2012 Winter Project Week:hybridMRS

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Project Title: Generation of a hybrid MR-Spectroscopic (MRS) dataset under 3DSlicer

Key Investigators

  • SPL: Jan Egger, Isaiah Norton, Tina Kapur, Alexandra Golby
  • UKGM: Daniel Hořínek, Jens Sommer, Christopher Nimsky
  • ETHZ: Bjoern Menze
  • IKEM: Antonín Škoch


Generating a hybrid MR-Spectroscopic (MRS) dataset under 3DSlicer that can be used for fusion with the anatomic dataset under iPlan of BrainLAB in AMIGO. A hybrid MR-Spectroscopic dataset can for example be used for biopsy targeting in brain tumors. Besides, the metabolic concentrations and ratios can help to diagnose lesions.

Approach, Plan

Try to process MRS data with the MRSI module from Bjoern Menze developed at a previous project week. The module interfaces SIVIC, which is an open-source standards-based software framework and application suite for processing and visualization of DICOM MR Spectroscopy data.


Loaded/integrated processed chemical shift-MRS data from Uni. Marburg into Slicer4.


- updating SIVIC-Slicer module to latest revision of SIVIC

- port module to Slicer4 -

Delivery Mechanism

Towards a 3DSlicer module...


Preoperative Grading of Gliomas by Using Metabolite Quantification with High-Spatial-Resolution Proton MR Spectroscopic Imaging. Radiology 2006 Mar;238(3):958-69.

Imaging of brain tumors: MR spectroscopy and metabolic imaging. Neuroimaging Clin N Am. 2010 Aug;20(3):293-310.

Use of in vivo two-dimensional MR spectroscopy to compare the biochemistry of the human brain to that of glioblastoma. Radiology. 2011 May;259(2):540-9. Epub 2011 Feb 25.


Sivic Sivic plugin for Slicer 3.?






jSIPRO - MR Spectroscopic Imaging Processing Tool