Thanks.  Unfortunately, this is only for the GLM, is there an equivalent version for the linear mixed model? I haven’t seen one.  I guess we could figure out how to integrate lme into mri_glmsim, but I’m not sure that’s a better use of our time than manually running the simulations.  Your thoughts?  

Thanks for the help.

FreeSurfer has its own permutation software
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We also have a handy interface to palm
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On 7/27/2019 9:33 PM, Mark Wagshul wrote:

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Great, thanks!

Mark

_______________________

Mark Wagshul, PhD

Albert Einstein College of Medicine

Bronx, NY

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On Jul 27, 2019, at 2:43 PM, Antonin Skoch <ansk@ikem.cz> wrote:

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Dear Mark,

I would suggest to use PALM instead:

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PALM supports surface-based data. Each vertex has different area, which has to be accounted when the cluster size is computed.

Antonin Skoch



Dear Freesurfer experts,

Hi.  We are analyzing cortical thickness data in Freesurfer, longitudinal data 
in 55 subjects using the linear mixed effects package.  We are finding a number 
of siginificant clusters, and would like to correct for multiple comparisons 
with permutation testing.  We have already run about 2000 permutations, and 
would like to use TFCE available in randomise rather than empirical methods to 
set parameters such as the cluster forming threshold.

So, the simple question is, how do we convert our FS format data (these are F 
statistics at each vertex) into a format which can be read into randomise?

Thanks for any advice you can provide.

Best,

Mark

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