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: