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Overview

SIVIC is an open-source standards-based software framework and application suite for processing and visualization of DICOM MR Spectroscopy data.

The SIVIC project provides a standalone, cross platform visualization application and plug-ins for OsiriX and Slicer. The SIVIC c++ framework extends VTK and supports reading, writing, algorithms and visualization classes for MR spectroscopy (MRS) data. The framework is extensible, and community participation and contributions are encouraged to facilitate accessibility and validation of MRS processing methodologies (recon, post-processing, quantification).

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Supported File Formats

• supported file formats

SIVIC Applications

• SIVIC standalone MRI/MRS Visualization and Processing GUI
• SIVIC Application and Plug-in for OsiriX
• SIVIC Module for Slicer
• svk_file_convert? - Command line tool for converting between different MRI/MRS formats.
• svk_gepfile_reader? - Command line tool for converting GE PFiles to DICOM MRS. Provides more GE pfile specific functionality than svk_file_convert.
• svk_quick_view? - Command line tool that loads a lightweight MRI/MRS display window
• svk_multi_view? - Command line tool for loading multiple images with spectra and overlay image
• svk_create_dcmraw? - Command line tool for encapsulating a raw file inside a DICOM Raw Storage SOP instance.
• svk_dcmdump? - Command line tool that shows DICOM header data structure used by SIVIC internally to store meta data for loaded data sets.
• svk_get_filetype? - Command line utility that returns the svk reader type that supports the input data file.
• svk_integrate_dynamic? - Command line utility that reads in a time series of spectra (5D data), integrates the magnitude spectrum at each time point over the specified interval, and outputs a 4D data set representing the time evolution of the integrated magnitude peak vs time.
• svk_quantify? - Command line tool that returns peak ht, integrated area, ratios or z-scores from a spectroscopy data set.
• svk_reslice? - Command line utility that reslices an 3D image to the orientation of a reference MRS data set.
• svk_spec_diff? - Command line utility that returns the difference between 2 MRS data sets.
• svk_svrecon? - Command line utility that performs a simple single voxel multi-channel recon.
• auto_mrsi_prescription - Automate Prescription for 3D Brain MRSI

Documentation and Support

• Supported file formats
• Get help, report a bug, request a feature
• SIVIC Application User's Guide
• mailing listarchive
• DICOM Conformance (DICOM IODs supported by SIVIC)
• FAQ
• Tutorials

Downloads

• download applications, source code and sample data sets

For Developers

• Building from source and Using the SIVIC Library and Application Suite
• SIVIC API Documentation
• Join the SIVIC development team
• SIVIC CDash Dashboard

Leadership

• Nelson Lab, UCSF

Collaborators and Contributors

• SIVIC Committers
• Don Bigler (Penn State)
• Jason Crane (UCSF)
• Emma Essock-Burns (UCSF)
• Bob Kraft (WFU)
• Christine Leon (UCSF)
• Janine Lupo (UCSF)
• Bjoern Menze (MIT) - Lead, SIVIC module for3D Slicer
• Beck Olson (UCSF)
• Eugene Ozhinsky (UCSF)
• Mangpo Phitchaya Phothilimthana (MIT)
• Martin Wilson (University of Birmingham)

References

• RSNA 2010 (Exhibit LL-INE1208-SUB) - SIVIC: A Vendor Agnostic Extensible Open Source Software Framework for Processing and Visualizing MR Spectroscopy Data Using the DICOM Standard
• ISMRM 2010 (program 3354) - SIVIC: An Extensible Open-Source DICOM MR Spectroscopy Software Framework and Application Suite
• RSNA 2009 (Exhibit LL-IN3522-D) - Open Source DICOM MR Spectroscopy Software Framework and Plug-in for OsiriX

Funding

SIVIC is funded by NIH P41EB013598, NIH P01 CA11816 and NIH RO1 CA127612

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