|
|
|
|
@ -0,0 +1,467 @@
|
|
|
|
|
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
|
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|
|
|
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)
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|
|
|
vector<int> G;
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|
|
|
|
vector<string> titles;
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|
|
|
|
float tr, mult, trmult, nltffwhm=0, maxconvwin=0;
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|
|
|
|
- char fl[10000], *FSLDIR;
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|
|
|
|
+ char fl[10000];
|
|
|
|
|
string fn, filename;
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|
|
|
|
FONT_DATA *font_data = new FONT_DATA[1];
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|
|
|
|
|
|
|
|
|
@@ -763,8 +763,6 @@ int main(int argc, char **argv)
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|
|
|
if (argc==3)
|
|
|
|
|
motionparams=remmean(read_ascii_matrix(argv[2]));
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|
|
|
|
|
|
|
|
|
- FSLDIR=getenv("FSLDIR");
|
|
|
|
|
-
|
|
|
|
|
fn = string(argv[1])+".fsf";
|
|
|
|
|
|
|
|
|
|
level = atoi(find_line(fn, "fmri(level)", fl));
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|
|
|
|
@@ -1510,7 +1508,7 @@ int main(int argc, char **argv)
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|
|
|
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 ";
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|
|
|
|
+ filename="wpng -q -overwrite "+string(argv[1])+".ppm ";
|
|
|
|
|
system(filename.c_str());
|
|
|
|
|
|
|
|
|
|
return(0);
|
|
|
|
|
@@ -2161,6 +2159,6 @@ char the_string[10000];
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|
|
|
|
|
|
|
|
|
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
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|
|
|
|
index ae191fd..3a02b55 100644
|
|
|
|
|
--- a/src/feat5/tsplot.cc
|
|
|
|
|
+++ b/src/feat5/tsplot.cc
|
|
|
|
|
@@ -293,7 +293,7 @@ int main(int argc, char **argv)
|
|
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|
|
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");
|
Horea Christian