diff options
Diffstat (limited to 'sci-biology/fsl/files')
| -rw-r--r-- | sci-biology/fsl/files/fsl-6.0.2-cuda_buildsettings.patch | 12 | ||||
| -rw-r--r-- | sci-biology/fsl/files/fsl-6.0.2-eddy_cuda.patch | 21 | ||||
| -rw-r--r-- | sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p1.patch | 240 | ||||
| -rw-r--r-- | sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p2.patch | 255 | ||||
| -rw-r--r-- | sci-biology/fsl/files/fsl-6.0.2-gcc10_include.patch | 10 | ||||
| -rw-r--r-- | sci-biology/fsl/files/fsl-6.0.2-setup.patch | 198 |
6 files changed, 0 insertions, 736 deletions
diff --git a/sci-biology/fsl/files/fsl-6.0.2-cuda_buildsettings.patch b/sci-biology/fsl/files/fsl-6.0.2-cuda_buildsettings.patch deleted file mode 100644 index a3872acf0..000000000 --- a/sci-biology/fsl/files/fsl-6.0.2-cuda_buildsettings.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -Naur fsl.orig/config/buildSettings.mk fsl/config/buildSettings.mk ---- fsl.orig/config/buildSettings.mk 2020-07-23 15:43:42.277064365 -0400 -+++ fsl/config/buildSettings.mk 2020-07-23 15:45:17.705069496 -0400 -@@ -141,7 +141,7 @@ - # CUDA development environment - CUDAVER := $(or $(CUDAVER),9.1) - #$(info $$CUDAVER is [${CUDAVER}]) --CUDA_INSTALLATION = /opt/cuda-${CUDAVER} -+CUDA_INSTALLATION = /opt/cuda - GENCODE_FLAGS = $(shell ${FSLDIR}/config/common/supportedGencodes.sh ${CUDA_INSTALLATION}) - LIB_CUDA = ${CUDA_INSTALLATION}/lib64 - INC_CUDA = ${CUDA_INSTALLATION}/include diff --git a/sci-biology/fsl/files/fsl-6.0.2-eddy_cuda.patch b/sci-biology/fsl/files/fsl-6.0.2-eddy_cuda.patch deleted file mode 100644 index 40409ec08..000000000 --- a/sci-biology/fsl/files/fsl-6.0.2-eddy_cuda.patch +++ /dev/null @@ -1,21 +0,0 @@ -diff -Naur fsl.orig/src/eddy/Makefile fsl/src/eddy/Makefile ---- fsl.orig/src/eddy/Makefile 2020-07-30 14:30:06.414884410 -0400 -+++ fsl/src/eddy/Makefile 2020-07-30 14:33:03.400889914 -0400 -@@ -29,6 +29,8 @@ - TMPCXXFLAGS_2= - TMPNAME_1= - TMPNAME_2= -+cuda=1 -+cpu=1 - - ifndef cuda - ifndef cpu #Default single cpu, no threading -@@ -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 diff --git a/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p1.patch b/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p1.patch deleted file mode 100644 index ca3945442..000000000 --- a/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p1.patch +++ /dev/null @@ -1,240 +0,0 @@ -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; diff --git a/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p2.patch b/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p2.patch deleted file mode 100644 index 74bf19169..000000000 --- a/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p2.patch +++ /dev/null @@ -1,255 +0,0 @@ -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 --git a/src/siena/siena_diff.cc b/src/siena/siena_diff.cc -index e19193a..17d8701 100644 ---- a/src/siena/siena_diff.cc -+++ b/src/siena/siena_diff.cc -@@ -107,7 +107,7 @@ int main(int argc,char *argv[]) - { - // {{{ 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 @@ if (argc<3) - - string argv1(argv[1]), argv2(argv[2]); - --sprintf(fsldir,"%s",getenv("FSLDIR")); -- - for (i = 3; i < argc; i++) { - if (!strcmp(argv[i], "-i")) - ignore_z=1; -@@ -209,26 +207,26 @@ for (i = 3; i < argc; i++) { - // }}} - // {{{ 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); - } - -@@ -287,8 +285,8 @@ if(1) // always done unless the above uncommented and used instead of this test - 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 - diff --git a/sci-biology/fsl/files/fsl-6.0.2-gcc10_include.patch b/sci-biology/fsl/files/fsl-6.0.2-gcc10_include.patch deleted file mode 100644 index 9ddb11a2b..000000000 --- a/sci-biology/fsl/files/fsl-6.0.2-gcc10_include.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- a/src/newimage/newimageio.h 2020-06-18 06:05:51.287864975 -0400 -+++ b/src/newimage/newimageio.h 2020-06-18 06:06:27.535129711 -0400 -@@ -75,6 +75,7 @@ - #include <iostream> - #include <fstream> - #include <sstream> -+#include <stdexcept> - #include "NewNifti/NewNifti.h" - #include "newmatio.h" - #include "newimage.h" diff --git a/sci-biology/fsl/files/fsl-6.0.2-setup.patch b/sci-biology/fsl/files/fsl-6.0.2-setup.patch deleted file mode 100644 index 39737fd85..000000000 --- a/sci-biology/fsl/files/fsl-6.0.2-setup.patch +++ /dev/null @@ -1,198 +0,0 @@ -From baae97cc3c8d0cadcabb7ed16559f4e4de26ddbe Mon Sep 17 00:00:00 2001 -From: François Bissey <frp.bissey@gmail.com> -Date: Mon, 20 Jan 2020 11:54:37 +1300 -Subject: [PATCH] Adjust the build system so it doesnt build packages - externally provided by portage. Make the compilation flags more generic and - easily adjustable. Make the build system stop at the first fault. - ---- - build | 6 +++--- - config/buildSettings.mk | 20 ++++++++++---------- - config/common/buildproj | 8 +++++--- - config/common/vars.mk | 10 +++++----- - extras/build | 8 ++++---- - src/mist-clean/Makefile | 2 +- - 6 files changed, 28 insertions(+), 26 deletions(-) - -diff --git a/build b/build -index 05dac06c..d90e407b 100755 ---- a/build -+++ b/build -@@ -3,7 +3,7 @@ - if [ $# -ge 1 ] ; then - PROJECTS="$@"; - else -- MASTERPROJECTS="CiftiLib-master utils znzlib NewNifti niftiio fslio giftiio miscmaths newimage libhfunc libvis first_lib \ -+ MASTERPROJECTS="utils znzlib NewNifti niftiio fslio giftiio miscmaths newimage libhfunc libvis first_lib \ - meshclass fslvtkio misc_tcl basisfield warpfns bint shapeModel MVdisc fslvtkconv fslsurface libmeshutils newmesh \ - DiscreteOpt FastPDlib MSMRegLib misc_c dpm topup \ - asl_mfree \ -@@ -80,8 +80,8 @@ xtract"; - done - fi - --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 --git a/config/buildSettings.mk b/config/buildSettings.mk -index b2e1f150..04532fc2 100644 ---- a/config/buildSettings.mk -+++ b/config/buildSettings.mk -@@ -18,7 +18,7 @@ MV = /bin/mv - CHMOD = /bin/chmod - MKDIR = /bin/mkdir - INSTALL = install -p --TCLSH = ${FSLDIR}/bin/fsltclsh -+TCLSH = tclsh - DEPENDFLAGS = -MM - MACHDBGFLAGS = -g - ##################################################################### -@@ -124,19 +124,19 @@ endif # if Darwin - ##################################################################### - 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) -@@ -148,8 +148,8 @@ INC_CUDA = ${CUDA_INSTALLATION}/include - NVCC = ${CUDA_INSTALLATION}/bin/nvcc - ############### External Libs ##################################### - # ZLIB library --LIB_ZLIB = /lib64 --INC_ZLIB = /usr/include -+#LIB_ZLIB = /lib64 -+#INC_ZLIB = /usr/include - # QT library - QTDIR = /usr/lib/qt3 - LIB_QT = ${QTDIR}/lib -diff --git a/config/common/buildproj b/config/common/buildproj -index 2f0f2b8f..48624a1f 100755 ---- a/config/common/buildproj -+++ b/config/common/buildproj -@@ -11,10 +11,10 @@ if [ X$1 = X-strict ] ; then - fi - PROJECTS="$@" ; 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 @@ for projname in $PROJECTS; do - 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 @@ for projname in $PROJECTS; do - if [ $installok = false ] ; then - echo " " - echo "ERROR::Could not install $projname successfully" ; -+ exit 1 - fi - else - echo " " -@@ -90,6 +91,7 @@ for projname in $PROJECTS; do - echo " " - echo " " - errorprojs="$errorprojs $projname" ; export errorprojs ; -+ exit 1 - fi - fi - done -diff --git a/config/common/vars.mk b/config/common/vars.mk -index b027b010..aeeae67c 100755 ---- a/config/common/vars.mk -+++ b/config/common/vars.mk -@@ -24,15 +24,15 @@ USRINCFLAGS = - 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} ${USERCXXFLAGS} - - HFILES = *.h - AFILES = *.a -diff --git a/extras/build b/extras/build -index 59e7a2ed..0d68232e 100755 ---- a/extras/build -+++ b/extras/build -@@ -96,16 +96,16 @@ if [ X"${OS}" = "XDarwin" ]; then - 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 --git a/src/mist-clean/Makefile b/src/mist-clean/Makefile -index 20402cca..6918bee4 100755 ---- a/src/mist-clean/Makefile -+++ b/src/mist-clean/Makefile -@@ -52,6 +52,6 @@ installpython: - 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 --- -2.24.1 - |