NAMIC Wiki - User contributions [en]

https://www.na-mic.org/w/api.php?action=feedcontributions&feedformat=atom&user=Yong NAMIC Wiki - User contributions [en] 2026-04-06T08:19:29Z User contributions MediaWiki 1.33.0 https://www.na-mic.org/w/index.php?title=2010_Winter_Project_Week_catalyst&diff=47225 2010 Winter Project Week catalyst 2010-01-06T19:10:53Z

<p>Yong: /* Key Investigators */</p> <hr /> <div>==Key Investigators==<br /> * Yong Gao<br /> * Randy Gollub<br /> * John Paulett<br /> * Tim Olsen<br /> * Dan Marcus<br /> <br /> <div style="margin: 20px;"><br /> <div style="width: 27%; float: left; padding-right: 3%;"><br /> <br /> <h3>Objective</h3><br /> Provide support to the Harvard Catalyst as they work to stand up XNAT throughout their user community. Investigate the possibility that the Harvard Catalyst use case could be a model for additional CTSC sites that are also using the i2b2 framework, such as Emory University. <br /> <br /> </div><br /> <br /> <div style="width: 27%; float: left; padding-right: 3%;"><br /> <br /> <h3>Approach, Plan</h3><br /> Specific open issues:<br /> #Review data modeling requirement for XNAT from a MGH PI<br /> #Contributing SubjectHandler Yong wrote into DicomServer release.<br /> #Scan Level search capabilities for queries like "find all mr sessions with a usable MPRAGE scan". According to Tim, this is not an out-of-the-box thing offered by the REST API.<br /> #Processing and loading images in NRRD format.<br /> <br /> </div><br /> <br /> <div style="width: 40%; float: left;"><br /> <br /> <h3>Progress</h3><br /> #Most of the data should have a close map to XNAT schema. Extensions to XNAT are needed to cover Testing session and Clinic Visit. XNAT will add a new field for "site".<br /> #The SubjectHandler code was sent to Kevin Archie for consideration.<br /> #This is now supported in xnat 1.4 rc3. Tim's example request would get a list of sessions with at least one usable MPRAGE from XNAT central: http://central.xnat.org/REST/experiments?xsiType=xnat:mrSessionData&format=xml&columns=ID,label,project&xnat:mrSessionData/scans/scan/quality=usable&xnat:mrSessionData/scans/scan/type=MPRAGE<br /> #NRRD files can be loaded just as any other files. New parser is needed to be written if it's is desired to get header information from the NRRD files.<br /> <br /> </div><br /> <br /> <div style="width: 97%; float: left;"><br /> <br /> <br /> <br /> </div><br /> <br /> ==References==<br /> <div><br /> [http://nrg.wikispaces.com/XNAT+Imaging+Data+Strategies http://nrg.wikispaces.com/XNAT+Imaging+Data+Strategies]<br /> <br /> </div></div>

Yong https://www.na-mic.org/w/index.php?title=2010_Winter_Project_Week_catalyst&diff=47221 2010 Winter Project Week catalyst 2010-01-06T19:00:57Z

<p>Yong: /* Key Investigators */</p> <hr /> <div>==Key Investigators==<br /> * Yong Gao<br /> * Randy Gollub<br /> * John Paulett<br /> * Tim Olsen<br /> * Dan Marcus<br /> <br /> <div style="margin: 20px;"><br /> <div style="width: 27%; float: left; padding-right: 3%;"><br /> <br /> <h3>Objective</h3><br /> Provide support to the Harvard Catalyst as they work to stand up XNAT throughout their user community. Investigate the possibility that the Harvard Catalyst use case could be a model for additional CTSC sites that are also using the i2b2 framework, such as Emory University. <br /> <br /> </div><br /> <br /> <div style="width: 27%; float: left; padding-right: 3%;"><br /> <br /> <h3>Approach, Plan</h3><br /> Specific open issues:<br /> #Review data modeling requirement for XNAT from a MGH PI<br /> #Contributing SubjectHandler Yong wrote into DicomServer release.<br /> #Scan Level search capabilities for queries like "find all mr sessions with a usable MPRAGE scan". According to Tim, this is not an out-of-the-box thing offered by the REST API.<br /> #Processing and loading images in NRRD format.<br /> <br /> </div><br /> <br /> <div style="width: 40%; float: left;"><br /> <br /> <h3>Progress</h3><br /> #Most of the data should have a close map to XNAT schema. Extensions to XNAT are needed to cover Testing session and Clinic Visit. XNAT will add a new field for "site".<br /> #The SubjectHandler code was sent to Kevin Archie for consideration.<br /> #This is now supported in xnat 1.4 rc3.<br /> #NRRD files can be loaded just as any other files. New parser is needed to be written if it's is desired to get header information from the NRRD files.<br /> <br /> </div><br /> <br /> <div style="width: 97%; float: left;"><br /> <br /> <br /> <br /> </div><br /> <br /> ==References==<br /> <div><br /> [http://nrg.wikispaces.com/XNAT+Imaging+Data+Strategies http://nrg.wikispaces.com/XNAT+Imaging+Data+Strategies]<br /> <br /> </div></div>

Yong https://www.na-mic.org/w/index.php?title=2010_Winter_Project_Week&diff=45950 2010 Winter Project Week 2009-12-08T17:33:45Z

<p>Yong: /* Informatics */</p> <hr /> <div> Back to [[Project Events]], [[AHM_2010]], [[Events]]<br /> <br /> __NOTOC__<br /> <br /> ==Background==<br /> <br /> From January 4-8, 2010, the tenth project week for hands-on research and development activity in Image-Guided Therapy and Neuroscience applications will be hosted in Salt Lake City, Utah. Participant engange in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers ([http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions. <br /> <br /> Active preparation for this conference begins with a kick-off teleconference. Invitations to this call are sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties expressing an interest in working with these centers. The main goal of the initial teleconference is to gather information about which groups/projects would be active at the upcoming event to ensure that there were sufficient resources available to meet everyone's needs. Focused discussions about individual projects are conducted during several subsequent teleconferences and permits the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in break-out sessions. In the final days leading up to the meeting, all project teams are asked to complete a template page on the wiki describing the objectives and research plan for each project. <br /> <br /> On the first day of the conference, each project team leader delivers a short presentation to introduce their topic and individual members of their team. These brief presentations serve to both familiarize other teams doing similar work about common problems or practical solutions, and to identify potential subsets of individuals who might benefit from collaborative work. For the remainder of the conference, about 50% time is devoted to break-out discussions on topics of common interest to particular subsets and 50% to hands-on project work. For hands-on project work, attendees are organized into 30-50 small teams comprised of 2-4 individuals with a mix of multi-disciplinary expertise. To facilitate this work, a large room is setup with ample work tables, internet connection, and power access. This enables each computer software development-based team to gather on a table with their individual laptops, connect to the internet, download their software and data, and work on specific projects. On the final day of the event, each project team summarizes their accomplishments in a closing presentation.<br /> <br /> A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].<br /> <br /> == Dates.Venue.Registration ==<br /> <br /> Please [[AHM_2010#Dates._Venue._Registration| click here for Dates, Venue, and Registration]] for this event.<br /> <br /> == Agenda==<br /> <br /> Please [[AHM_2010#Agenda|click here for the agenda for AHM 2010 and Project Week]].<br /> <br /> == Modules and extensions==<br /> <br /> <br /> * [[Media:3DSlicer-Modules%2BExtensions-2009-11-27.ppt|Overview]]<br /> * [http://wiki.slicer.org/slicerWiki/index.php/Documentation-3.5#Requirements_for_Modules Requirements for modules]<br /> * [http://wiki.slicer.org/slicerWiki/index.php/Documentation-3.5#Introduction User-side explanations]<br /> * [http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Extensions Developer-side explanations]<br /> <br /> ==Projects==<br /> <br /> === Segmentation ===<br /> #[[2010_Winter_Project_Week_Spine_Segmentation_Module_in_Slicer3|Spine Segmentation Module in Slicer3]] (Martin Loepprich, Sylvain Jaume, Polina Golland, Ron Kikinis, Steve Pieper)<br /> #[[2010_Winter_Project_Week_The_Vascular_Modeling_Toolkit_in_3D_Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Steve Pieper)<br /> #[[2010_Winter_Project_Week_RobustStatisticsDrivenActiveContourSegmentation|Active contour segmentation using robust statistics]] (Yi Gao, Allen Tannenbaum, GT; Andriy Fedorov, Katie Hayes Ron Kikinis, BWH)<br /> #[[2010_Winter_Project_Week_SegmentationWizard|High Level Wizard for Segmentation of Images]] (Mark Scully, Jeremy Bockholt, Steve Pieper)<br /> #[[2010_Winter_Project_Week_LongitudinalLupusAnalyses|Longitudinal Analyses of Lesions in Lupus]] (Mark Scully, Jeremy Bockholt, Steve Pieper)<br /> #[[2010_Winter_Project_Week_MultiscaleLupusAnalyses|Multiscale Analyses of Lupus Patients]] (Mark Scully, Jeremy Bockholt, Steve Pieper)<br /> #[[2010_Winter_Project_Week_ProstateSeg|Prostate segmentation using shape-based method]] (Andras Lasso, Yi Gao)<br /> #[[2010_Winter_Project_Week_TubularTreeSeg|Tubular Tree Segmentation for brain and cardiac imagery]] (Vandana Mohan, Allen Tannenbaum, GT; Marek Kubicki, BWH)<br /> #[[2010_Winter_Project_Week_SegmentationEpicardialWall|Epicardial Wall Segmentation]] (Behnood Gholami, Yi Gao, Allen Tannenbaum, GT; Rob MacLeod, Josh Blauer, University of Utah)<br /> #[[2010_Winter_Project_Week_SegmentationMeshEmbeddedContours|Segmentation on Mesh Surfaces Using Geometric Information]] (Peter Karasev, Matias Perez, Allen Tannenbaum, GT; Ron Kikinis, BWH)<br /> #[[2010_Winter_Project_Week_TBISegmentation|Segmentation of TBI (Traumatic Brain Injury) Subjects from Multimodal MRI]] (Marcel Prastawa, Guido Gerig, Ron Kikinis)<br /> <br /> === Registration ===<br /> #[[2010_Winter_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library Project]] (Dominik Meier, Casey Goodlett, Ron Kikinis)<br /> #[[Tissue_Dependent_Registration|Registration with Varying Elastic Parameters]] (Petter Risholm, Sandy Wells)<br /> <br /> === IGT ===<br /> # [[2010_Winter_Project_Week_Fast_Imaging_Library_%2B_Siemens_EPI]] (Scott Hoge, Nick Todd, Dennis Parker, Katie Hayes)<br /> # [[2010_Winter_Project_Week_MRI_Guided_Robotic_Prostate_Intervention| MRI-guided Robotic Prostate Intervention]] (Andras Lasso and Junichi Tokuda)<br /> <br /> === Radiotherapy ===<br /> # [[2010_Winter_Project_Week_DicomRT_Plugin]] (Greg Sharp, others)<br /> # [[Adaptive Radiotherapy for Head, Neck, and Thorax]] (Ivan Kolesov, Vandana Mohan, Greg Sharp)<br /> <br /> === Analysis ===<br /> <br /> === Informatics ===<br /> #XNAT Desktop User Interface (Dan M, Wendy P, Ron K)<br /> #Slicer 3 XNAT Performance Tuning (Wendy P, Dan M, Tim Olson, Nicole Aucoin)<br /> #Harvard CTSC XNAT (Yong Gao, Dan M, Tim Olson, John Paulett)<br /> ##Contributing SubjectHandler Yong wrote into DicomServer release.<br /> ##Scan Level search capabilities for queries like "find all mr sessions with a usable MPRAGE scan". According to Tim, this is not an out-of-the-box thing offered by the REST API.<br /> ##Processing and loading images in NRRD format.<br /> <br /> === Diffusion ===<br /> #[[ 2010_Winter_Project_Week_HARDI_RSH|Integration of Real Spherical Harmonic basis for HARDI models]] (Luke Bloy, C-F Westin)<br /> #[[ 2010_Winter_Project_Week_Tractography|Filtered tractography]] (James Malcolm, Peter Savadjiev, Yogesh Rathi, C-F Westin, Casey Goodlett)<br /> #[[ 2010_Winter_Project_Week_HARDI_CONNECTIVITY|Connectivity Study of Neonatal Brain Data using HARDI Techniques]] ( Yundi(Wendy) Shi, Deepika Mahalingam, Martin Styner )<br /> #[[ 2010_Winter_Project_Week_WM_ATLAS|Atlas-Based White Matter Segmentation]] (Lauren O'Donnell, C-F Westin, Alexandra J. Golby)<br /> <br /> === Python ===<br /> <br /> <br /> === NA-MIC Kit Internals ===<br /> #Testing for Extensions (Steve, Andre, Jim, Julien Jomier, Katie Hayes, Stuart Wallace)<br /> #[[2010_Winter_Project_Week_SPECTRE_3DSlicer_Integration|Integration of SPECTRE Java module into 3D Slicer]] (Nicole Aucoin, Aaron Carass, Min Chen)<br /> #VTK 3D Widgets in Slicer3 (Nicole Aucoin, Karthik, Will)<br /> #Updates to Slicer3 Colors Module (Nicole Aucoin)<br /> #Whole Body CT/MR open source data set publishing (Dan Marcus)<br /> #CMAKE Build process (Dave Partyka, Katie Hayes)<br /> #Integration of XNAT Packaging for Slicer Internals (Dan, Tim Olsen, Dave Partyka, Wendy, Randy)<br /> <br /> === NA-MIC Outreach ===<br /> #[[AHM 2010 Tutorial Polishing | Tutorial Polishing]] (Stuart Wallace, Randy Gollub, Sonia Pujol, all contributing tutorial contest developers)<br /> <br /> === Execution Model ===<br /> <br /> <br /> === Preparation ===<br /> <br /> # Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]<br /> # Starting Thursday, October 15th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:<br /> #*October 15: Engineering Infrastructure Projects<br /> #*October 22: Funded External Collaboration Projects<br /> #*October 29: Funded External Collaboration Projects<br /> #*November 5: DPB Projects <br /> #*November 19: DPB Projects <br /> #*December 3: Other/new collaborations<br /> #*December 10: Finalize Engineering Projects<br /> #*December 17: Loose Ends<br /> #By December 17, 2010: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.<br /> # By December 17, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)<br /> ##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]<br /> ## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)<br /> ## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)<br /> ## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)<br /> # Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...</div>

Yong https://www.na-mic.org/w/index.php?title=CTSC:ARRA_supplement&diff=45103 CTSC:ARRA supplement 2009-11-19T19:17:22Z

<p>Yong: /* Installation Instructions for x86_64 Linux, Centos */</p> <hr /> <div>= Harvard Catalyst Medical Imaging Informatics ARRA Administrative Supplement=<br /> <br /> {|<br /> |align="left"|<br /> <br /> == Medical Imaging Informatics Bench to Bedside (mi2b2) ==<br /> <br>This Medical Imaging Informatics project was funded by an Administrative Supplement to the Harvard Catalyst through the federal stimulus package aka ARRA. The project will enable clinical imaging data to be used, with appropriate human subject and institutional protections, for secondary research purposes.<br /> |[[image:ARRA.png|thumb|px=250|Go to the [http://www.recovery.gov ARRA website]]]<br /> |}<br /> <br /> =Mission Statement=<br /> <br /> To facilitate access to and use of the extensive collection of valuable medical images obtained during clinical care in a manner that does not negatively impact clinical care, enhances oversight of access and is in compliance with all local and national regulatory requirements. The target audiences for this project are clinical translational scientists (Radiologists and other physicians), basic scientists, and medical image analysis algorithm developers.<br /> <br /> =Key Personnel and Resources=<br /> <br /> Our hospitals are international leaders in the development and deployment of new and advanced biomedical imaging technologies (MRI, high speed CT, ultrasound, PET and others) for clinical practice (although old tried and true technologies are also extensively used). The Picture Archive and Communication Systems (PACS) within each of the Departments of Radiology in our participating hospitals (Massachusetts General Hospital, Brigham and Women’s Hospital, Beth Israel Deaconess Medical Center, and Children’s Hospital Boston) contain a wealth of medical images that equal or exceed the quality of clinical research imaging data, and greatly exceed its volume in terms of the number of patients and disease types. <br /> <br /> This project uses software that is free and open source from currently funded government projects. This software includes the i2b2 (Informatics for Integrating Biology & the Bedside), a National Center for Biomedical Computing suite of open source software tools that extract and integrate data from of the electronic medical records, laboratory data, billing information systems and genomic data. It also includes XNAT (http://xnat.org/) software that is supported by NIH through the National Center for Research Resources (NCRR) sponsored Biomedical Informatics Research Network (BIRN) initiative and NA-MIC.<br /> <br /> = Upcoming Events =<br /> <br /> ===Weekly Meetings===<br /> Tuesday (10:30- 11:30 AM), call: 1-866-890-3820<br /> <br /> *[[CTSC:ARRA.111709| November 17, 2009]] Harvard School of Public Health, 655 Huntington Ave, Building SPH2, 4th Floor, Room 426<br /> *[[CTSC:ARRA.112409| November 24, 2009]] Countway, Ware Room, 5th floor<br /> *[[CTSC:ARRA.120109| December 1, 2009]] <br /> *[[CTSC:ARRA.120809| December 8, 2009]] Ware room, Countway 5th floor (! XNAT demo from Dan Marcus WashU)<br /> *[[CTSC:ARRA.121509| December 15, 2009]] Harvard School of Public Health, 655 Huntington Ave, Building SPH2, 4th Floor, Room 426<br /> *[[CTSC:ARRA.122209| December 22, 2009]] Ware room, Countway 5th floor<br /> *[[CTSC:ARRA.122909| December 29, 2009]] Ware room, Countway 5th floor<br /> <br /> =Past Events =<br /> ===2009 meetings===<br /> <br /> *[[CTSC:ARRA.111009| November 10, 2009]] <br /> *[[CTSC:ARRA.110309| November 3, 2009]] <br /> *[[CTSC:ARRA.102709| October 27, 2009]] <br /> *[[CTSC:ARRA.102009| October 20, 2009]]<br /> *[[CTSC:ARRA.101309| October 13, 2009]]<br /> *[[CTSC:ARRA.100609| October 6, 2009]]<br /> <br /> =Using DCM4CHEE =<br /> ===Installation Instructions for x86_64 Linux, Centos ===<br /> *Download the latest DCM4CHEE for Postgresql<br /> **wget http://sourceforge.net/projects/dcm4che/files/dcm4chee/2.14.7/dcm4chee-psql-2.14.7.zip/download<br /> *Install Postgresql<br /> **sudo yum install postgresql postgresql-server<br /> <br /> *Install DCM4CHEE<br /> **Follow instructions at http://www.dcm4che.org/confluence/display/ee2/Installation<br /> **Special Steps<br /> ***Download Sun's Java Advanced Imaging Image I/O Tools 1.1 for 64bit Linux:<br /> ****wget http://download.java.net/media/jai-imageio/builds/release/1.1/jai_imageio-1_1-lib-linux-i586.tar.gz<br /> ***Download the binary distribution package of JBoss Application Server 4.2.3.GA<br /> ****wget http://sourceforge.net/projects/jboss/files/JBoss/JBoss-4.2.3.GA/jboss-4.2.3.GA.zip/download<br /> ***Download the Audit Record Repository (ARR)<br /> ****wget http://sourceforge.net/projects/dcm4che/files/dcm4chee-arr/3.0.8/dcm4chee-arr-psql-3.0.8.zip/download <br /> ***Unarchive the downloaded files.<br /> ***sudo cp -rp dcm4chee-psql-2.14.7 /opt<br /> ***sudo cp -p jai_imageio-1_1/lib/libclib_jiio.so /opt/dcm4chee-psql-2.14.7/bin/native/<br /> ***sudo /opt/dcm4chee-psql-2.14.7/bin/install_jboss.sh jboss-4.2.3.GA<br /> ***sudo /opt/dcm4chee-psql-2.14.7/bin/install_arr.sh dcm4chee-arr-psql-3.0.8/<br /> ***Start Postgresql server<br /> ****sudo mkdir /opt/pgdata<br /> ****sudo chown /opt/pgdata postgres<br /> ****sudo -s -H -u postgres<br /> ****initdb -D /opt/pgdata/ -U postgres -W (enter postgres as password)<br /> ***Create databases<br /> ****createdb pacsdb<br /> ****psql pacsdb -f /opt/dcm4chee-psql-2.14.7/sql/create.psql<br /> ****createdb arrdb<br /> ****set password in files /opt/dcm4chee-psql-2.14.7/server/default/deploy/arr-psql-ds.xml and pacs-postgres-ds.xml<br /> <br /> *Running DCM4CHEE<br /> **sudo /opt/dcm4chee-psql-2.14.7/bin/run.sh<br /> **change default AETitle to MI2B2 (See step 12. at http://www.dcm4che.org/confluence/display/ee2/Installation)<br /> **test then stop run.sh<br /> **Run as a service (See step 18 at http://www.dcm4che.org/confluence/display/ee2/Installation)<br /> ***edit /opt/dcm4chee-psql-2.14.7/server/default/conf/jboss-log4j.xml to comment out "<appender-ref ref="CONSOLE"/>"<br /> ***sudo cp /opt/dcm4chee-psql-2.14.7/bin/dcm4chee_init_redhat.sh /etc/init.d/dcm4chee<br /> ***Modify JBOSS_HOME, JBOSS_USER and JAVAPTH in /etc/init.d/dcm4chee<br /> ***sudo /sbin/chkconfig dcm4chee on<br /> ***sudo service dcm4chee start<br /> *Stop DCM4CHEE<br /> **sudo /sbin/service dcm4chee stop<br /> <br /> <br /> Back to [[Collaboration:Harvard_CTSC|Collaboration:Harvard_CTSC]]<br /> <br></div>

Yong https://www.na-mic.org/w/index.php?title=CTSC:ARRA_supplement&diff=45102 CTSC:ARRA supplement 2009-11-19T19:12:47Z

<p>Yong: /* Installation Instructions for x86_64 Linux, Centos */</p> <hr /> <div>= Harvard Catalyst Medical Imaging Informatics ARRA Administrative Supplement=<br /> <br /> {|<br /> |align="left"|<br /> <br /> == Medical Imaging Informatics Bench to Bedside (mi2b2) ==<br /> <br>This Medical Imaging Informatics project was funded by an Administrative Supplement to the Harvard Catalyst through the federal stimulus package aka ARRA. The project will enable clinical imaging data to be used, with appropriate human subject and institutional protections, for secondary research purposes.<br /> |[[image:ARRA.png|thumb|px=250|Go to the [http://www.recovery.gov ARRA website]]]<br /> |}<br /> <br /> =Mission Statement=<br /> <br /> To facilitate access to and use of the extensive collection of valuable medical images obtained during clinical care in a manner that does not negatively impact clinical care, enhances oversight of access and is in compliance with all local and national regulatory requirements. The target audiences for this project are clinical translational scientists (Radiologists and other physicians), basic scientists, and medical image analysis algorithm developers.<br /> <br /> =Key Personnel and Resources=<br /> <br /> Our hospitals are international leaders in the development and deployment of new and advanced biomedical imaging technologies (MRI, high speed CT, ultrasound, PET and others) for clinical practice (although old tried and true technologies are also extensively used). The Picture Archive and Communication Systems (PACS) within each of the Departments of Radiology in our participating hospitals (Massachusetts General Hospital, Brigham and Women’s Hospital, Beth Israel Deaconess Medical Center, and Children’s Hospital Boston) contain a wealth of medical images that equal or exceed the quality of clinical research imaging data, and greatly exceed its volume in terms of the number of patients and disease types. <br /> <br /> This project uses software that is free and open source from currently funded government projects. This software includes the i2b2 (Informatics for Integrating Biology & the Bedside), a National Center for Biomedical Computing suite of open source software tools that extract and integrate data from of the electronic medical records, laboratory data, billing information systems and genomic data. It also includes XNAT (http://xnat.org/) software that is supported by NIH through the National Center for Research Resources (NCRR) sponsored Biomedical Informatics Research Network (BIRN) initiative and NA-MIC.<br /> <br /> = Upcoming Events =<br /> <br /> ===Weekly Meetings===<br /> Tuesday (10:30- 11:30 AM), call: 1-866-890-3820<br /> <br /> *[[CTSC:ARRA.111709| November 17, 2009]] Harvard School of Public Health, 655 Huntington Ave, Building SPH2, 4th Floor, Room 426<br /> *[[CTSC:ARRA.112409| November 24, 2009]] Countway, Ware Room, 5th floor<br /> *[[CTSC:ARRA.120109| December 1, 2009]] <br /> *[[CTSC:ARRA.120809| December 8, 2009]] Ware room, Countway 5th floor (! XNAT demo from Dan Marcus WashU)<br /> *[[CTSC:ARRA.121509| December 15, 2009]] Harvard School of Public Health, 655 Huntington Ave, Building SPH2, 4th Floor, Room 426<br /> *[[CTSC:ARRA.122209| December 22, 2009]] Ware room, Countway 5th floor<br /> *[[CTSC:ARRA.122909| December 29, 2009]] Ware room, Countway 5th floor<br /> <br /> =Past Events =<br /> ===2009 meetings===<br /> <br /> *[[CTSC:ARRA.111009| November 10, 2009]] <br /> *[[CTSC:ARRA.110309| November 3, 2009]] <br /> *[[CTSC:ARRA.102709| October 27, 2009]] <br /> *[[CTSC:ARRA.102009| October 20, 2009]]<br /> *[[CTSC:ARRA.101309| October 13, 2009]]<br /> *[[CTSC:ARRA.100609| October 6, 2009]]<br /> <br /> =Using DCM4CHEE =<br /> ===Installation Instructions for x86_64 Linux, Centos ===<br /> *Download the latest DCM4CHEE for Postgresql<br /> **wget http://sourceforge.net/projects/dcm4che/files/dcm4chee/2.14.7/dcm4chee-psql-2.14.7.zip/download<br /> *Install Postgresql<br /> **sudo yum install postgresql postgresql-server<br /> <br /> *Install DCM4CHEE<br /> **Follow instructions at http://www.dcm4che.org/confluence/display/ee2/Installation<br /> **Special Steps<br /> ***Download Sun's Java Advanced Imaging Image I/O Tools 1.1 for 64bit Linux:<br /> ****wget http://download.java.net/media/jai-imageio/builds/release/1.1/jai_imageio-1_1-lib-linux-i586.tar.gz<br /> ***Download the binary distribution package of JBoss Application Server 4.2.3.GA<br /> ****wget http://sourceforge.net/projects/jboss/files/JBoss/JBoss-4.2.3.GA/jboss-4.2.3.GA.zip/download<br /> ***Download the Audit Record Repository (ARR)<br /> ****wget http://sourceforge.net/projects/dcm4che/files/dcm4chee-arr/3.0.8/dcm4chee-arr-psql-3.0.8.zip/download <br /> ***Unarchive the downloaded files.<br /> ***sudo cp -rp dcm4chee-psql-2.14.7 /opt<br /> ***sudo cp -p jai_imageio-1_1/lib/libclib_jiio.so /opt/dcm4chee-psql-2.14.7/bin/native/<br /> ***sudo /opt/dcm4chee-psql-2.14.7/bin/install_jboss.sh jboss-4.2.3.GA<br /> ***sudo /opt/dcm4chee-psql-2.14.7/bin/install_arr.sh dcm4chee-arr-psql-3.0.8/<br /> ***Start Postgresql server<br /> ****sudo mkdir /opt/pgdata<br /> ****sudo chown /opt/pgdata postgres<br /> ****sudo -s -H -u postgres<br /> ****initdb -D /opt/pgdata/ -U postgres -W (enter postgres as password)<br /> ***Create databases<br /> ****createdb pacsdb<br /> ****psql pacsdb -f /opt/dcm4chee-psql-2.14.7/sql/create.psql<br /> ****createdb arrdb<br /> ****set password in files /opt/dcm4chee-psql-2.14.7/server/default/deploy/arr-psql-ds.xml and pacs-postgres-ds.xml<br /> <br /> *Running DCM4CHEE<br /> **sudo /opt/dcm4chee-psql-2.14.7/bin/run.sh<br /> **change default AETitle to MI2B2 (See step 12. at http://www.dcm4che.org/confluence/display/ee2/Installation)<br /> **test then stop run.sh<br /> **Run as a service (See step 18 at http://www.dcm4che.org/confluence/display/ee2/Installation)<br /> ***edit /opt/dcm4chee-psql-2.14.7/server/default/conf/jboss-log4j.xml to comment out "<appender-ref ref="CONSOLE"/>"<br /> ***sudo cp /opt/dcm4chee-psql-2.14.7/bin/dcm4chee_init_redhat.sh /etc/init.d/dcm4chee<br /> ***Modify JBOSS_HOME, JBOSS_USER and JAVAPTH in /etc/init.d/dcm4chee<br /> ***sudo /sbin/chkconfig dcm4chee on<br /> <br /> <br /> <br /> Back to [[Collaboration:Harvard_CTSC|Collaboration:Harvard_CTSC]]<br /> <br></div>

Yong https://www.na-mic.org/w/index.php?title=CTSC:ARRA_supplement&diff=45101 CTSC:ARRA supplement 2009-11-19T19:12:00Z

<p>Yong: /* Using DCM4CHEE */</p> <hr /> <div>= Harvard Catalyst Medical Imaging Informatics ARRA Administrative Supplement=<br /> <br /> {|<br /> |align="left"|<br /> <br /> == Medical Imaging Informatics Bench to Bedside (mi2b2) ==<br /> <br>This Medical Imaging Informatics project was funded by an Administrative Supplement to the Harvard Catalyst through the federal stimulus package aka ARRA. The project will enable clinical imaging data to be used, with appropriate human subject and institutional protections, for secondary research purposes.<br /> |[[image:ARRA.png|thumb|px=250|Go to the [http://www.recovery.gov ARRA website]]]<br /> |}<br /> <br /> =Mission Statement=<br /> <br /> To facilitate access to and use of the extensive collection of valuable medical images obtained during clinical care in a manner that does not negatively impact clinical care, enhances oversight of access and is in compliance with all local and national regulatory requirements. The target audiences for this project are clinical translational scientists (Radiologists and other physicians), basic scientists, and medical image analysis algorithm developers.<br /> <br /> =Key Personnel and Resources=<br /> <br /> Our hospitals are international leaders in the development and deployment of new and advanced biomedical imaging technologies (MRI, high speed CT, ultrasound, PET and others) for clinical practice (although old tried and true technologies are also extensively used). The Picture Archive and Communication Systems (PACS) within each of the Departments of Radiology in our participating hospitals (Massachusetts General Hospital, Brigham and Women’s Hospital, Beth Israel Deaconess Medical Center, and Children’s Hospital Boston) contain a wealth of medical images that equal or exceed the quality of clinical research imaging data, and greatly exceed its volume in terms of the number of patients and disease types. <br /> <br /> This project uses software that is free and open source from currently funded government projects. This software includes the i2b2 (Informatics for Integrating Biology & the Bedside), a National Center for Biomedical Computing suite of open source software tools that extract and integrate data from of the electronic medical records, laboratory data, billing information systems and genomic data. It also includes XNAT (http://xnat.org/) software that is supported by NIH through the National Center for Research Resources (NCRR) sponsored Biomedical Informatics Research Network (BIRN) initiative and NA-MIC.<br /> <br /> = Upcoming Events =<br /> <br /> ===Weekly Meetings===<br /> Tuesday (10:30- 11:30 AM), call: 1-866-890-3820<br /> <br /> *[[CTSC:ARRA.111709| November 17, 2009]] Harvard School of Public Health, 655 Huntington Ave, Building SPH2, 4th Floor, Room 426<br /> *[[CTSC:ARRA.112409| November 24, 2009]] Countway, Ware Room, 5th floor<br /> *[[CTSC:ARRA.120109| December 1, 2009]] <br /> *[[CTSC:ARRA.120809| December 8, 2009]] Ware room, Countway 5th floor (! XNAT demo from Dan Marcus WashU)<br /> *[[CTSC:ARRA.121509| December 15, 2009]] Harvard School of Public Health, 655 Huntington Ave, Building SPH2, 4th Floor, Room 426<br /> *[[CTSC:ARRA.122209| December 22, 2009]] Ware room, Countway 5th floor<br /> *[[CTSC:ARRA.122909| December 29, 2009]] Ware room, Countway 5th floor<br /> <br /> =Past Events =<br /> ===2009 meetings===<br /> <br /> *[[CTSC:ARRA.111009| November 10, 2009]] <br /> *[[CTSC:ARRA.110309| November 3, 2009]] <br /> *[[CTSC:ARRA.102709| October 27, 2009]] <br /> *[[CTSC:ARRA.102009| October 20, 2009]]<br /> *[[CTSC:ARRA.101309| October 13, 2009]]<br /> *[[CTSC:ARRA.100609| October 6, 2009]]<br /> <br /> =Using DCM4CHEE =<br /> ===Installation Instructions for x86_64 Linux, Centos ===<br /> *Download the latest DCM4CHEE for Postgresql<br /> **wget http://sourceforge.net/projects/dcm4che/files/dcm4chee/2.14.7/dcm4chee-psql-2.14.7.zip/download<br /> *Install Postgresql<br /> **sudo yum install postgresql postgresql-server<br /> <br /> *Install DCM4CHEE<br /> **Follow instructions at http://www.dcm4che.org/confluence/display/ee2/Installation<br /> **Special Steps<br /> ***Download Sun's Java Advanced Imaging Image I/O Tools 1.1 for 64bit Linux:<br /> ****wget http://download.java.net/media/jai-imageio/builds/release/1.1/jai_imageio-1_1-lib-linux-i586.tar.gz<br /> ***Download the binary distribution package of JBoss Application Server 4.2.3.GA<br /> ****wget http://sourceforge.net/projects/jboss/files/JBoss/JBoss-4.2.3.GA/jboss-4.2.3.GA.zip/download<br /> ***Download the Audit Record Repository (ARR)<br /> ****wget http://sourceforge.net/projects/dcm4che/files/dcm4chee-arr/3.0.8/dcm4chee-arr-psql-3.0.8.zip/download <br /> ***Unarchive the downloaded files.<br /> ***sudo cp -rp dcm4chee-psql-2.14.7 /opt<br /> ***sudo cp -p jai_imageio-1_1/lib/libclib_jiio.so /opt/dcm4chee-psql-2.14.7/bin/native/<br /> ***sudo /opt/dcm4chee-psql-2.14.7/bin/install_jboss.sh jboss-4.2.3.GA<br /> ***sudo /opt/dcm4chee-psql-2.14.7/bin/install_arr.sh dcm4chee-arr-psql-3.0.8/<br /> ***Start Postgresql server<br /> ****sudo mkdir /opt/pgdata<br /> ****sudo chown /opt/pgdata postgres<br /> ****sudo -s -H -u postgres<br /> ****initdb -D /opt/pgdata/ -U postgres -W (enter postgres as password)<br /> ***Create databases<br /> ****createdb pacsdb<br /> ****psql pacsdb -f /opt/dcm4chee-psql-2.14.7/sql/create.psql<br /> ****createdb arrdb<br /> ****set password in files /opt/dcm4chee-psql-2.14.7/server/default/deploy/arr-psql-ds.xml and pacs-postgres-ds.xml<br /> <br /> *Running DCM4CHEE<br /> **sudo /opt/dcm4chee-psql-2.14.7/bin/run.sh<br /> **change default AETitle to MI2B2 (See step 12. at http://www.dcm4che.org/confluence/display/ee2/Installation)<br /> **Run as a service (See step 18 at http://www.dcm4che.org/confluence/display/ee2/Installation)<br /> ***edit /opt/dcm4chee-psql-2.14.7/server/default/conf/jboss-log4j.xml to comment out "<appender-ref ref="CONSOLE"/>"<br /> ***sudo cp /opt/dcm4chee-psql-2.14.7/bin/dcm4chee_init_redhat.sh /etc/init.d/dcm4chee<br /> ***Modify JBOSS_HOME, JBOSS_USER and JAVAPTH in /etc/init.d/dcm4chee<br /> ***sudo /sbin/chkconfig dcm4chee on<br /> <br /> <br /> <br /> Back to [[Collaboration:Harvard_CTSC|Collaboration:Harvard_CTSC]]<br /> <br></div>

Yong https://www.na-mic.org/w/index.php?title=CTSC:ARRA_supplement&diff=45062 CTSC:ARRA supplement 2009-11-18T02:07:53Z

<p>Yong: /* Installation Instructions for x86_64 Linux, Centos */</p> <hr /> <div>= Harvard Catalyst Medical Imaging Informatics ARRA Administrative Supplement=<br /> <br /> {|<br /> |align="left"|<br /> <br /> == Medical Imaging Informatics Bench to Bedside (mi2b2) ==<br /> <br>This Medical Imaging Informatics project was funded by an Administrative Supplement to the Harvard Catalyst through the federal stimulus package aka ARRA. The project will enable clinical imaging data to be used, with appropriate human subject and institutional protections, for secondary research purposes.<br /> |[[image:ARRA.png|thumb|px=250|Go to the [http://www.recovery.gov ARRA website]]]<br /> |}<br /> <br /> =Mission Statement=<br /> <br /> To facilitate access to and use of the extensive collection of valuable medical images obtained during clinical care in a manner that does not negatively impact clinical care, enhances oversight of access and is in compliance with all local and national regulatory requirements. The target audiences for this project are clinical translational scientists (Radiologists and other physicians), basic scientists, and medical image analysis algorithm developers.<br /> <br /> =Key Personnel and Resources=<br /> <br /> Our hospitals are international leaders in the development and deployment of new and advanced biomedical imaging technologies (MRI, high speed CT, ultrasound, PET and others) for clinical practice (although old tried and true technologies are also extensively used). The Picture Archive and Communication Systems (PACS) within each of the Departments of Radiology in our participating hospitals (Massachusetts General Hospital, Brigham and Women’s Hospital, Beth Israel Deaconess Medical Center, and Children’s Hospital Boston) contain a wealth of medical images that equal or exceed the quality of clinical research imaging data, and greatly exceed its volume in terms of the number of patients and disease types. <br /> <br /> This project uses software that is free and open source from currently funded government projects. This software includes the i2b2 (Informatics for Integrating Biology & the Bedside), a National Center for Biomedical Computing suite of open source software tools that extract and integrate data from of the electronic medical records, laboratory data, billing information systems and genomic data. It also includes XNAT (http://xnat.org/) software that is supported by NIH through the National Center for Research Resources (NCRR) sponsored Biomedical Informatics Research Network (BIRN) initiative and NA-MIC.<br /> <br /> = Upcoming Events =<br /> <br /> ===Weekly Meetings===<br /> Tuesday (10:30- 11:30 AM), call: 1-866-890-3820<br /> <br /> *[[CTSC:ARRA.111709| November 17, 2009]] Harvard School of Public Health, 655 Huntington Ave, Building SPH2, 4th Floor, Room 426<br /> *[[CTSC:ARRA.112409| November 24, 2009]] Countway, Ware Room, 5th floor<br /> *[[CTSC:ARRA.120109| December 1, 2009]] <br /> *[[CTSC:ARRA.120809| December 8, 2009]] Ware room, Countway 5th floor (! XNAT demo from Dan Marcus WashU)<br /> *[[CTSC:ARRA.121509| December 15, 2009]] Harvard School of Public Health, 655 Huntington Ave, Building SPH2, 4th Floor, Room 426<br /> *[[CTSC:ARRA.122209| December 22, 2009]] Ware room, Countway 5th floor<br /> *[[CTSC:ARRA.122909| December 29, 2009]] Ware room, Countway 5th floor<br /> <br /> =Past Events =<br /> ===2009 meetings===<br /> <br /> *[[CTSC:ARRA.111009| November 10, 2009]] <br /> *[[CTSC:ARRA.110309| November 3, 2009]] <br /> *[[CTSC:ARRA.102709| October 27, 2009]] <br /> *[[CTSC:ARRA.102009| October 20, 2009]]<br /> *[[CTSC:ARRA.101309| October 13, 2009]]<br /> *[[CTSC:ARRA.100609| October 6, 2009]]<br /> <br /> =Using DCM4CHEE =<br /> ===Installation Instructions for x86_64 Linux, Centos ===<br /> *Download the latest DCM4CHEE for Postgresql<br /> **wget http://sourceforge.net/projects/dcm4che/files/dcm4chee/2.14.7/dcm4chee-psql-2.14.7.zip/download<br /> *Install Postgresql<br /> **sudo yum install postgresql postgresql-server<br /> <br /> *Install DCM4CHEE<br /> **Follow instructions at http://www.dcm4che.org/confluence/display/ee2/Installation<br /> **Special Steps<br /> ***Download Sun's Java Advanced Imaging Image I/O Tools 1.1 for 64bit Linux:<br /> ****wget http://download.java.net/media/jai-imageio/builds/release/1.1/jai_imageio-1_1-lib-linux-i586.tar.gz<br /> ***Download the binary distribution package of JBoss Application Server 4.2.3.GA<br /> ****wget http://sourceforge.net/projects/jboss/files/JBoss/JBoss-4.2.3.GA/jboss-4.2.3.GA.zip/download<br /> ***Download the Audit Record Repository (ARR)<br /> ****wget http://sourceforge.net/projects/dcm4che/files/dcm4chee-arr/3.0.8/dcm4chee-arr-psql-3.0.8.zip/download <br /> ***Unarchive the downloaded files.<br /> ***sudo cp -rp dcm4chee-psql-2.14.7 /opt<br /> ***sudo cp -p jai_imageio-1_1/lib/libclib_jiio.so /opt/dcm4chee-psql-2.14.7/bin/native/<br /> ***sudo /opt/dcm4chee-psql-2.14.7/bin/install_jboss.sh jboss-4.2.3.GA<br /> ***sudo /opt/dcm4chee-psql-2.14.7/bin/install_arr.sh dcm4chee-arr-psql-3.0.8/<br /> ***Start Postgresql server<br /> ****sudo mkdir /opt/pgdata<br /> ****sudo chown /opt/pgdata postgres<br /> ****sudo -s -H -u postgres<br /> ****initdb -D /opt/pgdata/ -U postgres -W (enter postgres as password)<br /> ***Create databases<br /> ****createdb pacsdb<br /> ****psql pacsdb -f /opt/dcm4chee-psql-2.14.7/sql/create.psql<br /> ****createdb arrdb<br /> ****set password in files /opt/dcm4chee-psql-2.14.7/server/default/deploy/arr-psql-ds.xml and pacs-postgres-ds.xml<br /> <br /> <br /> Back to [[Collaboration:Harvard_CTSC|Collaboration:Harvard_CTSC]]<br /> <br></div>

Yong https://www.na-mic.org/w/index.php?title=CTSC:ARRA_supplement&diff=45061 CTSC:ARRA supplement 2009-11-18T02:03:00Z

<p>Yong: /* Installation Instructions for x86_64 Linux, Centos */</p> <hr /> <div>= Harvard Catalyst Medical Imaging Informatics ARRA Administrative Supplement=<br /> <br /> {|<br /> |align="left"|<br /> <br /> == Medical Imaging Informatics Bench to Bedside (mi2b2) ==<br /> <br>This Medical Imaging Informatics project was funded by an Administrative Supplement to the Harvard Catalyst through the federal stimulus package aka ARRA. The project will enable clinical imaging data to be used, with appropriate human subject and institutional protections, for secondary research purposes.<br /> |[[image:ARRA.png|thumb|px=250|Go to the [http://www.recovery.gov ARRA website]]]<br /> |}<br /> <br /> =Mission Statement=<br /> <br /> To facilitate access to and use of the extensive collection of valuable medical images obtained during clinical care in a manner that does not negatively impact clinical care, enhances oversight of access and is in compliance with all local and national regulatory requirements. The target audiences for this project are clinical translational scientists (Radiologists and other physicians), basic scientists, and medical image analysis algorithm developers.<br /> <br /> =Key Personnel and Resources=<br /> <br /> Our hospitals are international leaders in the development and deployment of new and advanced biomedical imaging technologies (MRI, high speed CT, ultrasound, PET and others) for clinical practice (although old tried and true technologies are also extensively used). The Picture Archive and Communication Systems (PACS) within each of the Departments of Radiology in our participating hospitals (Massachusetts General Hospital, Brigham and Women’s Hospital, Beth Israel Deaconess Medical Center, and Children’s Hospital Boston) contain a wealth of medical images that equal or exceed the quality of clinical research imaging data, and greatly exceed its volume in terms of the number of patients and disease types. <br /> <br /> This project uses software that is free and open source from currently funded government projects. This software includes the i2b2 (Informatics for Integrating Biology & the Bedside), a National Center for Biomedical Computing suite of open source software tools that extract and integrate data from of the electronic medical records, laboratory data, billing information systems and genomic data. It also includes XNAT (http://xnat.org/) software that is supported by NIH through the National Center for Research Resources (NCRR) sponsored Biomedical Informatics Research Network (BIRN) initiative and NA-MIC.<br /> <br /> = Upcoming Events =<br /> <br /> ===Weekly Meetings===<br /> Tuesday (10:30- 11:30 AM), call: 1-866-890-3820<br /> <br /> *[[CTSC:ARRA.111709| November 17, 2009]] Harvard School of Public Health, 655 Huntington Ave, Building SPH2, 4th Floor, Room 426<br /> *[[CTSC:ARRA.112409| November 24, 2009]] Countway, Ware Room, 5th floor<br /> *[[CTSC:ARRA.120109| December 1, 2009]] <br /> *[[CTSC:ARRA.120809| December 8, 2009]] Ware room, Countway 5th floor (! XNAT demo from Dan Marcus WashU)<br /> *[[CTSC:ARRA.121509| December 15, 2009]] Harvard School of Public Health, 655 Huntington Ave, Building SPH2, 4th Floor, Room 426<br /> *[[CTSC:ARRA.122209| December 22, 2009]] Ware room, Countway 5th floor<br /> *[[CTSC:ARRA.122909| December 29, 2009]] Ware room, Countway 5th floor<br /> <br /> =Past Events =<br /> ===2009 meetings===<br /> <br /> *[[CTSC:ARRA.111009| November 10, 2009]] <br /> *[[CTSC:ARRA.110309| November 3, 2009]] <br /> *[[CTSC:ARRA.102709| October 27, 2009]] <br /> *[[CTSC:ARRA.102009| October 20, 2009]]<br /> *[[CTSC:ARRA.101309| October 13, 2009]]<br /> *[[CTSC:ARRA.100609| October 6, 2009]]<br /> <br /> =Using DCM4CHEE =<br /> ===Installation Instructions for x86_64 Linux, Centos ===<br /> *Download the latest DCM4CHEE for Postgresql<br /> **wget http://sourceforge.net/projects/dcm4che/files/dcm4chee/2.14.7/dcm4chee-psql-2.14.7.zip/download<br /> *Install Postgresql<br /> **sudo yum install postgresql postgresql-server<br /> <br /> *Install DCM4CHEE<br /> **Follow instructions at http://www.dcm4che.org/confluence/display/ee2/Installation<br /> **Special Steps<br /> ***Download Sun's Java Advanced Imaging Image I/O Tools 1.1 for 64bit Linux:<br /> ****wget http://download.java.net/media/jai-imageio/builds/release/1.1/jai_imageio-1_1-lib-linux-i586.tar.gz<br /> ***Download the binary distribution package of JBoss Application Server 4.2.3.GA<br /> ****wget http://sourceforge.net/projects/jboss/files/JBoss/JBoss-4.2.3.GA/jboss-4.2.3.GA.zip/download<br /> ***Download the Audit Record Repository (ARR)<br /> ****wget http://sourceforge.net/projects/dcm4che/files/dcm4chee-arr/3.0.8/dcm4chee-arr-psql-3.0.8.zip/download <br /> ***Unarchive the downloaded files.<br /> ***sudo cp -rp dcm4chee-psql-2.14.7 /opt<br /> ***sudo cp -p jai_imageio-1_1/lib/libclib_jiio.so /opt/dcm4chee-psql-2.14.7/bin/native/<br /> ***sudo /opt/dcm4chee-psql-2.14.7/bin/install_jboss.sh jboss-4.2.3.GA<br /> ***sudo /opt/dcm4chee-psql-2.14.7/bin/install_arr.sh dcm4chee-arr-psql-3.0.8/<br /> ***Start Postgresql server<br /> ****sudo mkdir /opt/pgdata<br /> ****sudo chown /opt/pgdata postgres<br /> ****sudo -s -H -u postgres<br /> ****initdb -D /opt/pgdata/ -U postgres -W (enter postgres as password)<br /> ***Create databases<br /> ****createdb pacsdb<br /> ****psql pacsdb -f /opt/dcm4chee-psql-2.14.7/sql/create.psql<br /> ****createdb arrdb<br /> <br /> <br /> Back to [[Collaboration:Harvard_CTSC|Collaboration:Harvard_CTSC]]<br /> <br></div>

Yong https://www.na-mic.org/w/index.php?title=CTSC:ARRA_supplement&diff=45060 CTSC:ARRA supplement 2009-11-18T01:57:16Z

<p>Yong: /* Installation Instructions for x86_64 Linux, Centos */</p> <hr /> <div>= Harvard Catalyst Medical Imaging Informatics ARRA Administrative Supplement=<br /> <br /> {|<br /> |align="left"|<br /> <br /> == Medical Imaging Informatics Bench to Bedside (mi2b2) ==<br /> <br>This Medical Imaging Informatics project was funded by an Administrative Supplement to the Harvard Catalyst through the federal stimulus package aka ARRA. The project will enable clinical imaging data to be used, with appropriate human subject and institutional protections, for secondary research purposes.<br /> |[[image:ARRA.png|thumb|px=250|Go to the [http://www.recovery.gov ARRA website]]]<br /> |}<br /> <br /> =Mission Statement=<br /> <br /> To facilitate access to and use of the extensive collection of valuable medical images obtained during clinical care in a manner that does not negatively impact clinical care, enhances oversight of access and is in compliance with all local and national regulatory requirements. The target audiences for this project are clinical translational scientists (Radiologists and other physicians), basic scientists, and medical image analysis algorithm developers.<br /> <br /> =Key Personnel and Resources=<br /> <br /> Our hospitals are international leaders in the development and deployment of new and advanced biomedical imaging technologies (MRI, high speed CT, ultrasound, PET and others) for clinical practice (although old tried and true technologies are also extensively used). The Picture Archive and Communication Systems (PACS) within each of the Departments of Radiology in our participating hospitals (Massachusetts General Hospital, Brigham and Women’s Hospital, Beth Israel Deaconess Medical Center, and Children’s Hospital Boston) contain a wealth of medical images that equal or exceed the quality of clinical research imaging data, and greatly exceed its volume in terms of the number of patients and disease types. <br /> <br /> This project uses software that is free and open source from currently funded government projects. This software includes the i2b2 (Informatics for Integrating Biology & the Bedside), a National Center for Biomedical Computing suite of open source software tools that extract and integrate data from of the electronic medical records, laboratory data, billing information systems and genomic data. It also includes XNAT (http://xnat.org/) software that is supported by NIH through the National Center for Research Resources (NCRR) sponsored Biomedical Informatics Research Network (BIRN) initiative and NA-MIC.<br /> <br /> = Upcoming Events =<br /> <br /> ===Weekly Meetings===<br /> Tuesday (10:30- 11:30 AM), call: 1-866-890-3820<br /> <br /> *[[CTSC:ARRA.111709| November 17, 2009]] Harvard School of Public Health, 655 Huntington Ave, Building SPH2, 4th Floor, Room 426<br /> *[[CTSC:ARRA.112409| November 24, 2009]] Countway, Ware Room, 5th floor<br /> *[[CTSC:ARRA.120109| December 1, 2009]] <br /> *[[CTSC:ARRA.120809| December 8, 2009]] Ware room, Countway 5th floor (! XNAT demo from Dan Marcus WashU)<br /> *[[CTSC:ARRA.121509| December 15, 2009]] Harvard School of Public Health, 655 Huntington Ave, Building SPH2, 4th Floor, Room 426<br /> *[[CTSC:ARRA.122209| December 22, 2009]] Ware room, Countway 5th floor<br /> *[[CTSC:ARRA.122909| December 29, 2009]] Ware room, Countway 5th floor<br /> <br /> =Past Events =<br /> ===2009 meetings===<br /> <br /> *[[CTSC:ARRA.111009| November 10, 2009]] <br /> *[[CTSC:ARRA.110309| November 3, 2009]] <br /> *[[CTSC:ARRA.102709| October 27, 2009]] <br /> *[[CTSC:ARRA.102009| October 20, 2009]]<br /> *[[CTSC:ARRA.101309| October 13, 2009]]<br /> *[[CTSC:ARRA.100609| October 6, 2009]]<br /> <br /> =Using DCM4CHEE =<br /> ===Installation Instructions for x86_64 Linux, Centos ===<br /> *Download the latest DCM4CHEE for Postgresql<br /> **wget http://sourceforge.net/projects/dcm4che/files/dcm4chee/2.14.7/dcm4chee-psql-2.14.7.zip/download<br /> *Install Postgresql<br /> **sudo yum install postgresql postgresql-server<br /> <br /> *Install DCM4CHEE<br /> **Follow instructions at http://www.dcm4che.org/confluence/display/ee2/Installation<br /> **Special Steps<br /> ***Download Sun's Java Advanced Imaging Image I/O Tools 1.1 for 64bit Linux:<br /> ****wget http://download.java.net/media/jai-imageio/builds/release/1.1/jai_imageio-1_1-lib-linux-i586.tar.gz<br /> ***Download the binary distribution package of JBoss Application Server 4.2.3.GA<br /> ****wget http://sourceforge.net/projects/jboss/files/JBoss/JBoss-4.2.3.GA/jboss-4.2.3.GA.zip/download<br /> ***Download the Audit Record Repository (ARR)<br /> ****wget http://sourceforge.net/projects/dcm4che/files/dcm4chee-arr/3.0.8/dcm4chee-arr-psql-3.0.8.zip/download <br /> ***Unarchive the downloaded files.<br /> ***sudo cp -rp dcm4chee-psql-2.14.7 /opt<br /> ***sudo cp -p jai_imageio-1_1/lib/libclib_jiio.so /opt/dcm4chee-psql-2.14.7/bin/native/<br /> ***sudo /opt/dcm4chee-psql-2.14.7/bin/install_jboss.sh jboss-4.2.3.GA<br /> ***sudo /opt/dcm4chee-psql-2.14.7/bin/install_arr.sh dcm4chee-arr-psql-3.0.8/<br /> ***Start Postgresql server<br /> ****sudo mkdir /opt/pgdata<br /> ****sudo chown /opt/pgdata postgres<br /> ****sudo -s -H -u postgres<br /> ****initdb -D /opt/pgdata/ -U postgres -W (enter postgres as password)<br /> ***Create pacsdb<br /> ****createdb pacsdb<br /> ****psql pacsdb -f /opt/dcm4chee-psql-2.14.7/sql/create.psql<br /> <br /> <br /> Back to [[Collaboration:Harvard_CTSC|Collaboration:Harvard_CTSC]]<br /> <br></div>

Yong https://www.na-mic.org/w/index.php?title=CTSC:ARRA_supplement&diff=45059 CTSC:ARRA supplement 2009-11-17T23:13:11Z

<p>Yong: /* Installation Instructions for x86_64 Linux, Centos */</p> <hr /> <div>= Harvard Catalyst Medical Imaging Informatics ARRA Administrative Supplement=<br /> <br /> {|<br /> |align="left"|<br /> <br /> == Medical Imaging Informatics Bench to Bedside (mi2b2) ==<br /> <br>This Medical Imaging Informatics project was funded by an Administrative Supplement to the Harvard Catalyst through the federal stimulus package aka ARRA. The project will enable clinical imaging data to be used, with appropriate human subject and institutional protections, for secondary research purposes.<br /> |[[image:ARRA.png|thumb|px=250|Go to the [http://www.recovery.gov ARRA website]]]<br /> |}<br /> <br /> =Mission Statement=<br /> <br /> To facilitate access to and use of the extensive collection of valuable medical images obtained during clinical care in a manner that does not negatively impact clinical care, enhances oversight of access and is in compliance with all local and national regulatory requirements. The target audiences for this project are clinical translational scientists (Radiologists and other physicians), basic scientists, and medical image analysis algorithm developers.<br /> <br /> =Key Personnel and Resources=<br /> <br /> Our hospitals are international leaders in the development and deployment of new and advanced biomedical imaging technologies (MRI, high speed CT, ultrasound, PET and others) for clinical practice (although old tried and true technologies are also extensively used). The Picture Archive and Communication Systems (PACS) within each of the Departments of Radiology in our participating hospitals (Massachusetts General Hospital, Brigham and Women’s Hospital, Beth Israel Deaconess Medical Center, and Children’s Hospital Boston) contain a wealth of medical images that equal or exceed the quality of clinical research imaging data, and greatly exceed its volume in terms of the number of patients and disease types. <br /> <br /> This project uses software that is free and open source from currently funded government projects. This software includes the i2b2 (Informatics for Integrating Biology & the Bedside), a National Center for Biomedical Computing suite of open source software tools that extract and integrate data from of the electronic medical records, laboratory data, billing information systems and genomic data. It also includes XNAT (http://xnat.org/) software that is supported by NIH through the National Center for Research Resources (NCRR) sponsored Biomedical Informatics Research Network (BIRN) initiative and NA-MIC.<br /> <br /> = Upcoming Events =<br /> <br /> ===Weekly Meetings===<br /> Tuesday (10:30- 11:30 AM), call: 1-866-890-3820<br /> <br /> *[[CTSC:ARRA.111709| November 17, 2009]] Harvard School of Public Health, 655 Huntington Ave, Building SPH2, 4th Floor, Room 426<br /> *[[CTSC:ARRA.112409| November 24, 2009]] Countway, Ware Room, 5th floor<br /> *[[CTSC:ARRA.120109| December 1, 2009]] <br /> *[[CTSC:ARRA.120809| December 8, 2009]] Ware room, Countway 5th floor (! XNAT demo from Dan Marcus WashU)<br /> *[[CTSC:ARRA.121509| December 15, 2009]] Harvard School of Public Health, 655 Huntington Ave, Building SPH2, 4th Floor, Room 426<br /> *[[CTSC:ARRA.122209| December 22, 2009]] Ware room, Countway 5th floor<br /> *[[CTSC:ARRA.122909| December 29, 2009]] Ware room, Countway 5th floor<br /> <br /> =Past Events =<br /> ===2009 meetings===<br /> <br /> *[[CTSC:ARRA.111009| November 10, 2009]] <br /> *[[CTSC:ARRA.110309| November 3, 2009]] <br /> *[[CTSC:ARRA.102709| October 27, 2009]] <br /> *[[CTSC:ARRA.102009| October 20, 2009]]<br /> *[[CTSC:ARRA.101309| October 13, 2009]]<br /> *[[CTSC:ARRA.100609| October 6, 2009]]<br /> <br /> =Using DCM4CHEE =<br /> ===Installation Instructions for x86_64 Linux, Centos ===<br /> *Download the latest DCM4CHEE for Postgresql<br /> **wget http://sourceforge.net/projects/dcm4che/files/dcm4chee/2.14.7/dcm4chee-psql-2.14.7.zip/download<br /> *Install Postgresql<br /> **sudo yum install postgresql postgresql-server<br /> *Start Postgresql<br /> **sudo /sbin/chkconfig postgresql on<br /> **sudo /sbin/service postgresql start<br /> *Install DCM4CHEE<br /> **Follow instructions at http://www.dcm4che.org/confluence/display/ee2/Installation<br /> **Special Steps<br /> ***Download Sun's Java Advanced Imaging Image I/O Tools 1.1 for 64bit Linux:<br /> ****wget http://download.java.net/media/jai-imageio/builds/release/1.1/jai_imageio-1_1-lib-linux-i586.tar.gz<br /> ***Download the binary distribution package of JBoss Application Server 4.2.3.GA<br /> ****wget http://sourceforge.net/projects/jboss/files/JBoss/JBoss-4.2.3.GA/jboss-4.2.3.GA.zip/download<br /> ***Download the Audit Record Repository (ARR)<br /> ****wget http://sourceforge.net/projects/dcm4che/files/dcm4chee-arr/3.0.8/dcm4chee-arr-psql-3.0.8.zip/download <br /> ***Unarchive the downloaded files.<br /> ***sudo cp -rp dcm4chee-psql-2.14.7 /opt<br /> ***sudo cp -p jai_imageio-1_1/lib/libclib_jiio.so /opt/dcm4chee-psql-2.14.7/bin/native/<br /> ***sudo /opt/dcm4chee-psql-2.14.7/bin/install_jboss.sh jboss-4.2.3.GA<br /> ***sudo /opt/dcm4chee-psql-2.14.7/bin/install_arr.sh dcm4chee-arr-psql-3.0.8/<br /> ***sudo -u postgres createdb pacsdb<br /> ***sudo -u postgres psql pacsdb -f /opt/dcm4chee-psql-2.14.7/sql/create.psql<br /> <br /> <br /> Back to [[Collaboration:Harvard_CTSC|Collaboration:Harvard_CTSC]]<br /> <br></div>

Yong https://www.na-mic.org/w/index.php?title=CTSC:ARRA_supplement&diff=45058 CTSC:ARRA supplement 2009-11-17T22:30:52Z

<p>Yong: </p> <hr /> <div>= Harvard Catalyst Medical Imaging Informatics ARRA Administrative Supplement=<br /> <br /> {|<br /> |align="left"|<br /> <br /> == Medical Imaging Informatics Bench to Bedside (mi2b2) ==<br /> <br>This Medical Imaging Informatics project was funded by an Administrative Supplement to the Harvard Catalyst through the federal stimulus package aka ARRA. The project will enable clinical imaging data to be used, with appropriate human subject and institutional protections, for secondary research purposes.<br /> |[[image:ARRA.png|thumb|px=250|Go to the [http://www.recovery.gov ARRA website]]]<br /> |}<br /> <br /> =Mission Statement=<br /> <br /> To facilitate access to and use of the extensive collection of valuable medical images obtained during clinical care in a manner that does not negatively impact clinical care, enhances oversight of access and is in compliance with all local and national regulatory requirements. The target audiences for this project are clinical translational scientists (Radiologists and other physicians), basic scientists, and medical image analysis algorithm developers.<br /> <br /> =Key Personnel and Resources=<br /> <br /> Our hospitals are international leaders in the development and deployment of new and advanced biomedical imaging technologies (MRI, high speed CT, ultrasound, PET and others) for clinical practice (although old tried and true technologies are also extensively used). The Picture Archive and Communication Systems (PACS) within each of the Departments of Radiology in our participating hospitals (Massachusetts General Hospital, Brigham and Women’s Hospital, Beth Israel Deaconess Medical Center, and Children’s Hospital Boston) contain a wealth of medical images that equal or exceed the quality of clinical research imaging data, and greatly exceed its volume in terms of the number of patients and disease types. <br /> <br /> This project uses software that is free and open source from currently funded government projects. This software includes the i2b2 (Informatics for Integrating Biology & the Bedside), a National Center for Biomedical Computing suite of open source software tools that extract and integrate data from of the electronic medical records, laboratory data, billing information systems and genomic data. It also includes XNAT (http://xnat.org/) software that is supported by NIH through the National Center for Research Resources (NCRR) sponsored Biomedical Informatics Research Network (BIRN) initiative and NA-MIC.<br /> <br /> = Upcoming Events =<br /> <br /> ===Weekly Meetings===<br /> Tuesday (10:30- 11:30 AM), call: 1-866-890-3820<br /> <br /> *[[CTSC:ARRA.111709| November 17, 2009]] Harvard School of Public Health, 655 Huntington Ave, Building SPH2, 4th Floor, Room 426<br /> *[[CTSC:ARRA.112409| November 24, 2009]] Countway, Ware Room, 5th floor<br /> *[[CTSC:ARRA.120109| December 1, 2009]] <br /> *[[CTSC:ARRA.120809| December 8, 2009]] Ware room, Countway 5th floor (! XNAT demo from Dan Marcus WashU)<br /> *[[CTSC:ARRA.121509| December 15, 2009]] Harvard School of Public Health, 655 Huntington Ave, Building SPH2, 4th Floor, Room 426<br /> *[[CTSC:ARRA.122209| December 22, 2009]] Ware room, Countway 5th floor<br /> *[[CTSC:ARRA.122909| December 29, 2009]] Ware room, Countway 5th floor<br /> <br /> =Past Events =<br /> ===2009 meetings===<br /> <br /> *[[CTSC:ARRA.111009| November 10, 2009]] <br /> *[[CTSC:ARRA.110309| November 3, 2009]] <br /> *[[CTSC:ARRA.102709| October 27, 2009]] <br /> *[[CTSC:ARRA.102009| October 20, 2009]]<br /> *[[CTSC:ARRA.101309| October 13, 2009]]<br /> *[[CTSC:ARRA.100609| October 6, 2009]]<br /> <br /> =Using DCM4CHEE =<br /> ===Installation Instructions for x86_64 Linux, Centos ===<br /> *Download the latest DCM4CHEE for Postgresql<br /> **wget http://sourceforge.net/projects/dcm4che/files/dcm4chee/2.14.7/dcm4chee-psql-2.14.7.zip/download<br /> *Install Postgresql<br /> **sudo yum install postgresql postgresql-server<br /> *Start Postgresql<br /> **sudo /sbin/chkconfig postgresql on<br /> **sudo /sbin/service postgresql start<br /> *Install DCM4CHEE<br /> **Follow instructions at http://www.dcm4che.org/confluence/display/ee2/Installation<br /> **Special Steps<br /> ***Download Sun's Java Advanced Imaging Image I/O Tools 1.1 for 64bit Linux:<br /> ****wget http://download.java.net/media/jai-imageio/builds/release/1.1/jai_imageio-1_1-lib-linux-i586.tar.gz<br /> ***Download the binary distribution package of JBoss Application Server 4.2.3.GA<br /> ****wget http://sourceforge.net/projects/jboss/files/JBoss/JBoss-4.2.3.GA/jboss-4.2.3.GA.zip/download<br /> ***Download the Audit Record Repository (ARR)<br /> ****wget http://sourceforge.net/projects/dcm4che/files/dcm4chee-arr/3.0.8/dcm4chee-arr-psql-3.0.8.zip/download <br /> ***Unarchive the downloaded files.<br /> ***sudo cp -rp dcm4chee-psql-2.14.7 /opt<br /> ***sudo cp -p jai_imageio-1_1/lib/libclib_jiio.so /opt/dcm4chee-psql-2.14.7/bin/native/<br /> ***sudo /opt/dcm4chee-psql-2.14.7/bin/install_jboss.sh jboss-4.2.3.GA<br /> ***sudo -u postgres createdb pacsdb<br /> ***sudo -u postgres psql pacsdb -f /opt/dcm4chee-psql-2.14.7/sql/create.psql<br /> <br /> <br /> Back to [[Collaboration:Harvard_CTSC|Collaboration:Harvard_CTSC]]<br /> <br></div>

Yong https://www.na-mic.org/w/index.php?title=CTSC:ARRA_supplement&diff=45057 CTSC:ARRA supplement 2009-11-17T22:22:50Z

<p>Yong: </p> <hr /> <div>= Harvard Catalyst Medical Imaging Informatics ARRA Administrative Supplement=<br /> <br /> {|<br /> |align="left"|<br /> <br /> == Medical Imaging Informatics Bench to Bedside (mi2b2) ==<br /> <br>This Medical Imaging Informatics project was funded by an Administrative Supplement to the Harvard Catalyst through the federal stimulus package aka ARRA. The project will enable clinical imaging data to be used, with appropriate human subject and institutional protections, for secondary research purposes.<br /> |[[image:ARRA.png|thumb|px=250|Go to the [http://www.recovery.gov ARRA website]]]<br /> |}<br /> <br /> =Mission Statement=<br /> <br /> To facilitate access to and use of the extensive collection of valuable medical images obtained during clinical care in a manner that does not negatively impact clinical care, enhances oversight of access and is in compliance with all local and national regulatory requirements. The target audiences for this project are clinical translational scientists (Radiologists and other physicians), basic scientists, and medical image analysis algorithm developers.<br /> <br /> =Key Personnel and Resources=<br /> <br /> Our hospitals are international leaders in the development and deployment of new and advanced biomedical imaging technologies (MRI, high speed CT, ultrasound, PET and others) for clinical practice (although old tried and true technologies are also extensively used). The Picture Archive and Communication Systems (PACS) within each of the Departments of Radiology in our participating hospitals (Massachusetts General Hospital, Brigham and Women’s Hospital, Beth Israel Deaconess Medical Center, and Children’s Hospital Boston) contain a wealth of medical images that equal or exceed the quality of clinical research imaging data, and greatly exceed its volume in terms of the number of patients and disease types. <br /> <br /> This project uses software that is free and open source from currently funded government projects. This software includes the i2b2 (Informatics for Integrating Biology & the Bedside), a National Center for Biomedical Computing suite of open source software tools that extract and integrate data from of the electronic medical records, laboratory data, billing information systems and genomic data. It also includes XNAT (http://xnat.org/) software that is supported by NIH through the National Center for Research Resources (NCRR) sponsored Biomedical Informatics Research Network (BIRN) initiative and NA-MIC.<br /> <br /> = Upcoming Events =<br /> <br /> ===Weekly Meetings===<br /> Tuesday (10:30- 11:30 AM), call: 1-866-890-3820<br /> <br /> *[[CTSC:ARRA.111709| November 17, 2009]] Harvard School of Public Health, 655 Huntington Ave, Building SPH2, 4th Floor, Room 426<br /> *[[CTSC:ARRA.112409| November 24, 2009]] Countway, Ware Room, 5th floor<br /> *[[CTSC:ARRA.120109| December 1, 2009]] <br /> *[[CTSC:ARRA.120809| December 8, 2009]] Ware room, Countway 5th floor (! XNAT demo from Dan Marcus WashU)<br /> *[[CTSC:ARRA.121509| December 15, 2009]] Harvard School of Public Health, 655 Huntington Ave, Building SPH2, 4th Floor, Room 426<br /> *[[CTSC:ARRA.122209| December 22, 2009]] Ware room, Countway 5th floor<br /> *[[CTSC:ARRA.122909| December 29, 2009]] Ware room, Countway 5th floor<br /> <br /> =Past Events =<br /> ===2009 meetings===<br /> <br /> *[[CTSC:ARRA.111009| November 10, 2009]] <br /> *[[CTSC:ARRA.110309| November 3, 2009]] <br /> *[[CTSC:ARRA.102709| October 27, 2009]] <br /> *[[CTSC:ARRA.102009| October 20, 2009]]<br /> *[[CTSC:ARRA.101309| October 13, 2009]]<br /> *[[CTSC:ARRA.100609| October 6, 2009]]<br /> <br /> =Using DCM4CHEE =<br /> ===Installation Instructions for x86_64 Linux, Centos ===<br /> *Download the latest DCM4CHEE for Postgresql<br /> **wget http://sourceforge.net/projects/dcm4che/files/dcm4chee/2.14.7/dcm4chee-psql-2.14.7.zip/download<br /> *Install Postgresql<br /> **sudo yum install postgresql postgresql-server<br /> *Start Postgresql<br /> **sudo /sbin/chkconfig postgresql on<br /> **sudo /sbin/service postgresql start<br /> *Install DCM4CHEE<br /> **Follow instructions at http://www.dcm4che.org/confluence/display/ee2/Installation<br /> **Special Steps<br /> ***Get Sun's Java Advanced Imaging Image I/O Tools 1.1 for 64bit Linux:<br /> wget http://download.java.net/media/jai-imageio/builds/release/1.1/jai_imageio-1_1-lib-linux-i586.tar.gz<br /> ***Download the binary distribution package of JBoss Application Server 4.2.3.GA<br /> wget http://sourceforge.net/projects/jboss/files/JBoss/JBoss-4.2.3.GA/jboss-4.2.3.GA.zip/download<br /> ***Unarchive the downloaded files.<br /> ***sudo cp -rp dcm4chee-psql-2.14.7 /opt<br /> ***sudo cp -p jai_imageio-1_1/lib/libclib_jiio.so /opt/dcm4chee-psql-2.14.7/bin/native/<br /> ***sudo /opt/dcm4chee-psql-2.14.7/bin/install_jboss.sh jboss-4.2.3.GA<br /> ***sudo -u postgres createdb pacsdb<br /> ***sudo -u postgres psql pacsdb -f /opt/dcm4chee-psql-2.14.7/sql/create.psql<br /> <br /> <br /> Back to [[Collaboration:Harvard_CTSC|Collaboration:Harvard_CTSC]]<br /> <br></div>

Yong https://www.na-mic.org/w/index.php?title=CTSC:ARRA_supplement&diff=45056 CTSC:ARRA supplement 2009-11-17T21:32:57Z

<p>Yong: </p> <hr /> <div>= Harvard Catalyst Medical Imaging Informatics ARRA Administrative Supplement=<br /> <br /> {|<br /> |align="left"|<br /> <br /> == Medical Imaging Informatics Bench to Bedside (mi2b2) ==<br /> <br>This Medical Imaging Informatics project was funded by an Administrative Supplement to the Harvard Catalyst through the federal stimulus package aka ARRA. The project will enable clinical imaging data to be used, with appropriate human subject and institutional protections, for secondary research purposes.<br /> |[[image:ARRA.png|thumb|px=250|Go to the [http://www.recovery.gov ARRA website]]]<br /> |}<br /> <br /> =Mission Statement=<br /> <br /> To facilitate access to and use of the extensive collection of valuable medical images obtained during clinical care in a manner that does not negatively impact clinical care, enhances oversight of access and is in compliance with all local and national regulatory requirements. The target audiences for this project are clinical translational scientists (Radiologists and other physicians), basic scientists, and medical image analysis algorithm developers.<br /> <br /> =Key Personnel and Resources=<br /> <br /> Our hospitals are international leaders in the development and deployment of new and advanced biomedical imaging technologies (MRI, high speed CT, ultrasound, PET and others) for clinical practice (although old tried and true technologies are also extensively used). The Picture Archive and Communication Systems (PACS) within each of the Departments of Radiology in our participating hospitals (Massachusetts General Hospital, Brigham and Women’s Hospital, Beth Israel Deaconess Medical Center, and Children’s Hospital Boston) contain a wealth of medical images that equal or exceed the quality of clinical research imaging data, and greatly exceed its volume in terms of the number of patients and disease types. <br /> <br /> This project uses software that is free and open source from currently funded government projects. This software includes the i2b2 (Informatics for Integrating Biology & the Bedside), a National Center for Biomedical Computing suite of open source software tools that extract and integrate data from of the electronic medical records, laboratory data, billing information systems and genomic data. It also includes XNAT (http://xnat.org/) software that is supported by NIH through the National Center for Research Resources (NCRR) sponsored Biomedical Informatics Research Network (BIRN) initiative and NA-MIC.<br /> <br /> = Upcoming Events =<br /> <br /> ===Weekly Meetings===<br /> Tuesday (10:30- 11:30 AM), call: 1-866-890-3820<br /> <br /> *[[CTSC:ARRA.111709| November 17, 2009]] Harvard School of Public Health, 655 Huntington Ave, Building SPH2, 4th Floor, Room 426<br /> *[[CTSC:ARRA.112409| November 24, 2009]] Countway, Ware Room, 5th floor<br /> *[[CTSC:ARRA.120109| December 1, 2009]] <br /> *[[CTSC:ARRA.120809| December 8, 2009]] Ware room, Countway 5th floor (! XNAT demo from Dan Marcus WashU)<br /> *[[CTSC:ARRA.121509| December 15, 2009]] Harvard School of Public Health, 655 Huntington Ave, Building SPH2, 4th Floor, Room 426<br /> *[[CTSC:ARRA.122209| December 22, 2009]] Ware room, Countway 5th floor<br /> *[[CTSC:ARRA.122909| December 29, 2009]] Ware room, Countway 5th floor<br /> <br /> =Past Events =<br /> ===2009 meetings===<br /> <br /> *[[CTSC:ARRA.111009| November 10, 2009]] <br /> *[[CTSC:ARRA.110309| November 3, 2009]] <br /> *[[CTSC:ARRA.102709| October 27, 2009]] <br /> *[[CTSC:ARRA.102009| October 20, 2009]]<br /> *[[CTSC:ARRA.101309| October 13, 2009]]<br /> *[[CTSC:ARRA.100609| October 6, 2009]]<br /> <br /> =Using DCM4CHEE =<br /> ===Installation Instructions for x86_64 Linux, Centos ===<br /> *Download the latest DCM4CHEE for Postgresql<br /> **wget http://sourceforge.net/projects/dcm4che/files/dcm4chee/2.14.7/dcm4chee-psql-2.14.7.zip/download<br /> *Install Postgresql<br /> **sudo yum install postgresql postgresql-server<br /> *Start Postgresql<br /> **sudo /sbin/chkconfig postgresql on<br /> **sudo /sbin/service postgresql start<br /> *Install DCM4CHEE<br /> **Follow instructions at http://www.dcm4che.org/confluence/display/ee2/Installation<br /> **Special Steps<br /> ***Get Sun's Java Advanced Imaging Image I/O Tools 1.1 for 64bit Linux:<br /> wget http://download.java.net/media/jai-imageio/builds/release/1.1/jai_imageio-1_1-lib-linux-i586.tar.gz<br /> *** Download the binary distribution package of JBoss Application Server 4.2.3.GA<br /> wget http://sourceforge.net/projects/jboss/files/JBoss/JBoss-4.2.3.GA/jboss-4.2.3.GA.zip/download<br /> <br /> Back to [[Collaboration:Harvard_CTSC|Collaboration:Harvard_CTSC]]<br /> <br></div>

Yong https://www.na-mic.org/w/index.php?title=CTSC:ARRA_supplement&diff=45049 CTSC:ARRA supplement 2009-11-17T19:09:26Z

<p>Yong: </p> <hr /> <div>= Harvard Catalyst Medical Imaging Informatics ARRA Administrative Supplement=<br /> <br /> {|<br /> |align="left"|<br /> <br /> == Medical Imaging Informatics Bench to Bedside (mi2b2) ==<br /> <br>This Medical Imaging Informatics project was funded by an Administrative Supplement to the Harvard Catalyst through the federal stimulus package aka ARRA. The project will enable clinical imaging data to be used, with appropriate human subject and institutional protections, for secondary research purposes.<br /> |[[image:ARRA.png|thumb|px=250|Go to the [http://www.recovery.gov ARRA website]]]<br /> |}<br /> <br /> =Mission Statement=<br /> <br /> To facilitate access to and use of the extensive collection of valuable medical images obtained during clinical care in a manner that does not negatively impact clinical care, enhances oversight of access and is in compliance with all local and national regulatory requirements. The target audiences for this project are clinical translational scientists (Radiologists and other physicians), basic scientists, and medical image analysis algorithm developers.<br /> <br /> =Key Personnel and Resources=<br /> <br /> Our hospitals are international leaders in the development and deployment of new and advanced biomedical imaging technologies (MRI, high speed CT, ultrasound, PET and others) for clinical practice (although old tried and true technologies are also extensively used). The Picture Archive and Communication Systems (PACS) within each of the Departments of Radiology in our participating hospitals (Massachusetts General Hospital, Brigham and Women’s Hospital, Beth Israel Deaconess Medical Center, and Children’s Hospital Boston) contain a wealth of medical images that equal or exceed the quality of clinical research imaging data, and greatly exceed its volume in terms of the number of patients and disease types. <br /> <br /> This project uses software that is free and open source from currently funded government projects. This software includes the i2b2 (Informatics for Integrating Biology & the Bedside), a National Center for Biomedical Computing suite of open source software tools that extract and integrate data from of the electronic medical records, laboratory data, billing information systems and genomic data. It also includes XNAT (http://xnat.org/) software that is supported by NIH through the National Center for Research Resources (NCRR) sponsored Biomedical Informatics Research Network (BIRN) initiative and NA-MIC.<br /> <br /> = Upcoming Events =<br /> <br /> ===Weekly Meetings===<br /> Tuesday (10:30- 11:30 AM), call: 1-866-890-3820<br /> <br /> *[[CTSC:ARRA.111709| November 17, 2009]] Harvard School of Public Health, 655 Huntington Ave, Building SPH2, 4th Floor, Room 426<br /> *[[CTSC:ARRA.112409| November 24, 2009]] Countway, Ware Room, 5th floor<br /> *[[CTSC:ARRA.120109| December 1, 2009]] <br /> *[[CTSC:ARRA.120809| December 8, 2009]] Ware room, Countway 5th floor (! XNAT demo from Dan Marcus WashU)<br /> *[[CTSC:ARRA.121509| December 15, 2009]] Harvard School of Public Health, 655 Huntington Ave, Building SPH2, 4th Floor, Room 426<br /> *[[CTSC:ARRA.122209| December 22, 2009]] Ware room, Countway 5th floor<br /> *[[CTSC:ARRA.122909| December 29, 2009]] Ware room, Countway 5th floor<br /> <br /> =Past Events =<br /> ===2009 meetings===<br /> <br /> *[[CTSC:ARRA.111009| November 10, 2009]] <br /> *[[CTSC:ARRA.110309| November 3, 2009]] <br /> *[[CTSC:ARRA.102709| October 27, 2009]] <br /> *[[CTSC:ARRA.102009| October 20, 2009]]<br /> *[[CTSC:ARRA.101309| October 13, 2009]]<br /> *[[CTSC:ARRA.100609| October 6, 2009]]<br /> <br /> =Using DCM4CHEE =<br /> ===Installation Instructions===<br /> *Download the latest DCM4CHEE for Postgresql<br /> **wget http://sourceforge.net/projects/dcm4che/files/dcm4chee/2.14.7/dcm4chee-psql-2.14.7.zip/download<br /> *Install Postgresql<br /> **sudo yum install postgresql postgresql-server<br /> *Start Postgresql<br /> **sudo /sbin/chkconfig postgresql on<br /> **sudo /sbin/service postgresql start<br /> *Install DCM4CHEE<br /> **Follow instructions at http://www.dcm4che.org/confluence/display/ee2/Installation<br /> **Special Steps<br /> ***Get Sun's Java Advanced Imaging Image I/O Tools 1.1 for 64bit Linux:<br /> wget http://download.java.net/media/jai-imageio/builds/release/1.1/jai_imageio-1_1-lib-linux-i586.tar.gz<br /> <br /> Back to [[Collaboration:Harvard_CTSC|Collaboration:Harvard_CTSC]]<br /> <br></div>

Yong https://www.na-mic.org/w/index.php?title=CTSC:ARRA_supplement&diff=45048 CTSC:ARRA supplement 2009-11-17T18:52:05Z

<p>Yong: </p> <hr /> <div>= Harvard Catalyst Medical Imaging Informatics ARRA Administrative Supplement=<br /> <br /> {|<br /> |align="left"|<br /> <br /> == Medical Imaging Informatics Bench to Bedside (mi2b2) ==<br /> <br>This Medical Imaging Informatics project was funded by an Administrative Supplement to the Harvard Catalyst through the federal stimulus package aka ARRA. The project will enable clinical imaging data to be used, with appropriate human subject and institutional protections, for secondary research purposes.<br /> |[[image:ARRA.png|thumb|px=250|Go to the [http://www.recovery.gov ARRA website]]]<br /> |}<br /> <br /> =Mission Statement=<br /> <br /> To facilitate access to and use of the extensive collection of valuable medical images obtained during clinical care in a manner that does not negatively impact clinical care, enhances oversight of access and is in compliance with all local and national regulatory requirements. The target audiences for this project are clinical translational scientists (Radiologists and other physicians), basic scientists, and medical image analysis algorithm developers.<br /> <br /> =Key Personnel and Resources=<br /> <br /> Our hospitals are international leaders in the development and deployment of new and advanced biomedical imaging technologies (MRI, high speed CT, ultrasound, PET and others) for clinical practice (although old tried and true technologies are also extensively used). The Picture Archive and Communication Systems (PACS) within each of the Departments of Radiology in our participating hospitals (Massachusetts General Hospital, Brigham and Women’s Hospital, Beth Israel Deaconess Medical Center, and Children’s Hospital Boston) contain a wealth of medical images that equal or exceed the quality of clinical research imaging data, and greatly exceed its volume in terms of the number of patients and disease types. <br /> <br /> This project uses software that is free and open source from currently funded government projects. This software includes the i2b2 (Informatics for Integrating Biology & the Bedside), a National Center for Biomedical Computing suite of open source software tools that extract and integrate data from of the electronic medical records, laboratory data, billing information systems and genomic data. It also includes XNAT (http://xnat.org/) software that is supported by NIH through the National Center for Research Resources (NCRR) sponsored Biomedical Informatics Research Network (BIRN) initiative and NA-MIC.<br /> <br /> = Upcoming Events =<br /> <br /> ===Weekly Meetings===<br /> Tuesday (10:30- 11:30 AM), call: 1-866-890-3820<br /> <br /> *[[CTSC:ARRA.111709| November 17, 2009]] Harvard School of Public Health, 655 Huntington Ave, Building SPH2, 4th Floor, Room 426<br /> *[[CTSC:ARRA.112409| November 24, 2009]] Countway, Ware Room, 5th floor<br /> *[[CTSC:ARRA.120109| December 1, 2009]] <br /> *[[CTSC:ARRA.120809| December 8, 2009]] Ware room, Countway 5th floor (! XNAT demo from Dan Marcus WashU)<br /> *[[CTSC:ARRA.121509| December 15, 2009]] Harvard School of Public Health, 655 Huntington Ave, Building SPH2, 4th Floor, Room 426<br /> *[[CTSC:ARRA.122209| December 22, 2009]] Ware room, Countway 5th floor<br /> *[[CTSC:ARRA.122909| December 29, 2009]] Ware room, Countway 5th floor<br /> <br /> =Past Events =<br /> ===2009 meetings===<br /> <br /> *[[CTSC:ARRA.111009| November 10, 2009]] <br /> *[[CTSC:ARRA.110309| November 3, 2009]] <br /> *[[CTSC:ARRA.102709| October 27, 2009]] <br /> *[[CTSC:ARRA.102009| October 20, 2009]]<br /> *[[CTSC:ARRA.101309| October 13, 2009]]<br /> *[[CTSC:ARRA.100609| October 6, 2009]]<br /> <br /> =Using DCM4CHEE =<br /> ===Installation Instructions===<br /> *Download the latest DCM4CHEE for Postgresql<br /> **wget http://sourceforge.net/projects/dcm4che/files/dcm4chee/2.14.7/dcm4chee-psql-2.14.7.zip/download<br /> *Install Postgresql<br /> **sudo yum install postgresql postgresql-server<br /> *Start Postgresql<br /> **sudo /sbin/chkconfig postgresql on<br /> **sudo /sbin/service postgresql start<br /> *Install DCM4CHEE<br /> **Follow instructions at http://www.dcm4che.org/confluence/display/ee2/Installation<br /> <br /> Back to [[Collaboration:Harvard_CTSC|Collaboration:Harvard_CTSC]]<br /> <br></div>

Yong https://www.na-mic.org/w/index.php?title=CTSC:ARRA_supplement&diff=45047 CTSC:ARRA supplement 2009-11-17T18:15:16Z

<p>Yong: </p> <hr /> <div>= Harvard Catalyst Medical Imaging Informatics ARRA Administrative Supplement=<br /> <br /> {|<br /> |align="left"|<br /> <br /> == Medical Imaging Informatics Bench to Bedside (mi2b2) ==<br /> <br>This Medical Imaging Informatics project was funded by an Administrative Supplement to the Harvard Catalyst through the federal stimulus package aka ARRA. The project will enable clinical imaging data to be used, with appropriate human subject and institutional protections, for secondary research purposes.<br /> |[[image:ARRA.png|thumb|px=250|Go to the [http://www.recovery.gov ARRA website]]]<br /> |}<br /> <br /> =Mission Statement=<br /> <br /> To facilitate access to and use of the extensive collection of valuable medical images obtained during clinical care in a manner that does not negatively impact clinical care, enhances oversight of access and is in compliance with all local and national regulatory requirements. The target audiences for this project are clinical translational scientists (Radiologists and other physicians), basic scientists, and medical image analysis algorithm developers.<br /> <br /> =Key Personnel and Resources=<br /> <br /> Our hospitals are international leaders in the development and deployment of new and advanced biomedical imaging technologies (MRI, high speed CT, ultrasound, PET and others) for clinical practice (although old tried and true technologies are also extensively used). The Picture Archive and Communication Systems (PACS) within each of the Departments of Radiology in our participating hospitals (Massachusetts General Hospital, Brigham and Women’s Hospital, Beth Israel Deaconess Medical Center, and Children’s Hospital Boston) contain a wealth of medical images that equal or exceed the quality of clinical research imaging data, and greatly exceed its volume in terms of the number of patients and disease types. <br /> <br /> This project uses software that is free and open source from currently funded government projects. This software includes the i2b2 (Informatics for Integrating Biology & the Bedside), a National Center for Biomedical Computing suite of open source software tools that extract and integrate data from of the electronic medical records, laboratory data, billing information systems and genomic data. It also includes XNAT (http://xnat.org/) software that is supported by NIH through the National Center for Research Resources (NCRR) sponsored Biomedical Informatics Research Network (BIRN) initiative and NA-MIC.<br /> <br /> = Upcoming Events =<br /> <br /> ===Weekly Meetings===<br /> Tuesday (10:30- 11:30 AM), call: 1-866-890-3820<br /> <br /> *[[CTSC:ARRA.111709| November 17, 2009]] Harvard School of Public Health, 655 Huntington Ave, Building SPH2, 4th Floor, Room 426<br /> *[[CTSC:ARRA.112409| November 24, 2009]] Countway, Ware Room, 5th floor<br /> *[[CTSC:ARRA.120109| December 1, 2009]] <br /> *[[CTSC:ARRA.120809| December 8, 2009]] Ware room, Countway 5th floor (! XNAT demo from Dan Marcus WashU)<br /> *[[CTSC:ARRA.121509| December 15, 2009]] Harvard School of Public Health, 655 Huntington Ave, Building SPH2, 4th Floor, Room 426<br /> *[[CTSC:ARRA.122209| December 22, 2009]] Ware room, Countway 5th floor<br /> *[[CTSC:ARRA.122909| December 29, 2009]] Ware room, Countway 5th floor<br /> <br /> =Past Events =<br /> ===2009 meetings===<br /> <br /> *[[CTSC:ARRA.111009| November 10, 2009]] <br /> *[[CTSC:ARRA.110309| November 3, 2009]] <br /> *[[CTSC:ARRA.102709| October 27, 2009]] <br /> *[[CTSC:ARRA.102009| October 20, 2009]]<br /> *[[CTSC:ARRA.101309| October 13, 2009]]<br /> *[[CTSC:ARRA.100609| October 6, 2009]]<br /> <br /> =Using DCM4CHEE =<br /> ===Installation Instructions===<br /> *Download the latest DCM4CHEE for Postgresql<br /> **wget http://sourceforge.net/projects/dcm4che/files/dcm4chee/2.14.7/dcm4chee-psql-2.14.7.zip/download<br /> *Install Postgresql<br /> **sudo yum install postgresql postgresql-server<br /> *Start Postgresql<br /> **sudo /sbin/chkconfig postgresql on<br /> **sudo /sbin/service postgresql start<br /> *Install DCM4CHEE<br /> <br /> <br /> Back to [[Collaboration:Harvard_CTSC|Collaboration:Harvard_CTSC]]<br /> <br></div>

Yong https://www.na-mic.org/w/index.php?title=2009_Summer_Project_Week_XNAT_i2b2&diff=40403 2009 Summer Project Week XNAT i2b2 2009-07-07T20:06:29Z

<p>Yong: Blanked the page</p> <hr /> <div></div>

Yong https://www.na-mic.org/w/index.php?title=2009_Summer_Project_Week&diff=40402 2009 Summer Project Week 2009-07-07T20:05:59Z

<p>Yong: /* Informatics */</p> <hr /> <div>__NOTOC__<br /> <br /> Back to [[Project Events]], [[Events]]<br /> <br /> [[Image:PW2009-v3.png|300px]]<br /> [[Image:2009_Project_Week_Group_Picture.jpg|300px]]<br /> <br /> ==Summary==<br /> <br /> The FIRST JOINT PROJECT WEEK (and the nineth NA-MIC Project event) was held during June 22-26, 2009 in Boston, at MIT and Brigham and Women's Hospital. It recorded 125+ registered attendees.<br /> <br /> Some (many!) pictures from the event are available [http://picasaweb.google.com/tokjun/ProjectWeek2009?authkey=Gv1sRgCOmyn6fPrcSTwwE&feat=directlink here]. <br /> <br /> ==Introduction to the FIRST JOINT PROJECT WEEK==<br /> <br /> We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. <br /> <br /> Active preparation begins on Thursday, April 16th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects. <br /> <br /> The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.<br /> <br /> This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January. <br /> <br /> A summary of all past NA-MIC Project Events that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].<br /> <br /> == Agenda==<br /> Breakout Rooms: 32-D451, 38-413<br /> <br /> === Monday=== <br /> ** noon-1pm lunch <br /> **1pm: Welcome (Ron Kikinis)<br /> ** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template]) <br /> ** 3:30-5:30pm Start project work<br /> === Tuesday ===<br /> ** 8:30am breakfast<br /> ** 8:30am-9:30am [[2009_Summer_Project_Week_4D_Imaging_discussion| 4D Imaging Meeting]]<br /> **9:30-10am: NA-MIC Kit Overview (Jim Miller)<br /> ** 10-10:30am Slicer 3.4 Update (Steve Pieper) ([[media:2009 NA-MIC Project Week Slicer3.4.ppt|Slides]], [[2009_Summer_Project_Week_Extension_Manager|Project Page]])<br /> ** 10:30-11am Slicer IGT and Imaging Kit Update Update (Noby Hata [[Media:2009SummerProgrammingWeekHataIGT.ppt‎|Slides]], Scott Hoge [ [[Media:2009_NA-MIC_Project_Week_FastImagingLibrary.ppt|slides]] ])<br /> ** noon lunch<br /> ** 1pm Breakout Session: [[2009 Project Week Breakout Session: Slicer-Python]] (Demian W) (Star D463 Star Conference Room in Stata)<br /> ** 2:00pm-3.00pm: [[2009 Project Week Data Clinic|Data Clinic]] (Ron Kikinis) (In Grier)<br /> ** 4:00pm: GWE End-To-End Live Demo (Marco Ruiz)<br /> ** 4:30pm [http://www.cimit.org/forum-current.html CIMIT Forum (At BWH / Carl J. and Ruth Shapiro Cardiovascular Center) Open Source Software for Translational IGT Research and Commercial Use, Clif Burdette, Acoustic MedSystems, Inc. ]<br /> ** 5:30pm adjourn for day<br /> <br /> === Wednesday ===<br /> ** 8:30am breakfast<br /> ** 9am-12pm Breakout Session: [[2009 Project Week Breakout Session: ITK]] (32-G451) (Luis Ibanez)<br /> ** 10am - 11am 32-D451 taken by Megason Lab.<br /> ** noon lunch<br /> ** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: 3D+T Microscopy Cell Dataset Segmentation]] (D463 Star conference room) (Alexandre Gouaillard, Arnaud Gelas, Lydie Souhait, Badri Roysam, Curtis Rueden)<br /> ** 5:30pm adjourn for day<br /> <br /> === Thursday===<br /> ** 8:30am breakfast<br /> ** 10-11am [[Events:TutorialContestJune2009|Tutorial Contest Presentations]]<br /> ** 11am: Breakout Session: Linking atlases, labels, and ontologies<br /> ** noon lunch<br /> ** 1:00pm: Breakout Session: [[2009 Project Week Breakout Session: XNAT for Programmers]] (32-D451) (Dan M.)<br /> ** 5:30pm adjourn for day<br /> <br /> === Friday=== <br /> ** 8:30am breakfast<br /> ** 10am-noon: [[Events:TutorialContestJune2009|Tutorial Contest Winner Announcement]] and [[#Projects|Project Progress Updates]]<br /> *** Noon: Lunch boxes and adjourn by 1:30pm.<br /> ***We need to empty room by 1:30. You are welcome to use wireless in Stata.<br /> ***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]<br /> ***Next Project Week [[AHM_2010|in Utah, January 4-8, 2010]]<br /> <br /> ==Projects==<br /> <br /> === Segmentation ===<br /> <br /> #[[2009_Summer_Project_Week_Lupus_Lesion_Segmentation|Lupus Lesion Segmentation]] (Mark Scully MRN)<br /> #[[2009_Summer_Project_Week_WML_SEgmentation|White Matter Lesion segmentation]] (Minjeong Kim UNC)<br /> #[[2009_Summer_Project_Week_Skull_Stripping|Skull Stripping]] (Snehashis Roy JHU)<br /> #[[EMSegment|EM Segment]] (Sylvain Jaume MIT, Nicolas Rannou BWH)<br /> #[[2009_Summer_Project_Week-FastMarching_for_brain_tumor_segmentation|FastMarching for brain tumor segmentation]] (Andrey Fedorov BWH)<br /> #[[2009_Summer_Project_Week_New_ITK_Level_Set_Framework|New Level Set Framework in ITK]] (Arnaud Gelas, Harvard Medical School)<br /> #[[2009_Summer_Project_Week_TubularSurfaceSeg|Tubular Surface Segmentation in Slicer]] (Vandana Mohan, Georgia Tech)<br /> #[[Summer2009:The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn BWH)<br /> #[[2009_Summer_Project_Week_Slicer3_Cortical_Thickness_Pipeline|Cortical Thickness Pipeline]] (Clement Vachet UNC)<br /> #[[2009_Summer_Project_Week_Automatic_Brain_MRI_Pipeline|Automatic brain MRI processing pipeline]] (Marcel Prastawa Utah)<br /> #[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images|Segmentation of Knee Structures]] (Harish Doddi Stanford)<br /> <br /> === Registration ===<br /> <br /> #[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration|Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez Kitware)<br /> #[[BSpline Registration in Slicer3|BSpline Registration in Slicer3]] (Samuel Gerber Utah)<br /> #[[Summer2009:Registration reproducibility in Slicer|Registration reproducibility in Slicer3]] (Andrey Fedorov BWH)<br /> #[[2009_Summer_project_week_prostate_registration|Prostate Registration Slicer Module]] (Yi Gao, Georgia Tech)<br /> #[[2009_Summer_Project_Week_Slicer3_registration|Slicer 3 registration ]] (Andrew Rausch BWH PNL)<br /> #[[EPI Correction in Slicer3|EPI Correction in Slicer3]] (Ran Tao Utah)<br /> #[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Tina Kapur BWH)<br /> #[[Measuring Alcohol Stress Interaction]] (Vidya Rajgopalan Virginia Tech)<br /> #[[2009_Summer_Project_Week_TrigeminalNerve|Atlas to CT Registration in Trigeminal Neuralgia]] (Marta Peroni PoliMI)<br /> #[[2009_Summer_Project_Week_HAMMER_Registration|HAMMER Registration]] (Guorong Wu UNC)<br /> #[[2009_Summer_Project_Week_MCMC_Cuda_Registration|Elastic Non-Rigid Registration using MCMC and CUDA]] (Petter Risholm BWH)<br /> #[[2009_Summer_Project_Week_Cardiac_Blood_Pool_Registration|Cardiac Blood Pool Registration]] (Michal Depa MIT)<br /> <br /> === IGT ===<br /> <br /> #[[2009_Summer_Project_Week_Transrectal_Prostate_biopsy|Transrectal Prostate Biopsy]] (Andras Lasso Queen's)<br /> #[[2009_Summer_Project_Week_Prostate_Robotics|Prostate Robotics]] (Junichi Tokuda BWH)<br /> #[[2009_Summer_Project_Week_Liver_Ablation_Slicer|Liver Ablation in Slicer]] (Ziv Yaniv Georgetown)<br /> #[[2009_Summer_Project_Week_Slicer3_Brainlab_Introduction|Demo of Neuronavigation using Brainlab, Slicer3, BioImage Suite]] (Haiying Liu BWH)<br /> #[[2009_Summer_Project_Week_3DGRASE|3D GRASE]] (Scott Hoge BWH)<br /> #[[2009_Summer_Project_Week_RTHawk_MR_Navigation|Using RTHawk to Implement MR Navigation]] (Ben Schwartz BWH)<br /> #[[2009_Summer_Project_Week_Slicer|Integration of Flexible Surgical Instrument Modeling and Virtual Catheter with Slicer]] (Jayender Jagadeesan BWH)<br /> #[[Integration of stereo video into Slicer3]] (Mehdi Esteghamatian Robarts Institute)<br /> #[[Enhanced Neurosuregery navigation]] (Haytham Elhawary, Brigham and Women's Hospital)<br /> #[[GPU accelerated FEM for simulation and segmentation]] (Megumi Nakao, Brigham and Women's Hospital)<br /> #[[Liver EM segmentation]] (Padma Akella, Brigham and Women's Hospital)<br /> <br /> === Radiotherapy ===<br /> <br /> #[[2009_Summer_Project_Week_Slicer3_Adaptive_Radiotherapy|DicomRT]] (Greg Sharp)<br /> #[[2009_Summer_Project_Week_Adaptive_RT|Adaptive Radiotherapy for Head,Neck, and Thorax]] (Ivan Kolesov GATech)<br /> #[[2009_Summer_Project_Week_Cone_Beam_backprojection]](James Balter U Michigan)<br /> #[[2009_Summer_project_week_3d_Deformable_alignment]](Dan McShan U Michigan)<br /> #[[2009_Summer_project_week_adaptive_radiation_planning_visualization]](Cal Hisley, Des Moines University/Mercy Des Moines Medical Center)<br /> <br /> === Analysis ===<br /> <br /> #[[2009_Summer_Project_Week_Meningioma_growth_simulation|Meningioma growth simulation]] (Andrey Fedorov BWH)<br /> #[[2009_Summer_Project_Week_Multimodal_SPL_Brain_Atlas|Linking atlas data with ontologies of brain morphology and function]] (Michael Halle BWH)<br /> #[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze MIT)<br /> #[[2009_Summer_Project_Week_4D_Imaging|4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi Tokuda BWH)<br /> #[[2009_Summer_Project_Week_4D_Gated_US_In_Slicer|Gated 4D ultrasound reconstruction for Slicer3]] (Danielle Pace Robarts Institute)<br /> #[[2009_Summer_Project_Week_Statistical_Toolbox|multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor Robarts Institute)<br /> #[[2009_Summer_Project_Week_Photograph|Photograph Project]] (Junichi Tokuda, BWH)<br /> <br /> === Informatics ===<br /> <br /> #[[2009_Summer_Project_Week_XNAT_UI|XNAT user interface improvements for NA-MIC]] (Dan Marcus WUSTL)<br /> #[[2009_Summer_Project_Week_XNATFS|XNAT File System with FUSE]] (Dan Marcus WUSTL)<br /> #[[2009_Summer_Project_Week_GWE_XNAT|GWE-XNAT Integration]] (Marco Ruiz UCSD)<br /> #[[2009_Summer_Project_Week_GWE_Results_Browser|GWE Results Browser Improvements]] (Marco Ruiz UCSD)<br /> #[[Projects:ShapeCorrespondence_UNCOrthoApp|XNAT & Ortho App]] (Beatriz Paniagua UNC)<br /> <br /> === Diffusion ===<br /> <br /> #[[Summer2009:VCFS|Stochastic Tractography to study VCFS and Schizophrenia]] (Sylvain Bouix BWH)<br /> #[[2009_Summer_Project_Week_FunctionalClusteringAnalysis|Functional Analysis of White Matter in Whole Brain Clustering of Schizophrenic Patients]] (Doug Terry BWH)<br /> #[[2009_Summer_Project_Week_Slicer3_Fibre_Dispersion|Slicer module for the computation of fibre dispersion and curving measures]] (Peter Savadjiev BWH)<br /> #[[2009_Summer_Project_Week_DWI_/_DTI_QC_and_Prepare_Tool:_DTIPrep|DWI/DTI QC and Preparation Tool: DTIPrep]] (Zhexing Liu UNC)<br /> #[[2009_Summer_Project_Week_Hageman_DTIDigitalPhantom|DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA ]] (Nathan Hageman UCLA)<br /> #[[2009_Summer_Project_Week_Hageman_FMTractography|Fluid mechanics tractography and visualization]] (Nathan Hageman UCLA)<br /> #[[Summer2009:Using_CUDA_for_stochastic_tractography|Developing interactive stochastic tractography using CUDA]] (Julien de Siebenthal BWH)<br /> <br /> <br /> <br /> === Python ===<br /> <br /> #[[Summer2009:Using_ITK_in_python|Using ITK in python]] (Steve Pieper BWH)<br /> #[[Summer2009:Using_cython|Accelerating python with cython: application to stochastic tractography]] (Julien de Siebenthal BWH)<br /> #[[Summer2009:Implementing_parallelism_in_python|Taking advantage of multicore machines & clusters with python]] (Julien de Siebenthal BWH)<br /> #[[Summer2009:Using_client_server_paradigm_with_python_and_slicer|Deferring heavy computational tasks with Slicer python]] (Julien de Siebenthal BWH)<br /> <br /> === Slicer Internals ===<br /> <br /> #[[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole Aucoin BWH)<br /> #[[2009_Summer_Project_Week_Colors_Module|Updates to Slicer3 Colors module]] (Nicole Aucoin BWH)<br /> #[[2009_Summer_Project_Week_Orthogonal_Reformat_Widget|Orthogonal Planes in Reformat Widget]] (Michal Depa MIT)<br /> #[[Slicer3_FlexibleLayouts | Slicer3 Flexible Layouts]] (Wendy Plesniak BWH)<br /> #[[2009_Summer_Project_Week_Extension_Manager|Slicer3 Extension Manager]] (Katie Hayes BWH)<br /> #[[MeshingSummer2009|IAFE Mesh Modules - improvements and testing]] (Curt Lisle Knowledge Vis)<br /> <br /> === Execution Model ===<br /> <br /> #[[Plug-In 3D Viewer based on XIP|Plug-in 3D Viewer based on XIP]] (Lining Yang Siemens Research)<br /> #[[Summer2009:Extension of the Command Line XML Syntax/Interface|Extension of the Command Line XML Syntax/Interface]] (Bennett Landman)<br /> <br /> == Preparation ==<br /> <br /> # Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list<br /> # Join the kickoff TCON on April 16, 3pm ET.<br /> # [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.<br /> # By 3pm ET on June 11, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.<br /> # By 3pm on June 18, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)<br /> ## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)<br /> ## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)<br /> ## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)<br /> # Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...<br /> # People doing Slicer related projects should come to project week with slicer built on your laptop.<br /> ## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-4/#dirlist Slicer-3-4 branch] (new code should not be checked into the branch).<br /> ## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].<br /> <br /> <br /> <br /> == Logistics ==<br /> *'''Dates:''' June 22-26, 2009<br /> *'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].<br /> *32-D451 (Stata)<br /> ** Mon, noon - end<br /> ** Tues, Wed, Thurs, all day<br /> *38-413 (Lg Conference room inside EECS Headquarters)<br /> **Mon, noon-end<br /> **Tues, Wed, Thurs, 9-end<br /> **Fri, 9-1:00<br /> *'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 12th, 2009. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139. Receipts will be provided by email as checks are received. Please send questions to dkauf at mit.edu. '''If this is your first event and you are attending for only one day, the registration fee is waived.''' Please let us know, so that we can cover the costs with one of our grants.<br /> *'''Registration Method''' Add your name to the Attendee List section of this page<br /> *'''Hotel:''' We have a group rate of $189/night (plus tax) at the Le Meridien (which used to be the Hotel at MIT). [http://www.starwoodmeeting.com/Book/MITDECSE Please click here to reserve.] This rate is good only through June 1.<br /> *Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.<br /> *2009 Summer Project Week [[NA-MIC/Projects/Theme/Template|'''Template''']]<br /> *[[2008_Summer_Project_Week#Projects|Last Year's Projects as a reference]]<br /> *For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]<br /> <br /> ==Attendee List==<br /> <br /> '''Please do not add any more names here. If you need to register, please send an email to tkapur at bwh.harvard.edu and we will accommodate you if we can.'''<br /> {|<br /> |-<br /> |<br /> {|class="wikitable"<br /> !Number<br /> |- style=&#34height:50px&#34<br /> |1<br /> |- style=&#34height:50px&#34<br /> |2<br /> |- style=&#34height:50px&#34<br /> |3<br /> |- style=&#34height:50px&#34<br /> |4<br /> |- style=&#34height:50px&#34<br /> |5<br /> |- style=&#34height:50px&#34<br /> |6<br /> |- style=&#34height:50px&#34<br /> |7<br /> |- style=&#34height:50px&#34<br /> |8<br /> |- style=&#34height:50px&#34<br /> |9<br /> |- style=&#34height:50px&#34<br /> |10<br /> |- style=&#34height:50px&#34<br /> |11<br /> |- style=&#34height:50px&#34<br /> |12<br /> |- style=&#34height:50px&#34<br /> |13<br /> |- style=&#34height:50px&#34<br /> |14<br /> |- style=&#34height:50px&#34<br /> |15<br /> |- style=&#34height:50px&#34<br /> |16<br /> |- style=&#34height:50px&#34<br /> |17<br /> |- style=&#34height:50px&#34<br /> |18<br /> |- 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style=&#34height:50px&#34<br /> |Robert<br /> |Yaffe<br /> |MGH - Mon<br /> |- style=&#34height:50px&#34<br /> |Sylvain<br /> |Jaume<br /> |MIT<br /> |- style=&#34height:50px&#34<br /> |Bjoern<br /> |Menze<br /> |MIT<br /> |- style=&#34height:50px&#34<br /> |Jeremy<br /> |Bockholt<br /> |MRN (NAMIC Lupus DBP)<br /> |- style=&#34height:50px&#34<br /> |Mark<br /> |Scully<br /> |MRN (NAMIC Lupus DBP) Tue-Th<br /> |- style=&#34height:50px&#34<br /> |Joe<br /> |Stam<br /> |NVIDIA (Wed &amp; Thurs)<br /> |- style=&#34height:50px&#34<br /> |Kimberly<br /> |Powell<br /> |NVIDIA (Wed)<br /> |- style=&#34height:50px&#34<br /> |Marta<br /> |Peroni<br /> |Politecnico di Milano<br /> |- style=&#34height:50px&#34<br /> |Andras<br /> |Lasso<br /> |Queen's (NAMIC DBP)<br /> |- style=&#34height:50px&#34<br /> |Yanling<br /> |Liu<br /> |SAIC/NCI-Frederick<br /> |- style=&#34height:50px&#34<br /> |Melanie<br /> |Grebe<br /> |Siemens Corporate Research<br /> |- style=&#34height:50px&#34<br /> |Lining<br /> |Yang<br /> |Siemens Corporate Research<br /> |- style=&#34height:50px&#34<br /> |Harish<br /> |Doddi<br /> |Stanford University<br /> |- style=&#34height:50px&#34<br /> |Marco<br /> |Ruiz<br /> |UCSD<br /> |- style=&#34height:50px&#34<br /> |Nathan<br /> |Hageman<br /> |UCLA (Mon-Thurs)<br /> |- style=&#34height:50px&#34<br /> |Hans<br /> |Johnson<br /> |U Iowa<br /> |- style=&#34height:50px&#34<br /> |Vincent<br /> |Magnotta<br /> |U Iowa<br /> |- style=&#34height:50px&#34<br /> |Jeffrey<br /> |Yager<br /> |U Iowa<br /> |- style=&#34height:50px&#34<br /> |Manasi<br /> |Ramachandran<br /> |U Iowa<br /> |- style=&#34height:50px&#34<br /> |Dave<br /> |Welch<br /> |U Iowa<br /> |- style=&#34height:50px&#34<br /> |Andrzej<br /> |Przybyszewski<br /> |UMass Med (Mon)<br /> |- style=&#34height:50px&#34<br /> |James<br /> |Balter<br /> |U Michigan<br /> |- style=&#34height:50px&#34<br /> |Dan<br /> |McShan<br /> |U Michigan<br /> |- style=&#34height:50px&#34<br /> |Zhou<br /> |Shen<br /> 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|Archie<br /> |WUSTL<br /> |- style=&#34height:50px&#34<br /> |Tim<br /> |Olsen<br /> |WUSTL<br /> |- style=&#34height:50px&#34<br /> |Mehdi<br /> |Esteghamatian<br /> |Robarts Research Inst. / Western Ontario<br /> |- style=&#34height:50px&#34<br /> |Diego<br /> |Cantor<br /> |Robarts Research Inst. / Western Ontario<br /> |- style=&#34height:50px&#34<br /> |Danielle<br /> |Pace<br /> |Robarts Research Inst. / Western Ontario<br /> |- style=&#34height:50px&#34<br /> |Vidya<br /> |Rajagopalan<br /> |VA Tech<br /> |- style=&#34height:50px&#34<br /> |Gregory<br /> |Fischer<br /> |WPI<br /> |- style=&#34height:50px&#34<br /> |Dominique<br /> |Belhachemi<br /> |Yale U (Tu &amp; Wed)<br /> |- style=&#34height:50px&#34<br /> |Alark<br /> |Joshi<br /> |Yale U (Tu &amp; Wed)<br /> |- style=&#34height:50px&#34<br /> |Xenios<br /> |Papademetris<br /> |Yale U (Tu &amp; Wed)<br /> |- style=&#34height:50px&#34<br /> |Dustin<br /> |Scheinost<br /> |Yale U (Tu &amp; Wed)<br /> |- style=&#34height:50px&#34<br /> |Michelle<br /> |Borkin<br /> |Harvard SEAS (Mon only)<br /> |- style=&#34height:50px&#34<br /> |Renxin<br /> |Chu<br /> |BWH (NCIGT) (Mon, Tue)<br /> |- style=&#34height:50px&#34<br /> |Ben<br /> |Schwartz<br /> |BWH (NCIGT) (Mon, Tue)<br /> |- style=&#34height:50px&#34<br /> |Marianna<br /> |Jakab<br /> |BWH (NCIGT, NAC) (Mon, Tue)<br /> |- style=&#34height:50px&#34<br /> |Viswanath <br /> |Avasarala<br /> |GE (Wed, Thurs)<br /> |- style=&#34height:50px&#34<br /> |Michal<br /> |Depa<br /> |MIT<br /> |- style=&#34height:50px&#34<br /> |}<br /> |}<br /> <br /> <br /> '''Please do not add any more names here. If you need to register, please send an email to tkapur at bwh.harvard.edu and we will accommodate you if we can.'''<br /> <br /> The following was used to convert from excel to mediawiki markup: http://area23.brightbyte.de/csv2wp.php</div>

Yong https://www.na-mic.org/w/index.php?title=2009_Summer_Project_Week_XNAT_i2b2&diff=38388 2009 Summer Project Week XNAT i2b2 2009-06-08T21:00:35Z

<p>Yong: Created page with '__NOTOC__ <gallery> Image:PW2009-v3.png|Project Week Main Page </gallery> ==Key Investigators== * WUSTL: Dan Marcus * Harvard CTSC: Yong Gao * othe...'</p> <hr /> <div>__NOTOC__<br /> <gallery><br /> Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]<br /> </gallery><br /> <br /> <br /> ==Key Investigators==<br /> * WUSTL: Dan Marcus<br /> * Harvard CTSC: Yong Gao<br /> * others who will join, please add your names!<br /> <br /> <div style="margin: 20px;"><br /> <div style="width: 27%; float: left; padding-right: 3%;"><br /> <br /> <h3>Objective</h3><br /> * Learn about new API for XNAT Desktop and XNAT Enterprise <br /> * Review use cases<br /> * Work out solutions for<br /> ** Configurable DICOM fields extraction into XNAT xml format<br /> ** Programmable linking of subject data wil uploaded DICOM images<br /> ** Distributed images storage<br /> <br /> <br /> </div><br /> <br /> <div style="width: 27%; float: left; padding-right: 3%;"><br /> <br /> <h3>Approach, Plan</h3><br /> <br /> <br /> <br /> </div><br /> <br /> <div style="width: 40%; float: left;"><br /> <br /> <h3>Progress</h3><br /> <br /> <br /> </div><br /> </div><br /> <br /> ==References==</div>

Yong https://www.na-mic.org/w/index.php?title=2009_Summer_Project_Week&diff=38385 2009 Summer Project Week 2009-06-08T20:52:06Z

<p>Yong: /* Collaboration Projects */</p> <hr /> <div>Back to [[Project Events]], [[Events]]<br /> <br /> [[Image:PW2009-v3.png|300px]]<br /> <br /> *'''Dates:''' June 22-26, 2009<br /> *'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].<br /> <br /> <br /> ==Introduction to the FIRST JOINT PROJECT WEEK==<br /> <br /> We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. <br /> <br /> Active preparation will begin on''' Thursday, April 16th at 3pm ET''', with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects. <br /> <br /> The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.<br /> <br /> This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January. <br /> <br /> A summary of all past NA-MIC Project Events that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].<br /> <br /> == Agenda==<br /> * Monday <br /> ** noon-1pm lunch <br /> **1pm: Welcome (Ron Kikinis)<br /> ** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template]) <br /> ** 3:30-5:30pm Start project work<br /> * Tuesday <br /> ** 8:30am breakfast<br /> **9:30-10am: NA-MIC Kit Overview (Jim Miller)<br /> ** 10-10:30am Slicer 3.4 Update (Steve Pieper)<br /> ** 10:30-11am Slicer IGT and Imaging Kit Update Update (Noby Hata, Scott Hoge)<br /> ** 11am-12:00pm Breakout Session: [[2009 Project Week Breakout Session: Slicer-Python]] (Demian W)<br /> ** noon lunch<br /> ** 2:30pm-5pm: [[2009 Project Week Data Clinic|Data Clinic]] (Ron Kikinis)<br /> ** 5:30pm adjourn for day<br /> * Wednesday <br /> ** 8:30am breakfast<br /> ** 9am-12pm Breakout Session: [[2009 Project Week Breakout Session: ITK]] (Luis Ibanez)<br /> ** noon lunch<br /> ** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: 3D+T Microscopy Cell Dataset Segmentation]] (Alex G.)<br /> ** 5:30pm adjourn for day<br /> * Thursday<br /> ** 8:30am breakfast<br /> ** 9-11pm Tutorial Contest Presentations<br /> ** noon lunch<br /> ** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: XNAT]] (Dan M.)<br /> ** 5:30pm adjourn for day<br /> * Friday <br /> ** 8:30am breakfast<br /> ** 10am-noon: [[Events:TutorialContestJune2009|Tutorial Contest Winner Announcement]] and [[#Projects|Project Progress Updates]]<br /> *** Noon: Lunch boxes and adjourn by 1:30pm.<br /> ***We need to empty room by 1:30. You are welcome to use wireless in Stata.<br /> ***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]<br /> ***Next Project Week [[AHM_2010|in Utah, January 4-8, 2010]]<br /> <br /> == Projects ==<br /> <br /> The list of projects for this week will go here.<br /> === Collaboration Projects ===<br /> #[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images]] (Saikat Pal)<br /> #[[2009_Summer_Project_Week_4D_Imaging| 4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi Tokuda)<br /> #[[2009_Summer_Project_Week_Liver_Ablation_Slicer|Liver Ablation in Slicer]] (Haiying Liu)<br /> #[[2009_Summer_Project_Week_Slicer3_Brainlab_Introduction|SLicer3, BioImage Suite and Brainlab - Introduction to UCLA]] (Haiying Liu)<br /> #[[2009_Summer_Project_Week_Slicer3_Adaptive_Radiotherapy|Adaptive Radiotherapy - Deformable registration and DICOMRT]] (Greg Sharp)<br /> #[[2009_Summer_Project_Week_Multimodal_SPL_Brain_Atlas|Segmentation of thalamic nuclei from DTI]] (Ion-Florin Talos)<br /> #Slicer module for the computation of fibre dispersion and curving measures (Peter Savadjiev, C-F Westin)<br /> #Xnat user interface improvements for NA-MIC (Dan M, Florin, Ron, Wendy)<br /> #[[2009_Summer_Project_Week_Hageman_FMTractography | Fluid mechanics tractography and visualization]] (Nathan Hageman UCLA)<br /> #[[2009_Summer_Project_Week_Hageman_DTIDigitalPhantom | DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA ]] (Nathan Hageman UCLA)<br /> #[[2009_Summer_Project_Week_Slicer3_Cortical_Thickness_Pipeline|Cortical Thickness Pipeline (Clement Vachet)]]<br /> #[[2009_Summer_Project_Week_Slicer3_Brainlab_Demo|Demo Brainlab-BioImage Suite-Slicer in BWH OR (Haiying, Isaiah, Nathan Hageman, Haytham)]]<br /> #[[2009_Summer_Project_Week_Skull_Stripping | Skull Stripping]] (Xiaodong, Snehashis Roy, Nicole Aucoin)<br /> #[[2009_Summer_Project_Week_HAMMER_Registration | HAMMER Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller)<br /> #[[2009_Summer_Project_Week_WML_SEgmentation |White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller)<br /> #[[2009_Summer_Project_Week-FastMarching_for_brain_tumor_segmentation |FastMarching for brain tumor segmentation]] (Fedorov, GeorgiaTech)<br /> #[[2009_Summer_Project_Week_Meningioma_growth_simulation|Meningioma growth simulation]] (Fedorov, Marcel, Ron)<br /> #[[2009_Summer_Project_Week_Automatic_Brain_MRI_Pipeline|Automatic brain MRI processing pipeline]] (Marcel, Hans)<br /> #[[2009_Summer_Project_Week_XNAT_i2b2|XNAT integration into Harvard Catalyst i2b2 framework]] (Yong, Marcus)<br /> #[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration |Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez,Thomas Yeo, Polina Goland), - (Mon, Tue, Wed)<br /> #[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze, Jeff Yager, Vince Magnotta)<br /> #[[Measuring Alcohol Stress Interaction]] (Vidya Rajgopalan, Andrey Fedorov)<br /> #[[2009_Summer_Project_Week_DWI_/_DTI_QC_and_Prepare_Tool:_DTIPrep | DWI/DTI QC and Preparation Tool: DTIPrep]] (Zhexing Liu)<br /> <br /> ===IGT Projects:===<br /> #[[2009_Summer_Project_Week_Prostate_Robotics |Prostate Robotics]] (Junichi, Sam, Nathan Cho, Jack), - Mon, Tue, Thursday 7pm-midnight)<br /> #[[2009_Summer_Project_Week_4D_Gated_US_In_Slicer |Gated 4D ultrasound reconstruction for Slicer3]] (Danielle Pace)<br /> #integration of stereo video into Slicer (Mehdi)<br /> #[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor, Sylvain Jaume, Nicholas, Noby)<br /> <br /> ===NA-MIC Engineering Projects===<br /> # [[Summer2009:Using_ITK_in_python| Using ITK in python]] (Steve, Demian, Jim)<br /> # [[Summer2009:Implementing_parallelism_in_python| Taking advantage of multicore machines & clusters with python]] (Julien de Siebenthal, Sylvain Bouix)<br /> # [[Summer2009:Using_client_server_paradigm_with_python_and_slicer| Deferring heavy computational tasks with python]] (Julien de Siebenthal, Sylvain Bouix)<br /> # [[Summer2009:Using_CUDA_for_stochastic_tractography| Developing realtime feedback using CUDA]] (Julien de Siebenthal, Sylvain Bouix)<br /> # [[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole, Karthik, Sebastien, Wendy)<br /> # [[2009_Summer_Project_Week_Colors_Module |Updates to Slicer3 Colors module]] (Nicole)<br /> # [[EMSegment|EM Segment]] (Sylvain Jaume, Nicolas Rannou)<br /> # [[Plug-In 3D Viewer based on XIP|Plug-in 3D Viewer based on XIP]] (Lining Yang, Melanie Grebe)<br /> # [[MeshingSummer2009 | IAFE Mesh Modules - improvements and testing]] (Curt, Steve, Vince)<br /> # [[Slicer3 Informatics Workflow Design & XNAT updates | Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wen, Steve, Dan M, Dan B)<br /> # [[BSpline Registration in Slicer3 | BSpline Registration in Slicer3]] (Samuel Gerber,Jim Miller, Ross Whitaker)<br /> # [[EPI Correction in Slicer3 | EPI Correction in Slicer3]] (Ran Tao, Jim Miller, Sylvain Bouix, Tom Fletcher, Ross Whitaker, Julien de Siebenthal)<br /> # [[Summer2009:Registration reproducibility in Slicer|Registration reproducibility in Slicer3]] (Andriy, Luis, Bill, Jim, Steve)<br /> # [[Summer2009:The Vascular Modeling Toolkit in 3D Slicer | The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn)<br /> # [[Summer2009:Extension of the Command Line XML Syntax/Interface | Extension of the Command Line XML Syntax/Interface]] (Bennett Landman)<br /> <br /> ===CUDA Projects===<br /> #[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Sandy Wells, Jim Balter, and others)<br /> #[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor, Sylvain Jaume, Nicholas, Noby)<br /> #[[2009_Summer_Project_Week_Dose_Calculation |accelerate calculation for LDR seeds]] (Jack Blevins)<br /> #[[2009_Summer_Project_Week_Cone_Beam_backprojection]](Zhou Shen, Greg Sharp, James Balter)<br /> #[[2009_Summer_project_week_3d_Deformable_alignment]](Dan McShan, Greg Sharp, ??)<br /> <br /> == Preparation ==<br /> <br /> # Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list<br /> # Join the kickoff TCON on April 16, 3pm ET.<br /> # [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.<br /> # By 3pm ET on June 11, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.<br /> # By 3pm on June 18, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)<br /> ## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)<br /> ## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)<br /> ## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)<br /> # Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...<br /> # People doing Slicer related projects should come to project week with slicer built on your laptop.<br /> ## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-4/#dirlist Slicer-3-4 branch] (new code should not be checked into the branch).<br /> ## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].<br /> <br /> ==Attendee List==<br /> If you plan to attend, please add your name here.<br /> <br /> #Ron Kikinis, BWH (NA-MIC, NAC, NCIGT)<br /> #Clare Tempany, BWH (NCIGT)<br /> #Tina Kapur, BWH (NA-MIC, NCIGT)<br /> #Steve Pieper, Isomics Inc<br /> #Jim Miller, GE Research<br /> #Xiaodong Tao, GE Research<br /> #Randy Gollub, MGH<br /> #Nicole Aucoin, BWH (NA-MIC)<br /> #Dan Marcus, WUSTL<br /> #Junichi Tokuda, BWH (NCIGT)<br /> #Alex Gouaillard, Harvard Systems Biology<br /> #Arnaud Gelas, Harvard Systems Biology <br /> #Kishore Mosanliganti, Harvard Systems Biology<br /> #Lydie Souhait, Harvard Systems Biology<br /> #Luis Ibanez, Kitware Inc (Attending: Monday/Tuesday/Wednesday)<br /> #Vincent Magnotta, UIowa<br /> #Hans Johnson, UIowa<br /> #Xenios Papademetris, Yale<br /> #Gregory S. Fischer, WPI (Mon, Tue, Wed)<br /> #Daniel Blezek, Mayo (Tue-Fri)<br /> #Danielle Pace, Robarts Research Institute / UWO<br /> #Clement Vachet, UNC-Chapel Hill<br /> #Dave Welch, UIowa<br /> #Demian Wassermann, Odyssée lab, INRIA, France<br /> #Manasi Ramachandran, UIowa<br /> #Greg Sharp, MGH<br /> #Rui Li, MGH<br /> #Mehdi Esteghamatian, Robarts Research Institute / UWO<br /> #Misha Milchenko, WUSTL<br /> #Kevin Archie, WUSTL<br /> #Tim Olsen, WUSTL<br /> #Wendy Plesniak BWH (NAC)<br /> #Haiying Liu BWH (NCIGT)<br /> #Curtis Lisle, KnowledgeVis / Isomics<br /> #Diego Cantor, Robarts Research Institute / UWO<br /> #Daniel Haehn, BWH<br /> #Nicolas Rannou, BWH<br /> #Sylvain Jaume, MIT<br /> #Alex Yarmarkovich, Isomics<br /> #Marco Ruiz, UCSD<br /> #Andriy Fedorov, BWH (NA-MIC)<br /> #Harish Doddi, Stanford University<br /> #Saikat Pal, Stanford University<br /> #Scott Hoge, BWH (NCIGT)<br /> #Vandana Mohan, Georgia Tech<br /> #Ivan Kolosev, Georgia Tech<br /> #Behnood Gholami, Georgia Tech<br /> #James Balter, U Michigan<br /> #Dan McShan, U Michigan<br /> #Zhou Shen, U Michigan<br /> #Maria Francesca Spadea, Italy<br /> #Lining Yang, Siemens Corporate Research<br /> #Beatriz Paniagua, UNC-Chapel Hill<br /> #Bennett Landman, Johns Hopkins University <br /> #Snehashis Roy, Johns Hopkins University<br /> #Marta Peroni, Politecnico di Milano<br /> #Sebastien Barre, Kitware, Inc.<br /> #Samuel Gerber, SCI University of Utah<br /> #Ran Tao, SCI University of Utah<br /> #Marcel Prastawa, SCI University of Utah<br /> #Katie Hayes, BWH (NA-MIC)<br /> #Sonia Pujol, BWH (NA-MIC)<br /> #Andras Lasso, Queen's University<br /> #Yong Gao, MGH<br /> #Minjeong Kim, UNC-Chapel Hill<br /> #Guorong Wu, UNC-Chapel Hill<br /> #Jeffrey Yager, UIowa<br /> #Yanling Liu, SAIC/NCI-Frederick<br /> #Ziv Yaniv, Georgetown<br /> #Bjoern Menze, MIT<br /> #Vidya Rajagopalan, Virginia Tech<br /> #Sandy Wells, BWH (NAC, NCIGT)<br /> #Lilla Zollei, MGH (NAC)<br /> #Lauren O'Donnell, BWH<br /> #Florin Talos, BWH (NAC)<br /> #Nobuhiko Hata, BWH (NCIGT)<br /> #Alark Joshi, Yale<br /> #Yogesh Rathi, BWH<br /> #Jimi Malcolm, BWH<br /> #Dustin Scheinost, Yale<br /> #Dominique Belhachemi, Yale<br /> #Sam Song, JHU<br /> #Nathan Cho, JHU<br /> #Julien de Siebenthal, BWH<br /> #Peter Savadjiev, BWH<br /> #Carl-Fredrik Westin, BWH<br /> #John Melonakos, AccelerEyes (Wed & Thu morning)<br /> #Yi Gao, Georgia Tech<br /> #Sylvain Bouix, BWH<br /> #Zhexing Liu, UNC-CH<br /> #Eric Melonakos, BWH<br /> #Lei Qin, BWH<br /> #Giovanna Danagoulian, BWH<br /> #Andrew Rausch, BWH (1st day only)<br /> #Haytham Elhawary, BWH<br /> #Jayender Jagadeesan, BWH<br /> #Marek Kubicki, BWH<br /> #Doug Terry, BWH<br /> #Nathan Hageman, LONI (UCLA)<br /> #Dana Peters, Beth Israel Deaconess<br /> #Sun Woo Lee, BWH<br /> # Melanie Grebe, Siemens Corporate Research<br /> # Megumi Nakao, BWH/NAIST<br /> # Moti Freiman, The Hebrew Univ. of Jerusalem<br /> #Jack Blevins, Acoustic Med Systems<br /> #Michael Halle, BWH<br /> #Amanda Peters, Harvard SEAS<br /> #Joe Stam, NVIDIA (Wednesday, Thursday)<br /> #Petter Risholm, BWH (NCIGT)<br /> <br /> == Logistics ==<br /> *'''Dates:''' June 22-26, 2009<br /> *'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].<br /> *'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 12th, 2009. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139. Receipts will be provided by email as checks are received. Please send questions to dkauf at mit.edu. '''If this is your first event and you are attending for only one day, the registration fee is waived.''' Please let us know, so that we can cover the costs with one of our grants.<br /> *'''Registration Method''' Add your name to the Attendee List section of this page<br /> *'''Hotel:''' We have a group rate of $189/night (plus tax) at the Le Meridien (which used to be the Hotel at MIT). [http://www.starwoodmeeting.com/Book/MITDECSE Please click here to reserve.] This rate is good only through June 1.<br /> *Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.<br /> *2009 Summer Project Week [[NA-MIC/Projects/Theme/Template|'''Template''']]<br /> *[[2008_Summer_Project_Week#Projects|Last Year's Projects as a reference]]<br /> *For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]</div>

Yong https://www.na-mic.org/w/index.php?title=2009_Summer_Project_Week&diff=38384 2009 Summer Project Week 2009-06-08T20:51:38Z

<p>Yong: /* Collaboration Projects */</p> <hr /> <div>Back to [[Project Events]], [[Events]]<br /> <br /> [[Image:PW2009-v3.png|300px]]<br /> <br /> *'''Dates:''' June 22-26, 2009<br /> *'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].<br /> <br /> <br /> ==Introduction to the FIRST JOINT PROJECT WEEK==<br /> <br /> We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. <br /> <br /> Active preparation will begin on''' Thursday, April 16th at 3pm ET''', with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects. <br /> <br /> The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.<br /> <br /> This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January. <br /> <br /> A summary of all past NA-MIC Project Events that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].<br /> <br /> == Agenda==<br /> * Monday <br /> ** noon-1pm lunch <br /> **1pm: Welcome (Ron Kikinis)<br /> ** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template]) <br /> ** 3:30-5:30pm Start project work<br /> * Tuesday <br /> ** 8:30am breakfast<br /> **9:30-10am: NA-MIC Kit Overview (Jim Miller)<br /> ** 10-10:30am Slicer 3.4 Update (Steve Pieper)<br /> ** 10:30-11am Slicer IGT and Imaging Kit Update Update (Noby Hata, Scott Hoge)<br /> ** 11am-12:00pm Breakout Session: [[2009 Project Week Breakout Session: Slicer-Python]] (Demian W)<br /> ** noon lunch<br /> ** 2:30pm-5pm: [[2009 Project Week Data Clinic|Data Clinic]] (Ron Kikinis)<br /> ** 5:30pm adjourn for day<br /> * Wednesday <br /> ** 8:30am breakfast<br /> ** 9am-12pm Breakout Session: [[2009 Project Week Breakout Session: ITK]] (Luis Ibanez)<br /> ** noon lunch<br /> ** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: 3D+T Microscopy Cell Dataset Segmentation]] (Alex G.)<br /> ** 5:30pm adjourn for day<br /> * Thursday<br /> ** 8:30am breakfast<br /> ** 9-11pm Tutorial Contest Presentations<br /> ** noon lunch<br /> ** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: XNAT]] (Dan M.)<br /> ** 5:30pm adjourn for day<br /> * Friday <br /> ** 8:30am breakfast<br /> ** 10am-noon: [[Events:TutorialContestJune2009|Tutorial Contest Winner Announcement]] and [[#Projects|Project Progress Updates]]<br /> *** Noon: Lunch boxes and adjourn by 1:30pm.<br /> ***We need to empty room by 1:30. You are welcome to use wireless in Stata.<br /> ***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]<br /> ***Next Project Week [[AHM_2010|in Utah, January 4-8, 2010]]<br /> <br /> == Projects ==<br /> <br /> The list of projects for this week will go here.<br /> === Collaboration Projects ===<br /> #[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images]] (Saikat Pal)<br /> #[[2009_Summer_Project_Week_4D_Imaging| 4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi Tokuda)<br /> #[[2009_Summer_Project_Week_Liver_Ablation_Slicer|Liver Ablation in Slicer]] (Haiying Liu)<br /> #[[2009_Summer_Project_Week_Slicer3_Brainlab_Introduction|SLicer3, BioImage Suite and Brainlab - Introduction to UCLA]] (Haiying Liu)<br /> #[[2009_Summer_Project_Week_Slicer3_Adaptive_Radiotherapy|Adaptive Radiotherapy - Deformable registration and DICOMRT]] (Greg Sharp)<br /> #[[2009_Summer_Project_Week_Multimodal_SPL_Brain_Atlas|Segmentation of thalamic nuclei from DTI]] (Ion-Florin Talos)<br /> #Slicer module for the computation of fibre dispersion and curving measures (Peter Savadjiev, C-F Westin)<br /> #Xnat user interface improvements for NA-MIC (Dan M, Florin, Ron, Wendy)<br /> #[[2009_Summer_Project_Week_Hageman_FMTractography | Fluid mechanics tractography and visualization]] (Nathan Hageman UCLA)<br /> #[[2009_Summer_Project_Week_Hageman_DTIDigitalPhantom | DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA ]] (Nathan Hageman UCLA)<br /> #[[2009_Summer_Project_Week_Slicer3_Cortical_Thickness_Pipeline|Cortical Thickness Pipeline (Clement Vachet)]]<br /> #[[2009_Summer_Project_Week_Slicer3_Brainlab_Demo|Demo Brainlab-BioImage Suite-Slicer in BWH OR (Haiying, Isaiah, Nathan Hageman, Haytham)]]<br /> #[[2009_Summer_Project_Week_Skull_Stripping | Skull Stripping]] (Xiaodong, Snehashis Roy, Nicole Aucoin)<br /> #[[2009_Summer_Project_Week_HAMMER_Registration | HAMMER Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller)<br /> #[[2009_Summer_Project_Week_WML_SEgmentation |White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller)<br /> #[[2009_Summer_Project_Week-FastMarching_for_brain_tumor_segmentation |FastMarching for brain tumor segmentation]] (Fedorov, GeorgiaTech)<br /> #[[2009_Summer_Project_Week_Meningioma_growth_simulation|Meningioma growth simulation]] (Fedorov, Marcel, Ron)<br /> #[[2009_Summer_Project_Week_Automatic_Brain_MRI_Pipeline|Automatic brain MRI processing pipeline]] (Marcel, Hans)<br /> #[[2009_Summer_Project_Week_XNAT_i2b2|XNAT integration into Harvard Catalyst i2b2 framework]] (Yong, Marcus)<br /> <br /> #[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration |Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez,Thomas Yeo, Polina Goland), - (Mon, Tue, Wed)<br /> #[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze, Jeff Yager, Vince Magnotta)<br /> #[[Measuring Alcohol Stress Interaction]] (Vidya Rajgopalan, Andrey Fedorov)<br /> #[[2009_Summer_Project_Week_DWI_/_DTI_QC_and_Prepare_Tool:_DTIPrep | DWI/DTI QC and Preparation Tool: DTIPrep]] (Zhexing Liu)<br /> <br /> ===IGT Projects:===<br /> #[[2009_Summer_Project_Week_Prostate_Robotics |Prostate Robotics]] (Junichi, Sam, Nathan Cho, Jack), - Mon, Tue, Thursday 7pm-midnight)<br /> #[[2009_Summer_Project_Week_4D_Gated_US_In_Slicer |Gated 4D ultrasound reconstruction for Slicer3]] (Danielle Pace)<br /> #integration of stereo video into Slicer (Mehdi)<br /> #[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor, Sylvain Jaume, Nicholas, Noby)<br /> <br /> ===NA-MIC Engineering Projects===<br /> # [[Summer2009:Using_ITK_in_python| Using ITK in python]] (Steve, Demian, Jim)<br /> # [[Summer2009:Implementing_parallelism_in_python| Taking advantage of multicore machines & clusters with python]] (Julien de Siebenthal, Sylvain Bouix)<br /> # [[Summer2009:Using_client_server_paradigm_with_python_and_slicer| Deferring heavy computational tasks with python]] (Julien de Siebenthal, Sylvain Bouix)<br /> # [[Summer2009:Using_CUDA_for_stochastic_tractography| Developing realtime feedback using CUDA]] (Julien de Siebenthal, Sylvain Bouix)<br /> # [[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole, Karthik, Sebastien, Wendy)<br /> # [[2009_Summer_Project_Week_Colors_Module |Updates to Slicer3 Colors module]] (Nicole)<br /> # [[EMSegment|EM Segment]] (Sylvain Jaume, Nicolas Rannou)<br /> # [[Plug-In 3D Viewer based on XIP|Plug-in 3D Viewer based on XIP]] (Lining Yang, Melanie Grebe)<br /> # [[MeshingSummer2009 | IAFE Mesh Modules - improvements and testing]] (Curt, Steve, Vince)<br /> # [[Slicer3 Informatics Workflow Design & XNAT updates | Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wen, Steve, Dan M, Dan B)<br /> # [[BSpline Registration in Slicer3 | BSpline Registration in Slicer3]] (Samuel Gerber,Jim Miller, Ross Whitaker)<br /> # [[EPI Correction in Slicer3 | EPI Correction in Slicer3]] (Ran Tao, Jim Miller, Sylvain Bouix, Tom Fletcher, Ross Whitaker, Julien de Siebenthal)<br /> # [[Summer2009:Registration reproducibility in Slicer|Registration reproducibility in Slicer3]] (Andriy, Luis, Bill, Jim, Steve)<br /> # [[Summer2009:The Vascular Modeling Toolkit in 3D Slicer | The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn)<br /> # [[Summer2009:Extension of the Command Line XML Syntax/Interface | Extension of the Command Line XML Syntax/Interface]] (Bennett Landman)<br /> <br /> ===CUDA Projects===<br /> #[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Sandy Wells, Jim Balter, and others)<br /> #[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor, Sylvain Jaume, Nicholas, Noby)<br /> #[[2009_Summer_Project_Week_Dose_Calculation |accelerate calculation for LDR seeds]] (Jack Blevins)<br /> #[[2009_Summer_Project_Week_Cone_Beam_backprojection]](Zhou Shen, Greg Sharp, James Balter)<br /> #[[2009_Summer_project_week_3d_Deformable_alignment]](Dan McShan, Greg Sharp, ??)<br /> <br /> == Preparation ==<br /> <br /> # Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list<br /> # Join the kickoff TCON on April 16, 3pm ET.<br /> # [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.<br /> # By 3pm ET on June 11, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.<br /> # By 3pm on June 18, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)<br /> ## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)<br /> ## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)<br /> ## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)<br /> # Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...<br /> # People doing Slicer related projects should come to project week with slicer built on your laptop.<br /> ## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-4/#dirlist Slicer-3-4 branch] (new code should not be checked into the branch).<br /> ## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].<br /> <br /> ==Attendee List==<br /> If you plan to attend, please add your name here.<br /> <br /> #Ron Kikinis, BWH (NA-MIC, NAC, NCIGT)<br /> #Clare Tempany, BWH (NCIGT)<br /> #Tina Kapur, BWH (NA-MIC, NCIGT)<br /> #Steve Pieper, Isomics Inc<br /> #Jim Miller, GE Research<br /> #Xiaodong Tao, GE Research<br /> #Randy Gollub, MGH<br /> #Nicole Aucoin, BWH (NA-MIC)<br /> #Dan Marcus, WUSTL<br /> #Junichi Tokuda, BWH (NCIGT)<br /> #Alex Gouaillard, Harvard Systems Biology<br /> #Arnaud Gelas, Harvard Systems Biology <br /> #Kishore Mosanliganti, Harvard Systems Biology<br /> #Lydie Souhait, Harvard Systems Biology<br /> #Luis Ibanez, Kitware Inc (Attending: Monday/Tuesday/Wednesday)<br /> #Vincent Magnotta, UIowa<br /> #Hans Johnson, UIowa<br /> #Xenios Papademetris, Yale<br /> #Gregory S. Fischer, WPI (Mon, Tue, Wed)<br /> #Daniel Blezek, Mayo (Tue-Fri)<br /> #Danielle Pace, Robarts Research Institute / UWO<br /> #Clement Vachet, UNC-Chapel Hill<br /> #Dave Welch, UIowa<br /> #Demian Wassermann, Odyssée lab, INRIA, France<br /> #Manasi Ramachandran, UIowa<br /> #Greg Sharp, MGH<br /> #Rui Li, MGH<br /> #Mehdi Esteghamatian, Robarts Research Institute / UWO<br /> #Misha Milchenko, WUSTL<br /> #Kevin Archie, WUSTL<br /> #Tim Olsen, WUSTL<br /> #Wendy Plesniak BWH (NAC)<br /> #Haiying Liu BWH (NCIGT)<br /> #Curtis Lisle, KnowledgeVis / Isomics<br /> #Diego Cantor, Robarts Research Institute / UWO<br /> #Daniel Haehn, BWH<br /> #Nicolas Rannou, BWH<br /> #Sylvain Jaume, MIT<br /> #Alex Yarmarkovich, Isomics<br /> #Marco Ruiz, UCSD<br /> #Andriy Fedorov, BWH (NA-MIC)<br /> #Harish Doddi, Stanford University<br /> #Saikat Pal, Stanford University<br /> #Scott Hoge, BWH (NCIGT)<br /> #Vandana Mohan, Georgia Tech<br /> #Ivan Kolosev, Georgia Tech<br /> #Behnood Gholami, Georgia Tech<br /> #James Balter, U Michigan<br /> #Dan McShan, U Michigan<br /> #Zhou Shen, U Michigan<br /> #Maria Francesca Spadea, Italy<br /> #Lining Yang, Siemens Corporate Research<br /> #Beatriz Paniagua, UNC-Chapel Hill<br /> #Bennett Landman, Johns Hopkins University <br /> #Snehashis Roy, Johns Hopkins University<br /> #Marta Peroni, Politecnico di Milano<br /> #Sebastien Barre, Kitware, Inc.<br /> #Samuel Gerber, SCI University of Utah<br /> #Ran Tao, SCI University of Utah<br /> #Marcel Prastawa, SCI University of Utah<br /> #Katie Hayes, BWH (NA-MIC)<br /> #Sonia Pujol, BWH (NA-MIC)<br /> #Andras Lasso, Queen's University<br /> #Yong Gao, MGH<br /> #Minjeong Kim, UNC-Chapel Hill<br /> #Guorong Wu, UNC-Chapel Hill<br /> #Jeffrey Yager, UIowa<br /> #Yanling Liu, SAIC/NCI-Frederick<br /> #Ziv Yaniv, Georgetown<br /> #Bjoern Menze, MIT<br /> #Vidya Rajagopalan, Virginia Tech<br /> #Sandy Wells, BWH (NAC, NCIGT)<br /> #Lilla Zollei, MGH (NAC)<br /> #Lauren O'Donnell, BWH<br /> #Florin Talos, BWH (NAC)<br /> #Nobuhiko Hata, BWH (NCIGT)<br /> #Alark Joshi, Yale<br /> #Yogesh Rathi, BWH<br /> #Jimi Malcolm, BWH<br /> #Dustin Scheinost, Yale<br /> #Dominique Belhachemi, Yale<br /> #Sam Song, JHU<br /> #Nathan Cho, JHU<br /> #Julien de Siebenthal, BWH<br /> #Peter Savadjiev, BWH<br /> #Carl-Fredrik Westin, BWH<br /> #John Melonakos, AccelerEyes (Wed & Thu morning)<br /> #Yi Gao, Georgia Tech<br /> #Sylvain Bouix, BWH<br /> #Zhexing Liu, UNC-CH<br /> #Eric Melonakos, BWH<br /> #Lei Qin, BWH<br /> #Giovanna Danagoulian, BWH<br /> #Andrew Rausch, BWH (1st day only)<br /> #Haytham Elhawary, BWH<br /> #Jayender Jagadeesan, BWH<br /> #Marek Kubicki, BWH<br /> #Doug Terry, BWH<br /> #Nathan Hageman, LONI (UCLA)<br /> #Dana Peters, Beth Israel Deaconess<br /> #Sun Woo Lee, BWH<br /> # Melanie Grebe, Siemens Corporate Research<br /> # Megumi Nakao, BWH/NAIST<br /> # Moti Freiman, The Hebrew Univ. of Jerusalem<br /> #Jack Blevins, Acoustic Med Systems<br /> #Michael Halle, BWH<br /> #Amanda Peters, Harvard SEAS<br /> #Joe Stam, NVIDIA (Wednesday, Thursday)<br /> #Petter Risholm, BWH (NCIGT)<br /> <br /> == Logistics ==<br /> *'''Dates:''' June 22-26, 2009<br /> *'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].<br /> *'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 12th, 2009. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139. Receipts will be provided by email as checks are received. Please send questions to dkauf at mit.edu. '''If this is your first event and you are attending for only one day, the registration fee is waived.''' Please let us know, so that we can cover the costs with one of our grants.<br /> *'''Registration Method''' Add your name to the Attendee List section of this page<br /> *'''Hotel:''' We have a group rate of $189/night (plus tax) at the Le Meridien (which used to be the Hotel at MIT). [http://www.starwoodmeeting.com/Book/MITDECSE Please click here to reserve.] This rate is good only through June 1.<br /> *Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.<br /> *2009 Summer Project Week [[NA-MIC/Projects/Theme/Template|'''Template''']]<br /> *[[2008_Summer_Project_Week#Projects|Last Year's Projects as a reference]]<br /> *For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]</div>

Yong https://www.na-mic.org/w/index.php?title=CTSC_Imaging_Informatics_Initiative&diff=37895 CTSC Imaging Informatics Initiative 2009-06-01T15:10:14Z

<p>Yong: /* Overview */</p> <hr /> <div>__TOC__<br /> <br /> Back to [[CTSC:CrossSiteImagingIdeas|CTSC_CrossSiteImagingIdeas]]<br /> <br /> = Overview =<br /> The Harvard Catalyst Medical Imaging Informatics Bench to Bedside (mi2b2) Initiative is preparing to provide services for setting up imaging data management systems (IDMS) to support research and clinical efforts involving imaging for Harvard Catalyst affiliated investigators. Two simultaneous (and potentially conflicting) priorities are to 1) provide optimal, customized hardware and software tools for each investigator/ laboratory and 2) to harmonized these solutions to allow for aggregation of the raw and derived medical imaging data for subsequent sharing beyond the investigator/ laboratory. <br /> <br /> <br><br /> XNAT has been identified as a potential software solution for providing the core functionalities of a Harvard Catalyst IDMS.<br /> A typical IDMS service engagement will include the following steps:<br /> *Requirement gathering<br /> *Gap analysis<br /> *Infrastructure setup<br /> *Data modeling<br /> *IDMS installation and setup<br /> *Data loading<br /> *Testing and evaluation<br /> *Ongoing data entry, data loading/transfer, and system monitoring and maintenance<br /> *System upgrade<br /> <br /> = mi2b2 Phases =<br /> == Planning and Information Gathering ==<br /> <br /> The goals of current phase of the initiative are to:<br /> #Gather concrete and specific requirements for imaging data transfer and management from a number of high-volume imaging projects led by Harvard Catalyst-affiliated investigators that are generating valuable derived image data with the intention to share that data beyond their own laboratory; <br /> #Generate a list of overlapping requirements from these specific investigators; <br /> #Prioritize the projects to determine next steps; <br /> #Deploy a demo IDMS based on the default XNAT source code;<br /> #Assess the effort required to extend XNAT code to support the features identified.<br /> <br /> == Prototype Development ==<br /> ===CHB===<br /> *Grant Lab<br /> <br /> ===MGH===<br /> *Dickerson Lab<br /> <br /> == Production System Development for Selective projects==<br /> <br /> ===CHB===<br /> <br /> ===MGH===<br /> <br /> ===BWH===<br /> <br /> = Use Cases =<br /> <br /> (Template<br /> *Mission<br /> **Description of big picture, goal(s) of project<br /> *Participants<br /> *Data Types<br /> **Project<br /> **Imaging Modalities<br /> **Genetic<br /> *Storage needs<br /> *Workflow<br /> **Other software to be integrated (e.g., Osirix)<br /> **other features<br /> *Data transfer<br /> *Data Management)<br /> <br /> The use cases presented here are based on on-going informal interviews with various labs and email communications.<br /> <br /> ==Clinical==<br /> <br /> *[[CTSC_Dan Iosifescu, MGH| Dan Iosifescu, MGH]]<br /> *[[CTSC_biomarkers_appendicitis| Biomarkers for appendicitis]]<br /> *[[CTSC_MCI| Mild cognitive impairment]]<br /> <br /> ==Research==<br /> <br /> *[[CTSC_Ellen Grant, CHB| Ellen Grant, CHB]]<br /> *[[CTSC_Stephan Voss, CHB| Stephan Voss, CHB]]<br /> *[[CTSC_Simon Warfield, CHB| Simon Warfield, CHB]]<br /> *[[CTSC_Bill Hanlon, DF/HCC| Bill Hanlon, DF/HCC]]<br /> *[[CTSC_COPD Gene Project, BWH| COPD Gene Project, BWH]]<br /> *[[CTSC_Brad Dickerson, MGH| Brad Dickerson]]<br /> <br /> = Project Prioritization Criteria=<br /> Possible criteria include:<br /> *Impact<br /> **Number of users<br /> **Duration of the project<br /> **Amount of data (# of subjects, # of scans ...)<br /> <br /> *Success Potential<br /> **Commitment of PI<br /> **Feasibility: is it a good fit for using XNAT?<br /> **Availability of project support at each stage of the effort, including requirement gathering, data collection, system testing, continuing IT and informatics support.<br /> <br /> = Current Status =<br /> Test installations of XNAT (1.4 release candidate 2) were done on Windows XP and Linux in VMware. Minor issues in the setup process needs to be fixed to make successful installation on Windows Vista. <br /> <br /> Requirement gathering from several research and clinical projects have been conducted.<br /> <br /> XNAT 1.4R2 setup/installation process semi-automated.<br /> <br /> XNAT extension prototype built.<br /> <br /> Explored ways of extracting and loading additional DICOM fields.<br /> <br /> = Other Software =<br /> <br /> In addition, an evaluation of dcm4chee|[http://www.dcm4che.org] (a DICOM Implementation in JAVA) is in progress. Simon's group runs an instance of dcm4chee. XNAT's DicomServer and DicomBrowser are based on dcm4che.<br /> <br /> The Globus MEDICUS (Medical Imaging and Computing for Unified Information Sharing)|[http://dev.globus.org/wiki/Incubator/MEDICUS] has been proposed to provide an image sharing solution.<br /> <br /> Reporting and database management of radiological data for clinical trials offered by http://tumormetrics.org/<br /> <br /> Evorad Medical Imaging Workstation from http://www.evorad.com/</div>

Yong https://www.na-mic.org/w/index.php?title=CTSC_Imaging_Informatics_Initiative&diff=37894 CTSC Imaging Informatics Initiative 2009-06-01T14:53:01Z

<p>Yong: /* Current Status */</p> <hr /> <div>__TOC__<br /> <br /> Back to [[CTSC:CrossSiteImagingIdeas|CTSC_CrossSiteImagingIdeas]]<br /> <br /> = Overview =<br /> The Harvard Catalyst Medical Imaging Informatics Bench to Bedside (mi2b2) Initiative is preparing to provide services for setting up imaging data management systems (IDMS) to support research and clinical efforts involving imaging for Harvard Catalyst affiliated investigators. Two simultaneous (and potentially conflicting) priorities are to 1) provide optimal, customized hardware and software tools for each investigator/ laboratory and 2) to harmonized these solutions to allow for aggregation of the raw and derived medical imaging data for subsequent sharing beyond the investigator/ laboratory. <br /> <br /> <br><br /> XNAT has been identified as a potential software solution for providing the core functionalities of a Harvard Catalyst IDMS.<br /> A typical IDMS service will include the following steps:<br /> *Requirement gathering<br /> *Gap analysis<br /> *Infrastructure setup<br /> *Data modeling<br /> *IDMS installation and setup<br /> *Data loading<br /> *Testing and evaluation<br /> *Ongoing data entry, data loading/transfer, and system monitoring and maintenance<br /> *System upgrade<br /> <br /> = mi2b2 Phases =<br /> == Planning and Information Gathering ==<br /> <br /> The goals of current phase of the initiative are to:<br /> #Gather concrete and specific requirements for imaging data transfer and management from a number of high-volume imaging projects led by Harvard Catalyst-affiliated investigators that are generating valuable derived image data with the intention to share that data beyond their own laboratory; <br /> #Generate a list of overlapping requirements from these specific investigators; <br /> #Prioritize the projects to determine next steps; <br /> #Deploy a demo IDMS based on the default XNAT source code;<br /> #Assess the effort required to extend XNAT code to support the features identified.<br /> <br /> == Prototype Development ==<br /> ===CHB===<br /> *Grant Lab<br /> <br /> ===MGH===<br /> *Dickerson Lab<br /> <br /> == Production System Development for Selective projects==<br /> <br /> ===CHB===<br /> <br /> ===MGH===<br /> <br /> ===BWH===<br /> <br /> = Use Cases =<br /> <br /> (Template<br /> *Mission<br /> **Description of big picture, goal(s) of project<br /> *Participants<br /> *Data Types<br /> **Project<br /> **Imaging Modalities<br /> **Genetic<br /> *Storage needs<br /> *Workflow<br /> **Other software to be integrated (e.g., Osirix)<br /> **other features<br /> *Data transfer<br /> *Data Management)<br /> <br /> The use cases presented here are based on on-going informal interviews with various labs and email communications.<br /> <br /> ==Clinical==<br /> <br /> *[[CTSC_Dan Iosifescu, MGH| Dan Iosifescu, MGH]]<br /> *[[CTSC_biomarkers_appendicitis| Biomarkers for appendicitis]]<br /> *[[CTSC_MCI| Mild cognitive impairment]]<br /> <br /> ==Research==<br /> <br /> *[[CTSC_Ellen Grant, CHB| Ellen Grant, CHB]]<br /> *[[CTSC_Stephan Voss, CHB| Stephan Voss, CHB]]<br /> *[[CTSC_Simon Warfield, CHB| Simon Warfield, CHB]]<br /> *[[CTSC_Bill Hanlon, DF/HCC| Bill Hanlon, DF/HCC]]<br /> *[[CTSC_COPD Gene Project, BWH| COPD Gene Project, BWH]]<br /> *[[CTSC_Brad Dickerson, MGH| Brad Dickerson]]<br /> <br /> = Project Prioritization Criteria=<br /> Possible criteria include:<br /> *Impact<br /> **Number of users<br /> **Duration of the project<br /> **Amount of data (# of subjects, # of scans ...)<br /> <br /> *Success Potential<br /> **Commitment of PI<br /> **Feasibility: is it a good fit for using XNAT?<br /> **Availability of project support at each stage of the effort, including requirement gathering, data collection, system testing, continuing IT and informatics support.<br /> <br /> = Current Status =<br /> Test installations of XNAT (1.4 release candidate 2) were done on Windows XP and Linux in VMware. Minor issues in the setup process needs to be fixed to make successful installation on Windows Vista. <br /> <br /> Requirement gathering from several research and clinical projects have been conducted.<br /> <br /> XNAT 1.4R2 setup/installation process semi-automated.<br /> <br /> XNAT extension prototype built.<br /> <br /> Explored ways of extracting and loading additional DICOM fields.<br /> <br /> = Other Software =<br /> <br /> In addition, an evaluation of dcm4chee|[http://www.dcm4che.org] (a DICOM Implementation in JAVA) is in progress. Simon's group runs an instance of dcm4chee. XNAT's DicomServer and DicomBrowser are based on dcm4che.<br /> <br /> The Globus MEDICUS (Medical Imaging and Computing for Unified Information Sharing)|[http://dev.globus.org/wiki/Incubator/MEDICUS] has been proposed to provide an image sharing solution.<br /> <br /> Reporting and database management of radiological data for clinical trials offered by http://tumormetrics.org/<br /> <br /> Evorad Medical Imaging Workstation from http://www.evorad.com/</div>

Yong https://www.na-mic.org/w/index.php?title=2009_Summer_Project_Week&diff=37632 2009 Summer Project Week 2009-05-20T16:58:13Z

<p>Yong: /* Collaboration Projects */</p> <hr /> <div>Back to [[Project Events]], [[Events]]<br /> <br /> *'''Dates:''' June 22-26, 2009<br /> *'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].<br /> <br /> <br /> ==Introduction to the FIRST JOINT PROJECT WEEK==<br /> <br /> We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. <br /> <br /> Active preparation will begin on''' Thursday, April 16th at 3pm ET''', with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects. <br /> <br /> The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.<br /> <br /> This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January. <br /> <br /> A summary of all past NA-MIC Project Events that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].<br /> <br /> == Agenda==<br /> * Monday <br /> ** noon-1pm lunch <br /> **1pm: Welcome (Ron Kikinis)<br /> ** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]]) <br /> ** 3:30-5:30pm Start project work<br /> * Tuesday <br /> ** 8:30am breakfast<br /> **9:30-10am: NA-MIC Kit Overview (Jim Miller)<br /> ** 10-10:30am Slicer 3.4 Update (Steve Pieper)<br /> ** 10:30-11am Slicer IGT and Imaging Kit Update Update (Noby Hata, Scott Hoge)<br /> ** 11am-12:00pm Breakout Session: [[2009 Project Week Breakout Session: Slicer-Python]] (Demian W)<br /> ** noon lunch<br /> ** 2:30pm-5pm: [[2009 Project Week Data Clinic|Data Clinic]]<br /> ** 5:30pm adjourn for day<br /> * Wednesday <br /> ** 8:30am breakfast<br /> ** 9am-12pm Breakout Session: [[2009 Project Week Breakout Session: ITK]] (Luis Ibanez)<br /> ** noon lunch<br /> ** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: 3D+T Microscopy Cell Dataset Segmentation]] (Alex G.)<br /> ** 5:30pm adjourn for day<br /> * Thursday<br /> ** 8:30am breakfast<br /> ** 9-11pm Tutorial Contest Presentations<br /> ** noon lunch<br /> ** 2:30pm: Breakout Session: TBD<br /> ** 5:30pm adjourn for day<br /> * Friday <br /> ** 8:30am breakfast<br /> ** 10am-noon: Tutorial Contest Winner Announcement and Project Progress using update [[#Projects|Project Wiki pages]]<br /> *** Noon: Lunch boxes and adjourn by 1:30pm.<br /> ***We need to empty room by 1:30. You are welcome to use wireless in Stata.<br /> ***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]<br /> ***Next Project Week [[AHM_2010|in Utah, January 4-8, 2010]]<br /> <br /> == Projects ==<br /> <br /> The list of projects for this week will go here.<br /> === Collaboration Projects ===<br /> #[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images]]<br /> #Prostate Robotics (Junichi, Sam, Nathan Cho, Jack), - Mon, Tue, Thursday 7pm-midnight)<br /> #4D Imaging - currently used for Lung Perfusion (Junichi, Dan Blezek?, Steve, Alex G?)<br /> #Liver Ablation in Slicer (Haiying, Georgetown?)<br /> #SLicer3 and Brainlab - introduction to UCLA (Haiying, Xenios, Pratik, Nathan Hageman)<br /> #Adaptive Radiotherapy - Deformable registration and DICOMRT (Greg Sharp, Steve, Wendy)<br /> #gpu based registration acceleration (James Balter, Greg Sharp, Alark Joshi?, Aditya K., Yogesh Rathi?, Jimi Malcolm, Sandy Wells, Tina Kapur)<br /> #Brain DTI Atlas? (Florin, Utah, UNC, GeorgiaTech)<br /> #Xnat user interface improvements for NA-MIC (Dan M, Tina, Florin, Ron, Wendy)<br /> #xnat and DICOMRT (Greg Sharp, Dan M) - might be done?<br /> #Xnat user clinic - combine with data clinic<br /> #xnat programmer clinic<br /> #Grid Wizard+xnat clinic (Clement)<br /> #?Fluid Mechanincs Module (Nathan Hageman)<br /> #?DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA (Nathan Hageman)<br /> #Cortical Thickness Pipeline (Clement, Ipek)<br /> #Demo Brainlab/Slicer in BWH OR (Haiying, Nathan Hageman)<br /> #Skull Stripping (Xiaodong, Snehashis Roy)<br /> #FastMarching for brain tumor segmentation (Fedorov, GeorgiaTech)<br /> #Meningioma growth simulation for validation (Fedorov, Marcel, Ron)<br /> #Automatic brain MRI processing pipeline (Marcel, Hans)<br /> #XNAT integration into Harvard Catalyst i2b2 framework(Gao, Yong)<br /> <br /> ===IGT Projects:===<br /> #port 4d gated ultrasound code to Slicer - (Danielle)<br /> #integration of stereo video into Slicer (Mehdi)<br /> #multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data (Diego, sylvain jaume, nicholas, noby)<br /> #neuroendoscope workflow presentation (sebastien barre)<br /> #slicer integration of mri compatible prostate biopsy robot(sid, queens)<br /> #breakout session on Dynamic Patient Models (James Balter)<br /> #gpu acceleration of 2d-3d registration (james balter, greg sharp, sandy wells, noby hata, terry peters proxy)<br /> <br /> ===NA-MIC Engineering Projects===<br /> # DICOM Validation and Cleanup Tool (Luis, Sid, Steve, Greg)<br /> # [[Summer2009:Using_ITK_in_python| Using ITK in python]] (Steve, Demian, Jim)<br /> # VTK 3d Widgets in Slicer3 (Nicole, Will/Karthik)<br /> # Update to Slicer3 Colors module (Nicole)<br /> # EM Segmenter (Sylvain, Nicolas)<br /> # Plug-in 3D Viewer based on XIP (Lining)<br /> # IAFE Mesh Modules - improvements and testing (Curt, Steve, Vince)<br /> # Informatics workflow Design (Wen, Steve, Dan M, Dan B)<br /> # [[BSpline Registration in Slicer3 | BSpline Registration in Slicer3]] (Jim Miller, Ross Whitaker, Samuel Gerber)<br /> # [[EPI Correction in Slicer3 | EPI Correction in Slicer3]] (Jim Miller, Sylvain Bouix, Tom Fletcher, Ross Whitaker, Julien Siebenthal, Ran Tao )<br /> # Fix [http://www.na-mic.org/Bug/view.php?id=416 bug 416] in registration (Andriy, Luis, Bill, Jim, Steve)<br /> # [[Summer2009:The Vascular Modeling Toolkit in 3D Slicer | The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn)<br /> <br /> == Preparation ==<br /> <br /> # Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list<br /> # Join the kickoff TCON on April 16, 3pm ET.<br /> # [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.<br /> # By 3pm ET on June 11, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.<br /> # By 3pm on June 18, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)<br /> ## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)<br /> ## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)<br /> ## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)<br /> # Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...<br /> # People doing Slicer related projects should come to project week with slicer built on your laptop.<br /> ## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-4/#dirlist Slicer-3-4 branch] (new code should not be checked into the branch).<br /> ## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].<br /> <br /> ==Attendee List==<br /> If you plan to attend, please add your name here.<br /> <br /> #Ron Kikinis, BWH<br /> #Ferenc Jolesz, BWH<br /> #Clare Tempany, BWH<br /> #Tina Kapur, BWH<br /> #Steve Pieper, Isomics Inc<br /> #Jim Miller, GE Research<br /> #Xiaodong Tao, GE Research<br /> #Bill Lorensen, EAB<br /> #Randy Gollub, MGH<br /> #Nicole Aucoin, BWH<br /> #Dan Marcus, WUSTL<br /> #Junichi Tokuda, BWH<br /> #Alex Gouaillard, Harvard Systems Biology<br /> #Arnaud Gelas, Harvard Systems Biology <br /> #Kishore Mosanliganti, Harvard Systems Biology<br /> #Lydie Souhait, Harvard Systems Biology<br /> #Luis Ibanez, Kitware Inc<br /> #Vincent Magnotta, UIowa<br /> #Hans Johnson, UIowa<br /> #Xenios Papademetris, Yale<br /> #Gregory S. Fischer, WPI (Mon, Tue, Wed)<br /> #Daniel Blezek, Mayo (Tue-Fri)<br /> #Danielle Pace, Robarts Research Institute / UWO<br /> #Clement Vachet, UNC-Chapel Hill<br /> #Dave Welch, UIowa<br /> #Demian Wassermann, Odyssée lab, INRIA, France<br /> #Manasi Ramachandran, UIowa<br /> #Greg Sharp, MGH<br /> #Rui Li, MGH<br /> #Mehdi Esteghamatian, Robarts Research Institute / UWO<br /> #Misha Milchenko, WUSTL<br /> #Kevin Archie, WUSTL<br /> #Tim Olsen, WUSTL<br /> #Wendy Plesniak BWH<br /> #Haiying Liu BWH<br /> #Curtis Lisle, KnowledgeVis / Isomics<br /> #Diego Cantor, Robarts Research Institute / UWO<br /> #Daniel Haehn, BWH<br /> #Nicolas Rannou, BWH<br /> #Sylvain Jaume, MIT<br /> #Alex Yarmarkovich, Isomics<br /> #Marco Ruiz, UCSD<br /> #Andriy Fedorov, BWH<br /> #Harish Doddi, Stanford University<br /> #Saikat Pal, Stanford University<br /> #Scott Hoge, BWH<br /> #Vandana Mohan, Georgia Tech<br /> #Ivan Kolosev, Georgia Tech<br /> #Behnood Gholami, Georgia Tech<br /> #James Balter, U Michigan<br /> #Dan McShan, U Michigan<br /> #Zhou Shen, U Michigan<br /> #Maria Francesca Spadea, Italy<br /> #Lining Yang, Siemens Corporate Research<br /> #Beatriz Paniagua, UNC-Chapel Hill<br /> #Bennett Landman, Johns Hopkins University <br /> #Snehashis Roy, Johns Hopkins University<br /> #Marta Peroni, Politecnico di Milano<br /> #Sebastien Barre, Kitware, Inc.<br /> #Samuel Gerber, SCI University of Utah<br /> #Ran Tao, SCI University of Utah<br /> #Marcel Prastawa, SCI University of Utah<br /> #Katie Hayes, BWH<br /> #Sonia Pujol, BWH<br /> #Andras Lasso, Queen's University<br /> #Yong Gao, MGH<br /> <br /> == Logistics ==<br /> *'''Dates:''' June 22-26, 2009<br /> *'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].<br /> *'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 12th, 2009. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139. Receipts will be provided by email as checks are received. Please send questions to dkauf at mit.edu. '''If this is your first event and you are attending for only one day, the registration fee is waived.''' Please let us know, so that we can cover the costs with one of our grants.<br /> *'''Registration Method''' Add your name to the Attendee List section of this page<br /> *'''Hotel:''' We have a group rate of $189/night (plus tax) at the Le Meridien (which used to be the Hotel at MIT). [http://www.starwoodmeeting.com/Book/MITDECSE Please click here to reserve.] This rate is good only through June 1.<br /> *Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.<br /> *2009 Summer Project Week [[NA-MIC/Projects/Theme/Template|'''Template''']]<br /> *[[2008_Summer_Project_Week#Projects|Last Year's Projects as a reference]]<br /> *For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]</div>

Yong https://www.na-mic.org/w/index.php?title=CTSC_Brad_Dickerson,_MGH&diff=37631 CTSC Brad Dickerson, MGH 2009-05-20T16:08:01Z

<p>Yong: </p> <hr /> <div>Back to [[CTSC Imaging Informatics Initiative|CTSC Imaging Informatics Initiative]]<br /> <br /> <br /> =Mission=<br /> See http://www.nmr.mgh.harvard.edu/~bradd/research.html<br /> <br /> =Participants=<br /> * sites involved: MGH NMR center<br /> * number of users: >10<br /> * PI: Brad Dickerson<br /> * staff: Akram Bakkour (Study coordinator/MRI technician/Lab manager) <br /> * clinicians<br /> * IT staff: NMR could provide IT support<br /> <br /> =Data=<br /> The Dickerson lab has about 250 scans for their own studies, and 150 scans for collaborators. Scans include both MRI and fMRI. <br /> Other data are stored with Excel spreadsheets.<br /> <br /> **Project<br /> **Imaging Modalities<br /> **Genetic<br /> <br /> *Storage needs<br /> Images files are currently scattered over several file servers on the same network.<br /> <br /> <br /> =Current Workflow=<br /> DICOM files are transferred from the scanners (PACS?) to a local DICOM Server, and then copied to lab machines<br /> Images are processed with FreeSurfer.<br /> <br /> **Other software to be integrated (e.g., Osirix)<br /> **other features<br /> <br /> <br /> =Other Information=<br /> <br /> There have been at least two serious attempts using XNAT, working with XNAT support group (NRG) at Harvard. An XNAT with customized schema was developed by Eli White a couple of years ago on Dory at NMR.<br /> <br /> The lab recognizes the need for an XNAT-based system to manage images and other data.</div>

Yong https://www.na-mic.org/w/index.php?title=CTSC_Imaging_Informatics_Initiative&diff=37630 CTSC Imaging Informatics Initiative 2009-05-20T16:05:49Z

<p>Yong: /* Use Cases */</p> <hr /> <div>__TOC__<br /> <br /> Back to [[CTSC:CrossSiteImagingIdeas|CTSC_CrossSiteImagingIdeas]]<br /> <br /> = Overview =<br /> The Harvard Catalyst Medical Imaging Informatics Bench to Bedside (mi2b2) Initiative is preparing to provide services for setting up imaging data management systems (IDMS) to support research and clinical efforts involving imaging for Harvard Catalyst affiliated investigators. Two simultaneous (and potentially conflicting) priorities are to 1) provide optimal, customized hardware and software tools for each investigator/ laboratory and 2) to harmonized these solutions to allow for aggregation of the raw and derived medical imaging data for subsequent sharing beyond the investigator/ laboratory. <br /> <br /> <br><br /> XNAT has been identified as a potential software solution for providing the core functionalities of a Harvard Catalyst IDMS.<br /> A typical IDMS service will include the following steps:<br /> *Requirement gathering<br /> *Gap analysis<br /> *Infrastructure setup<br /> *Data modeling<br /> *IDMS installation and setup<br /> *Data loading<br /> *Testing and evaluation<br /> *Ongoing data entry, data loading/transfer, and system monitoring and maintenance<br /> *System upgrade<br /> <br /> = mi2b2 Phases =<br /> == Planning and Information Gathering ==<br /> <br /> The goals of current phase of the initiative are to:<br /> #Gather concrete and specific requirements for imaging data transfer and management from a number of high-volume imaging projects led by Harvard Catalyst-affiliated investigators that are generating valuable derived image data with the intention to share that data beyond their own laboratory; <br /> #Generate a list of overlapping requirements from these specific investigators; <br /> #Prioritize the projects to determine next steps; <br /> #Deploy a demo IDMS based on the default XNAT source code;<br /> #Assess the effort required to extend XNAT code to support the features identified.<br /> <br /> == Prototype Development ==<br /> ===CHB===<br /> *Grant Lab<br /> <br /> ===MGH===<br /> *Dickerson Lab<br /> <br /> == Production System Development for Selective projects==<br /> <br /> ===CHB===<br /> <br /> ===MGH===<br /> <br /> ===BWH===<br /> <br /> = Use Cases =<br /> <br /> (Template<br /> *Mission<br /> **Description of big picture, goal(s) of project<br /> *Participants<br /> *Data Types<br /> **Project<br /> **Imaging Modalities<br /> **Genetic<br /> *Storage needs<br /> *Workflow<br /> **Other software to be integrated (e.g., Osirix)<br /> **other features<br /> *Data transfer<br /> *Data Management)<br /> <br /> The use cases presented here are based on on-going informal interviews with various labs and email communications.<br /> <br /> ==Clinical==<br /> <br /> *[[CTSC_Dan Iosifescu, MGH| Dan Iosifescu, MGH]]<br /> *[[CTSC_biomarkers_appendicitis| Biomarkers for appendicitis]]<br /> *[[CTSC_MCI| Mild cognitive impairment]]<br /> <br /> ==Research==<br /> <br /> *[[CTSC_Ellen Grant, CHB| Ellen Grant, CHB]]<br /> *[[CTSC_Stephan Voss, CHB| Stephan Voss, CHB]]<br /> *[[CTSC_Simon Warfield, CHB| Simon Warfield, CHB]]<br /> *[[CTSC_Bill Hanlon, DF/HCC| Bill Hanlon, DF/HCC]]<br /> *[[CTSC_COPD Gene Project, BWH| COPD Gene Project, BWH]]<br /> *[[CTSC_Brad Dickerson, MGH| Brad Dickerson]]<br /> <br /> = Project Prioritization Criteria=<br /> Possible criteria include:<br /> *Impact<br /> **Number of users<br /> **Duration of the project<br /> **Amount of data (# of subjects, # of scans ...)<br /> <br /> *Success Potential<br /> **Commitment of PI<br /> **Feasibility: is it a good fit for using XNAT?<br /> **Availability of project support at each stage of the effort, including requirement gathering, data collection, system testing, continuing IT and informatics support.<br /> <br /> = Current Status =<br /> Test installations of XNAT (1.4 release candidate 2) were done on Windows XP and Linux in VMware. Minor issues in the setup process needs to be fixed to make successful installation on Windows Vista. <br /> <br /> Requirement gathering from several research and clinical projects have been conducted. <br /> <br /> <br /> = Other Software =<br /> <br /> In addition, an evaluation of dcm4chee|[http://www.dcm4che.org] (a DICOM Implementation in JAVA) is in progress. Simon's group runs an instance of dcm4chee. XNAT's DicomServer and DicomBrowser are based on dcm4che.<br /> <br /> The Globus MEDICUS (Medical Imaging and Computing for Unified Information Sharing)|[http://dev.globus.org/wiki/Incubator/MEDICUS] has been proposed to provide an image sharing solution.<br /> <br /> Reporting and database management of radiological data for clinical trials offered by http://tumormetrics.org/<br /> <br /> Evorad Medical Imaging Workstation from http://www.evorad.com/</div>

Yong https://www.na-mic.org/w/index.php?title=2009_Summer_Project_Week&diff=37629 2009 Summer Project Week 2009-05-20T15:52:46Z

<p>Yong: /* Attendee List */</p> <hr /> <div>Back to [[Project Events]], [[Events]]<br /> <br /> *'''Dates:''' June 22-26, 2009<br /> *'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].<br /> <br /> <br /> ==Introduction to the FIRST JOINT PROJECT WEEK==<br /> <br /> We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. <br /> <br /> Active preparation will begin on''' Thursday, April 16th at 3pm ET''', with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects. <br /> <br /> The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.<br /> <br /> This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January. <br /> <br /> A summary of all past NA-MIC Project Events that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].<br /> <br /> == Agenda==<br /> * Monday <br /> ** noon-1pm lunch <br /> **1pm: Welcome (Ron Kikinis)<br /> ** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]]) <br /> ** 3:30-5:30pm Start project work<br /> * Tuesday <br /> ** 8:30am breakfast<br /> **9:30-10am: NA-MIC Kit Overview (Jim Miller)<br /> ** 10-10:30am Slicer 3.4 Update (Steve Pieper)<br /> ** 10:30-11am Slicer IGT and Imaging Kit Update Update (Noby Hata, Scott Hoge)<br /> ** 11am-12:00pm Breakout Session: [[2009 Project Week Breakout Session: Slicer-Python]] (Demian W)<br /> ** noon lunch<br /> ** 2:30pm-5pm: [[2009 Project Week Data Clinic|Data Clinic]]<br /> ** 5:30pm adjourn for day<br /> * Wednesday <br /> ** 8:30am breakfast<br /> ** 9am-12pm Breakout Session: [[2009 Project Week Breakout Session: ITK]] (Luis Ibanez)<br /> ** noon lunch<br /> ** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: 3D+T Microscopy Cell Dataset Segmentation]] (Alex G.)<br /> ** 5:30pm adjourn for day<br /> * Thursday<br /> ** 8:30am breakfast<br /> ** 9-11pm Tutorial Contest Presentations<br /> ** noon lunch<br /> ** 2:30pm: Breakout Session: TBD<br /> ** 5:30pm adjourn for day<br /> * Friday <br /> ** 8:30am breakfast<br /> ** 10am-noon: Tutorial Contest Winner Announcement and Project Progress using update [[#Projects|Project Wiki pages]]<br /> *** Noon: Lunch boxes and adjourn by 1:30pm.<br /> ***We need to empty room by 1:30. You are welcome to use wireless in Stata.<br /> ***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]<br /> ***Next Project Week [[AHM_2010|in Utah, January 4-8, 2010]]<br /> <br /> == Projects ==<br /> <br /> The list of projects for this week will go here.<br /> === Collaboration Projects ===<br /> #[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images]]<br /> #Prostate Robotics (Junichi, Sam, Nathan Cho, Jack), - Mon, Tue, Thursday 7pm-midnight)<br /> #4D Imaging - currently used for Lung Perfusion (Junichi, Dan Blezek?, Steve, Alex G?)<br /> #Liver Ablation in Slicer (Haiying, Georgetown?)<br /> #SLicer3 and Brainlab - introduction to UCLA (Haiying, Xenios, Pratik, Nathan Hageman)<br /> #Adaptive Radiotherapy - Deformable registration and DICOMRT (Greg Sharp, Steve, Wendy)<br /> #gpu based registration acceleration (James Balter, Greg Sharp, Alark Joshi?, Aditya K., Yogesh Rathi?, Jimi Malcolm, Sandy Wells, Tina Kapur)<br /> #Brain DTI Atlas? (Florin, Utah, UNC, GeorgiaTech)<br /> #Xnat user interface improvements for NA-MIC (Dan M, Tina, Florin, Ron, Wendy)<br /> #xnat and DICOMRT (Greg Sharp, Dan M) - might be done?<br /> #Xnat user clinic - combine with data clinic<br /> #xnat programmer clinic<br /> #Grid Wizard+xnat clinic (Clement)<br /> #?Fluid Mechanincs Module (Nathan Hageman)<br /> #?DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA (Nathan Hageman)<br /> #Cortical Thickness Pipeline (Clement, Ipek)<br /> #Demo Brainlab/Slicer in BWH OR (Haiying, Nathan Hageman)<br /> #Skull Stripping (Xiaodong, Snehashis Roy)<br /> #FastMarching for brain tumor segmentation (Fedorov, GeorgiaTech)<br /> #Meningioma growth simulation for validation (Fedorov, Marcel, Ron)<br /> #Automatic brain MRI processing pipeline (Marcel, Hans)<br /> <br /> ===IGT Projects:===<br /> #port 4d gated ultrasound code to Slicer - (Danielle)<br /> #integration of stereo video into Slicer (Mehdi)<br /> #multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data (Diego, sylvain jaume, nicholas, noby)<br /> #neuroendoscope workflow presentation (sebastien barre)<br /> #slicer integration of mri compatible prostate biopsy robot(sid, queens)<br /> #breakout session on Dynamic Patient Models (James Balter)<br /> #gpu acceleration of 2d-3d registration (james balter, greg sharp, sandy wells, noby hata, terry peters proxy)<br /> <br /> ===NA-MIC Engineering Projects===<br /> # DICOM Validation and Cleanup Tool (Luis, Sid, Steve, Greg)<br /> # [[Summer2009:Using_ITK_in_python| Using ITK in python]] (Steve, Demian, Jim)<br /> # VTK 3d Widgets in Slicer3 (Nicole, Will/Karthik)<br /> # Update to Slicer3 Colors module (Nicole)<br /> # EM Segmenter (Sylvain, Nicolas)<br /> # Plug-in 3D Viewer based on XIP (Lining)<br /> # IAFE Mesh Modules - improvements and testing (Curt, Steve, Vince)<br /> # Informatics workflow Design (Wen, Steve, Dan M, Dan B)<br /> # [[BSpline Registration in Slicer3 | BSpline Registration in Slicer3]] (Jim Miller, Ross Whitaker, Samuel Gerber)<br /> # [[EPI Correction in Slicer3 | EPI Correction in Slicer3]] (Jim Miller, Sylvain Bouix, Tom Fletcher, Ross Whitaker, Julien Siebenthal, Ran Tao )<br /> # Fix [http://www.na-mic.org/Bug/view.php?id=416 bug 416] in registration (Andriy, Luis, Bill, Jim, Steve)<br /> # [[Summer2009:The Vascular Modeling Toolkit in 3D Slicer | The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn)<br /> <br /> == Preparation ==<br /> <br /> # Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list<br /> # Join the kickoff TCON on April 16, 3pm ET.<br /> # [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.<br /> # By 3pm ET on June 11, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.<br /> # By 3pm on June 18, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)<br /> ## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)<br /> ## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)<br /> ## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)<br /> # Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...<br /> # People doing Slicer related projects should come to project week with slicer built on your laptop.<br /> ## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-4/#dirlist Slicer-3-4 branch] (new code should not be checked into the branch).<br /> ## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].<br /> <br /> ==Attendee List==<br /> If you plan to attend, please add your name here.<br /> <br /> #Ron Kikinis, BWH<br /> #Ferenc Jolesz, BWH<br /> #Clare Tempany, BWH<br /> #Tina Kapur, BWH<br /> #Steve Pieper, Isomics Inc<br /> #Jim Miller, GE Research<br /> #Xiaodong Tao, GE Research<br /> #Bill Lorensen, EAB<br /> #Randy Gollub, MGH<br /> #Nicole Aucoin, BWH<br /> #Dan Marcus, WUSTL<br /> #Junichi Tokuda, BWH<br /> #Alex Gouaillard, Harvard Systems Biology<br /> #Arnaud Gelas, Harvard Systems Biology <br /> #Kishore Mosanliganti, Harvard Systems Biology<br /> #Lydie Souhait, Harvard Systems Biology<br /> #Luis Ibanez, Kitware Inc<br /> #Vincent Magnotta, UIowa<br /> #Hans Johnson, UIowa<br /> #Xenios Papademetris, Yale<br /> #Gregory S. Fischer, WPI (Mon, Tue, Wed)<br /> #Daniel Blezek, Mayo (Tue-Fri)<br /> #Danielle Pace, Robarts Research Institute / UWO<br /> #Clement Vachet, UNC-Chapel Hill<br /> #Dave Welch, UIowa<br /> #Demian Wassermann, Odyssée lab, INRIA, France<br /> #Manasi Ramachandran, UIowa<br /> #Greg Sharp, MGH<br /> #Rui Li, MGH<br /> #Mehdi Esteghamatian, Robarts Research Institute / UWO<br /> #Misha Milchenko, WUSTL<br /> #Kevin Archie, WUSTL<br /> #Tim Olsen, WUSTL<br /> #Wendy Plesniak BWH<br /> #Haiying Liu BWH<br /> #Curtis Lisle, KnowledgeVis / Isomics<br /> #Diego Cantor, Robarts Research Institute / UWO<br /> #Daniel Haehn, BWH<br /> #Nicolas Rannou, BWH<br /> #Sylvain Jaume, MIT<br /> #Alex Yarmarkovich, Isomics<br /> #Marco Ruiz, UCSD<br /> #Andriy Fedorov, BWH<br /> #Harish Doddi, Stanford University<br /> #Saikat Pal, Stanford University<br /> #Scott Hoge, BWH<br /> #Vandana Mohan, Georgia Tech<br /> #Ivan Kolosev, Georgia Tech<br /> #Behnood Gholami, Georgia Tech<br /> #James Balter, U Michigan<br /> #Dan McShan, U Michigan<br /> #Zhou Shen, U Michigan<br /> #Maria Francesca Spadea, Italy<br /> #Lining Yang, Siemens Corporate Research<br /> #Beatriz Paniagua, UNC-Chapel Hill<br /> #Bennett Landman, Johns Hopkins University <br /> #Snehashis Roy, Johns Hopkins University<br /> #Marta Peroni, Politecnico di Milano<br /> #Sebastien Barre, Kitware, Inc.<br /> #Samuel Gerber, SCI University of Utah<br /> #Ran Tao, SCI University of Utah<br /> #Marcel Prastawa, SCI University of Utah<br /> #Katie Hayes, BWH<br /> #Sonia Pujol, BWH<br /> #Andras Lasso, Queen's University<br /> #Yong Gao, MGH<br /> <br /> == Logistics ==<br /> *'''Dates:''' June 22-26, 2009<br /> *'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].<br /> *'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 12th, 2009. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139. Receipts will be provided by email as checks are received. Please send questions to dkauf at mit.edu. '''If this is your first event and you are attending for only one day, the registration fee is waived.''' Please let us know, so that we can cover the costs with one of our grants.<br /> *'''Registration Method''' Add your name to the Attendee List section of this page<br /> *'''Hotel:''' We have a group rate of $189/night (plus tax) at the Le Meridien (which used to be the Hotel at MIT). [http://www.starwoodmeeting.com/Book/MITDECSE Please click here to reserve.] This rate is good only through June 1.<br /> *Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.<br /> *2009 Summer Project Week [[NA-MIC/Projects/Theme/Template|'''Template''']]<br /> *[[2008_Summer_Project_Week#Projects|Last Year's Projects as a reference]]<br /> *For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]</div>

Yong https://www.na-mic.org/w/index.php?title=CTSC_Imaging_Informatics_Initiative&diff=37279 CTSC Imaging Informatics Initiative 2009-05-13T17:42:35Z

<p>Yong: /* I3 Phases */</p> <hr /> <div>__TOC__<br /> <br /> Back to [[CTSC:CrossSiteImagingIdeas|CTSC_CrossSiteImagingIdeas]]<br /> <br /> = Overview =<br /> The CTSC Imaging Informatics Initiative (I3) is planning to provide services for setting up imaging data management systems (IDMS) in support of research and clinical efforts involving imaging in Harvard CTSC. XNAT has been identified for providing the core functionalities of the IDMS.<br /> A typical IDMS service will include the following steps:<br /> *Requirement gathering<br /> *Gap analysis<br /> *Infrastructure setup<br /> *Data modeling<br /> *IDMS installation and setup<br /> *Data loading<br /> *Testing and evaluation<br /> *Ongoing data entry, data loading/transfer, and system monitoring and maintenance<br /> *System upgrade<br /> <br /> = I3 Phases =<br /> == Planning and Information Gathering ==<br /> <br /> The goals of current phase of the initiative are to:<br /> #Gather concrete and specific requirements for imaging data transfer and management from a number of labs in Harvard CTSC; <br /> #Generate overlapping requirements from these specific needs; <br /> #Prioritize the potential projects to determine next steps; <br /> #Deploy a demo IDMS based on XNAT.<br /> <br /> == Prototype Development ==<br /> ===CHB===<br /> *Grant Lab<br /> <br /> ===MGH===<br /> *Dickerson Lab<br /> <br /> == Production System Development for Selective projects==<br /> <br /> ===CHB===<br /> <br /> ===MGH===<br /> <br /> ===BWH===<br /> <br /> = Use Cases =<br /> <br /> (Template<br /> *Mission<br /> **Description of big picture, goal(s) of project<br /> *Participants<br /> *Data<br /> **Project<br /> **Imaging Modalities<br /> **Genetic<br /> *Workflow<br /> **Other software to be integrated (e.g., Osirix)<br /> **other features<br /> *Data transfer<br /> *Data Management)<br /> <br /> The use cases presented here are based on on-going informal interviews with various labs and email communications.<br /> <br /> ==Clinical==<br /> <br /> *[[CTSC_Dan Iosifescu, MGH| Dan Iosifescu, MGH]]<br /> *[[CTSC_biomarkers_appendicitis| Biomarkers for appendicitis]]<br /> *[[CTSC_MCI| Mild cognitive impairment]]<br /> <br /> ==Research==<br /> <br /> *[[CTSC_Ellen Grant, CHB| Ellen Grant, CHB]]<br /> *[[CTSC_Stephan Voss, CHB| Stephan Voss, CHB]]<br /> *[[CTSC_Simon Warfield, CHB| Simon Warfield, CHB]]<br /> *[[CTSC_Bill Hanlon, DF/HCC| Bill Hanlon, DF/HCC]]<br /> *[[CTSC_COPD Gene Project, BWH| COPD Gene Project, BWH]]<br /> *[[CTSC_Brad Dickerson, MGH| Brad Dickerson]]<br /> <br /> = Project Prioritization Criteria=<br /> Possible criteria include:<br /> *Impact<br /> **Number of users<br /> **Duration of the project<br /> **Amount of data (# of subjects, # of scans ...)<br /> <br /> *Success Potential<br /> **Commitment of PI<br /> **Feasibility: is it a good fit for using XNAT?<br /> **Availability of project support at each stage of the effort, including requirement gathering, data collection, system testing, continuing IT and informatics support.<br /> <br /> = Current Status =<br /> Test installations of XNAT (1.4 release candidate 2) were done on Windows XP and Linux in VMware. Minor issues in the setup process needs to be fixed to make successful installation on Windows Vista. <br /> <br /> Requirement gathering from several research and clinical projects have been conducted. <br /> <br /> <br /> = Other Software =<br /> <br /> In addition, an evaluation of dcm4chee|[http://www.dcm4che.org] (a DICOM Implementation in JAVA) is in progress. Simon's group runs an instance of dcm4chee. XNAT's DicomServer and DicomBrowser are based on dcm4che.<br /> <br /> The Globus MEDICUS (Medical Imaging and Computing for Unified Information Sharing)|[http://dev.globus.org/wiki/Incubator/MEDICUS] has been proposed to provide an image sharing solution.<br /> <br /> Reporting and database management of radiological data for clinical trials offered by http://tumormetrics.org/<br /> <br /> Evorad Medical Imaging Workstation from http://www.evorad.com/</div>

Yong https://www.na-mic.org/w/index.php?title=CTSC_Brad_Dickerson,_MGH&diff=37278 CTSC Brad Dickerson, MGH 2009-05-13T17:37:03Z

<p>Yong: </p> <hr /> <div>Back to [[CTSC Imaging Informatics Initiative|CTSC Imaging Informatics Initiative]]<br /> <br /> <br /> =Mission=<br /> See http://www.nmr.mgh.harvard.edu/~bradd/research.html<br /> <br /> =Participants=<br /> * sites involved: MGH NMR center<br /> * number of users: >10<br /> * PI: Brad Dickerson<br /> * staff: Akram Bakkour (Study coordinator/MRI technician/Lab manager) <br /> * clinicians<br /> * IT staff: NMR could provide IT support<br /> <br /> =Data=<br /> The Dickerson lab has about 250 scans for their own studies, and 150 scans for collaborators. Scans include both MRI and fMRI. Images files are current scattered over several file servers.<br /> <br /> Other data are stored with Excel spreadsheets.<br /> <br /> =Current Workflow=<br /> DICOM files are transferred from the scanners (PACS?) to a local DICOM Server, and then copied to lab machines<br /> Images are processed with FreeSurfer.<br /> <br /> <br /> =Other Information=<br /> <br /> There have been at least two serious attempts using XNAT, working with XNAT support group (NRG) at Harvard. An XNAT with customized schema was developed by Eli White a couple of years ago on Dory at NMR.<br /> <br /> The lab recognizes the need for an XNAT-based system to manage images and other data.</div>

Yong https://www.na-mic.org/w/index.php?title=CTSC_Ellen_Grant,_CHB&diff=37277 CTSC Ellen Grant, CHB 2009-05-13T17:12:02Z

<p>Yong: </p> <hr /> <div>Back to [[CTSC Imaging Informatics Initiative|CTSC Imaging Informatics Initiative]]<br /> <br /> <br /> =Mission=<br /> <br /> <br /> =Participants=<br /> * sites involved: MGH NMR center, MGH Radiology, CHB Radiology<br /> * number of users: ~10<br /> * PI: Ellen Grant<br /> * staff: Rudolph Pienaar<br /> * clinicians<br /> * IT staff<br /> <br /> =Data=<br /> There are currently about 1540 studies, each with about 1k images<br /> * Multiple studies<br /> * Imaging Modalities: MRI<br /> * Genetic:<br /> <br /> =Current Workflow=<br /> <br /> DICOM raw images are produced at radiology PACS at MGH, and are manually pushed to the PACS hosted on KAOS resided at MGH NMR center. The images are processed by a set of PERL scripts to be renamed and re-organized into a file structure where all images for a study are saved into a directory named for the study.<br /> <br /> DICOM images are currently viewed with Osiris on Macs.<br /> <br /> = Data Management need=<br /> <br /> It is desired to develop an Image Management System for BDC (IMS4BDC) with which at least the following can be done:<br /> <br /> * Move images from MGH (KAOS) to a BDC machine at Childrens <br /> * Import legacy data into IMS4BDC from existing file structure and CDs<br /> * Query capabilities: (example) Show all diffusion studies where patients ages are < 6<br /> * Mange post-processed images<br /> * Sharing images with clinical physicians; export post-processed data back to clinical PACS<br /> <br /> =Other Information=<br /> <br /> Rudolph has worked with XNAT support group at Harvard.</div>

Yong https://www.na-mic.org/w/index.php?title=CTSC_Ellen_Grant,_CHB&diff=37276 CTSC Ellen Grant, CHB 2009-05-13T17:11:45Z

<p>Yong: </p> <hr /> <div>Back to [[CTSC Imaging Informatics Initiative|CTSC Imaging Informatics Initiative]]<br /> <br /> <br /> =Mission=<br /> <br /> <br /> =Participants=<br /> * sites involved: MGH NMR center, MGH Radiology, CHB Radiology<br /> * number of users: ~10<br /> * PI: Ellen Grant<br /> * staff: Rudolph Pienaar<br /> * clinicians<br /> * IT staff<br /> <br /> =Data=<br /> There are currently about 1540 studies, each with about 1k images<br /> * Multiple studies<br /> * Imaging Modalities: MRI<br /> * Genetic:<br /> =Current Workflow=<br /> <br /> DICOM raw images are produced at radiology PACS at MGH, and are manually pushed to the PACS hosted on KAOS resided at MGH NMR center. The images are processed by a set of PERL scripts to be renamed and re-organized into a file structure where all images for a study are saved into a directory named for the study.<br /> <br /> DICOM images are currently viewed with Osiris on Macs.<br /> <br /> = Data Management need=<br /> <br /> It is desired to develop an Image Management System for BDC (IMS4BDC) with which at least the following can be done:<br /> <br /> * Move images from MGH (KAOS) to a BDC machine at Childrens <br /> * Import legacy data into IMS4BDC from existing file structure and CDs<br /> * Query capabilities: (example) Show all diffusion studies where patients ages are < 6<br /> * Mange post-processed images<br /> * Sharing images with clinical physicians; export post-processed data back to clinical PACS<br /> <br /> =Other Information=<br /> <br /> Rudolph has worked with XNAT support group at Harvard.</div>

Yong https://www.na-mic.org/w/index.php?title=CTSC_Ellen_Grant,_CHB&diff=37275 CTSC Ellen Grant, CHB 2009-05-13T17:09:50Z

<p>Yong: </p> <hr /> <div>Back to [[CTSC Imaging Informatics Initiative|CTSC Imaging Informatics Initiative]]<br /> <br /> <br /> =Mission=<br /> <br /> <br /> =Participants=<br /> * sites involved: MGH NMR center, MGH Radiology, CHB Radiology<br /> * number of users: ~10<br /> * PI: Ellen Grant<br /> * staff: Rudolph Pienaar<br /> * clinicians<br /> * IT staff<br /> <br /> =Data=<br /> There are currently about 1540 studies, each with about 1k images<br /> <br /> =Current Workflow=<br /> <br /> DICOM raw images are produced at radiology PACS at MGH, and are manually pushed to the PACS hosted on KAOS resided at MGH NMR center. The images are processed by a set of PERL scripts to be renamed and re-organized into a file structure where all images for a study are saved into a directory named for the study.<br /> <br /> DICOM images are currently viewed with Osiris on Macs.<br /> <br /> = Data Management need=<br /> <br /> It is desired to develop an Image Management System for BDC (IMS4BDC) with which at least the following can be done:<br /> <br /> * Move images from MGH (KAOS) to a BDC machine at Childrens <br /> * Import legacy data into IMS4BDC from existing file structure and CDs<br /> * Query capabilities: (example) Show all diffusion studies where patients ages are < 6<br /> * Mange post-processed images<br /> * Sharing images with clinical physicians; export post-processed data back to clinical PACS<br /> <br /> =Other Information=<br /> <br /> Rudolph has worked with XNAT support group at Harvard.</div>

Yong https://www.na-mic.org/w/index.php?title=CTSC_Ellen_Grant,_CHB&diff=37274 CTSC Ellen Grant, CHB 2009-05-13T17:01:24Z

<p>Yong: </p> <hr /> <div>Back to [[CTSC Imaging Informatics Initiative|CTSC Imaging Informatics Initiative]]<br /> <br /> <br /> =Mission=<br /> <br /> <br /> =Participants=<br /> * PI: Ellen Grant<br /> * staff: Rudolph Pienaar<br /> * clinicians<br /> * IT staff<br /> <br /> =Data=<br /> There are currently about 1540 studies, each with about 1k images<br /> <br /> =Current Workflow=<br /> <br /> DICOM raw images are produced at radiology PACS at MGH, and are manually pushed to the PACS hosted on KAOS resided at MGH NMR center. The images are processed by a set of PERL scripts to be renamed and re-organized into a file structure where all images for a study are saved into a directory named for the study.<br /> <br /> DICOM images are currently viewed with Osiris on Macs.<br /> <br /> = Data Management need=<br /> <br /> It is desired to develop an Image Management System for BDC (IMS4BDC) with which at least the following can be done:<br /> <br /> * Move images from MGH (KAOS) to a BDC machine at Childrens <br /> * Import legacy data into IMS4BDC from existing file structure and CDs<br /> * Query capabilities: (example) Show all diffusion studies where patients ages are < 6<br /> * Mange post-processed images<br /> * Sharing images with clinical physicians; export post-processed data back to clinical PACS<br /> <br /> =Other Information=<br /> <br /> Rudolph has worked with XNAT support group at Harvard.</div>

Yong https://www.na-mic.org/w/index.php?title=CTSC_Imaging_Informatics_Initiative&diff=37273 CTSC Imaging Informatics Initiative 2009-05-13T16:06:54Z

<p>Yong: /* Use Cases */</p> <hr /> <div>__TOC__<br /> <br /> Back to [[CTSC:CrossSiteImagingIdeas|CTSC_CrossSiteImagingIdeas]]<br /> <br /> = Overview =<br /> The CTSC Imaging Informatics Initiative (I3) is planning to provide services for setting up imaging data management systems (IDMS) in support of research and clinical efforts involving imaging in Harvard CTSC. XNAT has been identified for providing the core functionalities of the IDMS.<br /> A typical IDMS service will include the following steps:<br /> *Requirement gathering<br /> *Gap analysis<br /> *Infrastructure setup<br /> *Data modeling<br /> *IDMS installation and setup<br /> *Data loading<br /> *Testing and evaluation<br /> *Ongoing data entry, data loading/transfer, and system monitoring and maintenance<br /> *System upgrade<br /> <br /> = I3 Phases =<br /> == Planning and Information Gathering ==<br /> <br /> <br /> The goals of current phase of the initiative are to:<br /> #Gather concrete and specific requirements for imaging data transfer and management from a number of labs in Harvard CTSC; <br /> #Generate overlapping requirements from these specific needs; <br /> #Prioritize the potential projects to determine next steps; <br /> #Deploy a demo IDMS based on XNAT.<br /> <br /> = Use Cases =<br /> <br /> (Template<br /> *Mission<br /> **Description of big picture, goal(s) of project<br /> *Participants<br /> *Data<br /> **Project<br /> **Imaging Modalities<br /> **Genetic<br /> *Workflow<br /> **Other software to be integrated (e.g., Osirix)<br /> **other features<br /> *Data transfer<br /> *Data Management)<br /> <br /> The use cases presented here are based on on-going informal interviews with various labs and email communications.<br /> <br /> ==Clinical==<br /> <br /> *[[CTSC_Dan Iosifescu, MGH| Dan Iosifescu, MGH]]<br /> *[[CTSC_biomarkers_appendicitis| Biomarkers for appendicitis]]<br /> *[[CTSC_MCI| Mild cognitive impairment]]<br /> <br /> ==Research==<br /> <br /> *[[CTSC_Ellen Grant, CHB| Ellen Grant, CHB]]<br /> *[[CTSC_Stephan Voss, CHB| Stephan Voss, CHB]]<br /> *[[CTSC_Simon Warfield, CHB| Simon Warfield, CHB]]<br /> *[[CTSC_Bill Hanlon, DF/HCC| Bill Hanlon, DF/HCC]]<br /> *[[CTSC_COPD Gene Project, BWH| COPD Gene Project, BWH]]<br /> *[[CTSC_Brad Dickerson, MGH| Brad Dickerson]]<br /> <br /> = Project Prioritization Criteria=<br /> Possible criteria include:<br /> *Impact<br /> **Number of users<br /> **Duration of the project<br /> **Amount of data (# of subjects, # of scans ...)<br /> <br /> *Success Potential<br /> **Commitment of PI<br /> **Feasibility: is it a good fit for using XNAT?<br /> **Availability of project support at each stage of the effort, including requirement gathering, data collection, system testing, continuing IT and informatics support.<br /> <br /> = Current Status =<br /> Test installations of XNAT (1.4 release candidate 2) were done on Windows XP and Linux in VMware. Minor issues in the setup process needs to be fixed to make successful installation on Windows Vista. <br /> <br /> Requirement gathering from several research and clinical projects have been conducted. <br /> <br /> <br /> = Other Software =<br /> <br /> In addition, an evaluation of dcm4chee|[http://www.dcm4che.org] (a DICOM Implementation in JAVA) is in progress. Simon's group runs an instance of dcm4chee. XNAT's DicomServer and DicomBrowser are based on dcm4che.<br /> <br /> The Globus MEDICUS (Medical Imaging and Computing for Unified Information Sharing)|[http://dev.globus.org/wiki/Incubator/MEDICUS] has been proposed to provide an image sharing solution.<br /> <br /> Reporting and database management of radiological data for clinical trials offered by http://tumormetrics.org/<br /> <br /> Evorad Medical Imaging Workstation from http://www.evorad.com/</div>

Yong https://www.na-mic.org/w/index.php?title=CTSC_Imaging_Informatics_Initiative&diff=37272 CTSC Imaging Informatics Initiative 2009-05-13T16:06:28Z

<p>Yong: /* I3 Phases */</p> <hr /> <div>__TOC__<br /> <br /> Back to [[CTSC:CrossSiteImagingIdeas|CTSC_CrossSiteImagingIdeas]]<br /> <br /> = Overview =<br /> The CTSC Imaging Informatics Initiative (I3) is planning to provide services for setting up imaging data management systems (IDMS) in support of research and clinical efforts involving imaging in Harvard CTSC. XNAT has been identified for providing the core functionalities of the IDMS.<br /> A typical IDMS service will include the following steps:<br /> *Requirement gathering<br /> *Gap analysis<br /> *Infrastructure setup<br /> *Data modeling<br /> *IDMS installation and setup<br /> *Data loading<br /> *Testing and evaluation<br /> *Ongoing data entry, data loading/transfer, and system monitoring and maintenance<br /> *System upgrade<br /> <br /> = I3 Phases =<br /> == Planning and Information Gathering ==<br /> <br /> <br /> The goals of current phase of the initiative are to:<br /> #Gather concrete and specific requirements for imaging data transfer and management from a number of labs in Harvard CTSC; <br /> #Generate overlapping requirements from these specific needs; <br /> #Prioritize the potential projects to determine next steps; <br /> #Deploy a demo IDMS based on XNAT.<br /> <br /> = Use Cases =<br /> (Template<br /> *Mission<br /> **Description of big picture, goal(s) of project<br /> *Participants<br /> *Data<br /> **Project<br /> **Imaging Modalities<br /> **Genetic<br /> *Workflow<br /> **Other software to be integrated (e.g., Osirix)<br /> **other features<br /> *Data transfer<br /> *Data Management)<br /> <br /> ==Clinical==<br /> <br /> *[[CTSC_Dan Iosifescu, MGH| Dan Iosifescu, MGH]]<br /> *[[CTSC_biomarkers_appendicitis| Biomarkers for appendicitis]]<br /> *[[CTSC_MCI| Mild cognitive impairment]]<br /> <br /> ==Research==<br /> <br /> *[[CTSC_Ellen Grant, CHB| Ellen Grant, CHB]]<br /> *[[CTSC_Stephan Voss, CHB| Stephan Voss, CHB]]<br /> *[[CTSC_Simon Warfield, CHB| Simon Warfield, CHB]]<br /> *[[CTSC_Bill Hanlon, DF/HCC| Bill Hanlon, DF/HCC]]<br /> *[[CTSC_COPD Gene Project, BWH| COPD Gene Project, BWH]]<br /> *[[CTSC_Brad Dickerson, MGH| Brad Dickerson]]<br /> <br /> = Project Prioritization Criteria=<br /> Possible criteria include:<br /> *Impact<br /> **Number of users<br /> **Duration of the project<br /> **Amount of data (# of subjects, # of scans ...)<br /> <br /> *Success Potential<br /> **Commitment of PI<br /> **Feasibility: is it a good fit for using XNAT?<br /> **Availability of project support at each stage of the effort, including requirement gathering, data collection, system testing, continuing IT and informatics support.<br /> <br /> = Current Status =<br /> Test installations of XNAT (1.4 release candidate 2) were done on Windows XP and Linux in VMware. Minor issues in the setup process needs to be fixed to make successful installation on Windows Vista. <br /> <br /> Requirement gathering from several research and clinical projects have been conducted. <br /> <br /> <br /> = Other Software =<br /> <br /> In addition, an evaluation of dcm4chee|[http://www.dcm4che.org] (a DICOM Implementation in JAVA) is in progress. Simon's group runs an instance of dcm4chee. XNAT's DicomServer and DicomBrowser are based on dcm4che.<br /> <br /> The Globus MEDICUS (Medical Imaging and Computing for Unified Information Sharing)|[http://dev.globus.org/wiki/Incubator/MEDICUS] has been proposed to provide an image sharing solution.<br /> <br /> Reporting and database management of radiological data for clinical trials offered by http://tumormetrics.org/<br /> <br /> Evorad Medical Imaging Workstation from http://www.evorad.com/</div>

Yong https://www.na-mic.org/w/index.php?title=CTSC_Stephan_Voss,_CHB&diff=37227 CTSC Stephan Voss, CHB 2009-05-12T14:53:10Z

<p>Yong: /* Data Transfer */</p> <hr /> <div>Back to [[CTSC Imaging Informatics Initiative|CTSC Imaging Informatics Initiative]]<br /> <br /> <br /> =Mission=<br /> Description of big picture, goal(s) of project<br /> <br /> =Participants=<br /> * PI, clinicians, IT staff, CT investigator, etc<br /> * staff missing<br /> <br /> = Data =<br /> <br /> COG [http://www.childrensoncologygroup.org/ (Children's Oncology Group)] phase I consortium imaging/clinical trial ADVL0712. <br /> *25 patients (with multiple imaging studies per patient, including CT, MRI and PET imaging)<br /> *In addition to DICOM files, much data exist on various Excel spreadsheets, in file folders, and as email attachments, in LA and Boston. Currently, the only way to integrate all of the data available about a patient is to manually assemble all of these pieces of information. This is a common scenario for multi-institutional clinical trials.<br /> <br /> =Data Transfer =<br /> Diagnostic imaging and meta data reside at the COG Phase I Image Center in LA, and can be easily pulled to a local workstation at Children¹s Boston via the COG Grid.<br /> <br /> =Work Flow =<br /> <br /> Osirix is the preferred image viewer. <br /> Other tools provided by COG.<br /> <br /> = Data Management Need =<br /> *All of the non-protected DICOM header info should be extractable and searchable (not just study name and protocol ID, but other data such as FDG dose and pt weight)<br /> *The studies must be referenced to therapy surveillance dates, i.e. post-treatment week 4, off-study scan, etc<br /> *The surveillance period and actual imaging studies dates may not coincide for various practical reason related to patient care. We are currently logging this information on spreadsheets<br /> *The institutions are usually asked to submit the local radiologist’s report along with the images. These reports come in various formats, ranging from electronic reports included with the image files to PDFs. These are currently sent by email.<br /> *Measurements are made to determine treatment response; there is no way of posting those annotated images used to determine response back to the Grid. Posting the measurements and the annotated images used to make the assessment would be VERY useful when disagreements arise between central reviews and institutional assessments.<br /> *Genetic and pathology data. <br /> * As a research study progresses and new information is learned, supplemental data is often required (by the FDA, for example). It is very common for us to go back to institutions and request additional clinical data based on our interim analyses. We would need a “placeholder” for such future data.<br /> *launch image analysis tools – such as Simon, Karl, and others have been developing, DCE-MRI for example – and use XNAT to access the appropriate imaging data hosted on the GRID and subsequently post the analyses back to the GRID. Again, these are currently manual operations.<br /> <br /> ==The new BIRNCC could potentially provide informatics support(?)==</div>

Yong https://www.na-mic.org/w/index.php?title=CTSC_Imaging_Informatics_Initiative&diff=37226 CTSC Imaging Informatics Initiative 2009-05-12T14:51:13Z

<p>Yong: /* Use Cases */</p> <hr /> <div>__TOC__<br /> <br /> Back to [[CTSC:CrossSiteImagingIdeas|CTSC_CrossSiteImagingIdeas]]<br /> <br /> = Overview =<br /> The CTSC Imaging Informatics Initiative (I3) is planning to provide services for setting up imaging data management systems (IDMS) in support of research and clinical efforts involving imaging in Harvard CTSC. XNAT has been identified for providing the core functionalities of the IDMS.<br /> A typical IDMS service will include the following steps:<br /> *Requirement gathering<br /> *Gap analysis<br /> *Infrastructure setup<br /> *Data modeling<br /> *IDMS installation and setup<br /> *Data loading<br /> *Testing and evaluation<br /> *Ongoing data entry, data loading/transfer, and system monitoring and maintenance<br /> *System upgrade<br /> <br /> = I3 Phases =<br /> == Planning and Information Gathering ==<br /> <br /> <br /> The goals of current phase of the initiative are to:<br /> #Gather concrete and specific requirements for imaging data transfer and management from a number of labs in Harvard CTSC; <br /> #Generate overlapping requirements from these specific needs; <br /> #Prioritize the potential projects to determine next steps; <br /> #Deploy a demo IDMS based on XNAT.<br /> <br /> The use cases presented here are based on on-going informal interviews with various labs and email communications.<br /> <br /> = Use Cases =<br /> (Template<br /> *Mission<br /> **Description of big picture, goal(s) of project<br /> *Participants<br /> *Data<br /> **Project<br /> **Imaging Modalities<br /> **Genetic<br /> *Workflow<br /> **Other software to be integrated (e.g., Osirix)<br /> **other features<br /> *Data transfer<br /> *Data Management)<br /> <br /> ==Clinical==<br /> <br /> *[[CTSC_Dan Iosifescu, MGH| Dan Iosifescu, MGH]]<br /> *[[CTSC_biomarkers_appendicitis| Biomarkers for appendicitis]]<br /> *[[CTSC_MCI| Mild cognitive impairment]]<br /> <br /> ==Research==<br /> <br /> *[[CTSC_Ellen Grant, CHB| Ellen Grant, CHB]]<br /> *[[CTSC_Stephan Voss, CHB| Stephan Voss, CHB]]<br /> *[[CTSC_Simon Warfield, CHB| Simon Warfield, CHB]]<br /> *[[CTSC_Bill Hanlon, DF/HCC| Bill Hanlon, DF/HCC]]<br /> *[[CTSC_COPD Gene Project, BWH| COPD Gene Project, BWH]]<br /> *[[CTSC_Brad Dickerson, MGH| Brad Dickerson]]<br /> <br /> = Project Prioritization Criteria=<br /> Possible criteria include:<br /> *Impact<br /> **Number of users<br /> **Duration of the project<br /> **Amount of data (# of subjects, # of scans ...)<br /> <br /> *Success Potential<br /> **Commitment of PI<br /> **Feasibility: is it a good fit for using XNAT?<br /> **Availability of project support at each stage of the effort, including requirement gathering, data collection, system testing, continuing IT and informatics support.<br /> <br /> = Current Status =<br /> Test installations of XNAT (1.4 release candidate 2) were done on Windows XP and Linux in VMware. Minor issues in the setup process needs to be fixed to make successful installation on Windows Vista. <br /> <br /> Requirement gathering from several research and clinical projects have been conducted. <br /> <br /> <br /> = Other Software =<br /> <br /> In addition, an evaluation of dcm4chee|[http://www.dcm4che.org] (a DICOM Implementation in JAVA) is in progress. Simon's group runs an instance of dcm4chee. XNAT's DicomServer and DicomBrowser are based on dcm4che.<br /> <br /> The Globus MEDICUS (Medical Imaging and Computing for Unified Information Sharing)|[http://dev.globus.org/wiki/Incubator/MEDICUS] has been proposed to provide an image sharing solution.<br /> <br /> Reporting and database management of radiological data for clinical trials offered by http://tumormetrics.org/<br /> <br /> Evorad Medical Imaging Workstation from http://www.evorad.com/</div>

Yong https://www.na-mic.org/w/index.php?title=CTSC_Imaging_Informatics_Initiative&diff=37225 CTSC Imaging Informatics Initiative 2009-05-12T14:49:30Z

<p>Yong: /* Current Status */</p> <hr /> <div>__TOC__<br /> <br /> Back to [[CTSC:CrossSiteImagingIdeas|CTSC_CrossSiteImagingIdeas]]<br /> <br /> = Overview =<br /> The CTSC Imaging Informatics Initiative (I3) is planning to provide services for setting up imaging data management systems (IDMS) in support of research and clinical efforts involving imaging in Harvard CTSC. XNAT has been identified for providing the core functionalities of the IDMS.<br /> A typical IDMS service will include the following steps:<br /> *Requirement gathering<br /> *Gap analysis<br /> *Infrastructure setup<br /> *Data modeling<br /> *IDMS installation and setup<br /> *Data loading<br /> *Testing and evaluation<br /> *Ongoing data entry, data loading/transfer, and system monitoring and maintenance<br /> *System upgrade<br /> <br /> = I3 Phases =<br /> == Planning and Information Gathering ==<br /> <br /> <br /> The goals of current phase of the initiative are to:<br /> #Gather concrete and specific requirements for imaging data transfer and management from a number of labs in Harvard CTSC; <br /> #Generate overlapping requirements from these specific needs; <br /> #Prioritize the potential projects to determine next steps; <br /> #Deploy a demo IDMS based on XNAT.<br /> <br /> The use cases presented here are based on on-going informal interviews with various labs and email communications.<br /> <br /> = Use Cases =<br /> (Template<br /> *Mission<br /> **Description of big picture, goal(s) of project<br /> *Participants<br /> *Data<br /> **Project<br /> **Imaging Modalities<br /> **Genetic<br /> **Workflow<br /> **other<br /> *Data transfer<br /> *Data Management)<br /> <br /> ==Clinical==<br /> <br /> *[[CTSC_Dan Iosifescu, MGH| Dan Iosifescu, MGH]]<br /> *[[CTSC_biomarkers_appendicitis| Biomarkers for appendicitis]]<br /> *[[CTSC_MCI| Mild cognitive impairment]]<br /> <br /> ==Research==<br /> <br /> *[[CTSC_Ellen Grant, CHB| Ellen Grant, CHB]]<br /> *[[CTSC_Stephan Voss, CHB| Stephan Voss, CHB]]<br /> *[[CTSC_Simon Warfield, CHB| Simon Warfield, CHB]]<br /> *[[CTSC_Bill Hanlon, DF/HCC| Bill Hanlon, DF/HCC]]<br /> *[[CTSC_COPD Gene Project, BWH| COPD Gene Project, BWH]]<br /> *[[CTSC_Brad Dickerson, MGH| Brad Dickerson]]<br /> <br /> = Project Prioritization Criteria=<br /> Possible criteria include:<br /> *Impact<br /> **Number of users<br /> **Duration of the project<br /> **Amount of data (# of subjects, # of scans ...)<br /> <br /> *Success Potential<br /> **Commitment of PI<br /> **Feasibility: is it a good fit for using XNAT?<br /> **Availability of project support at each stage of the effort, including requirement gathering, data collection, system testing, continuing IT and informatics support.<br /> <br /> = Current Status =<br /> Test installations of XNAT (1.4 release candidate 2) were done on Windows XP and Linux in VMware. Minor issues in the setup process needs to be fixed to make successful installation on Windows Vista. <br /> <br /> Requirement gathering from several research and clinical projects have been conducted. <br /> <br /> <br /> = Other Software =<br /> <br /> In addition, an evaluation of dcm4chee|[http://www.dcm4che.org] (a DICOM Implementation in JAVA) is in progress. Simon's group runs an instance of dcm4chee. XNAT's DicomServer and DicomBrowser are based on dcm4che.<br /> <br /> The Globus MEDICUS (Medical Imaging and Computing for Unified Information Sharing)|[http://dev.globus.org/wiki/Incubator/MEDICUS] has been proposed to provide an image sharing solution.<br /> <br /> Reporting and database management of radiological data for clinical trials offered by http://tumormetrics.org/<br /> <br /> Evorad Medical Imaging Workstation from http://www.evorad.com/</div>

Yong https://www.na-mic.org/w/index.php?title=CTSC_Imaging_Informatics_Initiative&diff=37224 CTSC Imaging Informatics Initiative 2009-05-12T14:16:35Z

<p>Yong: /* Current Status */</p> <hr /> <div>__TOC__<br /> <br /> Back to [[CTSC:CrossSiteImagingIdeas|CTSC_CrossSiteImagingIdeas]]<br /> <br /> = Overview =<br /> The CTSC Imaging Informatics Initiative (I3) is planning to provide services for setting up imaging data management systems (IDMS) in support of research and clinical efforts involving imaging in Harvard CTSC. XNAT has been identified for providing the core functionalities of the IDMS.<br /> A typical IDMS service will include the following steps:<br /> *Requirement gathering<br /> *Gap analysis<br /> *Infrastructure setup<br /> *Data modeling<br /> *IDMS installation and setup<br /> *Data loading<br /> *Testing and evaluation<br /> *Ongoing data entry, data loading/transfer, and system monitoring and maintenance<br /> *System upgrade<br /> <br /> = I3 Phases =<br /> == Planning and Information Gathering ==<br /> <br /> <br /> The goals of current phase of the initiative are to:<br /> #Gather concrete and specific requirements for imaging data transfer and management from a number of labs in Harvard CTSC; <br /> #Generate overlapping requirements from these specific needs; <br /> #Prioritize the potential projects to determine next steps; <br /> #Deploy a demo IDMS based on XNAT.<br /> <br /> The use cases presented here are based on on-going informal interviews with various labs and email communications.<br /> <br /> = Use Cases =<br /> (Template<br /> *Mission<br /> **Description of big picture, goal(s) of project<br /> *Participants<br /> *Data<br /> **Project<br /> **Imaging Modalities<br /> **Genetic<br /> **Workflow<br /> **other<br /> *Data transfer<br /> *Data Management)<br /> <br /> ==Clinical==<br /> <br /> *[[CTSC_Dan Iosifescu, MGH| Dan Iosifescu, MGH]]<br /> *[[CTSC_biomarkers_appendicitis| Biomarkers for appendicitis]]<br /> *[[CTSC_MCI| Mild cognitive impairment]]<br /> <br /> ==Research==<br /> <br /> *[[CTSC_Ellen Grant, CHB| Ellen Grant, CHB]]<br /> *[[CTSC_Stephan Voss, CHB| Stephan Voss, CHB]]<br /> *[[CTSC_Simon Warfield, CHB| Simon Warfield, CHB]]<br /> *[[CTSC_Bill Hanlon, DF/HCC| Bill Hanlon, DF/HCC]]<br /> *[[CTSC_COPD Gene Project, BWH| COPD Gene Project, BWH]]<br /> *[[CTSC_Brad Dickerson, MGH| Brad Dickerson]]<br /> <br /> = Project Prioritization Criteria=<br /> Possible criteria include:<br /> *Impact<br /> **Number of users<br /> **Duration of the project<br /> **Amount of data (# of subjects, # of scans ...)<br /> <br /> *Success Potential<br /> **Commitment of PI<br /> **Feasibility: is it a good fit for using XNAT?<br /> **Availability of project support at each stage of the effort, including requirement gathering, data collection, system testing, continuing IT and informatics support.<br /> <br /> = Current Status =<br /> Test installations of XNAT (1.4 release candidate 2) were done on Windows XP and Linux in VMware. Minor issues in the setup process needs to be fixed to make successful installation on Windows Vista. <br /> <br /> Requirement gathering from several research and clinical projects have been conducted. <br /> <br /> In addition, an evaluation of dcm4chee|[http://www.dcm4che.org] (a DICOM Implementation in JAVA) is in progress. Simon's group runs an instance of dcm4chee. XNAT's DicomServer and DicomBrowser are based on dcm4che.<br /> <br /> The Globus MEDICUS (Medical Imaging and Computing for Unified Information Sharing)|[http://dev.globus.org/wiki/Incubator/MEDICUS] has been proposed to provide an image sharing solution.</div>

Yong https://www.na-mic.org/w/index.php?title=CTSC:TTIC.050509&diff=37058 CTSC:TTIC.050509 2009-05-07T03:24:07Z

<p>Yong: </p> <hr /> <div>Back to [[Collaboration:Harvard_CTSC|Collaboration:Harvard_CTSC]]<br /> <br><br /> '''Agenda '''<br /> <br /> # Update of the consultation requests: (Dr MacCabe, pediatric fMRI, Dr Halberg, cardiovascular MRI, Dr Dodson, lingual nerve imaging, Dr Buijze, Orthopaedic 3D project)<br /> # Procedure when several groups offer their expertise for a consultation request.<br /> # Feedback on the evaluation plan<br /> # Use of TMIC software for COG project<br /> <br /> <br><br /> <br /> == Harvard Translational Imaging Consortium Meeting Minutes May 5, 2009 ==<br /> <br /> In attendance:<br /> * Gordon Williams<br /> * Randy Gollub<br /> * Valerie Humblet<br /> * Clare Tempany<br /> * Simon Warfield<br /> * Laura Alice<br /> * Bob Lenkinski<br /> * Bill Hanlon<br /> * Stephan Voss<br /> * Gordon Harris <br /> * Jeff Yapp<br /> * Annick Van den Abbeelle<br /> * Yong Gao<br /> <br /> <br><br /> <br /> '''1. Update on imaging consultation requests''' <br><br /> <br /> * Valerie gave an update on the ongoing consultation requests. All the investigators have been contacted by at least one imaging expert and the collaborative work is in process.<br /> <br /> <br><br /> <br /> '''2. Procedure when several groups offer their expertise for a consultation request'''<br><br /> <br /> * Until the web-based consultation tracking tool JIRA is up and running, all members working on a consultation request should e-mail the rest of the group via the listserv whenever they contact and investigator.<br /> <br /> <br><br /> <br /> '''3. Feedback on the evaluation plan'''<br><br /> <br /> * Randy sent a copy of the evaluation plan last week and reminded all the members to have a look at it and get back to her with comments.<br /> <br /> <br><br /> <br /> '''4. Use of TIMC software for COG project''' <br><br /> <br /> * The BIRN project proposed the use of XNAT to provide COG with an informatics tool to help with data visualization and data management/transfer.<br /> ** This project is viewed by the consortium as a good test case for XNAT integration.<br /> * In the mean time, Bill and Gordon Harris proposed to give Valerie, Yong, Stephan and Simon a demo of the TIMC software to evaluate if it could fits COG needs.<br /> ** As a multi-institution informatics tool for image analysis and data management/transfer, the software created by TIMC could be used as a model for what COG is trying to build.<br /> ** Annick reminded that TMIC works on a fee-for-service structure and NCI guidelines and grant rules must be followed. It might not be possible for TIMC to share the software and waived the fee-for-service if they don't provide software support. TIMC could definitively and easily add another site and helping support COG but first the regulations attached to TIMC must be reviewed by Annick, Gordon and Bill.<br /> * Randy gave an overview of BIRN mission: provide tools for the medical community, open source software anybody can use if they have the IT people to support it. She will be circulating BIRN grant aim to the group</div>

Yong https://www.na-mic.org/w/index.php?title=CTSC_Imaging_Informatics_Initiative&diff=36964 CTSC Imaging Informatics Initiative 2009-05-01T22:16:29Z

<p>Yong: </p> <hr /> <div>__TOC__<br /> <br /> Back to [[CTSC:CrossSiteImagingIdeas|CTSC_CrossSiteImagingIdeas]]<br /> <br /> = Overview =<br /> The CTSC Imaging Informatics Initiative (I3) is planning to provide services for setting up imaging data management systems (IDMS) in support of research and clinical efforts involving imaging in Harvard CTSC. XNAT has been identified for providing the core functionalities of the IDMS.<br /> A typical IDMS service will include the following steps:<br /> *Requirement gathering<br /> *Gap analysis<br /> *Infrastructure setup<br /> *Data modeling<br /> *IDMS installation and setup<br /> *Data loading<br /> *Testing and evaluation<br /> *Ongoing data entry, data loading/transfer, and system monitoring and maintenance<br /> *System upgrade<br /> <br /> = I3 Phases =<br /> == Planning and Information Gathering ==<br /> <br /> <br /> The goals of current phase of the initiative are to:<br /> #Gather concrete and specific requirements for imaging data transfer and management from a number of labs in Harvard CTSC; <br /> #Generate overlapping requirements from these specific needs; <br /> #Prioritize the potential projects to determine next steps; <br /> #Deploy a demo IDMS based on XNAT.<br /> <br /> The use cases presented here are based on on-going informal interviews with various labs and email communications.<br /> <br /> = Use Cases =<br /> (Template<br /> *Mission<br /> **Description of big picture, goal(s) of project<br /> *Participants<br /> *Data<br /> **Project<br /> **Imaging Modalities<br /> **Genetic<br /> **Workflow<br /> **other<br /> *Data transfer<br /> *Data Management)<br /> <br /> ==Clinical==<br /> <br /> *[[CTSC_Dan Iosifescu, MGH| Dan Iosifescu, MGH]]<br /> *[[CTSC_biomarkers_appendicitis| Biomarkers for appendicitis]]<br /> *[[CTSC_MCI| Mild cognitive impairment]]<br /> <br /> ==Research==<br /> <br /> *[[CTSC_Ellen Grant, CHB| Ellen Grant, CHB]]<br /> *[[CTSC_Stephan Voss, CHB| Stephan Voss, CHB]]<br /> *[[CTSC_Simon Warfield, CHB| Simon Warfield, CHB]]<br /> *[[CTSC_Bill Hanlon, DF/HCC| Bill Hanlon, DF/HCC]]<br /> *[[CTSC_COPD Gene Project, BWH| COPD Gene Project, BWH]]<br /> *[[CTSC_Brad Dickerson, MGH| Brad Dickerson]]<br /> <br /> = Project Prioritization Criteria=<br /> Possible criteria include:<br /> *Impact<br /> **Number of users<br /> **Duration of the project<br /> **Amount of data (# of subjects, # of scans ...)<br /> <br /> *Success Potential<br /> **Commitment of PI<br /> **Feasibility: is it a good fit for using XNAT?<br /> **Availability of project support at each stage of the effort, including requirement gathering, data collection, system testing, continuing IT and informatics support.<br /> <br /> = Current Status =<br /> Test installations of XNAT (1.4 release candidate 2) were done on Windows XP. Minor issues in the setup process needs to be fixed to make successful installation on Windows Vista. Effort on setting up XNAT on Linux running in VMware is underway. <br /> <br /> In addition, an evaluation of dcm4chee|[http://www.dcm4che.org] (a DICOM Implementation in JAVA) is in progress. Simon's group runs an instance of dcm4chee. XNAT's DicomServer and DicomBrowser are based on dcm4che.<br /> <br /> The Globus MEDICUS (Medical Imaging and Computing for Unified Information Sharing)|[http://dev.globus.org/wiki/Incubator/MEDICUS] has been proposed to provide an image sharing solution.</div>

Yong https://www.na-mic.org/w/index.php?title=CTSC_Imaging_Informatics_Initiative&diff=36963 CTSC Imaging Informatics Initiative 2009-05-01T22:14:46Z

<p>Yong: </p> <hr /> <div>__TOC__<br /> <br /> Back to [[CTSC:CrossSiteImagingIdeas|CTSC_CrossSiteImagingIdeas]]<br /> <br /> = Overview =<br /> The CTSC Imaging Informatics Initiative (I3) is planning to provide services for setting up imaging data management systems (IDMS) in support of research and clinical efforts involving imaging in Harvard CTSC. XNAT has been identified for providing the core functionalities of the IDMS.<br /> A typical IDMS service will include the following steps:<br /> *Requirement gathering<br /> *Gap analysis<br /> *Infrastructure setup<br /> *Data modeling<br /> *IDMS installation and setup<br /> *Data loading<br /> *Testing and evaluation<br /> *Ongoing data entry, data loading/transfer, and system monitoring and maintenance<br /> *System upgrade<br /> <br /> = I3 Phases =<br /> == Planning and Information Gathering ==<br /> <br /> <br /> The goals of current phase of the initiative are to:<br /> #Gather concrete and specific requirements for imaging data transfer and management from a number of labs in Harvard CTSC; <br /> #Generate overlapping requirements from these specific needs; <br /> #Prioritize the potential projects to determine next steps; <br /> #Deploy a demo IDMS based on XNAT.<br /> <br /> The use cases presented here are based on on-going informal interviews with various labs and email communications.<br /> <br /> = Use Cases =<br /> (Template<br /> *Mission<br /> **Description of big picture, goal(s) of project<br /> *Participants<br /> *Data<br /> **Project<br /> **Imaging Modalities<br /> **Genetic<br /> **Workflow<br /> **other<br /> *Data transfer<br /> *Data Management)<br /> <br /> ==Clinical==<br /> <br /> *[[CTSC_Dan Iosifescu, MGH| Dan Iosifescu, MGH]]<br /> *[[CTSC_biomarkers_appendicitis| Biomarkers for appendicitis]]<br /> *[[CTSC_MCI| Mild cognitive impairment]]<br /> <br /> ==Research==<br /> <br /> *[[CTSC_Ellen Grant, CHB| Ellen Grant, CHB]]<br /> *[[CTSC_Stephan Voss, CHB| Stephan Voss, CHB]]<br /> *[[CTSC_Simon Warfield, CHB| Simon Warfield, CHB]]<br /> *[[CTSC_Bill Hanlon, DF/HCC| Bill Hanlon, DF/HCC]]<br /> *[[CTSC_COPD Gene Project, BWH| COPD Gene Project, BWH]]<br /> *[[CTSC_Brad Dickerson, MGH| Brad Dickerson]]<br /> <br /> = Project Prioritization Criteria=<br /> Possible criteria include:<br /> *Impact<br /> **Number of users<br /> **Duration of the project<br /> **Amount of data (# of subjects, # of scans ...)<br /> <br /> *Success Potential<br /> **Commitment of PI<br /> **Feasibility: is it a good fit for using XNAT?<br /> **Availability of project support at each stage of the effort, including requirement gathering, data collection, system testing, continuing IT and informatics support.<br /> <br /> = Status =<br /> Test installations of XNAT (1.4 release candidate 2) were done on Windows XP. Minor issues in the setup process needs to be fixed to make successful installation on Windows Vista. Effort on setting up XNAT on Linux running in VMware is underway. <br /> <br /> In addition, an evaluation of dcm4chee|[http://www.dcm4che.org] (a DICOM Implementation in JAVA) is in progress. Simon's group runs an instance of dcm4chee. XNAT's DicomServer and DicomBrowser are based on dcm4che.<br /> <br /> The Globus MEDICUS (Medical Imaging and Computing for Unified Information Sharing)|[http://dev.globus.org/wiki/Incubator/MEDICUS] has been proposed to provide an image sharing solution.</div>

Yong https://www.na-mic.org/w/index.php?title=CTSC_Imaging_Informatics_Initiative&diff=36949 CTSC Imaging Informatics Initiative 2009-05-01T13:22:02Z

<p>Yong: </p> <hr /> <div>__TOC__<br /> <br /> Back to [[CTSC:CrossSiteImagingIdeas|CTSC_CrossSiteImagingIdeas]]<br /> <br /> = Overview =<br /> The CTSC Imaging Informatics Initiative (I3) is planning to provide services for setting up imaging data management systems (IDMS) in support of research and clinical efforts involving imaging in Harvard CTSC. XNAT has been identified for providing the core functionalities of the IDMS.<br /> A typical IDMS service will include the following steps:<br /> *Requirement gathering<br /> *Gap analysis<br /> *Infrastructure setup<br /> *Data modeling<br /> *IDMS installation and setup<br /> *Data loading<br /> *Testing and evaluation<br /> *Ongoing data entry, data loading/transfer, and system monitoring and maintenance<br /> *System upgrade<br /> <br /> = I3 Phases =<br /> == Planning and Information Gathering ==<br /> <br /> <br /> The goals of current phase of the initiative are to:<br /> #Gather concrete and specific requirements for imaging data transfer and management from a number of labs in Harvard CTSC; <br /> #Generate overlapping requirements from these specific needs; <br /> #Prioritize the potential projects to determine next steps; <br /> #Deploy a demo IDMS based on XNAT.<br /> <br /> The use cases presented here are based on on-going informal interviews with various labs and email communications.<br /> <br /> = Use Cases =<br /> <br /> ==Clinical==<br /> <br /> *[[CTSC_Dan Iosifescu, MGH| Dan Iosifescu, MGH]]<br /> *[[CTSC_biomarkers_appendicitis| Biomarkers for appendicitis]]<br /> *[[CTSC_MCI| Mild cognitive impairment]]<br /> <br /> ==Research==<br /> <br /> *[[CTSC_Ellen Grant, CHB| Ellen Grant, CHB]]<br /> *[[CTSC_Stephan Voss, CHB| Stephan Voss, CHB]]<br /> *[[CTSC_Simon Warfield, CHB| Simon Warfield, CHB]]<br /> *[[CTSC_Bill Hanlon, DF/HCC| Bill Hanlon, DF/HCC]]<br /> *[[CTSC_COPD Gene Project, BWH| COPD Gene Project, BWH]]<br /> *[[CTSC_Brad Dickerson, MGH| Brad Dickerson]]<br /> <br /> = Project Prioritization Criteria=<br /> Possible criteria include:<br /> *Impact<br /> **Number of users<br /> **Duration of the project<br /> **Amount of data (# of subjects, # of scans ...)<br /> <br /> *Success Potential<br /> **Commitment of PI<br /> **Feasibility: is it a good fit for using XNAT?<br /> **Availability of project support at each stage of the effort, including requirement gathering, data collection, system testing, continuing IT and informatics support.<br /> <br /> = Status =<br /> Test installations of XNAT (1.4 release candidate 2) were done on Windows XP. Minor issues in the setup process needs to be fixed to make successful installation on Windows Vista. Effort on setting up XNAT on Linux running in VMware is underway. <br /> <br /> In addition, an evaluation of dcm4chee|[http://www.dcm4che.org] (a DICOM Implementation in JAVA) is in progress. Simon's group runs an instance of dcm4chee. XNAT's DicomServer and DicomBrowser are based on dcm4che.<br /> <br /> The Globus MEDICUS (Medical Imaging and Computing for Unified Information Sharing)|[http://dev.globus.org/wiki/Incubator/MEDICUS] has been proposed to provide an image sharing solution.</div>

Yong https://www.na-mic.org/w/index.php?title=CTSC_COPD_Gene_Project,_BWH&diff=36948 CTSC COPD Gene Project, BWH 2009-05-01T02:43:59Z

<p>Yong: </p> <hr /> <div>Back to [[CTSC Imaging Informatics Initiative|CTSC Imaging Informatics Initiative]]<br /> <br /> <br /> =Mission=<br /> <br /> Sent by Ron Kikinis, James Ross at Surgical Planning and Channing labs made contact for a potential data management project based on XNAT. James Ross and Raúl San José Estépar have met with Randy Gollub and Dan Marcus before.<br /> <br /> =Participants=<br /> <br /> * PI, clinicians, IT staff, CT investigator, etc<br /> * staff missing<br /> <br /> = Data =<br /> The COPD (chronic obstructive pulmonary disease) Gene project is a five year research study being conducted by a group of doctors and scientists throughout the United States. The scope of the project is quite large, with a patient recruitment goal of 10,000 over five years (approximately 3,000 currently). Data includes:<br /> *CT scans used to phenotype the disease<br /> *Genetic information<br /> *Various derived data files (either additional, filtered datasets or summary statistics files in Excel) produced by a CT image-processing chain.<br /> <br /> = Data Management =<br /> <br /> There is currently no automated systematic mechanism for data transfer and data management. CT data was received on a hard disk drive and then transferred to local computers.<br /> <br /> Both James Ross and Raúl San José focus on image analysis. However they have the necessary training and willingness to take over a developed XNAT installation. They'd need help on developing customized data model (XML schema) and consultation on jump starting the project.</div>

Yong https://www.na-mic.org/w/index.php?title=CTSC_Imaging_Informatics_Initiative&diff=36779 CTSC Imaging Informatics Initiative 2009-04-29T00:21:08Z

<p>Yong: </p> <hr /> <div>__TOC__<br /> <br /> == Overview ==<br /> The CTSC Imaging Informatics Initiative (I3) is planning to provide services for setting up imaging data management systems (IDMS) in support of research and clinical efforts involving imaging in Harvard CTSC. XNAT has been identified for providing the core functionalities of the IDMS.<br /> A typical IDMS service will include the following steps:<br /> *Requirement gathering<br /> *Gap analysis<br /> *Infrastructure setup<br /> *Data modeling<br /> *IDMS installation and setup<br /> *Data loading<br /> *Testing and evaluation<br /> *Ongoing data entry, data loading/transfer, and system monitoring and maintenance<br /> *System upgrade<br /> <br /> The goals of current phase of the initiative are to: 1) gather concrete and specific requirements for imaging data transfer and management from a number of labs in Harvard CTSC; 2)generate overlapping requirements from these specific needs; 3) prioritize the potential projects to determine next steps; 4)Deploy a demo IDMS based on XNAT.<br /> <br /> The use cases presented here are based on on-going informal interviews with various labs and email communications.<br /> <br /> == Use Cases ==<br /> *[[Ellen Grant, CHB]]<br /> *[[Stephan Voss, CHB]]<br /> *[[Simon Warfield, CHB]]<br /> *[[Bill Hanlon, DF/HCC]]<br /> *[[COPD Gene Project, BWH]]<br /> *[[Brad Dickerson, MGH]]<br /> *[[Dan Iosifescu, MGH]]<br /> <br /> <br /> == Project Prioritization Criteria==<br /> Possible criteria include:<br /> *Impact<br /> **Number of users<br /> **Duration of the project<br /> **Amount of data (# of subjects, # of scans ...)<br /> <br /> *Success Potential<br /> **Commitment of PI<br /> **Feasibility: is it a good fit for using XNAT?<br /> **Availability of project support at each stage of the effort, including requirement gathering, data collection, system testing, continuing IT and informatics support.<br /> <br /> == Status ==<br /> Test installations of XNAT (1.4 release candidate 2) were done on Windows XP. Minor issues in the setup process needs to be fixed to make successful installation on Windows Vista. Effort on setting up XNAT on Linux running in VMware is underway. <br /> <br /> In addition, an evaluation of dcm4chee|[http://www.dcm4che.org] (a DICOM Implementation in JAVA) is in progress. Simon's group runs an instance of dcm4chee. XNAT's DicomServer and DicomBrowser are based on dcm4che.<br /> <br /> The Globus MEDICUS (Medical Imaging and Computing for Unified Information Sharing)|[http://dev.globus.org/wiki/Incubator/MEDICUS] has been proposed to provide an image sharing solution.</div>

Yong https://www.na-mic.org/w/index.php?title=CTSC_Bill_Hanlon,_DF/HCC&diff=36778 CTSC Bill Hanlon, DF/HCC 2009-04-28T20:21:47Z

<p>Yong: </p> <hr /> <div>See |[http://www.na-mic.org/Wiki/index.php/TIMC_Requirements_/_Use_Case]<br /> <br /> An XNAT-based IDMS is needed to function as a gateway between TIMC and RIS, HIS and PACS at all five DF/HCC institutions.<br /> <br /> In addition to image data, reports, schedules and patient history are also to be managed. <br /> <br /> Features such as ordering exams are beyond current XNAT offerings.</div>

Yong https://www.na-mic.org/w/index.php?title=CTSC_Imaging_Informatics_Initiative&diff=36776 CTSC Imaging Informatics Initiative 2009-04-28T16:41:00Z

<p>Yong: </p> <hr /> <div>__TOC__<br /> <br /> == Overview ==<br /> The CTSC Imaging Informatics Initiative (I3) is planning to provide services for setting up imaging data management systems (IDMS) in support of research and clinical efforts involving imaging in Harvard CTSC. XNAT has been identified for providing the core functionalities of the IDMS.<br /> A typical IDMS service will include the following steps:<br /> *Requirement gathering<br /> *Gap analysis<br /> *Infrastructure setup<br /> *Data modeling<br /> *IDMS installation and setup<br /> *Data loading<br /> *Testing and evaluation<br /> *Ongoing data entry, data loading/transfer, and system monitoring and maintenance<br /> *System upgrade<br /> <br /> The goals of current phase of the initiative are to: 1) gather concrete and specific requirements for imaging data transfer and management from a number of labs in Harvard CTSC; 2)generate overlapping requirements from these specific needs; 3) prioritize the potential projects to determine next steps; 4)Deploy a demo IDMS based on XNAT.<br /> <br /> The use cases presented here are based on on-going informal interviews with various labs and email communications.<br /> <br /> == Use Cases ==<br /> *[[Ellen Grant, CHB]]<br /> *[[Stephan Voss, CHB]]<br /> *[[Simon Warfield, CHB]]<br /> *[[Bill Hanlon, DF/HCC]]<br /> *[[COPD Gene Project, BWH]]<br /> *[[Brad Dickerson, MGH]]<br /> *[[Dan Iosifescu, MGH]]<br /> <br /> <br /> == Project Prioritization Criteria==<br /> Possible criteria include:<br /> *Impact<br /> **Number of users<br /> **Duration of the project<br /> **Amount of data (# of subjects, # of scans ...)<br /> <br /> *Success Potential<br /> **Commitment of PI<br /> **Feasibility: is it a good fit for using XNAT?<br /> **Availability of project support at each stage of the effort, including requirement gathering, data collection, system testing, continuing IT and informatics support.<br /> <br /> == Status ==<br /> Test installations of XNAT (1.4 release candidate 2) were done on Windows XP. Minor issues in the setup process needs to be fixed to make successful installation on Windows Vista. Effort on setting up XNAT on Linux running in VMware is underway. <br /> <br /> In addition, an evaluation of dcm4chee|[http://www.dcm4che.org] (a DICOM Implementation in JAVA) is in progress. Simon's group runs an instance of dcm4chee. XNAT's DicomServer and DicomBrowser are based on dcm4che.<br /> <br /> The Globus MEDICUS (Medical Imaging and Computing for Unified Information Sharing)|[http://dev.globus.org/wiki/Incubator/MEDICUS] has been discussed to provide an image sharing solution.</div>

Yong https://www.na-mic.org/w/index.php?title=CTSC_Imaging_Informatics_Initiative&diff=36775 CTSC Imaging Informatics Initiative 2009-04-28T15:31:36Z

<p>Yong: </p> <hr /> <div>__TOC__<br /> <br /> == Overview ==<br /> The CTSC Imaging Informatics Initiative (I3) is planning to provide services for setting up imaging data management systems (IDMS) in support of research and clinical efforts involving imaging in Harvard CTSC. XNAT has been identified for providing the core functionalities of the IDMS.<br /> A typical IDMS service will include the following steps:<br /> *Requirement gathering<br /> *Gap analysis<br /> *Infrastructure setup<br /> *Data modeling<br /> *IDMS installation and setup<br /> *Data loading<br /> *Testing and evaluation<br /> *Ongoing data entry, data loading/transfer, and system monitoring and maintenance<br /> *System upgrade<br /> <br /> The goals of current phase of the initiative are to: 1) gather concrete and specific requirements for imaging data transfer and management from a number of labs in Harvard CTSC; 2)generate overlapping requirements from these specific needs; 3) prioritize the potential projects to determine next steps; 4)Deploy a demo IDMS based on XNAT.<br /> <br /> The use cases presented here are based on on-going informal interviews with various labs and email communications.<br /> <br /> == Use Cases ==<br /> *[[Ellen Grant, CHB]]<br /> *[[Stephan Voss, CHB]]<br /> *[[Simon Warfield, CHB]]<br /> *[[Bill Hanlon, MGH]]<br /> *[[COPD Gene Project, BWH]]<br /> *[[Brad Dickerson, MGH]]<br /> *[[Dan Iosifescu, MGH]]<br /> <br /> <br /> == Project Prioritization Criteria==<br /> Possible criteria include:<br /> *Impact<br /> **Number of users<br /> **Duration of the project<br /> **Amount of data (# of subjects, # of scans ...)<br /> <br /> *Success Potential<br /> **Commitment of PI<br /> **Feasibility: is it a good fit for using XNAT?<br /> **Availability of project support at each stage of the effort, including requirement gathering, data collection, system testing, continuing IT and informatics support.<br /> <br /> == Status ==<br /> Test installations of XNAT (1.4 release candidate 2) were done on Windows XP. Minor issues in the setup process needs to be fixed to make successful installation on Windows Vista. Effort on setting up XNAT on Linux running in VMware is underway. <br /> <br /> In addition, an evaluation of dcm4chee|[http://www.dcm4che.org] (a DICOM Implementation in JAVA) is in progress. Simon's group runs an instance of dcm4chee. XNAT's DicomServer and DicomBrowser are based on dcm4che.<br /> <br /> The Globus MEDICUS (Medical Imaging and Computing for Unified Information Sharing)|[http://dev.globus.org/wiki/Incubator/MEDICUS] has been discussed to provide an image sharing solution.</div>

Yong https://www.na-mic.org/w/index.php?title=CTSC_Bill_Hanlon,_DF/HCC&diff=36773 CTSC Bill Hanlon, DF/HCC 2009-04-28T15:30:29Z

<p>Yong: moved Bill Hanlon, MGH to Bill Hanlon, DF/HCC</p> <hr /> <div>See |[http://www.na-mic.org/Wiki/index.php/TIMC_Requirements_/_Use_Case]</div>

Yong https://www.na-mic.org/w/index.php?title=Bill_Hanlon,_MGH&diff=36774 Bill Hanlon, MGH 2009-04-28T15:30:29Z

<p>Yong: moved Bill Hanlon, MGH to Bill Hanlon, DF/HCC</p> <hr /> <div>#REDIRECT [[Bill Hanlon, DF/HCC]]</div>

Yong