24 files changed, 1488 insertions, 1933 deletions
diff --git a/sci-biology/fsl/files/fsl-5.0.11-setup.patch b/sci-biology/fsl/files/fsl-5.0.11-setup.patch
deleted file mode 100644
index cf9cb785d..000000000
--- a/sci-biology/fsl/files/fsl-5.0.11-setup.patch
+++ /dev/null
@@ -1,158 +0,0 @@
-diff --git a/build b/build
-index 6827443..19b2002 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 avwutils basil bet2 cluster dpm copain tissue fast4 feat5 film filmbabe flirt fabber baycest \
-@@ -25,8 +25,8 @@ flameo oxford_asl relax qboot topup ptx2 lesions eddy dwssfp verbena MSM bianca
-   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/common/buildproj b/config/common/buildproj
-index 3450bda..ec3edc1 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`
- export FSLDIR FSLDEVDIR FSLCONFDIR FSLMACHTYPE
- 
- buildmessages="" ; export buildmessages ;
-@@ -66,7 +66,7 @@ for projname in $PROJECTS; do
- 	  if [ -x ./fslconfig ] ; then
- 	    . ./fslconfig ;
- 	  fi
--	  if ${MAKE} -k ${MAKEOPTIONS} ; then 
-+	  if ${MAKE} ${MAKEOPTIONS} ${MAKEOPTS} ; then 
- 	    if ${MAKE} ${MAKEOPTIONS} install ; then
- 	      installok=true;
- 	      # Clean up after ourselves
-@@ -81,6 +81,7 @@ for projname in $PROJECTS; do
- 	    if [ $installok = false ]  ; then
- 	      echo " "
- 	      echo "ERROR::Could not install $projname successfully" ;
-+	      exit 1
- 	    fi
- 	  else
- 	    echo " "
-@@ -89,6 +90,7 @@ 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 53754be..ff7a117 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/config/generic/systemvars.mk b/config/generic/systemvars.mk
-index e40e3d6..ddb5bfe 100755
---- a/config/generic/systemvars.mk
-+++ b/config/generic/systemvars.mk
-@@ -4,20 +4,20 @@ SHELL = /bin/sh
- 
- # 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 @@ ARCHFLAGS =
- 
- DEPENDFLAGS = -MM
- 
--OPTFLAGS =  -O3 -fexpensive-optimizations ${ARCHFLAGS}
-+OPTFLAGS =
- MACHDBGFLAGS =
- GNU_ANSI_FLAGS = -Wall -ansi -pedantic
- SGI_ANSI_FLAGS = -ansi -fullwarn
-diff --git a/extras/build b/extras/build
-index 6133a1b..caeae2d 100755
---- a/extras/build
-+++ b/extras/build
-@@ -104,8 +104,8 @@ PROJECTS="${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 libxml++-2.34.0 libsqlite libnlopt ../include/armawrap/dummy_newmat"
-+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 b3a32fc..e949ba1 100755
---- a/src/mist-clean/Makefile
-+++ b/src/mist-clean/Makefile
-@@ -52,7 +52,7 @@ installpython:
- 		cp -r python/* ${DESTDIR}/python/mist
- 
- clean:
--			rm ${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
- 
diff --git a/sci-biology/fsl/files/fsl-5.0.4-headers.patch b/sci-biology/fsl/files/fsl-5.0.4-headers.patch
deleted file mode 100644
index 803151bb7..000000000
--- a/sci-biology/fsl/files/fsl-5.0.4-headers.patch
+++ /dev/null
@@ -1,32 +0,0 @@
---- src/avwutils/fslmaths.cc.orig	2013-10-19 00:17:44.765129309 +1300
-+++ src/avwutils/fslmaths.cc	2013-10-19 00:18:02.975157728 +1300
-@@ -71,7 +71,7 @@
- #include "newimage/newimageall.h"
- #include "miscmaths/miscmaths.h"
- #include "utils/fsl_isfinite.h"
--#include "libprob/libprob.h"
-+#include "libprob.h"
- 
- using namespace MISCMATHS;
- using namespace NEWIMAGE;
---- src/miscvis/writepng.c.orig	2013-10-19 00:18:32.415203592 +1300
-+++ 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 */
- 
---- src/ptx2/surfmaths.cc.orig	2013-10-19 00:19:51.595327317 +1300
-+++ src/ptx2/surfmaths.cc	2013-10-19 00:20:09.284354805 +1300
-@@ -72,7 +72,7 @@
- #include "csv_mesh.h"
- #include "miscmaths/miscmaths.h"
- #include "utils/fsl_isfinite.h"
--#include "libprob/libprob.h"
-+#include "libprob.h"
- 
- using namespace MISCMATHS;
- 
diff --git a/sci-biology/fsl/files/fsl-5.0.4-setup.patch b/sci-biology/fsl/files/fsl-5.0.4-setup.patch
deleted file mode 100644
index 0b961492a..000000000
--- a/sci-biology/fsl/files/fsl-5.0.4-setup.patch
+++ /dev/null
@@ -1,110 +0,0 @@
---- extras/build.orig	2013-10-18 21:37:53.533939550 +1300
-+++ extras/build	2013-10-18 21:40:42.283158471 +1300
-@@ -41,7 +41,7 @@
- 
- errorprojs="" ; export errorprojs ;
- 
--PROJECTS="tcl tk zlib libpng libiconv libgd libgdc libprob libcprob newmat cprob newran cephes fftw"
-+PROJECTS="libgdc libprob libcprob newmat cprob newran cephes"
- 
- for projname in $PROJECTS; do
- 
---- build.orig	2013-10-18 22:24:22.312777248 +1300
-+++ build	2013-10-18 22:24:59.161835107 +1300
-@@ -11,8 +11,7 @@
- ifit load_varian load_dicom misc_scripts fdt first possum sgeutils flameo oxford_asl relax qboot topup ptx2 lesions eddy dwssfp";
- 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 $PROJECTS
-+echo "Finished build"
- 
---- config/common/buildproj.orig	2013-10-18 22:28:40.683182435 +1300
-+++ config/common/buildproj	2013-10-18 22:29:09.612227825 +1300
-@@ -11,10 +11,10 @@
- fi
- PROJECTS="$@" ; 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 ;
---- config/generic/systemvars.mk.orig	2007-07-13 23:00:20.000000000 +1200
-+++ config/generic/systemvars.mk	2013-10-18 23:13:06.472693414 +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
---- config/common/vars.mk.orig	2013-10-18 23:39:26.384029157 +1300
-+++ config/common/vars.mk	2013-10-18 23:40:49.489145387 +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} ${DBGFLAGS} ${USEDCSTATICFLAGS} ${USRCFLAGS} ${ARCHFLAGS} ${OPTFLAGS}  \
--	${AccumulatedIncFlags}
-+	${AccumulatedIncFlags} ${USERCFLAGS}
- 
- CXXFLAGS = ${ANSI_FLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS}  \
--	${AccumulatedIncFlags}
-+	${AccumulatedIncFlags} ${USERCXXFLAGS}
- 
- HFILES = *.h
- AFILES = *.a
---- config/common/buildproj.orig	2013-10-19 23:27:10.477238469 +1300
-+++ config/common/buildproj	2013-10-19 23:28:32.207370622 +1300
-@@ -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 --git a/sci-biology/fsl/files/fsl-5.0.6-fsldir_redux.patch b/sci-biology/fsl/files/fsl-5.0.6-fsldir_redux.patch
deleted file mode 100644
index a4fff260f..000000000
--- a/sci-biology/fsl/files/fsl-5.0.6-fsldir_redux.patch
+++ /dev/null
@@ -1,456 +0,0 @@
---- src/fast4/fast_two.cc.orig	2013-10-19 23:45:02.636971888 +1300
-+++ src/fast4/fast_two.cc	2013-10-19 23:46:45.436138299 +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);
---- src/feat5/tsplot.cc.orig	2013-10-19 23:48:08.997273362 +1300
-+++ src/feat5/tsplot.cc	2013-10-19 23:50:59.376548902 +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 */
---- src/feat5/feat_model.cc.orig	2013-10-19 23:52:13.456668655 +1300
-+++ src/feat5/feat_model.cc	2013-10-19 23:53:31.655795065 +1300
-@@ -734,7 +734,6 @@
-   vector<int> G;
-   vector<string> titles;
-   float  tr, mult, trmult, nltffwhm=0, maxconvwin=0;
--  char   fl[10000], *FSLDIR;
-   string fn, filename;
-   FONT_DATA *font_data = new FONT_DATA[1];
- 
-@@ -753,8 +752,6 @@
-   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));
-@@ -1479,7 +1476,7 @@
-   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);
-@@ -2122,6 +2119,6 @@
- 
-     fclose(outputfile);
- 
--    filename=string(getenv("FSLDIR")) + "/bin/wpng -q -overwrite  " + filename;
-+    filename="wpng -q -overwrite  " + filename;
-     system(filename.c_str());
- }
---- src/first/first_utils.cc.orig	2013-10-19 23:54:30.375890034 +1300
-+++ src/first/first_utils.cc	2013-10-19 23:59:11.706344887 +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;
---- src/fnirt/fnirtfns.cpp.orig	2013-10-20 00:00:18.106452166 +1300
-+++ src/fnirt/fnirtfns.cpp	2013-10-20 00:04:56.005901533 +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");
---- src/fslsurface/fslsurface_first.cc.orig	2013-10-20 00:05:35.495965454 +1300
-+++ src/fslsurface/fslsurface_first.cc	2013-10-20 00:06:54.346092913 +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);
- 			
---- src/fslsurface/fslsurfacemaths.cpp.orig	2013-10-20 00:07:39.457165850 +1300
-+++ src/fslsurface/fslsurfacemaths.cpp	2013-10-20 00:09:28.396341998 +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;
---- src/libvis/miscpic.h.orig	2013-10-20 00:11:03.706496109 +1300
-+++ src/libvis/miscpic.h	2013-10-20 00:12:24.515626764 +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;
---- src/melodic/melreport.cc.orig	2013-10-20 00:13:01.475686492 +1300
-+++ src/melodic/melreport.cc	2013-10-20 00:15:02.795882687 +1300
-@@ -85,7 +85,7 @@
- 
-       {//start IC page
- 				IChtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
--					(string) getenv("FSLDIR") +"/doc/fsl.css>" << endl
-+					"@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 
-@@ -488,7 +488,7 @@
-       {//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
-+					"@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;
- 	
---- src/melodic/meloptions.cc.orig	2013-10-20 00:15:46.755953769 +1300
-+++ src/melodic/meloptions.cc	2013-10-20 00:18:26.176211442 +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++);
- 
---- src/melodic/meloptions.h.orig	2013-10-20 00:19:32.176318206 +1300
-+++ src/melodic/meloptions.h	2013-10-20 00:19:53.455352701 +1300
-@@ -93,7 +93,6 @@
-   	~MelodicOptions() { delete gopt; }
-   
-   	string version;
--  	string binpath;
-   	string logfname;
-   	bool   filtermode;
-   	bool   explicitnums;
---- src/melodic/meldata.cc.orig	2013-10-20 00:20:45.856437466 +1300
-+++ src/melodic/meldata.cc	2013-10-20 00:21:48.655538924 +1300
-@@ -921,7 +921,7 @@
-   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){
-@@ -1086,7 +1086,7 @@
- 				// 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";
- 
---- src/melodic/melreport.h.orig	2013-10-20 00:22:41.816624872 +1300
-+++ src/melodic/melreport.h	2013-10-20 00:24:25.555792499 +1300
-@@ -105,20 +105,20 @@
- 		    		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>" 
-+							"@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>" 
-+							"@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;
-+							"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>"  << endl;
- 						head << "<link REL=stylesheet TYPE=text/css href=file:"+
--							(string) getenv("FSLDIR") +"/doc/fsl.css>"  << endl;
-+							"@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;
---- src/mm/mixture_model.cc.orig	2013-10-20 00:25:00.355848878 +1300
-+++ src/mm/mixture_model.cc	2013-10-20 00:25:32.185900186 +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;
---- src/siena/siena_diff.cc.orig	2013-10-20 00:26:13.215966685 +1300
-+++ src/siena/siena_diff.cc	2013-10-20 00:28:03.925145734 +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);
-   }
---- src/topup/topupfns.cpp.orig	2013-10-20 00:28:36.456198320 +1300
-+++ src/topup/topupfns.cpp	2013-10-20 00:29:37.905297565 +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");
---- etc/matlab/call_fsl.m.orig	2013-10-20 23:17:58.626045346 +1300
-+++ etc/matlab/call_fsl.m	2013-10-20 23:20:06.556252150 +1300
-@@ -8,7 +8,7 @@
- % Debian/Ubuntu users should uncomment as
- % indicated
- 
--fsldir=getenv('FSLDIR');
-+%fsldir=getenv('FSLDIR');
- 
- % Debian/Ubuntu - uncomment the following
- %fsllibdir=sprintf('%s/%s', fsldir, 'bin');
---- etc/js/label-div.html.orig	2013-10-20 23:22:04.906443685 +1300
-+++ etc/js/label-div.html	2013-10-20 23:23:35.006589232 +1300
-@@ -2,12 +2,12 @@
-   <head>
-     <title>label-div</title>
-     <!--[if IE]>
--    <script type="text/javascript" src="FSLDIR/etc/js/excanvas.js"></script>
-+    <script type="text/javascript" src="@GENTOO_PORTAGE_EPREFIX@/etc/js/excanvas.js"></script>
-     <![endif]-->
--    <script type="text/javascript" src="FSLDIR/etc/js/strftime-min.js"></script>
--    <script type="text/javascript" src="FSLDIR/etc/js/rgbcolor.js"></script>
--    <script type="text/javascript" src="FSLDIR/etc/js/dygraph-canvas.js"></script>
--    <script type="text/javascript" src="FSLDIR/etc/js/dygraph.js"></script>
-+    <script type="text/javascript" src="@GENTOO_PORTAGE_EPREFIX@/etc/js/strftime-min.js"></script>
-+    <script type="text/javascript" src="@GENTOO_PORTAGE_EPREFIX@/etc/js/rgbcolor.js"></script>
-+    <script type="text/javascript" src="@GENTOO_PORTAGE_EPREFIX@/etc/js/dygraph-canvas.js"></script>
-+    <script type="text/javascript" src="@GENTOO_PORTAGE_EPREFIX@/etc/js/dygraph.js"></script>
-     <script type="text/javascript" src="PNMDATA.js"></script>
-   </head>
-   <body>
diff --git a/sci-biology/fsl/files/fsl-5.0.8-fsldir_redux.patch b/sci-biology/fsl/files/fsl-5.0.8-fsldir_redux.patch
deleted file mode 100644
index 593c1c807..000000000
--- a/sci-biology/fsl/files/fsl-5.0.8-fsldir_redux.patch
+++ /dev/null
@@ -1,452 +0,0 @@
-diff -Naur src.orig/fast4/fast_two.cc src/fast4/fast_two.cc
---- src.orig/fast4/fast_two.cc	2015-03-30 11:54:10.522550233 +1300
-+++ src/fast4/fast_two.cc	2015-03-30 11:54:18.412569892 +1300
-@@ -166,7 +166,7 @@
- string csfPriorName, grayPriorName, whitePriorName;
-   if(alternatePriors.unset())
-   {
--    string priorRootName=string(getenv("FSLDIR")) + "/data/standard/tissuepriors/avg152T1_";
-+    string priorRootName="@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/tissuepriors/avg152T1_";
-     csfPriorName = priorRootName+"csf";
-     grayPriorName = priorRootName+"gray";
-     whitePriorName = priorRootName+"white";
-@@ -215,15 +215,15 @@
-     if(bapused>0)
-       {
- 	char reg[1024];
--	sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), csfPriorName.c_str(), (main_prior_vol+"_csf_stdspace").c_str(),  bapriori.value().c_str());
-+	sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), csfPriorName.c_str(), (main_prior_vol+"_csf_stdspace").c_str(),  bapriori.value().c_str());
-         if(verbose.value())
- 	  cout<<reg<<endl;
- 	system(reg);
--	sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), grayPriorName.c_str(), (main_prior_vol+"_gm_stdspace").c_str(),  bapriori.value().c_str());
-+	sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), grayPriorName.c_str(), (main_prior_vol+"_gm_stdspace").c_str(),  bapriori.value().c_str());
- 	if(verbose.value())
- 	  cout<<reg<<endl;
-         system(reg);
--	sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), whitePriorName.c_str(), (main_prior_vol+"_wm_stdspace").c_str(),  bapriori.value().c_str());
-+	sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), whitePriorName.c_str(), (main_prior_vol+"_wm_stdspace").c_str(),  bapriori.value().c_str());
- 	if(verbose.value())
- 	  cout << reg << endl;
- 	system(reg);
-diff -Naur src.orig/feat5/feat_model.cc src/feat5/feat_model.cc
---- src.orig/feat5/feat_model.cc	2015-03-30 11:54:10.502550183 +1300
-+++ src/feat5/feat_model.cc	2015-03-30 11:54:18.412569892 +1300
-@@ -741,7 +741,7 @@
-   vector<int> G;
-   vector<string> titles;
-   float  tr, mult, trmult, nltffwhm=0, maxconvwin=0;
--  char   fl[10000], *FSLDIR;
-+  char   fl[10000];
-   string fn, filename;
-   FONT_DATA *font_data = new FONT_DATA[1];
- 
-@@ -760,8 +760,6 @@
-   if (argc==3)
-     motionparams=remmean(read_ascii_matrix(argv[2]));
- 
--  FSLDIR=getenv("FSLDIR");
--
-   fn = string(argv[1])+".fsf";
- 
-   level      = atoi(find_line(fn, "fmri(level)", fl));
-@@ -1491,7 +1489,7 @@
-   writeCovarianceImage(string(argv[1])+"_cov.ppm", contrasts, F, nftests, realDesign, level, evs.eigenvals, font_data, contrasts.RE);
-   writeImagePreview(string(argv[1])+".ppm", contrasts, F, nftests, realDesign, level, evs, font_data, titles, tr, nltffwhm, nTimepoints, G);
- 
--  filename=string(getenv("FSLDIR"))+"/bin/wpng -q -overwrite  "+string(argv[1])+".ppm ";
-+  filename="wpng -q -overwrite  "+string(argv[1])+".ppm ";
-   system(filename.c_str());
- 
-   return(0);
-@@ -2134,6 +2132,6 @@
- 
-     fclose(outputfile);
- 
--    filename=string(getenv("FSLDIR")) + "/bin/wpng -q -overwrite  " + filename;
-+    filename="wpng -q -overwrite  " + filename;
-     system(filename.c_str());
- }
-diff -Naur src.orig/feat5/tsplot.cc src/feat5/tsplot.cc
---- src.orig/feat5/tsplot.cc	2015-03-30 11:54:10.502550183 +1300
-+++ src/feat5/tsplot.cc	2015-03-30 11:54:18.412569892 +1300
-@@ -293,7 +293,7 @@
- ofstream     outputFile;
- int          numEVs, npts, numContrasts=1, nftests=0, GRPHSIZE(600), PSSIZE(600); 
- vector<double> normalisedContrasts, model, triggers;
-- string       fmriFileName, fslPath, featdir, vType, indexText;
-+ string       fmriFileName, featdir, vType, indexText;
- ColumnVector NewimageVoxCoord(4),NiftiVoxCoord(4);
- bool outputText(true), useCoordinate(false), prewhiten(false), useTriggers(false), customMask(false), modelFree(false), isHigherLevel(false), outputDataOnly(false);
- bool zWeightClusters(true);
-@@ -307,7 +307,6 @@
-   if (argc<2) usage("");
-   featdir=string(argv[1]);
-   fmriFileName=featdir+"/filtered_func_data";
--  fslPath=string(getenv("FSLDIR"));
- 
-   string outputName(featdir);
- 
-@@ -725,7 +724,7 @@
- 	cerr << "Can't open output report file " << outputName << endl;
- 	exit(1);
-       }
--      outputFile << "<HTML>\n<TITLE>"<< statType << num2str(i) <<"</TITLE>\n<BODY BACKGROUND=\"file:"<< fslPath <<"/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report - "<< statType << num2str(i) <<"</H1>\n</CENTER>\n<hr><b>Full plots</b><p>\n"<< graphText;
-+      outputFile << "<HTML>\n<TITLE>"<< statType << num2str(i) <<"</TITLE>\n<BODY BACKGROUND=\"file:"<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report - "<< statType << num2str(i) <<"</H1>\n</CENTER>\n<hr><b>Full plots</b><p>\n"<< graphText;
-       if (useTriggers) outputFile << "\n<hr><b>Peristimulus plots</b><p>\n"<< peristimulusText <<"\n<HR></BODY></HTML>\n\n";
-       else outputFile << "\n</BODY></HTML>\n\n";
-       outputFile.close();
-@@ -740,7 +739,7 @@
-       cerr << "Can't open output report file " << outputName << endl;
-       exit(1);
-   }
--  outputFile << "<HTML>\n<TITLE>FEAT Time Series Report</TITLE>\n<BODY BACKGROUND=\"file:" << fslPath << "/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report</H1>\n</CENTER>\n<hr>" << indexText << "<HR></BODY></HTML>" << endl << endl;
-+  outputFile << "<HTML>\n<TITLE>FEAT Time Series Report</TITLE>\n<BODY BACKGROUND=\"file:" << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report</H1>\n</CENTER>\n<hr>" << indexText << "<HR></BODY></HTML>" << endl << endl;
-   outputFile.close();
- 
-   /* now output same thing without start and end, for inclusion in feat report */
-diff -Naur src.orig/first/first_utils.cc src/first/first_utils.cc
---- src.orig/first/first_utils.cc	2015-03-30 11:54:10.482550135 +1300
-+++ src/first/first_utils.cc	2015-03-30 11:54:18.412569892 +1300
-@@ -1954,8 +1954,8 @@
-     if (!surfaceVAout.value()) {
-       // do not output on the surface, instead do the new default of outputting a volume with the scalar normal dot product values (for use with randomise)
-       volume<float> refim;
--      if (useReconMNI.value()) { read_volume(refim,string(getenv("FSLDIR")) + "/data/standard/MNI152_T1_1mm"); } 
--      else { read_volume(refim,string(getenv("FSLDIR")) + "/data/standard/MNI152_T1_1mm"); } 
-+      if (useReconMNI.value()) { read_volume(refim,"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); } 
-+      else { read_volume(refim,"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); } 
-       volume<float> maskvol(refim);
-       maskvol=0.0f;
-       volume4D<float> volnormals;
-diff -Naur src.orig/fnirt/fnirtfns.cpp src/fnirt/fnirtfns.cpp
---- src.orig/fnirt/fnirtfns.cpp	2015-03-30 11:54:10.522550233 +1300
-+++ src/fnirt/fnirtfns.cpp	2015-03-30 11:54:18.412569892 +1300
-@@ -1203,8 +1203,7 @@
-       return(string(ref_fname));
-     }
-     else {
--      const char *fsldir_ptr = getenv("FSLDIR");
--      string eref_fname = string(fsldir_ptr) + string("/data/standard/") + ref_fname;
-+      string eref_fname = string("@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/") + ref_fname;
-       if (NEWIMAGE::fsl_imageexists(eref_fname)) return(eref_fname);
-       else return(string(""));
-     }
-@@ -1230,9 +1229,8 @@
-       NEWIMAGE::read_volume_hdr_only(vref,ref_fname); // Throws if file dont exist
-       eref_fname = ref_fname;
-     }
--    catch(...) { // Didn't exist in current directory, try in ${FSLDIR}/data/standard
--      const char *fsldir_ptr = getenv("FSLDIR");
--      eref_fname = string(fsldir_ptr) + string("/data/standard/") + ref_fname;
-+    catch(...) { // Didn't exist in current directory, try in .../data/standard
-+      eref_fname = string("@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/") + ref_fname;
-       try {
-         cout << "Could not find " << ref_fname << ", now checking " << eref_fname << endl;
-         NEWIMAGE::read_volume_hdr_only(vref,eref_fname); // Throws if file dont exist
-@@ -1267,8 +1265,7 @@
-     if (check_exist(ecfname)) return(ecfname);
-   }
-   if (!FNIRT::path(cfname).length()) {              // If no path explicitly given
--    const char *fsldir_ptr = getenv("FSLDIR");
--    ecfname = string(fsldir_ptr) + string("/etc/flirtsch/") + cfname;
-+    ecfname = string("@GENTOO_PORTAGE_EPREFIX@/etc/flirtsch/") + cfname;
-     if (check_exist(ecfname)) return(ecfname);
-     else if (!FNIRT::extension(ecfname).length()) { // If no path _and_ no extension given
-       ecfname += string(".cnf");
-diff -Naur src.orig/fslsurface/fslsurface_first.cc src/fslsurface/fslsurface_first.cc
---- src.orig/fslsurface/fslsurface_first.cc	2015-03-30 11:54:10.522550233 +1300
-+++ src/fslsurface/fslsurface_first.cc	2015-03-30 11:54:18.412569892 +1300
-@@ -500,8 +500,7 @@
-             
- 			volume<float>* immni = new volume<float>();
-             
--            char* fsldir = getenv("FSLDIR");
--            read_volume_hdr_only(*immni, string(fsldir) + "/data/standard/MNI152_T1_1mm");
-+            read_volume_hdr_only(*immni, "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm");
-             
- 			//read_volume_hdr_only(*immni, template_name);
- 			
-@@ -699,8 +698,7 @@
-           
- 			volume<float>* immni = new volume<float>();
-             
--            char* fsldir = getenv("FSLDIR");
--            read_volume_hdr_only(*immni, string(fsldir) + "/data/standard/MNI152_T1_1mm");
-+            read_volume_hdr_only(*immni, "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm");
-             
- 			//read_volume_hdr_only(*immni, template_name);
- 			
-diff -Naur src.orig/fslsurface/fslsurfacemaths.cpp src/fslsurface/fslsurfacemaths.cpp
---- src.orig/fslsurface/fslsurfacemaths.cpp	2015-03-30 11:54:10.522550233 +1300
-+++ src/fslsurface/fslsurfacemaths.cpp	2015-03-30 11:54:18.412569892 +1300
-@@ -598,12 +598,6 @@
- 
-         }else if (command == "-reconFromBvars"){
-             cout<<"do recon "<<endl;
--            char* fsldir = getenv("FSLDIR");
--            if (fsldir == NULL)
--            {
--                cerr<<"FSLDIR has not been set. "<<endl;
--                exit(EXIT_FAILURE); 
--            }
-             //file.bvars,mni_template.nii.gz
-            // string mni = string(fsldir)+"/data/standard/MNI152_T1_1mm";
-             reconSurface_from_bvars( surf, string(argv[i_arg+1]));
-@@ -612,12 +606,6 @@
- 
-         }else if (command == "-reconAllFromBvarsAndSave"){
-             cout<<"do recon+save "<<argc<<" "<<i_arg<<endl;
--            char* fsldir = getenv("FSLDIR");
--            if (fsldir == NULL)
--            {
--                cerr<<"FSLDIR has not been set. "<<endl;
--                exit(EXIT_FAILURE); 
--            }
-             //file.bvars,mni_template.nii.gz
-             // string mni = string(fsldir)+"/data/standard/MNI152_T1_1mm";
-             cout<<"recon "<< string(argv[i_arg+1])<<endl;
-diff -Naur src.orig/libvis/miscpic.h src/libvis/miscpic.h
---- src.orig/libvis/miscpic.h	2015-03-30 11:54:10.482550135 +1300
-+++ src/libvis/miscpic.h	2015-03-30 11:54:18.412569892 +1300
-@@ -89,12 +89,7 @@
- 	LR_label_flag = true;
- 	trans= -10;
- 	edgethresh = 0.0;
--	if(getenv("FSLDIR")!=0){
--	  lutbase = string(getenv("FSLDIR")) + "/etc/luts/";
--	}
--	else{
--	  lutbase = string("/");
--	}
-+	lutbase = "@GENTOO_PORTAGE_EPREFIX@/etc/luts/";
- 	title = string("");
- 	cbartype = string("");
- 	cbarptr = NULL;
-diff -Naur src.orig/melodic/meldata.cc src/melodic/meldata.cc
---- src.orig/melodic/meldata.cc	2015-03-30 11:54:10.502550183 +1300
-+++ src/melodic/meldata.cc	2015-03-30 11:54:18.412569892 +1300
-@@ -971,7 +971,7 @@
-   void MelodicData::est_smoothness()
-   {
-     if(Resels == 0){
--      string SM_path = opts.binpath + "smoothest";
-+      string SM_path = "smoothest";
-       string Mask_fname = logger.appendDir("mask");
- 
-       if(opts.segment.value().length()>0){
-@@ -1136,7 +1136,7 @@
- 				// set up all strings
- 				string BET_outputfname = string(Mean_fname)+"_brain";
- 
--				string BET_path = opts.binpath + "bet";
-+				string BET_path = "bet";
- 				string BET_optarg = "-m -f 0.4"; // see man bet
- 				string Mask_fname = BET_outputfname+"_mask";
- 
-diff -Naur src.orig/melodic/meloptions.cc src/melodic/meloptions.cc
---- src.orig/melodic/meloptions.cc	2015-03-30 11:54:10.502550183 +1300
-+++ src/melodic/meloptions.cc	2015-03-30 11:54:18.412569892 +1300
-@@ -93,14 +93,6 @@
-   		explicitnums = false;
-   		logfname = string("log.txt");
- 
--  		// work out the path to the $FSLDIR/bin directory
--  		if(getenv("FSLDIR")!=0){
--    		binpath = (string) getenv("FSLDIR") + "/bin/";
--  		} else{
--    		binpath = argv[0];
--    		binpath = binpath.substr(0,binpath.length()-7);
--  		}
--
-   		// parse once to establish log directory name
-   		for(int a = options.parse_command_line(argc, argv); a < argc; a++);
- 
-diff -Naur src.orig/melodic/meloptions.h src/melodic/meloptions.h
---- src.orig/melodic/meloptions.h	2015-03-30 11:54:10.502550183 +1300
-+++ src/melodic/meloptions.h	2015-03-30 11:54:18.412569892 +1300
-@@ -93,7 +93,6 @@
-   	~MelodicOptions() { delete gopt; }
-   
-   	string version;
--  	string binpath;
-   	string logfname;
-   	bool   filtermode;
-   	bool   explicitnums;
-diff -Naur src.orig/melodic/melreport.cc src/melodic/melreport.cc
---- src.orig/melodic/melreport.cc	2015-03-30 11:54:10.502550183 +1300
-+++ src/melodic/melreport.cc	2015-03-30 11:54:18.412569892 +1300
-@@ -84,8 +84,8 @@
- 			IChtml.setDir(report.getDir(),mmodel.get_prefix()+".html");
- 
-       {//start IC page
--				IChtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
--					(string) getenv("FSLDIR") +"/doc/fsl.css>" << endl
-+				IChtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
-+				       << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl
- 					<< "<style type=\"text/css\">OBJECT { width: 100% }</style>"
- 	       	<< "<TITLE>FSL</TITLE></HEAD>" << endl
- 	  			<< "<IFRAME  height=" << int(melodat.get_numfiles()/30 + 1)*50 
-@@ -487,8 +487,8 @@
- 
-       {//start IC2 page
- 				IChtml2.setDir(report.getDir(),mmodel.get_prefix()+"_MM.html");
--				IChtml2 << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
--					(string) getenv("FSLDIR") +"/doc/fsl.css>" << endl
-+				IChtml2 << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
-+					<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl
- 					<< "<style type=\"text/css\">OBJECT { width: 100% }</style>"
- 	       	<< "<TITLE>FSL</TITLE></HEAD>" << endl
- 					<< "<IFRAME  height="<< int(melodat.get_numfiles()/30 + 1)*50 
-@@ -666,8 +666,8 @@
- 				IChtml << "<HTML> " << endl
- 	       	<< "<TITLE>MELODIC Component " << num2str(cnum)
- 	       	<< "</TITLE>" << endl
--	       	<< "<BODY BACKGROUND=\"file:" << getenv("FSLDIR") 
--	    		<< "/doc/images/fsl-bg.jpg\">" << endl 
-+	       	<< "<BODY BACKGROUND=\"file:"  
-+	    		<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl 
- 	     		<< "<hr><CENTER><H1>MELODIC Component " << num2str(cnum)
- 	       	<< "</H1>"<< endl;
- 	
-diff -Naur src.orig/melodic/melreport.h src/melodic/melreport.h
---- src.orig/melodic/melreport.h	2015-03-30 11:54:10.502550183 +1300
-+++ src/melodic/melreport.h	2015-03-30 12:11:17.995116883 +1300
-@@ -104,21 +104,21 @@
- 	  				const time_t tmptime = time(NULL);
- 		    		system(("mkdir "+ logger.appendDir("report") + " 2>/dev/null").c_str());
- 				report.setDir(logger.appendDir("report"),"00index.html",true,false,ios::out);
--						report << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
--							(string) getenv("FSLDIR") +"/doc/fsl.css>" 
-+						report << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
-+							<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" 
- 						  << "<TITLE>MELODIC report</TITLE></HEAD><BODY>"
- 							<< endl <<endl;
- 						loghtml.setDir(report.getDir(),"log.html");
--						loghtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
--							(string) getenv("FSLDIR") +"/doc/fsl.css>" 
-+						loghtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
-+							<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" 
- 						  << "<TITLE>MELODIC report</TITLE></HEAD><BODY>"
- 							<< endl <<endl;						
- 						navigator.setDir(report.getDir(),"nav.html");
- 						head.setDir(report.getDir(),"head.html");
--	  				navigator << "<link REL=stylesheet TYPE=text/css href=file:"+
--							(string) getenv("FSLDIR") +"/doc/fsl.css>"  << endl;
--						head << "<link REL=stylesheet TYPE=text/css href=file:"+
--							(string) getenv("FSLDIR") +"/doc/fsl.css>"  << endl;
-+	  				navigator << "<link REL=stylesheet TYPE=text/css href=file:"
-+						<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>"  << endl;
-+						head << "<link REL=stylesheet TYPE=text/css href=file:"
-+							<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>"  << endl;
- 						head  <<"<TABLE BORDER=0><TR>" << endl
- 							<<" <TD ALIGN=CENTER WIDTH=100%>"<< endl
- 							<<"<TABLE BORDER=0>"<< endl
-@@ -130,8 +130,8 @@
- 							<< "</tr></table>" << endl
- 							<< "<TD ALIGN=RIGHT>" << endl
- 							<< "<a href=http://www.fmrib.ox.ac.uk/fsl target=_top>" << endl
--						  << "<IMG BORDER=0 SRC=file:"<< getenv("FSLDIR")
--							<< "/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl
-+						  << "<IMG BORDER=0 SRC=file:"
-+							<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl
- 							<< "</TD>"<<endl<<"</TR></TABLE> <hr>"<<endl;
- 						if(opts.guireport.value()==""){
- 							report <<"<OBJECT data=head.html></OBJECT>" <<  endl;
-diff -Naur src.orig/mm/mixture_model.cc src/mm/mixture_model.cc
---- src.orig/mm/mixture_model.cc	2015-03-30 11:54:10.522550233 +1300
-+++ src/mm/mixture_model.cc	2015-03-30 11:54:18.412569892 +1300
-@@ -2224,8 +2224,8 @@
- 
- 	htmllog << "<HTML> " << endl
- 		<< "<TITLE>Mixture Model fit for" << data_name << "</TITLE>" << endl
--		<< "<BODY BACKGROUND=\"file:" << getenv("FSLDIR") 
--		<< "/doc/images/fsl-bg.jpg\">" << endl 
-+		<< "<BODY BACKGROUND=\"file:"  
-+		<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl 
- 		<< "<hr><CENTER><H1>Mixture Model fit for<br>" << data_name << " </H1>"<< endl;
-      	
- 	htmllog << "<hr><p>" << endl;
-diff -Naur src.orig/siena/siena_diff.cc src/siena/siena_diff.cc
---- src.orig/siena/siena_diff.cc	2015-03-30 11:54:10.482550135 +1300
-+++ src/siena/siena_diff.cc	2015-03-30 11:54:18.412569892 +1300
-@@ -107,7 +107,7 @@
- {
-   // {{{  vars
- 
--char   thestring[10000], segoptions[10000], fsldir[10000];
-+char   thestring[10000], segoptions[10000];
- int    x_size, y_size, z_size, size, x, y, z, i, count,
-   seg2=0, ignore_z=0, ignore_top_slices=0, //erode_mask=0, 
-   ignore_bottom_slices=0, debug=0, flow_output=1, edge_masking=0;
-@@ -124,8 +124,6 @@
- 
- string argv1(argv[1]), argv2(argv[2]);
- 
--sprintf(fsldir,"%s",getenv("FSLDIR"));
--
- for (i = 3; i < argc; i++) {
-   if (!strcmp(argv[i], "-i"))
-     ignore_z=1;
-@@ -209,26 +207,26 @@
- // }}}
-   // {{{  transform images and masks
- 
--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
--	fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
-+sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
-+	argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
- printf("%s\n",thestring); system(thestring);
- 
--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
--	fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
-+sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
-+	argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
- printf("%s\n",thestring); system(thestring);
- 
--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
--	fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
-+sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
-+	argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
- printf("%s\n",thestring); system(thestring);
- 
--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
--	fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
-+sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
-+	argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
- printf("%s\n",thestring); system(thestring);
- 
- if (edge_masking)
- {
--  sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s",
--	  fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
-+  sprintf(thestring,"flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s",
-+	  argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
-   printf("%s\n",thestring); system(thestring);
- }
- 
-@@ -287,8 +285,8 @@
-     cout << "saving image 1 to disk prior to segmentation" << endl;
-     save_volume(in1,argv1+"_halfwayto_"+argv2+"_brain");
-     in1.destroy();
--    sprintf(thestring,"%s/bin/fast %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1",
--	    fsldir,segtype,segoptions,argv[1],argv[2],argv[1],argv[2]);
-+    sprintf(thestring,"fast %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1",
-+	    segtype,segoptions,argv[1],argv[2],argv[1],argv[2]);
-     cout << thestring << endl;
-     system(thestring);
-   }
-diff -Naur src.orig/topup/topupfns.cpp src/topup/topupfns.cpp
---- src.orig/topup/topupfns.cpp	2015-03-30 11:54:10.522550233 +1300
-+++ src/topup/topupfns.cpp	2015-03-30 11:54:18.412569892 +1300
-@@ -463,8 +463,7 @@
-     if (TOPUP::check_exist(ecfname)) return(ecfname);
-   }
-   if (!TOPUP::path(cfname).length()) {              // If no path explicitly given
--    const char *fsldir_ptr = getenv("FSLDIR");
--    ecfname = string(fsldir_ptr) + string("/etc/flirtsch/") + cfname;
-+    ecfname = string("@GENTOO_PORTAGE_EPREFIX@/etc/flirtsch/") + cfname;
-     if (TOPUP::check_exist(ecfname)) return(ecfname);
-     else if (!TOPUP::extension(ecfname).length()) { // If no path _and_ no extension given
-       ecfname += string(".cnf");
-
diff --git a/sci-biology/fsl/files/fsl-5.0.8-headers.patch b/sci-biology/fsl/files/fsl-5.0.8-headers.patch
deleted file mode 100644
index ab2ab3da3..000000000
--- a/sci-biology/fsl/files/fsl-5.0.8-headers.patch
+++ /dev/null
@@ -1,21 +0,0 @@
---- src/miscvis/writepng.c.orig	2013-10-19 00:18:32.415203592 +1300
-+++ 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 */
- 
---- src/ptx2/surfmaths.cc.orig	2013-10-19 00:19:51.595327317 +1300
-+++ src/ptx2/surfmaths.cc	2013-10-19 00:20:09.284354805 +1300
-@@ -72,7 +72,7 @@
- #include "csv_mesh.h"
- #include "miscmaths/miscmaths.h"
- #include "utils/fsl_isfinite.h"
--#include "libprob/libprob.h"
-+#include "libprob.h"
- 
- using namespace MISCMATHS;
- 
diff --git a/sci-biology/fsl/files/fsl-5.0.8-setup.patch b/sci-biology/fsl/files/fsl-5.0.8-setup.patch
deleted file mode 100644
index 0cbda5d5c..000000000
--- a/sci-biology/fsl/files/fsl-5.0.8-setup.patch
+++ /dev/null
@@ -1,113 +0,0 @@
-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
-@@ -11,8 +11,7 @@
- ifit load_varian load_dicom misc_scripts fdt first possum sgeutils flameo oxford_asl relax qboot topup ptx2 lesions eddy dwssfp";
- 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
-@@ -60,7 +60,7 @@
- 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"
- for projname in $PROJECTS; do
- 
-     if [ -d $FSLESRCDIR/$projname ] ; then
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
deleted file mode 100644
index c28fabe42..000000000
--- a/sci-biology/fsl/files/fsl-5.0.9-fsldir_redux.patch
+++ /dev/null
@@ -1,456 +0,0 @@
-# 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
index 663dc565c..f4da2bb50 100644
--- a/sci-biology/fsl/files/fsl-5.0.9-headers.patch
+++ b/sci-biology/fsl/files/fsl-5.0.9-headers.patch
@@ -1,6 +1,6 @@
 # Include zlib header directly.
 # From: Francois Bissey <frp.bissey@gmail.com>
-# Signed-off-by: Horea Christian <horea.christ@gmail.com>
+# Signed-off-by: Horea Christian <gentoo@chymera.eu>
 # 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
diff --git a/sci-biology/fsl/files/fsl-5.0.9-setup.patch b/sci-biology/fsl/files/fsl-5.0.9-setup.patch
deleted file mode 100644
index c688cd6e8..000000000
--- a/sci-biology/fsl/files/fsl-5.0.9-setup.patch
+++ /dev/null
@@ -1,115 +0,0 @@
-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/files/fsl-5.0.11-no_xmlpp.patch b/sci-biology/fsl/files/fsl-6.0.2-no_xmlpp.patch
index bccf0e238..6eccc4370 100644
--- a/sci-biology/fsl/files/fsl-5.0.11-no_xmlpp.patch
+++ b/sci-biology/fsl/files/fsl-6.0.2-no_xmlpp.patch
@@ -1,5 +1,16 @@
+From 9de29e5141afa43c06f347ca158b67168fbb0031 Mon Sep 17 00:00:00 2001
+From: François Bissey <frp.bissey@gmail.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 5389e2f..52785c3 100644
+index d22eb965..e967e682 100644
 --- a/src/flameo/Makefile
 +++ b/src/flameo/Makefile
 @@ -2,7 +2,7 @@ include ${FSLCONFDIR}/default.mk
@@ -15,13 +26,13 @@ index 5389e2f..52785c3 100644
          LIBS = -liconv
  endif
  
--LIBS += -lutils -lnewimage -lmiscmaths -lm -lnewmat -lfslio -lniftiio -lcifti -lxml++-2.6 -lxml2 -lboost_filesystem -lboost_system -lznz -lprob -lz 
-+LIBS += -lutils -lnewimage -lmiscmaths -lm -lnewmat -lfslio -lniftiio ${CIFTILIBS} -lboost_filesystem -lboost_system -lznz -lprob -lz 
+-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 53b951a..803c39e 100644
+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
@@ -37,8 +48,11 @@ index 53b951a..803c39e 100644
          LIBS = -liconv
  endif
  
--LIBS += -lutils -lnewimage -lmiscplot -lmiscpic -lmiscmaths -lfslio -lniftiio -lcifti -lxml++-2.6 -lxml2 -lboost_filesystem -lboost_system -lznz -lnewmat -lprob -lm  -lgdc -lgd -lpng -lz
-+LIBS += -lutils -lnewimage -lmiscplot -lmiscpic -lmiscmaths -lfslio -lniftiio ${CIFTILIBS} -lboost_filesystem -lboost_system -lznz -lnewmat -lprob -lm  -lgdc -lgd -lpng -lz
+-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-5.0.11-qstring_compat.patch b/sci-biology/fsl/files/fsl-6.0.2-qstring_compat.patch
index 78aa020c6..9e6682a48 100644
--- a/sci-biology/fsl/files/fsl-5.0.11-qstring_compat.patch
+++ b/sci-biology/fsl/files/fsl-6.0.2-qstring_compat.patch
@@ -1,8 +1,8 @@
-From bbd60f634cdcdfbbb3eb8f3b6d00f366d9f34bf9 Mon Sep 17 00:00:00 2001
-From: =?UTF-8?q?Fran=C3=A7ois=20Bissey?= <frp.bissey@gmail.com>
-Date: Thu, 18 Oct 2018 11:21:05 +1300
-Subject: [PATCH] Basic compatibility between for AString built with either
- glib ustring or QString
+From 5a5ab3c80eaaea1fe9a43659e2ea5b773b587bb0 Mon Sep 17 00:00:00 2001
+From: François Bissey <frp.bissey@gmail.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 ++--
@@ -11,15 +11,15 @@ Subject: [PATCH] Basic compatibility between for AString built with either
  3 files changed, 4 insertions(+), 4 deletions(-)
 
 diff --git a/src/flameo/gsa.cc b/src/flameo/gsa.cc
-index 6a477f9..0860d46 100644
+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(fslbasename(filename)+".nii");
-+      inputCifti.openFile((fslbasename(filename)+".nii").c_str());
+-      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;
@@ -27,13 +27,13 @@ index 6a477f9..0860d46 100644
        scalarsMap.setLength(data.Nrows());
        ciftiExemplar.setMap(0, scalarsMap);
        CiftiFile outputFile;
--      outputFile.setWritingFile(fslbasename(filename)+extension+".nii");//sets up on-disk writing with default writing version
-+      outputFile.setWritingFile((fslbasename(filename)+extension+".nii").c_str());//sets up on-disk writing with default writing version
+-      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 f310dc7..5e9bc18 100644
+index c4ad2349..1515e702 100644
 --- a/src/melodic/meldata.cc
 +++ b/src/melodic/meldata.cc
 @@ -118,7 +118,7 @@ namespace Melodic{
@@ -46,7 +46,7 @@ index f310dc7..5e9bc18 100644
  	  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 1e1adfc..d898152 100644
+index 49774003..f5326bdd 100644
 --- a/src/melodic/meldata.h
 +++ b/src/melodic/meldata.h
 @@ -109,7 +109,7 @@ namespace Melodic{
@@ -59,5 +59,5 @@ index 1e1adfc..d898152 100644
  	  cifti::CiftiScalarsMap scalarsMap;
  	  std::vector<char> foo = xml.writeXMLToVector();
 -- 
-2.18.1
+2.24.1
 
diff --git a/sci-biology/fsl/files/fsl-6.0.2-template.patch b/sci-biology/fsl/files/fsl-6.0.2-template.patch
new file mode 100644
index 000000000..597241a3b
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.2-template.patch
@@ -0,0 +1,55 @@
+Subject: as discussed in https://github.com/gentoo/sci/issues/963
+
+--- a/src/newimage/generalio.cc	2019-09-11 09:24:32.000000000 -0400
++++ b/src/newimage/generalio.cc §2020-08-07 20:30:20.037494201 -0400
+@@ -308,6 +308,41 @@
+   return 0;
+ }
+
++template
++int readGeneralVolume<double>(volume<double>& target, const string& filename,
++		  short& dtype, const bool swap2radiological,
++		  int64_t x0, int64_t y0, int64_t z0, int64_t t0, int64_t d50, int64_t d60, int64_t d70,
++		  int64_t x1, int64_t y1, int64_t z1, int64_t t1, int64_t d51, int64_t d61, int64_t d71,
++		  const bool readAs4D);
++
++template
++int readGeneralVolume<float>(volume<float>& target, const string& filename,
++		  short& dtype, const bool swap2radiological,
++		  int64_t x0, int64_t y0, int64_t z0, int64_t t0, int64_t d50, int64_t d60, int64_t d70,
++		  int64_t x1, int64_t y1, int64_t z1, int64_t t1, int64_t d51, int64_t d61, int64_t d71,
++		  const bool readAs4D);
++
++template
++int readGeneralVolume<short>(volume<short>& target, const string& filename,
++		  short& dtype, const bool swap2radiological,
++		  int64_t x0, int64_t y0, int64_t z0, int64_t t0, int64_t d50, int64_t d60, int64_t d70,
++		  int64_t x1, int64_t y1, int64_t z1, int64_t t1, int64_t d51, int64_t d61, int64_t d71,
++		  const bool readAs4D);
++
++template
++int readGeneralVolume<char>(volume<char>& target, const string& filename,
++		  short& dtype, const bool swap2radiological,
++		  int64_t x0, int64_t y0, int64_t z0, int64_t t0, int64_t d50, int64_t d60, int64_t d70,
++		  int64_t x1, int64_t y1, int64_t z1, int64_t t1, int64_t d51, int64_t d61, int64_t d71,
++		  const bool readAs4D);
++
++template
++int readGeneralVolume<int>(volume<int>& target, const string& filename,
++		  short& dtype, const bool swap2radiological,
++		  int64_t x0, int64_t y0, int64_t z0, int64_t t0, int64_t d50, int64_t d60, int64_t d70,
++		  int64_t x1, int64_t y1, int64_t z1, int64_t t1, int64_t d51, int64_t d61, int64_t d71,
++		  const bool readAs4D);
++
+ template int read_volumeROI(volume<char>& target, const string& filename,
+ 			      short& dtype,
+ 			      int64_t x0, int64_t y0, int64_t z0, int64_t t0,
+
+--- a/src/fslsurface/fslsurfaceio.cc	2019-09-11 09:23:11.000000000 -0400
++++ b/src/fslsurface/fslsurfaceio.cc	2020-08-08 04:17:55.917387550 -0400
+@@ -1055,6 +1055,7 @@
+ 	  return 0;
+ 	}
+
++  template int readGIFTI<float, unsigned int>( fslSurface<float, unsigned int> & surf, const string & filename);
+   template int writeGIFTI<float, unsigned int>( const fslSurface<float, unsigned int> & surf, const std::string & filename, int enc);
diff --git a/sci-biology/fsl/files/fsl-6.0.4-cuda_buildsettings.patch b/sci-biology/fsl/files/fsl-6.0.4-cuda_buildsettings.patch
new file mode 100644
index 000000000..749e80623
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-cuda_buildsettings.patch
@@ -0,0 +1,12 @@
+diff -Naur fsl.orig/config/buildSettings.mk fsl/config/buildSettings.mk
+--- fsl.orig/config/buildSettings.mk	2020-12-02 16:22:57.999912865 -0500
++++ fsl/config/buildSettings.mk	2020-12-02 16:24:15.332915270 -0500
+@@ -144,7 +144,7 @@
+ # CUDA development environment
+ CUDAVER := $(or $(CUDAVER),9.1)
+ #$(info $$CUDAVER is [${CUDAVER}])
+-CUDA_INSTALLATION = /opt/cuda-${CUDAVER}
++CUDA_INSTALLATION = /opt/cuda
+ ifdef SINGULARITY_NAME
+ CUDA_INSTALLATION = /usr/local/cuda-${CUDAVER}
+ endif
diff --git a/sci-biology/fsl/files/fsl-6.0.4-eddy_cuda.patch b/sci-biology/fsl/files/fsl-6.0.4-eddy_cuda.patch
new file mode 100644
index 000000000..ad118c39a
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-eddy_cuda.patch
@@ -0,0 +1,21 @@
+diff -Naur fsl.orig/src/eddy/Makefile fsl/src/eddy/Makefile
+--- fsl.orig/src/eddy/Makefile	2020-12-02 16:07:47.327884548 -0500
++++ fsl/src/eddy/Makefile	2020-12-02 16:11:21.149891196 -0500
+@@ -29,6 +29,8 @@
+ TMPCXXFLAGS_2=
+ TMPNAME_1=
+ TMPNAME_2=
++cuda=1
++cpu=1
+ TOPUP_DIR=../topup
+ 
+ ifndef cuda
+@@ -74,7 +75,7 @@
+ ifdef NVCC11
+ 	NVCC=${NVCC11}
+ endif
+-NVCCFLAGS=-c -DCOMPILE_GPU -O3 -m 64 -std=c++11
++NVCCFLAGS=-c -DCOMPILE_GPU -O3 -m 64 -std=c++11 @@GENTOO_NVCC_FLAGS@@
+ ifeq ($(CLOBBER_CLANG),1)
+    NVCCFLAGS+= -DCLOBBER_CLANG
+ endif
diff --git a/sci-biology/fsl/files/fsl-6.0.4-fdt_cuda.patch b/sci-biology/fsl/files/fsl-6.0.4-fdt_cuda.patch
new file mode 100644
index 000000000..7f322027b
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-fdt_cuda.patch
@@ -0,0 +1,14 @@
+diff -Naur fsl.orig/src/fdt/Makefile fsl/src/fdt/Makefile
+--- fsl.orig/src/fdt/Makefile	2020-12-02 19:06:55.826218772 -0500
++++ fsl/src/fdt/Makefile	2020-12-02 19:08:02.883220858 -0500
+@@ -6,7 +6,9 @@
+      $(eval $($(PROJNAME)_MASTERBUILD))
+ endif
+ 
+-ifeq ($(COMPILE_GPU), 1)
++# disable CUDA support for fdt
++#ifeq ($(COMPILE_GPU), 1)
++ifeq (0, 1)
+ 	COMPILE_WITH_GPU=libbedpostx_cuda.so merge_parts_gpu xfibres_gpu CUDA/split_parts_gpu
+ 	SCRIPTS_GPU=CUDA/bedpostx_gpu CUDA/bedpostx_postproc_gpu.sh
+ endif
diff --git a/sci-biology/fsl/files/fsl-6.0.4-flameo_std.patch b/sci-biology/fsl/files/fsl-6.0.4-flameo_std.patch
new file mode 100644
index 000000000..a991f1ed3
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-flameo_std.patch
@@ -0,0 +1,11 @@
+diff -Naur fsl.orig/src/flameo/Makefile fsl/src/flameo/Makefile
+--- fsl.orig/src/flameo/Makefile	2021-01-06 14:04:35.728274475 -0500
++++ fsl/src/flameo/Makefile	2021-01-06 14:08:18.204269285 -0500
+@@ -4,6 +4,7 @@
+ 
+ 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
+ USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_ZLIB}
++USRCXXFLAGS = -std=c++11
+ 
+ UNAME := $(shell uname)
+ ifeq (${UNAME},Darwin)
diff --git a/sci-biology/fsl/files/fsl-6.0.4-fsldir_redux-p1.patch b/sci-biology/fsl/files/fsl-6.0.4-fsldir_redux-p1.patch
new file mode 100644
index 000000000..ca3945442
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-fsldir_redux-p1.patch
@@ -0,0 +1,240 @@
+From 2bc4be1f55b27a733e1e624b34bc570187ba95e1 Mon Sep 17 00:00:00 2001
+From: François Bissey <frp.bissey@gmail.com>
+Date: Mon, 20 Jan 2020 11:40:53 +1300
+Subject: [PATCH] Making sure fsl code and executable can find other executable
+ and data in standard location.
+
+---
+ src/fast4/fast_two.cc              |  8 ++++----
+ src/feat5/feat_model.cc            |  8 +++-----
+ src/feat5/tsplot.cc                |  7 +++----
+ src/first/first_utils.cc           |  4 ++--
+ src/fnirt/fnirtfns.cpp             | 11 ++++-------
+ src/fslsurface/fslsurface_first.cc |  6 ++----
+ src/fslsurface/fslsurfacemaths.cpp | 12 ------------
+ src/libvis/miscpic.h               |  7 +------
+ src/melodic/meldata.cc             |  4 ++--
+ src/melodic/meloptions.cc          |  8 --------
+ src/melodic/meloptions.h           |  1 -
+ src/melodic/melreport.cc           | 12 ++++++------
+ src/melodic/melreport.h            | 20 ++++++++++----------
+ src/mm/mixture_model.cc            |  4 ++--
+ src/siena/siena_diff.cc            | 28 +++++++++++++---------------
+ src/topup/topupfns.cpp             |  3 +--
+ 16 files changed, 53 insertions(+), 90 deletions(-)
+
+diff --git a/src/fast4/fast_two.cc b/src/fast4/fast_two.cc
+index 592b5df..b525444 100644
+--- a/src/fast4/fast_two.cc
++++ b/src/fast4/fast_two.cc
+@@ -166,7 +166,7 @@ int prior_registration(string inname, string main_prior_vol, NEWIMAGE::volume<fl
+ string csfPriorName, grayPriorName, whitePriorName;
+   if(alternatePriors.unset())
+   {
+-    string priorRootName=string(getenv("FSLDIR")) + "/data/standard/tissuepriors/avg152T1_";
++    string priorRootName="@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/tissuepriors/avg152T1_";
+     csfPriorName = priorRootName+"csf";
+     grayPriorName = priorRootName+"gray";
+     whitePriorName = priorRootName+"white";
+@@ -215,15 +215,15 @@ string csfPriorName, grayPriorName, whitePriorName;
+     if(bapused>0)
+       {
+ 	char reg[1024];
+-	sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), csfPriorName.c_str(), (main_prior_vol+"_csf_stdspace").c_str(),  bapriori.value().c_str());
++	sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), csfPriorName.c_str(), (main_prior_vol+"_csf_stdspace").c_str(),  bapriori.value().c_str());
+         if(verbose.value())
+ 	  cout<<reg<<endl;
+ 	system(reg);
+-	sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), grayPriorName.c_str(), (main_prior_vol+"_gm_stdspace").c_str(),  bapriori.value().c_str());
++	sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), grayPriorName.c_str(), (main_prior_vol+"_gm_stdspace").c_str(),  bapriori.value().c_str());
+ 	if(verbose.value())
+ 	  cout<<reg<<endl;
+         system(reg);
+-	sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), whitePriorName.c_str(), (main_prior_vol+"_wm_stdspace").c_str(),  bapriori.value().c_str());
++	sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), whitePriorName.c_str(), (main_prior_vol+"_wm_stdspace").c_str(),  bapriori.value().c_str());
+ 	if(verbose.value())
+ 	  cout << reg << endl;
+ 	system(reg);
+diff --git a/src/feat5/feat_model.cc b/src/feat5/feat_model.cc
+index 399a13e..e15e43c 100644
+--- a/src/feat5/feat_model.cc
++++ b/src/feat5/feat_model.cc
+@@ -744,7 +744,7 @@ int main(int argc, char **argv)
+   vector<int> G;
+   vector<string> titles;
+   float  tr, mult, trmult, nltffwhm=0, maxconvwin=0;
+-  char   fl[10000], *FSLDIR;
++  char   fl[10000];
+   string fn, filename;
+   FONT_DATA *font_data = new FONT_DATA[1];
+ 
+@@ -763,8 +763,6 @@ int main(int argc, char **argv)
+   if (argc==3)
+     motionparams=remmean(read_ascii_matrix(argv[2]));
+ 
+-  FSLDIR=getenv("FSLDIR");
+-
+   fn = string(argv[1])+".fsf";
+ 
+   level      = atoi(find_line(fn, "fmri(level)", fl));
+@@ -1510,7 +1508,7 @@ int main(int argc, char **argv)
+   writeCovarianceImage(string(argv[1])+"_cov.ppm", contrasts, F, nftests, realDesign, level, evs.eigenvals, font_data, contrasts.RE);
+   writeImagePreview(string(argv[1])+".ppm", contrasts, F, nftests, realDesign, level, evs, font_data, titles, tr, nltffwhm, nTimepoints, G);
+ 
+-  filename=string(getenv("FSLDIR"))+"/bin/wpng -q -overwrite  "+string(argv[1])+".ppm ";
++  filename="wpng -q -overwrite  "+string(argv[1])+".ppm ";
+   system(filename.c_str());
+ 
+   return(0);
+@@ -2161,6 +2159,6 @@ char the_string[10000];
+ 
+     fclose(outputfile);
+ 
+-    filename=string(getenv("FSLDIR")) + "/bin/wpng -q -overwrite  " + filename;
++    filename="wpng -q -overwrite  " + filename;
+     system(filename.c_str());
+ }
+diff --git a/src/feat5/tsplot.cc b/src/feat5/tsplot.cc
+index ae191fd..3a02b55 100644
+--- a/src/feat5/tsplot.cc
++++ b/src/feat5/tsplot.cc
+@@ -293,7 +293,7 @@ int main(int argc, char **argv)
+ ofstream     outputFile;
+ int          numEVs, npts, numContrasts=1, nftests=0, GRPHSIZE(600), PSSIZE(600); 
+ vector<double> normalisedContrasts, model, triggers;
+- string       fmriFileName, fslPath, featdir, vType, indexText;
++ string       fmriFileName, featdir, vType, indexText;
+ ColumnVector NewimageVoxCoord(4),NiftiVoxCoord(4);
+ bool outputText(true), useCoordinate(false), prewhiten(false), useTriggers(false), customMask(false), modelFree(false), isHigherLevel(false), outputDataOnly(false);
+ bool zWeightClusters(true);
+@@ -307,7 +307,6 @@ volume<float> immask;
+   if (argc<2) usage("");
+   featdir=string(argv[1]);
+   fmriFileName=featdir+"/filtered_func_data";
+-  fslPath=string(getenv("FSLDIR"));
+ 
+   string outputName(featdir);
+ 
+@@ -753,7 +752,7 @@ volume4D<float> acs;
+ 	cerr << "Can't open output report file " << outputName << endl;
+ 	exit(1);
+       }
+-      outputFile << "<HTML>\n<TITLE>"<< statType << num2str(i) <<"</TITLE>\n<BODY BACKGROUND=\"file:"<< fslPath <<"/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report - "<< statType << num2str(i) <<"</H1>\n</CENTER>\n<hr><b>Full plots</b><p>\n"<< graphText;
++      outputFile << "<HTML>\n<TITLE>"<< statType << num2str(i) <<"</TITLE>\n<BODY BACKGROUND=\"file:"<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report - "<< statType << num2str(i) <<"</H1>\n</CENTER>\n<hr><b>Full plots</b><p>\n"<< graphText;
+       if (useTriggers) outputFile << "\n<hr><b>Peristimulus plots</b><p>\n"<< peristimulusText <<"\n<HR></BODY></HTML>\n\n";
+       else outputFile << "\n</BODY></HTML>\n\n";
+       outputFile.close();
+@@ -768,7 +767,7 @@ volume4D<float> acs;
+       cerr << "Can't open output report file " << outputName << endl;
+       exit(1);
+   }
+-  outputFile << "<HTML>\n<TITLE>FEAT Time Series Report</TITLE>\n<BODY BACKGROUND=\"file:" << fslPath << "/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report</H1>\n</CENTER>\n<hr>" << indexText << "<HR></BODY></HTML>" << endl << endl;
++  outputFile << "<HTML>\n<TITLE>FEAT Time Series Report</TITLE>\n<BODY BACKGROUND=\"file:" << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report</H1>\n</CENTER>\n<hr>" << indexText << "<HR></BODY></HTML>" << endl << endl;
+   outputFile.close();
+ 
+   /* now output same thing without start and end, for inclusion in feat report */
+diff --git a/src/first/first_utils.cc b/src/first/first_utils.cc
+index 68be44b..85960f4 100644
+--- a/src/first/first_utils.cc
++++ b/src/first/first_utils.cc
+@@ -1954,8 +1954,8 @@ void do_work_bvars(){
+     if (!surfaceVAout.value()) {
+       // do not output on the surface, instead do the new default of outputting a volume with the scalar normal dot product values (for use with randomise)
+       volume<float> refim;
+-      if (useReconMNI.value()) { read_volume(refim,string(getenv("FSLDIR")) + "/data/standard/MNI152_T1_1mm"); } 
+-      else { read_volume(refim,string(getenv("FSLDIR")) + "/data/standard/MNI152_T1_1mm"); } 
++      if (useReconMNI.value()) { read_volume(refim,"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); } 
++      else { read_volume(refim,"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); } 
+       volume<float> maskvol(refim);
+       maskvol=0.0f;
+       volume4D<float> volnormals;
+diff --git a/src/fnirt/fnirtfns.cpp b/src/fnirt/fnirtfns.cpp
+index 24e26fd..77899e7 100644
+--- a/src/fnirt/fnirtfns.cpp
++++ b/src/fnirt/fnirtfns.cpp
+@@ -1203,8 +1203,7 @@ string existing_ref_fname(const string& ref_fname)
+       return(string(ref_fname));
+     }
+     else {
+-      const char *fsldir_ptr = getenv("FSLDIR");
+-      string eref_fname = string(fsldir_ptr) + string("/data/standard/") + ref_fname;
++      string eref_fname = string("@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/") + ref_fname;
+       if (NEWIMAGE::FslFileExists(eref_fname)) return(eref_fname);
+       else return(string(""));
+     }
+@@ -1230,9 +1229,8 @@ string existing_ref_fname(const string& ref_fname)
+       NEWIMAGE::read_volume_hdr_only(vref,ref_fname); // Throws if file dont exist
+       eref_fname = ref_fname;
+     }
+-    catch(...) { // Didn't exist in current directory, try in ${FSLDIR}/data/standard
+-      const char *fsldir_ptr = getenv("FSLDIR");
+-      eref_fname = string(fsldir_ptr) + string("/data/standard/") + ref_fname;
++    catch(...) { // Didn't exist in current directory, try in .../data/standard
++      eref_fname = string("@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/") + ref_fname;
+       try {
+         cout << "Could not find " << ref_fname << ", now checking " << eref_fname << endl;
+         NEWIMAGE::read_volume_hdr_only(vref,eref_fname); // Throws if file dont exist
+@@ -1267,8 +1265,7 @@ string existing_conf_file(const string& cfname)
+     if (check_exist(ecfname)) return(ecfname);
+   }
+   if (!FNIRT::path(cfname).length()) {              // If no path explicitly given
+-    const char *fsldir_ptr = getenv("FSLDIR");
+-    ecfname = string(fsldir_ptr) + string("/etc/flirtsch/") + cfname;
++    ecfname = string("@GENTOO_PORTAGE_EPREFIX@/etc/flirtsch/") + cfname;
+     if (check_exist(ecfname)) return(ecfname);
+     else if (!FNIRT::extension(ecfname).length()) { // If no path _and_ no extension given
+       ecfname += string(".cnf");
+diff --git a/src/fslsurface/fslsurface_first.cc b/src/fslsurface/fslsurface_first.cc
+index faec642..b2ef794 100644
+--- a/src/fslsurface/fslsurface_first.cc
++++ b/src/fslsurface/fslsurface_first.cc
+@@ -500,8 +500,7 @@ namespace fslsurface_name {
+             
+ 			volume<float>* immni = new volume<float>();
+             
+-            char* fsldir = getenv("FSLDIR");
+-            read_volume_hdr_only(*immni, string(fsldir) + "/data/standard/MNI152_T1_1mm");
++            read_volume_hdr_only(*immni, "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm");
+             
+ 			//read_volume_hdr_only(*immni, template_name);
+ 			
+@@ -699,8 +698,7 @@ namespace fslsurface_name {
+           
+ 			volume<float>* immni = new volume<float>();
+             
+-            char* fsldir = getenv("FSLDIR");
+-            read_volume_hdr_only(*immni, string(fsldir) + "/data/standard/MNI152_T1_1mm");
++            read_volume_hdr_only(*immni, "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm");
+             
+ 			//read_volume_hdr_only(*immni, template_name);
+ 			
+diff --git a/src/fslsurface/fslsurfacemaths.cpp b/src/fslsurface/fslsurfacemaths.cpp
+index eaf55eb..3dc184d 100644
+--- a/src/fslsurface/fslsurfacemaths.cpp
++++ b/src/fslsurface/fslsurfacemaths.cpp
+@@ -598,12 +598,6 @@ int main (int argc, char * argv[])
+ 
+         }else if (command == "-reconFromBvars"){
+             cout<<"do recon "<<endl;
+-            char* fsldir = getenv("FSLDIR");
+-            if (fsldir == NULL)
+-            {
+-                cerr<<"FSLDIR has not been set. "<<endl;
+-                exit(EXIT_FAILURE); 
+-            }
+             //file.bvars,mni_template.nii.gz
+            // string mni = string(fsldir)+"/data/standard/MNI152_T1_1mm";
+             reconSurface_from_bvars( surf, string(argv[i_arg+1]));
+@@ -612,12 +606,6 @@ int main (int argc, char * argv[])
+ 
+         }else if (command == "-reconAllFromBvarsAndSave"){
+             cout<<"do recon+save "<<argc<<" "<<i_arg<<endl;
+-            char* fsldir = getenv("FSLDIR");
+-            if (fsldir == NULL)
+-            {
+-                cerr<<"FSLDIR has not been set. "<<endl;
+-                exit(EXIT_FAILURE); 
+-            }
+             //file.bvars,mni_template.nii.gz
+             // string mni = string(fsldir)+"/data/standard/MNI152_T1_1mm";
+             cout<<"recon "<< string(argv[i_arg+1])<<endl;
diff --git a/sci-biology/fsl/files/fsl-6.0.4-fsldir_redux-p2.patch b/sci-biology/fsl/files/fsl-6.0.4-fsldir_redux-p2.patch
new file mode 100644
index 000000000..af498b400
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-fsldir_redux-p2.patch
@@ -0,0 +1,254 @@
+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 -Naur fsl.orig/src/siena/siena_diff.cc fsl/src/siena/siena_diff.cc
+--- fsl.orig/src/siena/siena_diff.cc	2020-12-02 15:52:50.359856656 -0500
++++ fsl/src/siena/siena_diff.cc	2020-12-02 16:03:25.699876412 -0500
+@@ -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"))
+@@ -206,26 +204,26 @@
+ // }}}
+   // {{{  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);
+ }
+ 
+@@ -284,8 +282,8 @@
+     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 --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-6.0.4-gcc10_include.patch b/sci-biology/fsl/files/fsl-6.0.4-gcc10_include.patch
new file mode 100644
index 000000000..ae836c065
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-gcc10_include.patch
@@ -0,0 +1,11 @@
+diff -Naur fsl.orig/src/newimage/newimageio.h fsl/src/newimage/newimageio.h
+--- fsl.orig/src/newimage/newimageio.h	2020-12-02 15:15:27.012786899 -0500
++++ fsl/src/newimage/newimageio.h	2020-12-02 15:19:51.046795110 -0500
+@@ -75,6 +75,7 @@
+ #include <iostream>
+ #include <fstream>
+ #include <sstream>
++#include <stdexcept>
+ #include "NewNifti/NewNifti.h"
+ #include "newmatio.h"
+ #include "newimage.h"
diff --git a/sci-biology/fsl/files/fsl-6.0.4-melodic_std.patch b/sci-biology/fsl/files/fsl-6.0.4-melodic_std.patch
new file mode 100644
index 000000000..83b5b9932
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-melodic_std.patch
@@ -0,0 +1,11 @@
+diff -Naur fsl.orig/src/melodic/Makefile fsl/src/melodic/Makefile
+--- fsl.orig/src/melodic/Makefile	2021-01-06 14:04:35.743274475 -0500
++++ fsl/src/melodic/Makefile	2021-01-06 14:11:27.924264859 -0500
+@@ -9,6 +9,7 @@
+ 
+ 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
+ USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_GD} -L${LIB_GDC} -L${LIB_PNG} -L${LIB_ZLIB}
++USRCXXFLAGS = -std=c++11
+ 
+ UNAME := $(shell uname)
+ ifeq (${UNAME},Darwin)
diff --git a/sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p1.patch b/sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p1.patch
new file mode 100644
index 000000000..434dc9cf6
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p1.patch
@@ -0,0 +1,303 @@
+diff -Naur fsl.orig/src/fslio/imln fsl/src/fslio/imln
+--- fsl.orig/src/fslio/imln	2021-02-01 15:29:34.842752994 -0500
++++ fsl/src/fslio/imln	1969-12-31 19:00:00.000000000 -0500
+@@ -1,90 +0,0 @@
+-#!/bin/sh
+-
+-#   imln - make symbolic link(s) to image file(s)
+-#
+-#   Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group
+-#
+-#   Copyright (C) 1999-2004 University of Oxford
+-#
+-#   Part of FSL - FMRIB's Software Library
+-#   http://www.fmrib.ox.ac.uk/fsl
+-#   fsl@fmrib.ox.ac.uk
+-#
+-#   Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+-#   Imaging of the Brain), Department of Clinical Neurology, Oxford
+-#   University, Oxford, UK
+-#
+-#
+-#   LICENCE
+-#
+-#   FMRIB Software Library, Release 6.0 (c) 2018, The University of
+-#   Oxford (the "Software")
+-#
+-#   The Software remains the property of the Oxford University Innovation
+-#   ("the University").
+-#
+-#   The Software is distributed "AS IS" under this Licence solely for
+-#   non-commercial use in the hope that it will be useful, but in order
+-#   that the University as a charitable foundation protects its assets for
+-#   the benefit of its educational and research purposes, the University
+-#   makes clear that no condition is made or to be implied, nor is any
+-#   warranty given or to be implied, as to the accuracy of the Software,
+-#   or that it will be suitable for any particular purpose or for use
+-#   under any specific conditions. Furthermore, the University disclaims
+-#   all responsibility for the use which is made of the Software. It
+-#   further disclaims any liability for the outcomes arising from using
+-#   the Software.
+-#
+-#   The Licensee agrees to indemnify the University and hold the
+-#   University harmless from and against any and all claims, damages and
+-#   liabilities asserted by third parties (including claims for
+-#   negligence) which arise directly or indirectly from the use of the
+-#   Software or the sale of any products based on the Software.
+-#
+-#   No part of the Software may be reproduced, modified, transmitted or
+-#   transferred in any form or by any means, electronic or mechanical,
+-#   without the express permission of the University. The permission of
+-#   the University is not required if the said reproduction, modification,
+-#   transmission or transference is done without financial return, the
+-#   conditions of this Licence are imposed upon the receiver of the
+-#   product, and all original and amended source code is included in any
+-#   transmitted product. You may be held legally responsible for any
+-#   copyright infringement that is caused or encouraged by your failure to
+-#   abide by these terms and conditions.
+-#
+-#   You are not permitted under this Licence to use this Software
+-#   commercially. Use for which any financial return is received shall be
+-#   defined as commercial use, and includes (1) integration of all or part
+-#   of the source code or the Software into a product for sale or license
+-#   by or on behalf of Licensee to third parties or (2) use of the
+-#   Software or any derivative of it for research with the final aim of
+-#   developing software products for sale or license to a third party or
+-#   (3) use of the Software or any derivative of it for research with the
+-#   final aim of developing non-software products for sale or license to a
+-#   third party, or (4) use of the Software to provide any service to an
+-#   external organisation for which payment is received. If you are
+-#   interested in using the Software commercially, please contact Oxford
+-#   University Innovation ("OUI"), the technology transfer company of the
+-#   University, to negotiate a licence. Contact details are:
+-#   fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.
+-export LC_ALL=C
+-
+-if [ $# -lt 2 ] ; then
+-  echo "Usage: $0 <file1> <file2>"
+-  echo "  Makes a link (called file2) to file1"
+-  echo "  NB: filenames can be basenames or include an extension"
+-  exit 1;
+-fi
+-
+-f1=`${FSLDIR}/bin/remove_ext $1`;
+-f2=`${FSLDIR}/bin/remove_ext $2`;
+-
+-if [ -f ${f1}.hdr ] ; then ln -fs ${f1}.hdr ${f2}.hdr ; fi
+-if [ -f ${f1}.hdr.gz ] ; then ln -fs ${f1}.hdr.gz ${f2}.hdr.gz ; fi 
+-if [ -f ${f1}.img ] ; then ln -fs ${f1}.img ${f2}.img ; fi 
+-if [ -f ${f1}.img.gz ] ; then ln -fs ${f1}.img.gz ${f2}.img.gz ; fi 
+-if [ -f ${f1}.nii ] ; then ln -fs ${f1}.nii ${f2}.nii ; fi 
+-if [ -f ${f1}.nii.gz ] ; then ln -fs ${f1}.nii.gz ${f2}.nii.gz ; fi 
+-if [ -f ${f1}.mnc ] ; then ln -fs ${f1}.mnc ${f2}.mnc ; fi 
+-if [ -f ${f1}.mnc.gz ] ; then ln -fs ${f1}.mnc.gz ${f2}.mnc.gz ; fi 
+-
+diff -Naur fsl.orig/src/fslio/imrm fsl/src/fslio/imrm
+--- fsl.orig/src/fslio/imrm	2021-02-01 15:29:34.842752994 -0500
++++ fsl/src/fslio/imrm	1969-12-31 19:00:00.000000000 -0500
+@@ -1,83 +0,0 @@
+-#!/bin/sh
+-
+-#   imrm - remove image files
+-#
+-#   Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group
+-#
+-#   Copyright (C) 1999-2004 University of Oxford
+-#
+-#   Part of FSL - FMRIB's Software Library
+-#   http://www.fmrib.ox.ac.uk/fsl
+-#   fsl@fmrib.ox.ac.uk
+-#
+-#   Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+-#   Imaging of the Brain), Department of Clinical Neurology, Oxford
+-#   University, Oxford, UK
+-#
+-#
+-#   LICENCE
+-#
+-#   FMRIB Software Library, Release 6.0 (c) 2018, The University of
+-#   Oxford (the "Software")
+-#
+-#   The Software remains the property of the Oxford University Innovation
+-#   ("the University").
+-#
+-#   The Software is distributed "AS IS" under this Licence solely for
+-#   non-commercial use in the hope that it will be useful, but in order
+-#   that the University as a charitable foundation protects its assets for
+-#   the benefit of its educational and research purposes, the University
+-#   makes clear that no condition is made or to be implied, nor is any
+-#   warranty given or to be implied, as to the accuracy of the Software,
+-#   or that it will be suitable for any particular purpose or for use
+-#   under any specific conditions. Furthermore, the University disclaims
+-#   all responsibility for the use which is made of the Software. It
+-#   further disclaims any liability for the outcomes arising from using
+-#   the Software.
+-#
+-#   The Licensee agrees to indemnify the University and hold the
+-#   University harmless from and against any and all claims, damages and
+-#   liabilities asserted by third parties (including claims for
+-#   negligence) which arise directly or indirectly from the use of the
+-#   Software or the sale of any products based on the Software.
+-#
+-#   No part of the Software may be reproduced, modified, transmitted or
+-#   transferred in any form or by any means, electronic or mechanical,
+-#   without the express permission of the University. The permission of
+-#   the University is not required if the said reproduction, modification,
+-#   transmission or transference is done without financial return, the
+-#   conditions of this Licence are imposed upon the receiver of the
+-#   product, and all original and amended source code is included in any
+-#   transmitted product. You may be held legally responsible for any
+-#   copyright infringement that is caused or encouraged by your failure to
+-#   abide by these terms and conditions.
+-#
+-#   You are not permitted under this Licence to use this Software
+-#   commercially. Use for which any financial return is received shall be
+-#   defined as commercial use, and includes (1) integration of all or part
+-#   of the source code or the Software into a product for sale or license
+-#   by or on behalf of Licensee to third parties or (2) use of the
+-#   Software or any derivative of it for research with the final aim of
+-#   developing software products for sale or license to a third party or
+-#   (3) use of the Software or any derivative of it for research with the
+-#   final aim of developing non-software products for sale or license to a
+-#   third party, or (4) use of the Software to provide any service to an
+-#   external organisation for which payment is received. If you are
+-#   interested in using the Software commercially, please contact Oxford
+-#   University Innovation ("OUI"), the technology transfer company of the
+-#   University, to negotiate a licence. Contact details are:
+-#   fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.
+-export LC_ALL=C
+-
+-if [ $# -lt 1 ] ; then
+-  echo "Usage: $0 <list of image names to remove>"
+-  echo "NB: filenames can be basenames or not"
+-  exit 1;
+-fi
+-
+-for f in $@ ; do
+-  fn=`${FSLDIR}/bin/remove_ext $f`;
+-  # do the rm silently
+-  /bin/rm -f ${fn}.img ${fn}.hdr ${fn}.hdr.gz ${fn}.img.gz ${fn}.nii ${fn}.nii.gz ${fn}.mnc ${fn}.mnc.gz
+-done
+-
+diff -Naur fsl.orig/src/fslio/imtest fsl/src/fslio/imtest
+--- fsl.orig/src/fslio/imtest	2021-02-01 15:29:34.842752994 -0500
++++ fsl/src/fslio/imtest	1969-12-31 19:00:00.000000000 -0500
+@@ -1,118 +0,0 @@
+-#!/bin/sh
+-
+-#   imtest - test to see if a valid image file exists with this name (root)
+-#
+-#   Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group
+-#
+-#   Copyright (C) 1999-2004 University of Oxford
+-#
+-#   Part of FSL - FMRIB's Software Library
+-#   http://www.fmrib.ox.ac.uk/fsl
+-#   fsl@fmrib.ox.ac.uk
+-#
+-#   Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+-#   Imaging of the Brain), Department of Clinical Neurology, Oxford
+-#   University, Oxford, UK
+-#
+-#
+-#   LICENCE
+-#
+-#   FMRIB Software Library, Release 6.0 (c) 2018, The University of
+-#   Oxford (the "Software")
+-#
+-#   The Software remains the property of the Oxford University Innovation
+-#   ("the University").
+-#
+-#   The Software is distributed "AS IS" under this Licence solely for
+-#   non-commercial use in the hope that it will be useful, but in order
+-#   that the University as a charitable foundation protects its assets for
+-#   the benefit of its educational and research purposes, the University
+-#   makes clear that no condition is made or to be implied, nor is any
+-#   warranty given or to be implied, as to the accuracy of the Software,
+-#   or that it will be suitable for any particular purpose or for use
+-#   under any specific conditions. Furthermore, the University disclaims
+-#   all responsibility for the use which is made of the Software. It
+-#   further disclaims any liability for the outcomes arising from using
+-#   the Software.
+-#
+-#   The Licensee agrees to indemnify the University and hold the
+-#   University harmless from and against any and all claims, damages and
+-#   liabilities asserted by third parties (including claims for
+-#   negligence) which arise directly or indirectly from the use of the
+-#   Software or the sale of any products based on the Software.
+-#
+-#   No part of the Software may be reproduced, modified, transmitted or
+-#   transferred in any form or by any means, electronic or mechanical,
+-#   without the express permission of the University. The permission of
+-#   the University is not required if the said reproduction, modification,
+-#   transmission or transference is done without financial return, the
+-#   conditions of this Licence are imposed upon the receiver of the
+-#   product, and all original and amended source code is included in any
+-#   transmitted product. You may be held legally responsible for any
+-#   copyright infringement that is caused or encouraged by your failure to
+-#   abide by these terms and conditions.
+-#
+-#   You are not permitted under this Licence to use this Software
+-#   commercially. Use for which any financial return is received shall be
+-#   defined as commercial use, and includes (1) integration of all or part
+-#   of the source code or the Software into a product for sale or license
+-#   by or on behalf of Licensee to third parties or (2) use of the
+-#   Software or any derivative of it for research with the final aim of
+-#   developing software products for sale or license to a third party or
+-#   (3) use of the Software or any derivative of it for research with the
+-#   final aim of developing non-software products for sale or license to a
+-#   third party, or (4) use of the Software to provide any service to an
+-#   external organisation for which payment is received. If you are
+-#   interested in using the Software commercially, please contact Oxford
+-#   University Innovation ("OUI"), the technology transfer company of the
+-#   University, to negotiate a licence. Contact details are:
+-#   fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.
+-export LC_ALL=C
+-
+-# return 0 if no image exists or 1 if the image exists
+-
+-if [ $# -lt 1 ] ; then
+- echo "0";
+- exit;
+-fi
+-
+-inputfile=$1
+-
+-
+-
+-for i in 1 2 3 4 5 6 7 8 9 10 11 12
+-do
+-if [ -h $inputfile ] ; then 
+-inputfile=`readlink $inputfile`;
+-fi
+-done
+-
+-filename=`${FSLDIR}/bin/remove_ext $inputfile`;
+-
+-if [ -r ${filename}.nii ] || [ -r ${filename}.nii.gz ] ; then
+-  echo "1";
+-  exit;
+-fi
+-
+-if [ -r ${filename}.mnc ] || [ -r ${filename}.mnc.gz ] ; then
+-  echo "1";
+-  exit;
+-fi
+-
+-if [ ! -r ${filename}.hdr ] && [ ! -r ${filename}.hdr.gz ] ; then
+-  # return 0 here as no header exists and no single image means no image!
+-  echo "0";
+-  exit;
+-fi
+-
+-if [ ! -r ${filename}.img ] && [ ! -r ${filename}.img.gz ] ; then
+-  # return 0 here as no img file exists and no single image means no image!
+-  echo "0";
+-  exit;
+-fi
+-
+-# only gets to here if there was a hdr and an img file
+-
+-echo "1";
+-exit;
+-
diff --git a/sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p2.patch b/sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p2.patch
new file mode 100644
index 000000000..ddb7cfb67
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p2.patch
@@ -0,0 +1,348 @@
+diff -Naur fsl.orig/src/fslio/Makefile fsl/src/fslio/Makefile
+--- fsl.orig/src/fslio/Makefile	2021-02-01 15:29:34.842752994 -0500
++++ fsl/src/fslio/Makefile	2021-02-01 15:32:19.723761859 -0500
+@@ -6,7 +6,7 @@
+ 
+ OBJS=fslio.o
+ 
+-SCRIPTS = remove_ext fsloutputtype imtest imglob imcp imln imrm immv
++SCRIPTS = fsloutputtype imglob imcp immv
+ 
+ all: 
+ 
+diff -Naur fsl.orig/src/fslio/remove_ext fsl/src/fslio/remove_ext
+--- fsl.orig/src/fslio/remove_ext	2021-02-01 15:29:34.842752994 -0500
++++ fsl/src/fslio/remove_ext	1969-12-31 19:00:00.000000000 -0500
+@@ -1,87 +0,0 @@
+-#!/bin/sh
+-
+-#   remove_ext - remove extension from image filename
+-#
+-#   Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group
+-#
+-#   Copyright (C) 1999-2004 University of Oxford
+-#
+-#   Part of FSL - FMRIB's Software Library
+-#   http://www.fmrib.ox.ac.uk/fsl
+-#   fsl@fmrib.ox.ac.uk
+-#
+-#   Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+-#   Imaging of the Brain), Department of Clinical Neurology, Oxford
+-#   University, Oxford, UK
+-#
+-#
+-#   LICENCE
+-#
+-#   FMRIB Software Library, Release 6.0 (c) 2018, The University of
+-#   Oxford (the "Software")
+-#
+-#   The Software remains the property of the Oxford University Innovation
+-#   ("the University").
+-#
+-#   The Software is distributed "AS IS" under this Licence solely for
+-#   non-commercial use in the hope that it will be useful, but in order
+-#   that the University as a charitable foundation protects its assets for
+-#   the benefit of its educational and research purposes, the University
+-#   makes clear that no condition is made or to be implied, nor is any
+-#   warranty given or to be implied, as to the accuracy of the Software,
+-#   or that it will be suitable for any particular purpose or for use
+-#   under any specific conditions. Furthermore, the University disclaims
+-#   all responsibility for the use which is made of the Software. It
+-#   further disclaims any liability for the outcomes arising from using
+-#   the Software.
+-#
+-#   The Licensee agrees to indemnify the University and hold the
+-#   University harmless from and against any and all claims, damages and
+-#   liabilities asserted by third parties (including claims for
+-#   negligence) which arise directly or indirectly from the use of the
+-#   Software or the sale of any products based on the Software.
+-#
+-#   No part of the Software may be reproduced, modified, transmitted or
+-#   transferred in any form or by any means, electronic or mechanical,
+-#   without the express permission of the University. The permission of
+-#   the University is not required if the said reproduction, modification,
+-#   transmission or transference is done without financial return, the
+-#   conditions of this Licence are imposed upon the receiver of the
+-#   product, and all original and amended source code is included in any
+-#   transmitted product. You may be held legally responsible for any
+-#   copyright infringement that is caused or encouraged by your failure to
+-#   abide by these terms and conditions.
+-#
+-#   You are not permitted under this Licence to use this Software
+-#   commercially. Use for which any financial return is received shall be
+-#   defined as commercial use, and includes (1) integration of all or part
+-#   of the source code or the Software into a product for sale or license
+-#   by or on behalf of Licensee to third parties or (2) use of the
+-#   Software or any derivative of it for research with the final aim of
+-#   developing software products for sale or license to a third party or
+-#   (3) use of the Software or any derivative of it for research with the
+-#   final aim of developing non-software products for sale or license to a
+-#   third party, or (4) use of the Software to provide any service to an
+-#   external organisation for which payment is received. If you are
+-#   interested in using the Software commercially, please contact Oxford
+-#   University Innovation ("OUI"), the technology transfer company of the
+-#   University, to negotiate a licence. Contact details are:
+-#   fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.
+-export LC_ALL=C
+-
+-
+-if [ $# -lt 1 ] ; then
+-  exit 1
+-fi
+-
+-lst="";
+-for fn in $@ ; do
+-    # for the ones at the end of the line
+-  f=`echo "$fn" | sed 's/\.hdr\.gz$//' | sed 's/\.img\.gz$//' | sed 's/\.hdr$//' | sed 's/\.img$//' | sed 's/\.nii.gz$//' | sed 's/\.nii$//' | sed 's/\.mnc.gz$//' | sed 's/\.mnc$//' | sed 's/\.$//'`;
+-    # for the ones in the middle of the line
+-  f=`echo "$f" | sed 's/\.hdr\.gz[ 	]/ /g' | sed 's/\.img\.gz[ 	]/ /g' | sed 's/\.hdr[ 	]/ /g' | sed 's/\.img[ 	]/ /g' | sed 's/\.nii\.gz[ 	]/ /g' | sed 's/\.nii[ 	]/ /g' | sed 's/\.mnc\.gz[ 	]/ /g' | sed 's/\.mnc[ 	]/ /g' |sed 's/\.[ 	]/ /g'`;
+-  lst="$lst $f";
+-done
+-echo $lst;
+-
+-
+diff -Naur fsl.orig/src/misc_scripts/fsl_abspath fsl/src/misc_scripts/fsl_abspath
+--- fsl.orig/src/misc_scripts/fsl_abspath	2021-02-01 15:29:34.828752994 -0500
++++ fsl/src/misc_scripts/fsl_abspath	1969-12-31 19:00:00.000000000 -0500
+@@ -1,71 +0,0 @@
+-#!/usr/bin/env fslpython
+-#   fsl_abspath - return true file path
+-#   Matthew Webster FMRIB Image Analysis Group
+-#   Copyright (C) 2009 University of Oxford 
+-#   Part of FSL - FMRIB's Software Library
+-#   http://www.fmrib.ox.ac.uk/fsl
+-#   fsl@fmrib.ox.ac.uk
+-#
+-#   Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+-#   Imaging of the Brain), Department of Clinical Neurology, Oxford
+-#   University, Oxford, UK
+-#
+-#
+-#   LICENCE
+-#
+-#   FMRIB Software Library, Release 6.0 (c) 2018, The University of
+-#   Oxford (the "Software")
+-#
+-#   The Software remains the property of the Oxford University Innovation
+-#   ("the University").
+-#
+-#   The Software is distributed "AS IS" under this Licence solely for
+-#   non-commercial use in the hope that it will be useful, but in order
+-#   that the University as a charitable foundation protects its assets for
+-#   the benefit of its educational and research purposes, the University
+-#   makes clear that no condition is made or to be implied, nor is any
+-#   warranty given or to be implied, as to the accuracy of the Software,
+-#   or that it will be suitable for any particular purpose or for use
+-#   under any specific conditions. Furthermore, the University disclaims
+-#   all responsibility for the use which is made of the Software. It
+-#   further disclaims any liability for the outcomes arising from using
+-#   the Software.
+-#
+-#   The Licensee agrees to indemnify the University and hold the
+-#   University harmless from and against any and all claims, damages and
+-#   liabilities asserted by third parties (including claims for
+-#   negligence) which arise directly or indirectly from the use of the
+-#   Software or the sale of any products based on the Software.
+-#
+-#   No part of the Software may be reproduced, modified, transmitted or
+-#   transferred in any form or by any means, electronic or mechanical,
+-#   without the express permission of the University. The permission of
+-#   the University is not required if the said reproduction, modification,
+-#   transmission or transference is done without financial return, the
+-#   conditions of this Licence are imposed upon the receiver of the
+-#   product, and all original and amended source code is included in any
+-#   transmitted product. You may be held legally responsible for any
+-#   copyright infringement that is caused or encouraged by your failure to
+-#   abide by these terms and conditions.
+-#
+-#   You are not permitted under this Licence to use this Software
+-#   commercially. Use for which any financial return is received shall be
+-#   defined as commercial use, and includes (1) integration of all or part
+-#   of the source code or the Software into a product for sale or license
+-#   by or on behalf of Licensee to third parties or (2) use of the
+-#   Software or any derivative of it for research with the final aim of
+-#   developing software products for sale or license to a third party or
+-#   (3) use of the Software or any derivative of it for research with the
+-#   final aim of developing non-software products for sale or license to a
+-#   third party, or (4) use of the Software to provide any service to an
+-#   external organisation for which payment is received. If you are
+-#   interested in using the Software commercially, please contact Oxford
+-#   University Innovation ("OUI"), the technology transfer company of the
+-#   University, to negotiate a licence. Contact details are:
+-#   fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.
+-from __future__ import print_function
+-import sys
+-import os
+-
+-print (os.path.realpath(sys.argv[1]))
+-sys.exit(0)
+diff -Naur fsl.orig/src/misc_scripts/Makefile fsl/src/misc_scripts/Makefile
+--- fsl.orig/src/misc_scripts/Makefile	2021-02-01 15:29:34.828752994 -0500
++++ fsl/src/misc_scripts/Makefile	2021-02-01 15:32:56.027763811 -0500
+@@ -2,6 +2,6 @@
+ 
+ PROJNAME = misc_scripts
+ 
+-SCRIPTS = fslecho regscript remove_vols replace_and_average_fmrib linkbedpost ocmr_preproc correct_and_average eddy_correct Text2Vest Vest2Text AnatomicalAverage fsl_abspath fsl_anat fslFixText
++SCRIPTS = fslecho regscript remove_vols replace_and_average_fmrib linkbedpost ocmr_preproc correct_and_average eddy_correct AnatomicalAverage fsl_anat fslFixText
+ 
+ all:
+diff -Naur fsl.orig/src/misc_scripts/Text2Vest fsl/src/misc_scripts/Text2Vest
+--- fsl.orig/src/misc_scripts/Text2Vest	2021-02-01 15:29:34.828752994 -0500
++++ fsl/src/misc_scripts/Text2Vest	1969-12-31 19:00:00.000000000 -0500
+@@ -1,80 +0,0 @@
+-#!/bin/sh
+-#   Copyright (C) 2012 University of Oxford
+-#
+-#   Part of FSL - FMRIB's Software Library
+-#   http://www.fmrib.ox.ac.uk/fsl
+-#   fsl@fmrib.ox.ac.uk
+-#
+-#   Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+-#   Imaging of the Brain), Department of Clinical Neurology, Oxford
+-#   University, Oxford, UK
+-#
+-#
+-#   LICENCE
+-#
+-#   FMRIB Software Library, Release 6.0 (c) 2018, The University of
+-#   Oxford (the "Software")
+-#
+-#   The Software remains the property of the Oxford University Innovation
+-#   ("the University").
+-#
+-#   The Software is distributed "AS IS" under this Licence solely for
+-#   non-commercial use in the hope that it will be useful, but in order
+-#   that the University as a charitable foundation protects its assets for
+-#   the benefit of its educational and research purposes, the University
+-#   makes clear that no condition is made or to be implied, nor is any
+-#   warranty given or to be implied, as to the accuracy of the Software,
+-#   or that it will be suitable for any particular purpose or for use
+-#   under any specific conditions. Furthermore, the University disclaims
+-#   all responsibility for the use which is made of the Software. It
+-#   further disclaims any liability for the outcomes arising from using
+-#   the Software.
+-#
+-#   The Licensee agrees to indemnify the University and hold the
+-#   University harmless from and against any and all claims, damages and
+-#   liabilities asserted by third parties (including claims for
+-#   negligence) which arise directly or indirectly from the use of the
+-#   Software or the sale of any products based on the Software.
+-#
+-#   No part of the Software may be reproduced, modified, transmitted or
+-#   transferred in any form or by any means, electronic or mechanical,
+-#   without the express permission of the University. The permission of
+-#   the University is not required if the said reproduction, modification,
+-#   transmission or transference is done without financial return, the
+-#   conditions of this Licence are imposed upon the receiver of the
+-#   product, and all original and amended source code is included in any
+-#   transmitted product. You may be held legally responsible for any
+-#   copyright infringement that is caused or encouraged by your failure to
+-#   abide by these terms and conditions.
+-#
+-#   You are not permitted under this Licence to use this Software
+-#   commercially. Use for which any financial return is received shall be
+-#   defined as commercial use, and includes (1) integration of all or part
+-#   of the source code or the Software into a product for sale or license
+-#   by or on behalf of Licensee to third parties or (2) use of the
+-#   Software or any derivative of it for research with the final aim of
+-#   developing software products for sale or license to a third party or
+-#   (3) use of the Software or any derivative of it for research with the
+-#   final aim of developing non-software products for sale or license to a
+-#   third party, or (4) use of the Software to provide any service to an
+-#   external organisation for which payment is received. If you are
+-#   interested in using the Software commercially, please contact Oxford
+-#   University Innovation ("OUI"), the technology transfer company of the
+-#   University, to negotiate a licence. Contact details are:
+-#   fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.
+-export LC_ALL=C
+-if [ $# -lt 2 ] ; then 
+-  echo "`basename $0` <text file> <vest file>"
+-  exit 0
+-fi
+-
+-NumPoints=`grep -cve '^\s*$' $1`
+-NumWaves=`wc $1 | awk '{ print $2 }'`
+-NumWaves=`expr $NumWaves / $NumPoints`
+-
+-echo /NumWaves $NumWaves    > $2
+-echo /NumPoints $NumPoints >> $2
+-echo /Matrix               >> $2
+-
+-cat $1 >> $2
+-
+diff -Naur fsl.orig/src/misc_scripts/Vest2Text fsl/src/misc_scripts/Vest2Text
+--- fsl.orig/src/misc_scripts/Vest2Text	2021-02-01 15:29:34.828752994 -0500
++++ fsl/src/misc_scripts/Vest2Text	1969-12-31 19:00:00.000000000 -0500
+@@ -1,71 +0,0 @@
+-#!/bin/sh
+-#   Copyright (C) 2012 University of Oxford
+-#
+-#   Part of FSL - FMRIB's Software Library
+-#   http://www.fmrib.ox.ac.uk/fsl
+-#   fsl@fmrib.ox.ac.uk
+-#
+-#   Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+-#   Imaging of the Brain), Department of Clinical Neurology, Oxford
+-#   University, Oxford, UK
+-#
+-#
+-#   LICENCE
+-#
+-#   FMRIB Software Library, Release 6.0 (c) 2018, The University of
+-#   Oxford (the "Software")
+-#
+-#   The Software remains the property of the Oxford University Innovation
+-#   ("the University").
+-#
+-#   The Software is distributed "AS IS" under this Licence solely for
+-#   non-commercial use in the hope that it will be useful, but in order
+-#   that the University as a charitable foundation protects its assets for
+-#   the benefit of its educational and research purposes, the University
+-#   makes clear that no condition is made or to be implied, nor is any
+-#   warranty given or to be implied, as to the accuracy of the Software,
+-#   or that it will be suitable for any particular purpose or for use
+-#   under any specific conditions. Furthermore, the University disclaims
+-#   all responsibility for the use which is made of the Software. It
+-#   further disclaims any liability for the outcomes arising from using
+-#   the Software.
+-#
+-#   The Licensee agrees to indemnify the University and hold the
+-#   University harmless from and against any and all claims, damages and
+-#   liabilities asserted by third parties (including claims for
+-#   negligence) which arise directly or indirectly from the use of the
+-#   Software or the sale of any products based on the Software.
+-#
+-#   No part of the Software may be reproduced, modified, transmitted or
+-#   transferred in any form or by any means, electronic or mechanical,
+-#   without the express permission of the University. The permission of
+-#   the University is not required if the said reproduction, modification,
+-#   transmission or transference is done without financial return, the
+-#   conditions of this Licence are imposed upon the receiver of the
+-#   product, and all original and amended source code is included in any
+-#   transmitted product. You may be held legally responsible for any
+-#   copyright infringement that is caused or encouraged by your failure to
+-#   abide by these terms and conditions.
+-#
+-#   You are not permitted under this Licence to use this Software
+-#   commercially. Use for which any financial return is received shall be
+-#   defined as commercial use, and includes (1) integration of all or part
+-#   of the source code or the Software into a product for sale or license
+-#   by or on behalf of Licensee to third parties or (2) use of the
+-#   Software or any derivative of it for research with the final aim of
+-#   developing software products for sale or license to a third party or
+-#   (3) use of the Software or any derivative of it for research with the
+-#   final aim of developing non-software products for sale or license to a
+-#   third party, or (4) use of the Software to provide any service to an
+-#   external organisation for which payment is received. If you are
+-#   interested in using the Software commercially, please contact Oxford
+-#   University Innovation ("OUI"), the technology transfer company of the
+-#   University, to negotiate a licence. Contact details are:
+-#   fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.
+-export LC_ALL=C
+-if [ $# -lt 2 ] ; then 
+-  echo "`basename $0` <vest file> <text file>"
+-  exit 0
+-fi
+-sed -e "/\//d" $1 | sed '/^$/d' > $2
+-
diff --git a/sci-biology/fsl/files/fsl-6.0.4-setup.patch b/sci-biology/fsl/files/fsl-6.0.4-setup.patch
new file mode 100644
index 000000000..061e1a22a
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-setup.patch
@@ -0,0 +1,174 @@
+diff -Naur fsl.orig/build fsl/build
+--- fsl.orig/build	2020-12-02 15:29:12.180812558 -0500
++++ fsl/build	2020-12-02 15:34:03.854821628 -0500
+@@ -28,7 +28,6 @@
+     # The build order for MASTERLIBS is very important, and should not be modified unless you know what
+     # you are doing. 
+     MASTERLIBS="
+-    CiftiLib-master \
+     utils \
+     znzlib \
+     NewNifti \
+@@ -157,8 +156,8 @@
+     done #project (MASTERPROJECTS)
+ fi #full build
+ 
+-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 -Naur fsl.orig/config/buildSettings.mk fsl/config/buildSettings.mk
+--- fsl.orig/config/buildSettings.mk	2020-12-02 15:29:11.993812552 -0500
++++ fsl/config/buildSettings.mk	2020-12-02 15:39:37.269831995 -0500
+@@ -18,7 +18,7 @@
+ CHMOD = /bin/chmod
+ MKDIR = /bin/mkdir
+ INSTALL = install -p
+-TCLSH = ${FSLDIR}/bin/fsltclsh
++TCLSH = tclsh
+ DEPENDFLAGS = -MM
+ MACHDBGFLAGS = -g
+ #####################################################################
+@@ -127,19 +127,19 @@
+ #####################################################################
+ 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)
+@@ -158,8 +158,8 @@
+ NVCC = ${CUDA_INSTALLATION}/bin/nvcc
+ ###############   External Libs   #####################################
+ # ZLIB library
+-LIB_ZLIB = ${FSLEXTLIB}
+-INC_ZLIB = ${FSLEXTINC}
++#LIB_ZLIB = ${FSLEXTLIB}
++#INC_ZLIB = ${FSLEXTINC}
+ # QT library
+ QTDIR = /usr/lib/qt3
+ LIB_QT = ${QTDIR}/lib
+diff -Naur fsl.orig/config/common/buildproj fsl/config/common/buildproj
+--- fsl.orig/config/common/buildproj	2020-12-02 15:29:11.993812552 -0500
++++ fsl/config/common/buildproj	2020-12-02 15:41:25.579835363 -0500
+@@ -11,10 +11,10 @@
+ fi
+ PROJECTS="$@" ; export PROJECTS ;
+ 
+-FSLDIR=`pwd`
++#FSLDIR=`pwd`
+ FSLDEVDIR=${FSLDIR}
+ FSLCONFDIR=${FSLDIR}/config
+-FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh`
++#FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh`
+ FSLMASTERBUILD=1
+ export FSLDIR FSLDEVDIR FSLCONFDIR FSLMACHTYPE FSLMASTERBUILD
+ 
+@@ -67,7 +67,7 @@
+ 	  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 @@
+ 	    if [ $installok = false ]  ; then
+ 	      echo " "
+ 	      echo "ERROR::Could not install $projname successfully" ;
++          exit 1
+ 	    fi
+ 	  else
+ 	    echo " "
+@@ -90,6 +91,7 @@
+ 	    echo " "
+ 	    echo " "
+ 	    errorprojs="$errorprojs $projname" ; export errorprojs ;
++        exit 1
+ 	  fi
+     fi
+ done
+diff -Naur fsl.orig/config/common/vars.mk fsl/config/common/vars.mk
+--- fsl.orig/config/common/vars.mk	2020-12-02 15:29:11.993812552 -0500
++++ fsl/config/common/vars.mk	2020-12-02 15:43:00.602838318 -0500
+@@ -24,15 +24,15 @@
+ 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 -Naur fsl.orig/extras/build fsl/extras/build
+--- fsl.orig/extras/build	2020-12-02 15:29:12.404812565 -0500
++++ fsl/extras/build	2020-12-02 15:44:06.906840380 -0500
+@@ -96,16 +96,16 @@
+ 	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 -Naur fsl.orig/src/mist/Makefile fsl/src/mist/Makefile
+--- fsl.orig/src/mist/Makefile	2020-12-02 15:29:12.875812580 -0500
++++ fsl/src/mist/Makefile	2020-12-02 15:45:09.805842335 -0500
+@@ -52,6 +52,8 @@
+ 		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