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bioRxiv · 10.1101/2021.11.09.467912

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

Clarke, W. T.·Mikkelsen, M.·Oeltzschner, G.·Bell, T.·Shamaei, A.·Soher, B. J.·Emir, U. E.·Wilson, M.
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Abstract

PurposeThe 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. MethodsA 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. ResultsAlongside 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. ConclusionThe 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.

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Clarke, W. T., Mikkelsen, M., Oeltzschner, G., Bell, T., Shamaei, A., Soher, B. J., Emir, U. E., Wilson, M.. 2021-11-11. NIfTI-MRS: A standard format for magnetic resonance spectroscopic data. https://doi.org/10.1101/2021.11.09.467912

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