Dear FreeSurfer Experts,
I have two questions about freesurfer troubleshoot.
My subjects are people with multiple sclerosis, so for most of them I need to add control points as well as edit white matter due to lesions. As far as I know, I should add control points and do recon-all -autorecon2-cp -autorecon3 to my subject and then edit white matter, do recon-all -autorecon2-wm -autorecon3.
My question is, it seems there are some repeated steps for those two recon steps, and it takes so long to run them. Is there anyway that I can save some process steps and leave it to the last recon? To be specific, can I do recon-all -autorecon2-cp only after I added control points, then do recon-all -autorecon2-wm -autorecon3 after wm edits? I think it is reasonable as after -autorecon2-cp the new white matter surface is already generated and can help to detect wm failure. But I am not sure whether this makes sense to you guys.
Another question is, some of my subjects they have degenerated white matter and grey matter, so some parts get so dark that freesurfer would not include it even in the pial surface. I attached one figure for your referece. If there is no white matter detected in that unlabled part (at the top of the figure), what should I do? should I leave it or just add some white matter and control points myself to get a better segmentation and surface? [The case I show in the attachment is much better than some other cases, whose brain has some parts so dark that even I can not tell which is grey matter or white matter from my experience..]