Deep learning pipeline for quality filtering of MRSI spectra

With the rise of novel 3D magnetic resonance spectroscopy imaging (MRSI) acquisition protocols in clinical practice, which are capable of capturing a large number of spectra from a subject's brain, there is a need for an automated preprocessing pipeline that filters out bad‐quality spectra and identifies contaminated but salvageable spectra prior to the metabolite quantification step. This work introduces such a pipeline based on an ensemble of deep‐learning classifiers. The dataset consists of 36,338 spectra from one healthy subject and five brain tumor patients, acquired with an EPSI variant, which implemented a novel type of spectral editing named SLOtboom–Weng (SLOW) editing on a 7T MR scanner. The spectra were labeled manually by an expert into four classes of spectral quality as follows: (i) noise, (ii) spectra greatly influenced by lipid‐related artifacts (deemed not to contain clinical information), (iii) spectra containing metabolic information slightly contaminated by lipid signals, and (iv) good‐quality spectra. The AI model consists of three pairs of networks, each comprising a convolutional autoencoder and a multilayer perceptron network. In the classification step, the encoding half of the autoencoder is kept as a dimensionality reduction tool, while the fully connected layers are added to its output. Each of the three pairs of networks is trained on different representations of spectra (real, imaginary, or both), aiming at robust decision‐making. The final class is assigned via a majority voting scheme. The F1 scores obtained on the test dataset for the four previously defined classes are 0.96, 0.93, 0.82, and 0.90, respectively. The arguably lower value of 0.82 was reached for the least represented class of spectra mildly influenced by lipids. Not only does the proposed model minimise the required user interaction, but it also greatly reduces the computation time at the metabolite quantification step (by selecting a subset of spectra worth quantifying) and enforces the display of only clinically relevant information. We introduce an automated robust deep‐learning pipeline for quality filtering of MRSI spectra. Spectra are classified into four classes and the bad‐quality spectra are filtered out prior to the metabolite quantification step. The network is an ensemble of convolutional autoencoders and multilayer perceptrons trained on spectra in the frequency domain.