If you are trying to obtain a Desikan-Killiany atlas from a lesioned brain you can't process with FreeSurfer, you could try processing it using CAT12 or FastSurfer:
- https://neuroimage.usc.edu/brainstorm/Tutorials/SegCAT12
- https://neuroimage.usc.edu/brainstorm/Tutorials/SegFastSurfer
Alternatively, if your initial plan was to work with the AICHA atlas, you can work with volume head models and volume scouts:
https://neuroimage.usc.edu/brainstorm/Tutorials/TutVolSource
Sorry for the response delay...