main

#!/bin/bash
#PBS -l nodes=1:ppn=16,walltime=4:00:00
#PBS -l vmem=31gb
#PBS -N tractseg
#PBS -V

#needed for bridges (it must be set via the resource ENV)
##SBATCH -p GPU-shared
##SBATCH --gres=gpu:p100:2

module load cuda/10.0

set -x
set -e

echo "running tractseg and tractometry on peak length"
rm -rf tractseg_output && mkdir -p tractseg_output
time singularity exec --nv -e docker://brainlife/tractseg:2.7 ./run.sh

echo "creating wmc"
mkdir -p wmc/tracts
singularity exec -e docker://brainlife/dipy:1.1.1 ./create_wmc.py
mkdir -p wmc/surfaces
singularity exec -e docker://brainlife/pythonvtk:1.1 ./mask2surface.py

echo "merging .tck into 1"
mkdir -p tck
singularity exec -e docker://brainlife/mrtrix3:3.0.0 tckedit -force tractseg_output/TOM_trackings/*.tck tck/track.tck
#check size of tractogram
actualsize=$(wc -c <"tck/track.tck")
if [ $actualsize -le 10000 ]; then
    echo "tck/track.tck seems empty. exiting"
    exit 1
fi

#create tractseg output
mkdir -p output
ln -sf ../tractseg_output/bundle_segmentations output/masks

#create tractmasks output
mkdir -p endingmasks
ln -sf ../tractseg_output/endings_segmentations endingmasks/masks

#create tractometry output
mkdir -p tractseg_tractometry
ln -sf ../tractseg_output/Tractometry_peaks.csv tractseg_tractometry/tractmeasures.csv
echo "all done"