Large medical imaging data sets are becoming increasingly available, but ensuring sample quality without significant artefacts is challenging. Existing methods for identifying imperfections in medical imaging rely on data-intensive approaches, compounded by a scarcity of artefact-rich scans for training machine learning models in clinical research. To tackle this problem, we propose a framework with four main components: 1) artefact generators inspired by magnetic resonance physics to corrupt brain MRI scans and augment a training dataset, 2) abstract and engineered features to represent images compactly, 3) a feature selection process depending on the artefact class to improve classification, and 4) SVM classifiers to identify artefacts. Our contributions are threefold: first, physics-based artefact generators produce synthetic brain MRI scans with controlled artefacts for data augmentation. This will avoid the labour-intensive collection and labelling process of scans with rare artefacts. Second, we propose a pool of abstract and engineered image features to identify 9 different artefacts for structural MRI. Finally, we use an artefact-based feature selection block that, for each class of artefacts, finds the set of features providing the best classification performance. We performed validation experiments on a large data set of scans with artificially-generated artefacts, and in a multiple sclerosis clinical trial where real artefacts were identified by experts, showing that the proposed pipeline outperforms traditional methods. In particular, our data augmentation increases performance by up to 12.5 percentage points on accuracy, precision, and recall. The computational efficiency of our pipeline enables potential real-time deployment, promising high-throughput clinical applications through automated image-processing pipelines driven by quality control systems.

Simulating images representative of neurodegenerative diseases is important for predicting patient outcomes and for validation of computational models of disease progression. This capability is valuable for secondary prevention clinical trials where outcomes and screening criteria involve neuroimaging. Traditional computational methods are limited by imposing a parametric model for atrophy and are extremely resource-demanding. Recent advances in deep learning have yielded data-driven models for longitudinal studies (e.g., face ageing) that are capable of generating synthetic images in real-time. Similar solutions can be used to model trajectories of atrophy in the brain, although new challenges need to be addressed to ensure accurate disease progression modelling. Here we propose Degenerative Adversarial NeuroImage Net (DaniNet) --- a new deep learning approach that learns to emulate the effect of neurodegeneration on MRI. DaniNet uses an underlying set of Support Vector Regressors (SVRs) trained to capture the patterns of regional intensity changes that accompany disease progression. DaniNet produces whole output images, consisting of 2D-MRI slices that are constrained to match regional predictions from the SVRs. DaniNet is also able to condition the progression on non-imaging characteristics (age, diagnosis, etc.) while it maintains the unique brain morphology of individuals. Adversarial training ensures realistic brain images and smooth temporal progression. We train our model using 9652 T1-weighted (longitudinal) MRI extracted from the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset. We perform quantitative and qualitative evaluations on a separate test set of 1283 images (also from ADNI) demonstrating the ability of DaniNet to produce accurate and convincing synthetic images that emulate disease progression.