Publication detail

NIfTI-MRS: A standard data format for magnetic resonance spectroscopy

CLARKE, W. MIKKELSEN, M. OELTZSCHNER, G. BELL, T. SHAMAEI, A. SOHER, B. EMIR, U. WILSON, M.

Original Title

NIfTI-MRS: A standard data format for magnetic resonance spectroscopy

Type

journal article in Web of Science

Language

English

Original Abstract

Purpose The use of multiple data formats in the MRS community currently hinders data sharing and integration. NIfTI-MRS is proposed as a standard MR spectroscopy data format, which is implemented as an extension to the neuroimaging informatics technology initiative (NIfTI) format. Using this standardised format will facilitate data sharing, ease algorithm development, and encourage the integration of MRS analysis with other imaging modalities. Methods A file format based on the NIfTI header extension framework was designed to incorporate essential spectroscopic metadata and additional encoding dimensions. A detailed description of the specification is provided. An open-source command-line conversion program is implemented to enable conversion of single-voxel and spectroscopic imaging data to NIfTI-MRS. To provide visualisation of data in NIfTI-MRS, a dedicated plugin is implemented for FSLeyes, the FSL image viewer. Results Alongside online documentation, ten example datasets are provided in the proposed format. In addition, minimal examples of NIfTI-MRS readers have been implemented. The conversion software, spec2nii, currently converts fourteen formats to NIfTI-MRS, including DICOM and vendor proprietary formats. Conclusion The proposed format aims to solve the issue of multiple data formats being used in the MRS community. By providing a single conversion point, it aims to simplify the processing and analysis of MRS data, thereby lowering the barrier to use of MRS. Furthermore, it can serve as the basis for open data sharing, collaboration, and interoperability of analysis programs. It also opens possibility of greater standardisation and harmonisation. By aligning with the dominant format in neuroimaging, NIfTI-MRS enables the use of mature tools present in the imaging community, demonstrated in this work by using a dedicated imaging tool, FSLeyes, as a viewer.

Keywords

Spectroscopy; MRS; MRSI; reproducible; visualisation

Authors

CLARKE, W.; MIKKELSEN, M.; OELTZSCHNER, G.; BELL, T.; SHAMAEI, A.; SOHER, B.; EMIR, U.; WILSON, M.

Released

29. 7. 2022

Publisher

John Wiley & Sons, Inc

ISBN

0740-3194

Periodical

MAGNETIC RESONANCE IN MEDICINE

State

United States of America

Pages from

2358

Pages to

2370

Pages count

13

URL

https://ora.ox.ac.uk/objects/uuid:4675d22d-fac5-40da-a095-ba9960a38bb9

BibTex

@article{BUT178848,
  author="William T {Clarke} and mark {mikkelsen} and Georg {Oeltzschner} and Tiffany {Bell} and Amirmohammad {Shamaei} and Brian J {Soher} and Uzay {Emir} and Martin {Wilson}",
  title="NIfTI-MRS: A standard data format for magnetic resonance spectroscopy",
  journal="MAGNETIC RESONANCE IN MEDICINE",
  year="2022",
  number="0",
  pages="2358--2370",
  doi="10.1002/mrm.29418",
  issn="0740-3194",
  url="https://ora.ox.ac.uk/objects/uuid:4675d22d-fac5-40da-a095-ba9960a38bb9"
}