https://github.com/mckib2/rawdatarinator

Read Siemens raw data
https://github.com/mckib2/rawdatarinator

Last synced: about 1 month ago
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Read Siemens raw data

• Host: GitHub
• URL: https://github.com/mckib2/rawdatarinator
• Owner: mckib2
• License: gpl-3.0
• Created: 2017-12-23T19:41:27.000Z (about 7 years ago)
• Default Branch: master
• Last Pushed: 2024-09-03T21:19:13.000Z (4 months ago)
• Last Synced: 2024-11-20T09:29:42.697Z (about 2 months ago)
• Language: Cython
• Homepage:
• Size: 1.09 MB
• Stars: 11
• Watchers: 3
• Forks: 2
• Open Issues: 2
• Metadata Files:
  • Readme: README.rst
  • License: LICENSE.txt

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README

        
RawDatarInator

==============

Python bindings for BART's `twixread` function ([1]_).  This new

version of rawdatarinator replaces the old Python port of a MATLAB

script.  Consequently, this one runs much faster and breaks less

often.  A cleaner interface is provided which will break all old

code.  See usage for examples.  In general, this new release has

fewer features that work better.

The name of the project pays homage to the naming convention of the

main antagonist in Disney's hit cartoon "Phineas and Ferb" ([2]_).

Installation

============

This package is known to work with Python 3.6.8 using Ubuntu 18.04.

If it doesn't work on your system, please submit an issue and we can

try to figure something out.  The goal is to provide a simple

pip-installable Python interface for BART's twixread function.  The

Cythonized BART code is compiled during the installation, so you will

need a C compiler installed.

Use pip to install:

.. code-block:: bash

    pip install rawdatarinator

Usage

=====

You get a few functions:

.. code-block:: python

    # BART's twixread function can be invoked right from a Python

    # script:

    from rawdatarinator import twixread

    twixread('path/to/input/data.dat', 'path/to/output')

    # A pair of .cfl, .hdr will be created: path/to/output.[cfl/hdr]

    # as BART normally does.  However, if you're using these Python

    # bindings, you might want to just grab the data straight away.

    # You can do this by not providing any output file:

    data = twixread('path/to/data.dat', A=True)

    # You can read existing BART files like this:

    from rawdatarinator import read

    data = read('path/to/file/without/extentsion')

    # If you've used BART's Python interface, this is a modified

    # verison of readcfl.  It works just like that.  Similarly,

    # BART's writecfl functionality can be found:

    from rawdatarinator import write

    write('path/to/out', data)

References

==========

.. [1] Uecker, Martin, et al. "Berkeley advanced reconstruction

       toolbox." Proc. Intl. Soc. Mag. Reson. Med. Vol. 23. 2015.

.. [2] `List of Doofenshmirtz's schemes and inventions `_