Graham,
In general, you should be careful when selecting the '-nosomething' options, as recon-all does not perform much checking for these flags (only the -autorecon1,2,3 flags contain the validity checks).
An option when experimenting with the flags is to use the -dontrun flag, which just prints all the commands it will run without executing. Then you can manually check for validity.
Also, perusing the recon-all script is the next best thing. In the case of the -noskullstrip flag, this just skips the mri_watershed block of code, so that means brainmask.auto.mgz is not created.
This means, I suppose, that you could just name your own skullstripped volume brainmask.auto.mgz (and copy that to brainmask.mgz, which is the one that should be edited, if need be), and then run:
recon-all -autorecon2 -normneck -noskull-lta
Nick
On Thu, 2006-07-13 at 13:10 -0700, 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer