Hi, all. Because the FEAT GUI registration tab (first level analysis) doesn't offer advanced settings (e.g. cost function), which can produce much better registration results for some data, I use FLIRT independent of FEAT to register 4D BOLD files. I then turn off the "registration" when running a first level analysis. However, when I then try to use FEAT to do the higher level analysis, it exits prematurely with the "can't find filtered_func header files" - Not surprising given there is no first level reg directory. So, the conundrum is how to run a higher level analysis on first level feat directories that don't contain a reg directory? I've looked through the forum archives and the use of the CLI "flameo" may be one answer, but I'm not clear about how to set that up for a higher order analysis; e.g., can two cope files be fed in? What would a tcontrastsfile or a designfile look like? Another possibility would be to edit the design.fsf file to incorporate the advanced registration function(s) that I'm interested in during the first level analysis, but I'm not sure if I'd simply add the FLIRT CLI lines to the design.fsf file or if this is even an option. Any clarification of either option -- or a different one -- would be greatly appreciated.
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