diff --git a/brainglobe_registration/elastix/register.py b/brainglobe_registration/elastix/register.py
index 51e0fab..f38f3ff 100644
--- a/brainglobe_registration/elastix/register.py
+++ b/brainglobe_registration/elastix/register.py
@@ -115,10 +115,17 @@ def run_registration(
     )[..., ::-1]
 
     if output_directory:
-        # Remove the deformationField.tiff file generated by elastix
-        os.unlink(output_directory / "deformationField.tiff")
+        working_directory = output_directory
     else:
-        os.unlink("deformationField.tiff")
+        working_directory = Path.cwd()
+
+    # Cleanup files generated by elastix
+    os.remove(working_directory / "deformationField.tiff")
+    for i in range(len(parameter_lists)):
+        try:
+            os.remove(working_directory / f"result.{i}.tiff")
+        except FileNotFoundError:
+            continue
 
     return (
         np.asarray(result_image),
diff --git a/brainglobe_registration/parameters/ara_tools/affine.txt b/brainglobe_registration/parameters/ara_tools/affine.txt
index cabe450..b6f281e 100644
--- a/brainglobe_registration/parameters/ara_tools/affine.txt
+++ b/brainglobe_registration/parameters/ara_tools/affine.txt
@@ -4,9 +4,9 @@
 
 //ImageTypes
 (FixedInternalImagePixelType "float")
-(FixedImageDimension 3)
+(FixedImageDimension 2)
 (MovingInternalImagePixelType "float")
-(MovingImageDimension 3)
+(MovingImageDimension 2)
 
 //Components
 (Registration "MultiResolutionRegistration")
diff --git a/brainglobe_registration/parameters/ara_tools/bspline.txt b/brainglobe_registration/parameters/ara_tools/bspline.txt
index e87a225..a7a51f9 100644
--- a/brainglobe_registration/parameters/ara_tools/bspline.txt
+++ b/brainglobe_registration/parameters/ara_tools/bspline.txt
@@ -2,9 +2,9 @@
 
 //ImageTypes
 (FixedInternalImagePixelType "float")
-(FixedImageDimension 3)
+(FixedImageDimension 2)
 (MovingInternalImagePixelType "float")
-(MovingImageDimension 3)
+(MovingImageDimension 2)
 
 //Components
 (Registration "MultiResolutionRegistration")
diff --git a/brainglobe_registration/parameters/elastix_default/affine.txt b/brainglobe_registration/parameters/elastix_default/affine.txt
index f53b17b..dfd5765 100644
--- a/brainglobe_registration/parameters/elastix_default/affine.txt
+++ b/brainglobe_registration/parameters/elastix_default/affine.txt
@@ -21,4 +21,4 @@
 (ResultImageFormat "tiff")
 (Transform "AffineTransform")
 (WriteIterationInfo "false")
-(WriteResultImage "false")
+(WriteResultImage "true")
diff --git a/brainglobe_registration/parameters/elastix_default/bspline.txt b/brainglobe_registration/parameters/elastix_default/bspline.txt
index 6e2d6d7..16b7736 100644
--- a/brainglobe_registration/parameters/elastix_default/bspline.txt
+++ b/brainglobe_registration/parameters/elastix_default/bspline.txt
@@ -24,4 +24,4 @@
 (ResultImageFormat "tiff")
 (Transform "BSplineTransform")
 (WriteIterationInfo "false")
-(WriteResultImage "false")
+(WriteResultImage "true")
diff --git a/brainglobe_registration/parameters/elastix_default/rigid.txt b/brainglobe_registration/parameters/elastix_default/rigid.txt
index 9213652..5339da1 100644
--- a/brainglobe_registration/parameters/elastix_default/rigid.txt
+++ b/brainglobe_registration/parameters/elastix_default/rigid.txt
@@ -21,4 +21,4 @@
 (ResultImageFormat "tiff")
 (Transform "EulerTransform")
 (WriteIterationInfo "false")
-(WriteResultImage "false")
+(WriteResultImage "true")