script to do 2D registration on each slice of a 3D+time
dataset, and glue the results back together at the end
This script is structured to operate only on an AFNI
+orig.HEAD dataset. The one input on the command line
is the prefix for the dataset.
Modified 07 Dec 2010 by RWC to use 3dAllineate instead
of 3dWarpDrive, with nonlinear slice-wise warping.
Set prefix of input 3D+time dataset here.
In this example with 'wilma' as the command line
argument, the output dataset will be 'wilma_reg+orig'.
The output registration parameters files will
be 'wilma_param_ssss.1D', where 'ssss' is the slice number.
usage: @2dwarper.Allin [options] INPUT_PREFIX
example: @2dwarper.Allin epi_run1
example: @2dwarper.Allin -mask my_mask epi_run1
options:
-mask MSET : provide the prefix of an existing mask dataset
-prefix PREFIX : provide the prefix for output datasets
