Hi Anthony,
we need more info about why the AFNI guys think it's our problem. You should look at the ?h.sphere surface to see if it's okay, and also send us the recon-all.log to see if the spherical mapping worked okay (you can look for the distance error at the end of mris_sphere - it should be around 20%).
Bruce
On Mon, 13 Nov 2006, Anthony Steven Dick wrote:
Hello all-
We have encountered a problem interfacing Freesurfer with AFNI/SUMA. The problem occurs specifically with the creation of standard meshes (using the MapIcosahedron program in SUMA)--they come out very distorted. This occurs even though the individual's surface looks pretty good. We have talked to the people at AFNI, and they have told us that our surfaces from Freesurfer are the problem, and that we need to do some manual editing.
We think our surfaces are pretty good. Additionally, we have never encountered this problem in the 3 years we have been using Freesurfer and interfacing with AFNI. The problem began when we downloaded and used Freesurfer 3.0.1. Of course it could be our surfaces require more manual edits, and we are looking into that. However, I wanted to post to find out if:
a) Anyone else is encountering this problem, especially recently b) Does anyone have any other ideas about why it would just be appearing now?
We know it was not a problem in the past. Additionally, we have recently tried a very old freesurfed brain (over 2 years old), and it comes out pretty good.
Any ideas?
Thanks.
Anthony