Hi Hinke

mri_em_register, mri_ca_label, mri_ca_register and mri_ca_normalize all take -lh and -rh commands to indicate that only one hemisphere exists. Try including them and see if it fixes things (you should be able to use expert options for this). We have only used it for ex vivo analysis in the past, but hopefully it will do the trick for you


On Wed, 12 Oct 2016, Halbertsma, HN (ohk) wrote:

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

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
E. h.n.halbert...@umcg.nl

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