diff --git a/fmriprep/workflows/bold/resampling.py b/fmriprep/workflows/bold/resampling.py
index 30069a323..c51098121 100644
--- a/fmriprep/workflows/bold/resampling.py
+++ b/fmriprep/workflows/bold/resampling.py
@@ -201,10 +201,10 @@ def select_target(subject_id, space):
         ]),
         (inputnode, targets, [("subject_id", "subject_id")]),
         (inputnode, itk2lta, [
-            ("bold_t1w", "reference"),
+            ("bold_t1w", "moving"),
             ("fsnative2t1w_xfm", "in_xfms"),
         ]),
-        (get_fsnative, itk2lta, [("T1", "moving")]),
+        (get_fsnative, itk2lta, [("T1", "reference")]),
         (inputnode, sampler, [
             ("subjects_dir", "subjects_dir"),
             ("subject_id", "subject_id"),