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There are numerous scripts used to automatically linearly and nonlinearly register one MINC volume to another.
mritotal, mritoself, best_lin_reg.pl and other MNI AutoReg tools with additional documentation in wikibooks.
best_nonlin_reg.pl is the most commonly used tool.
ANIMAL is also part of MNI Autoreg and was designed to label the major anatomical regions (the different lobes, corpus callosum, etc.) of a MRI.
monkey_best_lin_reg.pl and monkey_mritotal.pl are the scripts used to linearly and nonlinearly register monkeys to a monkey atlas such as the MNI Macaque Atlas.