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

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
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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