Type of objective function to be minimized

There are four different objective functions that can be used for minimization in the optimization routines. These functions are cross-correlation, normalized intensity difference, stochastic sign change and minimization of the variance of the pixel ratios (vol1/vol2). When masks are specified on the command line, only data in the masked region participates in the evaluation of the objective function.

from minctracc -help:
Optimization objective functions. (default = -xcorr)
 -xcorr:             Use cross correlation.
 -zscore:            Use normalized difference.
 -ssc:               Use stochastic sign change.
 -vr:                Use variance of ratio vol1/vol2
 -groups:            Number of groups for ratio calculations.
		Default value: 16
 -threshold:         Lower limit for voxel threshold
		Default value: 0 0
 -speckle:           percent speckle noise to add to source
		Default value: 5

In more detail, the choices are:

-xcorr

cross correlation. the value returned has a maximum value of 1 and a minimum value of 0. The correlation value is calculated as:

where:
(point to point multiply)
(sum of all points squared)
(sum of all points squared)

-zscore

normalized intensity. For both source and target volumes, each pixel in the volume is replaced by

where is the old voxel value, is the mean voxel value (within the mask) for the one volume and is the standard deviation of voxels (in the mask) for the volume. The objective function is:

where the summation is done over all voxels in the lattice.

-ssc

stochastic sign change - see Minoshima
-speckle option is used to specify the percent speckle noise to add to the source volume.

-vr

variance of ratio - see Woods
-groups is used to specify the number of classification groups to be used when calculating the variance.
-threshold specifies the two threshold values form vol1 and vol2