diff --git a/docs/changes/newsfragments/331.bugfix b/docs/changes/newsfragments/331.bugfix
new file mode 100644
index 000000000..61d03f105
--- /dev/null
+++ b/docs/changes/newsfragments/331.bugfix
@@ -0,0 +1 @@
+Remove extra dimension from parcellations warped via ANTs when merging parcellations by `Synchon Mandal`_
diff --git a/junifer/data/parcellations.py b/junifer/data/parcellations.py
index fbd9d8fba..947c3acbc 100644
--- a/junifer/data/parcellations.py
+++ b/junifer/data/parcellations.py
@@ -326,7 +326,9 @@ def get_parcellation(
             # Call antsApplyTransforms
             run_ext_cmd(name="antsApplyTransforms", cmd=apply_transforms_cmd)
 
-            img = nib.load(warped_parcellation_path)
+            raw_img = nib.load(warped_parcellation_path)
+            # Remove extra dimension added by ANTs
+            img = image.math_img("np.squeeze(img)", img=raw_img)
 
         # Resample parcellation to target image
         img_to_merge = image.resample_to_img(