added instacorr option

meldata.cc

@@ -115,6 +115,19 @@ namespace Melodic{
       message(" done" << endl);
     }
 
+	//convert to instacorrs
+	if(opts.insta_fn.value()>""){
+		Matrix vscales = pow(stdev(tmpData,1),-1);
+		varnorm(tmpData,vscales);
+		
+		Matrix tmpTC = tmpData * insta_mask.t();
+		varnorm(tmpTC,pow(stdev(tmpTC),-1));
+		
+		for(int ctr=1; ctr <=tmpData.Ncols();ctr++)
+			tmpData.Column(ctr) = SP(tmpData.Column(ctr),tmpTC);
+
+	}
+
 	tmpData.Release();
 	dbgmsg(string("END: process_file") << endl);	
     return tmpData;
@@ -607,6 +620,19 @@ namespace Melodic{
       create_RXweight();
     }
 
+	//set up instacorr mask image
+	if(opts.insta_fn.value()>""){
+		dbgmsg(string(" Setting up instacorr mask") << endl);
+		volume4D<float> tmp_im;
+		read_volume4D(tmp_im,opts.insta_fn.value());
+	
+		if(!samesize(Mean,tmp_im[0])){
+	        	cerr << "ERROR:: instacorr mask and data have different voxel dimensions  \n\n";
+	        	exit(2);
+		}	
+		insta_mask = tmp_im.matrix(Mask); 
+	}
+
     //seed the random number generator
     double tmptime = time(NULL);
     if ( opts.seed.value() != -1 ) {

meldata.h

@@ -241,6 +241,7 @@ namespace Melodic{
       volume<float> Mask;
       volume<float> Mean;
       volume<float> background;
+      Matrix insta_mask;	
 
       Matrix Data;
       Matrix PPCA;

melhlprfns.cc

@@ -164,6 +164,8 @@ namespace Melodic{
     return tmpD;
   }  //RowVector varnorm
 
+
+
   Matrix SP2(const Matrix& in, const Matrix& weights, int econ)
   {
     Matrix Res;

melodic.h

@@ -66,7 +66,7 @@
 
 namespace Melodic{
 
-const string version = "3.13";  
+const string version = "3.131";  
 
 // The two strings below specify the title and example usage that is	
 // printed out as the help or usage message

meloptions.cc

@@ -155,6 +155,9 @@ MelodicOptions* MelodicOptions::gopt = NULL;
   		if (numICs.value() > 0){
     		explicitnums = true;
   		}
+		if (insta_fn.value() > ""){
+			varnorm.set_T(false);
+		}
   
   		//in the case of indirect inputs, create the vector of input names here
   		if(!fsl_imageexists(inputfname.value().at(0))){

meloptions.h

-/*  MELODIC - Multivariate exploratory linear optimized decomposition into 
+ /*  MELODIC - Multivariate exploratory linear optimized decomposition into 
               independent components
     
     meloptions.h - class for command line options
@@ -125,6 +125,7 @@ class MelodicOptions {
   	Option<float> nlconst1;
   	Option<float> nlconst2;
   	Option<float> smooth_probmap;
+	Option<string> insta_fn;
 
   	Option<bool> remove_meanvol;
   	Option<bool> remove_meantc;
@@ -391,6 +392,9 @@ class MelodicOptions {
    smooth_probmap(string("--smooth_pm"),  0.0,
 	   string("width of smoothing kernel for probability maps"), 
 	   false, requires_argument, false),
+   insta_fn(string("--insta_fn"), string(""),
+	   string(" mask file name for instacorr calculation"),
+       false, requires_argument, false),
    remove_meanvol(string("--keep_meanvol"), true,
 	   string("do not subtract mean volume"), 
 	   false, no_argument, false),
@@ -496,6 +500,7 @@ class MelodicOptions {
 	    options.add(nlconst1);
 	    options.add(nlconst2);
 	    options.add(smooth_probmap);
+		options.add(insta_fn);
 	    options.add(remove_meanvol);
 	    options.add(remove_meantc);
 	    options.add(remove_endslices);