Advancing GABA-edited MRS Research through a Reconstruction Challenge

Abstract

Purpose To create a benchmark for the comparison of machine learning-based Gamma-Aminobutyric Acid (GABA)-edited Magnetic Resonance Spectroscopy (MRS) reconstruction models using one quarter of the transients typically acquired during a complete scan. Methods The Edited-MRS reconstruction challenge had three tracks with the purpose of evaluating machine learning models trained to reconstruct simulated (Track 1), homogeneous in vivo (Track 2), and heterogeneous in vivo (Track 3) GABA-edited MRS data. Four quantitative metrics were used to evaluate the results: mean squared error (MSE), signal-to-noise ratio (SNR), linewidth, and a shape score metric that we proposed. Challenge participants were given three months to create, train and submit their models. Challenge organizers provided open access to a baseline U-NET model for initial comparison, as well as simulated data, in vivo data, and tutorials and guides for adding synthetic noise to the simulations. Results The most successful approach for Track 1 simulated data was a covariance matrix convolutional neural network model, while for Track 2 and Track 3 in vivo data, a vision transformer model operating on a spectrogram representation of the data achieved the most success. Deep learning (DL) based reconstructions with reduced transients achieved equivalent or better SNR, linewidth and fit error as conventional reconstructions with the full amount of transients. However, some DL models also showed the ability to optimize the linewidth and SNR values without actually improving overall spectral quality, pointing to the need for more robust metrics. Conclusion The edited-MRS reconstruction challenge showed that the top performing DL based edited-MRS reconstruction pipelines can obtain with a reduced number of transients equivalent metrics to conventional reconstruction pipelines using the full amount of transients. The proposed metric shape score was positively correlated with challenge track outcome indicating that it is well-suited to evaluate spectral quality.