On 04/04/2013 03:56 PM, Gabriel Gonzalez Escamilla wrote:

Dear Doug,

Thank you so much as always for your answer.

When you said that the permutation test is done normally, do you mean that does not take account of the nuisance variables, and only test for the groups comparison?

It creates the full matrix including nuisance, then it permutes the rows of the matrix.

Now I'm wondering if you have something implemented on matlab or anything that could do a correction for multiple comparisons? different than the cluster-wise correction (of mri_surfcluster), and without having to wait the long time that the mc-z simulations (of mri_glmfit-sim) take.

If you're doing whole hemisphere, then you can used the cached mc-z with mri_glmfit-sim. Run mri_glmfit-sim with --help to get more info. There's also stuff on the wiki. doug

Regards, Gabriel.

El 04/04/13, *Douglas N Greve * greve@nmr.mgh.harvard.edu escribió:

...

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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