Nam,

The csurf application is no longer supported (and has been removed from the newest release). The recon-all script now performs all processing stages, where the three main stages are -autorecon1, -autorecon2 and - autorecon3 (-stage1 is a deprecated option).

You may want to see our new tutorial, here:

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial

to learn what sorts of problems can occur during the various stages.

It's hard to say from your email what the problem may be, but it could be a bad Talairach alignment. The tutorial discusses this. Note: you should not see the brain stem after the image has been skull-stripped (which occurs during the -autorecon1 stage).

Nick

On Thu, 2006-06-01 at 14:40 -0400, Joongnam Yang wrote:

Hi all,

I posted a question, but for some reason, I didn't get any response. Please help me on this. Here is the question.

I ran 'process volume' and 'create surface' on csurf. The created surface (left inflated) has brain stem attached to it. So, I editted 'wm' slices to get rid of it, and ran 'create surface' again. No change took place. I tried commandline 'recon-all -stage1 -subjid ID', with no luck.

Would someone suggest any comment on this?

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