How to save beta maps from the first level GLM?

I am trying to use beta maps for second-level GLM analysis.
However, I cannot find a way to save the beta maps from the first-level GLM function. Does anyone know how to save the beta map as nii file?

I also found that nilearn default setting of the 2nd level ‘effect_size’ map. Is ‘effect size’ map beta map?

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Yes - see this code snippet in second-level analysis:

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Just to +1 @HaoTing_Wang 's answer, you can find this idea in the narrative documentation here :slightly_smiling_face:

https://nilearn.github.io/auto_examples/plot_single_subject_single_run.html#detecting-voxels-with-significant-effects

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I am also trying to understand this.

In the link there is:

1. Does this mean that in order to get a beta map (as the beta_xxxx.nii from SPM), we need to use effect_size as input argument?

2. And the z_score argument will produce the z-scored version of the t-map produced from the beta map?

  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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Clear. Thanks for clarifying this!

I’m sorry I have the same problem. I need a second-level GLM analysis between groups. Do I understand correctly that I need to save contrast maps between selected events at the first GLM level in order to calculate the contrast between groups at the second GLM level?

Excuse me, if you managed to perform a second-level analysis for fNIRS data, can you tell the sequence? Please , I 'm desperate , I can 't do anything