Ejemplo n.º 1
0
def get_config(
    subject: Optional[str] = None,
    session: Optional[str] = None
) -> BunchConst:
    cfg = BunchConst(
        process_er=config.process_er,
        runs=config.get_runs(subject=subject),
        use_maxwell_filter=config.use_maxwell_filter,
        proc=config.proc,
        task=config.get_task(),
        datatype=config.get_datatype(),
        session=session,
        acq=config.acq,
        rec=config.rec,
        space=config.space,
        bids_root=config.get_bids_root(),
        deriv_root=config.get_deriv_root(),
        interactive=config.interactive,
        epochs_tmin=config.epochs_tmin,
        epochs_tmax=config.epochs_tmax,
        epochs_metadata_tmin=config.epochs_metadata_tmin,
        epochs_metadata_tmax=config.epochs_metadata_tmax,
        epochs_metadata_keep_first=config.epochs_metadata_keep_first,
        epochs_metadata_keep_last=config.epochs_metadata_keep_last,
        event_repeated=config.event_repeated,
        decim=config.decim,
        ch_types=config.ch_types,
        eeg_reference=config.get_eeg_reference()
    )
    return cfg
Ejemplo n.º 2
0
def get_config(subject: Optional[str] = None,
               session: Optional[str] = None) -> SimpleNamespace:
    # Deal with configurations where `deriv_root` was specified, but not
    # `fs_subjects_dir`. We normally raise an exception in this case in
    # `get_fs_subjects_dir()`. However, in situations where users only run the
    # sensor-space scripts, we never call this function, so everything works
    # totally fine at first (which is expected). Yet, when creating the
    # reports, the pipeline would fail with an exception – which is
    # unjustified, as it would not make sense to force users to provide an
    # `fs_subjects_dir` if they don't care about source analysis anyway! So
    # simply assign a dummy value in such cases.
    # `get_fs_subject()` calls `get_fs_subjects_dir()`, so take care of this
    # too.
    try:
        fs_subjects_dir = config.get_fs_subjects_dir()
    except ValueError:
        fs_subjects_dir = None
        fs_subject = None
    else:
        fs_subject = config.get_fs_subject(subject=subject)

    cfg = SimpleNamespace(
        task=config.get_task(),
        runs=config.get_runs(subject=subject),
        datatype=config.get_datatype(),
        acq=config.acq,
        rec=config.rec,
        space=config.space,
        proc=config.proc,
        analyze_channels=config.analyze_channels,
        process_er=config.process_er,
        find_noisy_channels_meg=config.find_noisy_channels_meg,
        h_freq=config.h_freq,
        spatial_filter=config.spatial_filter,
        ica_reject=config.ica_reject,
        conditions=config.conditions,
        contrasts=config.contrasts,
        time_frequency_conditions=config.time_frequency_conditions,
        decode=config.decode,
        decoding_metric=config.decoding_metric,
        n_boot=config.n_boot,
        inverse_method=config.inverse_method,
        fs_subject=fs_subject,
        fs_subjects_dir=fs_subjects_dir,
        deriv_root=config.get_deriv_root(),
        bids_root=config.get_bids_root(),
        use_template_mri=config.use_template_mri,
        interactive=config.interactive,
        plot_psd_for_runs=config.plot_psd_for_runs,
    )
    return cfg
Ejemplo n.º 3
0
def main() -> None:
    """Run freesurfer recon-all command on BIDS dataset.

    The script allows to run the freesurfer recon-all
    command on all subjects of your BIDS dataset. It can
    run in parallel with the --n_jobs parameter.

    It is built on top of the FreeSurfer BIDS app:

    https://github.com/BIDS-Apps/freesurfer

    and the MNE BIDS Pipeline

    https://mne.tools/mne-bids-pipeline

    You must have freesurfer available on your system.

    Run via the MNE BIDS Pipeline's `run.py`:

    python run.py --steps=freesurfer --config=your_pipeline_config.py

    """  # noqa

    logger.info('Running FreeSurfer')

    subjects = config.get_subjects()
    root_dir = config.get_bids_root()
    subjects_dir = Path(config.get_fs_subjects_dir())
    subjects_dir.mkdir(parents=True, exist_ok=True)

    with config.get_parallel_backend():
        n_jobs = config.get_n_jobs()
        parallel, run_func, _ = parallel_func(run_recon, n_jobs=n_jobs)
        parallel(run_func(root_dir, subject, fs_bids_app)
                 for subject in subjects)

        # Handle fsaverage
        fsaverage_dir = subjects_dir / 'fsaverage'
        if fsaverage_dir.exists():
            if fsaverage_dir.is_symlink():
                fsaverage_dir.unlink()
            else:
                shutil.rmtree(fsaverage_dir)

        env = os.environ
        shutil.copytree(f"{env['FREESURFER_HOME']}/subjects/fsaverage",
                        subjects_dir / 'fsaverage')
Ejemplo n.º 4
0
def get_config(subject: Optional[str] = None,
               session: Optional[str] = None) -> SimpleNamespace:
    cfg = SimpleNamespace(
        task=config.get_task(),
        runs=config.get_runs(subject=subject),
        datatype=config.get_datatype(),
        acq=config.acq,
        rec=config.rec,
        space=config.space,
        mindist=config.mindist,
        spacing=config.spacing,
        use_template_mri=config.use_template_mri,
        source_info_path_update=config.source_info_path_update,
        ch_types=config.ch_types,
        fs_subject=config.get_fs_subject(subject=subject),
        fs_subjects_dir=config.get_fs_subjects_dir(),
        deriv_root=config.get_deriv_root(),
        bids_root=config.get_bids_root(),
        n_jobs=config.get_n_jobs())
    return cfg
def get_config(subject: Optional[str] = None,
               session: Optional[str] = None) -> BunchConst:
    cfg = BunchConst(
        process_er=config.process_er,
        runs=config.get_runs(subject=subject),
        use_maxwell_filter=config.use_maxwell_filter,
        proc=config.proc,
        task=config.get_task(),
        datatype=config.get_datatype(),
        acq=config.acq,
        rec=config.rec,
        space=config.space,
        bids_root=config.get_bids_root(),
        deriv_root=config.get_deriv_root(),
        l_freq=config.l_freq,
        h_freq=config.h_freq,
        l_trans_bandwidth=config.l_trans_bandwidth,
        h_trans_bandwidth=config.h_trans_bandwidth,
        resample_sfreq=config.resample_sfreq,
        crop_runs=config.crop_runs,
        interactive=config.interactive,
        rename_events=config.rename_events,
        eeg_bipolar_channels=config.eeg_bipolar_channels,
        eeg_template_montage=config.eeg_template_montage,
        fix_stim_artifact=config.fix_stim_artifact,
        stim_artifact_tmin=config.stim_artifact_tmin,
        stim_artifact_tmax=config.stim_artifact_tmax,
        find_flat_channels_meg=config.find_flat_channels_meg,
        find_noisy_channels_meg=config.find_noisy_channels_meg,
        reference_run=config.get_mf_reference_run(),
        drop_channels=config.drop_channels,
        find_breaks=config.find_breaks,
        min_break_duration=config.min_break_duration,
        t_break_annot_start_after_previous_event=config.
        t_break_annot_start_after_previous_event,  # noqa:E501
        t_break_annot_stop_before_next_event=config.
        t_break_annot_stop_before_next_event,  # noqa:E501
    )
    return cfg
def get_config(
    subject: Optional[str] = None,
    session: Optional[str] = None
) -> BunchConst:
    cfg = BunchConst(
        task=config.get_task(),
        runs=config.get_runs(subject=subject),
        datatype=config.get_datatype(),
        acq=config.acq,
        rec=config.rec,
        space=config.space,
        mindist=config.mindist,
        spacing=config.spacing,
        use_template_mri=config.use_template_mri,
        ch_types=config.ch_types,
        fs_subject=config.get_fs_subject(subject=subject),
        fs_subjects_dir=config.get_fs_subjects_dir(),
        deriv_root=config.get_deriv_root(),
        bids_root=config.get_bids_root(),
        n_jobs=config.get_n_jobs()
    )
    return cfg
def get_config(
    subject: Optional[str] = None,
    session: Optional[str] = None
) -> BunchConst:
    cfg = BunchConst(
        mf_cal_fname=config.get_mf_cal_fname(subject, session),
        mf_ctc_fname=config.get_mf_ctc_fname(subject, session),
        mf_st_duration=config.mf_st_duration,
        mf_head_origin=config.mf_head_origin,
        process_er=config.process_er,
        runs=config.get_runs(subject=subject),  # XXX needs to accept session!
        use_maxwell_filter=config.use_maxwell_filter,
        proc=config.proc,
        task=config.get_task(),
        datatype=config.get_datatype(),
        acq=config.acq,
        rec=config.rec,
        space=config.space,
        bids_root=config.get_bids_root(),
        deriv_root=config.get_deriv_root(),
        crop_runs=config.crop_runs,
        interactive=config.interactive,
        rename_events=config.rename_events,
        eeg_template_montage=config.eeg_template_montage,
        fix_stim_artifact=config.fix_stim_artifact,
        stim_artifact_tmin=config.stim_artifact_tmin,
        stim_artifact_tmax=config.stim_artifact_tmax,
        find_flat_channels_meg=config.find_flat_channels_meg,
        find_noisy_channels_meg=config.find_noisy_channels_meg,
        mf_reference_run=config.get_mf_reference_run(),
        drop_channels=config.drop_channels,
        find_breaks=config.find_breaks,
        min_break_duration=config.min_break_duration,
        t_break_annot_start_after_previous_event=config.t_break_annot_start_after_previous_event,  # noqa:E501
        t_break_annot_stop_before_next_event=config.t_break_annot_stop_before_next_event,  # noqa:E501
    )
    return cfg