Tutorials
The following are 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.
HMTRC Workshops
SIVIC Quick Start
SIVIC GUI Quick Start - anatomy of the SIVIC GUI
2019 Workshop Tutorials
- SIVIC Analysis: This tutorial demonstrates visualization and analysis of HP 13C data using the SIVIC GUI and command line tools.
2019 HMTRC 13C Workshop SIVIC Analysis Tutorial
2019 HMTRC 13C Workshop SIVIC Analysis Tutorial Sample Data
- SIVIC Development: This tutorial demonstrates the use of Docker to access a SIVIC C++ software environment and walks the user through the development of a new kinetic model and applies it to fit simulated dynamic HP 13C sample data.
SIVIC Software Development With Docker Tutorial
Docker Image With Data (This does not need to be downloaded manually and will be downloaded as part of the tutorial)
- Workshop presentations:
SIVIC Hands On Tutorial Slides
2018 Workshop Tutorials
- SIVIC Analysis: This tutorial demonstrates visualization and analysis of HP 13C data using the SIVIC GUI and command line tools.
2018 HMTRC 13C Workshop SIVIC Analysis Tutorial
2018 HMTRC 13C Workshop SIVIC Analysis Tutorial Sample Data
- SIVIC Development: This tutorial demonstrates the use of Docker to access a SIVIC C++ software environment and walks the user through the development of a new kinetic model and applies it to fit simulated dynamic HP 13C sample data.
SIVIC Software Development With Docker Tutorial
Docker Image With Data (This does not need to be downloaded manually and will be downloaded as part of the tutorial)
- Workshop presentations:
SIVIC Hands On Tutorial Slides
2017 Workshop Tutorials
- SIVIC GUI Introduction: This tutorial demonstrates interactive visualization and analysis of HP 13C data using the SIVIC GUI.
2017 HMTRC 13C Workshop SIVIC GUI Tutorial Cookbook
2017 HMTRC 13C Workshop SIVIC GUI Tutorial Sample Data
- SIVIC Command Line Scripting: This tutorial demonstrates command line analysis of HP 13C data using SIVIC command line tools for batch mode data analysis.
GE 3T 13C Dual Band Variable Flip Angle Dynamic Spectroscopy Tutorial Cookbook for LINUX/Mac OsX Users
GE 3T 13C Dual Band Variable Flip Angle Dynamic Spectroscopy Tutorial Cookbook for Windows Users
GE 3T 13C Dual Band Variable Flip Angle Dynamic Spectroscopy Sample Data
- SIVIC Development: This tutorial introduces the SIVIC C++ software framework and walks the user through the development of a new kinetic model and applies it to fit simulated dynamic HP 13C sample data.
SIVIC software development tutorial
Sample data for kinetic modeling development tutorial
- Workshop presentations:
SIVIC Introduction Overview
SIVIC with MATLAB and Creating Figures with SIVIC
2016 Workshop Tutorials
- GE 3T 2D EPSI Dual Band Variable Flip Angle 13C Dynamic Spectroscopy Recon, Quantification and Kinetic Modeling
Load a dynamic MRS animal data set acquired on a GE 3T scanner. This data was acquired with an EPSI sequence using a dual-band variable flip angle pulse scheme. You will reconstruct the data, combine the EPSI lobes, combine the coils and then correct for the dual-band and variable-flip pulse profiles using a Data Acquisition Description (DAD) file produced for the sequence. Then you will generate metabolite maps for pyruvate and lactate at each time point and also manually create an ROI mask of the animal. These results will be saved as DICOM images and used as input to a kinetic modeling program that will fit the observed dynamic signal changes to a 2-site exchange model within the ROI and generate 3D maps of Kpl and T1all.
GE 3T 13C Dual Band Variable Flip Angle Dynamic Spectroscopy Tutorial Cookbook
GE 3T 13C Dual Band Variable Flip Angle Dynamic Spectroscopy Sample Data
2014 Workshop Tutorials
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Varian 13C 2D CSI Mouse Reconstruction and Quantification
Load 13C Varian MRS and MRI data, reconstruct and quantify metabolites. Demonstrates export of DICOM data in the following formats: Secondary Capture, MRI (metabolite maps) and MR Spectroscopy data.
Varian 13C 2DCSI Mouse Brain Tutorial Cookbook
Varian 13C 2DCSI Mouse Brain Data
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GE 3T 13C Dynamic Human Prostate Recon, Quantification and Kinetic Modeling
Load dynamic 13C GE MRS and MRI data, reconstruct and quantify metabolites at each time point and display time variation of metabolites. Use svk command line tools to fit metabolite concentrations vs time to a kinetic model of pyruvate to lactate conversion and display fitted parameter maps. Demonstrates customization of quantification ranges and export of DICOM data in the following formats: Secondary Capture, MRI (metabolite maps) and MR Spectroscopy data.
GE 3T 13C Dynamic Human Prostate Tutorial Cookbook
GE 3T 13C Dynamic Human Prostate Sample Data
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Varian 14T 13C 2D EPSI Recon and Quantification
Load 13C Varian MRS and MRI data, reconstruct and quantify metabolites. Demonstrates customization of quantification ranges and export of DICOM data in the following formats: Secondary Capture, MRI (metabolite maps) and MR Spectroscopy data.
Varian 14T 13C 2D EPSI Phantom Tutorial Cookbook
Varian 14T 13C 2D EPSI Phantom Sample Data
Special Topics
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MRSI Quantification
This document describes how to customize the SIVIC quantification.
[MRSI_quantification] -
SIVIC Auto MRS Documentation
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This document describes the use of the MATLAB atlas MRS prescription tool:
http://sourceforge.net/p/sivic/sivicwiki/Tutorials/attachment/SIVIC_Atlas_RX_SDC1.pdf -
This document shows the code for reading an MRS prescription embedded into a GE PSD:
https://sourceforge.net/p/sivic/sivicwiki/Tutorials/attachment/SIVIC_GE_PSD_SDC2.pdf -
This document provides the SOP for operating the SIVIC MRS recon on the GE console:
https://sourceforge.net/p/sivic/sivicwiki/Tutorials/attachment/SIVIC_GE_CONSOLE_RECON_SDC3.pdf
Sample Data
HMTRC-2016: GE 3T 13C Dual Band Variable Flip Angle Dynamic Spectroscopy Sample Data
Varian 13C 2DCSI Mouse Brain Data
GE 3T 13C Dynamic Human Prostate Data
Varian 14T 13C 2D EPSI Phantom Data
