:orphan: .. _ahelp_@Align_Centers: ************** @Align_Centers ************** .. contents:: :local: | .. code-block:: none 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 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 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.