StandardBasisTools

Tools to generate standardized basis spectra and LCM fitting results representations

We have released initial guidelines for a standardized data format to store basis spectra and LCM results. This standard will:

• provide a common format for data sharing
• reduce workload to support file formats specific to a single density matrix simulation software
• increase transparency and reproducibility by adding relevant metadata
• increase between-software compatibility; and e) maximize the integration of MRS into existing software- and data-sharing efforts.

The development is spearheaded by the Code and Data Sharing Committee of the ISMRM MRS study group, encouraging community feedback and contributions via the community forum (forum.mrshub.org).

Preliminary Example data

This repository currently contains an example analysis of an HERCULES MRS dataset. The data is provided in NIfTI-MRS format (MRSHub forum thread or full manuscript for reference) and anlyzed using Osprey.

The example script generates the following outputs:

• Processed data in NIfTI-MRS format including model provenance
• Linear-combination model results in NIfTI-MRS format following a preliminiary proposal to store LCM fitting results
• low-level HERCULES basis set in NIfTI-MRS format

Next step

• Generalize guidelines to leverage NIfTI-MRS to store low-level basis sets and LCM fitting results
• Introduce a data format to store high-level basis sets
• Write conversion scripts for LCM algorithms with discontinued support (LCModel)

Contact & Feedback

If you are interested to contribute please contact Helge J. Zöllner.

Contributors

These efforts are spearheaded by the Code and Data Sharing Committee of the ISMRM MRS study group:

• Helge J. Zöllner (Johns Hopkins University, Baltimore, MD)
• Kelley M. Swanberg (Columbia University, New York, NY)
• John LaMaster (Technische Universität München, München, Germany)
• Antonia Kaiser (University of Amsterdam, Amsterdam, The Netherlands)
• Jamie Near (University of Toronto, Toronto, Canada)
• Candace Fleischer (Georgia Institute of Technology and Emory University, Atlanta, GA)
• Georg Oeltzschner (Johns Hopkins University, Baltimore, MD)

And by other interested MRS software developers:

• Brian J. Soher (University of Oxford, Oxford, United Kingdom)
• William T. Clarke (Duke University Medical Center, Durham, NC)