Index

_

__initialize_parameter_object() (brainles_preprocessing.registration.elastix.elastix.ElastixRegistrator method) _abc_impl (brainles_preprocessing.defacing.defacer.Defacer attribute) (brainles_preprocessing.defacing.quickshear.quickshear.QuickshearDefacer attribute) (brainles_preprocessing.n4_bias_correction.n4_bias_corrector.N4BiasCorrector attribute) (brainles_preprocessing.n4_bias_correction.sitk.sitk_n4_bias_corrector.SitkN4BiasCorrector attribute) (brainles_preprocessing.preprocessor.atlas_centric_preprocessor.AtlasCentricPreprocessor attribute) (brainles_preprocessing.preprocessor.native_space_preprocessor.NativeSpacePreprocessor attribute) (brainles_preprocessing.preprocessor.preprocessor.BasePreprocessor attribute) (brainles_preprocessing.registration.ANTs.ANTs.ANTsRegistrator attribute) (brainles_preprocessing.registration.elastix.elastix.ElastixRegistrator attribute) (brainles_preprocessing.registration.greedy.greedy.GreedyRegistrator attribute) (brainles_preprocessing.registration.niftyreg.niftyreg.NiftyRegRegistrator attribute) (brainles_preprocessing.registration.registrator.Registrator attribute)

_add_log_file_handler() (brainles_preprocessing.preprocessor.preprocessor.BasePreprocessor method) _check_for_name_conflicts() (brainles_preprocessing.preprocessor.preprocessor.BasePreprocessor method) _compose_affine_transforms() (brainles_preprocessing.registration.niftyreg.niftyreg.NiftyRegRegistrator method) _configure_gpu() (brainles_preprocessing.preprocessor.preprocessor.BasePreprocessor method) _conform() (brainles_preprocessing.brain_extraction.synthstrip.SynthStripExtractor method) _cuda_is_available() (brainles_preprocessing.preprocessor.preprocessor.BasePreprocessor static method) _find_transformation_matrix() (brainles_preprocessing.modality.Modality method) _invert_affine_transform() (brainles_preprocessing.registration.niftyreg.niftyreg.NiftyRegRegistrator method) _log_to_file() (brainles_preprocessing.registration.ANTs.ANTs.ANTsRegistrator static method) _resample_like() (brainles_preprocessing.brain_extraction.synthstrip.SynthStripExtractor method) _save_output() (brainles_preprocessing.preprocessor.preprocessor.BasePreprocessor method) _setup_model() (brainles_preprocessing.brain_extraction.synthstrip.SynthStripExtractor method)

A

ACCURATE (brainles_preprocessing.brain_extraction.brain_extractor.Mode attribute) all_modalities (brainles_preprocessing.preprocessor.preprocessor.BasePreprocessor property) ANTsRegistrator (class in brainles_preprocessing.registration.ANTs.ANTs) apply() (brainles_preprocessing.transform.Transform method) 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 (class in brainles_preprocessing.constants) ATLAS_CORRECTED (brainles_preprocessing.constants.PreprocessorSteps attribute) atlas_correction (brainles_preprocessing.modality.CenterModality attribute) (brainles_preprocessing.modality.Modality attribute) ATLAS_REGISTERED (brainles_preprocessing.constants.PreprocessorSteps attribute) AtlasCentricPreprocessor (class in brainles_preprocessing.preprocessor.atlas_centric_preprocessor)

B

BasePreprocessor (class in brainles_preprocessing.preprocessor.preprocessor) BET (brainles_preprocessing.constants.PreprocessorSteps attribute) 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.brain_extraction.synthstrip module brainles_preprocessing.constants module brainles_preprocessing.defacing.defacer module brainles_preprocessing.defacing.quickshear.quickshear module brainles_preprocessing.modality module brainles_preprocessing.n4_bias_correction.n4_bias_corrector module brainles_preprocessing.n4_bias_correction.sitk.sitk_n4_bias_corrector module

brainles_preprocessing.preprocessor.atlas_centric_preprocessor module brainles_preprocessing.preprocessor.native_space_preprocessor module brainles_preprocessing.preprocessor.preprocessor module brainles_preprocessing.registration.ANTs.ANTs module brainles_preprocessing.registration.elastix.elastix module brainles_preprocessing.registration.greedy.greedy module brainles_preprocessing.registration.niftyreg.niftyreg module brainles_preprocessing.registration.registrator module brainles_preprocessing.transform module BRATS_MNI152 (brainles_preprocessing.constants.Atlas attribute) BRATS_SRI24 (brainles_preprocessing.constants.Atlas attribute) BRATS_SRI24_SKULLSTRIPPED (brainles_preprocessing.constants.Atlas attribute)

C

CenterModality (class in brainles_preprocessing.modality) compute_mask() (brainles_preprocessing.n4_bias_correction.sitk.sitk_n4_bias_corrector.SitkN4BiasCorrector method) COREGISTERED (brainles_preprocessing.constants.PreprocessorSteps attribute)

coregistration_transform_path (brainles_preprocessing.modality.Modality attribute) correct() (brainles_preprocessing.n4_bias_correction.n4_bias_corrector.N4BiasCorrector method) (brainles_preprocessing.n4_bias_correction.sitk.sitk_n4_bias_corrector.SitkN4BiasCorrector method)

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)

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

E

ElastixRegistrator (class in brainles_preprocessing.registration.elastix.elastix) extract() (brainles_preprocessing.brain_extraction.brain_extractor.BrainExtractor method) (brainles_preprocessing.brain_extraction.brain_extractor.HDBetExtractor method) (brainles_preprocessing.brain_extraction.synthstrip.SynthStripExtractor method)

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

F

FAST (brainles_preprocessing.brain_extraction.brain_extractor.Mode attribute)

G

GreedyRegistrator (class in brainles_preprocessing.registration.greedy.greedy)

H

HDBetExtractor (class in brainles_preprocessing.brain_extraction.brain_extractor)

I

INPUT (brainles_preprocessing.constants.PreprocessorSteps attribute) input_path (brainles_preprocessing.modality.CenterModality attribute) (brainles_preprocessing.modality.Modality attribute) inverse_transform() (brainles_preprocessing.registration.ANTs.ANTs.ANTsRegistrator method) (brainles_preprocessing.registration.elastix.elastix.ElastixRegistrator method) (brainles_preprocessing.registration.greedy.greedy.GreedyRegistrator method) (brainles_preprocessing.registration.niftyreg.niftyreg.NiftyRegRegistrator method) (brainles_preprocessing.registration.registrator.Registrator method)

M

MNI152 (brainles_preprocessing.constants.Atlas attribute) 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.brain_extraction.synthstrip brainles_preprocessing.constants brainles_preprocessing.defacing.defacer brainles_preprocessing.defacing.quickshear.quickshear brainles_preprocessing.modality brainles_preprocessing.n4_bias_correction.n4_bias_corrector brainles_preprocessing.n4_bias_correction.sitk.sitk_n4_bias_corrector brainles_preprocessing.preprocessor.atlas_centric_preprocessor brainles_preprocessing.preprocessor.native_space_preprocessor brainles_preprocessing.preprocessor.preprocessor brainles_preprocessing.registration.ANTs.ANTs brainles_preprocessing.registration.elastix.elastix brainles_preprocessing.registration.greedy.greedy brainles_preprocessing.registration.niftyreg.niftyreg brainles_preprocessing.registration.registrator brainles_preprocessing.transform

N

N4_BIAS_CORRECTED (brainles_preprocessing.constants.PreprocessorSteps attribute) n4_bias_correction (brainles_preprocessing.modality.CenterModality attribute) (brainles_preprocessing.modality.Modality attribute) N4BiasCorrector (class in brainles_preprocessing.n4_bias_correction.n4_bias_corrector) NativeSpacePreprocessor (class in brainles_preprocessing.preprocessor.native_space_preprocessor) 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

PreprocessorSteps (class in brainles_preprocessing.constants)

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.elastix.elastix.ElastixRegistrator method) (brainles_preprocessing.registration.greedy.greedy.GreedyRegistrator 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.BasePreprocessor property) run() (brainles_preprocessing.preprocessor.atlas_centric_preprocessor.AtlasCentricPreprocessor method) (brainles_preprocessing.preprocessor.native_space_preprocessor.NativeSpacePreprocessor method) (brainles_preprocessing.preprocessor.preprocessor.BasePreprocessor method) run_atlas_correction() (brainles_preprocessing.preprocessor.atlas_centric_preprocessor.AtlasCentricPreprocessor method) run_atlas_registration() (brainles_preprocessing.preprocessor.atlas_centric_preprocessor.AtlasCentricPreprocessor method) run_brain_extraction() (brainles_preprocessing.preprocessor.preprocessor.BasePreprocessor method) run_coregistration() (brainles_preprocessing.preprocessor.preprocessor.BasePreprocessor method) run_defacing() (brainles_preprocessing.preprocessor.atlas_centric_preprocessor.AtlasCentricPreprocessor method) (brainles_preprocessing.preprocessor.native_space_preprocessor.NativeSpacePreprocessor method) run_n4_bias_correction() (brainles_preprocessing.preprocessor.preprocessor.BasePreprocessor method)

S

save_current_image() (brainles_preprocessing.modality.Modality method) save_mask() (brainles_preprocessing.modality.CenterModality method) SitkN4BiasCorrector (class in brainles_preprocessing.n4_bias_correction.sitk.sitk_n4_bias_corrector)

SRI24 (brainles_preprocessing.constants.Atlas attribute) SRI24_SKULLSTRIPPED (brainles_preprocessing.constants.Atlas attribute) SynthStripExtractor (class in brainles_preprocessing.brain_extraction.synthstrip)

T

Transform (class in brainles_preprocessing.transform) transform() (brainles_preprocessing.modality.Modality method) (brainles_preprocessing.registration.ANTs.ANTs.ANTsRegistrator method) (brainles_preprocessing.registration.elastix.elastix.ElastixRegistrator method) (brainles_preprocessing.registration.greedy.greedy.GreedyRegistrator method) (brainles_preprocessing.registration.niftyreg.niftyreg.NiftyRegRegistrator method) (brainles_preprocessing.registration.registrator.Registrator method)