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dicom2nifti

tit.pre.dicom2nifti

DICOM to NIfTI conversion with BIDS-compliant naming.

Converts DICOM images to NIfTI format following BIDS naming conventions.

run_dicom_to_nifti 

run_dicom_to_nifti(project_dir: str, subject_id: str, *, logger, runner: CommandRunner | None = None) -> None

Convert DICOMs to BIDS-compliant NIfTI for a subject.

Parameters

project_dir : str BIDS project root directory. subject_id : str Subject identifier without the 'sub-' prefix. logger : logging.Logger Logger for progress and command output. runner : CommandRunner, optional Subprocess runner for streaming output.

Source code in tit/pre/dicom2nifti.py 
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def run_dicom_to_nifti(
    project_dir: str,
    subject_id: str,
    *,
    logger,
    runner: CommandRunner | None = None,
) -> None:
    """Convert DICOMs to BIDS-compliant NIfTI for a subject.

    Parameters
    ----------
    project_dir : str
        BIDS project root directory.
    subject_id : str
        Subject identifier without the 'sub-' prefix.
    logger : logging.Logger
        Logger for progress and command output.
    runner : CommandRunner, optional
        Subprocess runner for streaming output.
    """

    pm = get_path_manager(project_dir)

    sourcedata_dir = Path(pm.sourcedata_subject(subject_id))
    bids_anat_dir = Path(pm.bids_anat(subject_id))
    bids_anat_dir.mkdir(parents=True, exist_ok=True)

    converted = False
    for modality in ("T1w", "T2w"):
        if _process_modality(
            modality,
            sourcedata_dir,
            bids_anat_dir,
            subject_id,
            pm,
            logger,
            runner,
        ):
            converted = True

    if not converted:
        logger.warning("No DICOM files found or converted")