Index

A

acquisition (cmtklib.bids.io.CustomBIDSFile attribute) act_tracking (cmp.stages.preprocessing.preprocessing.PreprocessingConfig attribute) (cmp.stages.registration.registration.RegistrationConfig attribute) aggregate_outputs() (cmtklib.interfaces.fsl.Orient method) anat_flow (cmp.pipelines.common.Pipeline attribute) anat_load_config_json() (in module cmtklib.config) anat_save_config() (in module cmtklib.config) AnatomicalPipeline (class in cmp.pipelines.anatomical.anatomical) AnatomicalPipelineUI (class in cmp.bidsappmanager.pipelines.anatomical.anatomical) ants_bspline_interpolation_parameters (cmp.stages.registration.registration.RegistrationConfig attribute) ants_convergence_thresh (cmp.stages.registration.registration.RegistrationConfig attribute) ants_convergence_winsize (cmp.stages.registration.registration.RegistrationConfig attribute) ants_gauss_interpolation_parameters (cmp.stages.registration.registration.RegistrationConfig attribute) ants_interpolation (cmp.stages.registration.registration.RegistrationConfig attribute) ants_linear_cost (cmp.stages.registration.registration.RegistrationConfig attribute) ants_linear_gradient_step (cmp.stages.registration.registration.RegistrationConfig attribute) ants_linear_sampling_perc (cmp.stages.registration.registration.RegistrationConfig attribute) ants_linear_sampling_strategy (cmp.stages.registration.registration.RegistrationConfig attribute) ants_lower_quantile (cmp.stages.registration.registration.RegistrationConfig attribute) ants_multilab_interpolation_parameters (cmp.stages.registration.registration.RegistrationConfig attribute) ants_nonlinear_cost (cmp.stages.registration.registration.RegistrationConfig attribute)

ants_nonlinear_gradient_step (cmp.stages.registration.registration.RegistrationConfig attribute) ants_nonlinear_total_field_variance (cmp.stages.registration.registration.RegistrationConfig attribute) ants_nonlinear_update_field_variance (cmp.stages.registration.registration.RegistrationConfig attribute) ants_perform_syn (cmp.stages.registration.registration.RegistrationConfig attribute) ants_precision_type (cmp.stages.parcellation.parcellation.ParcellationConfig attribute) ants_probmaskfile (cmp.stages.segmentation.segmentation.SegmentationConfig attribute) ants_regmaskfile (cmp.stages.segmentation.segmentation.SegmentationConfig attribute) ants_templatefile (cmp.stages.segmentation.segmentation.SegmentationConfig attribute) ants_upper_quantile (cmp.stages.registration.registration.RegistrationConfig attribute) apply_inverse_epochs_cartool() (cmtklib.interfaces.pycartool.CartoolInverseSolutionROIExtraction static method) apply_scrubbing (cmp.stages.connectome.fmri_connectome.ConnectomeConfig attribute) apply_to_eroded_brain (cmp.stages.registration.registration.RegistrationConfig attribute) apply_to_eroded_csf (cmp.stages.registration.registration.RegistrationConfig attribute) apply_to_eroded_wm (cmp.stages.registration.registration.RegistrationConfig attribute) ApplymultipleMRConvert ApplymultipleMRCrop ApplymultipleMRTransforms ApplymultipleWarp ApplymultipleXfm atlas (cmtklib.bids.io.CustomBIDSFile attribute) atlas_info (cmp.stages.parcellation.parcellation.ParcellationConfig attribute)

B

Bandpass BBRegister BColors (class in cmtklib.util) bias_field_algo (cmp.stages.preprocessing.preprocessing.PreprocessingConfig attribute) bias_field_correction (cmp.stages.preprocessing.preprocessing.PreprocessingConfig attribute) bids_dir (cmp.stages.common.Stage attribute)

bids_electrodes_file (cmp.stages.eeg.preprocessing.EEGPreprocessingConfig attribute) bids_session_label (cmp.stages.common.Stage attribute) bids_subject_label (cmp.stages.common.Stage attribute) BinaryThreshold BOLD (cmtklib.util.BColors attribute) brain_mask_extraction_tool (cmp.stages.segmentation.segmentation.SegmentationConfig attribute)

C

cartool_electrodes_file (cmp.stages.eeg.preprocessing.EEGPreprocessingConfig attribute) cartool_esi_lamb (cmp.stages.eeg.esi.EEGSourceImagingConfig attribute) cartool_esi_method (cmp.stages.eeg.esi.EEGSourceImagingConfig attribute) cartool_invsol_file (cmp.stages.eeg.esi.EEGSourceImagingConfig attribute) cartool_spi_file (cmp.stages.eeg.esi.EEGSourceImagingConfig attribute) cartool_svd_toi_begin (cmp.stages.eeg.esi.EEGSourceImagingConfig attribute) cartool_svd_toi_end (cmp.stages.eeg.esi.EEGSourceImagingConfig attribute) CartoolInverseSolutionROIExtraction check_config() (cmp.pipelines.anatomical.anatomical.AnatomicalPipeline method) (cmp.pipelines.functional.eeg.EEGPipeline method) (cmp.pipelines.functional.fMRI.fMRIPipeline method) check_configuration_format() (in module cmtklib.config) check_configuration_version() (in module cmtklib.config) check_directory_exists() (in module cmtklib.util) check_input() (cmp.bidsappmanager.pipelines.anatomical.anatomical.AnatomicalPipelineUI method) (cmp.bidsappmanager.pipelines.functional.fMRI.fMRIPipelineUI method) (cmp.pipelines.anatomical.anatomical.AnatomicalPipeline method) (cmp.pipelines.functional.eeg.EEGPipeline method) (cmp.pipelines.functional.fMRI.fMRIPipeline method) check_output() (cmp.bidsappmanager.pipelines.anatomical.anatomical.AnatomicalPipelineUI method) (cmp.pipelines.anatomical.anatomical.AnatomicalPipeline method) circular_layout (cmp.bidsappmanager.stages.connectome.connectome.ConnectomeStageUI attribute) (cmp.bidsappmanager.stages.connectome.eeg_connectome.EEGConnectomeStageUI attribute) (cmp.bidsappmanager.stages.connectome.fmri_connectome.ConnectomeStageUI attribute) (cmp.stages.connectome.connectome.ConnectomeConfig attribute) (cmp.stages.connectome.fmri_connectome.ConnectomeConfig attribute) clear_stages_outputs() (cmp.pipelines.common.Pipeline method) cmat() (in module cmtklib.connectome) cmp module, [1] cmp.bidsappmanager module cmp.bidsappmanager.gui module cmp.bidsappmanager.gui.globals module cmp.bidsappmanager.gui.traits module cmp.bidsappmanager.images module cmp.bidsappmanager.pipelines module cmp.bidsappmanager.pipelines.anatomical module cmp.bidsappmanager.pipelines.anatomical.anatomical module cmp.bidsappmanager.pipelines.diffusion module cmp.bidsappmanager.pipelines.functional module cmp.bidsappmanager.pipelines.functional.eeg module cmp.bidsappmanager.pipelines.functional.fMRI module cmp.bidsappmanager.stages module cmp.bidsappmanager.stages.connectome module cmp.bidsappmanager.stages.connectome.connectome module cmp.bidsappmanager.stages.connectome.eeg_connectome module cmp.bidsappmanager.stages.connectome.fmri_connectome module cmp.bidsappmanager.stages.diffusion module cmp.bidsappmanager.stages.eeg module cmp.bidsappmanager.stages.eeg.esi module cmp.bidsappmanager.stages.eeg.preprocessing module cmp.bidsappmanager.stages.functional module cmp.bidsappmanager.stages.functional.functionalMRI module cmp.bidsappmanager.stages.parcellation module cmp.bidsappmanager.stages.parcellation.parcellation module cmp.bidsappmanager.stages.preprocessing module cmp.bidsappmanager.stages.preprocessing.fmri_preprocessing module cmp.bidsappmanager.stages.preprocessing.preprocessing module cmp.bidsappmanager.stages.registration module cmp.bidsappmanager.stages.registration.registration module cmp.bidsappmanager.stages.segmentation module cmp.bidsappmanager.stages.segmentation.segmentation module cmp.cli module cmp.cli.showmatrix_gpickle module cmp.cli.visualize_eeg_pipeline_outputs module cmp.config module cmp.parser module cmp.pipelines module cmp.pipelines.anatomical module cmp.pipelines.anatomical.anatomical module cmp.pipelines.common module cmp.pipelines.diffusion module cmp.pipelines.functional module cmp.pipelines.functional.eeg module cmp.pipelines.functional.fMRI module cmp.stages module cmp.stages.common module cmp.stages.connectome module cmp.stages.connectome.connectome module cmp.stages.connectome.eeg_connectome module cmp.stages.connectome.fmri_connectome module cmp.stages.diffusion module cmp.stages.eeg module cmp.stages.eeg.esi module cmp.stages.eeg.preprocessing module cmp.stages.functional module cmp.stages.functional.functionalMRI module cmp.stages.parcellation module cmp.stages.parcellation.parcellation module cmp.stages.preprocessing module cmp.stages.preprocessing.fmri_preprocessing module cmp.stages.preprocessing.preprocessing module cmp.stages.registration module cmp.stages.registration.registration module cmp.stages.segmentation module cmp.stages.segmentation.segmentation module cmp.viz module cmp.viz.reports module cmtklib module, [1]

cmtklib.bids module cmtklib.bids.io module cmtklib.bids.network module cmtklib.bids.utils module cmtklib.config module cmtklib.connectome module cmtklib.data module cmtklib.data.parcellation module cmtklib.data.parcellation.util module cmtklib.data.parcellation.viz module cmtklib.diffusion module cmtklib.eeg module cmtklib.functionalMRI module cmtklib.interfaces module cmtklib.interfaces.afni module cmtklib.interfaces.ants module cmtklib.interfaces.freesurfer module cmtklib.interfaces.fsl module cmtklib.interfaces.misc module cmtklib.interfaces.mne module cmtklib.interfaces.mrtrix3 module cmtklib.interfaces.pycartool module cmtklib.parcellation module cmtklib.process module cmtklib.util module CombineParcellations compute_curvature (cmp.stages.connectome.connectome.ConnectomeConfig attribute) compute_curvature_array() (in module cmtklib.connectome) compute_length_array() (in module cmtklib.diffusion) ComputeParcellationRoiVolumes ConcatOutputsAsTuple config (cmp.stages.common.Stage attribute) config_view (cmp.bidsappmanager.stages.connectome.connectome.ConnectomeStageUI attribute) (cmp.bidsappmanager.stages.connectome.eeg_connectome.EEGConnectomeStageUI attribute) (cmp.bidsappmanager.stages.connectome.fmri_connectome.ConnectomeStageUI attribute) (cmp.bidsappmanager.stages.eeg.esi.EEGSourceImagingStageUI attribute) (cmp.bidsappmanager.stages.eeg.preprocessing.EEGPreprocessingStageUI attribute) (cmp.bidsappmanager.stages.functional.functionalMRI.FunctionalMRIStageUI attribute) (cmp.bidsappmanager.stages.parcellation.parcellation.ParcellationStageUI attribute) (cmp.bidsappmanager.stages.preprocessing.fmri_preprocessing.PreprocessingStageUI attribute) (cmp.bidsappmanager.stages.preprocessing.preprocessing.PreprocessingStageUI attribute) (cmp.bidsappmanager.stages.registration.registration.RegistrationStageUI attribute) (cmp.bidsappmanager.stages.segmentation.segmentation.SegmentationStageUI attribute) connectivity_metrics (cmp.bidsappmanager.stages.connectome.connectome.ConnectomeConfigUI attribute) (cmp.bidsappmanager.stages.connectome.eeg_connectome.EEGConnectomeConfigUI attribute) (cmp.stages.connectome.connectome.ConnectomeConfig attribute) (cmp.stages.connectome.eeg_connectome.EEGConnectomeConfig attribute) connectome (cmp.bidsappmanager.pipelines.functional.eeg.EEGPipelineUI attribute) (cmp.bidsappmanager.pipelines.functional.fMRI.fMRIPipelineUI attribute) ConnectomeConfig (class in cmp.stages.connectome.connectome) (class in cmp.stages.connectome.fmri_connectome) ConnectomeConfigUI (class in cmp.bidsappmanager.stages.connectome.connectome) (class in cmp.bidsappmanager.stages.connectome.fmri_connectome) ConnectomeStage (class in cmp.stages.connectome.connectome) (class in cmp.stages.connectome.fmri_connectome) ConnectomeStageUI (class in cmp.bidsappmanager.stages.connectome.connectome) (class in cmp.bidsappmanager.stages.connectome.fmri_connectome) ConstrainedSphericalDeconvolutionMultiTissue ConstrainedSphericalDeconvolutionSingleTissue contrast_type (cmp.stages.registration.registration.RegistrationConfig attribute) convert_config_ini_2_json() (in module cmtklib.config) convert_list_to_tuple() (in module cmtklib.util) copyBrainMaskToFreesurfer copyFileToFreesurfer create_ants_workflow() (cmp.stages.registration.registration.RegistrationStage method) create_bbregister_workflow() (cmp.stages.registration.registration.RegistrationStage method) create_cartool_workflow() (cmp.stages.eeg.esi.EEGSourceImagingStage method) create_configparser_from_pipeline() (in module cmtklib.config) create_datagrabber_node() (cmp.pipelines.anatomical.anatomical.AnatomicalPipeline method) (cmp.pipelines.functional.eeg.EEGPipeline method) (cmp.pipelines.functional.fMRI.fMRIPipeline method) create_datasinker_node() (cmp.pipelines.anatomical.anatomical.AnatomicalPipeline method) (cmp.pipelines.functional.eeg.EEGPipeline method) (cmp.pipelines.functional.fMRI.fMRIPipeline method) create_endpoints_array() (in module cmtklib.connectome) create_flirt_workflow() (cmp.stages.registration.registration.RegistrationStage method) create_mne_workflow() (cmp.stages.eeg.esi.EEGSourceImagingStage method) create_parser() (in module cmp.cli.visualize_eeg_pipeline_outputs) create_pipeline_flow() (cmp.pipelines.anatomical.anatomical.AnatomicalPipeline method) (cmp.pipelines.functional.eeg.EEGPipeline method) (cmp.pipelines.functional.fMRI.fMRIPipeline method) create_roi() (in module cmtklib.parcellation) create_roi_labels() (in module cmp.cli.visualize_eeg_pipeline_outputs) create_stage_flow() (cmp.pipelines.common.Pipeline method) create_subject_configuration_from_ref() (in module cmtklib.config) create_T1_and_Brain() (in module cmtklib.parcellation) create_wm_mask() (in module cmtklib.parcellation) create_workflow() (cmp.stages.connectome.connectome.ConnectomeStage method), [1] (cmp.stages.connectome.eeg_connectome.EEGConnectomeStage method) (cmp.stages.connectome.fmri_connectome.ConnectomeStage method), [1] (cmp.stages.eeg.esi.EEGSourceImagingStage method) (cmp.stages.eeg.preprocessing.EEGPreprocessingStage method) (cmp.stages.functional.functionalMRI.FunctionalMRIStage method), [1] (cmp.stages.parcellation.parcellation.ParcellationStage method), [1] (cmp.stages.preprocessing.fmri_preprocessing.PreprocessingStage method), [1] (cmp.stages.preprocessing.preprocessing.PreprocessingStage method), [1] (cmp.stages.registration.registration.RegistrationStage method), [1] (cmp.stages.segmentation.segmentation.SegmentationStage method), [1] create_workflow_custom() (cmp.stages.parcellation.parcellation.ParcellationStage method) (cmp.stages.segmentation.segmentation.SegmentationStage method) CreateAcqpFile CreateBEM CreateBIDSStandardParcellationLabelIndexMappingFile CreateCMPParcellationNodeDescriptionFilesFromBIDSFile CreateCov CreateFwd CreateIndexFile CreateMultipleCMPParcellationNodeDescriptionFilesFromBIDSFile CreateSpiRoisMapping CreateSrc crop_and_move_datasets() (in module cmtklib.parcellation) crop_and_move_WM_and_GM() (in module cmtklib.parcellation) csf (cmp.stages.functional.functionalMRI.FunctionalMRIConfig attribute) custom_aparcaseg (cmp.stages.segmentation.segmentation.SegmentationConfig attribute) custom_aparcaseg_group (cmp.bidsappmanager.stages.segmentation.segmentation.SegmentationConfigUI attribute) custom_brainmask (cmp.stages.segmentation.segmentation.SegmentationConfig attribute) custom_brainmask_group (cmp.bidsappmanager.stages.segmentation.segmentation.SegmentationConfigUI attribute) custom_csf_mask (cmp.stages.segmentation.segmentation.SegmentationConfig attribute) custom_csf_mask_group (cmp.bidsappmanager.stages.segmentation.segmentation.SegmentationConfigUI attribute) custom_gm_mask (cmp.stages.segmentation.segmentation.SegmentationConfig attribute) custom_gm_mask_group (cmp.bidsappmanager.stages.segmentation.segmentation.SegmentationConfigUI attribute) custom_parcellation (cmp.stages.parcellation.parcellation.ParcellationConfig attribute) custom_parcellation_view (cmp.bidsappmanager.stages.parcellation.parcellation.ParcellationConfigUI attribute) custom_wm_mask (cmp.stages.segmentation.segmentation.SegmentationConfig attribute) custom_wm_mask_group (cmp.bidsappmanager.stages.segmentation.segmentation.SegmentationConfigUI attribute) CustomAparcAsegBIDSFile (class in cmtklib.bids.io) CustomBIDSFile (class in cmtklib.bids.io) CustomBrainMaskBIDSFile (class in cmtklib.bids.io) CustomCSFMaskBIDSFile (class in cmtklib.bids.io) CustomEEGCartoolElectrodesBIDSFile (class in cmtklib.bids.io) CustomEEGCartoolInvSolBIDSFile (class in cmtklib.bids.io) CustomEEGCartoolMapSpiRoisBIDSFile (class in cmtklib.bids.io) CustomEEGCartoolSpiBIDSFile (class in cmtklib.bids.io) CustomEEGElectrodesBIDSFile (class in cmtklib.bids.io) CustomEEGEpochsBIDSFile (class in cmtklib.bids.io) CustomEEGEventsBIDSFile (class in cmtklib.bids.io) CustomEEGMNETransformBIDSFile (class in cmtklib.bids.io) CustomEEGPreprocBIDSFile (class in cmtklib.bids.io) CustomGMMaskBIDSFile (class in cmtklib.bids.io) CustomParcellationBIDSFile (class in cmtklib.bids.io) CustomWMMaskBIDSFile (class in cmtklib.bids.io)

D

datatype (cmtklib.bids.io.CustomBIDSFile attribute) define_custom_mapping() (cmp.pipelines.anatomical.anatomical.AnatomicalPipeline method) (cmp.pipelines.functional.fMRI.fMRIPipeline method) define_inspect_outputs() (cmp.stages.connectome.connectome.ConnectomeStage method) (cmp.stages.connectome.eeg_connectome.EEGConnectomeStage method) (cmp.stages.connectome.fmri_connectome.ConnectomeStage method) (cmp.stages.eeg.esi.EEGSourceImagingStage method) (cmp.stages.eeg.preprocessing.EEGPreprocessingStage method) (cmp.stages.functional.functionalMRI.FunctionalMRIStage method) (cmp.stages.parcellation.parcellation.ParcellationStage method) (cmp.stages.preprocessing.fmri_preprocessing.PreprocessingStage method) (cmp.stages.preprocessing.preprocessing.PreprocessingStage method) (cmp.stages.registration.registration.RegistrationStage method) (cmp.stages.segmentation.segmentation.SegmentationStage method) denoising (cmp.stages.preprocessing.preprocessing.PreprocessingConfig attribute) denoising_algo (cmp.stages.preprocessing.preprocessing.PreprocessingConfig attribute) desc (cmtklib.bids.io.CustomBIDSFile attribute)

description (cmp.stages.preprocessing.preprocessing.PreprocessingConfig attribute) (setup_pypi.VerifyVersionCommand attribute) Despike despiking (cmp.stages.preprocessing.fmri_preprocessing.PreprocessingConfig attribute) Detrending diffusion_imaging_model (cmp.stages.registration.registration.RegistrationConfig attribute) dipy_noise_model (cmp.stages.preprocessing.preprocessing.PreprocessingConfig attribute) discard_n_volumes (cmp.stages.preprocessing.fmri_preprocessing.PreprocessingConfig attribute) DiscardTP dmri_load_config_json() (in module cmtklib.config) dmri_save_config() (in module cmtklib.config) DmriCmat dof (cmp.stages.registration.registration.RegistrationConfig attribute) DVARS_thr (cmp.stages.connectome.fmri_connectome.ConnectomeConfig attribute) DWI2Tensor DWIBiasCorrect DWIDenoise

E

Eddy eddy_correct_motion_correction (cmp.stages.preprocessing.preprocessing.PreprocessingConfig attribute) eddy_correction_algo (cmp.stages.preprocessing.preprocessing.PreprocessingConfig attribute) eddy_current_and_motion_correction (cmp.stages.preprocessing.preprocessing.PreprocessingConfig attribute) EddyOpenMP eeg_load_config_json() (in module cmtklib.config) eeg_save_config() (in module cmtklib.config) eeg_ts_file (cmp.stages.eeg.preprocessing.EEGPreprocessingConfig attribute) EEGConnectomeConfig (class in cmp.stages.connectome.eeg_connectome) EEGConnectomeConfigUI (class in cmp.bidsappmanager.stages.connectome.eeg_connectome) EEGConnectomeStage (class in cmp.stages.connectome.eeg_connectome) EEGConnectomeStageUI (class in cmp.bidsappmanager.stages.connectome.eeg_connectome) EEGLAB2fif EEGPipeline (class in cmp.pipelines.functional.eeg) EEGPipelineUI (class in cmp.bidsappmanager.pipelines.functional.eeg) EEGPreprocessingConfig (class in cmp.stages.eeg.preprocessing) EEGPreprocessingConfigUI (class in cmp.bidsappmanager.stages.eeg.preprocessing) EEGPreprocessingStage (class in cmp.stages.eeg.preprocessing) EEGPreprocessingStageUI (class in cmp.bidsappmanager.stages.eeg.preprocessing) EEGSourceImagingConfig (class in cmp.stages.eeg.esi) EEGSourceImagingConfigUI (class in cmp.bidsappmanager.stages.eeg.esi)

EEGSourceImagingStage (class in cmp.stages.eeg.esi) EEGSourceImagingStageUI (class in cmp.bidsappmanager.stages.eeg.esi) electrodes_file_fmt (cmp.stages.eeg.preprocessing.EEGPreprocessingConfig attribute) Element (class in cmp.viz.reports) enabled (cmp.stages.common.Stage attribute), [1] ENDC (cmtklib.util.BColors attribute) Erode erode_mask() (in module cmtklib.parcellation) esi_tool (cmp.stages.eeg.esi.EEGSourceImagingConfig attribute) EstimateResponseForSHMultiTissue EstimateResponseForSHSingleTissue events_file (cmp.stages.eeg.preprocessing.EEGPreprocessingConfig attribute) extension (cmtklib.bids.io.CustomBIDSFile attribute) extract() (in module cmtklib.parcellation) extract_event_ids_from_json_sidecar() (cmtklib.bids.io.CustomEEGEventsBIDSFile method) extract_freesurfer_subject_dir() (in module cmtklib.util) extract_reconall_base_dir() (in module cmtklib.util) ExtractFSLGrad ExtractHeaderVoxel2WorldMatrix ExtractImageVoxelSizes ExtractMRTrixGrad ExtractPVEsFrom5TT

F

FAIL (cmtklib.util.BColors attribute) fast_use_priors (cmp.stages.preprocessing.preprocessing.PreprocessingConfig attribute) FD_thr (cmp.stages.connectome.fmri_connectome.ConnectomeConfig attribute) fill_stages_outputs() (cmp.pipelines.common.Pipeline method) filter_fibers() (in module cmtklib.diffusion) FilterTractogram find_toolbox_derivatives_containing_file() (in module cmtklib.util) FlipBvec FlipTable flirt_args (cmp.stages.registration.registration.RegistrationConfig attribute) fmri_load_config_json() (in module cmtklib.config) fmri_save_config() (in module cmtklib.config) fMRIPipeline (class in cmp.pipelines.functional.fMRI)

fMRIPipelineUI (class in cmp.bidsappmanager.pipelines.functional.fMRI) freesurfer_args (cmp.stages.segmentation.segmentation.SegmentationConfig attribute) freesurfer_subject_id (cmp.stages.segmentation.segmentation.SegmentationConfig attribute) freesurfer_subjects_dir (cmp.stages.segmentation.segmentation.SegmentationConfig attribute) fs_subject_id (cmp.stages.registration.registration.RegistrationStage attribute) fs_subjects_dir (cmp.stages.registration.registration.RegistrationStage attribute) fsl_cost (cmp.stages.registration.registration.RegistrationConfig attribute) FSLCreateHD functionalMRI (cmp.bidsappmanager.pipelines.functional.fMRI.fMRIPipelineUI attribute) FunctionalMRIConfig (class in cmp.stages.functional.functionalMRI) FunctionalMRIConfigUI (class in cmp.bidsappmanager.stages.functional.functionalMRI) FunctionalMRIStage (class in cmp.stages.functional.functionalMRI) FunctionalMRIStageUI (class in cmp.bidsappmanager.stages.functional.functionalMRI)

G

Generate5tt generate_name_title() (in module cmp.viz.reports) generate_report() (cmp.viz.reports.Report method) generate_reports() (in module cmp.viz.reports) generate_WM_and_GM_mask() (in module cmtklib.parcellation) GenerateGMWMInterface get() (in module cmp.parser) get_anat_process_detail_json() (in module cmtklib.config) get_basename() (in module cmtklib.util) get_dmri_process_detail_json() (in module cmtklib.config) get_docker_wrapper_parser() (in module cmp.parser) get_eeg_process_detail_json() (in module cmtklib.config) get_filename() (cmtklib.bids.io.CustomBIDSFile method) get_filename_path() (cmtklib.bids.io.CustomBIDSFile method) get_fmri_process_detail_json() (in module cmtklib.config) get_freesurfer_subject_id() (in module cmtklib.util) get_icon() (in module cmp.bidsappmanager.gui.globals) get_lausanne2018_parcellation_annot() (in module cmtklib.data.parcellation.util) get_lausanne2018_parcellation_mni_coords() (in module cmtklib.data.parcellation.util) get_native_space_files() (in module cmtklib.bids.utils)

get_native_space_no_desc_files() (in module cmtklib.bids.utils) get_native_space_tsv_sidecar_files() (in module cmtklib.bids.utils) get_nb_of_regions() (cmtklib.bids.io.CustomParcellationBIDSFile method) get_nipype_eeg_pipeline_subject_dir() (cmp.pipelines.functional.eeg.EEGPipeline method) get_parcellation() (in module cmtklib.parcellation) get_pipeline_dictionary_outputs() (in module cmtklib.util) get_process_detail_json() (in module cmtklib.config) get_query_dict() (cmtklib.bids.io.CustomBIDSFile method) get_singularity_wrapper_parser() (in module cmp.parser) get_toolbox_derivatives_dir() (cmtklib.bids.io.CustomBIDSFile method) get_wrapper_parser() (in module cmp.parser) global_conf (cmp.pipelines.anatomical.anatomical.AnatomicalPipeline attribute) (cmp.pipelines.functional.eeg.EEGPipeline attribute) (cmp.pipelines.functional.fMRI.fMRIPipeline attribute) global_nuisance (cmp.stages.functional.functionalMRI.FunctionalMRIConfig attribute) GlobalConfig (class in cmp.pipelines.anatomical.anatomical) (class in cmp.pipelines.functional.eeg) (class in cmp.pipelines.functional.fMRI) gmwmi_seeding (cmp.stages.preprocessing.preprocessing.PreprocessingConfig attribute) (cmp.stages.registration.registration.RegistrationConfig attribute) group_analysis_sconn() (in module cmtklib.connectome)

H

HEADER (cmtklib.util.BColors attribute)

I

imaging_model (cmp.pipelines.functional.fMRI.GlobalConfig attribute) include_thalamic_nuclei_parcellation (cmp.stages.parcellation.parcellation.ParcellationConfig attribute) index() (cmp.viz.reports.Report method) index_error_dir() (cmp.viz.reports.Report method) init (cmp.stages.registration.registration.RegistrationConfig attribute) init_subject_derivatives_dirs() (cmp.pipelines.anatomical.anatomical.AnatomicalPipeline method) (cmp.pipelines.functional.eeg.EEGPipeline method) (cmp.pipelines.functional.fMRI.fMRIPipeline method) input_folders (cmp.pipelines.anatomical.anatomical.AnatomicalPipeline attribute) (cmp.pipelines.functional.eeg.EEGPipeline attribute) (cmp.pipelines.functional.fMRI.fMRIPipeline attribute) inspect_output_button (cmp.bidsappmanager.stages.connectome.connectome.ConnectomeStageUI attribute) (cmp.bidsappmanager.stages.connectome.eeg_connectome.EEGConnectomeStageUI attribute) (cmp.bidsappmanager.stages.connectome.fmri_connectome.ConnectomeStageUI attribute) (cmp.bidsappmanager.stages.eeg.esi.EEGSourceImagingStageUI attribute) (cmp.bidsappmanager.stages.eeg.preprocessing.EEGPreprocessingStageUI attribute) (cmp.bidsappmanager.stages.functional.functionalMRI.FunctionalMRIStageUI attribute) (cmp.bidsappmanager.stages.parcellation.parcellation.ParcellationStageUI attribute) (cmp.bidsappmanager.stages.preprocessing.fmri_preprocessing.PreprocessingStageUI attribute) (cmp.bidsappmanager.stages.preprocessing.preprocessing.PreprocessingStageUI attribute) (cmp.bidsappmanager.stages.registration.registration.RegistrationStageUI attribute) (cmp.bidsappmanager.stages.segmentation.segmentation.SegmentationStageUI attribute)

inspect_outputs (cmp.stages.common.Stage attribute), [1] inspect_outputs_enum (cmp.stages.common.Stage attribute) inspect_outputs_view (cmp.bidsappmanager.stages.connectome.connectome.ConnectomeStageUI attribute) (cmp.bidsappmanager.stages.connectome.eeg_connectome.EEGConnectomeStageUI attribute) (cmp.bidsappmanager.stages.connectome.fmri_connectome.ConnectomeStageUI attribute) (cmp.bidsappmanager.stages.eeg.esi.EEGSourceImagingStageUI attribute) (cmp.bidsappmanager.stages.eeg.preprocessing.EEGPreprocessingStageUI attribute) (cmp.bidsappmanager.stages.functional.functionalMRI.FunctionalMRIStageUI attribute) (cmp.bidsappmanager.stages.parcellation.parcellation.ParcellationStageUI attribute) (cmp.bidsappmanager.stages.preprocessing.fmri_preprocessing.PreprocessingStageUI attribute) (cmp.bidsappmanager.stages.preprocessing.preprocessing.PreprocessingStageUI attribute) (cmp.bidsappmanager.stages.registration.registration.RegistrationStageUI attribute) (cmp.bidsappmanager.stages.segmentation.segmentation.SegmentationStageUI attribute) interpolation (cmp.stages.preprocessing.preprocessing.PreprocessingConfig attribute) is_running() (cmp.stages.common.Stage method) isavailable() (in module cmtklib.util) ismember() (cmtklib.parcellation.CombineParcellations method) isotropic_interpolation (cmp.stages.segmentation.segmentation.SegmentationConfig attribute) isotropic_vox_size (cmp.stages.segmentation.segmentation.SegmentationConfig attribute)

L

label (cmtklib.bids.io.CustomBIDSFile attribute) lausanne2018_parcellation_res (cmp.stages.connectome.eeg_connectome.EEGConnectomeConfig attribute) (cmp.stages.eeg.esi.EEGSourceImagingConfig attribute) length() (in module cmtklib.util) load_graphs() (in module cmtklib.bids.network)

log_visualization (cmp.bidsappmanager.stages.connectome.connectome.ConnectomeStageUI attribute) (cmp.bidsappmanager.stages.connectome.eeg_connectome.EEGConnectomeStageUI attribute) (cmp.bidsappmanager.stages.connectome.fmri_connectome.ConnectomeStageUI attribute) (cmp.stages.connectome.connectome.ConnectomeConfig attribute) (cmp.stages.connectome.fmri_connectome.ConnectomeConfig attribute)

M

magn() (in module cmtklib.util) main() (in module cmp.cli.showmatrix_gpickle) (in module cmp.cli.visualize_eeg_pipeline_outputs) (in module setup_pypi) make_isotropic (cmp.stages.segmentation.segmentation.SegmentationConfig attribute) MathsCommand mean_curvature() (in module cmtklib.util) mne_apply_electrode_transform (cmp.stages.eeg.esi.EEGSourceImagingConfig attribute) mne_electrode_transform_file (cmp.stages.eeg.esi.EEGSourceImagingConfig attribute) mne_esi_method (cmp.stages.eeg.esi.EEGSourceImagingConfig attribute) mne_esi_method_snr (cmp.stages.eeg.esi.EEGSourceImagingConfig attribute) MNEInverseSolutionROI MNESpectralConnectivity module cmp, [1] cmp.bidsappmanager cmp.bidsappmanager.gui cmp.bidsappmanager.gui.globals cmp.bidsappmanager.gui.traits cmp.bidsappmanager.images cmp.bidsappmanager.pipelines cmp.bidsappmanager.pipelines.anatomical cmp.bidsappmanager.pipelines.anatomical.anatomical cmp.bidsappmanager.pipelines.diffusion cmp.bidsappmanager.pipelines.functional cmp.bidsappmanager.pipelines.functional.eeg cmp.bidsappmanager.pipelines.functional.fMRI cmp.bidsappmanager.stages cmp.bidsappmanager.stages.connectome cmp.bidsappmanager.stages.connectome.connectome cmp.bidsappmanager.stages.connectome.eeg_connectome cmp.bidsappmanager.stages.connectome.fmri_connectome cmp.bidsappmanager.stages.diffusion cmp.bidsappmanager.stages.eeg cmp.bidsappmanager.stages.eeg.esi cmp.bidsappmanager.stages.eeg.preprocessing cmp.bidsappmanager.stages.functional cmp.bidsappmanager.stages.functional.functionalMRI cmp.bidsappmanager.stages.parcellation cmp.bidsappmanager.stages.parcellation.parcellation cmp.bidsappmanager.stages.preprocessing cmp.bidsappmanager.stages.preprocessing.fmri_preprocessing cmp.bidsappmanager.stages.preprocessing.preprocessing cmp.bidsappmanager.stages.registration cmp.bidsappmanager.stages.registration.registration cmp.bidsappmanager.stages.segmentation cmp.bidsappmanager.stages.segmentation.segmentation cmp.cli cmp.cli.showmatrix_gpickle cmp.cli.visualize_eeg_pipeline_outputs cmp.config cmp.parser cmp.pipelines cmp.pipelines.anatomical cmp.pipelines.anatomical.anatomical cmp.pipelines.common cmp.pipelines.diffusion cmp.pipelines.functional cmp.pipelines.functional.eeg cmp.pipelines.functional.fMRI cmp.stages cmp.stages.common cmp.stages.connectome cmp.stages.connectome.connectome cmp.stages.connectome.eeg_connectome cmp.stages.connectome.fmri_connectome cmp.stages.diffusion cmp.stages.eeg cmp.stages.eeg.esi cmp.stages.eeg.preprocessing cmp.stages.functional cmp.stages.functional.functionalMRI cmp.stages.parcellation cmp.stages.parcellation.parcellation cmp.stages.preprocessing cmp.stages.preprocessing.fmri_preprocessing cmp.stages.preprocessing.preprocessing cmp.stages.registration cmp.stages.registration.registration cmp.stages.segmentation cmp.stages.segmentation.segmentation cmp.viz cmp.viz.reports cmtklib, [1] cmtklib.bids cmtklib.bids.io cmtklib.bids.network cmtklib.bids.utils cmtklib.config cmtklib.connectome cmtklib.data cmtklib.data.parcellation cmtklib.data.parcellation.util cmtklib.data.parcellation.viz cmtklib.diffusion cmtklib.eeg cmtklib.functionalMRI cmtklib.interfaces cmtklib.interfaces.afni cmtklib.interfaces.ants cmtklib.interfaces.freesurfer cmtklib.interfaces.fsl cmtklib.interfaces.misc cmtklib.interfaces.mne cmtklib.interfaces.mrtrix3 cmtklib.interfaces.pycartool cmtklib.parcellation cmtklib.process cmtklib.util setup_pypi

motion (cmp.stages.functional.functionalMRI.FunctionalMRIConfig attribute) motion_correction (cmp.stages.preprocessing.fmri_preprocessing.PreprocessingConfig attribute) MRConvert MRCrop MRThreshold MRTransform MRTrix3Base MRtrix_mul MultipleANTsApplyTransforms MultiSelectAdapter (class in cmp.bidsappmanager.gui.traits)

N

no_search (cmp.stages.registration.registration.RegistrationConfig attribute) now (cmp.pipelines.anatomical.anatomical.AnatomicalPipeline attribute) (cmp.pipelines.functional.eeg.EEGPipeline attribute) (cmp.pipelines.functional.fMRI.fMRIPipeline attribute)

NuisanceRegression number_of_cores (cmp.pipelines.common.Pipeline attribute) number_of_threads (cmp.stages.segmentation.segmentation.SegmentationConfig attribute)

O

OKBLUE (cmtklib.util.BColors attribute) OKGREEN (cmtklib.util.BColors attribute) order_by_run() (in module cmp.viz.reports) ordered_stage_list (cmp.pipelines.anatomical.anatomical.AnatomicalPipeline attribute) (cmp.pipelines.functional.eeg.EEGPipeline attribute) (cmp.pipelines.functional.fMRI.fMRIPipeline attribute) Orient

output_dir (cmp.stages.common.Stage attribute) output_types (cmp.bidsappmanager.stages.connectome.connectome.ConnectomeConfigUI attribute) (cmp.bidsappmanager.stages.connectome.eeg_connectome.EEGConnectomeConfigUI attribute) (cmp.bidsappmanager.stages.connectome.fmri_connectome.ConnectomeConfigUI attribute) (cmp.stages.connectome.connectome.ConnectomeConfig attribute) (cmp.stages.connectome.eeg_connectome.EEGConnectomeConfig attribute) (cmp.stages.connectome.fmri_connectome.ConnectomeConfig attribute)

P

Parcellate ParcellateBrainstemStructures ParcellateHippocampalSubfields ParcellateThalamus parcellation (cmp.bidsappmanager.pipelines.anatomical.anatomical.AnatomicalPipelineUI attribute) parcellation_scheme (cmp.stages.connectome.eeg_connectome.EEGConnectomeConfig attribute) (cmp.stages.eeg.esi.EEGSourceImagingConfig attribute) (cmp.stages.parcellation.parcellation.ParcellationConfig attribute) parcellation_scheme_editor (cmp.stages.parcellation.parcellation.ParcellationConfig attribute) ParcellationConfig (class in cmp.stages.parcellation.parcellation) ParcellationConfigUI (class in cmp.bidsappmanager.stages.parcellation.parcellation) ParcellationStage (class in cmp.stages.parcellation.parcellation) ParcellationStageUI (class in cmp.bidsappmanager.stages.parcellation.parcellation) partial_volume_estimation (cmp.stages.preprocessing.preprocessing.PreprocessingConfig attribute) Pipeline (class in cmp.pipelines.common) pipeline (cmp.stages.registration.registration.RegistrationConfig attribute) pipeline_group (cmp.bidsappmanager.pipelines.anatomical.anatomical.AnatomicalPipelineUI attribute) (cmp.bidsappmanager.pipelines.functional.eeg.EEGPipelineUI attribute) (cmp.bidsappmanager.pipelines.functional.fMRI.fMRIPipelineUI attribute) pipeline_mode (cmp.stages.parcellation.parcellation.ParcellationConfig attribute) plot_connectivity_circle() (in module cmp.cli.showmatrix_gpickle)

plot_lausanne2018_surface_ctx() (in module cmtklib.data.parcellation.viz) plot_roi_time_series() (in module cmp.cli.visualize_eeg_pipeline_outputs) preprocessing (cmp.bidsappmanager.pipelines.functional.eeg.EEGPipelineUI attribute) (cmp.bidsappmanager.pipelines.functional.fMRI.fMRIPipelineUI attribute) PreprocessingConfig (class in cmp.stages.preprocessing.fmri_preprocessing) (class in cmp.stages.preprocessing.preprocessing) PreprocessingConfigUI (class in cmp.bidsappmanager.stages.preprocessing.fmri_preprocessing) (class in cmp.bidsappmanager.stages.preprocessing.preprocessing) PreprocessingStage (class in cmp.stages.preprocessing.fmri_preprocessing) (class in cmp.stages.preprocessing.preprocessing) PreprocessingStageUI (class in cmp.bidsappmanager.stages.preprocessing.fmri_preprocessing) (class in cmp.bidsappmanager.stages.preprocessing.preprocessing) print_blue() (in module cmtklib.util) print_error() (in module cmtklib.util) print_warning() (in module cmtklib.util) process() (cmp.pipelines.anatomical.anatomical.AnatomicalPipeline method) (cmp.pipelines.functional.eeg.EEGPipeline method) (cmp.pipelines.functional.fMRI.fMRIPipeline method) process_type (cmp.pipelines.anatomical.anatomical.GlobalConfig attribute) (cmp.pipelines.functional.eeg.GlobalConfig attribute) (cmp.pipelines.functional.fMRI.GlobalConfig attribute)

R

rec (cmtklib.bids.io.CustomBIDSFile attribute) registration (cmp.bidsappmanager.pipelines.functional.fMRI.fMRIPipelineUI attribute) registration_mode (cmp.stages.registration.registration.RegistrationConfig attribute) registration_mode_trait (cmp.stages.registration.registration.RegistrationConfig attribute) RegistrationConfig (class in cmp.stages.registration.registration) RegistrationConfigUI (class in cmp.bidsappmanager.stages.registration.registration) RegistrationStage (class in cmp.stages.registration.registration) RegistrationStageUI (class in cmp.bidsappmanager.stages.registration.registration) Rename001

repetition_time (cmp.stages.preprocessing.fmri_preprocessing.PreprocessingConfig attribute) Report (class in cmp.viz.reports) Reportlet (class in cmp.viz.reports) res (cmtklib.bids.io.CustomBIDSFile attribute) resampling (cmp.stages.preprocessing.preprocessing.PreprocessingConfig attribute) return_button_style_sheet() (in module cmtklib.util) RsfmriCmat run() (in module cmtklib.process) (setup_pypi.VerifyVersionCommand method) run_reports() (in module cmp.viz.reports)

S

save_configparser_as_json() (in module cmtklib.config) save_eeg_connectome_file() (in module cmtklib.eeg) save_fibers() (in module cmtklib.connectome) Scrubbing seg_tool (cmp.stages.segmentation.segmentation.SegmentationConfig attribute) segment_brainstem (cmp.stages.parcellation.parcellation.ParcellationConfig attribute) segment_hippocampal_subfields (cmp.stages.parcellation.parcellation.ParcellationConfig attribute) segmentation (cmp.bidsappmanager.pipelines.anatomical.anatomical.AnatomicalPipelineUI attribute) SegmentationConfig (class in cmp.stages.segmentation.segmentation) SegmentationConfigUI (class in cmp.bidsappmanager.stages.segmentation.segmentation) SegmentationStage (class in cmp.stages.segmentation.segmentation) SegmentationStageUI (class in cmp.bidsappmanager.stages.segmentation.segmentation) set_pipeline_attributes_from_config() (in module cmtklib.config) setup_pypi module

SIFT2 slice_timing (cmp.stages.preprocessing.fmri_preprocessing.PreprocessingConfig attribute) sourceimaging (cmp.bidsappmanager.pipelines.functional.eeg.EEGPipelineUI attribute) Stage (class in cmp.stages.common) StreamlineTrack subject (cmp.pipelines.anatomical.anatomical.GlobalConfig attribute) (cmp.pipelines.common.Pipeline attribute) (cmp.pipelines.functional.eeg.GlobalConfig attribute) (cmp.stages.connectome.connectome.ConnectomeConfig attribute) (cmp.stages.connectome.fmri_connectome.ConnectomeConfig attribute) subject_session (cmp.pipelines.anatomical.anatomical.GlobalConfig attribute) (cmp.pipelines.functional.eeg.GlobalConfig attribute) subjects (cmp.pipelines.anatomical.anatomical.GlobalConfig attribute) (cmp.pipelines.functional.eeg.GlobalConfig attribute) SubReport (class in cmp.viz.reports) suffix (cmtklib.bids.io.CustomBIDSFile attribute)

T

t_max (cmp.stages.eeg.preprocessing.EEGPreprocessingConfig attribute) t_min (cmp.stages.eeg.preprocessing.EEGPreprocessingConfig attribute) task (cmtklib.bids.io.CustomBIDSFile attribute) task_label (cmp.stages.connectome.eeg_connectome.EEGConnectomeConfig attribute) (cmp.stages.eeg.esi.EEGSourceImagingConfig attribute) (cmp.stages.eeg.preprocessing.EEGPreprocessingConfig attribute) Tck2Trk Tensor2Vector Tkregister2 toolbox_derivatives_dir (cmtklib.bids.io.CustomBIDSFile attribute) total_readout (cmp.stages.preprocessing.preprocessing.PreprocessingConfig attribute) tracking_tool (cmp.stages.preprocessing.preprocessing.PreprocessingConfig attribute) (cmp.stages.registration.registration.RegistrationConfig attribute)

traits_view (cmp.bidsappmanager.pipelines.anatomical.anatomical.AnatomicalPipelineUI attribute) (cmp.bidsappmanager.pipelines.functional.eeg.EEGPipelineUI attribute) (cmp.bidsappmanager.pipelines.functional.fMRI.fMRIPipelineUI attribute) (cmp.bidsappmanager.stages.connectome.connectome.ConnectomeConfigUI attribute) (cmp.bidsappmanager.stages.connectome.eeg_connectome.EEGConnectomeConfigUI attribute) (cmp.bidsappmanager.stages.connectome.fmri_connectome.ConnectomeConfigUI attribute) (cmp.bidsappmanager.stages.eeg.esi.EEGSourceImagingConfigUI attribute) (cmp.bidsappmanager.stages.eeg.preprocessing.EEGPreprocessingConfigUI attribute) (cmp.bidsappmanager.stages.functional.functionalMRI.FunctionalMRIConfigUI attribute) (cmp.bidsappmanager.stages.parcellation.parcellation.ParcellationConfigUI attribute) (cmp.bidsappmanager.stages.preprocessing.fmri_preprocessing.PreprocessingConfigUI attribute) (cmp.bidsappmanager.stages.preprocessing.preprocessing.PreprocessingConfigUI attribute) (cmp.bidsappmanager.stages.registration.registration.RegistrationConfigUI attribute) (cmp.bidsappmanager.stages.segmentation.segmentation.SegmentationConfigUI attribute)

U

UNDERLINE (cmtklib.util.BColors attribute) unicode2str() (in module cmtklib.util) update_nuisance_requirements() (cmp.pipelines.functional.fMRI.fMRIPipeline method) update_registration() (cmp.pipelines.functional.fMRI.fMRIPipeline method) update_scrubbing() (cmp.pipelines.functional.fMRI.fMRIPipeline method)

UpdateGMWMInterfaceSeeding use_existing_freesurfer_data (cmp.stages.segmentation.segmentation.SegmentationConfig attribute) use_float_precision (cmp.stages.registration.registration.RegistrationConfig attribute) use_fsl_brain_mask (cmp.stages.segmentation.segmentation.SegmentationConfig attribute) uses_qform (cmp.stages.registration.registration.RegistrationConfig attribute)

V

VerifyVersionCommand (class in setup_pypi) view_mode (cmp.bidsappmanager.pipelines.anatomical.anatomical.AnatomicalPipelineUI attribute) (cmp.bidsappmanager.pipelines.functional.eeg.EEGPipelineUI attribute) (cmp.bidsappmanager.pipelines.functional.fMRI.fMRIPipelineUI attribute)

W

WARNING (cmtklib.util.BColors attribute)

wm (cmp.stages.functional.functionalMRI.FunctionalMRIConfig attribute) write_derivative_description() (in module cmtklib.bids.utils)