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Commit e9dbbcca authored by Michael Hanke's avatar Michael Hanke
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Imported upstream version 4.0~pre1

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LICENCE 0 → 100644
View file @ e9dbbcca
FMRIB Software Library, Release 3.3 (c) 2006, The University of
Oxford (the "Software")
The Software remains the property of the University of Oxford ("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 Isis
Innovation Limited ("Isis"), the technology transfer company of the
University, to negotiate a licence. Contact details are:
innovation@isis.ox.ac.uk quoting reference DE/1112.
README 0 → 100644
View file @ e9dbbcca
For instructions on installing and compiling FSL see doc/index.html
build 0 → 100755
View file @ e9dbbcca
#!/bin/sh
if [ $# -ge 1 ] ; then
PROJECTS="$@";
else
PROJECTS="freeware utils znzlib niftiio fslio miscmaths \
newimage libhfunc libss libvis meshclass misc_tcl bint \
afni avwutils bet bet2 cluster fast fdt feat5 film filmbabe flame flirt \
fslpres fugue mcflirt melodic2 misc_c miscvis mm \
randomise siena slicetimer susan tbss \
dropouts ifit load_varian taldaemon misc_scripts fast4 shapeModel first possum";
fi
echo "Building projects - see build.log file for progress..."
./config/common/buildproj $PROJECTS > ./build.log 2>&1
echo "Finished build : end of log file shows ..."
tail -10 build.log
config/Makefile 0 → 100644
View file @ e9dbbcca
FSLCONFDIR=.
include default.mk
PROJNAME = config
install:
@${MAKE} "DESTDIR=${FSLDEVDIR}" install-general
install-fmrib:
@${MAKE} "DESTDIR=${FSLDIR}" install-general
install-general:
${CP} -R -f . ${DESTDIR}/config
${RM} -rf ${DESTDIR}/config/CVS ${DESTDIR}/config/*/CVS
config/apple-darwin7-gcc3.1/externallibs.mk 0 → 100644
View file @ e9dbbcca
# $Id: externallibs.mk,v 1.3 2007/06/29 14:22:27 duncan Exp $
# External Library and Include Paths
FSLEXTLIB=${FSLDIR}/extras/lib
FSLEXTINC=${FSLDIR}/extras/include
# CEPHES library
LIB_CEPHES = ${FSLEXTLIB}
INC_CEPHES = ${FSLEXTINC}/cephes
# GD library
LIB_GD = ${FSLEXTLIB}
INC_GD = ${FSLEXTINC}
# GDC library
LIB_GDC = ${FSLEXTLIB}
INC_GDC = ${FSLEXTINC}/libgdc
# GSL library
LIB_GSL = ${FSLEXTLIB}
INC_GSL = ${FSLEXTINC}/gsl
# PNG library
LIB_PNG = ${FSLEXTLIB}
INC_PNG = ${FSLEXTINC}
# PROB library
LIB_PROB = ${FSLEXTLIB}
INC_PROB = ${FSLEXTINC}/libprob
# CPROB library
LIB_CPROB = ${FSLEXTLIB}
INC_CPROB = ${FSLEXTINC}/libcprob
# NEWMAT library
LIB_NEWMAT = ${FSLEXTLIB}
INC_NEWMAT = ${FSLEXTINC}/newmat
# NEWRAN library
LIB_NEWRAN = ${FSLEXTLIB}
INC_NEWRAN = ${FSLEXTINC}/newran
# ZLIB library
LIB_ZLIB = ${FSLEXTLIB}
INC_ZLIB = ${FSLEXTINC}
# QT library
QTDIR = /sw
LIB_QT = ${QTDIR}/lib
INC_QT = ${QTDIR}/include
# BOOST library
BOOSTDIR = ${FSLEXTINC}/boost
LIB_BOOST = ${BOOSTDIR}
INC_BOOST = ${BOOSTDIR}
# QWT library
QWTDIR = /usr/local/qwt
INC_QWT = ${QWTDIR}/include
LIB_QWT = ${QWTDIR}/lib
# FFTW3 library
LIB_FFTW3 = ${FSLEXTLIB}
INC_FFTW3 = ${FSLEXTINC}/fftw3
config/apple-darwin7-gcc3.1/systemvars.mk 0 → 100644
View file @ e9dbbcca
# for SHELL, do not change the type of shell - only use Bourne or BASH
SHELL = /bin/sh
# Compiler dependent variables
CC = cc
CXX = c++
CSTATICFLAGS =
CXXSTATICFLAGS =
ARCHFLAGS =
DEPENDFLAGS = -MM
OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS}
MACHDBGFLAGS = -g
GNU_ANSI_FLAGS = -traditional-cpp -Wall -Wno-long-long -Wno-long-double -ansi -pedantic
SGI_ANSI_FLAGS = -ansi -fullwarn
ANSI_FLAGS = ${GNU_ANSI_FLAGS}
# Variables determined with AUTOCONFIG:
INSTALL = install -p -c
RM = /bin/rm
CP = /bin/cp
CHMOD = /bin/chmod
MKDIR = /bin/mkdir
RANLIB = ranlib
TCLSH = ${FSLDIR}/bin/fsltclsh
config/apple-darwin7-gcc3.3/externallibs.mk 0 → 100644
View file @ e9dbbcca
# $Id: externallibs.mk,v 1.3 2007/06/29 14:22:27 duncan Exp $
# External Library and Include Paths
FSLEXTLIB=${FSLDIR}/extras/lib
FSLEXTINC=${FSLDIR}/extras/include
# CEPHES library
LIB_CEPHES = ${FSLEXTLIB}
INC_CEPHES = ${FSLEXTINC}/cephes
# GD library
LIB_GD = ${FSLEXTLIB}
INC_GD = ${FSLEXTINC}
# GDC library
LIB_GDC = ${FSLEXTLIB}
INC_GDC = ${FSLEXTINC}/libgdc
# GSL library
LIB_GSL = ${FSLEXTLIB}
INC_GSL = ${FSLEXTINC}/gsl
# PNG library
LIB_PNG = ${FSLEXTLIB}
INC_PNG = ${FSLEXTINC}
# PROB library
LIB_PROB = ${FSLEXTLIB}
INC_PROB = ${FSLEXTINC}/libprob
# CPROB library
LIB_CPROB = ${FSLEXTLIB}
INC_CPROB = ${FSLEXTINC}/libcprob
# NEWMAT library
LIB_NEWMAT = ${FSLEXTLIB}
INC_NEWMAT = ${FSLEXTINC}/newmat
# NEWRAN library
LIB_NEWRAN = ${FSLEXTLIB}
INC_NEWRAN = ${FSLEXTINC}/newran
# ZLIB library
LIB_ZLIB = ${FSLEXTLIB}
INC_ZLIB = ${FSLEXTINC}
# QT library
QTDIR = /sw
LIB_QT = ${QTDIR}/lib
INC_QT = ${QTDIR}/include
# BOOST library
BOOSTDIR = ${FSLEXTINC}/boost
LIB_BOOST = ${BOOSTDIR}
INC_BOOST = ${BOOSTDIR}
# QWT library
QWTDIR = /usr/local/qwt
INC_QWT = ${QWTDIR}/include
LIB_QWT = ${QWTDIR}/lib
# FFTW3 library
LIB_FFTW3 = ${FSLEXTLIB}
INC_FFTW3 = ${FSLEXTINC}/fftw3
config/apple-darwin7-gcc3.3/systemvars.mk 0 → 100644
View file @ e9dbbcca
# for SHELL, do not change the type of shell - only use Bourne or BASH
SHELL = /bin/sh
# Compiler dependent variables
CC = cc
CXX = c++
CSTATICFLAGS =
CXXSTATICFLAGS =
ARCHFLAGS =
DEPENDFLAGS = -MM
OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS}
MACHDBGFLAGS = -g
GNU_ANSI_FLAGS = -Wall -Wno-long-long -Wno-long-double -ansi -pedantic
SGI_ANSI_FLAGS = -ansi -fullwarn
ANSI_FLAGS = ${GNU_ANSI_FLAGS}
# Variables determined with AUTOCONFIG:
INSTALL = install -p -c
RM = /bin/rm
CP = /bin/cp
CHMOD = /bin/chmod
MKDIR = /bin/mkdir
RANLIB = ranlib
TCLSH = ${FSLDIR}/bin/fsltclsh
config/apple-darwin8-gcc4.0/configure.sh 0 → 100644
View file @ e9dbbcca
# Auto-configure options for Mac OS X Universal build
# Written by Duncan Mortimer
macosx_universal_opts="-isysroot /Developer/SDKs/MacOSX10.4u.sdk -arch ppc -arch ppc64 -arch i386 -arch x86_64"
cflags="${cflags} ${macosx_universal_opts}"
cxxflags="${cxxflags} ${macosx_universal_opts}"
ldflags="${ldflags} -Wl,-search_paths_first ${macosx_universal_opts}"
configure_opts="${configure_opts} --disable-dependency-tracking"
config/apple-darwin8-gcc4.0/externallibs.mk 0 → 100644
View file @ e9dbbcca
# $Id: externallibs.mk,v 1.3 2007/06/29 14:22:27 duncan Exp $
# External Library and Include Paths
FSLEXTLIB=${FSLDIR}/extras/lib
FSLEXTINC=${FSLDIR}/extras/include
# CEPHES library
LIB_CEPHES = ${FSLEXTLIB}
INC_CEPHES = ${FSLEXTINC}/cephes
# GD library
LIB_GD = ${FSLEXTLIB}
INC_GD = ${FSLEXTINC}
# GDC library
LIB_GDC = ${FSLEXTLIB}
INC_GDC = ${FSLEXTINC}/libgdc
# GSL library
LIB_GSL = ${FSLEXTLIB}
INC_GSL = ${FSLEXTINC}/gsl
# PNG library
LIB_PNG = ${FSLEXTLIB}
INC_PNG = ${FSLEXTINC}
# PROB library
LIB_PROB = ${FSLEXTLIB}
INC_PROB = ${FSLEXTINC}/libprob
# CPROB library
LIB_CPROB = ${FSLEXTLIB}
INC_CPROB = ${FSLEXTINC}/libcprob
# NEWMAT library
LIB_NEWMAT = ${FSLEXTLIB}
INC_NEWMAT = ${FSLEXTINC}/newmat
# NEWRAN library
LIB_NEWRAN = ${FSLEXTLIB}
INC_NEWRAN = ${FSLEXTINC}/newran
# ZLIB library
LIB_ZLIB = ${FSLEXTLIB}
INC_ZLIB = ${FSLEXTINC}
# QT library
QTDIR = /sw
LIB_QT = ${QTDIR}/lib
INC_QT = ${QTDIR}/include
# BOOST library
BOOSTDIR = ${FSLEXTINC}/boost
LIB_BOOST = ${BOOSTDIR}
INC_BOOST = ${BOOSTDIR}
# QWT library
QWTDIR = /usr/local/qwt
INC_QWT = ${QWTDIR}/include
LIB_QWT = ${QWTDIR}/lib
# FFTW3 library
LIB_FFTW3 = ${FSLEXTLIB}
INC_FFTW3 = ${FSLEXTINC}/fftw3
config/apple-darwin8-gcc4.0/systemvars.mk 0 → 100644
View file @ e9dbbcca
# for SHELL, do not change the type of shell - only use Bourne or BASH
SHELL = /bin/sh
# Compiler dependent variables
CC = cc
CXX = c++
CSTATICFLAGS =
CXXSTATICFLAGS =
ARCHFLAGS = -arch ppc -arch ppc64 -arch i386 -arch x86_64 -DPPC64 -isysroot /Developer/SDKs/MacOSX10.4u.sdk
ARCHLDFLAGS = -Wl,-search_paths_first -arch ppc -arch ppc64 -arch i386 -arch x86_64 -isysroot /Developer/SDKs/MacOSX10.4u.sdk
PER_ARCH_CFLAGS_i386 = -msse3
PER_ARCH_CFLAGS_ppc =
PER_ARCH_CFLAGS_ppc64 = -mcpu=G5
PER_ARCH_CFLAGS_x86_64= -msse3
DEPENDFLAGS = -MM
OPTFLAGS = -O3 -fexpensive-optimizations
MACHDBGFLAGS = -g
GNU_ANSI_FLAGS = -Wall -Wno-long-long -Wno-long-double -ansi -pedantic
SGI_ANSI_FLAGS = -ansi -fullwarn
ANSI_FLAGS = ${GNU_ANSI_FLAGS}
# Variables determined with AUTOCONFIG:
INSTALL = install -p -c
RM = /bin/rm
CP = /bin/cp
CHMOD = /bin/chmod
MKDIR = /bin/mkdir
RANLIB = ranlib
TCLSH = ${FSLDIR}/bin/fsltclsh
config/common/buildproj 0 → 100755
View file @ e9dbbcca
#!/bin/sh
if [ $# -lt 1 ] ; then
echo "Usage: $0 <list of projects>"
exit 2 ;
fi
strict=false; export strict;
if [ X$1 = X-strict ] ; then
strict=true; export strict;
fi
PROJECTS="$@" ; export PROJECTS ;
FSLDIR=`pwd`
FSLDEVDIR=${FSLDIR}
FSLCONFDIR=${FSLDIR}/config
FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh`
export FSLDIR FSLDEVDIR FSLCONFDIR FSLMACHTYPE
buildmessages="" ; export buildmessages ;
if [ $strict = false ] ; then
# If this machine doesn't exist in standard config, link to the generic form
if [ ! -d ${FSLCONFDIR}/${FSLMACHTYPE} ] ; then
( cd ${FSLCONFDIR} ; ln -s generic ${FSLMACHTYPE} ; buildmessages="WARNING: Did not find specific configuration for ${FSLMACHTYPE} - trying generic version instead"; echo "$buildmessages" ; )
fi
# Make freeware if it exists
if [ -d ${FSLDIR}/src/freeware ] ; then
( cd ${FSLDIR}/src/freeware ; make FSLDIR=${FSLDIR} FSLCONFDIR=${FSLCONFDIR} )
fi
# Make the extras if they are installed in the same fsl tree
if [ -d ${FSLDIR}/extras ] ; then
( cd ${FSLDIR}/extras ; ./build ) ;
MAKEOPTIONS="${MAKEOPTIONS} FSLEXTLIB=${FSLDIR}/extras/lib FSLEXTINC=${FSLDIR}/extras/include" ;
fi
fi
# Determine which make command to use
MAKE=none
if [ X"`make --version 2>&1 | grep -i gnu`"X != XX ] ; then
MAKE=make;
else if [ X"`gmake --version 2>&1 | grep -i gnu`"X != XX ] ; then
MAKE=gmake;
fi; fi
if [ ${MAKE} = none ] ; then
echo "Could not find the gnu make utility in path" ;
exit 1 ;
fi
errorprojs="" ; export errorprojs ;
errorinstall="" ; export errorinstall ;
for projname in $PROJECTS; do
if [ -d $FSLDIR/src/$projname ] ; then
echo " " ;
echo " " ;
echo "Making project src/$projname" ;
echo " " ;
cd $FSLDIR/src/$projname ;
${MAKE} distclean ;
if [ -x fslconfig ] ; then
./fslconfig ;
fi
if ${MAKE} -k ${MAKEOPTIONS} ; then
if ${MAKE} install ; then
installok=true;
else
installok=false;
errorinstall="$errorinstall $projname" ; export errorinstall ;
fi
echo " "
echo " ------------------------- "
echo "Successfully made $projname";
if [ $installok = false ] ; then
echo " "
echo "ERROR::Could not install $projname successfully" ;
fi
else
echo " "
echo " ========================= "
echo "ERROR::Could not make $projname successfully" ;
echo " "
echo " "
errorprojs="$errorprojs $projname" ; export errorprojs ;
fi
fi
done
cd $FSLDIR
echo " ";
echo " ";
echo " ";
if [ "X${errorprojs}X" != XX ] ; then
echo "!!ERROR in BUILD!!" ;
echo " Could not make the following projects successfully:" ;
echo " $errorprojs" ;
else
echo "BUILD successfully made all projects" ;
fi
echo " ";
if [ "X${errorinstall}X" != XX ] ; then
echo "!!ERROR in INSTALL!!" ;
echo " Could not fully install the following projects successfully:" ;
echo " $errorinstall" ;
else
echo " ";
fi
echo " ";
echo "${buildmessages}"
config/common/copyrights/ccopyright.c 0 → 100644
View file @ e9dbbcca
/* 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 3.3 (c) 2006, The University of
Oxford (the "Software")
The Software remains the property of the University of Oxford ("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 Isis
Innovation Limited ("Isis"), the technology transfer company of the
University, to negotiate a licence. Contact details are:
innovation@isis.ox.ac.uk quoting reference DE/1112. */
config/common/copyrights/shcopyright.sh 0 → 100644
View file @ e9dbbcca
# 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 3.3 (c) 2006, The University of
# Oxford (the "Software")
#
# The Software remains the property of the University of Oxford ("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.
#