Replace data loading for long template resampling

Author: kaitj

src/rbc/bids/longitudinal/anatomical.py

@@ -43,7 +43,7 @@ def resolve_longitudinal_anat(
         Dict with keys matching ``longitudinal_process`` parameters.
     """
     return {
-        "template": tpl_q.expect(tpl_df, suffix=Suffix.T1W),
+        "template": tpl_q.expect(tpl_df, suffix=Suffix.T1W, without=["res"]),
         "subj_to_template_xfm": tpl_q.expect(
             tpl_df,
             suffix="xfm",

src/rbc/core/longitudinal/resampling.py

@@ -1,4 +1,4 @@
-"""Resampling utiltiies for longitudinal templates."""
+"""Resampling utilities for longitudinal templates."""
 
 from __future__ import annotations
 
@@ -13,7 +13,7 @@
 from rbc.core.niwrap import generate_exec_folder
 
 
-def resample_template_to_bold(bold_ref: Path, template: Path) -> Path:
+def resample_template_to_bold_grid(bold_ref: Path, template: Path) -> Path:
     """Resample template to BOLD grid if shapes differ.
 
     Args:
@@ -32,7 +32,7 @@ def resample_template_to_bold(bold_ref: Path, template: Path) -> Path:
 
     # If 4D, extract first volume
     if len(bold_ref_img.shape) > 3:
-        bold_ref_img = bold_ref_img[..., 0]
+        bold_ref_img = nib.four_to_three(bold_ref_img)[0]
     # If same shape, no need to resample
     if bold_ref_img.shape == template_img.shape:
         return template_img

src/rbc/workflows/longitudinal/template.py

@@ -14,7 +14,7 @@
     fs_to_itk_xfm,
     generate_robust_template,
 )
-from rbc.core.longitudinal.resampling import resample_template_to_bold
+from rbc.core.longitudinal.resampling import resample_template_to_bold_grid
 
 if TYPE_CHECKING:
     from collections.abc import Sequence
@@ -71,7 +71,7 @@ def generate_subject_template(
     )
 
     if bold_ref is not None:
-        bold_ref = resample_template_to_bold(bold_ref, robust.template)
+        bold_ref = resample_template_to_bold_grid(bold_ref, robust.template)
 
     return LongitudinalTemplateOutputs(
         template=robust.template,

tests/unit/bids/test_longitudinal_anatomical.py

@@ -99,6 +99,7 @@ def _anat_row(
         "sub": sub,
         "ses": ses,
         "desc": desc,
+        "res": None,
         "root": "/data",
         "path": path,
         "extra_entities": extra or [],