An alternative approach would be to use bootstrapping to determine the significance as was done by Gross et al. 2012. *Cortical signatures of cognition and their relationship to Alzheimer's disease.*

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On Thu, Apr 4, 2013 at 12:16 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:

Correct, you cannot do a permutation test with continuous variables (or with any non-orthogonal design matrix). If you use the --perm-force, it will do the permutation test as normal (by randomly swapping the rows), but technically the test is not legal. Having said that, I suspect that LOTS of people do exactly that. doug

On 04/04/2013 10:03 AM, Gabriel Gonzalez Escamilla wrote:

...

Dear Freesurfer experts,

I'm having troubles when setting a permutation test, I'm making group comparisons, but I'm introducing the Age, and cortical thickness as niusance variables (as previously recommended).

It seems that permutations only work for orthogonal matrices, does this means that I cannot set any niusance variable?

If so, this is telling me that I can run the command with the flag "--perm-force", and I'm wondering, which would be the implications of force to run the permutations with niusance variables?

Many thanks in advance, Gabriel

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Yes, I know, I just have not implemented them:). doug

On 04/04/2013 12:47 PM, Michael Harms wrote:

Hi Doug, There are approaches/methods available for permutation testing with non-orthogonal design matrices -- see for example the documentation for FSL's randomise and the references cited therein.

cheers, -MH