ATOMMIC User Guide# Getting Started Introduction Installation Conda Pip From source Docker containers Quick Start Guide Training & Testing Configuration Collections MRI Datasets License Citation References Contact Disclaimer & Acknowledgements Projects MultiTask Learning (MTL) Stanford Knee MRI Multi-Task Evaluation (SKM-TEA) 2021 Dataset quantitative MR Imaging (qMRI) AHEAD MRI Reconstruction (REC) CC359 fastMRI Brains Multicoil fastMRI Knees Multicoil fastMRI Knees Singlecoil Stanford Knee MRI Multi-Task Evaluation (SKM-TEA) 2021 Dataset Stanford Fullysampled 3D FSE Knees 2019 Dataset MRI Segmentation (SEG) BraTS 2023 Adult Glioma ISLES 2022 Sub Acute Stroke Stanford Knee MRI Multi-Task Evaluation (SKM-TEA) 2021 Dataset Tutorials ATOMMIC MRI Collections & Models MultiTask Learning (MTL) Quantitative MR Imaging (qMRI) MRI Reconstruction (REC) MRI Segmentation (SEG) Losses AggregatorLoss Metrics Pre-processing Cropper EstimateCoilSensitivityMaps GeometricDecompositionCoilCompression MotionSimulation N2R NoisePreWhitening Normalizer SNREstimator SSDU ZeroFillingPadding Composer MRIDataTransforms qMRIDataTransforms RSMRIDataTransforms ReconstructionMRIDataTransforms SegmentationMRIDataTransforms Full Example Undersampling Prospective Undersampling Retrospective Undersampling ATOMMIC Core Training & Testing Basics Training Configuration Optimization Save and Restore Register Artifacts Nested ATOMMIC Models Dynamic Layer Freezing Experiment Manager Resume Training Experiment Loggers Exponential Moving Average Support for Preemption Hydra Multi-Run with ATOMMIC ExpManagerConfig Exporting ATOMMIC Models Exporting Models How to Use Model Export How to Make Model Exportable API Core Base class for all ATOMMIC models ModelPT Base Mixin classes Base Connector classes SaveRestoreConnector Neural Type checking typecheck Neural Type classes NeuralType AxisType ElementType NeuralTypeComparisonResult Experiment manager exp_manager ExpManagerConfig Exportable Exportable Common MRI collection Callbacks Exponential Moving Average (EMA) Common MRI Data Classes MRIDataset MaskFunc Equispaced1DMaskFunc Equispaced2DMaskFunc Gaussian1DMaskFunc Gaussian2DMaskFunc Poisson2DMaskFunc Random1DMaskFunc create_masker() Common MRI Losses AggregatorLoss SinkhornDistance Common MRI Metrics GlobalAverageLossMetric Common MRI Neural Networks Common MRI Parts Coil Sensitivity Maps FFT Common MRI Transforms Common MRI Utils MRI Multitask Learning (MTL) Multitask MRI Reconstruction & Segmentation Multitask MRI Reconstruction & Segmentation Data Classes Multitask MRI Reconstruction & Segmentation Neural Networks Multitask MRI Reconstruction & Segmentation Parts MRI Reconstruction (REC) MRI Reconstruction Data Classes ReconstructionMRIDataset CC359ReconstructionMRIDataset SKMTEAReconstructionMRIDataset StanfordKneesReconstructionMRIDataset MRI Reconstruction Losses NoiseAwareLoss SSIMLoss MRI Reconstruction Metrics MRI Reconstruction Neural Networks MRI Reconstruction Parts MRI Segmentation (SEG) MRI Segmentation Data Classes SegmentationMRIDataset BraTS2023AdultGliomaSegmentationMRIDataset ISLES2022SubAcuteStrokeSegmentationMRIDataset SKMTEASegmentationMRIDataset MRI Segmentation Losses CrossEntropyLoss Dice MRI Segmentation Metrics MRI Segmentation Neural Networks MRI Segmentation Parts Quantitative MRI (qMRI) Quantitative MRI Data Classes qMRIDataset AHEADqMRIDataset Quantitative MRI Neural Networks Quantitative MRI Parts
