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diff=lfs merge=lfs -text +mridata_knee_3dfse/VORTEX_Image/model-raw-gpu.ckpt filter=lfs diff=lfs merge=lfs -text +mridata_knee_3dfse/VORTEX_Image/model-raw.ckpt filter=lfs diff=lfs merge=lfs -text +mridata_knee_3dfse/VORTEX_Image/model.ckpt filter=lfs diff=lfs merge=lfs -text +mridata_knee_3dfse/VORTEX_Physics/model-gpu.ckpt filter=lfs diff=lfs merge=lfs -text +mridata_knee_3dfse/VORTEX_Physics/model-raw-gpu.ckpt filter=lfs diff=lfs merge=lfs -text +mridata_knee_3dfse/VORTEX_Physics/model-raw.ckpt filter=lfs diff=lfs merge=lfs -text +mridata_knee_3dfse/VORTEX_Physics/model.ckpt filter=lfs diff=lfs merge=lfs -text diff --git a/fastmri_brain_mini/Aug_Motion/config.yaml b/fastmri_brain_mini/Aug_Motion/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..fabf332a438fa0780d3339e9960afcb653a7e89b --- /dev/null +++ b/fastmri_brain_mini/Aug_Motion/config.yaml @@ -0,0 +1,227 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 8 +AUG_TRAIN: + MOTION_P: 0.2 + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + gamma: 5.0 + max_iter: -200 + name: WarmupStepTF + warmup_method: exp + warmup_milestones: + - -1 + TRANSFORMS: + - name: RandomMRIMotion + p: 0.2 + std_devs: + - 0.2 + - 0.5 + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 8 + CALIBRATION_SIZE: 0 + CENTER_FRACTIONS: + - 0.04 + MAX_ATTEMPTS: 30 + NAME: RandomMaskFunc1D + USE_MOTION: false + USE_NOISE: false +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: + - - target + - jsense-8-cf=4/target + - - maps + - jsense-8-cf=4/maps + DROP_LAST: true + FILTER: + BY: + - - acquisition + - AXT2 + - - systemFieldStrength_T + - 2.8936 + GROUP_SAMPLER: + AS_BATCH_SAMPLER: true + BATCH_BY: + - receiverChannels + - inplane_shape + NUM_WORKERS: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: GroupSampler + SUBSAMPLE_TRAIN: + NUM_TOTAL: 18 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: 50 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + TEST: + - fastMRI_brain_multicoil_mini_v0.0.1_test + TRAIN: + - fastMRI_brain_multicoil_mini_v0.0.1_train + VAL: + - fastMRI_brain_multicoil_mini_v0.0.1_val +DESCRIPTION: + BRIEF: 'U-NET LR = 1e-3 Aug2Recon 8x fastMRI brain-mc mini \(MRAugment\) - Exp: + fastmri brain - motion/heavy/version_009 - MRAugment + motion, heavy, p=0.2' + ENTITY_NAME: '' + EXP_NAME: vortex/fastmri_brain_mini/Aug_Motion + PROJECT_NAME: '' + TAGS: + - baseline + - aug + - 8x + - fastmri_brain_mini +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://vortex/fastmri_brain_mini/Aug_Motion +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + BIAS_LR_FACTOR: 1.0 + CHECKPOINT_PERIOD: -10 + GAMMA: 0.1 + GRAD_ACCUM_ITERS: 2 + LR_SCHEDULER_NAME: '' + MAX_ITER: -200 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: [] + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 12 + 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: -10 + 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: 100 diff --git a/fastmri_brain_mini/Aug_Motion/model-gpu.ckpt b/fastmri_brain_mini/Aug_Motion/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..c096151cef3b6e701e313ebc6b61a0b5dfce368c --- /dev/null +++ b/fastmri_brain_mini/Aug_Motion/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:2c2bded991652d43b63878ae5637c43909450e3d4c2d30d4dfb8b478ec153a65 +size 93109239 diff --git a/fastmri_brain_mini/Aug_Motion/model-raw-gpu.ckpt b/fastmri_brain_mini/Aug_Motion/model-raw-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..6c3915cbbf8e5c66afe8dabe3017facedf2301c5 --- /dev/null +++ b/fastmri_brain_mini/Aug_Motion/model-raw-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:7ef44b5a909c62f2a4fbf020cdc668539fc079750a2930a7116d6126a84da778 +size 93109239 diff --git 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0000000000000000000000000000000000000000..a659bea44e525fbbf067b0561be853dd972d4f7a --- /dev/null +++ b/fastmri_brain_mini/Aug_Motion__super-heavy/config.yaml @@ -0,0 +1,228 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 8 +AUG_TRAIN: + MOTION_P: 0.2 + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + gamma: 5.0 + max_iter: -200 + name: WarmupStepTF + warmup_method: exp + warmup_milestones: + - -1 + TRANSFORMS: + - name: RandomMRIMotion + p: 0.2 + std_devs: + - 0.5 + - 0.7 + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 8 + CALIBRATION_SIZE: 0 + CENTER_FRACTIONS: + - 0.04 + MAX_ATTEMPTS: 30 + NAME: RandomMaskFunc1D + USE_MOTION: false + USE_NOISE: false +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: + - - target + - jsense-8-cf=4/target + - - maps + - jsense-8-cf=4/maps + DROP_LAST: true + FILTER: + BY: + - - acquisition + - AXT2 + - - systemFieldStrength_T + - 2.8936 + GROUP_SAMPLER: + AS_BATCH_SAMPLER: true + BATCH_BY: + - receiverChannels + - inplane_shape + NUM_WORKERS: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: GroupSampler + SUBSAMPLE_TRAIN: + NUM_TOTAL: 18 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: 50 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + TEST: + - fastMRI_brain_multicoil_mini_v0.0.1_test + TRAIN: + - fastMRI_brain_multicoil_mini_v0.0.1_train + VAL: + - fastMRI_brain_multicoil_mini_v0.0.1_val +DESCRIPTION: + BRIEF: 'U-NET LR = 1e-3 Aug2Recon 8x fastMRI brain-mc mini \(MRAugment\) - Exp: + fastmri brain - motion/super-heavy/version_009 - MRAugment + motion, super-heavy, + p=0.2' + ENTITY_NAME: '' + EXP_NAME: vortex/fastmri_brain_mini/Aug_Motion__super-heavy + PROJECT_NAME: '' + TAGS: + - baseline + - aug + - 8x + - fastmri_brain_mini +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://vortex/fastmri_brain_mini/Aug_Motion__super-heavy +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + BIAS_LR_FACTOR: 1.0 + CHECKPOINT_PERIOD: -10 + GAMMA: 0.1 + GRAD_ACCUM_ITERS: 2 + LR_SCHEDULER_NAME: '' + MAX_ITER: -200 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: [] + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 12 + 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: -10 + 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: 100 diff --git a/fastmri_brain_mini/Aug_Motion__super-heavy/model-gpu.ckpt b/fastmri_brain_mini/Aug_Motion__super-heavy/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..3d1bd8699576509b885bf467a00c5ecb387d9075 --- /dev/null +++ b/fastmri_brain_mini/Aug_Motion__super-heavy/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:7daf8e22659bfa26015b7668691331f6e2bb667598e2e8fe34fda5caf481bd97 +size 93109239 diff --git a/fastmri_brain_mini/Aug_Motion__super-heavy/model-raw-gpu.ckpt b/fastmri_brain_mini/Aug_Motion__super-heavy/model-raw-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..d091e024a6cae4cf935095e83019595a9f5fde70 --- /dev/null +++ b/fastmri_brain_mini/Aug_Motion__super-heavy/model-raw-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:32b010785e07dcd3e87d354036525d6b7d8414d60396e6bb1daf8045418ca78c +size 93109239 diff --git a/fastmri_brain_mini/Aug_Motion__super-heavy/model-raw.ckpt b/fastmri_brain_mini/Aug_Motion__super-heavy/model-raw.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..e19cf7aa86a512ef42d1ece8998ac5a1de3fa521 --- /dev/null +++ b/fastmri_brain_mini/Aug_Motion__super-heavy/model-raw.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a31448787ff97797c01a46626f30c40e2a70920494aea64a51f3f6ee27801a54 +size 93103415 diff --git a/fastmri_brain_mini/Aug_Motion__super-heavy/model.ckpt b/fastmri_brain_mini/Aug_Motion__super-heavy/model.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..e19cf7aa86a512ef42d1ece8998ac5a1de3fa521 --- /dev/null +++ b/fastmri_brain_mini/Aug_Motion__super-heavy/model.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a31448787ff97797c01a46626f30c40e2a70920494aea64a51f3f6ee27801a54 +size 93103415 diff --git a/fastmri_brain_mini/MRAugment_Image/config.yaml b/fastmri_brain_mini/MRAugment_Image/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..178d44c9bd5fd0b4f9a1a86bc3d0ce818d954b45 --- /dev/null +++ b/fastmri_brain_mini/MRAugment_Image/config.yaml @@ -0,0 +1,247 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 8 +AUG_TRAIN: + MOTION_P: 0.2 + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + gamma: 5.0 + max_iter: -200 + name: WarmupStepTF + warmup_method: exp + warmup_milestones: + - -1 + TRANSFORMS: + - dims: -1 + name: RandomFlip + p: 0.275 + - dims: -2 + name: RandomFlip + p: 0.275 + - ks: + - 2 + name: RandomRot90 + p: 0.275 + - name: RandomTranslation + p: 0.55 + pad_mode: reflect + translate: + - 0.08 + - 0.125 + - angle: 180.0 + name: RandomAffine + p: + angle: 0.275 + scale: 0.55 + shear: 0.55 + pad_like: MRAugment + scale: 0.25 + shear: 15.0 + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 8 + CALIBRATION_SIZE: 0 + CENTER_FRACTIONS: + - 0.04 + MAX_ATTEMPTS: 30 + NAME: RandomMaskFunc1D + USE_MOTION: false + USE_NOISE: false +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: + - - target + - jsense-8-cf=4/target + - - maps + - jsense-8-cf=4/maps + DROP_LAST: true + FILTER: + BY: + - - acquisition + - AXT2 + - - systemFieldStrength_T + - 2.8936 + GROUP_SAMPLER: + AS_BATCH_SAMPLER: true + BATCH_BY: + - receiverChannels + - inplane_shape + NUM_WORKERS: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: GroupSampler + SUBSAMPLE_TRAIN: + NUM_TOTAL: 18 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: 50 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + TEST: + - fastMRI_brain_multicoil_mini_v0.0.1_test + TRAIN: + - fastMRI_brain_multicoil_mini_v0.0.1_train + VAL: + - fastMRI_brain_multicoil_mini_v0.0.1_val +DESCRIPTION: + BRIEF: 'U-NET LR = 1e-3 Aug2Recon 8x fastMRI brain-mc mini \(MRAugment\) - Exp: + fastmri brain - image/version_008 - MRAugment + image, light, p=0.2' + ENTITY_NAME: '' + EXP_NAME: vortex/fastmri_brain_mini/MRAugment_Image + PROJECT_NAME: '' + TAGS: + - baseline + - mraugment + - 8x + - fastmri_brain_mini +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://vortex/fastmri_brain_mini/MRAugment_Image +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + BIAS_LR_FACTOR: 1.0 + CHECKPOINT_PERIOD: -10 + GAMMA: 0.1 + GRAD_ACCUM_ITERS: 2 + LR_SCHEDULER_NAME: '' + MAX_ITER: -200 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: [] + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 12 + 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: -10 + 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: 100 diff --git a/fastmri_brain_mini/MRAugment_Image/model-gpu.ckpt b/fastmri_brain_mini/MRAugment_Image/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..ea3df30e8ae0bf2177f5bc7f7f536e4bafc40493 --- /dev/null +++ b/fastmri_brain_mini/MRAugment_Image/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:940b8db5d9742bdb070d9bdaf3c78afab741b5781678bdb5aa8bee15a3053949 +size 93109239 diff --git a/fastmri_brain_mini/MRAugment_Image/model-raw-gpu.ckpt b/fastmri_brain_mini/MRAugment_Image/model-raw-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..dc663f2b88cb5980c54410db7a3055101da81686 --- /dev/null +++ b/fastmri_brain_mini/MRAugment_Image/model-raw-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:6462f8465ce571cbc0770b8f50a8236bac0e48079500204bd7fb5803a1bab119 +size 93109239 diff --git a/fastmri_brain_mini/MRAugment_Image/model-raw.ckpt b/fastmri_brain_mini/MRAugment_Image/model-raw.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..518f10ec030136cbfbc21fe563d517c88f55ce96 --- /dev/null +++ b/fastmri_brain_mini/MRAugment_Image/model-raw.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:21c561c74189d3cfdeb2af76084e69d29be35226913444b8d4b44cca6842d08d +size 93103415 diff --git a/fastmri_brain_mini/MRAugment_Image/model.ckpt b/fastmri_brain_mini/MRAugment_Image/model.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..518f10ec030136cbfbc21fe563d517c88f55ce96 --- /dev/null +++ b/fastmri_brain_mini/MRAugment_Image/model.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:21c561c74189d3cfdeb2af76084e69d29be35226913444b8d4b44cca6842d08d +size 93103415 diff --git a/fastmri_brain_mini/Noise2Recon_super-heavy/config.yaml b/fastmri_brain_mini/Noise2Recon_super-heavy/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..ede1a48ea77f338228d05090c982d08da907177f --- /dev/null +++ b/fastmri_brain_mini/Noise2Recon_super-heavy/config.yaml @@ -0,0 +1,222 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 8 +AUG_TRAIN: + MOTION_P: 0.2 + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 8 + CALIBRATION_SIZE: 0 + CENTER_FRACTIONS: + - 0.04 + MAX_ATTEMPTS: 30 + NAME: RandomMaskFunc1D + USE_MOTION: false + USE_NOISE: false +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: + - - target + - jsense-8-cf=4/target + - - maps + - jsense-8-cf=4/maps + DROP_LAST: true + FILTER: + BY: + - - acquisition + - AXT2 + - - systemFieldStrength_T + - 2.8936 + GROUP_SAMPLER: + AS_BATCH_SAMPLER: true + BATCH_BY: + - receiverChannels + - inplane_shape + NUM_WORKERS: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: AlternatingGroupSampler + SUBSAMPLE_TRAIN: + NUM_TOTAL: 54 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 36 + NUM_VAL: 50 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + TEST: + - fastMRI_brain_multicoil_mini_v0.0.1_test + TRAIN: + - fastMRI_brain_multicoil_mini_v0.0.1_train + VAL: + - fastMRI_brain_multicoil_mini_v0.0.1_val +DESCRIPTION: + BRIEF: 'U-NET LR = 1e-3 Aug2Recon 8x fastMRI brain-mc mini (Aug2Recon) - noise/super-heavy/version_001 + - Data ratio - 18 supervised : 36 unsupervised, 1:1 alt sampling, noise/super-heavy/version_001' + ENTITY_NAME: '' + EXP_NAME: vortex/fastmri_brain_mini/Noise2Recon_super-heavy + PROJECT_NAME: '' + TAGS: + - baseline + - noise2recon + - 8x + - fastmri_brain_mini +MODEL: + A2R: + META_ARCHITECTURE: UnetModel + 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: + - name: RandomNoise + p: 1.0 + std_devs: + - 0.5 + - 0.7 + use_mask: true + 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: A2RModel + 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://vortex/fastmri_brain_mini/Noise2Recon_super-heavy +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + BIAS_LR_FACTOR: 1.0 + CHECKPOINT_PERIOD: -10 + GAMMA: 0.1 + GRAD_ACCUM_ITERS: 2 + LR_SCHEDULER_NAME: '' + MAX_ITER: -200 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: [] + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 12 + 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: 100 diff --git a/fastmri_brain_mini/Noise2Recon_super-heavy/model-gpu.ckpt b/fastmri_brain_mini/Noise2Recon_super-heavy/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..cdab719d5ce6742e3853b17b39a092dceec46382 --- /dev/null +++ b/fastmri_brain_mini/Noise2Recon_super-heavy/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:77762f28bc196b6c747210ddc6016232d50d7bb016107e6d0d5541d921e8ac9a +size 93110071 diff --git a/fastmri_brain_mini/Noise2Recon_super-heavy/model-raw-gpu.ckpt b/fastmri_brain_mini/Noise2Recon_super-heavy/model-raw-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..2cd8de6c2ee8ee15eb9304aec045cceaeed8aca0 --- /dev/null +++ b/fastmri_brain_mini/Noise2Recon_super-heavy/model-raw-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:19157a4f1e79aa91da5d7ce65268bc546c29e4f1ec6ab594ea88b9eed98e7382 +size 93110071 diff --git a/fastmri_brain_mini/Noise2Recon_super-heavy/model-raw.ckpt b/fastmri_brain_mini/Noise2Recon_super-heavy/model-raw.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..e2e0f79c49ac09611dc38b47792135c0ee437958 --- /dev/null +++ b/fastmri_brain_mini/Noise2Recon_super-heavy/model-raw.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:fbef095285933a9499dac8d6c1ff4e90382df53108021dba97cf739783658d42 +size 93103607 diff --git a/fastmri_brain_mini/Noise2Recon_super-heavy/model.ckpt b/fastmri_brain_mini/Noise2Recon_super-heavy/model.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..e2e0f79c49ac09611dc38b47792135c0ee437958 --- /dev/null +++ b/fastmri_brain_mini/Noise2Recon_super-heavy/model.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:fbef095285933a9499dac8d6c1ff4e90382df53108021dba97cf739783658d42 +size 93103607 diff --git a/fastmri_brain_mini/SSDU/config.yaml b/fastmri_brain_mini/SSDU/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..842b273effa46076c2a685c51efdaf409be92b62 --- /dev/null +++ b/fastmri_brain_mini/SSDU/config.yaml @@ -0,0 +1,220 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 8 +AUG_TRAIN: + MOTION_P: 0.2 + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 8 + CALIBRATION_SIZE: 0 + CENTER_FRACTIONS: + - 0.04 + MAX_ATTEMPTS: 30 + NAME: RandomMaskFunc1D + USE_MOTION: false + USE_NOISE: false +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: + - - target + - jsense-8-cf=4/target + - - maps + - jsense-8-cf=4/maps + DROP_LAST: true + FILTER: + BY: + - - acquisition + - AXT2 + - - systemFieldStrength_T + - 2.8936 + GROUP_SAMPLER: + AS_BATCH_SAMPLER: true + BATCH_BY: + - receiverChannels + - inplane_shape + NUM_WORKERS: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: GroupSampler + SUBSAMPLE_TRAIN: + NUM_TOTAL: 54 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 18 + NUM_VAL: 50 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + TEST: + - fastMRI_brain_multicoil_mini_v0.0.1_test + TRAIN: + - fastMRI_brain_multicoil_mini_v0.0.1_train + VAL: + - fastMRI_brain_multicoil_mini_v0.0.1_val +DESCRIPTION: + BRIEF: SSDU U-Net 8x fastMRI brain-mc mini - rho=0.2, uniform/rho=2e-01/version_009 + ENTITY_NAME: '' + EXP_NAME: vortex/fastmri_brain_mini/SSDU + PROJECT_NAME: '' + TAGS: + - baseline + - ssdu + - 8x + - fastmri_brain_mini +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: SSDUModel + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NM2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + RECON_LOSS: + NAME: k_l1_l2_sum_normalized + RENORMALIZE_DATA: false + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + SSDU: + MASKER: + PARAMS: + kind: uniform + p: 1.0 + per_example: true + rhos: 0.2 + std_scale: 4 + META_ARCHITECTURE: UnetModel + 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://vortex/fastmri_brain_mini/SSDU +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + BIAS_LR_FACTOR: 1.0 + CHECKPOINT_PERIOD: -10 + GAMMA: 0.1 + GRAD_ACCUM_ITERS: 3 + LR_SCHEDULER_NAME: '' + MAX_ITER: -200 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: [] + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 8 + 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: -10 + 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: 100 diff --git a/fastmri_brain_mini/SSDU/model-gpu.ckpt b/fastmri_brain_mini/SSDU/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..07b5fff988827e7de92e4c87e66597fb52d23168 --- /dev/null +++ b/fastmri_brain_mini/SSDU/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:4d55d05b9be7bd5d1c02b0059dff576f86e331e47bf668f8058093bfe3816a4e +size 93110071 diff --git a/fastmri_brain_mini/SSDU/model-raw-gpu.ckpt b/fastmri_brain_mini/SSDU/model-raw-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..d3fd0fd0838b3e19c68d34a4381ab0fe35a83530 --- /dev/null +++ b/fastmri_brain_mini/SSDU/model-raw-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c71257f00538451de2264f62e31aeb2cee35a46f2ea75d95713624fb7a9e7c7c +size 93110071 diff --git a/fastmri_brain_mini/SSDU/model-raw.ckpt b/fastmri_brain_mini/SSDU/model-raw.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..ac8e3a81601a943d37b48d9440c48426fd0cf607 --- /dev/null +++ b/fastmri_brain_mini/SSDU/model-raw.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:588b65426755ec783907d2435c3b26fa0789e54ef0b2b7a37761b67fbc68e10a +size 93103607 diff --git a/fastmri_brain_mini/SSDU/model.ckpt b/fastmri_brain_mini/SSDU/model.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..ac8e3a81601a943d37b48d9440c48426fd0cf607 --- /dev/null +++ b/fastmri_brain_mini/SSDU/model.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:588b65426755ec783907d2435c3b26fa0789e54ef0b2b7a37761b67fbc68e10a +size 93103607 diff --git a/fastmri_brain_mini/Supervised/config.yaml b/fastmri_brain_mini/Supervised/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..7940b2de8c691aa7285c1d12c3f30904c54a3742 --- /dev/null +++ b/fastmri_brain_mini/Supervised/config.yaml @@ -0,0 +1,215 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 8 +AUG_TRAIN: + MOTION_P: 0.2 + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 8 + CALIBRATION_SIZE: 0 + CENTER_FRACTIONS: + - 0.04 + MAX_ATTEMPTS: 30 + NAME: RandomMaskFunc1D + USE_MOTION: false + USE_NOISE: false +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: + - - target + - jsense-8-cf=4/target + - - maps + - jsense-8-cf=4/maps + DROP_LAST: true + FILTER: + BY: + - - acquisition + - AXT2 + - - systemFieldStrength_T + - 2.8936 + GROUP_SAMPLER: + AS_BATCH_SAMPLER: true + BATCH_BY: + - receiverChannels + - inplane_shape + NUM_WORKERS: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: GroupSampler + SUBSAMPLE_TRAIN: + NUM_TOTAL: 18 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: 50 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + TEST: + - fastMRI_brain_multicoil_mini_v0.0.1_test + TRAIN: + - fastMRI_brain_multicoil_mini_v0.0.1_train + VAL: + - fastMRI_brain_multicoil_mini_v0.0.1_val +DESCRIPTION: + BRIEF: U-NET LR = 1e-3 Aug2Recon 8x fastMRI brain-mc mini baseline + ENTITY_NAME: '' + EXP_NAME: vortex/fastmri_brain_mini/Supervised + PROJECT_NAME: '' + TAGS: + - baseline + - supervised + - 8x + - fastmri_brain_mini +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://vortex/fastmri_brain_mini/Supervised +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + BIAS_LR_FACTOR: 1.0 + CHECKPOINT_PERIOD: -10 + GAMMA: 0.1 + GRAD_ACCUM_ITERS: 2 + LR_SCHEDULER_NAME: '' + MAX_ITER: -200 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: [] + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 12 + 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: -10 + 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/fastmri_brain_mini/Supervised/model-gpu.ckpt b/fastmri_brain_mini/Supervised/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..bb77e6db61175efc00bd38fe28cfe94d21216b9a --- /dev/null +++ b/fastmri_brain_mini/Supervised/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:fa8537512d781c843465cac20d51deede67fbb16f17aa20a3d1155f7ed3ae577 +size 93109239 diff --git a/fastmri_brain_mini/Supervised/model-raw-gpu.ckpt b/fastmri_brain_mini/Supervised/model-raw-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..f43742634660efd362cd5ec4d6ab5b8066f77eea --- /dev/null +++ b/fastmri_brain_mini/Supervised/model-raw-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:0fc1022d8b6744d8d701744c9b0993cd707088a55874b86d3115cbc45c914bcc +size 93109239 diff --git a/fastmri_brain_mini/Supervised/model-raw.ckpt b/fastmri_brain_mini/Supervised/model-raw.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..42f10c41e9476db41d704474ad77a6babec7c3cb --- /dev/null +++ b/fastmri_brain_mini/Supervised/model-raw.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:d10a8fb756af50946d712b1e5174e88f5e2c8fd6ed21abbc70bbb6913d859f7d +size 93103415 diff --git a/fastmri_brain_mini/Supervised/model.ckpt b/fastmri_brain_mini/Supervised/model.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..42f10c41e9476db41d704474ad77a6babec7c3cb --- /dev/null +++ b/fastmri_brain_mini/Supervised/model.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:d10a8fb756af50946d712b1e5174e88f5e2c8fd6ed21abbc70bbb6913d859f7d +size 93103415 diff --git a/fastmri_brain_mini/VORTEX_Image+Motion__super-heavy/config.yaml b/fastmri_brain_mini/VORTEX_Image+Motion__super-heavy/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..f51f77f9ebef8fdf423440400c4c4019e80d655d --- /dev/null +++ b/fastmri_brain_mini/VORTEX_Image+Motion__super-heavy/config.yaml @@ -0,0 +1,246 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 8 +AUG_TRAIN: + MOTION_P: 0.2 + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 8 + CALIBRATION_SIZE: 0 + CENTER_FRACTIONS: + - 0.04 + MAX_ATTEMPTS: 30 + NAME: RandomMaskFunc1D + USE_MOTION: false + USE_NOISE: false +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: + - - target + - jsense-8-cf=4/target + - - maps + - jsense-8-cf=4/maps + DROP_LAST: true + FILTER: + BY: + - - acquisition + - AXT2 + - - systemFieldStrength_T + - 2.8936 + GROUP_SAMPLER: + AS_BATCH_SAMPLER: true + BATCH_BY: + - receiverChannels + - inplane_shape + NUM_WORKERS: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: AlternatingGroupSampler + SUBSAMPLE_TRAIN: + NUM_TOTAL: 54 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 36 + NUM_VAL: 50 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + TEST: + - fastMRI_brain_multicoil_mini_v0.0.1_test + TRAIN: + - fastMRI_brain_multicoil_mini_v0.0.1_train + VAL: + - fastMRI_brain_multicoil_mini_v0.0.1_val +DESCRIPTION: + BRIEF: 'U-NET LR = 1e-3 Aug2Recon 8x fastMRI brain-mc mini \(Aug2Recon\) - 18sup36unsup/super-heavy/version_030 + - Data ratio - 18 supervised : 36 unsupervised, 1:1 alt sampling, 18sup36unsup/super-heavy/version_030' + ENTITY_NAME: '' + EXP_NAME: vortex/fastmri_brain_mini/VORTEX_Image+Motion__super-heavy + PROJECT_NAME: '' + TAGS: + - vortex + - vortex + - 8x + - fastmri_brain_mini +MODEL: + A2R: + META_ARCHITECTURE: UnetModel + 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: + - dims: -1 + name: RandomFlip + p: 0.5 + - dims: -2 + name: RandomFlip + p: 0.5 + - ks: + - 2 + name: RandomRot90 + p: 0.5 + - name: RandomTranslation + p: 1.0 + pad_mode: reflect + translate: + - 0.1 + - 0.1 + - angle: 180.0 + name: RandomAffine + p: + angle: 0.5 + scale: 1.0 + shear: 1.0 + pad_like: MRAugment + scale: 0.25 + shear: 15.0 + - name: RandomMRIMotion + p: 1.0 + std_devs: + - 0.5 + - 0.7 + 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: A2RModel + 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://vortex/fastmri_brain_mini/VORTEX_Image+Motion__super-heavy +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + BIAS_LR_FACTOR: 1.0 + CHECKPOINT_PERIOD: -10 + GAMMA: 0.1 + GRAD_ACCUM_ITERS: 2 + LR_SCHEDULER_NAME: '' + MAX_ITER: -200 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: [] + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 12 + 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: -10 + 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: 100 diff --git a/fastmri_brain_mini/VORTEX_Image+Motion__super-heavy/model-gpu.ckpt b/fastmri_brain_mini/VORTEX_Image+Motion__super-heavy/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..6eb29b84c390d97d78f124161188b4ad308f2b81 --- /dev/null +++ b/fastmri_brain_mini/VORTEX_Image+Motion__super-heavy/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:2caf870e4f520cc7624becbb0fdd95006316a5bb32d9eb0e9d8ff58ffc6ac424 +size 93110071 diff --git a/fastmri_brain_mini/VORTEX_Image+Motion__super-heavy/model-raw-gpu.ckpt b/fastmri_brain_mini/VORTEX_Image+Motion__super-heavy/model-raw-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..1750b7666fa015bafc0f8b446be8a8bfbc6772c7 --- /dev/null +++ b/fastmri_brain_mini/VORTEX_Image+Motion__super-heavy/model-raw-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:d995b5c5d923dc17f9914508bc2a46564a4088cf3fe9e6bcf1af10cfa13b8860 +size 93110071 diff --git a/fastmri_brain_mini/VORTEX_Image+Motion__super-heavy/model-raw.ckpt b/fastmri_brain_mini/VORTEX_Image+Motion__super-heavy/model-raw.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..9cc98204c1f637d163521af8dec22fbd008166ac --- /dev/null +++ b/fastmri_brain_mini/VORTEX_Image+Motion__super-heavy/model-raw.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:4bff226d3d6abbf0fb48df2ba673b9d85c7f128ce919fa040328f1567f14729c +size 93103607 diff --git a/fastmri_brain_mini/VORTEX_Image+Motion__super-heavy/model.ckpt b/fastmri_brain_mini/VORTEX_Image+Motion__super-heavy/model.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..9cc98204c1f637d163521af8dec22fbd008166ac --- /dev/null +++ b/fastmri_brain_mini/VORTEX_Image+Motion__super-heavy/model.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:4bff226d3d6abbf0fb48df2ba673b9d85c7f128ce919fa040328f1567f14729c +size 93103607 diff --git a/fastmri_brain_mini/VORTEX_Image+Physics__super-heavy/config.yaml b/fastmri_brain_mini/VORTEX_Image+Physics__super-heavy/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..fd401f3ae7d6f553112105b92ab508550de3f307 --- /dev/null +++ b/fastmri_brain_mini/VORTEX_Image+Physics__super-heavy/config.yaml @@ -0,0 +1,252 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 8 +AUG_TRAIN: + MOTION_P: 0.2 + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 8 + CALIBRATION_SIZE: 0 + CENTER_FRACTIONS: + - 0.04 + MAX_ATTEMPTS: 30 + NAME: RandomMaskFunc1D + USE_MOTION: false + USE_NOISE: false +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: + - - target + - jsense-8-cf=4/target + - - maps + - jsense-8-cf=4/maps + DROP_LAST: true + FILTER: + BY: + - - acquisition + - AXT2 + - - systemFieldStrength_T + - 2.8936 + GROUP_SAMPLER: + AS_BATCH_SAMPLER: true + BATCH_BY: + - receiverChannels + - inplane_shape + NUM_WORKERS: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: AlternatingGroupSampler + SUBSAMPLE_TRAIN: + NUM_TOTAL: 54 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 36 + NUM_VAL: 50 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + TEST: + - fastMRI_brain_multicoil_mini_v0.0.1_test + TRAIN: + - fastMRI_brain_multicoil_mini_v0.0.1_train + VAL: + - fastMRI_brain_multicoil_mini_v0.0.1_val +DESCRIPTION: + BRIEF: 'U-NET LR = 1e-3 Aug2Recon 8x fastMRI brain-mc mini \(Aug2Recon\) - 18sup36unsup/super-heavy/version_029 + - Data ratio - 18 supervised : 36 unsupervised, 1:1 alt sampling, 18sup36unsup/super-heavy/version_029' + ENTITY_NAME: '' + EXP_NAME: vortex/fastmri_brain_mini/VORTEX_Image+Physics__super-heavy + PROJECT_NAME: '' + TAGS: + - vortex + - vortex + - 8x + - fastmri_brain_mini +MODEL: + A2R: + META_ARCHITECTURE: UnetModel + 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: + - dims: -1 + name: RandomFlip + p: 0.5 + - dims: -2 + name: RandomFlip + p: 0.5 + - ks: + - 2 + name: RandomRot90 + p: 0.5 + - name: RandomTranslation + p: 1.0 + pad_mode: reflect + translate: + - 0.1 + - 0.1 + - angle: 180.0 + name: RandomAffine + p: + angle: 0.5 + scale: 1.0 + shear: 1.0 + pad_like: MRAugment + scale: 0.25 + shear: 15.0 + - name: RandomMRIMotion + p: 1.0 + std_devs: + - 0.5 + - 0.7 + - name: RandomNoise + p: 1.0 + std_devs: + - 0.5 + - 0.7 + use_mask: true + 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: A2RModel + 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://vortex/fastmri_brain_mini/VORTEX_Image+Physics__super-heavy +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + BIAS_LR_FACTOR: 1.0 + CHECKPOINT_PERIOD: -10 + GAMMA: 0.1 + GRAD_ACCUM_ITERS: 2 + LR_SCHEDULER_NAME: '' + MAX_ITER: -200 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: [] + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 12 + 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: -10 + 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: 100 diff --git a/fastmri_brain_mini/VORTEX_Image+Physics__super-heavy/model-gpu.ckpt b/fastmri_brain_mini/VORTEX_Image+Physics__super-heavy/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..d280aa41e2cf3fbd0f03e56fb516f08f0232e1ee --- /dev/null +++ b/fastmri_brain_mini/VORTEX_Image+Physics__super-heavy/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:3da2867cae6908f3538973246146aba5e779d01c580501ec876e499dc06d82d8 +size 93110071 diff --git a/fastmri_brain_mini/VORTEX_Image+Physics__super-heavy/model-raw-gpu.ckpt b/fastmri_brain_mini/VORTEX_Image+Physics__super-heavy/model-raw-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..d75c51d91d996f2c50abfc91e6fd7844b290bfe6 --- /dev/null +++ b/fastmri_brain_mini/VORTEX_Image+Physics__super-heavy/model-raw-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:767a0836904121e0cd15fffd314b478eb1a2c5aa215b63eeb33c0f59c13b3b5f +size 93110071 diff --git a/fastmri_brain_mini/VORTEX_Image+Physics__super-heavy/model-raw.ckpt b/fastmri_brain_mini/VORTEX_Image+Physics__super-heavy/model-raw.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..01080c68fa4e15da6b390b5e237dead6a1531665 --- /dev/null +++ b/fastmri_brain_mini/VORTEX_Image+Physics__super-heavy/model-raw.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:0549c1ac6ee0662280038956156d4356ac5cc749d08ad857eaa4ad030ecf8a20 +size 93103607 diff --git a/fastmri_brain_mini/VORTEX_Image+Physics__super-heavy/model.ckpt b/fastmri_brain_mini/VORTEX_Image+Physics__super-heavy/model.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..01080c68fa4e15da6b390b5e237dead6a1531665 --- /dev/null +++ b/fastmri_brain_mini/VORTEX_Image+Physics__super-heavy/model.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:0549c1ac6ee0662280038956156d4356ac5cc749d08ad857eaa4ad030ecf8a20 +size 93103607 diff --git a/fastmri_brain_mini/VORTEX_Motion/config.yaml b/fastmri_brain_mini/VORTEX_Motion/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..d410950327234e9abeb04c67b1dbdba5c588a80a --- /dev/null +++ b/fastmri_brain_mini/VORTEX_Motion/config.yaml @@ -0,0 +1,221 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 8 +AUG_TRAIN: + MOTION_P: 0.2 + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 8 + CALIBRATION_SIZE: 0 + CENTER_FRACTIONS: + - 0.04 + MAX_ATTEMPTS: 30 + NAME: RandomMaskFunc1D + USE_MOTION: false + USE_NOISE: false +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: + - - target + - jsense-8-cf=4/target + - - maps + - jsense-8-cf=4/maps + DROP_LAST: true + FILTER: + BY: + - - acquisition + - AXT2 + - - systemFieldStrength_T + - 2.8936 + GROUP_SAMPLER: + AS_BATCH_SAMPLER: true + BATCH_BY: + - receiverChannels + - inplane_shape + NUM_WORKERS: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: AlternatingGroupSampler + SUBSAMPLE_TRAIN: + NUM_TOTAL: 54 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 18 + NUM_VAL: 50 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + TEST: + - fastMRI_brain_multicoil_mini_v0.0.1_test + TRAIN: + - fastMRI_brain_multicoil_mini_v0.0.1_train + VAL: + - fastMRI_brain_multicoil_mini_v0.0.1_val +DESCRIPTION: + BRIEF: U-NET LR = 1e-3 Aug2Recon 8x fastMRI brain-mc mini \(Aug2Recon\) - Spatial + Transforms + ENTITY_NAME: '' + EXP_NAME: vortex/fastmri_brain_mini/VORTEX_Motion + PROJECT_NAME: '' + TAGS: + - vortex + - vortex + - 8x + - fastmri_brain_mini +MODEL: + A2R: + META_ARCHITECTURE: UnetModel + 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: + - name: RandomMRIMotion + p: 1.0 + std_devs: + - 0.2 + - 0.5 + 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: A2RModel + 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://vortex/fastmri_brain_mini/VORTEX_Motion +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + BIAS_LR_FACTOR: 1.0 + CHECKPOINT_PERIOD: -10 + GAMMA: 0.1 + GRAD_ACCUM_ITERS: 2 + LR_SCHEDULER_NAME: '' + MAX_ITER: -200 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: [] + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 12 + 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: -10 + 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: 100 diff --git a/fastmri_brain_mini/VORTEX_Motion/model-gpu.ckpt b/fastmri_brain_mini/VORTEX_Motion/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..cf3d4281414326367ca6880be74571182594938c --- /dev/null +++ b/fastmri_brain_mini/VORTEX_Motion/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f70e896c274c0d87d3ccd0395c7d96d5b8db309c564941457a97443ed9294890 +size 93110071 diff --git a/fastmri_brain_mini/VORTEX_Motion/model-raw-gpu.ckpt b/fastmri_brain_mini/VORTEX_Motion/model-raw-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..d915d5d6475ed2d74774f8db0d91f985b0956e90 --- /dev/null +++ b/fastmri_brain_mini/VORTEX_Motion/model-raw-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:d9d27f35e087b8b1ec2dd4db248315c5812f85537aed878fd42e3858b1274a87 +size 93110071 diff --git a/fastmri_brain_mini/VORTEX_Motion/model-raw.ckpt b/fastmri_brain_mini/VORTEX_Motion/model-raw.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..c419787e17d67166d1ea66e92870b6e839653b83 --- /dev/null +++ b/fastmri_brain_mini/VORTEX_Motion/model-raw.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:2ee156063542141ac3032685d431cf63b0697308d31d781b31b1efa1c042dd7f +size 93103607 diff --git a/fastmri_brain_mini/VORTEX_Motion/model.ckpt b/fastmri_brain_mini/VORTEX_Motion/model.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..c419787e17d67166d1ea66e92870b6e839653b83 --- /dev/null +++ b/fastmri_brain_mini/VORTEX_Motion/model.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:2ee156063542141ac3032685d431cf63b0697308d31d781b31b1efa1c042dd7f +size 93103607 diff --git a/fastmri_brain_mini/VORTEX_Motion__super-heavy/config.yaml b/fastmri_brain_mini/VORTEX_Motion__super-heavy/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..399f404d07b151777faecdc75f02dc99f2189cf8 --- /dev/null +++ b/fastmri_brain_mini/VORTEX_Motion__super-heavy/config.yaml @@ -0,0 +1,221 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 8 +AUG_TRAIN: + MOTION_P: 0.2 + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + TRANSFORMS: [] + NOISE_P: 0.2 + UNDERSAMPLE: + ACCELERATIONS: + - 8 + CALIBRATION_SIZE: 0 + CENTER_FRACTIONS: + - 0.04 + MAX_ATTEMPTS: 30 + NAME: RandomMaskFunc1D + USE_MOTION: false + USE_NOISE: false +CUDNN_BENCHMARK: false +DATALOADER: + ALT_SAMPLER: + PERIOD_SUPERVISED: 1 + PERIOD_UNSUPERVISED: 1 + DATA_KEYS: + - - target + - jsense-8-cf=4/target + - - maps + - jsense-8-cf=4/maps + DROP_LAST: true + FILTER: + BY: + - - acquisition + - AXT2 + - - systemFieldStrength_T + - 2.8936 + GROUP_SAMPLER: + AS_BATCH_SAMPLER: true + BATCH_BY: + - receiverChannels + - inplane_shape + NUM_WORKERS: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: AlternatingGroupSampler + SUBSAMPLE_TRAIN: + NUM_TOTAL: 54 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 36 + NUM_VAL: 50 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + TEST: + - fastMRI_brain_multicoil_mini_v0.0.1_test + TRAIN: + - fastMRI_brain_multicoil_mini_v0.0.1_train + VAL: + - fastMRI_brain_multicoil_mini_v0.0.1_val +DESCRIPTION: + BRIEF: 'U-NET LR = 1e-3 Aug2Recon 8x fastMRI brain-mc mini \(Aug2Recon\) - 18sup36unsup/super-heavy/version_032 + - Data ratio - 18 supervised : 36 unsupervised, 1:1 alt sampling, 18sup36unsup/super-heavy/version_032' + ENTITY_NAME: '' + EXP_NAME: vortex/fastmri_brain_mini/VORTEX_Motion__super-heavy + PROJECT_NAME: '' + TAGS: + - vortex + - vortex + - 8x + - fastmri_brain_mini +MODEL: + A2R: + META_ARCHITECTURE: UnetModel + 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: + - name: RandomMRIMotion + p: 1.0 + std_devs: + - 0.5 + - 0.7 + 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: A2RModel + 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://vortex/fastmri_brain_mini/VORTEX_Motion__super-heavy +SEED: 1000 +SOLVER: + BASE_LR: 0.001 + BIAS_LR_FACTOR: 1.0 + CHECKPOINT_PERIOD: -10 + GAMMA: 0.1 + GRAD_ACCUM_ITERS: 2 + LR_SCHEDULER_NAME: '' + MAX_ITER: -200 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: [] + TEST_BATCH_SIZE: 16 + TRAIN_BATCH_SIZE: 12 + 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: -10 + 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: 100 diff --git a/fastmri_brain_mini/VORTEX_Motion__super-heavy/model-gpu.ckpt b/fastmri_brain_mini/VORTEX_Motion__super-heavy/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..15ffd6c857468bb8fa1f977805c4d02d26b65656 --- /dev/null +++ b/fastmri_brain_mini/VORTEX_Motion__super-heavy/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:b5e8586d40e60dd69a5d8bb67b5fbb506d89d6682c6a3840b760140264d40877 +size 93110071 diff --git a/fastmri_brain_mini/VORTEX_Motion__super-heavy/model-raw-gpu.ckpt b/fastmri_brain_mini/VORTEX_Motion__super-heavy/model-raw-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..5238cb356955bb6715606daf04d4beb7a48c5363 --- /dev/null +++ b/fastmri_brain_mini/VORTEX_Motion__super-heavy/model-raw-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:95a82cc67e177121023aead06465be4cf9bb95463a51ade8a62cd0514e7b0803 +size 93110071 diff --git a/fastmri_brain_mini/VORTEX_Motion__super-heavy/model-raw.ckpt b/fastmri_brain_mini/VORTEX_Motion__super-heavy/model-raw.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..8066c8940cf49e2e38fb04d19329a8f530aabbfe --- /dev/null +++ b/fastmri_brain_mini/VORTEX_Motion__super-heavy/model-raw.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:727269d95580626fe402eb59054538cddcfd71099bf23674aaefe6adc8f224be +size 93103607 diff --git a/fastmri_brain_mini/VORTEX_Motion__super-heavy/model.ckpt b/fastmri_brain_mini/VORTEX_Motion__super-heavy/model.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..8066c8940cf49e2e38fb04d19329a8f530aabbfe --- /dev/null +++ b/fastmri_brain_mini/VORTEX_Motion__super-heavy/model.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:727269d95580626fe402eb59054538cddcfd71099bf23674aaefe6adc8f224be +size 93103607 diff --git a/mridata_knee_3dfse/Aug_Image+Physics/config.yaml b/mridata_knee_3dfse/Aug_Image+Physics/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..2120f9cfd08bb35a933de516b0608dbc3a0e32c3 --- /dev/null +++ b/mridata_knee_3dfse/Aug_Image+Physics/config.yaml @@ -0,0 +1,247 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 16 +AUG_TRAIN: + MOTION_P: 0.2 + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + gamma: 5.0 + max_iter: -200 + name: WarmupStepTF + warmup_method: exp + warmup_milestones: + - -1 + TRANSFORMS: + - dims: -1 + name: RandomFlip + p: 0.275 + - dims: -2 + name: RandomFlip + p: 0.275 + - ks: + - 2 + name: RandomRot90 + p: 0.275 + - name: RandomTranslation + p: 0.55 + pad_mode: reflect + translate: + - 0.1 + - 0.1 + - angle: 180.0 + name: RandomAffine + p: + angle: 0.275 + scale: 0.55 + shear: 0.55 + pad_like: MRAugment + scale: 0.25 + shear: 15.0 + - name: RandomMRIMotion + p: 0.2 + std_devs: + - 0.2 + - 0.5 + - name: RandomNoise + p: 0.2 + std_devs: + - 0.2 + - 0.5 + use_mask: true + 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: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: '' + SUBSAMPLE_TRAIN: + NUM_TOTAL: 1 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + TEST: + - mridata_knee_2019_test + TRAIN: + - mridata_knee_2019_train + VAL: + - mridata_knee_2019_val +DESCRIPTION: + BRIEF: Aug2Recon 16x mridata baseline + augmentations - MRAugment + image+motion+noise, + heavy, p=0.2 + ENTITY_NAME: '' + EXP_NAME: vortex/mridata_knee_3dfse/Aug_Image+Physics + PROJECT_NAME: '' + TAGS: + - baseline + - 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: + - 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://vortex/mridata_knee_3dfse/Aug_Image+Physics +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: -200 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: [] + TEST_BATCH_SIZE: 24 + TRAIN_BATCH_SIZE: 24 + 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/Aug_Image+Physics/model-gpu.ckpt b/mridata_knee_3dfse/Aug_Image+Physics/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..b0d13a6765f384c001ffccebbdb939ef4d492bac --- /dev/null +++ b/mridata_knee_3dfse/Aug_Image+Physics/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:22dd5674accc35023a3f0c087f6bd08eff1fba647ccaff53014369fa4148cb11 +size 93109175 diff --git a/mridata_knee_3dfse/Aug_Image+Physics/model-raw-gpu.ckpt b/mridata_knee_3dfse/Aug_Image+Physics/model-raw-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..adf56751074076fba10257d91400565c5fdabe9e --- /dev/null +++ b/mridata_knee_3dfse/Aug_Image+Physics/model-raw-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:820bfc60e419761ee24e785def3afc42eb9eb4f227f3543e8a8b49a3be2bb555 +size 93109175 diff --git a/mridata_knee_3dfse/Aug_Image+Physics/model-raw.ckpt b/mridata_knee_3dfse/Aug_Image+Physics/model-raw.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..c7b3cd681cc3bb0df6147c3d1404065165771f32 --- /dev/null +++ b/mridata_knee_3dfse/Aug_Image+Physics/model-raw.ckpt @@ -0,0 +1,3 @@ +version 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IGNORE: false + gamma: 5.0 + max_iter: -200 + name: WarmupStepTF + warmup_method: exp + warmup_milestones: + - -1 + TRANSFORMS: + - name: RandomMRIMotion + p: 0.2 + std_devs: + - 0.2 + - 0.5 + 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: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: '' + SUBSAMPLE_TRAIN: + NUM_TOTAL: 1 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + TEST: + - mridata_knee_2019_test + TRAIN: + - mridata_knee_2019_train + VAL: + - mridata_knee_2019_val +DESCRIPTION: + BRIEF: Aug2Recon 16x mridata baseline + augmentations - MRAugment + motion, heavy, + p=0.2 + ENTITY_NAME: '' + EXP_NAME: vortex/mridata_knee_3dfse/Aug_Motion + PROJECT_NAME: '' + TAGS: + - baseline + - 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: + - 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://vortex/mridata_knee_3dfse/Aug_Motion +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: -200 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: [] + TEST_BATCH_SIZE: 24 + TRAIN_BATCH_SIZE: 24 + 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/Aug_Motion/model-gpu.ckpt b/mridata_knee_3dfse/Aug_Motion/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..90813238efe6f36e09ae03767a7129c13343f4de --- /dev/null +++ b/mridata_knee_3dfse/Aug_Motion/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:28a6bf0ea557d882a43c778ab2c0bea0b7f7edaf27b3fff88bbec8acd204b637 +size 93109175 diff --git a/mridata_knee_3dfse/Aug_Motion/model-raw-gpu.ckpt b/mridata_knee_3dfse/Aug_Motion/model-raw-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..c10eab55ab45f9b572212c2c411ea79098e4171e --- /dev/null +++ b/mridata_knee_3dfse/Aug_Motion/model-raw-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:da952b2af789e64f5be2352f72a8b6c666a7ee6bb0601138011b0b8bf28dfd0c +size 93109175 diff --git a/mridata_knee_3dfse/Aug_Motion/model-raw.ckpt b/mridata_knee_3dfse/Aug_Motion/model-raw.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..9f284cbf7eb14f25e9234269bb44181fc10dcf07 --- /dev/null +++ b/mridata_knee_3dfse/Aug_Motion/model-raw.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:d11bc600cffc00a6e9b4b68b4cf23cc55341a6d5a6974d6962db50ced06afca6 +size 93103415 diff --git a/mridata_knee_3dfse/Aug_Motion/model.ckpt b/mridata_knee_3dfse/Aug_Motion/model.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..9f284cbf7eb14f25e9234269bb44181fc10dcf07 --- /dev/null +++ b/mridata_knee_3dfse/Aug_Motion/model.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:d11bc600cffc00a6e9b4b68b4cf23cc55341a6d5a6974d6962db50ced06afca6 +size 93103415 diff --git a/mridata_knee_3dfse/Aug_Noise/config.yaml b/mridata_knee_3dfse/Aug_Noise/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..b8903dee0e38a4ac9f50ab811ac03b2f2aaad0c7 --- /dev/null +++ b/mridata_knee_3dfse/Aug_Noise/config.yaml @@ -0,0 +1,217 @@ +AUG_TEST: + UNDERSAMPLE: + ACCELERATIONS: + - 16 +AUG_TRAIN: + MOTION_P: 0.2 + MRI_RECON: + AUG_SENSITIVITY_MAPS: true + SCHEDULER_P: + IGNORE: false + gamma: 5.0 + max_iter: -200 + name: WarmupStepTF + warmup_method: exp + warmup_milestones: + - -1 + TRANSFORMS: + - name: RandomNoise + p: 0.2 + std_devs: + - 0.2 + - 0.5 + use_mask: true + 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: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: '' + SUBSAMPLE_TRAIN: + NUM_TOTAL: 1 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + TEST: + - mridata_knee_2019_test + TRAIN: + - mridata_knee_2019_train + VAL: + - mridata_knee_2019_val +DESCRIPTION: + BRIEF: Aug2Recon 16x mridata baseline + augmentations - MRAugment + noise, heavy, + p=0.2 + ENTITY_NAME: '' + EXP_NAME: vortex/mridata_knee_3dfse/Aug_Noise + PROJECT_NAME: '' + TAGS: + - baseline + - 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: + - 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://vortex/mridata_knee_3dfse/Aug_Noise +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: -200 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: [] + TEST_BATCH_SIZE: 24 + TRAIN_BATCH_SIZE: 24 + 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/Aug_Noise/model-gpu.ckpt b/mridata_knee_3dfse/Aug_Noise/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..3678807895c19a8fb6feb4ad7c6b579906f2fb3c --- /dev/null +++ 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warmup_method: exp + warmup_milestones: + - -1 + TRANSFORMS: + - name: RandomMRIMotion + p: 0.2 + std_devs: + - 0.2 + - 0.5 + - name: RandomNoise + p: 0.2 + std_devs: + - 0.2 + - 0.5 + use_mask: true + 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: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: '' + SUBSAMPLE_TRAIN: + NUM_TOTAL: 1 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + TEST: + - mridata_knee_2019_test + TRAIN: + - mridata_knee_2019_train + VAL: + - mridata_knee_2019_val +DESCRIPTION: + BRIEF: Aug2Recon 16x mridata baseline + augmentations - MRAugment + motion+noise, + heavy, p=0.2 + ENTITY_NAME: '' + EXP_NAME: vortex/mridata_knee_3dfse/Aug_Physics + PROJECT_NAME: '' + TAGS: + - baseline + - 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: + - 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://vortex/mridata_knee_3dfse/Aug_Physics +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: -200 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: [] + TEST_BATCH_SIZE: 24 + TRAIN_BATCH_SIZE: 24 + 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/Aug_Physics/model-gpu.ckpt b/mridata_knee_3dfse/Aug_Physics/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..3ac2762ee9f94389b48531e853ebbd46bbfdedaf --- /dev/null +++ b/mridata_knee_3dfse/Aug_Physics/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:3d4e726b7d3bde0b6654b093deb97ab111fb0a0a0c8dc02c69f43a662c207749 +size 93109175 diff --git a/mridata_knee_3dfse/Aug_Physics/model-raw-gpu.ckpt b/mridata_knee_3dfse/Aug_Physics/model-raw-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..f67cde342c3b9e2aaa355e63bfdef62d45527fcb --- /dev/null +++ b/mridata_knee_3dfse/Aug_Physics/model-raw-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8e8a37b0301699a16f647dc14992b3e43cb2c062b07b796e9a7144e44b7ee9fc +size 93109175 diff --git a/mridata_knee_3dfse/Aug_Physics/model-raw.ckpt b/mridata_knee_3dfse/Aug_Physics/model-raw.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..f535c66dbe7e4c8a53adf681dc6d4e7a1791a84e --- /dev/null +++ b/mridata_knee_3dfse/Aug_Physics/model-raw.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid 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name: WarmupStepTF + warmup_method: exp + warmup_milestones: + - -1 + TRANSFORMS: + - dims: -1 + name: RandomFlip + p: 0.275 + - dims: -2 + name: RandomFlip + p: 0.275 + - ks: + - 2 + name: RandomRot90 + p: 0.275 + - name: RandomTranslation + p: 0.55 + pad_mode: reflect + translate: + - 0.1 + - 0.1 + - angle: 180.0 + name: RandomAffine + p: + angle: 0.275 + scale: 0.55 + shear: 0.55 + pad_like: MRAugment + scale: 0.25 + shear: 15.0 + 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: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: '' + SUBSAMPLE_TRAIN: + NUM_TOTAL: 1 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + TEST: + - mridata_knee_2019_test + TRAIN: + - mridata_knee_2019_train + VAL: + - mridata_knee_2019_val +DESCRIPTION: + BRIEF: Aug2Recon 16x mridata baseline + augmentations - MRAugment + image, light, + p=0.2 + ENTITY_NAME: '' + EXP_NAME: vortex/mridata_knee_3dfse/MRAugment_Image + PROJECT_NAME: '' + TAGS: + - baseline + - mraugment + - 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://vortex/mridata_knee_3dfse/MRAugment_Image +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: -200 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: [] + TEST_BATCH_SIZE: 24 + TRAIN_BATCH_SIZE: 24 + 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 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0000000000000000000000000000000000000000..8d3fa7a18f18ddd2ec348da0ea56f0e0e01ffcfe --- /dev/null +++ b/mridata_knee_3dfse/SSDU/config.yaml @@ -0,0 +1,209 @@ +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: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: '' + SUBSAMPLE_TRAIN: + NUM_TOTAL: 6 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 5 + 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: SSDU 16x mridata - loss=k_l1, uniform/loss=k_l1/version_001 + ENTITY_NAME: '' + EXP_NAME: vortex/mridata_knee_3dfse/SSDU + PROJECT_NAME: '' + TAGS: + - baseline + - ssdu + - 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: SSDUModel + N2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NM2R: + META_ARCHITECTURE: GeneralizedUnrolledCNN + USE_SUPERVISED_CONSISTENCY: false + NORMALIZER: + KEYWORDS: [] + NAME: TopMagnitudeNormalizer + RECON_LOSS: + NAME: k_l1 + RENORMALIZE_DATA: false + SEG: + ACTIVATION: sigmoid + CLASSES: [] + INCLUDE_BACKGROUND: false + SSDU: + MASKER: + PARAMS: + kind: uniform + p: 1.0 + per_example: true + rhos: 0.4 + std_scale: 4 + META_ARCHITECTURE: UnetModel + 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://vortex/mridata_knee_3dfse/SSDU +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: -200 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: [] + TEST_BATCH_SIZE: 24 + TRAIN_BATCH_SIZE: 24 + 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: 100 diff --git a/mridata_knee_3dfse/SSDU/model-gpu.ckpt b/mridata_knee_3dfse/SSDU/model-gpu.ckpt new file mode 100644 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@@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f7829da7675cfaea640770427fe5f108a2a6f349747002c140c1a946451b0883 +size 93103543 diff --git a/mridata_knee_3dfse/SSDU/model.ckpt b/mridata_knee_3dfse/SSDU/model.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..7ef6f7a079e78c61e743cbe66423f618b39f5dd9 --- /dev/null +++ b/mridata_knee_3dfse/SSDU/model.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f7829da7675cfaea640770427fe5f108a2a6f349747002c140c1a946451b0883 +size 93103543 diff --git a/mridata_knee_3dfse/Supervised/config.yaml b/mridata_knee_3dfse/Supervised/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..7d88ffcb891c2550b48742f04881f45f7ed7b38c --- /dev/null +++ b/mridata_knee_3dfse/Supervised/config.yaml @@ -0,0 +1,203 @@ +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: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: '' + SUBSAMPLE_TRAIN: + NUM_TOTAL: 1 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 0 + NUM_VAL: -1 + NUM_VAL_BY_GROUP: [] + SEED: 1000 +DATASETS: + TEST: + - mridata_knee_2019_test + TRAIN: + - mridata_knee_2019_train + VAL: + - mridata_knee_2019_val +DESCRIPTION: + BRIEF: Aug2Recon 16x mridata baseline + ENTITY_NAME: '' + EXP_NAME: vortex/mridata_knee_3dfse/Supervised + 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: &id001 + - 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: *id001 + 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://vortex/mridata_knee_3dfse/Supervised +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: -200 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: [] + TEST_BATCH_SIZE: 24 + TRAIN_BATCH_SIZE: 24 + 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/Supervised/model-gpu.ckpt b/mridata_knee_3dfse/Supervised/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..ee7e03ef3000aa3701f3d3d053fe57843baff4ea --- /dev/null +++ b/mridata_knee_3dfse/Supervised/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:2175c3218ca7e17e8a3d80d98ea4350f2618f5ffaff6c546932633af15dac382 +size 93109175 diff --git a/mridata_knee_3dfse/Supervised/model-raw-gpu.ckpt 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0000000000000000000000000000000000000000..c69abdac4d514bb6e4a64f53e4e68728465a95c2 --- /dev/null +++ b/mridata_knee_3dfse/Supervised/model.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:e1eb8397fabc275a9945655d8a01b7f541f26ece1153355bade4f166bdf9777c +size 93103415 diff --git a/mridata_knee_3dfse/VORTEX_Curricula_Motion/config.yaml b/mridata_knee_3dfse/VORTEX_Curricula_Motion/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..56c4b836f735d5f8c35247a674066422cbf872d7 --- /dev/null +++ b/mridata_knee_3dfse/VORTEX_Curricula_Motion/config.yaml @@ -0,0 +1,216 @@ +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: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: AlternatingSampler + SUBSAMPLE_TRAIN: + NUM_TOTAL: 6 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 5 + 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: Aug2Recon 16x mridata A2R - curricula - exp @ 200 epochs, gamma=5, heavy/exp-200e-gamma=5/version_001 + ENTITY_NAME: '' + EXP_NAME: vortex/mridata_knee_3dfse/VORTEX_Curricula_Motion + PROJECT_NAME: '' + TAGS: + - vortex + - vortex + - 16x + - mridata_knee_3dfse +MODEL: + A2R: + META_ARCHITECTURE: UnetModel + 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: + - name: RandomMRIMotion + p: 1.0 + scheduler: + gamma: 5 + name: WarmupTF + params: + - std_devs + warmup_iters: -200 + warmup_method: exp + std_devs: + - 0.2 + - 0.5 + 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: A2RModel + 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://vortex/mridata_knee_3dfse/VORTEX_Curricula_Motion +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: -200 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: [] + TEST_BATCH_SIZE: 24 + TRAIN_BATCH_SIZE: 24 + 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: 100 diff --git a/mridata_knee_3dfse/VORTEX_Curricula_Motion/model-gpu.ckpt b/mridata_knee_3dfse/VORTEX_Curricula_Motion/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..e37a7fcbcf1139b23b4d2c9bf57efd4f4c3aca76 --- /dev/null +++ b/mridata_knee_3dfse/VORTEX_Curricula_Motion/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid 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sha256:173e506b4050cc40604ba583fd55c4949e40e1f13d7db7c65be637ff2b1f4e6f +size 93103543 diff --git a/mridata_knee_3dfse/VORTEX_Curricula_Motion/model.ckpt b/mridata_knee_3dfse/VORTEX_Curricula_Motion/model.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..0f05c2b7f2cdf31a7656dbc921463ac7f808bc96 --- /dev/null +++ b/mridata_knee_3dfse/VORTEX_Curricula_Motion/model.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:173e506b4050cc40604ba583fd55c4949e40e1f13d7db7c65be637ff2b1f4e6f +size 93103543 diff --git a/mridata_knee_3dfse/VORTEX_Curricula_Noise/config.yaml b/mridata_knee_3dfse/VORTEX_Curricula_Noise/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..d56477e4aec1ef37ad6e752892b66550667c8b9f --- /dev/null +++ b/mridata_knee_3dfse/VORTEX_Curricula_Noise/config.yaml @@ -0,0 +1,216 @@ +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: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: AlternatingSampler + SUBSAMPLE_TRAIN: + NUM_TOTAL: 6 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 5 + 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: Aug2Recon 16x mridata A2R - curricula - linear @ 200 epochs, gamma=1, heavy/linear-200e-gamma=1/version_001 + ENTITY_NAME: '' + EXP_NAME: vortex/mridata_knee_3dfse/VORTEX_Curricula_Noise + PROJECT_NAME: '' + TAGS: + - vortex + - vortex + - 16x + - mridata_knee_3dfse +MODEL: + A2R: + META_ARCHITECTURE: UnetModel + 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: + - name: RandomNoise + p: 1.0 + scheduler: + name: WarmupTF + params: + - std_devs + warmup_iters: -200 + warmup_method: linear + std_devs: + - 0.2 + - 0.5 + use_mask: true + 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: A2RModel + 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://vortex/mridata_knee_3dfse/VORTEX_Curricula_Noise +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: -200 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: [] + TEST_BATCH_SIZE: 24 + TRAIN_BATCH_SIZE: 24 + 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: 100 diff --git a/mridata_knee_3dfse/VORTEX_Curricula_Noise/model-gpu.ckpt b/mridata_knee_3dfse/VORTEX_Curricula_Noise/model-gpu.ckpt new file mode 100644 index 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0000000000000000000000000000000000000000..faa3867230d65a2164abd89d662b9be16ec9cdf6 --- /dev/null +++ b/mridata_knee_3dfse/VORTEX_Curricula_Physics/config.yaml @@ -0,0 +1,227 @@ +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: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: AlternatingSampler + SUBSAMPLE_TRAIN: + NUM_TOTAL: 6 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 5 + 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: Aug2Recon 16x mridata A2R - curricula - linear @ 200 epochs, gamma=1, heavy/linear-200e-gamma=1/version_001 + ENTITY_NAME: '' + EXP_NAME: vortex/mridata_knee_3dfse/VORTEX_Curricula_Physics + PROJECT_NAME: '' + TAGS: + - vortex + - vortex + - 16x + - mridata_knee_3dfse +MODEL: + A2R: + META_ARCHITECTURE: UnetModel + 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: + - name: RandomMRIMotion + p: 1.0 + scheduler: + name: WarmupTF + params: + - std_devs + warmup_iters: -200 + warmup_method: linear + std_devs: + - 0.2 + - 0.5 + - name: RandomNoise + p: 1.0 + scheduler: + name: WarmupTF + params: + - std_devs + warmup_iters: -200 + warmup_method: linear + std_devs: + - 0.2 + - 0.5 + use_mask: true + 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: A2RModel + 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://vortex/mridata_knee_3dfse/VORTEX_Curricula_Physics +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: -200 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: [] + TEST_BATCH_SIZE: 24 + TRAIN_BATCH_SIZE: 24 + 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: 100 diff --git a/mridata_knee_3dfse/VORTEX_Curricula_Physics/model-gpu.ckpt b/mridata_knee_3dfse/VORTEX_Curricula_Physics/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..c913e9e8cf004913b5db4f5f4872ab91be73474c --- /dev/null +++ b/mridata_knee_3dfse/VORTEX_Curricula_Physics/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:d6fe8d469be40f76e523f33741946c2d94270b2c637fc1ed5f2fd2eb8b0f5785 +size 93110007 diff --git a/mridata_knee_3dfse/VORTEX_Curricula_Physics/model-raw-gpu.ckpt b/mridata_knee_3dfse/VORTEX_Curricula_Physics/model-raw-gpu.ckpt new file mode 100644 index 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0000000000000000000000000000000000000000..8b9d4d1db204a8600e4d908771b1f1ba356a3b9b --- /dev/null +++ b/mridata_knee_3dfse/VORTEX_Curricula_Physics/model.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:15ed7f5afe88b5a5f1d3d3e646b11f9476e32fc6c30cc8c147a6bcbb7606ad47 +size 93103543 diff --git a/mridata_knee_3dfse/VORTEX_Image+Physics/config.yaml b/mridata_knee_3dfse/VORTEX_Image+Physics/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..cae2177f11946cb7ba5dfef39ac32bd3634e226f --- /dev/null +++ b/mridata_knee_3dfse/VORTEX_Image+Physics/config.yaml @@ -0,0 +1,241 @@ +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: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: AlternatingSampler + SUBSAMPLE_TRAIN: + NUM_TOTAL: 6 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 5 + 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: Aug2Recon 16x mridata A2R - alternate sampling - 1:1 supervised:unsupervised, + alt-sampling/1-1/heavy/version_001 + ENTITY_NAME: '' + EXP_NAME: vortex/mridata_knee_3dfse/VORTEX_Image+Physics + PROJECT_NAME: '' + TAGS: + - vortex + - vortex + - 16x + - mridata_knee_3dfse +MODEL: + A2R: + META_ARCHITECTURE: UnetModel + 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: + - dims: -1 + name: RandomFlip + p: 0.5 + - dims: -2 + name: RandomFlip + p: 0.5 + - ks: + - 2 + name: RandomRot90 + p: 0.5 + - name: RandomTranslation + p: 1.0 + pad_mode: reflect + translate: + - 0.1 + - 0.1 + - angle: 180.0 + name: RandomAffine + p: + angle: 0.5 + scale: 1.0 + shear: 1.0 + pad_like: MRAugment + scale: 0.25 + shear: 15.0 + - name: RandomMRIMotion + p: 1.0 + std_devs: + - 0.2 + - 0.5 + - name: RandomNoise + p: 1.0 + std_devs: + - 0.2 + - 0.5 + use_mask: true + 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: A2RModel + 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://vortex/mridata_knee_3dfse/VORTEX_Image+Physics +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: -200 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: [] + TEST_BATCH_SIZE: 24 + TRAIN_BATCH_SIZE: 24 + 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: 100 diff --git a/mridata_knee_3dfse/VORTEX_Image+Physics/model-gpu.ckpt b/mridata_knee_3dfse/VORTEX_Image+Physics/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..698edc46fbf4e2df3faefb7c0b6d5e3458071118 --- /dev/null +++ b/mridata_knee_3dfse/VORTEX_Image+Physics/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ab21c8b8c86f08953f8cf665996acfd5738f6431d058dce5486dae3a010ea331 +size 93110007 diff --git a/mridata_knee_3dfse/VORTEX_Image+Physics/model-raw-gpu.ckpt b/mridata_knee_3dfse/VORTEX_Image+Physics/model-raw-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..df077f56e04ea96a23e21eb59e3dcb080304c067 --- /dev/null +++ b/mridata_knee_3dfse/VORTEX_Image+Physics/model-raw-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8c37b268bbcbbea6edbababe6a06dcf2e397193aee68bd67591e1c32f50feaa9 +size 93110007 diff --git a/mridata_knee_3dfse/VORTEX_Image+Physics/model-raw.ckpt b/mridata_knee_3dfse/VORTEX_Image+Physics/model-raw.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..43e1595f3212c9465713fb19a27d17129bbae6d6 --- /dev/null +++ b/mridata_knee_3dfse/VORTEX_Image+Physics/model-raw.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:984fc28eeebe5052a1e88653a42e651648db67554dcbbfd02d8bb2c5fc8f1217 +size 93103543 diff --git a/mridata_knee_3dfse/VORTEX_Image+Physics/model.ckpt b/mridata_knee_3dfse/VORTEX_Image+Physics/model.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..43e1595f3212c9465713fb19a27d17129bbae6d6 --- /dev/null +++ b/mridata_knee_3dfse/VORTEX_Image+Physics/model.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:984fc28eeebe5052a1e88653a42e651648db67554dcbbfd02d8bb2c5fc8f1217 +size 93103543 diff --git a/mridata_knee_3dfse/VORTEX_Image/config.yaml b/mridata_knee_3dfse/VORTEX_Image/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..98376653610028e1122c43c3a7a988e3ea447830 --- /dev/null +++ b/mridata_knee_3dfse/VORTEX_Image/config.yaml @@ -0,0 +1,230 @@ +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: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: AlternatingSampler + SUBSAMPLE_TRAIN: + NUM_TOTAL: 6 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 5 + 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: Aug2Recon 16x mridata A2R - alternate sampling - 1:1 supervised:unsupervised, + alt-sampling/1-1/version_001 + ENTITY_NAME: '' + EXP_NAME: vortex/mridata_knee_3dfse/VORTEX_Image + PROJECT_NAME: '' + TAGS: + - vortex + - vortex + - 16x + - mridata_knee_3dfse +MODEL: + A2R: + META_ARCHITECTURE: UnetModel + 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: + - dims: -1 + name: RandomFlip + p: 0.5 + - dims: -2 + name: RandomFlip + p: 0.5 + - ks: + - 2 + name: RandomRot90 + p: 0.5 + - name: RandomTranslation + p: 1.0 + pad_mode: reflect + translate: + - 0.1 + - 0.1 + - angle: 180.0 + name: RandomAffine + p: + angle: 0.5 + scale: 1.0 + shear: 1.0 + pad_like: MRAugment + scale: 0.25 + shear: 15.0 + 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: A2RModel + 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://vortex/mridata_knee_3dfse/VORTEX_Image +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: -200 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: [] + TEST_BATCH_SIZE: 24 + TRAIN_BATCH_SIZE: 24 + 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: 100 diff --git a/mridata_knee_3dfse/VORTEX_Image/model-gpu.ckpt b/mridata_knee_3dfse/VORTEX_Image/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..9af7e09bfedda5f459d1d155e0b755533103eb34 --- /dev/null +++ b/mridata_knee_3dfse/VORTEX_Image/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c917c29f0dc2a5e0d323b0cd0515652c3d2b459630b804726d65b71abd3e459d +size 93110007 diff --git a/mridata_knee_3dfse/VORTEX_Image/model-raw-gpu.ckpt b/mridata_knee_3dfse/VORTEX_Image/model-raw-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..3e134c7bed0942f19ab8160b2e6fb38bc29634f7 --- /dev/null +++ b/mridata_knee_3dfse/VORTEX_Image/model-raw-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:11a644afeaa1cd384e4bb1fdccad4a8e682c499afc42b7427a96414dab715d65 +size 93110007 diff --git a/mridata_knee_3dfse/VORTEX_Image/model-raw.ckpt b/mridata_knee_3dfse/VORTEX_Image/model-raw.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..a5b7ff96d54c37cf17085f8b4c1dce53f6fe326e --- /dev/null +++ b/mridata_knee_3dfse/VORTEX_Image/model-raw.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:85ed0890e0a690cf4e2ea5b0334023f2b4b0aa967ea43d9f3524030c4b7537d5 +size 93103543 diff --git a/mridata_knee_3dfse/VORTEX_Image/model.ckpt b/mridata_knee_3dfse/VORTEX_Image/model.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..a5b7ff96d54c37cf17085f8b4c1dce53f6fe326e --- /dev/null +++ b/mridata_knee_3dfse/VORTEX_Image/model.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:85ed0890e0a690cf4e2ea5b0334023f2b4b0aa967ea43d9f3524030c4b7537d5 +size 93103543 diff --git a/mridata_knee_3dfse/VORTEX_Physics/config.yaml b/mridata_knee_3dfse/VORTEX_Physics/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..c11374e6df9aa7fdb32fd2b38c40ae297463fc6c --- /dev/null +++ b/mridata_knee_3dfse/VORTEX_Physics/config.yaml @@ -0,0 +1,216 @@ +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: 8 + PREFETCH_FACTOR: 2 + SAMPLER_TRAIN: AlternatingSampler + SUBSAMPLE_TRAIN: + NUM_TOTAL: 6 + NUM_TOTAL_BY_GROUP: [] + NUM_UNDERSAMPLED: 5 + 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: Aug2Recon 16x mridata A2R - alternate sampling - 1:1 supervised:unsupervised, + alt-sampling/1-1/heavy/version_001 + ENTITY_NAME: '' + EXP_NAME: vortex/mridata_knee_3dfse/VORTEX_Physics + PROJECT_NAME: '' + TAGS: + - vortex + - vortex + - 16x + - mridata_knee_3dfse +MODEL: + A2R: + META_ARCHITECTURE: UnetModel + 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: + - name: RandomMRIMotion + p: 1.0 + std_devs: + - 0.2 + - 0.5 + - name: RandomNoise + p: 1.0 + std_devs: + - 0.2 + - 0.5 + use_mask: true + 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: A2RModel + 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://vortex/mridata_knee_3dfse/VORTEX_Physics +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: -200 + MOMENTUM: 0.9 + OPTIMIZER: Adam + STEPS: [] + TEST_BATCH_SIZE: 24 + TRAIN_BATCH_SIZE: 24 + 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: 100 diff --git a/mridata_knee_3dfse/VORTEX_Physics/model-gpu.ckpt b/mridata_knee_3dfse/VORTEX_Physics/model-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..6a801607b103c187514e8e9ee4c8c9ebe482d479 --- /dev/null +++ b/mridata_knee_3dfse/VORTEX_Physics/model-gpu.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ca4214bdb66062cdfb46acd5996d7d6ef583191c3519337652d174faa4c818f5 +size 93110007 diff --git a/mridata_knee_3dfse/VORTEX_Physics/model-raw-gpu.ckpt b/mridata_knee_3dfse/VORTEX_Physics/model-raw-gpu.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..90284309ee8a72aebd0cc6e40003591b5d00b423 --- /dev/null +++ b/mridata_knee_3dfse/VORTEX_Physics/model-raw-gpu.ckpt @@ -0,0 +1,3 @@ +version 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