Education & Training:
- (HP MRI Course 2023) - DNP Hardware: HyperSense, SpinAligner, and SPINlab:  As part of our TR&D2 project we are proud to offer this presentation on the preclinical and clinical polarizers. Watch this presentation to learn more about: the requirements for DNP Hardware, the different types of commerical dissolution DNP systems, and the technological advances in dissolution DNP

- Clinical translation of hyperpolarized ¹³C pyruvate and urea (Co-Pol) imaging agents: This presentation given by Dr. Andrew Riselli, PharmD, RPh, HP Research Pharmacist goes over:

• Developing a formulation and procedure to prepare a sterile HP ¹³C pyruvate and urea injection product.
• Conducting nonclinical studies including toxicology. 
• Submitting the clinical protocol, Chemistry Manufacturing and Controls (CMC), and toxicology reports to the FDA for approval.
• General guidelines for submitting the clinical protocol to the IRB for approval. 

- Production of Filled Pharmacy Kits (cassettes) and Terminal Sterilization For Human Studies: As part of our TR&D1 project we are proud to offer training in Production of Filled Pharmacy Kits (cassettes) and Terminal Sterilization For Human Studies. Click on the button to the right to learn more about: Manufacturing Methods & Facilities, Acceptance Testing, Quality Control, Manufacturing and Release, Documentation and Analysis

- Sample Methods for GE SPINlab Polarizer: Methods for Pharmakit Filling & Polarizer Set-up 

- HP Probe Preparation Training in Novel Hyperpolarized MR Molecular Imaging Probes: As part of our TR&D2 project we are proud to offer HP Probe Preparation Training in novel hyperpolarized MR molecular imaging probes.

Education & Training:
- Overview Hyperpolarized ¹³C MRI: Polarization Physics & Hardware:
As part of our TR&D1 project we are proud to offer this seminar lecture on the overview of Polarization Physics & Hardware for Hyperpolarized ¹³C MRI. Please see the outline below for topics covered. To view the presentation please see the links to the right. 

DNP Physics: Magnetization, Boltzmann Distribution, Signal-to-Noise Ratio, Sensitivity, Thermal Polarization, Brute-Force Polarization, Dynamic Nuclear Polarization, DNP Hyperpolarization, DNP Requirements, Solid Effect, Cross Effect, Thermal Mixing, Spin Diffusion, Effect of Temperature and Field Strength, Effect of Radical

Polarizer Hardware: HyperSense Polarizer (Buildup, Dissolution Procedure, Key Considerations) ; SPINlab Polarizer (Comparison with HyperSense, Fluid Path, Key Considerations, Clinical Applications)

Suggestions on Further Readings

- Preclinical DNP Polarizer training for improved DNP Methodology: As part of our TR&D1 project we are proud to offer Preclinical DNP Polarizer training for improved DNP Methodology. This training is hands-on which allows users to learn through experience with support from members of our Center. For more information please email [email protected].

Education & Training:
- Overview Hyperpolarized ¹³C MRI: Polarization Physics & Hardware:
As part of our TR&D1 project we are proud to offer this seminar lecture on the overview of Polarization Physics & Hardware for Hyperpolarized ¹³C MRI. Please see the outline below for topics covered. To view the presentation please see the links to the right. 

DNP Physics: Magnetization, Boltzmann Distribution, Signal-to-Noise Ratio, Sensitivity, Thermal Polarization, Brute-Force Polarization, Dynamic Nuclear Polarization, DNP Hyperpolarization, DNP Requirements, Solid Effect, Cross Effect, Thermal Mixing, Spin Diffusion, Effect of Temperature and Field Strength, Effect of Radical

Polarizer Hardware: HyperSense Polarizer (Buildup, Dissolution Procedure, Key Considerations) ; SPINlab Polarizer (Comparison with HyperSense, Fluid Path, Key Considerations, Clinical Applications)

Suggestions on Further Readings

- National Cancer Institute - IND Regulatory & Manufacturing Resources on Hyperpolarized [¹³C]  Pyruvate: This resource provides links to the component documents for an IND for hyperpolarized [13C] Pyruvate. For more information please email [email protected].

- Human DNP Polarizer training for improved DNP Methodology: As part of our TR&D1 project we are proud to offer Human DNP Polarizer training for improved DNP Methodology. This training is hands-on which allows users to learn through experience with support from members of our Center. For more information please email [email protected].

Education & Training:
- Coil Design: Coil images & descriptions used for Human Research Acquisition - Coming soon. Interested in trying our coil designs for human research? Email us at [email protected].

Description: The goal of this toolbox is to provide research-level and prototyping software tools for hyperpolarized MRI experiments. It is currently based on Matlab code, and includes code for designing radiofrequency (RF) pulses, readout gradients, and data reconstruction. This toolbox also contains pulse sequence construction tools such as the Spectral-Spatial RF Pulse Design for MRI and MRSI Matlab Package. This package includes Matlab functions to design spectral-spatial RF pulses (also known as spatial-spectral RF pulses) for application to magnetic resonance spectroscopy and imaging. 

Description: SIVIC is an open-source, standards-based software framework and application suite for processing and visualization of DICOM MR Spectroscopy data. Through the use of DICOM, SIVIC aims to facilitate the application of MRS in medical imaging studies. This program features a PyDICOM Tool Box.

Supporting  Resources:

• Tutorials and Users Guide
• Download Sample C-13 Data
• Data Analysis Review Article
• Source Code on GitHub
• Training: SIVIC Open-Source Software Training 

External RF MRI: This Matlab code helps the user control a Agilent RF vector electronic signal generator (ESG) from a PC, for the purpose of generating RF excitation pulses for magnetic resonance imaging (MRI). This is especially useful for equipping a standard "single nucleus" MRI scanner with a supplementary RF transmission channel for enabling heteronuclear MRI experiments. Questions? Email us at [email protected]. 

Multiband RF Pulse Design: This is a Matlab toolbox for RF pulse design used in Magnetic Resonance Imaging (MRI). It features design of 1D selective RF pulse with multiband magnitude profile, arbitrary phase profile and generalized flip angle. The implementation is built on Shinnar-Le Roux (SLR) algorithm and convex optimization. Spectral sparsity was exploited to further improve pulse performance, such as minimizing pulse duration, transition width or total energy with flexible trade-off. Questions? Email us at [email protected]. 

Bruker 3T Packages (PV6): 

Bruker 3T 2D CSI: Contains SIVIC 2D CSI sequences and the associated scripts for SIVIC processing and slab 1D sequence that are used at UCSF. 

Bruker 3T EPSI - Pulse Sequence Program: This SPSP pulse acquisition package for Bruker 3T includes instructions and resources on how to calculate and calibrate the pulse & gradient profile for the hyperpolarize probe of interest as well as how to acquire data. Also, through this resource you can find the custom Matlab codes for the analysis of 2D EPSI data in preclinical brain tumor models which was acquired on a Bruker horizontal MR system.

Bruker 3T Slab Spectroscopy - Pulse Sequence Program: This SPSP pulse acquisition package for Bruker 3T includes instructions and resources on how to calculate and calibrate the pulse & gradient profile for the hyperpolarize probe of interest as well as how to acquire data.

Bruker ParaVision 6 hpMR Method Fiiles: Created from The University of Texas MD Anderson Cancer Center, Department of Imaging Physics by Keith Michael, this repository contains Bruker ParaVision 6 hpMR method files and associated Matlab tools for the design and implementation of hyperpolarized imaging experiments using snapshot EPI readouts, IDEAL encoding and/or spectral-spatial RF excitations. Please note, this method has currently been tested only on the CentOS 5.11 operating system.

- (HP MRI Course 2021) - Hyperpolarized C-13 MRI Pulse Sequence Strategies: This presentation is an overview of Data Processing provided from the 2021 HP MRI Course and includes topics such as:
- Imaging Trade-offs: T₁ Decay, ¹H vs ¹³C Imaging
- Coils & Calibration: RF Coils, Multichannel Arrays, ¹³C Frequency Calibration, RF Power Calibration, Autonomous Scanning, Flip Angle, Dynamic Imaging
- Imaging Approaches: k-space, HP Imaging of Inert Substrates, SSFP, Metabolically Active Substrates, Dealing with Off-Resonance, Spectroscopic Imaging Techniques, Chemical Shift Imaging, Rapid Spectroscopic Techniques, Model-Based Reconstructions, Signal Model in k-space, Model-Based Reconstructions, Signal Model in k-space, Spectral Selectivity, Slice-Selective Excitation, Spectral-Spatial RF Pulses/Excitation, Metabolite-Specific Imaging, Acquisition Scheme Comparison, Sequence Trade-offs

Description: The goal of this toolbox is to provide research-level and prototyping software tools for hyperpolarized MRI experiments. It is currently based on Matlab code, and includes code for designing radiofrequency (RF) pulses, readout gradients, and data reconstruction. This toolbox also contains pulse sequence construction tools such as the Spectral-Spatial RF Pulse Design for MRI and MRSI Matlab Package. This package includes Matlab functions to design spectral-spatial RF pulses (also known as spatial-spectral RF pulses) for application to magnetic resonance spectroscopy and imaging. 

Description: SIVIC is an open-source, standards-based software framework and application suite for processing and visualization of DICOM MR Spectroscopy data. Through the use of DICOM, SIVIC aims to facilitate the application of MRS in medical imaging studies. This program features a PyDICOM Tool Box.

Supporting  Resources:

• Tutorials and Users Guide
• Download Sample C-13 Data
• Data Analysis Review Article
• Source Code on GitHub
• Training: SIVIC Open-Source Software Training 

External RF MRI: This Matlab code helps the user control a Agilent RF vector electronic signal generator (ESG) from a PC, for the purpose of generating RF excitation pulses for magnetic resonance imaging (MRI). This is especially useful for equipping a standard "single nucleus" MRI scanner with a supplementary RF transmission channel for enabling heteronuclear MRI experiments. Questions? Email us at [email protected]. 

Multiband RF Pulse Design: This is a Matlab toolbox for RF pulse design used in Magnetic Resonance Imaging (MRI). It features design of 1D selective RF pulse with multiband magnitude profile, arbitrary phase profile and generalized flip angle. The implementation is built on Shinnar-Le Roux (SLR) algorithm and convex optimization. Spectral sparsity was exploited to further improve pulse performance, such as minimizing pulse duration, transition width or total energy with flexible trade-off. Questions? Email us at [email protected]. 

EPI pulse sequence: In order to enable faster, more robust hyperpolarized (HP) MRI for patient studies, we developed a new metabolite-specific broadband EPI pulse sequence for rapid volumetric imaging of HP [1-¹³C]pyruvate and other molecules. This pulse sequence contains commonly used features such as ramp-sampling, partial-Fourier, and Nyquist ghost correction. It includes built-in spectral-spatial RF pulses and flip angle schemes for pyruvate and other probes, as well as the capability to integrate user-designed pulses and flip angles. This pulse sequence is compatible with clinical MR scanners and includes reconstruction and analysis software, facilitating the integration of metabolic data into the clinical workflow. 

MNS Research Pack (GE Healthcare): The MNS Research Pack is a software acquisition package for GE MRI scanners focused on multi-nuclear imaging and spectroscopy for hyperpolarized [1-¹³C]pyruvate research.  It includes different sequences and semi-automatic pre-scanning. In addition to pre-installed methods, additional RF pulses and trajectories can be designed off-line in Matlab, saved in a file, and read into the sequence. The package is available on request, contact: Rolf.Schulte_at_Research.ge.com

RT Hawk: RThawk is an interactive platform for hyperpolarized [1-¹³C]pyruvate multislice spiral imaging, providing wide coverage and featuring automatic frequency and power calibrations. Originally developed for cardiac MRI applications, it offers specialized cardiac-gated C13 acquisition techniques integrated into standard proton heart studies, which are tailored for short-axis, long-axis views and more. It also comes with pulse programming environment that allows technical development and adaptation for other imaging targets.

- (HP MRI Course 2023) - Hyperpolarized MR Experimental Methods - Human: This presentation is an overview of Data Processing provided from the 2023 HP MRI Course. Objectives of this presentation are:

•  Identify the necessary components involved in a human HP C-13 MR study.​
• Give an overview of major areas of interest for clinical studies at UCSF.​
• Examine the MR hardware, pulse sequences and processing techniques.​
• Highlight the importance of patient safety and sterility for C-13 stable-isotope clinical studies/trials.

- (HP MRI Course 2021) - Hyperpolarized C-13 MRI Pulse Sequence Strategies: This presentation is an overview of Data Processing provided from the 2021 HP MRI Course and includes topics such as:
- Imaging Trade-offs: T₁ Decay, ¹H vs ¹³C Imaging
- Coils & Calibration: RF Coils, Multichannel Arrays, ¹³C Frequency Calibration, RF Power Calibration, Autonomous Scanning, Flip Angle, Dynamic Imaging
- Imaging Approaches: k-space, HP Imaging of Inert Substrates, SSFP, Metabolically Active Substrates, Dealing with Off-Resonance, Spectroscopic Imaging Techniques, Chemical Shift Imaging, Rapid Spectroscopic Techniques, Model-Based Reconstructions, Signal Model in k-space, Model-Based Reconstructions, Signal Model in k-space, Spectral Selectivity, Slice-Selective Excitation, Spectral-Spatial RF Pulses/Excitation, Metabolite-Specific Imaging, Acquisition Scheme Comparison, Sequence Trade-offs

Description: The goal of this toolbox is to provide research-level and prototyping software tools for hyperpolarized MRI experiments. It is currently based on Matlab code, and includes code for designing radiofrequency (RF) pulses, readout gradients, and data reconstruction. This toolbox also contains pulse sequence construction tools such as the Spectral-Spatial RF Pulse Design for MRI and MRSI Matlab Package. This package includes Matlab functions to design spectral-spatial RF pulses (also known as spatial-spectral RF pulses) for application to magnetic resonance spectroscopy and imaging. 

Description: SIVIC is an open-source, standards-based software framework and application suite for processing and visualization of DICOM MR Spectroscopy data. Through the use of DICOM, SIVIC aims to facilitate the application of MRS in medical imaging studies. This program features a PyDICOM Tool Box.

Supporting  Resources:

• Tutorials and Users Guide
• Download Sample C-13 Data
• Data Analysis Review Article
• Source Code on GitHub
• Training: SIVIC Open-Source Software Training 

- (HP MRI Course 2023) Storage, Visualization, and Analysis of Hyperpolarized C-13 MR Data by Dr. Peder Larson: This presentation is from the 2023 HP MRI Course and includes topics such as:
- Data storage and preparation – ensure data is ready for analysis​ (File formats​, Preprocessing e.g. phasing​)
- Data visualization – inspect data​ (High dimensional data​, Tools​)
- Model-free metrics – alternatives to kinetic models​ (Ratios​)
- Kinetic/pharmacokinetic modeling – fit data to a model for quantification
- Data Analysis, Live Demo

- Di-chromatic Interpolation of Metabolic Magnetic Resonance Images by Dr. Nicholas Dwork, Postdoctoral Scholar: This presentation is an overview of a publication by Dr. Nicholas Dwork:
Dwork N, Gordon JW, Tang S, O'Connor D, Hansen ESS, Laustsen C, Larson PEZ. Di-chromatic interpolation of magnetic resonance metabolic images. MAGMA. 2021; 34(1):57-72. PMCID: PMC7983744 

Preclinical Raw & Processed Data Examples, Disease Model Images: Examples of in vivo animal  hyperpolarized MRI data can be found using the links to the right. These data sets were acquired with different methods and are described more in detail below.

• SIVIC Tutorials using Sample in vivo Hyperpolarized datasets: On our SOURCEFORGE page, you can find links to SIVIC tutorials that have been presented at live workshops. The data sets are from specific vendors, but the general concepts should applicable to data from any vendor.
• Sample in vivo Hyperpolarized MRI Data on GitHub: In the hyperpolarized-mri-toolbox on GitHub, you can access several in vivo hyperpolarized MRI data sets that come from animal and human studies that are acquired with a variety of different methods. Below are some selected examples:

Description: The goal of this toolbox is to provide research-level and prototyping software tools for hyperpolarized MRI experiments. It is currently based on Matlab code, and includes code for designing radiofrequency (RF) pulses, readout gradients, and data reconstruction. This toolbox also contains pulse sequence construction tools such as the Spectral-Spatial RF Pulse Design for MRI and MRSI Matlab Package. This package includes Matlab functions to design spectral-spatial RF pulses (also known as spatial-spectral RF pulses) for application to magnetic resonance spectroscopy and imaging. 

Description: SIVIC is an open-source, standards-based software framework and application suite for processing and visualization of DICOM MR Spectroscopy data. Through the use of DICOM, SIVIC aims to facilitate the application of MRS in medical imaging studies. This program features a PyDICOM Tool Box.

Supporting  Resources:

• Tutorials and Users Guide
• Download Sample C-13 Data
• Data Analysis Review Article
• Source Code on GitHub
• Training: SIVIC Open-Source Software Training 

- (HP MRI Course 2023) - Storage, Visualization, and Analysis of Hyperpolarized C-13 MR Data by Dr. Peder Larson: This presentation is from the 2023 HP MRI Course and includes topics such as:

• Data storage and preparation – ensure data is ready for analysis​ (File formats​, Preprocessing e.g. phasing​)
•  Data visualization – inspect data​ (High dimensional data​, Tools​)
• Model-free metrics – alternatives to kinetic models​ (Ratios​)
• Kinetic/pharmacokinetic modeling – fit data to a model for quantification
• Data Analysis, Live Demo

- Using EPI to investigate HP [1-¹³C]pyruvate metabolism in glioma patients and healthy volunteers by Dr. Adam Autry: This presentation is from the 2019 HP MRI Course and includes topics such as: Dynamic Echo Planar Imaging (EPI), Dynamic frequency-selective ¹³C EPI, EPI Processing Framework, Optimal Weights Coil Combination, Voxel-wise Phasing, Regions of Interest, Kinetic traces and fitting: NAWMl, k_pl & k_pb Maps with ROIs, Serial HP Data.

- Image Analysis Techniques ¹³C MRI in Clinical Study by Dr. Hsin-Yu Chen: This presentation is from the 2019 HP MRI Course and includes topics such as: Challenges in Clinical Mangement of Prostate Cancer, processing HP-¹³C Prostate Data, Peak Quantification, Phased Detection of Spectra, Phase Correction, Other Quantification Techniques, Receiver Correction, Receiver Correction - Case Study, Transmitter Considerations, Image Display, Masking and ROIs, Quantification of Cancer Metabolism. 

- Di-chromatic Interpolation of Metabolic Magnetic Resonance Images by Dr. Nicholas Dwork, Postdoctoral Scholar: This presentation is an overview of a publication by Dr. Nicholas Dwork:
Dwork N, Gordon JW, Tang S, O'Connor D, Hansen ESS, Laustsen C, Larson PEZ. Di-chromatic interpolation of magnetic resonance metabolic images. MAGMA. 2021; 34(1):57-72. PMCID: PMC7983744 

- Denoising of HP C-13 MR Images of the Human Brain using Patch-based Higher-order Singular Value Decomposition: This presentation is an overview of a publication by Dr. Yaewon Kim: Kim Y, Chen HY, Autry AW, Villanueva-Meyer J, Chang SM, Li Y, Larson PEZ, Brender JR, Krishna MC, Xu D, Vigneron DB, Gordon JW. Denoising of hyperpolarized ¹³C MR images of the human brain using patch-based higher-order singular value decomposition. Magn Reson Med. 2021 Jun 25. doi: 10.1002/mrm.28887. Epub ahead of print. PMID: 34173268.

- Specialized Computational Methods for Denoising, B₁ Correction & Kinetic Modeling in HP ¹³C MR EPSI Studies of Liver Tumors: This presentation is an overview of a publication by Graduate Student Philip Lee from the Vigneron Group: Lee PM, Chen HY, Gordon JW, Zhu Z, Larson PEZ, Dwork N, Van Criekinge M, Carvajal L, Ohliger MA, Wang ZJ, Xu D, Kurhanewicz J, Bok RA, Aggarwal R, Munster PN, Vigneron DB. Specialized computational methods for denoising, B₁ correction, and kinetic modeling in hyperpolarized ¹³C MR EPSI studies of liver tumors. Magn Reson Med. 2021 Jul 3. doi: 10.1002/mrm.28901. Epub ahead of print. PMID: 34216051.

HP C-13 EPI HOSVD Denoising: This GitHub repository contains Matlab codes for denoising hyperpolarized 13C MR images of the human brain using patch-based higher-order singular value decomposition and sample data from a healthy brain volunteer and simulations. The description of the method and results can be found in the paper published in Magnetic Resonance in Medicine (doi: 10.1002/mrm.28887.)

Human Research Raw & Processed Data Examples, Disease Model Images: Examples of in vivo human hyperpolarized MRI data can be found using the links to the right. These data sets were acquired with different methods and are described more in detail below.

• SIVIC Tutorials using Sample in vivo Hyperpolarized datasets: On our SOURCEFORGE page, you can find links to SIVIC tutorials that have been presented at live workshops. The data sets are from specific vendors, but the general concepts should applicable to data from any vendor.
• Sample in vivo Hyperpolarized MRI Data on GitHub: In the hyperpolarized-mri-toolbox on GitHub, you can access several in vivo hyperpolarized MRI data sets that come from animal and human studies that are acquired with a variety of different methods. Below is a selected example:

Human Brain: This dataset contains pyruvate, lactate, and bicarbonate dynamic imaging using metabolite-specific imaging with EPI in the head of a healthy volunteer.