main

#!/bin/bash
#PBS -l nodes=1:ppn=8,vmem=15gb,walltime=60:00:00
#PBS -N ensembletracking
#PBS -V

#make the script to fail if any of the commands ran fails.
set -e


#validate some input parameters
if [ $(jq -r '.num_or_fibers' config.json) -gt 25 ]; then
    echo "num_or_fibers should be less than 25"
    exit 1
fi

if [ ! -f convertfiles.success ]; then
    echo "converting aparc+aseg.mgz"
    [ -z "$FREESURFER_LICENSE" ] && echo "Please set FREESURFER_LICENSE in .bashrc" && exit 1;
    echo $FREESURFER_LICENSE > license.txt
    #export SINGULARITYENV_FS_LICENSE=`pwd`/license.txt
    time singularity exec -e -B `pwd`/license.txt:/usr/local/freesurfer/license.txt docker://brainlife/freesurfer:6.0.0 ./convertfiles.sh
fi

if [ ! -f wmmask.success ]; then
    echo "creating exclude ROI with FSL"
    time singularity exec -e docker://brainlife/fsl:5.0.9 ./make_fsl_roi.sh
fi

if [ ! -f track.tck ]; then
    echo "running ensembetracking"
    time singularity exec -e docker://brainlife/mrtrix:0.2.12 ./ensembletracking.sh
fi