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charm

tit.pre.charm

SimNIBS charm (m2m) creation + subject atlas segmentation.

run_charm 

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

Run SimNIBS charm for a subject.

Parameters

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

Source code in tit/pre/charm.py 
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def run_charm(
    project_dir: str,
    subject_id: str,
    *,
    logger,
    runner: CommandRunner | None = None,
) -> None:
    """Run SimNIBS charm for a subject.

    Parameters
    ----------
    project_dir : str
        BIDS project root.
    subject_id : str
        Subject identifier without the `sub-` prefix.
    logger : logging.Logger
        Logger used for progress and command output.
    runner : CommandRunner, optional
        Subprocess runner used to stream output.
    """
    pm = get_path_manager(project_dir)

    simnibs_subject_dir = Path(pm.sub(subject_id))
    simnibs_subject_dir.mkdir(parents=True, exist_ok=True)
    m2m_dir = Path(pm.m2m(subject_id))

    t1_file, t2_file = _find_anat_files(subject_id)
    if not t1_file:
        bids_anat_dir = Path(pm.bids_anat(subject_id))
        raise PreprocessError(f"No T1 image found in {bids_anat_dir}")

    if m2m_dir.exists():
        raise PreprocessError(
            f"m2m output already exists at {m2m_dir}. "
            "Remove the directory manually before rerunning."
        )

    cmd = ["charm", "--forcesform", subject_id, str(t1_file)]
    if t2_file:
        cmd.append(str(t2_file))

    logger.info(f"Running SimNIBS charm for subject {subject_id}")
    if runner is None:
        runner = CommandRunner()
    exit_code = runner.run(cmd, logger=logger, cwd=str(simnibs_subject_dir))

    if exit_code != 0:
        raise PreprocessError(
            f"charm failed for subject {subject_id} (exit {exit_code})."
        )

run_subject_atlas 

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

Run subject_atlas to create .annot files for a subject.

This should be called after charm completes successfully. Generates all three atlases: a2009s, DK40, and HCP_MMP1.

Parameters

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

Source code in tit/pre/charm.py 
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def run_subject_atlas(
    project_dir: str,
    subject_id: str,
    *,
    logger,
    runner: CommandRunner | None = None,
) -> None:
    """Run subject_atlas to create .annot files for a subject.

    This should be called after charm completes successfully.
    Generates all three atlases: a2009s, DK40, and HCP_MMP1.

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

    pm = get_path_manager(project_dir)
    m2m_dir = Path(pm.m2m(subject_id))

    if not m2m_dir.exists():
        raise PreprocessError(f"m2m folder not found at {m2m_dir}. Run charm first.")

    # Output directory for atlas segmentation
    output_dir = m2m_dir / "segmentation"
    output_dir.mkdir(parents=True, exist_ok=True)

    if runner is None:
        runner = CommandRunner()

    logger.info(
        f"Running subject_atlas for subject {subject_id} with atlases: {', '.join(ATLASES)}"
    )

    for atlas in ATLASES:
        cmd = [
            "subject_atlas",
            "-a",
            atlas,
            "-o",
            str(output_dir),
            subject_id,
        ]

        logger.info(f"  Creating {atlas} atlas...")
        exit_code = runner.run(cmd, logger=logger)
        if exit_code != 0:
            raise PreprocessError(
                f"subject_atlas failed for atlas {atlas} (exit code {exit_code})"
            )

    logger.info(f"All atlases created successfully for subject {subject_id}")