You can use mri_binarize with the --match option to spec the index, eg:
mri_binarize --i aseg.mgz --match 17 --o hippo.lh.nii
doug
Martin Ystad wrote:
Hi, I'd like to create binary masks in the nifti-format from each of
the subcortical segmentations in freesurfer, separately (one for
hippocampus, one for thalamus, and so forth..). Is there any way to do
this automatically from the command line?
Thanks,
Martin Ystad
Ph.D. candidate,
University of Bergen
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Douglas N. Greve, Ph.D.
MGH-NMR Center
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