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 > _______________________________________________ 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.
