Hi there, 

 

Resending this as there seemed to be an issue with my previous email. We want to implement the Glasser atlas for cortical parcellation on a sample of participants that have been run through FreeSurfer 8.0. I found this example in the listserv and have adapted 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. Am I also able to use the same script with the HCPex atlas file instead?

 

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