Index A | B | C | D | E | F | G | H | I | J | L | M | N | O | P | R | S | T | U | V | W | Z A 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_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) are_all_subject_files() (FastSurferCNN.utils.common.SubjectList method) args2cfg() (in module FastSurferCNN.run_prediction) argument_parse() (in module recon_surf.paint_cc_into_pred) as_future() (FastSurferCNN.utils.run_tools.Popen method) asegdkt_segfile (FastSurferCNN.utils.common.SubjectDirectory property) assert_no_root() (in module FastSurferCNN.utils.common) 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 calculate_flip_orientation() (in module HypVINN.data_loader.data_utils) calculate_merged_labels() (in module FastSurferCNN.segstats) call() (in module recon_surf.spherically_project_wrapper) can_resolve_attribute() (FastSurferCNN.utils.common.SubjectDirectory method) can_resolve_filename() (FastSurferCNN.utils.common.SubjectDirectory method) CanAddArguments (class in FastSurferCNN.utils.parser_defaults) 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.metrics 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_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_cortex_labels() (in module FastSurferCNN.data_loader.data_utils) 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) comput_dice_cnf() (FastSurferCNN.utils.metrics.DiceScore method) compute() (CerebNet.utils.metrics.DiceScore method) compute_dsc() (FastSurferCNN.utils.metrics.DiceScore method) conf_name (FastSurferCNN.utils.common.SubjectDirectory property) conform() (in module FastSurferCNN.data_loader.conform) conform_and_save_orig() (FastSurferCNN.run_prediction.RunModelOnData method) construct_adj_cluster() (in module recon_surf.sample_parc) copy_orig_name (FastSurferCNN.utils.common.SubjectDirectory property) correct_cereb_brainstem() (in module CerebNet.datasets.wm_merge_clean) 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_hdf5_dataset() (CerebNet.datasets.generate_hdf5.CerebNetDataset method) (FastSurferCNN.generate_hdf5.H5pyDataset method) create_mask() (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) Criteria (class in FastSurferCNN.data_loader.conform) 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 CerebNet.datasets.utils) CrossEntropy2D (class in FastSurferCNN.models.losses) D dataframe() (FastSurferCNN.utils.mapper.JsonColorLookupTable method) (FastSurferCNN.utils.mapper.TSVLookupTable method) decay_base_lr() (CerebNet.utils.lr_scheduler.CosineAnnealingWarmRestartsDecay method) deep_sulci_and_wm_strand_mask() (in module FastSurferCNN.data_loader.data_utils) dice_score() (in module CerebNet.utils.metrics) (in module FastSurferCNN.utils.metrics) DiceLoss (class in FastSurferCNN.models.losses) DiceScore (class in CerebNet.utils.metrics) (class in FastSurferCNN.utils.metrics) disable_confusion_mat() (FastSurferCNN.utils.meters.Meter method) 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) eval() (FastSurferCNN.inference.Inference method) (HypVINN.inference.Inference method) 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.sub_module module FastSurferCNN.quick_qc module FastSurferCNN.reduce_to_aseg module FastSurferCNN.run_prediction module FastSurferCNN.segstats module FastSurferCNN.utils.arg_types module FastSurferCNN.utils.checkpoint module FastSurferCNN.utils.common module FastSurferCNN.utils.load_config module FastSurferCNN.utils.logging module FastSurferCNN.utils.lr_scheduler module FastSurferCNN.utils.mapper module FastSurferCNN.utils.meters module FastSurferCNN.utils.metrics module FastSurferCNN.utils.misc module FastSurferCNN.utils.parser_defaults module FastSurferCNN.utils.run_tools module FastSurferCNN.utils.threads module FastSurferCNN.version module FastSurferCNNBase (class in FastSurferCNN.models.networks) FastSurferVINN (class in FastSurferCNN.models.networks) 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_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_device() (in module FastSurferCNN.utils.common) find_img_size_by_fov() (in module FastSurferCNN.data_loader.conform) find_latest_experiment() (in module FastSurferCNN.utils.misc) find_min_size() (in module FastSurferCNN.data_loader.conform) 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_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) 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_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_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) get_conformed_vox_img_size() (in module FastSurferCNN.data_loader.conform) 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_image_mean() (in module recon_surf.N4_bias_correct) 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_max_size() (FastSurferCNN.inference.Inference method) (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.threads) get_plane() (FastSurferCNN.inference.Inference method) (HypVINN.inference.Inference method) get_prediction() (FastSurferCNN.run_prediction.RunModelOnData method) (in module HypVINN.run_prediction) 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_tal_origin_voxel() (in module recon_surf.N4_bias_correct) get_thick_slices() (in module FastSurferCNN.data_loader.data_utils) get_ventricle_bg_intersection_volume() (in module FastSurferCNN.quick_qc) get_vox2ras() (in module recon_surf.align_seg) 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 CerebNet.utils.metrics) hd95() (in module CerebNet.utils.metrics) HelpFormatter (class in FastSurferCNN.segstats) 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 HypVINNDataset (class in HypVINN.data_loader.dataset) I id (FastSurferCNN.utils.common.SubjectDirectory property) 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) InputDenseBlock (class in FastSurferCNN.models.sub_module) int_ge_zero() (in module FastSurferCNN.utils.arg_types) int_gt_zero() (in module FastSurferCNN.utils.arg_types) 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_int() (in module FastSurferCNN.utils.mapper) is_lia() (in module FastSurferCNN.data_loader.conform) is_resampling_vox2vox() (in module FastSurferCNN.data_loader.conform) iterate() (in module FastSurferCNN.utils.common) 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) 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) load_from_checkpoint() (in module CerebNet.utils.checkpoint) (in module FastSurferCNN.utils.checkpoint) load_image() (in module FastSurferCNN.data_loader.data_utils) load_maybe_conform() (in module FastSurferCNN.data_loader.data_utils) load_subject() (CerebNet.datasets.load_data.SubjectLoader method) load_test_subject() (CerebNet.datasets.load_data.SubjectLoader method) load_volumes() (in module HypVINN.run_prediction) 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 CerebNet.datasets.utils) M main() (in module CerebNet.apply_warp) (in module CerebNet.run_prediction) (in module FastSurferCNN.segstats) (in module FastSurferCNN.version) (in module HypVINN.run_prediction) (in module recon_surf.smooth_aparc) main_segfile (FastSurferCNN.utils.common.SubjectDirectory property) make_arguments() (in module FastSurferCNN.segstats) make_classmapper() (FastSurferCNN.utils.mapper.Mapper class method) make_parser() (in module FastSurferCNN.run_prediction) (in module FastSurferCNN.version) (in module recon_surf.rewrite_oriented_surface) make_subjects_dir() (FastSurferCNN.utils.common.SubjectList method) map() (FastSurferCNN.utils.common.SerialExecutor method) (FastSurferCNN.utils.mapper.Mapper method) map_aparc_aseg2label() (in module FastSurferCNN.data_loader.data_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) Mapper (class in FastSurferCNN.utils.mapper) mapSurfLabel() (in module recon_surf.map_surf_label) max_label (FastSurferCNN.utils.mapper.Mapper property) MessageBuffer (class in FastSurferCNN.utils.run_tools) Meter (class in CerebNet.utils.meters) (class in FastSurferCNN.utils.meters) metrics_per_class() (CerebNet.utils.meters.TestMeter method) mode_filter() (in module recon_surf.smooth_aparc) 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.metrics CerebNet.utils.misc 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.sub_module FastSurferCNN.quick_qc FastSurferCNN.reduce_to_aseg FastSurferCNN.run_prediction FastSurferCNN.segstats FastSurferCNN.utils.arg_types FastSurferCNN.utils.checkpoint FastSurferCNN.utils.common FastSurferCNN.utils.load_config FastSurferCNN.utils.logging FastSurferCNN.utils.lr_scheduler FastSurferCNN.utils.mapper FastSurferCNN.utils.meters FastSurferCNN.utils.metrics FastSurferCNN.utils.misc FastSurferCNN.utils.parser_defaults FastSurferCNN.utils.run_tools FastSurferCNN.utils.threads FastSurferCNN.version HypVINN.data_loader.data_utils HypVINN.data_loader.dataset HypVINN.inference HypVINN.models.networks HypVINN.run_prediction recon_surf.align_points recon_surf.align_seg recon_surf.create_annotation recon_surf.fs_balabels recon_surf.lta recon_surf.map_surf_label recon_surf.N4_bias_correct recon_surf.paint_cc_into_pred 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_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.mapper.ColorLookupTable property) (FastSurferCNN.utils.mapper.Mapper property) 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) O option_parse() (in module HypVINN.run_prediction) optional_path() (in module HypVINN.run_prediction) options_parse() (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) 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 recon_surf.paint_cc_into_pred) 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) pipeline() (in module FastSurferCNN.utils.common) pipeline_conform_and_save_orig() (FastSurferCNN.run_prediction.RunModelOnData method) plane (CerebNet.data_loader.dataset.SubjectDataset property) plot_confusion_matrix() (in module CerebNet.utils.misc) (in module FastSurferCNN.utils.misc) plot_predictions() (in module CerebNet.utils.misc) (in module FastSurferCNN.utils.misc) pool (FastSurferCNN.run_prediction.RunModelOnData property) Popen (class in FastSurferCNN.utils.run_tools) precision_recall() (in module FastSurferCNN.utils.metrics) prediction_visualize() (CerebNet.utils.meters.Meter method) prepare_checkpoints() (in module HypVINN.run_prediction) preproc_image() (in module FastSurferCNN.segstats) print_build_file() (in module FastSurferCNN.version) pv_calc() (in module FastSurferCNN.segstats) pv_calc_patch() (in module FastSurferCNN.segstats) 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_lta() (in module CerebNet.datasets.utils) read_multiple_labels() (in module recon_surf.create_annotation) read_talairach_xfm() (in module recon_surf.N4_bias_correct) read_version_from_project_file() (in module FastSurferCNN.version) recon_surf.align_points module recon_surf.align_seg module recon_surf.create_annotation module recon_surf.fs_balabels module recon_surf.lta module recon_surf.map_surf_label module recon_surf.N4_bias_correct module recon_surf.paint_cc_into_pred 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_wrapper module reduce_to_aseg() (in module FastSurferCNN.reduce_to_aseg) ReduceLROnPlateauWithRestarts (class in CerebNet.utils.lr_scheduler) remove_ckpt() (in module FastSurferCNN.utils.checkpoint) reorient_img() (in module HypVINN.data_loader.data_utils) 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) (CerebNet.utils.metrics.DiceScore 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) (HypVINN.inference.Inference method) 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_checkpoint() (in module CerebNet.utils.checkpoint) (in module FastSurferCNN.utils.checkpoint) save_image() (in module FastSurferCNN.data_loader.data_utils) save_img() (FastSurferCNN.run_prediction.RunModelOnData method) save_mgh_image() (in module CerebNet.datasets.wm_merge_clean) save_nii_image() (in module CerebNet.apply_warp) scalecrop() (in module FastSurferCNN.data_loader.conform) section() (in module FastSurferCNN.version) seg_borders() (in module FastSurferCNN.segstats) segfile (FastSurferCNN.utils.common.SubjectDirectory property) SerialExecutor (class in FastSurferCNN.utils.common) set_cfg() (FastSurferCNN.inference.Inference method) (HypVINN.inference.Inference method) set_lr() (CerebNet.utils.lr_scheduler.CosineLR method) set_model() (FastSurferCNN.run_prediction.RunModelOnData method) (HypVINN.inference.Inference method) set_plane() (CerebNet.data_loader.dataset.SubjectDataset method) set_summary_path() (in module CerebNet.utils.misc) set_up_cfgs() (in module FastSurferCNN.run_prediction) (in module HypVINN.run_prediction) set_up_model_params() (FastSurferCNN.run_prediction.RunModelOnData 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) slice_lia2ras() (in module CerebNet.data_loader.data_utils) slice_ras2lia() (in module CerebNet.data_loader.data_utils) smooth_aparc() (in module recon_surf.smooth_aparc) source_space (FastSurferCNN.utils.mapper.Mapper property) sphere() (in module CerebNet.datasets.wm_merge_clean) spherical_wrapper() (in module recon_surf.spherically_project_wrapper) split_cortex_labels() (in module FastSurferCNN.data_loader.data_utils) step() (CerebNet.utils.lr_scheduler.ReduceLROnPlateauWithRestarts method) subject_dir (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.common.SerialExecutor method) T table_to_dataframe() (in module FastSurferCNN.segstats) target_dtype() (in module FastSurferCNN.utils.arg_types) target_space (FastSurferCNN.utils.mapper.Mapper property) TestLoader (class in CerebNet.data_loader.dataset) TestMeter (class in CerebNet.utils.meters) to() (FastSurferCNN.inference.Inference method) to_same_type() (in module FastSurferCNN.utils.mapper) 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) 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) 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) unquote_str() (in module FastSurferCNN.utils.arg_types) update() (CerebNet.utils.metrics.DiceScore method) (FastSurferCNN.utils.mapper.Mapper method) (FastSurferCNN.utils.metrics.DiceScore method) update_num_steps() (in module FastSurferCNN.utils.misc) 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 VersionDict (class in FastSurferCNN.version) visualize_batch() (in module CerebNet.utils.misc) volume_similarity() (in module CerebNet.utils.metrics) vox_size() (in module FastSurferCNN.utils.arg_types) W WarmupCosineLR (class in CerebNet.utils.lr_scheduler) write_annot() (in module recon_surf.create_annotation) write_statsfile() (in module FastSurferCNN.segstats) write_summary() (CerebNet.utils.meters.Meter method) (FastSurferCNN.utils.meters.Meter method) writeLTA() (in module recon_surf.lta) 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)