https://www.na-mic.org/w/api.php?action=feedcontributions&user=RandyGollub&feedformat=atomNAMIC Wiki - User contributions [en]2024-03-28T16:35:30ZUser contributionsMediaWiki 1.33.0https://www.na-mic.org/w/index.php?title=2016_Winter_Project_Week&diff=916092016 Winter Project Week2016-01-04T18:23:19Z<p>RandyGollub: /* Image Analysis */</p>
<hr />
<div>__NOTOC__<br />
[[image:PW-MIT2016.png|300px]]<br />
<br />
'''Dates:''' January 4-8, 2016<br />
<br />
'''Location:''' [https://www.google.com/maps/place/MIT:+Computer+Science+and+Artificial+Intelligence+Laboratory/@42.361864,-71.090563,16z/data=!4m2!3m1!1s0x0:0x303ada1e9664dfed?hl=en MIT CSAIL], Cambridge, MA. (Rooms: [[MIT_Project_Week_Rooms#Kiva|Kiva]], R&D)<br />
<br />
'''REGISTRATION:''' Register [https://www.regonline.com/namic16 here].<br />
<br><br />
<br />
== Introduction ==<br />
Founded in 2005, the National Alliance for Medical Image Computing (NAMIC), was chartered with building a computational infrastructure to support biomedical research as part of the NIH funded [http://www.ncbcs.org/ NCBC] program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform [http://www.slicer.org 3D Slicer], built using [http://www.vtk.org VTK], [http://www.itk.org ITK], [http://www.cmake.org CMake], and [http://www.cdash.org CDash], and the creation of a community of algorithm researchers, biomedical scientists and software engineers who are committed to open science. This community meets twice a year in an event called Project Week. <br />
<br />
[[Engineering:Programming_Events|Project Week]] is a semi-annual event which draws 80-120 researchers. As of August 2014, it is a [http://www.miccai.org/organization MICCAI] endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event. <br />
<br />
Project Week activities: Everyone shows up with a project. Some people are working on the platform. Some people are developing algorithms. Some people are applying the tools to their research problems. We begin the week by introducing projects and connecting teams. We end the week by reporting progress. In addition to the ongoing working sessions, breakout sessions are organized ad-hoc on a variety of special topics. These topics include: discussions of software architecture, presentations of new features and approaches and topics such as Image-Guided Therapy.<br />
<br />
Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], and [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO]. <br />
<br />
A summary of all previous Project Events is available [[Project_Events#Past|here]].<br />
<br />
This project week is an event [[Post-NCBC-2014|endorsed]] by the MICCAI society.<br />
<br />
Please make sure that you are on the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]<br />
<br />
==Agenda==<br />
<br />
{|border="1"<br />
|-style="background:#b0d5e6;color:#02186f" <br />
!style="width:10%" |Time<br />
!style="width:18%" |Monday, January 4<br />
!style="width:18%" |Tuesday, January 5<br />
!style="width:18%" |Wednesday, January 6<br />
!style="width:18%" |Thursday, January 7<br />
!style="width:18%" |Friday, January 8<br />
|-<br />
|<br />
|bgcolor="#dbdbdb"|'''Project Presentations''' <br />
|bgcolor="#6494ec"| '''Work on Projects'''<br />
|bgcolor="#6494ec"| '''Work on Projects'''<br />
|bgcolor="#88aaae"|'''IGT Day'''<br />
|bgcolor="#faedb6"|'''Reporting Day'''<br />
|-<br />
|bgcolor="#ffffdd"|'''8:30am'''<br />
|<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast <br />
|-<br />
|bgcolor="#ffffdd"|'''9:00am-12:00pm'''<br />
|'''10:30am-12pm:''' [Tutorial] Diffeomorphic registration and geodesic shooting methods (I). (Sarang Joshi)<br> Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].<br />
|'''10:00-11:30am:''' Breakout Session:[[2016_Winter_Project_Week/Breakout_Sessions/NewSlicerExtensions | Slicer Extensions Birds of a Feather]]<br />
|<br />
'''10:00-11:30am:''' Breakout Session: [[2016_Winter_Project_Week/Breakout_Sessions/SlicerForMedicalRoboticsResearch| Slicer for Medical Robotics Research]]<br />
<br><br />
|'''8:30-9:30am''' [[2016_Winter_Project_Week/Breakout_Sessions/IGT#Image-guided Breast Surgery| MR, US, Mass Spect guided Breast Surgery]] (Melissa Mallory, Nathalie Agar, Gabrielle Gauvin, Andras Lasso) <br><br />
'''9:30-10:30am''' [[2016_Winter_Project_Week/Breakout_Sessions/IGT#Image-guided Neurosurgery| Clinical perspective on Image Guided Neurosurgery]] (Alexandra Golby) <br><br />
'''10:30-11:30am''' [[2016_Winter_Project_Week/Breakout_Sessions/IGT#Multiparametric MRI| Clinical perspective on Multiparametric MRI]] (Fiona Fennessy)<br><br />
'''11:30am-12pm''' [[2016_Winter_Project_Week/Breakout_Sessions/IGT#Drug Delivery to Brain|Drug Delivery to Brain]] <br><br />
|'''10:00am-12:00pm:''' [[#Projects|Project Progress Updates]]<br> <br />
[[MIT_Project_Week_Rooms#Kiva|Kiva]]<br />
<br>-----------------<br><br />
'''12pm:''' [[Events:TutorialContestJanuary2016|Tutorial Contest Winner Announcement]]<br> <br />
[[MIT_Project_Week_Rooms#Kiva|Kiva]]<br />
|-<br />
|bgcolor="#ffffdd"|'''12:00pm-1:00pm'''<br />
|bgcolor="#ffffaa"|Lunch <br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm<br />
|-<br />
|bgcolor="#ffffdd"|'''1:00-5:30pm'''<br />
|'''1:00pm-1:05pm: <font color="#503020">Welcome</font>'''<br> <br />
[[MIT_Project_Week_Rooms#Kiva|Kiva]]<br />
<br>-----------------<br><br />
'''1:05-2:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)<br><br />
[[MIT_Project_Week_Rooms#Kiva|Kiva]]<br />
<br>-----------------<br><br />
'''2:45-4:00pm:''' Breakout Session: [[2016_Winter_Project_Week/Breakout_Sessions/Ultrasound| Ultrasound]]<br><br />
[[MIT_Project_Week_Rooms#Kiva|Kiva]]<br />
<br>-----------------<br><br />
<br />
'''4:00-5:30pm:''' [Tutorial] Diffeomorphic registration geodesic shooting methods (II). (Sarang Joshi) <br> Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].<br />
|<br />
|'''1:00-2:30pm:''' Breakout Session:[[2016_Winter_Project_Week/Breakout_Sessions/DiffusionMRI| Diffusion MRI]]<br><br />
[[MIT_Project_Week_Rooms#Kiva|Kiva]] <br><br />
'''3:00-4:30pm:''' Breakout Session:[[2016_Winter_Project_Week/Breakout_Sessions/QIICRTools| QIICR Tools]]<br />
|'''1:00-3:00pm:''' Breakout Session:[[2016_Winter_Project_Week/Breakout_Session/What's_Planned_for_Slicer_Core|What's Planned for Slicer Core]]<br><br />
[[MIT_Project_Week_Rooms#Kiva|Kiva]] <br />
|<br />
|-<br />
|bgcolor="#ffffdd"|'''5:30pm'''<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|<br />
|}<br />
<br />
==Calendar==<br />
{{#widget:Google Calendar<br />
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com<br />
|timezone=America/New_York&dates=20160103%2F20160110<br />
|title=NAMIC Winter Project Week<br />
|view=WEEK<br />
|dates=20160103/20160110<br />
}}<br />
<br />
iCal (.ics) link: https://calendar.google.com/calendar/ical/kitware.com_sb07i171olac9aavh46ir495c4%40group.calendar.google.com/public/basic.ics<br />
<br />
='''Projects'''=<br />
*Use this [[2016_Project_Week_Template | Updated Template for project pages]]<br />
<br />
== IGT ==<br />
* [[2016_Winter_Project_Week/Projects/SlicerROSIntegration | 3D Slicer + ROS Integration]] (Junichi Tokuda, Axel Krieger, Simon Leonard, Jayender Jagadeesan)<br />
* [[2016_Winter_Project_Week/Projects/External_beam_planning | External Beam Radiotherapy Planning]] (Greg Sharp, others)<br />
* [[2016_Winter_Project_Week/Projects/CryoPlanningSlicerModule | CryoPlanning Module in Slicer]] (Jayender Jagadeesan, Steve Pieper, Sandy Wells)<br />
* [[2016_Winter_Project_Week/Projects/TrackedUltrasoundStandardization | Tracked Ultrasound Standardization]] (Andras Lasso, Christian Askeland, Simon Drouin, Junichi Tokuda, Steve Pieper, Adam Rankin)<br />
*[[2016_Winter_Project_Week/Projects/IntegrationCustusX|Integration of CustusX with PLUS on BK System]] (Christian A, Andras Lasso, Adam Rankin)<br />
*[[2016_Winter_Project_Week/Projects/MITK_Plus_Integration | Integration of Plus and MITK]] (Thomas Kirchner, Janek Groehl)<br />
*[[2016_Winter_Project_Week/Projects/IntegrationImFusion| Integration of ImFusion MR-US Registration with BWH AMIGO Neurosurgery Setup]] (Sarah Frisken, Tina Kapur, Steve Pieper, Sandy Wells, Andras Lasso, Christian Askelan)<br />
* [[2016_Winter_Project_Week/Projects/PLUS | Improvement of PLUS communication with Slicer]] (Adam Rankin)<br />
* [[2016_Winter_Project_Week/Projects/SliceTracker | Prostate motion tracking and navigation in Slicer ]] (Christian Herz, Andrey Fedorov)<br />
* [[2016_Winter_Project_Week/Projects/EVD |Measuring Anatomic Factors for Extraventricular Drain Placement]] (Kirby Vosburgh, P. Jason White)<br />
* [[2016_Winter_Project_Week/Projects/GABA_Delivery |Localized GABA delivery via BBB disruption]] (Nick Todd)<br />
<br />
== Tractography ==<br />
* [[2016_Winter_Project_Week/Projects/Tractography_format_interoperability | Tractography Format Interoperability]] (Isaiah Norton, Michael Onken, Lauren O'Donnell, others)<br />
* [[2016_Winter_Project_Week/Projects/SlicerDMRI_documentation | Slicer Diffusion MR / tractography workflow documentation]] (Pegah Kahaliardabili, Fan Zhang, Isaiah Norton, Lauren O'Donnell, others)<br />
* [[2016_Winter_Project_Week/Projects/TractographyModuleDevelop&Test | Tractography Analysis Module Development and Testing]] (Fan Zhang, Pegah Kahaliardabili, Isaiah Norton, Lauren O'Donnell, others)<br />
<br />
==Image Analysis==<br />
* [[2016_Winter_Project_Week/Projects/ImageRestoration | Image Restoration via Patch GMMs]] (Adrian Dalca, Katie Bouman, Polina Golland)<br />
* [[2016_Winter_Project_Week/Projects/PatchRegistration | Patch Based Discrete Registration for Difficult Images]] (Adrian Dalca, Andreea Bobu, Polina Golland)<br />
* [[2016_Winter_Project_Week/Projects/SphericalWaveletShapeAnalysis|Spherical Wavelet Shape Analysis]] (Yi Gao, Erich Bremer, Allen Tannenbaum, Ron Kikinis)<br />
* [[2016_Winter_Project_Week/Projects/DigitalPathologyNuclearSegmentation|Digital Pathology Nuclear Segmentation]] (Erich Bremer, Kelli Xu, Yi Gao, Nicole Aucoin, Andrey Fedorov)<br />
* [[2016_Winter_Project_Week/Projects/SlicerCMFNextSteps | Moving beyond SlicerCMF and Future Projects]] (Beatriz Paniagua, Lucia Cevidanes, Steve Pieper, Juan Prieto)<br />
*[[2016_Winter_Project_Week/Projects/ChestImagingPlatform|Chest Imaging Platform: COPD and Other Pulmonary Diseases]] (Raúl San José, Jorge Onieva, James Ross)<br />
* [[2016_Winter_Project_Week/Projects/ChestImagingPlatformWorkflows|Nipype Workflows for the Chest Imaging Platform]] (James Ross, Raúl San José)<br />
* [[2016 Winter Project Week/Projects/Cluster-Driven Lung Segmentation | Cluster-Driven Segmentation of Lung Nodules]] (Vivek Narayan, Raúl San José, Daniel Blezek, Steve Pieper, Chintan Parmar)<br />
* [[2016_Winter_Project_Week/Projects/BatchImageAnalysis | Batch Clinical Image Analysis]] (Sandy Wells, Kalli Retzepi, Yangming Ou, Matt Toews, Steve Pieper, Randy Gollub)<br />
* [[2016_Winter_Project_Week/Projects/SlicerOpenCVExtension | Slicer OpenCV Extension]] (Nicole Aucoin, Erich Bremer, Andrey Fedorov)<br />
* [[2016_Winter_Project_Week/Projects/Interactive4DSegmentation | Interactive 4D Segmentation Module]] (Ethan Ulrich, Andrey Fedorov)<br />
* [[2016_Winter_Project_Week/Projects/CongenitalHeart | Interactive patch-based segmentation for congenital heart disease]] (Danielle Pace, Adrian Dalca, Polina Golland)<br />
* [[2016_Winter_Project_Week/Projects/DSCAnalysis | Dynamic Susceptibility Contrast (DSC) MRI Analysis]] (Xiao Da, Yangming Ou, Andriy Fedorov, Steve Pieper, Jayashree Kalpathy-Cramer)<br />
<br />
* [[2016_Winter_Project_Week/Projects/ShapeAnalysis | Low-dimensional Principal Geodesic Analysis On the Manifold of Diffeomorphisms]] (Miaomiao Zhang, Polina Golland)<br />
<br />
==Infrastructure==<br />
*[[2016_Winter_Project_Week/Projects/UpgradeNAMICSlicerWiki|Upgrade the NAMIC (and Slicer?) Wiki]] (Mike Halle, JC)<br />
* [[2016_Winter_Project_Week/Projects/CommonDataStructure | Common Data Structure for CMF modules in Slicer]] (Jean-Baptiste Vimort, François Budin, Lucia Cevidanes, Beatriz Paniagua, Steve Pieper, Juan Prieto)<br />
* [[2016_Winter_Project_Week/Projects/StatisticalShapeModeling | Statistical Shape Modeling in Slicer: OA Index]] (Laura Pascal, Beatriz Paniagua, François Budin, Lucia Cevidanes, Steve Pieper, Juan Prieto)<br />
* [[2016_Winter_Project_Week/Projects/CommonGL | CommonGL]] (Steve Pieper, Jim Miller)<br />
* [[2016_Winter_Project_Week/Projects/CLIModules Backgrounding in MeVisLab | Running CLI Modules in MeVisLab Asynchronously]] (Hans Meine)<br />
* [[2016_Winter_Project_Week/Projects/BRAINSFit_in_MeVisLab | Interoperability Tests with BRAINSFit (or other interesting CLIs) in MeVisLab]] (Hans Meine, Steve Pieper)<br />
* [[2016_Winter_Project_Week/Projects/CLI_Dashboard | Kibana Dashboard for Browsing All Available CLI Modules]] (Hans Meine, JC?)<br />
* [[2016_Winter_Project_Week/Projects/SegmentationEditorWidget | Editor Widget using Segmentations]] (Csaba Pinter, Andras Lasso, Andrey Fedorov, Steve Pieper)<br />
* [[2016_Winter_Project_Week/Projects/SlicerTerminologyEditor | Terminology Editor]] (Nicole Aucoin, Csaba Pinter, Andrey Fedorov)<br />
* [[2016_Winter_Project_Week/Projects/DICOMSegObjIntegration | Integration of DICOM Segmentation Image Storage with Segmentations Module]] (Kyle Sunderland, Csaba Pinter, Andras Lasso, Andrey Fedorov, Steve Pieper?)<br />
* [[2016_Winter_Project_Week/Projects/CondaSlicer | Integration of Anaconda Python in Slicer]] (JC, Raúl San José, Jorge Onieva, Slicer Community?)<br />
* [[2016_Winter_Project_Week/Projects/Data Persisting | Mechanism to Persist Clinical User Data from Different Modules Based on SQLite and/or other Database Engines ]] (Raúl San José, Jorge Onieva)<br />
* [[2016_Winter_Project_Week/Projects/Workflows | Workflow Module that Enables the Navigation and Data Sharing between Different Modules in a Clinical Workflow ]] (Raúl San José, Jorge Onieva)<br />
* [[2016_Winter_Project_Week/Projects/AIMInteroperability | AIM for Interoperability]] (Hans Meine, Andrey Fedorov, ??)<br />
* [[2016_Winter_Project_Week/Projects/PLUSOCR | Exploration of open-source OCR libraries for device meta-data capture without research interface ]] (Adam Rankin)<br />
* [[2016_Winter_Project_Week/Projects/3DNrrdSequences | Sequences extension support for 3D+t NRRD]] (Adam Rankin)<br />
* [[2016_Winter_Project_Week/Projects/SlicerEnhancedMR | Developing support for Enhanced MR in Slicer]] (Michael Onken, Andrey Fedorov)<br />
* [[2016_Winter_Project_Week/Projects/CLIImprovement| Improve CLI robustness and testing]] (Johan Andruejol)<br />
<br />
= '''Logistics''' =<br />
<br />
*'''Dates:''' January 4-8, 2016<br />
*'''Location:''' MIT, Kiva Conference room; 4th floor of Building 32.<br />
*'''REGISTRATION:''' Register [https://www.regonline.com/namic16 here]. Registration Fee: $300.<br />
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.<br />
*'''Room sharing''': If interested, add your name to the list [[2016_Winter_Project_Week/RoomSharing|here]]<br />
<br />
= '''Registrants''' =<br />
<br />
Do not add your name to this list - it is maintained by the organizers based on your paid registration. To register, visit this [https://www.regonline.com/namic16 registration site].<br />
<br />
<br />
#Polina Golland, MIT<br />
#Ron Kikinis, BWH<br />
#Nicole Aucoin, BWH/SPL<br />
#Peter Anderson<br />
#Daniel Blezek, Isomics, Inc.<br />
#Lucia Cevidanes, University of Michigan<br />
#Adrian Dalca, MIT<br />
#Simon Drouin, Montreal Neurological Institute<br />
#Janek Groehl, German Cancer Research Center<br />
#Tina Kapur, BWH/HMS<br />
#Thomas Kirchner, German Cancer Research Center<br />
#Hans Meine, University of Bremen/MEVIS<br />
#Vivek Narayan, Dana Farber Cancer Institute<br />
#Danielle Pace, MIT<br />
#Laura Pascal, University of Michigan<br />
#Steve Pieper, Isomics, Inc.<br />
#Csaba Pinter, Queen's University<br />
#Gregory Sharp, MGH<br />
#James Miller, GE Research<br />
#Kyle Sunderland, Queen's University<br />
#Ethan Ulrich, University of Iowa<br />
#Jean-Baptiste Vimort, University of Michigan<br />
#Miaomiao Zhang, MIT<br />
#Beatriz Paniagua, University of North Carolina at Chapel Hill<br />
#Sonia Pujol, BWH<br />
#Junichi Tokuda, BWH<br />
#Katie Mastrogiacomo, BWH<br />
#Niravkumar Patel, Worcester Polytechnic Institute <br />
#Michael Onken, Open Connections (Germany)<br />
#Erich Bremer, Stony Brook University<br />
#Xiao Da, MGH<br />
#Tobias Frank, Leibniz Universität Hannover<br />
#Kirby Vosburgh, BWH<br />
#P. Jason White, BWH<br />
#Lauren O'Donnell, BWH<br />
#Pegah Kahali, BWH<br />
#Fan Zhang, BWH<br />
#Adam Rankin, Robarts Research Institute <br />
#Simon Leoard, Johns Hopkins University<br />
#David Gering, HealthMyne<br />
#Johan Andruejol, Kitware<br />
#Jean-Christophe Fillion-Robin, Kitware<br />
#Kelli Xu, MIT<br />
#Christian Askeland, SINTEF<br />
#Katharine Carter, BWH<br />
#Nick Todd, BWH<br />
#Ye Cheng, BWH<br />
#Andriy Fedorov, BWH/HMS<br />
#Sudhanshu Semwal, UCCS Professor<br />
#Michael Halle, BWH<br />
#Kallirroi Retzepi, MGH<br />
#Jayender Jagadeesan, BWH<br />
#Nathalie Agar, BWH<br />
#Curtis Lisle, KnowledgeVis, LLC<br />
#Andras Lasso, PerkLab, Queen's University<br />
#Sarah Frisken, BWH<br />
#Yi Gao, Stony Brook University<br />
#Christian Herz, BWH<br />
#Prashin Unadkat, SPL/BWH<br />
#Jorge Onieva, BWH<br />
#James Ross, BWH<br />
#Raul SanJose, BWH<br />
#Jayashree Kalpathy-Cramer, MGH/HMS<br />
#Daniel Glazer, BWH<br />
#Valentin Demeusy, SPL Intern<br />
#Ameet Jain, Phillips Research<br />
#Utsav Soni, BWH<br />
#Matthew Toews, Ecole de Technologie Superieure<br />
#Isaiah Norton, BWH<br />
#Sean Doyle, MGH<br />
#Stuart Pomerantz, MGH<br />
#Randy Gollub, MGH<br />
#Melissa Mallory, BWH<br />
#Axel Krieger, Children's National Medical Center<br />
#Nobuhiko Hata, BWH</div>RandyGollubhttps://www.na-mic.org/w/index.php?title=2016_Winter_Project_Week/Projects/BatchImageAnalysis&diff=907162016 Winter Project Week/Projects/BatchImageAnalysis2015-12-10T15:22:16Z<p>RandyGollub: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2016.png|[[2016_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Kalli Retzepi (MGH)<br />
* Yangming Ou (MGH)<br />
* Matt Toews (?)<br />
* Steve Pieper (BWH)<br />
* Sandy Wells (BWH)<br />
* Randy Gollub (MGH)<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
*<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
*<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
*<br />
</div><br />
</div></div>RandyGollubhttps://www.na-mic.org/w/index.php?title=2016_Winter_Project_Week/Projects/BatchImageAnalysis&diff=907152016 Winter Project Week/Projects/BatchImageAnalysis2015-12-10T15:21:16Z<p>RandyGollub: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2016.png|[[2016_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Kalli Retzepi<br />
* Yangming Ou<br />
* Matt Toews<br />
* Steve Pieper<br />
* Sandy Wells<br />
* Randy Gollub<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
*<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
*<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
*<br />
</div><br />
</div></div>RandyGollubhttps://www.na-mic.org/w/index.php?title=2016_Winter_Project_Week/Projects/BatchImageAnalysis&diff=907142016 Winter Project Week/Projects/BatchImageAnalysis2015-12-10T15:17:06Z<p>RandyGollub: /* Key Investigators */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2016.png|[[2016_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
Kalli Retzepi<br />
Yangming Ou<br />
Matt Toews<br />
Steve Pieper<br />
Sandy Wells<br />
Randy Gollub<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
*<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
*<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
*<br />
</div><br />
</div></div>RandyGollubhttps://www.na-mic.org/w/index.php?title=2016_Winter_Project_Week&diff=905702016 Winter Project Week2015-11-24T21:49:53Z<p>RandyGollub: /* Projects */</p>
<hr />
<div>__NOTOC__<br />
<br />
[[image:PW-MIT2016.png|300px|left]]<br />
<br><br><br><br><br><br><br><br><br><br><br><br><br />
'''Dates:''' January 4-8, 2016<br />
<br />
'''Location:''' MIT, Cambridge, MA. (Rooms: [[MIT_Project_Week_Rooms#Kiva|Kiva]], R&D)<br />
<br><br />
<br />
== Introduction ==<br />
Founded in 2005, the National Alliance for Medical Image Computing (NAMIC), was chartered with building a computational infrastructure to support biomedical research as part of the NIH funded [http://www.ncbcs.org/ NCBC] program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform [http://www.slicer.org 3D Slicer], built using [http://www.vtk.org VTK], [http://www.itk.org ITK], [http://www.cmake.org CMake], and [http://www.cdash.org CDash], and the creation of a community of algorithm researchers, biomedical scientists and software engineers who are committed to open science. This community meets twice a year in an event called Project Week. <br />
<br />
[[Engineering:Programming_Events|Project Week]] is a semi-annual event which draws 80-120 researchers. As of August 2014, it is a MICCAI endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event. <br />
<br />
Project Week activities: Everyone shows up with a project. Some people are working on the platform. Some people are developing algorithms. Some people are applying the tools to their research problems. We begin the week by introducing projects and connecting teams. We end the week by reporting progress. In addition to the ongoing working sessions, breakout sessions are organized ad-hoc on a variety of special topics. These topics include: discussions of software architecture, presentations of new features and approaches and topics such as Image-Guided Therapy.<br />
<br />
Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], and [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO]. <br />
<br />
A summary of all previous Project Events is available [[Project_Events#Past|here]].<br />
<br />
This project week is an event [[Post-NCBC-2014|endorsed]] by the MICCAI society.<br />
<br />
Please make sure that you are on the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]<br />
<br />
==Agenda==<br />
<br />
Tentative Agenda<br />
<br />
{|border="1"<br />
|-style="background:#b0d5e6;color:#02186f" <br />
!style="width:10%" |Time<br />
!style="width:18%" |Monday, January 4<br />
!style="width:18%" |Tuesday, January 5<br />
!style="width:18%" |Wednesday, January 6<br />
!style="width:18%" |Thursday, January 7<br />
!style="width:18%" |Friday, January 8<br />
|-<br />
|<br />
|bgcolor="#dbdbdb"|'''Project Presentations''' <br />
|bgcolor="#6494ec"|<br />
|<br />
|bgcolor="#88aaae"|'''IGT Day'''<br />
|bgcolor="#faedb6"|'''Reporting Day'''<br />
|-<br />
|bgcolor="#ffffdd"|'''8:30am'''<br />
|<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast <br />
|-<br />
|bgcolor="#ffffdd"|'''9am-12pm'''<br />
|'''10:30am-12pm:''' '''Diffeomorphic registration and the more recent geodesic shooting methods for diffeomorphic registration.''' (Tutorial Part 1 by Sarang Joshi)<br> Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].<br />
|'''10-11:30am:''' <font color="#503020">Breakout Session: New Slicer Extensions'''</font><br><br />
|<br />
'''10-11:30am:''' <font color="#503020">Breakout Session: [[2015_Winter_Project_Week:SlicerROSIntegration| Slicer for Medical Robotics Research]] </font><br />
<br><br />
|'''9:00-10:30am''' TBD <br><br />
<br>----------------------------------------<br><br />
'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>TBD <br><br />
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]<br><br />
[[MIT_Project_Week_Rooms#Kiva|Kiva]]<br />
<br>----------------------------------------<br><br />
'''12pm''' [[Events:TutorialContestJune2014|Tutorial Contest Winner Announcement]]<br><br />
[[MIT_Project_Week_Rooms#Kiva|Kiva]]<br />
|-<br />
|bgcolor="#ffffdd"|'''12pm-1pm'''<br />
|bgcolor="#ffffaa"|Lunch <br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm<br />
|-<br />
|bgcolor="#ffffdd"|'''1pm-5:30pm'''<br />
|'''1-1:05pm: <font color="#503020">Welcome</font>'''<br><br />
[[MIT_Project_Week_Rooms#Kiva|Kiva]]<br />
<br>----------------------------------------<br><br />
'''1:05-2:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)<br><br />
[[MIT_Project_Week_Rooms#Kiva|Kiva]]<br />
<br>----------------------------------------<br><br />
'''2:45-4pm:''' [[Breakout Session: Ultrasound]]<br />
[[MIT_Project_Week_Rooms#Kiva|Kiva]]<br />
<br>----------------------------------------<br><br />
<br />
'''4:00pm-5:30pm:''' '''Diffeomorphic registration and the more recent geodesic shooting methods for diffeomorphic registration.''' (Tutorial Part 2 by Sarang Joshi) <br> Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].<br />
|'''1-3pm:''' <font color="#503020"> [[Breakout Session: What's Planned for Slicer Core]]<br><br />
[[MIT_Project_Week_Rooms#Kiva|Kiva]] <br />
|'''1-2:30pm:''' <font color="#503020">Breakout Session:'''</font><br>[[Breakout Session: Diffusion MRI]]<br />
[[MIT_Project_Week_Rooms#Kiva|Kiva]] <br />
|<br />
|<br />
|-<br />
|bgcolor="#ffffdd"|'''5:30pm'''<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|<br />
|}<br />
<br />
<googlecalendar>kitware.com_sb07i171olac9aavh46ir495c4</googlecalendar><br />
<br />
='''Projects'''=<br />
* [[2016_Project_Week_Template | Template for project pages]]<br />
<br />
<br />
* [[2015_Winter_Project_Week:SlicerROSIntegration | 3D Slicer + ROS Integration]] (Junichi Tokuda, Axel Krieger, Simon Leonard)<br />
* [[2016_Winter_Project_Week:TrackedUltrasoundStandardization | Tracked ultrasound standardization]] (Andras Lasso, Christian Askeland, Simon Drouin, Junichi Tokuda, Steve Pieper, Adam Rankin)<br />
*Integration of CustusX with PLUS on BK System (Christian A)<br />
*Integration of ImFusion MR-US registration with BWH AMIGO neurosurgery setup (Christian A, Tina Kapur, Steve Pieper, Sandy Wells, Andras Lasso)<br />
*Digital Pathology Nuclear Segmentation (Erich Bremer, Nicole Aucoin)<br />
*Chest Imaging Platform: COPD and other pulmonary diseases (Raúl San José, Jorge Onieva)<br />
*Upgrade the namic wiki (JC, Mike Halle)<br />
* [[2016_Winter_Project_Week:BatchImageAnalysis | Batch Clinical Image Analysis]] (Kalli Retzepi, Yangming Ou, Matt Toews, Steve Pieper, Sandy Wells, Randy Gollub)<br />
<br />
==Infrastructure==<br />
* [[2016_Winter_Project_Week:SlicerProjectName | Project Name]] (List of people working on this project)<br />
* [[2016_Winter_Project_Week:CommonGL | CommonGL]] (Steve Pieper, Jim Miller)<br />
* [[2016_Winter_Project_Week:WebTechnologies | Web Technologies and Slicer]] (Steve Pieper, Hans Meine)<br />
<br />
= '''Logistics''' =<br />
<br />
*'''Dates:''' January 4-8, 2016<br />
*'''Location:''' MIT<br />
*'''REGISTRATION:''' Registration link will go live as the event gets closer. <br />
**Please note that as you proceed to the checkout portion of the registration process, RegOnline will offer you a chance to opt into a free trial of ACTIVEAdvantage -- click on "No thanks" in order to finish your Project Week registration.<br />
*'''Registration Fee:''' $300.<br />
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.<br />
*'''Room sharing''': If interested, add your name to the list [[2016_Winter_Project_Week/RoomSharing|here]]<br />
<br />
= '''Registrants''' =<br />
<br />
Do not add your name to this list - it is maintained by the organizers based on your paid registration.</div>RandyGollubhttps://www.na-mic.org/w/index.php?title=2016_Winter_Project_Week&diff=905692016 Winter Project Week2015-11-24T21:46:50Z<p>RandyGollub: /* Projects */</p>
<hr />
<div>__NOTOC__<br />
<br />
[[image:PW-MIT2016.png|300px|left]]<br />
<br><br><br><br><br><br><br><br><br><br><br><br><br />
'''Dates:''' January 4-8, 2016<br />
<br />
'''Location:''' MIT, Cambridge, MA. (Rooms: [[MIT_Project_Week_Rooms#Kiva|Kiva]], R&D)<br />
<br><br />
<br />
== Introduction ==<br />
Founded in 2005, the National Alliance for Medical Image Computing (NAMIC), was chartered with building a computational infrastructure to support biomedical research as part of the NIH funded [http://www.ncbcs.org/ NCBC] program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform [http://www.slicer.org 3D Slicer], built using [http://www.vtk.org VTK], [http://www.itk.org ITK], [http://www.cmake.org CMake], and [http://www.cdash.org CDash], and the creation of a community of algorithm researchers, biomedical scientists and software engineers who are committed to open science. This community meets twice a year in an event called Project Week. <br />
<br />
[[Engineering:Programming_Events|Project Week]] is a semi-annual event which draws 80-120 researchers. As of August 2014, it is a MICCAI endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event. <br />
<br />
Project Week activities: Everyone shows up with a project. Some people are working on the platform. Some people are developing algorithms. Some people are applying the tools to their research problems. We begin the week by introducing projects and connecting teams. We end the week by reporting progress. In addition to the ongoing working sessions, breakout sessions are organized ad-hoc on a variety of special topics. These topics include: discussions of software architecture, presentations of new features and approaches and topics such as Image-Guided Therapy.<br />
<br />
Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], and [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO]. <br />
<br />
A summary of all previous Project Events is available [[Project_Events#Past|here]].<br />
<br />
This project week is an event [[Post-NCBC-2014|endorsed]] by the MICCAI society.<br />
<br />
Please make sure that you are on the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]<br />
<br />
==Agenda==<br />
<br />
Tentative Agenda<br />
<br />
{|border="1"<br />
|-style="background:#b0d5e6;color:#02186f" <br />
!style="width:10%" |Time<br />
!style="width:18%" |Monday, January 4<br />
!style="width:18%" |Tuesday, January 5<br />
!style="width:18%" |Wednesday, January 6<br />
!style="width:18%" |Thursday, January 7<br />
!style="width:18%" |Friday, January 8<br />
|-<br />
|<br />
|bgcolor="#dbdbdb"|'''Project Presentations''' <br />
|bgcolor="#6494ec"|<br />
|<br />
|bgcolor="#88aaae"|'''IGT Day'''<br />
|bgcolor="#faedb6"|'''Reporting Day'''<br />
|-<br />
|bgcolor="#ffffdd"|'''8:30am'''<br />
|<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast <br />
|-<br />
|bgcolor="#ffffdd"|'''9am-12pm'''<br />
|'''10:30am-12pm:''' '''Diffeomorphic registration and the more recent geodesic shooting methods for diffeomorphic registration.''' (Tutorial Part 1 by Sarang Joshi)<br> Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].<br />
|'''10-11:30am:''' <font color="#503020">Breakout Session: New Slicer Extensions'''</font><br><br />
|<br />
'''10-11:30am:''' <font color="#503020">Breakout Session: [[2015_Winter_Project_Week:SlicerROSIntegration| Slicer for Medical Robotics Research]] </font><br />
<br><br />
|'''9:00-10:30am''' TBD <br><br />
<br>----------------------------------------<br><br />
'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>TBD <br><br />
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]<br><br />
[[MIT_Project_Week_Rooms#Kiva|Kiva]]<br />
<br>----------------------------------------<br><br />
'''12pm''' [[Events:TutorialContestJune2014|Tutorial Contest Winner Announcement]]<br><br />
[[MIT_Project_Week_Rooms#Kiva|Kiva]]<br />
|-<br />
|bgcolor="#ffffdd"|'''12pm-1pm'''<br />
|bgcolor="#ffffaa"|Lunch <br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm<br />
|-<br />
|bgcolor="#ffffdd"|'''1pm-5:30pm'''<br />
|'''1-1:05pm: <font color="#503020">Welcome</font>'''<br><br />
[[MIT_Project_Week_Rooms#Kiva|Kiva]]<br />
<br>----------------------------------------<br><br />
'''1:05-2:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)<br><br />
[[MIT_Project_Week_Rooms#Kiva|Kiva]]<br />
<br>----------------------------------------<br><br />
'''2:45-4pm:''' [[Breakout Session: Ultrasound]]<br />
[[MIT_Project_Week_Rooms#Kiva|Kiva]]<br />
<br>----------------------------------------<br><br />
<br />
'''4:00pm-5:30pm:''' '''Diffeomorphic registration and the more recent geodesic shooting methods for diffeomorphic registration.''' (Tutorial Part 2 by Sarang Joshi) <br> Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].<br />
|'''1-3pm:''' <font color="#503020"> [[Breakout Session: What's Planned for Slicer Core]]<br><br />
[[MIT_Project_Week_Rooms#Kiva|Kiva]] <br />
|'''1-2:30pm:''' <font color="#503020">Breakout Session:'''</font><br>[[Breakout Session: Diffusion MRI]]<br />
[[MIT_Project_Week_Rooms#Kiva|Kiva]] <br />
|<br />
|<br />
|-<br />
|bgcolor="#ffffdd"|'''5:30pm'''<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|<br />
|}<br />
<br />
<googlecalendar>kitware.com_sb07i171olac9aavh46ir495c4</googlecalendar><br />
<br />
='''Projects'''=<br />
* [[2016_Project_Week_Template | Template for project pages]]<br />
<br />
<br />
* [[2015_Winter_Project_Week:SlicerROSIntegration | 3D Slicer + ROS Integration]] (Junichi Tokuda, Axel Krieger, Simon Leonard)<br />
* [[2016_Winter_Project_Week:TrackedUltrasoundStandardization | Tracked ultrasound standardization]] (Andras Lasso, Christian Askeland, Simon Drouin, Junichi Tokuda, Steve Pieper, Adam Rankin)<br />
*Integration of CustusX with PLUS on BK System (Christian A)<br />
*Integration of ImFusion MR-US registration with BWH AMIGO neurosurgery setup (Christian A, Tina Kapur, Steve Pieper, Sandy Wells, Andras Lasso)<br />
*Digital Pathology Nuclear Segmentation (Erich Bremer, Nicole Aucoin)<br />
*Chest Imaging Platform: COPD and other pulmonary diseases (Raúl San José, Jorge Onieva)<br />
*Upgrade the namic wiki (JC, Mike Halle)<br />
* [[2016_Winter_Project_Week:BatchImageAnalysis | Batch Clinical Image Analysis]] (Kalli Retzepi, Nasim Maleki, Yangming Ou, Matt Toews, Steve Pieper, Sandy Wells, Randy Gollub)<br />
<br />
==Infrastructure==<br />
* [[2016_Winter_Project_Week:SlicerProjectName | Project Name]] (List of people working on this project)<br />
* [[2016_Winter_Project_Week:CommonGL | CommonGL]] (Steve Pieper, Jim Miller)<br />
* [[2016_Winter_Project_Week:WebTechnologies | Web Technologies and Slicer]] (Steve Pieper, Hans Meine)<br />
<br />
= '''Logistics''' =<br />
<br />
*'''Dates:''' January 4-8, 2016<br />
*'''Location:''' MIT<br />
*'''REGISTRATION:''' Registration link will go live as the event gets closer. <br />
**Please note that as you proceed to the checkout portion of the registration process, RegOnline will offer you a chance to opt into a free trial of ACTIVEAdvantage -- click on "No thanks" in order to finish your Project Week registration.<br />
*'''Registration Fee:''' $300.<br />
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.<br />
*'''Room sharing''': If interested, add your name to the list [[2016_Winter_Project_Week/RoomSharing|here]]<br />
<br />
= '''Registrants''' =<br />
<br />
Do not add your name to this list - it is maintained by the organizers based on your paid registration.</div>RandyGollubhttps://www.na-mic.org/w/index.php?title=2014_Tutorial_Contest&diff=866392014 Tutorial Contest2014-06-25T19:05:29Z<p>RandyGollub: </p>
<hr />
<div>'''NA-MIC Tutorial Contest, Thursday June 26, 9-10:30 am'''<br />
<br />
[[2014_Summer_Project_Week#Agenda|Back to Summer project week Agenda]]<br />
<br />
[http://www.slicer.org Slicer4] is used to perform meaningful research tasks. As part of the NA-MIC Training Core activities we are building a curated portfolio of tutorials for the basic functions and specialized functionality available in Slicer. <br />
<br />
The primary purpose of the Summer 2014 tutorial contest is to enrich the training materials that are available to end-users and developers using 3D Slicer and the NA-MIC kit. We believe participants will be motivated to join this event to enhance the dissemination of their own algorithms that they have incorporated into the Slicer4 platform and/or to enhance training of Slicer4 functionality for their own laboratory groups.<br />
<br />
<br />
[http://wiki.na-mic.org/Wiki/index.php/2013_Tutorial_Contest 2013 Summer Tutorial 2013 Contest page]<br />
<br />
There will be three categories:<br />
*Category 0: '''EXTENSION TUTORIAL''' <br> In this category, the tutorial will teach a user how to use an Extension of Slicer.<br />
*Category 1: '''END TO END SOLUTION TUTORIAL''' <br> In this category, the tutorial will teach a user how to solve a particular clinical problem using the NA-MIC Kit. <br> Example: [http://www.slicer.org/slicerWiki/images/f/f1/NeurosurgicalPlanning_SoniaPujol.pdf White Matter Exploration for Neurosurgical Planning]<br />
*Category 2: '''ALGORITHM TUTORIAL:''' In this category the tutorial will teach a user how to make an algorithm work on their data.<br> Examples: [http://www.slicer.org/slicerWiki/images/c/c6/Slicer4QuantitativeImaging.pdf Quantitative Imaging tutorial]<br><br />
*Category 3: '''METHODOLOGY TUTORIAL'''. Application-level tutorials for users and developers.<br> Examples:[[Slicer3:Fiducials_TutorialContestSummer2010 | '''Fiducials''']] <br />
<br />
<br />
Entries in each category require the following material: <br />
* scientific background and application motivation<br />
* step-by-step instructions<br />
* anonymized sample dataset<br />
<br />
=Rules=<br />
<br />
The [[Summer2014_Tutorial_Contest | evaluation criteria]] for the 2014 tutorial contest are below:<br />
*Tutorial must be based on the Slicer nightly build of June 2,2014:<br />
Windows: <br />
*[http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.3.1-2014-06-02-win-amd64.exe&checksum=f464d190dda72957d1ab7f43b58843e2 Slicer4.4.2014-06.03]<br />
Mac:<br />
*[http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.3.1-2014-06-02-macosx-amd64.dmg&checksum=b5c99307995cbb1292d1789a4cf6c7a9 Slicer4.4.2014-06.03]<br />
Linux:<br />
*[http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.3.1-2014-06-02-linux-amd64.tar.gz&checksum=eebf24ed14aaf46ccd0f47311e96f1fe Slicer4.4.2014-06.03]<br />
<br />
*To enter the contest, you must provide a self-test that can be run in Slicer and '''a version of the tutorial that works on all supported platforms (Mac,Windows,Linux)+'''.<br />
Example of self-tests can be found in the RSNA2012Quant module of Slicer4.3.<br />
*Tutorial and all of its components (data, powerpoints/pdfs, additional modules etc.) must be released under the [http://www.slicer.org/slicerWiki/index.php/Slicer:license Slicer license]<br />
*Tutorial data must be anonymized<br />
*Tutorial must include contact information of the primary author (e-mail and phone number) <br />
*Tutorial must follow the guidelines specified above and use the [[Media:TutorialContest_Template_2014.ppt | Summer 2014 contest tutorial template]].<br />
*If applicable, the tutorial must provide clear directions for downloading and installing additional modules <br><br />
+Applicants will work with the NA-MIC Training Core in advance to do the multi-platform testing.<br />
<br />
NOTE: If you plan on sending the DTI data, we are currently experiencing a [http://na-mic.org/Mantis/view.php?id=3723 bug] that is being worked on. Please refer to these useful debugging hints:<br />
*Load DTI and get bad display as shown in bug report<br />
*Go to volumes module<br />
*Select perpendicular diffusivity mode (possible others work too)<br />
*Switch back to Color Orientation and display is working<br />
*FA now works as well.<br />
<br />
=Submission Dead-line and Presentation=<br />
<br />
'''<span style="background-color: pink"> Submission dead-line: Monday June 23, 2014'''</span><br />
* '''Submission process''': to enter the contest, please follow the 5 steps below:<br />
**1. Create a wiki page for your tutorial on the NA-MIC wiki.<br />
**2. Upload your slides and tutorial dataset. Your tutorial and data must be named as 'TutorialName_TutorialContestSummer2014.pdf' and 'TutorialData_TutorialContestSummer2014.zip'<br />
**3. Add a link to the uploaded tutorial and datasets on your tutorial page. <br />
**4. Copy the template of the [http://wiki.na-mic.org/Wiki/index.php/Training:Summer_2014_Contest_Table Summer 2014 test table ] on your tutorial page, and enter the results of your cross-platform testing (Mac, Windows XP &7, Linux 64, Linux 32).<br />
**5. Once you have completed step 1-4, add a link to your tutorial page in the list below and send a notification email to Sonia Pujol (spujol at bwh.harvard.edu) to receive a confirmation of your submission.<br />
<br />
* '''Presentation at the NA-MIC Project week''': Brief highlights of tutorials will be presented by the authors at the Summer 2014 Project Week. Each presentation should be 5-minute summary of the submission.<br />
<br />
*Tutorial contest entries<br />
#[http://wiki.na-mic.org/Wiki/index.php/CMRToolkitLAWorkflow_TutorialContestSummer2014 Cardiac MRI Toolkit LA Segmentation Workflow. Salma Bengali, Josh Cates, SCI, Utah]<br />
#[http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014 Cardiac Agatston Scoring Slicer Module. Jessica Forbes, Hans Johnson, Iowa City, Iowa]<br />
<br />
Contest judges: <br />
*Randy Gollub, MD, PhD, Massachusetts General Hospital, Harvard Medical School<br />
*Greg Sharp, PhD, Massachusetts General Hospital, Harvard Medical School<br />
*Sidong Liu, MSc, Brigham and Women's Hospital, Harvard Medical School - University of Sydney <br />
*Sonia Pujol, PhD, Brigham and Women's Hospital, Harvard Medical School</div>RandyGollubhttps://www.na-mic.org/w/index.php?title=Imaging_in_Neuroscience&diff=80866Imaging in Neuroscience2013-04-08T03:11:21Z<p>RandyGollub: </p>
<hr />
<div>The 3D Slicer software platform will be presented as part of the Harvard Catalyst course "Advanced Imaging: Imaging in Neuroscience" course organized by Dr. Randy Gollub <br />
<br />
==Course Faculty==<br />
*Junichi Tokuda, Brigham and Women's Hospital, Harvard Medical School (Presenter)<br />
*Nicole Aucoin, Brigham and Women's Hospital, Harvard Medical School <br />
*Sonia Pujol, Brigham and Women's Hospital, Harvard Medical School<br />
*Randy L. Gollub, Massachusetts General Hospital, Harvard Medical School<br />
*P. Ellen Grant, Boston Children's Hospital, Harvard Medical School<br />
*Daniel Haehn, Boston Children's Hospital, Harvard Medical School<br />
*Nicolas Rannou, Boston Children's Hospital, Harvard Medical School<br />
*Nathaniel A Reynolds, Massachusetts General Hospital, Harvard Medical School<br />
<br />
==Course Logistics==<br />
Date: April 8, 2013, 11:30-12:00<br />
Location: Sheraton Commander Hotel, Boston, MA<br />
<br />
==Agenda== <br />
*11:30-12:00: The 3D Slicer open-source platform for image analysis and 3D visualization of medical image data (lecture)<br />
*12:00-1:00: Slicer4 minute tutorial (hands-on session) and Diffusion tractography (demo)<br />
<br />
[[Media:ImagingInNeuroscience_April8-3DSlicer_SoniaPujol.pdf | 3D Slicer course - Imaging in Neuroscience]]<br />
<br />
<font color=red>Note:<br />
* Slide page 37 (For those who downloaded the slide before Apr 7): "Load scene" menu is not available in the current version of 3D Slicer (version 4.2.2). Please choose "Add data" instead.<br />
* Slide page 48: If the white matter surface does not appear, please select "hemisphelic_white_matter.vtk" and uncheck "Clip" (see the screenshot bellow). <br />
[[Image:ImagingInNeuroscience_April8_Clipping.png|300px]]<br />
<br />
</font><br />
<br />
== Course Materials ==<br />
In preparation for the hands-on session, please download the 3D Slicer release version 4.2.2-1 and the Slicer4 minute datasets.<br />
<br />
[http://download.slicer.org 3D Slicer 4.x (blue download button)]<br />
<br />
[http://www.slicer.org/slicerWiki/index.php/File:Slicer4minute.zip Slicer4minute dataset (hands-on)]<br />
<br />
[[media:Dti.zip |DTI dataset (demo)]]<br />
<br />
Additional materials for learning more about 3D Slicer are available on the Slicer 101 page.</div>RandyGollubhttps://www.na-mic.org/w/index.php?title=CTSC:ARRA.071712&diff=77222CTSC:ARRA.0717122012-07-17T16:28:02Z<p>RandyGollub: Created page with 'Back to CTSC:ARRA supplement <br> <br> == Harvard Catalyst Medical Informatics group Meeting Minutes July 17, 2012 == In attendance: * Bill Wang * Shawn Murphy * Randy Goll…'</p>
<hr />
<div>Back to [[CTSC:ARRA supplement]]<br />
<br> <br />
<br><br />
== Harvard Catalyst Medical Informatics group Meeting Minutes July 17, 2012 ==<br />
<br />
In attendance:<br />
* Bill Wang<br />
* Shawn Murphy<br />
* Randy Gollub <br />
* Chris Herrick<br />
* Darren Sack<br />
<br />
'''Agenda'''<br />
# NIBIB Baby Brains R01 grant update<br />
# mi2b2 software update <br />
# manuscript<br />
<br />
<br />
===NIBIB Baby Brains R01 grant update===<br />
* We have confirmation that NIBIB will fund the originally submitted mi2b2 grant. <br />
* Randy submitted a new IRB application specifically for the MGH/BWH site aspects of the project. It has been approved and linked into the Just In Time material for the original grant.<br />
* The JIT paperwork is submitted.<br />
<br />
===mi2b2 software update===<br />
* The mi2b2 software version 1.2 that allows one or more XNAT instances and/or DICOM receivers such as OSIRIX-MD to be specified per project is now deployed at MGH. Internal testing is done and has been all stable. Next step is to have users test it. Randy will contact Jayashree to follow up on the email Bill sent to get her launched on this. There is a step where the mi2b2 team has to confirm that the transfer site for data to be received is actually within firewall. Chris will try using the Infosec team to accomplish this. <br />
<br />
===manuscript===<br />
* Progress is slow, on agenda for next meeting.</div>RandyGollubhttps://www.na-mic.org/w/index.php?title=Collaboration:Harvard_CTSC&diff=77141Collaboration:Harvard CTSC2012-06-25T22:33:03Z<p>RandyGollub: </p>
<hr />
<div>__NOTOC__<br />
=Harvard Catalyst | The Harvard Clinical and Translational Science Center, Imaging Consortium Workspace=<br />
<br />
{| border="00" cellpadding="2" cellspacing="0"<br />
|-<br />
| rowspan="2"| Welcome to this on-line archive of current and past HMS affiliated medical imaging activity! The original intent of these wiki pages was to encourage quick and efficient communication among the Harvard Catalyst Imaging Consortium and the broader Harvard Catalyst community. However, changes in the structure of support for imaging in the Harvard Catalyst has resulted in new leadership and new offerings. Please visit the main web page for the current organization: [http://catalyst.harvard.edu/ Harvard Catalyst]. This site is being maintained for archival purposes and also for support of the still active [[CTSC:ARRA_supplement| '''(mi2b2)''']] project.<br />
|-<br />
| style="background: #ebeced"| [[Image:Catalyst_logo_final.jpg]]<br />
| style="background: #ebeced"| [[Image:NCRR-logo.jpg]]<br />
| style="background: #ebeced"| [[Image:Harvard shield.jpg]]<br />
|}<br />
<br />
<br />
<br />
----<br />
<br />
== Mission statement==<br />
<br />
The [http://catalyst.harvard.edu/programs/imaging/ '''Imaging Consortium''']:<br />
* provides expert [http://catalyst.harvard.edu/services/imagingconsult/ '''consultation'''] to assist clinical and translational investigators in the planning and design of medical imaging research. <br />
* [[CTSC:education| '''educates''']] about both general and current state of the art medical imaging and image processing capabilities. The courses are designed to better acquaint clinicians and scientists with the tools and technologies available in this important field. <br />
* guides the CTSC participants about available [[CTSC:resources| '''resources''']] in the use of imaging as part of clinical translational research.<br />
* develops, through the Harvard Catalyst Medical Imaging Informatics Bench to Bedside Initiative [[CTSC:ARRA_supplement| '''(mi2b2)''']] and cross-institutional harmonization efforts, medical imaging informatics to support the clinical and translational research community and enable current and future large-scale medical image data exploration.<br />
<br />
<br />
<br />
----<br />
<br />
==Key Personnel==<br />
{| class="wikitable1" border="1" cellpadding="5" border="1" align="center"<br />
| style="width:30%" | '''Sites'''<br />
| style="width:70%" | '''Imaging Consortium Personnel''' <br />
|-<br />
|[[Image:MGH.png|160px]]<br />
|'''[http://www.nmr.mgh.harvard.edu/martinos/people/showPerson.php?people_id=141 Bruce Rosen]''', Director <br>[[User:Randy |'''Randy Gollub''']], Co-Director <br>'''[http://www2.massgeneral.org/radiology/index.asp?page=staff&subpage=harris Gordon J. Harris]''', Consultant <br> '''[http://connects.catalyst.harvard.edu/profiles/profile/person/73215 William Hanlon]''', Consultant<br />
|-<br />
|[[Image:BIDMC.png|160px]]<br />
|'''Valerie Humblet''', Medical Imaging Liaison<br><br />
|-<br />
|[[Image:BWH.png|160px]]<br />
|'''[http://www.spl.harvard.edu/~ctempany Clare Tempany]''', Consultant<br>'''[http://spl.harvard.edu/~kikinis Ron Kikinis]''', Consultant<br>'''[http://cni.bwh.harvard.edu/personnel/charles.html Charles Guttmann]''', Consultant <br>'''[http://connects.catalyst.harvard.edu/profiles/profile/person/21262 Todd Perlstein]''', Consultant <br> '''[http://www.brighamandwomens.org/endocrine/Research/Gordon_Williams.aspx Gordon Williams]''', PI for CTSC Translational Technologies<br />
|-<br />
|[[Image:Children's.png|160px]]<br />
|'''[http://www.childrenshospital.org/cfapps/research/data_admin/Site190/mainpageS190P0.html Stephan Voss]''', Consultant<br>'''[http://www.crl.med.harvard.edu/people/warfield/ Simon Warfield]''', Consultant<br />
|-<br />
|[[Image:DFCI.png|160px]]<br />
|'''[http://physicians.dana-farber.org/directory/profile.asp?dbase=main&setsize=10&last=Van+Den+Abbeele&grouptype_typeid=1&display=Y&nxtfmt=pc&pgt=Annick+D.+Van+den+Abbeele%2C+MD&gs=pc&pict_id=8172418 Annick D. Van den Abbeele]''',Consultant<br>'''[http://www.jpnm.org/faculty/yap.html Jeffrey Yap]''', Consultant and Director of Education<br />
|-<br />
<br />
|}<br />
<br />
<br />
----<br />
<br />
==Upcoming Events==<br />
<br />
<br />
<br />
<br />
----<br />
<br />
== Multicenter Clinical Trial working group==<br />
<br />
The objective of this group is the establishment of an infrastructure to support multi-center imaging projects.<br />
<br />
*[[CTSC:multicenter101410| October 14, 2010]]<br />
*[[CTSC:multicenter061510| June 15, 2010]]<br />
*[[CTSC:multicenter042110| April 21, 2010]]<br />
<br />
<br />
----<br />
<br />
==Harvard Catalyst Medical Imaging Informatics mi2b2 initiative==<br />
On September 24, 2009, Harvard Catalyst was awarded an [[CTSC:ARRA_supplement|ARRA administrative supplement]] to enable clinical imaging data to be used for secondary research purposes.<br />
<br />
<br />
<br />
----<br />
<br />
== Medical Imaging Informatics and Data Management==<br />
<br />
[[CTSC:CrossSiteImagingIdeas|Use Cases and Development of Goals]]<br />
<br />
<br />
<br />
----<br />
<br />
==MRI Compatible Physiological Monitoring System ==<br />
Here you can find [[CTSC:monitoring.system|Information for users]] about the specifications of a monitoring system supported by Harvard Catalyst. There is also information about the LabChart software.<br />
<br />
<br />
----<br />
<br />
==Past Events ==<br />
<br />
===2011 meetings===<br />
* [[CTSC:TTiC.092711| September 27, 2011]]<br />
*[[CTSC:TTiC.091311| September 13, 2011]] face-to-face<br />
*[[CTSC:TTiC.0802311| August 23, 2011]] meeting canceled<br />
*[[CTSC:TTiC.080911| August 09, 2011]] face-to-face<br />
*[[CTSC:TTiC.072611| July 26, 2011]] t-con<br />
*[[CTSC:TTiC.071211| July 12, 2011]] face-to-face<br />
*[[CTSC:TTiC.062811| June 28, 2011]] t-con<br />
*[[CTSC:TTiC.061411| June 14, 2011]] face-to-face<br />
*[[CTSC:TTiC.052411| May 24, 2011]] face-to-face<br />
*[[CTSC:TTiC.051011| May 10, 2011]] Meeting canceled<br />
*[[CTSC:TTiC.042611| April 26, 2011]]<br />
*[[CTSC:TTiC.041211| April 12, 2011]]<br />
*[[CTSC:TTIC.032211| March 22, 2011]]<br />
*[[CTSC:TTIC.030811| March 8, 2011]]<br />
*[[CTSC:TTIC.022211| February 22, 2011]]<br />
*[[CTSC:TTIC.020811| February 08, 2011]] Face-to-face<br />
*[[CTSC:TTIC.012511| January 25, 2011]] t-con<br />
*[[CTSC:TTIC.011111| January 11, 2011]] Face-to-face<br />
<br />
===2010 ===<br />
*[[CTSC:TTIC.01to05| t-con 2010]]<br />
*[[CTSC:TTIC.RSNA2010| RSNA 2010]] <br />
<br />
===2009 ===<br />
* [[CTSC:TTIC.2009|t-con, meetings and presentations 2009]]<br />
* [[CTSC:TTIC.progress|Progress Report Y2]]<br />
<br />
===2008===<br />
* [[CTSC:TTIC.2008|t-con and meetings 2008]]<br />
<br />
<br />
<br />
----<br />
<br />
== JIRA system==<br />
We use JIRA to monitor our consultation requests. Here are some information for our consultants: links to the [[media:JIRA_user.ppt |user guide]], [[media: JIRA_screens shots.ppt |screenshots]] and the [https://jira.cbmi.med.harvard.edu/jira/secure/Dashboard.jspa website]<br />
<br />
<br />
<br />
----<br />
<br />
== External imaging core collaborative efforts ==<br />
<br />
The Harvard Catalyst Imaging Consortium integrates with national clinical and translational efforts through the CTSA Imaging Working Group and Steering Committee<br />
<br />
*[http://wiki.ctsa-imaging.org/index.php?title=Main_Page CTSA Imaging Working Group wiki]<br />
<br />
<br />
----<br />
<br />
== Additional Resources ==<br />
<br />
{| class="wikitable1" border="1" cellpadding="5" border="1" align="center"<br />
|[[Image:BIRN-logo.jpg|160px]]<br />
|'''Biomedical Informatics Research Network'''<br>BIRN<br />
| [[CTSC:BIRNresources|BIRN Imaging Resources]]<br />
| [[CTSC:BIRN.Education|BIRN Training Resources]]<br />
|-<br />
|align="center"|[[Image:NAMIC 380x463.jpg|100px]]<br />
| '''National Alliance for Medical Image Computing'''<br>NA-MIC<br />
| [[Resources|NA-MIC Resources]]<br />
| [[Training:Main|NA-MIC Training Resources]]<br />
|-<br />
|align="center"|[[Image:Logo_nac.gif|100px]]<br />
| '''Neuroimage Analysis Center'''<br>NAC<br />
| [http://nac.spl.harvard.edu Resources]<br />
| [http://nac.spl.harvard.edu/pages/Training Training Resources]<br />
|}<br />
<br />
<br />
<br />
----<br />
<br />
The Harvard CTSC Imaging Consortium would like to thank its gracious host NA-MIC for providing communication tools to facilitate the rapid deployment of expertise in medical imaging acquisition, analysis and visualization to clinical translational investigators.<br />
<br />
<br />
Back to [[NA-MIC_External_Collaborations|NA-MIC External Collaborations]]</div>RandyGollubhttps://www.na-mic.org/w/index.php?title=Collaboration:Harvard_CTSC&diff=77140Collaboration:Harvard CTSC2012-06-25T22:32:15Z<p>RandyGollub: </p>
<hr />
<div>__NOTOC__<br />
=Harvard Catalyst | The Harvard Clinical and Translational Science Center, Imaging Consortium Workspace=<br />
<br />
{| border="00" cellpadding="2" cellspacing="0"<br />
|-<br />
| rowspan="2"| Welcome to this on-line archive of current and past HMS affiliated medical imaging activity! The original intent of these wiki pages was to encourage quick and efficient communication among the Harvard Catalyst Imaging Consortium and the broader Harvard Catalyst community. However, changes in the structure of support for imaging in the Harvard Catalyst has been transitioned to new leadership and new offerings. Please visit the main web page for the current organization: [http://catalyst.harvard.edu/ Harvard Catalyst]. This site is being maintained for archival purposes and also for support of the still active [[CTSC:ARRA_supplement| '''(mi2b2)''']] project.<br />
|-<br />
| style="background: #ebeced"| [[Image:Catalyst_logo_final.jpg]]<br />
| style="background: #ebeced"| [[Image:NCRR-logo.jpg]]<br />
| style="background: #ebeced"| [[Image:Harvard shield.jpg]]<br />
|}<br />
<br />
<br />
<br />
----<br />
<br />
== Mission statement==<br />
<br />
The [http://catalyst.harvard.edu/programs/imaging/ '''Imaging Consortium''']:<br />
* provides expert [http://catalyst.harvard.edu/services/imagingconsult/ '''consultation'''] to assist clinical and translational investigators in the planning and design of medical imaging research. <br />
* [[CTSC:education| '''educates''']] about both general and current state of the art medical imaging and image processing capabilities. The courses are designed to better acquaint clinicians and scientists with the tools and technologies available in this important field. <br />
* guides the CTSC participants about available [[CTSC:resources| '''resources''']] in the use of imaging as part of clinical translational research.<br />
* develops, through the Harvard Catalyst Medical Imaging Informatics Bench to Bedside Initiative [[CTSC:ARRA_supplement| '''(mi2b2)''']] and cross-institutional harmonization efforts, medical imaging informatics to support the clinical and translational research community and enable current and future large-scale medical image data exploration.<br />
<br />
<br />
<br />
----<br />
<br />
==Key Personnel==<br />
{| class="wikitable1" border="1" cellpadding="5" border="1" align="center"<br />
| style="width:30%" | '''Sites'''<br />
| style="width:70%" | '''Imaging Consortium Personnel''' <br />
|-<br />
|[[Image:MGH.png|160px]]<br />
|'''[http://www.nmr.mgh.harvard.edu/martinos/people/showPerson.php?people_id=141 Bruce Rosen]''', Director <br>[[User:Randy |'''Randy Gollub''']], Co-Director <br>'''[http://www2.massgeneral.org/radiology/index.asp?page=staff&subpage=harris Gordon J. Harris]''', Consultant <br> '''[http://connects.catalyst.harvard.edu/profiles/profile/person/73215 William Hanlon]''', Consultant<br />
|-<br />
|[[Image:BIDMC.png|160px]]<br />
|'''Valerie Humblet''', Medical Imaging Liaison<br><br />
|-<br />
|[[Image:BWH.png|160px]]<br />
|'''[http://www.spl.harvard.edu/~ctempany Clare Tempany]''', Consultant<br>'''[http://spl.harvard.edu/~kikinis Ron Kikinis]''', Consultant<br>'''[http://cni.bwh.harvard.edu/personnel/charles.html Charles Guttmann]''', Consultant <br>'''[http://connects.catalyst.harvard.edu/profiles/profile/person/21262 Todd Perlstein]''', Consultant <br> '''[http://www.brighamandwomens.org/endocrine/Research/Gordon_Williams.aspx Gordon Williams]''', PI for CTSC Translational Technologies<br />
|-<br />
|[[Image:Children's.png|160px]]<br />
|'''[http://www.childrenshospital.org/cfapps/research/data_admin/Site190/mainpageS190P0.html Stephan Voss]''', Consultant<br>'''[http://www.crl.med.harvard.edu/people/warfield/ Simon Warfield]''', Consultant<br />
|-<br />
|[[Image:DFCI.png|160px]]<br />
|'''[http://physicians.dana-farber.org/directory/profile.asp?dbase=main&setsize=10&last=Van+Den+Abbeele&grouptype_typeid=1&display=Y&nxtfmt=pc&pgt=Annick+D.+Van+den+Abbeele%2C+MD&gs=pc&pict_id=8172418 Annick D. Van den Abbeele]''',Consultant<br>'''[http://www.jpnm.org/faculty/yap.html Jeffrey Yap]''', Consultant and Director of Education<br />
|-<br />
<br />
|}<br />
<br />
<br />
----<br />
<br />
==Upcoming Events==<br />
<br />
<br />
<br />
<br />
----<br />
<br />
== Multicenter Clinical Trial working group==<br />
<br />
The objective of this group is the establishment of an infrastructure to support multi-center imaging projects.<br />
<br />
*[[CTSC:multicenter101410| October 14, 2010]]<br />
*[[CTSC:multicenter061510| June 15, 2010]]<br />
*[[CTSC:multicenter042110| April 21, 2010]]<br />
<br />
<br />
----<br />
<br />
==Harvard Catalyst Medical Imaging Informatics mi2b2 initiative==<br />
On September 24, 2009, Harvard Catalyst was awarded an [[CTSC:ARRA_supplement|ARRA administrative supplement]] to enable clinical imaging data to be used for secondary research purposes.<br />
<br />
<br />
<br />
----<br />
<br />
== Medical Imaging Informatics and Data Management==<br />
<br />
[[CTSC:CrossSiteImagingIdeas|Use Cases and Development of Goals]]<br />
<br />
<br />
<br />
----<br />
<br />
==MRI Compatible Physiological Monitoring System ==<br />
Here you can find [[CTSC:monitoring.system|Information for users]] about the specifications of a monitoring system supported by Harvard Catalyst. There is also information about the LabChart software.<br />
<br />
<br />
----<br />
<br />
==Past Events ==<br />
<br />
===2011 meetings===<br />
* [[CTSC:TTiC.092711| September 27, 2011]]<br />
*[[CTSC:TTiC.091311| September 13, 2011]] face-to-face<br />
*[[CTSC:TTiC.0802311| August 23, 2011]] meeting canceled<br />
*[[CTSC:TTiC.080911| August 09, 2011]] face-to-face<br />
*[[CTSC:TTiC.072611| July 26, 2011]] t-con<br />
*[[CTSC:TTiC.071211| July 12, 2011]] face-to-face<br />
*[[CTSC:TTiC.062811| June 28, 2011]] t-con<br />
*[[CTSC:TTiC.061411| June 14, 2011]] face-to-face<br />
*[[CTSC:TTiC.052411| May 24, 2011]] face-to-face<br />
*[[CTSC:TTiC.051011| May 10, 2011]] Meeting canceled<br />
*[[CTSC:TTiC.042611| April 26, 2011]]<br />
*[[CTSC:TTiC.041211| April 12, 2011]]<br />
*[[CTSC:TTIC.032211| March 22, 2011]]<br />
*[[CTSC:TTIC.030811| March 8, 2011]]<br />
*[[CTSC:TTIC.022211| February 22, 2011]]<br />
*[[CTSC:TTIC.020811| February 08, 2011]] Face-to-face<br />
*[[CTSC:TTIC.012511| January 25, 2011]] t-con<br />
*[[CTSC:TTIC.011111| January 11, 2011]] Face-to-face<br />
<br />
===2010 ===<br />
*[[CTSC:TTIC.01to05| t-con 2010]]<br />
*[[CTSC:TTIC.RSNA2010| RSNA 2010]] <br />
<br />
===2009 ===<br />
* [[CTSC:TTIC.2009|t-con, meetings and presentations 2009]]<br />
* [[CTSC:TTIC.progress|Progress Report Y2]]<br />
<br />
===2008===<br />
* [[CTSC:TTIC.2008|t-con and meetings 2008]]<br />
<br />
<br />
<br />
----<br />
<br />
== JIRA system==<br />
We use JIRA to monitor our consultation requests. Here are some information for our consultants: links to the [[media:JIRA_user.ppt |user guide]], [[media: JIRA_screens shots.ppt |screenshots]] and the [https://jira.cbmi.med.harvard.edu/jira/secure/Dashboard.jspa website]<br />
<br />
<br />
<br />
----<br />
<br />
== External imaging core collaborative efforts ==<br />
<br />
The Harvard Catalyst Imaging Consortium integrates with national clinical and translational efforts through the CTSA Imaging Working Group and Steering Committee<br />
<br />
*[http://wiki.ctsa-imaging.org/index.php?title=Main_Page CTSA Imaging Working Group wiki]<br />
<br />
<br />
----<br />
<br />
== Additional Resources ==<br />
<br />
{| class="wikitable1" border="1" cellpadding="5" border="1" align="center"<br />
|[[Image:BIRN-logo.jpg|160px]]<br />
|'''Biomedical Informatics Research Network'''<br>BIRN<br />
| [[CTSC:BIRNresources|BIRN Imaging Resources]]<br />
| [[CTSC:BIRN.Education|BIRN Training Resources]]<br />
|-<br />
|align="center"|[[Image:NAMIC 380x463.jpg|100px]]<br />
| '''National Alliance for Medical Image Computing'''<br>NA-MIC<br />
| [[Resources|NA-MIC Resources]]<br />
| [[Training:Main|NA-MIC Training Resources]]<br />
|-<br />
|align="center"|[[Image:Logo_nac.gif|100px]]<br />
| '''Neuroimage Analysis Center'''<br>NAC<br />
| [http://nac.spl.harvard.edu Resources]<br />
| [http://nac.spl.harvard.edu/pages/Training Training Resources]<br />
|}<br />
<br />
<br />
<br />
----<br />
<br />
The Harvard CTSC Imaging Consortium would like to thank its gracious host NA-MIC for providing communication tools to facilitate the rapid deployment of expertise in medical imaging acquisition, analysis and visualization to clinical translational investigators.<br />
<br />
<br />
Back to [[NA-MIC_External_Collaborations|NA-MIC External Collaborations]]</div>RandyGollubhttps://www.na-mic.org/w/index.php?title=CTSC:ARRA_supplement&diff=77139CTSC:ARRA supplement2012-06-25T22:26:43Z<p>RandyGollub: </p>
<hr />
<div>[[Projects:ARRASuplements|Back to our ARRA home page]]<br />
== Harvard Catalyst Medical Imaging Informatics ARRA Administrative Supplement==<br />
{|<br />
|align="left"|<br />
=Medical Imaging Informatics Bench to Bedside (mi2b2) =<br />
<br>This Medical Imaging Informatics project was funded by an Administrative Supplement to 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. Please go to our main wiki page (http://www.mi2b2.org) for the most up-to-date information and to download the software.<br />
|[[image:ARRA.png|thumb|px=250|Go to the [http://www.recovery.gov ARRA website]]]<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. Furthermore, the current practice of excellent medical care includes extensive use of diagnostic and prognostic medical imaging using standardized image acquisition methods. 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 />
= Human Subject's Protection Training =<br />
All project personnel who access the medical imaging data for this effort must secure appropriate IRB approval. If you haven't already done it, take the CITI human subject's protection training course (https://www.citiprogram.org/) and then have your site i2b2 PI add you to their i2b2 IRB development protocol. <br />
<br />
= Mockup used for initial development =<br />
<br />
The mi2b2 installation at HMS hospitals requires careful attention to patient privacy and operational integrity of critical hospital information systems (e.g. clinical PACS). Therefore the software related to this project was developed and tested extensively before deployment in the clinical setting.<br />
<br />
In order to develop the software in isolation, a [[CTSC:ARRA:Mockup|virtualized mockup]] was set up that included a PACS system with phantom and anonymized DICOM data, an instance of i2b2 software, and a test installation of XNAT. The guidelines for this are being left intact on this web site for historical purposes and for the use by the community as they do their own development. But please see the main download site for mi2b2 for primary instructions for how to proceed.<br />
<br />
= mi2b2 software download site and installation instructions =<br />
<br />
The Medical Imaging Informatics Bench to Bedside web site (http://www.mi2b2.org) that hosts the download of the software, developer guidelines for installation and user tutorials are hosted on the i2b2 Community Wiki.<br />
= Upcoming Events =<br />
<br />
<br />
===Weekly Meetings===<br />
Wednesdays on weeks without monthly meetings OCC 299, Shawn's Office (9:00- 10:00 AM) <br />
<br />
===Monthly Meetings===<br />
Tuesdays (10:30- 11:30 AM), call: number in email reminder<br />
<br />
* [[CTSC:ARRA.071712| July 17, 2012]] Countway Library, conference room 319B<br />
<br />
=Past Events =<br />
<br />
===2012 meetings===<br />
* [[CTSC:ARRA.011712| January 17, 2012]] <br />
* [[CTSC:ARRA.022112| February 21, 2012]]<br />
* [[CTSC:ARRA.031312| March 13, 2012]] <br />
* [[CTSC:ARRA.041012| April 10, 2012]]<br />
* [[CTSC:ARRA.051512| May 15, 2012]] <br />
* [[CTSC:ARRA.061912| June 19, 2012]]<br />
<br />
===2011 meetings===<br />
'''[[CTSC:ARRA.tconJantoMay2011| January 2011 through May 2011 meeting minutes]]'''<br><br />
'''[[CTSC:ARRA.tconJunetoDec2011| June 2011 through December 2011 meeting minutes]]'''<br />
<br />
===2010 meetings===<br />
'''[[CTSC:ARRA.tconJantoJune2010| January 2010 through May 2010 t-con meeting minutes]]'''<br><br />
'''[[CTSC:ARRA.tconJunetoDec2010| June 2010 through December 2010 t-con and face to face meeting minutes]]'''<br />
<br />
===2009 meetings===<br />
'''[[CTSC:ARRA.2009tcon| 2009 t-con meeting minutes]]'''<br />
<br />
===Meeting presentations===<br />
* [[CTSC:ARRA.OHBM2011| Abstract presentation at the Organization for Human Brain Mapping meeting, Quebec City, CANADA, June, 2011]] <br />
* [[CTSC:ARRA.SIIM2011| Presentation at the Society for Imaging Informatics in Medicine annual meeting, Washington DC, June, 2011]] <br />
* [[CTSC:ARRA.ACRIN2010| ACRIN Medical Imaging Informatics Session, September 29, 2010]] <br />
* [[CTSC:ARRA.SFN2011| Abstract presentation at the Society for Neurosciences annual meeting, Washington DC, November, 2011]] <br />
* SIIM 2012 Open Source Plug Fest, June 2012<br />
<br />
=Using DCM4CHEE =<br />
[[CTSC:ARRA:dcm4chee_install|Installation instructions for DCM4CHEE]]<br />
<br />
Back to [[Collaboration:Harvard_CTSC|Collaboration:Harvard_CTSC]]<br />
<br></div>RandyGollubhttps://www.na-mic.org/w/index.php?title=CTSC:ARRA_supplement&diff=77138CTSC:ARRA supplement2012-06-25T22:25:54Z<p>RandyGollub: </p>
<hr />
<div>[[Projects:ARRASuplements|Back to our ARRA home page]]<br />
== Harvard Catalyst Medical Imaging Informatics ARRA Administrative Supplement==<br />
{|<br />
|align="left"|<br />
=Medical Imaging Informatics Bench to Bedside (mi2b2) =<br />
<br>This Medical Imaging Informatics project was funded by an Administrative Supplement to 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. Please go to our main wiki page (http://www.mi2b2.org) for the most up-to-date information and to download the software.<br />
|[[image:ARRA.png|thumb|px=250|Go to the [http://www.recovery.gov ARRA website]]]<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. Furthermore, the current practice of excellent medical care includes extensive use of diagnostic and prognostic medical imaging using standardized image acquisition methods. 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 />
= Human Subject's Protection Training =<br />
All project personnel who access the medical imaging data for this effort must secure appropriate IRB approval. If you haven't already done it, take the CITI human subject's protection training course (https://www.citiprogram.org/) and then have your site i2b2 PI add you to their i2b2 IRB development protocol. <br />
<br />
= Mockup used for initial development =<br />
<br />
The mi2b2 installation at HMS hospitals requires careful attention to patient privacy and operational integrity of critical hospital information systems (e.g. clinical PACS). Therefore the software related to this project was developed and tested extensively before deployment in the clinical setting.<br />
<br />
In order to develop the software in isolation, a [[CTSC:ARRA:Mockup|virtualized mockup]] was set up that included a PACS system with phantom and anonymized DICOM data, an instance of i2b2 software, and a test installation of XNAT. The guidelines for this are being left intact on this web site for historical purposes and for the use by the community as they do their own development. But please see the main download site for mi2b2 for primary instructions for how to proceed.<br />
<br />
= mi2b2 software download site and installation instructions =<br />
<br />
The Medical Imaging Informatics Bench to Bedside web site (http://www.mi2b2.org) that hosts the download of the software, developer guidelines for installation and user tutorials are hosted on the i2b2 Community Wiki.<br />
= Upcoming Events =<br />
* SIIM 2012 Open Source Plug Fest, June 2012<br />
<br />
===Weekly Meetings===<br />
Wednesdays on weeks without monthly meetings OCC 299, Shawn's Office (9:00- 10:00 AM) <br />
<br />
===Monthly Meetings===<br />
Tuesdays (10:30- 11:30 AM), call: number in email reminder<br />
<br />
* [[CTSC:ARRA.071712| July 17, 2012]] Countway Library, conference room 319B<br />
<br />
=Past Events =<br />
<br />
===2012 meetings===<br />
* [[CTSC:ARRA.011712| January 17, 2012]] <br />
* [[CTSC:ARRA.022112| February 21, 2012]]<br />
* [[CTSC:ARRA.031312| March 13, 2012]] <br />
* [[CTSC:ARRA.041012| April 10, 2012]]<br />
* [[CTSC:ARRA.051512| May 15, 2012]] <br />
* [[CTSC:ARRA.061912| June 19, 2012]]<br />
<br />
===2011 meetings===<br />
'''[[CTSC:ARRA.tconJantoMay2011| January 2011 through May 2011 meeting minutes]]'''<br><br />
'''[[CTSC:ARRA.tconJunetoDec2011| June 2011 through December 2011 meeting minutes]]'''<br />
<br />
===2010 meetings===<br />
'''[[CTSC:ARRA.tconJantoJune2010| January 2010 through May 2010 t-con meeting minutes]]'''<br><br />
'''[[CTSC:ARRA.tconJunetoDec2010| June 2010 through December 2010 t-con and face to face meeting minutes]]'''<br />
<br />
===2009 meetings===<br />
'''[[CTSC:ARRA.2009tcon| 2009 t-con meeting minutes]]'''<br />
<br />
===Meeting presentations===<br />
* [[CTSC:ARRA.OHBM2011| Abstract presentation at the Organization for Human Brain Mapping meeting, Quebec City, CANADA, June, 2011]] <br />
* [[CTSC:ARRA.SIIM2011| Presentation at the Society for Imaging Informatics in Medicine annual meeting, Washington DC, June, 2011]] <br />
* [[CTSC:ARRA.ACRIN2010| ACRIN Medical Imaging Informatics Session, September 29, 2010]] <br />
* [[CTSC:ARRA.SFN2011| Abstract presentation at the Society for Neurosciences annual meeting, Washington DC, November, 2011]] <br />
<br />
=Using DCM4CHEE =<br />
[[CTSC:ARRA:dcm4chee_install|Installation instructions for DCM4CHEE]]<br />
<br />
Back to [[Collaboration:Harvard_CTSC|Collaboration:Harvard_CTSC]]<br />
<br></div>RandyGollubhttps://www.na-mic.org/w/index.php?title=CTSC:ARRA.061912&diff=77137CTSC:ARRA.0619122012-06-25T22:24:57Z<p>RandyGollub: Created page with 'Back to CTSC:ARRA supplement <br> <br> == Harvard Catalyst Medical Informatics group Meeting Minutes June 19, 2012 == In attendance: * David Wang * Bill Wang * Shawn Murphy…'</p>
<hr />
<div>Back to [[CTSC:ARRA supplement]]<br />
<br> <br />
<br><br />
== Harvard Catalyst Medical Informatics group Meeting Minutes June 19, 2012 ==<br />
<br />
In attendance:<br />
* David Wang<br />
* Bill Wang<br />
* Shawn Murphy<br />
* Randy Gollub <br />
* Chris Herrick<br />
* Darren Sack<br />
* Jesse Wei (phone)<br />
<br />
<br />
'''Agenda'''<br />
# NIBIB Baby Brains R01 grant update<br />
# mi2b2 software update <br />
# manuscript<br />
# SIIM Plug Fest<br />
<br />
===NIBIB Baby Brains R01 grant update===<br />
* Our resubmitted grant was reviewed and received a very favorable score. <br />
* Shawn's admin team will reach out to the co-investigators for information that is required to submit for the Just In Time requirements.<br />
<br />
===mi2b2 software update===<br />
* BIDMC update from Jesse is that he is discussion with his departmental team and the BIDMC IT leadership regarding how best to proceed and will keep up posted.<br />
* The mi2b2 software version 1.2 that allows one or more XNAT instances and/or DICOM receivers such as OSIRIX-MD to be specified per project is being deployed now at MGH. <br />
* Development work is focused on enhanced integration with i2b2 to improve performance when used in that mode.<br />
<br />
===manuscript===<br />
* Progress is slow, on agenda for next meeting. Randy will circulate updated version for mi2b2 dev team to update the methods/results section with text about the XNAT/DICOM receiver enhancements.<br />
<br />
=== SIIM Plug Fest ===<br />
* Bill reported that attendance at our demo was excellent with non-stop crowds watching our video demonstration and asking questions. Most common questions were on the topics of de-identification and data sharing. In response to question about sharing images across institutions. Bill gave an excellent response to the question</div>RandyGollubhttps://www.na-mic.org/w/index.php?title=CTSC:ARRA.051512&diff=75255CTSC:ARRA.0515122012-05-15T15:29:17Z<p>RandyGollub: Created page with 'Back to CTSC:ARRA supplement <br> <br> == Harvard Catalyst Medical Informatics group Meeting Minutes April 10, 2012 == In attendance: * David Wang * Bill Wang * Shawn Murph…'</p>
<hr />
<div>Back to [[CTSC:ARRA supplement]]<br />
<br> <br />
<br><br />
== Harvard Catalyst Medical Informatics group Meeting Minutes April 10, 2012 ==<br />
<br />
In attendance:<br />
* David Wang<br />
* Bill Wang<br />
* Shawn Murphy<br />
* Randy Gollub <br />
* Chris Herrick<br />
* Steve Pieper<br />
* Darren Sack<br />
<br />
<br />
'''Agenda'''<br />
# mi2b2 software update <br />
# manuscript<br />
# SIIM Plug Fest<br />
<br />
===mi2b2 software update===<br />
* The mi2b2 software version 1.2 that allows one or more XNAT instances and/or DICOM receivers such as OSIRIX-MD to be specified per project is still being tested. Code for the UI was revised to allow the client to remember the "libraries" or directories where the user was working when they quit from the previous session. This allows each work session to be more time efficient for the user. Also improved the persistence of the users image view from session to session. Attempt is to enhance the fluidity of the experience. This logging feature can be disabled. This is the endpoint of new development for mi2b2 software until new specific funding is obtained. <br />
* With the remaining funding we will be enhancing integration with i2b2 to improve performance when used in that mode.<br />
* Chris checked out the Clinical Trial Processor (CTP). CTP is a Java based software tool developed by the CaBIG community comprised of a DICOM listener that can be configured to anonymize/de-identify files and a DICOM server to store the images. Appeared to be a good tool that might help mi2b2 users.<br />
<br />
===manuscript===<br />
* Discussed the literary style, the content and the use cases to be included. Plans for the next set of edits made.<br />
<br />
=== SIIM Plug Fest ===<br />
* Bill will be attending the meeting and presenting mi2b2 using a video demonstration.</div>RandyGollubhttps://www.na-mic.org/w/index.php?title=CTSC:ARRA_supplement&diff=74722CTSC:ARRA supplement2012-04-10T19:43:51Z<p>RandyGollub: </p>
<hr />
<div>[[Projects:ARRASuplements|Back to our ARRA home page]]<br />
== Harvard Catalyst Medical Imaging Informatics ARRA Administrative Supplement==<br />
{|<br />
|align="left"|<br />
=Medical Imaging Informatics Bench to Bedside (mi2b2) =<br />
<br>This Medical Imaging Informatics project was funded by an Administrative Supplement to 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. Please go to our main wiki page (http://www.mi2b2.org) for the most up-to-date information and to download the software.<br />
|[[image:ARRA.png|thumb|px=250|Go to the [http://www.recovery.gov ARRA website]]]<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. Furthermore, the current practice of excellent medical care includes extensive use of diagnostic and prognostic medical imaging using standardized image acquisition methods. 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 />
= Human Subject's Protection Training =<br />
All project personnel who access the medical imaging data for this effort must secure appropriate IRB approval. If you haven't already done it, take the CITI human subject's protection training course (https://www.citiprogram.org/) and then have your site i2b2 PI add you to their i2b2 IRB development protocol. <br />
<br />
= Mockup used for initial development =<br />
<br />
The mi2b2 installation at HMS hospitals requires careful attention to patient privacy and operational integrity of critical hospital information systems (e.g. clinical PACS). Therefore the software related to this project was developed and tested extensively before deployment in the clinical setting.<br />
<br />
In order to develop the software in isolation, a [[CTSC:ARRA:Mockup|virtualized mockup]] was set up that included a PACS system with phantom and anonymized DICOM data, an instance of i2b2 software, and a test installation of XNAT. The guidelines for this are being left intact on this web site for historical purposes and for the use by the community as they do their own development. But please see the main download site for mi2b2 for primary instructions for how to proceed.<br />
<br />
= mi2b2 software download site and installation instructions =<br />
<br />
The Medical Imaging Informatics Bench to Bedside web site (http://www.mi2b2.org) that hosts the download of the software, developer guidelines for installation and user tutorials are hosted on the i2b2 Community Wiki.<br />
= Upcoming Events =<br />
* SIIM 2012 Open Source Plug Fest, June 2012<br />
<br />
===Weekly Meetings===<br />
Wednesdays on weeks without monthly meetings OCC 299, Shawn's Office (9:00- 10:00 AM) <br />
<br />
===Monthly Meetings===<br />
Tuesdays (10:30- 11:30 AM), call: number in email reminder<br />
<br />
* [[CTSC:ARRA.051512| May 15, 2012]] Countway Library, conference room 319B<br />
* [[CTSC:ARRA.061912| June 19, 2012]] Countway Library, conference room 319B<br />
* [[CTSC:ARRA.071712| July 17, 2012]] Countway Library, conference room 319B<br />
<br />
=Past Events =<br />
<br />
===2012 meetings===<br />
* [[CTSC:ARRA.011712| January 17, 2012]] <br />
* [[CTSC:ARRA.022112| February 21, 2012]]<br />
* [[CTSC:ARRA.031312| March 13, 2012]] <br />
* [[CTSC:ARRA.041012| April 10, 2012]]<br />
<br />
===2011 meetings===<br />
'''[[CTSC:ARRA.tconJantoMay2011| January 2011 through May 2011 meeting minutes]]'''<br><br />
'''[[CTSC:ARRA.tconJunetoDec2011| June 2011 through December 2011 meeting minutes]]'''<br />
<br />
===2010 meetings===<br />
'''[[CTSC:ARRA.tconJantoJune2010| January 2010 through May 2010 t-con meeting minutes]]'''<br><br />
'''[[CTSC:ARRA.tconJunetoDec2010| June 2010 through December 2010 t-con and face to face meeting minutes]]'''<br />
<br />
===2009 meetings===<br />
'''[[CTSC:ARRA.2009tcon| 2009 t-con meeting minutes]]'''<br />
<br />
===Meeting presentations===<br />
* [[CTSC:ARRA.OHBM2011| Abstract presentation at the Organization for Human Brain Mapping meeting, Quebec City, CANADA, June, 2011]] <br />
* [[CTSC:ARRA.SIIM2011| Presentation at the Society for Imaging Informatics in Medicine annual meeting, Washington DC, June, 2011]] <br />
* [[CTSC:ARRA.ACRIN2010| ACRIN Medical Imaging Informatics Session, September 29, 2010]] <br />
* [[CTSC:ARRA.SFN2011| Abstract presentation at the Society for Neurosciences annual meeting, Washington DC, November, 2011]] <br />
<br />
=Using DCM4CHEE =<br />
[[CTSC:ARRA:dcm4chee_install|Installation instructions for DCM4CHEE]]<br />
<br />
Back to [[Collaboration:Harvard_CTSC|Collaboration:Harvard_CTSC]]<br />
<br></div>RandyGollubhttps://www.na-mic.org/w/index.php?title=CTSC:ARRA_supplement&diff=74721CTSC:ARRA supplement2012-04-10T19:43:29Z<p>RandyGollub: </p>
<hr />
<div>[[Projects:ARRASuplements|Back to our ARRA home page]]<br />
== Harvard Catalyst Medical Imaging Informatics ARRA Administrative Supplement==<br />
{|<br />
|align="left"|<br />
=Medical Imaging Informatics Bench to Bedside (mi2b2) =<br />
<br>This Medical Imaging Informatics project was funded by an Administrative Supplement to 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. Please go to our main wiki page (http://www.mi2b2.org) for the most up-to-date information and to download the software.<br />
|[[image:ARRA.png|thumb|px=250|Go to the [http://www.recovery.gov ARRA website]]]<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. Furthermore, the current practice of excellent medical care includes extensive use of diagnostic and prognostic medical imaging using standardized image acquisition methods. 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 />
= Human Subject's Protection Training =<br />
All project personnel who access the medical imaging data for this effort must secure appropriate IRB approval. If you haven't already done it, take the CITI human subject's protection training course (https://www.citiprogram.org/) and then have your site i2b2 PI add you to their i2b2 IRB development protocol. <br />
<br />
= Mockup used for initial development =<br />
<br />
The mi2b2 installation at HMS hospitals requires careful attention to patient privacy and operational integrity of critical hospital information systems (e.g. clinical PACS). Therefore the software related to this project was developed and tested extensively before deployment in the clinical setting.<br />
<br />
In order to develop the software in isolation, a [[CTSC:ARRA:Mockup|virtualized mockup]] was set up that included a PACS system with phantom and anonymized DICOM data, an instance of i2b2 software, and a test installation of XNAT. The guidelines for this are being left intact on this web site for historical purposes and for the use by the community as they do their own development. But please see the main download site for mi2b2 for primary instructions for how to proceed.<br />
<br />
= mi2b2 software download site and installation instructions =<br />
<br />
The Medical Imaging Informatics Bench to Bedside web site (http://www.mi2b2.org) that hosts the download of the software, developer guidelines for installation and user tutorials are hosted on the i2b2 Community Wiki.<br />
= Upcoming Events =<br />
* SIIM 2012 Open Source Plug Fest, June 2012<br />
<br />
===Weekly Meetings===<br />
Wednesdays on weeks without monthly meetings OCC 299, Shawn's Office (9:00- 10:00 AM) <br />
<br />
===Monthly Meetings===<br />
Tuesdays (10:30- 11:30 AM), call: number in email reminder<br />
<br />
* [[CTSC:ARRA.041012| April 10, 2012]]<br />
* [[CTSC:ARRA.051512| May 15, 2012]] Countway Library, conference room 319B<br />
* [[CTSC:ARRA.061912| June 19, 2012]] Countway Library, conference room 319B<br />
* [[CTSC:ARRA.071712| July 17, 2012]] Countway Library, conference room 319B<br />
<br />
=Past Events =<br />
<br />
===2012 meetings===<br />
* [[CTSC:ARRA.011712| January 17, 2012]] <br />
* [[CTSC:ARRA.022112| February 21, 2012]]<br />
* [[CTSC:ARRA.031312| March 13, 2012]] <br />
* [[CTSC:ARRA.041012| April 10, 2012]]<br />
<br />
===2011 meetings===<br />
'''[[CTSC:ARRA.tconJantoMay2011| January 2011 through May 2011 meeting minutes]]'''<br><br />
'''[[CTSC:ARRA.tconJunetoDec2011| June 2011 through December 2011 meeting minutes]]'''<br />
<br />
===2010 meetings===<br />
'''[[CTSC:ARRA.tconJantoJune2010| January 2010 through May 2010 t-con meeting minutes]]'''<br><br />
'''[[CTSC:ARRA.tconJunetoDec2010| June 2010 through December 2010 t-con and face to face meeting minutes]]'''<br />
<br />
===2009 meetings===<br />
'''[[CTSC:ARRA.2009tcon| 2009 t-con meeting minutes]]'''<br />
<br />
===Meeting presentations===<br />
* [[CTSC:ARRA.OHBM2011| Abstract presentation at the Organization for Human Brain Mapping meeting, Quebec City, CANADA, June, 2011]] <br />
* [[CTSC:ARRA.SIIM2011| Presentation at the Society for Imaging Informatics in Medicine annual meeting, Washington DC, June, 2011]] <br />
* [[CTSC:ARRA.ACRIN2010| ACRIN Medical Imaging Informatics Session, September 29, 2010]] <br />
* [[CTSC:ARRA.SFN2011| Abstract presentation at the Society for Neurosciences annual meeting, Washington DC, November, 2011]] <br />
<br />
=Using DCM4CHEE =<br />
[[CTSC:ARRA:dcm4chee_install|Installation instructions for DCM4CHEE]]<br />
<br />
Back to [[Collaboration:Harvard_CTSC|Collaboration:Harvard_CTSC]]<br />
<br></div>RandyGollubhttps://www.na-mic.org/w/index.php?title=CTSC:ARRA.041012&diff=74720CTSC:ARRA.0410122012-04-10T19:42:23Z<p>RandyGollub: Created page with 'Back to CTSC:ARRA supplement <br> <br> == Harvard Catalyst Medical Informatics group Meeting Minutes April 10, 2012 == In attendance: * David Wang * Bill Wang * Shawn Murph…'</p>
<hr />
<div>Back to [[CTSC:ARRA supplement]]<br />
<br> <br />
<br><br />
== Harvard Catalyst Medical Informatics group Meeting Minutes April 10, 2012 ==<br />
<br />
In attendance:<br />
* David Wang<br />
* Bill Wang<br />
* Shawn Murphy<br />
* Randy Gollub <br />
* Chris Herrick<br />
* Steve Pieper<br />
* Jesse Wei (phone)<br />
* Kathy Andriole (phone)<br />
<br />
'''Agenda'''<br />
# mi2b2 software update <br />
# manuscript<br />
# To Do List<br />
<br />
===mi2b2 software update===<br />
* In the newly designed workflow for the mi2b2 software version 1.2 that allows one or more XNAT instances and/or DICOM receivers such as OSIRIX-MD to be specified per project. We can now move images from a PACS to our mi2b2 server cache and then to the user's desired location(s). Uses DICOM commands not through REST calls.<br />
* User interface design is now the focus of software development in version 1.2. Goal is to enable users to be able to view the images that they have downloaded into their own specified location and have the information persist from session to session.<br />
<br />
===manuscript===<br />
* No progress in past 4 weeks. Will be primary focus of next meeting. ;)<br />
<br />
===To Do List ===<br />
* Discussed the idea of integrating our mi2b2 software with the Clinical Trial Processor (CTP). CTP is a Java based software tool developed by the CaBIG community comprised of a DICOM listener that can be configured to anonymize/de-identify files and a DICOM server to store the images. Shawn and Chris will look into this.<br />
<br />
* In past meetings we discussed the idea that at MGH (and perhaps other of our sites) that we might query and retrieve for images from their Radiology Department archives rather than the Clinical PACS. This needs to be further discussed in future meetings since it might be a much more stable architecture (fewer upgrades, etc) and also might allow for increased access as mi2b2 grows.</div>RandyGollubhttps://www.na-mic.org/w/index.php?title=CTSC:ARRA_supplement&diff=74340CTSC:ARRA supplement2012-03-13T16:38:33Z<p>RandyGollub: </p>
<hr />
<div>[[Projects:ARRASuplements|Back to our ARRA home page]]<br />
== Harvard Catalyst Medical Imaging Informatics ARRA Administrative Supplement==<br />
{|<br />
|align="left"|<br />
=Medical Imaging Informatics Bench to Bedside (mi2b2) =<br />
<br>This Medical Imaging Informatics project was funded by an Administrative Supplement to 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. Please go to our main wiki page (http://www.mi2b2.org) for the most up-to-date information and to download the software.<br />
|[[image:ARRA.png|thumb|px=250|Go to the [http://www.recovery.gov ARRA website]]]<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. Furthermore, the current practice of excellent medical care includes extensive use of diagnostic and prognostic medical imaging using standardized image acquisition methods. 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 />
= Human Subject's Protection Training =<br />
All project personnel who access the medical imaging data for this effort must secure appropriate IRB approval. If you haven't already done it, take the CITI human subject's protection training course (https://www.citiprogram.org/) and then have your site i2b2 PI add you to their i2b2 IRB development protocol. <br />
<br />
= Mockup used for initial development =<br />
<br />
The mi2b2 installation at HMS hospitals requires careful attention to patient privacy and operational integrity of critical hospital information systems (e.g. clinical PACS). Therefore the software related to this project was developed and tested extensively before deployment in the clinical setting.<br />
<br />
In order to develop the software in isolation, a [[CTSC:ARRA:Mockup|virtualized mockup]] was set up that included a PACS system with phantom and anonymized DICOM data, an instance of i2b2 software, and a test installation of XNAT. The guidelines for this are being left intact on this web site for historical purposes and for the use by the community as they do their own development. But please see the main download site for mi2b2 for primary instructions for how to proceed.<br />
<br />
= mi2b2 software download site and installation instructions =<br />
<br />
The Medical Imaging Informatics Bench to Bedside web site (http://www.mi2b2.org) that hosts the download of the software, developer guidelines for installation and user tutorials are hosted on the i2b2 Community Wiki.<br />
= Upcoming Events =<br />
* SIIM 2012 Open Source Plug Fest, June 2012<br />
<br />
===Weekly Meetings===<br />
Wednesdays on weeks without monthly meetings OCC 299, Shawn's Office (9:00- 10:00 AM) <br />
<br />
===Monthly Meetings===<br />
Tuesdays (10:30- 11:30 AM), call: 1-866-890-3820 <br />
<br />
* [[CTSC:ARRA.041012| April 10, 2012]] Countway Library, conference room 319B<br />
* [[CTSC:ARRA.051512| May 15, 2012]] Countway Library, conference room 319B<br />
* [[CTSC:ARRA.061912| June 19, 2012]] Countway Library, conference room 319B<br />
* [[CTSC:ARRA.071712| July 17, 2012]] Countway Library, conference room 319B<br />
<br />
=Past Events =<br />
<br />
===2012 meetings===<br />
* [[CTSC:ARRA.011712| January 17, 2012]] <br />
* [[CTSC:ARRA.022112| February 21, 2012]]<br />
* [[CTSC:ARRA.031312| March 13, 2012]] <br />
<br />
===2011 meetings===<br />
'''[[CTSC:ARRA.tconJantoMay2011| January 2011 through May 2011 meeting minutes]]'''<br><br />
'''[[CTSC:ARRA.tconJunetoDec2011| June 2011 through December 2011 meeting minutes]]'''<br />
<br />
===2010 meetings===<br />
'''[[CTSC:ARRA.tconJantoJune2010| January 2010 through May 2010 t-con meeting minutes]]'''<br><br />
'''[[CTSC:ARRA.tconJunetoDec2010| June 2010 through December 2010 t-con and face to face meeting minutes]]'''<br />
<br />
===2009 meetings===<br />
'''[[CTSC:ARRA.2009tcon| 2009 t-con meeting minutes]]'''<br />
<br />
===Meeting presentations===<br />
* [[CTSC:ARRA.OHBM2011| Abstract presentation at the Organization for Human Brain Mapping meeting, Quebec City, CANADA, June, 2011]] <br />
* [[CTSC:ARRA.SIIM2011| Presentation at the Society for Imaging Informatics in Medicine annual meeting, Washington DC, June, 2011]] <br />
* [[CTSC:ARRA.ACRIN2010| ACRIN Medical Imaging Informatics Session, September 29, 2010]] <br />
* [[CTSC:ARRA.SFN2011| Abstract presentation at the Society for Neurosciences annual meeting, Washington DC, November, 2011]] <br />
<br />
=Using DCM4CHEE =<br />
[[CTSC:ARRA:dcm4chee_install|Installation instructions for DCM4CHEE]]<br />
<br />
Back to [[Collaboration:Harvard_CTSC|Collaboration:Harvard_CTSC]]<br />
<br></div>RandyGollubhttps://www.na-mic.org/w/index.php?title=CTSC:ARRA.031312&diff=74339CTSC:ARRA.0313122012-03-13T15:37:21Z<p>RandyGollub: Created page with 'Back to CTSC:ARRA supplement <br> <br> == Harvard Catalyst Medical Informatics group Meeting Minutes March 13, 2012 == In attendance: * David Wang * Bill Wang * Shawn Murph…'</p>
<hr />
<div>Back to [[CTSC:ARRA supplement]]<br />
<br> <br />
<br><br />
== Harvard Catalyst Medical Informatics group Meeting Minutes March 13, 2012 ==<br />
<br />
In attendance:<br />
* David Wang<br />
* Bill Wang<br />
* Shawn Murphy<br />
* Randy Gollub<br />
* Darren Sack <br />
* Chris Herrick<br />
* Steve Pieper<br />
* Nandan Patibandla<br />
<br />
'''Agenda'''<br />
# mi2b2 software update <br />
# grant<br />
# manuscript<br />
<br />
===mi2b2 software update===<br />
* The team is working on the software design for the next mi2b2 software version that will allow one or more XNAT instances and/or DICOM receiver such as OSIRIX-MD to be specified per project.<br />
* Discussed the idea of integrating our mi2b2 software with the Clinical Trial Processor (CTP). CTP is a Java based software tool developed by the CaBIG community comprised of a DICOM listener that can be configured to anonymize/de-identify files and a DICOM server to store the images. Shawn and Chris will look into this.<br />
* Discussed the idea that at MGH (and perhaps other of our sites) that we might query and retrieve for images from the Radiology Department archives rather than the <br />
<br />
===mi2b2 Grant resubmission===<br />
* The revised grant was submitted on time and is in the pipeline to be reviewed by the same study section as the initial review.<br />
<br />
===manuscript===<br />
* Reviewed who needs to do what and Shawn will circulate a new version to work from. Will be primary focus of next meeting.</div>RandyGollubhttps://www.na-mic.org/w/index.php?title=CTSC:ARRA_supplement&diff=74197CTSC:ARRA supplement2012-02-21T16:36:21Z<p>RandyGollub: </p>
<hr />
<div>[[Projects:ARRASuplements|Back to our ARRA home page]]<br />
== Harvard Catalyst Medical Imaging Informatics ARRA Administrative Supplement==<br />
{|<br />
|align="left"|<br />
=Medical Imaging Informatics Bench to Bedside (mi2b2) =<br />
<br>This Medical Imaging Informatics project was funded by an Administrative Supplement to 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. Please go to our main wiki page (http://www.mi2b2.org) for the most up-to-date information and to download the software.<br />
|[[image:ARRA.png|thumb|px=250|Go to the [http://www.recovery.gov ARRA website]]]<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. Furthermore, the current practice of excellent medical care includes extensive use of diagnostic and prognostic medical imaging using standardized image acquisition methods. 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 />
= Human Subject's Protection Training =<br />
All project personnel who access the medical imaging data for this effort must secure appropriate IRB approval. If you haven't already done it, take the CITI human subject's protection training course (https://www.citiprogram.org/) and then have your site i2b2 PI add you to their i2b2 IRB development protocol. <br />
<br />
= Mockup used for initial development =<br />
<br />
The mi2b2 installation at HMS hospitals requires careful attention to patient privacy and operational integrity of critical hospital information systems (e.g. clinical PACS). Therefore the software related to this project was developed and tested extensively before deployment in the clinical setting.<br />
<br />
In order to develop the software in isolation, a [[CTSC:ARRA:Mockup|virtualized mockup]] was set up that included a PACS system with phantom and anonymized DICOM data, an instance of i2b2 software, and a test installation of XNAT. The guidelines for this are being left intact on this web site for historical purposes and for the use by the community as they do their own development. But please see the main download site for mi2b2 for primary instructions for how to proceed.<br />
<br />
= mi2b2 software download site and installation instructions =<br />
<br />
The Medical Imaging Informatics Bench to Bedside web site (http://www.mi2b2.org) that hosts the download of the software, developer guidelines for installation and user tutorials are hosted on the i2b2 Community Wiki.<br />
= Upcoming Events =<br />
* SIIM 2012 Open Source Plug Fest, June 2012<br />
<br />
===Weekly Meetings===<br />
Wednesdays on weeks without monthly meetings OCC 299, Shawn's Office (9:00- 10:00 AM) <br />
<br />
===Monthly Meetings===<br />
Tuesdays (10:30- 11:30 AM), call: 1-866-890-3820 <br />
<br />
* [[CTSC:ARRA.031312| March 13, 2012]] Countway Library, conference room 319B<br />
<br />
=Past Events =<br />
<br />
===2012 meetings===<br />
* [[CTSC:ARRA.011712| January 17, 2012]] <br />
* [[CTSC:ARRA.022112| February 21, 2012]]<br />
<br />
===2011 meetings===<br />
'''[[CTSC:ARRA.tconJantoMay2011| January 2011 through May 2011 meeting minutes]]'''<br><br />
'''[[CTSC:ARRA.tconJunetoDec2011| June 2011 through December 2011 meeting minutes]]'''<br />
<br />
===2010 meetings===<br />
'''[[CTSC:ARRA.tconJantoJune2010| January 2010 through May 2010 t-con meeting minutes]]'''<br><br />
'''[[CTSC:ARRA.tconJunetoDec2010| June 2010 through December 2010 t-con and face to face meeting minutes]]'''<br />
<br />
===2009 meetings===<br />
'''[[CTSC:ARRA.2009tcon| 2009 t-con meeting minutes]]'''<br />
<br />
===Meeting presentations===<br />
* [[CTSC:ARRA.OHBM2011| Abstract presentation at the Organization for Human Brain Mapping meeting, Quebec City, CANADA, June, 2011]] <br />
* [[CTSC:ARRA.SIIM2011| Presentation at the Society for Imaging Informatics in Medicine annual meeting, Washington DC, June, 2011]] <br />
* [[CTSC:ARRA.ACRIN2010| ACRIN Medical Imaging Informatics Session, September 29, 2010]] <br />
* [[CTSC:ARRA.SFN2011| Abstract presentation at the Society for Neurosciences annual meeting, Washington DC, November, 2011]] <br />
<br />
=Using DCM4CHEE =<br />
[[CTSC:ARRA:dcm4chee_install|Installation instructions for DCM4CHEE]]<br />
<br />
Back to [[Collaboration:Harvard_CTSC|Collaboration:Harvard_CTSC]]<br />
<br></div>RandyGollubhttps://www.na-mic.org/w/index.php?title=CTSC:ARRA_supplement&diff=74196CTSC:ARRA supplement2012-02-21T16:35:39Z<p>RandyGollub: </p>
<hr />
<div>[[Projects:ARRASuplements|Back to our ARRA home page]]<br />
== Harvard Catalyst Medical Imaging Informatics ARRA Administrative Supplement==<br />
{|<br />
|align="left"|<br />
=Medical Imaging Informatics Bench to Bedside (mi2b2) =<br />
<br>This Medical Imaging Informatics project was funded by an Administrative Supplement to 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. Please go to our main wiki page (http://www.mi2b2.org) for the most up-to-date information and to download the software.<br />
|[[image:ARRA.png|thumb|px=250|Go to the [http://www.recovery.gov ARRA website]]]<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. Furthermore, the current practice of excellent medical care includes extensive use of diagnostic and prognostic medical imaging using standardized image acquisition methods. 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 />
= Human Subject's Protection Training =<br />
All project personnel who access the medical imaging data for this effort must secure appropriate IRB approval. If you haven't already done it, take the CITI human subject's protection training course (https://www.citiprogram.org/) and then have your site i2b2 PI add you to their i2b2 IRB development protocol. <br />
<br />
= Mockup used for initial development =<br />
<br />
The mi2b2 installation at HMS hospitals requires careful attention to patient privacy and operational integrity of critical hospital information systems (e.g. clinical PACS). Therefore the software related to this project was developed and tested extensively before deployment in the clinical setting.<br />
<br />
In order to develop the software in isolation, a [[CTSC:ARRA:Mockup|virtualized mockup]] was set up that included a PACS system with phantom and anonymized DICOM data, an instance of i2b2 software, and a test installation of XNAT. The guidelines for this are being left intact on this web site for historical purposes and for the use by the community as they do their own development. But please see the main download site for mi2b2 for primary instructions for how to proceed.<br />
<br />
= mi2b2 software download site and installation instructions =<br />
<br />
The Medical Imaging Informatics Bench to Bedside web site (http://www.mi2b2.org) that hosts the download of the software, developer guidelines for installation and user tutorials are hosted on the i2b2 Community Wiki.<br />
= Upcoming Events =<br />
* SIIM 2012 Open Source Plug Fest, June 2012<br />
<br />
===Weekly Meetings===<br />
Wednesdays on weeks without monthly meetings OCC 299, Shawn's Office (9:00- 10:00 AM) <br />
<br />
===Monthly Meetings===<br />
Tuesdays (10:30- 11:30 AM), call: 1-866-890-3820 <br />
<br />
* [[CTSC:ARRA.022112| February 21, 2012]]<br />
* [[CTSC:ARRA.031312| March 13, 2012]]<br />
<br />
=Past Events =<br />
<br />
===2012 meetings===<br />
* [[CTSC:ARRA.011712| January 17, 2012]] Countway Library, conference room 319B<br />
<br />
===2011 meetings===<br />
'''[[CTSC:ARRA.tconJantoMay2011| January 2011 through May 2011 meeting minutes]]'''<br><br />
'''[[CTSC:ARRA.tconJunetoDec2011| June 2011 through December 2011 meeting minutes]]'''<br />
<br />
===2010 meetings===<br />
'''[[CTSC:ARRA.tconJantoJune2010| January 2010 through May 2010 t-con meeting minutes]]'''<br><br />
'''[[CTSC:ARRA.tconJunetoDec2010| June 2010 through December 2010 t-con and face to face meeting minutes]]'''<br />
<br />
===2009 meetings===<br />
'''[[CTSC:ARRA.2009tcon| 2009 t-con meeting minutes]]'''<br />
<br />
===Meeting presentations===<br />
* [[CTSC:ARRA.OHBM2011| Abstract presentation at the Organization for Human Brain Mapping meeting, Quebec City, CANADA, June, 2011]] <br />
* [[CTSC:ARRA.SIIM2011| Presentation at the Society for Imaging Informatics in Medicine annual meeting, Washington DC, June, 2011]] <br />
* [[CTSC:ARRA.ACRIN2010| ACRIN Medical Imaging Informatics Session, September 29, 2010]] <br />
* [[CTSC:ARRA.SFN2011| Abstract presentation at the Society for Neurosciences annual meeting, Washington DC, November, 2011]] <br />
<br />
=Using DCM4CHEE =<br />
[[CTSC:ARRA:dcm4chee_install|Installation instructions for DCM4CHEE]]<br />
<br />
Back to [[Collaboration:Harvard_CTSC|Collaboration:Harvard_CTSC]]<br />
<br></div>RandyGollubhttps://www.na-mic.org/w/index.php?title=CTSC:ARRA.022112&diff=74195CTSC:ARRA.0221122012-02-21T16:35:03Z<p>RandyGollub: Created page with 'Back to CTSC:ARRA supplement <br> <br> == Harvard Catalyst Medical Informatics group Meeting Minutes February 21, 2012 == In attendance: * David Wang * Shawn Murphy (phone)…'</p>
<hr />
<div>Back to [[CTSC:ARRA supplement]]<br />
<br> <br />
<br><br />
== Harvard Catalyst Medical Informatics group Meeting Minutes February 21, 2012 ==<br />
<br />
In attendance:<br />
* David Wang<br />
* Shawn Murphy (phone)<br />
* Randy Gollub<br />
* Darren Sack <br />
* Chris Herrick<br />
<br />
'''Agenda'''<br />
# mi2b2 software update <br />
# manuscript<br />
# grant<br />
<br />
===mi2b2 software update===<br />
* The newest version of mi2b2 software tool that now can transfer files using DICOM send command from the temporary cache to an XNAT instance or other DICOM receiver is now completed. The team has uploaded the code to the mi2b2 wiki page. Shawn will notify the BIRN senior leadership of this tremendous accomplishment. <br />
* This mi2b2 version is not yet installed on the Catalyst affiliated servers because this version is coded such that it must be configured to send the images to a single XNAT instance. <br />
* Discussed options for next mi2b2 software version to allow the XNAT instance to be specified per user or per project.<br />
<br />
===mi2b2 Grant resubmission===<br />
* The team has worked to generate the 1 page introduction and revision as well as new letters of support. We have been on time with all our deadlines and so we expect the resubmission will go in on time.<br />
<br />
===manuscript===<br />
* Little progress has been made since all efforts have been put towards grant and software. Agreed that next meeting will be devoted to working on manuscript. Meeting moved to March 13th so Shawn can be present.</div>RandyGollubhttps://www.na-mic.org/w/index.php?title=CTSC:ARRA_supplement&diff=74193CTSC:ARRA supplement2012-02-21T15:40:32Z<p>RandyGollub: </p>
<hr />
<div>[[Projects:ARRASuplements|Back to our ARRA home page]]<br />
== Harvard Catalyst Medical Imaging Informatics ARRA Administrative Supplement==<br />
{|<br />
|align="left"|<br />
=Medical Imaging Informatics Bench to Bedside (mi2b2) =<br />
<br>This Medical Imaging Informatics project was funded by an Administrative Supplement to 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. Please go to our main wiki page (http://www.mi2b2.org) for the most up-to-date information and to download the software.<br />
|[[image:ARRA.png|thumb|px=250|Go to the [http://www.recovery.gov ARRA website]]]<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. Furthermore, the current practice of excellent medical care includes extensive use of diagnostic and prognostic medical imaging using standardized image acquisition methods. 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 />
= Human Subject's Protection Training =<br />
All project personnel who access the medical imaging data for this effort must secure appropriate IRB approval. If you haven't already done it, take the CITI human subject's protection training course (https://www.citiprogram.org/) and then have your site i2b2 PI add you to their i2b2 IRB development protocol. <br />
<br />
= Mockup used for initial development =<br />
<br />
The mi2b2 installation at HMS hospitals requires careful attention to patient privacy and operational integrity of critical hospital information systems (e.g. clinical PACS). Therefore the software related to this project was developed and tested extensively before deployment in the clinical setting.<br />
<br />
In order to develop the software in isolation, a [[CTSC:ARRA:Mockup|virtualized mockup]] was set up that included a PACS system with phantom and anonymized DICOM data, an instance of i2b2 software, and a test installation of XNAT. The guidelines for this are being left intact on this web site for historical purposes and for the use by the community as they do their own development. But please see the main download site for mi2b2 for primary instructions for how to proceed.<br />
<br />
= mi2b2 software download site and installation instructions =<br />
<br />
The Medical Imaging Informatics Bench to Bedside web site (http://www.mi2b2.org) that hosts the download of the software, developer guidelines for installation and user tutorials are hosted on the i2b2 Community Wiki.<br />
= Upcoming Events =<br />
* SIIM 2012 Open Source Plug Fest, June 2012<br />
<br />
===Weekly Meetings===<br />
Wednesdays on weeks without monthly meetings OCC 299, Shawn's Office (9:00- 10:00 AM) <br />
<br />
===Monthly Meetings===<br />
Tuesdays (10:30- 11:30 AM), call: 1-866-890-3820 <br />
<br />
* [[CTSC:ARRA.022112| February 21, 2012]]<br />
* [[CTSC:ARRA.032012| March 20, 2012]]<br />
<br />
=Past Events =<br />
<br />
===2012 meetings===<br />
* [[CTSC:ARRA.011712| January 17, 2012]] Countway Library, conference room 319B<br />
<br />
===2011 meetings===<br />
'''[[CTSC:ARRA.tconJantoMay2011| January 2011 through May 2011 meeting minutes]]'''<br><br />
'''[[CTSC:ARRA.tconJunetoDec2011| June 2011 through December 2011 meeting minutes]]'''<br />
<br />
===2010 meetings===<br />
'''[[CTSC:ARRA.tconJantoJune2010| January 2010 through May 2010 t-con meeting minutes]]'''<br><br />
'''[[CTSC:ARRA.tconJunetoDec2010| June 2010 through December 2010 t-con and face to face meeting minutes]]'''<br />
<br />
===2009 meetings===<br />
'''[[CTSC:ARRA.2009tcon| 2009 t-con meeting minutes]]'''<br />
<br />
===Meeting presentations===<br />
* [[CTSC:ARRA.OHBM2011| Abstract presentation at the Organization for Human Brain Mapping meeting, Quebec City, CANADA, June, 2011]] <br />
* [[CTSC:ARRA.SIIM2011| Presentation at the Society for Imaging Informatics in Medicine annual meeting, Washington DC, June, 2011]] <br />
* [[CTSC:ARRA.ACRIN2010| ACRIN Medical Imaging Informatics Session, September 29, 2010]] <br />
* [[CTSC:ARRA.SFN2011| Abstract presentation at the Society for Neurosciences annual meeting, Washington DC, November, 2011]] <br />
<br />
=Using DCM4CHEE =<br />
[[CTSC:ARRA:dcm4chee_install|Installation instructions for DCM4CHEE]]<br />
<br />
Back to [[Collaboration:Harvard_CTSC|Collaboration:Harvard_CTSC]]<br />
<br></div>RandyGollubhttps://www.na-mic.org/w/index.php?title=Mi2b2_(i2b2_instance_with_the_STAR-D_software)_specifications_and_installation_instructions&diff=73888Mi2b2 (i2b2 instance with the STAR-D software) specifications and installation instructions2012-02-01T14:52:26Z<p>RandyGollub: Blanked the page</p>
<hr />
<div></div>RandyGollubhttps://www.na-mic.org/w/index.php?title=CTSC:ARRA_supplement&diff=73887CTSC:ARRA supplement2012-02-01T14:51:00Z<p>RandyGollub: </p>
<hr />
<div>[[Projects:ARRASuplements|Back to our ARRA home page]]<br />
== Harvard Catalyst Medical Imaging Informatics ARRA Administrative Supplement==<br />
{|<br />
|align="left"|<br />
=Medical Imaging Informatics Bench to Bedside (mi2b2) =<br />
<br>This Medical Imaging Informatics project was funded by an Administrative Supplement to 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. Please go to our main wiki page (http://www.mi2b2.org) for the most up-to-date information and to download the software.<br />
|[[image:ARRA.png|thumb|px=250|Go to the [http://www.recovery.gov ARRA website]]]<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. Furthermore, the current practice of excellent medical care includes extensive use of diagnostic and prognostic medical imaging using standardized image acquisition methods. 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 />
= Human Subject's Protection Training =<br />
All project personnel who access the medical imaging data for this effort must secure appropriate IRB approval. If you haven't already done it, take the CITI human subject's protection training course (https://www.citiprogram.org/) and then have your site i2b2 PI add you to their i2b2 IRB development protocol. <br />
<br />
= Mockup used for initial development =<br />
<br />
The mi2b2 installation at HMS hospitals requires careful attention to patient privacy and operational integrity of critical hospital information systems (e.g. clinical PACS). Therefore the software related to this project was developed and tested extensively before deployment in the clinical setting.<br />
<br />
In order to develop the software in isolation, a [[CTSC:ARRA:Mockup|virtualized mockup]] was set up that included a PACS system with phantom and anonymized DICOM data, an instance of i2b2 software, and a test installation of XNAT. The guidelines for this are being left intact on this web site for historical purposes and for the use by the community as they do their own development. But please see the main download site for mi2b2 for primary instructions for how to proceed.<br />
<br />
= mi2b2 software download site and installation instructions =<br />
<br />
The Medical Imaging Informatics Bench to Bedside web site (http://www.mi2b2.org) that hosts the download of the software, developer guidelines for installation and user tutorials are hosted on the i2b2 Community Wiki.<br />
= Upcoming Events =<br />
* SIIM 2012 Open Source Plug Fest, June 2012<br />
<br />
===Weekly Meetings===<br />
Wednesdays on weeks without monthly meetings OCC 299, Shawn's Office (9:00- 10:00 AM) <br />
<br />
===Monthly Meetings===<br />
Tuesdays (10:30- 11:30 AM), call: 1-866-890-3820 <br />
<br />
*<br />
<br />
=Past Events =<br />
<br />
===2012 meetings===<br />
* [[CTSC:ARRA.011712| January 17, 2012]] Countway Library, conference room 319B<br />
<br />
===2011 meetings===<br />
'''[[CTSC:ARRA.tconJantoMay2011| January 2011 through May 2011 meeting minutes]]'''<br><br />
'''[[CTSC:ARRA.tconJunetoDec2011| June 2011 through December 2011 meeting minutes]]'''<br />
<br />
===2010 meetings===<br />
'''[[CTSC:ARRA.tconJantoJune2010| January 2010 through May 2010 t-con meeting minutes]]'''<br><br />
'''[[CTSC:ARRA.tconJunetoDec2010| June 2010 through December 2010 t-con and face to face meeting minutes]]'''<br />
<br />
===2009 meetings===<br />
'''[[CTSC:ARRA.2009tcon| 2009 t-con meeting minutes]]'''<br />
<br />
===Meeting presentations===<br />
* [[CTSC:ARRA.OHBM2011| Abstract presentation at the Organization for Human Brain Mapping meeting, Quebec City, CANADA, June, 2011]] <br />
* [[CTSC:ARRA.SIIM2011| Presentation at the Society for Imaging Informatics in Medicine annual meeting, Washington DC, June, 2011]] <br />
* [[CTSC:ARRA.ACRIN2010| ACRIN Medical Imaging Informatics Session, September 29, 2010]] <br />
* [[CTSC:ARRA.SFN2011| Abstract presentation at the Society for Neurosciences annual meeting, Washington DC, November, 2011]] <br />
<br />
=Using DCM4CHEE =<br />
[[CTSC:ARRA:dcm4chee_install|Installation instructions for DCM4CHEE]]<br />
<br />
Back to [[Collaboration:Harvard_CTSC|Collaboration:Harvard_CTSC]]<br />
<br></div>RandyGollubhttps://www.na-mic.org/w/index.php?title=CTSC:ARRA_supplement&diff=73886CTSC:ARRA supplement2012-02-01T14:49:45Z<p>RandyGollub: </p>
<hr />
<div>[[Projects:ARRASuplements|Back to our ARRA home page]]<br />
== Harvard Catalyst Medical Imaging Informatics ARRA Administrative Supplement==<br />
{|<br />
|align="left"|<br />
=Medical Imaging Informatics Bench to Bedside (mi2b2) =<br />
<br>This Medical Imaging Informatics project was funded by an Administrative Supplement to 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. Please go to our main wiki page (http://www.mi2b2.org) for the most up-to-date information and to download the software.<br />
|[[image:ARRA.png|thumb|px=250|Go to the [http://www.recovery.gov ARRA website]]]<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. Furthermore, the current practice of excellent medical care includes extensive use of diagnostic and prognostic medical imaging using standardized image acquisition methods. 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 />
= Human Subject's Protection Training =<br />
All project personnel who access the medical imaging data for this effort must secure appropriate IRB approval. If you haven't already done it, take the CITI human subject's protection training course (https://www.citiprogram.org/) and then have your site i2b2 PI add you to their i2b2 IRB development protocol. <br />
<br />
= Mockup used for initial development =<br />
<br />
The mi2b2 installation at HMS hospitals requires careful attention to patient privacy and operational integrity of critical hospital information systems (e.g. clinical PACS). Therefore the software related to this project was developed and tested extensively before deployment in the clinical setting.<br />
<br />
In order to develop the software in isolation, a [[CTSC:ARRA:Mockup|virtualized mockup]] was set up that included a PACS system with phantom and anonymized DICOM data, an instance of i2b2 software, and a test installation of XNAT. The guidelines for this are being left intact on this web site for historical purposes and for the use by the community as they do their own development. But please see the main download site for mi2b2 for primary instructions for how to proceed.<br />
<br />
= mi2b2 software download site and installation instructions =<br />
<br />
The Medical Imaging Informatics Bench to Bedside web site (http://www.mi2b2.org) that hosts the download of the software, developer guidelines for installation and user tutorials are hosted on the i2b2 Community Wiki.<br />
= Upcoming Events =<br />
<br />
* [[CTSC:ARRA.SFN2011| Abstract presentation at the Society for Neurosciences annual meeting, Washington DC, November, 2011]] <br />
<br />
<br />
===Weekly Meetings===<br />
Wednesdays on weeks without monthly meetings OCC 299, Shawn's Office (9:00- 10:00 AM) <br />
<br />
===Monthly Meetings===<br />
Tuesdays (10:30- 11:30 AM), call: 1-866-890-3820 <br />
<br />
*<br />
<br />
=Past Events =<br />
<br />
===2012 meetings===<br />
* [[CTSC:ARRA.011712| January 17, 2012]] Countway Library, conference room 319B<br />
<br />
===2011 meetings===<br />
'''[[CTSC:ARRA.tconJantoMay2011| January 2011 through May 2011 meeting minutes]]'''<br><br />
'''[[CTSC:ARRA.tconJunetoDec2011| June 2011 through December 2011 meeting minutes]]'''<br />
<br />
===2010 meetings===<br />
'''[[CTSC:ARRA.tconJantoJune2010| January 2010 through May 2010 t-con meeting minutes]]'''<br><br />
'''[[CTSC:ARRA.tconJunetoDec2010| June 2010 through December 2010 t-con and face to face meeting minutes]]'''<br />
<br />
===2009 meetings===<br />
'''[[CTSC:ARRA.2009tcon| 2009 t-con meeting minutes]]'''<br />
<br />
===Meeting presentations===<br />
* [[CTSC:ARRA.OHBM2011| Abstract presentation at the Organization for Human Brain Mapping meeting, Quebec City, CANADA, June, 2011]] <br />
* [[CTSC:ARRA.SIIM2011| Presentation at the Society for Imaging Informatics in Medicine annual meeting, Washington DC, June, 2011]] <br />
* [[CTSC:ARRA.ACRIN2010| ACRIN Medical Imaging Informatics Session, September 29, 2010]] <br />
<br />
=Using DCM4CHEE =<br />
[[CTSC:ARRA:dcm4chee_install|Installation instructions for DCM4CHEE]]<br />
<br />
Back to [[Collaboration:Harvard_CTSC|Collaboration:Harvard_CTSC]]<br />
<br></div>RandyGollubhttps://www.na-mic.org/w/index.php?title=CTSC:ARRA_supplement&diff=73885CTSC:ARRA supplement2012-02-01T14:49:15Z<p>RandyGollub: </p>
<hr />
<div>[[Projects:ARRASuplements|Back to our ARRA home page]]<br />
== 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 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. Please go to our main wiki page (http://www.mi2b2.org) for the most up-to-date information and to download the software.<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. Furthermore, the current practice of excellent medical care includes extensive use of diagnostic and prognostic medical imaging using standardized image acquisition methods. 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 />
= Human Subject's Protection Training =<br />
All project personnel who access the medical imaging data for this effort must secure appropriate IRB approval. If you haven't already done it, take the CITI human subject's protection training course (https://www.citiprogram.org/) and then have your site i2b2 PI add you to their i2b2 IRB development protocol. <br />
<br />
= Mockup used for initial development =<br />
<br />
The mi2b2 installation at HMS hospitals requires careful attention to patient privacy and operational integrity of critical hospital information systems (e.g. clinical PACS). Therefore the software related to this project was developed and tested extensively before deployment in the clinical setting.<br />
<br />
In order to develop the software in isolation, a [[CTSC:ARRA:Mockup|virtualized mockup]] was set up that included a PACS system with phantom and anonymized DICOM data, an instance of i2b2 software, and a test installation of XNAT. The guidelines for this are being left intact on this web site for historical purposes and for the use by the community as they do their own development. But please see the main download site for mi2b2 for primary instructions for how to proceed.<br />
<br />
= mi2b2 software download site and installation instructions =<br />
<br />
The Medical Imaging Informatics Bench to Bedside web site (http://www.mi2b2.org) that hosts the download of the software, developer guidelines for installation and user tutorials are hosted on the i2b2 Community Wiki.<br />
= Upcoming Events =<br />
<br />
* [[CTSC:ARRA.SFN2011| Abstract presentation at the Society for Neurosciences annual meeting, Washington DC, November, 2011]] <br />
<br />
<br />
===Weekly Meetings===<br />
Wednesdays on weeks without monthly meetings OCC 299, Shawn's Office (9:00- 10:00 AM) <br />
<br />
===Monthly Meetings===<br />
Tuesdays (10:30- 11:30 AM), call: 1-866-890-3820 <br />
<br />
*<br />
<br />
=Past Events =<br />
<br />
===2012 meetings===<br />
* [[CTSC:ARRA.011712| January 17, 2012]] Countway Library, conference room 319B<br />
<br />
===2011 meetings===<br />
'''[[CTSC:ARRA.tconJantoMay2011| January 2011 through May 2011 meeting minutes]]'''<br><br />
'''[[CTSC:ARRA.tconJunetoDec2011| June 2011 through December 2011 meeting minutes]]'''<br />
<br />
===2010 meetings===<br />
'''[[CTSC:ARRA.tconJantoJune2010| January 2010 through May 2010 t-con meeting minutes]]'''<br><br />
'''[[CTSC:ARRA.tconJunetoDec2010| June 2010 through December 2010 t-con and face to face meeting minutes]]'''<br />
<br />
===2009 meetings===<br />
'''[[CTSC:ARRA.2009tcon| 2009 t-con meeting minutes]]'''<br />
<br />
===Meeting presentations===<br />
* [[CTSC:ARRA.OHBM2011| Abstract presentation at the Organization for Human Brain Mapping meeting, Quebec City, CANADA, June, 2011]] <br />
* [[CTSC:ARRA.SIIM2011| Presentation at the Society for Imaging Informatics in Medicine annual meeting, Washington DC, June, 2011]] <br />
* [[CTSC:ARRA.ACRIN2010| ACRIN Medical Imaging Informatics Session, September 29, 2010]] <br />
<br />
=Using DCM4CHEE =<br />
[[CTSC:ARRA:dcm4chee_install|Installation instructions for DCM4CHEE]]<br />
<br />
Back to [[Collaboration:Harvard_CTSC|Collaboration:Harvard_CTSC]]<br />
<br></div>RandyGollubhttps://www.na-mic.org/w/index.php?title=CTSC:ARRA_supplement&diff=73884CTSC:ARRA supplement2012-02-01T14:47:33Z<p>RandyGollub: </p>
<hr />
<div>[[Projects:ARRASuplements|Back to our ARRA home page]]<br />
== 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 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. Furthermore, the current practice of excellent medical care includes extensive use of diagnostic and prognostic medical imaging using standardized image acquisition methods. 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 />
= Human Subject's Protection Training =<br />
All project personnel who access the medical imaging data for this effort must secure appropriate IRB approval. If you haven't already done it, take the CITI human subject's protection training course (https://www.citiprogram.org/) and then have your site i2b2 PI add you to their i2b2 IRB development protocol. <br />
<br />
= Mockup used for initial development =<br />
<br />
The mi2b2 installation at HMS hospitals requires careful attention to patient privacy and operational integrity of critical hospital information systems (e.g. clinical PACS). Therefore the software related to this project was developed and tested extensively before deployment in the clinical setting.<br />
<br />
In order to develop the software in isolation, a [[CTSC:ARRA:Mockup|virtualized mockup]] was set up that included a PACS system with phantom and anonymized DICOM data, an instance of i2b2 software, and a test installation of XNAT. The guidelines for this are being left intact on this web site for historical purposes and for the use by the community as they do their own development. But please see the main download site for mi2b2 for primary instructions for how to proceed.<br />
<br />
= mi2b2 software download site and installation instructions =<br />
<br />
The Medical Imaging Informatics Bench to Bedside web site (http://www.mi2b2.org) that hosts the download of the software, developer guidelines for installation and user tutorials are hosted on the i2b2 Community Wiki.<br />
= Upcoming Events =<br />
<br />
* [[CTSC:ARRA.SFN2011| Abstract presentation at the Society for Neurosciences annual meeting, Washington DC, November, 2011]] <br />
<br />
<br />
===Weekly Meetings===<br />
Wednesdays on weeks without monthly meetings OCC 299, Shawn's Office (9:00- 10:00 AM) <br />
<br />
===Monthly Meetings===<br />
Tuesdays (10:30- 11:30 AM), call: 1-866-890-3820 <br />
<br />
*<br />
<br />
=Past Events =<br />
<br />
===2012 meetings===<br />
* [[CTSC:ARRA.011712| January 17, 2012]] Countway Library, conference room 319B<br />
<br />
===2011 meetings===<br />
'''[[CTSC:ARRA.tconJantoMay2011| January 2011 through May 2011 meeting minutes]]'''<br><br />
'''[[CTSC:ARRA.tconJunetoDec2011| June 2011 through December 2011 meeting minutes]]'''<br />
<br />
===2010 meetings===<br />
'''[[CTSC:ARRA.tconJantoJune2010| January 2010 through May 2010 t-con meeting minutes]]'''<br><br />
'''[[CTSC:ARRA.tconJunetoDec2010| June 2010 through December 2010 t-con and face to face meeting minutes]]'''<br />
<br />
===2009 meetings===<br />
'''[[CTSC:ARRA.2009tcon| 2009 t-con meeting minutes]]'''<br />
<br />
===Meeting presentations===<br />
* [[CTSC:ARRA.OHBM2011| Abstract presentation at the Organization for Human Brain Mapping meeting, Quebec City, CANADA, June, 2011]] <br />
* [[CTSC:ARRA.SIIM2011| Presentation at the Society for Imaging Informatics in Medicine annual meeting, Washington DC, June, 2011]] <br />
* [[CTSC:ARRA.ACRIN2010| ACRIN Medical Imaging Informatics Session, September 29, 2010]] <br />
<br />
=Using DCM4CHEE =<br />
[[CTSC:ARRA:dcm4chee_install|Installation instructions for DCM4CHEE]]<br />
<br />
Back to [[Collaboration:Harvard_CTSC|Collaboration:Harvard_CTSC]]<br />
<br></div>RandyGollubhttps://www.na-mic.org/w/index.php?title=CTSC:ARRA_supplement&diff=73883CTSC:ARRA supplement2012-02-01T14:45:02Z<p>RandyGollub: /* Upcoming Events */</p>
<hr />
<div>[[Projects:ARRASuplements|Back to our ARRA home page]]<br />
== 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 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. Furthermore, the current practice of excellent medical care includes extensive use of diagnostic and prognostic medical imaging using standardized image acquisition methods. 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 />
= Human Subject's Protection Training =<br />
All project personnel who access the medical imaging data for this effort must secure appropriate IRB approval. If you haven't already done it, take the CITI human subject's protection training course (https://www.citiprogram.org/) and then have your site i2b2 PI add you to their i2b2 IRB development protocol. <br />
<br />
= Mockup used for initial development =<br />
<br />
The mi2b2 installation at HMS hospitals requires careful attention to patient privacy and operational integrity of critical hospital information systems (e.g. clinical PACS). Therefore the software related to this project was developed and tested extensively before deployment in the clinical setting.<br />
<br />
In order to develop the software in isolation, a [[CTSC:ARRA:Mockup|virtualized mockup]] was set up that included a PACS system with phantom and anonymized DICOM data, an instance of i2b2 software, and a test installation of XNAT. The guidelines for this are being left intact on this web site for historical purposes and for the use by the community as they do their own development. But please see the main download site for mi2b2 for primary instructions for how to proceed.<br />
<br />
= mi2b2 software download site and installation instructions =<br />
<br />
The Medical Imaging Informatics Bench to Bedside web site (http://www.mi2b2.org) that hosts the download of the software, developer guidelines for installation and user tutorials are hosted on the i2b2 Community Wiki.<br />
= Upcoming Events =<br />
<br />
* [[CTSC:ARRA.SFN2011| Abstract presentation at the Society for Neurosciences annual meeting, Washington DC, November, 2011]] <br />
<br />
<br />
===Weekly Meetings===<br />
Wednesdays on weeks without monthly meetings OCC 299, Shawn's Office (9:00- 10:00 AM) <br />
<br />
===Monthly Meetings===<br />
Tuesdays (10:30- 11:30 AM), call: 1-866-890-3820 <br />
<br />
* [[CTSC:ARRA.011712| January 17, 2012]] Countway Library, conference room 319B<br />
<br />
=Past Events =<br />
<br />
===2011 meetings===<br />
<br />
<br><br />
* [[CTSC:ARRA.OHBM2011| Abstract presentation at the Organization for Human Brain Mapping meeting, Quebec City, CANADA, June, 2011]] <br />
* [[CTSC:ARRA.SIIM2011| Presentation at the Society for Imaging Informatics in Medicine annual meeting, Washington DC, June, 2011]] <br />
* [[CTSC:ARRA.ACRIN2010| ACRIN Medical Imaging Informatics Session, September 29, 2010]] <br />
<br />
<br />
'''[[CTSC:ARRA.tconJantoMay2011| January 2011 through May 2011 meeting minutes]]'''<br />
<br><br />
'''[[CTSC:ARRA.tconJunetoDec2011| June 2011 through December 2011 meeting minutes]]'''<br />
<br />
===2010 meetings===<br />
<br />
'''[[CTSC:ARRA.tconJantoJune2010| January 2010 through May 2010 t-con meeting minutes]]'''<br><br />
'''[[CTSC:ARRA.tconJunetoDec2010| June 2010 through December 2010 t-con and face to face meeting minutes]]'''<br />
<br />
===2009 meetings===<br />
<br />
'''[[CTSC:ARRA.2009tcon| 2009 t-con meeting minutes]]<br />
'''<br />
=Using DCM4CHEE =<br />
[[CTSC:ARRA:dcm4chee_install|Installation instructions for DCM4CHEE]]<br />
<br />
Back to [[Collaboration:Harvard_CTSC|Collaboration:Harvard_CTSC]]<br />
<br></div>RandyGollubhttps://www.na-mic.org/w/index.php?title=CTSC:ARRA_supplement&diff=73882CTSC:ARRA supplement2012-02-01T14:14:50Z<p>RandyGollub: </p>
<hr />
<div>[[Projects:ARRASuplements|Back to our ARRA home page]]<br />
== 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 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. Furthermore, the current practice of excellent medical care includes extensive use of diagnostic and prognostic medical imaging using standardized image acquisition methods. 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 />
= Human Subject's Protection Training =<br />
All project personnel who access the medical imaging data for this effort must secure appropriate IRB approval. If you haven't already done it, take the CITI human subject's protection training course (https://www.citiprogram.org/) and then have your site i2b2 PI add you to their i2b2 IRB development protocol. <br />
<br />
= Mockup used for initial development =<br />
<br />
The mi2b2 installation at HMS hospitals requires careful attention to patient privacy and operational integrity of critical hospital information systems (e.g. clinical PACS). Therefore the software related to this project was developed and tested extensively before deployment in the clinical setting.<br />
<br />
In order to develop the software in isolation, a [[CTSC:ARRA:Mockup|virtualized mockup]] was set up that included a PACS system with phantom and anonymized DICOM data, an instance of i2b2 software, and a test installation of XNAT. The guidelines for this are being left intact on this web site for historical purposes and for the use by the community as they do their own development. But please see the main download site for mi2b2 for primary instructions for how to proceed.<br />
<br />
= mi2b2 software download site and installation instructions =<br />
<br />
The Medical Imaging Informatics Bench to Bedside web site (http://www.mi2b2.org) that hosts the download of the software, developer guidelines for installation and user tutorials are hosted on the i2b2 Community Wiki.<br />
= Upcoming Events =<br />
<br />
* [[CTSC:ARRA.SFN2011| Abstract presentation at the Society for Neurosciences annual meeting, Washington DC, November, 2011]] <br />
<br />
<br />
===Weekly Meetings===<br />
Wednesday (9:00- 10:00 AM), call: 1-866-890-3820 <br />
* [[CTSC:ARRA.110211| November 2, 2011]] OCC 299, Shawn's Office<br />
* [[CTSC:ARRA.110911| November 9, 2011]] OCC 299, Shawn's Office<br />
* [[CTSC:ARRA.111611| November 16, 2011]] OCC 299, Shawn's Office<br />
* [[CTSC:ARRA.113011| November 30, 2011]] OCC 299, Shawn's Office (Note: conflicts with RSNA)<br />
<br />
===Monthly Meetings===<br />
Tuesday (10:30- 11:30 AM), call: 1-866-890-3820 <br />
<br />
* [[CTSC:ARRA.011712| January 17, 2012]] Ware room, Countway 5th floor<br />
<br />
=Past Events =<br />
<br />
===2011 meetings===<br />
<br />
<br><br />
* [[CTSC:ARRA.OHBM2011| Abstract presentation at the Organization for Human Brain Mapping meeting, Quebec City, CANADA, June, 2011]] <br />
* [[CTSC:ARRA.SIIM2011| Presentation at the Society for Imaging Informatics in Medicine annual meeting, Washington DC, June, 2011]] <br />
* [[CTSC:ARRA.ACRIN2010| ACRIN Medical Imaging Informatics Session, September 29, 2010]] <br />
<br />
<br />
'''[[CTSC:ARRA.tconJantoMay2011| January 2011 through May 2011 meeting minutes]]'''<br />
<br><br />
'''[[CTSC:ARRA.tconJunetoDec2011| June 2011 through December 2011 meeting minutes]]'''<br />
<br />
===2010 meetings===<br />
<br />
'''[[CTSC:ARRA.tconJantoJune2010| January 2010 through May 2010 t-con meeting minutes]]'''<br><br />
'''[[CTSC:ARRA.tconJunetoDec2010| June 2010 through December 2010 t-con and face to face meeting minutes]]'''<br />
<br />
===2009 meetings===<br />
<br />
'''[[CTSC:ARRA.2009tcon| 2009 t-con meeting minutes]]<br />
'''<br />
=Using DCM4CHEE =<br />
[[CTSC:ARRA:dcm4chee_install|Installation instructions for DCM4CHEE]]<br />
<br />
Back to [[Collaboration:Harvard_CTSC|Collaboration:Harvard_CTSC]]<br />
<br></div>RandyGollubhttps://www.na-mic.org/w/index.php?title=CTSC:ARRA.tconJunetoDec2011&diff=73881CTSC:ARRA.tconJunetoDec20112012-02-01T14:14:13Z<p>RandyGollub: </p>
<hr />
<div>Back to [[CTSC:ARRA supplement]]<br />
<br><br />
* [[CTSC:ARRA.060711| June 07, 2011]]<br />
* [[CTSC:ARRA.061411| June 14, 2011]]<br />
* [[CTSC:ARRA.062111| June 21, 2011]] Cancelled<br />
* [[CTSC:ARRA.062811| June 28, 2011]] Cancelled<br />
* [[CTSC:ARRA.070511| July 5, 2011]] <br />
* [[CTSC:ARRA.071211| July 12, 2011]]<br />
* [[CTSC:ARRA.071911| July 19, 2011]]<br />
* [[CTSC:ARRA.072611| July 26, 2011]]<br />
* [[CTSC:ARRA.080211| August 2, 2011]]<br />
* [[CTSC:ARRA.080911| August 9, 2011]]<br />
* [[CTSC:ARRA.081611| August 16, 2011]]<br />
* [[CTSC:ARRA.082311| August 23, 2011]]<br />
* [[CTSC:ARRA.083011| August 30, 2011]]<br />
* [[CTSC:ARRA.090611| September 6, 2011]]<br />
* [[CTSC:ARRA.091311| September 13, 2011]]<br />
* [[CTSC:ARRA.092011| September 20, 2011]]<br />
* [[CTSC:ARRA.092711| September 27, 2011]]<br />
* [[CTSC:ARRA.101811| October 18, 2011]]<br />
* [[CTSC:ARRA.112211| November 22, 2011]]<br />
* [[CTSC:ARRA.122011| December 20, 2011]]</div>RandyGollubhttps://www.na-mic.org/w/index.php?title=CTSC:ARRA.tconJunetoDec2011&diff=73880CTSC:ARRA.tconJunetoDec20112012-02-01T14:13:38Z<p>RandyGollub: Created page with ' * June 07, 2011 * June 14, 2011 * June 21, 2011 Cancelled * June 28, 2011 Cancelled * [[…'</p>
<hr />
<div><br />
<br />
* [[CTSC:ARRA.060711| June 07, 2011]]<br />
* [[CTSC:ARRA.061411| June 14, 2011]]<br />
* [[CTSC:ARRA.062111| June 21, 2011]] Cancelled<br />
* [[CTSC:ARRA.062811| June 28, 2011]] Cancelled<br />
* [[CTSC:ARRA.070511| July 5, 2011]] <br />
* [[CTSC:ARRA.071211| July 12, 2011]]<br />
* [[CTSC:ARRA.071911| July 19, 2011]]<br />
* [[CTSC:ARRA.072611| July 26, 2011]]<br />
* [[CTSC:ARRA.080211| August 2, 2011]]<br />
* [[CTSC:ARRA.080911| August 9, 2011]]<br />
* [[CTSC:ARRA.081611| August 16, 2011]]<br />
* [[CTSC:ARRA.082311| August 23, 2011]]<br />
* [[CTSC:ARRA.083011| August 30, 2011]]<br />
* [[CTSC:ARRA.090611| September 6, 2011]]<br />
* [[CTSC:ARRA.091311| September 13, 2011]]<br />
* [[CTSC:ARRA.092011| September 20, 2011]]<br />
* [[CTSC:ARRA.092711| September 27, 2011]]<br />
* [[CTSC:ARRA.101811| October 18, 2011]]<br />
* [[CTSC:ARRA.112211| November 22, 2011]]<br />
* [[CTSC:ARRA.122011| December 20, 2011]]</div>RandyGollubhttps://www.na-mic.org/w/index.php?title=CTSC:ARRA_supplement&diff=73879CTSC:ARRA supplement2012-02-01T14:13:06Z<p>RandyGollub: </p>
<hr />
<div>[[Projects:ARRASuplements|Back to our ARRA home page]]<br />
== 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 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. Furthermore, the current practice of excellent medical care includes extensive use of diagnostic and prognostic medical imaging using standardized image acquisition methods. 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 />
= Human Subject's Protection Training =<br />
All project personnel who access the medical imaging data for this effort must secure appropriate IRB approval. If you haven't already done it, take the CITI human subject's protection training course (https://www.citiprogram.org/) and then have your site i2b2 PI add you to their i2b2 IRB development protocol. <br />
<br />
= Mockup used for initial development =<br />
<br />
The mi2b2 installation at HMS hospitals requires careful attention to patient privacy and operational integrity of critical hospital information systems (e.g. clinical PACS). Therefore the software related to this project was developed and tested extensively before deployment in the clinical setting.<br />
<br />
In order to develop the software in isolation, a [[CTSC:ARRA:Mockup|virtualized mockup]] was set up that included a PACS system with phantom and anonymized DICOM data, an instance of i2b2 software, and a test installation of XNAT. The guidelines for this are being left intact on this web site for historical purposes and for the use by the community as they do their own development. But please see the main download site for mi2b2 for primary instructions for how to proceed.<br />
<br />
= mi2b2 software download site and installation instructions =<br />
<br />
The Medical Imaging Informatics Bench to Bedside web site (http://www.mi2b2.org) that hosts the download of the software, developer guidelines for installation and user tutorials are hosted on the i2b2 Community Wiki.<br />
= Upcoming Events =<br />
<br />
* [[CTSC:ARRA.SFN2011| Abstract presentation at the Society for Neurosciences annual meeting, Washington DC, November, 2011]] <br />
<br />
<br />
===Weekly Meetings===<br />
Wednesday (9:00- 10:00 AM), call: 1-866-890-3820 <br />
* [[CTSC:ARRA.110211| November 2, 2011]] OCC 299, Shawn's Office<br />
* [[CTSC:ARRA.110911| November 9, 2011]] OCC 299, Shawn's Office<br />
* [[CTSC:ARRA.111611| November 16, 2011]] OCC 299, Shawn's Office<br />
* [[CTSC:ARRA.113011| November 30, 2011]] OCC 299, Shawn's Office (Note: conflicts with RSNA)<br />
<br />
===Monthly Meetings===<br />
Tuesday (10:30- 11:30 AM), call: 1-866-890-3820 <br />
<br />
* [[CTSC:ARRA.011712| January 17, 2012]] Ware room, Countway 5th floor<br />
<br />
=Past Events =<br />
<br />
===2011 meetings===<br />
<br />
* [[CTSC:ARRA.060711| June 07, 2011]]<br />
* [[CTSC:ARRA.061411| June 14, 2011]]<br />
* [[CTSC:ARRA.062111| June 21, 2011]] Cancelled<br />
* [[CTSC:ARRA.062811| June 28, 2011]] Cancelled<br />
* [[CTSC:ARRA.070511| July 5, 2011]] <br />
* [[CTSC:ARRA.071211| July 12, 2011]]<br />
* [[CTSC:ARRA.071911| July 19, 2011]]<br />
* [[CTSC:ARRA.072611| July 26, 2011]]<br />
* [[CTSC:ARRA.080211| August 2, 2011]]<br />
* [[CTSC:ARRA.080911| August 9, 2011]]<br />
* [[CTSC:ARRA.081611| August 16, 2011]]<br />
* [[CTSC:ARRA.082311| August 23, 2011]]<br />
* [[CTSC:ARRA.083011| August 30, 2011]]<br />
* [[CTSC:ARRA.090611| September 6, 2011]]<br />
* [[CTSC:ARRA.091311| September 13, 2011]]<br />
* [[CTSC:ARRA.092011| September 20, 2011]]<br />
* [[CTSC:ARRA.092711| September 27, 2011]]<br />
* [[CTSC:ARRA.101811| October 18, 2011]]<br />
* [[CTSC:ARRA.112211| November 22, 2011]]<br />
* [[CTSC:ARRA.122011| December 20, 2011]] <br />
<br><br />
<br><br />
* [[CTSC:ARRA.OHBM2011| Abstract presentation at the Organization for Human Brain Mapping meeting, Quebec City, CANADA, June, 2011]] <br />
* [[CTSC:ARRA.SIIM2011| Presentation at the Society for Imaging Informatics in Medicine annual meeting, Washington DC, June, 2011]] <br />
* [[CTSC:ARRA.ACRIN2010| ACRIN Medical Imaging Informatics Session, September 29, 2010]] <br />
<br />
<br />
'''[[CTSC:ARRA.tconJantoMay2011| January 2011 through May 2011 meeting minutes]]'''<br />
'''[[CTSC:ARRA.tconJunetoDec2011| June 2011 through December 2011 meeting minutes]]'''<br />
<br />
===2010 meetings===<br />
<br />
'''[[CTSC:ARRA.tconJantoJune2010| January 2010 through May 2010 t-con meeting minutes]]'''<br><br />
'''[[CTSC:ARRA.tconJunetoDec2010| June 2010 through December 2010 t-con and face to face meeting minutes]]'''<br />
<br />
===2009 meetings===<br />
<br />
'''[[CTSC:ARRA.2009tcon| 2009 t-con meeting minutes]]<br />
'''<br />
=Using DCM4CHEE =<br />
[[CTSC:ARRA:dcm4chee_install|Installation instructions for DCM4CHEE]]<br />
<br />
Back to [[Collaboration:Harvard_CTSC|Collaboration:Harvard_CTSC]]<br />
<br></div>RandyGollubhttps://www.na-mic.org/w/index.php?title=CTSC:ARRA_supplement&diff=73878CTSC:ARRA supplement2012-02-01T14:04:40Z<p>RandyGollub: </p>
<hr />
<div>[[Projects:ARRASuplements|Back to our ARRA home page]]<br />
== 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 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. Furthermore, the current practice of excellent medical care includes extensive use of diagnostic and prognostic medical imaging using standardized image acquisition methods. 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 />
= Human Subject's Protection Training =<br />
All project personnel who access the medical imaging data for this effort must secure appropriate IRB approval. If you haven't already done it, take the CITI human subject's protection training course (https://www.citiprogram.org/) and then have your site i2b2 PI add you to their i2b2 IRB development protocol. <br />
<br />
= Mockup used for initial development =<br />
<br />
The mi2b2 installation at HMS hospitals requires careful attention to patient privacy and operational integrity of critical hospital information systems (e.g. clinical PACS). Therefore the software related to this project was developed and tested extensively before deployment in the clinical setting.<br />
<br />
In order to develop the software in isolation, a [[CTSC:ARRA:Mockup|virtualized mockup]] was set up that included a PACS system with phantom and anonymized DICOM data, an instance of i2b2 software, and a test installation of XNAT. The guidelines for this are being left intact on this web site for historical purposes and for the use by the community as they do their own development. But please see the main download site for mi2b2 for primary instructions for how to proceed.<br />
<br />
= mi2b2 software download site and installation instructions [http://www.mi2b2.org] =<br />
<br />
= Upcoming Events =<br />
<br />
* [[CTSC:ARRA.SFN2011| Abstract presentation at the Society for Neurosciences annual meeting, Washington DC, November, 2011]] <br />
<br />
<br />
===Weekly Meetings===<br />
Wednesday (9:00- 10:00 AM), call: 1-866-890-3820 <br />
* [[CTSC:ARRA.110211| November 2, 2011]] OCC 299, Shawn's Office<br />
* [[CTSC:ARRA.110911| November 9, 2011]] OCC 299, Shawn's Office<br />
* [[CTSC:ARRA.111611| November 16, 2011]] OCC 299, Shawn's Office<br />
* [[CTSC:ARRA.113011| November 30, 2011]] OCC 299, Shawn's Office (Note: conflicts with RSNA)<br />
<br />
===Monthly Meetings===<br />
Tuesday (10:30- 11:30 AM), call: 1-866-890-3820 <br />
<br />
* [[CTSC:ARRA.011712| January 17, 2012]] Ware room, Countway 5th floor<br />
<br />
=Past Events =<br />
<br />
===2011 meetings===<br />
<br />
* [[CTSC:ARRA.060711| June 07, 2011]]<br />
* [[CTSC:ARRA.061411| June 14, 2011]]<br />
* [[CTSC:ARRA.062111| June 21, 2011]] Cancelled<br />
* [[CTSC:ARRA.062811| June 28, 2011]] Cancelled<br />
* [[CTSC:ARRA.070511| July 5, 2011]] <br />
* [[CTSC:ARRA.071211| July 12, 2011]]<br />
* [[CTSC:ARRA.071911| July 19, 2011]]<br />
* [[CTSC:ARRA.072611| July 26, 2011]]<br />
* [[CTSC:ARRA.080211| August 2, 2011]]<br />
* [[CTSC:ARRA.080911| August 9, 2011]]<br />
* [[CTSC:ARRA.081611| August 16, 2011]]<br />
* [[CTSC:ARRA.082311| August 23, 2011]]<br />
* [[CTSC:ARRA.083011| August 30, 2011]]<br />
* [[CTSC:ARRA.090611| September 6, 2011]]<br />
* [[CTSC:ARRA.091311| September 13, 2011]]<br />
* [[CTSC:ARRA.092011| September 20, 2011]]<br />
* [[CTSC:ARRA.092711| September 27, 2011]]<br />
* [[CTSC:ARRA.101811| October 18, 2011]]<br />
* [[CTSC:ARRA.112211| November 22, 2011]]<br />
* [[CTSC:ARRA.122011| December 20, 2011]] <br />
<br><br />
<br><br />
* [[CTSC:ARRA.OHBM2011| Abstract presentation at the Organization for Human Brain Mapping meeting, Quebec City, CANADA, June, 2011]] <br />
* [[CTSC:ARRA.SIIM2011| Presentation at the Society for Imaging Informatics in Medicine annual meeting, Washington DC, June, 2011]] <br />
* [[CTSC:ARRA.ACRIN2010| ACRIN Medical Imaging Informatics Session, September 29, 2010]] <br />
<br />
<br />
'''[[CTSC:ARRA.tconJantoMay2011| January 2011 through May 2011 t-con meeting minutes]]'''<br />
<br />
===2010 meetings===<br />
<br />
'''[[CTSC:ARRA.tconJantoJune2010| January 2010 through May 2010 t-con meeting minutes]]'''<br><br />
'''[[CTSC:ARRA.tconJunetoDec2010| June 2010 through December 2010 t-con and face to face meeting minutes]]'''<br />
<br />
===2009 meetings===<br />
<br />
'''[[CTSC:ARRA.2009tcon| 2009 t-con meeting minutes]]<br />
'''<br />
=Using DCM4CHEE =<br />
[[CTSC:ARRA:dcm4chee_install|Installation instructions for DCM4CHEE]]<br />
<br />
Back to [[Collaboration:Harvard_CTSC|Collaboration:Harvard_CTSC]]<br />
<br></div>RandyGollubhttps://www.na-mic.org/w/index.php?title=CTSC:ARRA.011712&diff=73799CTSC:ARRA.0117122012-01-17T16:34:28Z<p>RandyGollub: </p>
<hr />
<div>Back to [[CTSC:ARRA supplement]]<br />
<br> <br />
<br><br />
== Harvard Catalyst Medical Informatics group Meeting Minutes January 17, 2012 ==<br />
<br />
In attendance:<br />
* Bill Wang<br />
* Shawn Murphy<br />
* Randy Gollub<br />
* Chris Herrick <br />
* Steve Pieper<br />
* Darren Sack<br />
* Jon Bickel (phone)<br />
* Kathy Andriole (phone)<br />
<br />
'''Agenda'''<br />
# mi2b2 software update <br />
# grant<br />
# manuscript<br />
# Open Source Plug-Fest at SIIM<br />
<br><br />
===mi2b2 software update===<br />
* The mi2b2 software has now been shared with the full scientific community via the i2b2 community wiki. This happened the last week in December. Strong work team (especially Bill Wang!).<br />
* CHB mi2b2 is fully operational and in production mode. User training will resume after the grant and manuscript are submitted with Randy being the "training guinea pig".<br />
* MGH production server is now reconfigured back to MGH from BWH.<br />
* Two new users are now active on the MGH production server, the Baby Brain project with Randy as user and a new glioblastoma study with Jayashree Calpathy-Kramer as the user.<br />
* One new technical development that just started is to enable mi2b2 to be interoperable with XNAT, particularly to be able to directly transfer image data via mi2b2 to an XNAT instance. Bill is standing up an XNAT instance at MGH to use for this purpose.<br />
* The other new technical feature is to improve the integration of mi2b2 with the existing RPDR to increase the automation of getting a new user set up.<br />
<br><br />
===grant===<br />
* Our new program officer, Vinay Pai, requested that we send him a 2-3 page summary of our response to the reviewers and update on our progress since first submission. We worked hard and did it. Waiting to hear. <br />
* Subcontract paperwork for the planned resubmission is in. <br />
* Steve and Randy with help from colleagues finished a rough prototype for the software that will support the mi2b2 Radiology Decision Support Toolkit.<br />
* Now gathering the letters of support.<br />
<br><br />
===manuscript===<br />
* Targeting Journal of Digital Imaging<br />
* Shawn circulated to the group a detailed outline that included: Questions to be answered, proposed content, names for who should be responsible for writing and editing each section. We reviewed and agreed upon the text that Shawn had prepared.<br />
* All references need to be in EndNote format or provide PMID.<br />
* Deadline to finish text is next month's meeting.<br />
<br><br />
===Open Source Plug-Fest at SIIM 2012===<br />
* All agree that this is an excellent venue to demonstrate this software to the appropriate community. Kathy sent us the information for how to submit. Bill and Chris agreed to be responsible for submitting and for doing the presentation at the meeting in June.</div>RandyGollubhttps://www.na-mic.org/w/index.php?title=CTSC:ARRA.011712&diff=73798CTSC:ARRA.0117122012-01-17T16:21:49Z<p>RandyGollub: Created page with 'Back to CTSC:ARRA supplement <br> <br> == Harvard Catalyst Medical Informatics group Meeting Minutes January 17, 2012 == In attendance: * Bill Wang * Shawn Murphy * Randy G…'</p>
<hr />
<div>Back to [[CTSC:ARRA supplement]]<br />
<br> <br />
<br><br />
== Harvard Catalyst Medical Informatics group Meeting Minutes January 17, 2012 ==<br />
<br />
In attendance:<br />
* Bill Wang<br />
* Shawn Murphy<br />
* Randy Gollub<br />
* Chris Herrick <br />
* Steve Pieper<br />
* Darren Sack<br />
* Jon Bickel (phone)<br />
* Kathy Andriole (phone)<br />
<br />
'''Agenda'''<br />
# mi2b2 software update <br />
# grant<br />
# manuscript<br />
# Open Source Plug-Fest at SIIM<br />
<br />
===mi2b2 software update===<br />
* The mi2b2 software has now been shared with the full scientific community via the i2b2 community wiki. This happened the last week in December. Strong work team (especially Bill Wang!).<br />
* CHB mi2b2 is fully operational and in production mode. User training will resume after the grant and manuscript are submitted with Randy being the "training guinea pig".<br />
* MGH production server is now reconfigured back to MGH from BWH.<br />
* Two new users are now active on the MGH production server, the Baby Brain project with Randy as user and a new glioblastoma study with Jayashree Calpathy-Kramer as the user.<br />
* One new technical development that just started is to enable mi2b2 to be interoperable with XNAT, particularly to be able to directly transfer image data via mi2b2 to an XNAT instance. Bill is standing up an XNAT instance at MGH to use for this purpose.<br />
* The other new technical feature is to improve the integration of mi2b2 with the existing RPDR to increase the automation of getting a new user set up.<br />
<br><br />
===grant===<br />
* Our new program officer, Vinay Pai, <br />
* Randy contacted all subcontract PI's to initiate the preparation of updated paperwork for the planned resubmission. Deadline for subcontract paperwork is January 10, 2011. Deadline for scientific content is February 14, 2012. <br />
* Steve and Randy are working on a prototype for the software that will support the mi2b2 Radiology Decision Support Toolkit.<br />
<br><br />
===manuscript===<br />
* Targeting Journal of Digital Imaging<br />
* Shawn circulated to the group a detailed outline that included: Questions to be answered, proposed content, names for who should be responsible.<br />
<br><br />
===Open Source Plug-Fest at SIIM 2012===<br />
* All agree that this is an excellent venue to demonstrate this software to the appropriate community. Kathy sent us the information for how to submit. Bill and Chris agreed to be responsible for submitting and for doing the presentation at the meeting in June.</div>RandyGollubhttps://www.na-mic.org/w/index.php?title=CTSC:ARRA_supplement&diff=72609CTSC:ARRA supplement2011-12-20T19:38:12Z<p>RandyGollub: </p>
<hr />
<div>[[Projects:ARRASuplements|Back to our ARRA home page]]<br />
== 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 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. Furthermore, the current practice of excellent medical care includes extensive use of diagnostic and prognostic medical imaging using standardized image acquisition methods. 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 />
= Human Subject's Protection Training =<br />
All project personnel who access the medical imaging data for this effort must secure appropriate IRB approval. If you haven't already done it, take the CITI human subject's protection training course (https://www.citiprogram.org/) and then have your site i2b2 PI add you to their i2b2 IRB development protocol. <br />
<br />
= Mockup =<br />
<br />
The mi2b2 installation at HMS hospitals will require careful attention to patient privacy and operational integrity of critical hospital information systems (e.g. clinical PACS). Therefore the software related to this project will be developed and tested extensively before any deployment in a clinical setting.<br />
<br />
In order to develop the software in isolation, a [[CTSC:ARRA:Mockup|virtualized mockup]] is being set up that includes a PACS system with phantom and anonymized DICOM data, an instance of i2b2 software, and a test installation of XNAT.<br />
<br />
= [[mi2b2 (i2b2 instance with the STAR-D software) specifications and installation instructions]] =<br />
<br />
= Upcoming Events =<br />
<br />
* [[CTSC:ARRA.SFN2011| Abstract presentation at the Society for Neurosciences annual meeting, Washington DC, November, 2011]] <br />
<br />
<br />
===Weekly Meetings===<br />
Wednesday (9:00- 10:00 AM), call: 1-866-890-3820 <br />
* [[CTSC:ARRA.110211| November 2, 2011]] OCC 299, Shawn's Office<br />
* [[CTSC:ARRA.110911| November 9, 2011]] OCC 299, Shawn's Office<br />
* [[CTSC:ARRA.111611| November 16, 2011]] OCC 299, Shawn's Office<br />
* [[CTSC:ARRA.113011| November 30, 2011]] OCC 299, Shawn's Office (Note: conflicts with RSNA)<br />
<br />
===Monthly Meetings===<br />
Tuesday (10:30- 11:30 AM), call: 1-866-890-3820 <br />
<br />
* [[CTSC:ARRA.011712| January 17, 2012]] Ware room, Countway 5th floor<br />
<br />
=Past Events =<br />
<br />
===2011 meetings===<br />
<br />
* [[CTSC:ARRA.060711| June 07, 2011]]<br />
* [[CTSC:ARRA.061411| June 14, 2011]]<br />
* [[CTSC:ARRA.062111| June 21, 2011]] Cancelled<br />
* [[CTSC:ARRA.062811| June 28, 2011]] Cancelled<br />
* [[CTSC:ARRA.070511| July 5, 2011]] <br />
* [[CTSC:ARRA.071211| July 12, 2011]]<br />
* [[CTSC:ARRA.071911| July 19, 2011]]<br />
* [[CTSC:ARRA.072611| July 26, 2011]]<br />
* [[CTSC:ARRA.080211| August 2, 2011]]<br />
* [[CTSC:ARRA.080911| August 9, 2011]]<br />
* [[CTSC:ARRA.081611| August 16, 2011]]<br />
* [[CTSC:ARRA.082311| August 23, 2011]]<br />
* [[CTSC:ARRA.083011| August 30, 2011]]<br />
* [[CTSC:ARRA.090611| September 6, 2011]]<br />
* [[CTSC:ARRA.091311| September 13, 2011]]<br />
* [[CTSC:ARRA.092011| September 20, 2011]]<br />
* [[CTSC:ARRA.092711| September 27, 2011]]<br />
* [[CTSC:ARRA.101811| October 18, 2011]]<br />
* [[CTSC:ARRA.112211| November 22, 2011]]<br />
* [[CTSC:ARRA.122011| December 20, 2011]] <br />
<br><br />
<br><br />
* [[CTSC:ARRA.OHBM2011| Abstract presentation at the Organization for Human Brain Mapping meeting, Quebec City, CANADA, June, 2011]] <br />
* [[CTSC:ARRA.SIIM2011| Presentation at the Society for Imaging Informatics in Medicine annual meeting, Washington DC, June, 2011]] <br />
* [[CTSC:ARRA.ACRIN2010| ACRIN Medical Imaging Informatics Session, September 29, 2010]] <br />
<br />
<br />
'''[[CTSC:ARRA.tconJantoMay2011| January 2011 through May 2011 t-con meeting minutes]]'''<br />
<br />
===2010 meetings===<br />
<br />
'''[[CTSC:ARRA.tconJantoJune2010| January 2010 through May 2010 t-con meeting minutes]]'''<br><br />
'''[[CTSC:ARRA.tconJunetoDec2010| June 2010 through December 2010 t-con and face to face meeting minutes]]'''<br />
<br />
===2009 meetings===<br />
<br />
'''[[CTSC:ARRA.2009tcon| 2009 t-con meeting minutes]]<br />
'''<br />
=Using DCM4CHEE =<br />
[[CTSC:ARRA:dcm4chee_install|Installation instructions for DCM4CHEE]]<br />
<br />
Back to [[Collaboration:Harvard_CTSC|Collaboration:Harvard_CTSC]]<br />
<br></div>RandyGollubhttps://www.na-mic.org/w/index.php?title=CTSC:ARRA.122011&diff=72570CTSC:ARRA.1220112011-12-20T16:18:47Z<p>RandyGollub: Created page with 'Back to CTSC:ARRA supplement <br> <br> == Harvard Catalyst Medical Informatics group Meeting Minutes December 20, 2011 == In attendance: * Bill Wang * Shawn Murphy * Randy …'</p>
<hr />
<div>Back to [[CTSC:ARRA supplement]]<br />
<br> <br />
<br><br />
== Harvard Catalyst Medical Informatics group Meeting Minutes December 20, 2011 ==<br />
<br />
In attendance:<br />
* Bill Wang<br />
* Shawn Murphy<br />
* Randy Gollub<br />
* Darren Sack (phone) <br />
* Steve Pieper<br />
<br />
'''Agenda'''<br />
# mi2b2 software update <br />
# XNAT<br />
# Grant<br />
<br />
===mi2b2 software update===<br />
<br />
* CHB mi2b2 is fully operational and in production mode. Nandan began training the mi2b2 CHB personnel on it last week. User testing will begin when Nandan is back. <br />
* Both BWH servers, development and production, are now up and operational.<br />
* Next step is to reconfigure MGH production server back to MGH from BWH.<br />
* Team is now full steam forward on getting the mi2b2 software ready to share with the full scientific community via the i2b2 community wiki. <br />
* Once that is done, the team will be ready to support one additional development study. <br />
* The next study to be supported will be Jayashree Calpathy-Kramer's IRB approved glioblastoma study. <br />
* Steve tested the new version of mi2b2 client server workbench using batch queries to the PACS and it all worked fine except for some minor usability issues which he reported to Bill. <br />
<br />
<br><br />
<br />
===XNAT===<br />
<br />
* We are planning to integrate XNAT in the next version. Work will begin on this in January.<br />
<br />
<br><br />
<br />
===Grant===<br />
<br />
* Randy contacted all subcontract PI's to initiate the preparation of updated paperwork for the planned resubmission. Deadline for subcontract paperwork is January 10, 2011. Deadline for scientific content is February 14, 2012. <br />
* Steve and Randy are working on a prototype for the software that will support the mi2b2 Radiology Decision Support Toolkit.</div>RandyGollubhttps://www.na-mic.org/w/index.php?title=SFN2011_Diffusion_Tensor_Imaging_Analysis_Workshop&diff=71911SFN2011 Diffusion Tensor Imaging Analysis Workshop2011-11-11T22:31:21Z<p>RandyGollub: </p>
<hr />
<div>{| class="wikitable" border="1" cellpadding="8" cellspacing="1"<br />
| colspan="3" style="width:450px" |[[Image:Am2011_header.jpg]]<br />
|-<br />
| style="width:150px" |[[Image:NAMIC.jpg]]<br />
| style="width:150px" |[[Image:Logo_nac.gif]]<br />
| style="width:150px" |[[Image:NCIGTlogo.gif]]<br />
|}<br />
[[File:NA-MIC_DTI_workshop_SfN2011_flyer.png | 600 px | right]]<br />
==White Matter Exploration with Diffusion Tensor Imaging: Fundamentals and Perspectives - A Hands-On Workshop by the National Alliance for Medical Imaging Computing (NA-MIC)==<br />
Diffusion Tensor Magnetic Resonance Imaging (DT-MRI) provides a non-invasive window on the complex organization of the brain white matter in-vivo. The technique offers tremendous opportunities for gaining insights into the architecture of major white matter pathways, and DT-MRI findings have the potential to play a critical role in the extraction of meaningful information for diagnosis, prognosis and following of treatment response. The workshop will guide participants through the fundamentals of the acquisition, analysis and interpretation of DT-MRI data. The format will alternate a series of lectures and hands-on sessions with the participants running DT-MRI analysis on their own laptops, to provide a conceptual understanding of the underlying theory of Diffusion Imaging, and a practical experience of extracting relevant clinical information from DT-MRI images. The hands-on sessions will use the 3DSlicer software, an open-source software package for medical image analysis and 3D visualization used in biomedical and clinical research worldwide. The workshop will educate the participants on the fundamentals of DT-MRI data required to make decisions about how to analyze their own data for neuroscience studies.<br />
<br />
Next DTI course will be at the SPIE 2012 conference in San Diego, Ca.<br />
<br />
==Introduction==<br />
This workshop is a satellite event of the [http://www.sfn.org/am2011/ Annual Meeting of the Society for Neuroscience], November 12-16, Washington, DC<br />
<br />
= Satellite Workshop Goals =<br />
* To provide tutorials on DTI data validation and management (including how to put your image data into NRRD format).<br /><br />
* To provide hands on tutorials in the use of NA-MIC DTI analysis tools.<br /><br />
* To establish contact between NA-MIC Tookit experts (users and developers) and basic and clinical researchers in the global neuroimaging community.<br /><br />
<br />
== Workshop Faculty ==<br />
<br />
* [[User:SPujol|Sonia Pujol, PhD]], Harvard Medical School, Surgical Planning Laboratory, Department of Radiology, Brigham and Women's Hospital<br />
* [[User:Randy|Randy Gollub, MD, PhD]], Harvard Medical School, Department of Psychiatry and Martinos Center, Department of Radiology, Massachusetts General Hospital<br />
* [http://www.nmr.mgh.harvard.edu/martinos/people/showPerson.php?people_id=572 Anastasia Yendiki, PhD], Harvard Medical School, Martinos Center, Department of Radiology, Massachussets General Hospital<br />
* [http://www.med.unc.edu/psych/directories/faculty/ipek-oguz-phd/ Ipek Oguz, PhD], University of North Carolina Chapel Hill<br />
<br />
== '''Tentative Agenda''' == <br />
* 9:00 - 9:10 AM '''Goals of Workshop''' (Randy Gollub/Sonia Pujol) <br />
* 9:10 - 10:10 AM [[media:Dmri,namic,11.11.11.pdf | '''Theoretical foundations of Diffusion Imaging''' ]](Anastasia Yendiki)<br />
* 10:10 - 10:45 AM '''Getting to Know DTI really, really well- tensors, glyphs and more''' (Sonia Pujol) <br />
* 10:45 -11:00 Coffee Break <br />
* 11:00 - 12:00 PM [[Media:Oguz-DTIApps-SfN11.pdf | '''DTI in research and in the clinics: current uses and future roadmap''' ]](Ipek Oguz)<br />
* 12:00 - 1:30 Lunch on own<br />
* 1:30 - 2:00 '''Challenges in clinical transfer of DT-MRI: towards validation of tractography''' (Sonia Pujol) <br />
* 2:00 - 3:00 '''Hands-on Session 1- Diffusion Tensor Imaging Analysis within 3DSlicer: from DWI images to 3D fiber bundles''' (Sonia Pujol/Randy Gollub/Anastasia Yendiki/Ipek Oguz) <br />
* 3:15 - 3:30 Coffee Break <br />
* 3:30 - 4:45 '''Hands-on Session 2- White Matter Exploration for Neurosurgical Planning''' (Sonia Pujol/Randy Gollub/Anastasia Yendiki/Ipek Oguz)<br />
* 4:45 - 5:15 [[Media:DTI-cross.site.pdf |'''Lessons in Multi-site DTI Acquisition- the BIRN experience''']] (Randy Gollub)] <br />
* 5:15 - 5:30 Concluding remarks and Discussion <br />
<br /><br />
<br />
==Logistics and Registration==<br />
* The workshop will be held on Friday November 11 from 9:00 am to 5:30 pm in '''Room 159A''' of the Walter E. Washington Convention Center, 801 Mount Vernon Place, NW, Washington.<br />
* '''<span style="background-color: yellow"> Registration Fee: $50. Please register [http://www.cvent.com/d/xcq82y/4W here]. Only credit card payments are accepted.</span>'''<br />
* For questions related to the workshop and to pre-register to the event, send an e-mail to Sonia Pujol (spujol at bwh.harvard.edu). Please include your contact information including full spelling of your name, degree, current institution, preferred email address for communication, your educational background and training and your reason for attending. We would also appreciate it if you would indicate the characteristics of the computer you will be using for the workshop (OS, RAM, Processor).<br />
<br />
== Preparation for Workshop -- ''Important Information for all attendees'' ==<br />
<br />
<span style="background-color: yellow">'''This is hands-on training. All participants must come with their own computer and install the software and data at the links below. Windows XP, Linux or MacOS 10.4 or greater computers are supported. A minimum of 1 GB of RAM (2 GB if possible) and a dedicated graphic accelerator with 64mb of on board graphic memory are required.'''</span><br /> <br />
<br />
*Software installation: Please install the Slicer3.6.3 release version appropriate to the laptop computer you'll be bringing to the workshop<br />
* Windows: [http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.3-2011-03-04-win32.exe Slicer3-3.6.3-2011-03-04-win32.exe]<br />
* Linux 64: [http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz] <br />
* Linux 32: [http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz ]<br />
* Mac Darwin: [http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz ] <br />
<br />
*Datasets: Please download the [[media:DiffusionDataset.zip| Diffusion dataset]], and [[media:WhiteMatterExplorationData.zip| White Matter Exploration dataset]] in preparation for the workshop.<br />
<br />
<br />
Suggested background reading for workshop:<br /><br />
<br />
* Le Bihan D, Mangin JF, Poupon C, et al. Diffusion tensor imaging:. concepts and applications. J Magn Reson Imaging 2001;13:534–546 [http://www.meteoreservice.com/PDFs/JMRI_DTI.PDF [pdf download]]<br />
* Westin CF, Maier SE, Mamata H, Nabavi A, Jolesz FA, Kikinis R., Processing and Visualization for Diffusion Tensor MRI. Medical Image Analysis, 6(2)::93-108, June 2002 [http://lmi.bwh.harvard.edu/papers/papers/westinMEDIA02.html [pdf dowload]]<br />
* S. Mori and P.C.M. van Zijl, Fiber tracking: principles and strategies – a technical review. NMR in Biomedicine, 15(7-8):468-480, 2002 [[Media:Mori-intro-2002.pdf| [pdf download]]]<br /><br /><br />
* Mukherjee P, Berman JI, Chung SW, Hess CP, Henry RG. Diffusion tensor MR imaging and fiber tractography: theoretic underpinnings. AJNR American journal of neuroradiology (2008) vol. 29 (4) pp. 632-41<br />
* Mukherjee P, Chung SW, Berman JI, Hess CP, Henry RG. Diffusion tensor MR imaging and fiber tractography: technical considerations. AJNR American journal of neuroradiology (2008) vol. 29 (5) pp. 843-52<br />
* Diffusion MRI: Theory, Methods, and Applications. Edited by Derek K. Jones. Oxford University Press, 2011.<br />
<br />
==To learn more about the NA-MIC Toolkit== <br />
Please visit our [[Main_Page|Wiki page]] for general information and [[NA-MIC-Kit|the NA-MIC Kit pages]] for specific information.<br />
<br />
== Slicer3 Training Survey ==<br />
<br />
[http://www.surveymonkey.com/s/GZDXKXQ Click here to take the Slicer3 Training Survey]<br />
<br />
==Slicer Community ==<br />
Participants are invited to join the [http://www.slicer.org/pages/Mailinglist Slicer user and Slicer developer community] prior to the workshop, for questions and feature requests related to the software.</div>RandyGollubhttps://www.na-mic.org/w/index.php?title=File:DTI-cross.site.pdf&diff=71909File:DTI-cross.site.pdf2011-11-11T22:13:51Z<p>RandyGollub: </p>
<hr />
<div></div>RandyGollubhttps://www.na-mic.org/w/index.php?title=File:DTI-cross.site.pptx&diff=71908File:DTI-cross.site.pptx2011-11-11T22:07:37Z<p>RandyGollub: </p>
<hr />
<div></div>RandyGollubhttps://www.na-mic.org/w/index.php?title=CTSC:ARRA.101811&diff=71459CTSC:ARRA.1018112011-10-18T15:35:48Z<p>RandyGollub: Created page with 'Back to CTSC:ARRA supplement <br> <br> == Harvard Catalyst Medical Informatics group Meeting Minutes October 18, 2011 == In attendance: * Bill Wang * Chris Herrick * David …'</p>
<hr />
<div>Back to [[CTSC:ARRA supplement]]<br />
<br> <br />
<br><br />
== Harvard Catalyst Medical Informatics group Meeting Minutes October 18, 2011 ==<br />
<br />
In attendance:<br />
* Bill Wang<br />
* Chris Herrick<br />
* David Wang <br />
* Shawn Murphy<br />
* Randy Gollub<br />
* Darren Sack<br />
* Jayashree Kalpathy <br />
* Nandan Patibandla <br />
* Bill Hanlon<br />
* Valerie Humblet (phone)<br />
* Jesse Wei (phone)<br />
* Kathy Andriole (phone)<br />
<br />
=== Partners Advisory Board Meeting this afternoon ===<br />
At the Prudential. Focus is on update of current capabilities, what will be to users in the near future. Randy and Steve will send Shawn slides to illustrate current IRB approved mi2b2 projects. Reviewed details of Steve and Ron's project so we are ready to present more details.<br />
<br />
=== mi2b2 software/hardware update ===<br />
* The second set of production servers for Partners is now "racked" and is being connected to the system. Progress is expected in the next weeks. We are looking into funds to replace missing test server at BWH site. Note there was no PHI on the missing server. <br />
* Dave has developed an improved workflow to address issues related to failures during the download step. He has divided each request for a long list of MRN/accession numbers that are sent for C-find into sets of three so that if anyone fails, only a those three will be marked as failed. At the end of the whole command the user will get back a report with successes, failures and missing data along with links to resubmit request for failed downloads. <br />
<br />
=== BIDMC ===<br />
* Jesse is running into additional technical hurdles trying to use his mac mini since it is running the Lion OSX, since there is no Oracle Express Lion version which is necessary for the PM module. He is leaning back towards the VMware version.<br />
<br />
=== Baby brain project ===<br />
* Valerie attended Ellen Grant's lab meeting last week to present her update on the mi2b2 clinical database mining efforts. There is strong interest in pushing this project forward as fast as possible- they would like data soon enough to generate a meeting abstract by mid-November. Valerie is working on setting up a meeting with the CHB mi2b2 team members (Nandan and Jon Bickel) and Ellen Grant's lab team to work out a plan for how to move mi2b2 development forward at the CHB.<br />
<br />
* Ellen's junior faculty fellow, Katyucia de Macedo Rodrigues, won one of the Department of Radiology Research Awards (along with $500) for her poster "The impact of maximum turning angle in different deterministic tractography algorithms applied in pediatric populations" that used data obtained through the mi2b2 project.<br />
<br />
=== Radiology Decision Support Workflow in Reading Room ===<br />
* Randy raised the idea of initiating some effort towards developing the technology proposed in the R01 grant's Project 3. Agreed that in principal it is worthwhile to pursue this and need to identify the best driving biological project be it baby brains and/or other. Group will look for most appropriate examples in addition to the baby brain project.</div>RandyGollubhttps://www.na-mic.org/w/index.php?title=CTSC:ARRA_supplement&diff=71041CTSC:ARRA supplement2011-09-20T15:52:10Z<p>RandyGollub: </p>
<hr />
<div>[[Projects:ARRASuplements|Back to our ARRA home page]]<br />
== 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 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. Furthermore, the current practice of excellent medical care includes extensive use of diagnostic and prognostic medical imaging using standardized image acquisition methods. 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 />
= Human Subject's Protection Training =<br />
All project personnel who access the medical imaging data for this effort must secure appropriate IRB approval. If you haven't already done it, take the CITI human subject's protection training course (https://www.citiprogram.org/) and then have your site i2b2 PI add you to their i2b2 IRB development protocol. <br />
<br />
= Mockup =<br />
<br />
The mi2b2 installation at HMS hospitals will require careful attention to patient privacy and operational integrity of critical hospital information systems (e.g. clinical PACS). Therefore the software related to this project will be developed and tested extensively before any deployment in a clinical setting.<br />
<br />
In order to develop the software in isolation, a [[CTSC:ARRA:Mockup|virtualized mockup]] is being set up that includes a PACS system with phantom and anonymized DICOM data, an instance of i2b2 software, and a test installation of XNAT.<br />
<br />
= [[mi2b2 (i2b2 instance with the STAR-D software) specifications and installation instructions]] =<br />
<br />
= Upcoming Events =<br />
<br />
* [[CTSC:ARRA.SFN2011| Abstract presentation at the Society for Neurosciences annual meeting, Washington DC, November, 2011]] <br />
<br />
<br />
===Weekly Meetings===<br />
Wednesday (9:00- 10:00 AM), call: 1-866-890-3820 <br />
* [[CTSC:ARRA.100511| October 5, 2011]] OCC 299, Shawn's Office<br />
* [[CTSC:ARRA.101211| October 12, 2011]] OCC 299, Shawn's Office<br />
* [[CTSC:ARRA.102611| October 26, 2011]] OCC 299, Shawn's Office<br />
* [[CTSC:ARRA.110211| November 2, 2011]] OCC 299, Shawn's Office<br />
* [[CTSC:ARRA.110911| November 9, 2011]] OCC 299, Shawn's Office<br />
* [[CTSC:ARRA.111611| November 16, 2011]] OCC 299, Shawn's Office<br />
* [[CTSC:ARRA.113011| November 30, 2011]] OCC 299, Shawn's Office (Note: conflicts with RSNA)<br />
<br />
===Monthly Meetings===<br />
Tuesday (10:30- 11:30 AM), call: 1-866-890-3820 <br />
<br />
* [[CTSC:ARRA.092711| September 27, 2011]] Ware room, Countway 5th floor<br />
* [[CTSC:ARRA.101811| October 18, 2011]] Ware room, Countway 5th floor<br />
* [[CTSC:ARRA.112211| November 22, 2011]] Ware room, Countway 5th floor<br />
* [[CTSC:ARRA.122011| December 20, 2011]] Ware room, Countway 5th floor<br />
<br />
=Past Events =<br />
<br />
===2011 meetings===<br />
<br />
* [[CTSC:ARRA.060711| June 07, 2011]]<br />
* [[CTSC:ARRA.061411| June 14, 2011]]<br />
* [[CTSC:ARRA.062111| June 21, 2011]] Cancelled<br />
* [[CTSC:ARRA.062811| June 28, 2011]] Cancelled<br />
* [[CTSC:ARRA.070511| July 5, 2011]] <br />
* [[CTSC:ARRA.071211| July 12, 2011]]<br />
* [[CTSC:ARRA.071911| July 19, 2011]]<br />
* [[CTSC:ARRA.072611| July 26, 2011]]<br />
* [[CTSC:ARRA.080211| August 2, 2011]]<br />
* [[CTSC:ARRA.080911| August 9, 2011]]<br />
* [[CTSC:ARRA.081611| August 16, 2011]]<br />
* [[CTSC:ARRA.082311| August 23, 2011]]<br />
* [[CTSC:ARRA.083011| August 30, 2011]]<br />
* [[CTSC:ARRA.090611| September 6, 2011]]<br />
* [[CTSC:ARRA.091311| September 13, 2011]]<br />
* [[CTSC:ARRA.092011| September 20, 2011]]<br />
<br><br />
<br><br />
* [[CTSC:ARRA.OHBM2011| Abstract presentation at the Organization for Human Brain Mapping meeting, Quebec City, CANADA, June, 2011]] <br />
* [[CTSC:ARRA.SIIM2011| Presentation at the Society for Imaging Informatics in Medicine annual meeting, Washington DC, June, 2011]] <br />
* [[CTSC:ARRA.ACRIN2010| ACRIN Medical Imaging Informatics Session, September 29, 2010]] <br />
<br />
<br />
'''[[CTSC:ARRA.tconJantoMay2011| January 2011 through May 2011 t-con meeting minutes]]'''<br />
<br />
===2010 meetings===<br />
<br />
'''[[CTSC:ARRA.tconJantoJune2010| January 2010 through May 2010 t-con meeting minutes]]'''<br><br />
'''[[CTSC:ARRA.tconJunetoDec2010| June 2010 through December 2010 t-con and face to face meeting minutes]]'''<br />
<br />
===2009 meetings===<br />
<br />
'''[[CTSC:ARRA.2009tcon| 2009 t-con meeting minutes]]<br />
'''<br />
=Using DCM4CHEE =<br />
[[CTSC:ARRA:dcm4chee_install|Installation instructions for DCM4CHEE]]<br />
<br />
Back to [[Collaboration:Harvard_CTSC|Collaboration:Harvard_CTSC]]<br />
<br></div>RandyGollubhttps://www.na-mic.org/w/index.php?title=CTSC:ARRA_supplement&diff=71040CTSC:ARRA supplement2011-09-20T15:49:06Z<p>RandyGollub: </p>
<hr />
<div>[[Projects:ARRASuplements|Back to our ARRA home page]]<br />
== 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 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. Furthermore, the current practice of excellent medical care includes extensive use of diagnostic and prognostic medical imaging using standardized image acquisition methods. 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 />
= Human Subject's Protection Training =<br />
All project personnel who access the medical imaging data for this effort must secure appropriate IRB approval. If you haven't already done it, take the CITI human subject's protection training course (https://www.citiprogram.org/) and then have your site i2b2 PI add you to their i2b2 IRB development protocol. <br />
<br />
= Mockup =<br />
<br />
The mi2b2 installation at HMS hospitals will require careful attention to patient privacy and operational integrity of critical hospital information systems (e.g. clinical PACS). Therefore the software related to this project will be developed and tested extensively before any deployment in a clinical setting.<br />
<br />
In order to develop the software in isolation, a [[CTSC:ARRA:Mockup|virtualized mockup]] is being set up that includes a PACS system with phantom and anonymized DICOM data, an instance of i2b2 software, and a test installation of XNAT.<br />
<br />
= [[mi2b2 (i2b2 instance with the STAR-D software) specifications and installation instructions]] =<br />
<br />
= Upcoming Events =<br />
<br />
* [[CTSC:ARRA.SFN2011| Abstract presentation at the Society for Neurosciences annual meeting, Washington DC, November, 2011]] <br />
<br />
<br />
===Weekly Meetings===<br />
Wednesday (9:00- 10:00 AM), call: 1-866-890-3820 <br />
* [[CTSC:ARRA.100511| October 5, 2011]] OCC, Shawn's Office<br />
<br />
<br />
<br />
===Monthly Meetings===<br />
Tuesday (10:30- 11:30 AM), call: 1-866-890-3820 <br />
<br />
* [[CTSC:ARRA.092711| September 27, 2011]] Ware room, Countway 5th floor<br />
* [[CTSC:ARRA.101811| October 18, 2011]] Ware room, Countway 5th floor<br />
* [[CTSC:ARRA.112211| November 22, 2011]] Ware room, Countway 5th floor<br />
* [[CTSC:ARRA.122011| December 20, 2011]] Ware room, Countway 5th floor<br />
<br />
=Past Events =<br />
<br />
===2011 meetings===<br />
<br />
* [[CTSC:ARRA.060711| June 07, 2011]]<br />
* [[CTSC:ARRA.061411| June 14, 2011]]<br />
* [[CTSC:ARRA.062111| June 21, 2011]] Cancelled<br />
* [[CTSC:ARRA.062811| June 28, 2011]] Cancelled<br />
* [[CTSC:ARRA.070511| July 5, 2011]] <br />
* [[CTSC:ARRA.071211| July 12, 2011]]<br />
* [[CTSC:ARRA.071911| July 19, 2011]]<br />
* [[CTSC:ARRA.072611| July 26, 2011]]<br />
* [[CTSC:ARRA.080211| August 2, 2011]]<br />
* [[CTSC:ARRA.080911| August 9, 2011]]<br />
* [[CTSC:ARRA.081611| August 16, 2011]]<br />
* [[CTSC:ARRA.082311| August 23, 2011]]<br />
* [[CTSC:ARRA.083011| August 30, 2011]]<br />
* [[CTSC:ARRA.090611| September 6, 2011]]<br />
* [[CTSC:ARRA.091311| September 13, 2011]]<br />
* [[CTSC:ARRA.092011| September 20, 2011]]<br />
<br><br />
<br><br />
* [[CTSC:ARRA.OHBM2011| Abstract presentation at the Organization for Human Brain Mapping meeting, Quebec City, CANADA, June, 2011]] <br />
* [[CTSC:ARRA.SIIM2011| Presentation at the Society for Imaging Informatics in Medicine annual meeting, Washington DC, June, 2011]] <br />
* [[CTSC:ARRA.ACRIN2010| ACRIN Medical Imaging Informatics Session, September 29, 2010]] <br />
<br />
<br />
'''[[CTSC:ARRA.tconJantoMay2011| January 2011 through May 2011 t-con meeting minutes]]'''<br />
<br />
===2010 meetings===<br />
<br />
'''[[CTSC:ARRA.tconJantoJune2010| January 2010 through May 2010 t-con meeting minutes]]'''<br><br />
'''[[CTSC:ARRA.tconJunetoDec2010| June 2010 through December 2010 t-con and face to face meeting minutes]]'''<br />
<br />
===2009 meetings===<br />
<br />
'''[[CTSC:ARRA.2009tcon| 2009 t-con meeting minutes]]<br />
'''<br />
=Using DCM4CHEE =<br />
[[CTSC:ARRA:dcm4chee_install|Installation instructions for DCM4CHEE]]<br />
<br />
Back to [[Collaboration:Harvard_CTSC|Collaboration:Harvard_CTSC]]<br />
<br></div>RandyGollubhttps://www.na-mic.org/w/index.php?title=CTSC:ARRA.092011&diff=71039CTSC:ARRA.0920112011-09-20T15:43:36Z<p>RandyGollub: </p>
<hr />
<div>Back to [[CTSC:ARRA supplement]]<br />
<br> <br />
<br><br />
== Harvard Catalyst Medical Informatics group Meeting Minutes September 20, 2011 ==<br />
<br />
In attendance:<br />
* Bill Wang<br />
* Chris Herrick<br />
* David Wang <br />
* Shawn Murphy<br />
* Randy Gollub<br />
* Steve Pieper<br />
* Bill Tellier<br />
* Darren Sack<br />
* Jayashree Kalpathy (new Medical Informatics researcher at Martinos Center at MGH who is interested in using mi2b2 and meeting this team) <br />
* Nandan Patibandla (works with Jon Bickel at CHB in the Clinical Informatics department)<br />
* Kathy Andriole (phone)<br />
* Alex Zeitsev - transitioning from BWH SPL/NAMIC/CTSC to MGH Psychiatric Neurogenetics group under Jordan Smoller where he will be a mi2b2 user<br />
<br />
=== End of Initial ARRA Funding Period ===<br />
* Today is the final meeting under the original 2 year ARRA funded grant. We bid farewell and grateful thanks to the site representatives from the Radiology Departments at CHB, Bill Tellier and Paul Lamonica. We welcomed Nandan who has been working at CHB on Clinical Informatics (including i2b2) and will now be the CHB mi2b2 representative. Support via the no-cost extension will enable continued work at Partners- these personnel will support work at CHB and BIDMC with Jesse Wei. <br />
* Agreed to post all our Presentations on our site hosted by i2b2, Randy will do this with help from Bill and Dave as needed.<br />
<br />
=== new meeting schedule ===<br />
We will continue meeting weekly, but will hold them primarily in Charlestown in the OCC in Shawn's office. Once a month (usually the 4th Tuesday, but alternating with the 3rd Tuesday to accommodate holidays) we will hold the meeting in the Harvard Longwood area, typically in the Ware Room of Countway Library where we have been meeting. These monthly meetings will continue to be held on Tuesdays at 10:30- 11:30 AM. The next ones will be:<br />
*9/27<br />
*10/18<br />
*11/22<br />
*12/20<br />
<br><br />
The weekly meetings will shift to Wednesdays at 9 AM OCC 299 (aka Shawn's office). The next ones will be:<br />
*10/5<br />
*10/12<br />
*10/26<br />
*11/2<br />
*11/9<br />
*11/16<br />
*11/30<br />
<br />
<br />
=== mi2b2 software/hardware update ===<br />
* No news on the BWH production server yet.<br />
* Bill figured out that the problems that Steve was having when he tried to use mi2b2 at BWH last week were due to a process problem during the C-find command execution. Bill has the list of the MRNs and accession numbers for Steve and Ron's project, he will use them to finish working out a solution to fixing the problem and hopes to have it ready for Steve and Ron to use when they are back from their work travels.</div>RandyGollubhttps://www.na-mic.org/w/index.php?title=CTSC:ARRA.092011&diff=71038CTSC:ARRA.0920112011-09-20T15:40:27Z<p>RandyGollub: Created page with 'Back to CTSC:ARRA supplement <br> <br> == Harvard Catalyst Medical Informatics group Meeting Minutes September 20, 2011 == In attendance: * Bill Wang * Chris Herrick * Davi…'</p>
<hr />
<div>Back to [[CTSC:ARRA supplement]]<br />
<br> <br />
<br><br />
== Harvard Catalyst Medical Informatics group Meeting Minutes September 20, 2011 ==<br />
<br />
In attendance:<br />
* Bill Wang<br />
* Chris Herrick<br />
* David Wang <br />
* Shawn Murphy<br />
* Randy Gollub<br />
* Steve Pieper<br />
* Bill Tellier<br />
* Darren Sack<br />
* Jayashree Kalpathy (new Medical Informatics researcher at Martinos Center at MGH who is interested in using mi2b2 and meeting this team) <br />
* Nandan Patibandla (works with Jon Bickel at CHB in the Clinical Informatics department)<br />
* Kathy Andriole (phone)<br />
* Alex Zeitsev - transitioning from BWH SPL/NAMIC/CTSC to MGH Psychiatric Neurogenetics group under Jordan Smoller where he will be a mi2b2 user<br />
<br />
=== End of Initial ARRA Funding Period ===<br />
* Today is the final meeting under the original 2 year ARRA funded grant. We bid farewell and grateful thanks to the site representatives from the Radiology Departments at CHB, Bill Tellier and Paul Lamonica. We welcomed Nandan who has been working at CHB on Clinical Informatics (including i2b2) and will now be the CHB mi2b2 representative. Support via the no-cost extension will enable continued work at Partners- these personnel will support work at CHB and BIDMC with Jesse Wei. <br />
<br />
=== new meeting schedule ===<br />
We will continue meeting weekly, but will hold them primarily in Charlestown in the OCC in Shawn's office. Once a month (usually the 4th Tuesday, but alternating with the 3rd Tuesday to accommodate holidays) we will hold the meeting in the Harvard Longwood area, typically in the Ware Room of Countway Library where we have been meeting. These monthly meetings will continue to be held on Tuesdays at 10:30- 11:30 AM. The next ones will be:<br />
*9/27<br />
*10/18<br />
*11/22<br />
*12/20<br />
<br><br />
The weekly meetings will shift to Wednesdays at 9 AM OCC 299 (aka Shawn's office). The next ones will be:<br />
*10/5<br />
<br />
=== mi2b2 software/hardware update ===<br />
* No news on the BWH production server yet.<br />
* Bill figured out that the problems that Steve was having when he tried to use mi2b2 at BWH last week were due to a process problem during the C-find command execution. Bill has the list of the MRNs and accession numbers for Steve and Ron's project, he will use them to finish working out a solution to fixing the problem and hopes to have it ready for Steve and Ron to use when they are back from their work travels.</div>RandyGollubhttps://www.na-mic.org/w/index.php?title=CTSC:ARRA.090611&diff=70839CTSC:ARRA.0906112011-09-06T15:30:40Z<p>RandyGollub: /* Harvard Catalyst Medical Informatics group Meeting Minutes September 06, 2011 */</p>
<hr />
<div>Back to [[CTSC:ARRA supplement]]<br />
<br> <br />
<br><br />
== Harvard Catalyst Medical Informatics group Meeting Minutes September 06, 2011 ==<br />
<br />
In attendance:<br />
* Bill Wang<br />
* Chris Herrick<br />
* David Wang <br />
* Shawn Murphy<br />
* Randy Gollub<br />
* Steve Pieper<br />
* Alex Zeitsev (phone)<br />
* Kathy Andriole (phone)<br />
<br />
== mi2b2 software/hardware update ==<br />
* Steve reports that the BWH enabled version 6 mi2b2 software and the Mac client version of the client software has worked perfectly to download all the data from 327 MRNs associated with their IRB, there were 165 that were requested of which only one failed. Steve will go back to Ron to complete the requests for downloading all additional images that they need for their project. Note that this marks the achievement of a number of new milestones. Steve has a few suggestions based on using it that could improve the interface that he passed along to the development team. <br />
* New cache management software is set up such that each Project has an allocated cache of 500GB disk space. Until that cache is filled, the users mi2b2 Workbench will continue to work to down load images. If it is full, an error message will be generated.<br />
* To manage the time limit for each Project, a parameter will be entered into the i2b2/RPDR Project Management cell for study expiration date. That way if a person applies for an extension it is easy for our team to implement. Need to work out the administrative details (e.g. training materials, email notifications, etc). <br />
* Kathy reported a theft of the mi2b2 dev server from their facility in Brookline. She is reporting the theft to the appropriate authorities and will report back on what next. <br />
* CHB is still working on incorporating mi2b2 Version 6. Apparently the security issue has been resolved. Randy will check in again with him to see if we can do anything to help.<br />
* BIDMC is waiting for the mac mini server that was ordered to arrive then Jesse will try to deploy that version of mi2b2 there.<br />
<br />
== Development of an initial mi2b2 manuscript == <br />
# Targeting a submission for Journal of Digital Imaging (JDI)<br />
# Shawn, Randy, Steve to brainstorm initial framework for content<br />
# Kathy suggests that in addition to the technical details of the programming and a clinical example (and future applications) for illustration, to also include the important information regarding privacy, HIPAA and regulatory compliance.<br />
# Normal baby brain atlas is really a great showcase, with important societal relevance</div>RandyGollubhttps://www.na-mic.org/w/index.php?title=CTSC:ARRA.090611&diff=70838CTSC:ARRA.0906112011-09-06T15:30:18Z<p>RandyGollub: </p>
<hr />
<div>Back to [[CTSC:ARRA supplement]]<br />
<br> <br />
<br><br />
== Harvard Catalyst Medical Informatics group Meeting Minutes September 06, 2011 ==<br />
<br />
In attendance:<br />
* Bill Wang<br />
* Chris Herrick<br />
* David Wang <br />
* Shawn Murphy<br />
* Randy Gollub<br />
* Steve Pieper<br />
* Alex Zeitsev (phone)<br />
<br />
<br />
== mi2b2 software/hardware update ==<br />
* Steve reports that the BWH enabled version 6 mi2b2 software and the Mac client version of the client software has worked perfectly to download all the data from 327 MRNs associated with their IRB, there were 165 that were requested of which only one failed. Steve will go back to Ron to complete the requests for downloading all additional images that they need for their project. Note that this marks the achievement of a number of new milestones. Steve has a few suggestions based on using it that could improve the interface that he passed along to the development team. <br />
* New cache management software is set up such that each Project has an allocated cache of 500GB disk space. Until that cache is filled, the users mi2b2 Workbench will continue to work to down load images. If it is full, an error message will be generated.<br />
* To manage the time limit for each Project, a parameter will be entered into the i2b2/RPDR Project Management cell for study expiration date. That way if a person applies for an extension it is easy for our team to implement. Need to work out the administrative details (e.g. training materials, email notifications, etc). <br />
* Kathy reported a theft of the mi2b2 dev server from their facility in Brookline. She is reporting the theft to the appropriate authorities and will report back on what next. <br />
* CHB is still working on incorporating mi2b2 Version 6. Apparently the security issue has been resolved. Randy will check in again with him to see if we can do anything to help.<br />
* BIDMC is waiting for the mac mini server that was ordered to arrive then Jesse will try to deploy that version of mi2b2 there.<br />
<br />
== Development of an initial mi2b2 manuscript == <br />
# Targeting a submission for Journal of Digital Imaging (JDI)<br />
# Shawn, Randy, Steve to brainstorm initial framework for content<br />
# Kathy suggests that in addition to the technical details of the programming and a clinical example (and future applications) for illustration, to also include the important information regarding privacy, HIPAA and regulatory compliance.<br />
# Normal baby brain atlas is really a great showcase, with important societal relevance</div>RandyGollubhttps://www.na-mic.org/w/index.php?title=CTSC:ARRA_supplement&diff=70836CTSC:ARRA supplement2011-09-06T15:26:40Z<p>RandyGollub: </p>
<hr />
<div>[[Projects:ARRASuplements|Back to our ARRA home page]]<br />
== 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 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. Furthermore, the current practice of excellent medical care includes extensive use of diagnostic and prognostic medical imaging using standardized image acquisition methods. 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 />
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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 />
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= Human Subject's Protection Training =<br />
All project personnel who access the medical imaging data for this effort must secure appropriate IRB approval. If you haven't already done it, take the CITI human subject's protection training course (https://www.citiprogram.org/) and then have your site i2b2 PI add you to their i2b2 IRB development protocol. <br />
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= Mockup =<br />
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The mi2b2 installation at HMS hospitals will require careful attention to patient privacy and operational integrity of critical hospital information systems (e.g. clinical PACS). Therefore the software related to this project will be developed and tested extensively before any deployment in a clinical setting.<br />
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In order to develop the software in isolation, a [[CTSC:ARRA:Mockup|virtualized mockup]] is being set up that includes a PACS system with phantom and anonymized DICOM data, an instance of i2b2 software, and a test installation of XNAT.<br />
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= [[mi2b2 (i2b2 instance with the STAR-D software) specifications and installation instructions]] =<br />
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= Upcoming Events =<br />
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* [[CTSC:ARRA.SFN2011| Abstract presentation at the Society for Neurosciences annual meeting, Washington DC, November, 2011]] <br />
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===Weekly Meetings===<br />
Tuesday (10:30- 11:30 AM), call: 1-866-890-3820 <br />
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* [[CTSC:ARRA.091311| September 13, 2011]] Ware room, Countway 5th floor<br />
* [[CTSC:ARRA.092011| September 20, 2011]] Ware room, Countway 5th floor<br />
* [[CTSC:ARRA.092711| September 27, 2011]] Ware room, Countway 5th floor<br />
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=Past Events =<br />
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===2011 meetings===<br />
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* [[CTSC:ARRA.060711| June 07, 2011]]<br />
* [[CTSC:ARRA.061411| June 14, 2011]]<br />
* [[CTSC:ARRA.062111| June 21, 2011]] Cancelled<br />
* [[CTSC:ARRA.062811| June 28, 2011]] Cancelled<br />
* [[CTSC:ARRA.070511| July 5, 2011]] <br />
* [[CTSC:ARRA.071211| July 12, 2011]]<br />
* [[CTSC:ARRA.071911| July 19, 2011]]<br />
* [[CTSC:ARRA.072611| July 26, 2011]]<br />
* [[CTSC:ARRA.080211| August 2, 2011]]<br />
* [[CTSC:ARRA.080911| August 9, 2011]]<br />
* [[CTSC:ARRA.081611| August 16, 2011]]<br />
* [[CTSC:ARRA.082311| August 23, 2011]]<br />
* [[CTSC:ARRA.083011| August 30, 2011]]<br />
* [[CTSC:ARRA.090611| September 6, 2011]]<br />
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* [[CTSC:ARRA.OHBM2011| Abstract presentation at the Organization for Human Brain Mapping meeting, Quebec City, CANADA, June, 2011]] <br />
* [[CTSC:ARRA.SIIM2011| Presentation at the Society for Imaging Informatics in Medicine annual meeting, Washington DC, June, 2011]] <br />
* [[CTSC:ARRA.ACRIN2010| ACRIN Medical Imaging Informatics Session, September 29, 2010]] <br />
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'''[[CTSC:ARRA.tconJantoMay2011| January 2011 through May 2011 t-con meeting minutes]]'''<br />
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===2010 meetings===<br />
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'''[[CTSC:ARRA.tconJantoJune2010| January 2010 through May 2010 t-con meeting minutes]]'''<br><br />
'''[[CTSC:ARRA.tconJunetoDec2010| June 2010 through December 2010 t-con and face to face meeting minutes]]'''<br />
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===2009 meetings===<br />
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'''[[CTSC:ARRA.2009tcon| 2009 t-con meeting minutes]]<br />
'''<br />
=Using DCM4CHEE =<br />
[[CTSC:ARRA:dcm4chee_install|Installation instructions for DCM4CHEE]]<br />
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Back to [[Collaboration:Harvard_CTSC|Collaboration:Harvard_CTSC]]<br />
<br></div>RandyGollub