you can also use mri_vol2vol with --regheader. Bruce Fischl wrote: > 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 > > >
-- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
