[gentoo-commits] proj/sci:master commit in: sci-biology/fsl/, sci-biology/fsl/files/

[Horea Christian]

commit:     f672571c8517da492b59e914aaa25e8786a6af61
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Thu Jan 30 15:22:28 2020 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Thu Jan 30 15:22:28 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f672571c

sci-biology/fsl: version bump 6.0.2

Thanks to François Bissey <frp.bissey <AT> gmail.com>

Package-Manager: Portage-2.3.84, Repoman-2.3.20
Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 sci-biology/fsl/files/fsl-6.0.2-fsldir_redux.patch | 495 +++++++++++++++++++++
 sci-biology/fsl/files/fsl-6.0.2-no_xmlpp.patch     |  58 +++
 .../fsl/files/fsl-6.0.2-qstring_compat.patch       |  63 +++
 sci-biology/fsl/files/fsl-6.0.2-setup.patch        | 198 +++++++++
 sci-biology/fsl/fsl-6.0.2.ebuild                   | 164 +++++++
 5 files changed, 978 insertions(+)

diff --git a/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux.patch b/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux.patch
new file mode 100644
index 000000000..dc1babd48
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux.patch
@@ -0,0 +1,495 @@
+From 2bc4be1f55b27a733e1e624b34bc570187ba95e1 Mon Sep 17 00:00:00 2001
+From: François Bissey <frp.bissey@×××××.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/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
+

diff --git a/sci-biology/fsl/files/fsl-6.0.2-no_xmlpp.patch b/sci-biology/fsl/files/fsl-6.0.2-no_xmlpp.patch
new file mode 100644
index 000000000..6eccc4370
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.2-no_xmlpp.patch
@@ -0,0 +1,58 @@
+From 9de29e5141afa43c06f347ca158b67168fbb0031 Mon Sep 17 00:00:00 2001
+From: François Bissey <frp.bissey@×××××.com>
+Date: Mon, 20 Jan 2020 11:46:52 +1300
+Subject: [PATCH] Build without xmlpp since we use an external ciftilib that
+ doesnt require it. Replace it and other ciftilib flags with CIFTICFLAGS.
+
+---
+ src/flameo/Makefile  | 4 ++--
+ src/melodic/Makefile | 4 ++--
+ 2 files changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/src/flameo/Makefile b/src/flameo/Makefile
+index d22eb965..e967e682 100644
+--- a/src/flameo/Makefile
++++ b/src/flameo/Makefile
+@@ -2,7 +2,7 @@ include ${FSLCONFDIR}/default.mk
+ 
+ PROJNAME = flame
+ 
+-USRINCFLAGS = -I${INC_NEWMAT} -I${INC_PROB} -I${INC_ZLIB} -DCIFTILIB_USE_XMLPP -I${FSLEXTINC} -I${INC_XML2} -I${INC_XML++} -I${INC_XML++CONF} -I${INC_BOOST} -I${FSLDIR}/include/ciftiio
++USRINCFLAGS = -fPIC -I${INC_NEWMAT} -I${INC_PROB} -I${INC_ZLIB} -I${FSLEXTINC} ${CIFTICFLAGS} -I${INC_BOOST} -I${FSLDIR}/include/ciftiio
+ USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_ZLIB}
+ 
+ UNAME := $(shell uname)
+@@ -10,7 +10,7 @@ ifeq (${UNAME},Darwin)
+         LIBS = -liconv
+ endif
+ 
+-LIBS += -lutils -lnewimage -lmiscmaths -lm -lnewmat -lNewNifti -lcifti -lxml++-2.6 -lxml2 -lboost_filesystem -lboost_system -lznz -lprob -lz 
++LIBS += -lutils -lnewimage -lmiscmaths -lm -lnewmat -lNewNifti ${CIFTILIBS} -lboost_filesystem -lboost_system -lznz -lprob -lz 
+ 
+ XFILES = flameo
+ 
+diff --git a/src/melodic/Makefile b/src/melodic/Makefile
+index 50666517..0c356a2d 100644
+--- a/src/melodic/Makefile
++++ b/src/melodic/Makefile
+@@ -7,7 +7,7 @@ OPTFLAGS_alphaev6-dec-osf5.0-gcc2.95.2 = -O3 -mieee -mfp-trap-mode=sui
+ 
+ PROJNAME = melodic
+ 
+-USRINCFLAGS = -I${INC_NEWMAT} -I${INC_PROB} -I${INC_GD} -I${INC_GDC} -I${INC_PNG} -I${INC_ZLIB} -DCIFTILIB_USE_XMLPP -I${FSLEXTINC} -I${INC_XML2} -I${INC_XML++} -I${INC_XML++CONF} -I${INC_BOOST} -I${FSLDIR}/include/ciftiio
++USRINCFLAGS = -fPIC -I${INC_NEWMAT} -I${INC_PROB} -I${INC_GD} -I${INC_GDC} -I${INC_PNG} -I${INC_ZLIB} -I${FSLEXTINC} ${CIFTICFLAGS} -I${INC_BOOST} -I${FSLDIR}/include/ciftiio
+ USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_GD} -L${LIB_GDC} -L${LIB_PNG} -L${LIB_ZLIB}
+ 
+ UNAME := $(shell uname)
+@@ -15,7 +15,7 @@ ifeq (${UNAME},Darwin)
+         LIBS = -liconv
+ endif
+ 
+-LIBS += -lutils -lnewimage -lmiscplot -lmiscpic -lmiscmaths -lNewNifti -lcifti -lxml++-2.6 -lxml2 -lboost_filesystem -lboost_system -lznz -lnewmat -lprob -lm  -lgdc -lgd -lpng -lz
++LIBS += -lutils -lnewimage -lmiscplot -lmiscpic -lmiscmaths -lNewNifti ${CIFTILIBS} -lboost_filesystem -lboost_system -lznz -lnewmat -lprob -lm  -lgdc -lgd -lpng -lz
+ 
+ TEST_OBJS = test.o 
+ 
+-- 
+2.24.1
+

diff --git a/sci-biology/fsl/files/fsl-6.0.2-qstring_compat.patch b/sci-biology/fsl/files/fsl-6.0.2-qstring_compat.patch
new file mode 100644
index 000000000..9e6682a48
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.2-qstring_compat.patch
@@ -0,0 +1,63 @@
+From 5a5ab3c80eaaea1fe9a43659e2ea5b773b587bb0 Mon Sep 17 00:00:00 2001
+From: François Bissey <frp.bissey@×××××.com>
+Date: Mon, 20 Jan 2020 11:51:52 +1300
+Subject: [PATCH] Because we use qstrings in ciftilib, calls to ciftilib file
+ function have to be made into compatible c strings.
+
+---
+ src/flameo/gsa.cc      | 4 ++--
+ src/melodic/meldata.cc | 2 +-
+ src/melodic/meldata.h  | 2 +-
+ 3 files changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/src/flameo/gsa.cc b/src/flameo/gsa.cc
+index 70f8f385..16167abe 100644
+--- a/src/flameo/gsa.cc
++++ b/src/flameo/gsa.cc
+@@ -74,7 +74,7 @@ namespace GSA {
+     sourceType=mode;
+     if ( sourceType.compare("CIFTI") == 0 ) {
+       cifti::CiftiFile inputCifti;
+-      inputCifti.openFile(make_basename(filename)+".nii");
++      inputCifti.openFile((make_basename(filename)+".nii").c_str());
+       ciftiExemplar=inputCifti.getCiftiXML();
+       cerr << "ndim " << ciftiExemplar.getNumberOfDimensions() << endl;
+       cerr << "type1 " << ciftiExemplar.getMappingType(0) << endl;
+@@ -194,7 +194,7 @@ namespace GSA {
+       scalarsMap.setLength(data.Nrows());
+       ciftiExemplar.setMap(0, scalarsMap);
+       CiftiFile outputFile;
+-      outputFile.setWritingFile(make_basename(filename)+extension+".nii");//sets up on-disk writing with default writing version
++      outputFile.setWritingFile((make_basename(filename)+extension+".nii").c_str());//sets up on-disk writing with default writing version
+       outputFile.setCiftiXML(ciftiExemplar,false);	    
+       vector<float> scratchRow(data.Nrows());//read/write a row at a time
+       for (int64_t row=0;row<data.Ncols();row++) {	    
+diff --git a/src/melodic/meldata.cc b/src/melodic/meldata.cc
+index c4ad2349..1515e702 100644
+--- a/src/melodic/meldata.cc
++++ b/src/melodic/meldata.cc
+@@ -118,7 +118,7 @@ namespace Melodic{
+     	tmpData = RawData.matrix(Mask);
+ 		memmsg(" after reshape ");	  
+ 	} else { //Read in Cifti
+-	  inputCifti.openFile(fname+".nii");
++	  inputCifti.openFile((fname+".nii").c_str());
+ 	  const vector<int64_t>& dims = inputCifti.getDimensions();
+ 	  tmpData.ReSize(dims[0],dims[1]); //swapped compared to cifti
+ 	  vector<float> scratchRow(dims[0]);//read/write a row at a time
+diff --git a/src/melodic/meldata.h b/src/melodic/meldata.h
+index 49774003..f5326bdd 100644
+--- a/src/melodic/meldata.h
++++ b/src/melodic/meldata.h
+@@ -109,7 +109,7 @@ namespace Melodic{
+ 	  message("  " << logger.appendDir(fname) << endl);
+ 	} else { //Process CIFTI save ICs as float
+ 	  cifti::CiftiFile outputFile;
+-	  outputFile.setWritingFile(logger.appendDir(fname)+".nii");//sets up on-disk writing with default writing version
++	  outputFile.setWritingFile((logger.appendDir(fname)+".nii").c_str());//sets up on-disk writing with default writing version
+ 	  cifti::CiftiXML xml(inputCifti.getCiftiXML());
+ 	  cifti::CiftiScalarsMap scalarsMap;
+ 	  std::vector<char> foo = xml.writeXMLToVector();
+-- 
+2.24.1
+

diff --git a/sci-biology/fsl/files/fsl-6.0.2-setup.patch b/sci-biology/fsl/files/fsl-6.0.2-setup.patch
new file mode 100644
index 000000000..39737fd85
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.2-setup.patch
@@ -0,0 +1,198 @@
+From baae97cc3c8d0cadcabb7ed16559f4e4de26ddbe Mon Sep 17 00:00:00 2001
+From: François Bissey <frp.bissey@×××××.com>
+Date: Mon, 20 Jan 2020 11:54:37 +1300
+Subject: [PATCH] Adjust the build system so it doesnt build packages
+ externally provided by portage. Make the compilation flags more generic and
+ easily adjustable. Make the build system stop at the first fault.
+
+---
+ build                   |  6 +++---
+ config/buildSettings.mk | 20 ++++++++++----------
+ config/common/buildproj |  8 +++++---
+ config/common/vars.mk   | 10 +++++-----
+ extras/build            |  8 ++++----
+ src/mist-clean/Makefile |  2 +-
+ 6 files changed, 28 insertions(+), 26 deletions(-)
+
+diff --git a/build b/build
+index 05dac06c..d90e407b 100755
+--- a/build
++++ b/build
+@@ -3,7 +3,7 @@
+ if [ $# -ge 1 ] ; then
+   PROJECTS="$@";
+ else
+-  MASTERPROJECTS="CiftiLib-master utils znzlib NewNifti niftiio fslio giftiio miscmaths newimage libhfunc libvis first_lib \
++  MASTERPROJECTS="utils znzlib NewNifti niftiio fslio giftiio miscmaths newimage libhfunc libvis first_lib \
+ meshclass fslvtkio misc_tcl basisfield warpfns bint shapeModel MVdisc fslvtkconv fslsurface libmeshutils newmesh \
+ DiscreteOpt FastPDlib MSMRegLib misc_c dpm topup \
+ asl_mfree \
+@@ -80,8 +80,8 @@ xtract";
+   done
+ fi
+ 
+-echo "Building projects - see build.log file for progress..."
+-./config/common/buildproj $PROJECTS > ./build.log 2>&1
++echo "Building projects"
++./config/common/buildproj $PROJECTS
+ finalStatus=$?
+ if [ $finalStatus -eq 0 ]; then
+     echo "Build completed successfully.";
+diff --git a/config/buildSettings.mk b/config/buildSettings.mk
+index b2e1f150..04532fc2 100644
+--- a/config/buildSettings.mk
++++ b/config/buildSettings.mk
+@@ -18,7 +18,7 @@ MV = /bin/mv
+ CHMOD = /bin/chmod
+ MKDIR = /bin/mkdir
+ INSTALL = install -p 
+-TCLSH = ${FSLDIR}/bin/fsltclsh
++TCLSH = tclsh
+ DEPENDFLAGS = -MM
+ MACHDBGFLAGS = -g
+ #####################################################################
+@@ -124,19 +124,19 @@ endif # if Darwin
+ #####################################################################
+ ifeq ($(SYSTYPE), Linux)
+ ###############   System Vars   #####################################
+-CC = gcc
+-CXX = c++
+-CXX11 = c++
++CC = @@GENTOO_CC@@
++CXX = @@GENTOO_CXX@@
++CXX11 = @@GENTOO_CXX@@
+ CSTATICFLAGS = -static
+ CXXSTATICFLAGS = -static
+-ARCHFLAGS = -m64
+-ARCHLDFLAGS = -Wl,-rpath,'$$ORIGIN/../lib'
++ARCHFLAGS =
++ARCHLDFLAGS =
+ PARALLELFLAGS = -fopenmp
+-OPTFLAGS = -g -O3 -fexpensive-optimizations ${ARCHFLAGS}
++OPTFLAGS =
+ GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long
+ SGI_ANSI_FLAGS = -ansi -fullwarn
+ ANSI_FLAGS = ${GNU_ANSI_FLAGS}
+-RANLIB = echo
++RANLIB = @@GENTOO_RANLIB@@
+ FSLML = ${FSLDIR}/bin/fslml
+ # CUDA development environment
+ CUDAVER := $(or $(CUDAVER),9.1)
+@@ -148,8 +148,8 @@ INC_CUDA = ${CUDA_INSTALLATION}/include
+ NVCC = ${CUDA_INSTALLATION}/bin/nvcc
+ ###############   External Libs   #####################################
+ # ZLIB library
+-LIB_ZLIB = /lib64
+-INC_ZLIB = /usr/include
++#LIB_ZLIB = /lib64
++#INC_ZLIB = /usr/include
+ # QT library
+ QTDIR = /usr/lib/qt3
+ LIB_QT = ${QTDIR}/lib
+diff --git a/config/common/buildproj b/config/common/buildproj
+index 2f0f2b8f..48624a1f 100755
+--- a/config/common/buildproj
++++ b/config/common/buildproj
+@@ -11,10 +11,10 @@ if [ X$1 = X-strict ] ; then
+ fi
+ PROJECTS="$@" ; export PROJECTS ;
+ 
+-FSLDIR=`pwd`
++#FSLDIR=`pwd`
+ FSLDEVDIR=${FSLDIR}
+ FSLCONFDIR=${FSLDIR}/config
+-FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh`
++#FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh`
+ FSLMASTERBUILD=1
+ export FSLDIR FSLDEVDIR FSLCONFDIR FSLMACHTYPE FSLMASTERBUILD
+ 
+@@ -67,7 +67,7 @@ for projname in $PROJECTS; do
+ 	  if [ -x ./fslconfig ] ; then
+ 	    . ./fslconfig ;
+ 	  fi
+-	  if ${MAKE} -k ${MAKEOPTIONS} ; then 
++	  if ${MAKE} ${MAKEOPTIONS} ; then 
+ 	    if ${MAKE} ${MAKEOPTIONS} install ; then
+ 	      installok=true;
+ 	      # Clean up after ourselves
+@@ -82,6 +82,7 @@ for projname in $PROJECTS; do
+ 	    if [ $installok = false ]  ; then
+ 	      echo " "
+ 	      echo "ERROR::Could not install $projname successfully" ;
++	      exit 1
+ 	    fi
+ 	  else
+ 	    echo " "
+@@ -90,6 +91,7 @@ for projname in $PROJECTS; do
+ 	    echo " "
+ 	    echo " "
+ 	    errorprojs="$errorprojs $projname" ; export errorprojs ;
++	    exit 1
+ 	  fi
+     fi
+ done
+diff --git a/config/common/vars.mk b/config/common/vars.mk
+index b027b010..aeeae67c 100755
+--- a/config/common/vars.mk
++++ b/config/common/vars.mk
+@@ -24,15 +24,15 @@ USRINCFLAGS =
+ USRCFLAGS = 
+ USRCXXFLAGS =
+ 
+-LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR}
++LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR} ${USERLDFLAGS}
+ 
+-AccumulatedIncFlags = -I${INC_BOOST} ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR}
++AccumulatedIncFlags = ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR} ${CPPFLAGS}
+ 
+ CFLAGS = ${ANSI_FLAGS} ${ANSI_CFLAGS} ${DBGFLAGS} ${USEDCSTATICFLAGS} ${USRCFLAGS} ${ARCHFLAGS} ${OPTFLAGS}  \
+-	${AccumulatedIncFlags}
++	${AccumulatedIncFlags} ${USERCFLAGS}
+ 
+-CXXFLAGS = ${ANSI_FLAGS} ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS}  \
+-	${AccumulatedIncFlags}
++CXXFLAGS = ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS}  \
++	${AccumulatedIncFlags} ${USERCXXFLAGS}
+ 
+ HFILES = *.h
+ AFILES = *.a
+diff --git a/extras/build b/extras/build
+index 59e7a2ed..0d68232e 100755
+--- a/extras/build
++++ b/extras/build
+@@ -96,16 +96,16 @@ if [ X"${OS}" = "XDarwin" ]; then
+ 	BUILDICONV=1
+     fi
+ fi
+-PROJECTS="tcl tk"
++#PROJECTS="tcl tk"
+ if [ ${BUILDZLIB} -eq 1 ]; then
+   PROJECTS="${PROJECTS} zlib"
+ fi
+-PROJECTS="${PROJECTS} libpng"
++#PROJECTS="${PROJECTS} libpng"
+ if [ ${BUILDICONV} -eq 1 ]; then
+   PROJECTS="${PROJECTS} libiconv"
+ fi
+-PROJECTS="${PROJECTS} libgd libgdc libprob libcprob newmat cprob newran fftw"
+-PROJECTS="${PROJECTS} boost libxml2-2.9.2 libxmlpp libsqlite libnlopt ../include/armawrap/dummy_newmat"
++PROJECTS="${PROJECTS} libgdc libprob libcprob newmat cprob newran"
++PROJECTS="${PROJECTS} ../include/armawrap/dummy_newmat"
+ for projname in $PROJECTS; do
+     if [ -d $FSLESRCDIR/$projname ] ; then
+        buildIt $FSLESRCDIR $projname 1
+diff --git a/src/mist-clean/Makefile b/src/mist-clean/Makefile
+index 20402cca..6918bee4 100755
+--- a/src/mist-clean/Makefile
++++ b/src/mist-clean/Makefile
+@@ -52,6 +52,6 @@ installpython:
+ 		cp -r python/* ${DESTDIR}/python/mist
+ 
+ clean:
+-			rm -f ${OBJS} mist/mist.o mist/mist
++			rm -f ${OBJS} mist/mist.o mist/mist || echo "CLEAN could not locate some files scheduled for deletion."
+ 
+ .PHONY:		all clean installdata
+-- 
+2.24.1
+

diff --git a/sci-biology/fsl/fsl-6.0.2.ebuild b/sci-biology/fsl/fsl-6.0.2.ebuild
new file mode 100644
index 000000000..cde479421
--- /dev/null
+++ b/sci-biology/fsl/fsl-6.0.2.ebuild
@@ -0,0 +1,164 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit flag-o-matic toolchain-funcs prefix
+
+DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging data"
+HOMEPAGE="http://www.fmrib.ox.ac.uk/fsl"
+SRC_URI="https://fsl.fmrib.ox.ac.uk/fsldownloads/${P}-sources.tar.gz -> ${P}.tar.gz"
+
+LICENSE="FSL BSD-2 newmat"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND="
+	dev-libs/boost
+	dev-python/fslpy
+	media-gfx/graphviz
+	media-libs/gd
+	media-libs/glu
+	media-libs/libpng:0=
+	sci-libs/ciftilib
+	sci-libs/nlopt
+	sys-libs/zlib
+	dev-lang/tcl:0=
+	dev-lang/tk:0=
+	>=virtual/lapack-3.8
+	>=virtual/blas-3.8
+	"
+RDEPEND="${DEPEND}"
+
+S=${WORKDIR}/${PN}
+UPSTREAM_FSLDIR="/usr/share/fsl"
+
+PATCHES=(
+	"${FILESDIR}/${PN}"-6.0.2-setup.patch
+	"${FILESDIR}/${PN}"-6.0.2-no_xmlpp.patch
+	"${FILESDIR}/${PN}"-5.0.11-niftiio_var_fix.patch
+	"${FILESDIR}/${PN}"-5.0.11-ifstream_use.patch
+	"${FILESDIR}/${PN}"-5.0.11-fslsurface_parallel_make.patch
+	"${FILESDIR}/${PN}"-6.0.2-qstring_compat.patch
+	"${FILESDIR}/${PN}"-5.0.9-headers.patch
+	"${FILESDIR}/${PN}"-6.0.2-fsldir_redux.patch
+)
+
+src_prepare(){
+	default
+
+	sed -i \
+		-e "s:@@GENTOO_RANLIB@@:$(tc-getRANLIB):" \
+		-e "s:@@GENTOO_CC@@:$(tc-getCC):" \
+		-e "s:@@GENTOO_CXX@@:$(tc-getCXX):" \
+		config/buildSettings.mk || die
+
+	eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX src/*) \
+		etc/js/label-div.html
+
+	# Disable mist-clean the hard way for now.
+	rm -rf src/mist-clean
+
+	makefilelist=$(find src/ -name Makefile)
+
+	sed -i \
+		-e "s:-I\${INC_BOOST}::" \
+		-e "s:-I\${INC_ZLIB}::" \
+		-e "s:-I\${INC_GD}::" \
+		-e "s:-I\${INC_PNG}::" \
+		-e "s:-L\${LIB_GD}::" \
+		-e "s:-L\${LIB_PNG}::" \
+		-e "s:-L\${LIB_ZLIB}::" \
+		${makefilelist} || die
+
+	sed -e "s:\${FSLDIR}/bin/::g" \
+		-e "s:\$FSLDIR/bin/::g" \
+		-i $(grep -rl "\${FSLDIR}/bin" src/*) \
+		-i $(grep -rl "\$FSLDIR/bin" src/*) \
+		$(grep -rl "\${FSLDIR}/bin" etc/matlab/*)\
+		$(grep -rl "\$FSLDIR/bin" etc/matlab/*) || die
+
+	sed -e "s:\$FSLDIR/data:${EPREFIX}/usr/share/fsl/data:g" \
+		-e "s:\${FSLDIR}/data:${EPREFIX}/usr/share/fsl/data:g" \
+		-i $(grep -rl "\$FSLDIR/data" src/*) \
+		$(grep -rl "\${FSLDIR}/data" src/*) || die
+
+	sed -e "s:\$FSLDIR/doc:${EPREFIX}/usr/share/fsl/doc:g" \
+		-e "s:\${FSLDIR}/doc:${EPREFIX}/usr/share/fsl/doc:g" \
+		-i $(grep -rl "\$FSLDIR/doc" src/*) \
+		$(grep -rl "\${FSLDIR}/doc" src/*) || die
+
+	sed -e "s:/usr/share/fsl/doc:${EPREFIX}/usr/share/fsl/doc:g" \
+		-i $(grep -rl "/usr/share/fsl/doc" src/*) || die
+
+	sed -e "s:\$FSLDIR/etc:${EPREFIX}/etc:g" \
+		-e "s:\${FSLDIR}/etc:${EPREFIX}/etc:g" \
+		-i $(grep -rlI "\$FSLDIR/etc" *) \
+		-i $(grep -rlI "\${FSLDIR}/etc" *) || die
+
+	# Use generic blas/lapack rather than openblas
+	sed -e "s:-lopenblas:-llapack -lblas:g" \
+		-i $(grep -rlI lopenblas *) || die
+
+	# script wanting to have access to flsversion at buildtime
+	sed -e "s:/etc/fslversion:${S}/etc/fslversion:g" \
+		-i ${makefilelist} || die
+}
+
+src_compile() {
+	export FSLDIR=${WORKDIR}/${PN}
+	export FSLCONDIR=${WORKDIR}/${PN}/config
+	export FSLMACHTYPE=generic
+
+	export USERLDFLAGS="${LDFLAGS}"
+	export USERCFLAGS="${CFLAGS}"
+	export USERCXXFLAGS="${CXXFLAGS}"
+
+	export CIFTICFLAGS="$($(tc-getPKG_CONFIG) --cflags CiftiLib)"
+	export CIFTILIBS="$($(tc-getPKG_CONFIG) --libs-only-l CiftiLib)"
+
+	./build || die
+}
+
+src_install() {
+	sed -i "s:\${FSLDIR}/tcl:/usr/libexec/fsl:g" \
+		$(grep -lI "\${FSLDIR}/tcl" bin/*) \
+		$(grep -l "\${FSLDIR}/tcl"  tcl/*) || die
+	sed -i "s:\$FSLDIR/tcl:/usr/libexec/fsl:g" \
+		$(grep -l "\$FSLDIR/tcl" tcl/*) || die
+
+	dobin bin/*
+
+	insinto /usr/share/${PN}
+	doins -r data
+	dodoc -r doc/. refdoc
+
+	insinto /usr/libexec/fsl
+	doins -r tcl/*
+
+	insinto /etc/fslconf
+	doins etc/fslconf/fsl.sh
+
+	insinto /etc
+	doins etc/fslversion
+	doins -r etc/default_flobs.flobs etc/flirtsch etc/js etc/luts
+
+	#the following is needed for FSL and depending programs to be able
+	#to find its files, since FSL uses an uncommon installation path:
+	#https://github.com/gentoo-science/sci/pull/612#r60289295
+	dosym ../../../etc ${UPSTREAM_FSLDIR}/etc
+	dosym ../doc/${PF} ${UPSTREAM_FSLDIR}/doc
+	dosym ../../bin ${UPSTREAM_FSLDIR}/bin
+
+	doenvd "$(prefixify_ro "${FILESDIR}"/99fsl)"
+	mv "${ED}"/usr/bin/{,fsl_}cluster || die
+}
+
+pkg_postinst() {
+	echo
+	einfo "Please run the following commands if you"
+	einfo "intend to use fsl from an existing shell:"
+	einfo "env-update && source /etc/profile"
+	echo
+}