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I have not used TumorSynth, so I can't speak to that. But I have used tumor masks a colleague made using ITK-SNAP with manual edits as input to VBG:

Radwan AM, Emsell L, Blommaert J, Zhylka A, Kovacs S, Theys T, Sollmann N, Dupont P, Sunaert S. Virtual brain grafting: Enabling whole brain parcellation in the presence of large lesions. Neuroimage. 2021 Apr 1;229:117731. doi: 10.1016/j.neuroimage.2021.117731. Epub 2021 Jan 14. PMID: 33454411.

VBG calls recon-all as part of its pipeline.

I ran 80 tumor patients through this process, and 54 of them turned out well. Seven of them had messy brainmasks (even beyond the tumor). Five of them had "funky fills", e.g.:

https://secure-web.cisco.com/1URCXEdfnF5nMqwz2hNRwwe4JJ-USXxr-5-pDgbgJzIIRt1...

We were primarily interested in the contralateral hemisphere, and using freesurfer's hemisphere specific flags didn't work for us reliably, though it's not designed for tumor patients. (Maybe freesurfer 8 clinical/robust?) Our priorities shifted and I transferred to another lab, so it didn't make it to publication.

Ahmed Radwan was very responsive whenever I needed help. I even attended his dissertation defense virtually!

________________________________ From: nooshin Safari noonoosh91@gmail.com Sent: Sunday, May 31, 2026 10:07 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Question on FreeSurfer recon-all workflow for brain tumor MRI

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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

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