Date: Fri, 01 Feb 2008 15:08:58 -0600 From: "Teddy Youn" To: Subject: Talairach transformations in tkregister2 and WM editing for aseg.stats Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: quoted-printable Content-Disposition: inline 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 registrati= on 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=20 Doris Duke Clinical Research Fellow '07-'08=20 North Texas TBI Research Center UT Southwestern Medical Center at Dallas=20 Warren Alpert School of Medicine at Brown University, MD '09 Teddy.Youn@utsouthwestern.edu=20 (401)-714-2847=20