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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Hello DTI Studio users<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Is there any way to save my own gradient file(s) on the computer?<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Thanks<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Ned <o:p></o:p></span></p><p class=MsoNormal><a name="_MailEndCompose"><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></a></p><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> mristudio-users-bounces@mristudio.org [mailto:mristudio-users-bounces@mristudio.org] <b>On Behalf Of </b>skhekmat<br><b>Sent:</b> Friday, April 05, 2013 2:02 PM<br><b>To:</b> 'DTI Studio, ROI Editor, DiffeoMap Questions/Support'<br><b>Subject:</b> Re: [Mristudio-users] masking<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Hello Susumu<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Thanks for providing suggestions, I tried to follow that, I do have some questions on that…<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> <a href="mailto:mristudio-users-bounces@mristudio.org">mristudio-users-bounces@mristudio.org</a> [<a href="mailto:mristudio-users-bounces@mristudio.org">mailto:mristudio-users-bounces@mristudio.org</a>] <b>On Behalf Of </b>susumu mori<br><b>Sent:</b> Thursday, April 04, 2013 5:34 PM<br><b>To:</b> DTI Studio, ROI Editor, DiffeoMap Questions/Support<br><b>Subject:</b> Re: [Mristudio-users] masking<o:p></o:p></span></p></div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>Hi Ned,<o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>The simplest masking you can use is the intensity threshold.<o:p></o:p></p></div><div><p class=MsoNormal>When you click "tensor" calculation, there is a section to define an intensity threshold. This should suppress most of the background noise floor.<o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>My question is, In DTI map option ( in tensor calculation) does it create and save a mask file using threshold option 10 %) somewhere explicitly in my computer? If so, I could not find it.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>More sophisticated method is to apply for skull-strip.<o:p></o:p></p></div><div><p class=MsoNormal>You can do this at the tensor calculation by loading a masking file, again, within the tensor calculation window.<o:p></o:p></p></div><div><p class=MsoNormal>The brain mask file should contain 1/0 information. <o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Using this option, I created a roi mask file in binary format and but unable to load at tensor calculation, may be it reads only rec file<o:p></o:p></span></p></div><div><p class=MsoNormal>Or, you can skull-strip after tensor calculation.<o:p></o:p></p></div><div><p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Using this, is a better option, after tensor calculation, I do not know how to apply to resultant images. <o:p></o:p></span></p></div><div><p class=MsoNormal>For the skull-strip, you can use any software out there. We use our own skull-strip function in RoiEditor.<o:p></o:p></p></div><div><p class=MsoNormal>You can load FA, trace, and other images with b0 or iDWI (the sum of all DWIs you can calculate in DtiStudi).<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>You can use b0 or iDWI for skull stripping and the resultant masking is applied to all loaded images.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Hope this will help.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Susumu<o:p></o:p></p></div></div><div><p class=MsoNormal style='margin-bottom:12.0pt'><o:p> </o:p></p><div><p class=MsoNormal>On Thu, Apr 4, 2013 at 12:34 PM, skhekmat <<a href="mailto:skhekmat@hotmail.com" target="_blank">skhekmat@hotmail.com</a>> wrote:<o:p></o:p></p><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#1F497D'>Hello All</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#1F497D'>Is there any function to create a mask in DTI studio, so that I will apply in Tensor mapping? I could create using other softwares, however, transformation causes so many issues.</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#1F497D'>Thanks</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#1F497D'>Ned</span><o:p></o:p></p></div></div><p class=MsoNormal style='margin-bottom:12.0pt'><br>_______________________________________________<br>mristudio-users mailing list<br><a href="mailto:mristudio-users@mristudio.org">mristudio-users@mristudio.org</a><br><a href="http://lists.mristudio.org/mailman/listinfo/" target="_blank">http://lists.mristudio.org/mailman/listinfo/</a><br>Unsubscribe, send a blank email to: <a href="mailto:mristudio-users-unsubscribe@mristudio.org">mristudio-users-unsubscribe@mristudio.org</a><o:p></o:p></p></div><p class=MsoNormal><o:p> </o:p></p></div></div></body></html>