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