I spent a year of my life working on DL for Neuro. The huge problem is data availability. It's just unfeasible to train anything "deep" with the datasets available today. Until some well funded organisation / government comes along and open sources a dataset in the correct order of magnitude of samples - it's just not going to happen.

Still - you can have great successes with classic linear models, and the underlying effects of fMRI are very real. I look forward to the day a multimodal dataset of cutting edge DTI, fMRI and MRI is released.