Index

_

__init__() (CPAC.pipeline.nipype_pipeline_engine.MapNode method) (CPAC.pipeline.nipype_pipeline_engine.Node method) (CPAC.pipeline.nipype_pipeline_engine.Workflow method) (CPAC.utils.interfaces.function.Function method) (nipype.interfaces.base.core.Interface method)

A

add_nodes() (CPAC.pipeline.nipype_pipeline_engine.Workflow method) aggregate_outputs() (CPAC.utils.interfaces.function.Function method) (nipype.interfaces.base.core.Interface method)

always_run (CPAC.utils.interfaces.function.Function property) (nipype.interfaces.base.core.Interface property)

B

bandpass_voxels() (in module CPAC.nuisance) base_dir (CPAC.pipeline.nipype_pipeline_engine.MapNode attribute) (CPAC.pipeline.nipype_pipeline_engine.Node attribute) (CPAC.pipeline.nipype_pipeline_engine.Workflow attribute)

C

calculate_DVARS() (in module CPAC.generate_motion_statistics) calculate_FD_J() (in module CPAC.generate_motion_statistics) calculate_FD_P() (in module CPAC.generate_motion_statistics) calculate_overlap() (in module CPAC.qc.xcp) calculate_resource_timeseries() (in module CPAC.utils.monitoring.draw_gantt_chart) can_resume (CPAC.utils.interfaces.function.Function property) (nipype.interfaces.base.core.Interface property) check_if_file_is_empty() (in module CPAC.seg_preproc) clone() (CPAC.pipeline.nipype_pipeline_engine.MapNode method) (CPAC.pipeline.nipype_pipeline_engine.Node method) (CPAC.pipeline.nipype_pipeline_engine.Workflow method) compute_fisher_z_score() (in module CPAC.sca) compute_reho() (in module CPAC.reho) connect() (CPAC.pipeline.nipype_pipeline_engine.Workflow method) convert_pvalue_to_r() (in module CPAC.network_centrality) copy_geom() (in module CPAC.easy_thresh) cosine_filter() (in module CPAC.nuisance) CPAC.alff module CPAC.cwas module CPAC.easy_thresh module CPAC.func_preproc module CPAC.generate_motion_statistics module CPAC.group_analysis module CPAC.isc module CPAC.network_centrality module CPAC.nuisance module

CPAC.qc.xcp module CPAC.registration module CPAC.reho module CPAC.sca module CPAC.scrubbing module CPAC.seg_preproc module CPAC.timeseries module CPAC.utils.monitoring.draw_gantt_chart module CPAC.vmhc module create_bbregister_func_to_anat() (in module CPAC.registration) create_cwas() (in module CPAC.cwas) create_event_dict() (in module CPAC.utils.monitoring.draw_gantt_chart) create_fsl_flame_wf() (in module CPAC.group_analysis) create_fsl_fnirt_nonlinear_reg() (in module CPAC.registration) create_fsl_fnirt_nonlinear_reg_nhp() (in module CPAC.registration) create_register_func_to_anat() (in module CPAC.registration) create_register_func_to_anat_use_T2() (in module CPAC.registration) create_regressor_workflow() (in module CPAC.nuisance) create_reho() (in module CPAC.reho) create_sca() (in module CPAC.sca) create_scrubbing_preproc() (in module CPAC.scrubbing) create_seg_preproc_antsJointLabel_method() (in module CPAC.seg_preproc) create_temporal_reg() (in module CPAC.sca) create_wf_calculate_ants_warp() (in module CPAC.registration)

D

disconnect() (CPAC.pipeline.nipype_pipeline_engine.Workflow method)

draw_nodes() (in module CPAC.utils.monitoring.draw_gantt_chart) dvcorr() (in module CPAC.qc.xcp)

E

easy_thresh() (in module CPAC.easy_thresh)

erosion() (in module CPAC.seg_preproc) export() (CPAC.pipeline.nipype_pipeline_engine.Workflow method)

F

f_kendall() (in module CPAC.reho) find_offending_time_points() (in module CPAC.nuisance) fullname (CPAC.pipeline.nipype_pipeline_engine.MapNode property) (CPAC.pipeline.nipype_pipeline_engine.Node property) (CPAC.pipeline.nipype_pipeline_engine.Workflow property)

Function (class in CPAC.utils.interfaces.function)

G

gen_motion_parameters() (in module CPAC.generate_motion_statistics) gen_power_parameters() (in module CPAC.generate_motion_statistics) gen_roi_timeseries() (in module CPAC.timeseries) gen_vertices_timeseries() (in module CPAC.timeseries) gen_voxel_timeseries() (in module CPAC.timeseries) generate_gantt_chart() (in module CPAC.utils.monitoring.draw_gantt_chart) generate_summarize_tissue_mask() (in module CPAC.nuisance) generate_xcp_qc() (in module CPAC.qc.xcp) get_idx() (in module CPAC.func_preproc) get_img_nvols() (in module CPAC.vmhc) get_indx() (in module CPAC.scrubbing) get_mov_parameters() (in module CPAC.scrubbing)

get_node() (CPAC.pipeline.nipype_pipeline_engine.Workflow method) get_operand_expression() (in module CPAC.vmhc) get_operation() (in module CPAC.group_analysis) get_output() (CPAC.pipeline.nipype_pipeline_engine.MapNode method) (CPAC.pipeline.nipype_pipeline_engine.Node method) get_roi_timeseries() (in module CPAC.timeseries) get_spatial_map_timeseries() (in module CPAC.timeseries) get_standard_background_img() (in module CPAC.easy_thresh) get_subnodes() (CPAC.pipeline.nipype_pipeline_engine.MapNode method) get_tuple() (in module CPAC.easy_thresh) get_vertices_timeseries() (in module CPAC.timeseries) get_voxel_timeseries() (in module CPAC.timeseries) getOpString() (in module CPAC.reho)

H

hardcoded_antsJointLabelFusion() (in module CPAC.seg_preproc) hash_exists() (CPAC.pipeline.nipype_pipeline_engine.MapNode method) (CPAC.pipeline.nipype_pipeline_engine.Node method)

help() (CPAC.pipeline.nipype_pipeline_engine.MapNode method) (CPAC.pipeline.nipype_pipeline_engine.Node method) (CPAC.utils.interfaces.function.Function class method) (nipype.interfaces.base.core.Interface class method)

I

ImageTo1D (class in CPAC.generate_motion_statistics) input_spec (CPAC.generate_motion_statistics.ImageTo1D attribute) (CPAC.utils.interfaces.function.Function attribute) inputs (CPAC.pipeline.nipype_pipeline_engine.MapNode property) (CPAC.pipeline.nipype_pipeline_engine.Node property) Interface (class in nipype.interfaces.base.core)

interface (CPAC.pipeline.nipype_pipeline_engine.MapNode property) (CPAC.pipeline.nipype_pipeline_engine.Node property) is_cached() (CPAC.pipeline.nipype_pipeline_engine.MapNode method) (CPAC.pipeline.nipype_pipeline_engine.Node method) itername (CPAC.pipeline.nipype_pipeline_engine.MapNode property) (CPAC.pipeline.nipype_pipeline_engine.Node property) (CPAC.pipeline.nipype_pipeline_engine.Workflow property)

J

joint_mask() (in module CPAC.cwas)

L

list_node_names() (CPAC.pipeline.nipype_pipeline_engine.Workflow method) load() (CPAC.pipeline.nipype_pipeline_engine.MapNode static method) (CPAC.pipeline.nipype_pipeline_engine.Node static method) (CPAC.pipeline.nipype_pipeline_engine.Workflow static method)

load_inputs_from_json() (CPAC.utils.interfaces.function.Function method) log_nodes_cb() (in module CPAC.utils.monitoring)

M

map_to_roi() (in module CPAC.sca) MapNode (class in CPAC.pipeline.nipype_pipeline_engine) mask_erosion() (in module CPAC.seg_preproc) mem_gb (CPAC.pipeline.nipype_pipeline_engine.MapNode property) (CPAC.pipeline.nipype_pipeline_engine.Node property) mem_x (CPAC.pipeline.nipype_pipeline_engine.MapNode property) (CPAC.pipeline.nipype_pipeline_engine.Node property) module CPAC.alff CPAC.cwas CPAC.easy_thresh CPAC.func_preproc CPAC.generate_motion_statistics CPAC.group_analysis CPAC.isc CPAC.network_centrality CPAC.nuisance CPAC.qc.xcp CPAC.registration CPAC.reho CPAC.sca CPAC.scrubbing CPAC.seg_preproc CPAC.timeseries CPAC.utils.monitoring.draw_gantt_chart CPAC.vmhc

motion_power_statistics() (in module CPAC.generate_motion_statistics)

N

n_procs (CPAC.pipeline.nipype_pipeline_engine.MapNode property) (CPAC.pipeline.nipype_pipeline_engine.Node property) name (CPAC.pipeline.nipype_pipeline_engine.MapNode property) (CPAC.pipeline.nipype_pipeline_engine.Node property) (CPAC.pipeline.nipype_pipeline_engine.Workflow property)

nifti_cwas() (in module CPAC.cwas) Node (class in CPAC.pipeline.nipype_pipeline_engine) num_subnodes() (CPAC.pipeline.nipype_pipeline_engine.MapNode method)

O

output_dir() (CPAC.pipeline.nipype_pipeline_engine.MapNode method) (CPAC.pipeline.nipype_pipeline_engine.Node method) output_spec (CPAC.generate_motion_statistics.ImageTo1D attribute) (CPAC.utils.interfaces.function.Function attribute)

outputs (CPAC.pipeline.nipype_pipeline_engine.MapNode property) (CPAC.pipeline.nipype_pipeline_engine.Node property)

P

pick_tissue_from_labels_file() (in module CPAC.seg_preproc) pick_wm_class_0() (in module CPAC.seg_preproc) pick_wm_class_1() (in module CPAC.seg_preproc) pick_wm_class_2() (in module CPAC.seg_preproc)

pick_wm_prob_0() (in module CPAC.seg_preproc) pick_wm_prob_1() (in module CPAC.seg_preproc) pick_wm_prob_2() (in module CPAC.seg_preproc) process_segment_map() (in module CPAC.seg_preproc)

Q

qc_xcp_native() (in module CPAC.qc.xcp)

qc_xcp_skullstripped() (in module CPAC.qc.xcp) qc_xcp_template() (in module CPAC.qc.xcp)

R

random_seed_flags() (in module CPAC.pipeline.random_state.seed) remove_nodes() (CPAC.pipeline.nipype_pipeline_engine.Workflow method) resource_overusage_report() (in module CPAC.utils.monitoring.draw_gantt_chart) resource_report() (in module CPAC.utils.monitoring.draw_gantt_chart) result (CPAC.pipeline.nipype_pipeline_engine.MapNode property) (CPAC.pipeline.nipype_pipeline_engine.Node property)

run() (CPAC.pipeline.nipype_pipeline_engine.MapNode method) (CPAC.pipeline.nipype_pipeline_engine.Node method) (CPAC.pipeline.nipype_pipeline_engine.Workflow method) (CPAC.utils.interfaces.function.Function method) (nipype.interfaces.base.core.Interface method)

S

save() (CPAC.pipeline.nipype_pipeline_engine.MapNode method) (CPAC.pipeline.nipype_pipeline_engine.Node method) (CPAC.pipeline.nipype_pipeline_engine.Workflow method)

save_inputs_to_json() (CPAC.utils.interfaces.function.Function method) set_input() (CPAC.pipeline.nipype_pipeline_engine.MapNode method) (CPAC.pipeline.nipype_pipeline_engine.Node method) strings_from_bids() (in module CPAC.qc.xcp)

U

update() (CPAC.pipeline.nipype_pipeline_engine.MapNode method) (CPAC.pipeline.nipype_pipeline_engine.Node method)

V

version (CPAC.utils.interfaces.function.Function property) (nipype.interfaces.base.core.Interface property)

W

Workflow (class in CPAC.pipeline.nipype_pipeline_engine)

write_graph() (CPAC.pipeline.nipype_pipeline_engine.Workflow method)