Re: [Freesurfer] Unknown regions in cortical parcellation

[Aidan Murphy]

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 
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: jakeri...@gmail.com
>>
>> On Thu, Sep 7, 2017 at 6:17 PM, Douglas N Greve <
>> gr...@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
>> gr...@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 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.

Re: [Freesurfer] Unknown regions in cortical parcellation

[Bruce Fischl]

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: jakeri...@gmail.com

On Thu, Sep 7, 2017 at 6:17 PM, Douglas N Greve  
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
gr...@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.

Re: [Freesurfer] Unknown regions in cortical parcellation

[Jake Rieke]

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: jakeri...@gmail.com

On Thu, Sep 7, 2017 at 6:17 PM, Douglas N Greve 
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
> gr...@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.

Re: [Freesurfer] Unknown regions in cortical parcellation

[Douglas N Greve]

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
gr...@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.