Hi,
Thanks, Chris. I followed your instructions and set up the third-level analysis to be run for each cope separately. I ran this across copes using a bash script.
While this worked fine it is hard for me to believe that there isn't a more automated way to do this? For some reason, simply running a third level mixed effects analysis with the FE results by selecting each person's feat directory so that the analysis is done on all contrasts simultaneously does not work for me either. This would be a lot more efficient/user-friendly. In case it's of relevance, I'm using FSL 4.1 (2008).
In any case, the instructions that are currently specified on the FSL webpage (http://www.fmrib.ox.ac.uk/fsl/feat5/detail.html#MultiSessionMultiSubject) listed under the section entitled Multi-Session & Multi-Subject (Repeated Measures - Three Level Analysis) appear to be incorrect. Given how common it is to conduct an analysis using multiple runs per subject, it would be very helpful if the webpage could be updated.
Cheers,
-Erie
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