Let me give you an example here:

Suppose you have a target image: target.tif
and target landmarks saved as: target.csv
and a subject image: subject.tif

1) global alignment;

./vaa3d /x brainaligner /f brainaligner /p "#t target.tif #s subject.tif #w 0 #o subject_ga.tif"

2) local alignment:

./vaa3d /x brainaligner /f brainaligner /p "#t target.tif #s subject_ga.tif #w 10 #o aligned_subject.tif #L target.csv"

The found corresponding landmarks in subject_ga.tif will be saved as csv file as well.

The brainaligner will efficient align your images but it might need you carefully pick control points to ensure your alignment meaningful. Good luck!

Best,
Yang