I'm not sure what is going wrong. The FLAIR looks a little strange to me but it is hard to judge without being able to load it in freeview. I would probably not use the FLAIR. If you have the option to upgrade to 8.2, I would do that as much of the benefit of the FLAIR is realized in 8.2 without a FLAIR.

On 4/3/2026 7:55 PM, Boa Sorte Silva, Narlon wrote:

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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>

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