commit: 3ef3c15bafb5079dd2018f02ea63c50a36e51002
Author: Aisha Tammy <gentoo <AT> aisha <DOT> cc>
AuthorDate: Thu Dec 31 15:07:13 2020 +0000
Commit: Aisha Tammy <gentoo <AT> aisha <DOT> cc>
CommitDate: Thu Dec 31 15:07:13 2020 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=3ef3c15b
sci-biology/fsl: break large patch into two
this should fix up the build
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Aisha Tammy <gentoo <AT> aisha.cc>
...redux.patch => fsl-6.0.2-fsldir_redux-p1.patch} | 255 ---------------------
.../fsl/files/fsl-6.0.2-fsldir_redux-p2.patch | 255 +++++++++++++++++++++
sci-biology/fsl/fsl-6.0.2-r1.ebuild | 3 +-
sci-biology/fsl/fsl-6.0.2.ebuild | 3 +-
sci-biology/fsl/metadata.xml | 3 -
5 files changed, 259 insertions(+), 260 deletions(-)
diff --git a/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux.patch
b/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p1.patch
similarity index 52%
rename from sci-biology/fsl/files/fsl-6.0.2-fsldir_redux.patch
rename to sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p1.patch
index dc1babd48..ca3945442 100644
--- a/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux.patch
+++ b/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p1.patch
@@ -238,258 +238,3 @@ index eaf55eb..3dc184d 100644
//file.bvars,mni_template.nii.gz
// string mni = string(fsldir)+"/data/standard/MNI152_T1_1mm";
cout<<"recon "<< string(argv[i_arg+1])<<endl;
-diff --git a/src/libvis/miscpic.h b/src/libvis/miscpic.h
-index a2f3855..5f440f2 100644
---- a/src/libvis/miscpic.h
-+++ b/src/libvis/miscpic.h
-@@ -90,12 +90,7 @@ namespace MISCPIC{
- markRight=false;
- trans= -10;
- edgethresh = 0.0;
-- if(getenv("FSLDIR")!=0){
-- lutbase = string(getenv("FSLDIR")) + "/etc/luts/";
-- }
-- else{
-- lutbase = string("/");
-- }
-+ lutbase = "@GENTOO_PORTAGE_EPREFIX@/etc/luts/";
- title = string("");
- cbartype = string("");
- cbarptr = NULL;
-diff --git a/src/melodic/meldata.cc b/src/melodic/meldata.cc
-index 1749a45..c4ad234 100644
---- a/src/melodic/meldata.cc
-+++ b/src/melodic/meldata.cc
-@@ -992,7 +992,7 @@ namespace Melodic{
- void MelodicData::est_smoothness()
- {
- if(Resels == 0){
-- string SM_path = opts.binpath + "smoothest";
-+ string SM_path = "smoothest";
- string Mask_fname = logger.appendDir("mask");
-
- if(opts.segment.value().length()>0){
-@@ -1157,7 +1157,7 @@ namespace Melodic{
- // set up all strings
- string BET_outputfname =
string(Mean_fname)+"_brain";
-
-- string BET_path = opts.binpath + "bet";
-+ string BET_path = "bet";
- string BET_optarg = "-m -f 0.4"; // see man bet
- string Mask_fname = BET_outputfname+"_mask";
-
-diff --git a/src/melodic/meloptions.cc b/src/melodic/meloptions.cc
-index 08170c7..252e72b 100644
---- a/src/melodic/meloptions.cc
-+++ b/src/melodic/meloptions.cc
-@@ -93,14 +93,6 @@ MelodicOptions* MelodicOptions::gopt = NULL;
- explicitnums = false;
- logfname = string("log.txt");
-
-- // work out the path to the $FSLDIR/bin directory
-- if(getenv("FSLDIR")!=0){
-- binpath = (string) getenv("FSLDIR") + "/bin/";
-- } else{
-- binpath = argv[0];
-- binpath = binpath.substr(0,binpath.length()-7);
-- }
--
- // parse once to establish log directory name
- for(int a = options.parse_command_line(argc, argv); a < argc;
a++);
-
-diff --git a/src/melodic/meloptions.h b/src/melodic/meloptions.h
-index f546125..b964b7d 100644
---- a/src/melodic/meloptions.h
-+++ b/src/melodic/meloptions.h
-@@ -93,7 +93,6 @@ class MelodicOptions {
- ~MelodicOptions() { delete gopt; }
-
- string version;
-- string binpath;
- string logfname;
- bool filtermode;
- bool explicitnums;
-diff --git a/src/melodic/melreport.cc b/src/melodic/melreport.cc
-index 141b6c2..2625059 100644
---- a/src/melodic/melreport.cc
-+++ b/src/melodic/melreport.cc
-@@ -84,8 +84,8 @@ namespace Melodic{
-
IChtml.setDir(report.getDir(),mmodel.get_prefix()+".html");
-
- {//start IC page
-- IChtml << "<HTML><HEAD><link REL=stylesheet
TYPE=text/css href=file:" +
-- (string) getenv("FSLDIR")
+"/doc/fsl.css>" << endl
-+ IChtml << "<HTML><HEAD><link REL=stylesheet
TYPE=text/css href=file:"
-+ <<
"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl
- << "<style type=\"text/css\">OBJECT {
width: 100% }</style>"
- << "<TITLE>FSL</TITLE></HEAD>" << endl
- << "<IFRAME height=" <<
int(melodat.get_numfiles()/30 + 1)*50
-@@ -486,8 +486,8 @@ namespace Melodic{
-
- {//start IC2 page
-
IChtml2.setDir(report.getDir(),mmodel.get_prefix()+"_MM.html");
-- IChtml2 << "<HTML><HEAD><link REL=stylesheet
TYPE=text/css href=file:" +
-- (string) getenv("FSLDIR")
+"/doc/fsl.css>" << endl
-+ IChtml2 << "<HTML><HEAD><link REL=stylesheet
TYPE=text/css href=file:"
-+ <<
"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl
- << "<style type=\"text/css\">OBJECT {
width: 100% }</style>"
- << "<TITLE>FSL</TITLE></HEAD>" << endl
- << "<IFRAME height="<<
int(melodat.get_numfiles()/30 + 1)*50
-@@ -665,8 +665,8 @@ namespace Melodic{
- IChtml << "<HTML> " << endl
- << "<TITLE>MELODIC Component " << num2str(cnum)
- << "</TITLE>" << endl
-- << "<BODY BACKGROUND=\"file:" << getenv("FSLDIR")
-- << "/doc/images/fsl-bg.jpg\">" << endl
-+ << "<BODY BACKGROUND=\"file:"
-+ <<
"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl
- << "<hr><CENTER><H1>MELODIC Component " << num2str(cnum)
- << "</H1>"<< endl;
-
-diff --git a/src/melodic/melreport.h b/src/melodic/melreport.h
-index 574fc4c..e444681 100644
---- a/src/melodic/melreport.h
-+++ b/src/melodic/melreport.h
-@@ -104,21 +104,21 @@ namespace Melodic{
- const time_t tmptime = time(NULL);
- system(("mkdir "+ logger.appendDir("report") +
" 2>/dev/null").c_str());
-
report.setDir(logger.appendDir("report"),"00index.html",true,false,ios::out);
-- report << "<HTML><HEAD><link
REL=stylesheet TYPE=text/css href=file:" +
-- (string)
getenv("FSLDIR") +"/doc/fsl.css>"
-+ report << "<HTML><HEAD><link
REL=stylesheet TYPE=text/css href=file:"
-+ <<
"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>"
- << "<TITLE>MELODIC
report</TITLE></HEAD><BODY>"
- << endl <<endl;
-
loghtml.setDir(report.getDir(),"log.html");
-- loghtml << "<HTML><HEAD><link
REL=stylesheet TYPE=text/css href=file:" +
-- (string)
getenv("FSLDIR") +"/doc/fsl.css>"
-+ loghtml << "<HTML><HEAD><link
REL=stylesheet TYPE=text/css href=file:"
-+ <<
"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>"
- << "<TITLE>MELODIC
report</TITLE></HEAD><BODY>"
- << endl <<endl;
-
navigator.setDir(report.getDir(),"nav.html");
-
head.setDir(report.getDir(),"head.html");
-- navigator << "<link REL=stylesheet
TYPE=text/css href=file:"+
-- (string)
getenv("FSLDIR") +"/doc/fsl.css>" << endl;
-- head << "<link REL=stylesheet
TYPE=text/css href=file:"+
-- (string)
getenv("FSLDIR") +"/doc/fsl.css>" << endl;
-+ navigator << "<link REL=stylesheet
TYPE=text/css href=file:"
-+ <<
"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl;
-+ head << "<link REL=stylesheet
TYPE=text/css href=file:"
-+ <<
"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl;
- head <<"<TABLE BORDER=0><TR>"
<< endl
- <<" <TD ALIGN=CENTER
WIDTH=100%>"<< endl
- <<"<TABLE BORDER=0>"<<
endl
-@@ -130,8 +130,8 @@ namespace Melodic{
- << "</tr></table>" <<
endl
- << "<TD ALIGN=RIGHT>"
<< endl
- << "<a
href=http://www.fmrib.ox.ac.uk/fsl target=_top>" << endl
-- << "<IMG BORDER=0
SRC=file:"<< getenv("FSLDIR")
-- <<
"/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl
-+ << "<IMG BORDER=0 SRC=file:"
-+ <<
"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-logo-big.jpg
WIDTH=165></a>" << endl
- <<
"</TD>"<<endl<<"</TR></TABLE> <hr>"<<endl;
- if(opts.guireport.value()==""){
- report <<"<OBJECT
data=head.html></OBJECT>" << endl;
-diff --git a/src/mm/mixture_model.cc b/src/mm/mixture_model.cc
-index b8e6167..5f00693 100644
---- a/src/mm/mixture_model.cc
-+++ b/src/mm/mixture_model.cc
-@@ -2224,8 +2224,8 @@ namespace Mm {
-
- htmllog << "<HTML> " << endl
- << "<TITLE>Mixture Model fit for" << data_name << "</TITLE>" <<
endl
-- << "<BODY BACKGROUND=\"file:" << getenv("FSLDIR")
-- << "/doc/images/fsl-bg.jpg\">" << endl
-+ << "<BODY BACKGROUND=\"file:"
-+ <<
"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl
- << "<hr><CENTER><H1>Mixture Model fit for<br>" << data_name <<
" </H1>"<< endl;
-
- htmllog << "<hr><p>" << endl;
-diff --git a/src/siena/siena_diff.cc b/src/siena/siena_diff.cc
-index e19193a..17d8701 100644
---- a/src/siena/siena_diff.cc
-+++ b/src/siena/siena_diff.cc
-@@ -107,7 +107,7 @@ int main(int argc,char *argv[])
- {
- // {{{ vars
-
--char thestring[10000], segoptions[10000], fsldir[10000];
-+char thestring[10000], segoptions[10000];
- int x_size, y_size, z_size, size, x, y, z, i, count,
- seg2=0, ignore_z=0, ignore_top_slices=0, //erode_mask=0,
- ignore_bottom_slices=0, debug=0, flow_output=1, edge_masking=0;
-@@ -124,8 +124,6 @@ if (argc<3)
-
- string argv1(argv[1]), argv2(argv[2]);
-
--sprintf(fsldir,"%s",getenv("FSLDIR"));
--
- for (i = 3; i < argc; i++) {
- if (!strcmp(argv[i], "-i"))
- ignore_z=1;
-@@ -209,26 +207,26 @@ for (i = 3; i < argc; i++) {
- // }}}
- // {{{ transform images and masks
-
--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1
-paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
-- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
-+sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0
-init %s_halfwayto_%s.mat -ref %s -in %s",
-+ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
- printf("%s\n",thestring); system(thestring);
-
--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1
-paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
-- fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
-+sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0
-init %s_halfwayto_%s.mat -ref %s -in %s",
-+ argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
- printf("%s\n",thestring); system(thestring);
-
--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1
-paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
-- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
-+sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize
0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
-+ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
- printf("%s\n",thestring); system(thestring);
-
--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1
-paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
-- fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
-+sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize
0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
-+ argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
- printf("%s\n",thestring); system(thestring);
-
- if (edge_masking)
- {
-- sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm
1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s",
-- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
-+ sprintf(thestring,"flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm 1
-paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s",
-+ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
- printf("%s\n",thestring); system(thestring);
- }
-
-@@ -287,8 +285,8 @@ if(1) // always done unless the above uncommented and used
instead of this test
- cout << "saving image 1 to disk prior to segmentation" << endl;
- save_volume(in1,argv1+"_halfwayto_"+argv2+"_brain");
- in1.destroy();
-- sprintf(thestring,"%s/bin/fast %s %s %s_halfwayto_%s_brain >
%s_halfwayto_%s_brain.vol 2>&1",
-- fsldir,segtype,segoptions,argv[1],argv[2],argv[1],argv[2]);
-+ sprintf(thestring,"fast %s %s %s_halfwayto_%s_brain >
%s_halfwayto_%s_brain.vol 2>&1",
-+ segtype,segoptions,argv[1],argv[2],argv[1],argv[2]);
- cout << thestring << endl;
- system(thestring);
- }
-diff --git a/src/topup/topupfns.cpp b/src/topup/topupfns.cpp
-index 6873758..9e8b956 100644
---- a/src/topup/topupfns.cpp
-+++ b/src/topup/topupfns.cpp
-@@ -463,8 +463,7 @@ string existing_conf_file(const string& cfname)
- if (TOPUP::check_exist(ecfname)) return(ecfname);
- }
- if (!TOPUP::path(cfname).length()) { // If no path explicitly
given
-- const char *fsldir_ptr = getenv("FSLDIR");
-- ecfname = string(fsldir_ptr) + string("/etc/flirtsch/") + cfname;
-+ ecfname = string("@GENTOO_PORTAGE_EPREFIX@/etc/flirtsch/") + cfname;
- if (TOPUP::check_exist(ecfname)) return(ecfname);
- else if (!TOPUP::extension(ecfname).length()) { // If no path _and_ no
extension given
- ecfname += string(".cnf");
---
-2.24.1
-
diff --git a/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p2.patch
b/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p2.patch
new file mode 100644
index 000000000..74bf19169
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p2.patch
@@ -0,0 +1,255 @@
+diff --git a/src/libvis/miscpic.h b/src/libvis/miscpic.h
+index a2f3855..5f440f2 100644
+--- a/src/libvis/miscpic.h
++++ b/src/libvis/miscpic.h
+@@ -90,12 +90,7 @@ namespace MISCPIC{
+ markRight=false;
+ trans= -10;
+ edgethresh = 0.0;
+- if(getenv("FSLDIR")!=0){
+- lutbase = string(getenv("FSLDIR")) + "/etc/luts/";
+- }
+- else{
+- lutbase = string("/");
+- }
++ lutbase = "@GENTOO_PORTAGE_EPREFIX@/etc/luts/";
+ title = string("");
+ cbartype = string("");
+ cbarptr = NULL;
+diff --git a/src/melodic/meldata.cc b/src/melodic/meldata.cc
+index 1749a45..c4ad234 100644
+--- a/src/melodic/meldata.cc
++++ b/src/melodic/meldata.cc
+@@ -992,7 +992,7 @@ namespace Melodic{
+ void MelodicData::est_smoothness()
+ {
+ if(Resels == 0){
+- string SM_path = opts.binpath + "smoothest";
++ string SM_path = "smoothest";
+ string Mask_fname = logger.appendDir("mask");
+
+ if(opts.segment.value().length()>0){
+@@ -1157,7 +1157,7 @@ namespace Melodic{
+ // set up all strings
+ string BET_outputfname =
string(Mean_fname)+"_brain";
+
+- string BET_path = opts.binpath + "bet";
++ string BET_path = "bet";
+ string BET_optarg = "-m -f 0.4"; // see man bet
+ string Mask_fname = BET_outputfname+"_mask";
+
+diff --git a/src/melodic/meloptions.cc b/src/melodic/meloptions.cc
+index 08170c7..252e72b 100644
+--- a/src/melodic/meloptions.cc
++++ b/src/melodic/meloptions.cc
+@@ -93,14 +93,6 @@ MelodicOptions* MelodicOptions::gopt = NULL;
+ explicitnums = false;
+ logfname = string("log.txt");
+
+- // work out the path to the $FSLDIR/bin directory
+- if(getenv("FSLDIR")!=0){
+- binpath = (string) getenv("FSLDIR") + "/bin/";
+- } else{
+- binpath = argv[0];
+- binpath = binpath.substr(0,binpath.length()-7);
+- }
+-
+ // parse once to establish log directory name
+ for(int a = options.parse_command_line(argc, argv); a < argc;
a++);
+
+diff --git a/src/melodic/meloptions.h b/src/melodic/meloptions.h
+index f546125..b964b7d 100644
+--- a/src/melodic/meloptions.h
++++ b/src/melodic/meloptions.h
+@@ -93,7 +93,6 @@ class MelodicOptions {
+ ~MelodicOptions() { delete gopt; }
+
+ string version;
+- string binpath;
+ string logfname;
+ bool filtermode;
+ bool explicitnums;
+diff --git a/src/melodic/melreport.cc b/src/melodic/melreport.cc
+index 141b6c2..2625059 100644
+--- a/src/melodic/melreport.cc
++++ b/src/melodic/melreport.cc
+@@ -84,8 +84,8 @@ namespace Melodic{
+
IChtml.setDir(report.getDir(),mmodel.get_prefix()+".html");
+
+ {//start IC page
+- IChtml << "<HTML><HEAD><link REL=stylesheet
TYPE=text/css href=file:" +
+- (string) getenv("FSLDIR")
+"/doc/fsl.css>" << endl
++ IChtml << "<HTML><HEAD><link REL=stylesheet
TYPE=text/css href=file:"
++ <<
"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl
+ << "<style type=\"text/css\">OBJECT {
width: 100% }</style>"
+ << "<TITLE>FSL</TITLE></HEAD>" << endl
+ << "<IFRAME height=" <<
int(melodat.get_numfiles()/30 + 1)*50
+@@ -486,8 +486,8 @@ namespace Melodic{
+
+ {//start IC2 page
+
IChtml2.setDir(report.getDir(),mmodel.get_prefix()+"_MM.html");
+- IChtml2 << "<HTML><HEAD><link REL=stylesheet
TYPE=text/css href=file:" +
+- (string) getenv("FSLDIR")
+"/doc/fsl.css>" << endl
++ IChtml2 << "<HTML><HEAD><link REL=stylesheet
TYPE=text/css href=file:"
++ <<
"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl
+ << "<style type=\"text/css\">OBJECT {
width: 100% }</style>"
+ << "<TITLE>FSL</TITLE></HEAD>" << endl
+ << "<IFRAME height="<<
int(melodat.get_numfiles()/30 + 1)*50
+@@ -665,8 +665,8 @@ namespace Melodic{
+ IChtml << "<HTML> " << endl
+ << "<TITLE>MELODIC Component " << num2str(cnum)
+ << "</TITLE>" << endl
+- << "<BODY BACKGROUND=\"file:" << getenv("FSLDIR")
+- << "/doc/images/fsl-bg.jpg\">" << endl
++ << "<BODY BACKGROUND=\"file:"
++ <<
"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl
+ << "<hr><CENTER><H1>MELODIC Component " << num2str(cnum)
+ << "</H1>"<< endl;
+
+diff --git a/src/melodic/melreport.h b/src/melodic/melreport.h
+index 574fc4c..e444681 100644
+--- a/src/melodic/melreport.h
++++ b/src/melodic/melreport.h
+@@ -104,21 +104,21 @@ namespace Melodic{
+ const time_t tmptime = time(NULL);
+ system(("mkdir "+ logger.appendDir("report") +
" 2>/dev/null").c_str());
+
report.setDir(logger.appendDir("report"),"00index.html",true,false,ios::out);
+- report << "<HTML><HEAD><link
REL=stylesheet TYPE=text/css href=file:" +
+- (string)
getenv("FSLDIR") +"/doc/fsl.css>"
++ report << "<HTML><HEAD><link
REL=stylesheet TYPE=text/css href=file:"
++ <<
"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>"
+ << "<TITLE>MELODIC
report</TITLE></HEAD><BODY>"
+ << endl <<endl;
+
loghtml.setDir(report.getDir(),"log.html");
+- loghtml << "<HTML><HEAD><link
REL=stylesheet TYPE=text/css href=file:" +
+- (string)
getenv("FSLDIR") +"/doc/fsl.css>"
++ loghtml << "<HTML><HEAD><link
REL=stylesheet TYPE=text/css href=file:"
++ <<
"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>"
+ << "<TITLE>MELODIC
report</TITLE></HEAD><BODY>"
+ << endl <<endl;
+
navigator.setDir(report.getDir(),"nav.html");
+
head.setDir(report.getDir(),"head.html");
+- navigator << "<link REL=stylesheet
TYPE=text/css href=file:"+
+- (string)
getenv("FSLDIR") +"/doc/fsl.css>" << endl;
+- head << "<link REL=stylesheet
TYPE=text/css href=file:"+
+- (string)
getenv("FSLDIR") +"/doc/fsl.css>" << endl;
++ navigator << "<link REL=stylesheet
TYPE=text/css href=file:"
++ <<
"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl;
++ head << "<link REL=stylesheet
TYPE=text/css href=file:"
++ <<
"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl;
+ head <<"<TABLE BORDER=0><TR>"
<< endl
+ <<" <TD ALIGN=CENTER
WIDTH=100%>"<< endl
+ <<"<TABLE BORDER=0>"<<
endl
+@@ -130,8 +130,8 @@ namespace Melodic{
+ << "</tr></table>" <<
endl
+ << "<TD ALIGN=RIGHT>"
<< endl
+ << "<a
href=http://www.fmrib.ox.ac.uk/fsl target=_top>" << endl
+- << "<IMG BORDER=0
SRC=file:"<< getenv("FSLDIR")
+- <<
"/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl
++ << "<IMG BORDER=0 SRC=file:"
++ <<
"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-logo-big.jpg
WIDTH=165></a>" << endl
+ <<
"</TD>"<<endl<<"</TR></TABLE> <hr>"<<endl;
+ if(opts.guireport.value()==""){
+ report <<"<OBJECT
data=head.html></OBJECT>" << endl;
+diff --git a/src/mm/mixture_model.cc b/src/mm/mixture_model.cc
+index b8e6167..5f00693 100644
+--- a/src/mm/mixture_model.cc
++++ b/src/mm/mixture_model.cc
+@@ -2224,8 +2224,8 @@ namespace Mm {
+
+ htmllog << "<HTML> " << endl
+ << "<TITLE>Mixture Model fit for" << data_name << "</TITLE>" <<
endl
+- << "<BODY BACKGROUND=\"file:" << getenv("FSLDIR")
+- << "/doc/images/fsl-bg.jpg\">" << endl
++ << "<BODY BACKGROUND=\"file:"
++ <<
"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl
+ << "<hr><CENTER><H1>Mixture Model fit for<br>" << data_name <<
" </H1>"<< endl;
+
+ htmllog << "<hr><p>" << endl;
+diff --git a/src/siena/siena_diff.cc b/src/siena/siena_diff.cc
+index e19193a..17d8701 100644
+--- a/src/siena/siena_diff.cc
++++ b/src/siena/siena_diff.cc
+@@ -107,7 +107,7 @@ int main(int argc,char *argv[])
+ {
+ // {{{ vars
+
+-char thestring[10000], segoptions[10000], fsldir[10000];
++char thestring[10000], segoptions[10000];
+ int x_size, y_size, z_size, size, x, y, z, i, count,
+ seg2=0, ignore_z=0, ignore_top_slices=0, //erode_mask=0,
+ ignore_bottom_slices=0, debug=0, flow_output=1, edge_masking=0;
+@@ -124,8 +124,6 @@ if (argc<3)
+
+ string argv1(argv[1]), argv2(argv[2]);
+
+-sprintf(fsldir,"%s",getenv("FSLDIR"));
+-
+ for (i = 3; i < argc; i++) {
+ if (!strcmp(argv[i], "-i"))
+ ignore_z=1;
+@@ -209,26 +207,26 @@ for (i = 3; i < argc; i++) {
+ // }}}
+ // {{{ transform images and masks
+
+-sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1
-paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
+- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
++sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0
-init %s_halfwayto_%s.mat -ref %s -in %s",
++ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
+ printf("%s\n",thestring); system(thestring);
+
+-sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1
-paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
+- fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
++sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0
-init %s_halfwayto_%s.mat -ref %s -in %s",
++ argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
+ printf("%s\n",thestring); system(thestring);
+
+-sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1
-paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
+- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
++sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize
0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
++ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
+ printf("%s\n",thestring); system(thestring);
+
+-sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1
-paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
+- fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
++sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize
0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
++ argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
+ printf("%s\n",thestring); system(thestring);
+
+ if (edge_masking)
+ {
+- sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm
1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s",
+- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
++ sprintf(thestring,"flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm 1
-paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s",
++ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
+ printf("%s\n",thestring); system(thestring);
+ }
+
+@@ -287,8 +285,8 @@ if(1) // always done unless the above uncommented and used
instead of this test
+ cout << "saving image 1 to disk prior to segmentation" << endl;
+ save_volume(in1,argv1+"_halfwayto_"+argv2+"_brain");
+ in1.destroy();
+- sprintf(thestring,"%s/bin/fast %s %s %s_halfwayto_%s_brain >
%s_halfwayto_%s_brain.vol 2>&1",
+- fsldir,segtype,segoptions,argv[1],argv[2],argv[1],argv[2]);
++ sprintf(thestring,"fast %s %s %s_halfwayto_%s_brain >
%s_halfwayto_%s_brain.vol 2>&1",
++ segtype,segoptions,argv[1],argv[2],argv[1],argv[2]);
+ cout << thestring << endl;
+ system(thestring);
+ }
+diff --git a/src/topup/topupfns.cpp b/src/topup/topupfns.cpp
+index 6873758..9e8b956 100644
+--- a/src/topup/topupfns.cpp
++++ b/src/topup/topupfns.cpp
+@@ -463,8 +463,7 @@ string existing_conf_file(const string& cfname)
+ if (TOPUP::check_exist(ecfname)) return(ecfname);
+ }
+ if (!TOPUP::path(cfname).length()) { // If no path explicitly
given
+- const char *fsldir_ptr = getenv("FSLDIR");
+- ecfname = string(fsldir_ptr) + string("/etc/flirtsch/") + cfname;
++ ecfname = string("@GENTOO_PORTAGE_EPREFIX@/etc/flirtsch/") + cfname;
+ if (TOPUP::check_exist(ecfname)) return(ecfname);
+ else if (!TOPUP::extension(ecfname).length()) { // If no path _and_ no
extension given
+ ecfname += string(".cnf");
+--
+2.24.1
+
diff --git a/sci-biology/fsl/fsl-6.0.2-r1.ebuild
b/sci-biology/fsl/fsl-6.0.2-r1.ebuild
index 0cadd4e4b..c9162fd0e 100644
--- a/sci-biology/fsl/fsl-6.0.2-r1.ebuild
+++ b/sci-biology/fsl/fsl-6.0.2-r1.ebuild
@@ -51,7 +51,8 @@ PATCHES=(
"${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}/${PN}"-6.0.2-fsldir_redux.patch
+ "${FILESDIR}/${PN}"-6.0.2-fsldir_redux-p1.patch
+ "${FILESDIR}/${PN}"-6.0.2-fsldir_redux-p2.patch
)
src_prepare() {
diff --git a/sci-biology/fsl/fsl-6.0.2.ebuild b/sci-biology/fsl/fsl-6.0.2.ebuild
index 94603ced6..8a7e0eebb 100644
--- a/sci-biology/fsl/fsl-6.0.2.ebuild
+++ b/sci-biology/fsl/fsl-6.0.2.ebuild
@@ -44,7 +44,8 @@ PATCHES=(
"${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}/${PN}"-6.0.2-fsldir_redux.patch
+ "${FILESDIR}/${PN}"-6.0.2-fsldir_redux-p1.patch
+ "${FILESDIR}/${PN}"-6.0.2-fsldir_redux-p2.patch
)
src_prepare(){
diff --git a/sci-biology/fsl/metadata.xml b/sci-biology/fsl/metadata.xml
index 9d12c769d..e171f1431 100644
--- a/sci-biology/fsl/metadata.xml
+++ b/sci-biology/fsl/metadata.xml
@@ -5,9 +5,6 @@
<email>[email protected]</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>
<use>
<flag name="cuda">Add support for CUDA</flag>
</use>
