Difference between revisions of "CTSC:ARRA:Mockup"

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Back to [[CTSC:ARRA_supplement|CTSC ARRA Supplement]]
 
Back to [[CTSC:ARRA_supplement|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.'''
  
 
== Goals ==
 
== Goals ==
  
 
The mockup installation allows the development team to conduct experiments outside of the clinical network environment.
 
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 ==
 
== Implementation ==
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CentOS 64 bit linux is the standard OS used in this project (compatible with i2b2 standard usage).
 
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 ===
 
=== PACS ===
  
 +
[[image:Dcm4chee-mi2b2-query-2010-03-16.png|thumb|200px|right|Web administration screen of dcm4chee instance at mi2b2.slicer.org showing results of query for patient name starting with the letter F.]]
 +
[[image:OsiriX-query-mi2b2-2010-03-16.png|thumb|200px|right|OsiriX query of dcm4chee instance at mi2b2.slicer.org showing results of query for patient name starting with the letter F.]]
 +
[[image:Aeskulap-query-mi2b2-2010-03-16.png|thumb|200px|right|Aeskulap query of dcm4chee instance at mi2b2.slicer.org showing results of query for patient name starting with the letter F.]]
 
The [http://www.dcm4che.org/ dcm4chee] software allows implementation of basic PACS functionality.
 
The [http://www.dcm4che.org/ dcm4chee] software allows implementation of basic PACS functionality.
  
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The server can be accessed at: http://mi2b2.slicer.org:8080/dcm4chee-web/
 
The server can be accessed at: http://mi2b2.slicer.org:8080/dcm4chee-web/
  
−
(Contact a mi2b2 researcher for username and password.)
+
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
  
−
This server is being populated by phantom datasets and anonymized generic data.
+
These parameters have been tested and are working with [http://osirix-viewer.com OsiriX] on Mac OSX and [http://aeskulap.nongnu.org Aeskulap] on linux.  Other DICOM clients should also work.
 +
 
 +
==== Access the PACS using [http://dicom.offis.de dcmtk] ====
 +
 
 +
'''Push a set of DICOM files:'''
 +
 
 +
storescu -aec MI2B2 mi2b2.slicer.org 11112 dicom/*
 +
 
 +
''Warning: be sure there is no [http://en.wikipedia.org/wiki/Protected_health_information 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 ===
 
=== 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 ===
 
=== XNAT ===
  
−
== Client Software ==
+
Initially [http://central.xnat.org 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

Latest revision as of 17:46, 8 February 2016

Home < 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.

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

Web administration screen of dcm4chee instance at mi2b2.slicer.org showing results of query for patient name starting with the letter F.
OsiriX query of dcm4chee instance at mi2b2.slicer.org showing results of query for patient name starting with the letter F.
Aeskulap query of dcm4chee instance at mi2b2.slicer.org showing results of query for patient name starting with the letter F.

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
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