Generate bold ref once after template created

Author: kaitj

src/rbc/bids/longitudinal/functional.py

@@ -51,7 +51,7 @@ def resolve_longitudinal_func(
         )
 
     return {
-        "template": tpl_q.expect(tpl_df, suffix="T1w"),
+        "template": tpl_q.expect(tpl_df, res="bold", suffix="T1w"),
         "anat_to_template_xfm": tpl_q.expect(
             tpl_df,
             suffix="xfm",

src/rbc/bids/longitudinal/template.py

@@ -21,11 +21,13 @@ class TemplateInputs(NamedTuple):
         sub: Subject label.
         sessions: Per-input session labels (parallel to ``files``).
         files: Per-session preprocessed T1w brain volumes.
+        bold_ref: First BOLD volume for grid reference
     """
 
     sub: str
     sessions: list[str]
     files: list[Path]
+    bold_ref: Path | None
 
 
 def discover_template_inputs(
@@ -56,6 +58,17 @@ def discover_template_inputs(
         # the mri_robust_template invocation.
         pl.col("space").is_null(),
     )
+    bold_ref_rows = df.filter(
+        pl.col("ses") != "longitudinal",
+        pl.col("datatype") == "func",
+        pl.col("suffix") == "bold",
+        pl.col("space").is_null(),
+    )
+    bold_ref = (
+        None
+        if bold_ref_rows.is_empty()
+        else Path(bold_ref_rows["root"][0]) / bold_ref_rows["path"][0]
+    )
 
     inputs: list[TemplateInputs] = []
     skipped: list[str] = []
@@ -68,7 +81,9 @@ def discover_template_inputs(
         files = [
             Path(row["root"]) / row["path"] for row in sub_group.iter_rows(named=True)
         ]
-        inputs.append(TemplateInputs(sub=sub, sessions=sessions, files=files))
+        inputs.append(
+            TemplateInputs(sub=sub, sessions=sessions, files=files, bold_ref=bold_ref)
+        )
     return inputs, skipped
 
 
@@ -81,6 +96,8 @@ def export_template(tpl: Bids, outputs: LongitudinalTemplateOutputs) -> None:
         outputs: Results from the longitudinal template workflow.
     """
     tpl.save(outputs.template, suffix=Suffix.T1W)
+    if outputs.bold_template is not None:
+        tpl.save(outputs.bold_template, res="bold", suffix=Suffix.T1W)
     for ses, xfm in zip(outputs.sessions, outputs.transforms, strict=True):
         ses_label = bids_safe_label(ses)
         tpl.save(

src/rbc/orchestration/longitudinal/template.py

@@ -49,6 +49,7 @@ def process_subject(
         sub=inputs.sub,
         sessions=inputs.sessions,
         in_files=inputs.files,
+        bold_ref=inputs.bold_ref,
     )
     tpl = pipe_ctx.bids(datatype=Datatype.ANAT).derive(ses="longitudinal")
     export_template(tpl, outputs)

src/rbc/workflows/longitudinal/functional.py

@@ -12,7 +12,6 @@
 from typing import TYPE_CHECKING, NamedTuple
 
 from rbc.core.functional import apply_regression, apply_regression_bandpass
-from rbc.core.longitudinal.resampling import resample_template_to_bold
 from rbc.core.longitudinal.transform import (
     compose_transform,
     func_transform,
@@ -83,10 +82,8 @@ def longitudinal_process(
         :class:`FunctionalLongOutputs` with all inputs transformed to
         longitudinal template space and per-regressor regression outputs.
     """
-    template_resampled = resample_template_to_bold(bold_ref=sbref, template=template)
-
     bold_to_tpl_xfm = compose_transform(
-        ref=template_resampled,
+        ref=template,
         bold_to_anat_itk=bold_to_anat_itk,
         anat_to_tpl_xfm=anat_to_template_xfm,
     )

src/rbc/workflows/longitudinal/template.py

@@ -14,6 +14,7 @@
     fs_to_itk_xfm,
     generate_robust_template,
 )
+from rbc.core.longitudinal.resampling import resample_template_to_bold
 
 if TYPE_CHECKING:
     from collections.abc import Sequence
@@ -27,11 +28,13 @@ class LongitudinalTemplateOutputs(NamedTuple):
 
     Attributes:
         template: Robust within-subject template volume.
+        bold_template: Within-subject template volume resampled to BOLD resolution.
         sessions: Session labels in the same order as ``transforms``.
         transforms: Per-session ITK-format session-to-template transforms.
     """
 
     template: Path
+    bold_template: Path | None
     sessions: list[str]
     transforms: list[Path]
 
@@ -40,13 +43,15 @@ def generate_subject_template(
     sub: str,
     sessions: Sequence[str],
     in_files: Sequence[Path],
+    bold_ref: Path | None = None,
 ) -> LongitudinalTemplateOutputs:
     """Build a robust template and ITK transforms for one subject.
 
     Args:
         sub: Subject label (without the ``sub-`` prefix).
         sessions: Session labels parallel to ``in_files``.
         in_files: Per-session preprocessed T1w volumes (e.g. brain-extracted).
+        bold_ref: Reference bold volume to resample template for functional data.
 
     Returns:
         :class:`LongitudinalTemplateOutputs` ready for BIDS export.
@@ -65,8 +70,12 @@ def generate_subject_template(
         in_xfms=robust.transforms,
     )
 
+    if bold_ref is not None:
+        bold_ref = resample_template_to_bold(bold_ref, robust.template)
+
     return LongitudinalTemplateOutputs(
         template=robust.template,
+        bold_template=bold_ref,
         sessions=list(sessions),
         transforms=itk_xfms,
     )