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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
