usually it's because the bias field brings the gm too low, so if you find nearby white matter (that is *not* partial volumed) that is below 110, putting some control points there will also move the pial surface out a bit. Or the skull strip could have removed it. Or the topology fixer might have done something strange. This can be checked by looking at the ?h.orig.nofix surface and seeing if it is more accurate than the ?h.orig. If this is the case you'll need to identify and correct the topological defect in the wm.mgz volume.

cheers, Bruce

On Mon, 9 Jul 2007, Sebastian Moeller wrote:

Hi,

not being an expert, please take my rambling with a grain of salt. But I am somewhat curious to learn better ways ;)

On Jul 9, 2007, at 11:03 PM, freesurfer-request@nmr.mgh.harvard.edu wrote:

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Message: 9 Date: Mon, 9 Jul 2007 17:01:42 -0400 From: "Wang, Xin" Xin.Wang2@utoledo.edu Subject: [Freesurfer] add the gray matter To: "freesurfer" freesurfer@nmr.mgh.harvard.edu Message-ID: B8C005270B26F04CAA5A0F779FD8DEBD056A85@MSG02CV04.utad.utoledo.edu Content-Type: text/plain; charset="iso-8859-1"

Hello, Group

I need to edit the pial surface. I learned to remove points with tkmedit from the tutorial. But how to add gray matter in the pial surface?

1. If you have nothing where gray matter should be, then check

brainmask.mgz, if this is missing gray matter, around where your problems occur edit the bainmask.mgz volume and pick up your reconstruction from there. (IIRC there is something in the tutorial about this) 2) If there is white matter where gray matter should be, be sure to to check nu.mgz and brainmask.mgz at the critical parts for too high intensity in the supposed gray matter. Either control points might helo (unlikely) or redoing the intensity correction (and then starting again from that point). At least for my data, acquired with surface coils, sub-optimal intensity correction is really annoying.

ahoi & good luck Sebastian

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Thank you in advance.

Xin