Index

A

add() (sdcflows.utils.bimap.bidict method) analysis_level (sdcflows.config.workflow attribute) ants_float (sdcflows.config.execution attribute) apply() (sdcflows.transform.B0FieldTransform method)

ApplyCoeffsField (class in sdcflows.interfaces.bspline) as_path() (sdcflows.data.load method) (sdcflows.data.Loader method) au2rads() (in module sdcflows.utils.phasemanip)

B

B0FieldTransform (class in sdcflows.transform) bidict (class in sdcflows.utils.bimap) bids_database_dir (sdcflows.config.execution attribute) bids_database_wipe (sdcflows.config.execution attribute) bids_description_hash (sdcflows.config.execution attribute) bids_dir (sdcflows.config.execution attribute) bids_filters (sdcflows.config.execution attribute)

bids_id (sdcflows.fieldmaps.FieldmapEstimation attribute) bids_root (sdcflows.fieldmaps.FieldmapFile attribute) BinaryDilation (class in sdcflows.interfaces.brainmask) brain_masker() (in module sdcflows.utils.tools) BrainExtraction (class in sdcflows.interfaces.brainmask) bspline_grid() (in module sdcflows.interfaces.bspline) BSplineApprox (class in sdcflows.interfaces.bspline) build_workflow() (in module sdcflows.cli.workflow)

C

cached() (sdcflows.data.load method) (sdcflows.data.Loader method) check_path() (sdcflows.fieldmaps.FieldmapFile method) CheckB0Units (class in sdcflows.interfaces.fmap) CheckRegister (class in sdcflows.interfaces.fmap) clear() (sdcflows.utils.bimap.bidict method) clear_registry() (in module sdcflows.fieldmaps)

cli (sdcflows.config.loggers attribute) coeffs (sdcflows.transform.B0FieldTransform attribute) ConvertWarp (class in sdcflows.interfaces.utils) coolwarm_transparent() (in module sdcflows.viz.utils) cpu_count (sdcflows.config.environment attribute) crashfile_format (sdcflows.config.nipype attribute) cwd (sdcflows.config.execution attribute)

D

debug (sdcflows.config.execution attribute) default (sdcflows.config.loggers attribute) delta_te() (in module sdcflows.utils.phasemanip) DenoiseImage (class in sdcflows.interfaces.utils) Deoblique (class in sdcflows.interfaces.utils)

deoblique_and_zooms() (in module sdcflows.utils.tools) DerivativesDataSink (class in sdcflows.workflows.outputs) disp_to_fmap() (in module sdcflows.transform) DisplacementsField2Fieldmap (class in sdcflows.interfaces.fmap) dry_run (sdcflows.config.execution attribute) dumps() (in module sdcflows.config)

E

ensure_positive_cosines() (in module sdcflows.utils.tools) entities (sdcflows.fieldmaps.FieldmapFile attribute) environment (class in sdcflows.config) epi_mask() (in module sdcflows.utils.epimanip)

EstimatorRegistry (class in sdcflows.utils.bimap) EstimatorType (class in sdcflows.fieldmaps) exec_docker_version (sdcflows.config.environment attribute) exec_env (sdcflows.config.environment attribute) execution (class in sdcflows.config)

F

FieldmapEstimation (class in sdcflows.fieldmaps) FieldmapFile (class in sdcflows.fieldmaps) FieldmapReportlet (class in sdcflows.interfaces.reportlets) file_path (in module sdcflows.config) find_anatomical_estimators() (in module sdcflows.utils.wrangler) find_estimators() (in module sdcflows.utils.wrangler) find_meta (sdcflows.fieldmaps.FieldmapFile attribute)

fit() (sdcflows.transform.B0FieldTransform method) Flatten (class in sdcflows.interfaces.utils) fmap_to_disp() (in module sdcflows.transform) fmapless (sdcflows.config.workflow attribute) free_mem (sdcflows.config.environment attribute) from_dict() (in module sdcflows.config) front() (in module sdcflows.utils.misc)

G

get() (in module sdcflows.config) get_free_mem() (in module sdcflows.utils.misc) get_identifier() (in module sdcflows.fieldmaps) get_key() (sdcflows.utils.bimap.EstimatorRegistry method) get_linked_libs (sdcflows.config.nipype attribute)

get_plugin() (sdcflows.config.nipype class method) get_trt() (in module sdcflows.utils.epimanip) get_workflow() (sdcflows.fieldmaps.FieldmapEstimation method) getLogger() (sdcflows.config.loggers class method) GetReadoutTime (class in sdcflows.interfaces.epi) grid_bspline_weights() (in module sdcflows.transform)

I

init() (sdcflows.config.execution class method) (sdcflows.config.loggers class method) (sdcflows.config.nipype class method) init_3dQwarp_wf() (in module sdcflows.workflows.fit.pepolar) init_brainextraction_wf() (in module sdcflows.workflows.ancillary) init_coeff2epi_wf() (in module sdcflows.workflows.apply.registration) init_fmap_derivatives_wf() (in module sdcflows.workflows.outputs) init_fmap_preproc_wf() (in module sdcflows.workflows.base) init_fmap_reports_wf() (in module sdcflows.workflows.outputs)

init_fmap_wf() (in module sdcflows.workflows.fit.fieldmap) init_magnitude_wf() (in module sdcflows.workflows.fit.fieldmap) init_phdiff_wf() (in module sdcflows.workflows.fit.fieldmap) init_sdcflows_wf() (in module sdcflows.workflows.fit.base) init_syn_preprocessing_wf() (in module sdcflows.workflows.fit.syn) init_syn_sdc_wf() (in module sdcflows.workflows.fit.syn) init_topup_wf() (in module sdcflows.workflows.fit.pepolar) init_unwarp_wf() (in module sdcflows.workflows.apply.correction) interface (sdcflows.config.loggers attribute)

L

last() (in module sdcflows.utils.misc) layout (sdcflows.config.execution attribute) load() (in module sdcflows.config) (in module sdcflows.data)

Loader (class in sdcflows.data) local_hash_check (sdcflows.config.nipype attribute) log_dir (sdcflows.config.execution attribute) log_level (sdcflows.config.execution attribute) loggers (class in sdcflows.config)

M

main() (in module sdcflows.cli.main) mapped (sdcflows.transform.B0FieldTransform attribute) match_histogram() (in module sdcflows.workflows.fit.syn) memory_gb (sdcflows.config.nipype attribute) metadata (sdcflows.fieldmaps.FieldmapFile attribute) MetadataError method (sdcflows.fieldmaps.FieldmapEstimation attribute) module sdcflows.cli sdcflows.cli.main sdcflows.cli.parser sdcflows.cli.workflow sdcflows.config sdcflows.data sdcflows.fieldmaps sdcflows.interfaces sdcflows.interfaces.brainmask sdcflows.interfaces.bspline sdcflows.interfaces.epi sdcflows.interfaces.fmap sdcflows.interfaces.reportlets sdcflows.interfaces.utils sdcflows.transform sdcflows.utils sdcflows.utils.bimap sdcflows.utils.epimanip sdcflows.utils.misc sdcflows.utils.phasemanip sdcflows.utils.telemetry sdcflows.utils.tools sdcflows.utils.wrangler sdcflows.viz sdcflows.viz.utils sdcflows.workflows sdcflows.workflows.ancillary sdcflows.workflows.apply sdcflows.workflows.apply.correction sdcflows.workflows.apply.registration sdcflows.workflows.base sdcflows.workflows.fit sdcflows.workflows.fit.base sdcflows.workflows.fit.fieldmap sdcflows.workflows.fit.pepolar sdcflows.workflows.fit.syn sdcflows.workflows.outputs

N

nipype (class in sdcflows.config) nipype_version (sdcflows.config.environment attribute)

notrack (sdcflows.config.execution attribute) nprocs (sdcflows.config.nipype attribute)

O

omp_nthreads (sdcflows.config.nipype attribute) output_dir (sdcflows.config.execution attribute)

overcommit_limit (sdcflows.config.environment attribute) overcommit_policy (sdcflows.config.environment attribute)

P

PadSlices (class in sdcflows.interfaces.utils) parse_args() (in module sdcflows.cli.parser) participant_label (sdcflows.config.execution attribute) path (sdcflows.fieldmaps.FieldmapFile attribute) paths() (sdcflows.fieldmaps.FieldmapEstimation method) pdb (sdcflows.config.execution attribute)

Phasediff2Fieldmap (class in sdcflows.interfaces.fmap) PhaseMap2rads (class in sdcflows.interfaces.fmap) phdiff2fmap() (in module sdcflows.utils.phasemanip) plot_registration() (in module sdcflows.viz.utils) plugin (sdcflows.config.nipype attribute) plugin_args (sdcflows.config.nipype attribute) PositiveDirectionCosines (class in sdcflows.interfaces.utils)

R

readable() (sdcflows.data.load method) (sdcflows.data.Loader method) remove_node_directories (sdcflows.config.nipype attribute) Reoblique (class in sdcflows.interfaces.utils) reorient_pedir() (in module sdcflows.utils.tools)

ReorientImageAndMetadata (class in sdcflows.interfaces.utils) resample_to_zooms() (in module sdcflows.utils.tools) resource_monitor (sdcflows.config.nipype attribute) restore_env() (in module sdcflows.config) run_uuid (sdcflows.config.execution attribute)

S

sanitized_id (sdcflows.fieldmaps.FieldmapEstimation attribute) sdcflows.cli module sdcflows.cli.main module sdcflows.cli.parser module sdcflows.cli.workflow module sdcflows.config module sdcflows.data module sdcflows.fieldmaps module sdcflows.interfaces module sdcflows.interfaces.brainmask module sdcflows.interfaces.bspline module sdcflows.interfaces.epi module sdcflows.interfaces.fmap module sdcflows.interfaces.reportlets module sdcflows.interfaces.utils module sdcflows.transform module sdcflows.utils module sdcflows.utils.bimap module sdcflows.utils.epimanip module sdcflows.utils.misc module sdcflows.utils.phasemanip module sdcflows.utils.telemetry module

sdcflows.utils.tools module sdcflows.utils.wrangler module sdcflows.viz module sdcflows.viz.utils module sdcflows.workflows module sdcflows.workflows.ancillary module sdcflows.workflows.apply module sdcflows.workflows.apply.correction module sdcflows.workflows.apply.registration module sdcflows.workflows.base module sdcflows.workflows.fit module sdcflows.workflows.fit.base module sdcflows.workflows.fit.fieldmap module sdcflows.workflows.fit.pepolar module sdcflows.workflows.fit.syn module sdcflows.workflows.outputs module send_crumb() (in module sdcflows.utils.telemetry) session_label (sdcflows.config.execution attribute) setup_migas() (in module sdcflows.utils.telemetry) sloppy (sdcflows.config.execution attribute) SortPEBlips (class in sdcflows.interfaces.epi) sources (sdcflows.fieldmaps.FieldmapEstimation attribute) (sdcflows.utils.bimap.EstimatorRegistry property) species (sdcflows.config.workflow attribute) stop_on_first_crash (sdcflows.config.nipype attribute) subtract_phases() (in module sdcflows.utils.phasemanip) SubtractPhases (class in sdcflows.interfaces.fmap) suffix (sdcflows.fieldmaps.FieldmapFile attribute)

T

template_id (sdcflows.config.workflow attribute) templateflow_home (sdcflows.config.execution attribute) templateflow_version (sdcflows.config.environment attribute) to_displacements() (sdcflows.transform.B0FieldTransform method)

to_filename() (in module sdcflows.config) TOPUPCoeffReorient (class in sdcflows.interfaces.bspline) total_memory (sdcflows.config.environment attribute) TransformCoefficients (class in sdcflows.interfaces.bspline)

U

UniformGrid (class in sdcflows.interfaces.utils) Union (class in sdcflows.interfaces.brainmask)

unwarp_parallel() (in module sdcflows.transform) utils (sdcflows.config.loggers attribute)

V

version (sdcflows.config.environment attribute)

W

work_dir (sdcflows.config.execution attribute) worker() (in module sdcflows.transform)

workflow (class in sdcflows.config) (sdcflows.config.loggers attribute) write_graph (sdcflows.config.execution attribute)