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Dear Freesurfer experts,

I ran a glm analysis a while back and corrected for MC using the glm-fit_sim --cache option / Monte Carlo simulation. I now saw that the AlphaSim algorithm this is based on is not recommended anymore (https://secure-web.cisco.com/1A4g1vq2U_gugbf-mlVAUZcEyLmp9YkEcL2Vw_tFG_wyrNF...). Instead, it suggests using 3DClustSim.

1. Does that mean the Monte Carlo simulation as it is implemented in FreeSurfer does not allow for valid analyses / MC corrections anymore?

2. Is 3DClustSim implemented in Freesurfer? And if not, would I need to export the FreeSurfer files as a volume (i.e. 3D) file and analyse it externally?

What would you recommend? (My analysis is a regression analysis for one group, so the design matrix is not really suitable for a permutation).

Thanks in advance,

Meike