An efficient data strategy for the detection of brain aneurysms from MRA with deep learning

Youssef Assis, Liang Liao, Fabien Pierre, René Anxionnat, Erwan Kerrien

Abstract: The detection of intracranial aneurysms from Magnetic Resonance Angiography images is a problem of rapidly growing clinical importance. In the last 3 years, the raise of deep convolutional neural networks has instigated a streak of methods that have shown promising performance. The major issue to address is the very severe class imbalance. Previous authors have focused their efforts on the network architecture and loss function. This paper tackles the data. A rough but fast annotation is considered: each aneurysm is approximated by a sphere defined by two points. Second, a small patch approach is taken so as to increase the number of samples. Third, samples are generated by a combination of data selection (negative patches are centered half on blood vessels and half on parenchyma) and data synthesis (patches containing an aneurysm are duplicated and deformed by a 3D spline transform). This strategy is applied to train a 3D U-net model, with a binary cross entropy loss, on a data set of 111 patients (155 aneurysms, mean size 3.86mm ± 2.39mm, min 1.23mm, max 19.63mm). A 5-fold cross-validation evaluation provides state of the art results (sensitivity 0.72, false positive count 0.14, as per ADAM challenge criteria). The study also reports a comparison with the focal loss, and Cohen’s Kappa coefficient is shown to be a better metric than Dice for this highly unbalanced detection problem.