Rendering Freesurfer regional volumes in Effect size or Z-score ColourMaps


I am analyzing the volume of 20 Freesurfer automated segmented structures, which can be visualized label statistics as per FreeSurfer’s atlas labels.

As I have several MR subjects, groups and time points, without creating a GLM .mgh Freesurfer files, is it possible to input each of the group mean differences (e.g. Cohen’s d effect size or Z-score) and project these difference with color-gradient labels?


There’s nothing pre-programmed for that exact calculation I think, but it should be pretty straightforward to write a script for that. You can get all the scalar data as numpy arrays and perform all the statisics.

Thanks, Steve. I think I wasn’t clear with my question. I already have the effect sizes statistics. I just need to input these numbers so that I can get a color-gradient label maps. Is it possible, and where, to input the effect size or Z-scores in color-gradient?


Okay, thanks for the clarification. Are these z scores defined per-vertex of the freesurfer model? If so you can assign these as scalar field data for the model, easiest to do that with a numpy array, something like this.

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