Add single subject anat workflow

Author: kaitj

src/rbc/core/anatomical/registration.py

@@ -124,11 +124,12 @@ def ants_registration(
             ),
         ],
         output=ants.ants_apply_transforms_composite_displacement_field_output(
-            composite_displacement_field=f"{output_prefix}_from-T1w_to-template_mode-image_xfm.nii.gz"
+            composite_displacement_field=f"{output_prefix}_from-T1w_to-template_mode-image_xfm.nii.gz",
+            print_out_composite_warp_file=True,
         ),
     )
     rev = ants.ants_apply_transforms(
-        reference_image=str(in_file),
+        reference_image=in_file,
         transform=[
             ants.ants_apply_transforms_transform_file_name(
                 registration.root / f"{output_prefix}_1InverseWarp.nii.gz"
@@ -138,7 +139,8 @@ def ants_registration(
             ),
         ],
         output=ants.ants_apply_transforms_composite_displacement_field_output(
-            composite_displacement_field=f"{output_prefix}_from-template_to-T1w_mode-image_xfm.nii.gz"
+            composite_displacement_field=f"{output_prefix}_from-template_to-T1w_mode-image_xfm.nii.gz",
+            print_out_composite_warp_file=True,
         ),
     )
     return SimpleNamespace(forward=fwd.output, inverse=rev.output)

src/rbc/workflows/anatomical.py

@@ -0,0 +1,52 @@
+"""Anatomical workflows."""
+
+from functools import partial
+from pathlib import Path
+
+import niwrap_helper
+
+from rbc.core.anatomical import ants_brain_extraction, ants_registration
+from rbc.core.common import reorient
+from rbc.core.utils import get_base_entities, rename
+
+
+def single_session(in_t1w: Path, output_dir: Path) -> None:
+    """Workflow for preprocessing anatomical data.
+
+    Args:
+        in_t1w: Input T1w image to process.
+        output_dir: Parent output directory to save data to.
+
+    Raises:
+        FileNotFoundError: If brain extracted file could not be found.
+    """
+    bids_entities = get_base_entities(in_t1w)
+    bids = partial(niwrap_helper.bids_path, **bids_entities)
+
+    reoriented_t1w = reorient(
+        in_file=in_t1w,
+        output_fname=str(bids(desc="reoriented", suffix="T1w", ext=".nii.gz")),
+    )
+    extracted_t1w = ants_brain_extraction(
+        in_file=reoriented_t1w.out_file, output_prefix=str(bids())
+    )
+    transforms = ants_registration(
+        extracted_t1w.brain_extracted_image, output_prefix=str(bids())
+    )
+
+    # Prep files to save
+    extracted_t1w_outputs = [
+        (extracted_t1w.brain_extracted_image, "brain", "T1w"),
+        (extracted_t1w.brain_mask, "T1w", "mask"),
+        (extracted_t1w.csf_segmentation, "csf", "dseg"),
+        (extracted_t1w.wm_segmentation, "wm", "dseg"),
+        (extracted_t1w.gm_segmentation, "gm", "dseg"),
+    ]
+    renamed_files = [
+        rename(Path(out_file), str(bids(desc=desc, suffix=suffix, ext=".nii.gz")))
+        for out_file, desc, suffix in extracted_t1w_outputs
+    ]
+    niwrap_helper.save(
+        [*renamed_files, transforms.forward, transforms.inverse],
+        out_dir=output_dir / bids(datatype="anat", directory=True),
+    )