Step-by-Step Guide

Brain Extraction

• Initial processing (dicom conversion, fslreorient2std, robustfov/fslroi)

• Run the BET tool:

  • from the GUI (simply fill in the input image; default output image is created, but can be changed)
  • from the command line (specify input and output image names)
• Check outputs:
  • load brain extracted image over original image in FSLView (use colour map with brain extracted image)
  • for registration purposes small errors do not matter ; for segmentations it is important to be very accurate (at least no loss of brain tissue, but extra CSF/dark tissue is fine)
• Troubleshooting:
  • try different options (e.g. "fractional intensity threshold" or -f ; "robust brain centre" or -R; see BET page; and many others)
• Alternative methods:

  • fsl_anat

  • non-linear registration with fnirt (transforming brain mask from standard space back to the native space)