MIRIAD converter to BIDS

clinica/iotools/bids_utils.py

@@ -26,6 +26,7 @@ class StudyName(str, Enum):
     OASIS3 = "OASIS3"
     UKB = "UKB"
     IXI = "IXI"
+    MIRIAD = "MIRIAD"
 
 
 BIDS_VALIDATOR_CONFIG = {
@@ -93,7 +94,8 @@ def bids_id_factory(study: StudyName) -> Type[BIDSSubjectID]:
         return HABSBIDSSubjectID
     if study == StudyName.IXI:
         return IXIBIDSSubjectID
-
+    if study == StudyName.MIRIAD:
+        return MIRIADBIDSSubjectID
 
 class ADNIBIDSSubjectID(BIDSSubjectID):
     """Implementation for ADNI of the BIDSSubjectIDClass, allowing to go from the source id XXX_S_XXXX
@@ -319,6 +321,29 @@ def from_original_study_id(cls, study_id: str) -> str:
     def to_original_study_id(self) -> str:
         return str(self.replace("sub-", ""))
 
+class MIRIADBIDSSubjectID(BIDSSubjectID):
+    """Implementation for MIRIAD of the BIDSSubjectIDClass, allowing to go from the source id MIRIAD###
+    to a bids id sub-MIRAD### and reciprocally."""
+
+    def validate(self, value: str) -> str:
+        if re.fullmatch(r"sub-MIRIAD\d{3}", value):
+            return value
+        raise ValueError(
+            f"BIDS MIRIAD subject ID {value} is not properly formatted. "
+            "Expecting a 'sub-MIRIAD' format."
+        )
+
+    @classmethod
+    def from_original_study_id(cls, study_id: str) -> str:
+        if re.fullmatch(r"MIRIAD\d{3}", study_id):
+            return f"sub-{study_id}"
+        raise ValueError(
+            f"Raw MIRIAD subject ID {study_id} is not properly formatted. "
+            "Expecting a 'Y' format."
+        )
+
+    def to_original_study_id(self) -> str:
+        return str(self.replace("sub-", ""))
 
 # -- Methods for the clinical data --
 def create_participants_df(

clinica/iotools/converters/cli.py

@@ -9,6 +9,7 @@
 from .oasis3_to_bids import oasis3_to_bids_cli
 from .oasis_to_bids import oasis_to_bids_cli
 from .ukb_to_bids import ukb_to_bids_cli
+from .miriad_to_bids import miriad_to_bids_cli
 
 
 @click.group("convert")
@@ -26,6 +27,7 @@ def cli() -> None:
 cli.add_command(ukb_to_bids_cli.cli)
 cli.add_command(genfi_to_bids_cli.cli)
 cli.add_command(ixi_to_bids_cli.cli)
+cli.add_command(miriad_to_bids_cli.cli)
 
 if __name__ == "__main__":
     cli()

clinica/iotools/converters/factory.py

@@ -40,6 +40,8 @@ def get_converter_name(study: Union[str, StudyName]) -> str:
         return "UkbToBids"
     if study == StudyName.IXI:
         return "IxiToBids"
+    if study == StudyName.MIRIAD:
+        return "MiriadToBids"
 
 
 def converter_factory(study: Union[str, StudyName]) -> Callable:
@@ -62,4 +64,6 @@ def converter_factory(study: Union[str, StudyName]) -> Callable:
         from .ukb_to_bids import convert
     if study == StudyName.IXI:
         from .ixi_to_bids import convert
+    if study == StudyName.MIRIAD:
+        from .miriad_to_bids import convert
     return convert

clinica/iotools/converters/miriad_to_bids/__init__.py

@@ -0,0 +1,3 @@
+from .miriad_to_bids import convert
+
+__all__ = ["convert"]

clinica/iotools/converters/miriad_to_bids/miriad_to_bids.py

@@ -0,0 +1,64 @@
+"""Convert MIRIAD dataset to BIDS."""
+
+from pathlib import Path
+from typing import Optional
+
+import os
+import shutil
+import csv
+from clinica.utils.filemanip import UserProvidedPath
+
+# Paths
+input_dir = 'your_input_directory'  # Where the original data is located
+output_dir = 'your_output_directory'  # Where the BIDS data will be written
+csv_file = 'metadata.csv'  # Metadata CSV file to store extracted information
+
+def convert(
+    path_to_dataset: UserProvidedPath,
+    bids_dir: UserProvidedPath,
+    path_to_clinical: UserProvidedPath,
+    subjects: Optional[UserProvidedPath] = None,
+    n_procs: Optional[int] = 1,
+    **kwargs,
+):
+    """_summary_
+
+    Args:
+        path_to_dataset (UserProvidedPath): _description_
+        bids_dir (UserProvidedPath): _description_
+        path_to_clinical (UserProvidedPath): _description_
+        subjects (Optional[UserProvidedPath], optional): _description_. Defaults to None.
+        n_procs (Optional[int], optional): _description_. Defaults to 1.
+    """
+    from clinica.iotools.converters.miriad_to_bids.miriad_to_bids_utils import create_bids_structure
+    # Prepare CSV
+    with open(csv_file, 'w', newline='') as csvfile:
+        csvwriter = csv.writer(csvfile)
+        csvwriter.writerow(['cohort', 'subject_id', 'diagnosis', 'gender', 'session', 'input_file', 'output_file'])
+
+        # Traverse the input directory
+        for root, dirs, files in os.walk(path_to_dataset):
+            for file in files:
+                if file.endswith('.nii'):
+                    # Example: miriad_215_AD_M_01_MR_1.nii
+                    parts = file.split('_')
+
+                    # Extract information from filename
+                    cohort = parts[0]   # miriad
+                    subject_id = parts[1]  # 215
+                    diagnosis = parts[2]  # AD (Alzheimer's) or HC (Healthy Control)
+                    gender = parts[3]     # M or F
+                    session = parts[4]    # Session number
+
+                    # Full path of input file
+                    input_file = os.path.join(root, file)
+
+                    # Create BIDS structure and move the file
+                    create_bids_structure(subject_id, session, cohort, diagnosis, gender, input_file, path_to_dataset, bids_dir, path_to_clinical)
+
+                    # Write the extracted information to CSV
+                    bids_filename = f"sub-{subject_id}_ses-{session}_T1w.nii.gz"
+                    output_file = os.path.join(f"sub-{subject_id}", f"ses-{session}", 'anat', bids_filename)
+                    csvwriter.writerow([cohort, subject_id, diagnosis, gender, session, input_file, output_file])
+
+    print("Conversion to BIDS format and metadata extraction completed.")

clinica/iotools/converters/miriad_to_bids/miriad_to_bids_cli.py

@@ -0,0 +1,27 @@
+from os import PathLike
+from typing import Optional
+
+import click
+
+from clinica.iotools.converters import cli_param
+
+
+@click.command(name="miriad-to-bids")
+@cli_param.dataset_directory
+@cli_param.bids_directory
+@cli_param.clinical_data_directory
+@cli_param.subjects_list
+def cli(
+    dataset_directory: PathLike,
+    bids_directory: PathLike,
+    clinical_data_directory: PathLike,
+    subjects_list: Optional[PathLike] = None,
+) -> None:
+    """MIRIAD to BIDS converter."""
+    from .miriad_to_bids import convert
+
+    convert(dataset_directory, bids_directory, clinical_data_directory, subjects_list)
+
+
+if __name__ == "__main__":
+    cli()

clinica/iotools/converters/miriad_to_bids/miriad_to_bids_utils.py

@@ -0,0 +1,30 @@
+import os
+import shutil
+
+# Helper function to create BIDS folders and move files
+def create_bids_structure(subject_id, session, cohort, diagnosis, gender, input_file, path_to_dataset, output_dir, path_to_clinical
+):
+
+    """_summary_
+
+    Args:
+        session (_type_): _description_
+        cohort (_type_): _description_
+        diagnosis (_type_): _description_
+        gender (_type_): _description_
+        input_file (_type_): _description_
+        output_dir (_type_): _description_
+        path_to_dataset (_type_, optional): _description_. Defaults to None, n_procs: Optional[int] = 1, **kwargs, ):#subject_id.
+    """
+    sub_id = f"sub-MIRIAD{subject_id}"
+    ses_id = f"ses-{session}"
+
+    # Create output directory for this subject/session
+    anat_dir = os.path.join(output_dir, sub_id, ses_id, 'anat')
+    os.makedirs(anat_dir, exist_ok=True)
+
+    # Destination filename in BIDS format
+    bids_filename = f"{sub_id}_{ses_id}_T1w.nii.gz"
+
+    # Copy and rename the file to BIDS format
+    shutil.copy(input_file, os.path.join(anat_dir, bids_filename))