Bruker2nifti is an open source medical image format converter from raw Bruker ParaVision to NifTi, without any intermediate step through the DICOM standard formats.
Bruker2nifti is a pip-installable Python tool provided with a Graphical User Interface and a Command Line Utility to access the conversion method.
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Requirements
- Python 3 backward compatible with python 2.7
- Libraries in requirements.txt.
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Installation
- Install the latest stable release with
pip install bruker2nifti
. - Install the latest development version.
- Install the latest stable release with
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Real data examples
- To access the Graphical User interface and convert some data with no python knowledge required.
- GUI instructions and real data examples.
- API documentation.
- Wiki documentation with additional notes and examples.
- Links and list of available Bruker converter.
- Unit testing with nosetest.
Type
nosetests
in a terminal at the cloned repository. - Tests are based on the open dataset in the folder test_data.
- Bruker2nifti_qa provides more Bruker raw data for further experiments (thanks to Mikaël Naveau).
- Coverage percentage. Created with:
nosetests --with-coverage --cover-package=bruker2nifti &> nose_coverage.txt
Use
nosetests --with-coverage --cover-package=bruker2nifti --cover-erase --cover-html
open cover/index.html
to see the HTML output.
- Current deployment version undergoes continuous integration on travis-ci.
Please see the contribution guideline for bugs report, feature requests and code style.
- Copyright (c) 2017, Sebastiano Ferraris, University College London.
- Bruker2nifti is available as free open-source software under MIT License.
- To cite the code in your research please follow this link.
- This repository is developed within the gift-SURG research project.
- Funding sources and authors list can be found in the JOSS submission paper.
- Thanks to Bernard Siow (Centre for Advanced Biomedical Imaging, University College London), Chris Rorden (McCausland Center for Brain Imaging, University of South Carolina) and Matthew Brett (Berkeley Brain Imaging Center).