main

#!/bin/bash
#PBS -l nodes=1:ppn=16
#PBS -l walltime=02:00:00

set -xe

INPUT=$(jq -r .bold config.json)
MASK=$(jq -r .mask config.json)
NHOOD=$(jq -r .neighborhood config.json)
FWHM=$(jq -r .fwhm config.json)

if [ $MASK == "null" ]; then
    MASK=""
fi

OPTS=""
if [ ! -z "$MASK" ]; then
    OPTS="$OPTS -mask $MASK"
fi

mkdir -p reho

time singularity run -e \
    docker://anibalsolon/app-reho:v0.0.1 \
    /opt/afni/3dReHo \
    -inset $INPUT \
    -prefix reho/reho.nii.gz \
    -nneigh $NHOOD \
    $OPTS

time singularity run -e \
    docker://anibalsolon/app-reho:v0.0.1 \
        sh ./zscore.sh reho/reho.nii.gz reho/reho_norm.nii.gz

mv reho/reho_norm.nii.gz reho/reho.nii.gz

if [ "$FWHM" != "0" ]; then
    time singularity run -e \
        docker://anibalsolon/app-reho:v0.0.1 \
        /opt/afni/3dBlurToFWHM \
        -input reho/reho.nii.gz \
        -prefix reho/reho_smooth.nii.gz \
        -FWHM $FWHM \
        $OPTS

    mv reho/reho_smooth.nii.gz reho/reho.nii.gz
fi