Migrated to Gentoo Science
https://gitweb.gentoo.org/proj/sci.git/commit/?id=f672571c8517da492b59e914aaa25e8786a6af61
This commit is contained in:
Horea Christian
parent
be2d622d7f
commit
b0bd24b30d
@ -1,50 +0,0 @@
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19 Jan 2020; François Bissey <frp.bissey@gmail.com>
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files/fsl-6.0.2-fsldir_redux.patch, files/fsl-6.0.2-no_xmlpp.patch,
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files/fsl-6.0.2-qstring_compat.patch, files/fsl-6.0.2-setup.patch:
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sci-biology/fsl: credit and detail the patches.
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16 Jan 2020; <chymera@gentoo.org> fsl-6.0.2.ebuild:
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sci-biology/fsl: dropped commented matlab USE flag
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15 Jan 2020; <chymera@gentoo.org> fsl-6.0.2.ebuild:
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sci-biology/fsl: added dependency and bumped EAPI
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14 Nov 2019; François Bissey <frp.bissey@gmail.com> fsl-6.0.2.ebuild:
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sci-biology/fsl: use generic blas/lapack revert stuff.
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08 Nov 2019; François Bissey <frp.bissey@gmail.com> fsl-6.0.2.ebuild:
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sci-biology/fsl: final touches. Skip mist-clean.
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07 Nov 2019; François Bissey <frp.bissey@gmail.com>
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+files/fsl-6.0.2-fsldir_redux.patch, fsl-6.0.2.ebuild:
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sci-biology/fsl: Work on fsldir elimination
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07 Nov 2019; François Bissey <frp.bissey@gmail.com>
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+files/fsl-6.0.2-no_xmlpp.patch, +files/fsl-6.0.2-qstring_compat.patch,
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fsl-6.0.2.ebuild:
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sci-biology/fsl: patch porting to deal with cifti
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07 Nov 2019; François Bissey <frp.bissey@gmail.com> fsl-6.0.2.ebuild:
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sci-biology/fsl: tcl/tk is needed at build time
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07 Nov 2019; François Bissey <frp.bissey@gmail.com>
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files/fsl-6.0.2-setup.patch:
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sci-biology/fsl: do not build tcl/tk/libpng
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07 Nov 2019; François Bissey <frp.bissey@gmail.com>
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+files/fsl-6.0.2-setup.patch, fsl-6.0.2.ebuild:
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sci-biology/fsl: Initial fix to fsl 6.0.2
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*fsl-6.0.2 (06 Nov 2019)
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06 Nov 2019; <chymera@gentoo.org> +files/99fsl,
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+files/fsl-5.0.11-fslsurface_parallel_make.patch,
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+files/fsl-5.0.11-ifstream_use.patch, +files/fsl-5.0.11-niftiio_var_fix.patch,
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+files/fsl-5.0.11-no_xmlpp.patch, +files/fsl-5.0.11-qstring_compat.patch,
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+files/fsl-5.0.11-setup.patch, +files/fsl-5.0.4-headers.patch,
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+files/fsl-5.0.4-setup.patch, +files/fsl-5.0.6-fsldir_redux.patch,
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+files/fsl-5.0.8-fsldir_redux.patch, +files/fsl-5.0.8-headers.patch,
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+files/fsl-5.0.8-setup.patch, +files/fsl-5.0.9-fsldir_redux.patch,
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+files/fsl-5.0.9-headers.patch, +files/fsl-5.0.9-setup.patch,
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+fsl-6.0.2.ebuild, +metadata.xml:
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sci-biology/fsl: attempt at version bump 6.0.2
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@ -1 +0,0 @@
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DIST fsl-6.0.2.tar.gz 2505331864 SHA256 c118b351c6cedb441af7e1b9d194cf344505ff53b417063f697b86305a908afd SHA512 fe308393076c51c50b086f9bf7ff5ddebcf8b1284128e734b9d9e501019917ceba7c0ee5cd5aa1ed44452bcd042ad72653c1a8693f94eab9b83a80fe508a56ca WHIRLPOOL ecb62e9d09cc34ac926353e4a9a131be875428b729bcf2d6f1433d9ea1a7e2b9382d1a1b305651705449a48eb3c576899f09f82ae4254b149a6219096eb45d3d
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@ -1,5 +0,0 @@
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FSLOUTPUTTYPE=NIFTI_GZ
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FSLMULTIFILEQUIT=TRUE
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FSLTCLSH=tclsh
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FSLWISH=wish
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FSLDIR=/usr/share/fsl
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@ -1,14 +0,0 @@
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diff --git a/src/fslsurface/Makefile b/src/fslsurface/Makefile
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index 37f459c..008f443 100644
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--- a/src/fslsurface/Makefile
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+++ b/src/fslsurface/Makefile
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@@ -57,7 +57,7 @@ fslsurfacegl.a: fslsurfacegl.o fslsurface.a
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${AR} -r libfslsurfacegl.a fslsurfacegl.o
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fslsurface_backcompat.a: fslsurface_first.o fslsurface_dataconv.o fslsurface.a
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${AR} -r libfslsurface_backcompat.a fslsurface_first.o fslsurface_dataconv.o
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-fslsurfacemaths: fslsurface.a fslsurfacemaths.o
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+fslsurfacemaths: fslsurface.a fslsurfacemaths.o fslsurfaceio.o fslsurfacefns.o fslsurface_first.o fslsurface.o
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${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ fslsurfacemaths.o fslsurfaceio.o fslsurfacefns.o fslsurface_first.o fslsurface.o ${LIBS} ${FMLIBS}
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-marching_cubes: fslsurface.a marching_cubes.o
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+marching_cubes: fslsurface.a marching_cubes.o fslsurfaceio.o fslsurfacefns.o
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${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ marching_cubes.o fslsurfaceio.o fslsurfacefns.o ${LIBS} ${FMLIBS}
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@ -1,13 +0,0 @@
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diff --git a/src/melodic/meldata.cc b/src/melodic/meldata.cc
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index f310dc7..03fe8bb 100644
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--- a/src/melodic/meldata.cc
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+++ b/src/melodic/meldata.cc
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@@ -1015,7 +1015,7 @@ namespace Melodic{
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Resels = 1.0;
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in.open(logger.appendDir("smoothest").c_str(), ios::in);
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- if(in>0){
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+ if(in.is_open()){
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for(int ctr=1; ctr<7; ctr++)
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in >> str;
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in.close();
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@ -1,24 +0,0 @@
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diff --git a/src/fslio/dbh.h b/src/fslio/dbh.h
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index eff0a50a..fbce1770 100644
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--- a/src/fslio/dbh.h
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+++ b/src/fslio/dbh.h
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@@ -79,19 +79,6 @@ struct dsr /* dsr */
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struct data_history hist; /* 148 + 200 */
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}; /* total=348 */
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-/* Acceptable values for hdr.dime.datatype */
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-
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-#define DT_NONE 0
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-#define DT_UNKNOWN 0
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-#define DT_BINARY 1
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-#define DT_UNSIGNED_CHAR 2
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-#define DT_SIGNED_SHORT 4
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-#define DT_SIGNED_INT 8
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-#define DT_FLOAT 16
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-#define DT_COMPLEX 32
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-#define DT_DOUBLE 64
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-#define DT_RGB 128
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-#define DT_ALL 255
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typedef struct
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{
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@ -1,44 +0,0 @@
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diff --git a/src/flameo/Makefile b/src/flameo/Makefile
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index 5389e2f..52785c3 100644
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--- a/src/flameo/Makefile
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+++ b/src/flameo/Makefile
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@@ -2,7 +2,7 @@ include ${FSLCONFDIR}/default.mk
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PROJNAME = flame
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-USRINCFLAGS = -I${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
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+USRINCFLAGS = -fPIC -I${INC_NEWMAT} -I${INC_PROB} -I${INC_ZLIB} -I${FSLEXTINC} ${CIFTICFLAGS} -I${INC_BOOST} -I${FSLDIR}/include/ciftiio
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USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_ZLIB}
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UNAME := $(shell uname)
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@@ -10,7 +10,7 @@ ifeq (${UNAME},Darwin)
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LIBS = -liconv
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endif
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-LIBS += -lutils -lnewimage -lmiscmaths -lm -lnewmat -lfslio -lniftiio -lcifti -lxml++-2.6 -lxml2 -lboost_filesystem -lboost_system -lznz -lprob -lz
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+LIBS += -lutils -lnewimage -lmiscmaths -lm -lnewmat -lfslio -lniftiio ${CIFTILIBS} -lboost_filesystem -lboost_system -lznz -lprob -lz
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XFILES = flameo
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diff --git a/src/melodic/Makefile b/src/melodic/Makefile
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index 53b951a..803c39e 100644
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--- a/src/melodic/Makefile
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+++ b/src/melodic/Makefile
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@@ -7,7 +7,7 @@ OPTFLAGS_alphaev6-dec-osf5.0-gcc2.95.2 = -O3 -mieee -mfp-trap-mode=sui
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PROJNAME = melodic
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-USRINCFLAGS = -I${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${FSLDIR}/include/ciftiio
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+USRINCFLAGS = -fPIC -I${INC_NEWMAT} -I${INC_PROB} -I${INC_GD} -I${INC_GDC} -I${INC_PNG} -I${INC_ZLIB} -I${FSLEXTINC} ${CIFTICFLAGS} -I${INC_BOOST} -I${FSLDIR}/include/ciftiio
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USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_GD} -L${LIB_GDC} -L${LIB_PNG} -L${LIB_ZLIB}
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UNAME := $(shell uname)
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@@ -15,7 +15,7 @@ ifeq (${UNAME},Darwin)
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LIBS = -liconv
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endif
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-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
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+LIBS += -lutils -lnewimage -lmiscplot -lmiscpic -lmiscmaths -lfslio -lniftiio ${CIFTILIBS} -lboost_filesystem -lboost_system -lznz -lnewmat -lprob -lm -lgdc -lgd -lpng -lz
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TEST_OBJS = test.o
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@ -1,63 +0,0 @@
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From bbd60f634cdcdfbbb3eb8f3b6d00f366d9f34bf9 Mon Sep 17 00:00:00 2001
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From: =?UTF-8?q?Fran=C3=A7ois=20Bissey?= <frp.bissey@gmail.com>
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Date: Thu, 18 Oct 2018 11:21:05 +1300
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Subject: [PATCH] Basic compatibility between for AString built with either
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glib ustring or QString
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---
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src/flameo/gsa.cc | 4 ++--
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src/melodic/meldata.cc | 2 +-
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src/melodic/meldata.h | 2 +-
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3 files changed, 4 insertions(+), 4 deletions(-)
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diff --git a/src/flameo/gsa.cc b/src/flameo/gsa.cc
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index 6a477f9..0860d46 100644
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--- a/src/flameo/gsa.cc
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+++ b/src/flameo/gsa.cc
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@@ -74,7 +74,7 @@ namespace GSA {
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sourceType=mode;
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if ( sourceType.compare("CIFTI") == 0 ) {
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cifti::CiftiFile inputCifti;
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- inputCifti.openFile(fslbasename(filename)+".nii");
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|
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+ inputCifti.openFile((fslbasename(filename)+".nii").c_str());
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|
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ciftiExemplar=inputCifti.getCiftiXML();
|
|
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cerr << "ndim " << ciftiExemplar.getNumberOfDimensions() << endl;
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|
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cerr << "type1 " << ciftiExemplar.getMappingType(0) << endl;
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|
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@@ -194,7 +194,7 @@ namespace GSA {
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|
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scalarsMap.setLength(data.Nrows());
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|
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ciftiExemplar.setMap(0, scalarsMap);
|
|
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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.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
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|
||||||
index f310dc7..5e9bc18 100644
|
|
||||||
--- a/src/melodic/meldata.cc
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|
||||||
+++ b/src/melodic/meldata.cc
|
|
||||||
@@ -118,7 +118,7 @@ namespace Melodic{
|
|
||||||
tmpData = RawData.matrix(Mask);
|
|
||||||
memmsg(" after reshape ");
|
|
||||||
} else { //Read in Cifti
|
|
||||||
- inputCifti.openFile(fname+".nii");
|
|
||||||
+ inputCifti.openFile((fname+".nii").c_str());
|
|
||||||
const vector<int64_t>& dims = inputCifti.getDimensions();
|
|
||||||
tmpData.ReSize(dims[0],dims[1]); //swapped compared to cifti
|
|
||||||
vector<float> scratchRow(dims[0]);//read/write a row at a time
|
|
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diff --git a/src/melodic/meldata.h b/src/melodic/meldata.h
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|
||||||
index 1e1adfc..d898152 100644
|
|
||||||
--- a/src/melodic/meldata.h
|
|
||||||
+++ b/src/melodic/meldata.h
|
|
||||||
@@ -109,7 +109,7 @@ namespace Melodic{
|
|
||||||
message(" " << logger.appendDir(fname) << endl);
|
|
||||||
} else { //Process CIFTI save ICs as float
|
|
||||||
cifti::CiftiFile outputFile;
|
|
||||||
- outputFile.setWritingFile(logger.appendDir(fname)+".nii");//sets up on-disk writing with default writing version
|
|
||||||
+ outputFile.setWritingFile((logger.appendDir(fname)+".nii").c_str());//sets up on-disk writing with default writing version
|
|
||||||
cifti::CiftiXML xml(inputCifti.getCiftiXML());
|
|
||||||
cifti::CiftiScalarsMap scalarsMap;
|
|
||||||
std::vector<char> foo = xml.writeXMLToVector();
|
|
||||||
--
|
|
||||||
2.18.1
|
|
||||||
|
|
||||||
@ -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$1 = X-strict ] ; then
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|
||||||
fi
|
|
||||||
PROJECTS="$@" ; export PROJECTS ;
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|
||||||
|
|
||||||
-FSLDIR=`pwd`
|
|
||||||
+#FSLDIR=`pwd`
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|
||||||
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
|
|
||||||
|
|
||||||
@ -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;
|
|
||||||
|
|
||||||
@ -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
|
|
||||||
@ -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>
|
|
||||||
@ -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");
|
|
||||||
|
|
||||||
@ -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;
|
|
||||||
|
|
||||||
@ -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
|
|
||||||
@ -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");
|
|
||||||
|
|
||||||
@ -1,15 +0,0 @@
|
|||||||
# Include zlib header directly.
|
|
||||||
# From: Francois Bissey <frp.bissey@gmail.com>
|
|
||||||
# Signed-off-by: Horea Christian <horea.christ@gmail.com>
|
|
||||||
# Submitted upstream: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1709&L=FSL&F=&S=&X=95C10F0B7D62EAAE7A&P=169254
|
|
||||||
|
|
||||||
--- fsl/src/miscvis/writepng.c.orig 2013-10-19 00:18:32.415203592 +1300
|
|
||||||
+++ fsl/src/miscvis/writepng.c 2013-10-19 00:19:05.414255132 +1300
|
|
||||||
@@ -32,6 +32,7 @@
|
|
||||||
|
|
||||||
#include <stdlib.h> /* for exit() prototype */
|
|
||||||
|
|
||||||
+#include "zlib.h"
|
|
||||||
#include "png.h" /* libpng header; includes zlib.h and setjmp.h */
|
|
||||||
#include "writepng.h" /* typedefs, common macros, public prototypes */
|
|
||||||
|
|
||||||
@ -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
|
|
||||||
@ -1,495 +0,0 @@
|
|||||||
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/src/libvis/miscpic.h b/src/libvis/miscpic.h
|
|
||||||
index a2f3855..5f440f2 100644
|
|
||||||
--- a/src/libvis/miscpic.h
|
|
||||||
+++ b/src/libvis/miscpic.h
|
|
||||||
@@ -90,12 +90,7 @@ namespace MISCPIC{
|
|
||||||
markRight=false;
|
|
||||||
trans= -10;
|
|
||||||
edgethresh = 0.0;
|
|
||||||
- if(getenv("FSLDIR")!=0){
|
|
||||||
- lutbase = string(getenv("FSLDIR")) + "/etc/luts/";
|
|
||||||
- }
|
|
||||||
- else{
|
|
||||||
- lutbase = string("/");
|
|
||||||
- }
|
|
||||||
+ lutbase = "@GENTOO_PORTAGE_EPREFIX@/etc/luts/";
|
|
||||||
title = string("");
|
|
||||||
cbartype = string("");
|
|
||||||
cbarptr = NULL;
|
|
||||||
diff --git a/src/melodic/meldata.cc b/src/melodic/meldata.cc
|
|
||||||
index 1749a45..c4ad234 100644
|
|
||||||
--- a/src/melodic/meldata.cc
|
|
||||||
+++ b/src/melodic/meldata.cc
|
|
||||||
@@ -992,7 +992,7 @@ namespace Melodic{
|
|
||||||
void MelodicData::est_smoothness()
|
|
||||||
{
|
|
||||||
if(Resels == 0){
|
|
||||||
- string SM_path = opts.binpath + "smoothest";
|
|
||||||
+ string SM_path = "smoothest";
|
|
||||||
string Mask_fname = logger.appendDir("mask");
|
|
||||||
|
|
||||||
if(opts.segment.value().length()>0){
|
|
||||||
@@ -1157,7 +1157,7 @@ namespace Melodic{
|
|
||||||
// set up all strings
|
|
||||||
string BET_outputfname = string(Mean_fname)+"_brain";
|
|
||||||
|
|
||||||
- string BET_path = opts.binpath + "bet";
|
|
||||||
+ string BET_path = "bet";
|
|
||||||
string BET_optarg = "-m -f 0.4"; // see man bet
|
|
||||||
string Mask_fname = BET_outputfname+"_mask";
|
|
||||||
|
|
||||||
diff --git a/src/melodic/meloptions.cc b/src/melodic/meloptions.cc
|
|
||||||
index 08170c7..252e72b 100644
|
|
||||||
--- a/src/melodic/meloptions.cc
|
|
||||||
+++ b/src/melodic/meloptions.cc
|
|
||||||
@@ -93,14 +93,6 @@ MelodicOptions* MelodicOptions::gopt = NULL;
|
|
||||||
explicitnums = false;
|
|
||||||
logfname = string("log.txt");
|
|
||||||
|
|
||||||
- // work out the path to the $FSLDIR/bin directory
|
|
||||||
- if(getenv("FSLDIR")!=0){
|
|
||||||
- binpath = (string) getenv("FSLDIR") + "/bin/";
|
|
||||||
- } else{
|
|
||||||
- binpath = argv[0];
|
|
||||||
- binpath = binpath.substr(0,binpath.length()-7);
|
|
||||||
- }
|
|
||||||
-
|
|
||||||
// parse once to establish log directory name
|
|
||||||
for(int a = options.parse_command_line(argc, argv); a < argc; a++);
|
|
||||||
|
|
||||||
diff --git a/src/melodic/meloptions.h b/src/melodic/meloptions.h
|
|
||||||
index f546125..b964b7d 100644
|
|
||||||
--- a/src/melodic/meloptions.h
|
|
||||||
+++ b/src/melodic/meloptions.h
|
|
||||||
@@ -93,7 +93,6 @@ class MelodicOptions {
|
|
||||||
~MelodicOptions() { delete gopt; }
|
|
||||||
|
|
||||||
string version;
|
|
||||||
- string binpath;
|
|
||||||
string logfname;
|
|
||||||
bool filtermode;
|
|
||||||
bool explicitnums;
|
|
||||||
diff --git a/src/melodic/melreport.cc b/src/melodic/melreport.cc
|
|
||||||
index 141b6c2..2625059 100644
|
|
||||||
--- a/src/melodic/melreport.cc
|
|
||||||
+++ b/src/melodic/melreport.cc
|
|
||||||
@@ -84,8 +84,8 @@ namespace Melodic{
|
|
||||||
IChtml.setDir(report.getDir(),mmodel.get_prefix()+".html");
|
|
||||||
|
|
||||||
{//start IC page
|
|
||||||
- IChtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
|
|
||||||
- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl
|
|
||||||
+ IChtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
|
|
||||||
+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl
|
|
||||||
<< "<style type=\"text/css\">OBJECT { width: 100% }</style>"
|
|
||||||
<< "<TITLE>FSL</TITLE></HEAD>" << endl
|
|
||||||
<< "<IFRAME height=" << int(melodat.get_numfiles()/30 + 1)*50
|
|
||||||
@@ -486,8 +486,8 @@ namespace Melodic{
|
|
||||||
|
|
||||||
{//start IC2 page
|
|
||||||
IChtml2.setDir(report.getDir(),mmodel.get_prefix()+"_MM.html");
|
|
||||||
- IChtml2 << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
|
|
||||||
- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl
|
|
||||||
+ IChtml2 << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
|
|
||||||
+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl
|
|
||||||
<< "<style type=\"text/css\">OBJECT { width: 100% }</style>"
|
|
||||||
<< "<TITLE>FSL</TITLE></HEAD>" << endl
|
|
||||||
<< "<IFRAME height="<< int(melodat.get_numfiles()/30 + 1)*50
|
|
||||||
@@ -665,8 +665,8 @@ namespace Melodic{
|
|
||||||
IChtml << "<HTML> " << endl
|
|
||||||
<< "<TITLE>MELODIC Component " << num2str(cnum)
|
|
||||||
<< "</TITLE>" << endl
|
|
||||||
- << "<BODY BACKGROUND=\"file:" << getenv("FSLDIR")
|
|
||||||
- << "/doc/images/fsl-bg.jpg\">" << endl
|
|
||||||
+ << "<BODY BACKGROUND=\"file:"
|
|
||||||
+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl
|
|
||||||
<< "<hr><CENTER><H1>MELODIC Component " << num2str(cnum)
|
|
||||||
<< "</H1>"<< endl;
|
|
||||||
|
|
||||||
diff --git a/src/melodic/melreport.h b/src/melodic/melreport.h
|
|
||||||
index 574fc4c..e444681 100644
|
|
||||||
--- a/src/melodic/melreport.h
|
|
||||||
+++ b/src/melodic/melreport.h
|
|
||||||
@@ -104,21 +104,21 @@ namespace Melodic{
|
|
||||||
const time_t tmptime = time(NULL);
|
|
||||||
system(("mkdir "+ logger.appendDir("report") + " 2>/dev/null").c_str());
|
|
||||||
report.setDir(logger.appendDir("report"),"00index.html",true,false,ios::out);
|
|
||||||
- report << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
|
|
||||||
- (string) getenv("FSLDIR") +"/doc/fsl.css>"
|
|
||||||
+ report << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
|
|
||||||
+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>"
|
|
||||||
<< "<TITLE>MELODIC report</TITLE></HEAD><BODY>"
|
|
||||||
<< endl <<endl;
|
|
||||||
loghtml.setDir(report.getDir(),"log.html");
|
|
||||||
- loghtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
|
|
||||||
- (string) getenv("FSLDIR") +"/doc/fsl.css>"
|
|
||||||
+ loghtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
|
|
||||||
+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>"
|
|
||||||
<< "<TITLE>MELODIC report</TITLE></HEAD><BODY>"
|
|
||||||
<< endl <<endl;
|
|
||||||
navigator.setDir(report.getDir(),"nav.html");
|
|
||||||
head.setDir(report.getDir(),"head.html");
|
|
||||||
- navigator << "<link REL=stylesheet TYPE=text/css href=file:"+
|
|
||||||
- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl;
|
|
||||||
- head << "<link REL=stylesheet TYPE=text/css href=file:"+
|
|
||||||
- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl;
|
|
||||||
+ navigator << "<link REL=stylesheet TYPE=text/css href=file:"
|
|
||||||
+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl;
|
|
||||||
+ head << "<link REL=stylesheet TYPE=text/css href=file:"
|
|
||||||
+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl;
|
|
||||||
head <<"<TABLE BORDER=0><TR>" << endl
|
|
||||||
<<" <TD ALIGN=CENTER WIDTH=100%>"<< endl
|
|
||||||
<<"<TABLE BORDER=0>"<< endl
|
|
||||||
@@ -130,8 +130,8 @@ namespace Melodic{
|
|
||||||
<< "</tr></table>" << endl
|
|
||||||
<< "<TD ALIGN=RIGHT>" << endl
|
|
||||||
<< "<a href=http://www.fmrib.ox.ac.uk/fsl target=_top>" << endl
|
|
||||||
- << "<IMG BORDER=0 SRC=file:"<< getenv("FSLDIR")
|
|
||||||
- << "/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl
|
|
||||||
+ << "<IMG BORDER=0 SRC=file:"
|
|
||||||
+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl
|
|
||||||
<< "</TD>"<<endl<<"</TR></TABLE> <hr>"<<endl;
|
|
||||||
if(opts.guireport.value()==""){
|
|
||||||
report <<"<OBJECT data=head.html></OBJECT>" << endl;
|
|
||||||
diff --git a/src/mm/mixture_model.cc b/src/mm/mixture_model.cc
|
|
||||||
index b8e6167..5f00693 100644
|
|
||||||
--- a/src/mm/mixture_model.cc
|
|
||||||
+++ b/src/mm/mixture_model.cc
|
|
||||||
@@ -2224,8 +2224,8 @@ namespace Mm {
|
|
||||||
|
|
||||||
htmllog << "<HTML> " << endl
|
|
||||||
<< "<TITLE>Mixture Model fit for" << data_name << "</TITLE>" << endl
|
|
||||||
- << "<BODY BACKGROUND=\"file:" << getenv("FSLDIR")
|
|
||||||
- << "/doc/images/fsl-bg.jpg\">" << endl
|
|
||||||
+ << "<BODY BACKGROUND=\"file:"
|
|
||||||
+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl
|
|
||||||
<< "<hr><CENTER><H1>Mixture Model fit for<br>" << data_name << " </H1>"<< endl;
|
|
||||||
|
|
||||||
htmllog << "<hr><p>" << endl;
|
|
||||||
diff --git a/src/siena/siena_diff.cc b/src/siena/siena_diff.cc
|
|
||||||
index e19193a..17d8701 100644
|
|
||||||
--- a/src/siena/siena_diff.cc
|
|
||||||
+++ b/src/siena/siena_diff.cc
|
|
||||||
@@ -107,7 +107,7 @@ int main(int argc,char *argv[])
|
|
||||||
{
|
|
||||||
// {{{ vars
|
|
||||||
|
|
||||||
-char thestring[10000], segoptions[10000], fsldir[10000];
|
|
||||||
+char thestring[10000], segoptions[10000];
|
|
||||||
int x_size, y_size, z_size, size, x, y, z, i, count,
|
|
||||||
seg2=0, ignore_z=0, ignore_top_slices=0, //erode_mask=0,
|
|
||||||
ignore_bottom_slices=0, debug=0, flow_output=1, edge_masking=0;
|
|
||||||
@@ -124,8 +124,6 @@ if (argc<3)
|
|
||||||
|
|
||||||
string argv1(argv[1]), argv2(argv[2]);
|
|
||||||
|
|
||||||
-sprintf(fsldir,"%s",getenv("FSLDIR"));
|
|
||||||
-
|
|
||||||
for (i = 3; i < argc; i++) {
|
|
||||||
if (!strcmp(argv[i], "-i"))
|
|
||||||
ignore_z=1;
|
|
||||||
@@ -209,26 +207,26 @@ for (i = 3; i < argc; i++) {
|
|
||||||
// }}}
|
|
||||||
// {{{ transform images and masks
|
|
||||||
|
|
||||||
-sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
|
|
||||||
- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
|
|
||||||
+sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
|
|
||||||
+ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
|
|
||||||
printf("%s\n",thestring); system(thestring);
|
|
||||||
|
|
||||||
-sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
|
|
||||||
- fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
|
|
||||||
+sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
|
|
||||||
+ argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
|
|
||||||
printf("%s\n",thestring); system(thestring);
|
|
||||||
|
|
||||||
-sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
|
|
||||||
- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
|
|
||||||
+sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
|
|
||||||
+ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
|
|
||||||
printf("%s\n",thestring); system(thestring);
|
|
||||||
|
|
||||||
-sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
|
|
||||||
- fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
|
|
||||||
+sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
|
|
||||||
+ argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
|
|
||||||
printf("%s\n",thestring); system(thestring);
|
|
||||||
|
|
||||||
if (edge_masking)
|
|
||||||
{
|
|
||||||
- sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s",
|
|
||||||
- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
|
|
||||||
+ sprintf(thestring,"flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s",
|
|
||||||
+ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
|
|
||||||
printf("%s\n",thestring); system(thestring);
|
|
||||||
}
|
|
||||||
|
|
||||||
@@ -287,8 +285,8 @@ if(1) // always done unless the above uncommented and used instead of this test
|
|
||||||
cout << "saving image 1 to disk prior to segmentation" << endl;
|
|
||||||
save_volume(in1,argv1+"_halfwayto_"+argv2+"_brain");
|
|
||||||
in1.destroy();
|
|
||||||
- sprintf(thestring,"%s/bin/fast %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1",
|
|
||||||
- fsldir,segtype,segoptions,argv[1],argv[2],argv[1],argv[2]);
|
|
||||||
+ sprintf(thestring,"fast %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1",
|
|
||||||
+ segtype,segoptions,argv[1],argv[2],argv[1],argv[2]);
|
|
||||||
cout << thestring << endl;
|
|
||||||
system(thestring);
|
|
||||||
}
|
|
||||||
diff --git a/src/topup/topupfns.cpp b/src/topup/topupfns.cpp
|
|
||||||
index 6873758..9e8b956 100644
|
|
||||||
--- a/src/topup/topupfns.cpp
|
|
||||||
+++ b/src/topup/topupfns.cpp
|
|
||||||
@@ -463,8 +463,7 @@ string existing_conf_file(const string& cfname)
|
|
||||||
if (TOPUP::check_exist(ecfname)) return(ecfname);
|
|
||||||
}
|
|
||||||
if (!TOPUP::path(cfname).length()) { // If no path explicitly given
|
|
||||||
- const char *fsldir_ptr = getenv("FSLDIR");
|
|
||||||
- ecfname = string(fsldir_ptr) + string("/etc/flirtsch/") + cfname;
|
|
||||||
+ ecfname = string("@GENTOO_PORTAGE_EPREFIX@/etc/flirtsch/") + cfname;
|
|
||||||
if (TOPUP::check_exist(ecfname)) return(ecfname);
|
|
||||||
else if (!TOPUP::extension(ecfname).length()) { // If no path _and_ no extension given
|
|
||||||
ecfname += string(".cnf");
|
|
||||||
--
|
|
||||||
2.24.1
|
|
||||||
|
|
||||||
@ -1,58 +0,0 @@
|
|||||||
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 d22eb965..e967e682 100644
|
|
||||||
--- a/src/flameo/Makefile
|
|
||||||
+++ b/src/flameo/Makefile
|
|
||||||
@@ -2,7 +2,7 @@ include ${FSLCONFDIR}/default.mk
|
|
||||||
|
|
||||||
PROJNAME = flame
|
|
||||||
|
|
||||||
-USRINCFLAGS = -I${INC_NEWMAT} -I${INC_PROB} -I${INC_ZLIB} -DCIFTILIB_USE_XMLPP -I${FSLEXTINC} -I${INC_XML2} -I${INC_XML++} -I${INC_XML++CONF} -I${INC_BOOST} -I${FSLDIR}/include/ciftiio
|
|
||||||
+USRINCFLAGS = -fPIC -I${INC_NEWMAT} -I${INC_PROB} -I${INC_ZLIB} -I${FSLEXTINC} ${CIFTICFLAGS} -I${INC_BOOST} -I${FSLDIR}/include/ciftiio
|
|
||||||
USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_ZLIB}
|
|
||||||
|
|
||||||
UNAME := $(shell uname)
|
|
||||||
@@ -10,7 +10,7 @@ ifeq (${UNAME},Darwin)
|
|
||||||
LIBS = -liconv
|
|
||||||
endif
|
|
||||||
|
|
||||||
-LIBS += -lutils -lnewimage -lmiscmaths -lm -lnewmat -lNewNifti -lcifti -lxml++-2.6 -lxml2 -lboost_filesystem -lboost_system -lznz -lprob -lz
|
|
||||||
+LIBS += -lutils -lnewimage -lmiscmaths -lm -lnewmat -lNewNifti ${CIFTILIBS} -lboost_filesystem -lboost_system -lznz -lprob -lz
|
|
||||||
|
|
||||||
XFILES = flameo
|
|
||||||
|
|
||||||
diff --git a/src/melodic/Makefile b/src/melodic/Makefile
|
|
||||||
index 50666517..0c356a2d 100644
|
|
||||||
--- a/src/melodic/Makefile
|
|
||||||
+++ b/src/melodic/Makefile
|
|
||||||
@@ -7,7 +7,7 @@ OPTFLAGS_alphaev6-dec-osf5.0-gcc2.95.2 = -O3 -mieee -mfp-trap-mode=sui
|
|
||||||
|
|
||||||
PROJNAME = melodic
|
|
||||||
|
|
||||||
-USRINCFLAGS = -I${INC_NEWMAT} -I${INC_PROB} -I${INC_GD} -I${INC_GDC} -I${INC_PNG} -I${INC_ZLIB} -DCIFTILIB_USE_XMLPP -I${FSLEXTINC} -I${INC_XML2} -I${INC_XML++} -I${INC_XML++CONF} -I${INC_BOOST} -I${FSLDIR}/include/ciftiio
|
|
||||||
+USRINCFLAGS = -fPIC -I${INC_NEWMAT} -I${INC_PROB} -I${INC_GD} -I${INC_GDC} -I${INC_PNG} -I${INC_ZLIB} -I${FSLEXTINC} ${CIFTICFLAGS} -I${INC_BOOST} -I${FSLDIR}/include/ciftiio
|
|
||||||
USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_GD} -L${LIB_GDC} -L${LIB_PNG} -L${LIB_ZLIB}
|
|
||||||
|
|
||||||
UNAME := $(shell uname)
|
|
||||||
@@ -15,7 +15,7 @@ ifeq (${UNAME},Darwin)
|
|
||||||
LIBS = -liconv
|
|
||||||
endif
|
|
||||||
|
|
||||||
-LIBS += -lutils -lnewimage -lmiscplot -lmiscpic -lmiscmaths -lNewNifti -lcifti -lxml++-2.6 -lxml2 -lboost_filesystem -lboost_system -lznz -lnewmat -lprob -lm -lgdc -lgd -lpng -lz
|
|
||||||
+LIBS += -lutils -lnewimage -lmiscplot -lmiscpic -lmiscmaths -lNewNifti ${CIFTILIBS} -lboost_filesystem -lboost_system -lznz -lnewmat -lprob -lm -lgdc -lgd -lpng -lz
|
|
||||||
|
|
||||||
TEST_OBJS = test.o
|
|
||||||
|
|
||||||
--
|
|
||||||
2.24.1
|
|
||||||
|
|
||||||
@ -1,63 +0,0 @@
|
|||||||
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 ++--
|
|
||||||
src/melodic/meldata.cc | 2 +-
|
|
||||||
src/melodic/meldata.h | 2 +-
|
|
||||||
3 files changed, 4 insertions(+), 4 deletions(-)
|
|
||||||
|
|
||||||
diff --git a/src/flameo/gsa.cc b/src/flameo/gsa.cc
|
|
||||||
index 70f8f385..16167abe 100644
|
|
||||||
--- a/src/flameo/gsa.cc
|
|
||||||
+++ b/src/flameo/gsa.cc
|
|
||||||
@@ -74,7 +74,7 @@ namespace GSA {
|
|
||||||
sourceType=mode;
|
|
||||||
if ( sourceType.compare("CIFTI") == 0 ) {
|
|
||||||
cifti::CiftiFile inputCifti;
|
|
||||||
- inputCifti.openFile(make_basename(filename)+".nii");
|
|
||||||
+ inputCifti.openFile((make_basename(filename)+".nii").c_str());
|
|
||||||
ciftiExemplar=inputCifti.getCiftiXML();
|
|
||||||
cerr << "ndim " << ciftiExemplar.getNumberOfDimensions() << endl;
|
|
||||||
cerr << "type1 " << ciftiExemplar.getMappingType(0) << endl;
|
|
||||||
@@ -194,7 +194,7 @@ namespace GSA {
|
|
||||||
scalarsMap.setLength(data.Nrows());
|
|
||||||
ciftiExemplar.setMap(0, scalarsMap);
|
|
||||||
CiftiFile outputFile;
|
|
||||||
- outputFile.setWritingFile(make_basename(filename)+extension+".nii");//sets up on-disk writing with default writing version
|
|
||||||
+ outputFile.setWritingFile((make_basename(filename)+extension+".nii").c_str());//sets up on-disk writing with default writing version
|
|
||||||
outputFile.setCiftiXML(ciftiExemplar,false);
|
|
||||||
vector<float> scratchRow(data.Nrows());//read/write a row at a time
|
|
||||||
for (int64_t row=0;row<data.Ncols();row++) {
|
|
||||||
diff --git a/src/melodic/meldata.cc b/src/melodic/meldata.cc
|
|
||||||
index c4ad2349..1515e702 100644
|
|
||||||
--- a/src/melodic/meldata.cc
|
|
||||||
+++ b/src/melodic/meldata.cc
|
|
||||||
@@ -118,7 +118,7 @@ namespace Melodic{
|
|
||||||
tmpData = RawData.matrix(Mask);
|
|
||||||
memmsg(" after reshape ");
|
|
||||||
} else { //Read in Cifti
|
|
||||||
- inputCifti.openFile(fname+".nii");
|
|
||||||
+ inputCifti.openFile((fname+".nii").c_str());
|
|
||||||
const vector<int64_t>& dims = inputCifti.getDimensions();
|
|
||||||
tmpData.ReSize(dims[0],dims[1]); //swapped compared to cifti
|
|
||||||
vector<float> scratchRow(dims[0]);//read/write a row at a time
|
|
||||||
diff --git a/src/melodic/meldata.h b/src/melodic/meldata.h
|
|
||||||
index 49774003..f5326bdd 100644
|
|
||||||
--- a/src/melodic/meldata.h
|
|
||||||
+++ b/src/melodic/meldata.h
|
|
||||||
@@ -109,7 +109,7 @@ namespace Melodic{
|
|
||||||
message(" " << logger.appendDir(fname) << endl);
|
|
||||||
} else { //Process CIFTI save ICs as float
|
|
||||||
cifti::CiftiFile outputFile;
|
|
||||||
- outputFile.setWritingFile(logger.appendDir(fname)+".nii");//sets up on-disk writing with default writing version
|
|
||||||
+ outputFile.setWritingFile((logger.appendDir(fname)+".nii").c_str());//sets up on-disk writing with default writing version
|
|
||||||
cifti::CiftiXML xml(inputCifti.getCiftiXML());
|
|
||||||
cifti::CiftiScalarsMap scalarsMap;
|
|
||||||
std::vector<char> foo = xml.writeXMLToVector();
|
|
||||||
--
|
|
||||||
2.24.1
|
|
||||||
|
|
||||||
@ -1,198 +0,0 @@
|
|||||||
From baae97cc3c8d0cadcabb7ed16559f4e4de26ddbe Mon Sep 17 00:00:00 2001
|
|
||||||
From: François Bissey <frp.bissey@gmail.com>
|
|
||||||
Date: Mon, 20 Jan 2020 11:54:37 +1300
|
|
||||||
Subject: [PATCH] Adjust the build system so it doesnt build packages
|
|
||||||
externally provided by portage. Make the compilation flags more generic and
|
|
||||||
easily adjustable. Make the build system stop at the first fault.
|
|
||||||
|
|
||||||
---
|
|
||||||
build | 6 +++---
|
|
||||||
config/buildSettings.mk | 20 ++++++++++----------
|
|
||||||
config/common/buildproj | 8 +++++---
|
|
||||||
config/common/vars.mk | 10 +++++-----
|
|
||||||
extras/build | 8 ++++----
|
|
||||||
src/mist-clean/Makefile | 2 +-
|
|
||||||
6 files changed, 28 insertions(+), 26 deletions(-)
|
|
||||||
|
|
||||||
diff --git a/build b/build
|
|
||||||
index 05dac06c..d90e407b 100755
|
|
||||||
--- a/build
|
|
||||||
+++ b/build
|
|
||||||
@@ -3,7 +3,7 @@
|
|
||||||
if [ $# -ge 1 ] ; then
|
|
||||||
PROJECTS="$@";
|
|
||||||
else
|
|
||||||
- MASTERPROJECTS="CiftiLib-master utils znzlib NewNifti niftiio fslio giftiio miscmaths newimage libhfunc libvis first_lib \
|
|
||||||
+ MASTERPROJECTS="utils znzlib NewNifti niftiio fslio giftiio miscmaths newimage libhfunc libvis first_lib \
|
|
||||||
meshclass fslvtkio misc_tcl basisfield warpfns bint shapeModel MVdisc fslvtkconv fslsurface libmeshutils newmesh \
|
|
||||||
DiscreteOpt FastPDlib MSMRegLib misc_c dpm topup \
|
|
||||||
asl_mfree \
|
|
||||||
@@ -80,8 +80,8 @@ xtract";
|
|
||||||
done
|
|
||||||
fi
|
|
||||||
|
|
||||||
-echo "Building projects - see build.log file for progress..."
|
|
||||||
-./config/common/buildproj $PROJECTS > ./build.log 2>&1
|
|
||||||
+echo "Building projects"
|
|
||||||
+./config/common/buildproj $PROJECTS
|
|
||||||
finalStatus=$?
|
|
||||||
if [ $finalStatus -eq 0 ]; then
|
|
||||||
echo "Build completed successfully.";
|
|
||||||
diff --git a/config/buildSettings.mk b/config/buildSettings.mk
|
|
||||||
index b2e1f150..04532fc2 100644
|
|
||||||
--- a/config/buildSettings.mk
|
|
||||||
+++ b/config/buildSettings.mk
|
|
||||||
@@ -18,7 +18,7 @@ MV = /bin/mv
|
|
||||||
CHMOD = /bin/chmod
|
|
||||||
MKDIR = /bin/mkdir
|
|
||||||
INSTALL = install -p
|
|
||||||
-TCLSH = ${FSLDIR}/bin/fsltclsh
|
|
||||||
+TCLSH = tclsh
|
|
||||||
DEPENDFLAGS = -MM
|
|
||||||
MACHDBGFLAGS = -g
|
|
||||||
#####################################################################
|
|
||||||
@@ -124,19 +124,19 @@ endif # if Darwin
|
|
||||||
#####################################################################
|
|
||||||
ifeq ($(SYSTYPE), Linux)
|
|
||||||
############### System Vars #####################################
|
|
||||||
-CC = gcc
|
|
||||||
-CXX = c++
|
|
||||||
-CXX11 = c++
|
|
||||||
+CC = @@GENTOO_CC@@
|
|
||||||
+CXX = @@GENTOO_CXX@@
|
|
||||||
+CXX11 = @@GENTOO_CXX@@
|
|
||||||
CSTATICFLAGS = -static
|
|
||||||
CXXSTATICFLAGS = -static
|
|
||||||
-ARCHFLAGS = -m64
|
|
||||||
-ARCHLDFLAGS = -Wl,-rpath,'$$ORIGIN/../lib'
|
|
||||||
+ARCHFLAGS =
|
|
||||||
+ARCHLDFLAGS =
|
|
||||||
PARALLELFLAGS = -fopenmp
|
|
||||||
-OPTFLAGS = -g -O3 -fexpensive-optimizations ${ARCHFLAGS}
|
|
||||||
+OPTFLAGS =
|
|
||||||
GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long
|
|
||||||
SGI_ANSI_FLAGS = -ansi -fullwarn
|
|
||||||
ANSI_FLAGS = ${GNU_ANSI_FLAGS}
|
|
||||||
-RANLIB = echo
|
|
||||||
+RANLIB = @@GENTOO_RANLIB@@
|
|
||||||
FSLML = ${FSLDIR}/bin/fslml
|
|
||||||
# CUDA development environment
|
|
||||||
CUDAVER := $(or $(CUDAVER),9.1)
|
|
||||||
@@ -148,8 +148,8 @@ INC_CUDA = ${CUDA_INSTALLATION}/include
|
|
||||||
NVCC = ${CUDA_INSTALLATION}/bin/nvcc
|
|
||||||
############### External Libs #####################################
|
|
||||||
# ZLIB library
|
|
||||||
-LIB_ZLIB = /lib64
|
|
||||||
-INC_ZLIB = /usr/include
|
|
||||||
+#LIB_ZLIB = /lib64
|
|
||||||
+#INC_ZLIB = /usr/include
|
|
||||||
# QT library
|
|
||||||
QTDIR = /usr/lib/qt3
|
|
||||||
LIB_QT = ${QTDIR}/lib
|
|
||||||
diff --git a/config/common/buildproj b/config/common/buildproj
|
|
||||||
index 2f0f2b8f..48624a1f 100755
|
|
||||||
--- a/config/common/buildproj
|
|
||||||
+++ b/config/common/buildproj
|
|
||||||
@@ -11,10 +11,10 @@ if [ X$1 = X-strict ] ; then
|
|
||||||
fi
|
|
||||||
PROJECTS="$@" ; export PROJECTS ;
|
|
||||||
|
|
||||||
-FSLDIR=`pwd`
|
|
||||||
+#FSLDIR=`pwd`
|
|
||||||
FSLDEVDIR=${FSLDIR}
|
|
||||||
FSLCONFDIR=${FSLDIR}/config
|
|
||||||
-FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh`
|
|
||||||
+#FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh`
|
|
||||||
FSLMASTERBUILD=1
|
|
||||||
export FSLDIR FSLDEVDIR FSLCONFDIR FSLMACHTYPE FSLMASTERBUILD
|
|
||||||
|
|
||||||
@@ -67,7 +67,7 @@ for projname in $PROJECTS; do
|
|
||||||
if [ -x ./fslconfig ] ; then
|
|
||||||
. ./fslconfig ;
|
|
||||||
fi
|
|
||||||
- if ${MAKE} -k ${MAKEOPTIONS} ; then
|
|
||||||
+ if ${MAKE} ${MAKEOPTIONS} ; then
|
|
||||||
if ${MAKE} ${MAKEOPTIONS} install ; then
|
|
||||||
installok=true;
|
|
||||||
# Clean up after ourselves
|
|
||||||
@@ -82,6 +82,7 @@ for projname in $PROJECTS; do
|
|
||||||
if [ $installok = false ] ; then
|
|
||||||
echo " "
|
|
||||||
echo "ERROR::Could not install $projname successfully" ;
|
|
||||||
+ exit 1
|
|
||||||
fi
|
|
||||||
else
|
|
||||||
echo " "
|
|
||||||
@@ -90,6 +91,7 @@ for projname in $PROJECTS; do
|
|
||||||
echo " "
|
|
||||||
echo " "
|
|
||||||
errorprojs="$errorprojs $projname" ; export errorprojs ;
|
|
||||||
+ exit 1
|
|
||||||
fi
|
|
||||||
fi
|
|
||||||
done
|
|
||||||
diff --git a/config/common/vars.mk b/config/common/vars.mk
|
|
||||||
index b027b010..aeeae67c 100755
|
|
||||||
--- a/config/common/vars.mk
|
|
||||||
+++ b/config/common/vars.mk
|
|
||||||
@@ -24,15 +24,15 @@ USRINCFLAGS =
|
|
||||||
USRCFLAGS =
|
|
||||||
USRCXXFLAGS =
|
|
||||||
|
|
||||||
-LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR}
|
|
||||||
+LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR} ${USERLDFLAGS}
|
|
||||||
|
|
||||||
-AccumulatedIncFlags = -I${INC_BOOST} ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR}
|
|
||||||
+AccumulatedIncFlags = ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR} ${CPPFLAGS}
|
|
||||||
|
|
||||||
CFLAGS = ${ANSI_FLAGS} ${ANSI_CFLAGS} ${DBGFLAGS} ${USEDCSTATICFLAGS} ${USRCFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \
|
|
||||||
- ${AccumulatedIncFlags}
|
|
||||||
+ ${AccumulatedIncFlags} ${USERCFLAGS}
|
|
||||||
|
|
||||||
-CXXFLAGS = ${ANSI_FLAGS} ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \
|
|
||||||
- ${AccumulatedIncFlags}
|
|
||||||
+CXXFLAGS = ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \
|
|
||||||
+ ${AccumulatedIncFlags} ${USERCXXFLAGS}
|
|
||||||
|
|
||||||
HFILES = *.h
|
|
||||||
AFILES = *.a
|
|
||||||
diff --git a/extras/build b/extras/build
|
|
||||||
index 59e7a2ed..0d68232e 100755
|
|
||||||
--- a/extras/build
|
|
||||||
+++ b/extras/build
|
|
||||||
@@ -96,16 +96,16 @@ if [ X"${OS}" = "XDarwin" ]; then
|
|
||||||
BUILDICONV=1
|
|
||||||
fi
|
|
||||||
fi
|
|
||||||
-PROJECTS="tcl tk"
|
|
||||||
+#PROJECTS="tcl tk"
|
|
||||||
if [ ${BUILDZLIB} -eq 1 ]; then
|
|
||||||
PROJECTS="${PROJECTS} zlib"
|
|
||||||
fi
|
|
||||||
-PROJECTS="${PROJECTS} libpng"
|
|
||||||
+#PROJECTS="${PROJECTS} libpng"
|
|
||||||
if [ ${BUILDICONV} -eq 1 ]; then
|
|
||||||
PROJECTS="${PROJECTS} libiconv"
|
|
||||||
fi
|
|
||||||
-PROJECTS="${PROJECTS} libgd libgdc libprob libcprob newmat cprob newran fftw"
|
|
||||||
-PROJECTS="${PROJECTS} boost libxml2-2.9.2 libxmlpp libsqlite libnlopt ../include/armawrap/dummy_newmat"
|
|
||||||
+PROJECTS="${PROJECTS} libgdc libprob libcprob newmat cprob newran"
|
|
||||||
+PROJECTS="${PROJECTS} ../include/armawrap/dummy_newmat"
|
|
||||||
for projname in $PROJECTS; do
|
|
||||||
if [ -d $FSLESRCDIR/$projname ] ; then
|
|
||||||
buildIt $FSLESRCDIR $projname 1
|
|
||||||
diff --git a/src/mist-clean/Makefile b/src/mist-clean/Makefile
|
|
||||||
index 20402cca..6918bee4 100755
|
|
||||||
--- a/src/mist-clean/Makefile
|
|
||||||
+++ b/src/mist-clean/Makefile
|
|
||||||
@@ -52,6 +52,6 @@ installpython:
|
|
||||||
cp -r python/* ${DESTDIR}/python/mist
|
|
||||||
|
|
||||||
clean:
|
|
||||||
- rm -f ${OBJS} mist/mist.o mist/mist
|
|
||||||
+ rm -f ${OBJS} mist/mist.o mist/mist || echo "CLEAN could not locate some files scheduled for deletion."
|
|
||||||
|
|
||||||
.PHONY: all clean installdata
|
|
||||||
--
|
|
||||||
2.24.1
|
|
||||||
|
|
||||||
@ -1,164 +0,0 @@
|
|||||||
# Copyright 1999-2020 Gentoo Authors
|
|
||||||
# Distributed under the terms of the GNU General Public License v2
|
|
||||||
|
|
||||||
EAPI=7
|
|
||||||
|
|
||||||
inherit flag-o-matic toolchain-funcs prefix
|
|
||||||
|
|
||||||
DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging data"
|
|
||||||
HOMEPAGE="http://www.fmrib.ox.ac.uk/fsl"
|
|
||||||
SRC_URI="https://fsl.fmrib.ox.ac.uk/fsldownloads/${P}-sources.tar.gz -> ${P}.tar.gz"
|
|
||||||
|
|
||||||
LICENSE="FSL BSD-2 newmat"
|
|
||||||
SLOT="0"
|
|
||||||
KEYWORDS="~amd64"
|
|
||||||
IUSE=""
|
|
||||||
|
|
||||||
DEPEND="
|
|
||||||
dev-libs/boost
|
|
||||||
dev-python/fslpy
|
|
||||||
media-gfx/graphviz
|
|
||||||
media-libs/gd
|
|
||||||
media-libs/glu
|
|
||||||
media-libs/libpng:0=
|
|
||||||
sci-libs/ciftilib
|
|
||||||
sci-libs/nlopt
|
|
||||||
sys-libs/zlib
|
|
||||||
dev-lang/tcl:0=
|
|
||||||
dev-lang/tk:0=
|
|
||||||
>=virtual/lapack-3.8
|
|
||||||
>=virtual/blas-3.8
|
|
||||||
"
|
|
||||||
RDEPEND="${DEPEND}"
|
|
||||||
|
|
||||||
S=${WORKDIR}/${PN}
|
|
||||||
UPSTREAM_FSLDIR="/usr/share/fsl"
|
|
||||||
|
|
||||||
PATCHES=(
|
|
||||||
"${FILESDIR}/${PN}"-6.0.2-setup.patch
|
|
||||||
"${FILESDIR}/${PN}"-6.0.2-no_xmlpp.patch
|
|
||||||
"${FILESDIR}/${PN}"-5.0.11-niftiio_var_fix.patch
|
|
||||||
"${FILESDIR}/${PN}"-5.0.11-ifstream_use.patch
|
|
||||||
"${FILESDIR}/${PN}"-5.0.11-fslsurface_parallel_make.patch
|
|
||||||
"${FILESDIR}/${PN}"-6.0.2-qstring_compat.patch
|
|
||||||
"${FILESDIR}/${PN}"-5.0.9-headers.patch
|
|
||||||
"${FILESDIR}/${PN}"-6.0.2-fsldir_redux.patch
|
|
||||||
)
|
|
||||||
|
|
||||||
src_prepare(){
|
|
||||||
default
|
|
||||||
|
|
||||||
sed -i \
|
|
||||||
-e "s:@@GENTOO_RANLIB@@:$(tc-getRANLIB):" \
|
|
||||||
-e "s:@@GENTOO_CC@@:$(tc-getCC):" \
|
|
||||||
-e "s:@@GENTOO_CXX@@:$(tc-getCXX):" \
|
|
||||||
config/buildSettings.mk || die
|
|
||||||
|
|
||||||
eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX src/*) \
|
|
||||||
etc/js/label-div.html
|
|
||||||
|
|
||||||
# Disable mist-clean the hard way for now.
|
|
||||||
rm -rf src/mist-clean
|
|
||||||
|
|
||||||
makefilelist=$(find src/ -name Makefile)
|
|
||||||
|
|
||||||
sed -i \
|
|
||||||
-e "s:-I\${INC_BOOST}::" \
|
|
||||||
-e "s:-I\${INC_ZLIB}::" \
|
|
||||||
-e "s:-I\${INC_GD}::" \
|
|
||||||
-e "s:-I\${INC_PNG}::" \
|
|
||||||
-e "s:-L\${LIB_GD}::" \
|
|
||||||
-e "s:-L\${LIB_PNG}::" \
|
|
||||||
-e "s:-L\${LIB_ZLIB}::" \
|
|
||||||
${makefilelist} || die
|
|
||||||
|
|
||||||
sed -e "s:\${FSLDIR}/bin/::g" \
|
|
||||||
-e "s:\$FSLDIR/bin/::g" \
|
|
||||||
-i $(grep -rl "\${FSLDIR}/bin" src/*) \
|
|
||||||
-i $(grep -rl "\$FSLDIR/bin" src/*) \
|
|
||||||
$(grep -rl "\${FSLDIR}/bin" etc/matlab/*)\
|
|
||||||
$(grep -rl "\$FSLDIR/bin" etc/matlab/*) || die
|
|
||||||
|
|
||||||
sed -e "s:\$FSLDIR/data:${EPREFIX}/usr/share/fsl/data:g" \
|
|
||||||
-e "s:\${FSLDIR}/data:${EPREFIX}/usr/share/fsl/data:g" \
|
|
||||||
-i $(grep -rl "\$FSLDIR/data" src/*) \
|
|
||||||
$(grep -rl "\${FSLDIR}/data" src/*) || die
|
|
||||||
|
|
||||||
sed -e "s:\$FSLDIR/doc:${EPREFIX}/usr/share/fsl/doc:g" \
|
|
||||||
-e "s:\${FSLDIR}/doc:${EPREFIX}/usr/share/fsl/doc:g" \
|
|
||||||
-i $(grep -rl "\$FSLDIR/doc" src/*) \
|
|
||||||
$(grep -rl "\${FSLDIR}/doc" src/*) || die
|
|
||||||
|
|
||||||
sed -e "s:/usr/share/fsl/doc:${EPREFIX}/usr/share/fsl/doc:g" \
|
|
||||||
-i $(grep -rl "/usr/share/fsl/doc" src/*) || die
|
|
||||||
|
|
||||||
sed -e "s:\$FSLDIR/etc:${EPREFIX}/etc:g" \
|
|
||||||
-e "s:\${FSLDIR}/etc:${EPREFIX}/etc:g" \
|
|
||||||
-i $(grep -rlI "\$FSLDIR/etc" *) \
|
|
||||||
-i $(grep -rlI "\${FSLDIR}/etc" *) || die
|
|
||||||
|
|
||||||
# Use generic blas/lapack rather than openblas
|
|
||||||
sed -e "s:-lopenblas:-llapack -lblas:g" \
|
|
||||||
-i $(grep -rlI lopenblas *) || die
|
|
||||||
|
|
||||||
# script wanting to have access to flsversion at buildtime
|
|
||||||
sed -e "s:/etc/fslversion:${S}/etc/fslversion:g" \
|
|
||||||
-i ${makefilelist} || die
|
|
||||||
}
|
|
||||||
|
|
||||||
src_compile() {
|
|
||||||
export FSLDIR=${WORKDIR}/${PN}
|
|
||||||
export FSLCONDIR=${WORKDIR}/${PN}/config
|
|
||||||
export FSLMACHTYPE=generic
|
|
||||||
|
|
||||||
export USERLDFLAGS="${LDFLAGS}"
|
|
||||||
export USERCFLAGS="${CFLAGS}"
|
|
||||||
export USERCXXFLAGS="${CXXFLAGS}"
|
|
||||||
|
|
||||||
export CIFTICFLAGS="$($(tc-getPKG_CONFIG) --cflags CiftiLib)"
|
|
||||||
export CIFTILIBS="$($(tc-getPKG_CONFIG) --libs-only-l CiftiLib)"
|
|
||||||
|
|
||||||
./build || die
|
|
||||||
}
|
|
||||||
|
|
||||||
src_install() {
|
|
||||||
sed -i "s:\${FSLDIR}/tcl:/usr/libexec/fsl:g" \
|
|
||||||
$(grep -lI "\${FSLDIR}/tcl" bin/*) \
|
|
||||||
$(grep -l "\${FSLDIR}/tcl" tcl/*) || die
|
|
||||||
sed -i "s:\$FSLDIR/tcl:/usr/libexec/fsl:g" \
|
|
||||||
$(grep -l "\$FSLDIR/tcl" tcl/*) || die
|
|
||||||
|
|
||||||
dobin bin/*
|
|
||||||
|
|
||||||
insinto /usr/share/${PN}
|
|
||||||
doins -r data
|
|
||||||
dodoc -r doc/. refdoc
|
|
||||||
|
|
||||||
insinto /usr/libexec/fsl
|
|
||||||
doins -r tcl/*
|
|
||||||
|
|
||||||
insinto /etc/fslconf
|
|
||||||
doins etc/fslconf/fsl.sh
|
|
||||||
|
|
||||||
insinto /etc
|
|
||||||
doins etc/fslversion
|
|
||||||
doins -r etc/default_flobs.flobs etc/flirtsch etc/js etc/luts
|
|
||||||
|
|
||||||
#the following is needed for FSL and depending programs to be able
|
|
||||||
#to find its files, since FSL uses an uncommon installation path:
|
|
||||||
#https://github.com/gentoo-science/sci/pull/612#r60289295
|
|
||||||
dosym ../../../etc ${UPSTREAM_FSLDIR}/etc
|
|
||||||
dosym ../doc/${PF} ${UPSTREAM_FSLDIR}/doc
|
|
||||||
dosym ../../bin ${UPSTREAM_FSLDIR}/bin
|
|
||||||
|
|
||||||
doenvd "$(prefixify_ro "${FILESDIR}"/99fsl)"
|
|
||||||
mv "${ED}"/usr/bin/{,fsl_}cluster || die
|
|
||||||
}
|
|
||||||
|
|
||||||
pkg_postinst() {
|
|
||||||
echo
|
|
||||||
einfo "Please run the following commands if you"
|
|
||||||
einfo "intend to use fsl from an existing shell:"
|
|
||||||
einfo "env-update && source /etc/profile"
|
|
||||||
echo
|
|
||||||
}
|
|
||||||
@ -1,11 +0,0 @@
|
|||||||
<?xml version="1.0" encoding="UTF-8"?>
|
|
||||||
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
|
|
||||||
<pkgmetadata>
|
|
||||||
<maintainer type="project">
|
|
||||||
<email>sci-biology@gentoo.org</email>
|
|
||||||
<name>Gentoo Biology Project</name>
|
|
||||||
</maintainer>
|
|
||||||
<longdescription>
|
|
||||||
FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.
|
|
||||||
</longdescription>
|
|
||||||
</pkgmetadata>
|
|
||||||
Loading…
x
Reference in New Issue
Block a user