Thank you for your feedback! I mistakenly assumed that the self-connection parameters defaulted to -1. In case you are wondering, the R package I used was FIAR (not FAIR): http://www.jstatsoft.org/v44/i13. I will try fixing the A matrix and running in SPM as well.
If you have the time, I have a follow up question:
That makes sense that my problem might have something to do with the EM algorithm settling on a relatively poor local maximum for the correct model. How can one mitigate this risk? If the EM algorithm starts at an arbitrary point, then it would seem that increasing subject or run number would help. Are there properties of a specific model structure (or space) that would make one more or less susceptible to this?
Thank you again,
Becky
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