that shouldn't create much blurring. How are you assessing this? By overlaying on the DTI volume? If so, how did you register it?
On Thu, 1 Apr 2010, Walimuni, Indika S wrote: > Hi Bruce > Sure, Its 170x256x256 axial > Truly, > Indika Walimuni > Research Associate > University of Texas Health Science Center > Houston, TX. > ________________________________________ > From: Bruce Fischl [[email protected]] > Sent: Thursday, April 01, 2010 1:45 PM > To: Walimuni, Indika S > Subject: RE: [Freesurfer] Volume masks > > Hi Indika, > > can you post these to the list so others can answer? What is the "native" > space you are using? > > Bruce > > > > On Thu, 1 Apr 2010, Walimuni, Indika S wrote: > >> Hi Bruce >> Thanks for the reply. I used wmparc.mgz file for all the > cortical and sub-cortical WM/GM masks. This was the command, mri_binarize > --i wmparc.mgz --match "index from LUT" --o outputfile. This effect becomes > even more significant after I register the mask to like DTI/FA. But I don't > think it is a FreeSufer issue. I think I may have judged based on that. The > masks seems fine in the FreeSurfer space and the masks are OK. But when I > convert them to our native space using "mri_convert" I see a broadening > around the edges. I just want to test if there is another way and see the > difference. Am I using the wrong file? If I am to use aparc+aseg.mgz file > can I use it for all cortical, subcortical, WM and GM masks? > >> Truly, >> Indika Walimuni >> Research Associate >> University of Texas Health Science Center >> Houston, TX. >> ________________________________________ >> From: Bruce Fischl [[email protected]] >> Sent: Thursday, April 01, 2010 11:38 AM >> To: Walimuni, Indika S >> Cc: [email protected] >> Subject: Re: [Freesurfer] Volume masks >> >> Hi Indika, >> >> you should be able to do this using the aparc+aseg.mgz volume and >> mri_binarize. What command line did you use and can you give us an example >> of the "spilling"? >> >> cheers, >> Bruce >> >> >> On Thu, 1 Apr 2010, >> Walimuni, Indika S wrote: >> >>> Hi FreeSurfer List >>> Is their any way that I can generate cortical >> and sub-cortical volume masks by using the surfaces generated by >> FreeSurfer. If I can could anyone give me the proper command. Apparently, >> The masks I already generated using mri_binarize command, are little bigger >> and spilling into the surrounding. >>> Thank you in advance, >>> Truly, >>> Indika Walimuni >>> Research Associate >>> University of Texas Health Science Center >>> Houston, TX. >>> _______________________________________________ >>> Freesurfer mailing list >>> [email protected] >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> >> >> > > > _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
