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Hi there, A full flame analysis only carries out MCMC on voxels which are "near" threshold. The two parameters you mention here tell flame when to run mcmc -zlt is the lower threshold -zut is the upper threshold mcmc is actually run for stage-1 z values slightly outside this band to account for the potential errors stage-1 flame. Anyway - if you set --zut=100000 and --zlut=100000 Then flame stage-1 must return a z-value of 10000ish before mcmc gets run. This never happens , hence "stage 1 only" Hope this answers your question Tim ------------------------------------------------------------------------------- Tim Behrens Centre for Functional MRI of the Brain The John Radcliffe Hospital Headley Way Oxford OX3 9DU Oxford University Work 01865 222782 Mobile 07980 884537 ------------------------------------------------------------------------------- On Tue, 2 Mar 2004, Jonathan E. Dan wrote: > 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 >