RBX: Robex 3dSS: 3dSkullStrip us: useskull ) (“Manual” is the manually extracted ‘golden-standard’ to which all other extractions are compared. some Ubuntu installations), please start optiBET by typing: * 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.

Optibet fsl