diff options
Diffstat (limited to 'sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p2.patch')
| -rw-r--r-- | sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p2.patch | 348 |
1 files changed, 348 insertions, 0 deletions
diff --git a/sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p2.patch b/sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p2.patch new file mode 100644 index 000000000..ddb7cfb67 --- /dev/null +++ b/sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p2.patch @@ -0,0 +1,348 @@ +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 +- |