:orphan:

.. _ahelp_convert_cdiflist_to_grads.py:

****************************
convert_cdiflist_to_grads.py
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.. contents:: :local:


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PURPOSE
=======

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      This program reads in a GE cdiflist and outputs gradient file + file
      of bvalues, which can be used in subsequent processing.
    
      Ver  : 0.4
      Date : Jan 10, 2023
      Auth : PA Taylor
    
    

INPUTS
======

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      + cdiflist (from GE DWI scanning)
      + max bvalue used (in using s/mm^2), e.g., 1000 or 1100. 
    
    

OUTPUTS
=======

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      + row gradient file (unscaled, unit-magnitude)
      + col gradient file (scaled by b-magn)
      + row bval file     (bvalues)
    
    

RUNNING
=======

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     -cdiflist CDIFLIST
                    :(req) name(s) of cdiflist text file, which can be
                     output by GE scanners when acquiring DWIs and has the
                     following format:
                     + first line is 1 number, which is the number of grads N
                       used in the acquisition
                     + N rows of 3 values each, which relate to the gradient
                       direction+strength (but they are *not* directly the 
                       grads themselves)
    
     -bval_max BBB  :(req) max bvalue used, which provides a reference value
                     for scaling everything else
    
     -prefix PP     :(req) output basename for the subsequent grad and bvalue
                     files.
                     Note that this can include path information, but both 
                     a suffix and a file extensions will be added for the
                     main outputs: 
                        _rvec.dat  (row-format of gradients, unit magn)
                        _bval.dat  (row-format of bvals)
                        _cvec.dat  (col-format of grads, scaled by b-values)
    
     -ver           :display current version
                     (0.4)
    
     -date          :display release/editing date of current version
                     (Jan 10, 2023)
    
     -help          :display help (in terminal)
     -h             :display help (in terminal)
    
     -hview         :display help (in separate text editor)
    
    

NOTES
=====

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    At this point in time, this program should only be used if the DWI
    acquisition used *axial slices*.  This tends to be (by far) the most
    common way to acquire the data, so this probably isn't a very
    prohibitive restriction.  However, more option(s) would need to be
    added for dealing with other slice acquisitions (based on how GE
    stores the data).
    
    Also, if you have any questions/uncertainty about the gradient info,
    just ask.  And if you *really* want a correct answer, of course you
    should ask Joelle, the real expert!
    
    

EXAMPLES
========

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    convert_cdiflist_to_grads.py             \
        -cdiflist  cdiflist45                \
        -bval_max  1100                      \
        -prefix    grads_ge_45