Dear FSL experts,
through the FSL logs I have managed to write a bash script that runs the first level analysis. However, for the higher level analysis it seems like some commands are missing in the logs. I understand that the results from the first level analysis are transformed into MNI space and concatenated into one cope and varcope file for each contrast, but I can't see the actual call to flame. In another log file I found the following command,
flameo --cope=filtered_func_data --vc=var_filtered_func_data --dvc=tdof_filtered_func_data --mask=mask --ld=stats --dm=design.mat --cs=design.grp --tc=design.con --runmode=fe
but I can't find how filtered_func_data and var_filtered_func_data are calculated, are these simply equal to the cope and varcope files?
It would be great if anyone could tell me which source file to look into.
Cheers,
Anders
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