Rename CompositeTransforms to RegistrationOutputs and improve tests

The NamedTuple now includes a brain image alongside transforms, so the
old name was misleading. Also adds a comment explaining the manual
_Warped.nii.gz path, asserts the warped brain exists in the integration
test, and adds a unit test verifying the MNI-space BIDS filename.

Author: nx10

tests/integration/test_anatomical.py

@@ -35,6 +35,7 @@ def test_tissue_segmentation(test_subject: TestSubjectData) -> None:
 @pytest.mark.slow
 def test_registration(test_subject: TestSubjectData) -> None:
     """Test anatomical registration."""
-    composite_xfms = anatomical.ants_registration(in_file=test_subject.t1w)
-    assert composite_xfms.forward.exists()
-    assert composite_xfms.inverse.exists()
+    reg_outputs = anatomical.ants_registration(in_file=test_subject.t1w)
+    assert reg_outputs.brain.exists()
+    assert reg_outputs.forward.exists()
+    assert reg_outputs.inverse.exists()

tests/unit/bids/test_exports.py

@@ -128,10 +128,10 @@ def func_bids(pipe_ctx: RunContext) -> Bids:
 class TestExportAnatomical:
     """Tests for export_anatomical."""
 
-    def test_creates_8_files(
+    def test_creates_9_files(
         self, anat_bids: Bids, workdir: Path, pipe_ctx: RunContext
     ) -> None:
-        """All 8 anatomical outputs are saved."""
+        """All 9 anatomical outputs are saved."""
         outputs = _make_anat_outputs(workdir)
         export_anatomical(anat_bids, outputs)
         saved = list(pipe_ctx.output_dir.rglob("*.*"))
@@ -147,6 +147,21 @@ def test_filenames_contain_expected_entities(
             assert "sub-01" in p.name
             assert "ses-baseline" in p.name
 
+    def test_template_space_t1w_has_space_entity(
+        self, anat_bids: Bids, workdir: Path, pipe_ctx: RunContext
+    ) -> None:
+        """Template-space T1w is saved with the MNI space entity."""
+        outputs = _make_anat_outputs(workdir)
+        export_anatomical(anat_bids, outputs)
+        mni_files = [
+            p.name
+            for p in pipe_ctx.output_dir.rglob("*.*")
+            if "space-MNI152NLin6Asym" in p.name
+        ]
+        assert len(mni_files) == 1
+        assert "T1w" in mni_files[0]
+        assert "desc-brain" in mni_files[0]
+
 
 # ---------------------------------------------------------------------------
 # Functional exports