path: root/sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p2.patch

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
-