Hi Graham,
the EM Registration with Skull is for generating ICV measures, which of
course you won't be able to get with the skull gone.
Bruce
On Thu, 13 Jul 2006,
Graham Wideman wrote:
Nick, Doug or anyone with thoughts on the matter,
This is a return to a similar question I raised in June-2nd thread "Some FS input
questions", but a little less awkward.
We'd like to present to FS already brain-extracted volumes that are already
"conformed", ie: 256^3, and 1 mm isotropic
This would appear to avoid the necessity to turn off aseg (mentioned by Nick in
previous thread).
I also see the enticing looking options like "noskullstrip", but... I'm wary of
two things:
a) In general, when you select a "nosomething" option, does recon-all do the right thing
to "pass the data through" (usually a copy I suspect) so that subsequent steps receive
their input file(s)?
b) There may be steps that expect the skull or neck to be in place? "EM Registration
with Skull" (skull-lta) sounds like it might be one?
So I'd like to know if there are such, and whether I should care?
According to my chart here:
grahamwideman.com/gw/brain/fs/fsunderstanding2006/processvsdata2006.htm
...looks like I *should* be able to bypass rmneck and skull-lta (or just let
them run unsatisfactorily) with no downstream impact.
Any thoughts?
Thanks,
Graham
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