Dear Matthieu,

Which version did you use? The FireANTs version, I presume?

Can you please share some screenshots of the incorrect registration?

Cheers,

/Eugenio

 

--

Juan Eugenio Iglesias

http://www.jeiglesias.com

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Chourrout, Matthieu <m.chourrout@ucl.ac.uk>
Date: Tuesday, May 13, 2025 at 6:17 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Cc: Keenlyside, Andrew <andrew.keenlyside.23@ucl.ac.uk>
Subject: [Freesurfer] Run NextBrain on a high-res 3D dataset: tweaks required for 200um on Edlow brain?

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Hi Freesurfer Community,

 

The NextBrain page showcases the results of the pipeline on the Edlow brain binned at 200um, but we weren't able to reproduce this on our data with a voxel size < 300 um (thus we binned the data). With my colleague Andrew, we've pinpointed the issue to the cartoon fitting step.

 

On what system was the NextBrain run at this resolution? I assume it was run on CPU only? Did you have to tweak the cartoon or other key steps to make it run?

 

Best regards,

 

Dr Matthieu Chourrout orcid logo 16px

Research Fellow on Correlative X-ray Imaging for the Large-scale Imaging of Neural Circuits

UCL Mechanical Engineering

Materials, Structure and Manufacturing at Harwell (MSMaH)

Rm 4.17 Malet Place Eng. Building, Torrington Place, London, WC1E 7JE

Bloomsbury Campus, University College London