Tidied up inits

film_gls.cc

@@ -40,20 +40,19 @@ int main(int argc, char *argv[])
     volume4D<float> input_data;
     volumeinfo vinfo;
     read_volume4D(input_data,globalopts.inputfname,vinfo);
-    volume<float> mask(input_data[0]);
-    int sizeTS = input_data.tsize();
+    int sizeTS(input_data.tsize());
 
-    volume4D<float> reference(mask.xsize(),mask.ysize(),mask.zsize(),1);
-    reference[0]=input_data[int(sizeTS/2)-1];
+    volume4D<float> reference;
+    reference=input_data[int(sizeTS/2)-1];
     copybasicproperties(input_data,reference);
 
-    mask=meanvol(input_data);
+    volume<float> mask(meanvol(input_data));
     volume<float> variance(variancevol(input_data));
     input_data-=mask;
 
     mask.binarise(globalopts.thresh,mask.max()+1,exclusive);
-    variance.binarise(1e-10,variance.max()+1,exclusive);
-    mask*=variance;
+    variance.binarise(1e-10,variance.max()+1,exclusive); //variance mask needed if thresh is -ve to remove background voxels (0 variance)
+    mask*=variance; //convolved mask ensures that only super-threshold non-background voxels pass
 
     Matrix datam(input_data.matrix(mask));