changes to use chunk- entity when multiple FoV are converted in separate niftis for the same series

Author: bpinsard

heudiconv/bids.py

@@ -1088,6 +1088,12 @@ class BIDSFile:
         "mt",
         "part",
         "recording",
+        "chunk",
+        "nuc",
+        "tracksys",
+        "voi",
+        "stain",
+        "trc",
     ]
 
     def __init__(

heudiconv/convert.py

@@ -525,24 +525,35 @@ def update_uncombined_name(
 def update_multiorient_name(
     metadata: dict[str, Any],
     filename: str,
+    iops: set,
 ) -> str:
+    """
+    Insert `_chunk-<num>` entity into filename if data are from a sequence
+    that outputs multiple FoV (localizer, multi-FoV bold)
+
+    Parameters
+    ----------
+    metadata : dict
+        Scan metadata dictionary from BIDS sidecar file.
+    filename : str
+        Incoming filename
+
+    Returns
+    -------
+    filename : str
+        Updated filename with chunk entity added, if appropriate.
+    """
     bids_file = BIDSFile.parse(filename)
-    if bids_file["acq"]:
+    if bids_file["chunk"]:
         lgr.warning(
-            "Not embedding multi-orientation information as `%r` already uses acq- parameter.",
+            "Not embedding multi-orientation information as `%r` already uses chunk- parameter.",
             filename,
         )
         return filename
-    iop = metadata.get("ImageOrientationPatientDICOM")
-    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_file["acq"] = slice_orient
+    iops = sorted(list(iops))
+    bids_file["chunk"] = str(
+        iops.index(str(metadata["ImageOrientationPatientDICOM"])) + 1
+    )
     return str(bids_file)
 
 
@@ -1117,7 +1128,7 @@ def rename_files() -> None:
 
                 if is_multiorient:
                     this_prefix_basename = update_multiorient_name(
-                        bids_meta, this_prefix_basename
+                        bids_meta, this_prefix_basename, iops
                     )
 
             # Fallback option:

heudiconv/tests/test_bids.py

@@ -1385,12 +1385,12 @@ def test_convert_multiorient(
 
     # 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 orient in [1, 2, 3]:
         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)
-            )
+            fname = op.join(
+                outdir, "sub-%s", "anat", "sub-%s_chunk-%d_localizer.%s"
+            ) % (subID, subID, orient, ext)
+            assert op.exists(fname)
 
 
 @pytest.mark.skipif(not have_datalad, reason="no datalad")

heudiconv/tests/test_convert.py

@@ -146,13 +146,15 @@ def test_update_uncombined_name() -> None:
 
 def test_update_multiorient_name() -> None:
     """Unit testing for heudiconv.convert.update_multiorient_name(), which updates
-    filenames with the acq field if appropriate.
+    filenames with the chunk 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_task-Z_acq-sagittal_run-01_bold"
-    out_fn_test = update_multiorient_name(metadata, base_fn)
+    out_fn_true = "sub-X_ses-Y_task-Z_run-01_chunk-1_bold"
+    out_fn_test = update_multiorient_name(
+        metadata, base_fn, set(["[0, 1, 0, 0, 0, -1]"])
+    )
     assert out_fn_test == out_fn_true