  Deep learning methods have recently made notable advances in the tasks of
classification and representation learning. These tasks are important for brain
imaging and neuroscience discovery, making the methods attractive for porting
to a neuroimager's toolbox. Success of these methods is, in part, explained by
the flexibility of deep learning models. However, this flexibility makes the
process of porting to new areas a difficult parameter optimization problem. In
this work we demonstrate our results (and feasible parameter ranges) in
application of deep learning methods to structural and functional brain imaging
data. We also describe a novel constraint-based approach to visualizing high
dimensional data. We use it to analyze the effect of parameter choices on data
transformations. Our results show that deep learning methods are able to learn
physiologically important representations and detect latent relations in
neuroimaging data.
