CTSC:ARRA supplement

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 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.

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 (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.

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.

Upcoming Events

Weekly Meetings

Tuesday (10:30- 11:30 AM), call: 1-866-890-3820

• November 17, 2009 Harvard School of Public Health, 655 Huntington Ave, Building SPH2, 4th Floor, Room 426
• November 24, 2009 Countway, Ware Room, 5th floor
• December 1, 2009
• December 8, 2009 Ware room, Countway 5th floor (! XNAT demo from Dan Marcus WashU)
• December 15, 2009 Harvard School of Public Health, 655 Huntington Ave, Building SPH2, 4th Floor, Room 426
• December 22, 2009 Ware room, Countway 5th floor
• December 29, 2009 Ware room, Countway 5th floor

Past Events

2009 meetings

• November 10, 2009
• November 3, 2009
• October 27, 2009
• October 20, 2009
• October 13, 2009
• October 6, 2009

Using DCM4CHEE

Installation Instructions for x86_64 Linux, Centos

• Download the latest DCM4CHEE for Postgresql
  • wget http://sourceforge.net/projects/dcm4che/files/dcm4chee/2.14.7/dcm4chee-psql-2.14.7.zip/download
• Install Postgresql
  • sudo yum install postgresql postgresql-server

• Install DCM4CHEE
  • Follow instructions at http://www.dcm4che.org/confluence/display/ee2/Installation
  • Special Steps
    • Download Sun's Java Advanced Imaging Image I/O Tools 1.1 for 64bit Linux:
      • wget http://download.java.net/media/jai-imageio/builds/release/1.1/jai_imageio-1_1-lib-linux-i586.tar.gz
    • Download the binary distribution package of JBoss Application Server 4.2.3.GA
      • wget http://sourceforge.net/projects/jboss/files/JBoss/JBoss-4.2.3.GA/jboss-4.2.3.GA.zip/download
    • Download the Audit Record Repository (ARR)
      • wget http://sourceforge.net/projects/dcm4che/files/dcm4chee-arr/3.0.8/dcm4chee-arr-psql-3.0.8.zip/download
    • Unarchive the downloaded files.
    • sudo cp -rp dcm4chee-psql-2.14.7 /opt
    • sudo cp -p jai_imageio-1_1/lib/libclib_jiio.so /opt/dcm4chee-psql-2.14.7/bin/native/
    • sudo /opt/dcm4chee-psql-2.14.7/bin/install_jboss.sh jboss-4.2.3.GA
    • sudo /opt/dcm4chee-psql-2.14.7/bin/install_arr.sh dcm4chee-arr-psql-3.0.8/
    • Start Postgresql server
      • sudo mkdir /opt/pgdata
      • sudo chown /opt/pgdata postgres
      • sudo -s -H -u postgres
      • initdb -D /opt/pgdata/ -U postgres -W (enter postgres as password)
    • Create databases
      • createdb pacsdb
      • psql pacsdb -f /opt/dcm4chee-psql-2.14.7/sql/create.psql
      • createdb arrdb
      • set password in files /opt/dcm4chee-psql-2.14.7/server/default/deploy/arr-psql-ds.xml and pacs-postgres-ds.xml

• Running DCM4CHEE
  • sudo /opt/dcm4chee-psql-2.14.7/bin/run.sh
  • change default AETitle to MI2B2 (See step 12. at http://www.dcm4che.org/confluence/display/ee2/Installation)
  • test then stop run.sh
  • Run as a service (See step 18 at http://www.dcm4che.org/confluence/display/ee2/Installation)
    • edit /opt/dcm4chee-psql-2.14.7/server/default/conf/jboss-log4j.xml to comment out "<appender-ref ref="CONSOLE"/>"
    • sudo cp /opt/dcm4chee-psql-2.14.7/bin/dcm4chee_init_redhat.sh /etc/init.d/dcm4chee
    • Modify JBOSS_HOME, JBOSS_USER and JAVAPTH in /etc/init.d/dcm4chee
    • sudo /sbin/chkconfig dcm4chee on

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