:orphan:

.. _ahelp_@xyz_to_ijk:

***********
@xyz_to_ijk
***********

.. contents:: :local:


| 

    

OVERVIEW
========

.. code-block:: none

    
    Basic helper script to convert a set of (x, y, z) coordinates to (i,
    j, k) indices for a dset.  
    
    Essentially, this was created by stealing sage advice written by DR
    Glen in a helpful Message Board post.
    
    Ver. 1.4 (PA Taylor, Feb 12, 2019)
    
    # ========================================================================
    

USAGE
=====

.. code-block:: none

    
    Inputs:
        + the name of a volumetric file
        + 3 coordinates: x y z
    
    Outputs:
        + 3 indices: i j k
    
    The IJK output is output to screen and can be saved directly to a
    variable in a script or redirected to a file with ">" or ">>".  There
    is also a '-prefix ...' option to write to a text file directly
    (screen output is still produced).
    
    If any of 'i j k' are outside the dset's matrix, an error is returned.
    
    If you just get an error message "argv: Subscript out of range.",
    then you have probably provided too few coordinates.  The user is
    required to put in all three (and only three).
    
    Make sure you are interpreting your input xyz and output ijk trios as
    you wish, if you are using a dset with non-xyz-like orientation (such
    as AIL, SPR, etc.).
    
    # =========================================================================
    

COMMAND OPTIONS
===============

.. code-block:: none

    
      -inset VV  :(req) volume VV whose header information sets the FOV and
                  coordinates
    
      -xyz X Y Z :(req) three coordinates (in units of the dset, like mm),
                  that will be translated to 'i j k' values by the
                  program.
    
      -prefix PP :(opt) file name, which can include path, to output the
                  three indices
    
    # ========================================================================
    

EXAMPLES
========

.. code-block:: none

    
        ### Output to screen.
        @xyz_to_ijk                 \
            -inset FILE.nii.gz      \
            -xyz 30 -10.5 0
    
        ### Script example, save result to a variable: tcsh syntax.
        set IJK = `@xyz_to_ijk                 \
                       -inset FILE.nii.gz      \
                       -xyz 30 -10.5 0`
    
        ### Redirect result to a file.
        @xyz_to_ijk                 \
            -inset FILE.nii.gz      \
            -xyz 30 -10.5 0         > ../saved_ijk.txt
    
        ### Another way to write to a file.
        @xyz_to_ijk                 \
            -inset FILE.nii.gz      \
            -xyz 30 -10.5 0         \
            -prefix ../saved_ijk.txt