Difference between revisions of "CTSC:ARRA supplement"

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= Harvard Catalyst Medical Imaging Informatics ARRA Administrative Supplement=
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[[Projects:ARRASuplements|Back to our ARRA home page]]
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== Harvard Catalyst Medical Imaging Informatics ARRA Administrative Supplement==
 
{|
 
{|
 
|align="left"|
 
|align="left"|
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=Medical Imaging Informatics Bench to Bedside (mi2b2) =
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== Medical Imaging Informatics Bench to Bedside (mi2b2) ==
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<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.
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<br>This Medical Imaging Informatics project was funded by an Administrative Supplement to the Harvard Catalyst through the federal stimulus package aka ARRA. The project will enable clinical imaging data to be used, with appropriate human subject and institutional protections, for secondary research purposes.
 
 
|[[image:ARRA.png|thumb|px=250|Go to the [http://www.recovery.gov ARRA website]]]
 
|[[image:ARRA.png|thumb|px=250|Go to the [http://www.recovery.gov ARRA website]]]
 
|}
 
|}
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=Mission Statement=
 
=Mission Statement=
  
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=Key Personnel and Resources=
 
=Key Personnel and Resources=
  
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Our hospitals are international leaders in the development and deployment of new and advanced biomedical imaging technologies (MRI, high speed CT, ultrasound, PET and others) for clinical practice (although old tried and true technologies are also extensively used).  The Picture Archive and Communication Systems (PACS) within each of the Departments of Radiology in our participating hospitals (Massachusetts General Hospital, Brigham and Women’s Hospital, Beth Israel Deaconess Medical Center, and Children’s Hospital Boston) contain a wealth of medical images that equal or exceed the quality of clinical research imaging data, and greatly exceed its volume in terms of the number of patients and disease types.     
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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.     
  
 
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.
 
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.
  
 +
= Human Subject's Protection Training =
 +
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. 
 +
 +
= Mockup used for initial development =
 +
 +
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.
 +
 +
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.
 +
 +
= mi2b2 software download site and installation instructions =
 +
 +
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.
 
= Upcoming Events =
 
= Upcoming Events =
 +
  
 
===Weekly Meetings===
 
===Weekly Meetings===
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Tuesday (10:30- 11:30 AM), call: 1-866-890-3820
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Wednesdays on weeks without monthly meetings OCC 299, Shawn's Office (9:00- 10:00 AM)
 +
 
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===Monthly Meetings===
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Tuesdays (10:30- 11:30 AM), call: number in email reminder
  
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*[[CTSC:ARRA.111709| November 17, 2009]] Harvard School of Public Health, 655 Huntington Ave, Building SPH2, 4th Floor, Room 426
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* [[CTSC:ARRA.071712| July 17, 2012]] Countway Library, conference room 319B
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*[[CTSC:ARRA.112409| November 24, 2009]] Countway, Ware Room, 5th floor
 
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*[[CTSC:ARRA.120109| December 1, 2009]]
 
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*[[CTSC:ARRA.120809| December 8, 2009]]  Ware room, Countway 5th floor (! XNAT demo from Dan Marcus WashU)
 
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*[[CTSC:ARRA.121509| December 15, 2009]] Harvard School of Public Health, 655 Huntington Ave, Building SPH2, 4th Floor, Room 426
 
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*[[CTSC:ARRA.122209| December 22, 2009]] Ware room, Countway 5th floor
 
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*[[CTSC:ARRA.122909| December 29, 2009]] Ware room, Countway 5th floor
 
  
 
=Past Events =
 
=Past Events =
 +
 +
===2012 meetings===
 +
* [[CTSC:ARRA.011712| January 17, 2012]]
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* [[CTSC:ARRA.022112| February 21, 2012]]
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* [[CTSC:ARRA.031312| March 13, 2012]]
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* [[CTSC:ARRA.041012| April 10, 2012]]
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* [[CTSC:ARRA.051512| May 15, 2012]]
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* [[CTSC:ARRA.061912| June 19, 2012]]
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===2011 meetings===
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'''[[CTSC:ARRA.tconJantoMay2011| January 2011 through May 2011 meeting minutes]]'''<br>
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'''[[CTSC:ARRA.tconJunetoDec2011| June 2011 through December 2011 meeting minutes]]'''
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===2010 meetings===
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'''[[CTSC:ARRA.tconJantoJune2010| January 2010 through May 2010 t-con meeting minutes]]'''<br>
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'''[[CTSC:ARRA.tconJunetoDec2010| June 2010 through December 2010 t-con and face to face meeting minutes]]'''
 +
 
===2009 meetings===
 
===2009 meetings===
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'''[[CTSC:ARRA.2009tcon| 2009 t-con meeting minutes]]'''
  
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*[[CTSC:ARRA.111009| November 10, 2009]]  
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===Meeting presentations===
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*[[CTSC:ARRA.110309| November 3, 2009]]  
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* [[CTSC:ARRA.OHBM2011| Abstract presentation at the Organization for Human Brain Mapping meeting, Quebec City, CANADA, June, 2011]]  
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*[[CTSC:ARRA.102709| October 27, 2009]]  
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* [[CTSC:ARRA.SIIM2011| Presentation at the Society for Imaging Informatics in Medicine annual meeting, Washington DC, June, 2011]]  
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*[[CTSC:ARRA.102009| October 20, 2009]]
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* [[CTSC:ARRA.ACRIN2010| ACRIN Medical Imaging Informatics Session, September 29, 2010]]  
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*[[CTSC:ARRA.101309| October 13, 2009]]
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* [[CTSC:ARRA.SFN2011| Abstract presentation at the Society for Neurosciences annual meeting, Washington DC, November, 2011]]  
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*[[CTSC:ARRA.100609| October 6, 2009]]
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* SIIM 2012 Open Source Plug Fest, June 2012
  
 
=Using DCM4CHEE =
 
=Using DCM4CHEE =
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===Installation Instructions for x86_64 Linux, Centos ===
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[[CTSC:ARRA:dcm4chee_install|Installation instructions for DCM4CHEE]]
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*Download the latest DCM4CHEE for Postgresql
 
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**wget http://sourceforge.net/projects/dcm4che/files/dcm4chee/2.14.7/dcm4chee-psql-2.14.7.zip/download
 
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*Install Postgresql
 
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**sudo yum install postgresql postgresql-server
 
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*Start Postgresql
 
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**sudo /sbin/chkconfig postgresql on
 
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**sudo /sbin/service postgresql start
 
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*Install DCM4CHEE
 
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**Follow instructions at http://www.dcm4che.org/confluence/display/ee2/Installation
 
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**Special Steps
 
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***Download Sun's Java Advanced Imaging Image I/O Tools 1.1 for 64bit Linux:
 
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****wget http://download.java.net/media/jai-imageio/builds/release/1.1/jai_imageio-1_1-lib-linux-i586.tar.gz
 
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***Download the binary distribution package of JBoss Application Server 4.2.3.GA
 
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****wget http://sourceforge.net/projects/jboss/files/JBoss/JBoss-4.2.3.GA/jboss-4.2.3.GA.zip/download
 
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***Download the Audit Record Repository (ARR)
 
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****wget http://sourceforge.net/projects/dcm4che/files/dcm4chee-arr/3.0.8/dcm4chee-arr-psql-3.0.8.zip/download
 
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***Unarchive the downloaded files.
 
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***sudo cp -rp dcm4chee-psql-2.14.7 /opt
 
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***sudo cp -p jai_imageio-1_1/lib/libclib_jiio.so /opt/dcm4chee-psql-2.14.7/bin/native/
 
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***sudo /opt/dcm4chee-psql-2.14.7/bin/install_jboss.sh jboss-4.2.3.GA
 
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***sudo -u postgres createdb pacsdb
 
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***sudo -u postgres psql pacsdb -f /opt/dcm4chee-psql-2.14.7/sql/create.psql
 
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Back to [[Collaboration:Harvard_CTSC|Collaboration:Harvard_CTSC]]
 
Back to [[Collaboration:Harvard_CTSC|Collaboration:Harvard_CTSC]]
 
<br>
 
<br>

Latest revision as of 22:26, 25 June 2012

Home < CTSC:ARRA supplement

Back to our ARRA home page

Harvard Catalyst Medical Imaging Informatics ARRA Administrative Supplement

Medical Imaging Informatics Bench to Bedside (mi2b2)


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.

Go to the ARRA website

Mission Statement

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.

Key Personnel and Resources

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.

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.

Human Subject's Protection Training

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.

Mockup used for initial development

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.

In order to develop the software in isolation, a 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.

mi2b2 software download site and installation instructions

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.

Upcoming Events

Weekly Meetings

Wednesdays on weeks without monthly meetings OCC 299, Shawn's Office (9:00- 10:00 AM)

Monthly Meetings

Tuesdays (10:30- 11:30 AM), call: number in email reminder

Past Events

2012 meetings

2011 meetings

January 2011 through May 2011 meeting minutes
June 2011 through December 2011 meeting minutes

2010 meetings

January 2010 through May 2010 t-con meeting minutes
June 2010 through December 2010 t-con and face to face meeting minutes

2009 meetings

2009 t-con meeting minutes

Meeting presentations

Using DCM4CHEE

Installation instructions for DCM4CHEE

Back to Collaboration:Harvard_CTSC

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