hi - I've been trying to run a set of MP-RAGE images collected on our allegra through the first part of the autorecon process, and I've run into somewhat of a problem with the skull-stripping. In all 8 of the brains that I have tried, there is a substantial amount of scalp left over after stripping (primarily on the dorsal posterior surface of the skull). I have tried the recommendations from the wiki (reducing the wsthresh to 5, and using -wsatlas) to no avail, there is still skull left over. Short of editing out the scalp by hand, are there any other tricks I might try to get the automated stripping to work?
for what it's worth, we have found these Allegra MP-RAGE images to wreak havoc on BSE and BET as well. Any suggestions would be most appreciated!
cheers
russ
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Russell A. Poldrack, Ph.d.
Associate Professor
UCLA Department of Psychology
Franz Hall, Box 951563
Los Angeles, CA 90095-1563
phone: 310-794-1224
fax: 310-206-5895