feedsRun

#!/usr/bin/env bash

set -e

outdir=$1
indir=$(pwd)

pushd $outdir

for i in {1..172}; do
   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
done