AFNI program: @Align_Centers
Output of -help
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 \
-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 transform 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. You can also replace BASE with RAI:X,Y,Z to have the script set the center of dset to RAI X,Y,Z
-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.
-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.
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Thu Feb 22 18:37:26 EST 2024