What do you mean you only get one vertex for the medial wall? Can you send the make_average_{subject,surface,volume}.log files (located in the scripts folder of the average subject)

On 11/22/2017 05:01 AM, M del Mar Velasco wrote:

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

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