Hi Tom, we've never really used our skull stripping for primates, so I'm not surprised to hear that it fails. It's good to know that BET works well, so I would definitely use it instead of ours. In general, we have been working over the last year or so to integrate with the Oxford tools, so hopefully things are pretty interchangeable now.
However, I would investigate the error message you got a bit further, as it sounds like something went wrong in your intensity normalization. Did you look at your T1 volume? It should have wm intensities at or close to 110. For primates, this is usually done by selecting a couple of control points in the white matter, and running the normalization with them (with humans is uses the auto-talairaching, which of course will fail on a monkey). As for the libppm stuff, I think we have fixed that in the most recent version (since we don't really use ppm). Try getting a new version. 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 Mon, 15 Jul 2002, Tom Schoenemann wrote: > Hello, > > When we try to strip the skull on a primate brain, it fails with the > following message: > > <lots of stuff deleted> > **********WATERSHED********* > preflooding height equal to 25 percent > Sorting... > first estimation of the COG coord: x=129 y=91 z=127 r=73 > first estimation of the main basin volume: 1647886 voxels > Error > intensity too high...probable pbm > > Command Finished > > > In the manual is says to try setting seed points using TKmedit. > However, when we try to open TKmedit we get: > > /home/opt2/freesurfer_alpha/bin/Linux/tkmedit bonobo.jill orig -csurf > /home/opt2/freesurfer_alpha/bin/Linux/tkmedit: error while loading shared > libraries: libppm.so.1: cannot open shared object file: No such file or > directory > > Command Finished > > > Clearly we are missing something. The operating system was recently > upgraded. Is it possible something was left out? Any suggestions what > we might try? > > -Tom > > ________________________________________________ > P. Thomas Schoenemann > Assistant Professor > Department of Anthropology > University of Pennsylvania > Philadelphia, PA 19104-6398 > > Phone: (215) 573-7671 > Fax: (215) 898-7462 > E-mail: [EMAIL PROTECTED] > Homepage: http://www.sas.upenn.edu/~ptschoen/ >
