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From: "Andrew Ammerlaan" <andrewammerlaan@gentoo.org>
To: gentoo-commits@lists.gentoo.org
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Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/fsl/files/
X-VCS-Repository: proj/sci
X-VCS-Files: sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p1.patch sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p2.patch
X-VCS-Directories: sci-biology/fsl/files/
X-VCS-Committer: andrewammerlaan
X-VCS-Committer-Name: Andrew Ammerlaan
X-VCS-Revision: 3e155035c382ba0c3e76d69636ac6eff56d2bc35
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commit:     3e155035c382ba0c3e76d69636ac6eff56d2bc35
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Jan 25 15:33:21 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Jan 25 15:33:21 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=3e155035

sci-biology/fsl: drop unused patches

Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 .../fsl/files/fsl-6.0.2-fsldir_redux-p1.patch      | 240 -------------------
 .../fsl/files/fsl-6.0.2-fsldir_redux-p2.patch      | 255 ---------------------
 2 files changed, 495 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;

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
-