Hi Teddy,
1. Our newest versions don't use mri_total, but Avi Snyder's algorithm
instead, which we have found to be more robust. You might try that, but
althernatively you can use tkregister2 to fix the transform.
2. The wm.mgz won't contribute to the aseg.stats, only the aseg.mgz, so
feel free to fix things in it. Note that it is essentially a binary volume
with "on" (>5) meaning interior to the gray/white boundary and "off" (<5)
meaning exterior. It's not [0,1] because we keep track of things that were
manually changed to on or off.
cheers,
Bruce
On Fri, 1 Feb 2008, Teddy Youn wrote:
Hi,
Our group is currently trying to use FS on a cohort of DAI/TBI patients and
have encountered several problems. We recognize the limitations with using FS
on brains that may have severe deformation; however, we wanted to get some
feedback:
1) When loading the talairach transformation on tkregister2, the registration
of some of our more severe TBI brains has been pretty bad. Some have loaded
coronal orientations twice for the corresponding axial and coronal orientations
of the T1 images. Others are poorly rotated and even flipped in orientation.
For poorly registered images, is it better to use a program like SPM to
manipulate the image and then convert to a register.dat format for FS, or is
MRItotal sufficient (through FS)?
2) For some of our more severely injured DAI patients, the wm.mgz is missing a lot of voxels in
subcortical structures (single voxels all along the white matter areas. Should we be filling in
these areas with "white" or "grey" with the volume brush if we do not want to
those voxels to be counted in the aseg.stats file? Our assumption is that the DAI in these
patients is causing the white matter missing voxels. (We know that this may only apply for the
volumes-based Desikan-Killany atlas and not for the Destrieux surface-based atlas.)
Any help you can provide would be great,
-Teddy
Doris Duke Clinical Research Fellow '07-'08
North Texas TBI Research Center
UT Southwestern Medical Center at Dallas
Warren Alpert School of Medicine at Brown University, MD '09
[EMAIL PROTECTED]
(401)-714-2847
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