sci-biology/fsl: add version 6.0.4

Closes: https://github.com/gentoo/sci/pull/1074
Co-authored-by: Paul Polak <paul.polak@med-image.info>
Package-Manager: Portage-3.0.20, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
master
Andrew Ammerlaan 1 year ago
parent 5c39cf0660
commit 1c4f022505
No known key found for this signature in database
GPG Key ID: A2E2304370447E8E
  1. 1
      sci-biology/fsl/Manifest
  2. 12
      sci-biology/fsl/files/fsl-6.0.4-cuda_buildsettings.patch
  3. 21
      sci-biology/fsl/files/fsl-6.0.4-eddy_cuda.patch
  4. 14
      sci-biology/fsl/files/fsl-6.0.4-fdt_cuda.patch
  5. 11
      sci-biology/fsl/files/fsl-6.0.4-flameo_std.patch
  6. 240
      sci-biology/fsl/files/fsl-6.0.4-fsldir_redux-p1.patch
  7. 254
      sci-biology/fsl/files/fsl-6.0.4-fsldir_redux-p2.patch
  8. 11
      sci-biology/fsl/files/fsl-6.0.4-gcc10_include.patch
  9. 11
      sci-biology/fsl/files/fsl-6.0.4-melodic_std.patch
  10. 303
      sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p1.patch
  11. 348
      sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p2.patch
  12. 174
      sci-biology/fsl/files/fsl-6.0.4-setup.patch
  13. 4
      sci-biology/fsl/fsl-6.0.2-r1.ebuild
  14. 6
      sci-biology/fsl/fsl-6.0.2.ebuild
  15. 217
      sci-biology/fsl/fsl-6.0.4.ebuild

@ -1 +1,2 @@
DIST fsl-6.0.2.tar.gz 2505331864 BLAKE2B 0fbc23c788e0960e41a895f8eddd346e8facfae448c637eca18d39b142f8aabd9531427ce4ff97c634fdc5d16a74163947c7bade219a8900722815321144b41e SHA512 fe308393076c51c50b086f9bf7ff5ddebcf8b1284128e734b9d9e501019917ceba7c0ee5cd5aa1ed44452bcd042ad72653c1a8693f94eab9b83a80fe508a56ca
DIST fsl-6.0.4.tar.gz 2507673220 BLAKE2B 21e7437f8a3fde03ec6711b8022ee203ae159c07b5a3b998f37db768205d3335ffe9b28ad05b859e6bde4916933ea58e4e188012f147648f00fd6e6253ce1a12 SHA512 c65edcf5728920752e6dceea440dc2b528d007b7e4f56390a3d7eed91b1014457544563f699cae77f62c44cdfbdfcc5031265a5fd619fe0ecb99cad5653080d3

@ -0,0 +1,12 @@
diff -Naur fsl.orig/config/buildSettings.mk fsl/config/buildSettings.mk
--- fsl.orig/config/buildSettings.mk 2020-12-02 16:22:57.999912865 -0500
+++ fsl/config/buildSettings.mk 2020-12-02 16:24:15.332915270 -0500
@@ -144,7 +144,7 @@
# CUDA development environment
CUDAVER := $(or $(CUDAVER),9.1)
#$(info $$CUDAVER is [${CUDAVER}])
-CUDA_INSTALLATION = /opt/cuda-${CUDAVER}
+CUDA_INSTALLATION = /opt/cuda
ifdef SINGULARITY_NAME
CUDA_INSTALLATION = /usr/local/cuda-${CUDAVER}
endif

@ -0,0 +1,21 @@
diff -Naur fsl.orig/src/eddy/Makefile fsl/src/eddy/Makefile
--- fsl.orig/src/eddy/Makefile 2020-12-02 16:07:47.327884548 -0500
+++ fsl/src/eddy/Makefile 2020-12-02 16:11:21.149891196 -0500
@@ -29,6 +29,8 @@
TMPCXXFLAGS_2=
TMPNAME_1=
TMPNAME_2=
+cuda=1
+cpu=1
TOPUP_DIR=../topup
ifndef cuda
@@ -74,7 +75,7 @@
ifdef NVCC11
NVCC=${NVCC11}
endif
-NVCCFLAGS=-c -DCOMPILE_GPU -O3 -m 64 -std=c++11
+NVCCFLAGS=-c -DCOMPILE_GPU -O3 -m 64 -std=c++11 @@GENTOO_NVCC_FLAGS@@
ifeq ($(CLOBBER_CLANG),1)
NVCCFLAGS+= -DCLOBBER_CLANG
endif

@ -0,0 +1,14 @@
diff -Naur fsl.orig/src/fdt/Makefile fsl/src/fdt/Makefile
--- fsl.orig/src/fdt/Makefile 2020-12-02 19:06:55.826218772 -0500
+++ fsl/src/fdt/Makefile 2020-12-02 19:08:02.883220858 -0500
@@ -6,7 +6,9 @@
$(eval $($(PROJNAME)_MASTERBUILD))
endif
-ifeq ($(COMPILE_GPU), 1)
+# disable CUDA support for fdt
+#ifeq ($(COMPILE_GPU), 1)
+ifeq (0, 1)
COMPILE_WITH_GPU=libbedpostx_cuda.so merge_parts_gpu xfibres_gpu CUDA/split_parts_gpu
SCRIPTS_GPU=CUDA/bedpostx_gpu CUDA/bedpostx_postproc_gpu.sh
endif

@ -0,0 +1,11 @@
diff -Naur fsl.orig/src/flameo/Makefile fsl/src/flameo/Makefile
--- fsl.orig/src/flameo/Makefile 2021-01-06 14:04:35.728274475 -0500
+++ fsl/src/flameo/Makefile 2021-01-06 14:08:18.204269285 -0500
@@ -4,6 +4,7 @@
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${FSLDIR}/include/ciftiio
USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_ZLIB}
+USRCXXFLAGS = -std=c++11
UNAME := $(shell uname)
ifeq (${UNAME},Darwin)

@ -0,0 +1,240 @@
From 2bc4be1f55b27a733e1e624b34bc570187ba95e1 Mon Sep 17 00:00:00 2001
From: François Bissey <frp.bissey@gmail.com>
Date: Mon, 20 Jan 2020 11:40:53 +1300
Subject: [PATCH] Making sure fsl code and executable can find other executable
and data in standard location.
---
src/fast4/fast_two.cc | 8 ++++----
src/feat5/feat_model.cc | 8 +++-----
src/feat5/tsplot.cc | 7 +++----
src/first/first_utils.cc | 4 ++--
src/fnirt/fnirtfns.cpp | 11 ++++-------
src/fslsurface/fslsurface_first.cc | 6 ++----
src/fslsurface/fslsurfacemaths.cpp | 12 ------------
src/libvis/miscpic.h | 7 +------
src/melodic/meldata.cc | 4 ++--
src/melodic/meloptions.cc | 8 --------
src/melodic/meloptions.h | 1 -
src/melodic/melreport.cc | 12 ++++++------
src/melodic/melreport.h | 20 ++++++++++----------
src/mm/mixture_model.cc | 4 ++--
src/siena/siena_diff.cc | 28 +++++++++++++---------------
src/topup/topupfns.cpp | 3 +--
16 files changed, 53 insertions(+), 90 deletions(-)
diff --git a/src/fast4/fast_two.cc b/src/fast4/fast_two.cc
index 592b5df..b525444 100644
--- a/src/fast4/fast_two.cc
+++ b/src/fast4/fast_two.cc
@@ -166,7 +166,7 @@ int prior_registration(string inname, string main_prior_vol, NEWIMAGE::volume<fl
string csfPriorName, grayPriorName, whitePriorName;
if(alternatePriors.unset())
{
- string priorRootName=string(getenv("FSLDIR")) + "/data/standard/tissuepriors/avg152T1_";
+ string priorRootName="@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/tissuepriors/avg152T1_";
csfPriorName = priorRootName+"csf";
grayPriorName = priorRootName+"gray";
whitePriorName = priorRootName+"white";
@@ -215,15 +215,15 @@ string csfPriorName, grayPriorName, whitePriorName;
if(bapused>0)
{
char reg[1024];
- 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());
+ 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());
if(verbose.value())
cout<<reg<<endl;
system(reg);
- 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());
+ 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());
if(verbose.value())
cout<<reg<<endl;
system(reg);
- 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());
+ 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());
if(verbose.value())
cout << reg << endl;
system(reg);
diff --git a/src/feat5/feat_model.cc b/src/feat5/feat_model.cc
index 399a13e..e15e43c 100644
--- a/src/feat5/feat_model.cc
+++ b/src/feat5/feat_model.cc
@@ -744,7 +744,7 @@ int main(int argc, char **argv)
vector<int> G;
vector<string> titles;
float tr, mult, trmult, nltffwhm=0, maxconvwin=0;
- char fl[10000], *FSLDIR;
+ char fl[10000];
string fn, filename;
FONT_DATA *font_data = new FONT_DATA[1];
@@ -763,8 +763,6 @@ int main(int argc, char **argv)
if (argc==3)
motionparams=remmean(read_ascii_matrix(argv[2]));
- FSLDIR=getenv("FSLDIR");
-
fn = string(argv[1])+".fsf";
level = atoi(find_line(fn, "fmri(level)", fl));
@@ -1510,7 +1508,7 @@ int main(int argc, char **argv)
writeCovarianceImage(string(argv[1])+"_cov.ppm", contrasts, F, nftests, realDesign, level, evs.eigenvals, font_data, contrasts.RE);
writeImagePreview(string(argv[1])+".ppm", contrasts, F, nftests, realDesign, level, evs, font_data, titles, tr, nltffwhm, nTimepoints, G);
- filename=string(getenv("FSLDIR"))+"/bin/wpng -q -overwrite "+string(argv[1])+".ppm ";
+ filename="wpng -q -overwrite "+string(argv[1])+".ppm ";
system(filename.c_str());
return(0);
@@ -2161,6 +2159,6 @@ char the_string[10000];
fclose(outputfile);
- filename=string(getenv("FSLDIR")) + "/bin/wpng -q -overwrite " + filename;
+ filename="wpng -q -overwrite " + filename;
system(filename.c_str());
}
diff --git a/src/feat5/tsplot.cc b/src/feat5/tsplot.cc
index ae191fd..3a02b55 100644
--- a/src/feat5/tsplot.cc
+++ b/src/feat5/tsplot.cc
@@ -293,7 +293,7 @@ int main(int argc, char **argv)
ofstream outputFile;
int numEVs, npts, numContrasts=1, nftests=0, GRPHSIZE(600), PSSIZE(600);
vector<double> normalisedContrasts, model, triggers;
- string fmriFileName, fslPath, featdir, vType, indexText;
+ string fmriFileName, featdir, vType, indexText;
ColumnVector NewimageVoxCoord(4),NiftiVoxCoord(4);
bool outputText(true), useCoordinate(false), prewhiten(false), useTriggers(false), customMask(false), modelFree(false), isHigherLevel(false), outputDataOnly(false);
bool zWeightClusters(true);
@@ -307,7 +307,6 @@ volume<float> immask;
if (argc<2) usage("");
featdir=string(argv[1]);
fmriFileName=featdir+"/filtered_func_data";
- fslPath=string(getenv("FSLDIR"));
string outputName(featdir);
@@ -753,7 +752,7 @@ volume4D<float> acs;
cerr << "Can't open output report file " << outputName << endl;
exit(1);
}
- 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;
+ 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;
if (useTriggers) outputFile << "\n<hr><b>Peristimulus plots</b><p>\n"<< peristimulusText <<"\n<HR></BODY></HTML>\n\n";
else outputFile << "\n</BODY></HTML>\n\n";
outputFile.close();
@@ -768,7 +767,7 @@ volume4D<float> acs;
cerr << "Can't open output report file " << outputName << endl;
exit(1);
}
- 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;
+ 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;
outputFile.close();
/* now output same thing without start and end, for inclusion in feat report */
diff --git a/src/first/first_utils.cc b/src/first/first_utils.cc
index 68be44b..85960f4 100644
--- a/src/first/first_utils.cc
+++ b/src/first/first_utils.cc
@@ -1954,8 +1954,8 @@ void do_work_bvars(){
if (!surfaceVAout.value()) {
// 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)
volume<float> refim;
- if (useReconMNI.value()) { read_volume(refim,string(getenv("FSLDIR")) + "/data/standard/MNI152_T1_1mm"); }
- else { read_volume(refim,string(getenv("FSLDIR")) + "/data/standard/MNI152_T1_1mm"); }
+ if (useReconMNI.value()) { read_volume(refim,"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); }
+ else { read_volume(refim,"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); }
volume<float> maskvol(refim);
maskvol=0.0f;
volume4D<float> volnormals;
diff --git a/src/fnirt/fnirtfns.cpp b/src/fnirt/fnirtfns.cpp
index 24e26fd..77899e7 100644
--- a/src/fnirt/fnirtfns.cpp
+++ b/src/fnirt/fnirtfns.cpp
@@ -1203,8 +1203,7 @@ string existing_ref_fname(const string& ref_fname)
return(string(ref_fname));
}
else {
- const char *fsldir_ptr = getenv("FSLDIR");
- string eref_fname = string(fsldir_ptr) + string("/data/standard/") + ref_fname;
+ string eref_fname = string("@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/") + ref_fname;
if (NEWIMAGE::FslFileExists(eref_fname)) return(eref_fname);
else return(string(""));
}
@@ -1230,9 +1229,8 @@ string existing_ref_fname(const string& ref_fname)
NEWIMAGE::read_volume_hdr_only(vref,ref_fname); // Throws if file dont exist
eref_fname = ref_fname;
}
- catch(...) { // Didn't exist in current directory, try in ${FSLDIR}/data/standard
- const char *fsldir_ptr = getenv("FSLDIR");
- eref_fname = string(fsldir_ptr) + string("/data/standard/") + ref_fname;
+ catch(...) { // Didn't exist in current directory, try in .../data/standard
+ eref_fname = string("@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/") + ref_fname;
try {
cout << "Could not find " << ref_fname << ", now checking " << eref_fname << endl;
NEWIMAGE::read_volume_hdr_only(vref,eref_fname); // Throws if file dont exist
@@ -1267,8 +1265,7 @@ string existing_conf_file(const string& cfname)
if (check_exist(ecfname)) return(ecfname);
}
if (!FNIRT::path(cfname).length()) { // If no path explicitly given
- const char *fsldir_ptr = getenv("FSLDIR");
- ecfname = string(fsldir_ptr) + string("/etc/flirtsch/") + cfname;
+ ecfname = string("@GENTOO_PORTAGE_EPREFIX@/etc/flirtsch/") + cfname;
if (check_exist(ecfname)) return(ecfname);
else if (!FNIRT::extension(ecfname).length()) { // If no path _and_ no extension given
ecfname += string(".cnf");
diff --git a/src/fslsurface/fslsurface_first.cc b/src/fslsurface/fslsurface_first.cc
index faec642..b2ef794 100644
--- a/src/fslsurface/fslsurface_first.cc
+++ b/src/fslsurface/fslsurface_first.cc
@@ -500,8 +500,7 @@ namespace fslsurface_name {
volume<float>* immni = new volume<float>();
- char* fsldir = getenv("FSLDIR");
- read_volume_hdr_only(*immni, string(fsldir) + "/data/standard/MNI152_T1_1mm");
+ read_volume_hdr_only(*immni, "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm");
//read_volume_hdr_only(*immni, template_name);
@@ -699,8 +698,7 @@ namespace fslsurface_name {
volume<float>* immni = new volume<float>();
- char* fsldir = getenv("FSLDIR");
- read_volume_hdr_only(*immni, string(fsldir) + "/data/standard/MNI152_T1_1mm");
+ read_volume_hdr_only(*immni, "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm");
//read_volume_hdr_only(*immni, template_name);
diff --git a/src/fslsurface/fslsurfacemaths.cpp b/src/fslsurface/fslsurfacemaths.cpp
index eaf55eb..3dc184d 100644
--- a/src/fslsurface/fslsurfacemaths.cpp
+++ b/src/fslsurface/fslsurfacemaths.cpp
@@ -598,12 +598,6 @@ int main (int argc, char * argv[])
}else if (command == "-reconFromBvars"){
cout<<"do recon "<<endl;
- char* fsldir = getenv("FSLDIR");
- if (fsldir == NULL)
- {
- cerr<<"FSLDIR has not been set. "<<endl;
- exit(EXIT_FAILURE);
- }
//file.bvars,mni_template.nii.gz
// string mni = string(fsldir)+"/data/standard/MNI152_T1_1mm";
reconSurface_from_bvars( surf, string(argv[i_arg+1]));
@@ -612,12 +606,6 @@ int main (int argc, char * argv[])
}else if (command == "-reconAllFromBvarsAndSave"){
cout<<"do recon+save "<<argc<<" "<<i_arg<<endl;
- char* fsldir = getenv("FSLDIR");
- if (fsldir == NULL)
- {
- cerr<<"FSLDIR has not been set. "<<endl;
- exit(EXIT_FAILURE);
- }
//file.bvars,mni_template.nii.gz
// string mni = string(fsldir)+"/data/standard/MNI152_T1_1mm";
cout<<"recon "<< string(argv[i_arg+1])<<endl;

@ -0,0 +1,254 @@
diff --git a/src/libvis/miscpic.h b/src/libvis/miscpic.h
index a2f3855..5f440f2 100644
--- a/src/libvis/miscpic.h
+++ b/src/libvis/miscpic.h
@@ -90,12 +90,7 @@ namespace MISCPIC{
markRight=false;
trans= -10;
edgethresh = 0.0;
- if(getenv("FSLDIR")!=0){
- lutbase = string(getenv("FSLDIR")) + "/etc/luts/";
- }
- else{
- lutbase = string("/");
- }
+ lutbase = "@GENTOO_PORTAGE_EPREFIX@/etc/luts/";
title = string("");
cbartype = string("");
cbarptr = NULL;
diff --git a/src/melodic/meldata.cc b/src/melodic/meldata.cc
index 1749a45..c4ad234 100644
--- a/src/melodic/meldata.cc
+++ b/src/melodic/meldata.cc
@@ -992,7 +992,7 @@ namespace Melodic{
void MelodicData::est_smoothness()
{
if(Resels == 0){
- string SM_path = opts.binpath + "smoothest";
+ string SM_path = "smoothest";
string Mask_fname = logger.appendDir("mask");
if(opts.segment.value().length()>0){
@@ -1157,7 +1157,7 @@ namespace Melodic{
// set up all strings
string BET_outputfname = string(Mean_fname)+"_brain";
- string BET_path = opts.binpath + "bet";
+ string BET_path = "bet";
string BET_optarg = "-m -f 0.4"; // see man bet
string Mask_fname = BET_outputfname+"_mask";
diff --git a/src/melodic/meloptions.cc b/src/melodic/meloptions.cc
index 08170c7..252e72b 100644
--- a/src/melodic/meloptions.cc
+++ b/src/melodic/meloptions.cc
@@ -93,14 +93,6 @@ MelodicOptions* MelodicOptions::gopt = NULL;
explicitnums = false;
logfname = string("log.txt");
- // work out the path to the $FSLDIR/bin directory
- if(getenv("FSLDIR")!=0){
- binpath = (string) getenv("FSLDIR") + "/bin/";
- } else{
- binpath = argv[0];
- binpath = binpath.substr(0,binpath.length()-7);
- }
-
// parse once to establish log directory name
for(int a = options.parse_command_line(argc, argv); a < argc; a++);
diff --git a/src/melodic/meloptions.h b/src/melodic/meloptions.h
index f546125..b964b7d 100644
--- a/src/melodic/meloptions.h
+++ b/src/melodic/meloptions.h
@@ -93,7 +93,6 @@ class MelodicOptions {
~MelodicOptions() { delete gopt; }
string version;
- string binpath;
string logfname;
bool filtermode;
bool explicitnums;
diff --git a/src/melodic/melreport.cc b/src/melodic/melreport.cc
index 141b6c2..2625059 100644
--- a/src/melodic/melreport.cc
+++ b/src/melodic/melreport.cc
@@ -84,8 +84,8 @@ namespace Melodic{
IChtml.setDir(report.getDir(),mmodel.get_prefix()+".html");
{//start IC page
- IChtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl
+ IChtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl
<< "<style type=\"text/css\">OBJECT { width: 100% }</style>"
<< "<TITLE>FSL</TITLE></HEAD>" << endl
<< "<IFRAME height=" << int(melodat.get_numfiles()/30 + 1)*50
@@ -486,8 +486,8 @@ namespace Melodic{
{//start IC2 page
IChtml2.setDir(report.getDir(),mmodel.get_prefix()+"_MM.html");
- IChtml2 << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl
+ IChtml2 << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl
<< "<style type=\"text/css\">OBJECT { width: 100% }</style>"
<< "<TITLE>FSL</TITLE></HEAD>" << endl
<< "<IFRAME height="<< int(melodat.get_numfiles()/30 + 1)*50
@@ -665,8 +665,8 @@ namespace Melodic{
IChtml << "<HTML> " << endl
<< "<TITLE>MELODIC Component " << num2str(cnum)
<< "</TITLE>" << endl
- << "<BODY BACKGROUND=\"file:" << getenv("FSLDIR")
- << "/doc/images/fsl-bg.jpg\">" << endl
+ << "<BODY BACKGROUND=\"file:"
+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl
<< "<hr><CENTER><H1>MELODIC Component " << num2str(cnum)
<< "</H1>"<< endl;
diff --git a/src/melodic/melreport.h b/src/melodic/melreport.h
index 574fc4c..e444681 100644
--- a/src/melodic/melreport.h
+++ b/src/melodic/melreport.h
@@ -104,21 +104,21 @@ namespace Melodic{
const time_t tmptime = time(NULL);
system(("mkdir "+ logger.appendDir("report") + " 2>/dev/null").c_str());
report.setDir(logger.appendDir("report"),"00index.html",true,false,ios::out);
- report << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
- (string) getenv("FSLDIR") +"/doc/fsl.css>"
+ report << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>"
<< "<TITLE>MELODIC report</TITLE></HEAD><BODY>"
<< endl <<endl;
loghtml.setDir(report.getDir(),"log.html");
- loghtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
- (string) getenv("FSLDIR") +"/doc/fsl.css>"
+ loghtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>"
<< "<TITLE>MELODIC report</TITLE></HEAD><BODY>"
<< endl <<endl;
navigator.setDir(report.getDir(),"nav.html");
head.setDir(report.getDir(),"head.html");
- navigator << "<link REL=stylesheet TYPE=text/css href=file:"+
- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl;
- head << "<link REL=stylesheet TYPE=text/css href=file:"+
- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl;
+ navigator << "<link REL=stylesheet TYPE=text/css href=file:"
+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl;
+ head << "<link REL=stylesheet TYPE=text/css href=file:"
+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl;
head <<"<TABLE BORDER=0><TR>" << endl
<<" <TD ALIGN=CENTER WIDTH=100%>"<< endl
<<"<TABLE BORDER=0>"<< endl
@@ -130,8 +130,8 @@ namespace Melodic{
<< "</tr></table>" << endl
<< "<TD ALIGN=RIGHT>" << endl
<< "<a href=http://www.fmrib.ox.ac.uk/fsl target=_top>" << endl
- << "<IMG BORDER=0 SRC=file:"<< getenv("FSLDIR")
- << "/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl
+ << "<IMG BORDER=0 SRC=file:"
+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl
<< "</TD>"<<endl<<"</TR></TABLE> <hr>"<<endl;
if(opts.guireport.value()==""){
report <<"<OBJECT data=head.html></OBJECT>" << endl;
diff --git a/src/mm/mixture_model.cc b/src/mm/mixture_model.cc
index b8e6167..5f00693 100644
--- a/src/mm/mixture_model.cc
+++ b/src/mm/mixture_model.cc
@@ -2224,8 +2224,8 @@ namespace Mm {
htmllog << "<HTML> " << endl
<< "<TITLE>Mixture Model fit for" << data_name << "</TITLE>" << endl
- << "<BODY BACKGROUND=\"file:" << getenv("FSLDIR")
- << "/doc/images/fsl-bg.jpg\">" << endl
+ << "<BODY BACKGROUND=\"file:"
+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl
<< "<hr><CENTER><H1>Mixture Model fit for<br>" << data_name << " </H1>"<< endl;
htmllog << "<hr><p>" << endl;
diff -Naur fsl.orig/src/siena/siena_diff.cc fsl/src/siena/siena_diff.cc
--- fsl.orig/src/siena/siena_diff.cc 2020-12-02 15:52:50.359856656 -0500
+++ fsl/src/siena/siena_diff.cc 2020-12-02 16:03:25.699876412 -0500
@@ -107,7 +107,7 @@
{
// {{{ vars
-char thestring[10000], segoptions[10000], fsldir[10000];
+char thestring[10000], segoptions[10000];
int x_size, y_size, z_size, size, x, y, z, i, count,
seg2=0, ignore_z=0, ignore_top_slices=0, //erode_mask=0,
ignore_bottom_slices=0, debug=0, flow_output=1, edge_masking=0;
@@ -124,8 +124,6 @@
string argv1(argv[1]), argv2(argv[2]);
-sprintf(fsldir,"%s",getenv("FSLDIR"));
-
for (i = 3; i < argc; i++)
{
if (!strcmp(argv[i], "-i"))
@@ -206,26 +204,26 @@
// }}}
// {{{ transform images and masks
-sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
+sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
+ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
printf("%s\n",thestring); system(thestring);
-sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
- fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
+sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
+ argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
printf("%s\n",thestring); system(thestring);
-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",
- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
+sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
+ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
printf("%s\n",thestring); system(thestring);
-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",
- fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
+sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
+ argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
printf("%s\n",thestring); system(thestring);
if (edge_masking)
{
- 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",
- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
+ 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",
+ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
printf("%s\n",thestring); system(thestring);
}
@@ -284,8 +282,8 @@
cout << "saving image 1 to disk prior to segmentation" << endl;
save_volume(in1,argv1+"_halfwayto_"+argv2+"_brain");
in1.destroy();
- sprintf(thestring,"%s/bin/fast %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1",
- fsldir,segtype,segoptions,argv[1],argv[2],argv[1],argv[2]);
+ sprintf(thestring,"fast %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1",
+ segtype,segoptions,argv[1],argv[2],argv[1],argv[2]);
cout << thestring << endl;
system(thestring);
}
diff --git a/src/topup/topupfns.cpp b/src/topup/topupfns.cpp
index 6873758..9e8b956 100644
--- a/src/topup/topupfns.cpp
+++ b/src/topup/topupfns.cpp
@@ -463,8 +463,7 @@ string existing_conf_file(const string& cfname)
if (TOPUP::check_exist(ecfname)) return(ecfname);
}
if (!TOPUP::path(cfname).length()) { // If no path explicitly given
- const char *fsldir_ptr = getenv("FSLDIR");
- ecfname = string(fsldir_ptr) + string("/etc/flirtsch/") + cfname;
+ ecfname = string("@GENTOO_PORTAGE_EPREFIX@/etc/flirtsch/") + cfname;
if (TOPUP::check_exist(ecfname)) return(ecfname);
else if (!TOPUP::extension(ecfname).length()) { // If no path _and_ no extension given
ecfname += string(".cnf");
--
2.24.1

@ -0,0 +1,11 @@
diff -Naur fsl.orig/src/newimage/newimageio.h fsl/src/newimage/newimageio.h
--- fsl.orig/src/newimage/newimageio.h 2020-12-02 15:15:27.012786899 -0500
+++ fsl/src/newimage/newimageio.h 2020-12-02 15:19:51.046795110 -0500
@@ -75,6 +75,7 @@
#include <iostream>
#include <fstream>
#include <sstream>
+#include <stdexcept>
#include "NewNifti/NewNifti.h"
#include "newmatio.h"
#include "newimage.h"

@ -0,0 +1,11 @@
diff -Naur fsl.orig/src/melodic/Makefile fsl/src/melodic/Makefile
--- fsl.orig/src/melodic/Makefile 2021-01-06 14:04:35.743274475 -0500
+++ fsl/src/melodic/Makefile 2021-01-06 14:11:27.924264859 -0500
@@ -9,6 +9,7 @@
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
USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_GD} -L${LIB_GDC} -L${LIB_PNG} -L${LIB_ZLIB}
+USRCXXFLAGS = -std=c++11
UNAME := $(shell uname)
ifeq (${UNAME},Darwin)

@ -0,0 +1,303 @@
diff -Naur fsl.orig/src/fslio/imln fsl/src/fslio/imln
--- fsl.orig/src/fslio/imln 2021-02-01 15:29:34.842752994 -0500
+++ fsl/src/fslio/imln 1969-12-31 19:00:00.000000000 -0500
@@ -1,90 +0,0 @@
-#!/bin/sh
-
-# imln - make symbolic link(s) to image file(s)
-#
-# Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group
-#
-# Copyright (C) 1999-2004 University of Oxford
-#
-# Part of FSL - FMRIB's Software Library
-# http://www.fmrib.ox.ac.uk/fsl
-# fsl@fmrib.ox.ac.uk
-#
-# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
-# Imaging of the Brain), Department of Clinical Neurology, Oxford
-# University, Oxford, UK
-#
-#
-# LICENCE
-#
-# FMRIB Software Library, Release 6.0 (c) 2018, The University of
-# Oxford (the "Software")
-#
-# The Software remains the property of the Oxford University Innovation
-# ("the University").
-#
-# The Software is distributed "AS IS" under this Licence solely for
-# non-commercial use in the hope that it will be useful, but in order
-# that the University as a charitable foundation protects its assets for
-# the benefit of its educational and research purposes, the University
-# makes clear that no condition is made or to be implied, nor is any
-# warranty given or to be implied, as to the accuracy of the Software,
-# or that it will be suitable for any particular purpose or for use
-# under any specific conditions. Furthermore, the University disclaims
-# all responsibility for the use which is made of the Software. It
-# further disclaims any liability for the outcomes arising from using
-# the Software.
-#
-# The Licensee agrees to indemnify the University and hold the
-# University harmless from and against any and all claims, damages and
-# liabilities asserted by third parties (including claims for
-# negligence) which arise directly or indirectly from the use of the
-# Software or the sale of any products based on the Software.
-#
-# No part of the Software may be reproduced, modified, transmitted or
-# transferred in any form or by any means, electronic or mechanical,
-# without the express permission of the University. The permission of
-# the University is not required if the said reproduction, modification,
-# transmission or transference is done without financial return, the
-# conditions of this Licence are imposed upon the receiver of the
-# product, and all original and amended source code is included in any
-# transmitted product. You may be held legally responsible for any
-# copyright infringement that is caused or encouraged by your failure to
-# abide by these terms and conditions.
-#
-# You are not permitted under this Licence to use this Software
-# commercially. Use for which any financial return is received shall be
-# defined as commercial use, and includes (1) integration of all or part
-# of the source code or the Software into a product for sale or license
-# by or on behalf of Licensee to third parties or (2) use of the
-# Software or any derivative of it for research with the final aim of
-# developing software products for sale or license to a third party or
-# (3) use of the Software or any derivative of it for research with the
-# final aim of developing non-software products for sale or license to a
-# third party, or (4) use of the Software to provide any service to an
-# external organisation for which payment is received. If you are
-# interested in using the Software commercially, please contact Oxford
-# University Innovation ("OUI"), the technology transfer company of the
-# University, to negotiate a licence. Contact details are:
-# fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.
-export LC_ALL=C
-
-if [ $# -lt 2 ] ; then
- echo "Usage: $0 <file1> <file2>"
- echo " Makes a link (called file2) to file1"
- echo " NB: filenames can be basenames or include an extension"
- exit 1;
-fi
-
-f1=`${FSLDIR}/bin/remove_ext $1`;
-f2=`${FSLDIR}/bin/remove_ext $2`;
-
-if [ -f ${f1}.hdr ] ; then ln -fs ${f1}.hdr ${f2}.hdr ; fi
-if [ -f ${f1}.hdr.gz ] ; then ln -fs ${f1}.hdr.gz ${f2}.hdr.gz ; fi
-if [ -f ${f1}.img ] ; then ln -fs ${f1}.img ${f2}.img ; fi
-if [ -f ${f1}.img.gz ] ; then ln -fs ${f1}.img.gz ${f2}.img.gz ; fi
-if [ -f ${f1}.nii ] ; then ln -fs ${f1}.nii ${f2}.nii ; fi
-if [ -f ${f1}.nii.gz ] ; then ln -fs ${f1}.nii.gz ${f2}.nii.gz ; fi
-if [ -f ${f1}.mnc ] ; then ln -fs ${f1}.mnc ${f2}.mnc ; fi
-if [ -f ${f1}.mnc.gz ] ; then ln -fs ${f1}.mnc.gz ${f2}.mnc.gz ; fi
-
diff -Naur fsl.orig/src/fslio/imrm fsl/src/fslio/imrm
--- fsl.orig/src/fslio/imrm 2021-02-01 15:29:34.842752994 -0500
+++ fsl/src/fslio/imrm 1969-12-31 19:00:00.000000000 -0500
@@ -1,83 +0,0 @@
-#!/bin/sh
-
-# imrm - remove image files
-#
-# Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group
-#
-# Copyright (C) 1999-2004 University of Oxford
-#
-# Part of FSL - FMRIB's Software Library
-# http://www.fmrib.ox.ac.uk/fsl
-# fsl@fmrib.ox.ac.uk
-#
-# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
-# Imaging of the Brain), Department of Clinical Neurology, Oxford
-# University, Oxford, UK
-#
-#
-# LICENCE
-#
-# FMRIB Software Library, Release 6.0 (c) 2018, The University of
-# Oxford (the "Software")
-#
-# The Software remains the property of the Oxford University Innovation
-# ("the University").
-#
-# The Software is distributed "AS IS" under this Licence solely for
-# non-commercial use in the hope that it will be useful, but in order
-# that the University as a charitable foundation protects its assets for
-# the benefit of its educational and research purposes, the University
-# makes clear that no condition is made or to be implied, nor is any
-# warranty given or to be implied, as to the accuracy of the Software,
-# or that it will be suitable for any particular purpose or for use
-# under any specific conditions. Furthermore, the University disclaims
-# all responsibility for the use which is made of the Software. It
-# further disclaims any liability for the outcomes arising from using
-# the Software.
-#
-# The Licensee agrees to indemnify the University and hold the
-# University harmless from and against any and all claims, damages and
-# liabilities asserted by third parties (including claims for
-# negligence) which arise directly or indirectly from the use of the
-# Software or the sale of any products based on the Software.
-#
-# No part of the Software may be reproduced, modified, transmitted or
-# transferred in any form or by any means, electronic or mechanical,
-# without the express permission of the University. The permission of
-# the University is not required if the said reproduction, modification,
-# transmission or transference is done without financial return, the
-# conditions of this Licence are imposed upon the receiver of the
-# product, and all original and amended source code is included in any
-# transmitted product. You may be held legally responsible for any
-# copyright infringement that is caused or encouraged by your failure to
-# abide by these terms and conditions.
-#
-# You are not permitted under this Licence to use this Software
-# commercially. Use for which any financial return is received shall be
-# defined as commercial use, and includes (1) integration of all or part
-# of the source code or the Software into a product for sale or license
-# by or on behalf of Licensee to third parties or (2) use of the
-# Software or any derivative of it for research with the final aim of
-# developing software products for sale or license to a third party or
-# (3) use of the Software or any derivative of it for research with the
-# final aim of developing non-software products for sale or license to a
-# third party, or (4) use of the Software to provide any service to an
-# external organisation for which payment is received. If you are
-# interested in using the Software commercially, please contact Oxford
-# University Innovation ("OUI"), the technology transfer company of the
-# University, to negotiate a licence. Contact details are:
-# fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.
-export LC_ALL=C
-
-if [ $# -lt 1 ] ; then
- echo "Usage: $0 <list of image names to remove>"
- echo "NB: filenames can be basenames or not"
- exit 1;
-fi
-
-for f in $@ ; do
- fn=`${FSLDIR}/bin/remove_ext $f`;
- # do the rm silently
- /bin/rm -f ${fn}.img ${fn}.hdr ${fn}.hdr.gz ${fn}.img.gz ${fn}.nii ${fn}.nii.gz ${fn}.mnc ${fn}.mnc.gz
-done
-
diff -Naur fsl.orig/src/fslio/imtest fsl/src/fslio/imtest
--- fsl.orig/src/fslio/imtest 2021-02-01 15:29:34.842752994 -0500
+++ fsl/src/fslio/imtest 1969-12-31 19:00:00.000000000 -0500
@@ -1,118 +0,0 @@
-#!/bin/sh
-
-# imtest - test to see if a valid image file exists with this name (root)
-#
-# Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group
-#
-# Copyright (C) 1999-2004 University of Oxford
-#
-# Part of FSL - FMRIB's Software Library
-# http://www.fmrib.ox.ac.uk/fsl
-# fsl@fmrib.ox.ac.uk
-#
-# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
-# Imaging of the Brain), Department of Clinical Neurology, Oxford
-# University, Oxford, UK
-#
-#
-# LICENCE
-#
-# FMRIB Software Library, Release 6.0 (c) 2018, The University of
-# Oxford (the "Software")
-#
-# The Software remains the property of the Oxford University Innovation
-# ("the University").
-#
-# The Software is distributed "AS IS" under this Licence solely for
-# non-commercial use in the hope that it will be useful, but in order
-# that the University as a charitable foundation protects its assets for
-# the benefit of its educational and research purposes, the University
-# makes clear that no condition is made or to be implied, nor is any
-# warranty given or to be implied, as to the accuracy of the Software,
-# or that it will be suitable for any particular purpose or for use
-# under any specific conditions. Furthermore, the University disclaims
-# all responsibility for the use which is made of the Software. It
-# further disclaims any liability for the outcomes arising from using
-# the Software.
-#
-# The Licensee agrees to indemnify the University and hold the
-# University harmless from and against any and all claims, damages and
-# liabilities asserted by third parties (including claims for
-# negligence) which arise directly or indirectly from the use of the
-# Software or the sale of any products based on the Software.
-#
-# No part of the Software may be reproduced, modified, transmitted or
-# transferred in any form or by any means, electronic or mechanical,
-# without the express permission of the University. The permission of
-# the University is not required if the said reproduction, modification,
-# transmission or transference is done without financial return, the
-# conditions of this Licence are imposed upon the receiver of the
-# product, and all original and amended source code is included in any
-# transmitted product. You may be held legally responsible for any
-# copyright infringement that is caused or encouraged by your failure to
-# abide by these terms and conditions.
-#
-# You are not permitted under this Licence to use this Software
-# commercially. Use for which any financial return is received shall be
-# defined as commercial use, and includes (1) integration of all or part
-# of the source code or the Software into a product for sale or license
-# by or on behalf of Licensee to third parties or (2) use of the
-# Software or any derivative of it for research with the final aim of
-# developing software products for sale or license to a third party or
-# (3) use of the Software or any derivative of it for research with the
-# final aim of developing non-software products for sale or license to a
-# third party, or (4) use of the Software to provide any service to an
-# external organisation for which payment is received. If you are
-# interested in using the Software commercially, please contact Oxford
-# University Innovation ("OUI"), the technology transfer company of the
-# University, to negotiate a licence. Contact details are:
-# fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.
-export LC_ALL=C
-
-# return 0 if no image exists or 1 if the image exists
-
-if [ $# -lt 1 ] ; then
- echo "0";
- exit;
-fi
-
-inputfile=$1
-
-
-
-for i in 1 2 3 4 5 6 7 8 9 10 11 12
-do
-if [ -h $inputfile ] ; then
-inputfile=`readlink $inputfile`;
-fi
-done
-
-filename=`${FSLDIR}/bin/remove_ext $inputfile`;
-
-if [ -r ${filename}.nii ] || [ -r ${filename}.nii.gz ] ; then
- echo "1";
- exit;
-fi
-
-if [ -r ${filename}.mnc ] || [ -r ${filename}.mnc.gz ] ; then
- echo "1";
- exit;
-fi
-
-if [ ! -r ${filename}.hdr ] && [ ! -r ${filename}.hdr.gz ] ; then
- # return 0 here as no header exists and no single image means no image!
- echo "0";
- exit;
-fi
-
-if [ ! -r ${filename}.img ] && [ ! -r ${filename}.img.gz ] ; then
- # return 0 here as no img file exists and no single image means no image!
- echo "0";
- exit;
-fi
-
-# only gets to here if there was a hdr and an img file
-
-echo "1";
-exit;
-

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

@ -0,0 +1,174 @@
diff -Naur fsl.orig/build fsl/build
--- fsl.orig/build 2020-12-02 15:29:12.180812558 -0500
+++ fsl/build 2020-12-02 15:34:03.854821628 -0500
@@ -28,7 +28,6 @@
# The build order for MASTERLIBS is very important, and should not be modified unless you know what
# you are doing.
MASTERLIBS="
- CiftiLib-master \
utils \
znzlib \
NewNifti \
@@ -157,8 +156,8 @@
done #project (MASTERPROJECTS)
fi #full build
-echo "Building projects - see build.log file for progress..."
-./config/common/buildproj $PROJECTS > ./build.log 2>&1
+echo "Building projects"
+./config/common/buildproj $PROJECTS
finalStatus=$?
if [ $finalStatus -eq 0 ]; then
echo "Build completed successfully.";
diff -Naur fsl.orig/config/buildSettings.mk fsl/config/buildSettings.mk
--- fsl.orig/config/buildSettings.mk 2020-12-02 15:29:11.993812552 -0500
+++ fsl/config/buildSettings.mk 2020-12-02 15:39:37.269831995 -0500
@@ -18,7 +18,7 @@
CHMOD = /bin/chmod
MKDIR = /bin/mkdir
INSTALL = install -p
-TCLSH = ${FSLDIR}/bin/fsltclsh
+TCLSH = tclsh
DEPENDFLAGS = -MM
MACHDBGFLAGS = -g
#####################################################################
@@ -127,19 +127,19 @@
#####################################################################
ifeq ($(SYSTYPE), Linux)
############### System Vars #####################################
-CC = gcc
-CXX = c++
-CXX11 = c++
+CC = @@GENTOO_CC@@
+CXX = @@GENTOO_CXX@@
+CXX11 = @@GENTOO_CXX@@
CSTATICFLAGS = -static
CXXSTATICFLAGS = -static
-ARCHFLAGS = -m64
-ARCHLDFLAGS = -Wl,-rpath,'$$ORIGIN/../lib'
+ARCHFLAGS =
+ARCHLDFLAGS =
PARALLELFLAGS = -fopenmp
-OPTFLAGS = -g -O3 -fexpensive-optimizations ${ARCHFLAGS}
+OPTFLAGS =
GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long
SGI_ANSI_FLAGS = -ansi -fullwarn
ANSI_FLAGS = ${GNU_ANSI_FLAGS}
-RANLIB = echo
+RANLIB = @@GENTOO_RANLIB@@
FSLML = ${FSLDIR}/bin/fslml
# CUDA development environment
CUDAVER := $(or $(CUDAVER),9.1)
@@ -158,8 +158,8 @@
NVCC = ${CUDA_INSTALLATION}/bin/nvcc
############### External Libs #####################################
# ZLIB library
-LIB_ZLIB = ${FSLEXTLIB}
-INC_ZLIB = ${FSLEXTINC}
+#LIB_ZLIB = ${FSLEXTLIB}
+#INC_ZLIB = ${FSLEXTINC}
# QT library
QTDIR = /usr/lib/qt3
LIB_QT = ${QTDIR}/lib
diff -Naur fsl.orig/config/common/buildproj fsl/config/common/buildproj
--- fsl.orig/config/common/buildproj 2020-12-02 15:29:11.993812552 -0500
+++ fsl/config/common/buildproj 2020-12-02 15:41:25.579835363 -0500
@@ -11,10 +11,10 @@
fi
PROJECTS="$@" ; export PROJECTS ;
-FSLDIR=`pwd`
+#FSLDIR=`pwd`
FSLDEVDIR=${FSLDIR}
FSLCONFDIR=${FSLDIR}/config
-FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh`
+#FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh`
FSLMASTERBUILD=1
export FSLDIR FSLDEVDIR FSLCONFDIR FSLMACHTYPE FSLMASTERBUILD
@@ -67,7 +67,7 @@
if [ -x ./fslconfig ] ; then
. ./fslconfig ;
fi
- if ${MAKE} -k ${MAKEOPTIONS} ; then
+ if ${MAKE} ${MAKEOPTIONS} ; then
if ${MAKE} ${MAKEOPTIONS} install ; then
installok=true;
# Clean up after ourselves
@@ -82,6 +82,7 @@
if [ $installok = false ] ; then
echo " "
echo "ERROR::Could not install $projname successfully" ;
+ exit 1
fi
else
echo " "
@@ -90,6 +91,7 @@
echo " "
echo " "
errorprojs="$errorprojs $projname" ; export errorprojs ;
+ exit 1
fi
fi
done
diff -Naur fsl.orig/config/common/vars.mk fsl/config/common/vars.mk
--- fsl.orig/config/common/vars.mk 2020-12-02 15:29:11.993812552 -0500
+++ fsl/config/common/vars.mk 2020-12-02 15:43:00.602838318 -0500
@@ -24,15 +24,15 @@
USRCFLAGS =
USRCXXFLAGS =
-LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR}
+LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR} ${USERLDFLAGS}
-AccumulatedIncFlags = -I${INC_BOOST} ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR}
+AccumulatedIncFlags = ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR} ${CPPFLAGS}
CFLAGS = ${ANSI_FLAGS} ${ANSI_CFLAGS} ${DBGFLAGS} ${USEDCSTATICFLAGS} ${USRCFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \
- ${AccumulatedIncFlags}
+ ${AccumulatedIncFlags} ${USERCFLAGS}
-CXXFLAGS = ${ANSI_FLAGS} ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \
- ${AccumulatedIncFlags}
+CXXFLAGS = ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \
+ ${AccumulatedIncFlags} ${USERCXXFLAGS}
HFILES = *.h
AFILES = *.a
diff -Naur fsl.orig/extras/build fsl/extras/build
--- fsl.orig/extras/build 2020-12-02 15:29:12.404812565 -0500
+++ fsl/extras/build 2020-12-02 15:44:06.906840380 -0500
@@ -96,16 +96,16 @@
BUILDICONV=1
fi
fi
-PROJECTS="tcl tk"
+#PROJECTS="tcl tk"
if [ ${BUILDZLIB} -eq 1 ]; then
PROJECTS="${PROJECTS} zlib"
fi
-PROJECTS="${PROJECTS} libpng"
+#PROJECTS="${PROJECTS} libpng"
if [ ${BUILDICONV} -eq 1 ]; then
PROJECTS="${PROJECTS} libiconv"
fi
-PROJECTS="${PROJECTS} libgd libgdc libprob libcprob newmat cprob newran fftw"
-PROJECTS="${PROJECTS} boost libxml2-2.9.2 libxmlpp libsqlite libnlopt ../include/armawrap/dummy_newmat"
+PROJECTS="${PROJECTS} libgdc libprob libcprob newmat cprob newran"
+PROJECTS="${PROJECTS} ../include/armawrap/dummy_newmat"
for projname in $PROJECTS; do
if [ -d $FSLESRCDIR/$projname ] ; then
buildIt $FSLESRCDIR $projname 1
diff -Naur fsl.orig/src/mist/Makefile fsl/src/mist/Makefile
--- fsl.orig/src/mist/Makefile 2020-12-02 15:29:12.875812580 -0500
+++ fsl/src/mist/Makefile 2020-12-02 15:45:09.805842335 -0500
@@ -52,6 +52,8 @@
cp -r python/* ${DESTDIR}/python/mist
clean:
- rm -f ${OBJS} mist/mist.o mist/mist
+ rm -f ${OBJS} mist/mist.o mist/mist || echo "CLEAN could not locate some files scheduled for deletion."
+
+
.PHONY: all clean installdata

@ -6,7 +6,7 @@ EAPI=7
inherit cuda flag-o-matic toolchain-funcs prefix
DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging data"
HOMEPAGE="http://www.fmrib.ox.ac.uk/fsl"
HOMEPAGE="https://www.fmrib.ox.ac.uk/fsl"
SRC_URI="https://fsl.fmrib.ox.ac.uk/fsldownloads/${P}-sources.tar.gz -> ${P}.tar.gz"
LICENSE="FSL BSD-2 newmat"
@ -16,7 +16,7 @@ IUSE="cuda"
DEPEND="
dev-libs/boost
dev-python/fslpy
<dev-python/fslpy-3
media-gfx/graphviz
media-libs/gd
media-libs/glu

@ -1,4 +1,4 @@
# Copyright 1999-2020 Gentoo Authors
# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@ -6,7 +6,7 @@ EAPI=7
inherit flag-o-matic toolchain-funcs prefix
DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging data"
HOMEPAGE="http://www.fmrib.ox.ac.uk/fsl"
HOMEPAGE="https://www.fmrib.ox.ac.uk/fsl"
SRC_URI="https://fsl.fmrib.ox.ac.uk/fsldownloads/${P}-sources.tar.gz -> ${P}.tar.gz"
LICENSE="FSL BSD-2 newmat"
@ -16,7 +16,7 @@ IUSE=""
DEPEND="
dev-libs/boost
dev-python/fslpy
<dev-python/fslpy-3
media-gfx/graphviz
media-libs/gd
media-libs/glu

@ -0,0 +1,217 @@
# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
inherit cuda flag-o-matic toolchain-funcs prefix
DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging data"
HOMEPAGE="https://www.fmrib.ox.ac.uk/fsl"
SRC_URI="https://fsl.fmrib.ox.ac.uk/fsldownloads/${P}-sources.tar.gz -> ${P}.tar.gz"
LICENSE="FSL BSD-2 newmat"
SLOT="0"
KEYWORDS="~amd64"
IUSE="cuda"
DEPEND="
dev-libs/boost
>=dev-python/fslpy-3
media-gfx/graphviz
media-libs/gd
media-libs/glu
media-libs/libpng:0=
sci-libs/ciftilib
sci-libs/nlopt
sys-libs/zlib
dev-lang/tcl:0=
dev-lang/tk:0=
>=virtual/lapack-3.8
>=virtual/blas-3.8
cuda? (
|| (
( =dev-util/nvidia-cuda-toolkit-10* =sys-devel/gcc-8*:* )
( =dev-util/nvidia-cuda-toolkit-11* =sys-devel/gcc-9*:* )
)
)
"
RDEPEND="${DEPEND}"
S=${WORKDIR}/${PN}
UPSTREAM_FSLDIR="/usr/share/fsl"
PATCHES=(
"${FILESDIR}/${P}"-gcc10_include.patch
"${FILESDIR}/${P}"-setup.patch
"${FILESDIR}/${PN}"-6.0.2-template.patch
"${FILESDIR}/${PN}"-6.0.2-no_xmlpp.patch
"${FILESDIR}/${PN}"-5.0.11-niftiio_var_fix.patch
"${FILESDIR}/${PN}"-5.0.11-ifstream_use.patch
"${FILESDIR}/${PN}"-5.0.11-fslsurface_parallel_make.patch
"${FILESDIR}/${PN}"-6.0.2-qstring_compat.patch
"${FILESDIR}/${PN}"-5.0.9-headers.patch
"${FILESDIR}/${P}"-fsldir_redux-p1.patch
"${FILESDIR}/${P}"-fsldir_redux-p2.patch
"${FILESDIR}/${P}"-flameo_std.patch
"${FILESDIR}/${P}"-melodic_std.patch
"${FILESDIR}/${P}"-remove_fslpy_collisions-p1.patch
"${FILESDIR}/${P}"-remove_fslpy_collisions-p2.patch
"${FILESDIR}/${P}"-fdt_cuda.patch
)
src_prepare() {
default
sed -i \
-e "s:@@GENTOO_RANLIB@@:$(tc-getRANLIB):" \
-e "s:@@GENTOO_CC@@:$(tc-getCC):" \
-e "s:@@GENTOO_CXX@@:$(tc-getCXX):" \
config/buildSettings.mk || die
eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX src/*) \
etc/js/label-div.html
# Disable mist the hard way for now.
rm -r src/mist || die
# Disable ptx2 for now
rm -r src/ptx2 || die
makefilelist=$(find src/ -name Makefile)
sed -i \
-e "s:-I\${INC_BOOST}::" \
-e "s:-I\${INC_ZLIB}::" \
-e "s:-I\${INC_GD}::" \
-e "s:-I\${INC_PNG}::" \
-e "s:-L\${LIB_GD}::" \
-e "s:-L\${LIB_PNG}::" \