Index

A

aggr_ses_reports (qsirecon.config.execution attribute), [1] ants (qsirecon.config.seeds attribute) assert_circular() (qsirecon.utils.testing.TestWorkflow method)

assert_inputs_set() (qsirecon.utils.testing.TestWorkflow method) assertIsAlmostExpectedWorkflow() (qsirecon.utils.testing.TestWorkflow method) assertIsSubsetOfList() (qsirecon.utils.testing.TestWorkflow method)

B

b0_threshold (qsirecon.config.workflow attribute), [1] before_send() (in module qsirecon.utils.sentry) bids_database_dir (qsirecon.config.execution attribute), [1] bids_description_hash (qsirecon.config.execution attribute), [1] bids_dir (qsirecon.config.execution attribute), [1]

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

C

check_deps() (in module qsirecon.utils.misc) check_latest() (in module qsirecon.cli.version) clean_datasinks() (in module qsirecon.utils.bids) cli (qsirecon.config.loggers attribute), [1] collect_participants() (in module qsirecon.utils.bids)

collect_ukb_participants() (in module qsirecon.utils.ingress) copy_boilerplate() (in module qsirecon.cli.workflow) cpu_count (qsirecon.config.environment attribute), [1] crashfile_format (qsirecon.config.nipype attribute), [1] create_ukb_layout() (in module qsirecon.utils.ingress)

D

dataset_links (qsirecon.config.execution attribute), [1] debug (qsirecon.config.execution attribute), [1] default (qsirecon.config.loggers attribute), [1]

derivatives (qsirecon.config.execution attribute), [1] DerivativesDataSink (class in qsirecon.interfaces.bids) dumps() (in module qsirecon.config)

E

environment (class in qsirecon.config), [1] exec_docker_version (qsirecon.config.environment attribute), [1]

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

F

free_mem (qsirecon.config.environment attribute), [1] freesurfer_input (qsirecon.config.execution attribute), [1]

from_dict() (in module qsirecon.config) fs_license_file (qsirecon.config.execution attribute), [1] fs_subjects_dir (qsirecon.config.execution attribute), [1]

G

get() (in module qsirecon.config) get_atlases() (in module qsirecon.utils.atlases) get_bids_params() (in module qsirecon.interfaces.bids)

get_inputs_outputs() (qsirecon.utils.testing.TestWorkflow method) get_linked_libs (qsirecon.config.nipype attribute), [1] get_plugin() (qsirecon.config.nipype class method), [1] get_recon_output_name() (in module qsirecon.interfaces.bids)

I

infant (qsirecon.config.workflow attribute), [1] init() (qsirecon.config.execution class method), [1] (qsirecon.config.loggers class method), [1] (qsirecon.config.nipype class method), [1] (qsirecon.config.seeds class method) (qsirecon.config.workflow class method) init_qsirecon_wf() (in module qsirecon.workflows.base)

init_single_subject_recon_wf() (in module qsirecon.workflows.base) init_spaces() (in module qsirecon.config) input_dir (qsirecon.config.execution attribute), [1] input_type (qsirecon.config.workflow attribute), [1] interactive_reports_only (qsirecon.config.execution attribute), [1] interface (qsirecon.config.loggers attribute), [1] is_flagged() (in module qsirecon.cli.version) is_interactive() (in module qsirecon.utils.debug)

L

layout (qsirecon.config.execution attribute), [1] load() (in module qsirecon.config) load_yaml() (in module qsirecon.utils.misc)

log_dir (qsirecon.config.execution attribute), [1] log_level (qsirecon.config.execution attribute), [1] loggers (class in qsirecon.config), [1] low_mem (qsirecon.config.execution attribute), [1]

M

main() (in module qsirecon.cli.run) make_sloppy() (in module qsirecon.utils.sloppy_recon) master (qsirecon.config.seeds attribute) memory_gb (qsirecon.config.nipype attribute), [1] missing_from_ukb_directory() (in module qsirecon.utils.ingress) module qsirecon qsirecon.cli qsirecon.cli.parser qsirecon.cli.run qsirecon.cli.version qsirecon.cli.workflow qsirecon.config qsirecon.interfaces.bids qsirecon.utils qsirecon.utils.atlases qsirecon.utils.bids qsirecon.utils.debug qsirecon.utils.ingress qsirecon.utils.misc qsirecon.utils.sentry qsirecon.utils.sloppy_recon qsirecon.utils.testing qsirecon.workflows qsirecon.workflows.base qsirecon.workflows.recon

N

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

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

O

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

output_dir (qsirecon.config.execution attribute), [1] output_resolution (qsirecon.config.workflow attribute), [1] overcommit_limit (qsirecon.config.environment attribute), [1] overcommit_policy (qsirecon.config.environment attribute), [1]

P

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

plugin (qsirecon.config.nipype attribute), [1] plugin_args (qsirecon.config.nipype attribute), [1] process_crashfile() (in module qsirecon.utils.sentry)

Q

qsirecon module qsirecon.cli module qsirecon.cli.parser module qsirecon.cli.run module qsirecon.cli.version module qsirecon.cli.workflow module qsirecon.config module qsirecon.interfaces.bids module qsirecon.utils module qsirecon.utils.atlases module

qsirecon.utils.bids module qsirecon.utils.debug module qsirecon.utils.ingress module qsirecon.utils.misc module qsirecon.utils.sentry module qsirecon.utils.sloppy_recon module qsirecon.utils.testing module qsirecon.workflows module qsirecon.workflows.base module qsirecon.workflows.recon module qsirecon_suffixes (qsirecon.config.workflow attribute), [1]

R

recon_spec (qsirecon.config.workflow attribute), [1] ReconDerivativesDataSink (class in qsirecon.interfaces.bids) remove_non_alphanumeric() (in module qsirecon.utils.misc)

remove_unnecessary_outputs (qsirecon.config.nipype attribute), [1] reports_only (qsirecon.config.execution attribute), [1] resource_monitor (qsirecon.config.nipype attribute), [1] run_uuid (qsirecon.config.execution attribute), [1]

S

seeds (class in qsirecon.config) sentry_setup() (in module qsirecon.utils.sentry) setup_exceptionhook() (in module qsirecon.utils.debug) skip_odf_reports (qsirecon.config.execution attribute), [1]

sloppy (qsirecon.config.execution attribute), [1] spec_needs_to_template_transform() (in module qsirecon.workflows.base) start_ping() (in module qsirecon.utils.sentry) stop_on_first_crash (qsirecon.config.nipype attribute), [1]

T

templateflow_home (qsirecon.config.execution attribute), [1] templateflow_version (qsirecon.config.environment attribute), [1]

TestWorkflow (class in qsirecon.utils.testing) to_filename() (in module qsirecon.config)

U

ukb_dirname_to_bids() (in module qsirecon.utils.ingress)

update_params() (in module qsirecon.utils.sloppy_recon) utils (qsirecon.config.loggers attribute), [1]

V

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

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

W

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

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