Hi Tom

I'll cc Flo who wrote this code (a long time ago!). I think the -brain_atlas flag takes a gca atlas and uses it to avoid large-scale errors, while -atlas uses some built-in statistics about the shape and size of e.g. the cerebellum to avoid erasing it accidentally. Flo can correct me if I'm wrong :)

cheers Bruce

On Tue, 4 Nov 2014, tvg[fs] wrote:

• This is a repost. It seems it did not come trough yesterday.

Apologies if this becomes a double post -

Hi all,

I noticed that during skull stripping the standard recon-all pipeline uses option "-brain_atlas" in the routine "mri_watershed". However documentation of this argument cannot be found in the help section or on the website.

mri_watershed --help | less -p atlas https://surfer.nmr.mgh.harvard.edu/fswiki/mri_watershed?highlight=(atlas)

Is this an undocumented flag or simply a synonym for "-atlas"? Does the "-brain_atlas" flag take an extra argument to specify the atlas?

Thanks, Tom

Specs: Mac OS X 10.8.5 freesurfer-Darwin-lion-stable-pub-v5.3.0 $ mri_watershed --version stable5 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer