sci-biology/fsl: version bump.

  made env.dfile prefix-compatible

Closes: https://github.com/gentoo/sci/pull/804
Package-Manager: Portage-2.3.8, Repoman-2.3.3

6 files changed, 732 insertions, 1 deletions

diff --git a/sci-biology/fsl/Manifest b/sci-biology/fsl/Manifest
index 25155a2fa..c54ea85b0 100644
--- a/sci-biology/fsl/Manifest
+++ b/sci-biology/fsl/Manifest
@@ -1 +1,2 @@
 DIST fsl-5.0.8-sources.tar.gz 1420879532 SHA256 2053cc42782360b191bd9610dbbc0a56677b40796cceb4680420b93d5eddfc15 SHA512 8dedf13d633d71fa28c5dd6591fab4adda4893b76467affa6f58aee917ee3fdc83da07d8f505feb61ac2733de1bfb84f7f9ff74589756946be21cdb9f057f0f0 WHIRLPOOL 2a64245f6b4da2642237aad96270b65799f868bb7a5294f1576470173a9393296b4c26e0ddfffe2198665d068c82f6d7b64548729cfa3aff07f6809c13d57554
+DIST fsl-5.0.9-sources.tar.gz 1491426239 SHA256 4b58183ab11abcf4ff61283af5cc0b792f7a0de2ccbdbb2e2562d1522e0a81d9 SHA512 86a33084cf880ea1341ff8622eb13a364a462018a0fac55ee291dd8917e8453701db57f35529e144d419ea744397906b586b88acaf9a2dea0291fa3101ebb27d WHIRLPOOL a8f839e384cf3928eea003a07df1dfeae36999bc9439a327e1d93e2bbec124eaaef920960e928ac935194b1647d2bfa76711c7dba25eac4bc394428b268011d7
diff --git a/sci-biology/fsl/files/fsl-5.0.9-fsldir_redux.patch b/sci-biology/fsl/files/fsl-5.0.9-fsldir_redux.patch
new file mode 100644
index 000000000..c28fabe42
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-5.0.9-fsldir_redux.patch
@@ -0,0 +1,456 @@
+# 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");

+

diff --git a/sci-biology/fsl/files/fsl-5.0.9-headers.patch b/sci-biology/fsl/files/fsl-5.0.9-headers.patch
new file mode 100644
index 000000000..663dc565c
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-5.0.9-headers.patch
@@ -0,0 +1,15 @@
+# Include zlib header directly.
+# From: Francois Bissey <frp.bissey@gmail.com>
+# Signed-off-by: Horea Christian <horea.christ@gmail.com>
+# Submitted upstream: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1709&L=FSL&F=&S=&X=95C10F0B7D62EAAE7A&P=169254
+
+--- fsl/src/miscvis/writepng.c.orig	2013-10-19 00:18:32.415203592 +1300
++++ fsl/src/miscvis/writepng.c	2013-10-19 00:19:05.414255132 +1300
+@@ -32,6 +32,7 @@
+ 
+ #include <stdlib.h>     /* for exit() prototype */
+ 
++#include "zlib.h"
+ #include "png.h"        /* libpng header; includes zlib.h and setjmp.h */
+ #include "writepng.h"   /* typedefs, common macros, public prototypes */
+ 
diff --git a/sci-biology/fsl/files/fsl-5.0.9-setup.patch b/sci-biology/fsl/files/fsl-5.0.9-setup.patch
new file mode 100644
index 000000000..c688cd6e8
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-5.0.9-setup.patch
@@ -0,0 +1,115 @@
+diff -Naur fsl.orig/build fsl/build
+--- fsl.orig/build	2015-03-29 00:10:39.845936000 +1300
++++ fsl/build	2015-03-29 00:12:37.160487000 +1300
+@@ -11,9 +11,8 @@
+ ifit load_varian load_dicom misc_scripts fdt first possum sgeutils \
+ flameo oxford_asl relax qboot topup ptx2 lesions eddy dwssfp verbena";
+ fi
+ 
+-echo "Building projects - see build.log file for progress..."
+-./config/common/buildproj $PROJECTS > ./build.log 2>&1
+-echo "Finished build : end of log file shows ..."
+-tail -10 build.log
++echo "Building projects"
++./config/common/buildproj $PROJECTS
++echo "Finished build"
+ 
+diff -Naur fsl.orig/config/common/buildproj fsl/config/common/buildproj
+--- fsl.orig/config/common/buildproj	2015-03-29 00:11:47.130998000 +1300
++++ fsl/config/common/buildproj	2015-03-29 00:12:37.164319000 +1300
+@@ -11,10 +11,10 @@
+ fi
+ PROJECTS="$@" ; export PROJECTS ;
+ 
+-FSLDIR=`pwd`
++#FSLDIR=`pwd`
+ FSLDEVDIR=${FSLDIR}
+ FSLCONFDIR=${FSLDIR}/config
+-FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh`
++#FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh`
+ export FSLDIR FSLDEVDIR FSLCONFDIR FSLMACHTYPE
+ 
+ buildmessages="" ; export buildmessages ;
+@@ -66,7 +66,7 @@
+ 	  if [ -x fslconfig ] ; then
+ 	    ./fslconfig ;
+ 	  fi
+-	  if ${MAKE} -k ${MAKEOPTIONS} ; then 
++	  if ${MAKE} ${MAKEOPTIONS} ${MAKEOPTS} ; then 
+ 	    if ${MAKE} install ; then
+ 	      installok=true;
+ 	      # Clean up after ourselves
+diff -Naur fsl.orig/config/common/vars.mk fsl/config/common/vars.mk
+--- fsl.orig/config/common/vars.mk	2015-03-29 00:11:47.183520000 +1300
++++ fsl/config/common/vars.mk	2015-03-29 00:18:53.151222000 +1300
+@@ -24,15 +24,15 @@
+ USRCFLAGS = 
+ USRCXXFLAGS =
+ 
+-LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR}
++LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR} ${USERLDFLAGS}
+ 
+-AccumulatedIncFlags = ${USRINCFLAGS} -I. -I${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}
++	${AccumulatedIncFlags} ${USERCXXFLAGS}
+ 
+ HFILES = *.h
+ AFILES = *.a
+diff -Naur fsl.orig/config/generic/systemvars.mk fsl/config/generic/systemvars.mk
+--- fsl.orig/config/generic/systemvars.mk	2015-03-29 00:11:47.534246000 +1300
++++ fsl/config/generic/systemvars.mk	2015-03-29 00:12:37.162129000 +1300
+@@ -4,20 +4,20 @@
+ 
+ # System dependent commands (NB: the first two are the most platform dependent)
+ 
+-INSTALL = ginstall -p
+-RANLIB = ranlib
++INSTALL = install -p
++RANLIB = @@GENTOO_RANLIB@@
+ 
+ RM = /bin/rm
+ CP = /bin/cp
+ MV = /bin/mv
+ CHMOD = /bin/chmod
+ MKDIR = /bin/mkdir
+-TCLSH = ${FSLDIR}/bin/fsltclsh
++TCLSH = tclsh
+ 
+ # Compiler dependent variables
+ 
+-CC = gcc
+-CXX = c++
++CC = @@GENTOO_CC@@
++CXX = @@GENTOO_CXX@@
+ CSTATICFLAGS = -static
+ CXXSTATICFLAGS = -static
+ 
+@@ -25,7 +25,7 @@
+ 
+ DEPENDFLAGS = -MM
+ 
+-OPTFLAGS =  -O3 -fexpensive-optimizations ${ARCHFLAGS}
++OPTFLAGS =
+ MACHDBGFLAGS =
+ GNU_ANSI_FLAGS = -Wall -ansi -pedantic
+ SGI_ANSI_FLAGS = -ansi -fullwarn
+diff -Naur fsl.orig/extras/build fsl/extras/build
+--- fsl.orig/extras/build	2015-03-29 00:11:15.080236000 +1300
++++ fsl/extras/build	2015-03-29 00:15:53.170496000 +1300
+@@ -104,8 +104,8 @@
+ if [ ${BUILDICONV} -eq 1 ]; then
+   PROJECTS="${PROJECTS} libiconv"
+ fi
+-PROJECTS="${PROJECTS} libgd libgdc libprob libcprob newmat cprob newran fftw"
++PROJECTS="libgdc libprob libcprob newmat cprob newran"
+ PROJECTS="${PROJECTS} boost libxml2-2.9.2 libxml++-2.34.0"
+ for projname in $PROJECTS; do
+ 
+     if [ -d $FSLESRCDIR/$projname ] ; then
diff --git a/sci-biology/fsl/fsl-5.0.8.ebuild b/sci-biology/fsl/fsl-5.0.8.ebuild
index 467255c5f..7916c0811 100644
--- a/sci-biology/fsl/fsl-5.0.8.ebuild
+++ b/sci-biology/fsl/fsl-5.0.8.ebuild
@@ -133,7 +133,9 @@ src_install() {
 	dosym /etc /usr/share/fsl/etc
 	dosym /usr/share/doc/${P} /usr/share/fsl/doc
 
-	doenvd "${FILESDIR}"/99fsl
+	cp "${FILESDIR}"/99fsl "${TMPDIR}"/99fsl || die
+	eprefixify "${TMPDIR}"/99fsl
+	doenvd "${TMPDIR}"/99fsl
 	mv "${ED}"/usr/bin/{,fsl_}cluster || die
 }
 
diff --git a/sci-biology/fsl/fsl-5.0.9.ebuild b/sci-biology/fsl/fsl-5.0.9.ebuild
new file mode 100644
index 000000000..bc96cec06
--- /dev/null
+++ b/sci-biology/fsl/fsl-5.0.9.ebuild
@@ -0,0 +1,142 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit 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://dev.gentoo.org/~jlec/distfiles/${P}-sources.tar.gz"
+
+LICENSE="FSL BSD-2 newmat"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+COMMON_DEPEND="
+	dev-libs/boost
+	media-gfx/graphviz
+	media-libs/gd
+	media-libs/glu
+	media-libs/libpng:0=
+	sys-libs/zlib
+	"
+DEPEND="${COMMON_DEPEND}"
+RDEPEND="${COMMON_DEPEND}
+	dev-lang/tcl:0=
+	dev-lang/tk:0=
+	"
+
+S=${WORKDIR}/${PN}
+UPSTREAM_FSLDIR="/usr/share/fsl"
+
+PATCHES=(
+	"${FILESDIR}/${PN}"-5.0.9-setup.patch
+	"${FILESDIR}/${PN}"-5.0.9-headers.patch
+	"${FILESDIR}/${PN}"-5.0.9-fsldir_redux.patch
+)
+
+src_prepare(){
+	default
+	sed -i \
+		-e "s:@@GENTOO_RANLIB@@:$(tc-getRANLIB):" \
+		-e "s:@@GENTOO_CC@@:$(tc-getCC):" \
+		-e "s:@@GENTOO_CXX@@:$(tc-getCXX):" \
+		config/generic/systemvars.mk || die
+
+	eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX src/*) \
+		etc/js/label-div.html
+
+	makefilelist=$(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/*) \
+		$(grep -rl "\${FSLDIR}/bin" etc/matlab/*) || die
+
+	sed -e "s:\$FSLDIR/data:${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" \
+		$(grep -rl "/usr/share/fsl/doc" src/*) || die
+
+	sed -e "s:\$FSLDIR/etc:${EPREFIX}/etc:g" \
+		-e "s:\${FSLDIR}/etc:${EPREFIX}/etc:g" \
+		-i $(grep -rlI "\$FSLDIR/etc" *) \
+		-i $(grep -rlI "\${FSLDIR}/etc" *) || die
+}
+
+src_compile() {
+	export FSLDIR=${WORKDIR}/${PN}
+	export FSLCONDIR=${WORKDIR}/${PN}/config
+	export FSLMACHTYPE=generic
+
+	export USERLDFLAGS="${LDFLAGS}"
+	export USERCFLAGS="${CFLAGS}"
+	export USERCXXFLAGS="${CXXFLAGS}"
+
+	./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
+	#if use matlab; then
+	#	doins etc/matlab
+	#fi
+
+	#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 ${UPSTREAM_FSLDIR}/etc
+	dosym /usr/share/doc/${PF} ${UPSTREAM_FSLDIR}/doc
+	dosym /usr/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
+}