FSL 6.0.5

6 files changed, 632 insertions, 102 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 1e3913504d29..b53db7dd851d 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,7 +1,7 @@
 pkgbase = fsl
 	pkgdesc = A comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data
-	pkgver = 6.0.4
-	pkgrel = 2
+	pkgver = 6.0.5
+	pkgrel = 1
 	url = http://www.fmrib.ox.ac.uk/fsl/
 	arch = x86_64
 	license = custom
@@ -24,34 +24,23 @@ pkgbase = fsl
 	depends = vtk
 	depends = sqlite
 	depends = python3
-	depends = fslpy
+	depends = fslpy>=3.7.0
 	depends = bc
 	depends = openblas
 	optdepends = cuda
-	source = https://www.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.4-sources.tar.gz
-	source = https://www.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.4-feeds.tar.gz
+	source = https://www.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.5-sources.tar.gz
+	source = https://www.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.5-feeds.tar.gz
 	source = buildSettings.mk
-	source = imcp
-	source = imglob
-	source = immv
+	source = fsl_sub
 	source = 001-use_distribution_environment.patch
-	source = 002-fix_meldata_usage_of_ifstream.patch
-	source = 003-fix_fsl_exec_empty_errorCode.patch
-	source = 004-fix_missing_LIB_PROB.patch
-	source = 005-fix_cuda_thrust_include.patch
-	source = 006-compile_ptx2_without_std-c++11.patch
-	sha256sums = 58b88f38e080b05d70724d57342f58e1baf56e2bd3b98506a72b4446cad5033e
-	sha256sums = 411daed14287d6ba536cb531450941ab1f570309cd561de4e2a4b0ec43a7e9f7
-	sha256sums = c7f93adcf037a73182ae42ae6a59d3eb04a492888b6c2a6b528f9cd16539b2b2
-	sha256sums = 8aac3a2ea61bb4c38eb363262ab7f89e55c49a5feb9912fd2ff71f2439f11fc9
-	sha256sums = b3280bafc86d04dfa8835ef21f50469f2645bf09c36edcdd3f04349ce2c74225
-	sha256sums = 8e343b0ff93477280fd9a980822ddc9980afa7201dea51c886376c189c234c99
+	source = 002-fix_fsl_exec_empty_errorCode.patch
+	source = 003-fix_missing_LIB_PROB.patch
+	sha256sums = df12b0b1161a26470ddf04e4c5d5d81580a04493890226207667ed8fd2b4b83f
+	sha256sums = e68e1efeb45750f876f350442f56c4830d211e9fb16daa5ad134bb8e1ef1ae18
+	sha256sums = 880c46d4ef8a8ee1401e1fdb71dadd0f79aad2154967a03232844845227394a3
+	sha256sums = 2516982d151ab9e450a9ac6d5a6fc87099a7acc067514d80422c69950e618170
 	sha256sums = 906ac7de8068e5a5487b083844b50b6afd7562866088a4175fd88030182affdd
-	sha256sums = 13d4cf35343e7a73bc2534c94b1b0d4db41c338d374e6982091e4cf7a421d420
 	sha256sums = 64b4ccefa63a3cf920b185dd52e94b918c24f2cedaebcec8efb767bd80a6418a
 	sha256sums = adea0372f42026e72e385f1bec19ecc8cffa46de1f617271f14c9345c6b83c04
-	sha256sums = 9471addfc2f880350eedadcb99cb8b350abf42be1c0652ccddf49e34e5e48734
-	sha256sums = ab68cb802243ce715eff0d1136cfa29fa34a3e09934e5e20e02a092d69028df1
 
 pkgname = fsl
-
diff --git a/002-fix_fsl_exec_empty_errorCode.patch b/002-fix_fsl_exec_empty_errorCode.patch
new file mode 100644
index 000000000000..5e8cb0269cd2
--- /dev/null
+++ b/002-fix_fsl_exec_empty_errorCode.patch
@@ -0,0 +1,12 @@
+--- a/fsl/src/misc_tcl/fsl_exec.tcl	2018-10-23 18:49:44.000000000 +0200
++++ b/fsl/src/misc_tcl/fsl_exec.tcl	2018-11-25 18:52:30.636934316 +0100
+@@ -175,6 +175,9 @@
+ 	set logout ""
+     }
+ 
++    # make sure errorCode is set
++    if { ! [ info exists ::errorCode ] } { set ::errorCode "NONE" }
++
+     # run and log the actual command
+     if { $do_logout } {
+ 	fsl:echo $logout "\n$thecommand"
diff --git a/003-fix_missing_LIB_PROB.patch b/003-fix_missing_LIB_PROB.patch
new file mode 100644
index 000000000000..abd3dbb4b631
--- /dev/null
+++ b/003-fix_missing_LIB_PROB.patch
@@ -0,0 +1,35 @@
+--- a/fsl/src/eddy/Makefile	2019-09-29 21:41:53.118138982 +0200
++++ b/fsl/src/eddy/Makefile	2019-09-29 21:25:19.118338652 +0200
+@@ -62,7 +62,7 @@
+         endif
+ 	EXENAME=eddy${TMPNAME_1}${TMPNAME_2}
+ endif
+-USRLDFLAGS=-L${LIB_NEWMAT} -Wl,-rpath,/opt/fmrib/fsl/lib -rdynamic
++USRLDFLAGS=-L${LIB_NEWMAT} -L${LIB_PROB} -Wl,-rpath,/opt/fmrib/fsl/lib -rdynamic 
+ USRINCFLAGS=-I. -I${INC_NEWMAT} -I${INC_PROB} -I${INC_BOOST} -I${INC_CUDA} -I$(CBF_DIR) -I$(INC_BASISFIELD)
+ 
+ OBJS=eddy.o BiasFieldEstimatorImpl.o MoveBySuscCF.o PostEddyAlignShellsFunctions.o EddyCommandLineOptions.o ECModels.o KMatrix.o HyParEstimator.o ECScanClasses.o EddyUtils.o EddyHelperClasses.o DiffusionGP.o b0Predictor.o
+
+--- a/fsl/src/asl_mfree/Makefile	2019-09-29 22:52:54.221367251 +0200
++++ b/fsl/src/asl_mfree/Makefile	2019-09-29 22:53:23.577360889 +0200
+@@ -3,7 +3,7 @@
+ PROJNAME = asl_mfree
+ 
+ USRINCFLAGS = -I${INC_NEWMAT} -I${INC_ZLIB}
+-USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_ZLIB}
++USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_ZLIB} -L${LIB_PROB}
+ 
+ FSLVERSION= $(shell cat ${FSLDIR}/etc/fslversion | head -c 1)
+ ifeq ($(FSLVERSION), 5) 
+
+--- a/fsl/src/oxford_asl/Makefile	2019-09-29 22:52:27.621373018 +0200
++++ b/fsl/src/oxford_asl/Makefile	2019-09-29 22:53:41.237357074 +0200
+@@ -3,7 +3,7 @@
+ PROJNAME = oxford_asl
+ 
+ USRINCFLAGS = -I${INC_NEWMAT} -I${INC_ZLIB}
+-USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_ZLIB}
++USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_ZLIB} -L${LIB_PROB}
+ 
+ FSLVERSION= $(shell cat ${FSLDIR}/etc/fslversion | head -c 1)
+ ifeq ($(FSLVERSION), 5) 
diff --git a/PKGBUILD b/PKGBUILD
index 8de8a5634ed7..a9985e364426 100755
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,41 +1,35 @@
 # Maintainer: Tobias Bachmann <tobachmann@gmx.de>
 # Contributor: fishburn <frankthefishburn@gmail.com>
 
+# Set number of parallel compile jobs, default equals number of CPUs
+NJOBS=$(nproc)
+NJOBS=8
+
 pkgname=fsl
-pkgver=6.0.4
-pkgrel=2
+pkgver=6.0.5
+pkgrel=1
 pkgdesc="A comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data"
 arch=("x86_64")
 url="http://www.fmrib.ox.ac.uk/fsl/"
 license=(custom)
-depends=(gd libxml2 libxml++2.6 gsl libpng nlopt newmat tcl tk zlib python glu boost-libs vtk sqlite python3 fslpy bc openblas)
+depends=(gd libxml2 libxml++2.6 gsl libpng nlopt newmat tcl tk zlib python glu boost-libs vtk sqlite python3 'fslpy>=3.7.0' bc openblas)
 makedepends=(boost fftw gcc9)
 optdepends=(cuda)
 source=("https://www.fmrib.ox.ac.uk/fsldownloads/fsl-${pkgver}-sources.tar.gz"
         "https://www.fmrib.ox.ac.uk/fsldownloads/fsl-${pkgver}-feeds.tar.gz"
 	"buildSettings.mk"
-        "imcp"
-	"imglob"
-	"immv"
+	"fsl_sub"
 	"001-use_distribution_environment.patch"
-	"002-fix_meldata_usage_of_ifstream.patch"
-	"003-fix_fsl_exec_empty_errorCode.patch"
-	"004-fix_missing_LIB_PROB.patch"
-	"005-fix_cuda_thrust_include.patch"
-	"006-compile_ptx2_without_std-c++11.patch")
+	"002-fix_fsl_exec_empty_errorCode.patch"
+	"003-fix_missing_LIB_PROB.patch")
 
-sha256sums=('58b88f38e080b05d70724d57342f58e1baf56e2bd3b98506a72b4446cad5033e'
-	    '411daed14287d6ba536cb531450941ab1f570309cd561de4e2a4b0ec43a7e9f7'
-	    'c7f93adcf037a73182ae42ae6a59d3eb04a492888b6c2a6b528f9cd16539b2b2'
-            '8aac3a2ea61bb4c38eb363262ab7f89e55c49a5feb9912fd2ff71f2439f11fc9'
-	    'b3280bafc86d04dfa8835ef21f50469f2645bf09c36edcdd3f04349ce2c74225'
-	    '8e343b0ff93477280fd9a980822ddc9980afa7201dea51c886376c189c234c99'
+sha256sums=('df12b0b1161a26470ddf04e4c5d5d81580a04493890226207667ed8fd2b4b83f'
+	    'e68e1efeb45750f876f350442f56c4830d211e9fb16daa5ad134bb8e1ef1ae18'
+	    '880c46d4ef8a8ee1401e1fdb71dadd0f79aad2154967a03232844845227394a3'
+	    '2516982d151ab9e450a9ac6d5a6fc87099a7acc067514d80422c69950e618170'
 	    '906ac7de8068e5a5487b083844b50b6afd7562866088a4175fd88030182affdd'
-	    '13d4cf35343e7a73bc2534c94b1b0d4db41c338d374e6982091e4cf7a421d420'
 	    '64b4ccefa63a3cf920b185dd52e94b918c24f2cedaebcec8efb767bd80a6418a'
-	    'adea0372f42026e72e385f1bec19ecc8cffa46de1f617271f14c9345c6b83c04'
-    	    '9471addfc2f880350eedadcb99cb8b350abf42be1c0652ccddf49e34e5e48734'
-            'ab68cb802243ce715eff0d1136cfa29fa34a3e09934e5e20e02a092d69028df1')
+	    'adea0372f42026e72e385f1bec19ecc8cffa46de1f617271f14c9345c6b83c04')
 
 prepare() {
 	cd "${srcdir}"
@@ -48,15 +42,10 @@ prepare() {
 
 	# Apply patches
 	patch -Np1 -i "${srcdir}"/001-use_distribution_environment.patch
-	patch -Np1 -i "${srcdir}"/002-fix_meldata_usage_of_ifstream.patch
 	# From https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=fsl;e8fa48c1.1501
 	patch -Np1 -i "${srcdir}"/003-fix_fsl_exec_empty_errorCode.patch
 	# I'm not sure why -L${LIB_PROB} is missing in some Makefiles 
 	patch -Np1 -i "${srcdir}"/004-fix_missing_LIB_PROB.patch
-	# Adapted from Caspar van Leeuwen's patch: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;2b74023.2006
-	patch -Np1 -i "${srcdir}"/005-fix_cuda_thrust_include.patch
-	# ptx2 does not compile when assuming C++11 standard
-	patch -Np1 -i "${srcdir}"/006-compile_ptx2_without_std-c++11.patch
 
 	# Insert makepkg build flags into configuration
 	sed -i '0,/${AccumulatedIncFlags}/{s^${AccumulatedIncFlags}^& '"${CFLAGS}"'^}' "${srcdir}/fsl/config/common/vars.mk"
@@ -69,16 +58,22 @@ prepare() {
 build() {
 	export FSLDIR="${srcdir}/fsl"
 	cd "${FSLDIR}"
-	./build
-
-	# Install missing binaries, which are no longer shipped (depends on fslpy)	
-	/usr/bin/install -m 755 "${srcdir}"/{imcp,imglob,immv} "${srcdir}/fsl/bin"
+	MAKEOPTIONS="-j $NJOBS" ./build extras CiftiLib-master utils znzlib NewNifti fslio giftiio miscmaths newimage libvis first_lib meshclass fslvtkio misc_tcl basisfield warpfns bint shapeModel MVdisc
+        MAKEOPTIONS="" ./build fslsurface # fslsurface does not like parallel compiling
+        MAKEOPTIONS="-j $NJOBS" ./build libmeshutils newmesh DiscreteOpt FastPDlib MSMRegLib misc_c topup asl_mfree avwutils basil baycest bet2 bianca cluster fsl_deface eddy fabber_core fabber_models_asl fabber_models_cest fabber_models_dce fabber_models_dsc fabber_models_dualecho fabber_models_dwi fabber_models_pet fabber_models_qbold fabber_models_t1 fast4 fdt feat5 film filmbabe first flameo flirt fnirt fslvbm fugue gps lesions mcflirt melodic misc_scripts miscvis mist mm MSM oxford_asl possum ptx2 qboot randomise siena slicetimer susan swe tbss verbena xtract
+	# Install missing binaries, which are now Python scripts and shipped with fslpy
+	/usr/bin/install -m 755 /usr/bin/{imcp,imglob,immv} "${srcdir}"/fsl/bin
+	# Install missing fsl_sub script from 6.0.4
+	/usr/bin/install -m 755 "${srcdir}"/fsl_sub "${srcdir}"/fsl/bin
+	# Create fake fslpython environment (all dependencies have been taken care of system-wide)
+	ln -s /usr/bin/python "${srcdir}"/fsl/bin/fslpython
 }
 
 check() {
 	export FSLDIR="${srcdir}/fsl"
 	export FEEDSDIR="${srcdir}/feeds"
 	. "${FSLDIR}/etc/fslconf/fsl.sh"
+	export PATH="${FSLDIR}/bin":${PATH}
 	cd "${FEEDSDIR}"
 	time ./RUN all
 }
diff --git a/buildSettings.mk b/buildSettings.mk
index 52b59563fbb3..d15aada3c4d3 100644
--- a/buildSettings.mk
+++ b/buildSettings.mk
@@ -44,9 +44,9 @@ INC_GSL = /usr/include/gsl
 # PNG library
 LIB_PNG = /usr/lib
 INC_PNG = /usr/include/libpng16
-# PROB library
+# PROB library; added -I${FSLEXTINC} for 6.0.5
 LIB_PROB = ${FSLEXTLIB}
-INC_PROB = ${FSLEXTINC}/cprob
+INC_PROB = ${FSLEXTINC}/cprob -I${FSLEXTINC}
 # CPROB library
 LIB_CPROB = ${FSLEXTLIB}
 INC_CPROB = ${FSLEXTINC}/
@@ -73,51 +73,6 @@ INC_XML++CONF = /usr/lib/libxml++-2.6/include
 INC_NEWMAT = ${FSLEXTINC}/armawrap/armawrap -DARMA_USE_LAPACK -DARMA_USE_BLAS -DARMA_64BIT_WORD
 #####################################################################
 #
-#       Darwin specific sys vars and ext libs
-#
-#####################################################################
-ifeq ($(SYSTYPE), Darwin)
-###############   System Vars   #####################################
-CC = cc-9
-CXX = c++-9
-CXX11 = clang++-9
-CSTATICFLAGS =
-CXXSTATICFLAGS =
-CFLAGS = -std=c99
-ARCHFLAGS = -arch x86_64
-ARCHLDFLAGS = -Wl,-search_paths_first -arch x86_64
-PER_ARCH_CFLAGS_x86_64 = -msse3
-OPTFLAGS =  -O3
-GNU_ANSI_FLAGS = -Wall -pedantic -ansi -Wno-long-long
-ANSI_CFLAGS = ${GNU_ANSI_FLAGS}
-ANSI_CXXFLAGS = ${GNU_ANSI_FLAGS} -ansi
-RANLIB = ranlib
-###############   External Libs   #####################################
-# Armadillo library
-LIB_NEWMAT = ${FSLEXTLIB} -llapack -lblas
-# ZLIB library
-LIB_ZLIB = /usr/lib
-INC_ZLIB = /usr/include
-# QT library
-QTDIR = /usr
-LIB_QT = ${QTDIR}/lib
-INC_QT = ${QTDIR}/include/qt
-# VTK library
-VTKDIR_INC = /Users/cowboy/VTK7/include/vtk-7.0
-VTKDIR_LIB = /Users/cowboy/VTK7/lib
-VTKSUFFIX = -7.0
-# CUDA library
-CUDAVER := $(or $(CUDAVER),7.5)
-CUDA_INSTALLATION = /Developer/NVIDIA/CUDA-${CUDAVER}
-GENCODE_FLAGS = $(shell ${FSLDIR}/config/common/supportedGencodes.sh ${CUDA_INSTALLATION})
-LIB_CUDA = ${CUDA_INSTALLATION}/lib
-INC_CUDA = ${CUDA_INSTALLATION}/include
-NVCC = ${CUDA_INSTALLATION}/bin/nvcc
-#Project specific variables
-EDDYBUILDPARAMETERS="cuda=1 CUDAVER=7.5" "cpu=1"
-endif # if Darwin
-#####################################################################
-#
 #       Linux specific sys vars and ext libs
 #				Makefile auto-detects gcc version for Linux
 #
@@ -173,8 +128,8 @@ LIB_NEWMAT = /usr/lib -llapack -lopenblas
 
 #Project specific variables
 EDDYBUILDPARAMETERS = "cuda=1 CUDAVER=8.0" "cuda=1 CUDAVER=9.1" "cpu=1"
-fdt_MASTERBUILD     = COMPILE_GPU = 1
-ptx2_MASTERBUILD    = COMPILE_GPU = 1
+fdt_MASTERBUILD     = COMPILE_GPU = 0
+ptx2_MASTERBUILD    = COMPILE_GPU = 0
 define newline
 
 
diff --git a/fsl_sub b/fsl_sub
new file mode 100644
index 000000000000..cf74a2795289
--- /dev/null
+++ b/fsl_sub
@@ -0,0 +1,544 @@
+#!/bin/bash
+
+# Copyright (C) 2007-2017 University of Oxford
+# Authors: Dave Flitney, Stephen Smith, Matthew Webster and Duncan Mortimer
+
+#   Part of FSL - FMRIB's Software Library
+#   http://www.fmrib.ox.ac.uk/fsl
+#   fsl@fmrib.ox.ac.uk
+#
+#   Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+#   Imaging of the Brain), Department of Clinical Neurology, Oxford
+#   University, Oxford, UK
+#
+#
+#   LICENCE
+#
+#   FMRIB Software Library, Release 6.0 (c) 2018, The University of
+#   Oxford (the "Software")
+#
+#   The Software remains the property of the Oxford University Innovation
+#   ("the University").
+#
+#   The Software is distributed "AS IS" under this Licence solely for
+#   non-commercial use in the hope that it will be useful, but in order
+#   that the University as a charitable foundation protects its assets for
+#   the benefit of its educational and research purposes, the University
+#   makes clear that no condition is made or to be implied, nor is any
+#   warranty given or to be implied, as to the accuracy of the Software,
+#   or that it will be suitable for any particular purpose or for use
+#   under any specific conditions. Furthermore, the University disclaims
+#   all responsibility for the use which is made of the Software. It
+#   further disclaims any liability for the outcomes arising from using
+#   the Software.
+#
+#   The Licensee agrees to indemnify the University and hold the
+#   University harmless from and against any and all claims, damages and
+#   liabilities asserted by third parties (including claims for
+#   negligence) which arise directly or indirectly from the use of the
+#   Software or the sale of any products based on the Software.
+#
+#   No part of the Software may be reproduced, modified, transmitted or
+#   transferred in any form or by any means, electronic or mechanical,
+#   without the express permission of the University. The permission of
+#   the University is not required if the said reproduction, modification,
+#   transmission or transference is done without financial return, the
+#   conditions of this Licence are imposed upon the receiver of the
+#   product, and all original and amended source code is included in any
+#   transmitted product. You may be held legally responsible for any
+#   copyright infringement that is caused or encouraged by your failure to
+#   abide by these terms and conditions.
+#
+#   You are not permitted under this Licence to use this Software
+#   commercially. Use for which any financial return is received shall be
+#   defined as commercial use, and includes (1) integration of all or part
+#   of the source code or the Software into a product for sale or license
+#   by or on behalf of Licensee to third parties or (2) use of the
+#   Software or any derivative of it for research with the final aim of
+#   developing software products for sale or license to a third party or
+#   (3) use of the Software or any derivative of it for research with the
+#   final aim of developing non-software products for sale or license to a
+#   third party, or (4) use of the Software to provide any service to an
+#   external organisation for which payment is received. If you are
+#   interested in using the Software commercially, please contact Oxford
+#   University Innovation ("OUI"), the technology transfer company of the
+#   University, to negotiate a licence. Contact details are:
+#   fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.
+export LC_ALL=C
+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.
+###########################################################################