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cox1-preproc.bash
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#!/bin/bash
#
# Location of mapping file, each line has
# - sub-name
# - ses-name
# - bids pet img sidecar (json)
# - pet imaging timeseries file
# - bloodstram file
MAP_FILE="cox1-preproc-mapping.txt"
SUBJECTS_DIR="/autofs/vast/gerenuk/pwighton/pet/fs-subs"
# Top level directory of pet imaging data
IMG_REF_DIR="/autofs/vast/gerenuk/pwighton/pet/ds004230-plus-cox1blocked"
# Top level directory of motion corrected pet imaging data
MOCO_REF_DIR="/autofs/vast/gerenuk/pwighton/pet/ds004230-plus-cox1blocked--petprep-hmc--384176a6cc6b"
# Top level directory of bloodstream data
BLOOD_REF_DIR="/autofs/vast/gerenuk/pwighton/pet/ds004230-plus-cox1blocked--bloodstream2023-08-28_id-tfK8--martin"
# Location of integrate.py
CALC_FRAMEWISE_AIF_PY="/autofs/vast/gerenuk/pwighton/pet/miba/calc_framewise_aif.py"
echo "SUBJECTS_DIR: "$SUBJECTS_DIR
echo "MAP_FILE: "$MAP_FILE
echo "IMG_REF_DIR: "$IMG_REF_DIR
echo "MOCO_REF_DIR: "$MOCO_REF_DIR
echo "BLOOD_REF_DIR: "$BLOOD_REF_DIR
# Make the file tsec.txt
# Assumes consistent frame timing across dataset
PET_JSON_FILE=$(cat $MAP_FILE | sed -n "1p" | awk '{print $3}')
echo "jq '.FrameTimesStart[]' ${IMG_REF_DIR}/${PET_JSON_FILE} > $SUBJECTS_DIR/tsec.txt"
jq '.FrameTimesStart[]' ${IMG_REF_DIR}/${PET_JSON_FILE} > $SUBJECTS_DIR/tsec.txt
NUM_LINES=$(cat $MAP_FILE|wc -l)
for LINE_NUM in $(seq $NUM_LINES)
do
SUB_NAME=$(cat $MAP_FILE| sed -n "${LINE_NUM}p" | awk '{print $1}')
PET_SUBDIR=$(cat $MAP_FILE | sed -n "${LINE_NUM}p" | awk '{print $2}')
PET_JSON_FILE=$(cat $MAP_FILE | sed -n "${LINE_NUM}p" | awk '{print $3}')
PET_MOCO_FILE=$(cat $MAP_FILE | sed -n "${LINE_NUM}p" | awk '{print $4}')
BLOODSTREAM_FILE=$(cat $MAP_FILE | sed -n "${LINE_NUM}p" | awk '{print $5}')
echo "SUB_NAME: "$SUB_NAME
echo "PET_SUBDIR: "$PET_SUBDIR
echo "BLOODSTREAM_FILE: "$BLOODSTREAM_FILE
echo "PET_JSON_FILE: "$PET_JSON_FILE
PET_IMG_FILE=$(echo "${PET_JSON_FILE%%.*}")".nii.gz"
echo "PET_IMG_FILE: "$PET_IMG_FILE
echo "PET_MOCO_FILE: "$PET_MOCO_FILE
PETSURFER_DIR=$SUBJECTS_DIR/$SUB_NAME/$PET_SUBDIR
echo "PETSURFER_DIR: "$PETSURFER_DIR
echo "rm -rf ${PETSURFER_DIR}"
rm -rf ${PETSURFER_DIR}
echo "mkdir -p ${PETSURFER_DIR}"
mkdir -p ${PETSURFER_DIR}
echo "cp ${MOCO_REF_DIR}/${PET_MOCO_FILE} ${PETSURFER_DIR}/pet.nii.gz"
cp ${MOCO_REF_DIR}/${PET_MOCO_FILE} ${PETSURFER_DIR}/pet.nii.gz
echo "mri_concat ${PETSURFER_DIR}/pet.nii.gz --mean --o ${PETSURFER_DIR}/pet.mn.nii.gz"
mri_concat ${PETSURFER_DIR}/pet.nii.gz --mean --o ${PETSURFER_DIR}/pet.mn.nii.gz
echo "${CALC_FRAMEWISE_AIF_PY} -a ${BLOOD_REF_DIR}/${BLOODSTREAM_FILE} -b ${IMG_REF_DIR}/${PET_JSON_FILE} -o ${PETSURFER_DIR}/aif.bloodstream.dat"
${CALC_FRAMEWISE_AIF_PY} -a ${BLOOD_REF_DIR}/${BLOODSTREAM_FILE} -b ${IMG_REF_DIR}/${PET_JSON_FILE} -o ${PETSURFER_DIR}/aif.bloodstream.dat
done