From cbf24ba52206e674fbf1a48fa6b6423d977cebe5 Mon Sep 17 00:00:00 2001
From: AliceJoubert <158147135+AliceJoubert@users.noreply.github.com>
Date: Fri, 4 Oct 2024 08:54:26 +0200
Subject: [PATCH 01/13] [FIX] Fix OASIS1 BIDSSubjectID Method (#1312)

---
 clinica/iotools/bids_utils.py             | 2 +-
 test/unittests/iotools/test_bids_utils.py | 3 +--
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/clinica/iotools/bids_utils.py b/clinica/iotools/bids_utils.py
index de47302ad..738882d1b 100644
--- a/clinica/iotools/bids_utils.py
+++ b/clinica/iotools/bids_utils.py
@@ -242,7 +242,7 @@ def from_original_study_id(cls, study_id: str) -> str:
         )
 
     def to_original_study_id(self) -> str:
-        return "OAS1" + self.split("OASIS1")[1] + "MR1"
+        return f"OAS1_{self.split('OASIS1')[1]}_MR1"
 
 
 class OASIS3BIDSSubjectID(BIDSSubjectID):
diff --git a/test/unittests/iotools/test_bids_utils.py b/test/unittests/iotools/test_bids_utils.py
index 6fe0ca75d..65ef601ed 100644
--- a/test/unittests/iotools/test_bids_utils.py
+++ b/test/unittests/iotools/test_bids_utils.py
@@ -102,8 +102,7 @@ def test_study_to_bids_id_value_error(study, study_id):
         (StudyName.GENFI, "MAPT009", "sub-MAPT009"),
         (StudyName.OASIS3, "OAS30001", "sub-OAS30001"),
         (StudyName.HABS, "P_INIBUB", "sub-HABSINIBUB"),
-        # (StudyName.OASIS, "OAS1_0001_MR1", "sub-OASIS10001"),
-        # todo : check OASIS
+        (StudyName.OASIS, "OAS1_0001_MR1", "sub-OASIS10001"),
         (StudyName.IXI, "IXI001", "sub-IXI001"),
     ],
 )

From 3772efdcf30e66f46f3c47367c32f4b05e84dedd Mon Sep 17 00:00:00 2001
From: AliceJoubert <158147135+AliceJoubert@users.noreply.github.com>
Date: Wed, 9 Oct 2024 14:46:23 +0200
Subject: [PATCH 02/13] [FIX] IXI-to-BIDS function `define_participants` should
 output sorted participants list (#1318)

---
 clinica/iotools/converters/ixi_to_bids/ixi_to_bids_utils.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/clinica/iotools/converters/ixi_to_bids/ixi_to_bids_utils.py b/clinica/iotools/converters/ixi_to_bids/ixi_to_bids_utils.py
index 8bebe8643..3f296a280 100644
--- a/clinica/iotools/converters/ixi_to_bids/ixi_to_bids_utils.py
+++ b/clinica/iotools/converters/ixi_to_bids/ixi_to_bids_utils.py
@@ -59,7 +59,7 @@ def define_participants(
 
     list_from_data = _get_subjects_list_from_data(data_directory)
     if subjs_list_path is None:
-        return list_from_data
+        return sorted(list_from_data)
     cprint("Loading a subjects list provided by the user...")
     list_from_file = _get_subjects_list_from_file(subjs_list_path)
     list_filtered = [subject for subject in list_from_file if subject in list_from_data]
@@ -69,7 +69,7 @@ def define_participants(
             f"The subjects : {' , '.join(invalid_subjects)} do not have any associated data inside the directory {data_directory}"
             f" and can not be converted."
         )
-    return list_filtered
+    return sorted(list_filtered)
 
 
 def _rename_clinical_data_to_bids(column: str) -> str:

From 1a6e0fdd5f1ee444f9f8d96d01e4f5a661d2c791 Mon Sep 17 00:00:00 2001
From: AliceJoubert <158147135+AliceJoubert@users.noreply.github.com>
Date: Wed, 9 Oct 2024 17:08:52 +0200
Subject: [PATCH 03/13] [TEST][REF] Move functions specific to OASIS1 converter
 in a dedicated utils file and add unit tests (#1313)

* Move functions from bids_utils to oasis_to_bids_utils + create test script

* WIP 1

* Remove unused optional argument subj_to_remove

* WIP2

* Finish tests

* Fix

* Add last test

* Changes upon suggestions

* Changes 2
---
 clinica/iotools/bids_utils.py                 | 186 +----------------
 .../converters/oasis_to_bids/oasis_to_bids.py |  12 +-
 .../oasis_to_bids/oasis_to_bids_utils.py      | 148 +++++++++++++
 .../oasis_to_bids/test_oasis_to_bids_utils.py | 196 ++++++++++++++++++
 4 files changed, 349 insertions(+), 193 deletions(-)
 create mode 100644 clinica/iotools/converters/oasis_to_bids/oasis_to_bids_utils.py
 create mode 100644 test/unittests/iotools/converters/oasis_to_bids/test_oasis_to_bids_utils.py

diff --git a/clinica/iotools/bids_utils.py b/clinica/iotools/bids_utils.py
index 738882d1b..38c6f1808 100644
--- a/clinica/iotools/bids_utils.py
+++ b/clinica/iotools/bids_utils.py
@@ -464,146 +464,6 @@ def create_participants_df(
     return participant_df
 
 
-def create_sessions_dict_oasis(
-    clinical_data_dir: Path,
-    bids_dir: Path,
-    study_name: StudyName,
-    clinical_specifications_folder: Path,
-    bids_ids: list[str],
-    name_column_ids: str,
-    subj_to_remove: Optional[list[str]] = None,
-    participants_df: Optional[pd.DataFrame] = None,
-) -> dict:
-    """Extract the information regarding the sessions and store them in a dictionary (session M00 only).
-
-    Parameters
-    ----------
-    clinical_data_dir : Path
-        The path to the input folder.
-
-    bids_dir : Path
-        The path to the BIDS directory.
-
-    study_name : StudyName
-        The name of the study (Ex: ADNI).
-
-    clinical_specifications_folder : Path
-        The path to the clinical file.
-
-    bids_ids : list of str
-        The list of bids ids.
-
-    name_column_ids : str
-        The name of the column where the subject ids are stored.
-
-    subj_to_remove : list of str, optional
-        The list of subject IDs to remove.
-
-    participants_df : pd.DataFrame, optional
-        A pandas dataframe that contains the participants data (required for OASIS3 only).
-
-    Returns
-    -------
-    dict :
-        Session dict.
-    """
-    import numpy as np
-
-    from clinica.utils.stream import cprint
-
-    subj_to_remove = subj_to_remove or []
-    location = f"{study_name.value} location"
-    sessions = pd.read_csv(clinical_specifications_folder / "sessions.tsv", sep="\t")
-    sessions_fields = sessions[study_name.value]
-    field_location = sessions[location]
-    sessions_fields_bids = sessions["BIDS CLINICA"]
-    fields_dataset = []
-    fields_bids = []
-    sessions_dict = {}
-
-    for i in range(0, len(sessions_fields)):
-        if not pd.isnull(sessions_fields[i]):
-            fields_bids.append(sessions_fields_bids[i])
-            fields_dataset.append(sessions_fields[i])
-
-    for i in range(0, len(sessions_fields)):
-        # If the i-th field is available
-        if not pd.isnull(sessions_fields[i]):
-            # Load the file
-            tmp = field_location[i].split("/")
-            location = tmp[0]
-            if len(tmp) > 1:
-                sheet = tmp[1]
-            else:
-                sheet = ""
-
-            file_to_read_path = clinical_data_dir / location
-            file_ext = os.path.splitext(location)[1]
-            if file_ext == ".xlsx":
-                file_to_read = pd.read_excel(file_to_read_path, sheet_name=sheet)
-            elif file_ext == ".csv":
-                file_to_read = pd.read_csv(file_to_read_path)
-            else:
-                raise ValueError(
-                    f"Unknown file extension {file_ext}. Expecting either .xlsx or .csv."
-                )
-
-            for r in range(0, len(file_to_read.values)):
-                # Extracts the subject ids columns from the dataframe
-                subj_id = file_to_read.iloc[r][name_column_ids]
-                if hasattr(subj_id, "dtype"):
-                    if subj_id.dtype == np.int64:
-                        subj_id = str(subj_id)
-                # Removes all the - from
-                subj_id_alpha = str(subj_id[0:3] + "IS" + subj_id[3] + subj_id[5:9])
-
-                # Extract the corresponding BIDS id and create the output file if doesn't exist
-                subj_bids = [s for s in bids_ids if subj_id_alpha in s]
-                if len(subj_bids) == 0:
-                    # If the subject is not an excluded one
-                    if subj_id not in subj_to_remove:
-                        cprint(
-                            f"{sessions_fields[i]} for {subj_id} not found in the BIDS converted.",
-                            "info",
-                        )
-                else:
-                    subj_bids = subj_bids[0]
-                    subj_dir = bids_dir / subj_bids
-                    session_names = get_bids_sess_list(subj_dir)
-                    for s in session_names:
-                        s_name = s.replace("ses-", "")
-                        if study_name == StudyName.OASIS3:
-                            row = file_to_read[
-                                file_to_read["MR ID"].str.startswith(subj_id)
-                                & file_to_read["MR ID"].str.endswith(s_name)
-                            ].iloc[0]
-                        else:
-                            row = file_to_read.iloc[r]
-                        if subj_bids not in sessions_dict:
-                            sessions_dict.update({subj_bids: {}})
-                        if s_name not in sessions_dict[subj_bids].keys():
-                            sessions_dict[subj_bids].update({s_name: {"session_id": s}})
-                        (sessions_dict[subj_bids][s_name]).update(
-                            {sessions_fields_bids[i]: row[sessions_fields[i]]}
-                        )
-                        # Calculate the difference in months for OASIS3 only
-                        if (
-                            study_name == StudyName.OASIS3
-                            and sessions_fields_bids[i] == "age"
-                        ):
-                            diff_years = (
-                                float(sessions_dict[subj_bids][s_name]["age"])
-                                - participants_df[
-                                    participants_df["participant_id"] == subj_bids
-                                ]["age_bl"]
-                            )
-                            (sessions_dict[subj_bids][s_name]).update(
-                                {"diff_months": round(float(diff_years) * 12)}
-                            )
-
-    return sessions_dict
-
-
 def create_scans_dict(
     clinical_data_dir: Path,
     study_name: StudyName,
@@ -836,51 +696,6 @@ def write_modality_agnostic_files(
     _write_bidsignore(bids_dir)
 
 
-# todo : move to oasis utils ?
-def write_sessions_tsv(bids_dir: Path, sessions_dict: dict) -> None:
-    """Create <participant_id>_sessions.tsv files.
-
-    Basically writes the content of the function
-    `clinica.iotools.bids_utils.create_sessions_dict` in several TSV files
-    following the BIDS specification.
-
-    Parameters
-    ----------
-    bids_dir : Path
-        The path to the BIDS directory.
-
-    sessions_dict : dict
-        Dictionary containing sessions metadata.
-
-        .. note::
-            This is the output of the function
-            `clinica.iotools.bids_utils.create_sessions_dict`.
-
-    See also
-    --------
-    create_sessions_dict
-    write_scans_tsv
-    """
-    for subject_path in bids_dir.glob("sub-*"):
-        if subject_path.name in sessions_dict:
-            session_df = pd.DataFrame.from_dict(
-                sessions_dict[subject_path.name], orient="index"
-            )
-            cols = session_df.columns.tolist()
-            cols = cols[-1:] + cols[:-1]
-            session_df = session_df[cols]
-        else:
-            print(f"No session data available for {subject_path}")
-            session_df = pd.DataFrame(columns=["session_id"])
-            session_df["session_id"] = pd.Series("M000")
-        session_df = session_df.set_index("session_id").fillna("n/a")
-        session_df.to_csv(
-            subject_path / f"{subject_path.name}_sessions.tsv",
-            sep="\t",
-            encoding="utf8",
-        )
-
-
 def _get_pet_tracer_from_filename(filename: str) -> Tracer:
     """Return the PET tracer from the provided filename.
 
@@ -1227,6 +1042,7 @@ def identify_modality(filename: str) -> Optional[str]:
         return np.nan
 
 
+# todo : use more ?
 def write_to_tsv(df: pd.DataFrame, buffer: Union[Path, BinaryIO]) -> None:
     """Save dataframe as a BIDS-compliant TSV file.
 
diff --git a/clinica/iotools/converters/oasis_to_bids/oasis_to_bids.py b/clinica/iotools/converters/oasis_to_bids/oasis_to_bids.py
index f5d281562..9f0a1808d 100644
--- a/clinica/iotools/converters/oasis_to_bids/oasis_to_bids.py
+++ b/clinica/iotools/converters/oasis_to_bids/oasis_to_bids.py
@@ -108,20 +108,16 @@ def _create_sessions_tsv(
         bids_dir: Path,
         bids_ids: list[str],
     ) -> dict:
-        from clinica.iotools.bids_utils import (
-            StudyName,
-            create_sessions_dict_oasis,
-            write_sessions_tsv,
-        )
+        from .oasis_to_bids_utils import create_sessions_dict, write_sessions_tsv
 
-        sessions_dict = create_sessions_dict_oasis(
+        sessions_dict = create_sessions_dict(
             clinical_data_dir=clinical_data_dir,
             bids_dir=bids_dir,
-            study_name=StudyName.OASIS,
             clinical_specifications_folder=Path(__file__).parents[1] / "specifications",
             bids_ids=bids_ids,
-            name_column_ids="ID",
         )
+
+        # todo : when tested add to create_sessions_dict bc specific to oasis1
         for bids_id in bids_ids:
             sessions_dict[bids_id]["M000"]["diagnosis"] = (
                 "AD" if sessions_dict[bids_id]["M000"]["diagnosis"] > 0 else "CN"
diff --git a/clinica/iotools/converters/oasis_to_bids/oasis_to_bids_utils.py b/clinica/iotools/converters/oasis_to_bids/oasis_to_bids_utils.py
new file mode 100644
index 000000000..1290be8d8
--- /dev/null
+++ b/clinica/iotools/converters/oasis_to_bids/oasis_to_bids_utils.py
@@ -0,0 +1,148 @@
+import os
+from pathlib import Path
+from typing import Iterable
+
+import numpy as np
+import pandas as pd
+
+from clinica.iotools.bids_utils import StudyName, get_bids_sess_list
+from clinica.utils.stream import cprint
+
+__all__ = ["create_sessions_dict", "write_sessions_tsv"]
+
+
+def create_sessions_dict(
+    clinical_data_dir: Path,
+    bids_dir: Path,
+    clinical_specifications_folder: Path,
+    bids_ids: Iterable[str],
+) -> dict:
+    """Extract the information regarding the sessions and store them in a dictionary (session M000 only).
+
+    Parameters
+    ----------
+    clinical_data_dir : Path
+        The path to the input folder.
+
+    bids_dir : Path
+        The path to the BIDS directory.
+
+    clinical_specifications_folder : Path
+        The path to the clinical file.
+
+    bids_ids : list of str
+        The list of bids ids.
+
+    Returns
+    -------
+    dict :
+        Session dict.
+    """
+
+    location = f"{StudyName.OASIS.value} location"
+    sessions = pd.read_csv(clinical_specifications_folder / "sessions.tsv", sep="\t")
+    sessions_fields = sessions[StudyName.OASIS.value]
+    field_location = sessions[location]
+    sessions_fields_bids = sessions["BIDS CLINICA"]
+    fields_dataset = []
+    fields_bids = []
+    sessions_dict = {}
+
+    for i in range(0, len(sessions_fields)):
+        if not pd.isnull(sessions_fields[i]):
+            fields_bids.append(sessions_fields_bids[i])
+            fields_dataset.append(sessions_fields[i])
+
+    for i in range(0, len(sessions_fields)):
+        # If the i-th field is available
+        if not pd.isnull(sessions_fields[i]):
+            # Load the file
+            tmp = field_location[i].split("/")
+            location = tmp[0]
+            if len(tmp) > 1:
+                sheet = tmp[1]
+            else:
+                sheet = ""
+
+            file_to_read_path = clinical_data_dir / location
+            file_ext = os.path.splitext(location)[1]
+            if file_ext == ".xlsx":
+                file_to_read = pd.read_excel(file_to_read_path, sheet_name=sheet)
+            elif file_ext == ".csv":
+                file_to_read = pd.read_csv(file_to_read_path)
+            else:
+                raise ValueError(
+                    f"Unknown file extension {file_ext}. Expecting either .xlsx or .csv."
+                )
+
+            for r in range(0, len(file_to_read.values)):
+                # Extracts the subject ids columns from the dataframe
+                subj_id = file_to_read.iloc[r]["ID"]
+                if hasattr(subj_id, "dtype"):
+                    if subj_id.dtype == np.int64:
+                        subj_id = str(subj_id)
+                # Removes all the - from
+                subj_id_alpha = str(subj_id[0:3] + "IS" + subj_id[3] + subj_id[5:9])
+
+                # Extract the corresponding BIDS id and create the output file if doesn't exist
+                subj_bids = [s for s in bids_ids if subj_id_alpha in s]
+                if subj_bids:
+                    subj_bids = subj_bids[0]
+                    subj_dir = bids_dir / subj_bids
+                    session_names = get_bids_sess_list(subj_dir)
+                    for s in session_names:
+                        s_name = s.replace("ses-", "")
+                        row = file_to_read.iloc[r]
+                        if subj_bids not in sessions_dict:
+                            sessions_dict.update({subj_bids: {}})
+                        if s_name not in sessions_dict[subj_bids].keys():
+                            sessions_dict[subj_bids].update({s_name: {"session_id": s}})
+                        (sessions_dict[subj_bids][s_name]).update(
+                            {sessions_fields_bids[i]: row[sessions_fields[i]]}
+                        )
+
+    return sessions_dict
+
+
+def write_sessions_tsv(bids_dir: Path, sessions_dict: dict) -> None:
+    """Create <participant_id>_sessions.tsv files.
+
+    Basically writes the content of the function
+    `clinica.iotools.bids_utils.create_sessions_dict` in several TSV files
+    following the BIDS specification.
+
+    Parameters
+    ----------
+    bids_dir : Path
+        The path to the BIDS directory.
+
+    sessions_dict : dict
+        Dictionary containing sessions metadata.
+
+        .. note::
+            This is the output of the function
+            `clinica.iotools.bids_utils.create_sessions_dict`.
+
+    See also
+    --------
+    create_sessions_dict
+    write_scans_tsv
+    """
+    for subject_path in bids_dir.glob("sub-*"):
+        if subject_path.name in sessions_dict:
+            session_df = pd.DataFrame.from_dict(
+                sessions_dict[subject_path.name], orient="index"
+            )
+            cols = session_df.columns.tolist()
+            cols = cols[-1:] + cols[:-1]
+            session_df = session_df[cols]
+        else:
+            print(f"No session data available for {subject_path}")
+            session_df = pd.DataFrame(columns=["session_id"])
+            session_df["session_id"] = pd.Series("M000")
+        session_df = session_df.set_index("session_id").fillna("n/a")
+        session_df.to_csv(
+            subject_path / f"{subject_path.name}_sessions.tsv",
+            sep="\t",
+            encoding="utf8",
+        )
diff --git a/test/unittests/iotools/converters/oasis_to_bids/test_oasis_to_bids_utils.py b/test/unittests/iotools/converters/oasis_to_bids/test_oasis_to_bids_utils.py
new file mode 100644
index 000000000..72e9de84a
--- /dev/null
+++ b/test/unittests/iotools/converters/oasis_to_bids/test_oasis_to_bids_utils.py
@@ -0,0 +1,196 @@
+from pathlib import Path
+
+import numpy as np
+import pandas as pd
+import pytest
+from pandas.testing import assert_frame_equal
+
+from clinica.iotools.converters.oasis_to_bids.oasis_to_bids_utils import (
+    create_sessions_dict,
+    write_sessions_tsv,
+)
+
+
+@pytest.fixture
+def clinical_data_path(tmp_path: Path) -> Path:
+    clinical_data_path = tmp_path / "clinical"
+    _build_clinical_data(clinical_data_path)
+    return clinical_data_path
+
+
+def _build_clinical_data(clinical_data_path: Path) -> None:
+    clinical_data_path.mkdir()
+
+    df = pd.DataFrame(
+        {
+            "ID": ["OAS1_0001_MR1", "OAS1_0002_MR1"],
+            "M/F": ["F", "M"],
+            "Hand": ["R", "L"],
+            "Age": [74, 67],
+            "Educ": [2, 2],
+            "SES": [3, 3],
+            "MMSE": [29, 29],
+            "CDR": [0, 0],
+            "eTIV": [1344, 1344],
+            "nWBV": [0.704, 0.645],
+            "ASF": [1.306, 1.100],
+            "Delay": [float("nan"), float("nan")],
+        }
+    )
+    df.to_csv(clinical_data_path / "oasis_cross-sectional.csv", index=False)
+
+    # todo : future with excel
+
+
+@pytest.fixture
+def sessions_path_success(tmp_path: Path) -> Path:
+    sessions_path_success = tmp_path / "spec"
+    _build_spec_sessions_success(sessions_path_success)
+    return sessions_path_success
+
+
+def _build_spec_sessions_success(sessions_path_success: Path) -> None:
+    sessions_path_success.mkdir()
+    spec = pd.DataFrame(
+        {
+            "BIDS CLINICA": ["cdr_global", "MMS", "diagnosis", "foo"],
+            "ADNI": [np.nan, np.nan, np.nan, "foo"],
+            "OASIS": ["CDR", "MMSE", "CDR", np.nan],
+            "OASIS location": [
+                "oasis_cross-sectional.csv",
+                "oasis_cross-sectional.csv",
+                "oasis_cross-sectional.csv",
+                np.nan,
+            ],
+        }
+    )
+    spec.to_csv(sessions_path_success / "sessions.tsv", index=False, sep="\t")
+
+
+@pytest.fixture
+def sessions_path_error(tmp_path: Path) -> Path:
+    sessions_path_error = tmp_path / "spec"
+    _build_spec_sessions_error(sessions_path_error)
+    return sessions_path_error
+
+
+def _build_spec_sessions_error(sessions_path_error: Path) -> None:
+    sessions_path_error.mkdir()
+    spec = pd.DataFrame(
+        {
+            "BIDS CLINICA": ["foo"],
+            "OASIS": ["foo"],
+            "OASIS location": [
+                "foo.csv",
+            ],
+        }
+    )
+    spec.to_csv(sessions_path_error / "sessions.tsv", index=False, sep="\t")
+
+
+@pytest.fixture
+def bids_dir(tmp_path: Path) -> Path:
+    bids_dir = tmp_path / "BIDS"
+    _build_bids_dir(bids_dir)
+    return bids_dir
+
+
+def _build_bids_dir(bids_dir: Path) -> None:
+    (bids_dir / "sub-OASIS10001" / "ses-M000").mkdir(parents=True)
+    (bids_dir / "sub-OASIS10001" / "ses-M006").mkdir(parents=True)
+    (bids_dir / "sub-OASIS10002" / "ses-M000").mkdir(parents=True)
+
+
+@pytest.fixture
+def expected() -> dict:
+    expected = {
+        "sub-OASIS10001": {
+            "M000": {
+                "session_id": "ses-M000",
+                "cdr_global": 0,
+                "MMS": 29,
+                "diagnosis": 0,
+            },
+            "M006": {
+                "session_id": "ses-M006",
+                "cdr_global": 0,
+                "MMS": 29,
+                "diagnosis": 0,
+            },
+        },
+        "sub-OASIS10002": {
+            "M000": {
+                "session_id": "ses-M000",
+                "cdr_global": 0,
+                "MMS": 29,
+                "diagnosis": 0,
+            }
+        },
+    }
+
+    return expected
+
+
+def test_create_sessions_dict_success(
+    tmp_path,
+    clinical_data_path: Path,
+    bids_dir: Path,
+    sessions_path_success: Path,
+    expected: dict,
+):
+    # todo : how does it handle nan inside excel/csv ? verify with excel
+
+    result = create_sessions_dict(
+        clinical_data_path,
+        bids_dir,
+        sessions_path_success,
+        ["sub-OASIS10001", "sub-OASIS10002"],
+    )
+
+    assert result == expected
+
+
+def test_create_sessions_dict_error(
+    tmp_path,
+    clinical_data_path: Path,
+    bids_dir: Path,
+    sessions_path_error: Path,
+    expected: dict,
+):
+    # todo : how does it handle nan inside excel/csv ? verify with excel
+
+    with pytest.raises(FileNotFoundError):
+        create_sessions_dict(
+            clinical_data_path,
+            bids_dir,
+            sessions_path_error,
+            ["sub-OASIS10001", "sub-OASIS10002"],
+        )
+
+
+def test_write_sessions_tsv(
+    tmp_path,
+    clinical_data_path: Path,
+    bids_dir: Path,
+    sessions_path_success: Path,
+    expected: dict,
+):
+    sessions = create_sessions_dict(
+        clinical_data_path,
+        bids_dir,
+        sessions_path_success,
+        ["sub-OASIS10001", "sub-OASIS10002"],
+    )
+    write_sessions_tsv(tmp_path / "BIDS", sessions)
+    sessions_files = list((tmp_path / "BIDS").rglob("*.tsv"))
+    assert len(sessions_files) == 2
+    for file in sessions_files:
+        assert_frame_equal(
+            pd.read_csv(file, sep="\t").set_index("session_id", drop=False),
+            pd.DataFrame(expected[file.parent.name]).T.set_index(
+                "session_id", drop=False
+            ),
+            check_like=True,
+            check_dtype=False,
+        )
+        assert file.name == f"{file.parent.name}_sessions.tsv"

From 949a8edee9868369238f44363af8fe3129c55f14 Mon Sep 17 00:00:00 2001
From: AliceJoubert <158147135+AliceJoubert@users.noreply.github.com>
Date: Thu, 10 Oct 2024 09:26:15 +0200
Subject: [PATCH 04/13] [FIX] OASIS-to-BIDS is not up to date with online data
 (#1321)

* First pass

* Small fix

* Update bids_utils test

* Changes 1'
'

* Make change in oasis utils

* Remove duplicate function
---
 clinica/iotools/bids_utils.py                 |   3 +-
 .../oasis_to_bids/oasis_to_bids_utils.py      |   6 +-
 .../converters/specifications/participant.tsv |  78 +-
 .../converters/specifications/sessions.tsv    | 858 +++++++++---------
 test/unittests/iotools/test_bids_utils.py     |   8 +-
 5 files changed, 476 insertions(+), 477 deletions(-)

diff --git a/clinica/iotools/bids_utils.py b/clinica/iotools/bids_utils.py
index 38c6f1808..19ec84547 100644
--- a/clinica/iotools/bids_utils.py
+++ b/clinica/iotools/bids_utils.py
@@ -360,6 +360,7 @@ def create_participants_df(
 
     fields_bids = ["participant_id"]
     prev_location = ""
+    prev_sheet = 0
     index_to_drop = []
     subjects_to_drop = []
     study_name = StudyName(study_name)
@@ -387,7 +388,7 @@ def create_participants_df(
             tmp = field_location[i].split("/")
             location = tmp[0]
             # If a sheet is available
-            sheet = tmp[1] if len(tmp) > 1 else ""
+            sheet = tmp[1] if len(tmp) > 1 else 0
             # Check if the file to open for a certain field is the same of the previous field
             if location == prev_location and sheet == prev_sheet:
                 pass
diff --git a/clinica/iotools/converters/oasis_to_bids/oasis_to_bids_utils.py b/clinica/iotools/converters/oasis_to_bids/oasis_to_bids_utils.py
index 1290be8d8..89022e6a0 100644
--- a/clinica/iotools/converters/oasis_to_bids/oasis_to_bids_utils.py
+++ b/clinica/iotools/converters/oasis_to_bids/oasis_to_bids_utils.py
@@ -59,11 +59,7 @@ def create_sessions_dict(
             # Load the file
             tmp = field_location[i].split("/")
             location = tmp[0]
-            if len(tmp) > 1:
-                sheet = tmp[1]
-            else:
-                sheet = ""
-
+            sheet = tmp[1] if len(tmp) > 1 else 0
             file_to_read_path = clinical_data_dir / location
             file_ext = os.path.splitext(location)[1]
             if file_ext == ".xlsx":
diff --git a/clinica/iotools/converters/specifications/participant.tsv b/clinica/iotools/converters/specifications/participant.tsv
index 7d80bb8d7..abe689229 100644
--- a/clinica/iotools/converters/specifications/participant.tsv
+++ b/clinica/iotools/converters/specifications/participant.tsv
@@ -1,40 +1,40 @@
 Field	BIDS CLINICA	BIDS format	BIDS type	AIBL	AIBL location	OASIS	OASIS location	OASIS3	OASIS3 location
-BIDS id of the participant	participant_id	Keyword 'sub-' followed by one of the original subject IDs without special characters or symbols	string						
-Second participant id	alternative_id_1		string	RID	aibl_ptdemog_*.csv	ID	oasis_cross-sectional.csv	Subject	oasis3_participants.csv
-Third participant id	alternative_id_2		string						
-Fourth participant id	alternative_id_3		string						
-Type of subj in PrevDemAls dataset	prevdemals_status	A or R (A = patients, R = relatives)	char						
-Date of birth	date_of_birth	YYYY-MM-DD HH:MM:SS	string	PTDOB	aibl_ptdemog_*.csv				
-Sex	sex	M or F	char	PTGENDER	aibl_ptdemog_*.csv	M/F	oasis_cross-sectional.csv	M/F	oasis3_participants.csv
-Educational level	education_level	Free format	string			Educ	oasis_cross-sectional.csv	Education	oasis3_participants.csv
-Deceased	deceased	Y or N							
-Age in years	age_bl	In years with, possibly, decimals	float			Age	oasis_cross-sectional.csv	ageAtEntry	oasis3_participants.csv
-Civil status	marital_status	Free format	string						
-	adni_rid								
-Site in which the patient was studied	site	Free format	string	SITEID	aibl_ptdemog_*.csv				
-	original_study								
-	cdr					CDR	oasis_cross-sectional.csv	cdr	oasis3_participants.csv
-Diagnosis at baseline	diagnosis_bl	AD=Alzheimer's disease - bvFTD=behavioral variant Fronto Temporal Dementia	string			CDR	oasis_cross-sectional.csv	cdr	oasis3_participants.csv
-Score of mmse test at the baseline	mmse_bl								
-APOE (number of E4 alleles)	apoe4	0, 1 or 2 (number of E4 alleles)	int						
-	apoe_gen1			APGEN1	aibl_apoeres_*.csv				
-	apoe_gen2			APGEN2	aibl_apoeres_*.csv				
-	prevdemals_age_at_onset_patients	In years with, possibly, decimals	float						
-Laterality of the subject	laterality					Hand	oasis_cross-sectional.csv	Hand	oasis3_participants.csv
-	inclusion_date	YYYY-MM-DD HH:MM:SS	string						
-									
-	prevdemals_parent_transmitting_ftd	Y or N	char						
-	prevdemals_parent_transmitting_als	Y or N	char						
-	prevdemals_parent_transmitting	father or mother	string						
-Indicate if the genotype is mutated or not	prevdemals_genetic_status_mutated	Y (mutated) or N (not mutated)	bool						
-									
-	prevdemals_aoo_transmitting_parent	in years							
-	prevdemals_family_phenotype_als	Y or N							
-	prevdemals_family_phenotype_ftd	Y or N							
-Average age onset disease in all the family member	prevdemals_aoo_mean_family		float						
-	prevdemals_expected_years_aoo_bl		signed float						
-	age_first_symptoms								
-	clinad_inclusion								
-	clinad_final_inclusion								
-	prevdemals_distance_aoo_transmitting_parent								
-	prevdemals_family_code								
+BIDS id of the participant	participant_id	Keyword 'sub-' followed by one of the original subject IDs without special characters or symbols	string
+Second participant id	alternative_id_1		string	RID	aibl_ptdemog_*.csv	ID	oasis_cross-sectional-5708aa0a98d82080.xlsx	Subject	oasis3_participants.csv
+Third participant id	alternative_id_2		string
+Fourth participant id	alternative_id_3		string
+Type of subj in PrevDemAls dataset	prevdemals_status	A or R (A = patients, R = relatives)	char
+Date of birth	date_of_birth	YYYY-MM-DD HH:MM:SS	string	PTDOB	aibl_ptdemog_*.csv
+Sex	sex	M or F	char	PTGENDER	aibl_ptdemog_*.csv	M/F	oasis_cross-sectional-5708aa0a98d82080.xlsx	M/F	oasis3_participants.csv
+Educational level	education_level	Free format	string			Educ	oasis_cross-sectional-5708aa0a98d82080.xlsx	Education	oasis3_participants.csv
+Deceased	deceased	Y or N
+Age in years	age_bl	In years with, possibly, decimals	float			Age	oasis_cross-sectional-5708aa0a98d82080.xlsx	ageAtEntry	oasis3_participants.csv
+Civil status	marital_status	Free format	string
+	adni_rid
+Site in which the patient was studied	site	Free format	string	SITEID	aibl_ptdemog_*.csv
+	original_study
+	cdr					CDR	oasis_cross-sectional-5708aa0a98d82080.xlsx	cdr	oasis3_participants.csv
+Diagnosis at baseline	diagnosis_bl	AD=Alzheimer's disease - bvFTD=behavioral variant Fronto Temporal Dementia	string			CDR	oasis_cross-sectional-5708aa0a98d82080.xlsx	cdr	oasis3_participants.csv
+Score of mmse test at the baseline	mmse_bl
+APOE (number of E4 alleles)	apoe4	0, 1 or 2 (number of E4 alleles)	int
+	apoe_gen1			APGEN1	aibl_apoeres_*.csv
+	apoe_gen2			APGEN2	aibl_apoeres_*.csv
+	prevdemals_age_at_onset_patients	In years with, possibly, decimals	float
+Laterality of the subject	laterality					Hand	oasis_cross-sectional-5708aa0a98d82080.xlsx	Hand	oasis3_participants.csv
+	inclusion_date	YYYY-MM-DD HH:MM:SS	string
+
+	prevdemals_parent_transmitting_ftd	Y or N	char
+	prevdemals_parent_transmitting_als	Y or N	char
+	prevdemals_parent_transmitting	father or mother	string
+Indicate if the genotype is mutated or not	prevdemals_genetic_status_mutated	Y (mutated) or N (not mutated)	bool
+
+	prevdemals_aoo_transmitting_parent	in years
+	prevdemals_family_phenotype_als	Y or N
+	prevdemals_family_phenotype_ftd	Y or N
+Average age onset disease in all the family member	prevdemals_aoo_mean_family		float
+	prevdemals_expected_years_aoo_bl		signed float
+	age_first_symptoms
+	clinad_inclusion
+	clinad_final_inclusion
+	prevdemals_distance_aoo_transmitting_parent
+	prevdemals_family_code
diff --git a/clinica/iotools/converters/specifications/sessions.tsv b/clinica/iotools/converters/specifications/sessions.tsv
index db4955f65..7d7f23a2d 100644
--- a/clinica/iotools/converters/specifications/sessions.tsv
+++ b/clinica/iotools/converters/specifications/sessions.tsv
@@ -1,431 +1,431 @@
 Field	BIDS CLINICA	BIDS format	BIDS type	INSIGHT	INSIGHT location	CLINAD	AIBL	AIBL location	OASIS	OASIS location	OASIS3	OASIS3 location
-BIDS session id	session_id	Keyword 'ses-' followed by the original session id of each dataset without special characters or symbols	string									
-Date of the examination	examination_date	YYYY-MM-DD HH:MM:SS	string	 		date d'evaluation	EXAMDATE	aibl_neurobat_*.csv				
+BIDS session id	session_id	Keyword 'ses-' followed by the original session id of each dataset without special characters or symbols	string
+Date of the examination	examination_date	YYYY-MM-DD HH:MM:SS	string	 		date d'evaluation	EXAMDATE	aibl_neurobat_*.csv
 Age at the session	age		float				PTDOB	aibl_ptdemog_*.csv			Age	oasis3_sessions.csv
-	current_study	free format										
-	adni_fdg	free format										
-	adni_pib	free format										
-	adni_av45	free format										
-	cdr_global						CDGLOBAL	aibl_cdr_*.csv	CDR	oasis_cross-sectional.csv	cdr	oasis3_sessions.csv
-	cdr_sb											
-	adas11											
-	adas13											
-Mini-mental state exam	MMS		int			MMS	MMSCORE	aibl_mmse_*.csv	MMSE	oasis_cross-sectional.csv	mmse	oasis3_sessions.csv
-	FAQ											
-	adni_ventricles_vol											
-	adni_hippocampus_vol											
-	adni_brain_vol											
-	adni_entorhinal_vol											
-Intracranial volume	adni_icv											
-Diagnosis at current session	diagnosis						DXCURREN	aibl_pdxconv_*.csv	CDR	oasis_cross-sectional.csv	cdr	oasis3_sessions.csv
-	cati_sacha_vol_left_hippocampus	cm3	float	vol_left_hippocampus	Analyses_INSIGHT_M0_20151201/Analyses_HPC_SACHA							
-	cati_sacha_vol_right_hippocampus	cm3	float	vol_right_hippocampus	Analyses_INSIGHT_M0_20151202/Analyses_HPC_SACHA							
-	cati_whasa_volume	cm3	float	volume (cm3)	Analyses_INSIGHT_M0_20151203/Analyses_HPC_WHASA							
-	mattis_attention											
-	mattis_initiation											
-	mattis_construction											
-	mattis_concepts											
-	mattis_memory											
-	MATTIS		int									
-	FBI											
-Verbal Fluency Test	categorical_fluency		int	Categorical Verbal Fluency	Tst_NRO_NP							
-Verbal Fluency Test	p_fluency		int									
-Grober and Buschke test	grober_buschke_free_cued_recall		int									
-Frontal assessment battery	FAB		int			BREF						
-	freesurfer_rh_mean_thickness			rh_MeanThickness_thickness (mm)	Analyses_INSIGHT_M0_20151201/Analyses_thichness_Freesurfer							
-	freesurfer_lh_mean_thickness			lh_MeanThickness_thickness (mm)	Analyses_INSIGHT_M0_20151201/Analyses_thichness_Freesurfer							
-	EQ			EQ_SCORE	TST_NRO_NL.xls/EQ5D							
-	SPPB			Total Score	TST_NRO_NL.xls/SPPB							
-	AD8			AD8_SCORE	Tst_NRO_NP.xlsx/AD8							
-	MEM			MEM_SCORE	Tst_NRO_NP.xlsx/MCQ							
-	AD			AD_SCORE	Tst_NRO_NP.xlsx/AD8							
-Grober and Buschke test	grober_buschke_free_recall		int			RL						
-Grober and Buschke test	grober_buschke_total_recall		int			RT						
-	grober_buschke_free_recall_delayed		int			RLD						
-	grober_buschke_total_recall_delayed		int			RTD						
-	motivation_starkstein			(Starkstein) Motivation scale	Tst_NRO_NP.xlsx/(Starkstein)							
-	verbal_fluency			Lexical Verbal Fluency Score	Tst_NRO_NP.xlsx/(Verbal Fluency)							
-Innotest amyloid/tau index	IATI		float			IATI						
-	clinad_CSF					CSF AD profile						
-	clinad_amyloidB		int			B-Amyloide						
-	clinad_tau		int			Tau						
-	clinad_p_tau		int			P-Tau						
-	clinad_p_tau_Aß		float			PTau/Aß						
-	clinad_delay_MRI_CSF					Délai IRM PL						
-	clinad_date_MRI_closest_to_CSF					Date IRM proche PL						
-												
-	prevdemals_benson_copy											
-	prevdemals_benson_rappel											
-	prevdemals_benson_total											
-	prevdemals_faux_pas											
-	praxies_dexterity											
-	praxies_gesture_kinetic											
-	praxies_non_meaning_gestures											
-	praxies_intransitive gestures											
-	praxies_transitive_gestures											
-	praxies_total											
-	prevdemals_emotion_total											
-	prevdemals_als											
-	prevdemals_ftd											
-												
-												
-												
-												
-												
-												
-	clinad_amnestic_syndrome_of_hippocampal_type					Sd amn hip						
-Number of words that was not cointaned in the original dataset of words	grober_buschke_intrusions					intrusions						
-												
-	clinad_reac_indic					Réac indic						
-	clinad_correct_recognitions					reconnaissances correctes						
-	clinad_false_recognitions					fausses reconnaissnces						
-												
-	clinad_date_csf					Date PL						
-	clinad_spm_vol_gm					Vol_SG						
-	clinad_spm_vol_wm					Vol_SB						
-	clinad_spm_vol_csf					Vol_CSF						
-	clinad_spm_vol_total					Vol_Total						
-	clinad_volbrain_scale_factor					Scale factor						
-	clinad_volbrain_snr		float			SNR						
-	clinad_volbrain_msnr		float			mSNR						
-	clinad_volbrain_qc		float			QC						
-	clinad_volbrain_tissue_wm_cm3		float			Tissue WM cm3						
-	clinad_volbrain_tissue_wm_%		float			Tissue WM %						
-	clinad_volbrain_tissue_gm_cm3		float			Tissue GM cm3						
-	clinad_volbrain_tissue_gm_%		float			Tissue GM %						
-	clinad_volbrain_tissue_csf_cm3		float			Tissue CSF cm3						
-	clinad_volbrain_tissue_csf_%		float			Tissue CSF %						
-	clinad_volbrain_tissue_brain_cm3		float			Tissue Brain cm3						
-	clinad_volbrain_tissue_brain_%		float			Tissue Brain %						
-	clinad_volbrain_tissue_ic_cm3		float			Tissue IC cm3						
-	clinad_volbrain_tissue_ic_%		float			Tissue IC %						
-	clinad_volbrain_cerebrum_total_cm3		float			Cerebrum Total cm3						
-	clinad_volbrain_cerebrum_total_%		float			Cerebrum Total %						
-	clinad_volbrain_cerebrum_t_gm_cm3		float			Cerebrum T GM cm3						
-	clinad_volbrain_cerebrum_t_gm_%		float			Cerebrum T GM %						
-	clinad_volbrain_cerebrum_t_wm_cm3		float			Cerebrum T WM cm3						
-	clinad_volbrain_cerebrum_t_wm_%		float			Cerebrum T WM %						
-	clinad_volbrain_cerebrum_right_cm3		float			Cerebrum Right cm3						
-	clinad_volbrain_cerebrum_right_%		float			Cerebrum Right %						
-	clinad_volbrain_cerebrum_r_gm_cm3		float			Cerebrum R GM cm3						
-	clinad_volbrain_cerebrum_r_gm_%		float			Cerebrum R GM %						
-	clinad_volbrain_cerebrum_r_wm_cm3		float			Cerebrum R WM cm3						
-	clinad_volbrain_cerebrum_r_wm_%		float			Cerebrum R WM %						
-	clinad_volbrain_cerebrum_left_cm3		float			Cerebrum Left cm3						
-	clinad_volbrain_cerebrum_left_%		float			Cerebrum Left %						
-	clinad_volbrain_cerebrum_l_gm_cm3		float			Cerebrum L GM cm3						
-	clinad_volbrain_cerebrum_l_gm_%		float			Cerebrum L GM %						
-	clinad_volbrain_cerebrum_l_wm_cm3		float			Cerebrum L WM cm3						
-	clinad_volbrain_cerebrum_l_wm_%		float			Cerebrum L WM %						
-	clinad_volbrain_cerebrum_assymetry		float			Cerebrum Asymmetry						
-	clinad_volbrain_cerebelum_total_cm3		float			Cerebelum Total cm3						
-	clinad_volbrain_cerebelum_total_%		float			Cerebelum Total %						
-	clinad_volbrain_cerebelum_t_gm_cm3		float			Cerebelum T GM cm3						
-	clinad_volbrain_cerebelum_t_gm_%		float			Cerebelum T GM %						
-	clinad_volbrain_cerebelum_t_wm_cm3		float			Cerebelum T WM cm3						
-	clinad_volbrain_cerebelum_t_wm_%		float			Cerebelum T WM %						
-	clinad_volbrain_cerebelum_right_cm3		float			Cerebelum Right cm3						
-	clinad_volbrain_cerebelum_right_%		float			Cerebelum Right %						
-	clinad_volbrain_cerebelum_r_gm_cm3		float			Cerebelum R GM cm3						
-	clinad_volbrain_cerebelum_r_gm_%		float			Cerebelum R GM %						
-	clinad_volbrain_cerebelum_r_wm_cm3		float			Cerebelum R WM cm3						
-	clinad_volbrain_cerebelum_r_wm_%		float			Cerebelum R WM %						
-	clinad_volbrain_cerebelum_left_cm3		float			Cerebelum Left cm3						
-	clinad_volbrain_cerebelum_left_%		float			Cerebelum Left %						
-	clinad_volbrain_cerebelum_l_gm_cm3		float			Cerebelum L GM cm3						
-	clinad_volbrain_cerebelum_l_gm_%		float			Cerebelum L GM %						
-	clinad_volbrain_cerebelum_l_wm_cm3		float			Cerebelum L WM cm3						
-	clinad_volbrain_cerebelum_l_wm_%		float			Cerebelum L WM %						
-	clinad_volbrain_cerebelum_assymetry		float			Cerebelum Asymmetry						
-	clinad_volbrain_brainstem_cm3		float			Brainstem cm3						
-	clinad_volbrain_brainstem_%		float			Brainstem %						
-	clinad_volbrain_lateral_ventricles_total_cm3		float			Lateral ventricles Total cm3						
-	clinad_volbrain_lateral_ventricles_total_%		float			Lateral ventricles Total %						
-	clinad_volbrain_lateral_ventricles_right_cm3		float			Lateral ventricles Right cm3						
-	clinad_volbrain_lateral_ventricles_right_%		float			Lateral ventricles Right %						
-	clinad_volbrain_lateral_ventricles_left_cm3		float			Lateral ventricles Left cm3						
-	clinad_volbrain_lateral_ventricles_left_%		float			Lateral ventricles Left %						
-	clinad_volbrain_lateral_ventricles_asymmetry		float			Lateral ventricles Asymmetry						
-	clinad_volbrain_caudate_total_cm3		float			Caudate Total cm3						
-	clinad_volbrain_caudate_total_%		float			Caudate Total %						
-	clinad_volbrain_caudate_right_cm3		float			Caudate Right cm3						
-	clinad_volbrain_caudate_right_%		float			Caudate Right %						
-	clinad_volbrain_caudate_left_cm3		float			Caudate Left cm3						
-	clinad_volbrain_caudate_left_%		float			Caudate Left %						
-	clinad_volbrain_caudate_asymmetry		float			Caudate Asymmetry						
-	clinad_volbrain_putamen_total_cm3		float			Putamen Total cm3						
-	clinad_volbrain_putamen_total_%		float			Putamen Total %						
-	clinad_volbrain_putamen_right_cm3		float			Putamen Right cm3						
-	clinad_volbrain_putamen_right_%		float			Putamen Right %						
-	clinad_volbrain_putamen_left_cm3		float			Putamen Left cm3						
-	clinad_volbrain_putamen_left_%		float			Putamen Left %						
-	clinad_volbrain_putamen_asymmetry		float			Putamen Asymmetry						
-	clinad_volbrain_thalamus_total_cm3		float			Thalamus Total cm3						
-	clinad_volbrain_thalamus_total_%		float			Thalamus Total %						
-	clinad_volbrain_thalamus_right_cm3		float			Thalamus Right cm3						
-	clinad_volbrain_thalamus_right_%		float			Thalamus Right %						
-	clinad_volbrain_thalamus_left_cm3		float			Thalamus Left cm3						
-	clinad_volbrain_thalamus_left_%		float			Thalamus Left %						
-	clinad_volbrain_thalamus_asymmetry		float			Thalamus Asymmetry						
-	clinad_volbrain_globus_pallidus_total_cm3		float			Globus Pallidus Total cm3						
-	clinad_volbrain_globus_pallidus_total_%		float			Globus Pallidus Total %						
-	clinad_volbrain_globus_pallidus_right_cm3		float			Globus Pallidus Right cm3						
-	clinad_volbrain_globus_pallidus_right_%		float			Globus Pallidus Right %						
-	clinad_volbrain_globus_pallidus_left_cm3		float			Globus Pallidus Left cm3						
-	clinad_volbrain_globus_pallidus_left_%		float			Globus Pallidus Left %						
-	clinad_volbrain_globus_pallidus_asymmetry		float			Globus Pallidus Asymmetry						
-	clinad_volbrain_hippocampus_total_cm3		float			Hippocampus Total cm3						
-	clinad_volbrain_hippocampus_total_%		float			Hippocampus Total %						
-	clinad_volbrain_hippocampus_right_cm3		float			Hippocampus Right cm3						
-	clinad_volbrain_hippocampus_right_%		float			Hippocampus Right %						
-	clinad_volbrain_hippocampus_left_cm3		float			Hippocampus Left cm3						
-	clinad_volbrain_hippocampus_left_%		float			Hippocampus Left %						
-	clinad_volbrain_hippocampus_asymmetry		float			Hippocampus Asymmetry						
-	clinad_volbrain_amygdala_total_cm3		float			Amygdala Total cm3						
-	clinad_volbrain_amygdala_total_%		float			Amygdala Total %						
-	clinad_volbrain_amygdala_right_cm3		float			Amygdala Right cm3						
-	clinad_volbrain_amygdala_right_%		float			Amygdala Right %						
-	clinad_volbrain_amygdala_left_cm3		float			Amygdala Left cm3						
-	clinad_volbrain_amygdala_left_%		float			Amygdala Left %						
-	clinad_volbrain_amygdala_asymmetry		float			Amygdala Asymmetry						
-	clinad_volbrain_accumbens_total_cm3					Accumbens Total cm3						
-	clinad_volbrain_accumbens_total_%					Accumbens Total %						
-	clinad_volbrain_accumbens_right_cm3					Accumbens Right cm3						
-	clinad_volbrain_accumbens_right_%					Accumbens Right %						
-	clinad_volbrain_accumbens_left_cm3					Accumbens Left cm3						
-	clinad_volbrain_accumbens_left_%					Accumbens Left %						
-	clinad_volbrain_accumbens_asymmetry					Accumbens Asymmetry						
-	clinad_brainreader_id_rm					MR ID						
-	clinad_brainreader_clinical_image_id					Clinical image id						
-	clinad_brainreader_filename					Filename						
-	clinad_brainreader_nr_version					NR version						
-	clinad_brainreader_mtiv_in_ml		float			The measured total intracranial volume (mTIV) in ml						
-	clinad_brainreader_hippocampal_left_right_asymmetry_index		float			Hippocampal Left-Right Asymmetry Index						
-	clinad_brainreader_hippocampal_left_right_asymmetry_index_nr_index		float			Hippocampal Left-Right Asymmetry Index NR Index						
-	clinad_brainreader_hippocampal_left_right_asymmetry_index_z_score		float			Hippocampal Left-Right Asymmetry Index z-score						
-	clinad_brainreader_hippocampal_left_right_asymmetry_index_percentile		float			Hippocampal Left-Right Asymmetry Index percentile						
-	clinad_brainreader_whole_brain_matter_volume_in_ml		float			Whole-Brain-Matter volume in ml						
-	clinad_brainreader_whole_brain_matter_vol_mtiv_ratio		float			Whole-Brain-Matter Vol/mTIV ratio						
-	clinad_brainreader_whole_brain_matter_nr_index		float			Whole-Brain-Matter NR Index						
-	clinad_brainreader_whole_brain_matter_z_score		float			Whole-Brain-Matter z-score						
-	clinad_brainreader_whole_brain_matter_percentile		float			Whole-Brain-Matter percentile						
-	clinad_brainreader_white_matter_volume_in_ml		float			White-Matter volume in ml						
-	clinad_brainreader_white_matter_vol_mtiv_ratio		float			White-Matter Vol/mTIV ratio						
-	clinad_brainreader_white_matter_nr_index		float			White-Matter NR Index						
-	clinad_brainreader_white_matter_z_score		float			White-Matter z-score						
-	clinad_brainreader_white_matter_percentile		float			White-Matter percentile						
-	clinad_brainreader_gray_matter_volume_in_ml		float			Gray-Matter volume in ml						
-	clinad_brainreader_gray_matter_vol_mtiv_ratio		float			Gray-Matter Vol/mTIV ratio						
-	clinad_brainreader_gray_matter_nr_index		float			Gray-Matter NR Index						
-	clinad_brainreader_gray_matter_z_score		float			Gray-Matter z-score						
-	clinad_brainreader_gray_matter_percentile		float			Gray-Matter percentile						
-	clinad_brainreader_csf_dura_volume_in_ml		float			CSF-(+-dura) volume in ml						
-	clinad_brainreader_csf_dura_vol_mtiv_ratio		float			CSF-(+-dura) Vol/mTIV ratio						
-	clinad_brainreader_csf_dura_nr_index		float			CSF-(+-dura) NR Index						
-	clinad_brainreader_csf_dura_z_score		float			CSF-(+-dura) z-score						
-	clinad_brainreader_csf_dura_percentile		float			CSF-(+-dura) percentile						
-	clinad_brainreader_left_hippocampus_volume_in_ml		float			Left-Hippocampus volume in ml						
-	clinad_brainreader_left_hippocampus_vol_mtiv_ratio		float			Left-Hippocampus Vol/mTIV ratio						
-	clinad_brainreader_left_hippocampus_nr_index		float			Left-Hippocampus NR Index						
-	clinad_brainreader_left_hippocampus_z_score		float			Left-Hippocampus z-score						
-	clinad_brainreader_left_hippocampus_percentile		float			Left-Hippocampus percentile						
-	clinad_brainreader_right_hippocampus_volume_in_ml		float			Right-Hippocampus volume in ml						
-	clinad_brainreader_right_hippocampus_vol_mtiv_ratio		float			Right-Hippocampus Vol/mTIV ratio						
-	clinad_brainreader_right_hippocampus_nr_index		float			Right-Hippocampus NR Index						
-	clinad_brainreader_right_hippocampus_z_score		float			Right-Hippocampus z-score						
-	clinad_brainreader_right_hippocampus_percentile		float			Right-Hippocampus percentile						
-	clinad_brainreader_hippocampus_volume_in_ml		float			Hippocampus volume in ml						
-	clinad_brainreader_hippocampus_vol_mtiv_ratio		float			Hippocampus Vol/mTIV ratio						
-	clinad_brainreader_hippocampus_nr_index		float			Hippocampus NR Index						
-	clinad_brainreader_hippocampus_z_score		float			Hippocampus z-score						
-	clinad_brainreader_hippocampus_percentile		float			Hippocampus percentile						
-	clinad_brainreader_left_amygdala_volume_in_ml		float			Left-Amygdala volume in ml						
-	clinad_brainreader_left_amygdala_vol_mtiv_ratio		float			Left-Amygdala Vol/mTIV ratio						
-	clinad_brainreader_left_amygdala_nr_index		float			Left-Amygdala NR Index						
-	clinad_brainreader_left_amygdala_z_score		float			Left-Amygdala z-score						
-	clinad_brainreader_left_amygdala_percentile		float			Left-Amygdala percentile						
-	clinad_brainreader_right_amygdala_volume_in_ml		float			Right-Amygdala volume in ml						
-	clinad_brainreader_right_amygdala_vol_mtiv_ratio		float			Right-Amygdala Vol/mTIV ratio						
-	clinad_brainreader_right_amygdala_nr_index		float			Right-Amygdala NR Index						
-	clinad_brainreader_right_amygdala_z_score		float			Right-Amygdala z-score						
-	clinad_brainreader_right_amygdala_percentile		float			Right-Amygdala percentile						
-	clinad_brainreader_amygdala_volume_in_ml		float			Amygdala volume in ml						
-	clinad_brainreader_amygdala_vol_mtiv_ratio		float			Amygdala Vol/mTIV ratio						
-	clinad_brainreader_amygdala_nr_index		float			Amygdala NR Index						
-	clinad_brainreader_amygdala_z_score		float			Amygdala z-score						
-	clinad_brainreader_amygdala_percentile		float			Amygdala percentile						
-	clinad_brainreader_brain_stem_volume_in_ml		float			Brain-Stem volume in ml						
-	clinad_brainreader_brain_stem_vol_mtiv_ratio		float			Brain-Stem Vol/mTIV ratio						
-	clinad_brainreader_brain_stem_nr_index		float			Brain-Stem NR Index						
-	clinad_brainreader_brain_stem_z_score		float			Brain-Stem z-score						
-	clinad_brainreader_brain_stem_percentile		float			Brain-Stem percentile						
-	clinad_brainreader_caudate_volume_in_ml		float			Caudate volume in ml						
-	clinad_brainreader_caudate_vol_mtiv_ratio		float			Caudate Vol/mTIV ratio						
-	clinad_brainreader_caudate_nr_index		float			Caudate NR Index						
-	clinad_brainreader_caudate_z_score		float			Caudate z-score						
-	clinad_brainreader_caudate_percentile		float			Caudate percentile						
-	clinad_brainreader_left_caudate_volume_in_ml		float			Left-Caudate volume in ml						
-	clinad_brainreader_left_caudate_vol_mtiv_ratio		float			Left-Caudate Vol/mTIV ratio						
-	clinad_brainreader_left_caudate_nr_index		float			Left-Caudate NR Index						
-	clinad_brainreader_left_caudate_z_score		float			Left-Caudate z-score						
-	clinad_brainreader_left_caudate_percentile		float			Left-Caudate percentile						
-	clinad_brainreader_right_caudate_volume_in_ml		float			Right-Caudate volume in ml						
-	clinad_brainreader_right_caudate_vol_mtiv_ratio		float			Right-Caudate Vol/mTIV ratio						
-	clinad_brainreader_right_caudate_nr_index		float			Right-Caudate NR Index						
-	clinad_brainreader_right_caudate_z_score		float			Right-Caudate z-score						
-	clinad_brainreader_right_caudate_percentile		float			Right-Caudate percentile						
-	clinad_brainreader_left_cerebellum_volume_in_ml		float			Left-Cerebellum volume in ml						
-	clinad_brainreader_left_cerebellum_vol_mtiv_ratio		float			Left-Cerebellum Vol/mTIV ratio						
-	clinad_brainreader_left_cerebellum_nr_index		float			Left-Cerebellum NR Index						
-	clinad_brainreader_left_cerebellum_z_score		float			Left-Cerebellum z-score						
-	clinad_brainreader_left_cerebellum_percentile		float			Left-Cerebellum percentile						
-	clinad_brainreader_right_cerebellum_volume_in_ml		float			Right-Cerebellum volume in ml						
-	clinad_brainreader_right_cerebellum_vol_mtiv_ratio		float			Right-Cerebellum Vol/mTIV ratio						
-	clinad_brainreader_right_cerebellum_nr_index		float			Right-Cerebellum NR Index						
-	clinad_brainreader_right_cerebellum_z_score		float			Right-Cerebellum z-score						
-	clinad_brainreader_right_cerebellum_percentile		float			Right-Cerebellum percentile						
-	clinad_brainreader_cerebellum_volume_in_ml		float			Cerebellum volume in ml						
-	clinad_brainreader_cerebellum_vol_mtiv_ratio		float			Cerebellum Vol/mTIV ratio						
-	clinad_brainreader_cerebellum_nr_index		float			Cerebellum NR Index						
-	clinad_brainreader_cerebellum_z_score		float			Cerebellum z-score						
-	clinad_brainreader_cerebellum_percentile		float			Cerebellum percentile						
-	clinad_brainreader_lateral_ventricle_volume_in_ml		float			Lateral-Ventricle volume in ml						
-	clinad_brainreader_lateral_ventricle_vol_mtiv_ratio		float			Lateral-Ventricle Vol/mTIV ratio						
-	clinad_brainreader_lateral_ventricle_nr_index		float			Lateral-Ventricle NR Index						
-	clinad_brainreader_lateral_ventricle_z_score		float			Lateral-Ventricle z-score						
-	clinad_brainreader_lateral_ventricle_percentile		float			Lateral-Ventricle percentile						
-	clinad_brainreader_left_lateral_ventricle_volume_in_ml		float			Left-Lateral-Ventricle volume in ml						
-	clinad_brainreader_left_lateral_ventricle_vol_mtiv_ratio		float			Left-Lateral-Ventricle Vol/mTIV ratio						
-	clinad_brainreader_left_lateral_ventricle_nr_index		float			Left-Lateral-Ventricle NR Index						
-	clinad_brainreader_left_lateral_ventricle_z_score		float			Left-Lateral-Ventricle z-score						
-	clinad_brainreader_left_lateral_ventricle_percentile		float			Left-Lateral-Ventricle percentile						
-	clinad_brainreader_right_lateral_ventricle_volume_in_ml		float			Right-Lateral-Ventricle volume in ml						
-	clinad_brainreader_right_lateral_ventricle_vol_mtiv_ratio		float			Right-Lateral-Ventricle Vol/mTIV ratio						
-	clinad_brainreader_right_lateral_ventricle_nr_index		float			Right-Lateral-Ventricle NR Index						
-	clinad_brainreader_right_lateral_ventricle_z_score		float			Right-Lateral-Ventricle z-score						
-	clinad_brainreader_right_lateral_ventricle_percentile		float			Right-Lateral-Ventricle percentile						
-	clinad_brainreader_putamen_volume_in_ml		float			Putamen volume in ml						
-	clinad_brainreader_putamen_vol_mtiv_ratio		float			Putamen Vol/mTIV ratio						
-	clinad_brainreader_putamen_nr_index		float			Putamen NR Index						
-	clinad_brainreader_putamen_z_score		float			Putamen z-score						
-	clinad_brainreader_putamen_percentile		float			Putamen percentile						
-	clinad_brainreader_left_putamen_volume_in_ml		float			Left-Putamen volume in ml						
-	clinad_brainreader_left_putamen_vol_mtiv_ratio		float			Left-Putamen Vol/mTIV ratio						
-	clinad_brainreader_left_putamen_nr_index		float			Left-Putamen NR Index						
-	clinad_brainreader_left_putamen_z_score		float			Left-Putamen z-score						
-	clinad_brainreader_left_putamen_percentile		float			Left-Putamen percentile						
-	clinad_brainreader_right_putamen_volume_in_ml		float			Right-Putamen volume in ml						
-	clinad_brainreader_right_putamen_vol_mtiv_ratio		float			Right-Putamen Vol/mTIV ratio						
-	clinad_brainreader_right_putamen_nr_index		float			Right-Putamen NR Index						
-	clinad_brainreader_right_putamen_z_score		float			Right-Putamen z-score						
-	clinad_brainreader_right_putamen_percentile		float			Right-Putamen percentile						
-	clinad_brainreader_thalamus_volume_in_ml		float			Thalamus volume in ml						
-	clinad_brainreader_thalamus_vol_mtiv_ratio		float			Thalamus Vol/mTIV ratio						
-	clinad_brainreader_thalamus_nr_index		float			Thalamus NR Index						
-	clinad_brainreader_thalamus_z_score		float			Thalamus z-score						
-	clinad_brainreader_thalamus_percentile		float			Thalamus percentile						
-	clinad_brainreader_left_thalamus_volume_in_ml		float			Left-Thalamus volume in ml						
-	clinad_brainreader_left_thalamus_vol_mtiv_ratio		float			Left-Thalamus Vol/mTIV ratio						
-	clinad_brainreader_left_thalamus_nr_index		float			Left-Thalamus NR Index						
-	clinad_brainreader_left_thalamus_z_score		float			Left-Thalamus z-score						
-	clinad_brainreader_left_thalamus_percentile		float			Left-Thalamus percentile						
-	clinad_brainreader_right_thalamus_volume_in_ml		float			Right-Thalamus volume in ml						
-	clinad_brainreader_right_thalamus_vol_mtiv_ratio		float			Right-Thalamus Vol/mTIV ratio						
-	clinad_brainreader_right_thalamus_nr_index		float			Right-Thalamus NR Index						
-	clinad_brainreader_right_thalamus_z_score		float			Right-Thalamus z-score						
-	clinad_brainreader_right_thalamus_percentile		float			Right-Thalamus percentile						
-	clinad_brainreader_ventral_diencephalon_volume_in_ml		float			Ventral-Diencephalon volume in ml						
-	clinad_brainreader_ventral_diencephalon_vol_mtiv_ratio		float			Ventral-Diencephalon Vol/mTIV ratio						
-	clinad_brainreader_ventral_diencephalon_nr_index		float			Ventral-Diencephalon NR Index						
-	clinad_brainreader_ventral_diencephalon_z_score		float			Ventral-Diencephalon z-score						
-	clinad_brainreader_ventral_diencephalon_percentile		float			Ventral-Diencephalon percentile						
-	clinad_brainreader_left_ventral_diencephalon_volume_in_ml		float			Left-Ventral-Diencephalon volume in ml						
-	clinad_brainreader_left_ventral_diencephalon_vol_mtiv_ratio		float			Left-Ventral-Diencephalon Vol/mTIV ratio						
-	clinad_brainreader_left_ventral_diencephalon_nr_index		float			Left-Ventral-Diencephalon NR Index						
-	clinad_brainreader_left_ventral_diencephalon_z_score		float			Left-Ventral-Diencephalon z-score						
-	clinad_brainreader_left_ventral_diencephalon_percentile		float			Left-Ventral-Diencephalon percentile						
-	clinad_brainreader_right_ventral_diencephalon_volume_in_ml		float			Right-Ventral-Diencephalon volume in ml						
-	clinad_brainreader_right_ventral_diencephalon_vol_mtiv_ratio		float			Right-Ventral-Diencephalon Vol/mTIV ratio						
-	clinad_brainreader_right_ventral_diencephalon_nr_index		float			Right-Ventral-Diencephalon NR Index						
-	clinad_brainreader_right_ventral_diencephalon_z_score		float			Right-Ventral-Diencephalon z-score						
-	clinad_brainreader_right_ventral_diencephalon_percentile		float			Right-Ventral-Diencephalon percentile						
-	clinad_brainreader_left_frontal_lobe_volume_in_ml		float			Left-Frontal-Lobe volume in ml						
-	clinad_brainreader_left_frontal_lobe_vol_mtiv_ratio		float			Left-Frontal-Lobe Vol/mTIV ratio						
-	clinad_brainreader_left_frontal_lobe_nr_index		float			Left-Frontal-Lobe NR Index						
-	clinad_brainreader_left_frontal_lobe_z_score		float			Left-Frontal-Lobe z-score						
-	clinad_brainreader_left_frontal_lobe_percentile		float			Left-Frontal-Lobe percentile						
-	clinad_brainreader_right_frontal_lobe_volume_in_ml		float			Right-Frontal-Lobe volume in ml						
-	clinad_brainreader_right_frontal_lobe_vol_mtiv_ratio		float			Right-Frontal-Lobe Vol/mTIV ratio						
-	clinad_brainreader_right_frontal_lobe_nr_index		float			Right-Frontal-Lobe NR Index						
-	clinad_brainreader_right_frontal_lobe_z_score		float			Right-Frontal-Lobe z-score						
-	clinad_brainreader_right_frontal_lobe_percentile		float			Right-Frontal-Lobe percentile						
-	clinad_brainreader_left_parietal_lobe_volume_in_ml		float			Left-Parietal-Lobe volume in ml						
-	clinad_brainreader_left_parietal_lobe_vol_mtiv_ratio		float			Left-Parietal-Lobe Vol/mTIV ratio						
-	clinad_brainreader_left_parietal_lobe_nr_index		float			Left-Parietal-Lobe NR Index						
-	clinad_brainreader_left_parietal_lobe_z_score		float			Left-Parietal-Lobe z-score						
-	clinad_brainreader_left_parietal_lobe_percentile		float			Left-Parietal-Lobe percentile						
-	clinad_brainreader_right_parietal_lobe_volume_in_ml		float			Right-Parietal-Lobe volume in ml						
-	clinad_brainreader_right_parietal_lobe_vol_mtiv_ratio		float			Right-Parietal-Lobe Vol/mTIV ratio						
-	clinad_brainreader_right_parietal_lobe_nr_index		float			Right-Parietal-Lobe NR Index						
-	clinad_brainreader_right_parietal_lobe_z_score		float			Right-Parietal-Lobe z-score						
-	clinad_brainreader_right_parietal_lobe_percentile		float			Right-Parietal-Lobe percentile						
-	clinad_brainreader_left_occipital_lobe_volume_in_ml		float			Left-Occipital-Lobe volume in ml						
-	clinad_brainreader_left_occipital_lobe_vol_mtiv_ratio		float			Left-Occipital-Lobe Vol/mTIV ratio						
-	clinad_brainreader_left_occipital_lobe_nr_index		float			Left-Occipital-Lobe NR Index						
-	clinad_brainreader_left_occipital_lobe_z_score		float			Left-Occipital-Lobe z-score						
-	clinad_brainreader_left_occipital_lobe_percentile		float			Left-Occipital-Lobe percentile						
-	clinad_brainreader_right_occipital_lobe_volume_in_ml		float			Right-Occipital-Lobe volume in ml						
-	clinad_brainreader_right_occipital_lobe_vol_mtiv_ratio		float			Right-Occipital-Lobe Vol/mTIV ratio						
-	clinad_brainreader_right_occipital_lobe_nr_index		float			Right-Occipital-Lobe NR Index						
-	clinad_brainreader_right_occipital_lobe_z_score		float			Right-Occipital-Lobe z-score						
-	clinad_brainreader_right_occipital_lobe_percentile		float			Right-Occipital-Lobe percentile						
-	clinad_brainreader_left_temporal_lobe_volume_in_ml		float			Left-Temporal-Lobe volume in ml						
-	clinad_brainreader_left_temporal_lobe_vol_mtiv_ratio		float			Left-Temporal-Lobe Vol/mTIV ratio						
-	clinad_brainreader_left_temporal_lobe_nr_index		float			Left-Temporal-Lobe NR Index						
-	clinad_brainreader_left_temporal_lobe_z_score		float			Left-Temporal-Lobe z-score						
-	clinad_brainreader_left_temporal_lobe_percentile		float			Left-Temporal-Lobe percentile						
-	clinad_brainreader_right_temporal_lobe_volume_in_ml		float			Right-Temporal-Lobe volume in ml						
-	clinad_brainreader_right_temporal_lobe_vol_mtiv_ratio		float			Right-Temporal-Lobe Vol/mTIV ratio						
-	clinad_brainreader_right_temporal_lobe_nr_index		float			Right-Temporal-Lobe NR Index						
-	clinad_brainreader_right_temporal_lobe_z_score		float			Right-Temporal-Lobe z-score						
-	clinad_brainreader_right_temporal_lobe_percentile		float			Right-Temporal-Lobe percentile						
-	clinad_brainreader_frontal_lobe_volume_in_ml		float			Frontal-Lobe volume in ml						
-	clinad_brainreader_frontal_lobe_vol_mtiv_ratio		float			Frontal-Lobe Vol/mTIV ratio						
-	clinad_brainreader_frontal_lobe_nr_index		float			Frontal-Lobe NR Index						
-	clinad_brainreader_frontal_lobe_z_score		float			Frontal-Lobe z-score						
-	clinad_brainreader_frontal_lobe_percentile		float			Frontal-Lobe percentile						
-	clinad_brainreader_parietal_lobe_volume_in_ml		float			Parietal-Lobe volume in ml						
-	clinad_brainreader_parietal_lobe_vol_mtiv_ratio		float			Parietal-Lobe Vol/mTIV ratio						
-	clinad_brainreader_parietal_lobe_nr_index		float			Parietal-Lobe NR Index						
-	clinad_brainreader_parietal_lobe_z_score		float			Parietal-Lobe z-score						
-	clinad_brainreader_parietal_lobe_percentile		float			Parietal-Lobe percentile						
-	clinad_brainreader_occipital_lobe_volume_in_ml		float			Occipital-Lobe volume in ml						
-	clinad_brainreader_occipital_lobe_vol_mtiv_ratio		float			Occipital-Lobe Vol/mTIV ratio						
-	clinad_brainreader_occipital_lobe_nr_index		float			Occipital-Lobe NR Index						
-	clinad_brainreader_occipital_lobe_z_score		float			Occipital-Lobe z-score						
-	clinad_brainreader_occipital_lobe_percentile		float			Occipital-Lobe percentile						
-	clinad_brainreader_temporal_lobe_volume_in_ml		float			Temporal-Lobe volume in ml						
-	clinad_brainreader_temporal_lobe_vol_mtiv_ratio		float			Temporal-Lobe Vol/mTIV ratio						
-	clinad_brainreader_temporal_lobe_nr_index		float			Temporal-Lobe NR Index						
-	clinad_brainreader_temporal_lobe_z_score		float			Temporal-Lobe z-score						
-	clinad_brainreader_temporal_lobe_percentile		float			Temporal-Lobe percentile						
-	clinad_brainreader_left_pallidum_volume_in_ml		float			Left-Pallidum volume in ml						
-	clinad_brainreader_left_pallidum_vol_mtiv_ratio		float			Left-Pallidum Vol/mTIV ratio						
-	clinad_brainreader_left_pallidum_nr_index		float			Left-Pallidum NR Index						
-	clinad_brainreader_left_pallidum_z_score		float			Left-Pallidum z-score						
-	clinad_brainreader_left_pallidum_percentile		float			Left-Pallidum percentile						
-	clinad_brainreader_right_pallidum_volume_in_ml		float			Right-Pallidum volume in ml						
-	clinad_brainreader_right_pallidum_vol_mtiv_ratio		float			Right-Pallidum Vol/mTIV ratio						
-	clinad_brainreader_right_pallidum_nr_index		float			Right-Pallidum NR Index						
-	clinad_brainreader_right_pallidum_z_score		float			Right-Pallidum z-score						
-	clinad_brainreader_right_pallidum_percentile		float			Right-Pallidum percentile						
-	clinad_brainreader_pallidum_volume_in_ml		float			Pallidum volume in ml						
-	clinad_brainreader_pallidum_vol_mtiv_ratio		float			Pallidum Vol/mTIV ratio						
-	clinad_brainreader_pallidum_nr_index		float			Pallidum NR Index						
-	clinad_brainreader_pallidum_z_score		float			Pallidum z-score						
-	clinad_brainreader_pallidum_percentile		float			Pallidum percentile						
-	clinad_brainreader_pallidum_volume_in_ml		float			Pallidum volume in ml						
-	clinad_brainreader_pallidum_vol_mtiv_ratio		float			Pallidum Vol/mTIV ratio						
-	clinad_brainreader_pallidum_nr_index		float			Pallidum NR Index						
-	clinad_brainreader_pallidum_z_score		float			Pallidum z-score						
-	clinad_brainreader_pallidum_percentile		float			Pallidum percentile						
+	current_study	free format
+	adni_fdg	free format
+	adni_pib	free format
+	adni_av45	free format
+	cdr_global						CDGLOBAL	aibl_cdr_*.csv	CDR	oasis_cross-sectional-5708aa0a98d82080.xlsx	cdr	oasis3_sessions.csv
+	cdr_sb
+	adas11
+	adas13
+Mini-mental state exam	MMS		int			MMS	MMSCORE	aibl_mmse_*.csv	MMSE	oasis_cross-sectional-5708aa0a98d82080.xlsx	mmse	oasis3_sessions.csv
+	FAQ
+	adni_ventricles_vol
+	adni_hippocampus_vol
+	adni_brain_vol
+	adni_entorhinal_vol
+Intracranial volume	adni_icv
+Diagnosis at current session	diagnosis						DXCURREN	aibl_pdxconv_*.csv	CDR	oasis_cross-sectional-5708aa0a98d82080.xlsx	cdr	oasis3_sessions.csv
+	cati_sacha_vol_left_hippocampus	cm3	float	vol_left_hippocampus	Analyses_INSIGHT_M0_20151201/Analyses_HPC_SACHA
+	cati_sacha_vol_right_hippocampus	cm3	float	vol_right_hippocampus	Analyses_INSIGHT_M0_20151202/Analyses_HPC_SACHA
+	cati_whasa_volume	cm3	float	volume (cm3)	Analyses_INSIGHT_M0_20151203/Analyses_HPC_WHASA
+	mattis_attention
+	mattis_initiation
+	mattis_construction
+	mattis_concepts
+	mattis_memory
+	MATTIS		int
+	FBI
+Verbal Fluency Test	categorical_fluency		int	Categorical Verbal Fluency	Tst_NRO_NP
+Verbal Fluency Test	p_fluency		int
+Grober and Buschke test	grober_buschke_free_cued_recall		int
+Frontal assessment battery	FAB		int			BREF
+	freesurfer_rh_mean_thickness			rh_MeanThickness_thickness (mm)	Analyses_INSIGHT_M0_20151201/Analyses_thichness_Freesurfer
+	freesurfer_lh_mean_thickness			lh_MeanThickness_thickness (mm)	Analyses_INSIGHT_M0_20151201/Analyses_thichness_Freesurfer
+	EQ			EQ_SCORE	TST_NRO_NL.xls/EQ5D
+	SPPB			Total Score	TST_NRO_NL.xls/SPPB
+	AD8			AD8_SCORE	Tst_NRO_NP.xlsx/AD8
+	MEM			MEM_SCORE	Tst_NRO_NP.xlsx/MCQ
+	AD			AD_SCORE	Tst_NRO_NP.xlsx/AD8
+Grober and Buschke test	grober_buschke_free_recall		int			RL
+Grober and Buschke test	grober_buschke_total_recall		int			RT
+	grober_buschke_free_recall_delayed		int			RLD
+	grober_buschke_total_recall_delayed		int			RTD
+	motivation_starkstein			(Starkstein) Motivation scale	Tst_NRO_NP.xlsx/(Starkstein)
+	verbal_fluency			Lexical Verbal Fluency Score	Tst_NRO_NP.xlsx/(Verbal Fluency)
+Innotest amyloid/tau index	IATI		float			IATI
+	clinad_CSF					CSF AD profile
+	clinad_amyloidB		int			B-Amyloide
+	clinad_tau		int			Tau
+	clinad_p_tau		int			P-Tau
+	clinad_p_tau_Aß		float			PTau/Aß
+	clinad_delay_MRI_CSF					Délai IRM PL
+	clinad_date_MRI_closest_to_CSF					Date IRM proche PL
+
+	prevdemals_benson_copy
+	prevdemals_benson_rappel
+	prevdemals_benson_total
+	prevdemals_faux_pas
+	praxies_dexterity
+	praxies_gesture_kinetic
+	praxies_non_meaning_gestures
+	praxies_intransitive gestures
+	praxies_transitive_gestures
+	praxies_total
+	prevdemals_emotion_total
+	prevdemals_als
+	prevdemals_ftd
+
+
+
+
+
+
+	clinad_amnestic_syndrome_of_hippocampal_type					Sd amn hip
+Number of words that was not cointaned in the original dataset of words	grober_buschke_intrusions					intrusions
+
+	clinad_reac_indic					Réac indic
+	clinad_correct_recognitions					reconnaissances correctes
+	clinad_false_recognitions					fausses reconnaissnces
+
+	clinad_date_csf					Date PL
+	clinad_spm_vol_gm					Vol_SG
+	clinad_spm_vol_wm					Vol_SB
+	clinad_spm_vol_csf					Vol_CSF
+	clinad_spm_vol_total					Vol_Total
+	clinad_volbrain_scale_factor					Scale factor
+	clinad_volbrain_snr		float			SNR
+	clinad_volbrain_msnr		float			mSNR
+	clinad_volbrain_qc		float			QC
+	clinad_volbrain_tissue_wm_cm3		float			Tissue WM cm3
+	clinad_volbrain_tissue_wm_%		float			Tissue WM %
+	clinad_volbrain_tissue_gm_cm3		float			Tissue GM cm3
+	clinad_volbrain_tissue_gm_%		float			Tissue GM %
+	clinad_volbrain_tissue_csf_cm3		float			Tissue CSF cm3
+	clinad_volbrain_tissue_csf_%		float			Tissue CSF %
+	clinad_volbrain_tissue_brain_cm3		float			Tissue Brain cm3
+	clinad_volbrain_tissue_brain_%		float			Tissue Brain %
+	clinad_volbrain_tissue_ic_cm3		float			Tissue IC cm3
+	clinad_volbrain_tissue_ic_%		float			Tissue IC %
+	clinad_volbrain_cerebrum_total_cm3		float			Cerebrum Total cm3
+	clinad_volbrain_cerebrum_total_%		float			Cerebrum Total %
+	clinad_volbrain_cerebrum_t_gm_cm3		float			Cerebrum T GM cm3
+	clinad_volbrain_cerebrum_t_gm_%		float			Cerebrum T GM %
+	clinad_volbrain_cerebrum_t_wm_cm3		float			Cerebrum T WM cm3
+	clinad_volbrain_cerebrum_t_wm_%		float			Cerebrum T WM %
+	clinad_volbrain_cerebrum_right_cm3		float			Cerebrum Right cm3
+	clinad_volbrain_cerebrum_right_%		float			Cerebrum Right %
+	clinad_volbrain_cerebrum_r_gm_cm3		float			Cerebrum R GM cm3
+	clinad_volbrain_cerebrum_r_gm_%		float			Cerebrum R GM %
+	clinad_volbrain_cerebrum_r_wm_cm3		float			Cerebrum R WM cm3
+	clinad_volbrain_cerebrum_r_wm_%		float			Cerebrum R WM %
+	clinad_volbrain_cerebrum_left_cm3		float			Cerebrum Left cm3
+	clinad_volbrain_cerebrum_left_%		float			Cerebrum Left %
+	clinad_volbrain_cerebrum_l_gm_cm3		float			Cerebrum L GM cm3
+	clinad_volbrain_cerebrum_l_gm_%		float			Cerebrum L GM %
+	clinad_volbrain_cerebrum_l_wm_cm3		float			Cerebrum L WM cm3
+	clinad_volbrain_cerebrum_l_wm_%		float			Cerebrum L WM %
+	clinad_volbrain_cerebrum_assymetry		float			Cerebrum Asymmetry
+	clinad_volbrain_cerebelum_total_cm3		float			Cerebelum Total cm3
+	clinad_volbrain_cerebelum_total_%		float			Cerebelum Total %
+	clinad_volbrain_cerebelum_t_gm_cm3		float			Cerebelum T GM cm3
+	clinad_volbrain_cerebelum_t_gm_%		float			Cerebelum T GM %
+	clinad_volbrain_cerebelum_t_wm_cm3		float			Cerebelum T WM cm3
+	clinad_volbrain_cerebelum_t_wm_%		float			Cerebelum T WM %
+	clinad_volbrain_cerebelum_right_cm3		float			Cerebelum Right cm3
+	clinad_volbrain_cerebelum_right_%		float			Cerebelum Right %
+	clinad_volbrain_cerebelum_r_gm_cm3		float			Cerebelum R GM cm3
+	clinad_volbrain_cerebelum_r_gm_%		float			Cerebelum R GM %
+	clinad_volbrain_cerebelum_r_wm_cm3		float			Cerebelum R WM cm3
+	clinad_volbrain_cerebelum_r_wm_%		float			Cerebelum R WM %
+	clinad_volbrain_cerebelum_left_cm3		float			Cerebelum Left cm3
+	clinad_volbrain_cerebelum_left_%		float			Cerebelum Left %
+	clinad_volbrain_cerebelum_l_gm_cm3		float			Cerebelum L GM cm3
+	clinad_volbrain_cerebelum_l_gm_%		float			Cerebelum L GM %
+	clinad_volbrain_cerebelum_l_wm_cm3		float			Cerebelum L WM cm3
+	clinad_volbrain_cerebelum_l_wm_%		float			Cerebelum L WM %
+	clinad_volbrain_cerebelum_assymetry		float			Cerebelum Asymmetry
+	clinad_volbrain_brainstem_cm3		float			Brainstem cm3
+	clinad_volbrain_brainstem_%		float			Brainstem %
+	clinad_volbrain_lateral_ventricles_total_cm3		float			Lateral ventricles Total cm3
+	clinad_volbrain_lateral_ventricles_total_%		float			Lateral ventricles Total %
+	clinad_volbrain_lateral_ventricles_right_cm3		float			Lateral ventricles Right cm3
+	clinad_volbrain_lateral_ventricles_right_%		float			Lateral ventricles Right %
+	clinad_volbrain_lateral_ventricles_left_cm3		float			Lateral ventricles Left cm3
+	clinad_volbrain_lateral_ventricles_left_%		float			Lateral ventricles Left %
+	clinad_volbrain_lateral_ventricles_asymmetry		float			Lateral ventricles Asymmetry
+	clinad_volbrain_caudate_total_cm3		float			Caudate Total cm3
+	clinad_volbrain_caudate_total_%		float			Caudate Total %
+	clinad_volbrain_caudate_right_cm3		float			Caudate Right cm3
+	clinad_volbrain_caudate_right_%		float			Caudate Right %
+	clinad_volbrain_caudate_left_cm3		float			Caudate Left cm3
+	clinad_volbrain_caudate_left_%		float			Caudate Left %
+	clinad_volbrain_caudate_asymmetry		float			Caudate Asymmetry
+	clinad_volbrain_putamen_total_cm3		float			Putamen Total cm3
+	clinad_volbrain_putamen_total_%		float			Putamen Total %
+	clinad_volbrain_putamen_right_cm3		float			Putamen Right cm3
+	clinad_volbrain_putamen_right_%		float			Putamen Right %
+	clinad_volbrain_putamen_left_cm3		float			Putamen Left cm3
+	clinad_volbrain_putamen_left_%		float			Putamen Left %
+	clinad_volbrain_putamen_asymmetry		float			Putamen Asymmetry
+	clinad_volbrain_thalamus_total_cm3		float			Thalamus Total cm3
+	clinad_volbrain_thalamus_total_%		float			Thalamus Total %
+	clinad_volbrain_thalamus_right_cm3		float			Thalamus Right cm3
+	clinad_volbrain_thalamus_right_%		float			Thalamus Right %
+	clinad_volbrain_thalamus_left_cm3		float			Thalamus Left cm3
+	clinad_volbrain_thalamus_left_%		float			Thalamus Left %
+	clinad_volbrain_thalamus_asymmetry		float			Thalamus Asymmetry
+	clinad_volbrain_globus_pallidus_total_cm3		float			Globus Pallidus Total cm3
+	clinad_volbrain_globus_pallidus_total_%		float			Globus Pallidus Total %
+	clinad_volbrain_globus_pallidus_right_cm3		float			Globus Pallidus Right cm3
+	clinad_volbrain_globus_pallidus_right_%		float			Globus Pallidus Right %
+	clinad_volbrain_globus_pallidus_left_cm3		float			Globus Pallidus Left cm3
+	clinad_volbrain_globus_pallidus_left_%		float			Globus Pallidus Left %
+	clinad_volbrain_globus_pallidus_asymmetry		float			Globus Pallidus Asymmetry
+	clinad_volbrain_hippocampus_total_cm3		float			Hippocampus Total cm3
+	clinad_volbrain_hippocampus_total_%		float			Hippocampus Total %
+	clinad_volbrain_hippocampus_right_cm3		float			Hippocampus Right cm3
+	clinad_volbrain_hippocampus_right_%		float			Hippocampus Right %
+	clinad_volbrain_hippocampus_left_cm3		float			Hippocampus Left cm3
+	clinad_volbrain_hippocampus_left_%		float			Hippocampus Left %
+	clinad_volbrain_hippocampus_asymmetry		float			Hippocampus Asymmetry
+	clinad_volbrain_amygdala_total_cm3		float			Amygdala Total cm3
+	clinad_volbrain_amygdala_total_%		float			Amygdala Total %
+	clinad_volbrain_amygdala_right_cm3		float			Amygdala Right cm3
+	clinad_volbrain_amygdala_right_%		float			Amygdala Right %
+	clinad_volbrain_amygdala_left_cm3		float			Amygdala Left cm3
+	clinad_volbrain_amygdala_left_%		float			Amygdala Left %
+	clinad_volbrain_amygdala_asymmetry		float			Amygdala Asymmetry
+	clinad_volbrain_accumbens_total_cm3					Accumbens Total cm3
+	clinad_volbrain_accumbens_total_%					Accumbens Total %
+	clinad_volbrain_accumbens_right_cm3					Accumbens Right cm3
+	clinad_volbrain_accumbens_right_%					Accumbens Right %
+	clinad_volbrain_accumbens_left_cm3					Accumbens Left cm3
+	clinad_volbrain_accumbens_left_%					Accumbens Left %
+	clinad_volbrain_accumbens_asymmetry					Accumbens Asymmetry
+	clinad_brainreader_id_rm					MR ID
+	clinad_brainreader_clinical_image_id					Clinical image id
+	clinad_brainreader_filename					Filename
+	clinad_brainreader_nr_version					NR version
+	clinad_brainreader_mtiv_in_ml		float			The measured total intracranial volume (mTIV) in ml
+	clinad_brainreader_hippocampal_left_right_asymmetry_index		float			Hippocampal Left-Right Asymmetry Index
+	clinad_brainreader_hippocampal_left_right_asymmetry_index_nr_index		float			Hippocampal Left-Right Asymmetry Index NR Index
+	clinad_brainreader_hippocampal_left_right_asymmetry_index_z_score		float			Hippocampal Left-Right Asymmetry Index z-score
+	clinad_brainreader_hippocampal_left_right_asymmetry_index_percentile		float			Hippocampal Left-Right Asymmetry Index percentile
+	clinad_brainreader_whole_brain_matter_volume_in_ml		float			Whole-Brain-Matter volume in ml
+	clinad_brainreader_whole_brain_matter_vol_mtiv_ratio		float			Whole-Brain-Matter Vol/mTIV ratio
+	clinad_brainreader_whole_brain_matter_nr_index		float			Whole-Brain-Matter NR Index
+	clinad_brainreader_whole_brain_matter_z_score		float			Whole-Brain-Matter z-score
+	clinad_brainreader_whole_brain_matter_percentile		float			Whole-Brain-Matter percentile
+	clinad_brainreader_white_matter_volume_in_ml		float			White-Matter volume in ml
+	clinad_brainreader_white_matter_vol_mtiv_ratio		float			White-Matter Vol/mTIV ratio
+	clinad_brainreader_white_matter_nr_index		float			White-Matter NR Index
+	clinad_brainreader_white_matter_z_score		float			White-Matter z-score
+	clinad_brainreader_white_matter_percentile		float			White-Matter percentile
+	clinad_brainreader_gray_matter_volume_in_ml		float			Gray-Matter volume in ml
+	clinad_brainreader_gray_matter_vol_mtiv_ratio		float			Gray-Matter Vol/mTIV ratio
+	clinad_brainreader_gray_matter_nr_index		float			Gray-Matter NR Index
+	clinad_brainreader_gray_matter_z_score		float			Gray-Matter z-score
+	clinad_brainreader_gray_matter_percentile		float			Gray-Matter percentile
+	clinad_brainreader_csf_dura_volume_in_ml		float			CSF-(+-dura) volume in ml
+	clinad_brainreader_csf_dura_vol_mtiv_ratio		float			CSF-(+-dura) Vol/mTIV ratio
+	clinad_brainreader_csf_dura_nr_index		float			CSF-(+-dura) NR Index
+	clinad_brainreader_csf_dura_z_score		float			CSF-(+-dura) z-score
+	clinad_brainreader_csf_dura_percentile		float			CSF-(+-dura) percentile
+	clinad_brainreader_left_hippocampus_volume_in_ml		float			Left-Hippocampus volume in ml
+	clinad_brainreader_left_hippocampus_vol_mtiv_ratio		float			Left-Hippocampus Vol/mTIV ratio
+	clinad_brainreader_left_hippocampus_nr_index		float			Left-Hippocampus NR Index
+	clinad_brainreader_left_hippocampus_z_score		float			Left-Hippocampus z-score
+	clinad_brainreader_left_hippocampus_percentile		float			Left-Hippocampus percentile
+	clinad_brainreader_right_hippocampus_volume_in_ml		float			Right-Hippocampus volume in ml
+	clinad_brainreader_right_hippocampus_vol_mtiv_ratio		float			Right-Hippocampus Vol/mTIV ratio
+	clinad_brainreader_right_hippocampus_nr_index		float			Right-Hippocampus NR Index
+	clinad_brainreader_right_hippocampus_z_score		float			Right-Hippocampus z-score
+	clinad_brainreader_right_hippocampus_percentile		float			Right-Hippocampus percentile
+	clinad_brainreader_hippocampus_volume_in_ml		float			Hippocampus volume in ml
+	clinad_brainreader_hippocampus_vol_mtiv_ratio		float			Hippocampus Vol/mTIV ratio
+	clinad_brainreader_hippocampus_nr_index		float			Hippocampus NR Index
+	clinad_brainreader_hippocampus_z_score		float			Hippocampus z-score
+	clinad_brainreader_hippocampus_percentile		float			Hippocampus percentile
+	clinad_brainreader_left_amygdala_volume_in_ml		float			Left-Amygdala volume in ml
+	clinad_brainreader_left_amygdala_vol_mtiv_ratio		float			Left-Amygdala Vol/mTIV ratio
+	clinad_brainreader_left_amygdala_nr_index		float			Left-Amygdala NR Index
+	clinad_brainreader_left_amygdala_z_score		float			Left-Amygdala z-score
+	clinad_brainreader_left_amygdala_percentile		float			Left-Amygdala percentile
+	clinad_brainreader_right_amygdala_volume_in_ml		float			Right-Amygdala volume in ml
+	clinad_brainreader_right_amygdala_vol_mtiv_ratio		float			Right-Amygdala Vol/mTIV ratio
+	clinad_brainreader_right_amygdala_nr_index		float			Right-Amygdala NR Index
+	clinad_brainreader_right_amygdala_z_score		float			Right-Amygdala z-score
+	clinad_brainreader_right_amygdala_percentile		float			Right-Amygdala percentile
+	clinad_brainreader_amygdala_volume_in_ml		float			Amygdala volume in ml
+	clinad_brainreader_amygdala_vol_mtiv_ratio		float			Amygdala Vol/mTIV ratio
+	clinad_brainreader_amygdala_nr_index		float			Amygdala NR Index
+	clinad_brainreader_amygdala_z_score		float			Amygdala z-score
+	clinad_brainreader_amygdala_percentile		float			Amygdala percentile
+	clinad_brainreader_brain_stem_volume_in_ml		float			Brain-Stem volume in ml
+	clinad_brainreader_brain_stem_vol_mtiv_ratio		float			Brain-Stem Vol/mTIV ratio
+	clinad_brainreader_brain_stem_nr_index		float			Brain-Stem NR Index
+	clinad_brainreader_brain_stem_z_score		float			Brain-Stem z-score
+	clinad_brainreader_brain_stem_percentile		float			Brain-Stem percentile
+	clinad_brainreader_caudate_volume_in_ml		float			Caudate volume in ml
+	clinad_brainreader_caudate_vol_mtiv_ratio		float			Caudate Vol/mTIV ratio
+	clinad_brainreader_caudate_nr_index		float			Caudate NR Index
+	clinad_brainreader_caudate_z_score		float			Caudate z-score
+	clinad_brainreader_caudate_percentile		float			Caudate percentile
+	clinad_brainreader_left_caudate_volume_in_ml		float			Left-Caudate volume in ml
+	clinad_brainreader_left_caudate_vol_mtiv_ratio		float			Left-Caudate Vol/mTIV ratio
+	clinad_brainreader_left_caudate_nr_index		float			Left-Caudate NR Index
+	clinad_brainreader_left_caudate_z_score		float			Left-Caudate z-score
+	clinad_brainreader_left_caudate_percentile		float			Left-Caudate percentile
+	clinad_brainreader_right_caudate_volume_in_ml		float			Right-Caudate volume in ml
+	clinad_brainreader_right_caudate_vol_mtiv_ratio		float			Right-Caudate Vol/mTIV ratio
+	clinad_brainreader_right_caudate_nr_index		float			Right-Caudate NR Index
+	clinad_brainreader_right_caudate_z_score		float			Right-Caudate z-score
+	clinad_brainreader_right_caudate_percentile		float			Right-Caudate percentile
+	clinad_brainreader_left_cerebellum_volume_in_ml		float			Left-Cerebellum volume in ml
+	clinad_brainreader_left_cerebellum_vol_mtiv_ratio		float			Left-Cerebellum Vol/mTIV ratio
+	clinad_brainreader_left_cerebellum_nr_index		float			Left-Cerebellum NR Index
+	clinad_brainreader_left_cerebellum_z_score		float			Left-Cerebellum z-score
+	clinad_brainreader_left_cerebellum_percentile		float			Left-Cerebellum percentile
+	clinad_brainreader_right_cerebellum_volume_in_ml		float			Right-Cerebellum volume in ml
+	clinad_brainreader_right_cerebellum_vol_mtiv_ratio		float			Right-Cerebellum Vol/mTIV ratio
+	clinad_brainreader_right_cerebellum_nr_index		float			Right-Cerebellum NR Index
+	clinad_brainreader_right_cerebellum_z_score		float			Right-Cerebellum z-score
+	clinad_brainreader_right_cerebellum_percentile		float			Right-Cerebellum percentile
+	clinad_brainreader_cerebellum_volume_in_ml		float			Cerebellum volume in ml
+	clinad_brainreader_cerebellum_vol_mtiv_ratio		float			Cerebellum Vol/mTIV ratio
+	clinad_brainreader_cerebellum_nr_index		float			Cerebellum NR Index
+	clinad_brainreader_cerebellum_z_score		float			Cerebellum z-score
+	clinad_brainreader_cerebellum_percentile		float			Cerebellum percentile
+	clinad_brainreader_lateral_ventricle_volume_in_ml		float			Lateral-Ventricle volume in ml
+	clinad_brainreader_lateral_ventricle_vol_mtiv_ratio		float			Lateral-Ventricle Vol/mTIV ratio
+	clinad_brainreader_lateral_ventricle_nr_index		float			Lateral-Ventricle NR Index
+	clinad_brainreader_lateral_ventricle_z_score		float			Lateral-Ventricle z-score
+	clinad_brainreader_lateral_ventricle_percentile		float			Lateral-Ventricle percentile
+	clinad_brainreader_left_lateral_ventricle_volume_in_ml		float			Left-Lateral-Ventricle volume in ml
+	clinad_brainreader_left_lateral_ventricle_vol_mtiv_ratio		float			Left-Lateral-Ventricle Vol/mTIV ratio
+	clinad_brainreader_left_lateral_ventricle_nr_index		float			Left-Lateral-Ventricle NR Index
+	clinad_brainreader_left_lateral_ventricle_z_score		float			Left-Lateral-Ventricle z-score
+	clinad_brainreader_left_lateral_ventricle_percentile		float			Left-Lateral-Ventricle percentile
+	clinad_brainreader_right_lateral_ventricle_volume_in_ml		float			Right-Lateral-Ventricle volume in ml
+	clinad_brainreader_right_lateral_ventricle_vol_mtiv_ratio		float			Right-Lateral-Ventricle Vol/mTIV ratio
+	clinad_brainreader_right_lateral_ventricle_nr_index		float			Right-Lateral-Ventricle NR Index
+	clinad_brainreader_right_lateral_ventricle_z_score		float			Right-Lateral-Ventricle z-score
+	clinad_brainreader_right_lateral_ventricle_percentile		float			Right-Lateral-Ventricle percentile
+	clinad_brainreader_putamen_volume_in_ml		float			Putamen volume in ml
+	clinad_brainreader_putamen_vol_mtiv_ratio		float			Putamen Vol/mTIV ratio
+	clinad_brainreader_putamen_nr_index		float			Putamen NR Index
+	clinad_brainreader_putamen_z_score		float			Putamen z-score
+	clinad_brainreader_putamen_percentile		float			Putamen percentile
+	clinad_brainreader_left_putamen_volume_in_ml		float			Left-Putamen volume in ml
+	clinad_brainreader_left_putamen_vol_mtiv_ratio		float			Left-Putamen Vol/mTIV ratio
+	clinad_brainreader_left_putamen_nr_index		float			Left-Putamen NR Index
+	clinad_brainreader_left_putamen_z_score		float			Left-Putamen z-score
+	clinad_brainreader_left_putamen_percentile		float			Left-Putamen percentile
+	clinad_brainreader_right_putamen_volume_in_ml		float			Right-Putamen volume in ml
+	clinad_brainreader_right_putamen_vol_mtiv_ratio		float			Right-Putamen Vol/mTIV ratio
+	clinad_brainreader_right_putamen_nr_index		float			Right-Putamen NR Index
+	clinad_brainreader_right_putamen_z_score		float			Right-Putamen z-score
+	clinad_brainreader_right_putamen_percentile		float			Right-Putamen percentile
+	clinad_brainreader_thalamus_volume_in_ml		float			Thalamus volume in ml
+	clinad_brainreader_thalamus_vol_mtiv_ratio		float			Thalamus Vol/mTIV ratio
+	clinad_brainreader_thalamus_nr_index		float			Thalamus NR Index
+	clinad_brainreader_thalamus_z_score		float			Thalamus z-score
+	clinad_brainreader_thalamus_percentile		float			Thalamus percentile
+	clinad_brainreader_left_thalamus_volume_in_ml		float			Left-Thalamus volume in ml
+	clinad_brainreader_left_thalamus_vol_mtiv_ratio		float			Left-Thalamus Vol/mTIV ratio
+	clinad_brainreader_left_thalamus_nr_index		float			Left-Thalamus NR Index
+	clinad_brainreader_left_thalamus_z_score		float			Left-Thalamus z-score
+	clinad_brainreader_left_thalamus_percentile		float			Left-Thalamus percentile
+	clinad_brainreader_right_thalamus_volume_in_ml		float			Right-Thalamus volume in ml
+	clinad_brainreader_right_thalamus_vol_mtiv_ratio		float			Right-Thalamus Vol/mTIV ratio
+	clinad_brainreader_right_thalamus_nr_index		float			Right-Thalamus NR Index
+	clinad_brainreader_right_thalamus_z_score		float			Right-Thalamus z-score
+	clinad_brainreader_right_thalamus_percentile		float			Right-Thalamus percentile
+	clinad_brainreader_ventral_diencephalon_volume_in_ml		float			Ventral-Diencephalon volume in ml
+	clinad_brainreader_ventral_diencephalon_vol_mtiv_ratio		float			Ventral-Diencephalon Vol/mTIV ratio
+	clinad_brainreader_ventral_diencephalon_nr_index		float			Ventral-Diencephalon NR Index
+	clinad_brainreader_ventral_diencephalon_z_score		float			Ventral-Diencephalon z-score
+	clinad_brainreader_ventral_diencephalon_percentile		float			Ventral-Diencephalon percentile
+	clinad_brainreader_left_ventral_diencephalon_volume_in_ml		float			Left-Ventral-Diencephalon volume in ml
+	clinad_brainreader_left_ventral_diencephalon_vol_mtiv_ratio		float			Left-Ventral-Diencephalon Vol/mTIV ratio
+	clinad_brainreader_left_ventral_diencephalon_nr_index		float			Left-Ventral-Diencephalon NR Index
+	clinad_brainreader_left_ventral_diencephalon_z_score		float			Left-Ventral-Diencephalon z-score
+	clinad_brainreader_left_ventral_diencephalon_percentile		float			Left-Ventral-Diencephalon percentile
+	clinad_brainreader_right_ventral_diencephalon_volume_in_ml		float			Right-Ventral-Diencephalon volume in ml
+	clinad_brainreader_right_ventral_diencephalon_vol_mtiv_ratio		float			Right-Ventral-Diencephalon Vol/mTIV ratio
+	clinad_brainreader_right_ventral_diencephalon_nr_index		float			Right-Ventral-Diencephalon NR Index
+	clinad_brainreader_right_ventral_diencephalon_z_score		float			Right-Ventral-Diencephalon z-score
+	clinad_brainreader_right_ventral_diencephalon_percentile		float			Right-Ventral-Diencephalon percentile
+	clinad_brainreader_left_frontal_lobe_volume_in_ml		float			Left-Frontal-Lobe volume in ml
+	clinad_brainreader_left_frontal_lobe_vol_mtiv_ratio		float			Left-Frontal-Lobe Vol/mTIV ratio
+	clinad_brainreader_left_frontal_lobe_nr_index		float			Left-Frontal-Lobe NR Index
+	clinad_brainreader_left_frontal_lobe_z_score		float			Left-Frontal-Lobe z-score
+	clinad_brainreader_left_frontal_lobe_percentile		float			Left-Frontal-Lobe percentile
+	clinad_brainreader_right_frontal_lobe_volume_in_ml		float			Right-Frontal-Lobe volume in ml
+	clinad_brainreader_right_frontal_lobe_vol_mtiv_ratio		float			Right-Frontal-Lobe Vol/mTIV ratio
+	clinad_brainreader_right_frontal_lobe_nr_index		float			Right-Frontal-Lobe NR Index
+	clinad_brainreader_right_frontal_lobe_z_score		float			Right-Frontal-Lobe z-score
+	clinad_brainreader_right_frontal_lobe_percentile		float			Right-Frontal-Lobe percentile
+	clinad_brainreader_left_parietal_lobe_volume_in_ml		float			Left-Parietal-Lobe volume in ml
+	clinad_brainreader_left_parietal_lobe_vol_mtiv_ratio		float			Left-Parietal-Lobe Vol/mTIV ratio
+	clinad_brainreader_left_parietal_lobe_nr_index		float			Left-Parietal-Lobe NR Index
+	clinad_brainreader_left_parietal_lobe_z_score		float			Left-Parietal-Lobe z-score
+	clinad_brainreader_left_parietal_lobe_percentile		float			Left-Parietal-Lobe percentile
+	clinad_brainreader_right_parietal_lobe_volume_in_ml		float			Right-Parietal-Lobe volume in ml
+	clinad_brainreader_right_parietal_lobe_vol_mtiv_ratio		float			Right-Parietal-Lobe Vol/mTIV ratio
+	clinad_brainreader_right_parietal_lobe_nr_index		float			Right-Parietal-Lobe NR Index
+	clinad_brainreader_right_parietal_lobe_z_score		float			Right-Parietal-Lobe z-score
+	clinad_brainreader_right_parietal_lobe_percentile		float			Right-Parietal-Lobe percentile
+	clinad_brainreader_left_occipital_lobe_volume_in_ml		float			Left-Occipital-Lobe volume in ml
+	clinad_brainreader_left_occipital_lobe_vol_mtiv_ratio		float			Left-Occipital-Lobe Vol/mTIV ratio
+	clinad_brainreader_left_occipital_lobe_nr_index		float			Left-Occipital-Lobe NR Index
+	clinad_brainreader_left_occipital_lobe_z_score		float			Left-Occipital-Lobe z-score
+	clinad_brainreader_left_occipital_lobe_percentile		float			Left-Occipital-Lobe percentile
+	clinad_brainreader_right_occipital_lobe_volume_in_ml		float			Right-Occipital-Lobe volume in ml
+	clinad_brainreader_right_occipital_lobe_vol_mtiv_ratio		float			Right-Occipital-Lobe Vol/mTIV ratio
+	clinad_brainreader_right_occipital_lobe_nr_index		float			Right-Occipital-Lobe NR Index
+	clinad_brainreader_right_occipital_lobe_z_score		float			Right-Occipital-Lobe z-score
+	clinad_brainreader_right_occipital_lobe_percentile		float			Right-Occipital-Lobe percentile
+	clinad_brainreader_left_temporal_lobe_volume_in_ml		float			Left-Temporal-Lobe volume in ml
+	clinad_brainreader_left_temporal_lobe_vol_mtiv_ratio		float			Left-Temporal-Lobe Vol/mTIV ratio
+	clinad_brainreader_left_temporal_lobe_nr_index		float			Left-Temporal-Lobe NR Index
+	clinad_brainreader_left_temporal_lobe_z_score		float			Left-Temporal-Lobe z-score
+	clinad_brainreader_left_temporal_lobe_percentile		float			Left-Temporal-Lobe percentile
+	clinad_brainreader_right_temporal_lobe_volume_in_ml		float			Right-Temporal-Lobe volume in ml
+	clinad_brainreader_right_temporal_lobe_vol_mtiv_ratio		float			Right-Temporal-Lobe Vol/mTIV ratio
+	clinad_brainreader_right_temporal_lobe_nr_index		float			Right-Temporal-Lobe NR Index
+	clinad_brainreader_right_temporal_lobe_z_score		float			Right-Temporal-Lobe z-score
+	clinad_brainreader_right_temporal_lobe_percentile		float			Right-Temporal-Lobe percentile
+	clinad_brainreader_frontal_lobe_volume_in_ml		float			Frontal-Lobe volume in ml
+	clinad_brainreader_frontal_lobe_vol_mtiv_ratio		float			Frontal-Lobe Vol/mTIV ratio
+	clinad_brainreader_frontal_lobe_nr_index		float			Frontal-Lobe NR Index
+	clinad_brainreader_frontal_lobe_z_score		float			Frontal-Lobe z-score
+	clinad_brainreader_frontal_lobe_percentile		float			Frontal-Lobe percentile
+	clinad_brainreader_parietal_lobe_volume_in_ml		float			Parietal-Lobe volume in ml
+	clinad_brainreader_parietal_lobe_vol_mtiv_ratio		float			Parietal-Lobe Vol/mTIV ratio
+	clinad_brainreader_parietal_lobe_nr_index		float			Parietal-Lobe NR Index
+	clinad_brainreader_parietal_lobe_z_score		float			Parietal-Lobe z-score
+	clinad_brainreader_parietal_lobe_percentile		float			Parietal-Lobe percentile
+	clinad_brainreader_occipital_lobe_volume_in_ml		float			Occipital-Lobe volume in ml
+	clinad_brainreader_occipital_lobe_vol_mtiv_ratio		float			Occipital-Lobe Vol/mTIV ratio
+	clinad_brainreader_occipital_lobe_nr_index		float			Occipital-Lobe NR Index
+	clinad_brainreader_occipital_lobe_z_score		float			Occipital-Lobe z-score
+	clinad_brainreader_occipital_lobe_percentile		float			Occipital-Lobe percentile
+	clinad_brainreader_temporal_lobe_volume_in_ml		float			Temporal-Lobe volume in ml
+	clinad_brainreader_temporal_lobe_vol_mtiv_ratio		float			Temporal-Lobe Vol/mTIV ratio
+	clinad_brainreader_temporal_lobe_nr_index		float			Temporal-Lobe NR Index
+	clinad_brainreader_temporal_lobe_z_score		float			Temporal-Lobe z-score
+	clinad_brainreader_temporal_lobe_percentile		float			Temporal-Lobe percentile
+	clinad_brainreader_left_pallidum_volume_in_ml		float			Left-Pallidum volume in ml
+	clinad_brainreader_left_pallidum_vol_mtiv_ratio		float			Left-Pallidum Vol/mTIV ratio
+	clinad_brainreader_left_pallidum_nr_index		float			Left-Pallidum NR Index
+	clinad_brainreader_left_pallidum_z_score		float			Left-Pallidum z-score
+	clinad_brainreader_left_pallidum_percentile		float			Left-Pallidum percentile
+	clinad_brainreader_right_pallidum_volume_in_ml		float			Right-Pallidum volume in ml
+	clinad_brainreader_right_pallidum_vol_mtiv_ratio		float			Right-Pallidum Vol/mTIV ratio
+	clinad_brainreader_right_pallidum_nr_index		float			Right-Pallidum NR Index
+	clinad_brainreader_right_pallidum_z_score		float			Right-Pallidum z-score
+	clinad_brainreader_right_pallidum_percentile		float			Right-Pallidum percentile
+	clinad_brainreader_pallidum_volume_in_ml		float			Pallidum volume in ml
+	clinad_brainreader_pallidum_vol_mtiv_ratio		float			Pallidum Vol/mTIV ratio
+	clinad_brainreader_pallidum_nr_index		float			Pallidum NR Index
+	clinad_brainreader_pallidum_z_score		float			Pallidum z-score
+	clinad_brainreader_pallidum_percentile		float			Pallidum percentile
+	clinad_brainreader_pallidum_volume_in_ml		float			Pallidum volume in ml
+	clinad_brainreader_pallidum_vol_mtiv_ratio		float			Pallidum Vol/mTIV ratio
+	clinad_brainreader_pallidum_nr_index		float			Pallidum NR Index
+	clinad_brainreader_pallidum_z_score		float			Pallidum z-score
+	clinad_brainreader_pallidum_percentile		float			Pallidum percentile
diff --git a/test/unittests/iotools/test_bids_utils.py b/test/unittests/iotools/test_bids_utils.py
index 65ef601ed..f39bdef63 100644
--- a/test/unittests/iotools/test_bids_utils.py
+++ b/test/unittests/iotools/test_bids_utils.py
@@ -133,9 +133,9 @@ def create_clinical_data(tmp_path: Path, study_name: StudyName) -> Path:
             "OASIS": [np.nan, "ID", np.nan, "M/F", np.nan],
             "OASIS location": [
                 np.nan,
-                "oasis_cross-sectional.csv",
+                "oasis_cross-sectional-5708aa0a98d82080.xlsx",
                 np.nan,
-                "oasis_cross-sectional.csv",
+                "oasis_cross-sectional-5708aa0a98d82080.xlsx",
                 np.nan,
             ],
         }
@@ -182,7 +182,9 @@ def create_clinical_data(tmp_path: Path, study_name: StudyName) -> Path:
                 "Age": ["45", "50", "55", "60", "60"],
             }
         )
-        df_oasis.to_csv(clinical_path / "oasis_cross-sectional.csv", index=False)
+        df_oasis.to_excel(
+            clinical_path / "oasis_cross-sectional-5708aa0a98d82080.xlsx", index=False
+        )
     return clinical_path
 
 

From 3cb533853b62a6bdbacd86c03319d508167d728e Mon Sep 17 00:00:00 2001
From: AliceJoubert <158147135+AliceJoubert@users.noreply.github.com>
Date: Thu, 10 Oct 2024 09:29:14 +0200
Subject: [PATCH 05/13] [DOC] Modify download instructions for OASIS-to-BIDS
 data (#1324)

---
 docs/Converters/OASIS2BIDS.md | 17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

diff --git a/docs/Converters/OASIS2BIDS.md b/docs/Converters/OASIS2BIDS.md
index 63c6d29ea..85fbf1dc3 100644
--- a/docs/Converters/OASIS2BIDS.md
+++ b/docs/Converters/OASIS2BIDS.md
@@ -1,7 +1,10 @@
 <!-- markdownlint-disable MD046 -->
 # `oasis-to-bids` – Conversion of the Open Access Series of Imaging Studies (OASIS) to BIDS
 
-!!! quote "Description reproduced from the [OASIS' webpage](https://sites.wustl.edu/oasisbrains)"
+!!! warning
+    We do not currently support the conversion of OASIS-2.
+
+??? quote "Description reproduced from the [OASIS' webpage](https://sites.wustl.edu/oasisbrains)"
     The Open Access Series of Imaging Studies (OASIS) is a project aimed at making MRI data sets of the brain freely available to the scientific community.
     By compiling and freely distributing MRI data sets, we hope to facilitate future discoveries in basic and clinical neuroscience.
     OASIS is made available by the Washington University Alzheimer’s Disease Research Center, Dr. Randy Buckner at the Howard Hughes Medical Institute (HHMI) at Harvard University, the Neuroinformatics Research Group (NRG) at Washington University School of Medicine, and the Biomedical Informatics Research Network (BIRN).
@@ -22,13 +25,14 @@ If you installed the core of Clinica, this converter needs no further dependenci
 
 The OASIS to BIDS converter requires the user to have downloaded the OASIS-1 (also called *Cross-sectional MRI Data in Young, Middle Aged, Nondemented and Demented Older Adults*) imaging and clinical data.
 
-To do so, visit the [OASIS website](https://sites.wustl.edu/oasisbrains/), click on `DATASETS` then `OASIS-1`. You can download the imaging data via FTP or XNAT (if you click on `Browse Data`). Download the clinical data by clicking on `Download CSV`.
+To do so, visit the OASIS website page [specific to OASIS-1](https://sites.wustl.edu/oasisbrains/home/oasis-1/), and go to `Download Instructions`.
 
-!!! note
-    You do not have to modify the original folder name or rename the clinical data file before using the converter.
+- Download clinical data by clicking on `OASIS-1 : Demographic and Clinical Data`, then `CSV File with Demographic, and Clinical Data`.
+- Download image data by clicking on `OASIS-1 : Raw Data Download` then any archive link.
 
 !!! warning
-    We do not currently support the conversion of OASIS-2.
+    All subjects to be converted should be placed in the same folder, which means the archives downloaded from the website should be unzipped in the same folder.
+
 
 ## Modalities supported
 
@@ -38,7 +42,6 @@ To convert the imaging data to BIDS, the list of subjects is obtained from the d
 
 For each subject, among the multiple T1w MR images available, we select the average of the motion-corrected co-registered individual images resampled to 1 mm isotropic voxels, located in the `SUBJ_111` subfolder.
 
-The clinical data being converted are defined in a spreadsheet (`clinical_specifications.xlsx`) available with the code of the converter, which the user can modify.
 
 ## Using the converter
 
@@ -67,7 +70,7 @@ DATASET_DIRECTORY
 ├── ...
 ```
 
-- `CLINICAL_DATA_DIRECTORY` is the path to the directory containing the [CSV](../glossary.md#csv) file called `oasis_cross-sectional.csv`.
+- `CLINICAL_DATA_DIRECTORY` is the path to the directory containing the excel file called `oasis_cross-sectional-5708aa0a98d82080.xlsx`.
 
 - `BIDS_DIRECTORY` is the path to the output directory, where the BIDS-converted version of OASIS will be stored.
 

From 7cbc43d27701dd6f49abd217b9ead754ba106460 Mon Sep 17 00:00:00 2001
From: AliceJoubert <158147135+AliceJoubert@users.noreply.github.com>
Date: Fri, 11 Oct 2024 14:42:16 +0200
Subject: [PATCH 06/13] [FIX] Add import for `ClinicaMissingDependencyError` in
 `anat_linear_utils.py` (#1329)

---
 clinica/pipelines/t1_linear/anat_linear_utils.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/clinica/pipelines/t1_linear/anat_linear_utils.py b/clinica/pipelines/t1_linear/anat_linear_utils.py
index 1f24a6e1d..0d2a35046 100644
--- a/clinica/pipelines/t1_linear/anat_linear_utils.py
+++ b/clinica/pipelines/t1_linear/anat_linear_utils.py
@@ -108,6 +108,7 @@ def run_n4biasfieldcorrection(
     bias_corrected_output_path : Path
         The path to the bias corrected image.
     """
+    from clinica.utils.exceptions import ClinicaMissingDependencyError
     from clinica.utils.stream import cprint, log_and_raise
 
     try:

From d6123b30669255281804f273852fba0b9538be1b Mon Sep 17 00:00:00 2001
From: AliceJoubert <158147135+AliceJoubert@users.noreply.github.com>
Date: Wed, 16 Oct 2024 08:41:45 +0200
Subject: [PATCH 07/13] [FIX] Fix method `BIDSubjectID.to_study_id()` (#1335)

---
 clinica/iotools/bids_utils.py             | 4 ++--
 test/unittests/iotools/test_bids_utils.py | 6 +++---
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/clinica/iotools/bids_utils.py b/clinica/iotools/bids_utils.py
index 19ec84547..324ef4571 100644
--- a/clinica/iotools/bids_utils.py
+++ b/clinica/iotools/bids_utils.py
@@ -292,7 +292,7 @@ def from_original_study_id(cls, study_id: str) -> str:
         )
 
     def to_original_study_id(self) -> str:
-        return str(self.replace("sub-HABS", "P_"))
+        return str(self).replace("sub-HABS", "P_")
 
 
 class IXIBIDSSubjectID(BIDSSubjectID):
@@ -317,7 +317,7 @@ def from_original_study_id(cls, study_id: str) -> str:
         )
 
     def to_original_study_id(self) -> str:
-        return str(self.replace("sub-", ""))
+        return str(self).replace("sub-", "")
 
 
 # -- Methods for the clinical data --
diff --git a/test/unittests/iotools/test_bids_utils.py b/test/unittests/iotools/test_bids_utils.py
index f39bdef63..a26dbe03b 100644
--- a/test/unittests/iotools/test_bids_utils.py
+++ b/test/unittests/iotools/test_bids_utils.py
@@ -93,7 +93,7 @@ def test_study_to_bids_id_value_error(study, study_id):
 
 
 @pytest.mark.parametrize(
-    "study,expected,bids_id",
+    "study,source_id,bids_id",
     [
         (StudyName.ADNI, "001_S_0001", "sub-ADNI001S0001"),
         (StudyName.NIFD, "1_S_0001", "sub-NIFD1S0001"),
@@ -106,10 +106,10 @@ def test_study_to_bids_id_value_error(study, study_id):
         (StudyName.IXI, "IXI001", "sub-IXI001"),
     ],
 )
-def test_bids_to_study(study, bids_id, expected):
+def test_bids_to_study(study, bids_id, source_id):
     from clinica.iotools.bids_utils import bids_id_factory
 
-    assert bids_id_factory(study).to_original_study_id(bids_id) == expected
+    assert bids_id_factory(study)(bids_id).to_original_study_id() == source_id
 
 
 def create_clinical_data(tmp_path: Path, study_name: StudyName) -> Path:

From 999cd3df306b36ad248b60f59cdcbad9cb7f7b7e Mon Sep 17 00:00:00 2001
From: AliceJoubert <158147135+AliceJoubert@users.noreply.github.com>
Date: Thu, 17 Oct 2024 12:14:15 +0200
Subject: [PATCH 08/13] [FIX] Fix logging in OASIS and AIBL converters (#1340)

---
 clinica/iotools/converters/aibl_to_bids/utils/bids.py     | 8 ++++++++
 clinica/iotools/converters/oasis_to_bids/oasis_to_bids.py | 8 ++++++++
 2 files changed, 16 insertions(+)

diff --git a/clinica/iotools/converters/aibl_to_bids/utils/bids.py b/clinica/iotools/converters/aibl_to_bids/utils/bids.py
index 88cfc4327..15a12f21b 100644
--- a/clinica/iotools/converters/aibl_to_bids/utils/bids.py
+++ b/clinica/iotools/converters/aibl_to_bids/utils/bids.py
@@ -630,11 +630,19 @@ def _create_file(
     Path or None :
         Path to file
     """
+    from clinica.cmdline import setup_clinica_logging
     from clinica.iotools.bids_utils import StudyName, bids_id_factory, json_from_dcm
     from clinica.iotools.converter_utils import viscode_to_session
     from clinica.iotools.utils.data_handling import center_nifti_origin
     from clinica.utils.stream import cprint
 
+    # This function is executed in a multiprocessing context
+    # such that we need to re-configure the clinica logger in the child processes.
+    # Note that logging messages could easily be lost (for example when logging
+    # to a file from two different processes). A better solution would be to
+    # implement a logging process consuming logging messages from a multiprocessing.Queue...
+    setup_clinica_logging("INFO")
+
     participant_id = bids_id_factory(StudyName.AIBL).from_original_study_id(
         image.Subjects_ID
     )
diff --git a/clinica/iotools/converters/oasis_to_bids/oasis_to_bids.py b/clinica/iotools/converters/oasis_to_bids/oasis_to_bids.py
index 9f0a1808d..d57ea0e8c 100644
--- a/clinica/iotools/converters/oasis_to_bids/oasis_to_bids.py
+++ b/clinica/iotools/converters/oasis_to_bids/oasis_to_bids.py
@@ -172,9 +172,17 @@ def _create_modality_agnostic_files(self, bids_dir: Path):
 
     @staticmethod
     def convert_single_subject(subj_folder: Path, dest_dir: Path):
+        from clinica.cmdline import setup_clinica_logging
         from clinica.iotools.bids_utils import StudyName, bids_id_factory
         from clinica.utils.stream import cprint
 
+        # This function is executed in a multiprocessing context
+        # such that we need to re-configure the clinica logger in the child processes.
+        # Note that logging messages could easily be lost (for example when logging
+        # to a file from two different processes). A better solution would be to
+        # implement a logging process consuming logging messages from a multiprocessing.Queue...
+        setup_clinica_logging("INFO")
+
         t1_folder = subj_folder / "PROCESSED" / "MPRAGE" / "SUBJ_111"
         cprint(f"Converting {subj_folder.name}", lvl="info")
         participant_id = bids_id_factory(StudyName.OASIS).from_original_study_id(

From 539cc4eeea3d6b070ef6b2a18a872bc6b6b98659 Mon Sep 17 00:00:00 2001
From: AliceJoubert <158147135+AliceJoubert@users.noreply.github.com>
Date: Tue, 22 Oct 2024 18:12:58 +0200
Subject: [PATCH 09/13] [FIX] ADNI utils `load_clinical_csv` should avoid
 hidden files (#1343)

---
 clinica/iotools/converters/adni_to_bids/adni_utils.py        | 2 +-
 .../iotools/converters/adni_to_bids/test_adni_utils.py       | 5 ++---
 2 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/clinica/iotools/converters/adni_to_bids/adni_utils.py b/clinica/iotools/converters/adni_to_bids/adni_utils.py
index 2ac56a99d..c79631787 100644
--- a/clinica/iotools/converters/adni_to_bids/adni_utils.py
+++ b/clinica/iotools/converters/adni_to_bids/adni_utils.py
@@ -1109,7 +1109,7 @@ def load_clinical_csv(clinical_dir: Path, filename: str) -> pd.DataFrame:
 
     pattern = filename + r"(_\d{1,2}[A-Za-z]{3}\d{4})?.csv"
     files_matching_pattern = [
-        f for f in clinical_dir.rglob("*.csv") if re.search(pattern, f.name)
+        f for f in clinical_dir.rglob("[!.]*.csv") if re.search(pattern, f.name)
     ]
     if len(files_matching_pattern) != 1:
         raise IOError(
diff --git a/test/unittests/iotools/converters/adni_to_bids/test_adni_utils.py b/test/unittests/iotools/converters/adni_to_bids/test_adni_utils.py
index 951d7ce36..540391a98 100644
--- a/test/unittests/iotools/converters/adni_to_bids/test_adni_utils.py
+++ b/test/unittests/iotools/converters/adni_to_bids/test_adni_utils.py
@@ -236,7 +236,7 @@ def test_compute_session_id(csv_filename, visit_code_column_name):
 
 
 @pytest.fixture
-def input_df():
+def input_df() -> pd.DataFrame:
     return pd.DataFrame(
         {
             "foo": ["foo1", "foo2", "foo3"],
@@ -255,6 +255,7 @@ def test_load_clinical_csv(tmp_path, input_df, csv_name, csv_to_look_for):
     from clinica.iotools.converters.adni_to_bids.adni_utils import load_clinical_csv
 
     input_df.to_csv(tmp_path / csv_name, index=False)
+    pd.DataFrame().to_csv(tmp_path / f".{csv_name}")
     assert_frame_equal(load_clinical_csv(tmp_path, csv_to_look_for), input_df)
 
 
@@ -278,8 +279,6 @@ def test_load_clinical_csv_error(
 
 
 def test_load_clinical_csv_value_error(tmp_path):
-    import re
-
     from clinica.iotools.converters.adni_to_bids.adni_utils import load_clinical_csv
 
     with open(tmp_path / "adnimerge.csv", "w") as fp:

From 1fad1c3a3ccbd56b9b4c5f3fc1884ec602be4e55 Mon Sep 17 00:00:00 2001
From: Ravi Hassanaly <42928557+ravih18@users.noreply.github.com>
Date: Thu, 24 Oct 2024 13:17:58 +0200
Subject: [PATCH 10/13] [FIX] Correct the `pet-linear` pipeline (#1348)

* Use T1W linear for non linear registration

* run precommit

* Update clinica/pipelines/pet/linear/pipeline.py

* Update clinica/pipelines/pet/linear/pipeline.py

---------

Co-authored-by: Gensollen <nicolas.gensollen@gmail.com>
---
 clinica/pipelines/pet/linear/pipeline.py | 30 ++++++++++++++++++++----
 1 file changed, 26 insertions(+), 4 deletions(-)

diff --git a/clinica/pipelines/pet/linear/pipeline.py b/clinica/pipelines/pet/linear/pipeline.py
index 9e877c5a8..aae24d09c 100644
--- a/clinica/pipelines/pet/linear/pipeline.py
+++ b/clinica/pipelines/pet/linear/pipeline.py
@@ -38,7 +38,7 @@ def get_input_fields(self) -> List[str]:
         list of str :
             A list of (string) input fields name.
         """
-        return ["pet", "t1w", "t1w_to_mni"]
+        return ["pet", "t1w", "t1w_to_mni", "t1w_linear"]
 
     def get_output_fields(self) -> List[str]:
         """Specify the list of possible outputs of this pipeline.
@@ -66,7 +66,12 @@ def _build_input_node(self):
             ClinicaException,
         )
         from clinica.utils.image import get_mni_template
-        from clinica.utils.input_files import T1W_NII, T1W_TO_MNI_TRANSFORM
+        from clinica.utils.input_files import (
+            T1W_LINEAR,
+            T1W_LINEAR_CROPPED,
+            T1W_NII,
+            T1W_TO_MNI_TRANSFORM,
+        )
         from clinica.utils.inputs import clinica_file_reader
         from clinica.utils.stream import cprint
         from clinica.utils.ux import print_images_to_process
@@ -102,6 +107,21 @@ def _build_input_node(self):
             raise ClinicaBIDSError(err)
 
         # Inputs from t1-linear pipeline
+        # T1w images registered
+        t1w_linear_file_pattern = (
+            T1W_LINEAR
+            if self.parameters.get("uncropped_image", False)
+            else T1W_LINEAR_CROPPED
+        )
+        try:
+            t1w_linear_files, _ = clinica_file_reader(
+                self.subjects,
+                self.sessions,
+                self.caps_directory,
+                t1w_linear_file_pattern,
+            )
+        except ClinicaException as e:
+            raise ClinicaCAPSError(e)
         # Transformation files from T1w files to MNI:
         try:
             t1w_to_mni_transformation_files, _ = clinica_file_reader(
@@ -124,6 +144,7 @@ def _build_input_node(self):
                 ("t1w", t1w_files),
                 ("pet", pet_files),
                 ("t1w_to_mni", t1w_to_mni_transformation_files),
+                ("t1w_linear", t1w_linear_files),
             ],
             synchronize=True,
             interface=nutil.IdentityInterface(fields=self.get_input_fields()),
@@ -133,6 +154,7 @@ def _build_input_node(self):
                 (read_input_node, self.input_node, [("t1w", "t1w")]),
                 (read_input_node, self.input_node, [("pet", "pet")]),
                 (read_input_node, self.input_node, [("t1w_to_mni", "t1w_to_mni")]),
+                (read_input_node, self.input_node, [("t1w_linear", "t1w_linear")]),
             ]
         )
 
@@ -394,12 +416,12 @@ def _build_core_nodes(self):
                 (
                     self.input_node,
                     ants_registration_nonlinear_node,
-                    [("t1w", "moving_image")],
+                    [("t1w_linear", "moving_image")],
                 ),
                 (
                     ants_registration_nonlinear_node,
                     ants_applytransform_nonlinear_node,
-                    [("reverse_forward_transforms", "transforms")],
+                    [("forward_transforms", "transforms")],
                 ),
                 (
                     ants_applytransform_node,

From 876298c76c5fdfc435ad20a5f58c1ec2f40e2cd3 Mon Sep 17 00:00:00 2001
From: AliceJoubert <158147135+AliceJoubert@users.noreply.github.com>
Date: Thu, 24 Oct 2024 15:37:59 +0200
Subject: [PATCH 11/13] [FIX] ADNI-to-BIDS : incorporate the fix for KeyError
 "APGEN" (#1342)

* Proposition

* Changes upon suggestions

* Modify unit test

* Small fix
---
 clinica/iotools/bids_utils.py             | 15 +++++++++
 test/unittests/iotools/test_bids_utils.py | 39 ++++++++++++++++++-----
 2 files changed, 46 insertions(+), 8 deletions(-)

diff --git a/clinica/iotools/bids_utils.py b/clinica/iotools/bids_utils.py
index 324ef4571..e4eb8cedf 100644
--- a/clinica/iotools/bids_utils.py
+++ b/clinica/iotools/bids_utils.py
@@ -401,6 +401,21 @@ def create_participants_df(
                     file_to_read = load_clinical_csv(
                         clinical_data_dir, location.split(".")[0]
                     )
+                    # Condition to handle ADNI modification of file APOERES.csv
+                    # See issue https://github.com/aramis-lab/clinica/issues/1294
+                    if study_name == StudyName.ADNI and location == "APOERES.csv":
+                        if (
+                            participant_fields_db[i] not in file_to_read.columns
+                            and "GENOTYPE" in file_to_read.columns
+                        ):
+                            # Split the 'GENOTYPE' column into 'APGEN1' and 'APGEN2'
+                            genotype = file_to_read["GENOTYPE"].str.split(
+                                "/", expand=True
+                            )
+                            file_to_read = file_to_read.assign(
+                                APGEN1=genotype[0], APGEN2=genotype[1]
+                            )
+
                 prev_location = location
                 prev_sheet = sheet
 
diff --git a/test/unittests/iotools/test_bids_utils.py b/test/unittests/iotools/test_bids_utils.py
index a26dbe03b..c014dbc7e 100644
--- a/test/unittests/iotools/test_bids_utils.py
+++ b/test/unittests/iotools/test_bids_utils.py
@@ -1,6 +1,6 @@
 from pathlib import Path
 from string import Template
-from typing import Union
+from typing import Optional, Union
 
 import numpy as np
 import pandas as pd
@@ -112,7 +112,7 @@ def test_bids_to_study(study, bids_id, source_id):
     assert bids_id_factory(study)(bids_id).to_original_study_id() == source_id
 
 
-def create_clinical_data(tmp_path: Path, study_name: StudyName) -> Path:
+def create_participants_spec(tmp_path: Path) -> Path:
     spec_df = pd.DataFrame(
         {
             "BIDS CLINICA": [
@@ -142,6 +142,12 @@ def create_clinical_data(tmp_path: Path, study_name: StudyName) -> Path:
     )
     spec_df.to_csv(tmp_path / "participant.tsv", sep="\t", index=False)
 
+    return tmp_path
+
+
+def create_clinical_data(
+    tmp_path: Path, study_name: StudyName, adni_genotype: Optional[bool] = False
+) -> Path:
     clinical_path = tmp_path / "clinical_data"
     clinical_path.mkdir()
 
@@ -160,14 +166,25 @@ def create_clinical_data(tmp_path: Path, study_name: StudyName) -> Path:
                 "AGE": ["40", "50", "60", "70", "80", None],
             }
         )
+
         df_apoeres = pd.DataFrame(
             {
                 "APGEN1": ["3", "3", "3", "3", None, "3"],
                 "GEN2": ["2", "2", "2", "2", None, "2"],
             }
         )
+
+        if adni_genotype:
+            df_apoeres = pd.DataFrame(
+                {
+                    "GENOTYPE": ["3/2", "3/2", "3/2", "3/2", None, "3/2"],
+                    "GEN2": ["2", "2", "2", "2", None, "2"],
+                }
+            )
+
         df_adnimerge.to_csv(clinical_path / "ADNIMERGE.csv", index=False)
         df_apoeres.to_csv(clinical_path / "APOERES.csv", index=False)
+
     if study_name == StudyName.OASIS:
         df_oasis = pd.DataFrame(
             {
@@ -189,7 +206,7 @@ def create_clinical_data(tmp_path: Path, study_name: StudyName) -> Path:
 
 
 @pytest.mark.parametrize(
-    "study_name, bids_ids, expected",
+    "study_name, bids_ids, expected, adni_genotype",
     [
         (
             StudyName.OASIS,
@@ -201,6 +218,7 @@ def create_clinical_data(tmp_path: Path, study_name: StudyName) -> Path:
                     "sex": ["F"],
                 }
             ),
+            False,
         ),
         (
             StudyName.ADNI,
@@ -210,9 +228,10 @@ def create_clinical_data(tmp_path: Path, study_name: StudyName) -> Path:
                     "participant_id": ["sub-ADNI001S0001"],
                     "alternative_id_1": ["001_S_0001"],
                     "sex": ["Male"],
-                    "apoegen1": [3.0],
+                    "apoegen1": ["3"],
                 }
             ),
+            True,
         ),
         (
             StudyName.OASIS,
@@ -224,6 +243,7 @@ def create_clinical_data(tmp_path: Path, study_name: StudyName) -> Path:
                     "sex": ["M", "M"],
                 }
             ),
+            False,
         ),
         (
             StudyName.ADNI,
@@ -236,6 +256,7 @@ def create_clinical_data(tmp_path: Path, study_name: StudyName) -> Path:
                     "apoegen1": ["n/a"],
                 }
             ),
+            False,
         ),
         (
             StudyName.ADNI,
@@ -248,18 +269,20 @@ def create_clinical_data(tmp_path: Path, study_name: StudyName) -> Path:
                     "apoegen1": [3.0],
                 }
             ),
+            False,
         ),
     ],
 )
-def test_create_participants_df(tmp_path, bids_ids, expected, study_name):
+def test_create_participants_df(
+    tmp_path, bids_ids, expected, study_name, adni_genotype
+):
     from clinica.iotools.bids_utils import create_participants_df
 
-    clinical_path = create_clinical_data(tmp_path, study_name)
     assert (
         create_participants_df(
             study_name,
-            clinical_specifications_folder=tmp_path,
-            clinical_data_dir=clinical_path,
+            clinical_specifications_folder=create_participants_spec(tmp_path),
+            clinical_data_dir=create_clinical_data(tmp_path, study_name, adni_genotype),
             bids_ids=bids_ids,
         )
         .reset_index(drop=True)

From df56362a7369a2a68cc395ddc203010962716970 Mon Sep 17 00:00:00 2001
From: Gensollen <nicolas.gensollen@gmail.com>
Date: Fri, 25 Oct 2024 14:17:33 +0200
Subject: [PATCH 12/13] Revert "[FIX] Correct the `pet-linear` pipeline
 (#1348)" (#1357)

This reverts commit 1fad1c3a3ccbd56b9b4c5f3fc1884ec602be4e55.
---
 clinica/pipelines/pet/linear/pipeline.py | 30 ++++--------------------
 1 file changed, 4 insertions(+), 26 deletions(-)

diff --git a/clinica/pipelines/pet/linear/pipeline.py b/clinica/pipelines/pet/linear/pipeline.py
index aae24d09c..9e877c5a8 100644
--- a/clinica/pipelines/pet/linear/pipeline.py
+++ b/clinica/pipelines/pet/linear/pipeline.py
@@ -38,7 +38,7 @@ def get_input_fields(self) -> List[str]:
         list of str :
             A list of (string) input fields name.
         """
-        return ["pet", "t1w", "t1w_to_mni", "t1w_linear"]
+        return ["pet", "t1w", "t1w_to_mni"]
 
     def get_output_fields(self) -> List[str]:
         """Specify the list of possible outputs of this pipeline.
@@ -66,12 +66,7 @@ def _build_input_node(self):
             ClinicaException,
         )
         from clinica.utils.image import get_mni_template
-        from clinica.utils.input_files import (
-            T1W_LINEAR,
-            T1W_LINEAR_CROPPED,
-            T1W_NII,
-            T1W_TO_MNI_TRANSFORM,
-        )
+        from clinica.utils.input_files import T1W_NII, T1W_TO_MNI_TRANSFORM
         from clinica.utils.inputs import clinica_file_reader
         from clinica.utils.stream import cprint
         from clinica.utils.ux import print_images_to_process
@@ -107,21 +102,6 @@ def _build_input_node(self):
             raise ClinicaBIDSError(err)
 
         # Inputs from t1-linear pipeline
-        # T1w images registered
-        t1w_linear_file_pattern = (
-            T1W_LINEAR
-            if self.parameters.get("uncropped_image", False)
-            else T1W_LINEAR_CROPPED
-        )
-        try:
-            t1w_linear_files, _ = clinica_file_reader(
-                self.subjects,
-                self.sessions,
-                self.caps_directory,
-                t1w_linear_file_pattern,
-            )
-        except ClinicaException as e:
-            raise ClinicaCAPSError(e)
         # Transformation files from T1w files to MNI:
         try:
             t1w_to_mni_transformation_files, _ = clinica_file_reader(
@@ -144,7 +124,6 @@ def _build_input_node(self):
                 ("t1w", t1w_files),
                 ("pet", pet_files),
                 ("t1w_to_mni", t1w_to_mni_transformation_files),
-                ("t1w_linear", t1w_linear_files),
             ],
             synchronize=True,
             interface=nutil.IdentityInterface(fields=self.get_input_fields()),
@@ -154,7 +133,6 @@ def _build_input_node(self):
                 (read_input_node, self.input_node, [("t1w", "t1w")]),
                 (read_input_node, self.input_node, [("pet", "pet")]),
                 (read_input_node, self.input_node, [("t1w_to_mni", "t1w_to_mni")]),
-                (read_input_node, self.input_node, [("t1w_linear", "t1w_linear")]),
             ]
         )
 
@@ -416,12 +394,12 @@ def _build_core_nodes(self):
                 (
                     self.input_node,
                     ants_registration_nonlinear_node,
-                    [("t1w_linear", "moving_image")],
+                    [("t1w", "moving_image")],
                 ),
                 (
                     ants_registration_nonlinear_node,
                     ants_applytransform_nonlinear_node,
-                    [("forward_transforms", "transforms")],
+                    [("reverse_forward_transforms", "transforms")],
                 ),
                 (
                     ants_applytransform_node,

From 44b1691f230d5dd682e7719a6058b353341771d2 Mon Sep 17 00:00:00 2001
From: Gensollen <nicolas.gensollen@gmail.com>
Date: Fri, 25 Oct 2024 14:29:29 +0200
Subject: [PATCH 13/13] Release `0.9.2` (#1356)

* update version number

* update changelog

* remove pet-linear fix from release
---
 docs/CHANGELOG.md | 13 +++++++++++++
 pyproject.toml    |  2 +-
 2 files changed, 14 insertions(+), 1 deletion(-)

diff --git a/docs/CHANGELOG.md b/docs/CHANGELOG.md
index 29c979824..7a3669bef 100644
--- a/docs/CHANGELOG.md
+++ b/docs/CHANGELOG.md
@@ -6,6 +6,19 @@ Main changes to this code/ project are documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## Clinica 0.9.2
+
+### Fixed
+
+- [Converters] Fix KeyError "APGEN" in adni-to-bids (see PR [#1342](https://github.com/aramis-lab/clinica/pull/1342))
+- [Converters] Fix function `load_clinical_csv` to avoid hidden files (see PR [#1343](https://github.com/aramis-lab/clinica/pull/1343))
+- [Converters] Fix logging in oasis-to-bids and aibl-to-bids (see PR [#1340](https://github.com/aramis-lab/clinica/pull/1340))
+- [Converters] Fix method `BIDSSubjectID.to_study_id()` (see PR [#1335](https://github.com/aramis-lab/clinica/pull/1335))
+- [T1Linear] Fix missing import in utility function (see PR [#1329](https://github.com/aramis-lab/clinica/pull/1329))
+- [Converters] Fix oasis-to-bids to work with new clinical data (see PR [#1321](https://github.com/aramis-lab/clinica/pull/1321))
+- [Converters] Fix function `define_participants` in ixi-to-bids, which is now deterministic (see PR [#1318](https://github.com/aramis-lab/clinica/pull/1318))
+- [Converters] Fix Oasis1 `BIDSSubjectID` method (see PR [#1312](https://github.com/aramis-lab/clinica/pull/1312))
+
 ## Clinica 0.9.1
 
 ### Fixed
diff --git a/pyproject.toml b/pyproject.toml
index 9935d4795..dbcd5b513 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "clinica"
-version = "0.9.1"
+version = "0.9.2"
 description = "Software platform for clinical neuroimaging studies"
 license = "MIT"
 authors = ["ARAMIS Lab"]