Difference between revisions of "2012 Winter Project Week:hybridMRS"

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Image:MRS2.png|Fusion of an anatomic dataset with the hybrid MRS dataset under iPlan (AMIGO)
 
Image:MRS2.png|Fusion of an anatomic dataset with the hybrid MRS dataset under iPlan (AMIGO)
 
Image:MRS1.png|Segmentation result of the MRS region under iPlan (AMIGO):
 
Image:MRS1.png|Segmentation result of the MRS region under iPlan (AMIGO):
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Image:Marburg-csi+slicer.png|Fusion of anatomic dataset with MRS dataset using Slicer
 
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==Key Investigators==
 
==Key Investigators==
* SPL: Isaiah Norton, Jan Egger, Christopher Nimsky, Tina Kapur
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* SPL: Jan Egger, Isaiah Norton, Tina Kapur, Alexandra Golby
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* UKGM: Daniel Hořínek, Jens Sommer, Christopher Nimsky
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* ETHZ: Bjoern Menze
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* IKEM: Antonín Škoch
  
 
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<h3>Objective</h3>
 
<h3>Objective</h3>
  
Generating a hybrid MR-Spectroscopic (MRS) dataset under 3DSlicer.
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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.
  
 
</div>
 
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<h3>Approach, Plan</h3>
 
<h3>Approach, Plan</h3>
  
-
+
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.
  
 
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<h3>Progress</h3>
 
<h3>Progress</h3>
 +
Loaded/integrated processed chemical shift-MRS data from Uni. Marburg into Slicer4.
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Pending:
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- updating SIVIC-Slicer module to latest revision of SIVIC
  
 +
- port module to Slicer4
 
-
 
-
  
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Towards a 3DSlicer module...
 
Towards a 3DSlicer module...
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 +
==Bibliography==
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[http://www.ncbi.nlm.nih.gov/pubmed/16424238 Preoperative Grading of Gliomas by Using Metabolite Quantification with High-Spatial-Resolution Proton MR Spectroscopic Imaging.] Radiology 2006 Mar;238(3):958-69.
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[http://www.ncbi.nlm.nih.gov/pubmed/20708548 Imaging of brain tumors: MR spectroscopy and metabolic imaging.] Neuroimaging Clin N Am. 2010 Aug;20(3):293-310.
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[http://www.ncbi.nlm.nih.gov/pubmed/21357517 Use of in vivo two-dimensional MR spectroscopy to compare the biochemistry of the human brain to that of glioblastoma.]
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Radiology. 2011 May;259(2):540-9. Epub 2011 Feb 25.
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 +
==Resources==
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[http://sourceforge.net/apps/trac/sivic/ Sivic]
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[http://sourceforge.net/apps/trac/sivic/browser/trunk/applications/slicer_plugin Sivic plugin for Slicer 3.?]
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http://www.brighamandwomens.org/Departments_and_Services/radiology/Research/Spectroscopy/Default.aspx
 +
 +
https://scion.duhs.duke.edu/svn/sample_data/siemens_rda_export/read_rda102.m
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http://www.acrin.org/portals/0/protocols/6677/imaging/6677spectro_files_siemens.pdf
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http://hci.iwr.uni-heidelberg.de/MIP/Software/csitools.php
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 +
http://tarquin.sourceforge.net/
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[http://www.sites.google.com/site/jsiprotool/ jSIPRO - MR Spectroscopic Imaging Processing Tool]
  
 
</div>
 
</div>

Latest revision as of 15:33, 13 January 2012

Home < 2012 Winter Project Week:hybridMRS

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

Objective

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.

Progress

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

Pending:

- updating SIVIC-Slicer module to latest revision of SIVIC

- port module to Slicer4 -

Delivery Mechanism

Towards a 3DSlicer module...

Bibliography

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.

Resources

Sivic Sivic plugin for Slicer 3.?

http://www.brighamandwomens.org/Departments_and_Services/radiology/Research/Spectroscopy/Default.aspx

https://scion.duhs.duke.edu/svn/sample_data/siemens_rda_export/read_rda102.m

http://www.acrin.org/portals/0/protocols/6677/imaging/6677spectro_files_siemens.pdf

http://hci.iwr.uni-heidelberg.de/MIP/Software/csitools.php

http://tarquin.sourceforge.net/

jSIPRO - MR Spectroscopic Imaging Processing Tool