Hello,

I am trying to use MRIcroGL via a notebook to generate a volume with edges from a cluster image. However, the save function, gl.saveimg(), seems to be limited to saving the bg image. Is there any way you can specify an overlay for saving to an .nii image?

MRIcroGL is a visualization tool not a image processing tool. If you are proficient in Python, nibabel allows you to load images and apply many methods. fslmaths is another outstanding tool. You might even like my clone of fslmaths:

https://github.com/rordenlab/niimath