Brain Imaging & Analysis Center

usage: -align dataset flag ncycles nsteps nbits imin shift1 shift2 doff drot dscale

ALIGN superimposes the data set to be aligned onto the current (reference) data set and then adjusts the alignment data set to optimize its registration with the reference data set. The adjustment is done by stepping through several possible alignment settings and calculating a “mutual information” index for each step. The parameter settings that can be adjusted are Translation, Rotation, and Scaling along each of the 3 cardinal image axes (X, Y, and Z). For each parameter being adjusted, ALIGN tests NSTEPS values (default=5), with NSTEPS/2 values on either side of the starting value. It performs NCYCLES of adjustment (default=3) of all parameters, decreasing the step size on each cycle.

The adjustment stepsize is specified by a combination of the FLAG, NCYCLES, DOFF, DROT, and DSCALE parameters. The finest adjustment step for the last adjustment cycle is (assuming no Coarse FLAG option):

• DOFF - translation offset step (default=0.25 mm)
• DROT - rotation step (default=0.25 degrees)
• DSALE - scale step (default=1.0)

FLAG (combine options by adding values):

• 1 -
• 2 -
• 4 -
• 8 -

See Also:
fScan Home, fScan Manual, CmdLineOptions, Manual Help