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Read Siemens raw data.

Project description

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:

pip install rawdatarinator

Usage

You get a few functions:

# 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

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