Grabs output from mris_anatomical_stats

anatomical_stats_scraper.sh

usage() { echo "Usage: $0 [-i <mris_anatomical_stats output>]" 1>&2; exit 1; }

while getopts ":i:" o; do
	case "${o}" in
		i)
			i=${OPTARG}
			;;
		*)
			usage
			;;
	esac
done
shift "$((OPTIND-1))"

if [ -z "${i}" ]; then
    usage
fi

name=`echo $i | cut -d "." -f 1`
output=${name}_stats.csv

if [ ! -f $output ]; then
	touch $output
else 
    echo "WARNING: Scraper already used on this mris_anatomical_stats output. Resulting output may contain redundant information."
fi

echo "subject,thickness" > $output

mkdir temporary
csplit -s $i '/^structure/' '{*}'
rm -f xx00
mv xx* temporary/

for j in temporary/xx*; do 
	subj=`cat $j | grep structure | cut -d " " -f 3 | cut -d "/" -f 1 | tr -d "\""`
	thick=`cat $j | grep "average cortical thickness" | tr -s " " | cut -d " " -f 5`
	echo $subj,$thick >> $output
done

rm -fr temporary