Added transpose option and tidied up indenting of the code

fslmeants.cc

@@ -66,6 +66,10 @@ Option<bool> bin_mask(string("--no_bin"), true,
 Option<int> order(string("--order"), 1,
 		  string("        select number of Eigenvariates (default 1)"),
 		  false, requires_argument);
+Option<bool> transpose(string("--transpose"), false,
+		  string("        output results in transpose format (one row per voxel/mean)"),
+		  false, no_argument);
+
 int nonoptarg;
 
 
@@ -85,6 +89,7 @@ int main(int argc,char *argv[])
   options.add(eig);
   options.add(order);
   options.add(bin_mask);
+  options.add(transpose);
   options.add(verbose);
   options.add(help);
   
@@ -145,34 +150,36 @@ int main(int argc,char *argv[])
   mask.binarise(1e-8);  // arbitrary "0" threshold
 
   if(eig.value()){
-	Matrix dat, evecs, scales;
-	scales = mask_nonbin.matrix(mask);
-	dat = vin.matrix(mask);
-	if(!bin_mask.value())
-		dat = SP (dat, ones(dat.Nrows(),1) * scales);
-	dat = remmean(dat,1);
-	
-	if (verbose.value()) {
+    Matrix dat, evecs, scales;
+    scales = mask_nonbin.matrix(mask);
+    dat = vin.matrix(mask);
+    if(!bin_mask.value())
+      dat = SP (dat, ones(dat.Nrows(),1) * scales);
+    dat = remmean(dat,1);
+    
+    if (verbose.value()) {
       cout << "Number of voxels used = " << dat.Ncols() << endl;
     }
-
-	SymmetricMatrix Corr;
-	Corr << dat * dat.t() / dat.Ncols();
-	DiagonalMatrix tmpD;
+    
+    SymmetricMatrix Corr;
+    Corr << dat * dat.t() / dat.Ncols();
+    DiagonalMatrix tmpD;
     EigenValues(Corr,tmpD,evecs);	
-	evecs = fliplr(evecs.Columns(evecs.Ncols()-order.value()+1 , evecs.Ncols())) * std::sqrt(dat.Nrows());
-	
-	Matrix res2 = mean(dat,2);
-	res2 = res2.Column(1).t() * evecs.Column(1);
-	
-	if((float)res2.AsScalar()<0)  
-		evecs = -1.0 * evecs;
-	
-	if (outmat.set()) {
+    evecs = fliplr(evecs.Columns(evecs.Ncols()-order.value()+1 , evecs.Ncols())) * std::sqrt(dat.Nrows());
+    
+    Matrix res2 = mean(dat,2);
+    res2 = res2.Column(1).t() * evecs.Column(1);
+    
+    if((float)res2.AsScalar()<0)  
+      evecs = -1.0 * evecs;
+    
+    if (transpose.value()) { evecs=evecs.t(); }
+    if (outmat.set()) {
       write_ascii_matrix(evecs,outmat.value());
     } else {
       cout << evecs << endl;
     }
+    if (transpose.value()) { evecs=evecs.t(); }
   }
   else{	
     int nt = vin.tsize();
@@ -184,43 +191,45 @@ int main(int argc,char *argv[])
     Matrix meants(nt,nvox);
     meants = 0;
     long int num=0;
-
+    
     for (int z=mask.minz(); z<=mask.maxz(); z++) {
       for (int y=mask.miny(); y<=mask.maxy(); y++) {
         for (int x=mask.minx(); x<=mask.maxx(); x++) {
-        	if (mask(x,y,z)>0.5) {
-	           num++;
-	           if (showall.value()) {
-	              ColumnVector v(4);
-	              v << x << y << z << 1.0;
-	              v = (vin[0].niftivox2newimagevox_mat()).i() * v;
-	              meants(1,num) = v(1);
-	              meants(2,num) = v(2);
-	              meants(3,num) = v(3);
-	              meants.SubMatrix(4,nt,num,num) = vin.voxelts(x,y,z);
-	           } else {
-	              meants += vin.voxelts(x,y,z);
-	             }
-	        }
+	  if (mask(x,y,z)>0.5) {
+	    num++;
+	    if (showall.value()) {
+	      ColumnVector v(4);
+	      v << x << y << z << 1.0;
+	      v = (vin[0].niftivox2newimagevox_mat()).i() * v;
+	      meants(1,num) = v(1);
+	      meants(2,num) = v(2);
+	      meants(3,num) = v(3);
+	      meants.SubMatrix(4,nt,num,num) = vin.voxelts(x,y,z);
+	    } else {
+	      meants += vin.voxelts(x,y,z);
+	    }
+	  }
         }
       }
     }
-
+    
     if (verbose.value()) {
       cout << "Number of voxels used = " << num << endl;
     }
-
+    
     // normalise for number of valid entries if averaging
     if (!showall.value()) {
       if (num>0) meants /= (float) num;
     }
-
+    
     // save the result
+    if (transpose.value()) { meants=meants.t(); }
     if (outmat.set()) {
       write_ascii_matrix(meants,outmat.value());
     } else {
       cout << meants << endl;
     }
+    if (transpose.value()) { meants=meants.t(); }
   }
   return 0;
 }