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commit: 1c4f022505e83357adc3fbab929ea55396aee27d |
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Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> |
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AuthorDate: Sun Jul 18 10:47:25 2021 +0000 |
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Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> |
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CommitDate: Sun Jul 18 10:47:25 2021 +0000 |
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URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=1c4f0225 |
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|
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sci-biology/fsl: add version 6.0.4 |
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|
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Closes: https://github.com/gentoo/sci/pull/1074 |
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Co-authored-by: Paul Polak <paul.polak <AT> med-image.info> |
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Package-Manager: Portage-3.0.20, Repoman-3.0.3 |
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Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org> |
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|
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.../fsl/files/fsl-6.0.4-cuda_buildsettings.patch | 12 + |
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sci-biology/fsl/files/fsl-6.0.4-eddy_cuda.patch | 21 ++ |
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sci-biology/fsl/files/fsl-6.0.4-fdt_cuda.patch | 14 + |
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sci-biology/fsl/files/fsl-6.0.4-flameo_std.patch | 11 + |
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.../fsl/files/fsl-6.0.4-fsldir_redux-p1.patch | 240 ++++++++++++++ |
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.../fsl/files/fsl-6.0.4-fsldir_redux-p2.patch | 254 +++++++++++++++ |
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.../fsl/files/fsl-6.0.4-gcc10_include.patch | 11 + |
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sci-biology/fsl/files/fsl-6.0.4-melodic_std.patch | 11 + |
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.../fsl-6.0.4-remove_fslpy_collisions-p1.patch | 303 ++++++++++++++++++ |
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.../fsl-6.0.4-remove_fslpy_collisions-p2.patch | 348 +++++++++++++++++++++ |
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sci-biology/fsl/files/fsl-6.0.4-setup.patch | 174 +++++++++++ |
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sci-biology/fsl/fsl-6.0.2-r1.ebuild | 4 +- |
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sci-biology/fsl/fsl-6.0.2.ebuild | 6 +- |
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.../fsl/{fsl-6.0.2-r1.ebuild => fsl-6.0.4.ebuild} | 36 ++- |
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14 files changed, 1429 insertions(+), 16 deletions(-) |
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|
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diff --git a/sci-biology/fsl/files/fsl-6.0.4-cuda_buildsettings.patch b/sci-biology/fsl/files/fsl-6.0.4-cuda_buildsettings.patch |
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new file mode 100644 |
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index 000000000..749e80623 |
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--- /dev/null |
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+++ b/sci-biology/fsl/files/fsl-6.0.4-cuda_buildsettings.patch |
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@@ -0,0 +1,12 @@ |
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+diff -Naur fsl.orig/config/buildSettings.mk fsl/config/buildSettings.mk |
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+--- fsl.orig/config/buildSettings.mk 2020-12-02 16:22:57.999912865 -0500 |
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++++ fsl/config/buildSettings.mk 2020-12-02 16:24:15.332915270 -0500 |
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+@@ -144,7 +144,7 @@ |
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+ # CUDA development environment |
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+ CUDAVER := $(or $(CUDAVER),9.1) |
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+ #$(info $$CUDAVER is [${CUDAVER}]) |
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+-CUDA_INSTALLATION = /opt/cuda-${CUDAVER} |
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++CUDA_INSTALLATION = /opt/cuda |
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+ ifdef SINGULARITY_NAME |
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+ CUDA_INSTALLATION = /usr/local/cuda-${CUDAVER} |
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+ endif |
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|
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diff --git a/sci-biology/fsl/files/fsl-6.0.4-eddy_cuda.patch b/sci-biology/fsl/files/fsl-6.0.4-eddy_cuda.patch |
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new file mode 100644 |
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index 000000000..ad118c39a |
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--- /dev/null |
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+++ b/sci-biology/fsl/files/fsl-6.0.4-eddy_cuda.patch |
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@@ -0,0 +1,21 @@ |
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+diff -Naur fsl.orig/src/eddy/Makefile fsl/src/eddy/Makefile |
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+--- fsl.orig/src/eddy/Makefile 2020-12-02 16:07:47.327884548 -0500 |
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++++ fsl/src/eddy/Makefile 2020-12-02 16:11:21.149891196 -0500 |
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+@@ -29,6 +29,8 @@ |
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+ TMPCXXFLAGS_2= |
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+ TMPNAME_1= |
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+ TMPNAME_2= |
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++cuda=1 |
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++cpu=1 |
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+ TOPUP_DIR=../topup |
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+ |
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+ ifndef cuda |
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+@@ -74,7 +75,7 @@ |
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+ ifdef NVCC11 |
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+ NVCC=${NVCC11} |
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+ endif |
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+-NVCCFLAGS=-c -DCOMPILE_GPU -O3 -m 64 -std=c++11 |
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++NVCCFLAGS=-c -DCOMPILE_GPU -O3 -m 64 -std=c++11 @@GENTOO_NVCC_FLAGS@@ |
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+ ifeq ($(CLOBBER_CLANG),1) |
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+ NVCCFLAGS+= -DCLOBBER_CLANG |
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+ endif |
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|
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diff --git a/sci-biology/fsl/files/fsl-6.0.4-fdt_cuda.patch b/sci-biology/fsl/files/fsl-6.0.4-fdt_cuda.patch |
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new file mode 100644 |
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index 000000000..7f322027b |
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--- /dev/null |
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+++ b/sci-biology/fsl/files/fsl-6.0.4-fdt_cuda.patch |
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@@ -0,0 +1,14 @@ |
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+diff -Naur fsl.orig/src/fdt/Makefile fsl/src/fdt/Makefile |
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+--- fsl.orig/src/fdt/Makefile 2020-12-02 19:06:55.826218772 -0500 |
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++++ fsl/src/fdt/Makefile 2020-12-02 19:08:02.883220858 -0500 |
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+@@ -6,7 +6,9 @@ |
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+ $(eval $($(PROJNAME)_MASTERBUILD)) |
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+ endif |
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+ |
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+-ifeq ($(COMPILE_GPU), 1) |
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++# disable CUDA support for fdt |
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++#ifeq ($(COMPILE_GPU), 1) |
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++ifeq (0, 1) |
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+ COMPILE_WITH_GPU=libbedpostx_cuda.so merge_parts_gpu xfibres_gpu CUDA/split_parts_gpu |
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+ SCRIPTS_GPU=CUDA/bedpostx_gpu CUDA/bedpostx_postproc_gpu.sh |
97 |
+ endif |
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|
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diff --git a/sci-biology/fsl/files/fsl-6.0.4-flameo_std.patch b/sci-biology/fsl/files/fsl-6.0.4-flameo_std.patch |
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new file mode 100644 |
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index 000000000..a991f1ed3 |
102 |
--- /dev/null |
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+++ b/sci-biology/fsl/files/fsl-6.0.4-flameo_std.patch |
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@@ -0,0 +1,11 @@ |
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+diff -Naur fsl.orig/src/flameo/Makefile fsl/src/flameo/Makefile |
106 |
+--- fsl.orig/src/flameo/Makefile 2021-01-06 14:04:35.728274475 -0500 |
107 |
++++ fsl/src/flameo/Makefile 2021-01-06 14:08:18.204269285 -0500 |
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+@@ -4,6 +4,7 @@ |
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+ |
110 |
+ USRINCFLAGS = -I${INC_NEWMAT} -I${INC_PROB} -I${INC_ZLIB} -DCIFTILIB_USE_XMLPP -I${FSLEXTINC} -I${INC_XML2} -I${INC_XML++} -I${INC_XML++CONF} -I${INC_BOOST} -I${FSLDIR}/include/ciftiio |
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+ USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_ZLIB} |
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++USRCXXFLAGS = -std=c++11 |
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+ |
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+ UNAME := $(shell uname) |
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+ ifeq (${UNAME},Darwin) |
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|
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diff --git a/sci-biology/fsl/files/fsl-6.0.4-fsldir_redux-p1.patch b/sci-biology/fsl/files/fsl-6.0.4-fsldir_redux-p1.patch |
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new file mode 100644 |
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index 000000000..ca3945442 |
120 |
--- /dev/null |
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+++ b/sci-biology/fsl/files/fsl-6.0.4-fsldir_redux-p1.patch |
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@@ -0,0 +1,240 @@ |
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+From 2bc4be1f55b27a733e1e624b34bc570187ba95e1 Mon Sep 17 00:00:00 2001 |
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+From: François Bissey <frp.bissey@×××××.com> |
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+Date: Mon, 20 Jan 2020 11:40:53 +1300 |
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+Subject: [PATCH] Making sure fsl code and executable can find other executable |
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+ and data in standard location. |
128 |
+ |
129 |
+--- |
130 |
+ src/fast4/fast_two.cc | 8 ++++---- |
131 |
+ src/feat5/feat_model.cc | 8 +++----- |
132 |
+ src/feat5/tsplot.cc | 7 +++---- |
133 |
+ src/first/first_utils.cc | 4 ++-- |
134 |
+ src/fnirt/fnirtfns.cpp | 11 ++++------- |
135 |
+ src/fslsurface/fslsurface_first.cc | 6 ++---- |
136 |
+ src/fslsurface/fslsurfacemaths.cpp | 12 ------------ |
137 |
+ src/libvis/miscpic.h | 7 +------ |
138 |
+ src/melodic/meldata.cc | 4 ++-- |
139 |
+ src/melodic/meloptions.cc | 8 -------- |
140 |
+ src/melodic/meloptions.h | 1 - |
141 |
+ src/melodic/melreport.cc | 12 ++++++------ |
142 |
+ src/melodic/melreport.h | 20 ++++++++++---------- |
143 |
+ src/mm/mixture_model.cc | 4 ++-- |
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+ src/siena/siena_diff.cc | 28 +++++++++++++--------------- |
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+ src/topup/topupfns.cpp | 3 +-- |
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+ 16 files changed, 53 insertions(+), 90 deletions(-) |
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+ |
148 |
+diff --git a/src/fast4/fast_two.cc b/src/fast4/fast_two.cc |
149 |
+index 592b5df..b525444 100644 |
150 |
+--- a/src/fast4/fast_two.cc |
151 |
++++ b/src/fast4/fast_two.cc |
152 |
+@@ -166,7 +166,7 @@ int prior_registration(string inname, string main_prior_vol, NEWIMAGE::volume<fl |
153 |
+ string csfPriorName, grayPriorName, whitePriorName; |
154 |
+ if(alternatePriors.unset()) |
155 |
+ { |
156 |
+- string priorRootName=string(getenv("FSLDIR")) + "/data/standard/tissuepriors/avg152T1_"; |
157 |
++ string priorRootName="@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/tissuepriors/avg152T1_"; |
158 |
+ csfPriorName = priorRootName+"csf"; |
159 |
+ grayPriorName = priorRootName+"gray"; |
160 |
+ whitePriorName = priorRootName+"white"; |
161 |
+@@ -215,15 +215,15 @@ string csfPriorName, grayPriorName, whitePriorName; |
162 |
+ if(bapused>0) |
163 |
+ { |
164 |
+ char reg[1024]; |
165 |
+- sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), csfPriorName.c_str(), (main_prior_vol+"_csf_stdspace").c_str(), bapriori.value().c_str()); |
166 |
++ sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), csfPriorName.c_str(), (main_prior_vol+"_csf_stdspace").c_str(), bapriori.value().c_str()); |
167 |
+ if(verbose.value()) |
168 |
+ cout<<reg<<endl; |
169 |
+ system(reg); |
170 |
+- sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), grayPriorName.c_str(), (main_prior_vol+"_gm_stdspace").c_str(), bapriori.value().c_str()); |
171 |
++ sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), grayPriorName.c_str(), (main_prior_vol+"_gm_stdspace").c_str(), bapriori.value().c_str()); |
172 |
+ if(verbose.value()) |
173 |
+ cout<<reg<<endl; |
174 |
+ system(reg); |
175 |
+- sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), whitePriorName.c_str(), (main_prior_vol+"_wm_stdspace").c_str(), bapriori.value().c_str()); |
176 |
++ sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), whitePriorName.c_str(), (main_prior_vol+"_wm_stdspace").c_str(), bapriori.value().c_str()); |
177 |
+ if(verbose.value()) |
178 |
+ cout << reg << endl; |
179 |
+ system(reg); |
180 |
+diff --git a/src/feat5/feat_model.cc b/src/feat5/feat_model.cc |
181 |
+index 399a13e..e15e43c 100644 |
182 |
+--- a/src/feat5/feat_model.cc |
183 |
++++ b/src/feat5/feat_model.cc |
184 |
+@@ -744,7 +744,7 @@ int main(int argc, char **argv) |
185 |
+ vector<int> G; |
186 |
+ vector<string> titles; |
187 |
+ float tr, mult, trmult, nltffwhm=0, maxconvwin=0; |
188 |
+- char fl[10000], *FSLDIR; |
189 |
++ char fl[10000]; |
190 |
+ string fn, filename; |
191 |
+ FONT_DATA *font_data = new FONT_DATA[1]; |
192 |
+ |
193 |
+@@ -763,8 +763,6 @@ int main(int argc, char **argv) |
194 |
+ if (argc==3) |
195 |
+ motionparams=remmean(read_ascii_matrix(argv[2])); |
196 |
+ |
197 |
+- FSLDIR=getenv("FSLDIR"); |
198 |
+- |
199 |
+ fn = string(argv[1])+".fsf"; |
200 |
+ |
201 |
+ level = atoi(find_line(fn, "fmri(level)", fl)); |
202 |
+@@ -1510,7 +1508,7 @@ int main(int argc, char **argv) |
203 |
+ writeCovarianceImage(string(argv[1])+"_cov.ppm", contrasts, F, nftests, realDesign, level, evs.eigenvals, font_data, contrasts.RE); |
204 |
+ writeImagePreview(string(argv[1])+".ppm", contrasts, F, nftests, realDesign, level, evs, font_data, titles, tr, nltffwhm, nTimepoints, G); |
205 |
+ |
206 |
+- filename=string(getenv("FSLDIR"))+"/bin/wpng -q -overwrite "+string(argv[1])+".ppm "; |
207 |
++ filename="wpng -q -overwrite "+string(argv[1])+".ppm "; |
208 |
+ system(filename.c_str()); |
209 |
+ |
210 |
+ return(0); |
211 |
+@@ -2161,6 +2159,6 @@ char the_string[10000]; |
212 |
+ |
213 |
+ fclose(outputfile); |
214 |
+ |
215 |
+- filename=string(getenv("FSLDIR")) + "/bin/wpng -q -overwrite " + filename; |
216 |
++ filename="wpng -q -overwrite " + filename; |
217 |
+ system(filename.c_str()); |
218 |
+ } |
219 |
+diff --git a/src/feat5/tsplot.cc b/src/feat5/tsplot.cc |
220 |
+index ae191fd..3a02b55 100644 |
221 |
+--- a/src/feat5/tsplot.cc |
222 |
++++ b/src/feat5/tsplot.cc |
223 |
+@@ -293,7 +293,7 @@ int main(int argc, char **argv) |
224 |
+ ofstream outputFile; |
225 |
+ int numEVs, npts, numContrasts=1, nftests=0, GRPHSIZE(600), PSSIZE(600); |
226 |
+ vector<double> normalisedContrasts, model, triggers; |
227 |
+- string fmriFileName, fslPath, featdir, vType, indexText; |
228 |
++ string fmriFileName, featdir, vType, indexText; |
229 |
+ ColumnVector NewimageVoxCoord(4),NiftiVoxCoord(4); |
230 |
+ bool outputText(true), useCoordinate(false), prewhiten(false), useTriggers(false), customMask(false), modelFree(false), isHigherLevel(false), outputDataOnly(false); |
231 |
+ bool zWeightClusters(true); |
232 |
+@@ -307,7 +307,6 @@ volume<float> immask; |
233 |
+ if (argc<2) usage(""); |
234 |
+ featdir=string(argv[1]); |
235 |
+ fmriFileName=featdir+"/filtered_func_data"; |
236 |
+- fslPath=string(getenv("FSLDIR")); |
237 |
+ |
238 |
+ string outputName(featdir); |
239 |
+ |
240 |
+@@ -753,7 +752,7 @@ volume4D<float> acs; |
241 |
+ cerr << "Can't open output report file " << outputName << endl; |
242 |
+ exit(1); |
243 |
+ } |
244 |
+- outputFile << "<HTML>\n<TITLE>"<< statType << num2str(i) <<"</TITLE>\n<BODY BACKGROUND=\"file:"<< fslPath <<"/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report - "<< statType << num2str(i) <<"</H1>\n</CENTER>\n<hr><b>Full plots</b><p>\n"<< graphText; |
245 |
++ outputFile << "<HTML>\n<TITLE>"<< statType << num2str(i) <<"</TITLE>\n<BODY BACKGROUND=\"file:"<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report - "<< statType << num2str(i) <<"</H1>\n</CENTER>\n<hr><b>Full plots</b><p>\n"<< graphText; |
246 |
+ if (useTriggers) outputFile << "\n<hr><b>Peristimulus plots</b><p>\n"<< peristimulusText <<"\n<HR></BODY></HTML>\n\n"; |
247 |
+ else outputFile << "\n</BODY></HTML>\n\n"; |
248 |
+ outputFile.close(); |
249 |
+@@ -768,7 +767,7 @@ volume4D<float> acs; |
250 |
+ cerr << "Can't open output report file " << outputName << endl; |
251 |
+ exit(1); |
252 |
+ } |
253 |
+- outputFile << "<HTML>\n<TITLE>FEAT Time Series Report</TITLE>\n<BODY BACKGROUND=\"file:" << fslPath << "/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report</H1>\n</CENTER>\n<hr>" << indexText << "<HR></BODY></HTML>" << endl << endl; |
254 |
++ outputFile << "<HTML>\n<TITLE>FEAT Time Series Report</TITLE>\n<BODY BACKGROUND=\"file:" << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report</H1>\n</CENTER>\n<hr>" << indexText << "<HR></BODY></HTML>" << endl << endl; |
255 |
+ outputFile.close(); |
256 |
+ |
257 |
+ /* now output same thing without start and end, for inclusion in feat report */ |
258 |
+diff --git a/src/first/first_utils.cc b/src/first/first_utils.cc |
259 |
+index 68be44b..85960f4 100644 |
260 |
+--- a/src/first/first_utils.cc |
261 |
++++ b/src/first/first_utils.cc |
262 |
+@@ -1954,8 +1954,8 @@ void do_work_bvars(){ |
263 |
+ if (!surfaceVAout.value()) { |
264 |
+ // do not output on the surface, instead do the new default of outputting a volume with the scalar normal dot product values (for use with randomise) |
265 |
+ volume<float> refim; |
266 |
+- if (useReconMNI.value()) { read_volume(refim,string(getenv("FSLDIR")) + "/data/standard/MNI152_T1_1mm"); } |
267 |
+- else { read_volume(refim,string(getenv("FSLDIR")) + "/data/standard/MNI152_T1_1mm"); } |
268 |
++ if (useReconMNI.value()) { read_volume(refim,"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); } |
269 |
++ else { read_volume(refim,"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); } |
270 |
+ volume<float> maskvol(refim); |
271 |
+ maskvol=0.0f; |
272 |
+ volume4D<float> volnormals; |
273 |
+diff --git a/src/fnirt/fnirtfns.cpp b/src/fnirt/fnirtfns.cpp |
274 |
+index 24e26fd..77899e7 100644 |
275 |
+--- a/src/fnirt/fnirtfns.cpp |
276 |
++++ b/src/fnirt/fnirtfns.cpp |
277 |
+@@ -1203,8 +1203,7 @@ string existing_ref_fname(const string& ref_fname) |
278 |
+ return(string(ref_fname)); |
279 |
+ } |
280 |
+ else { |
281 |
+- const char *fsldir_ptr = getenv("FSLDIR"); |
282 |
+- string eref_fname = string(fsldir_ptr) + string("/data/standard/") + ref_fname; |
283 |
++ string eref_fname = string("@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/") + ref_fname; |
284 |
+ if (NEWIMAGE::FslFileExists(eref_fname)) return(eref_fname); |
285 |
+ else return(string("")); |
286 |
+ } |
287 |
+@@ -1230,9 +1229,8 @@ string existing_ref_fname(const string& ref_fname) |
288 |
+ NEWIMAGE::read_volume_hdr_only(vref,ref_fname); // Throws if file dont exist |
289 |
+ eref_fname = ref_fname; |
290 |
+ } |
291 |
+- catch(...) { // Didn't exist in current directory, try in ${FSLDIR}/data/standard |
292 |
+- const char *fsldir_ptr = getenv("FSLDIR"); |
293 |
+- eref_fname = string(fsldir_ptr) + string("/data/standard/") + ref_fname; |
294 |
++ catch(...) { // Didn't exist in current directory, try in .../data/standard |
295 |
++ eref_fname = string("@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/") + ref_fname; |
296 |
+ try { |
297 |
+ cout << "Could not find " << ref_fname << ", now checking " << eref_fname << endl; |
298 |
+ NEWIMAGE::read_volume_hdr_only(vref,eref_fname); // Throws if file dont exist |
299 |
+@@ -1267,8 +1265,7 @@ string existing_conf_file(const string& cfname) |
300 |
+ if (check_exist(ecfname)) return(ecfname); |
301 |
+ } |
302 |
+ if (!FNIRT::path(cfname).length()) { // If no path explicitly given |
303 |
+- const char *fsldir_ptr = getenv("FSLDIR"); |
304 |
+- ecfname = string(fsldir_ptr) + string("/etc/flirtsch/") + cfname; |
305 |
++ ecfname = string("@GENTOO_PORTAGE_EPREFIX@/etc/flirtsch/") + cfname; |
306 |
+ if (check_exist(ecfname)) return(ecfname); |
307 |
+ else if (!FNIRT::extension(ecfname).length()) { // If no path _and_ no extension given |
308 |
+ ecfname += string(".cnf"); |
309 |
+diff --git a/src/fslsurface/fslsurface_first.cc b/src/fslsurface/fslsurface_first.cc |
310 |
+index faec642..b2ef794 100644 |
311 |
+--- a/src/fslsurface/fslsurface_first.cc |
312 |
++++ b/src/fslsurface/fslsurface_first.cc |
313 |
+@@ -500,8 +500,7 @@ namespace fslsurface_name { |
314 |
+ |
315 |
+ volume<float>* immni = new volume<float>(); |
316 |
+ |
317 |
+- char* fsldir = getenv("FSLDIR"); |
318 |
+- read_volume_hdr_only(*immni, string(fsldir) + "/data/standard/MNI152_T1_1mm"); |
319 |
++ read_volume_hdr_only(*immni, "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); |
320 |
+ |
321 |
+ //read_volume_hdr_only(*immni, template_name); |
322 |
+ |
323 |
+@@ -699,8 +698,7 @@ namespace fslsurface_name { |
324 |
+ |
325 |
+ volume<float>* immni = new volume<float>(); |
326 |
+ |
327 |
+- char* fsldir = getenv("FSLDIR"); |
328 |
+- read_volume_hdr_only(*immni, string(fsldir) + "/data/standard/MNI152_T1_1mm"); |
329 |
++ read_volume_hdr_only(*immni, "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); |
330 |
+ |
331 |
+ //read_volume_hdr_only(*immni, template_name); |
332 |
+ |
333 |
+diff --git a/src/fslsurface/fslsurfacemaths.cpp b/src/fslsurface/fslsurfacemaths.cpp |
334 |
+index eaf55eb..3dc184d 100644 |
335 |
+--- a/src/fslsurface/fslsurfacemaths.cpp |
336 |
++++ b/src/fslsurface/fslsurfacemaths.cpp |
337 |
+@@ -598,12 +598,6 @@ int main (int argc, char * argv[]) |
338 |
+ |
339 |
+ }else if (command == "-reconFromBvars"){ |
340 |
+ cout<<"do recon "<<endl; |
341 |
+- char* fsldir = getenv("FSLDIR"); |
342 |
+- if (fsldir == NULL) |
343 |
+- { |
344 |
+- cerr<<"FSLDIR has not been set. "<<endl; |
345 |
+- exit(EXIT_FAILURE); |
346 |
+- } |
347 |
+ //file.bvars,mni_template.nii.gz |
348 |
+ // string mni = string(fsldir)+"/data/standard/MNI152_T1_1mm"; |
349 |
+ reconSurface_from_bvars( surf, string(argv[i_arg+1])); |
350 |
+@@ -612,12 +606,6 @@ int main (int argc, char * argv[]) |
351 |
+ |
352 |
+ }else if (command == "-reconAllFromBvarsAndSave"){ |
353 |
+ cout<<"do recon+save "<<argc<<" "<<i_arg<<endl; |
354 |
+- char* fsldir = getenv("FSLDIR"); |
355 |
+- if (fsldir == NULL) |
356 |
+- { |
357 |
+- cerr<<"FSLDIR has not been set. "<<endl; |
358 |
+- exit(EXIT_FAILURE); |
359 |
+- } |
360 |
+ //file.bvars,mni_template.nii.gz |
361 |
+ // string mni = string(fsldir)+"/data/standard/MNI152_T1_1mm"; |
362 |
+ cout<<"recon "<< string(argv[i_arg+1])<<endl; |
363 |
|
364 |
diff --git a/sci-biology/fsl/files/fsl-6.0.4-fsldir_redux-p2.patch b/sci-biology/fsl/files/fsl-6.0.4-fsldir_redux-p2.patch |
365 |
new file mode 100644 |
366 |
index 000000000..af498b400 |
367 |
--- /dev/null |
368 |
+++ b/sci-biology/fsl/files/fsl-6.0.4-fsldir_redux-p2.patch |
369 |
@@ -0,0 +1,254 @@ |
370 |
+diff --git a/src/libvis/miscpic.h b/src/libvis/miscpic.h |
371 |
+index a2f3855..5f440f2 100644 |
372 |
+--- a/src/libvis/miscpic.h |
373 |
++++ b/src/libvis/miscpic.h |
374 |
+@@ -90,12 +90,7 @@ namespace MISCPIC{ |
375 |
+ markRight=false; |
376 |
+ trans= -10; |
377 |
+ edgethresh = 0.0; |
378 |
+- if(getenv("FSLDIR")!=0){ |
379 |
+- lutbase = string(getenv("FSLDIR")) + "/etc/luts/"; |
380 |
+- } |
381 |
+- else{ |
382 |
+- lutbase = string("/"); |
383 |
+- } |
384 |
++ lutbase = "@GENTOO_PORTAGE_EPREFIX@/etc/luts/"; |
385 |
+ title = string(""); |
386 |
+ cbartype = string(""); |
387 |
+ cbarptr = NULL; |
388 |
+diff --git a/src/melodic/meldata.cc b/src/melodic/meldata.cc |
389 |
+index 1749a45..c4ad234 100644 |
390 |
+--- a/src/melodic/meldata.cc |
391 |
++++ b/src/melodic/meldata.cc |
392 |
+@@ -992,7 +992,7 @@ namespace Melodic{ |
393 |
+ void MelodicData::est_smoothness() |
394 |
+ { |
395 |
+ if(Resels == 0){ |
396 |
+- string SM_path = opts.binpath + "smoothest"; |
397 |
++ string SM_path = "smoothest"; |
398 |
+ string Mask_fname = logger.appendDir("mask"); |
399 |
+ |
400 |
+ if(opts.segment.value().length()>0){ |
401 |
+@@ -1157,7 +1157,7 @@ namespace Melodic{ |
402 |
+ // set up all strings |
403 |
+ string BET_outputfname = string(Mean_fname)+"_brain"; |
404 |
+ |
405 |
+- string BET_path = opts.binpath + "bet"; |
406 |
++ string BET_path = "bet"; |
407 |
+ string BET_optarg = "-m -f 0.4"; // see man bet |
408 |
+ string Mask_fname = BET_outputfname+"_mask"; |
409 |
+ |
410 |
+diff --git a/src/melodic/meloptions.cc b/src/melodic/meloptions.cc |
411 |
+index 08170c7..252e72b 100644 |
412 |
+--- a/src/melodic/meloptions.cc |
413 |
++++ b/src/melodic/meloptions.cc |
414 |
+@@ -93,14 +93,6 @@ MelodicOptions* MelodicOptions::gopt = NULL; |
415 |
+ explicitnums = false; |
416 |
+ logfname = string("log.txt"); |
417 |
+ |
418 |
+- // work out the path to the $FSLDIR/bin directory |
419 |
+- if(getenv("FSLDIR")!=0){ |
420 |
+- binpath = (string) getenv("FSLDIR") + "/bin/"; |
421 |
+- } else{ |
422 |
+- binpath = argv[0]; |
423 |
+- binpath = binpath.substr(0,binpath.length()-7); |
424 |
+- } |
425 |
+- |
426 |
+ // parse once to establish log directory name |
427 |
+ for(int a = options.parse_command_line(argc, argv); a < argc; a++); |
428 |
+ |
429 |
+diff --git a/src/melodic/meloptions.h b/src/melodic/meloptions.h |
430 |
+index f546125..b964b7d 100644 |
431 |
+--- a/src/melodic/meloptions.h |
432 |
++++ b/src/melodic/meloptions.h |
433 |
+@@ -93,7 +93,6 @@ class MelodicOptions { |
434 |
+ ~MelodicOptions() { delete gopt; } |
435 |
+ |
436 |
+ string version; |
437 |
+- string binpath; |
438 |
+ string logfname; |
439 |
+ bool filtermode; |
440 |
+ bool explicitnums; |
441 |
+diff --git a/src/melodic/melreport.cc b/src/melodic/melreport.cc |
442 |
+index 141b6c2..2625059 100644 |
443 |
+--- a/src/melodic/melreport.cc |
444 |
++++ b/src/melodic/melreport.cc |
445 |
+@@ -84,8 +84,8 @@ namespace Melodic{ |
446 |
+ IChtml.setDir(report.getDir(),mmodel.get_prefix()+".html"); |
447 |
+ |
448 |
+ {//start IC page |
449 |
+- IChtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" + |
450 |
+- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl |
451 |
++ IChtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" |
452 |
++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl |
453 |
+ << "<style type=\"text/css\">OBJECT { width: 100% }</style>" |
454 |
+ << "<TITLE>FSL</TITLE></HEAD>" << endl |
455 |
+ << "<IFRAME height=" << int(melodat.get_numfiles()/30 + 1)*50 |
456 |
+@@ -486,8 +486,8 @@ namespace Melodic{ |
457 |
+ |
458 |
+ {//start IC2 page |
459 |
+ IChtml2.setDir(report.getDir(),mmodel.get_prefix()+"_MM.html"); |
460 |
+- IChtml2 << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" + |
461 |
+- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl |
462 |
++ IChtml2 << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" |
463 |
++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl |
464 |
+ << "<style type=\"text/css\">OBJECT { width: 100% }</style>" |
465 |
+ << "<TITLE>FSL</TITLE></HEAD>" << endl |
466 |
+ << "<IFRAME height="<< int(melodat.get_numfiles()/30 + 1)*50 |
467 |
+@@ -665,8 +665,8 @@ namespace Melodic{ |
468 |
+ IChtml << "<HTML> " << endl |
469 |
+ << "<TITLE>MELODIC Component " << num2str(cnum) |
470 |
+ << "</TITLE>" << endl |
471 |
+- << "<BODY BACKGROUND=\"file:" << getenv("FSLDIR") |
472 |
+- << "/doc/images/fsl-bg.jpg\">" << endl |
473 |
++ << "<BODY BACKGROUND=\"file:" |
474 |
++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl |
475 |
+ << "<hr><CENTER><H1>MELODIC Component " << num2str(cnum) |
476 |
+ << "</H1>"<< endl; |
477 |
+ |
478 |
+diff --git a/src/melodic/melreport.h b/src/melodic/melreport.h |
479 |
+index 574fc4c..e444681 100644 |
480 |
+--- a/src/melodic/melreport.h |
481 |
++++ b/src/melodic/melreport.h |
482 |
+@@ -104,21 +104,21 @@ namespace Melodic{ |
483 |
+ const time_t tmptime = time(NULL); |
484 |
+ system(("mkdir "+ logger.appendDir("report") + " 2>/dev/null").c_str()); |
485 |
+ report.setDir(logger.appendDir("report"),"00index.html",true,false,ios::out); |
486 |
+- report << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" + |
487 |
+- (string) getenv("FSLDIR") +"/doc/fsl.css>" |
488 |
++ report << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" |
489 |
++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" |
490 |
+ << "<TITLE>MELODIC report</TITLE></HEAD><BODY>" |
491 |
+ << endl <<endl; |
492 |
+ loghtml.setDir(report.getDir(),"log.html"); |
493 |
+- loghtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" + |
494 |
+- (string) getenv("FSLDIR") +"/doc/fsl.css>" |
495 |
++ loghtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" |
496 |
++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" |
497 |
+ << "<TITLE>MELODIC report</TITLE></HEAD><BODY>" |
498 |
+ << endl <<endl; |
499 |
+ navigator.setDir(report.getDir(),"nav.html"); |
500 |
+ head.setDir(report.getDir(),"head.html"); |
501 |
+- navigator << "<link REL=stylesheet TYPE=text/css href=file:"+ |
502 |
+- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl; |
503 |
+- head << "<link REL=stylesheet TYPE=text/css href=file:"+ |
504 |
+- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl; |
505 |
++ navigator << "<link REL=stylesheet TYPE=text/css href=file:" |
506 |
++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl; |
507 |
++ head << "<link REL=stylesheet TYPE=text/css href=file:" |
508 |
++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl; |
509 |
+ head <<"<TABLE BORDER=0><TR>" << endl |
510 |
+ <<" <TD ALIGN=CENTER WIDTH=100%>"<< endl |
511 |
+ <<"<TABLE BORDER=0>"<< endl |
512 |
+@@ -130,8 +130,8 @@ namespace Melodic{ |
513 |
+ << "</tr></table>" << endl |
514 |
+ << "<TD ALIGN=RIGHT>" << endl |
515 |
+ << "<a href=http://www.fmrib.ox.ac.uk/fsl target=_top>" << endl |
516 |
+- << "<IMG BORDER=0 SRC=file:"<< getenv("FSLDIR") |
517 |
+- << "/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl |
518 |
++ << "<IMG BORDER=0 SRC=file:" |
519 |
++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl |
520 |
+ << "</TD>"<<endl<<"</TR></TABLE> <hr>"<<endl; |
521 |
+ if(opts.guireport.value()==""){ |
522 |
+ report <<"<OBJECT data=head.html></OBJECT>" << endl; |
523 |
+diff --git a/src/mm/mixture_model.cc b/src/mm/mixture_model.cc |
524 |
+index b8e6167..5f00693 100644 |
525 |
+--- a/src/mm/mixture_model.cc |
526 |
++++ b/src/mm/mixture_model.cc |
527 |
+@@ -2224,8 +2224,8 @@ namespace Mm { |
528 |
+ |
529 |
+ htmllog << "<HTML> " << endl |
530 |
+ << "<TITLE>Mixture Model fit for" << data_name << "</TITLE>" << endl |
531 |
+- << "<BODY BACKGROUND=\"file:" << getenv("FSLDIR") |
532 |
+- << "/doc/images/fsl-bg.jpg\">" << endl |
533 |
++ << "<BODY BACKGROUND=\"file:" |
534 |
++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl |
535 |
+ << "<hr><CENTER><H1>Mixture Model fit for<br>" << data_name << " </H1>"<< endl; |
536 |
+ |
537 |
+ htmllog << "<hr><p>" << endl; |
538 |
+diff -Naur fsl.orig/src/siena/siena_diff.cc fsl/src/siena/siena_diff.cc |
539 |
+--- fsl.orig/src/siena/siena_diff.cc 2020-12-02 15:52:50.359856656 -0500 |
540 |
++++ fsl/src/siena/siena_diff.cc 2020-12-02 16:03:25.699876412 -0500 |
541 |
+@@ -107,7 +107,7 @@ |
542 |
+ { |
543 |
+ // {{{ vars |
544 |
+ |
545 |
+-char thestring[10000], segoptions[10000], fsldir[10000]; |
546 |
++char thestring[10000], segoptions[10000]; |
547 |
+ int x_size, y_size, z_size, size, x, y, z, i, count, |
548 |
+ seg2=0, ignore_z=0, ignore_top_slices=0, //erode_mask=0, |
549 |
+ ignore_bottom_slices=0, debug=0, flow_output=1, edge_masking=0; |
550 |
+@@ -124,8 +124,6 @@ |
551 |
+ |
552 |
+ string argv1(argv[1]), argv2(argv[2]); |
553 |
+ |
554 |
+-sprintf(fsldir,"%s",getenv("FSLDIR")); |
555 |
+- |
556 |
+ for (i = 3; i < argc; i++) |
557 |
+ { |
558 |
+ if (!strcmp(argv[i], "-i")) |
559 |
+@@ -206,26 +204,26 @@ |
560 |
+ // }}} |
561 |
+ // {{{ transform images and masks |
562 |
+ |
563 |
+-sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s", |
564 |
+- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]); |
565 |
++sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s", |
566 |
++ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]); |
567 |
+ printf("%s\n",thestring); system(thestring); |
568 |
+ |
569 |
+-sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s", |
570 |
+- fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]); |
571 |
++sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s", |
572 |
++ argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]); |
573 |
+ printf("%s\n",thestring); system(thestring); |
574 |
+ |
575 |
+-sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask", |
576 |
+- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]); |
577 |
++sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask", |
578 |
++ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]); |
579 |
+ printf("%s\n",thestring); system(thestring); |
580 |
+ |
581 |
+-sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask", |
582 |
+- fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]); |
583 |
++sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask", |
584 |
++ argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]); |
585 |
+ printf("%s\n",thestring); system(thestring); |
586 |
+ |
587 |
+ if (edge_masking) |
588 |
+ { |
589 |
+- sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s", |
590 |
+- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]); |
591 |
++ sprintf(thestring,"flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s", |
592 |
++ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]); |
593 |
+ printf("%s\n",thestring); system(thestring); |
594 |
+ } |
595 |
+ |
596 |
+@@ -284,8 +282,8 @@ |
597 |
+ cout << "saving image 1 to disk prior to segmentation" << endl; |
598 |
+ save_volume(in1,argv1+"_halfwayto_"+argv2+"_brain"); |
599 |
+ in1.destroy(); |
600 |
+- sprintf(thestring,"%s/bin/fast %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1", |
601 |
+- fsldir,segtype,segoptions,argv[1],argv[2],argv[1],argv[2]); |
602 |
++ sprintf(thestring,"fast %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1", |
603 |
++ segtype,segoptions,argv[1],argv[2],argv[1],argv[2]); |
604 |
+ cout << thestring << endl; |
605 |
+ system(thestring); |
606 |
+ } |
607 |
+diff --git a/src/topup/topupfns.cpp b/src/topup/topupfns.cpp |
608 |
+index 6873758..9e8b956 100644 |
609 |
+--- a/src/topup/topupfns.cpp |
610 |
++++ b/src/topup/topupfns.cpp |
611 |
+@@ -463,8 +463,7 @@ string existing_conf_file(const string& cfname) |
612 |
+ if (TOPUP::check_exist(ecfname)) return(ecfname); |
613 |
+ } |
614 |
+ if (!TOPUP::path(cfname).length()) { // If no path explicitly given |
615 |
+- const char *fsldir_ptr = getenv("FSLDIR"); |
616 |
+- ecfname = string(fsldir_ptr) + string("/etc/flirtsch/") + cfname; |
617 |
++ ecfname = string("@GENTOO_PORTAGE_EPREFIX@/etc/flirtsch/") + cfname; |
618 |
+ if (TOPUP::check_exist(ecfname)) return(ecfname); |
619 |
+ else if (!TOPUP::extension(ecfname).length()) { // If no path _and_ no extension given |
620 |
+ ecfname += string(".cnf"); |
621 |
+-- |
622 |
+2.24.1 |
623 |
+ |
624 |
|
625 |
diff --git a/sci-biology/fsl/files/fsl-6.0.4-gcc10_include.patch b/sci-biology/fsl/files/fsl-6.0.4-gcc10_include.patch |
626 |
new file mode 100644 |
627 |
index 000000000..ae836c065 |
628 |
--- /dev/null |
629 |
+++ b/sci-biology/fsl/files/fsl-6.0.4-gcc10_include.patch |
630 |
@@ -0,0 +1,11 @@ |
631 |
+diff -Naur fsl.orig/src/newimage/newimageio.h fsl/src/newimage/newimageio.h |
632 |
+--- fsl.orig/src/newimage/newimageio.h 2020-12-02 15:15:27.012786899 -0500 |
633 |
++++ fsl/src/newimage/newimageio.h 2020-12-02 15:19:51.046795110 -0500 |
634 |
+@@ -75,6 +75,7 @@ |
635 |
+ #include <iostream> |
636 |
+ #include <fstream> |
637 |
+ #include <sstream> |
638 |
++#include <stdexcept> |
639 |
+ #include "NewNifti/NewNifti.h" |
640 |
+ #include "newmatio.h" |
641 |
+ #include "newimage.h" |
642 |
|
643 |
diff --git a/sci-biology/fsl/files/fsl-6.0.4-melodic_std.patch b/sci-biology/fsl/files/fsl-6.0.4-melodic_std.patch |
644 |
new file mode 100644 |
645 |
index 000000000..83b5b9932 |
646 |
--- /dev/null |
647 |
+++ b/sci-biology/fsl/files/fsl-6.0.4-melodic_std.patch |
648 |
@@ -0,0 +1,11 @@ |
649 |
+diff -Naur fsl.orig/src/melodic/Makefile fsl/src/melodic/Makefile |
650 |
+--- fsl.orig/src/melodic/Makefile 2021-01-06 14:04:35.743274475 -0500 |
651 |
++++ fsl/src/melodic/Makefile 2021-01-06 14:11:27.924264859 -0500 |
652 |
+@@ -9,6 +9,7 @@ |
653 |
+ |
654 |
+ USRINCFLAGS = -I${INC_NEWMAT} -I${INC_PROB} -I${INC_GD} -I${INC_GDC} -I${INC_PNG} -I${INC_ZLIB} -DCIFTILIB_USE_XMLPP -I${FSLEXTINC} -I${INC_XML2} -I${INC_XML++} -I${INC_XML++CONF} -I${INC_BOOST} -I${FSLDIR}/include/ciftiio |
655 |
+ USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_GD} -L${LIB_GDC} -L${LIB_PNG} -L${LIB_ZLIB} |
656 |
++USRCXXFLAGS = -std=c++11 |
657 |
+ |
658 |
+ UNAME := $(shell uname) |
659 |
+ ifeq (${UNAME},Darwin) |
660 |
|
661 |
diff --git a/sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p1.patch b/sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p1.patch |
662 |
new file mode 100644 |
663 |
index 000000000..434dc9cf6 |
664 |
--- /dev/null |
665 |
+++ b/sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p1.patch |
666 |
@@ -0,0 +1,303 @@ |
667 |
+diff -Naur fsl.orig/src/fslio/imln fsl/src/fslio/imln |
668 |
+--- fsl.orig/src/fslio/imln 2021-02-01 15:29:34.842752994 -0500 |
669 |
++++ fsl/src/fslio/imln 1969-12-31 19:00:00.000000000 -0500 |
670 |
+@@ -1,90 +0,0 @@ |
671 |
+-#!/bin/sh |
672 |
+- |
673 |
+-# imln - make symbolic link(s) to image file(s) |
674 |
+-# |
675 |
+-# Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group |
676 |
+-# |
677 |
+-# Copyright (C) 1999-2004 University of Oxford |
678 |
+-# |
679 |
+-# Part of FSL - FMRIB's Software Library |
680 |
+-# http://www.fmrib.ox.ac.uk/fsl |
681 |
+-# fsl@×××××××××××.uk |
682 |
+-# |
683 |
+-# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance |
684 |
+-# Imaging of the Brain), Department of Clinical Neurology, Oxford |
685 |
+-# University, Oxford, UK |
686 |
+-# |
687 |
+-# |
688 |
+-# LICENCE |
689 |
+-# |
690 |
+-# FMRIB Software Library, Release 6.0 (c) 2018, The University of |
691 |
+-# Oxford (the "Software") |
692 |
+-# |
693 |
+-# The Software remains the property of the Oxford University Innovation |
694 |
+-# ("the University"). |
695 |
+-# |
696 |
+-# The Software is distributed "AS IS" under this Licence solely for |
697 |
+-# non-commercial use in the hope that it will be useful, but in order |
698 |
+-# that the University as a charitable foundation protects its assets for |
699 |
+-# the benefit of its educational and research purposes, the University |
700 |
+-# makes clear that no condition is made or to be implied, nor is any |
701 |
+-# warranty given or to be implied, as to the accuracy of the Software, |
702 |
+-# or that it will be suitable for any particular purpose or for use |
703 |
+-# under any specific conditions. Furthermore, the University disclaims |
704 |
+-# all responsibility for the use which is made of the Software. It |
705 |
+-# further disclaims any liability for the outcomes arising from using |
706 |
+-# the Software. |
707 |
+-# |
708 |
+-# The Licensee agrees to indemnify the University and hold the |
709 |
+-# University harmless from and against any and all claims, damages and |
710 |
+-# liabilities asserted by third parties (including claims for |
711 |
+-# negligence) which arise directly or indirectly from the use of the |
712 |
+-# Software or the sale of any products based on the Software. |
713 |
+-# |
714 |
+-# No part of the Software may be reproduced, modified, transmitted or |
715 |
+-# transferred in any form or by any means, electronic or mechanical, |
716 |
+-# without the express permission of the University. The permission of |
717 |
+-# the University is not required if the said reproduction, modification, |
718 |
+-# transmission or transference is done without financial return, the |
719 |
+-# conditions of this Licence are imposed upon the receiver of the |
720 |
+-# product, and all original and amended source code is included in any |
721 |
+-# transmitted product. You may be held legally responsible for any |
722 |
+-# copyright infringement that is caused or encouraged by your failure to |
723 |
+-# abide by these terms and conditions. |
724 |
+-# |
725 |
+-# You are not permitted under this Licence to use this Software |
726 |
+-# commercially. Use for which any financial return is received shall be |
727 |
+-# defined as commercial use, and includes (1) integration of all or part |
728 |
+-# of the source code or the Software into a product for sale or license |
729 |
+-# by or on behalf of Licensee to third parties or (2) use of the |
730 |
+-# Software or any derivative of it for research with the final aim of |
731 |
+-# developing software products for sale or license to a third party or |
732 |
+-# (3) use of the Software or any derivative of it for research with the |
733 |
+-# final aim of developing non-software products for sale or license to a |
734 |
+-# third party, or (4) use of the Software to provide any service to an |
735 |
+-# external organisation for which payment is received. If you are |
736 |
+-# interested in using the Software commercially, please contact Oxford |
737 |
+-# University Innovation ("OUI"), the technology transfer company of the |
738 |
+-# University, to negotiate a licence. Contact details are: |
739 |
+-# fsl@××××××××××××××××.uk quoting Reference Project 9564, FSL. |
740 |
+-export LC_ALL=C |
741 |
+- |
742 |
+-if [ $# -lt 2 ] ; then |
743 |
+- echo "Usage: $0 <file1> <file2>" |
744 |
+- echo " Makes a link (called file2) to file1" |
745 |
+- echo " NB: filenames can be basenames or include an extension" |
746 |
+- exit 1; |
747 |
+-fi |
748 |
+- |
749 |
+-f1=`${FSLDIR}/bin/remove_ext $1`; |
750 |
+-f2=`${FSLDIR}/bin/remove_ext $2`; |
751 |
+- |
752 |
+-if [ -f ${f1}.hdr ] ; then ln -fs ${f1}.hdr ${f2}.hdr ; fi |
753 |
+-if [ -f ${f1}.hdr.gz ] ; then ln -fs ${f1}.hdr.gz ${f2}.hdr.gz ; fi |
754 |
+-if [ -f ${f1}.img ] ; then ln -fs ${f1}.img ${f2}.img ; fi |
755 |
+-if [ -f ${f1}.img.gz ] ; then ln -fs ${f1}.img.gz ${f2}.img.gz ; fi |
756 |
+-if [ -f ${f1}.nii ] ; then ln -fs ${f1}.nii ${f2}.nii ; fi |
757 |
+-if [ -f ${f1}.nii.gz ] ; then ln -fs ${f1}.nii.gz ${f2}.nii.gz ; fi |
758 |
+-if [ -f ${f1}.mnc ] ; then ln -fs ${f1}.mnc ${f2}.mnc ; fi |
759 |
+-if [ -f ${f1}.mnc.gz ] ; then ln -fs ${f1}.mnc.gz ${f2}.mnc.gz ; fi |
760 |
+- |
761 |
+diff -Naur fsl.orig/src/fslio/imrm fsl/src/fslio/imrm |
762 |
+--- fsl.orig/src/fslio/imrm 2021-02-01 15:29:34.842752994 -0500 |
763 |
++++ fsl/src/fslio/imrm 1969-12-31 19:00:00.000000000 -0500 |
764 |
+@@ -1,83 +0,0 @@ |
765 |
+-#!/bin/sh |
766 |
+- |
767 |
+-# imrm - remove image files |
768 |
+-# |
769 |
+-# Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group |
770 |
+-# |
771 |
+-# Copyright (C) 1999-2004 University of Oxford |
772 |
+-# |
773 |
+-# Part of FSL - FMRIB's Software Library |
774 |
+-# http://www.fmrib.ox.ac.uk/fsl |
775 |
+-# fsl@×××××××××××.uk |
776 |
+-# |
777 |
+-# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance |
778 |
+-# Imaging of the Brain), Department of Clinical Neurology, Oxford |
779 |
+-# University, Oxford, UK |
780 |
+-# |
781 |
+-# |
782 |
+-# LICENCE |
783 |
+-# |
784 |
+-# FMRIB Software Library, Release 6.0 (c) 2018, The University of |
785 |
+-# Oxford (the "Software") |
786 |
+-# |
787 |
+-# The Software remains the property of the Oxford University Innovation |
788 |
+-# ("the University"). |
789 |
+-# |
790 |
+-# The Software is distributed "AS IS" under this Licence solely for |
791 |
+-# non-commercial use in the hope that it will be useful, but in order |
792 |
+-# that the University as a charitable foundation protects its assets for |
793 |
+-# the benefit of its educational and research purposes, the University |
794 |
+-# makes clear that no condition is made or to be implied, nor is any |
795 |
+-# warranty given or to be implied, as to the accuracy of the Software, |
796 |
+-# or that it will be suitable for any particular purpose or for use |
797 |
+-# under any specific conditions. Furthermore, the University disclaims |
798 |
+-# all responsibility for the use which is made of the Software. It |
799 |
+-# further disclaims any liability for the outcomes arising from using |
800 |
+-# the Software. |
801 |
+-# |
802 |
+-# The Licensee agrees to indemnify the University and hold the |
803 |
+-# University harmless from and against any and all claims, damages and |
804 |
+-# liabilities asserted by third parties (including claims for |
805 |
+-# negligence) which arise directly or indirectly from the use of the |
806 |
+-# Software or the sale of any products based on the Software. |
807 |
+-# |
808 |
+-# No part of the Software may be reproduced, modified, transmitted or |
809 |
+-# transferred in any form or by any means, electronic or mechanical, |
810 |
+-# without the express permission of the University. The permission of |
811 |
+-# the University is not required if the said reproduction, modification, |
812 |
+-# transmission or transference is done without financial return, the |
813 |
+-# conditions of this Licence are imposed upon the receiver of the |
814 |
+-# product, and all original and amended source code is included in any |
815 |
+-# transmitted product. You may be held legally responsible for any |
816 |
+-# copyright infringement that is caused or encouraged by your failure to |
817 |
+-# abide by these terms and conditions. |
818 |
+-# |
819 |
+-# You are not permitted under this Licence to use this Software |
820 |
+-# commercially. Use for which any financial return is received shall be |
821 |
+-# defined as commercial use, and includes (1) integration of all or part |
822 |
+-# of the source code or the Software into a product for sale or license |
823 |
+-# by or on behalf of Licensee to third parties or (2) use of the |
824 |
+-# Software or any derivative of it for research with the final aim of |
825 |
+-# developing software products for sale or license to a third party or |
826 |
+-# (3) use of the Software or any derivative of it for research with the |
827 |
+-# final aim of developing non-software products for sale or license to a |
828 |
+-# third party, or (4) use of the Software to provide any service to an |
829 |
+-# external organisation for which payment is received. If you are |
830 |
+-# interested in using the Software commercially, please contact Oxford |
831 |
+-# University Innovation ("OUI"), the technology transfer company of the |
832 |
+-# University, to negotiate a licence. Contact details are: |
833 |
+-# fsl@××××××××××××××××.uk quoting Reference Project 9564, FSL. |
834 |
+-export LC_ALL=C |
835 |
+- |
836 |
+-if [ $# -lt 1 ] ; then |
837 |
+- echo "Usage: $0 <list of image names to remove>" |
838 |
+- echo "NB: filenames can be basenames or not" |
839 |
+- exit 1; |
840 |
+-fi |
841 |
+- |
842 |
+-for f in $@ ; do |
843 |
+- fn=`${FSLDIR}/bin/remove_ext $f`; |
844 |
+- # do the rm silently |
845 |
+- /bin/rm -f ${fn}.img ${fn}.hdr ${fn}.hdr.gz ${fn}.img.gz ${fn}.nii ${fn}.nii.gz ${fn}.mnc ${fn}.mnc.gz |
846 |
+-done |
847 |
+- |
848 |
+diff -Naur fsl.orig/src/fslio/imtest fsl/src/fslio/imtest |
849 |
+--- fsl.orig/src/fslio/imtest 2021-02-01 15:29:34.842752994 -0500 |
850 |
++++ fsl/src/fslio/imtest 1969-12-31 19:00:00.000000000 -0500 |
851 |
+@@ -1,118 +0,0 @@ |
852 |
+-#!/bin/sh |
853 |
+- |
854 |
+-# imtest - test to see if a valid image file exists with this name (root) |
855 |
+-# |
856 |
+-# Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group |
857 |
+-# |
858 |
+-# Copyright (C) 1999-2004 University of Oxford |
859 |
+-# |
860 |
+-# Part of FSL - FMRIB's Software Library |
861 |
+-# http://www.fmrib.ox.ac.uk/fsl |
862 |
+-# fsl@×××××××××××.uk |
863 |
+-# |
864 |
+-# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance |
865 |
+-# Imaging of the Brain), Department of Clinical Neurology, Oxford |
866 |
+-# University, Oxford, UK |
867 |
+-# |
868 |
+-# |
869 |
+-# LICENCE |
870 |
+-# |
871 |
+-# FMRIB Software Library, Release 6.0 (c) 2018, The University of |
872 |
+-# Oxford (the "Software") |
873 |
+-# |
874 |
+-# The Software remains the property of the Oxford University Innovation |
875 |
+-# ("the University"). |
876 |
+-# |
877 |
+-# The Software is distributed "AS IS" under this Licence solely for |
878 |
+-# non-commercial use in the hope that it will be useful, but in order |
879 |
+-# that the University as a charitable foundation protects its assets for |
880 |
+-# the benefit of its educational and research purposes, the University |
881 |
+-# makes clear that no condition is made or to be implied, nor is any |
882 |
+-# warranty given or to be implied, as to the accuracy of the Software, |
883 |
+-# or that it will be suitable for any particular purpose or for use |
884 |
+-# under any specific conditions. Furthermore, the University disclaims |
885 |
+-# all responsibility for the use which is made of the Software. It |
886 |
+-# further disclaims any liability for the outcomes arising from using |
887 |
+-# the Software. |
888 |
+-# |
889 |
+-# The Licensee agrees to indemnify the University and hold the |
890 |
+-# University harmless from and against any and all claims, damages and |
891 |
+-# liabilities asserted by third parties (including claims for |
892 |
+-# negligence) which arise directly or indirectly from the use of the |
893 |
+-# Software or the sale of any products based on the Software. |
894 |
+-# |
895 |
+-# No part of the Software may be reproduced, modified, transmitted or |
896 |
+-# transferred in any form or by any means, electronic or mechanical, |
897 |
+-# without the express permission of the University. The permission of |
898 |
+-# the University is not required if the said reproduction, modification, |
899 |
+-# transmission or transference is done without financial return, the |
900 |
+-# conditions of this Licence are imposed upon the receiver of the |
901 |
+-# product, and all original and amended source code is included in any |
902 |
+-# transmitted product. You may be held legally responsible for any |
903 |
+-# copyright infringement that is caused or encouraged by your failure to |
904 |
+-# abide by these terms and conditions. |
905 |
+-# |
906 |
+-# You are not permitted under this Licence to use this Software |
907 |
+-# commercially. Use for which any financial return is received shall be |
908 |
+-# defined as commercial use, and includes (1) integration of all or part |
909 |
+-# of the source code or the Software into a product for sale or license |
910 |
+-# by or on behalf of Licensee to third parties or (2) use of the |
911 |
+-# Software or any derivative of it for research with the final aim of |
912 |
+-# developing software products for sale or license to a third party or |
913 |
+-# (3) use of the Software or any derivative of it for research with the |
914 |
+-# final aim of developing non-software products for sale or license to a |
915 |
+-# third party, or (4) use of the Software to provide any service to an |
916 |
+-# external organisation for which payment is received. If you are |
917 |
+-# interested in using the Software commercially, please contact Oxford |
918 |
+-# University Innovation ("OUI"), the technology transfer company of the |
919 |
+-# University, to negotiate a licence. Contact details are: |
920 |
+-# fsl@××××××××××××××××.uk quoting Reference Project 9564, FSL. |
921 |
+-export LC_ALL=C |
922 |
+- |
923 |
+-# return 0 if no image exists or 1 if the image exists |
924 |
+- |
925 |
+-if [ $# -lt 1 ] ; then |
926 |
+- echo "0"; |
927 |
+- exit; |
928 |
+-fi |
929 |
+- |
930 |
+-inputfile=$1 |
931 |
+- |
932 |
+- |
933 |
+- |
934 |
+-for i in 1 2 3 4 5 6 7 8 9 10 11 12 |
935 |
+-do |
936 |
+-if [ -h $inputfile ] ; then |
937 |
+-inputfile=`readlink $inputfile`; |
938 |
+-fi |
939 |
+-done |
940 |
+- |
941 |
+-filename=`${FSLDIR}/bin/remove_ext $inputfile`; |
942 |
+- |
943 |
+-if [ -r ${filename}.nii ] || [ -r ${filename}.nii.gz ] ; then |
944 |
+- echo "1"; |
945 |
+- exit; |
946 |
+-fi |
947 |
+- |
948 |
+-if [ -r ${filename}.mnc ] || [ -r ${filename}.mnc.gz ] ; then |
949 |
+- echo "1"; |
950 |
+- exit; |
951 |
+-fi |
952 |
+- |
953 |
+-if [ ! -r ${filename}.hdr ] && [ ! -r ${filename}.hdr.gz ] ; then |
954 |
+- # return 0 here as no header exists and no single image means no image! |
955 |
+- echo "0"; |
956 |
+- exit; |
957 |
+-fi |
958 |
+- |
959 |
+-if [ ! -r ${filename}.img ] && [ ! -r ${filename}.img.gz ] ; then |
960 |
+- # return 0 here as no img file exists and no single image means no image! |
961 |
+- echo "0"; |
962 |
+- exit; |
963 |
+-fi |
964 |
+- |
965 |
+-# only gets to here if there was a hdr and an img file |
966 |
+- |
967 |
+-echo "1"; |
968 |
+-exit; |
969 |
+- |
970 |
|
971 |
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 |
972 |
new file mode 100644 |
973 |
index 000000000..ddb7cfb67 |
974 |
--- /dev/null |
975 |
+++ b/sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p2.patch |
976 |
@@ -0,0 +1,348 @@ |
977 |
+diff -Naur fsl.orig/src/fslio/Makefile fsl/src/fslio/Makefile |
978 |
+--- fsl.orig/src/fslio/Makefile 2021-02-01 15:29:34.842752994 -0500 |
979 |
++++ fsl/src/fslio/Makefile 2021-02-01 15:32:19.723761859 -0500 |
980 |
+@@ -6,7 +6,7 @@ |
981 |
+ |
982 |
+ OBJS=fslio.o |
983 |
+ |
984 |
+-SCRIPTS = remove_ext fsloutputtype imtest imglob imcp imln imrm immv |
985 |
++SCRIPTS = fsloutputtype imglob imcp immv |
986 |
+ |
987 |
+ all: |
988 |
+ |
989 |
+diff -Naur fsl.orig/src/fslio/remove_ext fsl/src/fslio/remove_ext |
990 |
+--- fsl.orig/src/fslio/remove_ext 2021-02-01 15:29:34.842752994 -0500 |
991 |
++++ fsl/src/fslio/remove_ext 1969-12-31 19:00:00.000000000 -0500 |
992 |
+@@ -1,87 +0,0 @@ |
993 |
+-#!/bin/sh |
994 |
+- |
995 |
+-# remove_ext - remove extension from image filename |
996 |
+-# |
997 |
+-# Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group |
998 |
+-# |
999 |
+-# Copyright (C) 1999-2004 University of Oxford |
1000 |
+-# |
1001 |
+-# Part of FSL - FMRIB's Software Library |
1002 |
+-# http://www.fmrib.ox.ac.uk/fsl |
1003 |
+-# fsl@×××××××××××.uk |
1004 |
+-# |
1005 |
+-# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance |
1006 |
+-# Imaging of the Brain), Department of Clinical Neurology, Oxford |
1007 |
+-# University, Oxford, UK |
1008 |
+-# |
1009 |
+-# |
1010 |
+-# LICENCE |
1011 |
+-# |
1012 |
+-# FMRIB Software Library, Release 6.0 (c) 2018, The University of |
1013 |
+-# Oxford (the "Software") |
1014 |
+-# |
1015 |
+-# The Software remains the property of the Oxford University Innovation |
1016 |
+-# ("the University"). |
1017 |
+-# |
1018 |
+-# The Software is distributed "AS IS" under this Licence solely for |
1019 |
+-# non-commercial use in the hope that it will be useful, but in order |
1020 |
+-# that the University as a charitable foundation protects its assets for |
1021 |
+-# the benefit of its educational and research purposes, the University |
1022 |
+-# makes clear that no condition is made or to be implied, nor is any |
1023 |
+-# warranty given or to be implied, as to the accuracy of the Software, |
1024 |
+-# or that it will be suitable for any particular purpose or for use |
1025 |
+-# under any specific conditions. Furthermore, the University disclaims |
1026 |
+-# all responsibility for the use which is made of the Software. It |
1027 |
+-# further disclaims any liability for the outcomes arising from using |
1028 |
+-# the Software. |
1029 |
+-# |
1030 |
+-# The Licensee agrees to indemnify the University and hold the |
1031 |
+-# University harmless from and against any and all claims, damages and |
1032 |
+-# liabilities asserted by third parties (including claims for |
1033 |
+-# negligence) which arise directly or indirectly from the use of the |
1034 |
+-# Software or the sale of any products based on the Software. |
1035 |
+-# |
1036 |
+-# No part of the Software may be reproduced, modified, transmitted or |
1037 |
+-# transferred in any form or by any means, electronic or mechanical, |
1038 |
+-# without the express permission of the University. The permission of |
1039 |
+-# the University is not required if the said reproduction, modification, |
1040 |
+-# transmission or transference is done without financial return, the |
1041 |
+-# conditions of this Licence are imposed upon the receiver of the |
1042 |
+-# product, and all original and amended source code is included in any |
1043 |
+-# transmitted product. You may be held legally responsible for any |
1044 |
+-# copyright infringement that is caused or encouraged by your failure to |
1045 |
+-# abide by these terms and conditions. |
1046 |
+-# |
1047 |
+-# You are not permitted under this Licence to use this Software |
1048 |
+-# commercially. Use for which any financial return is received shall be |
1049 |
+-# defined as commercial use, and includes (1) integration of all or part |
1050 |
+-# of the source code or the Software into a product for sale or license |
1051 |
+-# by or on behalf of Licensee to third parties or (2) use of the |
1052 |
+-# Software or any derivative of it for research with the final aim of |
1053 |
+-# developing software products for sale or license to a third party or |
1054 |
+-# (3) use of the Software or any derivative of it for research with the |
1055 |
+-# final aim of developing non-software products for sale or license to a |
1056 |
+-# third party, or (4) use of the Software to provide any service to an |
1057 |
+-# external organisation for which payment is received. If you are |
1058 |
+-# interested in using the Software commercially, please contact Oxford |
1059 |
+-# University Innovation ("OUI"), the technology transfer company of the |
1060 |
+-# University, to negotiate a licence. Contact details are: |
1061 |
+-# fsl@××××××××××××××××.uk quoting Reference Project 9564, FSL. |
1062 |
+-export LC_ALL=C |
1063 |
+- |
1064 |
+- |
1065 |
+-if [ $# -lt 1 ] ; then |
1066 |
+- exit 1 |
1067 |
+-fi |
1068 |
+- |
1069 |
+-lst=""; |
1070 |
+-for fn in $@ ; do |
1071 |
+- # for the ones at the end of the line |
1072 |
+- 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/\.$//'`; |
1073 |
+- # for the ones in the middle of the line |
1074 |
+- 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'`; |
1075 |
+- lst="$lst $f"; |
1076 |
+-done |
1077 |
+-echo $lst; |
1078 |
+- |
1079 |
+- |
1080 |
+diff -Naur fsl.orig/src/misc_scripts/fsl_abspath fsl/src/misc_scripts/fsl_abspath |
1081 |
+--- fsl.orig/src/misc_scripts/fsl_abspath 2021-02-01 15:29:34.828752994 -0500 |
1082 |
++++ fsl/src/misc_scripts/fsl_abspath 1969-12-31 19:00:00.000000000 -0500 |
1083 |
+@@ -1,71 +0,0 @@ |
1084 |
+-#!/usr/bin/env fslpython |
1085 |
+-# fsl_abspath - return true file path |
1086 |
+-# Matthew Webster FMRIB Image Analysis Group |
1087 |
+-# Copyright (C) 2009 University of Oxford |
1088 |
+-# Part of FSL - FMRIB's Software Library |
1089 |
+-# http://www.fmrib.ox.ac.uk/fsl |
1090 |
+-# fsl@×××××××××××.uk |
1091 |
+-# |
1092 |
+-# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance |
1093 |
+-# Imaging of the Brain), Department of Clinical Neurology, Oxford |
1094 |
+-# University, Oxford, UK |
1095 |
+-# |
1096 |
+-# |
1097 |
+-# LICENCE |
1098 |
+-# |
1099 |
+-# FMRIB Software Library, Release 6.0 (c) 2018, The University of |
1100 |
+-# Oxford (the "Software") |
1101 |
+-# |
1102 |
+-# The Software remains the property of the Oxford University Innovation |
1103 |
+-# ("the University"). |
1104 |
+-# |
1105 |
+-# The Software is distributed "AS IS" under this Licence solely for |
1106 |
+-# non-commercial use in the hope that it will be useful, but in order |
1107 |
+-# that the University as a charitable foundation protects its assets for |
1108 |
+-# the benefit of its educational and research purposes, the University |
1109 |
+-# makes clear that no condition is made or to be implied, nor is any |
1110 |
+-# warranty given or to be implied, as to the accuracy of the Software, |
1111 |
+-# or that it will be suitable for any particular purpose or for use |
1112 |
+-# under any specific conditions. Furthermore, the University disclaims |
1113 |
+-# all responsibility for the use which is made of the Software. It |
1114 |
+-# further disclaims any liability for the outcomes arising from using |
1115 |
+-# the Software. |
1116 |
+-# |
1117 |
+-# The Licensee agrees to indemnify the University and hold the |
1118 |
+-# University harmless from and against any and all claims, damages and |
1119 |
+-# liabilities asserted by third parties (including claims for |
1120 |
+-# negligence) which arise directly or indirectly from the use of the |
1121 |
+-# Software or the sale of any products based on the Software. |
1122 |
+-# |
1123 |
+-# No part of the Software may be reproduced, modified, transmitted or |
1124 |
+-# transferred in any form or by any means, electronic or mechanical, |
1125 |
+-# without the express permission of the University. The permission of |
1126 |
+-# the University is not required if the said reproduction, modification, |
1127 |
+-# transmission or transference is done without financial return, the |
1128 |
+-# conditions of this Licence are imposed upon the receiver of the |
1129 |
+-# product, and all original and amended source code is included in any |
1130 |
+-# transmitted product. You may be held legally responsible for any |
1131 |
+-# copyright infringement that is caused or encouraged by your failure to |
1132 |
+-# abide by these terms and conditions. |
1133 |
+-# |
1134 |
+-# You are not permitted under this Licence to use this Software |
1135 |
+-# commercially. Use for which any financial return is received shall be |
1136 |
+-# defined as commercial use, and includes (1) integration of all or part |
1137 |
+-# of the source code or the Software into a product for sale or license |
1138 |
+-# by or on behalf of Licensee to third parties or (2) use of the |
1139 |
+-# Software or any derivative of it for research with the final aim of |
1140 |
+-# developing software products for sale or license to a third party or |
1141 |
+-# (3) use of the Software or any derivative of it for research with the |
1142 |
+-# final aim of developing non-software products for sale or license to a |
1143 |
+-# third party, or (4) use of the Software to provide any service to an |
1144 |
+-# external organisation for which payment is received. If you are |
1145 |
+-# interested in using the Software commercially, please contact Oxford |
1146 |
+-# University Innovation ("OUI"), the technology transfer company of the |
1147 |
+-# University, to negotiate a licence. Contact details are: |
1148 |
+-# fsl@××××××××××××××××.uk quoting Reference Project 9564, FSL. |
1149 |
+-from __future__ import print_function |
1150 |
+-import sys |
1151 |
+-import os |
1152 |
+- |
1153 |
+-print (os.path.realpath(sys.argv[1])) |
1154 |
+-sys.exit(0) |
1155 |
+diff -Naur fsl.orig/src/misc_scripts/Makefile fsl/src/misc_scripts/Makefile |
1156 |
+--- fsl.orig/src/misc_scripts/Makefile 2021-02-01 15:29:34.828752994 -0500 |
1157 |
++++ fsl/src/misc_scripts/Makefile 2021-02-01 15:32:56.027763811 -0500 |
1158 |
+@@ -2,6 +2,6 @@ |
1159 |
+ |
1160 |
+ PROJNAME = misc_scripts |
1161 |
+ |
1162 |
+-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 |
1163 |
++SCRIPTS = fslecho regscript remove_vols replace_and_average_fmrib linkbedpost ocmr_preproc correct_and_average eddy_correct AnatomicalAverage fsl_anat fslFixText |
1164 |
+ |
1165 |
+ all: |
1166 |
+diff -Naur fsl.orig/src/misc_scripts/Text2Vest fsl/src/misc_scripts/Text2Vest |
1167 |
+--- fsl.orig/src/misc_scripts/Text2Vest 2021-02-01 15:29:34.828752994 -0500 |
1168 |
++++ fsl/src/misc_scripts/Text2Vest 1969-12-31 19:00:00.000000000 -0500 |
1169 |
+@@ -1,80 +0,0 @@ |
1170 |
+-#!/bin/sh |
1171 |
+-# Copyright (C) 2012 University of Oxford |
1172 |
+-# |
1173 |
+-# Part of FSL - FMRIB's Software Library |
1174 |
+-# http://www.fmrib.ox.ac.uk/fsl |
1175 |
+-# fsl@×××××××××××.uk |
1176 |
+-# |
1177 |
+-# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance |
1178 |
+-# Imaging of the Brain), Department of Clinical Neurology, Oxford |
1179 |
+-# University, Oxford, UK |
1180 |
+-# |
1181 |
+-# |
1182 |
+-# LICENCE |
1183 |
+-# |
1184 |
+-# FMRIB Software Library, Release 6.0 (c) 2018, The University of |
1185 |
+-# Oxford (the "Software") |
1186 |
+-# |
1187 |
+-# The Software remains the property of the Oxford University Innovation |
1188 |
+-# ("the University"). |
1189 |
+-# |
1190 |
+-# The Software is distributed "AS IS" under this Licence solely for |
1191 |
+-# non-commercial use in the hope that it will be useful, but in order |
1192 |
+-# that the University as a charitable foundation protects its assets for |
1193 |
+-# the benefit of its educational and research purposes, the University |
1194 |
+-# makes clear that no condition is made or to be implied, nor is any |
1195 |
+-# warranty given or to be implied, as to the accuracy of the Software, |
1196 |
+-# or that it will be suitable for any particular purpose or for use |
1197 |
+-# under any specific conditions. Furthermore, the University disclaims |
1198 |
+-# all responsibility for the use which is made of the Software. It |
1199 |
+-# further disclaims any liability for the outcomes arising from using |
1200 |
+-# the Software. |
1201 |
+-# |
1202 |
+-# The Licensee agrees to indemnify the University and hold the |
1203 |
+-# University harmless from and against any and all claims, damages and |
1204 |
+-# liabilities asserted by third parties (including claims for |
1205 |
+-# negligence) which arise directly or indirectly from the use of the |
1206 |
+-# Software or the sale of any products based on the Software. |
1207 |
+-# |
1208 |
+-# No part of the Software may be reproduced, modified, transmitted or |
1209 |
+-# transferred in any form or by any means, electronic or mechanical, |
1210 |
+-# without the express permission of the University. The permission of |
1211 |
+-# the University is not required if the said reproduction, modification, |
1212 |
+-# transmission or transference is done without financial return, the |
1213 |
+-# conditions of this Licence are imposed upon the receiver of the |
1214 |
+-# product, and all original and amended source code is included in any |
1215 |
+-# transmitted product. You may be held legally responsible for any |
1216 |
+-# copyright infringement that is caused or encouraged by your failure to |
1217 |
+-# abide by these terms and conditions. |
1218 |
+-# |
1219 |
+-# You are not permitted under this Licence to use this Software |
1220 |
+-# commercially. Use for which any financial return is received shall be |
1221 |
+-# defined as commercial use, and includes (1) integration of all or part |
1222 |
+-# of the source code or the Software into a product for sale or license |
1223 |
+-# by or on behalf of Licensee to third parties or (2) use of the |
1224 |
+-# Software or any derivative of it for research with the final aim of |
1225 |
+-# developing software products for sale or license to a third party or |
1226 |
+-# (3) use of the Software or any derivative of it for research with the |
1227 |
+-# final aim of developing non-software products for sale or license to a |
1228 |
+-# third party, or (4) use of the Software to provide any service to an |
1229 |
+-# external organisation for which payment is received. If you are |
1230 |
+-# interested in using the Software commercially, please contact Oxford |
1231 |
+-# University Innovation ("OUI"), the technology transfer company of the |
1232 |
+-# University, to negotiate a licence. Contact details are: |
1233 |
+-# fsl@××××××××××××××××.uk quoting Reference Project 9564, FSL. |
1234 |
+-export LC_ALL=C |
1235 |
+-if [ $# -lt 2 ] ; then |
1236 |
+- echo "`basename $0` <text file> <vest file>" |
1237 |
+- exit 0 |
1238 |
+-fi |
1239 |
+- |
1240 |
+-NumPoints=`grep -cve '^\s*$' $1` |
1241 |
+-NumWaves=`wc $1 | awk '{ print $2 }'` |
1242 |
+-NumWaves=`expr $NumWaves / $NumPoints` |
1243 |
+- |
1244 |
+-echo /NumWaves $NumWaves > $2 |
1245 |
+-echo /NumPoints $NumPoints >> $2 |
1246 |
+-echo /Matrix >> $2 |
1247 |
+- |
1248 |
+-cat $1 >> $2 |
1249 |
+- |
1250 |
+diff -Naur fsl.orig/src/misc_scripts/Vest2Text fsl/src/misc_scripts/Vest2Text |
1251 |
+--- fsl.orig/src/misc_scripts/Vest2Text 2021-02-01 15:29:34.828752994 -0500 |
1252 |
++++ fsl/src/misc_scripts/Vest2Text 1969-12-31 19:00:00.000000000 -0500 |
1253 |
+@@ -1,71 +0,0 @@ |
1254 |
+-#!/bin/sh |
1255 |
+-# Copyright (C) 2012 University of Oxford |
1256 |
+-# |
1257 |
+-# Part of FSL - FMRIB's Software Library |
1258 |
+-# http://www.fmrib.ox.ac.uk/fsl |
1259 |
+-# fsl@×××××××××××.uk |
1260 |
+-# |
1261 |
+-# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance |
1262 |
+-# Imaging of the Brain), Department of Clinical Neurology, Oxford |
1263 |
+-# University, Oxford, UK |
1264 |
+-# |
1265 |
+-# |
1266 |
+-# LICENCE |
1267 |
+-# |
1268 |
+-# FMRIB Software Library, Release 6.0 (c) 2018, The University of |
1269 |
+-# Oxford (the "Software") |
1270 |
+-# |
1271 |
+-# The Software remains the property of the Oxford University Innovation |
1272 |
+-# ("the University"). |
1273 |
+-# |
1274 |
+-# The Software is distributed "AS IS" under this Licence solely for |
1275 |
+-# non-commercial use in the hope that it will be useful, but in order |
1276 |
+-# that the University as a charitable foundation protects its assets for |
1277 |
+-# the benefit of its educational and research purposes, the University |
1278 |
+-# makes clear that no condition is made or to be implied, nor is any |
1279 |
+-# warranty given or to be implied, as to the accuracy of the Software, |
1280 |
+-# or that it will be suitable for any particular purpose or for use |
1281 |
+-# under any specific conditions. Furthermore, the University disclaims |
1282 |
+-# all responsibility for the use which is made of the Software. It |
1283 |
+-# further disclaims any liability for the outcomes arising from using |
1284 |
+-# the Software. |
1285 |
+-# |
1286 |
+-# The Licensee agrees to indemnify the University and hold the |
1287 |
+-# University harmless from and against any and all claims, damages and |
1288 |
+-# liabilities asserted by third parties (including claims for |
1289 |
+-# negligence) which arise directly or indirectly from the use of the |
1290 |
+-# Software or the sale of any products based on the Software. |
1291 |
+-# |
1292 |
+-# No part of the Software may be reproduced, modified, transmitted or |
1293 |
+-# transferred in any form or by any means, electronic or mechanical, |
1294 |
+-# without the express permission of the University. The permission of |
1295 |
+-# the University is not required if the said reproduction, modification, |
1296 |
+-# transmission or transference is done without financial return, the |
1297 |
+-# conditions of this Licence are imposed upon the receiver of the |
1298 |
+-# product, and all original and amended source code is included in any |
1299 |
+-# transmitted product. You may be held legally responsible for any |
1300 |
+-# copyright infringement that is caused or encouraged by your failure to |
1301 |
+-# abide by these terms and conditions. |
1302 |
+-# |
1303 |
+-# You are not permitted under this Licence to use this Software |
1304 |
+-# commercially. Use for which any financial return is received shall be |
1305 |
+-# defined as commercial use, and includes (1) integration of all or part |
1306 |
+-# of the source code or the Software into a product for sale or license |
1307 |
+-# by or on behalf of Licensee to third parties or (2) use of the |
1308 |
+-# Software or any derivative of it for research with the final aim of |
1309 |
+-# developing software products for sale or license to a third party or |
1310 |
+-# (3) use of the Software or any derivative of it for research with the |
1311 |
+-# final aim of developing non-software products for sale or license to a |
1312 |
+-# third party, or (4) use of the Software to provide any service to an |
1313 |
+-# external organisation for which payment is received. If you are |
1314 |
+-# interested in using the Software commercially, please contact Oxford |
1315 |
+-# University Innovation ("OUI"), the technology transfer company of the |
1316 |
+-# University, to negotiate a licence. Contact details are: |
1317 |
+-# fsl@××××××××××××××××.uk quoting Reference Project 9564, FSL. |
1318 |
+-export LC_ALL=C |
1319 |
+-if [ $# -lt 2 ] ; then |
1320 |
+- echo "`basename $0` <vest file> <text file>" |
1321 |
+- exit 0 |
1322 |
+-fi |
1323 |
+-sed -e "/\//d" $1 | sed '/^$/d' > $2 |
1324 |
+- |
1325 |
|
1326 |
diff --git a/sci-biology/fsl/files/fsl-6.0.4-setup.patch b/sci-biology/fsl/files/fsl-6.0.4-setup.patch |
1327 |
new file mode 100644 |
1328 |
index 000000000..061e1a22a |
1329 |
--- /dev/null |
1330 |
+++ b/sci-biology/fsl/files/fsl-6.0.4-setup.patch |
1331 |
@@ -0,0 +1,174 @@ |
1332 |
+diff -Naur fsl.orig/build fsl/build |
1333 |
+--- fsl.orig/build 2020-12-02 15:29:12.180812558 -0500 |
1334 |
++++ fsl/build 2020-12-02 15:34:03.854821628 -0500 |
1335 |
+@@ -28,7 +28,6 @@ |
1336 |
+ # The build order for MASTERLIBS is very important, and should not be modified unless you know what |
1337 |
+ # you are doing. |
1338 |
+ MASTERLIBS=" |
1339 |
+- CiftiLib-master \ |
1340 |
+ utils \ |
1341 |
+ znzlib \ |
1342 |
+ NewNifti \ |
1343 |
+@@ -157,8 +156,8 @@ |
1344 |
+ done #project (MASTERPROJECTS) |
1345 |
+ fi #full build |
1346 |
+ |
1347 |
+-echo "Building projects - see build.log file for progress..." |
1348 |
+-./config/common/buildproj $PROJECTS > ./build.log 2>&1 |
1349 |
++echo "Building projects" |
1350 |
++./config/common/buildproj $PROJECTS |
1351 |
+ finalStatus=$? |
1352 |
+ if [ $finalStatus -eq 0 ]; then |
1353 |
+ echo "Build completed successfully."; |
1354 |
+diff -Naur fsl.orig/config/buildSettings.mk fsl/config/buildSettings.mk |
1355 |
+--- fsl.orig/config/buildSettings.mk 2020-12-02 15:29:11.993812552 -0500 |
1356 |
++++ fsl/config/buildSettings.mk 2020-12-02 15:39:37.269831995 -0500 |
1357 |
+@@ -18,7 +18,7 @@ |
1358 |
+ CHMOD = /bin/chmod |
1359 |
+ MKDIR = /bin/mkdir |
1360 |
+ INSTALL = install -p |
1361 |
+-TCLSH = ${FSLDIR}/bin/fsltclsh |
1362 |
++TCLSH = tclsh |
1363 |
+ DEPENDFLAGS = -MM |
1364 |
+ MACHDBGFLAGS = -g |
1365 |
+ ##################################################################### |
1366 |
+@@ -127,19 +127,19 @@ |
1367 |
+ ##################################################################### |
1368 |
+ ifeq ($(SYSTYPE), Linux) |
1369 |
+ ############### System Vars ##################################### |
1370 |
+-CC = gcc |
1371 |
+-CXX = c++ |
1372 |
+-CXX11 = c++ |
1373 |
++CC = @@GENTOO_CC@@ |
1374 |
++CXX = @@GENTOO_CXX@@ |
1375 |
++CXX11 = @@GENTOO_CXX@@ |
1376 |
+ CSTATICFLAGS = -static |
1377 |
+ CXXSTATICFLAGS = -static |
1378 |
+-ARCHFLAGS = -m64 |
1379 |
+-ARCHLDFLAGS = -Wl,-rpath,'$$ORIGIN/../lib' |
1380 |
++ARCHFLAGS = |
1381 |
++ARCHLDFLAGS = |
1382 |
+ PARALLELFLAGS = -fopenmp |
1383 |
+-OPTFLAGS = -g -O3 -fexpensive-optimizations ${ARCHFLAGS} |
1384 |
++OPTFLAGS = |
1385 |
+ GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long |
1386 |
+ SGI_ANSI_FLAGS = -ansi -fullwarn |
1387 |
+ ANSI_FLAGS = ${GNU_ANSI_FLAGS} |
1388 |
+-RANLIB = echo |
1389 |
++RANLIB = @@GENTOO_RANLIB@@ |
1390 |
+ FSLML = ${FSLDIR}/bin/fslml |
1391 |
+ # CUDA development environment |
1392 |
+ CUDAVER := $(or $(CUDAVER),9.1) |
1393 |
+@@ -158,8 +158,8 @@ |
1394 |
+ NVCC = ${CUDA_INSTALLATION}/bin/nvcc |
1395 |
+ ############### External Libs ##################################### |
1396 |
+ # ZLIB library |
1397 |
+-LIB_ZLIB = ${FSLEXTLIB} |
1398 |
+-INC_ZLIB = ${FSLEXTINC} |
1399 |
++#LIB_ZLIB = ${FSLEXTLIB} |
1400 |
++#INC_ZLIB = ${FSLEXTINC} |
1401 |
+ # QT library |
1402 |
+ QTDIR = /usr/lib/qt3 |
1403 |
+ LIB_QT = ${QTDIR}/lib |
1404 |
+diff -Naur fsl.orig/config/common/buildproj fsl/config/common/buildproj |
1405 |
+--- fsl.orig/config/common/buildproj 2020-12-02 15:29:11.993812552 -0500 |
1406 |
++++ fsl/config/common/buildproj 2020-12-02 15:41:25.579835363 -0500 |
1407 |
+@@ -11,10 +11,10 @@ |
1408 |
+ fi |
1409 |
+ PROJECTS="$@" ; export PROJECTS ; |
1410 |
+ |
1411 |
+-FSLDIR=`pwd` |
1412 |
++#FSLDIR=`pwd` |
1413 |
+ FSLDEVDIR=${FSLDIR} |
1414 |
+ FSLCONFDIR=${FSLDIR}/config |
1415 |
+-FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh` |
1416 |
++#FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh` |
1417 |
+ FSLMASTERBUILD=1 |
1418 |
+ export FSLDIR FSLDEVDIR FSLCONFDIR FSLMACHTYPE FSLMASTERBUILD |
1419 |
+ |
1420 |
+@@ -67,7 +67,7 @@ |
1421 |
+ if [ -x ./fslconfig ] ; then |
1422 |
+ . ./fslconfig ; |
1423 |
+ fi |
1424 |
+- if ${MAKE} -k ${MAKEOPTIONS} ; then |
1425 |
++ if ${MAKE} ${MAKEOPTIONS} ; then |
1426 |
+ if ${MAKE} ${MAKEOPTIONS} install ; then |
1427 |
+ installok=true; |
1428 |
+ # Clean up after ourselves |
1429 |
+@@ -82,6 +82,7 @@ |
1430 |
+ if [ $installok = false ] ; then |
1431 |
+ echo " " |
1432 |
+ echo "ERROR::Could not install $projname successfully" ; |
1433 |
++ exit 1 |
1434 |
+ fi |
1435 |
+ else |
1436 |
+ echo " " |
1437 |
+@@ -90,6 +91,7 @@ |
1438 |
+ echo " " |
1439 |
+ echo " " |
1440 |
+ errorprojs="$errorprojs $projname" ; export errorprojs ; |
1441 |
++ exit 1 |
1442 |
+ fi |
1443 |
+ fi |
1444 |
+ done |
1445 |
+diff -Naur fsl.orig/config/common/vars.mk fsl/config/common/vars.mk |
1446 |
+--- fsl.orig/config/common/vars.mk 2020-12-02 15:29:11.993812552 -0500 |
1447 |
++++ fsl/config/common/vars.mk 2020-12-02 15:43:00.602838318 -0500 |
1448 |
+@@ -24,15 +24,15 @@ |
1449 |
+ USRCFLAGS = |
1450 |
+ USRCXXFLAGS = |
1451 |
+ |
1452 |
+-LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR} |
1453 |
++LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR} ${USERLDFLAGS} |
1454 |
+ |
1455 |
+-AccumulatedIncFlags = -I${INC_BOOST} ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR} |
1456 |
++AccumulatedIncFlags = ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR} ${CPPFLAGS} |
1457 |
+ |
1458 |
+ CFLAGS = ${ANSI_FLAGS} ${ANSI_CFLAGS} ${DBGFLAGS} ${USEDCSTATICFLAGS} ${USRCFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \ |
1459 |
+- ${AccumulatedIncFlags} |
1460 |
++ ${AccumulatedIncFlags} ${USERCFLAGS} |
1461 |
+ |
1462 |
+-CXXFLAGS = ${ANSI_FLAGS} ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \ |
1463 |
+- ${AccumulatedIncFlags} |
1464 |
++CXXFLAGS = ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \ |
1465 |
++ ${AccumulatedIncFlags} ${USERCXXFLAGS} |
1466 |
+ |
1467 |
+ HFILES = *.h |
1468 |
+ AFILES = *.a |
1469 |
+diff -Naur fsl.orig/extras/build fsl/extras/build |
1470 |
+--- fsl.orig/extras/build 2020-12-02 15:29:12.404812565 -0500 |
1471 |
++++ fsl/extras/build 2020-12-02 15:44:06.906840380 -0500 |
1472 |
+@@ -96,16 +96,16 @@ |
1473 |
+ BUILDICONV=1 |
1474 |
+ fi |
1475 |
+ fi |
1476 |
+-PROJECTS="tcl tk" |
1477 |
++#PROJECTS="tcl tk" |
1478 |
+ if [ ${BUILDZLIB} -eq 1 ]; then |
1479 |
+ PROJECTS="${PROJECTS} zlib" |
1480 |
+ fi |
1481 |
+-PROJECTS="${PROJECTS} libpng" |
1482 |
++#PROJECTS="${PROJECTS} libpng" |
1483 |
+ if [ ${BUILDICONV} -eq 1 ]; then |
1484 |
+ PROJECTS="${PROJECTS} libiconv" |
1485 |
+ fi |
1486 |
+-PROJECTS="${PROJECTS} libgd libgdc libprob libcprob newmat cprob newran fftw" |
1487 |
+-PROJECTS="${PROJECTS} boost libxml2-2.9.2 libxmlpp libsqlite libnlopt ../include/armawrap/dummy_newmat" |
1488 |
++PROJECTS="${PROJECTS} libgdc libprob libcprob newmat cprob newran" |
1489 |
++PROJECTS="${PROJECTS} ../include/armawrap/dummy_newmat" |
1490 |
+ for projname in $PROJECTS; do |
1491 |
+ if [ -d $FSLESRCDIR/$projname ] ; then |
1492 |
+ buildIt $FSLESRCDIR $projname 1 |
1493 |
+diff -Naur fsl.orig/src/mist/Makefile fsl/src/mist/Makefile |
1494 |
+--- fsl.orig/src/mist/Makefile 2020-12-02 15:29:12.875812580 -0500 |
1495 |
++++ fsl/src/mist/Makefile 2020-12-02 15:45:09.805842335 -0500 |
1496 |
+@@ -52,6 +52,8 @@ |
1497 |
+ cp -r python/* ${DESTDIR}/python/mist |
1498 |
+ |
1499 |
+ clean: |
1500 |
+- rm -f ${OBJS} mist/mist.o mist/mist |
1501 |
++ rm -f ${OBJS} mist/mist.o mist/mist || echo "CLEAN could not locate some files scheduled for deletion." |
1502 |
++ |
1503 |
++ |
1504 |
+ |
1505 |
+ .PHONY: all clean installdata |
1506 |
|
1507 |
diff --git a/sci-biology/fsl/fsl-6.0.2-r1.ebuild b/sci-biology/fsl/fsl-6.0.2-r1.ebuild |
1508 |
index 71314a8f8..ae12098ec 100644 |
1509 |
--- a/sci-biology/fsl/fsl-6.0.2-r1.ebuild |
1510 |
+++ b/sci-biology/fsl/fsl-6.0.2-r1.ebuild |
1511 |
@@ -6,7 +6,7 @@ EAPI=7 |
1512 |
inherit cuda flag-o-matic toolchain-funcs prefix |
1513 |
|
1514 |
DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging data" |
1515 |
-HOMEPAGE="http://www.fmrib.ox.ac.uk/fsl" |
1516 |
+HOMEPAGE="https://www.fmrib.ox.ac.uk/fsl" |
1517 |
SRC_URI="https://fsl.fmrib.ox.ac.uk/fsldownloads/${P}-sources.tar.gz -> ${P}.tar.gz" |
1518 |
|
1519 |
LICENSE="FSL BSD-2 newmat" |
1520 |
@@ -16,7 +16,7 @@ IUSE="cuda" |
1521 |
|
1522 |
DEPEND=" |
1523 |
dev-libs/boost |
1524 |
- dev-python/fslpy |
1525 |
+ <dev-python/fslpy-3 |
1526 |
media-gfx/graphviz |
1527 |
media-libs/gd |
1528 |
media-libs/glu |
1529 |
|
1530 |
diff --git a/sci-biology/fsl/fsl-6.0.2.ebuild b/sci-biology/fsl/fsl-6.0.2.ebuild |
1531 |
index 8a7e0eebb..f490b6e7c 100644 |
1532 |
--- a/sci-biology/fsl/fsl-6.0.2.ebuild |
1533 |
+++ b/sci-biology/fsl/fsl-6.0.2.ebuild |
1534 |
@@ -1,4 +1,4 @@ |
1535 |
-# Copyright 1999-2020 Gentoo Authors |
1536 |
+# Copyright 1999-2021 Gentoo Authors |
1537 |
# Distributed under the terms of the GNU General Public License v2 |
1538 |
|
1539 |
EAPI=7 |
1540 |
@@ -6,7 +6,7 @@ EAPI=7 |
1541 |
inherit flag-o-matic toolchain-funcs prefix |
1542 |
|
1543 |
DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging data" |
1544 |
-HOMEPAGE="http://www.fmrib.ox.ac.uk/fsl" |
1545 |
+HOMEPAGE="https://www.fmrib.ox.ac.uk/fsl" |
1546 |
SRC_URI="https://fsl.fmrib.ox.ac.uk/fsldownloads/${P}-sources.tar.gz -> ${P}.tar.gz" |
1547 |
|
1548 |
LICENSE="FSL BSD-2 newmat" |
1549 |
@@ -16,7 +16,7 @@ IUSE="" |
1550 |
|
1551 |
DEPEND=" |
1552 |
dev-libs/boost |
1553 |
- dev-python/fslpy |
1554 |
+ <dev-python/fslpy-3 |
1555 |
media-gfx/graphviz |
1556 |
media-libs/gd |
1557 |
media-libs/glu |
1558 |
|
1559 |
diff --git a/sci-biology/fsl/fsl-6.0.2-r1.ebuild b/sci-biology/fsl/fsl-6.0.4.ebuild |
1560 |
similarity index 83% |
1561 |
copy from sci-biology/fsl/fsl-6.0.2-r1.ebuild |
1562 |
copy to sci-biology/fsl/fsl-6.0.4.ebuild |
1563 |
index 71314a8f8..e0feb82d9 100644 |
1564 |
--- a/sci-biology/fsl/fsl-6.0.2-r1.ebuild |
1565 |
+++ b/sci-biology/fsl/fsl-6.0.4.ebuild |
1566 |
@@ -6,7 +6,7 @@ EAPI=7 |
1567 |
inherit cuda flag-o-matic toolchain-funcs prefix |
1568 |
|
1569 |
DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging data" |
1570 |
-HOMEPAGE="http://www.fmrib.ox.ac.uk/fsl" |
1571 |
+HOMEPAGE="https://www.fmrib.ox.ac.uk/fsl" |
1572 |
SRC_URI="https://fsl.fmrib.ox.ac.uk/fsldownloads/${P}-sources.tar.gz -> ${P}.tar.gz" |
1573 |
|
1574 |
LICENSE="FSL BSD-2 newmat" |
1575 |
@@ -16,7 +16,7 @@ IUSE="cuda" |
1576 |
|
1577 |
DEPEND=" |
1578 |
dev-libs/boost |
1579 |
- dev-python/fslpy |
1580 |
+ >=dev-python/fslpy-3 |
1581 |
media-gfx/graphviz |
1582 |
media-libs/gd |
1583 |
media-libs/glu |
1584 |
@@ -42,8 +42,8 @@ S=${WORKDIR}/${PN} |
1585 |
UPSTREAM_FSLDIR="/usr/share/fsl" |
1586 |
|
1587 |
PATCHES=( |
1588 |
- "${FILESDIR}/${PN}"-6.0.2-gcc10_include.patch |
1589 |
- "${FILESDIR}/${PN}"-6.0.2-setup.patch |
1590 |
+ "${FILESDIR}/${P}"-gcc10_include.patch |
1591 |
+ "${FILESDIR}/${P}"-setup.patch |
1592 |
"${FILESDIR}/${PN}"-6.0.2-template.patch |
1593 |
"${FILESDIR}/${PN}"-6.0.2-no_xmlpp.patch |
1594 |
"${FILESDIR}/${PN}"-5.0.11-niftiio_var_fix.patch |
1595 |
@@ -51,8 +51,13 @@ PATCHES=( |
1596 |
"${FILESDIR}/${PN}"-5.0.11-fslsurface_parallel_make.patch |
1597 |
"${FILESDIR}/${PN}"-6.0.2-qstring_compat.patch |
1598 |
"${FILESDIR}/${PN}"-5.0.9-headers.patch |
1599 |
- "${FILESDIR}/${PN}"-6.0.2-fsldir_redux-p1.patch |
1600 |
- "${FILESDIR}/${PN}"-6.0.2-fsldir_redux-p2.patch |
1601 |
+ "${FILESDIR}/${P}"-fsldir_redux-p1.patch |
1602 |
+ "${FILESDIR}/${P}"-fsldir_redux-p2.patch |
1603 |
+ "${FILESDIR}/${P}"-flameo_std.patch |
1604 |
+ "${FILESDIR}/${P}"-melodic_std.patch |
1605 |
+ "${FILESDIR}/${P}"-remove_fslpy_collisions-p1.patch |
1606 |
+ "${FILESDIR}/${P}"-remove_fslpy_collisions-p2.patch |
1607 |
+ "${FILESDIR}/${P}"-fdt_cuda.patch |
1608 |
) |
1609 |
|
1610 |
src_prepare() { |
1611 |
@@ -67,8 +72,11 @@ src_prepare() { |
1612 |
eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX src/*) \ |
1613 |
etc/js/label-div.html |
1614 |
|
1615 |
- # Disable mist-clean the hard way for now. |
1616 |
- rm -rf src/mist-clean |
1617 |
+ # Disable mist the hard way for now. |
1618 |
+ rm -r src/mist || die |
1619 |
+ |
1620 |
+ # Disable ptx2 for now |
1621 |
+ rm -r src/ptx2 || die |
1622 |
|
1623 |
makefilelist=$(find src/ -name Makefile) |
1624 |
|
1625 |
@@ -111,7 +119,7 @@ src_prepare() { |
1626 |
sed -e "s:-lopenblas:-llapack -lblas:g" \ |
1627 |
-i $(grep -rlI lopenblas *) || die |
1628 |
|
1629 |
- # script wanting to have access to flsversion at buildtime |
1630 |
+ # script wanting to have access to fslversion at buildtime |
1631 |
sed -e "s:/etc/fslversion:${S}/etc/fslversion:g" \ |
1632 |
-i ${makefilelist} || die |
1633 |
|
1634 |
@@ -129,8 +137,8 @@ src_prepare() { |
1635 |
CUDA_INSTALLATION="/opt/cuda" |
1636 |
CUDAVER=`cuda_toolkit_version` |
1637 |
|
1638 |
- eapply "${FILESDIR}/${PN}-6.0.2-eddy_cuda.patch" |
1639 |
- eapply "${FILESDIR}/${PN}-6.0.2-cuda_buildsettings.patch" |
1640 |
+ eapply "${FILESDIR}/${P}-eddy_cuda.patch" |
1641 |
+ eapply "${FILESDIR}/${P}-cuda_buildsettings.patch" |
1642 |
|
1643 |
sed -i \ |
1644 |
-e "s:@@GENTOO_NVCC_FLAGS@@:${cuda_NVCC_flags}:" \ |
1645 |
@@ -145,8 +153,14 @@ src_compile() { |
1646 |
export FSLCONDIR=${WORKDIR}/${PN}/config |
1647 |
export FSLMACHTYPE=generic |
1648 |
|
1649 |
+ # define the default build system to match upstream official standard |
1650 |
+ # -> individual projects may overwrite the '-std=' flag |
1651 |
+ export ANSI_CFLAGS="-std=c99" |
1652 |
+ export ANSI_CXXFLAGS="-std=c++98" |
1653 |
+ |
1654 |
export USERLDFLAGS="${LDFLAGS}" |
1655 |
export USERCFLAGS="${CFLAGS}" |
1656 |
+ export USERCPPFLAGS="${CPPFLAGS}" |
1657 |
export USERCXXFLAGS="${CXXFLAGS}" |
1658 |
|
1659 |
export CIFTICFLAGS="$($(tc-getPKG_CONFIG) --cflags CiftiLib)" |