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ALERT

Except for the six topics relating to the User Authentication Tool, this page consists of outdated documentation describing an older version of TCIA's search interface as well as the NBIA 7.4 TCIA Patch. The latest search interface is at https://nbia.cancerimagingarchive.net/nbia-search/. Please refer to the Cancer Imaging Archive User's Guide for current documentation for the TCIA Radiology Portal.

Registering a New User

To access both the TCIA wiki and the archive of DICOM images, you must follow these steps to register as a new user.

  1. Start at https://www.cancerimagingarchive.net. Click Search Data Portal button.
  2. Click the Register Now link in the Register Now panel as shown below.
    Register Now
    The legal provisions page appears.
  3. Review the text on the page and click the CLICKING HERE link at the bottom to indicate your agreement.
  4. Enter the challenge word(s) on the CAPCHA page. Click Verify.
    The registration form appears.
    New User Registration. Password Self-Service page.
  5. All fields are required. The username may have a period and an @ symbol, but no other special characters are allowed in usernames. The password can have any special characters.
  6. Click Create.
    Once you have submitted your entry form, an automated handshake email will be sent to your address. Once you confirm the account registration, your account is registered.

    If you are registering here for access to a private space within TCIA's wiki, you may additionally need to request access to that restricted space by sending an email to TCIA Help Desk. In this email, include your username and the URL of the wiki to which you want access.

Logging into TCIA

Open the TCIA data portal. The welcome page appears.

If you do not have a User ID or password, click Register Now to apply for a user account. For more information, see Registering a New User.

If you have already registered, perform the following steps to log in.

  1. In the User Login panel, enter your User ID and password.
    User Login dialog box
  2. Click Login. If your login is successful, the data portal appears.

    Tip

    TCIA uses popups. To prevent problems accessing the application, in your browser, enable a popup blocker exception for https://public.cancerimagingarchive.net/ncia/login.jsf.

    If you have persistent difficulty logging in, click I cannot access my account on the TCIA login page. A TCIA Account Help topic opens, describing help options for resolving your login problem. Alternately, contact the TCIA Help Desk.

Using the TCIA Home Page

When you first open the TCIA Data Portal, you can search images without logging in. You can also view information about obtaining DICOM Viewers, learn about persistent references (DOIs), learn about programmatic interfaces (APIs), and get support.

TCIA home page before you log in

After you log in, you have more options.
TCIA home page if you log in

Options available from this page and links to more information about them follow.

Menu

Menu Option

Description

For more information, see

Try the Beta Search
The Beta Search features a new interface for the TCIA Data Portal. You can submit feedback and suggestions on this new interface.TCIA Data Portal User Guide

Home


Return to the TCIA Home page.


Search Images

Simple Search

Open the Simple Search page.

Performing a Simple Search


Text SearchOpen the Text Search page.Performing a Text Search

Advanced SearchOpen the Advanced Search page.Performing an Advanced Search

Manage Data Basket


Open the My Data Basket page. This is the same option as choosing Manage Data Basket from the menu bar.

Working with the Data Basket

Tools

List DICOM Image Viewers

Open a page displaying links to freeware DICOM image viewers.

Obtaining DICOM Viewers


Persistent References (DOIs)Opens TCIA Analysis Results.

Programmatic Interface (APIs)Opens the TCIA Programmatic Interface (REST API) Usage Guide.

View Saved QueriesOpen the Saved Queries page.Working with Saved Queries

View Query HistoryOpen the Query History page.Viewing Query History

Create Shared ListOpen the Create Shared List page.Creating a Shared List

Edit Shared ListOpen the Edit Shared List page.Editing a Shared List

Search Shared ListOpen the Search Shared List page.Searching a Shared List
Admin

Perform QC

Evaluate a submission and assign a QC status.

Only administrative users have access to this menu. If you believe you should have access, contact the TCIA helpdesk.

Using the Quality Control (QC) Tool


Approve DeletionsApprove the deletion of image series marked for deletion.
Approving Image Deletions

Manage Shared ListDelete shared lists created by other users.Managing a Shared List

View Submission ReportsRun reports to verify that images have been received and to monitor the status of the submitted images.Viewing Submission Reports

Perform Online DeletionsImmediately remove images that are marked as approved for deletion.Manually Deleting Image Series

Edit Collection DescriptionsAdd a brief description for a collection so that TCIA users know what data is in the collection.Editing a Collection Description

Manage Workflow ItemsCreate, edit, and delete workflow items that involve changing the visibility status of an image series and/or trigger a web service call to a URL.Managing Workflow Items

Manage Saved QueriesReview and delete saved queries.Managing Saved Queries

User Authorization ToolManage users and their access, protection elements, protection groups, user groups, and roles.

Managing Users

Managing PE

Managing Protection Groups

Managing User Groups

Adding Protection Groups and Assigning Roles

Support


Open a browser window with support options.

TCIA Support

Logout
Log out of TCIA and return to the TCIA home page.

Using TCIA Online Help

The TCIA online help retrieves topics from the TCIA User's Guide. It explains how to use all of the features of the TCIA data portal.

Not logged in?

You can open the user's guide without being logged into TCIA.

Click Help > User Guides in the top menu bar to open the TCIA User's Guide on the TCIA wiki.

On any application page, click help button to open the help topic that applies to features available on that TCIA page.

Performing a Simple Search

A simple search allows you to search for image studies based on a combination of the following search filters: Collection(s), Image Modality(ies), Anatomical Site, Manufacturer Model(s), Available date, Subject IDs, and Baseline Plus. The more criteria you select, the fewer results you receive. After you select your search criteria, you can create a saved query to use later.

To perform a simple search

  • On the TCIA home page, click Simple Search or Search Images > Simple Search.
    The Simple Search page appears.
    Simple Search page
    Choose the search criteria as described in the following table.

    DescriptionSimple Search Criteria
    Results per Page

    Select the number of search results per page the search will return.

    Collection(s)
    Collections are NCI-defined groupings of image data sets. Select from the collections to which you can access. If none are selected, then the search returns data for all collections.

    Click the Collection help buttonicon next to the collection name to display a popup with the collection description if it exists.

    Click Collection Descriptions for more information about the collections.

    Image Modality(ies)

    Select from the available image classifications. If none are selected, then the search returns data for all modalities. 

    Specify whether to Return cases that include All or ANY Modality.

    Modality description

    Descriptive text for the modality displays when you hover the cursor over the option.

    The TCIA data portal can perform ultrasound-specific searches. To launch an ultrasound image search, select US in the list of Image Modalities. When you do so, three additional search options display on the page, shown below. Configure the options appropriately for the ultrasound data you want to search.

    Image Modalities when US is selected

    • Number of frames: One ultrasound DICOM file can consist of multiple frames which you can specify in this option.
    • Specify if Ultrasound Color Data is present.
    • Specify one or more Ultrasound Image Modes.

    If you choose to view an ultrasound DICOM file in animation, TCIA loops through all of the images in the file.

    Anatomical SiteTo further restrict the search, optionally choose the anatomical site of interest.
    Manufacturer ModelTo restrict manufacturer model results, uncheck All Manufacturers. Expand and display the list as needed, and select the items to restrict the search.


    Available (mm/dd/yyyy)

    To restrict results to the date the image became available in the system, expand the panel, enter from and to dates and select Add Criteria to perform the search.
    Available panel

    Subject ID(s)

    To restrict results to a comma separated list of patient IDs, expand the panel, enter the list of patient IDs, and select Add Criteria to perform the search.
    Subject ID(s) enter comma separated ID(s)

    Baseline Plus

    Expand the panel and specify the Minimum Number of Additional Studies.
    Baseline Plus

    To clear the search criteria and start over, click Reset button.

    The search results appear.

    Simple Search results page

    Save the Query

    You can save your search criteria to make it easier to repeat this query in the future. After you have selected one or more search criteria, the Save Query link appears at the bottom left of the page.

    To save a search query
    1. Select search criteria.
    2. In the box above the Save Query link, enter a name for your query.


      Save Query link

    3. Click Save Query.
      The query is saved. You can see it by selecting Tools > View Saved Queries.

    For more information, see Managing Saved Queries.

    Navigation Tips

    • Click the down arrow next to a column title to sort the column by that item.
    • 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.

    The Search Results (Studies for Subject) page shows studies associated with the subject that you selected on the Search Results by Subject page. Each study, identified by Study Instance ID, Description, and Date, is followed by a table with rows for each image series in the study. At the top and bottom of the page, breadcrumbs in the format Search >> Study show the level of the data on the page. Clicking Search in those breadcrumbs returns you to your original search results.

    The following table describes the data available for each study and image series in that study.

    Field

    Description

    Series

    Series identification number

    Description

    Description of the Series

    Modality

    Image modality

    Manufacturer

    Name of the manufacturer of the image series

    Images

    Displays the number of images in the series. This number includes visible images that meet the search criteria.

    Thumbnails

    Click Magnifying glass iconto display thumbnails of the series' images. For more information, see Search Results (Images for Series).

    Cine Mode

    Click Cine mode button in a series record to launch an animation of the series. This feature is only available when two or more thumbnails are available for the series. For more information, see Viewing Image Animation.

    DICOM

    Click DICOM button to open a new window that displays DICOM metadata about the first image in the series. 

    DICOM tags for first image in the series. Columns are Element, Name, and Data
    Each image series can have multiple images whose thumbnails display in this search results page. While each image has its own DICOM file whose attributes may vary slightly from the others in the series, the DICOM file that opens displays values for only the first image in the series. These values represent the values for all images in the series.

    Add to Basket


     

    • Click add to basket button to select the series and remove from basket button to clear it.
    • To mark all series in the search results as records you want to add to your data basket, click the basket icon in the column header or click Add all found to basket button

    For more information, see Managing the Data Basket.

    Add a Study series to Basket

    To add only the series in a single study in the search results to your basket, click basket button in the Add This Study to Basket section.

Performing a Text Search

A text search allows for searching of many of the database text fields, DICOM image tag data, and annotation files that are not available in the normal Simple and Advanced searches. For example, you can find all patients associated with the term glioma, as shown below.

To perform a text search

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

    empty text search fields

  2. Select the number of search results per page the search will return.
  3. In the box at the top of the page, enter a text string.
    Use Lucene conventions for wildcards. Do not use colons as TCIA automatically filters them from the criteria. Lucene designates colons as fields. Since the text search searches all fields, colons are not necessary.
  4. Click Submit.
    The search results appear.
    search results from search term of brain

    Navigation Tips

    • Click the down arrow next to a column title to sort the column by that item.
    • 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.

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

    Search ResultDescription
    Collection IDCollection 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

    Total StudiesTotal number of studies for the subject
    Total SeriesTotal number of image series for the subject
    basket

    Add the images for a single series or the entire study to your data basket. When you have marked a record for addition to the data basket, it is highlighted in yellow.

    • Click add to data basket to select the record and remove from basket to clear it.
    • To mark all records in the search results as records you want to add to your data basket, click the basket icon in the column header or click add found to basket.

    For more information, see Managing the Data Basket.

Performing an Advanced Search

An advanced search allows you to search against multiple combinations of values within Collections, Patient, Study,  Series, or Image objects. You can build search criteria based on data values or ranges at the image series level.

To perform an advanced search

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

    Advanced Search criteria
  2. Select the number of search results per page the search will return.
  3. From the Match options, select ALL to find image series that meet all of your search criteria or select ANY Criteria to find image series that meet any of your search criteria.
  4. From the first Criteria list, select a TCIA entity. Your selection here determines the options available for the rest of the search criteria.
  5. Select options from the lists or enter text into the box as needed to perform your search. If you enter text into the box, click the Add icon (plus sign button) for each set of criteria you define.
    As soon as you specify the final criterion, the criteria you selected appear in the box below the criteria and the search results appear to the right.

    Modality searches

    Modality searches only support the CT and MR modalities.

     

    advanced search results page

    Navigation Tips

    • Click the down arrow next to a column title to sort the column by that item.
    • 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.

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

    Search ResultDescription
    Collection IDCollection 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).

    Matched Studies

    Total number of studies for this subject that match the search criteria

    Total StudiesTotal number of studies for the subject
    Matched SeriesTotal number of image series for the subject that match the search criteria
    Total SeriesTotal number of image series for the subject
    basket

    Add the images for a single series or the entire study to your data basket. When you have marked a record for addition to the data basket, it is highlighted in yellow.

    • Click add to data basket to select the record and remove from data basket to clear it.
    • To mark all records in the search results as records you want to add to your data basket, click the basket icon in the column header or click add found to basket.

    For more information, see Managing the Data Basket.

  6. To further refine your results, select new search criteria. These new criteria filter your existing results and as with the previous search, the criteria you selected appear in a box below the criteria. Click the close button to delete the record from the page or click reset button  to delete all criteria and start over.

Viewing Image Animation

You can launch an image animation where there are more than two images in the series using one of these methods:
  • On the Search Results (Studies for Subject) page, you can launch an animation of thumbnails if there is more than one image in the series. Click Cine mode in a series record in the search results.

    OR
  • You can launch the animation of an image series from the data basket. In the View column of the data basket, click the magnifying glass symbol,Magnifying glass, corresponding to the series you want to view. On the View Series Images page, click the View Series in Cine Mode link.
    Animation viewer, described in text
    When the viewer opens (figure above), the animation controls display below the image. When you use the controls, TCIA proceeds to display the images sequentially, like a movie.

The following table describes the action of each of the animation controls.

Animation Controls

Action

Reset start and end button

Reset start and end.

Yellow bar

Drag ends of the yellow bar to vary the range of images playing.

Fast backward

Click to return to the first image in the set.

Back arrow

Click to play animation backward through the series.

Minus

Click to stop the animation; click again to display one image at a time, moving backward through the series.

Arrow slider on a line

Drag the arrow to set which frame of the movie displays. This also monitors the progress of the animation.

Plus sign

Click to stop the animation; click again to display one image at a time, moving forward through the series.

Forward arrow

Click to play animation forward through the series.

Fast forward double arrow

Click to progress to the last image in the set.

Cycle arrow

Click to cycle the animation forward or backward. Once set, the animation continues.


Tip

If the animation is very sluggish, you may want to preload the entire animation by clicking the link at the bottom of the series animation page. Also heed the note at the bottom of the page, which reads:

Warning: Especially on low-bandwidth connections, please ensure your browser is configured to cache data on SSL connections. Otherwise, the performance of theslide showcan be poor. For example, to enable caching on Firefox, set browser.cache.disk_cache_ssl to true. If viewing Ultrasound Cine Loop, note that it is not playing at acquired frame rate - please download to local computer and run with separate DICOM viewer.

Creating Saved Queries

To save a search query
  1. Select search criteria.
  2. In the box above the Save Query link, enter a name for your query.


    Save Query link

  3. Click Save Query.
    The query is saved. You can see it by selecting Tools > View Saved Queries.

Working with Saved Queries

While performing a Simple Search, you can save your choice of Collection(s), Image Modality(ies), and Anatomical Site as a named query. You can then run that query in the future or edit it, if you want to change any of the search criteria. That edited query can either update your original query or become a new query with a new name.

The following procedures are associated with saved search queries.

Editing Saved Queries

You can view your saved queries and then edit and resubmit them. You can also view your query history.

Disallowed Collections and Saved Queries

If you save a query when you have access to a collection then subsequently lose that access, you do not lose the saved query. However, records from a disallowed collection are not included in the search results.

To view, edit, and resubmit saved queries

  • Select Tools > View Saved Queries.
    The Saved Queries page appears.

    Saved Queries page

    The query table is sorted in descending order by Last Executed date by default. You can also sort by Query Name by clicking on the down arrow next to the column title.

    The following table describes the information about your saved queries on this page.

Saved Query

Description

Query Name

The name of the query displays as a link. The default is that the criteria themselves do not display. The link toggles whether the criteria for the saved query displays. Click the link to display/not display the criteria selected for the query.

Last Executed

The most recent date and time you executed the query displays. The time is displayed for the Eastern Time (US and Canada) time zone.

New Data Available

An icon (New data available icon) appears if new data is available for the saved query. Click the icon to display the results (new data only) on the Search Results page.

Resubmit Query

Click this button to open the Simple Search page showing all available results of the currently saved search criteria. A message appears in the lower left corner identifying the source of the search results.

message says these are the results of the CR saved query

Edit Query

Click this button to open the Simple Search page with the currently saved search criteria selected. In the lower left corner of the page, the Save Query section provides the options to update the saved query with new criteria or to save these criteria as a new saved query, with a box for the new query name.

Select an option and click Save Query.

edit query section of Simple Search page

Check Box

Click the check box to mark the query for deletion. You can click the check box in the header to select all queries or you can select queries individually. Click Remove Selected Items. The Manage Saved Queries page displays a message indicating success or failure and any additional actions that are required.

You can also perform the following action on the Saved Queries page.

ActionDescription
View Query HistoryClick the Query History tab. The View Query History page appears. For more information, see Viewing Query History.

Viewing Query History

To view query history
  • Select Tools > View Query History link
    or
    Click the Query History tab from the Saved Queries page.
    The Query History page appears. The Query History page displays a table of the last twenty queries that you executed. These include saved queries that you resubmitted as well as queries you have not saved.
    query history page

The Query History page contains the following information:

Field Name

Description

Query Name

The name of the query displays as a link. The link toggles whether the criteria for the executed query is displayed. The text of the link can appear three different ways depending on the situation.

  • If the query was not saved, No Name Provided displays as the link.
  • If the query is a saved query that has not been edited since the last execution date, the name of the saved query is displayed.
  • If the query is a saved query that has been edited since the last execution date, the name of the saved query is displayed with an asterisk. The asterisk refers to a message at the bottom of the page which is a warning to you that the results are based on the criteria that were used at the time the query was run, not the criteria that is currently saved for the query.

Last Executed

The date and time that you executed the query. The time is displayed for the Eastern Time (US & Canada) time zone.

Resubmit Query

Click the Resubmit Query button to submit the query using the saved criteria. The results display on the Search Results page.

Click the Saved Queries tab to view, edit, or resubmit saved queries (see Managing Saved Queries).

Search Results Studies for Subject

The Search Results (Studies for Subject) page shows studies associated with the subject that you selected on the Search Results by Subject page. Each study, identified by Study Instance ID, Description, and Date, is followed by a table with rows for each image series in the study. At the top and bottom of the page, breadcrumbs in the format Search >> Study show the level of the data on the page. Clicking Search in those breadcrumbs returns you to your original search results.

The following table describes the data available for each study and image series in that study.

Field

Description

Series

Series identification number

Description

Description of the Series

Modality

Image modality

Manufacturer

Name of the manufacturer of the image series

Images

Displays the number of images in the series. This number includes visible images that meet the search criteria.

Thumbnails

Click Magnifying glass iconto display thumbnails of the series' images. For more information, see Search Results (Images for Series).

Cine Mode

Click Cine mode button in a series record to launch an animation of the series. This feature is only available when two or more thumbnails are available for the series. For more information, see Viewing Image Animation.

DICOM

Click DICOM button to open a new window that displays DICOM metadata about the first image in the series. 

DICOM tags for first image in the series. Columns are Element, Name, and Data
Each image series can have multiple images whose thumbnails display in this search results page. While each image has its own DICOM file whose attributes may vary slightly from the others in the series, the DICOM file that opens displays values for only the first image in the series. These values represent the values for all images in the series.

Add to Basket


 

  • Click add to basket button to select the series and remove from basket button to clear it.
  • To mark all series in the search results as records you want to add to your data basket, click the basket icon in the column header or click Add all found to basket button

For more information, see Managing the Data Basket.

Add a Study series to Basket

To add only the series in a single study in the search results to your basket, click basket button in the Add This Study to Basket section.

Creating a Shared List

You can create a shared list by clicking Tools > Create Shared List link or by putting a series in the data basket, as explained below.

Who can create a shared list?

Anyone can create a shared list. Once you do so, you must record the exact name of the shared list to distribute to others who may want to use the list. That is the only way they can access it.

To create a shared list

You can create a shared list from data basket or the Tools menu. Procedures for both methods follow.

Data Basket

  1. Add an image series that you want to include in the shared list to the data basket.
  2. Click the Create Shared List button.
  3. Do the following:
    1. Enter a Name for the list (required).
    2. Optionally, add a description and a URL. The URL links to relevant or more detailed information about the list.
    3. Click Browse to upload a file in comma separated value format (.csv) that includes all of the series instance IDs you want to be in the shared list. This file should have one series instance UID per line.
  4. Click Submit.
    The image series from the uploaded file is added to the data basket.

Access to your list

TCIA warns you that not all public users will have access to your list if the list contains any non-public image series.

Menu Option:

  1. Click Tools > Create Shared List.
    The Create Shared List page appears.
    Create Shared List page
  2. On this page, do the following:
    1. Enter a Name for the list (required).
    2. Add Comments and a Hyperlink, where appropriate, which links to relevant or more detailed information about the list (optional).
    3. In the Upload File field, enter the name of a file that includes all of the series instance IDs you want to be in the shared list. This file should have a series instance UID per line.
    4. For your convenience, a Java tool is available to aid in generating a CSV of your series instance UIDs. 
      Download: ExtractSeriesUIDs.zip
      Do the following to use this tool to generate the file to upload in the last field of our online Create Shared List form:
      1. Download the zip file, then move it to a top-level directory of DICOM files you want indexed.
      2. Extract the zip file to the top level directory where your DICOM data resides (all sub-directories will be scanned). It should extract two things.
      3. Then run ExtractSeriesUIDs.bat which should flash a quick command line window and then automatically disappear.
        A file with a name similar to SeriesUIDs.CSV is created as an output.
      4. Enter the output filename into the form.
  3. Click Submit.
    The image series from the uploaded file is added to the data basket.


Searching a Shared List

Any user can search for a shared list.

To search for a shared list

  1. From http://www.cancerimagingarchive.net/, click Search Data Portal button.
  2. Click Tools > Search Shared List.
    The Search Shared List page appears.
    Search Shared List page
  3. Enter the name of an existing shared list. To retrieve the list, you must know the exact name given to the shared list.
  4. Click Submit to launch the search or Reset to clear the field and start again.

If the search is successful, all image series in the shared list are added to the data basket. If the shared list includes series for which you do not have visibility rights, a message appears that informs you that the displayed shared list is not complete.

Editing a Shared List

You can edit the list only by uploading a .csv file with all the series instance IDs for the list. You can only edit/delete shared lists you have created yourself.

Shared List

From the data basket, you can export image series instance IDs to a .csv file for later use in creating or editing a shared list. See Exporting a Shared List for more information.

To edit a shared list

  1. Click the Edit Shared List link under Tools on the menu bar.
    The Edit My Shared List page appears, displaying a list of shared lists you have created.
    Edit My Shared List page
  2. Click the name of the shared list you want to edit.
    List details appear.
    expanded Edit My Shared List page showing details about the list
  3. In the description field, optionally enter a comment about the list or your edit.
  4. In the URL field, optionally enter a web address that provides more information about the shared list.
  5. Click Browse to locate the file you want to upload. Doing this replaces the current shared list.

To delete a shared list

  1. Click Tools > Edit Shared List.
    The Edit My Shared List page appears, displaying a list of Shared Lists you have created.
  2. In the row of the shared list you want to delete, click Delete button.

Because editing a shared list is only possible by replacing it, you might consider backing up a shared list when you create it. To do so, export the shared list as a file when you create it. See Exporting a Shared List.

Managing a Shared List

Users with the appropriate administrative privileges can delete shared lists created by other users.

Permissions

This administrative feature is available only to logged in users who have "manage visibility" privileges, as defined in UPT.

 To delete a shared list, follow these steps:

  1. Click Admin > Manage Shared List.
    The Manage Shared List page appears.
    Manage Shared List page with a user name dropdown option only
  2. Select a user name from the list.
    That user's shared list(s) appear.
    Manage Shared List page displaying a selected user's shared list
  3. Click the name link to review the shared list's details or click delete button to delete shared the shared list.

Managing the Data Basket

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Adding Items to Your Basket

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Downloading the Data Basket

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Download Manager

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Downloading TCIA Images


Topics in this section

Downloading the NBIA Data Retriever 

After you search for images of interest and add them to your data basket, you can download them.

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.

Get the NBIA Data Retriever

Click one of the following links to download the NBIA Data Retriever for that operating system.

  • RPM (tested on centOS)
    To run this file, type the following at the command prompt:
    sudo yum -v -y remove NBIADataRetriever-3.5-1.x86_64.rpm;sudo yum -y install NBIADataRetriever-3.6-1.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-3.5.deb;sudo -S dpkg -i nbia-data-retriever-3.6.deb
  • NBIA Data Retriever in the Mac App Store
  • Windows

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

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

The Mac version of the NBIA Data Retriever is only available through the iOS App Store. It requires a manifest file to work. You can download the app first or create a manifest file first. If you download the app first, right-click the manifest file and select Open With NBIA Data Retriever. If you create a manifest file first, right-click it and select Open With App Store. This installs the app and then opens the manifest file in the app.

  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.

Downloading Images Using the NBIA Data Retriever

When you download images you have added to your cart, TCIA provides a list of these images in a manifest file (manifest-xxx.tcia). You must have already installed the NBIA Data Retriever to open this manifest file and download the images.

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 Cart icon.
    The cart contents appear.
    Cart contents showing three image series ready to be downloaded
  4. Click Download button.
    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 Download button. Otherwise, click Get Data Retriever button to go to a page with links for downloads for each operating system.
    Message box prompting you to download the Data Retriever
  5. Open the manifest-xxx.tcia file.
    The  NBIA Data Retriever appears, with the items you added to your cart in the Downloads table. See the note about the file naming system that appears in the manifest file.
    NBIA Data Retriever in the process of downloading data
    The NBIA Data Retriever lists all items you selected in the cart. 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. 

    NBIA Data Retriever File Naming System

    The file naming system used by the NBIA Data Retriever has been revised to provide a more natural ordering of the files within each series. This has been accomplished by first ordering the DICOM files 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.

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

  7. Click Start to begin the download. You can monitor the download 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.

    Note that files downloaded this way are not compressed. 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 saving an error report, which you can share with the TCIA help desk, or of retrying just the failed series.

    NBIA Data Retriever download in progress with errors



Downloading Private Data

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Viewing Submission Reports


Permissions

This administrative feature is available only to logged in users who have "manage visibility" privileges, as defined in UPT. For more information, see Registering a New TCIA User.

When a site submits images to TCIA, a user with admin privileges can run various reports to verify that the images have been received and to monitor the status of the submitted images. This is accomplished in TCIA by generating a report with this information.

To view submission reports, follow these steps:

  1. Click Admin > View Submission Reports.
    The Submission Reports page appears.
    Submission Reports page
    The Collection//Site section displays all collections for which you, as an Admin, have permissions to view.
  2. Select a collection.
  3. Enter a valid date range or select one by clicking the calendar icons.
  4. Click the report type you want to run: Accrual, Image, or Annotation.
    The search begins and may take a few moments.

To assist in viewing the reports, use the following icons:

  • In the report results in the upper right segment of the page, click the Help button (help button) to learn details about the report type you selected.
  • Click the arrow at the left of the section to hide (hide button) or show (show button) the results.
  • To view an expanded view of the image report results, click the Expand icon (Expand icon) preceding each row of the New Image or Corrected summaries.

The results display Count by Day details of the submissions. For example, for each day in the time frame, you can view a list of affected patient IDs, study instance UIDs and series instance UIDs.

Accrual Report

After you have submitted a query for viewing accrual reports, TCIA displays the results on a page shown in the following figure.
accrual report

Fields that appear on the report are described in the following table.

Submitted Files Counts Fields

Description

New Image

An image that does not exist in the system at the time of submission

Corrected Image

An Image that has been successfully submitted more than once. The time of the original image submission does not affect whether a subsequent image is considered as "corrected". Each time, an image is re-submitted in the time frame, the count is incremented.

New Patient

A patient that had no images submissions prior to the start of the date range, but at least one image submission within the date range

Updated Patient

A patient that had at least one image submission prior to the start of the date range, and at least one image submission within the date range

Corrected Patient

A patient that has at least one image submission in the time frame that has been corrected.

New Study

A study that had no image submissions prior to the start of the date range, but has at least one image submission within the date range

Updated Study

A study that had at least one image submission prior to the start of the date range, and at least one image submission within the date range

Corrected Study

A study that has at least one image submission in the time frame that has been corrected.

New Series

A series that no image submissions prior to the start of the date range, but has at least one image submission within the date range

Updated Series

A series that had at least one image submission prior to the start of the date range, and at least one image submission within the date range

Corrected Series

A series that has at least one image submission in the time frame that has been corrected

Report content

The reports contain a count of patient/study, series or images that have been affected during the date range in the specified collection/site.

Image Submission Report

After you have submitted a query for viewing image submission results, TCIA displays the report on a page as shown in the following figure.
Submission Report window

Image submission results display a count of patients, studies or series for or to which an image was submitted during the specified date range in the collection or site you selected. Fields that appear on the report are described in the following table.

Submitted Files Counts Fields

Description

New Image

An image that does not exist in the system at the time of submission

Corrected Image

An Image that has been successfully submitted more than once. The time of the original image submission does not affect whether a subsequent image is considered as "corrected". Each time, an image is re-submitted in the time frame, the count is incremented

Affected Patient/Study/Series

A patient/study/series is one for which there was at least one new image submission

Corrected Patient/Study/Series

A patient/study/series that has at least one image submission that has been corrected in the time frame.

Report content

The reports contain a count of patient/study, series or images that have been affected during the date range in the specified collection/site.

Annotation Submission Report

After you have submitted a query for viewing annotation submission results, TCIA displays the report on a page as shown in the following figure.
annotation submission report

The annotation submission report contains a count of annotations submitted and affected patient/study/series during the specified date range for that collection site. Fields that appear on the report are described in the following table.

Submitted Files Counts Fields

Description

Annotation

An annotation that has never been submitted in the system prior to the start of the date range

Corrected Image

A patient/study/series is one for which there was at least one new annotation submission

Report content

The reports contain a count of patient/study, series or images that have been affected during the date range in the specified collection/site.

Using the Quality Control Tool


Permissions

This administrative feature is available only to logged in users who have the MANAGE_VISIBILITY_STATUS privilege, as defined in UPT/UAT. For more information, see Registering a New TCIA User.

When an image is uploaded to TCIA, it is not made public immediately. A curator takes it through a quality control process to ensure that no private patient data is available, the image is of good quality, and so forth. Using the QC tool as a curator, you can define search criteria to locate image series for you to evaluate. You can then evaluate the submission and assign the QC status to an image or image series.

QC tool search visibility

The QC tool allows a curator to search images with any QC status. A regular user using the search tool can only see approved public or private image series that have the QC status of "visible."

Classic Search

To perform a classic search

  1. Click Admin > Perform QC. This opens the QC Tool page to the Classic tab, shown below. You can specify basic search criteria on this tab. You can construct more specific search criteria on the Dynamic tab.

    QC Tool, Classic View

    Do not click your browser's Back or Refresh button while following these steps. This logs you out.

  2. Check the QC Status for the series you want to locate. The options are described in the following table:

    Submitted Object Status

    Description

    Not VisibleNo images in the series are visible.

    Not Yet Reviewed

    This status (selected by default) is automatically assigned to an image upon submission to the NBIA database.

    First Review to Seventh A configurable user-defined stage in the workflow of an image series.

    To Be Deleted

    Selected image series are to be deleted from the system.

    VisibleAll images in the series are visible.
    DownloadableUse this option to identify series that are not ready for release but are available for curators to download so they can study them with their own tool. Downloadable series do not appear in search results. Administrators can include series flagged as downloadable in a manifest and download them.

    Administrators can download any image, no matter what its status is.

  3. In the Collection(s) field, select one collection (site) that you want to search. You cannot search multiple collections (sites) at one time.

  4. In the Batch Number field, select the batch number of the images/series for which you want to search. You can also select Any, to find all batches that have a batch number, or None, to find all batches that do not have a batch number.
  5. In the Confirmed as COMPLETE field, select Yes to search for a set of images/series that has been confirmed as complete, or No to search for a set of images/series that is ongoing.
  6. In the Released field, select Yes to search for images/series that have been released or No to search for images/series that have not been released.

  7. To restrict results to a list of patient IDs, in the Patient ID panel, enter the list of patient IDs and select Add Criteria to perform the search. Separate multiple patient IDs with commas.

    Patient ID field with patient IDs.

  8. In the From and To boxes, enter the most recent submission date range by selecting a date in the calendar or by using the format mm/dd/yyyy.

  9. Click Submit. NBIA searches for image series that match the criteria you define.

See also Understanding QC Tool Search Results.

Dynamic Search

To perform a dynamic search

  1. Click Admin > Perform QC. Select the Dynamic tab, shown in the following figure. The Dynamic tab allows you to construct specific search criteria.

    Do not use the back button nor the refresh button in these steps, either of which will return the page back to the previous page.

    QC Tool, Dynamic View

  2. Check the QC Status for the series you want to locate. The status options are described in the following table.

    QC Status

    Description

    Not VisibleNo images in the series are visible.

    Not Yet Reviewed

    This status (selected by default) is automatically assigned to an image upon submission to the NBIA database.

    First Review to Seventh A configurable user-defined stage in the workflow of an image series.
    To Be DeletedSelected image series are to be deleted from the system.

    Visible

    All images in the series are visible.

    DownloadableUse this option to identify series that are not ready for release but are available for curators to download so they can study them with their own tool. Downloadable series do not appear in search results. Administrators can include series flagged as downloadable in a manifest and download them.

    Administrators can download any image, no matter what its status is.

  3. In the Batch Number field, select the batch number of the images/series for which you want to search. You can also select Any, to find all batches that have a batch number, or None, to find all batches that do not have a batch number.
  4. In the Confirmed as COMPLETE field, select Yes to search for a set of images/series that has been confirmed as complete, or No to search for a set of images/series that is ongoing.
  5. In the Released field, select Yes to search for images/series that have been released or No to search for images/series that have not been released.
  6. In the From and To boxes, enter the most recent submission date range by selecting a date in the calendar or by using the format mm/dd/yyyy.
  7. For each criterion you select, click the green (+) symbol. This confirms the selection and displays the criterion above the first Submit button.
  8. To select more criteria, do so in the Construct Criteria section. Options under the drop-down arrows change according to the group you select. You can also specify the Boolean AND or OR to express relationships among criteria.
  9. Click Submit. NBIA searches for image series that match the criteria you define.

See also Understanding QC Tool Search Results.

Understanding QC Tool Search Results

Curators use the QC tool to work with images that are not yet available to the public.

After you submit search criteria in the QC tool, you can do the following on the search results page.

QC Tool

Viewing Image Series

Your search results appear in a table in the QC Images by Series section of the QC Tool page.

QC Images by Series showing one result

In addition to viewing image series details in the table, you can view them as thumbnails or in the DICOM viewer.

Viewing Thumbnails

In the Thumbnails column, click View to see image series details.

The Series Details page appears, displaying the first image in the series on the left and the DICOM tags for the image on the right. If there is more than one image in the series and DICOM tags for each image, you can view an animated slide show of the images in the series. For more information about the controls in the animated slide show, see Viewing Image Animation. The DICOM tags change when you view a different image in the series.

If the image series modality is Ultrasound, you can view each image in the series in multi-frame, as shown below. You can move to other images in the series by selecting them from the list.


Series Details page

If the collection you selected for viewing includes sequence information, the annotations show the sequence data identified by a (>) to the left of the Element column, as shown below.

Series Details page showing arrows that indicate sequence data

Viewing Image Series in the DICOM Viewer

In the DICOM Viewer column, click View to open the image series in the Oviyam DICOM viewer. For more information, see QC Tool Search Results.

Changing Image Series Status

As a curator, you may need to change the status of one or more images or image series. You can change the status of one or more selected images or image series individually or as a batch update.

Before you can change the status of an image or image series, you must use the QC Tool to find it. You must then select the image or image series you want to change.

Status options include:

QC Status

Description

Not Yet Reviewed

This status (selected by default) is automatically assigned to an image upon submission to the TCIA database.

Visible

All images in the series are visible.

Not Visible

No images in the series are visible.

To Be Deleted

Selected image series are to be deleted from the system.

First Review to SeventhA configurable user-defined stage in the workflow of an image series.
DownloadableUse this option to identify series that are not ready for release but are available for curators to download so they can study them with their own tool. Downloadable series do not appear in search results. Administrators can include seriesflagged as downloadable in a manifest and download them..

Administrators can download any image, no matter what its status is.

If you change the status of an image series, the change is also reflected in any shared lists to which the image series belongs. If you attempt to change the status of an image series that is in a shared list, an alert message appears, detailing to which shared lists the selected image series belong(s).

To change image series status

  1. Select Admin > Perform QC. The QC Tool page appears.
    Scroll down to the QC Images by Series section. The images you selected in the Classic search or Dynamic search appear in the table.

    QC Tool, QC Images by Series and Perform Bulk QC Operations

  2. Select the image(s) or series for which you want to change the status.
    • To select a single image in a series, click View in the Thumbnails column, then use the cine tool to locate the image you want to change.
    • To select a single series, select the box in the search results table corresponding to the image series you want to change.
    • For a bulk update, select multiple image series in the search results table or click Check All, which is above and below the search results table.

      Selecting images to QC

      The Check All and Uncheck All buttons in the QC Images by Series section of the QC Tool page apply to all of the results of your search. The box to the left of the Submission Date column only selects the series in that row of the results table.

  3. In the Perform Bulk QC Operations section, select the new status you want to assign to the selected image or series. If you are applying the status change to many collections at once, click Run in background to run the bulk operation in a separate thread, improving system performance.

  4. In the Change Log box, describe the nature of the image status change. This text will be part of the QC Status report you can generate to track changes in visibility. See Generating a QC Status Report.

  5. Click Update to update the selected image(s) or series.

After the image series' status has been changed, the status column of the image series in the search results table on the QC Tool page also changes.

Generating a QC Status History Report

To view the status change log from the QC Tool page search results, select the series you want to appear in the report and then click Generate Report.

The QC Status History Report appears, displaying all changes that have been made to the status of the series you selected.

QC Status History Report Page

Click Back to QC Tool to close this window and return to the QC tool.

Generating a QC Status Report

To view the status change log from the QC Tool page search results, select the series you want to appear in the report and then click Generate Report.

The QC Status History Report appears, displaying all changes that have been made to the status of the series you selected.

QC Status History Report Page

Click Back to QC Tool to close this window and return to the QC tool.

Approving Image Deletions

This function is part of a two-tier deletion process. You, as a super curator, can approve the deletion of image series that have been identified as "To be deleted".

To approve series deletions, follow these steps:

  1. Click Admin > Approve Deletions.
    The Approve Deletions page appears.
    Approve Deletions window
  2. From the Collection(s) list, select a collection (site).
  3. Optionally, enter Patient IDs. Separate multiple IDs by commas.
  4. Click Submit to initiate a search for the series marked for deletion.
  5. From the results, click View to review the detail for an individual series. From the page that opens, click Delete to approve the deletion. Click the Skip button to go to the next series.

    Tip

    If you click Skip, this signals that you do not approve the deletion. If that is so, you should generate a report to see who requested the deletion and work with that person to resolve any deletion disagreement.

  6. For batch deletion, select the checkbox for one or more series and click Delete to approve the deletion.

Image series approved for deletion are still visible in the system, identified as "To Be Deleted". They are removed from the system at a system-configured time, such as at midnight (called an "off-line deletion"), unless a manual deletion (called an "online deletion") is performed. For more information, see Manually Deleting Image Series.

About deletions

  • After an image series is approved for deletion, the action cannot be reversed.
  • Any new image submissions to a series identified "To be deleted" will be successful, but the status of the series does not change.
  • Images submitted to files that are identified as "Deleted" are quarantined.

Manually Deleting Image Series


Permissions

This administrative feature is available only to logged in users who have "manage visibility" privileges, as defined in UPT. For more information, see Registering a New TCIA User.

This function is part of a two-tier deletion process. You, as a Delete Admin, can execute the online deletion of image series that are "approved for deletion". This function immediately removes images that are approved for deletion rather than waiting for the next scheduled system-wide deletion job.

To manually delete series, follow these steps:

  1. Click Admin > Perform Online Deletion.
    A list of image series that have been approved for deletion appears.
  2. Click Delete to execute the real time series removal.

    Deleting individual series?

    All series listed in this page are deleted. There is no way to specify individual series for online deletion.

Editing a Collection Description


Permissions

This administrative feature is available only to logged in users who have "manage visibility" privileges, as defined in UPT. For more information, see Registering a New TCIA User.

This feature allows you as an administrator to enter a brief description for a collection so the TCIA user knows what type of data comprises the collection.

To edit a collection description, follow these steps:

  1. Click Admin > Edit Collection Description.
    The Edit Collection Descriptions page appears.
    Edit Collection Descriptions dialog box
  2. From the Select Collection Name list, select a collection name.
  3. In the text box, enter a description or edit an existing description for the collection. Use the text formatting tools to format the text, if you like. If appropriate, you can add a hyperlink to a resource such as a wiki with a longer description.

The description displays on the simple/advanced search screen when you click the (?) button next to the collection name.

Creating a clickable link

To make a link clickable in this section, select Rich for Toolbar Selection, select Source (Source button), and create a link as shown in the following example:

         <span contenteditable="false"><a href="https://www.google.com" target="_blank"><span>Link To Be Created</span> </a></span></p>

If you want to edit the link, select the Source button and set contenteditable to true.

Managing Workflow Items 


Permissions

This administrative feature is available only to logged in users who have "manage visibility" privileges, as defined in UPT. For more information, see Registering a New TCIA User.

A workflow is a business process that, in the case of TCIA, an image series must pass through before it is published. Since it is a business process, these steps must be defined first within an organization. TCIA allows you to change the visibility status of an image series. This visibility change is part of the definition of a workflow item. Workflow items can also trigger a web service call to a URL. When you define a workflow item, you specify a name for it, the type of action that will take place during it (such as a visibility change), which image collection and site are involved, and the URL of a web service if the information resulting from this workflow item should be sent to one.

You can create, edit, and delete workflow items

Creating a Workflow Item

To create a workflow item
  1. Select Admin > Manage Workflow Items.
    The Manage Workflow Items page appears.
    Manage Workflow Items page
  2. Click Create Workflow.
    The Workflow Item page appears.

    Workflow Item page

  3. In the Name box, specify a name for the new workflow item. The name cannot be longer than 50 characters.

  4. From the Type list, select Visibility Change or New Series.


    • Select the Visibility Change option when editing an existing workflow item. A visibility change occurs when the workflow item triggers a web service call to the URL you have entered in the URL field on this page.

    • Select the New Series option if you want the result of this workflow item to create a new image series. You can add this new series to a collection in the next step.

  5. From the Collection list, select an existing image collection to which this workflow item should apply. Existing image collections are in the Collection list.  If you need to create a new collection to apply to this workflow item, enter it in the New Collection for List box and then click Add to Collection List.
  6. From the Site list, select an existing site. Existing sites are in the Site list. If you need to create a new site to apply to this workflow item, enter it in the New Site for List box and then click Add to Site List.
  7. To send information in this workflow item to a web service, enter the web service's URL in the URL box.
  8. Click Save.
    The new workflow item appears on the Manage Workflow Items page.

Editing a Workflow Item

You can edit a workflow item's name and collection/site.

To edit a workflow item

  1. Select Admin > Manage Workflow Items.
    The Manage Workflow Items page appears.
    Manage Workflow Items page
  2. Click the Edit button in the row of the workflow item you want to edit.
    The Workflow Item page appears, showing the values already set for the workflow item you selected.
    Workflow Item page
  3. Edit the name, type, collection, site, or URL as needed, consulting Creating a Workflow Item for details on these steps.
  4. Click Save.

Deleting a Workflow Item

To delete a workflow item

  1. Select Admin > Manage Workflow Items.
    The Manage Workflow Items page appears.
    Manage Workflow Items page
  2. Click delete button in the row of the workflow item you want to delete.
    You are prompted to confirm the deletion.

Creating Workflow items

To create a workflow item
  1. Select Admin > Manage Workflow Items.
    The Manage Workflow Items page appears.
    Manage Workflow Items page
  2. Click Create Workflow.
    The Workflow Item page appears.

    Workflow Item page

  3. In the Name box, specify a name for the new workflow item. The name cannot be longer than 50 characters.

  4. From the Type list, select Visibility Change or New Series.


    • Select the Visibility Change option when editing an existing workflow item. A visibility change occurs when the workflow item triggers a web service call to the URL you have entered in the URL field on this page.

    • Select the New Series option if you want the result of this workflow item to create a new image series. You can add this new series to a collection in the next step.

  5. From the Collection list, select an existing image collection to which this workflow item should apply. Existing image collections are in the Collection list.  If you need to create a new collection to apply to this workflow item, enter it in the New Collection for List box and then click Add to Collection List.
  6. From the Site list, select an existing site. Existing sites are in the Site list. If you need to create a new site to apply to this workflow item, enter it in the New Site for List box and then click Add to Site List.
  7. To send information in this workflow item to a web service, enter the web service's URL in the URL box.
  8. Click Save.
    The new workflow item appears on the Manage Workflow Items page.

Managing Saved Queries

You can review and delete queries saved by users in TCIA.

Permissions

This administrative feature is available only to logged in users who have "manage visibility" privileges, as defined in UPT. For more information, see Registering a New TCIA User.

Reviewing Saved Query Information

To review a saved query

  1. Select Admin > Manage Saved Queries.
    The Manage Saved Queries page appears listing all the queries saved by TCIA users.
    Manage Saved Queries page
  2. The following information is listed for each query.

    Sorting the table

    By default the table is sorted by Query Name, but you can also sort by the Last Executed or Query Creator columns.

    Column NameDescription
    Query Name

    Click the name of the query to display the Criteria Selected by the user. The selected field name(s) and data are listed.

    Query Name Criteria Selected

    Last ExecutedLists the date and time that the query was run.
    New Data Available
    New Data icon. Exclamation pointindicates that new data is available.
    Query CreatorUser name of the person who saved the query.

Deleting a Saved Query

To delete a saved query

  1. Select Admin > Manage Saved Queries.
    The Manage Saved Queries page appears.
    Manage Saved Queries page
  2. Check the box next to the Query Creator column of a query to be removed. You can delete multiple queries at once.

    Removing All Saved Queriese

    To remove all of the saved queries, check the box next to column name, Query Creator. All queries are selected.

    Delete Saved Queries page

  3. Click Remove Selected Items.
    You are prompted to confirm the deletion and the selected queries are removed.

Managing Protection Elements

The TCIA administrator can create new protection elements, which consist of collection names and site names, so that when new images are submitted, they can be associated with these protection elements. Administrators can then add these protection elements to a protection group or remove these protection elements from a protection group.

Topics in this section include:

Adding a Protection Element to a Protection Group

  1. Log in to the TCIA Radiology Portal and select the User Admin tab.
    The User Authorization Tool appears.
  2. Select the Protection Element tab.
    The Protection Element tab appears.

    Protection Element tab of the User Authentication Tool

    You can sort the list of Collections and Sites by clicking the arrows. If both arrows are showing (Two arrows pointing on top of one another, one pointing up and one pointing down), that column is displaying its default sort order. If one arrow is showing, the column is sorted alphabetically in the direction the arrow is pointing.

  3. Click Add Protection Element button.
    The Protection Element Details window appears.
    Protection Element Details window with text boxes for Collection and Site and a Save button.
  4. Enter a name for the new collection and new site.
  5. Click Save button.

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Managing Protection Groups

A TCIA administrator uses the Protection Group tab to create protection groups and assign protection elements to them to limit data access and visibility by image collection and site.

Protection elements are created automatically

TCIA automatically creates protection elements when data is submitted.

Managing protection groups involves:

Adding a Protection Group

  1. Log in to the TCIA Radiology Portal and select the User Admin tab.
    The User Authorization Tool appears.
  2. Select the Protection Group tab.
  3. Scroll to the end of the page and click Add Protection Group button.
    The Protection Group Details dialog box appears.
    Protection Group Details dialog box with two text boxes, Protection Group Name and Description, a Save button, and a Delete button
    • In the Protection Group Name field, start the name with "NCIA” followed by a dot, then enter your name of choice. For example: NCIA.Prostate-3T.

      No Special Characters

      Do not use special characters such as # or \ in group names.

    • Optionally, enter a description.

  4. Click Save button to save the changes.
    The protection group is added to the table.

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Associating Protection Elements with a Protection Group

Seting up security for a collection's visibility in TCIA involves creating a protection group for it and then assigning protection element(s) to it. The protection element identifies the collection and site associated with the data.

Data Access and Protection Elements

To associate a protection element with a protection group

  1. On the Protection Group tab, find the protection group you want to edit.
  2. Click Assign Protection Element icon in the Assign/Remove Protection Element(s) column.
    The Add Protection Element(s) to Protection Group window appears.
    Add Protection Element(s) to Protection Group dialog box
  3. Open the list next to Available Protection Elements.

  4. Select the elements to be associated with the protection group by clicking the box to the left of the element name. You can select more than one.

    Narrowing a List

    To narrow the list of protection elements, type the name or part of the name next to the magnifying glass icon (Magnifying glass icon).

    Filter box with a checkbox, text box where you can enter a protection element name or partial name, and magnifying glass icon. In this example, it says No results found.

  5. Click Add button to save the changes.

    The Associated Protection Element(s) column lists the elements that you added.

    In the following example protection element, NCIA.SportInjury//ACL

    • NCIA.SportInjury is the collection.
    • ACL is the site.

      Multiple Sites

      If there are multiple sites for a collection, you might want to create a protection group for each site. This process would grant access to verify submissions per site.

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Removing Protection Elements from a Protection Group

  1. Click Remove protection elements icon in the Remove Protection Element(s) column.
    The Remove Protection Element(s) from Protection Group window appears.
    Remove Protection Elements from Protection Groups with two text boxes, Protection Group Name and Included Protection Elements, and a Remove button.
    The Protection Group Name cannot be changed.
  2. Open the list next to Included Protection Elements, and select the elements to remove.

    Narrowing a List

    To narrow the list of protection elements, type the name or part of the name next to the magnifying glass icon (Magnifying glass icon). 

    Filter box with a checkbox, text box where you can enter a protection element name or partial name, and magnifying glass icon. In this example, it says No results found.

    Click x to return without saving.

  3. Select the elements you want to remove by clicking the box to the left of the element name. You can select more than one.
  4. Click Remove button to save the changes.
    The protection element you removed is no longer listed in the Associated Protection Elements column.

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Finding a Protection Group

On the Protection Group tab, you can perform a global search or a column search, which are both described in the following table.

 You can perform both searching techniques to filter a list, but do not forget to clear the search boxes to expand the list.

Type of SearchPerforming a Search
Global Search

You can search for a term or part of a term in all the protection group columns in the table. All protection groups with the characters you entered are returned.

In the following example, a Global Search on brain finds protection groups with "brain" in the Protection Group name and the Associated Protection Elements.

List of protection groups with search word of brain
Column Search

You can also find protection groups in the table by adding a term to a column header or more than one column header to further narrow the list.

In the following example, searching for pilot in the Protection Group column displays the following results.

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Updating a Protection Group Description

  1. On the Protection Group tab, find the protection group you want to update.
  2. Click Edit protection group button.
    The Protection Group Details window appears.

  3. Update the group description.
    Note that you cannot update the protection group name.

  4. Click Save button to save the changes.

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Deleting a Protection Group

  1. On the Protection Group tab, find the protection group you want to delete.
  2. Click Edit protection group button.
    The Protection Group Details window appears.

  3. Click Delete button.
    The row is removed from the table.

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Managing User Groups

TCIA administrators create user groups to limit data access and visibility by protection group and user role. Before or after creating user groups, you can assign users and roles to protection groups.

Managing user groups involves:

Editing or Deleting a User Group

You can edit a user group's name and description. If you choose to delete a user group, you do not delete the users in it.

  1. Log in to the TCIA Radiology Portal and select the User Admin tab.
    The User Authorization Tool appears.
  2. Select the User Group tab.

    User Group tab in the User Authentication Tool

  3. In the row for the user group you want to edit or delete, click Edit button in the Edit User Group column.
    The Edit or Delete Group dialog box appears.
    Edit or Delete the Group dialog box with two text fields, User Group Name and Description, and two buttons, Delete the Group and Save

  4. Edit the User Group Name and/or Description and click Save button.
    or
    Click Delete Group button.

    Warning!

    Clicking the Delete Group button deletes the group immediately. There is no confirmation message in case you change your mind about this action.

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Assigning a Protection Group with Roles to a User Group

An administrator uses protection groups to limit data access and visibility by image collection and site(s). You can assign roles to a protection group and associate that protection group with a user group.

  1. On the User Group tab, in the row of the user group you want to assign protection groups with roles to, click Plus sign button in the Assign Protection Group(s) with Role(s) column.
    The Add Protection Group to Selected User Group dialog box appears. 
  2. From the Protection Group list, select the Protection Group (already created on the Protection Group tab) you want to assign to the selected user group.
  3. From the Role list, select one or more roles to that the user group should have. For more information about these roles and what they are designed to do, see Creating a New NBIA User
  4. Click Save button.
    The user group is now associated with the selected protection group and role(s).

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Modifying the Authorization for a User Group

The authorization for a user group consists of the protection group and its roles assigned to a user group. You can remove the protection group you assigned to the user group. You can then assign a new protection group to that user group. You can also change the assignment of roles to the existing protection group. 

  • On the User Group tab, find the user group you want to modify and expand it by clicking the arrow to the left of the user group name.
    The user group's protection group and assigned role(s) appears.
    the User Group tab of the User Authentication Tool
  • In the row you expanded, click .
    The Modify Authorization for Selected User Group dialog box appears.
    Modify Authorization for Selected User Group dialog box, showing text boxes for User Group Name and Protection Group Name, Remove PG and Update Role a dropdown list for Role, and two buttons, Remove PG and Update Role
  • Click the Role list to open it. Click or clear the checkboxes you want to add or remove, respectively. Click Update Role button.
    or
    To remove this protection group from this user group, click Remove PG button.

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Showing Users Associated with a User Group

You can view the users associated with a user group on the User Group tab but if you want to modify which group those users belong to, you need to authorize them with protection groups.

  1. On the User Group tab, find the user group you want to view.
    Row of the User Group tab showing the 4d-Lung-VCU user group
  2. In that row, clickShow Associated Users button in the Show Associated User(s) column.
    The Users in User Group window appears.
    Users in User Group 4D-Lung-VCU window. No users are in the list.

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Managing Users

Once a user submits data, an administrator adds the user to TCIA. The administrator must create the user in LDAP to manage data access privileges.

What to do if the user is not in LDAP

Contact the Help Desk to request that a user be added to LDAP.

Managing users involves:

Adding a User to TCIA

  1. Log in to the TCIA Radiology Portal and select the User Admin tab.
    The User Authorization Tool appears.
  2. Select the User tab.
    User tab of the User Authentication Tool
  3. Click Add User button.
    The User Details dialog box appears.
  4. Add the user's Login Name. The login name is not case-sensitive.
  5. Add a valid Email address of the user.
  6. To activate the user, set Active Status to True. To deactivate the user in TCIA, set Active Status to False.

  7. Click Save button to save the changes.
    The user is added to TCIA and the table on the User tab.

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Finding a User

To find a user on the User tab, narrow the list by adding one or more characters to one or more column header boxes.

In the following example, the displayed users have aa as part of their login name.

Filter of users by login name

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Updating User Information

  1. On the User tab, find the user whose information you want to update.
  2. Click Edit User button.
    The user information becomes editable.
    User details including email address and status, and a checkmark icon and X icon.

  3. Update the email address and status as needed. Note that a user cannot be deleted from TCIA, only deactivated. The Login Name cannot be updated.

  4. Click Checkmark iconto save the changes or X mark icon to cancel the change.
    The user information is updated in the table.

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Adding Protection Groups and Assigning Roles

A TCIA administrator creates protection groups to limit data access and visibility by image collection and site(s). Administrators add users to protection groups and can then further manage their access by assigning them one or more roles. Users can only access the protection group data in the way that the role specifies.

For example, John Smith needs to be a curator within the Mouse Astrocytoma protection group, so user johnsmith is assigned to protection group TCIA Mouse Astrocytoma with the role of CURATOR.

Topics in this section include:

Adding a Protection Group

  1. Log in to the TCIA Radiology Portal and select the User Admin tab.
    The User Authorization Tool appears.
  2. Select the Protection Group tab.
  3. Scroll down to the bottom of the page and click Add Protection Group button.
    The Protection Group Details window appears.
  4. Enter a name for the new group and optionally, a description.

    No Special Characters

    Do not use special characters such as # or \ in group names.

  5. Click Save button.
    The protection group appears on the Protection Group tab.

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Assigning a User to a Protection Group with Roles

Super Administrator

If you are a Super Administrator for one protection group, your privileges extend to all of the protection groups.

To assign a user to a protection group and assign roles

  1. Log in to the TCIA Radiology Portal and select the User Admin tab.
    The User Authorization Tool appears.
  2. Select the User Authorization w/PG tab.
    User Authorization with PG tab
  3. Select a user name from the list at the top left.
    A page listing the protection groups and access roles associated with the selected user appears.

  4. Click Add Protection Group and Access Role button.
    The Grant Access to Selected User window opens.
    Grant Access to Selected User page

  5. From the Protection Group list, select the group to which you want to assign the user.
  6. From the Role list, select the access role that the user should have in that protection group.
    The following table lists and describes the access roles available in TCIA.

    Access Role
    Description of Access Role
    NCIA ADMIN

    Access the User Authorization Tool to manage users

    NCIA CURATE

    Add or modify curation data

    NCIA DELETE_ADMIN

    Super Administrator role for deletions

    NCIA MANAGE_COLLECTION_DESCRIPTION

    Manage collection descriptions

    NCIA MANAGE_VISIBILITY_STATUS

    Access the Quality Control (QC) Tool

    NCIA READ

    Public role for searching

    NCIA SUPER_CURATOR

    Super Administrator role for approving deletions

    NCIA VIEW_SUBMISSION_REPORT

    Access the Submission Reports option to verify submissions.

  7. Click Save to save the changes.

    The row is added to the table.

    Working with the table

    To adjust how the table is sorted, click the arrows in the column header. To narrow the list, type the name or part of the name in the column header. You can also enter information in multiple column headers to further narrow the list.

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Changing a User's Access Role Within a Protection Group

  1. Log in to the TCIA Radiology Portal and select the User Admin tab.
    The User Authorization Tool appears.
  2. Select the Protection Group tab.
  3. Select a user from the list in the top left.
    A page listing the protection groups and access roles associated with the selected user opens.

  4. In the row of the protection group you want to change, click Change Access button.
    The Grant Access to Selected User dialog box opens.

    Grant Access to Selected User, Update

  5. To change the user's access to roles in this protection group, click the down arrow to open the Role list. Select the boxes next to roles you want to assign to the selected user. Clear the boxes next to roles you do not want the user to have. Click Update button to save your changes.

    To delete a role, open the Role list, select a role, and click Delete button.

    The User Authentication tab appears.

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Authorizing Protection Groups

An administrator can grant access for a selected user to a protection group with an associated access role. 

To grant access to a protection group and access role

  1. Log in to the TCIA Radiology Portal.
  2. Select the User Admin tab.
  3. Select User Authorization w/ PG.
  4. Select a user name from the list by starting to enter it and selecting the name you want, or by clicking the arrow and selecting a name in the list.
  5. Click Add Protection Group and Access Role button.

    If you know the name of the protection group and access role, you can enter them into the respective fields. As you type, the tool will suggest options matching the characters you entered.

  6. Click Save.

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To change a user's access to a protection group and access role

  1. In the Change the Access column for a selected user, click Change the access button, which is a pencil image.
    The Grant Access to Selected User window appears.
    Grant Access to Selected User window with a Login Name field (grayed out), Protection Group field (grayed out), and Role field (selectable), Delete button, and Update button.
  2. Select a different role and then click Update,
    or
    Click Delete to remove the user's access to that protection group.

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Authorizing User Groups

An administrator can grant a user access to a user group and remove a user's access from a user group.

Granting a User Access to a User Group

  1. Log in to the TCIA Radiology Portal.
  2. Select the User Admin tab.
    The User Authorization Tool appears.
  3. Select User Authorization w/ User Group.
  4. Select a user name from the list at the top of the screen.
    User Authorization with User Group tab of the User Authorization Tool

    Click the arrow in the Select a user name list to open a text box where you can find a user name quickly by entering a name or partial name. 

  5. Click the user whose access you want to change.
    The page refreshes with a list of user groups the user has access to.
    User Authorization with User Group tab showing a selected user, NBIAtest1, and a list of user groups this user can access.
  6. Click Add Group button.
    The Assign Group(s) to Selected User window appears.
  7. Click the arrow next to the Groups box. 
    A list of groups you can select appears.
    An empty text box with a magnifying class, followed by a list of user groups. Each group has a box to the left of it you can click to select the group.
  8. Click the box to the left of the user group you want to authorize for this user. You can select as many as you want. When you are done selecting groups, click the X at the top of the list of user groups or click outside the list.
    The groups you selected appear in the Assign Group(s) to Selected User window.

    To find the user group quickly, enter the whole or partial user group name in the search box at the top. If you only want to select one user group, enter it into the search box and then click the box to the left of the search box. If you want to select more than one user group, do not do this but rather select the groups in the user group list.

  9. Click Save button.

Removing a User's Access from a User Group

  1. Log in to the TCIA Radiology Portal.
  2. Select the User Admin tab.
    The User Authorization Tool appears.
  3. Select User Authorization w/ User Group.
  4. Select a user name from the list at the top of the screen.
    User Authorization with User Group tab of the User Authorization Tool

    Click the arrow in the Select a user name list to open a text box where you can find a user name quickly by entering a name or partial name. 

  5. Click the user whose access you want to change.
    The page refreshes with a list of user groups the user has access to.
    User Authorization with User Group tab showing a selected user, NBIAtest1, and a list of user groups this user can access.
  6. Find the user group you want to deassign from the user. To find the user group quickly, enter a name or partial name in the User Group box.
  7. Click  next to that user group.
    A confirmation message appears. Click Yes or No as appropriate.

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