On Wed, 5 Jan 2005, Joongnam Yang wrote:
Hi,
Sounds like trivial questions...
(1) How do you check if the talairach.xfm is OK?
You load the mri/orig in tkmedit as main volume, then:
File--> Load Transform for Main Volume --> and select SUBJECTNAME/mri/transforms/talairach.xfm *or* talairach.lta
now you should be able to toggle between the two volumes -- check to make sure the talairach is aligned properly (e.g. corpus callosum, anterior commissure, temporal lobes are roughly where they should be, the entire talairach transform should also be in the field of view)
if one of them is good, then use that one if one of them is bad, rename it to talairach_xfm.bad of neither one is good, remake it by running:
talairach_mgh SUBJECTNAME
(should take about 20 minutes)
2) that depends on what you're using tkregister2 to register -- if you're using it for the talairach transform then you should use it as soon as possible in the process... what volumes are you registering? it can also be used after recon-all to register functional data of course, but this seems an obvious point so probably not what you meant
(2) Either during the command-line option of recon-all -stage 1 thru 4, when do you use tkregister2 for registeration?
Thanks for the help.
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