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0000000000000000000000000000000000000000..9cf2f0bbe4c4bbb981dbbb08451554b8324d860e --- /dev/null +++ b/mridata_knee_3dfse/12x/Noise2Recon_1sub/config.yaml @@ -0,0 +1,207 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 12 +AUG_TRAIN: + MOTION_P: 0.2 + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 12 + CALIBRATION_SIZE: 20 + CENTER_FRACTIONS: [] + MAX_ATTEMPTS: 30 + NAME: PoissonDiskMaskFunc + USE_MOTION: false + 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: false + BATCH_BY: [] + NUM_WORKERS: 12 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: AlternatingSampler + SUBSAMPLE_TRAIN: + NUM_TOTAL: -1 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 13 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + TEST: + - mridata_knee_2019_test + TRAIN: + - mridata_knee_2019_train + VAL: + - mridata_knee_2019_val +DESCRIPTION: + BRIEF: U-NET LR = 1e-3 N2R 12x mridata.org - 1 subject, 13 unsupervised alternating + sampler (1/1), Std Dev [0.2, 0.5) + ENTITY_NAME: '' + EXP_NAME: noise2recon/mridata_knee_3dfse/12x/Noise2Recon_1sub + PROJECT_NAME: '' + TAGS: + - noise2recon + - noise2recon + - 12x + - mridata_knee_3dfse +MODEL: + A2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + CONSISTENCY: + AUG: + MOTION: + RANGE: + - 0.2 + - 0.5 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE: + MASK: + RHO: 1.0 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + STD_DEV: + - 0.2 + - 0.5 + LATENT_LOSS_NAME: mag_l1 + LATENT_LOSS_WEIGHT: 0.1 + LOSS_NAME: l1 + LOSS_WEIGHT: 0.1 + NUM_LATENT_LAYERS: 1 + USE_CONSISTENCY: true + USE_LATENT: 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 + M2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + META_ARCHITECTURE: N2RModel + N2R: + META_ARCHITECTURE: UnetModel + USE_SUPERVISED_CONSISTENCY: false + NM2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + SSDU: + MASKER: + PARAMS: {} + META_ARCHITECTURE: GeneralizedUnrolledCNN + UNET: + BLOCK_ORDER: + - conv + - relu + - conv + - relu + - batchnorm + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NORMALIZE: false + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + BLOCK_ARCHITECTURE: ResNet + 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://noise2recon/mridata_knee_3dfse/12x/Noise2Recon_1sub +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + BIAS_LR_FACTOR: 1.0 + CHECKPOINT_PERIOD: -10 + GAMMA: 0.1 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: StepLR + MAX_ITER: 80000 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: + - 320000 + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 16 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_BIAS: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: -10 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 0 + VAL_AS_TEST: true + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim (Wang) +TIME_SCALE: iter +VERSION: 1 +VIS_PERIOD: 400 diff --git 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0000000000000000000000000000000000000000..7bf8cafbeb207d052438ef414b302457e9a57ba7 --- /dev/null +++ b/mridata_knee_3dfse/12x/Noise2Recon_2sub/config.yaml @@ -0,0 +1,207 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 12 +AUG_TRAIN: + MOTION_P: 0.2 + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 12 + CALIBRATION_SIZE: 20 + CENTER_FRACTIONS: [] + MAX_ATTEMPTS: 30 + NAME: PoissonDiskMaskFunc + USE_MOTION: false + 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: false + BATCH_BY: [] + NUM_WORKERS: 12 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: AlternatingSampler + SUBSAMPLE_TRAIN: + NUM_TOTAL: -1 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 12 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + TEST: + - mridata_knee_2019_test + TRAIN: + - mridata_knee_2019_train + VAL: + - mridata_knee_2019_val +DESCRIPTION: + BRIEF: U-NET LR = 1e-3 N2R 12x mridata.org - 2 subject, 12 unsupervised alternating + sampler (1/1), lambda=0.02, Std Dev [0.2, 0.5) + ENTITY_NAME: '' + EXP_NAME: noise2recon/mridata_knee_3dfse/12x/Noise2Recon_2sub + PROJECT_NAME: '' + TAGS: + - noise2recon + - noise2recon + - 12x + - mridata_knee_3dfse +MODEL: + A2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + CONSISTENCY: + AUG: + MOTION: + RANGE: + - 0.2 + - 0.5 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE: + MASK: + RHO: 1.0 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + STD_DEV: + - 0.2 + - 0.5 + LATENT_LOSS_NAME: mag_l1 + LATENT_LOSS_WEIGHT: 0.1 + LOSS_NAME: l1 + LOSS_WEIGHT: 0.1 + NUM_LATENT_LAYERS: 1 + USE_CONSISTENCY: true + USE_LATENT: 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 + M2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + META_ARCHITECTURE: N2RModel + N2R: + META_ARCHITECTURE: UnetModel + USE_SUPERVISED_CONSISTENCY: false + NM2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + SSDU: + MASKER: + PARAMS: {} + META_ARCHITECTURE: GeneralizedUnrolledCNN + UNET: + BLOCK_ORDER: + - conv + - relu + - conv + - relu + - batchnorm + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NORMALIZE: false + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + BLOCK_ARCHITECTURE: ResNet + 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://noise2recon/mridata_knee_3dfse/12x/Noise2Recon_2sub +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + BIAS_LR_FACTOR: 1.0 + CHECKPOINT_PERIOD: -10 + GAMMA: 0.1 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: StepLR + MAX_ITER: 80000 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: + - 320000 + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 16 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_BIAS: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: -10 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 0 + VAL_AS_TEST: true + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim (Wang) +TIME_SCALE: iter +VERSION: 1 +VIS_PERIOD: 400 diff --git 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0000000000000000000000000000000000000000..a750d6872f31dca7845ea283c03d542c33fd6cd7 --- /dev/null +++ b/mridata_knee_3dfse/12x/Noise2Recon_3sub/config.yaml @@ -0,0 +1,207 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 12 +AUG_TRAIN: + MOTION_P: 0.2 + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 12 + CALIBRATION_SIZE: 20 + CENTER_FRACTIONS: [] + MAX_ATTEMPTS: 30 + NAME: PoissonDiskMaskFunc + USE_MOTION: false + 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: false + BATCH_BY: [] + NUM_WORKERS: 12 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: AlternatingSampler + SUBSAMPLE_TRAIN: + NUM_TOTAL: -1 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 11 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + TEST: + - mridata_knee_2019_test + TRAIN: + - mridata_knee_2019_train + VAL: + - mridata_knee_2019_val +DESCRIPTION: + BRIEF: U-NET LR = 1e-3 N2R 12x mridata.org - 3 subject, 9 unsupervised alternating + sampler (1/1), lambda=0.02, Std Dev [0.2, 0.5) + ENTITY_NAME: '' + EXP_NAME: noise2recon/mridata_knee_3dfse/12x/Noise2Recon_3sub + PROJECT_NAME: '' + TAGS: + - noise2recon + - noise2recon + - 12x + - mridata_knee_3dfse +MODEL: + A2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + CONSISTENCY: + AUG: + MOTION: + RANGE: + - 0.2 + - 0.5 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE: + MASK: + RHO: 1.0 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + STD_DEV: + - 0.2 + - 0.5 + LATENT_LOSS_NAME: mag_l1 + LATENT_LOSS_WEIGHT: 0.1 + LOSS_NAME: l1 + LOSS_WEIGHT: 0.1 + NUM_LATENT_LAYERS: 1 + USE_CONSISTENCY: true + USE_LATENT: 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 + M2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + META_ARCHITECTURE: N2RModel + N2R: + META_ARCHITECTURE: UnetModel + USE_SUPERVISED_CONSISTENCY: false + NM2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + SSDU: + MASKER: + PARAMS: {} + META_ARCHITECTURE: GeneralizedUnrolledCNN + UNET: + BLOCK_ORDER: + - conv + - relu + - conv + - relu + - batchnorm + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NORMALIZE: false + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + BLOCK_ARCHITECTURE: ResNet + 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://noise2recon/mridata_knee_3dfse/12x/Noise2Recon_3sub +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + BIAS_LR_FACTOR: 1.0 + CHECKPOINT_PERIOD: -10 + GAMMA: 0.1 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: StepLR + MAX_ITER: 80000 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: + - 320000 + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 16 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_BIAS: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: -10 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 0 + VAL_AS_TEST: true + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim (Wang) +TIME_SCALE: iter +VERSION: 1 +VIS_PERIOD: 400 diff --git a/mridata_knee_3dfse/12x/Noise2Recon_3sub/model-gpu.ckpt b/mridata_knee_3dfse/12x/Noise2Recon_3sub/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..e79595041dc7f82cdc6f3bffb2717735247efcd1 --- /dev/null +++ b/mridata_knee_3dfse/12x/Noise2Recon_3sub/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:0a6201364edd10545e8616fb9d414d261d9b1ce18767c0ec211d8fd6bffc5f1c +size 93110199 diff --git a/mridata_knee_3dfse/12x/Noise2Recon_3sub/model-raw-gpu.ckpt b/mridata_knee_3dfse/12x/Noise2Recon_3sub/model-raw-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..c4d318bbb68a88795a89110de9120f225adf7d3d --- /dev/null +++ b/mridata_knee_3dfse/12x/Noise2Recon_3sub/model-raw-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:6ad3ccfa8f5622301d621f4a9c2aa2cbc7766f9657548c6488f2646c90e7dad3 +size 93110199 diff --git a/mridata_knee_3dfse/12x/Noise2Recon_3sub/model-raw.ckpt 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index 0000000000000000000000000000000000000000..c4854c936287dcc6048b43db5e7f9c65064efbcc --- /dev/null +++ b/mridata_knee_3dfse/12x/Supervised+Aug-FT_1sub/config.yaml @@ -0,0 +1,208 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 12 +AUG_TRAIN: + MOTION_P: 0.2 + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 12 + CALIBRATION_SIZE: 20 + CENTER_FRACTIONS: [] + MAX_ATTEMPTS: 30 + NAME: PoissonDiskMaskFunc + USE_MOTION: false + USE_NOISE: true +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: [] + DROP_LAST: true + FILTER: + BY: [] + GROUP_SAMPLER: + AS_BATCH_SAMPLER: false + BATCH_BY: [] + NUM_WORKERS: 12 + 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: + TEST: + - mridata_knee_2019_test + TRAIN: + - mridata_knee_2019_train + VAL: + - mridata_knee_2019_val +DESCRIPTION: + BRIEF: Denoiser finetuning w/ noise aug U-Net 12x - augmentation std_dev=(0.2, 0.5), + 1 supervised scan(s), 0 unsupervised scan(s), 40k iterations, restart-iteration-count + = True + ENTITY_NAME: '' + EXP_NAME: noise2recon/mridata_knee_3dfse/12x/Supervised+Aug-FT_1sub + PROJECT_NAME: '' + TAGS: + - baseline + - supervised+aug-ft + - 12x + - mridata_knee_3dfse +MODEL: + A2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + CONSISTENCY: + AUG: + MOTION: + RANGE: + - 0.2 + - 0.5 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE: + MASK: + RHO: 1.0 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + STD_DEV: + - 0.2 + - 0.5 + LATENT_LOSS_NAME: mag_l1 + LATENT_LOSS_WEIGHT: 0.1 + LOSS_NAME: l1 + LOSS_WEIGHT: 0.1 + NUM_LATENT_LAYERS: 1 + USE_CONSISTENCY: true + USE_LATENT: 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 + M2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + META_ARCHITECTURE: UnetModel + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NM2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + SSDU: + MASKER: + PARAMS: {} + META_ARCHITECTURE: GeneralizedUnrolledCNN + UNET: + BLOCK_ORDER: + - conv + - relu + - conv + - relu + - batchnorm + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NORMALIZE: false + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + BLOCK_ARCHITECTURE: ResNet + 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: /bmrNAS/people/arjun/results/ss_recon/n2r-experiments/denoise-pretrainer/version_010/model_0039199.pth +OUTPUT_DIR: results://noise2recon/mridata_knee_3dfse/12x/Supervised+Aug-FT_1sub +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + BIAS_LR_FACTOR: 1.0 + CHECKPOINT_PERIOD: -20 + GAMMA: 0.1 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: '' + MAX_ITER: 40000 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: + - 320000 + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 16 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_BIAS: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: -20 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 0 + VAL_AS_TEST: true + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim (Wang) +TIME_SCALE: iter +VERSION: 1 +VIS_PERIOD: 400 diff --git a/mridata_knee_3dfse/12x/Supervised+Aug-FT_1sub/model-gpu.ckpt b/mridata_knee_3dfse/12x/Supervised+Aug-FT_1sub/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..55845b14108a9dce7014b34de758fd215b53d9be --- /dev/null +++ b/mridata_knee_3dfse/12x/Supervised+Aug-FT_1sub/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:832927e6a3116e16ff09849f3014ed1067a6f6d1581c7dae62e6a8276aff5fc4 +size 93109175 diff --git a/mridata_knee_3dfse/12x/Supervised+Aug-FT_1sub/model-raw-gpu.ckpt b/mridata_knee_3dfse/12x/Supervised+Aug-FT_1sub/model-raw-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..85aca02eb2ecfc4e7e1544c333625256d42494ef --- /dev/null +++ b/mridata_knee_3dfse/12x/Supervised+Aug-FT_1sub/model-raw-gpu.ckpt @@ -0,0 +1,3 @@ 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sha256:ee736009b02e29e4abf8e79ee705eef2c39181e8f2a27080cd78d33f529bfb1c +size 93103415 diff --git a/mridata_knee_3dfse/12x/Supervised+Aug-FT_2sub/config.yaml b/mridata_knee_3dfse/12x/Supervised+Aug-FT_2sub/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..242a5e13955c40c347d299c6bfe2cc2ddcdadc3f --- /dev/null +++ b/mridata_knee_3dfse/12x/Supervised+Aug-FT_2sub/config.yaml @@ -0,0 +1,208 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 12 +AUG_TRAIN: + MOTION_P: 0.2 + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 12 + CALIBRATION_SIZE: 20 + CENTER_FRACTIONS: [] + MAX_ATTEMPTS: 30 + NAME: PoissonDiskMaskFunc + USE_MOTION: false + USE_NOISE: true +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: [] + DROP_LAST: true + FILTER: + BY: [] + GROUP_SAMPLER: + AS_BATCH_SAMPLER: false + BATCH_BY: [] + NUM_WORKERS: 12 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: '' + SUBSAMPLE_TRAIN: + NUM_TOTAL: 2 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + TEST: + - mridata_knee_2019_test + TRAIN: + - mridata_knee_2019_train + VAL: + - mridata_knee_2019_val +DESCRIPTION: + BRIEF: Denoiser finetuning w/ noise aug U-Net 12x - augmentation std_dev=(0.2, 0.5), + 2 supervised scan(s), 0 unsupervised scan(s), 40k iterations, restart-iteration-count + = True + ENTITY_NAME: '' + EXP_NAME: noise2recon/mridata_knee_3dfse/12x/Supervised+Aug-FT_2sub + PROJECT_NAME: '' + TAGS: + - baseline + - supervised+aug-ft + - 12x + - mridata_knee_3dfse +MODEL: + A2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + CONSISTENCY: + AUG: + MOTION: + RANGE: + - 0.2 + - 0.5 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE: + MASK: + RHO: 1.0 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + STD_DEV: + - 0.2 + - 0.5 + LATENT_LOSS_NAME: mag_l1 + LATENT_LOSS_WEIGHT: 0.1 + LOSS_NAME: l1 + LOSS_WEIGHT: 0.1 + NUM_LATENT_LAYERS: 1 + USE_CONSISTENCY: true + USE_LATENT: 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 + M2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + META_ARCHITECTURE: UnetModel + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NM2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + SSDU: + MASKER: + PARAMS: {} + META_ARCHITECTURE: GeneralizedUnrolledCNN + UNET: + BLOCK_ORDER: + - conv + - relu + - conv + - relu + - batchnorm + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NORMALIZE: false + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + BLOCK_ARCHITECTURE: ResNet + 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: /bmrNAS/people/arjun/results/ss_recon/n2r-experiments/denoise-pretrainer/version_014/model_0039199.pth +OUTPUT_DIR: results://noise2recon/mridata_knee_3dfse/12x/Supervised+Aug-FT_2sub +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + BIAS_LR_FACTOR: 1.0 + CHECKPOINT_PERIOD: -10 + GAMMA: 0.1 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: '' + MAX_ITER: 40000 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: + - 320000 + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 16 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_BIAS: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: -10 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 0 + VAL_AS_TEST: true + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim (Wang) +TIME_SCALE: iter +VERSION: 1 +VIS_PERIOD: 400 diff --git a/mridata_knee_3dfse/12x/Supervised+Aug-FT_2sub/model-gpu.ckpt b/mridata_knee_3dfse/12x/Supervised+Aug-FT_2sub/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..be464d149ba3501bfb5d0f3fefd021a82c0b6983 --- /dev/null +++ b/mridata_knee_3dfse/12x/Supervised+Aug-FT_2sub/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:3240a814b96a955bc8301643ea6eb5f34fd3fa5a8802ca1e44abf0bcaf7be9a0 +size 93109175 diff --git a/mridata_knee_3dfse/12x/Supervised+Aug-FT_2sub/model-raw-gpu.ckpt 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[] + MAX_ATTEMPTS: 30 + NAME: PoissonDiskMaskFunc + USE_MOTION: false + USE_NOISE: true +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: [] + DROP_LAST: true + FILTER: + BY: [] + GROUP_SAMPLER: + AS_BATCH_SAMPLER: false + BATCH_BY: [] + NUM_WORKERS: 12 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: '' + SUBSAMPLE_TRAIN: + NUM_TOTAL: 3 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + TEST: + - mridata_knee_2019_test + TRAIN: + - mridata_knee_2019_train + VAL: + - mridata_knee_2019_val +DESCRIPTION: + BRIEF: Denoiser finetuning w/ noise aug U-Net 12x - augmentation std_dev=(0.2, 0.5), + 3 supervised scan(s), 0 unsupervised scan(s), 40k iterations, restart-iteration-count + = True + ENTITY_NAME: '' + EXP_NAME: noise2recon/mridata_knee_3dfse/12x/Supervised+Aug-FT_3sub + PROJECT_NAME: '' + TAGS: + - baseline + - supervised+aug-ft + - 12x + - mridata_knee_3dfse +MODEL: + A2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + CONSISTENCY: + AUG: + MOTION: + RANGE: + - 0.2 + - 0.5 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE: + MASK: + RHO: 1.0 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + STD_DEV: + - 0.2 + - 0.5 + LATENT_LOSS_NAME: mag_l1 + LATENT_LOSS_WEIGHT: 0.1 + LOSS_NAME: l1 + LOSS_WEIGHT: 0.1 + NUM_LATENT_LAYERS: 1 + USE_CONSISTENCY: true + USE_LATENT: 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 + M2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + META_ARCHITECTURE: UnetModel + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NM2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + SSDU: + MASKER: + PARAMS: {} + META_ARCHITECTURE: GeneralizedUnrolledCNN + UNET: + BLOCK_ORDER: + - conv + - relu + - conv + - relu + - batchnorm + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NORMALIZE: false + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + BLOCK_ARCHITECTURE: ResNet + 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: /bmrNAS/people/arjun/results/ss_recon/n2r-experiments/denoise-pretrainer/version_015/model_0036399.pth +OUTPUT_DIR: results://noise2recon/mridata_knee_3dfse/12x/Supervised+Aug-FT_3sub +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + BIAS_LR_FACTOR: 1.0 + CHECKPOINT_PERIOD: -10 + GAMMA: 0.1 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: '' + MAX_ITER: 40000 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: + - 320000 + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 16 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_BIAS: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: -10 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 0 + VAL_AS_TEST: true + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim (Wang) +TIME_SCALE: iter +VERSION: 1 +VIS_PERIOD: 400 diff --git a/mridata_knee_3dfse/12x/Supervised+Aug-FT_3sub/model-gpu.ckpt b/mridata_knee_3dfse/12x/Supervised+Aug-FT_3sub/model-gpu.ckpt new file mode 100644 index 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0000000000000000000000000000000000000000..d2fc5d2e5b534bf3a3700be7a8ac6b76f8b0659a --- /dev/null +++ b/mridata_knee_3dfse/12x/Supervised+Aug_1sub/config.yaml @@ -0,0 +1,207 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 12 +AUG_TRAIN: + MOTION_P: 0.2 + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 12 + CALIBRATION_SIZE: 20 + CENTER_FRACTIONS: [] + MAX_ATTEMPTS: 30 + NAME: PoissonDiskMaskFunc + USE_MOTION: false + USE_NOISE: true +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: [] + DROP_LAST: true + FILTER: + BY: [] + GROUP_SAMPLER: + AS_BATCH_SAMPLER: false + BATCH_BY: [] + NUM_WORKERS: 12 + 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: + TEST: + - mridata_knee_2019_test + TRAIN: + - mridata_knee_2019_train + VAL: + - mridata_knee_2019_val +DESCRIPTION: + BRIEF: U-NET LR = 1e-3 Baseline 12x mridata.org w/ Noise augmentation - 1 subject, + p=0.2, Std Dev [0.2, 0.5) + ENTITY_NAME: '' + EXP_NAME: noise2recon/mridata_knee_3dfse/12x/Supervised+Aug_1sub + PROJECT_NAME: '' + TAGS: + - baseline + - supervised+aug + - 12x + - mridata_knee_3dfse +MODEL: + A2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + CONSISTENCY: + AUG: + MOTION: + RANGE: + - 0.2 + - 0.5 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE: + MASK: + RHO: 1.0 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + STD_DEV: + - 0.2 + - 0.5 + LATENT_LOSS_NAME: mag_l1 + LATENT_LOSS_WEIGHT: 0.1 + LOSS_NAME: l1 + LOSS_WEIGHT: 0.1 + NUM_LATENT_LAYERS: 1 + USE_CONSISTENCY: true + USE_LATENT: 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 + M2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + META_ARCHITECTURE: UnetModel + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NM2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + SSDU: + MASKER: + PARAMS: {} + META_ARCHITECTURE: GeneralizedUnrolledCNN + UNET: + BLOCK_ORDER: + - conv + - relu + - conv + - relu + - batchnorm + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NORMALIZE: false + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + BLOCK_ARCHITECTURE: ResNet + 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://noise2recon/mridata_knee_3dfse/12x/Supervised+Aug_1sub +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + BIAS_LR_FACTOR: 1.0 + CHECKPOINT_PERIOD: -20 + GAMMA: 0.1 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: '' + MAX_ITER: 80000 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: + - 160000 + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 16 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_BIAS: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: -20 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 0 + VAL_AS_TEST: true + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim (Wang) +TIME_SCALE: iter +VERSION: 1 +VIS_PERIOD: 400 diff --git a/mridata_knee_3dfse/12x/Supervised+Aug_1sub/model-gpu.ckpt b/mridata_knee_3dfse/12x/Supervised+Aug_1sub/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..070cbc8b359a02e13c42fc736f88199cc89fe817 --- /dev/null +++ b/mridata_knee_3dfse/12x/Supervised+Aug_1sub/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:3e623f4af95845ca5daba5ea3d658656f8b51884fdfe98824b9905ea6e77aa4f +size 93109175 diff --git a/mridata_knee_3dfse/12x/Supervised+Aug_1sub/model-raw-gpu.ckpt b/mridata_knee_3dfse/12x/Supervised+Aug_1sub/model-raw-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..9b9b82b6f710904ebcce26b83e1df7653ba4c7c9 --- /dev/null +++ b/mridata_knee_3dfse/12x/Supervised+Aug_1sub/model-raw-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:7b4b74ce02dc8b52c5c1eec8bd5b1f81dbff3475a34e592a9c32944b81f70df3 +size 93109175 diff --git 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b/mridata_knee_3dfse/12x/Supervised+Aug_2sub/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..6adc27c243c589c1f81b94d748d9c7fdd90e6bdd --- /dev/null +++ b/mridata_knee_3dfse/12x/Supervised+Aug_2sub/config.yaml @@ -0,0 +1,198 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 12 +AUG_TRAIN: + MOTION_P: 0.2 + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 12 + CALIBRATION_SIZE: 20 + CENTER_FRACTIONS: [] + MAX_ATTEMPTS: 30 + NAME: PoissonDiskMaskFunc + USE_MOTION: false + USE_NOISE: true +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: [] + DROP_LAST: true + FILTER: + BY: [] + GROUP_SAMPLER: + AS_BATCH_SAMPLER: false + BATCH_BY: [] + NUM_WORKERS: 12 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: '' + SUBSAMPLE_TRAIN: + NUM_TOTAL: 2 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + TEST: + - mridata_knee_2019_test + TRAIN: + - mridata_knee_2019_train + VAL: + - mridata_knee_2019_val +DESCRIPTION: + BRIEF: U-NET LR = 1e-3 Baseline 12x mridata.org w/ Noise augmentation - 2 subject, + p=0.2, Std Dev [0.2, 0.5) + ENTITY_NAME: '' + EXP_NAME: noise2recon/mridata_knee_3dfse/12x/Supervised+Aug_2sub + PROJECT_NAME: '' + TAGS: + - baseline + - supervised+aug + - 12x + - mridata_knee_3dfse +MODEL: + A2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + CONSISTENCY: + AUG: + MOTION: + RANGE: + - 0.2 + - 0.5 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE: + MASK: + RHO: 1.0 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + STD_DEV: + - 0.2 + - 0.5 + LATENT_LOSS_NAME: mag_l1 + LATENT_LOSS_WEIGHT: 0.1 + LOSS_NAME: l1 + LOSS_WEIGHT: 0.1 + NUM_LATENT_LAYERS: 1 + USE_CONSISTENCY: true + USE_LATENT: 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 + M2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + META_ARCHITECTURE: UnetModel + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NM2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + SSDU: + MASKER: + PARAMS: {} + META_ARCHITECTURE: GeneralizedUnrolledCNN + UNET: + BLOCK_ORDER: + - conv + - relu + - conv + - relu + - batchnorm + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NORMALIZE: false + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + BLOCK_ARCHITECTURE: ResNet + 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://noise2recon/mridata_knee_3dfse/12x/Supervised+Aug_2sub +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + BIAS_LR_FACTOR: 1.0 + CHECKPOINT_PERIOD: -10 + GAMMA: 0.1 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: StepLR + MAX_ITER: 160000 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: + - 160000 + TEST_BATCH_SIZE: 1 + TRAIN_BATCH_SIZE: 4 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_BIAS: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: -10 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 0 + VAL_AS_TEST: true + VAL_METRICS: + RECON: [] +TIME_SCALE: iter +VERSION: 1 +VIS_PERIOD: 400 diff --git a/mridata_knee_3dfse/12x/Supervised+Aug_2sub/model-gpu.ckpt b/mridata_knee_3dfse/12x/Supervised+Aug_2sub/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..28b4ec1b0b3b5b681eed755a28decde1398ce190 --- /dev/null +++ b/mridata_knee_3dfse/12x/Supervised+Aug_2sub/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:2a968a569791b60cbc17170bb6c31abfc331c5b4063dbd79fb83cef2aa1df2af +size 93109303 diff --git a/mridata_knee_3dfse/12x/Supervised+Aug_2sub/model-raw-gpu.ckpt b/mridata_knee_3dfse/12x/Supervised+Aug_2sub/model-raw-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..140e31e6047f645f4291ff629c70f1ab526a9213 --- /dev/null +++ b/mridata_knee_3dfse/12x/Supervised+Aug_2sub/model-raw-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:9fd89e3e2845e5fafdf610dc80a21f8a22873968cd492944a74af3cec6422566 +size 93109303 diff --git a/mridata_knee_3dfse/12x/Supervised+Aug_2sub/model-raw.ckpt b/mridata_knee_3dfse/12x/Supervised+Aug_2sub/model-raw.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..ecfe80a131229c923f7e22c4bd92bdeee15135ab --- /dev/null +++ b/mridata_knee_3dfse/12x/Supervised+Aug_2sub/model-raw.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:88ec23a1c845c43b510a297abd19720185da69926ef87db4b759872ff00d2c4f +size 93103543 diff --git a/mridata_knee_3dfse/12x/Supervised+Aug_2sub/model.ckpt b/mridata_knee_3dfse/12x/Supervised+Aug_2sub/model.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..ecfe80a131229c923f7e22c4bd92bdeee15135ab --- /dev/null +++ b/mridata_knee_3dfse/12x/Supervised+Aug_2sub/model.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:88ec23a1c845c43b510a297abd19720185da69926ef87db4b759872ff00d2c4f +size 93103543 diff --git a/mridata_knee_3dfse/12x/Supervised+Aug_3sub/config.yaml b/mridata_knee_3dfse/12x/Supervised+Aug_3sub/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..2fda2ca7c9b3b2311470a5a36cf38a944fd4b2a1 --- /dev/null +++ b/mridata_knee_3dfse/12x/Supervised+Aug_3sub/config.yaml @@ -0,0 +1,207 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 12 +AUG_TRAIN: + MOTION_P: 0.2 + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 12 + CALIBRATION_SIZE: 20 + CENTER_FRACTIONS: [] + MAX_ATTEMPTS: 30 + NAME: PoissonDiskMaskFunc + USE_MOTION: false + USE_NOISE: true +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: [] + DROP_LAST: true + FILTER: + BY: [] + GROUP_SAMPLER: + AS_BATCH_SAMPLER: false + BATCH_BY: [] + NUM_WORKERS: 12 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: '' + SUBSAMPLE_TRAIN: + NUM_TOTAL: 3 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + TEST: + - mridata_knee_2019_test + TRAIN: + - mridata_knee_2019_train + VAL: + - mridata_knee_2019_val +DESCRIPTION: + BRIEF: U-NET LR = 1e-3 Baseline 12x mridata.org w/ Noise augmentation - 3 subject, + p=0.2, Std Dev [0.2, 0.5) + ENTITY_NAME: '' + EXP_NAME: noise2recon/mridata_knee_3dfse/12x/Supervised+Aug_3sub + PROJECT_NAME: '' + TAGS: + - baseline + - supervised+aug + - 12x + - mridata_knee_3dfse +MODEL: + A2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + CONSISTENCY: + AUG: + MOTION: + RANGE: + - 0.2 + - 0.5 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE: + MASK: + RHO: 1.0 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + STD_DEV: + - 0.2 + - 0.5 + LATENT_LOSS_NAME: mag_l1 + LATENT_LOSS_WEIGHT: 0.1 + LOSS_NAME: l1 + LOSS_WEIGHT: 0.1 + NUM_LATENT_LAYERS: 1 + USE_CONSISTENCY: true + USE_LATENT: 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 + M2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + META_ARCHITECTURE: UnetModel + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NM2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + SSDU: + MASKER: + PARAMS: {} + META_ARCHITECTURE: GeneralizedUnrolledCNN + UNET: + BLOCK_ORDER: + - conv + - relu + - conv + - relu + - batchnorm + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NORMALIZE: false + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + BLOCK_ARCHITECTURE: ResNet + 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://noise2recon/mridata_knee_3dfse/12x/Supervised+Aug_3sub +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + BIAS_LR_FACTOR: 1.0 + CHECKPOINT_PERIOD: -10 + GAMMA: 0.1 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: StepLR + MAX_ITER: 80000 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: + - 80000 + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 16 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_BIAS: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: -10 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 0 + VAL_AS_TEST: true + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim (Wang) +TIME_SCALE: iter +VERSION: 1 +VIS_PERIOD: 400 diff --git a/mridata_knee_3dfse/12x/Supervised+Aug_3sub/model-gpu.ckpt b/mridata_knee_3dfse/12x/Supervised+Aug_3sub/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..0d38282ac6ac19f5b7cf98dff289f096fbcb6a70 --- /dev/null +++ b/mridata_knee_3dfse/12x/Supervised+Aug_3sub/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:0686682c3c93243fbcdec80a86e1186984f51428e8d94f43945ca3af00e767e4 +size 93109367 diff --git a/mridata_knee_3dfse/12x/Supervised+Aug_3sub/model-raw-gpu.ckpt b/mridata_knee_3dfse/12x/Supervised+Aug_3sub/model-raw-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..eb1b2e77c9e08198444d3dd6da69fe020ccf60cd --- /dev/null +++ b/mridata_knee_3dfse/12x/Supervised+Aug_3sub/model-raw-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:08453d35cfbd92590338f4b558e7bc80acf4d725173aee91d0893da47f9bccb9 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a/mridata_knee_3dfse/12x/Supervised-FT_1sub/config.yaml b/mridata_knee_3dfse/12x/Supervised-FT_1sub/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..8d8d0e61200c3350b3f0e759963aea333cf725f0 --- /dev/null +++ b/mridata_knee_3dfse/12x/Supervised-FT_1sub/config.yaml @@ -0,0 +1,207 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 12 +AUG_TRAIN: + MOTION_P: 0.2 + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 12 + CALIBRATION_SIZE: 20 + CENTER_FRACTIONS: [] + MAX_ATTEMPTS: 30 + NAME: PoissonDiskMaskFunc + USE_MOTION: false + 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: false + BATCH_BY: [] + NUM_WORKERS: 12 + 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: + TEST: + - mridata_knee_2019_test + TRAIN: + - mridata_knee_2019_train + VAL: + - mridata_knee_2019_val +DESCRIPTION: + BRIEF: Denoiser finetuning U-Net 12x - std_dev=(0.2, 0.5), 1 supervised scan(s), + 0 unsupervised scan(s), 40k iterations, restart-iteration-count = True + ENTITY_NAME: '' + EXP_NAME: noise2recon/mridata_knee_3dfse/12x/Supervised-FT_1sub + PROJECT_NAME: '' + TAGS: + - baseline + - supervised-ft + - 12x + - mridata_knee_3dfse +MODEL: + A2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + CONSISTENCY: + AUG: + MOTION: + RANGE: + - 0.2 + - 0.5 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE: + MASK: + RHO: 1.0 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + STD_DEV: + - 1 + LATENT_LOSS_NAME: mag_l1 + LATENT_LOSS_WEIGHT: 0.1 + LOSS_NAME: l1 + LOSS_WEIGHT: 0.1 + NUM_LATENT_LAYERS: 1 + USE_CONSISTENCY: true + USE_LATENT: false + CS: + MAX_ITER: 200 + REGULARIZATION: 0.005 + DENOISING: + META_ARCHITECTURE: GeneralizedUnrolledCNN + NOISE: + STD_DEV: + - 0.2 + - 0.5 + USE_FULLY_SAMPLED_TARGET: true + USE_FULLY_SAMPLED_TARGET_EVAL: null + DEVICE: cpu + M2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + META_ARCHITECTURE: UnetModel + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NM2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + SSDU: + MASKER: + PARAMS: {} + META_ARCHITECTURE: GeneralizedUnrolledCNN + UNET: + BLOCK_ORDER: + - conv + - relu + - conv + - relu + - batchnorm + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NORMALIZE: false + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + BLOCK_ARCHITECTURE: ResNet + 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: /bmrNAS/people/arjun/results/ss_recon/n2r-experiments/denoise-pretrainer/version_010/model_0039199.pth +OUTPUT_DIR: results://noise2recon/mridata_knee_3dfse/12x/Supervised-FT_1sub +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + BIAS_LR_FACTOR: 1.0 + CHECKPOINT_PERIOD: -20 + GAMMA: 0.1 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: '' + MAX_ITER: 40000 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: + - 320000 + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 16 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_BIAS: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: -20 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 0 + VAL_AS_TEST: true + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim (Wang) +TIME_SCALE: iter +VERSION: 1 +VIS_PERIOD: 400 diff --git a/mridata_knee_3dfse/12x/Supervised-FT_1sub/model-gpu.ckpt b/mridata_knee_3dfse/12x/Supervised-FT_1sub/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..d7b00895d080d5ad9752db6c8018a58dcc21818d --- /dev/null +++ b/mridata_knee_3dfse/12x/Supervised-FT_1sub/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:11be2ab474bbb641404cd5404c5a79ca41dec8697dc257e6223ad4399600bd5e +size 93109175 diff --git a/mridata_knee_3dfse/12x/Supervised-FT_1sub/model-raw-gpu.ckpt b/mridata_knee_3dfse/12x/Supervised-FT_1sub/model-raw-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..62bbb993f2250217fd87009ad6a506f359df75ca --- /dev/null +++ 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@@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f2b495d81a094d71902f3a42fd4b589df0b4257104596c3905b8b3f00641c53f +size 93103415 diff --git a/mridata_knee_3dfse/12x/Supervised-FT_2sub/config.yaml b/mridata_knee_3dfse/12x/Supervised-FT_2sub/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..8b03b5544cee4367559f2514fc38b87d42428360 --- /dev/null +++ b/mridata_knee_3dfse/12x/Supervised-FT_2sub/config.yaml @@ -0,0 +1,207 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 12 +AUG_TRAIN: + MOTION_P: 0.2 + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 12 + CALIBRATION_SIZE: 20 + CENTER_FRACTIONS: [] + MAX_ATTEMPTS: 30 + NAME: PoissonDiskMaskFunc + USE_MOTION: false + 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: false + BATCH_BY: [] + NUM_WORKERS: 12 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: '' + SUBSAMPLE_TRAIN: + NUM_TOTAL: 2 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + TEST: + - mridata_knee_2019_test + TRAIN: + - mridata_knee_2019_train + VAL: + - mridata_knee_2019_val +DESCRIPTION: + BRIEF: Denoiser finetuning U-Net 12x - std_dev=(0.2, 0.5), 2 supervised scan(s), + 0 unsupervised scan(s), 40k iterations, restart-iteration-count = True + ENTITY_NAME: '' + EXP_NAME: noise2recon/mridata_knee_3dfse/12x/Supervised-FT_2sub + PROJECT_NAME: '' + TAGS: + - baseline + - supervised-ft + - 12x + - mridata_knee_3dfse +MODEL: + A2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + CONSISTENCY: + AUG: + MOTION: + RANGE: + - 0.2 + - 0.5 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE: + MASK: + RHO: 1.0 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + STD_DEV: + - 1 + LATENT_LOSS_NAME: mag_l1 + LATENT_LOSS_WEIGHT: 0.1 + LOSS_NAME: l1 + LOSS_WEIGHT: 0.1 + NUM_LATENT_LAYERS: 1 + USE_CONSISTENCY: true + USE_LATENT: false + CS: + MAX_ITER: 200 + REGULARIZATION: 0.005 + DENOISING: + META_ARCHITECTURE: GeneralizedUnrolledCNN + NOISE: + STD_DEV: + - 0.2 + - 0.5 + USE_FULLY_SAMPLED_TARGET: true + USE_FULLY_SAMPLED_TARGET_EVAL: null + DEVICE: cpu + M2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + META_ARCHITECTURE: UnetModel + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NM2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + SSDU: + MASKER: + PARAMS: {} + META_ARCHITECTURE: GeneralizedUnrolledCNN + UNET: + BLOCK_ORDER: + - conv + - relu + - conv + - relu + - batchnorm + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NORMALIZE: false + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + BLOCK_ARCHITECTURE: ResNet + 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: /bmrNAS/people/arjun/results/ss_recon/n2r-experiments/denoise-pretrainer/version_014/model_0039199.pth +OUTPUT_DIR: results://noise2recon/mridata_knee_3dfse/12x/Supervised-FT_2sub +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + BIAS_LR_FACTOR: 1.0 + CHECKPOINT_PERIOD: -10 + GAMMA: 0.1 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: '' + MAX_ITER: 40000 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: + - 320000 + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 16 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_BIAS: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: -10 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 0 + VAL_AS_TEST: true + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim (Wang) +TIME_SCALE: iter +VERSION: 1 +VIS_PERIOD: 400 diff --git a/mridata_knee_3dfse/12x/Supervised-FT_2sub/model-gpu.ckpt b/mridata_knee_3dfse/12x/Supervised-FT_2sub/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..2661b507f92511ced73f6fc34d85441e0eff4a30 --- /dev/null +++ b/mridata_knee_3dfse/12x/Supervised-FT_2sub/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:eeef714747833641096120464ae56998e00295795e738e3b7e3c134d4c168789 +size 93109175 diff --git a/mridata_knee_3dfse/12x/Supervised-FT_2sub/model-raw-gpu.ckpt 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file mode 100644 index 0000000000000000000000000000000000000000..283da99dd323c66d0123d5c2aac77af9a735287f --- /dev/null +++ b/mridata_knee_3dfse/12x/Supervised-FT_2sub/model.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:5aa7dbca2903919127adcbb54a2870c90695ab1ab3ec8d0cb7b2c9099e508301 +size 93103415 diff --git a/mridata_knee_3dfse/12x/Supervised-FT_3sub/config.yaml b/mridata_knee_3dfse/12x/Supervised-FT_3sub/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..52a6e30f4107b6182ffffaca7fd17c629e2e20d2 --- /dev/null +++ b/mridata_knee_3dfse/12x/Supervised-FT_3sub/config.yaml @@ -0,0 +1,207 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 12 +AUG_TRAIN: + MOTION_P: 0.2 + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 12 + CALIBRATION_SIZE: 20 + CENTER_FRACTIONS: [] + MAX_ATTEMPTS: 30 + NAME: PoissonDiskMaskFunc + USE_MOTION: false + 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: false + BATCH_BY: [] + NUM_WORKERS: 12 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: '' + SUBSAMPLE_TRAIN: + NUM_TOTAL: 3 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + TEST: + - mridata_knee_2019_test + TRAIN: + - mridata_knee_2019_train + VAL: + - mridata_knee_2019_val +DESCRIPTION: + BRIEF: Denoiser finetuning U-Net 12x - std_dev=(0.2, 0.5), 3 supervised scan(s), + 0 unsupervised scan(s), 40k iterations, restart-iteration-count = True + ENTITY_NAME: '' + EXP_NAME: noise2recon/mridata_knee_3dfse/12x/Supervised-FT_3sub + PROJECT_NAME: '' + TAGS: + - baseline + - supervised-ft + - 12x + - mridata_knee_3dfse +MODEL: + A2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + CONSISTENCY: + AUG: + MOTION: + RANGE: + - 0.2 + - 0.5 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE: + MASK: + RHO: 1.0 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + STD_DEV: + - 1 + LATENT_LOSS_NAME: mag_l1 + LATENT_LOSS_WEIGHT: 0.1 + LOSS_NAME: l1 + LOSS_WEIGHT: 0.1 + NUM_LATENT_LAYERS: 1 + USE_CONSISTENCY: true + USE_LATENT: false + CS: + MAX_ITER: 200 + REGULARIZATION: 0.005 + DENOISING: + META_ARCHITECTURE: GeneralizedUnrolledCNN + NOISE: + STD_DEV: + - 0.2 + - 0.5 + USE_FULLY_SAMPLED_TARGET: true + USE_FULLY_SAMPLED_TARGET_EVAL: null + DEVICE: cpu + M2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + META_ARCHITECTURE: UnetModel + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NM2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + SSDU: + MASKER: + PARAMS: {} + META_ARCHITECTURE: GeneralizedUnrolledCNN + UNET: + BLOCK_ORDER: + - conv + - relu + - conv + - relu + - batchnorm + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NORMALIZE: false + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + BLOCK_ARCHITECTURE: ResNet + 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: /bmrNAS/people/arjun/results/ss_recon/n2r-experiments/denoise-pretrainer/version_015/model_0036399.pth +OUTPUT_DIR: results://noise2recon/mridata_knee_3dfse/12x/Supervised-FT_3sub +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + BIAS_LR_FACTOR: 1.0 + CHECKPOINT_PERIOD: -10 + GAMMA: 0.1 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: '' + MAX_ITER: 40000 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: + - 320000 + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 16 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_BIAS: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: -10 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 0 + VAL_AS_TEST: true + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim (Wang) +TIME_SCALE: iter +VERSION: 1 +VIS_PERIOD: 400 diff --git a/mridata_knee_3dfse/12x/Supervised-FT_3sub/model-gpu.ckpt b/mridata_knee_3dfse/12x/Supervised-FT_3sub/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..cca9f5d6e3c9b8e03cb8f27d2f2f938cfb091b55 --- /dev/null +++ b/mridata_knee_3dfse/12x/Supervised-FT_3sub/model-gpu.ckpt @@ -0,0 +1,3 @@ +version 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sha256:2e96011be40863df450565777138bce5f51a6e2689732ead1eea4fc6f8383112 +size 93103415 diff --git a/mridata_knee_3dfse/12x/Supervised-FT_3sub/model.ckpt b/mridata_knee_3dfse/12x/Supervised-FT_3sub/model.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..48b301aa378d7cbef918a9f5e8330449e3a3ec5e --- /dev/null +++ b/mridata_knee_3dfse/12x/Supervised-FT_3sub/model.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:2e96011be40863df450565777138bce5f51a6e2689732ead1eea4fc6f8383112 +size 93103415 diff --git a/mridata_knee_3dfse/12x/Supervised_14sub/config.yaml b/mridata_knee_3dfse/12x/Supervised_14sub/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..63e7a0bfa4c2d8f8f2e1de6ad1e06138da6efc58 --- /dev/null +++ b/mridata_knee_3dfse/12x/Supervised_14sub/config.yaml @@ -0,0 +1,205 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 12 +AUG_TRAIN: + MOTION_P: 0.2 + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 12 + CALIBRATION_SIZE: 20 + CENTER_FRACTIONS: [] + MAX_ATTEMPTS: 30 + NAME: PoissonDiskMaskFunc + USE_MOTION: false + 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: false + BATCH_BY: [] + NUM_WORKERS: 12 + 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: + TEST: + - mridata_knee_2019_test + TRAIN: + - mridata_knee_2019_train + VAL: + - mridata_knee_2019_val +DESCRIPTION: + BRIEF: U-NET LR = 1e-3 Baseline 12x mridata.org 14 subject, BS=16 + ENTITY_NAME: '' + EXP_NAME: noise2recon/mridata_knee_3dfse/12x/Supervised_14sub + PROJECT_NAME: '' + TAGS: + - baseline + - supervised + - 12x + - mridata_knee_3dfse +MODEL: + A2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + CONSISTENCY: + AUG: + MOTION: + RANGE: + - 0.2 + - 0.5 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE: + MASK: + RHO: 1.0 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + STD_DEV: + - 1 + LATENT_LOSS_NAME: mag_l1 + LATENT_LOSS_WEIGHT: 0.1 + LOSS_NAME: l1 + LOSS_WEIGHT: 0.1 + NUM_LATENT_LAYERS: 1 + USE_CONSISTENCY: true + USE_LATENT: 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 + M2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + META_ARCHITECTURE: UnetModel + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NM2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + SSDU: + MASKER: + PARAMS: {} + META_ARCHITECTURE: GeneralizedUnrolledCNN + UNET: + BLOCK_ORDER: + - conv + - relu + - conv + - relu + - batchnorm + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NORMALIZE: false + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + BLOCK_ARCHITECTURE: ResNet + 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://noise2recon/mridata_knee_3dfse/12x/Supervised_14sub +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + BIAS_LR_FACTOR: 1.0 + CHECKPOINT_PERIOD: -10 + GAMMA: 0.1 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: '' + MAX_ITER: 80000 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: + - 320000 + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 16 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_BIAS: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: -10 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 0 + VAL_AS_TEST: true + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim (Wang) +TIME_SCALE: iter +VERSION: 1 +VIS_PERIOD: 400 diff --git a/mridata_knee_3dfse/12x/Supervised_14sub/model-gpu.ckpt b/mridata_knee_3dfse/12x/Supervised_14sub/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..0ec222dba395fb62ea5f551d65ea955063dc5d28 --- /dev/null +++ b/mridata_knee_3dfse/12x/Supervised_14sub/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid 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false + TRANSFORMS: [] + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 12 + CALIBRATION_SIZE: 20 + CENTER_FRACTIONS: [] + MAX_ATTEMPTS: 30 + NAME: PoissonDiskMaskFunc + USE_MOTION: false + 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: false + BATCH_BY: [] + NUM_WORKERS: 12 + 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: + TEST: + - mridata_knee_2019_test + TRAIN: + - mridata_knee_2019_train + VAL: + - mridata_knee_2019_val +DESCRIPTION: + BRIEF: U-NET LR = 1e-3 Baseline 12x mridata.org w/ Noise augmentation - 1 subject, + p=0.2, Std Dev [0.2, 0.5) + ENTITY_NAME: '' + EXP_NAME: noise2recon/mridata_knee_3dfse/12x/Supervised_1sub + PROJECT_NAME: '' + TAGS: + - baseline + - supervised + - 12x + - mridata_knee_3dfse +MODEL: + A2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + CONSISTENCY: + AUG: + MOTION: + RANGE: + - 0.2 + - 0.5 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE: + MASK: + RHO: 1.0 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + STD_DEV: + - 1 + LATENT_LOSS_NAME: mag_l1 + LATENT_LOSS_WEIGHT: 0.1 + LOSS_NAME: l1 + LOSS_WEIGHT: 0.1 + NUM_LATENT_LAYERS: 1 + USE_CONSISTENCY: true + USE_LATENT: 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 + M2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + META_ARCHITECTURE: UnetModel + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NM2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + SSDU: + MASKER: + PARAMS: {} + META_ARCHITECTURE: GeneralizedUnrolledCNN + UNET: + BLOCK_ORDER: + - conv + - relu + - conv + - relu + - batchnorm + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NORMALIZE: false + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + BLOCK_ARCHITECTURE: ResNet + 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://noise2recon/mridata_knee_3dfse/12x/Supervised_1sub +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + BIAS_LR_FACTOR: 1.0 + CHECKPOINT_PERIOD: -20 + GAMMA: 0.1 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: '' + MAX_ITER: 320000 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: + - 320000 + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 4 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_BIAS: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: -20 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 0 + VAL_AS_TEST: true + VAL_METRICS: + RECON: [] +TIME_SCALE: iter +VERSION: 1 +VIS_PERIOD: 400 diff --git a/mridata_knee_3dfse/12x/Supervised_1sub/model-gpu.ckpt b/mridata_knee_3dfse/12x/Supervised_1sub/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..c04b5d8235f1b3c4efd545c991bb46783c764194 --- /dev/null +++ b/mridata_knee_3dfse/12x/Supervised_1sub/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:2a10fdb83a750064f844e4d38389c96e6acbb56541e504ff01be3068aedd6b7e +size 93109239 diff --git a/mridata_knee_3dfse/12x/Supervised_1sub/model-raw-gpu.ckpt b/mridata_knee_3dfse/12x/Supervised_1sub/model-raw-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..d6da6eef56986b6cd6427a86d0647b7f011efd3a --- /dev/null +++ b/mridata_knee_3dfse/12x/Supervised_1sub/model-raw-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:4c6e9c99465bad9838781edad65cc448e36453b3aaa26a11090714fbd4b32a51 +size 93109239 diff --git a/mridata_knee_3dfse/12x/Supervised_1sub/model-raw.ckpt b/mridata_knee_3dfse/12x/Supervised_1sub/model-raw.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..96b0de35e8ede44868515c3371f0b0f9f4c4944e --- /dev/null +++ b/mridata_knee_3dfse/12x/Supervised_1sub/model-raw.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ea63195f461f406775bf0ef328a55bbaee65f2b3595927eedfc7d3d650eb1a9e +size 93103479 diff --git a/mridata_knee_3dfse/12x/Supervised_1sub/model.ckpt b/mridata_knee_3dfse/12x/Supervised_1sub/model.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..96b0de35e8ede44868515c3371f0b0f9f4c4944e --- /dev/null +++ b/mridata_knee_3dfse/12x/Supervised_1sub/model.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ea63195f461f406775bf0ef328a55bbaee65f2b3595927eedfc7d3d650eb1a9e +size 93103479 diff --git a/mridata_knee_3dfse/12x/Supervised_2sub/config.yaml b/mridata_knee_3dfse/12x/Supervised_2sub/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..2b88abb203771f255d433d82262219cc20eee7a9 --- /dev/null +++ b/mridata_knee_3dfse/12x/Supervised_2sub/config.yaml @@ -0,0 +1,205 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 12 +AUG_TRAIN: + MOTION_P: 0.2 + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 12 + CALIBRATION_SIZE: 20 + CENTER_FRACTIONS: [] + MAX_ATTEMPTS: 30 + NAME: PoissonDiskMaskFunc + USE_MOTION: false + 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: false + BATCH_BY: [] + NUM_WORKERS: 12 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: '' + SUBSAMPLE_TRAIN: + NUM_TOTAL: 2 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + TEST: + - mridata_knee_2019_test + TRAIN: + - mridata_knee_2019_train + VAL: + - mridata_knee_2019_val +DESCRIPTION: + BRIEF: U-NET LR = 1e-3 Baseline 12x mridata.org 2 subject, BS=16, magnitude l1 loss + ENTITY_NAME: '' + EXP_NAME: noise2recon/mridata_knee_3dfse/12x/Supervised_2sub + PROJECT_NAME: '' + TAGS: + - baseline + - supervised + - 12x + - mridata_knee_3dfse +MODEL: + A2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + CONSISTENCY: + AUG: + MOTION: + RANGE: + - 0.2 + - 0.5 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE: + MASK: + RHO: 1.0 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + STD_DEV: + - 1 + LATENT_LOSS_NAME: mag_l1 + LATENT_LOSS_WEIGHT: 0.1 + LOSS_NAME: l1 + LOSS_WEIGHT: 0.1 + NUM_LATENT_LAYERS: 1 + USE_CONSISTENCY: true + USE_LATENT: 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 + M2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + META_ARCHITECTURE: UnetModel + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NM2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + SSDU: + MASKER: + PARAMS: {} + META_ARCHITECTURE: GeneralizedUnrolledCNN + UNET: + BLOCK_ORDER: + - conv + - relu + - conv + - relu + - batchnorm + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NORMALIZE: false + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + BLOCK_ARCHITECTURE: ResNet + 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://noise2recon/mridata_knee_3dfse/12x/Supervised_2sub +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + BIAS_LR_FACTOR: 1.0 + CHECKPOINT_PERIOD: -10 + GAMMA: 0.1 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: '' + MAX_ITER: 80000 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: + - 320000 + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 16 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_BIAS: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: -10 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 0 + VAL_AS_TEST: true + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim (Wang) +TIME_SCALE: iter +VERSION: 1 +VIS_PERIOD: 400 diff --git a/mridata_knee_3dfse/12x/Supervised_2sub/model-gpu.ckpt b/mridata_knee_3dfse/12x/Supervised_2sub/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..0b01fabc8b67028adec44a5eebb963e2320cfac2 --- /dev/null +++ b/mridata_knee_3dfse/12x/Supervised_2sub/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:6d626a86e602daab85cf13f59b73467177d1d6086143f2d720368b6c9ea3066e +size 93109175 diff --git 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b/mridata_knee_3dfse/12x/Supervised_2sub/model.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..f34c22d32fff21296ac3745f22dfa5962069ad36 --- /dev/null +++ b/mridata_knee_3dfse/12x/Supervised_2sub/model.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:d624e1b02537f7403aa9689c2f79a898ea8eadaeda4a1e2ee963e0d18c3ea238 +size 93103415 diff --git a/mridata_knee_3dfse/12x/Supervised_3sub/config.yaml b/mridata_knee_3dfse/12x/Supervised_3sub/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..9f57da6c6a6a8149fc0a593725aba308110057ab --- /dev/null +++ b/mridata_knee_3dfse/12x/Supervised_3sub/config.yaml @@ -0,0 +1,206 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 12 +AUG_TRAIN: + MOTION_P: 0.2 + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 12 + CALIBRATION_SIZE: 20 + CENTER_FRACTIONS: [] + MAX_ATTEMPTS: 30 + NAME: PoissonDiskMaskFunc + USE_MOTION: false + 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: false + BATCH_BY: [] + NUM_WORKERS: 12 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: '' + SUBSAMPLE_TRAIN: + NUM_TOTAL: 3 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + TEST: + - mridata_knee_2019_test + TRAIN: + - mridata_knee_2019_train + VAL: + - mridata_knee_2019_val +DESCRIPTION: + BRIEF: U-NET LR = 1e-3 Baseline 12x mridata.org, 3 subject, BS=16, magnitude l1 + loss + ENTITY_NAME: '' + EXP_NAME: noise2recon/mridata_knee_3dfse/12x/Supervised_3sub + PROJECT_NAME: '' + TAGS: + - baseline + - supervised + - 12x + - mridata_knee_3dfse +MODEL: + A2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + CONSISTENCY: + AUG: + MOTION: + RANGE: + - 0.2 + - 0.5 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE: + MASK: + RHO: 1.0 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + STD_DEV: + - 1 + LATENT_LOSS_NAME: mag_l1 + LATENT_LOSS_WEIGHT: 0.1 + LOSS_NAME: l1 + LOSS_WEIGHT: 0.1 + NUM_LATENT_LAYERS: 1 + USE_CONSISTENCY: true + USE_LATENT: 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 + M2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + META_ARCHITECTURE: UnetModel + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NM2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + SSDU: + MASKER: + PARAMS: {} + META_ARCHITECTURE: GeneralizedUnrolledCNN + UNET: + BLOCK_ORDER: + - conv + - relu + - conv + - relu + - batchnorm + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NORMALIZE: false + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + BLOCK_ARCHITECTURE: ResNet + 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://noise2recon/mridata_knee_3dfse/12x/Supervised_3sub +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + BIAS_LR_FACTOR: 1.0 + CHECKPOINT_PERIOD: -10 + GAMMA: 0.1 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: '' + MAX_ITER: 80000 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: + - 320000 + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 16 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_BIAS: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: -10 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 0 + VAL_AS_TEST: true + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim (Wang) +TIME_SCALE: iter +VERSION: 1 +VIS_PERIOD: 400 diff --git a/mridata_knee_3dfse/12x/Supervised_3sub/model-gpu.ckpt b/mridata_knee_3dfse/12x/Supervised_3sub/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..dea4e50d79fdff01831649f7d5f2639f7ce5fabe --- /dev/null +++ b/mridata_knee_3dfse/12x/Supervised_3sub/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:67b79d5b03fb7d35ee5a39610c3bb0024d7d581141eda9335634f8a853b4832e +size 93109239 diff --git 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b/mridata_knee_3dfse/12x/Supervised_3sub/model.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..d655230c5d0ce380f7d2948fd0de1518f1bd4bc8 --- /dev/null +++ b/mridata_knee_3dfse/12x/Supervised_3sub/model.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:b1a484e3e94cfced9f52dff849aa7bbff2c25915e45a4c354d7d9b035e8f2462 +size 93103479 diff --git a/mridata_knee_3dfse/16x/Noise2Recon_1sub/config.yaml b/mridata_knee_3dfse/16x/Noise2Recon_1sub/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..c11b012145ba52f01bf2519d44212959d98d76b4 --- /dev/null +++ b/mridata_knee_3dfse/16x/Noise2Recon_1sub/config.yaml @@ -0,0 +1,207 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 16 +AUG_TRAIN: + MOTION_P: 0.2 + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 16 + CALIBRATION_SIZE: 20 + CENTER_FRACTIONS: [] + MAX_ATTEMPTS: 30 + NAME: PoissonDiskMaskFunc + USE_MOTION: false + 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: false + BATCH_BY: [] + NUM_WORKERS: 12 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: AlternatingSampler + SUBSAMPLE_TRAIN: + NUM_TOTAL: -1 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 13 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + TEST: + - mridata_knee_2019_test + TRAIN: + - mridata_knee_2019_train + VAL: + - mridata_knee_2019_val +DESCRIPTION: + BRIEF: U-NET LR = 1e-3 N2R 16x mridata.org - 1 subject, 13 unsupervised random sampler + with supervised consistency, Std Dev [0.2, 0.5) + ENTITY_NAME: '' + EXP_NAME: noise2recon/mridata_knee_3dfse/16x/Noise2Recon_1sub + PROJECT_NAME: '' + TAGS: + - noise2recon + - noise2recon + - 16x + - mridata_knee_3dfse +MODEL: + A2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + CONSISTENCY: + AUG: + MOTION: + RANGE: + - 0.2 + - 0.5 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE: + MASK: + RHO: 1.0 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + STD_DEV: + - 0.2 + - 0.5 + LATENT_LOSS_NAME: mag_l1 + LATENT_LOSS_WEIGHT: 0.1 + LOSS_NAME: l1 + LOSS_WEIGHT: 0.1 + NUM_LATENT_LAYERS: 1 + USE_CONSISTENCY: true + USE_LATENT: 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 + M2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + META_ARCHITECTURE: N2RModel + N2R: + META_ARCHITECTURE: UnetModel + USE_SUPERVISED_CONSISTENCY: false + NM2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + SSDU: + MASKER: + PARAMS: {} + META_ARCHITECTURE: GeneralizedUnrolledCNN + UNET: + BLOCK_ORDER: + - conv + - relu + - conv + - relu + - batchnorm + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NORMALIZE: false + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + BLOCK_ARCHITECTURE: ResNet + 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://noise2recon/mridata_knee_3dfse/16x/Noise2Recon_1sub +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + BIAS_LR_FACTOR: 1.0 + CHECKPOINT_PERIOD: -10 + GAMMA: 0.1 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: StepLR + MAX_ITER: 80000 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: + - 320000 + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 16 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_BIAS: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: -10 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 0 + VAL_AS_TEST: true + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim (Wang) +TIME_SCALE: iter +VERSION: 1 +VIS_PERIOD: 400 diff --git a/mridata_knee_3dfse/16x/Noise2Recon_1sub/model-gpu.ckpt b/mridata_knee_3dfse/16x/Noise2Recon_1sub/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..624fc1bf6ef5e9df24d92db8516862554687fbdf --- /dev/null +++ b/mridata_knee_3dfse/16x/Noise2Recon_1sub/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:bf0755cde6dcdb4459f6f7edc3ab914bd52b174cc0d30f1f7d543ce2685f44ef +size 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a/mridata_knee_3dfse/16x/Noise2Recon_1sub/model.ckpt b/mridata_knee_3dfse/16x/Noise2Recon_1sub/model.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..38ccfc348076308bbe7e3dfae354bffef4865fa4 --- /dev/null +++ b/mridata_knee_3dfse/16x/Noise2Recon_1sub/model.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:b697401a6530ea4dfc083632b9b6ac024a2df8afb694210554ca2661643bdc94 +size 93103671 diff --git a/mridata_knee_3dfse/16x/Noise2Recon_2sub/config.yaml b/mridata_knee_3dfse/16x/Noise2Recon_2sub/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..ff336989ff5ccf63908020c54d2d906695606f49 --- /dev/null +++ b/mridata_knee_3dfse/16x/Noise2Recon_2sub/config.yaml @@ -0,0 +1,207 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 16 +AUG_TRAIN: + MOTION_P: 0.2 + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 16 + CALIBRATION_SIZE: 20 + CENTER_FRACTIONS: [] + MAX_ATTEMPTS: 30 + NAME: PoissonDiskMaskFunc + USE_MOTION: false + 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: false + BATCH_BY: [] + NUM_WORKERS: 12 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: AlternatingSampler + SUBSAMPLE_TRAIN: + NUM_TOTAL: -1 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 12 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + TEST: + - mridata_knee_2019_test + TRAIN: + - mridata_knee_2019_train + VAL: + - mridata_knee_2019_val +DESCRIPTION: + BRIEF: U-NET LR = 1e-3 N2R 16x mridata.org - 2 subject, 12 unsupervised random sampler + with supervised consistency, Std Dev [0.2, 0.5) + ENTITY_NAME: '' + EXP_NAME: noise2recon/mridata_knee_3dfse/16x/Noise2Recon_2sub + PROJECT_NAME: '' + TAGS: + - noise2recon + - noise2recon + - 16x + - mridata_knee_3dfse +MODEL: + A2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + CONSISTENCY: + AUG: + MOTION: + RANGE: + - 0.2 + - 0.5 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE: + MASK: + RHO: 1.0 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + STD_DEV: + - 0.2 + - 0.5 + LATENT_LOSS_NAME: mag_l1 + LATENT_LOSS_WEIGHT: 0.1 + LOSS_NAME: l1 + LOSS_WEIGHT: 0.1 + NUM_LATENT_LAYERS: 1 + USE_CONSISTENCY: true + USE_LATENT: 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 + M2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + META_ARCHITECTURE: N2RModel + N2R: + META_ARCHITECTURE: UnetModel + USE_SUPERVISED_CONSISTENCY: false + NM2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + SSDU: + MASKER: + PARAMS: {} + META_ARCHITECTURE: GeneralizedUnrolledCNN + UNET: + BLOCK_ORDER: + - conv + - relu + - conv + - relu + - batchnorm + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NORMALIZE: false + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + BLOCK_ARCHITECTURE: ResNet + 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://noise2recon/mridata_knee_3dfse/16x/Noise2Recon_2sub +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + BIAS_LR_FACTOR: 1.0 + CHECKPOINT_PERIOD: -10 + GAMMA: 0.1 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: StepLR + MAX_ITER: 80000 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: + - 320000 + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 16 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_BIAS: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: -10 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 0 + VAL_AS_TEST: true + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim (Wang) +TIME_SCALE: iter +VERSION: 1 +VIS_PERIOD: 400 diff --git a/mridata_knee_3dfse/16x/Noise2Recon_2sub/model-gpu.ckpt b/mridata_knee_3dfse/16x/Noise2Recon_2sub/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..66bcc003847ab2d7cee01e70ebb224bc03860fee --- /dev/null +++ b/mridata_knee_3dfse/16x/Noise2Recon_2sub/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid 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false + TRANSFORMS: [] + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 16 + CALIBRATION_SIZE: 20 + CENTER_FRACTIONS: [] + MAX_ATTEMPTS: 30 + NAME: PoissonDiskMaskFunc + USE_MOTION: false + 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: false + BATCH_BY: [] + NUM_WORKERS: 12 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: AlternatingSampler + SUBSAMPLE_TRAIN: + NUM_TOTAL: -1 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 11 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + TEST: + - mridata_knee_2019_test + TRAIN: + - mridata_knee_2019_train + VAL: + - mridata_knee_2019_val +DESCRIPTION: + BRIEF: U-NET LR = 1e-3 N2R 16x mridata.org - 3 subject, 12 unsupervised random sampler + with supervised consistency, Std Dev [0.2, 0.5) + ENTITY_NAME: '' + EXP_NAME: noise2recon/mridata_knee_3dfse/16x/Noise2Recon_3sub + PROJECT_NAME: '' + TAGS: + - noise2recon + - noise2recon + - 16x + - mridata_knee_3dfse +MODEL: + A2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + CONSISTENCY: + AUG: + MOTION: + RANGE: + - 0.2 + - 0.5 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE: + MASK: + RHO: 1.0 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + STD_DEV: + - 0.2 + - 0.5 + LATENT_LOSS_NAME: mag_l1 + LATENT_LOSS_WEIGHT: 0.1 + LOSS_NAME: l1 + LOSS_WEIGHT: 0.1 + NUM_LATENT_LAYERS: 1 + USE_CONSISTENCY: true + USE_LATENT: 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 + M2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + META_ARCHITECTURE: N2RModel + N2R: + META_ARCHITECTURE: UnetModel + USE_SUPERVISED_CONSISTENCY: false + NM2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + SSDU: + MASKER: + PARAMS: {} + META_ARCHITECTURE: GeneralizedUnrolledCNN + UNET: + BLOCK_ORDER: + - conv + - relu + - conv + - relu + - batchnorm + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NORMALIZE: false + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + BLOCK_ARCHITECTURE: ResNet + 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://noise2recon/mridata_knee_3dfse/16x/Noise2Recon_3sub +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + BIAS_LR_FACTOR: 1.0 + CHECKPOINT_PERIOD: -10 + GAMMA: 0.1 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: StepLR + MAX_ITER: 80000 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: + - 320000 + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 16 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_BIAS: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: -10 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 0 + VAL_AS_TEST: true + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim (Wang) +TIME_SCALE: iter +VERSION: 1 +VIS_PERIOD: 400 diff --git a/mridata_knee_3dfse/16x/Noise2Recon_3sub/model-gpu.ckpt b/mridata_knee_3dfse/16x/Noise2Recon_3sub/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..e97a6fbadec3e0501c325f5fa0c8743daf839bb0 --- /dev/null +++ b/mridata_knee_3dfse/16x/Noise2Recon_3sub/model-gpu.ckpt @@ -0,0 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SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 16 + CALIBRATION_SIZE: 20 + CENTER_FRACTIONS: [] + MAX_ATTEMPTS: 30 + NAME: PoissonDiskMaskFunc + USE_MOTION: false + USE_NOISE: true +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: [] + DROP_LAST: true + FILTER: + BY: [] + GROUP_SAMPLER: + AS_BATCH_SAMPLER: false + BATCH_BY: [] + NUM_WORKERS: 12 + 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: + TEST: + - mridata_knee_2019_test + TRAIN: + - mridata_knee_2019_train + VAL: + - mridata_knee_2019_val +DESCRIPTION: + BRIEF: Denoiser finetuning w/ noise aug U-Net 16x - augmentation std_dev=(0.2, 0.5), + 1 supervised scan(s), 0 unsupervised scan(s), 40k iterations, restart-iteration-count + = True + ENTITY_NAME: '' + EXP_NAME: noise2recon/mridata_knee_3dfse/16x/Supervised+Aug-FT_1sub + PROJECT_NAME: '' + TAGS: + - baseline + - supervised+aug-ft + - 16x + - mridata_knee_3dfse +MODEL: + A2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + CONSISTENCY: + AUG: + MOTION: + RANGE: + - 0.2 + - 0.5 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE: + MASK: + RHO: 1.0 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + STD_DEV: + - 0.2 + - 0.5 + LATENT_LOSS_NAME: mag_l1 + LATENT_LOSS_WEIGHT: 0.1 + LOSS_NAME: l1 + LOSS_WEIGHT: 0.1 + NUM_LATENT_LAYERS: 1 + USE_CONSISTENCY: true + USE_LATENT: 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 + M2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + META_ARCHITECTURE: UnetModel + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NM2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + SSDU: + MASKER: + PARAMS: {} + META_ARCHITECTURE: GeneralizedUnrolledCNN + UNET: + BLOCK_ORDER: + - conv + - relu + - conv + - relu + - batchnorm + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NORMALIZE: false + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + BLOCK_ARCHITECTURE: ResNet + 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: /bmrNAS/people/arjun/results/ss_recon/n2r-experiments/denoise-pretrainer/version_017/model_0039199.pth +OUTPUT_DIR: results://noise2recon/mridata_knee_3dfse/16x/Supervised+Aug-FT_1sub +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + BIAS_LR_FACTOR: 1.0 + CHECKPOINT_PERIOD: -20 + GAMMA: 0.1 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: '' + MAX_ITER: 40000 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: + - 320000 + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 16 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_BIAS: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: -20 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 0 + VAL_AS_TEST: true + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim (Wang) +TIME_SCALE: iter +VERSION: 1 +VIS_PERIOD: 400 diff --git a/mridata_knee_3dfse/16x/Supervised+Aug-FT_1sub/model-gpu.ckpt 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b/mridata_knee_3dfse/16x/Supervised+Aug-FT_2sub/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..5831e9fc3488ea614ab56d7f3c573fcd1a6f7933 --- /dev/null +++ b/mridata_knee_3dfse/16x/Supervised+Aug-FT_2sub/config.yaml @@ -0,0 +1,208 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 16 +AUG_TRAIN: + MOTION_P: 0.2 + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 16 + CALIBRATION_SIZE: 20 + CENTER_FRACTIONS: [] + MAX_ATTEMPTS: 30 + NAME: PoissonDiskMaskFunc + USE_MOTION: false + USE_NOISE: true +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: [] + DROP_LAST: true + FILTER: + BY: [] + GROUP_SAMPLER: + AS_BATCH_SAMPLER: false + BATCH_BY: [] + NUM_WORKERS: 12 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: '' + SUBSAMPLE_TRAIN: + NUM_TOTAL: 2 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + TEST: + - mridata_knee_2019_test + TRAIN: + - mridata_knee_2019_train + VAL: + - mridata_knee_2019_val +DESCRIPTION: + BRIEF: Denoiser finetuning w/ noise aug U-Net 16x - augmentation std_dev=(0.2, 0.5), + 2 supervised scan(s), 0 unsupervised scan(s), 40k iterations, restart-iteration-count + = True + ENTITY_NAME: '' + EXP_NAME: noise2recon/mridata_knee_3dfse/16x/Supervised+Aug-FT_2sub + PROJECT_NAME: '' + TAGS: + - baseline + - supervised+aug-ft + - 16x + - mridata_knee_3dfse +MODEL: + A2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + CONSISTENCY: + AUG: + MOTION: + RANGE: + - 0.2 + - 0.5 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE: + MASK: + RHO: 1.0 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + STD_DEV: + - 0.2 + - 0.5 + LATENT_LOSS_NAME: mag_l1 + LATENT_LOSS_WEIGHT: 0.1 + LOSS_NAME: l1 + LOSS_WEIGHT: 0.1 + NUM_LATENT_LAYERS: 1 + USE_CONSISTENCY: true + USE_LATENT: 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 + M2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + META_ARCHITECTURE: UnetModel + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NM2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + SSDU: + MASKER: + PARAMS: {} + META_ARCHITECTURE: GeneralizedUnrolledCNN + UNET: + BLOCK_ORDER: + - conv + - relu + - conv + - relu + - batchnorm + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NORMALIZE: false + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + BLOCK_ARCHITECTURE: ResNet + 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: /bmrNAS/people/arjun/results/ss_recon/n2r-experiments/denoise-pretrainer/version_018/model_0019599.pth +OUTPUT_DIR: results://noise2recon/mridata_knee_3dfse/16x/Supervised+Aug-FT_2sub +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + BIAS_LR_FACTOR: 1.0 + CHECKPOINT_PERIOD: -10 + GAMMA: 0.1 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: '' + MAX_ITER: 40000 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: + - 320000 + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 16 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_BIAS: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: -10 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 0 + VAL_AS_TEST: true + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim (Wang) +TIME_SCALE: iter +VERSION: 1 +VIS_PERIOD: 400 diff --git a/mridata_knee_3dfse/16x/Supervised+Aug-FT_2sub/model-gpu.ckpt b/mridata_knee_3dfse/16x/Supervised+Aug-FT_2sub/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..015b7ebcb3b8fbecf5ae44daae82ce52283c7654 --- /dev/null +++ b/mridata_knee_3dfse/16x/Supervised+Aug-FT_2sub/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:5f162d591a962fdd07af2cdbf330643236a2def069f51215e29c279b461baf3f +size 93109175 diff --git a/mridata_knee_3dfse/16x/Supervised+Aug-FT_2sub/model-raw-gpu.ckpt b/mridata_knee_3dfse/16x/Supervised+Aug-FT_2sub/model-raw-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..0f45be77c00bd42bcfe220db2f8ac7212da9cc0f --- 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b/mridata_knee_3dfse/16x/Supervised+Aug-FT_2sub/model.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ee7a5b35e13f925c21c8ba2c7a661c93a732d3e6aabb33af61ae410ad561e39e +size 93103415 diff --git a/mridata_knee_3dfse/16x/Supervised+Aug-FT_3sub/config.yaml b/mridata_knee_3dfse/16x/Supervised+Aug-FT_3sub/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..adb22a1d027e756735300a91bbecc1d043e99b8a --- /dev/null +++ b/mridata_knee_3dfse/16x/Supervised+Aug-FT_3sub/config.yaml @@ -0,0 +1,208 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 16 +AUG_TRAIN: + MOTION_P: 0.2 + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 16 + CALIBRATION_SIZE: 20 + CENTER_FRACTIONS: [] + MAX_ATTEMPTS: 30 + NAME: PoissonDiskMaskFunc + USE_MOTION: false + USE_NOISE: true +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: [] + DROP_LAST: true + FILTER: + BY: [] + GROUP_SAMPLER: + AS_BATCH_SAMPLER: false + BATCH_BY: [] + NUM_WORKERS: 12 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: '' + SUBSAMPLE_TRAIN: + NUM_TOTAL: 3 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + TEST: + - mridata_knee_2019_test + TRAIN: + - mridata_knee_2019_train + VAL: + - mridata_knee_2019_val +DESCRIPTION: + BRIEF: Denoiser finetuning w/ noise aug U-Net 16x - augmentation std_dev=(0.2, 0.5), + 3 supervised scan(s), 0 unsupervised scan(s), 40k iterations, restart-iteration-count + = True + ENTITY_NAME: '' + EXP_NAME: noise2recon/mridata_knee_3dfse/16x/Supervised+Aug-FT_3sub + PROJECT_NAME: '' + TAGS: + - baseline + - supervised+aug-ft + - 16x + - mridata_knee_3dfse +MODEL: + A2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + CONSISTENCY: + AUG: + MOTION: + RANGE: + - 0.2 + - 0.5 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE: + MASK: + RHO: 1.0 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + STD_DEV: + - 0.2 + - 0.5 + LATENT_LOSS_NAME: mag_l1 + LATENT_LOSS_WEIGHT: 0.1 + LOSS_NAME: l1 + LOSS_WEIGHT: 0.1 + NUM_LATENT_LAYERS: 1 + USE_CONSISTENCY: true + USE_LATENT: 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 + M2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + META_ARCHITECTURE: UnetModel + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NM2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + SSDU: + MASKER: + PARAMS: {} + META_ARCHITECTURE: GeneralizedUnrolledCNN + UNET: + BLOCK_ORDER: + - conv + - relu + - conv + - relu + - batchnorm + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NORMALIZE: false + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + BLOCK_ARCHITECTURE: ResNet + 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: /bmrNAS/people/arjun/results/ss_recon/n2r-experiments/denoise-pretrainer/version_019/model_0036399.pth +OUTPUT_DIR: results://noise2recon/mridata_knee_3dfse/16x/Supervised+Aug-FT_3sub +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + BIAS_LR_FACTOR: 1.0 + CHECKPOINT_PERIOD: -10 + GAMMA: 0.1 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: '' + MAX_ITER: 40000 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: + - 320000 + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 16 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_BIAS: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: -10 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 0 + VAL_AS_TEST: true + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim (Wang) +TIME_SCALE: iter +VERSION: 1 +VIS_PERIOD: 400 diff --git a/mridata_knee_3dfse/16x/Supervised+Aug-FT_3sub/model-gpu.ckpt b/mridata_knee_3dfse/16x/Supervised+Aug-FT_3sub/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..dd45a302a8972e38cb4675ec3e0ed392b6af20fa --- /dev/null +++ b/mridata_knee_3dfse/16x/Supervised+Aug-FT_3sub/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:15dc1b48ec2c9d44c3c663223ce1cb3c808dcbb320affa05ccbb23c3335e8097 +size 93109175 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a/mridata_knee_3dfse/16x/Supervised+Aug-FT_3sub/model.ckpt b/mridata_knee_3dfse/16x/Supervised+Aug-FT_3sub/model.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..526de8504e1103bdeac8d39765dfb6caa6e3fb67 --- /dev/null +++ b/mridata_knee_3dfse/16x/Supervised+Aug-FT_3sub/model.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:41ad83faaa2385a9ac671da01a117954411afb2a23277265464bdf7f17fc0cef +size 93103415 diff --git a/mridata_knee_3dfse/16x/Supervised+Aug_1sub/config.yaml b/mridata_knee_3dfse/16x/Supervised+Aug_1sub/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..c2a9454a969fcbe7c11ce06dc308fcfb3266aadd --- /dev/null +++ b/mridata_knee_3dfse/16x/Supervised+Aug_1sub/config.yaml @@ -0,0 +1,207 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 16 +AUG_TRAIN: + MOTION_P: 0.2 + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 16 + CALIBRATION_SIZE: 20 + CENTER_FRACTIONS: [] + MAX_ATTEMPTS: 30 + NAME: PoissonDiskMaskFunc + USE_MOTION: false + USE_NOISE: true +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: [] + DROP_LAST: true + FILTER: + BY: [] + GROUP_SAMPLER: + AS_BATCH_SAMPLER: false + BATCH_BY: [] + NUM_WORKERS: 12 + 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: + TEST: + - mridata_knee_2019_test + TRAIN: + - mridata_knee_2019_train + VAL: + - mridata_knee_2019_val +DESCRIPTION: + BRIEF: U-NET LR = 1e-3 Baseline 16x mridata.org w/ Noise augmentation - 1 subject, + l1 loss, p=0.2, Std Dev [0.2, 0.5) + ENTITY_NAME: '' + EXP_NAME: noise2recon/mridata_knee_3dfse/16x/Supervised+Aug_1sub + PROJECT_NAME: '' + TAGS: + - baseline + - supervised+aug + - 16x + - mridata_knee_3dfse +MODEL: + A2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + CONSISTENCY: + AUG: + MOTION: + RANGE: + - 0.2 + - 0.5 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE: + MASK: + RHO: 1.0 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + STD_DEV: + - 0.2 + - 0.5 + LATENT_LOSS_NAME: mag_l1 + LATENT_LOSS_WEIGHT: 0.1 + LOSS_NAME: l1 + LOSS_WEIGHT: 0.1 + NUM_LATENT_LAYERS: 1 + USE_CONSISTENCY: true + USE_LATENT: 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 + M2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + META_ARCHITECTURE: UnetModel + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NM2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + SSDU: + MASKER: + PARAMS: {} + META_ARCHITECTURE: GeneralizedUnrolledCNN + UNET: + BLOCK_ORDER: + - conv + - relu + - conv + - relu + - batchnorm + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NORMALIZE: false + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + BLOCK_ARCHITECTURE: ResNet + 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://noise2recon/mridata_knee_3dfse/16x/Supervised+Aug_1sub +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + BIAS_LR_FACTOR: 1.0 + CHECKPOINT_PERIOD: -10 + GAMMA: 0.1 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: '' + MAX_ITER: 80000 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: + - 160000 + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 16 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_BIAS: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: -10 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 0 + VAL_AS_TEST: true + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim (Wang) +TIME_SCALE: iter +VERSION: 1 +VIS_PERIOD: 400 diff --git a/mridata_knee_3dfse/16x/Supervised+Aug_1sub/model-gpu.ckpt b/mridata_knee_3dfse/16x/Supervised+Aug_1sub/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..825198601abb841fca916d0f6bf397dfd9f4fa55 --- /dev/null +++ b/mridata_knee_3dfse/16x/Supervised+Aug_1sub/model-gpu.ckpt @@ -0,0 +1,3 @@ +version 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SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 16 + CALIBRATION_SIZE: 20 + CENTER_FRACTIONS: [] + MAX_ATTEMPTS: 30 + NAME: PoissonDiskMaskFunc + USE_MOTION: false + USE_NOISE: true +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: [] + DROP_LAST: true + FILTER: + BY: [] + GROUP_SAMPLER: + AS_BATCH_SAMPLER: false + BATCH_BY: [] + NUM_WORKERS: 12 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: '' + SUBSAMPLE_TRAIN: + NUM_TOTAL: 2 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + TEST: + - mridata_knee_2019_test + TRAIN: + - mridata_knee_2019_train + VAL: + - mridata_knee_2019_val +DESCRIPTION: + BRIEF: U-NET LR = 1e-3 Baseline 16x mridata.org w/ Noise augmentation - 2 subject, + l1 loss, p=0.2, Std Dev [0.2, 0.5) + ENTITY_NAME: '' + EXP_NAME: noise2recon/mridata_knee_3dfse/16x/Supervised+Aug_2sub + PROJECT_NAME: '' + TAGS: + - baseline + - supervised+aug + - 16x + - mridata_knee_3dfse +MODEL: + A2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + CONSISTENCY: + AUG: + MOTION: + RANGE: + - 0.2 + - 0.5 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE: + MASK: + RHO: 1.0 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + STD_DEV: + - 0.2 + - 0.5 + LATENT_LOSS_NAME: mag_l1 + LATENT_LOSS_WEIGHT: 0.1 + LOSS_NAME: l1 + LOSS_WEIGHT: 0.1 + NUM_LATENT_LAYERS: 1 + USE_CONSISTENCY: true + USE_LATENT: 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 + M2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + META_ARCHITECTURE: UnetModel + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NM2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + SSDU: + MASKER: + PARAMS: {} + META_ARCHITECTURE: GeneralizedUnrolledCNN + UNET: + BLOCK_ORDER: + - conv + - relu + - conv + - relu + - batchnorm + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NORMALIZE: false + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + BLOCK_ARCHITECTURE: ResNet + 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://noise2recon/mridata_knee_3dfse/16x/Supervised+Aug_2sub +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + BIAS_LR_FACTOR: 1.0 + CHECKPOINT_PERIOD: -10 + GAMMA: 0.1 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: '' + MAX_ITER: 80000 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: + - 160000 + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 16 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_BIAS: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: -10 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 0 + VAL_AS_TEST: true + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim (Wang) +TIME_SCALE: iter +VERSION: 1 +VIS_PERIOD: 400 diff --git a/mridata_knee_3dfse/16x/Supervised+Aug_2sub/model-gpu.ckpt b/mridata_knee_3dfse/16x/Supervised+Aug_2sub/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..61efdafeec61a1042b8d189253a93f67f67767b8 --- /dev/null +++ b/mridata_knee_3dfse/16x/Supervised+Aug_2sub/model-gpu.ckpt @@ 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MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 16 + CALIBRATION_SIZE: 20 + CENTER_FRACTIONS: [] + MAX_ATTEMPTS: 30 + NAME: PoissonDiskMaskFunc + USE_MOTION: false + USE_NOISE: true +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: [] + DROP_LAST: true + FILTER: + BY: [] + GROUP_SAMPLER: + AS_BATCH_SAMPLER: false + BATCH_BY: [] + NUM_WORKERS: 12 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: '' + SUBSAMPLE_TRAIN: + NUM_TOTAL: 3 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + TEST: + - mridata_knee_2019_test + TRAIN: + - mridata_knee_2019_train + VAL: + - mridata_knee_2019_val +DESCRIPTION: + BRIEF: U-NET LR = 1e-3 Baseline 16x mridata.org w/ Noise augmentation - 3 subject, + l1 loss, p=0.2, Std Dev [0.2, 0.5) + ENTITY_NAME: '' + EXP_NAME: noise2recon/mridata_knee_3dfse/16x/Supervised+Aug_3sub + PROJECT_NAME: '' + TAGS: + - baseline + - supervised+aug + - 16x + - mridata_knee_3dfse +MODEL: + A2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + CONSISTENCY: + AUG: + MOTION: + RANGE: + - 0.2 + - 0.5 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE: + MASK: + RHO: 1.0 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + STD_DEV: + - 0.2 + - 0.5 + LATENT_LOSS_NAME: mag_l1 + LATENT_LOSS_WEIGHT: 0.1 + LOSS_NAME: l1 + LOSS_WEIGHT: 0.1 + NUM_LATENT_LAYERS: 1 + USE_CONSISTENCY: true + USE_LATENT: 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 + M2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + META_ARCHITECTURE: UnetModel + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NM2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + SSDU: + MASKER: + PARAMS: {} + META_ARCHITECTURE: GeneralizedUnrolledCNN + UNET: + BLOCK_ORDER: + - conv + - relu + - conv + - relu + - batchnorm + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NORMALIZE: false + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + BLOCK_ARCHITECTURE: ResNet + 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://noise2recon/mridata_knee_3dfse/16x/Supervised+Aug_3sub +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + BIAS_LR_FACTOR: 1.0 + CHECKPOINT_PERIOD: -10 + GAMMA: 0.1 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: '' + MAX_ITER: 80000 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: + - 160000 + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 16 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_BIAS: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: -10 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 0 + VAL_AS_TEST: true + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim (Wang) +TIME_SCALE: iter +VERSION: 1 +VIS_PERIOD: 400 diff --git a/mridata_knee_3dfse/16x/Supervised+Aug_3sub/model-gpu.ckpt b/mridata_knee_3dfse/16x/Supervised+Aug_3sub/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..191b054d9bd43c730cfe6db37f70a09edd1c2a50 --- /dev/null +++ b/mridata_knee_3dfse/16x/Supervised+Aug_3sub/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c2210a3b6bbc258aa3a051437e0c655d11d16384bf8e93e1d9b246366fcc930c +size 93109239 diff --git a/mridata_knee_3dfse/16x/Supervised+Aug_3sub/model-raw-gpu.ckpt b/mridata_knee_3dfse/16x/Supervised+Aug_3sub/model-raw-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..6eb5207787709bd330e5207361d2e285b98e12db --- /dev/null +++ b/mridata_knee_3dfse/16x/Supervised+Aug_3sub/model-raw-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:75ab7591941bacc1bfb0301c7c7971584477c644e65b5953188590581380287a +size 93109239 diff --git a/mridata_knee_3dfse/16x/Supervised+Aug_3sub/model-raw.ckpt b/mridata_knee_3dfse/16x/Supervised+Aug_3sub/model-raw.ckpt new file mode 100644 index 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0000000000000000000000000000000000000000..bd2e91db119544feb042eff8af034a58f0953dde --- /dev/null +++ b/mridata_knee_3dfse/16x/Supervised-FT_1sub/config.yaml @@ -0,0 +1,205 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 16 +AUG_TRAIN: + MOTION_P: 0.2 + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 16 + CALIBRATION_SIZE: 20 + CENTER_FRACTIONS: [] + MAX_ATTEMPTS: 30 + NAME: PoissonDiskMaskFunc + USE_MOTION: false + 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: false + BATCH_BY: [] + NUM_WORKERS: 12 + 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: + TEST: + - mridata_knee_2019_test + TRAIN: + - mridata_knee_2019_train + VAL: + - mridata_knee_2019_val +DESCRIPTION: + BRIEF: Denoiser finetuning U-Net 16x - augmentation std_dev=(), 1 supervised scan(s), + 0 unsupervised scan(s), 40k iterations, restart-iteration-count = True + ENTITY_NAME: '' + EXP_NAME: noise2recon/mridata_knee_3dfse/16x/Supervised-FT_1sub + PROJECT_NAME: '' + TAGS: + - baseline + - supervised-ft + - 16x + - mridata_knee_3dfse +MODEL: + A2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + CONSISTENCY: + AUG: + MOTION: + RANGE: + - 0.2 + - 0.5 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE: + MASK: + RHO: 1.0 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + STD_DEV: [] + LATENT_LOSS_NAME: mag_l1 + LATENT_LOSS_WEIGHT: 0.1 + LOSS_NAME: l1 + LOSS_WEIGHT: 0.1 + NUM_LATENT_LAYERS: 1 + USE_CONSISTENCY: true + USE_LATENT: 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 + M2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + META_ARCHITECTURE: UnetModel + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NM2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + SSDU: + MASKER: + PARAMS: {} + META_ARCHITECTURE: GeneralizedUnrolledCNN + UNET: + BLOCK_ORDER: + - conv + - relu + - conv + - relu + - batchnorm + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NORMALIZE: false + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + BLOCK_ARCHITECTURE: ResNet + 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: /bmrNAS/people/arjun/results/ss_recon/n2r-experiments/denoise-pretrainer/version_017/model_0039199.pth +OUTPUT_DIR: results://noise2recon/mridata_knee_3dfse/16x/Supervised-FT_1sub +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + BIAS_LR_FACTOR: 1.0 + CHECKPOINT_PERIOD: -20 + GAMMA: 0.1 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: '' + MAX_ITER: 40000 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: + - 320000 + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 16 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_BIAS: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: -20 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 0 + VAL_AS_TEST: true + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim (Wang) +TIME_SCALE: iter +VERSION: 1 +VIS_PERIOD: 400 diff --git a/mridata_knee_3dfse/16x/Supervised-FT_1sub/model-gpu.ckpt b/mridata_knee_3dfse/16x/Supervised-FT_1sub/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..bb027cc5c0959b1281586f811c1e9a183e66c651 --- /dev/null +++ b/mridata_knee_3dfse/16x/Supervised-FT_1sub/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ecfe5cac17e59e9a197e0f598efe2fb0c4bf1c45c55ea9187df1e00918980205 +size 93109175 diff --git a/mridata_knee_3dfse/16x/Supervised-FT_1sub/model-raw-gpu.ckpt b/mridata_knee_3dfse/16x/Supervised-FT_1sub/model-raw-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..92275713116c36f1f19dd66501672619e92bc730 --- /dev/null +++ b/mridata_knee_3dfse/16x/Supervised-FT_1sub/model-raw-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid 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+size 93103415 diff --git a/mridata_knee_3dfse/16x/Supervised-FT_2sub/config.yaml b/mridata_knee_3dfse/16x/Supervised-FT_2sub/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..22227b5048a1dc86c6fe2350efeba1e6daa9316b --- /dev/null +++ b/mridata_knee_3dfse/16x/Supervised-FT_2sub/config.yaml @@ -0,0 +1,205 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 16 +AUG_TRAIN: + MOTION_P: 0.2 + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 16 + CALIBRATION_SIZE: 20 + CENTER_FRACTIONS: [] + MAX_ATTEMPTS: 30 + NAME: PoissonDiskMaskFunc + USE_MOTION: false + 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: false + BATCH_BY: [] + NUM_WORKERS: 12 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: '' + SUBSAMPLE_TRAIN: + NUM_TOTAL: 2 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + TEST: + - mridata_knee_2019_test + TRAIN: + - mridata_knee_2019_train + VAL: + - mridata_knee_2019_val +DESCRIPTION: + BRIEF: Denoiser finetuning U-Net 16x - augmentation std_dev=(), 2 supervised scan(s), + 0 unsupervised scan(s), 40k iterations, restart-iteration-count = True + ENTITY_NAME: '' + EXP_NAME: noise2recon/mridata_knee_3dfse/16x/Supervised-FT_2sub + PROJECT_NAME: '' + TAGS: + - baseline + - supervised-ft + - 16x + - mridata_knee_3dfse +MODEL: + A2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + CONSISTENCY: + AUG: + MOTION: + RANGE: + - 0.2 + - 0.5 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE: + MASK: + RHO: 1.0 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + STD_DEV: [] + LATENT_LOSS_NAME: mag_l1 + LATENT_LOSS_WEIGHT: 0.1 + LOSS_NAME: l1 + LOSS_WEIGHT: 0.1 + NUM_LATENT_LAYERS: 1 + USE_CONSISTENCY: true + USE_LATENT: 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 + M2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + META_ARCHITECTURE: UnetModel + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NM2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + SSDU: + MASKER: + PARAMS: {} + META_ARCHITECTURE: GeneralizedUnrolledCNN + UNET: + BLOCK_ORDER: + - conv + - relu + - conv + - relu + - batchnorm + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NORMALIZE: false + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + BLOCK_ARCHITECTURE: ResNet + 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: /bmrNAS/people/arjun/results/ss_recon/n2r-experiments/denoise-pretrainer/version_018/model_0019599.pth +OUTPUT_DIR: results://noise2recon/mridata_knee_3dfse/16x/Supervised-FT_2sub +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + BIAS_LR_FACTOR: 1.0 + CHECKPOINT_PERIOD: -10 + GAMMA: 0.1 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: '' + MAX_ITER: 40000 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: + - 320000 + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 16 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_BIAS: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: -10 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 0 + VAL_AS_TEST: true + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim (Wang) +TIME_SCALE: iter +VERSION: 1 +VIS_PERIOD: 400 diff --git a/mridata_knee_3dfse/16x/Supervised-FT_2sub/model-gpu.ckpt b/mridata_knee_3dfse/16x/Supervised-FT_2sub/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..57ef26adff671b3eafcbe60086a15a606b1582d2 --- /dev/null +++ b/mridata_knee_3dfse/16x/Supervised-FT_2sub/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:97d5178110127211c2e8e4c5598c212594d353b0ff46d9c0716983244f9a3773 +size 93109175 diff --git a/mridata_knee_3dfse/16x/Supervised-FT_2sub/model-raw-gpu.ckpt b/mridata_knee_3dfse/16x/Supervised-FT_2sub/model-raw-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..6e5719d16145cee9d3f7945cc0f9d20534d49b85 --- /dev/null +++ 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@@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a0171051f69d2a07d318fbbfbc36c1c03bc4a236e4010eb83cd06162e07dc411 +size 93103415 diff --git a/mridata_knee_3dfse/16x/Supervised-FT_3sub/config.yaml b/mridata_knee_3dfse/16x/Supervised-FT_3sub/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..b325c343c745f0a15b4852f95b360548b69ccc62 --- /dev/null +++ b/mridata_knee_3dfse/16x/Supervised-FT_3sub/config.yaml @@ -0,0 +1,205 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 16 +AUG_TRAIN: + MOTION_P: 0.2 + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 16 + CALIBRATION_SIZE: 20 + CENTER_FRACTIONS: [] + MAX_ATTEMPTS: 30 + NAME: PoissonDiskMaskFunc + USE_MOTION: false + 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: false + BATCH_BY: [] + NUM_WORKERS: 12 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: '' + SUBSAMPLE_TRAIN: + NUM_TOTAL: 3 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + TEST: + - mridata_knee_2019_test + TRAIN: + - mridata_knee_2019_train + VAL: + - mridata_knee_2019_val +DESCRIPTION: + BRIEF: Denoiser finetuning U-Net 16x - augmentation std_dev=(), 3 supervised scan(s), + 0 unsupervised scan(s), 40k iterations, restart-iteration-count = True + ENTITY_NAME: '' + EXP_NAME: noise2recon/mridata_knee_3dfse/16x/Supervised-FT_3sub + PROJECT_NAME: '' + TAGS: + - baseline + - supervised-ft + - 16x + - mridata_knee_3dfse +MODEL: + A2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + CONSISTENCY: + AUG: + MOTION: + RANGE: + - 0.2 + - 0.5 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE: + MASK: + RHO: 1.0 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + STD_DEV: [] + LATENT_LOSS_NAME: mag_l1 + LATENT_LOSS_WEIGHT: 0.1 + LOSS_NAME: l1 + LOSS_WEIGHT: 0.1 + NUM_LATENT_LAYERS: 1 + USE_CONSISTENCY: true + USE_LATENT: 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 + M2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + META_ARCHITECTURE: UnetModel + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NM2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + SSDU: + MASKER: + PARAMS: {} + META_ARCHITECTURE: GeneralizedUnrolledCNN + UNET: + BLOCK_ORDER: + - conv + - relu + - conv + - relu + - batchnorm + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NORMALIZE: false + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + BLOCK_ARCHITECTURE: ResNet + 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: /bmrNAS/people/arjun/results/ss_recon/n2r-experiments/denoise-pretrainer/version_019/model_0036399.pth +OUTPUT_DIR: results://noise2recon/mridata_knee_3dfse/16x/Supervised-FT_3sub +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + BIAS_LR_FACTOR: 1.0 + CHECKPOINT_PERIOD: -10 + GAMMA: 0.1 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: '' + MAX_ITER: 40000 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: + - 320000 + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 16 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_BIAS: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: -10 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 0 + VAL_AS_TEST: true + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim (Wang) +TIME_SCALE: iter +VERSION: 1 +VIS_PERIOD: 400 diff --git a/mridata_knee_3dfse/16x/Supervised-FT_3sub/model-gpu.ckpt b/mridata_knee_3dfse/16x/Supervised-FT_3sub/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..607e0e107142e1272c8eef749fe6529d15e3c324 --- /dev/null +++ b/mridata_knee_3dfse/16x/Supervised-FT_3sub/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:16ff522e6cab3e56505356ccb2132a33ff5900bb84f6878f0ed89549fe26a750 +size 93109175 diff --git a/mridata_knee_3dfse/16x/Supervised-FT_3sub/model-raw-gpu.ckpt 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file mode 100644 index 0000000000000000000000000000000000000000..eb41f2a6a11dd805b11b875b86facaa8a03cfb61 --- /dev/null +++ b/mridata_knee_3dfse/16x/Supervised-FT_3sub/model.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ef4340f4d3695b539a0c27b2e168dc70a57fb52e0c77e51d83102c32d16cd984 +size 93103415 diff --git a/mridata_knee_3dfse/16x/Supervised_14sub/config.yaml b/mridata_knee_3dfse/16x/Supervised_14sub/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..02337d63d881cfd4a93d3c57f8a4441513cca8da --- /dev/null +++ b/mridata_knee_3dfse/16x/Supervised_14sub/config.yaml @@ -0,0 +1,205 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 16 +AUG_TRAIN: + MOTION_P: 0.2 + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 16 + CALIBRATION_SIZE: 20 + CENTER_FRACTIONS: [] + MAX_ATTEMPTS: 30 + NAME: PoissonDiskMaskFunc + USE_MOTION: false + 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: false + BATCH_BY: [] + NUM_WORKERS: 12 + 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: + TEST: + - mridata_knee_2019_test + TRAIN: + - mridata_knee_2019_train + VAL: + - mridata_knee_2019_val +DESCRIPTION: + BRIEF: U-NET LR = 1e-3 Baseline 16x mridata.org, 3 subject, BS=16, l1 loss + ENTITY_NAME: '' + EXP_NAME: noise2recon/mridata_knee_3dfse/16x/Supervised_14sub + PROJECT_NAME: '' + TAGS: + - baseline + - supervised + - 16x + - mridata_knee_3dfse +MODEL: + A2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + CONSISTENCY: + AUG: + MOTION: + RANGE: + - 0.2 + - 0.5 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE: + MASK: + RHO: 1.0 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + STD_DEV: + - 1 + LATENT_LOSS_NAME: mag_l1 + LATENT_LOSS_WEIGHT: 0.1 + LOSS_NAME: l1 + LOSS_WEIGHT: 0.1 + NUM_LATENT_LAYERS: 1 + USE_CONSISTENCY: true + USE_LATENT: 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 + M2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + META_ARCHITECTURE: UnetModel + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NM2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + SSDU: + MASKER: + PARAMS: {} + META_ARCHITECTURE: GeneralizedUnrolledCNN + UNET: + BLOCK_ORDER: + - conv + - relu + - conv + - relu + - batchnorm + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NORMALIZE: false + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + BLOCK_ARCHITECTURE: ResNet + 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://noise2recon/mridata_knee_3dfse/16x/Supervised_14sub +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + BIAS_LR_FACTOR: 1.0 + CHECKPOINT_PERIOD: -10 + GAMMA: 0.1 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: '' + MAX_ITER: 80000 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: + - 320000 + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 16 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_BIAS: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: -10 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 0 + VAL_AS_TEST: true + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim (Wang) +TIME_SCALE: iter +VERSION: 1 +VIS_PERIOD: 400 diff --git a/mridata_knee_3dfse/16x/Supervised_14sub/model-gpu.ckpt b/mridata_knee_3dfse/16x/Supervised_14sub/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..3aa2b27a68a20eca790166cfef1e2420e9ffb964 --- /dev/null +++ b/mridata_knee_3dfse/16x/Supervised_14sub/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:0a3476f2bda953ce8f64573933de52854693850a535c6e61c9b0be16075fee25 +size 93109175 diff --git a/mridata_knee_3dfse/16x/Supervised_14sub/model-raw-gpu.ckpt b/mridata_knee_3dfse/16x/Supervised_14sub/model-raw-gpu.ckpt 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0000000000000000000000000000000000000000..3199b426c5e244355a37d212936bb5f9bdf206e2 --- /dev/null +++ b/mridata_knee_3dfse/16x/Supervised_14sub/model.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ef80581fdd6f631aea8742b14b97308764b5161e52af6522e6b80f4c43cef479 +size 93103415 diff --git a/mridata_knee_3dfse/16x/Supervised_1sub/config.yaml b/mridata_knee_3dfse/16x/Supervised_1sub/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..f70895219bcba9bdccb81dabe6fe4ea3493b8680 --- /dev/null +++ b/mridata_knee_3dfse/16x/Supervised_1sub/config.yaml @@ -0,0 +1,205 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 16 +AUG_TRAIN: + MOTION_P: 0.2 + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 16 + CALIBRATION_SIZE: 20 + CENTER_FRACTIONS: [] + MAX_ATTEMPTS: 30 + NAME: PoissonDiskMaskFunc + USE_MOTION: false + 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: false + BATCH_BY: [] + NUM_WORKERS: 12 + 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: + TEST: + - mridata_knee_2019_test + TRAIN: + - mridata_knee_2019_train + VAL: + - mridata_knee_2019_val +DESCRIPTION: + BRIEF: U-NET LR = 1e-3 Baseline 16x mridata.org, 1 subject, BS=16, l1 loss + ENTITY_NAME: '' + EXP_NAME: noise2recon/mridata_knee_3dfse/16x/Supervised_1sub + PROJECT_NAME: '' + TAGS: + - baseline + - supervised + - 16x + - mridata_knee_3dfse +MODEL: + A2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + CONSISTENCY: + AUG: + MOTION: + RANGE: + - 0.2 + - 0.5 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE: + MASK: + RHO: 1.0 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + STD_DEV: + - 1 + LATENT_LOSS_NAME: mag_l1 + LATENT_LOSS_WEIGHT: 0.1 + LOSS_NAME: l1 + LOSS_WEIGHT: 0.1 + NUM_LATENT_LAYERS: 1 + USE_CONSISTENCY: true + USE_LATENT: 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 + M2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + META_ARCHITECTURE: UnetModel + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NM2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + SSDU: + MASKER: + PARAMS: {} + META_ARCHITECTURE: GeneralizedUnrolledCNN + UNET: + BLOCK_ORDER: + - conv + - relu + - conv + - relu + - batchnorm + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NORMALIZE: false + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + BLOCK_ARCHITECTURE: ResNet + 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://noise2recon/mridata_knee_3dfse/16x/Supervised_1sub +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + BIAS_LR_FACTOR: 1.0 + CHECKPOINT_PERIOD: -10 + GAMMA: 0.1 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: '' + MAX_ITER: 80000 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: + - 320000 + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 16 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_BIAS: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: -10 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 0 + VAL_AS_TEST: true + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim (Wang) +TIME_SCALE: iter +VERSION: 1 +VIS_PERIOD: 400 diff --git a/mridata_knee_3dfse/16x/Supervised_1sub/model-gpu.ckpt b/mridata_knee_3dfse/16x/Supervised_1sub/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..38d47c4061bbbac73be8129501283617884c2ac8 --- /dev/null +++ b/mridata_knee_3dfse/16x/Supervised_1sub/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:b5ebce9868e730d8aee5f8bf34d505b9f9eee1c221c838fa8e1bfdd6cc770ca2 +size 93109175 diff --git a/mridata_knee_3dfse/16x/Supervised_1sub/model-raw-gpu.ckpt b/mridata_knee_3dfse/16x/Supervised_1sub/model-raw-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..5da19d58e32b008c6f4e0b95824499e56e10e803 --- /dev/null +++ b/mridata_knee_3dfse/16x/Supervised_1sub/model-raw-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:248d127eccc17906bafcda75f126e9d144efbdcbe059eb9595ad4a45ab3b4f8f +size 93109175 diff --git a/mridata_knee_3dfse/16x/Supervised_1sub/model-raw.ckpt b/mridata_knee_3dfse/16x/Supervised_1sub/model-raw.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..1d9fb81cc8a197d2277cdc97afd05c7fef2bcc54 --- /dev/null +++ b/mridata_knee_3dfse/16x/Supervised_1sub/model-raw.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a6ce2e140670d822497943d1ae1f2c94b2228050b018e59f416435a3ded09fa4 +size 93103415 diff --git a/mridata_knee_3dfse/16x/Supervised_1sub/model.ckpt b/mridata_knee_3dfse/16x/Supervised_1sub/model.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..1d9fb81cc8a197d2277cdc97afd05c7fef2bcc54 --- /dev/null +++ b/mridata_knee_3dfse/16x/Supervised_1sub/model.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a6ce2e140670d822497943d1ae1f2c94b2228050b018e59f416435a3ded09fa4 +size 93103415 diff --git a/mridata_knee_3dfse/16x/Supervised_2sub/config.yaml b/mridata_knee_3dfse/16x/Supervised_2sub/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..9fa8d584b710feb2216238ec70d366b165b626f9 --- /dev/null +++ b/mridata_knee_3dfse/16x/Supervised_2sub/config.yaml @@ -0,0 +1,205 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 16 +AUG_TRAIN: + MOTION_P: 0.2 + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 16 + CALIBRATION_SIZE: 20 + CENTER_FRACTIONS: [] + MAX_ATTEMPTS: 30 + NAME: PoissonDiskMaskFunc + USE_MOTION: false + 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: false + BATCH_BY: [] + NUM_WORKERS: 12 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: '' + SUBSAMPLE_TRAIN: + NUM_TOTAL: 2 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + TEST: + - mridata_knee_2019_test + TRAIN: + - mridata_knee_2019_train + VAL: + - mridata_knee_2019_val +DESCRIPTION: + BRIEF: U-NET LR = 1e-3 Baseline 16x mridata.org, 2 subject, BS=16, l1 loss + ENTITY_NAME: '' + EXP_NAME: noise2recon/mridata_knee_3dfse/16x/Supervised_2sub + PROJECT_NAME: '' + TAGS: + - baseline + - supervised + - 16x + - mridata_knee_3dfse +MODEL: + A2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + CONSISTENCY: + AUG: + MOTION: + RANGE: + - 0.2 + - 0.5 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE: + MASK: + RHO: 1.0 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + STD_DEV: + - 1 + LATENT_LOSS_NAME: mag_l1 + LATENT_LOSS_WEIGHT: 0.1 + LOSS_NAME: l1 + LOSS_WEIGHT: 0.1 + NUM_LATENT_LAYERS: 1 + USE_CONSISTENCY: true + USE_LATENT: 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 + M2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + META_ARCHITECTURE: UnetModel + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NM2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + SSDU: + MASKER: + PARAMS: {} + META_ARCHITECTURE: GeneralizedUnrolledCNN + UNET: + BLOCK_ORDER: + - conv + - relu + - conv + - relu + - batchnorm + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NORMALIZE: false + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + BLOCK_ARCHITECTURE: ResNet + 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://noise2recon/mridata_knee_3dfse/16x/Supervised_2sub +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + BIAS_LR_FACTOR: 1.0 + CHECKPOINT_PERIOD: -10 + GAMMA: 0.1 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: '' + MAX_ITER: 80000 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: + - 320000 + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 16 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_BIAS: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: -10 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 0 + VAL_AS_TEST: true + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim (Wang) +TIME_SCALE: iter +VERSION: 1 +VIS_PERIOD: 400 diff --git a/mridata_knee_3dfse/16x/Supervised_2sub/model-gpu.ckpt b/mridata_knee_3dfse/16x/Supervised_2sub/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..ddd9d9c5d6875fd929cbba8a700de494bf7ce0a1 --- /dev/null +++ b/mridata_knee_3dfse/16x/Supervised_2sub/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:e270027c9549265cd5a907d844b17bf9af4c0066af7e9382b69cc9930ecc0d60 +size 93109175 diff --git a/mridata_knee_3dfse/16x/Supervised_2sub/model-raw-gpu.ckpt b/mridata_knee_3dfse/16x/Supervised_2sub/model-raw-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..39fc21c15cda662cb934a2861578f65bf32db4f2 --- /dev/null +++ b/mridata_knee_3dfse/16x/Supervised_2sub/model-raw-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:bb22c35b128e2fae7f1b38b68c2269429ff263aac9288c0db392c4e1d580b181 +size 93109175 diff --git a/mridata_knee_3dfse/16x/Supervised_2sub/model-raw.ckpt b/mridata_knee_3dfse/16x/Supervised_2sub/model-raw.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..a79a7c4a5ffdbf851db291d7462eeea3ba9291f1 --- /dev/null +++ b/mridata_knee_3dfse/16x/Supervised_2sub/model-raw.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:37f73ac06ff6adcce9a1bb0af921cb8b63750026c7ed1f0752760ffec114e0b7 +size 93103415 diff --git a/mridata_knee_3dfse/16x/Supervised_2sub/model.ckpt b/mridata_knee_3dfse/16x/Supervised_2sub/model.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..a79a7c4a5ffdbf851db291d7462eeea3ba9291f1 --- /dev/null +++ b/mridata_knee_3dfse/16x/Supervised_2sub/model.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:37f73ac06ff6adcce9a1bb0af921cb8b63750026c7ed1f0752760ffec114e0b7 +size 93103415 diff --git a/mridata_knee_3dfse/16x/Supervised_3sub/config.yaml b/mridata_knee_3dfse/16x/Supervised_3sub/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..01c4ecda29d2018bfb6cf08451e3f03ab4cbc0d0 --- /dev/null +++ b/mridata_knee_3dfse/16x/Supervised_3sub/config.yaml @@ -0,0 +1,205 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 16 +AUG_TRAIN: + MOTION_P: 0.2 + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 16 + CALIBRATION_SIZE: 20 + CENTER_FRACTIONS: [] + MAX_ATTEMPTS: 30 + NAME: PoissonDiskMaskFunc + USE_MOTION: false + 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: false + BATCH_BY: [] + NUM_WORKERS: 12 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: '' + SUBSAMPLE_TRAIN: + NUM_TOTAL: 3 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + TEST: + - mridata_knee_2019_test + TRAIN: + - mridata_knee_2019_train + VAL: + - mridata_knee_2019_val +DESCRIPTION: + BRIEF: U-NET LR = 1e-3 Baseline 16x mridata.org, 3 subject, BS=16, l1 loss + ENTITY_NAME: '' + EXP_NAME: noise2recon/mridata_knee_3dfse/16x/Supervised_3sub + PROJECT_NAME: '' + TAGS: + - baseline + - supervised + - 16x + - mridata_knee_3dfse +MODEL: + A2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + CONSISTENCY: + AUG: + MOTION: + RANGE: + - 0.2 + - 0.5 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE: + MASK: + RHO: 1.0 + SCHEDULER: + WARMUP_ITERS: 0 + WARMUP_METHOD: '' + STD_DEV: + - 1 + LATENT_LOSS_NAME: mag_l1 + LATENT_LOSS_WEIGHT: 0.1 + LOSS_NAME: l1 + LOSS_WEIGHT: 0.1 + NUM_LATENT_LAYERS: 1 + USE_CONSISTENCY: true + USE_LATENT: 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 + M2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + META_ARCHITECTURE: UnetModel + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NM2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + RECON_LOSS: + NAME: l1 + RENORMALIZE_DATA: false + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + SSDU: + MASKER: + PARAMS: {} + META_ARCHITECTURE: GeneralizedUnrolledCNN + UNET: + BLOCK_ORDER: + - conv + - relu + - conv + - relu + - batchnorm + - dropout + CHANNELS: 32 + DROPOUT: 0.0 + IN_CHANNELS: 2 + NORMALIZE: false + NUM_POOL_LAYERS: 4 + OUT_CHANNELS: 2 + UNROLLED: + BLOCK_ARCHITECTURE: ResNet + 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://noise2recon/mridata_knee_3dfse/16x/Supervised_3sub +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + BIAS_LR_FACTOR: 1.0 + CHECKPOINT_PERIOD: -10 + GAMMA: 0.1 + GRAD_ACCUM_ITERS: 1 + LR_SCHEDULER_NAME: '' + MAX_ITER: 80000 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: + - 320000 + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 16 + WARMUP_FACTOR: 0.001 + WARMUP_ITERS: 1000 + WARMUP_METHOD: linear + WEIGHT_DECAY: 0.0001 + WEIGHT_DECAY_BIAS: 0.0001 + WEIGHT_DECAY_NORM: 0.0 +TEST: + EVAL_PERIOD: -10 + EXPECTED_RESULTS: [] + FLUSH_PERIOD: 0 + VAL_AS_TEST: true + VAL_METRICS: + RECON: + - psnr + - psnr_scan + - psnr_mag + - psnr_mag_scan + - nrmse + - nrmse_scan + - nrmse_mag + - nrmse_mag_scan + - ssim (Wang) +TIME_SCALE: iter +VERSION: 1 +VIS_PERIOD: 400 diff --git a/mridata_knee_3dfse/16x/Supervised_3sub/model-gpu.ckpt b/mridata_knee_3dfse/16x/Supervised_3sub/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..45983a76a1ca8603a8579f6a8156057dfa4af11b --- /dev/null +++ b/mridata_knee_3dfse/16x/Supervised_3sub/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8ef6a4d9b154b642ab872e31a55df3b9d74bfe6ef91efc79045e84d151b6d27f +size 93109175 diff --git a/mridata_knee_3dfse/16x/Supervised_3sub/model-raw-gpu.ckpt b/mridata_knee_3dfse/16x/Supervised_3sub/model-raw-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..efc548385ed621241067d533a28ca3c46a8554cf --- /dev/null +++ b/mridata_knee_3dfse/16x/Supervised_3sub/model-raw-gpu.ckpt @@ -0,0 +1,3 @@ +version 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