Hello Freesurfer List, I am looking to use freesurfer to analyse MRI images from some patients which have diverse traumatic pathology, with gross lesions occurring in WM and GM as well as some occurring across the boundary. I have run these through recon-all with freesurfer v6 but am concerned about the ability of the Taliarch transform step to spatially normalize the images due to the distortions introduced by the lesion.
I would therefore like to use an enantiomorphic approach such as Nachev et al (2008) Neuroimage using a replacement approach which mirrors volumes from the undamaged hemisphere to 'Fill' the lesion. If I was to do this, what would I need to generate to feed into the freesurfer pipeline and what would I replace? I assume I would need to rerun recon -all without the Taliarch step and use the new output instead? Will these lesions effect any other downstream functions such as the registration step or do these use the taliarch transform? Any help would be greatly appreciated! Best wishes, Dan King
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