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On Apr 2, 2026, at 10:03 AM, Boa Sorte Silva, Narlon narlon.silva@ubc.ca wrote:
Hi there,
I am running recon-all (freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460) on a number of participants with both T1w and FLAIR images.
For some participants, we noticed that the pial segmentation does not improve as a result of using the FLAIR (screenshot #1 attached, lh.pial.FLAIR in red). In checking the mri subfolder files, I notice that the was some type of error with the FLAIR.prenorm.mgz —> FLAIR.norm.mgz conversion (screenshot #2 and #3). The log is also attached.
I wanted to ask if there’s a way to prevent this from happening or should I just go with the T1w-only recon-all in these cases?
For context, I have tested FLAIR with preprocessing (biasfield correction, denoising, registration to T1w space) and without preprocessing, same outcome.
Thanks for your help!
Best regards Nárlon <Surfaces.png> <FLAIR.prenorm.png> <FLAIR.norm.png> <recon-all.log>
