Index: /branches/pap_branch_080207/ppStack/src/ppStackMatch.c
===================================================================
--- /branches/pap_branch_080207/ppStack/src/ppStackMatch.c	(revision 16423)
+++ /branches/pap_branch_080207/ppStack/src/ppStackMatch.c	(revision 16424)
@@ -141,5 +141,11 @@
         while ((item = psMetadataGetAndIncrement(iter))) {
             assert(item->type == PS_DATA_UNKNOWN);
-            *kernels = psArrayAdd(*kernels, ARRAY_BUFFER, item->data.V);
+            // Set the normalisation dimensions, since these will be otherwise unavailable when reading the
+            // images by scans.
+            pmSubtractionKernels *kernel = item->data.V; // Kernel used in subtraction
+            kernel->numCols = readout->image->numCols;
+            kernel->numRows = readout->image->numRows;
+
+            *kernels = psArrayAdd(*kernels, ARRAY_BUFFER, kernel);
         }
         psFree(iter);
Index: /branches/pap_branch_080207/ppStack/src/ppStackReadout.c
===================================================================
--- /branches/pap_branch_080207/ppStack/src/ppStackReadout.c	(revision 16423)
+++ /branches/pap_branch_080207/ppStack/src/ppStackReadout.c	(revision 16424)
@@ -137,6 +137,12 @@
     for (int i = 0; i < num; i++) {
         pmStackData *data = stack->data[i]; // Data for this image
-        psPixels *reject = pmStackReject(data->pixels, threshold, regions->data[i],
+        pmReadout *readout = data->readout; // Readout of interest
+        int col0 = readout->col0, row0 = readout->row0; // Offset for readout
+        int numCols = readout->image->numCols, numRows = readout->image->numRows; // Size of image
+
+        psRegion *valid = psRegionAlloc(col0, col0 + numCols, row0, row0 + numRows); // Valid region for rej
+        psPixels *reject = pmStackReject(data->pixels, valid, threshold, regions->data[i],
                                          kernels->data[i]); // Pixels to reject
+        psFree(valid);
         psFree(data->pixels);
         data->pixels = reject;