[Freesurfer] Re: 7.2.0 -notal-check talairach.xfm relevant beyond eTIV?

There is only one small spot with talairach.xfm is used, and that is when rescaling after nu_correct. If the nu.mgz and the norm.mgz and the surfaces look ok, then I think you can safely ignore it.

On 12/16/2025 7:05 AM, Dr. Cornelius Kronlage wrote:

     External Email - Use Caution

Dear freesurfer team,

using freesurfer 7.2.0, recon-all fails for some subjects in a certain dataset (denoised MP2RAGEs) for me at this stage:

     #@# Talairach Failure Detection Wed Dec 10 11:30:01 GMT 2025
     /data/output/fs_outputs/sub-007/mri

      talairach_afd -T 0.005 -xfm transforms/talairach.xfm

     ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0056, pval=0.0000 < threshold=0.0050)
     Command exited with non-zero status 1

The talairach.xfm registration indeed looks completely off. However, if I use "-notal-check", recon-all runs through with outputs (surfaces etc.) that look fine. It seems like the talairach.lta created by mri_em_register a couple of steps later is correct and downstream steps use this. The incorrect talairach.xfm only appears to have have an impact on the eTIV estimation (not so relevant for me).

Is it appropriate to run recon-all with -notal-check with an incorrect talairach.xfm but an accurate talairach.lta - or are there other issues this might cause?

Thank you and best wishes,

Cornelius

---

Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.e...