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Hi, I am working with sienax to get some volumetric info on a group of patients, but the brains are so pathological that automatic bet and registration are really thrown off. Indeed, for many of these patients I had to manually go in and delete bits of skull/eyeballs/neck that I just can't seem to remove with bet. Now, I do have (manually adjusted) brain extracted images for each of these patients, so I am trying to see if I can use them to work-aroud the sienax script. This would require 2 things: 1) generate a skull image (which unfortunately I do not have..). Is there a way I could generate them from the bet-ted brain (e.g. if I subtracted the bet-ted brain from the original image, would that be usable for the purposes of sienax as a *_skull.nii.gz image)? 2) Once I have _brain and _skull images I should be able to comment out the bet command in the sienax script and run it from there? Does it sound possible? Is there a better/different way to work with these "unbettable" brains? cheers Martin -- Martin M Monti, PhD Assistant Professor 7461E Franz Hall UCLA Department of Psychology BOX 951563, Los Angeles, CA 90095-1563 310-825-8546 http://montilab.psych.ucla.edu http://faculty.psych.ucla.edu/directory/faculty.php?id=187&area=3 <http://faculty.psych.ucla.edu/directory/faculty.php?id=187&area=3%20> “Well! I’ve often seen a cat without a grin,” thought Alice, “but a grin without a cat! It’s the most curious thing I ever saw in my life!” [Lewis Carroll, Alice in Wonderland]