Index

_

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

A

add() (qsiprep.niworkflows.due.InactiveDueCreditCollector method) add_suffix() (in module qsiprep.niworkflows.utils.misc) (in module qsiprep.utils.misc) aggregate_reports() (in module qsiprep.cli.group_report)

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

before_send() (in module qsiprep.utils.sentry) BibTeX() (in module qsiprep.niworkflows.due) BIDSError

BIDSWarning build_qsiprep_workflow() (in module qsiprep.cli.run) build_recon_workflow() (in module qsiprep.cli.run)

C

check_deps() (in module qsiprep.cli.run) check_latest() (in module qsiprep.cli.version) cite() (qsiprep.niworkflows.due.InactiveDueCreditCollector method) collect_data() (in module qsiprep.utils.bids) collect_participants() (in module qsiprep.utils.bids)

collect_ukb_participants() (in module qsiprep.utils.ingress) compose_view() (in module qsiprep.niworkflows.viz.utils) compute_affine() (in module qsiprep.utils.bspline) confoundplot() (in module qsiprep.niworkflows.viz.plots) create_ukb_layout() (in module qsiprep.utils.ingress) cuts_from_bbox() (in module qsiprep.niworkflows.viz.utils)

D

dcite() (qsiprep.niworkflows.due.InactiveDueCreditCollector method)

Doi() (in module qsiprep.niworkflows.due)

E

Element (class in qsiprep.niworkflows.viz.reports) (class in qsiprep.viz.reports)

extract_svg() (in module qsiprep.niworkflows.viz.utils)

F

fetch_file() (in module qsiprep.niworkflows.data.utils) find_ukb_directory() (in module qsiprep.utils.ingress)

fix_multi_source_name() (in module qsiprep.utils.misc) fix_multi_T1w_source_name() (in module qsiprep.niworkflows.utils.misc) (in module qsiprep.utils.misc)

G

generate_interactive_report_summary() (in module qsiprep.viz.reports) generate_name_title() (in module qsiprep.niworkflows.viz.reports) (in module qsiprep.viz.reports) generate_report() (qsiprep.niworkflows.viz.reports.Report method) (qsiprep.viz.reports.Report method) generate_reports() (in module qsiprep.niworkflows.viz.reports) (in module qsiprep.viz.reports) get_atlases() (in module qsiprep.utils.atlases)

get_bids_examples() (in module qsiprep.niworkflows.data.getters) get_brainweb_1mm_normal() (in module qsiprep.niworkflows.data.getters) get_dataset() (in module qsiprep.niworkflows.data.getters) get_ds003_downsampled() (in module qsiprep.niworkflows.data.getters) get_grouping_test_data() (in module qsiprep.utils.testing) get_ijk() (in module qsiprep.utils.bspline) get_inputs_outputs() (qsiprep.utils.testing.TestWorkflow method) get_parser() (in module qsiprep.cli.run) get_template() (in module qsiprep.niworkflows.data.getters)

I

InactiveDueCreditCollector (class in qsiprep.niworkflows.due) index() (qsiprep.niworkflows.viz.reports.Report method) (qsiprep.viz.reports.Report method)

index_error_dir() (qsiprep.niworkflows.viz.reports.Report method) (qsiprep.viz.reports.Report method) is_flagged() (in module qsiprep.cli.version)

L

LiterateWorkflow (class in qsiprep.engine.workflows) (class in qsiprep.niworkflows.engine.workflows)

load() (qsiprep.niworkflows.due.InactiveDueCreditCollector method)

M

main() (in module qsiprep.cli.run) make_sloppy() (in module qsiprep.utils.sloppy_recon) missing_from_ukb_directory() (in module qsiprep.utils.ingress) module qsiprep qsiprep.cli qsiprep.cli.group_report qsiprep.cli.run qsiprep.cli.version qsiprep.engine qsiprep.engine.workflows qsiprep.niworkflows qsiprep.niworkflows.common qsiprep.niworkflows.common.orient qsiprep.niworkflows.data qsiprep.niworkflows.data.getters qsiprep.niworkflows.data.utils qsiprep.niworkflows.due qsiprep.niworkflows.dwi qsiprep.niworkflows.engine qsiprep.niworkflows.engine.workflows qsiprep.niworkflows.func qsiprep.niworkflows.utils qsiprep.niworkflows.utils.bids qsiprep.niworkflows.utils.misc qsiprep.niworkflows.viz qsiprep.niworkflows.viz.plots qsiprep.niworkflows.viz.reports qsiprep.niworkflows.viz.utils qsiprep.utils qsiprep.utils.atlases qsiprep.utils.bids qsiprep.utils.bspline qsiprep.utils.ingress qsiprep.utils.misc qsiprep.utils.sentry qsiprep.utils.sloppy_recon qsiprep.utils.testing qsiprep.viz qsiprep.viz.reports qsiprep.workflows qsiprep.workflows.dwi, [1]

O

order_by_run() (in module qsiprep.niworkflows.viz.reports) (in module qsiprep.viz.reports)

P

plot_acpc() (in module qsiprep.niworkflows.viz.utils) plot_carpet() (in module qsiprep.niworkflows.viz.plots) plot_denoise() (in module qsiprep.niworkflows.viz.utils) plot_melodic_components() (in module qsiprep.niworkflows.viz.utils)

plot_registration() (in module qsiprep.niworkflows.viz.utils) plot_rpe_sdc() (in module qsiprep.niworkflows.viz.utils) plot_segs() (in module qsiprep.niworkflows.viz.utils) process_crashfile() (in module qsiprep.utils.sentry)

Q

qsiprep module qsiprep.cli module qsiprep.cli.group_report module qsiprep.cli.run module qsiprep.cli.version module qsiprep.engine module qsiprep.engine.workflows module qsiprep.niworkflows module qsiprep.niworkflows.common module qsiprep.niworkflows.common.orient module qsiprep.niworkflows.data module qsiprep.niworkflows.data.getters module qsiprep.niworkflows.data.utils module qsiprep.niworkflows.due module qsiprep.niworkflows.dwi module qsiprep.niworkflows.engine module qsiprep.niworkflows.engine.workflows module qsiprep.niworkflows.func module qsiprep.niworkflows.utils module

qsiprep.niworkflows.utils.bids module qsiprep.niworkflows.utils.misc module qsiprep.niworkflows.viz module qsiprep.niworkflows.viz.plots module qsiprep.niworkflows.viz.reports module qsiprep.niworkflows.viz.utils module qsiprep.utils module qsiprep.utils.atlases module qsiprep.utils.bids module qsiprep.utils.bspline module qsiprep.utils.ingress module qsiprep.utils.misc module qsiprep.utils.sentry module qsiprep.utils.sloppy_recon module qsiprep.utils.testing module qsiprep.viz module qsiprep.viz.reports module qsiprep.workflows module qsiprep.workflows.dwi module, [1]

R

read_crashfile() (in module qsiprep.niworkflows.utils.misc) readlinkabs() (in module qsiprep.niworkflows.data.utils) reorient_wf() (in module qsiprep.niworkflows.common.orient) Report (class in qsiprep.niworkflows.viz.reports) (class in qsiprep.viz.reports)

Reportlet (class in qsiprep.niworkflows.viz.reports) (class in qsiprep.viz.reports) robust_set_limits() (in module qsiprep.niworkflows.viz.utils) run_reports() (in module qsiprep.niworkflows.viz.reports) (in module qsiprep.viz.reports)

S

sentry_setup() (in module qsiprep.utils.sentry) set_freesurfer_license() (in module qsiprep.cli.run) slices_from_bbox() (in module qsiprep.niworkflows.viz.utils) spikesplot() (in module qsiprep.niworkflows.viz.plots) spikesplot_cb() (in module qsiprep.niworkflows.viz.plots)

splitext() (in module qsiprep.niworkflows.utils.misc) start_ping() (in module qsiprep.utils.sentry) SubReport (class in qsiprep.niworkflows.viz.reports) (class in qsiprep.viz.reports) svg2str() (in module qsiprep.niworkflows.viz.utils) svg_compress() (in module qsiprep.niworkflows.viz.utils)

T

tbspl_eval() (in module qsiprep.utils.bspline)

TestWorkflow (class in qsiprep.utils.testing) transform_to_2d() (in module qsiprep.niworkflows.viz.utils)

U

ukb_dirname_to_bids() (in module qsiprep.utils.ingress) update_metadata_from_nifti_header() (in module qsiprep.utils.bids)

update_params() (in module qsiprep.utils.sloppy_recon) Url() (in module qsiprep.niworkflows.due)

V

validate_bids() (in module qsiprep.cli.run) validate_input_dir() (in module qsiprep.utils.bids)

visit_desc() (qsiprep.engine.workflows.LiterateWorkflow method) (qsiprep.niworkflows.engine.workflows.LiterateWorkflow method)

W

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