NIfTI‐MRS: a standard data format for magnetic resonance spectroscopy

William T. Clarke*, Tiffany K. Bell, Uzay E. Emir, Mark Mikkelsen, Georg Oeltzschner, Amirmohammad Shamaei, Brian J. Soher, Martin Wilson

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

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Abstract

Purpose: Multiple data formats in the MRS community currently hinder data sharing and integration. NIfTI‐MRS is proposed as a standard spectroscopy data format, implemented as an extension to the Neuroimaging informatics technology initiative (NIfTI) format. This standardized format can facilitate data sharing and algorithm development as well as ease integration of MRS analysis alongside other imaging modalities.

Methods: A file format using the NIfTI header extension framework incorporates 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 convert single‐voxel and spectroscopic imaging data to NIfTI‐MRS. Visualization of data in NIfTI‐MRS is provided by development of a dedicated plugin for FSLeyes, the FMRIB Software Library (FSL) image viewer.

Results: Online documentation and 10 example datasets in the proposed format are provided. Code examples of NIfTI‐MRS readers are implemented in common programming languages. Conversion software, spec2nii, currently converts 14 formats where data is stored in image‐space to NIfTI‐MRS, including Digital Imaging and Communications in Medicine (DICOM) and vendor proprietary formats.

Conclusion: NIfTI‐MRS aims to solve issues arising from multiple data formats being used in the MRS community. Through a single conversion point, processing and analysis of MRS data are simplified, 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. Greater standardization and harmonization become possible. 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, for visualization.
Original languageEnglish
Pages (from-to)2358-2370
Number of pages13
JournalMagnetic Resonance in Medicine
Volume88
Issue number6
Early online date11 Sept 2022
DOIs
Publication statusPublished - Dec 2022

Bibliographical note

Funding Information:
Support provided by funding from the Wellcome Trust and the Royal Society, grant 102584/Z/13/Z (William T. Clarke.); the National Institutes of Health (NIH), grants K99/R00 AG062230, S10 OD021648, P41 EB031771, P41 EB015909, R01 EB016089, R01 EB023963, and R01 EB028259 (Georg Oeltzschner); and funding from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska‐Curie grant agreement no. 813120 (Amir M. Shamaei.). The Wellcome Centre for Integrative Neuroimaging is supported by core funding from the Wellcome Trust, grant 203139/Z/16/Z.

The authors thank all contributors of test data and source code to the spec2nii program— especially Jack Miller and Tomas Psorn —and Paul McCarthy, the FSLeyes developer, for his extensive advice in creating the NIfTI-MRS visualization plugin.

Publisher Copyright:
© 2022 The Authors. Magnetic Resonance in Medicine published by Wiley Periodicals LLC on behalf of International Society for Magnetic Resonance in Medicine.

Keywords

  • MRS
  • MRSI
  • RESEARCH ARTICLE
  • RESEARCH ARTICLES
  • open data format
  • spectroscopy
  • visualization

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