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

Journal Article (Journal Article)

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.

Full Text

Duke Authors

Cited Authors

  • Clarke, WT; Bell, TK; Emir, UE; Mikkelsen, M; Oeltzschner, G; Shamaei, A; Soher, BJ; Wilson, M

Published Date

  • December 2022

Published In

Volume / Issue

  • 88 / 6

Start / End Page

  • 2358 - 2370

PubMed ID

  • 36089825

Pubmed Central ID

  • PMC7613677

Electronic International Standard Serial Number (EISSN)

  • 1522-2594

Digital Object Identifier (DOI)

  • 10.1002/mrm.29418


  • eng

Conference Location

  • United States