Yes, 3 is p<.001, which is converted to a z before thresholding the map. Note that we are trying to push people to use permutation instead of MC.

On 07/09/2018 05:22 PM, Dincer, Aylin wrote:

Hi FreeSurfer experts,

I am trying to understand the Monte Carlo Z simulation in FreeSufer (/mri_glmfit/-/sim/) and have a question about the vertex wise /cluster forming threshold.

In the simulation, a vertex wise threshold (ex. -cache 3 abs) is set and the threshold is applied to a z map. Is the 3 threshold (p value of 0.001) converted to a z score using the z table before it is applied to the map?

Thanks!

Aylin

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