Through-plane super-resolution with autoencoders in diffusion magnetic resonance imaging of the developing human brain

Kebiri, H.; Canales-Rodriguez, E. J.; Lajous, H.; de Dumast, P.; Girard, G.; Aleman-Gomez, Y.; Koob, M.; Jakab, A.; Cuadra, M. B.

doi:10.1101/2021.12.06.471406

bioRxiv · 10.1101/2021.12.06.471406

Through-plane super-resolution with autoencoders in diffusion magnetic resonance imaging of the developing human brain

Kebiri, H.·Canales-Rodriguez, E. J.·Lajous, H.·de Dumast, P.·Girard, G.·Aleman-Gomez, Y.·Koob, M.·Jakab, A.·Cuadra, M. B.

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Abstract

Fetal brain diffusion magnetic resonance images are often acquired with a lower through-plane than in-plane resolution. This anisotropy is often overcome by classical upsampling methods such as linear or cubic interpolation. In this work, we employ an unsupervised learning algorithm using an autoencoder neural network to enhance the through-plane resolution by leveraging a large amount of data. Our framework, which can also be used for slice outliers replacement, overperformed conventional interpolations quantitatively and qualitatively on pre-term newborns of the developing Human Connectome Project. The evaluation was performed on both the original diffusion-weighted signal and on the estimated diffusion tensor maps. A byproduct of our autoencoder was its ability to act as a denoiser. The network was able to generalize to fetal data with different levels of motion and we qualitatively showed its consistency, hence supporting the relevance of pre-term datasets to improve the processing of fetal brain images.

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Kebiri, H., Canales-Rodriguez, E. J., Lajous, H., de Dumast, P., Girard, G., Aleman-Gomez, Y., Koob, M., Jakab, A., Cuadra, M. B.. 2021-12-07. Through-plane super-resolution with autoencoders in diffusion magnetic resonance imaging of the developing human brain. https://doi.org/10.1101/2021.12.06.471406

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