AFNI program: 3dROIstats

Usage: 3dROIstats -mask[n] mset [options] datasets
Options:
  -mask[n] mset Means to use the dataset 'mset' as a mask:
                 If n is present, it specifies which sub-brick
                 in mset to use a la 3dcalc.  Note: do not include
                 the brackets if specifing a sub-brick, they are
                 there to indicate that they are optional.  If not
                 present, 0 is assumed
                 Voxels with the same nonzero values in 'mset'
                 will be statisticized from 'dataset'.  This will
                 be repeated for all the different values in mset.
                 I.e. all of the 1s in mset are one ROI, as are all
                 of the 2s, etc.
                 Note that the mask dataset and the input dataset
                 must have the same number of voxels and that mset
                 must be BYTE or SHORT (i.e., float masks won't work).
  -numROI n     Forces the assumption that the mask dataset's ROIs are
                 denoted by 1 to n inclusive.  Normally, the program
                 figures out the ROIs on its own.  This option is 
                 useful if a) you are certain that the mask dataset
                 has no values outside the range [0 n], b) there may 
                 be some ROIs missing between [1 n] in the mask data-
                 set and c) you want those columns in the output any-
                 way so the output lines up with the output from other
                 invocations of 3dROIstats.  Confused?  Then don't use
                 this option!

  -debug        Print out debugging information
  -quiet        Do not print out labels for columns or rows

The following options specify what stats are computed.  By default
the mean is always computed.

  -nzmean       Compute the mean using only non_zero voxels.  Implies
                 the oppisite for the normal mean computed
  -nzvoxels     Compute the number of non_zero voxels
  -minmax       Compute the min/max of all voxels
  -nzminmax     Compute the min/max of non_zero voxels
  -sigma        Means to compute the standard deviation as well
                 as the mean.
  -summary      Only output a summary line with the grand mean across all briks
                 in the input dataset. 

The output is printed to stdout (the terminal), and can be
saved to a file using the usual redirection operation '>'.

N.B.: The input datasets and the mask dataset can use sub-brick
      selectors, as detailed in the output of 3dcalc -help.

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'.