[Freesurfer] Misregistration of T2 FLAIR during recon-all

Hello,

I’m trying to update recon-all (with freesurfer-6) on a number of subjects using T2 FLAIR images and the following command: recon-all -subjid <subject_name> -FLAIR <path_to_FLAIR.nii.gz> -FLAIRpial -autorecon3

For a substantial portion of subjects, the registration of the FLAIR image to the T1 fails. I’ve run a few trials where I pre-registered the FLAIR to the T1 and made sure the header information was the same (with fslcpgeom), but the registration during recon-all still fails (see images below).

I saw a few posts from a couple years back about a recon-all patch that may fix the registration issue: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg39378.html Is this the best way to deal with this issue?

Thanks very much,

Dan

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