bruker2bart

A Python package providing data format conversion between Bruker and The Berkeley Advanced Reconstruction Toolbox (BART) data formats. It also provides several examples preforming reconstruction of Bruker data using BART.

Install

Using pip:

pip install bruker2bart

From source:

git clone https://github.com/isi-nmr/bruker2bart.git
cd bruker2bart
python setup.py build
python setup.py install

Examples

We provide a set of examples to demonstrate the functionality of bruker2bart. To run these examples, please download our testing data set:

pip install zenodo_get
zenodo_get 10.5281/zenodo.3894651
unzip 20200612_094625_lego_phantom_3_1_2.zip

Now it is necessary to set two environment variables. The PATH_DATA variable should be set to the parent directory of the downloaded data. The PATH_RESULTS variable should be set to the directory where you wish to store store results of the reconstructions.

export PATH_DATA=/home/user/data
export PATH_RESULTS=/home/user/tmp

Then you can run any of the scripts located in the examples folder such as the 2D NUFFT.

./bruker-2d-nufft.sh

The following reconstruction examples are currently avaliable:

• 2D FFT (bruker-2d-fft.sh)
• 3D FFT (bruker-3d-fft.sh)
• 2D NUFFT (bruker-2d-nufft.sh)
• 3D NUFFT (bruker-3d-nufft.sh)

Acknowledgement

Part of this software is the clf.py file from BART official repository created by:

• Martin Uecker <[email protected]>
• Jonathan Tamir <[email protected]>