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

0560982 - ÚPT 2023 RIV US eng J - Journal Article
Clarke, W. T. - Bell, T. K. - Emir, U. E. - Mikkelsen, M. - Oeltzschner, G. - Shamaei, Amirmohammad - Soher, B. J. - Wilson, M.
NIfTI-MRS: A standard data format for magnetic resonance spectroscopy.
Magnetic Resonance in Medicine. Roč. 88, č. 6 (2022), s. 2358-2370. ISSN 0740-3194. E-ISSN 1522-2594
EU Projects: European Commission(XE) 813120 - INSPiRE-MED
Institutional support: RVO:68081731
Keywords : MRS * MRSI * open data format * spectroscopy * visualization
OECD category: Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)
Impact factor: 3.3, year: 2022
Method of publishing: Open access
https://onlinelibrary.wiley.com/doi/10.1002/mrm.29418

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.
Permanent Link: https://hdl.handle.net/11104/0333741


Research data: Zenodo