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