Topics in this chapter include:

Introduction to the TCIA Data Portal

TCIA Data Portal enables you to search for images in the local TCIA in vivo image repository. If available, you can also search remote imaging archives.

TCIA submissions are organized in the following hierarchy, which is important to remember in creating your search query and reviewing search results:

In other words, a Collection is the largest organizing concept within TCIA and it includes data about Patients (also called Subjects). As you continue to drill down to more granular concepts, Patients contain Studies, Studies contain (Image) Series, and Series contain individual Images.

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Browser Support

TCIA supports the latest versions of Google Chrome and Mozilla Firefox browsers.

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Searching for Image Studies

You can search and download public data without logging in to the TCIA Data Portal. To access restricted data, however, you must log in first to see that data in your search results.

TCIA provides two ways to search for image studies:

• Simple Search
• Text Search

When you first open TCIA Data Portal, the Summary tab displays filters for a simple search and pie charts.

Click one or more boxes next to each search filter to select it. As you select search filters, they move to the top of the list. They also appear in Boolean query format above the pie charts. This query specifies the filters you have applied to your search. Click Clear if you want to remove all of your filters at once and start over. You can save your query as a URL for later use or to put in an email to a colleague. For more information about sharing, go to Sharing a Query.

You can filter (narrow) your search by Collections, Image Modality, Anatomical Site, Date released on TCIA, and Subject IDs. You can also specify the minimum number of image studies you want to match each search filter. For Collections, if you know the name of the collection, click  to enter it instead of finding and clicking the collection's box.

The Simple Search page shows a summary of image studies that match your search criteria. Your selections appear in the following ways:

• Boxes you selected are checked.
• Pie charts update to show the exact search results.
• Breadcrumb-style labels at the top of the page show the applied search filters (not all may display due to space constraints).
• Count of search results appears.

The pie charts show the count of image studies in your search results by Collection, Image Modality, and Anatomical Site. Click a pie slice or hover over it to see the name of the Collection, Image Modality, or Anatomical Site, and number of each, in your search results.

The Search Results tab shows the same results as the pie charts but in tabular form.

Text searches involve entering any text that might appear in any search filter.

Results are displayed in pie charts and a table, just as with the simple search.

Accessing Limited-Access Collections

You can search and download public data without logging in to the TCIA Data Portal. To access restricted data, however, you must log in first to see that data in your search results. Consult the TCIA Collections page to learn which collections have limited access.

1. In the top menu bar, click .
   The Login window appears.
   
2. Enter your user name and password, then click Log In.

Performing a Simple Search

A simple search allows you to search for image studies based on a combination of the following search filters: Collections, Image Modality, Anatomical Site, Date released on TCIA, and Subject IDs. The more criteria you select, the fewer results you receive. After you select your search criteria, you can save your query to use later.

To perform a simple search

1. On the TCIA home page, click the Simple Search tab.
   The Simple Search page appears.
   

2. Select filters to narrow down the available image series.

   To Select	Do This
   Collections	Option 1: Click the box next to each collection name you want to select.
   	Option 2: Click the magnifying glass to enter a name.
   Image Modality	Option 1: Click the box next to one or more image modalities. If you select more than one image modality, clicking ANY will returns any study that is associated with any of the modalities you selected. Clicking ALL returns all studies that are associated with all of the modalities you selected.
   Anatomical Site	Option 1: Click the box next to each anatomical site you want to select.
   At least X time point (DICOM studies)	Enter the minimum number of time points that match the criteria of your search. This filter allows you to see subjects that have more than one DICOM study (that is, the patient was seen at multiple time points).
   Date released on TCIA	Enter a From and To date to narrow your search results to studies that TCIA first made available during that date range. Alternately, select the Apply "Available" date range box to exclude studies that were unavailable to TCIA during the selected date range.
   Subject IDs	Enter Subject IDs associated with the image series you want to receive in your search results. Separate each Subject ID with a comma and then click Apply Subject IDs.

   The Summary tab shows updated pie charts and the number of image series in the search results.
   
   Click the Search Results tab for more detailed results.

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Performing a Text Search

Viewing Subject Details

The search results from your query are presented both on the Summary tab in pie charts and on the Search Results tab in a table. Each record in the table corresponds to one subject (patient) and displays the collection(s), study(ies), and image series associated with that subject.

From the Search Results tab, you can view subject details, view all image series associated with the subject, and add image series to your cart for download. You can also view the DICOM header for a selected image series. In the future, you will be able to view the image.

To view subject details

1. Search for studies that match criteria that interest you.
   The Summary tab refreshes to show your search results in pie chart form.
2. Click the Search Results tab.
   The search results that match your criteria appear sorted by Subject ID.
   

   
   You can now add all studies associated with a subject to your cart at the same time or drill down to an individual study and add it to your cart instead.

3. Click a Subject ID link.
   All studies associated with this subject appear. In this example, this subject is only associated with one study, and only one image series is associated with that study.
   

   The red asterisk indicates that the date, which is the date that this series was first available at TCIA, has been offset to protect private health information.

4. Click the arrow to the left of the cart icon to view details about the selected study.
   All of the image series associated with that study appear.
   
   You can now

• • Add an image series to your cart
  • View the series description, modality, manufacturer, number of images, and series ID
  • View thumbnails of the image series
  • View an animation of the image series (feature not yet available)
  • View DICOM data for this image series

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Viewing Thumbnails of the Image Series

You can view thumbnails of all images in the selected series and then open selected images for further analysis in another image system.

To view thumbnails

1. View the details for a subject.
2. Select a study and view its details.
3. In the row for an image series, click .
   
   Thumbnails of all of the images in the selected image series appear.
   
   
4. Click any image to download it to your computer. 
   Follow your browser's instructions to open or save the file.
   

Viewing DICOM Data

Digital Imaging and Communications in Medicine (DICOM) is a standard for handling, storing, printing, and transmitting information in medical imaging.

You can view the DICOM tags that form the header of the selected image series.

To view DICOM data

1. View the details for a subject.
2. Select a study and view its details.
3. In the row for an image series, click .
   The DICOM tags associated with the image series appear.
   

Downloading Study Data

You can download items you add during the current work session. Before you download items you must download and then install the NBIA Data Retriever.

You select items to download by first searching for them in TCIA and then adding them to your cart.

Adding Data to the Cart

Your cart is a holding place for data you have selected to download. You can add all image series associated with a subject, all image series associated with a study, or one or more selected image series to your cart. 

To add all image series associated with a subject to the cart

1. Search for the subject.
2. Click the Search Results tab.

3. Click the cart icon in the row of one or more subjects.
   The cart icon turns green and the number of image series now in your cart appears next to the cart. The cart itself, in the upper-right of the window, shows how many image series are in it and how large the download will be.

   To remove all of the data associated with this subject from the cart, click the cart icon again.

   
   

To add all image series associated with a study to the cart

1. Search for the subject.
2. Click the Search Results tab.
3. Click a Subject ID link.
   All of the studies associated with this subject appear.

4. Click the cart icon next to one or more studies.
   All of the image series in the selected studies are added to the cart.

• • The cart icon in the study row turns green. If you did not select all of the studies associated with the subject, the cart icon in the subject row turns yellow.

  • The cart itself, in the upper-right of the window, shows how many image series are in it and how large the download will be.

    To remove all of the data associated with this subject from the cart, click the cart icon again.

    

To add one or more image series to the cart

1. Search for the subject.
2. Click the Search Results tab.
3. Click a Subject ID link to open all series associated with that subject.
4. Click the cart icon for one or more series.
   The cart icon you select turns green.
   The cart icon for the subject turns yellow, indicating that you have not selected all available series for this subject.
   

Downloading the NBIA Data Retriever

Installing the NBIA Data Retriever

To install the NBIA Data Retriever on Windows

1. Download the installer package for Windows using the Windows link above.
2. Save the installer package file to your computer.
3. Install the app by double-clicking the installer package file.
4. Agree to the terms in the License Agreement and click Install.
5. When the Setup Wizard ends, click Finish.

To install the NBIA Data Retriever on Mac

1. On your Mac, find the NBIA Data Retriever on the Mac App Store.

   The NBIA Data Retriever is free but still requires you to log in to download it. Consider changing your iOS Password Settings so that you can download free software without having to log in separately for it.

2. Click Get, then click Install App. The NBIA Data Retriever is free.
   The app starts downloading to your Mac. When the download is complete, you can open a manifest file with the NBIA Data Retriever.

To install the NBIA Data Retriever on Linux (centOS or Ubuntu)

You must have the sudo privilege on your computer and a sudo password to install the NBIA Data Retriever on CentOS and Ubuntu.

1. Download the installer package for centOS or Ubuntu using the links above.
2. Save the installer package file to your computer.
3. Open a command window and go to the location where you saved the installer.

• For a centOS system, enter the following at the command prompt:
  sudo yum -v -y remove TCIADownloader.x86_64;sudo yum -y install NBIADataRetriever-3.3-1.x86_64.rpm
• For a Ubuntu system, enter the following at the command prompt:
  sudo -S dpkg -r tciadownloader;sudo -S dpkg -i nbia-data-retriever-3.3.deb
  Enter the sudo password when prompted.

Downloading Images Using the NBIA Data Retriever

Sharing a Query

You can save your query for later use or share it with a colleague by email.

To share a query

1. In the top menu bar, click  and then select Share my query.
   The Query URL box appears.
   
   
2. Click Copy URL.
   The URL copies into your Clipboard.

3. Paste the URL into an email or other document.

   Shared queries honor data permissions that may exist. Each person that runs the shared query will only see search results that he or she is allowed to see.

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Sharing Data in Your Cart

Once you have added data to your cart, you can share it as a URL to a static set of data. When you or a colleague opens the URL in a browser window, the new TCIA Graphical User Interface (GUI) opens to the cart page. 

In the legacy TCIA data portal, this was called a shared list. This is a similar concept in the new TCIA GUI. 

To share data in your cart

1. Add data to your cart.
2. In the top menu bar, click  and then select Share My Cart.
   The Retrieve Cart Data URL box appears.
   
   
3. Click Copy URL.
   The URL copies into your Clipboard.
4. Paste the URL into an email or other document.

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