Hi Jamie,

I think:

recon-all -gca <new atlas> ...

should do the trick (at least it's supposed to)

Bruce On Mon, 4 May 2009, Jamie Hanson wrote:

Hi Freesurfer folks-

So I have been trying to create a custom aseg atlas (which I did, thanks much to Bruce and Nick!)... Now I want to run recon-all w/ that new custom aseg atlas (on additional subjects not included in .gca / atlas creation)...

I checked the web and the listserv archive, but might have missed it... Is there an easy way to simple specify this new aseg atlas to run w/ recon-all? Or do I just need to run each command for autorecon1 and autorecon2 and just replace the default .gca file when I run mri_em_register, mri_watershed, mri_ca_normalize, mri_ca_register, mri_remove_neck, and mri_ca_label?

Thanks much! jamie.