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348 lines
17 KiB
348 lines
17 KiB
diff -Naur fsl.orig/src/fslio/Makefile fsl/src/fslio/Makefile |
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--- fsl.orig/src/fslio/Makefile 2021-02-01 15:29:34.842752994 -0500 |
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+++ fsl/src/fslio/Makefile 2021-02-01 15:32:19.723761859 -0500 |
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@@ -6,7 +6,7 @@ |
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OBJS=fslio.o |
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-SCRIPTS = remove_ext fsloutputtype imtest imglob imcp imln imrm immv |
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+SCRIPTS = fsloutputtype imglob imcp immv |
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all: |
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diff -Naur fsl.orig/src/fslio/remove_ext fsl/src/fslio/remove_ext |
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--- fsl.orig/src/fslio/remove_ext 2021-02-01 15:29:34.842752994 -0500 |
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+++ fsl/src/fslio/remove_ext 1969-12-31 19:00:00.000000000 -0500 |
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@@ -1,87 +0,0 @@ |
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-#!/bin/sh |
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- |
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-# remove_ext - remove extension from image filename |
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-# |
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-# Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group |
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-# |
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-# Copyright (C) 1999-2004 University of Oxford |
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-# |
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-# Part of FSL - FMRIB's Software Library |
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-# http://www.fmrib.ox.ac.uk/fsl |
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-# fsl@fmrib.ox.ac.uk |
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-# |
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-# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance |
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-# Imaging of the Brain), Department of Clinical Neurology, Oxford |
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-# University, Oxford, UK |
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-# |
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-# |
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-# LICENCE |
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-# |
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-# FMRIB Software Library, Release 6.0 (c) 2018, The University of |
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-# Oxford (the "Software") |
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-# |
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-# The Software remains the property of the Oxford University Innovation |
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-# ("the University"). |
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-# |
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-# The Software is distributed "AS IS" under this Licence solely for |
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-# non-commercial use in the hope that it will be useful, but in order |
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-# that the University as a charitable foundation protects its assets for |
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-# the benefit of its educational and research purposes, the University |
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-# makes clear that no condition is made or to be implied, nor is any |
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-# warranty given or to be implied, as to the accuracy of the Software, |
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-# or that it will be suitable for any particular purpose or for use |
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-# under any specific conditions. Furthermore, the University disclaims |
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-# all responsibility for the use which is made of the Software. It |
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-# further disclaims any liability for the outcomes arising from using |
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-# the Software. |
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-# |
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-# The Licensee agrees to indemnify the University and hold the |
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-# University harmless from and against any and all claims, damages and |
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-# liabilities asserted by third parties (including claims for |
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-# negligence) which arise directly or indirectly from the use of the |
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-# Software or the sale of any products based on the Software. |
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-# |
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-# No part of the Software may be reproduced, modified, transmitted or |
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-# transferred in any form or by any means, electronic or mechanical, |
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-# without the express permission of the University. The permission of |
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-# the University is not required if the said reproduction, modification, |
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-# transmission or transference is done without financial return, the |
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-# conditions of this Licence are imposed upon the receiver of the |
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-# product, and all original and amended source code is included in any |
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-# transmitted product. You may be held legally responsible for any |
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-# copyright infringement that is caused or encouraged by your failure to |
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-# abide by these terms and conditions. |
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-# |
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-# You are not permitted under this Licence to use this Software |
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-# commercially. Use for which any financial return is received shall be |
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-# defined as commercial use, and includes (1) integration of all or part |
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-# of the source code or the Software into a product for sale or license |
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-# by or on behalf of Licensee to third parties or (2) use of the |
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-# Software or any derivative of it for research with the final aim of |
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-# developing software products for sale or license to a third party or |
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-# (3) use of the Software or any derivative of it for research with the |
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-# final aim of developing non-software products for sale or license to a |
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-# third party, or (4) use of the Software to provide any service to an |
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-# external organisation for which payment is received. If you are |
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-# interested in using the Software commercially, please contact Oxford |
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-# University Innovation ("OUI"), the technology transfer company of the |
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-# University, to negotiate a licence. Contact details are: |
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-# fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL. |
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-export LC_ALL=C |
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- |
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- |
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-if [ $# -lt 1 ] ; then |
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- exit 1 |
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-fi |
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- |
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-lst=""; |
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-for fn in $@ ; do |
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- # for the ones at the end of the line |
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- f=`echo "$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/\.$//'`; |
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- # for the ones in the middle of the line |
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- f=`echo "$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'`; |
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- lst="$lst $f"; |
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-done |
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-echo $lst; |
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- |
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- |
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diff -Naur fsl.orig/src/misc_scripts/fsl_abspath fsl/src/misc_scripts/fsl_abspath |
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--- fsl.orig/src/misc_scripts/fsl_abspath 2021-02-01 15:29:34.828752994 -0500 |
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+++ fsl/src/misc_scripts/fsl_abspath 1969-12-31 19:00:00.000000000 -0500 |
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@@ -1,71 +0,0 @@ |
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-#!/usr/bin/env fslpython |
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-# fsl_abspath - return true file path |
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-# Matthew Webster FMRIB Image Analysis Group |
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-# Copyright (C) 2009 University of Oxford |
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-# Part of FSL - FMRIB's Software Library |
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-# http://www.fmrib.ox.ac.uk/fsl |
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-# fsl@fmrib.ox.ac.uk |
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-# |
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-# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance |
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-# Imaging of the Brain), Department of Clinical Neurology, Oxford |
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-# University, Oxford, UK |
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-# |
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-# |
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-# LICENCE |
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-# |
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-# FMRIB Software Library, Release 6.0 (c) 2018, The University of |
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-# Oxford (the "Software") |
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-# |
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-# The Software remains the property of the Oxford University Innovation |
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-# ("the University"). |
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-# |
|
-# 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 |
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-# external organisation for which payment is received. If you are |
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-# interested in using the Software commercially, please contact Oxford |
|
-# University Innovation ("OUI"), the technology transfer company of the |
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-# University, to negotiate a licence. Contact details are: |
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-# fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL. |
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-from __future__ import print_function |
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-import sys |
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-import os |
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- |
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-print (os.path.realpath(sys.argv[1])) |
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-sys.exit(0) |
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diff -Naur fsl.orig/src/misc_scripts/Makefile fsl/src/misc_scripts/Makefile |
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--- fsl.orig/src/misc_scripts/Makefile 2021-02-01 15:29:34.828752994 -0500 |
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+++ fsl/src/misc_scripts/Makefile 2021-02-01 15:32:56.027763811 -0500 |
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@@ -2,6 +2,6 @@ |
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PROJNAME = misc_scripts |
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-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 |
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+SCRIPTS = fslecho regscript remove_vols replace_and_average_fmrib linkbedpost ocmr_preproc correct_and_average eddy_correct AnatomicalAverage fsl_anat fslFixText |
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all: |
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diff -Naur fsl.orig/src/misc_scripts/Text2Vest fsl/src/misc_scripts/Text2Vest |
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--- fsl.orig/src/misc_scripts/Text2Vest 2021-02-01 15:29:34.828752994 -0500 |
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+++ fsl/src/misc_scripts/Text2Vest 1969-12-31 19:00:00.000000000 -0500 |
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@@ -1,80 +0,0 @@ |
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-#!/bin/sh |
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-# Copyright (C) 2012 University of Oxford |
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-# |
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-# Part of FSL - FMRIB's Software Library |
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-# http://www.fmrib.ox.ac.uk/fsl |
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-# fsl@fmrib.ox.ac.uk |
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-# |
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-# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance |
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-# Imaging of the Brain), Department of Clinical Neurology, Oxford |
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-# University, Oxford, UK |
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-# |
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-# |
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-# LICENCE |
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-# |
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-# 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. |
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-export LC_ALL=C |
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-if [ $# -lt 2 ] ; then |
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- echo "`basename $0` <text file> <vest file>" |
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- exit 0 |
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-fi |
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- |
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-NumPoints=`grep -cve '^\s*$' $1` |
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-NumWaves=`wc $1 | awk '{ print $2 }'` |
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-NumWaves=`expr $NumWaves / $NumPoints` |
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- |
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-echo /NumWaves $NumWaves > $2 |
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-echo /NumPoints $NumPoints >> $2 |
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-echo /Matrix >> $2 |
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- |
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-cat $1 >> $2 |
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- |
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diff -Naur fsl.orig/src/misc_scripts/Vest2Text fsl/src/misc_scripts/Vest2Text |
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--- fsl.orig/src/misc_scripts/Vest2Text 2021-02-01 15:29:34.828752994 -0500 |
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+++ fsl/src/misc_scripts/Vest2Text 1969-12-31 19:00:00.000000000 -0500 |
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@@ -1,71 +0,0 @@ |
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-#!/bin/sh |
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-# Copyright (C) 2012 University of Oxford |
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-# |
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-# Part of FSL - FMRIB's Software Library |
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-# http://www.fmrib.ox.ac.uk/fsl |
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-# fsl@fmrib.ox.ac.uk |
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-# |
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-# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance |
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-# Imaging of the Brain), Department of Clinical Neurology, Oxford |
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-# 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 |
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-if [ $# -lt 2 ] ; then |
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- echo "`basename $0` <vest file> <text file>" |
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- exit 0 |
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-fi |
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-sed -e "/\//d" $1 | sed '/^$/d' > $2 |
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-
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