FWIW: In FS 5.3, -autorecon2-cp and -autorecon2-wm invoke the exact same set of flags. (This wasn't the case in earlier versions).

cheers, -MH

-- Michael Harms, Ph.D.

----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mharms@wustl.edu

On 6/12/14 10:15 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:

Hi Jidan

for your first point, if you make both wm edits and add control points you can run -autorecon2-cp -autorecon3 as it is a superset of -autorecon2-wm.

For the second one, it's hard to diagnose from the single slice. Is there white matter through-plane that is not included in the white surface or the wm.mgz?

cheers Bruce

On Thu, 12 Jun 2014, Jidan Zhong wrote:

...

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..]

Thanks!

-- Regards,

Jidan

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