Hi Mike,
it is used a bit in mri_fill I think, although it might actually have
been removed now that we use the aseg. There is also the option of using
it to initialize the spherical morph, but that is disabled by default, so
it's not used very much. Generally as long as it's not dramatically wrong
it won't effect the processing, but will of course mean the tal coords
you report are wrong.
cheers,
Bruce
On Fri, 12 Oct 2007, Michael Harms wrote:
Is talairach.xfm even used as input for any stage of autorecon2 or 3?
(Or, is it just the talairach.lta and talairach.m3z files?)
thanks,
Mike H.
On Thu, 2007-10-11 at 16:28 -0400, Doug Greve wrote:
It is not that important from a recon standpoint. However, if you intend
to report talairach coods, create an average surface, or use that
talairach transform in any way, it will be a problem.
doug
Michael Harms wrote:
Hello,
We are running FS v3.0.5 on some elderly brains, and the talairach
transform (as assessed via tkregister2 with fstal flag) is inaccurate in
an appreciable number of the scans we have examined so far. Frequently,
the inaccuracies involve primarily scaling or translation, although in
one instance the rotation was way-off (such that the cardinal axes were
basically swapped). However, even for this worst case, the white and
pial surfaces, as well as the aseg, look reasonable. (I haven't run
autorecon3 to create the surface parcellations yet).
To what extent is talairach.xfm important for the autorecon2 & 3 stages?
If surfaces and aseg look ok, can an inaccurate talairach.xfm just be
ignored if we are not going to be averaging functional data? Will the
surface parcellations perhaps be affected somehow?
Looking at ReconAllDevTable it appears that talairach.lta and
talairach.m3z are the primary inputs to stages 2 and 3. So, I'm
wondering how the .xfm relates to the .lta and .m3z files...?
Lastly, the particularly bad .xfm under v3.0.5 looks fine when created
using v4.0.1. If we need or want accurate .xfm's would it be
appropriate to run autorecon1 under v4 but then switch to v3 for
autorecon2 & 3 so as to maintain compatibility with other subjects
processed under v3?
thanks,
Mike H.
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