[Freesurfer] Fwd: Overinclusion of brain volume during segmentation - Question

Hi!

I've attached 2 pictures of some brain scans on Freesurfer -- is there any way we can fix the huge underinclusion of the gray matter, hopefully without changing the surfaces of the white matter? What should be done with these scans to fix them?

Thanks! Christina

On Thu, Mar 20, 2014 at 2:32 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:

cortical stats reported by asegstats2table use the surfaces, not the cortical segmentation in aseg.mgz doug

On 03/20/2014 05:29 PM, Christina Chen wrote:

...

Thanks a lot!! I have a follow up question:

We use the command

asegstats2table

to output the subcortical volumes (and other whole brain volumes) to table. If the aseg is incorrect, can we still believe those values?

Thanks, Christina

On Thu, Mar 20, 2014 at 1:27 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:

Hi Christina

if the aseg is incorrect but the surfaces are right, then you
don't need to worry about it. This is the reason we typically use
the surfaces instead of the aseg for things like brain
volume/cortex modeling.

cheers
Bruce

On Thu, 20 Mar 2014, Christina Chen wrote:

    Hi!
    If the cortical surface outlines are fine, but there is an
    overinclusion of
    brain volume during segmentation, how should I fix this?  Can
    we calculate
    brain volume based on the cortical surface outlines -- if so,

how?

...

    Thanks!
    Christina




_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto:

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

-- 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