BrkRaw: A comprehensive tool to access raw Bruker Biospin MRI data

Version: 0.3.11

Description

The ‘BrkRaw’ is a python module designed to provide a comprehensive tool to access raw data acquired from Bruker Biospin preclinical MRI scanner. This module is also compatible with the zip compressed data to enable use of the archived data directly.
The module is comprised of four components, including graphical user interface (GUI), command-line tools, high-level and low-level python APIs.

• For the GUI, we focused on improving convenience for checking metadata and previewing the reconstructed image.
• For the command-line tool, we focused on providing tools for converting, organizing, archiving, and managing data. The command-line tool also provides easy-to-use function to convert large set of raw data into organized structure according to BIDS.
• For the high-level python API, we focused on enhancing the accessibility of reconstructed image data with preserved image orientation and metadata for the image analysis. It compatible users' convenient objects type (nibabel or SimpleITK) without the conversion step.
• For the low-level python API, we focused on providing a consistent method to access raw Bruker data including parameter and binary files with the python compatible datatype while keeping the sake of simplicity.

Conversion reliability

We've tested our converter using the sample dataset from Bruker2Nifti_QA and the results showed correct geometry and orientation for all datasets. We are still looking for more datasets showing orientation issue, if you have any shareable dataset, please contact the developer.

Website

For more detail information including installation, usage and examples, please visit our GitPage.

• Installation
• Command-line tool usage examples
• Converting dataset into BIDS
• Python API usage examples
• GUI
• Interactive Tutorial

Credits:

Authors

• SungHo Lee (shlee@unc.edu): main developer
• Woomi Ban (banwoomi@unc.edu): sub-developer who tested and refined the module structure
• Jaiden Dumas: proofreading of documents and update contents for the user community.
• Dr. Gabriel A. Devenyi: The vast contributions to refinement of module functionality and troubleshooting.
• Yen-Yu Ian Shih (shihy@neurology.unc.edu): technical and academical advisory on this project (as well as funding)

Contributors

• Drs. Chris Rorden and Sebastiano Ferraris: The pioneers related this project who had been inspired the developer through their great tools including dcm2niix and bruker2nifti, as well as their comments to improve this project.
• Dr. Mikael Naveau: The publisher of bruker2nifti_qa, the set of data to help benchmark testing of Bruker converter.

License:

GNU General Public License v3.0

How to get Support

If you are experiencing any problem or have questions, please report it through Issues

Citing BrkRaw

Lee, Sung-Ho, Ban, Woomi, & Shih, Yen-Yu Ian. (2020, June 4). BrkRaw/bruker: BrkRaw v0.3.3 (Version 0.3.3). Zenodo. http://doi.org/10.5281/zenodo.3877179

BibTeX

@software{lee_sung_ho_2020_3907018,
  author       = {Lee, Sung-Ho and
                  Ban, Woomi and
                  Shih, Yen-Yu Ian},
  title        = {BrkRaw/bruker: BrkRaw v0.3.4},
  month        = jun,
  year         = 2020,
  publisher    = {Zenodo},
  version      = {0.3.4},
  doi          = {10.5281/zenodo.3907018},
  url          = {https://doi.org/10.5281/zenodo.3907018}
}