Index

_

_abc_impl (brainles_preprocessing.defacing.defacer.Defacer attribute) (brainles_preprocessing.defacing.quickshear.quickshear.QuickshearDefacer attribute) (brainles_preprocessing.registration.ANTs.ANTs.ANTsRegistrator attribute) (brainles_preprocessing.registration.niftyreg.niftyreg.NiftyRegRegistrator attribute) (brainles_preprocessing.registration.registrator.Registrator attribute)

_configure_gpu() (brainles_preprocessing.preprocessor.Preprocessor method) _cuda_is_available() (brainles_preprocessing.preprocessor.Preprocessor static method) _log_to_file() (brainles_preprocessing.registration.ANTs.ANTs.ANTsRegistrator static method) _save_output() (brainles_preprocessing.preprocessor.Preprocessor method)

A

ACCURATE (brainles_preprocessing.brain_extraction.brain_extractor.Mode attribute) all_modalities (brainles_preprocessing.preprocessor.Preprocessor property) ANTsRegistrator (class in brainles_preprocessing.registration.ANTs.ANTs) apply_bet_mask() (brainles_preprocessing.modality.Modality method)

apply_deface_mask() (brainles_preprocessing.modality.Modality method) apply_mask() (brainles_preprocessing.brain_extraction.brain_extractor.BrainExtractor method) (brainles_preprocessing.defacing.defacer.Defacer method) atlas_correction (brainles_preprocessing.modality.CenterModality attribute) (brainles_preprocessing.modality.Modality attribute)

B

bet (brainles_preprocessing.modality.CenterModality attribute) (brainles_preprocessing.modality.Modality attribute) (brainles_preprocessing.modality.Modality property) bet_mask_output_path (brainles_preprocessing.modality.CenterModality attribute) BrainExtractor (class in brainles_preprocessing.brain_extraction.brain_extractor) brainles_preprocessing.brain_extraction.brain_extractor module brainles_preprocessing.defacing.defacer module brainles_preprocessing.defacing.quickshear.quickshear module

brainles_preprocessing.modality module brainles_preprocessing.preprocessor module brainles_preprocessing.registration.ANTs.ANTs module brainles_preprocessing.registration.niftyreg.niftyreg module brainles_preprocessing.registration.registrator module

C

CenterModality (class in brainles_preprocessing.modality)

D

deface() (brainles_preprocessing.defacing.defacer.Defacer method) (brainles_preprocessing.defacing.quickshear.quickshear.QuickshearDefacer method) (brainles_preprocessing.modality.CenterModality method) (brainles_preprocessing.modality.Modality method)

Defacer (class in brainles_preprocessing.defacing.defacer) defacing_mask_output_path (brainles_preprocessing.modality.CenterModality attribute)

E

ensure_remove_log_file_handler() (brainles_preprocessing.preprocessor.Preprocessor method) extract() (brainles_preprocessing.brain_extraction.brain_extractor.BrainExtractor method) (brainles_preprocessing.brain_extraction.brain_extractor.HDBetExtractor method)

extract_brain_region() (brainles_preprocessing.modality.CenterModality method) (brainles_preprocessing.modality.Modality method)

F

FAST (brainles_preprocessing.brain_extraction.brain_extractor.Mode attribute)

H

HDBetExtractor (class in brainles_preprocessing.brain_extraction.brain_extractor)

I

input_path (brainles_preprocessing.modality.CenterModality attribute) (brainles_preprocessing.modality.Modality attribute)

M

Modality (class in brainles_preprocessing.modality) modality_name (brainles_preprocessing.modality.CenterModality attribute) (brainles_preprocessing.modality.Modality attribute) Mode (class in brainles_preprocessing.brain_extraction.brain_extractor) module brainles_preprocessing.brain_extraction.brain_extractor brainles_preprocessing.defacing.defacer brainles_preprocessing.defacing.quickshear.quickshear brainles_preprocessing.modality brainles_preprocessing.preprocessor brainles_preprocessing.registration.ANTs.ANTs brainles_preprocessing.registration.niftyreg.niftyreg brainles_preprocessing.registration.registrator

N

NiftyRegRegistrator (class in brainles_preprocessing.registration.niftyreg.niftyreg) normalize() (brainles_preprocessing.modality.Modality method) normalized_bet_output_path (brainles_preprocessing.modality.CenterModality attribute) (brainles_preprocessing.modality.Modality attribute) normalized_defaced_output_path (brainles_preprocessing.modality.CenterModality attribute) (brainles_preprocessing.modality.Modality attribute)

normalized_skull_output_path (brainles_preprocessing.modality.CenterModality attribute) (brainles_preprocessing.modality.Modality attribute) normalizer (brainles_preprocessing.modality.CenterModality attribute) (brainles_preprocessing.modality.Modality attribute)

P

Preprocessor (class in brainles_preprocessing.preprocessor)

Q

QuickshearDefacer (class in brainles_preprocessing.defacing.quickshear.quickshear)

R

raw_bet_output_path (brainles_preprocessing.modality.CenterModality attribute) (brainles_preprocessing.modality.Modality attribute) raw_defaced_output_path (brainles_preprocessing.modality.CenterModality attribute) (brainles_preprocessing.modality.Modality attribute) raw_skull_output_path (brainles_preprocessing.modality.CenterModality attribute) (brainles_preprocessing.modality.Modality attribute) register() (brainles_preprocessing.modality.Modality method) (brainles_preprocessing.registration.ANTs.ANTs.ANTsRegistrator method) (brainles_preprocessing.registration.niftyreg.niftyreg.NiftyRegRegistrator method) (brainles_preprocessing.registration.registrator.Registrator method)

Registrator (class in brainles_preprocessing.registration.registrator) requires_deface (brainles_preprocessing.modality.Modality property) requires_defacing (brainles_preprocessing.preprocessor.Preprocessor property) run() (brainles_preprocessing.preprocessor.Preprocessor method) run_atlas_correction() (brainles_preprocessing.preprocessor.Preprocessor method) run_atlas_registration() (brainles_preprocessing.preprocessor.Preprocessor method) run_brain_extraction() (brainles_preprocessing.preprocessor.Preprocessor method) run_coregistration() (brainles_preprocessing.preprocessor.Preprocessor method) run_defacing() (brainles_preprocessing.preprocessor.Preprocessor method)

S

save_current_image() (brainles_preprocessing.modality.Modality method)

save_mask() (brainles_preprocessing.modality.CenterModality method)

T

transform() (brainles_preprocessing.modality.Modality method) (brainles_preprocessing.registration.ANTs.ANTs.ANTsRegistrator method) (brainles_preprocessing.registration.niftyreg.niftyreg.NiftyRegRegistrator method) (brainles_preprocessing.registration.registrator.Registrator method)