31 May
2026
31 May
'26
11:12 p.m.
External Email - Use Caution
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