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
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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
freesurfer@nmr.mgh.harvard.edu
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Allison Stevens -
Gregg, Brian E.