#!/bin/bash

for d in \
"mgh_1001" \
"mgh_1002" \
"mgh_1003" \
"mgh_1004" \
"mgh_1005" \
"mgh_1006" \
"mgh_1007" \
"mgh_1008" \
"mgh_1009" \
"mgh_1010" \
"mgh_1011" \
"mgh_1012" \
"mgh_1013" \
"mgh_1014" \
"mgh_1015" \
"mgh_1016" \
"mgh_1017" \
"mgh_1018" \
"mgh_1019" \
"mgh_1021" \
"mgh_1022" \
"mgh_1023" \
"mgh_1024" \
"mgh_1025" \
"mgh_1026" \
"mgh_1027" \
"mgh_1028" \
"mgh_1029" \
"mgh_1030" \
"mgh_1031" \
"mgh_1032" \
"mgh_1033" \
"mgh_1034";

do
    echo "Processing $d"
	cd /mnt/d/HCP35/unzipped/$d/anat/T1;
	docker run -it --rm --name sthomas -v ${PWD}:/data -w /data --user ${UID}:$(id -g) anagrammarian/sthomastest hipsthomas.sh -v -t1 -i T1.nii.gz
	echo "Processed $d"
done
