From: "Francois Bissey" <f.r.bissey@massey.ac.nz>
To: gentoo-commits@lists.gentoo.org
Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/fsl/files/, sci-biology/fsl/
Date: Mon, 20 Apr 2015 01:11:36 +0000 (UTC) [thread overview]
Message-ID: <1427732081.5d5c08d1c7bca1b5ae4278cac0b9d5536b345ccb.fbissey@gentoo> (raw)
commit: 5d5c08d1c7bca1b5ae4278cac0b9d5536b345ccb
Author: Horea Christian <h.chr <AT> mail <DOT> ru>
AuthorDate: Mon Mar 30 16:14:41 2015 +0000
Commit: Francois Bissey <f.r.bissey <AT> massey <DOT> ac <DOT> nz>
CommitDate: Mon Mar 30 16:14:41 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=5d5c08d1
5.0.8 redux patch by François Bissey
Package-Manager: portage-2.2.18
sci-biology/fsl/ChangeLog | 3 +
sci-biology/fsl/files/fsl-5.0.8-redux.patch | 452 ++++++++++++++++++++++++++++
2 files changed, 455 insertions(+)
diff --git a/sci-biology/fsl/ChangeLog b/sci-biology/fsl/ChangeLog
index a8447db..9157f64 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: $
+ 30 Mar 2015; <chymera@gentoo.org> +files/fsl-5.0.8-redux.patch:
+ 5.0.8 redux patch by François Bissey
+
29 Mar 2015; <chymera@gentoo.org> fsl-5.0.8.ebuild:
using the 5.0.8 headers patch
diff --git a/sci-biology/fsl/files/fsl-5.0.8-redux.patch b/sci-biology/fsl/files/fsl-5.0.8-redux.patch
new file mode 100644
index 0000000..593c1c8
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-5.0.8-redux.patch
@@ -0,0 +1,452 @@
+diff -Naur src.orig/fast4/fast_two.cc src/fast4/fast_two.cc
+--- src.orig/fast4/fast_two.cc 2015-03-30 11:54:10.522550233 +1300
++++ src/fast4/fast_two.cc 2015-03-30 11:54:18.412569892 +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);
+diff -Naur src.orig/feat5/feat_model.cc src/feat5/feat_model.cc
+--- src.orig/feat5/feat_model.cc 2015-03-30 11:54:10.502550183 +1300
++++ src/feat5/feat_model.cc 2015-03-30 11:54:18.412569892 +1300
+@@ -741,7 +741,7 @@
+ 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];
+
+@@ -760,8 +760,6 @@
+ 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));
+@@ -1491,7 +1489,7 @@
+ 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);
+@@ -2134,6 +2132,6 @@
+
+ fclose(outputfile);
+
+- filename=string(getenv("FSLDIR")) + "/bin/wpng -q -overwrite " + filename;
++ filename="wpng -q -overwrite " + filename;
+ system(filename.c_str());
+ }
+diff -Naur src.orig/feat5/tsplot.cc src/feat5/tsplot.cc
+--- src.orig/feat5/tsplot.cc 2015-03-30 11:54:10.502550183 +1300
++++ src/feat5/tsplot.cc 2015-03-30 11:54:18.412569892 +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 */
+diff -Naur src.orig/first/first_utils.cc src/first/first_utils.cc
+--- src.orig/first/first_utils.cc 2015-03-30 11:54:10.482550135 +1300
++++ src/first/first_utils.cc 2015-03-30 11:54:18.412569892 +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;
+diff -Naur src.orig/fnirt/fnirtfns.cpp src/fnirt/fnirtfns.cpp
+--- src.orig/fnirt/fnirtfns.cpp 2015-03-30 11:54:10.522550233 +1300
++++ src/fnirt/fnirtfns.cpp 2015-03-30 11:54:18.412569892 +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");
+diff -Naur src.orig/fslsurface/fslsurface_first.cc src/fslsurface/fslsurface_first.cc
+--- src.orig/fslsurface/fslsurface_first.cc 2015-03-30 11:54:10.522550233 +1300
++++ src/fslsurface/fslsurface_first.cc 2015-03-30 11:54:18.412569892 +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);
+
+diff -Naur src.orig/fslsurface/fslsurfacemaths.cpp src/fslsurface/fslsurfacemaths.cpp
+--- src.orig/fslsurface/fslsurfacemaths.cpp 2015-03-30 11:54:10.522550233 +1300
++++ src/fslsurface/fslsurfacemaths.cpp 2015-03-30 11:54:18.412569892 +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;
+diff -Naur src.orig/libvis/miscpic.h src/libvis/miscpic.h
+--- src.orig/libvis/miscpic.h 2015-03-30 11:54:10.482550135 +1300
++++ src/libvis/miscpic.h 2015-03-30 11:54:18.412569892 +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;
+diff -Naur src.orig/melodic/meldata.cc src/melodic/meldata.cc
+--- src.orig/melodic/meldata.cc 2015-03-30 11:54:10.502550183 +1300
++++ src/melodic/meldata.cc 2015-03-30 11:54:18.412569892 +1300
+@@ -971,7 +971,7 @@
+ 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){
+@@ -1136,7 +1136,7 @@
+ // 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";
+
+diff -Naur src.orig/melodic/meloptions.cc src/melodic/meloptions.cc
+--- src.orig/melodic/meloptions.cc 2015-03-30 11:54:10.502550183 +1300
++++ src/melodic/meloptions.cc 2015-03-30 11:54:18.412569892 +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++);
+
+diff -Naur src.orig/melodic/meloptions.h src/melodic/meloptions.h
+--- src.orig/melodic/meloptions.h 2015-03-30 11:54:10.502550183 +1300
++++ src/melodic/meloptions.h 2015-03-30 11:54:18.412569892 +1300
+@@ -93,7 +93,6 @@
+ ~MelodicOptions() { delete gopt; }
+
+ string version;
+- string binpath;
+ string logfname;
+ bool filtermode;
+ bool explicitnums;
+diff -Naur src.orig/melodic/melreport.cc src/melodic/melreport.cc
+--- src.orig/melodic/melreport.cc 2015-03-30 11:54:10.502550183 +1300
++++ src/melodic/melreport.cc 2015-03-30 11:54:18.412569892 +1300
+@@ -84,8 +84,8 @@
+ 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
+@@ -487,8 +487,8 @@
+
+ {//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
+@@ -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;
+
+diff -Naur src.orig/melodic/melreport.h src/melodic/melreport.h
+--- src.orig/melodic/melreport.h 2015-03-30 11:54:10.502550183 +1300
++++ src/melodic/melreport.h 2015-03-30 12:11:17.995116883 +1300
+@@ -104,21 +104,21 @@
+ 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 @@
+ << "</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 -Naur src.orig/mm/mixture_model.cc src/mm/mixture_model.cc
+--- src.orig/mm/mixture_model.cc 2015-03-30 11:54:10.522550233 +1300
++++ src/mm/mixture_model.cc 2015-03-30 11:54:18.412569892 +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;
+diff -Naur src.orig/siena/siena_diff.cc src/siena/siena_diff.cc
+--- src.orig/siena/siena_diff.cc 2015-03-30 11:54:10.482550135 +1300
++++ src/siena/siena_diff.cc 2015-03-30 11:54:18.412569892 +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);
+ }
+diff -Naur src.orig/topup/topupfns.cpp src/topup/topupfns.cpp
+--- src.orig/topup/topupfns.cpp 2015-03-30 11:54:10.522550233 +1300
++++ src/topup/topupfns.cpp 2015-03-30 11:54:18.412569892 +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");
+
next reply other threads:[~2015-04-20 1:11 UTC|newest]
Thread overview: 9+ messages / expand[flat|nested] mbox.gz Atom feed top
2015-04-20 1:11 Francois Bissey [this message]
-- strict thread matches above, loose matches on Subject: below --
2020-12-31 15:07 [gentoo-commits] proj/sci:master commit in: sci-biology/fsl/files/, sci-biology/fsl/ Aisha Tammy
2020-09-17 15:15 Horea Christian
2020-08-09 4:50 Horea Christian
2020-06-19 5:37 Horea Christian
2020-06-19 5:30 Horea Christian
2017-09-21 2:39 Benda XU
2015-04-20 1:11 Francois Bissey
2015-04-20 1:11 Francois Bissey
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