We're running QA on Freesurfer's aseg and aparc+aseg volumes. On the aparc volume we're noticing fairly large unknown regions in what should be entorhinal cortex, specifically where it comes up against the hippocampus and amygdala. The aseg volumes label these unknown regions as cortex. I've searched the archives and haven't been able to find anything similar from recent years. I've attached some axial screenshots of the raw T1, the aseg and the aparc+aseg.
what version of FS are you using?
On 09/07/2017 03:19 PM, Aidan Murphy wrote:
We're running QA on Freesurfer's aseg and aparc+aseg volumes. On the aparc volume we're noticing fairly large unknown regions in what should be entorhinal cortex, specifically where it comes up against the hippocampus and amygdala. The aseg volumes label these unknown regions as cortex. I've searched the archives and haven't been able to find anything similar from recent years.
I've attached some axial screenshots of the raw T1, the aseg and the aparc+aseg.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Freesurfer expert,
I am writing regarding the local gyrification index (lGI), pipeline now available with Freesurfer.
In order to better understand the results obtained it would be important to better understand the relationship between lGI to other metrics provided by the freesurfer analysis.
I understand lGI is the ratio between the sulcal surface / outer surface.
Which is the relationship between lGI and area, area_pial, sulcation and curvature and even thickness (available for the qdec analysis)? Has it been evaluated yet?
Edu
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Thursday, September 7, 2017 3:17 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Unknown regions in cortical parcellation
what version of FS are you using?
On 09/07/2017 03:19 PM, Aidan Murphy wrote:
We're running QA on Freesurfer's aseg and aparc+aseg volumes. On the aparc volume we're noticing fairly large unknown regions in what should be entorhinal cortex, specifically where it comes up against the hippocampus and amygdala. The aseg volumes label these unknown regions as cortex. I've searched the archives and haven't been able to find anything similar from recent years.
I've attached some axial screenshots of the raw T1, the aseg and the aparc+aseg.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Martinos Center File Drophttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html www.nmr.mgh.harvard.edu 11/15/2012 -- There is a new version of Filedrop. Please help us test it https://gate.nmr.mgh.harvard.edu/filedrop2/ Welcome to the Martinos Center file drop area ...
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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We are using Freesurfer v6.0
Biomedical Engineer, Brain Rehabilitation Research Center Malcolm Randall VA Medical Center, 1601 SW Archer Road, Gainesville, FL 32608 Phone: 1-352-376-1611 ext. 5249, E-mail: jakerieke@gmail.com
On Thu, Sep 7, 2017 at 6:17 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
what version of FS are you using?
On 09/07/2017 03:19 PM, Aidan Murphy wrote:
We're running QA on Freesurfer's aseg and aparc+aseg volumes. On the aparc volume we're noticing fairly large unknown regions in what should be entorhinal cortex, specifically where it comes up against the hippocampus and amygdala. The aseg volumes label these unknown regions as cortex. I've searched the archives and haven't been able to find anything similar from recent years.
I've attached some axial screenshots of the raw T1, the aseg and the aparc+aseg.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 Jake
if you upload a subject and send us the voxel coords you are looking at one of us will take a look
cheers Bruce On Wed, 13 Sep 2017, Jake Rieke wrote:
We are using Freesurfer v6.0
Biomedical Engineer, Brain Rehabilitation Research CenterMalcolm Randall VA Medical Center, 1601 SW Archer Road, Gainesville, FL 32608 Phone: 1-352-376-1611 ext. 5249, E-mail: jakerieke@gmail.com
On Thu, Sep 7, 2017 at 6:17 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote: what version of FS are you using?
On 09/07/2017 03:19 PM, Aidan Murphy wrote: > > We're running QA on Freesurfer's aseg and aparc+aseg volumes. On the > aparc volume we're noticing fairly large unknown regions in what > should be entorhinal cortex, specifically where it comes up against > the hippocampus and amygdala. The aseg volumes label these unknown > regions as cortex. I've searched the archives and haven't been able to > find anything similar from recent years. > > I've attached some axial screenshots of the raw T1, the aseg and the > aparc+aseg. > >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Bruce,
I've uploaded one of our subjects to the FileDrop
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=31qhh4docnq
The areas we're concerned with are temporal regions. [151,150,131] is one instance of these unknown entorhinal regions.
Aidan
On Wed, Sep 13, 2017 at 2:43 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Jake
if you upload a subject and send us the voxel coords you are looking at one of us will take a look
cheers Bruce On Wed, 13 Sep 2017, Jake Rieke wrote:
We are using Freesurfer v6.0
Biomedical Engineer, Brain Rehabilitation Research CenterMalcolm Randall VA Medical Center, 1601 SW
Archer Road, Gainesville, FL 32608 Phone: 1-352-376-1611 ext. 5249, E-mail: jakerieke@gmail.com
On Thu, Sep 7, 2017 at 6:17 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote: what version of FS are you using?
On 09/07/2017 03:19 PM, Aidan Murphy wrote: > > We're running QA on Freesurfer's aseg and aparc+aseg volumes. Onthe > aparc volume we're noticing fairly large unknown regions in what > should be entorhinal cortex, specifically where it comes up against > the hippocampus and amygdala. The aseg volumes label these unknown > regions as cortex. I've searched the archives and haven't been able to > find anything similar from recent years. > > I've attached some axial screenshots of the raw T1, the aseg and the > aparc+aseg. > >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
freesurfer@nmr.mgh.harvard.edu
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Aidan Murphy -
Bruce Fischl -
Caverzasi, Eduardo -
Douglas N Greve -
Jake Rieke