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CALIBRATION_SIZE: 24 + CENTER_FRACTIONS: [] + NAME: PoissonDiskMaskFunc + PRECOMPUTE: + NUM: 100000 + SEED: -1 + USE_NOISE: false +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: [] + DROP_LAST: true + FILTER: + BY: [] + GROUP_SAMPLER: + AS_BATCH_SAMPLER: true + BATCH_BY: + - num_coils + - matrix_shape + NUM_WORKERS: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: GroupSampler + SUBSAMPLE_TRAIN: + NUM_TOTAL: -1 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + QDESS: + DATASET_TYPE: '' + ECHO_KIND: echo1+echo2 + KWARGS: [] + TEST: + - stanford_qdess_v0.1.0_test + TRAIN: + - stanford_qdess_v0.1.0_train + VAL: + - stanford_qdess_v0.1.0_val +DESCRIPTION: + BRIEF: Recon only unet baseline - 4 pooling layers, 32 channels, L1 loss, lr=1e-3, + echo=echo1+echo2, acc=6 + ENTITY_NAME: mtrecon + EXP_NAME: recon-baseline/unet-6x-echo1+echo2/version_002 + PROJECT_NAME: mtrecon + TAGS: + - neurips + - recon-baseline + - baseline + - unet + - unet_6x +MODEL: + CASCADE: + ITFS: + PERIOD: 0 + RECON_MODEL_NAME: '' + SEG_MODEL_NAME: '' + SEG_NORMALIZE: '' + USE_MAGNITUDE: false + ZERO_FILL: false + CS: + MAX_ITER: 200 + REGULARIZATION: 0.005 + DENOISING: + META_ARCHITECTURE: GeneralizedUnrolledCNN + NOISE: + STD_DEV: + - 1 + USE_FULLY_SAMPLED_TARGET: true + USE_FULLY_SAMPLED_TARGET_EVAL: null + DEVICE: cpu + META_ARCHITECTURE: UnetModel + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + PARAMETERS: + INIT: [] + USE_COMPLEX_WEIGHTS: false + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + WEIGHT: 1.0 + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + IN_CHANNELS: null + LOSS_NAME: DiceLoss + LOSS_WEIGHT: 1.0 + MODEL: + DYNUNET_MONAI: + DEEP_SUPERVISION: false + DEEP_SUPR_NUM: 1 + KERNEL_SIZE: + - 3 + NORM_NAME: instance + RES_BLOCK: false + STRIDES: + - 1 + UPSAMPLE_KERNEL_SIZE: + - 2 + UNET_MONAI: + ACTIVATION: + - prelu + - {} + CHANNELS: [] + DROPOUT: 0.0 + KERNEL_SIZE: + - 3 + NORM: + - instance + - {} + NUM_RES_UNITS: 0 + STRIDES: [] + UP_KERNEL_SIZE: + - 3 + VNET_MONAI: + ACTIVATION: + - elu + - inplace: true + DROPOUT_DIM: 3 + DROPOUT_PROB: 0.5 + USE_MAGNITUDE: true + TASKS: + - recon + TB_RECON: + CHANNELS: + - 16 + - 32 + - 64 + DEC_NUM_CONV_BLOCKS: + - 2 + - 3 + ENC_NUM_CONV_BLOCKS: + - 1 + - 2 + - 3 + KERNEL_SIZE: + - 5 + MULTI_CONCAT: [] + ORDER: + - conv + - relu + STRIDES: + - 2 + USE_MAGNITUDE: false + UNET: + BLOCK_ORDER: + - conv + - instancenorm + - - leakyrelu + - negative_slope: 0.2 + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + CONV_BLOCK: + ACTIVATION: relu + NORM: none + NORM_AFFINE: false + ORDER: + - norm + - act + - drop + - conv + DROPOUT: 0.0 + FIX_STEP_SIZE: false + KERNEL_SIZE: + - 3 + NUM_EMAPS: 1 + NUM_FEATURES: 256 + NUM_RESBLOCKS: 2 + NUM_UNROLLED_STEPS: 5 + PADDING: '' + SHARE_WEIGHTS: false + WEIGHTS: '' +OUTPUT_DIR: results://skm-tea/neurips2021/6x/U-Net_E1+E2 +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + CHECKPOINT_MONITOR: val_loss + CHECKPOINT_PERIOD: 1 + EARLY_STOPPING: + MIN_DELTA: 0.0 + MONITOR: val_loss + PATIENCE: 0 + GAMMA: 1.0 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: '' + MAX_ITER: 20 + MIN_LR: null + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: [] + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 24 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: 1 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 1000 + QDESS_EVALUATOR: + ADDITIONAL_PATHS: [] + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim (Wang) + SEM_SEG: [] +TIME_SCALE: epoch +VERSION: 1 +VIS_PERIOD: -400 diff --git a/neurips2021/recon-models/6x/U-Net_E1+E2/model-gpu.ckpt 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b/neurips2021/recon-models/6x/U-Net_E1-oplus-E2/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..1cb391db448dad3ef05be79d9aeac4ae76ec179f --- /dev/null +++ b/neurips2021/recon-models/6x/U-Net_E1-oplus-E2/config.yaml @@ -0,0 +1,240 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 6 +AUG_TRAIN: + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 6 + CALIBRATION_SIZE: 24 + CENTER_FRACTIONS: [] + NAME: PoissonDiskMaskFunc + PRECOMPUTE: + NUM: 100000 + SEED: -1 + USE_NOISE: false +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: [] + DROP_LAST: true + FILTER: + BY: [] + GROUP_SAMPLER: + AS_BATCH_SAMPLER: true + BATCH_BY: + - num_coils + - matrix_shape + NUM_WORKERS: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: GroupSampler + SUBSAMPLE_TRAIN: + NUM_TOTAL: -1 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + QDESS: + DATASET_TYPE: '' + ECHO_KIND: echo1-echo2-mc + KWARGS: [] + TEST: + - stanford_qdess_v0.1.0_test + TRAIN: + - stanford_qdess_v0.1.0_train + VAL: + - stanford_qdess_v0.1.0_val +DESCRIPTION: + BRIEF: Recon only unet baseline - 4 pooling layers, 32 channels, L1 loss, lr=1e-3, + echo=echo1-echo2-mc, acc=6 + ENTITY_NAME: mtrecon + EXP_NAME: recon-baseline/unet-6x-echo1-echo2-mc/version_001 + PROJECT_NAME: mtrecon + TAGS: + - neurips + - recon-baseline + - baseline + - unet + - unet_6x +MODEL: + CASCADE: + ITFS: + PERIOD: 0 + RECON_MODEL_NAME: '' + SEG_MODEL_NAME: '' + SEG_NORMALIZE: '' + USE_MAGNITUDE: false + ZERO_FILL: false + CS: + MAX_ITER: 200 + REGULARIZATION: 0.005 + DENOISING: + META_ARCHITECTURE: GeneralizedUnrolledCNN + NOISE: + STD_DEV: + - 1 + USE_FULLY_SAMPLED_TARGET: true + USE_FULLY_SAMPLED_TARGET_EVAL: null + DEVICE: cpu + META_ARCHITECTURE: UnetModel + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + PARAMETERS: + INIT: [] + USE_COMPLEX_WEIGHTS: false + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + WEIGHT: 1.0 + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + IN_CHANNELS: null + LOSS_NAME: DiceLoss + LOSS_WEIGHT: 1.0 + MODEL: + DYNUNET_MONAI: + DEEP_SUPERVISION: false + DEEP_SUPR_NUM: 1 + KERNEL_SIZE: + - 3 + NORM_NAME: instance + RES_BLOCK: false + STRIDES: + - 1 + UPSAMPLE_KERNEL_SIZE: + - 2 + UNET_MONAI: + ACTIVATION: + - prelu + - {} + CHANNELS: [] + DROPOUT: 0.0 + KERNEL_SIZE: + - 3 + NORM: + - instance + - {} + NUM_RES_UNITS: 0 + STRIDES: [] + UP_KERNEL_SIZE: + - 3 + VNET_MONAI: + ACTIVATION: + - elu + - inplace: true + DROPOUT_DIM: 3 + DROPOUT_PROB: 0.5 + USE_MAGNITUDE: true + TASKS: + - recon + TB_RECON: + CHANNELS: + - 16 + - 32 + - 64 + DEC_NUM_CONV_BLOCKS: + - 2 + - 3 + ENC_NUM_CONV_BLOCKS: + - 1 + - 2 + - 3 + KERNEL_SIZE: + - 5 + MULTI_CONCAT: [] + ORDER: + - conv + - relu + STRIDES: + - 2 + USE_MAGNITUDE: false + UNET: + BLOCK_ORDER: + - conv + - instancenorm + - - leakyrelu + - negative_slope: 0.2 + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 4 + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 4 + UNROLLED: + CONV_BLOCK: + ACTIVATION: relu + NORM: none + NORM_AFFINE: false + ORDER: + - norm + - act + - drop + - conv + DROPOUT: 0.0 + FIX_STEP_SIZE: false + KERNEL_SIZE: + - 3 + NUM_EMAPS: 1 + NUM_FEATURES: 256 + NUM_RESBLOCKS: 2 + NUM_UNROLLED_STEPS: 5 + PADDING: '' + SHARE_WEIGHTS: false + WEIGHTS: '' +OUTPUT_DIR: results://skm-tea/neurips2021/6x/U-Net_E1-oplus-E2 +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + CHECKPOINT_MONITOR: val_loss + CHECKPOINT_PERIOD: 1 + EARLY_STOPPING: + MIN_DELTA: 0.0 + MONITOR: val_loss + PATIENCE: 0 + GAMMA: 1.0 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: '' + MAX_ITER: 20 + MIN_LR: null + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: [] + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 24 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: 1 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 1000 + QDESS_EVALUATOR: + ADDITIONAL_PATHS: [] + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim (Wang) + SEM_SEG: [] +TIME_SCALE: epoch +VERSION: 1 +VIS_PERIOD: -400 diff --git a/neurips2021/recon-models/6x/U-Net_E1-oplus-E2/model-gpu.ckpt b/neurips2021/recon-models/6x/U-Net_E1-oplus-E2/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..3600893936186a4f893b265f88e1bc40e26b3674 --- /dev/null +++ b/neurips2021/recon-models/6x/U-Net_E1-oplus-E2/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:1173877575b67651ae894c0c6ccd33bdce9c58cbfd181b0aeea699497466ad83 +size 93115533 diff --git a/neurips2021/recon-models/6x/U-Net_E1-oplus-E2/model-raw-gpu.ckpt b/neurips2021/recon-models/6x/U-Net_E1-oplus-E2/model-raw-gpu.ckpt new file mode 100644 index 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b/neurips2021/recon-models/6x/U-Net_E1/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..ac7f218532a43650e7fc6e02d06714cec5d84ce3 --- /dev/null +++ b/neurips2021/recon-models/6x/U-Net_E1/config.yaml @@ -0,0 +1,241 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 6 +AUG_TRAIN: + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 6 + CALIBRATION_SIZE: 24 + CENTER_FRACTIONS: [] + NAME: PoissonDiskMaskFunc + PRECOMPUTE: + NUM: 100000 + SEED: -1 + USE_NOISE: false +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: [] + DROP_LAST: true + FILTER: + BY: [] + GROUP_SAMPLER: + AS_BATCH_SAMPLER: true + BATCH_BY: + - num_coils + - matrix_shape + NUM_WORKERS: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: GroupSampler + SUBSAMPLE_TRAIN: + NUM_TOTAL: -1 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + QDESS: + DATASET_TYPE: '' + ECHO_KIND: echo1 + KWARGS: [] + TEST: + - skmtea_v1_test + TRAIN: + - skmtea_v1_train + VAL: + - skmtea_v1_val +DESCRIPTION: + BRIEF: Recon only unet baseline - 4 pooling layers, 32 channels, L1 loss, lr=1e-3, + echo=echo1, acc=6 + ENTITY_NAME: mtrecon + EXP_NAME: recon-baseline/unet-6x-echo1/version_001 + PROJECT_NAME: mtrecon + TAGS: + - baseline + - unet + - neurips + - recon-baseline + - unet_6x +MODEL: + CASCADE: + ITFS: + PERIOD: 0 + RECON_MODEL_NAME: '' + SEG_MODEL_NAME: '' + SEG_NORMALIZE: '' + USE_MAGNITUDE: false + ZERO_FILL: false + CS: + MAX_ITER: 200 + REGULARIZATION: 0.005 + DENOISING: + META_ARCHITECTURE: GeneralizedUnrolledCNN + NOISE: + STD_DEV: + - 1 + USE_FULLY_SAMPLED_TARGET: true + USE_FULLY_SAMPLED_TARGET_EVAL: null + DEVICE: cpu + META_ARCHITECTURE: UnetModel + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + PARAMETERS: + INIT: [] + USE_COMPLEX_WEIGHTS: false + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + WEIGHT: 1.0 + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + IN_CHANNELS: null + LOSS_NAME: DiceLoss + LOSS_WEIGHT: 1.0 + MODEL: + DYNUNET_MONAI: + DEEP_SUPERVISION: false + DEEP_SUPR_NUM: 1 + KERNEL_SIZE: + - 3 + NORM_NAME: instance + RES_BLOCK: false + STRIDES: + - 1 + UPSAMPLE_KERNEL_SIZE: + - 2 + UNET_MONAI: + ACTIVATION: + - prelu + - {} + CHANNELS: [] + DROPOUT: 0.0 + KERNEL_SIZE: + - 3 + NORM: + - instance + - {} + NUM_RES_UNITS: 0 + STRIDES: [] + UP_KERNEL_SIZE: + - 3 + VNET_MONAI: + ACTIVATION: + - elu + - inplace: true + DROPOUT_DIM: 3 + DROPOUT_PROB: 0.5 + USE_MAGNITUDE: true + TASKS: + - recon + TB_RECON: + CHANNELS: + - 16 + - 32 + - 64 + DEC_NUM_CONV_BLOCKS: + - 2 + - 3 + ENC_NUM_CONV_BLOCKS: + - 1 + - 2 + - 3 + KERNEL_SIZE: + - 5 + MULTI_CONCAT: [] + ORDER: + - conv + - relu + STRIDES: + - 2 + USE_MAGNITUDE: false + UNET: + BLOCK_ORDER: + - conv + - instancenorm + - - leakyrelu + - negative_slope: 0.2 + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + CONV_BLOCK: + ACTIVATION: relu + NORM: none + NORM_AFFINE: false + ORDER: + - norm + - act + - drop + - conv + DROPOUT: 0.0 + FIX_STEP_SIZE: false + KERNEL_SIZE: + - 3 + NUM_EMAPS: 1 + NUM_FEATURES: 256 + NUM_RESBLOCKS: 2 + NUM_UNROLLED_STEPS: 5 + PADDING: '' + SHARE_WEIGHTS: false + WEIGHTS: '' +OUTPUT_DIR: results://skm-tea/neurips2021/6x/U-Net_E1 +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + CHECKPOINT_MONITOR: val_loss + CHECKPOINT_PERIOD: 1 + EARLY_STOPPING: + MIN_DELTA: 0.0 + MONITOR: val_loss + PATIENCE: 0 + GAMMA: 1.0 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: '' + MAX_ITER: 20 + MIN_LR: null + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: [] + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 24 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: 1 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 1000 + QDESS_EVALUATOR: + ADDITIONAL_PATHS: [] + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim_old + - ssim (Wang) + SEM_SEG: [] +TIME_SCALE: epoch +VERSION: 1 +VIS_PERIOD: -400 diff --git a/neurips2021/recon-models/6x/U-Net_E1/model-gpu.ckpt b/neurips2021/recon-models/6x/U-Net_E1/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..91361054802e70c6fe051db8b41bb64326f3303d --- /dev/null +++ b/neurips2021/recon-models/6x/U-Net_E1/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a64b865cc263317552cd157a56baa321271884a3ab0f0da0d273d8d9e6187861 +size 93107853 diff --git a/neurips2021/recon-models/6x/U-Net_E1/model-raw-gpu.ckpt b/neurips2021/recon-models/6x/U-Net_E1/model-raw-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..91361054802e70c6fe051db8b41bb64326f3303d --- /dev/null +++ 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b/neurips2021/recon-models/6x/U-Net_E2/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..831b0780a6c89ff93824f50502825dd4b7de97c4 --- /dev/null +++ b/neurips2021/recon-models/6x/U-Net_E2/config.yaml @@ -0,0 +1,241 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 6 +AUG_TRAIN: + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 6 + CALIBRATION_SIZE: 24 + CENTER_FRACTIONS: [] + NAME: PoissonDiskMaskFunc + PRECOMPUTE: + NUM: 100000 + SEED: -1 + USE_NOISE: false +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: [] + DROP_LAST: true + FILTER: + BY: [] + GROUP_SAMPLER: + AS_BATCH_SAMPLER: true + BATCH_BY: + - num_coils + - matrix_shape + NUM_WORKERS: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: GroupSampler + SUBSAMPLE_TRAIN: + NUM_TOTAL: -1 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + QDESS: + DATASET_TYPE: '' + ECHO_KIND: echo2 + KWARGS: [] + TEST: + - stanford_qdess_v0.1.0_test + TRAIN: + - stanford_qdess_v0.1.0_train + VAL: + - stanford_qdess_v0.1.0_val +DESCRIPTION: + BRIEF: Recon only unet baseline - 4 pooling layers, 32 channels, L1 loss, lr=1e-3, + echo=echo2, acc=6 + ENTITY_NAME: mtrecon + EXP_NAME: recon-baseline/unet-6x-echo2/version_001 + PROJECT_NAME: mtrecon + TAGS: + - baseline + - unet + - neurips + - recon-baseline + - unet_6x +MODEL: + CASCADE: + ITFS: + PERIOD: 0 + RECON_MODEL_NAME: '' + SEG_MODEL_NAME: '' + SEG_NORMALIZE: '' + USE_MAGNITUDE: false + ZERO_FILL: false + CS: + MAX_ITER: 200 + REGULARIZATION: 0.005 + DENOISING: + META_ARCHITECTURE: GeneralizedUnrolledCNN + NOISE: + STD_DEV: + - 1 + USE_FULLY_SAMPLED_TARGET: true + USE_FULLY_SAMPLED_TARGET_EVAL: null + DEVICE: cpu + META_ARCHITECTURE: UnetModel + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + PARAMETERS: + INIT: [] + USE_COMPLEX_WEIGHTS: false + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + WEIGHT: 1.0 + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + IN_CHANNELS: null + LOSS_NAME: DiceLoss + LOSS_WEIGHT: 1.0 + MODEL: + DYNUNET_MONAI: + DEEP_SUPERVISION: false + DEEP_SUPR_NUM: 1 + KERNEL_SIZE: + - 3 + NORM_NAME: instance + RES_BLOCK: false + STRIDES: + - 1 + UPSAMPLE_KERNEL_SIZE: + - 2 + UNET_MONAI: + ACTIVATION: + - prelu + - {} + CHANNELS: [] + DROPOUT: 0.0 + KERNEL_SIZE: + - 3 + NORM: + - instance + - {} + NUM_RES_UNITS: 0 + STRIDES: [] + UP_KERNEL_SIZE: + - 3 + VNET_MONAI: + ACTIVATION: + - elu + - inplace: true + DROPOUT_DIM: 3 + DROPOUT_PROB: 0.5 + USE_MAGNITUDE: true + TASKS: + - recon + TB_RECON: + CHANNELS: + - 16 + - 32 + - 64 + DEC_NUM_CONV_BLOCKS: + - 2 + - 3 + ENC_NUM_CONV_BLOCKS: + - 1 + - 2 + - 3 + KERNEL_SIZE: + - 5 + MULTI_CONCAT: [] + ORDER: + - conv + - relu + STRIDES: + - 2 + USE_MAGNITUDE: false + UNET: + BLOCK_ORDER: + - conv + - instancenorm + - - leakyrelu + - negative_slope: 0.2 + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + CONV_BLOCK: + ACTIVATION: relu + NORM: none + NORM_AFFINE: false + ORDER: + - norm + - act + - drop + - conv + DROPOUT: 0.0 + FIX_STEP_SIZE: false + KERNEL_SIZE: + - 3 + NUM_EMAPS: 1 + NUM_FEATURES: 256 + NUM_RESBLOCKS: 2 + NUM_UNROLLED_STEPS: 5 + PADDING: '' + SHARE_WEIGHTS: false + WEIGHTS: '' +OUTPUT_DIR: results://skm-tea/neurips2021/6x/U-Net_E2 +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + CHECKPOINT_MONITOR: val_loss + CHECKPOINT_PERIOD: 1 + EARLY_STOPPING: + MIN_DELTA: 0.0 + MONITOR: val_loss + PATIENCE: 0 + GAMMA: 1.0 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: '' + MAX_ITER: 20 + MIN_LR: null + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: [] + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 24 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: 1 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 1000 + QDESS_EVALUATOR: + ADDITIONAL_PATHS: [] + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim_old + - ssim (Wang) + SEM_SEG: [] +TIME_SCALE: epoch +VERSION: 1 +VIS_PERIOD: -400 diff --git a/neurips2021/recon-models/6x/U-Net_E2/model-gpu.ckpt b/neurips2021/recon-models/6x/U-Net_E2/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..60286c8cab5e1e3728b7fab98d30ec9c7cb24aa3 --- /dev/null +++ b/neurips2021/recon-models/6x/U-Net_E2/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:cd15a1c2267ad24ed56d30d2ed8ebae3000b8135b418fd68f0cd28b5b741fac2 +size 93107853 diff --git a/neurips2021/recon-models/6x/U-Net_E2/model-raw-gpu.ckpt b/neurips2021/recon-models/6x/U-Net_E2/model-raw-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..60286c8cab5e1e3728b7fab98d30ec9c7cb24aa3 --- /dev/null +++ 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(Wang)_scan diff --git a/neurips2021/recon-models/6x/Unrolled_E1+E2/config.yaml b/neurips2021/recon-models/6x/Unrolled_E1+E2/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..30362594654582de571428f1d5afefa9ccaab560 --- /dev/null +++ b/neurips2021/recon-models/6x/Unrolled_E1+E2/config.yaml @@ -0,0 +1,239 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 6 +AUG_TRAIN: + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 6 + CALIBRATION_SIZE: 24 + CENTER_FRACTIONS: [] + NAME: PoissonDiskMaskFunc + PRECOMPUTE: + NUM: 100000 + SEED: -1 + USE_NOISE: false +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: [] + DROP_LAST: true + FILTER: + BY: [] + GROUP_SAMPLER: + AS_BATCH_SAMPLER: true + BATCH_BY: + - num_coils + - matrix_shape + NUM_WORKERS: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: GroupSampler + SUBSAMPLE_TRAIN: + NUM_TOTAL: -1 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + QDESS: + DATASET_TYPE: '' + ECHO_KIND: echo1+echo2 + KWARGS: [] + TEST: + - stanford_qdess_v0.1.0_test + TRAIN: + - stanford_qdess_v0.1.0_train + VAL: + - stanford_qdess_v0.1.0_val +DESCRIPTION: + BRIEF: Recon only unrolled baseline - 8 unrolled, 2 resblocks, 256 features, L1 + loss, lr=8e-4- echo=echo1+echo2, acc=6 + ENTITY_NAME: mtrecon + EXP_NAME: recon-baseline/unrolled-6x-echo1+echo2/version_005 + PROJECT_NAME: mtrecon + TAGS: + - unrolled + - baseline + - neurips + - unrolled_6x + - gcp + - recon-baseline +MODEL: + CASCADE: + ITFS: + PERIOD: 0 + RECON_MODEL_NAME: '' + SEG_MODEL_NAME: '' + SEG_NORMALIZE: '' + USE_MAGNITUDE: false + ZERO_FILL: false + CS: + MAX_ITER: 200 + REGULARIZATION: 0.005 + DENOISING: + META_ARCHITECTURE: GeneralizedUnrolledCNN + NOISE: + STD_DEV: + - 1 + USE_FULLY_SAMPLED_TARGET: true + USE_FULLY_SAMPLED_TARGET_EVAL: null + DEVICE: cpu + META_ARCHITECTURE: GeneralizedUnrolledCNN + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + PARAMETERS: + INIT: [] + USE_COMPLEX_WEIGHTS: false + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + WEIGHT: 1.0 + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + IN_CHANNELS: null + LOSS_NAME: DiceLoss + LOSS_WEIGHT: 1.0 + MODEL: + DYNUNET_MONAI: + DEEP_SUPERVISION: false + DEEP_SUPR_NUM: 1 + KERNEL_SIZE: + - 3 + NORM_NAME: instance + RES_BLOCK: false + STRIDES: + - 1 + UPSAMPLE_KERNEL_SIZE: + - 2 + UNET_MONAI: + ACTIVATION: + - prelu + - {} + CHANNELS: [] + DROPOUT: 0.0 + KERNEL_SIZE: + - 3 + NORM: + - instance + - {} + NUM_RES_UNITS: 0 + STRIDES: [] + UP_KERNEL_SIZE: + - 3 + VNET_MONAI: + ACTIVATION: + - elu + - inplace: true + DROPOUT_DIM: 3 + DROPOUT_PROB: 0.5 + USE_MAGNITUDE: true + TASKS: + - recon + TB_RECON: + CHANNELS: + - 16 + - 32 + - 64 + DEC_NUM_CONV_BLOCKS: + - 2 + - 3 + ENC_NUM_CONV_BLOCKS: + - 1 + - 2 + - 3 + KERNEL_SIZE: + - 5 + MULTI_CONCAT: [] + ORDER: + - conv + - relu + STRIDES: + - 2 + USE_MAGNITUDE: false + UNET: + BLOCK_ORDER: + - conv + - instancenorm + - - leakyrelu + - negative_slope: 0.2 + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + CONV_BLOCK: + ACTIVATION: relu + NORM: none + NORM_AFFINE: false + ORDER: + - act + - conv + DROPOUT: 0.0 + FIX_STEP_SIZE: false + KERNEL_SIZE: + - 3 + NUM_EMAPS: 1 + NUM_FEATURES: 128 + NUM_RESBLOCKS: 2 + NUM_UNROLLED_STEPS: 8 + PADDING: '' + SHARE_WEIGHTS: false + WEIGHTS: '' +OUTPUT_DIR: results://skm-tea/neurips2021/6x/Unrolled_E1+E2 +SEED: 1000 +SOLVER: + BASE_LR: 0.0008 + CHECKPOINT_MONITOR: val_loss + CHECKPOINT_PERIOD: 1 + EARLY_STOPPING: + MIN_DELTA: 0.0 + MONITOR: val_loss + PATIENCE: 0 + GAMMA: 1.0 + GRAD_ACCUM_ITERS: 6 + LR_SCHEDULER_NAME: '' + MAX_ITER: 20 + MIN_LR: null + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: [] + TEST_BATCH_SIZE: 8 + TRAIN_BATCH_SIZE: 4 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: 1 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 1000 + QDESS_EVALUATOR: + ADDITIONAL_PATHS: [] + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim (Wang) + SEM_SEG: [] +TIME_SCALE: epoch +VERSION: 1 +VIS_PERIOD: -400 diff --git a/neurips2021/recon-models/6x/Unrolled_E1+E2/model-gpu.ckpt b/neurips2021/recon-models/6x/Unrolled_E1+E2/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..2096c19beb187a6d2b7274581352c3f8a16e01db --- /dev/null +++ b/neurips2021/recon-models/6x/Unrolled_E1+E2/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:2b9103e924dc78e28b190c57ae7b3ffba5c17109b1b01ef3d5a11cf54c31612b +size 43117073 diff --git a/neurips2021/recon-models/6x/Unrolled_E1+E2/model-raw-gpu.ckpt 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a/neurips2021/recon-models/6x/Unrolled_E1-oplus-E2/config.yaml b/neurips2021/recon-models/6x/Unrolled_E1-oplus-E2/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..fd0bf351d6c0b0256fe490fb12827e3768342ba9 --- /dev/null +++ b/neurips2021/recon-models/6x/Unrolled_E1-oplus-E2/config.yaml @@ -0,0 +1,238 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 6 +AUG_TRAIN: + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 6 + CALIBRATION_SIZE: 24 + CENTER_FRACTIONS: [] + NAME: PoissonDiskMaskFunc + PRECOMPUTE: + NUM: 100000 + SEED: -1 + USE_NOISE: false +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: [] + DROP_LAST: true + FILTER: + BY: [] + GROUP_SAMPLER: + AS_BATCH_SAMPLER: true + BATCH_BY: + - num_coils + - matrix_shape + NUM_WORKERS: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: GroupSampler + SUBSAMPLE_TRAIN: + NUM_TOTAL: -1 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + QDESS: + DATASET_TYPE: '' + ECHO_KIND: echo1-echo2-mc + KWARGS: [] + TEST: + - stanford_qdess_v0.1.0_test + TRAIN: + - stanford_qdess_v0.1.0_train + VAL: + - stanford_qdess_v0.1.0_val +DESCRIPTION: + BRIEF: Recon only unrolled baseline - 8 unrolled, 2 resblocks, 256 features, L1 + loss, lr=8e-4, echo=echo1-echo2-mc, acc=6 + ENTITY_NAME: mtrecon + EXP_NAME: recon-baseline/unrolled-6x-echo1-echo2-mc/version_001 + PROJECT_NAME: mtrecon + TAGS: + - neurips + - recon-baseline + - unrolled + - baseline + - unrolled_6x +MODEL: + CASCADE: + ITFS: + PERIOD: 0 + RECON_MODEL_NAME: '' + SEG_MODEL_NAME: '' + SEG_NORMALIZE: '' + USE_MAGNITUDE: false + ZERO_FILL: false + CS: + MAX_ITER: 200 + REGULARIZATION: 0.005 + DENOISING: + META_ARCHITECTURE: GeneralizedUnrolledCNN + NOISE: + STD_DEV: + - 1 + USE_FULLY_SAMPLED_TARGET: true + USE_FULLY_SAMPLED_TARGET_EVAL: null + DEVICE: cpu + META_ARCHITECTURE: GeneralizedUnrolledCNN + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + PARAMETERS: + INIT: [] + USE_COMPLEX_WEIGHTS: false + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + WEIGHT: 1.0 + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + IN_CHANNELS: null + LOSS_NAME: DiceLoss + LOSS_WEIGHT: 1.0 + MODEL: + DYNUNET_MONAI: + DEEP_SUPERVISION: false + DEEP_SUPR_NUM: 1 + KERNEL_SIZE: + - 3 + NORM_NAME: instance + RES_BLOCK: false + STRIDES: + - 1 + UPSAMPLE_KERNEL_SIZE: + - 2 + UNET_MONAI: + ACTIVATION: + - prelu + - {} + CHANNELS: [] + DROPOUT: 0.0 + KERNEL_SIZE: + - 3 + NORM: + - instance + - {} + NUM_RES_UNITS: 0 + STRIDES: [] + UP_KERNEL_SIZE: + - 3 + VNET_MONAI: + ACTIVATION: + - elu + - inplace: true + DROPOUT_DIM: 3 + DROPOUT_PROB: 0.5 + USE_MAGNITUDE: true + TASKS: + - recon + TB_RECON: + CHANNELS: + - 16 + - 32 + - 64 + DEC_NUM_CONV_BLOCKS: + - 2 + - 3 + ENC_NUM_CONV_BLOCKS: + - 1 + - 2 + - 3 + KERNEL_SIZE: + - 5 + MULTI_CONCAT: [] + ORDER: + - conv + - relu + STRIDES: + - 2 + USE_MAGNITUDE: false + UNET: + BLOCK_ORDER: + - conv + - instancenorm + - - leakyrelu + - negative_slope: 0.2 + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + CONV_BLOCK: + ACTIVATION: relu + NORM: none + NORM_AFFINE: false + ORDER: + - act + - conv + DROPOUT: 0.0 + FIX_STEP_SIZE: false + KERNEL_SIZE: + - 3 + NUM_EMAPS: 2 + NUM_FEATURES: 128 + NUM_RESBLOCKS: 2 + NUM_UNROLLED_STEPS: 8 + PADDING: '' + SHARE_WEIGHTS: false + WEIGHTS: '' +OUTPUT_DIR: results://skm-tea/neurips2021/6x/Unrolled_E1-oplus-E2 +SEED: 1000 +SOLVER: + BASE_LR: 0.0008 + CHECKPOINT_MONITOR: val_loss + CHECKPOINT_PERIOD: 1 + EARLY_STOPPING: + MIN_DELTA: 0.0 + MONITOR: val_loss + PATIENCE: 0 + GAMMA: 1.0 + GRAD_ACCUM_ITERS: 6 + LR_SCHEDULER_NAME: '' + MAX_ITER: 20 + MIN_LR: null + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: [] + TEST_BATCH_SIZE: 8 + TRAIN_BATCH_SIZE: 4 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: 1 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 1000 + QDESS_EVALUATOR: + ADDITIONAL_PATHS: [] + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim (Wang) + SEM_SEG: [] +TIME_SCALE: epoch +VERSION: 1 +VIS_PERIOD: -400 diff --git a/neurips2021/recon-models/6x/Unrolled_E1-oplus-E2/model-gpu.ckpt b/neurips2021/recon-models/6x/Unrolled_E1-oplus-E2/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..be8dce040d5397a928288970dc53c00e8ddfbd00 --- /dev/null +++ b/neurips2021/recon-models/6x/Unrolled_E1-oplus-E2/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:fef0aca6680bbaaaccc262cc720721b3d94a613036863d43deadb97bd589f6b7 +size 43583825 diff --git a/neurips2021/recon-models/6x/Unrolled_E1-oplus-E2/model-raw-gpu.ckpt 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b/neurips2021/recon-models/6x/Unrolled_E1/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..d21d22ff99e670a2f3e8e055e8aa29321a62db19 --- /dev/null +++ b/neurips2021/recon-models/6x/Unrolled_E1/config.yaml @@ -0,0 +1,240 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 6 +AUG_TRAIN: + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 6 + CALIBRATION_SIZE: 24 + CENTER_FRACTIONS: [] + NAME: PoissonDiskMaskFunc + PRECOMPUTE: + NUM: 100000 + SEED: -1 + USE_NOISE: false +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: [] + DROP_LAST: true + FILTER: + BY: [] + GROUP_SAMPLER: + AS_BATCH_SAMPLER: true + BATCH_BY: + - num_coils + - matrix_shape + NUM_WORKERS: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: GroupSampler + SUBSAMPLE_TRAIN: + NUM_TOTAL: -1 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + QDESS: + DATASET_TYPE: '' + ECHO_KIND: echo1 + KWARGS: [] + TEST: + - stanford_qdess_v0.1.0_test + TRAIN: + - stanford_qdess_v0.1.0_train + VAL: + - stanford_qdess_v0.1.0_val +DESCRIPTION: + BRIEF: Recon only unrolled baseline - 8 unrolled, 2 resblocks, 256 features, L1 + loss, lr=8e-4- echo=echo1, acc=6 + ENTITY_NAME: mtrecon + EXP_NAME: recon-baseline/unrolled-6x-echo1/version_004 + PROJECT_NAME: mtrecon + TAGS: + - unrolled + - gcp + - unrolled_6x + - neurips + - recon-baseline + - baseline +MODEL: + CASCADE: + ITFS: + PERIOD: 0 + RECON_MODEL_NAME: '' + SEG_MODEL_NAME: '' + SEG_NORMALIZE: '' + USE_MAGNITUDE: false + ZERO_FILL: false + CS: + MAX_ITER: 200 + REGULARIZATION: 0.005 + DENOISING: + META_ARCHITECTURE: GeneralizedUnrolledCNN + NOISE: + STD_DEV: + - 1 + USE_FULLY_SAMPLED_TARGET: true + USE_FULLY_SAMPLED_TARGET_EVAL: null + DEVICE: cpu + META_ARCHITECTURE: GeneralizedUnrolledCNN + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + PARAMETERS: + INIT: [] + USE_COMPLEX_WEIGHTS: false + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + WEIGHT: 1.0 + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + IN_CHANNELS: null + LOSS_NAME: DiceLoss + LOSS_WEIGHT: 1.0 + MODEL: + DYNUNET_MONAI: + DEEP_SUPERVISION: false + DEEP_SUPR_NUM: 1 + KERNEL_SIZE: + - 3 + NORM_NAME: instance + RES_BLOCK: false + STRIDES: + - 1 + UPSAMPLE_KERNEL_SIZE: + - 2 + UNET_MONAI: + ACTIVATION: + - prelu + - {} + CHANNELS: [] + DROPOUT: 0.0 + KERNEL_SIZE: + - 3 + NORM: + - instance + - {} + NUM_RES_UNITS: 0 + STRIDES: [] + UP_KERNEL_SIZE: + - 3 + VNET_MONAI: + ACTIVATION: + - elu + - inplace: true + DROPOUT_DIM: 3 + DROPOUT_PROB: 0.5 + USE_MAGNITUDE: true + TASKS: + - recon + TB_RECON: + CHANNELS: + - 16 + - 32 + - 64 + DEC_NUM_CONV_BLOCKS: + - 2 + - 3 + ENC_NUM_CONV_BLOCKS: + - 1 + - 2 + - 3 + KERNEL_SIZE: + - 5 + MULTI_CONCAT: [] + ORDER: + - conv + - relu + STRIDES: + - 2 + USE_MAGNITUDE: false + UNET: + BLOCK_ORDER: + - conv + - instancenorm + - - leakyrelu + - negative_slope: 0.2 + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + CONV_BLOCK: + ACTIVATION: relu + NORM: none + NORM_AFFINE: false + ORDER: + - act + - conv + DROPOUT: 0.0 + FIX_STEP_SIZE: false + KERNEL_SIZE: + - 3 + NUM_EMAPS: 1 + NUM_FEATURES: 128 + NUM_RESBLOCKS: 2 + NUM_UNROLLED_STEPS: 8 + PADDING: '' + SHARE_WEIGHTS: false + WEIGHTS: '' +OUTPUT_DIR: results://skm-tea/neurips2021/6x/Unrolled_E1 +SEED: 1000 +SOLVER: + BASE_LR: 0.0008 + CHECKPOINT_MONITOR: val_loss + CHECKPOINT_PERIOD: 1 + EARLY_STOPPING: + MIN_DELTA: 0.0 + MONITOR: val_loss + PATIENCE: 0 + GAMMA: 1.0 + GRAD_ACCUM_ITERS: 6 + LR_SCHEDULER_NAME: '' + MAX_ITER: 20 + MIN_LR: null + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: [] + TEST_BATCH_SIZE: 8 + TRAIN_BATCH_SIZE: 4 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: 1 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 1000 + QDESS_EVALUATOR: + ADDITIONAL_PATHS: [] + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim_old + - ssim (Wang) + SEM_SEG: [] +TIME_SCALE: epoch +VERSION: 1 +VIS_PERIOD: -400 diff --git a/neurips2021/recon-models/6x/Unrolled_E1/model-gpu.ckpt b/neurips2021/recon-models/6x/Unrolled_E1/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..9d69d6427dd5d01febf1ce7161605e19c5fdb130 --- /dev/null +++ b/neurips2021/recon-models/6x/Unrolled_E1/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:810e539a7f02fbb1dda3e60d4c0f9af559ec824f516a50328347dd094f08e0f9 +size 43116881 diff --git a/neurips2021/recon-models/6x/Unrolled_E1/model-raw-gpu.ckpt b/neurips2021/recon-models/6x/Unrolled_E1/model-raw-gpu.ckpt new file mode 100644 index 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b/neurips2021/recon-models/6x/Unrolled_E2/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..5a12ff09365e623ee5d5985b51f93c9212ed85c6 --- /dev/null +++ b/neurips2021/recon-models/6x/Unrolled_E2/config.yaml @@ -0,0 +1,239 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 6 +AUG_TRAIN: + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 6 + CALIBRATION_SIZE: 24 + CENTER_FRACTIONS: [] + NAME: PoissonDiskMaskFunc + PRECOMPUTE: + NUM: 100000 + SEED: -1 + USE_NOISE: false +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: [] + DROP_LAST: true + FILTER: + BY: [] + GROUP_SAMPLER: + AS_BATCH_SAMPLER: true + BATCH_BY: + - num_coils + - matrix_shape + NUM_WORKERS: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: GroupSampler + SUBSAMPLE_TRAIN: + NUM_TOTAL: -1 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + QDESS: + DATASET_TYPE: '' + ECHO_KIND: echo2 + KWARGS: [] + TEST: + - stanford_qdess_v0.1.0_test + TRAIN: + - stanford_qdess_v0.1.0_train + VAL: + - stanford_qdess_v0.1.0_val +DESCRIPTION: + BRIEF: Recon only unrolled baseline - 8 unrolled, 2 resblocks, 256 features, L1 + loss, lr=8e-4- echo=echo2, acc=6 + ENTITY_NAME: mtrecon + EXP_NAME: recon-baseline/unrolled-6x-echo2/version_001 + PROJECT_NAME: mtrecon + TAGS: + - recon-baseline + - unrolled + - baseline + - unrolled_6x + - neurips +MODEL: + CASCADE: + ITFS: + PERIOD: 0 + RECON_MODEL_NAME: '' + SEG_MODEL_NAME: '' + SEG_NORMALIZE: '' + USE_MAGNITUDE: false + ZERO_FILL: false + CS: + MAX_ITER: 200 + REGULARIZATION: 0.005 + DENOISING: + META_ARCHITECTURE: GeneralizedUnrolledCNN + NOISE: + STD_DEV: + - 1 + USE_FULLY_SAMPLED_TARGET: true + USE_FULLY_SAMPLED_TARGET_EVAL: null + DEVICE: cpu + META_ARCHITECTURE: GeneralizedUnrolledCNN + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + PARAMETERS: + INIT: [] + USE_COMPLEX_WEIGHTS: false + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + WEIGHT: 1.0 + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + IN_CHANNELS: null + LOSS_NAME: DiceLoss + LOSS_WEIGHT: 1.0 + MODEL: + DYNUNET_MONAI: + DEEP_SUPERVISION: false + DEEP_SUPR_NUM: 1 + KERNEL_SIZE: + - 3 + NORM_NAME: instance + RES_BLOCK: false + STRIDES: + - 1 + UPSAMPLE_KERNEL_SIZE: + - 2 + UNET_MONAI: + ACTIVATION: + - prelu + - {} + CHANNELS: [] + DROPOUT: 0.0 + KERNEL_SIZE: + - 3 + NORM: + - instance + - {} + NUM_RES_UNITS: 0 + STRIDES: [] + UP_KERNEL_SIZE: + - 3 + VNET_MONAI: + ACTIVATION: + - elu + - inplace: true + DROPOUT_DIM: 3 + DROPOUT_PROB: 0.5 + USE_MAGNITUDE: true + TASKS: + - recon + TB_RECON: + CHANNELS: + - 16 + - 32 + - 64 + DEC_NUM_CONV_BLOCKS: + - 2 + - 3 + ENC_NUM_CONV_BLOCKS: + - 1 + - 2 + - 3 + KERNEL_SIZE: + - 5 + MULTI_CONCAT: [] + ORDER: + - conv + - relu + STRIDES: + - 2 + USE_MAGNITUDE: false + UNET: + BLOCK_ORDER: + - conv + - instancenorm + - - leakyrelu + - negative_slope: 0.2 + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + CONV_BLOCK: + ACTIVATION: relu + NORM: none + NORM_AFFINE: false + ORDER: + - act + - conv + DROPOUT: 0.0 + FIX_STEP_SIZE: false + KERNEL_SIZE: + - 3 + NUM_EMAPS: 1 + NUM_FEATURES: 128 + NUM_RESBLOCKS: 2 + NUM_UNROLLED_STEPS: 8 + PADDING: '' + SHARE_WEIGHTS: false + WEIGHTS: '' +OUTPUT_DIR: results://skm-tea/neurips2021/6x/Unrolled_E2 +SEED: 1000 +SOLVER: + BASE_LR: 0.0008 + CHECKPOINT_MONITOR: val_loss + CHECKPOINT_PERIOD: 1 + EARLY_STOPPING: + MIN_DELTA: 0.0 + MONITOR: val_loss + PATIENCE: 0 + GAMMA: 1.0 + GRAD_ACCUM_ITERS: 6 + LR_SCHEDULER_NAME: '' + MAX_ITER: 20 + MIN_LR: null + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: [] + TEST_BATCH_SIZE: 8 + TRAIN_BATCH_SIZE: 4 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: 1 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 1000 + QDESS_EVALUATOR: + ADDITIONAL_PATHS: [] + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim_old + - ssim (Wang) + SEM_SEG: [] +TIME_SCALE: epoch +VERSION: 1 +VIS_PERIOD: -400 diff --git a/neurips2021/recon-models/6x/Unrolled_E2/model-gpu.ckpt b/neurips2021/recon-models/6x/Unrolled_E2/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..dd11856f2ee198c79bcfcee93db1a83ec98a96c1 --- /dev/null +++ b/neurips2021/recon-models/6x/Unrolled_E2/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:828e88bc6ee47f1409c5731a231d5f918c8bb59b0452a388db7157970b8595c4 +size 43116881 diff --git a/neurips2021/recon-models/6x/Unrolled_E2/model-raw-gpu.ckpt b/neurips2021/recon-models/6x/Unrolled_E2/model-raw-gpu.ckpt new file mode 100644 index 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num_coils + - matrix_shape + NUM_WORKERS: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: GroupSampler + SUBSAMPLE_TRAIN: + NUM_TOTAL: -1 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + QDESS: + DATASET_TYPE: '' + ECHO_KIND: echo1+echo2 + KWARGS: [] + TEST: + - stanford_qdess_v0.1.0_test + TRAIN: + - stanford_qdess_v0.1.0_train + VAL: + - stanford_qdess_v0.1.0_val +DESCRIPTION: + BRIEF: Recon only unet baseline - 4 pooling layers, 32 channels, L1 loss, lr=1e-3, + echo=echo1+echo2, acc=8 + ENTITY_NAME: mtrecon + EXP_NAME: recon-baseline/unet-8x-echo1+echo2/version_002 + PROJECT_NAME: mtrecon + TAGS: + - neurips + - recon-baseline + - unet_8x + - baseline + - unet +MODEL: + CASCADE: + ITFS: + PERIOD: 0 + RECON_MODEL_NAME: '' + SEG_MODEL_NAME: '' + SEG_NORMALIZE: '' + USE_MAGNITUDE: false + ZERO_FILL: false + CS: + MAX_ITER: 200 + REGULARIZATION: 0.005 + DENOISING: + META_ARCHITECTURE: GeneralizedUnrolledCNN + NOISE: + STD_DEV: + - 1 + USE_FULLY_SAMPLED_TARGET: true + USE_FULLY_SAMPLED_TARGET_EVAL: null + DEVICE: cpu + META_ARCHITECTURE: UnetModel + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + PARAMETERS: + INIT: [] + USE_COMPLEX_WEIGHTS: false + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + WEIGHT: 1.0 + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + IN_CHANNELS: null + LOSS_NAME: DiceLoss + LOSS_WEIGHT: 1.0 + MODEL: + DYNUNET_MONAI: + DEEP_SUPERVISION: false + DEEP_SUPR_NUM: 1 + KERNEL_SIZE: + - 3 + NORM_NAME: instance + RES_BLOCK: false + STRIDES: + - 1 + UPSAMPLE_KERNEL_SIZE: + - 2 + UNET_MONAI: + ACTIVATION: + - prelu + - {} + CHANNELS: [] + DROPOUT: 0.0 + KERNEL_SIZE: + - 3 + NORM: + - instance + - {} + NUM_RES_UNITS: 0 + STRIDES: [] + UP_KERNEL_SIZE: + - 3 + VNET_MONAI: + ACTIVATION: + - elu + - inplace: true + DROPOUT_DIM: 3 + DROPOUT_PROB: 0.5 + USE_MAGNITUDE: true + TASKS: + - recon + TB_RECON: + CHANNELS: + - 16 + - 32 + - 64 + DEC_NUM_CONV_BLOCKS: + - 2 + - 3 + ENC_NUM_CONV_BLOCKS: + - 1 + - 2 + - 3 + KERNEL_SIZE: + - 5 + MULTI_CONCAT: [] + ORDER: + - conv + - relu + STRIDES: + - 2 + USE_MAGNITUDE: false + UNET: + BLOCK_ORDER: + - conv + - instancenorm + - - leakyrelu + - negative_slope: 0.2 + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + CONV_BLOCK: + ACTIVATION: relu + NORM: none + NORM_AFFINE: false + ORDER: + - norm + - act + - drop + - conv + DROPOUT: 0.0 + FIX_STEP_SIZE: false + KERNEL_SIZE: + - 3 + NUM_EMAPS: 1 + NUM_FEATURES: 256 + NUM_RESBLOCKS: 2 + NUM_UNROLLED_STEPS: 5 + PADDING: '' + SHARE_WEIGHTS: false + WEIGHTS: '' +OUTPUT_DIR: results://skm-tea/neurips2021/8x/U-Net_E1+E2 +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + CHECKPOINT_MONITOR: val_loss + CHECKPOINT_PERIOD: 1 + EARLY_STOPPING: + MIN_DELTA: 0.0 + MONITOR: val_loss + PATIENCE: 0 + GAMMA: 1.0 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: '' + MAX_ITER: 20 + MIN_LR: null + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: [] + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 24 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: 1 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 1000 + QDESS_EVALUATOR: + ADDITIONAL_PATHS: [] + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim (Wang) + SEM_SEG: [] +TIME_SCALE: epoch +VERSION: 1 +VIS_PERIOD: -400 diff --git a/neurips2021/recon-models/8x/U-Net_E1+E2/model-gpu.ckpt b/neurips2021/recon-models/8x/U-Net_E1+E2/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..7d08af331ee6af3d310b6d9de361deb9e0972e45 --- /dev/null +++ b/neurips2021/recon-models/8x/U-Net_E1+E2/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid 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b/neurips2021/recon-models/8x/U-Net_E1-oplus-E2/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..485be81483717a844b88972cdc71a852b7daee6a --- /dev/null +++ b/neurips2021/recon-models/8x/U-Net_E1-oplus-E2/config.yaml @@ -0,0 +1,240 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 8 +AUG_TRAIN: + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 8 + CALIBRATION_SIZE: 24 + CENTER_FRACTIONS: [] + NAME: PoissonDiskMaskFunc + PRECOMPUTE: + NUM: 100000 + SEED: -1 + USE_NOISE: false +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: [] + DROP_LAST: true + FILTER: + BY: [] + GROUP_SAMPLER: + AS_BATCH_SAMPLER: true + BATCH_BY: + - num_coils + - matrix_shape + NUM_WORKERS: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: GroupSampler + SUBSAMPLE_TRAIN: + NUM_TOTAL: -1 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + QDESS: + DATASET_TYPE: '' + ECHO_KIND: echo1-echo2-mc + KWARGS: [] + TEST: + - stanford_qdess_v0.1.0_test + TRAIN: + - stanford_qdess_v0.1.0_train + VAL: + - stanford_qdess_v0.1.0_val +DESCRIPTION: + BRIEF: Recon only unet baseline - 4 pooling layers, 32 channels, L1 loss, lr=1e-3, + echo=echo1-echo2-mc, acc=8 + ENTITY_NAME: mtrecon + EXP_NAME: recon-baseline/unet-8x-echo1-echo2-mc/version_001 + PROJECT_NAME: mtrecon + TAGS: + - neurips + - recon-baseline + - unet_8x + - baseline + - unet +MODEL: + CASCADE: + ITFS: + PERIOD: 0 + RECON_MODEL_NAME: '' + SEG_MODEL_NAME: '' + SEG_NORMALIZE: '' + USE_MAGNITUDE: false + ZERO_FILL: false + CS: + MAX_ITER: 200 + REGULARIZATION: 0.005 + DENOISING: + META_ARCHITECTURE: GeneralizedUnrolledCNN + NOISE: + STD_DEV: + - 1 + USE_FULLY_SAMPLED_TARGET: true + USE_FULLY_SAMPLED_TARGET_EVAL: null + DEVICE: cpu + META_ARCHITECTURE: UnetModel + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + PARAMETERS: + INIT: [] + USE_COMPLEX_WEIGHTS: false + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + WEIGHT: 1.0 + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + IN_CHANNELS: null + LOSS_NAME: DiceLoss + LOSS_WEIGHT: 1.0 + MODEL: + DYNUNET_MONAI: + DEEP_SUPERVISION: false + DEEP_SUPR_NUM: 1 + KERNEL_SIZE: + - 3 + NORM_NAME: instance + RES_BLOCK: false + STRIDES: + - 1 + UPSAMPLE_KERNEL_SIZE: + - 2 + UNET_MONAI: + ACTIVATION: + - prelu + - {} + CHANNELS: [] + DROPOUT: 0.0 + KERNEL_SIZE: + - 3 + NORM: + - instance + - {} + NUM_RES_UNITS: 0 + STRIDES: [] + UP_KERNEL_SIZE: + - 3 + VNET_MONAI: + ACTIVATION: + - elu + - inplace: true + DROPOUT_DIM: 3 + DROPOUT_PROB: 0.5 + USE_MAGNITUDE: true + TASKS: + - recon + TB_RECON: + CHANNELS: + - 16 + - 32 + - 64 + DEC_NUM_CONV_BLOCKS: + - 2 + - 3 + ENC_NUM_CONV_BLOCKS: + - 1 + - 2 + - 3 + KERNEL_SIZE: + - 5 + MULTI_CONCAT: [] + ORDER: + - conv + - relu + STRIDES: + - 2 + USE_MAGNITUDE: false + UNET: + BLOCK_ORDER: + - conv + - instancenorm + - - leakyrelu + - negative_slope: 0.2 + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 4 + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 4 + UNROLLED: + CONV_BLOCK: + ACTIVATION: relu + NORM: none + NORM_AFFINE: false + ORDER: + - norm + - act + - drop + - conv + DROPOUT: 0.0 + FIX_STEP_SIZE: false + KERNEL_SIZE: + - 3 + NUM_EMAPS: 1 + NUM_FEATURES: 256 + NUM_RESBLOCKS: 2 + NUM_UNROLLED_STEPS: 5 + PADDING: '' + SHARE_WEIGHTS: false + WEIGHTS: '' +OUTPUT_DIR: results://skm-tea/neurips2021/8x/U-Net_E1-oplus-E2 +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + CHECKPOINT_MONITOR: val_loss + CHECKPOINT_PERIOD: 1 + EARLY_STOPPING: + MIN_DELTA: 0.0 + MONITOR: val_loss + PATIENCE: 0 + GAMMA: 1.0 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: '' + MAX_ITER: 20 + MIN_LR: null + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: [] + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 24 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: 1 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 1000 + QDESS_EVALUATOR: + ADDITIONAL_PATHS: [] + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim (Wang) + SEM_SEG: [] +TIME_SCALE: epoch +VERSION: 1 +VIS_PERIOD: -400 diff --git a/neurips2021/recon-models/8x/U-Net_E1-oplus-E2/model-gpu.ckpt b/neurips2021/recon-models/8x/U-Net_E1-oplus-E2/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..a55bf38938ec26fe3da8340c2ecf9631eb659441 --- /dev/null +++ b/neurips2021/recon-models/8x/U-Net_E1-oplus-E2/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:4c983b3efe6db2bbecface96e59e8415bebecea39aa96e3505e5346df47b1df6 +size 93115533 diff --git a/neurips2021/recon-models/8x/U-Net_E1-oplus-E2/model-raw-gpu.ckpt b/neurips2021/recon-models/8x/U-Net_E1-oplus-E2/model-raw-gpu.ckpt new file mode 100644 index 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b/neurips2021/recon-models/8x/U-Net_E1/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..5204f97575417fd154a21d47e0e1fc38a5a603a6 --- /dev/null +++ b/neurips2021/recon-models/8x/U-Net_E1/config.yaml @@ -0,0 +1,241 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 8 +AUG_TRAIN: + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 8 + CALIBRATION_SIZE: 24 + CENTER_FRACTIONS: [] + NAME: PoissonDiskMaskFunc + PRECOMPUTE: + NUM: 100000 + SEED: -1 + USE_NOISE: false +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: [] + DROP_LAST: true + FILTER: + BY: [] + GROUP_SAMPLER: + AS_BATCH_SAMPLER: true + BATCH_BY: + - num_coils + - matrix_shape + NUM_WORKERS: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: GroupSampler + SUBSAMPLE_TRAIN: + NUM_TOTAL: -1 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + QDESS: + DATASET_TYPE: '' + ECHO_KIND: echo1 + KWARGS: [] + TEST: + - stanford_qdess_v0.1.0_test + TRAIN: + - stanford_qdess_v0.1.0_train + VAL: + - stanford_qdess_v0.1.0_val +DESCRIPTION: + BRIEF: Recon only unet baseline - 4 pooling layers, 32 channels, L1 loss, lr=1e-3, + echo=echo1, acc=8 + ENTITY_NAME: mtrecon + EXP_NAME: recon-baseline/unet-8x-echo1/version_001 + PROJECT_NAME: mtrecon + TAGS: + - neurips + - recon-baseline + - unet_8x + - unet + - baseline +MODEL: + CASCADE: + ITFS: + PERIOD: 0 + RECON_MODEL_NAME: '' + SEG_MODEL_NAME: '' + SEG_NORMALIZE: '' + USE_MAGNITUDE: false + ZERO_FILL: false + CS: + MAX_ITER: 200 + REGULARIZATION: 0.005 + DENOISING: + META_ARCHITECTURE: GeneralizedUnrolledCNN + NOISE: + STD_DEV: + - 1 + USE_FULLY_SAMPLED_TARGET: true + USE_FULLY_SAMPLED_TARGET_EVAL: null + DEVICE: cpu + META_ARCHITECTURE: UnetModel + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + PARAMETERS: + INIT: [] + USE_COMPLEX_WEIGHTS: false + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + WEIGHT: 1.0 + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + IN_CHANNELS: null + LOSS_NAME: DiceLoss + LOSS_WEIGHT: 1.0 + MODEL: + DYNUNET_MONAI: + DEEP_SUPERVISION: false + DEEP_SUPR_NUM: 1 + KERNEL_SIZE: + - 3 + NORM_NAME: instance + RES_BLOCK: false + STRIDES: + - 1 + UPSAMPLE_KERNEL_SIZE: + - 2 + UNET_MONAI: + ACTIVATION: + - prelu + - {} + CHANNELS: [] + DROPOUT: 0.0 + KERNEL_SIZE: + - 3 + NORM: + - instance + - {} + NUM_RES_UNITS: 0 + STRIDES: [] + UP_KERNEL_SIZE: + - 3 + VNET_MONAI: + ACTIVATION: + - elu + - inplace: true + DROPOUT_DIM: 3 + DROPOUT_PROB: 0.5 + USE_MAGNITUDE: true + TASKS: + - recon + TB_RECON: + CHANNELS: + - 16 + - 32 + - 64 + DEC_NUM_CONV_BLOCKS: + - 2 + - 3 + ENC_NUM_CONV_BLOCKS: + - 1 + - 2 + - 3 + KERNEL_SIZE: + - 5 + MULTI_CONCAT: [] + ORDER: + - conv + - relu + STRIDES: + - 2 + USE_MAGNITUDE: false + UNET: + BLOCK_ORDER: + - conv + - instancenorm + - - leakyrelu + - negative_slope: 0.2 + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + CONV_BLOCK: + ACTIVATION: relu + NORM: none + NORM_AFFINE: false + ORDER: + - norm + - act + - drop + - conv + DROPOUT: 0.0 + FIX_STEP_SIZE: false + KERNEL_SIZE: + - 3 + NUM_EMAPS: 1 + NUM_FEATURES: 256 + NUM_RESBLOCKS: 2 + NUM_UNROLLED_STEPS: 5 + PADDING: '' + SHARE_WEIGHTS: false + WEIGHTS: '' +OUTPUT_DIR: results://skm-tea/neurips2021/8x/U-Net_E1 +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + CHECKPOINT_MONITOR: val_loss + CHECKPOINT_PERIOD: 1 + EARLY_STOPPING: + MIN_DELTA: 0.0 + MONITOR: val_loss + PATIENCE: 0 + GAMMA: 1.0 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: '' + MAX_ITER: 20 + MIN_LR: null + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: [] + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 24 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: 1 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 1000 + QDESS_EVALUATOR: + ADDITIONAL_PATHS: [] + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim_old + - ssim (Wang) + SEM_SEG: [] +TIME_SCALE: epoch +VERSION: 1 +VIS_PERIOD: -400 diff --git a/neurips2021/recon-models/8x/U-Net_E1/model-gpu.ckpt b/neurips2021/recon-models/8x/U-Net_E1/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..47572db8ebde2beb0dbacbf9db14d71bcf90b233 --- /dev/null +++ b/neurips2021/recon-models/8x/U-Net_E1/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:fd855f1e5f59dda60637e0c39ee6442899f782758e875ba0533070d85ca92ccd +size 93107853 diff --git a/neurips2021/recon-models/8x/U-Net_E1/model-raw-gpu.ckpt b/neurips2021/recon-models/8x/U-Net_E1/model-raw-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..47572db8ebde2beb0dbacbf9db14d71bcf90b233 --- /dev/null +++ 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b/neurips2021/recon-models/8x/U-Net_E2/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..2be28da9b66d1962ff979f4ff20f4c2a56ed7e7d --- /dev/null +++ b/neurips2021/recon-models/8x/U-Net_E2/config.yaml @@ -0,0 +1,241 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 8 +AUG_TRAIN: + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 8 + CALIBRATION_SIZE: 24 + CENTER_FRACTIONS: [] + NAME: PoissonDiskMaskFunc + PRECOMPUTE: + NUM: 100000 + SEED: -1 + USE_NOISE: false +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: [] + DROP_LAST: true + FILTER: + BY: [] + GROUP_SAMPLER: + AS_BATCH_SAMPLER: true + BATCH_BY: + - num_coils + - matrix_shape + NUM_WORKERS: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: GroupSampler + SUBSAMPLE_TRAIN: + NUM_TOTAL: -1 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + QDESS: + DATASET_TYPE: '' + ECHO_KIND: echo2 + KWARGS: [] + TEST: + - stanford_qdess_v0.1.0_test + TRAIN: + - stanford_qdess_v0.1.0_train + VAL: + - stanford_qdess_v0.1.0_val +DESCRIPTION: + BRIEF: Recon only unet baseline - 4 pooling layers, 32 channels, L1 loss, lr=1e-3, + echo=echo2, acc=8 + ENTITY_NAME: mtrecon + EXP_NAME: recon-baseline/unet-8x-echo2/version_001 + PROJECT_NAME: mtrecon + TAGS: + - neurips + - recon-baseline + - unet_8x + - unet + - baseline +MODEL: + CASCADE: + ITFS: + PERIOD: 0 + RECON_MODEL_NAME: '' + SEG_MODEL_NAME: '' + SEG_NORMALIZE: '' + USE_MAGNITUDE: false + ZERO_FILL: false + CS: + MAX_ITER: 200 + REGULARIZATION: 0.005 + DENOISING: + META_ARCHITECTURE: GeneralizedUnrolledCNN + NOISE: + STD_DEV: + - 1 + USE_FULLY_SAMPLED_TARGET: true + USE_FULLY_SAMPLED_TARGET_EVAL: null + DEVICE: cpu + META_ARCHITECTURE: UnetModel + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + PARAMETERS: + INIT: [] + USE_COMPLEX_WEIGHTS: false + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + WEIGHT: 1.0 + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + IN_CHANNELS: null + LOSS_NAME: DiceLoss + LOSS_WEIGHT: 1.0 + MODEL: + DYNUNET_MONAI: + DEEP_SUPERVISION: false + DEEP_SUPR_NUM: 1 + KERNEL_SIZE: + - 3 + NORM_NAME: instance + RES_BLOCK: false + STRIDES: + - 1 + UPSAMPLE_KERNEL_SIZE: + - 2 + UNET_MONAI: + ACTIVATION: + - prelu + - {} + CHANNELS: [] + DROPOUT: 0.0 + KERNEL_SIZE: + - 3 + NORM: + - instance + - {} + NUM_RES_UNITS: 0 + STRIDES: [] + UP_KERNEL_SIZE: + - 3 + VNET_MONAI: + ACTIVATION: + - elu + - inplace: true + DROPOUT_DIM: 3 + DROPOUT_PROB: 0.5 + USE_MAGNITUDE: true + TASKS: + - recon + TB_RECON: + CHANNELS: + - 16 + - 32 + - 64 + DEC_NUM_CONV_BLOCKS: + - 2 + - 3 + ENC_NUM_CONV_BLOCKS: + - 1 + - 2 + - 3 + KERNEL_SIZE: + - 5 + MULTI_CONCAT: [] + ORDER: + - conv + - relu + STRIDES: + - 2 + USE_MAGNITUDE: false + UNET: + BLOCK_ORDER: + - conv + - instancenorm + - - leakyrelu + - negative_slope: 0.2 + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + CONV_BLOCK: + ACTIVATION: relu + NORM: none + NORM_AFFINE: false + ORDER: + - norm + - act + - drop + - conv + DROPOUT: 0.0 + FIX_STEP_SIZE: false + KERNEL_SIZE: + - 3 + NUM_EMAPS: 1 + NUM_FEATURES: 256 + NUM_RESBLOCKS: 2 + NUM_UNROLLED_STEPS: 5 + PADDING: '' + SHARE_WEIGHTS: false + WEIGHTS: '' +OUTPUT_DIR: results://skm-tea/neurips2021/8x/U-Net_E2 +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + CHECKPOINT_MONITOR: val_loss + CHECKPOINT_PERIOD: 1 + EARLY_STOPPING: + MIN_DELTA: 0.0 + MONITOR: val_loss + PATIENCE: 0 + GAMMA: 1.0 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: '' + MAX_ITER: 20 + MIN_LR: null + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: [] + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 24 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: 1 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 1000 + QDESS_EVALUATOR: + ADDITIONAL_PATHS: [] + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim_old + - ssim (Wang) + SEM_SEG: [] +TIME_SCALE: epoch +VERSION: 1 +VIS_PERIOD: -400 diff --git a/neurips2021/recon-models/8x/U-Net_E2/model-gpu.ckpt b/neurips2021/recon-models/8x/U-Net_E2/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..43b65c7cf52630ab7cd63ab2fe188cd57594db83 --- /dev/null +++ b/neurips2021/recon-models/8x/U-Net_E2/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:554e1f0be903d5ed6fb765d741519adb64ece1cbe05d59e208a211e6865cb182 +size 93107853 diff --git a/neurips2021/recon-models/8x/U-Net_E2/model-raw-gpu.ckpt b/neurips2021/recon-models/8x/U-Net_E2/model-raw-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..43b65c7cf52630ab7cd63ab2fe188cd57594db83 --- /dev/null +++ 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+179,MTR_223,0.64731306,ssim (Wang)_scan diff --git a/neurips2021/recon-models/8x/Unrolled_E1+E2/config.yaml b/neurips2021/recon-models/8x/Unrolled_E1+E2/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..d6ce5f9fbb1316e65588c14910cd72c52d11440a --- /dev/null +++ b/neurips2021/recon-models/8x/Unrolled_E1+E2/config.yaml @@ -0,0 +1,239 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 8 +AUG_TRAIN: + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 8 + CALIBRATION_SIZE: 24 + CENTER_FRACTIONS: [] + NAME: PoissonDiskMaskFunc + PRECOMPUTE: + NUM: 100000 + SEED: -1 + USE_NOISE: false +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: [] + DROP_LAST: true + FILTER: + BY: [] + GROUP_SAMPLER: + AS_BATCH_SAMPLER: true + BATCH_BY: + - num_coils + - matrix_shape + NUM_WORKERS: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: GroupSampler + SUBSAMPLE_TRAIN: + NUM_TOTAL: -1 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + QDESS: + DATASET_TYPE: '' + ECHO_KIND: echo1+echo2 + KWARGS: [] + TEST: + - stanford_qdess_v0.1.0_test + TRAIN: + - stanford_qdess_v0.1.0_train + VAL: + - stanford_qdess_v0.1.0_val +DESCRIPTION: + BRIEF: Recon only unrolled baseline - 8 unrolled, 2 resblocks, 256 features, L1 + loss, lr=8e-4- echo=echo1+echo2, acc=8 + ENTITY_NAME: mtrecon + EXP_NAME: recon-baseline/unrolled-8x-echo1+echo2/version_006 + PROJECT_NAME: mtrecon + TAGS: + - unrolled + - unrolled_8x + - baseline + - neurips + - gcp + - recon-baseline +MODEL: + CASCADE: + ITFS: + PERIOD: 0 + RECON_MODEL_NAME: '' + SEG_MODEL_NAME: '' + SEG_NORMALIZE: '' + USE_MAGNITUDE: false + ZERO_FILL: false + CS: + MAX_ITER: 200 + REGULARIZATION: 0.005 + DENOISING: + META_ARCHITECTURE: GeneralizedUnrolledCNN + NOISE: + STD_DEV: + - 1 + USE_FULLY_SAMPLED_TARGET: true + USE_FULLY_SAMPLED_TARGET_EVAL: null + DEVICE: cpu + META_ARCHITECTURE: GeneralizedUnrolledCNN + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + PARAMETERS: + INIT: [] + USE_COMPLEX_WEIGHTS: false + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + WEIGHT: 1.0 + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + IN_CHANNELS: null + LOSS_NAME: DiceLoss + LOSS_WEIGHT: 1.0 + MODEL: + DYNUNET_MONAI: + DEEP_SUPERVISION: false + DEEP_SUPR_NUM: 1 + KERNEL_SIZE: + - 3 + NORM_NAME: instance + RES_BLOCK: false + STRIDES: + - 1 + UPSAMPLE_KERNEL_SIZE: + - 2 + UNET_MONAI: + ACTIVATION: + - prelu + - {} + CHANNELS: [] + DROPOUT: 0.0 + KERNEL_SIZE: + - 3 + NORM: + - instance + - {} + NUM_RES_UNITS: 0 + STRIDES: [] + UP_KERNEL_SIZE: + - 3 + VNET_MONAI: + ACTIVATION: + - elu + - inplace: true + DROPOUT_DIM: 3 + DROPOUT_PROB: 0.5 + USE_MAGNITUDE: true + TASKS: + - recon + TB_RECON: + CHANNELS: + - 16 + - 32 + - 64 + DEC_NUM_CONV_BLOCKS: + - 2 + - 3 + ENC_NUM_CONV_BLOCKS: + - 1 + - 2 + - 3 + KERNEL_SIZE: + - 5 + MULTI_CONCAT: [] + ORDER: + - conv + - relu + STRIDES: + - 2 + USE_MAGNITUDE: false + UNET: + BLOCK_ORDER: + - conv + - instancenorm + - - leakyrelu + - negative_slope: 0.2 + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + CONV_BLOCK: + ACTIVATION: relu + NORM: none + NORM_AFFINE: false + ORDER: + - act + - conv + DROPOUT: 0.0 + FIX_STEP_SIZE: false + KERNEL_SIZE: + - 3 + NUM_EMAPS: 1 + NUM_FEATURES: 128 + NUM_RESBLOCKS: 2 + NUM_UNROLLED_STEPS: 8 + PADDING: '' + SHARE_WEIGHTS: false + WEIGHTS: '' +OUTPUT_DIR: results://skm-tea/neurips2021/8x/Unrolled_E1+E2 +SEED: 1000 +SOLVER: + BASE_LR: 0.0008 + CHECKPOINT_MONITOR: val_loss + CHECKPOINT_PERIOD: 1 + EARLY_STOPPING: + MIN_DELTA: 0.0 + MONITOR: val_loss + PATIENCE: 0 + GAMMA: 1.0 + GRAD_ACCUM_ITERS: 6 + LR_SCHEDULER_NAME: '' + MAX_ITER: 20 + MIN_LR: null + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: [] + TEST_BATCH_SIZE: 8 + TRAIN_BATCH_SIZE: 4 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: 1 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 1000 + QDESS_EVALUATOR: + ADDITIONAL_PATHS: [] + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim (Wang) + SEM_SEG: [] +TIME_SCALE: epoch +VERSION: 1 +VIS_PERIOD: -400 diff --git a/neurips2021/recon-models/8x/Unrolled_E1+E2/model-gpu.ckpt b/neurips2021/recon-models/8x/Unrolled_E1+E2/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..fdc0ff7b9870e13b97714fd531c1d194494ee503 --- /dev/null +++ b/neurips2021/recon-models/8x/Unrolled_E1+E2/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:6711012f8f67a9c4b548ebf53e9d7b0422a77e6b1e01d5692ea0f08d3cfce14b +size 43116881 diff --git a/neurips2021/recon-models/8x/Unrolled_E1+E2/model-raw-gpu.ckpt 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a/neurips2021/recon-models/8x/Unrolled_E1-oplus-E2/config.yaml b/neurips2021/recon-models/8x/Unrolled_E1-oplus-E2/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..eaad29a6d9259131f468af14f6aeaa6ab71e8594 --- /dev/null +++ b/neurips2021/recon-models/8x/Unrolled_E1-oplus-E2/config.yaml @@ -0,0 +1,238 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 8 +AUG_TRAIN: + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 8 + CALIBRATION_SIZE: 24 + CENTER_FRACTIONS: [] + NAME: PoissonDiskMaskFunc + PRECOMPUTE: + NUM: 100000 + SEED: -1 + USE_NOISE: false +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: [] + DROP_LAST: true + FILTER: + BY: [] + GROUP_SAMPLER: + AS_BATCH_SAMPLER: true + BATCH_BY: + - num_coils + - matrix_shape + NUM_WORKERS: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: GroupSampler + SUBSAMPLE_TRAIN: + NUM_TOTAL: -1 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + QDESS: + DATASET_TYPE: '' + ECHO_KIND: echo1-echo2-mc + KWARGS: [] + TEST: + - stanford_qdess_v0.1.0_test + TRAIN: + - stanford_qdess_v0.1.0_train + VAL: + - stanford_qdess_v0.1.0_val +DESCRIPTION: + BRIEF: Recon only unrolled baseline - 8 unrolled, 2 resblocks, 256 features, L1 + loss, lr=8e-4, echo=echo1-echo2-mc, acc=8 + ENTITY_NAME: mtrecon + EXP_NAME: recon-baseline/unrolled-8x-echo1-echo2-mc/version_001 + PROJECT_NAME: mtrecon + TAGS: + - neurips + - recon-baseline + - unrolled + - baseline + - unrolled_8x +MODEL: + CASCADE: + ITFS: + PERIOD: 0 + RECON_MODEL_NAME: '' + SEG_MODEL_NAME: '' + SEG_NORMALIZE: '' + USE_MAGNITUDE: false + ZERO_FILL: false + CS: + MAX_ITER: 200 + REGULARIZATION: 0.005 + DENOISING: + META_ARCHITECTURE: GeneralizedUnrolledCNN + NOISE: + STD_DEV: + - 1 + USE_FULLY_SAMPLED_TARGET: true + USE_FULLY_SAMPLED_TARGET_EVAL: null + DEVICE: cpu + META_ARCHITECTURE: GeneralizedUnrolledCNN + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + PARAMETERS: + INIT: [] + USE_COMPLEX_WEIGHTS: false + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + WEIGHT: 1.0 + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + IN_CHANNELS: null + LOSS_NAME: DiceLoss + LOSS_WEIGHT: 1.0 + MODEL: + DYNUNET_MONAI: + DEEP_SUPERVISION: false + DEEP_SUPR_NUM: 1 + KERNEL_SIZE: + - 3 + NORM_NAME: instance + RES_BLOCK: false + STRIDES: + - 1 + UPSAMPLE_KERNEL_SIZE: + - 2 + UNET_MONAI: + ACTIVATION: + - prelu + - {} + CHANNELS: [] + DROPOUT: 0.0 + KERNEL_SIZE: + - 3 + NORM: + - instance + - {} + NUM_RES_UNITS: 0 + STRIDES: [] + UP_KERNEL_SIZE: + - 3 + VNET_MONAI: + ACTIVATION: + - elu + - inplace: true + DROPOUT_DIM: 3 + DROPOUT_PROB: 0.5 + USE_MAGNITUDE: true + TASKS: + - recon + TB_RECON: + CHANNELS: + - 16 + - 32 + - 64 + DEC_NUM_CONV_BLOCKS: + - 2 + - 3 + ENC_NUM_CONV_BLOCKS: + - 1 + - 2 + - 3 + KERNEL_SIZE: + - 5 + MULTI_CONCAT: [] + ORDER: + - conv + - relu + STRIDES: + - 2 + USE_MAGNITUDE: false + UNET: + BLOCK_ORDER: + - conv + - instancenorm + - - leakyrelu + - negative_slope: 0.2 + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + CONV_BLOCK: + ACTIVATION: relu + NORM: none + NORM_AFFINE: false + ORDER: + - act + - conv + DROPOUT: 0.0 + FIX_STEP_SIZE: false + KERNEL_SIZE: + - 3 + NUM_EMAPS: 2 + NUM_FEATURES: 128 + NUM_RESBLOCKS: 2 + NUM_UNROLLED_STEPS: 8 + PADDING: '' + SHARE_WEIGHTS: false + WEIGHTS: '' +OUTPUT_DIR: results://skm-tea/neurips2021/8x/Unrolled_E1-oplus-E2 +SEED: 1000 +SOLVER: + BASE_LR: 0.0008 + CHECKPOINT_MONITOR: val_loss + CHECKPOINT_PERIOD: 1 + EARLY_STOPPING: + MIN_DELTA: 0.0 + MONITOR: val_loss + PATIENCE: 0 + GAMMA: 1.0 + GRAD_ACCUM_ITERS: 6 + LR_SCHEDULER_NAME: '' + MAX_ITER: 20 + MIN_LR: null + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: [] + TEST_BATCH_SIZE: 8 + TRAIN_BATCH_SIZE: 4 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: 1 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 1000 + QDESS_EVALUATOR: + ADDITIONAL_PATHS: [] + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim (Wang) + SEM_SEG: [] +TIME_SCALE: epoch +VERSION: 1 +VIS_PERIOD: -400 diff --git a/neurips2021/recon-models/8x/Unrolled_E1-oplus-E2/model-gpu.ckpt b/neurips2021/recon-models/8x/Unrolled_E1-oplus-E2/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..bc6ad947910144c94b4d97926bec40a667c0fd82 --- /dev/null +++ b/neurips2021/recon-models/8x/Unrolled_E1-oplus-E2/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:def77b0ce529ab2820ecce4421d4ac59f6eccded3f5b7ce78be8ced5e9a398ef +size 43583825 diff --git a/neurips2021/recon-models/8x/Unrolled_E1-oplus-E2/model-raw-gpu.ckpt 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b/neurips2021/recon-models/8x/Unrolled_E1/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..7735d70275fb2f6565ddec032a0f989abb4f1b5c --- /dev/null +++ b/neurips2021/recon-models/8x/Unrolled_E1/config.yaml @@ -0,0 +1,237 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 8 +AUG_TRAIN: + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 8 + CALIBRATION_SIZE: 24 + CENTER_FRACTIONS: [] + NAME: PoissonDiskMaskFunc + PRECOMPUTE: + NUM: 100000 + SEED: -1 + USE_NOISE: false +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: [] + DROP_LAST: true + FILTER: + BY: [] + GROUP_SAMPLER: + AS_BATCH_SAMPLER: true + BATCH_BY: + - num_coils + - matrix_shape + NUM_WORKERS: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: GroupSampler + SUBSAMPLE_TRAIN: + NUM_TOTAL: -1 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + QDESS: + DATASET_TYPE: '' + ECHO_KIND: echo1 + KWARGS: [] + TEST: + - stanford_qdess_v0.1.0_test + TRAIN: + - stanford_qdess_v0.1.0_train + VAL: + - stanford_qdess_v0.1.0_val +DESCRIPTION: + BRIEF: Recon only unrolled baseline - 8 unrolled, 2 resblocks, 256 features, L1 + loss, lr=8e-4, echo=echo1, acc=8 + ENTITY_NAME: mtrecon + EXP_NAME: recon-baseline/unrolled-8x-echo1/version_001 + PROJECT_NAME: mtrecon + TAGS: + - recon-baseline + - unrolled_8x + - unrolled +MODEL: + CASCADE: + ITFS: + PERIOD: 0 + RECON_MODEL_NAME: '' + SEG_MODEL_NAME: '' + SEG_NORMALIZE: '' + USE_MAGNITUDE: false + ZERO_FILL: false + CS: + MAX_ITER: 200 + REGULARIZATION: 0.005 + DENOISING: + META_ARCHITECTURE: GeneralizedUnrolledCNN + NOISE: + STD_DEV: + - 1 + USE_FULLY_SAMPLED_TARGET: true + USE_FULLY_SAMPLED_TARGET_EVAL: null + DEVICE: cpu + META_ARCHITECTURE: GeneralizedUnrolledCNN + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + PARAMETERS: + INIT: [] + USE_COMPLEX_WEIGHTS: false + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + WEIGHT: 1.0 + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + IN_CHANNELS: null + LOSS_NAME: DiceLoss + LOSS_WEIGHT: 1.0 + MODEL: + DYNUNET_MONAI: + DEEP_SUPERVISION: false + DEEP_SUPR_NUM: 1 + KERNEL_SIZE: + - 3 + NORM_NAME: instance + RES_BLOCK: false + STRIDES: + - 1 + UPSAMPLE_KERNEL_SIZE: + - 2 + UNET_MONAI: + ACTIVATION: + - prelu + - {} + CHANNELS: [] + DROPOUT: 0.0 + KERNEL_SIZE: + - 3 + NORM: + - instance + - {} + NUM_RES_UNITS: 0 + STRIDES: [] + UP_KERNEL_SIZE: + - 3 + VNET_MONAI: + ACTIVATION: + - elu + - inplace: true + DROPOUT_DIM: 3 + DROPOUT_PROB: 0.5 + USE_MAGNITUDE: true + TASKS: + - recon + TB_RECON: + CHANNELS: + - 16 + - 32 + - 64 + DEC_NUM_CONV_BLOCKS: + - 2 + - 3 + ENC_NUM_CONV_BLOCKS: + - 1 + - 2 + - 3 + KERNEL_SIZE: + - 5 + MULTI_CONCAT: [] + ORDER: + - conv + - relu + STRIDES: + - 2 + USE_MAGNITUDE: false + UNET: + BLOCK_ORDER: + - conv + - instancenorm + - - leakyrelu + - negative_slope: 0.2 + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + CONV_BLOCK: + ACTIVATION: relu + NORM: none + NORM_AFFINE: false + ORDER: + - act + - conv + DROPOUT: 0.0 + FIX_STEP_SIZE: false + KERNEL_SIZE: + - 3 + NUM_EMAPS: 1 + NUM_FEATURES: 128 + NUM_RESBLOCKS: 2 + NUM_UNROLLED_STEPS: 8 + PADDING: '' + SHARE_WEIGHTS: false + WEIGHTS: '' +OUTPUT_DIR: results://skm-tea/neurips2021/8x/Unrolled_E1 +SEED: 1000 +SOLVER: + BASE_LR: 0.0008 + CHECKPOINT_MONITOR: val_loss + CHECKPOINT_PERIOD: 1 + EARLY_STOPPING: + MIN_DELTA: 0.0 + MONITOR: val_loss + PATIENCE: 0 + GAMMA: 1.0 + GRAD_ACCUM_ITERS: 6 + LR_SCHEDULER_NAME: '' + MAX_ITER: 20 + MIN_LR: null + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: [] + TEST_BATCH_SIZE: 8 + TRAIN_BATCH_SIZE: 4 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: 1 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 1000 + QDESS_EVALUATOR: + ADDITIONAL_PATHS: [] + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim_old + - ssim (Wang) + SEM_SEG: [] +TIME_SCALE: epoch +VERSION: 1 +VIS_PERIOD: -400 diff --git a/neurips2021/recon-models/8x/Unrolled_E1/model-gpu.ckpt b/neurips2021/recon-models/8x/Unrolled_E1/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..d4170d493d4f641a4896702ae64832d9bfa9a57d --- /dev/null +++ b/neurips2021/recon-models/8x/Unrolled_E1/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:274a131d2808461417364a121c4abf83d953db0c777d99c32d27159dd8e6dd87 +size 43116881 diff --git a/neurips2021/recon-models/8x/Unrolled_E1/model-raw-gpu.ckpt b/neurips2021/recon-models/8x/Unrolled_E1/model-raw-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..d4170d493d4f641a4896702ae64832d9bfa9a57d --- 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b/neurips2021/recon-models/8x/Unrolled_E2/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..2acaad0eebc7c1f8f6c76e7ee9f0f6549d472d4a --- /dev/null +++ b/neurips2021/recon-models/8x/Unrolled_E2/config.yaml @@ -0,0 +1,237 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 8 +AUG_TRAIN: + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 8 + CALIBRATION_SIZE: 24 + CENTER_FRACTIONS: [] + NAME: PoissonDiskMaskFunc + PRECOMPUTE: + NUM: 100000 + SEED: -1 + USE_NOISE: false +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: [] + DROP_LAST: true + FILTER: + BY: [] + GROUP_SAMPLER: + AS_BATCH_SAMPLER: true + BATCH_BY: + - num_coils + - matrix_shape + NUM_WORKERS: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: GroupSampler + SUBSAMPLE_TRAIN: + NUM_TOTAL: -1 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + QDESS: + DATASET_TYPE: '' + ECHO_KIND: echo2 + KWARGS: [] + TEST: + - stanford_qdess_v0.1.0_test + TRAIN: + - stanford_qdess_v0.1.0_train + VAL: + - stanford_qdess_v0.1.0_val +DESCRIPTION: + BRIEF: Recon only unrolled baseline - 8 unrolled, 2 resblocks, 256 features, L1 + loss, lr=8e-4, echo=echo2, acc=8 + ENTITY_NAME: mtrecon + EXP_NAME: recon-baseline/unrolled-8x-echo2/version_001 + PROJECT_NAME: mtrecon + TAGS: + - recon-baseline + - unrolled_8x + - unrolled +MODEL: + CASCADE: + ITFS: + PERIOD: 0 + RECON_MODEL_NAME: '' + SEG_MODEL_NAME: '' + SEG_NORMALIZE: '' + USE_MAGNITUDE: false + ZERO_FILL: false + CS: + MAX_ITER: 200 + REGULARIZATION: 0.005 + DENOISING: + META_ARCHITECTURE: GeneralizedUnrolledCNN + NOISE: + STD_DEV: + - 1 + USE_FULLY_SAMPLED_TARGET: true + USE_FULLY_SAMPLED_TARGET_EVAL: null + DEVICE: cpu + META_ARCHITECTURE: GeneralizedUnrolledCNN + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + PARAMETERS: + INIT: [] + USE_COMPLEX_WEIGHTS: false + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + WEIGHT: 1.0 + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + IN_CHANNELS: null + LOSS_NAME: DiceLoss + LOSS_WEIGHT: 1.0 + MODEL: + DYNUNET_MONAI: + DEEP_SUPERVISION: false + DEEP_SUPR_NUM: 1 + KERNEL_SIZE: + - 3 + NORM_NAME: instance + RES_BLOCK: false + STRIDES: + - 1 + UPSAMPLE_KERNEL_SIZE: + - 2 + UNET_MONAI: + ACTIVATION: + - prelu + - {} + CHANNELS: [] + DROPOUT: 0.0 + KERNEL_SIZE: + - 3 + NORM: + - instance + - {} + NUM_RES_UNITS: 0 + STRIDES: [] + UP_KERNEL_SIZE: + - 3 + VNET_MONAI: + ACTIVATION: + - elu + - inplace: true + DROPOUT_DIM: 3 + DROPOUT_PROB: 0.5 + USE_MAGNITUDE: true + TASKS: + - recon + TB_RECON: + CHANNELS: + - 16 + - 32 + - 64 + DEC_NUM_CONV_BLOCKS: + - 2 + - 3 + ENC_NUM_CONV_BLOCKS: + - 1 + - 2 + - 3 + KERNEL_SIZE: + - 5 + MULTI_CONCAT: [] + ORDER: + - conv + - relu + STRIDES: + - 2 + USE_MAGNITUDE: false + UNET: + BLOCK_ORDER: + - conv + - instancenorm + - - leakyrelu + - negative_slope: 0.2 + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + CONV_BLOCK: + ACTIVATION: relu + NORM: none + NORM_AFFINE: false + ORDER: + - act + - conv + DROPOUT: 0.0 + FIX_STEP_SIZE: false + KERNEL_SIZE: + - 3 + NUM_EMAPS: 1 + NUM_FEATURES: 128 + NUM_RESBLOCKS: 2 + NUM_UNROLLED_STEPS: 8 + PADDING: '' + SHARE_WEIGHTS: false + WEIGHTS: '' +OUTPUT_DIR: results://skm-tea/neurips2021/8x/Unrolled_E2 +SEED: 1000 +SOLVER: + BASE_LR: 0.0008 + CHECKPOINT_MONITOR: val_loss + CHECKPOINT_PERIOD: 1 + EARLY_STOPPING: + MIN_DELTA: 0.0 + MONITOR: val_loss + PATIENCE: 0 + GAMMA: 1.0 + GRAD_ACCUM_ITERS: 6 + LR_SCHEDULER_NAME: '' + MAX_ITER: 20 + MIN_LR: null + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: [] + TEST_BATCH_SIZE: 8 + TRAIN_BATCH_SIZE: 4 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: 1 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 1000 + QDESS_EVALUATOR: + ADDITIONAL_PATHS: [] + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim_old + - ssim (Wang) + SEM_SEG: [] +TIME_SCALE: epoch +VERSION: 1 +VIS_PERIOD: -400 diff --git a/neurips2021/recon-models/8x/Unrolled_E2/model-gpu.ckpt b/neurips2021/recon-models/8x/Unrolled_E2/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..45b8cd5b32c96f91af558a54ebc045c81deb17cb --- /dev/null +++ b/neurips2021/recon-models/8x/Unrolled_E2/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:99253e488a42994473fe5634292b227cb683365753984cbb2c0624e5557fbd03 +size 43116881 diff --git a/neurips2021/recon-models/8x/Unrolled_E2/model-raw-gpu.ckpt b/neurips2021/recon-models/8x/Unrolled_E2/model-raw-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..45b8cd5b32c96f91af558a54ebc045c81deb17cb --- 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(Wang)_scan +178,MTR_178,0.70392567,ssim (Wang)_scan +179,MTR_223,0.70678115,ssim (Wang)_scan diff --git a/neurips2021/segmentation-models/U-Net_E1-oplus-E2/config.yaml b/neurips2021/segmentation-models/U-Net_E1-oplus-E2/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..041e5d51d4d5ac66b0ca7e15466e266b6f2bb4fe --- /dev/null +++ b/neurips2021/segmentation-models/U-Net_E1-oplus-E2/config.yaml @@ -0,0 +1,251 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 6 +AUG_TRAIN: + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 6 + CALIBRATION_SIZE: 24 + CENTER_FRACTIONS: [] + NAME: PoissonDiskMaskFunc + PRECOMPUTE: + NUM: -1 + SEED: -1 + USE_NOISE: false +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: [] + DROP_LAST: true + FILTER: + BY: [] + GROUP_SAMPLER: + AS_BATCH_SAMPLER: true + BATCH_BY: + - inplane_shape + NUM_WORKERS: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: '' + SUBSAMPLE_TRAIN: + NUM_TOTAL: -1 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + QDESS: + DATASET_TYPE: qDESSImageDataset + ECHO_KIND: echo1-echo2-mc + KWARGS: + - orientation + - sagittal + TEST: + - stanford_qdess_v0.1.0_test + TRAIN: + - stanford_qdess_v0.1.0_train + VAL: + - stanford_qdess_v0.1.0_val +DESCRIPTION: + BRIEF: UNet segmentation following parameters used in MedSegPy - input=echo1-echo2-mc, + 100 epochs, 0.001 lr w/ 0.9x decay every (2,) epochs, early stopping- T=12, delta=1e-05, + bsz=16, qdess args=('orientation', 'sagittal') + ENTITY_NAME: ss_recon + EXP_NAME: seg-baseline/unet-medsegpy-echo1-echo2-mc + PROJECT_NAME: ss_recon + TAGS: + - seg-baseline + - baseline + - unet-medsegpy + - neurips +MODEL: + CASCADE: + ITFS: + PERIOD: 0 + RECON_MODEL_NAME: '' + SEG_MODEL_NAME: '' + SEG_NORMALIZE: '' + USE_MAGNITUDE: false + ZERO_FILL: false + CS: + MAX_ITER: 200 + REGULARIZATION: 0.005 + DENOISING: + META_ARCHITECTURE: GeneralizedUnrolledCNN + NOISE: + STD_DEV: + - 1 + USE_FULLY_SAMPLED_TARGET: true + USE_FULLY_SAMPLED_TARGET_EVAL: null + DEVICE: cpu + META_ARCHITECTURE: GeneralizedUNet + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + PARAMETERS: + INIT: + - initializers: (("kaiming_normal_", {"nonlinearity":"relu"}), "zeros_") + kind: conv + patterns: (".*weight", ".*bias") + - initializers: ("ones_", "zeros_") + kind: norm + patterns: (".*weight", ".*bias") + - initializers: ("xavier_uniform_",) + patterns: ("output_block\.weight",) + USE_COMPLEX_WEIGHTS: false + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: true + WEIGHT: 1.0 + SEG: + ACTIVATION: sigmoid + CLASSES: + - pc + - fc + - men + - tc + INCLUDE_BACKGROUND: false + IN_CHANNELS: 2 + LOSS_NAME: FlattenedDiceLoss + LOSS_WEIGHT: 1.0 + MODEL: + DYNUNET_MONAI: + DEEP_SUPERVISION: false + DEEP_SUPR_NUM: 1 + KERNEL_SIZE: + - 3 + NORM_NAME: instance + RES_BLOCK: false + STRIDES: + - 1 + UPSAMPLE_KERNEL_SIZE: + - 2 + UNET_MONAI: + ACTIVATION: + - prelu + - {} + CHANNELS: [] + DROPOUT: 0.0 + KERNEL_SIZE: + - 3 + NORM: + - instance + - {} + NUM_RES_UNITS: 0 + STRIDES: [] + UP_KERNEL_SIZE: + - 3 + VNET_MONAI: + ACTIVATION: + - elu + - inplace: true + DROPOUT_DIM: 3 + DROPOUT_PROB: 0.5 + USE_MAGNITUDE: true + TASKS: + - sem_seg + TB_RECON: + CHANNELS: + - 16 + - 32 + - 64 + DEC_NUM_CONV_BLOCKS: + - 2 + - 3 + ENC_NUM_CONV_BLOCKS: + - 1 + - 2 + - 3 + KERNEL_SIZE: + - 5 + MULTI_CONCAT: [] + ORDER: + - conv + - relu + STRIDES: + - 2 + USE_MAGNITUDE: false + UNET: + BLOCK_ORDER: + - conv + - relu + - conv + - relu + - bn + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NUM_POOL_LAYERS: 5 + OUT_CHANNELS: 2 + UNROLLED: + CONV_BLOCK: + ACTIVATION: relu + NORM: none + NORM_AFFINE: false + ORDER: + - norm + - act + - drop + - conv + DROPOUT: 0.0 + FIX_STEP_SIZE: false + KERNEL_SIZE: + - 3 + NUM_EMAPS: 1 + NUM_FEATURES: 256 + NUM_RESBLOCKS: 2 + NUM_UNROLLED_STEPS: 5 + PADDING: '' + SHARE_WEIGHTS: false + WEIGHTS: '' +OUTPUT_DIR: results://skm-tea/neurips2021/U-Net_E1-oplus-E2 +SEED: 9001 +SOLVER: + BASE_LR: 0.001 + CHECKPOINT_MONITOR: val_loss + CHECKPOINT_PERIOD: 1 + EARLY_STOPPING: + MIN_DELTA: 1.0e-05 + MONITOR: val_loss + PATIENCE: 12 + GAMMA: 0.9 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: StepLR + MAX_ITER: 100 + MIN_LR: 1.0e-08 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: + - 2 + TEST_BATCH_SIZE: 40 + TRAIN_BATCH_SIZE: 16 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: 1 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: -5 + QDESS_EVALUATOR: + ADDITIONAL_PATHS: [] + VAL_METRICS: + RECON: [] + SEM_SEG: + - DSC + - VOE + - CV + - DSC_scan + - VOE_scan + - CV_scan +TIME_SCALE: epoch +VERSION: 1 +VIS_PERIOD: -100 diff --git a/neurips2021/segmentation-models/U-Net_E1-oplus-E2/model-gpu.ckpt b/neurips2021/segmentation-models/U-Net_E1-oplus-E2/model-gpu.ckpt new file mode 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+7,MTR_066,0.9143593311309814,0.6419733762741089,2.1347105503082275,1.7407081127166748,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +8,MTR_079,0.5439184308052063,0.29178330302238464,0.24208058416843414,0.2605423331260681,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +9,MTR_080,0.6634348630905151,0.2694576680660248,0.2859136164188385,0.37396422028541565,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +10,MTR_096,0.66550612449646,0.16107384860515594,0.3428915739059448,0.20093251764774323,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +11,MTR_099,0.3433677852153778,0.2624264061450958,0.5805190205574036,0.3889078199863434,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +12,MTR_120,0.38432198762893677,0.39642685651779175,0.9085205793380737,0.2635924816131592,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +13,MTR_126,0.341908723115921,0.3907257616519928,0.5540884137153625,0.3021378815174103,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +14,MTR_144,0.23121793568134308,0.20119518041610718,0.34915032982826233,0.3637676537036896,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +15,MTR_156,0.7034190893173218,0.41106048226356506,0.8612309098243713,0.4868907332420349,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +16,MTR_158,0.2653937041759491,0.22426319122314453,0.8720167279243469,0.3838661313056946,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +17,MTR_173,0.8381838798522949,0.6861959099769592,1.5677005052566528,1.20004403591156,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +18,MTR_176,0.5174118876457214,0.25879424810409546,0.6959963440895081,0.4089217782020569,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +19,MTR_178,0.35023632645606995,0.22542783617973328,0.43747007846832275,0.29235875606536865,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +20,MTR_188,0.31424272060394287,0.26567769050598145,0.40628382563591003,0.2529151737689972,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +21,MTR_196,0.2341042309999466,0.214219331741333,0.292239248752594,0.19310057163238525,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +22,MTR_198,0.28855064511299133,0.270192950963974,0.5131471157073975,0.328682541847229,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +23,MTR_199,0.18851439654827118,0.18983609974384308,0.24388037621974945,0.3716196119785309,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +24,MTR_218,0.2382664978504181,0.2695496082305908,0.3608667552471161,0.22938752174377441,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +25,MTR_219,0.170353502035141,0.19879421591758728,0.3357918858528137,0.26863497495651245,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +26,MTR_221,1.2306691408157349,0.37679430842399597,1.072572946548462,0.9538949131965637,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +27,MTR_223,0.19674532115459442,0.13253438472747803,0.23329222202301025,0.23415972292423248,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +28,MTR_224,0.2770971655845642,0.19604367017745972,0.7987090945243835,0.32593467831611633,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +29,MTR_227,0.19974727928638458,0.1997690200805664,0.26892703771591187,0.33484214544296265,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +30,MTR_235,0.6891064643859863,0.30579760670661926,0.5654111504554749,0.37253808975219727,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +31,MTR_237,0.6711770296096802,0.43098175525665283,1.2241162061691284,0.7944031357765198,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +32,MTR_240,0.5573195219039917,0.5866793990135193,1.5685185194015503,1.5502426624298096,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +33,MTR_241,2.1767258644104004,0.36145567893981934,0.8418861031532288,0.37867894768714905,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +34,MTR_244,0.46337538957595825,0.2534797787666321,0.3120173513889313,0.2037997990846634,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +35,MTR_248,0.7354440689086914,0.2555910646915436,0.5314398407936096,0.3068937361240387,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +36,MTR_005,0.015090095810592175,0.03494710102677345,0.14434832334518433,0.10332661867141724,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +37,MTR_006,0.056294240057468414,0.027574097737669945,0.14794115722179413,0.025668608024716377,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +38,MTR_030,0.17492187023162842,0.16415159404277802,0.3876723051071167,0.24065415561199188,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +39,MTR_034,0.0379873663187027,0.008813182823359966,0.09765714406967163,0.03000643104314804,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +40,MTR_048,0.012587819248437881,0.00260717561468482,0.04809258133172989,0.0462503544986248,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +41,MTR_052,0.528147280216217,0.044268712401390076,0.11742245405912399,0.30087950825691223,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +42,MTR_065,0.02845708839595318,0.03376426175236702,0.09023167937994003,0.06437956541776657,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +43,MTR_066,0.1614505648612976,0.14852046966552734,0.05106304585933685,0.09255339205265045,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +44,MTR_079,0.049040280282497406,0.03222357854247093,0.05750184506177902,0.0864972174167633,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +45,MTR_080,0.11105679720640182,0.08933334797620773,0.032584890723228455,0.03710023686289787,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +46,MTR_096,0.010771919041872025,0.008340505883097649,0.010310618206858635,0.026904407888650894,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +47,MTR_099,0.04469810053706169,0.011781850829720497,0.05794510245323181,0.10533343255519867,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +48,MTR_120,0.03782304376363754,0.17719581723213196,0.15352074801921844,0.09271388500928879,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +49,MTR_126,0.11551379412412643,0.11472896486520767,0.11763399094343185,0.11447528749704361,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +50,MTR_144,0.010296890512108803,0.005280316807329655,0.03647913038730621,0.11693073809146881,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +51,MTR_156,0.06035338342189789,0.1233508288860321,0.0878678485751152,0.11623043566942215,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +52,MTR_158,0.006805751007050276,0.06883958727121353,0.34076544642448425,0.012022482231259346,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +53,MTR_173,0.055385522544384,0.16777019202709198,0.015563559718430042,0.10242705047130585,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +54,MTR_176,0.17804725468158722,0.0665600448846817,0.0467827208340168,0.2323489934206009,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +55,MTR_178,0.06750041246414185,0.1025744304060936,0.01988658308982849,0.03966332599520683,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +56,MTR_188,0.036535609513521194,0.10745441168546677,0.0435425341129303,0.1054958626627922,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +57,MTR_196,0.05547858402132988,0.034128159284591675,0.044190965592861176,0.0031849017832428217,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +58,MTR_198,0.010960804298520088,0.08607818186283112,0.022533414885401726,0.05014127865433693,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +59,MTR_199,0.04421696066856384,0.0492313876748085,0.04634902626276016,0.06213749945163727,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +60,MTR_218,0.10521146655082703,0.11828745901584625,0.04931224137544632,0.02078036405146122,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +61,MTR_219,0.009416676126420498,0.011687921360135078,0.03991403430700302,0.008471186272799969,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +62,MTR_221,0.2796025574207306,0.130060613155365,0.11262083798646927,0.22744686901569366,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +63,MTR_223,0.022261012345552444,0.004843758884817362,0.027457941323518753,0.01886933296918869,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +64,MTR_224,0.07676300406455994,0.10508226603269577,0.03774541988968849,0.015229438431560993,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +65,MTR_227,0.0848088413476944,0.11243901401758194,0.06485845893621445,0.12514165043830872,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +66,MTR_235,0.02550112083554268,0.09128269553184509,0.03523727506399155,0.009313588961958885,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +67,MTR_237,0.006959094665944576,0.03654209151864052,0.049998942762613297,0.062423285096883774,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +68,MTR_240,0.004543726798146963,0.15647250413894653,0.06116779148578644,0.15513519942760468,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +69,MTR_241,0.20122119784355164,0.19435814023017883,0.1599939614534378,0.21244238317012787,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +70,MTR_244,0.148358553647995,0.09665791690349579,0.02094634808599949,0.09377110749483109,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +71,MTR_248,0.13041526079177856,0.010546904057264328,0.015354477800428867,0.017540184780955315,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +72,MTR_005,0.9236449003219604,0.9094212055206299,0.8413504958152771,0.8815556168556213,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +73,MTR_006,0.8992171883583069,0.886679470539093,0.8565671443939209,0.8673000931739807,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +74,MTR_030,0.8494676947593689,0.777649462223053,0.5612945556640625,0.7256202697753906,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +75,MTR_034,0.9041615724563599,0.8973108530044556,0.8843852281570435,0.8865505456924438,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +76,MTR_048,0.9396041035652161,0.9230778217315674,0.8170496225357056,0.8864918947219849,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +77,MTR_052,0.4256972670555115,0.8553723692893982,0.726078450679779,0.7395787835121155,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +78,MTR_065,0.9015911817550659,0.8906841278076172,0.8437927961349487,0.8531747460365295,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +79,MTR_066,0.8463056683540344,0.8312106728553772,0.8036180138587952,0.8473788499832153,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +80,MTR_079,0.8539755344390869,0.8650503158569336,0.8766957521438599,0.8758289813995361,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +81,MTR_080,0.891828179359436,0.8573805689811707,0.9003974795341492,0.8853724002838135,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +82,MTR_096,0.8854777216911316,0.9236134886741638,0.8794867396354675,0.9187476634979248,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +83,MTR_099,0.8935242295265198,0.8941799998283386,0.8653241991996765,0.8595367670059204,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +84,MTR_120,0.9052129983901978,0.8366498947143555,0.7757421135902405,0.8887786865234375,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +85,MTR_126,0.9008354544639587,0.884673535823822,0.8684430122375488,0.8853261470794678,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +86,MTR_144,0.943692684173584,0.9291747808456421,0.889099657535553,0.8726003766059875,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +87,MTR_156,0.8818686604499817,0.8719728589057922,0.8505139946937561,0.8703563809394836,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +88,MTR_158,0.8858409523963928,0.892939031124115,0.7074703574180603,0.8370899558067322,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +89,MTR_173,0.8924335837364197,0.8332111239433289,0.8611457347869873,0.8478399515151978,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +90,MTR_176,0.8521327376365662,0.8940837383270264,0.8131666779518127,0.8279393911361694,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +91,MTR_178,0.9200910925865173,0.8879504203796387,0.8653814792633057,0.875770628452301,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +92,MTR_188,0.9062780141830444,0.8736145496368408,0.865487813949585,0.8744412660598755,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +93,MTR_196,0.9038245677947998,0.8961519598960876,0.8880942463874817,0.8993690609931946,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +94,MTR_198,0.898862361907959,0.8837215900421143,0.8285742998123169,0.881549596786499,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +95,MTR_199,0.9268282651901245,0.898245632648468,0.8995294570922852,0.86257004737854,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +96,MTR_218,0.8855654001235962,0.8553997874259949,0.8492271900177002,0.8310981392860413,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +97,MTR_219,0.9351403713226318,0.9097878336906433,0.8726843595504761,0.895695149898529,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +98,MTR_221,0.7558638453483582,0.850595235824585,0.82075035572052,0.7995122075080872,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +99,MTR_223,0.9338782429695129,0.9216018915176392,0.9000134468078613,0.9026006460189819,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +100,MTR_224,0.8842537999153137,0.8797767162322998,0.8087581396102905,0.8318050503730774,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +101,MTR_227,0.9180117249488831,0.8773121237754822,0.8771461248397827,0.8506946563720703,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +102,MTR_235,0.867315411567688,0.8777615427970886,0.8534198999404907,0.8859329223632812,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +103,MTR_237,0.9158650040626526,0.8809974193572998,0.8353029489517212,0.8577969670295715,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +104,MTR_240,0.8644216656684875,0.8555413484573364,0.8641403317451477,0.826995849609375,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +105,MTR_241,0.7316427826881409,0.8038256764411926,0.7521077394485474,0.8109821677207947,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +106,MTR_244,0.8586469292640686,0.8561699390411377,0.9017816185951233,0.8824970722198486,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +107,MTR_248,0.8750433325767517,0.9110010862350464,0.869335412979126,0.8804072737693787,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +108,MTR_005,0.14187711477279663,0.16611140966415405,0.27385246753692627,0.21180206537246704,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +109,MTR_006,0.18311119079589844,0.20357215404510498,0.2508811354637146,0.23430728912353516,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +110,MTR_030,0.261674165725708,0.36380815505981445,0.6098613739013672,0.4306090474128723,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +111,MTR_034,0.1749134063720703,0.1862521767616272,0.2072664499282837,0.20378011465072632,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +112,MTR_048,0.11391198635101318,0.14285558462142944,0.30931204557418823,0.20387476682662964,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +113,MTR_052,0.7295963168144226,0.2527068257331848,0.43004459142684937,0.4132288694381714,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, 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b/neurips2021/segmentation-models/U-Net_E1/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..b8060a27a275fd51ee8f9c33ebc68933d629fba7 --- /dev/null +++ b/neurips2021/segmentation-models/U-Net_E1/config.yaml @@ -0,0 +1,251 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 6 +AUG_TRAIN: + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 6 + CALIBRATION_SIZE: 24 + CENTER_FRACTIONS: [] + NAME: PoissonDiskMaskFunc + PRECOMPUTE: + NUM: -1 + SEED: -1 + USE_NOISE: false +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: [] + DROP_LAST: true + FILTER: + BY: [] + GROUP_SAMPLER: + AS_BATCH_SAMPLER: true + BATCH_BY: + - inplane_shape + NUM_WORKERS: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: '' + SUBSAMPLE_TRAIN: + NUM_TOTAL: -1 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + QDESS: + DATASET_TYPE: qDESSImageDataset + ECHO_KIND: echo1 + KWARGS: + - orientation + - sagittal + TEST: + - stanford_qdess_v0.1.0_test + TRAIN: + - stanford_qdess_v0.1.0_train + VAL: + - stanford_qdess_v0.1.0_val +DESCRIPTION: + BRIEF: UNet segmentation following parameters used in MedSegPy - input=echo1, 100 + epochs, 0.001 lr w/ 0.9x decay every (2,) epochs, early stopping- T=12, delta=1e-05, + bsz=16, qdess args=('orientation', 'sagittal') + ENTITY_NAME: ss_recon + EXP_NAME: seg-baseline/unet-medsegpy-echo1 + PROJECT_NAME: ss_recon + TAGS: + - seg-baseline + - baseline + - unet-medsegpy + - neurips +MODEL: + CASCADE: + ITFS: + PERIOD: 0 + RECON_MODEL_NAME: '' + SEG_MODEL_NAME: '' + SEG_NORMALIZE: '' + USE_MAGNITUDE: false + ZERO_FILL: false + CS: + MAX_ITER: 200 + REGULARIZATION: 0.005 + DENOISING: + META_ARCHITECTURE: GeneralizedUnrolledCNN + NOISE: + STD_DEV: + - 1 + USE_FULLY_SAMPLED_TARGET: true + USE_FULLY_SAMPLED_TARGET_EVAL: null + DEVICE: cpu + META_ARCHITECTURE: GeneralizedUNet + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + PARAMETERS: + INIT: + - initializers: (("kaiming_normal_", {"nonlinearity":"relu"}), "zeros_") + kind: conv + patterns: (".*weight", ".*bias") + - initializers: ("ones_", "zeros_") + kind: norm + patterns: (".*weight", ".*bias") + - initializers: ("xavier_uniform_",) + patterns: ("output_block\.weight",) + USE_COMPLEX_WEIGHTS: false + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: true + WEIGHT: 1.0 + SEG: + ACTIVATION: sigmoid + CLASSES: + - pc + - fc + - men + - tc + INCLUDE_BACKGROUND: false + IN_CHANNELS: null + LOSS_NAME: FlattenedDiceLoss + LOSS_WEIGHT: 1.0 + MODEL: + DYNUNET_MONAI: + DEEP_SUPERVISION: false + DEEP_SUPR_NUM: 1 + KERNEL_SIZE: + - 3 + NORM_NAME: instance + RES_BLOCK: false + STRIDES: + - 1 + UPSAMPLE_KERNEL_SIZE: + - 2 + UNET_MONAI: + ACTIVATION: + - prelu + - {} + CHANNELS: [] + DROPOUT: 0.0 + KERNEL_SIZE: + - 3 + NORM: + - instance + - {} + NUM_RES_UNITS: 0 + STRIDES: [] + UP_KERNEL_SIZE: + - 3 + VNET_MONAI: + ACTIVATION: + - elu + - inplace: true + DROPOUT_DIM: 3 + DROPOUT_PROB: 0.5 + USE_MAGNITUDE: true + TASKS: + - sem_seg + TB_RECON: + CHANNELS: + - 16 + - 32 + - 64 + DEC_NUM_CONV_BLOCKS: + - 2 + - 3 + ENC_NUM_CONV_BLOCKS: + - 1 + - 2 + - 3 + KERNEL_SIZE: + - 5 + MULTI_CONCAT: [] + ORDER: + - conv + - relu + STRIDES: + - 2 + USE_MAGNITUDE: false + UNET: + BLOCK_ORDER: + - conv + - relu + - conv + - relu + - bn + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NUM_POOL_LAYERS: 5 + OUT_CHANNELS: 2 + UNROLLED: + CONV_BLOCK: + ACTIVATION: relu + NORM: none + NORM_AFFINE: false + ORDER: + - norm + - act + - drop + - conv + DROPOUT: 0.0 + FIX_STEP_SIZE: false + KERNEL_SIZE: + - 3 + NUM_EMAPS: 1 + NUM_FEATURES: 256 + NUM_RESBLOCKS: 2 + NUM_UNROLLED_STEPS: 5 + PADDING: '' + SHARE_WEIGHTS: false + WEIGHTS: '' +OUTPUT_DIR: results://skm-tea/neurips2021/U-Net_E1 +SEED: 9001 +SOLVER: + BASE_LR: 0.001 + CHECKPOINT_MONITOR: val_loss + CHECKPOINT_PERIOD: 1 + EARLY_STOPPING: + MIN_DELTA: 1.0e-05 + MONITOR: val_loss + PATIENCE: 12 + GAMMA: 0.9 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: StepLR + MAX_ITER: 100 + MIN_LR: 1.0e-08 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: + - 2 + TEST_BATCH_SIZE: 40 + TRAIN_BATCH_SIZE: 16 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: 1 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: -5 + QDESS_EVALUATOR: + ADDITIONAL_PATHS: [] + VAL_METRICS: + RECON: [] + SEM_SEG: + - DSC + - VOE + - CV + - DSC_scan + - VOE_scan + - CV_scan +TIME_SCALE: epoch +VERSION: 1 +VIS_PERIOD: -100 diff --git a/neurips2021/segmentation-models/U-Net_E1/model-gpu.ckpt b/neurips2021/segmentation-models/U-Net_E1/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..08c65e54b7302787b1b299ac4c482f03eaab357b --- /dev/null +++ b/neurips2021/segmentation-models/U-Net_E1/model-gpu.ckpt @@ -0,0 +1,3 @@ +version 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+37,MTR_006,0.02212401106953621,0.02018326334655285,0.13666824996471405,0.07447195053100586,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +38,MTR_030,0.06452371925115585,0.11490757018327713,0.18744853138923645,0.09283938258886337,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +39,MTR_034,0.0037599289789795876,0.023647304624319077,0.10954733937978745,0.034002549946308136,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +40,MTR_048,0.012613569386303425,0.0013317358680069447,0.035371363162994385,0.06897865235805511,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +41,MTR_052,0.042013175785541534,0.13044297695159912,0.00046347902389243245,0.1943112164735794,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +42,MTR_065,0.021692462265491486,0.025255048647522926,0.1030970960855484,0.04205805063247681,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +43,MTR_066,0.19131875038146973,0.1717379093170166,0.06623969972133636,0.08828575164079666,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +44,MTR_079,0.040446069091558456,0.014196100644767284,0.06968682259321213,0.1170908510684967,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +45,MTR_080,0.020318692550063133,0.08360917121171951,0.028399288654327393,0.037420500069856644,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +46,MTR_096,0.042988136410713196,0.0174123365432024,0.018064817413687706,0.03360949829220772,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +47,MTR_099,0.01154419593513012,0.010871350765228271,0.05901400372385979,0.08734744787216187,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +48,MTR_120,0.09017810970544815,0.2026098370552063,0.16271162033081055,0.08939206600189209,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +49,MTR_126,0.1400926560163498,0.12723982334136963,0.11172673851251602,0.08117066323757172,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +50,MTR_144,0.006705067120492458,0.0038107815198600292,0.031088892370462418,0.11763302981853485,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +51,MTR_156,0.04672016575932503,0.12769551575183868,0.08999978005886078,0.1088155135512352,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +52,MTR_158,0.03880405053496361,0.042705386877059937,0.34179502725601196,0.023312876001000404,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +53,MTR_173,0.05873686447739601,0.13740837574005127,0.03394399210810661,0.060186393558979034,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +54,MTR_176,0.0947176143527031,0.04500226676464081,0.02212589606642723,0.223920539021492,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +55,MTR_178,0.019901027902960777,0.10586608946323395,0.008753295056521893,0.02059784345328808,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +56,MTR_188,0.0837240070104599,0.04242175072431564,0.032873932272195816,0.07694055140018463,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +57,MTR_196,0.029745565727353096,0.0470355749130249,0.0502554327249527,0.03532540425658226,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +58,MTR_198,0.04520373418927193,0.08388325572013855,0.04083763435482979,0.0554143562912941,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +59,MTR_199,0.0060273041017353535,0.03922855854034424,0.060118772089481354,0.06070864573121071,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +60,MTR_218,0.08684471249580383,0.11849534511566162,0.027363566681742668,0.12462389469146729,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +61,MTR_219,0.018180225044488907,0.0011989225167781115,0.0018390852492302656,0.00932182464748621,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +62,MTR_221,0.07061450183391571,0.1491185575723648,0.15361644327640533,0.22058671712875366,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +63,MTR_223,0.015497132204473019,0.009070714935660362,0.023943426087498665,0.03026888519525528,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +64,MTR_224,0.04971715807914734,0.11674898117780685,0.06208270415663719,0.029340960085392,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +65,MTR_227,0.08111622929573059,0.12192036211490631,0.06198796629905701,0.13896849751472473,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +66,MTR_235,0.046707212924957275,0.09058228880167007,0.04264659062027931,0.006734809372574091,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +67,MTR_237,0.01588555984199047,0.02011517807841301,0.06486650556325912,0.04417978972196579,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +68,MTR_240,0.05210087448358536,0.14386412501335144,0.050306908786296844,0.1548478752374649,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +69,MTR_241,0.4958447217941284,0.2027941197156906,0.14827831089496613,0.16675622761249542,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +70,MTR_244,0.1041666641831398,0.06876658648252487,0.005783123429864645,0.0677657350897789,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +71,MTR_248,0.12214773148298264,0.013198877684772015,0.020023353397846222,0.006726089399307966,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +72,MTR_005,0.9295270442962646,0.9068014621734619,0.8367829918861389,0.875062882900238,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +73,MTR_006,0.8888997435569763,0.8847068548202515,0.8610689043998718,0.8615976572036743,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +74,MTR_030,0.9045374989509583,0.8145965933799744,0.6065145134925842,0.7856277227401733,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +75,MTR_034,0.9192677736282349,0.897968053817749,0.860870361328125,0.8856141567230225,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +76,MTR_048,0.9246695637702942,0.9243132472038269,0.8352878093719482,0.8755961656570435,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +77,MTR_052,0.43140363693237305,0.8031963109970093,0.7129420042037964,0.7586319446563721,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +78,MTR_065,0.8857285380363464,0.8883572220802307,0.8360772132873535,0.8676100373268127,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +79,MTR_066,0.8067388534545898,0.8151824474334717,0.8206250667572021,0.8442268371582031,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +80,MTR_079,0.8841174244880676,0.8810343146324158,0.8707148432731628,0.8665427565574646,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +81,MTR_080,0.9182842969894409,0.8632466793060303,0.9022944569587708,0.8920270204544067,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +82,MTR_096,0.8716283440589905,0.9237892031669617,0.8822237849235535,0.9134107828140259,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +83,MTR_099,0.902835488319397,0.8877477645874023,0.8645874261856079,0.859222412109375,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +84,MTR_120,0.8659950494766235,0.8221021294593811,0.7985163927078247,0.8825384974479675,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +85,MTR_126,0.8820981979370117,0.8746423721313477,0.8613418340682983,0.882002592086792,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +86,MTR_144,0.9291123151779175,0.9237654209136963,0.8815479278564453,0.8710201382637024,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +87,MTR_156,0.8693913817405701,0.8675782084465027,0.8599072694778442,0.8669359683990479,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +88,MTR_158,0.8793877363204956,0.8913748860359192,0.69092857837677,0.8361682295799255,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +89,MTR_173,0.8771227598190308,0.8365439772605896,0.8649854063987732,0.8563120365142822,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +90,MTR_176,0.8820719718933105,0.8883743286132812,0.826951265335083,0.8319445848464966,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +91,MTR_178,0.9180708527565002,0.8842431902885437,0.8715128302574158,0.8800150752067566,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +92,MTR_188,0.8936734199523926,0.8871076107025146,0.8631354570388794,0.881800651550293,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +93,MTR_196,0.9103290438652039,0.8934664726257324,0.8828545212745667,0.8896697759628296,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +94,MTR_198,0.8904716372489929,0.875152051448822,0.8343939781188965,0.8728156685829163,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +95,MTR_199,0.9237392544746399,0.8998357057571411,0.8950158953666687,0.8699742555618286,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +96,MTR_218,0.897334098815918,0.8632585406303406,0.854594886302948,0.7835652828216553,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +97,MTR_219,0.9338517189025879,0.9115905165672302,0.8872124552726746,0.8981868028640747,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +98,MTR_221,0.7911089062690735,0.8472604155540466,0.8293736577033997,0.7945564985275269,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +99,MTR_223,0.943804144859314,0.9242792129516602,0.9032800793647766,0.9062101244926453,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +100,MTR_224,0.8802997469902039,0.8767812848091125,0.8152319192886353,0.8262422680854797,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +101,MTR_227,0.9233275651931763,0.8732049465179443,0.8818652629852295,0.8458190560340881,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +102,MTR_235,0.8710024952888489,0.8702384233474731,0.8551830053329468,0.88474041223526,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +103,MTR_237,0.926277220249176,0.880925178527832,0.8253725171089172,0.8522472381591797,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +104,MTR_240,0.8666337132453918,0.858770489692688,0.8514552116394043,0.8412485122680664,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +105,MTR_241,0.5766523480415344,0.785715639591217,0.7521868348121643,0.8233054876327515,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +106,MTR_244,0.8690298795700073,0.8638811707496643,0.9021347165107727,0.8835206627845764,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +107,MTR_248,0.8672751784324646,0.9127659201622009,0.8773717284202576,0.8859477043151855,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +108,MTR_005,0.13166695833206177,0.17050617933273315,0.2806304097175598,0.22212284803390503,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +109,MTR_006,0.19998246431350708,0.20674943923950195,0.2439674735069275,0.2431519627571106,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +110,MTR_030,0.17428714036941528,0.31281065940856934,0.564750075340271,0.3530586361885071,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +111,MTR_034,0.14940285682678223,0.18517053127288818,0.2442736029624939,0.20528948307037354,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +112,MTR_048,0.14010661840438843,0.14072269201278687,0.28283756971359253,0.22127968072891235,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +113,MTR_052,0.7249747514724731,0.3288821578025818,0.4460684657096863,0.38887423276901245,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +114,MTR_065,0.2051052451133728,0.200860857963562,0.28167301416397095,0.2338239550590515,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +115,MTR_066,0.3239209055900574,0.31197643280029297,0.3041864037513733,0.2695566415786743,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +116,MTR_079,0.20769673585891724,0.2126350998878479,0.22896820306777954,0.23548704385757446,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +117,MTR_080,0.15108537673950195,0.24060332775115967,0.1780177354812622,0.19490182399749756,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +118,MTR_096,0.22753435373306274,0.14162802696228027,0.2107330560684204,0.15937799215316772,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +119,MTR_099,0.17711925506591797,0.20184671878814697,0.23852580785751343,0.24680989980697632,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +120,MTR_120,0.236339271068573,0.30205994844436646,0.3353913426399231,0.21022921800613403,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +121,MTR_126,0.2109341025352478,0.22278714179992676,0.24354666471481323,0.21108704805374146,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +122,MTR_144,0.13239049911499023,0.14166903495788574,0.211814284324646,0.2284892201423645,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +123,MTR_156,0.2310413122177124,0.23387360572814941,0.24575674533843994,0.23487472534179688,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +124,MTR_158,0.21526139974594116,0.19596362113952637,0.4721994400024414,0.28153854608535767,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +125,MTR_173,0.2188614010810852,0.2809836268424988,0.23790806531906128,0.2512713074684143,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +126,MTR_176,0.21097612380981445,0.20083320140838623,0.295041024684906,0.2877524495124817,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +127,MTR_178,0.15145015716552734,0.20749467611312866,0.22771579027175903,0.21426165103912354,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +128,MTR_188,0.19221556186676025,0.20288103818893433,0.240775465965271,0.21141016483306885,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +129,MTR_196,0.1645835041999817,0.1925535798072815,0.20972281694412231,0.1987341046333313,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +130,MTR_198,0.197432279586792,0.22198188304901123,0.28415435552597046,0.2256672978401184,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +131,MTR_199,0.1417142152786255,0.18208974599838257,0.19001924991607666,0.23012882471084595,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +132,MTR_218,0.18621397018432617,0.24058502912521362,0.2538928985595703,0.3558509945869446,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +133,MTR_219,0.1240883469581604,0.16245627403259277,0.20271176099777222,0.18481028079986572,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +134,MTR_221,0.34559130668640137,0.2650027871131897,0.2915128469467163,0.34085965156555176,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +135,MTR_223,0.10641175508499146,0.1407814621925354,0.17638039588928223,0.171495258808136,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +136,MTR_224,0.21380770206451416,0.21940290927886963,0.3119059205055237,0.2960708737373352,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +137,MTR_227,0.1424248218536377,0.2250543236732483,0.21130681037902832,0.2671694755554199,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +138,MTR_235,0.22851693630218506,0.22971493005752563,0.25299590826034546,0.206695556640625,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +139,MTR_237,0.1373218297958374,0.21280944347381592,0.2973325848579407,0.2574644684791565,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +140,MTR_240,0.2353454828262329,0.2475041151046753,0.2586660385131836,0.27400439977645874,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +141,MTR_241,0.5948618650436401,0.3529393672943115,0.3971959948539734,0.300323486328125,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +142,MTR_244,0.23160666227340698,0.23962080478668213,0.17828291654586792,0.20865470170974731,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +143,MTR_248,0.23434609174728394,0.16046977043151855,0.2184664011001587,0.2047520875930786,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, 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+145,MTR_006,36.34393420610943,41.94742243818081,23.5937001128338,34.62910223168812,t2_seg_gt,29.310650294449317,27.586141678129298,37.67713292033475,37.75029408372737,29.600368324125235,41.63888488344148,47.35857477968681,43.934851771511205,45.68953017194174,53.70395076201641,47.6200243902439,52.159889934598816,38.28235590709986,35.55843469063987,41.6666957612787,45.66201081583997,38.349846044528654,46.910950801326884,30.28020847434683,29.351463020144095,41.541140308582456,43.08257596496031,36.23702097812919,36.462791521939465,33.87932981927711,25.366933661942905,31.79944925255704,31.45607075850978,22.80644805297178,29.89075098814229,42.72100371747212,34.75651860744298,40.72764650283555,51.52426205903527,44.952625250501,44.369369074861055,37.836751247920134,29.695871153420413,35.85528123658222,40.02104777999693,32.55756639901174,36.35268456375839,23.5937001128338,22.361268299087506,24.169137164750953 +146,MTR_030,35.421287998594266,41.528312302839126,22.151798252457482,35.78327354039709,t2_seg_gt,35.95078609221466,26.723869413968426,38.6321863940228,44.19220380029806,29.61854803010181,35.54636120780377,45.791170327691745,35.108798283261805,47.979344294575164,51.42207780235988,41.098307379823964,45.63493812375249,40.99182220582811,30.910637727759916,43.3034582841401,47.828029285019234,35.30262599173091,40.62570452261306,30.86565774155995,30.994315904536343,38.9828735826705,39.72488731487444,35.2012474012474,35.6293308264251,27.418396458435804,31.728917503273678,37.076013513513516,32.38985781990522,28.958905800082274,30.99000221190002,36.115977443609026,42.756667506932196,45.67159699892819,35.93849114703619,43.50745109321059,39.38648789377766,31.24351060898319,36.84613405076617,41.04943022295623,33.989606107929895,35.02399856080595,34.84684286055967,21.616360601001666,21.19825918762089,22.40372056719136 +147,MTR_034,29.199275056306305,32.102552435767805,19.70699424961129,27.82992052012347,t2_seg_gt,29.005250438039994,22.77817915547962,28.699740905793345,27.826941704035878,24.536760409057703,27.687192216044483,39.953305263157894,36.90799894403379,36.57349391402599,37.630887146506915,36.384399117971334,32.64385167464115,34.49165008741786,29.56646372399797,32.65461345990146,32.772506666666665,30.443618873110395,30.21117093850502,23.91694113006607,22.877428968805884,34.360082702797826,34.49708623653968,29.43592318779932,28.95825638111474,25.689172510518937,23.21234684260132,28.396021903688194,23.452701181767022,22.542881688757976,24.268974250738708,35.09712837837838,31.510090898630768,32.44300603400987,34.58899488926747,29.644896542146924,30.819891142998515,29.95699616858238,27.16605811403509,30.291291317006337,28.48969024503005,25.874799661215715,27.28478359908884,19.70699424961129,20.6979303048337,19.1169042368877 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+149,MTR_052,33.87351437699681,34.093083843622324,20.153348041492492,26.239667343290815,t2_seg_gt,20.93252777236406,27.73556370302475,31.609859658532226,29.17519330579388,26.335491651205942,33.2691675598428,31.440317059989194,36.65641199008339,41.3093446714114,40.42150015497469,35.28056059689453,40.215601816805446,26.393800917688925,32.2329848880809,36.37992272727272,34.870771645304735,30.621020585677,36.64241655638877,66.28392857142858,29.036708860759497,78.52272727272728,36.750870406189556,69.73589743589744,32.95697903014417,20.446993865030674,21.766024555461474,21.261421695668272,25.56347283406755,23.8194609297725,27.204251386321626,27.33642857142857,29.077104050448703,28.442491007194246,31.75909482758621,29.10970012239902,34.124598930481284,23.63023102310231,25.173233864586866,24.50420304568528,28.413164155432195,26.183862144420132,30.231791005978685,20.153348041492492,19.714336352894836,20.33689005982765 +150,MTR_065,30.85599448067122,29.008563878482526,20.848785017187563,25.43286496003867,t2_seg_gt,25.03344769148101,19.86665811746602,26.10192074180373,22.849722756591603,21.06336616847826,28.474290756074385,34.51285146942018,26.355306574735284,31.19345356276197,31.90205309000415,29.903501129396584,35.12377996433995,29.868380223207954,23.177010050251255,28.648670344827583,27.574397965257862,25.59755895738519,31.84562648545509,24.499537483137406,23.58698549941457,38.87241224928366,35.5082057961576,31.949470899470903,29.848595373498096,20.47570325427468,18.83280182232346,25.613164996144953,19.595468148781528,20.400243871133362,23.03316719528772,30.850919181408255,29.40538740043447,34.06308694675354,29.536863599237684,30.971224609949957,29.164648117839604,25.071147641726842,23.76315256297697,29.515084552339452,23.967967908034964,25.324429208090503,25.81509900990099,20.848785017187563,20.274288346830904,21.243714371437143 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b/neurips2021/segmentation-models/U-Net_E2/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..b45a4978361093c81f425c1dc5a9bc1df5c913ff --- /dev/null +++ b/neurips2021/segmentation-models/U-Net_E2/config.yaml @@ -0,0 +1,251 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 6 +AUG_TRAIN: + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 6 + CALIBRATION_SIZE: 24 + CENTER_FRACTIONS: [] + NAME: PoissonDiskMaskFunc + PRECOMPUTE: + NUM: -1 + SEED: -1 + USE_NOISE: false +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: [] + DROP_LAST: true + FILTER: + BY: [] + GROUP_SAMPLER: + AS_BATCH_SAMPLER: true + BATCH_BY: + - inplane_shape + NUM_WORKERS: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: '' + SUBSAMPLE_TRAIN: + NUM_TOTAL: -1 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + QDESS: + DATASET_TYPE: qDESSImageDataset + ECHO_KIND: echo2 + KWARGS: + - orientation + - sagittal + TEST: + - stanford_qdess_v0.1.0_test + TRAIN: + - stanford_qdess_v0.1.0_train + VAL: + - stanford_qdess_v0.1.0_val +DESCRIPTION: + BRIEF: UNet segmentation following parameters used in MedSegPy - input=echo2, 100 + epochs, 0.001 lr w/ 0.9x decay every (2,) epochs, early stopping- T=12, delta=1e-05, + bsz=16, qdess args=('orientation', 'sagittal') + ENTITY_NAME: ss_recon + EXP_NAME: seg-baseline/unet-medsegpy-echo2 + PROJECT_NAME: ss_recon + TAGS: + - seg-baseline + - baseline + - unet-medsegpy + - neurips +MODEL: + CASCADE: + ITFS: + PERIOD: 0 + RECON_MODEL_NAME: '' + SEG_MODEL_NAME: '' + SEG_NORMALIZE: '' + USE_MAGNITUDE: false + ZERO_FILL: false + CS: + MAX_ITER: 200 + REGULARIZATION: 0.005 + DENOISING: + META_ARCHITECTURE: GeneralizedUnrolledCNN + NOISE: + STD_DEV: + - 1 + USE_FULLY_SAMPLED_TARGET: true + USE_FULLY_SAMPLED_TARGET_EVAL: null + DEVICE: cpu + META_ARCHITECTURE: GeneralizedUNet + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + PARAMETERS: + INIT: + - initializers: (("kaiming_normal_", {"nonlinearity":"relu"}), "zeros_") + kind: conv + patterns: (".*weight", ".*bias") + - initializers: ("ones_", "zeros_") + kind: norm + patterns: (".*weight", ".*bias") + - initializers: ("xavier_uniform_",) + patterns: ("output_block\.weight",) + USE_COMPLEX_WEIGHTS: false + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: true + WEIGHT: 1.0 + SEG: + ACTIVATION: sigmoid + CLASSES: + - pc + - fc + - men + - tc + INCLUDE_BACKGROUND: false + IN_CHANNELS: null + LOSS_NAME: FlattenedDiceLoss + LOSS_WEIGHT: 1.0 + MODEL: + DYNUNET_MONAI: + DEEP_SUPERVISION: false + DEEP_SUPR_NUM: 1 + KERNEL_SIZE: + - 3 + NORM_NAME: instance + RES_BLOCK: false + STRIDES: + - 1 + UPSAMPLE_KERNEL_SIZE: + - 2 + UNET_MONAI: + ACTIVATION: + - prelu + - {} + CHANNELS: [] + DROPOUT: 0.0 + KERNEL_SIZE: + - 3 + NORM: + - instance + - {} + NUM_RES_UNITS: 0 + STRIDES: [] + UP_KERNEL_SIZE: + - 3 + VNET_MONAI: + ACTIVATION: + - elu + - inplace: true + DROPOUT_DIM: 3 + DROPOUT_PROB: 0.5 + USE_MAGNITUDE: true + TASKS: + - sem_seg + TB_RECON: + CHANNELS: + - 16 + - 32 + - 64 + DEC_NUM_CONV_BLOCKS: + - 2 + - 3 + ENC_NUM_CONV_BLOCKS: + - 1 + - 2 + - 3 + KERNEL_SIZE: + - 5 + MULTI_CONCAT: [] + ORDER: + - conv + - relu + STRIDES: + - 2 + USE_MAGNITUDE: false + UNET: + BLOCK_ORDER: + - conv + - relu + - conv + - relu + - bn + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NUM_POOL_LAYERS: 5 + OUT_CHANNELS: 2 + UNROLLED: + CONV_BLOCK: + ACTIVATION: relu + NORM: none + NORM_AFFINE: false + ORDER: + - norm + - act + - drop + - conv + DROPOUT: 0.0 + FIX_STEP_SIZE: false + KERNEL_SIZE: + - 3 + NUM_EMAPS: 1 + NUM_FEATURES: 256 + NUM_RESBLOCKS: 2 + NUM_UNROLLED_STEPS: 5 + PADDING: '' + SHARE_WEIGHTS: false + WEIGHTS: '' +OUTPUT_DIR: results://skm-tea/neurips2021/U-Net_E2 +SEED: 9001 +SOLVER: + BASE_LR: 0.001 + CHECKPOINT_MONITOR: val_loss + CHECKPOINT_PERIOD: 1 + EARLY_STOPPING: + MIN_DELTA: 1.0e-05 + MONITOR: val_loss + PATIENCE: 12 + GAMMA: 0.9 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: StepLR + MAX_ITER: 100 + MIN_LR: 1.0e-08 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: + - 2 + TEST_BATCH_SIZE: 40 + TRAIN_BATCH_SIZE: 16 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: 1 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: -5 + QDESS_EVALUATOR: + ADDITIONAL_PATHS: [] + VAL_METRICS: + RECON: [] + SEM_SEG: + - DSC + - VOE + - CV + - DSC_scan + - VOE_scan + - CV_scan +TIME_SCALE: epoch +VERSION: 1 +VIS_PERIOD: -100 diff --git a/neurips2021/segmentation-models/U-Net_E2/model-gpu.ckpt b/neurips2021/segmentation-models/U-Net_E2/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..c770a099776f6a7c4f0cdbca007ebe4122f54ad3 --- /dev/null +++ b/neurips2021/segmentation-models/U-Net_E2/model-gpu.ckpt @@ -0,0 +1,3 @@ +version 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+49,MTR_126,0.09787901490926743,0.09300176799297333,0.09108856320381165,0.05051295459270477,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +50,MTR_144,0.008857959881424904,0.039339520037174225,0.04227210953831673,0.06460422277450562,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +51,MTR_156,0.04117966070771217,0.11446963995695114,0.17020410299301147,0.0990329459309578,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +52,MTR_158,0.06513401120901108,0.06262306123971939,0.25950291752815247,0.025113428011536598,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +53,MTR_173,0.007667133584618568,0.05097329616546631,0.12734054028987885,0.020509174093604088,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +54,MTR_176,0.07533715665340424,0.08864696323871613,0.031257957220077515,0.24639387428760529,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +55,MTR_178,0.04040101170539856,0.036809343844652176,0.027403904125094414,0.015496300533413887,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +56,MTR_188,0.07348722964525223,0.09245070070028305,0.04738210141658783,0.1402563601732254,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +57,MTR_196,0.018248390406370163,0.03059099055826664,0.019095528870821,0.06074057146906853,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +58,MTR_198,0.04281500726938248,0.10717059671878815,0.0472584068775177,0.1536429524421692,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +59,MTR_199,0.018288420513272285,0.003005440579727292,0.09579751640558243,0.001788345747627318,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +60,MTR_218,0.12044703960418701,0.11564849317073822,0.009105381555855274,0.08667933940887451,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +61,MTR_219,0.004295910242944956,0.04250854253768921,0.01925058662891388,0.043719347566366196,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +62,MTR_221,0.13285255432128906,0.12867631018161774,0.1207108125090599,0.30282407999038696,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +63,MTR_223,0.04389471933245659,0.004932434763759375,0.018808087334036827,0.041240591555833817,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +64,MTR_224,0.02943491004407406,0.11152051389217377,0.020325174555182457,0.04132413864135742,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +65,MTR_227,0.06433049589395523,0.13083888590335846,0.04690801724791527,0.1123124212026596,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +66,MTR_235,0.03250668942928314,0.09230971336364746,0.06372526288032532,0.026682032272219658,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +67,MTR_237,0.010348253883421421,0.006446915213018656,0.06281182169914246,0.04148738086223602,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +68,MTR_240,0.023257162421941757,0.1631159782409668,0.04538200423121452,0.20076364278793335,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +69,MTR_241,0.29470938444137573,0.22278042137622833,0.17617283761501312,0.2685149013996124,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +70,MTR_244,0.14244432747364044,0.10015890002250671,0.01813376322388649,0.01314563862979412,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +71,MTR_248,0.0635717585682869,0.018929993733763695,0.051839832216501236,0.015103014186024666,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +72,MTR_005,0.9074127078056335,0.89936763048172,0.829882800579071,0.8738064169883728,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +73,MTR_006,0.8779573440551758,0.8616470098495483,0.8175961375236511,0.8276863694190979,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +74,MTR_030,0.8702338337898254,0.8147145509719849,0.6660059690475464,0.7155471444129944,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +75,MTR_034,0.8490073680877686,0.8890221118927002,0.8619851469993591,0.8721633553504944,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +76,MTR_048,0.9312244653701782,0.910110354423523,0.7987940311431885,0.867448627948761,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +77,MTR_052,0.32280129194259644,0.8092705011367798,0.7566059827804565,0.6694784164428711,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +78,MTR_065,0.8794987797737122,0.8542212247848511,0.8265916109085083,0.8197543621063232,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +79,MTR_066,0.8377010822296143,0.8014096021652222,0.7442533373832703,0.7768973708152771,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +80,MTR_079,0.836719274520874,0.8435468077659607,0.8193774819374084,0.8524438738822937,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +81,MTR_080,0.8772074580192566,0.8556467890739441,0.8907279372215271,0.8617706298828125,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +82,MTR_096,0.8902410268783569,0.9000743627548218,0.8389107584953308,0.8942571878433228,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +83,MTR_099,0.8892515301704407,0.8744412064552307,0.8579866886138916,0.8391996622085571,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +84,MTR_120,0.8785565495491028,0.813485324382782,0.7687046527862549,0.8424336910247803,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +85,MTR_126,0.8893985748291016,0.8736304044723511,0.8500651121139526,0.8499869704246521,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +86,MTR_144,0.9197397828102112,0.905643880367279,0.8566105961799622,0.8575153946876526,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +87,MTR_156,0.8739175200462341,0.8618000149726868,0.8145204186439514,0.8519650101661682,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +88,MTR_158,0.9017723798751831,0.8893325924873352,0.7704703211784363,0.8175163269042969,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +89,MTR_173,0.8407629728317261,0.8296810984611511,0.7932701110839844,0.7920462489128113,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +90,MTR_176,0.8331130146980286,0.8768303394317627,0.798613429069519,0.8092402219772339,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +91,MTR_178,0.8853055238723755,0.8687329292297363,0.8333504796028137,0.8420011401176453,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +92,MTR_188,0.8628362417221069,0.8493354320526123,0.8477913737297058,0.8179817199707031,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +93,MTR_196,0.8909674882888794,0.8795653581619263,0.8803490400314331,0.8581398129463196,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +94,MTR_198,0.8885155320167542,0.8580005764961243,0.7845185399055481,0.8247603178024292,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +95,MTR_199,0.910291850566864,0.8803904056549072,0.8723211884498596,0.8256436586380005,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +96,MTR_218,0.8624261617660522,0.8378828763961792,0.8042147755622864,0.7935042381286621,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +97,MTR_219,0.9249133467674255,0.8727426528930664,0.8537716269493103,0.8633641600608826,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +98,MTR_221,0.8147806525230408,0.8263961672782898,0.825887143611908,0.7331605553627014,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +99,MTR_223,0.9139251112937927,0.9021177291870117,0.8657800555229187,0.8802691698074341,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +100,MTR_224,0.884033203125,0.8659017086029053,0.7909799218177795,0.8227153420448303,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +101,MTR_227,0.9034095406532288,0.854703426361084,0.8736887574195862,0.8187759518623352,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +102,MTR_235,0.8562478423118591,0.8541876673698425,0.8327094912528992,0.858645498752594,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +103,MTR_237,0.9211888313293457,0.8745014667510986,0.8166402578353882,0.8189830780029297,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +104,MTR_240,0.8116084337234497,0.8482944369316101,0.8446165919303894,0.7801195383071899,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +105,MTR_241,0.5067617893218994,0.7693167924880981,0.7538635730743408,0.7393350005149841,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +106,MTR_244,0.8444444537162781,0.832025945186615,0.8905701041221619,0.8351953625679016,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +107,MTR_248,0.8864706158638,0.8803346157073975,0.8536321520805359,0.8433730006217957,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +108,MTR_005,0.16948264837265015,0.18286287784576416,0.2907695174217224,0.22410643100738525,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +109,MTR_006,0.2175365686416626,0.24307572841644287,0.3085305690765381,0.2939719557762146,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +110,MTR_030,0.22972214221954346,0.31264275312423706,0.5007429122924805,0.44291675090789795,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +111,MTR_034,0.26236945390701294,0.19978421926498413,0.2425537109375,0.2266935110092163,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +112,MTR_048,0.12869971990585327,0.16495180130004883,0.33500659465789795,0.23407572507858276,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +113,MTR_052,0.8075354099273682,0.32035738229751587,0.391499400138855,0.4968301057815552,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +114,MTR_065,0.2150844931602478,0.2544623017311096,0.29556357860565186,0.30543750524520874,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +115,MTR_066,0.279272198677063,0.33137327432632446,0.4073220491409302,0.36481428146362305,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +116,MTR_079,0.28072458505630493,0.2705742120742798,0.3059784770011902,0.2571658492088318,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +117,MTR_080,0.2187269926071167,0.2522878050804138,0.19701582193374634,0.24288487434387207,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +118,MTR_096,0.19780689477920532,0.18169522285461426,0.27747952938079834,0.19126111268997192,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +119,MTR_099,0.1994122862815857,0.2231048345565796,0.2487068772315979,0.27705079317092896,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +120,MTR_120,0.2165842056274414,0.31439077854156494,0.3756943345069885,0.27223724126815796,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +121,MTR_126,0.1991739273071289,0.2243838906288147,0.26077115535736084,0.2608892321586609,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +122,MTR_144,0.1485942006111145,0.172441303730011,0.25081467628479004,0.2494293451309204,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +123,MTR_156,0.22393113374710083,0.242839515209198,0.31291908025741577,0.25789278745651245,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +124,MTR_158,0.17888391017913818,0.19928091764450073,0.3733617663383484,0.30864477157592773,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +125,MTR_173,0.2747272849082947,0.2910640835762024,0.3426283001899719,0.34430742263793945,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +126,MTR_176,0.28603798151016235,0.21932512521743774,0.3352569341659546,0.3204001188278198,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +127,MTR_178,0.20578640699386597,0.2320709228515625,0.285689115524292,0.2728825807571411,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +128,MTR_188,0.2412382960319519,0.2618739604949951,0.26420319080352783,0.3079787492752075,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +129,MTR_196,0.19662630558013916,0.21497845649719238,0.21372896432876587,0.24847203493118286,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +130,MTR_198,0.2006046175956726,0.24868559837341309,0.3545615077018738,0.2982194423675537,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +131,MTR_199,0.16464614868164062,0.21366310119628906,0.22644537687301636,0.2969394326210022,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +132,MTR_218,0.2418723702430725,0.2790031433105469,0.32745885848999023,0.3423066735267639,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +133,MTR_219,0.139684796333313,0.22578227519989014,0.25514698028564453,0.24042147397994995,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +134,MTR_221,0.31254857778549194,0.2958473563194275,0.29658621549606323,0.4212679862976074,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +135,MTR_223,0.1585063934326172,0.17831099033355713,0.23667359352111816,0.21385645866394043,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +136,MTR_224,0.20783203840255737,0.23648446798324585,0.3457677960395813,0.3011755347251892,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +137,MTR_227,0.17616504430770874,0.25372743606567383,0.2242918610572815,0.30684107542037964,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +138,MTR_235,0.2513694167137146,0.2545135021209717,0.28663045167922974,0.24769604206085205,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +139,MTR_237,0.14610737562179565,0.2230096459388733,0.3098968267440796,0.30654412508010864,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +140,MTR_240,0.31705302000045776,0.26344501972198486,0.2689729332923889,0.36049509048461914,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +141,MTR_241,0.6606289744377136,0.3748864531517029,0.39503931999206543,0.4135357141494751,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +142,MTR_244,0.26923078298568726,0.28763318061828613,0.19727236032485962,0.28297388553619385,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +143,MTR_248,0.20390909910202026,0.21375209093093872,0.2553592920303345,0.2708340883255005,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, 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b/neurips2021/segmentation-models/U-Net_RSS/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..7948b97b621a49f65bb9568a7a211a15211f6c49 --- /dev/null +++ b/neurips2021/segmentation-models/U-Net_RSS/config.yaml @@ -0,0 +1,250 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 6 +AUG_TRAIN: + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 6 + CALIBRATION_SIZE: 24 + CENTER_FRACTIONS: [] + NAME: PoissonDiskMaskFunc + PRECOMPUTE: + NUM: -1 + SEED: -1 + USE_NOISE: false +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: [] + DROP_LAST: true + FILTER: + BY: [] + GROUP_SAMPLER: + AS_BATCH_SAMPLER: true + BATCH_BY: + - inplane_shape + NUM_WORKERS: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: '' + SUBSAMPLE_TRAIN: + NUM_TOTAL: -1 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + QDESS: + DATASET_TYPE: qDESSImageDataset + ECHO_KIND: rms + KWARGS: + - orientation + - sagittal + TEST: + - stanford_qdess_v0.1.0_test + TRAIN: + - stanford_qdess_v0.1.0_train + VAL: + - stanford_qdess_v0.1.0_val +DESCRIPTION: + BRIEF: UNet segmentation following parameters used in MedSegPy - 100 epochs, 0.001 + lr w/ 0.9x decay every (2,) epochs, early stopping- T=12, delta=1e-05, bsz=16 + ENTITY_NAME: ss_recon + EXP_NAME: seg-baseline/unet-medsegpy-rms + PROJECT_NAME: ss_recon + TAGS: + - seg-baseline + - baseline + - unet-medsegpy + - neurips +MODEL: + CASCADE: + ITFS: + PERIOD: 0 + RECON_MODEL_NAME: '' + SEG_MODEL_NAME: '' + SEG_NORMALIZE: '' + USE_MAGNITUDE: false + ZERO_FILL: false + CS: + MAX_ITER: 200 + REGULARIZATION: 0.005 + DENOISING: + META_ARCHITECTURE: GeneralizedUnrolledCNN + NOISE: + STD_DEV: + - 1 + USE_FULLY_SAMPLED_TARGET: true + USE_FULLY_SAMPLED_TARGET_EVAL: null + DEVICE: cpu + META_ARCHITECTURE: GeneralizedUNet + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + PARAMETERS: + INIT: + - initializers: (("kaiming_normal_", {"nonlinearity":"relu"}), "zeros_") + kind: conv + patterns: (".*weight", ".*bias") + - initializers: ("ones_", "zeros_") + kind: norm + patterns: (".*weight", ".*bias") + - initializers: ("xavier_uniform_",) + patterns: ("output_block\.weight",) + USE_COMPLEX_WEIGHTS: false + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: true + WEIGHT: 1.0 + SEG: + ACTIVATION: sigmoid + CLASSES: + - pc + - fc + - men + - tc + INCLUDE_BACKGROUND: false + IN_CHANNELS: null + LOSS_NAME: FlattenedDiceLoss + LOSS_WEIGHT: 1.0 + MODEL: + DYNUNET_MONAI: + DEEP_SUPERVISION: false + DEEP_SUPR_NUM: 1 + KERNEL_SIZE: + - 3 + NORM_NAME: instance + RES_BLOCK: false + STRIDES: + - 1 + UPSAMPLE_KERNEL_SIZE: + - 2 + UNET_MONAI: + ACTIVATION: + - prelu + - {} + CHANNELS: [] + DROPOUT: 0.0 + KERNEL_SIZE: + - 3 + NORM: + - instance + - {} + NUM_RES_UNITS: 0 + STRIDES: [] + UP_KERNEL_SIZE: + - 3 + VNET_MONAI: + ACTIVATION: + - elu + - inplace: true + DROPOUT_DIM: 3 + DROPOUT_PROB: 0.5 + USE_MAGNITUDE: true + TASKS: + - sem_seg + TB_RECON: + CHANNELS: + - 16 + - 32 + - 64 + DEC_NUM_CONV_BLOCKS: + - 2 + - 3 + ENC_NUM_CONV_BLOCKS: + - 1 + - 2 + - 3 + KERNEL_SIZE: + - 5 + MULTI_CONCAT: [] + ORDER: + - conv + - relu + STRIDES: + - 2 + USE_MAGNITUDE: false + UNET: + BLOCK_ORDER: + - conv + - relu + - conv + - relu + - bn + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NUM_POOL_LAYERS: 5 + OUT_CHANNELS: 2 + UNROLLED: + CONV_BLOCK: + ACTIVATION: relu + NORM: none + NORM_AFFINE: false + ORDER: + - norm + - act + - drop + - conv + DROPOUT: 0.0 + FIX_STEP_SIZE: false + KERNEL_SIZE: + - 3 + NUM_EMAPS: 1 + NUM_FEATURES: 256 + NUM_RESBLOCKS: 2 + NUM_UNROLLED_STEPS: 5 + PADDING: '' + SHARE_WEIGHTS: false + WEIGHTS: '' +OUTPUT_DIR: results://skm-tea/neurips2021/U-Net_RSS +SEED: 9001 +SOLVER: + BASE_LR: 0.001 + CHECKPOINT_MONITOR: val_loss + CHECKPOINT_PERIOD: 1 + EARLY_STOPPING: + MIN_DELTA: 1.0e-05 + MONITOR: val_loss + PATIENCE: 12 + GAMMA: 0.9 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: StepLR + MAX_ITER: 100 + MIN_LR: 1.0e-08 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: + - 2 + TEST_BATCH_SIZE: 40 + TRAIN_BATCH_SIZE: 16 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: 1 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: -5 + QDESS_EVALUATOR: + ADDITIONAL_PATHS: [] + VAL_METRICS: + RECON: [] + SEM_SEG: + - DSC + - VOE + - CV + - DSC_scan + - VOE_scan + - CV_scan +TIME_SCALE: epoch +VERSION: 1 +VIS_PERIOD: -100 diff --git a/neurips2021/segmentation-models/U-Net_RSS/model-gpu.ckpt b/neurips2021/segmentation-models/U-Net_RSS/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..5872ba29cae2f417037a59441383555151af7fee --- /dev/null +++ b/neurips2021/segmentation-models/U-Net_RSS/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid 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+68,MTR_240,0.010622981935739517,0.14990736544132233,0.07410570979118347,0.15206365287303925,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +69,MTR_241,0.33407050371170044,0.2150997668504715,0.17926804721355438,0.19320976734161377,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +70,MTR_244,0.1209590956568718,0.08708211034536362,0.011128231883049011,0.07773476094007492,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +71,MTR_248,0.14771033823490143,0.026691125705838203,0.02005666121840477,0.014866267330944538,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +72,MTR_005,0.9219050407409668,0.9100983142852783,0.8451095223426819,0.8791824579238892,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +73,MTR_006,0.8693647980690002,0.8791186213493347,0.8549365997314453,0.8695983290672302,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +74,MTR_030,0.89816814661026,0.8165270686149597,0.597481369972229,0.7609648704528809,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +75,MTR_034,0.9091578722000122,0.8973803520202637,0.8723298907279968,0.8833739161491394,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +76,MTR_048,0.9418829679489136,0.9268865585327148,0.8351551294326782,0.8786815404891968,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +77,MTR_052,0.3447740375995636,0.8321766257286072,0.6771296858787537,0.773423433303833,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +78,MTR_065,0.8781542778015137,0.8906920552253723,0.8507571816444397,0.8605091571807861,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +79,MTR_066,0.8486568331718445,0.8236023187637329,0.8230592608451843,0.8410748243331909,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +80,MTR_079,0.8487823009490967,0.880473256111145,0.8674097657203674,0.8688566088676453,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +81,MTR_080,0.8910571932792664,0.8615880012512207,0.9003907442092896,0.894715428352356,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +82,MTR_096,0.8709500432014465,0.924530029296875,0.881277322769165,0.9186829924583435,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +83,MTR_099,0.8950940370559692,0.8915026783943176,0.8572351932525635,0.8562943339347839,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +84,MTR_120,0.9021332263946533,0.831328809261322,0.7607322335243225,0.8898916840553284,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +85,MTR_126,0.8800268769264221,0.8718947768211365,0.8589417338371277,0.8748513460159302,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +86,MTR_144,0.9331567883491516,0.9283435940742493,0.8823719620704651,0.880225419998169,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +87,MTR_156,0.8788729906082153,0.8663358092308044,0.8575131893157959,0.8674426078796387,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +88,MTR_158,0.8719838261604309,0.8937276005744934,0.705916702747345,0.8350951075553894,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +89,MTR_173,0.8646222949028015,0.8640962839126587,0.8436346054077148,0.842669665813446,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +90,MTR_176,0.8705307245254517,0.8944916129112244,0.8233960866928101,0.8238459825515747,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +91,MTR_178,0.9086140394210815,0.8828178644180298,0.8793442845344543,0.8782248497009277,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +92,MTR_188,0.879605233669281,0.8822118043899536,0.8583341836929321,0.8743698596954346,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +93,MTR_196,0.8972801566123962,0.8942623138427734,0.8805685639381409,0.8953593969345093,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +94,MTR_198,0.9047837853431702,0.882041335105896,0.8319216370582581,0.8749909400939941,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +95,MTR_199,0.9250754714012146,0.9047987461090088,0.8999673128128052,0.8671358823776245,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +96,MTR_218,0.8873530626296997,0.8638935089111328,0.8623564839363098,0.7905629873275757,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +97,MTR_219,0.9348620176315308,0.9136488437652588,0.8834797739982605,0.8912865519523621,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +98,MTR_221,0.8108533620834351,0.8496642112731934,0.8085405230522156,0.7898183465003967,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +99,MTR_223,0.9423832297325134,0.9238612055778503,0.8983287811279297,0.9053111672401428,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +100,MTR_224,0.8791038393974304,0.8764901161193848,0.8105789422988892,0.8326277136802673,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +101,MTR_227,0.8998649716377258,0.8695251941680908,0.865810215473175,0.8430389165878296,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +102,MTR_235,0.8824625611305237,0.8734445571899414,0.8598636984825134,0.8799973130226135,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +103,MTR_237,0.9209623336791992,0.8861808776855469,0.8163763880729675,0.8449102640151978,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +104,MTR_240,0.8787201642990112,0.8570781350135803,0.8597403168678284,0.83963543176651,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +105,MTR_241,0.6786357164382935,0.7967535853385925,0.7549519538879395,0.8196799159049988,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +106,MTR_244,0.8599404096603394,0.8625174760818481,0.8929749727249146,0.8811340928077698,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +107,MTR_248,0.8711242079734802,0.9116851091384888,0.8821452856063843,0.8860065340995789,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +108,MTR_005,0.1448758840560913,0.16497212648391724,0.2682340145111084,0.21558821201324463,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +109,MTR_006,0.23108279705047607,0.21568983793258667,0.25337183475494385,0.23071742057800293,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +110,MTR_030,0.18484103679656982,0.3100585341453552,0.5739940404891968,0.3858407735824585,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +111,MTR_034,0.16655409336090088,0.18613791465759277,0.22643166780471802,0.2088901400566101,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +112,MTR_048,0.10984987020492554,0.13626408576965332,0.28303319215774536,0.2163853645324707,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +113,MTR_052,0.7917057275772095,0.28741222620010376,0.4881359934806824,0.36944544315338135,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +114,MTR_065,0.2172236442565918,0.19707411527633667,0.2597237825393677,0.24483013153076172,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +115,MTR_066,0.26289844512939453,0.29989469051361084,0.300679087638855,0.27426308393478394,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +116,MTR_079,0.2627091407775879,0.21353089809417725,0.23413628339767456,0.2318776249885559,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +117,MTR_080,0.19648051261901855,0.24316680431365967,0.18117213249206543,0.19051122665405273,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +118,MTR_096,0.2285991907119751,0.1403478980064392,0.21224689483642578,0.1504036784172058,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +119,MTR_099,0.18989121913909912,0.1957557201385498,0.24985861778259277,0.25129836797714233,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +120,MTR_120,0.17828530073165894,0.288654625415802,0.3861438035964966,0.19837403297424316,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +121,MTR_126,0.2142428159713745,0.22711575031280518,0.24724113941192627,0.22245711088180542,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +122,MTR_144,0.12531030178070068,0.13373017311096191,0.21049588918685913,0.21392619609832764,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +123,MTR_156,0.21608078479766846,0.23580920696258545,0.24943280220031738,0.2340850830078125,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +124,MTR_158,0.22697573900222778,0.1921270489692688,0.45450448989868164,0.28312164545059204,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +125,MTR_173,0.2384716272354126,0.2392873764038086,0.2704429030418396,0.2718849182128906,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +126,MTR_176,0.22925686836242676,0.19087761640548706,0.300192654132843,0.2995424270629883,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +127,MTR_178,0.16746771335601807,0.20978158712387085,0.2153306007385254,0.2171115279197693,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +128,MTR_188,0.21491485834121704,0.21075224876403809,0.24817389249801636,0.2232174277305603,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +129,MTR_196,0.18630272150039673,0.1912527084350586,0.21337878704071045,0.18945640325546265,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +130,MTR_198,0.17387652397155762,0.21102505922317505,0.287786066532135,0.2222365140914917,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +131,MTR_199,0.13940423727035522,0.1738516092300415,0.1818721890449524,0.23456323146820068,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +132,MTR_218,0.20248454809188843,0.23960161209106445,0.24198001623153687,0.34633803367614746,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +133,MTR_219,0.12230896949768066,0.15897470712661743,0.20872026681900024,0.1961073875427246,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +134,MTR_221,0.31812161207199097,0.2613772749900818,0.321386456489563,0.34735554456710815,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +135,MTR_223,0.10895580053329468,0.14150363206863403,0.18457633256912231,0.17299675941467285,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +136,MTR_224,0.21571344137191772,0.21986430883407593,0.31850963830947876,0.2867504358291626,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +137,MTR_227,0.18204128742218018,0.23083186149597168,0.23662668466567993,0.27133333683013916,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +138,MTR_235,0.21035081148147583,0.22467684745788574,0.24582374095916748,0.21429002285003662,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +139,MTR_237,0.14649659395217896,0.20437628030776978,0.3102736473083496,0.26853275299072266,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +140,MTR_240,0.21632391214370728,0.2500991225242615,0.2460135817527771,0.2764037847518921,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +141,MTR_241,0.48641282320022583,0.3378300666809082,0.3936363458633423,0.305544376373291,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +142,MTR_244,0.2457057237625122,0.24173122644424438,0.19335609674453735,0.21247565746307373,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +143,MTR_248,0.22832590341567993,0.1622965931892395,0.21085870265960693,0.20465731620788574,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +144,MTR_005,33.83510886947964,33.54902315906958,19.94319690149691,28.65864023402811,t2_seg_gt,27.017055247768543,22.75142489428204,32.36600669615178,27.764334605026928,22.502823067632853,27.59828543958979,40.6999190844989,39.48220306513411,40.59641900937082,38.90543218122113,35.52807071014934,36.24807178720222,33.85427207269647,30.945045974854573,36.456636726546904,33.35720033528918,28.985278725824802,31.92269643715613,26.25622752834885,27.789217134416546,36.04663812641652,43.99635008744582,31.380707381370826,35.98249788575382,25.464399038461536,24.31219534883721,28.88050648741598,23.318091253237696,21.79466999791797,21.45406107862248,33.26625352112676,33.52151216037448,36.767036254839844,41.45783617424242,30.272781937826185,30.209551706571574,29.05669260700389,28.710307625018224,32.59035516185115,31.607854592664722,25.851460369163952,25.47771274727847,19.94319690149691,20.812161485847742,19.418497750318984 +145,MTR_006,36.34393420610943,41.94742243818081,23.5937001128338,34.62910223168812,t2_seg_gt,29.310650294449317,27.586141678129298,37.67713292033475,37.75029408372737,29.600368324125235,41.63888488344148,47.35857477968681,43.934851771511205,45.68953017194174,53.70395076201641,47.6200243902439,52.159889934598816,38.28235590709986,35.55843469063987,41.6666957612787,45.66201081583997,38.349846044528654,46.910950801326884,30.28020847434683,29.351463020144095,41.541140308582456,43.08257596496031,36.23702097812919,36.462791521939465,33.87932981927711,25.366933661942905,31.79944925255704,31.45607075850978,22.80644805297178,29.89075098814229,42.72100371747212,34.75651860744298,40.72764650283555,51.52426205903527,44.952625250501,44.369369074861055,37.836751247920134,29.695871153420413,35.85528123658222,40.02104777999693,32.55756639901174,36.35268456375839,23.5937001128338,22.361268299087506,24.169137164750953 +146,MTR_030,35.421287998594266,41.528312302839126,22.151798252457482,35.78327354039709,t2_seg_gt,35.95078609221466,26.723869413968426,38.6321863940228,44.19220380029806,29.61854803010181,35.54636120780377,45.791170327691745,35.108798283261805,47.979344294575164,51.42207780235988,41.098307379823964,45.63493812375249,40.99182220582811,30.910637727759916,43.3034582841401,47.828029285019234,35.30262599173091,40.62570452261306,30.86565774155995,30.994315904536343,38.9828735826705,39.72488731487444,35.2012474012474,35.6293308264251,27.418396458435804,31.728917503273678,37.076013513513516,32.38985781990522,28.958905800082274,30.99000221190002,36.115977443609026,42.756667506932196,45.67159699892819,35.93849114703619,43.50745109321059,39.38648789377766,31.24351060898319,36.84613405076617,41.04943022295623,33.989606107929895,35.02399856080595,34.84684286055967,21.616360601001666,21.19825918762089,22.40372056719136 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a/neurips2021/segmentation-models/V-Net_E1-oplus-E2/config.yaml b/neurips2021/segmentation-models/V-Net_E1-oplus-E2/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..c2616152f63ff0b5ae474cc864e8f0421dccdb7b --- /dev/null +++ b/neurips2021/segmentation-models/V-Net_E1-oplus-E2/config.yaml @@ -0,0 +1,252 @@ +# DEPENDENCY: monai>=0.5.3,<=0.6.0 +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 6 +AUG_TRAIN: + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 6 + CALIBRATION_SIZE: 24 + CENTER_FRACTIONS: [] + NAME: PoissonDiskMaskFunc + PRECOMPUTE: + NUM: -1 + SEED: -1 + USE_NOISE: false +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: [] + DROP_LAST: true + FILTER: + BY: [] + GROUP_SAMPLER: + AS_BATCH_SAMPLER: true + BATCH_BY: + - inplane_shape + NUM_WORKERS: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: '' + SUBSAMPLE_TRAIN: + NUM_TOTAL: -1 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + QDESS: + DATASET_TYPE: qDESSImageDataset + ECHO_KIND: echo1-echo2-mc + KWARGS: + - orientation + - sagittal + TEST: + - stanford_qdess_v0.1.0_test + TRAIN: + - stanford_qdess_v0.1.0_train + VAL: + - stanford_qdess_v0.1.0_val +DESCRIPTION: + BRIEF: VNet segmentation following parameters used in MONAI - input=echo1-echo2-mc, + 100 epochs, 0.001 lr w/ 0.9x decay every (2,) epochs, early stopping- T=0, delta=0.0, + bsz=16, qdess args=('orientation', 'sagittal') + ENTITY_NAME: ss_recon + EXP_NAME: seg-baseline/vnet-medsegpy-echo1-echo2-mc-bsz=16 + PROJECT_NAME: ss_recon + TAGS: + - seg-baseline + - baseline + - vnet-monai + - neurips +MODEL: + CASCADE: + ITFS: + PERIOD: 0 + RECON_MODEL_NAME: '' + SEG_MODEL_NAME: '' + SEG_NORMALIZE: '' + USE_MAGNITUDE: false + ZERO_FILL: false + CS: + MAX_ITER: 200 + REGULARIZATION: 0.005 + DENOISING: + META_ARCHITECTURE: GeneralizedUnrolledCNN + NOISE: + STD_DEV: + - 1 + USE_FULLY_SAMPLED_TARGET: true + USE_FULLY_SAMPLED_TARGET_EVAL: null + DEVICE: cpu + META_ARCHITECTURE: VNetMONAI + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + PARAMETERS: + INIT: + - initializers: (("kaiming_normal_", {"nonlinearity":"relu"}), "zeros_") + kind: conv + patterns: (".*weight", ".*bias") + - initializers: ("ones_", "zeros_") + kind: norm + patterns: (".*weight", ".*bias") + - initializers: ("xavier_uniform_",) + patterns: ("output_block\.weight",) + USE_COMPLEX_WEIGHTS: false + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: true + WEIGHT: 1.0 + SEG: + ACTIVATION: sigmoid + CLASSES: + - pc + - fc + - tc + - men + INCLUDE_BACKGROUND: false + IN_CHANNELS: 2 + LOSS_NAME: FlattenedDiceLoss + LOSS_WEIGHT: 1.0 + MODEL: + DYNUNET_MONAI: + DEEP_SUPERVISION: false + DEEP_SUPR_NUM: 1 + KERNEL_SIZE: + - 3 + NORM_NAME: instance + RES_BLOCK: false + STRIDES: + - 1 + UPSAMPLE_KERNEL_SIZE: + - 2 + UNET_MONAI: + ACTIVATION: + - prelu + - {} + CHANNELS: [] + DROPOUT: 0.0 + KERNEL_SIZE: + - 3 + NORM: + - instance + - {} + NUM_RES_UNITS: 0 + STRIDES: [] + UP_KERNEL_SIZE: + - 3 + VNET_MONAI: + ACTIVATION: + - elu + - inplace: true + DROPOUT_DIM: 2 + DROPOUT_PROB: 0.0 + USE_MAGNITUDE: true + TASKS: + - sem_seg + TB_RECON: + CHANNELS: + - 16 + - 32 + - 64 + DEC_NUM_CONV_BLOCKS: + - 2 + - 3 + ENC_NUM_CONV_BLOCKS: + - 1 + - 2 + - 3 + KERNEL_SIZE: + - 5 + MULTI_CONCAT: [] + ORDER: + - conv + - relu + STRIDES: + - 2 + USE_MAGNITUDE: false + UNET: + BLOCK_ORDER: + - conv + - instancenorm + - - leakyrelu + - negative_slope: 0.2 + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + CONV_BLOCK: + ACTIVATION: relu + NORM: none + NORM_AFFINE: false + ORDER: + - norm + - act + - drop + - conv + DROPOUT: 0.0 + FIX_STEP_SIZE: false + KERNEL_SIZE: + - 3 + NUM_EMAPS: 1 + NUM_FEATURES: 256 + NUM_RESBLOCKS: 2 + NUM_UNROLLED_STEPS: 5 + PADDING: '' + SHARE_WEIGHTS: false + WEIGHTS: '' +OUTPUT_DIR: results://skm-tea/neurips2021/V-Net_E1-oplus-E2 +SEED: 9001 +SOLVER: + BASE_LR: 0.001 + CHECKPOINT_MONITOR: val_loss + CHECKPOINT_PERIOD: 1 + EARLY_STOPPING: + MIN_DELTA: 0.0 + MONITOR: val_loss + PATIENCE: 0 + GAMMA: 0.9 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: StepLR + MAX_ITER: 100 + MIN_LR: 1.0e-08 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: + - 2 + TEST_BATCH_SIZE: 40 + TRAIN_BATCH_SIZE: 16 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: 1 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: -5 + QDESS_EVALUATOR: + ADDITIONAL_PATHS: [] + VAL_METRICS: + RECON: [] + SEM_SEG: + - DSC + - VOE + - CV + - DSC_scan + - VOE_scan + - CV_scan +TIME_SCALE: epoch +VERSION: 1 +VIS_PERIOD: -100 diff --git a/neurips2021/segmentation-models/V-Net_E1-oplus-E2/model-gpu.ckpt b/neurips2021/segmentation-models/V-Net_E1-oplus-E2/model-gpu.ckpt new file mode 100644 index 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+,id,pc,fc,tc,men,Metric,fc/deep-lateral-anterior,fc/deep-lateral-central,fc/deep-lateral-posterior,fc/deep-medial-anterior,fc/deep-medial-central,fc/deep-medial-posterior,fc/superficial-lateral-anterior,fc/superficial-lateral-central,fc/superficial-lateral-posterior,fc/superficial-medial-anterior,fc/superficial-medial-central,fc/superficial-medial-posterior,fc/total-lateral-anterior,fc/total-lateral-central,fc/total-lateral-posterior,fc/total-medial-anterior,fc/total-medial-central,fc/total-medial-posterior,pc/deep-lateral,pc/deep-medial,pc/superficial-lateral,pc/superficial-medial,pc/total-lateral,pc/total-medial,tc/inferior-lateral-anterior,tc/inferior-lateral-central,tc/inferior-lateral-posterior,tc/inferior-medial-anterior,tc/inferior-medial-central,tc/inferior-medial-posterior,tc/superior-lateral-anterior,tc/superior-lateral-central,tc/superior-lateral-posterior,tc/superior-medial-anterior,tc/superior-medial-central,tc/superior-medial-posterior,tc/total-lateral-anterior,tc/total-lateral-central,tc/total-lateral-posterior,tc/total-medial-anterior,tc/total-medial-central,tc/total-medial-posterior,total,total-total-lateral,total-total-medial +0,MTR_005,0.1657014638185501,0.2289450615644455,0.33889350295066833,0.5954583287239075,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +1,MTR_006,0.35838133096694946,0.1995224803686142,0.3119296729564667,0.32594743371009827,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +2,MTR_030,0.22883936762809753,0.4033767580986023,0.6260076761245728,1.6781666278839111,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +3,MTR_034,0.19230525195598602,0.17033801972866058,0.41339218616485596,0.46243607997894287,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +4,MTR_048,0.14953933656215668,0.1480960249900818,0.19217103719711304,0.7192777991294861,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +5,MTR_052,4.042993545532227,0.454937219619751,0.5948723554611206,1.2637532949447632,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +6,MTR_065,0.21877595782279968,0.2394418716430664,0.35361069440841675,0.5475689768791199,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +7,MTR_066,0.3615928888320923,0.24216830730438232,0.32861649990081787,0.4389665722846985,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +8,MTR_079,0.19080978631973267,0.24724721908569336,0.23886893689632416,0.2015867829322815,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +9,MTR_080,0.17201481759548187,0.23814263939857483,0.23302991688251495,0.2931031286716461,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +10,MTR_096,0.5481988787651062,0.15052995085716248,0.18775705993175507,0.24844631552696228,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +11,MTR_099,0.23770450055599213,0.22469185292720795,0.349893182516098,0.5431647300720215,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +12,MTR_120,0.2207055389881134,0.3681889772415161,0.2719559073448181,0.7836833000183105,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +13,MTR_126,0.2943664789199829,0.4265807569026947,0.30632296204566956,0.4684223234653473,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +14,MTR_144,0.19823220372200012,0.17483565211296082,0.3200378715991974,0.2819545865058899,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +15,MTR_156,0.3729424774646759,0.3081037402153015,0.272862046957016,0.4871142506599426,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +16,MTR_158,0.2113960087299347,0.22825931012630463,0.3377453684806824,0.6667215824127197,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +17,MTR_173,0.2934550940990448,0.2954985499382019,0.3241516947746277,0.298988938331604,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +18,MTR_176,0.31827956438064575,0.29959559440612793,0.3557453751564026,0.4862624406814575,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +19,MTR_178,0.20496609807014465,0.19958022236824036,0.2353595793247223,0.3638806641101837,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +20,MTR_188,0.24660645425319672,0.2771489918231964,0.25025150179862976,0.26968422532081604,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +21,MTR_196,0.223397895693779,0.15699177980422974,0.18833909928798676,0.2684807777404785,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +22,MTR_198,0.27761539816856384,0.24341756105422974,0.3294076919555664,0.49537986516952515,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +23,MTR_199,0.19156156480312347,0.15451179444789886,0.2959902882575989,0.28483477234840393,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +24,MTR_218,0.2023109644651413,0.23355703055858612,0.2855930030345917,0.3386743664741516,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +25,MTR_219,0.14756092429161072,0.1647716462612152,0.2349052131175995,0.29848790168762207,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +26,MTR_221,0.40432044863700867,0.2856084704399109,0.5146405100822449,0.5135337710380554,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +27,MTR_223,0.14265882968902588,0.12308201193809509,0.19488272070884705,0.25536221265792847,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +28,MTR_224,0.244828000664711,0.1656142771244049,0.29090118408203125,0.5277572870254517,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +29,MTR_227,0.18965551257133484,0.20833821594715118,0.3619515597820282,0.2501888573169708,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +30,MTR_235,0.31167322397232056,0.27598610520362854,0.3743235468864441,0.4985992908477783,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +31,MTR_237,0.17844942212104797,0.21366478502750397,0.3187253177165985,0.4251432418823242,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +32,MTR_240,0.18690454959869385,0.33397406339645386,0.4302504062652588,0.46797794103622437,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +33,MTR_241,0.48095372319221497,0.3609231114387512,0.39396238327026367,0.8657984733581543,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +34,MTR_244,0.25378143787384033,0.23805207014083862,0.2025841623544693,0.35402414202690125,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +35,MTR_248,0.3514583706855774,0.23274271190166473,0.2706693410873413,0.4181951880455017,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +36,MTR_005,0.02565942518413067,0.05406671762466431,0.13275490701198578,0.13535520434379578,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +37,MTR_006,0.02694677747786045,0.0304989255964756,0.03719807416200638,0.11597808450460434,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +38,MTR_030,0.11928465217351913,0.16406410932540894,0.2163003832101822,0.28252485394477844,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +39,MTR_034,0.011794942431151867,0.0006321072578430176,0.06383258104324341,0.1100674718618393,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +40,MTR_048,0.0062246122397482395,0.003354960586875677,0.03128169849514961,0.03661719709634781,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +41,MTR_052,0.5330233573913574,0.028469864279031754,0.21942628920078278,0.17371387779712677,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +42,MTR_065,0.022175682708621025,0.023614810779690742,0.0661456361413002,0.10645194351673126,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +43,MTR_066,0.13185152411460876,0.1439550220966339,0.09920644760131836,0.04917425289750099,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +44,MTR_079,0.010436851531267166,0.03349611535668373,0.08816078305244446,0.024376679211854935,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +45,MTR_080,0.03835858777165413,0.08818506449460983,0.05368031561374664,0.019795171916484833,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +46,MTR_096,0.02575836516916752,0.0032146552111953497,0.004572954028844833,0.003747051814571023,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +47,MTR_099,0.03002481535077095,0.015384750440716743,0.12559503316879272,0.06938246637582779,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +48,MTR_120,0.03820689022541046,0.16888339817523956,0.11264000087976456,0.15735499560832977,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +49,MTR_126,0.11889083683490753,0.13247759640216827,0.14780494570732117,0.10975600779056549,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +50,MTR_144,0.020879996940493584,0.021050093695521355,0.16135554015636444,0.020385080948472023,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +51,MTR_156,0.05209283530712128,0.11781560629606247,0.1394851803779602,0.08753059804439545,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +52,MTR_158,0.05720739811658859,0.07667236775159836,0.016147460788488388,0.23781873285770416,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +53,MTR_173,0.02906252257525921,0.11095103621482849,0.13505476713180542,0.04423677921295166,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +54,MTR_176,0.11175806075334549,0.08360042423009872,0.23841403424739838,0.012925880961120129,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +55,MTR_178,0.04519575834274292,0.09979158639907837,0.06009767949581146,0.015887966379523277,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +56,MTR_188,0.05237432196736336,0.11127715557813644,0.102257639169693,0.027363041415810585,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +57,MTR_196,0.03267447277903557,0.03631826862692833,0.0015438246773555875,0.023288780823349953,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +58,MTR_198,0.02610972337424755,0.07212703675031662,0.019461490213871002,0.06760895252227783,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +59,MTR_199,0.03797469660639763,0.045300111174583435,0.08468585461378098,0.08006157726049423,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +60,MTR_218,0.09246756881475449,0.14057113230228424,0.02066119574010372,0.0013574426993727684,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +61,MTR_219,0.004073800519108772,0.007519484497606754,0.009118163958191872,0.03582434356212616,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +62,MTR_221,0.19891706109046936,0.12671130895614624,0.23287099599838257,0.15880441665649414,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +63,MTR_223,0.008552276529371738,0.031301870942115784,0.013094100169837475,0.019854944199323654,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +64,MTR_224,0.07525721192359924,0.07979170233011246,0.005563951563090086,0.0027611071709543467,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +65,MTR_227,0.07845485210418701,0.12663833796977997,0.15642093122005463,0.0616711787879467,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +66,MTR_235,0.04336782544851303,0.07122533023357391,0.0268784798681736,0.03281790763139725,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +67,MTR_237,0.008490201085805893,0.04902882128953934,0.0713915005326271,0.08371981233358383,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +68,MTR_240,0.009549683891236782,0.15349134802818298,0.13793393969535828,0.06461201608181,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +69,MTR_241,0.060681141912937164,0.18849429488182068,0.227763369679451,0.18869636952877045,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +70,MTR_244,0.10147274285554886,0.08106377720832825,0.10998652875423431,0.006466601975262165,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +71,MTR_248,0.08654569089412689,0.030358145013451576,0.03223472833633423,0.007378807291388512,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +72,MTR_005,0.9345265626907349,0.910575270652771,0.8779734969139099,0.8414575457572937,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +73,MTR_006,0.8955982327461243,0.8926647901535034,0.8612118363380432,0.8792807459831238,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +74,MTR_030,0.8959267139434814,0.831056535243988,0.7785588502883911,0.6211625933647156,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +75,MTR_034,0.920164942741394,0.9042659997940063,0.8845170140266418,0.8764739632606506,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +76,MTR_048,0.9400127530097961,0.929072380065918,0.9058462381362915,0.8474905490875244,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +77,MTR_052,0.4293628931045532,0.8542391061782837,0.7930694818496704,0.757767915725708,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +78,MTR_065,0.9053743481636047,0.8947157859802246,0.8612571358680725,0.8451206684112549,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +79,MTR_066,0.8548106551170349,0.8477591872215271,0.8443272113800049,0.8163706064224243,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +80,MTR_079,0.8771049976348877,0.8766021132469177,0.8792076110839844,0.8864805102348328,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +81,MTR_080,0.9291232824325562,0.8709756135940552,0.8952300548553467,0.9052321314811707,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +82,MTR_096,0.8894017338752747,0.9271852374076843,0.9219684600830078,0.896720826625824,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +83,MTR_099,0.9064977169036865,0.9001171588897705,0.859717845916748,0.8642564415931702,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +84,MTR_120,0.9059598445892334,0.8413021564483643,0.8889632225036621,0.7905887961387634,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +85,MTR_126,0.9000892639160156,0.8829622268676758,0.8666740655899048,0.8644670844078064,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +86,MTR_144,0.937800943851471,0.929918646812439,0.8741773366928101,0.9008418321609497,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +87,MTR_156,0.8919023871421814,0.8782606720924377,0.8674644827842712,0.8644729852676392,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +88,MTR_158,0.9135138392448425,0.8963929414749146,0.8488125205039978,0.7705063223838806,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +89,MTR_173,0.8945860862731934,0.8649174571037292,0.858213484287262,0.8615425825119019,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +90,MTR_176,0.8837378025054932,0.8955211043357849,0.8269646167755127,0.8313782215118408,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +91,MTR_178,0.9293366074562073,0.8916239738464355,0.8868228793144226,0.8728170990943909,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +92,MTR_188,0.9132509827613831,0.8766846060752869,0.8692234754562378,0.8923816084861755,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +93,MTR_196,0.9094802141189575,0.9016420245170593,0.9022147059440613,0.9038193821907043,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +94,MTR_198,0.8981516361236572,0.8914814591407776,0.887474775314331,0.849246621131897,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +95,MTR_199,0.9299729466438293,0.9112248420715332,0.8652554154396057,0.8901671171188354,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +96,MTR_218,0.8992107510566711,0.86278235912323,0.8206787705421448,0.8549301028251648,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +97,MTR_219,0.9331833124160767,0.9216015934944153,0.9053030014038086,0.8829059600830078,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +98,MTR_221,0.8159935474395752,0.8587053418159485,0.8023601770401001,0.8388232588768005,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +99,MTR_223,0.9442488551139832,0.9276868104934692,0.90947425365448,0.8980122208595276,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, 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b/neurips2021/segmentation-models/V-Net_E1/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..4fdc3a464130a6e9370806910b85a7c994d035cc --- /dev/null +++ b/neurips2021/segmentation-models/V-Net_E1/config.yaml @@ -0,0 +1,252 @@ +# DEPENDENCY: monai>=0.5.3,<=0.6.0 +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 6 +AUG_TRAIN: + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 6 + CALIBRATION_SIZE: 24 + CENTER_FRACTIONS: [] + NAME: PoissonDiskMaskFunc + PRECOMPUTE: + NUM: -1 + SEED: -1 + USE_NOISE: false +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: [] + DROP_LAST: true + FILTER: + BY: [] + GROUP_SAMPLER: + AS_BATCH_SAMPLER: true + BATCH_BY: + - inplane_shape + NUM_WORKERS: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: '' + SUBSAMPLE_TRAIN: + NUM_TOTAL: -1 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + QDESS: + DATASET_TYPE: qDESSImageDataset + ECHO_KIND: echo1 + KWARGS: + - orientation + - sagittal + TEST: + - stanford_qdess_v0.1.0_test + TRAIN: + - stanford_qdess_v0.1.0_train + VAL: + - stanford_qdess_v0.1.0_val +DESCRIPTION: + BRIEF: VNet segmentation following parameters used in MONAI - input=echo1, 100 epochs, + 0.001 lr w/ 0.9x decay every (2,) epochs, early stopping- T=0, delta=0.0, bsz=16, + qdess args=('orientation', 'sagittal') + ENTITY_NAME: ss_recon + EXP_NAME: seg-baseline/vnet-medsegpy-echo1-bsz=16 + PROJECT_NAME: ss_recon + TAGS: + - seg-baseline + - baseline + - vnet-monai + - neurips +MODEL: + CASCADE: + ITFS: + PERIOD: 0 + RECON_MODEL_NAME: '' + SEG_MODEL_NAME: '' + SEG_NORMALIZE: '' + USE_MAGNITUDE: false + ZERO_FILL: false + CS: + MAX_ITER: 200 + REGULARIZATION: 0.005 + DENOISING: + META_ARCHITECTURE: GeneralizedUnrolledCNN + NOISE: + STD_DEV: + - 1 + USE_FULLY_SAMPLED_TARGET: true + USE_FULLY_SAMPLED_TARGET_EVAL: null + DEVICE: cpu + META_ARCHITECTURE: VNetMONAI + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + PARAMETERS: + INIT: + - initializers: (("kaiming_normal_", {"nonlinearity":"relu"}), "zeros_") + kind: conv + patterns: (".*weight", ".*bias") + - initializers: ("ones_", "zeros_") + kind: norm + patterns: (".*weight", ".*bias") + - initializers: ("xavier_uniform_",) + patterns: ("output_block\.weight",) + USE_COMPLEX_WEIGHTS: false + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: true + WEIGHT: 1.0 + SEG: + ACTIVATION: sigmoid + CLASSES: + - pc + - fc + - tc + - men + INCLUDE_BACKGROUND: false + IN_CHANNELS: null + LOSS_NAME: FlattenedDiceLoss + LOSS_WEIGHT: 1.0 + MODEL: + DYNUNET_MONAI: + DEEP_SUPERVISION: false + DEEP_SUPR_NUM: 1 + KERNEL_SIZE: + - 3 + NORM_NAME: instance + RES_BLOCK: false + STRIDES: + - 1 + UPSAMPLE_KERNEL_SIZE: + - 2 + UNET_MONAI: + ACTIVATION: + - prelu + - {} + CHANNELS: [] + DROPOUT: 0.0 + KERNEL_SIZE: + - 3 + NORM: + - instance + - {} + NUM_RES_UNITS: 0 + STRIDES: [] + UP_KERNEL_SIZE: + - 3 + VNET_MONAI: + ACTIVATION: + - elu + - inplace: true + DROPOUT_DIM: 2 + DROPOUT_PROB: 0.0 + USE_MAGNITUDE: true + TASKS: + - sem_seg + TB_RECON: + CHANNELS: + - 16 + - 32 + - 64 + DEC_NUM_CONV_BLOCKS: + - 2 + - 3 + ENC_NUM_CONV_BLOCKS: + - 1 + - 2 + - 3 + KERNEL_SIZE: + - 5 + MULTI_CONCAT: [] + ORDER: + - conv + - relu + STRIDES: + - 2 + USE_MAGNITUDE: false + UNET: + BLOCK_ORDER: + - conv + - instancenorm + - - leakyrelu + - negative_slope: 0.2 + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + CONV_BLOCK: + ACTIVATION: relu + NORM: none + NORM_AFFINE: false + ORDER: + - norm + - act + - drop + - conv + DROPOUT: 0.0 + FIX_STEP_SIZE: false + KERNEL_SIZE: + - 3 + NUM_EMAPS: 1 + NUM_FEATURES: 256 + NUM_RESBLOCKS: 2 + NUM_UNROLLED_STEPS: 5 + PADDING: '' + SHARE_WEIGHTS: false + WEIGHTS: '' +OUTPUT_DIR: results://skm-tea/neurips2021/V-Net_E1 +SEED: 9001 +SOLVER: + BASE_LR: 0.001 + CHECKPOINT_MONITOR: val_loss + CHECKPOINT_PERIOD: 1 + EARLY_STOPPING: + MIN_DELTA: 0.0 + MONITOR: val_loss + PATIENCE: 0 + GAMMA: 0.9 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: StepLR + MAX_ITER: 100 + MIN_LR: 1.0e-08 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: + - 2 + TEST_BATCH_SIZE: 40 + TRAIN_BATCH_SIZE: 16 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: 1 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: -5 + QDESS_EVALUATOR: + ADDITIONAL_PATHS: [] + VAL_METRICS: + RECON: [] + SEM_SEG: + - DSC + - VOE + - CV + - DSC_scan + - VOE_scan + - CV_scan +TIME_SCALE: epoch +VERSION: 1 +VIS_PERIOD: -100 diff --git a/neurips2021/segmentation-models/V-Net_E1/model-gpu.ckpt b/neurips2021/segmentation-models/V-Net_E1/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..bb7e4c96be454c92fad61ea6a9fc1b6e4ad69cc1 --- /dev/null +++ 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+24,MTR_218,0.22501488029956818,0.24870334565639496,0.3046933114528656,0.2873273193836212,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +25,MTR_219,0.14186526834964752,0.16560176014900208,0.24229809641838074,0.2599131464958191,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +26,MTR_221,0.38598546385765076,0.29067015647888184,0.3899329900741577,0.5594061017036438,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +27,MTR_223,0.12993185222148895,0.11875476688146591,0.18779295682907104,0.2130742073059082,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +28,MTR_224,0.3152425289154053,0.1713484525680542,0.31180498003959656,0.650810956954956,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +29,MTR_227,0.21247431635856628,0.24811294674873352,0.37636464834213257,0.2630906105041504,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +30,MTR_235,0.31157422065734863,0.27393990755081177,0.3859555125236511,0.47210800647735596,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +31,MTR_237,0.17216646671295166,0.2223154455423355,0.3610258996486664,0.46320539712905884,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +32,MTR_240,0.22644326090812683,0.335957407951355,0.4828551113605499,0.5816373229026794,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +33,MTR_241,1.2159479856491089,0.41952913999557495,0.3143857717514038,0.8800555467605591,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +34,MTR_244,0.2764907479286194,0.2114619016647339,0.18721719086170197,0.28782522678375244,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +35,MTR_248,0.35685959458351135,0.208378866314888,0.27562662959098816,0.3691002130508423,ASSD_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +36,MTR_005,0.06777329742908478,0.06245548278093338,0.13267283141613007,0.1579711139202118,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +37,MTR_006,0.02532789669930935,0.021115228533744812,0.019388347864151,0.08939266949892044,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +38,MTR_030,0.10707204788923264,0.15838459134101868,0.18130351603031158,0.2917274534702301,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +39,MTR_034,0.021651022136211395,0.015179785899817944,0.058431319892406464,0.12033823132514954,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +40,MTR_048,0.019161663949489594,0.016126682981848717,0.08420392125844955,0.06216825544834137,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +41,MTR_052,0.043721556663513184,0.10277989506721497,0.22086024284362793,0.11113523691892624,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +42,MTR_065,0.04961097985506058,0.013343578204512596,0.1077871099114418,0.14235983788967133,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +43,MTR_066,0.1817641258239746,0.18716280162334442,0.12852540612220764,0.09691902250051498,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +44,MTR_079,0.005380596965551376,0.0166175477206707,0.08925393968820572,0.005420222878456116,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +45,MTR_080,0.07801021635532379,0.09871110320091248,0.049909159541130066,0.01929592341184616,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +46,MTR_096,0.013069616630673409,0.004650238435715437,0.013385770842432976,0.015474166721105576,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +47,MTR_099,0.05198495090007782,0.03720562160015106,0.10859555751085281,0.0743485763669014,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +48,MTR_120,0.05462139844894409,0.2023499608039856,0.09105056524276733,0.19544288516044617,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +49,MTR_126,0.13049152493476868,0.15040017664432526,0.12583550810813904,0.1260223090648651,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +50,MTR_144,0.014894799329340458,0.037471458315849304,0.14424557983875275,0.05229808762669563,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +51,MTR_156,0.07644669711589813,0.14523954689502716,0.13204628229141235,0.08798779547214508,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +52,MTR_158,0.06084887310862541,0.07661183923482895,0.0031349207274615765,0.1897466629743576,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +53,MTR_173,0.033812690526247025,0.0971011146903038,0.0829998105764389,0.03738127648830414,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +54,MTR_176,0.12089815735816956,0.07615181803703308,0.243174210190773,0.0033023476134985685,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +55,MTR_178,0.02602783963084221,0.12161478400230408,0.05358103662729263,0.024635447189211845,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +56,MTR_188,0.04981177672743797,0.09763238579034805,0.10607920587062836,0.04470941424369812,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +57,MTR_196,0.06127909943461418,0.03783790394663811,0.017540615051984787,0.00563422916457057,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +58,MTR_198,0.025739416480064392,0.058595601469278336,0.018178697675466537,0.09889303892850876,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +59,MTR_199,0.062313806265592575,0.0564064122736454,0.07560376822948456,0.08467578887939453,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +60,MTR_218,0.11625482887029648,0.15842773020267487,0.14300085604190826,0.04010801389813423,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +61,MTR_219,0.024311598390340805,0.012003920041024685,0.00771032040938735,0.04065408930182457,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +62,MTR_221,0.1810104101896286,0.16931398212909698,0.24935929477214813,0.1986633539199829,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +63,MTR_223,0.00787055492401123,0.03415917232632637,0.0052573950961232185,0.0042504617013037205,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +64,MTR_224,0.10678993165493011,0.08574004471302032,0.017987854778766632,0.03766836225986481,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +65,MTR_227,0.10868827253580093,0.14338558912277222,0.15223191678524017,0.06735438853502274,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +66,MTR_235,0.0468861423432827,0.07198025286197662,0.024909578263759613,0.06463062018156052,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +67,MTR_237,0.004034056328237057,0.003770739771425724,0.08294615894556046,0.1266489326953888,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +68,MTR_240,0.11767484992742538,0.14670445024967194,0.1552947610616684,0.08056145906448364,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +69,MTR_241,0.49209821224212646,0.21207603812217712,0.1923743337392807,0.2235739678144455,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +70,MTR_244,0.12278110533952713,0.08575375378131866,0.0913788452744484,0.015151336789131165,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +71,MTR_248,0.10008465498685837,0.033699870109558105,0.01412444282323122,0.005157093051820993,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +72,MTR_005,0.9295967817306519,0.9089572429656982,0.8767604827880859,0.8343166708946228,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +73,MTR_006,0.8977779150009155,0.884456217288971,0.8739137649536133,0.8946497440338135,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +74,MTR_030,0.9036492705345154,0.8172301054000854,0.7747490406036377,0.6147688627243042,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +75,MTR_034,0.9237051010131836,0.903491199016571,0.8888026475906372,0.873386025428772,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +76,MTR_048,0.9375925660133362,0.9270583391189575,0.882987380027771,0.8318222165107727,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +77,MTR_052,0.5350962281227112,0.7985262274742126,0.7904945611953735,0.7428597211837769,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +78,MTR_065,0.9105134606361389,0.8913821578025818,0.8404716849327087,0.8383215665817261,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +79,MTR_066,0.8403481841087341,0.8202046155929565,0.8397454023361206,0.803834080696106,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +80,MTR_079,0.8756388425827026,0.885723352432251,0.8763404488563538,0.8814425468444824,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +81,MTR_080,0.9220676422119141,0.8647005558013916,0.9011810421943665,0.9067593216896057,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +82,MTR_096,0.8798947930335999,0.9299572706222534,0.9190993309020996,0.8925923109054565,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +83,MTR_099,0.9010067582130432,0.8927373886108398,0.8605170845985413,0.8708084225654602,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +84,MTR_120,0.9006636142730713,0.8292588591575623,0.8905640840530396,0.8016237020492554,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +85,MTR_126,0.8905823230743408,0.8719807267189026,0.8775614500045776,0.8596640825271606,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +86,MTR_144,0.9284356236457825,0.924738883972168,0.8691850900650024,0.8939490914344788,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +87,MTR_156,0.8784096240997314,0.8635517954826355,0.8667359948158264,0.8504721522331238,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +88,MTR_158,0.9074296951293945,0.89286869764328,0.8461918830871582,0.7803304195404053,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +89,MTR_173,0.8988182544708252,0.8708680272102356,0.8707987666130066,0.8789613842964172,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +90,MTR_176,0.8666440844535828,0.9009354114532471,0.8235434293746948,0.8283612728118896,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +91,MTR_178,0.9192041158676147,0.8863670825958252,0.8867982625961304,0.8755258321762085,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +92,MTR_188,0.911051869392395,0.8813515305519104,0.8749844431877136,0.8857319951057434,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +93,MTR_196,0.9082781672477722,0.8981993198394775,0.8936914205551147,0.8986847400665283,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +94,MTR_198,0.9140322804450989,0.8931373357772827,0.8865798711776733,0.8452810049057007,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +95,MTR_199,0.9150630831718445,0.9081775546073914,0.8716989159584045,0.8916003108024597,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +96,MTR_218,0.8884283304214478,0.8559640049934387,0.7924484014511108,0.8773421049118042,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +97,MTR_219,0.9363604187965393,0.9226204752922058,0.9036257266998291,0.8944181203842163,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +98,MTR_221,0.8303492069244385,0.8422299027442932,0.7864153385162354,0.8204634785652161,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +99,MTR_223,0.9478751420974731,0.9274701476097107,0.9107517600059509,0.9028372168540955,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +100,MTR_224,0.8696578145027161,0.8902853727340698,0.8340570330619812,0.8164788484573364,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +101,MTR_227,0.9136652946472168,0.8708105087280273,0.8401105403900146,0.87981116771698,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +102,MTR_235,0.8827247619628906,0.885550320148468,0.8831884264945984,0.8594696521759033,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +103,MTR_237,0.9317821860313416,0.8829624652862549,0.8454875946044922,0.8135561943054199,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +104,MTR_240,0.8603678345680237,0.8632349371910095,0.845360279083252,0.8677250742912292,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +105,MTR_241,0.5961560606956482,0.7878244519233704,0.824623703956604,0.7420312762260437,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +106,MTR_244,0.8737807869911194,0.8716752529144287,0.8923935294151306,0.9029333591461182,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +107,MTR_248,0.8955393433570862,0.911931037902832,0.8949016332626343,0.8978028297424316,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +108,MTR_005,0.13154524564743042,0.16689127683639526,0.21943581104278564,0.28426820039749146,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +109,MTR_006,0.1854836344718933,0.2071523666381836,0.22393709421157837,0.19061881303787231,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +110,MTR_030,0.17576628923416138,0.30905401706695557,0.3676813244819641,0.5561976432800293,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +111,MTR_034,0.14177316427230835,0.17602920532226562,0.20013964176177979,0.22476905584335327,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +112,MTR_048,0.11748301982879639,0.1359657645225525,0.20950990915298462,0.28793179988861084,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +113,MTR_052,0.6347225904464722,0.33537769317626953,0.34643155336380005,0.4090876579284668,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +114,MTR_065,0.16427290439605713,0.19595187902450562,0.27516067028045654,0.278353214263916,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +115,MTR_066,0.2753444314002991,0.30479079484939575,0.27624034881591797,0.3279911279678345,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +116,MTR_079,0.22121214866638184,0.20511358976364136,0.2201014757156372,0.21198278665542603,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +117,MTR_080,0.14459604024887085,0.2383502721786499,0.17986392974853516,0.17057663202285767,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +118,MTR_096,0.21445345878601074,0.13091576099395752,0.1496911644935608,0.1939803957939148,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, 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+137,MTR_227,0.15894681215286255,0.22881805896759033,0.2756977677345276,0.2145867943763733,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +138,MTR_235,0.20993083715438843,0.20539230108261108,0.20918762683868408,0.24642986059188843,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +139,MTR_237,0.12772268056869507,0.20954984426498413,0.2676669955253601,0.3142901659011841,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +140,MTR_240,0.24504774808883667,0.24062150716781616,0.2678579092025757,0.2336445450782776,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +141,MTR_241,0.575340211391449,0.35007399320602417,0.298417329788208,0.4101353883743286,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +142,MTR_244,0.2241467833518982,0.22746068239212036,0.19430452585220337,0.17695671319961548,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +143,MTR_248,0.18916136026382446,0.16188114881515503,0.1902063488960266,0.18544262647628784,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, 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+145,MTR_006,36.34393420610943,41.94742243818081,34.62910223168812,23.5937001128338,t2_seg_gt,29.310650294449317,27.586141678129298,37.67713292033475,37.75029408372737,29.600368324125235,41.63888488344148,47.35857477968681,43.934851771511205,45.68953017194174,53.70395076201641,47.6200243902439,52.159889934598816,38.28235590709986,35.55843469063987,41.6666957612787,45.66201081583997,38.349846044528654,46.910950801326884,30.28020847434683,29.351463020144095,41.541140308582456,43.08257596496031,36.23702097812919,36.462791521939465,33.87932981927711,25.366933661942905,31.79944925255704,31.45607075850978,22.80644805297178,29.89075098814229,42.72100371747212,34.75651860744298,40.72764650283555,51.52426205903527,44.952625250501,44.369369074861055,37.836751247920134,29.695871153420413,35.85528123658222,40.02104777999693,32.55756639901174,36.35268456375839,23.5937001128338,22.361268299087506,24.169137164750953 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b/neurips2021/segmentation-models/V-Net_E2/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..5325ddbd6c6e93b7ead017c7c102e765d3dc5a86 --- /dev/null +++ b/neurips2021/segmentation-models/V-Net_E2/config.yaml @@ -0,0 +1,252 @@ +# DEPENDENCY: monai>=0.5.3,<=0.6.0 +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 6 +AUG_TRAIN: + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 6 + CALIBRATION_SIZE: 24 + CENTER_FRACTIONS: [] + NAME: PoissonDiskMaskFunc + PRECOMPUTE: + NUM: -1 + SEED: -1 + USE_NOISE: false +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: [] + DROP_LAST: true + FILTER: + BY: [] + GROUP_SAMPLER: + AS_BATCH_SAMPLER: true + BATCH_BY: + - inplane_shape + NUM_WORKERS: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: '' + SUBSAMPLE_TRAIN: + NUM_TOTAL: -1 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + QDESS: + DATASET_TYPE: qDESSImageDataset + ECHO_KIND: echo2 + KWARGS: + - orientation + - sagittal + TEST: + - stanford_qdess_v0.1.0_test + TRAIN: + - stanford_qdess_v0.1.0_train + VAL: + - stanford_qdess_v0.1.0_val +DESCRIPTION: + BRIEF: VNet segmentation following parameters used in MONAI - input=echo2, 100 epochs, + 0.001 lr w/ 0.9x decay every (2,) epochs, early stopping- T=0, delta=0.0, bsz=16, + qdess args=('orientation', 'sagittal') + ENTITY_NAME: ss_recon + EXP_NAME: seg-baseline/vnet-medsegpy-echo2-bsz=16 + PROJECT_NAME: ss_recon + TAGS: + - seg-baseline + - baseline + - vnet-monai + - neurips +MODEL: + CASCADE: + ITFS: + PERIOD: 0 + RECON_MODEL_NAME: '' + SEG_MODEL_NAME: '' + SEG_NORMALIZE: '' + USE_MAGNITUDE: false + ZERO_FILL: false + CS: + MAX_ITER: 200 + REGULARIZATION: 0.005 + DENOISING: + META_ARCHITECTURE: GeneralizedUnrolledCNN + NOISE: + STD_DEV: + - 1 + USE_FULLY_SAMPLED_TARGET: true + USE_FULLY_SAMPLED_TARGET_EVAL: null + DEVICE: cpu + META_ARCHITECTURE: VNetMONAI + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + PARAMETERS: + INIT: + - initializers: (("kaiming_normal_", {"nonlinearity":"relu"}), "zeros_") + kind: conv + patterns: (".*weight", ".*bias") + - initializers: ("ones_", "zeros_") + kind: norm + patterns: (".*weight", ".*bias") + - initializers: ("xavier_uniform_",) + patterns: ("output_block\.weight",) + USE_COMPLEX_WEIGHTS: false + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: true + WEIGHT: 1.0 + SEG: + ACTIVATION: sigmoid + CLASSES: + - pc + - fc + - tc + - men + INCLUDE_BACKGROUND: false + IN_CHANNELS: null + LOSS_NAME: FlattenedDiceLoss + LOSS_WEIGHT: 1.0 + MODEL: + DYNUNET_MONAI: + DEEP_SUPERVISION: false + DEEP_SUPR_NUM: 1 + KERNEL_SIZE: + - 3 + NORM_NAME: instance + RES_BLOCK: false + STRIDES: + - 1 + UPSAMPLE_KERNEL_SIZE: + - 2 + UNET_MONAI: + ACTIVATION: + - prelu + - {} + CHANNELS: [] + DROPOUT: 0.0 + KERNEL_SIZE: + - 3 + NORM: + - instance + - {} + NUM_RES_UNITS: 0 + STRIDES: [] + UP_KERNEL_SIZE: + - 3 + VNET_MONAI: + ACTIVATION: + - elu + - inplace: true + DROPOUT_DIM: 2 + DROPOUT_PROB: 0.0 + USE_MAGNITUDE: true + TASKS: + - sem_seg + TB_RECON: + CHANNELS: + - 16 + - 32 + - 64 + DEC_NUM_CONV_BLOCKS: + - 2 + - 3 + ENC_NUM_CONV_BLOCKS: + - 1 + - 2 + - 3 + KERNEL_SIZE: + - 5 + MULTI_CONCAT: [] + ORDER: + - conv + - relu + STRIDES: + - 2 + USE_MAGNITUDE: false + UNET: + BLOCK_ORDER: + - conv + - instancenorm + - - leakyrelu + - negative_slope: 0.2 + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + CONV_BLOCK: + ACTIVATION: relu + NORM: none + NORM_AFFINE: false + ORDER: + - norm + - act + - drop + - conv + DROPOUT: 0.0 + FIX_STEP_SIZE: false + KERNEL_SIZE: + - 3 + NUM_EMAPS: 1 + NUM_FEATURES: 256 + NUM_RESBLOCKS: 2 + NUM_UNROLLED_STEPS: 5 + PADDING: '' + SHARE_WEIGHTS: false + WEIGHTS: '' +OUTPUT_DIR: results://skm-tea/neurips2021/V-Net_E2 +SEED: 9001 +SOLVER: + BASE_LR: 0.001 + CHECKPOINT_MONITOR: val_loss + CHECKPOINT_PERIOD: 1 + EARLY_STOPPING: + MIN_DELTA: 0.0 + MONITOR: val_loss + PATIENCE: 0 + GAMMA: 0.9 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: StepLR + MAX_ITER: 100 + MIN_LR: 1.0e-08 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: + - 2 + TEST_BATCH_SIZE: 40 + TRAIN_BATCH_SIZE: 16 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: 1 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: -5 + QDESS_EVALUATOR: + ADDITIONAL_PATHS: [] + VAL_METRICS: + RECON: [] + SEM_SEG: + - DSC + - VOE + - CV + - DSC_scan + - VOE_scan + - CV_scan +TIME_SCALE: epoch +VERSION: 1 +VIS_PERIOD: -100 diff --git a/neurips2021/segmentation-models/V-Net_E2/model-gpu.ckpt b/neurips2021/segmentation-models/V-Net_E2/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..6117bbad1b3c16a7b1b3e6c69287dcd393be2d2e --- /dev/null +++ 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+42,MTR_065,0.025593925267457962,0.057264022529125214,0.007627751678228378,0.08090483397245407,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +43,MTR_066,0.1725369542837143,0.16692334413528442,0.10889188945293427,0.12371101975440979,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +44,MTR_079,0.058479778468608856,0.03953976184129715,0.03587557375431061,0.05086350440979004,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +45,MTR_080,0.0779699981212616,0.0888332650065422,0.04637167230248451,0.006031572353094816,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +46,MTR_096,0.03601206839084625,0.023594453930854797,0.030487418174743652,0.022257039323449135,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +47,MTR_099,0.08459018915891647,0.025914140045642853,0.07568597048521042,0.052303247153759,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +48,MTR_120,0.06150159612298012,0.1882663369178772,0.12548254430294037,0.1419423669576645,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +49,MTR_126,0.1318766474723816,0.11686033755540848,0.11282603442668915,0.09865713119506836,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +50,MTR_144,0.031550828367471695,0.005694868508726358,0.14994367957115173,0.01685490272939205,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +51,MTR_156,0.07412337511777878,0.1237872838973999,0.10987267643213272,0.1868070513010025,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +52,MTR_158,0.09840397536754608,0.06773308664560318,0.03511735051870346,0.18397264182567596,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +53,MTR_173,0.031844839453697205,0.05507958307862282,0.007448446936905384,0.088172048330307,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +54,MTR_176,0.15154603123664856,0.10841833800077438,0.2878066599369049,0.01984071545302868,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +55,MTR_178,0.09850499033927917,0.06732680648565292,0.003359589958563447,0.017276447266340256,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +56,MTR_188,0.03724072501063347,0.12044787406921387,0.13860802352428436,0.049606986343860626,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +57,MTR_196,0.04645829647779465,0.01696920394897461,0.043198637664318085,0.017849138006567955,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +58,MTR_198,0.006546050775796175,0.06138964742422104,0.0820544883608818,0.04762718454003334,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +59,MTR_199,0.0526423305273056,0.021406227722764015,0.05150337144732475,0.1151786670088768,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +60,MTR_218,0.15149419009685516,0.12969093024730682,0.15628167986869812,0.0335879810154438,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +61,MTR_219,0.026650775223970413,0.030453799292445183,0.018858304247260094,0.023947887122631073,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +62,MTR_221,0.25836092233657837,0.14930301904678345,0.3056642413139343,0.14003215730190277,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +63,MTR_223,0.003457058686763048,0.023372605443000793,0.015152649953961372,0.008424959145486355,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +64,MTR_224,0.07079055905342102,0.09393846988677979,0.019093822687864304,0.011184758506715298,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +65,MTR_227,0.10384541004896164,0.14187300205230713,0.15142132341861725,0.03167693689465523,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +66,MTR_235,0.07308614999055862,0.060393448919057846,0.0010262973373755813,0.07749202847480774,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +67,MTR_237,0.03667295351624489,0.010836650617420673,0.08978825807571411,0.10938447713851929,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +68,MTR_240,0.056447114795446396,0.1658434271812439,0.17745749652385712,0.015095295384526253,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +69,MTR_241,0.034206610172986984,0.21517570316791534,0.23805786669254303,0.20686563849449158,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +70,MTR_244,0.14437174797058105,0.0909058004617691,0.04383460804820061,0.020356129854917526,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +71,MTR_248,0.12233937531709671,0.0019889608956873417,0.021027496084570885,0.01267724484205246,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +72,MTR_005,0.9177122116088867,0.9019318222999573,0.8716568350791931,0.8253166079521179,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +73,MTR_006,0.8863639831542969,0.8740639686584473,0.8273348212242126,0.8547115921974182,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +74,MTR_030,0.8408095240592957,0.8178430199623108,0.7330905199050903,0.6305364370346069,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +75,MTR_034,0.8542568683624268,0.8905510902404785,0.8677757382392883,0.8664563894271851,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +76,MTR_048,0.9325270652770996,0.9082947969436646,0.8764554858207703,0.8328916430473328,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +77,MTR_052,0.26978856325149536,0.8140846490859985,0.6640866994857788,0.7913925051689148,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +78,MTR_065,0.8929394483566284,0.852789580821991,0.8242378830909729,0.823561429977417,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +79,MTR_066,0.8177183270454407,0.8051437735557556,0.7939997315406799,0.7595763802528381,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +80,MTR_079,0.8528972864151001,0.853083610534668,0.8541089296340942,0.8231499791145325,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +81,MTR_080,0.9069477915763855,0.8580383062362671,0.8745980858802795,0.8935357332229614,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +82,MTR_096,0.9121062159538269,0.9080669283866882,0.901324987411499,0.8493991494178772,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +83,MTR_099,0.8835805058479309,0.8805959820747375,0.8389318585395813,0.8615545630455017,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +84,MTR_120,0.8791080713272095,0.8235206604003906,0.8246083855628967,0.7415639162063599,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +85,MTR_126,0.8791035413742065,0.8761459589004517,0.8553377985954285,0.8383159041404724,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +86,MTR_144,0.9233294129371643,0.9098515510559082,0.8528621196746826,0.8808098435401917,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +87,MTR_156,0.8695861101150513,0.8641736507415771,0.8560326099395752,0.7954275608062744,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +88,MTR_158,0.9011154770851135,0.891755223274231,0.8343536257743835,0.8016236424446106,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +89,MTR_173,0.8513011932373047,0.8322060108184814,0.8173275589942932,0.8244031071662903,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +90,MTR_176,0.8306997418403625,0.8745494484901428,0.7881201505661011,0.8000353574752808,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +91,MTR_178,0.8973045945167542,0.875758707523346,0.8534644246101379,0.8514931797981262,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +92,MTR_188,0.8621776700019836,0.8537060618400574,0.8281780481338501,0.8655144572257996,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +93,MTR_196,0.8869510293006897,0.8836468458175659,0.8676848411560059,0.8973837494850159,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +94,MTR_198,0.8904597163200378,0.8722609877586365,0.8545814752578735,0.8239138722419739,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +95,MTR_199,0.903243362903595,0.891838014125824,0.8330540060997009,0.8634086847305298,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +96,MTR_218,0.8560149669647217,0.8459317684173584,0.7963665723800659,0.820103108882904,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +97,MTR_219,0.9275654554367065,0.8962188959121704,0.8716645240783691,0.8670091032981873,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +98,MTR_221,0.7619780898094177,0.8294514417648315,0.7489773035049438,0.8296552896499634,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +99,MTR_223,0.9305514693260193,0.9076875448226929,0.8947538137435913,0.8634099960327148,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +100,MTR_224,0.8711875081062317,0.8755418062210083,0.8231107592582703,0.7987794876098633,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +101,MTR_227,0.9028385877609253,0.8537717461585999,0.8125744462013245,0.8816103935241699,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +102,MTR_235,0.8504101634025574,0.8634083271026611,0.8656537532806396,0.8319172859191895,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +103,MTR_237,0.9156495332717896,0.88133704662323,0.808465301990509,0.8117854595184326,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +104,MTR_240,0.8152520656585693,0.8469302654266357,0.7968625426292419,0.8369151949882507,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +105,MTR_241,0.6640343070030212,0.7741750478744507,0.7517348527908325,0.7463666796684265,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +106,MTR_244,0.848279595375061,0.8421662449836731,0.845190167427063,0.8899329304695129,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +107,MTR_248,0.8820486068725586,0.8981403112411499,0.8651267886161804,0.87484210729599,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +108,MTR_005,0.15206271409988403,0.17861950397491455,0.22748959064483643,0.29741358757019043,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +109,MTR_006,0.20408105850219727,0.2237001657485962,0.2944833040237427,0.25371497869491577,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +110,MTR_030,0.2746580243110657,0.30817729234695435,0.42135530710220337,0.539574146270752,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +111,MTR_034,0.25440800189971924,0.1973031759262085,0.23356550931930542,0.23562151193618774,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +112,MTR_048,0.12641620635986328,0.16800355911254883,0.21991926431655884,0.28636306524276733,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +113,MTR_052,0.8440719246864319,0.31353896856307983,0.5028968453407288,0.3452030420303345,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +114,MTR_065,0.1934140920639038,0.2566406726837158,0.29897570610046387,0.2999536991119385,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +115,MTR_066,0.3083556890487671,0.32615846395492554,0.3416256308555603,0.3876475691795349,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +116,MTR_079,0.2564769387245178,0.25619369745254517,0.25463342666625977,0.30054807662963867,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +117,MTR_080,0.1702612042427063,0.24862778186798096,0.22285711765289307,0.19244050979614258,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +118,MTR_096,0.16158521175384521,0.16838586330413818,0.17962545156478882,0.26177775859832764,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +119,MTR_099,0.20855867862701416,0.21333497762680054,0.27744823694229126,0.24321836233139038,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +120,MTR_120,0.21570664644241333,0.30001264810562134,0.29843950271606445,0.41072583198547363,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +121,MTR_126,0.21571391820907593,0.22040951251983643,0.2527596354484558,0.27836155891418457,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +122,MTR_144,0.1424216628074646,0.16538745164871216,0.2565304636955261,0.21299362182617188,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +123,MTR_156,0.23073649406433105,0.23916739225387573,0.25169843435287476,0.33965981006622314,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +124,MTR_158,0.17997252941131592,0.19534450769424438,0.2842137813568115,0.33107519149780273,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +125,MTR_173,0.2588995695114136,0.2873691916465759,0.3089147210121155,0.2987365126609802,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +126,MTR_176,0.28957533836364746,0.22293394804000854,0.3496714234352112,0.3332841992378235,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +127,MTR_178,0.18626254796981812,0.22102248668670654,0.25561457872390747,0.25860852003097534,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +128,MTR_188,0.2422562837600708,0.2552468180656433,0.2932560443878174,0.23708641529083252,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +129,MTR_196,0.20313388109207153,0.2084522843360901,0.2337072491645813,0.1861322522163391,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +130,MTR_198,0.197451651096344,0.22654008865356445,0.25391334295272827,0.2994442582130432,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +131,MTR_199,0.17644143104553223,0.19520968198776245,0.28612464666366577,0.2403525710105896,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +132,MTR_218,0.25172531604766846,0.2670001983642578,0.33836448192596436,0.30493664741516113,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +133,MTR_219,0.135084331035614,0.18804651498794556,0.22747749090194702,0.23476070165634155,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +134,MTR_221,0.38451969623565674,0.29139941930770874,0.40130800008773804,0.2911018133163452,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +135,MTR_223,0.1298772692680359,0.1690220832824707,0.19044840335845947,0.24035054445266724,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +136,MTR_224,0.22822654247283936,0.2213655710220337,0.30060476064682007,0.3350268006324768,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +137,MTR_227,0.17711418867111206,0.2551468014717102,0.31568384170532227,0.21171438694000244,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +138,MTR_235,0.2602490186691284,0.24035316705703735,0.2368699312210083,0.287792444229126,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +139,MTR_237,0.15557783842086792,0.2121514081954956,0.32149243354797363,0.3168022632598877,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +140,MTR_240,0.31187719106674194,0.265499472618103,0.33767956495285034,0.2804349660873413,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +141,MTR_241,0.5029555559158325,0.3684456944465637,0.3977763056755066,0.4046371579170227,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +142,MTR_244,0.26346737146377563,0.272636353969574,0.2681131362915039,0.19830703735351562,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +143,MTR_248,0.21101349592208862,0.1848868727684021,0.23768854141235352,0.2224717140197754,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, 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+145,MTR_006,36.34393420610943,41.94742243818081,34.62910223168812,23.5937001128338,t2_seg_gt,29.310650294449317,27.586141678129298,37.67713292033475,37.75029408372737,29.600368324125235,41.63888488344148,47.35857477968681,43.934851771511205,45.68953017194174,53.70395076201641,47.6200243902439,52.159889934598816,38.28235590709986,35.55843469063987,41.6666957612787,45.66201081583997,38.349846044528654,46.910950801326884,30.28020847434683,29.351463020144095,41.541140308582456,43.08257596496031,36.23702097812919,36.462791521939465,33.87932981927711,25.366933661942905,31.79944925255704,31.45607075850978,22.80644805297178,29.89075098814229,42.72100371747212,34.75651860744298,40.72764650283555,51.52426205903527,44.952625250501,44.369369074861055,37.836751247920134,29.695871153420413,35.85528123658222,40.02104777999693,32.55756639901174,36.35268456375839,23.5937001128338,22.361268299087506,24.169137164750953 +146,MTR_030,35.421287998594266,41.528312302839126,35.78327354039709,22.151798252457482,t2_seg_gt,35.95078609221466,26.723869413968426,38.6321863940228,44.19220380029806,29.61854803010181,35.54636120780377,45.791170327691745,35.108798283261805,47.979344294575164,51.42207780235988,41.098307379823964,45.63493812375249,40.99182220582811,30.910637727759916,43.3034582841401,47.828029285019234,35.30262599173091,40.62570452261306,30.86565774155995,30.994315904536343,38.9828735826705,39.72488731487444,35.2012474012474,35.6293308264251,27.418396458435804,31.728917503273678,37.076013513513516,32.38985781990522,28.958905800082274,30.99000221190002,36.115977443609026,42.756667506932196,45.67159699892819,35.93849114703619,43.50745109321059,39.38648789377766,31.24351060898319,36.84613405076617,41.04943022295623,33.989606107929895,35.02399856080595,34.84684286055967,21.616360601001666,21.19825918762089,22.40372056719136 +147,MTR_034,29.199275056306305,32.102552435767805,27.82992052012347,19.70699424961129,t2_seg_gt,29.005250438039994,22.77817915547962,28.699740905793345,27.826941704035878,24.536760409057703,27.687192216044483,39.953305263157894,36.90799894403379,36.57349391402599,37.630887146506915,36.384399117971334,32.64385167464115,34.49165008741786,29.56646372399797,32.65461345990146,32.772506666666665,30.443618873110395,30.21117093850502,23.91694113006607,22.877428968805884,34.360082702797826,34.49708623653968,29.43592318779932,28.95825638111474,25.689172510518937,23.21234684260132,28.396021903688194,23.452701181767022,22.542881688757976,24.268974250738708,35.09712837837838,31.510090898630768,32.44300603400987,34.58899488926747,29.644896542146924,30.819891142998515,29.95699616858238,27.16605811403509,30.291291317006337,28.48969024503005,25.874799661215715,27.28478359908884,19.70699424961129,20.6979303048337,19.1169042368877 +148,MTR_048,31.37581665205306,34.502520589408476,30.584988437923613,23.76331191753742,t2_seg_gt,27.094259944146728,22.67999535855187,26.10402932113176,27.996046776363446,28.26819114629141,32.48965642390515,42.951009072394,35.689247058823526,35.457913601207316,44.13911173352005,45.60190788493069,43.30457512276993,35.09811758108234,29.140453376957232,30.757788414162032,36.201333197638924,36.86267090385042,37.82391390992427,24.024080702896192,24.707992761272813,38.384981472062776,37.1387372252555,31.60992132028402,31.154399593436906,21.9510989010989,21.35192307692308,27.196883704735374,27.587170647623736,23.772973331564287,30.594706084565143,33.395728496196604,34.006700801424756,37.350452079566004,46.71257783312578,40.60361101780315,42.62250380131779,27.22161142549178,27.362206597589342,31.91046544165656,36.03358999037536,31.20085983248091,35.45559197050389,23.76314358838584,19.623452117403414,27.80992355754127 +149,MTR_052,33.87351437699681,34.093083843622324,26.239667343290815,20.153348041492492,t2_seg_gt,20.93252777236406,27.73556370302475,31.609859658532226,29.17519330579388,26.335491651205942,33.2691675598428,31.440317059989194,36.65641199008339,41.3093446714114,40.42150015497469,35.28056059689453,40.215601816805446,26.393800917688925,32.2329848880809,36.37992272727272,34.870771645304735,30.621020585677,36.64241655638877,66.28392857142858,29.036708860759497,78.52272727272728,36.750870406189556,69.73589743589744,32.95697903014417,20.446993865030674,21.766024555461474,21.261421695668272,25.56347283406755,23.8194609297725,27.204251386321626,27.33642857142857,29.077104050448703,28.442491007194246,31.75909482758621,29.10970012239902,34.124598930481284,23.63023102310231,25.173233864586866,24.50420304568528,28.413164155432195,26.183862144420132,30.231791005978685,20.153348041492492,19.714336352894836,20.33689005982765 +150,MTR_065,30.85599448067122,29.008563878482526,25.43286496003867,20.848785017187563,t2_seg_gt,25.03344769148101,19.86665811746602,26.10192074180373,22.849722756591603,21.06336616847826,28.474290756074385,34.51285146942018,26.355306574735284,31.19345356276197,31.90205309000415,29.903501129396584,35.12377996433995,29.868380223207954,23.177010050251255,28.648670344827583,27.574397965257862,25.59755895738519,31.84562648545509,24.499537483137406,23.58698549941457,38.87241224928366,35.5082057961576,31.949470899470903,29.848595373498096,20.47570325427468,18.83280182232346,25.613164996144953,19.595468148781528,20.400243871133362,23.03316719528772,30.850919181408255,29.40538740043447,34.06308694675354,29.536863599237684,30.971224609949957,29.164648117839604,25.071147641726842,23.76315256297697,29.515084552339452,23.967967908034964,25.324429208090503,25.81509900990099,20.848785017187563,20.274288346830904,21.243714371437143 +151,MTR_066,27.612478031634446,32.628557826367874,29.350897597977244,27.923943661971833,t2_seg_gt,30.592013949433305,30.26406570841889,29.787547169811326,30.256843652397574,30.793211488250652,31.489715536105034,36.94934448033441,33.263466666666666,31.948601558917925,34.99424272818456,36.184297520661154,32.92133995037221,33.64215507826721,31.551699029126212,30.730487321711568,32.52576092174748,33.17529585798817,32.19628205128205,22.994853801169594,23.980099091659785,30.360598943041694,32.18975270250259,26.91573024927717,28.308627420362274,27.476521739130437,26.640294117647063,26.477348066298344,27.085537190082647,30.53498098859315,28.66363636363636,31.740199335548176,32.37355212355212,29.278873239436617,29.575370919881305,33.19405099150141,30.034285714285716,29.89340866290019,30.101631701631703,27.708978328173373,28.534715025906735,32.058766233766235,29.270886075949363,27.923943661971833,28.03,20.5 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b/neurips2021/segmentation-models/V-Net_RSS/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..4e80cfaa6c04aedf523f792ef2526b57e99408c0 --- /dev/null +++ b/neurips2021/segmentation-models/V-Net_RSS/config.yaml @@ -0,0 +1,252 @@ +# DEPENDENCY: monai>=0.5.3,<=0.6.0 +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 6 +AUG_TRAIN: + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 6 + CALIBRATION_SIZE: 24 + CENTER_FRACTIONS: [] + NAME: PoissonDiskMaskFunc + PRECOMPUTE: + NUM: -1 + SEED: -1 + USE_NOISE: false +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: [] + DROP_LAST: true + FILTER: + BY: [] + GROUP_SAMPLER: + AS_BATCH_SAMPLER: true + BATCH_BY: + - inplane_shape + NUM_WORKERS: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: '' + SUBSAMPLE_TRAIN: + NUM_TOTAL: -1 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + QDESS: + DATASET_TYPE: qDESSImageDataset + ECHO_KIND: rms + KWARGS: + - orientation + - sagittal + TEST: + - stanford_qdess_v0.1.0_test + TRAIN: + - stanford_qdess_v0.1.0_train + VAL: + - stanford_qdess_v0.1.0_val +DESCRIPTION: + BRIEF: VNet segmentation following parameters used in MONAI - input=rms, 100 epochs, + 0.001 lr w/ 0.9x decay every (2,) epochs, early stopping- T=0, delta=0.0, bsz=16, + qdess args=('orientation', 'sagittal') + ENTITY_NAME: ss_recon + EXP_NAME: seg-baseline/vnet-medsegpy-rms-bsz=16 + PROJECT_NAME: ss_recon + TAGS: + - seg-baseline + - baseline + - vnet-monai + - neurips +MODEL: + CASCADE: + ITFS: + PERIOD: 0 + RECON_MODEL_NAME: '' + SEG_MODEL_NAME: '' + SEG_NORMALIZE: '' + USE_MAGNITUDE: false + ZERO_FILL: false + CS: + MAX_ITER: 200 + REGULARIZATION: 0.005 + DENOISING: + META_ARCHITECTURE: GeneralizedUnrolledCNN + NOISE: + STD_DEV: + - 1 + USE_FULLY_SAMPLED_TARGET: true + USE_FULLY_SAMPLED_TARGET_EVAL: null + DEVICE: cpu + META_ARCHITECTURE: VNetMONAI + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + PARAMETERS: + INIT: + - initializers: (("kaiming_normal_", {"nonlinearity":"relu"}), "zeros_") + kind: conv + patterns: (".*weight", ".*bias") + - initializers: ("ones_", "zeros_") + kind: norm + patterns: (".*weight", ".*bias") + - initializers: ("xavier_uniform_",) + patterns: ("output_block\.weight",) + USE_COMPLEX_WEIGHTS: false + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: true + WEIGHT: 1.0 + SEG: + ACTIVATION: sigmoid + CLASSES: + - pc + - fc + - tc + - men + INCLUDE_BACKGROUND: false + IN_CHANNELS: null + LOSS_NAME: FlattenedDiceLoss + LOSS_WEIGHT: 1.0 + MODEL: + DYNUNET_MONAI: + DEEP_SUPERVISION: false + DEEP_SUPR_NUM: 1 + KERNEL_SIZE: + - 3 + NORM_NAME: instance + RES_BLOCK: false + STRIDES: + - 1 + UPSAMPLE_KERNEL_SIZE: + - 2 + UNET_MONAI: + ACTIVATION: + - prelu + - {} + CHANNELS: [] + DROPOUT: 0.0 + KERNEL_SIZE: + - 3 + NORM: + - instance + - {} + NUM_RES_UNITS: 0 + STRIDES: [] + UP_KERNEL_SIZE: + - 3 + VNET_MONAI: + ACTIVATION: + - elu + - inplace: true + DROPOUT_DIM: 2 + DROPOUT_PROB: 0.0 + USE_MAGNITUDE: true + TASKS: + - sem_seg + TB_RECON: + CHANNELS: + - 16 + - 32 + - 64 + DEC_NUM_CONV_BLOCKS: + - 2 + - 3 + ENC_NUM_CONV_BLOCKS: + - 1 + - 2 + - 3 + KERNEL_SIZE: + - 5 + MULTI_CONCAT: [] + ORDER: + - conv + - relu + STRIDES: + - 2 + USE_MAGNITUDE: false + UNET: + BLOCK_ORDER: + - conv + - instancenorm + - - leakyrelu + - negative_slope: 0.2 + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + CONV_BLOCK: + ACTIVATION: relu + NORM: none + NORM_AFFINE: false + ORDER: + - norm + - act + - drop + - conv + DROPOUT: 0.0 + FIX_STEP_SIZE: false + KERNEL_SIZE: + - 3 + NUM_EMAPS: 1 + NUM_FEATURES: 256 + NUM_RESBLOCKS: 2 + NUM_UNROLLED_STEPS: 5 + PADDING: '' + SHARE_WEIGHTS: false + WEIGHTS: '' +OUTPUT_DIR: results://skm-tea/neurips2021/V-Net_RSS +SEED: 9001 +SOLVER: + BASE_LR: 0.001 + CHECKPOINT_MONITOR: val_loss + CHECKPOINT_PERIOD: 1 + EARLY_STOPPING: + MIN_DELTA: 0.0 + MONITOR: val_loss + PATIENCE: 0 + GAMMA: 0.9 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: StepLR + MAX_ITER: 100 + MIN_LR: 1.0e-08 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: + - 2 + TEST_BATCH_SIZE: 40 + TRAIN_BATCH_SIZE: 16 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: 1 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: -5 + QDESS_EVALUATOR: + ADDITIONAL_PATHS: [] + VAL_METRICS: + RECON: [] + SEM_SEG: + - DSC + - VOE + - CV + - DSC_scan + - VOE_scan + - CV_scan +TIME_SCALE: epoch +VERSION: 1 +VIS_PERIOD: -100 diff --git a/neurips2021/segmentation-models/V-Net_RSS/model-gpu.ckpt b/neurips2021/segmentation-models/V-Net_RSS/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..1d792521d1b2563424a2037056e46b04ce54fdf4 --- /dev/null +++ b/neurips2021/segmentation-models/V-Net_RSS/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:440b53540f14d7762090e8b235d7942ea448ac0fc46108612340c7a7822fbeb1 +size 112508197 diff --git a/neurips2021/segmentation-models/V-Net_RSS/model-raw-gpu.ckpt b/neurips2021/segmentation-models/V-Net_RSS/model-raw-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..7bb5bd6cff590ca7bd5c89cca4f87df6588ff1a4 --- /dev/null +++ b/neurips2021/segmentation-models/V-Net_RSS/model-raw-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:76b4cf54e4df031fe26170ee1348b2382dbc5378740d1b1c76c644caec13bc5b +size 112517005 diff --git a/neurips2021/segmentation-models/V-Net_RSS/model-raw.ckpt b/neurips2021/segmentation-models/V-Net_RSS/model-raw.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..afa8b7ae96b405c7f71046805994e7f4c4c1d12b --- /dev/null +++ b/neurips2021/segmentation-models/V-Net_RSS/model-raw.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ec32745811dd4f03911d82bdb864e88ffdc1c8360a0328d656c7e797a03f6e81 +size 112496229 diff --git a/neurips2021/segmentation-models/V-Net_RSS/model.ckpt b/neurips2021/segmentation-models/V-Net_RSS/model.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..afa8b7ae96b405c7f71046805994e7f4c4c1d12b --- /dev/null +++ b/neurips2021/segmentation-models/V-Net_RSS/model.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ec32745811dd4f03911d82bdb864e88ffdc1c8360a0328d656c7e797a03f6e81 +size 112496229 diff --git a/neurips2021/segmentation-models/V-Net_RSS/scan_metrics.csv b/neurips2021/segmentation-models/V-Net_RSS/scan_metrics.csv new file mode 100644 index 0000000000000000000000000000000000000000..fae2c2cbfde3021e33578a5f664afc9a02b13baa --- /dev/null +++ b/neurips2021/segmentation-models/V-Net_RSS/scan_metrics.csv @@ -0,0 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+48,MTR_120,0.057534199208021164,0.18224766850471497,0.09372781217098236,0.17096096277236938,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +49,MTR_126,0.12150900065898895,0.13273200392723083,0.11795201152563095,0.105599045753479,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +50,MTR_144,0.028418047353625298,0.03488866984844208,0.14893408119678497,0.02706117369234562,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +51,MTR_156,0.0829211175441742,0.1352158933877945,0.12947295606136322,0.07957811653614044,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +52,MTR_158,0.06659311056137085,0.07936018705368042,0.006437851581722498,0.20143014192581177,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +53,MTR_173,0.012511929497122765,0.08276050537824631,0.05504780635237694,0.04930376634001732,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +54,MTR_176,0.1504553109407425,0.07447739690542221,0.2407558560371399,0.019115136936306953,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +55,MTR_178,0.041846659034490585,0.10916314274072647,0.0563165508210659,0.008257109671831131,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +56,MTR_188,0.032642725855112076,0.10924332588911057,0.11550303548574448,0.024063128978013992,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +57,MTR_196,0.056317608803510666,0.03889421746134758,0.024785736575722694,0.0065057361498475075,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +58,MTR_198,0.02856782265007496,0.06856007874011993,0.03891783580183983,0.08748161792755127,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +59,MTR_199,0.06929711997509003,0.06068959832191467,0.08435201644897461,0.06524426490068436,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +60,MTR_218,0.11237850785255432,0.15562309324741364,0.11473403871059418,0.021514516323804855,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +61,MTR_219,0.012308239936828613,0.0005020370008423924,0.008836820721626282,0.009929582476615906,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +62,MTR_221,0.1960577815771103,0.14972244203090668,0.2354838103055954,0.1817261278629303,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +63,MTR_223,0.010219765827059746,0.03331078216433525,0.011911465786397457,0.015595423057675362,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +64,MTR_224,0.10004027932882309,0.08787216991186142,0.0013376619899645448,0.02078266069293022,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +65,MTR_227,0.09989354014396667,0.14057835936546326,0.14748284220695496,0.05937851220369339,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +66,MTR_235,0.03381237015128136,0.07682438939809799,0.02687070704996586,0.04188160598278046,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +67,MTR_237,0.004403200000524521,0.023549331352114677,0.07649101316928864,0.10163436830043793,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +68,MTR_240,0.07692882418632507,0.14084739983081818,0.1606011688709259,0.08783240616321564,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +69,MTR_241,0.5680974721908569,0.20195439457893372,0.20357483625411987,0.21698901057243347,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +70,MTR_244,0.10894983261823654,0.07404600083827972,0.09679683297872543,0.00354452570900321,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +71,MTR_248,0.10314491391181946,0.030731240287423134,0.029607154428958893,0.01417397242039442,CV_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +72,MTR_005,0.9329108595848083,0.9110988974571228,0.8771148920059204,0.8362975716590881,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +73,MTR_006,0.9080170392990112,0.8845127820968628,0.8760808706283569,0.8798457384109497,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +74,MTR_030,0.8991954922676086,0.8205572366714478,0.7823833227157593,0.6344825625419617,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +75,MTR_034,0.9212129712104797,0.9058229923248291,0.8855125904083252,0.8731973171234131,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +76,MTR_048,0.942180335521698,0.9283422231674194,0.8950326442718506,0.8362076282501221,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +77,MTR_052,0.528206467628479,0.8155542612075806,0.8197968006134033,0.6972540020942688,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +78,MTR_065,0.9108235239982605,0.891692042350769,0.8506147861480713,0.8439436554908752,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +79,MTR_066,0.8509498834609985,0.8361793160438538,0.8521293997764587,0.8160973191261292,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +80,MTR_079,0.8678830862045288,0.8848276138305664,0.8748447299003601,0.8806440830230713,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +81,MTR_080,0.9224624037742615,0.8653242588043213,0.8979371786117554,0.9062609076499939,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +82,MTR_096,0.8924998044967651,0.9283172488212585,0.9223676323890686,0.8943003416061401,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +83,MTR_099,0.8981724381446838,0.8944852352142334,0.8558196425437927,0.8775269389152527,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +84,MTR_120,0.903820812702179,0.8385910987854004,0.8914644718170166,0.7917487025260925,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +85,MTR_126,0.8987666964530945,0.8813385367393494,0.8806441426277161,0.8698762059211731,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +86,MTR_144,0.93980872631073,0.9270457625389099,0.8694530725479126,0.8987070918083191,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +87,MTR_156,0.8821567296981812,0.8694760203361511,0.865490734577179,0.861066460609436,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +88,MTR_158,0.9069228172302246,0.8936834335327148,0.8384463787078857,0.7756134867668152,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +89,MTR_173,0.9053589105606079,0.869281530380249,0.8646447062492371,0.8863630890846252,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +90,MTR_176,0.866951048374176,0.8988289833068848,0.8253175616264343,0.831032395362854,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +91,MTR_178,0.9242530465126038,0.8902398347854614,0.8862374424934387,0.877177357673645,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +92,MTR_188,0.9136106371879578,0.8785037994384766,0.8719537258148193,0.8786308765411377,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +93,MTR_196,0.909945547580719,0.8973978161811829,0.895876944065094,0.9033947587013245,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +94,MTR_198,0.9060601592063904,0.8913540840148926,0.8905182480812073,0.8554282188415527,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +95,MTR_199,0.9180846214294434,0.9083184599876404,0.8716754913330078,0.8967759013175964,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +96,MTR_218,0.8923112750053406,0.8586907386779785,0.7988782525062561,0.875087320804596,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +97,MTR_219,0.9422319531440735,0.92169189453125,0.904172420501709,0.8930217027664185,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +98,MTR_221,0.8208339810371399,0.8520300984382629,0.7956987023353577,0.8290535807609558,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +99,MTR_223,0.9491242170333862,0.9285876750946045,0.9125765562057495,0.9008967280387878,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +100,MTR_224,0.8763229846954346,0.8919821381568909,0.8337783217430115,0.8148403763771057,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +101,MTR_227,0.9185953736305237,0.8707360625267029,0.8463161587715149,0.8910553455352783,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +102,MTR_235,0.888340175151825,0.8849444389343262,0.8844512104988098,0.8678064346313477,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +103,MTR_237,0.9319841265678406,0.8882602453231812,0.8465230464935303,0.8236825466156006,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +104,MTR_240,0.8687503337860107,0.8642932176589966,0.8401480913162231,0.8696262836456299,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +105,MTR_241,0.5530585646629333,0.7918583154678345,0.8227630257606506,0.7464345693588257,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +106,MTR_244,0.8802180886268616,0.8737220168113708,0.8917877674102783,0.8986556529998779,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +107,MTR_248,0.8996874094009399,0.9109242558479309,0.8953928351402283,0.8939618468284607,DSC_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +108,MTR_005,0.12574231624603271,0.16328591108322144,0.21887391805648804,0.2813475728034973,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +109,MTR_006,0.1684696078300476,0.2070615291595459,0.2205125093460083,0.21453166007995605,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +110,MTR_030,0.18314695358276367,0.3042839765548706,0.35744696855545044,0.5353537201881409,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +111,MTR_034,0.14606600999832153,0.1721421480178833,0.2054530382156372,0.22506630420684814,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +112,MTR_048,0.1093185544013977,0.1337326169013977,0.18999183177947998,0.28148043155670166,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +113,MTR_052,0.6411137580871582,0.31144654750823975,0.3053765892982483,0.4647812843322754,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +114,MTR_065,0.16375023126602173,0.1954473853111267,0.2599393129348755,0.2699804902076721,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +115,MTR_066,0.2594318389892578,0.2815222144126892,0.25764334201812744,0.31067192554473877,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +116,MTR_079,0.23339802026748657,0.20655536651611328,0.2224675416946411,0.21325820684432983,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +117,MTR_080,0.1439163088798523,0.23738187551498413,0.18522149324417114,0.17141032218933105,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +118,MTR_096,0.19413131475448608,0.13377606868743896,0.14407950639724731,0.19119054079055786,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +119,MTR_099,0.18483394384384155,0.19088804721832275,0.25202375650405884,0.21821999549865723,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +120,MTR_120,0.17548078298568726,0.2779536247253418,0.19581782817840576,0.3447151780128479,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +121,MTR_126,0.18385440111160278,0.21214896440505981,0.21325814723968506,0.23028242588043213,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +122,MTR_144,0.11354798078536987,0.13598763942718506,0.23094475269317627,0.18395274877548218,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +123,MTR_156,0.2108404040336609,0.2309088110923767,0.2371232509613037,0.24397128820419312,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +124,MTR_158,0.17030298709869385,0.19219917058944702,0.2781682014465332,0.36652886867523193,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +125,MTR_173,0.1729171872138977,0.23121309280395508,0.23843687772750854,0.20408254861831665,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +126,MTR_176,0.2348511815071106,0.18375170230865479,0.2974121570587158,0.2890886068344116,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +127,MTR_178,0.14082670211791992,0.19780880212783813,0.20428508520126343,0.21877485513687134,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +128,MTR_188,0.1590394377708435,0.2166680097579956,0.22702306509017944,0.21646595001220703,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +129,MTR_196,0.16522926092147827,0.18610912561416626,0.18860769271850586,0.17618966102600098,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +130,MTR_198,0.1717458963394165,0.1959974765777588,0.19735658168792725,0.252621591091156,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +131,MTR_199,0.15142661333084106,0.16796386241912842,0.22746026515960693,0.18713164329528809,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +132,MTR_218,0.19443857669830322,0.24762660264968872,0.33488988876342773,0.22208422422409058,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +133,MTR_219,0.1092262864112854,0.1452425718307495,0.17489540576934814,0.19327980279922485,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +134,MTR_221,0.30388593673706055,0.25779402256011963,0.33928602933883667,0.29197990894317627,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +135,MTR_223,0.0968254804611206,0.13330501317977905,0.1607900857925415,0.18033474683761597,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +136,MTR_224,0.2201290726661682,0.1949748992919922,0.28506016731262207,0.31246358156204224,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +137,MTR_227,0.15055346488952637,0.22893482446670532,0.26642274856567383,0.19648349285125732,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +138,MTR_235,0.20088845491409302,0.2063673734664917,0.20716041326522827,0.233517587184906,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +139,MTR_237,0.12736862897872925,0.20101779699325562,0.2661118507385254,0.29977869987487793,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +140,MTR_240,0.23204362392425537,0.23898208141326904,0.2756419777870178,0.2306736707687378,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +141,MTR_241,0.6177740097045898,0.3445650339126587,0.30110669136047363,0.4045507311820984,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +142,MTR_244,0.2139379382133484,0.22423940896987915,0.19529151916503906,0.18403750658035278,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +143,MTR_248,0.18233466148376465,0.16358047723770142,0.18940162658691406,0.1917441487312317,VOE_scan,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, 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