Index: branches/pap/ppStack/src/ppStackConvolve.c
===================================================================
--- branches/pap/ppStack/src/ppStackConvolve.c	(revision 25830)
+++ branches/pap/ppStack/src/ppStackConvolve.c	(revision 25911)
@@ -39,5 +39,6 @@
     options->weightings = psVectorAlloc(num, PS_TYPE_F32); // Combination weightings for images (1/noise^2)
     psVectorInit(options->weightings, 0.0);
-    options->covariances = psArrayAlloc(num); // Covariance matrices
+    options->origCovars = psArrayAlloc(num);
+    options->convCovars = psArrayAlloc(num); // Covariance matrices
 
     psList *fpaList = psListAlloc(NULL); // List of input FPAs, for concept averaging
@@ -79,4 +80,5 @@
         // Background subtraction, scaling and normalisation is performed automatically by the image matching
         psTimerStart("PPSTACK_MATCH");
+        options->origCovars->data[i] = psMemIncrRefCounter(readout->covariance);
         if (!ppStackMatch(readout, options, i, config)) {
             psErrorStackPrint(stderr, "Unable to match image %d --- ignoring.", i);
@@ -85,5 +87,5 @@
             continue;
         }
-        options->covariances->data[i] = psMemIncrRefCounter(readout->covariance);
+        options->convCovars->data[i] = psMemIncrRefCounter(readout->covariance);
 
         if (options->stats) {