Index

A

ApplyTransforms (class in xcp_d.interfaces.ants)

atlases (xcp_d.config.execution attribute), [1]

B

band_stop_max (xcp_d.config.workflow attribute), [1] band_stop_min (xcp_d.config.workflow attribute), [1] bandpass_filter (xcp_d.config.workflow attribute), [1] bids_database_dir (xcp_d.config.execution attribute), [1] bids_description_hash (xcp_d.config.execution attribute), [1] bids_filters (xcp_d.config.execution attribute), [1]

BIDSError BIDSWarning boilerplate_only (xcp_d.config.execution attribute), [1] bpf_order (xcp_d.config.workflow attribute), [1] build_boilerplate() (in module xcp_d.cli.workflow) build_workflow() (in module xcp_d.cli.workflow)

C

C3d (class in xcp_d.interfaces.c3) check_deps() (in module xcp_d.cli.parser_utils) check_latest() (in module xcp_d.cli.version) check_pipeline_version() (in module xcp_d.utils.bids) cifti (xcp_d.config.workflow attribute), [1] cli (xcp_d.config.loggers attribute), [1] collect_data() (in module xcp_d.utils.bids) collect_mesh_data() (in module xcp_d.utils.bids) collect_morphometry_data() (in module xcp_d.utils.bids)

collect_participants() (in module xcp_d.utils.bids) collect_run_data() (in module xcp_d.utils.bids) CollectRegistrationFiles (class in xcp_d.interfaces.bids) combineruns (xcp_d.config.workflow attribute), [1] CompositeInvTransformUtil (class in xcp_d.interfaces.ants) ConvertTransformFile (class in xcp_d.interfaces.ants) CopyAtlas (class in xcp_d.interfaces.bids) cpu_count (xcp_d.config.environment attribute), [1] crashfile_format (xcp_d.config.nipype attribute), [1] custom_confounds (xcp_d.config.execution attribute), [1]

D

dcan_qc (xcp_d.config.workflow attribute), [1] debug (xcp_d.config.execution attribute), [1] default (xcp_d.config.loggers attribute), [1] DerivativesDataSink (class in xcp_d.interfaces.bids)

despike (xcp_d.config.workflow attribute), [1] download_example_data() (in module xcp_d.utils.doc) dummy_scans (xcp_d.config.workflow attribute), [1] dumps() (in module xcp_d.config)

E

ensure_list() (in module xcp_d.utils.filemanip) environment (class in xcp_d.config), [1] exact_time (xcp_d.config.workflow attribute), [1]

exec_docker_version (xcp_d.config.environment attribute), [1] exec_env (xcp_d.config.environment attribute), [1] execution (class in xcp_d.config), [1]

F

fd_thresh (xcp_d.config.workflow attribute), [1] fill_doc() (in module xcp_d.utils.doc) fmri_dir (xcp_d.config.execution attribute), [1]

fname_presuffix() (in module xcp_d.utils.filemanip) free_mem (xcp_d.config.environment attribute), [1] from_dict() (in module xcp_d.config) fs_license_file (xcp_d.config.execution attribute), [1]

G

get() (in module xcp_d.config) get_atlas_cifti() (in module xcp_d.utils.atlas) get_atlas_nifti() (in module xcp_d.utils.atlas) get_entity() (in module xcp_d.utils.bids) get_freesurfer_dir() (in module xcp_d.utils.bids)

get_linked_libs (xcp_d.config.nipype attribute), [1] get_parser() (in module xcp_d.cli.combineqc) get_plugin() (xcp_d.config.nipype class method), [1] get_preproc_pipeline_info() (in module xcp_d.utils.bids) group_across_runs() (in module xcp_d.utils.bids)

H

head_radius (xcp_d.config.workflow attribute), [1]

high_pass (xcp_d.config.workflow attribute), [1]

I

init() (xcp_d.config.execution class method), [1] (xcp_d.config.loggers class method), [1] (xcp_d.config.nipype class method), [1] (xcp_d.config.seeds class method) (xcp_d.config.workflow class method)

input_type (xcp_d.config.workflow attribute), [1] interface (xcp_d.config.loggers attribute), [1] is_flagged() (in module xcp_d.cli.version)

J

json_file() (in module xcp_d.cli.parser_utils)

L

layout (xcp_d.config.execution attribute), [1] load() (in module xcp_d.config) log_dir (xcp_d.config.execution attribute), [1]

log_level (xcp_d.config.execution attribute), [1] loggers (class in xcp_d.config), [1] low_mem (xcp_d.config.execution attribute), [1] low_pass (xcp_d.config.workflow attribute), [1]

M

main() (in module xcp_d.cli.combineqc) (in module xcp_d.cli.run) master (xcp_d.config.seeds attribute) md_only_boilerplate (xcp_d.config.execution attribute), [1] memory_gb (xcp_d.config.nipype attribute), [1] min_coverage (xcp_d.config.workflow attribute), [1] min_time (xcp_d.config.workflow attribute), [1] module xcp_d xcp_d.cli xcp_d.cli.combineqc xcp_d.cli.parser xcp_d.cli.parser_utils xcp_d.cli.run xcp_d.cli.version xcp_d.cli.workflow xcp_d.config xcp_d.interfaces.ants xcp_d.interfaces.bids xcp_d.interfaces.c3 xcp_d.utils.atlas xcp_d.utils.bids xcp_d.utils.doc xcp_d.utils.filemanip

motion_filter_order (xcp_d.config.workflow attribute), [1] motion_filter_type (xcp_d.config.workflow attribute), [1]

N

nipype (class in xcp_d.config), [1] nipype_version (xcp_d.config.environment attribute), [1]

notrack (xcp_d.config.execution attribute), [1] nprocs (xcp_d.config.nipype attribute), [1]

O

omp_nthreads (xcp_d.config.nipype attribute), [1] out_path_base (xcp_d.interfaces.bids.DerivativesDataSink attribute)

output_dir (xcp_d.config.execution attribute), [1] overcommit_limit (xcp_d.config.environment attribute), [1] overcommit_policy (xcp_d.config.environment attribute), [1]

P

params (xcp_d.config.workflow attribute), [1] parse_args() (in module xcp_d.cli.parser) participant_label (xcp_d.config.execution attribute), [1]

plugin (xcp_d.config.nipype attribute), [1] plugin_args (xcp_d.config.nipype attribute), [1] process_surfaces (xcp_d.config.workflow attribute), [1]

R

reports_only (xcp_d.config.execution attribute), [1]

resource_monitor (xcp_d.config.nipype attribute), [1] run_uuid (xcp_d.config.execution attribute), [1]

S

seeds (class in xcp_d.config) select_atlases() (in module xcp_d.utils.atlas)

smoothing (xcp_d.config.workflow attribute), [1] split_filename() (in module xcp_d.utils.filemanip) stop_on_first_crash (xcp_d.config.nipype attribute), [1]

T

task_id (xcp_d.config.execution attribute), [1] templateflow_home (xcp_d.config.execution attribute), [1]

templateflow_version (xcp_d.config.environment attribute), [1] to_filename() (in module xcp_d.config)

U

utils (xcp_d.config.loggers attribute), [1]

V

version (xcp_d.config.environment attribute), [1]

W

work_dir (xcp_d.config.execution attribute), [1] workflow (class in xcp_d.config), [1] (xcp_d.config.loggers attribute), [1]

write_atlas_dataset_description() (in module xcp_d.utils.bids) write_dataset_description() (in module xcp_d.utils.bids) write_graph (xcp_d.config.execution attribute), [1]

X

xcp_d module xcp_d.cli module xcp_d.cli.combineqc module xcp_d.cli.parser module xcp_d.cli.parser_utils module xcp_d.cli.run module xcp_d.cli.version module xcp_d.cli.workflow module

xcp_d.config module xcp_d.interfaces.ants module xcp_d.interfaces.bids module xcp_d.interfaces.c3 module xcp_d.utils.atlas module xcp_d.utils.bids module xcp_d.utils.doc module xcp_d.utils.filemanip module xcp_d_dir (xcp_d.config.execution attribute), [1]