Jeff,

You can skip the talairach quality check by adding the flag -notal-check to recon-all. In versions prior to v4.1.0, the threshold for the check was too conservative, and the z-score threshold has been reduced from -4 to -6 in v4.1.0. I see your score is -4, so that is a valid transform (one that is hard to beat by manually registering with tkregister2).

If you wanted you could also modify your recon-all script to change that threshold. Look for the 'zscoreThreshold' variable, and change it to -6.

Nick

On Wed, 2009-01-21 at 17:58 -0500, Jeff Phillips wrote:

Hi all,

I have an MPRAGE which consistently fails the Talairach quality check (see attached error) in autorecon1. (A 32-channel coil was used in this scan, and I suspect that might be a cause of the failure.) Per the wiki's suggestion, I have tried to manually fix the transform in tkregister2 and rerun reconstruction, but despite multiple attempts, I haven't been able to get a transform which satisfies the quality check. From similar list posts, I thought it might be possible for me to Talairach in an external program (BET, AFNI, etc.) and create a transform file that FreeSurfer can read. If this is possible, could you give me an overview of the process, or point me to existing documentation?

Thanks,

Jeff Phillips _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer