Dear surfers,
I ran the recon-all -s bert -autorecon1 recon-all -s bert -autorecon2 recon-all -s bert -autorecon3
commands and all of them finished without any error. The log files of the commands and the file list of the resultant bert folder are attached to the mail. I can see the surface of the pial and the white with the tksurfer and try to load the ?h.thickness files as curvature files to the surfaces. But I only get fully red colored surface. What may be wrong? Also how can I read the ?h.thickness files manually to check is there any meaningful information there. The curvature maps are working but the thickness is not working. The snapshots of the the thickness and curvature are also attached.
For the next step I want to ask one more question. In a previous mail in the list it is said that
"we compute the closest vertex on the pial from each vertex on the white, and visa-versa, then set the thickness to the average of the two." for the thickness calculation.
I understand from this statement that the thickness is just measured for the surface vertices but not for the voxels in the original volume. For voxel based morphometry do you have any advice to get thickness values for the voxels of the grey matter?
Thanks in advance for any advice and reply.
Burak
It sounds like you need to change the tksurfer color scale to give it more dynamic range.
On Wed, 11 Apr 2007, burak ozkalayci wrote:
Dear surfers,
I ran the recon-all -s bert -autorecon1 recon-all -s bert -autorecon2 recon-all -s bert -autorecon3
commands and all of them finished without any error. The log files of the commands and the file list of the resultant bert folder are attached to the mail. I can see the surface of the pial and the white with the tksurfer and try to load the ?h.thickness files as curvature files to the surfaces. But I only get fully red colored surface. What may be wrong? Also how can I read the ?h.thickness files manually to check is there any meaningful information there. The curvature maps are working but the thickness is not working. The snapshots of the the thickness and curvature are also attached.
For the next step I want to ask one more question. In a previous mail in the list it is said that
"we compute the closest vertex on the pial from each vertex on the white, and visa-versa, then set the thickness to the average of the two." for the thickness calculation.
I understand from this statement that the thickness is just measured for the surface vertices but not for the voxels in the original volume. For voxel based morphometry do you have any advice to get thickness values for the voxels of the grey matter?
Thanks in advance for any advice and reply.
Burak
Hi Burak,
it's all red because the red/green inflection point is at 0. You need to change it for the thickness to show up well (set it the midpoint at 2 or so). And no, the thickness is a property of the surface(s), so you can't make voxel maps of it
Bruce
On Wed, 11 Apr 2007, burak ozkalayci wrote:
Dear surfers,
I ran the recon-all -s bert -autorecon1 recon-all -s bert -autorecon2 recon-all -s bert -autorecon3
commands and all of them finished without any error. The log files of the commands and the file list of the resultant bert folder are attached to the mail. I can see the surface of the pial and the white with the tksurfer and try to load the ?h.thickness files as curvature files to the surfaces. But I only get fully red colored surface. What may be wrong? Also how can I read the ?h.thickness files manually to check is there any meaningful information there. The curvature maps are working but the thickness is not working. The snapshots of the the thickness and curvature are also attached.
For the next step I want to ask one more question. In a previous mail in the list it is said that
"we compute the closest vertex on the pial from each vertex on the white, and visa-versa, then set the thickness to the average of the two." for the thickness calculation.
I understand from this statement that the thickness is just measured for the surface vertices but not for the voxels in the original volume. For voxel based morphometry do you have any advice to get thickness values for the voxels of the grey matter?
Thanks in advance for any advice and reply.
Burak
Burak,
The file bert/stats/?h.aparc.stats contains thickness data for parcellated regions.
You can get the raw thickness data with:
mris_convert -c lh.thickness lh.white lh.thickness.asc
where lh.thickness.asc will contain:
<vertex> <x> <y> <z> <thickness in mm>
noting that the x,y,z pertains to the lh.white surface.
Nick
On Wed, 2007-04-11 at 18:46 +0200, burak ozkalayci wrote:
Dear surfers,
I ran the recon-all -s bert -autorecon1 recon-all -s bert -autorecon2 recon-all -s bert -autorecon3
commands and all of them finished without any error. The log files of the commands and the file list of the resultant bert folder are attached to the mail. I can see the surface of the pial and the white with the tksurfer and try to load the ?h.thickness files as curvature files to the surfaces. But I only get fully red colored surface. What may be wrong? Also how can I read the ?h.thickness files manually to check is there any meaningful information there. The curvature maps are working but the thickness is not working. The snapshots of the the thickness and curvature are also attached.
For the next step I want to ask one more question. In a previous mail in the list it is said that
"we compute the closest vertex on the pial from each vertex on the white, and visa-versa, then set the thickness to the average of the two." for the thickness calculation.
I understand from this statement that the thickness is just measured for the surface vertices but not for the voxels in the original volume. For voxel based morphometry do you have any advice to get thickness values for the voxels of the grey matter?
Thanks in advance for any advice and reply.
Burak
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Nick Schmansky