... and fixed indices

functions/phaseRetrieval/utilities/rescaleDefocusSeries.m

@@ -291,11 +291,11 @@ for imageIdx = idxMaxMagnification+direction:direction:idxMaxMagnification+direc
     else
         % align the cropped image to the reference using alignImages and dftregistration
         [~, shifts, rotAngleDegree, imFiltered] = alignImages(imScaled(...
-            settings.cutTop : size(imScaled,1)-settings.cutBottom ...
-            , settings.cutLeft : size(imScaled,2)-settings.cutRight) ...
+            settings.cutTop + 1: size(imScaled,1)-settings.cutBottom ...
+            , settings.cutLeft + 1 : size(imScaled,2)-settings.cutRight) ...
             , imReference(...
-            settings.cutTop : size(imReference,1)-settings.cutBottom ...
-            , settings.cutLeft : size(imReference,2)-settings.cutRight) ...
+            settings.cutTop + 1 : size(imReference,1)-settings.cutBottom ...
+            , settings.cutLeft + 1 : size(imReference,2)-settings.cutRight) ...
             ,settings);
     end