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
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
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
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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi John,
I don't believe this atlas is FLAIR based. Could you please attach a recon-all log for one of these subjects?
Thank you,
Emma
________________________________ 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 3:25:43 PM To: Boyd, Emma Cc: Freesurfer support list Subject: Re: [Freesurfer] aparc.DKTatlas+aseg.mgz
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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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: 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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Right, I think this is a new file with version 6.
On 08/31/2017 04:32 PM, John Anderson wrote:
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: 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
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
The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners
Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to
you in error
but does not contain patient information, please contact the sender
and properly
dispose of the e-mail.
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Bruce Fischl -
Douglas N Greve -
John Anderson