The way you probably want to do this is to register the CT to the MRI (bbregister, creates an LTA registration file), then run mri_vol2surf, passing it the LTA you created with bbregister. Then just load the result as an overlay in freeview and specify whatever surface you want (white, pial, inflated). It is generally set up to sample inside the brain, so when you run mri_vol2surf, you may have to play with it a little bit to make sure that it samples the electrodes. You can try using the  pial surface instead of the white (--surf) and use --projdist-max. Run any of the programs with --help to get more details.

Hi Freesurfer developers,

I am rather new (a few days in fact) to Freesurfer, so forgive me if I have some lack of knowledge.

I am currently working with T1 MRI and CT scans of patients that are undergoing epilepsy surgery, and am interested in using the transformation that freesurfer uses to "inflate" the cortical surface into a sphere for "inflating" the electrode contacts onto the spherical surface as well. 

However, I am not sure if Freesurfer saves this transformation matrix done on the cortical surface? If so, is there a way I can extract that? 

Thank you!

--

Best Regards,

Adam Li

Graduate Student in Biomedical Engineering

Johns Hopkins University & School of Medicine

(805) 807-5898 | LinkedIn | Personal Website | ali39@jhu.edu

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