There is actually an option called --thresh where you can give it a threshold to use. Somehow it did not make it onto the help docs

On 09/13/2017 11:39 AM, Jahn, Andrew wrote:

Hi Doug,

Thank you for the custom permutation script; it is very helpful.

However, it is still not clear how to use mri_mcsim to create tables with different thresholds. I understand how to use it to restrict the search space and how to use it on different subjects, but I don't see any option for specifying different thresholds. Is there a specific option in mri_mcsim for doing this?

Thank you,

-Andy

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*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu *Sent:* Thursday, September 7, 2017 5:55:30 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Cluster-Defining Threshold of p=0.025 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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