Hi Bob et al, I prefer mri_strip_skull to mri_watershed. I think the former was a previous method that has now been replaced by the latter. Please find attached a small csh script (process_anatomy.csh) that I find useful for doing the skull strip and segmentation (note that mri_watershed is hashed out). I use another script to loop over subjects (process_allanatomy.bash).
Kind regards, Darren ----- Original Message ----- From: "Bob Thoma" <[EMAIL PROTECTED]> To: <[EMAIL PROTECTED]> Sent: Thursday, October 17, 2002 3:58 AM Subject: skull stripping > All, > > I've been having some difficulty with skull stripping, it doesn't appear to > be removing enough. I have tried changing the remove skull settings under > expert preferences, but have had no luck. I found a previous email with a > similar problem. Bruce, I believe you replied as such: > > are you using a talairaching procedure? If so, please check that it worked > properly. If it fails, everything after it fails as well. Please also check > your T1 volume by bringing it up in tkmedit. The vast majority of the white > matter should have an intensity of exactly 110. If this is not the case,then > the intensity normalization didn't work properly, possibly because of a > talairach failure, or for some other reason. The segmentation itself usually > works pretty well, so I suspect that it is one of the previous steps that is > causing you problems. > > cheers, > Bruce > > I have two questions, one, how can i check to see if the talairaching > procedure worked properly or how to not run the talairaching procedure. > Second, where do I locate the white matter intensity that you stated to be > 110. > > Or if anyone has any other suggestions, I would be grateful. > > Thanks > Natalie > > > > > > > > _________________________________________________________________ > Protect your PC - get McAfee.com VirusScan Online > http://clinic.mcafee.com/clinic/ibuy/campaign.asp?cid=3963 > >
process_anatomy.csh
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process_allanatomy.bash
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