@Align_Centers


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
                     way.
   -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.
   -shift_xform xxx.1D : apply shift translation from 1D file
   -shift_xform_inv xxx.1D : apply inverse of shift translation

   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.