We did this for the hippocampal subfields (full-FOV T1 and high-res T2 slab), but haven’t implemented anything similar in NextBrain yet. It’s a great suggestion, though, and I’ll add it to the (admittedly too long) to-do list 😉
From: Gabriella Monopoli <gabriella.monopoli@phd.unich.it>
Date: Friday, March 20, 2026 at 3:32 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] NextBrain atlas at different resolution images
External Email - Use Caution
I would like to ask for your advice regarding the use of NextBrain with MRI datasets acquired at different resolutions and coverage.
Specifically, I have:
• A 3D T1-weighted image covering the whole brain with 1×1×1 mm voxel size
• A second T1-weighted acquisition focused only on the brainstem, with higher resolution (0.5×0.5×0.5 mm)
Would it be possible (and methodologically sound) to combine these two datasets within the NextBrain pipeline? In particular, I am interested in whether the high-resolution brainstem scan can be integrated with the whole-brain image to improve segmentation
or analysis in that region.
If this approach is feasible, I would appreciate any recommendations on preprocessing steps (e.g., registration, resampling, or intensity normalization) to ensure compatibility between the two images.
Thank you very much for your help.
Best regards,
Gabriella Monopoli