Merge branch 'master' of github.com:TheChymera/overlay
This commit is contained in:
commit
5ef500305a
@ -1,3 +1,22 @@
|
|||||||
|
08 Nov 2019; François Bissey <frp.bissey@gmail.com> fsl-6.0.2.ebuild:
|
||||||
|
sci-biology/fsl: final touches. Skip mist-clean.
|
||||||
|
|
||||||
|
07 Nov 2019; François Bissey <frp.bissey@gmail.com>
|
||||||
|
+files/fsl-6.0.2-fsldir_redux.patch, fsl-6.0.2.ebuild:
|
||||||
|
sci-biology/fsl: Work on fsldir elimination
|
||||||
|
|
||||||
|
07 Nov 2019; François Bissey <frp.bissey@gmail.com>
|
||||||
|
+files/fsl-6.0.2-no_xmlpp.patch, +files/fsl-6.0.2-qstring_compat.patch,
|
||||||
|
fsl-6.0.2.ebuild:
|
||||||
|
sci-biology/fsl: patch porting to deal with cifti
|
||||||
|
|
||||||
|
07 Nov 2019; François Bissey <frp.bissey@gmail.com> fsl-6.0.2.ebuild:
|
||||||
|
sci-biology/fsl: tcl/tk is needed at build time
|
||||||
|
|
||||||
|
07 Nov 2019; François Bissey <frp.bissey@gmail.com>
|
||||||
|
files/fsl-6.0.2-setup.patch:
|
||||||
|
sci-biology/fsl: do not build tcl/tk/libpng
|
||||||
|
|
||||||
07 Nov 2019; François Bissey <frp.bissey@gmail.com>
|
07 Nov 2019; François Bissey <frp.bissey@gmail.com>
|
||||||
+files/fsl-6.0.2-setup.patch, fsl-6.0.2.ebuild:
|
+files/fsl-6.0.2-setup.patch, fsl-6.0.2.ebuild:
|
||||||
sci-biology/fsl: Initial fix to fsl 6.0.2
|
sci-biology/fsl: Initial fix to fsl 6.0.2
|
||||||
|
467
sci-biology/fsl/files/fsl-6.0.2-fsldir_redux.patch
Normal file
467
sci-biology/fsl/files/fsl-6.0.2-fsldir_redux.patch
Normal file
@ -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
|
||||||
|
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");
|
44
sci-biology/fsl/files/fsl-6.0.2-no_xmlpp.patch
Normal file
44
sci-biology/fsl/files/fsl-6.0.2-no_xmlpp.patch
Normal file
@ -0,0 +1,44 @@
|
|||||||
|
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
|
||||||
|
|
48
sci-biology/fsl/files/fsl-6.0.2-qstring_compat.patch
Normal file
48
sci-biology/fsl/files/fsl-6.0.2-qstring_compat.patch
Normal file
@ -0,0 +1,48 @@
|
|||||||
|
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 1749a459..b76f052d 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();
|
@ -1,5 +1,5 @@
|
|||||||
diff --git a/build b/build
|
diff --git a/build b/build
|
||||||
index 05dac06..d90e407 100755
|
index 05dac06c..d90e407b 100755
|
||||||
--- a/build
|
--- a/build
|
||||||
+++ b/build
|
+++ b/build
|
||||||
@@ -3,7 +3,7 @@
|
@@ -3,7 +3,7 @@
|
||||||
@ -23,7 +23,7 @@ index 05dac06..d90e407 100755
|
|||||||
if [ $finalStatus -eq 0 ]; then
|
if [ $finalStatus -eq 0 ]; then
|
||||||
echo "Build completed successfully.";
|
echo "Build completed successfully.";
|
||||||
diff --git a/config/buildSettings.mk b/config/buildSettings.mk
|
diff --git a/config/buildSettings.mk b/config/buildSettings.mk
|
||||||
index b2e1f15..04532fc 100644
|
index b2e1f150..04532fc2 100644
|
||||||
--- a/config/buildSettings.mk
|
--- a/config/buildSettings.mk
|
||||||
+++ b/config/buildSettings.mk
|
+++ b/config/buildSettings.mk
|
||||||
@@ -18,7 +18,7 @@ MV = /bin/mv
|
@@ -18,7 +18,7 @@ MV = /bin/mv
|
||||||
@ -74,7 +74,7 @@ index b2e1f15..04532fc 100644
|
|||||||
QTDIR = /usr/lib/qt3
|
QTDIR = /usr/lib/qt3
|
||||||
LIB_QT = ${QTDIR}/lib
|
LIB_QT = ${QTDIR}/lib
|
||||||
diff --git a/config/common/buildproj b/config/common/buildproj
|
diff --git a/config/common/buildproj b/config/common/buildproj
|
||||||
index 2f0f2b8..48624a1 100755
|
index 2f0f2b8f..48624a1f 100755
|
||||||
--- a/config/common/buildproj
|
--- a/config/common/buildproj
|
||||||
+++ b/config/common/buildproj
|
+++ b/config/common/buildproj
|
||||||
@@ -11,10 +11,10 @@ if [ X$1 = X-strict ] ; then
|
@@ -11,10 +11,10 @@ if [ X$1 = X-strict ] ; then
|
||||||
@ -116,7 +116,7 @@ index 2f0f2b8..48624a1 100755
|
|||||||
fi
|
fi
|
||||||
done
|
done
|
||||||
diff --git a/config/common/vars.mk b/config/common/vars.mk
|
diff --git a/config/common/vars.mk b/config/common/vars.mk
|
||||||
index b027b01..aeeae67 100755
|
index b027b010..aeeae67c 100755
|
||||||
--- a/config/common/vars.mk
|
--- a/config/common/vars.mk
|
||||||
+++ b/config/common/vars.mk
|
+++ b/config/common/vars.mk
|
||||||
@@ -24,15 +24,15 @@ USRINCFLAGS =
|
@@ -24,15 +24,15 @@ USRINCFLAGS =
|
||||||
@ -141,10 +141,20 @@ index b027b01..aeeae67 100755
|
|||||||
HFILES = *.h
|
HFILES = *.h
|
||||||
AFILES = *.a
|
AFILES = *.a
|
||||||
diff --git a/extras/build b/extras/build
|
diff --git a/extras/build b/extras/build
|
||||||
index 59e7a2e..2cead09 100755
|
index 59e7a2ed..0d68232e 100755
|
||||||
--- a/extras/build
|
--- a/extras/build
|
||||||
+++ b/extras/build
|
+++ b/extras/build
|
||||||
@@ -104,8 +104,8 @@ PROJECTS="${PROJECTS} libpng"
|
@@ -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
|
if [ ${BUILDICONV} -eq 1 ]; then
|
||||||
PROJECTS="${PROJECTS} libiconv"
|
PROJECTS="${PROJECTS} libiconv"
|
||||||
fi
|
fi
|
||||||
@ -156,7 +166,7 @@ index 59e7a2e..2cead09 100755
|
|||||||
if [ -d $FSLESRCDIR/$projname ] ; then
|
if [ -d $FSLESRCDIR/$projname ] ; then
|
||||||
buildIt $FSLESRCDIR $projname 1
|
buildIt $FSLESRCDIR $projname 1
|
||||||
diff --git a/src/mist-clean/Makefile b/src/mist-clean/Makefile
|
diff --git a/src/mist-clean/Makefile b/src/mist-clean/Makefile
|
||||||
index 20402cc..6918bee 100755
|
index 20402cca..6918bee4 100755
|
||||||
--- a/src/mist-clean/Makefile
|
--- a/src/mist-clean/Makefile
|
||||||
+++ b/src/mist-clean/Makefile
|
+++ b/src/mist-clean/Makefile
|
||||||
@@ -52,6 +52,6 @@ installpython:
|
@@ -52,6 +52,6 @@ installpython:
|
||||||
|
@ -14,7 +14,7 @@ SLOT="0"
|
|||||||
KEYWORDS="~amd64"
|
KEYWORDS="~amd64"
|
||||||
IUSE=""
|
IUSE=""
|
||||||
|
|
||||||
COMMON_DEPEND="
|
DEPEND="
|
||||||
dev-libs/boost
|
dev-libs/boost
|
||||||
media-gfx/graphviz
|
media-gfx/graphviz
|
||||||
media-libs/gd
|
media-libs/gd
|
||||||
@ -23,25 +23,25 @@ COMMON_DEPEND="
|
|||||||
sci-libs/ciftilib
|
sci-libs/ciftilib
|
||||||
sci-libs/nlopt
|
sci-libs/nlopt
|
||||||
sys-libs/zlib
|
sys-libs/zlib
|
||||||
"
|
|
||||||
DEPEND="${COMMON_DEPEND}"
|
|
||||||
RDEPEND="${COMMON_DEPEND}
|
|
||||||
dev-lang/tcl:0=
|
dev-lang/tcl:0=
|
||||||
dev-lang/tk:0=
|
dev-lang/tk:0=
|
||||||
|
virtual/lapack
|
||||||
|
virtual/blas
|
||||||
"
|
"
|
||||||
|
RDEPEND="${DEPEND}"
|
||||||
|
|
||||||
S=${WORKDIR}/${PN}
|
S=${WORKDIR}/${PN}
|
||||||
UPSTREAM_FSLDIR="/usr/share/fsl"
|
UPSTREAM_FSLDIR="/usr/share/fsl"
|
||||||
|
|
||||||
PATCHES=(
|
PATCHES=(
|
||||||
"${FILESDIR}/${PN}"-6.0.2-setup.patch
|
"${FILESDIR}/${PN}"-6.0.2-setup.patch
|
||||||
#"${FILESDIR}/${PN}"-5.0.11-no_xmlpp.patch
|
"${FILESDIR}/${PN}"-6.0.2-no_xmlpp.patch
|
||||||
"${FILESDIR}/${PN}"-5.0.11-niftiio_var_fix.patch
|
"${FILESDIR}/${PN}"-5.0.11-niftiio_var_fix.patch
|
||||||
"${FILESDIR}/${PN}"-5.0.11-ifstream_use.patch
|
"${FILESDIR}/${PN}"-5.0.11-ifstream_use.patch
|
||||||
"${FILESDIR}/${PN}"-5.0.11-fslsurface_parallel_make.patch
|
"${FILESDIR}/${PN}"-5.0.11-fslsurface_parallel_make.patch
|
||||||
#"${FILESDIR}/${PN}"-5.0.11-qstring_compat.patch
|
"${FILESDIR}/${PN}"-6.0.2-qstring_compat.patch
|
||||||
"${FILESDIR}/${PN}"-5.0.9-headers.patch
|
"${FILESDIR}/${PN}"-5.0.9-headers.patch
|
||||||
#"${FILESDIR}/${PN}"-5.0.9-fsldir_redux.patch
|
"${FILESDIR}/${PN}"-6.0.2-fsldir_redux.patch
|
||||||
)
|
)
|
||||||
|
|
||||||
src_prepare(){
|
src_prepare(){
|
||||||
@ -56,6 +56,9 @@ src_prepare(){
|
|||||||
eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX src/*) \
|
eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX src/*) \
|
||||||
etc/js/label-div.html
|
etc/js/label-div.html
|
||||||
|
|
||||||
|
# Disable mist-clean the hard way for now.
|
||||||
|
rm -rf src/mist-clean
|
||||||
|
|
||||||
makefilelist=$(find src/ -name Makefile)
|
makefilelist=$(find src/ -name Makefile)
|
||||||
|
|
||||||
sed -i \
|
sed -i \
|
||||||
@ -71,7 +74,13 @@ src_prepare(){
|
|||||||
sed -e "s:\${FSLDIR}/bin/::g" \
|
sed -e "s:\${FSLDIR}/bin/::g" \
|
||||||
-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/*) || die
|
-i $(grep -rl "\$FSLDIR/bin" src/*) \
|
||||||
|
$(grep -rl "\${FSLDIR}/bin" etc/matlab/*)\
|
||||||
|
$(grep -rl "\$FSLDIR/bin" etc/matlab/*) || die
|
||||||
|
|
||||||
|
# Not caught by the previous sed. Usually append
|
||||||
|
sed -e "s:\${FSLDIR}/bin::g" \
|
||||||
|
-i $(grep -rl "\${FSLDIR}/bin" src/*) || die
|
||||||
|
|
||||||
sed -e "s:\$FSLDIR/data:${EPREFIX}/usr/share/fsl/data:g" \
|
sed -e "s:\$FSLDIR/data:${EPREFIX}/usr/share/fsl/data:g" \
|
||||||
-e "s:\${FSLDIR}/data:${EPREFIX}/usr/share/fsl/data:g" \
|
-e "s:\${FSLDIR}/data:${EPREFIX}/usr/share/fsl/data:g" \
|
||||||
|
Loading…
Reference in New Issue
Block a user