main

#!/bin/bash
#PBS -l nodes=1:ppn=4,vmem=28gb,walltime=10:00:00
#PBS -N wmaSeg

rm -rf tracts

[ -z "$FREESURFER_LICENSE" ] && echo "Please set FREESURFER_LICENSE in .bashrc" && exit 1;
echo $FREESURFER_LICENSE > license.txt

set -e
set -x

if [ ! -f aparc+aseg.nii.gz ]; then
    echo "converting aparc.a2009+aseg file to nifti"
    singularity exec -e -B `pwd`/license.txt:/usr/local/freesurfer/license.txt \
        docker://brainlife/freesurfer-mini:6.0.1 ./convertaseg.sh
fi

echo "running segmentation"
singularity exec -e docker://brainlife/mcr:r2019a ./compiled/main
if [ ! -s classification/classification.mat ]; then
	echo "output missing"
	exit 1
fi

#TODO - will be deprecated soon by wmc datatype validator
echo "Generating surfaces/ vtk from aparc+aseg.mgz"
time singularity exec -e docker://brainlife/pythonvtk:1.1 ./freesurfer2vtks.py

#cp labels.json classification
#cp aparc.a2009s+aseg.nii.gz classification/parc.nii.gz

echo "all done"