Hi there,

 

We want to implement the Glasser atlas for our cortical parcellation. I found this example in the listserv and have adapted it. However, in the response, it seemed as though this may not be an ideal way to do it.

Is someone able to confirm if this script would give me a reliable output? I also hope to do the same with the HCPex atlas, so if you happen to be able to address that as well, that would be amazing!

 

Thanks so much!

Carly

 

 

mri_surf2surf \

  --hemi lh \

  --srcsubject fsaverage \

  --trgsubject $subj \

  --sval-annot $datadir/fsaverage/label/lh.HCPMMP1.annot \

  --tval ${SUBJECTS_DIR}/$subj/label/lh.HCPMMP1.annot

 

 

mri_surf2surf \

  --hemi rh \

  --srcsubject fsaverage \

  --trgsubject $subj \

  --sval-annot $datadir/fsaverage/label/rh.HCPMMP1.annot \

  --tval $SUBJECTS_DIR/$subj/label/rh.HCPMMP1.annot

 

 

# Extract Thickness and Volume stats

mris_anatomical_stats \

                -a $SUBJECTS_DIR/$subj/label/lh.HCPMMP1.annot \

                -f ${SUBJECTS_DIR}/$subj/stats/lh.HCPMMP1.stats \

                -b $subj lh

 

 

# Extract Thickness and Volume stats

mris_anatomical_stats \

                -a $SUBJECTS_DIR/$subj/label/rh.HCPMMP1.annot \

                -f ${SUBJECTS_DIR}/$subj/stats/rh.HCPMMP1.stats \

                -b $subj rh

 

 

FREESURFER VERSION: 8.0.0

OS: macOS Monterey