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sci/sci-biology/fsl/files/fsl-6.0.4-fsldir_redux-p2.p...

255 lines
11 KiB

diff --git a/src/libvis/miscpic.h b/src/libvis/miscpic.h
index a2f3855..5f440f2 100644
--- a/src/libvis/miscpic.h
+++ b/src/libvis/miscpic.h
@@ -90,12 +90,7 @@ namespace MISCPIC{
markRight=false;
trans= -10;
edgethresh = 0.0;
- if(getenv("FSLDIR")!=0){
- lutbase = string(getenv("FSLDIR")) + "/etc/luts/";
- }
- else{
- lutbase = string("/");
- }
+ lutbase = "@GENTOO_PORTAGE_EPREFIX@/etc/luts/";
title = string("");
cbartype = string("");
cbarptr = NULL;
diff --git a/src/melodic/meldata.cc b/src/melodic/meldata.cc
index 1749a45..c4ad234 100644
--- a/src/melodic/meldata.cc
+++ b/src/melodic/meldata.cc
@@ -992,7 +992,7 @@ namespace Melodic{
void MelodicData::est_smoothness()
{
if(Resels == 0){
- string SM_path = opts.binpath + "smoothest";
+ string SM_path = "smoothest";
string Mask_fname = logger.appendDir("mask");
if(opts.segment.value().length()>0){
@@ -1157,7 +1157,7 @@ namespace Melodic{
// set up all strings
string BET_outputfname = string(Mean_fname)+"_brain";
- string BET_path = opts.binpath + "bet";
+ string BET_path = "bet";
string BET_optarg = "-m -f 0.4"; // see man bet
string Mask_fname = BET_outputfname+"_mask";
diff --git a/src/melodic/meloptions.cc b/src/melodic/meloptions.cc
index 08170c7..252e72b 100644
--- a/src/melodic/meloptions.cc
+++ b/src/melodic/meloptions.cc
@@ -93,14 +93,6 @@ MelodicOptions* MelodicOptions::gopt = NULL;
explicitnums = false;
logfname = string("log.txt");
- // work out the path to the $FSLDIR/bin directory
- if(getenv("FSLDIR")!=0){
- binpath = (string) getenv("FSLDIR") + "/bin/";
- } else{
- binpath = argv[0];
- binpath = binpath.substr(0,binpath.length()-7);
- }
-
// parse once to establish log directory name
for(int a = options.parse_command_line(argc, argv); a < argc; a++);
diff --git a/src/melodic/meloptions.h b/src/melodic/meloptions.h
index f546125..b964b7d 100644
--- a/src/melodic/meloptions.h
+++ b/src/melodic/meloptions.h
@@ -93,7 +93,6 @@ class MelodicOptions {
~MelodicOptions() { delete gopt; }
string version;
- string binpath;
string logfname;
bool filtermode;
bool explicitnums;
diff --git a/src/melodic/melreport.cc b/src/melodic/melreport.cc
index 141b6c2..2625059 100644
--- a/src/melodic/melreport.cc
+++ b/src/melodic/melreport.cc
@@ -84,8 +84,8 @@ namespace Melodic{
IChtml.setDir(report.getDir(),mmodel.get_prefix()+".html");
{//start IC page
- IChtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl
+ IChtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl
<< "<style type=\"text/css\">OBJECT { width: 100% }</style>"
<< "<TITLE>FSL</TITLE></HEAD>" << endl
<< "<IFRAME height=" << int(melodat.get_numfiles()/30 + 1)*50
@@ -486,8 +486,8 @@ namespace Melodic{
{//start IC2 page
IChtml2.setDir(report.getDir(),mmodel.get_prefix()+"_MM.html");
- IChtml2 << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl
+ IChtml2 << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl
<< "<style type=\"text/css\">OBJECT { width: 100% }</style>"
<< "<TITLE>FSL</TITLE></HEAD>" << endl
<< "<IFRAME height="<< int(melodat.get_numfiles()/30 + 1)*50
@@ -665,8 +665,8 @@ namespace Melodic{
IChtml << "<HTML> " << endl
<< "<TITLE>MELODIC Component " << num2str(cnum)
<< "</TITLE>" << endl
- << "<BODY BACKGROUND=\"file:" << getenv("FSLDIR")
- << "/doc/images/fsl-bg.jpg\">" << endl
+ << "<BODY BACKGROUND=\"file:"
+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl
<< "<hr><CENTER><H1>MELODIC Component " << num2str(cnum)
<< "</H1>"<< endl;
diff --git a/src/melodic/melreport.h b/src/melodic/melreport.h
index 574fc4c..e444681 100644
--- a/src/melodic/melreport.h
+++ b/src/melodic/melreport.h
@@ -104,21 +104,21 @@ namespace Melodic{
const time_t tmptime = time(NULL);
system(("mkdir "+ logger.appendDir("report") + " 2>/dev/null").c_str());
report.setDir(logger.appendDir("report"),"00index.html",true,false,ios::out);
- report << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
- (string) getenv("FSLDIR") +"/doc/fsl.css>"
+ report << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>"
<< "<TITLE>MELODIC report</TITLE></HEAD><BODY>"
<< endl <<endl;
loghtml.setDir(report.getDir(),"log.html");
- loghtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
- (string) getenv("FSLDIR") +"/doc/fsl.css>"
+ loghtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>"
<< "<TITLE>MELODIC report</TITLE></HEAD><BODY>"
<< endl <<endl;
navigator.setDir(report.getDir(),"nav.html");
head.setDir(report.getDir(),"head.html");
- navigator << "<link REL=stylesheet TYPE=text/css href=file:"+
- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl;
- head << "<link REL=stylesheet TYPE=text/css href=file:"+
- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl;
+ navigator << "<link REL=stylesheet TYPE=text/css href=file:"
+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl;
+ head << "<link REL=stylesheet TYPE=text/css href=file:"
+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl;
head <<"<TABLE BORDER=0><TR>" << endl
<<" <TD ALIGN=CENTER WIDTH=100%>"<< endl
<<"<TABLE BORDER=0>"<< endl
@@ -130,8 +130,8 @@ namespace Melodic{
<< "</tr></table>" << endl
<< "<TD ALIGN=RIGHT>" << endl
<< "<a href=http://www.fmrib.ox.ac.uk/fsl target=_top>" << endl
- << "<IMG BORDER=0 SRC=file:"<< getenv("FSLDIR")
- << "/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl
+ << "<IMG BORDER=0 SRC=file:"
+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl
<< "</TD>"<<endl<<"</TR></TABLE> <hr>"<<endl;
if(opts.guireport.value()==""){
report <<"<OBJECT data=head.html></OBJECT>" << endl;
diff --git a/src/mm/mixture_model.cc b/src/mm/mixture_model.cc
index b8e6167..5f00693 100644
--- a/src/mm/mixture_model.cc
+++ b/src/mm/mixture_model.cc
@@ -2224,8 +2224,8 @@ namespace Mm {
htmllog << "<HTML> " << endl
<< "<TITLE>Mixture Model fit for" << data_name << "</TITLE>" << endl
- << "<BODY BACKGROUND=\"file:" << getenv("FSLDIR")
- << "/doc/images/fsl-bg.jpg\">" << endl
+ << "<BODY BACKGROUND=\"file:"
+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl
<< "<hr><CENTER><H1>Mixture Model fit for<br>" << data_name << " </H1>"<< endl;
htmllog << "<hr><p>" << endl;
diff -Naur fsl.orig/src/siena/siena_diff.cc fsl/src/siena/siena_diff.cc
--- fsl.orig/src/siena/siena_diff.cc 2020-12-02 15:52:50.359856656 -0500
+++ fsl/src/siena/siena_diff.cc 2020-12-02 16:03:25.699876412 -0500
@@ -107,7 +107,7 @@
{
// {{{ vars
-char thestring[10000], segoptions[10000], fsldir[10000];
+char thestring[10000], segoptions[10000];
int x_size, y_size, z_size, size, x, y, z, i, count,
seg2=0, ignore_z=0, ignore_top_slices=0, //erode_mask=0,
ignore_bottom_slices=0, debug=0, flow_output=1, edge_masking=0;
@@ -124,8 +124,6 @@
string argv1(argv[1]), argv2(argv[2]);
-sprintf(fsldir,"%s",getenv("FSLDIR"));
-
for (i = 3; i < argc; i++)
{
if (!strcmp(argv[i], "-i"))
@@ -206,26 +204,26 @@
// }}}
// {{{ transform images and masks
-sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
+sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
+ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
printf("%s\n",thestring); system(thestring);
-sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
- fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
+sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
+ argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
printf("%s\n",thestring); system(thestring);
-sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
+sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
+ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
printf("%s\n",thestring); system(thestring);
-sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
- fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
+sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
+ argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
printf("%s\n",thestring); system(thestring);
if (edge_masking)
{
- sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s",
- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
+ sprintf(thestring,"flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s",
+ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
printf("%s\n",thestring); system(thestring);
}
@@ -284,8 +282,8 @@
cout << "saving image 1 to disk prior to segmentation" << endl;
save_volume(in1,argv1+"_halfwayto_"+argv2+"_brain");
in1.destroy();
- sprintf(thestring,"%s/bin/fast %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1",
- fsldir,segtype,segoptions,argv[1],argv[2],argv[1],argv[2]);
+ sprintf(thestring,"fast %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1",
+ segtype,segoptions,argv[1],argv[2],argv[1],argv[2]);
cout << thestring << endl;
system(thestring);
}
diff --git a/src/topup/topupfns.cpp b/src/topup/topupfns.cpp
index 6873758..9e8b956 100644
--- a/src/topup/topupfns.cpp
+++ b/src/topup/topupfns.cpp
@@ -463,8 +463,7 @@ string existing_conf_file(const string& cfname)
if (TOPUP::check_exist(ecfname)) return(ecfname);
}
if (!TOPUP::path(cfname).length()) { // If no path explicitly given
- const char *fsldir_ptr = getenv("FSLDIR");
- ecfname = string(fsldir_ptr) + string("/etc/flirtsch/") + cfname;
+ ecfname = string("@GENTOO_PORTAGE_EPREFIX@/etc/flirtsch/") + cfname;
if (TOPUP::check_exist(ecfname)) return(ecfname);
else if (!TOPUP::extension(ecfname).length()) { // If no path _and_ no extension given
ecfname += string(".cnf");
--
2.24.1