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, /E

-- 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

External Email - Use Caution 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