diff --git a/Makefile b/Makefile
index d12cd48eb98142d302a08afee1d38b9565cb45a3..ecf8f167d14960069060d83e344e8ccce88bd0df 100644
--- a/Makefile
+++ b/Makefile
@@ -12,7 +12,7 @@ USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_GD} -L${LIB_GDC} -L${LIB_PNG}
LIBS = -lutils -lnewimage -lmiscplot -lmiscpic -lmiscmaths -lfslio -lniftiio -lznz -lnewmat -lprob -lm -lgdc -lgd -lpng -lz
-TEST_OBJS = melhlprfns.o test.o
+TEST_OBJS = test.o test2.o
GGMIX_OBJS = ggmix.o
diff --git a/fsl_glm.cc b/fsl_glm.cc
index 0398b2992ce5e9fb7f4b327ca72b86e5f979c866..e1f98736fd6c520a20e5e643d62dd3c310a36208 100644
--- a/fsl_glm.cc
+++ b/fsl_glm.cc
@@ -44,7 +44,7 @@ using namespace std;
false, requires_argument);
Option<string> fncontrasts(string("-c,--contrasts"), string(""),
string("matrix of t-statistics contrasts"),
- false, requires_argument, false);
+ true, requires_argument);
Option<string> fnftest(string("-f,--ftests"), string(""),
string("matrix of F-tests on contrasts"),
false, requires_argument);
diff --git a/meldata.cc b/meldata.cc
index 54b0dd55731e2a9dd0d2cf7c64d86a8bc0bb4dee..a1115ec9f420ca47afc1ad9f58b91d3ac62f291c 100644
--- a/meldata.cc
+++ b/meldata.cc
@@ -87,9 +87,11 @@ namespace Melodic{
if(opts.varnorm.value()){
message(" Normalising by voxel-wise variance ...");
if(stdDev.Storage()==0)
- stdDev = varnorm(tmpData,std::min(30,tmpData.Nrows()-1),2.3)/numfiles;
+ stdDev = varnorm(tmpData,std::min(30,tmpData.Nrows()-1),
+ opts.vn_level.value())/numfiles;
else
- stdDev += varnorm(tmpData,std::min(30,tmpData.Nrows()-1),2.3)/numfiles;
+ stdDev += varnorm(tmpData,std::min(30,tmpData.Nrows()-1),
+ opts.vn_level.value())/numfiles;
stdDevi = pow(stdDev,-1);
message(" done" << endl);
}
@@ -490,7 +492,9 @@ namespace Melodic{
save4D(PCAmaps,opts.outputfname.value() + "_pca");
}
- } //void save()
+
+ message("...done" << endl);
+ } //void save()
int MelodicData::remove_components()
{
@@ -748,14 +752,19 @@ namespace Melodic{
// Setup external call to BET:
- char callBETstr[1000];
- ostrstream betosc(callBETstr,1000);
- betosc << BET_path << " " << Mean_fname << " "
- << BET_outputfname << " " << BET_optarg << " > /dev/null " << '\0';
-
- message(" Calling BET: " << callBETstr << endl);
- system(callBETstr);
+ // char callBETstr[1000];
+ // ostrstream betosc(callBETstr,1000);
+// betosc << BET_path << " " << Mean_fname << " "
+// << BET_outputfname << " " << BET_optarg << " > /dev/null " << '\0';
+// message(" Calling BET: " << callBETstr << endl);
+// system(callBETstr);
+
+ string tmpstr = BET_path + string(" ") +
+ Mean_fname + string(" ") + BET_outputfname + string(" ") +
+ BET_optarg + string(" > /dev/null ");
+ system(tmpstr.c_str());
+
// read back the Mask file
read_volume(theMask,Mask_fname);
diff --git a/melodic.cc b/melodic.cc
index 0d04f18e8bdbdbd4eb344d13109351de76bef407..fef92f1086bb0e5d1ebb0f9831df4bdf0d29db4e 100644
--- a/melodic.cc
+++ b/melodic.cc
@@ -135,7 +135,8 @@ int main(int argc, char *argv[]){
melodat.save();
Matrix pmaps;//(melodat.get_IC());
Matrix mmres;
-
+
+ message("Creating report index page ...");
if( bool(opts.genreport.value()) ){
report.analysistxt();
if(melodat.get_numfiles()>1)
@@ -143,6 +144,7 @@ int main(int argc, char *argv[]){
report.PPCA_rep();
}
+ message("done"<< endl <<endl);
if(opts.perf_mm.value())
mmres = mmall(logger,opts,melodat,report,pmaps);
else{
diff --git a/meloptions.h b/meloptions.h
index 534a1cfa698bcf27f387f8d23fdad040141acc44..ca1eec87c6d44800cc60d234ed01d9fc5f9e7e99 100644
--- a/meloptions.h
+++ b/meloptions.h
@@ -55,6 +55,7 @@ class MelodicOptions {
Option<string> pca_est;
Option<bool> joined_whiten;
Option<bool> joined_vn;
+ Option<float> vn_level;
Option<int> numICs;
Option<string> approach;
Option<string> nonlinearity;
@@ -186,8 +187,11 @@ class MelodicOptions {
string("switch on separate whitening"),
false, no_argument),
joined_vn(string("--sep_vn"), true,
- string("switch off joined variance nomalisation"),
- false, no_argument, false),
+ string("switch off joined variance nomalisation"),
+ false, no_argument, false),
+ vn_level(string("--vn_level"), float(2.3),
+ string("variance nomalisation threshold level (Z> value is ignored)"),
+ false, requires_argument, false),
numICs(string("-n,--numICs"), -1,
string("numer of IC's to extract (for deflation approach)"),
false, requires_argument),
@@ -379,6 +383,7 @@ class MelodicOptions {
options.add(pca_est);
options.add(joined_whiten);
options.add(joined_vn);
+ options.add(vn_level);
options.add(numICs);
options.add(approach);
options.add(nonlinearity);
diff --git a/melreport.cc b/melreport.cc
index beeb33272001c3d97c0dedda50f670eef6c6611a..b851f86ee761c0efc5a7888f87095cbd335d9e08 100644
--- a/melreport.cc
+++ b/melreport.cc
@@ -289,7 +289,7 @@ namespace Melodic{
newplot.boxplot((Matrix)smode.Column(1),
report.appendDir(string("b")+num2str(cnum)+".png"),
- string("Subject/Session mode"));
+ string("Subject/Session mode"));
write_ascii_matrix(report.appendDir(string("s")
+num2str(cnum)+".txt"), smode);
IChtml << "<A HREF=\"" << string("s")
@@ -789,16 +789,18 @@ namespace Melodic{
<< "session/subject domain (" << melodat.get_numfiles()
<< " input files). Components have been sorted in decreasing order of "
<< " the median response per component. <br><br>";
+
+ outMsize("Smode.at(0)", melodat.get_Smodes().at(0));
Matrix allmodes = melodat.get_Smodes().at(0);
for(int ctr = 1; ctr < (int)melodat.get_Smodes().size();++ctr)
allmodes |= melodat.get_Smodes().at(ctr);
-
+
+ outMsize("allmodes", allmodes);
newplot.add_xlabel("Component No.");
newplot.add_ylabel("");
newplot.set_xysize(100+30*allmodes.Ncols(),300);
newplot.boxplot(allmodes,report.appendDir(string("bp_Smodes.png")),
- string("Subject/Session modes"));
-
- report << "<img BORDER=0 SRC=\"bp_Smodes.png\"><p>" << endl;
+ string("Subject/Session modes"));
+ report << "<img BORDER=0 SRC=\"bp_Smodes.png\"><p>" << endl;
}
}