Hi Laouchedi, You'll have to run autorecon3 as well to regenerate the pial surfaces. FYI: aseg.mgz, brain.finalsurfs.mgz, wm.mgz and filled.mgz are all volumes, not surfaces. All play a part in generating the surfaces though. -Louis
On Fri, 19 Jul 2013, LAOUCHEDI MAKHLOUF wrote:
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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