In one aspect the disclosed technology relates to embodiments of a method which, includes acquiring magnetic resonance imaging data, for a plurality of images, of the heart of a subject. The method also includes segmenting, using cascaded convolutional neural networks (CNN), respective portions of the images corresponding to respective epicardium layers and endocardium layers for a left ventricle (LV) and a right ventricle (RV) of the heart. The segmenting is used for extracting biomarker data from segmented portions of the images and, in one embodiment, assessing hypertrophic cardiomyopathy from the biomarker data. The method further includes segmenting processes for T1 MRI data and LGE MRI data.