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

**URL:** <https://discourse.slicer.org/t/rendering-freesurfer-regional-volumes-in-effect-size-or-z-score-colourmaps/11692>\
**Category:** Support\
**Tags:** segmentation\
**Created:** [May 25, 2020, 12:57pm UTC](https://discourse.slicer.org/t/rendering-freesurfer-regional-volumes-in-effect-size-or-z-score-colourmaps/11692 "2020-05-25T12:57:53Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![p.wib](https://avatars.discourse-cdn.com/v4/letter/p/77aa72/32.png) [@p.wib](https://discourse.slicer.org/u/p.wib)\
**Post date:** [May 25, 2020, 12:57pm UTC](https://discourse.slicer.org/t/rendering-freesurfer-regional-volumes-in-effect-size-or-z-score-colourmaps/11692/1 "2020-05-25T12:57:54Z")

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Hi

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?

Thanks!  
Pierre

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**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [May 25, 2020, 4:13pm UTC](https://discourse.slicer.org/t/rendering-freesurfer-regional-volumes-in-effect-size-or-z-score-colourmaps/11692/2 "2020-05-25T16:13:34Z")

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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.

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**Author:** ![p.wib](https://avatars.discourse-cdn.com/v4/letter/p/77aa72/32.png) [@p.wib](https://discourse.slicer.org/u/p.wib)\
**Post date:** [May 26, 2020, 1:27am UTC](https://discourse.slicer.org/t/rendering-freesurfer-regional-volumes-in-effect-size-or-z-score-colourmaps/11692/3 "2020-05-26T01:27:29Z")

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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?

Thanks

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**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [May 26, 2020, 5:45pm UTC](https://discourse.slicer.org/t/rendering-freesurfer-regional-volumes-in-effect-size-or-z-score-colourmaps/11692/4 "2020-05-26T17:45:42Z")

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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](https://gist.github.com/pieper/f9da3e0a73c70981b48d0747132526d5#file-guide-py-L48-L54).

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**Author:** ![coco](https://avatars.discourse-cdn.com/v4/letter/c/8797f3/32.png) [@coco](https://discourse.slicer.org/u/coco)\
**Post date:** [March 12, 2024, 3:47pm UTC](https://discourse.slicer.org/t/rendering-freesurfer-regional-volumes-in-effect-size-or-z-score-colourmaps/11692/5 "2024-03-12T15:47:07Z")

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Hi Pierre, I have the same paradigm here (trying to visualise segments based on size statistics. wondering if you managed to get this to work ?  
If so, could you share a script, please ?  
s