fs_stats_generation.sh

#!/bin/bash

# Environment variable $SUBJECTS_DIR needs to point to the freesurfer derivatives directory
list=$(ls $SUBJECTS_DIR)

### asegstats2table ###

# Store segmentation-specific measurement arguments (excluding volume)
declare -a s_arr=("Area_mm2" "nvoxels" "nvertices" "mean" "std" "max")

# Store numbers corresponding to regions for all ROIs
seg_numbers=(4 5 7 8 10 11 12 13 14 15 16 17 18 24 26 28 30 31 43 44 46 47 49 50 51 52 53 54 58 60 62 63 72 77 78 79 80 81 82 85 251 252 253 254 255)

# Fetch global stats for measurement 'volume' with option --no-segno to exclude all regions
asegstats2table --subjects $list --meas volume --no-segno ${seg_numbers[@]} --skip --tablefile asegstats_global.csv

# Fetch stats for measurement 'volume' and use --no-vol-extras option
asegstats2table --subjects $list --meas volume --common-segs  --no-vol-extras --skip --tablefile asegstats_volume.csv

# Fetch stats for all other measuresments
for measure in ${s_arr[@]}
do
   asegstats2table --subjects $list --meas $measure --common-segs --skip --tablefile asegstats_"$measure".csv
done

### aparcstats2table ###

# Store parcellation-specific measurement arguments
declare -a p_arr=("area" "volume" "thickness" "thicknessstd" "thickness.T1" "meancurv" "gauscurv" "foldind" "curvind")

## Desikan/Killiany ##

# Fetch stats for all measurements of left hemisphere from lh.aparc.stats
for measure in ${p_arr[@]}
do
   aparcstats2table --hemi lh --subjects $list --meas $measure --skip --tablefile lh_aparc_aparcstats_"$measure".csv
done

# Fetch stats for all measurements of right hemisphere from rh.aparc.stats
for measure in ${p_arr[@]}
do
   aparcstats2table --hemi rh --subjects $list --meas $measure --skip --tablefile rh_aparc_aparcstats_"$measure".csv
done

## Destrieux ##

# Fetch stats for all measurements of left hemisphere from lh.aparc.a2009.stats
for measure in ${p_arr[@]}
do
   aparcstats2table --hemi lh --subjects $list --parc aparc.a2009s --meas $measure --skip --tablefile lh_a2009s_aparcstats_"$measure".csv
done

# Fetch stats for all measurements of right hemisphere from rh.aparc.a2009.stats
for measure in ${p_arr[@]}
do
   aparcstats2table --hemi rh --subjects $list --parc aparc.a2009s --meas $measure --skip --tablefile rh_a2009s_aparcstats_"$measure".csv
done