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Hi Lilla,
Thank you for your quick response!
Infant freesurfer is only for use up to age 2, right?
I would be interested in trying the pipeline for older infants.
And also willing to discuss the lesion issue too.
Thank you!! Stef
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Zollei, Lilla,Ph.D. LZOLLEI@mgh.harvard.edu Sent: Monday, March 17, 2025 10:11 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Question - Pediatric pathology
You don't often get email from lzollei@mgh.harvard.edu. Learn why this is importanthttps://secure-web.cisco.com/1QHz0vejszmx5Kj6r4Ul601cxmQg56xAqNuanZUrCBVxYISNhRTmOnvx011OtERPHG7mPiQ7tR27snyQx9IDb0jhhSBuZxxpZbNVXg3g9ZJdoZT18A5GySxCGbBc7m0LIA8P42XHIf8StHHkOQlYS4shYdoqjTaxAOsfxJmqp-3U4xjBseicaMpodscVJl2-HV3-dCRh008dAlQdsoYxiSGafIgL7dqk13GJixIqiwE0eF_tHzD_L4qYN3mgl70jOrVJEy2QqpRxgY6jQkrupzrvRcW4Z6f85mhFz69ckV3Q4u0Wo3bXzKWlFC6e6xnqE/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification 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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