NAMIC Wiki - User contributions [en]

CTSC:ARRA.011811

2011-01-24T20:28:59Z

Cherrick: /* Update on Phase 3 and Phase 4 mi2b2 software/hardware */

Back to [[CTSC:ARRA supplement]]
 

'''Agenda'''
* Update on Phase 3 and Phase 4 mi2b2 software
* Policies and Procedures for PACS access at each institution
* Organization for Human Brain Mapping (OHBM) Conference Abstract
 
== Harvard Catalyst Medical Informatics group Meeting Minutes January 18, 2011 ==

In attendance:
* Bill Wang
* Shawn Murphy
* Alex Zeitsev
* Chris Herrick
* Vincent Roch
* Charles McGow
* Steve Pieper
* Randy Gollub
* Wendy Plesniak (phone)
* Mark Anderson (phone)
* Yong Gao

=== Update on Phase 3 and Phase 4 mi2b2 software/hardware ===

* This week Jesse made good progress on the BIDMC mi2b2 installation, using the VMWare. We learned from tests using his research PACS that not all PACS support patient level query roots. mi2b2 currently uses patient level queries to validate medical record numbers against a PACS and return patient demographic information. The alternative to using a patient level query is to query by study and "clean up" the returned data in the mi2b2 server software. Raises the question of what mi2b2 should use as its standard so that it will be most flexible in being able to interface with as many PACS as possible. Would need to change from study level to patient level query root. Dave is thinking through how this would effect the subsequent data query, retrieve and display steps. Chris will contact Dan Marcus to find out best strategy for mi2b2 at Wash U and other sites.

* The Windows 2008 software on the new MGH 64 bit server continues to cause problems for the mi2b2 software. The JAI (Java Advanced Imaging) library software in particular was troublesome so we need to find alternative options. Also ran into problems using Axis2 1.1 - web services were not being registered properly.

* Running into problem retrieving large image data sets (>2000 images/study). Currently, retrieve stops at 2000 images exactly. Not sure source of problem. This is being investigated by Chris and Bill.

=== Policies and Procedures for PACS access at each institution ===

We will ask each of our institutional representatives (hopefully at our next meeting) to give us their recommendations for these parameters to use for development and initial implementation. Shawn will send out an email to them asking, Do you want us to exclude archived images? If so, how will we know what images are archived and hence off limits? Are there limitations necessary with respect to the rates and times of day images are retrieved? Any other restrictions that we need to consider? There answers will be used to draft a first proposal to the External Advisory Board indicating:
# Any limitations by dates of study being retrieved
# Any limitations by types of studies being retrieved (interaction of first two)
# Any limitations rates of pull
# Any limitations as to time of day (interaction of second two)
# Need for emergency pause capability

=== Organization for Human Brain Mapping (OHBM) Conference Abstract ===

Randy and Vincent submitted, with input from many of our team, an abstract for OHBM based on Vincent's analysis of the first preliminary mi2b2 data. She will circulate the final draft to the author list and post the abstract at the time of the meeting in June 2011.

Mi2b2 (i2b2 instance with the STAR-D software) specifications and installation instructions

2010-05-20T14:48:14Z

Cherrick: /* mi2b2 Installation Instructions */

Back to [[CTSC:ARRA supplement]]
 

== Specifications ==
This server will need to be inside the institutional firewall, have PACS access via institutional intranet, and a fixed IP address. It will not need access to the outside world. 
2 GHZ processor 
2 GB RAM 
40 GB free space 
 
'''Software''' 
Windows XP SP1 or CentOS (other Linux version possible) 
JDK 6.0 
JBoss 4.2.2 
Apache Ant 1.6.5 
Apache Axis2 1.1 
Oracle 10g Express Edition (for Linux Servers) or Sql Server 2005 Express Edition (for Windows) 

== mi2b2 Installation Instructions ==

''' Prerequisites '''

* For Windows XP, make sure all of the latest updates are installed to your machine
* Make sure that DotNet framework 2.0 is installed on your workstation.

''' Download Software '''

* Download the zip file (mi2b2.zip) by going to i2b2.slicer.org/downloads [http://i2b2.slicer.org/downloads]
* Save MI2B2 file to your desktop.
* Extract the zipped file to C:\

''' Install JDK '''

* Navigate to C:\MI2B2\installs, and double click on ''jdk-6u20-windows-i586.exe''
* Accept the license agreement
* Click next on all prompts accepting default settings.
* Reboot Workstation

''' Install Sql Server Express '''

* Navigate to C:\MI2B2\installs, and double click on ''SQLEXPR32.exe''
* Wait for extraction to finish, accept license, and click next.
* Continue to click Next until you come to the Registration Information screen
* On the Registration Information screen, uncheck ''Hide advanced configuration options''. Click Next.
* Accept Default settings and click next
* On the Instance Name screen, change to ''Default instance''
* Use the default settings for service account. Click Next.
* On Database Security selection screen. Select ''MIXED MODE'', and enter a password (you choose)
* Click Next three more times (accepting default settings each time), and click Install to finish.

''' Modify Sql Server Configuration '''

* Click Start > Programs > Microsoft SQL Server 2005 > Configuration Tools > SQL Server Configuration Manager
* Expand SQL Server 2005 Network Connection on the left.
* Click on PROTOCOLS for MSSQLSERVER
* Right Click on TCP/IP and select ''Enable''
* Click on SQL Server 2005 Services
* On the right, right click on SQL Server (MSSQLSERVER) and select Restart.

''' Modify Enviroment Variables '''

* Right Click on My Computer and select Properties, select Advanced, select Environment Variables, select new System Variable.
** Name: ''JAVA_HOME''
** Variable: ''C:\Program Files\Java\jdk1.6.0_20''
* Select New System Variable again
** Name: ''JBOSS_HOME''
** Variable: ''C:\Mi2b2\jboss-4.2.2.GA''
* Reboot Workstation

''' Install Databases and Windows Service '''

* Click Start > Run > Type ''CMD'' and press enter.
* In the command window, type ''cd C:\MI2B2\Database'' and press enter
* In the command winder, type ''install_database'' and press enter
* Let the Database install finish
* Next in the same command window, type ''cd C:\Mi2b2\jboss-4.2.2.GA\Bin'' and press enter
* Type ''install_service server''' and press enter
* Close command window.

''' Modify MI2B2 Configurations '''

* Navigate to this directory C:\Mi2b2\jboss-4.2.2.GA\server\default\conf\stardapp
* Open the File stard.properties with Wordpad
* Add your local PACS Server information to the section below without the parenthesis.
** #######################################
** # Remote PACS System Registration
** #######################################
** #stard.pacs.remote.aetitle=DCM4CHEE
** #stard.pacs.remote.address=
** #stard.pacs.remote.port=11112
** stard.pacs.remote.aetitle=(''YOUR TEST AETITLE'')
** stard.pacs.remote.address=(''YOUR TEST PACS IP OR HOSTNAME'')
** stard.pacs.remote.port=(''YOUR TEST PACS PORT'')
* Save File
* Edit Same File and give the local I2B2 workstation an AETitle, Hostname and Port.
** #######################################
** # Local PACS System Registration
** #######################################
** stard.pacs.local.aetitle=(''Your MI2B2 workstation Name'')
** stard.pacs.local.address=(''Your MI2B2 workstation Hostname'')
** stard.pacs.local.port=104
* Save the file again and reboot workstation.

''' Start I2B2 Hive Server '''

* Right Click on My Computer and select services.
* Right Click on I2B2 Hive Server Service and select start (if not already started)

''' Test Software '''

* Navigate to C:\MI2B2\ C:\Mi2b2\mi2b2_workbench\
* Double Click on i2b2workbench.exe
* Logon as
** User: Demo
** Password: demouser
* You should be able to search your local Test Pacs System via MRN.

Mi2b2 (i2b2 instance with the STAR-D software) specifications and installation instructions

2010-05-20T14:40:41Z

Cherrick: /* mi2b2 Installation Instructions */

Back to [[CTSC:ARRA supplement]]
 

== Specifications ==
This server will need to be inside the institutional firewall, have PACS access via institutional intranet, and a fixed IP address. It will not need access to the outside world. 
2 GHZ processor 
2 GB RAM 
40 GB free space 
 
'''Software''' 
Windows XP SP1 or CentOS (other Linux version possible) 
JDK 6.0 
JBoss 4.2.2 
Apache Ant 1.6.5 
Apache Axis2 1.1 
Oracle 10g Express Edition (for Linux Servers) or Sql Server 2005 Express Edition (for Windows) 

== mi2b2 Installation Instructions ==

* For Windows XP, make sure all of the latest updates are installed to your machine
* Make sure that DotNet framework 2.0 is installed on your workstation.

* Download the zip file (mi2b2.zip) by going to i2b2.slicer.org/downloads [http://i2b2.slicer.org/downloads]
* Save MI2B2 file to your desktop.
* Extract the zipped file to C:\

* Navigate to C:\MI2B2\installs, and double click on '''jdk-6u20-windows-i586.exe'''
* Accept the license agreement
* Click next on all prompts accepting default settings.
* Reboot Workstation

* Navigate to C:\MI2B2\installs, and double click on '''SQLEXPR32.exe'''
* Wait for extraction to finish, accept license, and click next.
* Continue to click Next until you come to the Registration Information screen
* On the Registration Information screen, uncheck '''Hide advanced configuration options'''. Click Next.
* Accept Default settings and click next
* On the Instance Name screen, change to '''Default instance'''
* Use the default settings for service account. Click Next.
* On Database Security selection screen. Select '''MIXED MODE''', and enter a password (you choose)
* Click Next three more times (accepting default settings each time), and click Install to finish.

* Right Click on My Computer and select Properties, select Advanced, select Environment Variables, select new System Variable.
** Name: '''JAVA_HOME'''
** Variable: '''C:\Program Files\Java\jdk1.6.0_20'''
* Select New System Variable again
** Name: '''JBOSS_HOME'''
** Variable: '''C:\Mi2b2\jboss-4.2.2.GA'''
* Reboot Workstation

* Click Start > Run > Type '''CMD''' and press enter.
* In the command window, type '''cd C:\MI2B2\Database''' and press enter
* In the command winder, type '''install_database''' and press enter
* Let the Database install finish
* Next in the same command window, type '''cd C:\Mi2b2\jboss-4.2.2.GA\Bin''' and press enter
* Type '''install_service server''' and press enter
* Close command window.

* Click Start > Programs > Microsoft SQL Server 2005 > Configuration Tools > SQL Server Configuration Manager
* Expand SQL Server 2005 Network Connection on the left.
* Click on PROTOCOLS for MSSQLSERVER
* Right Click on TCP/IP and select '''Enable'''
* Click on SQL Server 2005 Services
* On the right, right click on SQL Server (MSSQLSERVER) and select Restart.

* Navigate to this directory C:\Mi2b2\jboss-4.2.2.GA\server\default\conf\stardapp
* Open the File stard.properties with Wordpad
* Add your local PACS Server information to the section below without the parenthesis.
** #######################################
** # Remote PACS System Registration
** #######################################
** #stard.pacs.remote.aetitle=DCM4CHEE
** #stard.pacs.remote.address=
** #stard.pacs.remote.port=11112
** stard.pacs.remote.aetitle=('''YOUR TEST AETITLE''')
** stard.pacs.remote.address=('''YOUR TEST PACS IP OR HOSTNAME''')
** stard.pacs.remote.port=('''YOUR TEST PACS PORT''')
* Save File
* Edit Same File and give the local I2B2 workstation an AETitle, Hostname and Port.
** #######################################
** # Local PACS System Registration
** #######################################
** stard.pacs.local.aetitle=('''Your MI2B2 workstation Name''')
** stard.pacs.local.address=('''Your MI2B2 workstation Hostname''')
** stard.pacs.local.port=104
* Save the file again and reboot workstation.

* Right Click on My Computer and select services.
* Right Click on I2B2 Hive Server Service and select start (if not already started)

* Navigate to C:\MI2B2\ C:\Mi2b2\mi2b2_workbench\
* Double Click on i2b2workbench.exe
* Logon as
** User: Demo
** Password: demouser
* You should be able to search your local Test Pacs System via MRN.

Mi2b2 (i2b2 instance with the STAR-D software) specifications and installation instructions

2010-05-20T14:38:16Z

Cherrick: /* mi2b2 Installation Instructions */

Back to [[CTSC:ARRA supplement]]
 

== Specifications ==
This server will need to be inside the institutional firewall, have PACS access via institutional intranet, and a fixed IP address. It will not need access to the outside world. 
2 GHZ processor 
2 GB RAM 
40 GB free space 
 
'''Software''' 
Windows XP SP1 or CentOS (other Linux version possible) 
JDK 6.0 
JBoss 4.2.2 
Apache Ant 1.6.5 
Apache Axis2 1.1 
Oracle 10g Express Edition (for Linux Servers) or Sql Server 2005 Express Edition (for Windows) 

== mi2b2 Installation Instructions ==

* For Windows XP, make sure all of the latest updates are installed to your machine
* Make sure that DotNet framework 2.0 is installed on your workstation.

* Download the zip file (mi2b2.zip) by going to i2b2.slicer.org/downloads [http://i2b2.slicer.org/downloads]
* Save MI2B2 file to your desktop.
* Extract the zipped file to C:\

* Navigate to C:\MI2B2\installs, and double click on ''jdk-6u20-windows-i586.exe''
* Accept the license agreement
* Click next on all prompts accepting default settings.
* Reboot Workstation

* Navigate to C:\MI2B2\installs, and double click on ''SQLEXPR32.exe''
* Wait for extraction to finish, accept license, and click next.
* Continue to click Next until you come to the Registration Information screen
* On the Registration Information screen, uncheck ''Hide advanced configuration options''. Click Next.
* Accept Default settings and click next
* On the Instance Name screen, change to ''Default instance''
* Use the default settings for service account. Click Next.
* On Database Security selection screen. Select ''MIXED MODE'', and enter a password (you choose)
* Click Next three more times (accepting default settings each time), and click Install to finish.

* Right Click on My Computer and select Properties, select Advanced, select Environment Variables, select new System Variable.
** Name: ''JAVA_HOME''
** Variable: ''C:\Program Files\Java\jdk1.6.0_20''
* Select New System Variable again
** Name: ''JBOSS_HOME''
** Variable: ''C:\Mi2b2\jboss-4.2.2.GA''
* Reboot Workstation

* Click Start > Run > Type ''CMD'' and press enter.
* In the command window, type ''cd C:\MI2B2\Database'' and press enter
* In the command winder, type ''install_database'' and press enter
* Let the Database install finish
* Next in the same command window, type ''cd C:\Mi2b2\jboss-4.2.2.GA\Bin'' and press enter
* Type ''install_service server'' and press enter
* Close command window.

* Click Start > Programs > Microsoft SQL Server 2005 > Configuration Tools > SQL Server Configuration Manager
* Expand SQL Server 2005 Network Connection on the left.
* Click on PROTOCOLS for MSSQLSERVER
* Right Click on TCP/IP and select ''Enable''
* Click on SQL Server 2005 Services
* On the right, right click on SQL Server (MSSQLSERVER) and select Restart.

* Navigate to this directory C:\Mi2b2\jboss-4.2.2.GA\server\default\conf\stardapp
* Open the File stard.properties with Wordpad
* Add your local PACS Server information to the section below without the parenthesis.
** #######################################
** # Remote PACS System Registration
** #######################################
** #stard.pacs.remote.aetitle=DCM4CHEE
** #stard.pacs.remote.address=
** #stard.pacs.remote.port=11112
** stard.pacs.remote.aetitle=(*YOUR TEST AETITLE*)
** stard.pacs.remote.address=(*YOUR TEST PACS IP OR HOSTNAME*)
** stard.pacs.remote.port=(*YOUR TEST PACS PORT*)
* Save File
* Edit Same File and give the local I2B2 workstation an AETitle, Hostname and Port.
** #######################################
** # Local PACS System Registration
** #######################################
** stard.pacs.local.aetitle=(Your I2B2 workstation Name)
** stard.pacs.local.address=(Your I2B2 workstation Hostname)
** stard.pacs.local.port=104
* Save the file again and reboot workstation.

* Right Click on My Computer and select services.
* Right Click on I2B2 Hive Server Service and select start (if not already started)

* Navigate to C:\MI2B2\ C:\Mi2b2\mi2b2_workbench\
* Double Click on i2b2workbench.exe
* Logon as
** User: Demo
** Password: demouser
* You should be able to search your local Test Pacs System via MRN.

Mi2b2 (i2b2 instance with the STAR-D software) specifications and installation instructions

2010-05-20T14:37:44Z

Cherrick: /* mi2b2 Installation Instructions */

Back to [[CTSC:ARRA supplement]]
 

== Specifications ==
This server will need to be inside the institutional firewall, have PACS access via institutional intranet, and a fixed IP address. It will not need access to the outside world. 
2 GHZ processor 
2 GB RAM 
40 GB free space 
 
'''Software''' 
Windows XP SP1 or CentOS (other Linux version possible) 
JDK 6.0 
JBoss 4.2.2 
Apache Ant 1.6.5 
Apache Axis2 1.1 
Oracle 10g Express Edition (for Linux Servers) or Sql Server 2005 Express Edition (for Windows) 

== mi2b2 Installation Instructions ==

* For Windows XP, make sure all of the latest updates are installed to your machine
* Make sure that DotNet framework 2.0 is installed on your workstation.

* Download the zip file (mi2b2.zip) by going to i2b2.slicer.org/downloads [http://i2b2.slicer.org/downloads]
* Save MI2B2 file to your desktop.
* Extract the zipped file to C:\

* Navigate to C:\MI2B2\installs, and double click on ''jdk-6u20-windows-i586.exe''
* Accept the license agreement
* Click next on all prompts accepting default settings.
* Reboot Workstation

* Navigate to C:\MI2B2\installs, and double click on ''SQLEXPR32.exe''
* Wait for extraction to finish, accept license, and click next.
* Continue to click Next until you come to the Registration Information screen
* On the Registration Information screen, uncheck ''Hide advanced configuration options''. Click Next.
* Accept Default settings and click next
* On the Instance Name screen, change to ''Default instance''
* Use the default settings for service account. Click Next.
* On Database Security selection screen. Select ''MIXED MODE'', and enter a password (you choose)
* Click Next three more times (accepting default settings each time), and click Install to finish.

* Right Click on My Computer and select Properties, select Advanced, select Environment Variables, select new System Variable.
** Name: ''JAVA_HOME''
** Variable: ''C:\Program Files\Java\jdk1.6.0_20''
* Select New System Variable again
** Name: ''JBOSS_HOME''
** Variable: ''C:\Mi2b2\jboss-4.2.2.GA''
* Reboot Workstation

* Click Start > Run > Type ''CMD'' and press enter.
* In the command window, type ''cd C:\MI2B2\Database'' and press enter
* In the command winder, type ''install_database'' and press enter
* Let the Database install finish
* Next in the same command window, type ''cd C:\Mi2b2\jboss-4.2.2.GA\Bin'' and press enter
* Type ''install_service server'' and press enter
* Close command window.

* Click Start > Programs > Microsoft SQL Server 2005 > Configuration Tools > SQL Server Configuration Manager
* Expand SQL Server 2005 Network Connection on the left.
* Click on PROTOCOLS for MSSQLSERVER
* Right Click on TCP/IP and select ''Enable''
* Click on SQL Server 2005 Services
* On the right, right click on SQL Server (MSSQLSERVER) and select Restart.

* Navigate to this directory C:\Mi2b2\jboss-4.2.2.GA\server\default\conf\stardapp
* Open the File stard.properties with Wordpad
* Add your local PACS Server information to the section below without the parenthesis.
** #######################################
** # Remote PACS System Registration
** #######################################
** #stard.pacs.remote.aetitle=DCM4CHEE
** #stard.pacs.remote.address=infra11.partners.org
** #stard.pacs.remote.port=11112
** stard.pacs.remote.aetitle=(*YOUR TEST AETITLE*)
** stard.pacs.remote.address=(*YOUR TEST PACS IP OR HOSTNAME*)
** stard.pacs.remote.port=(*YOUR TEST PACS PORT*)
* Save File
* Edit Same File and give the local I2B2 workstation an AETitle, Hostname and Port.
** #######################################
** # Local PACS System Registration
** #######################################
** stard.pacs.local.aetitle=(Your I2B2 workstation Name)
** stard.pacs.local.address=(Your I2B2 workstation Hostname)
** stard.pacs.local.port=104
* Save the file again and reboot workstation.

* Right Click on My Computer and select services.
* Right Click on I2B2 Hive Server Service and select start (if not already started)

* Navigate to C:\MI2B2\ C:\Mi2b2\mi2b2_workbench\
* Double Click on i2b2workbench.exe
* Logon as
** User: Demo
** Password: demouser
* You should be able to search your local Test Pacs System via MRN.