how are you doing the nonlinear registration? And why not using a rigid transform? It is the same subject, isn't it? Are you correcting for eddy currents?
On Thu, 1 Apr 2010, Walimuni, Indika S wrote: > Yes, After non-linear registration to DTI space then overlay. > Truly, > Indika Walimuni > Research Associate > University of Texas Health Science Center > Houston, TX. > ________________________________________ > From: Bruce Fischl [[email protected]] > Sent: Thursday, April 01, 2010 2:06 PM > To: Walimuni, Indika S > Cc: [email protected] > Subject: RE: [Freesurfer] Volume masks > > 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
