AFNI program: 3dmaskave

Usage: 3dmaskave [options] dataset

Computes average of all voxels in the input dataset
which satisfy the criterion in the options list.
If no options are given, then all voxels are included.

------------------------------------------------------------
Examples:

1. compute the average timeseries in epi_r1+orig, over voxels
   that are set (any non-zero value) in the dataset, ROI+orig:

    3dmaskave -mask ROI+orig epi_r1+orig

2. restrict the ROI to values of 3 or 4, and save (redirect)
   the output to the text file run1_roi_34.txt:

    3dmaskave -mask ROI+orig -quiet -mrange 3 4   \
              epi_r1+orig > run1_roi_34.txt
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Options:
  -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.
               SPECIAL CASE: If 'mset' is the string 'SELF',
                             then the input dataset will be
                             used to mask itself.  That is,
                             only nonzero voxels from the
                             #miv sub-brick will be used.
  -mindex miv  Means to use sub-brick #'miv' from the mask
                 dataset.  If not given, miv=0.
  -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.

  -dindex div  Means to use sub-brick #'div' from the dataset.
                 If not given, all sub-bricks will be processed.
  -drange a b  Means to only include voxels from the dataset whose
                 values fall in the range 'a' to 'b' (inclusive).
                 Otherwise, all voxel values are included.

  -slices p q  Means to only included voxels from the dataset
                 whose slice numbers are in the range 'p' to 'q'
                 (inclusive).  Slice numbers range from 0 to
                 NZ-1, where NZ can be determined from the output
                 of program 3dinfo.  The default is to include
                 data from all slices.
                 [There is no provision for geometrical voxel]
                 [selection except in the slice (z) direction]

  -sigma       Means to compute the standard deviation as well
                 as the mean.
  -median      Means to compute the median instead of the mean.
  -max         Means to compute the max instead of the mean.
  -min         Means to compute the min instead of the mean.
                 (-sigma is ignored with -median, -max, or -min)
  -dump        Means to print out all the voxel values that
                 go into the average.
  -udump       Means to print out all the voxel values that
                 go into the average, UNSCALED by any internal
                 factors.
                 N.B.: the scale factors for a sub-brick
                       can be found using program 3dinfo.
  -indump      Means to print out the voxel indexes (i,j,k) for
                 each dumped voxel.  Has no effect if -dump
                 or -udump is not also used.
                 N.B.: if nx,ny,nz are the number of voxels in
                       each direction, then the array offset
                       in the brick corresponding to (i,j,k)
                       is i+j*nx+k*nx*ny.
 -q     or
 -quiet        Means to print only the minimal results.
               This is useful if you want to create a *.1D file.

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

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'.

++ Compile date = Jan 29 2009