run_structural_qa

#!/bin/bash -e

progname=`basename $0`

if [ $# -ne 2 ]
then
    echo "usage: $progname <source file> <working directory>"
    exit 1
fi

source="$1"
working_dir="$2"

cd "$working_dir"

ndar_unpack "$source" -v anat.nii.gz

fslreorient2std anat anat_r

bet anat_r anat_brain -A -m
fslmaths anat_brain_outskin_mask -sub 1 -mul -1 external
fast -t 1 anat_brain
fslstats anat_r -k external -R -r -m -s -v > external.stats
fslstats anat_r -k anat_brain_mask -R -r -m -s -v > brain.stats

fslmaths anat_brain_seg -thr 1 -uthr 1 -bin csf
fslstats anat_r -k csf -R -r -m -s -v > csf.stats

fslmaths anat_brain_seg -thr 2 -uthr 2 -bin gm
fslstats anat_r -k gm -R -r -m -s -v > gm.stats

fslmaths anat_brain_seg -thr 3 -uthr 3 -bin wm
fslstats anat_r -k wm -R -r -m -s -v > wm.stats

exit 0

# eof