[pymvpa] Searchlights and Permutation testing

Bill Broderick billbrod at gmail.com
Tue Jun 16 18:50:24 UTC 2015

Hi all,

I'm trying to implement permutation testing with searchlights and, after
going through the manual and the mailing list archives, I'm still not sure
how to do it.

According to this thread
the fastest way to get searchlight permutations is to use the GNB
searchlight; otherwise it takes so long as to be impractical. However, when
trying to set up the GNB searchlight with a null_dist, as shown in here
I get a NotImplementedError: "GNBSearchlight does not yet support
partitions altering the target (e.g. permutators)", as warned about on the
documentation page for GNB searchlight and mentioned in this thread

However, if I can't use an attribute permutator with the GNB searchlight,
how can I use it to run permutation tests and get a null probability? What
am I missing?

Additionally, and this is a side note, is there any way to pass the null
distribution from the searchlight's null_dist attribute to the results
dataset? Or should I just give up on that, because trying to save the
distribution for each searchlight would result in a huge file?

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