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Hello FreeSurfer Developers,

I'm attempting to map CT-electrode-xyz coordinates to Freesurfer space. Now, there are two approaches:

1. Coregistering CT -> T1 MRI and then localizing contacts on the CT_in_T1 image volume 2. Localizing contacts in CT and then mapping those coordinates with the affine transformation

Afterwards, I have a Nx3 matrix denoting the CT-xyz coordinates in the T1 image volume space. I usually run this with the T1.nii nifti image created from the raw .dicoms. However, my impression of the surfaces and overall Freesurfer analysis is that they are resampled into "Freesurfer space". The problem with this is then any sort of analysis to try to link the CT-xyz coordinates to any parcellation, or analysis done by FreeSurfer isn't correct (I am pretty sure). My end goal is to map these electrode coordinates to either:

1. White matter contact 2. Gray matter contact - mapped to an atlas label 3. Outside brain contact - if it lays outside the brain

I am wondering how I can perform the NativeSpace -> FreeSurfer space mapping.

I looked at the following:

1. https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat which explains how to convert surfaces/volumes/coords to Native Space, but I want to do the reverse. It seems that it is possible for me to just map all the surfaces, volumes, etc. of interest into native space, but that seems like a lot of extra work compared to doing what I am proposing. Any comments on the pros/cons of either approach would also be helpful!

I've searched the list and no one has had a detailed similar problem. Does anyone have any thoughts on how to go about this and can also possibly provide a link to more information that can explain things further?

Thank you!

Best Regards,

Adam Li PhD Student in Biomedical Engineering Johns Hopkins University & School of Medicine