Index

_

__init__() (qsiprep.engine.workflows.LiterateWorkflow method)

A

add_suffix() (in module qsiprep.utils.misc) aggr_ses_reports (qsiprep.config.execution attribute) anat_modality (qsiprep.config.workflow attribute), [1], [2] anat_only (qsiprep.config.workflow attribute), [1], [2] anatomical_template (qsiprep.config.workflow attribute), [1], [2]

ants (qsiprep.config.seeds attribute) assert_circular() (qsiprep.utils.testing.TestWorkflow method) assert_inputs_set() (qsiprep.utils.testing.TestWorkflow method) assertIsAlmostExpectedWorkflow() (qsiprep.utils.testing.TestWorkflow method) assertIsSubsetOfList() (qsiprep.utils.testing.TestWorkflow method)

B

b0_motion_corr_to (qsiprep.config.workflow attribute), [1], [2] b0_threshold (qsiprep.config.workflow attribute), [1], [2] b0_to_t1w_transform (qsiprep.config.workflow attribute), [1], [2] b1_biascorrect_stage (qsiprep.config.workflow attribute), [1], [2] before_send() (in module qsiprep.utils.sentry) bids_database_dir (qsiprep.config.execution attribute), [1], [2] bids_description_hash (qsiprep.config.execution attribute), [1], [2] bids_dir (qsiprep.config.execution attribute), [1], [2]

bids_filters (qsiprep.config.execution attribute), [1], [2] BIDSDataGrabber (class in qsiprep.interfaces.bids) BIDSError BIDSInfo (class in qsiprep.interfaces.bids) BIDSWarning boilerplate_only (qsiprep.config.execution attribute), [1], [2] build_boilerplate() (in module qsiprep.cli.workflow) build_workflow() (in module qsiprep.cli.workflow)

C

check_deps() (in module qsiprep.utils.misc) check_latest() (in module qsiprep.cli.version) cli (qsiprep.config.loggers attribute), [1], [2] collect_data() (in module qsiprep.utils.bids)

collect_participants() (in module qsiprep.utils.bids) compute_affine() (in module qsiprep.utils.bspline) cpu_count (qsiprep.config.environment attribute), [1], [2] crashfile_format (qsiprep.config.nipype attribute), [1], [2]

D

dataset_links (qsiprep.config.execution attribute), [1], [2] debug (qsiprep.config.execution attribute), [1], [2] default (qsiprep.config.loggers attribute), [1], [2] denoise_after_combining (qsiprep.config.workflow attribute), [1], [2] denoise_method (qsiprep.config.workflow attribute), [1], [2] derivatives (qsiprep.config.execution attribute), [1], [2]

DerivativesDataSink (class in qsiprep.interfaces.bids) DerivativesMaybeDataSink (class in qsiprep.interfaces.bids) distortion_group_merge (qsiprep.config.workflow attribute), [1], [2] dumps() (in module qsiprep.config), [1] dwi_denoise_window (qsiprep.config.workflow attribute), [1], [2] dwi_no_biascorr (qsiprep.config.workflow attribute), [1], [2] dwi_only (qsiprep.config.workflow attribute), [1], [2]

E

eddy_config (qsiprep.config.workflow attribute), [1], [2] environment (class in qsiprep.config), [1], [2]

exec_docker_version (qsiprep.config.environment attribute), [1], [2] exec_env (qsiprep.config.environment attribute), [1], [2] execution (class in qsiprep.config), [1], [2]

F

FileNotFoundError find_fieldmaps_from_other_dwis() (in module qsiprep.utils.grouping) fix_multi_source_name() (in module qsiprep.utils.misc) fix_multi_T1w_source_name() (in module qsiprep.utils.misc)

fmap_bspline (qsiprep.config.workflow attribute), [1], [2] fmap_demean (qsiprep.config.workflow attribute), [1], [2] force_syn (qsiprep.config.workflow attribute), [1], [2] free_mem (qsiprep.config.environment attribute), [1], [2] from_dict() (in module qsiprep.config), [1]

G

get() (in module qsiprep.config), [1] get_bids_params() (in module qsiprep.interfaces.bids) get_concatenated_bids_name() (in module qsiprep.utils.grouping) get_grouping_test_data() (in module qsiprep.utils.testing) get_highest_priority_fieldmap() (in module qsiprep.utils.grouping) get_ijk() (in module qsiprep.utils.bspline) get_inputs_outputs() (qsiprep.utils.testing.TestWorkflow method)

get_linked_libs (qsiprep.config.nipype attribute), [1], [2] get_plugin() (qsiprep.config.nipype class method), [1], [2] get_session_groups() (in module qsiprep.utils.grouping) group_by_warpspace() (in module qsiprep.utils.grouping) group_dwi_scans() (in module qsiprep.utils.grouping) group_for_concatenation() (in module qsiprep.utils.grouping) group_for_eddy() (in module qsiprep.utils.grouping)

H

hmc_model (qsiprep.config.workflow attribute), [1], [2]

hmc_transform (qsiprep.config.workflow attribute), [1], [2]

I

ignore (qsiprep.config.workflow attribute), [1], [2] infant (qsiprep.config.workflow attribute), [1], [2] init() (qsiprep.config.execution class method), [1], [2] (qsiprep.config.loggers class method), [1], [2] (qsiprep.config.nipype class method), [1], [2] (qsiprep.config.seeds class method)

init_spaces() (in module qsiprep.config), [1] interface (qsiprep.config.loggers attribute), [1], [2] intramodal_template_iters (qsiprep.config.workflow attribute), [1], [2] intramodal_template_transform (qsiprep.config.workflow attribute), [1], [2] is_flagged() (in module qsiprep.cli.version) is_interactive() (in module qsiprep.utils.debug)

L

layout (qsiprep.config.execution attribute), [1], [2] LiterateWorkflow (class in qsiprep.engine.workflows) load() (in module qsiprep.config), [1] log_dir (qsiprep.config.execution attribute), [1], [2]

log_level (qsiprep.config.execution attribute), [1], [2] loggers (class in qsiprep.config), [1], [2] longitudinal (qsiprep.config.workflow attribute), [1], [2] low_mem (qsiprep.config.execution attribute), [1], [2]

M

main() (in module qsiprep.cli.run) master (qsiprep.config.seeds attribute) memory_gb (qsiprep.config.nipype attribute), [1], [2] merge_dwi_groups() (in module qsiprep.utils.grouping) module qsiprep qsiprep.cli qsiprep.cli.parser qsiprep.cli.run qsiprep.cli.version qsiprep.cli.workflow qsiprep.config, [1] qsiprep.engine qsiprep.engine.workflows qsiprep.interfaces.bids qsiprep.utils qsiprep.utils.bids qsiprep.utils.bspline qsiprep.utils.debug qsiprep.utils.grouping qsiprep.utils.misc qsiprep.utils.sentry qsiprep.utils.testing qsiprep.viz qsiprep.viz.utils qsiprep.workflows qsiprep.workflows.dwi

N

nipype (class in qsiprep.config), [1], [2] nipype_version (qsiprep.config.environment attribute), [1], [2] no_b0_harmonization (qsiprep.config.workflow attribute), [1], [2]

notrack (qsiprep.config.execution attribute), [1], [2] nprocs (qsiprep.config.nipype attribute), [1], [2] numpy (qsiprep.config.seeds attribute)

O

omp_nthreads (qsiprep.config.nipype attribute), [1], [2] out_path_base (qsiprep.interfaces.bids.DerivativesDataSink attribute) output_dir (qsiprep.config.execution attribute), [1], [2]

output_layout (qsiprep.config.execution attribute), [1], [2] output_resolution (qsiprep.config.workflow attribute), [1], [2] overcommit_limit (qsiprep.config.environment attribute), [1], [2] overcommit_policy (qsiprep.config.environment attribute), [1], [2]

P

parse_args() (in module qsiprep.cli.parser) participant_label (qsiprep.config.execution attribute), [1], [2] pepolar_method (qsiprep.config.workflow attribute), [1], [2] plot_acpc() (in module qsiprep.viz.utils)

plot_denoise() (in module qsiprep.viz.utils) plugin (qsiprep.config.nipype attribute), [1], [2] plugin_args (qsiprep.config.nipype attribute), [1], [2] process_crashfile() (in module qsiprep.utils.sentry)

Q

qsiprep module qsiprep.cli module qsiprep.cli.parser module qsiprep.cli.run module qsiprep.cli.version module qsiprep.cli.workflow module qsiprep.config module, [1] qsiprep.engine module qsiprep.engine.workflows module qsiprep.interfaces.bids module qsiprep.utils module

qsiprep.utils.bids module qsiprep.utils.bspline module qsiprep.utils.debug module qsiprep.utils.grouping module qsiprep.utils.misc module qsiprep.utils.sentry module qsiprep.utils.testing module qsiprep.viz module qsiprep.viz.utils module qsiprep.workflows module qsiprep.workflows.dwi module

R

remove_unnecessary_outputs (qsiprep.config.nipype attribute), [1], [2] reports_only (qsiprep.config.execution attribute), [1], [2]

resource_monitor (qsiprep.config.nipype attribute), [1], [2] run_uuid (qsiprep.config.execution attribute), [1], [2]

S

seeds (class in qsiprep.config) sentry_setup() (in module qsiprep.utils.sentry) separate_all_dwis (qsiprep.config.workflow attribute), [1], [2] setup_exceptionhook() (in module qsiprep.utils.debug) shoreline_iters (qsiprep.config.workflow attribute), [1], [2]

skip_anat_based_spatial_normalization (qsiprep.config.execution attribute), [1], [2] sloppy (qsiprep.config.execution attribute), [1], [2] split_by_phase_encoding_direction() (in module qsiprep.utils.grouping) start_ping() (in module qsiprep.utils.sentry) stop_on_first_crash (qsiprep.config.nipype attribute), [1], [2]

T

tbspl_eval() (in module qsiprep.utils.bspline) templateflow_home (qsiprep.config.execution attribute), [1], [2]

templateflow_version (qsiprep.config.environment attribute), [1], [2] TestWorkflow (class in qsiprep.utils.testing) to_filename() (in module qsiprep.config), [1]

U

unringing_method (qsiprep.config.workflow attribute), [1], [2] update_metadata_from_nifti_header() (in module qsiprep.utils.bids)

use_syn_sdc (qsiprep.config.workflow attribute), [1], [2] utils (qsiprep.config.loggers attribute), [1], [2]

V

validate_input_dir() (in module qsiprep.utils.bids)

version (qsiprep.config.environment attribute), [1], [2] visit_desc() (qsiprep.engine.workflows.LiterateWorkflow method)

W

work_dir (qsiprep.config.execution attribute), [1], [2] workflow (class in qsiprep.config), [1], [2] (qsiprep.config.loggers attribute), [1], [2]

write_bidsignore() (in module qsiprep.utils.bids) write_derivative_description() (in module qsiprep.utils.bids) write_graph (qsiprep.config.execution attribute), [1], [2]