Hi
  in fact, the wm intensities are mostly below 110 so i seeded control points in the wm (across many slices) and then i run recon-all with only autorecon2. at the end i notices that the problem still not fixed. according to ReconAllDevTable section, the final surfaces (aseg.mgz, brain.finalsurfs.mgz, wm.mgz, filled.mgz) are done at the autorecon2 step; Or should i run autorecon3 to fix the problem ?

Thanks


De : Bruce Fischl <fischl@nmr.mgh.harvard.edu>
À : LAOUCHEDI MAKHLOUF <laoumakhl@yahoo.fr>
Cc : "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Envoyé le : Jeudi 18 juillet 2013 15h31
Objet : Re: [Freesurfer] WM and pial surfaces problem

Hi Laouchedi

what are the intensities in the white matter in that region in the
brain.mgz? If significantly below 110, try sprinkling a few control
points there
cheers
BruceOn Thu, 18 Jul 2013, LAOUCHEDI MAKHLOUF wrote:

> Hi
>     i run recon-all on a subject and when checking the surfaces, i noticed that a big part of the temporal part is badly
> segmented; this concerned WM as well as the grey matter. on the RecommendedReconstruction page, it is explained how to remove
> parts of non-pial structures considered as so, but not how to move the red surface to include missed wm and grey matter.
>
> thank you for help
>
>


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