Yes, you can use mri_mcsim. I've put the latest version for linux here:

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/mri_mcsim.linux

Run it something like

mri_mcsim --o $FREESURFER_HOME/average/mult-comp-cor \ --base mc-z --surface yoursubject lh --nreps 10000

And one for the right hemi too.

This will create a directory structure similar to $FREESURFER_HOME/average/mult-comp-cor/fsaverage

It may take a couple of days to run but once it is done, you don't need to run it again. After that you can just run mri_glmfit-sim

Note, you can put it into a different directory and then spec that folder when you run mri_glmfit-sim with the --cache-dir flag.

doug

On 01/20/2014 11:30 AM, Sophie Maingault wrote:

Dear FreeSurfer experts,

We are running group analyses in 430 young healthy volunteers using Qdec interface and FreeSurfer 5.3.

FDR correction seems to be not enough restrictive and on the contrary use a Bonferroni correction with the total number of vertices would be too much restrictive.

In this context we would like to use the Monte Carlo simulation but we built our specific template and as you may know this is not possible in this case, this error message being displayed: " Erreur in Monte Carlo simulation: This function only works when using fsaverage as the common-space subject ".

Thus I have two questions: 1) is it possible to adapt the Monte Carlo simulation to our template using some command line or something else? 2) If not what advice can you give to us?

Thanks a lot, Best regards,

Sophie Maingault

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