• The NBIA Data Retriever has been updated to version 4.1.
• A command line interface is now available for Linux (CentOS and Ubuntu) users that does not require the desktop environment. 
• As of version 4.0, the Data Description URI is included in the metadata file you download if you export the cart as a spreadsheet. 
• You can now resume a download if you closed the NBIA Data Retriever in the middle of a download, as long as you choose the same download directory as you originally did before the interruption. You can specify whether you want to download just the missing series or download all of the series in the original manifest file. See Downloading Images Using the NBIA Data Retriever for an updated procedure.
• You must now accept the TCIA Data Usage Policy before proceeding to download data. This policy is now also included in the license file. See Downloading Images Using the NBIA Data Retriever for an updated procedure.
• The NBIA Data Retriever now warns you if there are series in your download that have commercial use restrictions.
• More technical features in this release include replacing Oracle Java 8 with Amazon-Corretto as the embedded Java runtime environment and several bug fixes.

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 showing counts of collections, image modalities, and anatomical sites in the database. Each pie "slice" is a filter you can use to narrow the data in the portal. Hover over a pie chart slice to view the name of each filter. The size of each pie slice is relative to the size of that filter's representation in the database. 

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 Data in Your Cart.

You can narrow your search by the following filters:

• Collections
• Image Modality
• Anatomical Site
• Species
• Phantoms
• 3rd-Party Analysis Results
• Clinical Time Points
• Exclude collections with commercial use restrictions
• Date Released
• 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.

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. Hovering over a collection name opens a window with information about the collection in it. Quickly move your mouse to this window, where you can select text and click links. The window stays open until you move your mouse away from it.
   	Option 2: Click the magnifying glass to enter a name.
   Image Modality	Click the box next to one or more image modalities. If you select more than one image modality, clicking ANY 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. When you select the ANY search modifier here, only the studies that match your search criteria are returned. Be aware that these may be only be a subset of the studies belonging to a single subject (patient). The potential difference between total studies available and the number of studies returned by your search  becomes clearer when you select the Total Studies and Total Series columns to appear in your search results. To do so, click at the top of the Search Results tab. Select Total Studies and Total Series in the Pick Columns list.
   Anatomical Site	Click the box next to each anatomical site you want to select. Click alpha or num to sort the list alphabetically or numerically. Select Not Specified to find data for which the BodyPartExamined field is empty.
   Species	Click the box next to the species you want your search results to represent, either human or Mus musculus (mouse).
   Phantoms	Click the box next to the phantom option you want to select.
   3rd-Party Analysis Results	Third-party analysis results are derived data (e.g. segmentations) that were contributed by researchers who were not part of the group that originally submitted a collection to TCIA. To enhance the value of TCIA collections, TCIA encourages the research community to publish their analyses of existing TCIA image collections. Examples of this kind of data includes radiologist or pathologist annotations, image classifications, segmentations, radiomics features, or derived/reprocessed images. Click the box next to each third-party analysis results option you want to select. Only DICOM data from third-party analysis results appear when using this search filter. A full listing of all third-party analysis data inclusive of non-DICOM formats appears in the Analysis Results Directory.
   Clinical Time Points	Some datasets encode Clinical Time Point information in the image metadata. This filter allows you to refine search results based on how many days have passed since a particular clinical event occurred when these metadata are included by the data submitter (e.g. "Days since diagnosis"). Click select to view the types that are available in the database, plus their available date range. In the from and to boxes, enter numbers that correspond to the range of days from and to that time point.
   Exclude collections with commercial use restrictions	TCIA supports collections with different types of licenses. Some licenses prohibit the commercial use of the collection. You can filter your search results to exclude those collections that have commercial use restrictions.
   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	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. Click the  button to return the dates to the default 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.

3. Select which columns you want to have appear in the detailed search results on the Search Results tab by clicking at the top of the Search Results tab. The Pick Columns panel appears. 

   
   
   

   Search results are shown in two different ways, as a summary and as detailed search results, and which one appears first matches your last choice. 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.

The text search does have some restrictions. These are:

• The text string you use must have more than one character. The search won't return any values if the text string has only one character.
• Do not use a forward slash (/) in your text string.
• Do not use complex searches with AND or OR statements (text search supports Lucene syntax but only a single field can be searched at a time).

To perform a text search

1. On the TCIA home page, click Text Search or Search Images > Text Search.
   The Text Search page appears.

   

2. In the Text Search box, enter a text string of two characters or more.

3. Click .
   The search results appear.
   
   
   

   Navigation Tips

   • Click the down arrow next to the Subject ID column header to sort the results alphabetically (A to Z or Z to A) by Subject ID.
   • Click the arrows at the bottom of the table to display the first, previous, next, or last page of results.
   • Click the page number links to move to a specific page of results.
   • In the Show (10) entries box in the bottom left, edit the default 10 to the number of entries you want to see on a search results page.

   The following table describes each item in the search results table.

   Search Result	Description
   	Click the caret to view the subject details. Click the cart symbol to add image series to your cart.
   Collection ID	Collection identifier
   Subject ID	Click the Subject ID to view all study images for this subject in a DICOM web viewer, a single series' thumbnails, or the DICOM header for the first image in the series. See Search Results (Studies for Subject).
   Hit	The field in the study where the text string you entered as your search criteria appears.

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

• • View the series description, modality, manufacturer, number of images, and series ID.
  • View thumbnails of the image series.
  • View DICOM data for this image series.
  • View an animation of the image series.
  • Download study data.

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.
   

To view a TCIA collection

1. View the details for a subject.
2. Click the study date link for the collection you want to view.
   The image series associated with this study appear.
   
3. In the row for an image series, click.
   The images in the series open in the Open Health Imaging Foundation (OHIF) Viewer.
   
4. Click to display the images in the series sequentially.

To add all subjects to the cart

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

3. Click the subject cart icon in the row of one or more subjects. This selects all studies associated with each subject.
   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 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 selected studies to the cart

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

To add selected series to the cart

1. Search for the subject.
2. Click the Search Results tab.
3. Click a Subject ID link or click the arrow to the left of the subject cart to open all series associated with that subject.
4. Click a study date link or click the arrow to the left of the study cart to open all the series associated with that study.
5. Click the cart icon for one or more series.
   • The series cart icons you select turn green.
   • The study cart icon for the subject turns yellow, indicating that you have not selected all available series for this study.
   • The subject cart icon for the subject turns yellow, indicating that you have not selected all available studies and series for this subject.
     
     

The most convenient method of downloading is by using the NBIA Data Retriever. You must install the NBIA Data Retriever before you begin downloading. You only have to install it once to use it in future downloading sessions.

Consult the NBIA Data Retriever FAQ for more information about NBIA Data Retriever versions and usage.

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.

To download images using the NBIA Data Retriever

1. Search for images of interest.
2. Add those images to your cart.
3. Click the cart icon in the top-right of the page .
   The cart contents appear.
   
4. Click .
   A message appears reminding you to download the NBIA Data Retriever. If you have already downloaded it, click Do not show this message again and click . Otherwise, click  to go to a page with links for downloads for each operating system.
   

5. Open the manifest-xxx.tcia file.
   The Data Usage Policy notification appears. 
   

6. Click Agree. You must agree to the data usage policy before you can proceed with downloading the data in your cart. Note that this policy is included in the license file accompanying your download.

   • If you have added limited-access series to your cart, the NBIA Data Retriever login window appears. Enter your user name and password and click Submit.
     

   • If all of the series you have added to your cart are public, the NBIA Data Retriever appears, showing the items you added to your cart in the Downloads table.
     
     
     If there are series in your download that have commercial use restrictions, the NBIA Data Retriever displays a message referring you to the license information for these series.
     

     You can hover your mouse over the Patient ID, Study Instance, and Series Instance columns to reveal the complete corresponding IDs. You can also resize a column by selecting and dragging the column border.

     If you do not want to download any of those items, select them in the Downloads table and then click Delete. When you remove an item from the Downloads table, it stays in your cart in the Radiology Portal. 
     
     

     If you close the NBIA Data Retriever in the middle of a download, NBIA Data Retriever remembers the partial download. When you restart the NBIA Data Retriever, choosing the same download directory as before, and click Start, you are prompted to specify whether you want to download just the missing series or download all of the series in the original manifest file. 

     

     If you choose Download all, the existing download folder will be overwritten with all of the series in the original manifest file. If you choose Download missing series, only those series you have not previously downloaded appear in the Downloads table in the NBIA Data Retriever window, then download only those series.

     NBIA Data Retriever File Naming System

     The file naming system used by the NBIA Data Retriever provides a natural ordering of the files within each series. The DICOM files are first ordered by ordinal position of acquisition number and then by ordinal position of instance number. The files are then assigned numbers with the lowest acquisition being 1 and the lowest instance number within that acquisition being 1, separated by a dash. The numbers are incremented by 1 as the next values are encountered. All values are left-padded with zeros to provide for the ordering within the file system. 

     As an example, a series with 2 acquisition numbers with each acquisition having 42 instance numbers would start with 1-01.dcm for the lowest acquisition number and the lowest instance number in that acquisition. The last file in that acquisition would be 1-42.dcm.  Then the second acquisition would start with 2-01.dcm, ending with 2-42.dcm, in that acquisition. For the purposes of ordering, an empty value in either acquisition number or instance number is lower than an file having a value for those number.

7. Click Browse to navigate to the destination where you want the images/annotations to be downloaded.

8. Click Start to begin the download. You can monitor the status of the full download in the progress bar on top, and for each collection in the Progress column. The Status column indicates when the download for each item is complete.

   At any point in the process, you can click the Pause and Resume buttons to temporarily stop and restart the process.

   The downloaded files are stored in a child folder under the destination folder such as Collection Name > Patient ID > part of Study Date + part of Study ID + part of Study Description + last 5 digits of Study Instance UID > part of Series Number + part of Series Description + last 5 digits of Series Instance UID.

   Network Error?

   If network errors occur during large downloads, the NBIA Data Retriever retries downloading the series in the manifest file the number of times that your administrator has configured. The default is four times.

   After the automatic retries, you have the option of retrying just the failed series, saving an error report, which you can share with the TCIA help desk, and exiting.

   

To export your cart

• Add data to your cart.
• Click .
  The cart appears.
  
• Click .
  A CSV file called "metadata" opens in your browser. This file provides an overview of the downloaded files. 
  
  Metadata file in the manifest folder
  
  This file includes the following columns: 
  
  • Series Instance UID
  • Collection
  • 3rd Party Analysis
  • Data Description URI
  • Subject ID
  • Study UID
  • Study Description
  • Study Date
  • Series Description
  • Modality
  • Manufacturer
  • SOP Class Name
  • SOP Class UID
  • Number of Images
  • File size
  • File Location
  • Download Time Stamp
    
    
    Metadata file opened in Microsoft Excel