Save normalized t1w brain

Author: kaitj

src/rbc/core/anatomical/registration.py

@@ -21,9 +21,16 @@
 _PREFIX = "ants_reg"
 
 
-class CompositeTransforms(NamedTuple):
-    """Forward and inverse composite transformation paths."""
+class RegistrationOutputs(NamedTuple):
+    """Outputs from ANTs registration to a standard-space template.
 
+    Attributes:
+        brain: Warped (template-space) skull-stripped brain.
+        forward: T1w-to-template composite displacement field.
+        inverse: Template-to-T1w composite displacement field.
+    """
+
+    brain: Path
     forward: Path
     inverse: Path
 
@@ -32,7 +39,7 @@ def ants_registration(
     in_file: Path,
     seed: int = CPAC_ANTS_SEED,
     registration_template: Path = REGISTRATION_TEMPLATES.brain_1mm,
-) -> CompositeTransforms:
+) -> RegistrationOutputs:
     """Register a skull-stripped T1w to a standard-space template with ANTs.
 
     Runs a three-stage registration (Rigid -> Affine -> SyN) and then
@@ -171,6 +178,10 @@ def ants_registration(
             print_out_composite_warp_file=True,
         ),
     )
-    return CompositeTransforms(
-        forward=fwd.output.output_image_outfile, inverse=rev.output.output_image_outfile
+    # 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,
     )

src/rbc/workflows/anatomical.py

@@ -38,6 +38,7 @@ class AnatomicalOutputs(NamedTuple):
     Attributes:
         brain: Skull-stripped T1w brain.
         brain_mask: Binary brain mask.
+        brain_tpl: Skull-stripped T1w brain in template space.
         csf_mask: CSF tissue mask.
         gm_mask: GM tissue mask.
         wm_mask: WM tissue mask.
@@ -48,6 +49,7 @@ class AnatomicalOutputs(NamedTuple):
 
     brain: Path
     brain_mask: Path
+    brain_tpl: Path
     csf_mask: Path
     gm_mask: Path
     wm_mask: Path
@@ -105,6 +107,7 @@ def single_session_preprocess(
     return AnatomicalOutputs(
         brain=extracted_t1w.brain,
         brain_mask=extracted_t1w.brain_mask,
+        brain_tpl=transforms.brain,
         csf_mask=tissue_masks.csf,
         gm_mask=tissue_masks.gm,
         wm_mask=tissue_masks.wm,