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REC_CIRIM_AHEAD_gaussian2d_12x

PyTorch
English
atommic
image-reconstruction
CIRIM
ATOMMIC
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REC_CIRIM_AHEAD_gaussian2d_12x
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---
language:
- en
license: apache-2.0
library_name: atommic
datasets:
- AHEAD
thumbnail: null
tags:
- image-reconstruction
- CIRIM
- ATOMMIC
- pytorch
model-index:
- name: REC_CIRIM_AHEAD_gaussian2d_12x
  results: []

---


## Model Overview

Cascades of Independently Recurrent Inference Machines (CIRIM) for 12x accelerated MRI Reconstruction on the AHEAD 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/AHEAD/conf).


### Automatically instantiate the model

```base
pretrained: true
checkpoint: https://huggingface.co./wdika/REC_CIRIM_AHEAD_gaussian2d_12x/blob/main/REC_CIRIM_AHEAD_gaussian2d_12x.atommic
mode: test
```

### Usage

You need to download the AHEAD dataset to effectively use this model. Check the [AHEAD](https://github.com/wdika/atommic/blob/main/projects/REC/AHEAD/README.md) page for more information.


## Model Architecture
```base
model:
  model_name: CIRIM
  recurrent_layer: IndRNN
  conv_filters:
    - 64
    - 64
    - 2
  conv_kernels:
    - 5
    - 3
    - 3
  conv_dilations:
    - 1
    - 2
    - 1
  conv_bias:
    - true
    - true
    - false
  recurrent_filters:
    - 64
    - 64
    - 0
  recurrent_kernels:
    - 1
    - 1
    - 0
  recurrent_dilations:
    - 1
    - 1
    - 0
  recurrent_bias:
    - true
    - true
    - false
  depth: 2
  time_steps: 8
  conv_dim: 2
  num_cascades: 5
  no_dc: true
  keep_prediction: true
  accumulate_predictions: true
  dimensionality: 2
  num_echoes: 4
  reconstruction_loss:
    ssim: 1.0
```

## Training
```base
  optim:
    name: adamw
    lr: 1e-4
    betas:
      - 0.9
      - 0.999
    weight_decay: 0.0
    sched:
        name: PolynomialHoldDecayAnnealing
        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/AHEAD/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 SENSE targets
--------------------------------
12x: MSE = 0.0009594 +/- 0.003039 NMSE = 0.04406 +/- 0.07482 PSNR = 32.89 +/- 8.596 SSIM = 0.909 +/- 0.08273


## Limitations

This model was trained on very few subjects on the AHEAD dataset. It is not guaranteed to generalize to other datasets.


## References

[1] [ATOMMIC](https://github.com/wdika/atommic)

[2] Alkemade A, Mulder MJ, Groot JM, et al. The Amsterdam Ultra-high field adult lifespan database (AHEAD): A freely available multimodal 7 Tesla submillimeter magnetic resonance imaging database. NeuroImage 2020;221.