Dear Freesurfer experts,

I have a question related to make_average_subject command and Freesurfer versions.

When I used to create my average subject with Freesurfer 5.3, I got lh.cortex.label and rh.cortex.label files inside label folder with 149955 vertexs. Moreover, lh.Medial_Wall.label and rh.Medial_Wall.label had 13887 vertexs.

However, with new Freesurfer 6, I get 163841 vertexs for cortex and only one vertex for medial wall. That's why I have problems with mri_glmfit when I use rh or lh.cortex.label files as label mask. I am considering all vertexs, and I would like to use only real cortex vertexs.

Are label files outputs from make_average_subject wrong? How can I fit this problem?

Thanks in advance,

M del Mar