Sending DICOM files between IRIS for Health and PACS software

Welcome community members to a new article! this time we are going to test the interoperability capabilities of IRIS for Health to work with DICOM files.

Let's go to configure a short workshop using Docker. You'll find at the end of the article the URL to access to GitHub if you want to make it run in your own computer.

Previously to any configuration we are going to explain what is DICOM:

• DICOM is the acronym of Digital Imaging and Communication in Medicine and it's a images and medic data transmission standard. In this protocol is included the format of the DICOM file and the communication protocol based on TCP/IP.
• DICOM files support images and clinical documentation (you can include in a DICOM file images or documents "dicomized" as images).
• DICOM protocol define services/operations for the DICOM files. You can request the storages of an image (C-STORE), execute queries (C-FIND) o move this images among the systems of the medical organizations (C-MOVE). You can review all these available services from this URL .
• All the systems involved in a DICOM based communication request a DICOM message as response.

You can see here a typical example of the architecture for a system designed to work with DICOM:

We have some "modalities" (these modalities could be machines as scanners, MRIs or just the software that will store it) identified by the AE Title o AET (Application Entity Title). This AET will be unique for each modality and must be configured in those other modalities or systems that are going to communicate with it, in such a way that communication between both modalities is allowed.

As you can see in the graph, the modalities are configured to store their images in a DICOM file server that may or may not belong to a PACS (Picture Archiving and Communication System) that is later consulted from a PACS web interface. It is increasingly common to include a VNA (Vendor Neutral Archive) system in organizations that is responsible for centralized storage and viewing of all DICOM files used by the organization.

In general, in the most modern modalities, the destination of the generated images can be configured, but on many occasions it may be necessary or to carry out some type of action on the DICOM image fields (modify the patient identifier, include the clinical episode to the one with which it is related, etc) or, due to the inability of the modality, to take charge of capturing and forwarding the generated image to the system responsible for archiving. It is in these cases that the existence of an integration engine that provides us with such functionality is necessary, and there is none better than IRIS for Health!

For our example we will consider the following scenario:

• A certain modality is generating images that need to be sent to a PACS for registration.
• Our DICOM or PACS server will receive these images and must forward them to a specific VNA.

To simulate our PACS we will use Orthanc, an open source tool that will provide us with the basic functionalities for archiving and viewing DICOM images (more information here). Orthanc is kind enough to provide us with its use through an image that we can mount in Docker without any complications. Finally we will deploy an IRIS for Health container (it depends on when you read this article, the license may have expired, in that case you just have to update the docker-compose file of the code) in which we can mount our production.

Let's take a look at the docker-compose we've configured:

version: '3.1'  # Secrets are only available since this version of Docker Compose
services:
  orthanc:
    image: jodogne/orthanc-plugins:1.11.0
    command: /run/secrets/  # Path to the configuration files (stored as secrets)
    ports:
      - 4242:4242
      - 8042:8042
    secrets:
      - orthanc.json
    environment:
      - ORTHANC_NAME=orthanc
    volumes:
      - /tmp/orthanc-db/:/var/lib/orthanc/db/
    hostname: orthanc
  iris:
    container_name: iris
    build:
      context: .
      dockerfile: iris/Dockerfile
    ports:
    - "52773:52773"
    - "2010:2010"
    - "23:2323"
    - "1972:1972"
    volumes:
    - ./shared:/shared
    command:
      --check-caps false
    hostname: iris
secrets:
  orthanc.json:
    file: orthanc.json

Access to the Orthanc web viewer will be done through port 8042 (http://localhost:8042), the IP destined to receive images via TCP/IP will be 4242 and its configuration will be done from the orthanc.json file. The management portal of our IRIS for Health will be 52773.

Let's see what orthanc.json contains:

{
    "Name" : "${ORTHANC_NAME} in Docker Compose",
    "RemoteAccessAllowed" : true,
    "AuthenticationEnabled": true,
    "RegisteredUsers": {
        "demo": "demo-pwd"
    },
    "DicomAssociationCloseDelay": 0,
    "DicomModalities" : {
        "iris" : [ "IRIS", "host.docker.internal", 2010 ]
      }
}

 

As you can see we have defined a demo user with a password demo-pwd and we have declared a mode called IRIS that will use port 2010 to receive images from Orthanc, "host.docker.internal" is the mask used by Docker to access other deployed containers.

Let's check that after running the docker-compose build and docker-compose up -d we can access our IRIS for Health and Orthanc without problems:

IRIS for Health is successfully deployed.

Orthanc works too, so come on, get messy!

Let's access the namespace called DICOM and open its production. We can see in it the following business components:

We are going to review just the necessary components to manage the first case that we have presented for now. A modality that generates DICOM images but from which we cannot send them to our PACS. To do this we will use a Business Service of the standard class EnsLib.DICOM.Service.File configured to read all the .dcm files stored in the /shared/durable/in/ directory and send them to the Business Process of the Workshop.DICOM.Production.StorageFile class.

Let's take a closer look at the main method of this Business Process:

/// Messages received here are instances of EnsLib.DICOM.Document sent to this
/// process by the service or operation config items. In this demo, the process is ever
/// in one of two states, the Operation is connected or not.
Method OnMessage(pSourceConfigName As %String, pInput As %Library.Persistent) As %Status
{
    #dim tSC As %Status = $$$OK
    #dim tMsgType As %String
    do {
        
        If pInput.%Extends("Ens.AlarmResponse") {
            
            #; We are retrying, simulate 1st call
            #; Make sure we have a document
            Set pInput=..DocumentFromService
            $$$ASSERT(..CurrentState="OperationNotConnected")
        }
            
        #; If its a document sent from the service
        If pSourceConfigName'=..OperationDuplexName {
            
            #; If the operation has not been connected yet
            If ..CurrentState="OperationNotConnected" {
                
                #; We need to establish a connection to the operation,
                #; Keep hold of the incoming document
                Set ..DocumentFromService=pInput
                
                #; We will be called back at OnAssociationEstablished()
                Set tSC=..EstablishAssociation(..OperationDuplexName)
                
            } elseif ..CurrentState="OperationConnected" {
                
                #; The Operation is connected
                #; Get the CommandField, it contains the type of request, it should ALWAYS be present
                Set tMsgType=$$$MsgTyp2Str(pInput.GetValueAt("CommandSet.CommandField",,.tSC))
                If $$$ISERR(tSC) Quit
                #; We are only handling storage requests at present
                $$$ASSERT(tMsgType="C-STORE-RQ")
        		
        		// set patientId = pInput.GetValueAt("DataSet.PatientID",,.tSC)
        		// Set ^PatientImageReceived(patientId) = pInput.GetValueAt("DataSet.PatientName",,.tSC)
                #; We can forward the document to the operation
                Set tSC=..SendRequestAsync(..OperationDuplexName,pInput,0)
            }
            
        } elseif pSourceConfigName=..OperationDuplexName {
            
            #; We have received a document from the operation
            Set tMsgType=$$$MsgTyp2Str(pInput.GetValueAt("CommandSet.CommandField",,.tSC))
            If $$$ISERR(tSC) Quit
            #; Should only EVER get a C-STORE-RSP
            $$$ASSERT(tMsgType="C-STORE-RSP")

            #; Now close the Association with the operation, we will be called back at
            #; OnAssociationReleased()
            Set tSC=..ReleaseAssociation(..OperationDuplexName)
            
            #; Finished with this document
            Set ..DocumentFromService="",..OriginatingMessageID=""
        }
    } while (0)
    
    Quit tSC
}

As we can see, this class is configured to check the origin of the DICOM file, if it does not come from the Business Operation defined in the OperationDuplexName parameter, it will mean that we must forward it to the PACS and therefore the metadata of the DICOM message located in the CommandSet section under the name CommandField shall be of type C-STORE-RQ (store request) prior to connection establishment. In this URL you can check the different values ​​that this metadata can take (in hexadecimal).

In the case that the message comes from the indicated Business Operation, it is a sign that it corresponds to a DICOM response message to our previously sent DICOM, therefore it is validating that the CommandField of said message is of type C-STORE-RSP.

Let's analyze a little more in detail the key configuration of the Business Operation EnsLib.DICOM.Operation.TCP used to send our DICOM to our PACS via TCP/IP:

We have declared as IP the name of the hostname specified in the docker-compose in which Orthanc is deployed, as well as the port.

Hemos configurado dos elementos clave para el envío a PACS, el AET de nuestro IRIS for Health (IRIS) y el AET de nuestro PACS (ORTHANC). Sin esta configuración no es posible ningún envío de imágenes, ya que tanto IRIS como Orthanc validarán que la modalidad que envía/recibe tiene permiso para hacerlo.

¿Dónde se configura a qué modalidades se pueden enviar imágenes desde IRIS y qué modalidades nos pueden enviar imágenes? Muy sencillo, tenemos desde el portal de gestión de IRIS acceso a la funcionalidad de DICOM settings:

From this menu we can not only indicate which modalities can send us and to which we can send DICOM images, we can also indicate what type of images we will be able to send and receive, in such a way that we can reject any image that falls outside of this parameterization. As you can see in the image above we have configured connections both from IRIS to Orthanc and from Orthanc to IRIS. By default Orthanc supports any type of image, so we don't need to modify anything in its configuration.

In order not to have problems with the images that we can send and receive from IRIS, we will configure the "Presentation Context" call, made up of "Abstract Syntax" made up of the combination of DICOM services (Store, Get, Find...) and an object (MR images , CT, etc...) and the "Transfer Syntax" that defines how information is exchanged and how data is represented.

Well, we already have configured any possible connection between IRIS and Orthanc and vice versa. Let's proceed to launch a test including a DICOM file in the path defined in our Business Service:

Very good! Here we have registered our DICOM files and we can see how they have gone through our production until they are sent to Orthanc. Let's go into more detail by checking out a message.

Here we have our message with its CommandField set to 1, corresponding to C-STORE-RQ, now let's review the response we received from Orthanc:

We can see that the value of CommandFile 32769 corresponds in hexadecimal to 8001, which, as we have seen in this URL, is equivalent to type C-STORE-RSP. We can also see that the response message is a DICOM message that only contains the values ​​defined in the Command Set.

Let's check from Orthanc that we have received the messages correctly:

Here are our messages successfully archived in our PACS. Goal achieved! We can now store the DICOM images of our modality in our PACS without any problem.

In the next article we will deal with the opposite direction of communication, sending from the PACS to our modality configured in IRIS.

Here you have available the code used for this article: https://github.com/intersystems-ib/workshop-dicom-orthanc