diff --git a/docs/changes/newsfragments/324.bugfix b/docs/changes/newsfragments/324.bugfix
new file mode 100644
index 000000000..ee6e3d25e
--- /dev/null
+++ b/docs/changes/newsfragments/324.bugfix
@@ -0,0 +1 @@
+Remove extra dimension from parcellations warped via ANTs to other template spaces by `Synchon Mandal`_
diff --git a/junifer/markers/parcel_aggregation.py b/junifer/markers/parcel_aggregation.py
index a97abfa1d..a24f2eef7 100644
--- a/junifer/markers/parcel_aggregation.py
+++ b/junifer/markers/parcel_aggregation.py
@@ -195,7 +195,9 @@ class ParcelAggregation(BaseMarker):
         )
 
         # Get binarized parcellation image for masking
-        parcellation_bin = math_img("img != 0", img=parcellation_img)
+        parcellation_bin = math_img(
+            "np.squeeze(img) != 0", img=parcellation_img
+        )
 
         # Load mask
         if self.masks is not None: