Hi, 

This task will be a bit easy using  fslmaths

- convert mgz file to nii using mri_convert
-then use fslmaths <labeled nii file> -thr <label> -uthr <label> <outputfile.nii>

example:
fslmaths wmparc.nii -thr 1006 -uthr 1006 lh_entorhinal.nii

On Thu, May 12, 2016 at 9:12 AM Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:
What version of FS are you using? You may need a newer version of
mri_aparc2aseg. Try this one

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_aparc2aseg

On 05/12/2016 06:53 AM, Caroline Beelen wrote:
>
> If we changed the command –-ribbon to –- no ribbon, the script ran,
> but when we looked at the stats-file, only cortical grey matte
>

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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