Thank you Dr Bruce,
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.
I see aseg.mgz, aseg+aparc.mgz and wmparc.mgz
> -------- 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: fis...@nmr.mgh.harvard.edu
> To: John Anderson <john.ande...@protonmail.com>, Freesurfer support list
> <freesurfer@nmr.mgh.harvard.edu>
> "Boyd, Emma" <ebo...@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: ebo...@mgh.harvard.edu
>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>, John Anderson
>> <john.ande...@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-boun...@nmr.mgh.harvard.edu
>> <freesurfer-boun...@nmr.mgh.harvard.edu> on
>> behalf of John Anderson <john.ande...@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.ande...@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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