2D and 3D U-Nets for skull stripping in a large and heterogeneous set of head MRI using fastai

Skull stripping in brain imaging is the removal of the parts of images corresponding to non-brain tissue. Fast and accurate skull stripping is a crucial step for numerous medical brain imaging applications, e.g. registration, segmentation and feature extraction, as it eases subsequent image processing steps. In this work, we propose and compare two novel skull stripping methods based on 2D and 3D convolutional neural networks trained on a large, heterogeneous collection of 2777 clinical 3D T1-weighted MRI images from 1681 healthy subjects. We investigated the performance of the models by testing them on 927 images from 324 subjects set aside from our collection of data, in addition to images from an independent, large brain imaging study: the IXI dataset (n = 556). Our models achieved mean Dice scores higher than 0.978 and Jaccard indices higher than 0.957 on all tests sets, making predictions on new unseen brain MR images in approximately 1.4s for the 3D model and 12.4s for the 2D model. A preliminary exploration of the models’ robustness to variation in the input data showed favourable results when compared to a traditional, well-established skull stripping method. With further research aimed at increasing the models’ robustness, such accurate and fast skull stripping methods can potentially form a useful component of brain MRI analysis pipelines.