Teddy,

You can use mri_annotation2label (use the --help flag for usage) to break apart a .annot file into multiple .label files. The .label files are ascii files listing the vertices of that label.

Nick

On Thu, 2008-02-28 at 17:09 -0600, Teddy Youn wrote:

Hi everyone,

Thanks again for your help from my previous query. I had a question about how to convert the binary format of the annotation file to ascii format, similar to using mris_convert to surface files from binary to ascii. Is there an equivalent program that does the same thing for annotation files?

Thanks very much,

-Teddy Youn

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 Teddy.Youn@utsouthwestern.edu (401)-714-2847 email message attachment On Thu, 2008-02-28 at 17:09 -0600, 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 Teddy.Youn@utsouthwestern.edu (401)-714-2847

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