If you want to use that threshold, you will have to create tables for that threshold using mri_mcsim. See
https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo
Alternatively, I have a version of mri_glmfit-sim that will run permutation with non-orthogonal designs.
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_glmfit-sim
This is the direction I'm pushing people in. To run it, use the normal permutation options and add --perm-resid
This uses the ter Braak method. Run mri_glmfit-sim --help to get more info
On 09/07/2017 11:05 AM, Jahn, Andrew wrote:
Hello,
Is it possible to use cluster-defining thresholds such as p = 0.025 with mri_glmfit-sim? (This would roughly correspond to a negative log value of 1.6.) My design doesn't allow the use of permutations for simulating cluster sizes, so I have to use the mczsim option; however, from what I can tell it doesn't allow using any non-cached options.
Thanks,
-Andy
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