Deeplearning/Neural Network

I’ve processed the t1 weighted unlabelled mri data using freesurfer.Now I have preprocessed data from freesurfer and got multiple outputs like .mgz, ctab and label files i don’t know how to use these data to feed my network to get some distrubution. kindly suggest me a paper or guide me how can i feed this data/which data to feed to the neural network i.e(VAE)/ which data to be used to feed to the network to get some feature distribution/clustering.