realign

realign is a command-line implementation of the rigid registration routine from SPM96. It performs rigid-body (6 parameter) motion correction with volumes in 4D image data files. Even though it's based on very old code, it still does a fairly good job. Here's the help text:

VoxBo realign (v1.8.5pre7/Jan  4 2010)
usage: realign [flags] file [file ...]
flags:
    -r <refimage>        refimage is the reference image
    -n <num>             number of the reference image
    -o <outfile>         set the name for the realigned file
    -p <paramfile>       set the name for the param file to be saved
    -t <tolerance>       tolerance for (in voxels, default 0.5)
    -i <maxiter>         max # of iterations (default 4)
    -s <spikethresh>     spike warning threshold (in voxels, default 0.5)
    -d <driftthresh>     drift warning threshold (in voxels, default 0.5)
    -c <file> [file ...] check parameters from each file
    -q <file> [file ...] summarize parameters from each file