Upload config

readme_template.md

@@ -0,0 +1,129 @@
+---
+language:
+- en
+license: apache-2.0
+library_name: atommic
+datasets:
+- CC359
+thumbnail: null
+tags:
+- image-reconstruction
+- JointICNet
+- ATOMMIC
+- pytorch
+model-index:
+- name: REC_JointICNet_CC359_12_channel_poisson2d_5x_10x_NNEstimationCSM
+  results: []
+
+---
+
+
+## Model Overview
+
+Joint Deep Model-Based MR Image and Coil Sensitivity Reconstruction Network (JointICNet) for 5x & 10x accelerated MRI Reconstruction on the CC359 dataset.
+
+
+## ATOMMIC: Training
+
+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.
+```
+pip install atommic['all']
+```
+
+## How to Use this Model
+
+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.
+
+Corresponding configuration YAML files can be found [here](https://github.com/wdika/atommic/tree/main/projects/REC/CC359/conf).
+
+### Automatically instantiate the model
+
+```base
+pretrained: true
+checkpoint: https://huggingface.co/wdika/REC_JointICNet_CC359_12_channel_poisson2d_5x_10x_NNEstimationCSM/blob/main/REC_JointICNet_CC359_12_channel_poisson2d_5x_10x_NNEstimationCSM.atommic
+mode: test
+```
+
+### Usage
+
+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.
+
+
+## Model Architecture
+```base
+model:
+  model_name: JointICNet
+  num_iter: 2
+  kspace_unet_num_filters: 16
+  kspace_unet_num_pool_layers: 2
+  kspace_unet_dropout_probability: 0.0
+  kspace_unet_padding_size: 11
+  kspace_unet_normalize: true
+  imspace_unet_num_filters: 16
+  imspace_unet_num_pool_layers: 2
+  imspace_unet_dropout_probability: 0.0
+  imspace_unet_padding_size: 11
+  imspace_unet_normalize: true
+  sens_unet_num_filters: 16
+  sens_unet_num_pool_layers: 2
+  sens_unet_dropout_probability: 0.0
+  sens_unet_padding_size: 11
+  sens_unet_normalize: true
+  dimensionality: 2
+```
+
+## Training
+```base
+  optim:
+    name: adamw
+    lr: 1e-4
+    betas:
+      - 0.9
+      - 0.999
+    weight_decay: 0.0
+    sched:
+        name: CosineAnnealing
+        min_lr: 0.0
+        last_epoch: -1
+        warmup_ratio: 0.1
+
+trainer:
+  strategy: ddp_find_unused_parameters_false
+  accelerator: gpu
+  devices: 1
+  num_nodes: 1
+  max_epochs: 20
+  precision: 16-mixed
+  enable_checkpointing: false
+  logger: false
+  log_every_n_steps: 50
+  check_val_every_n_epoch: -1
+  max_steps: -1
+```
+
+## Performance
+
+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.
+
+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.
+
+Results
+-------
+
+Evaluation against RSS targets
+------------------------------
+5x: MSE = 0.001306 +/- 0.001178 NMSE = 0.02018 +/- 0.02082 PSNR = 29.28 +/- 3.99 SSIM = 0.8719 +/- 0.06531
+
+10x: MSE = 0.002043 +/- 0.001908 NMSE = 0.03181 +/- 0.03297 PSNR = 27.36 +/- 4.101 SSIM = 0.8278 +/- 0.0864
+
+
+## Limitations
+
+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.
+
+
+## References
+
+[1] [ATOMMIC](https://github.com/wdika/atommic)
+
+[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