afni.nimh.nih.gov

The general case from the documentation is:

Example 1: Segmenting a skull-stripped T1 volume with:
Brain mask, No prior volumes, Uniform mixing fraction
3dSeg -anat anat.nii -mask AUTO \
-classes 'CSF ; GM ; WM' -bias_classes 'GM ; WM' \
-bias_fwhm 25 -mixfrac UNI -main_N 5 \
-blur_meth BFT

In your case, a good starting point may be substituting anat.nii above with spgr.nii. In my tests, I get CSF, GM, and WM in the Classes+orig dataset. I then used 3dcalc to extract just the grey matter or WM or CSF into a single dataset.



Edited 1 time(s). Last edit at 10/24/2012 02:24PM by Peter Molfese.