Thanks Bruce. Following that, to convert the rth.mgz back to native space I think I can use the following command: mri_convert -rl orig/001.mgz -rt nearest rth.mgz rth.nii
thanks Mehul On Sun, Apr 11, 2010 at 1:38 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>wrote: > Hi Mehul, > try mri_binarize instead. It would be something like: > > mri_binarize --match 49 --i aseg.mgz --o rth.mgz > > where 49 is the index for right thalamus proper (from the > FreeSurferColorLUT.txt file) and rth.mgz is the output volume > > cheers, > Bruce > > On Sun, 11 Apr 2010, Mehul Sampat wrote: > > Hi Folks, >> >> I would like to create a binary mask volume for the Right-Thalamus (all >> voxels of right-thalamus as 1 and 0 otherwise). >> >> I looked at this help page >> http://surfer.nmr.mgh.harvard.edu/fswiki/mri_vol2roi >> and i think I should use the following command described on this page: >> >> mri_vol2roi --label your.label --srcvol f --srcreg register.dat >> --finalmskvol labelbinmask --roiavg /tmp/not.wanted.dat >> >> is this correct ? also could someone give me an example? i am not sure >> what >> all of the parameters are. >> thanks >> Mehul >> >> > > 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. > >
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