MTL_SegNet_SKMTEA_poisson2d_4x

Model Overview

Segmentation Network MRI (SegNet) 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. 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.

Automatically instantiate the model

pretrained: true
checkpoint: https://huggingface.co/wdika/MTL_SegNet_SKMTEA_poisson2d_4x/blob/main/MTL_SegNet_SKMTEA_poisson2d_4x.atommic
mode: test

Usage

You need to download the SKMTEA dataset to effectively use this model. Check the SKMTEA page for more information.

Model Architecture

model:
  model_name: SEGNET
  use_reconstruction_module: true
  input_channels: 64  # coils * 2
  reconstruction_module_output_channels: 64  # coils * 2
  segmentation_module_output_channels: 4
  channels: 64
  num_pools: 2
  padding_size: 11
  drop_prob: 0.0
  normalize: true
  padding: true
  norm_groups: 2
  num_cascades: 5
  segmentation_final_layer_conv_dim: 2
  segmentation_final_layer_kernel_size: 3
  segmentation_final_layer_dilation: 1
  segmentation_final_layer_bias: False
  segmentation_final_layer_nonlinear: relu
  segmentation_loss:
    dice: 1.0
  dice_loss_include_background: true  # always set to true if the background is removed
  dice_loss_to_onehot_y: false
  dice_loss_sigmoid: false
  dice_loss_softmax: false
  dice_loss_other_act: none
  dice_loss_squared_pred: false
  dice_loss_jaccard: false
  dice_loss_flatten: false
  dice_loss_reduction: mean_batch
  dice_loss_smooth_nr: 1e-5
  dice_loss_smooth_dr: 1e-5
  dice_loss_batch: true
  dice_metric_include_background: true  # always set to true if the background is removed
  dice_metric_to_onehot_y: false
  dice_metric_sigmoid: false
  dice_metric_softmax: false
  dice_metric_other_act: none
  dice_metric_squared_pred: false
  dice_metric_jaccard: false
  dice_metric_flatten: false
  dice_metric_reduction: mean_batch
  dice_metric_smooth_nr: 1e-5
  dice_metric_smooth_dr: 1e-5
  dice_metric_batch: true
  segmentation_classes_thresholds: [0.5, 0.5, 0.5, 0.5]
  segmentation_activation: sigmoid
  reconstruction_loss:
    l1: 1.0
  kspace_reconstruction_loss: false
  total_reconstruction_loss_weight: 0.5
  total_segmentation_loss_weight: 0.5

Training

  optim:
    name: adam
    lr: 1e-4
    betas:
      - 0.9
      - 0.98
    weight_decay: 0.0
    sched:
      name: InverseSquareRootAnnealing
      min_lr: 0.0
      last_epoch: -1
      warmup_ratio: 0.1

trainer:
  strategy: ddp
  accelerator: gpu
  devices: 1
  num_nodes: 1
  max_epochs: 10
  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 configuration files.

Evaluation can be performed using the reconstruction evaluation and segmentation scripts for the reconstruction and the segmentation tasks, with --evaluation_type per_slice.

Results

Evaluation against SENSE targets

4x: MSE = 0.001247 +/- 0.002092 NMSE = 0.02623 +/- 0.05875 PSNR = 29.95 +/- 5.115 SSIM = 0.8396 +/- 0.1071 DICE = 0.9154 +/- 0.1138 F1 = 0.2703 +/- 0.2842 HD95 = 3.002 +/- 1.449 IOU = 0.2904 +/- 0.3491

Limitations

This model was trained on the SKM-TEA dataset for 4x accelerated MRI reconstruction and MRI segmentation with MultiTask Learning (MTL) of the axial plane.

References

[1] ATOMMIC

[2] Desai AD, Schmidt AM, Rubin EB, et al. SKM-TEA: A Dataset for Accelerated MRI Reconstruction with Dense Image Labels for Quantitative Clinical Evaluation. 2022