How to use mriqc - 10 common examples

# Check physical memory
    total_memory = opts.mem_gb
    if total_memory < 0:
        try:
            from psutil import virtual_memory
            total_memory = virtual_memory().total // (1024 ** 3) + 1
        except ImportError:
            MRIQC_LOG.warn('Total physical memory could not be estimated, using %d'
                           'GB as default', DEFAULT_MEM_GB)
            total_memory = DEFAULT_MEM_GB

    if total_memory > 0:
        av_procs = total_memory // 4
        if av_procs < 1:
            MRIQC_LOG.warn('Total physical memory is less than 4GB, memory allocation'
                           ' problems are likely to occur.')
            n_procs = 1
        elif n_procs > av_procs:
            n_procs = av_procs

    settings = {
        'bids_dir': bids_dir,
        'write_graph': opts.write_graph,
        'testing': opts.testing,
        'hmc_afni': opts.hmc_afni,
        'n_procs': n_procs,
        'ants_nthreads': opts.ants_nthreads,
        'output_dir': op.abspath(opts.output_dir),
        'work_dir': op.abspath(opts.work_dir),
        'verbose_reports': opts.verbose_reports or opts.testing
    }

'considered for preprocessing')
    g_afni.add_argument('--stop-idx', action='store', type=int,
                        help='Final volume in functional timeseries that should be '
                             'considered for preprocessing')
    g_afni.add_argument('--correct-slice-timing', action='store_true', default=False,
                        help='Perform slice timing correction')

    opts = parser.parse_args()

    # Build settings dict
    bids_dir = op.abspath(opts.bids_dir)

    # Number of processes
    n_procs = 0
    if opts.nthreads is not None:
        MRIQC_LOG.warn('Option --nthreads has been deprecated in mriqc 0.8.8. '
                       'Please use --n_procs instead.')
        n_procs = opts.nthreads
    if opts.n_procs is not None:
        n_procs = opts.n_procs

    # Check physical memory
    total_memory = opts.mem_gb
    if total_memory < 0:
        try:
            from psutil import virtual_memory
            total_memory = virtual_memory().total // (1024 ** 3) + 1
        except ImportError:
            MRIQC_LOG.warn('Total physical memory could not be estimated, using %d'
                           'GB as default', DEFAULT_MEM_GB)
            total_memory = DEFAULT_MEM_GB

n_procs = 0
    if opts.nthreads is not None:
        MRIQC_LOG.warn('Option --nthreads has been deprecated in mriqc 0.8.8. '
                       'Please use --n_procs instead.')
        n_procs = opts.nthreads
    if opts.n_procs is not None:
        n_procs = opts.n_procs

    # Check physical memory
    total_memory = opts.mem_gb
    if total_memory < 0:
        try:
            from psutil import virtual_memory
            total_memory = virtual_memory().total // (1024 ** 3) + 1
        except ImportError:
            MRIQC_LOG.warn('Total physical memory could not be estimated, using %d'
                           'GB as default', DEFAULT_MEM_GB)
            total_memory = DEFAULT_MEM_GB

    if total_memory > 0:
        av_procs = total_memory // 4
        if av_procs < 1:
            MRIQC_LOG.warn('Total physical memory is less than 4GB, memory allocation'
                           ' problems are likely to occur.')
            n_procs = 1
        elif n_procs > av_procs:
            n_procs = av_procs

    settings = {
        'bids_dir': bids_dir,
        'write_graph': opts.write_graph,
        'testing': opts.testing,

plugin_settings = loadyml(pfile)
    else:
        # Setup multiprocessing
        if settings['n_procs'] == 0:
            settings['n_procs'] = 1
            max_parallel_ants = cpu_count() // settings['ants_nthreads']
            if max_parallel_ants > 1:
                settings['n_procs'] = max_parallel_ants

        if settings['n_procs'] > 1:
            plugin_settings['plugin'] = 'MultiProc'
            plugin_settings['plugin_args'] = {'n_procs': settings['n_procs']}

    MRIQC_LOG.info(
        'Running MRIQC-%s (analysis_level=%s, participant_label=%s)\n\tSettings=%s',
        __version__, opts.analysis_level, opts.participant_label, settings)

    # Set up participant level
    if opts.analysis_level == 'participant':
        for qctype in opts.data_type:
            ms_func = getattr(mwc, 'ms_' + qctype)
            workflow = ms_func(subject_id=opts.participant_label, session_id=opts.session_id,
                               run_id=opts.run_id, settings=settings)
            if workflow is None:
                MRIQC_LOG.warn(
                    '%s QC workflow - no scans were found for the given inputs',
                    'Anatomical' if qctype[:4] == 'anat' else 'Functional')
                continue

            workflow.base_dir = settings['work_dir']
            if settings.get('write_graph', False):
                workflow.write_graph()

from yaml import load as loadyml
        with open(opts.use_plugin) as pfile:
            plugin_settings = loadyml(pfile)
    else:
        # Setup multiprocessing
        if settings['n_procs'] == 0:
            settings['n_procs'] = 1
            max_parallel_ants = cpu_count() // settings['ants_nthreads']
            if max_parallel_ants > 1:
                settings['n_procs'] = max_parallel_ants

        if settings['n_procs'] > 1:
            plugin_settings['plugin'] = 'MultiProc'
            plugin_settings['plugin_args'] = {'n_procs': settings['n_procs']}

    MRIQC_LOG.info(
        'Running MRIQC-%s (analysis_level=%s, participant_label=%s)\n\tSettings=%s',
        __version__, opts.analysis_level, opts.participant_label, settings)

    # Set up participant level
    if opts.analysis_level == 'participant':
        for qctype in opts.data_type:
            ms_func = getattr(mwc, 'ms_' + qctype)
            workflow = ms_func(subject_id=opts.participant_label, session_id=opts.session_id,
                               run_id=opts.run_id, settings=settings)
            if workflow is None:
                MRIQC_LOG.warn(
                    '%s QC workflow - no scans were found for the given inputs',
                    'Anatomical' if qctype[:4] == 'anat' else 'Functional')
                continue

            workflow.base_dir = settings['work_dir']

def mock_config():
    """Create a mock config for documentation and testing purposes."""
    from . import config

    filename = Path(pkgrf("mriqc", "data/config-example.toml"))
    settings = loads(filename.read_text())
    for sectionname, configs in settings.items():
        if sectionname != "environment":
            section = getattr(config, sectionname)
            section.load(configs, init=False)
    config.nipype.init()
    config.loggers.init()

    config.execution.work_dir = Path(mkdtemp())
    config.execution.bids_dir = Path(pkgrf("mriqc", "data/tests/ds000005")).absolute()
    config.execution.init()

    yield

def mock_config():
    """Create a mock config for documentation and testing purposes."""
    from . import config

    filename = Path(pkgrf("mriqc", "data/config-example.toml"))
    settings = loads(filename.read_text())
    for sectionname, configs in settings.items():
        if sectionname != "environment":
            section = getattr(config, sectionname)
            section.load(configs, init=False)
    config.nipype.init()
    config.loggers.init()

    config.execution.work_dir = Path(mkdtemp())
    config.execution.bids_dir = Path(pkgrf("mriqc", "data/tests/ds000005")).absolute()
    config.execution.init()

    yield

scale = {"G": 1, "T": 10 ** 3, "M": 1e-3, "K": 1e-6, "B": 1e-9}
        digits = "".join([c for c in value if c.isdigit()])
        units = value[len(digits):] or "G"
        return int(digits) * scale[units[0]]

    def _drop_sub(value):
        value = str(value)
        return value.lstrip("sub-")

    def _bids_filter(value):
        from json import loads

        if value and Path(value).exists():
            return loads(Path(value).read_text())

    verstr = f"MRIQC v{config.environment.version}"
    currentv = Version(config.environment.version)

    parser = ArgumentParser(
        description=f"""\
MRIQC {config.environment.version}
Automated Quality Control and visual reports for Quality Assesment of structural \
(T1w, T2w) and functional MRI of the brain.

{config.DSA_MESSAGE}""",
        formatter_class=ArgumentDefaultsHelpFormatter,
    )
    PathExists = partial(_path_exists, parser=parser)
    PositiveInt = partial(_min_one, parser=parser)

    # Arguments as specified by BIDS-Apps
    # required, positional arguments

def dumps():
    """Format config into toml."""
    from toml import dumps

    return dumps(get())


def to_filename(filename):
    """Write settings to file."""
    filename = Path(filename)
    filename.write_text(dumps())


# Make sure loggers are started
loggers.init()

def git_versions_from_keywords(keywords, tag_prefix, verbose):
    """Get version information from git keywords."""
    if not keywords:
        raise NotThisMethod("no keywords at all, weird")
    date = keywords.get("date")
    if date is not None:
        # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant
        # datestamp. However we prefer "%ci" (which expands to an "ISO-8601
        # -like" string, which we must then edit to make compliant), because
        # it's been around since git-1.5.3, and it's too difficult to
        # discover which version we're using, or to work around using an
        # older one.
        date = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
    refnames = keywords["refnames"].strip()
    if refnames.startswith("$Format"):
        if verbose:
            print("keywords are unexpanded, not using")
        raise NotThisMethod("unexpanded keywords, not a git-archive tarball")
    refs = set([r.strip() for r in refnames.strip("()").split(",")])
    # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of