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 > -- Evelina
