You can also look in pctsurfcon. This compute the percent gray/white contrast. It does so on the T1w, but you could look inside the script to see how it does it and adapt to your situation.

On 2/23/2022 3:26 PM, Adam Martersteck wrote:

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Hi Dylan,

Give this a try:
fscalc gm_lh.nii.gz div wm_lh.nii.gz --o gmwmratio_lh.nii.gz

On Wed, Feb 23, 2022 at 12:24 PM Tisdall, Dylan <mtisdall@pennmedicine.upenn.edu> wrote:

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Hi all,

I've generated two surface overlays, using mri_vol2surf with positive and negative projfrac to get a GM and WM samples (gm_lh.nii.gz and wm_lh.nii.gz). I'd now like to take the vertex-wise ratio of these two overlays, and make a new one (gmwmratio_lh.nii.gz). I've tried doing this as:

fslmaths gm_lh.nii.gz -div wm_lh.nii.gz gmwmratio_lh.nii.gz

but the result is:

Image Exception: #22 :: Failed to read volume gm_lh.nii.gz
Error : Error: Nonsensical ROI for gm_lh.nii.gz

Is there another tool I can use to compute this ratio? Is there a better workflow than making two surfaces and dividing?

Thanks,
Dylan

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