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): | ||
| + | Image:Marburg-csi+slicer.png|Fusion of anatomic dataset with MRS dataset using Slicer | ||
</gallery> | </gallery> | ||
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==Key Investigators== | ==Key Investigators== | ||
| − | * SPL: Jan Egger, Isaiah Norton, Tina Kapur | + | * SPL: Jan Egger, Isaiah Norton, Tina Kapur, Alexandra Golby |
| − | * | + | * UKGM: Daniel Hořínek, Jens Sommer, Christopher Nimsky |
* ETHZ: Bjoern Menze | * ETHZ: Bjoern Menze | ||
| + | * IKEM: Antonín Škoch | ||
<div style="margin: 20px;"> | <div style="margin: 20px;"> | ||
| Line 18: | Line 20: | ||
<h3>Objective</h3> | <h3>Objective</h3> | ||
| − | 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. | + | 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> | </div> | ||
| Line 26: | Line 28: | ||
<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. |
</div> | </div> | ||
| Line 33: | Line 35: | ||
<h3>Progress</h3> | <h3>Progress</h3> | ||
| + | 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 | ||
- | - | ||
| Line 44: | Line 52: | ||
Towards a 3DSlicer module... | Towards a 3DSlicer module... | ||
| + | |||
| + | ==Bibliography== | ||
| + | [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. | ||
| + | |||
| + | [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. | ||
| + | |||
| + | [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.] | ||
| + | Radiology. 2011 May;259(2):540-9. Epub 2011 Feb 25. | ||
| + | |||
| + | ==Resources== | ||
| + | [http://sourceforge.net/apps/trac/sivic/ Sivic] | ||
| + | [http://sourceforge.net/apps/trac/sivic/browser/trunk/applications/slicer_plugin 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/ | ||
| + | |||
| + | [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
Fusion of an anatomic dataset with the hybrid MRS dataset under iPlan (AMIGO)
Segmentation result of the MRS region under iPlan (AMIGO):
Fusion of anatomic dataset with MRS dataset using Slicer
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.?
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
