Yes, that would be great if you guys could take a look. What's the process to upload?
Thanks, Vina
Bruce Fischl wrote:
do you want to upload one of them for us to look at? On Wed, 16 Jul 2008, Vina Goghari wrote:
I would say it's pretty typical. I tried a random set of 4 subjects of the ~70 and I get the same error and similar mis-alignment between talairach and original.
Any thoughts?
Thanks, Vina
Doug Greve wrote:
That would just do the conversion, it won't fix the problem. Does this happen with all your subjects? How is the quality of your T1s (the one you sent looks a little funny).
doug
Allison Stevens wrote:
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 > #-------------------------------------------- > #@# 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 > > > ------------------------------------------------------------------------ > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
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