We have imported Freesurfer 6.0 models and EEG data into Brainstorm and are now trying to understand the effect of injury and misalignment of C1/C2 vertebrae on brain function. I have a CT scan of the cervical spine. What would be the best way of building a 3D model that could be registered with my anatomy files so as to be able to be viewed in Brainstorm?
Thanks,
-Matt
I’m not sure what you expect from constructing a model of the spine in Brainstorm. The forward models available in Brainstorm are designed to estimate the brain sources: cerebral cortex and cerebellum.
If you simply want to have additional for display in Brainstorm, you’d need to find a way to create a mask of the structures you are interested in, and then find a way to create a mesh based on these masks, then import the meshes in Brainstorm. But I don’t know how to help you with this.
Thanks Francois, yes I am simply looking to have it displayed in place for context. Currently we switch between BrainStorm and other 3D software to facilitate discussion. It would be easier if they were all in the same place.
We can easily combine, for example, 3D models of the brain with 3D models of upper cervical spine, but were hoping to be able to use the combined model in our BrainStorm analyses.
For now, we will just leave them separate.
Kind regards,
-Matt
So your questions are related only to display, not to source computation?
It’s a bit difficult to give you technical answers without knowing exactly what you have in input and what you’d like to have in output, but there are maybe solutions with existing tools in Brainstorm. For instance, if you have 3D masks or atlases in patient’s space or MNI space, you could import them directly as volumes, as meshed surfaces or as 3D source atlases:
https://neuroimage.usc.edu/brainstorm/News#Volume_atlases
If you need any additional directions for us, please post screen captures explaining what you’re expecting to observe and the types of files you have in input.