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Bruker2nifti: Magnetic Resonance Images converter from Bruker ParaVision to Nifti format

Ferraris, S; Shakir, DI; Van Der Merwe, J; Gsell, W; Deprest, J; Vercauteren, T; (2017) Bruker2nifti: Magnetic Resonance Images converter from Bruker ParaVision to Nifti format. Journal Of Open Source Software , 2 (16) p. 354. 10.21105/joss.00354. Green open access

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Abstract

In clinical and pre-clinical research involving medical images, the first step following a Magnetic Resonance Imaging dataset acquisition, usually entails the conversion of image data from the native scanner format to a format suitable for the intended analysis. The proprietary [Bruker ParaVision](https://www.bruker.com/products/mr/preclinical-mri/software/service-support.html) software currently does not provide the tools for conversion of the data to suitable and open formats for research, such as nifti [@cox2004sort], for which most of the available tools for medical image analysis are implemented. For this purpose we have designed and developed [bruker2nifti](https://github.com/SebastianoF/bruker2nifti), a pip-installable Python tool provided with a Graphical User Interface to convert from the native MRI Bruker format to the nifti format, without any intermediate step through the DICOM standard formats [@Mildenberger2002]. Bruker2nifti is intended to be a tool to access the data structure and to parse all parameter files of the Bruker ParaVision format into python dictionaries, to select the relevant information to fill the Nifti header and data volume. Lastly it is meant to be a starting point where to integrate possible future variations in Bruker hardware and ParaVision software future releases.

Type: Article
Title: Bruker2nifti: Magnetic Resonance Images converter from Bruker ParaVision to Nifti format
Open access status: An open access version is available from UCL Discovery
DOI: 10.21105/joss.00354
Publisher version: http://dx.doi.org/10.21105/joss.00354
Language: English
Additional information: Authors of JOSS papers retain copyright and release the work under a Creative Commons Attribution 4.0 International License (CC-BY) (http://creativecommons.org/licenses/by/4.0/).
UCL classification: UCL
UCL > Provost and Vice Provost Offices > UCL BEAMS
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science > Dept of Med Phys and Biomedical Eng
URI: https://discovery.ucl.ac.uk/id/eprint/1571768
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