I have also been getting error messages, after Talairach correction using
tkregister2
*...@# Talairach Failure Detection Mon May 3 09:57:40 EDT 2010
/usr/local/freesurfer/subjects/FS060828cr/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6064,
pval=0.2817 >= threshold=0.0050)
awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk
/usr/local/freesurfer/subjects/FS060828cr/mri/transforms/talairach_avi.log
TalAviQA: 0.93168
z-score: -10
ERROR: Talairach QA check failed!
z-score = -10 <= -6 = threshold
Manual Talairach alignment may be necessary, or
include the -notal-check flag to skip this test,
making sure the -notal-check flag follows -all
or -autorecon1 in the command string.
See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
Linux venus.mbni.med.umich.edu 2.6.18-128.1.10.el5 #1 SMP Thu May 7 10:35:59
EDT 2009 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Mon May 3 09:57:40 EDT 2010*
On 3 May 2010 10:44, Janani Dhinakaran <janinthe...@gmail.com> wrote:
> Hello experts,
>
> I've been having some trouble with the talairach during recon. I followed
> previous instructions and checked the rawavg image and found that it was in
> wrongly oriented.
> The sagittal picture was appearing under coronal but upsidedown, the
> coronal picture was sideways in the transverse section and the transverse
> was in the sagital section. I wonder if there is a place where I can send
> the data for someone to see and tell me how exaclty to flip the orientation
> of it to suit FreeSurfer.
>
> I would also like to know whether there is a shorter way of processing the
> data for only mri-stats without running recon-all for all the subjects' data
> we have.
>
> Thank you
>
> Jan
>
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