pacs_integration.adoc

PACS Integration

Abstract

This document describes, in some detail, the steps required to connect a ChRIS instance to a PACS resource. The intended audience is system’s developers.

Setting environment variables

export HOST_IP=$(ip route | grep -v docker | awk '{if(NF==11) print $9}')
export HOST_PORT=4055

Make note of the values of each of these variables as some of the steps that follow require manual insertion of the values.

Setting up Orthanc

Clone the orthanc-fnndsc repo

git clone https://github.com/FNNDSC/orthanc-fnndsc.git

Switch to the persistent-db branch

cd orthanc-fnndsc
git checkout persistent-db

Set the list of DICOM Modalities in orthanc.json

Ensure that the following setting is listed under the DicomModalities block of orthanc.json, being sure to replace <HOST_IP> with its appropriate value.

  "DicomModalities" : {
    /**
     * CHIPS CALLING AET.
     * Dicom listener running on
     **/
    "chips" : [ "CHIPS", "<HOST_IP>", 10402 ]

    ...

  },

Start orthanc

docker-compose up

An alternative method that might provide a bit more guidance in starting up orthanc is to run the makefile.

sudo ./make.sh -h ${HOST_IP}:10402

Push DICOM data to orthanc

Navigate to http://localhost:8042 in a browser and sign into the orthanc web GUI. Use orthanc as the username and password. Upload DICOM files on the "Upload" page.

Setting up pfdcm

Install pfdcm

Since the system requires the installation of some system-level companion services, the recommend vector is via the docker mechanism.

docker pull fnndsc/pfdcm

Start pfdcm

docker run --name pfdcm     \
            -v /home:/Users \
            --rm -ti        \
            fnndsc/pfdcm    \
            --forever --httpResponse

It may be necessary to add a --network="host" flag to allow orthanc to be reachable by pypx within its container. Note that this should only be used for development purposes:

docker run --name pfdcm     \
            -v /home:/Users \
            --network="host"\
            --rm -ti        \
            fnndsc/pfdcm    \
            --forever --httpResponse

Set internal values specifying the remote PACS host

Be sure to replace <HOST_IP> and <HOST_PORT> with their respective values.

docker run --rm --name pfurl fnndsc/pfurl --verb POST \
      --raw \
      --http ${HOST_IP}:${HOST_PORT}/api/v1/cmd   \
      --jsonwrapper 'payload' \
      --msg \
'{  "action": "internalctl",
    "meta": {
                "var":     "/PACS",
                "set":     {
                             "orthanc" : {
                                  "serverIP": "<HOST_IP>",
                                  "aet": "CHIPS",
                                  "aet_listener": "CHIPS",
                                  "aec": "ORTHANC",
                                  "serverPort": "<HOST_PORT>"
                               }
                           }
            }
}'

Set up the listener infrastructure

docker run --rm --name pfurl fnndsc/pfurl --verb POST \
        --raw                                   \
        --http ${HOST_IP}:${HOST_PORT}/api/v1/cmd   \
        --jsonwrapper 'payload'                 \
        --msg                                   \
        '{
            "action": "xinetd",
            "meta": {
                "object" : "service",
                "do":      "everything"
            }
        }'

Check the internal data tree

The following command can be run to check the state of the tree.

docker run --rm --name pfurl fnndsc/pfurl   --verb POST                             \
        --raw                                   \
        --http ${HOST_IP}:${HOST_PORT}/api/v1/cmd       \
        --jsonwrapper 'payload'                 \
        --msg                                   \
        '{
            "action": "internalctl",
            "meta":
            {
                "var":     "/",
                "get":      "value"
            }
        }'

Query the PACS server

Query by PatientID

Replace <patient-id> with the desired PatientID.

docker run --rm --name pfurl fnndsc/pfurl --verb POST --raw \
            --http ${HOST_IP}:${HOST_PORT}/api/v1/cmd     \
            --jsonwrapper 'payload'    \
            --msg '{
            "action": "PACSinteract",
            "meta": {
                "do":  "query",
                "on" : {
                   "PatientID": "<patient-id>"
                },
                "PACS" : "orthanc"
            }
        }'

Retrieve from the PACS server

Retrieve by PatientID

Use the <study-instance-uid> and <series-instance-uid> obtained from a query to retrieve the PACS files.

docker run --rm --name pfurl fnndsc/pfurl   --verb POST  \
        --raw                                   \
        --http ${HOST_IP}:${HOST_PORT}/api/v1/cmd        \
        --jsonwrapper 'payload'                 \
        --msg '{
            "action": "PACSinteract",
            "meta": {
                "do":  "retrieve",
                "on" : {
                    "StudyInstanceUID":  "<study-instance-uid>",
                    "SeriesInstanceUID": "<series-instance-uid>"
                },
                "PACS" : "orthanc"
            }
        }'

Check status of PACS retrieve

docker run --rm --name pfurl fnndsc/pfurl   --verb POST  \
        --raw                                   \
        --http ${HOST_IP}:${HOST_PORT}/api/v1/cmd       \
        --jsonwrapper 'payload'                 \
        --msg '{
            "action": "PACSinteract",
            "meta": {
                "do":  "retrieveStatus",
                "on" : {
                   "series_uid": "<series-instance-uid>"
                 },
                "PACS" : "orthanc"
            }
        }'