Hi Stefanie,
We have an in-house preschooler version of the script and for 4.5 / 5 yr-olds
(depending on your data quality) you could also try to use the regular
pipeline. We also wrote up a manual QC / editing guideline for 4-6 year-olds
that you might want to look at:
https://surfer.nmr.mgh.harvard.edu/fswiki/ChildBrainManualEdits
Lilla
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Stefanie Bradley
<stefanie.brad...@mail.utoronto.ca>
Sent: Wednesday, March 19, 2025 9:55 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Freesurfer Question - Pediatric pathology
External Email - Use Caution
Hi Lilla,
Just following up about this Freesurfer question. I've been using the NIH
pediatric atlas for children aged 4.5-8 years old for parts of my analysis.
I'd be interested in hearing about the pipeline for older infants that you
mentioned?
Thank you,
Stefanie
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Stefanie Bradley
<stefanie.brad...@mail.utoronto.ca>
Sent: Monday, March 17, 2025 10:29 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Freesurfer Question - Pediatric pathology
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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
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From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zollei, Lilla,Ph.D.
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Sent: Monday, March 17, 2025 10:11 AM
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Subject: Re: [Freesurfer] Freesurfer Question - Pediatric pathology
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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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Stefanie Bradley
<stefanie.brad...@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.brad...@mail.utoronto.ca
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