3.0 alpha 1

meldata.cc

@@ -155,6 +155,8 @@ namespace Melodic{
   { 
     setup_misc();
     numfiles = (int)opts.inputfname.value().size();
+    if((numfiles > 1) && (opts.approach.value()==string("defl") || opts.approach.value()==string("symm")))
+      opts.approach.set_T("tica");
 
     Matrix alldat, tmpData;
     alldat = process_file(opts.inputfname.value().at(0), numfiles) / numfiles;
@@ -324,6 +326,10 @@ namespace Melodic{
 	  save4D(stdNoisei,string("Noise_stddev_inv"));
       }
 
+      //Output T- & S-modes
+      save_Tmodes();
+      save_Smodes();
+
     //Output mixMatrix
     if(mixMatrix.Storage()>0){
       saveascii(mixMatrix, opts.outputfname.value() + "_mix");

meldata.h

@@ -77,10 +77,22 @@ namespace Melodic{
       inline vector<Matrix>& get_Smodes() {return Smodes;}
       inline Matrix& get_Smodes(int what) {return Smodes.at(what);}
       inline void add_Smodes(Matrix& Arg) {Smodes.push_back(Arg);}      
+      inline void save_Smodes(){
+	Matrix tmp = Smodes.at(0); 
+	for(unsigned int ctr = 1; ctr < Smodes.size(); ctr++)
+	  tmp |= Smodes.at(ctr);
+	saveascii(tmp,opts.outputfname.value() + "_Smodes");
+      }
 
       inline vector<Matrix>& get_Tmodes() {return Tmodes;}
       inline Matrix& get_Tmodes(int what) {return Tmodes.at(what);}
-      inline void add_Tmodes(Matrix& Arg) {Tmodes.push_back(Arg);}      
+      inline void add_Tmodes(Matrix& Arg) {Tmodes.push_back(Arg);}
+      inline void save_Tmodes(){
+	Matrix tmp = Tmodes.at(0); 
+	for(unsigned int ctr = 1; ctr < Tmodes.size(); ctr++)
+	  tmp |= Tmodes.at(ctr);
+	saveascii(tmp,opts.outputfname.value() + "_Tmodes");
+      }
 
       void set_TSmode();
 

melica.cc

@@ -90,8 +90,9 @@ namespace Melodic{
       
       
       // rank 1 approximation in the case of multiple input files
-      if(melodat.get_numfiles() > 1)
+      if(opts.approach.value() == string("tica"))
 	{
+	  message("  Rank-1 approximation of the time courses; ");
 	  Matrix temp(melodat.get_dewhite() * redUMM);
 	  temp = melodat.expand_dimred(temp);
 	  temp = krapprox(temp,int(temp.Nrows()/melodat.get_numfiles())); 
@@ -460,7 +461,10 @@ write_ascii_matrix("Xim",Data.Row(1));
     //switch to the chosen method
     
     //      cout << endl << "Dim = " << dim << endl << "Samples = " << samples << endl;
-    if(opts.approach.value()==string("symm")){
+    if(opts.approach.value()==string("symm") ||
+       opts.approach.value()==string("tica") ||
+       opts.approach.value()==string("parafac") ||
+       opts.approach.value()==string("concat")){
       ica_fastica_symm(Data);}
     if(opts.approach.value()==string("defl")){
       ica_fastica_defl(Data);}
@@ -468,6 +472,7 @@ write_ascii_matrix("Xim",Data.Row(1));
       ica_jade(Data);}
     if(opts.approach.value()==string("maxent")){
       ica_maxent(Data);}
+  
     
     if(!no_convergence){//calculate the IC
       Matrix temp(melodat.get_unmix()*melodat.get_Data());

melodic.cc

@@ -313,11 +313,13 @@ Matrix mmall(Log& logger, MelodicOptions& opts,
 		  wherelog,ctr,
 		  melodat.get_mask(), 
 		  melodat.get_mean(),3);
+    message("   calculating mixture-model fit "<<endl);
     mixmod.fit("GGM");
 
     if(opts.output_MMstats.value()){
+      message("   saving probability map:");
       melodat.save4D(mixmod.get_probmap(),
-		    string("stats/probmap_")+num2str(ctr));
+		     string("stats/probmap_")+num2str(ctr));
     }
 
     //re-scale spatial maps to mean 0 for nht
@@ -380,6 +382,7 @@ Matrix mmall(Log& logger, MelodicOptions& opts,
 	    << " Means :  " << mixmod.get_means() << endl
 	    << " Vars. :  " << mixmod.get_vars()  << endl
 	    << " Prop. :  " << mixmod.get_pi()    << endl << endl;
+      message("   saving thresholded Z-stats image:");
       melodat.save4D(mixmod.get_threshmaps(),
 		     string("stats/thresh_zstat")+num2str(ctr));
     }

melodic.h

@@ -32,7 +32,7 @@
 
 namespace Melodic{
 
-const string version = "3.02";  
+const string version = "3.0 alpha 1";  
 
 }
 

meloptions.cc

@@ -80,7 +80,7 @@ MelodicOptions* MelodicOptions::gopt = NULL;
   }
   if (approach.value() != "symm" && approach.value() != "defl"  && 
       approach.value() != "jade" && approach.value() != "maxent" &&
-      approach.value() != "tica" && approach.value() != "parafac"){
+      approach.value() != "tica" && approach.value() != "concat"){
     cerr << "ERROR:: unknown approach \n\n";
     print_usage(argc,argv);
     exit(2);

meloptions.h

@@ -171,7 +171,7 @@ class MelodicOptions {
 	   string("numer of IC's to extract (for deflation approach)"), 
 	   false, requires_argument),
    approach(string("-a,--approach"),  string("symm"),
-	   string("approach for decomposition: defl, symm"), 
+	   string("approach for decomposition, 2D: defl, symm (default), 3D: tica (default), concat"), 
 	   false, requires_argument),
    nonlinearity(string("--nl"), string("pow3"),
 	   string("\tnonlinearity: gauss, tanh, pow3, pow4"), 

melreport.cc

@@ -146,10 +146,10 @@ namespace Melodic{
 
       {//plot subject mode 
 	Matrix smode;
-	smode = melodat.get_Smodes(0);
+	smode = melodat.get_Smodes(cnum-1);
 	if(smode.Nrows() > 1){
 	  miscplot newplot;
-	  newplot.timeseries(smode, 
+	  newplot.timeseries(smode.t(), 
 			  report.appendDir(string("s")+num2str(cnum)+".png"),
 			  string("Subject/Session mode"));
 	  write_ascii_matrix(report.appendDir(string("s")
@@ -161,7 +161,6 @@ namespace Melodic{
 	    +string("s")+num2str(cnum)+".png\"></A><p>" << endl;
 	}
       }//subject mode plot
-      cerr << "after subject plot " << endl;
       {//plot frequency 
 	miscplot newplot;
 	RowVector empty(1);