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