I'm puzzling over why freesurfer is not including a chunk of white matter in the final surface and how I can fix it. The culprit appears to be the topology fixer. If you look at the attached screenshots, you can see that the offending bit of left frontal lobe is well-connected to the rest of the brain in wm.mgz (and, for completeness, filled.mgz). The yellow surface, which corresponds to lh.smoothwm.nofix, includes the desired white matter. Thus, neither tessellation nor smoothing would seem to be the problem. The green (white matter) and red (pial) surfaces from lh.orig exclude the desired white matter. Thus, I'm assuming the topology fixer is cutting off what it perceives to be a defect... but I can't figure out why or how to fix it. Although I will try, I do not expect that filling in the few missing white matter voxels or adding control points in that region will have any effect. Any other ideas?
