How to save beta maps from the first level GLM?

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  1. Pure beta maps will come from individual conditions (that is, those that go into a contrast). The effect size here would be analogous to the “con_XXX” maps from SPM.
  2. Yes. You have beta maps for your individual conditions, contrast maps for the difference between the beta maps, t-maps for the statistical significance of the contrasts, and z-maps for a normalized version of the t-maps. Outputting the z-score will get you directly to the last step, which will likely be useful for the next step in your analyses.

Hope this helps,
Steven

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