Abstract: The present invention relates to a method and a system for the segmentation of white matter hyperintensities (WMHs) present in magnetic resonance brain images, comprising: providing an array of trained convolutional neural networks (CNNs) with a magnetic resonance brain image; determining, for each of the CNNs and for each voxel, the probability that the given voxel corresponds to a pathological hyperintensity; calculating the average of all the probabilities determined for each voxel; comparing the averaged probabilities for each voxel with a threshold; generating an image mask with the voxels that exceed the threshold.