I suspect that the bright WM is causing your problem. N4 is run as part of recon-all v7 and beyond. You might try running v8 as that uses synthstrip, which is much more robust.
On 2/18/2026 7:57 AM, Chanelle Hendrikse wrote:
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Dear FreeSurfer developers
I am processing longitudinal 3T T1-weighted data (Freesurfer 7.1.1) from the same scanner and protocol at 3 timepoints across childhood. The first two waves processed without major issues, but in the current pre-adolescent wave I am seeing consistent segmentation failures, mainly in occipital regions (sometimes frontal/parietal). Recon-all “misses” these regions, which were also excluded from the brain mask.
I managed to correct the brain masks by fixing skull stripping (using ms_watershed) and rerunning recon-all, but the segmentation issues persisted. Inspection of norm.mgz suggests residual intensity inhomogeneity as posterior white matter intensity is substantially higher than expected (up to ~140–150). The brain mask also appears brighter here. Could this be causing recon-all to “miss” these regions?
From what I’ve read, a potential solution is running N4BiasFieldCorrection on the raw T1 prior to recon-all (then processing from scratch), and only using control points if needed afterward.
Would this be an acceptable approach, particularly in a longitudinal developmental dataset? Any alternative suggestions are also welcome!
Many thanks in advance for your advice.
Kind regards, Chanelle
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