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 <gr...@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 > gr...@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/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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. > >
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