Hi,
you can try adding control points in the white matter that is dimmer than you want it to be then rerun autorecon2-cp and autorecon3. Make sure that you only select control points in locations that are *not* partial volumed, and that have an intensity in the brain.mgz of <110.
If you want to tar and gzip the subject and put it on our website we'll take a look.
cheers, Bruce
On Fri, 8 Aug 2008, [ks_c_5601-1987] ·ùöÇü wrote:
Dear freesurfer
I¡¯m one of the neurologists in South Korea and having an interest in the functional neuroimaging studies in neurodegenerative diseases.
Recently, I¡¯m planning to study the cortical thickness of various degenerative disorders and trying to learn the freesurfer (version 4.0.5), which is running on the brand new MacBook Pro (leopard) with core2duo intel CPU of 2.5GHz speed and 4MB internal RAM.
Now, I am facing with some troubles.
First, how can I edit or correct the underestimated pial surface.
The MR signals (GE 3.0T, T1 axial SPGR sequence, 1mm slice thickness) acquired in the vertex gray matter and lower part of cerebellum were rather attenuated than the center of brain. Therefore, the freesurfer would classify upper part of the vertex gray matter into the extra-cerebral tissue. In other words, the thickness of the vertex was underestimated.
How can I manually expand the boundary of vertex gray matter with tkmedit ?
Second, the scuba did not work.
When I type the scuba in the terminal, the ¡®bus error¡¯ come out and it do not work at all.
Alternatively, I tried the scuba1 and it worked with some errors (stopping of scuba program and I have to force quit the X11 application).
How can I correct the bus errors and use more advanced viewing and editing software in the freesurfer ?
Thank you for reading my questions and I¡¯m waiting for your kind answer.
Chul Hyoung Lyoo, MD, PhD
Instructor
Department of Neurology
Youngdong Severance Hospital
Yonsei University College of Medicine
612 Eonjuro, Gangnam-gu
Seoul, Korea
Phone: +82-2-2019-3327
Fax: +82-2-3462-5904
E-mail: lyoochel@yuhs.ac