Hi, you might also want to get an updated version of mri_watershed, as Florent Segonne has made it much more robust. You can find it in the latest snapshot in the downloads section of surfer.nmr.mgh.harvard.edu.
cheers, Bruce -------------------------------------------------------- Bruce Fischl email: [EMAIL PROTECTED] Mass. General Hosp. NMR Center. tel:(617)-726-4897 Rm. 2328, Building 149, 13th Street fax:(617)-726-7422 Charlestown, MA 02129 USA On Wed, 16 Oct 2002, Evelina Busa wrote: > > Hi, > > The answers are in the body of your email: > > On Wed, 16 Oct 2002, Bob Thoma wrote: > > > 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. > > You can load the talairach transform (assuming it exists) using the > TkMedit Tools 'FILE' menu. First load your T1 volume, then select 'Load > Transform For Main Volume' from the 'File' menu. You should see a 'Load > Transform File' dialog box. From here, browse to the subject's > mri/transforms directory, and you should see 'talairach.xfm'. Click on > this, then click OK and OK again, to load. You should now see the > talairach transform in your tkmedit graphics window. What you are > checking for is alignment. The talairach transformation fails if the > talairached volume is askew or dramatically out of scale. > > If you find that this is the case, you can opt not to use it by manually > editing the COR-.info file of the mri/wm volume. Simply remove the line > that would currently read: > > xform /space/yoursubjectpath/yoursubjectname/mri/transforms/talairach.xfm > > ... if the talairach transform exists. > > Note that there are other options available with the skull strip that have > not been well documented. If you prefer to run it from the command line, > cd to the subject's mri directory. Just type "mri_watershed" (no > quotation marks) to get all the options, i.e.: > > Usage: mri_watershed [options] input_file output_file > optional command -less : to shrink the surface > optional command -more : to expand the surface > optional command -wat : only the watershed algorithm > optional command -wat+temp : watershed algo and first template smoothing > optional command -surf: to save the surfaces > optional command -s int_i int_j int_k : to add a seed point > optional command -t int_threshold: to change the threshold in the > watershed analyze process > optional command -h int_hpf : to precize the preflooding height (in > percent) > optional command -n : not to use the watershed analyze process > > You may want to try changing the preflooding height to something lower > than the default if you find it's stripping too much, for example: > > mri_watershed -h 22 T1 brain > > > Second, where do I locate the white matter intensity that you stated to be > > 110. > > The white matter intensity of any voxel in the volume is displayed in the > lower portion of the TkMedit Tools window. If you just rest your cursor > on the area of interest, you should get a value displayed. > > Good luck, I hope this helps. > > > > > > 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 > > > >
