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
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
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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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
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@nmr.mgh.harvard.edu
-
Bruce Fischl -
LAOUCHEDI MAKHLOUF -
Louis Nicholas Vinke