2011 Winter Project Week:MRSI module and SIVIC interface

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Home < 2011 Winter Project Week:MRSI module and SIVIC interface

Key Investigators

  • MIT: Bjoern Menze, Mangpo Phothilimthana, Polina Golland
  • UCSF: Beck Olson, Jason Crane, Sarah Nelson (Nelson Lab)
  • BWH: Nicole Aucoin



Magnetic resonance spectroscopic imaging (MRSI) is a non-invasive diagnostic method used to determine the relative abundance of specific metabolites at arbitrary locations in vivo. Certain diseases -- such as tumors in brain, breast and prostate -- can be can be associated with characteristic changes in the metabolic level.

The objective of the current project is to develop a module proving the means for the processing and visualization of MRSI -- and thus for a joint analysis of magnetic resonance spectroscopic images together with other imaging modalities -- in Slicer.

Approach, Plan

Spectral fitting routines have been implemented, using a HSVD filter for water peak removal and baseline estimation, and a constrained non-linear least squares optimization for the fit of the resonance line models. Current fitting routines require, however, several external software libraries not to be distributed, installed and used easily.

We want to integrate the currently available MRSI quantitation routines with the SIVIC Slicer interface developed at the UCSF. More specifically we want to integrate the previously developed signal processing routines (Fig. 1) into the svk library of the SIVIC framework, and realize the joint display of metabolic maps (Fig. 2) and spectral information (Fig. 3) within the current prototype of the Slicer module.


  • We implemented a basic quantification algorithm (Fig. 4) integrating over predefined spectral regions and made progress towards implementing the other fitting routines.
  • Metabolic maps generated in Slicer can now be displayed (Fig. 4).
  • The display of individual spectra in Slicer now also supports multiple traces from the spectral fitting (Fig. 5).
  • We improved the integration of SIVIC with Slicer through a better use of the MRML architecture.
  • The new functionality is now available through SIVIC and a Slicer Module prototype.

Delivery Mechanism

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

  1. ITK Module
  2. Slicer Module
    1. Built-in
    2. Extension -- commandline
    3. Extension -- loadable YES
  3. Other (Please specify) YES: part of the 'vtk style' svk library of the SIVIC framework


  • Jason C. Crane, Marram P. Olson, Sarah J. Nelson. SIVIC: An Extensible Open-Source DICOM MR Spectroscopy Software Framework and Application Suite. Proc ISMRM 2010. 3354.