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