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diff -Naur fsl.orig/src/fslio/Makefile fsl/src/fslio/Makefile
--- fsl.orig/src/fslio/Makefile 2021-02-01 15:29:34.842752994 -0500
+++ fsl/src/fslio/Makefile 2021-02-01 15:32:19.723761859 -0500
@@ -6,7 +6,7 @@
OBJS=fslio.o
-SCRIPTS = remove_ext fsloutputtype imtest imglob imcp imln imrm immv
+SCRIPTS = fsloutputtype imglob imcp immv
all:
diff -Naur fsl.orig/src/fslio/remove_ext fsl/src/fslio/remove_ext
--- fsl.orig/src/fslio/remove_ext 2021-02-01 15:29:34.842752994 -0500
+++ fsl/src/fslio/remove_ext 1969-12-31 19:00:00.000000000 -0500
@@ -1,87 +0,0 @@
-#!/bin/sh
-
-# remove_ext - remove extension from image filename
-#
-# Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group
-#
-# Copyright (C) 1999-2004 University of Oxford
-#
-# 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
-
-
-if [ $# -lt 1 ] ; then
- exit 1
-fi
-
-lst="";
-for fn in $@ ; do
- # for the ones at the end of the line
- f=`echo "$fn" | sed 's/\.hdr\.gz$//' | sed 's/\.img\.gz$//' | sed 's/\.hdr$//' | sed 's/\.img$//' | sed 's/\.nii.gz$//' | sed 's/\.nii$//' | sed 's/\.mnc.gz$//' | sed 's/\.mnc$//' | sed 's/\.$//'`;
- # for the ones in the middle of the line
- f=`echo "$f" | sed 's/\.hdr\.gz[ ]/ /g' | sed 's/\.img\.gz[ ]/ /g' | sed 's/\.hdr[ ]/ /g' | sed 's/\.img[ ]/ /g' | sed 's/\.nii\.gz[ ]/ /g' | sed 's/\.nii[ ]/ /g' | sed 's/\.mnc\.gz[ ]/ /g' | sed 's/\.mnc[ ]/ /g' |sed 's/\.[ ]/ /g'`;
- lst="$lst $f";
-done
-echo $lst;
-
-
diff -Naur fsl.orig/src/misc_scripts/fsl_abspath fsl/src/misc_scripts/fsl_abspath
--- fsl.orig/src/misc_scripts/fsl_abspath 2021-02-01 15:29:34.828752994 -0500
+++ fsl/src/misc_scripts/fsl_abspath 1969-12-31 19:00:00.000000000 -0500
@@ -1,71 +0,0 @@
-#!/usr/bin/env fslpython
-# fsl_abspath - return true file path
-# Matthew Webster FMRIB Image Analysis Group
-# Copyright (C) 2009 University of Oxford
-# 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.
-from __future__ import print_function
-import sys
-import os
-
-print (os.path.realpath(sys.argv[1]))
-sys.exit(0)
diff -Naur fsl.orig/src/misc_scripts/Makefile fsl/src/misc_scripts/Makefile
--- fsl.orig/src/misc_scripts/Makefile 2021-02-01 15:29:34.828752994 -0500
+++ fsl/src/misc_scripts/Makefile 2021-02-01 15:32:56.027763811 -0500
@@ -2,6 +2,6 @@
PROJNAME = misc_scripts
-SCRIPTS = fslecho regscript remove_vols replace_and_average_fmrib linkbedpost ocmr_preproc correct_and_average eddy_correct Text2Vest Vest2Text AnatomicalAverage fsl_abspath fsl_anat fslFixText
+SCRIPTS = fslecho regscript remove_vols replace_and_average_fmrib linkbedpost ocmr_preproc correct_and_average eddy_correct AnatomicalAverage fsl_anat fslFixText
all:
diff -Naur fsl.orig/src/misc_scripts/Text2Vest fsl/src/misc_scripts/Text2Vest
--- fsl.orig/src/misc_scripts/Text2Vest 2021-02-01 15:29:34.828752994 -0500
+++ fsl/src/misc_scripts/Text2Vest 1969-12-31 19:00:00.000000000 -0500
@@ -1,80 +0,0 @@
-#!/bin/sh
-# Copyright (C) 2012 University of Oxford
-#
-# 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
-if [ $# -lt 2 ] ; then
- echo "`basename $0` <text file> <vest file>"
- exit 0
-fi
-
-NumPoints=`grep -cve '^\s*$' $1`
-NumWaves=`wc $1 | awk '{ print $2 }'`
-NumWaves=`expr $NumWaves / $NumPoints`
-
-echo /NumWaves $NumWaves > $2
-echo /NumPoints $NumPoints >> $2
-echo /Matrix >> $2
-
-cat $1 >> $2
-
diff -Naur fsl.orig/src/misc_scripts/Vest2Text fsl/src/misc_scripts/Vest2Text
--- fsl.orig/src/misc_scripts/Vest2Text 2021-02-01 15:29:34.828752994 -0500
+++ fsl/src/misc_scripts/Vest2Text 1969-12-31 19:00:00.000000000 -0500
@@ -1,71 +0,0 @@
-#!/bin/sh
-# Copyright (C) 2012 University of Oxford
-#
-# 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
-if [ $# -lt 2 ] ; then
- echo "`basename $0` <vest file> <text file>"
- exit 0
-fi
-sed -e "/\//d" $1 | sed '/^$/d' > $2
-