#This is the FAQ template
# Make sure you "Add to" CategoryFaq
<<FslToolContents>>
= Step-by-Step Guide =
== Brain Extraction ==

 * [[InitialProcessing|Initial processing]] (dicom conversion, fslreorient2std, robustfov/fslroi) 
 * Run the [[Bet/UserGuide|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|fsl_anat]]
   * non-linear registration with [[fnirt/UserGuide|fnirt]] (transforming brain mask from standard space back to the native space)