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.edu> wrote:

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