#!/usr/bin/env bash

set -e

outdir=$1
indir=$(pwd)

pushd $outdir

for i in {1..172}; do
  job_id=$(fsl_sub --coprocessor=cuda probtrackx2_gpu            \
                   -x $indir/masks/$i.nii.gz                     \
                   --dir=$indir/probtrackx/$i --forcedir  -P 200 \
                   -s $indir/bedpost.bedpostX/merged             \
                   -m $indir/bedpost.bedpostX/nodif_brain_mask   \
                   --opd --pd -l -c 0.2 --distthresh=0)
  touch ${outdir}/wait
  fsl_sub --jobhold ${job_id} rm wait
  while [ -e ${outdir}/wait ]; do
    sleep 1m
  done
done