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For images showing pathology, consider using binary cost function weighting images - a zero for areas of a pathological nature and one elsewhere do not put zero outside the brain. Consider using the Group facility GUI only for running the registration on a collection of images this is also easily achieved with the command-line version by scripting.
Accurate and robust brain image alignment using boundary-based registration. Medical Image Analysis, 5 2: Improved optimisation for the robust and accurate linear registration and motion correction of brain images.
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