Classifying subjects as healthy or diseased using neuroimaging data has gained a lot of attention during the last 10 years, and recently, different deep learning approaches have been used. Despite this fact, there has not been any investigation regarding how 3D augmentation can help to create larger datasets, required to train deep networks with millions of parameters. In this study, deep learning was applied to derivatives from resting state functional MRI data, to investigate how different 3D augmentation techniques affect the test accuracy. Specifically, resting state derivatives from 1112 subjects in ABIDE (Autism Brain Imaging Data Exchange) preprocessed were used to train a 3D convolutional neural network (CNN) to classify each subject according to presence or absence of autism spectrum disorder. The results show that augmentation only provide minor improvements to the test accuracy.