now with static vxt option

fsl_glm.cc

@@ -103,8 +103,11 @@ using namespace std;
 	Option<string> outvnscales(string("--out_vnscales"),string(""),
 		string("output file name for scaling factors for variance normalisation"),
 		false, requires_argument);
+        Option<vector<string> > textConfounds(string("--vxt"), vector<string>(), 
+         string("\tlist of text files containing text matrix confounds. caution BETA option."), 
+         false, requires_argument);
         Option<vector<string> > voxelwiseConfounds(string("--vxf"), vector<string>(), 
-         string("\tlist of 4D images containing voxelwise EVs (list order corresponds to numbers in vxl option). caution BETA option."), 
+         string("\tlist of 4D images containing voxelwise confounds. caution BETA option."), 
          false, requires_argument);
 		/*
 }
@@ -203,11 +206,19 @@ int setup(int &dof){
 	}
 
         dof=(int)ols_dof(design);
+	Matrix baseConfounds;
+	if ( textConfounds.set() ) {
+	  baseConfounds=read_ascii_matrix( textConfounds.value().at(0) );
+	  for(unsigned int i=1; i< textConfounds.value().size(); i++) 
+		baseConfounds|=read_ascii_matrix( textConfounds.value().at(i) );
+	  dof-=textConfounds.value().size();
+	  if ( !voxelwiseConfounds.set() )
+	    data=(IdentityMatrix(baseConfounds.Nrows())-baseConfounds*pinv(baseConfounds))*data;
+	    }
 
 	if ( voxelwiseConfounds.set() ) {
 	  vector<Matrix> confounds;
 	  confounds.resize(voxelwiseConfounds.value().size());
-	  cerr << confounds.size() << endl;
 	  volume4D<float> input;
 	  for(unsigned int i=0; i< confounds.size(); i++) {
 	    read_volume4D(input,voxelwiseConfounds.value().at(i));
@@ -220,11 +231,15 @@ int setup(int &dof){
 	    Matrix confound(confounds.at(0).Column(voxel) );
 	    for(unsigned int i=1; i< confounds.size(); i++) 
 	    confound|=confounds.at(i).Column(voxel);
-	    data.Column(voxel)=(IdentityMatrix(confound.Nrows())-confound*pinv(confound))*data.Column(voxel);	    
-	    }
-	  dof-=2;
+	    if ( textConfounds.set() )
+	      confound=baseConfounds | confound;
+	    data.Column(voxel)=(IdentityMatrix(confound.Nrows())-confound*pinv(confound))*data.Column(voxel);	  
+	  }
+	  dof-=confounds.size();
 	}
 
+
+
 	if(perf_demean.value()){
 		if(debug.value())
 			cout << "De-meaning the data matrix" << endl;
@@ -329,6 +344,7 @@ int main(int argc,char *argv[]){
 			options.add(outsigsq);
 			options.add(outdata);
 			options.add(outvnscales);
+			options.add(textConfounds);
 			options.add(voxelwiseConfounds);
 	    options.parse_command_line(argc, argv);