SYMBOL INDEX (371 symbols across 59 files)

FILE: .maint/update_authors.py
  function read_md_table (line 11) | def read_md_table(md_text):
  function sort_contributors (line 59) | def sort_contributors(entries, git_lines, exclude=None, last=None):
  function get_git_lines (line 109) | def get_git_lines(fname='line-contributors.txt'):
  function _namelast (line 144) | def _namelast(inlist):
  function cli (line 155) | def cli():
  function zenodo (line 167) | def zenodo(
  function publication (line 246) | def publication(

FILE: mriqc/_warnings.py
  class _LogFormatter (line 50) | class _LogFormatter(logging.Formatter):
    method __init__ (line 55) | def __init__(self, datefmt=None, colored=True, **kwargs):
    method format (line 65) | def format(self, record):

FILE: mriqc/bin/abide2bids.py
  function main (line 46) | def main():
  function fetch (line 103) | def fetch(args: (str, str, str, str)) -> (str, str):
  function _myerror (line 179) | def _myerror(message: str):

FILE: mriqc/bin/dfcheck.py
  function read_iqms (line 38) | def read_iqms(feat_file):
  function main (line 74) | def main():

FILE: mriqc/bin/fs2gif.py
  function main (line 40) | def main():
  function _xvfb_run (line 240) | def _xvfb_run(wait=5, server_args='-screen 0, 1600x1200x24', logs=None):
  function _myerror (line 259) | def _myerror(msg):

FILE: mriqc/bin/labeler.py
  function num_rows (line 32) | def num_rows(data):
  function main (line 39) | def main():

FILE: mriqc/bin/mriqcwebapi_test.py
  function get_parser (line 26) | def get_parser():
  function main (line 57) | def main():

FILE: mriqc/bin/nib_hash.py
  function get_parser (line 35) | def get_parser() -> ArgumentParser:
  function get_hash (line 53) | def get_hash(nii_file: str) -> str:
  function main (line 71) | def main():

FILE: mriqc/bin/subject_wrangler.py
  function main (line 37) | def main():

FILE: mriqc/cli/parser.py
  function _parse_participant_labels (line 30) | def _parse_participant_labels(value):
  function _build_parser (line 51) | def _build_parser():
  function parse_args (line 488) | def parse_args(args=None, namespace=None):

FILE: mriqc/cli/run.py
  function format_elapsed_time (line 26) | def format_elapsed_time(elapsed_timedelta):
  function main (line 35) | def main(argv=None):

FILE: mriqc/cli/version.py
  function check_latest (line 37) | def check_latest():
  function is_flagged (line 85) | def is_flagged():

FILE: mriqc/cli/workflow.py
  function build_workflow (line 34) | def build_workflow(config_file, retval):

FILE: mriqc/config.py
  class _Config (line 234) | class _Config:
    method __init__ (line 240) | def __init__(self):
    method load (line 245) | def load(cls, sections, init=True):
    method get (line 263) | def get(cls) -> dict[str, Any]:
  class settings (line 279) | class settings(_Config):
  class environment (line 290) | class environment(_Config):
  class nipype (line 334) | class nipype(_Config):
    method get_plugin (line 364) | def get_plugin(cls) -> dict[str, Any]:
    method init (line 377) | def init(cls) -> None:
  class execution (line 394) | class execution(_Config):
    method init (line 491) | def init(cls) -> None:
  class workflow (line 576) | class workflow(_Config):
    method init (line 616) | def init(cls) -> None:
  class loggers (line 629) | class loggers:
    method init (line 648) | def init(cls) -> None:
    method getLogger (line 691) | def getLogger(cls, name) -> logging.Logger:
  function from_dict (line 700) | def from_dict(sections: dict) -> None:
  function load (line 707) | def load(filename: str | os.PathLike) -> None:
  function get (line 727) | def get(flat: bool = False) -> dict[str, dict[str, Any]]:
  function dumps (line 746) | def dumps() -> str:
  function to_filename (line 753) | def to_filename(
  function _process_initializer (line 785) | def _process_initializer(config_file: Path) -> None:
  function restore_env (line 810) | def restore_env() -> None:

FILE: mriqc/conftest.py
  function expand_namespace (line 45) | def expand_namespace(doctest_namespace):
  function testdata_path (line 74) | def testdata_path():
  function workdir (line 79) | def workdir():
  function outdir (line 84) | def outdir():

FILE: mriqc/data/config.py
  class GroupTemplate (line 30) | class GroupTemplate:
    method __init__ (line 38) | def __init__(self):
    method compile (line 49) | def compile(self, configs):
    method generate_conf (line 54) | def generate_conf(self, configs, path):

FILE: mriqc/data/reports/embed_resources/boxplots.js
  function makeDistroChart (line 22) | function makeDistroChart(settings) {

FILE: mriqc/data/reports/resources/boxplots.js
  function makeDistroChart (line 22) | function makeDistroChart(settings) {

FILE: mriqc/engine/plugin.py
  function run_node (line 41) | def run_node(node, updatehash, taskid):
  class PluginBase (line 82) | class PluginBase:
    method __init__ (line 85) | def __init__(self, plugin_args=None):
    method run (line 93) | def run(self, graph, config, updatehash=False):
  class DistributedPluginBase (line 114) | class DistributedPluginBase(PluginBase):
    method __init__ (line 147) | def __init__(self, plugin_args=None):
    method _prerun_check (line 160) | def _prerun_check(self, graph):
    method _postrun_check (line 163) | def _postrun_check(self):
    method run (line 166) | def run(self, graph, config, updatehash=False):
    method _get_result (line 238) | def _get_result(self, taskid):
    method _submit_job (line 241) | def _submit_job(self, node, updatehash=False):
    method _clear_task (line 244) | def _clear_task(self, taskid):
    method _clean_queue (line 247) | def _clean_queue(self, jobid, graph, result=None):
    method _send_procs_to_workers (line 271) | def _send_procs_to_workers(self, updatehash=False, graph=None):
    method _submit_mapnode (line 274) | def _submit_mapnode(self, jobid):
    method _local_hash_check (line 299) | def _local_hash_check(self, jobid, graph):
    method _task_finished_cb (line 323) | def _task_finished_cb(self, jobid, cached=False):
    method _generate_dependency_list (line 342) | def _generate_dependency_list(self, graph):
    method _remove_node_deps (line 358) | def _remove_node_deps(self, jobid, graph):
    method _remove_node_dirs (line 375) | def _remove_node_dirs(self):
  class MultiProcPlugin (line 394) | class MultiProcPlugin(DistributedPluginBase):
    method __init__ (line 423) | def __init__(self, pool=None, plugin_args=None):
    method _async_callback (line 455) | def _async_callback(self, args):
    method _get_result (line 459) | def _get_result(self, taskid):
    method _clear_task (line 462) | def _clear_task(self, taskid):
    method _submit_job (line 465) | def _submit_job(self, node, updatehash=False):
    method _prerun_check (line 477) | def _prerun_check(self, graph):
    method _postrun_check (line 493) | def _postrun_check(self):
    method _check_resources (line 496) | def _check_resources(self, running_tasks):
    method _send_procs_to_workers (line 506) | def _send_procs_to_workers(self, updatehash=False, graph=None):
    method _sort_jobs (line 611) | def _sort_jobs(self, jobids, scheduler='tsort'):
  function report_crash (line 620) | def report_crash(node, traceback=None, hostname=None):

FILE: mriqc/instrumentation/resources.py
  function FindProcess (line 48) | def FindProcess(process_name):
  function sample (line 74) | def sample(
  function parse_sample (line 108) | def parse_sample(datapoint, timestamp=None, attrs=SAMPLE_ATTRS):
  function sample2file (line 130) | def sample2file(pid=None, recursive=True, timestamp=None, fd=None, flush...
  class ResourceRecorder (line 147) | class ResourceRecorder(Process):
    method __init__ (line 150) | def __init__(self, pid, frequency=0.2, log_file=None, exclude_probe=Tr...
    method run (line 169) | def run(self, *args, **kwargs):
    method stop (line 214) | def stop(self, *args):

FILE: mriqc/instrumentation/viz.py
  function plot (line 32) | def plot(filename, param='mem_vsm_mb', mask_processes=(), out_file=None):

FILE: mriqc/interfaces/__init__.py
  class DerivativesDataSink (line 40) | class DerivativesDataSink(_DDSink):

FILE: mriqc/interfaces/anatomical.py
  class StructuralQCInputSpec (line 57) | class StructuralQCInputSpec(BaseInterfaceInputSpec):
  class StructuralQCOutputSpec (line 77) | class StructuralQCOutputSpec(TraitedSpec):
  class StructuralQC (line 98) | class StructuralQC(SimpleInterface):
    method _run_interface (line 108) | def _run_interface(self, runtime):  # pylint: disable=R0914,E1101
  class _ArtifactMaskInputSpec (line 270) | class _ArtifactMaskInputSpec(BaseInterfaceInputSpec):
  class _ArtifactMaskOutputSpec (line 289) | class _ArtifactMaskOutputSpec(TraitedSpec):
  class ArtifactMask (line 295) | class ArtifactMask(SimpleInterface):
    method _run_interface (line 303) | def _run_interface(self, runtime):
  class ComputeQI2InputSpec (line 356) | class ComputeQI2InputSpec(BaseInterfaceInputSpec):
  class ComputeQI2OutputSpec (line 361) | class ComputeQI2OutputSpec(TraitedSpec):
  class ComputeQI2 (line 366) | class ComputeQI2(SimpleInterface):
    method _run_interface (line 374) | def _run_interface(self, runtime):
  class HarmonizeInputSpec (line 383) | class HarmonizeInputSpec(BaseInterfaceInputSpec):
  class HarmonizeOutputSpec (line 392) | class HarmonizeOutputSpec(TraitedSpec):
  class Harmonize (line 396) | class Harmonize(SimpleInterface):
    method _run_interface (line 404) | def _run_interface(self, runtime):
  class RotationMaskInputSpec (line 435) | class RotationMaskInputSpec(BaseInterfaceInputSpec):
  class RotationMaskOutputSpec (line 439) | class RotationMaskOutputSpec(TraitedSpec):
  class RotationMask (line 443) | class RotationMask(SimpleInterface):
    method _run_interface (line 451) | def _run_interface(self, runtime):
  function artifact_mask (line 487) | def artifact_mask(imdata, airdata, distance, zscore=10.0):
  function fuzzy_jaccard (line 511) | def fuzzy_jaccard(in_tpms, in_mni_tpms):

FILE: mriqc/interfaces/bids.py
  class IQMFileSinkInputSpec (line 43) | class IQMFileSinkInputSpec(DynamicTraitedSpec, BaseInterfaceInputSpec):
    method __setattr__ (line 65) | def __setattr__(self, key, value):
  class IQMFileSinkOutputSpec (line 76) | class IQMFileSinkOutputSpec(TraitedSpec):
  class IQMFileSink (line 80) | class IQMFileSink(SimpleInterface):
    method __init__ (line 85) | def __init__(self, fields=None, force_run=True, **inputs):
    method _add_field (line 102) | def _add_field(self, name, value=Undefined):
    method _gen_outfile (line 107) | def _gen_outfile(self):
    method _run_interface (line 133) | def _run_interface(self, runtime):
  function _process_name (line 204) | def _process_name(name, val):

FILE: mriqc/interfaces/common/conform_image.py
  class ConformImageInputSpec (line 58) | class ConformImageInputSpec(BaseInterfaceInputSpec):
  class ConformImageOutputSpec (line 68) | class ConformImageOutputSpec(TraitedSpec):
  class ConformImage (line 76) | class ConformImage(SimpleInterface):
    method _warn_suspicious_dtype (line 137) | def _warn_suspicious_dtype(self, dtype: int) -> None:
    method _check_dtype (line 152) | def _check_dtype(self, nii: nib.Nifti1Image) -> nib.Nifti1Image:
    method _run_interface (line 179) | def _run_interface(self, runtime):

FILE: mriqc/interfaces/common/ensure_size.py
  class EnsureSizeInputSpec (line 51) | class EnsureSizeInputSpec(BaseInterfaceInputSpec):
  class EnsureSizeOutputSpec (line 61) | class EnsureSizeOutputSpec(TraitedSpec):
  class EnsureSize (line 70) | class EnsureSize(SimpleInterface):
    method _check_size (line 78) | def _check_size(self, nii: nib.Nifti1Image) -> bool:
    method _run_interface (line 91) | def _run_interface(self, runtime):

FILE: mriqc/interfaces/diffusion.py
  class _DiffusionQCInputSpec (line 74) | class _DiffusionQCInputSpec(_BaseInterfaceInputSpec):
  class _DiffusionQCOutputSpec (line 155) | class _DiffusionQCOutputSpec(TraitedSpec):
  class DiffusionQC (line 175) | class DiffusionQC(SimpleInterface):
    method _run_interface (line 181) | def _run_interface(self, runtime):
  class _ReadDWIMetadataOutputSpec (line 318) | class _ReadDWIMetadataOutputSpec(_ReadSidecarJSONOutputSpec):
  class ReadDWIMetadata (line 328) | class ReadDWIMetadata(ReadSidecarJSON):
    method _run_interface (line 335) | def _run_interface(self, runtime):
  class _WeightedStatInputSpec (line 352) | class _WeightedStatInputSpec(_BaseInterfaceInputSpec):
  class _WeightedStatOutputSpec (line 363) | class _WeightedStatOutputSpec(_TraitedSpec):
  class WeightedStat (line 367) | class WeightedStat(SimpleInterface):
    method _run_interface (line 373) | def _run_interface(self, runtime):
  class _NumberOfShellsInputSpec (line 398) | class _NumberOfShellsInputSpec(_BaseInterfaceInputSpec):
  class _NumberOfShellsOutputSpec (line 404) | class _NumberOfShellsOutputSpec(_TraitedSpec):
  class NumberOfShells (line 432) | class NumberOfShells(SimpleInterface):
    method _run_interface (line 453) | def _run_interface(self, runtime):
  class _ExtractOrientationsInputSpec (line 521) | class _ExtractOrientationsInputSpec(_BaseInterfaceInputSpec):
  class _ExtractOrientationsOutputSpec (line 527) | class _ExtractOrientationsOutputSpec(_TraitedSpec):
  class ExtractOrientations (line 536) | class ExtractOrientations(SimpleInterface):
    method _run_interface (line 542) | def _run_interface(self, runtime):
  class _CorrectSignalDriftInputSpec (line 568) | class _CorrectSignalDriftInputSpec(_BaseInterfaceInputSpec):
  class _CorrectSignalDriftOutputSpec (line 581) | class _CorrectSignalDriftOutputSpec(_TraitedSpec):
  class CorrectSignalDrift (line 588) | class CorrectSignalDrift(SimpleInterface):
    method _run_interface (line 594) | def _run_interface(self, runtime):
  class _SplitShellsInputSpec (line 677) | class _SplitShellsInputSpec(_BaseInterfaceInputSpec):
  class _SplitShellsOutputSpec (line 682) | class _SplitShellsOutputSpec(_TraitedSpec):
  class SplitShells (line 686) | class SplitShells(SimpleInterface):
    method _run_interface (line 692) | def _run_interface(self, runtime):
  class _FilterShellsInputSpec (line 716) | class _FilterShellsInputSpec(_BaseInterfaceInputSpec):
  class _FilterShellsOutputSpec (line 723) | class _FilterShellsOutputSpec(_TraitedSpec):
  class FilterShells (line 730) | class FilterShells(SimpleInterface):
    method _run_interface (line 736) | def _run_interface(self, runtime):
  class _DiffusionModelInputSpec (line 777) | class _DiffusionModelInputSpec(_BaseInterfaceInputSpec):
  class _DiffusionModelOutputSpec (line 786) | class _DiffusionModelOutputSpec(_TraitedSpec):
  class DiffusionModel (line 797) | class DiffusionModel(SimpleInterface):
    method _run_interface (line 809) | def _run_interface(self, runtime):
  class _CCSegmentationInputSpec (line 948) | class _CCSegmentationInputSpec(_BaseInterfaceInputSpec):
  class _CCSegmentationOutputSpec (line 967) | class _CCSegmentationOutputSpec(_TraitedSpec):
  class CCSegmentation (line 973) | class CCSegmentation(SimpleInterface):
    method _run_interface (line 979) | def _run_interface(self, runtime):
  class _SpikingVoxelsMaskInputSpec (line 1070) | class _SpikingVoxelsMaskInputSpec(_BaseInterfaceInputSpec):
  class _SpikingVoxelsMaskOutputSpec (line 1082) | class _SpikingVoxelsMaskOutputSpec(_TraitedSpec):
  class SpikingVoxelsMask (line 1086) | class SpikingVoxelsMask(SimpleInterface):
    method _run_interface (line 1092) | def _run_interface(self, runtime):
  class _PIESNOInputSpec (line 1130) | class _PIESNOInputSpec(_BaseInterfaceInputSpec):
  class _PIESNOOutputSpec (line 1135) | class _PIESNOOutputSpec(_TraitedSpec):
  class PIESNO (line 1140) | class PIESNO(SimpleInterface):
    method _run_interface (line 1146) | def _run_interface(self, runtime):
  class _RotateVectorsInputSpec (line 1175) | class _RotateVectorsInputSpec(_BaseInterfaceInputSpec):
  class _RotateVectorsOutputSpec (line 1189) | class _RotateVectorsOutputSpec(_TraitedSpec):
  class RotateVectors (line 1202) | class RotateVectors(SimpleInterface):
    method _run_interface (line 1208) | def _run_interface(self, runtime):
  function _rms (line 1244) | def _rms(estimator, X):
  function _exp_func (line 1261) | def _exp_func(t, A, K, C):
  function segment_corpus_callosum (line 1265) | def segment_corpus_callosum(
  function get_spike_mask (line 1344) | def get_spike_mask(
  function noise_piesno (line 1393) | def noise_piesno(data: np.ndarray, n_channels: int = 4) -> (np.ndarray, ...

FILE: mriqc/interfaces/functional.py
  class FunctionalQCInputSpec (line 47) | class FunctionalQCInputSpec(BaseInterfaceInputSpec):
  class FunctionalQCOutputSpec (line 71) | class FunctionalQCOutputSpec(TraitedSpec):
  class FunctionalQC (line 87) | class FunctionalQC(SimpleInterface):
    method _run_interface (line 97) | def _run_interface(self, runtime):
  class SpikesInputSpec (line 191) | class SpikesInputSpec(BaseInterfaceInputSpec):
  class SpikesOutputSpec (line 211) | class SpikesOutputSpec(TraitedSpec):
  class Spikes (line 217) | class Spikes(SimpleInterface):
    method _run_interface (line 227) | def _run_interface(self, runtime):
  class _SelectEchoInputSpec (line 268) | class _SelectEchoInputSpec(BaseInterfaceInputSpec):
  class _SelectEchoOutputSpec (line 274) | class _SelectEchoOutputSpec(TraitedSpec):
  class SelectEcho (line 280) | class SelectEcho(SimpleInterface):
    method _run_interface (line 290) | def _run_interface(self, runtime):
  class GatherTimeseriesInputSpec (line 305) | class GatherTimeseriesInputSpec(TraitedSpec):
  class GatherTimeseriesOutputSpec (line 326) | class GatherTimeseriesOutputSpec(TraitedSpec):
  class GatherTimeseries (line 331) | class GatherTimeseries(SimpleInterface):
    method _run_interface (line 340) | def _run_interface(self, runtime):
  function _build_timeseries_metadata (line 383) | def _build_timeseries_metadata():
  function find_peaks (line 460) | def find_peaks(data):
  function find_spikes (line 465) | def find_spikes(data, spike_thresh):
  function _robust_zscore (line 483) | def _robust_zscore(data):
  function select_echo (line 487) | def select_echo(
  function _get_echotime (line 568) | def _get_echotime(inlist):

FILE: mriqc/interfaces/reports.py
  class _AddProvenanceInputSpec (line 38) | class _AddProvenanceInputSpec(BaseInterfaceInputSpec):
  class _AddProvenanceOutputSpec (line 45) | class _AddProvenanceOutputSpec(TraitedSpec):
  class AddProvenance (line 49) | class AddProvenance(SimpleInterface):
    method _run_interface (line 55) | def _run_interface(self, runtime):

FILE: mriqc/interfaces/synthstrip.py
  class _SynthStripInputSpec (line 43) | class _SynthStripInputSpec(CommandLineInputSpec):
  class _SynthStripOutputSpec (line 74) | class _SynthStripOutputSpec(TraitedSpec):
  class SynthStrip (line 79) | class SynthStrip(CommandLine):

FILE: mriqc/interfaces/transitional.py
  class GCORInputSpec (line 32) | class GCORInputSpec(CommandLineInputSpec):
  class GCOROutputSpec (line 57) | class GCOROutputSpec(TraitedSpec):
  class GCOR (line 61) | class GCOR(CommandLine):
    method _run_interface (line 84) | def _run_interface(self, runtime):
    method _list_outputs (line 96) | def _list_outputs(self):

FILE: mriqc/interfaces/webapi.py
  class UploadIQMsInputSpec (line 116) | class UploadIQMsInputSpec(BaseInterfaceInputSpec):
  class UploadIQMsOutputSpec (line 129) | class UploadIQMsOutputSpec(TraitedSpec):
  class UploadIQMs (line 134) | class UploadIQMs(SimpleInterface):
    method _run_interface (line 143) | def _run_interface(self, runtime):
  function upload_qc_metrics (line 204) | def upload_qc_metrics(
  function _hashfields (line 303) | def _hashfields(data):

FILE: mriqc/qc/anatomical.py
  function snr (line 220) | def snr(mu_fg, sigma_fg, n):
  function snr_dietrich (line 243) | def snr_dietrich(mu_fg, mad_air=0.0, sigma_air=1.0):
  function cnr (line 273) | def cnr(mu_wm, mu_gm, sigma_air, sigma_wm, sigma_gm):
  function cjv (line 299) | def cjv(mu_wm, mu_gm, sigma_wm, sigma_gm):
  function fber (line 323) | def fber(img, headmask, rotmask=None, decimals=4):
  function efc (line 355) | def efc(img, framemask=None, decimals=4):
  function wm2max (line 406) | def wm2max(img, mu_wm):
  function art_qi1 (line 421) | def art_qi1(airmask, artmask):
  function art_qi2 (line 448) | def art_qi2(
  function volume_fraction (line 515) | def volume_fraction(pvms):
  function rpve (line 540) | def rpve(pvms, seg):
  function summary_stats (line 568) | def summary_stats(
  function _prepare_mask (line 643) | def _prepare_mask(mask, label, erode=True):

FILE: mriqc/qc/diffusion.py
  class ExtremeValueWarning (line 109) | class ExtremeValueWarning(UserWarning):
  function noise_b0 (line 113) | def noise_b0(
  function cc_snr (line 165) | def cc_snr(
  function spike_ppm (line 266) | def spike_ppm(
  function neighboring_dwi_correlation (line 316) | def neighboring_dwi_correlation(

FILE: mriqc/qc/functional.py
  function gsr (line 217) | def gsr(epi_data, mask, direction='y', ref_file=None, out_file=None):

FILE: mriqc/qc/tests/test_anatomical.py
  class GroundTruth (line 38) | class GroundTruth:
    method get_data (line 39) | def get_data(self, sigma, noise='normal'):
  function gtruth (line 64) | def gtruth():
  function test_qi2 (line 107) | def test_qi2(gtruth, sigma):

FILE: mriqc/qc/tests/test_diffusion.py
  function test_spike_ppm (line 29) | def test_spike_ppm():

FILE: mriqc/reports/group.py
  function gen_html (line 33) | def gen_html(csv_file, mod, csv_failed=None, out_file=None):
  function _format_labels (line 338) | def _format_labels(row, id_labels):

FILE: mriqc/reports/individual.py
  function generate_reports (line 34) | def generate_reports():
  function _single_report (line 45) | def _single_report(in_file):

FILE: mriqc/synthstrip/cli.py
  function main (line 48) | def main():
  function conform (line 176) | def conform(input_nii):
  function resample_like (line 227) | def resample_like(image, target, output_dtype=None, cval=0):

FILE: mriqc/synthstrip/model.py
  class StripModel (line 52) | class StripModel(nn.Module):
    method __init__ (line 53) | def __init__(
    method forward (line 135) | def forward(self, x):
  class ConvBlock (line 159) | class ConvBlock(nn.Module):
    method __init__ (line 164) | def __init__(self, ndims, in_channels, out_channels, stride=1, activat...
    method forward (line 176) | def forward(self, x):

FILE: mriqc/testing.py
  function mock_config (line 36) | def mock_config():

FILE: mriqc/tests/test_config.py
  function _expand_bids (line 30) | def _expand_bids(tmp_path, testdata_path, testcase):
  function test_bids_indexing_manifest (line 66) | def test_bids_indexing_manifest(tmp_path, testdata_path, testcase):

FILE: mriqc/tests/test_main.py
  function set_command (line 32) | def set_command(monkeypatch):
  function test_help (line 38) | def test_help(capsys):
  function test_main (line 45) | def test_main(tmp_path):

FILE: mriqc/tests/test_parser.py
  function _create_set_bids_dir (line 35) | def _create_set_bids_dir(args, _tmp_path):
  function test_parser_errors (line 48) | def test_parser_errors(args, code):
  function test_parser_valid (line 62) | def test_parser_valid(tmp_path, args):
  function test_verbosity_arg (line 79) | def test_verbosity_arg(tmp_path, argdest, argstr, argval):
  function test_species_arg (line 97) | def test_species_arg(tmp_path, argval, _species):

FILE: mriqc/tests/test_reports.py
  function test_anat_reports (line 39) | def test_anat_reports(tmp_path, testdata_path, outdir, dataset, subject):

FILE: mriqc/utils/bids.py
  function write_bidsignore (line 34) | def write_bidsignore(deriv_dir):
  function write_derivative_description (line 47) | def write_derivative_description(bids_dir, deriv_dir):
  function derive_bids_fname (line 103) | def derive_bids_fname(

FILE: mriqc/utils/debug.py
  function is_interactive (line 47) | def is_interactive():
  function setup_exceptionhook (line 54) | def setup_exceptionhook(ipython=False):

FILE: mriqc/utils/misc.py
  function worker (line 72) | async def worker(job: Callable[[], R], semaphore) -> R:
  function reorder_csv (line 78) | def reorder_csv(csv_file, out_file=None):
  function rotate_files (line 111) | def rotate_files(fname):
  function bids_path (line 132) | def bids_path(subid, sesid=None, runid=None, prefix=None, out_path=None,...
  function generate_pred (line 150) | def generate_pred(derivatives_dir, output_dir, mod):
  function generate_tsv (line 192) | def generate_tsv(output_dir, mod):
  function _read_and_save (line 227) | def _read_and_save(in_file):
  function _flatten (line 231) | def _flatten(in_dict, parent_key='', sep='_'):
  function _flatten_dict (line 242) | def _flatten_dict(indict):
  function _flatten_list (line 257) | def _flatten_list(xs):
  function _datalad_get (line 265) | def _datalad_get(input_list, nprocs=None):
  function _file_meta_and_size (line 294) | def _file_meta_and_size(
  function _extract_meta_and_size (line 374) | async def _extract_meta_and_size(
  function initialize_meta_and_data (line 425) | def initialize_meta_and_data(
  function _merge_entities (line 508) | def _merge_entities(

FILE: mriqc/utils/telemetry.py
  function setup_migas (line 6) | def setup_migas(init_ping: bool = True, exit_ping: bool = True) -> None:
  function send_crumb (line 30) | def send_crumb(**kwargs) -> dict:

FILE: mriqc/workflows/anatomical/base.py
  function anat_qc_workflow (line 77) | def anat_qc_workflow(name='anatMRIQC'):
  function spatial_normalization (line 249) | def spatial_normalization(name='SpatialNormalization'):
  function init_brain_tissue_segmentation (line 332) | def init_brain_tissue_segmentation(name='brain_tissue_segmentation'):
  function compute_iqms (line 420) | def compute_iqms(name='ComputeIQMs'):
  function headmsk_wf (line 536) | def headmsk_wf(name='HeadMaskWorkflow', omp_nthreads=1):
  function airmsk_wf (line 615) | def airmsk_wf(name='AirMaskWorkflow'):
  function _binarize (line 684) | def _binarize(in_file, threshold=0.5, out_file=None):
  function _enhance (line 706) | def _enhance(in_file, wm_tpm, out_file=None):
  function image_gradient (line 733) | def image_gradient(in_file, brainmask, sigma=4.0, out_file=None):
  function gradient_threshold (line 761) | def gradient_threshold(in_file, brainmask, thresh=15.0, out_file=None, a...
  function _get_imgtype (line 816) | def _get_imgtype(in_file):
  function _get_mod (line 822) | def _get_mod(in_file):
  function _pop (line 830) | def _pop(inlist):

FILE: mriqc/workflows/anatomical/output.py
  function init_anat_report_wf (line 32) | def init_anat_report_wf(name: str = 'anat_report_wf'):

FILE: mriqc/workflows/core.py
  function init_mriqc_wf (line 38) | def init_mriqc_wf():

FILE: mriqc/workflows/diffusion/base.py
  function dmri_qc_workflow (line 55) | def dmri_qc_workflow(name='dwiMRIQC'):
  function compute_iqms (line 314) | def compute_iqms(name='ComputeIQMs'):
  function hmc_workflow (line 440) | def hmc_workflow(name='dMRI_HMC'):
  function epi_mni_align (line 518) | def epi_mni_align(name='SpatialNormalization'):
  function _mean (line 657) | def _mean(inlist):
  function _parse_tqual (line 663) | def _parse_tqual(in_file):
  function _parse_tout (line 671) | def _parse_tout(in_file):
  function _tolist (line 678) | def _tolist(value):
  function _get_bvals (line 682) | def _get_bvals(bmatrix):
  function _first (line 688) | def _first(inlist):
  function _all_but_first (line 695) | def _all_but_first(inlist):
  function _estimate_sigma (line 702) | def _estimate_sigma(in_file, mask):
  function _bvals_report (line 713) | def _bvals_report(in_file):
  function _filter_metadata (line 724) | def _filter_metadata(

FILE: mriqc/workflows/diffusion/output.py
  function init_dwi_report_wf (line 36) | def init_dwi_report_wf(name='dwi_report_wf'):
  function _carpet_parcellation (line 221) | def _carpet_parcellation(segmentation, crown_mask):
  function _get_tr (line 246) | def _get_tr(meta_dict):
  function _get_wm (line 250) | def _get_wm(in_file, radius=2):

FILE: mriqc/workflows/functional/base.py
  function fmri_qc_workflow (line 54) | def fmri_qc_workflow(name='funcMRIQC'):
  function compute_iqms (line 263) | def compute_iqms(name='ComputeIQMs'):
  function fmri_bmsk_workflow (line 465) | def fmri_bmsk_workflow(name='fMRIBrainMask'):
  function hmc (line 495) | def hmc(name='fMRI_HMC', omp_nthreads=None):
  function epi_mni_align (line 612) | def epi_mni_align(name='SpatialNormalization'):
  function _parse_tqual (line 751) | def _parse_tqual(in_file):
  function _parse_tout (line 762) | def _parse_tout(in_file):
  function _apply_transforms (line 772) | def _apply_transforms(in_file, in_xfm, max_concurrent):

FILE: mriqc/workflows/functional/output.py
  function init_func_report_wf (line 32) | def init_func_report_wf(name='func_report_wf'):
  function spikes_mask (line 345) | def spikes_mask(in_file, in_mask=None, out_file=None):
  function _carpet_parcellation (line 403) | def _carpet_parcellation(segmentation, crown_mask):
  function _get_tr (line 428) | def _get_tr(meta_dict):

FILE: mriqc/workflows/shared.py
  function synthstrip_wf (line 29) | def synthstrip_wf(name='synthstrip_wf', omp_nthreads=None):

FILE: mriqc/workflows/utils.py
  function _tofloat (line 26) | def _tofloat(inlist):
  function fwhm_dict (line 32) | def fwhm_dict(fwhm):
  function thresh_image (line 43) | def thresh_image(in_file, thres=0.5, out_file=None):
  function spectrum_mask (line 65) | def spectrum_mask(size):
  function slice_wise_fft (line 92) | def slice_wise_fft(in_file, ftmask=None, spike_thres=3.0, out_prefix=None):
  function get_fwhmx (line 174) | def get_fwhmx():
  function generate_filename (line 187) | def generate_filename(in_file, dirname=None, suffix='', extension=None):