Hi Falk,
can you really not afford the 6 minutes or so of scan time to get a good 1mm dataset? We have analyzed a bunch of 7T data successfully, although it probably isn't as automated as 1.5 and 3T. The error you are getting we only see when you have run out of disk space. It sounds like the surface file is corrupted. As for the cutting planes, you should be able to select a point in the pons above the cerebellar peduncle for the brainstem cutting plane. This should remove the cerebellum, which is required for analysis.
We certainly did many cortical thickness studies before the aseg stuff was integrated into the stream, so it should be possible, it just requires more work.
cheers, Bruce
On Thu, 30 Jul 2009, Falk Lüsebrink wrote:
Hi FreeSurfers,
As the subcortical segmentation fails fairly often on my high resolution data I want to skip it by using the noaseg flag, but Im currently encountering another issue.
1.) During the fix stage of autorecon2 I receive following error during mris_euler_numbers (also if I want to view the lh.orig or rh.orig in tksurfer):
rh.orig: face[233615].v[2] = 119048, but face 233615 not in vertex 119048 face list
lh.orig: face[196300].v[1] = 100366, but face 196300 not in vertex 100366 face list
2.) Normally the subcortical segmentation is also used to cut both hemisphere and to remove the cerebellum. The cutting plane between the hemispheres is done very well, but I have never been able to remove the cerebellum. Do I need to remove it manually or are there some ways to remove it automatically? Is it required to be removed?
3.) Im interested in measuring cortical thickness only. But do I need to keep something else in mind while not using the subcortical segmentation to process my data?
Thanks in advance,
Regards,
Falk