Hi Christina

it's pretty hard to diagnose from just a handful of slices. I also doubt that it's a huge underinclusion - probably if you move click on a point and change to sagittal you'll see it looks less dramatic. In any case, if you upload a dataset we'll take a look. Alternatively you can try the expert options to mris_make_surfaces to constrain the range of allowable intensities outside the pial surface.

cheers Bruce On Mon, 12 May 2014, Christina Chen wrote:

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

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