# Adapt hard-coded paths to the directory structure of Gentoo (including Prefix)
# From: Francois Bissey <frp.bissey@gmail.com>
# Signed-off-by: Horea Christian <horea.christ@gmail.com>

diff -Naur fsl.orig/src/fast4/fast_two.cc fsl/src/fast4/fast_two.cc
--- fsl.orig/src/fast4/fast_two.cc	2015-03-30 11:54:10.522550233 +1300
+++ fsl/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 fsl.orig/src/feat5/feat_model.cc fsl/src/feat5/feat_model.cc
--- fsl.orig/src/feat5/feat_model.cc	2015-03-30 11:54:10.502550183 +1300
+++ fsl/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 fsl.orig/src/feat5/tsplot.cc fsl/src/feat5/tsplot.cc
--- fsl.orig/src/feat5/tsplot.cc	2015-03-30 11:54:10.502550183 +1300
+++ fsl/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 fsl.orig/src/first/first_utils.cc fsl/src/first/first_utils.cc
--- fsl.orig/src/first/first_utils.cc	2015-03-30 11:54:10.482550135 +1300
+++ fsl/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 fsl.orig/src/fnirt/fnirtfns.cpp fsl/src/fnirt/fnirtfns.cpp
--- fsl.orig/src/fnirt/fnirtfns.cpp	2015-03-30 11:54:10.522550233 +1300
+++ fsl/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 fsl.orig/src/fslsurface/fslsurface_first.cc fsl/src/fslsurface/fslsurface_first.cc
--- fsl.orig/src/fslsurface/fslsurface_first.cc	2015-03-30 11:54:10.522550233 +1300
+++ fsl/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 fsl.orig/src/fslsurface/fslsurfacemaths.cpp fsl/src/fslsurface/fslsurfacemaths.cpp
--- fsl.orig/src/fslsurface/fslsurfacemaths.cpp	2015-03-30 11:54:10.522550233 +1300
+++ fsl/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 fsl.orig/src/libvis/miscpic.h fsl/src/libvis/miscpic.h
--- fsl.orig/src/libvis/miscpic.h	2015-03-30 11:54:10.482550135 +1300
+++ fsl/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 fsl.orig/src/melodic/meldata.cc fsl/src/melodic/meldata.cc
--- fsl.orig/src/melodic/meldata.cc	2015-03-30 11:54:10.502550183 +1300
+++ fsl/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 fsl.orig/src/melodic/meloptions.cc fsl/src/melodic/meloptions.cc
--- fsl.orig/src/melodic/meloptions.cc	2015-03-30 11:54:10.502550183 +1300
+++ fsl/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 fsl.orig/src/melodic/meloptions.h fsl/src/melodic/meloptions.h
--- fsl.orig/src/melodic/meloptions.h	2015-03-30 11:54:10.502550183 +1300
+++ fsl/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 fsl.orig/src/melodic/melreport.cc fsl/src/melodic/melreport.cc
--- fsl.orig/src/melodic/melreport.cc	2015-03-30 11:54:10.502550183 +1300
+++ fsl/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 fsl.orig/src/melodic/melreport.h fsl/src/melodic/melreport.h
--- fsl.orig/src/melodic/melreport.h	2015-03-30 11:54:10.502550183 +1300
+++ fsl/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 fsl.orig/src/mm/mixture_model.cc fsl/src/mm/mixture_model.cc
--- fsl.orig/src/mm/mixture_model.cc	2015-03-30 11:54:10.522550233 +1300
+++ fsl/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 fsl.orig/src/siena/siena_diff.cc fsl/src/siena/siena_diff.cc
--- fsl.orig/src/siena/siena_diff.cc	2015-03-30 11:54:10.482550135 +1300
+++ fsl/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 fsl.orig/src/topup/topupfns.cpp fsl/src/topup/topupfns.cpp
--- fsl.orig/src/topup/topupfns.cpp	2015-03-30 11:54:10.522550233 +1300
+++ fsl/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");