Usage: @Align_Centers <-base BASE> <-dset DSET> [-no_cp]
                     [-child CHILD_2 ... CHILD_N] [-echo]

   Moves the center of DSET to the center of BASE.
   By default, center refers to the center of the volume's voxel grid.
   Use -cm to use the brain's center of mass instead.

   AND/OR creates the transform matrix XFORM.1D needed for this shift.
   The transform can be used with 3dAllineate's -1Dmatrix_apply
      3dAllineate   -1Dmatrix_apply XFORM.1D    \
                    -prefix PREFIX -master BASE \
                    -input DSET

   -echo: Echo all commands to terminal for debugging
   -overwrite: You know what
   -prefix PREFIX:  Result will be named using PREFIX, instead of the
                    current prefix with _shft appended.
                  * Does not work with -child or -no_cp.
   -1Dmat_only: Only output the transfrom needed to align
                the centers. Do not shift any child volumes.
                The transform is named DSET_shft.1D
   -1Dmat_only_nodset: Like above, but no dsets at all
                are created or changed.
   -base BASE: Base volume, typically a template.
   -dset DSET: Typically an anatomical dset to be
               aligned to BASE.
   -child CHILD_'*': A bunch of datasets, originally
                     in register with DSET, that
                     should be shifted in the same
   -no_cp: Do not create new data, shift existing ones
           This is a good option if you know what you
           are doing. It will save you a lot of space.
           See NOTE below before using it.

    DSET and CHILD_'*' are typically all the datasets
    from a particular scanning session that
    you want to eventually align to BASE.
    Such an operation is needed when DSET and CHILD_'*'
    overlap very little, if at all with BASE

 Note that you can specify *.HEAD for the children even
 if the wildcard substitution would contain DSET
 and possibly even BASE. The script will not process
 a dataset twice in one execution.

 Center options:
   -grid: (default) Center is that of the volume's grid
   -cm : Center is the center of mass of the volume.
   -cm_no_amask : Implies -cm, but with no -automask.

   See also @Center_Distance

 NOTE: Running the script multiple times on the same data
       will cause a lot of trouble. That is why the default
       is to create new datasets as opposed to shifting the
       existing ones. Do not use -no_cp unless you know what
       you are doing.
       To undo errors caused by repeated executions
       look at the history of each dset and undo
       the excess 3drefit operations.

Requires 3drefit newer than Oct. 02/02.

Ziad Saad (saadz@mail.nih.gov)
SSCC/NIMH/ National Institutes of Health, Bethesda Maryland