If you want to use the AFNI option (which in our evaluation is sub-optimal!) then you will need both FSL and AFNI installed. The only requirement for the default options is to have FSL installed. INSTALLATION: just put the script in your path (and if needed make it executable e.g., “chmod 755 optibet.sh”).

(2014) Optimized Brain Extraction for Pathological Brains (optiBET). Lutkenhoff ES, Rosenberg M, Chiang J, Zhang K, Pickard JD, Owen AM, Monti MM. The script has now been tested on a set of more than 70 patient brains, and it performs better than all available tools ( see figure below). OptiBET is a shell script to perform brain-extractions even in patients brain, where extensive pathology is present.