From 1ba6f5acf7c5ead4bb9eb1f8614ca75af2e444ac Mon Sep 17 00:00:00 2001
From: Jason Kai <21226986+kaitj@users.noreply.github.com>
Date: Fri, 8 May 2026 10:52:03 -0400
Subject: [PATCH 01/12] Resample long templ to bold grid for ref

---
 src/rbc/core/longitudinal/resampling.py      | 46 ++++++++++++++++++++
 src/rbc/workflows/longitudinal/functional.py |  5 ++-
 2 files changed, 50 insertions(+), 1 deletion(-)
 create mode 100644 src/rbc/core/longitudinal/resampling.py

diff --git a/src/rbc/core/longitudinal/resampling.py b/src/rbc/core/longitudinal/resampling.py
new file mode 100644
index 00000000..da53c285
--- /dev/null
+++ b/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
diff --git a/src/rbc/workflows/longitudinal/functional.py b/src/rbc/workflows/longitudinal/functional.py
index fdf7b669..5926fba7 100644
--- a/src/rbc/workflows/longitudinal/functional.py
+++ b/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,
     )

From 05f0b3e6cec0dd1a9ed1f7f6d7e79cdb3beae858 Mon Sep 17 00:00:00 2001
From: Jason Kai <21226986+kaitj@users.noreply.github.com>
Date: Fri, 8 May 2026 13:13:20 -0400
Subject: [PATCH 02/12] Generate bold ref once after template created

---
 src/rbc/bids/longitudinal/functional.py       |  2 +-
 src/rbc/bids/longitudinal/template.py         | 19 ++++++++++++++++++-
 .../orchestration/longitudinal/template.py    |  1 +
 src/rbc/workflows/longitudinal/functional.py  |  5 +----
 src/rbc/workflows/longitudinal/template.py    |  9 +++++++++
 5 files changed, 30 insertions(+), 6 deletions(-)

diff --git a/src/rbc/bids/longitudinal/functional.py b/src/rbc/bids/longitudinal/functional.py
index 0ac9d457..3f156811 100644
--- a/src/rbc/bids/longitudinal/functional.py
+++ b/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",
diff --git a/src/rbc/bids/longitudinal/template.py b/src/rbc/bids/longitudinal/template.py
index 8b5784f9..12598201 100644
--- a/src/rbc/bids/longitudinal/template.py
+++ b/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(
diff --git a/src/rbc/orchestration/longitudinal/template.py b/src/rbc/orchestration/longitudinal/template.py
index 026c3b65..6091e776 100644
--- a/src/rbc/orchestration/longitudinal/template.py
+++ b/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)
diff --git a/src/rbc/workflows/longitudinal/functional.py b/src/rbc/workflows/longitudinal/functional.py
index 5926fba7..fdf7b669 100644
--- a/src/rbc/workflows/longitudinal/functional.py
+++ b/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,
     )
diff --git a/src/rbc/workflows/longitudinal/template.py b/src/rbc/workflows/longitudinal/template.py
index c76494b7..246d36a1 100644
--- a/src/rbc/workflows/longitudinal/template.py
+++ b/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]
 
@@ -40,6 +43,7 @@ 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.
 
@@ -47,6 +51,7 @@ def generate_subject_template(
         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,
     )

From 2f95effd83ecdb58f5aa7286c23181dbf5600c67 Mon Sep 17 00:00:00 2001
From: Jason Kai <21226986+kaitj@users.noreply.github.com>
Date: Fri, 8 May 2026 13:13:44 -0400
Subject: [PATCH 03/12] Update tests for bold ref template

---
 .../unit/bids/test_longitudinal_functional.py | 10 ++--
 tests/unit/bids/test_longitudinal_template.py | 48 +++++++++++++------
 2 files changed, 39 insertions(+), 19 deletions(-)

diff --git a/tests/unit/bids/test_longitudinal_functional.py b/tests/unit/bids/test_longitudinal_functional.py
index 98a17d41..861ba3e5 100644
--- a/tests/unit/bids/test_longitudinal_functional.py
+++ b/tests/unit/bids/test_longitudinal_functional.py
@@ -59,6 +59,7 @@ def _anat_row(
     sub: str,
     ses: str,
     suffix: str,
+    res: str | None = None,
     desc: str | None = None,
     ext: str = ".nii.gz",
     extra: list[dict[str, str]] | None = None,
@@ -73,6 +74,7 @@ def _anat_row(
         "sub": sub,
         "ses": ses,
         "space": None,
+        "res": res,
         "desc": desc,
         "root": "/data",
         "path": path,
@@ -143,7 +145,7 @@ def test_resolves_single_regressor(self, tmp_path: Path) -> None:
             ),
         )
         tpl_df = _df(
-            _anat_row(sub="01", ses="longitudinal", suffix="T1w"),
+            _anat_row(sub="01", ses="longitudinal", res="bold", suffix="T1w"),
             _anat_row(
                 sub="01",
                 ses="longitudinal",
@@ -218,7 +220,7 @@ def test_resolves_multiple_regressors(self, tmp_path: Path) -> None:
             ),
         )
         tpl_df = _df(
-            _anat_row(sub="01", ses="longitudinal", suffix="T1w"),
+            _anat_row(sub="01", ses="longitudinal", res="bold", suffix="T1w"),
             _anat_row(
                 sub="01",
                 ses="longitudinal",
@@ -275,7 +277,7 @@ def test_missing_regressor_raises(self, tmp_path: Path) -> None:
             ),
         )
         tpl_df = _df(
-            _anat_row(sub="01", ses="longitudinal", suffix="T1w"),
+            _anat_row(sub="01", ses="longitudinal", res="bold", suffix="T1w"),
             _anat_row(
                 sub="01",
                 ses="longitudinal",
@@ -328,7 +330,7 @@ def test_bold_mask_mandatory(self, tmp_path: Path) -> None:
             ),
         )
         tpl_df = _df(
-            _anat_row(sub="01", ses="longitudinal", suffix="T1w"),
+            _anat_row(sub="01", ses="longitudinal", res="bold", suffix="T1w"),
             _anat_row(
                 sub="01",
                 ses="longitudinal",
diff --git a/tests/unit/bids/test_longitudinal_template.py b/tests/unit/bids/test_longitudinal_template.py
index a9c80e63..f4b8ec7f 100644
--- a/tests/unit/bids/test_longitudinal_template.py
+++ b/tests/unit/bids/test_longitudinal_template.py
@@ -35,7 +35,7 @@ def _df(*rows: tuple) -> pl.DataFrame:
     return pl.DataFrame(dict(zip(_SCHEMA, zip(*rows, strict=True), strict=True)))
 
 
-def _brain_row(sub: str, ses: str, space: str | None = None) -> tuple:
+def _anat_row(sub: str, ses: str, space: str | None = None) -> tuple:
     space_part = f"_space-{space}" if space else ""
     path = (
         f"sub-{sub}/ses-{ses}/anat/"
@@ -56,16 +56,25 @@ def _brain_row(sub: str, ses: str, space: str | None = None) -> tuple:
     )
 
 
+def _func_row(sub: str, ses: str, task: str = "rest") -> tuple:
+    path = f"sub-{sub}/ses-{ses}/func/sub-{sub}_ses-{ses}_task-{task}_bold.nii.gz"
+    return ("func", "bold", ".nii.gz", sub, ses, None, task, None, None, "/data", path)
+
+
 class TestDiscoverTemplateInputs:
     """Tests for :func:`discover_template_inputs`."""
 
     def test_groups_by_subject(self) -> None:
         """Multi-session subjects yield one TemplateInputs each."""
         df = _df(
-            _brain_row("01", "baseline"),
-            _brain_row("01", "vis2"),
-            _brain_row("02", "baseline"),
-            _brain_row("02", "vis2"),
+            _anat_row("01", "baseline"),
+            _anat_row("01", "vis2"),
+            _anat_row("02", "baseline"),
+            _anat_row("02", "vis2"),
+            _func_row("01", "baseline"),
+            _func_row("01", "vis2"),
+            _func_row("02", "baseline"),
+            _func_row("02", "vis2"),
         )
         inputs, skipped = discover_template_inputs(df)
         assert {ti.sub for ti in inputs} == {"01", "02"}
@@ -77,9 +86,12 @@ def test_groups_by_subject(self) -> None:
     def test_reports_single_session_subject(self) -> None:
         """Single-session subjects are reported separately (bug #19)."""
         df = _df(
-            _brain_row("01", "baseline"),
-            _brain_row("01", "vis2"),
-            _brain_row("02", "baseline"),
+            _anat_row("01", "baseline"),
+            _anat_row("01", "vis2"),
+            _anat_row("02", "baseline"),
+            _func_row("01", "baseline"),
+            _func_row("01", "vis2"),
+            _func_row("02", "baseline"),
         )
         inputs, skipped = discover_template_inputs(df)
         assert [ti.sub for ti in inputs] == ["01"]
@@ -88,9 +100,12 @@ def test_reports_single_session_subject(self) -> None:
     def test_excludes_existing_longitudinal(self) -> None:
         """Pre-existing longitudinal templates are not re-included as inputs."""
         df = _df(
-            _brain_row("01", "baseline"),
-            _brain_row("01", "vis2"),
-            _brain_row("01", "longitudinal"),
+            _anat_row("01", "baseline"),
+            _anat_row("01", "vis2"),
+            _anat_row("01", "longitudinal"),
+            _func_row("01", "baseline"),
+            _func_row("01", "vis2"),
+            _func_row("01", "longitudinal"),
         )
         inputs, skipped = discover_template_inputs(df)
         assert len(inputs) == 1
@@ -111,10 +126,10 @@ def test_excludes_mni_registered_brains(self) -> None:
         duplicate LTA filenames in the mri_robust_template invocation.
         """
         df = _df(
-            _brain_row("01", "test"),
-            _brain_row("01", "test", space="MNI152NLin6Asym"),
-            _brain_row("01", "retest"),
-            _brain_row("01", "retest", space="MNI152NLin6Asym"),
+            _anat_row("01", "test"),
+            _anat_row("01", "test", space="MNI152NLin6Asym"),
+            _anat_row("01", "retest"),
+            _anat_row("01", "retest", space="MNI152NLin6Asym"),
         )
         inputs, skipped = discover_template_inputs(df)
         assert len(inputs) == 1
@@ -131,6 +146,8 @@ def test_writes_template_and_xfms(self, tmp_path: Path) -> None:
         """Template + per-session xfms land at the expected BIDS paths."""
         template_src = tmp_path / "src_template.nii.gz"
         template_src.write_bytes(b"\x00")
+        template_bold_src = tmp_path / "src_bold_template.nii.gz"
+        template_bold_src.write_bytes(b"\x00")
         xfm_baseline = tmp_path / "xfm_baseline.txt"
         xfm_baseline.write_text("baseline")
         xfm_vis2 = tmp_path / "xfm_vis2.txt"
@@ -138,6 +155,7 @@ def test_writes_template_and_xfms(self, tmp_path: Path) -> None:
 
         outputs = LongitudinalTemplateOutputs(
             template=template_src,
+            bold_template=template_bold_src,
             sessions=["baseline", "vis2"],
             transforms=[xfm_baseline, xfm_vis2],
         )

From 06929ef202bc8658783e54789d8f71b58556eb5d Mon Sep 17 00:00:00 2001
From: Jason Kai <21226986+kaitj@users.noreply.github.com>
Date: Fri, 8 May 2026 13:33:48 -0400
Subject: [PATCH 04/12] Replace data loading for long template resampling

---
 src/rbc/bids/longitudinal/anatomical.py         | 2 +-
 src/rbc/core/longitudinal/resampling.py         | 6 +++---
 src/rbc/workflows/longitudinal/template.py      | 4 ++--
 tests/unit/bids/test_longitudinal_anatomical.py | 1 +
 4 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/src/rbc/bids/longitudinal/anatomical.py b/src/rbc/bids/longitudinal/anatomical.py
index 8d8d4472..816b74eb 100644
--- a/src/rbc/bids/longitudinal/anatomical.py
+++ b/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",
diff --git a/src/rbc/core/longitudinal/resampling.py b/src/rbc/core/longitudinal/resampling.py
index da53c285..d84ed789 100644
--- a/src/rbc/core/longitudinal/resampling.py
+++ b/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
diff --git a/src/rbc/workflows/longitudinal/template.py b/src/rbc/workflows/longitudinal/template.py
index 246d36a1..ebc9a7df 100644
--- a/src/rbc/workflows/longitudinal/template.py
+++ b/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,
diff --git a/tests/unit/bids/test_longitudinal_anatomical.py b/tests/unit/bids/test_longitudinal_anatomical.py
index d80f6c89..59cc5064 100644
--- a/tests/unit/bids/test_longitudinal_anatomical.py
+++ b/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 [],

From 11b77227043266aaabd574db143b603fe7a0bc8d Mon Sep 17 00:00:00 2001
From: Jason Kai <21226986+kaitj@users.noreply.github.com>
Date: Fri, 8 May 2026 15:50:54 -0400
Subject: [PATCH 05/12] Resample longitudinal mask for QC

---
 src/rbc/core/longitudinal/resampling.py    | 23 +++++++++++-----------
 src/rbc/orchestration/longitudinal/qc.py   |  5 +++++
 src/rbc/workflows/longitudinal/template.py |  4 ++--
 3 files changed, 18 insertions(+), 14 deletions(-)

diff --git a/src/rbc/core/longitudinal/resampling.py b/src/rbc/core/longitudinal/resampling.py
index d84ed789..422fd57a 100644
--- a/src/rbc/core/longitudinal/resampling.py
+++ b/src/rbc/core/longitudinal/resampling.py
@@ -13,34 +13,33 @@
 from rbc.core.niwrap import generate_exec_folder
 
 
-def resample_template_to_bold_grid(bold_ref: Path, template: Path) -> Path:
+def resample_img_to_bold_grid(bold_ref: Path, img: 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.
+        img: 3D image in target space to resample.
 
     Returns:
-        Resampled template image with BOLD grid
+        Resampled 3D 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)
+    img_obj = nib.nifti1.load(img)
 
     # If 4D, extract first volume
     if len(bold_ref_img.shape) > 3:
         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
+    if bold_ref_img.shape == img_obj.shape:
+        return 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"
+    img_resampled = resample_from_to(img_obj, bold_ref_img)
+    img_resampled_path = (
+        generate_exec_folder("img_resample_to_bold_grid") / "resampled.nii.gz"
     )
-    nib.save(template_img, template_img_path)
-    return template_img_path
+    nib.save(img_resampled, img_resampled_path)
+    return img_resampled_path
diff --git a/src/rbc/orchestration/longitudinal/qc.py b/src/rbc/orchestration/longitudinal/qc.py
index 0fd8b7e0..df597657 100644
--- a/src/rbc/orchestration/longitudinal/qc.py
+++ b/src/rbc/orchestration/longitudinal/qc.py
@@ -21,6 +21,7 @@
     write_longitudinal_qc_tsv,
 )
 from rbc.bids.session import iter_session_files
+from rbc.core.longitudinal.resampling import resample_img_to_bold_grid
 from rbc.core.niwrap import generate_exec_folder
 from rbc.core.qc.registration import registration_qc_metrics
 from rbc.orchestration import Filters, RunnerConfig, init_runner
@@ -67,6 +68,10 @@ def process_qc(
     Returns:
         QC outputs with overlap metrics and pass/fail flag.
     """
+    # Resample longitudinal anatomical mask to bold grid for QC purposes.
+    # Longitudinal processed data are registered to the longitudinal template with
+    # respective modality's native resolution
+    anat_brain_mask = resample_img_to_bold_grid(bold_mask, anat_brain_mask)
     anat_mask_arr = nib.nifti1.load(anat_brain_mask).get_fdata()
     bold_mask_arr = nib.nifti1.load(bold_mask).get_fdata()
     reg_metrics = registration_qc_metrics(anat_mask_arr, bold_mask_arr)
diff --git a/src/rbc/workflows/longitudinal/template.py b/src/rbc/workflows/longitudinal/template.py
index ebc9a7df..efbf2fe7 100644
--- a/src/rbc/workflows/longitudinal/template.py
+++ b/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_grid
+from rbc.core.longitudinal.resampling import resample_img_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_grid(bold_ref, robust.template)
+        bold_ref = resample_img_to_bold_grid(bold_ref, robust.template)
 
     return LongitudinalTemplateOutputs(
         template=robust.template,

From 6553dc5b78375cc5203ac9b03d869d4eb0988389 Mon Sep 17 00:00:00 2001
From: Jason Kai <21226986+kaitj@users.noreply.github.com>
Date: Fri, 8 May 2026 17:09:43 -0400
Subject: [PATCH 06/12] Fix docstrings

---
 src/rbc/bids/longitudinal/template.py   | 2 +-
 src/rbc/core/longitudinal/resampling.py | 8 ++------
 2 files changed, 3 insertions(+), 7 deletions(-)

diff --git a/src/rbc/bids/longitudinal/template.py b/src/rbc/bids/longitudinal/template.py
index 12598201..12894884 100644
--- a/src/rbc/bids/longitudinal/template.py
+++ b/src/rbc/bids/longitudinal/template.py
@@ -21,7 +21,7 @@ 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
+        bold_ref: First BOLD volume for grid reference.
     """
 
     sub: str
diff --git a/src/rbc/core/longitudinal/resampling.py b/src/rbc/core/longitudinal/resampling.py
index 422fd57a..32921011 100644
--- a/src/rbc/core/longitudinal/resampling.py
+++ b/src/rbc/core/longitudinal/resampling.py
@@ -17,22 +17,18 @@ def resample_img_to_bold_grid(bold_ref: Path, img: Path) -> Path:
     """Resample template to BOLD grid if shapes differ.
 
     Args:
-        bold_ref: BOLD reference volume (used for ITK conversion).
+        bold_ref: BOLD reference volume.
         img: 3D image in target space to resample.
 
     Returns:
         Resampled 3D 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)
     img_obj = nib.nifti1.load(img)
 
     # If 4D, extract first volume
     if len(bold_ref_img.shape) > 3:
-        bold_ref_img = nib.four_to_three(bold_ref_img)[0]
+        bold_ref_img = nib.four_to_three(bold_ref_img.slicer[..., 0])[0]
     # If same shape, no need to resample
     if bold_ref_img.shape == img_obj.shape:
         return img

From ee0da2a3213aef7818f028c51b714dd671b123ae Mon Sep 17 00:00:00 2001
From: Jason Kai <21226986+kaitj@users.noreply.github.com>
Date: Fri, 8 May 2026 17:18:12 -0400
Subject: [PATCH 07/12] Rename bold_ref to bold_template due to shadowing

---
 src/rbc/core/longitudinal/resampling.py    | 2 +-
 src/rbc/workflows/longitudinal/template.py | 7 ++++---
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/src/rbc/core/longitudinal/resampling.py b/src/rbc/core/longitudinal/resampling.py
index 32921011..a2e87a1f 100644
--- a/src/rbc/core/longitudinal/resampling.py
+++ b/src/rbc/core/longitudinal/resampling.py
@@ -28,7 +28,7 @@ def resample_img_to_bold_grid(bold_ref: Path, img: Path) -> Path:
 
     # If 4D, extract first volume
     if len(bold_ref_img.shape) > 3:
-        bold_ref_img = nib.four_to_three(bold_ref_img.slicer[..., 0])[0]
+        bold_ref_img = bold_ref_img.slicer[..., 0]
     # If same shape, no need to resample
     if bold_ref_img.shape == img_obj.shape:
         return img
diff --git a/src/rbc/workflows/longitudinal/template.py b/src/rbc/workflows/longitudinal/template.py
index efbf2fe7..f7eee1c0 100644
--- a/src/rbc/workflows/longitudinal/template.py
+++ b/src/rbc/workflows/longitudinal/template.py
@@ -70,12 +70,13 @@ def generate_subject_template(
         in_xfms=robust.transforms,
     )
 
-    if bold_ref is not None:
-        bold_ref = resample_img_to_bold_grid(bold_ref, robust.template)
+    bold_template = (
+        resample_img_to_bold_grid(bold_ref, robust.template) if bold_ref else None
+    )
 
     return LongitudinalTemplateOutputs(
         template=robust.template,
-        bold_template=bold_ref,
+        bold_template=bold_template,
         sessions=list(sessions),
         transforms=itk_xfms,
     )

From 66085656400e3b6e2d93c90ecd400d76bdd51f9e Mon Sep 17 00:00:00 2001
From: Jason Kai <21226986+kaitj@users.noreply.github.com>
Date: Mon, 11 May 2026 15:22:18 -0400
Subject: [PATCH 08/12] Refactor to resample template per task

Templates for different takss _could_ be different resolutions. This refactors the resampling such that a template is generated per task for the longitudinal workflow.
---
 src/rbc/bids/longitudinal/functional.py       |  3 +-
 src/rbc/bids/longitudinal/template.py         | 28 +++++----
 .../orchestration/longitudinal/template.py    |  2 +-
 src/rbc/workflows/longitudinal/template.py    | 18 +++---
 .../unit/bids/test_longitudinal_functional.py | 57 +++++++++++++------
 tests/unit/bids/test_longitudinal_template.py |  2 +-
 6 files changed, 72 insertions(+), 38 deletions(-)

diff --git a/src/rbc/bids/longitudinal/functional.py b/src/rbc/bids/longitudinal/functional.py
index 3f156811..294679c2 100644
--- a/src/rbc/bids/longitudinal/functional.py
+++ b/src/rbc/bids/longitudinal/functional.py
@@ -50,8 +50,9 @@ def resolve_longitudinal_func(
             without=["space"],
         )
 
+    task = func_df["task"].unique()[0]
     return {
-        "template": tpl_q.expect(tpl_df, res="bold", suffix="T1w"),
+        "template": tpl_q.expect(tpl_df, suffix="T1w", res=task),
         "anat_to_template_xfm": tpl_q.expect(
             tpl_df,
             suffix="xfm",
diff --git a/src/rbc/bids/longitudinal/template.py b/src/rbc/bids/longitudinal/template.py
index 12894884..bde54a6a 100644
--- a/src/rbc/bids/longitudinal/template.py
+++ b/src/rbc/bids/longitudinal/template.py
@@ -21,13 +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.
+        bold_ref: Per-session preprocessed BOLD volumes (all tasks).
     """
 
     sub: str
     sessions: list[str]
     files: list[Path]
-    bold_ref: Path | None
+    bold_files: dict[str, Path]
 
 
 def discover_template_inputs(
@@ -58,17 +58,13 @@ def discover_template_inputs(
         # the mri_robust_template invocation.
         pl.col("space").is_null(),
     )
-    bold_ref_rows = df.filter(
+    bold_rows = df.filter(
         pl.col("ses") != "longitudinal",
         pl.col("datatype") == "func",
+        pl.col("desc") == "preproc",
         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] = []
@@ -81,8 +77,18 @@ def discover_template_inputs(
         files = [
             Path(row["root"]) / row["path"] for row in sub_group.iter_rows(named=True)
         ]
+        # Filter for first found session; only single reference per task is needed
+        sub_bold = bold_rows.filter(
+            (pl.col("sub") == sub) & (pl.col("ses") == sessions[0])
+        )
+        bold_files = {
+            row["task"]: Path(row["root"]) / row["path"]
+            for row in sub_bold.iter_rows(named=True)
+        }
         inputs.append(
-            TemplateInputs(sub=sub, sessions=sessions, files=files, bold_ref=bold_ref)
+            TemplateInputs(
+                sub=sub, sessions=sessions, files=files, bold_files=bold_files
+            )
         )
     return inputs, skipped
 
@@ -96,8 +102,8 @@ 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 btask, bold_template in outputs.bold_templates.items():
+        tpl.save(bold_template, res=btask, suffix=Suffix.T1W)
     for ses, xfm in zip(outputs.sessions, outputs.transforms, strict=True):
         ses_label = bids_safe_label(ses)
         tpl.save(
diff --git a/src/rbc/orchestration/longitudinal/template.py b/src/rbc/orchestration/longitudinal/template.py
index 6091e776..a76b0631 100644
--- a/src/rbc/orchestration/longitudinal/template.py
+++ b/src/rbc/orchestration/longitudinal/template.py
@@ -49,7 +49,7 @@ def process_subject(
         sub=inputs.sub,
         sessions=inputs.sessions,
         in_files=inputs.files,
-        bold_ref=inputs.bold_ref,
+        bold_files=inputs.bold_files,
     )
     tpl = pipe_ctx.bids(datatype=Datatype.ANAT).derive(ses="longitudinal")
     export_template(tpl, outputs)
diff --git a/src/rbc/workflows/longitudinal/template.py b/src/rbc/workflows/longitudinal/template.py
index f7eee1c0..5951a405 100644
--- a/src/rbc/workflows/longitudinal/template.py
+++ b/src/rbc/workflows/longitudinal/template.py
@@ -17,7 +17,7 @@
 from rbc.core.longitudinal.resampling import resample_img_to_bold_grid
 
 if TYPE_CHECKING:
-    from collections.abc import Sequence
+    from collections.abc import Mapping, Sequence
     from pathlib import Path
 
 _logger = logging.getLogger("rbc")
@@ -34,7 +34,7 @@ class LongitudinalTemplateOutputs(NamedTuple):
     """
 
     template: Path
-    bold_template: Path | None
+    bold_templates: dict[str, Path]
     sessions: list[str]
     transforms: list[Path]
 
@@ -43,7 +43,7 @@ def generate_subject_template(
     sub: str,
     sessions: Sequence[str],
     in_files: Sequence[Path],
-    bold_ref: Path | None = None,
+    bold_files: Mapping[str, Path],
 ) -> LongitudinalTemplateOutputs:
     """Build a robust template and ITK transforms for one subject.
 
@@ -51,7 +51,7 @@ def generate_subject_template(
         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.
+        bold_files: Reference bold volumes to resample template for functional data.
 
     Returns:
         :class:`LongitudinalTemplateOutputs` ready for BIDS export.
@@ -70,13 +70,15 @@ def generate_subject_template(
         in_xfms=robust.transforms,
     )
 
-    bold_template = (
-        resample_img_to_bold_grid(bold_ref, robust.template) if bold_ref else None
-    )
+    _logger.info("Creating reference volumes for each functional task")
+    bold_templates = {
+        btask: resample_img_to_bold_grid(bfile, robust.template)
+        for btask, bfile in bold_files.items()
+    }
 
     return LongitudinalTemplateOutputs(
         template=robust.template,
-        bold_template=bold_template,
+        bold_templates=bold_templates,
         sessions=list(sessions),
         transforms=itk_xfms,
     )
diff --git a/tests/unit/bids/test_longitudinal_functional.py b/tests/unit/bids/test_longitudinal_functional.py
index 861ba3e5..960cf96b 100644
--- a/tests/unit/bids/test_longitudinal_functional.py
+++ b/tests/unit/bids/test_longitudinal_functional.py
@@ -28,6 +28,7 @@ def _func_row(
     sub: str,
     ses: str,
     suffix: str,
+    task: str,
     desc: str | None = None,
     ext: str = ".nii.gz",
     space: str | None = None,
@@ -38,11 +39,12 @@ def _func_row(
     space_part = f"_space-{space}" if space else ""
     path = (
         f"sub-{sub}/ses-{ses}/func/"
-        f"sub-{sub}_ses-{ses}{space_part}{desc_part}_{suffix}{ext}"
+        f"sub-{sub}_ses-{ses}{space_part}_task-{task}{desc_part}_{suffix}{ext}"
     )
     return {
         "datatype": "func",
         "suffix": suffix,
+        "task": task,
         "ext": ext,
         "sub": sub,
         "ses": ses,
@@ -121,12 +123,17 @@ class TestResolveLongitudinalFunc:
     def test_resolves_single_regressor(self, tmp_path: Path) -> None:
         """Single regressor resolves raw regressor file from derivatives."""
         func_df = _df(
-            _func_row(sub="01", ses="baseline", suffix="sbref"),
-            _func_row(sub="01", ses="baseline", suffix="bold", desc="preproc"),
-            _func_row(sub="01", ses="baseline", suffix="mask", desc="brain"),
+            _func_row(sub="01", ses="baseline", task="rest", suffix="sbref"),
+            _func_row(
+                sub="01", ses="baseline", task="rest", suffix="bold", desc="preproc"
+            ),
+            _func_row(
+                sub="01", ses="baseline", task="rest", suffix="mask", desc="brain"
+            ),
             _func_row(
                 sub="01",
                 ses="baseline",
+                task="rest",
                 suffix="xfm",
                 desc="linearITK",
                 ext=".txt",
@@ -139,13 +146,14 @@ def test_resolves_single_regressor(self, tmp_path: Path) -> None:
             _func_row(
                 sub="01",
                 ses="baseline",
+                task="rest",
                 suffix="regressors",
                 desc="36parameter",
                 ext=".1D",
             ),
         )
         tpl_df = _df(
-            _anat_row(sub="01", ses="longitudinal", res="bold", suffix="T1w"),
+            _anat_row(sub="01", ses="longitudinal", res="rest", suffix="T1w"),
             _anat_row(
                 sub="01",
                 ses="longitudinal",
@@ -189,12 +197,17 @@ def test_resolves_single_regressor(self, tmp_path: Path) -> None:
     def test_resolves_multiple_regressors(self, tmp_path: Path) -> None:
         """Multiple regressors each get their own raw regressor file resolved."""
         func_df = _df(
-            _func_row(sub="01", ses="baseline", suffix="sbref"),
-            _func_row(sub="01", ses="baseline", suffix="bold", desc="preproc"),
-            _func_row(sub="01", ses="baseline", suffix="mask", desc="brain"),
+            _func_row(sub="01", ses="baseline", task="rest", suffix="sbref"),
+            _func_row(
+                sub="01", ses="baseline", task="rest", suffix="bold", desc="preproc"
+            ),
+            _func_row(
+                sub="01", ses="baseline", task="rest", suffix="mask", desc="brain"
+            ),
             _func_row(
                 sub="01",
                 ses="baseline",
+                task="rest",
                 suffix="xfm",
                 desc="linearITK",
                 ext=".txt",
@@ -207,6 +220,7 @@ def test_resolves_multiple_regressors(self, tmp_path: Path) -> None:
             _func_row(
                 sub="01",
                 ses="baseline",
+                task="rest",
                 suffix="regressors",
                 desc="36parameter",
                 ext=".1D",
@@ -214,13 +228,14 @@ def test_resolves_multiple_regressors(self, tmp_path: Path) -> None:
             _func_row(
                 sub="01",
                 ses="baseline",
+                task="rest",
                 suffix="regressors",
                 desc="aCompCor",
                 ext=".1D",
             ),
         )
         tpl_df = _df(
-            _anat_row(sub="01", ses="longitudinal", res="bold", suffix="T1w"),
+            _anat_row(sub="01", ses="longitudinal", res="rest", suffix="T1w"),
             _anat_row(
                 sub="01",
                 ses="longitudinal",
@@ -253,12 +268,17 @@ def test_resolves_multiple_regressors(self, tmp_path: Path) -> None:
     def test_missing_regressor_raises(self, tmp_path: Path) -> None:
         """Requesting a regressor not present in derivatives raises."""
         func_df = _df(
-            _func_row(sub="01", ses="baseline", suffix="sbref"),
-            _func_row(sub="01", ses="baseline", suffix="bold", desc="preproc"),
-            _func_row(sub="01", ses="baseline", suffix="mask", desc="brain"),
+            _func_row(sub="01", ses="baseline", task="rest", suffix="sbref"),
+            _func_row(
+                sub="01", ses="baseline", task="rest", suffix="bold", desc="preproc"
+            ),
+            _func_row(
+                sub="01", ses="baseline", task="rest", suffix="mask", desc="brain"
+            ),
             _func_row(
                 sub="01",
                 ses="baseline",
+                task="rest",
                 suffix="xfm",
                 desc="linearITK",
                 ext=".txt",
@@ -271,13 +291,14 @@ def test_missing_regressor_raises(self, tmp_path: Path) -> None:
             _func_row(
                 sub="01",
                 ses="baseline",
+                task="rest",
                 suffix="regressors",
                 desc="36parameter",
                 ext=".1D",
             ),
         )
         tpl_df = _df(
-            _anat_row(sub="01", ses="longitudinal", res="bold", suffix="T1w"),
+            _anat_row(sub="01", ses="longitudinal", res="rest", suffix="T1w"),
             _anat_row(
                 sub="01",
                 ses="longitudinal",
@@ -307,11 +328,14 @@ def test_missing_regressor_raises(self, tmp_path: Path) -> None:
     def test_bold_mask_mandatory(self, tmp_path: Path) -> None:
         """bold_mask is now resolved with expect(), so missing raises."""
         func_df = _df(
-            _func_row(sub="01", ses="baseline", suffix="sbref"),
-            _func_row(sub="01", ses="baseline", suffix="bold", desc="preproc"),
+            _func_row(sub="01", ses="baseline", task="rest", suffix="sbref"),
+            _func_row(
+                sub="01", ses="baseline", task="rest", suffix="bold", desc="preproc"
+            ),
             _func_row(
                 sub="01",
                 ses="baseline",
+                task="rest",
                 suffix="xfm",
                 desc="linearITK",
                 ext=".txt",
@@ -324,13 +348,14 @@ def test_bold_mask_mandatory(self, tmp_path: Path) -> None:
             _func_row(
                 sub="01",
                 ses="baseline",
+                task="rest",
                 suffix="regressors",
                 desc="36parameter",
                 ext=".1D",
             ),
         )
         tpl_df = _df(
-            _anat_row(sub="01", ses="longitudinal", res="bold", suffix="T1w"),
+            _anat_row(sub="01", ses="longitudinal", res="rest", suffix="T1w"),
             _anat_row(
                 sub="01",
                 ses="longitudinal",
diff --git a/tests/unit/bids/test_longitudinal_template.py b/tests/unit/bids/test_longitudinal_template.py
index f4b8ec7f..8ff7031a 100644
--- a/tests/unit/bids/test_longitudinal_template.py
+++ b/tests/unit/bids/test_longitudinal_template.py
@@ -155,7 +155,7 @@ def test_writes_template_and_xfms(self, tmp_path: Path) -> None:
 
         outputs = LongitudinalTemplateOutputs(
             template=template_src,
-            bold_template=template_bold_src,
+            bold_templates={"test": template_bold_src},
             sessions=["baseline", "vis2"],
             transforms=[xfm_baseline, xfm_vis2],
         )

From 6dc432d085cd664431291c6009e846118854aafc Mon Sep 17 00:00:00 2001
From: Jason Kai <21226986+kaitj@users.noreply.github.com>
Date: Tue, 12 May 2026 10:29:52 -0400
Subject: [PATCH 09/12] Address review comments

- Update stale docstring
- Use "ents['task']" instead of filtering for
- Address de-duping via assertion of grid for unique file paths
- Fix resampling order for mask
---
 src/rbc/bids/longitudinal/functional.py          |  3 ++-
 src/rbc/bids/longitudinal/template.py            | 16 +++++++++++++++-
 src/rbc/core/longitudinal/resampling.py          |  5 +++--
 src/rbc/orchestration/longitudinal/functional.py |  1 +
 src/rbc/orchestration/longitudinal/qc.py         |  2 +-
 src/rbc/workflows/longitudinal/template.py       |  3 ++-
 tests/unit/bids/test_longitudinal_functional.py  |  4 ++++
 7 files changed, 28 insertions(+), 6 deletions(-)

diff --git a/src/rbc/bids/longitudinal/functional.py b/src/rbc/bids/longitudinal/functional.py
index 294679c2..c4cb0eb9 100644
--- a/src/rbc/bids/longitudinal/functional.py
+++ b/src/rbc/bids/longitudinal/functional.py
@@ -23,6 +23,7 @@ def resolve_longitudinal_func(
     tpl_df: pl.DataFrame,
     *,
     ses: str,
+    task: str,
     regressors: Sequence[str] = ("36-parameter",),
 ) -> dict[str, Path | dict[str, Path]]:
     """Resolve inputs for longitudinal functional processing.
@@ -33,6 +34,7 @@ def resolve_longitudinal_func(
         func_df: DataFrame of functional derivatives.
         tpl_df: DataFrame of longitudinal template files.
         ses: Session label (used for template xfm lookup).
+        task: Task entity value to denote BOLD reference for template resampling.
         regressors: Regressor strategy names to resolve raw regressor
             files for.
 
@@ -50,7 +52,6 @@ def resolve_longitudinal_func(
             without=["space"],
         )
 
-    task = func_df["task"].unique()[0]
     return {
         "template": tpl_q.expect(tpl_df, suffix="T1w", res=task),
         "anat_to_template_xfm": tpl_q.expect(
diff --git a/src/rbc/bids/longitudinal/template.py b/src/rbc/bids/longitudinal/template.py
index bde54a6a..6cb25b9a 100644
--- a/src/rbc/bids/longitudinal/template.py
+++ b/src/rbc/bids/longitudinal/template.py
@@ -80,7 +80,21 @@ def discover_template_inputs(
         # Filter for first found session; only single reference per task is needed
         sub_bold = bold_rows.filter(
             (pl.col("sub") == sub) & (pl.col("ses") == sessions[0])
-        )
+        ).unique(subset=("task", "root", "path"))
+        # Check each task is unique, otherwise raise assertion error with details
+        if sub_bold.height != sub_bold["task"].n_unique():
+            conflicts = (
+                sub_bold.filter(pl.col("task").is_duplicated())
+                .group_by("task")
+                .agg(pl.format("{}/{}", "root", "path").alias("paths"))
+            )
+            raise AssertionError(
+                f"Found multiple non-matching grids for subject {sub}:\n"
+                + "\n".join(
+                    f"Task '{row['task']}': {row['paths']}"
+                    for row in conflicts.iter_rows(named=True)
+                )
+            )
         bold_files = {
             row["task"]: Path(row["root"]) / row["path"]
             for row in sub_bold.iter_rows(named=True)
diff --git a/src/rbc/core/longitudinal/resampling.py b/src/rbc/core/longitudinal/resampling.py
index a2e87a1f..ace508d8 100644
--- a/src/rbc/core/longitudinal/resampling.py
+++ b/src/rbc/core/longitudinal/resampling.py
@@ -13,12 +13,13 @@
 from rbc.core.niwrap import generate_exec_folder
 
 
-def resample_img_to_bold_grid(bold_ref: Path, img: Path) -> Path:
+def resample_img_to_bold_grid(bold_ref: Path, img: Path, order: int = 3) -> Path:
     """Resample template to BOLD grid if shapes differ.
 
     Args:
         bold_ref: BOLD reference volume.
         img: 3D image in target space to resample.
+        order: Interpolation order used during resampling
 
     Returns:
         Resampled 3D image with BOLD grid
@@ -33,7 +34,7 @@ def resample_img_to_bold_grid(bold_ref: Path, img: Path) -> Path:
     if bold_ref_img.shape == img_obj.shape:
         return img
 
-    img_resampled = resample_from_to(img_obj, bold_ref_img)
+    img_resampled = resample_from_to(img_obj, bold_ref_img, order=order)
     img_resampled_path = (
         generate_exec_folder("img_resample_to_bold_grid") / "resampled.nii.gz"
     )
diff --git a/src/rbc/orchestration/longitudinal/functional.py b/src/rbc/orchestration/longitudinal/functional.py
index dc971b38..c61e1628 100644
--- a/src/rbc/orchestration/longitudinal/functional.py
+++ b/src/rbc/orchestration/longitudinal/functional.py
@@ -64,6 +64,7 @@ def process_func(
         func_df,
         tpl_df,
         ses=pipe_ctx.ses,  # type: ignore[arg-type]
+        task=ents["task"],
         regressors=regressors,
     )
     func_outputs = functional_longitudinal(**resolved)  # type: ignore[arg-type]
diff --git a/src/rbc/orchestration/longitudinal/qc.py b/src/rbc/orchestration/longitudinal/qc.py
index df597657..aecda392 100644
--- a/src/rbc/orchestration/longitudinal/qc.py
+++ b/src/rbc/orchestration/longitudinal/qc.py
@@ -71,7 +71,7 @@ def process_qc(
     # Resample longitudinal anatomical mask to bold grid for QC purposes.
     # Longitudinal processed data are registered to the longitudinal template with
     # respective modality's native resolution
-    anat_brain_mask = resample_img_to_bold_grid(bold_mask, anat_brain_mask)
+    anat_brain_mask = resample_img_to_bold_grid(bold_mask, anat_brain_mask, order=0)
     anat_mask_arr = nib.nifti1.load(anat_brain_mask).get_fdata()
     bold_mask_arr = nib.nifti1.load(bold_mask).get_fdata()
     reg_metrics = registration_qc_metrics(anat_mask_arr, bold_mask_arr)
diff --git a/src/rbc/workflows/longitudinal/template.py b/src/rbc/workflows/longitudinal/template.py
index 5951a405..24474280 100644
--- a/src/rbc/workflows/longitudinal/template.py
+++ b/src/rbc/workflows/longitudinal/template.py
@@ -28,7 +28,8 @@ class LongitudinalTemplateOutputs(NamedTuple):
 
     Attributes:
         template: Robust within-subject template volume.
-        bold_template: Within-subject template volume resampled to BOLD resolution.
+        bold_templates: Within-subject template volumes resampled to task-specific BOLD
+            resolutions.
         sessions: Session labels in the same order as ``transforms``.
         transforms: Per-session ITK-format session-to-template transforms.
     """
diff --git a/tests/unit/bids/test_longitudinal_functional.py b/tests/unit/bids/test_longitudinal_functional.py
index 960cf96b..fece77c2 100644
--- a/tests/unit/bids/test_longitudinal_functional.py
+++ b/tests/unit/bids/test_longitudinal_functional.py
@@ -176,6 +176,7 @@ def test_resolves_single_regressor(self, tmp_path: Path) -> None:
             func_df,
             tpl_df,
             ses="baseline",
+            task="rest",
             regressors=["36-parameter"],
         )
 
@@ -258,6 +259,7 @@ def test_resolves_multiple_regressors(self, tmp_path: Path) -> None:
             func_df,
             tpl_df,
             ses="baseline",
+            task="rest",
             regressors=["36-parameter", "aCompCor"],
         )
 
@@ -322,6 +324,7 @@ def test_missing_regressor_raises(self, tmp_path: Path) -> None:
                 func_df,
                 tpl_df,
                 ses="baseline",
+                task="rest",
                 regressors=["aCompCor"],
             )
 
@@ -379,6 +382,7 @@ def test_bold_mask_mandatory(self, tmp_path: Path) -> None:
                 func_df,
                 tpl_df,
                 ses="baseline",
+                task="rest",
                 regressors=["36-parameter"],
             )
 

From 35ad7b1ecc1ad589eaad38d4c310d45c6cf55ac3 Mon Sep 17 00:00:00 2001
From: Jason Kai <21226986+kaitj@users.noreply.github.com>
Date: Mon, 18 May 2026 09:51:19 -0400
Subject: [PATCH 10/12] Extract row entities to find refs + file naming

---
 src/rbc/bids/longitudinal/template.py         | 16 ++++------
 src/rbc/orchestration/longitudinal/all.py     |  4 +--
 .../orchestration/longitudinal/anatomical.py  |  2 +-
 .../orchestration/longitudinal/functional.py  |  4 +--
 tests/unit/bids/test_longitudinal_template.py | 29 ++++++++++++++++++-
 .../test_longitudinal_template.py             | 10 +++++++
 6 files changed, 49 insertions(+), 16 deletions(-)

diff --git a/src/rbc/bids/longitudinal/template.py b/src/rbc/bids/longitudinal/template.py
index 6cb25b9a..1e0a243f 100644
--- a/src/rbc/bids/longitudinal/template.py
+++ b/src/rbc/bids/longitudinal/template.py
@@ -7,7 +7,7 @@
 
 import polars as pl
 
-from rbc.bids import Suffix, bids_safe_label
+from rbc.bids import FUNC_GROUP_ENTITIES, Suffix, bids_safe_label
 
 if TYPE_CHECKING:
     from rbc.bids import Bids
@@ -77,23 +77,19 @@ def discover_template_inputs(
         files = [
             Path(row["root"]) / row["path"] for row in sub_group.iter_rows(named=True)
         ]
-        # Filter for first found session; only single reference per task is needed
         sub_bold = bold_rows.filter(
             (pl.col("sub") == sub) & (pl.col("ses") == sessions[0])
-        ).unique(subset=("task", "root", "path"))
+        ).unique(subset=(*FUNC_GROUP_ENTITIES, "root", "path"))
         # Check each task is unique, otherwise raise assertion error with details
-        if sub_bold.height != sub_bold["task"].n_unique():
+        if sub_bold.height != sub_bold.unique().height:
             conflicts = (
-                sub_bold.filter(pl.col("task").is_duplicated())
-                .group_by("task")
+                sub_bold.filter(pl.struct(FUNC_GROUP_ENTITIES).is_duplicated())
+                .group_by(FUNC_GROUP_ENTITIES)
                 .agg(pl.format("{}/{}", "root", "path").alias("paths"))
             )
             raise AssertionError(
                 f"Found multiple non-matching grids for subject {sub}:\n"
-                + "\n".join(
-                    f"Task '{row['task']}': {row['paths']}"
-                    for row in conflicts.iter_rows(named=True)
-                )
+                + "\n".join(str(dict(row)) for row in conflicts.iter_rows(named=True))
             )
         bold_files = {
             row["task"]: Path(row["root"]) / row["path"]
diff --git a/src/rbc/orchestration/longitudinal/all.py b/src/rbc/orchestration/longitudinal/all.py
index bd8902d0..6bc0b1d2 100644
--- a/src/rbc/orchestration/longitudinal/all.py
+++ b/src/rbc/orchestration/longitudinal/all.py
@@ -18,7 +18,7 @@
 from rbc.bids import FUNC_GROUP_ENTITIES, Datatype, Suffix, extract_entities, load_table
 from rbc.bids.longitudinal.template import discover_template_inputs
 from rbc.bids.metrics import export_metrics
-from rbc.bids.session import iter_session_files
+from rbc.bids.session import _FUNC_ENTITY_KEYS, iter_session_files
 from rbc.context import RunContext
 from rbc.orchestration import Filters, RunnerConfig, init_runner
 from rbc.orchestration.longitudinal._iter import iter_sessions_with_template
@@ -124,7 +124,7 @@ def run(
             )
 
             row = func_df.filter(suffix=Suffix.BOLD).row(0, named=True)
-            ents = extract_entities(row, ["task", "run"])
+            ents = extract_entities(row, _FUNC_ENTITY_KEYS)
             func_q = pipe_ctx.bids(datatype=Datatype.FUNC, entities=ents)
             func_long = func_q.derive(space="longitudinal")
 
diff --git a/src/rbc/orchestration/longitudinal/anatomical.py b/src/rbc/orchestration/longitudinal/anatomical.py
index 509116d1..8a5ccfc0 100644
--- a/src/rbc/orchestration/longitudinal/anatomical.py
+++ b/src/rbc/orchestration/longitudinal/anatomical.py
@@ -51,7 +51,7 @@ def process_anat(
         Workflow outputs for in-memory handoff to downstream stages.
     """
     anat_df = anat_df.filter(pl.col("space").is_null())
-    ents = extract_entities(anat_df.row(0, named=True), ["run"])
+    ents = extract_entities(anat_df.row(0, named=True), ["run", "acq", "rec", "echo"])
 
     anat_q = pipe_ctx.bids(datatype=Datatype.ANAT)
     tpl_q = anat_q.derive(ses="longitudinal")
diff --git a/src/rbc/orchestration/longitudinal/functional.py b/src/rbc/orchestration/longitudinal/functional.py
index c61e1628..913084da 100644
--- a/src/rbc/orchestration/longitudinal/functional.py
+++ b/src/rbc/orchestration/longitudinal/functional.py
@@ -10,7 +10,7 @@
     export_longitudinal_func,
     resolve_longitudinal_func,
 )
-from rbc.bids.session import iter_session_files
+from rbc.bids.session import _FUNC_ENTITY_KEYS, iter_session_files
 from rbc.orchestration import Filters, RunnerConfig, init_runner
 from rbc.orchestration.longitudinal._iter import iter_sessions_with_template
 from rbc.workflows.longitudinal.functional import (
@@ -53,7 +53,7 @@ def process_func(
         Workflow outputs for in-memory handoff to downstream stages.
     """
     row = func_df.filter(suffix=Suffix.BOLD).row(0, named=True)
-    ents = extract_entities(row, ["task", "run"])
+    ents = extract_entities(row, list(_FUNC_ENTITY_KEYS))
 
     func_q = pipe_ctx.bids(datatype=Datatype.FUNC, entities=ents)
     tpl_q = pipe_ctx.bids(datatype=Datatype.ANAT).derive(ses="longitudinal")
diff --git a/tests/unit/bids/test_longitudinal_template.py b/tests/unit/bids/test_longitudinal_template.py
index 8ff7031a..71bfe5cb 100644
--- a/tests/unit/bids/test_longitudinal_template.py
+++ b/tests/unit/bids/test_longitudinal_template.py
@@ -23,6 +23,11 @@
     "sub",
     "ses",
     "space",
+    "acq",
+    "dir",
+    "echo",
+    "part",
+    "rec",
     "task",
     "run",
     "desc",
@@ -50,6 +55,11 @@ def _anat_row(sub: str, ses: str, space: str | None = None) -> tuple:
         space,
         None,
         None,
+        None,
+        None,
+        None,
+        None,
+        None,
         "brain",
         "/data",
         path,
@@ -58,7 +68,24 @@ def _anat_row(sub: str, ses: str, space: str | None = None) -> tuple:
 
 def _func_row(sub: str, ses: str, task: str = "rest") -> tuple:
     path = f"sub-{sub}/ses-{ses}/func/sub-{sub}_ses-{ses}_task-{task}_bold.nii.gz"
-    return ("func", "bold", ".nii.gz", sub, ses, None, task, None, None, "/data", path)
+    return (
+        "func",
+        "bold",
+        ".nii.gz",
+        sub,
+        ses,
+        None,
+        None,
+        None,
+        None,
+        None,
+        None,
+        task,
+        None,
+        None,
+        "/data",
+        path,
+    )
 
 
 class TestDiscoverTemplateInputs:
diff --git a/tests/unit/orchestration/test_longitudinal_template.py b/tests/unit/orchestration/test_longitudinal_template.py
index c2b6af28..5cdf8b2f 100644
--- a/tests/unit/orchestration/test_longitudinal_template.py
+++ b/tests/unit/orchestration/test_longitudinal_template.py
@@ -23,6 +23,11 @@
     "sub",
     "ses",
     "space",
+    "acq",
+    "dir",
+    "echo",
+    "part",
+    "rec",
     "task",
     "run",
     "desc",
@@ -42,6 +47,11 @@ def _brain_row(sub: str, ses: str) -> tuple:
         None,
         None,
         None,
+        None,
+        None,
+        None,
+        None,
+        None,
         "brain",
         "/data",
         path,

From 0cdaed6bb1b9ce1990acb0337e010918b1cf0371 Mon Sep 17 00:00:00 2001
From: Jason Kai <21226986+kaitj@users.noreply.github.com>
Date: Tue, 19 May 2026 10:15:07 -0400
Subject: [PATCH 11/12] Address reviews, round 2

- Removed check for uniqueness of bold dataframe
- Update stale docstring: `bold_ref` -> `bold_files`
- Wrap task with `bids_safe_label` when calling `tpl.save`
- Compare affines using `np.allclose` due to floating point precision
- Use a BoldKey NamedTuple as key to unique bold files
---
 src/rbc/bids/longitudinal/template.py         | 47 ++++++++++++-------
 src/rbc/core/longitudinal/resampling.py       |  5 +-
 src/rbc/orchestration/longitudinal/qc.py      |  4 +-
 src/rbc/workflows/longitudinal/template.py    |  6 ++-
 tests/unit/bids/test_longitudinal_template.py |  3 +-
 5 files changed, 42 insertions(+), 23 deletions(-)

diff --git a/src/rbc/bids/longitudinal/template.py b/src/rbc/bids/longitudinal/template.py
index 1e0a243f..cb8ad387 100644
--- a/src/rbc/bids/longitudinal/template.py
+++ b/src/rbc/bids/longitudinal/template.py
@@ -21,13 +21,36 @@ class TemplateInputs(NamedTuple):
         sub: Subject label.
         sessions: Per-input session labels (parallel to ``files``).
         files: Per-session preprocessed T1w brain volumes.
-        bold_ref: Per-session preprocessed BOLD volumes (all tasks).
+        bold_files: Per-session, unique preprocessed BOLD volumes (all tasks).
     """
 
     sub: str
     sessions: list[str]
     files: list[Path]
-    bold_files: dict[str, Path]
+    bold_files: dict[BoldKey, Path]
+
+
+# Use typing library instead of collections for static type hints
+class BoldKey(NamedTuple):
+    """Key with associated entities to use as dict key to represent bold filepath found.
+
+    Attributes:
+        task: Task associated with file.
+        run: Run associated with file.
+        acq: Acquisition associated with file.
+        dir: Direction associated with file.
+        echo: Echo associated with file.
+        part: Part associated with file.
+        rec: Recording associated with file.
+    """
+
+    task: str
+    run: str | None = None
+    acq: str | None = None
+    dir: str | None = None
+    echo: str | None = None
+    part: str | None = None
+    rec: str | None = None
 
 
 def discover_template_inputs(
@@ -80,19 +103,9 @@ def discover_template_inputs(
         sub_bold = bold_rows.filter(
             (pl.col("sub") == sub) & (pl.col("ses") == sessions[0])
         ).unique(subset=(*FUNC_GROUP_ENTITIES, "root", "path"))
-        # Check each task is unique, otherwise raise assertion error with details
-        if sub_bold.height != sub_bold.unique().height:
-            conflicts = (
-                sub_bold.filter(pl.struct(FUNC_GROUP_ENTITIES).is_duplicated())
-                .group_by(FUNC_GROUP_ENTITIES)
-                .agg(pl.format("{}/{}", "root", "path").alias("paths"))
-            )
-            raise AssertionError(
-                f"Found multiple non-matching grids for subject {sub}:\n"
-                + "\n".join(str(dict(row)) for row in conflicts.iter_rows(named=True))
-            )
-        bold_files = {
-            row["task"]: Path(row["root"]) / row["path"]
+        bold_files: dict[BoldKey, Path] = {
+            BoldKey(**{ent: row[ent] for ent in FUNC_GROUP_ENTITIES}): Path(row["root"])
+            / row["path"]
             for row in sub_bold.iter_rows(named=True)
         }
         inputs.append(
@@ -112,8 +125,8 @@ def export_template(tpl: Bids, outputs: LongitudinalTemplateOutputs) -> None:
         outputs: Results from the longitudinal template workflow.
     """
     tpl.save(outputs.template, suffix=Suffix.T1W)
-    for btask, bold_template in outputs.bold_templates.items():
-        tpl.save(bold_template, res=btask, suffix=Suffix.T1W)
+    for bold_key, bold_template in outputs.bold_templates.items():
+        tpl.save(bold_template, res=bids_safe_label(bold_key.task), suffix=Suffix.T1W)
     for ses, xfm in zip(outputs.sessions, outputs.transforms, strict=True):
         ses_label = bids_safe_label(ses)
         tpl.save(
diff --git a/src/rbc/core/longitudinal/resampling.py b/src/rbc/core/longitudinal/resampling.py
index ace508d8..0c1fdde6 100644
--- a/src/rbc/core/longitudinal/resampling.py
+++ b/src/rbc/core/longitudinal/resampling.py
@@ -5,6 +5,7 @@
 from typing import TYPE_CHECKING
 
 import nibabel as nib
+import numpy as np
 from nibabel.processing import resample_from_to
 
 if TYPE_CHECKING:
@@ -31,7 +32,9 @@ def resample_img_to_bold_grid(bold_ref: Path, img: Path, order: int = 3) -> Path
     if len(bold_ref_img.shape) > 3:
         bold_ref_img = bold_ref_img.slicer[..., 0]
     # If same shape, no need to resample
-    if bold_ref_img.shape == img_obj.shape:
+    if bold_ref_img.shape == img_obj.shape and np.allclose(
+        bold_ref_img.affine, img_obj.affine
+    ):
         return img
 
     img_resampled = resample_from_to(img_obj, bold_ref_img, order=order)
diff --git a/src/rbc/orchestration/longitudinal/qc.py b/src/rbc/orchestration/longitudinal/qc.py
index aecda392..33e55dab 100644
--- a/src/rbc/orchestration/longitudinal/qc.py
+++ b/src/rbc/orchestration/longitudinal/qc.py
@@ -20,7 +20,7 @@
     resolve_longitudinal_qc,
     write_longitudinal_qc_tsv,
 )
-from rbc.bids.session import iter_session_files
+from rbc.bids.session import _FUNC_ENTITY_KEYS, iter_session_files
 from rbc.core.longitudinal.resampling import resample_img_to_bold_grid
 from rbc.core.niwrap import generate_exec_folder
 from rbc.core.qc.registration import registration_qc_metrics
@@ -160,7 +160,7 @@ def run(
 
         for func_df, _ in iter_session_files(session, groupby=FUNC_GROUP_ENTITIES):
             row = func_df.filter(suffix=Suffix.BOLD).row(0, named=True)
-            ents = extract_entities(row, ["task", "run"])
+            ents = extract_entities(row, _FUNC_ENTITY_KEYS)
 
             func_q = pipe_ctx.bids(datatype=Datatype.FUNC, entities=ents)
             func_long_q = func_q.derive(space="longitudinal")
diff --git a/src/rbc/workflows/longitudinal/template.py b/src/rbc/workflows/longitudinal/template.py
index 24474280..7225749e 100644
--- a/src/rbc/workflows/longitudinal/template.py
+++ b/src/rbc/workflows/longitudinal/template.py
@@ -20,6 +20,8 @@
     from collections.abc import Mapping, Sequence
     from pathlib import Path
 
+    from rbc.bids.longitudinal.template import BoldKey
+
 _logger = logging.getLogger("rbc")
 
 
@@ -35,7 +37,7 @@ class LongitudinalTemplateOutputs(NamedTuple):
     """
 
     template: Path
-    bold_templates: dict[str, Path]
+    bold_templates: dict[BoldKey, Path]
     sessions: list[str]
     transforms: list[Path]
 
@@ -44,7 +46,7 @@ def generate_subject_template(
     sub: str,
     sessions: Sequence[str],
     in_files: Sequence[Path],
-    bold_files: Mapping[str, Path],
+    bold_files: Mapping[BoldKey, Path],
 ) -> LongitudinalTemplateOutputs:
     """Build a robust template and ITK transforms for one subject.
 
diff --git a/tests/unit/bids/test_longitudinal_template.py b/tests/unit/bids/test_longitudinal_template.py
index 71bfe5cb..25f3a4e5 100644
--- a/tests/unit/bids/test_longitudinal_template.py
+++ b/tests/unit/bids/test_longitudinal_template.py
@@ -7,6 +7,7 @@
 import polars as pl
 
 from rbc.bids.longitudinal.template import (
+    BoldKey,
     discover_template_inputs,
     export_template,
 )
@@ -182,7 +183,7 @@ def test_writes_template_and_xfms(self, tmp_path: Path) -> None:
 
         outputs = LongitudinalTemplateOutputs(
             template=template_src,
-            bold_templates={"test": template_bold_src},
+            bold_templates={BoldKey(task="test"): template_bold_src},
             sessions=["baseline", "vis2"],
             transforms=[xfm_baseline, xfm_vis2],
         )

From b0ca8efb090dedbc420c7478119362ea0abab3bd Mon Sep 17 00:00:00 2001
From: Jason Kai <21226986+kaitj@users.noreply.github.com>
Date: Wed, 20 May 2026 11:44:38 -0400
Subject: [PATCH 12/12] Apply session-to-longitudinal template xfm

---
 src/rbc/core/longitudinal/transform.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/rbc/core/longitudinal/transform.py b/src/rbc/core/longitudinal/transform.py
index 7a147271..e6b3947d 100644
--- a/src/rbc/core/longitudinal/transform.py
+++ b/src/rbc/core/longitudinal/transform.py
@@ -36,6 +36,7 @@ def anat_transform(in_file: Path, template: Path, xfm: Path) -> Path:
     return ants.ants_apply_transforms(
         reference_image=template,
         input_image=in_file,
+        transform=[ants.ants_apply_transforms_transform_file_name(xfm)],
         output=ants.ants_apply_transforms_warped_output("subject_to_template.nii.gz"),
         dimensionality=3,
         interpolation=ants.ants_apply_transforms_linear(),