Hi there-looking through the archives for pial surface questions I didn't see an answer to this: I've done autorecon1 and autorecon2 on this subject and I was checking the brain mask, wm, etc. There's a tip of temporal lobe lying outside the pial surface (red line), see attached, where the red cross is in both pictures. What are we supposed to do in this case? I can't put control points outside the red line, as I understand it?
Thanks,
Jess
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Jessica Turner, Ph.D.
Project Manager, FBIRN (www.nbirn.net)
Department of Psychiatry and Human Behavior
University of California, Irvine
Phone: (949) 824-3331
Fax: (949) 824-3324
Hi Jess,
If your surfaces are excluding white matter, you can put a control point in the white matter. You do not want to put a control point in grey matter, or a partial volumed voxel. It's not really a case of inside or outside the pial surface, as long as you pick a white matter voxel to put the control point on.
Jenni
On Thu, 19 Apr 2007, Turner, Jessica wrote:
Hi there-looking through the archives for pial surface questions I didn't see an answer to this: I've done autorecon1 and autorecon2 on this subject and I was checking the brain mask, wm, etc. There's a tip of temporal lobe lying outside the pial surface (red line), see attached, where the red cross is in both pictures. What are we supposed to do in this case? I can't put control points outside the red line, as I understand it?
Thanks,
Jess
Jessica Turner, Ph.D.
Project Manager, FBIRN (www.nbirn.net)
Department of Psychiatry and Human Behavior
University of California, Irvine
Phone: (949) 824-3331
Fax: (949) 824-3324
Dear List: I am trying to look for some papers in which differences in CTh among different areas of the brain are shown. Precisely, I would like to know if there is anything published regarding the fact that - as it appears on histopathology - the precentral gyrus is thicker than any other areas in human beings.
Any hints?
Thanks, Francesca
Hi Francesca,
we published some of what you are looking for in the PNAS thickness paper. It's on our wiki.
cheers, Bruce
On Thu, 19 Apr 2007, Bagnato, Francesca (NIH/NINDS) [E] wrote:
Dear List: I am trying to look for some papers in which differences in CTh among different areas of the brain are shown. Precisely, I would like to know if there is anything published regarding the fact that - as it appears on histopathology - the precentral gyrus is thicker than any other areas in human beings.
Any hints?
Thanks, Francesca
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Jess,
I agree with Jenni. It looks like it missed some of the white matter, which is why it also didn't get the pial surface. Was the wm.mgz accurate there? If it was, then the problem is probably the topology fixer. If not, then putting control points in the white matter would be my suggestion.
cheers, Bruce On Thu, 19 Apr 2007, Turner, Jessica wrote:
Hi there-looking through the archives for pial surface questions I didn't see an answer to this: I've done autorecon1 and autorecon2 on this subject and I was checking the brain mask, wm, etc. There's a tip of temporal lobe lying outside the pial surface (red line), see attached, where the red cross is in both pictures. What are we supposed to do in this case? I can't put control points outside the red line, as I understand it?
Thanks,
Jess
Jessica Turner, Ph.D.
Project Manager, FBIRN (www.nbirn.net)
Department of Psychiatry and Human Behavior
University of California, Irvine
Phone: (949) 824-3331
Fax: (949) 824-3324
freesurfer@nmr.mgh.harvard.edu
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Bagnato, Francesca (NIH/NINDS) [E] -
Bruce Fischl -
Jenni Pacheco -
Turner, Jessica