Extra Tree forests for sub-acute ischemic stroke lesion segmentation in MR sequences

Background: To analyse the relationship between structure and (dys-)function of the brain after stroke, accurate and repeatable segmentation of the lesion area in magnetic resonance (MR) images is required. Manual delineation, the current gold standard, is time consuming and suffers from high intra- and inter-observer differences. New method: A new approach is presented for the automatic and reproducible segmentation of sub-acute ischemic stroke lesions in MR images in the presence of other pathologies. The proposition is based on an Extra Tree forest framework for voxel-wise classification and mainly intensity derived image features are employed. Results: A thorough investigation of multi-spectral variants, which combine the information from multiple MR sequences, finds the fluid attenuated inversion recovery sequence to be both required and sufficient for a good segmentation result. The accuracy can be further improved by adding features extracted from the T1-weighted and the diffusion weighted sequences. The use of other sequences is discouraged, as they impact negatively on the results. Comparison with existing methods: Quantitative evaluation was carried out on 37 clinical cases. With a Dice coefficient of 0.65, the method outperforms earlier published methods. Conclusions: The approach proves especially suitable to differentiate between new stroke and other white matter lesions based on the FLAIR sequence alone. This, and the high overlap, renders it suitable for automatic screening of large databases of MR scans, e.g. for a subsequent neuropsychological investigation. Finally, each feature's importance is assessed in detail and the approach's statistical dependency on clinical and image characteristics is investigated. (C) 2014 Elsevier B.V. All rights reserved.