Hi Zheng,
I'll leave 2 for Nick. As for 1, we don't use the tal very much, and a
bad tal will not affect your thickness estimates. The newer versions
rarely have a bad tal since we changed over to Avi Synder's code (which
also fixes the problems we had with eTIV). You can manually correct it
using tkregister2, although this is probably only needed if you want to
report tal coords (or average in tal space).
cheers,
Bruce
On Wed, 8 Apr 2009, gmszh wrote:
Hi all,
I have two problems here.
1. talairach.xfm
By browsing through the mailing list, it seems that talairach.xfm was
not used much in the recon-all process which is quite different from the
table given at
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllFilesVsSteps. We did find
many subjects with bad talairach transformation but reasonable segmentation
and surface reconstruction (version 3.05). Are the results (volumes and
cortical thickness) for those subjects still trustworthy? Can you kindly
clarify the importance of talairach.xfm in the pipeline? And since the new
method of eTIV uses this transformation, is there any way to ensure manual
registration is fine enough to be used for this estimation, if I have to
manually register those subjects mentioned above?
2. recon-all -long
We processed our data with the longitudinal pipeline. So far we only
found 6 subjects failed among 200 subjects (tp1 corrected). All these 6
subjects seemed to have problem during the registration from tp2 to tp1. I
used the command "tkmedit -f tp2.long.tp1/mri/orig.mgz -aux
tp2.long.tp1/mri/orig_tp1_to_tp2.long.tp1.mgz" and realized they were not
aligned. I have tried different cost functions using
"fsl_rigid_registration". All of them gave the same result. Is there any way
I can do the manual registration? I used "fsl_rigid_registration" because no
matter which cost function I specified to recon-all -long, it would call
"fsl_rigid_registration" with corratio as the cost function.
Thanks in advance,
Zheng Hui
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