BrainQCNet: A Deep Learning attention-based model for the automated detection of artifacts in brain structural MRI scans

Analyses of structural MRI (sMRI) data depend on robust upstream data quality control (QC). It is also crucial that researchers seek to retain maximal amounts of data to ensure reproducible, generalizable models and to avoid wasted effort, including that of participants. The time-consuming and difficult task of manual QC evaluation has prompted the development of tools for the automatic assessment of brain sMRI scans. Existing tools have proved particularly valuable in this age of Big Data; as datasets continue to grow, reducing execution time for QC evaluation will be of considerable benefit. The development of Deep Learning (DL) models for artifact detection in structural MRI scans offers a promising avenue toward fast, accurate QC evaluation. In this study, we trained an interpretable Deep Learning model, ProtoPNet, to classify minimally preprocessed 2D slices of scans that had been manually annotated with a refined quality assessment (ABIDE 1; n = 980 scans). To evaluate the best model, we applied it to 2141 ABCD T1-weighted MRI scans for which gold-standard manual QC annotations were available. We obtained excellent accuracy: 82.4% for good quality scans (Pass), 91.4% for medium to low quality scans (Fail). Further validation using 799 T1w MRI scans from ABIDE 2 and 750 T1w MRI scans from ADHD-200 confirmed the reliability of our model. Accuracy was comparable to or exceeded that of existing ML models, with fast processing and prediction time (1 minute per scan, GPU machine, CUDA-compatible). Our attention model also performs better than traditional DL (i.e., convolutional neural network models) in detecting poor quality scans. To facilitate faster and more accurate QC prediction for the neuroimaging community, we have shared the model that returned the most reliable global quality scores as a BIDS-app (https://github.com/garciaml/BrainQCNet).