Index A | B | C | D | E | F | G | H | I | L | M | N | O | P | Q | R | S | T | U | W A ADC (pyalfe.data_structure.Modality attribute) add() (pyalfe.interfaces.c3d.C3D method) affine() (pyalfe.interfaces.greedy.Greedy method) AntsRegistration (class in pyalfe.image_registration) ASL (pyalfe.data_structure.Modality attribute) assign() (pyalfe.interfaces.c3d.C3D method) AXIAL (pyalfe.data_structure.Orientation attribute) B BACKGROUND (pyalfe.data_structure.Tissue attribute) BIDSDataDir (class in pyalfe.data_structure) binarize() (pyalfe.image_processing.Convert3DProcessor static method) (pyalfe.image_processing.ImageProcessor static method) (pyalfe.image_processing.NilearnProcessor static method) (pyalfe.interfaces.c3d.C3D method) BRAIN_STEM (pyalfe.data_structure.Tissue attribute) C C3D (class in pyalfe.interfaces.c3d) CBF (pyalfe.data_structure.Modality attribute) CEREBELLUM (pyalfe.data_structure.Tissue attribute) check_output() (pyalfe.interfaces.c3d.C3D method) clip() (pyalfe.interfaces.c3d.C3D method) comp() (pyalfe.interfaces.c3d.C3D method) Config (class in pyalfe.containers) Convert3DProcessor (class in pyalfe.image_processing) copy_matching_paths() (in module pyalfe.utils.archive) CORONAL (pyalfe.data_structure.Orientation attribute) CORTICAL_GRAY_MATTER (pyalfe.data_structure.Tissue attribute) create_dir() (pyalfe.data_structure.DefaultALFEDataDir method) crop_img() (pyalfe.image_processing.NilearnProcessor static method) cross_modality_registration (pyalfe.containers.PipelineContainer property) (pyalfe.pipeline.PyALFEPipelineRunner attribute) CrossModalityRegistration (class in pyalfe.tasks.registration) CSF (pyalfe.data_structure.Tissue attribute) D DeclarativeContainer (class in pyalfe.containers) DEEP_GRAY_MATTER (pyalfe.data_structure.Tissue attribute) DefaultALFEDataDir (class in pyalfe.data_structure) dicom_dir (pyalfe.containers.DicomProcessingContianer property) dicom_processing (pyalfe.containers.DicomProcessingContianer property) (pyalfe.pipeline.DicomProcessingPipelineRunner attribute) dicom_processing_pipeline_runner (pyalfe.containers.DicomProcessingContianer property) DicomProcessingContianer (class in pyalfe.containers) DicomProcessingPipelineRunner (class in pyalfe.pipeline) dilate() (pyalfe.image_processing.Convert3DProcessor static method) (pyalfe.image_processing.ImageProcessor static method) (pyalfe.image_processing.NilearnProcessor static method) (pyalfe.interfaces.c3d.C3D method) dim() (pyalfe.interfaces.greedy.Greedy method) distance_transform() (pyalfe.image_processing.Convert3DProcessor static method) (pyalfe.image_processing.ImageProcessor static method) (pyalfe.image_processing.NilearnProcessor static method) dof() (pyalfe.interfaces.greedy.Greedy method) dominant_tissue (pyalfe.tasks.quantification.Quantification attribute) download_archive() (in module pyalfe.utils.download) dup() (pyalfe.interfaces.c3d.C3D method) DWI (pyalfe.data_structure.Modality attribute) E EADC (pyalfe.data_structure.Modality attribute) enhancement_model (pyalfe.containers.PipelineContainer property) enhancement_segmentation (pyalfe.containers.PipelineContainer property) (pyalfe.pipeline.PyALFEPipelineRunner attribute) epsilon() (pyalfe.interfaces.greedy.Greedy method) extract_binary_from_archive() (in module pyalfe.utils.archive) extract_file_from_archive() (in module pyalfe.utils.archive) extract_file_from_dmg() (in module pyalfe.utils.archive) extract_file_from_tar() (in module pyalfe.utils.archive) extract_tar() (in module pyalfe.utils.archive) F FLAIR (pyalfe.data_structure.Modality attribute) flair_model (pyalfe.containers.PipelineContainer property) flair_segmentation (pyalfe.containers.PipelineContainer property) (pyalfe.pipeline.PyALFEPipelineRunner attribute) from_dict() (pyalfe.containers.Config method) from_ini() (pyalfe.containers.Config method) G generate_random_str() (in module pyalfe.utils.archive) get_all_dicom_series_instances() (pyalfe.data_structure.PatientDicomDataDir method) get_brain_volume_stats() (pyalfe.tasks.quantification.Quantification method) get_dims() (pyalfe.image_processing.Convert3DProcessor static method) (pyalfe.image_processing.ImageProcessor static method) (pyalfe.image_processing.NilearnProcessor static method) get_input_image() (pyalfe.data_structure.BIDSDataDir method) (pyalfe.data_structure.DefaultALFEDataDir method) (pyalfe.data_structure.PipelineDataDir method) get_lesion_stats() (pyalfe.tasks.quantification.Quantification method) get_output_image() (pyalfe.data_structure.BIDSDataDir method) (pyalfe.data_structure.DefaultALFEDataDir method) (pyalfe.data_structure.PipelineDataDir method) get_quantification_file() (pyalfe.data_structure.BIDSDataDir method) (pyalfe.data_structure.DefaultALFEDataDir method) (pyalfe.data_structure.PipelineDataDir method) get_radiomics() (pyalfe.tasks.quantification.Quantification method) get_series() (pyalfe.data_structure.PatientDicomDataDir method) get_summary_update_from_individual() (pyalfe.tasks.quantification.Quantification static method) Greedy (class in pyalfe.interfaces.greedy) greedy_path (pyalfe.image_registration.GreedyRegistration attribute) GreedyRegistration (class in pyalfe.image_registration) H holefill() (pyalfe.image_processing.Convert3DProcessor static method) (pyalfe.image_processing.ImageProcessor static method) (pyalfe.image_processing.NilearnProcessor static method) (pyalfe.interfaces.c3d.C3D method) I image_centers() (pyalfe.interfaces.greedy.Greedy method) image_processor (pyalfe.containers.PipelineContainer property) (pyalfe.tasks.registration.Resampling attribute) (pyalfe.tasks.registration.T1Registration attribute) (pyalfe.tasks.skullstripping.Skullstripping attribute) (pyalfe.tasks.t1_postprocessing.T1Postprocessing attribute) (pyalfe.tasks.t1_preprocessing.T1Preprocessing attribute) image_registration (pyalfe.containers.PipelineContainer property) (pyalfe.tasks.registration.CrossModalityRegistration attribute) (pyalfe.tasks.registration.Resampling attribute) (pyalfe.tasks.registration.T1Registration attribute) image_type (pyalfe.tasks.registration.CrossModalityRegistration attribute) (pyalfe.tasks.registration.Resampling attribute) ImageProcessor (class in pyalfe.image_processing) ImageRegistration (class in pyalfe.image_registration) inference_model (pyalfe.tasks.skullstripping.Skullstripping attribute) InferenceModel (class in pyalfe.inference) info() (pyalfe.interfaces.c3d.C3D method) init_resources() (pyalfe.containers.DeclarativeContainer method) Initialization (class in pyalfe.tasks.initialization) initialization (pyalfe.containers.PipelineContainer property) (pyalfe.pipeline.PyALFEPipelineRunner attribute) initialize_affine() (pyalfe.interfaces.greedy.Greedy method) input() (pyalfe.interfaces.greedy.Greedy method) input_output() (pyalfe.interfaces.greedy.Greedy method) instances (pyalfe.data_structure.Series attribute) interpolation() (pyalfe.interfaces.greedy.Greedy method) is_dicom_file() (pyalfe.data_structure.PatientDicomDataDir method) L label_mask_comp() (pyalfe.image_processing.Convert3DProcessor static method) (pyalfe.image_processing.ImageProcessor static method) (pyalfe.image_processing.NilearnProcessor static method) label_segmentation_components() (pyalfe.tasks.segmentation.Segmentation method) largest_mask_comp() (pyalfe.image_processing.Convert3DProcessor static method) (pyalfe.image_processing.ImageProcessor static method) (pyalfe.image_processing.NilearnProcessor static method) load() (pyalfe.tasks.quantification.Quantification method) load_modality_images() (pyalfe.tasks.quantification.Quantification method) load_nii_gz() (pyalfe.tasks.quantification.Quantification static method) load_template_images() (pyalfe.tasks.quantification.Quantification method) logger (pyalfe.data_structure.BIDSDataDir attribute) (pyalfe.image_registration.GreedyRegistration attribute) (pyalfe.tasks.initialization.Initialization attribute) (pyalfe.tasks.quantification.Quantification attribute) (pyalfe.tasks.registration.CrossModalityRegistration attribute) (pyalfe.tasks.registration.Resampling attribute) (pyalfe.tasks.registration.T1Registration attribute) (pyalfe.tasks.segmentation.MultiModalitySegmentation attribute) (pyalfe.tasks.segmentation.SingleModalitySegmentation attribute) (pyalfe.tasks.segmentation.SynthSegTissueSegmentation attribute) (pyalfe.tasks.segmentation.TissueWithPriorSegementation attribute) (pyalfe.tasks.skullstripping.Skullstripping attribute) (pyalfe.tasks.t1_postprocessing.T1Postprocessing attribute) (pyalfe.tasks.t1_preprocessing.T1Preprocessing attribute) M mask() (pyalfe.image_processing.Convert3DProcessor static method) (pyalfe.image_processing.ImageProcessor static method) (pyalfe.image_processing.NilearnProcessor static method) metric() (pyalfe.interfaces.greedy.Greedy method) modalities (pyalfe.tasks.initialization.Initialization attribute) (pyalfe.tasks.skullstripping.Skullstripping attribute) modalities_all (pyalfe.tasks.quantification.Quantification attribute) (pyalfe.tasks.registration.CrossModalityRegistration attribute) modalities_target (pyalfe.tasks.quantification.Quantification attribute) (pyalfe.tasks.registration.CrossModalityRegistration attribute) (pyalfe.tasks.registration.Resampling attribute) Modality (class in pyalfe.data_structure) modality_dict (pyalfe.data_structure.BIDSDataDir attribute) module pyalfe.containers pyalfe.data_structure pyalfe.image_processing pyalfe.image_registration pyalfe.inference pyalfe.interfaces.c3d pyalfe.interfaces.greedy pyalfe.main pyalfe.pipeline pyalfe.roi pyalfe.tasks.initialization pyalfe.tasks.quantification pyalfe.tasks.registration pyalfe.tasks.segmentation pyalfe.tasks.skullstripping pyalfe.tasks.t1_postprocessing pyalfe.tasks.t1_preprocessing pyalfe.utils.archive pyalfe.utils.download MultiModalitySegmentation (class in pyalfe.tasks.segmentation) multiply() (pyalfe.interfaces.c3d.C3D method) N NilearnProcessor (class in pyalfe.image_processing) NNUnet (class in pyalfe.inference) NNUnetV2 (class in pyalfe.inference) num_iter() (pyalfe.interfaces.greedy.Greedy method) O operand() (pyalfe.interfaces.c3d.C3D method) Orientation (class in pyalfe.data_structure) out() (pyalfe.interfaces.c3d.C3D method) (pyalfe.interfaces.greedy.Greedy method) overwrite (pyalfe.tasks.initialization.Initialization attribute) (pyalfe.tasks.registration.CrossModalityRegistration attribute) (pyalfe.tasks.registration.Resampling attribute) (pyalfe.tasks.registration.T1Registration attribute) (pyalfe.tasks.skullstripping.Skullstripping attribute) (pyalfe.tasks.t1_postprocessing.T1Postprocessing attribute) (pyalfe.tasks.t1_preprocessing.T1Preprocessing attribute) P PatientDicomDataDir (class in pyalfe.data_structure) PERFUSION (pyalfe.data_structure.Modality attribute) pipeline_dir (pyalfe.containers.DicomProcessingContianer property) (pyalfe.containers.PipelineContainer property) (pyalfe.tasks.initialization.Initialization attribute) (pyalfe.tasks.quantification.Quantification attribute) (pyalfe.tasks.registration.CrossModalityRegistration attribute) (pyalfe.tasks.registration.Resampling attribute) (pyalfe.tasks.registration.T1Registration attribute) (pyalfe.tasks.skullstripping.Skullstripping attribute) (pyalfe.tasks.t1_postprocessing.T1Postprocessing attribute) (pyalfe.tasks.t1_preprocessing.T1Preprocessing attribute) PipelineContainer (class in pyalfe.containers) PipelineDataDir (class in pyalfe.data_structure) PipelineRunner (class in pyalfe.pipeline) popas() (pyalfe.interfaces.c3d.C3D method) post_process() (pyalfe.tasks.segmentation.Segmentation method) (pyalfe.tasks.segmentation.SynthSegTissueSegmentation method) predict() (pyalfe.tasks.segmentation.Segmentation method) predict_cases() (pyalfe.inference.InferenceModel method) (pyalfe.inference.NNUnet method) (pyalfe.inference.NNUnetV2 method) (pyalfe.inference.SynthSeg method) process_dicom() (in module pyalfe.main) process_modalities() (pyalfe.tasks.skullstripping.Skullstripping method) push() (pyalfe.interfaces.c3d.C3D method) pyalfe.containers module pyalfe.data_structure module pyalfe.image_processing module pyalfe.image_registration module pyalfe.inference module pyalfe.interfaces.c3d module pyalfe.interfaces.greedy module pyalfe.main module pyalfe.pipeline module pyalfe.roi module pyalfe.tasks.initialization module pyalfe.tasks.quantification module pyalfe.tasks.registration module pyalfe.tasks.segmentation module pyalfe.tasks.skullstripping module pyalfe.tasks.t1_postprocessing module pyalfe.tasks.t1_preprocessing module pyalfe.utils.archive module pyalfe.utils.download module pyalfe_pipeline_runner (pyalfe.containers.PipelineContainer property) PyALFEPipelineRunner (class in pyalfe.pipeline) Q Quantification (class in pyalfe.tasks.quantification) quantification (pyalfe.containers.PipelineContainer property) (pyalfe.pipeline.PyALFEPipelineRunner attribute) R reference() (pyalfe.interfaces.greedy.Greedy method) register_affine() (pyalfe.image_registration.AntsRegistration method) (pyalfe.image_registration.GreedyRegistration method) (pyalfe.image_registration.ImageRegistration method) register_deformable() (pyalfe.image_registration.AntsRegistration method) (pyalfe.image_registration.GreedyRegistration method) (pyalfe.image_registration.ImageRegistration method) register_rigid() (pyalfe.image_registration.AntsRegistration method) (pyalfe.image_registration.GreedyRegistration method) (pyalfe.image_registration.ImageRegistration method) remap_labels() (pyalfe.image_processing.Convert3DProcessor static method) (pyalfe.image_processing.ImageProcessor static method) (pyalfe.image_processing.NilearnProcessor static method) resample() (pyalfe.interfaces.c3d.C3D method) resample_new_dim() (pyalfe.image_processing.Convert3DProcessor static method) (pyalfe.image_processing.ImageProcessor static method) (pyalfe.image_processing.NilearnProcessor static method) Resampling (class in pyalfe.tasks.registration) resampling (pyalfe.containers.PipelineContainer property) (pyalfe.pipeline.PyALFEPipelineRunner attribute) reslice() (pyalfe.image_registration.AntsRegistration method) (pyalfe.image_registration.GreedyRegistration method) (pyalfe.image_registration.ImageRegistration method) (pyalfe.interfaces.greedy.Greedy method) reslice_identity() (pyalfe.interfaces.c3d.C3D method) reslice_to_ref() (pyalfe.image_processing.Convert3DProcessor static method) (pyalfe.image_processing.ImageProcessor static method) (pyalfe.image_processing.NilearnProcessor static method) retain_labels() (pyalfe.interfaces.c3d.C3D method) run() (in module pyalfe.main) (pyalfe.interfaces.c3d.C3D method) (pyalfe.interfaces.greedy.Greedy method) (pyalfe.pipeline.PipelineRunner method) (pyalfe.tasks.initialization.Initialization method) (pyalfe.tasks.quantification.Quantification method) (pyalfe.tasks.registration.CrossModalityRegistration method) (pyalfe.tasks.registration.Resampling method) (pyalfe.tasks.registration.T1Registration method) (pyalfe.tasks.segmentation.MultiModalitySegmentation method) (pyalfe.tasks.segmentation.Segmentation method) (pyalfe.tasks.segmentation.SynthSegTissueSegmentation method) (pyalfe.tasks.segmentation.TissueWithPriorSegementation method) (pyalfe.tasks.skullstripping.Skullstripping method) (pyalfe.tasks.t1_postprocessing.T1Postprocessing method) (pyalfe.tasks.t1_preprocessing.T1Preprocessing method) S SAGITTAL (pyalfe.data_structure.Orientation attribute) save() (pyalfe.image_processing.NilearnProcessor static method) scale() (pyalfe.interfaces.c3d.C3D method) sdt() (pyalfe.interfaces.c3d.C3D method) Segmentation (class in pyalfe.tasks.segmentation) Series (class in pyalfe.data_structure) series_path (pyalfe.data_structure.Series attribute) set_subtract() (pyalfe.image_processing.Convert3DProcessor static method) (pyalfe.image_processing.ImageProcessor static method) (pyalfe.image_processing.NilearnProcessor static method) SingleDWI (pyalfe.data_structure.Modality attribute) SingleModalitySegmentation (class in pyalfe.tasks.segmentation) Skullstripping (class in pyalfe.tasks.skullstripping) skullstripping (pyalfe.containers.PipelineContainer property) (pyalfe.pipeline.PyALFEPipelineRunner attribute) skullstripping_model (pyalfe.containers.PipelineContainer property) SWI (pyalfe.data_structure.Modality attribute) SynthSeg (class in pyalfe.inference) SynthSegTissueSegmentation (class in pyalfe.tasks.segmentation) T T1 (pyalfe.data_structure.Modality attribute) t1_postprocessing (pyalfe.containers.PipelineContainer property) (pyalfe.pipeline.PyALFEPipelineRunner attribute) t1_preprocessing (pyalfe.containers.PipelineContainer property) (pyalfe.pipeline.PyALFEPipelineRunner attribute) t1_registration (pyalfe.containers.PipelineContainer property) (pyalfe.pipeline.PyALFEPipelineRunner attribute) T1Post (pyalfe.data_structure.Modality attribute) T1Postprocessing (class in pyalfe.tasks.t1_postprocessing) T1Preprocessing (class in pyalfe.tasks.t1_preprocessing) T1Registration (class in pyalfe.tasks.registration) T2 (pyalfe.data_structure.Modality attribute) threads (pyalfe.image_registration.GreedyRegistration attribute) threads() (pyalfe.interfaces.greedy.Greedy method) thresh() (pyalfe.interfaces.c3d.C3D method) threshold() (pyalfe.image_processing.Convert3DProcessor static method) (pyalfe.image_processing.ImageProcessor static method) (pyalfe.image_processing.NilearnProcessor static method) Tissue (class in pyalfe.data_structure) tissue_model (pyalfe.containers.PipelineContainer property) tissue_segmentation (pyalfe.containers.PipelineContainer property) (pyalfe.pipeline.PyALFEPipelineRunner attribute) TissueWithPriorSegementation (class in pyalfe.tasks.segmentation) transforms() (pyalfe.interfaces.greedy.Greedy method) trim() (pyalfe.interfaces.c3d.C3D method) trim_largest_comp() (pyalfe.image_processing.Convert3DProcessor static method) (pyalfe.image_processing.ImageProcessor static method) (pyalfe.image_processing.NilearnProcessor static method) U union() (pyalfe.image_processing.Convert3DProcessor static method) (pyalfe.image_processing.ImageProcessor static method) (pyalfe.image_processing.NilearnProcessor static method) W WHITE_MATTER (pyalfe.data_structure.Tissue attribute)
