Index

_

_always_run (fmridenoise.interfaces.bids.BIDSDataSink attribute) (fmridenoise.interfaces.report_creator.ReportCreator attribute) _calculate_quality_measures() (fmridenoise.interfaces.quality_measures.QualityMeasures method) _create_spike_regressors() (fmridenoise.interfaces.confounds.Confounds method) _create_summary_dict() (fmridenoise.interfaces.confounds.Confounds method) _distance_dependence() (fmridenoise.interfaces.quality_measures.QualityMeasures static method) _enough_clean_subjects() (fmridenoise.interfaces.quality_measures.QualityMeasures property) _fill_empty_lists() (in module fmridenoise.interfaces.bids) _filter_acompcors() (fmridenoise.interfaces.confounds.Confounds method) _filter_motion_parameters() (fmridenoise.interfaces.confounds.Confounds method) _filter_tissue_signals() (fmridenoise.interfaces.confounds.Confounds method) _inclusion_check() (fmridenoise.interfaces.confounds.Confounds method) _list_outputs() (fmridenoise.interfaces.bids.BIDSDataSink method) (fmridenoise.interfaces.utility.FlattenIdentityInterface method) _lists_to_entities() (in module fmridenoise.interfaces.bids) _load_confouds() (fmridenoise.interfaces.denoising.Denoise method) _make_summary_figures() (fmridenoise.interfaces.quality_measures.PipelinesQualityMeasures method) _perc_fc_fd_uncorr() (fmridenoise.interfaces.quality_measures.QualityMeasures class method)

_quality_measure() (fmridenoise.interfaces.quality_measures.QualityMeasures class method) _retain() (fmridenoise.interfaces.confounds.Confounds method) _run_interface() (fmridenoise.interfaces.bids.BIDSGrab method) (fmridenoise.interfaces.bids.BIDSValidate method) (fmridenoise.interfaces.confounds.Confounds method) (fmridenoise.interfaces.confounds.GroupConfounds method) (fmridenoise.interfaces.connectivity.Connectivity method) (fmridenoise.interfaces.connectivity.GroupConnectivity method) (fmridenoise.interfaces.denoising.Denoise method) (fmridenoise.interfaces.pipeline_selector.PipelineSelector method) (fmridenoise.interfaces.quality_measures.PipelinesQualityMeasures method) (fmridenoise.interfaces.quality_measures.QualityMeasures method) (fmridenoise.interfaces.report_creator.ReportCreator method) (fmridenoise.interfaces.smoothing.Smooth method) _select_one() (fmridenoise.interfaces.bids.BIDSGrab method) _validate_filtering() (fmridenoise.interfaces.denoising.Denoise method) _validate_fmri_prep_files() (fmridenoise.interfaces.denoising.Denoise method) _validate_group_conf_summary() (fmridenoise.interfaces.quality_measures.QualityMeasures method) _warnings() (fmridenoise.interfaces.quality_measures.QualityMeasures property)

A

asdict() (fmridenoise.utils.error_data.ErrorData method)

assert_all_entities_equal() (in module fmridenoise.utils.entities)

B

BIDSDataSink (class in fmridenoise.interfaces.bids) BIDSDataSinkInputSpec (class in fmridenoise.interfaces.bids) BIDSDataSinkOutputSpec (class in fmridenoise.interfaces.bids) BIDSGrab (class in fmridenoise.interfaces.bids) BIDSGrabInputSpec (class in fmridenoise.interfaces.bids) BIDSGrabOutputSpec (class in fmridenoise.interfaces.bids)

BIDSValidate (class in fmridenoise.interfaces.bids) BIDSValidateInputSpec (class in fmridenoise.interfaces.bids) BIDSValidateOutputSpec (class in fmridenoise.interfaces.bids) build() (fmridenoise.workflows.base.WorkflowBuilder method) build_message() (fmridenoise.utils.error_data.ErrorData method) build_path() (in module fmridenoise.utils.entities)

C

calculate_fc_fd_correlations() (fmridenoise.interfaces.quality_measures.QualityMeasures static method) carpet_plot_pattern (fmridenoise.interfaces.connectivity.Connectivity attribute) cast_bool() (in module fmridenoise.utils.utils) check_symmetry() (in module fmridenoise.utils.numeric) cleanup_tempdirs() (in module fmridenoise.utils.temps) compare() (in module fmridenoise.__main__) conf_prep_pattern (fmridenoise.interfaces.confounds.Confounds attribute) conf_summary_pattern (fmridenoise.interfaces.confounds.Confounds attribute) Confounds (class in fmridenoise.interfaces.confounds) ConfoundsInputSpec (class in fmridenoise.interfaces.confounds)

ConfoundsOutputSpec (class in fmridenoise.interfaces.confounds) conn_file_pattern (fmridenoise.interfaces.connectivity.Connectivity attribute) Connectivity (class in fmridenoise.interfaces.connectivity) ConnectivityInputSpec (class in fmridenoise.interfaces.connectivity) ConnectivityOutputSpec (class in fmridenoise.interfaces.connectivity) copy_as_dummy_dataset() (in module fmridenoise.utils.utils) create_dataset_description_json_content() (in module fmridenoise.utils.utils) create_flatten_identity_join_node() (in module fmridenoise.utils.utils) create_identity_join_node() (in module fmridenoise.utils.utils) create_report() (in module fmridenoise.utils.report_creator) critical (fmridenoise.utils.error_data.ErrorData attribute)

D

data_files_pattern (fmridenoise.interfaces.quality_measures.PipelinesQualityMeasures attribute) Denoise (class in fmridenoise.interfaces.denoising)

DenoiseInputSpec (class in fmridenoise.interfaces.denoising) DenoiseOutputSpec (class in fmridenoise.interfaces.denoising) dummy() (in module fmridenoise.__main__)

E

edges_weight_to_dataframe() (fmridenoise.interfaces.quality_measures.PipelinesQualityMeasures static method) entities (fmridenoise.utils.error_data.ErrorData attribute) entities() (fmridenoise.utils.dataclasses.excluded_subjects.ExcludedSubjects property) error() (fmridenoise.utils.error_data.ErrorData class method)

ErrorData (class in fmridenoise.utils.error_data) excluded (fmridenoise.utils.dataclasses.excluded_subjects.ExcludedSubjects attribute) ExcludedSubjects (class in fmridenoise.utils.dataclasses.excluded_subjects) extract_pipeline_from_path() (in module fmridenoise.pipelines)

F

fc_fd_corr_values_to_dataframe() (fmridenoise.interfaces.quality_measures.PipelinesQualityMeasures static method) file_pattern (fmridenoise.interfaces.confounds.GroupConfounds attribute) FlattenIdentityInterface (class in fmridenoise.interfaces.utility) fmri_denoised_pattern (fmridenoise.interfaces.denoising.Denoise attribute) fmridenoise module fmridenoise.__main__ module fmridenoise._version module fmridenoise.interfaces module fmridenoise.interfaces.bids module fmridenoise.interfaces.confounds module fmridenoise.interfaces.connectivity module fmridenoise.interfaces.denoising module fmridenoise.interfaces.pipeline_selector module fmridenoise.interfaces.quality_measures module fmridenoise.interfaces.report_creator module fmridenoise.interfaces.smoothing module fmridenoise.interfaces.utility module fmridenoise.parcellation module fmridenoise.pipelines module

fmridenoise.utils module fmridenoise.utils.dataclasses module fmridenoise.utils.dataclasses.excluded_subjects module fmridenoise.utils.dataclasses.runtime_info module fmridenoise.utils.entities module fmridenoise.utils.error_data module fmridenoise.utils.json_validator module fmridenoise.utils.numeric module fmridenoise.utils.plotting module fmridenoise.utils.profiling module fmridenoise.utils.report_creator module fmridenoise.utils.temps module fmridenoise.utils.traits module fmridenoise.utils.utils module fmridenoise.workflows module fmridenoise.workflows.base module

G

get_distance_matrix_file_path() (in module fmridenoise.parcellation) get_entity_files() (fmridenoise.interfaces.bids.BIDSValidate static method) get_parcellation_file_path() (in module fmridenoise.parcellation) get_parser() (in module fmridenoise.__main__) get_pipeline_name() (in module fmridenoise.pipelines) get_pipeline_path() (in module fmridenoise.pipelines) get_pipelines_names() (in module fmridenoise.pipelines) get_pipelines_paths() (in module fmridenoise.pipelines)

get_versions() (in module fmridenoise._version) group_corr_pattern (fmridenoise.interfaces.connectivity.GroupConnectivity attribute) GroupConfounds (class in fmridenoise.interfaces.confounds) GroupConfoundsInputSpec (class in fmridenoise.interfaces.confounds) GroupConfoundsOutputSpec (class in fmridenoise.interfaces.confounds) GroupConnectivity (class in fmridenoise.interfaces.connectivity) GroupConnectivityInputSpec (class in fmridenoise.interfaces.connectivity) GroupConnectivityOutputSpec (class in fmridenoise.interfaces.connectivity)

I

init_fmridenoise_wf() (in module fmridenoise.workflows.base) input_args (fmridenoise.utils.dataclasses.runtime_info.RuntimeInfo attribute) input_spec (fmridenoise.interfaces.bids.BIDSDataSink attribute) (fmridenoise.interfaces.bids.BIDSGrab attribute) (fmridenoise.interfaces.bids.BIDSValidate attribute) (fmridenoise.interfaces.confounds.Confounds attribute) (fmridenoise.interfaces.confounds.GroupConfounds attribute) (fmridenoise.interfaces.connectivity.Connectivity attribute) (fmridenoise.interfaces.connectivity.GroupConnectivity attribute) (fmridenoise.interfaces.denoising.Denoise attribute) (fmridenoise.interfaces.pipeline_selector.PipelineSelector attribute) (fmridenoise.interfaces.quality_measures.PipelinesQualityMeasures attribute) (fmridenoise.interfaces.quality_measures.QualityMeasures attribute) (fmridenoise.interfaces.report_creator.ReportCreator attribute) (fmridenoise.interfaces.smoothing.Smooth attribute)

is_booleanlike() (in module fmridenoise.utils.utils) is_entity_subset() (in module fmridenoise.utils.entities) is_IcaAROMA() (in module fmridenoise.pipelines) is_same_group() (fmridenoise.utils.dataclasses.excluded_subjects.ExcludedSubjects method) is_valid() (in module fmridenoise.utils.json_validator) is_valid_name() (in module fmridenoise.pipelines)

L

load_pipeline_from_json() (in module fmridenoise.pipelines)

M

main() (in module fmridenoise.__main__) make_carpetplot() (in module fmridenoise.utils.plotting) make_catplot() (in module fmridenoise.utils.plotting) make_corr_matrix_plot() (in module fmridenoise.utils.plotting) make_kdeplot() (in module fmridenoise.utils.plotting) make_motion_plot() (in module fmridenoise.utils.plotting) make_violinplot() (in module fmridenoise.utils.plotting) matrix_plot_pattern (fmridenoise.interfaces.connectivity.Connectivity attribute) message (fmridenoise.utils.error_data.ErrorData attribute) MissingFile mkdtemp() (in module fmridenoise.utils.temps) module fmridenoise fmridenoise.__main__ fmridenoise._version fmridenoise.interfaces fmridenoise.interfaces.bids fmridenoise.interfaces.confounds fmridenoise.interfaces.connectivity fmridenoise.interfaces.denoising fmridenoise.interfaces.pipeline_selector fmridenoise.interfaces.quality_measures fmridenoise.interfaces.report_creator fmridenoise.interfaces.smoothing fmridenoise.interfaces.utility fmridenoise.parcellation fmridenoise.pipelines fmridenoise.utils fmridenoise.utils.dataclasses fmridenoise.utils.dataclasses.excluded_subjects fmridenoise.utils.dataclasses.runtime_info fmridenoise.utils.entities fmridenoise.utils.error_data fmridenoise.utils.json_validator fmridenoise.utils.numeric fmridenoise.utils.plotting fmridenoise.utils.profiling fmridenoise.utils.report_creator fmridenoise.utils.temps fmridenoise.utils.traits fmridenoise.utils.utils fmridenoise.workflows fmridenoise.workflows.base

O

Optional() (in module fmridenoise.utils.traits) output_dir_pattern (fmridenoise.interfaces.bids.BIDSDataSink attribute) output_path_pattern (fmridenoise.interfaces.bids.BIDSDataSink attribute) output_spec (fmridenoise.interfaces.bids.BIDSDataSink attribute) (fmridenoise.interfaces.bids.BIDSGrab attribute) (fmridenoise.interfaces.bids.BIDSValidate attribute) (fmridenoise.interfaces.confounds.Confounds attribute) (fmridenoise.interfaces.confounds.GroupConfounds attribute) (fmridenoise.interfaces.connectivity.Connectivity attribute) (fmridenoise.interfaces.connectivity.GroupConnectivity attribute) (fmridenoise.interfaces.denoising.Denoise attribute) (fmridenoise.interfaces.pipeline_selector.PipelineSelector attribute) (fmridenoise.interfaces.quality_measures.PipelinesQualityMeasures attribute) (fmridenoise.interfaces.quality_measures.QualityMeasures attribute) (fmridenoise.interfaces.smoothing.Smooth attribute)

P

parse_file_entities_with_pipelines() (in module fmridenoise.utils.entities) parse_pipelines() (in module fmridenoise.__main__) pipeline_name (fmridenoise.utils.dataclasses.excluded_subjects.ExcludedSubjects attribute) pipeline_summaries_to_dataframe() (fmridenoise.interfaces.quality_measures.PipelinesQualityMeasures static method) PipelineSelector (class in fmridenoise.interfaces.pipeline_selector) PipelineSelectorInputSpecification (class in fmridenoise.interfaces.pipeline_selector) PipelineSelectorOutPutSpecification (class in fmridenoise.interfaces.pipeline_selector)

PipelinesQualityMeasures (class in fmridenoise.interfaces.quality_measures) PipelinesQualityMeasuresInputSpec (class in fmridenoise.interfaces.quality_measures) PipelinesQualityMeasuresOutputSpec (class in fmridenoise.interfaces.quality_measures) plot_pattern (fmridenoise.interfaces.quality_measures.PipelinesQualityMeasures attribute) (fmridenoise.interfaces.quality_measures.QualityMeasures attribute) profiler_callback() (in module fmridenoise.utils.profiling) pval_tresh (fmridenoise.interfaces.quality_measures.QualityMeasures attribute)

Q

QualityMeasures (class in fmridenoise.interfaces.quality_measures)

QualityMeasuresInputSpec (class in fmridenoise.interfaces.quality_measures) QualityMeasuresOutputSpec (class in fmridenoise.interfaces.quality_measures)

R

remove_undefined() (in module fmridenoise.utils.traits) ReportCreator (class in fmridenoise.interfaces.report_creator)

ReportCreatorInputSpec (class in fmridenoise.interfaces.report_creator) run (fmridenoise.utils.dataclasses.excluded_subjects.ExcludedSubjects attribute) RuntimeInfo (class in fmridenoise.utils.dataclasses.runtime_info)

S

select_one() (fmridenoise.interfaces.bids.BIDSGrab static method) session (fmridenoise.utils.dataclasses.excluded_subjects.ExcludedSubjects attribute) Smooth (class in fmridenoise.interfaces.smoothing) smooth_file_pattern (fmridenoise.interfaces.smoothing.Smooth attribute)

SmoothInputSpec (class in fmridenoise.interfaces.smoothing) SmoothOutputSpec (class in fmridenoise.interfaces.smoothing) source_name (fmridenoise.utils.error_data.ErrorData attribute) swap_booleans() (in module fmridenoise.utils.utils)

T

task (fmridenoise.utils.dataclasses.excluded_subjects.ExcludedSubjects attribute)

U

use_fmri_prep() (fmridenoise.workflows.base.WorkflowBuilder method)

use_fmri_prep_aroma() (fmridenoise.workflows.base.WorkflowBuilder method)

V

validate() (in module fmridenoise.utils.json_validator) validate_derivatives() (fmridenoise.interfaces.bids.BIDSValidate static method)

validate_files() (fmridenoise.interfaces.bids.BIDSValidate static method) version (fmridenoise.utils.dataclasses.runtime_info.RuntimeInfo attribute)

W

warning() (fmridenoise.utils.error_data.ErrorData class method) with_runs() (fmridenoise.workflows.base.WorkflowBuilder method)

with_sessions() (fmridenoise.workflows.base.WorkflowBuilder method) WorkflowBuilder (class in fmridenoise.workflows.base)