Skip to end of metadata
Go to start of metadata

Is NBIA Data Retriever open source?

Yes! The NBIA Data Retriever, like the backend server it talks to, is licensed under the 3-clause BSD license, sometimes referred to as the 'new' or 'modified' BSD license. The BSD license is very permissive, business-friendly, and approved by the Open Source Initiative. The source code is available from GitHub in the CBIIT/NBIA-TCIA repository, specifically in the software/nbia-download-manager subdirectory. Developers are free to review or fork to create derivative works. Of course, we would appreciate, but do not require, pull requests back to the repository if you have created nice new features or bug fixes that others might benefit from. They would be reviewed by the NBIA development team for inclusion, possibly after some tweaks, back into the main repository.

If you do create a derivative work, please keep in mind that the RESTful API that the NBIA Data Retriever uses to communicate back to the NBIA services is not standardized. The API could change in future versions of NBIA or the NBIA Data Retriever, though we do try to maintain some level of backwards compatibility. The same is true of the format for the manifest files that drive the NBIA Data Retriever. It is up to the maintainer of derivative works to stay up-to-date on the RESTful API and manifest file format.

Do I have to use NBIA Data Retriever to pull data from the archive?  Or are there alternatives?

Data in the archive is available through other methods. For example, a person versed in scripting or programming could easily pull data from the archive using the TCIA or NBIA Search RESTful interfaces, described at TCIA Programmatic Interface REST API Guides. Other organizations and people have also created software that can access data in TCIA. Many, but not all, of these tools and sites are listed in the Data Analysis Centers section of TCIA's web site. If you are interested in using TCIA data in the cloud, please check out NCI's Imaging Data Commons, which hosts public subsets (not all – yet) of TCIA data on a cloud platform for use by researchers. (IDC is still growing, and has not yet reached its full plan yet.)

Where are the installation files for the current version of the NBIA Data Retriever?

Click one of the following links to download the NBIA Data Retriever for that operating system. See Downloading Study Data for information on using this application to download data. 
  • RPM (tested on centOS)
    To run this file, type the following at the command prompt:
    sudo yum -v -y remove NBIADataRetriever-4.0-1.x86_64.rpm;sudo yum -y install NBIADataRetriever-4.1-1.x86_64.rpm
  • DEB (tested on Ubuntu)
    To run this file, type the following at the command prompt:
    sudo -S dpkg -r nbia-data-retriever-4.0.1.deb;sudo -S dpkg -i nbia-data-retriever-4.1.deb
  • NBIA Data Retriever in the Mac App Store
  • Windows

How do I know which version of the NBIA Data Retriever I am running?

For NBIA Data Retriever version 3.0 and later, the version information appears in the About menu. The version also appears at the bottom of the login windows when you download a private collection. The following steps explain how to find out which version of the app you are running for version 2.0 and earlier in different operating systems.

On Windows 10:

  1. Open the Start menu.
  2. Click Settings > System.
  3. From the left pane, select Apps & features.
  4. Search for NBIA Data Retriever.
  5. Click NBIA Data Retriever and the version number appears in the application details.

On Mac:

  1. Go to the Finder.
  2. Click an application to select it, then press the spacebar. A window appears, showing the version number, size, and last modification date.

On CentOS:

  • Type the following command at the command prompt of a terminal window:
    yum list installed | grep "NBIA"

On Ubuntu:

  • Type the following command at the command prompt of a terminal window:  
    dpkg -l |grep nbia

I generated a manifest file a while ago. How do I know which version of the NBIA Data Retriever to use with it?

Always use the latest version of the application. The application is backward-compatible. The following table shows the version compatibility between manifest files and the NBIA Data Retriever.

NBIA Data Retriever Version

Manifest v1.0

Manifest v2.0

Manifest v3.0

1.0

Working

Working with public data requests*

Not working

2.0

Working with public data requests

Working

Auto Upgrade and Manual Upgrade are working.

Remind Me Later does nothing.

3.0

Working with public data requests

Working

Working

4.0

Working with public data requests

Working

Working

4.1

Working with public data requests

Working

Working

What are the dependencies of the NBIA Data Retriever on Linux and how we can satisfy the dependencies?

On CentOS or Red Hat Linux, use the command sudo yum -v -y remove NBIADataRetriever-4.0-1.x86_64.rpm;sudo yum -y install NBIADataRetriever-4.1-1.x86_64.rpm  to install the NBIA Data Retriever. This command pulls and installs all missing dependent libraries when the NBIA Data Retriever is installed. If you install another way, you may not install all of the dependent libraries. Also, note that the NBIA Data Retriever always takes a manifest file as a parameter. In a GUI desktop environment, start the NBIA Data Retriever by clicking a manifest file.

How do I run the NBIA Data Retriever from the command line on RedHat/CentOS Linux?

The NBIA Data Retriever has two variants for Linux: the Graphical User Interface (GUI) app and a command-line interface.  The command-line interface is available for the NBIA Data Retriever starting with version 4.1 and documentation is available at NBIA Data Retriever Command Line Interface

The GUI app can also be started on the command line but needs the support of a desktop environment. For NBIA Data Retriever 3.2 and later, you can start the NBIA Data Retriever this way by entering the following command at the command prompt:

sudo /opt/NBIADataRetriever/NBIADataRetriever  <full path of manifest file including the file name>

This command assumes that the NBIA Data Retriever is installed on /opt/Downloader, which is the location it is installed at when installed with the command sudo yum -v -y remove NBIADataRetriever-4.0-1.x86_64.rpm;sudo yum -y install NBIADataRetriever-4.1-1.x86_64.rpm.

Once the NBIA Data Retriever is installed on the desktop, you can click any manifest file with the extension .tcia to invoke the app.

The NBIA Data Retriever requires a manifest file to run. You can create a manifest file in the TCIA Radiology Portal and with an API.

Failed to find library: jvm.dll

I clicked a manifest file and received the error “Failed to find library: jvm.dll” on Windows 10. How can I fix it?

This is a Java bug. This issue has a workaround. You must uninstall the NBIA Data Retriever and download the free community version of Visual Studio 2017. Install Visual Studio 2017 and then reinstall the NBIA Data Retriever.

How do I resolve the "xdg-desktop-menu: not found" error in the Ubuntu installation of the NBIA Data Retriever?

If the Ubuntu server does not have a desktop environment installed, it will not have the “xdg-utils” package. To solve this problem, run the following command.

$cd /tmp

$wget https://cbiit-download.nci.nih.gov/nbia/releases/ForTCIA/NBIADataRetriever_4.1/nbia-data-retriever-4.1.deb

$sudo apt install xdg-utils

$sudo -S dpkg -r nbia-data-retriever-4.0.1.deb;sudo -S dpkg -i nbia-data-retriever-4.1.deb

How do resolve the “xdg-desktop-menu: No writable system menu directory found” error in the Ubuntu installation of the NBIA Data Retriever?

Ubuntu has a bug that results in this error. To solve this problem, run the following command, then run the installation command again.

sudo mkdir /usr/share/desktop-directories/


  • No labels