yes, that sounds right Bruce On Sun, 11 Apr 2010, Mehul Sampat wrote:
> 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. >> >> > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
