Thank you for the prompt response. You sent exactly what I wanted. Everything worked great!
Brian
-----Original Message----- From: Allison Stevens [mailto:astevens@nmr.mgh.harvard.edu] Sent: Tuesday, November 19, 2013 8:03 AM To: Gregg, Brian E. Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] hippocampus region in an atlas?
The entire hippocampus is currently labeled by default in the recon-all stream. You can see it in the aseg.mgz (in the mri directory) and find volume information in stats/aseg.stats.
To get the hippocampal subfields you have to run recon-all with an additional flag. This is documented here:
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation
Allison
On Tue, 19 Nov 2013, Gregg, Brian E. wrote:
Hello,
I didn’t see hippocampus listed in the Desikan-Killiany, Destrieux, or DKTatlas40 atlases. Is there an existing atlas that contains the hippocampal subfields? If not, what options exist for getting the hippocampus into an atlas?
Thank you,
Brian