This chapter describes how to submit images to NBIA.
Topics in this chapter include:
When you submit an image to NBIA using FileSender, the process follows the path illustrated in the following flowchart:
In summary, the process involves the following steps. These steps are described in detail in the succeeding sections of this user's guide.
The submission process can be monitored using the CTP client (to see how many images were sent), CTP server (to see how many images were received) and the View Submission Reports tool within NBIA to ensure the images were successfully added to the database and file system. The View Submission Reports tool requires the “VIEW_SUBMISSION_REPORT” role in the UAT.
Once receipt of the images is confirmed, users with the “MANAGE_VISIBILITY_STATUS” role can use the QC Tool to review images, make them visible to users with read access to the collection, set them as invisible or mark them for deletion. In order for images to be deleted by a user with the “NCIA.SUPER_CURATOR” role must approve the images that are marked for deletion using the Approve Deletion tool within NBIA. Images that have been approved for deletion will be auto-deleted that night during off-peak hours to save system resources. This two-step process is designed to minimize accidental deletions.
See also Alternative Image Configuration/Submission Methods.
You can find the latest documentation for CTP on the Medical Imaging Research Center site.
To submit images, you must have the CTP client both installed and running on your machine. The installation of the CTP Client/Server is embedded into the NBIA application installation process.
For example, the installation path for the CTP in Windows is:
C:\apps\nbia\CTP-client
C:\apps\nbia\CTP-client\FileSender
C:\apps\nbia\CTP-server
As noted above, to submit images, you must have the FileSender and the CTP client both installed and running on your machine. For information regarding your specific installation issues, contact NCI Application Support.
To configure the CTP client, perform the following steps:
ctp.bat (ctp.sh
in Linux) in the CTP-Client/CTP folder. In Windows, the file path is: C:\apps\nbia\CTP-client\CTP\ctp.bat
.Open a browser and type in the CTP client URL for your local installation. You can find the port number by looking in the config.xml
file in the CTP folder. The third line of the standard file is "<Server port="24080" />"
. If changes are made to this number, the localhost port needed to access the CTP admin page changes in tandem.
Example URL for CTP client:
http://localhost:24080/
You may want to refer to the helpful information about this part of the CTP setup on the NCI wiki . Note that CTP only supports 32-bit Java. |
The CTP Client Console opens in your browser. The following image on the left shows the main menu when you are not logged in. The following image on the right shows the main menu when you are logged in.
Not logged in | Logged in |
---|---|
You do not need to be logged in to the CTP client to review some of the pages. See the first figure. You do need to be logged in to configure the anonymizer. |
config.xml
file referred to in step 2.da.script
file.The default configuration for submitting images to NBIA is detailed in the da.script
file. You can override that script by customizing anonymization parameters on the DICOM Anonymizer Configurator page, which follows. This page indicates how the image's DICOM tags are modified to anonymize the data, thus meeting HIPAA regulations to preserve patients' privacy. For example, the patient's birth date and patient ID are anonymized.
The following fields on this page are required:
SITE NAME – This identifies where data is coming from. Example = BioU. Several different collections could be submitted from there, but all would have same site name. The NBIA user does not see the source site for the data, except when using the Verify Submission feature, described in Viewing Submission Reports.
Authorization controls pay attention to the site. So a user, based on permissions, for example, may be able to search on collection X//site A, but not collection X//site B. |
The following field can also be configured.
Collection B, Site 2 UID Root = 555.4
Other fields can also be configured. For more information about the configuration and operation, see the CTP DICOM Anonymizer documentation .
The current CTP client contains a WG18 S142-compliant anonymization baseline. For more information about the Working Group 18, Supplement 142 profile, see Incorporation of DICOM WG18 Supplement 142 into CTP. |
Once the CTP client has been configured, you can begin the submission process in FileSender. See Submitting Images. Once the CTP server has been configured, you can verify that the images have been received and stored in the database. See Verifying Status of a Submitted Image.
Note the slight difference between the port numbers for the CTP client "24080" and the CTP server "23080". |
To start your local CTP server, execute the ctp.bat (ctp.sh
in Linux) in the CTP-Client/CTP folder. In Windows, the file path is: C:\apps\nbia\CTP-server\CTP\ctp.bat
.
Open a browser and enter the CTP Server URL for your local installation. You can find the port number by looking in the config.xml
file in the CTP folder. The third line of the standard file is "<Server port="23080" />"
. If changes are made to this number, the localhost port needed to access the CTP admin page changes in tandem. An example URL for the CTP server:
http://localhost:23080/
The CTP Server Console opens in your browser. To determine the status of an image you have submitted, as described in Submitting Images, continue with the steps in Verifying Status of a Submitted Image.
If you are not able to use User Manager of CTP server to create or delete a user, check if Apache is the front end server of the CTP server. If yes, add the following directive to the Apache configuration file at ctpconsole.conf
:
ProxyPreserveHost On
filesender.bat (filesender.sh
in Linux) in the CTP-Client/FileSender folder. The FileSender opens to a screen that displays a Source panel on the left and a Destination panel on the right (shown in the following figure.) C:\apps\nbia\CTP-client\FileSender\FileSender.bat
.Select the default URL for the destination in the Destination panel. This is the host and port number (the port number for the HttpImportService
defined in the config.xml
) where the CTP client is located.
The CTP client must be started to successfully submit images. |
Click Send to execute the submission process to the CTP client. The Destination panel displays the progress of the task.
To verify the images submitted, you must replace the default value in the URL field of the Processor tag or DatabaseVerifier tag in the config.xml
of CTP Client.
Replace the default value, url= http://localhost:23304
with url=https://ctpsubmission.nci.nih.gov/verifier.
To submit images using the user-defined username/password, follow these steps on the CTP Server:
config.xml
of the CTP Client.Once you have submitted one or more images, you can check their submission status. Click the Status button on the main page of the CTP client.
All of the fields supply information about the submission, but you might check especially the Last File Received At fields under each section. The following two figures show different examples. Correlate the date and time stamp when the submission was received with the time you sent the image(s). Refresh the page periodically to view the latest status.
CTP client showing in the HTTP Import section that a submitted image file has been received
The following figure shows that the file submitted was received by the CTP server, as shown in the Storage section:
The file shown as received in the previous figure is stored in the "storage" location. In windows, the storage location is: C:\apps\nbia\CTP-server\CTP\storage
. For example, the path to the file for the Last file stored as shown in the preceding figure is: C:\apps\nbia\CTP-server\CTP\storage\0000000000\000\000.dcm.
If the Status tab does not indicate that the file(s) were received, verify the URL on the Destination tab of File Sender.
Once the CTP Server receives the images, it extracts all the attributes/information related to the images and uploads the data, together with the images(URI) into the NBIA database.
Use the View Submission Reports tool within NBIA to ensure the images were successfully added to the database and file system. The View Submission Reports tool requires the “VIEW_SUBMISSION_REPORT” role in the User Authorization Tool.
If you suspect your files have not been submitted successfully to the CTP client, click the Quarantines button in the CTP client main page to see if any files have been received there. If no files are quarantined, the quarantine indicators remain at zero.
Each stage of processing in CTP can cause a quarantine, therefore, the quarantine count is broken down by stage. |
If something is quarantined in the Anonymizer stage, there is likely an error in the anonymization script. Common problems with the anonymization script are:
incorrect syntax (See the CTP section of the mircwiki for syntax.)
referring to parameters that don't exist. For example, if @PROJECTNAME is referred to in a rule, but not defined as a parameter.
To troubleshoot server-side submission problems or for other submission issues, contact Application Support.
You can use several other alternative methods for configuring and submitting images to the CTP client and/or servers. An example is the PACS radiology machine which takes DICOM images and sends them directly to a CTP server, circumventing the need to send the images and accompanying patient information over the internet. For more information about using these alternative submission methods, contact Application Support.