This is a newbie question as this is the first grossly abnormal scan on which I need to run freesurfer. There are very large CSF spaces and only a rim of cortex and white matter for many regions. Freesurfer fails very early on. Before I post errors, I would like to try to get it to complete if there are pointers online.
Is there a tutorial for running freesurfer on a grossly abnormal scan? Are there standard rules of thumb? Thanks - Don
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