Dear all,

I’m having troubles getting a good Freesurfer output from a hemispherectomised 
brain using recon-all. I was wondering whether there’s someone that has 
experience with running Freesurfer on such an unusual brain?

The first couple of issues I bumped into were failures regarding the talaraich 
alignment which I solved using registration matrices from FSL.

The issue I’m having now regards the labeling of subcortical structures. 
Apparently Freesurfer cannot deal with the fact that there’s just one 
hemisphere, and the fact that there is no clear corpus callosum. It looks like 
it’s trying to divide one hemisphere into two, which obviously messes up the 
subcortical labelling.
Any ideas on how to work around this issues?

Is there maybe a way to mirror the intact hemisphere pretending to form a full 
brain? Or are there any flags I can use to make sure the subcortical labelling 
works fine?

Thanks in advance

Hinke N. Halbertsma, MSc

PhD Student
University Medical Center Groningen (UMCG)
Department of Ophthalmology
NeuroImaging Center (Antonius Deusinglaan 2,  9713 AW Groningen), room 124
T. (+31) 050 363 4431

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