Hi Doug,

Typically, we are seeing these "ctx-unknown" voxels in insula or entorhinal cortex bordering amygdala so its a bit difficult to see from the surface view. On some subjects, it looks like the aparc surface annotation does not extend to cover the entire surface. I've attached a screenshot to help illustrate.

Best regards, Jake

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 21, 2017 at 5:04 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:

we don't have a path for editing aparc+aseg. Are the areas unknown on the surface?

On 09/21/2017 02:20 PM, Jake Rieke wrote:

...

Hi FreeSurfers,

I have a group of subjects with manual edits to the aparc+aseg volume. These edits were made to re-label unknown regions of cortex. I am wondering what recon-all flags I could use to implement the changes and re-generate cortical stats based on these edits. Thanks in advance.

Best regards, Jake

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Hi Dr. Greve,

I'm sorry for the delayed response. I tried responding earlier, but my response was not added to the thread in the freesurfer forum. Hope it goes through this time.

Typically, we are seeing these "ctx-unknown" voxels in insula or entorhinal cortex bordering amygdala so its a bit difficult to see from the surface view. On some subjects, it looks like the aparc surface annotation does not extend to cover the entire surface. I've attached a screenshot to help illustrate.

Best regards, Jake

On Thu, Sep 21, 2017 at 5:04 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:

we don't have a path for editing aparc+aseg. Are the areas unknown on the surface?

On 09/21/2017 02:20 PM, Jake Rieke wrote:

...

Hi FreeSurfers,

I have a group of subjects with manual edits to the aparc+aseg volume. These edits were made to re-label unknown regions of cortex. I am wondering what recon-all flags I could use to implement the changes and re-generate cortical stats based on these edits. Thanks in advance.

Best regards, Jake

---

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/

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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.