Merge pull request #384 from effigies/fix/transform_surfs

FIX: Update surfaces with fsnative2t1w_xfm

smriprep/interfaces/surf.py

@@ -199,18 +199,18 @@ def normalize_surfs(
 
     img = nb.load(in_file)
     if transform_file is None:
-        transform = np.eye(4)
+        transform = nt.linear.Affine()
     else:
         xfm_fmt = {
             ".txt": "itk",
             ".mat": "fsl",
             ".lta": "fs",
         }[Path(transform_file).suffix]
-        transform = nt.linear.load(transform_file, fmt=xfm_fmt).matrix
+        transform = nt.linear.load(transform_file, fmt=xfm_fmt)
     pointset = img.get_arrays_from_intent("NIFTI_INTENT_POINTSET")[0]
 
-    if not np.allclose(transform, np.eye(4)):
-        pointset.data = nb.affines.apply_affine(transform, pointset.data)
+    if not np.allclose(transform.matrix, np.eye(4)):
+        pointset.data = transform.map(pointset.data, inverse=True)
 
     fname = os.path.basename(in_file)
     if "graymid" in fname.lower():

smriprep/workflows/surfaces.py

@@ -919,10 +919,14 @@ def init_gifti_surfaces_wf(
         run_without_submitting=True,
     )
 
-    # fmt:off
     workflow.connect([
-        (inputnode, get_surfaces, [('subjects_dir', 'subjects_dir'),
-                                   ('subject_id', 'subject_id')]),
+        (inputnode, get_surfaces, [
+            ('subjects_dir', 'subjects_dir'),
+            ('subject_id', 'subject_id'),
+        ]),
+        (inputnode, fix_surfs, [
+            ('fsnative2t1w_xfm', 'transform_file'),
+        ]),
         (get_surfaces, surface_list, [
             (surf, f'in{i}') for i, surf in enumerate(surfaces, start=1)
         ]),
@@ -933,8 +937,7 @@ def init_gifti_surfaces_wf(
         (surface_groups, outputnode, [
             (f'out{i}', surf) for i, surf in enumerate(surfaces, start=1)
         ]),
-    ])
-    # fmt:on
+    ])  # fmt:skip
     return workflow