AFNI program: 3dmaskdump

Usage: 3dmaskdump [options] dataset dataset ...
Writes to an ASCII file values from the input datasets
which satisfy the mask criteria given in the options.
If no options are given, then all voxels are included.
This might result in a GIGANTIC output file.
Options:
  -mask mset   Means to use the dataset 'mset' as a mask:
                 Only voxels with nonzero values in 'mset'
                 will be printed 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.
  -index       Means to write out the dataset index values.
  -noijk       Means not to write out the i,j,k values.
  -xyz         Means to write the x,y,z coordinates from
                 the 1st input dataset at the start of each
                 output line.  These coordinates are in
                 the 'RAI' order.
  -o fname     Means to write output to file 'fname'.
                 [default = stdout, which you won't like]

  -cmask 'opts' Means to execute the options enclosed in single
                  quotes as a 3dcalc-like program, and produce
                  produce a mask from the resulting 3D brick.
       Examples:
        -cmask '-a fred+orig[7] -b zork+orig[3] -expr step(a-b)'
                  produces a mask that is nonzero only where
                  the 7th sub-brick of fred+orig is larger than
                  the 3rd sub-brick of zork+orig.
        -cmask '-a fred+orig -expr 1-bool(k-7)'
                  produces a mask that is nonzero only in the
                  7th slice (k=7); combined with -mask, you
                  could use this to extract just selected voxels
                  from particular slice(s).
       Notes: * You can use both -mask and -cmask in the same
                  run - in this case, only voxels present in
                  both masks will be dumped.
              * Only single sub-brick calculations can be
                  used in the 3dcalc-like calculations -
                  if you input a multi-brick dataset here,
                  without using a sub-brick index, then only
                  its 0th sub-brick will be used.
              * Do not use quotes inside the 'opts' string!

  -xbox x y z   Means to put a 'mask' down at the dataset (not DICOM)
                  coordinates of 'x y z' mm.  By default, this box is
                  1 voxel wide in each direction.  You can specify
                  instead a range of coordinates using a colon ':'
                  after the coordinates; for example:
                    -xbox 22:27 31:33 44
                  means a box from (x,y,z)=(22,31,44) to (27,33,44).

  -dbox x y z   Means the same as -xbox, but the coordinates are in
                  DICOM order (+x=Left, +y=Posterior, +z=Superior).
                  These coordinates correspond to those you'd enter
                  into the 'Jump to (xyz)' control in AFNI, and to
                  those output by default from 3dclust.
  -nbox x y z   Means the same as -xbot, but the coordinates are in
                  'neuroscience' order (+x=Right, +y=Anterior, +z=Superior)

  -ibox i j k   Means to put a 'mask' down at the voxel indexes
                  given by 'i j k'.  By default, this picks out
                  just 1 voxel.  Again, you can use a ':' to specify
                  a range (now in voxels) of locations.
       Notes: * Boxes are cumulative; that is, if you specify more
                  than 1 box, you'll get more than one region.
              * If a -mask and/or -cmask option is used, then
                  the intersection of the boxes with these masks
                  determines which voxels are output; that is,
                  a voxel must be inside some box AND inside the
                  mask in order to be selected for output.
              * If boxes select more than 1 voxel, the output lines
                  are NOT necessarily in the order of the options on
                  the command line.
              * Coordinates (for -xbox, -dbox, and -nbox) are relative
                  to the first dataset on the command line.

  -quiet        Means not to print progress messages to stderr.

Inputs after the last option are datasets whose values you
want to be dumped out.  These datasets (and the mask) can
use the sub-brick selection mechanism (described in the
output of '3dcalc -help') to choose which values you get.

Each selected voxel gets one line of output:
  i j k val val val ....
where (i,j,k) = 3D index of voxel in the dataset arrays,
and val = the actual voxel value.  Note that if you want
the mask value to be output, you have to include that
dataset in the dataset input list again, after you use
it in the '-mask' option.

N.B.: This program doesn't work with complex-valued datasets!

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'.