feat: rename BIDS files for multi-orientation series.

heudiconv/convert.py

@@ -523,6 +523,35 @@
     return filename
 
 
+def update_multiorient_name(
+    metadata: dict[str, Any],
+    filename: str,
+) -> str:
+    if "acq-" in filename:
+        lgr.warning(
+            "Not embedding multi-orientation information as prefix already uses acq- parameter."
+        )
+        return filename
+    iop = metadata.get("ImageOrientationPatientDICOM")
+    # iop = [round(x) for x in iop]
+    assert isinstance(iop, list)
+    cross_prod = [
+        iop[1] * iop[5] - iop[2] * iop[4],
+        iop[2] * iop[3] - iop[0] * iop[5],
+        iop[0] * iop[4] - iop[1] * iop[3],
+    ]
+    cross_prod = [abs(x) for x in cross_prod]
+    slice_orient = ["sagittal", "coronal", "axial"][cross_prod.index(1)]
+    bids_pairs = filename.split("_")
+    # acq needs to be inserted right after sub- or ses-
+    ses_or_sub_idx = sum(
+        [bids_pair.split("-")[0] in ["sub", "ses"] for bids_pair in bids_pairs]
+    )
+    bids_pairs.insert(ses_or_sub_idx, "acq-%s" % slice_orient)
+    filename = "_".join(bids_pairs)
+    return filename
+
+
 def convert(
     items: list[tuple[str, tuple[str, ...], list[str]]],
     converter: str,
@@ -953,6 +982,7 @@
         echo_times: set[float] = set()
         channel_names: set[str] = set()
         image_types: set[str] = set()
+        iops: set[str] = set()
         for metadata in bids_metas:
             if not metadata:
                 continue
@@ -968,6 +998,10 @@
                 image_types.update(metadata["ImageType"])
             except KeyError:
                 pass
+            try:
+                iops.add(str(metadata["ImageOrientationPatientDICOM"]))
+            except KeyError:
+                pass
 
         is_multiecho = (
             len(set(filter(bool, echo_times))) > 1
@@ -978,6 +1012,7 @@
         is_complex = (
             "M" in image_types and "P" in image_types
         )  # Determine if data are complex (magnitude + phase)
+        is_multiorient = len(iops) > 1
         echo_times_lst = sorted(echo_times)  # also converts to list
         channel_names_lst = sorted(channel_names)  # also converts to list
 
@@ -1008,6 +1043,11 @@
                         bids_meta, this_prefix_basename, channel_names_lst
                     )
 
+                if is_multiorient:
+                    this_prefix_basename = update_multiorient_name(
+                        bids_meta, this_prefix_basename
+                    )
+
             # Fallback option:
             # If we have failed to modify this_prefix_basename, because it didn't fall
             #   into any of the options above, just add the suffix at the end:

heudiconv/heuristics/bids_localizer.py

@@ -0,0 +1,44 @@
+"""Heuristic demonstrating conversion of the Multi-Echo sequences.
+
+It only cares about converting sequences which have _ME_ in their
+series_description and outputs to BIDS.
+"""
+
+from __future__ import annotations
+
+from typing import Optional
+
+from heudiconv.utils import SeqInfo
+
+
+def create_key(
+    template: Optional[str],
+    outtype: tuple[str, ...] = ("nii.gz",),
+    annotation_classes: None = None,
+) -> tuple[str, tuple[str, ...], None]:
+    if template is None or not template:
+        raise ValueError("Template must be a valid format string")
+    return (template, outtype, annotation_classes)
+
+
+def infotodict(
+    seqinfo: list[SeqInfo],
+) -> dict[tuple[str, tuple[str, ...], None], list[str]]:
+    """Heuristic evaluator for determining which runs belong where
+
+    allowed template fields - follow python string module:
+
+    item: index within category
+    subject: participant id
+    seqitem: run number during scanning
+    subindex: sub index within group
+    """
+    localizer = create_key("sub-{subject}/anat/sub-{subject}_localizer")
+
+    info: dict[tuple[str, tuple[str, ...], None], list[str]] = {
+        localizer: [],
+    }
+    for s in seqinfo:
+        if "localizer" in s.series_description:
+            info[localizer].append(s.series_id)
+    return info

heudiconv/heuristics/reproin.py

@@ -406,7 +406,11 @@
         # XXX: skip derived sequences, we don't store them to avoid polluting
         # the directory, unless it is the motion corrected ones
         # (will get _rec-moco suffix)
-        if skip_derived and curr_seqinfo.is_derived and not curr_seqinfo.is_motion_corrected:
+        if (
+            skip_derived
+            and curr_seqinfo.is_derived
+            and not curr_seqinfo.is_motion_corrected
+        ):
             skipped.append(curr_seqinfo.series_id)
             lgr.debug("Ignoring derived data %s", curr_seqinfo.series_id)
             continue
@@ -552,7 +556,10 @@
                         # XXX if we have a known earlier study, we need to always
                         # increase the run counter for phasediff because magnitudes
                         # were not acquired
-                        if get_study_hash([curr_seqinfo]) == "9d148e2a05f782273f6343507733309d":
+                        if (
+                            get_study_hash([curr_seqinfo])
+                            == "9d148e2a05f782273f6343507733309d"
+                        ):
                             current_run += 1
                         else:
                             raise RuntimeError(

heudiconv/tests/test_bids.py

@@ -1369,6 +1369,31 @@ def test_BIDSFile() -> None:
     assert my_bids_file["echo"] == "2"
 
 
+@pytest.mark.skipif(not have_datalad, reason="no datalad")
+def test_convert_multiorient(
+    tmp_path: Path,
+    heuristic: str = "bids_localizer.py",
+    subID: str = "loc",
+) -> None:
+    """Unit test for the case of multi-orient localizer data.
+    The different orientations should be labeled in `acq` entity.
+    """
+    datadir = op.join(TESTS_DATA_PATH, "01-localizer_64ch")
+    outdir = tmp_path / "out"
+    outdir.mkdir()
+    args = gen_heudiconv_args(datadir, str(outdir), subID, heuristic)
+    runner(args)
+
+    # Check that the expected files have been extracted.
+    # This also checks that the "echo" entity comes before "part":
+    for orient in ["sagittal", "coronal", "axial"]:
+        for ext in ["nii.gz", "json"]:
+            assert op.exists(
+                op.join(outdir, "sub-%s", "anat", "sub-%s_acq-%s_localizer.%s")
+                % (subID, subID, orient, ext)
+            )
+
+
 @pytest.mark.skipif(not have_datalad, reason="no datalad")
 def test_ME_mag_phase_conversion(
     monkeypatch: pytest.MonkeyPatch,

heudiconv/tests/test_convert.py

@@ -17,6 +17,7 @@
     bvals_are_zero,
     update_complex_name,
     update_multiecho_name,
+    update_multiorient_name,
     update_uncombined_name,
 )
 from heudiconv.utils import load_heuristic
@@ -143,6 +144,18 @@ def test_update_uncombined_name() -> None:
         update_uncombined_name(metadata, base_fn, set(channel_names))  # type: ignore[arg-type]
 
 
+def test_update_multiorient_name() -> None:
+    """Unit testing for heudiconv.convert.update_multiorient_name(), which updates
+    filenames with the acq field if appropriate.
+    """
+    # Standard name update
+    base_fn = "sub-X_ses-Y_task-Z_run-01_bold"
+    metadata = {"ImageOrientationPatientDICOM": [0, 1, 0, 0, 0, -1]}
+    out_fn_true = "sub-X_ses-Y_acq-sagittal_task-Z_run-01_bold"
+    out_fn_test = update_multiorient_name(metadata, base_fn)
+    assert out_fn_test == out_fn_true
+
+
 def test_b0dwi_for_fmap(tmp_path: Path, caplog: pytest.LogCaptureFixture) -> None:
     """Make sure we raise a warning when .bvec and .bval files
     are present but the modality is not dwi.