[CONV] IXI-to-BIDS modifications to fit BIDS specifications 1.10 (ara…

…mis-lab#1310)

* First pass

* Add dwi files

* Fix number of dwi volumes

* Fix tsv

* Fix broken unit test

clinica/iotools/converters/ixi_to_bids/dwi_b_files/bvals.txt

@@ -0,0 +1 @@
+0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000

clinica/iotools/converters/ixi_to_bids/dwi_b_files/bvecs.txt

@@ -0,0 +1,3 @@
+0.0 1.0 0.0 0.0 -0.179 -0.064 0.711 0.619 0.242 -0.259 -0.817 -0.844 -0.263 0.0 0.745 0.973
+0.0 0.0 -1.0 0.0 0.111 -0.377 -0.052 0.438 -0.784 0.618 -0.170 -0.526 -0.955 -0.969 -0.666 -0.232
+1.0 0.0 0.0 -1.0 0.978 0.924 0.701 0.651 0.571 0.742 0.551 0.106 0.139 -0.248 -0.024 -0.021

clinica/iotools/converters/ixi_to_bids/ixi_to_bids.py

@@ -11,6 +11,7 @@
     check_modalities,
     define_participants,
     read_clinical_data,
+    write_dwi_b_values,
     write_participants,
     write_scans,
     write_sessions,
@@ -65,6 +66,9 @@ def convert(
         )
         write_scans(bids_dir=bids_dir, participant=participant)
 
+    if list(bids_dir.rglob("dwi")):
+        write_dwi_b_values(bids_dir=bids_dir)
+
     readme_data = {
         "link": "https://brain-development.org/ixi-dataset/",
         "desc": (

clinica/iotools/converters/ixi_to_bids/ixi_to_bids_utils.py

@@ -20,9 +20,17 @@
     "write_scans",
     "write_participants",
     "check_modalities",
+    "write_dwi_b_values",
 ]
 
 
+def write_dwi_b_values(bids_dir: Path) -> None:
+    """Writes DWI bval and bvec files at the root of the BIDS directory"""
+    b_folder = Path(__file__).parents[0] / "dwi_b_files"
+    shutil.copy(b_folder / "bvals.txt", bids_dir / "dwi.bval")
+    shutil.copy(b_folder / "bvecs.txt", bids_dir / "dwi.bvec")
+
+
 def _get_subjects_list_from_data(data_directory: Path) -> List[str]:
     return list(
         dict.fromkeys(
@@ -308,7 +316,7 @@ def _write_subject_dti_if_exists(
 
 
 def _find_subject_dti_data(data_directory: Path, subject: str) -> List[Path]:
-    pattern = subject + r"(-\w*){2}-DTI(-\w*){1}.nii.gz$"
+    pattern = subject + r"(-\w*){2}-DTI(-(0[1-9]|[1-9][0-9])){1}.nii.gz$"
     return [
         path
         for path in data_directory.rglob(pattern="IXI*.nii.gz")
@@ -377,7 +385,7 @@ def write_participants(
     participants : List of converted subjects study source ids.
     """
     clinical_data.set_index("source_id", inplace=True, drop=False)
-    clinical_data.assign(
+    clinical_data = clinical_data.assign(
         participant_id=clinical_data.source_id.apply(
             lambda x: bids_id_factory(StudyName.IXI).from_original_study_id(x)
         )

test/unittests/iotools/converters/ixi_to_bids/test_ixi_to_bids_utils.py

@@ -28,12 +28,21 @@
     check_modalities,
     define_participants,
     read_clinical_data,
+    write_dwi_b_values,
     write_participants,
     write_scans,
     write_sessions,
 )
 
 
+def test_write_dwi_b_values(tmp_path):
+    write_dwi_b_values(tmp_path)
+    bvec_files = list(tmp_path.rglob("*.bvec"))
+    bval_files = list(tmp_path.rglob("*.bval"))
+    assert len(bvec_files) == 1 and bvec_files[0].name == "dwi.bvec"
+    assert len(bval_files) == 1 and bval_files[0].name == "dwi.bval"
+
+
 def test_get_subjects_list_from_data(tmp_path):
     for filename in ("IXI1", "IXI123", "IXIaaa", "foo"):
         (tmp_path / f"{filename}_T1w.nii.gz").touch()
@@ -219,7 +228,10 @@ def clinical_data_builder(tmp_path: Path) -> None:
 def test_read_clinical_data_success(tmp_path):
     clinical_data_builder(tmp_path)
     assert (
-        read_clinical_data(tmp_path).eq(formatted_clinical_data_builder()).all().all()
+        read_clinical_data(tmp_path)
+        .eq(formatted_clinical_data_builder().drop("participant_id", axis=1))
+        .all()
+        .all()
     )
 
 
@@ -531,7 +543,7 @@ def test_find_subject_dti_data(tmp_path):
     (tmp_path / "IXI001-Guys-1234-T1.nii.gz").touch()
     (tmp_path / "IXI001-Guys-1234-DTI").touch()
     (tmp_path / "IXI001-Guys-DTI.nii.gz").touch()
-    tmp_image = tmp_path / "IXI001-Guys-1234-DTI-00.nii.gz"
+    tmp_image = tmp_path / "IXI001-Guys-1234-DTI-01.nii.gz"
     tmp_image.touch()
     list_dti = _find_subject_dti_data(data_directory=tmp_path, subject="IXI001")
     assert len(list_dti) == 1 and list_dti[0] == tmp_image
@@ -564,6 +576,7 @@ def formatted_clinical_data_builder() -> pd.DataFrame:
     return pd.DataFrame(
         {
             "source_id": ["IXI001"],
+            "participant_id": ["sub-IXI001"],
             "session_id": ["ses-M000"],
             "acq_time": ["2024-08-23"],
             "sex": ["female"],