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--- |
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language: |
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- en |
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license: apache-2.0 |
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library_name: atommic |
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datasets: |
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- CC359 |
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thumbnail: null |
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tags: |
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- image-reconstruction |
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- UNet |
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- ATOMMIC |
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- pytorch |
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model-index: |
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- name: REC_UNet_CC359_12_channel_poisson2d_5x_10x_NNEstimationCSM |
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results: [] |
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--- |
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## Model Overview |
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UNet for 5x & 10x accelerated MRI Reconstruction on the CC359 dataset. |
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## ATOMMIC: Training |
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To train, fine-tune, or test the model you will need to install [ATOMMIC](https://github.com/wdika/atommic). We recommend you install it after you've installed latest Pytorch version. |
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``` |
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pip install atommic['all'] |
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``` |
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## How to Use this Model |
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The model is available for use in ATOMMIC, and can be used as a pre-trained checkpoint for inference or for fine-tuning on another dataset. |
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Corresponding configuration YAML files can be found [here](https://github.com/wdika/atommic/tree/main/projects/REC/CC359/conf). |
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### Automatically instantiate the model |
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```base |
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pretrained: true |
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checkpoint: https://huggingface.co/wdika/REC_UNet_CC359_12_channel_poisson2d_5x_10x_NNEstimationCSM/blob/main/REC_UNet_CC359_12_channel_poisson2d_5x_10x_NNEstimationCSM.atommic |
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mode: test |
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``` |
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### Usage |
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You need to download the CC359 dataset to effectively use this model. Check the [CC359](https://github.com/wdika/atommic/blob/main/projects/REC/CC359/README.md) page for more information. |
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## Model Architecture |
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```base |
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model: |
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model_name: UNet |
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channels: 64 |
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pooling_layers: 4 |
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in_channels: 2 |
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out_channels: 2 |
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padding_size: 11 |
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dropout: 0.0 |
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normalize: true |
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norm_groups: 2 |
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dimensionality: 2 |
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reconstruction_loss: |
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l1: 0.1 |
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ssim: 0.9 |
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estimate_coil_sensitivity_maps_with_nn: true |
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``` |
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## Training |
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```base |
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optim: |
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name: adamw |
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lr: 1e-4 |
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betas: |
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- 0.9 |
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- 0.999 |
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weight_decay: 0.0 |
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sched: |
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name: CosineAnnealing |
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min_lr: 0.0 |
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last_epoch: -1 |
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warmup_ratio: 0.1 |
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trainer: |
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strategy: ddp_find_unused_parameters_false |
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accelerator: gpu |
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devices: 1 |
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num_nodes: 1 |
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max_epochs: 20 |
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precision: 16-mixed |
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enable_checkpointing: false |
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logger: false |
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log_every_n_steps: 50 |
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check_val_every_n_epoch: -1 |
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max_steps: -1 |
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``` |
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## Performance |
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To compute the targets using the raw k-space and the chosen coil combination method, accompanied with the chosen coil sensitivity maps estimation method, you can use [targets](https://github.com/wdika/atommic/tree/main/projects/REC/CC359/conf/targets) configuration files. |
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Evaluation can be performed using the [evaluation](https://github.com/wdika/atommic/blob/main/tools/evaluation/reconstruction.py) script for the reconstruction task, with --evaluation_type per_slice. |
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Results |
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------- |
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Evaluation against RSS targets |
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------------------------------ |
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5x: MSE = 0.001429 +/- 0.001373 NMSE = 0.02208 +/- 0.02319 PSNR = 28.85 +/- 4.169 SSIM = 0.8487 +/- 0.07037 |
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10x: MSE = 0.002108 +/- 0.002 NMSE = 0.03273 +/- 0.03417 PSNR = 27.2 +/- 4.197 SSIM = 0.8095 +/- 0.09149 |
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## Limitations |
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This model was trained on the CC359 using a UNet coil sensitivity maps estimation and might differ from the results reported on the challenge leaderboard. |
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## References |
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[1] [ATOMMIC](https://github.com/wdika/atommic) |
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[2] Beauferris, Y., Teuwen, J., Karkalousos, D., Moriakov, N., Caan, M., Yiasemis, G., Rodrigues, L., Lopes, A., Pedrini, H., Rittner, L., Dannecker, M., Studenyak, V., Gröger, F., Vyas, D., Faghih-Roohi, S., Kumar Jethi, A., Chandra Raju, J., Sivaprakasam, M., Lasby, M., … Souza, R. (2022). Multi-Coil MRI Reconstruction Challenge—Assessing Brain MRI Reconstruction Models and Their Generalizability to Varying Coil Configurations. Frontiers in Neuroscience, 16. https://doi.org/10.3389/fnins.2022.919186 |
