AFNI program: 3ddot

Usage: 3ddot [options] dset1 dset2
Output = correlation coefficient between 2 dataset bricks
         - you can use sub-brick selectors on the dsets
         - the result is a number printed to stdoutOptions:
  -mask mset   Means to use the dataset 'mset' as a mask:
                 Only voxels with nonzero values in 'mset'
                 will be averaged from 'dataset'.  Note
                 that the mask dataset and the input dataset
                 must have the same number of voxels.
  -mrange a b  Means to further restrict the voxels from
                 'mset' so that only those mask values
                 between 'a' and 'b' (inclusive) will
                 be used.  If this option is not given,
                 all nonzero values from 'mset' are used.
                 Note that if a voxel is zero in 'mset', then
                 it won't be included, even if a < 0 < b.
  -demean      Means to remove the mean from each volume
                 prior to computing the correlation.

INPUT DATASET NAMES
-------------------
This program accepts datasets that are modified on input according to the
following schemes:
  'r1+orig[3..5]'                                    {sub-brick selector}
  'r1+orig<100.200>'                                 {sub-range selector}
  'r1+orig[3..5]<100..200>'                          {both selectors}
  '3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )'  {calculation}
For the gruesome details, see the output of 'afni -help'.