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

Publication ,  Journal Article
Clarke, WT; Bell, TK; Emir, UE; Mikkelsen, M; Oeltzschner, G; Shamaei, A; Soher, BJ; Wilson, M
Published in: Magn Reson Med
December 2022

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.

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Published In

Magn Reson Med

DOI

EISSN

1522-2594

Publication Date

December 2022

Volume

88

Issue

6

Start / End Page

2358 / 2370

Location

United States

Related Subject Headings

  • Technology
  • Software
  • Nuclear Medicine & Medical Imaging
  • Neuroimaging
  • Magnetic Resonance Spectroscopy
  • Magnetic Resonance Imaging
  • Informatics
  • 4003 Biomedical engineering
  • 0903 Biomedical Engineering
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Clarke, W. T., Bell, T. K., Emir, U. E., Mikkelsen, M., Oeltzschner, G., Shamaei, A., … Wilson, M. (2022). NIfTI-MRS: A standard data format for magnetic resonance spectroscopy. Magn Reson Med, 88(6), 2358–2370. https://doi.org/10.1002/mrm.29418
Clarke, William T., Tiffany K. Bell, Uzay E. Emir, Mark Mikkelsen, Georg Oeltzschner, Amirmohammad Shamaei, Brian J. Soher, and Martin Wilson. “NIfTI-MRS: A standard data format for magnetic resonance spectroscopy.Magn Reson Med 88, no. 6 (December 2022): 2358–70. https://doi.org/10.1002/mrm.29418.
Clarke WT, Bell TK, Emir UE, Mikkelsen M, Oeltzschner G, Shamaei A, et al. NIfTI-MRS: A standard data format for magnetic resonance spectroscopy. Magn Reson Med. 2022 Dec;88(6):2358–70.
Clarke, William T., et al. “NIfTI-MRS: A standard data format for magnetic resonance spectroscopy.Magn Reson Med, vol. 88, no. 6, Dec. 2022, pp. 2358–70. Pubmed, doi:10.1002/mrm.29418.
Clarke WT, Bell TK, Emir UE, Mikkelsen M, Oeltzschner G, Shamaei A, Soher BJ, Wilson M. NIfTI-MRS: A standard data format for magnetic resonance spectroscopy. Magn Reson Med. 2022 Dec;88(6):2358–2370.
Journal cover image

Published In

Magn Reson Med

DOI

EISSN

1522-2594

Publication Date

December 2022

Volume

88

Issue

6

Start / End Page

2358 / 2370

Location

United States

Related Subject Headings

  • Technology
  • Software
  • Nuclear Medicine & Medical Imaging
  • Neuroimaging
  • Magnetic Resonance Spectroscopy
  • Magnetic Resonance Imaging
  • Informatics
  • 4003 Biomedical engineering
  • 0903 Biomedical Engineering