Hi Stef,
The infant FreeSurfer pipeline does rely on an infant training data set. What atlas did you have in mind?
At the moment, there is no way to include a lesion mask into the pipeline, but I would be happy to discuss that option.
Also, for your population, older infants, we have another pipeline you might want to try. Le me know whether you are interested,
Lilla
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Stefanie Bradley stefanie.bradley@mail.utoronto.ca Sent: Monday, March 17, 2025 9:53 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Freesurfer Question - Pediatric pathology
External Email - Use Caution Hi there, I'm working with MRI scans from children aged 3-6 years old. I was wondering if there's a way to integrate pediatric atlases into the Freesurfer recon-all pipeline? I'm also wondering if it's possible to integrate a lesion mask into the pipeline in the case of brain pathology?
Thanks, Stef
STEFANIE BRADLEY
PHD CANDIDATE
Holland Bloorview Kids Rehab Hospital
150 Kilgour Rd, Toronto, ON M4G 1R8
stefanie.bradley@mail.utoronto.ca
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