I know someone that uses something like what is below to avoid using
tkregister:
mri_convert $subject/mri/T1.mgz $subject/mri/T1.mnc
mritotal -protocol icbm $subject/mri/T1.mnc $subject/mri/T1.xfm
mv $subject/mri/transforms/talairach.xfm
$subject/mri/transforms/oldtalairach.xfm
cp $subject/mri/T1.xfm $1/mri/transforms/talairach.xfm
Doug and Nick can correct me if this isn't a good idea. You can do:
mritotal -help
to learn more about it.
Allison
On Sat, 12 Jul 2008, Vina Goghari wrote:
Thanks Nick. I was wondering whether since this is a problem for all my
subjects (n=70) is there anything else that could fix the problem (i.e.
setting some parameter differently etc), so I wouldn't have to do it manually
for every subject?
Nick Schmansky wrote:
Vina,
See this page:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
(you won't need the tutorial data, just use your subject)
Nick
On Sat, 2008-07-12 at 11:05 -0500, Vina Goghari wrote:
Hi all,
I get this error:
Sat Jul 12 10:24:08 CDT 2008
talairach_avi done
#--------------------------------------------
[EMAIL PROTECTED] Talairach Failure Detection Sat Jul 12 10:24:08 CDT 2008
/pkg/bliss_all_labs/tricam/FEP_Aro/cbx02/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
***FAILED*** (p=0.0069, pval=0.0000 < threshold=0.0050)
Linux bliss 2.6.9-67.0.15.ELsmp #1 SMP Tue Apr 22 13:58:43 EDT 2008 x86_64
x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Sat Jul 12 10:24:08 CDT 2008
So I viewed the talairach transform using tkregister2 and this is what I
see for target and moveable. How would I go about fixing something like
this:
See attached images.
Thanks,
Vina
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