main

#!/bin/bash
#PBS -l nodes=1:ppn=8
#PBS -l vmem=16gb
#PBS -l walltime=10:00:00

export SINGULARITYENV_OMP_NUM_THREADS=7

set -e
set -x

mkdir -p output
cp $(jq -r .bvecs config.json) output/dwi.bvecs
cp $(jq -r .bvals config.json) output/dwi.bvals
chmod -R +w output

mkdir -p secondary
chmod -R +w secondary

AUTOCROP=$(jq -r .autocrop config.json)

if $AUTOCROP
then
    AUTOCROP="--autocrop"
else
    AUTOCROP=""
fi

DILATE=$(jq -r .dilate config.json)

if [[ $DILATE = null ]]
then
    DILATE=""
else
    DILATE="--dilate $DILATE"
fi

time singularity exec -e docker://brainlife/dipy:1.1.1 dipy_median_otsu \
    --force \
    --out_dir output \
    --save_masked \
    --median_radius $(jq -r .median_radius config.json) \
    --numpass $(jq -r .numpass config.json) \
    $AUTOCROP \
    --vol_idx $(jq -r .vol_idx config.json) \
    $DILATE \
    --out_mask mask.nii.gz \
    --out_masked dwi.nii.gz \
    $(jq -r .dwi config.json)

mv output/mask.nii.gz secondary/

echo "done"