yes, use mri_extract_label. The indices for the different labels are given in $FREESURFER_HOME/FreeSurferColorLUT.txt (if you specify the output volume as having a .nii extension it will write it in Niftii) On Mon, 20 Oct 2008, 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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