/Brain-MRI-Autoencoder

Deep Convolutional Autoencoders for reconstructing magnetic resonance images of the healthy brain

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Deep Convolutional Autoencoders for reconstructing magnetic resonance images of the healthy brain

PWC

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Deep Autoencoder for brain MRI

Master's Thesis. Master's in Data Science at Universitat Oberta de Catalunya.

Author

Tutor:



Convolutional Autoencoder Architectures used

Experiments:

  • With Data Augmentation:

    • 2 experiments (MSE and DSSIM Loss) for each of the following architectures:
      • Shallow residual autoencoder (full-pre)
      • Shallow residual autoencoder (full-pre) + L2 reg.
      • Skip connection autoencoder
      • Skip connection autoencoder + L2 reg.
      • Myronenko Autoencoder
      • RESIDUAL-UNET (proposed new improved architecture)
  • Without Data Augmentation:

    • MSE Loss
      • Shallow residual autoencoder (original)
      • Shallow residual autoencoder (full-pre)
      • Shallow residual autoencoder (full-pre) + L2 reg.
      • Skip connection autoencoder
      • Myronenko Autoencoder
      • Myronenko Autoencoder + L2 reg.

Results

Quantitative Results

Model loss L2 Val loss MSE DSSIM PSNR
Residual U-NET MSE No 3.58e-05 3.44e-05 2.95e-03 44.9
Shallow RES full-pre MSE No 1.55e-04 1.51e-04 6.75e-03 38.6
Skip connection CAE MSE Yes 2.69e-04 2.25e-04 1.65e-02 36.8
Skip connection CAE MSE No 3.10e-04 2.99e-04 9.36e-03 35.7
Myronenko CAE MSE No 3.38e-04 3.27e-04 1.57e-02 35.1
Shallow RES full-pre MSE Yes 3.72e-04 3.24e-04 1.14e-02 35.2
Residual U-NET DSSIM No 1.50e-03 7.49e-05 1.44e-03 41.8
Shallow RES full-pre DSSIM Yes 4.42e-03 2.34e-04 3.70e-03 36.7
Shallow RES full-pre DSSIM No 4.19e-03 2.88e-04 4.14e-03 35.9
Myronenko CAE DSSIM No 4.39e-03 6.69e-04 4.31e-03 32.1
Skip connection CAE DSSIM Yes 4.82e-03 4.08e-04 4.38e-03 34.2
Skip connection CAE DSSIM No 4.90e-03 4.57e-04 4.71e-03 33.7

Quanlitative Results

Char of test metrics and dependent sample t-test significances