diff options
| -rw-r--r-- | sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p1.patch (renamed from sci-biology/fsl/files/fsl-6.0.2-fsldir_redux.patch) | 255 | ||||
| -rw-r--r-- | sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p2.patch | 255 | ||||
| -rw-r--r-- | sci-biology/fsl/fsl-6.0.2-r1.ebuild | 3 | ||||
| -rw-r--r-- | sci-biology/fsl/fsl-6.0.2.ebuild | 3 | ||||
| -rw-r--r-- | 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 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>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> <use> <flag name="cuda">Add support for CUDA</flag> </use> |