Hello everyone,
I’m encountering an unexpected issue during label conversion using the following command:
labelconvert aparc+aseg.mgz FreeSurferColorLUT.txt fs_default.txt parc.mif
The input file aparc+aseg.mgz was generated via FreeSurfer’s recon-all pipeline and appears valid (no visible errors in FreeSurfer outputs). Both lookup tables (FreeSurferColorLUT.txt and fs_default.txt) have also been verified.
The output file nodes.mif shows abnormally low signal values (~2+) in the left hemisphere compared to normal tissue values (~50+). Visual inspection in mrview reveals a “hole-like” artifact localized to the left hemisphere (see attached screenshot).
The same artifact does not appear in the right hemisphere.While the warning actually occurs in Thalamus, which clearly not in the surface.
Is this left-hemisphere signal loss considered normal? If not, what troubleshooting steps would you recommend to resolve this issue?
