From 65c42961548fdd71e5b44fb089329ce65db5290a Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Wed, 10 Apr 2024 14:35:13 +0200 Subject: [PATCH 1/2] fix: use a numpy squeeze to take care of parcellation ndim when warped via ANTs specifically --- junifer/markers/parcel_aggregation.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) 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: -- 2.52.0 From c0c893b8ffd607d7ab739510842199c7f52a35a2 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Wed, 10 Apr 2024 16:24:55 +0200 Subject: [PATCH 2/2] chore: add changelog 324.bugfix --- docs/changes/newsfragments/324.bugfix | 1 + 1 file changed, 1 insertion(+) create mode 100644 docs/changes/newsfragments/324.bugfix 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`_ -- 2.52.0