BraTS 0.0.0.dev0__py3-none-any.whl

brats/data/meta/pediatric.yml

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+constants:
+  input_name_schema: &input_name_schema "BraTS-PED-{id:05d}-000"
+  challenge: &challenge "Pediatric Segmentation"
+  challenge_manuscript:
+    2025: &challenge_manuscript_2025 "https://arxiv.org/abs/2404.15009" # same as 2024
+    2024: &challenge_manuscript_2024 "https://arxiv.org/abs/2404.15009"
+    2023: &challenge_manuscript_2023 "https://arxiv.org/abs/2305.17033"
+  years:
+    2025: &year_2025 2025
+    2024: &year_2024 2024
+    2023: &year_2023 2023
+  ranks:
+    1st: &rank_1 1st
+    2nd: &rank_2 2nd
+    3rd: &rank_3 3rd
+
+algorithms:
+
+##### 2025 #####
+  BraTS25_1:
+    meta:
+      authors: Yuxiao Yi, et al.
+      paper: N/A
+      challenge: *challenge
+      challenge_manuscript: *challenge_manuscript_2025
+      rank: *rank_1
+      year: *year_2025
+    run_args:
+      docker_image: brainles/brats25_ped_joeyx:latest
+      input_name_schema: *input_name_schema
+      requires_root: true
+  
+  BraTS25_2:
+    meta:
+      authors: Meng-Yuan Chen, et al.
+      paper: N/A
+      challenge: *challenge
+      challenge_manuscript: *challenge_manuscript_2025
+      rank: *rank_2
+      year: *year_2025
+    run_args:
+      docker_image: brainles/brats25_ped_cmengynn:latest
+      input_name_schema: *input_name_schema
+      requires_root: true
+
+  BraTS25_3:
+    meta:
+      authors: Yu Haitao, et al.
+      paper: N/A
+      challenge: *challenge
+      challenge_manuscript: *challenge_manuscript_2025
+      rank: *rank_3
+      year: *year_2025
+    run_args:
+      docker_image: brainles/brats25_ped_qing:latest
+      input_name_schema: *input_name_schema
+      requires_root: true
+
+  # BraTS25_4?: # Removed after ranking updated
+  #   meta:
+  #     authors: Xiaolong Li, et al.
+  #     paper: N/A
+  #     challenge: *challenge
+  #     challenge_manuscript: *challenge_manuscript_2025
+  #     rank: *rank_1
+  #     year: *year_2025
+  #   run_args:
+  #     docker_image: brainles/brats25_ped_s1mpleee:latest
+  #     input_name_schema: *input_name_schema
+  #     requires_root: true
+
+
+##### 2024 #####
+  BraTS24_1:
+    meta:
+      authors: Mehdi Astaraki, et al.
+      paper: N/A
+      challenge: *challenge
+      challenge_manuscript: *challenge_manuscript_2024
+      rank: *rank_1
+      year: *year_2024
+    run_args:
+      docker_image: brainles/brats24_pediatric_astaraki:latest
+      input_name_schema: *input_name_schema
+      requires_root: false
+      parameters_file: true
+      shm_size: "8gb"
+
+  BraTS24_2:
+    meta:
+      authors: Tim Mulvany, et al.
+      paper: https://doi.org/10.48550/arXiv.2410.14020
+      challenge: *challenge
+      challenge_manuscript: *challenge_manuscript_2024
+      rank: *rank_2
+      year: *year_2024
+    run_args:
+      docker_image: brainles/brats24_pediatric_aipni:latest
+      input_name_schema: *input_name_schema
+      requires_root: false
+      parameters_file: true 
+      shm_size: "8gb"
+    additional_files:
+      record_id: "14446259"
+
+  BraTS24_3:
+    meta:
+      authors: Sarim Hashmi, et al.
+      paper: https://arxiv.org/abs/2411.15872
+      challenge: *challenge
+      challenge_manuscript: *challenge_manuscript_2024
+      rank: *rank_3
+      year: *year_2024
+    run_args:
+      docker_image: brainles/brats24_pediatric_biomedia-mbzu:latest
+      input_name_schema: *input_name_schema
+      requires_root: false
+      parameters_file: true
+      shm_size: "2gb"
+    additional_files:
+      record_id: "14446377"
+      param_name: ["checkpoint_dir"]
+
+##### 2023 #####
+  BraTS23_1:
+    meta:
+      authors: Daniel Capellán-Martín et al.
+      paper: https://api.semanticscholar.org/CorpusID:272599903
+      challenge: *challenge
+      challenge_manuscript: *challenge_manuscript_2023
+      rank: *rank_1
+      year: *year_2023
+    run_args:
+      docker_image: brainles/brats23_pediatric_cnmc_pmi2023:latest
+      input_name_schema: *input_name_schema
+      requires_root: true
+      parameters_file: false 
+      shm_size: "2gb"
+
+  BraTS23_2:
+    meta:
+      authors: Andriy Myronenko, et al.
+      paper: N/A
+      challenge: *challenge
+      challenge_manuscript: *challenge_manuscript_2023
+      rank: *rank_2
+      year: *year_2023
+    run_args:
+      docker_image: brainles/brats23_pediatric_nvauto:latest 
+      input_name_schema: *input_name_schema
+      requires_root: true
+      parameters_file: true
+      shm_size: "32gb"
+      
+  BraTS23_3:
+    meta:
+      authors: Yubo Zhou
+      paper: https://doi.org/10.1007/978-3-031-76163-8_5
+      challenge: *challenge
+      challenge_manuscript: *challenge_manuscript_2023
+      rank: *rank_3
+      year: *year_2023
+    run_args:
+      docker_image: brainles/brats23_pediatric_sherlock_zyb:latest
+      input_name_schema: *input_name_schema
+      requires_root: false
+      parameters_file: false
+      shm_size: "10gb"

brats/data/parameters/brats23_africa_sparkunn.yml

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+# Arguments of the data_preparation.py script
+
+# Arguments of the preprocess.py script
+prep_exec_mode: test
+ohe: true
+verbose: true
+task: "12" # testing
+dim: 3
+n_jobs: -1
+
+# Arguments of the main.py script
+exec_mode: predict
+config: None
+logname : logs.json
+gpus: 1
+nodes: 1
+learning_rate: 0.0003
+gradient_clip_val: 0
+negative_slope: 0.01
+tta: true
+brats: true
+deep_supervision: false
+invert_resampled_y: false
+amp: true
+benchmark: false
+focal: false
+save_ckpt: false
+nfolds: 10
+seed: null # "Random seed 
+skip_first_n_eval: 0 # Skip the evaluation for the first n epochs.
+# ckpt_path: null # Path for loading checkpoint #?
+# ckpt_store_dir: $results # Path for saving checkpoint #?
+# fold: 2 # Fold number
+patience: 100 # Early stopping patience
+batch_size: 2 # Batch size
+val_batch_size: 4 # Validation batch size
+momentum: 0.99 # Momentum factor
+weight_decay: 0.0001  #Weight decay (L2 penalty)
+save_preds: true # Enable prediction saving
+dim: 3 # UNet dimension
+resume_training: false # Resume training from the last checkpoint
+num_workers: 8 # Number of subprocesses to use for data loading
+epochs: 150 # Number of training epochs.
+warmup: 5 # Warmup iterations before collecting statistics
+nvol: 4  #Number of volumes which come into single batch size for 2D model
+depth: 5 # The depth of the encoder
+min_fmap: 4  #Minimal dimension of feature map in the bottleneck
+deep_supr_num: 2 # Number of deep supervision heads
+res_block: false # Enable residual blocks
+filters: null #  nargs="+", help="[Optional] Set U-Net filters"
+layout: NCDHW 
+brats22_model: true # Use BraTS22 model
+norm: instance # Normalization layer
+data2d_dim: 3 # Input data dimension for 2d model
+oversampling: 0.4 # Probability of crop to have some region with positive label
+overlap: 0.25 # Amount of overlap between scans during sliding window inference
+scheduler: true # Enable cosine rate scheduler with warmup
+optimizer: adam # Optimizer
+blend: constant # How to blend output of overlapping windows
+train_batches: 0 # Limit number of batches for training (used for benchmarking mode only)
+test_batches: 0 # Limit number of batches for inference (used for benchmarking mode only)
+
+#  Argument for the postprocess.py script

brats/data/parameters/brats23_inpainting_domaso.yml

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+slices_per_sampling: 32 # can be adjusted depending on GPU space, defines how many slices are sampled simultaneously
+gpu_id: 'cuda:0'
+attention_resolutions: '16'
+batch_size: 8
+channel_mult: ''
+class_cond: False
+data_dir: '' #./data_3d/raw_data_test'
+diffusion_steps: 1000
+dropout: 0.0
+ema_rate: '0.9999'
+fp16_scale_growth: 0.001
+image_size: 256
+learn_sigma: True
+log_interval: 1000
+lr: 0.0001
+lr_anneal_steps: 0
+microbatch: -1
+noise_schedule: 'linear'
+num_channels: 128
+num_head_channels: -1
+num_heads: 1
+num_heads_upsample: -1
+num_res_blocks: 2
+predict_xstart: False
+resblock_updown: False
+rescale_learned_sigmas: False
+rescale_timesteps: False
+resume_checkpoint: '' #./results_BraTS_transversal/savedmodel2170000.pt'
+save_interval: 5000
+schedule_sampler: 'uniform'
+timestep_respacing: ''
+use_checkpoint: False
+use_fp16: False
+use_kl: False
+use_new_attention_order: False
+use_scale_shift_norm: False
+weight_decay: 0.0
+num_samples: 1
+use_ddim: False
+clip_denoised: True,
+num_ensemble: 1
+#log_dir: 'predictions/'
+#model_path: 'additional_files/savedmodel2850000.pt'
+#data_dir: 'data/'

brats/data/parameters/brats23_missing_mri_onembyte.yml

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+t1n_model: t1n_model # logs/train/2023-08-01/08-19-59_w2aorpx3
+t1c_model: t1c_model # logs/train/2023-08-01/08-12-49_t75jck2e
+t2w_model: t2w_model # logs/train/2023-08-01/08-41-30_b24whwna
+t2f_model: t2f_model # logs/train/2023-08-01/08-54-29_hnx3ttp6
+phase: test

brats/data/parameters/brats24_adult_glioma_mist.yml

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+fast_inference: False
+overlap: 0.5
+blend_mode: "gaussian"
+tta: True
+no_preprocess: False
+output_std: False

brats/data/parameters/brats24_inpainting_smint.yml

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+attention_resolutions: '16'
+batch_size: 1
+channel_mult: ''
+class_cond: False
+clip_denoised: True
+diffusion_steps: 1000
+dropout: 0.0
+ema_rate: '0.9999'
+fp16_scale_growth: 0.001
+image_size: 256
+learn_sigma: True
+log_interval: 1000
+lr: 0.0001
+lr_anneal_steps: 0
+microbatch: -1
+noise_schedule: 'linear'
+num_channels: 128
+num_head_channels: -1
+num_heads: 1
+num_heads_upsample: -1
+num_res_blocks: 2
+predict_xstart: False
+resblock_updown: False
+rescale_learned_sigmas: False
+rescale_timesteps: False
+resume_checkpoint: ''
+save_interval: 5000
+schedule_sampler: 'uniform'
+subbatch: 16
+timestep_respacing: ''
+use_checkpoint: False
+use_ddim: False
+use_fp16: False
+use_kl: False
+use_new_attention_order: False
+use_scale_shift_norm: False
+weight_decay: 0.0

brats/data/parameters/brats24_missing_mri_cgv.yml

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+previous_exp_name: does_not_exist
+exp_name: refiner_fets_minmax_l1No_ssimYes_DiceYes
+
+# seg_model:
+#   seg_exp_name: seg_testing_merge
+#   path_suffix: epoch_100.pth
+
+dataset:
+  root: "/data_folder/"
+  folders: ["ASNR-MICCAI-BraTS2023-GLI-Challenge-TrainingData"]
+  val_folder: ["ASNR-MICCAI-BraTS2023-GLI-Challenge-ValidationData"]
+  suffix_modalities: ["t1", "t1ce", "t2", "flair"]
+  suffix_common: ".nii.gz"
+  resize: False
+  resize_input: 256
+  resize_output: 256
+  crop: True
+  random_crop: True
+  crop_size: 128
+  pad: True
+  normalize: True
+  norm_method: zscore # OPTIONS -  minmax01: [0,1], minmax11: [-1,1], zscore: z-score normalization
+  mask_input: False
+  mask_modality: True
+
+dataloader:
+  batch_size: 1
+  shuffle: True
+  num_workers: 1
+
+model:
+  spatial_dims: 3
+  in_channels: 4
+  out_channels: 4
+  latent_channels: 3
+  num_channels: [64, 128, 128, 128]
+  num_res_blocks: 1
+  norm_num_groups: 32
+  norm_eps: 1.0e-6
+  attention_levels: [
+    False,
+    False,
+    False,
+    False
+  ]
+  with_encoder_nonlocal_attn: False
+  with_decoder_nonlocal_attn: False
+  use_skip_connection: True
+  use_skip_squeeze: True
+  skip_squeeze_channels: 1
+  use_skip_connection_first_layer: False
+  skip_drop_rate: 0.0
+  training: True
+
+refiner:
+  hidden_size: 64
+  output_residual: True
+  use_final_conv: True
+
+discriminator:
+  hidden_size: 64
+
+training:
+  epoch: 1000
+  lr: 1.0e-5
+  cp_epoch: 2
+  pic_log_epoch: 1
+  cp_directory: "./checkpoints/"
+  use_scheduler: True
+  load_checkpoint: False
+  mask_loss_amp: 8.0
+  loss_coef: [1.0, 1.0]  # [L1, MSE]