Sulcal Depth from FreeSurfer Output

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1

Hi there,

I am struggling to calculate sulcal depth using FreeSurfer recon-all outputs for a set of subjects so that I can obtain the same metrics as the ABCD dataset (Structural Magnetic Resonance Imaging → sulcal depth Fischl, et al., 1999a).

I calculate area, volume, and thickness for the destrieux atlas for example, using aparcstats2table and asegstats2table for subcortical structures. I have been trying to use the mris_curvature_stats and mris_anatomical_stats commands to get sulcal depth with no success.

I can’t find it in the ABCD release notes or other documentation about how they did this.

Thank you so much for reading!

2

Hi! I realise that this was a while ago, but I was wondering whether you had any success with this?

3

Hi, yes I was able to do it with the following commands!

        "mris_anatomical_stats -a ${fs_dir}/sub-${pidn}/label/lh.${atlas}.annot -t ${fs_dir}/sub-${pidn}/surf/lh.sulc -f ${fs_dir}/sub-${pidn}/stats/lh.${atlas}_sulc.stats sub-${pidn} lh"
        "mris_anatomical_stats -a ${fs_dir}/sub-${pidn}/label/rh.${atlas}.annot -t ${fs_dir}/sub-${pidn}/surf/rh.sulc -f ${fs_dir}/sub-${pidn}/stats/rh.${atlas}_sulc.stats sub-${pidn} rh"

        "aparcstats2table --hemi lh --subjects sub-${pidn} --skip --delimiter comma --meas thickness --parc ${atlas}_sulc --tablefile ${subject_dir_met}/sub-${pidn}/sub-${pidn}_${atlas}_sulc_lh_stats.txt"
        "aparcstats2table --hemi rh --subjects sub-${pidn} --skip --delimiter comma --meas thickness --parc ${atlas}_sulc --tablefile ${subject_dir_met}/sub-${pidn}/sub-${pidn}_${atlas}_sulc_rh_stats.txt"

Where fs_dir is the freesurfer subject directory, pidn is the subject id, atlas is aparc (desikan) or aparc.a2009s (destrieux), and subject_dir_met is the output metrics dir for the subject.