reliably delineate a structure manually, the chance is high that
the automated method is not reliable either.

When you choose to use an automated method, you have to tell the computer
which structure you want to define, like hippocampus. Here, there are
several points I want to make;

1) There are often multiple ways to define a structure of interest. For
example, different anatomist may define the hippocampus in slightly
different ways. In literature, the size of the hippocampus could be
different as much as twice. In this context, "well-known ROI" means
"well-described definition  by a famous neuroanatomist about how to define
the hippocampus". You may find that there are surprisingly a small number of
publications for this type of topics. For the hippocampus, I recommend you
to go over some work by European consortium by Dr. Giovanni B. Frisoni
2) Some may want only a subregion of the hippocampus, like CA1, CA2, etc. As
you try to define more and more detailed structures, you find that the
smallest structure you can possibly define is the image pixels. Namely, you
can theoretically define corresponding pixel coordinates across subjects.
This is the idea of the voxel-based analysis. In this case, your ROI is one
pixel. One of the most "well-known ROIs" in this case is the MNI
coordinates. Instead of saying, "an ROI in the hippocampus", you can say,
"MNI coordinate X, Y, Z".
3) However, usually, when one says, "ROI", that is not a single pixel, but a
cluster of pixels that contain an anatomical representation, such as "the
hippocampus". In this case, computer algorithms often require a prior
definition. Many programs use a prior probabilistic map based on
manual delineation. I believe a program like FreeSurfer comes with prior
probabilistic maps. In this case, these maps serve as "well-known ROI".
4) Some other programs (like our MriStudio) use a pre-segmented atlas. As I
mentioned above (#1), there is some degree of arbitrariness when we define a
structure. However, once a structure is defined in an atlas, we can claim
that we can apply a consistent definition to all images. There are widely
used atlases for cortical ROIs (such as AAL and PickAtlas). The MriStudio
program family (RoiEditor) comes with a pre-segmented atlas called, "white
matter parcellation map (WMPM). This is a bit misnomer, because it also
contains parcellation of the gray matter. I'm not sure if we can call it
"well-known", but it is an option.
5) The approach I described in #4 is basically the same as the voxel-based
approach (#2) because you need to warp the atlas (e.g. WMPM) to other
subjects, which requires voxel-to-voxel mapping between the two images. The
voxel-to-voxel mapping is performed independent of any structural
definitions. This means, once voxel-to-voxel mapping (called image
normalization or transformation) is completed, you can define any arbitrary
structure in one brain and this definition is automatically transferred to
the other. Therefore, you can define your own ROI (do not have to use the
WMPM we provide). In this context, whether the ROI is "well-known" or not
seems not a critical issue to me. What is more critical is if the
voxel-to-voxel mapping is accurate or not.

I hope you find this helpful.

Susumu



On Wed, Jul 20, 2011 at 4:33 PM, Jacquie Hodge <
Jacquie.Hodge at albertahealthservices.ca> wrote:

> Hello All,
>
> I have been going through older emails to try and answer my own questions
> and came across this email. Can someone please share with me a "well known
> Atlas" and maybe elaborate a bit on the uses for these, how it would help me
> and what I do with it?
>
> Thank you in advance :)
>
> Jacquie
>
> Jacquie Hodge MSc candidate in Neuroscience, BSc
> Neuroscience, University of Calgary
> Research Assistant, Calgary Pediatric Stroke Program
> Alberta Children's Hospital
> 2888 Shaganappi Trail NW, Calgary, AB, Canada T3B 6A8
> Phone: 403-955-7733 Fax: 403-955-2922
> jacquie.hodge at albertahealthservices.ca
> Program website: www.perinatalstroke.com
> ________________________________________
> From: mristudio-users-bounces at mristudio.org [
> mristudio-users-bounces at mristudio.org] On Behalf Of [Seongjin] [
> choisj70 at gmail.com]
> Sent: February 28, 2011 10:15 AM
> To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
> Subject: Re: [Mristudio-users] About loaded ROI into my Anatomy Image
>
> I believe that you should do spatial normalization of your data to a well
> known ATLAS first.
>
> SC
>
>
>
> On Mon, Feb 28, 2011 at 8:15 AM, Yibao Wang <cmuwyb at gmail.com<mailto:
> cmuwyb at gmail.com>> wrote:
>
>
> Is there a method to load the well-known ROI into my Anatomy Image?
> I explain my question in detail,
> for example, the are lots of well-known ROI such as insular, hippocampus,
> it was diffcult to draw it in the anatomy image, sometimes because its poor
> resoultion.
> Could we loaded those ROI into my Image?
> I wonder is there any software could analysize the well-konwn interested
> ROI from the poor resolution anatomy image.
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org<mailto:mristudio-users at mristudio.org>
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org<mailto:
> mristudio-users-unsubscribe at mristudio.org>
>
>
>
>
>
>        <<
>                ATT00001..c     (0.3KB)
>
>                (0.3KB)
>        >>
>
> 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
>
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From susumu at mri.jhu.edu  Fri Jul 22 19:44:30 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Fri, 22 Jul 2011 19:44:30 -0400
Subject: [Mristudio-users] IFO, MdLF and EmC
In-Reply-To: <201107221458.p6MEwkUv016490@post.webmailer.de>
References: <201107221458.p6MEwkUv016490@post.webmailer.de>
Message-ID: <CAEq9apL6NZpSD8ZzL5edkTQEccL24ZJJejO5GrDZ=Gt8fx0Z-Q@mail.gmail.com>

Hi Andreas,

With 2-2.5mm resolution, the external and extreme capsules are difficult to
separate, but I agree that IFO seems to occupy a good portion of these
structures.

As for the different sections of the SLF, please refer to Yajing Zhang's
paper in NeuroImage about the automated tractography. She created
probabilistic maps of the different sections of the SLF in our atlas, which
are available for download. Please contact Yajing about the location of the
files. They may be already included in RoiEditor but I need to ask Xin.

MdLF is currently not defined in our atlas.

Susumu

On Fri, Jul 22, 2011 at 10:58 AM, Andreas Horn <mail at andreas-horn.de> wrote:

> Hello everybody, dear Susumu,
>
> I have read your response about IFO and SFO (
> http://lists.mristudio.org/pipermail/mristudio-users/2011/001928.html).
>
> Now I still wonder what anatomical structures are most likely included (or
> with which ones the cut-set is biggest) in IFO.
> When I look at the tract, it seems that the extreme capsule is definitely
> included, most likely also parts of external capsule, possibly uncinatus. Is
> this correct?
>
> I would also be very glad about three-dimensional data of the MdLF as
> delineated in Makris 2009 and/or the partialized SLF (I-III plus AF) but
> can't seem to find them anywhere. Do you have any ideas how to get access to
> these files?
>
> All I want to do is to assign our tracts to anatomical structures.
>
> Thank you so much for your help!
>
> Yours, sincerely, Andreas Horn
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
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From zhangyajing9996 at gmail.com  Sat Jul 23 11:22:07 2011
From: zhangyajing9996 at gmail.com (Yajing Zhang)
Date: Sat, 23 Jul 2011 11:22:07 -0400
Subject: [Mristudio-users] IFO, MdLF and EmC
In-Reply-To: <CAEq9apL6NZpSD8ZzL5edkTQEccL24ZJJejO5GrDZ=Gt8fx0Z-Q@mail.gmail.com>
References: <201107221458.p6MEwkUv016490@post.webmailer.de>
	<CAEq9apL6NZpSD8ZzL5edkTQEccL24ZJJejO5GrDZ=Gt8fx0Z-Q@mail.gmail.com>
Message-ID: <CADKVbtFWRjsZqLn5-2kjpW9sKMvFebF3Ap0CGJ9JZ7ptVCtZyg@mail.gmail.com>

Hi, Andreas

You can find the fiber atlas in:
http://lbam.med.jhmi.edu/cmrm/Data_Yajing/fiberMenu.htm
The components of SLF can be downloaded in:
http://lbam.med.jhmi.edu/cmrm/Data_Yajing/longAssociation.htm
The corresponding paper is: "Atlas-guided tract reconstruction for automated
and comprehensive examination of the white matter anatomy." Neuroimage
52(4):1289-1301 (2010).


Best regards,
Yajing



On Fri, Jul 22, 2011 at 7:44 PM, susumu mori <susumu at mri.jhu.edu> wrote:

> Hi Andreas,
>
> With 2-2.5mm resolution, the external and extreme capsules are difficult to
> separate, but I agree that IFO seems to occupy a good portion of these
> structures.
>
> As for the different sections of the SLF, please refer to Yajing Zhang's
> paper in NeuroImage about the automated tractography. She created
> probabilistic maps of the different sections of the SLF in our atlas, which
> are available for download. Please contact Yajing about the location of the
> files. They may be already included in RoiEditor but I need to ask Xin.
>
> MdLF is currently not defined in our atlas.
>
> Susumu
>
> On Fri, Jul 22, 2011 at 10:58 AM, Andreas Horn <mail at andreas-horn.de>wrote:
>
>> Hello everybody, dear Susumu,
>>
>> I have read your response about IFO and SFO (
>> http://lists.mristudio.org/pipermail/mristudio-users/2011/001928.html).
>>
>> Now I still wonder what anatomical structures are most likely included (or
>> with which ones the cut-set is biggest) in IFO.
>> When I look at the tract, it seems that the extreme capsule is definitely
>> included, most likely also parts of external capsule, possibly uncinatus. Is
>> this correct?
>>
>> I would also be very glad about three-dimensional data of the MdLF as
>> delineated in Makris 2009 and/or the partialized SLF (I-III plus AF) but
>> can't seem to find them anywhere. Do you have any ideas how to get access to
>> these files?
>>
>> All I want to do is to assign our tracts to anatomical structures.
>>
>> Thank you so much for your help!
>>
>> Yours, sincerely, Andreas Horn
>>
>> _______________________________________________
>> mristudio-users mailing 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
>
>
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From kmanoj at mail.med.upenn.edu  Tue Jul 26 09:16:33 2011
From: kmanoj at mail.med.upenn.edu (manoj kumar)
Date: Tue, 26 Jul 2011 09:16:33 -0400
Subject: [Mristudio-users] ROI analysis
Message-ID: <CAG11YAMTmsT15rryhcat_guD_dXAR0oc8oyUpzLVups1zKGGGA@mail.gmail.com>

Hello All user;

I am working on mouse animal model and have ex vivo brain DTI (high
resolution 3D) data. I want to co-registered  these data set and want to
analyse the data using DTI studio.
My problem is that when I have tried to co-register two data set using AIR
method in DTI studio and try to draw ROI and save it in Binary Image and
Binary map format and again try to import same ROI even in same data set
there was an error showing: unrecognized image-ROI data file.

Any help and suggestion are highly appreciated.

Thanks

Manoj
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From choisj70 at gmail.com  Tue Jul 26 11:35:33 2011
From: choisj70 at gmail.com (Seongjin)
Date: Tue, 26 Jul 2011 11:35:33 -0400
Subject: [Mristudio-users] ROI analysis
In-Reply-To: <CAG11YAMTmsT15rryhcat_guD_dXAR0oc8oyUpzLVups1zKGGGA@mail.gmail.com>
References: <CAG11YAMTmsT15rryhcat_guD_dXAR0oc8oyUpzLVups1zKGGGA@mail.gmail.com>
Message-ID: <CANM4YeWWaTr7zBQF50OWnAvCRj=izLw9sbO9u1GZyW7BmGKTmA@mail.gmail.com>

DTI studio is good for post-processing and deterministic tractography.
For ROI-based data analysis, it would be much better to try ROI-editor (a
sister software to DTI studio).

Best,
-SC

On Tue, Jul 26, 2011 at 9:16 AM, manoj kumar <kmanoj at mail.med.upenn.edu>wrote:

> Hello All user;
>
> I am working on mouse animal model and have ex vivo brain DTI (high
> resolution 3D) data. I want to co-registered  these data set and want to
> analyse the data using DTI studio.
> My problem is that when I have tried to co-register two data set using AIR
> method in DTI studio and try to draw ROI and save it in Binary Image and
> Binary map format and again try to import same ROI even in same data set
> there was an error showing: unrecognized image-ROI data file.
>
> Any help and suggestion are highly appreciated.
>
> Thanks
>
> 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
>
>
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From andreas.horn at uniklinik-freiburg.de  Sun Jul 24 05:45:21 2011
From: andreas.horn at uniklinik-freiburg.de (Andreas Horn)
Date: Sun, 24 Jul 2011 11:45:21 +0200
Subject: [Mristudio-users] IFO, MdLF and EmC
In-Reply-To: <CADKVbtFWRjsZqLn5-2kjpW9sKMvFebF3Ap0CGJ9JZ7ptVCtZyg@mail.gmail.com>
References: <201107221458.p6MEwkUv016490@post.webmailer.de>
	<CAEq9apL6NZpSD8ZzL5edkTQEccL24ZJJejO5GrDZ=Gt8fx0Z-Q@mail.gmail.com>
	<CADKVbtFWRjsZqLn5-2kjpW9sKMvFebF3Ap0CGJ9JZ7ptVCtZyg@mail.gmail.com>
Message-ID: <E7401B37-3DB5-4FC9-A577-4C903FBEFDFE@uniklinik-freiburg.de>

Dear Yajing,

thank you so much for your time to copy out the links for me. Unfortunately, I now realized that I had tried to use these tracts before and they don't seem to work with our software. Probably they only are to be displayed by your software bundle dtistudio/roieditor.

If I try to display them with SPM/Mricron, etc. they seem misplaced/shifted somehow (see picture).
Somehow they don't seem to be normalized into ICBM-Space or our software doesn't understand the normalization somehow - which is weird because e.g. the dti-81 atlas of the LONI-Institute works fine.

As an example, this is how SPM/mricron displays the left SLF-FT of your atlas.


Probably you don't have a solution for this coregistration-issue by hand and I completely understand if you don't have the time to go into it.

But I just thought that it could be worth it that you know about the issue.

Thank you so much in any case,

yours sincerely, Andreas


Am 23.07.2011 um 17:22 schrieb Yajing Zhang:

> Hi, Andreas
> 
> You can find the fiber atlas in: http://lbam.med.jhmi.edu/cmrm/Data_Yajing/fiberMenu.htm
> The components of SLF can be downloaded in: http://lbam.med.jhmi.edu/cmrm/Data_Yajing/longAssociation.htm
> The corresponding paper is: "Atlas-guided tract reconstruction for automated and comprehensive examination of the white matter anatomy." Neuroimage 52(4):1289-1301 (2010). 
> 
> 
> Best regards,
> Yajing
> 
> 
> 
> On Fri, Jul 22, 2011 at 7:44 PM, susumu mori <susumu at mri.jhu.edu> wrote:
> Hi Andreas,
> 
> With 2-2.5mm resolution, the external and extreme capsules are difficult to separate, but I agree that IFO seems to occupy a good portion of these structures.
> 
> As for the different sections of the SLF, please refer to Yajing Zhang's paper in NeuroImage about the automated tractography. She created probabilistic maps of the different sections of the SLF in our atlas, which are available for download. Please contact Yajing about the location of the files. They may be already included in RoiEditor but I need to ask Xin.
> 
> MdLF is currently not defined in our atlas.
> 
> Susumu
> 
> On Fri, Jul 22, 2011 at 10:58 AM, Andreas Horn <mail at andreas-horn.de> wrote:
> Hello everybody, dear Susumu,
> 
> I have read your response about IFO and SFO (http://lists.mristudio.org/pipermail/mristudio-users/2011/001928.html).
> 
> Now I still wonder what anatomical structures are most likely included (or with which ones the cut-set is biggest) in IFO.
> When I look at the tract, it seems that the extreme capsule is definitely included, most likely also parts of external capsule, possibly uncinatus. Is this correct?
> 
> I would also be very glad about three-dimensional data of the MdLF as delineated in Makris 2009 and/or the partialized SLF (I-III plus AF) but can't seem to find them anywhere. Do you have any ideas how to get access to these files?
> 
> All I want to do is to assign our tracts to anatomical structures.
> 
> Thank you so much for your help!
> 
> Yours, sincerely, Andreas Horn
> 
> _______________________________________________
> mristudio-users mailing 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

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From vermanojk at gmail.com  Tue Jul 26 09:13:51 2011
From: vermanojk at gmail.com (Manoj Kumar Verma)
Date: Tue, 26 Jul 2011 09:13:51 -0400
Subject: [Mristudio-users] ROI
Message-ID: <CAG11YAN46QrQLsnikzWvygC=TeFWp7ddWU4Ust25Z=NTuQ+h7w@mail.gmail.com>

Hello All user;

I am working on mouse animal model and have ex vivo brain DTI (high
resolution 3D) data. I want to co-registered  these data set and want to
analyse the data using DTI studio.
My problem is that when I have tried to co-register two data set using AIR
method in DTI studio and try to draw ROI and save it in Binary Image and
Binary map format and again try to import same ROI even in same data set
there was an error showing: unrecognized image-ROI data file.

Any help and suggestion are highly appreciated.

Thanks

Manoj
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From Harish.Poptani at uphs.upenn.edu  Tue Jul 26 11:39:27 2011
From: Harish.Poptani at uphs.upenn.edu (Poptani, Harish)
Date: Tue, 26 Jul 2011 11:39:27 -0400
Subject: [Mristudio-users] ex vivo DTI analysis
In-Reply-To: <CAG11YAMTmsT15rryhcat_guD_dXAR0oc8oyUpzLVups1zKGGGA@mail.gmail.com>
References: <CAG11YAMTmsT15rryhcat_guD_dXAR0oc8oyUpzLVups1zKGGGA@mail.gmail.com>
Message-ID: <506FBBF6FCB3404580679AC1AE1E48F038399C@uphmasphi010.UPHS.PENNHEALTH.PRV>

Hello Susumu,

 

 

Is there an easy way to co-register and analyze ex vivo DTI from the
mouse brain? We have been acquiring high-resolution DTI data of the
mouse brain and use DTI studio to process and analyze the data. Since
these are phenotypically different mice, the differences in anatomy are
not obvious and in order to assess DTI differences (FA for example), we
need to make sure that all the brains are aligned and matched to each
other. While there seems to be a way for performing the co-registration
step within DTI studio, I have not been able to figure out a way to save
the ROI such that it can be used for all the different samples. Can
you/anyone else please guide us through this?

 

Regards

 

Harish

 



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.
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From qzk2 at psu.edu  Tue Jul 26 13:02:32 2011
From: qzk2 at psu.edu (Susan Motch)
Date: Tue, 26 Jul 2011 13:02:32 -0400
Subject: [Mristudio-users] DtiMap Functions
Message-ID: <1311699751l.737398l.0l@psu.edu>

I have mouse brain data, and have just started using DTI-Studio. While the data
is displaying properly in the Image tab after loading using DTI Mapping, I am
repeatedly receiving the following error "An invalid argument was encountered."
for all DtiMap functions. Any suggestions would be appreciated. 
Thank you,
Susan




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From vermanojk at gmail.com  Tue Jul 26 13:36:12 2011
From: vermanojk at gmail.com (Manoj Kumar Verma)
Date: Tue, 26 Jul 2011 13:36:12 -0400
Subject: [Mristudio-users] ROI analysis
In-Reply-To: <CANM4YeWWaTr7zBQF50OWnAvCRj=izLw9sbO9u1GZyW7BmGKTmA@mail.gmail.com>
References: <CAG11YAMTmsT15rryhcat_guD_dXAR0oc8oyUpzLVups1zKGGGA@mail.gmail.com>
	<CANM4YeWWaTr7zBQF50OWnAvCRj=izLw9sbO9u1GZyW7BmGKTmA@mail.gmail.com>
Message-ID: <CAG11YAN=kcTunbOcETStWsx=0aoxfSTRJeUPS4EFShN07Y56+w@mail.gmail.com>

Hi Seongjin;
Thanks


On Tue, Jul 26, 2011 at 11:35 AM, [Seongjin] <choisj70 at gmail.com> wrote:

> DTI studio is good for post-processing and deterministic tractography.
> For ROI-based data analysis, it would be much better to try ROI-editor (a
> sister software to DTI studio).
>
> Best,
> -SC
>
> On Tue, Jul 26, 2011 at 9:16 AM, manoj kumar <kmanoj at mail.med.upenn.edu>wrote:
>
>> Hello All user;
>>
>> I am working on mouse animal model and have ex vivo brain DTI (high
>> resolution 3D) data. I want to co-registered  these data set and want to
>> analyse the data using DTI studio.
>> My problem is that when I have tried to co-register two data set using AIR
>> method in DTI studio and try to draw ROI and save it in Binary Image and
>> Binary map format and again try to import same ROI even in same data set
>> there was an error showing: unrecognized image-ROI data file.
>>
>> Any help and suggestion are highly appreciated.
>>
>> Thanks
>>
>> 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
>
>
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From zhangyajing9996 at gmail.com  Tue Jul 26 16:27:30 2011
From: zhangyajing9996 at gmail.com (Yajing Zhang)
Date: Tue, 26 Jul 2011 16:27:30 -0400
Subject: [Mristudio-users] IFO, MdLF and EmC
In-Reply-To: <E7401B37-3DB5-4FC9-A577-4C903FBEFDFE@uniklinik-freiburg.de>
References: <201107221458.p6MEwkUv016490@post.webmailer.de>
	<CAEq9apL6NZpSD8ZzL5edkTQEccL24ZJJejO5GrDZ=Gt8fx0Z-Q@mail.gmail.com>
	<CADKVbtFWRjsZqLn5-2kjpW9sKMvFebF3Ap0CGJ9JZ7ptVCtZyg@mail.gmail.com>
	<E7401B37-3DB5-4FC9-A577-4C903FBEFDFE@uniklinik-freiburg.de>
Message-ID: <CADKVbtFCp8S1OBj+RAo-5euf7eJx91YCsuhSJkt872o7UXP_MA@mail.gmail.com>

Hi, Andreas

It might be due to the data type issue. In your figure, the image was
flipped on the front-back direction. If you could flip the data, or treat
the .img as .dat data format, you'll get the overlay image as attached.
Thanks for pointing out the issue. Hope it will work in your software.

Regards,
Yajing



On Sun, Jul 24, 2011 at 5:45 AM, Andreas Horn <
andreas.horn at uniklinik-freiburg.de> wrote:

> Dear Yajing,
>
> thank you so much for your time to copy out the links for me.
> Unfortunately, I now realized that I had tried to use these tracts before
> and they don't seem to work with our software. Probably they only are to be
> displayed by your software bundle dtistudio/roieditor.
>
> If I try to display them with SPM/Mricron, etc. they seem misplaced/shifted
> somehow (see picture).
> Somehow they don't seem to be normalized into ICBM-Space or our software
> doesn't understand the normalization somehow - which is weird because e.g.
> the dti-81 atlas of the LONI-Institute works fine.
>
>
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From joanne.lin at auckland.ac.nz  Tue Jul 26 22:18:42 2011
From: joanne.lin at auckland.ac.nz (Joanne Lin)
Date: Wed, 27 Jul 2011 02:18:42 +0000
Subject: [Mristudio-users] DTI acquisition
Message-ID: <F2A353E188F5CD42BC66277361F0CDE417D1158A@FMHS-MBX1.fmhs.auckland.ac.nz>

Hi MriStudio users,



Apologies for this question that's outside the analysis tools, but I was hoping to draw on your expertise regarding parallel imaging for DTI.



I am starting a new trial and trying to decide on acquisition parameters.  We are using a 3 T Siemens Skyra system and acquiring EPIs for DTI and task fMRI, along with T1-weighted MPRAGE.



For parallel imaging (iPAT), there is the option to use GRAPPA or mSENESE - default is GRAPPA.



I realise that acquisition times of EPIs are not directly affected by iPAT, however it is meant to improve geometric distortion around sinuses etc but at a cost - up to 30% signal loss.  I am having trouble deciding whether to leave iPAT off - more SNR but possibly more distortion, or is the trade-off for less distortion and less signal worth it?



Any advice would be greatly appreciated.





Best regards,
Jo





Joanne Lin

BPharm (Hons), RegPharmNZ



Pharmacist/PhD Candidate
School of Pharmacy

Faculty of Medical & Health Sciences

The University of Auckland

Private Bag 92019

Auckland, New Zealand

+64 9 373 7599 Ext 88468



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From jeffm at mqmi.com.au  Tue Jul 26 22:42:29 2011
From: jeffm at mqmi.com.au (Jeff McIntosh)
Date: Tue, 26 Jul 2011 19:42:29 -0700
Subject: [Mristudio-users] DTI acquisition
In-Reply-To: <F2A353E188F5CD42BC66277361F0CDE417D1158A@FMHS-MBX1.fmhs.auckland.ac.nz>
References: <F2A353E188F5CD42BC66277361F0CDE417D1158A@FMHS-MBX1.fmhs.auckland.ac.nz>
Message-ID: <8814E86F9F9CCE41B79F7286F3BCC5060815FB90A2@SG1RD3XVS101.red003.local>

Would always use the parallel imaging options for EPI scans especially at 3T.

There are numerous articles that validate these methods as been more preferable. Siemens does also have some literature that supports this.

The main issue is the choice of technique, Siemens does emphasise the GRAPPA techniques as it does have fewer reconstruction artefacts but mSENSE may potential have a slight SNR advantage. You are using a SKYRA which is a great scanner it would be more beneficial if you are using the 32 Channel coil but take into account 3t has less SNR deep penetration so if you increase your parallel imaging factors to much your will strip out a disproportionality  large amounts of SNR centrally as compared to peripheral areas.

Kind Regards

Jeff McIntosh
Head of MRI and Research

[cid:image001.jpg at 01CC4C59.0656E4A0]

MACQUARIE MEDICAL IMAGING
Macquarie University Hospital
Ground Floor, 3 Technology Place
Macquarie University NSW 2109
P  02 9430 1108   F  02 9430 1199   M   041 477 1016
www.mqmi.com.au<http://www.mqmi.com.au>

From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Joanne Lin
Sent: Wednesday, July 27, 2011 12:19 PM
To: mristudio-users at mristudio.org
Subject: [Mristudio-users] DTI acquisition

Hi MriStudio users,

Apologies for this question that's outside the analysis tools, but I was hoping to draw on your expertise regarding parallel imaging for DTI.

I am starting a new trial and trying to decide on acquisition parameters.  We are using a 3 T Siemens Skyra system and acquiring EPIs for DTI and task fMRI, along with T1-weighted MPRAGE.

For parallel imaging (iPAT), there is the option to use GRAPPA or mSENESE - default is GRAPPA.

I realise that acquisition times of EPIs are not directly affected by iPAT, however it is meant to improve geometric distortion around sinuses etc but at a cost - up to 30% signal loss.  I am having trouble deciding whether to leave iPAT off - more SNR but possibly more distortion, or is the trade-off for less distortion and less signal worth it?

Any advice would be greatly appreciated.


Best regards,
Jo


Joanne Lin
BPharm (Hons), RegPharmNZ

Pharmacist/PhD Candidate
School of Pharmacy
Faculty of Medical & Health Sciences
The University of Auckland
Private Bag 92019
Auckland, New Zealand
+64 9 373 7599 Ext 88468



__________ Information from ESET NOD32 Antivirus, version of virus signature database 6327 (20110726) __________

The message was checked by ESET NOD32 Antivirus.

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From choisj70 at gmail.com  Wed Jul 27 11:11:27 2011
From: choisj70 at gmail.com (Seongjin)
Date: Wed, 27 Jul 2011 11:11:27 -0400
Subject: [Mristudio-users] DTI3DView
Message-ID: <CANM4YeVE7Xgx3orNC7WExEx1AvO6T5u=QtTtP=v+a38M5-Smsw@mail.gmail.com>

This is a question for the DTI3DView software (for visualizing fibers saved
in Amira format).

Included manual (in PPT) is not detailed enough to use DTI3DView and
panning, rotating, and zooming control are somewhat tricky confusing.

It might be better to have detailed manual for DTI3DView.

Anyone who knows about DTI3DView in depth?

Thanks,
-SC
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From sherrykhan78 at gmail.com  Wed Jul 27 19:30:05 2011
From: sherrykhan78 at gmail.com (Sheraz Khan)
Date: Wed, 27 Jul 2011 19:30:05 -0400
Subject: [Mristudio-users] Postdoctoral Fellowship: Multimodal Neuroimaging
 -MGH/ Harvard Medical School
Message-ID: <CALEzDDXCctEvs6L-yF_yuZFzM3p1-0EutFOw433ORZ3EoGpCCg@mail.gmail.com>

*Postdoctoral Fellowship: Multimodal Neuroimaging -MGH /Harvard Medical
School*

Job Description
A postdoctoral position is available with the TRANSCEND Research Program (
www.transcendresearch.org) at the Martinos Center for Biomedical Imaging in
Charlestown, MA (www.martinos.org) which is affiliated with the
Massachusetts General Hospital, Harvard Medical School and MIT.

We are seeking a candidate with a strong basis in magnetic resonance
imaging. Emphasis will be on MRI (DTI, spectroscopy, morphometry, ASL as
well as resting state fMRI), and on co-registering MEG with MRI. This
position will involve analysis of existing multimodal imaging data and
collection of new data.  The emphasis of the postdoctoral fellowship will be
analysis of existing datasets with secondary activity in piloting data for
new studies.  It will involve working closely with a multidisciplinary team
and with children, and will also involve some research oriented analysis of
data collected for clinical purposes.  After initial phase-in, ample
opportunity will also be provided to the candidate to self-explore and lead
research.

Datasets to be analyzed include:
MRI (including DTI and 1H-spectroscopy) and MEG data on 6-12 and teenage
matched autism spectrum and control subjects with phenotyping data
MRI data ( (morphometry, DTI, spectroscopy) plus laboratory and phenotyping
data) on 70 children with autism plus epilepsy and/or mitochondrial
dysfunction, along with one or more overnight EEGs on each patient
data from children ages 2-10 with and without autism.

Overall objectives:
To perform multimodal analyses of research and clinical research data, to
develop new approaches for performing these analyses, and to design
pipelines for data analysis.
To write papers and grants which will be high priorities all along the way
and will be actively supported by senior faculty.
To take advantage of the world class faculty and facilities of the Martinos
Center for Biomedical Imaging to perform the above activities to their
maximal potential.

The program?s emphasis is on pathophysiologically grounded brain research
and application of advanced imaging acquisition and analysis techniques to
neurological and sensory aspects of autism spectrum disorders.

Requirements:
Candidates must have PhD in neuroscience, physics, biomedical engineering,
electrical engineering, computer science or other related fields. Prior
experience in MRI analysis is required. Experience with EEG will be an added
advantage. Salary will be consistent with Massachusetts General Hospital,
Harvard Medical School policies for Postdoctoral trainees and will range
between $45,000 to $55,000 depending upon qualifications and experience.
Compensation also includes full staff benefits, including health insurance,
and vacation time.

Contact:
Interested applicants may send a CV and statement of interest addressing
background and specific pertinence of the candidate?s interest to Dr.
MarthaR. Herbert at
mherbert1 at partners.org and cc transcend at partners.org.
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From susumu at mri.jhu.edu  Thu Jul 28 07:58:26 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Thu, 28 Jul 2011 07:58:26 -0400
Subject: [Mristudio-users] DTI acquisition
In-Reply-To: <8814E86F9F9CCE41B79F7286F3BCC5060815FB90A2@SG1RD3XVS101.red003.local>
References: <F2A353E188F5CD42BC66277361F0CDE417D1158A@FMHS-MBX1.fmhs.auckland.ac.nz>
	<8814E86F9F9CCE41B79F7286F3BCC5060815FB90A2@SG1RD3XVS101.red003.local>
Message-ID: <CAEq9apLJX6w-_t2HLtNbPCWpJ2rg31CVMcYmwAHms--Ji=NFGA@mail.gmail.com>

I'm second to Jeff.

You should use iPAT. You can recover SNR loss by scanning longer but it's
very difficult to correct image distortion by B0 susceptibility.

My experience with Siemens mSENSE has not been very good and I always use
GRAPPA.

Susumu

On Tue, Jul 26, 2011 at 10:42 PM, Jeff McIntosh <jeffm at mqmi.com.au> wrote:

>  Would always use the parallel imaging options for EPI scans especially at
> 3T. ****
>
> ** **
>
> There are numerous articles that validate these methods as been more
> preferable. Siemens does also have some literature that supports this.****
>
> ** **
>
> The main issue is the choice of technique, Siemens does emphasise the
> GRAPPA techniques as it does have fewer reconstruction artefacts but mSENSE
> may potential have a slight SNR advantage. You are using a SKYRA which is a
> great scanner it would be more beneficial if you are using the 32 Channel
> coil but take into account 3t has less SNR deep penetration so if you
> increase your parallel imaging factors to much your will strip out a
> disproportionality  large amounts of SNR centrally as compared to p*
> eripheral** *areas.****
>
> ** **
>
> Kind Regards****
>
> ** **
>
> Jeff McIntosh****
>
> Head of MRI and Research****
>
> ** **
>
> [image: maquire medical imaging signage]****
>
> ** **
>
> MACQUARIE MEDICAL IMAGING****
>
> Macquarie University Hospital****
>
> Ground Floor, 3 Technology Place****
>
> Macquarie University NSW 2109****
>
> P  02 9430 1108   F  02 9430 1199   M   041 477 1016  ****
>
> www.mqmi.com.au****
>
> ** **
>
> *From:* mristudio-users-bounces at mristudio.org [mailto:
> mristudio-users-bounces at mristudio.org] *On Behalf Of *Joanne Lin
> *Sent:* Wednesday, July 27, 2011 12:19 PM
> *To:* mristudio-users at mristudio.org
> *Subject:* [Mristudio-users] DTI acquisition****
>
> ** **
>
> Hi MriStudio users,****
>
> ** **
>
> Apologies for this question that?s outside the analysis tools, but I was
> hoping to draw on your expertise regarding parallel imaging for DTI.****
>
> ** **
>
> I am starting a new trial and trying to decide on acquisition parameters.
> We are using a 3 T Siemens Skyra system and acquiring EPIs for DTI and task
> fMRI, along with T1-weighted MPRAGE.****
>
> ** **
>
> For parallel imaging (iPAT), there is the option to use GRAPPA or mSENESE ?
> default is GRAPPA.****
>
> ** **
>
> I realise that acquisition times of EPIs are not directly affected by iPAT,
> however it is meant to improve geometric distortion around sinuses etc but
> at a cost ? up to 30% signal loss.  I am having trouble deciding whether to
> leave iPAT off ? more SNR but possibly more distortion, or is the trade-off
> for less distortion and less signal worth it?****
>
> ** **
>
> Any advice would be greatly appreciated.****
>
> ** **
>
> ** **
>
> Best regards,
> Jo****
>
> ** **
>
> ** **
>
> *Joanne Lin*
>
> BPharm (Hons), RegPharmNZ****
>
> ** **
>
> Pharmacist/PhD Candidate
> School of Pharmacy****
>
> Faculty of Medical & Health Sciences****
>
> The University of Auckland****
>
> Private Bag 92019****
>
> Auckland, New Zealand****
>
> +64 9 373 7599 Ext 88468****
>
> ** **
>
>
>
> __________ Information from ESET NOD32 Antivirus, version of virus
> signature database 6327 (20110726) __________
>
> The message was checked by ESET NOD32 Antivirus.
>
> http://www.eset.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
>
>
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From susumu at mri.jhu.edu  Thu Jul 28 08:01:32 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Thu, 28 Jul 2011 08:01:32 -0400
Subject: [Mristudio-users] IFO, MdLF and EmC
In-Reply-To: <CADKVbtFCp8S1OBj+RAo-5euf7eJx91YCsuhSJkt872o7UXP_MA@mail.gmail.com>
References: <201107221458.p6MEwkUv016490@post.webmailer.de>
	<CAEq9apL6NZpSD8ZzL5edkTQEccL24ZJJejO5GrDZ=Gt8fx0Z-Q@mail.gmail.com>
	<CADKVbtFWRjsZqLn5-2kjpW9sKMvFebF3Ap0CGJ9JZ7ptVCtZyg@mail.gmail.com>
	<E7401B37-3DB5-4FC9-A577-4C903FBEFDFE@uniklinik-freiburg.de>
	<CADKVbtFCp8S1OBj+RAo-5euf7eJx91YCsuhSJkt872o7UXP_MA@mail.gmail.com>
Message-ID: <CAEq9apL5Us31qgjjYWrMAv9ARzO9RcbSo8x8ZH6Cr-Y7JR4S-w@mail.gmail.com>

Hi Andrea,

Please refer to FAQ15 in https://www.mristudio.org/wiki/faq.

Susumu

On Tue, Jul 26, 2011 at 4:27 PM, Yajing Zhang <zhangyajing9996 at gmail.com>wrote:

> Hi, Andreas
>
> It might be due to the data type issue. In your figure, the image was
> flipped on the front-back direction. If you could flip the data, or treat
> the .img as .dat data format, you'll get the overlay image as attached.
> Thanks for pointing out the issue. Hope it will work in your software.
>
> Regards,
> Yajing
>
>
>
> On Sun, Jul 24, 2011 at 5:45 AM, Andreas Horn <
> andreas.horn at uniklinik-freiburg.de> wrote:
>
>> Dear Yajing,
>>
>> thank you so much for your time to copy out the links for me.
>> Unfortunately, I now realized that I had tried to use these tracts before
>> and they don't seem to work with our software. Probably they only are to be
>> displayed by your software bundle dtistudio/roieditor.
>>
>> If I try to display them with SPM/Mricron, etc. they seem
>> misplaced/shifted somehow (see picture).
>> Somehow they don't seem to be normalized into ICBM-Space or our software
>> doesn't understand the normalization somehow - which is weird because e.g.
>> the dti-81 atlas of the LONI-Institute works fine.
>>
>>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From susumu at mri.jhu.edu  Thu Jul 28 08:22:28 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Thu, 28 Jul 2011 08:22:28 -0400
Subject: [Mristudio-users] ROI analysis
In-Reply-To: <CAG11YAN=kcTunbOcETStWsx=0aoxfSTRJeUPS4EFShN07Y56+w@mail.gmail.com>
References: <CAG11YAMTmsT15rryhcat_guD_dXAR0oc8oyUpzLVups1zKGGGA@mail.gmail.com>
	<CANM4YeWWaTr7zBQF50OWnAvCRj=izLw9sbO9u1GZyW7BmGKTmA@mail.gmail.com>
	<CAG11YAN=kcTunbOcETStWsx=0aoxfSTRJeUPS4EFShN07Y56+w@mail.gmail.com>
Message-ID: <CAEq9ap+oEPymjyX64+REFhZc02Upe1aHfsT7Ft3dy0Tzr3_j+Q@mail.gmail.com>

Hi Manoj,

Just add one thing. DtiStudio has AIR to coregister images within one DTI
data set. If you want to coregister images from different animals, you need
to use DiffeoMap.

As SC mentioned, after you process DTI and obtain FA, MD, etc, you'd better
move to RoiEditor, which has much better ROI drawing functions.

Susumu

On Tue, Jul 26, 2011 at 1:36 PM, Manoj Kumar Verma <vermanojk at gmail.com>wrote:

> Hi Seongjin;
> Thanks
>
>
>
> On Tue, Jul 26, 2011 at 11:35 AM, [Seongjin] <choisj70 at gmail.com> wrote:
>
>> DTI studio is good for post-processing and deterministic tractography.
>> For ROI-based data analysis, it would be much better to try ROI-editor (a
>> sister software to DTI studio).
>>
>> Best,
>> -SC
>>
>>  On Tue, Jul 26, 2011 at 9:16 AM, manoj kumar <kmanoj at mail.med.upenn.edu>wrote:
>>
>>>  Hello All user;
>>>
>>> I am working on mouse animal model and have ex vivo brain DTI (high
>>> resolution 3D) data. I want to co-registered  these data set and want to
>>> analyse the data using DTI studio.
>>> My problem is that when I have tried to co-register two data set using
>>> AIR method in DTI studio and try to draw ROI and save it in Binary Image and
>>> Binary map format and again try to import same ROI even in same data set
>>> there was an error showing: unrecognized image-ROI data file.
>>>
>>> Any help and suggestion are highly appreciated.
>>>
>>> Thanks
>>>
>>> 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
>
>
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From susumu at mri.jhu.edu  Thu Jul 28 08:30:01 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Thu, 28 Jul 2011 08:30:01 -0400
Subject: [Mristudio-users] DtiMap Functions
In-Reply-To: <1311699751l.737398l.0l@psu.edu>
References: <1311699751l.737398l.0l@psu.edu>
Message-ID: <CAEq9ap+WHVOcc36NJX-nkAob-zNCJT86GeT5b_T7C3OSLDP_MA@mail.gmail.com>

Hi Susan,

Are you using DICOM images? If so, one of the most common mistakes is that
the number of images do not match with the gradient table you specified.

For example, if DICOM file contains 12 images and your table contains only
10 gradient orientations, then you get the error.

Susumu

On Tue, Jul 26, 2011 at 1:02 PM, Susan Motch <qzk2 at psu.edu> wrote:

> I have mouse brain data, and have just started using DTI-Studio. While the
> data is displaying properly in the Image tab after loading using DTI
> Mapping, I am repeatedly receiving the following error "An invalid argument
> was encountered." for all DtiMap functions. Any suggestions would be
> appreciated.
> Thank you,
> Susan
>
>
>
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From susumu at mri.jhu.edu  Thu Jul 28 08:46:16 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Thu, 28 Jul 2011 08:46:16 -0400
Subject: [Mristudio-users] ex vivo DTI analysis
In-Reply-To: <506FBBF6FCB3404580679AC1AE1E48F038399C@uphmasphi010.UPHS.PENNHEALTH.PRV>
References: <CAG11YAMTmsT15rryhcat_guD_dXAR0oc8oyUpzLVups1zKGGGA@mail.gmail.com>
	<506FBBF6FCB3404580679AC1AE1E48F038399C@uphmasphi010.UPHS.PENNHEALTH.PRV>
Message-ID: <CAEq9apJXJXTPPgb1Ry6TjYOP0R4BFnz_TGWwVeZ5L896_7crag@mail.gmail.com>

Hi Harish,

Please take a look at our DiffeoMap and RoiEditor.
The former has many functions for image registration and the latter can do
ROI operations including automated atlas-based segmentation.

Please refer to papers by Jiangyang Zhang/Manisha Aggarwal/Duan in
NeuroImage about the mouse atlas-based brain segmentation. Let us know if
you want to use our pre-segmented mouse atlases.

You can find tutorials and some manual materials in www.mristudio.org.

Susumu

On Tue, Jul 26, 2011 at 11:39 AM, Poptani, Harish <
Harish.Poptani at uphs.upenn.edu> wrote:

>  Hello Susumu,****
>
> ** **
>
> ** **
>
> Is there an easy way to co-register and analyze ex vivo DTI from the mouse
> brain? We have been acquiring high-resolution DTI data of the mouse brain
> and use DTI studio to process and analyze the data. Since these are
> phenotypically different mice, the differences in anatomy are not obvious
> and in order to assess DTI differences (FA for example), we need to make
> sure that all the brains are aligned and matched to each other. While there
> seems to be a way for performing the co-registration step within DTI studio,
> I have not been able to figure out a way to save the ROI such that it can be
> used for all the different samples. Can you/anyone else please guide us
> through this?****
>
> ** **
>
> Regards****
>
> ** **
>
> Harish****
>
>  ****
>
> 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.
> _______________________________________________
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From saeede83 at gmail.com  Thu Jul 28 11:02:36 2011
From: saeede83 at gmail.com (Saeideh Bakhshi)
Date: Thu, 28 Jul 2011 11:02:36 -0400
Subject: [Mristudio-users] tracts from one ROI to another
Message-ID: <CALE4mdEEKCZbSUtpwYYLWJNBvU-cP_6hHqdXK-ivY6OhJVfpcQ@mail.gmail.com>

Hi all,

We are using DTIstudio to perform tractography our subjects. We have the
whole brain tracts, but I was wondering how we can identify tracts from a
source ROI to a target ROI. Our ROIs are masks in nifti format.


Appreciate your help.

-- 
--Saeideh
PhD candidate,
College of Computing,
Georgia Tech,
Atlanta, Ga
http://www.cc.gatech.edu/~sbakhshi/
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From choisj70 at gmail.com  Thu Jul 28 11:38:37 2011
From: choisj70 at gmail.com (Seongjin)
Date: Thu, 28 Jul 2011 11:38:37 -0400
Subject: [Mristudio-users] tracts from one ROI to another
In-Reply-To: <CALE4mdEEKCZbSUtpwYYLWJNBvU-cP_6hHqdXK-ivY6OhJVfpcQ@mail.gmail.com>
References: <CALE4mdEEKCZbSUtpwYYLWJNBvU-cP_6hHqdXK-ivY6OhJVfpcQ@mail.gmail.com>
Message-ID: <CANM4YeUEW5N46qyBbQmz9TTmoRwu_s0BUmwzFrKcRDCYLuX7-g@mail.gmail.com>

Nifti formatted mask image can be used to maks out noise in the outside
brain area in tensor cacluation.
However, I believe, you'd better to use ROIs defined in DTI studio or ROI
editor for fiber trakcing in DTI studio.

Sincerely,
-SC

On Thu, Jul 28, 2011 at 11:02 AM, Saeideh Bakhshi <saeede83 at gmail.com>wrote:

> Hi all,
>
> We are using DTIstudio to perform tractography our subjects. We have the
> whole brain tracts, but I was wondering how we can identify tracts from a
> source ROI to a target ROI. Our ROIs are masks in nifti format.
>
>
> Appreciate your help.
>
> --
> --Saeideh
> PhD candidate,
> College of Computing,
> Georgia Tech,
> Atlanta, Ga
> http://www.cc.gatech.edu/~sbakhshi/
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From joanne.lin at auckland.ac.nz  Thu Jul 28 16:28:26 2011
From: joanne.lin at auckland.ac.nz (Joanne Lin)
Date: Thu, 28 Jul 2011 20:28:26 +0000
Subject: [Mristudio-users] DTI acquisition
In-Reply-To: <CAEq9apLJX6w-_t2HLtNbPCWpJ2rg31CVMcYmwAHms--Ji=NFGA@mail.gmail.com>
References: <F2A353E188F5CD42BC66277361F0CDE417D1158A@FMHS-MBX1.fmhs.auckland.ac.nz>
	<8814E86F9F9CCE41B79F7286F3BCC5060815FB90A2@SG1RD3XVS101.red003.local>
	<CAEq9apLJX6w-_t2HLtNbPCWpJ2rg31CVMcYmwAHms--Ji=NFGA@mail.gmail.com>
Message-ID: <F2A353E188F5CD42BC66277361F0CDE417D11CB0@FMHS-MBX1.fmhs.auckland.ac.nz>

Thank you both for your advice - it's been very very helpful!!





Kind regards,

Joanne



From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori
Sent: Thursday, 28 July 2011 11:58 p.m.
To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
Subject: Re: [Mristudio-users] DTI acquisition



I'm second to Jeff.



You should use iPAT. You can recover SNR loss by scanning longer but it's very difficult to correct image distortion by B0 susceptibility.



My experience with Siemens mSENSE has not been very good and I always use GRAPPA.



Susumu

On Tue, Jul 26, 2011 at 10:42 PM, Jeff McIntosh <jeffm at mqmi.com.au<mailto:jeffm at mqmi.com.au>> wrote:

Would always use the parallel imaging options for EPI scans especially at 3T.



There are numerous articles that validate these methods as been more preferable. Siemens does also have some literature that supports this.



The main issue is the choice of technique, Siemens does emphasise the GRAPPA techniques as it does have fewer reconstruction artefacts but mSENSE may potential have a slight SNR advantage. You are using a SKYRA which is a great scanner it would be more beneficial if you are using the 32 Channel coil but take into account 3t has less SNR deep penetration so if you increase your parallel imaging factors to much your will strip out a disproportionality  large amounts of SNR centrally as compared to peripheral areas.



Kind Regards



Jeff McIntosh

Head of MRI and Research



Error! Filename not specified.



MACQUARIE MEDICAL IMAGING

Macquarie University Hospital

Ground Floor, 3 Technology Place

Macquarie University NSW 2109

P  02 9430 1108   F  02 9430 1199   M   041 477 1016

www.mqmi.com.au<http://www.mqmi.com.au>



From: mristudio-users-bounces at mristudio.org<mailto:mristudio-users-bounces at mristudio.org> [mailto:mristudio-users-bounces at mristudio.org<mailto:mristudio-users-bounces at mristudio.org>] On Behalf Of Joanne Lin
Sent: Wednesday, July 27, 2011 12:19 PM
To: mristudio-users at mristudio.org<mailto:mristudio-users at mristudio.org>
Subject: [Mristudio-users] DTI acquisition



Hi MriStudio users,



Apologies for this question that's outside the analysis tools, but I was hoping to draw on your expertise regarding parallel imaging for DTI.



I am starting a new trial and trying to decide on acquisition parameters.  We are using a 3 T Siemens Skyra system and acquiring EPIs for DTI and task fMRI, along with T1-weighted MPRAGE.



For parallel imaging (iPAT), there is the option to use GRAPPA or mSENESE - default is GRAPPA.



I realise that acquisition times of EPIs are not directly affected by iPAT, however it is meant to improve geometric distortion around sinuses etc but at a cost - up to 30% signal loss.  I am having trouble deciding whether to leave iPAT off - more SNR but possibly more distortion, or is the trade-off for less distortion and less signal worth it?



Any advice would be greatly appreciated.





Best regards,
Jo





Joanne Lin

BPharm (Hons), RegPharmNZ



Pharmacist/PhD Candidate
School of Pharmacy

Faculty of Medical & Health Sciences

The University of Auckland

Private Bag 92019

Auckland, New Zealand

+64 9 373 7599 Ext 88468





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From susumu at mri.jhu.edu  Fri Jul 29 19:22:10 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Fri, 29 Jul 2011 19:22:10 -0400
Subject: [Mristudio-users] tracts from one ROI to another
In-Reply-To: <CALE4mdEEKCZbSUtpwYYLWJNBvU-cP_6hHqdXK-ivY6OhJVfpcQ@mail.gmail.com>
References: <CALE4mdEEKCZbSUtpwYYLWJNBvU-cP_6hHqdXK-ivY6OhJVfpcQ@mail.gmail.com>
Message-ID: <CAEq9apLxDyFSag4ub-wkskseF+X82J2yGbKYi9aW0hsf7JWyxQ@mail.gmail.com>

Please refer to FAQ16 in https://www.mristudio.org/wiki/faq.
Also, please read FAQ15, if you want to use nifti format, because you may
find your ROI definition is front-back flipped.

On Thu, Jul 28, 2011 at 11:02 AM, Saeideh Bakhshi <saeede83 at gmail.com>wrote:

> Hi all,
>
> We are using DTIstudio to perform tractography our subjects. We have the
> whole brain tracts, but I was wondering how we can identify tracts from a
> source ROI to a target ROI. Our ROIs are masks in nifti format.
>
>
> Appreciate your help.
>
> --
> --Saeideh
> PhD candidate,
> College of Computing,
> Georgia Tech,
> Atlanta, Ga
> http://www.cc.gatech.edu/~sbakhshi/
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From sherrykhan78 at gmail.com  Sun Jul 31 19:11:45 2011
From: sherrykhan78 at gmail.com (Sheraz Khan)
Date: Sun, 31 Jul 2011 19:11:45 -0400
Subject: [Mristudio-users] Postdoctoral Fellowship: Multimodal Neuroimaging
 -MGH/Harvard Medical School
Message-ID: <CALEzDDX7p41Reaf_BCVpaxuMNO9AO=JPdZBFufLnxAVep0Cmxw@mail.gmail.com>

Postdoctoral Fellowship: Multimodal Neuroimaging -MGH/Harvard Medical School

Job Description
A postdoctoral position is available with the TRANSCEND Research Program (
www.transcendresearch.org) at the Martinos Center for Biomedical Imaging in
Charlestown, MA (www.martinos.org) which is affiliated with the
Massachusetts General Hospital, Harvard Medical School and MIT.

We are seeking a candidate with a strong basis in magnetic resonance
imaging. Emphasis will be on MRI (DTI, spectroscopy, morphometry, ASL as
well as resting state fMRI), and on co-registering MEG with MRI. This
position will involve analysis of existing multimodal imaging data and
collection of new data.  The emphasis of the postdoctoral fellowship will be
analysis of existing datasets with secondary activity in piloting data for
new studies.  It will involve working closely with a multidisciplinary team
and with children, and will also involve some research oriented analysis of
data collected for clinical purposes.  After initial phase-in, ample
opportunity will also be provided to the candidate to self-explore and lead
research.

Datasets to be analyzed include:
MRI (including DTI and 1H-spectroscopy) and MEG data on 6-12 and teenage
matched autism spectrum and control subjects with phenotyping data
MRI data ( (morphometry, DTI, spectroscopy) plus laboratory and phenotyping
data) on 70 children with autism plus epilepsy and/or mitochondrial
dysfunction, along with one or more overnight EEGs on each patient
data from children ages 2-10 with and without autism.

Overall objectives:
To perform multimodal analyses of research and clinical research data, to
develop new approaches for performing these analyses, and to design
pipelines for data analysis.
To write papers and grants which will be high priorities all along the way
and will be actively supported by senior faculty.
To take advantage of the world class faculty and facilities of the Martinos
Center for Biomedical Imaging to perform the above activities to their
maximal potential.

The program?s emphasis is on pathophysiologically grounded brain research
and application of advanced imaging acquisition and analysis techniques to
neurological and sensory aspects of autism spectrum disorders.

Requirements:
Candidates must have PhD in neuroscience, physics, biomedical engineering,
electrical engineering, computer science or other related fields. Prior
experience in MRI analysis is required. Experience with EEG will be an added
advantage. Salary will be consistent with Massachusetts General Hospital,
Harvard Medical School policies for Postdoctoral trainees and will range
between $45,000 to $55,000 depending upon qualifications and experience.
Compensation also includes full staff benefits, including health insurance,
and vacation time.

Contact:
Interested applicants may send a CV  to Dr. Martha R. Herbert at
mherbert1 at partners.org and cc transcend at partners.org.
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From vermanojk at gmail.com  Mon Aug  1 14:19:12 2011
From: vermanojk at gmail.com (Manoj Kumar Verma)
Date: Mon, 01 Aug 2011 14:19:12 -0400
Subject: [Mristudio-users] ROI analysis
In-Reply-To: <CAEq9ap+oEPymjyX64+REFhZc02Upe1aHfsT7Ft3dy0Tzr3_j+Q@mail.gmail.com>
References: <CAG11YAMTmsT15rryhcat_guD_dXAR0oc8oyUpzLVups1zKGGGA@mail.gmail.com>
	<CANM4YeWWaTr7zBQF50OWnAvCRj=izLw9sbO9u1GZyW7BmGKTmA@mail.gmail.com>
	<CAG11YAN=kcTunbOcETStWsx=0aoxfSTRJeUPS4EFShN07Y56+w@mail.gmail.com>
	<CAEq9ap+oEPymjyX64+REFhZc02Upe1aHfsT7Ft3dy0Tzr3_j+Q@mail.gmail.com>
Message-ID: <CAG11YAMh2iL+wLE_SacZVtPEKS=ZNqCQw3y9LNWQmcDSCE3Tyg@mail.gmail.com>

Hello Susumu and other users;

I have questions about the ROI editor and DiffeoMap.
I have ex vivo 3 D DTI data from mouse brain. I have generated FA and MD map
in analyze format then I open the FA map in ROI editor to draw the ROI and I
am able to draw the ROI but when I click on save button to save the ROI. The
message appeared that there is no ROI and I didn't get any statistical
number for the data.
I want to know that the way I am doing is correct or wrong way?
Can you suggest any tutorial for that how I can used these software. I also
saw there is a option for atlas template, Did I need these atlas for mouse
brain.

And for DiffeoMap almost same type of problem I got.
When I loaded the FA map on DiffeoMap and Click on AIR slice by slice linear
the message appeared makeaheader.

Any body can suggest what I can do, any suggestion and help will highly
appreciated.

Thanks

Manoj

On Thu, Jul 28, 2011 at 8:22 AM, susumu mori <susumu at mri.jhu.edu> wrote:

> Hi Manoj,
>
> Just add one thing. DtiStudio has AIR to coregister images within one DTI
> data set. If you want to coregister images from different animals, you need
> to use DiffeoMap.
>
> As SC mentioned, after you process DTI and obtain FA, MD, etc, you'd better
> move to RoiEditor, which has much better ROI drawing functions.
>
> Susumu
>
>
> On Tue, Jul 26, 2011 at 1:36 PM, Manoj Kumar Verma <vermanojk at gmail.com>wrote:
>
>> Hi Seongjin;
>> Thanks
>>
>>
>>
>> On Tue, Jul 26, 2011 at 11:35 AM, [Seongjin] <choisj70 at gmail.com> wrote:
>>
>>> DTI studio is good for post-processing and deterministic tractography.
>>> For ROI-based data analysis, it would be much better to try ROI-editor (a
>>> sister software to DTI studio).
>>>
>>> Best,
>>> -SC
>>>
>>>  On Tue, Jul 26, 2011 at 9:16 AM, manoj kumar <kmanoj at mail.med.upenn.edu
>>> > wrote:
>>>
>>>>  Hello All user;
>>>>
>>>> I am working on mouse animal model and have ex vivo brain DTI (high
>>>> resolution 3D) data. I want to co-registered  these data set and want to
>>>> analyse the data using DTI studio.
>>>> My problem is that when I have tried to co-register two data set using
>>>> AIR method in DTI studio and try to draw ROI and save it in Binary Image and
>>>> Binary map format and again try to import same ROI even in same data set
>>>> there was an error showing: unrecognized image-ROI data file.
>>>>
>>>> Any help and suggestion are highly appreciated.
>>>>
>>>> Thanks
>>>>
>>>> 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
>
>
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From kmanoj at mail.med.upenn.edu  Mon Aug  1 14:29:45 2011
From: kmanoj at mail.med.upenn.edu (manoj kumar)
Date: Mon, 01 Aug 2011 14:29:45 -0400
Subject: [Mristudio-users] ROI editor and DiffeoMap
Message-ID: <CAG11YAOOHAKp=TTQPwrDVbw3DFisc0OXWN9Ce=jgK98nFAs++Q@mail.gmail.com>

Hello Susumu and other users;

I have questions about the ROI editor and DiffeoMap.
I have ex vivo 3 D DTI data from mouse brain. I have generated FA and MD map
in analyze format then I open the FA map in ROI editor to draw the ROI and I
am able to draw the ROI but when I click on save button to save the ROI. The
message appeared that there is no ROI and I didn't get any statistical
number for the data.
I want to know that the way I am doing is correct or wrong way?
Can you suggest any tutorial for that how I can used these software. I also
saw there is a option for atlas template, Did I need these atlas for mouse
brain.

And for DiffeoMap almost same type of problem I got.
When I loaded the FA map on DiffeoMap and Click on AIR slice by slice linear
the message appeared makeaheader.

Any body can suggest what I can do, any suggestion and help will highly
appreciated.

Thanks

Manoj
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From khua1 at jhu.edu  Mon Aug  1 14:35:36 2011
From: khua1 at jhu.edu (HUA KEGANG)
Date: Mon, 01 Aug 2011 18:35:36 +0000
Subject: [Mristudio-users] DTI3DView
In-Reply-To: <CANM4YeVE7Xgx3orNC7WExEx1AvO6T5u=QtTtP=v+a38M5-Smsw@mail.gmail.com>
References: <CANM4YeVE7Xgx3orNC7WExEx1AvO6T5u=QtTtP=v+a38M5-Smsw@mail.gmail.com>
Message-ID: <BLU164-w11BF33F9BD91A47FFBF410B2380@phx.gbl>


Hi, SC

The DTI3DView software is developed with Visualization Toolkit(VTK).  The operations are consistent with VTK. Here is a snipt from VTK's documentation. Hope this can give you some idea.
 
vtkInteractorStyle implements the "joystick" style of interaction. That is, holding down the mouse keys generates a stream of events that cause continuous actions (e.g., rotate, translate, pan, zoom). (The class vtkInteractorStyleTrackball implements a grab and move style.) The event bindings for this class include the following:

Keypress j / Keypress t: toggle between joystick (position sensitive) and trackball (motion sensitive) styles. In joystick style, motion occurs continuously as long as a mouse button is pressed. In trackball style, motion occurs when the mouse button is pressed and the mouse pointer moves.
Keypress c / Keypress a: toggle between camera and actor modes. In camera mode, mouse events affect the camera position and focal point. In actor mode, mouse events affect the actor that is under the mouse pointer.
Button 1: rotate the camera around its focal point (if camera mode) or rotate the actor around its origin (if actor mode). The rotation is in the direction defined from the center of the renderer's viewport towards the mouse position. In joystick mode, the magnitude of the rotation is determined by the distance the mouse is from the center of the render window.
Button 2: pan the camera (if camera mode) or translate the actor (if actor mode). In joystick mode, the direction of pan or translation is from the center of the viewport towards the mouse position. In trackball mode, the direction of motion is the direction the mouse moves. (Note: with 2-button mice, pan is defined as <Shift>-Button 1.)
Button 3: zoom the camera (if camera mode) or scale the actor (if actor mode). Zoom in/increase scale if the mouse position is in the top half of the viewport; zoom out/decrease scale if the mouse position is in the bottom half. In joystick mode, the amount of zoom is controlled by the distance of the mouse pointer from the horizontal centerline of the window.
Keypress 3: toggle the render window into and out of stereo mode. By default, red-blue stereo pairs are created. Some systems support Crystal Eyes LCD stereo glasses; you have to invoke SetStereoTypeToCrystalEyes() on the rendering window.
Keypress e: exit the application.
Keypress f: fly to the picked point
Keypress p: perform a pick operation. The render window interactor has an internal instance of vtkCellPicker that it uses to pick.
Keypress r: reset the camera view along the current view direction. Centers the actors and moves the camera so that all actors are visible.
Keypress s: modify the representation of all actors so that they are surfaces.
Keypress u: invoke the user-defined function. Typically, this keypress will bring up an interactor that you can type commands in. Typing u calls UserCallBack() on the vtkRenderWindowInteractor, which invokes a vtkCommand::UserEvent. In other words, to define a user-defined callback, just add an observer to the vtkCommand::UserEvent on the vtkRenderWindowInteractor object.
Keypress w: modify the representation of all actors so that they are wireframe.

Thanks!
 
KEGANG(LUKE) HUA
Department of Radiology
Johns Hopkins University School of Medicine
720 Rutland Ave Traylor217
Baltimore, MD, 21205

 



Date: Wed, 27 Jul 2011 11:11:27 -0400
From: choisj70 at gmail.com
Subject: [Mristudio-users] DTI3DView
To: mristudio-users at mristudio.org

This is a question for the DTI3DView software (for visualizing fibers saved in Amira format).


Included manual (in PPT) is not detailed enough to use DTI3DView and panning, rotating, and zooming control are somewhat tricky confusing.


It might be better to have detailed manual for DTI3DView.


Anyone who knows about DTI3DView in depth?


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 		 	   		  
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From choisj70 at gmail.com  Mon Aug  1 15:03:48 2011
From: choisj70 at gmail.com (Seongjin)
Date: Mon, 01 Aug 2011 15:03:48 -0400
Subject: [Mristudio-users] DTI3DView
In-Reply-To: <BLU164-w11BF33F9BD91A47FFBF410B2380@phx.gbl>
References: <CANM4YeVE7Xgx3orNC7WExEx1AvO6T5u=QtTtP=v+a38M5-Smsw@mail.gmail.com>
	<BLU164-w11BF33F9BD91A47FFBF410B2380@phx.gbl>
Message-ID: <CANM4YeX_nhg21-0fi1Lj2PSxcfUAh0oG7Wi=RDZ0PfE0T6+y9A@mail.gmail.com>

Dear Kegang,

Thanks for your reply to my query.
I will give it a try.

Thansk again.
-SC

2011/8/1 HUA KEGANG <khua1 at jhu.edu>

>  Hi, SC
>
> The DTI3DView software is developed with Visualization Toolkit(VTK).  The
> operations are consistent with VTK. Here is a snipt from VTK's
> documentation. Hope this can give you some idea.
>
> vtkInteractorStyle <http://classvtkinteractorstyle.html/> implements the
> "joystick" style of interaction. That is, holding down the mouse keys
> generates a stream of events that cause continuous actions (e.g., rotate,
> translate, pan, zoom). (The class vtkInteractorStyleTrackball<http://classvtkinteractorstyletrackball.html/>implements a grab and move style.) The event bindings for this class include
> the following:
>
>    - Keypress j / Keypress t: toggle between joystick (position sensitive)
>    and trackball (motion sensitive) styles. In joystick style, motion occurs
>    continuously as long as a mouse button is pressed. In trackball style,
>    motion occurs when the mouse button is pressed and the mouse pointer moves.
>    - Keypress c / Keypress a: toggle between camera and actor modes. In
>    camera mode, mouse events affect the camera position and focal point. In
>    actor mode, mouse events affect the actor that is under the mouse pointer.
>    - Button 1: rotate the camera around its focal point (if camera mode)
>    or rotate the actor around its origin (if actor mode). The rotation is in
>    the direction defined from the center of the renderer's viewport towards the
>    mouse position. In joystick mode, the magnitude of the rotation is
>    determined by the distance the mouse is from the center of the render
>    window.
>    - Button 2: pan the camera (if camera mode) or translate the actor (if
>    actor mode). In joystick mode, the direction of pan or translation is from
>    the center of the viewport towards the mouse position. In trackball mode,
>    the direction of motion is the direction the mouse moves. (Note: with
>    2-button mice, pan is defined as <Shift>-Button 1.)
>    - Button 3: zoom the camera (if camera mode) or scale the actor (if
>    actor mode). Zoom in/increase scale if the mouse position is in the top half
>    of the viewport; zoom out/decrease scale if the mouse position is in the
>    bottom half. In joystick mode, the amount of zoom is controlled by the
>    distance of the mouse pointer from the horizontal centerline of the window.
>    - Keypress 3: toggle the render window into and out of stereo mode. By
>    default, red-blue stereo pairs are created. Some systems support Crystal
>    Eyes LCD stereo glasses; you have to invoke SetStereoTypeToCrystalEyes() on
>    the rendering window.
>    - Keypress e: exit the application.
>    - Keypress f: fly to the picked point
>    - Keypress p: perform a pick operation. The render window interactor
>    has an internal instance of vtkCellPicker<http://classvtkcellpicker.html/>that it uses to pick.
>    - Keypress r: reset the camera view along the current view direction.
>    Centers the actors and moves the camera so that all actors are visible.
>    - Keypress s: modify the representation of all actors so that they are
>    surfaces.
>    - Keypress u: invoke the user-defined function. Typically, this
>    keypress will bring up an interactor that you can type commands in. Typing u
>    calls UserCallBack() on the vtkRenderWindowInteractor<http://classvtkrenderwindowinteractor.html/>,
>    which invokes a vtkCommand::UserEvent<http://classvtkcommand.html/#a59a8690330ebcb1af6b66b0f3121f8feae177709a43a6bf74fa59806c157bd17f>.
>    In other words, to define a user-defined callback, just add an observer to
>    the vtkCommand::UserEvent<http://classvtkcommand.html/#a59a8690330ebcb1af6b66b0f3121f8feae177709a43a6bf74fa59806c157bd17f>on the
>    vtkRenderWindowInteractor <http://classvtkrenderwindowinteractor.html/>object.
>    - Keypress w: modify the representation of all actors so that they are
>    wireframe.
>
>
> Thanks!
>
> KEGANG(LUKE) HUA
> Department of Radiology
> Johns Hopkins University School of Medicine
> 720 Rutland Ave Traylor217
> Baltimore, MD, 21205
>
>
>  ------------------------------
> Date: Wed, 27 Jul 2011 11:11:27 -0400
> From: choisj70 at gmail.com
> Subject: [Mristudio-users] DTI3DView
> To: mristudio-users at mristudio.org
>
>
> This is a question for the DTI3DView software (for visualizing fibers saved
> in Amira format).
>
> Included manual (in PPT) is not detailed enough to use DTI3DView and
> panning, rotating, and zooming control are somewhat tricky confusing.
>
> It might be better to have detailed manual for DTI3DView.
>
> Anyone who knows about DTI3DView in depth?
>
> 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
>
>
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From joanne.lin at auckland.ac.nz  Mon Aug  1 22:01:46 2011
From: joanne.lin at auckland.ac.nz (Joanne Lin)
Date: Tue, 02 Aug 2011 02:01:46 +0000
Subject: [Mristudio-users] Skull Stripping
Message-ID: <F2A353E188F5CD42BC66277361F0CDE417D12F0C@FMHS-MBX1.fmhs.auckland.ac.nz>

Hello all,



I have a question around skull stripping in ROIEditor.



Based on previous questions and attending the tutorial, I tried skull stripping my participants' brains both manually and using the skull stripping tool in ROIEditor - both with mixed results.



I find that with the Seed Region Growing tool, it seems to include a lot of non-brain when I apply the threshold (and when I increase the threshold, there are lots of 'holes' in the ROI that I have to fix manually, and even then it doesn't always get rid of the non-brain).



When I use the Skull Stripping tool, I don't change many parameters - just change 'Segment Downsample' to 1 (as per a previous post).  This has generally worked well but for one participant, it has stripped out a part in the middle of the brain...



I hope I have explained it alright.  I would appreciate any advice for a consistent way to skull strip my data.



Thanks very much!





Kind regards,



Joanne

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From lydia.wachsmuth at uni-muenster.de  Tue Aug  2 07:49:27 2011
From: lydia.wachsmuth at uni-muenster.de (Lydia Wachsmuth)
Date: Tue, 02 Aug 2011 13:49:27 +0200
Subject: [Mristudio-users] how to create .flg file
Message-ID: <4E37E447.1030709@uni-muenster.de>

Hello,
I am trying to remove bad images from my DTI-datasets.
I work with Bruker data, 5 A0images, 30 directions (2 experiments / diff 
direction).
I can load the data to the original image window, and cross out selected 
images. How do I save at this step in order to get the .flg file?
Any suggestion will be appreciated
Thank you
Best,
Lydia

-- 
Dr. phil.nat. Lydia Wachsmuth
AG Experimentelle Magnetische Kernresonanz
Institut f?r Klinische Radiologie - Universit?tsklinikum M?nster
Westf?lische Wilhelms-Universit?t M?nster
Waldeyerstr. 1 (Haus Rosenbach)
48149 M?nster
GERMANY
Tel: +49 251 83 56146
Fax: +49 251 83 52067


From susumu at mri.jhu.edu  Tue Aug  2 08:02:02 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Tue, 02 Aug 2011 08:02:02 -0400
Subject: [Mristudio-users] how to create .flg file
In-Reply-To: <4E37E447.1030709@uni-muenster.de>
References: <4E37E447.1030709@uni-muenster.de>
Message-ID: <CAEq9apKkxdZrt918baP2wxqQrEg2mPoBB7FUxm64UU4MFFY+rg@mail.gmail.com>

Hi Lydia,

you first have to specify the filename in the opening data input window.
Then at the end of the session, DtiStudio asks where to save the info.

We recently start using pixel-rejection instead of manual slice-by-slice
quality check. Please see
https://www.mristudio.org/wiki/changelog/dtistudio-3.0.2 for detail.

Susumu

On Tue, Aug 2, 2011 at 7:49 AM, Lydia Wachsmuth <
lydia.wachsmuth at uni-muenster.de> wrote:

> Hello,
> I am trying to remove bad images from my DTI-datasets.
> I work with Bruker data, 5 A0images, 30 directions (2 experiments / diff
> direction).
> I can load the data to the original image window, and cross out selected
> images. How do I save at this step in order to get the .flg file?
> Any suggestion will be appreciated
> Thank you
> Best,
> Lydia
>
> --
> Dr. phil.nat. Lydia Wachsmuth
> AG Experimentelle Magnetische Kernresonanz
> Institut f?r Klinische Radiologie - Universit?tsklinikum M?nster
> Westf?lische Wilhelms-Universit?t M?nster
> Waldeyerstr. 1 (Haus Rosenbach)
> 48149 M?nster
> GERMANY
> Tel: +49 251 83 56146
> Fax: +49 251 83 52067
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From choisj70 at gmail.com  Tue Aug  2 08:34:45 2011
From: choisj70 at gmail.com (Seongjin)
Date: Tue, 02 Aug 2011 08:34:45 -0400
Subject: [Mristudio-users] how to create .flg file
In-Reply-To: <CAEq9apKkxdZrt918baP2wxqQrEg2mPoBB7FUxm64UU4MFFY+rg@mail.gmail.com>
References: <4E37E447.1030709@uni-muenster.de>
	<CAEq9apKkxdZrt918baP2wxqQrEg2mPoBB7FUxm64UU4MFFY+rg@mail.gmail.com>
Message-ID: <CANM4YeVeFXStxF6xRO9PTOWai_p+o5D6bW6iRPpFgqtRjRB9sg@mail.gmail.com>

Dear Susumu,

I wonder do you have any reference parameter sets for different filed
strenghts, e,g, 1.5 T, 3T, or 7T?

All of the best,
-SC

On Tue, Aug 2, 2011 at 8:02 AM, susumu mori <susumu at mri.jhu.edu> wrote:

> Hi Lydia,
>
> you first have to specify the filename in the opening data input window.
> Then at the end of the session, DtiStudio asks where to save the info.
>
> We recently start using pixel-rejection instead of manual slice-by-slice
> quality check. Please see
> https://www.mristudio.org/wiki/changelog/dtistudio-3.0.2 for detail.
>
> Susumu
>
>
> On Tue, Aug 2, 2011 at 7:49 AM, Lydia Wachsmuth <
> lydia.wachsmuth at uni-muenster.de> wrote:
>
>> Hello,
>> I am trying to remove bad images from my DTI-datasets.
>> I work with Bruker data, 5 A0images, 30 directions (2 experiments / diff
>> direction).
>> I can load the data to the original image window, and cross out selected
>> images. How do I save at this step in order to get the .flg file?
>> Any suggestion will be appreciated
>> Thank you
>> Best,
>> Lydia
>>
>> --
>> Dr. phil.nat. Lydia Wachsmuth
>> AG Experimentelle Magnetische Kernresonanz
>> Institut f?r Klinische Radiologie - Universit?tsklinikum M?nster
>> Westf?lische Wilhelms-Universit?t M?nster
>> Waldeyerstr. 1 (Haus Rosenbach)
>> 48149 M?nster
>> GERMANY
>> Tel: +49 251 83 56146
>> Fax: +49 251 83 52067
>>
>> _______________________________________________
>> mristudio-users mailing 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
>
>
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From choisj70 at gmail.com  Tue Aug  2 08:47:21 2011
From: choisj70 at gmail.com (Seongjin)
Date: Tue, 02 Aug 2011 08:47:21 -0400
Subject: [Mristudio-users] ROI editor and DiffeoMap
In-Reply-To: <CAG11YAOOHAKp=TTQPwrDVbw3DFisc0OXWN9Ce=jgK98nFAs++Q@mail.gmail.com>
References: <CAG11YAOOHAKp=TTQPwrDVbw3DFisc0OXWN9Ce=jgK98nFAs++Q@mail.gmail.com>
Message-ID: <CANM4YeUJzqJN8mEE61vpLmoDyArkK6MhcKkiNDioBZt=E=FKTA@mail.gmail.com>

Dear Manoj,

"Drawing and saving a ROI"  will not work.
Probably you did not fill the ROI and ADD it to a ROI object. They are under
SELECTION.
Take a look at the following instructions.

https://www.mristudio.org/wiki/user_manual/roieditor?highlight=%28ROI%29|%28editor%29

Best,
-SC

On Mon, Aug 1, 2011 at 2:29 PM, manoj kumar <kmanoj at mail.med.upenn.edu>wrote:

> Hello Susumu and other users;
>
> I have questions about the ROI editor and DiffeoMap.
> I have ex vivo 3 D DTI data from mouse brain. I have generated FA and MD
> map in analyze format then I open the FA map in ROI editor to draw the ROI
> and I am able to draw the ROI but when I click on save button to save the
> ROI. The message appeared that there is no ROI and I didn't get any
> statistical number for the data.
> I want to know that the way I am doing is correct or wrong way?
> Can you suggest any tutorial for that how I can used these software. I also
> saw there is a option for atlas template, Did I need these atlas for mouse
> brain.
>
> And for DiffeoMap almost same type of problem I got.
> When I loaded the FA map on DiffeoMap and Click on AIR slice by slice
> linear the message appeared makeaheader.
>
> Any body can suggest what I can do, any suggestion and help will highly
> appreciated.
>
> Thanks
>
> 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
>
>
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From vermanojk at gmail.com  Tue Aug  2 10:00:26 2011
From: vermanojk at gmail.com (Manoj Kumar Verma)
Date: Tue, 02 Aug 2011 10:00:26 -0400
Subject: [Mristudio-users] ROI editor and DiffeoMap
In-Reply-To: <CANM4YeUJzqJN8mEE61vpLmoDyArkK6MhcKkiNDioBZt=E=FKTA@mail.gmail.com>
References: <CAG11YAOOHAKp=TTQPwrDVbw3DFisc0OXWN9Ce=jgK98nFAs++Q@mail.gmail.com>
	<CANM4YeUJzqJN8mEE61vpLmoDyArkK6MhcKkiNDioBZt=E=FKTA@mail.gmail.com>
Message-ID: <CAG11YAOB7Vp0HsKA9b29YbdfvpvQwjyHgcTfVH+ZZm4E=XL+VQ@mail.gmail.com>

Hello Susumu and Seongjin,

Thanks a lot for your help.

Thanks

Manoj

On Tue, Aug 2, 2011 at 8:47 AM, [Seongjin] <choisj70 at gmail.com> wrote:

> Dear Manoj,
>
> "Drawing and saving a ROI"  will not work.
> Probably you did not fill the ROI and ADD it to a ROI object. They are
> under SELECTION.
> Take a look at the following instructions.
>
>
> https://www.mristudio.org/wiki/user_manual/roieditor?highlight=%28ROI%29|%28editor%29<https://www.mristudio.org/wiki/user_manual/roieditor?highlight=%28ROI%29%7C%28editor%29>
>
> Best,
> -SC
>
> On Mon, Aug 1, 2011 at 2:29 PM, manoj kumar <kmanoj at mail.med.upenn.edu>wrote:
>
>> Hello Susumu and other users;
>>
>> I have questions about the ROI editor and DiffeoMap.
>> I have ex vivo 3 D DTI data from mouse brain. I have generated FA and MD
>> map in analyze format then I open the FA map in ROI editor to draw the ROI
>> and I am able to draw the ROI but when I click on save button to save the
>> ROI. The message appeared that there is no ROI and I didn't get any
>> statistical number for the data.
>> I want to know that the way I am doing is correct or wrong way?
>> Can you suggest any tutorial for that how I can used these software. I
>> also saw there is a option for atlas template, Did I need these atlas for
>> mouse brain.
>>
>> And for DiffeoMap almost same type of problem I got.
>> When I loaded the FA map on DiffeoMap and Click on AIR slice by slice
>> linear the message appeared makeaheader.
>>
>> Any body can suggest what I can do, any suggestion and help will highly
>> appreciated.
>>
>> Thanks
>>
>> 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
>
>
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From yongxu324 at gmail.com  Wed Aug  3 10:23:25 2011
From: yongxu324 at gmail.com (Yong Xu)
Date: Wed, 03 Aug 2011 22:23:25 +0800
Subject: [Mristudio-users] =?big5?b?V2hhdCB0aGUgYnV0dG9uIG9mIKGlTUVBTiBT?=
	=?big5?b?VEShpmFjdHVhbGx5IGZvcqFI?=
Message-ID: <CAA4OH1FefK-YcJZL5-pAZPqfoehJdGB5doSG4FcD5EDF+NVBEA@mail.gmail.com>

Hi,
   I'm a master student just starting learning DTIstudio?and I'm
wondering about the actual function of the"MEAN STD"button.Suppose I
get MEAN and STD maps ,then what can I do more to make full use of
them?What can I get from looking at them on the interface of"Display
Images"?In addition,I tried to save MEAN maps as analyse format to see
if there is any difference between them and the original data,but I
can't import them into DTIstudio,and I don't why.
   A keen appreciation for giving any advice.Thank you for your time.


From susumu at mri.jhu.edu  Wed Aug  3 10:58:20 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Wed, 03 Aug 2011 10:58:20 -0400
Subject: [Mristudio-users] =?utf-8?q?_Re=3A__What_the_button_of_=E2=80=98M?=
 =?utf-8?b?RUFOIFNUROKAmWFjdHVhbGx5IGZvcu+8nw==?=
In-Reply-To: <CAA4OH1FefK-YcJZL5-pAZPqfoehJdGB5doSG4FcD5EDF+NVBEA@mail.gmail.com>
References: <CAA4OH1FefK-YcJZL5-pAZPqfoehJdGB5doSG4FcD5EDF+NVBEA@mail.gmail.com>
Message-ID: <CAEq9apKp88QWAbdOn+eptKZ+WZXkGc1NCD7P8sLF8LmPRzyCYw@mail.gmail.com>

Hi Yong,

Please see the documents in
https://www.mristudio.org/wiki/changelog/dtistudio-3.0.2. Here it explains
how to use the button.

Susumu

2011/8/3 Yong Xu <yongxu324 at gmail.com>

> Hi,   I'm a master student just starting learning DTIstudio?and
> I'mwondering about the actual function of the"MEAN STD"button.Suppose Iget
> MEAN and STD maps ,then what can I do more to make full use ofthem?What can
> I get from looking at them on the interface of"DisplayImages"?In addition,I
> tried to save MEAN maps as analyse format to seeif there is any difference
> between them and the original data,but Ican't import them into DTIstudio,and
> I don't why.   A keen appreciation for giving any advice.Thank you for your
> time.
> _______________________________________________mristudio-users mailing
> listmristudio-users at mristudio.orghttp://
> lists.mristudio.org/mailman/listinfo/Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
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From choisj70 at gmail.com  Wed Aug  3 11:49:23 2011
From: choisj70 at gmail.com (Seongjin)
Date: Wed, 03 Aug 2011 11:49:23 -0400
Subject: [Mristudio-users] Diffeomap question
Message-ID: <CANM4YeVe9xzgxjbQpq+_rUeRwfxKnHGL52EN2Fex2OTC093aHw@mail.gmail.com>

Dear all,

Mutual information registration works in Diffeomap without any problem.
However, when I tried AIR registration, I met the following error message.

"The version of this file is not compatible with the version of Windows
you're running.
Check your computer's sytem information to see weather you need an x86
(32-bit) or x64 (64-bit)
version of the program, and then contact the software publisher."

I downloaded fresh new files from the download site.

But I still have the same problem.

Is there any remedy for this?

Thanks in advance.
-SC
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From zhou1 at jhmi.edu  Wed Aug  3 13:59:02 2011
From: zhou1 at jhmi.edu (Zhipeng Hou)
Date: Wed, 03 Aug 2011 13:59:02 -0400
Subject: [Mristudio-users] DTI_STUDIO Tutorial Video for iPad
Message-ID: <CACeZz4jbxD3qoER4BB5_sqEAeixjzP3JaCjXWQMAq2fZ-z7zRg@mail.gmail.com>

http://162.129.247.245/Protocol/DTS/Tutorial/iPad.htm
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From pengdoctor1 at 163.com  Wed Aug  3 19:35:21 2011
From: pengdoctor1 at 163.com (pengdoctor1)
Date: Thu, 04 Aug 2011 07:35:21 +0800 (CST)
Subject: [Mristudio-users] how to import the mask of ROI into the DTIstudio
Message-ID: <66508c.738d.131920059df.Coremail.pengdoctor1@163.com>

hello,everyone:
Using the VBA method, i have found the activated brain regions,and saved them as the mask , and then i attempted to use the mask as a ROI,but i failed to import the ROI into the DTIstudio, how can i attain the aim,and if the DTIstudio only can use the drawing ROI method?              thank you very much.
                              David peng
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From susumu at mri.jhu.edu  Wed Aug  3 21:14:15 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Wed, 03 Aug 2011 21:14:15 -0400
Subject: [Mristudio-users] how to import the mask of ROI into the
	DTIstudio
In-Reply-To: <66508c.738d.131920059df.Coremail.pengdoctor1@163.com>
References: <66508c.738d.131920059df.Coremail.pengdoctor1@163.com>
Message-ID: <CAEq9apLcb03qVCv7R__jqD9wmQK9LMdmrAM+HzcmbS=AjiYiNg@mail.gmail.com>

Hi David, I hope FAQ#16 in https://www.mristudio.org/wiki/faq helps.

Susumu

2011/8/3 pengdoctor1 <pengdoctor1 at 163.com>

> hello,everyone:
> Using the VBA method, i have found the activated brain regions,and saved
> them as the mask , and then i attempted to use the mask as a ROI,but i
> failed to import the ROI into the DTIstudio, how can i attain the aim,and if
> the DTIstudio only can use the drawing ROI method?              thank you
> very much.
>                               David peng
>
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From pengdoctor1 at 163.com  Wed Aug  3 22:33:59 2011
From: pengdoctor1 at 163.com (pengdoctor1)
Date: Thu, 04 Aug 2011 10:33:59 +0800 (CST)
Subject: [Mristudio-users] how to import the mask of ROI into the
 DTIstudio
In-Reply-To: <CAEq9apLcb03qVCv7R__jqD9wmQK9LMdmrAM+HzcmbS=AjiYiNg@mail.gmail.com>
References: <CAEq9apLcb03qVCv7R__jqD9wmQK9LMdmrAM+HzcmbS=AjiYiNg@mail.gmail.com>
	<66508c.738d.131920059df.Coremail.pengdoctor1@163.com>
Message-ID: <4c533d43.13f28.13192a3e1f7.Coremail.pengdoctor1@163.com>

thank you ,susuma, i'try it.
                                 david peng


At 2011-08-04 09:14:15,"susumu mori" <susumu at mri.jhu.edu> wrote:
Hi David, I hope FAQ#16 in https://www.mristudio.org/wiki/faq helps.


Susumu


2011/8/3 pengdoctor1<pengdoctor1 at 163.com>

hello,everyone:
Using the VBA method, i have found the activated brain regions,and saved them as the mask , and then i attempted to use the mask as a ROI,but i failed to import the ROI into the DTIstudio, how can i attain the aim,and if the DTIstudio only can use the drawing ROI method?              thank you very much.
                              David peng



_______________________________________________
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mristudio-users at mristudio.org
http://lists.mristudio.org/mailman/listinfo/
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From mpinsk at gmail.com  Thu Aug  4 15:16:08 2011
From: mpinsk at gmail.com (Mark A. Pinsk)
Date: Thu, 04 Aug 2011 15:16:08 -0400
Subject: [Mristudio-users] checkered artifact
Message-ID: <94F6F842-C775-4077-911F-1A1D6A192156@gmail.com>

Hi everyone,

We're seeing an artifact in our DTI images (most visible in the non-DWI images, but they show up everywhere including the calculated FA maps).  I assume this will negatively impact any tracking analyses.   It's a checkered pattern that originates from high intensity regions (i.e. ventricles) and goes in both the frequency and the phase encode directions.  Links to snapshots below.   I was told by one person that they are Fourier truncation artifacts, but I was also told by another person that they are flow artifacts.

Can someone clarify for me (1) what they are, (2) should I be concerned, and (3) how do I avoid them ?

http://dl.dropbox.com/u/3889124/dti_snapshot1.tiff
http://dl.dropbox.com/u/3889124/dti_snapshot2.tiff

Thanks very much!
Mark



From alex.dresner at philips.com  Thu Aug  4 16:16:30 2011
From: alex.dresner at philips.com (Dresner, Alex)
Date: Thu, 04 Aug 2011 22:16:30 +0200
Subject: [Mristudio-users] checkered artifact
In-Reply-To: <94F6F842-C775-4077-911F-1A1D6A192156@gmail.com>
References: <94F6F842-C775-4077-911F-1A1D6A192156@gmail.com>
Message-ID: <F47DF122278D44439E845976F7C266D7436BA3D651@NLCLUEXM04.connect1.local>

Hi Mark,
Your first advisor was correct, these are Fourier truncation artifacts.  They show up most prominently around high signal areas--so it's the bright fluid, not specifically flow, that is the problem.  They show up in your FA maps because those are generated relative to the non-DWI or B0 image.  There are two physics solutions and one image processing approach:
1) increase your native (not just reconstructed) resolution to limit the ringing.  (It's also called Gibbs ringing, but that doesn't help you address it except in searching the literature.)  Since the ringing is in both directions, it will cost you some time (and SNR) to increase the resolution.  Are you using parallel imaging to accelerate the acquisition?  If so, you might be able to reduce the artifact just by cutting down on the acceleration factor.
2) suppress the bright fluid signal in your non-DWI image.  A few people have suggested using an isotropically-weighted b=20 instead of a b=0 image so suppress large free fluid signals; this is still minimal compared to the b=800 or b=1000 so this shouldn't produce a quantitative difference.
3) More filtering of your data.  There are more smoothing filters available than you could possibly test.  Simple interpolation will reduce the choppy (pixelated, checkered) appearance but will not address the underlying ringing.  The scanner should have some interpolation/filtering/ringing tools available; if these are already on maybe they're not performing the way you think they should.

Should you be concerned? I'll leave that to the processing and results experts.  But now you know more about it...

Regards,
Alex

____________________
M. Alex Dresner, Ph.D.
MR Clinical Scientist
Philips Healthcare
____________________




-----Original Message-----
From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Mark A. Pinsk
Sent: Thursday, August 04, 2011 3:16 PM
To: mristudio-users at mristudio.org
Subject: [Mristudio-users] checkered artifact

Hi everyone,

We're seeing an artifact in our DTI images (most visible in the non-DWI images, but they show up everywhere including the calculated FA maps).  I assume this will negatively impact any tracking analyses.   It's a checkered pattern that originates from high intensity regions (i.e. ventricles) and goes in both the frequency and the phase encode directions.  Links to snapshots below.   I was told by one person that they are Fourier truncation artifacts, but I was also told by another person that they are flow artifacts.

Can someone clarify for me (1) what they are, (2) should I be concerned, and (3) how do I avoid them ?

http://dl.dropbox.com/u/3889124/dti_snapshot1.tiff
http://dl.dropbox.com/u/3889124/dti_snapshot2.tiff

Thanks very much!
Mark


_______________________________________________
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mristudio-users at mristudio.org
http://lists.mristudio.org/mailman/listinfo/
Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org

The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message.



From susumu at mri.jhu.edu  Thu Aug  4 16:32:23 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Thu, 04 Aug 2011 16:32:23 -0400
Subject: [Mristudio-users] checkered artifact
In-Reply-To: <94F6F842-C775-4077-911F-1A1D6A192156@gmail.com>
References: <94F6F842-C775-4077-911F-1A1D6A192156@gmail.com>
Message-ID: <CAEq9apJ9EoLO1rDHVOnAS7a5yiBzJqmP33WjOZjcmf3eN8ZX_A@mail.gmail.com>

Hi Mark,

Unfortunately, this is a typical artifact we see in many EPI/DTI data. I
think it's a truncation error, but not sure. If it is a truncation error, it
may decrease by making the image matrix larger, but it causes loss of SNR
and larger deformation. So you win some and lose some. I personally like to
use a smaller matrix (use only the echoes with enough SNR) and take the
artifacts as part of the game....

On Thu, Aug 4, 2011 at 3:16 PM, Mark A. Pinsk <mpinsk at gmail.com> wrote:

> Hi everyone,
>
> We're seeing an artifact in our DTI images (most visible in the non-DWI
> images, but they show up everywhere including the calculated FA maps).  I
> assume this will negatively impact any tracking analyses.   It's a checkered
> pattern that originates from high intensity regions (i.e. ventricles) and
> goes in both the frequency and the phase encode directions.  Links to
> snapshots below.   I was told by one person that they are Fourier truncation
> artifacts, but I was also told by another person that they are flow
> artifacts.
>
> Can someone clarify for me (1) what they are, (2) should I be concerned,
> and (3) how do I avoid them ?
>
> http://dl.dropbox.com/u/3889124/dti_snapshot1.tiff
> http://dl.dropbox.com/u/3889124/dti_snapshot2.tiff
>
> Thanks very much!
> Mark
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
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From yongxu324 at gmail.com  Fri Aug  5 08:40:04 2011
From: yongxu324 at gmail.com (Yong Xu)
Date: Fri, 05 Aug 2011 20:40:04 +0800
Subject: [Mristudio-users] What's the difference among the format of philips
 rec and siemens dicom or other when import datasets under DTImapping?
Message-ID: <CAA4OH1FNXuW2=WkKx0Cb0KoC3qoLpAsYf+M2vhd7a4drjcMU6A@mail.gmail.com>

Hi,all
When I used DTI mapping,I found that SIEMENS MOSAIC files can be
imported both by format of PHILIPS REC or SIEMENS MOSAIC,while the
images via former were up-side down,and I only found difference in
total number of fiber until now.In addition, I found that after format
conversion,SIEMENS MOSAIC can't be used under seperation from the
original files.So I wonder if I can always use PHILIPS REC to import
datasets?Is there any severe error that could happen ?What's more,is
there any way to turn the up-side down images back?
Thanks for any advices.

From susumu at mri.jhu.edu  Fri Aug  5 11:03:47 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Fri, 05 Aug 2011 11:03:47 -0400
Subject: [Mristudio-users] What's the difference among the format of
 philips rec and siemens dicom or other when import datasets under
 DTImapping?
In-Reply-To: <CAA4OH1FNXuW2=WkKx0Cb0KoC3qoLpAsYf+M2vhd7a4drjcMU6A@mail.gmail.com>
References: <CAA4OH1FNXuW2=WkKx0Cb0KoC3qoLpAsYf+M2vhd7a4drjcMU6A@mail.gmail.com>
Message-ID: <CAEq9ap+CaLY0uVJo8uUH7LR=+vh5_bXyUijwBr9f1w5gCvdRKw@mail.gmail.com>

Hi Yong,

I'm not 100% sure about your question, but you should use Siemens Mosaic to
read Siemens Mosaic. If you see the images are upside-down, please be
careful and see FAQ#15 in https://www.mristudio.org/wiki/faq.

Once you read the data and process them, then we offer two ways to save
them; Raw or Analyze. The Raw files can be read by Philips REC because
Philips REC is RAW files.  So, RAW files can be read as the RAW format or as
the REC format. They are the same.

Hope this clarify your question.

Susumu

On Fri, Aug 5, 2011 at 8:40 AM, Yong Xu <yongxu324 at gmail.com> wrote:

> Hi,all
> When I used DTI mapping,I found that SIEMENS MOSAIC files can be
> imported both by format of PHILIPS REC or SIEMENS MOSAIC,while the
> images via former were up-side down,and I only found difference in
> total number of fiber until now.In addition, I found that after format
> conversion,SIEMENS MOSAIC can't be used under seperation from the
> original files.So I wonder if I can always use PHILIPS REC to import
> datasets?Is there any severe error that could happen ?What's more,is
> there any way to turn the up-side down images back?
> Thanks for any advices.
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
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From mpinsk at gmail.com  Fri Aug  5 12:28:03 2011
From: mpinsk at gmail.com (Mark A. Pinsk)
Date: Fri, 05 Aug 2011 12:28:03 -0400
Subject: [Mristudio-users] checkered artifact
In-Reply-To: <94F6F842-C775-4077-911F-1A1D6A192156@gmail.com>
References: <94F6F842-C775-4077-911F-1A1D6A192156@gmail.com>
Message-ID: <328B2A0B-E720-49DF-8383-B86185BA0602@gmail.com>

Thank you Alex and Susumu for the information.  I will explore further to see if I can reduce the artifact a bit.

To answer your questions Alex:
- We are using parallel imaging (GRAPPA 2) with a 256 FOV and 128 matrix size (2mm resolution).  So I don't think going to a higher resolution will help (not even sure the scanner will go much higher).

- I will check for interpolation/filtering/ringing tools at the scanner console to improve the situation, maybe they are turned off in my protocol.

- I will also attempt to increase b from 0 to 20 as you suggest to see if that helps.

Best,
Mark




From yongxu324 at gmail.com  Sat Aug  6 21:40:26 2011
From: yongxu324 at gmail.com (Yong Xu)
Date: Sun, 07 Aug 2011 09:40:26 +0800
Subject: [Mristudio-users] =?big5?b?aGmhQXRoZXJlJ3MgYSBwcm9ibGVt?=
Message-ID: <CAA4OH1FeUo-6bd+d6pn-+gL1yzG+=8SWTHZVP31SQ2MHGecGpw@mail.gmail.com>

hi,
I had sent an email to you about"What's the difference among the
format of philips
 rec and siemens dicom or other when import datasets under
DTImapping?"But there may be something wrong during the sending
process,and I don't know if you get the email ?Or maybe it happened
when you mail me back?Please let me know if there is any problem.Many
thanks.

From zhou1 at jhmi.edu  Sat Aug  6 21:47:36 2011
From: zhou1 at jhmi.edu (Zhipeng Hou)
Date: Sat, 06 Aug 2011 21:47:36 -0400
Subject: [Mristudio-users] =?utf-8?b?IFJlOiAgaGnvvIx0aGVyZSdzIGEgcHJvYmxl?=
 =?utf-8?q?m?=
In-Reply-To: <CACeZz4i2rDu3Fqs5SALoN7vSTzi+=rbFbJV-pfV=cv8VtHhNWA@mail.gmail.com>
References: <145933A2BE9E4F48AE079A201379BF2F2B22773AAC@RAD-EXCH1.win.ad.jhu.edu>
	<CACeZz4i2rDu3Fqs5SALoN7vSTzi+=rbFbJV-pfV=cv8VtHhNWA@mail.gmail.com>
Message-ID: <CACeZz4jJzSuC6cV28jJd=VQik-pKR-ax5O2+_88SsyvZDVRwZw@mail.gmail.com>

See Dr. Mori's reply:

http://lists.mristudio.org/pipermail/mristudio-users/2011/002173.html

Also all 2011 question and reply list at :

http://lists.mristudio.org/pipermail/mristudio-users/2011/





2011/8/6 Yong Xu <yongxu324 at gmail.com>

> hi,
> I had sent an email to you about"What's the difference among the
> format of philips
>  rec and siemens dicom or other when import datasets under
> DTImapping?"But there may be something wrong during the sending
> process,and I don't know if you get the email ?Or maybe it happened
> when you mail me back?Please let me know if there is any problem.Many
> thanks.
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
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From yongxu324 at gmail.com  Sat Aug  6 23:08:23 2011
From: yongxu324 at gmail.com (Yong Xu)
Date: Sun, 07 Aug 2011 11:08:23 +0800
Subject: [Mristudio-users] still my second question about import format,
	thank you
Message-ID: <CAA4OH1EfYYhDiyniPXq+Q+s=B418VTpod-s-DGUPL1EMibWHDQ@mail.gmail.com>

hi,all
maybe I didn't describe my question clearly,so I want to expain it again.
I just find that if I save the converted analyse format dataset in a
separate directory but not with the original PHILIPS DICOM date,I
can't import ".img"file via SIEMENS,GE or PHILIPS DICOM format with a
window"NO DICOM FILES BEING FOUND".But it can be imported via PHILIPS
REC,while with the image up-side down.And if I try some times,the
image may be turn back.
I don't know how to deal with this situation and thanks for any advice.

From susumu at mri.jhu.edu  Sun Aug  7 05:59:13 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Sun, 07 Aug 2011 05:59:13 -0400
Subject: [Mristudio-users] how to create .flg file
In-Reply-To: <CANM4YeVeFXStxF6xRO9PTOWai_p+o5D6bW6iRPpFgqtRjRB9sg@mail.gmail.com>
References: <4E37E447.1030709@uni-muenster.de>
	<CAEq9apKkxdZrt918baP2wxqQrEg2mPoBB7FUxm64UU4MFFY+rg@mail.gmail.com>
	<CANM4YeVeFXStxF6xRO9PTOWai_p+o5D6bW6iRPpFgqtRjRB9sg@mail.gmail.com>
Message-ID: <CAEq9apKvESAe0-_x4YTo4Oo9nj_9AC7O88+CHiMND_TQeZAF5A@mail.gmail.com>

Hi SC,

I don't have much experience with 7T yet.
For 1.5T and 3T, I use 2.5mm isotropic resolution for 1.5T and 2.2mm for 3T.
I think 2.0mm is possible with 3T, but I prefer to have higher SNR (2.2mm)
than higher resolution (2.0mm)

For both Ts, I use the same 96x96 matrix (zerofilled to 192x192 (Siemens) or
256x256 (Philips)) so the FOV is 240 (2.5mm) or 212 (2.2mm).

For 1.5T, I use at least 60 DWIs (about 8-9 min), preferably 90 DWIs (more
than 10 min less than 15 min) and for 3T 24 - 60 DWIs (4.5-9 min).

This means, for Siemens, 12-orientation x multiple scans and for Philips
32-orientation x multiple scans.

I prefer b-value = 700, but 1,000 is also fine.

Parallel imaging is "must".

TE/TR is shortest, although for Philips, I add 5-10 ms to the shortest TE
due to Eddy current and gradient load issue.



On Tue, Aug 2, 2011 at 8:34 AM, [Seongjin] <choisj70 at gmail.com> wrote:

> Dear Susumu,
>
> I wonder do you have any reference parameter sets for different filed
> strenghts, e,g, 1.5 T, 3T, or 7T?
>
> All of the best,
> -SC
>
>
> On Tue, Aug 2, 2011 at 8:02 AM, susumu mori <susumu at mri.jhu.edu> wrote:
>
>> Hi Lydia,
>>
>> you first have to specify the filename in the opening data input window.
>> Then at the end of the session, DtiStudio asks where to save the info.
>>
>> We recently start using pixel-rejection instead of manual slice-by-slice
>> quality check. Please see
>> https://www.mristudio.org/wiki/changelog/dtistudio-3.0.2 for detail.
>>
>> Susumu
>>
>>
>> On Tue, Aug 2, 2011 at 7:49 AM, Lydia Wachsmuth <
>> lydia.wachsmuth at uni-muenster.de> wrote:
>>
>>> Hello,
>>> I am trying to remove bad images from my DTI-datasets.
>>> I work with Bruker data, 5 A0images, 30 directions (2 experiments / diff
>>> direction).
>>> I can load the data to the original image window, and cross out selected
>>> images. How do I save at this step in order to get the .flg file?
>>> Any suggestion will be appreciated
>>> Thank you
>>> Best,
>>> Lydia
>>>
>>> --
>>> Dr. phil.nat. Lydia Wachsmuth
>>> AG Experimentelle Magnetische Kernresonanz
>>> Institut f?r Klinische Radiologie - Universit?tsklinikum M?nster
>>> Westf?lische Wilhelms-Universit?t M?nster
>>> Waldeyerstr. 1 (Haus Rosenbach)
>>> 48149 M?nster
>>> GERMANY
>>> Tel: +49 251 83 56146
>>> Fax: +49 251 83 52067
>>>
>>> _______________________________________________
>>> mristudio-users mailing 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
>
>
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From yongxu324 at gmail.com  Sun Aug  7 21:24:47 2011
From: yongxu324 at gmail.com (Yong Xu)
Date: Mon, 08 Aug 2011 09:24:47 +0800
Subject: [Mristudio-users] What's the function of RUN?
Message-ID: <CAA4OH1GmjMaLLwSwCuL4h1wewuNAk1kqUmOYmw7XbRRk=pS+Fg@mail.gmail.com>

hi,everyone
I'm using the DTIstudio of version 2.4.01.And I'm curious about the
function of "RUN" under the "image" tag. It shows like below:

run	
process one	setting
process two	setting

thanks for any advice.

From mliu4 at ualberta.ca  Thu Aug 11 18:35:24 2011
From: mliu4 at ualberta.ca (Min Liu)
Date: Thu, 11 Aug 2011 16:35:24 -0600
Subject: [Mristudio-users] AIR/MI/theory AIR, which is the best?
Message-ID: <CAPje6jRdFk4yT-2oghCT6iL7SphcAC1gx2H5RhHb=7z6X=4yOQ@mail.gmail.com>

Dear MRIStudio users,

I have four human brain datasets that are scanned sequentially (back
to back) of a single subject using the same DTI protocol. I want to
get an averaged dataset out of the four. Before doing that,
motion/eddy current correction is definitely needed. I am wondering
among the three methods provided by DTIStudio, i.e. AIR/MI?theory AIR.
By visual inspection, there is rotation/shifting between the very
first dataset and the very last by about 2 voxels. For this subtle
movement, is there a conclusion so far regarding which coregistration
is the best (without introducing errors! Sometimes AIR does more harm
than good by misalignment.) Thank you for your thoughts!!

Min

From susumu at mri.jhu.edu  Thu Aug 11 19:46:15 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Thu, 11 Aug 2011 19:46:15 -0400
Subject: [Mristudio-users] AIR/MI/theory AIR, which is the best?
In-Reply-To: <CAPje6jRdFk4yT-2oghCT6iL7SphcAC1gx2H5RhHb=7z6X=4yOQ@mail.gmail.com>
References: <CAPje6jRdFk4yT-2oghCT6iL7SphcAC1gx2H5RhHb=7z6X=4yOQ@mail.gmail.com>
Message-ID: <CAEq9apJrz80vACEGHuCTFopi1wEo401B+erRAJa5+7jaXas4Bw@mail.gmail.com>

If the scans are not co-registered (the subject went out and came back to
the scanner), I suggest you to calculate the tensor first and register the
tensor using DiffeoMap and linear registration (AIR or MI).

If you register the raw DWI data, you may get a bit better SNR (this is my
guess), but you have to make sure to use the b-table re-orientation scheme
in the AIR. I would recommend to use AIR or MI (MI may take a lot of time),
although I don't have much experience in the cross-scan registration.

I think the first method (calculate tensor and then register) is the
easiest.

On Thu, Aug 11, 2011 at 6:35 PM, Min Liu <mliu4 at ualberta.ca> wrote:

> Dear MRIStudio users,
>
> I have four human brain datasets that are scanned sequentially (back
> to back) of a single subject using the same DTI protocol. I want to
> get an averaged dataset out of the four. Before doing that,
> motion/eddy current correction is definitely needed. I am wondering
> among the three methods provided by DTIStudio, i.e. AIR/MI?theory AIR.
> By visual inspection, there is rotation/shifting between the very
> first dataset and the very last by about 2 voxels. For this subtle
> movement, is there a conclusion so far regarding which coregistration
> is the best (without introducing errors! Sometimes AIR does more harm
> than good by misalignment.) Thank you for your thoughts!!
>
> Min
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
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From rachaelg.uh at gmail.com  Mon Aug 15 18:31:31 2011
From: rachaelg.uh at gmail.com (Rachael Gonzales)
Date: Mon, 15 Aug 2011 12:31:31 -1000
Subject: [Mristudio-users] ADC-Map Calculation in DTIStudio
In-Reply-To: <AANLkTikZMJqg2fPA61UnxvPcewTNoT2PA5TOCyKL1A5z@mail.gmail.com>
References: <20110223013620.000068D1.0399@ib.k.u-tokyo.ac.jp>
	<0LH20086JO891D30@smtpauth1.wiscmail.wisc.edu>
	<AANLkTikZMJqg2fPA61UnxvPcewTNoT2PA5TOCyKL1A5z@mail.gmail.com>
Message-ID: <047F400A-E034-4A38-9D60-795FF8F5B758@gmail.com>

Hi DTI experts,

In DTIStudio, under the DTI map tab there is an ADC Map calculation available.  After the calculation, an ADC map - mean image is generated, is this the apparent or average diffusion coefficient?  


Thanks,

Rachael


*****************************************************************************************************************************

Judy, in DtiStudio, ADC (or also called MD) should be obtained from "Trace".

Trace is defined as Dxx+Dyy+Dzz. If you divide it by 3, it becomes
"Average diffusion constant (ADC)" or "Mean diffusivity (MD)". We like
to use the term "trace" because it has clear mathematical definition
while ADC is also used for "Apparent diffusion constant", which has a
different meaning from "average diffusion constant".

On Mon, Apr 11, 2011 at 11:58 AM, Judy James <jjames2 at umc.edu> wrote:
> Is any one in this group aware of how to calculate ADC maps from the
> original DWI images in DTI studio - not DTI images, like how to set the
> gradient table in such a case?
> Any input/help will be highly appreciated.
> 
> Thank you,
> Judy James "
> 
> 
> 
> *********************************************************************
> Judy Rose James, Ph.D.
> Clinical Physicist, MR Imaging Division
> Assistant Professor, Department of Radiology
> University of Mississippi Medical Center
> Jackson, MS - 39216
> Ph: (601) 984-2585; Pager: (601) 929-2442
> Email: jjames2 at umc.edu
> *********************************************************************
> 
> 
> ________________________________
> From: mristudio-users-bounces at mristudio.org
> [mristudio-users-bounces at mristudio.org] On Behalf Of Jacquie Hodge
> [Jacquie.Hodge at albertahealthservices.ca]
> Sent: Friday, April 08, 2011 11:56 AM
> To: mristudio-users at mristudio.org
> Subject: [Mristudio-users] Fa values
> 
> Good morning everyone,
> 
> I am using DTI studio for my project where I am interested in comparing the
> left and right CST's in children who have suffereed injury in that area and
> after reading many studies on DTI decided to compare average FA values of
> the tracts as one of my variables. However, I have come across this questino
> from one of my supervisors and cannot really answer it and am hoping for
> your help/expertise.
> Here is goes:
> Is the FA value still a viable measure to look at and use to make a
> correlation if you are using FA values to pull the white matter tract? It
> seems like if the tract is made from FA values then you should not be able
> to use the FA as an outcome variable. This question has come up as I
> presented my research idea and I'm not sure how to answer it. Most studies
> that use DTI use FA thresholds to pull the tracts and then also the FA
> values (eg. mean FA) to make comparisons between the tracts.
> 
> I really hope that my question makes sense as I have found it very hard to
> word properly.
> 
> Thank you very much,
> Jacquie
> 
> Jacquie Hodge MSc candidate in Neuroscience, BSc
> Neuroscience, University of Calgary
> Research Assistant, Calgary Pediatric Stroke Program
> Alberta Children's Hospital
> 2888 Shaganappi Trail NW, Calgary, AB, Canada T3B 6A8
> Phone: 403-955-7733 Fax: 403-955-2922
> jacquie.hodge at albertahealthservices.ca
> Program website:
> http://www.calgaryhealthregion.ca/programs/stroke/pediatric.htm
> ________________________________
> 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.
> 
> 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.
> _______________________________________________
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> 
> 

_______________________________________________
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On Feb 23, 2011, at 4:35 AM, susumu mori wrote:

> Andreas is right.
> So called ADC (average diffusion constant, apparent diffusion constant) and MD (mean diffusivity) are obtained by trace/3 (trace divided by 3), while the trace is (eigenvalue0+eigenvalue1+eigenvalue2).
> 
> also, axial diffusivity is same as eigenvalue0 and radial diffusivity is the average of eigenvalue1 and 2 [ (eigenvalue1+eigenvalue2)/2].
> 
> On Wed, Feb 23, 2011 at 8:31 AM, Andreas Buchmann <buchmann2 at wisc.edu> wrote:
> Dear Yo,
> 
> I'm using trace diffusivity, which is strongly related to mean diffusivity
> (I think, just multiplied with a constant factor, experts correct me if I'm
> wrong).
> 
> Andreas
> 
> 
> 
> -----Original Message-----
> From: mristudio-users-bounces at mristudio.org
> [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of
> 107310 at ib.k.u-tokyo.ac.jp
> Sent: Dienstag, 22. Februar 2011 19:36
> To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
> Subject: Re: [Mristudio-users] radial diffusivity, mean diffusivity
> 
> Dear Andreas, Ryuzo and DTI experts
> 
> 
> I also try to calculate mean diffusivity.
> But in DTI studio, only the radial diffusivity and ADCs can calculate at
> the 'Image'-tab with ROI.
> 
> Is there any function to measure mean diffusivity?
> Please give me any suggestion.
> 
> Many thanks.
> 
> 
> YO
> 
> 
> > Dear Andreas
> >
> >
> >
> > Thank you very much for your suggestion.  I will try.
> >
> >
> >
> > Ryuzo
> >
> >
> >
> > From: mristudio-users-bounces at mristudio.org
> > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Andreas
> Buchmann
> > Sent: Monday, February 21, 2011 11:03 PM
> > To: 'DTI Studio, ROI Editor, DiffeoMap Questions/Support'
> > Subject: Re: [Mristudio-users] radial diffusivity, mean diffusivity
> >
> >
> >
> > Dear Ryuzo,
> >
> >
> >
> > yes, you're on the right track with (1). After the estimation, DTI-
> Studio
> > appends the images to the list of images you have, and you can see
> them
> > under the 'Image'-tab and save them with right-click on the image.
> >
> >
> >
> > Good luck
> >
> > Andreas
> >
> >
> >
> >   _____
> >
> > From: mristudio-users-bounces at mristudio.org
> > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of hanaie
> > Sent: Montag, 21. Februar 2011 07:46
> > To: mristudio-users at mristudio.org
> > Subject: [Mristudio-users] radial diffusivity, mean diffusivity
> >
> >
> >
> > Dear DTI experts
> >
> >
> >
> > How can I do to obtain the radial diffusivity and mean diffusivity in
> DTI
> > studio?
> >
> >
> >
> > 1.     In the " Dti Map" tab, clicking "Tensor, color Map etc" button,
> and
> > checking the checkboxes "Radial", "Trace"
> >
> >
> >
> > 2.     After tensor calculation and fiber tracking, if I click "
> statistics"
> > button in the "Fiber" tab and
> >
> >  I choose the each image and click "go" button in the another window,
> can I
> > obtain radial and mean diffusivity?
> >
> >
> >
> >
> >
> > Please give me any suggestion.
> >
> >
> >
> > Many thanks.
> >
> >
> >
> > Ryuzo
> >
> >
> >
> >
> > _______________________________________________
> > mristudio-users mailing list
> > mristudio-users at mristudio.org
> > http://lists.mristudio.org/mailman/listinfo/
> > Unsubscribe, send a blank email to: mristudio-users-unsubscribe@
> 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

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From susumu at mri.jhu.edu  Mon Aug 15 18:49:50 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Mon, 15 Aug 2011 18:49:50 -0400
Subject: [Mristudio-users] ADC-Map Calculation in DTIStudio
In-Reply-To: <047F400A-E034-4A38-9D60-795FF8F5B758@gmail.com>
References: <20110223013620.000068D1.0399@ib.k.u-tokyo.ac.jp>
	<0LH20086JO891D30@smtpauth1.wiscmail.wisc.edu>
	<AANLkTikZMJqg2fPA61UnxvPcewTNoT2PA5TOCyKL1A5z@mail.gmail.com>
	<047F400A-E034-4A38-9D60-795FF8F5B758@gmail.com>
Message-ID: <CAEq9ap+QOoKAvU8mBoZ_et8NiYhAx8wN89=S01Rcfx7QgqzcjA@mail.gmail.com>

Hi Rachael,

Sorry for the confusion, but the "mean" in DtiStudio is NOT the "mean
diffusivity (MD)" widely used in the field. Hangyi, we should change the
name.

The "mean" in DtiStudio is the mean of individual ADC maps. For example, if
we use a 12-orientation method, it is possible to calculate ADC of the first
gradient orientation. Likewise, ADC of the second, third, and up to the 12th
gradient orientations can be calculated. Then, you can get 12 ADCs. The
"mean" in this case is the average of the 12 ADCs.

The "mean diffusivity" is calculated from the average of the three
eigenvalues. Therefore, we can get only after the tensor calculation.

I hope this clarify your question.

Susumu

On Mon, Aug 15, 2011 at 6:31 PM, Rachael Gonzales <rachaelg.uh at gmail.com>wrote:

> Hi DTI experts,
>
> In DTIStudio, under the DTI map tab there is an ADC Map calculation
> available.  After the calculation, an ADC map - mean image is generated, is
> this the *apparent *or *average* diffusion coefficient?
>
>
> Thanks,
>
> Rachael
>
>
>
> *****************************************************************************************************************************
>
> Judy, in DtiStudio, ADC (or also called MD) should be obtained from
> "Trace".
>
> Trace is defined as Dxx+Dyy+Dzz. If you divide it by 3, it becomes
> "Average diffusion constant (ADC)" or "Mean diffusivity (MD)". We like
> to use the term "trace" because it has clear mathematical definition
> while ADC is also used for "Apparent diffusion constant", which has a
> different meaning from "average diffusion constant".
>
> On Mon, Apr 11, 2011 at 11:58 AM, Judy James <jjames2 at umc.edu> wrote:
>
> Is any one in this group aware of how to calculate ADC maps from the
>
> original DWI images in DTI studio - not DTI images, like how to set the
>
> gradient table in such a case?
>
> Any input/help will be highly appreciated.
>
>
> Thank you,
>
> Judy James "
>
>
>
>
> *********************************************************************
>
> Judy Rose James, Ph.D.
>
> Clinical Physicist, MR Imaging Division
>
> Assistant Professor, Department of Radiology
>
> University of Mississippi Medical Center
>
> Jackson, MS - 39216
>
> Ph: (601) 984-2585; Pager: (601) 929-2442
>
> Email: jjames2 at umc.edu
>
> *********************************************************************
>
>
>
> ________________________________
>
> From: mristudio-users-bounces at mristudio.org
>
> [mristudio-users-bounces at mristudio.org] On Behalf Of Jacquie Hodge
>
> [Jacquie.Hodge at albertahealthservices.ca]
>
> Sent: Friday, April 08, 2011 11:56 AM
>
> To: mristudio-users at mristudio.org
>
> Subject: [Mristudio-users] Fa values
>
>
> Good morning everyone,
>
>
> I am using DTI studio for my project where I am interested in comparing the
>
> left and right CST's in children who have suffereed injury in that area and
>
> after reading many studies on DTI decided to compare average FA values of
>
> the tracts as one of my variables. However, I have come across this
> questino
>
> from one of my supervisors and cannot really answer it and am hoping for
>
> your help/expertise.
>
> Here is goes:
>
> Is the FA value still a viable measure to look at and use to make a
>
> correlation if you are using FA values to pull the white matter tract? It
>
> seems like if the tract is made from FA values then you should not be able
>
> to use the FA as an outcome variable. This question has come up as I
>
> presented my research idea and I'm not sure how to answer it. Most studies
>
> that use DTI use FA thresholds to pull the tracts and then also the FA
>
> values (eg. mean FA) to make comparisons between the tracts.
>
>
> I really hope that my question makes sense as I have found it very hard to
>
> word properly.
>
>
> Thank you very much,
>
> Jacquie
>
>
> Jacquie Hodge MSc candidate in Neuroscience, BSc
>
> Neuroscience, University of Calgary
>
> Research Assistant, Calgary Pediatric Stroke Program
>
> Alberta Children's Hospital
>
> 2888 Shaganappi Trail NW, Calgary, AB, Canada T3B 6A8
>
> Phone: 403-955-7733 Fax: 403-955-2922
>
> jacquie.hodge at albertahealthservices.ca
>
> Program website:
>
> http://www.calgaryhealthregion.ca/programs/stroke/pediatric.htm
>
> ________________________________
>
> 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.
>
>
> 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
>
>
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
> On Feb 23, 2011, at 4:35 AM, susumu mori wrote:
>
> Andreas is right.
> So called ADC (average diffusion constant, apparent diffusion constant) and
> MD (mean diffusivity) are obtained by trace/3 (trace divided by 3), while
> the trace is (eigenvalue0+eigenvalue1+eigenvalue2).
>
> also, axial diffusivity is same as eigenvalue0 and radial diffusivity is
> the average of eigenvalue1 and 2 [ (eigenvalue1+eigenvalue2)/2].
>
> On Wed, Feb 23, 2011 at 8:31 AM, Andreas Buchmann <buchmann2 at wisc.edu>wrote:
>
>> Dear Yo,
>>
>> I'm using trace diffusivity, which is strongly related to mean diffusivity
>> (I think, just multiplied with a constant factor, experts correct me if
>> I'm
>> wrong).
>>
>> Andreas
>>
>>
>>
>> -----Original Message-----
>> From: mristudio-users-bounces at mristudio.org
>> [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of
>> 107310 at ib.k.u-tokyo.ac.jp
>> Sent: Dienstag, 22. Februar 2011 19:36
>> To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
>> Subject: Re: [Mristudio-users] radial diffusivity, mean diffusivity
>>
>> Dear Andreas, Ryuzo and DTI experts
>>
>>
>> I also try to calculate mean diffusivity.
>> But in DTI studio, only the radial diffusivity and ADCs can calculate at
>> the 'Image'-tab with ROI.
>>
>> Is there any function to measure mean diffusivity?
>> Please give me any suggestion.
>>
>> Many thanks.
>>
>>
>> YO
>>
>>
>> > Dear Andreas
>> >
>> >
>> >
>> > Thank you very much for your suggestion.  I will try.
>> >
>> >
>> >
>> > Ryuzo
>> >
>> >
>> >
>> > From: mristudio-users-bounces at mristudio.org
>> > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Andreas
>> Buchmann
>> > Sent: Monday, February 21, 2011 11:03 PM
>> > To: 'DTI Studio, ROI Editor, DiffeoMap Questions/Support'
>> > Subject: Re: [Mristudio-users] radial diffusivity, mean diffusivity
>> >
>> >
>> >
>> > Dear Ryuzo,
>> >
>> >
>> >
>> > yes, you're on the right track with (1). After the estimation, DTI-
>> Studio
>> > appends the images to the list of images you have, and you can see
>> them
>> > under the 'Image'-tab and save them with right-click on the image.
>> >
>> >
>> >
>> > Good luck
>> >
>> > Andreas
>> >
>> >
>> >
>> >   _____
>> >
>> > From: mristudio-users-bounces at mristudio.org
>> > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of hanaie
>> > Sent: Montag, 21. Februar 2011 07:46
>> > To: mristudio-users at mristudio.org
>> > Subject: [Mristudio-users] radial diffusivity, mean diffusivity
>> >
>> >
>> >
>> > Dear DTI experts
>> >
>> >
>> >
>> > How can I do to obtain the radial diffusivity and mean diffusivity in
>> DTI
>> > studio?
>> >
>> >
>> >
>> > 1.     In the " Dti Map" tab, clicking "Tensor, color Map etc" button,
>> and
>> > checking the checkboxes "Radial", "Trace"
>> >
>> >
>> >
>> > 2.     After tensor calculation and fiber tracking, if I click "
>> statistics"
>> > button in the "Fiber" tab and
>> >
>> >  I choose the each image and click "go" button in the another window,
>> can I
>> > obtain radial and mean diffusivity?
>> >
>> >
>> >
>> >
>> >
>> > Please give me any suggestion.
>> >
>> >
>> >
>> > Many thanks.
>> >
>> >
>> >
>> > Ryuzo
>> >
>> >
>> >
>> >
>> > _______________________________________________
>> > mristudio-users mailing list
>> > mristudio-users at mristudio.org
>> > http://lists.mristudio.org/mailman/listinfo/
>> > Unsubscribe, send a blank email to: mristudio-users-unsubscribe@
>> 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
>
>
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From susumu at mri.jhu.edu  Mon Aug 15 18:53:26 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Mon, 15 Aug 2011 18:53:26 -0400
Subject: [Mristudio-users] ADC-Map Calculation in DTIStudio
In-Reply-To: <047F400A-E034-4A38-9D60-795FF8F5B758@gmail.com>
References: <20110223013620.000068D1.0399@ib.k.u-tokyo.ac.jp>
	<0LH20086JO891D30@smtpauth1.wiscmail.wisc.edu>
	<AANLkTikZMJqg2fPA61UnxvPcewTNoT2PA5TOCyKL1A5z@mail.gmail.com>
	<047F400A-E034-4A38-9D60-795FF8F5B758@gmail.com>
Message-ID: <CAEq9ap+WxteLTPumqR3KDaxdpuSPfETNsT-WbehPFmozyxGJVg@mail.gmail.com>

p.s. What I mean by "ADC" in my previous response is "apparent diffusion
constant", not "average diffusion constant". The latter is the same as "mean
diffusivity". The definition of the former is not well defined but in my
response, it means a diffusion constant calculated from one diffusion
orientation.

On Mon, Aug 15, 2011 at 6:31 PM, Rachael Gonzales <rachaelg.uh at gmail.com>wrote:

> Hi DTI experts,
>
> In DTIStudio, under the DTI map tab there is an ADC Map calculation
> available.  After the calculation, an ADC map - mean image is generated, is
> this the *apparent *or *average* diffusion coefficient?
>
>
> Thanks,
>
> Rachael
>
>
>
> *****************************************************************************************************************************
>
> Judy, in DtiStudio, ADC (or also called MD) should be obtained from
> "Trace".
>
> Trace is defined as Dxx+Dyy+Dzz. If you divide it by 3, it becomes
> "Average diffusion constant (ADC)" or "Mean diffusivity (MD)". We like
> to use the term "trace" because it has clear mathematical definition
> while ADC is also used for "Apparent diffusion constant", which has a
> different meaning from "average diffusion constant".
>
> On Mon, Apr 11, 2011 at 11:58 AM, Judy James <jjames2 at umc.edu> wrote:
>
> Is any one in this group aware of how to calculate ADC maps from the
>
> original DWI images in DTI studio - not DTI images, like how to set the
>
> gradient table in such a case?
>
> Any input/help will be highly appreciated.
>
>
> Thank you,
>
> Judy James "
>
>
>
>
> *********************************************************************
>
> Judy Rose James, Ph.D.
>
> Clinical Physicist, MR Imaging Division
>
> Assistant Professor, Department of Radiology
>
> University of Mississippi Medical Center
>
> Jackson, MS - 39216
>
> Ph: (601) 984-2585; Pager: (601) 929-2442
>
> Email: jjames2 at umc.edu
>
> *********************************************************************
>
>
>
> ________________________________
>
> From: mristudio-users-bounces at mristudio.org
>
> [mristudio-users-bounces at mristudio.org] On Behalf Of Jacquie Hodge
>
> [Jacquie.Hodge at albertahealthservices.ca]
>
> Sent: Friday, April 08, 2011 11:56 AM
>
> To: mristudio-users at mristudio.org
>
> Subject: [Mristudio-users] Fa values
>
>
> Good morning everyone,
>
>
> I am using DTI studio for my project where I am interested in comparing the
>
> left and right CST's in children who have suffereed injury in that area and
>
> after reading many studies on DTI decided to compare average FA values of
>
> the tracts as one of my variables. However, I have come across this
> questino
>
> from one of my supervisors and cannot really answer it and am hoping for
>
> your help/expertise.
>
> Here is goes:
>
> Is the FA value still a viable measure to look at and use to make a
>
> correlation if you are using FA values to pull the white matter tract? It
>
> seems like if the tract is made from FA values then you should not be able
>
> to use the FA as an outcome variable. This question has come up as I
>
> presented my research idea and I'm not sure how to answer it. Most studies
>
> that use DTI use FA thresholds to pull the tracts and then also the FA
>
> values (eg. mean FA) to make comparisons between the tracts.
>
>
> I really hope that my question makes sense as I have found it very hard to
>
> word properly.
>
>
> Thank you very much,
>
> Jacquie
>
>
> Jacquie Hodge MSc candidate in Neuroscience, BSc
>
> Neuroscience, University of Calgary
>
> Research Assistant, Calgary Pediatric Stroke Program
>
> Alberta Children's Hospital
>
> 2888 Shaganappi Trail NW, Calgary, AB, Canada T3B 6A8
>
> Phone: 403-955-7733 Fax: 403-955-2922
>
> jacquie.hodge at albertahealthservices.ca
>
> Program website:
>
> http://www.calgaryhealthregion.ca/programs/stroke/pediatric.htm
>
> ________________________________
>
> 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.
>
>
> 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
>
>
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
> On Feb 23, 2011, at 4:35 AM, susumu mori wrote:
>
> Andreas is right.
> So called ADC (average diffusion constant, apparent diffusion constant) and
> MD (mean diffusivity) are obtained by trace/3 (trace divided by 3), while
> the trace is (eigenvalue0+eigenvalue1+eigenvalue2).
>
> also, axial diffusivity is same as eigenvalue0 and radial diffusivity is
> the average of eigenvalue1 and 2 [ (eigenvalue1+eigenvalue2)/2].
>
> On Wed, Feb 23, 2011 at 8:31 AM, Andreas Buchmann <buchmann2 at wisc.edu>wrote:
>
>> Dear Yo,
>>
>> I'm using trace diffusivity, which is strongly related to mean diffusivity
>> (I think, just multiplied with a constant factor, experts correct me if
>> I'm
>> wrong).
>>
>> Andreas
>>
>>
>>
>> -----Original Message-----
>> From: mristudio-users-bounces at mristudio.org
>> [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of
>> 107310 at ib.k.u-tokyo.ac.jp
>> Sent: Dienstag, 22. Februar 2011 19:36
>> To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
>> Subject: Re: [Mristudio-users] radial diffusivity, mean diffusivity
>>
>> Dear Andreas, Ryuzo and DTI experts
>>
>>
>> I also try to calculate mean diffusivity.
>> But in DTI studio, only the radial diffusivity and ADCs can calculate at
>> the 'Image'-tab with ROI.
>>
>> Is there any function to measure mean diffusivity?
>> Please give me any suggestion.
>>
>> Many thanks.
>>
>>
>> YO
>>
>>
>> > Dear Andreas
>> >
>> >
>> >
>> > Thank you very much for your suggestion.  I will try.
>> >
>> >
>> >
>> > Ryuzo
>> >
>> >
>> >
>> > From: mristudio-users-bounces at mristudio.org
>> > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Andreas
>> Buchmann
>> > Sent: Monday, February 21, 2011 11:03 PM
>> > To: 'DTI Studio, ROI Editor, DiffeoMap Questions/Support'
>> > Subject: Re: [Mristudio-users] radial diffusivity, mean diffusivity
>> >
>> >
>> >
>> > Dear Ryuzo,
>> >
>> >
>> >
>> > yes, you're on the right track with (1). After the estimation, DTI-
>> Studio
>> > appends the images to the list of images you have, and you can see
>> them
>> > under the 'Image'-tab and save them with right-click on the image.
>> >
>> >
>> >
>> > Good luck
>> >
>> > Andreas
>> >
>> >
>> >
>> >   _____
>> >
>> > From: mristudio-users-bounces at mristudio.org
>> > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of hanaie
>> > Sent: Montag, 21. Februar 2011 07:46
>> > To: mristudio-users at mristudio.org
>> > Subject: [Mristudio-users] radial diffusivity, mean diffusivity
>> >
>> >
>> >
>> > Dear DTI experts
>> >
>> >
>> >
>> > How can I do to obtain the radial diffusivity and mean diffusivity in
>> DTI
>> > studio?
>> >
>> >
>> >
>> > 1.     In the " Dti Map" tab, clicking "Tensor, color Map etc" button,
>> and
>> > checking the checkboxes "Radial", "Trace"
>> >
>> >
>> >
>> > 2.     After tensor calculation and fiber tracking, if I click "
>> statistics"
>> > button in the "Fiber" tab and
>> >
>> >  I choose the each image and click "go" button in the another window,
>> can I
>> > obtain radial and mean diffusivity?
>> >
>> >
>> >
>> >
>> >
>> > Please give me any suggestion.
>> >
>> >
>> >
>> > Many thanks.
>> >
>> >
>> >
>> > Ryuzo
>> >
>> >
>> >
>> >
>> > _______________________________________________
>> > mristudio-users mailing list
>> > mristudio-users at mristudio.org
>> > http://lists.mristudio.org/mailman/listinfo/
>> > Unsubscribe, send a blank email to: mristudio-users-unsubscribe@
>> 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
>
>
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From rachaelg.uh at gmail.com  Mon Aug 15 19:29:41 2011
From: rachaelg.uh at gmail.com (Rachael Gonzales)
Date: Mon, 15 Aug 2011 13:29:41 -1000
Subject: [Mristudio-users] ADC-Map Calculation in DTIStudio
In-Reply-To: <CAEq9ap+WxteLTPumqR3KDaxdpuSPfETNsT-WbehPFmozyxGJVg@mail.gmail.com>
References: <20110223013620.000068D1.0399@ib.k.u-tokyo.ac.jp>
	<0LH20086JO891D30@smtpauth1.wiscmail.wisc.edu>
	<AANLkTikZMJqg2fPA61UnxvPcewTNoT2PA5TOCyKL1A5z@mail.gmail.com>
	<047F400A-E034-4A38-9D60-795FF8F5B758@gmail.com>
	<CAEq9ap+WxteLTPumqR3KDaxdpuSPfETNsT-WbehPFmozyxGJVg@mail.gmail.com>
Message-ID: <B7FB5D44-4ECD-4FC5-9005-CE2C769C020C@gmail.com>

Hi Dr. Mori,

Thank you so much for clearing that up!

Sincerely,

Rachael

Rachael M. K. Gonzales, B.A.
Graduate Student
Clinical Research - Neuroscience
John A. Burns School of Medicine
University of Hawaii - Manoa
(808) 545-8974 office
rachaelg at hawaii.edu





On Aug 15, 2011, at 12:53 PM, susumu mori wrote:

> p.s. What I mean by "ADC" in my previous response is "apparent diffusion constant", not "average diffusion constant". The latter is the same as "mean diffusivity". The definition of the former is not well defined but in my response, it means a diffusion constant calculated from one diffusion orientation.
> 
> On Mon, Aug 15, 2011 at 6:31 PM, Rachael Gonzales <rachaelg.uh at gmail.com> wrote:
> Hi DTI experts,
> 
> In DTIStudio, under the DTI map tab there is an ADC Map calculation available.  After the calculation, an ADC map - mean image is generated, is this the apparent or average diffusion coefficient?  
> 
> 
> Thanks,
> 
> Rachael
> 
> 
> *****************************************************************************************************************************
> 
> Judy, in DtiStudio, ADC (or also called MD) should be obtained from "Trace".
> 
> Trace is defined as Dxx+Dyy+Dzz. If you divide it by 3, it becomes
> "Average diffusion constant (ADC)" or "Mean diffusivity (MD)". We like
> to use the term "trace" because it has clear mathematical definition
> while ADC is also used for "Apparent diffusion constant", which has a
> different meaning from "average diffusion constant".
> 
> On Mon, Apr 11, 2011 at 11:58 AM, Judy James <jjames2 at umc.edu> wrote:
>> Is any one in this group aware of how to calculate ADC maps from the
>> original DWI images in DTI studio - not DTI images, like how to set the
>> gradient table in such a case?
>> Any input/help will be highly appreciated.
>> 
>> Thank you,
>> Judy James "
>> 
>> 
>> 
>> *********************************************************************
>> Judy Rose James, Ph.D.
>> Clinical Physicist, MR Imaging Division
>> Assistant Professor, Department of Radiology
>> University of Mississippi Medical Center
>> Jackson, MS - 39216
>> Ph: (601) 984-2585; Pager: (601) 929-2442
>> Email: jjames2 at umc.edu
>> *********************************************************************
>> 
>> 
>> ________________________________
>> From: mristudio-users-bounces at mristudio.org
>> [mristudio-users-bounces at mristudio.org] On Behalf Of Jacquie Hodge
>> [Jacquie.Hodge at albertahealthservices.ca]
>> Sent: Friday, April 08, 2011 11:56 AM
>> To: mristudio-users at mristudio.org
>> Subject: [Mristudio-users] Fa values
>> 
>> Good morning everyone,
>> 
>> I am using DTI studio for my project where I am interested in comparing the
>> left and right CST's in children who have suffereed injury in that area and
>> after reading many studies on DTI decided to compare average FA values of
>> the tracts as one of my variables. However, I have come across this questino
>> from one of my supervisors and cannot really answer it and am hoping for
>> your help/expertise.
>> Here is goes:
>> Is the FA value still a viable measure to look at and use to make a
>> correlation if you are using FA values to pull the white matter tract? It
>> seems like if the tract is made from FA values then you should not be able
>> to use the FA as an outcome variable. This question has come up as I
>> presented my research idea and I'm not sure how to answer it. Most studies
>> that use DTI use FA thresholds to pull the tracts and then also the FA
>> values (eg. mean FA) to make comparisons between the tracts.
>> 
>> I really hope that my question makes sense as I have found it very hard to
>> word properly.
>> 
>> Thank you very much,
>> Jacquie
>> 
>> Jacquie Hodge MSc candidate in Neuroscience, BSc
>> Neuroscience, University of Calgary
>> Research Assistant, Calgary Pediatric Stroke Program
>> Alberta Children's Hospital
>> 2888 Shaganappi Trail NW, Calgary, AB, Canada T3B 6A8
>> Phone: 403-955-7733 Fax: 403-955-2922
>> jacquie.hodge at albertahealthservices.ca
>> Program website:
>> http://www.calgaryhealthregion.ca/programs/stroke/pediatric.htm
>> ________________________________
>> 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.
>> 
>> 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
>> 
>> 
> 
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org
> 
> 
> On Feb 23, 2011, at 4:35 AM, susumu mori wrote:
> 
>> Andreas is right.
>> So called ADC (average diffusion constant, apparent diffusion constant) and MD (mean diffusivity) are obtained by trace/3 (trace divided by 3), while the trace is (eigenvalue0+eigenvalue1+eigenvalue2).
>> 
>> also, axial diffusivity is same as eigenvalue0 and radial diffusivity is the average of eigenvalue1 and 2 [ (eigenvalue1+eigenvalue2)/2].
>> 
>> On Wed, Feb 23, 2011 at 8:31 AM, Andreas Buchmann <buchmann2 at wisc.edu> wrote:
>> Dear Yo,
>> 
>> I'm using trace diffusivity, which is strongly related to mean diffusivity
>> (I think, just multiplied with a constant factor, experts correct me if I'm
>> wrong).
>> 
>> Andreas
>> 
>> 
>> 
>> -----Original Message-----
>> From: mristudio-users-bounces at mristudio.org
>> [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of
>> 107310 at ib.k.u-tokyo.ac.jp
>> Sent: Dienstag, 22. Februar 2011 19:36
>> To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
>> Subject: Re: [Mristudio-users] radial diffusivity, mean diffusivity
>> 
>> Dear Andreas, Ryuzo and DTI experts
>> 
>> 
>> I also try to calculate mean diffusivity.
>> But in DTI studio, only the radial diffusivity and ADCs can calculate at
>> the 'Image'-tab with ROI.
>> 
>> Is there any function to measure mean diffusivity?
>> Please give me any suggestion.
>> 
>> Many thanks.
>> 
>> 
>> YO
>> 
>> 
>> > Dear Andreas
>> >
>> >
>> >
>> > Thank you very much for your suggestion.  I will try.
>> >
>> >
>> >
>> > Ryuzo
>> >
>> >
>> >
>> > From: mristudio-users-bounces at mristudio.org
>> > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Andreas
>> Buchmann
>> > Sent: Monday, February 21, 2011 11:03 PM
>> > To: 'DTI Studio, ROI Editor, DiffeoMap Questions/Support'
>> > Subject: Re: [Mristudio-users] radial diffusivity, mean diffusivity
>> >
>> >
>> >
>> > Dear Ryuzo,
>> >
>> >
>> >
>> > yes, you're on the right track with (1). After the estimation, DTI-
>> Studio
>> > appends the images to the list of images you have, and you can see
>> them
>> > under the 'Image'-tab and save them with right-click on the image.
>> >
>> >
>> >
>> > Good luck
>> >
>> > Andreas
>> >
>> >
>> >
>> >   _____
>> >
>> > From: mristudio-users-bounces at mristudio.org
>> > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of hanaie
>> > Sent: Montag, 21. Februar 2011 07:46
>> > To: mristudio-users at mristudio.org
>> > Subject: [Mristudio-users] radial diffusivity, mean diffusivity
>> >
>> >
>> >
>> > Dear DTI experts
>> >
>> >
>> >
>> > How can I do to obtain the radial diffusivity and mean diffusivity in
>> DTI
>> > studio?
>> >
>> >
>> >
>> > 1.     In the " Dti Map" tab, clicking "Tensor, color Map etc" button,
>> and
>> > checking the checkboxes "Radial", "Trace"
>> >
>> >
>> >
>> > 2.     After tensor calculation and fiber tracking, if I click "
>> statistics"
>> > button in the "Fiber" tab and
>> >
>> >  I choose the each image and click "go" button in the another window,
>> can I
>> > obtain radial and mean diffusivity?
>> >
>> >
>> >
>> >
>> >
>> > Please give me any suggestion.
>> >
>> >
>> >
>> > Many thanks.
>> >
>> >
>> >
>> > Ryuzo
>> >
>> >
>> >
>> >
>> > _______________________________________________
>> > mristudio-users mailing list
>> > mristudio-users at mristudio.org
>> > http://lists.mristudio.org/mailman/listinfo/
>> > Unsubscribe, send a blank email to: mristudio-users-unsubscribe@
>> 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

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From jangouk at kennedykrieger.org  Wed Aug 17 20:45:48 2011
From: jangouk at kennedykrieger.org (Jangouk, Parastoo)
Date: Thu, 18 Aug 2011 00:45:48 +0000
Subject: [Mristudio-users] question on installation
Message-ID: <16C42831A84D3A4C9C4E7D16083952188F04EF@kki-gsp-mail2.kki.org>

 Hi everybody,

I am trying to install DTI Studio on a Windows 7 Professional system and I get this message: "The application has failed to start because its side-by side configuration is incorrect". Can somebody tell me how to fix the problem?
Thanks

Parastoo




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.
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From buchmann2 at wisc.edu  Thu Aug 18 09:50:42 2011
From: buchmann2 at wisc.edu (Andreas Buchmann)
Date: Thu, 18 Aug 2011 07:50:42 -0600
Subject: [Mristudio-users] number of fibers
In-Reply-To: <CAEq9apKkxdZrt918baP2wxqQrEg2mPoBB7FUxm64UU4MFFY+rg@mail.gmail.com>
Message-ID: <0LQ400J3SMGT5T40@smtpauth2.wiscmail.wisc.edu>

Dear DTI experts,

I've got two theoretical questions:

(1) in FACT, tract statistics give out a number of fibers. What does this
number mean? Is it possible that more than one fiber goes through one voxel?

(2) what is the physical measure of diffusivity values (e.g. radial
diffusivity: 10 exp-4 what? cm/s or m/s?)


Thanks a lot
Andreas


From xli16 at jhmi.edu  Thu Aug 18 10:11:40 2011
From: xli16 at jhmi.edu (Xin Li)
Date: Thu, 18 Aug 2011 10:11:40 -0400
Subject: [Mristudio-users] question on installation
In-Reply-To: <16C42831A84D3A4C9C4E7D16083952188F04EF@kki-gsp-mail2.kki.org>
References: <16C42831A84D3A4C9C4E7D16083952188F04EF@kki-gsp-mail2.kki.org>
Message-ID: <7010c4a825c37.4e4ce55c@johnshopkins.edu>

Hello Parastoo,

It seems that you need to install the Microsoft Visual Studio redistribution package. DtiStudio is developed with Visual C++. If your computer doesn't have Visual C++ 2005 and Service Pack 1 installed, please run vcredist_x86.exe (for 32 bit applications) or vcredist_x64.exe (for x64 applications). They can install runtime components of Visual C++ Libraries required on your computer. These two exe files are available at https://www.mristudio.org/wiki/installation.


Xin


----- Original Message -----
From: "Jangouk, Parastoo" <jangouk at kennedykrieger.org>
Date: Wednesday, August 17, 2011 8:46 pm
Subject: [Mristudio-users] question on installation
To: "mristudio-users at mristudio.org" <mristudio-users at mristudio.org>


>  Hi everybody,
>  
>  I am trying to install DTI Studio on a Windows 7 Professional system 
> and I get this message: "The application has failed to start because 
> its side-by side configuration is incorrect". Can somebody tell me how 
> to fix the problem?
>  Thanks
>  
>  Parastoo
>  
>  
>  
>  
>  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
>  
>  Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org 

From jangouk at kennedykrieger.org  Thu Aug 18 11:45:09 2011
From: jangouk at kennedykrieger.org (Jangouk, Parastoo)
Date: Thu, 18 Aug 2011 15:45:09 +0000
Subject: [Mristudio-users] question on installation
In-Reply-To: <7010c4a825c37.4e4ce55c@johnshopkins.edu>
References: <16C42831A84D3A4C9C4E7D16083952188F04EF@kki-gsp-mail2.kki.org>
	<7010c4a825c37.4e4ce55c@johnshopkins.edu>
Message-ID: <16C42831A84D3A4C9C4E7D16083952188F06F7@kki-gsp-mail2.kki.org>

Thanks so much Xin, It seems it is working now!
Perfect

Parastoo


-----Original Message-----
From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Xin Li
Sent: Thursday, August 18, 2011 10:12 AM
To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
Subject: Re: [Mristudio-users] question on installation

Hello Parastoo,

It seems that you need to install the Microsoft Visual Studio redistribution package. DtiStudio is developed with Visual C++. If your computer doesn't have Visual C++ 2005 and Service Pack 1 installed, please run vcredist_x86.exe (for 32 bit applications) or vcredist_x64.exe (for x64 applications). They can install runtime components of Visual C++ Libraries required on your computer. These two exe files are available at https://www.mristudio.org/wiki/installation.


Xin


----- Original Message -----
From: "Jangouk, Parastoo" <jangouk at kennedykrieger.org>
Date: Wednesday, August 17, 2011 8:46 pm
Subject: [Mristudio-users] question on installation
To: "mristudio-users at mristudio.org" <mristudio-users at mristudio.org>


>  Hi everybody,
>  
>  I am trying to install DTI Studio on a Windows 7 Professional system 
> and I get this message: "The application has failed to start because 
> its side-by side configuration is incorrect". Can somebody tell me how 
> to fix the problem?
>  Thanks
>  
>  Parastoo
>  
>  
>  
>  
>  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
>  
>  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  Thu Aug 18 18:17:41 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Thu, 18 Aug 2011 18:17:41 -0400
Subject: [Mristudio-users] number of fibers
In-Reply-To: <0LQ400J3SMGT5T40@smtpauth2.wiscmail.wisc.edu>
References: <CAEq9apKkxdZrt918baP2wxqQrEg2mPoBB7FUxm64UU4MFFY+rg@mail.gmail.com>
	<0LQ400J3SMGT5T40@smtpauth2.wiscmail.wisc.edu>
Message-ID: <CAEq9apL+rtrDo0jnagVaDsr7gEEXzxG4agJPZ_PKCXDULpeGQg@mail.gmail.com>

Hi Andreas,

please see below;


> (1) in FACT, tract statistics give out a number of fibers. What does this
> number mean? Is it possible that more than one fiber goes through one
> voxel?
>

The number of the fiber itself doesn't carry anatomical meaning. In
DtiStudio, we use the exhaustive approach, meaning fiber tracking is
initiated from the center of all pixels above the threshold. If the number
of the seed points is increased, the number of the fibers increases too. So,
it is parameter-dependent. You may be able to compare the numbers between
subjects but it may simply reflect the size of the tracts, which can be also
obtained from the number of pixels. The number of pixels is also reported in
DtiStudio and has a physical dimension, which may be easier to use.


>
> (2) what is the physical measure of diffusivity values (e.g. radial
> diffusivity: 10 exp-4 what? cm/s or m/s?)
>
>
It depends on the unit you use for the b-value.


>
> Thanks a lot
> Andreas
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
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From dzaca2 at jhmi.edu  Fri Aug 19 16:58:11 2011
From: dzaca2 at jhmi.edu (Domenico Zaca)
Date: Fri, 19 Aug 2011 16:58:11 -0400
Subject: [Mristudio-users] adc values measurement unit
Message-ID: <CA+sDYteEiVxyVivx90KWZvt8YKt5DDzdo1F693k5PvsycxdHWQ@mail.gmail.com>

Hi,

I got these results for ROI analysis of ADC data in 2 regions.
Values are expressed as mean? standard deviation.

GCC    843.3909 ? 148.6741
SCC   870.6035  ?  223.2440

Images were acquired on a 1.5 T Philips Scanner. b value was 700 s/mm2
What's the measurement unit Philips uses for ADC values?


Thanks
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From xperiax1 at mail.ustc.edu.cn  Sun Aug 21 02:39:26 2011
From: xperiax1 at mail.ustc.edu.cn (xperiax1 at mail.ustc.edu.cn)
Date: Sun, 21 Aug 2011 14:39:26 +0800 (CST)
Subject: [Mristudio-users] about the processor
Message-ID: <25115225.423771313908766493.JavaMail.coremail@mailweb>

Hello,

Would AFNI has a better performance on Xeon 7500 series than Opteron 6000 series?

Does AFNI support CUDA?

Thank You!

From xperiax1 at mail.ustc.edu.cn  Sun Aug 21 03:10:37 2011
From: xperiax1 at mail.ustc.edu.cn (xperiax1 at mail.ustc.edu.cn)
Date: Sun, 21 Aug 2011 15:10:37 +0800 (CST)
Subject: [Mristudio-users] about the processor
Message-ID: <27945797.424841313910637653.JavaMail.coremail@mailweb>

Hello,

Would DTIstudio has a better performance on Xeon 7500 series than Opteron 6000 series?

Does DTIstudio support CUDA?

Thank You!

(Sorry, I made a mistake in the prior mail.)

From susumu at mri.jhu.edu  Sun Aug 21 14:55:04 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Sun, 21 Aug 2011 14:55:04 -0400
Subject: [Mristudio-users] adc values measurement unit
In-Reply-To: <CA+sDYteEiVxyVivx90KWZvt8YKt5DDzdo1F693k5PvsycxdHWQ@mail.gmail.com>
References: <CA+sDYteEiVxyVivx90KWZvt8YKt5DDzdo1F693k5PvsycxdHWQ@mail.gmail.com>
Message-ID: <CAEq9apJJzASkBDTtvSe977nOfZ3q4dGUHpwQEjA-_GG6f+DxEQ@mail.gmail.com>

It seems that you didn't specify b-value so that DtiStudio used the default
(= 1)?
The unit depends on the unit of the b-value you use. If you used s/mm^2,
then, it should be s/mm^2.

Also please be careful, the trace value in DtiStudio is 3 x ADC (or 3x MD).

On Fri, Aug 19, 2011 at 4:58 PM, Domenico Zaca <dzaca2 at jhmi.edu> wrote:

> Hi,
>
> I got these results for ROI analysis of ADC data in 2 regions.
> Values are expressed as mean? standard deviation.
>
> GCC    843.3909 ? 148.6741
> SCC   870.6035  ?  223.2440
>
> Images were acquired on a 1.5 T Philips Scanner. b value was 700 s/mm2
> What's the measurement unit Philips uses for ADC values?
>
>
> Thanks
>
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From gnirkem at upstate.edu  Mon Aug 22 12:52:35 2011
From: gnirkem at upstate.edu (Matthew Gnirke)
Date: Mon, 22 Aug 2011 12:52:35 -0400
Subject: [Mristudio-users] FA stats question
Message-ID: <4E5251130200003D00045EA9@gwmta2.upstate.edu>

Hi

I have a question regarding the statistics profile in DTI-studio. I am
attempting to only measure the fibers between two extreme OR ROIs with an
AND ROI in between them. If I click statistics and then select the FA map,
and click stats profile, the program gives a breakdown of fibers by slice.
My question is what exactly is the mean FA value reflecting.. is it computed
from the FA of the fibers at that specific slice, or is it computed from the
average of the FA of the whole length of the fiber.  Lets say for example
(for simplicity), there is only one fiber... is each slices FA reflective of
the FA at that slice or of the average of that fiber along its entire
course?

Thank you for your help, and I hope my question made a little sense..
Matt

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From susumu at mri.jhu.edu  Mon Aug 22 19:35:12 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Mon, 22 Aug 2011 19:35:12 -0400
Subject: [Mristudio-users] FA stats question
In-Reply-To: <4E5251130200003D00045EA9@gwmta2.upstate.edu>
References: <4E5251130200003D00045EA9@gwmta2.upstate.edu>
Message-ID: <CAEq9apK6w7NMi+Sj6f2z8ykZ5anejecdK5MRixHHTyHo9AWFCw@mail.gmail.com>

Hi Matt,

The slice profile gives the average FA of the pixels within one given slice.
In your example, there should be only one pixel at each slice and thus you
get the FA of that single pixel.
If you want the average of the entire fiber, you need the reported FA before
you click "profile".

Also, if you want tracts between two ROIs, you may also want to try the
"CUT" operation, which waits for two ROI inputs and retain only the
trajectories between the two ROIs.

Susumu

On Mon, Aug 22, 2011 at 12:52 PM, Matthew Gnirke <gnirkem at upstate.edu>wrote:

> Hi
>
> I have a question regarding the statistics profile in DTI-studio. I am
> attempting to only measure the fibers between two extreme OR ROIs with an
> AND ROI in between them. If I click statistics and then select the FA map,
> and click stats profile, the program gives a breakdown of fibers by slice.
> My question is what exactly is the mean FA value reflecting.. is it computed
> from the FA of the fibers at that specific slice, or is it computed from the
> average of the FA of the whole length of the fiber.  Lets say for example
> (for simplicity), there is only one fiber... is each slices FA reflective of
> the FA at that slice or of the average of that fiber along its entire
> course?
>
> Thank you for your help, and I hope my question made a little sense..
> Matt
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From gnirkem at upstate.edu  Wed Aug 24 10:33:37 2011
From: gnirkem at upstate.edu (Matthew Gnirke)
Date: Wed, 24 Aug 2011 10:33:37 -0400
Subject: [Mristudio-users] FA stats question
Message-ID: <4E54D3810200003D0004601F@gwmta2.upstate.edu>

Thank you for your response and suggestions Dr Mori! I have a couple of more
specific questions if that's alright...

I have tryed the cut tool and it is not exactly what I am looking for, I
think the Or--And---Or set of ROIs better suits our needs. I am trying to 
calculate the average FA in between the two extreme Or ROIs. When I go to
the stat profile window, what I am currently doing is exporting the values
from the slices between my two OR ROIs into excell and calculating the mean
FA. My question centers around what, precisely, the values are. The table
has the following columns:


Slice  
#_Of_Fibers
Max_Val
Min_Val
Mean_Val
Std_Dev

Pixel#--
Max#--      
Min#--  
Mean#--     
Std_Dev-- (Fiber/Pixel)



Inorder to calculate a mean FA for a selected number of slices, would the
following be correct?: (ie for slice 1, 2, 3...)

((Pixel#)(Mean_val))1+((Pixel#)(Mean_val))2+((Pixel#)(Mean_val))3.......  /
total # of pixels


Or....

((#_Of_Fibers)(Mean_val))1+((#_Of_Fibers)(Mean_val))2+((#_Of_Fibers)(Mean_val))3.......
 / total #_Of_Fibers



Also, could you possibly explain what the rest of the values are?
(especially beyond pixel #)

Thank you again, I really appreciate the help
Matt Gnirke



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From susumu at mri.jhu.edu  Thu Aug 25 16:48:40 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Thu, 25 Aug 2011 16:48:40 -0400
Subject: [Mristudio-users] FA stats question
In-Reply-To: <4E54D3810200003D0004601F@gwmta2.upstate.edu>
References: <4E54D3810200003D0004601F@gwmta2.upstate.edu>
Message-ID: <CAEq9ap+6yLN2GCp4CEXzUS--pHA4ng-_gRzeOXc60cRv8RauWg@mail.gmail.com>

I have to confirm Hangyi, but my understanding is;


> Slice
> #_Of_Fibers: the number of reconstructed streamlines that penetrate the
> given slice
> Max_Val: The maximum pixel value (if you chose FA, then the FA value) that
> contains the streamlines in the given slice
> Min_Val
> Mean_Val: The mean of the pixel values that contain the streamlines in the
> given slice
> Std_Dev
>
> Pixel#--: The number of pixels that contain the streamlines in the given
> slice
> Max#--      : The maximum number of the streamlines a pixel holds in the
> given slice
> Min#--
> Mean#--     The mean number of the streamlines of the pixels that contain
> the streamlines in the given slice
> Std_Dev-- (Fiber/Pixel)
>
>
>
> Inorder to calculate a mean FA for a selected number of slices, would the
> following be correct?: (ie for slice 1, 2, 3...)
>

This number is already calculated in "Mean Val" column.

>
> ((Pixel#)(Mean_val))1+((Pixel#)(Mean_val))2+((Pixel#)(Mean_val))3.......  /
> total # of pixels
>
>
> Or....
>
> ((#_Of_Fibers)(Mean_val))1+((#_Of_Fibers)(Mean_val))2+((#_Of_Fibers)(Mean_val))3.......
> / total #_Of_Fibers
>
>
>
> Also, could you possibly explain what the rest of the values are?
> (especially beyond pixel #)
>
> Thank you again, I really appreciate the help
> Matt Gnirke
>
>
> ****
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From pengdoctor1 at 163.com  Mon Aug 29 21:28:12 2011
From: pengdoctor1 at 163.com (pengdoctor1)
Date: Tue, 30 Aug 2011 09:28:12 +0800 (CST)
Subject: [Mristudio-users] How to answer this question?
In-Reply-To: <CAEq9ap+6yLN2GCp4CEXzUS--pHA4ng-_gRzeOXc60cRv8RauWg@mail.gmail.com>
References: <CAEq9ap+6yLN2GCp4CEXzUS--pHA4ng-_gRzeOXc60cRv8RauWg@mail.gmail.com>
	<4E54D3810200003D0004601F@gwmta2.upstate.edu>
Message-ID: <30e9b40f.f335.132184d011a.Coremail.pengdoctor1@163.com>

Hello,everyone,
   I used ditstudio to produce FA,  and then used a VBA method to find a decreased FA brain region in my paper, but the referee asked a question, i don't know what it mean( the contents in yellow), who can tell me. thank you very much!
 

"Second, is it possible that the higher FA in the recovered scans is due to better quality of the scans? Maybe due to reduced movement artifact (coorelated with BDI)? Is it possible that simple filtering followed by VBA is more sensitive to such an artifact than TBSS would have been?Is this effect filter frequency dependent?"

 

 

? 2011-08-26 04:48:40?"susumu mori" <susumu at mri.jhu.edu> ???
I have to confirm Hangyi, but my understanding is;



Slice 
#_Of_Fibers: the number of reconstructed streamlines that penetrate the given slice
Max_Val: The maximum pixel value (if you chose FA, then the FA value) that contains the streamlines in the given slice
Min_Val
Mean_Val: The mean of the pixel values that contain the streamlines in the given slice
Std_Dev

Pixel#--: The number of pixels that contain the streamlines in the given slice
Max#--      : The maximum number of the streamlines a pixel holds in the given slice
Min#-- 
Mean#--     The mean number of the streamlines of the pixels that contain the streamlines in the given slice
Std_Dev-- (Fiber/Pixel)



Inorder to calculate a mean FA for a selected number of slices, would the following be correct?: (ie for slice 1, 2, 3...)



This number is already calculated in "Mean Val" column. 

((Pixel#)(Mean_val))1+((Pixel#)(Mean_val))2+((Pixel#)(Mean_val))3.......  / total # of pixels


Or....

((#_Of_Fibers)(Mean_val))1+((#_Of_Fibers)(Mean_val))2+((#_Of_Fibers)(Mean_val))3.......  / total #_Of_Fibers



Also, could you possibly explain what the rest of the values are? (especially beyond pixel #)

Thank you again, I really appreciate the help
Matt Gnirke




_______________________________________________
mristudio-users mailing list
mristudio-users at mristudio.org
http://lists.mristudio.org/mailman/listinfo/
Unsubscribe, send a blank email to:mristudio-users-unsubscribe at mristudio.org


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From naamab at stanford.edu  Thu Sep  1 19:15:14 2011
From: naamab at stanford.edu (Naama Barnea-Goraly)
Date: Thu, 01 Sep 2011 16:15:14 -0700
Subject: [Mristudio-users] How to run AIR on Siemens Mosaic data?
Message-ID: <9BEE6CA5-F7BF-41D2-BA10-0893D888EA1A@stanford.edu>


With GE data we have a B0 image to use as a reference. However in  
Mosaic there is no separate B0 image, what should I use for the  
reference image?

Thanks,

Naama




From susumu at mri.jhu.edu  Sat Sep  3 14:59:26 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Sat, 03 Sep 2011 14:59:26 -0400
Subject: [Mristudio-users] How to run AIR on Siemens Mosaic data?
In-Reply-To: <9BEE6CA5-F7BF-41D2-BA10-0893D888EA1A@stanford.edu>
References: <9BEE6CA5-F7BF-41D2-BA10-0893D888EA1A@stanford.edu>
Message-ID: <CAEq9apJtozNQFis9V+5+VLMRqxKW8U86G0teR-fh3RNq3uyr8w@mail.gmail.com>

Hi Naama,

Of course, we have b0 in Mosaic. You can't find it? Then you can't calculate
tensor either....

On Thu, Sep 1, 2011 at 7:15 PM, Naama Barnea-Goraly <naamab at stanford.edu>wrote:

>
> With GE data we have a B0 image to use as a reference. However in
> Mosaic there is no separate B0 image, what should I use for the
> reference image?
>
> Thanks,
>
> Naama
>
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
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From akolasny at jhu.edu  Tue Sep  6 07:44:49 2011
From: akolasny at jhu.edu (akolasny at jhu.edu)
Date: Tue, 06 Sep 2011 07:44:49 -0400 (EDT)
Subject: [Mristudio-users] Computational Anatomy Works (CAWorks) - LDDMM
 Region of Interest Processing
Message-ID: <54060.192.168.2.29.1315309489.squirrel@webmail.cis.jhu.edu>

Computational Anatomy Works (CAWorks) Software Announcement

CAWorks is available through mristudio.org under:

   https://www.mristudio.org/download/binaries/caworks/

The software application Computational Anatomy Works (CAWorks) was
developed to support Computational Anatomy and shape analysis. The
capabilities of CAWorks include:

   1. Interactive landmark placement to create segmentation (mask) of
desired region of interest

   2. Specialized landmark placement plugins for subcortical structures
such as hippocampus and amygdala

   3. Support for multiple Medical Imaging data formats, such as Nifti,
Analyze, Freesurfer, DICOM and landmark data

   4. Quadra Planar view visualization

   5. Shape Analysis plugin modules, such as Large Deformation
Diffeomorphic Metric Mapping (LDDMM)

Current enhancements to CAWorks have focused on interactive support for
landmarking of subcortical structures. Specific plugins are available for
landmark placement of the hippocampus, amygdala and entorhinal cortex
regions. After landmarking is completed, CAWorks facilitates submission
for automated segmentation processing. CAWorks is being used by the
Biomarkers for Older Controls At Risk for Dementia (BIOCARD), Resource for
Quantitative Functional MRI: TRD4, Validation of Structural/Functional MRI
Localization and Biomedical Informatics Research Network (BIRN) projects.

CAWorks extends ParaView, an open source, multi-platform, freely available
program for parallel, interactive, scientific visualization. An important
visualization tool for TeraGrid researchers, its client-server
architecture facilitates remote visualization of datasets and the
generation of level of detail (LOD) models that maintain interactive frame
rates for large datasets.

Tutorials describing CAWorks for the ROI feature are located at:

    http://caportal.cis.jhu.edu/tutorials


If you have questions regarding this software, please put CAWorks in your
subject line for the mristudio-users mailing list.

Thanks!
CAWorks Development Team


From jsadino.queens at gmail.com  Thu Sep  8 19:59:15 2011
From: jsadino.queens at gmail.com (Jeff Sadino)
Date: Thu, 08 Sep 2011 13:59:15 -1000
Subject: [Mristudio-users] LDDMM for Hematoma
Message-ID: <CAAK1NkfvbPZto-kY7Jp86ioKarfeze8AFWALaHPhOGcXbBGrhw@mail.gmail.com>

Hello again DTI Experts,

I have a group of patients that have suffered trauma to the head that I am
putting through the LDDMM pipeline.  A problem I ran across during AIR in
DiffeoMap is that since the trauma is causing a hematoma in the B0 image,
the registration is very poor.  On one subject, I performed DiffeoMap AIR
using the Mean DWI image and the registration came out pretty good.  I am
wondering if this is a valid approach to perform AIR registration.

For the LDDMM registration, usually I use the FA and the Trace image to
drive the Kimap.  However, I think I will get the same poor results.  Should
I use just the DWI image to drive the LDDMM registration?  There would be no
need to do "Intensity Normalization" on the DWI image, correct?

Thank you very much,
Jeff Sadino
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From susumu at mri.jhu.edu  Thu Sep  8 21:33:44 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Thu, 08 Sep 2011 21:33:44 -0400
Subject: [Mristudio-users] LDDMM for Hematoma
In-Reply-To: <CAAK1NkfvbPZto-kY7Jp86ioKarfeze8AFWALaHPhOGcXbBGrhw@mail.gmail.com>
References: <CAAK1NkfvbPZto-kY7Jp86ioKarfeze8AFWALaHPhOGcXbBGrhw@mail.gmail.com>
Message-ID: <CAEq9apLOqPN2GGNB11kjHPkH_S32KSUN_jr5R8eMVncjOz8_3g@mail.gmail.com>

Hi Jeff,

Before you start LDDMM, you have to make sure the linear registration (AIR)
is very good. This is similar to non-liner fitting of a XY plot, which
always requires you to do linear fitting first to get a good initial
estimate of the non-linear fitting parameters.

There are cases when AIR fails often due to high intensity inside or outside
the brains of patients. In this case, changing the contrast, as you did
could be one solution. You can't change the contrast ad hoc for LDDMM but
for linear transformation, it is just an initialization. So, all you want to
do is to bring the two brains as close as possible. So, it's ok to use
different approach for different data. What we often do is, 1) try mutual
information,  2) use landmarks, or 3) do skull strip.

Most important things is, to make sure that the linear transformation is
good. Be careful about the angle of the brain and the brainstem. The
sagittal rotation is one of the most difficult parameters, while X, Y, Z
translation and coronal / axial rotation is usually easy to register. If the
sagittal angle is not satisfactory, you should try different approaches.

Also, we recently start to use 9-mode affine (no shearing) very often, which
is now available in the latest DiffeoMap.

Susumu

On Thu, Sep 8, 2011 at 7:59 PM, Jeff Sadino <jsadino.queens at gmail.com>wrote:

> Hello again DTI Experts,
>
> I have a group of patients that have suffered trauma to the head that I am
> putting through the LDDMM pipeline.  A problem I ran across during AIR in
> DiffeoMap is that since the trauma is causing a hematoma in the B0 image,
> the registration is very poor.  On one subject, I performed DiffeoMap AIR
> using the Mean DWI image and the registration came out pretty good.  I am
> wondering if this is a valid approach to perform AIR registration.
>
> For the LDDMM registration, usually I use the FA and the Trace image to
> drive the Kimap.  However, I think I will get the same poor results.  Should
> I use just the DWI image to drive the LDDMM registration?  There would be no
> need to do "Intensity Normalization" on the DWI image, correct?
>
> Thank you very much,
> Jeff Sadino
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From jsadino.queens at gmail.com  Thu Sep  8 23:02:30 2011
From: jsadino.queens at gmail.com (Jeff Sadino)
Date: Thu, 08 Sep 2011 17:02:30 -1000
Subject: [Mristudio-users] LDDMM for Hematoma
In-Reply-To: <CAEq9apLOqPN2GGNB11kjHPkH_S32KSUN_jr5R8eMVncjOz8_3g@mail.gmail.com>
References: <CAAK1NkfvbPZto-kY7Jp86ioKarfeze8AFWALaHPhOGcXbBGrhw@mail.gmail.com>
	<CAEq9apLOqPN2GGNB11kjHPkH_S32KSUN_jr5R8eMVncjOz8_3g@mail.gmail.com>
Message-ID: <CAAK1Nkc87h-R3+ADySPnV85Wq+prOby5s42w_H792KMLkQL02g@mail.gmail.com>

Hi Dr. Mori,

Thank you for your quick and detailed reply.  It is good to know I am on the
right track by using the DWI image.  I am confused by this line: "You can't
change the contrast ad hoc for LDDMM."  Does this mean that I can only use
the B0, Trace, and FA images whenever I do the LDDMM registration?  I
skullstripped both the template and subject DWI images.  My thinking was to
use the skullstripped DWI images to drive the linear transformation, and
then (assuming a good AIR registration) use the linearly-registered subject
DWI image and the template DWI image to get a Kimap file that I could apply
to the rest of the linearly-registered subject images.  I would do this for
this entire cohort of 17 subjects.

Or am I to read your response to mean that I should only do a linear
registration on the subjects and then stop there without doing an LDDMM
transformation?  Or do I use the DWI image for the AIR, and then use the FA
and Trace for the LDDMM?  Some of the subjects have hematomas in about
10-15% of the brain, so it is a significant region.

Thank you very much!
Jeff

On Thu, Sep 8, 2011 at 3:33 PM, susumu mori <susumu at mri.jhu.edu> wrote:

> Hi Jeff,
>
> Before you start LDDMM, you have to make sure the linear registration (AIR)
> is very good. This is similar to non-liner fitting of a XY plot, which
> always requires you to do linear fitting first to get a good initial
> estimate of the non-linear fitting parameters.
>
> There are cases when AIR fails often due to high intensity inside or
> outside the brains of patients. In this case, changing the contrast, as you
> did could be one solution. You can't change the contrast ad hoc for LDDMM
> but for linear transformation, it is just an initialization. So, all you
> want to do is to bring the two brains as close as possible. So, it's ok to
> use different approach for different data. What we often do is, 1) try
> mutual information,  2) use landmarks, or 3) do skull strip.
>
> Most important things is, to make sure that the linear transformation is
> good. Be careful about the angle of the brain and the brainstem. The
> sagittal rotation is one of the most difficult parameters, while X, Y, Z
> translation and coronal / axial rotation is usually easy to register. If the
> sagittal angle is not satisfactory, you should try different approaches.
>
> Also, we recently start to use 9-mode affine (no shearing) very often,
> which is now available in the latest DiffeoMap.
>
> Susumu
>
> On Thu, Sep 8, 2011 at 7:59 PM, Jeff Sadino <jsadino.queens at gmail.com>wrote:
>
>> Hello again DTI Experts,
>>
>> I have a group of patients that have suffered trauma to the head that I am
>> putting through the LDDMM pipeline.  A problem I ran across during AIR in
>> DiffeoMap is that since the trauma is causing a hematoma in the B0 image,
>> the registration is very poor.  On one subject, I performed DiffeoMap AIR
>> using the Mean DWI image and the registration came out pretty good.  I am
>> wondering if this is a valid approach to perform AIR registration.
>>
>> For the LDDMM registration, usually I use the FA and the Trace image to
>> drive the Kimap.  However, I think I will get the same poor results.  Should
>> I use just the DWI image to drive the LDDMM registration?  There would be no
>> need to do "Intensity Normalization" on the DWI image, correct?
>>
>> Thank you very much,
>> Jeff Sadino
>>
>> _______________________________________________
>> mristudio-users mailing 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
>
>
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From sharmaatul11 at gmail.com  Fri Sep  9 03:19:35 2011
From: sharmaatul11 at gmail.com (Atul Kumar)
Date: Fri, 09 Sep 2011 00:19:35 -0700
Subject: [Mristudio-users] DTI analysis with Bruker image
Message-ID: <CAGPgYL7TW5kKCm7zeLM=QTb-kuDbKw_N3C4LzM=oYQ7a7gYhNA@mail.gmail.com>

Hi there,

I am very new to DTI area. I am trying to use Burker's  image for DTI
analysis. I am not able to do DTI mapping  and onwards ( just following the
documentation for DTI studio).

Please suggest me the best way to use Bruker's image for DTI analysis in DTI
studio.

Currently I  have tried '2dseq' images and dicom images created from Bruker.

Any help will be highly appreciated.

Regards,
Atul
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From chengfb04 at mails.jlu.edu.cn  Sat Sep 10 09:45:43 2011
From: chengfb04 at mails.jlu.edu.cn (chengfb04)
Date: Sat, 10 Sep 2011 21:45:43 +0800 (CST)
Subject: [Mristudio-users] Gradient Table for GE system
In-Reply-To: <CAEq9apLOqPN2GGNB11kjHPkH_S32KSUN_jr5R8eMVncjOz8_3g@mail.gmail.com>
References: <CAEq9apLOqPN2GGNB11kjHPkH_S32KSUN_jr5R8eMVncjOz8_3g@mail.gmail.com>
	<CAAK1NkfvbPZto-kY7Jp86ioKarfeze8AFWALaHPhOGcXbBGrhw@mail.gmail.com>
Message-ID: <3a4640fb.1164c.13253962ede.Coremail.chengfb04@mails.jlu.edu.cn>

Hi friends
 
Can you sent me a copy of Gradient Table for 15 directions in GE system?
Thank you very much!
Best wishes!
 
Fu Bo Cheng
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From buchmann2 at wisc.edu  Mon Aug 15 18:51:28 2011
From: buchmann2 at wisc.edu (Andreas Buchmann)
Date: Mon, 15 Aug 2011 22:51:28 -0000
Subject: [Mristudio-users] ADC-Map Calculation in DTIStudio
In-Reply-To: <047F400A-E034-4A38-9D60-795FF8F5B758@gmail.com>
Message-ID: <0LPZ00KA6RHP0Z30@smtpauth1.wiscmail.wisc.edu>

Dear Judy/ Rachael,

 

ADC is 'apparent diffusion coefficient'. It is defined for the three
coordinate directions, x,y,z (the space in which the subject was in the
scanner).

 

Note that mean ADC and mean diffusivity is not the same (at least if you
look at the definition). For mean diffusivity, the eigenvalues have to be
estimated from the tensors. In DTI Studio, you can get the 'trace
diffusivity' which equals 3 times the mean diffusivity.

 

 

Best

Andreas

 

  _____  

From: mristudio-users-bounces at mristudio.org
[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Rachael Gonzales
Sent: Montag, 15. August 2011 16:32
To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
Subject: [Mristudio-users] ADC-Map Calculation in DTIStudio

 

Hi DTI experts,

 

In DTIStudio, under the DTI map tab there is an ADC Map calculation
available.  After the calculation, an ADC map - mean image is generated, is
this the apparent or average diffusion coefficient?  

 

 

Thanks,

 

Rachael

 

 

****************************************************************************
*************************************************

 

Judy, in DtiStudio, ADC (or also called MD) should be obtained from "Trace".

Trace is defined as Dxx+Dyy+Dzz. If you divide it by 3, it becomes
"Average diffusion constant (ADC)" or "Mean diffusivity (MD)". We like
to use the term "trace" because it has clear mathematical definition
while ADC is also used for "Apparent diffusion constant", which has a
different meaning from "average diffusion constant".

On Mon, Apr 11, 2011 at 11:58 AM, Judy James <jjames2 at umc.edu> wrote:



Is any one in this group aware of how to calculate ADC maps from the

original DWI images in DTI studio - not DTI images, like how to set the

gradient table in such a case?

Any input/help will be highly appreciated.

 

Thank you,

Judy James "

 

 

 

*********************************************************************

Judy Rose James, Ph.D.

Clinical Physicist, MR Imaging Division

Assistant Professor, Department of Radiology

University of Mississippi Medical Center

Jackson, MS - 39216

Ph: (601) 984-2585; Pager: (601) 929-2442

Email: jjames2 at umc.edu

*********************************************************************

 

 

________________________________

From: mristudio-users-bounces at mristudio.org

[mristudio-users-bounces at mristudio.org] On Behalf Of Jacquie Hodge

[Jacquie.Hodge at albertahealthservices.ca]

Sent: Friday, April 08, 2011 11:56 AM

To: mristudio-users at mristudio.org

Subject: [Mristudio-users] Fa values

 

Good morning everyone,

 

I am using DTI studio for my project where I am interested in comparing the

left and right CST's in children who have suffereed injury in that area and

after reading many studies on DTI decided to compare average FA values of

the tracts as one of my variables. However, I have come across this questino

from one of my supervisors and cannot really answer it and am hoping for

your help/expertise.

Here is goes:

Is the FA value still a viable measure to look at and use to make a

correlation if you are using FA values to pull the white matter tract? It

seems like if the tract is made from FA values then you should not be able

to use the FA as an outcome variable. This question has come up as I

presented my research idea and I'm not sure how to answer it. Most studies

that use DTI use FA thresholds to pull the tracts and then also the FA

values (eg. mean FA) to make comparisons between the tracts.

 

I really hope that my question makes sense as I have found it very hard to

word properly.

 

Thank you very much,

Jacquie

 

Jacquie Hodge MSc candidate in Neuroscience, BSc

Neuroscience, University of Calgary

Research Assistant, Calgary Pediatric Stroke Program

Alberta Children's Hospital

2888 Shaganappi Trail NW, Calgary, AB, Canada T3B 6A8

Phone: 403-955-7733 Fax: 403-955-2922

jacquie.hodge at albertahealthservices.ca

Program website:

http://www.calgaryhealthregion.ca/programs/stroke/pediatric.htm

________________________________

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unauthorized review, use, retransmission, or other disclosure is strictly

prohibited. If you have received this message in error, please notify the

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On Feb 23, 2011, at 4:35 AM, susumu mori wrote:





Andreas is right.

So called ADC (average diffusion constant, apparent diffusion constant) and
MD (mean diffusivity) are obtained by trace/3 (trace divided by 3), while
the trace is (eigenvalue0+eigenvalue1+eigenvalue2).

 

also, axial diffusivity is same as eigenvalue0 and radial diffusivity is the
average of eigenvalue1 and 2 [ (eigenvalue1+eigenvalue2)/2].

On Wed, Feb 23, 2011 at 8:31 AM, Andreas Buchmann <buchmann2 at wisc.edu>
wrote:

Dear Yo,

I'm using trace diffusivity, which is strongly related to mean diffusivity
(I think, just multiplied with a constant factor, experts correct me if I'm
wrong).

Andreas




-----Original Message-----
From: mristudio-users-bounces at mristudio.org
[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of

107310 at ib.k.u-tokyo.ac.jp
Sent: Dienstag, 22. Februar 2011 19:36
To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
Subject: Re: [Mristudio-users] radial diffusivity, mean diffusivity

Dear Andreas, Ryuzo and DTI experts


I also try to calculate mean diffusivity.
But in DTI studio, only the radial diffusivity and ADCs can calculate at
the 'Image'-tab with ROI.

Is there any function to measure mean diffusivity?
Please give me any suggestion.

Many thanks.


YO


> Dear Andreas
>
>
>
> Thank you very much for your suggestion.  I will try.
>
>
>
> Ryuzo
>
>
>
> From: mristudio-users-bounces at mristudio.org
> [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Andreas
Buchmann
> Sent: Monday, February 21, 2011 11:03 PM
> To: 'DTI Studio, ROI Editor, DiffeoMap Questions/Support'
> Subject: Re: [Mristudio-users] radial diffusivity, mean diffusivity
>
>
>
> Dear Ryuzo,
>
>
>
> yes, you're on the right track with (1). After the estimation, DTI-
Studio
> appends the images to the list of images you have, and you can see
them
> under the 'Image'-tab and save them with right-click on the image.
>
>
>
> Good luck
>
> Andreas
>
>
>
>   _____
>
> From: mristudio-users-bounces at mristudio.org
> [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of hanaie
> Sent: Montag, 21. Februar 2011 07:46
> To: mristudio-users at mristudio.org
> Subject: [Mristudio-users] radial diffusivity, mean diffusivity
>
>
>
> Dear DTI experts
>
>
>
> How can I do to obtain the radial diffusivity and mean diffusivity in
DTI
> studio?
>
>
>
> 1.     In the " Dti Map" tab, clicking "Tensor, color Map etc" button,
and
> checking the checkboxes "Radial", "Trace"
>
>
>
> 2.     After tensor calculation and fiber tracking, if I click "
statistics"
> button in the "Fiber" tab and
>
>  I choose the each image and click "go" button in the another window,
can I
> obtain radial and mean diffusivity?
>
>
>
>
>
> Please give me any suggestion.
>
>
>
> Many thanks.
>
>
>
> Ryuzo
>
>
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to: mristudio-users-unsubscribe@
mristudio.org <http://mristudio.org/> 
>


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From jhaldar at usc.edu  Tue Aug 23 10:50:10 2011
From: jhaldar at usc.edu (Justin Haldar)
Date: Tue, 23 Aug 2011 14:50:10 -0000
Subject: [Mristudio-users] Siemens Mosaic Dicom question
Message-ID: <000c01cc61a3$e1439d10$a3cad730$@usc.edu>

Hi all,

I was recently given a collection of DW datasets from a Siemens scanner
(acquired with the product diffusion spin-echo EPI sequence) in Siemens
mosaic Dicom format.  I've been able to extract information like the
b-value, orientation, and b-matrix from the Dicom header.  However, I was
also hoping to get more detailed information about the diffusion timing
parameters (i.e., little delta and big delta).  Does anyone know if there is
a way to access these parameters from the Dicom header?

Thanks!

-- 
Justin



From adshereen at gmail.com  Sat Sep 10 08:48:30 2011
From: adshereen at gmail.com (Duke Shereen)
Date: Sat, 10 Sep 2011 08:48:30 -0400
Subject: [Mristudio-users] DTI analysis with Bruker image
In-Reply-To: <3ff196c7480744758fa544c6aa985ea1@SN2PRD0102HT028.prod.exchangelabs.com>
References: <3ff196c7480744758fa544c6aa985ea1@SN2PRD0102HT028.prod.exchangelabs.com>
Message-ID: <CAMiW9g89_rEa+c93FiRYmAbfNXFBJ4DkvCxb8rCuL+zh9KGEjQ@mail.gmail.com>

Hi Atul,

Try using the 2dseq's but first click on "Philips REC" under the "DTI
Calculation:  select file type" window.  Apparently, Philips REC is
the same as Bruker's 2dseq.

Good luck,
Duke

On Fri, Sep 9, 2011 at 3:19 AM, Atul Kumar <sharmaatul11 at gmail.com> wrote:
> Hi there,
> I am very new to DTI area. I am trying to use Burker's ?image for DTI
> analysis. I am not able to do DTI mapping ?and onwards ( just following the
> documentation for DTI studio).
> Please suggest me the best way to use Bruker's image for DTI analysis in DTI
> studio.
> Currently I ?have tried '2dseq' images and dicom images created from Bruker.
> Any help will be highly appreciated.
> Regards,
> Atul
>
>
>


From sharmaatul11 at gmail.com  Sat Sep 10 17:12:24 2011
From: sharmaatul11 at gmail.com (Atul Kumar)
Date: Sat, 10 Sep 2011 14:12:24 -0700
Subject: [Mristudio-users] DTI analysis with Bruker image
In-Reply-To: <CAMiW9g89_rEa+c93FiRYmAbfNXFBJ4DkvCxb8rCuL+zh9KGEjQ@mail.gmail.com>
References: <3ff196c7480744758fa544c6aa985ea1@SN2PRD0102HT028.prod.exchangelabs.com>
	<CAMiW9g89_rEa+c93FiRYmAbfNXFBJ4DkvCxb8rCuL+zh9KGEjQ@mail.gmail.com>
Message-ID: <CAGPgYL5GorwDo8xCcmgcw+uF0QYEtfrMHVqgOW61y4q2Os+pyg@mail.gmail.com>

Thank you so much.

Regards,
Atul

On Sat, Sep 10, 2011 at 5:48 AM, Duke Shereen <adshereen at gmail.com> wrote:

> Hi Atul,
>
> Try using the 2dseq's but first click on "Philips REC" under the "DTI
> Calculation:  select file type" window.  Apparently, Philips REC is
> the same as Bruker's 2dseq.
>
> Good luck,
> Duke
>
> On Fri, Sep 9, 2011 at 3:19 AM, Atul Kumar <sharmaatul11 at gmail.com> wrote:
> > Hi there,
> > I am very new to DTI area. I am trying to use Burker's  image for DTI
> > analysis. I am not able to do DTI mapping  and onwards ( just following
> the
> > documentation for DTI studio).
> > Please suggest me the best way to use Bruker's image for DTI analysis in
> DTI
> > studio.
> > Currently I  have tried '2dseq' images and dicom images created from
> Bruker.
> > Any help will be highly appreciated.
> > Regards,
> > Atul
> >
> >
> >
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
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From susumu at mri.jhu.edu  Mon Sep 12 13:23:51 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Mon, 12 Sep 2011 13:23:51 -0400
Subject: [Mristudio-users] LDDMM for Hematoma
In-Reply-To: <CAAK1Nkc87h-R3+ADySPnV85Wq+prOby5s42w_H792KMLkQL02g@mail.gmail.com>
References: <CAAK1NkfvbPZto-kY7Jp86ioKarfeze8AFWALaHPhOGcXbBGrhw@mail.gmail.com>
	<CAEq9apLOqPN2GGNB11kjHPkH_S32KSUN_jr5R8eMVncjOz8_3g@mail.gmail.com>
	<CAAK1Nkc87h-R3+ADySPnV85Wq+prOby5s42w_H792KMLkQL02g@mail.gmail.com>
Message-ID: <CAEq9apLRHDwCBML2Lf26C5TdM7qZHosuKsN23Nzmunv_BPZk_w@mail.gmail.com>

Hi Jeff,

Here is what I meant;

Suppose you have 10 images to normalize and there is 1 image failed to
linearly normalize. Also suppose you used b0 images for linear normalization
but it somehow didn't work well for the failed one. Then, it's ok to try
skull strip, mutual information, or use dwi for re-process the failed one,
because the linear normalization is just for the initialization.

On the other hand, for LDDMM, if you decide to use FA/trace, you need to use
the same contrasts for all 10 images and it's not good idea to change the
contrasts such as FA/b0, trace/b0, etc.

Susumu

On Thu, Sep 8, 2011 at 11:02 PM, Jeff Sadino <jsadino.queens at gmail.com>wrote:

> Hi Dr. Mori,
>
> Thank you for your quick and detailed reply.  It is good to know I am on
> the right track by using the DWI image.  I am confused by this line: "You
> can't change the contrast ad hoc for LDDMM."  Does this mean that I can only
> use the B0, Trace, and FA images whenever I do the LDDMM registration?  I
> skullstripped both the template and subject DWI images.  My thinking was to
> use the skullstripped DWI images to drive the linear transformation, and
> then (assuming a good AIR registration) use the linearly-registered subject
> DWI image and the template DWI image to get a Kimap file that I could apply
> to the rest of the linearly-registered subject images.  I would do this for
> this entire cohort of 17 subjects.
>
> Or am I to read your response to mean that I should only do a linear
> registration on the subjects and then stop there without doing an LDDMM
> transformation?  Or do I use the DWI image for the AIR, and then use the FA
> and Trace for the LDDMM?  Some of the subjects have hematomas in about
> 10-15% of the brain, so it is a significant region.
>
> Thank you very much!
> Jeff
>
> On Thu, Sep 8, 2011 at 3:33 PM, susumu mori <susumu at mri.jhu.edu> wrote:
>
>> Hi Jeff,
>>
>> Before you start LDDMM, you have to make sure the linear registration
>> (AIR) is very good. This is similar to non-liner fitting of a XY plot, which
>> always requires you to do linear fitting first to get a good initial
>> estimate of the non-linear fitting parameters.
>>
>> There are cases when AIR fails often due to high intensity inside or
>> outside the brains of patients. In this case, changing the contrast, as you
>> did could be one solution. You can't change the contrast ad hoc for LDDMM
>> but for linear transformation, it is just an initialization. So, all you
>> want to do is to bring the two brains as close as possible. So, it's ok to
>> use different approach for different data. What we often do is, 1) try
>> mutual information,  2) use landmarks, or 3) do skull strip.
>>
>> Most important things is, to make sure that the linear transformation is
>> good. Be careful about the angle of the brain and the brainstem. The
>> sagittal rotation is one of the most difficult parameters, while X, Y, Z
>> translation and coronal / axial rotation is usually easy to register. If the
>> sagittal angle is not satisfactory, you should try different approaches.
>>
>> Also, we recently start to use 9-mode affine (no shearing) very often,
>> which is now available in the latest DiffeoMap.
>>
>> Susumu
>>
>> On Thu, Sep 8, 2011 at 7:59 PM, Jeff Sadino <jsadino.queens at gmail.com>wrote:
>>
>>> Hello again DTI Experts,
>>>
>>> I have a group of patients that have suffered trauma to the head that I
>>> am putting through the LDDMM pipeline.  A problem I ran across during AIR in
>>> DiffeoMap is that since the trauma is causing a hematoma in the B0 image,
>>> the registration is very poor.  On one subject, I performed DiffeoMap AIR
>>> using the Mean DWI image and the registration came out pretty good.  I am
>>> wondering if this is a valid approach to perform AIR registration.
>>>
>>> For the LDDMM registration, usually I use the FA and the Trace image to
>>> drive the Kimap.  However, I think I will get the same poor results.  Should
>>> I use just the DWI image to drive the LDDMM registration?  There would be no
>>> need to do "Intensity Normalization" on the DWI image, correct?
>>>
>>> Thank you very much,
>>> Jeff Sadino
>>>
>>> _______________________________________________
>>> mristudio-users mailing 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:
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>
>
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From rajagov2 at ccf.org  Mon Sep 12 13:34:49 2011
From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran)
Date: Mon, 12 Sep 2011 13:34:49 -0400
Subject: [Mristudio-users] Number of fibers
Message-ID: <77A88E90A851594AAEF830450587C39D04183692@CCHSCLEXMB56.cc.ad.cchs.net>

Dear All,
 
After fiber tracking when I try to see statistics of FA along the fiber I could see in the stats file number of fibers in each slice. I am wondering what this number of fibers mean physiologically and how is this number of fibers calculated is it the number of the streamlines in a voxels.
 
Thanks in advance
Venkat

===================================

 Please consider the environment before printing this e-mail

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From susumu at mri.jhu.edu  Mon Sep 12 13:53:30 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Mon, 12 Sep 2011 13:53:30 -0400
Subject: [Mristudio-users] Number of fibers
In-Reply-To: <77A88E90A851594AAEF830450587C39D04183692@CCHSCLEXMB56.cc.ad.cchs.net>
References: <77A88E90A851594AAEF830450587C39D04183692@CCHSCLEXMB56.cc.ad.cchs.net>
Message-ID: <CAEq9apL0NtpUxpqW_GFjGPQ1LGCSR_GRGxq1NWJcBiu-6T7u4w@mail.gmail.com>

Hi Vankat,

This is one of the questions asked several times in the past. If you search
the Mailing List archive (
http://lists.mristudio.org/pipermail/mristudio-users/) with "number of
fibers" (using ctrl-f), you can find some past communications. My typical
reply is;

The number of the fiber itself doesn't carry anatomical meaning. In
DtiStudio, we use the exhaustive approach, meaning fiber tracking is
initiated from the center of all pixels above the threshold. If the number
of the seed points is increased, the number of the fibers increases too. So,
it is parameter-dependent. You may be able to compare the numbers between
subjects but it may simply reflect the size of the tracts, which can be also
obtained from the number of pixels. The number of pixels is also reported in
DtiStudio and has a physical dimension, which may be easier to use.

As you can imagine, it is not possible to link "the number of fibers" to the
real axonal fibers.
My lab doesn't use this metric.

Susumu


On Mon, Sep 12, 2011 at 1:34 PM, Rajagopalan, Venkateswaran <
rajagov2 at ccf.org> wrote:

>  Dear All,
>
> After fiber tracking when I try to see statistics of FA along the fiber I
> could see in the stats file number of fibers in each slice. I am wondering
> what this number of fibers mean physiologically and how is this number of
> fibers calculated is it the number of the streamlines in a voxels.
>
> Thanks in advance
> Venkat
>
> ===================================
>
>  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 (2010).
> 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
>
>
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From rajagov2 at ccf.org  Mon Sep 12 15:47:47 2011
From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran)
Date: Mon, 12 Sep 2011 15:47:47 -0400
Subject: [Mristudio-users] Number of fibers
References: <77A88E90A851594AAEF830450587C39D04183692@CCHSCLEXMB56.cc.ad.cchs.net>
	<CAEq9apL0NtpUxpqW_GFjGPQ1LGCSR_GRGxq1NWJcBiu-6T7u4w@mail.gmail.com>
Message-ID: <77A88E90A851594AAEF830450587C39D04183694@CCHSCLEXMB56.cc.ad.cchs.net>

Thanks very much Dr.Susumu, I am not able to understand this part sorry "If the number of the seed points is increased, the number of the fibers increases too. So,
it is parameter-dependent." 
 
Can you please throw more light on this I am not able to understand the following; according to my understanding DTI studio starts tracking from all voxels above the threshold say FA=0.2, bending angle =41 (which i set) after tracking from all voxels it will give me fibers running between the two ROIS which I choose in order to reconstruct CST or other tracts, so by seed points does it mean the size of these ROIs which I draw or something different, suppose if I keep the ROI size same in two conditions (two time points of scan in the same subject) then can number of fibers will make sense .
 
Thanks for your time.
 
Venkat

________________________________

From: mristudio-users-bounces at mristudio.org on behalf of susumu mori
Sent: Mon 9/12/2011 1:53 PM
To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
Subject: Re: [Mristudio-users] Number of fibers


Hi Vankat, 

This is one of the questions asked several times in the past. If you search the Mailing List archive (http://lists.mristudio.org/pipermail/mristudio-users/) with "number of fibers" (using ctrl-f), you can find some past communications. My typical reply is;

The number of the fiber itself doesn't carry anatomical meaning. In
DtiStudio, we use the exhaustive approach, meaning fiber tracking is
initiated from the center of all pixels above the threshold. If the number
of the seed points is increased, the number of the fibers increases too. So,
it is parameter-dependent. You may be able to compare the numbers between
subjects but it may simply reflect the size of the tracts, which can be also
obtained from the number of pixels. The number of pixels is also reported in
DtiStudio and has a physical dimension, which may be easier to use.
As you can imagine, it is not possible to link "the number of fibers" to the real axonal fibers. 
My lab doesn't use this metric.

Susumu


On Mon, Sep 12, 2011 at 1:34 PM, Rajagopalan, Venkateswaran <rajagov2 at ccf.org> wrote:


	Dear All,
	 
	After fiber tracking when I try to see statistics of FA along the fiber I could see in the stats file number of fibers in each slice. I am wondering what this number of fibers mean physiologically and how is this number of fibers calculated is it the number of the streamlines in a voxels.
	 
	Thanks in advance
	Venkat

	

	===================================

	 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 (2010).  
	Visit us online at http://www.clevelandclinic.org <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
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	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.

	


	_______________________________________________
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	http://lists.mristudio.org/mailman/listinfo/
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===================================

 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 (2010).  
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.
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From susumu at mri.jhu.edu  Mon Sep 12 18:06:14 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Mon, 12 Sep 2011 18:06:14 -0400
Subject: [Mristudio-users] Number of fibers
In-Reply-To: <77A88E90A851594AAEF830450587C39D04183694@CCHSCLEXMB56.cc.ad.cchs.net>
References: <77A88E90A851594AAEF830450587C39D04183692@CCHSCLEXMB56.cc.ad.cchs.net>
	<CAEq9apL0NtpUxpqW_GFjGPQ1LGCSR_GRGxq1NWJcBiu-6T7u4w@mail.gmail.com>
	<77A88E90A851594AAEF830450587C39D04183694@CCHSCLEXMB56.cc.ad.cchs.net>
Message-ID: <CAEq9apLO0GFDDjhH9N1HGcJ=W_rNTb=9mtZ78ery24yLr+DDtA@mail.gmail.com>

In the current implementation of DtiStudio, tracking starts from the center
of all voxels, but it is just a procedural division. As a matter of fact,
there are programs out there, in which you can control the number of seeds
per voxel, like 10 seeds randomly distributed inside a voxel. Then you may
get 10 more fibers that penetrate your ROIs.

Does it make sense?

On Mon, Sep 12, 2011 at 3:47 PM, Rajagopalan, Venkateswaran <
rajagov2 at ccf.org> wrote:

> Thanks very much Dr.Susumu, I am not able to understand this part sorry "If
> the number of the seed points is increased, the number of the fibers
> increases too. So,
> it is parameter-dependent."
>
> Can you please throw more light on this I am not able to understand the
> following; according to my understanding DTI studio starts tracking from all
> voxels above the threshold say FA=0.2, bending angle =41 (which i set) after
> tracking from all voxels it will give me fibers running between the two ROIS
> which I choose in order to reconstruct CST or other tracts, so by seed
> points does it mean the size of these ROIs which I draw or something
> different, suppose if I keep the ROI size same in two conditions (two time
> points of scan in the same subject) then can number of fibers will make
> sense .
>
> Thanks for your time.
>
> Venkat
>
> ________________________________
>
> From: mristudio-users-bounces at mristudio.org on behalf of susumu mori
> Sent: Mon 9/12/2011 1:53 PM
> To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
> Subject: Re: [Mristudio-users] Number of fibers
>
>
> Hi Vankat,
>
> This is one of the questions asked several times in the past. If you search
> the Mailing List archive (
> http://lists.mristudio.org/pipermail/mristudio-users/) with "number of
> fibers" (using ctrl-f), you can find some past communications. My typical
> reply is;
>
> The number of the fiber itself doesn't carry anatomical meaning. In
> DtiStudio, we use the exhaustive approach, meaning fiber tracking is
> initiated from the center of all pixels above the threshold. If the number
> of the seed points is increased, the number of the fibers increases too.
> So,
> it is parameter-dependent. You may be able to compare the numbers between
> subjects but it may simply reflect the size of the tracts, which can be
> also
> obtained from the number of pixels. The number of pixels is also reported
> in
> DtiStudio and has a physical dimension, which may be easier to use.
> As you can imagine, it is not possible to link "the number of fibers" to
> the real axonal fibers.
> My lab doesn't use this metric.
>
> Susumu
>
>
> On Mon, Sep 12, 2011 at 1:34 PM, Rajagopalan, Venkateswaran <
> rajagov2 at ccf.org> wrote:
>
>
>        Dear All,
>
>        After fiber tracking when I try to see statistics of FA along the
> fiber I could see in the stats file number of fibers in each slice. I am
> wondering what this number of fibers mean physiologically and how is this
> number of fibers calculated is it the number of the streamlines in a voxels.
>
>        Thanks in advance
>        Venkat
>
>
>
>        ===================================
>
>         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 (2010).
>         Visit us online at http://www.clevelandclinic.org <
> 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
>
>
>
>
>
> ===================================
>
>  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 (2010).
> 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
>
>
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From pkuclosed at gmail.com  Thu Sep 15 20:59:24 2011
From: pkuclosed at gmail.com (Chuyang Ye)
Date: Thu, 15 Sep 2011 20:59:24 -0400
Subject: [Mristudio-users] Visualizing Fibers in DTISTUDIO
Message-ID: <CAO_fy-MFmhfooye0kt63UmCN8kb=Lt4yF_W7dGJhm5UtDON+tQ@mail.gmail.com>

Dear All,

I am wondering if it is possible to color each point along a fiber
differently instead of using one color for a fiber in DTI Studio. For
instance, for a fiber f consisting points x_1,x_2,...,x_n, is this possible
to give each x_i a color so that the resulting fiber look "colorful"?

Thank you,
Chuyang
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From choisj70 at gmail.com  Fri Sep 23 11:14:52 2011
From: choisj70 at gmail.com (Seongjin)
Date: Fri, 23 Sep 2011 11:14:52 -0400
Subject: [Mristudio-users] To Developers
Message-ID: <CANM4YeV_BCi9KCF-aAoGESJrq726qHOBXQP1SzqUY-B80u0UOQ@mail.gmail.com>

Dear DTI studio developers,


I appreciate your efforts on developing your wonderful tools for us in MR
research field.

I have one request to you.

After processing images in DTI studio, I use ROI editor for ROI-based
analysis.

Occasionally, I need to see some information, e.g. Information on the image.
However to get the image info, I need to run DTI studio.

In DTI studio, in any image plane, there are couple of options are
available, such as Image level adjusting, Save this image as, copy,
Information on the image, Plain-Image view, and more.

In ROI editor, the options are only three: Image level adjusting, Save this
image as, and copy.

It might be very useful if we have the same options in ROI editor.

In addition, Plain-Image view will be a very handy function to add to ROI
editor to view 3D ROI drawn in a series of images at a glance.


All of the best,
SC
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From joeh at cis.jhu.edu  Tue Sep 27 12:29:51 2011
From: joeh at cis.jhu.edu (joeh at cis.jhu.edu)
Date: Tue, 27 Sep 2011 12:29:51 -0400 (EDT)
Subject: [Mristudio-users] Computational Anatomy Works (CAWorks) - LDDMM
 Region of Interest Processing
In-Reply-To: <41982.192.168.3.48.1317140413.squirrel@webmail.cis.jhu.edu>
References: <41982.192.168.3.48.1317140413.squirrel@webmail.cis.jhu.edu>
Message-ID: <42089.192.168.3.48.1317140991.squirrel@webmail.cis.jhu.edu>

There is a new version of CAWorks 381 b45 for linux
built using the cde version from 8/15/11 and having a
slightly modified run script.

caworks-package-381-b45-v2-32-bit-ubuntu-cde.tar.gz
caworks-package-381-b45-v2-64-bit-ubuntu-cde.tar.gz

The 32 bit version has been tested on 32 bit versions of
 Ubuntu 10.04, Ubuntu 11.04, and CentOS 6

and the 64 bit version has been tested on 64 bit versions of
 Ubuntu 10.04, Ubuntu 11.04, and CentOS 6

-Joseph Hennessey Ph.D.


> Computational Anatomy Works (CAWorks) Software Announcement
>
> CAWorks is available through mristudio.org under:
>
>    https://www.mristudio.org/download/binaries/caworks/
>
> The software application Computational Anatomy Works (CAWorks) was
> developed to support Computational Anatomy and shape analysis. The
> capabilities of CAWorks include:
>
>    1. Interactive landmark placement to create segmentation (mask) of
> desired region of interest
>
>    2. Specialized landmark placement plugins for subcortical structures
> such as hippocampus and amygdala
>
>    3. Support for multiple Medical Imaging data formats, such as Nifti,
> Analyze, Freesurfer, DICOM and landmark data
>
>    4. Quadra Planar view visualization
>
>    5. Shape Analysis plugin modules, such as Large Deformation
> Diffeomorphic Metric Mapping (LDDMM)
>
> Current enhancements to CAWorks have focused on interactive support for
> landmarking of subcortical structures. Specific plugins are available for
> landmark placement of the hippocampus, amygdala and entorhinal cortex
> regions. After landmarking is completed, CAWorks facilitates submission
> for automated segmentation processing. CAWorks is being used by the
> Biomarkers for Older Controls At Risk for Dementia (BIOCARD), Resource for
> Quantitative Functional MRI: TRD4, Validation of Structural/Functional MRI
> Localization and Biomedical Informatics Research Network (BIRN) projects.
>
> CAWorks extends ParaView, an open source, multi-platform, freely available
> program for parallel, interactive, scientific visualization. An important
> visualization tool for TeraGrid researchers, its client-server
> architecture facilitates remote visualization of datasets and the
> generation of level of detail (LOD) models that maintain interactive frame
> rates for large datasets.
>
> Tutorials describing CAWorks for the ROI feature are located at:
>
>     http://caportal.cis.jhu.edu/tutorials
>
>
> If you have questions regarding this software, please put CAWorks in your
> subject line for the mristudio-users mailing list.
>
> Thanks!
> CAWorks Development Team
>
>
>
>



From chyi.mark at msa.hinet.net  Wed Sep 28 09:42:01 2011
From: chyi.mark at msa.hinet.net (=?big5?B?wcKq+Kjk?=)
Date: Wed, 28 Sep 2011 21:42:01 +0800
Subject: [Mristudio-users] DiffeoMap Remote Processing
Message-ID: <000001cc7de4$67b06250$371126f0$%mark@msa.hinet.net>

Hi there,

I submitted a job through DiffeoMap's LDDMM for remote processing today

(Sep 28) and have not yet received any emails ... could someone

tell me how long does it usually take for a job to be complete or

whether I need to resubmit?

thanks,

 

Charng-Chyi Shieh

Radiological Technologist

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From xli16 at jhmi.edu  Wed Sep 28 09:55:02 2011
From: xli16 at jhmi.edu (Xin Li)
Date: Wed, 28 Sep 2011 09:55:02 -0400
Subject: [Mristudio-users] DiffeoMap Remote Processing
In-Reply-To: <000001cc7de4$67b06250$371126f0$%mark@msa.hinet.net>
References: <000001cc7de4$67b06250$371126f0$%mark@msa.hinet.net>
Message-ID: <71a0fa40b934.4e82eef6@johnshopkins.edu>

Hello,

Is the email address you submitted the one you registered at mristudio website?

You may check the block filter in your email box. Sometimes emails sent by the server will be blocked.


Xin

----- Original Message -----
From: ??? <chyi.mark at msa.hinet.net>
Date: Wednesday, September 28, 2011 9:42 am
Subject: [Mristudio-users] DiffeoMap Remote Processing
To: mristudio-users at mristudio.org


> Hi there,
>  
>  I submitted a job through DiffeoMap's LDDMM for remote processing today
>  
>  (Sep 28) and have not yet received any emails ... could someone
>  
>  tell me how long does it usually take for a job to be complete or
>  
>  whether I need to resubmit?
>  
>  thanks,
>  
>   
>  
>  Charng-Chyi Shieh
>  
>  Radiological Technologist
>   
> _______________________________________________
>  mristudio-users mailing list
>  mristudio-users at mristudio.org
>  
>  Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org 


From udayanbhaskar at gmail.com  Wed Sep 28 12:45:15 2011
From: udayanbhaskar at gmail.com (uday bhaskar)
Date: Wed, 28 Sep 2011 12:45:15 -0400
Subject: [Mristudio-users] Issues with Running DTI studio x64
Message-ID: <CALVL2mNdkVcvkzZ-Cm6+5N8MYM7Urkxvcxu1PoAEd-uoNu0dRA@mail.gmail.com>

Hi,

    I am a beginner and a new user of DTI studio. I am having a problem
running the DTIstudio-latest-x64. When I try to run it gives me an error
saying "The application failed to start because its
side-by-side configuration is incorrect".

 Please let me know how to overcome this. Any help is appreciated.

-- 
Thanks,
Uday.
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From chyi.mark at msa.hinet.net  Wed Sep 28 12:45:51 2011
From: chyi.mark at msa.hinet.net (Charng-Chyi Shieh)
Date: Thu, 29 Sep 2011 00:45:51 +0800
Subject: [Mristudio-users] DiffeoMap Remote Processing
In-Reply-To: <71a0fa40b934.4e82eef6@johnshopkins.edu>
References: <000001cc7de4$67b06250$371126f0$%mark@msa.hinet.net>
	<71a0fa40b934.4e82eef6@johnshopkins.edu>
Message-ID: <000001cc7dfe$15978b00$40c6a100$@msa.hinet.net>

Hi,

The email address I submitted is the one I registered at mristudio website.

And I check no emails blocked by the block filter.

Chyi

-----Original Message-----
From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Xin Li
Sent: Wednesday, September 28, 2011 9:55 PM
To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
Subject: Re: [Mristudio-users] DiffeoMap Remote Processing

Hello,

Is the email address you submitted the one you registered at mristudio website?

You may check the block filter in your email box. Sometimes emails sent by the server will be blocked.


Xin



From xli16 at jhmi.edu  Wed Sep 28 12:51:43 2011
From: xli16 at jhmi.edu (Xin Li)
Date: Wed, 28 Sep 2011 12:51:43 -0400
Subject: [Mristudio-users] Issues with Running DTI studio x64
In-Reply-To: <CALVL2mNdkVcvkzZ-Cm6+5N8MYM7Urkxvcxu1PoAEd-uoNu0dRA@mail.gmail.com>
References: <CALVL2mNdkVcvkzZ-Cm6+5N8MYM7Urkxvcxu1PoAEd-uoNu0dRA@mail.gmail.com>
Message-ID: <7220914c8ef5.4e83185f@johnshopkins.edu>

Hello,

It seems that you need to run vcredist_x64.exe on your computer first. The exe file is available at https://www.mristudio.org/wiki/installation

DtiStudio is a Microsoft Visual Studio applications. The Microsoft Visual Studio Redistribution package(vcredist_x64.exe) needs to be installed on your machine. 


Xin


----- Original Message -----
From: uday bhaskar <udayanbhaskar at gmail.com>
Date: Wednesday, September 28, 2011 12:45 pm
Subject: [Mristudio-users] Issues with Running DTI studio x64
To: mristudio-users at mristudio.org


> Hi,
>  
>      I am a beginner and a new user of DTI studio. I am having a problem
>  running the DTIstudio-latest-x64. When I try to run it gives me an error
>  saying "The application failed to start because its
>  side-by-side configuration is incorrect".
>  
>   Please let me know how to overcome this. Any help is appreciated.
>  
>  -- 
>  Thanks,
>  Uday. 
> _______________________________________________
>  mristudio-users mailing list
>  mristudio-users at mristudio.org
>  
>  Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org 

From udayanbhaskar at gmail.com  Wed Sep 28 12:57:45 2011
From: udayanbhaskar at gmail.com (uday bhaskar)
Date: Wed, 28 Sep 2011 12:57:45 -0400
Subject: [Mristudio-users] Issues with Running DTI studio x64
In-Reply-To: <7220914c8ef5.4e83185f@johnshopkins.edu>
References: <CALVL2mNdkVcvkzZ-Cm6+5N8MYM7Urkxvcxu1PoAEd-uoNu0dRA@mail.gmail.com>
	<7220914c8ef5.4e83185f@johnshopkins.edu>
Message-ID: <CALVL2mO=JX8qaVXSXUkxbzjsX811Sz-+Kr6Khv4vSDW8-nOirw@mail.gmail.com>

Thank you.

  Do you suggest some online tutorials for beginners.

-- 
Thanks,
Uday.

On Wed, Sep 28, 2011 at 12:51 PM, Xin Li <xli16 at jhmi.edu> wrote:

> Hello,
>
> It seems that you need to run vcredist_x64.exe on your computer first. The
> exe file is available at https://www.mristudio.org/wiki/installation
>
> DtiStudio is a Microsoft Visual Studio applications. The Microsoft Visual
> Studio Redistribution package(vcredist_x64.exe) needs to be installed on
> your machine.
>
>
> Xin
>
>
> ----- Original Message -----
> From: uday bhaskar <udayanbhaskar at gmail.com>
> Date: Wednesday, September 28, 2011 12:45 pm
> Subject: [Mristudio-users] Issues with Running DTI studio x64
> To: mristudio-users at mristudio.org
>
>
> > Hi,
> >
> >      I am a beginner and a new user of DTI studio. I am having a problem
> >  running the DTIstudio-latest-x64. When I try to run it gives me an error
> >  saying "The application failed to start because its
> >  side-by-side configuration is incorrect".
> >
> >   Please let me know how to overcome this. Any help is appreciated.
> >
> >  --
> >  Thanks,
> >  Uday.
> > _______________________________________________
> >  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
>
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From xli16 at jhmi.edu  Wed Sep 28 13:26:37 2011
From: xli16 at jhmi.edu (Xin Li)
Date: Wed, 28 Sep 2011 13:26:37 -0400
Subject: [Mristudio-users] Issues with Running DTI studio x64
In-Reply-To: <CALVL2mO=JX8qaVXSXUkxbzjsX811Sz-+Kr6Khv4vSDW8-nOirw@mail.gmail.com>
References: <CALVL2mNdkVcvkzZ-Cm6+5N8MYM7Urkxvcxu1PoAEd-uoNu0dRA@mail.gmail.com>
	<7220914c8ef5.4e83185f@johnshopkins.edu>
	<CALVL2mO=JX8qaVXSXUkxbzjsX811Sz-+Kr6Khv4vSDW8-nOirw@mail.gmail.com>
Message-ID: <72a0c06d9de5.4e83208d@johnshopkins.edu>

You are welcome.

The manuals and videos are at https://www.mristudio.org/wiki/user_manual


Xin

----- Original Message -----
From: uday bhaskar <udayanbhaskar at gmail.com>
Date: Wednesday, September 28, 2011 12:57 pm
Subject: Re: [Mristudio-users] Issues with Running DTI studio x64
To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" <mristudio-users at mristudio.org>


> Thank you.
>  
>    Do you suggest some online tutorials for beginners.
>  
>  -- 
>  Thanks,
>  Uday.
>  
>  On Wed, Sep 28, 2011 at 12:51 PM, Xin Li <xli16 at jhmi.edu> wrote:
>  
>  > Hello,
>  >
>  > It seems that you need to run vcredist_x64.exe on your computer 
> first. The
>  > exe file is available at 
>  >
>  > DtiStudio is a Microsoft Visual Studio applications. The Microsoft 
> Visual
>  > Studio Redistribution package(vcredist_x64.exe) needs to be 
> installed on
>  > your machine.
>  >
>  >
>  > Xin
>  >
>  >
>  > ----- Original Message -----
>  > From: uday bhaskar <udayanbhaskar at gmail.com>
>  > Date: Wednesday, September 28, 2011 12:45 pm
>  > Subject: [Mristudio-users] Issues with Running DTI studio x64
>  > To: mristudio-users at mristudio.org
>  >
>  >
>  > > Hi,
>  > >
>  > >      I am a beginner and a new user of DTI studio. I am having a 
> problem
>  > >  running the DTIstudio-latest-x64. When I try to run it gives me 
> an error
>  > >  saying "The application failed to start because its
>  > >  side-by-side configuration is incorrect".
>  > >
>  > >   Please let me know how to overcome this. Any help is appreciated.
>  > >
>  > >  --
>  > >  Thanks,
>  > >  Uday.
>  > > _______________________________________________
>  > >  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 toromed at gmail.com  Thu Sep 29 11:11:44 2011
From: toromed at gmail.com (Sue Mei Cheah)
Date: Thu, 29 Sep 2011 11:11:44 -0400
Subject: [Mristudio-users] Problem with AIR file
Message-ID: <CAKkuJNR7+QU2goUeonQEtef7XucKk8_4KGLZCDxcoyas4Y0oQA@mail.gmail.com>

Hi,

I am having a problem that seems to have been brought up last year; when I
attempt linear registration of my images in DiffeoMap, it tells me that it
"Cannot find air file" although linear registration with the air executables
correctly installed worked fine last week. I have double checked the
executables but it is still giving me that error message. I searched the
mristudio-users archive but could not find a fix for this problem. Please
advise, thank you!

Sincerely,
Sue Mei Cheah
Duke-NUS MS3
Class of 2013
toromed at gmail.com
919-348-7668
+65-93895910
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From xli16 at jhmi.edu  Thu Sep 29 11:45:52 2011
From: xli16 at jhmi.edu (Xin Li)
Date: Thu, 29 Sep 2011 11:45:52 -0400
Subject: [Mristudio-users] Problem with AIR file
In-Reply-To: <CAKkuJNR7+QU2goUeonQEtef7XucKk8_4KGLZCDxcoyas4Y0oQA@mail.gmail.com>
References: <CAKkuJNR7+QU2goUeonQEtef7XucKk8_4KGLZCDxcoyas4Y0oQA@mail.gmail.com>
Message-ID: <7260eb59107c8.4e845a70@johnshopkins.edu>

Hello, 

Are the AIR files directly in the "DiffeoMap" folder?


Xin

----- Original Message -----
From: Sue Mei Cheah <toromed at gmail.com>
Date: Thursday, September 29, 2011 11:12 am
Subject: [Mristudio-users] Problem with AIR file
To: mristudio-users at mristudio.org


> Hi,
>  
>  I am having a problem that seems to have been brought up last year; 
> when I
>  attempt linear registration of my images in DiffeoMap, it tells me 
> that it
>  "Cannot find air file" although linear registration with the air executables
>  correctly installed worked fine last week. I have double checked the
>  executables but it is still giving me that error message. I searched 
> the
>  mristudio-users archive but could not find a fix for this problem. Please
>  advise, thank you!
>  
>  Sincerely,
>  Sue Mei Cheah
>  Duke-NUS MS3
>  Class of 2013
>  toromed at gmail.com
>  919-348-7668
>  +65-93895910 
> _______________________________________________
>  mristudio-users mailing list
>  mristudio-users at mristudio.org
>  
>  Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org 

From ksupreet6 at gmail.com  Fri Sep 30 10:37:21 2011
From: ksupreet6 at gmail.com (Supreet kaur)
Date: Fri, 30 Sep 2011 10:37:21 -0400
Subject: [Mristudio-users] please help!!!
Message-ID: <CAMUw5-sg8kNYfSxczn0+kWmJ2Wjg2z7cdx0QxPmRfmGW+2xc3w@mail.gmail.com>

Hello all DTI experts,
                                       I am stuck at DTI problem as I am
progessing DTI images for Trachtography.
1) I have 17 blocks and 44 image sets, making it 748 dicom total images.
2) I need to convert those dicom files to FSL nifti format for image
processing in FSL. I did that using the MRI convert which converts my
dicom files into FSL nifti.
3) And then I transfered (copies and pasted my nifti file) into the FSL for
BET and eddy-motion correction. Everything seemed to work fine in the FSL.
4) Then I tranfered my final processed file in the windows for DTI fiber
tracking for Trachtography in DTI studio.
 Surprising I found out that my final images are only 44 images with 1 block
of image set, when I viewed them in DTI studio.
I was really disapponited that where did the rest of my images go after
processing ni FSL.

I will really appreciate your feedback and help, and I am struggling hard to
figure out this problem..


Sincerely,

Supreet kaur, BME engineer
Nationwide Childrens Hospital,
Columbus, OH
(614)355-3509
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From kajal5888 at yahoo.co.in  Fri Sep 30 14:21:01 2011
From: kajal5888 at yahoo.co.in (diljit singh)
Date: Fri, 30 Sep 2011 23:51:01 +0530 (IST)
Subject: [Mristudio-users] DTI protocol with cardiac gating required
Message-ID: <1317406861.33747.YahooMailNeo@web95513.mail.in.yahoo.com>

Hi Everyone,Can you please provide me with DTI Protocol 
for 1.5 T with Cardiac Gating 
?
Thanking You & Regards 

Diljit Singh Kajal
M.Tech (Clinical Engineering)
Indian Institute Of Technology Madras,
Christian Medical College- Vellore,
SCTIMST-Thiruvananthpuram,
INDIA
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From choisj70 at gmail.com  Fri Sep 30 16:09:10 2011
From: choisj70 at gmail.com (Seongjin)
Date: Fri, 30 Sep 2011 16:09:10 -0400
Subject: [Mristudio-users] AIR registration
Message-ID: <CANM4YeWsu8-6yat+K453ZdZitqsQ+HxHsJZ6OCnAoJ=DxM8t9A@mail.gmail.com>

Dear DTIstudio users and developers,


While I am playing with "AIR Slice by Slice Linear" option available on
DiffeoMap, I met couple of error message which I don't clearly understand.

Example is "Cannot find AirSlice8.air. There will be no registration for
Slice 8."

What I don't understand is "Cannot find AirSlice8.air." because there is no
missing slice in my test data volume.

If I click "OK", then the process continues.

The error message does not happen at all slice but couple of slices.

Is there any good explanation for this and possible method to avoid the
error message?


Thanks for your opinions and helps in advance.

SC
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From xli16 at jhmi.edu  Fri Sep 30 16:37:33 2011
From: xli16 at jhmi.edu (Xin Li)
Date: Fri, 30 Sep 2011 16:37:33 -0400
Subject: [Mristudio-users] AIR registration
In-Reply-To: <CANM4YeWsu8-6yat+K453ZdZitqsQ+HxHsJZ6OCnAoJ=DxM8t9A@mail.gmail.com>
References: <CANM4YeWsu8-6yat+K453ZdZitqsQ+HxHsJZ6OCnAoJ=DxM8t9A@mail.gmail.com>
Message-ID: <729091e613171.4e85f04d@johnshopkins.edu>

The message shows that AIR 2D registration cannot generate a AIR matrix file based on the slice data. When there is no air file on some slice, DiffeoMap won't transform that slice.


Xin


----- Original Message -----
From: "[Seongjin]" <choisj70 at gmail.com>
Date: Friday, September 30, 2011 4:09 pm
Subject: [Mristudio-users] AIR registration
To: "DTI Studio, ROI Editor, Landmarker Questions/Support" <mristudio-users at mristudio.org>


> Dear DTIstudio users and developers,
>  
>  
>  While I am playing with "AIR Slice by Slice Linear" option available 
> on
>  DiffeoMap, I met couple of error message which I don't clearly understand.
>  
>  Example is "Cannot find AirSlice8.air. There will be no registration 
> for
>  Slice 8."
>  
>  What I don't understand is "Cannot find AirSlice8.air." because there 
> is no
>  missing slice in my test data volume.
>  
>  If I click "OK", then the process continues.
>  
>  The error message does not happen at all slice but couple of slices.
>  
>  Is there any good explanation for this and possible method to avoid the
>  error message?
>  
>  
>  Thanks for your opinions and helps in advance.
>  
>  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  Tue Oct  4 09:21:50 2011
From: choisj70 at gmail.com (Seongjin)
Date: Tue, 04 Oct 2011 09:21:50 -0400
Subject: [Mristudio-users] compiled AIR file for 64-bit Windows 7 machine
Message-ID: <CANM4YeWxNmZ72geKVwxMaEJy46K+T+J56h8EF3JXpf3pYAVyeA@mail.gmail.com>

Dear DTI studio users and developers,


DiffeoMap is complaining that my AIR files are not compatible with 64-bit
machine.

I wonder if any could provide me with compiled AIR files for DiffeoMap
running on Windows 7 machine.

I need following files working on 64-bit Windows 7 machine.
1. aslign_warp
2. alignlinear
3. invert_air
4. makeheader

Thanks for your great helps in advance.


SC
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From choisj70 at gmail.com  Wed Oct  5 20:01:30 2011
From: choisj70 at gmail.com (Seongjin)
Date: Wed, 05 Oct 2011 20:01:30 -0400
Subject: [Mristudio-users] Nifti image question
Message-ID: <CANM4YeW2MQgmT5DJMGS+CbvMfV5Gm43L=dO+17YssdmKzxMNEA@mail.gmail.com>

Dear DtiStudio users and developers,

Recently I got nifti format images from my collaborator and tried to read
the images using ROI editor and DiffeoMap.
However, ROI editor and DiffeoMap complained they are unknown image type.
Interestingly, DtiStudio read the images successfully.
Any thought on this problem?

Thanks in advance,
SC
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From ccshieh1973 at gmail.com  Mon Oct 10 14:27:18 2011
From: ccshieh1973 at gmail.com (CC Shieh)
Date: Tue, 11 Oct 2011 02:27:18 +0800
Subject: [Mristudio-users] DiffeoMap Remote Processing
Message-ID: <CALSU1-8PE3+AtcFCzH_=AnX3jsBm7cFD2iTDxqjyEN98-g2pNg@mail.gmail.com>

Hi there,

I submitted several jobs through DiffeoMap's LDDMM for remote processing two
days ago

(Oct 9) and received the emails for  ICM Multichann?el Processing?... could
someone tell me

how long does it usually take for these jobs to be complete or whether I
need to resubmit?

thanks,


Charng-Chyi Shieh

Radiological Technologist
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From akolasny at jhu.edu  Mon Oct 10 16:58:14 2011
From: akolasny at jhu.edu (akolasny at jhu.edu)
Date: Mon, 10 Oct 2011 16:58:14 -0400 (EDT)
Subject: [Mristudio-users] lddmm processing status
Message-ID: <59032.68.50.209.72.1318280294.squirrel@webmail.cis.jhu.edu>

Greetings:

LDDMM processing is a little backlogged. The two reasons:

   1. Cluster nodes used 1 thread instead of 8 for processing starting
      on Oct. 7. It was corrected today, Oct. 10th.

   2. There was an email DNS resolution Oct. 10th between 2pm and 4:30pm.

Jobs are in the queue and being processed. It may be a day or two before
the normal processing resumes. Since some jobs are running with only
one thread, they may timeout and need to be restarted. If you see a second
email about your job starting, it was restarted.

I'm sorry for the delay.

-Anthony


From ccshieh1973 at gmail.com  Tue Oct 11 17:02:03 2011
From: ccshieh1973 at gmail.com (CC Shieh)
Date: Wed, 12 Oct 2011 05:02:03 +0800
Subject: [Mristudio-users] Q about Kimap
Message-ID: <CALSU1-8DuGDrUmmofaPt2+yC-S6iD7Wq4wiXn96v49yT1UdKaw@mail.gmail.com>

Hi,

I got the Kimap and Hmap by running Multichannel remote LDDMM.
*Could someone please verify my understanding of the difference in*
Kimap, Kimap001, Kimap002 and Kimap003? And How to choice
the ?/? ratio value in paper "Multi-contrast large deformation
diffeomorphic metric mapping for diffusion tensor imaging"?


*Thank you everyone for your continued help and support! *
**
Charng-Chyi Shieh
Radiological Technologist
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From susumu at mri.jhu.edu  Tue Oct 11 18:39:18 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Tue, 11 Oct 2011 18:39:18 -0400
Subject: [Mristudio-users] Q about Kimap
In-Reply-To: <CALSU1-8DuGDrUmmofaPt2+yC-S6iD7Wq4wiXn96v49yT1UdKaw@mail.gmail.com>
References: <CALSU1-8DuGDrUmmofaPt2+yC-S6iD7Wq4wiXn96v49yT1UdKaw@mail.gmail.com>
Message-ID: <CAEq9ap+WKXEz93oNXr8mFh2cnVDPe0wWaK1rL0K75dP5hWC-9w@mail.gmail.com>

> Kimap, Kimap001, Kimap002 and Kimap003?
>

If you use a 3-step cascading alpha method, you get the above 4 Kimaps.
Kimap001 is the result with the most linear-like (less elastic)
transformation. Kimap001+002 gives next step more elastic transformation.
Kimap001+002+003 (=Kimap) provides the most elastic transformation. You can
see how gradually transformation gets more and more elastic. When you apply
Kimap001 + Kimap002, you can transform the original image twice, first by
Kimap001 and then Kimap002; Kimap002(Kimap001(Image)). Or, you can combine
Kimap001 and Kimap002 to create one transformation matrix (say
"Kimap001+002") and then do transformation once; Kimap001+002 (Image). The
latter prevents too many interpolation steps.


> And How to choice
> the ?/? ratio value in paper "Multi-contrast large deformation
> diffeomorphic metric mapping for diffusion tensor imaging"?
>

If your data is mostly young adults without much atrophy, one-shot LDDMM
with alpha = 0.005 should give you a good result. If your subjects have a
large amount of anatomical changes (e.g. severe atrophy like AD patients),
then I would recommend 3-step cascading alpha with 0.01, 0.005, and 0.002,
although, in many cases, the final step (Kimap003) usually doesn't deform
the image much because most transformation is done by alpha=0.005
(Kimap001+002).


>
> *Thank you everyone for your continued help and support! *
> **
> Charng-Chyi Shieh
> Radiological Technologist
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From chyi.mark at msa.hinet.net  Tue Oct 11 20:59:01 2011
From: chyi.mark at msa.hinet.net (=?big5?B?wcKq+Kjk?=)
Date: Wed, 12 Oct 2011 08:59:01 +0800
Subject: [Mristudio-users]  Q about Kimap
Message-ID: <000501cc887a$224581f0$66d085d0$%mark@msa.hinet.net>

Dear Dr. Susumu Mori,

 

Thanks a lot for your kindly help!!

 

Charng-Chyi Shieh

Radiological Technologist

MRI Center

Department of Medical Imaging and Intervention

Linkou Chang Gung Memorial Hospital

No. 5, Fuhsing St., Kweishan, Taoyuan 333, Taiwan 

TEL: 886-3-3281200 ext. 8400  FAX: 886-3-3971936

E-mail: chyi.mark at msa.hinet.net

ccshieh1973 at gmail.com

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From mksarma at gmail.com  Tue Oct 11 21:33:50 2011
From: mksarma at gmail.com (manoj sarma)
Date: Tue, 11 Oct 2011 18:33:50 -0700
Subject: [Mristudio-users] Atlas based analysis using LDDMM
Message-ID: <CA+OMA6artacecdCObVSGxd88BsU2U+597BgyBsuQEBioxwEKXw@mail.gmail.com>

Hello DTI Experts,

I am trying to do an atlas based analysis using LDDMM. My goal is to do an
anlysis on my FA/MD map such as done in
http://www.ncbi.nlm.nih.gov/pubmed?term=20570617 (paper by Zhang).
Therefore, I have used the steps described in
https://www.mristudio.org/wiki/user_manual/diffeomap.

I first processed the DTI data using 'DTI-Studio' and then skull stripped.
To obtain the AIR and LDDMM transformation matrices
 I co-registered my skull stripped FA/MD/B0 map with 'JHU_MNI_SS_b0_ss'
template using AIR and then used 'FA + b0 dual-contrast LDDMM' with
'JHU_MNI_SS_b0_ss' and 'JHU_MNI_SS_FA_ss' templates.

After obtaining the LDDMM matrix, I apply the Hmap to the
'JHU_MNI_SS_WMPM_TypeII' template. But it looks to me the image I got is
having some problem. I am not sure if doing some mistakes. I used trilinear
interpolation for Hmap.

Can anyone please tell me if I am following the correct procedure? Where I
may go wrong?

Thanks in advance,
Manoj
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From susumu at mri.jhu.edu  Tue Oct 11 21:49:11 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Tue, 11 Oct 2011 21:49:11 -0400
Subject: [Mristudio-users] Atlas based analysis using LDDMM
In-Reply-To: <CA+OMA6artacecdCObVSGxd88BsU2U+597BgyBsuQEBioxwEKXw@mail.gmail.com>
References: <CA+OMA6artacecdCObVSGxd88BsU2U+597BgyBsuQEBioxwEKXw@mail.gmail.com>
Message-ID: <CAEq9apJ7eskqAzi3-XKfgmj1tHZabMp9Rp-G34_ZF0k8Ot3kOA@mail.gmail.com>

Well, if you could show me the image, I may be able to help you better, but
one thing I can tell now is, when you transform a WMPM, you need to use
"nearest neighbor". Each ROI in the WMPM contains artificially assigned
numbers; say, ROI-A is 12 and adjacent ROI-B is 20. If you transform this
map using trilinear, it would generate the number "16" right in the middle
of the region A and B, but the number 16 may be assigned to a totally
unrelated ROI.

So, please try nearest neighbor and see how it goes.

On Tue, Oct 11, 2011 at 9:33 PM, manoj sarma <mksarma at gmail.com> wrote:

> Hello DTI Experts,
>
> I am trying to do an atlas based analysis using LDDMM. My goal is to do an
> anlysis on my FA/MD map such as done in
> http://www.ncbi.nlm.nih.gov/pubmed?term=20570617 (paper by Zhang).
> Therefore, I have used the steps described in
> https://www.mristudio.org/wiki/user_manual/diffeomap.
>
> I first processed the DTI data using 'DTI-Studio' and then skull stripped.
> To obtain the AIR and LDDMM transformation matrices
>  I co-registered my skull stripped FA/MD/B0 map with 'JHU_MNI_SS_b0_ss'
> template using AIR and then used 'FA + b0 dual-contrast LDDMM' with
> 'JHU_MNI_SS_b0_ss' and 'JHU_MNI_SS_FA_ss' templates.
>
> After obtaining the LDDMM matrix, I apply the Hmap to the
> 'JHU_MNI_SS_WMPM_TypeII' template. But it looks to me the image I got is
> having some problem. I am not sure if doing some mistakes. I used trilinear
> interpolation for Hmap.
>
> Can anyone please tell me if I am following the correct procedure? Where I
> may go wrong?
>
> Thanks in advance,
> 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
>
>
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From xuli at mri.jhu.edu  Wed Oct 12 14:05:59 2011
From: xuli at mri.jhu.edu (xuli)
Date: Wed, 12 Oct 2011 14:05:59 -0400
Subject: [Mristudio-users] Can not upload data to LDDMM server
In-Reply-To: <CAEq9apJ7eskqAzi3-XKfgmj1tHZabMp9Rp-G34_ZF0k8Ot3kOA@mail.gmail.com>
References: <CA+OMA6artacecdCObVSGxd88BsU2U+597BgyBsuQEBioxwEKXw@mail.gmail.com>
	<CAEq9apJ7eskqAzi3-XKfgmj1tHZabMp9Rp-G34_ZF0k8Ot3kOA@mail.gmail.com>
Message-ID: <002101cc8909$9b92c560$d2b85020$@jhu.edu>

I am trying to do a LDDMM using DiffeoMap. However, it gives me the error 

"Cannot upload this file: xxxx.zip"

 

I was able to do the LDDMM several months before. I am wondering whether
there is anything wrong with the server or there might be some other
problems?

 

Thanks

 

Xu

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From xli16 at jhmi.edu  Wed Oct 12 14:59:49 2011
From: xli16 at jhmi.edu (Xin Li)
Date: Wed, 12 Oct 2011 14:59:49 -0400
Subject: [Mristudio-users] Can not upload data to LDDMM server
In-Reply-To: <002101cc8909$9b92c560$d2b85020$@jhu.edu>
References: <CA+OMA6artacecdCObVSGxd88BsU2U+597BgyBsuQEBioxwEKXw@mail.gmail.com>
	<CAEq9apJ7eskqAzi3-XKfgmj1tHZabMp9Rp-G34_ZF0k8Ot3kOA@mail.gmail.com>
	<002101cc8909$9b92c560$d2b85020$@jhu.edu>
Message-ID: <71d096792b839.4e95ab65@johnshopkins.edu>

Hello Xu,

I wonder if it is possible that the firewall in your work place blocked the data transfer. Or you may check if the firewall of Windows in your computer blocked the data transfer.


Xin

----- Original Message -----
From: xuli <xuli at mri.jhu.edu>
Date: Wednesday, October 12, 2011 2:06 pm
Subject: [Mristudio-users] Can not upload data to LDDMM server
To: "'DTI Studio, ROI Editor,	DiffeoMap Questions/Support'" <mristudio-users at mristudio.org>


> I am trying to do a LDDMM using DiffeoMap. However, it gives me the 
> error 
>  
>  "Cannot upload this file: xxxx.zip"
>  
>   
>  
>  I was able to do the LDDMM several months before. I am wondering whether
>  there is anything wrong with the server or there might be some other
>  problems?
>  
>   
>  
>  Thanks
>  
>   
>  
>  Xu
>   
> _______________________________________________
>  mristudio-users mailing list
>  mristudio-users at mristudio.org
>  
>  Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org 

From kumiko at cis.jhu.edu  Wed Oct 12 15:30:58 2011
From: kumiko at cis.jhu.edu (Kumiko Oishi)
Date: Wed, 12 Oct 2011 15:30:58 -0400 (EDT)
Subject: [Mristudio-users] Can not upload data to LDDMM server
In-Reply-To: <71d096792b839.4e95ab65@johnshopkins.edu>
References: <CA+OMA6artacecdCObVSGxd88BsU2U+597BgyBsuQEBioxwEKXw@mail.gmail.com>
	<CAEq9apJ7eskqAzi3-XKfgmj1tHZabMp9Rp-G34_ZF0k8Ot3kOA@mail.gmail.com>
	<002101cc8909$9b92c560$d2b85020$@jhu.edu>
	<71d096792b839.4e95ab65@johnshopkins.edu>
Message-ID: <49773.69.250.120.124.1318447858.squirrel@webmail.cis.jhu.edu>

Hello Xin and Xu,

I can not upload data to LDDMM, either. I could do yesterday. I have
nothing change with firewall...

Kumiko

> Hello Xu,
>
> I wonder if it is possible that the firewall in your work place blocked
> the data transfer. Or you may check if the firewall of Windows in your
> computer blocked the data transfer.
>
>
> Xin
>
> ----- Original Message -----
> From: xuli <xuli at mri.jhu.edu>
> Date: Wednesday, October 12, 2011 2:06 pm
> Subject: [Mristudio-users] Can not upload data to LDDMM server
> To: "'DTI Studio, ROI Editor,	DiffeoMap Questions/Support'"
> <mristudio-users at mristudio.org>
>
>
>> I am trying to do a LDDMM using DiffeoMap. However, it gives me the
>> error
>>
>>  "Cannot upload this file: xxxx.zip"
>>
>>
>>
>>  I was able to do the LDDMM several months before. I am wondering
>> whether
>>  there is anything wrong with the server or there might be some other
>>  problems?
>>
>>
>>
>>  Thanks
>>
>>
>>
>>  Xu
>>
>> _______________________________________________
>>  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 jangouk at kennedykrieger.org  Wed Oct 12 16:15:09 2011
From: jangouk at kennedykrieger.org (Jangouk, Parastoo)
Date: Wed, 12 Oct 2011 20:15:09 +0000
Subject: [Mristudio-users] LDDMM server?
Message-ID: <16C42831A84D3A4C9C4E7D16083952188F5AC3@kki-gsp-mail2.kki.org>

Hi there,

We are trying to submit our LDDMM data to the server to be analyzed since early afternoon today. However we constantly get the message that " The data can not be uploaded". Could you please check this issue and let us know if there is some problem with the server and when it is gonna be back to normal.

Thanks
Parastoo



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.
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From susumu at mri.jhu.edu  Wed Oct 12 16:38:25 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Wed, 12 Oct 2011 16:38:25 -0400
Subject: [Mristudio-users] Can not upload data to LDDMM server
In-Reply-To: <49773.69.250.120.124.1318447858.squirrel@webmail.cis.jhu.edu>
References: <CA+OMA6artacecdCObVSGxd88BsU2U+597BgyBsuQEBioxwEKXw@mail.gmail.com>
	<CAEq9apJ7eskqAzi3-XKfgmj1tHZabMp9Rp-G34_ZF0k8Ot3kOA@mail.gmail.com>
	<002101cc8909$9b92c560$d2b85020$@jhu.edu>
	<71d096792b839.4e95ab65@johnshopkins.edu>
	<49773.69.250.120.124.1318447858.squirrel@webmail.cis.jhu.edu>
Message-ID: <CAEq9ap+Dqq8hCe+VCcQwzZ=9MSx6AJB5Zx4jadTbp_O0E5E38w@mail.gmail.com>

Hi all users,

It seems our LDDMM pipeline is not working today.
We'll look into it and hopefully will be back tomorrow.
We'll keep you updated.

Thanks,

Susumu

On Wed, Oct 12, 2011 at 3:30 PM, Kumiko Oishi <kumiko at cis.jhu.edu> wrote:

> Hello Xin and Xu,
>
> I can not upload data to LDDMM, either. I could do yesterday. I have
> nothing change with firewall...
>
> Kumiko
>
> > Hello Xu,
> >
> > I wonder if it is possible that the firewall in your work place blocked
> > the data transfer. Or you may check if the firewall of Windows in your
> > computer blocked the data transfer.
> >
> >
> > Xin
> >
> > ----- Original Message -----
> > From: xuli <xuli at mri.jhu.edu>
> > Date: Wednesday, October 12, 2011 2:06 pm
> > Subject: [Mristudio-users] Can not upload data to LDDMM server
> > To: "'DTI Studio, ROI Editor, DiffeoMap Questions/Support'"
> > <mristudio-users at mristudio.org>
> >
> >
> >> I am trying to do a LDDMM using DiffeoMap. However, it gives me the
> >> error
> >>
> >>  "Cannot upload this file: xxxx.zip"
> >>
> >>
> >>
> >>  I was able to do the LDDMM several months before. I am wondering
> >> whether
> >>  there is anything wrong with the server or there might be some other
> >>  problems?
> >>
> >>
> >>
> >>  Thanks
> >>
> >>
> >>
> >>  Xu
> >>
> >> _______________________________________________
> >>  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
>
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From susumu at mri.jhu.edu  Wed Oct 12 16:44:27 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Wed, 12 Oct 2011 16:44:27 -0400
Subject: [Mristudio-users] LDDMM server?
In-Reply-To: <16C42831A84D3A4C9C4E7D16083952188F5AC3@kki-gsp-mail2.kki.org>
References: <16C42831A84D3A4C9C4E7D16083952188F5AC3@kki-gsp-mail2.kki.org>
Message-ID: <CAEq9ap+hwutbXzZtr4D_xOyMf5X8TDXSyi9ri6AbCxDbE7+hHw@mail.gmail.com>

Sorry. LDDMM pipeline is not working currently. I hope that it'll come back
by tomorrow.
I'll keep you updated.

On Wed, Oct 12, 2011 at 4:15 PM, Jangouk, Parastoo <
jangouk at kennedykrieger.org> wrote:

> Hi there,****
>
> ** **
>
> We are trying to submit our LDDMM data to the server to be analyzed since
> early afternoon today. However we constantly get the message that ? The data
> can not be uploaded?. Could you please check this issue and let us know if
> there is some problem with the server and when it is gonna be back to
> normal.****
>
> ** **
>
> Thanks****
>
> Parastoo****
>
>
>
> 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/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From akolasny at jhu.edu  Wed Oct 12 18:00:44 2011
From: akolasny at jhu.edu (akolasny at jhu.edu)
Date: Wed, 12 Oct 2011 18:00:44 -0400 (EDT)
Subject: [Mristudio-users] LDDMM server?
In-Reply-To: <CAEq9ap+hwutbXzZtr4D_xOyMf5X8TDXSyi9ri6AbCxDbE7+hHw@mail.gmail.com>
References: <16C42831A84D3A4C9C4E7D16083952188F5AC3@kki-gsp-mail2.kki.org>
	<CAEq9ap+hwutbXzZtr4D_xOyMf5X8TDXSyi9ri6AbCxDbE7+hHw@mail.gmail.com>
Message-ID: <35233.68.50.209.72.1318456844.squirrel@webmail.cis.jhu.edu>

Storage time for LDDMM processing has been reduced to 10 days.
This will allow extra storage space for the increase in
job processing.

If a job was reported as complete but data was not provided,
please resubmit the job. There appears to be about 5 jobs
that were not properly transferred due to the storage issue.

-Anthony

> Sorry. LDDMM pipeline is not working currently. I hope that it'll come
> back
> by tomorrow.
> I'll keep you updated.
>
> On Wed, Oct 12, 2011 at 4:15 PM, Jangouk, Parastoo <
> jangouk at kennedykrieger.org> wrote:
>
>> Hi there,****
>>
>> ** **
>>
>> We are trying to submit our LDDMM data to the server to be analyzed
>> since
>> early afternoon today. However we constantly get the message that ? The
>> data
>> can not be uploaded?. Could you please check this issue and let us know
>> if
>> there is some problem with the server and when it is gonna be back to
>> normal.****
>>
>> ** **
>>
>> Thanks****
>>
>> Parastoo****
>>
>>
>>
>> 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/
>> Unsubscribe, send a blank email to:
>> mristudio-users-unsubscribe at mristudio.org
>>
>>
>



From xuejie1201 at gmail.com  Wed Oct 12 21:46:56 2011
From: xuejie1201 at gmail.com (Xuejie Zhang)
Date: Thu, 13 Oct 2011 09:46:56 +0800
Subject: [Mristudio-users]  Question on Pediatric DTI data
Message-ID: <CAPzv0_UwAT2egHt=J_Xvvq2UNUfER6M-T_oPS17C=qHVgnRdGQ@mail.gmail.com>

Dear Prof. Mori and MRIstudio list members,

I am wondering the 0-2 years pediatric DTI data on the website (
http://lbam.med.jhmi.edu/) is in vivo data or ex vivo data ?

Thanks and Regards,

Xuejie
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From ruibinzhang at sina.cn  Thu Oct 13 03:40:27 2011
From: ruibinzhang at sina.cn (ruibinzhang at sina.cn)
Date: Thu, 13 Oct 2011 15:40:27 +0800
Subject: [Mristudio-users] How can I avoid the image to be reverted?
Message-ID: <20111013074027.89A2914D875@mail1.webapp.51uc.com>

Dear DTI experts:
        I am a new user of DTIstudio,recently I faced a problem that when I followed the DTI mapping,I found that the axial image was inversed.My data was acquired by Philips,1b0+32B?800?.According to the forum about the Philips' image,so I saved it as a raw data image,and did the DTI mapping again,but ?found that it was inversed too. How can I solve it?
       By the way,DTIstudio(automatic image registration),FSL(Flirt),which one is much better when i register diffusion-weighted image to the b0 image. I hope you suggestions.Thanks very much.
       Cheers!
                                                                                                                                                               yours sincerely
                                                                                                                                                                       Ruibin

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From susumu at mri.jhu.edu  Thu Oct 13 15:50:30 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Thu, 13 Oct 2011 15:50:30 -0400
Subject: [Mristudio-users] Question on Pediatric DTI data
In-Reply-To: <CAPzv0_UwAT2egHt=J_Xvvq2UNUfER6M-T_oPS17C=qHVgnRdGQ@mail.gmail.com>
References: <CAPzv0_UwAT2egHt=J_Xvvq2UNUfER6M-T_oPS17C=qHVgnRdGQ@mail.gmail.com>
Message-ID: <CAEq9apLnhAdQsYxDJQOy8pg+0UUbp58v52CiuDYEG9iq0qLa9Q@mail.gmail.com>

they are in vivo.

On Wed, Oct 12, 2011 at 9:46 PM, Xuejie Zhang <xuejie1201 at gmail.com> wrote:

> Dear Prof. Mori and MRIstudio list members,
>
> I am wondering the 0-2 years pediatric DTI data on the website (
> http://lbam.med.jhmi.edu/) is in vivo data or ex vivo data ?
>
> Thanks and Regards,
>
> Xuejie
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From Weihong.Yuan at cchmc.org  Thu Oct 13 23:00:38 2011
From: Weihong.Yuan at cchmc.org (Weihong Yuan)
Date: Thu, 13 Oct 2011 23:00:38 -0400
Subject: [Mristudio-users] Question about LDDMM
Message-ID: <4E976D960200004B00168594@n6mcgw16.cchmc.org>

Dear MRIStudio support team,
 
I submitted a 4-channel LDDMM task at around 11 am this morning but got an email message pretty soon. It is pasted as follows. I am not sure whether this means the job failed or I am supposed to continue to wait. So far, it's been approximately 12 hours. Can you help to have a look it, please? 
 
===================================================================
Status: ICM Multichannel Processing
Md5 String: 1d2fae2e4795230e54cd7a48634a3d3f
Command: lddmm-vmm -z -A Template.img -T Target.img -c lddmm-vmm1.conf -o ../result
Output: ftp://ftp.mristudio.org/pub/OUTGOING/lddmm-vmm/output/1d2fae2e4795230e54cd7a48634a3d3f 
lddmm-vmm1.conf:
VTK_INTERVAL=
ALPHA=0.01
HIST_MATCHING=2
D=3
SIMSTEPS=1000
TIMESTEPS=10
DELTA=0.1
EPSILON=0.0000000001
PROCS_Z=1
PROCS_Y=1
PROCS_X=1
GAMMA=1
POWERL=1
PADI=20
PADH=5
NORM_GRAD=1000
SIGMA=1
ERROR=0.02
CH_EPSILON=25
RESTART=0
===============================================================================
 
Thanks
 
Weihong
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From akolasny at jhu.edu  Fri Oct 14 06:12:38 2011
From: akolasny at jhu.edu (akolasny at jhu.edu)
Date: Fri, 14 Oct 2011 06:12:38 -0400 (EDT)
Subject: [Mristudio-users] Question about LDDMM
In-Reply-To: <4E976D960200004B00168594@n6mcgw16.cchmc.org>
References: <4E976D960200004B00168594@n6mcgw16.cchmc.org>
Message-ID: <57230.68.50.209.72.1318587158.squirrel@webmail.cis.jhu.edu>

Your job is still in the processing queue. Normally, a job is automatically
assigned a processor. Unfortunately, the cluster is overloaded and there
is a backlog. It may be two days before the job is complete.

I am looking at options to offload some of these jobs to other
prcessors.

-Anthony

> Dear MRIStudio support team,
>
> I submitted a 4-channel LDDMM task at around 11 am this morning but got an
> email message pretty soon. It is pasted as follows. I am not sure whether
> this means the job failed or I am supposed to continue to wait. So far,
> it's been approximately 12 hours. Can you help to have a look it, please?
>
> ===================================================================
> Status: ICM Multichannel Processing
> Md5 String: 1d2fae2e4795230e54cd7a48634a3d3f
> Command: lddmm-vmm -z -A Template.img -T Target.img -c lddmm-vmm1.conf -o
> ../result
> Output:
> ftp://ftp.mristudio.org/pub/OUTGOING/lddmm-vmm/output/1d2fae2e4795230e54cd7a48634a3d3f
> lddmm-vmm1.conf:
> VTK_INTERVAL=
> ALPHA=0.01
> HIST_MATCHING=2
> D=3
> SIMSTEPS=1000
> TIMESTEPS=10
> DELTA=0.1
> EPSILON=0.0000000001
> PROCS_Z=1
> PROCS_Y=1
> PROCS_X=1
> GAMMA=1
> POWERL=1
> PADI=20
> PADH=5
> NORM_GRAD=1000
> SIGMA=1
> ERROR=0.02
> CH_EPSILON=25
> RESTART=0
> ===============================================================================
>
> Thanks
>
> Weihong
> _______________________________________________
> mristudio-users mailing 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  Sun Oct 16 20:44:34 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Sun, 16 Oct 2011 20:44:34 -0400
Subject: [Mristudio-users] How can I avoid the image to be reverted?
In-Reply-To: <20111013074027.89A2914D875@mail1.webapp.51uc.com>
References: <20111013074027.89A2914D875@mail1.webapp.51uc.com>
Message-ID: <CAEq9apKQ465yaYc8Xcr3Gv3oABUP==Yt1Z5Gqi=KgKrfVzL1=g@mail.gmail.com>

This could happen if the data went through non-MriStudio software.
MriStudio uses Radiology convention while many image analysis programs were
developed by groups associated with Neurology, using Neurology convention.
Please read FAQ14 here (https://www.mristudio.org/wiki/faq).

2011/10/13 <ruibinzhang at sina.cn>

> Dear DTI experts:
>
>         I am a new user of DTIstudio,recently I faced a problem that when I
> followed the DTI mapping,I found that the axial image was inversed.My data
> was acquired by Philips,1b0+32B?800?.According to the forum about the
> Philips' image,so I saved it as a raw data image,and did the DTI mapping
> again,but ?found that it was inversed too. How can I solve it?
>
>        By the way,DTIstudio(automatic image registration),FSL(Flirt),which
> one is much better when i register diffusion-weighted image to the b0
> image. I hope you suggestions.Thanks very much.
>
>        Cheers!
>
>
> yours sincerely
>
>
>                                                                                                                                                                        Ruibin
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From amangupta2005 at gmail.com  Mon Oct 17 15:27:42 2011
From: amangupta2005 at gmail.com (aman gupta)
Date: Mon, 17 Oct 2011 14:27:42 -0500
Subject: [Mristudio-users] Fiber tractography image
Message-ID: <CALYsOkR72TuWED5gJtR4t9qTzmUg3wy4xK2W8_2B6NcJYdbBVQ@mail.gmail.com>

Hi

Can you please tell me how do i save the Fiber Tractography image as a
.jpg/.jpeg image?

Thanks,
Aman
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From jdthompson at eyecarecentre.org  Mon Oct 17 16:45:01 2011
From: jdthompson at eyecarecentre.org (Jodie Davies-Thompson)
Date: Mon, 17 Oct 2011 13:45:01 -0700
Subject: [Mristudio-users] Fiber tractography image
In-Reply-To: <CALYsOkR72TuWED5gJtR4t9qTzmUg3wy4xK2W8_2B6NcJYdbBVQ@mail.gmail.com>
References: <CALYsOkR72TuWED5gJtR4t9qTzmUg3wy4xK2W8_2B6NcJYdbBVQ@mail.gmail.com>
Message-ID: <7EFE6518F6AAEE40989E649BBF66418F01095BFB407E@srv1.eyecarecentre.org>

Hi Aman,

As far as I know, you can only do screen-grabs ('prt sc' button).

Jodie
________________________________________
From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of aman gupta [amangupta2005 at gmail.com]
Sent: Monday, October 17, 2011 12:27 PM
To: DTI Studio, ROI Editor, Landmarker Questions/Support
Subject: [Mristudio-users] Fiber tractography image

Hi

Can you please tell me how do i save the Fiber Tractography image as a .jpg/.jpeg image?

Thanks,
Aman



From amangupta2005 at gmail.com  Mon Oct 17 16:56:33 2011
From: amangupta2005 at gmail.com (aman gupta)
Date: Mon, 17 Oct 2011 15:56:33 -0500
Subject: [Mristudio-users] Fiber tractography image
In-Reply-To: <7EFE6518F6AAEE40989E649BBF66418F01095BFB407E@srv1.eyecarecentre.org>
References: <CALYsOkR72TuWED5gJtR4t9qTzmUg3wy4xK2W8_2B6NcJYdbBVQ@mail.gmail.com>
	<7EFE6518F6AAEE40989E649BBF66418F01095BFB407E@srv1.eyecarecentre.org>
Message-ID: <CALYsOkQ06O6eLwBuyH0-+u1d+WB7CX+QZJfhnJ_=++RYC-Xejg@mail.gmail.com>

Thanks Jodie, that's what i was wondering. Unlike other images (such B0, FA,
MD etc.) tractography "image" doesn't have right click and then "save image
as" option!

On Mon, Oct 17, 2011 at 3:45 PM, Jodie Davies-Thompson <
jdthompson at eyecarecentre.org> wrote:

> Hi Aman,
>
> As far as I know, you can only do screen-grabs ('prt sc' button).
>
> Jodie
> ________________________________________
> From: mristudio-users-bounces at mristudio.org [
> mristudio-users-bounces at mristudio.org] On Behalf Of aman gupta [
> amangupta2005 at gmail.com]
> Sent: Monday, October 17, 2011 12:27 PM
> To: DTI Studio, ROI Editor, Landmarker Questions/Support
> Subject: [Mristudio-users] Fiber tractography image
>
> Hi
>
> Can you please tell me how do i save the Fiber Tractography image as a
> .jpg/.jpeg image?
>
> Thanks,
> Aman
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>



-- 
Doubts and mistrust are the mere panic of timid imagination, which the
steadfast heart will conquer, and the large mind transcend.
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From joeh at cis.jhu.edu  Thu Oct 20 13:04:56 2011
From: joeh at cis.jhu.edu (joeh at cis.jhu.edu)
Date: Thu, 20 Oct 2011 13:04:56 -0400 (EDT)
Subject: [Mristudio-users] Computational Anatomy Works (CAWorks) Software
	Beta 46 Announcement
Message-ID: <25766.192.168.3.48.1319130296.squirrel@webmail.cis.jhu.edu>

Computational Anatomy Works (CAWorks) Software Beta 46 Announcement

CAWorks beta 46 is now available for windows 32 and 64 bit, mac osx, and
linux 32 and 64 bit

The new version includes

	Improvements to Dock panel layout and addition of tab for rapid surface
display and comparison

	Improvements to XnatBrowser beta plugin

	Bug fix for byu surface reading and writing

CAWorks is available through mristudio.org under:

   https://www.mristudio.org/download/binaries/caworks/

The software application Computational Anatomy Works (CAWorks) was
developed to support Computational Anatomy and shape analysis. The
capabilities of CAWorks include:

   1. Interactive landmark placement to create segmentation (mask) of
desired region of interest

   2. Specialized landmark placement plugins for subcortical structures
such as hippocampus and amygdala

   3. Support for multiple Medical Imaging data formats, such as Nifti,
Analyze, Freesurfer, DICOM and landmark data

   4. Quadra Planar view visualization

   5. Shape Analysis plugin modules, such as Large Deformation
Diffeomorphic Metric Mapping (LDDMM)

Current enhancements to CAWorks have focused on interactive support for
landmarking of subcortical structures. Specific plugins are available for
landmark placement of the hippocampus, amygdala and entorhinal cortex
regions. After landmarking is completed, CAWorks facilitates submission
for automated segmentation processing. CAWorks is being used by the
Biomarkers for Older Controls At Risk for Dementia (BIOCARD), Resource for
Quantitative Functional MRI: TRD4, Validation of Structural/Functional MRI
Localization and Biomedical Informatics Research Network (BIRN) projects.

CAWorks extends ParaView, an open source, multi-platform, freely available
program for parallel, interactive, scientific visualization. An important
visualization tool for TeraGrid researchers, its client-server
architecture facilitates remote visualization of datasets and the
generation of level of detail (LOD) models that maintain interactive frame
rates for large datasets.

Tutorials describing CAWorks for the ROI feature are located at:

    http://caportal.cis.jhu.edu/tutorials


If you have questions regarding this software, please put CAWorks in your
subject line for the mristudio-users mailing list.

Thanks!
CAWorks Development Team


From aman1986 at gmail.com  Fri Oct 21 15:35:39 2011
From: aman1986 at gmail.com (Amanmeet Garg)
Date: Fri, 21 Oct 2011 12:35:39 -0700
Subject: [Mristudio-users] ADC map from DTIstudio
Message-ID: <CAHpJ8K+R1qRTQ7OuPbRFQs3GM_qQVUe3vmtaTbWZD_0-KfhmwQ@mail.gmail.com>

Hi,
 Is the ADC map received from the DTIStudio calculation the Apparent
Diffusion Coeff or the "Average Diffusion coeff "

Regards
-- 
Amanmeet Garg

Graduate Student
Simon Fraser University
8888 University Drive,
Burnaby, BC, Canada
V5A1S6
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From susumu at mri.jhu.edu  Fri Oct 21 21:02:28 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Fri, 21 Oct 2011 21:02:28 -0400
Subject: [Mristudio-users] ADC map from DTIstudio
In-Reply-To: <CAHpJ8K+R1qRTQ7OuPbRFQs3GM_qQVUe3vmtaTbWZD_0-KfhmwQ@mail.gmail.com>
References: <CAHpJ8K+R1qRTQ7OuPbRFQs3GM_qQVUe3vmtaTbWZD_0-KfhmwQ@mail.gmail.com>
Message-ID: <CAEq9apJUNamfWZNMtWfxotmsiU0t091ww=O2GmAmhRDhTBt51w@mail.gmail.com>

The ADC in DtiStudio is "Apparent Diffusion Constant"
If your b-table has a 30-orientation scheme, you get 30 ADC maps. Suppose
the first line of the b-table is [1, 0, 0], then the first ADC is "apparent
diffusion constant" along X.

Obviously, we hardly use any of ADC values calculated in DtiStudio. If you
want "Average Diffusion Constant", then "Trace" is what you want which is 3
x "Average diffusion constant". In other words, if you divide Trace by 3,
you get "average diffusion constant".

On Fri, Oct 21, 2011 at 3:35 PM, Amanmeet Garg <aman1986 at gmail.com> wrote:

> Hi,
>  Is the ADC map received from the DTIStudio calculation the Apparent
> Diffusion Coeff or the "Average Diffusion coeff "
>
> Regards
> --
> Amanmeet Garg
>
> Graduate Student
> Simon Fraser University
> 8888 University Drive,
> Burnaby, BC, Canada
> V5A1S6
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From mborich at umn.edu  Mon Oct 24 13:41:02 2011
From: mborich at umn.edu (Michael Borich)
Date: Mon, 24 Oct 2011 12:41:02 -0500
Subject: [Mristudio-users] Issues with manual ROI drawing in the sagittal
	view
In-Reply-To: <72a0c06d9de5.4e83208d@johnshopkins.edu>
References: <CALVL2mNdkVcvkzZ-Cm6+5N8MYM7Urkxvcxu1PoAEd-uoNu0dRA@mail.gmail.com>
	<72a0c06d9de5.4e83208d@johnshopkins.edu>
Message-ID: <Gophermail.2.0.1110241241020.18687@vs-a.tc.umn.edu>

Hello DTIStudio users, 

I am attempting to use ROI editor to analyze some data and would like to 
manually partition the corpus callosum in the sagittal view and calculate 
FA values for each area; however I am having issues with drawing ROIs in 
the sagittal view. When I draw an ROI in the axial view with the pen 
function, then fill it, and add it, it works well (as shown in your 
tutorial). But when I try to draw in the sagittal or coronal view, when I 
click "add," the ROI that I have drawn shifts to the lowermost portion of 
the view instead of where I did the drawing and does not transfer and show 
up in the other views.

Have you encountered this problem previously and do you know of any 
possible solutions? Any information you can provide me with would be 
greatly appreciated.

Thanks in advance.   

Michael


From xli16 at jhmi.edu  Mon Oct 24 13:51:18 2011
From: xli16 at jhmi.edu (Xin Li)
Date: Mon, 24 Oct 2011 13:51:18 -0400
Subject: [Mristudio-users] Issues with manual ROI drawing in the
	sagittal	view
In-Reply-To: <Gophermail.2.0.1110241241020.18687@vs-a.tc.umn.edu>
References: <CALVL2mNdkVcvkzZ-Cm6+5N8MYM7Urkxvcxu1PoAEd-uoNu0dRA@mail.gmail.com>
	<72a0c06d9de5.4e83208d@johnshopkins.edu>
	<Gophermail.2.0.1110241241020.18687@vs-a.tc.umn.edu>
Message-ID: <7210d63c6795.4ea56d56@johnshopkins.edu>

It is a bug of ROIEditor. It happens when the image is not isotropic. Sorry for this. 

I am going to post a fixed version later.

Xin

----- Original Message -----
From: Michael Borich <mborich at umn.edu>
Date: Monday, October 24, 2011 1:41 pm
Subject: [Mristudio-users] Issues with manual ROI drawing in the sagittal	view
To: mristudio-users at mristudio.org


> Hello DTIStudio users, 
>  
>  I am attempting to use ROI editor to analyze some data and would like 
> to 
>  manually partition the corpus callosum in the sagittal view and 
> calculate 
>  FA values for each area; however I am having issues with drawing ROIs 
> in 
>  the sagittal view. When I draw an ROI in the axial view with the pen 
> 
>  function, then fill it, and add it, it works well (as shown in your 
>  tutorial). But when I try to draw in the sagittal or coronal view, 
> when I 
>  click "add," the ROI that I have drawn shifts to the lowermost 
> portion of 
>  the view instead of where I did the drawing and does not transfer and 
> show 
>  up in the other views.
>  
>  Have you encountered this problem previously and do you know of any 
>  possible solutions? Any information you can provide me with would be 
> 
>  greatly appreciated.
>  
>  Thanks in advance.   
>  
>  Michael
>  
>  _______________________________________________
>  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 Oct 24 14:27:07 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Mon, 24 Oct 2011 14:27:07 -0400
Subject: [Mristudio-users] Issues with manual ROI drawing in the
 sagittal view
In-Reply-To: <7210d63c6795.4ea56d56@johnshopkins.edu>
References: <CALVL2mNdkVcvkzZ-Cm6+5N8MYM7Urkxvcxu1PoAEd-uoNu0dRA@mail.gmail.com>
	<72a0c06d9de5.4e83208d@johnshopkins.edu>
	<Gophermail.2.0.1110241241020.18687@vs-a.tc.umn.edu>
	<7210d63c6795.4ea56d56@johnshopkins.edu>
Message-ID: <CAEq9ap+y670_+j3N0hOw8vCZ_T0RxoXDrL4fU=P_udpYcmPB_g@mail.gmail.com>

Michael,

In my understanding, the reason of you experience is due to interpolation.
When you draw an ROI, the ROI line is drawn based on the pixel resolution of
the display. When you confirm it as an ROI in your image, this
high-resolution ROI definition has to be converted to the low-resolution
image pixels. You won't feel this when you are working on axial slices
because the axial [X, Y] resolutions are high. However, if you draw ROIs in
sagittal or coronal, the Z orientation typically has much lower resolution.
When RoiEditor picks nearest pixel based on your high-res ROI drawing, you
notice the jump. This is something we can't fix.

Susumu

On Mon, Oct 24, 2011 at 1:51 PM, Xin Li <xli16 at jhmi.edu> wrote:

> It is a bug of ROIEditor. It happens when the image is not isotropic. Sorry
> for this.
>
> I am going to post a fixed version later.
>
> Xin
>
> ----- Original Message -----
> From: Michael Borich <mborich at umn.edu>
> Date: Monday, October 24, 2011 1:41 pm
> Subject: [Mristudio-users] Issues with manual ROI drawing in the sagittal
>     view
> To: mristudio-users at mristudio.org
>
>
> > Hello DTIStudio users,
> >
> >  I am attempting to use ROI editor to analyze some data and would like
> > to
> >  manually partition the corpus callosum in the sagittal view and
> > calculate
> >  FA values for each area; however I am having issues with drawing ROIs
> > in
> >  the sagittal view. When I draw an ROI in the axial view with the pen
> >
> >  function, then fill it, and add it, it works well (as shown in your
> >  tutorial). But when I try to draw in the sagittal or coronal view,
> > when I
> >  click "add," the ROI that I have drawn shifts to the lowermost
> > portion of
> >  the view instead of where I did the drawing and does not transfer and
> > show
> >  up in the other views.
> >
> >  Have you encountered this problem previously and do you know of any
> >  possible solutions? Any information you can provide me with would be
> >
> >  greatly appreciated.
> >
> >  Thanks in advance.
> >
> >  Michael
> >
> >  _______________________________________________
> >  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
>
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From mborich at umn.edu  Mon Oct 24 15:58:00 2011
From: mborich at umn.edu (Michael Borich)
Date: Mon, 24 Oct 2011 14:58:00 -0500
Subject: [Mristudio-users] Issues with manual ROI drawing in the
 sagittal view
In-Reply-To: <Gophermail.2.0.1110241241020.18687@vs-a.tc.umn.edu>
References: <CALVL2mNdkVcvkzZ-Cm6+5N8MYM7Urkxvcxu1PoAEd-uoNu0dRA@mail.gmail.com>
	<72a0c06d9de5.4e83208d@johnshopkins.edu>
	<Gophermail.2.0.1110241241020.18687@vs-a.tc.umn.edu>
Message-ID: <Gophermail.2.0.1110241458001.13603@vs-a.tc.umn.edu>

This issue appears to be resolved in the latest (4.1.1) version of 
ROIeditor. Thanks

Best,
Michael

On Oct 24 2011, Michael Borich wrote:

>Hello DTIStudio users, 
>
>I am attempting to use ROI editor to analyze some data and would like to 
>manually partition the corpus callosum in the sagittal view and calculate 
>FA values for each area; however I am having issues with drawing ROIs in 
>the sagittal view. When I draw an ROI in the axial view with the pen 
>function, then fill it, and add it, it works well (as shown in your 
>tutorial). But when I try to draw in the sagittal or coronal view, when I 
>click "add," the ROI that I have drawn shifts to the lowermost portion of 
>the view instead of where I did the drawing and does not transfer and show 
>up in the other views.
>
>Have you encountered this problem previously and do you know of any 
>possible solutions? Any information you can provide me with would be 
>greatly appreciated.
>
>Thanks in advance.   
>
>Michael
>
>

-- 
Michael Borich, DPT, PhD
Postdoctoral Research Fellow
University of British Columbia
604-827-3369


From udayanbhaskar at gmail.com  Sun Oct 30 16:37:34 2011
From: udayanbhaskar at gmail.com (uday bhaskar)
Date: Sun, 30 Oct 2011 16:37:34 -0400
Subject: [Mristudio-users] Getting Gradient directions
Message-ID: <CALVL2mMsBxs2kxTHSXf+RGz69SFqsCVRpHAYa=syG-eP6QLYEQ@mail.gmail.com>

Hi All,

       DTI studio is not able to load the DTI gradient from the header. I
have a 25 direction DTI data from a GE 1.5T scanner. Can anyone help me out
with getting the gradient directions. Any help is appreciated

Thank You

-- 
Thanks,
Uday.
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From weinmaya at gmail.com  Mon Nov  7 02:42:03 2011
From: weinmaya at gmail.com (maya weinstein)
Date: Mon, 07 Nov 2011 09:42:03 +0200
Subject: [Mristudio-users] Question regarding data quality assessment
Message-ID: <CACtX2RsUoYf9x4OP7FHh=hUdRextC9WGrfu-Y7BBeQQW6ppKug@mail.gmail.com>

Hi,

I'm running a study of preterms and I have allot of problems in my data do
to motion.
I have one dataset per subject so I cannot compare between repetitions to
check if there was motion.
I used the option of "automatic image registration" to run affine
registration and got AIR registered dataset.
Now, I wanted to remove corrupted images- so I run the outlier rejection.
My question is -after I manually mark additional corrupted images in the
display- will the program disregard these images automatically or do I need
to save the data again?  if yes- how do I save the corrected data so I can
load it to ROIeditor?


Thank you for your help!
Maya Weinstein
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From susumu at mri.jhu.edu  Mon Nov  7 05:22:54 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Mon, 07 Nov 2011 05:22:54 -0500
Subject: [Mristudio-users] Question regarding data quality assessment
In-Reply-To: <CACtX2RsUoYf9x4OP7FHh=hUdRextC9WGrfu-Y7BBeQQW6ppKug@mail.gmail.com>
References: <CACtX2RsUoYf9x4OP7FHh=hUdRextC9WGrfu-Y7BBeQQW6ppKug@mail.gmail.com>
Message-ID: <CAEq9apJG_=12MqXbxNYLtJ0NXX6oif8A4YXk-LDbAQxntvmg1Q@mail.gmail.com>

Hi Maya,

Please go over https://www.mristudio.org/wiki/changelog/dtistudio-3.0.2 to
find the functions for image quality check. Once slices (or pixels) are
rejected (manually or automatically), they are not used to calculate the
tensor (including the tensor-derived maps such as FA). In this process, you
can't save the raw data with your rejection information, although you can
save the information about which images you rejected. I think it doesn't
matter for image quantification using RoiEditor because what you need are
the tensor-derived maps which are already calculated with your rejection
information.

On Mon, Nov 7, 2011 at 2:42 AM, maya weinstein <weinmaya at gmail.com> wrote:

> Hi,
>
> I'm running a study of preterms and I have allot of problems in my data do
> to motion.
> I have one dataset per subject so I cannot compare between repetitions to
> check if there was motion.
> I used the option of "automatic image registration" to run affine
> registration and got AIR registered dataset.
> Now, I wanted to remove corrupted images- so I run the outlier rejection.
> My question is -after I manually mark additional corrupted images in the
> display- will the program disregard these images automatically or do I
> need to save the data again?  if yes- how do I save the corrected data so I
> can load it to ROIeditor?
>
>
> Thank you for your help!
> Maya Weinstein
>
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From ksupreet6 at gmail.com  Mon Nov  7 11:42:27 2011
From: ksupreet6 at gmail.com (Supreet kaur)
Date: Mon, 07 Nov 2011 11:42:27 -0500
Subject: [Mristudio-users] Mean diffusivity and standard errors
Message-ID: <CAMUw5-u_=x1qtv-ZTKYe5ESxy7Pot+Zqap5kSo2tXK43HP7Kxw@mail.gmail.com>

Hello DTI experts,
                   I just need to know that how do we get the MD (mean
diffusivity values) in DTI studio? Also is there
a way to calculate standard error in DTI studio?
I'll appreciate your feedback and help on this.

Thanks,

Sincerely,

Supreet,
Biomedical research engineer,
Nationwide Childrens Hospital,
Columbus, OH
(614)355-3509
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From cmang at ualberta.ca  Fri Oct 21 19:30:20 2011
From: cmang at ualberta.ca (Cameron Mang)
Date: Fri, 21 Oct 2011 23:30:20 -0000
Subject: [Mristudio-users] ROI editor question
Message-ID: <CAB2+1EyLyo6WXrRbx3vGunw8ua3_Fg1DfU64MniFS7-oSnNV1A@mail.gmail.com>

Hi there,

I am attempting to use ROI editor to analyze some data and would like to try
to partition the corpus callosum into a few different pieces and calculate
FA values for each area. The partitioning will be easiest to do in the
sagittal view as it is based on measurements from the anterior most part to
the posterior most part of the callosum; however I am having issues with
drawing ROIs in the sagittal view. When I draw an ROI in the axial view with
the pencil function, then fill it, and add it, it works really well (as
shown in your tutorial). But when I try to draw in the sagittal or coronal
view, when I click "add," the ROI that I have drawn shifts to the lowermost
portion of the view instead of where I did the drawing and does not transfer
and show up in the other views.

Have you encountered this problem previously and do you know of any possible
solutions? Any information you can provide me with would be greatly
appreciated.

Thanks in advance.

Cameron Mang
PhD student, Rehabilitation Sciences, University of British Columbia
BPE, MSc Neurophysiology, University of Alberta
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From ajaygarg1971 at yahoo.com  Sat Oct 22 14:18:31 2011
From: ajaygarg1971 at yahoo.com (AG)
Date: Sat, 22 Oct 2011 18:18:31 -0000
Subject: [Mristudio-users] Enhanced Gradient Mode on philips scanner
Message-ID: <1319307510.5019.YahooMailNeo@web30602.mail.mud.yahoo.com>

Hi Susumu and other DTI studio users,

I have few queries regarding data acquisition on Philips Achieve 3T scanner -


What is enhanced gradient mode? Does anyone is using it?

How can I acquire more than 1Bo image? We do have a research scanner.

Thanks,

Best,
-Ajay
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From weinmaya at gmail.com  Tue Nov  8 03:08:08 2011
From: weinmaya at gmail.com (maya weinstein)
Date: Tue, 08 Nov 2011 10:08:08 +0200
Subject: [Mristudio-users] Question regarding outlier rejection
Message-ID: <CACtX2Rt0OjD0iMnPSkE7BxFM7wo1sL5X=dYyJMH5q2etu9W+Cw@mail.gmail.com>

Hi,

I have a problem using outlier rejection, after I run it the calculated
maps ( FA, color map...) dissapeared- only a few pixels remained.
When I use the standard linear regression the data looks fine.
What could be the problem?
I'm attaching a print screen of the data.

Thanks,
Maya Weinstein
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From kamali2009res at hotmail.com  Tue Nov  8 23:16:06 2011
From: kamali2009res at hotmail.com (Arash Kamali)
Date: Tue, 08 Nov 2011 23:16:06 -0500
Subject: [Mristudio-users] Mean diffusivity and ADC value
In-Reply-To: <CAMUw5-u_=x1qtv-ZTKYe5ESxy7Pot+Zqap5kSo2tXK43HP7Kxw@mail.gmail.com>
References: <CAMUw5-u_=x1qtv-ZTKYe5ESxy7Pot+Zqap5kSo2tXK43HP7Kxw@mail.gmail.com>
Message-ID: <SNT127-W10B37688DF63430FCF8B0A3DF0@phx.gbl>


Hello Dr. Mori and Dr. LiMy question is also about measurement of the ADC or Mean diffusivity value like the recently asked question bellow. On DTI studio after ADC MAP calculation there are multiple ADC map being generated. For 2D ROI measurement of the ADC which map should be used and how we can get the number of the ADC value in DTI studio? Your help on this matter will be greatly appreciated. Arash Kamali MD 
 Date: Mon, 7 Nov 2011 11:42:27 -0500
From: ksupreet6 at gmail.com
To: mristudio-users at mristudio.org
Subject: [Mristudio-users] Mean diffusivity and standard errors

Hello DTI experts,
                   I just need to know that how do we get the MD (mean diffusivity values) in DTI studio? Also is there
a way to calculate standard error in DTI studio?
I'll appreciate your feedback and help on this.
 
Thanks,
 
Sincerely,

Supreet,
Biomedical research engineer,
Nationwide Childrens Hospital,
Columbus, OH
(614)355-3509


_______________________________________________
mristudio-users mailing list
mristudio-users at mristudio.org
http://lists.mristudio.org/mailman/listinfo/
Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org 		 	   		  
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From susumu at mri.jhu.edu  Wed Nov  9 19:16:00 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Wed, 09 Nov 2011 19:16:00 -0500
Subject: [Mristudio-users] Mean diffusivity and ADC value
In-Reply-To: <SNT127-W10B37688DF63430FCF8B0A3DF0@phx.gbl>
References: <CAMUw5-u_=x1qtv-ZTKYe5ESxy7Pot+Zqap5kSo2tXK43HP7Kxw@mail.gmail.com>
	<SNT127-W10B37688DF63430FCF8B0A3DF0@phx.gbl>
Message-ID: <CAEq9apL+k0B55xMLuKWz_v0=Ut6kzLCdeXD8_U32Bqy+Ogt8_g@mail.gmail.com>

Hi Arash,

For ADC or MD, please use "trace" in DtiStudio. Trace/3 is equivalent to
ADC or MD.

Susumu

On Tue, Nov 8, 2011 at 11:16 PM, Arash Kamali <kamali2009res at hotmail.com>wrote:

>  Hello Dr. Mori and Dr. Li
> My question is also about measurement of the ADC or Mean diffusivity value
> like the recently asked question bellow. On DTI studio after ADC MAP
> calculation there are multiple ADC map being generated. For 2D ROI
> measurement of the ADC which map should be used and how we can get the
> number of the ADC value in DTI studio?
>
> Your help on this matter will be greatly appreciated.
>
> Arash Kamali MD
>
>
>
> ------------------------------
> Date: Mon, 7 Nov 2011 11:42:27 -0500
> From: ksupreet6 at gmail.com
> To: mristudio-users at mristudio.org
> Subject: [Mristudio-users] Mean diffusivity and standard errors
>
> Hello DTI experts,
>                    I just need to know that how do we get the MD (mean
> diffusivity values) in DTI studio? Also is there
> a way to calculate standard error in DTI studio?
> I'll appreciate your feedback and help on this.
>
> Thanks,
>
> Sincerely,
>
> Supreet,
> Biomedical research engineer,
> Nationwide Childrens Hospital,
> Columbus, OH
> (614)355-3509
>
>
> _______________________________________________ mristudio-users mailing
> 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
>
>
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From kamali2009res at hotmail.com  Wed Nov  9 21:53:07 2011
From: kamali2009res at hotmail.com (Arash Kamali)
Date: Wed, 09 Nov 2011 21:53:07 -0500
Subject: [Mristudio-users] Mean diffusivity and ADC value
In-Reply-To: <CAEq9apL+k0B55xMLuKWz_v0=Ut6kzLCdeXD8_U32Bqy+Ogt8_g@mail.gmail.com>
References: <CAMUw5-u_=x1qtv-ZTKYe5ESxy7Pot+Zqap5kSo2tXK43HP7Kxw@mail.gmail.com>
	<SNT127-W10B37688DF63430FCF8B0A3DF0@phx.gbl>
	<CAEq9apL+k0B55xMLuKWz_v0=Ut6kzLCdeXD8_U32Bqy+Ogt8_g@mail.gmail.com>
Message-ID: <SNT127-W29CA963A071F6FFEB3C1DFA3DC0@phx.gbl>



 Thanks Dr. Mori for the response,In the  ROI statistics for Tensor value the bumbers are for example Mean:  2.59e-003 and Std:  1.90e-004 How I can devide these numbers by 3 to use for ADC value? Your input will be appreciated, ArashDate: Wed, 9 Nov 2011 19:16:00 -0500
From: susumu at mri.jhu.edu
To: mristudio-users at mristudio.org
Subject: Re: [Mristudio-users] Mean diffusivity and ADC value

Hi Arash,
For ADC or MD, please use "trace" in DtiStudio. Trace/3 is equivalent to ADC or MD.
Susumu

On Tue, Nov 8, 2011 at 11:16 PM, Arash Kamali <kamali2009res at hotmail.com> wrote:






Hello Dr. Mori and Dr. Li
My question is also about measurement of the ADC or Mean diffusivity value like the recently asked question bellow. On DTI studio after ADC MAP calculation there are multiple ADC map being generated. For 2D ROI measurement of the ADC which map should be used and how we can get the number of the ADC value in DTI studio?

 
Your help on this matter will be greatly appreciated.
 
Arash Kamali MD
 

 
Date: Mon, 7 Nov 2011 11:42:27 -0500
From: ksupreet6 at gmail.com

To: mristudio-users at mristudio.org
Subject: [Mristudio-users] Mean diffusivity and standard errors

Hello DTI experts,
                   I just need to know that how do we get the MD (mean diffusivity values) in DTI studio? Also is there
a way to calculate standard error in DTI studio?
I'll appreciate your feedback and help on this.
 
Thanks,
 
Sincerely,

Supreet,
Biomedical research engineer,
Nationwide Childrens Hospital,
Columbus, OH
(614)355-3509


_______________________________________________
mristudio-users mailing 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





_______________________________________________
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From susumu at mri.jhu.edu  Wed Nov  9 22:02:35 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Wed, 09 Nov 2011 22:02:35 -0500
Subject: [Mristudio-users] Enhanced Gradient Mode on philips scanner
In-Reply-To: <1319307510.5019.YahooMailNeo@web30602.mail.mud.yahoo.com>
References: <1319307510.5019.YahooMailNeo@web30602.mail.mud.yahoo.com>
Message-ID: <CAEq9apJg+fnW80xTeZWyCdPQkpBjHTDSrFh9Q+AB01M6mgSV9g@mail.gmail.com>

Hi Ajay,

I don't remember the meaning of "Enhanced" and other gradient modes. Craig,
would you know what they mean and which one we should use for DTI?

As for more than 1 b0 image acquisition, I think you have to use an option
called "Average high b" and set it to "User Defined". This is a very
confusing nomenclature.

Susumu

On Sat, Oct 22, 2011 at 2:18 PM, AG <ajaygarg1971 at yahoo.com> wrote:

> Hi Susumu and other DTI studio users,
>
> I have few queries regarding data acquisition on Philips Achieve 3T
> scanner -
>
>
> What is enhanced gradient mode? Does anyone is using it?
>
> How can I acquire more than 1Bo image? We do have a research scanner.
>
> Thanks,
>
> Best,
> -Ajay
>
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From joanne.lin at auckland.ac.nz  Wed Nov  9 23:24:06 2011
From: joanne.lin at auckland.ac.nz (Joanne Lin)
Date: Thu, 10 Nov 2011 04:24:06 +0000
Subject: [Mristudio-users] Using ROI for tractography
Message-ID: <F2A353E188F5CD42BC66277361F0CDE417D3D182@FMHS-MBX1.fmhs.auckland.ac.nz>

Hi all,

I have a question about saving ROIs from ROIEditor and then using them for tractography.

I was hoping to perform tractography for each of my participants, but because my anatomy knowledge is limited, I wanted to avoid having to manually delineating regions.  I have processed the data so the JHU_MNI_SS_WMPM_TypeII is in diffusion space; my question is this - is it valid to use one (or more) of these atlas-defined structures as ROIs for tractography?

If so, how can I isolate and save one (or more) of the atlas regions as a single ROI on its own?  I have tried 'hide all' and unhiding the one/s I am interested it but it doesn't appear to work.  Apart from deleting all of the (many) structures I'm not interested in, is there a way to do this properly?

Also, is 'binary map' the best format to save ROIs to use in fibre tracking?

Any advice greatly appreciated.  Thank you kindly for your help!

Kind regards,
Jo


Joanne Lin
BPharm (Hons), RegPharmNZ

Pharmacist/PhD Candidate
School of Pharmacy
Faculty of Medical & Health Sciences
The University of Auckland
Private Bag 92019
Auckland, New Zealand
+64 9 373 7599 Ext 88468

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From drajaygarg at gmail.com  Thu Nov 10 08:08:31 2011
From: drajaygarg at gmail.com (Ajay Garg)
Date: Thu, 10 Nov 2011 18:38:31 +0530
Subject: [Mristudio-users] Enhanced Gradient Mode on philips scanner
In-Reply-To: <CAEq9apJg+fnW80xTeZWyCdPQkpBjHTDSrFh9Q+AB01M6mgSV9g@mail.gmail.com>
References: <1319307510.5019.YahooMailNeo@web30602.mail.mud.yahoo.com>
	<CAEq9apJg+fnW80xTeZWyCdPQkpBjHTDSrFh9Q+AB01M6mgSV9g@mail.gmail.com>
Message-ID: <CA+DufhGBSom4BRHoYX6ZdLzQX67qDJf0u1kk-EC4s1_Dbo5N5Q@mail.gmail.com>

Hi Susumu,

Thanks for the reply. Tomorrow I will try to acquire data with average high
b values and get back to you. i am not sure how will the structure of
gradient table will change.

Ajay

On Thu, Nov 10, 2011 at 8:32 AM, susumu mori <susumu at mri.jhu.edu> wrote:

> Hi Ajay,
>
> I don't remember the meaning of "Enhanced" and other gradient modes.
> Craig, would you know what they mean and which one we should use for DTI?
>
> As for more than 1 b0 image acquisition, I think you have to use an option
> called "Average high b" and set it to "User Defined". This is a very
> confusing nomenclature.
>
> Susumu
>
> On Sat, Oct 22, 2011 at 2:18 PM, AG <ajaygarg1971 at yahoo.com> wrote:
>
>> Hi Susumu and other DTI studio users,
>>
>> I have few queries regarding data acquisition on Philips Achieve 3T
>> scanner -
>>
>>
>> What is enhanced gradient mode? Does anyone is using it?
>>
>> How can I acquire more than 1Bo image? We do have a research scanner.
>>
>> Thanks,
>>
>> Best,
>> -Ajay
>>
>>
>>
>> _______________________________________________
>> mristudio-users mailing list
>> mristudio-users at mristudio.org
>> http://lists.mristudio.org/mailman/listinfo/
>> Unsubscribe, send a blank email to:
>> mristudio-users-unsubscribe at mristudio.org
>>
>>
>


-- 
Dr Ajay Garg
Additional professor
Department of Neuroradiology
Neurosciences Centre
All India Institute of Medical sciences (A.I.I.M.S)
Ansari Nagar,
New Delhi
India- PIN  110029

E-mail:
ajaygarg1971 at yahoo.com
drajaygarg at gmail.com

Fax:  0091-11-26588641, 26588663
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From susumu at mri.jhu.edu  Thu Nov 10 09:08:18 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Thu, 10 Nov 2011 09:08:18 -0500
Subject: [Mristudio-users] Using ROI for tractography
In-Reply-To: <F2A353E188F5CD42BC66277361F0CDE417D3D182@FMHS-MBX1.fmhs.auckland.ac.nz>
References: <F2A353E188F5CD42BC66277361F0CDE417D3D182@FMHS-MBX1.fmhs.auckland.ac.nz>
Message-ID: <CAEq9ap++87aanugZfybAUrVnDoMFLO+846Jv85YfEs6_=a2zSg@mail.gmail.com>

Hi Joanne,

Please see;
Zhang YJ, Zhang JY, Oishi K, Faria AV, Jiang HY, Li X, Akhter K, Rosa-Neto
P, Pike GB, Evans A, Toga AW, Woods R, Mazziotta JC, Miller MI, van Zijl
PCM, Mori S. Atlas-guided tract reconstruction for automated and
comprehensive examination of the white matter anatomy. NeuroImage
2010;52(4):1289-1301. PMC2910162

This paper describes the same idea.
If you want to use WMPM as ROIs, you first have to register it to each
subject.
Assuming the registration is good, you can turn the WMPM into ROIs by the
following procedure;

1) Read the WMPM as an image, not as ROI into RoiEditor
2) By placing the cursor to a pacellated region of interest, you can read
the assigned value. For example, the splenium of the CC is "119".
3) Use the threshold tool and choose pixels with a value "119". This
operation selects all pixels in the splenium of the CC.
4) Register the selected pixels as "Object 1".
5) Repeat the procedure to the second region of interest and register the
selected pixels to "Object 2".
6) Once you define all regions of interest as separate Objects, save the
Objects (the "save" icon in the "ROI" section) as "Binary Map"
7) Read FAQ15 at https://www.mristudio.org/wiki/faq to learn how to use
Binary Map for fiber tracking in DtiStudio. You can combine multiple ROIs
with AND/OR/NOT operations.

For many white matter tracts, we already generated combinations of parcels
defined in the WMPM (e.g. a combination for CST, SLF, etc), which can be
registered to each patient and ready for fiber tracking. I believe these
WMPM-ROI files are posted somewhere in our website. Please contact Yajing
for more detail.

Susumu

On Wed, Nov 9, 2011 at 11:24 PM, Joanne Lin <joanne.lin at auckland.ac.nz>wrote:

>  Hi all,****
>
> ** **
>
> I have a question about saving ROIs from ROIEditor and then using them for
> tractography.****
>
> ** **
>
> I was hoping to perform tractography for each of my participants, but
> because my anatomy knowledge is limited, I wanted to avoid having to
> manually delineating regions.  I have processed the data so the
> JHU_MNI_SS_WMPM_TypeII is in diffusion space; my question is this ? is it
> valid to use one (or more) of these atlas-defined structures as ROIs for
> tractography?****
>
> ** **
>
> If so, how can I isolate and save one (or more) of the atlas regions as a
> single ROI on its own?  I have tried ?hide all? and unhiding the one/s I am
> interested it but it doesn?t appear to work.  Apart from deleting all of
> the (many) structures I?m not interested in, is there a way to do this
> properly?****
>
> ** **
>
> Also, is ?binary map? the best format to save ROIs to use in fibre
> tracking?****
>
> ** **
>
> Any advice greatly appreciated.  Thank you kindly for your help!  ****
>
> ** **
>
> Kind regards,****
>
> Jo****
>
> ** **
>
> ** **
>
> *Joanne Lin*
>
> BPharm (Hons), RegPharmNZ****
>
> ** **
>
> Pharmacist/PhD Candidate
> School of Pharmacy****
>
> Faculty of Medical & Health Sciences****
>
> The University of Auckland****
>
> Private Bag 92019****
>
> Auckland, New Zealand****
>
> +64 9 373 7599 Ext 88468****
>
> ** **
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From susumu at mri.jhu.edu  Thu Nov 10 09:13:38 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Thu, 10 Nov 2011 09:13:38 -0500
Subject: [Mristudio-users] Mean diffusivity and ADC value
In-Reply-To: <SNT127-W29CA963A071F6FFEB3C1DFA3DC0@phx.gbl>
References: <CAMUw5-u_=x1qtv-ZTKYe5ESxy7Pot+Zqap5kSo2tXK43HP7Kxw@mail.gmail.com>
	<SNT127-W10B37688DF63430FCF8B0A3DF0@phx.gbl>
	<CAEq9apL+k0B55xMLuKWz_v0=Ut6kzLCdeXD8_U32Bqy+Ogt8_g@mail.gmail.com>
	<SNT127-W29CA963A071F6FFEB3C1DFA3DC0@phx.gbl>
Message-ID: <CAEq9ap+=Ak3QLF4v6=qtXs03QkV3wtfRBO5EJE74qPQq_fZN3A@mail.gmail.com>

You can simply divide them by 3.
For example,  0.86 e-003 +/- 0.63e-004

On Wed, Nov 9, 2011 at 9:53 PM, Arash Kamali <kamali2009res at hotmail.com>wrote:

>
>
> Thanks Dr. Mori for the response,
> In the  ROI statistics for Tensor value the bumbers are for example *Mean:
> 2.59e-003* and *Std:  1.90e-004* How I can devide these numbers by 3 to
> use for ADC value?
>
> Your input will be appreciated,
>
> Arash
> ------------------------------
> Date: Wed, 9 Nov 2011 19:16:00 -0500
> From: susumu at mri.jhu.edu
> To: mristudio-users at mristudio.org
> Subject: Re: [Mristudio-users] Mean diffusivity and ADC value
>
> Hi Arash,
>
> For ADC or MD, please use "trace" in DtiStudio. Trace/3 is equivalent to
> ADC or MD.
>
> Susumu
>
> On Tue, Nov 8, 2011 at 11:16 PM, Arash Kamali <kamali2009res at hotmail.com>wrote:
>
>  Hello Dr. Mori and Dr. Li
> My question is also about measurement of the ADC or Mean diffusivity value
> like the recently asked question bellow. On DTI studio after ADC MAP
> calculation there are multiple ADC map being generated. For 2D ROI
> measurement of the ADC which map should be used and how we can get the
> number of the ADC value in DTI studio?
>
> Your help on this matter will be greatly appreciated.
>
> Arash Kamali MD
>
>
>
> ------------------------------
> Date: Mon, 7 Nov 2011 11:42:27 -0500
> From: ksupreet6 at gmail.com
> To: mristudio-users at mristudio.org
> Subject: [Mristudio-users] Mean diffusivity and standard errors
>
> Hello DTI experts,
>                    I just need to know that how do we get the MD (mean
> diffusivity values) in DTI studio? Also is there
> a way to calculate standard error in DTI studio?
> I'll appreciate your feedback and help on this.
>
> Thanks,
>
> Sincerely,
>
> Supreet,
> Biomedical research engineer,
> Nationwide Childrens Hospital,
> Columbus, OH
> (614)355-3509
>
>
> _______________________________________________ mristudio-users mailing
> 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
>
>
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From ksupreet6 at gmail.com  Thu Nov 10 13:42:55 2011
From: ksupreet6 at gmail.com (Supreet kaur)
Date: Thu, 10 Nov 2011 13:42:55 -0500
Subject: [Mristudio-users] mean diffusivity (MD)
Message-ID: <CAMUw5-tXzu+D=oL83gLtE2kt3bHMsajjPvsaRJ8xFkRtvXZvNg@mail.gmail.com>

Dear all DTI experts,
                                 How do you calculate the Mean diffusivity
(MD) values from DTI studio?
I'll appreciate your help and reply.

Thanks,

Sincerely,

Supreet kaur,
Biomedical research engineer,
Nationwide Childrens Hospital,
Columbus, OH
(614)355-3509
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From joanne.lin at auckland.ac.nz  Tue Nov 15 22:57:24 2011
From: joanne.lin at auckland.ac.nz (Joanne Lin)
Date: Wed, 16 Nov 2011 03:57:24 +0000
Subject: [Mristudio-users] Multichannel LDDMM error
Message-ID: <F2A353E188F5CD42BC66277361F0CDE417D3DCBB@FMHS-MBX1.fmhs.auckland.ac.nz>

Hi experts,

I just tried to download some results from multichannel LDDMM and came up with the error message 'cannot download the resultant data'.

This is the first time I've used multichannel so I'm not sure if it's a common error - could it have been something I did wrong?

(Md5 string af082fddfa4b139f2c6b1d5d449d34cc)

Thanks very much!

Kind regards,
Joanne

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From xli16 at jhmi.edu  Wed Nov 16 09:14:21 2011
From: xli16 at jhmi.edu (Xin Li)
Date: Wed, 16 Nov 2011 09:14:21 -0500
Subject: [Mristudio-users] Multichannel LDDMM error
In-Reply-To: <F2A353E188F5CD42BC66277361F0CDE417D3DCBB@FMHS-MBX1.fmhs.auckland.ac.nz>
References: <F2A353E188F5CD42BC66277361F0CDE417D3DCBB@FMHS-MBX1.fmhs.auckland.ac.nz>
Message-ID: <7270f73019224.4ec37eed@johnshopkins.edu>

Hello Joanne,

In the email the server sent you, there is a ftp link of the result file. Right click the ftp link and choose "Save target as". Then you can download the result.


Xin

----- Original Message -----
From: Joanne Lin <joanne.lin at auckland.ac.nz>
Date: Tuesday, November 15, 2011 10:57 pm
Subject: [Mristudio-users] Multichannel LDDMM error
To: "mristudio-users at mristudio.org" <mristudio-users at mristudio.org>


> Hi experts,
>  
>  I just tried to download some results from multichannel LDDMM and 
> came up with the error message 'cannot download the resultant data'.
>  
>  This is the first time I've used multichannel so I'm not sure if it's 
> a common error - could it have been something I did wrong?
>  
>  (Md5 string af082fddfa4b139f2c6b1d5d449d34cc)
>  
>  Thanks very much!
>  
>  Kind regards,
>  Joanne
>   
> _______________________________________________
>  mristudio-users mailing list
>  mristudio-users at mristudio.org
>  
>  Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org 

From weinmaya at gmail.com  Sun Nov 20 06:36:08 2011
From: weinmaya at gmail.com (maya weinstein)
Date: Sun, 20 Nov 2011 13:36:08 +0200
Subject: [Mristudio-users] can I use the neonatal brain atlas in ROIEDITOR?
Message-ID: <CACtX2RvC+aD7aU0MgBAdYiYGxeSEk4KBbu0jc_5DVfTmqcs_Lw@mail.gmail.com>

Hi MRIStudio support,

I read Oishi et al (2011) "Multi-contrast human neonatal brain atlas:
Application to normal neonate

development analysis" NeuroImage.

Is there a way to coregister my data to this atlas and then use this atlas
as a reference in the ROIEditor?

Thanks,

Maya


-- 
Maya Weinstein
Department of Psychology, Bar-Ilan University
Functional Brain Imaging Unit, Wohl Institute for Advanced Imaging,
Tel-Aviv Sourasky Medical Center
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From susumu at mri.jhu.edu  Sun Nov 20 07:25:18 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Sun, 20 Nov 2011 07:25:18 -0500
Subject: [Mristudio-users] can I use the neonatal brain atlas in
	ROIEDITOR?
In-Reply-To: <CACtX2RvC+aD7aU0MgBAdYiYGxeSEk4KBbu0jc_5DVfTmqcs_Lw@mail.gmail.com>
References: <CACtX2RvC+aD7aU0MgBAdYiYGxeSEk4KBbu0jc_5DVfTmqcs_Lw@mail.gmail.com>
Message-ID: <CAEq9ap+K9rp8GsKbYr6ShR-VY+JFYELW9uvCS=Xs85aWpf2EFQ@mail.gmail.com>

We currently have several atlases for pediatric populations. Please contact
following colleagues;

0 month: Dr. Kenichi Oishi
18 month and 24 month: Dr. Shoko Yoshida

You can use these atlases as a template in DiffeoMap. The rest of the
procedures will be the same as adult atlas-based studies.

On Sun, Nov 20, 2011 at 6:36 AM, maya weinstein <weinmaya at gmail.com> wrote:

> Hi MRIStudio support,
>
> I read Oishi et al (2011) "Multi-contrast human neonatal brain atlas:
> Application to normal neonate
>
> development analysis" NeuroImage.
>
> Is there a way to coregister my data to this atlas and then use this atlas
> as a reference in the ROIEditor?
>
> Thanks,
>
> Maya
>
>
> --
> Maya Weinstein
> Department of Psychology, Bar-Ilan University
> Functional Brain Imaging Unit, Wohl Institute for Advanced Imaging,
> Tel-Aviv Sourasky Medical Center
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From koishi at mri.jhu.edu  Sun Nov 20 09:31:57 2011
From: koishi at mri.jhu.edu (kenichioishi)
Date: Sun, 20 Nov 2011 09:31:57 -0500
Subject: [Mristudio-users] can I use the neonatal brain atlas in
	ROIEDITOR?
In-Reply-To: <CAEq9ap+K9rp8GsKbYr6ShR-VY+JFYELW9uvCS=Xs85aWpf2EFQ@mail.gmail.com>
References: <CACtX2RvC+aD7aU0MgBAdYiYGxeSEk4KBbu0jc_5DVfTmqcs_Lw@mail.gmail.com>
	<CAEq9ap+K9rp8GsKbYr6ShR-VY+JFYELW9uvCS=Xs85aWpf2EFQ@mail.gmail.com>
Message-ID: <B6AA5873-F5DD-488D-ACED-114E339825A2@mri.jhu.edu>

Dear Maya,

Thank you for your interest in our neonatal atlas.
Please visit
http://cmrm.med.jhmi.edu/
then click 'Atlas' then 'Neonate brain atlas' in the leftmost column.
After registration, you can download our neonatal atlas.
You can normalize your image to this atlas using DiffeoMap (or whatever software you want, including SPM or FSL).
The Diffeomap will output 2 transformation matrices at the same time. One is a Kimap (transformation from your image to the template) and the other is an Hmap (transformation from the template to your image). 
You can normalize you image to the template space by applying the Kimap to your image.
If you want to overlay our parcellation map to your image in original space, you can apply Hmap to our parcellation map to create the parcellation map in your original space. 
To measure scalar values (e.g., FA, MD, etc) of each structure (parcel), you can use the ROIeditor.
Hope this helps.

Best regards,

Kenichi Oishi
-------------------------------------------------------------
Kenichi Oishi, MD, PhD
Assistant Professor
Department of Radiology
Johns Hopkins University School of Medicine
koishi at mri.jhu.edu
-------------------------------------------------------------

On Nov 20, 2011, at 7:25 AM, susumu mori wrote:

> We currently have several atlases for pediatric populations. Please contact following colleagues;
> 
> 0 month: Dr. Kenichi Oishi
> 18 month and 24 month: Dr. Shoko Yoshida
> 
> You can use these atlases as a template in DiffeoMap. The rest of the procedures will be the same as adult atlas-based studies.
> 
> On Sun, Nov 20, 2011 at 6:36 AM, maya weinstein <weinmaya at gmail.com> wrote:
> Hi MRIStudio support,
>  
> I read Oishi et al (2011) "Multi-contrast human neonatal brain atlas: Application to normal neonate
> development analysis" NeuroImage.
> 
> Is there a way to coregister my data to this atlas and then use this atlas as a reference in the ROIEditor?
> 
> Thanks,
> 
> Maya
> 
> 
> 
> -- 
> Maya Weinstein
> Department of Psychology, Bar-Ilan University
> Functional Brain Imaging Unit, Wohl Institute for Advanced Imaging, Tel-Aviv Sourasky Medical Center
> 
> 
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org
> 
> 

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From shokoyoshida828 at gmail.com  Sun Nov 20 11:21:05 2011
From: shokoyoshida828 at gmail.com (Shoko Y)
Date: Sun, 20 Nov 2011 11:21:05 -0500
Subject: [Mristudio-users] can I use the neonatal brain atlas in
	ROIEDITOR?
In-Reply-To: <CAEq9ap+K9rp8GsKbYr6ShR-VY+JFYELW9uvCS=Xs85aWpf2EFQ@mail.gmail.com>
References: <CACtX2RvC+aD7aU0MgBAdYiYGxeSEk4KBbu0jc_5DVfTmqcs_Lw@mail.gmail.com>
	<CAEq9ap+K9rp8GsKbYr6ShR-VY+JFYELW9uvCS=Xs85aWpf2EFQ@mail.gmail.com>
Message-ID: <CAETTSdzcMKFrEbd0Yj6RT0MQC=g19T=eA5A97YuLS9k7Yv3fZQ@mail.gmail.com>

Hi Maya,

Pediatric atlases for 18months and 24months are not uploaded to our
website yet, while they are available to be used. I could give you
them by Dropbox etc..
If you need them for your pediatric subjects, could you please let me know?

Regards,

Shoko


2011/11/20 susumu mori <susumu at mri.jhu.edu>:
> We currently have several atlases for pediatric populations. Please contact
> following colleagues;
> 0 month: Dr. Kenichi Oishi
> 18 month and 24 month: Dr. Shoko Yoshida
> You can use these atlases as a template in DiffeoMap. The rest of the
> procedures will be the same as adult atlas-based studies.
>
> On Sun, Nov 20, 2011 at 6:36 AM, maya weinstein <weinmaya at gmail.com> wrote:
>>
>> Hi MRIStudio support,
>>
>> I read Oishi et al (2011) "Multi-contrast human neonatal brain atlas:
>> Application to normal neonate
>>
>> development analysis" NeuroImage.
>>
>> Is there a way to coregister my data to this atlas and then use this atlas
>> as a reference in the ROIEditor?
>>
>> Thanks,
>>
>> Maya
>>
>> --
>> Maya Weinstein
>> Department of Psychology,?Bar-Ilan University
>> Functional Brain Imaging Unit, Wohl Institute for Advanced Imaging,
>> Tel-Aviv Sourasky Medical Center
>>
>> _______________________________________________
>> mristudio-users mailing list
>> mristudio-users at mristudio.org
>> http://lists.mristudio.org/mailman/listinfo/
>> Unsubscribe, send a blank email to:
>> mristudio-users-unsubscribe at mristudio.org
>>
>
>



-- 
Shoko Yoshida

Research Associate,
Neuroscience group, MR Research Division,
The Russell H. Morgan Department of Radiology and Radiological Science,
Johns Hopkins University School of Medicine,
210, Traylor Building, 720 Rutland Avenue, Baltimore, MD, 21205, USA
tel: +1-410-614-3016 (Office)


From amangupta2005 at gmail.com  Mon Nov 28 16:24:00 2011
From: amangupta2005 at gmail.com (aman gupta)
Date: Mon, 28 Nov 2011 15:24:00 -0600
Subject: [Mristudio-users] Coherence index calculations
Message-ID: <CALYsOkRJwnT4tdABxj-yDkUD6JS6N=sa33mhQpAmbMTG+xdDiA@mail.gmail.com>

I searched DTI Studio to see if it does Coherence Index calculation but
couldn't find it, so just wanted to check with the forum if DTI studio does
Coherence index calculation or if any other program you could recommend?

Thanks,
Aman
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From susumu at mri.jhu.edu  Mon Nov 28 16:52:40 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Mon, 28 Nov 2011 16:52:40 -0500
Subject: [Mristudio-users] Coherence index calculations
In-Reply-To: <CALYsOkRJwnT4tdABxj-yDkUD6JS6N=sa33mhQpAmbMTG+xdDiA@mail.gmail.com>
References: <CALYsOkRJwnT4tdABxj-yDkUD6JS6N=sa33mhQpAmbMTG+xdDiA@mail.gmail.com>
Message-ID: <CAEq9ap+n186wHmBrLK3hAmDhe+WYXp217LOs199rrvgOExbKXg@mail.gmail.com>

Hi Aman,

Unfortunately, DtiStudio doesn't calculate it.

Susumu

On Mon, Nov 28, 2011 at 4:24 PM, aman gupta <amangupta2005 at gmail.com> wrote:

> I searched DTI Studio to see if it does Coherence Index calculation but
> couldn't find it, so just wanted to check with the forum if DTI studio does
> Coherence index calculation or if any other program you could recommend?
>
> Thanks,
> Aman
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From josselin.houenou at gmail.com  Sun Dec  4 18:45:00 2011
From: josselin.houenou at gmail.com (josselin houenou)
Date: Mon, 05 Dec 2011 00:45:00 +0100
Subject: [Mristudio-users] no mail for LDDMM
Message-ID: <CAD21SvbGz-EVF3A=NcNoGXhps6OF3em6Mko8gvfbJJoJ8qj38g@mail.gmail.com>

Dear all,

I am using DIffeoMap for LDDMM. I have sent today 3 pairs of files, but
have not received any emails from the server; neither for saying it begins
the process; nor to tell me that the process is over. Usually, I get both
emails without any problems. Any idea why ?

Thanks a lot !

Josselin
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From susumu at mri.jhu.edu  Sun Dec  4 19:26:48 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Sun, 04 Dec 2011 19:26:48 -0500
Subject: [Mristudio-users] no mail for LDDMM
In-Reply-To: <CAD21SvbGz-EVF3A=NcNoGXhps6OF3em6Mko8gvfbJJoJ8qj38g@mail.gmail.com>
References: <CAD21SvbGz-EVF3A=NcNoGXhps6OF3em6Mko8gvfbJJoJ8qj38g@mail.gmail.com>
Message-ID: <CAEq9apLH6CD1zUM_Tvf6TF+hEJNsSY_bCP853iECQO6vQxFbxg@mail.gmail.com>

Thank you for the report. We'll investigate it.

On Sun, Dec 4, 2011 at 6:45 PM, josselin houenou <josselin.houenou at gmail.com
> wrote:

> Dear all,
>
> I am using DIffeoMap for LDDMM. I have sent today 3 pairs of files, but
> have not received any emails from the server; neither for saying it begins
> the process; nor to tell me that the process is over. Usually, I get both
> emails without any problems. Any idea why ?
>
> Thanks a lot !
>
> Josselin
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From santoshyadav20076 at gmail.com  Sun Dec  4 19:29:16 2011
From: santoshyadav20076 at gmail.com (Santosh Yadav)
Date: Mon, 05 Dec 2011 05:59:16 +0530
Subject: [Mristudio-users] no mail for LDDMM
In-Reply-To: <CAEq9apLH6CD1zUM_Tvf6TF+hEJNsSY_bCP853iECQO6vQxFbxg@mail.gmail.com>
References: <CAD21SvbGz-EVF3A=NcNoGXhps6OF3em6Mko8gvfbJJoJ8qj38g@mail.gmail.com>
	<CAEq9apLH6CD1zUM_Tvf6TF+hEJNsSY_bCP853iECQO6vQxFbxg@mail.gmail.com>
Message-ID: <CA+7fnM29gevWB3D=N=gDGarTVCD81OWvXMeV0Jn5c9FPv3wttw@mail.gmail.com>

Dear all,

I am facing the same thing.

With regards

Santosh

On Mon, Dec 5, 2011 at 5:56 AM, susumu mori <susumu at mri.jhu.edu> wrote:

> Thank you for the report. We'll investigate it.
>
> On Sun, Dec 4, 2011 at 6:45 PM, josselin houenou <
> josselin.houenou at gmail.com> wrote:
>
>> Dear all,
>>
>> I am using DIffeoMap for LDDMM. I have sent today 3 pairs of files, but
>> have not received any emails from the server; neither for saying it begins
>> the process; nor to tell me that the process is over. Usually, I get both
>> emails without any problems. Any idea why ?
>>
>> Thanks a lot !
>>
>> Josselin
>>
>>
>> _______________________________________________
>> mristudio-users mailing 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
>
>


-- 
With Best Regards,

Neuroscience and MR Research Program

Department of Medicine, Queen's Medical Center

University of Hawaii

1356 Lusitana Street, 7th Floor, Honolulu, HI 96813

Phone No. 808-220-7152

Fax No.  808-545-8970
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From akolasny at jhu.edu  Mon Dec  5 08:04:56 2011
From: akolasny at jhu.edu (akolasny at jhu.edu)
Date: Mon, 05 Dec 2011 08:04:56 -0500 (EST)
Subject: [Mristudio-users] no mail for LDDMM
In-Reply-To: <CAD21SvbGz-EVF3A=NcNoGXhps6OF3em6Mko8gvfbJJoJ8qj38g@mail.gmail.com>
References: <CAD21SvbGz-EVF3A=NcNoGXhps6OF3em6Mko8gvfbJJoJ8qj38g@mail.gmail.com>
Message-ID: <37705.192.168.2.29.1323090296.squirrel@webmail.cis.jhu.edu>

We've had some hardware issues. This week, the processing may take
a little time. I'm working on resolving the issues. There may
be delays in the processing this week.

-Anthony


> Dear all,
>
> I am using DIffeoMap for LDDMM. I have sent today 3 pairs of files, but
> have not received any emails from the server; neither for saying it begins
> the process; nor to tell me that the process is over. Usually, I get both
> emails without any problems. Any idea why ?
>
> Thanks a lot !
>
> Josselin
> _______________________________________________
> mristudio-users mailing 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  7 21:23:03 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Wed, 07 Dec 2011 21:23:03 -0500
Subject: [Mristudio-users] no mail for LDDMM
In-Reply-To: <37705.192.168.2.29.1323090296.squirrel@webmail.cis.jhu.edu>
References: <CAD21SvbGz-EVF3A=NcNoGXhps6OF3em6Mko8gvfbJJoJ8qj38g@mail.gmail.com>
	<37705.192.168.2.29.1323090296.squirrel@webmail.cis.jhu.edu>
Message-ID: <CAEq9apLEGg6XDwp_02bRm-C_JzJG0P535mouaawKpByjTYwK1g@mail.gmail.com>

Hi Anthony,

How's the server going?
Did it come back?

Susumu

On Mon, Dec 5, 2011 at 8:04 AM, <akolasny at jhu.edu> wrote:

> We've had some hardware issues. This week, the processing may take
> a little time. I'm working on resolving the issues. There may
> be delays in the processing this week.
>
> -Anthony
>
>
> > Dear all,
> >
> > I am using DIffeoMap for LDDMM. I have sent today 3 pairs of files, but
> > have not received any emails from the server; neither for saying it
> begins
> > the process; nor to tell me that the process is over. Usually, I get both
> > emails without any problems. Any idea why ?
> >
> > Thanks a lot !
> >
> > Josselin
> > _______________________________________________
> > mristudio-users mailing 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
>
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From akolasny at jhu.edu  Thu Dec  8 05:58:34 2011
From: akolasny at jhu.edu (akolasny at jhu.edu)
Date: Thu, 08 Dec 2011 05:58:34 -0500 (EST)
Subject: [Mristudio-users] no mail for LDDMM
In-Reply-To: <CAEq9apLEGg6XDwp_02bRm-C_JzJG0P535mouaawKpByjTYwK1g@mail.gmail.com>
References: <CAD21SvbGz-EVF3A=NcNoGXhps6OF3em6Mko8gvfbJJoJ8qj38g@mail.gmail.com>
	<37705.192.168.2.29.1323090296.squirrel@webmail.cis.jhu.edu>
	<CAEq9apLEGg6XDwp_02bRm-C_JzJG0P535mouaawKpByjTYwK1g@mail.gmail.com>
Message-ID: <47795.68.50.209.72.1323341914.squirrel@webmail.cis.jhu.edu>

Susumu,

It's a little more involved than one server. This morning, I'll check
to see if the normal day to day lddmm processing is functioning correctly.

Our center is going through some major infrastructure changes. This will
provide greater stability for future growth.

-Anthony

> Hi Anthony,
>
> How's the server going?
> Did it come back?
>
> Susumu
>
> On Mon, Dec 5, 2011 at 8:04 AM, <akolasny at jhu.edu> wrote:
>
>> We've had some hardware issues. This week, the processing may take
>> a little time. I'm working on resolving the issues. There may
>> be delays in the processing this week.
>>
>> -Anthony
>>
>>
>> > Dear all,
>> >
>> > I am using DIffeoMap for LDDMM. I have sent today 3 pairs of files,
>> but
>> > have not received any emails from the server; neither for saying it
>> begins
>> > the process; nor to tell me that the process is over. Usually, I get
>> both
>> > emails without any problems. Any idea why ?
>> >
>> > Thanks a lot !
>> >
>> > Josselin
>> > _______________________________________________
>> > mristudio-users mailing 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 sd880131 at 126.com  Fri Dec  9 08:27:28 2011
From: sd880131 at 126.com (sd)
Date: Fri, 09 Dec 2011 21:27:28 +0800 (CST)
Subject: [Mristudio-users] no mail for LDDMM
In-Reply-To: <47795.68.50.209.72.1323341914.squirrel@webmail.cis.jhu.edu>
References: <47795.68.50.209.72.1323341914.squirrel@webmail.cis.jhu.edu>
	<CAD21SvbGz-EVF3A=NcNoGXhps6OF3em6Mko8gvfbJJoJ8qj38g@mail.gmail.com>
	<37705.192.168.2.29.1323090296.squirrel@webmail.cis.jhu.edu>
	<CAEq9apLEGg6XDwp_02bRm-C_JzJG0P535mouaawKpByjTYwK1g@mail.gmail.com>
Message-ID: <5dc7a3a6.12440.1342301d041.Coremail.sd880131@126.com>

Dear all,
I?m a new user,now I got a problem.When I click the''Retrieve Results From Remote Volume LDDMM,I find that I don't know the MD5 string.please do me a favor.
At 2011-12-08 18:58:34,akolasny at jhu.edu wrote:
>Susumu,
>
>It's a little more involved than one server. This morning, I'll check
>to see if the normal day to day lddmm processing is functioning correctly.
>
>Our center is going through some major infrastructure changes. This will
>provide greater stability for future growth.
>
>-Anthony
>
>> Hi Anthony,
>>
>> How's the server going?
>> Did it come back?
>>
>> Susumu
>>
>> On Mon, Dec 5, 2011 at 8:04 AM, <akolasny at jhu.edu> wrote:
>>
>>> We've had some hardware issues. This week, the processing may take
>>> a little time. I'm working on resolving the issues. There may
>>> be delays in the processing this week.
>>>
>>> -Anthony
>>>
>>>
>>> > Dear all,
>>> >
>>> > I am using DIffeoMap for LDDMM. I have sent today 3 pairs of files,
>>> but
>>> > have not received any emails from the server; neither for saying it
>>> begins
>>> > the process; nor to tell me that the process is over. Usually, I get
>>> both
>>> > emails without any problems. Any idea why ?
>>> >
>>> > Thanks a lot !
>>> >
>>> > Josselin
>>> > _______________________________________________
>>> > mristudio-users mailing 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 xli16 at jhmi.edu  Fri Dec  9 12:09:22 2011
From: xli16 at jhmi.edu (Xin Li)
Date: Fri, 09 Dec 2011 12:09:22 -0500
Subject: [Mristudio-users] no mail for LDDMM
In-Reply-To: <5dc7a3a6.12440.1342301d041.Coremail.sd880131@126.com>
References: <47795.68.50.209.72.1323341914.squirrel@webmail.cis.jhu.edu>
	<CAD21SvbGz-EVF3A=NcNoGXhps6OF3em6Mko8gvfbJJoJ8qj38g@mail.gmail.com>
	<37705.192.168.2.29.1323090296.squirrel@webmail.cis.jhu.edu>
	<CAEq9apLEGg6XDwp_02bRm-C_JzJG0P535mouaawKpByjTYwK1g@mail.gmail.com>
	<5dc7a3a6.12440.1342301d041.Coremail.sd880131@126.com>
Message-ID: <72608c2b2c33.4ee1fa72@johnshopkins.edu>

Hello,

Md5 string is a 32 character string. You can find it in the emails sent by the lddmm server.


Xin

----- Original Message -----
From: sd <sd880131 at 126.com>
Date: Friday, December 9, 2011 11:28 am
Subject: Re: [Mristudio-users] no mail for LDDMM
To: "DTI Studio, ROI Editor,	DiffeoMap Questions/Support" <mristudio-users at mristudio.org>
Cc: Michael Miller <mim at cis.jhu.edu>


> Dear all,
>  I?m a new user,now I got a problem.When I click the''Retrieve Results 
> From Remote Volume LDDMM,I find that I don't know the MD5 
> string.please do me a favor.
>  At 2011-12-08 18:58:34,akolasny at jhu.edu wrote:
>  >Susumu,
>  >
>  >It's a little more involved than one server. This morning, I'll check
>  >to see if the normal day to day lddmm processing is functioning correctly.
>  >
>  >Our center is going through some major infrastructure changes. This 
> will
>  >provide greater stability for future growth.
>  >
>  >-Anthony
>  >
>  >> Hi Anthony,
>  >>
>  >> How's the server going?
>  >> Did it come back?
>  >>
>  >> Susumu
>  >>
>  >> On Mon, Dec 5, 2011 at 8:04 AM, <akolasny at jhu.edu> wrote:
>  >>
>  >>> We've had some hardware issues. This week, the processing may take
>  >>> a little time. I'm working on resolving the issues. There may
>  >>> be delays in the processing this week.
>  >>>
>  >>> -Anthony
>  >>>
>  >>>
>  >>> > Dear all,
>  >>> >
>  >>> > I am using DIffeoMap for LDDMM. I have sent today 3 pairs of files,
>  >>> but
>  >>> > have not received any emails from the server; neither for 
> saying it
>  >>> begins
>  >>> > the process; nor to tell me that the process is over. Usually, 
> I get
>  >>> both
>  >>> > emails without any problems. Any idea why ?
>  >>> >
>  >>> > Thanks a lot !
>  >>> >
>  >>> > Josselin
>  >>> > _______________________________________________
>  >>> > 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 ksupreet6 at gmail.com  Fri Dec  9 13:02:39 2011
From: ksupreet6 at gmail.com (Supreet kaur)
Date: Fri, 09 Dec 2011 13:02:39 -0500
Subject: [Mristudio-users] DTI statistics need help!!!
Message-ID: <CAMUw5-sQFAn215KvHYvaZ=HCXpNu=W_SNT8ayH_fGyBXCO8JQw@mail.gmail.com>

hi DTI experts,
                             I need to ask you that is there any way that I
can export my statistics numbers in DTI studio (as I am doing Fiber
tractography, so I am interested in taking the mean FA, no. of fibers,
eigenvalue1, eigenvetor1, etc),
I need to export these numbers directly into excel. Do you have any code or
macros for importing those numbers directly into excel sheet?
I'll really appreciate your feedback on this.

Thanks,


Sincerely,

Supreet kaur,
Biomedical research engineer,
Nationwide Childrens Hospital,
Columbus, OH
(614)355-3509
-------------- next part --------------
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From LisaMarie.Langevin at albertahealthservices.ca  Fri Dec  9 14:07:57 2011
From: LisaMarie.Langevin at albertahealthservices.ca (Lisa Marie Langevin)
Date: Fri, 09 Dec 2011 12:07:57 -0700
Subject: [Mristudio-users] AIR/MI/theory AIR, which is the best?
In-Reply-To: <CAEq9apJrz80vACEGHuCTFopi1wEo401B+erRAJa5+7jaXas4Bw@mail.gmail.com>
References: <CAEq9apJrz80vACEGHuCTFopi1wEo401B+erRAJa5+7jaXas4Bw@mail.gmail.com>
Message-ID: <16D6DA47889FE44BA52573AAAE4493AE3C9261BE46@EXMBX10C.crha.bewell.ca>

Dear Dr. Mori,

I have been using your atlas to identify and trace the SLF on my pediatric DTI data.  I am interested in now subdividing the SLF into it's component parts, but from the literature, it seems as though the ROIs and tract images don't include the dorsomedial portion of the SLF, known as SLF I.  SLF II and III figure prominently, however.

According to the atlas, the region where the SLF I is usually found has been denoted as superior frontal gyrus white matter (SFG-WM) and superior parietal gyrus white matter (SPL-WM).

Is this the most recent terminology?

This link to a recent Nature article better illustrates the region I am trying to identify.

http://www.nature.com/neuro/journal/v14/n10/fig_tab/nn.2905_F1.html

Thank you!

Lisa Marie Langevin






Lisa Marie Langevin, PhD.
Postdoctoral Research Fellow
Behavioural Research Unit
Alberta Children's Hospital Research Institute for Child and Maternal Health
Tel: (403) 955-2785, Fax: (403) 955-2772
Email: lisamarie.langevin at albertahealthservices.ca
________________________________________
From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori [susumu at mri.jhu.edu]
Sent: August 11, 2011 5:46 PM
To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
Subject: Re: [Mristudio-users] AIR/MI/theory AIR, which is the best?

If the scans are not co-registered (the subject went out and came back to the scanner), I suggest you to calculate the tensor first and register the tensor using DiffeoMap and linear registration (AIR or MI).

If you register the raw DWI data, you may get a bit better SNR (this is my guess), but you have to make sure to use the b-table re-orientation scheme in the AIR. I would recommend to use AIR or MI (MI may take a lot of time), although I don't have much experience in the cross-scan registration.

I think the first method (calculate tensor and then register) is the easiest.


On Thu, Aug 11, 2011 at 6:35 PM, Min Liu <mliu4 at ualberta.ca<mailto:mliu4 at ualberta.ca>> wrote:


Dear MRIStudio users,

I have four human brain datasets that are scanned sequentially (back
to back) of a single subject using the same DTI protocol. I want to
get an averaged dataset out of the four. Before doing that,
motion/eddy current correction is definitely needed. I am wondering
among the three methods provided by DTIStudio, i.e. AIR/MI?theory AIR.
By visual inspection, there is rotation/shifting between the very
first dataset and the very last by about 2 voxels. For this subtle
movement, is there a conclusion so far regarding which coregistration
is the best (without introducing errors! Sometimes AIR does more harm
than good by misalignment.) Thank you for your thoughts!!

Min
_______________________________________________
mristudio-users mailing list
mristudio-users at mristudio.org<mailto:mristudio-users at mristudio.org>
http://lists.mristudio.org/mailman/listinfo/
Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org<mailto:mristudio-users-unsubscribe at mristudio.org>




        <<
                ATT00001..c     (0.3KB)

                (0.3KB)
        >>

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.


From susumu at mri.jhu.edu  Sun Dec 11 11:00:59 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Sun, 11 Dec 2011 11:00:59 -0500
Subject: [Mristudio-users] AIR/MI/theory AIR, which is the best?
In-Reply-To: <16D6DA47889FE44BA52573AAAE4493AE3C9261BE46@EXMBX10C.crha.bewell.ca>
References: <CAEq9apJrz80vACEGHuCTFopi1wEo401B+erRAJa5+7jaXas4Bw@mail.gmail.com>
	<16D6DA47889FE44BA52573AAAE4493AE3C9261BE46@EXMBX10C.crha.bewell.ca>
Message-ID: <CAEq9apLibtYyM9DrhkW2qaT6ObnnE5UOy2cR_rL2xRJnZpVFXA@mail.gmail.com>

Hi Lisa,

There are multiple terminologies in white matter anatomy and within each
terminology, the consensus is not always consistent.

In general, there are two different ways to define the white matter
anatomy. One is based on the location. For example, "The anterior limb of
internal capsule (ALIC)" is a white matter location between the caudate and
the putamen.

The second way to define the white matter is based on the pathway. In the
ALIC, there are corticothalamo and thalamocortical pathways. There are
also descending pathways such as cortiopontine, cortiobulbar, and
corticospinal tracts.

If I pick up, for example, the coritopontine fiber, it starts the motor
cortex and go through the peripheral white matter beneath the motor cortex,
the corona radiata, the internal capsule, the cerebral peduncle, and the
pons. This exemplifies how the same white matter area can be called in
different ways.

To me, the SLF I, II, and III are more based on pathway definition,
connecting different cortical areas.

The white matter parcellation maps (PM) we provide are purely based on
location information. Therefore, it is quite possible that the
pathway-defined structure, such as SLF I not only occupies a portion of the
our PM-based SLF and also a portion of SFG-WM.

I have to check Xin and Yajing, but the current RoiEditor also contains
probabilistic coordinates based on the pathway-based white matter
definition. I believe that contains SLF I, II, and III. If your RoiEditor
doesn't have these (should be RoiEditor/Images/Tracts), you can find them
in our website (lbam.med.jhmi.edu).

For the definition of these probabilistic coordinates, please refer to;

Zhang YJ, Zhang JY, Oishi K, Faria AV, Jiang HY, Li X, Akhter K, Rosa-Neto
P, Pike GB, Evans A, Toga AW, Woods R, Mazziotta JC, Miller MI, van Zijl
PCM, Mori S. Atlas-guided tract reconstruction for automated and
comprehensive examination of the white matter anatomy. NeuroImage
2010;52(4):1289-1301

Xin and Yajing, please let us know where exactly they are.

Susumu

On Fri, Dec 9, 2011 at 2:07 PM, Lisa Marie Langevin <
LisaMarie.Langevin at albertahealthservices.ca> wrote:

> Dear Dr. Mori,
>
> I have been using your atlas to identify and trace the SLF on my pediatric
> DTI data.  I am interested in now subdividing the SLF into it's component
> parts, but from the literature, it seems as though the ROIs and tract
> images don't include the dorsomedial portion of the SLF, known as SLF I.
>  SLF II and III figure prominently, however.
>
> According to the atlas, the region where the SLF I is usually found has
> been denoted as superior frontal gyrus white matter (SFG-WM) and superior
> parietal gyrus white matter (SPL-WM).
>
> Is this the most recent terminology?
>
> This link to a recent Nature article better illustrates the region I am
> trying to identify.
>
> http://www.nature.com/neuro/journal/v14/n10/fig_tab/nn.2905_F1.html
>
> Thank you!
>
> Lisa Marie Langevin
>
>
>
>
>
>
> Lisa Marie Langevin, PhD.
> Postdoctoral Research Fellow
> Behavioural Research Unit
> Alberta Children's Hospital Research Institute for Child and Maternal
> Health
> Tel: (403) 955-2785, Fax: (403) 955-2772
> Email: lisamarie.langevin at albertahealthservices.ca
> ________________________________________
> From: mristudio-users-bounces at mristudio.org [
> mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori [
> susumu at mri.jhu.edu]
> Sent: August 11, 2011 5:46 PM
> To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
> Subject: Re: [Mristudio-users] AIR/MI/theory AIR, which is the best?
>
> If the scans are not co-registered (the subject went out and came back to
> the scanner), I suggest you to calculate the tensor first and register the
> tensor using DiffeoMap and linear registration (AIR or MI).
>
> If you register the raw DWI data, you may get a bit better SNR (this is my
> guess), but you have to make sure to use the b-table re-orientation scheme
> in the AIR. I would recommend to use AIR or MI (MI may take a lot of time),
> although I don't have much experience in the cross-scan registration.
>
> I think the first method (calculate tensor and then register) is the
> easiest.
>
>
> On Thu, Aug 11, 2011 at 6:35 PM, Min Liu <mliu4 at ualberta.ca<mailto:
> mliu4 at ualberta.ca>> wrote:
>
>
> Dear MRIStudio users,
>
> I have four human brain datasets that are scanned sequentially (back
> to back) of a single subject using the same DTI protocol. I want to
> get an averaged dataset out of the four. Before doing that,
> motion/eddy current correction is definitely needed. I am wondering
> among the three methods provided by DTIStudio, i.e. AIR/MI?theory AIR.
> By visual inspection, there is rotation/shifting between the very
> first dataset and the very last by about 2 voxels. For this subtle
> movement, is there a conclusion so far regarding which coregistration
> is the best (without introducing errors! Sometimes AIR does more harm
> than good by misalignment.) Thank you for your thoughts!!
>
> Min
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org<mailto:mristudio-users at mristudio.org>
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org<mailto:
> mristudio-users-unsubscribe at mristudio.org>
>
>
>
>
>        <<
>                ATT00001..c     (0.3KB)
>
>                (0.3KB)
>        >>
>
> 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
>
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From zhangyajing9996 at gmail.com  Sun Dec 11 11:25:49 2011
From: zhangyajing9996 at gmail.com (Yajing Zhang)
Date: Sun, 11 Dec 2011 11:25:49 -0500
Subject: [Mristudio-users] AIR/MI/theory AIR, which is the best?
In-Reply-To: <CAEq9apLibtYyM9DrhkW2qaT6ObnnE5UOy2cR_rL2xRJnZpVFXA@mail.gmail.com>
References: <CAEq9apJrz80vACEGHuCTFopi1wEo401B+erRAJa5+7jaXas4Bw@mail.gmail.com>
	<16D6DA47889FE44BA52573AAAE4493AE3C9261BE46@EXMBX10C.crha.bewell.ca>
	<CAEq9apLibtYyM9DrhkW2qaT6ObnnE5UOy2cR_rL2xRJnZpVFXA@mail.gmail.com>
Message-ID: <CADKVbtFcfquqR8xTRiCZ+J_PocXcT_EMqYtq9ZJAnv8hz3rtvg@mail.gmail.com>

Hi, Lisa

In case your ROIeditor does not have these probabilistic pathway
definitions, you can download the files at this page:
http://lbam.med.jhmi.edu/cmrm/Data_Yajing/fiberMenu.htm . To use them in
ROIeditor, you can load the data as "raw image".


Yajing

On Sun, Dec 11, 2011 at 11:00 AM, susumu mori <susumu at mri.jhu.edu> wrote:

> Hi Lisa,
>
> There are multiple terminologies in white matter anatomy and within each
> terminology, the consensus is not always consistent.
>
> In general, there are two different ways to define the white matter
> anatomy. One is based on the location. For example, "The anterior limb of
> internal capsule (ALIC)" is a white matter location between the caudate and
> the putamen.
>
> The second way to define the white matter is based on the pathway. In the
> ALIC, there are corticothalamo and thalamocortical pathways. There are
> also descending pathways such as cortiopontine, cortiobulbar, and
> corticospinal tracts.
>
> If I pick up, for example, the coritopontine fiber, it starts the motor
> cortex and go through the peripheral white matter beneath the motor cortex,
> the corona radiata, the internal capsule, the cerebral peduncle, and the
> pons. This exemplifies how the same white matter area can be called in
> different ways.
>
> To me, the SLF I, II, and III are more based on pathway definition,
> connecting different cortical areas.
>
> The white matter parcellation maps (PM) we provide are purely based on
> location information. Therefore, it is quite possible that the
> pathway-defined structure, such as SLF I not only occupies a portion of the
> our PM-based SLF and also a portion of SFG-WM.
>
> I have to check Xin and Yajing, but the current RoiEditor also contains
> probabilistic coordinates based on the pathway-based white matter
> definition. I believe that contains SLF I, II, and III. If your RoiEditor
> doesn't have these (should be RoiEditor/Images/Tracts), you can find them
> in our website (lbam.med.jhmi.edu).
>
> For the definition of these probabilistic coordinates, please refer to;
>
> Zhang YJ, Zhang JY, Oishi K, Faria AV, Jiang HY, Li X, Akhter K, Rosa-Neto
> P, Pike GB, Evans A, Toga AW, Woods R, Mazziotta JC, Miller MI, van Zijl
> PCM, Mori S. Atlas-guided tract reconstruction for automated and
> comprehensive examination of the white matter anatomy. NeuroImage
> 2010;52(4):1289-1301
>
> Xin and Yajing, please let us know where exactly they are.
>
> Susumu
>
> On Fri, Dec 9, 2011 at 2:07 PM, Lisa Marie Langevin <
> LisaMarie.Langevin at albertahealthservices.ca> wrote:
>
>> Dear Dr. Mori,
>>
>> I have been using your atlas to identify and trace the SLF on my
>> pediatric DTI data.  I am interested in now subdividing the SLF into it's
>> component parts, but from the literature, it seems as though the ROIs and
>> tract images don't include the dorsomedial portion of the SLF, known as SLF
>> I.  SLF II and III figure prominently, however.
>>
>> According to the atlas, the region where the SLF I is usually found has
>> been denoted as superior frontal gyrus white matter (SFG-WM) and superior
>> parietal gyrus white matter (SPL-WM).
>>
>> Is this the most recent terminology?
>>
>> This link to a recent Nature article better illustrates the region I am
>> trying to identify.
>>
>> http://www.nature.com/neuro/journal/v14/n10/fig_tab/nn.2905_F1.html
>>
>> Thank you!
>>
>> Lisa Marie Langevin
>>
>>
>>
>>
>>
>>
>> Lisa Marie Langevin, PhD.
>> Postdoctoral Research Fellow
>> Behavioural Research Unit
>> Alberta Children's Hospital Research Institute for Child and Maternal
>> Health
>> Tel: (403) 955-2785, Fax: (403) 955-2772
>> Email: lisamarie.langevin at albertahealthservices.ca
>> ________________________________________
>> From: mristudio-users-bounces at mristudio.org [
>> mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori [
>> susumu at mri.jhu.edu]
>> Sent: August 11, 2011 5:46 PM
>> To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
>> Subject: Re: [Mristudio-users] AIR/MI/theory AIR, which is the best?
>>
>> If the scans are not co-registered (the subject went out and came back to
>> the scanner), I suggest you to calculate the tensor first and register the
>> tensor using DiffeoMap and linear registration (AIR or MI).
>>
>> If you register the raw DWI data, you may get a bit better SNR (this is
>> my guess), but you have to make sure to use the b-table re-orientation
>> scheme in the AIR. I would recommend to use AIR or MI (MI may take a lot of
>> time), although I don't have much experience in the cross-scan registration.
>>
>> I think the first method (calculate tensor and then register) is the
>> easiest.
>>
>>
>> On Thu, Aug 11, 2011 at 6:35 PM, Min Liu <mliu4 at ualberta.ca<mailto:
>> mliu4 at ualberta.ca>> wrote:
>>
>>
>> Dear MRIStudio users,
>>
>> I have four human brain datasets that are scanned sequentially (back
>> to back) of a single subject using the same DTI protocol. I want to
>> get an averaged dataset out of the four. Before doing that,
>> motion/eddy current correction is definitely needed. I am wondering
>> among the three methods provided by DTIStudio, i.e. AIR/MI?theory AIR.
>> By visual inspection, there is rotation/shifting between the very
>> first dataset and the very last by about 2 voxels. For this subtle
>> movement, is there a conclusion so far regarding which coregistration
>> is the best (without introducing errors! Sometimes AIR does more harm
>> than good by misalignment.) Thank you for your thoughts!!
>>
>> Min
>> _______________________________________________
>> mristudio-users mailing list
>> mristudio-users at mristudio.org<mailto:mristudio-users at mristudio.org>
>> http://lists.mristudio.org/mailman/listinfo/
>> Unsubscribe, send a blank email to:
>> mristudio-users-unsubscribe at mristudio.org<mailto:
>> mristudio-users-unsubscribe at mristudio.org>
>>
>>
>>
>>
>>        <<
>>                ATT00001..c     (0.3KB)
>>
>>                (0.3KB)
>>        >>
>>
>> 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
>>
>
>
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From susumu at mri.jhu.edu  Sun Dec 11 12:23:42 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Sun, 11 Dec 2011 12:23:42 -0500
Subject: [Mristudio-users] AIR/MI/theory AIR, which is the best?
In-Reply-To: <CADKVbtFcfquqR8xTRiCZ+J_PocXcT_EMqYtq9ZJAnv8hz3rtvg@mail.gmail.com>
References: <CAEq9apJrz80vACEGHuCTFopi1wEo401B+erRAJa5+7jaXas4Bw@mail.gmail.com>
	<16D6DA47889FE44BA52573AAAE4493AE3C9261BE46@EXMBX10C.crha.bewell.ca>
	<CAEq9apLibtYyM9DrhkW2qaT6ObnnE5UOy2cR_rL2xRJnZpVFXA@mail.gmail.com>
	<CADKVbtFcfquqR8xTRiCZ+J_PocXcT_EMqYtq9ZJAnv8hz3rtvg@mail.gmail.com>
Message-ID: <CAEq9ap+VNf9hK4_JKti211fvTvOAf1jvJk7QzNhK+Fxv09RH0w@mail.gmail.com>

I believe that you can also load the probabilistic maps as an ROI and
calculate the probability-weighted pixel intensity such as FA.

On Sun, Dec 11, 2011 at 11:25 AM, Yajing Zhang <zhangyajing9996 at gmail.com>wrote:

> Hi, Lisa
>
> In case your ROIeditor does not have these probabilistic pathway
> definitions, you can download the files at this page:
> http://lbam.med.jhmi.edu/cmrm/Data_Yajing/fiberMenu.htm . To use them in
> ROIeditor, you can load the data as "raw image".
>
>
> Yajing
>
> On Sun, Dec 11, 2011 at 11:00 AM, susumu mori <susumu at mri.jhu.edu> wrote:
>
>> Hi Lisa,
>>
>> There are multiple terminologies in white matter anatomy and within each
>> terminology, the consensus is not always consistent.
>>
>> In general, there are two different ways to define the white matter
>> anatomy. One is based on the location. For example, "The anterior limb of
>> internal capsule (ALIC)" is a white matter location between the caudate and
>> the putamen.
>>
>> The second way to define the white matter is based on the pathway. In the
>> ALIC, there are corticothalamo and thalamocortical pathways. There are
>> also descending pathways such as cortiopontine, cortiobulbar, and
>> corticospinal tracts.
>>
>> If I pick up, for example, the coritopontine fiber, it starts the motor
>> cortex and go through the peripheral white matter beneath the motor cortex,
>> the corona radiata, the internal capsule, the cerebral peduncle, and the
>> pons. This exemplifies how the same white matter area can be called in
>> different ways.
>>
>> To me, the SLF I, II, and III are more based on pathway definition,
>> connecting different cortical areas.
>>
>> The white matter parcellation maps (PM) we provide are purely based on
>> location information. Therefore, it is quite possible that the
>> pathway-defined structure, such as SLF I not only occupies a portion of the
>> our PM-based SLF and also a portion of SFG-WM.
>>
>> I have to check Xin and Yajing, but the current RoiEditor also contains
>> probabilistic coordinates based on the pathway-based white matter
>> definition. I believe that contains SLF I, II, and III. If your RoiEditor
>> doesn't have these (should be RoiEditor/Images/Tracts), you can find them
>> in our website (lbam.med.jhmi.edu).
>>
>> For the definition of these probabilistic coordinates, please refer to;
>>
>> Zhang YJ, Zhang JY, Oishi K, Faria AV, Jiang HY, Li X, Akhter K,
>> Rosa-Neto P, Pike GB, Evans A, Toga AW, Woods R, Mazziotta JC, Miller MI,
>> van Zijl PCM, Mori S. Atlas-guided tract reconstruction for automated and
>> comprehensive examination of the white matter anatomy. NeuroImage
>> 2010;52(4):1289-1301
>>
>> Xin and Yajing, please let us know where exactly they are.
>>
>> Susumu
>>
>> On Fri, Dec 9, 2011 at 2:07 PM, Lisa Marie Langevin <
>> LisaMarie.Langevin at albertahealthservices.ca> wrote:
>>
>>> Dear Dr. Mori,
>>>
>>> I have been using your atlas to identify and trace the SLF on my
>>> pediatric DTI data.  I am interested in now subdividing the SLF into it's
>>> component parts, but from the literature, it seems as though the ROIs and
>>> tract images don't include the dorsomedial portion of the SLF, known as SLF
>>> I.  SLF II and III figure prominently, however.
>>>
>>> According to the atlas, the region where the SLF I is usually found has
>>> been denoted as superior frontal gyrus white matter (SFG-WM) and superior
>>> parietal gyrus white matter (SPL-WM).
>>>
>>> Is this the most recent terminology?
>>>
>>> This link to a recent Nature article better illustrates the region I am
>>> trying to identify.
>>>
>>> http://www.nature.com/neuro/journal/v14/n10/fig_tab/nn.2905_F1.html
>>>
>>> Thank you!
>>>
>>> Lisa Marie Langevin
>>>
>>>
>>>
>>>
>>>
>>>
>>> Lisa Marie Langevin, PhD.
>>> Postdoctoral Research Fellow
>>> Behavioural Research Unit
>>> Alberta Children's Hospital Research Institute for Child and Maternal
>>> Health
>>> Tel: (403) 955-2785, Fax: (403) 955-2772
>>> Email: lisamarie.langevin at albertahealthservices.ca
>>> ________________________________________
>>> From: mristudio-users-bounces at mristudio.org [
>>> mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori [
>>> susumu at mri.jhu.edu]
>>> Sent: August 11, 2011 5:46 PM
>>> To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
>>> Subject: Re: [Mristudio-users] AIR/MI/theory AIR, which is the best?
>>>
>>> If the scans are not co-registered (the subject went out and came back
>>> to the scanner), I suggest you to calculate the tensor first and register
>>> the tensor using DiffeoMap and linear registration (AIR or MI).
>>>
>>> If you register the raw DWI data, you may get a bit better SNR (this is
>>> my guess), but you have to make sure to use the b-table re-orientation
>>> scheme in the AIR. I would recommend to use AIR or MI (MI may take a lot of
>>> time), although I don't have much experience in the cross-scan registration.
>>>
>>> I think the first method (calculate tensor and then register) is the
>>> easiest.
>>>
>>>
>>> On Thu, Aug 11, 2011 at 6:35 PM, Min Liu <mliu4 at ualberta.ca<mailto:
>>> mliu4 at ualberta.ca>> wrote:
>>>
>>>
>>> Dear MRIStudio users,
>>>
>>> I have four human brain datasets that are scanned sequentially (back
>>> to back) of a single subject using the same DTI protocol. I want to
>>> get an averaged dataset out of the four. Before doing that,
>>> motion/eddy current correction is definitely needed. I am wondering
>>> among the three methods provided by DTIStudio, i.e. AIR/MI?theory AIR.
>>> By visual inspection, there is rotation/shifting between the very
>>> first dataset and the very last by about 2 voxels. For this subtle
>>> movement, is there a conclusion so far regarding which coregistration
>>> is the best (without introducing errors! Sometimes AIR does more harm
>>> than good by misalignment.) Thank you for your thoughts!!
>>>
>>> Min
>>> _______________________________________________
>>> mristudio-users mailing list
>>> mristudio-users at mristudio.org<mailto:mristudio-users at mristudio.org>
>>> http://lists.mristudio.org/mailman/listinfo/
>>> Unsubscribe, send a blank email to:
>>> mristudio-users-unsubscribe at mristudio.org<mailto:
>>> mristudio-users-unsubscribe at mristudio.org>
>>>
>>>
>>>
>>>
>>>        <<
>>>                ATT00001..c     (0.3KB)
>>>
>>>                (0.3KB)
>>>        >>
>>>
>>> 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
>>>
>>
>>
>
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From yakira at kuhp.kyoto-u.ac.jp  Mon Dec 12 20:48:57 2011
From: yakira at kuhp.kyoto-u.ac.jp (Akira Yamamoto)
Date: Tue, 13 Dec 2011 10:48:57 +0900
Subject: [Mristudio-users] LDDMM awake?
Message-ID: <20111213104857.72F9.82258683@kuhp.kyoto-u.ac.jp>

Hello list,

I am using MRIstudio.
I have uploaded our data to LDDMM server yesterday. However, I have not
received confirmation mail yet.
I would like to know the status of LDDMM server. Is it available now?

Thanks.

Akira Yamamoto
-- 
Akira Yamamoto, M.D., Ph.D.
Assistant Professor
Department of Diagnostic Imaging and Nuclear Medicine
Kyoto University Hospital
54 Shogoin Kawahara-cho, Sakyo-ku, Kyoto-shi
Kyoto, JAPAN 6068507
Tel: +81-75-751-3760
Fax: +81-75-771-9709
Skype: yakira6454
yakira at kuhp.kyoto-u.ac.jp


From sd880131 at 126.com  Tue Dec 13 01:43:11 2011
From: sd880131 at 126.com (sd)
Date: Tue, 13 Dec 2011 14:43:11 +0800 (CST)
Subject: [Mristudio-users] LDDMM awake?
In-Reply-To: <20111213104857.72F9.82258683@kuhp.kyoto-u.ac.jp>
References: <20111213104857.72F9.82258683@kuhp.kyoto-u.ac.jp>
Message-ID: <5a80e0dd.cb3c.13436291d83.Coremail.sd880131@126.com>

Hello list,
I have received 2 messages from LDDMM.But when I wanted to retrieve the results,there came a caution said ''cannot download the result".What should I do to resolve this error?
Thanks.
At 2011-12-13 09:48:57,"Akira Yamamoto" <yakira at kuhp.kyoto-u.ac.jp> wrote:
>Hello list,
>
>I am using MRIstudio.
>I have uploaded our data to LDDMM server yesterday. However, I have not
>received confirmation mail yet.
>I would like to know the status of LDDMM server. Is it available now?
>
>Thanks.
>
>Akira Yamamoto
>-- 
>Akira Yamamoto, M.D., Ph.D.
>Assistant Professor
>Department of Diagnostic Imaging and Nuclear Medicine
>Kyoto University Hospital
>54 Shogoin Kawahara-cho, Sakyo-ku, Kyoto-shi
>Kyoto, JAPAN 6068507
>Tel: +81-75-751-3760
>Fax: +81-75-771-9709
>Skype: yakira6454
>yakira at kuhp.kyoto-u.ac.jp
>
>_______________________________________________
>mristudio-users mailing 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  Tue Dec 13 08:09:36 2011
From: xli16 at jhmi.edu (Xin Li)
Date: Tue, 13 Dec 2011 08:09:36 -0500
Subject: [Mristudio-users] LDDMM awake?
In-Reply-To: <5a80e0dd.cb3c.13436291d83.Coremail.sd880131@126.com>
References: <20111213104857.72F9.82258683@kuhp.kyoto-u.ac.jp>
	<5a80e0dd.cb3c.13436291d83.Coremail.sd880131@126.com>
Message-ID: <72f0ab4a19a2.4ee70840@johnshopkins.edu>

The LDDMM server have given you the ftp links of the results in the emails. You may right click the ftp links and choose the option "Save Target As" to download the results in Internet Explore directly. Or you may use any other ftp tools to download the results. 



----- Original Message -----
From: sd <sd880131 at 126.com>
Date: Tuesday, December 13, 2011 1:43 am
Subject: Re: [Mristudio-users] LDDMM awake?
To: "DTI Studio, ROI Editor,	DiffeoMap Questions/Support" <mristudio-users at mristudio.org>


> Hello list,
>  I have received 2 messages from LDDMM.But when I wanted to retrieve 
> the results,there came a caution said ''cannot download the 
> result".What should I do to resolve this error?
>  Thanks.
>  At 2011-12-13 09:48:57,"Akira Yamamoto" <yakira at kuhp.kyoto-u.ac.jp> wrote:
>  >Hello list,
>  >
>  >I am using MRIstudio.
>  >I have uploaded our data to LDDMM server yesterday. However, I have 
> not
>  >received confirmation mail yet.
>  >I would like to know the status of LDDMM server. Is it available now?
>  >
>  >Thanks.
>  >
>  >Akira Yamamoto
>  >-- 
>  >Akira Yamamoto, M.D., Ph.D.
>  >Assistant Professor
>  >Department of Diagnostic Imaging and Nuclear Medicine
>  >Kyoto University Hospital
>  >54 Shogoin Kawahara-cho, Sakyo-ku, Kyoto-shi
>  >Kyoto, JAPAN 6068507
>  >Tel: +81-75-751-3760
>  >Fax: +81-75-771-9709
>  >Skype: yakira6454
>  >yakira at kuhp.kyoto-u.ac.jp
>  >
>  >_______________________________________________
>  >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 billquinndme at yahoo.com  Tue Dec 13 10:32:47 2011
From: billquinndme at yahoo.com (Bill Quinn)
Date: Tue, 13 Dec 2011 15:32:47 +0000 (GMT)
Subject: [Mristudio-users] AIR image dimensions/ Talairach WMPM/Eigen vector
	flipping/ROI Error
Message-ID: <1323790367.60327.YahooMailNeo@web29616.mail.ird.yahoo.com>

Hi mri-studio users and programmers,

First of all, thank you for well written program and also your?fantastic 
follow up service. If possible I would like to ask a couple of questions 
just to clarify some questions that I have about the basic workings. 

1. In Diffeomap I perform Air Linear Registration in order to align my 
data with that of the Template (in my case I use the Talairach atlas). 
My images are 256*256*55 and I normalise it with the template of 
dimensions 192*192*136. How much does the difference in image size 
affect the accuracy and reliability of the subsequent analysis.
	* As an additional to ensure the best LDDMM result, is the contrast 
of the two images the most important in setting up the images before 
entering the LDDMM screen?
 

2. When I load the Talairach WMPM from diffeomap as an ROI the regions 
of interest are loaded as object 1,2 etc. Is it possible to get the name
 of each region of interest? When I perform the intensity measurements 
using the WMPM I get the a table listing a the same amount of parts as 
the objects i.e. in the case of Talairach 170. I then use the following 
paper to find what the abbreviations stand for:

Oishi et al,Atlas-based whole brain white matter analysis using large deformation diffeomorphic metric mapping: Application to 
normal elderly and Alzheimer?s disease participants
euroimage 2009 June ; 46(2): 486?499. (Appendix A part 4)

Is this the correct approach? Or is it the that the regions of interest 
in the ROI objects box contain these parts as can be seen when I choose 
the button under Atlas: WMPM of division of defined ROIs


3. When I load or create the tensor image file (.d file) in DIffeoMap I 
am asked if I want to flip the eigenvectors. If I save the file as 
eigenvectors being flipped when I created the file do I also have to 
flip them again while opening the file afterwards or do I assume they 
are now in the correct direction? 

4. Finally, when I create an ROI in either DTIStudio or ROI editor I 
save it as a binary map. When I then try to reload it in the fibre 
tracking section I am informed that the"Image parameters in this 
file are not consistent with with current ones, continue?" When I 
select yes the ROI loads in the expected position. Is it a normal 
occurance to get an error even though I created the ROI in the same image during the 
same DTIStudio session? 

 If any of these questions have already been answered, please just point 
me to the appropiate link.

Thank you for you time,

Best Regards,

William Quinn
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From susumu at mri.jhu.edu  Tue Dec 13 20:40:11 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Tue, 13 Dec 2011 20:40:11 -0500
Subject: [Mristudio-users] AIR image dimensions/ Talairach WMPM/Eigen
 vector flipping/ROI Error
In-Reply-To: <1323790367.60327.YahooMailNeo@web29616.mail.ird.yahoo.com>
References: <1323790367.60327.YahooMailNeo@web29616.mail.ird.yahoo.com>
Message-ID: <CAEq9ap+2_=DdFLAaDjzLezJTk8vDMm9F41p1zhYKf4J1ib+Oig@mail.gmail.com>

Hi Bill,


> 1. In Diffeomap I perform Air Linear Registration in order to align my
> data with that of the Template (in my case I use the Talairach atlas). My
> images are 256*256*55 and I normalise it with the template of dimensions
> 192*192*136. How much does the difference in image size affect the accuracy
> and reliability of the subsequent analysis.
>

because this is a simple upsampling, I assume that you don't have to worry
too much about the accuracy/reliability, but I don't have a definite
answer. Practically, I believe the accuracy is much more influenced by the
registration accuracy, not by the upsampling.

>
>    - As an additional to ensure the best LDDMM result, is the contrast of
>    the two images the most important in setting up the images before entering
>    the LDDMM screen?
>
>
>
when you do non-linear normalization, two images must have very similar
contrasts. Non-linear normalization aggressively deforms images to find the
best match. If the contrasts of the two images are different, the matching
becomes a very difficult task. So, please make sure that you use the same
contrast images and do intensity (histogram) matching before LDDMM.

2. When I load the Talairach WMPM from diffeomap as an ROI the regions of
> interest are loaded as object 1,2 etc. Is it possible to get the name of
> each region of interest? When I perform the intensity measurements using
> the WMPM I get the a table listing a the same amount of parts as the
> objects i.e. in the case of Talairach 170. I then use the following paper
> to find what the abbreviations stand for:
> *
> **Oishi et al,** Atlas-based whole brain white matter analysis using
> large deformation diffeomorphic metric mapping: Application to normal
> elderly and Alzheimer?s disease participants*
> euroimage 2009 June ; 46(2): 486?499. (Appendix A part 4)
>
> Is this the correct approach? Or is it the that the regions of interest in
> the ROI objects box contain these parts as can be seen when I choose the
> button under Atlas: *WMPM of division of defined ROIs*
>
>
If you load an ROI map (like WMPM) in the RoiEditor format, it loads the
ROI names too. If you load an ROI map in the binary format, you get the
generic ROI names (i.e. 1, 2, 3,,,). In this case, you need to find a
look-up table, which should be in the RoiEditor/Image directories.


>
> 3. When I load or create the tensor image file (.d file) in DIffeoMap I am
> asked if I want to flip the eigenvectors. If I save the file as
> eigenvectors being flipped when I created the file do I also have to flip
> them again while opening the file afterwards or do I assume they are now in
> the correct direction?
>
>
The "flipping" business is important only when you happened to use a table
with wrong +/- signs. I would suggest you to use a correct table and forget
about this business. In old days, before the table information was stored
in DICOM header, we had only one generic gradient table from each vendor.
These generic tables had arbitrary +/- definition and we had to figure out
the +/- sign empirically. In this case, we often calculated the tensor
using the generic table first and correct the sign later by "flipping" the
vector orientation. There are two occasions when the flipping becomes
important. One is tractography. We load the eigenvector, flip the sign, and
do tractography. The other is image transformation. We load the tensor
file, flip the sign, and transform. Here, once the transformation is done,
you don't have to do any further flipping.



> 4. Finally, when I create an ROI in either DTIStudio or ROI editor I save
> it as a binary map. When I then try to reload it in the fibre tracking
> section I am informed that the* "Image parameters in this file are not
> consistent with with current ones, continue?"* When I select yes the ROI
> loads in the expected position. Is it a normal occurance to get an error
> even though I created the ROI in the same image during the same DTIStudio
> session?
>
>
you get his message when the matrix size and file size don't match. Please
check if your file size is correct. Also, please check FAQ#15 in here (
https://www.mristudio.org/wiki/faq).

Susumu


>
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From sd880131 at 126.com  Wed Dec 14 01:40:56 2011
From: sd880131 at 126.com (sd)
Date: Wed, 14 Dec 2011 14:40:56 +0800 (CST)
Subject: [Mristudio-users] AIR image dimensions/ Talairach WMPM/Eigen
 vector flipping/ROI Error
In-Reply-To: <1323790367.60327.YahooMailNeo@web29616.mail.ird.yahoo.com>
References: <1323790367.60327.YahooMailNeo@web29616.mail.ird.yahoo.com>
Message-ID: <13a4f70a.18ba8.1343b4d6b41.Coremail.sd880131@126.com>

Hi?
I just wonder that which subject should I submit for the LDDMM process?The initial images or the images after linear transformation?
Sandy

At 2011-12-13 23:32:47,"Bill Quinn" <billquinndme at yahoo.com> wrote:

Hi mri-studio users and programmers,

First of all, thank you for well written program and also your fantastic follow up service. If possible I would like to ask a couple of questions just to clarify some questions that I have about the basic workings.

1. In Diffeomap I perform Air Linear Registration in order to align my data with that of the Template (in my case I use the Talairach atlas). My images are 256*256*55 and I normalise it with the template of dimensions 192*192*136. How much does the difference in image size affect the accuracy and reliability of the subsequent analysis.
As an additional to ensure the best LDDMM result, is the contrast of the two images the most important in setting up the images before entering the LDDMM screen?


2. When I load the Talairach WMPM from diffeomap as an ROI the regions of interest are loaded as object 1,2 etc. Is it possible to get the name of each region of interest? When I perform the intensity measurements using the WMPM I get the a table listing a the same amount of parts as the objects i.e. in the case of Talairach 170. I then use the following paper to find what the abbreviations stand for:

Oishi et al, Atlas-based whole brain white matter analysis using large deformation diffeomorphic metric mapping: Application to normal elderly and Alzheimer?s disease participants
euroimage 2009 June ; 46(2): 486?499. (Appendix A part 4)

Is this the correct approach? Or is it the that the regions of interest in the ROI objects box contain these parts as can be seen when I choose the button under Atlas: WMPM of division of defined ROIs


3. When I load or create the tensor image file (.d file) in DIffeoMap I am asked if I want to flip the eigenvectors. If I save the file as eigenvectors being flipped when I created the file do I also have to flip them again while opening the file afterwards or do I assume they are now in the correct direction?

4. Finally, when I create an ROI in either DTIStudio or ROI editor I save it as a binary map. When I then try to reload it in the fibre tracking section I am informed that the "Image parameters in this file are not consistent with with current ones, continue?" When I select yes the ROI loads in the expected position. Is it a normal occurance to get an error even though I created the ROI in the same image during the same DTIStudio session?

If any of these questions have already been answered, please just point me to the appropiate link.

Thank you for you time,

Best Regards,

William Quinn
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From santoshyadav20076 at gmail.com  Wed Dec 14 02:44:34 2011
From: santoshyadav20076 at gmail.com (Santosh Yadav)
Date: Wed, 14 Dec 2011 13:14:34 +0530
Subject: [Mristudio-users] g value
Message-ID: <CA+7fnM3DpAJQUoA_Gi=MzF5u6N7kC-XTsTodxfHAUDpGcJ9wyA@mail.gmail.com>

Hi DTI experts,


I was just wondering that what g value (optimum) should be used for making
the bet images in adult population.


With regards

Santosh
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From sd880131 at 126.com  Wed Dec 14 05:21:33 2011
From: sd880131 at 126.com (sd)
Date: Wed, 14 Dec 2011 18:21:33 +0800 (CST)
Subject: [Mristudio-users] some question about diffeomap
Message-ID: <1e5d18eb.1c977.1343c17670b.Coremail.sd880131@126.com>

Dear mristudio users?
Now I'm using the Diffeomap to aline my data,I find that  I can only submit 2 subjects  for the LDDMM multichannel process.After the successful mssage appeared,I need to rewrite my email and select  another 2 data and re-select my template. Is that right?Or just caused by my mistaken operation?In addition,should the 2 subjects I selected from the same sample?This has a ''Hmap'' and a ''Kimap'' in the result.zip I download from ftp,I want to know their meaning respectively.
Thank you for your kindness.
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From susumu at mri.jhu.edu  Wed Dec 14 07:27:03 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Wed, 14 Dec 2011 07:27:03 -0500
Subject: [Mristudio-users] some question about diffeomap
In-Reply-To: <1e5d18eb.1c977.1343c17670b.Coremail.sd880131@126.com>
References: <1e5d18eb.1c977.1343c17670b.Coremail.sd880131@126.com>
Message-ID: <CAEq9apLBHvkS6qe75H5OfAqn_xb8XZ5iVb=n_JEBcFhss2CZAA@mail.gmail.com>

Hi sd,

When we do multi-channel, you submit two different images from the same
subject. For example, if you did DTI, you can get b0 image, FA image, MD
image, etc.

If you submit two FA images; one from the atlas and one from your patient
data, it is "single-channel" LDDMM.

If you submit FA and b0; FA & b0 from the atlas and FA & b0 from your
patient data, it is "multi-channel" LDDMM.

The multi-channel LDDMM may give you more accurate registration between the
atlas and the subject. Both single and multi-channel LDDMM give you only
one set of Hmap/Kimap to match the atlas and subject images.

Hope this clarifies your question.

Susumu

2011/12/14 sd <sd880131 at 126.com>

> Dear mristudio users?
> Now I'm using the Diffeomap to aline my data,I find that  I can only
> submit 2 subjects  for the LDDMM multichannel process.After the successful
> mssage appeared,I need to rewrite my email and select  another 2 data and
> re-select my template. Is that right?Or just caused by my mistaken
> operation?In addition,should the 2 subjects I selected from the same
> sample?This has a ''Hmap'' and a ''Kimap'' in the result.zip I download
> from ftp,I want to know their meaning respectively.
> Thank you for your kindness.
>
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From susumu at mri.jhu.edu  Wed Dec 14 07:30:20 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Wed, 14 Dec 2011 07:30:20 -0500
Subject: [Mristudio-users] AIR image dimensions/ Talairach WMPM/Eigen
 vector flipping/ROI Error
In-Reply-To: <13a4f70a.18ba8.1343b4d6b41.Coremail.sd880131@126.com>
References: <1323790367.60327.YahooMailNeo@web29616.mail.ird.yahoo.com>
	<13a4f70a.18ba8.1343b4d6b41.Coremail.sd880131@126.com>
Message-ID: <CAEq9apJ82Sar-uVM5GvYZODRsVO2QbYvzs=xJ_3pnSvkTxp5cw@mail.gmail.com>

Before LDDMM, please make sure to do linear registration. Non-linear
solutions always depend on a good initial estimation by a linear solution.

On Wed, Dec 14, 2011 at 1:40 AM, sd <sd880131 at 126.com> wrote:

> Hi?
> I just wonder that which subject should I submit for the LDDMM process?The
> initial images or the images after linear transformation?
> Sandy
>
> At 2011-12-13 23:32:47,"Bill Quinn" <billquinndme at yahoo.com> wrote:
>
> Hi mri-studio users and programmers,
>
> First of all, thank you for well written program and also your fantastic
> follow up service. If possible I would like to ask a couple of questions
> just to clarify some questions that I have about the basic workings.
>
> 1. In Diffeomap I perform Air Linear Registration in order to align my
> data with that of the Template (in my case I use the Talairach atlas). My
> images are 256*256*55 and I normalise it with the template of dimensions
> 192*192*136. How much does the difference in image size affect the accuracy
> and reliability of the subsequent analysis.
>
>    - As an additional to ensure the best LDDMM result, is the contrast of
>    the two images the most important in setting up the images before entering
>    the LDDMM screen?
>
>
> 2. When I load the Talairach WMPM from diffeomap as an ROI the regions of
> interest are loaded as object 1,2 etc. Is it possible to get the name of
> each region of interest? When I perform the intensity measurements using
> the WMPM I get the a table listing a the same amount of parts as the
> objects i.e. in the case of Talairach 170. I then use the following paper
> to find what the abbreviations stand for:
> *
> **Oishi et al,** Atlas-based whole brain white matter analysis using
> large deformation diffeomorphic metric mapping: Application to normal
> elderly and Alzheimer?s disease participants*
> euroimage 2009 June ; 46(2): 486?499. (Appendix A part 4)
>
> Is this the correct approach? Or is it the that the regions of interest in
> the ROI objects box contain these parts as can be seen when I choose the
> button under Atlas: *WMPM of division of defined ROIs*
>
>
> 3. When I load or create the tensor image file (.d file) in DIffeoMap I am
> asked if I want to flip the eigenvectors. If I save the file as
> eigenvectors being flipped when I created the file do I also have to flip
> them again while opening the file afterwards or do I assume they are now in
> the correct direction?
>
> 4. Finally, when I create an ROI in either DTIStudio or ROI editor I save
> it as a binary map. When I then try to reload it in the fibre tracking
> section I am informed that the* "Image parameters in this file are not
> consistent with with current ones, continue?"* When I select yes the ROI
> loads in the expected position. Is it a normal occurance to get an error
> even though I created the ROI in the same image during the same DTIStudio
> session?
>
> If any of these questions have already been answered, please just point me
> to the appropiate link.
>
> Thank you for you time,
>
> Best Regards,
>
> William Quinn
>
>
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From susumu at mri.jhu.edu  Wed Dec 14 07:37:40 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Wed, 14 Dec 2011 07:37:40 -0500
Subject: [Mristudio-users] g value
In-Reply-To: <CA+7fnM3DpAJQUoA_Gi=MzF5u6N7kC-XTsTodxfHAUDpGcJ9wyA@mail.gmail.com>
References: <CA+7fnM3DpAJQUoA_Gi=MzF5u6N7kC-XTsTodxfHAUDpGcJ9wyA@mail.gmail.com>
Message-ID: <CAEq9ap+sN0pFkJAoL_0vsr_o2qHDyaeUKfuWZ0MGK-+QXWttzQ@mail.gmail.com>

Do you mean b-value?
Many simulation studies point 800-1,200 are good numbers.
I prefer a bit lower side like 700. It's personal preference. I like it
because of less motion artifacts and short TE. I came up with this number
based on my subjective experience, but I would say it's safer to use 1,000.

On Wed, Dec 14, 2011 at 2:44 AM, Santosh Yadav
<santoshyadav20076 at gmail.com>wrote:

> Hi DTI experts,
>
>
> I was just wondering that what g value (optimum) should be used for making
> the bet images in adult population.
>
>
> With regards
>
> Santosh
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From kamali2009res at hotmail.com  Fri Dec 16 00:39:12 2011
From: kamali2009res at hotmail.com (Arash Kamali)
Date: Fri, 16 Dec 2011 00:39:12 -0500
Subject: [Mristudio-users] Image data displaying function ?
In-Reply-To: <CAEq9ap+sN0pFkJAoL_0vsr_o2qHDyaeUKfuWZ0MGK-+QXWttzQ@mail.gmail.com>
References: <CA+7fnM3DpAJQUoA_Gi=MzF5u6N7kC-XTsTodxfHAUDpGcJ9wyA@mail.gmail.com>
	<CAEq9ap+sN0pFkJAoL_0vsr_o2qHDyaeUKfuWZ0MGK-+QXWttzQ@mail.gmail.com>
Message-ID: <SNT127-W501475841981901F8360B8A3A00@phx.gbl>


Hello Dr. Mori,I have two questions regarding the DTIstudio, 1)  Is it possible to include the anatomic data set for example the T1w images to the PAR REC data set aquired on the same subject to use in DTIstudio? 2)  Is there any function smiliar to the image data displayining function in dtistudio that instead of generating the matrix of the data from the pixels around the center of the image can generate the matrix of the data from the pixels inside the selected ROI? Thanks s lot, Arash
 Date: Wed, 14 Dec 2011 07:37:40 -0500
From: susumu at mri.jhu.edu
To: mristudio-users at mristudio.org
Subject: Re: [Mristudio-users] g value

Do you mean b-value?Many simulation studies point 800-1,200 are good numbers.I prefer a bit lower side like 700. It's personal preference. I like it because of less motion artifacts and short TE. I came up with this number based on my subjective experience, but I would say it's safer to use 1,000.


On Wed, Dec 14, 2011 at 2:44 AM, Santosh Yadav <santoshyadav20076 at gmail.com> wrote:

Hi DTI experts,


I was just wondering that what g value (optimum) should be
used for making the bet images in adult population.
With regards
Santosh


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mristudio-users at mristudio.org

http://lists.mristudio.org/mailman/listinfo/

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From susumu at mri.jhu.edu  Sat Dec 17 21:38:26 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Sat, 17 Dec 2011 21:38:26 -0500
Subject: [Mristudio-users] Image data displaying function ?
In-Reply-To: <SNT127-W501475841981901F8360B8A3A00@phx.gbl>
References: <CA+7fnM3DpAJQUoA_Gi=MzF5u6N7kC-XTsTodxfHAUDpGcJ9wyA@mail.gmail.com>
	<CAEq9ap+sN0pFkJAoL_0vsr_o2qHDyaeUKfuWZ0MGK-+QXWttzQ@mail.gmail.com>
	<SNT127-W501475841981901F8360B8A3A00@phx.gbl>
Message-ID: <CAEq9apJ76sujvxJOFOmprcppZ-UwRDn02vqMNXYkZgXC2kHVyw@mail.gmail.com>

Hi Arash,

On Fri, Dec 16, 2011 at 12:39 AM, Arash Kamali <kamali2009res at hotmail.com>wrote:

>  Hello Dr. Mori,
> I have two questions regarding the DTIstudio,
>
> 1)  Is it possible to include the anatomic data set for example the T1w
> images to the PAR REC data set aquired on the same subject to use in
> DTIstudio?
>

Not sure what you exactly meant, but it is possible to save T1w in PAR/REC
format by the scanner.
You can load and view the T1w in DtiStudio.


>
> 2)  Is there any function smiliar to the image data displayining function
> in dtistudio that instead of generating the matrix of the data from the
> pixels around the center of the image can generate the matrix of the data
> from the pixels inside the selected ROI?
>
>

Do you mean, recording the pixel intensities of all pixels within the ROI?


>
> ------------------------------
> Date: Wed, 14 Dec 2011 07:37:40 -0500
> From: susumu at mri.jhu.edu
> To: mristudio-users at mristudio.org
> Subject: Re: [Mristudio-users] g value
>
> Do you mean b-value?
> Many simulation studies point 800-1,200 are good numbers.
> I prefer a bit lower side like 700. It's personal preference. I like it
> because of less motion artifacts and short TE. I came up with this number
> based on my subjective experience, but I would say it's safer to use 1,000.
>
> On Wed, Dec 14, 2011 at 2:44 AM, Santosh Yadav <
> santoshyadav20076 at gmail.com> wrote:
>
> Hi DTI experts,
>
>
> I was just wondering that what g value (optimum) should be used for making
> the bet images in adult population.
>
>
> With regards
>
> Santosh
>
>
> _______________________________________________
> mristudio-users mailing 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
>
>
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From ruibinzhang at sina.cn  Sun Dec 18 22:37:20 2011
From: ruibinzhang at sina.cn (ruibinzhang at sina.cn)
Date: Mon, 19 Dec 2011 11:37:20 +0800
Subject: [Mristudio-users] how can i export the bet image to DTIstudio
Message-ID: <20111219033720.3B76141688E@mail1.webapp.51uc.com>

Dear experts of DTIstudio:
       Recently i met with a problem. Due to the slice thickness was 4mm, that is to say that was too thick, so i used the FSL bet to get the pure image. Then i wanted  to export the image after bet to DTI mapping, however when  i exported it , the image was the same to pre-bet. How can i solve this proble and export the image that after beting?
      By the way, my data was acquired by GE, and i exported the data in Simen, GE., Philips DIC, 
     With best wished for you, and Merry Christmas

                                                                                                                                                                                                                           Yours sincery 
                                                                                                                                                                                                                                Ruibin
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From kamali2009res at hotmail.com  Mon Dec 19 07:46:35 2011
From: kamali2009res at hotmail.com (Arash Kamali)
Date: Mon, 19 Dec 2011 07:46:35 -0500
Subject: [Mristudio-users] Image data displaying function ?
In-Reply-To: <CAEq9apJ76sujvxJOFOmprcppZ-UwRDn02vqMNXYkZgXC2kHVyw@mail.gmail.com>
References: <CA+7fnM3DpAJQUoA_Gi=MzF5u6N7kC-XTsTodxfHAUDpGcJ9wyA@mail.gmail.com>
	<CAEq9ap+sN0pFkJAoL_0vsr_o2qHDyaeUKfuWZ0MGK-+QXWttzQ@mail.gmail.com>
	<SNT127-W501475841981901F8360B8A3A00@phx.gbl>
	<CAEq9apJ76sujvxJOFOmprcppZ-UwRDn02vqMNXYkZgXC2kHVyw@mail.gmail.com>
Message-ID: <SNT127-W393FF122DFC9F5AE4D90F6A3A70@phx.gbl>


Thanks Dr. Mori,
 Yes, Thats exactly what I mean. Is there any way to have all the pixel signal intensities within the ROI?
 
and about my first quiestion, what is the  easiest way to load T1 map to DTI studio?
 
thanks for your time,
 
Arash



Date: Sat, 17 Dec 2011 21:38:26 -0500
From: susumu at mri.jhu.edu
To: mristudio-users at mristudio.org
Subject: Re: [Mristudio-users] Image data displaying function ?

Hi Arash,


On Fri, Dec 16, 2011 at 12:39 AM, Arash Kamali <kamali2009res at hotmail.com> wrote:



Hello Dr. Mori,
I have two questions regarding the DTIstudio,
 
1)  Is it possible to include the anatomic data set for example the T1w images to the PAR REC data set aquired on the same subject to use in DTIstudio?



Not sure what you exactly meant, but it is possible to save T1w in PAR/REC format by the scanner.
You can load and view the T1w in DtiStudio.
 


 
2)  Is there any function smiliar to the image data displayining function in dtistudio that instead of generating the matrix of the data from the pixels around the center of the image can generate the matrix of the data from the pixels inside the selected ROI?
 



Do you mean, recording the pixel intensities of all pixels within the ROI?
 


 




Date: Wed, 14 Dec 2011 07:37:40 -0500
From: susumu at mri.jhu.edu
To: mristudio-users at mristudio.org
Subject: Re: [Mristudio-users] g value

Do you mean b-value?
Many simulation studies point 800-1,200 are good numbers.
I prefer a bit lower side like 700. It's personal preference. I like it because of less motion artifacts and short TE. I came up with this number based on my subjective experience, but I would say it's safer to use 1,000.


On Wed, Dec 14, 2011 at 2:44 AM, Santosh Yadav <santoshyadav20076 at gmail.com> wrote:


Hi DTI experts,


I was just wondering that what g value (optimum) should be used for making the bet images in adult population.


With regards


Santosh

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mristudio-users mailing list
mristudio-users at mristudio.org
http://lists.mristudio.org/mailman/listinfo/
Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org



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From susumu at mri.jhu.edu  Wed Dec 21 20:39:02 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Wed, 21 Dec 2011 20:39:02 -0500
Subject: [Mristudio-users] Image data displaying function ?
In-Reply-To: <SNT127-W393FF122DFC9F5AE4D90F6A3A70@phx.gbl>
References: <CA+7fnM3DpAJQUoA_Gi=MzF5u6N7kC-XTsTodxfHAUDpGcJ9wyA@mail.gmail.com>
	<CAEq9ap+sN0pFkJAoL_0vsr_o2qHDyaeUKfuWZ0MGK-+QXWttzQ@mail.gmail.com>
	<SNT127-W501475841981901F8360B8A3A00@phx.gbl>
	<CAEq9apJ76sujvxJOFOmprcppZ-UwRDn02vqMNXYkZgXC2kHVyw@mail.gmail.com>
	<SNT127-W393FF122DFC9F5AE4D90F6A3A70@phx.gbl>
Message-ID: <CAEq9ap+uZEQOSezjtf=4VpoM8nsJx2uHxRetftkpPKcqhCxupA@mail.gmail.com>

>  Thanks Dr. Mori,
>  Yes, Thats exactly what I mean. Is there any way to have all the pixel
> signal intensities within the ROI?
>
>

Not by DitStudio. If you read the same image into RoiEditor and define
ROIs, there is "export pixel value" function, with which you can save and
read the pixel values by Excel.


> and about my first quiestion, what is the  easiest way to load T1 map to
> DTI studio?
>
>

You can directly read T1 to DtiStudio using DICOM, REC, Analyze, Nifti, and
raw, depending on the format of your T1.

Susumu
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From xiaogai.li at sth.kth.se  Thu Dec 22 12:35:37 2011
From: xiaogai.li at sth.kth.se (Xiaogai Li)
Date: Thu, 22 Dec 2011 17:35:37 +0000
Subject: [Mristudio-users] How to save fiber tracts in vtk format in DTI
	studio
Message-ID: <9E544B44F0CF0149BE0DB91E0C3ED25528AC9E92@EXDB4.ug.kth.se>

Hi all, 

Using DTI studio for fiber tract, the saved file format is an image.

Is there any way to save the fiber tracts as vtk polyline format like the way you can do it in Slicer 3D?
Otherwise, if there is any plugin to convert fibers to vtk polyline format?

Thanks a lot for your time.
Xiaogai Li

From billquinndme at yahoo.com  Fri Dec 23 07:47:56 2011
From: billquinndme at yahoo.com (Bill Quinn)
Date: Fri, 23 Dec 2011 12:47:56 +0000 (GMT)
Subject: [Mristudio-users] DiffeoMap - Returning Image to the native
	subject space after LDDMM
In-Reply-To: <1324582961.17459.YahooMailNeo@web29606.mail.ird.yahoo.com>
References: <1324582961.17459.YahooMailNeo@web29606.mail.ird.yahoo.com>
Message-ID: <1324644476.33955.YahooMailNeo@web29606.mail.ird.yahoo.com>

Hi all,


Just looking for a bit of help in using diffeomap as I seem to be doing something wrong in converting the Talairach_SS_WMPM to the native subject space. When I apply the Hmap from the LDDMM analysis to the WMPM the WMPM is converted perfectly. When I then apply the inverted AIR file I am running into a problem. The file does not seem to convert it correctly. 

I have searched through the forum and applied the approach suggested in a couple of posts but I am still having the same issue. If anyone has experience of this and could help me out it would be much appreciated.

The atlas?is 192*192*136 while my data is 256*256*55. When I apply the Inverted air file the WMPM gets converted but seems to remain in the original dimensions. For example, there are originally 136 slices and the air_inverted file also has 136 slices but an image occurs in only 55 of them. The image is also?compressed to the bottom right of the frame.

Procedure
????????? Load Template
o?? Talairach b0
????????? Load Sample
o?? b0
o?? FA
????????? Run AIR LINEAR
o?? Ensure both b0 images active
o?? Affine/Trilinear
o?? Save .air file
o?? Save converted files
????????? Run air invert_air_file
o?? Choose saved air file
????????? Close Diffeomap
?
????????? Open Template in Diffeomap
o?? Open FA image as subject (2nd time use WMPM of Talairach)
o?? Select Load Transformation Matrix
o?? Choose inverted file air
o?? Choose Trilinear or Nearest Neighbour

?If required I can send? the results I have gotten from the?process.?
Thank you in advance,

Bill
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From xli16 at jhmi.edu  Fri Dec 23 09:17:50 2011
From: xli16 at jhmi.edu (Xin Li)
Date: Fri, 23 Dec 2011 09:17:50 -0500
Subject: [Mristudio-users] DiffeoMap - Returning Image to the native
 subject space after LDDMM
In-Reply-To: <1324644476.33955.YahooMailNeo@web29606.mail.ird.yahoo.com>
References: <1324582961.17459.YahooMailNeo@web29606.mail.ird.yahoo.com>
	<1324644476.33955.YahooMailNeo@web29606.mail.ird.yahoo.com>
Message-ID: <72209a63774c.4ef4473e@johnshopkins.edu>

Hello Bill,

Your original data is 256*256*55. When the template is your original data (256*256*55) and the inverted air is applied, the WMPM is supposed to be converted to your original data space that is 256*256*55. 

Please take a look at the second slide on the webpage https://www.mristudio.org/wiki/user_manual/diffeomap/GetStarted_DualChannelNormalizationPipeline%3A
It shows the steps to convert the WMPM to the original data space.


By the way, when the WMPM is applied, please make sure to choose nearest neighbor as the interpolation method.


Xin


----- Original Message -----
From: Bill Quinn <billquinndme at yahoo.com>
Date: Friday, December 23, 2011 7:48 am
Subject: Re: [Mristudio-users] DiffeoMap - Returning Image to the native subject space after LDDMM
To: "mristudio-users at mristudio.org" <mristudio-users at mristudio.org>


> Hi all,
>  
>  
>  Just looking for a bit of help in using diffeomap as I seem to be 
> doing something wrong in converting the Talairach_SS_WMPM to the 
> native subject space. When I apply the Hmap from the LDDMM analysis to 
> the WMPM the WMPM is converted perfectly. When I then apply the 
> inverted AIR file I am running into a problem. The file does not seem 
> to convert it correctly. 
>  
>  I have searched through the forum and applied the approach suggested 
> in a couple of posts but I am still having the same issue. If anyone 
> has experience of this and could help me out it would be much appreciated.
>  
>  The atlas?is 192*192*136 while my data is 256*256*55. When I apply 
> the Inverted air file the WMPM gets converted but seems to remain in 
> the original dimensions. For example, there are originally 136 slices 
> and the air_inverted file also has 136 slices but an image occurs in 
> only 55 of them. The image is also?compressed to the bottom right of 
> the frame.
>  
>  Procedure
>  ????????? Load Template
>  o?? Talairach b0
>  ????????? Load Sample
>  o?? b0
>  o?? FA
>  ????????? Run AIR LINEAR
>  o?? Ensure both b0 images active
>  o?? Affine/Trilinear
>  o?? Save .air file
>  o?? Save converted files
>  ????????? Run air invert_air_file
>  o?? Choose saved air file
>  ????????? Close Diffeomap
>  ?
>  ????????? Open Template in Diffeomap
>  o?? Open FA image as subject (2nd time use WMPM of Talairach)
>  o?? Select Load Transformation Matrix
>  o?? Choose inverted file air
>  o?? Choose Trilinear or Nearest Neighbour
>  
>  ?If required I can send? the results I have gotten from the?process.?
>  Thank you in advance,
>   Bill
> _______________________________________________
>  mristudio-users mailing list
>  mristudio-users at mristudio.org
>  
>  Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org 


From billquinndme at yahoo.com  Fri Dec 23 10:11:02 2011
From: billquinndme at yahoo.com (Bill Quinn)
Date: Fri, 23 Dec 2011 15:11:02 +0000 (GMT)
Subject: [Mristudio-users] DiffeoMap - Returning Image to the native
 subject space after LDDMM
In-Reply-To: <72209a63774c.4ef4473e@johnshopkins.edu>
References: <1324582961.17459.YahooMailNeo@web29606.mail.ird.yahoo.com>
	<1324644476.33955.YahooMailNeo@web29606.mail.ird.yahoo.com>
	<72209a63774c.4ef4473e@johnshopkins.edu>
Message-ID: <1324653062.51739.YahooMailNeo@web29602.mail.ird.yahoo.com>

Hi Xin,
?
Thank you very much, the problem was my selection of the template as you described.
?
Thanks again for a quick and effective response.
?
Bill


________________________________
From: Xin Li <xli16 at jhmi.edu>
To: Bill Quinn <billquinndme at yahoo.com>; "DTI Studio, ROI Editor, DiffeoMap Questions/Support" <mristudio-users at mristudio.org> 
Sent: Friday, 23 December 2011, 14:17
Subject: Re: [Mristudio-users] DiffeoMap - Returning Image to the native subject space after LDDMM

Hello Bill,

Your original data is 256*256*55. When the template is your original data (256*256*55) and the inverted air is applied, the WMPM is supposed to be converted to your original data space that is 256*256*55. 

Please take a look at the second slide on the webpage https://www.mristudio.org/wiki/user_manual/diffeomap/GetStarted_DualChannelNormalizationPipeline%3A
It shows the steps to convert the WMPM to the original data space.


By the way, when the WMPM is applied, please make sure to choose nearest neighbor as the interpolation method.


Xin


----- Original Message -----
From: Bill Quinn <billquinndme at yahoo.com>
Date: Friday, December 23, 2011 7:48 am
Subject: Re: [Mristudio-users] DiffeoMap - Returning Image to the native subject space after LDDMM
To: "mristudio-users at mristudio.org" <mristudio-users at mristudio.org>


> Hi all,
>? 
>? 
>? Just looking for a bit of help in using diffeomap as I seem to be 
> doing something wrong in converting the Talairach_SS_WMPM to the 
> native subject space. When I apply the Hmap from the LDDMM analysis to 
> the WMPM the WMPM is converted perfectly. When I then apply the 
> inverted AIR file I am running into a problem. The file does not seem 
> to convert it correctly. 
>? 
>? I have searched through the forum and applied the approach suggested 
> in a couple of posts but I am still having the same issue. If anyone 
> has experience of this and could help me out it would be much appreciated.
>? 
>? The atlas?is 192*192*136 while my data is 256*256*55. When I apply 
> the Inverted air file the WMPM gets converted but seems to remain in 
> the original dimensions. For example, there are originally 136 slices 
> and the air_inverted file also has 136 slices but an image occurs in 
> only 55 of them. The image is also?compressed to the bottom right of 
> the frame.
>? 
>? Procedure
>? ????????? Load Template
>? o?? Talairach b0
>? ????????? Load Sample
>? o?? b0
>? o?? FA
>? ????????? Run AIR LINEAR
>? o?? Ensure both b0 images active
>? o?? Affine/Trilinear
>? o?? Save .air file
>? o?? Save converted files
>? ????????? Run air invert_air_file
>? o?? Choose saved air file
>? ????????? Close Diffeomap
>? ?
>? ????????? Open Template in Diffeomap
>? o?? Open FA image as subject (2nd time use WMPM of Talairach)
>? o?? Select Load Transformation Matrix
>? o?? Choose inverted file air
>? o?? Choose Trilinear or Nearest Neighbour
>? 
>? ?If required I can send? the results I have gotten from the?process.?
>? Thank you in advance,
>? Bill
> _______________________________________________
>? mristudio-users mailing list
>? mristudio-users at mristudio.org
>? 
>? Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org
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From susumu at mri.jhu.edu  Fri Dec 23 17:35:14 2011
From: susumu at mri.jhu.edu (susumu mori)
Date: Fri, 23 Dec 2011 17:35:14 -0500
Subject: [Mristudio-users] How to save fiber tracts in vtk format in DTI
 studio
In-Reply-To: <9E544B44F0CF0149BE0DB91E0C3ED25528AC9E92@EXDB4.ug.kth.se>
References: <AQHMwNAd+h50QNSXukWDxFz8weEaXw==@jhuin3.jhu.edu>
	<9E544B44F0CF0149BE0DB91E0C3ED25528AC9E92@EXDB4.ug.kth.se>
Message-ID: <CAEq9apJAgkaj3u8iwiFcbidJT7r9vTd5ydwy6Y9OkQrNZ=tLkw@mail.gmail.com>

DtiStudio saves the tract information as an image or a streamline. For the
latter, it has DtiStudio format as explained in FAQ#1 (
https://www.mristudio.org/wiki/faq#head-3015271ef8a43c43bd5f42e957a8591a3657e60a
).

Hangyi should know more about the vtk format but I don't think we currently
offer a tool to convert this tract format to a vtk format.

On Thu, Dec 22, 2011 at 12:35 PM, Xiaogai Li <xiaogai.li at sth.kth.se> wrote:

> Hi all,
>
> Using DTI studio for fiber tract, the saved file format is an image.
>
> Is there any way to save the fiber tracts as vtk polyline format like the
> way you can do it in Slicer 3D?
> Otherwise, if there is any plugin to convert fibers to vtk polyline format?
>
> Thanks a lot for your time.
> Xiaogai Li
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
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From santoshyadav20076 at gmail.com  Sat Dec 24 17:54:31 2011
From: santoshyadav20076 at gmail.com (Santosh Yadav)
Date: Sun, 25 Dec 2011 04:24:31 +0530
Subject: [Mristudio-users] LDDMM server Running?
Message-ID: <CA+7fnM1WqjFUNJZ4XjNvtYERH5PAy23F=FDXTrPaTSPu8dbiWQ@mail.gmail.com>

Hello All

I am using MRI studio.

I have uploaded our data to LDDMM server yesterday. However, I have
not received
any mail yet.

I would like to know the status of LDDMM server. Is it available now?

Thanks.

-- 
With Best Regards,

Neuroscience and MR Research Program

Department of Medicine, Queen's Medical Center

University of Hawaii

1356 Lusitana Street, 7th Floor, Honolulu, HI 96813

Phone No. 808-220-7152

Fax No.  808-545-8970
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From akolasny at jhu.edu  Sat Dec 24 19:06:42 2011
From: akolasny at jhu.edu (akolasny at jhu.edu)
Date: Sat, 24 Dec 2011 19:06:42 -0500 (EST)
Subject: [Mristudio-users] LDDMM server Running?
In-Reply-To: <CA+7fnM1WqjFUNJZ4XjNvtYERH5PAy23F=FDXTrPaTSPu8dbiWQ@mail.gmail.com>
References: <CA+7fnM1WqjFUNJZ4XjNvtYERH5PAy23F=FDXTrPaTSPu8dbiWQ@mail.gmail.com>
Message-ID: <45280.68.50.209.72.1324771602.squirrel@webmail.cis.jhu.edu>

There were a number of jobs that have been processed.
The system seems to be working correctly.

Did you get a successful upload message? I did not see an
error messages in the logs.

Is santoshyadav20076 at gmail.com registered with MRI Studio?
You should have got a messages that the process was started
and then one when it's completed.

Thanks,
Anthony

> Hello All
>
> I am using MRI studio.
>
> I have uploaded our data to LDDMM server yesterday. However, I have
> not received
> any mail yet.
>
> I would like to know the status of LDDMM server. Is it available now?
>
> Thanks.
>
> --
> With Best Regards,
>
> Neuroscience and MR Research Program
>
> Department of Medicine, Queen's Medical Center
>
> University of Hawaii
>
> 1356 Lusitana Street, 7th Floor, Honolulu, HI 96813
>
> Phone No. 808-220-7152
>
> Fax No.  808-545-8970
> _______________________________________________
> mristudio-users mailing 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 santoshyadav20076 at gmail.com  Sat Dec 24 20:59:59 2011
From: santoshyadav20076 at gmail.com (Santosh Yadav)
Date: Sun, 25 Dec 2011 07:29:59 +0530
Subject: [Mristudio-users] LDDMM server Running?
In-Reply-To: <45280.68.50.209.72.1324771602.squirrel@webmail.cis.jhu.edu>
References: <CA+7fnM1WqjFUNJZ4XjNvtYERH5PAy23F=FDXTrPaTSPu8dbiWQ@mail.gmail.com>
	<45280.68.50.209.72.1324771602.squirrel@webmail.cis.jhu.edu>
Message-ID: <CA+7fnM2-00X-c4rmhfGijWRaYOYncC0Bwi9eoAySJB3N6TXOHg@mail.gmail.com>

Hi Anthony,

Thanks for reply.

Yes this is my registered email id. In past I successfully received more
than 100 processed data. But yesterday I have submitted 15 data but
i didn't   received any email. After submitting i received only massage
that data has been submitted successfully to server you will notify when
data processed and even yesterday I didn't  received any email that the
process was started.

Regards

Santosh

On Sun, Dec 25, 2011 at 5:36 AM, <akolasny at jhu.edu> wrote:

> There were a number of jobs that have been processed.
> The system seems to be working correctly.
>
> Did you get a successful upload message? I did not see an
> error messages in the logs.
>
> Is santoshyadav20076 at gmail.com registered with MRI Studio?
> You should have got a messages that the process was started
> and then one when it's completed.
>
> Thanks,
> Anthony
>
> > Hello All
> >
> > I am using MRI studio.
> >
> > I have uploaded our data to LDDMM server yesterday. However, I have
> > not received
> > any mail yet.
> >
> > I would like to know the status of LDDMM server. Is it available now?
> >
> > Thanks.
> >
> > --
> > With Best Regards,
> >
> > Neuroscience and MR Research Program
> >
> > Department of Medicine, Queen's Medical Center
> >
> > University of Hawaii
> >
> > 1356 Lusitana Street, 7th Floor, Honolulu, HI 96813
> >
> > Phone No. 808-220-7152
> >
> > Fax No.  808-545-8970
> > _______________________________________________
> > mristudio-users mailing 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
>



-- 
With Best Regards,

Neuroscience and MR Research Program

Department of Medicine, Queen's Medical Center

University of Hawaii

1356 Lusitana Street, 7th Floor, Honolulu, HI 96813

Phone No. 808-220-7152

Fax No.  808-545-8970
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From akolasny at jhu.edu  Sun Dec 25 11:15:37 2011
From: akolasny at jhu.edu (akolasny at jhu.edu)
Date: Sun, 25 Dec 2011 11:15:37 -0500 (EST)
Subject: [Mristudio-users] LDDMM server Running?
In-Reply-To: <CA+7fnM2-00X-c4rmhfGijWRaYOYncC0Bwi9eoAySJB3N6TXOHg@mail.gmail.com>
References: <CA+7fnM1WqjFUNJZ4XjNvtYERH5PAy23F=FDXTrPaTSPu8dbiWQ@mail.gmail.com>
	<45280.68.50.209.72.1324771602.squirrel@webmail.cis.jhu.edu>
	<CA+7fnM2-00X-c4rmhfGijWRaYOYncC0Bwi9eoAySJB3N6TXOHg@mail.gmail.com>
Message-ID: <39285.68.50.209.72.1324829737.squirrel@webmail.cis.jhu.edu>

Santosh,

Strange, There are 4 jobs that are running since dec. 23. at 3pm.
Nothing else is in the queue.

Did something change with the data, parameters or submission software?
I don't have records of the submissions. If you have the MD5SUM, send
it to me in direct email. I'll try to trace it. From here, it doesn't
look like we received the submissions.

-Anthony

> Hi Anthony,
>
> Thanks for reply.
>
> Yes this is my registered email id. In past I successfully received more
> than 100 processed data. But yesterday I have submitted 15 data but
> i didn't   received any email. After submitting i received only massage
> that data has been submitted successfully to server you will notify when
> data processed and even yesterday I didn't  received any email that the
> process was started.
>
> Regards
>
> Santosh
>
> On Sun, Dec 25, 2011 at 5:36 AM, <akolasny at jhu.edu> wrote:
>
>> There were a number of jobs that have been processed.
>> The system seems to be working correctly.
>>
>> Did you get a successful upload message? I did not see an
>> error messages in the logs.
>>
>> Is santoshyadav20076 at gmail.com registered with MRI Studio?
>> You should have got a messages that the process was started
>> and then one when it's completed.
>>
>> Thanks,
>> Anthony
>>
>> > Hello All
>> >
>> > I am using MRI studio.
>> >
>> > I have uploaded our data to LDDMM server yesterday. However, I have
>> > not received
>> > any mail yet.
>> >
>> > I would like to know the status of LDDMM server. Is it available now?
>> >
>> > Thanks.
>> >
>> > --
>> > With Best Regards,
>> >
>> > Neuroscience and MR Research Program
>> >
>> > Department of Medicine, Queen's Medical Center
>> >
>> > University of Hawaii
>> >
>> > 1356 Lusitana Street, 7th Floor, Honolulu, HI 96813
>> >
>> > Phone No. 808-220-7152
>> >
>> > Fax No.  808-545-8970
>> > _______________________________________________
>> > mristudio-users mailing 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
>>
>
>
>
> --
> With Best Regards,
>
> Neuroscience and MR Research Program
>
> Department of Medicine, Queen's Medical Center
>
> University of Hawaii
>
> 1356 Lusitana Street, 7th Floor, Honolulu, HI 96813
>
> Phone No. 808-220-7152
>
> Fax No.  808-545-8970
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>