Hi Aicha,
Thank you for your quick response. Since I am new to freesurfer I have still a few questions... Thank you in advance for your time!
Where can I read more about building my own template?
On our wiki page there are several pages describing how to build the type of templates that we use in FreeSurfer.
And if I cannot plug this into the adult processing pipeline, what could I do with it?
It depends on how you construct it. The reason why you will not be able to plug it in directly is that some of the other recon steps will not work on infant data.
My ultimate goal would be to compare a neonate (TEA) with a reference template and to see where in the brain the cortical thinning would occur.
So do you want the template space to guide your surface generation or to serve as a "healthy control" template to be compared to or just as a common spatial coordinate space where you can do your comparison?
Best, Lilla
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Lilla Zollei [lzollei@nmr.mgh.harvard.edu] Sent: Monday, November 27, 2017 5:10 PM To: Freesurfer support list Subject: Re: [Freesurfer] neonatal brain
Hi Aicha,
We do have a pipeline and I am trying to get it released by the end of the year.
You should be able to build your own template independent from the adults, but you will not be able to just plug this new one in to the adult processing pipeline.
Lilla
On Mon, 27 Nov 2017, Dijkshoorn, A.B.C. (Aicha) wrote:
Dear all,
I want to build my own neonatal control reference template (n=35)to investigate cortical thickness measures and compare these to neonates with a rare type of bleeding. I read that freesurfer uses an adult reference atlas, but that a neonatal-infant (0-2y) is being made/has been made.
Is this new pipeline yet available in freesurfer? And can I build my own reference template in FREESURFER without interference from an adult brain template?
Kind regards,
Aicha Dijkshoorn
Stagiaire Onderzoek & Onderwijs | Divisie Vrouw en Baby, Neonatologie
Universitair Medisch Centrum Utrecht | Flexruimte voor Verpleegkundigen & Medisch personeel, afdeling Neonatologie | 3508 AB UTRECHT
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