Dear Jessica,

You can register your image to the atlas, and then apply the same transform to the segmentations (“propagate”). That will bring the segmentations to atlas (Brainnetome) space.

I hope this helps,

Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://www.jeiglesias.com

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Jessica Bourgin <jessica.bourgin@univ-smb.fr>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, 7 August 2019 at 13:44
To: freesurfer <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Transform hippocampal/amygdala segmentation to another space

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Dear Juan Eugenio,

Thanks a lot for your quick response.

I don't understand what you mean exactly by "propagate the hard segmentations".

And when you say to register the subjects to the Brainnetome, do you mean replace the atlas used by recon-all to do that ? (sorry, I am currently a PhD student with little experience in neuroimaging).

You also mention that the transformation is not trivial. But do you think this is "correct" to make it ?

Thanks for your help !

Cheers,

Jessica BOURGIN
Laboratoire de Psychologie et Neurocognition
CNRS UMR 5105
Université Savoie Mont Blanc (USMB)
BP 1104
73011 Chambery Cedex France