Hi - I don't quite understand the question - once you have FLAME higher-level zstats then the thresholding via the default FEAT route is straightforward?

If you want to speed up the higher-level stats then you can choose "FLAME 1" or even OLS instead of full FLAME 1+2.

Cheers.



On 28 Jul 2012, at 15:18, Pavel Hok wrote:

Hello FSL Team!

I would like to pre-threshold FLAME zstats without running the whole Higher-level analysis, as it takes a lot of time. I realized that cluster command requires DLH as input, but I am not sure how to use the smoothest command properly. First, I tried using the zstat as input for smoothest, but the results differ from the FEAT output when setting the pre-threshold mask in Post-stats. I found some threads in the mailing list which were dealing with similar issues, for instance calculating DLH from res4d instead of zstat was encouraged. However, I couldn't find any answer to following questions:

1) How is the DOF value for the smoothest command calculated? Should I just use the same value (e.g. 88) as the Feat script (from the log file)?

2) I noticed, that even when the pre-thresholding mask is set, the smoothest masks the res4d file only with whole-brain mask (i.e. mask.nii.gz from stats folder), ignoring the custom mask. So the question is, which mask should I use when running smoothest (whole brain mask or the custom one)?

Thanks!

Pavel



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