![]() * Depending on your shell and configuration (e.g. nii.gz image for input outputs binarized brain-extraction mask, saved as: _optiBET_brain_, and full-intensity brain-extraction, saved as: _optiBET_ *script requires proper installation of FSL and AFNIinput image should be in standard orientation use. d use debug mode (will NOT delete intermediate files) t script uses MNI152_T1_2mm_brain_ for mask o script uses MNI152_T1_1mm_brain_ for mask (default) a script uses AFNI for initial extraction f script uses FSL for initial extraction (default) ![]() Type sh optiBET.sh for a full list of options 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.
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