Hi Deirdre

I think the -noaseg is causing your problems. Can you point us at the tutorial that says to include that flag?

cheers Bruce On Thu, 1 Nov 2012, Deirdre O Shea wrote:

Hello FreeSurfer experts,

I am having a lot of trouble with the surfaces on some of my subjects. The main problem is that I am getting an overlap of the surfaces which can be clearly seen in the coronal view (see attached for an example). This has happened with several subjects even using different commands. One of the commands I used which produced this result was "recon-all -autorecon2-cp -autorecon3 -noaseg subjid (subject)". The other command i used which also produced these results was "recon-all -autorecon-pial -noaseg subjid (subject)" I was using the -noaseg flag after I was deleting some of the segmentation voxels that extended out from the cerrebellum as this was also a common edit. This was specified in the tutorial. Is this the correct procedure? I'm thinking maybe the problem I'm seeing is related to this flag. I hope someone can help.

Best Regards, Deirdre