U41:Service

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This page captures the Service Activities in the NCIGT U41.

Year 8 June 1, 2012-May 30, 2013

Year 7 June 1, 2011-May 30, 2012

  1. August 9 2011: Cristina Simoes-Franklin, PhD (cristinasimoesfranklin@beaumont.ie), a physicist/neuroscientist in Beaumont Hospital in Dubli, Ireland, consulted via an email exchange with the Golby Lab on use of Slicer and setting up a multimodal neurosurgical planning unit. Her desire is to fuse fMRI and DTI data to high resolution T1 images and make these maps available in the OR for neuronavigation.

Year 6 June 1, 2010-May 30, 2011

Year 5 (June 1, 2009-May 30, 2010)

  1. June, 2010: Prostate CT images provided to Georgia Tech for segmentation by Tempany/Cormack.
  2. HMS Research Tutorial Course, 2009-2010, Fridays 3:00-4:30pm DFCI Radiology Education Rm
  3. GPU Programming Lecture: NCIGT arranged an online lecture by Joe Stam, applications engineer from NVIDIA Corp, for a group of 50+ participants from 15+ universities/companies. This was prompted by requests from James Balter of U Michigan and Xenios Papademetris of Yale, to address specific IGT software engineering problems using the CUDA programming environment. This will be followed up by NVIDIA presence at the JOINT PROJECT Week.
  4. June 2010 Publication: Use of prostate datasets by Dr. Unal at Sabanci University, Faculty of Engineering and Natural Sciences, Istanbul, Turkey for publishing of Unal G. Nonparametric joint shape learning for customized shape modeling. Comput Med Imaging Graph. 2010 Jun;34(4):298-307. PMID: 20044237.

Year 4 (June 1, 2008-May 30, 2009)

  1. On-site visit to Univ of Utah by Scott Hoge to assist with library deployment, Dec 17-19, 2008.
  2. Provided consultation (Panych) to Hacene Serrai at National Research Council in Canada on solving artifact issues in MR wavelet encoding
  3. Provided DARTS software and assisted UofToronto, Sunnybrook researchers to set up real-time workstation for use with real-time reconstruction of temperature mapping data during FUS heating.
  4. Provided modified fast gradient echo pulse sequence to Dr. Kagayaki Kuroda's group (Medical Device Development Center, kagayaki@keyaki.cc.u-tokai.ac.jp) in Tokai University, Japan for image guided therapy research.
  5. Provided DARTS software and consultation to Giedrius Buracas (Salk Institute, UCSD MRI Center Faculty) for application in real-time dynamic fMRI.
  6. Provided functions from the 2DRF library along with consultation to collaborators at Duke University. Functions were used to improve pulse for 3D EPI imaging with applications in both fMRI and temperature mapping.
  7. The line scan diffusion imaging pulse sequence is shared with national and international sites. The most important projects include: spine diffusion imaging (Roland Bammer, Stanford, USA), high-b diffusion, imaging in animal tumor models and tumor patients (Yael Mardor, Sheba University Hospital, Israel), and diffusion imaging of tumors in the neck and inferior fossa (Masauyki Maeda, Mie University Hospital Japan).
  8. Feb 10, 2009: Bob Mulkern supplied Fabio Baselice, a PhD student at the Univ of Naples, Italy, with references about T2 mapping techniques including the paper: Roebuck JR, Haker SJ, Mitsouras D, Rybicki FJ, Tempany CM, Mulkern RV. Carr-Purcell-Meiboom-Gill imaging of prostate cancer: quantitative T(2) values for cancer discrimination. Magn Reson Imaging. 2008 Sep 25. PMID: 18823731.
  9. Oct 13-17, 2008: Alex Golby hosted Cliff Belden, a neuroradiologist transitioning from Albany Medical Center, Albany, NY to Dartmouth-Hitchcock in NH, to study clinical fMRI/DTI at the Advanced MRI Center.
  10. August 2008: Technical support to setup Slicer navigation for image guided surgery for Stephan Baron, a PhD student at Leibniz Universität Hannover, Germany. Haiying Liu and Junichi Tokuda. ALSO UNDER U41:Dissemination
  11. June - November 2008: Teleconference Workshop of Slicer IGT for graduate students at Shanghai Jiaotong University (SJTU), Shanghai, China. Technical support for building 3D ultrasound module in Slicer3. Haiying Liu.ALSO UNDER U41:Dissemination
  12. June - November 2008: Technical support to setup Slicer navigation with OpenIGTLink and NeuroNav for Peter Böttcher, Dr med vet, DipECVS at European Veterinary Specialist in Surgery, Universität Leipzig, Germany. Haiying Liu and Junichi Tokuda. ALSO UNDER U41:Dissemination

Year 3 (June 1, 2007-May 30, 2008)

  • May 2008: NCIGT team hosted Insightec Mini Symposium with Insight leadership at BWH to discuss status and plans for MRgFUS
  • March 3-31, 2008: Dr. Hata provided 3D Slicer IGT training through phone and Skype to researchers at Shanghai Jiaotong University, China
  • March 2008: Dr Hata hosted Dr. Tohru Tani, Professor and Chairman of Surgery at Shiga University of Medicine and Science Seta of Otsu-shi Shiga, Japan
  • February 7, 2008, Cleveland Clinic Visit: Cleveland Clinic is planning to build a large number of operating rooms and they are asking our advice. We will be offering a special edition of the ORF lecture plus significant glimpses of the next 5 years for 11 members of their design team. Participants include: Gene Barnett, MD, Brain Tumor and Neuro-oncology Center, Daphne Bascom, MD, Managing Director, eCleveland Clinic, Adam Fogelman, VP Technology, eCleveland Clinic, Ryan Goodwin, MD, Orthopedic Surgery, Louis Lannum, Radiology Informatics, Michael Modic, MD, Chairman of the Neurological Institute, David Piraino, MD, Radiology Informatics (Adhoc), Barbara Wilson, RN, Director of Surgical Services, Virginia Mannocchio, RN, Nursing, Surgical Services, and Dawn Schultz, RN, Nurse Manager, Surgical Services.
  • Provision of MRI-Guided FUS System and Expertise to assist in MGH Alzheimer’s Brain Research: From the NCIGT, Brian Bacskai, PhD, at the MGH, received help with targeted BBB disruption to his group’s mice. The NCIGT loaned the MGH group its ultrasound equipment to do the procedure without MRI guidance
  • A Slicer module called MRProstateCare was designed and implemented to guide prostate biopsy in the MR-guided imaging environment. The module is used for 1) Planning biopsy targets; 2) Controlling the scanner operations; and 3) Guiding the prostate biopsy procedure
  • Drs. Hata and Tokuda conducted a web-based tutorial on a device communication library, NaviTrack, for Johns Hopkins and Acoustic Med Systems
  • Drs. Hata and Tokuda conducted a consultation on 3D Slicer and tracking device integration for the Nagoya Institute of Technology, Japan.
  • Dr. Mulkern provided consultation on the development of high spatial resolution imaging in 3D formats with inner volume methods to BWH surgeons
  • November 13-14, 2007: Dr. Hata conducted a Slicer demonstration at CIMIT Innovation Congress, Boston, MA
  • Summer 2007: Dr. Hata served as a Prostate IGT Breakout Session Organizer at the NA-MIC/Project Week
  • Populated a brain tumor database prototype with 75 cases
  • Made available 10 non-rigidly registered MRT datasets on the NCIGT website under Downloads
  • Neurosurgery Core created a downloadable Tutorial on fMRI and DTI available on the NCIGT website under Downloads. The Neurosurgery Core continues to develop and refine fMRI and DTI imaging protocols for neurosurgical planning that have been validated through intraoperative electrophysiology. We will continue to make these well-tested protocols available for other neurosurgical sites. Specialized preoperative fMRI and DTI scan protocols are provided to physicians at local hospitals for their planning of resective neurosurgery. We have also created a tutorial entitled "Clincial Functional MRI and Diffusion Tensor Imaging for Surgical Planning" that can be downloaded by clinicians and researchers at other institutions PPT or PDF
  • Imaging Toolbox was made available on the NCIGT website under Downloads
  • Weekly, the Imaging Core held a two-hour pulse sequence programming workshop for MR physics researchers
  • Dr. Chang-Sheng Mei gave Course, Introduction to MRI: Following the Track of Nobel Laureates, at the Physics Department of Soochow University, Taiwan
  • Created and made available OpenIGTLink, a network protocol for data transfer of tracking and imaging, enabling IGTSK to interface with commercial trackers and to Slicer so that Slicer can work with the following commercial trackers: NDI Polaris, NDI Aurora, Ascension Flock of Birds, and Ascension Microbird.
  • November 8-9, 2007: NCIGT team invited to help JHU team setup iMRI. 2007_November_NCIGT_Delegation_to_JHU

Year 2 (June 1, 2006-May 30, 2007)

NCRR Service Definition with which the NCIGT is Aligned

“Providing biomedical investigators access to a Resource’s technology constitutes the service activity. This includes making available specialized instrumentation, equipment, software and techniques, and offering consultation and technical assistance in their use. Service is characterized by a routine operation of resource equipment or methods in which Resource Center personnel have little intellectual role and generally do not share in the intellectual property of the data or samples nor in authorship on resulting papers or patents. The Resource Center, however, is expected to be acknowledged in papers resulting from all projects, including service research projects. While service is one of the key elements of the Resource, the P41 mechanism is not intended to support centers that are predominantly service oriented.” NCRR Biotechnology Guidelines, page 2

There are two broad classes of service activities provided by our Center. One is through freely downloadable software and related documentation, and the other is through providing access to our specialized research facilities and techniques to external parties.

Freely Downloadable Software and Tutorials: The primary service activity of the NCIGT Computation Core, a collaborative service effort between NCIGT, the Neuroimage Analysis Center (NAC, U54 Kikinis/Jolesz), and the National Center for Medical Image Analysis (NA-MIC, U54 Kikinis), is the http://www.slicer.org website that has extensive documentation and support materials, including downloadable data sets for our open source research platform, 3D Slicer. The link to this site, URL: http://www.ncigt.org/slicer, is also available through the NCIGT website in the Service section. This site is augmented with the uploading of materials developed as part of joint development efforts by the NA-MIC, NCIGT, NAC, and others. Slicer services use publicly-visible email lists that allow investigators to actively engage with the user and developer communities to answer questions and resolve issues arising from the application of the technology in new environments or the influx of new data. The slicer-users@bwh.harvard.edu mailing list, for example, has 281 subscribers at US and international sites. This list serves as a forum for user issues. Archives of these exchanges are available to augment the standard documentation set. Similarly, slicer-devel@bwh.harvard.edu, with 194 subscribers, supports the exchange of information among the Core development group and between the Core group and the larger development community.

In Year 2 of the NCIGT, specifically, the Slicer service team leveraged the training infrastructure in Slicer that was initiated by NA-MIC to create training materials for the Slicer IGT extensions and made these publicly accessible through the Center website. As of May 1, 2007 since the start of the current funding period of NCIGT, 5,361 individuals have downloaded the package. The tutorial training is also available on request and has been implemented and tested. A recent example of its use was in one of the Center’s external collaborations (BRP grant- R01 CA 111288). The industrial partner in BRP; namely, Clif Burdette and his team at Acousticmed (formerly CMS), conducted an on-line tutorial led by Junichi Okuda (BWH). A second extensively supported service the NCIGT provided this year was the Slicer Image Guided Navigator (SIGN) platform for navigated procedures (http://www.ncigt.org/sign/). (A link to this website is also provided through the Service section of the NCIGT website.)

Access to Specialized MRI Intervention Resources: The Prostate Core provided access to personnel with appropriate expertise and time on the facility's MRI scanners to Steven Dubowsky, Professor of Mechanical Engineering at Massachusetts Institute of Technology. Dr. Dubowsky's group, led by Lauren Devita, has developed a dielectic elastomer actuator. Simon DiMaio, Ph.D., provided a set of specifications regarding working space in the MRI scanner, degrees of freedom, and ranges of motion necessary to insert a needle into the prostate with the Dubowsky technology. Daniel Kacher, M.S., provided advice on tailoring the device to be compatible with the MRI environment and conducted experiments in the MRI scanner with the group. Joseph Roebuck, M.D. (R25 training grant fellow), provided insight on appropriate tissue equivalent phantoms to gauge if the actuator was generating the necessary force to penetrate the skin and tissue to target a point within the prostate.

Access to Specialized FUS Protocols: FUS brain and prostate protocols are currently under development by our FUS Core and will be shared with several outside centers. Preliminary meetings have been held with Cornell and Memorial Sloan Kettering to develop the prostate cancer MRgFUS protocol. Insightec Inc. is supporting the device development.

Specialized fMRI/DTI Scans for Resective Neurosurgery: The Neurosurgery Core has developed a protocol for neurosurgical planning based on fMRI and DTI that has been validated through intraoperative electrophysiology. We will make this well-tested protocol available for other neurosurgical sites. Specialized fMRI and DTI scans are provided for local hospitals for resective neurosurgery. In future years of the Center, these protocols will be refined and made available to the broader research community through the NCIGT website.

Access to Parallel Imaging Library: The Imaging Core is currently developing a fast parallel imaging library that will be available for external investigators in Year 3 of the Center.

Prostate MR Database: Segmented by experts at the BWH, an anonymized data set of MR scans from the Prostate Core are available for other sites for algorithm development. To date, it has been used by groups at Johns Hopkins, Georgia Tech, UNC and Riverside Institute, NY.

Year 1 (June 1, 2005-May 30, 2006)

Service: The effort of the Service team has been mainly around MRT, FUS, and Slicer sites. Specifically, the following has been accomplished:

MRT and FUS: Service has been continued to MRT and FUS sites that were established prior to the start of the grant.

Slicer software: Service has been continued for the 3D Slicer open source software for medical image analysis and visualization. Specifically, Slicer 2.6 which contains IGT extensions and SIGN software for IGT were released this year.

Help Mailing List: A mailing list, ncigt-help@bwh.harvard.edu, was created and made accessible from both the external website and the more private center wiki. Year 2 Plans

Service: The MRT and FUS service effort will continue with in the same spirit as the first year. A specific goal for the Slicer service team is to leverage the training infrastructure in Slicer to add traiing materials for the IGT extensions.