Hi Rocco,
There were indeed some file configurations (only one time point) that were not compatible with newer developements (adaptive colormaps for t-test from @tvincent). I think I fixed it, please update Brainstorm and try again.
@tvincent: The corrected p-values returned by bst_stat_thresh are not necessarily a simple scalar. When applying a FDR correction independently for each dimension, you might obtain multiple values (or in Rocco's case, when the input file has only one time point, this one is replicated in time). You code was not handling this correctly. I use now the average of all these corrected p-values, I guess that this will work in most cases, but feel free to propose a different approach:
Francois