diff --git a/heudiconv/convert.py b/heudiconv/convert.py
index 8fc4f100..80fcaa61 100644
--- a/heudiconv/convert.py
+++ b/heudiconv/convert.py
@@ -11,7 +11,7 @@
import shutil
import sys
from types import ModuleType
-from typing import TYPE_CHECKING, Any, List, Optional, cast
+from typing import TYPE_CHECKING, Any, List, Optional, Tuple, cast
import filelock
from nipype import Node
@@ -849,6 +849,56 @@ def nipype_convert(
return eg, prov_file
+def filter_partial_volumes(
+ nii_files: list[str],
+ bids_files: list[str],
+ bids_metas: list[dict[str, Any]],
+) -> Tuple[list[str] | str, list[str] | str, list[Any] | Any]:
+ """filter interrupted 4D scans volumes with missing slices on XA: see dcm2niix #742
+
+ Parameters
+ ----------
+ nii_files : list[str]
+ converted nifti filepaths
+ bids_files: list[str]
+ converted BIDS json filepaths
+ bids_metas : list[dict[str, Any]]
+ list of metadata dict loaded from BIDS json files
+
+ Returns
+ -------
+ nii_files
+ filtered niftis
+ bids_files
+ filtered BIDS jsons
+ bids_metas
+ filtered BIDS metadata
+
+ """
+ partial_volumes = [not metadata.get("RawImage", True) for metadata in bids_metas]
+ no_partial_volumes = not any(partial_volumes) or all(partial_volumes)
+
+ if no_partial_volumes:
+ return nii_files, bids_files, bids_metas
+ else:
+ new_nii_files, new_bids_files, new_bids_metas = [], [], []
+ for fl, bids_file, bids_meta, is_pv in zip(
+ nii_files, bids_files, bids_metas, partial_volumes
+ ):
+ if is_pv:
+ # remove partial volume
+ os.remove(fl)
+ os.remove(bids_file)
+ lgr.warning(f"dropped {fl} partial volume from interrupted series")
+ else:
+ new_nii_files.append(fl)
+ new_bids_files.append(bids_file)
+ new_bids_metas.append(bids_meta)
+ if len(new_nii_files) == 1:
+ return new_nii_files[0], new_bids_files[0], new_bids_metas[0]
+ return new_nii_files, new_bids_files, new_bids_metas
+
+
def save_converted_files(
res: Node,
item_dicoms: list[str],
@@ -885,6 +935,7 @@ def save_converted_files(
bids_outfiles: list[str] = []
res_files = res.outputs.converted_files
+ bids_files = res.outputs.bids
if not len(res_files):
lgr.debug("DICOMs {} were not converted".format(item_dicoms))
@@ -925,6 +976,21 @@ def rename_files() -> None:
# we should provide specific handling for fmap,
# dwi etc which might spit out multiple files
+ # Also copy BIDS files although they might need to
+ # be merged/postprocessed later
+ bids_files = (
+ sorted(bids_files)
+ if len(bids_files) == len(res_files)
+ else [None] * len(res_files)
+ )
+ # preload since will be used in multiple spots
+ bids_metas = [load_json(b) for b in bids_files if b]
+
+ res_files, bids_files, bids_metas = filter_partial_volumes(
+ res_files, bids_files, bids_metas
+ )
+
+ if isinstance(res_files, list):
suffixes = (
[str(i + 1) for i in range(len(res_files))]
if (bids_options is not None)
@@ -941,16 +1007,6 @@ def rename_files() -> None:
)
suffixes = [str(-i - 1) for i in range(len(res_files))]
- # Also copy BIDS files although they might need to
- # be merged/postprocessed later
- bids_files = (
- sorted(res.outputs.bids)
- if len(res.outputs.bids) == len(res_files)
- else [None] * len(res_files)
- )
- # preload since will be used in multiple spots
- bids_metas = [load_json(b) for b in bids_files if b]
-
### Do we have a multi-echo series? ###
# Some Siemens sequences (e.g. CMRR's MB-EPI) set the label 'TE1',
# 'TE2', etc. in the 'ImageType' field. However, other seqs do not
@@ -1041,9 +1097,9 @@ def rename_files() -> None:
else:
outname = "{}.{}".format(prefix, outtype)
safe_movefile(res_files, outname, overwrite)
- if isdefined(res.outputs.bids):
+ if bids_files:
try:
- safe_movefile(res.outputs.bids, outname_bids, overwrite)
+ safe_movefile(bids_files, outname_bids, overwrite)
bids_outfiles.append(outname_bids)
except TypeError: ##catch lists
raise TypeError("Multiple BIDS sidecars detected.")
diff --git a/heudiconv/tests/data/xa_4d_interrupted/MRe.1.3.12.2.1107.5.2.43.167006.2025031213310724946301923 b/heudiconv/tests/data/xa_4d_interrupted/MRe.1.3.12.2.1107.5.2.43.167006.2025031213310724946301923
new file mode 100644
index 00000000..2b687cfc
Binary files /dev/null and b/heudiconv/tests/data/xa_4d_interrupted/MRe.1.3.12.2.1107.5.2.43.167006.2025031213310724946301923 differ
diff --git a/heudiconv/tests/data/xa_4d_interrupted/MRe.1.3.12.2.1107.5.2.43.167006.2025031213314325419905353 b/heudiconv/tests/data/xa_4d_interrupted/MRe.1.3.12.2.1107.5.2.43.167006.2025031213314325419905353
new file mode 100644
index 00000000..5581dd05
Binary files /dev/null and b/heudiconv/tests/data/xa_4d_interrupted/MRe.1.3.12.2.1107.5.2.43.167006.2025031213314325419905353 differ
diff --git a/heudiconv/tests/test_heuristics.py b/heudiconv/tests/test_heuristics.py
index 7f424108..00f1131d 100644
--- a/heudiconv/tests/test_heuristics.py
+++ b/heudiconv/tests/test_heuristics.py
@@ -183,6 +183,25 @@ def test_scout_conversion(tmp_path: Path) -> None:
assert j[HEUDICONV_VERSION_JSON_KEY] == __version__
+def test_partial_xa_conversion(tmp_path: Path) -> None:
+ args = [
+ "-b",
+ "-f",
+ "convertall",
+ "-s",
+ "test",
+ "--minmeta",
+ "--files",
+ op.join(TESTS_DATA_PATH, "xa_4d_interrupted"),
+ "-o",
+ str(tmp_path),
+ ]
+ runner(args)
+ n_output_files = len(list(tmp_path.glob("*.nii.gz")))
+ # partial volumes of interrupted scan should have been removed
+ assert n_output_files == 1
+
+
@pytest.mark.parametrize(
"bidsoptions",
[