Re: [Freesurfer] WmParc

you can also use mri_binarize --i wmparc.nii --match 1006 --o lh_entorhinal.nii

On 05/13/2016 06:12 PM, Pradeep wrote:

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 mailto: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
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Outgoing:
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