7.1.227. @2dwarper.AllinΒΆ

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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

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