Hello,

We are processing T1-weighted MRI from brain tumor patients and aim to run high-quality FreeSurfer recon-all for morphometric analysis.

We are considering this workflow: TumorSynth tumor mask → VBG/virtual-brain correction → recon-all.

Could you advise whether this is methodologically sound? Should tumor cases be handled with VBG/lesion filling before recon-all, by passing a mask directly, or another approach?

Any recommended flags, QC steps, manual edits, example commands, or references would be appreciated.

Best,
Nooshin