UCSF

Magnetic Resonance Spectroscopic Imaging (MRSI) allows us to visualize metabolites within the body without radioactive tracers, such as those used in PET scans. Hyperpolarized MRI exploits this process by using dynamic dissolution nuclear polarization to enhance the signal of and visualize previously difficult to detect metabolic intermediates such as pyruvate. 13C is a common hyperpolarized (HP) tracer, used for pyruvate imaging, that can help with cancer detection and tracking. MRSI and HP data contains varying numbers of spatial, spectral and temporal dimensions and is typically encoded using proprietary vendor-specific file formats, which presents challenges for post-processing and analysis using standard medical imaging software. The spectral data needs to be registered with the anatomical data, and temporal dimensions represented, if necessary. The Hyperpolarized MRI Technology Resource Center (HMTRC) was created for the dissemination of tools to make HP MRI more accessible, one of its aims being the development of free, open-source software (FOSS). At the University of California, San Francisco, the SIVIC (Spectroscopic Imaging, Visualization, and Computing) software package was developed to aid in this process. Bruker is one of these vendors, and proprietary data files from their newer 3T small animal scanner at UCSF cannot be directly inputted into SIVIC. This lack of standardization for spectral data causes problems across research, as each research group must manually pre-process the data before analysis. In this work, we aim to streamline this workflow by introducing a function that can take as input Bruker 2dseq files from an EPSI sequence and output in a standardized DICOM MRS format. Ultimately, this will provide a data pipeline that enables efficient analysis of Bruker HP data, allow for greater collaboration between research groups, and lines up with the HMTRC’s aim of developing additional FOSS. As of the time of this thesis submission, the pipeline can identify the 2dseq file and write metadata from parameter maps, but cannot fully handle spectral data.