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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
