Joel,

This page gives some info on how to correct a bad alignment:

http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach

but first I would inspect the nu.mgz file with tkmedit to make sure it looks ok.

Nick

On Thu, 2008-02-28 at 16:42 -0600, joel bruss wrote:

I was trying to run a single sujbect through recon-all and got the following error:

Thu Feb 28 16:34:57 CST 2008 talairach_avi done

cp transforms/talairach.auto.xfm transforms/talairach.xfm

#-------------------------------------------- #@# Talairach Failure Detection Thu Feb 28 16:34:58 CST 2008 /fmri/studies/retinotopic/new_retinotopic/3362/3362_resampled.dir/freesurfer_pipeline.dir/sub1/mri

talairach_afd -T 0.005 -xfm transforms/talairach.xfm

ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Linux dendrite 2.6.22.16-0.1-default #1 SMP 2008/01/23 14:28:52 UTC i686 i686 i386 GNU/Linux

recon-all exited with ERRORS at Thu Feb 28 16:34:58 CST 2008

I don't speak FreeSurfer and don't understand this error. Please help.

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