We have our own tools for doing this. When you run mri_glmfit-sim with the --cache option, it access precomputed simulation tables. If you need to create your own tables, see here
https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo
Note that the AFNI alphasim bug was not responsible for the elevated false positive rates found in Eklund 2016, and so fixing the bug will not make the problem go away. The FS implementation of the monte carlo simulation does not have (and never had) the bug. Also note that you can do permutation testing with mri_glmfit-sim as well.
On 11/18/2016 01:25 PM, Hubbard, Catherine S. wrote:
Hi, I’ve read previously on the archive that it is not possible to use AFNIs alphasim with freesurfer surfaces, however, I’m wondering if it might be possible to use 3dClustSim (recent version with fixed bug)? Thanks for your help.
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