Fix anat-to-tpl xfm grabbed

.github/workflows/test_full.yaml

@@ -27,6 +27,7 @@ jobs:
     - uses: actions/checkout@v6
     - uses: astral-sh/setup-uv@v8.0.0
       with:
+        version: "0.11.3"
         enable-cache: true # not automatic on self-hosted runners
     - run: uv sync
 

scripts/visualize_pipeline.py

@@ -146,9 +146,11 @@ def _resample_mosaic(
 def _build_mosaic(
     data: np.ndarray,
     n: int = 7,
+    slices: list[int] | None = None,
 ) -> np.ndarray:
     """Build an axial-slice mosaic resampled to standard dimensions."""
-    slices = _axial_slices(data, n)
+    if slices is None:
+        slices = _axial_slices(data, n)
     panels = [data[:, :, z].T for z in slices]
     mosaic = np.concatenate(panels, axis=1)
     return _resample_mosaic(mosaic)
@@ -285,8 +287,9 @@ def _render_stat_overlay(
 ) -> None:
     """Lightbox with thresholded stat map overlaid on background."""
     bg_vmax = _robust_vmax(bg_data)
-    bg_mosaic = _build_mosaic(bg_data, n)
-    stat_mosaic = _build_mosaic(stat_data, n)
+    slices = _axial_slices(bg_data, n)
+    bg_mosaic = _build_mosaic(bg_data, n, slices=slices)
+    stat_mosaic = _build_mosaic(stat_data, n, slices=slices)
 
     ax.imshow(
         bg_mosaic,

src/rbc/bids/anatomical.py

@@ -66,7 +66,7 @@ def export_anatomical(anat: Bids, outputs: AnatomicalOutputs) -> None:
     anat.save(outputs.wm_mask, suffix=Suffix.MASK, desc="wm")
     anat.save(outputs.wm_bbr_mask, suffix=Suffix.MASK, desc="wmBBR")
     anat.save(
-        outputs.forward_xfm,
+        outputs.anat_to_template_xfm,
         suffix="xfm",
         extra={
             "from": "T1w",
@@ -75,7 +75,7 @@ def export_anatomical(anat: Bids, outputs: AnatomicalOutputs) -> None:
         },
     )
     anat.save(
-        outputs.inverse_xfm,
+        outputs.template_to_anat_xfm,
         suffix="xfm",
         extra={
             "from": TemplateSpace.MNI152NLIN6ASYM,

src/rbc/bids/functional.py

@@ -91,8 +91,8 @@ def resolve_functional(
             anat_df,
             suffix="xfm",
             extra={
-                "from": TemplateSpace.MNI152NLIN6ASYM,
-                "to": "T1w",
+                "to": TemplateSpace.MNI152NLIN6ASYM,
+                "from": "T1w",
                 "mode": "image",
             },
         ),

src/rbc/bids/longitudinal.py

@@ -4,7 +4,7 @@
 
 from typing import TYPE_CHECKING
 
-from rbc.bids import Suffix
+from rbc.bids import Suffix, TemplateSpace
 
 if TYPE_CHECKING:
     from pathlib import Path
@@ -88,14 +88,22 @@ def export_longitudinal_anat(aex: Bids, outputs: AnatomicalLongOutputs) -> None:
         desc="wm",
     )
     aex.save(
-        outputs.forward_xfm,
+        outputs.long_to_template_xfm,
         suffix="xfm",
-        extra={"from": "T1w", "to": "longitudinal", "mode": "image"},
+        extra={
+            "from": "longitudinal",
+            "to": TemplateSpace.MNI152NLIN6ASYM,
+            "mode": "image",
+        },
     )
     aex.save(
-        outputs.inverse_xfm,
+        outputs.template_to_long_xfm,
         suffix="xfm",
-        extra={"from": "longitudinal", "to": "T1w", "mode": "image"},
+        extra={
+            "from": TemplateSpace.MNI152NLIN6ASYM,
+            "to": "longitudinal",
+            "mode": "image",
+        },
     )
 
 
@@ -154,7 +162,7 @@ def export_longitudinal_func(fex: Bids, outputs: FunctionalLongOutputs) -> None:
     fex.save(outputs.sbref, suffix=Suffix.SBREF)
     fex.save(outputs.bold, suffix=Suffix.BOLD, desc="preproc")
     fex.save(
-        outputs.forward_xfm,
+        outputs.bold_to_long_xfm,
         suffix="xfm",
         desc="composite",
         extra={"from": "bold", "to": "longitudinal", "mode": "image"},

src/rbc/core/anatomical/registration.py

@@ -26,13 +26,13 @@ class RegistrationOutputs(NamedTuple):
 
     Attributes:
         brain: Warped (template-space) skull-stripped brain.
-        forward: T1w-to-template composite displacement field.
-        inverse: Template-to-T1w composite displacement field.
+        forward: anat-to-template composite displacement field.
+        inverse: Template-to-anat composite displacement field.
     """
 
     brain: Path
-    forward: Path
-    inverse: Path
+    anat_to_template: Path
+    template_to_anat: Path
 
 
 def ants_registration(
@@ -53,8 +53,8 @@ def ants_registration(
             (default: MNI152 1 mm).
 
     Returns:
-        Forward (T1w -> template) and inverse (template -> T1w) composite
-        transforms.
+        Transformed brain in template space, forward (T1w -> template) and inverse
+        (template -> T1w) composite transforms.
     """
     registration = ants.ants_registration(
         stages=[
@@ -148,7 +148,7 @@ def ants_registration(
         interpolation="LanczosWindowedSinc",
         output=f"[{_PREFIX}_,{_PREFIX}_Warped.nii.gz]",
     )
-    fwd = ants.ants_apply_transforms(
+    anat_to_template = ants.ants_apply_transforms(
         reference_image=registration_template,
         transform=[
             ants.ants_apply_transforms_transform_file_name(
@@ -159,11 +159,11 @@ def ants_registration(
             ),
         ],
         output=ants.ants_apply_transforms_composite_displacement_field_output(
-            composite_displacement_field="forward_xfm.nii.gz",
+            composite_displacement_field="anat_to_template_xfm.nii.gz",
             print_out_composite_warp_file=True,
         ),
     )
-    rev = ants.ants_apply_transforms(
+    template_to_anat = ants.ants_apply_transforms(
         reference_image=in_file,
         transform=[
             ants.ants_apply_transforms_transform_file_name(
@@ -174,14 +174,14 @@ def ants_registration(
             ),
         ],
         output=ants.ants_apply_transforms_composite_displacement_field_output(
-            composite_displacement_field="inverse_xfm.nii.gz",
+            composite_displacement_field="template_to_anat_xfm.nii.gz",
             print_out_composite_warp_file=True,
         ),
     )
     # ANTs writes the warped image to {prefix}_Warped.nii.gz but NiWrap
     # does not expose this path, so we construct it from the output root.
     return RegistrationOutputs(
         brain=registration.root / f"{_PREFIX}_Warped.nii.gz",
-        forward=fwd.output.output_image_outfile,
-        inverse=rev.output.output_image_outfile,
+        anat_to_template=anat_to_template.output.output_image_outfile,
+        template_to_anat=template_to_anat.output.output_image_outfile,
     )

src/rbc/orchestration/all.py

@@ -118,7 +118,7 @@ def run(
                 "brain_mask": anat_outputs.brain_mask,
                 "csf_mask": anat_outputs.csf_mask,
                 "wm_mask": anat_outputs.wm_mask,
-                "anat_to_template": anat_outputs.inverse_xfm,
+                "anat_to_template": anat_outputs.anat_to_template_xfm,
             },
             tr=tr,
             func_template=func_template,

src/rbc/workflows/anatomical.py

@@ -43,8 +43,8 @@ class AnatomicalOutputs(NamedTuple):
         gm_mask: GM tissue mask.
         wm_mask: WM tissue mask.
         wm_bbr_mask: WM boundary mask for BBR coregistration.
-        forward_xfm: T1w-to-template composite warp.
-        inverse_xfm: Template-to-T1w composite warp.
+        anat_to_template_xfm: anat-to-template composite warp.
+        template_to_anat_xfm: Template-to-anat composite warp.
     """
 
     brain: Path
@@ -54,8 +54,8 @@ class AnatomicalOutputs(NamedTuple):
     gm_mask: Path
     wm_mask: Path
     wm_bbr_mask: Path
-    forward_xfm: Path
-    inverse_xfm: Path
+    anat_to_template_xfm: Path
+    template_to_anat_xfm: Path
 
 
 def single_session_preprocess(
@@ -112,8 +112,8 @@ def single_session_preprocess(
         gm_mask=tissue_masks.gm,
         wm_mask=tissue_masks.wm,
         wm_bbr_mask=wm_bbr,
-        forward_xfm=transforms.forward,
-        inverse_xfm=transforms.inverse,
+        anat_to_template_xfm=transforms.anat_to_template,
+        template_to_anat_xfm=transforms.template_to_anat,
     )
 
 
@@ -130,17 +130,17 @@ class AnatomicalLongOutputs(NamedTuple):
             or *None* if not provided.
         wm_mask: WM tissue mask warped to longitudinal template space,
             or *None* if not provided.
-        forward_xfm: Longitudinal template-to-MNI152 composite warp.
-        inverse_xfm: MNI152-to-longitudinal template composite warp.
+        long_to_template_xfm: Longitudinal template-to-MNI152 composite warp.
+        template_to_long_xfm: MNI152-to-longitudinal template composite warp.
     """
 
     brain: Path
     brain_mask: Path | None
     csf_mask: Path | None
     gm_mask: Path | None
     wm_mask: Path | None
-    forward_xfm: Path
-    inverse_xfm: Path
+    long_to_template_xfm: Path
+    template_to_long_xfm: Path
 
 
 def longitudinal_process(
@@ -193,6 +193,6 @@ def _xfm(val: Path | None) -> Path | None:
         csf_mask=_xfm(csf_mask),
         gm_mask=_xfm(gm_mask),
         wm_mask=_xfm(wm_mask),
-        forward_xfm=transforms.forward,
-        inverse_xfm=transforms.inverse,
+        long_to_template_xfm=transforms.anat_to_template,
+        template_to_long_xfm=transforms.template_to_anat,
     )

src/rbc/workflows/functional.py

@@ -387,14 +387,14 @@ class FunctionalLongOutputs(NamedTuple):
     """Outputs from the longitudinal functional preprocessing pipeline.
 
     Attributes:
-        forward_xfm: BOLD-to-longitudinal-template composite warp.
+        bold_to_long_xfm: BOLD-to-longitudinal-template composite warp.
         sbref: Motion reference volume warped to longitudinal template space.
         bold: Preprocessed BOLD warped to longitudinal template space.
         bold_mask: Brain mask warped to longitudinal template space,
             or *None* if no mask was provided.
     """
 
-    forward_xfm: Path
+    bold_to_long_xfm: Path
     sbref: Path
     bold: Path
     bold_mask: Path | None = None
@@ -443,5 +443,5 @@ def longitudinal_process(
         bold_mask=mask_transform(mask=bold_mask, template=template, xfm=bold_to_tpl_xfm)
         if bold_mask
         else None,
-        forward_xfm=bold_to_tpl_xfm,
+        bold_to_long_xfm=bold_to_tpl_xfm,
     )

tests/full_pipeline/conftest.py

@@ -105,11 +105,11 @@ def pipeline_data(
         brain_mask=anat.brain_mask,
         csf_mask=anat.csf_mask,
         wm_mask=anat.wm_mask,
-        anat_to_template=anat.forward_xfm,
+        anat_to_template=anat.anat_to_template_xfm,
         metadata=func_metadata,
     )
     template_brain_mask = _warp_mask_to_template(
-        anat.brain_mask, REGISTRATION_TEMPLATES.brain_2mm, anat.forward_xfm
+        anat.brain_mask, REGISTRATION_TEMPLATES.brain_2mm, anat.anat_to_template_xfm
     )
     manifest["anat"] = _to_dict(anat)
     manifest["func"] = _to_dict(func)

tests/integration/test_anatomical.py

@@ -37,5 +37,5 @@ def test_registration(test_subject: TestSubjectData) -> None:
     """Test anatomical registration."""
     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()
+    assert reg_outputs.anat_to_template.exists()
+    assert reg_outputs.template_to_anat.exists()

tests/unit/bids/test_exports.py

@@ -47,8 +47,8 @@ def _make_anat_outputs(w: Path) -> AnatomicalOutputs:
         gm_mask=_dummy(w, "gm_mask.nii.gz"),
         wm_mask=_dummy(w, "wm_mask.nii.gz"),
         wm_bbr_mask=_dummy(w, "wm_bbr_mask.nii.gz"),
-        forward_xfm=_dummy(w, "forward_xfm.nii.gz"),
-        inverse_xfm=_dummy(w, "inverse_xfm.nii.gz"),
+        anat_to_template_xfm=_dummy(w, "anat_to_template_xfm.nii.gz"),
+        template_to_anat_xfm=_dummy(w, "template_to_anat_xfm.nii.gz"),
     )
 
 

tests/unit/orchestration/test_functional.py

@@ -207,8 +207,8 @@ def test_anat_outputs_forwarded_as_anat_inputs(self, tmp_path: Path) -> None:
             gm_mask=_FAKE / "gm_mask.nii.gz",
             wm_mask=_FAKE / "wm_mask.nii.gz",
             wm_bbr_mask=_FAKE / "wm_bbr.nii.gz",
-            forward_xfm=_FAKE / "fwd.nii.gz",
-            inverse_xfm=_FAKE / "inv.nii.gz",
+            anat_to_template_xfm=_FAKE / "anat_to_template.nii.gz",
+            template_to_anat_xfm=_FAKE / "template_to_anat.nii.gz",
         )
 
         raw_df = pl.DataFrame(
@@ -260,4 +260,6 @@ def test_anat_outputs_forwarded_as_anat_inputs(self, tmp_path: Path) -> None:
             assert passed_inputs["csf_mask"] == anat_outputs.csf_mask
             assert passed_inputs["wm_mask"] == anat_outputs.wm_mask
             assert passed_inputs["wm_bbr_mask"] == anat_outputs.wm_bbr_mask
-            assert passed_inputs["anat_to_template"] == anat_outputs.inverse_xfm
+            assert (
+                passed_inputs["anat_to_template"] == anat_outputs.anat_to_template_xfm
+            )

tests/unit/orchestration/test_longitudinal.py

@@ -56,8 +56,8 @@ def _mock_anat_outputs() -> Mock:
     m.csf_mask = fake / "csf_mask.nii.gz"
     m.gm_mask = fake / "gm_mask.nii.gz"
     m.wm_mask = fake / "wm_mask.nii.gz"
-    m.forward_xfm = fake / "fwd_xfm.nii.gz"
-    m.inverse_xfm = fake / "inverse_xfm.nii.gz"
+    m.long_to_template_xfm = fake / "long_to_template_xfm.nii.gz"
+    m.template_to_long_xfm = fake / "template_to_long_xfm.nii.gz"
     return m
 
 
@@ -66,7 +66,7 @@ def _mock_func_outputs(*, with_bold_mask: bool = True) -> Mock:
     m = Mock()
     m.sbref = fake / "sbref.nii.gz"
     m.bold = fake / "bold.nii.gz"
-    m.forward_xfm = fake / "fwd_xfm.nii.gz"
+    m.bold_to_long_xfm = fake / "bold_to_long_xfm.nii.gz"
     m.bold_mask = (fake / "bold_mask.nii.gz") if with_bold_mask else None
     return m