Resample long templ to bold grid for ref

Author: kaitj

src/rbc/core/longitudinal/resampling.py

@@ -0,0 +1,46 @@
+"""Resampling utiltiies for longitudinal templates."""
+
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
+
+import nibabel as nib
+from nibabel.processing import resample_from_to
+
+if TYPE_CHECKING:
+    from pathlib import Path
+
+from rbc.core.niwrap import generate_exec_folder
+
+
+def resample_template_to_bold(bold_ref: Path, template: Path) -> Path:
+    """Resample template to BOLD grid if shapes differ.
+
+    Args:
+        bold_ref: BOLD reference volume (used for ITK conversion).
+        template: Brain template in target space.
+
+    Returns:
+        Resampled template image with BOLD grid
+
+    Raises:
+        FileNotFoundError: No motion .mat files found in the directory.
+        ValueError: Number of motion matrices does not match STC volumes.
+    """
+    bold_ref_img = nib.nifti1.load(bold_ref)
+    template_img = nib.nifti1.load(template)
+
+    # If 4D, extract first volume
+    if len(bold_ref_img.shape) > 3:
+        bold_ref_img = bold_ref_img[..., 0]
+    # If same shape, no need to resample
+    if bold_ref_img.shape == template_img.shape:
+        return template_img
+
+    template_img = resample_from_to(template_img, bold_ref_img)
+    template_img_path = (
+        generate_exec_folder("template_resample_to_bold_grid")
+        / "template_resampled.nii.gz"
+    )
+    nib.save(template_img, template_img_path)
+    return template_img_path

src/rbc/workflows/longitudinal/functional.py

@@ -12,6 +12,7 @@
 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,
@@ -82,8 +83,10 @@ 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,
+        ref=template_resampled,
         bold_to_anat_itk=bold_to_anat_itk,
         anat_to_tpl_xfm=anat_to_template_xfm,
     )