While I track down a bug in actually loading my simulated data from yesterday, I wanted to bring up another way of modelling sub-cortical structures. Another popular open source Matlab based application called Brainstorm, supports sub-cortical source localization by modelling sub-cortical structures as surfaces. Up until now, I've been modelling the amygdala as a volume and merging with the cortical surface, or modelling the whole brain as a volume.
Balderston et al. provide a video article using Brainstorm to look at amygdala activity. The video explicitly goes through the steps of recording and analyzing the data.
In addition, an MNE user from the University of Pennsylvania was kind enough to share his Python based implementation of modelling sub-cortical structures as surfaces. Another one of my goals this summer will be getting his code to work on the SPM face data set and comparing the results to my previous approaches.
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