It seems that FS5.3 doesn't output this file. I just checked many recons processed using FS5.3 without FLAIR and the file "aparc.DKTatlas+aseg.mgz" is missing in all these recons.
-------- Original Message --------
Subject: Re: [Freesurfer] aparc.DKTatlas+aseg.mgz
Local Time: August 31, 2017 4:04 PM
UTC Time: August 31, 2017 8:04 PM
From: fischl@nmr.mgh.harvard.edu
To: John Anderson <John.anderso@protonmail.com>, Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
"Boyd, Emma" <EBOYD2@mgh.harvard.edu>
Hi John
the atlas isn"t flair-based (and is done before the flair processing). I
thought we always generated both (plus Christophe"s for 3 total), so I"m
a bit confused
cheers
Bruce
On Thu, 31 Aug 2017, John Anderson wrote:
> 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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