William T Clarke1, Tiffany K Bell2,3,4, Uzay E Emir5,6, Mark Mikkelsen7, Georg Oeltzschner8,9, Amirmohammad Shamaei10,11, Brian J Soher12, Martin Wilson13. 1. Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom. 2. Department of Radiology, University of Calgary, Calgary, Alberta, Canada. 3. Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada. 4. Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada. 5. School of Health Sciences, Purdue University, West Lafayette, Indiana, USA. 6. Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana, USA. 7. Department of Radiology, Weill Cornell Medicine, New York, New York, USA. 8. Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA. 9. F. M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, Maryland, USA. 10. Czech Academy of Sciences, Institute of Scientific Instruments, Brno, Czech Republic. 11. Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic. 12. Center for Advanced MR Development, Department of Radiology, Duke University Medical Center, Durham, North Carolina, USA. 13. Centre for Human Brain Health and School of Psychology, University of Birmingham, Birmingham, United Kingdom.
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.
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.
Authors: Souheil J Inati; Joseph D Naegele; Nicholas R Zwart; Vinai Roopchansingh; Martin J Lizak; David C Hansen; Chia-Ying Liu; David Atkinson; Peter Kellman; Sebastian Kozerke; Hui Xue; Adrienne E Campbell-Washburn; Thomas S Sørensen; Michael S Hansen Journal: Magn Reson Med Date: 2016-01-29 Impact factor: 4.668
Authors: Christopher J Markiewicz; Krzysztof J Gorgolewski; Franklin Feingold; Ross Blair; Yaroslav O Halchenko; Eric Miller; Nell Hardcastle; Joe Wexler; Oscar Esteban; Mathias Goncavles; Anita Jwa; Russell Poldrack Journal: Elife Date: 2021-10-18 Impact factor: 8.713