How to save beta maps from the first level GLM?

hawe66 · July 20, 2021, 8:12am

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?

HaoTing_Wang · July 20, 2021, 11:00am

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

github.com

nilearn/nilearn/blob/ed9f2176df06a6cca1f2afcf4a614eab030c2dba/nilearn/glm/second_level/second_level.py#L206-L212


elif isinstance(second_level_input[0], FirstLevelModel):
    # Get the first level model maps
    effect_maps = []
    for model in second_level_input:
        effect_map = model.compute_contrast(contrast_def,
                                            output_type='effect_size')
        effect_maps.append(effect_map)

emdupre · July 20, 2021, 2:45pm

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

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