?Good morning,
I am editing a brain using FreeSurfer version 5.1 and I have a pial and white matter boundary issue that persists in the lateral ventricles, specifically where the software would draw a boundary between the right and left hemispheres of the brain. Upon running it through the recon-all pipeline, it reconstructed those ventricle boundaries in a way that the boundaries did not even touch the walls of the ventricles and had the boundary lines cutting through the middle of the left and right lateral ventricles.
After fully filling the ventricles with 255's on the wm.mgz file (to match the general reconstruction of other brains we have worked on), the issue still largely persists. The pial and white matter boundaries now more accurately follow the outer edges of the ventricles but the boundaries that separate the left and right hemisphere are still very messy. This issue can be found in over 60 slices throughout the brain.
Any and all help is appreciated.
Best,
Allison