Added MJ left-right changes back

cluster.cc

@@ -30,9 +30,6 @@ Option<bool> verbose(string("-v,--verbose"), false,
 Option<bool> help(string("-h,--help"), false,
 		  string("display this message"),
 		  false, no_argument);
-Option<bool> medxcoords(string("-m,--medx"), false,
-		  string("use MEDx coordinate conventions"),
-		  false, no_argument);
 Option<bool> mm(string("--mm"), false,
 		  string("use mm, not voxel, coordinates"),
 		  false, no_argument);
@@ -123,15 +120,6 @@ void copyconvert(const vector<triple<T> >& oldcoords,
 }
 
 
-template <class T, class S>
-void medx2voxcoord(vector<triple<T> >& coords, const volume<S>& vol)
-{
-  int ymax = vol.ysize();
-  for (unsigned int n=0; n<coords.size(); n++) {
-    coords[n].y = (T) (ymax - 1) - coords[n].y;
-  }
-}
-
 
 template <class S>
 void vox2mmcoord(vector<triple<float> >& coords, 
@@ -143,7 +131,7 @@ void vox2mmcoord(vector<triple<float> >& coords,
     cc(1) = coords[n].x;
     cc(2) = coords[n].y;
     cc(3) = coords[n].z;
-    cc = vol.sform_mat() * cc;
+    cc = vol.vox2mm_mat() * cc;
     coords[n].x = cc(1);
     coords[n].y = cc(2);
     coords[n].z = cc(3);
@@ -157,7 +145,7 @@ void applyvoxelxfm(vector<triple<T> >& coords, const Matrix& mat,
 	      const volume<S>& source, const volume<S>& dest)
 {
   Matrix voxmat;
-  voxmat = dest.sampling_mat().i() * mat * source.sampling_mat();
+  voxmat = Vox2VoxMatrix(mat,source,dest);
   ColumnVector vec(4);
   for (unsigned int n=0; n<coords.size(); n++) {
     vec << coords[n].x << coords[n].y << coords[n].z << 1.0;
@@ -306,15 +294,10 @@ void print_results(const vector<int>& idx,
     applyvoxelxfm(fcog,trans,zvol,stdvol);
     if (!copename.unset()) applyvoxelxfm(fcopemaxpos,trans,zvol,stdvol);
   }
-  if ( medxcoords.value() && (!mm.value()) ) {
-    medx2voxcoord(fmaxpos,zvol);
-    medx2voxcoord(fcog,zvol);
-    if (!copename.unset()) medx2voxcoord(fcopemaxpos,cope);
-  }
   if (mm.value()) {
     if ( !transformname.unset() && !stdvolname.unset() ) refvol = &stdvol;
     if (verbose.value()) { 
-      cout << "Using matrix : " << endl << refvol->sform_mat() << endl; 
+      cout << "Using matrix : " << endl << refvol->vox2mm_mat() << endl; 
     }
     vox2mmcoord(fmaxpos,*refvol);
     vox2mmcoord(fcog,*refvol);
@@ -413,8 +396,6 @@ void print_results(const vector<int>& idx,
 
 	if ( !transformname.unset() && !stdvolname.unset() )
 	  applyvoxelxfm(lmaxlistR,trans,zvol,stdvol);
-	if ( medxcoords.value() && (!mm.value()) )
-	  medx2voxcoord(lmaxlistR,zvol);
 	if (mm.value()) {
 	  vox2mmcoord(lmaxlistR,*refvol);
 	}
@@ -584,7 +565,6 @@ int main(int argc,char *argv[])
     options.add(dLh);
     options.add(fractional);
     options.add(numconnected);
-    options.add(medxcoords);
     options.add(mm);
     options.add(minv);
     options.add(no_table);