diff options
Diffstat (limited to 'sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p1.patch')
| -rw-r--r-- | sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p1.patch | 240 |
1 files changed, 0 insertions, 240 deletions
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; |