[Freesurfer] Starting with brain-extracted volume?

2006-07-13 Thread Graham Wideman
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 Thi

Re: [Freesurfer] Starting with brain-extracted volume?

2006-07-13 Thread Bruce Fischl
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 Jun

Re: [Freesurfer] Starting with brain-extracted volume?

2006-07-13 Thread Nick Schmansky
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 print

Re: [Freesurfer] Starting with brain-extracted volume?

2006-07-13 Thread Graham Wideman
OK Nick thanks, that's good insight into the intent behind the noxxx options etc. Graham At 7/13/2006 06:38 PM, Nick Schmansky wrote: >Graham, > >In general, you should be careful [...] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https: