Q&A $SUBJECT

#!/bin/bash -l ARGS=( "$@" ) if [ -z "$FSLDIR" ] ; then export FSLDIR="/usr/local/fsl" source ${FSLDIR}/etc/fslconf/fsl.sh fi #parse options SUBJECT_ID="" DIRBASE="" XNATBASE="" for ((n=0; n<${#ARGS[@]}; n++)) ; do case "${ARGS[$n]}" in --sid) let n=n+1 SUBJECT_ID="${ARGS[$n]}" ;; --wdir) let n=n+1 DIRBASE="${ARGS[$n]}" ;; --version) echo "RegisterPETwithMRImatch: mkSlicesQAhtm.sh" echo "v20201208" exit 0 ;; --help) echo "--help show help" echo "--sub subject ID" echo "--dir slicedir generated directory" echo "--version script version" exit 0 ;; esac done if [ -z "$DIRBASE" ] || [ -z "$SUBJECT_ID" ] ; then echo "Error: not enough parameters; use --help" >&2 exit 1 fi #QA with slices qaGIF=${SUBJECT_ID}_fbb_mni.gif ${FSLDIR}/bin/slices ${DIRBASE}/${SUBJECT_ID}_fbb_mni ${FSLDIR}/data/standard/MNI152_T1_2mm -o ${DIRBASE}/$qaGIF ( cat <<.EOF Q&A $SUBJECT_ID .EOF cat <<.EOF

$(echo "$qaGIF" | sed 's/\.gif.*$//')

.EOF cat <<.EOF

.EOF ) >>"$DIRBASE/qa.html"