SIVIC: Open-source, standards-based software for DICOM MR spectroscopy workflows

International Journal of Biomedical Imaging

Volumn 2013, Issue , 2013, Pages

  Crane, Jason C ^a   Olson, Marram P ^a   Nelson, Sarah J ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANATOMICAL IMAGES; FILE FORMATS; MAGNETIC RESONANCE SPECTROSCOPIC IMAGING; METABOLIC PARAMETERS; MR SPECTROSCOPY; OPEN-SOURCE; OPEN-SOURCE SOFTWARES; THERAPEUTIC MONITORING;

COMPUTER PROGRAMMING; DATA VISUALIZATION; MAGNETIC RESONANCE SPECTROSCOPY; SCANNING; TOOLS; VISUALIZATION;

COMPUTER AIDED DIAGNOSIS;

ALGORITHM; COMPUTER INTERFACE; COMPUTER PROGRAM; CONCEPTUAL FRAMEWORK; DIGITAL IMAGING AND COMMUNICATIONS IN MEDICINE; E-MAIL; HUMAN; IMAGE ANALYSIS; IMAGE RECONSTRUCTION; MAGNETIC RESONANCE SPECTROSCOPIC IMAGING; NUCLEAR MAGNETIC RESONANCE IMAGING; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PATIENT CARE; REVIEW; STANDARDIZATION; WORKFLOW;

EID: 84881398824     PISSN: 16874188     EISSN: 16874196     Source Type: Journal    
DOI: 10.1155/2013/169526     Document Type: Review

References (40)

1. Okuda D. T., Srinivasan R., Oksenberg J. R., Goodin D. S., Baranzini S. E., Beheshtian A., Waubant E., Zamvil S. S., Leppert D., Qualley P., Lincoln R., Gomez R., Caillier S., George M., Wang J., Nelson S. J., Cree B. A. C., Hauser S. L., Pelletier D., Genotype-phenotype correlations in multiple sclerosis: HLA genes influence disease severity inferred by 1HMR spectroscopy and MRI measures. Brain 2009 132 1 250 259 2-s2.0-58849146101 10.1093/brain/awn301
2. Laprie A., Catalaa I., Cassol E., McKnight T. R., Berchery D., Marre D., Bachaud J.-M., Berry I., Moyal E. C.-J., Proton magnetic resonance spectroscopic imaging in newly diagnosed glioblastoma: predictive value for the site of postradiotherapy relapse in a prospective longitudinal study. International Journal of Radiation Oncology Biology Physics 2008 70 3 773 781 2-s2.0-38849152924 10.1016/j.ijrobp.2007.10.039 (Pubitemid 351199728)
3. Chang J., Thakur S., Perera G., Kowalski A., Huang W., Karimi S., Hunt M., Koutcher J., Fuks Z., Amols H., Narayana A., Image-fusion of MR spectroscopic images for treatment planning of gliomas. Medical Physics 2006 33 1 32 40 2-s2.0-31044436014 10.1118/1.2128497 (Pubitemid 43121029)
4. Westman E., Wahlund L.-O., Foy C., Poppe M., Cooper A., Murphy D., Spenger C., Lovestone S., Simmons A., Magnetic resonance imaging and magnetic resonance spectroscopy for detection of early Alzheimers Disease. Journal of Alzheimer's Disease 2011 26 3 307 319 2-s2.0-80055044259 10.3233/JAD-2011-0028
5. 13C]pyruvate. NMR in Biomedicine 2012 25 8 993 999 2-s2.0-84856998872 10.1002/nbm.2762
6. Park I., Tamai G., Lee M. C., Chuang C. F., Chang S. M., Berger M. S., Nelson S. J., Pirzkall A., Patterns of recurrence analysis in newly diagnosed glioblastoma multiforme after three-dimensional conformal radiation therapy with respect to pre-radiation therapy magnetic resonance spectroscopic findings. International Journal of Radiation Oncology Biology Physics 2007 69 2 381 389 2-s2.0-34548507261 10.1016/j.ijrobp.2007.03.019 (Pubitemid 47380095)
7. Sankar T., Caramanos Z., Assina R., Villemure J.-G., Leblanc R., Langleben A., Arnold D. L., Preul M. C., Prospective serial proton MR spectroscopic assessment of response to tamoxifen for recurrent malignant glioma. Journal of Neuro-Oncology 2008 90 1 63 76 2-s2.0-50649121262 10.1007/s11060-008-9632-3
8. Stadlbauer A., Moser E., Gruber S., Nimsky C., Fahlbusch R., Ganslandt O., Integration of biochemical images of a tumor into frameless stereotaxy achieved using a magnetic resonance imaging/magnetic resonance spectroscopy hybrid data set. Journal of Neurosurgery 2004 101 2 287 294 2-s2.0-3242748189 (Pubitemid 38971006)
9. Tzika A. A., Proton magnetic resonance spectroscopic imaging as a cancer biomarker for pediatric brain tumors. International Journal of Oncology 2008 32 3 517 526 2-s2.0-40249091888 10.3892/ijo-32-3-517 (Pubitemid 351330457)
10. Crawford F. W., Khayal I. S., McGue C., Saraswathy S., Pirzkall A., Cha S., Lamborn K. R., Chang S. M., Berger M. S., Nelson S. J., Relationship of pre-surgery metabolic and physiological MR imaging parameters to survival for patients with untreated GBM. Journal of Neuro-Oncology 2009 91 3 337 351 2-s2.0-58149470593 10.1007/s11060-008-9719-x
11. Pinker K., Stadlbauer A., Bogner W., Gruber S., Helbich T. H., Molecular imaging of cancer: MR spectroscopy and beyond. European Journal of Radiology 2012 81 3 566 577 2-s2.0-84856963594 10.1016/j.ejrad.2010.04.028
12. DICOM, http://medical.nema.org/
13. DICOM Standard Part 3PS 3.3-2011, section A.36.3.3, http://medical.nema. org/standard.html
14. SIVIC, http://sourceforge.net/projects/sivic/
15. Crane J. C., Olson M. P., Nelson S. J., Open source DICOM MR spectroscopy software framework and plug-in for osiriX. RSNA Annual Meeting 2009
16. jMRUI, http://www.mrui.uab.es/mrui/mrui-Overview.shtml
17. MIDAS, http://mrir.med.miami.edu:8000/midas/
18. TARQUIN, http://tarquin.sourceforge.net/
19. VTK, http://www.vtk.org/
20. DCMTK, http://dicom.offis.de/dcmtk.php.en
21. 3D Slicer, http://www.slicer.org/
22. OsiriX, http://www.osirix-viewer.com/
23. SIVIC plug-in for OsiriX, http://sourceforge.net/projects/sivic/files/ osirix-plugin/
24. Slicer project week, 2010, http://www.na-mic.org/Wiki/index.php/2010- Summer-Project-Week-MRSI-module-and-SIVIC-interface
25. Slicer project week, 2011, http://www.na-mic.org/Wiki/index.php/2011- Winter-Project-Week:MRSI-module-and-SIVIC-interface
26. SIVIC command line tools, http://sivic.sourceforge.net/libsvk/html/index. html
27. SFTP, http://en.wikipedia.org/wiki/SSH-File-Transfer-Protocol
28. Crane J. C., Crawford F. W., Nelson S. J., Grid enabled magnetic resonance scanners for near real-time medical image processing. Journal of Parallel and Distributed Computing 2006 66 12 1524 1533 2-s2.0-33751014820 10.1016/j.jpdc.2006.03.009 (Pubitemid 44751385)
29. DCM4CHEE, http://www.dcm4che.org/confluence/display/ee2/Home
30. 1H magnetic resonance spectroscopy data. Magnetic Resonance in Medicine 2011 65 1 1 12 2-s2.0-79954426854
31. Stefan D., Cesare F. D., Andrasescu A., Popa E., Lazariev A., Vescovo E., Strbak O., Williams S., Starcuk Z., Cabanas M., Van Ormondt D., Graveron-Demilly D., Quantitation of magnetic resonance spectroscopy signals: the jMRUI software package. Measurement Science and Technology 2009 20 10 2-s2.0-70350695845 10.1088/0957-0233/20/10/104035 104035
32. Cunningham C. H., Vigneron D. B., Chen A. P., Xu D., Nelson S. J., Hurd R. E., Kelley D. A., Pauly J. M., Design of flyback echo-planar readout gradients for magnetic resonance spectroscopic imaging. Magnetic Resonance in Medicine 2005 54 5 1286 1289 2-s2.0-27644551824 10.1002/mrm.20663 (Pubitemid 41567210)
33. 13C MR spectroscopic imaging. Journal of Magnetic Resonance 2013 229 187 197
34. DCM4CHEE conformance, http://www.dcm4che.org/docs/conformance/dcm4chee- cs.pdf
35. OsiriX conformance, http://www.osirix-viewer.com/ DICOMConformanceStatements.pdf
36. http://www.carestream.com/pacsv11-dicom-8g8913.pdf
37. Philips conformance, http://incenter.medical.philips.com/doclib/getdoc. aspx?func=ll&objid=9332344&objaction=open
38. Agfa impax 6.5 conformance, http://www.agfahealthcare.com/global/en/he/ library/libraryopen?ID=28653428
39. svkImageReader2 classes, http://sivic.sourceforge.net/libsvk/html/ hierarchy.html
40. Sundararajan D., Digital Signal Processing: Theory and Practice 2003 World Scientific