diff --git a/bin/fsl_sub b/bin/fsl_sub
new file mode 100755
index 0000000000000000000000000000000000000000..e99349488d4ed8c1324a80ebaeb382207ffcab25
--- /dev/null
+++ b/bin/fsl_sub
@@ -0,0 +1,483 @@
+#!/bin/bash
+
+# Copyright (C) 2007-2017 University of Oxford
+# Authors: Dave Flitney, Stephen Smith, Matthew Webster and Duncan Mortimer
+
+# SHCOPYRIGHT
+export LC_ALL=C
+
+###########################################################################
+# Edit this file in order to setup FSL to use your local compute
+# cluster.
+###########################################################################
+set +o errexit
+
+###########################################################################
+# The following section determines what to do when fsl_sub is called
+# by an FSL program. If SGE_ROOT is set it will attempt to pass the
+# commands onto the cluster, otherwise it will run the commands
+# itself. There are two values for the METHOD variable, "SGE" and
+# "NONE". Note that a user can unset SGE_ROOT if they don't want the
+# cluster to be used.
+###########################################################################
+METHOD=SGE
+unset module
+if [[ "x$SGE_ROOT" = "x" ]] ; then
+ METHOD=NONE
+else
+ QCONF=$(which qconf)
+ if [[ "x$QCONF" = "x" ]]; then
+ METHOD=NONE
+ echo "Warning: SGE_ROOT environment variable is set but Grid Engine software not found, will run locally" >&2
+ fi
+fi
+
+# stop submitted scripts from submitting jobs themselves
+if [[ "X$FSLSUBALREADYRUN" = "Xtrue" ]] ; then
+ METHOD=NONE
+ echo "Warning: job on queue attempted to submit parallel jobs - running jobs serially instead" >&2
+fi
+
+if [[ "X$METHOD" = "XNONE" ]]; then
+ QCONF=echo
+fi
+FSLSUBALREADYRUN=true
+export FSLSUBALREADYRUN
+
+###########################################################################
+# The following auto-decides what cluster queue to use. The calling
+# FSL program will probably use the -T option when calling fsl_sub,
+# which tells fsl_sub how long (in minutes) the process is expected to
+# take (in the case of the -t option, how long each line in the
+# supplied file is expected to take). You need to setup the following
+# list to map ranges of timings into your cluster queues - it doesn't
+# matter how many you setup, that's up to you.
+###########################################################################
+
+map_qname ()
+{
+ if [[ "$1" -le 20 ]] ; then
+ queue=veryshort.q
+ elif [[ "$1" -le 120 ]] ; then
+ queue=short.q
+ elif [[ "$1" -le 1440 ]] ; then
+ queue=long.q
+ else
+ queue=verylong.q
+ fi
+ queueCmd=" -q $queue "
+
+ #echo "Estimated time was $1 mins: queue name is $queue"
+}
+
+###########################################################################
+# Don't change the following (but keep scrolling down!)
+###########################################################################
+
+if [[ ! -z "${POSIXLY_CORRECT}" ]]; then
+ OLD_POSIXLY_CORRECT=${POSIXLY_CORRECT}
+fi
+
+POSIXLY_CORRECT=1
+export POSIXLY_CORRECT
+command=$(basename "$0")
+
+usage ()
+{
+ cat <<EOF
+
+$command V1.1 - wrapper for job control system such as SGE
+
+Usage: $command [options] <command>
+
+$command gzip *.img *.hdr
+$command -q short.q gzip *.img *.hdr
+$command -a darwin regscript rawdata outputdir ...
+
+ -T <minutes> Estimated job length in minutes, used to auto-set queue name
+ -q <queuename> Possible values for <queuename> are "verylong.q", "long.q"
+ and "short.q". See below for details
+ Default is "long.q".
+ -a <arch-name> Architecture [e.g., darwin or lx24-amd64]
+ -p <job-priority> Lower priority [0:-1024] default = 0
+ -M <email-address> Who to email, default = $(whoami)@$(hostname -f | cut -d . -f 2-)
+ -j <jid> Place a hold on this task until job jid has completed
+ -t <filename> Specify a task file of commands to execute in parallel
+ -N <jobname> Specify jobname as it will appear on queue
+ -R <RAM> Max total RAM to use for job (integer in MB)
+ -l <logdirname> Where to output logfiles
+ -m <mailoptions> Change the SGE mail options, see qsub for details
+ -z <output> If <output> image or file already exists, do nothing and exit
+ -F Use flags embedded in scripts to set SGE queuing options
+ -s <pename>,<threads> Submit a multi-threaded task - requires a PE (<pename>) to be
+ configured for the requested queues.
+ <threads> specifies the number of threads to run
+ -v Verbose mode.
+
+Queues:
+
+There are several batch queues configured on the cluster, each with defined CPU
+time limits. All queues, except bigmem.q, have a 8GB memory limit.
+
+veryshort.q:This queue is for jobs which last under 30mins.
+short.q: This queue is for jobs which last up to 4h.
+long.q: This queue is for jobs which last less than 24h. Jobs run with a
+ nice value of 10.
+verylong.q: This queue is for jobs which will take longer than 24h CPU time.
+ There is one slot per node, and jobs on this queue have a nice value
+ of 15.
+bigmem.q: This queue is like the verylong.q but has no memory limits.
+
+EOF
+
+ exit 1
+}
+
+nargs=$#
+if [[ "$nargs" -eq 0 ]] ; then
+ usage
+fi
+
+#if the newer whitespace-safe getopt format is available, use it
+if [[ $(getopt -T >/dev/null 2>&1; echo $?) == 4 ]]; then
+ eval set -- $(getopt -s bash T:q:a:p:M:j:t:z:N:R:Fvm:l:s: "$@")
+ result=$?
+else
+ set -- $(getopt T:q:a:p:M:j:t:z:N:R:Fvm:l:s: "$@")
+ result=$?
+fi
+if [[ "$result" != 0 ]] ; then
+ echo "What? Your arguments make no sense!"
+fi
+
+if [[ "$nargs" -eq 0 ]] || [[ $result != 0 ]] ; then
+ usage
+fi
+
+if [[ -z "${OLD_POSIXLY_CORRECT}" ]]; then
+ unset POSIXLY_CORRECT
+else
+ POSIXLY_CORRECT=${OLD_POSIXLY_CORRECT}
+ export POSIXLY_CORRECT
+fi
+
+###########################################################################
+# If you have a Parallel Environment configured for OpenMP tasks then
+# the variable omp_pe should be set to the name you have defined for that
+# PE. The script will work out which queues have that PE setup on them.
+# Note, we support openmp tasks even when Grid Engine is not in use.
+###########################################################################
+
+omp_pe='openmp'
+
+
+###########################################################################
+# If you wish to disable processor affinities under Grid Engine then
+# comment the following line.
+# This instructs Grid Engine to bind the task to the number of job slots
+# allocated to the job (or PE)
+###########################################################################
+proc_affinities="-binding linear:slots"
+
+
+###########################################################################
+# The following sets up the default queue name, which you may want to
+# change. It also sets up the basic emailing control.
+###########################################################################
+
+queue=long.q
+queueCmd=" -q long.q "
+mailto=$(whoami)@$(hostname -f | cut -d . -f 2-)
+MailOpts="a"
+
+
+###########################################################################
+# In the following, you might want to change the behaviour of some
+# flags so that they prepare the right arguments for the actual
+# cluster queue submission program, in our case "qsub".
+#
+# -a sets is the cluster submission flag for controlling the required
+# hardware architecture (normally not set by the calling program)
+#
+# -p set the priority of the job - ignore this if your cluster
+# environment doesn't have priority control in this way.
+#
+# -j tells the cluster not to start this job until cluster job ID $jid
+# has completed. You will need this feature.
+#
+# -t will pass on to the cluster software the name of a text file
+# containing a set of commands to run in parallel; one command per
+# line.
+#
+# -N option determines what the command will be called when you list
+# running processes.
+#
+# -l tells the cluster what to call the standard output and standard
+# -error logfiles for the submitted program.
+###########################################################################
+
+if [[ -z "$FSLSUBVERBOSE" ]] ; then
+ verbose=0
+else
+ verbose=$FSLSUBVERBOSE;
+ echo "METHOD=$METHOD : args=$*" >&2
+fi
+
+scriptmode=0
+
+while [[ "$1" != -- ]] ; do
+ case "$1" in
+ -z)
+ if [[ -e "$2" || $("${FSLDIR}/bin/imtest" "$2") = 1 ]] ; then
+ exit 0
+ fi
+ shift;;
+ -T)
+ map_qname "$2"
+ shift;;
+ -q)
+ queue="$2"
+ queueCmd=" -q $queue "
+ "$QCONF" -sq "$queue" >/dev/null 2>&1
+ if [[ $? -eq 1 ]]; then
+ echo "Invalid queue specified!"
+ exit 127
+ fi
+ shift;;
+ -a)
+ acceptable_arch=no
+ available_archs=$(qhost | tail -n +4 | awk '{print $2}' | sort | uniq)
+ for a in $available_archs; do
+ if [[ "$2" = "$a" ]] ; then
+ acceptable_arch="yes"
+ fi
+ done
+ if [[ "$acceptable_arch" = "yes" ]]; then
+ sge_arch="-l arch=$2"
+ else
+ echo "Sorry arch of $2 is not supported on this SGE configuration!"
+ echo "Should be one of: $available_archs"
+ exit 127
+ fi
+ shift;;
+ -p)
+ # Not implmented
+ shift;;
+ -M)
+ mailto=$2
+ shift;;
+ -j)
+ jid=$2
+ sge_hold="-hold_jid $jid"
+ shift;;
+ -t)
+ taskfile=$2
+ if [[ -f "$taskfile" ]] ; then
+ tasks=$(wc -l "$taskfile" | awk '{print $1}')
+ if [[ "$tasks" -ne 0 ]]; then
+ sge_tasks="-t 1-$tasks"
+ else
+ echo "Task file ${taskfile} is empty"
+ echo "Should be a text file listing all the commands to run!"
+ exit -1
+ fi
+ else
+ echo "Task file (${taskfile}) does not exist"
+ exit -1
+ fi
+ shift;;
+ -N)
+ JobName=$2;
+ shift;;
+ -R)
+ RAM="-l mem_free=${2}M"
+ shift;;
+ -m)
+ MailOpts=$2;
+ shift;;
+ -l)
+ LogOpts="-o $2 -e $2";
+ LogDir="${2}/";
+ if [[ ! -e "${2}" ]]; then
+ mkdir -p "$2"
+ else
+ echo "${2}" | grep '/dev/null' >/dev/null 2>&1
+ if [[ $? -eq 1 ]] && [[ -f "${2}" ]]; then
+ echo "Log destination is a file (should be a folder)"
+ exit -1
+ fi
+ fi
+ shift;;
+ -F)
+ scriptmode=1;
+ ;;
+ -v)
+ verbose=1
+ ;;
+ -s)
+ pe_string=$2;
+ peName=$(echo "$pe_string" | cut -d',' -f 1)
+ peThreads=$(echo "$pe_string" | cut -d',' -f 2)
+ shift;;
+ esac
+ shift # next flag
+done
+shift
+
+###########################################################################
+# Don't change the following (but keep scrolling down!)
+###########################################################################
+commandline=("$@")
+command="${commandline[0]}"
+
+if [[ -z "$taskfile" ]] && [[ -z "$command" ]]; then
+ echo "Either supply a command to run or a parallel task file"
+ exit -1
+fi
+
+if [[ -z "$taskfile" ]] && [[ ! -x "$command" ]]; then
+ which "$command" >/dev/null 2>&1
+ if [[ $? -ne 0 ]]; then
+ echo "The command you have requested cannot be found or is not executable"
+ exit -1
+ fi
+fi
+
+if [[ "x$JobName" = x ]] ; then
+ if [[ "x$taskfile" != x ]] ; then
+ JobName=$(basename "$taskfile")
+ else
+ JobName=$(basename "$command")
+ fi
+fi
+
+if [[ -n "$tasks" ]] && [[ -n "${commandline[*]}" ]] ; then
+ echo "Spurious input after parsing command line: \"${commandline[*]}\"!"
+ echo "You appear to have specified both a task file and a command to run"
+ exit -1
+fi
+
+if [[ -n "$peName" ]]; then
+ # If the PE name is 'openmp' then limit the number of threads to those specified
+ if [[ "X$peName" = "X$omp_pe" ]]; then
+ OMP_NUM_THREADS=$peThreads
+ export OMP_NUM_THREADS
+ fi
+fi
+
+case "$METHOD" in
+
+###########################################################################
+# The following is the main call to the cluster, using the "qsub" SGE
+# program. If $tasks has not been set then qsub is running a single
+# command, otherwise qsub is processing a text file of parallel
+# commands.
+###########################################################################
+
+ SGE)
+ ###########################################################################
+ # Test Parallel environment options
+ ###########################################################################
+ if [[ -n "$peName" ]]; then
+ # Is this a configured PE?
+
+ "$QCONF" -sp "$peName" >/dev/null 2>&1
+
+ if [[ $? -eq 1 ]]; then
+ echo "${commandline[*]}"
+ echo "$peName is not a valid PE"
+ exit -1
+ fi
+
+ # Get a list of queues configured for this PE and confirm that the queue
+ # we have submitted to has that PE set up.
+ qstat -g c -pe "$peName" >/dev/null 2>&1
+ if [[ $? -eq 1 ]]; then
+ echo "No parallel environments configured!"
+ exit -1
+ fi
+
+ qstat -g c -pe "$peName" | sed '1,2d' | awk '{ print $1 }' | grep "^$queue" >/dev/null 2>&1
+
+ if [[ $? -eq 1 ]]; then
+ echo "${commandline[*]}"
+ echo "PE $peName is not configured on $queue"
+ exit -1
+ fi
+
+ # The -w e option will result in the job failing if there are insufficient slots
+ # on any of the cluster nodes
+ pe_options="-pe $peName $peThreads -w e"
+ fi
+
+ if [[ -z "$tasks" ]] ; then
+ if [[ "$scriptmode" -ne 1 ]] ; then
+ sge_command=(qsub -V -cwd -shell n -b y -r y $queueCmd $proc_affinities $pe_options -M $mailto -N "$JobName" -m $MailOpts $LogOpts $sge_arch $RAM $sge_hold)
+ else
+ sge_command=(qsub $proc_affinities $LogOpts $sge_arch $sge_hold)
+ fi
+ if [[ "$verbose" -eq 1 ]] ; then
+ echo "sge_command: ${sge_command[*]}" >&2
+ echo "executing: ${commandline[*]}" >&2
+ fi
+ exec "${sge_command[@]}" "${commandline[@]}" | awk '{print $3}'
+ else
+ sge_command=(qsub -V -cwd $queueCmd $proc_affinities $pe_options -M $mailto -N "$JobName" -m $MailOpts $LogOpts $sge_arch $RAM $sge_hold $sge_tasks)
+ if [[ "$verbose" -eq 1 ]] ; then
+ echo "sge_command: ${sge_command[*]}" >&2
+ echo "control file: $taskfile" >&2
+ fi
+ exec "${sge_command[@]}" <<EOF | awk '{print $3}' | awk -F. '{print $1}'
+#!/bin/sh
+
+#$ -S /bin/sh
+
+command=\`sed -n -e "\${SGE_TASK_ID}p" $taskfile\`
+
+exec /bin/sh -c "\$command"
+EOF
+ fi
+ ;;
+
+###########################################################################
+# Don't change the following - this runs the commands directly if a
+# cluster is not being used.
+###########################################################################
+
+ NONE)
+ if [[ "x$tasks" = "x" ]] ; then
+ if [[ "$verbose" -eq 1 ]] ; then
+ echo executing: "${commandline[*]}" >&2
+ fi
+
+ "${commandline[@]}" > "${LogDir}${JobName}.o$$" 2> "${LogDir}${JobName}.e$$"
+ ERR=$?
+ if [[ "$ERR" -ne 0 ]] ; then
+ cat "${LogDir}${JobName}.e$$" >&2
+ exit $ERR
+ fi
+ else
+ if [[ "$verbose" -eq 1 ]] ; then
+ echo "Running commands in: $taskfile" >&2
+ fi
+
+ n=1
+ while [[ "$n" -le "$tasks" ]] ; do
+ line=$(sed -n -e ''${n}'p' "$taskfile")
+ if [[ "$verbose" -eq 1 ]] ; then
+ echo "executing: $line" >&2
+ fi
+ /bin/sh <<EOF2 > "${LogDir}${JobName}.o$$.$n" 2> "${LogDir}${JobName}.e$$.$n"
+$line
+EOF2
+ n=$((n+1))
+ done
+ fi
+ echo $$
+ ;;
+
+esac
+
+###########################################################################
+# Done.
+###########################################################################
diff --git a/config/common/insertcopyright b/config/common/insertcopyright
old mode 100644
new mode 100755
diff --git a/config/common/supportedGencodes.sh b/config/common/supportedGencodes.sh
old mode 100644
new mode 100755
diff --git a/config/generic/configure.sh b/config/generic/configure.sh
deleted file mode 100644
index 5508366a9010430e6d40a01dca8bbbaa7629f1b0..0000000000000000000000000000000000000000
--- a/config/generic/configure.sh
+++ /dev/null
@@ -1,12 +0,0 @@
-# Auto-configure options for Mac OS X Universal build
-
-# Written by Duncan Mortimer
-case "$FSLMACHTYPE" in *darwin*)
- echo "BASE CONFIGURE"
- macosx_opts="-arch x86_64 -mmacosx-version-min=10.9"
- cflags="${cflags} ${macosx_opts}"
- cxxflags="${cxxflags} ${macosx_opts}"
- ldflags="${ldflags} -Wl,-search_paths_first ${macosx_opts}"
- configure_opts="${configure_opts} --disable-dependency-tracking"
-;;
-esac
\ No newline at end of file
diff --git a/config/generic/tclconfigure.sh b/config/generic/tclconfigure.sh
deleted file mode 100644
index fe05fdb374dbf1cd322e5aca9d284cefd9367804..0000000000000000000000000000000000000000
--- a/config/generic/tclconfigure.sh
+++ /dev/null
@@ -1,13 +0,0 @@
-# Auto-configure options for Mac OS X Universal build
-
-# Written by Duncan Mortimer
-case "$FSLMACHTYPE" in *darwin*)
- echo "TCL CONFIGURE"
- macosx_opts="-arch x86_64"
- macosx_version="-mmacosx-version-min=10.9"
- cflags="${cflags} ${macosx_opts} ${macosx_version}"
- cxxflags="${cxxflags} ${macosx_opts} ${macosx_version}"
- ldflags="${ldflags} -Wl,-search_paths_first ${macosx_opts}"
- configure_opts="${configure_opts} --disable-dependency-tracking"
-;;
-esac
diff --git a/config/generic/tkconfigure.sh b/config/generic/tkconfigure.sh
deleted file mode 100644
index 6a54c38ec8637ef32bcbffe1bc856aaa6ae7ef2d..0000000000000000000000000000000000000000
--- a/config/generic/tkconfigure.sh
+++ /dev/null
@@ -1,13 +0,0 @@
-# Auto-configure options for Mac OS X Universal build
-
-# Written by Duncan Mortimer
-case "$FSLMACHTYPE" in *darwin*)
- echo "TK CONFIGURE"
- macosx_opts="-arch x86_64"
- macosx_min="-mmacosx-version-min=10.9"
- cflags="${cflags} ${macosx_opts} ${macosx_min}"
- cxxflags="${cxxflags} ${macosx_opts} ${macosx_min}"
- ldflags="${ldflags} -Wl,-search_paths_first ${macosx_opts}"
- configure_opts="${configure_opts} --disable-dependency-tracking --x-includes=/usr/X11/include --x-libraries=/usr/X11/lib"
-;;
-esac