Skip no-op slice timing correction when timing metadata is absent (#294)

Author: nx10

src/rbc/metadata.py

@@ -117,6 +117,18 @@ def _validate_slice_timing(slice_timing: list[float], tr: float) -> None:
         raise ValueError(msg)
 
 
+def _header_slice_timing(hdr: nib.Nifti1Header) -> list[float] | None:
+    """Extract per-slice acquisition times from the NIfTI header, if present.
+
+    Returns *None* when the header lacks the necessary fields
+    (slice_code, slice_duration, dim_info).
+    """
+    try:
+        return list(hdr.get_slice_times())
+    except nib.spatialimages.HeaderDataError:
+        return None
+
+
 @dataclass(frozen=True)
 class FunctionalMetadata:
     """Validated, immutable metadata for a single BOLD run.
@@ -166,6 +178,23 @@ def load(
 
         slice_timing: list[float] | None = sidecar.get("SliceTiming")
         if slice_timing is not None:
+            _logger.info(
+                "SliceTiming: from BIDS sidecar (%d slices)", len(slice_timing)
+            )
             _validate_slice_timing(slice_timing, tr)
+        else:
+            slice_timing = _header_slice_timing(hdr)
+            if slice_timing is not None:
+                _logger.warning(
+                    "No SliceTiming in BIDS sidecar; "
+                    "falling back to NIfTI header (%d slices)",
+                    len(slice_timing),
+                )
+                _validate_slice_timing(slice_timing, tr)
+            else:
+                _logger.warning(
+                    "No SliceTiming in BIDS sidecar or NIfTI header; "
+                    "slice timing correction will be skipped"
+                )
 
         return cls(tr=tr, slice_timing=slice_timing)

src/rbc/workflows/functional.py

@@ -254,12 +254,18 @@ def single_session_preprocess(
     mc = fsl_motion_correction(in_file=despiked, ref_file=effective_ref)
 
     # 7. Slice timing correction
-    _logger.info("Slice timing correction")
-    st_corrected = slice_timing_correction(
-        in_file=despiked,
-        tr=metadata.tr,
-        tpattern=metadata.slice_timing,
-    )
+    if metadata.slice_timing is not None:
+        _logger.info("Slice timing correction")
+        st_corrected = slice_timing_correction(
+            in_file=despiked,
+            tr=metadata.tr,
+            tpattern=metadata.slice_timing,
+        )
+    else:
+        _logger.info(
+            "Skipping slice timing correction (no SliceTiming in sidecar or header)"
+        )
+        st_corrected = despiked
 
     # 8. Apply pre-STC motion transforms to STC BOLD
     # native-space MC + STC BOLD used in step 12

tests/unit/test_metadata.py

@@ -6,6 +6,7 @@
 from typing import TYPE_CHECKING
 from unittest.mock import MagicMock, patch
 
+import nibabel as nib
 import pytest
 
 from rbc.metadata import (
@@ -146,14 +147,15 @@ def test_load_with_override(self, tmp_path: Path) -> None:
         assert meta.tr == pytest.approx(1.5)
 
     def test_load_no_slice_timing(self, tmp_path: Path) -> None:
-        """load() sets slice_timing to None when absent from sidecar."""
+        """load() sets slice_timing to None when absent from sidecar and header."""
         bold = tmp_path / "bold.nii.gz"
         bold.touch()
 
         mock_hdr = MagicMock()
         mock_hdr.__getitem__ = lambda _, key: (
             [0, 1, 1, 1, 2.0] if key == "pixdim" else None
         )
+        mock_hdr.get_slice_times.side_effect = nib.spatialimages.HeaderDataError()
         mock_img = MagicMock()
         mock_img.header = mock_hdr
 
@@ -168,6 +170,32 @@ def test_load_no_slice_timing(self, tmp_path: Path) -> None:
 
         assert meta.slice_timing is None
 
+    def test_load_slice_timing_from_header(self, tmp_path: Path) -> None:
+        """load() falls back to NIfTI header when sidecar lacks SliceTiming."""
+        bold = tmp_path / "bold.nii.gz"
+        bold.touch()
+
+        header_times = [0.0, 0.5, 1.0, 1.5]
+
+        mock_hdr = MagicMock()
+        mock_hdr.__getitem__ = lambda _, key: (
+            [0, 1, 1, 1, 2.0] if key == "pixdim" else None
+        )
+        mock_hdr.get_slice_times.return_value = header_times
+        mock_img = MagicMock()
+        mock_img.header = mock_hdr
+
+        with (
+            patch(
+                "rbc.metadata.load_bids_metadata",
+                return_value={"RepetitionTime": 2.0},
+            ),
+            patch("rbc.metadata.nib.nifti1.load", return_value=mock_img),
+        ):
+            meta = FunctionalMetadata.load(bold)
+
+        assert meta.slice_timing == header_times
+
     def test_load_missing_tr_raises(self, tmp_path: Path) -> None:
         """load() raises when TR cannot be determined."""
         bold = tmp_path / "bold.nii.gz"