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