diff --git a/gpu_test/LICENSE b/gpu_test/LICENSE
new file mode 100644
index 0000000000000000000000000000000000000000..ca86e5eb5594344d33dc3b7648dba2931ed3d7b2
--- /dev/null
+++ b/gpu_test/LICENSE
@@ -0,0 +1,25 @@
+BSD 2-Clause License
+
+Copyright (c) 2019, Chris Rorden
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+ list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+ this list of conditions and the following disclaimer in the documentation
+ and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/gpu_test/README.md b/gpu_test/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..e908c017fcd64b8eb4e0838265a4a9d8cb4a321d
--- /dev/null
+++ b/gpu_test/README.md
@@ -0,0 +1,26 @@
+Cloned from https://github.com/neurolabusc/gpu_test/ on 22nd October 2021
+Commit: ff28eeb7f906564c67801f143a9a1da6e979a171
+
+
+## About
+
+Graphics cards (GPU) can dramatically accelerate some stages of brain imaging processing. In particular, the FSL tools Bedpostx, Eddy and Probtrackx are all commonly used for diffusion analyses and can be dramatically accelerations using an NVidia GPU that supports the CUDA language. While the performance benefits are huge, setting up these systems can be tricky. This repository contains minimal datasets and scripts for testing these tools.
+
+These sample datasets are only designed to validate the installation of these tools. They are not designed to showcase the performance benefits of GPU acceleration. Specifically, the datasets are designed to be small allowing for fast download and testing. Typical datasets are much larger and more computationally intensive. Several of these tests are probably constrained by memory speeds or the required CPU-based serial processing stages that precede and follow the parallel processing of the GPU.
+
+## Scripts
+
+* btest for [CUDA accelerated Bedpostx](https://users.fmrib.ox.ac.uk/~moisesf/Bedpostx_GPU/)
+ * The script `runme_gpu.sh` will run `Bedpostx_GPU`.
+ * If the script fails to run, make sure your version of Bedpostx_GPU matches your version of [CUDA](https://users.fmrib.ox.ac.uk/~moisesf/Bedpostx_GPU/Installation.html).
+
+* etest for [CUDA accelerated Eddy](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/eddy/UsersGuide#The_eddy_executables)
+ * Since there are different versions of Eddy for different generations of CUDA (e.g. `eddy_cuda9.1` only works with CUDA 9.1), the shell script assumes that the executable sym-link `eddy_cuda` exists. In theory, the FSL installer should create this for you, but this requires CUDA is setup prior to installing FSL. If this is not the case, this repository includes the installer script from FSL 6.0.4, which you can run `sudo ./configure_eddy.sh -f /usr/local/fsl`. In my experience, this can fail if you have multiple versions of CUDA installed. As an alternative, I include the script `configure_eddy_cr.sh` which you can run (e.g. `./configure_eddy.sh`) and it will suggest a command you can run to create the symbolic link (e.g. `sudo ln -s /usr/local/fsl/bin/eddy_cuda9.1 /usr/local/fsl/bin/eddy_cuda`.
+
+ * ptest for [CUDA accelerated Probtrackx](https://users.fmrib.ox.ac.uk/~moisesf/Probtrackx_GPU/index.html)
+ * The script `runme_gpu.sh` will run `Probtrackx_GPU`.
+ * If the script fails to run, make sure your version of Probtrackx_GPU matches your version of [CUDA](https://users.fmrib.ox.ac.uk/~moisesf/Probtrackx_GPU/Installation.html).
+
+## Lines
+
+ * [nii_preprocess](https://github.com/neurolabusc/nii_preprocess) leverages these GPU tools for processing datasets.
diff --git a/gpu_test/btest/bedpost/bvals b/gpu_test/btest/bedpost/bvals
new file mode 100755
index 0000000000000000000000000000000000000000..e93cc49473fa46ba896310c7e9d1f12fe7975ada
--- /dev/null
+++ b/gpu_test/btest/bedpost/bvals
@@ -0,0 +1 @@
+0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000
diff --git a/gpu_test/btest/bedpost/bvecs b/gpu_test/btest/bedpost/bvecs
new file mode 100755
index 0000000000000000000000000000000000000000..c6df476f2c182162c58cdcc12657937537b17c03
--- /dev/null
+++ b/gpu_test/btest/bedpost/bvecs
@@ -0,0 +1,3 @@
+0 0.99728941917419 0.52904087305069 0.09871383756399 0.57234114408493 0.29827025532722 0.91768813133239 0.74880933761596 0.20680364966392 0.90815126895904 0.52029657363891 0.37823864817619 0.50694638490676 0.54456895589828 0.64912503957748 0.51406991481781 0.83672642707824 0.92631632089614 0.35351040959358 0.14325453341007 0.76561915874481 0.49386376142501 0.7420095205307 0.93124419450759 0.18586841225624 -0.03146285563707 0.20657055079937 0.75862318277359 0.23452313244342 0.10333918780088 0.86848974227905 0.50137621164321 0.45120280981063 0.23461484909057 0.4041798710823 0.96193838119506 0.97203999757766 0.44904622435569 0.77852296829223 0.66199326515197 0.74761569499969 0.7154301404953 0.19648967683315 0.78184801340103 0.15366122126579 0.54266482591629 0.16201771795749 0.56601321697235 0.85948431491851 0.3078239262104 0.11971329897642 0.71542114019393 0.47409933805465 0.45725721120834 0.10556537657976 0.40082722902298 0.35262700915336 0.76099181175232 0.2868360877037 0.52904081344604 0.02763943001627 0.62969535589218 0.21067586541175 0.69069749116897 0.26768442988395
+0 -0.00284734903834 0.54523473978042 -0.64571571350097 -0.78070503473281 0.57210594415664 0.28155618906021 0.10069078207016 0.91472393274307 0.125328540802 -0.83553123474121 -0.82737815380096 -0.59940773248672 0.43447801470756 -0.65295654535293 0.06433679163456 0.53488200902938 -0.0186282005161 -0.50233364105224 -0.95033121109008 -0.43020704388618 0.8316284418106 -0.18899129331111 -0.24715395271778 0.75504666566848 0.12521325051784 -0.96539360284805 -0.61595100164413 -0.3140489757061 -0.77043581008911 0.40901958942413 -0.27910241484642 -0.09887818247079 0.15439313650131 0.18404148519039 0.27008816599845 -0.19787248969078 -0.8920806646347 -0.62485659122467 0.37998265027999 0.01863939128816 0.55868577957153 0.76543349027633 -0.36119017004966 -0.79607605934143 -0.62811416387558 0.39589694142341 0.80716812610626 -0.44485068321228 -0.60491567850112 -0.44497448205947 0.69407498836517 0.71679997444152 0.66466253995895 0.47108420729637 0.38376227021217 -0.83495903015136 0.2862249314785 0.90578305721283 0.54523473978042 -0.92563557624816 -0.26545673608779 -0.20174457132816 0.59173023700714 0.96348702907562
+0 -0.07352346181869 -0.65025752782821 0.75717025995254 -0.2508490383625 0.76402199268341 0.28031155467033 -0.65509229898452 -0.34714895486831 -0.39944213628768 0.17657575011253 0.41518783569335 0.61944794654846 0.71740752458572 0.39023640751838 -0.85533207654953 0.117431178689 0.3762859404087 0.78910791873931 0.27631270885467 -0.47827732563018 -0.25395408272743 -0.64319837093353 -0.26776704192161 -0.62877458333969 -0.99163085222244 -0.15919750928878 -0.21235628426075 0.91998487710952 -0.62908637523651 -0.28005090355873 -0.81897729635238 0.88692677021026 -0.9597492814064 0.89597284793853 -0.04155653342604 0.12643052637577 -0.05049291998148 0.05878961458802 -0.64604806900024 0.66386997699737 0.41955921053886 0.61278331279754 0.5081883072853 0.58536410331726 -0.55766254663467 0.90388929843902 0.16765642166137 0.25178271532058 -0.73438507318496 -0.88750571012497 -0.0802029967308 0.5112999677658 -0.59088027477264 -0.87574863433837 -0.83190387487411 -0.42248976230621 0.58220851421356 0.31190073490142 -0.65025752782821 -0.37740540504455 0.73007977008819 -0.95651179552078 -0.41568294167518 0.00614986103028
diff --git a/gpu_test/btest/bedpost/data.nii.gz b/gpu_test/btest/bedpost/data.nii.gz
new file mode 100644
index 0000000000000000000000000000000000000000..38fdc7d0c988550887afed6bc493efcf9e3ad933
--- /dev/null
+++ b/gpu_test/btest/bedpost/data.nii.gz
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:7cb90d53bc50cc842457224db37d3002eb143fd71698e23b315880c52d6f8d66
+size 523728
diff --git a/gpu_test/btest/bedpost/nodif_brain_mask.nii.gz b/gpu_test/btest/bedpost/nodif_brain_mask.nii.gz
new file mode 100644
index 0000000000000000000000000000000000000000..d93519dcf7475d320b316cff54e0573fe83e9112
--- /dev/null
+++ b/gpu_test/btest/bedpost/nodif_brain_mask.nii.gz
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:e5695011c246fce7c3efe09f290ebd3fabd169b5d61a7c41bdf1f45521f4627d
+size 1251
diff --git a/gpu_test/btest/dcm.sh b/gpu_test/btest/dcm.sh
new file mode 100755
index 0000000000000000000000000000000000000000..8be50991d565fe031788d458ef519aa343fc0e83
--- /dev/null
+++ b/gpu_test/btest/dcm.sh
@@ -0,0 +1,12 @@
+#!/bin/bash
+
+for i in $*;
+do
+ params=" $params $i"
+done
+exe=dcm2niix
+$exe -i y $params
+
+
+
+
diff --git a/gpu_test/btest/runme_gpu.sh b/gpu_test/btest/runme_gpu.sh
new file mode 100755
index 0000000000000000000000000000000000000000..8709bf1f6c05cf15c44677ee07117306c5405fa0
--- /dev/null
+++ b/gpu_test/btest/runme_gpu.sh
@@ -0,0 +1,11 @@
+#!/bin/bash
+
+pushd `dirname $0` > /dev/null
+SCRIPTPATH=`pwd -P`
+popd > /dev/null
+BEDPOSTDIR=$SCRIPTPATH/bedpost
+BEDPOSTOUTDIR=$BEDPOSTDIR.bedpostX
+rm -rf $BEDPOSTOUTDIR
+
+
+time bedpostx_gpu $BEDPOSTDIR
\ No newline at end of file
diff --git a/gpu_test/btest/runme_quick.sh b/gpu_test/btest/runme_quick.sh
new file mode 100755
index 0000000000000000000000000000000000000000..99a762af52280f76a9924bc28544567f2a02046c
--- /dev/null
+++ b/gpu_test/btest/runme_quick.sh
@@ -0,0 +1,20 @@
+#!/bin/bash
+
+pushd `dirname $0` > /dev/null
+SCRIPTPATH=`pwd -P`
+popd > /dev/null
+BEDPOSTDIR=$SCRIPTPATH/bedpost
+BEDPOSTOUTDIR=$BEDPOSTDIR.bedpostX
+
+rm -rf $BEDPOSTOUTDIR
+echo "fsl_sub running $COMMANDNAME with parallel processing disabled"
+FSLPARALLEL=0
+#time bedpostx $BEDPOSTDIR
+
+rm -rf $BEDPOSTOUTDIR
+echo "fsl_sub running $COMMANDNAME with parallel processing enabled"
+FSLPARALLEL=1
+time bedpostx $BEDPOSTDIR
+
+
+
diff --git a/gpu_test/eddy_setup/configure_eddy.sh b/gpu_test/eddy_setup/configure_eddy.sh
new file mode 100755
index 0000000000000000000000000000000000000000..f6d4c53802e2177417be29863fd48d58e08ed715
--- /dev/null
+++ b/gpu_test/eddy_setup/configure_eddy.sh
@@ -0,0 +1,187 @@
+#!/usr/bin/env bash
+#
+# This script configures eddy based on the current system (cuda found or not)
+#
+# Call with -f <FSLDIR path>, e.g. /usr/local/fsl (will use FSLDIR if given
+# no arguments)
+platform=`uname -s`
+# Where is this script?
+script_dir=$( cd $(dirname $0) ; pwd)
+script_name=${0##*/}
+# Set some defaults
+OPTIND=1
+fsl_dir=""
+quiet=0
+dryrun=0
+dropprivileges=0
+OLDIFS=$IFS
+# Have we been called by sudo?
+if [ ! -z "${SUDO_UID}" ]; then
+ dropprivileges=1
+fi
+
+function syntax {
+ echo "$script_name [-f <FSLDIR>] [-q] [-d]"
+ echo " -f <FSLDIR> Location of installed FSL, e.g. /usr/local/fsl"
+ echo " if not provided looks for FSLDIR in environment"
+ echo " -q Install quietly"
+ echo " -d Dry run. Does not actually make symlinks"
+}
+
+while getopts "h?qdf:" opt; do
+ case "${opt}" in
+ h|\?)
+ syntax
+ exit 0
+ ;;
+ q) quiet=1
+ ;;
+ f) fsl_dir=${OPTARG}
+ ;;
+ d) dryrun=1
+ ;;
+ esac
+done
+
+shift $((OPTIND-1))
+
+[ "$1" = "--" ] && shift
+
+if [ -z "${fsl_dir}" ]; then
+ if [ -z "${FSLDIR}" ]; then
+ echo "Error - FSLDIR not given as an argument and \$FSLDIR not set!" >&2
+ exit 1
+ else
+ fsl_dir=${FSLDIR}
+ fi
+fi
+
+if [ ! -e "${fsl_dir}/bin" ]; then
+ echo "Error - ${fsl_dir}/bin does not exist!" >&2
+ exit 1
+fi
+
+if [ ! -w "${fsl_dir}" ]; then
+ echo "Error - cannot write to ${fsl_dir}!" >&2
+ exit 1
+fi
+
+if [ ! -w "${fsl_dir}/bin" ]; then
+ echo "Error - cannot write to ${fsl_dir}/bin!" >&2
+ exit 1
+fi
+
+if [ ! -e "${fsl_dir}/etc/fslversion" ]; then
+ echo "${fsl_dir} doesn't look like an FSL installation folder!" >&2
+ exit 1
+fi
+
+function drop_sudo {
+ if [ ${dropprivileges} -eq 1 ]; then
+ sudo -u \#${SUDO_UID} "$@"
+ if [ $? -eq 1 ]; then
+ sudo -u \#${SUDO_UID} -g \#${SUDO_GID} "$@"
+ fi
+ else
+ "$@"
+ fi
+}
+
+#####################################
+# Configure eddy
+#####################################
+
+# If Darwin (macOS) then no need to configure eddy_openmp or eddy_cuda
+if [ "$platform" = "Darwin" ]; then
+ exit 0
+fi
+
+# If Linux, run the following configuration steps:
+# check if no eddy, but eddy_openmp exists, then link to eddy
+if [ ! -f "${fsl_dir}/bin/eddy" ]; then
+ if [ -f "${fsl_dir}/bin/eddy_openmp" ]; then
+ if [[ dryrun -eq 0 ]]
+ then
+ ln -sf ${fsl_dir}/bin/eddy_openmp ${fsl_dir}/bin/eddy
+ else
+ echo "would do: ln -sf ${fsl_dir}/bin/eddy_openmp ${fsl_dir}/bin/eddy"
+ fi
+ fi
+fi
+
+# does eddy_cuda exist?
+if [ -f "${fsl_dir}/bin/eddy_cuda" ]; then
+ exit 0
+else
+ # list installed fsl eddy_cuda versions (puts versions into array)
+ eddycudas=($(ls -d ${fsl_dir}/bin/eddy_cuda*))
+ if [ -z "$eddycudas" ]
+ then
+ exit 0
+ fi
+
+ # List installed cuda versions in /opt/cuda* (put into array)
+ ls -d /opt/cuda* > /dev/null 2>&1
+ if [ $? -eq 0 ]
+ then
+ syscudas=($(ls -d /opt/cuda* | sort -V))
+ else
+ ls -d /usr/local/cuda* > /dev/null 2>&1
+ if [ $? -eq 0 ]
+ then
+ syscudas=($(ls -d /usr/local/cuda* | sort -V))
+ else
+ exit 0
+ fi
+ fi
+ if [ -z "$syscudas" ]
+ then
+ exit 0
+ fi
+
+ # loop through eddy_cuda versions found
+ for eddycudaversionstring in "${eddycudas[@]}"
+ do
+ # parse full path string into parts separated by "/"
+ IFS='/' read -r -a parts <<< "$eddycudaversionstring"
+ # get the last part
+ len=${#parts[@]}
+ i=$((len-1))
+ fslcudastring="${parts[$i]}"
+ IFS=$OLDIFS
+ # parse again to get version string
+ IFS='eddy_cuda' read -a verstring <<< "$fslcudastring"
+ len=${#verstring[@]}
+ i=$((len-1))
+ fslcudaver="${verstring[$i]}"
+ IFS=$OLDIFS
+
+ for syscudaversionstring in "${syscudas[@]}"
+ do
+ # parse full path string into parts separated by "/"
+ IFS='/' read -a parts <<< "$syscudaversionstring"
+ # get the last part
+ len=${#parts[@]}
+ i=$((len-1))
+ syscudastring="${parts[$i]}"
+ IFS=$OLDIFS
+ # parse again to get version string
+ IFS='-' read -a verstring <<< "$syscudastring"
+ len=${#verstring[@]}
+ i=$((len-1))
+ syscudaver="${verstring[$i]}"
+ IFS=$OLDIFS
+ # if version strings are equal, we know that the user has version X available, so we can link to version X for eddy_cuda
+ if [ "$fslcudaver" == "$syscudaver" ]; then
+ if [[ dryrun -eq 0 ]]
+ then
+ ln -sf ${fsl_dir}/bin/eddy_cuda$fslcudaver ${fsl_dir}/bin/eddy_cuda
+ else
+ echo "would do: ln -sf ${fsl_dir}/bin/eddy_cuda$fslcudaver ${fsl_dir}/bin/eddy_cuda"
+ fi
+ fi
+ done
+ done
+fi
+
+
diff --git a/gpu_test/eddy_setup/configure_eddy_cr.sh b/gpu_test/eddy_setup/configure_eddy_cr.sh
new file mode 100755
index 0000000000000000000000000000000000000000..22ed693053402c63fc3b4180ca99ff288122b5c2
--- /dev/null
+++ b/gpu_test/eddy_setup/configure_eddy_cr.sh
@@ -0,0 +1,29 @@
+#!/bin/bash
+fnm=/usr/local/cuda/version.txt
+if [ ! -f $fnm ]; then
+ echo "CUDA not installed: unable to find '$fnm'"
+ exit 1
+fi
+value=`cat $fnm`
+#value = "CUDA Version 10.1.243"
+# echo "$value"
+var2=${value##* }
+#var2= "10.1.243" or "10.1"
+dots="${var2//[^.]}"
+dots=${#dots}
+if [[ "$dots" -eq 2 ]]; then
+ # "10.1.221" -> "10.1"
+ var2=${var2%.*}
+fi
+#var2 = "10.1"
+exe=eddy_cuda$var2
+pth=$(which $exe)
+if [ -z "$pth" ]; then
+ echo "CUDA version not supported: unable to find '$exe'"
+ exit 1
+fi
+# echo "Executing '$exe'"
+# $exe "$@"
+echo Run the following command:
+echo sudo ln -s $pth $(dirname $pth)/eddy_cuda
+
diff --git a/gpu_test/etest/DTIap.bval b/gpu_test/etest/DTIap.bval
new file mode 100644
index 0000000000000000000000000000000000000000..91168d5a36c06e0f56b63df43da0eb6ec25fce59
--- /dev/null
+++ b/gpu_test/etest/DTIap.bval
@@ -0,0 +1 @@
+0 1000 1000 1000 1000 1000 995 1000 1000 1000 0 1000 995 1000 995 1000 1000 995 1000 1000 0 995 1000 1000 1000 1000 995 995 1000 1000 0 1000 1000 1000 1000 1000 995 1000 1000 995 0
diff --git a/gpu_test/etest/DTIap.bvec b/gpu_test/etest/DTIap.bvec
new file mode 100644
index 0000000000000000000000000000000000000000..29bac659dedc6f1adbd579a86a3391f1092f50ef
--- /dev/null
+++ b/gpu_test/etest/DTIap.bvec
@@ -0,0 +1,3 @@
+0 0.0488851 0.725485 -0.682614 0.844537 -0.729888 -0.0513232 -0.0183529 -0.444238 -0.989383 0 -0.470038 0.412129 -0.551845 -0.123275 -0.848912 -0.340757 0.361164 -0.472463 -0.856466 0 0.797389 0.466211 0.0130422 0.882785 0.0166147 -0.442765 0.365204 0.976815 -0.405789 0 -0.627569 -0.353732 -0.65789 0.422267 0.212124 0.911878 -0.311432 0.678253 0.135593 0
+0 -0.923381 0.292673 0.246421 -0.503865 -0.6229 0.0514389 0.864488 0.503981 -0.0872866 0 -0.852204 0.4102 0.786223 -0.466669 0.147696 -0.793793 -0.520498 0.852957 -0.478704 0 0.169292 -0.0197333 0.99751 -0.384307 -0.545775 -0.64375 -0.0468793 -0.00673674 -0.903931 0 0.620526 0.764864 -0.478923 0.311514 -0.760891 -0.0995048 0.946037 0.62718 -0.274471 0
+0 0.380758 0.622908 0.687979 0.181324 0.28153 -0.997357 0.502318 -0.740713 0.116196 0 -0.229808 -0.813564 0.278065 -0.875798 -0.507479 0.503764 -0.77372 -0.221906 -0.193153 0 -0.579234 0.884453 0.0693107 -0.270183 0.837767 -0.624136 -0.929746 0.213978 0.13507 0 -0.470218 0.538384 0.581218 0.851264 0.613227 -0.398217 0.0895813 0.382909 -0.951987 0
diff --git a/gpu_test/etest/DTIap.nii.gz b/gpu_test/etest/DTIap.nii.gz
new file mode 100644
index 0000000000000000000000000000000000000000..0bf974d834fc4dd6863dce3198a58e16b5933a38
--- /dev/null
+++ b/gpu_test/etest/DTIap.nii.gz
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:acd55955eaf7a1267a6b2d0b529f5af895a5c11c63633ae4b3f4549c79932bf8
+size 18518301
diff --git a/gpu_test/etest/runme_gpu.sh b/gpu_test/etest/runme_gpu.sh
new file mode 100755
index 0000000000000000000000000000000000000000..980755f446d460f8b1cb2270c87adf693cd35055
--- /dev/null
+++ b/gpu_test/etest/runme_gpu.sh
@@ -0,0 +1,42 @@
+#!/bin/bash
+
+eddyExeName=eddy_cuda
+pth=$(which $eddyExeName)
+if [ -z "$pth" ]; then
+ echo "CUDA version not supported (try running `configure_eddy.sh`): unable to find '$eddyExeName'"
+ exit 1
+fi
+
+
+dti=DTIap
+
+if [ ! -e ${dti}.nii.gz ]; then
+ echo "Error: Unable to find ${dti}.nii.gz"
+ exit 1
+fi
+
+if ! hash $eddyExeName 2>/dev/null; then
+ echo "Error: Unable to find $eddyExeName"
+ exit 1
+fi
+
+dti_b=${dti}b #brain-extracted dti
+dti_b0=${dti}b0
+dti_u=${dti}u #undistorted dti
+dti_bvec=${dti}.bvec
+dti_bval=${dti}.bval
+
+fslroi $dti $dti_b0 0 1
+bet $dti_b0 $dti_b -f 0.2 -R -n -m
+dti_b=${dti}b_mask #masked brain-extracted dti
+#create acq_param: dummies as we will not run TOPUP
+dti_txt=${dti}_acq_param.txt
+printf "0 1 0 0.03388\n0 -1 0 0.03388\n" > $dti_txt
+#create index files: all = 1 as we will not run TOPUP
+dti_txt2=${dti}_index.txt
+nvol=$(fslnvols $dti)
+indx=""
+for ((i=1; i<=nvol; i+=1)); do indx="$indx 1"; done
+echo $indx > $dti_txt2
+echo $eddyExeName --imain=$dti --mask=$dti_b --acqp=$dti_txt --index=$dti_txt2 --bvecs=$dti_bvec --bvals=$dti_bval --repol --out=$dti_u
+time $eddyExeName --imain=$dti --mask=$dti_b --acqp=$dti_txt --index=$dti_txt2 --bvecs=$dti_bvec --bvals=$dti_bval --repol --out=$dti_u
diff --git a/gpu_test/ptest/bedpost.bedpostX/bvals b/gpu_test/ptest/bedpost.bedpostX/bvals
new file mode 100755
index 0000000000000000000000000000000000000000..b03537840b7848baaba1b6d90d012425cc802c60
--- /dev/null
+++ b/gpu_test/ptest/bedpost.bedpostX/bvals
@@ -0,0 +1 @@
+0 1000 1000 1000 1000 1000 995 1000 1000 1000 0 1000 995 1000 995 1000 1000 995 1000 1000 0 995 1000 1000 1000 1000 995 995 1000 1000 0 1000 1000 1000 1000 1000 995 1000 1000 995 0 0 1000 1000 1000 1000 1000 995 1000 1000 1000 0 1000 995 1000 995 1000 1000 995 1000 1000 0 995 1000 1000 1000 1000 995 995 1000 1000 0 1000 1000 1000 1000 1000 995 1000 1000 995 0
diff --git a/gpu_test/ptest/bedpost.bedpostX/bvecs b/gpu_test/ptest/bedpost.bedpostX/bvecs
new file mode 100755
index 0000000000000000000000000000000000000000..78b6d4ac62651ac69c20f165345137310d24f359
--- /dev/null
+++ b/gpu_test/ptest/bedpost.bedpostX/bvecs
@@ -0,0 +1,3 @@
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diff --git a/gpu_test/ptest/bedpost.bedpostX/commands.txt b/gpu_test/ptest/bedpost.bedpostX/commands.txt
new file mode 100755
index 0000000000000000000000000000000000000000..e825462d4b10fccea532bc89ff8443fc453916bd
--- /dev/null
+++ b/gpu_test/ptest/bedpost.bedpostX/commands.txt
@@ -0,0 +1,50 @@
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 0 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 1 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 2 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 3 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 4 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 5 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 6 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 7 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 8 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 9 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 10 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 11 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 12 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 13 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 14 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 15 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 16 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 17 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 18 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 19 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 20 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 21 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 22 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 23 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 24 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 25 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 26 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 27 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 28 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 29 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 30 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 31 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 32 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 33 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 34 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 35 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 36 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 37 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 38 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 39 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 40 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 41 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 42 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
+/usr/local/fsl/bin/bedpostx_single_slice.sh /home/crlab/Desktop/LM3/LM1045/bedpost 43 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear
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--- /dev/null
+++ b/gpu_test/ptest/bedpost.bedpostX/monitor
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+#!/bin/sh
+echo
+echo "----- Bedpostx Monitor -----"
+finished=0
+lastprinted=0
+havedad=2
+while [ $finished -eq 0 ] ; do
+ nfin=0
+ slice=0
+ errorFiles=`ls /home/crlab/Desktop/LM3/LM1045/bedpost.bedpostX/logs/*.e* 2> /dev/null `
+ for errorFile in $errorFiles
+ do
+ if [ -s $errorFile ]; then
+ echo An error ocurred. Please check file $errorFile
+ kill -9 4200
+ exit 1
+ fi
+ done
+ while [ $slice -le 50 ];do
+ if [ -e /home/crlab/Desktop/LM3/LM1045/bedpost.bedpostX/logs/monitor/$slice ]; then
+ nfin=$(($nfin + 1))
+ fi
+ slice=$(($slice + 1))
+ done
+ newmessages=$(($nfin - $lastprinted))
+ while [ "$newmessages" -gt 0 ];do
+ lastprinted=$(($lastprinted + 1))
+ echo $lastprinted slices processed out of 50
+ newmessages=$(($newmessages - 1))
+ done
+ if [ -f /home/crlab/Desktop/LM3/LM1045/bedpost.bedpostX/xfms/eye.mat ] ; then
+ finished=1
+ echo "All slices processed"
+ exit
+ fi
+ if [ ! $havedad -gt 0 ]; then
+ exit 0
+ fi
+ if [ "x" == "x" ]; then
+ havedad=`ps -e -o pid | grep "4200\b" | wc -l`
+ fi
+ sleep 180;
+done
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new file mode 100755
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--- /dev/null
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new file mode 100755
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--- /dev/null
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new file mode 100755
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--- /dev/null
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--- /dev/null
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new file mode 100755
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--- /dev/null
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new file mode 100755
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new file mode 100755
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--- /dev/null
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diff --git a/gpu_test/ptest/masks/94.nii.gz b/gpu_test/ptest/masks/94.nii.gz
new file mode 100755
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--- /dev/null
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diff --git a/gpu_test/ptest/masks/95.nii.gz b/gpu_test/ptest/masks/95.nii.gz
new file mode 100755
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--- /dev/null
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diff --git a/gpu_test/ptest/masks/96.nii.gz b/gpu_test/ptest/masks/96.nii.gz
new file mode 100755
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--- /dev/null
+++ b/gpu_test/ptest/masks/96.nii.gz
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diff --git a/gpu_test/ptest/masks/97.nii.gz b/gpu_test/ptest/masks/97.nii.gz
new file mode 100755
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--- /dev/null
+++ b/gpu_test/ptest/masks/97.nii.gz
@@ -0,0 +1,3 @@
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diff --git a/gpu_test/ptest/masks/98.nii.gz b/gpu_test/ptest/masks/98.nii.gz
new file mode 100755
index 0000000000000000000000000000000000000000..5f9d422632fa528b037291a812ec71e6230a054d
--- /dev/null
+++ b/gpu_test/ptest/masks/98.nii.gz
@@ -0,0 +1,3 @@
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diff --git a/gpu_test/ptest/masks/99.nii.gz b/gpu_test/ptest/masks/99.nii.gz
new file mode 100755
index 0000000000000000000000000000000000000000..3fad3e70b63240b47d52afb972ba86a79e3c5750
--- /dev/null
+++ b/gpu_test/ptest/masks/99.nii.gz
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
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diff --git a/gpu_test/ptest/runme_cpu.sh b/gpu_test/ptest/runme_cpu.sh
new file mode 100755
index 0000000000000000000000000000000000000000..7ca80553adf91c395244f4968bd2cfe367c48e96
--- /dev/null
+++ b/gpu_test/ptest/runme_cpu.sh
@@ -0,0 +1,22 @@
+
+
+pushd `dirname $0` > /dev/null
+SCRIPTPATH=`pwd -P`
+popd > /dev/null
+COMMANDNAME=$SCRIPTPATH/command.txt
+LOGNAME=$SCRIPTPATH/logs
+
+rm -f $COMMANDNAME
+for i in {1..4}
+do
+ echo "probtrackx2 -x $SCRIPTPATH/masks/$i.nii.gz --dir=$SCRIPTPATH/probtrackx/$i --forcedir -P 200 -s $SCRIPTPATH/bedpost.bedpostX/merged -m $SCRIPTPATH/bedpost.bedpostX/nodif_brain_mask --opd --pd -l -c 0.2 --distthresh=0" >> $COMMANDNAME
+done
+
+echo "fsl_sub running $COMMANDNAME with parallel processing enabled"
+FSLPARALLEL=1
+time fsl_sub -l $LOGNAME -N probtrackx -T 1 -t $COMMANDNAME
+
+echo "fsl_sub running $COMMANDNAME with parallel processing disabled"
+FSLPARALLEL=0
+time fsl_sub -l $LOGNAME -N probtrackx -T 1 -t $COMMANDNAME
+
diff --git a/gpu_test/ptest/runme_gpu.sh b/gpu_test/ptest/runme_gpu.sh
new file mode 100755
index 0000000000000000000000000000000000000000..ea4d16a5c8c2271fc5fb9a1112f923dee1405a19
--- /dev/null
+++ b/gpu_test/ptest/runme_gpu.sh
@@ -0,0 +1,17 @@
+#!/bin/bash
+
+pushd `dirname $0` > /dev/null
+SCRIPTPATH=`pwd -P`
+popd > /dev/null
+COMMANDNAME=$SCRIPTPATH/command.txt
+LOGNAME=$SCRIPTPATH/logs
+
+rm -f $COMMANDNAME
+for i in {1..4}
+do
+ echo "probtrackx2_gpu -x $SCRIPTPATH/masks/$i.nii.gz --dir=$SCRIPTPATH/probtrackx/$i --forcedir -P 200 -s $SCRIPTPATH/bedpost.bedpostX/merged -m $SCRIPTPATH/bedpost.bedpostX/nodif_brain_mask --opd --pd -l -c 0.2 --distthresh=0" >> $COMMANDNAME
+done
+
+echo "fsl_sub running $COMMANDNAME with the GPU"
+time fsl_sub -l $LOGNAME -N probtrackx -T 1 -t $COMMANDNAME
+
diff --git a/gpu_test/ptest/runme_slow_cpu.sh b/gpu_test/ptest/runme_slow_cpu.sh
new file mode 100755
index 0000000000000000000000000000000000000000..f5330c0310f756d21785a5884595c70d29510d43
--- /dev/null
+++ b/gpu_test/ptest/runme_slow_cpu.sh
@@ -0,0 +1,33 @@
+#!/bin/bash
+
+pushd `dirname $0` > /dev/null
+SCRIPTPATH=`pwd -P`
+popd > /dev/null
+COMMANDNAME=$SCRIPTPATH/command.txt
+LOGNAME=$SCRIPTPATH/logs
+
+rm -f $COMMANDNAME
+for i in {1..172}
+do
+ echo "probtrackx2 -x $SCRIPTPATH/masks/$i.nii.gz --dir=$SCRIPTPATH/probtrackx/$i --forcedir -P 200 -s $SCRIPTPATH/bedpost.bedpostX/merged -m $SCRIPTPATH/bedpost.bedpostX/nodif_brain_mask --opd --pd -l -c 0.2 --distthresh=0" >> $COMMANDNAME
+done
+
+echo "fsl_sub running $COMMANDNAME with parallel processing disabled"
+FSLPARALLEL=0; export FSLPARALLEL
+time fsl_sub -l $LOGNAME -N probtrackx -T 1 -t $COMMANDNAME
+
+echo "fsl_sub running $COMMANDNAME with x2 parallel processing enabled"
+FSLPARALLEL=2
+time fsl_sub -l $LOGNAME -N probtrackx -T 1 -t $COMMANDNAME
+
+echo "fsl_sub running $COMMANDNAME with x4 parallel processing enabled"
+FSLPARALLEL=4
+time fsl_sub -l $LOGNAME -N probtrackx -T 1 -t $COMMANDNAME
+
+echo "fsl_sub running $COMMANDNAME with x8 parallel processing enabled"
+FSLPARALLEL=8
+time fsl_sub -l $LOGNAME -N probtrackx -T 1 -t $COMMANDNAME
+
+echo "fsl_sub running $COMMANDNAME with x12 parallel processing enabled"
+FSLPARALLEL=12
+time fsl_sub -l $LOGNAME -N probtrackx -T 1 -t $COMMANDNAME
diff --git a/gpu_test/ptest/runme_slow_gpu.sh b/gpu_test/ptest/runme_slow_gpu.sh
new file mode 100755
index 0000000000000000000000000000000000000000..ab155554ecc55f4df47ff369fdcac6c52a51d602
--- /dev/null
+++ b/gpu_test/ptest/runme_slow_gpu.sh
@@ -0,0 +1,17 @@
+#!/bin/bash
+
+pushd `dirname $0` > /dev/null
+SCRIPTPATH=`pwd -P`
+popd > /dev/null
+COMMANDNAME=$SCRIPTPATH/command.txt
+LOGNAME=$SCRIPTPATH/logs
+
+rm -f $COMMANDNAME
+for i in {1..172}
+do
+ echo "probtrackx2_gpu -x $SCRIPTPATH/masks/$i.nii.gz --dir=$SCRIPTPATH/probtrackx/$i --forcedir -P 200 -s $SCRIPTPATH/bedpost.bedpostX/merged -m $SCRIPTPATH/bedpost.bedpostX/nodif_brain_mask --opd --pd -l -c 0.2 --distthresh=0" >> $COMMANDNAME
+done
+
+echo "fsl_sub running $COMMANDNAME with the GPU"
+time fsl_sub -l $LOGNAME -N probtrackx -T 1 -t $COMMANDNAME
+