Its possible that the alignment must be performed manually, at the very least confirmed. Use tkregister2 to do this:

tkregister2 --s <subj> -fstal

More instructions are here:

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

Nick

On Wed, 2008-02-27 at 20:19 +1100, wanlin wrote:

Hi, we met some errors as below when we run "recon-all -subjid SUBNAME -autorecon1". Similar questions have been asked in http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06452.html http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06739.html But the answer seems not useful for our situation. We are performing data processing pipeline with 3T MRI volume image. If we add -notal-check, the errors will disappear but we are not sure whether it's ok without Talairach check. Can anyone help us how to deal with them when such errors appeared?

thanks

#-------------------------------------------- #@# Talairach Failure Detection Wed Feb 27 07:43:35 EST 2008 /Data/MAS/FreeSurfer/CPU7/3914_20070206_3dt1/mri

talairach_afd -T 0.005 -xfm transforms/talairach.xfm

talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7627, pval=0.6675 >= threshold=0.0050)

awk -f /usr/local/freesurfer4.0.2/bin/extract_talairach_avi_QA.awk /Data/MAS/FreeSurfer/CPU7/3914_20070206_3dt1/mri/transforms/talairach_avi.log

TalAviQA: 0.94477 z-score: -7 ERROR: Talairach QA check failed! z-score = -7 < -5 = threshold Linux thalamus2007 2.6.23.15-80.fc7 #1 SMP Sun Feb 10 16:52:18 EST 2008 x86_64 x86_64 x86_64 GNU/Linux

recon-all exited with ERRORS at Wed Feb 27 07:43:35 EST 2008

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