Hello,
I am trying to use the skullstripping process of recon 1 to clean up the brains before importing into Brainvoyager QX. I convert the files to nifti in freesurfer then to VMR in Brainvoyager with the nifti gifti plugin. When I do this, however, the brain appears to be rotated and using Brainvoyager's manual spacial transformation makes the problem worse.
I've attached a screenshot of the brainvoyager window after importing it through nifti gifti.
Specs if needed: System: ubuntu 16.04 LTS Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
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