I've put a new version of mri_glmfit-sim here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_glmfit-sim This should run, though I'm not 100% sure this is the right way to do it. Let me know how it goes

On 3/19/19 10:58 AM, Victor Montal wrote:

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Dear Freesurfer experts,

I am very interested in using your permutation approach in order to correct our uncorr analyses using the newly proposed approach (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0...).

However, I am facing some problems that I hope you can assist me on.

We are computing the uncorrected stats using the mri_glmfit option --frame-mask. However, when I run the (latest) version of mri_glmfit-sim, as in the tutorial, I get the errors:

"""

INFO: unrecognized mri_glmfit cmd option --frame-mask  ... probably not a problem

INFO: unrecognized mri_glmfit cmd option ../rh.framemask.mgh  ... probably not a problem """

My concern is, since the command is not considering the frame-mask option, it will not also permutate the mask accordingly to the GLM design permutation.  Am I wrong or the sim command will permute the mask without problem?

I have also tried to run the mri_glmfit with the --sim option. In this case, I don't receive any warning/info, thus, I am assuming it takes into account the permutation of the frame-mask, or it does not?

One possible workaround would be to create the cluster-extension csd file by myself, but I would know if there is any solution for this already implemented in Freesurfer.

Thank you in advance for your help!

Victor M

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