:orphan:

.. _ahelp_adjunct_tort_read_dp_align.py:

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adjunct_tort_read_dp_align.py
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.. contents:: :local:


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Overview
========

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    This program is just meant to be used via: adjunct_tort_plot_mot.
    Please see that program for help usage.  It extracts the 3 translation
    (in mm) and 3 rotation (in deg) parameters estimated by TORTOISE's
    DIFF_PREP tool during DWI processing.
    
    auth:  PA Taylor
    

Usage
=====

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    If you really, really need to use this program separately (why?  you
    will miss out on the *pictures*!), then we will note that you can run
    this program with precisely two arguments, as:
    
    adjunct_tort_read_mot_transforms.py  \
        IN_FILE                          \
        OUT_FILE
    
    ... where:
    
       IN_FILE = *_transformations.txt file output by TORTOISE's DIFF_PREP.
    
      OUT_FILE = a '1D' file, in AFNI-ese.  Basically, a text file with 6
                 columns and with the same number of columns as input
                 DWIs.  The columns represent:
    
                      Column #0 : del x (for axial data, RL)
                      Column #1 : del y (for axial data, AP)
                      Column #2 : del z (for axial data, IS)
                      Column #3 : Rx
                      Column #4 : Ry
                      Column #5 : Rz
    

Note
====

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    This program (and its partner-in-crime, adjunct_tort_plot_mot) have
    been checked with TORTOISE versions 3.1* - 3.2.  Please contact the
    TORTOISE group if you have any doubts/questions about the input file
    format (you can cc us AFNI folks, too).