diff --git a/brainreg/napari/register.py b/brainreg/napari/register.py
index 0b59ca8..fd70780 100644
--- a/brainreg/napari/register.py
+++ b/brainreg/napari/register.py
@@ -560,11 +560,11 @@ def check_orientation(event=None):
         atlas = BrainGlobeAtlas(widget.atlas_key.value.name)
         if brain_geometry.value == "hemisphere_l":
             atlas.reference[
-                atlas.hemispheres == atlas.left_hemisphere_value
+                atlas.hemispheres == atlas.right_hemisphere_value
             ] = 0
         elif brain_geometry.value == "hemisphere_r":
             atlas.reference[
-                atlas.hemispheres == atlas.right_hemisphere_value
+                atlas.hemispheres == atlas.left_hemisphere_value
             ] = 0
         input_orientation = getattr(widget, "data_orientation").value
         data = getattr(widget, "img_layer").value.data
diff --git a/tests/test_brainreg_napari.py b/tests/test_brainreg_napari.py
index fdd5ac7..c03068e 100644
--- a/tests/test_brainreg_napari.py
+++ b/tests/test_brainreg_napari.py
@@ -116,6 +116,22 @@ def test_orientation_check(
     # run again and check previous output was deleted properly
     run_and_check_orientation_check(widget, viewer, brain_layer, atlas)
 
+    # "allen_mouse_50um" orientation is ASR
+    # so S-I projection will have origin AR
+    # so the columns 0 to half should be filled with zeros
+    # if we only want to register to the left hemisphere
+    # LR axis is 228
+    widget.brain_geometry.value = widget.brain_geometry.annotation[
+        "Left hemisphere"
+    ]
+    run_and_check_orientation_check(widget, viewer, brain_layer, atlas)
+    ar_projection = viewer.layers["Ref. proj. 1"].data
+    import numpy as np
+
+    assert ar_projection.shape[1] // 2 == 114
+    assert np.all(ar_projection[:, 114] == 0)
+    assert not np.all(ar_projection[:, 115] == 0)
+
 
 def run_and_check_orientation_check(widget, viewer, brain_layer, atlas):
     widget.check_orientation_button.clicked()