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Hi FSLers, I’m trying to determine the appropriate parameters to run a command line flame analysis. In particular, I would like to try the "FLAME stage 1 only" option. I ran both “stage 1” and “full flame” analysis with the GUI and the only difference in the parameters seemed to be the –zlt and –zut values (the relevant lines from the logfiles are below). What are these parameters? Is it true that they control whether the flame analysis goes to stage 1 only or whether it does the full MCMC estimation? Cheers, any help much appreciated, Marnie % “FLAME stage 1 only” /programs/fsl/bin/flame --cope=filtered_func_data -- vc=var_filtered_func_data --mask=mask --ld=stats --dm=design.mat -- cs=design.grp --tc=design.con --ols --nj=10000 --bi=500 --se=1 --fm -- zlt=100000 --zut=100000 % full MCMC flame /programs/fsl/bin/flame --cope=filtered_func_data -- vc=var_filtered_func_data --mask=mask --ld=stats --dm=design.mat -- cs=design.grp --tc=design.con --ols --nj=10000 --bi=500 --se=1 --fm -- zlt=2.25 --zut=2.65