Index A | B | C | D | E | F | G | H | I | J | L | M | N | O | P | R | S | T | U | V | W | Z A AbstractMeasure (class in FastSurferCNN.utils.brainvolstats) add_argument() (FastSurferCNN.utils.parser_defaults.CanAddArguments method) add_arguments() (in module FastSurferCNN.utils.parser_defaults) add_cereb_wm() (in module CerebNet.datasets.wm_merge_clean) add_computed_measure() (FastSurferCNN.utils.brainvolstats.Manager method) add_imported_measure() (FastSurferCNN.utils.brainvolstats.Manager method) add_measure_parser() (in module FastSurferCNN.segstats) add_plane_flags() (in module FastSurferCNN.utils.parser_defaults) add_two_help_messages() (in module FastSurferCNN.segstats) AddGaussianNoise (class in FastSurferCNN.data_loader.augmentation) align_aparc_centroids() (in module recon_surf.rotate_sphere) align_flipped() (in module recon_surf.align_seg) align_seg_centroids() (in module recon_surf.align_seg) angles2rmat() (in module recon_surf.align_points) apply_orientation() (in module FastSurferCNN.data_loader.conform) apply_transform_to_pt() (in module CorpusCallosum.utils.mapping_helpers) apply_transform_to_volume() (in module CorpusCallosum.utils.mapping_helpers) are_all_subject_files() (FastSurferCNN.utils.common.SubjectList method) area (CorpusCallosum.shape.contour.CCContour property) args2cfg() (in module FastSurferCNN.run_prediction) argument_parse() (in module CorpusCallosum.paint_cc_into_pred) ArgumentDefaultsHelpFormatter (class in CorpusCallosum.fastsurfer_cc) as_future() (FastSurferCNN.utils.run_tools.Popen method) as_tuple() (FastSurferCNN.utils.brainvolstats.AbstractMeasure method) asdict() (in module FastSurferCNN.utils.dataclasses) asegdkt_segfile (FastSurferCNN.utils.common.SubjectDirectory property) assert_measure_need_subject() (FastSurferCNN.utils.brainvolstats.Manager method) assert_measurefile_absolute() (FastSurferCNN.utils.brainvolstats.ImportedMeasure method) assert_no_root() (in module FastSurferCNN.utils.common) astuple() (in module FastSurferCNN.utils.dataclasses) async_save_img() (FastSurferCNN.run_prediction.RunModelOnData method) AugmentationPadImage (class in FastSurferCNN.data_loader.augmentation) AugmentationRandomCrop (class in FastSurferCNN.data_loader.augmentation) B bbox_3d() (in module FastSurferCNN.data_loader.data_utils) bincount2D_vectorized() (in module recon_surf.smooth_aparc) borders() (in module FastSurferCNN.segstats) bounding_volume_offset() (in module CerebNet.datasets.utils) build_annot() (in module recon_surf.create_annotation) build_model() (in module CerebNet.models.networks) (in module FastSurferCNN.models.networks) (in module HypVINN.models.networks) C calc_mapping_to_standard_space() (in module CorpusCallosum.utils.mapping_helpers) calc_ras_centroids_from_seg() (in module CorpusCallosum.data.read_write) calc_subsegment_areas() (in module CorpusCallosum.shape.subsegment_contour) calculate_cc_index() (in module CorpusCallosum.shape.metrics) calculate_curvature_metrics() (in module CorpusCallosum.shape.curvature) calculate_flip_orientation() (in module HypVINN.data_loader.data_utils) calculate_merged_labels() (in module FastSurferCNN.segstats) calculate_volume() (in module CorpusCallosum.shape.contour) can_resolve_attribute() (FastSurferCNN.utils.common.SubjectDirectory method) can_resolve_filename() (FastSurferCNN.utils.common.SubjectDirectory method) CanAddArguments (class in FastSurferCNN.utils.parser_defaults) cc_thickness() (in module CorpusCallosum.shape.thickness) CCContour (class in CorpusCallosum.shape.contour) CCMeasuresDict (class in CorpusCallosum.utils.types) CCMesh (class in CorpusCallosum.shape.mesh) cereb_subseg_lateral_mask() (in module CerebNet.datasets.wm_merge_clean) CerebDataset (class in CerebNet.data_loader.dataset) CerebNet.apply_warp module CerebNet.data_loader.augmentation module CerebNet.data_loader.data_utils module CerebNet.data_loader.dataset module CerebNet.data_loader.loader module CerebNet.datasets.generate_hdf5 module CerebNet.datasets.load_data module CerebNet.datasets.utils module CerebNet.datasets.wm_merge_clean module CerebNet.inference module CerebNet.models.networks module CerebNet.models.sub_module module CerebNet.run_prediction module CerebNet.utils.checkpoint module CerebNet.utils.load_config module CerebNet.utils.lr_scheduler module CerebNet.utils.meters module CerebNet.utils.misc module CerebNetDataset (class in CerebNet.datasets.generate_hdf5) chain() (FastSurferCNN.utils.mapper.Mapper method) check_affine_in_nifti() (in module FastSurferCNN.data_loader.conform) check_and_download_ckpts() (in module FastSurferCNN.utils.checkpoint) check_area_changes() (in module CorpusCallosum.shape.postprocessing) check_freesurfer() (in module recon_surf.long_compat_segmentHA) check_path() (in module FastSurferCNN.utils.misc) check_shape_affine() (in module FastSurferCNN.segstats) check_volume() (in module FastSurferCNN.quick_qc) CheckpointConfigDict (class in FastSurferCNN.utils.checkpoint) classes (FastSurferCNN.utils.mapper.ColorLookupTable property) ClassifierBlock (class in CerebNet.models.sub_module) (class in FastSurferCNN.models.sub_module) clean_cc_segmentation() (in module CorpusCallosum.segmentation.segmentation_postprocessing) clean_cortex_labels() (in module FastSurferCNN.data_loader.data_utils) clear() (FastSurferCNN.utils.brainvolstats.Manager method) color_palette (FastSurferCNN.utils.mapper.ColorLookupTable property) ColorLookupTable (class in FastSurferCNN.utils.mapper) colormap() (FastSurferCNN.utils.mapper.ColorLookupTable method) CombinedLoss (class in FastSurferCNN.models.losses) CompetitiveDecoderBlock (class in CerebNet.models.sub_module) (class in FastSurferCNN.models.sub_module) CompetitiveDenseBlock (class in CerebNet.models.sub_module) (class in FastSurferCNN.models.sub_module) CompetitiveDenseBlockInput (class in CerebNet.models.sub_module) (class in FastSurferCNN.models.sub_module) CompetitiveEncoderBlock (class in CerebNet.models.sub_module) (class in FastSurferCNN.models.sub_module) CompetitiveEncoderBlockInput (class in CerebNet.models.sub_module) (class in FastSurferCNN.models.sub_module) compute() (FastSurferCNN.utils.metrics.DiceScore method) compute_curvature() (in module CorpusCallosum.shape.curvature) compute_mean_curvature() (in module CorpusCallosum.shape.curvature) compute_non_derived_pv() (FastSurferCNN.utils.brainvolstats.Manager method) compute_stats() (in module HypVINN.utils.stats_utils) conf_name (FastSurferCNN.utils.common.SubjectDirectory property) conform() (in module FastSurferCNN.data_loader.conform) conform_and_save_orig() (FastSurferCNN.run_prediction.RunModelOnData method) conformed_vox_img_size() (in module FastSurferCNN.data_loader.conform) connect_diagonally_connected_components() (in module CorpusCallosum.shape.endpoint_heuristic) connect_nearby_components() (in module CorpusCallosum.segmentation.segmentation_postprocessing) construct_adj_cluster() (in module recon_surf.sample_parc) convert_numpy_to_json_serializable() (in module CorpusCallosum.data.read_write) copy() (CorpusCallosum.shape.contour.CCContour method) copy_orig_name (FastSurferCNN.utils.common.SubjectDirectory property) CorpusCallosum.cc_visualization module CorpusCallosum.data.constants module CorpusCallosum.data.fsaverage_cc_template module CorpusCallosum.data.generate_fsaverage_centroids module CorpusCallosum.data.read_write module CorpusCallosum.fastsurfer_cc module CorpusCallosum.localization.inference module CorpusCallosum.paint_cc_into_pred module CorpusCallosum.segmentation.inference module CorpusCallosum.segmentation.segmentation_postprocessing module CorpusCallosum.shape.contour module CorpusCallosum.shape.curvature module CorpusCallosum.shape.endpoint_heuristic module CorpusCallosum.shape.mesh module CorpusCallosum.shape.metrics module CorpusCallosum.shape.postprocessing module CorpusCallosum.shape.subsegment_contour module CorpusCallosum.shape.thickness module CorpusCallosum.transforms.localization module CorpusCallosum.transforms.segmentation module CorpusCallosum.utils.checkpoint module CorpusCallosum.utils.mapping_helpers module CorpusCallosum.utils.types module CorpusCallosum.utils.visualization module correct_cereb_brainstem() (in module CerebNet.datasets.wm_merge_clean) correct_nodding() (in module CorpusCallosum.utils.mapping_helpers) correct_wm_ventricles() (in module CorpusCallosum.paint_cc_into_pred) cortex_border_mask() (in module FastSurferCNN.data_loader.data_utils) CosineAnnealingWarmRestartsDecay (class in CerebNet.utils.lr_scheduler) CosineLR (class in CerebNet.utils.lr_scheduler) create_annotation() (in module recon_surf.create_annotation) create_checkpoint_dir() (in module CerebNet.utils.checkpoint) (in module FastSurferCNN.utils.checkpoint) create_connection_line() (in module CorpusCallosum.segmentation.segmentation_postprocessing) create_expand_output_directory() (in module HypVINN.utils.misc) create_hdf5_dataset() (CerebNet.datasets.generate_hdf5.CerebNetDataset method) (FastSurferCNN.generate_hdf5.H5pyDataset method) create_levelpaths() (CorpusCallosum.shape.contour.CCContour method) create_mask() (in module FastSurferCNN.reduce_to_aseg) create_mask_and_save() (in module FastSurferCNN.reduce_to_aseg) create_weight_mask() (in module FastSurferCNN.data_loader.data_utils) create_weight_mask2d() (in module CerebNet.data_loader.data_utils) crop_patch_to_mask() (in module FastSurferCNN.segstats) crop_position (FastSurferCNN.models.interpolation_layer.Zoom2d property) (FastSurferCNN.models.interpolation_layer.Zoom3d property) crop_transform() (in module FastSurferCNN.data_loader.conform) CropAroundACPC (class in CorpusCallosum.transforms.segmentation) CropAroundACPCFixedSize (class in CorpusCallosum.transforms.localization) CropAroundACPCtrack (class in CorpusCallosum.transforms.segmentation) CrossEntropy2D (class in FastSurferCNN.models.losses) D dataclass() (in module FastSurferCNN.utils.dataclasses) dataframe() (FastSurferCNN.utils.mapper.JsonColorLookupTable method) (FastSurferCNN.utils.mapper.TSVLookupTable method) dataframe_to_table() (in module FastSurferCNN.segstats) decay_base_lr() (CerebNet.utils.lr_scheduler.CosineAnnealingWarmRestartsDecay method) deep_sulci_and_wm_strand_mask() (in module FastSurferCNN.data_loader.data_utils) default() (FastSurferCNN.utils.brainvolstats.Manager method) default_measures (FastSurferCNN.utils.brainvolstats.Manager property) DerivedMeasure (class in FastSurferCNN.utils.brainvolstats) description (FastSurferCNN.utils.brainvolstats.AbstractMeasure property) dice_score() (in module FastSurferCNN.utils.metrics) DiceLoss (class in FastSurferCNN.models.losses) DiceScore (class in FastSurferCNN.utils.metrics) disable_confusion_mat() (FastSurferCNN.utils.meters.Meter method) does_vox2vox_rot_require_interpolation() (in module FastSurferCNN.data_loader.conform) download_checkpoint() (in module FastSurferCNN.utils.checkpoint) drop_disconnected_component() (in module CerebNet.datasets.wm_merge_clean) E empty() (in module FastSurferCNN.segstats) enable_confusion_mat() (FastSurferCNN.utils.meters.Meter method) ETIVMeasure (class in FastSurferCNN.utils.brainvolstats) eval() (FastSurferCNN.inference.Inference method) (FastSurferCNN.train.Trainer method) (HypVINN.inference.Inference method) extract_cc_contour() (in module CorpusCallosum.shape.endpoint_heuristic) extract_key_args() (FastSurferCNN.utils.brainvolstats.Manager method) extract_largest_connected_component() (in module CorpusCallosum.segmentation.segmentation_postprocessing) F FastSurferCNN (class in CerebNet.models.networks) (class in FastSurferCNN.models.networks) FastSurferCNN.data_loader.augmentation module FastSurferCNN.data_loader.conform module FastSurferCNN.data_loader.data_utils module FastSurferCNN.data_loader.dataset module FastSurferCNN.data_loader.loader module FastSurferCNN.download_checkpoints module FastSurferCNN.generate_hdf5 module FastSurferCNN.inference module FastSurferCNN.models.interpolation_layer module FastSurferCNN.models.losses module FastSurferCNN.models.networks module FastSurferCNN.models.optimizer module FastSurferCNN.models.sub_module module FastSurferCNN.mri_brainvol_stats module FastSurferCNN.mri_segstats module FastSurferCNN.quick_qc module FastSurferCNN.reduce_to_aseg module FastSurferCNN.run_model module FastSurferCNN.run_prediction module FastSurferCNN.segstats module FastSurferCNN.train module FastSurferCNN.utils.arg_types module FastSurferCNN.utils.brainvolstats module FastSurferCNN.utils.checkpoint module FastSurferCNN.utils.common module FastSurferCNN.utils.dataclasses module FastSurferCNN.utils.load_config module FastSurferCNN.utils.logging module FastSurferCNN.utils.lr_scheduler module FastSurferCNN.utils.lta module FastSurferCNN.utils.mapper module FastSurferCNN.utils.meters module FastSurferCNN.utils.metrics module FastSurferCNN.utils.misc module FastSurferCNN.utils.parallel module FastSurferCNN.utils.parser_defaults module FastSurferCNN.utils.run_tools module FastSurferCNN.version module FastSurferCNNBase (class in FastSurferCNN.models.networks) FastSurferCompatError FastSurferVINN (class in FastSurferCNN.models.networks) field() (in module FastSurferCNN.utils.dataclasses) fields() (in module FastSurferCNN.utils.dataclasses) fileexists_by_attribute() (FastSurferCNN.utils.common.SubjectDirectory method) fileexists_in_subject_folder() (FastSurferCNN.utils.common.SubjectDirectory method) filename_by_attribute() (FastSurferCNN.utils.common.SubjectDirectory method) filename_in_subject_folder() (FastSurferCNN.utils.common.SubjectDirectory method) fill_thickness_values() (CorpusCallosum.shape.contour.CCContour method) fill_unknown_labels_per_hemi() (in module FastSurferCNN.data_loader.data_utils) filling_unknown_labels() (in module CerebNet.datasets.wm_merge_clean) filter_blank_slices_thick() (in module CerebNet.data_loader.data_utils) (in module CerebNet.datasets.utils) (in module FastSurferCNN.data_loader.data_utils) filter_git_status() (in module FastSurferCNN.version) find_affine() (in module recon_surf.align_points) find_all_islands() (in module recon_surf.sample_parc) find_cc_endpoints() (in module CorpusCallosum.shape.endpoint_heuristic) find_closest_edge() (in module CorpusCallosum.shape.thickness) find_component_boundaries() (in module CorpusCallosum.segmentation.segmentation_postprocessing) find_device() (in module FastSurferCNN.utils.common) find_latest_experiment() (in module FastSurferCNN.utils.misc) find_minimal_connection_path() (in module CorpusCallosum.segmentation.segmentation_postprocessing) find_rigid() (in module recon_surf.align_points) find_rotation() (in module recon_surf.align_points) finish() (FastSurferCNN.utils.run_tools.Popen method) flags (FastSurferCNN.utils.common.SubjectList property) flip_wm_islands() (in module FastSurferCNN.reduce_to_aseg) float_gt_zero_and_le_one() (in module FastSurferCNN.utils.arg_types) format_classes() (in module FastSurferCNN.utils.brainvolstats) format_cmdline_args() (in module FastSurferCNN.mri_segstats) format_measure() (in module FastSurferCNN.utils.brainvolstats) format_measures() (FastSurferCNN.utils.brainvolstats.Manager method) format_parameters() (in module FastSurferCNN.segstats) forward() (CerebNet.models.networks.FastSurferCNN method) (CerebNet.models.sub_module.ClassifierBlock method) (CerebNet.models.sub_module.CompetitiveDecoderBlock method) (CerebNet.models.sub_module.CompetitiveDenseBlock method) (CerebNet.models.sub_module.CompetitiveDenseBlockInput method) (CerebNet.models.sub_module.CompetitiveEncoderBlock method) (CerebNet.models.sub_module.CompetitiveEncoderBlockInput method) (FastSurferCNN.models.losses.CombinedLoss method) (FastSurferCNN.models.losses.CrossEntropy2D method) (FastSurferCNN.models.losses.DiceLoss method) (FastSurferCNN.models.networks.FastSurferCNN method) (FastSurferCNN.models.networks.FastSurferCNNBase method) (FastSurferCNN.models.networks.FastSurferVINN method) (FastSurferCNN.models.sub_module.ClassifierBlock method) (FastSurferCNN.models.sub_module.CompetitiveDecoderBlock method) (FastSurferCNN.models.sub_module.CompetitiveDenseBlock method) (FastSurferCNN.models.sub_module.CompetitiveDenseBlockInput method) (FastSurferCNN.models.sub_module.CompetitiveEncoderBlock method) (FastSurferCNN.models.sub_module.CompetitiveEncoderBlockInput method) (FastSurferCNN.models.sub_module.GaussianNoise method) (FastSurferCNN.models.sub_module.InputDenseBlock method) (FastSurferCNN.models.sub_module.OutputDenseBlock method) (HypVINN.models.networks.HypVINN method) forward_output() (FastSurferCNN.utils.run_tools.MessageBuffer method) (FastSurferCNN.utils.run_tools.Popen method) from_contour_file() (CorpusCallosum.shape.contour.CCContour class method) from_contours() (CorpusCallosum.shape.mesh.CCMesh class method) from_mask_and_acpc() (CorpusCallosum.shape.contour.CCContour class method) FrozenInstanceError fuse_cortex_labels() (in module FastSurferCNN.data_loader.data_utils) G GaussianNoise (class in FastSurferCNN.models.sub_module) get_adjM() (in module recon_surf.smooth_aparc) get_aseg_cereb_mask() (in module CerebNet.data_loader.data_utils) get_attribute() (FastSurferCNN.utils.common.SubjectDirectory method) get_brain_centroid() (in module recon_surf.N4_bias_correct) get_cc_num_voxel() (in module CorpusCallosum.segmentation.segmentation_postprocessing) get_cfg() (FastSurferCNN.inference.Inference method) (HypVINN.inference.Inference method) get_checkpoint() (in module CerebNet.utils.checkpoint) (in module FastSurferCNN.utils.checkpoint) get_checkpoint_path() (in module CerebNet.utils.checkpoint) (in module FastSurferCNN.utils.checkpoint) get_checkpoints() (in module FastSurferCNN.utils.checkpoint) get_clean_labels() (in module HypVINN.utils.img_processing_utils) get_clean_mask() (in module HypVINN.utils.img_processing_utils) get_color_by_index() (FastSurferCNN.utils.mapper.ColorLookupTable method) get_common_suffix() (FastSurferCNN.utils.common.SubjectList method) get_config() (in module CerebNet.utils.load_config) (in module FastSurferCNN.utils.load_config) (in module HypVINN.utils.load_config) get_config_file() (in module FastSurferCNN.utils.checkpoint) get_contour_edge_lengths() (CorpusCallosum.shape.contour.CCContour method) get_dataloader() (in module CerebNet.data_loader.loader) (in module FastSurferCNN.data_loader.loader) get_default_version_info() (in module FastSurferCNN.version) get_device() (FastSurferCNN.inference.Inference method) (HypVINN.inference.Inference method) get_epoch_lr() (CerebNet.utils.lr_scheduler.CosineLR method) get_field() (in module FastSurferCNN.utils.dataclasses) get_hypinn_mode() (in module HypVINN.utils.mode_config) get_image_mean() (in module recon_surf.N4_bias_correct) get_imported_all_measures() (FastSurferCNN.utils.brainvolstats.Manager method) get_intersections() (in module CorpusCallosum.shape.metrics) get_labels_from_lut() (in module FastSurferCNN.data_loader.data_utils) get_largest_cc() (in module FastSurferCNN.data_loader.data_utils) get_loss_func() (in module FastSurferCNN.models.losses) get_lr() (CerebNet.utils.lr_scheduler.WarmupCosineLR method) get_lr_scheduler() (in module CerebNet.utils.lr_scheduler) (in module FastSurferCNN.utils.lr_scheduler) get_lut() (in module HypVINN.utils.visualization_utils) get_max_size() (HypVINN.inference.Inference method) get_model_height() (FastSurferCNN.inference.Inference method) (HypVINN.inference.Inference method) get_model_width() (FastSurferCNN.inference.Inference method) (HypVINN.inference.Inference method) get_modelname() (FastSurferCNN.inference.Inference method) (HypVINN.inference.Inference method) get_num_classes() (FastSurferCNN.inference.Inference method) (FastSurferCNN.run_prediction.RunModelOnData method) (HypVINN.inference.Inference method) get_num_threads() (in module FastSurferCNN.utils.parallel) get_optimizer() (in module FastSurferCNN.models.optimizer) get_plane() (FastSurferCNN.inference.Inference method) (HypVINN.inference.Inference method) get_prediction() (FastSurferCNN.run_prediction.RunModelOnData method) (in module HypVINN.run_prediction) get_primary_eigenvector() (in module CorpusCallosum.shape.subsegment_contour) get_region_bg_intersection_mask() (in module FastSurferCNN.quick_qc) get_seg_centroids() (in module recon_surf.align_seg) get_subject_names() (FastSurferCNN.data_loader.dataset.MultiScaleDataset method) (FastSurferCNN.data_loader.dataset.MultiScaleDatasetVal method) get_supported_freesurfer_version() (in module recon_surf.long_compat_segmentHA) get_tal_origin_voxel() (in module recon_surf.N4_bias_correct) get_thick_slices() (in module FastSurferCNN.data_loader.data_utils) get_transforms() (in module CorpusCallosum.localization.inference) get_ventricle_bg_intersection_volume() (in module FastSurferCNN.quick_qc) get_virtual_labels() (FastSurferCNN.utils.brainvolstats.Manager method) get_vox2ras() (in module recon_surf.align_seg) get_vox_vol() (FastSurferCNN.utils.brainvolstats.DerivedMeasure method) (FastSurferCNN.utils.brainvolstats.ImportedMeasure method) (FastSurferCNN.utils.brainvolstats.VolumeMeasure method) get_voxel_size() (in module recon_surf.long_compat_segmentHA) getitem_by_index() (FastSurferCNN.utils.mapper.ColorLookupTable method) (FastSurferCNN.utils.mapper.TSVLookupTable method) getscale() (in module FastSurferCNN.data_loader.conform) getSurfCorrespondence() (in module recon_surf.map_surf_label) global_stats() (in module FastSurferCNN.segstats) H H5pyDataset (class in FastSurferCNN.generate_hdf5) handle_cuda_memory_exception() (in module FastSurferCNN.utils.common) has_attribute() (FastSurferCNN.utils.common.SubjectDirectory method) has_git() (in module FastSurferCNN.version) hd() (in module FastSurferCNN.utils.metrics) hd95() (in module FastSurferCNN.utils.metrics) help() (FastSurferCNN.utils.brainvolstats.AbstractMeasure method) (FastSurferCNN.utils.brainvolstats.DerivedMeasure method) (FastSurferCNN.utils.brainvolstats.ETIVMeasure method) (FastSurferCNN.utils.brainvolstats.ImportedMeasure method) (FastSurferCNN.utils.brainvolstats.NullMeasure method) (FastSurferCNN.utils.brainvolstats.PVMeasure method) (FastSurferCNN.utils.brainvolstats.SurfaceHoles method) (FastSurferCNN.utils.brainvolstats.SurfaceVolume method) (FastSurferCNN.utils.brainvolstats.VolumeMeasure method) HelpFormatter (class in FastSurferCNN.segstats) hemi_masks_from_aseg() (in module FastSurferCNN.utils.brainvolstats) hypo_map_label2subseg() (in module HypVINN.data_loader.data_utils) hypo_map_prediction_sagittal2full() (in module HypVINN.data_loader.data_utils) hypo_map_subseg_2_fsseg() (in module HypVINN.data_loader.data_utils) HypVINN (class in HypVINN.models.networks) HypVINN.data_loader.data_utils module HypVINN.data_loader.dataset module HypVINN.inference module HypVINN.models.networks module HypVINN.run_prediction module HypVINN.utils.checkpoint module HypVINN.utils.img_processing_utils module HypVINN.utils.load_config module HypVINN.utils.misc module HypVINN.utils.mode_config module HypVINN.utils.preproc module HypVINN.utils.stats_utils module HypVINN.utils.visualization_utils module hypvinn_preproc() (in module HypVINN.utils.preproc) HypVINNDataset (class in HypVINN.data_loader.dataset) I id (FastSurferCNN.utils.common.SubjectDirectory property) img2axcodes() (in module HypVINN.utils.img_processing_utils) img_size() (in module FastSurferCNN.utils.arg_types) ImportedMeasure (class in FastSurferCNN.utils.brainvolstats) infer_labels_excludeid() (in module FastSurferCNN.segstats) infer_mapping_from_lut() (in module FastSurferCNN.data_loader.data_utils) infer_merged_labels() (in module FastSurferCNN.segstats) Inference (class in CerebNet.inference) (class in FastSurferCNN.inference) (class in HypVINN.inference) init_mgh_header() (in module CorpusCallosum.fastsurfer_cc) InputDenseBlock (class in FastSurferCNN.models.sub_module) insert_point_with_thickness() (in module CorpusCallosum.shape.thickness) instantiate_measures() (FastSurferCNN.utils.brainvolstats.Manager method) int_ge_zero() (in module FastSurferCNN.utils.arg_types) int_gt_zero() (in module FastSurferCNN.utils.arg_types) invalid_len_ratio() (FastSurferCNN.utils.brainvolstats.DerivedMeasure method) invalid_len_vox_vol() (FastSurferCNN.utils.brainvolstats.DerivedMeasure method) iou_score() (in module FastSurferCNN.utils.metrics) is_bijective() (FastSurferCNN.utils.mapper.Mapper method) is_checkpoint_epoch() (in module CerebNet.utils.checkpoint) is_conform() (in module FastSurferCNN.data_loader.conform) is_dataclass() (in module FastSurferCNN.utils.dataclasses) is_int() (in module FastSurferCNN.utils.mapper) is_orientation() (in module FastSurferCNN.data_loader.conform) iterate() (in module FastSurferCNN.utils.parallel) itk_n4_bfcorrection() (in module recon_surf.N4_bias_correct) J JsonColorLookupTable (class in FastSurferCNN.utils.mapper) L labelname2id() (FastSurferCNN.utils.mapper.ColorLookupTable method) (FastSurferCNN.utils.mapper.JsonColorLookupTable method) (FastSurferCNN.utils.mapper.TSVLookupTable method) labelname2index() (FastSurferCNN.utils.mapper.ColorLookupTable method) labels() (FastSurferCNN.utils.brainvolstats.PVMeasure method) load_and_conform_image() (in module FastSurferCNN.data_loader.data_utils) load_checkpoint() (FastSurferCNN.inference.Inference method) (HypVINN.inference.Inference method) load_checkpoint_config() (in module FastSurferCNN.utils.checkpoint) load_checkpoint_config_defaults() (in module FastSurferCNN.utils.checkpoint) load_classwise_weights() (in module CerebNet.utils.misc) load_config() (in module FastSurferCNN.utils.load_config) (in module HypVINN.utils.load_config) load_contours_from_template_dir() (in module CorpusCallosum.cc_visualization) load_from_checkpoint() (in module CerebNet.utils.checkpoint) (in module FastSurferCNN.utils.checkpoint) load_fsaverage_affine() (in module CorpusCallosum.data.read_write) load_fsaverage_cc_template() (in module CorpusCallosum.data.fsaverage_cc_template) load_fsaverage_centroids() (in module CorpusCallosum.data.read_write) load_fsaverage_data() (in module CorpusCallosum.data.read_write) load_image() (in module FastSurferCNN.data_loader.data_utils) load_maybe_conform() (in module FastSurferCNN.data_loader.data_utils) load_model() (in module CorpusCallosum.localization.inference) (in module CorpusCallosum.segmentation.inference) load_subject() (CerebNet.datasets.load_data.SubjectLoader method) load_talairach_coordinates() (in module CerebNet.datasets.utils) load_test_subject() (CerebNet.datasets.load_data.SubjectLoader method) load_thickness_values() (CorpusCallosum.shape.contour.CCContour method) load_validation_data() (in module CorpusCallosum.segmentation.inference) load_volumes() (in module HypVINN.run_prediction) localize_ac_pc() (in module CorpusCallosum.fastsurfer_cc) locate_mask_bbox() (CerebNet.data_loader.dataset.SubjectDataset method) locating_unknowns() (in module CerebNet.datasets.wm_merge_clean) log_epoch() (CerebNet.utils.meters.Meter method) (FastSurferCNN.utils.meters.Meter method) log_iter() (CerebNet.utils.meters.Meter method) (FastSurferCNN.utils.meters.Meter method) log_lr() (CerebNet.utils.meters.Meter method) lr_func_cosine() (CerebNet.utils.lr_scheduler.CosineLR method) LTADict (class in FastSurferCNN.utils.lta) M main() (in module CerebNet.apply_warp) (in module CerebNet.run_prediction) (in module CorpusCallosum.cc_visualization) (in module CorpusCallosum.data.generate_fsaverage_centroids) (in module CorpusCallosum.fastsurfer_cc) (in module FastSurferCNN.run_model) (in module FastSurferCNN.segstats) (in module FastSurferCNN.version) (in module HypVINN.run_prediction) (in module recon_surf.long_compat_segmentHA) (in module recon_surf.smooth_aparc) main_segfile (FastSurferCNN.utils.common.SubjectDirectory property) make_affine() (in module CorpusCallosum.utils.mapping_helpers) make_arguments() (in module FastSurferCNN.mri_brainvol_stats) (in module FastSurferCNN.mri_segstats) (in module FastSurferCNN.segstats) make_classmapper() (FastSurferCNN.utils.mapper.Mapper class method) make_dataclass() (in module FastSurferCNN.utils.dataclasses) make_mesh_from_contour() (in module CorpusCallosum.shape.thickness) make_midplane_affine() (in module CorpusCallosum.utils.mapping_helpers) make_parser() (in module CorpusCallosum.cc_visualization) (in module CorpusCallosum.fastsurfer_cc) (in module FastSurferCNN.data_loader.conform) (in module FastSurferCNN.run_model) (in module FastSurferCNN.run_prediction) (in module FastSurferCNN.version) (in module recon_surf.long_compat_segmentHA) (in module recon_surf.rewrite_oriented_surface) make_read_hook() (FastSurferCNN.utils.brainvolstats.Manager method) make_subdivision_mask() (in module CorpusCallosum.shape.postprocessing) make_subjects_dir() (FastSurferCNN.utils.common.SubjectList method) make_triangles_between_contours() (in module CorpusCallosum.shape.mesh) Manager (class in FastSurferCNN.utils.brainvolstats) map() (FastSurferCNN.utils.mapper.Mapper method) (FastSurferCNN.utils.parallel.SerialExecutor method) map_aparc_aseg2label() (in module FastSurferCNN.data_loader.data_utils) map_hyposeg2label() (in module HypVINN.utils.visualization_utils) map_image() (in module FastSurferCNN.data_loader.conform) map_label2aparc_aseg() (in module FastSurferCNN.data_loader.data_utils) map_label2subseg() (in module CerebNet.datasets.utils) map_multiple_labels() (in module recon_surf.create_annotation) map_prediction_sagittal2full() (in module CerebNet.data_loader.data_utils) (in module FastSurferCNN.data_loader.data_utils) map_sag2label() (in module CerebNet.data_loader.data_utils) map_size() (in module CerebNet.datasets.utils) map_softlabels_to_orig() (in module CorpusCallosum.utils.mapping_helpers) Mapper (class in FastSurferCNN.utils.mapper) mapSurfLabel() (in module recon_surf.map_surf_label) mask() (FastSurferCNN.utils.brainvolstats.MaskMeasure method) mask_in_array() (in module FastSurferCNN.utils.brainvolstats) mask_not_in_array() (in module FastSurferCNN.utils.brainvolstats) MaskMeasure (class in FastSurferCNN.utils.brainvolstats) max_label (FastSurferCNN.utils.mapper.Mapper property) Measure (class in FastSurferCNN.utils.brainvolstats) MessageBuffer (class in FastSurferCNN.utils.run_tools) messages() (FastSurferCNN.utils.run_tools.Popen method) Meter (class in CerebNet.utils.meters) (class in FastSurferCNN.utils.meters) metrics_per_class() (CerebNet.utils.meters.TestMeter method) mgh_from_sitk() (in module recon_surf.image_io) MGHHeaderDict (class in CorpusCallosum.data.read_write) minimum_bounding_rectangle() (in module CorpusCallosum.shape.subsegment_contour) mode_filter() (in module recon_surf.smooth_aparc) modify_argument() (in module FastSurferCNN.utils.parser_defaults) module CerebNet.apply_warp CerebNet.data_loader.augmentation CerebNet.data_loader.data_utils CerebNet.data_loader.dataset CerebNet.data_loader.loader CerebNet.datasets.generate_hdf5 CerebNet.datasets.load_data CerebNet.datasets.utils CerebNet.datasets.wm_merge_clean CerebNet.inference CerebNet.models.networks CerebNet.models.sub_module CerebNet.run_prediction CerebNet.utils.checkpoint CerebNet.utils.load_config CerebNet.utils.lr_scheduler CerebNet.utils.meters CerebNet.utils.misc CorpusCallosum.cc_visualization CorpusCallosum.data.constants CorpusCallosum.data.fsaverage_cc_template CorpusCallosum.data.generate_fsaverage_centroids CorpusCallosum.data.read_write CorpusCallosum.fastsurfer_cc CorpusCallosum.localization.inference CorpusCallosum.paint_cc_into_pred CorpusCallosum.segmentation.inference CorpusCallosum.segmentation.segmentation_postprocessing CorpusCallosum.shape.contour CorpusCallosum.shape.curvature CorpusCallosum.shape.endpoint_heuristic CorpusCallosum.shape.mesh CorpusCallosum.shape.metrics CorpusCallosum.shape.postprocessing CorpusCallosum.shape.subsegment_contour CorpusCallosum.shape.thickness CorpusCallosum.transforms.localization CorpusCallosum.transforms.segmentation CorpusCallosum.utils.checkpoint CorpusCallosum.utils.mapping_helpers CorpusCallosum.utils.types CorpusCallosum.utils.visualization FastSurferCNN.data_loader.augmentation FastSurferCNN.data_loader.conform FastSurferCNN.data_loader.data_utils FastSurferCNN.data_loader.dataset FastSurferCNN.data_loader.loader FastSurferCNN.download_checkpoints FastSurferCNN.generate_hdf5 FastSurferCNN.inference FastSurferCNN.models.interpolation_layer FastSurferCNN.models.losses FastSurferCNN.models.networks FastSurferCNN.models.optimizer FastSurferCNN.models.sub_module FastSurferCNN.mri_brainvol_stats FastSurferCNN.mri_segstats FastSurferCNN.quick_qc FastSurferCNN.reduce_to_aseg FastSurferCNN.run_model FastSurferCNN.run_prediction FastSurferCNN.segstats FastSurferCNN.train FastSurferCNN.utils.arg_types FastSurferCNN.utils.brainvolstats FastSurferCNN.utils.checkpoint FastSurferCNN.utils.common FastSurferCNN.utils.dataclasses FastSurferCNN.utils.load_config FastSurferCNN.utils.logging FastSurferCNN.utils.lr_scheduler FastSurferCNN.utils.lta FastSurferCNN.utils.mapper FastSurferCNN.utils.meters FastSurferCNN.utils.metrics FastSurferCNN.utils.misc FastSurferCNN.utils.parallel FastSurferCNN.utils.parser_defaults FastSurferCNN.utils.run_tools FastSurferCNN.version HypVINN.data_loader.data_utils HypVINN.data_loader.dataset HypVINN.inference HypVINN.models.networks HypVINN.run_prediction HypVINN.utils.checkpoint HypVINN.utils.img_processing_utils HypVINN.utils.load_config HypVINN.utils.misc HypVINN.utils.mode_config HypVINN.utils.preproc HypVINN.utils.stats_utils HypVINN.utils.visualization_utils recon_surf.align_points recon_surf.align_seg recon_surf.create_annotation recon_surf.fs_balabels recon_surf.image_io recon_surf.long_compat_segmentHA recon_surf.map_surf_label recon_surf.N4_bias_correct recon_surf.rewrite_mc_surface recon_surf.rewrite_oriented_surface recon_surf.rotate_sphere recon_surf.sample_parc recon_surf.smooth_aparc recon_surf.spherically_project recon_surf.spherically_project_wrapper MultiScaleDataset (class in FastSurferCNN.data_loader.dataset) MultiScaleDatasetVal (class in FastSurferCNN.data_loader.dataset) MultiScaleOrigDataThickSlices (class in FastSurferCNN.data_loader.dataset) N name (FastSurferCNN.utils.brainvolstats.AbstractMeasure property) (FastSurferCNN.utils.mapper.ColorLookupTable property) (FastSurferCNN.utils.mapper.Mapper property) needs_pv_calculation() (FastSurferCNN.utils.brainvolstats.Manager method) normalize_array() (in module CerebNet.datasets.utils) normalize_img() (in module recon_surf.N4_bias_correct) normalize_wm_aseg() (in module recon_surf.N4_bias_correct) normalize_wm_mask_ball() (in module recon_surf.N4_bias_correct) NullMeasure (class in FastSurferCNN.utils.brainvolstats) O offset_affine() (in module CorpusCallosum.shape.postprocessing) one_hot_to_label() (in module CorpusCallosum.segmentation.inference) option_parse() (in module HypVINN.run_prediction) optional_path() (in module HypVINN.run_prediction) options_parse() (in module CorpusCallosum.cc_visualization) (in module CorpusCallosum.fastsurfer_cc) (in module FastSurferCNN.data_loader.conform) (in module FastSurferCNN.quick_qc) (in module FastSurferCNN.reduce_to_aseg) (in module recon_surf.align_seg) (in module recon_surf.create_annotation) (in module recon_surf.fs_balabels) (in module recon_surf.map_surf_label) (in module recon_surf.N4_bias_correct) (in module recon_surf.rewrite_mc_surface) (in module recon_surf.rotate_sphere) (in module recon_surf.sample_parc) (in module recon_surf.smooth_aparc) (in module recon_surf.spherically_project) orientation() (in module FastSurferCNN.utils.arg_types) orientation_to_ornts() (in module FastSurferCNN.data_loader.conform) orig_name (FastSurferCNN.utils.common.SubjectDirectory property) OutputDenseBlock (class in FastSurferCNN.models.sub_module) P pad_slicer() (in module FastSurferCNN.segstats) paint_in_cc() (in module CorpusCallosum.paint_cc_into_pred) parents (FastSurferCNN.utils.brainvolstats.DerivedMeasure property) parents_items() (FastSurferCNN.utils.brainvolstats.DerivedMeasure method) parse_args() (FastSurferCNN.utils.brainvolstats.AbstractMeasure method) parse_build_file() (in module FastSurferCNN.version) parse_files() (in module FastSurferCNN.segstats) parse_version() (in module recon_surf.fs_balabels) patch_filter() (in module FastSurferCNN.segstats) patch_neighbors() (in module FastSurferCNN.segstats) path_or_none() (in module FastSurferCNN.utils.arg_types) pipeline() (in module FastSurferCNN.utils.parallel) pipeline_conform_and_save_orig() (FastSurferCNN.run_prediction.RunModelOnData method) plane (CerebNet.data_loader.dataset.SubjectDataset property) plot_cc_index_calculation() (in module CorpusCallosum.shape.metrics) plot_confusion_matrix() (in module CerebNet.utils.misc) (in module FastSurferCNN.utils.misc) plot_contour() (CorpusCallosum.shape.contour.CCContour method) plot_contour_colorfill() (CorpusCallosum.shape.contour.CCContour method) plot_contours() (in module CorpusCallosum.utils.visualization) plot_coronal_predictions() (in module HypVINN.utils.visualization_utils) plot_mesh() (CorpusCallosum.shape.mesh.CCMesh method) plot_predictions() (in module CerebNet.utils.misc) (in module FastSurferCNN.utils.misc) plot_qc_images() (in module HypVINN.utils.visualization_utils) plot_standardized_space() (in module CorpusCallosum.utils.visualization) pool (FastSurferCNN.run_prediction.RunModelOnData property) Popen (class in FastSurferCNN.utils.run_tools) precision_recall() (in module FastSurferCNN.utils.metrics) predict() (in module CorpusCallosum.localization.inference) prediction_visualize() (CerebNet.utils.meters.Meter method) prepare_checkpoints() (in module HypVINN.run_prediction) prepare_mgh_header() (in module FastSurferCNN.data_loader.conform) preproc_image() (in module FastSurferCNN.segstats) preprocess_volume() (in module CorpusCallosum.localization.inference) print_and_exit() (in module FastSurferCNN.mri_segstats) print_build_file() (in module FastSurferCNN.version) print_measures() (FastSurferCNN.utils.brainvolstats.Manager method) pv_calc() (in module FastSurferCNN.segstats) pv_calc_patch() (in module FastSurferCNN.segstats) PVMeasure (class in FastSurferCNN.utils.brainvolstats) PVStats (class in FastSurferCNN.segstats) PyPopen (class in FastSurferCNN.utils.run_tools) R RandomAffine (class in CerebNet.data_loader.augmentation) RandomBiasField (class in CerebNet.data_loader.augmentation) RandomFlip (class in CerebNet.data_loader.augmentation) RandomLabelsToImage (class in CerebNet.data_loader.augmentation) read_and_close_version() (in module FastSurferCNN.version) read_classes_from_lut() (in module FastSurferCNN.data_loader.data_utils) read_colortable() (in module recon_surf.create_annotation) read_colortables() (in module recon_surf.fs_balabels) read_file() (FastSurferCNN.utils.brainvolstats.ImportedMeasure static method) (FastSurferCNN.utils.brainvolstats.SurfaceMeasure static method) (FastSurferCNN.utils.brainvolstats.TransformMeasure static method) (FastSurferCNN.utils.brainvolstats.VolumeMeasure static method) read_lta() (in module FastSurferCNN.utils.lta) read_lta_transform_file() (in module FastSurferCNN.utils.brainvolstats) read_measure_file() (in module FastSurferCNN.utils.brainvolstats) read_mesh_file() (in module FastSurferCNN.utils.brainvolstats) read_multiple_labels() (in module recon_surf.create_annotation) read_statsfile() (in module FastSurferCNN.segstats) read_subject() (FastSurferCNN.utils.brainvolstats.AbstractMeasure method) (FastSurferCNN.utils.brainvolstats.DerivedMeasure method) (FastSurferCNN.utils.brainvolstats.ImportedMeasure method) (FastSurferCNN.utils.brainvolstats.Measure method) read_subject_on_parents (FastSurferCNN.utils.brainvolstats.DerivedMeasure property) read_subject_parents() (FastSurferCNN.utils.brainvolstats.Manager method) read_talairach_xfm() (in module recon_surf.N4_bias_correct) read_transform_file() (in module FastSurferCNN.utils.brainvolstats) read_version_from_project_file() (in module FastSurferCNN.version) read_volume_file() (in module FastSurferCNN.utils.brainvolstats) read_xfm_transform_file() (in module FastSurferCNN.utils.brainvolstats) ReadFileHook (class in FastSurferCNN.utils.brainvolstats) readITKimage() (in module recon_surf.image_io) recon_cc_surf_measure() (in module CorpusCallosum.shape.postprocessing) recon_cc_surf_measures_multi() (in module CorpusCallosum.shape.postprocessing) recon_surf.align_points module recon_surf.align_seg module recon_surf.create_annotation module recon_surf.fs_balabels module recon_surf.image_io module recon_surf.long_compat_segmentHA module recon_surf.map_surf_label module recon_surf.N4_bias_correct module recon_surf.rewrite_mc_surface module recon_surf.rewrite_oriented_surface module recon_surf.rotate_sphere module recon_surf.sample_parc module recon_surf.smooth_aparc module recon_surf.spherically_project module recon_surf.spherically_project_wrapper module reduce_to_aseg() (in module FastSurferCNN.reduce_to_aseg) reduce_to_aseg_and_save() (in module FastSurferCNN.reduce_to_aseg) ReduceLROnPlateauWithRestarts (class in CerebNet.utils.lr_scheduler) register_centroids_to_fsavg() (in module CorpusCallosum.fastsurfer_cc) remove_ckpt() (in module FastSurferCNN.utils.checkpoint) remove_values_from_list() (in module HypVINN.utils.visualization_utils) reorient_img() (in module HypVINN.data_loader.data_utils) replace() (in module FastSurferCNN.utils.dataclasses) replace_labels() (in module recon_surf.sample_parc) resafe_surface() (in module recon_surf.rewrite_mc_surface) (in module recon_surf.rewrite_oriented_surface) rescale() (in module FastSurferCNN.data_loader.conform) rescale_image() (in module HypVINN.data_loader.data_utils) reset() (CerebNet.utils.meters.Meter method) (FastSurferCNN.utils.meters.Meter method) (FastSurferCNN.utils.metrics.DiceScore method) reversed_dict() (FastSurferCNN.utils.mapper.Mapper method) rmat2angles() (in module recon_surf.align_points) roi (CerebNet.data_loader.dataset.SubjectDataset attribute) run() (FastSurferCNN.inference.Inference method) (FastSurferCNN.train.Trainer method) (HypVINN.inference.Inference method) (in module recon_surf.long_compat_segmentHA) run_inference() (in module CorpusCallosum.segmentation.inference) run_inference_on_slice() (in module CorpusCallosum.localization.inference) (in module CorpusCallosum.segmentation.inference) RunModelOnData (class in FastSurferCNN.run_prediction) S sagittal_coronal_remap_lookup() (in module FastSurferCNN.data_loader.data_utils) sample_img() (in module recon_surf.sample_parc) sample_intensity_stats_from_image() (in module CerebNet.data_loader.augmentation) sample_nearest_nonzero() (in module recon_surf.sample_parc) sample_parc() (in module recon_surf.sample_parc) save_cc_measures_json() (in module CorpusCallosum.fastsurfer_cc) save_checkpoint() (in module CerebNet.utils.checkpoint) (in module FastSurferCNN.utils.checkpoint) save_contour() (CorpusCallosum.shape.contour.CCContour method) save_image() (in module FastSurferCNN.data_loader.data_utils) save_img() (FastSurferCNN.run_prediction.RunModelOnData method) save_logits() (in module HypVINN.utils.img_processing_utils) save_mgh_image() (in module CerebNet.datasets.wm_merge_clean) save_nii_image() (in module CerebNet.apply_warp) save_segmentation() (in module HypVINN.utils.img_processing_utils) save_thickness_values() (CorpusCallosum.shape.contour.CCContour method) scalecrop() (in module FastSurferCNN.data_loader.conform) section() (in module FastSurferCNN.version) seg_borders() (in module FastSurferCNN.segstats) segfile (FastSurferCNN.utils.common.SubjectDirectory property) segment_cc() (in module CorpusCallosum.fastsurfer_cc) select_index_to_plot() (in module HypVINN.utils.visualization_utils) SerialExecutor (class in FastSurferCNN.utils.parallel) set_args() (FastSurferCNN.utils.brainvolstats.AbstractMeasure method) (FastSurferCNN.utils.brainvolstats.DerivedMeasure method) (FastSurferCNN.utils.brainvolstats.ETIVMeasure method) (FastSurferCNN.utils.brainvolstats.ImportedMeasure method) (FastSurferCNN.utils.brainvolstats.MaskMeasure method) (FastSurferCNN.utils.brainvolstats.Measure method) (FastSurferCNN.utils.brainvolstats.PVMeasure method) (FastSurferCNN.utils.brainvolstats.SurfaceMeasure method) (FastSurferCNN.utils.brainvolstats.TransformMeasure method) (FastSurferCNN.utils.brainvolstats.VolumeMeasure method) set_cfg() (FastSurferCNN.inference.Inference method) (HypVINN.inference.Inference method) set_contour_zero_idx() (in module CorpusCallosum.shape.thickness) set_lr() (CerebNet.utils.lr_scheduler.CosineLR method) set_model() (FastSurferCNN.run_prediction.RunModelOnData method) (HypVINN.inference.Inference method) set_num_threads() (in module FastSurferCNN.utils.parallel) set_plane() (CerebNet.data_loader.dataset.SubjectDataset method) set_summary_path() (in module CerebNet.utils.misc) set_thickness_values() (CorpusCallosum.shape.contour.CCContour method) set_up_cfgs() (in module FastSurferCNN.run_prediction) (in module HypVINN.run_prediction) set_up_model_params() (FastSurferCNN.run_prediction.RunModelOnData method) set_vox_vol() (FastSurferCNN.utils.brainvolstats.ImportedMeasure method) setup_logging() (in module FastSurferCNN.utils.logging) setup_model() (FastSurferCNN.inference.Inference method) (HypVINN.inference.Inference method) setup_options() (in module CerebNet.run_prediction) (in module recon_surf.spherically_project_wrapper) shutdown() (FastSurferCNN.utils.parallel.SerialExecutor method) shutdown_executors() (in module FastSurferCNN.utils.parallel) sitk_from_mgh() (in module recon_surf.image_io) slice_lia2ras() (in module CerebNet.data_loader.data_utils) slice_ras2lia() (in module CerebNet.data_loader.data_utils) smooth_() (CorpusCallosum.shape.mesh.CCMesh method) smooth_aparc() (in module recon_surf.smooth_aparc) smooth_contour() (CorpusCallosum.shape.contour.CCContour method) (in module CorpusCallosum.data.fsaverage_cc_template) (in module CorpusCallosum.shape.endpoint_heuristic) smooth_thickness_values() (CorpusCallosum.shape.contour.CCContour method) snap_cc_picture() (CorpusCallosum.shape.mesh.CCMesh method) softlink_or_copy() (in module recon_surf.long_compat_segmentHA) source_space (FastSurferCNN.utils.mapper.Mapper property) sphere() (in module CerebNet.datasets.wm_merge_clean) spherically_project_surface() (in module recon_surf.spherically_project) split_cortex_labels() (in module FastSurferCNN.data_loader.data_utils) start_read_subject() (FastSurferCNN.utils.brainvolstats.Manager method) step() (CerebNet.utils.lr_scheduler.ReduceLROnPlateauWithRestarts method) string_to_bool() (in module FastSurferCNN.utils.arg_types) subdivide_contour() (in module CorpusCallosum.shape.postprocessing) subdivide_contour_hampel() (in module CorpusCallosum.shape.subsegment_contour) subdivide_contour_vertical() (in module CorpusCallosum.shape.subsegment_contour) subject_dir (FastSurferCNN.utils.brainvolstats.AbstractMeasure property) (FastSurferCNN.utils.common.SubjectDirectory property) SubjectDataset (class in CerebNet.data_loader.dataset) SubjectDirectory (class in FastSurferCNN.utils.common) SubjectDirectoryConfig (class in FastSurferCNN.utils.parser_defaults) SubjectList (class in FastSurferCNN.utils.common) SubjectLoader (class in CerebNet.datasets.load_data) submit() (FastSurferCNN.utils.parallel.SerialExecutor method) subsegment_midline_orthogonal() (in module CorpusCallosum.shape.subsegment_contour) suppress_stderr() (in module FastSurferCNN.utils.common) suppress_stdout() (in module FastSurferCNN.utils.common) SurfaceHoles (class in FastSurferCNN.utils.brainvolstats) SurfaceMeasure (class in FastSurferCNN.utils.brainvolstats) SurfaceVolume (class in FastSurferCNN.utils.brainvolstats) T t1_to_t2_registration() (in module HypVINN.utils.preproc) table_to_dataframe() (in module FastSurferCNN.segstats) target_dtype() (in module FastSurferCNN.utils.arg_types) target_space (FastSurferCNN.utils.mapper.Mapper property) test_left_of_line() (in module CorpusCallosum.shape.postprocessing) TestLoader (class in CerebNet.data_loader.dataset) TestMeter (class in CerebNet.utils.meters) to() (FastSurferCNN.inference.Inference method) to_dtype() (in module FastSurferCNN.data_loader.conform) to_same_type() (in module FastSurferCNN.utils.mapper) to_target_orientation() (in module FastSurferCNN.data_loader.conform) to_vox_coordinates() (CorpusCallosum.shape.mesh.CCMesh method) ToTensor (class in CerebNet.data_loader.augmentation) (class in FastSurferCNN.data_loader.augmentation) ToTensorTest (class in CerebNet.data_loader.augmentation) (class in FastSurferCNN.data_loader.augmentation) train() (FastSurferCNN.train.Trainer method) Trainer (class in FastSurferCNN.train) transform() (FastSurferCNN.generate_hdf5.H5pyDataset method) transform_axial() (in module CerebNet.data_loader.data_utils) (in module FastSurferCNN.data_loader.data_utils) transform_axial2coronal() (in module HypVINN.data_loader.data_utils) transform_axial2sagittal() (in module CerebNet.data_loader.data_utils) (in module HypVINN.data_loader.data_utils) transform_coronal() (in module CerebNet.data_loader.data_utils) transform_sagittal() (in module CerebNet.data_loader.data_utils) (in module FastSurferCNN.data_loader.data_utils) transform_to_acpc_standard() (in module CorpusCallosum.shape.subsegment_contour) TransformMeasure (class in FastSurferCNN.utils.brainvolstats) tria_spherical_project() (in module recon_surf.spherically_project) TSVLookupTable (class in FastSurferCNN.utils.mapper) U uniform_filter() (in module FastSurferCNN.segstats) unify_imgs() (FastSurferCNN.data_loader.dataset.MultiScaleDataset method) unify_lateralized_labels() (in module FastSurferCNN.data_loader.data_utils) unit (FastSurferCNN.utils.brainvolstats.AbstractMeasure property) (FastSurferCNN.utils.brainvolstats.DerivedMeasure property) unquote_str() (in module FastSurferCNN.utils.arg_types) update() (FastSurferCNN.utils.mapper.Mapper method) (FastSurferCNN.utils.metrics.DiceScore method) update_data() (FastSurferCNN.utils.brainvolstats.PVMeasure method) update_docstring() (in module FastSurferCNN.utils.common) update_measures() (FastSurferCNN.utils.brainvolstats.Manager method) update_num_steps() (in module FastSurferCNN.utils.misc) update_pv_from_table() (FastSurferCNN.utils.brainvolstats.Manager method) update_results_dir() (in module CerebNet.utils.misc) update_split_path() (in module CerebNet.utils.misc) update_stats() (CerebNet.utils.meters.Meter method) (FastSurferCNN.utils.meters.Meter method) update_structnames() (in module FastSurferCNN.segstats) V validate_existing_file() (in module recon_surf.long_compat_segmentHA) validate_existing_subjects_dir() (in module recon_surf.long_compat_segmentHA) validate_inputs() (in module recon_surf.long_compat_segmentHA) VersionDict (class in FastSurferCNN.version) visualize_batch() (in module CerebNet.utils.misc) visualize_coordinate_spaces() (in module CorpusCallosum.utils.visualization) volume_similarity() (in module FastSurferCNN.utils.metrics) VolumeMeasure (class in FastSurferCNN.utils.brainvolstats) vox_size() (in module FastSurferCNN.utils.arg_types) vox_vol (FastSurferCNN.utils.brainvolstats.PVMeasure property) voxel_class (FastSurferCNN.utils.brainvolstats.Manager property) VoxelClassGenerator (class in FastSurferCNN.utils.brainvolstats) W wait_compute() (FastSurferCNN.utils.brainvolstats.Manager method) wait_read_subject() (FastSurferCNN.utils.brainvolstats.Manager method) wait_write_brainvolstats() (FastSurferCNN.utils.brainvolstats.Manager method) WarmupCosineLR (class in CerebNet.utils.lr_scheduler) with_subject() (FastSurferCNN.utils.brainvolstats.Manager method) write_annot() (in module recon_surf.create_annotation) write_fssurf() (CorpusCallosum.shape.mesh.CCMesh method) write_lta() (in module FastSurferCNN.utils.lta) write_morph_data() (CorpusCallosum.shape.mesh.CCMesh method) write_statsfile() (in module FastSurferCNN.segstats) write_summary() (CerebNet.utils.meters.Meter method) (FastSurferCNN.utils.meters.Meter method) writeITKimage() (in module recon_surf.image_io) writeSurfLabel() (in module recon_surf.map_surf_label) Z ZeroPad2D (class in FastSurferCNN.data_loader.augmentation) ZeroPad2DTest (class in FastSurferCNN.data_loader.augmentation) Zoom2d (class in FastSurferCNN.models.interpolation_layer) Zoom3d (class in FastSurferCNN.models.interpolation_layer)