main

#!/bin/bash
#PBS -l nodes=1:ppn=4,walltime=6:00:00,vmem=30g
#PBS -N app-mriqc

rm -rf output

set -e
set -x

VERSION=22.0.6

# identify datatype
TYPE=`jq -r '.type' config.json`
if [[ $(jq -r '.input' config.json) == *"t1"* ]]; then
    modality="T1w"
elif [[ $(jq -r '.input' config.json) == *"t2"* ]]; then
    modality="T2w"
elif [[ $(jq -r '.input' config.json) == *"bold"* ]]; then
    modality="bold"
fi

#copy input under input in bids format
mkdir -p input/sub-0/${TYPE} output regressors subject_html group_html subject_html/html group_html/html
ln -sf ../../../$(jq -r '.input' config.json) input/sub-0/${TYPE}/sub-0_${modality}.nii.gz

cat > input/dataset_description.json <<EOF
{
    "BIDSVersion": "1.0.0",
    "Name": "Temp dataset",
    "Authors": [
        "Soichi Hayashi"
    ]
}
EOF

# run mriqc
time singularity exec docker://nipreps/mriqc:${VERSION} mriqc input output participant --no-sub

# generate regressors tsv
time singularity exec -e docker://brainlife/dipy:1.4.1 ./create_regressors_table.py

# copy files to appropriate outputs
[ -f ./output/sub-0/${TYPE}/subj-0_*.json ] && cp ./output/sub-0/${TYPE}/subj-0_*.json ./product.json
[ -f ./output/group_${modality}.html ] && cp ./output/group_${modality}.html ./group_html/html/group_${modality}.html
[ -f ./output/sub-0_${modality}.html ] && cp ./output/sub-0_${modality}.html ./subject_html/html/sub-0_${modality}.html