commit: c936a53ac9ac5f4e923326f9dfbfac3739b2dde2 Author: Horea Christian <h.chr <AT> mail <DOT> ru> AuthorDate: Thu Apr 9 02:07:29 2015 +0000 Commit: Francois Bissey <f.r.bissey <AT> massey <DOT> ac <DOT> nz> CommitDate: Thu Apr 9 02:07:29 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c936a53a
removed 5.0.4 redux patch Package-Manager: portage-2.2.18 sci-biology/fsl/ChangeLog | 3 + sci-biology/fsl/files/fsl-5.0.4-fsldir_redux.patch | 467 --------------------- 2 files changed, 3 insertions(+), 467 deletions(-) diff --git a/sci-biology/fsl/ChangeLog b/sci-biology/fsl/ChangeLog index e509710..f97b5da 100644 --- a/sci-biology/fsl/ChangeLog +++ b/sci-biology/fsl/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 09 Apr 2015; <[email protected]> -files/fsl-5.0.4-fsldir_redux.patch: + removed 5.0.4 redux patch + 07 Apr 2015; <[email protected]> -fsl-5.0.4.ebuild, -fsl-5.0.5.ebuild: removed ebuilds with unavailable sources diff --git a/sci-biology/fsl/files/fsl-5.0.4-fsldir_redux.patch b/sci-biology/fsl/files/fsl-5.0.4-fsldir_redux.patch deleted file mode 100644 index 06f6445..0000000 --- a/sci-biology/fsl/files/fsl-5.0.4-fsldir_redux.patch +++ /dev/null @@ -1,467 +0,0 @@ ---- src/fast4/fast_two.cc.orig 2013-10-19 23:45:02.636971888 +1300 -+++ src/fast4/fast_two.cc 2013-10-19 23:46:45.436138299 +1300 -@@ -166,7 +166,7 @@ - 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 @@ - 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); ---- src/feat5/tsplot.cc.orig 2013-10-19 23:48:08.997273362 +1300 -+++ src/feat5/tsplot.cc 2013-10-19 23:50:59.376548902 +1300 -@@ -293,7 +293,7 @@ - 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 @@ - if (argc<2) usage(""); - featdir=string(argv[1]); - fmriFileName=featdir+"/filtered_func_data"; -- fslPath=string(getenv("FSLDIR")); - - string outputName(featdir); - -@@ -725,7 +724,7 @@ - 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(); -@@ -740,7 +739,7 @@ - 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 */ ---- src/feat5/feat_model.cc.orig 2013-10-19 23:52:13.456668655 +1300 -+++ src/feat5/feat_model.cc 2013-10-19 23:53:31.655795065 +1300 -@@ -734,7 +734,6 @@ - vector<int> G; - vector<string> titles; - float tr, mult, trmult, nltffwhm=0, maxconvwin=0; -- char fl[10000], *FSLDIR; - string fn, filename; - FONT_DATA *font_data = new FONT_DATA[1]; - -@@ -753,8 +752,6 @@ - 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)); -@@ -1479,7 +1476,7 @@ - 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); -@@ -2122,6 +2119,6 @@ - - fclose(outputfile); - -- filename=string(getenv("FSLDIR")) + "/bin/wpng -q -overwrite " + filename; -+ filename="wpng -q -overwrite " + filename; - system(filename.c_str()); - } ---- src/first/first_utils.cc.orig 2013-10-19 23:54:30.375890034 +1300 -+++ src/first/first_utils.cc 2013-10-19 23:59:11.706344887 +1300 -@@ -1954,8 +1954,8 @@ - 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; ---- src/fnirt/fnirtfns.cpp.orig 2013-10-20 00:00:18.106452166 +1300 -+++ src/fnirt/fnirtfns.cpp 2013-10-20 00:04:56.005901533 +1300 -@@ -1203,8 +1203,7 @@ - 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::fsl_imageexists(eref_fname)) return(eref_fname); - else return(string("")); - } -@@ -1230,9 +1229,8 @@ - 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 @@ - 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"); ---- src/fslsurface/fslsurface_first.cc.orig 2013-10-20 00:05:35.495965454 +1300 -+++ src/fslsurface/fslsurface_first.cc 2013-10-20 00:06:54.346092913 +1300 -@@ -500,8 +500,7 @@ - - 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 @@ - - 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); - ---- src/fslsurface/fslsurfacemaths.cpp.orig 2013-10-20 00:07:39.457165850 +1300 -+++ src/fslsurface/fslsurfacemaths.cpp 2013-10-20 00:09:28.396341998 +1300 -@@ -598,12 +598,6 @@ - - }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 @@ - - }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; ---- src/libvis/miscpic.h.orig 2013-10-20 00:11:03.706496109 +1300 -+++ src/libvis/miscpic.h 2013-10-20 00:12:24.515626764 +1300 -@@ -89,12 +89,7 @@ - LR_label_flag = true; - 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; ---- src/melodic/melreport.cc.orig 2013-10-20 00:13:01.475686492 +1300 -+++ src/melodic/melreport.cc 2013-10-20 00:15:02.795882687 +1300 -@@ -85,7 +85,7 @@ - - {//start IC page - IChtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" + -- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl -+ "@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 -@@ -488,7 +488,7 @@ - {//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 -+ "@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 -@@ -666,8 +666,8 @@ - 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; - ---- src/melodic/meloptions.cc.orig 2013-10-20 00:15:46.755953769 +1300 -+++ src/melodic/meloptions.cc 2013-10-20 00:18:26.176211442 +1300 -@@ -93,14 +93,6 @@ - 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++); - ---- src/melodic/meloptions.h.orig 2013-10-20 00:19:32.176318206 +1300 -+++ src/melodic/meloptions.h 2013-10-20 00:19:53.455352701 +1300 -@@ -93,7 +93,6 @@ - ~MelodicOptions() { delete gopt; } - - string version; -- string binpath; - string logfname; - bool filtermode; - bool explicitnums; ---- src/melodic/meldata.cc.orig 2013-10-20 00:20:45.856437466 +1300 -+++ src/melodic/meldata.cc 2013-10-20 00:21:48.655538924 +1300 -@@ -921,7 +921,7 @@ - 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){ -@@ -1086,7 +1086,7 @@ - // 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"; - ---- src/melodic/melreport.h.orig 2013-10-20 00:22:41.816624872 +1300 -+++ src/melodic/melreport.h 2013-10-20 00:24:25.555792499 +1300 -@@ -105,20 +105,20 @@ - 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>" -+ "@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>" -+ "@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; -+ "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl; - head << "<link REL=stylesheet TYPE=text/css href=file:"+ -- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl; -+ "@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 @@ - << "</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; ---- src/mm/mixture_model.cc.orig 2013-10-20 00:25:00.355848878 +1300 -+++ src/mm/mixture_model.cc 2013-10-20 00:25:32.185900186 +1300 -@@ -2224,8 +2224,8 @@ - - 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; ---- src/siena/siena_diff.cc.orig 2013-10-20 00:26:13.215966685 +1300 -+++ src/siena/siena_diff.cc 2013-10-20 00:28:03.925145734 +1300 -@@ -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")) - ignore_z=1; -@@ -209,26 +207,26 @@ - // }}} - // {{{ 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); - } - -@@ -287,8 +285,8 @@ - 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); - } ---- src/topup/topupfns.cpp.orig 2013-10-20 00:28:36.456198320 +1300 -+++ src/topup/topupfns.cpp 2013-10-20 00:29:37.905297565 +1300 -@@ -463,8 +463,7 @@ - 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"); ---- etc/matlab/call_fsl.m.orig 2013-10-20 23:17:58.626045346 +1300 -+++ etc/matlab/call_fsl.m 2013-10-20 23:20:06.556252150 +1300 -@@ -8,7 +8,7 @@ - % Debian/Ubuntu users should uncomment as - % indicated - --fsldir=getenv('FSLDIR'); -+%fsldir=getenv('FSLDIR'); - - % Debian/Ubuntu - uncomment the following - %fsllibdir=sprintf('%s/%s', fsldir, 'bin'); -@@ -23,8 +23,8 @@ - % setenv('LD_LIBRARY_PATH',fsllibdir); - end - --command = sprintf('/bin/sh -c ". ${FSLDIR}/etc/fslconf/fsl.sh; %s"\n', cmd); --[status,output] = system(command); -+%command = sprintf('/bin/sh -c ". ${FSLDIR}/etc/fslconf/fsl.sh; %s"\n', cmd); -+%[status,output] = system(command); - - if ismac - setenv('DYLD_LIBRARY_PATH', dylibpath); ---- etc/js/label-div.html.orig 2013-10-20 23:22:04.906443685 +1300 -+++ etc/js/label-div.html 2013-10-20 23:23:35.006589232 +1300 -@@ -2,12 +2,12 @@ - <head> - <title>label-div</title> - <!--[if IE]> -- <script type="text/javascript" src="FSLDIR/etc/js/excanvas.js"></script> -+ <script type="text/javascript" src="@GENTOO_PORTAGE_EPREFIX@/etc/js/excanvas.js"></script> - <![endif]--> -- <script type="text/javascript" src="FSLDIR/etc/js/strftime-min.js"></script> -- <script type="text/javascript" src="FSLDIR/etc/js/rgbcolor.js"></script> -- <script type="text/javascript" src="FSLDIR/etc/js/dygraph-canvas.js"></script> -- <script type="text/javascript" src="FSLDIR/etc/js/dygraph.js"></script> -+ <script type="text/javascript" src="@GENTOO_PORTAGE_EPREFIX@/etc/js/strftime-min.js"></script> -+ <script type="text/javascript" src="@GENTOO_PORTAGE_EPREFIX@/etc/js/rgbcolor.js"></script> -+ <script type="text/javascript" src="@GENTOO_PORTAGE_EPREFIX@/etc/js/dygraph-canvas.js"></script> -+ <script type="text/javascript" src="@GENTOO_PORTAGE_EPREFIX@/etc/js/dygraph.js"></script> - <script type="text/javascript" src="PNMDATA.js"></script> - </head> - <body>
