Hi Emma,
Thank you for your response. 
I am running my recons using V5.3 and V6.0
In the data base I have ~200  T1 images and for some I have FLAIR images.
When I run recon all with the flag FLAIR I get the file "aparc.DKTatlas+aseg.mgz" in FS5.3 and FS6.0
If I run recon-all without the flag FLAIR i don't see the file aparc.DKTatlas+aseg.mgz
as an output of FS5.3 or FS6.0

I am a bit confused about this!! Is this atlas FALIR-based or I am doing something wrong?!




-------- Original Message --------
Subject: Re: [Freesurfer] aparc.DKTatlas+aseg.mgz
Local Time: August 31, 2017 3:11 PM
UTC Time: August 31, 2017 7:11 PM
From: EBOYD2@mgh.harvard.edu
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>, John Anderson <John.anderso@protonmail.com>


Hi John,

Which version of FreeSurfer are you running?


Emma


---------

Emma Boyd

Research Technician II

Laboratory for Computational Neuroimaging

Martinos Center for Biomedical Imaging


From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of John Anderson <John.anderso@protonmail.com>
Sent: Thursday, August 31, 2017 12:17 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] aparc.DKTatlas+aseg.mgz
 
Dear experts,
looking into the output of Freesurfer in this page https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllOutputFiles
I see that there should be a file named "aparc.DKTatlas+aseg.mgz". Is this atlas can be generated with the presence of FLAIR images.

When i run recon-all without FLAIR or T2 I don't see this atlas!! Is this atlas FLAIR -based?

thank you for any clarification
John

-------- Original Message --------
Subject: aparc.DKTatlas+aseg.mgz
Local Time: August 30, 2017 7:49 PM
UTC Time: August 30, 2017 11:49 PM
From: John.anderso@protonmail.com
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>

Dear experts,
looking into the output of Freesurfer in this page https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllOutputFiles
I see that there should be a file named "aparc.DKTatlas+aseg.mgz". Do I need FLAIR images to get this file.

I ran the command recon-all --s subj --all and I can';t find this file


thank you for any clarification
John


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