CTSC:ARRA:Mockup
Back to CTSC ARRA Supplement
Note: as of March 2011 this mockup is disabled. The mi2b2 project has progressed to the point where this functionality is no longer required. If any users of the mi2b2.slicer.org dcm4chee installation would like access to a different machine, please contact Steve Pieper for IP address and AE title information.
Contents
Goals
The mockup installation allows the development team to conduct experiments outside of the clinical network environment.
WARNING: These services are not secured -- DO NOT upload any protected health information (PHI) or other confidential information to these servers.
Implementation
A set of virtual machine instances on the Amazon Web Services infrastructure allow our work to happen outside of the institutional firewalls. This minimizes the risk security issues on the clinical networks and allows developers to have control over server allocation, firewall rules, IP addresses, and similar issues that would otherwise require interaction with clinical IS staffs.
Servers
CentOS 64 bit linux is the standard OS used in this project (compatible with i2b2 standard usage).
Contact a mi2b2 researcher for username and password information for these servers.
PACS
The dcm4chee software allows implementation of basic PACS functionality.
The mi2b2 project provides instructions for installation on CentOS 64 bit linux.
The server can be accessed at: http://mi2b2.slicer.org:8080/dcm4chee-web/
This server is being populated by phantom datasets and anonymized generic data.
- IP Address: mi2b2.slicer.org (174.129.38.17) not currently on line - replace with your own dicom server
- Port: 11112
- AE Title: MI2B2
These parameters have been tested and are working with OsiriX on Mac OSX and Aeskulap on linux. Other DICOM clients should also work.
Access the PACS using dcmtk
Push a set of DICOM files:
storescu -aec MI2B2 mi2b2.slicer.org 11112 dicom/*
Warning: be sure there is no PHI in the dicom data!
To query by patient name:
Create a file patqry.dump containing the following:
# query patient names and IDs (0008,0052) CS [PATIENT] # QueryRetrieveLevel (0010,0010) PN [] # PatientsName (0010,0020) LO [] # PatientID
Run the following command to create a dicom (binary) file from the ascii description:
dump2dcm patqry.dump patqry.dcm
Use the CFind Service Class User (SCU) with the query file to ask for all patient with names starting with the letter F
findscu -aec MI2B2 -P -k 0010,0010=F* mi2b2.slicer.org 11112 patqry.dcm
As of this writing the query will return four response records:
$ findscu -aec MI2B2 -P -k 0010,0010=F* mi2b2.slicer.org 11112 patqry.dcm | grep PatientsName (0010,0010) PN [FROGG^KERMIE] # 12, 1 PatientsName (0010,0010) PN [FROG^KERMIT TCH ] # 16, 1 PatientsName (0010,0010) PN [FROG^KERMIT ] # 12, 1 PatientsName (0010,0010) PN [FROG^KERMIT ] # 12, 1 PatientsName
i2b2
- Webclient: An instance of i2b2 is installed at this address: http://i2b2.slicer.org/webclient
- Workbench:
- Download and install the workbench from www.i2b2.org.
- Edit i2b2workbench.properties file and add the following line at the end of the file:
I2b2.2=i2b2demo,REST,http://i2b2.slicer.org:9090/i2b2/rest/PMService/
XNAT
Initially XNAT Central is being used for testing. Optionally, an amazon instance may be set up to run XNAT locally.
See http://xnat.org for more information about XNAT interface, clients, and usage.
Issues and Considerations
- At each deployment site we will need a catalog of site-specific attributes that are not modeled accurately by this mockup. Possible issues include:
- Extra security layers and protocols
- Bandwidth caps to avoid disrupting clinical workflows
- Accounting for off-line (tape) storage that may require throttling accesses
- Bugs or other non-standard behavior of vendor PACS installations (or bugs in dcm4chee)
- Since the data in the mockup is non-clinical it may not accurately reflect the real installations
