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Dear authors, I'm trying to reconstruct a model of a brain from an MRI, and after completion of recon-all (without any errors) the results are truly poor. By looking through your tutorials I am quite confident to say that the problem is either one of intensity normalisation or of white matter segmentation (possibly, both), as you can see in the images attached.
My first attempt is to insert some control points, though I wonder if I might need instead to fix the segmentation with the brush tool. Could it be possible to receive some feedback about this issue?
Another issue regards the freeview software, as whenever I move with the arrows from a slice to another the loaded surfaces suddenly disappear and won't reappear unless I delete and reopen them, and it makes it really hard to insert control points if I can't see the surfaces' outlines. Also, I was wondering if the computational cost of the autorecon2-cp is dependent significantly on the number of control points.
The pictures shows the lh.white, rh.white files over the T1.mgz file and the wm.mgz and control.dat files over the brain mask.mgz file.
Thanks in advance for your help, Tommaso Mariani
