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Excerpt

This guide provides an overview of The Cancer Imaging Archive (TCIA) and explains how to use the National Biomedical Imaging Archive (NBIA) software, which powers TCIA to search for and download images.

The source of most of the instructions in this guide is the November 16, 2010 NBIA 5.0 User's Guide produced by the National Cancer Institute (NCI), Center for Biomedical Informatics and Information Technology.

The intended audience for this guide is anyone in the cancer research and medical community, industry, and academia that wishes to utilize TCIA to obtain Digital Imaging and Communications in Medicine (DICOM) and related meta data for use in their research.

The guide discusses the following topics:
Chapter 1 Getting Started provides an introduction to TCIA and describes how to access it.
Chapter 2 Searching for Images describes how to search the archive to find the data you're interested in.
Chapter 3 Viewing Search Results describes how to review results from TCIA database searches.

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Table of Contents

Executive Summary
Chapter 1 - GETTING STARTED
1.1 Introduction to The Cancer Imaging Archive
1.2 Registering a New User
1.3 Logging into The Cancer Imaging Archive
1.4 Using The Cancer Imaging Archive Home Page
1.5 Application Support
1.6 Using The Cancer Imaging Archive Online Help
Chapter 2 - SEARCHING FOR IMAGES
2.1 Performing Searches
2.2 Performing a Simple Search
2.3 Performing an Advanced Search
2.4 Performing a Dynamic Search
2.5 Specifying Remote Search Sites (disabled on TCIA - will restore this section if TCIA decides to support this feature in the future)
2.6 Working with Saved Search Queries
2.6.1 Saving a Search Query.
2.6.2 Managing Saved Queries.
2.6.3 Editing Saved Queries
2.6.4 Viewing a Query History
Chapter 3 --VIEWING SEARCH RESULTS
3.1 Search Results Overview
3.2 Search Results (by Subject)
3.3 Search Results (Studies for Subject)
3.4 Search Results (Images for Series)
3.5 Viewing Image Animation
3.6 Working with the Data Basket
3.6.1 Adding Items to Your Basket
3.6.2 Managing the Data Basket
3.7 Working With Shared Lists
3.7.1 Creating a Shared List
3.7.2 Editing a Shared List
3.7.3 Searching a Shared List
3.7.4 Exporting a Shared List
3.8 Downloading the Data Basket
3.8.1 Download Errors

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  • Lesion detection and classification software. 
  • Accelerated diagnostic imaging decision. 
  • Quantitative imaging assessment of drug response.

The archive provides access to improved cancer research imaging resources that increases the efficiency and reproducibility of cancer detection and diagnosis, providing an objective assessment of therapeutic response, and ultimately enabling the development of improved clinical decision support.

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To register a new user in TCIA, from http://cancerimagingarchive.net click LOG ON TO THE CANCER IMAGING ARCHIVE and follow these steps:
1. Click the Register Now hypertext link under User Login.

...

3. Enter the "Captcha" code on the verification screen to begin the account creation process.

4. Enter the required information on the New User Registration screen.

5. Enter a password and answer at least 4 security questions.

6. Click Register to execute the submission of the user information. Click Cancel to return to the login screen.

Once you have submitted your entry form, a message will be conveyed to TCIA User Support Center who will finish setting up your account and add permissions to access the archive. This typically takes less than 60 minutes during normal Support Center business hours which are Monday through Friday 6:30am – 5:00pm CST, excluding holidays.

When your account is ready, you will receive an email from the User Support Center. Until you receive that email, you may not be able to log into the archive.

If you have any questions, feel free to contact the User Support Center via email at help@cancerimagingarchive.net or by calling +1.314.747-4254 during business hours.

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If you have already registered with TCIA, perform the following steps to login:

1. Enter the login information, your USER ID and PASSWORD.

2. Click Login.

If your login is successful, The Cancer Imaging Archive opens to the home page.

In Case of Login Failure: 
Tip: If your USER ID or PASSWORD is not correct, "Invalid Username/password. Please try again." displays in red text on the login page. Additionally, a popup window opens, informing you of a failure to login and its possible reasons. In your browser, you should enable a popup blocker exception for TCIA's site URL. If you fail to do that, the login failure message may not appear.

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

2. If you have persistent difficulty logging in, click I cannot access my account on TCIA's login page. A Cancer Imaging Archive Account Help topic opens, describing help options for resolving your login problem.

3. Follow the directions on the Login Failed pop-up message and/or on TCIA's Help Account page. Note that you can contact User Support using the contact information on that page.

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TCIA's home page displays several panels and menu bars.

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Option

Description

See for More Information

Home

Returns you to TCIA's Home page

N/A

Search Images

Displays the Simple Search page

Performing a Simple Search

Manage Data Basket

Displays the My Data Basket page; This is the same option as choosing My Data Basket > View Contents from the side menu bar.

Managing the Data Basket

Help

Displays a separate online Help window

Using Cancer Imaging Archive Online Help

Logout

Logs you out of TCIA and returns you to the login page

N/A

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Option

Description

See for More Information

My Data Basket > View Contents

Displays the My Data Basket page.

Managing the Data Basket

My Queries >View
Saved Queries

Displays the Saved Queries page.

Managing Saved Queries

My Queries >View
Query History

Displays the Query History page.

Viewing a Query History

User's Guide

User's guide for searching collections. Can be downloaded and printed.

 

Collections

Description of collections available on TCIA.

 

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Option

Description

See for More Information

Feedback

Displays an email addressed to feedback@cancerimagingarchive.net so you can email comments or suggestions about TCIA.

N/A

Privacy Notice

Displays the Health and Human Services (HHS) Privacy Policy Notice.

N/A

Disclaimer

Displays TCIA's Legal Rules of the Road disclaimer.

N/A

Accessibility

Displays the NCI Web Accessibility Feedback Form to be used by users with disabilities who have comments about the accessibility of NCI's web pages.

N/A

Support

Displays information on contacting the User Support center.

N/A

 

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For any general information about TCIA, support questions, or to report a bug, contact TCIA User Support.

Email: help@cancerimagingarchive.net

When submitting support requests via email, please include:

  • Your contact information, including your telephone number.
  • The name of the application/tool you are using
  • The URL if it is a Web-based application
  • A description of the problem and steps to recreate it.
  • The text of any error messages you have received

Application Support URL

http://www.cancerimagingarchive.net/support.html

Telephone: +1-314-747-4254

Telephone support is available Monday to Friday, 8 am – 5 pm Central Time, excluding holidays.

 

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The online help has been written to help you master the NBIA software. To access online help in TCIA, use any of the following methods:

  • Click the Help menu option on the top menu bar to open online help.

Note: You can access online help without being logged into TCIA.

  • Click the Help icon or button at the top of each page to open a context sensitive topic.

Once you are in online help, an array of options helps you locate topics of interest.

  • Context-sensitive help displays online help topics that correspond to the "form" or the page from which help was opened. Click the table of contents (TOC) button ( Image Removed ) at the top left of the title bar to open the full online help directory.
  • Follow hypertext links or the Related Topics buttons in the help topics to open other closely related topics.
  • Locate topics using the TOC that displays in the left panel of the online help or the Index tab that displays at the top of the Table of Contents panel. Perform word searches by entering query text in the search text box.

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The NBIA software enables you to search for images in TCIA's local in vivo image repository. NBIA also supports a remote search function in other NBIA servers connected to caGrid; however, this functionality is not enabled within the TCIA deployment at this time. The NBIA software is designed to perform the following tasks: 

  • Search for images in simple or advanced search mode.
  • Combine search criteria defined with keyword searches of curated annotation data.
  • Save the search queries to be used repeatedly.
  • Review query histories.
  • As subjects, studies, series, or images are located, save them to your data basket for download.

Note: When you download a series that has annotation files (indicated by Yes in the Contains Annotations column), they are automatically downloaded as well. 

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

                           Collection > Patient (Subject) > Study > Series > Images

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  • Simple Search
  • Advanced Search
  • Annotation Keyword Search

Some search pages contain toggle buttons to allow you to switch back and forth between the Simple Search and Advanced Search pages.
Each search page contains selection boxes, drop-down lists, and text fields. Selected objects are used as search criteria.

1. Selection Boxes.

  • To move an item from the Available box to the Selected panel, highlight it in the Available box and click Select.
  • Click Select All to select all available items and move them to the Selected panel in one keystroke.
  • To remove an item from the Selected panel, highlight the item(s) and click Remove or Remove All.

2. Drop-down Lists. Click on a drop-down list arrow and select the appropriate choice.

3. Text fields. Enter the information requested.

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A simple search consists of basic criteria; they can be expanded for an advanced search. Criteria that you select helps narrow the data search.

Note: The data shown in the search results come from the supplied source, not from what the NBIA software derives unless explicitly stated.

Perform the following steps to complete a Simple Search:

1. Initiate the search by following one of these options:

  • Click Search Images from the top menu bar.
  • Click the Search Images link in the Welcome panel or on the menu bar.
  • Click the Simple Search link in the Welcome panel.
  • From the Advanced Search page, click the Simple Search button in the upper right hand corner. The Simple Search page displays with the basic criteria that may have already been selected.

Any of these options open the Simple Search page.

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Simple Search
Criteria

...

Image Modality(ies)

...

  • Select ALL to return only cases where all selections apply.
  • Select ANY to return cases to which one or more of the selections apply.

...

Contrast

...

Select either option:

  • Enhanced
  • Un-enhanced
    If you leave both options unselected, the results will be the same as though you had selected both options.

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Anatomical Site

...

Image Slice
Thickness

...

                                     Table 2.1 Simple Search criteria

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Simple Search
Criteria

...

Collection(s)

...

Available on NBIA (mm/dd/yyyy)

...

Using the date convention, enter a date range for images to be searched. All images submitted within that range and for which you have viewer privileges will be listed as part of the search results.

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Series Includes
Annotations

...

Select either option:

  • Annotated
  • Non-Annotated
    If you leave both options unselected, or if you select both options, then the search returns both series that have annotations and do not have annotations.

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Results per Page

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Subject IDs

...

Enter one or more subject ID strings, separated by commas.

                                                               Table 2.1 Simple Search criteria (Continued)

3. Click the appropriate button to initiate, enhance, or reset the search.

   a. Click Submit to start the search. The Search Criteria and Search Results (by Subject) pages display (see Initiating Searches from Other Applications).

   b. Click Reset to reset the search criteria to their default values.

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An Advanced Search has all fields available for a Simple Search, as well as expanded options. Criteria that you select helps narrow the data search. All advanced searches are made at the series level from the Advanced Search page.

 To perform an Advanced Search, follow these steps:

1. After logging in, click the Search Images link on TCIA's home page. The Simple Search page opens by default. Proceed to step 2.

– OR –

After logging in, bypass the Search Images link and click the Advanced Search link in the Search Images section. Proceed to step 3.

2. Click the Advanced Search link on the Simple Search page. Criteria that you may have already selected on the Simple Search page displays on the Advanced Search page. 

Image Removed
                          Figure 2.4 Advanced Search page

4. Choose the search criteria as described in Table 2.2.

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Advanced Search
Criteria

...

Image Modality(ies)

...

  • Select ALL to return only cases where all selections apply.
  • Select ANY to return cases to which one or more of the selections apply.

...

Contrast

...

Select either option:

  • Enhanced
  • Un-enhanced
    If you leave both options unselected, the results will be the same--as though you had selected both options.

...

Anatomical Site

...

Image Slice
Thickness

...

Previous Minimum
Number of Studies

...

Patients are selected if more than the entered number of studies has been performed on the patient. It is specified as baseline (first visit) plus the number of subsequent visits. Select a number from the drop-down list.

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Number of Months between Baseline and Final Study

...

This allows selection of cases with the desired amount of follow-up. Select equal (=), greater than (>), greater than or equal to (>=), less than (<) or less than or equal to (<=) from the drop-down list and enter the desired number of months.

                                                          Table 2.2 Advanced Search Criteria

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Advanced Search
Criteria

...

Collection(s)

...

Available on NBIA (mm/dd/yyyy)

...

Using the date convention, enter a date range for images to be searched. All images submitted within that range, and for which you have viewer privileges, will be listed as part of the search results.

...

Series Includes
Annotations

...

Select either option:

  • Annotated
  • Non-Annotated
    If you leave both options unselected, or if you select both options, then the search returns both series that have annotations and do not have annotations.

...

Subject IDs

...

Enter one or more subject ID strings, separated by commas.

...

The following criterion displays below the DICOM criteria on the search page:

...

 

...

Results per Page

...

Select the number of search results per page.
 
Note: This number also defines the number of thumbnail images that will display in the Search Results (Images for Series).

                                                              Table 2.2 Advanced Search Criteria (Continued)

5. Choose the modality manufacturer search criteria as shown in Figure 2.5 and described in Table 2.3.

Image Removed
                   Figure 2.5 Modality Manufacturer Search Criteria

Criteria

Description

Manufacturer
Model
Software Version

This option displays a tree view of the manufacturers, models, and software versions for the image modality. The number in parentheses indicates the number of items under that branch of the tree.

  • Click on the plus sign to expand a branch of the tree or click on the minus sign to collapse a branch of the tree.
  • Select a manufacturer, model, or software version for your search by clicking in the box next to the item. Any items under the branch you selected are automatically selected for you. For example, Phillips Medical Systems was selected above.
    If none are selected, then the search returns data for all manufacturers.

                                                                 Table 2.3 Modality Manufacturer Search Criteria

6. Choose the DICOM search criteria as shown in Figure 2.6 and described in Table 2.4. For more information on DICOM, see http://medical.nema.org/.

Image Removed
                              Figure 2.6 DICOM Search Criteria

Criteria

Description

Series Description

Enter your description of the series. The Series Description is a DICOM tag with a group number of 0008 and element number of 103E. The specified text must exactly match a portion of an existing series description (not case-sensitive).

Convolution Kernel

Select from the available convolution kernels, or algorithms, used to reconstruct the data. The DICOM tag group number is 0018 and the element number is 1210.  If none are selected, then the search returns data for all convolution kernels.

                                                                       Table 2.4 DICOM search criteria

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Criteria

...

Description

...

Kilovoltage Peak
Distribution

...

                                                                         Table 2.4 DICOM search criteria (Continued)

7. Click the appropriate button to initiate, enhance or reset the search.

    a. Click Submit to start the search. The Search Criteria and Search Results (by Subject) pages display (see Initiating Searches from Other Applications.

    b. Click Reset to reset the search criteria to their default values.

After the search is submitted, search criteria are summarized in a Criteria Selected table. Search results display below the table. See Viewing Search Results.

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A dynamic search allows you to build search criteria based on data values or ranges. To launch a dynamic search in TCIA's database at image series level, follow these steps:

1. After logging in, click the Search Images link on TCIA's home page. The Simple Search page opens by default. Proceed to step 2.

– OR –

After logging in, bypass the Search Images link and click the Dynamic Search link in the Search Images section. The Dynamic Search page opens
(Figure 2.7). Proceed to step 3.

2. Click the Dynamic Search button on the Simple Search page. The Dynamic Search page opens (Figure 2.7).

Image Removed
                                         Figure 2.7 Dynamic Search page

3. On the Dynamic Search page, define criteria for the Group category, using the following suggestions:

    a. Select an option in the first drop-down list. Options include TCIA entities.

    b. Your selection drives the options that display in the second drop-down as well as the options or text box that display for the rest of the category. Select from the third drop-down the operand appropriate for the other selection. Where appropriate, enter the value or selected text in the drop-down list.
4. Click the Add icon ( Image Removed ) for each set of criteria you define.

5. As you add criteria, they display in a table above the criteria fields. To remove criteria you have added, click the Remove icon ( Image Removed ).

6. Select the And or Or operand at the bottom of the page that determines whether the search finds image series that meet only all of the criteria or that meet any one of the criteria.

7. Indicate the number of results that will display per page. Default is set at 10.

8. To clear all fields and start again, click the Reset button.

9. To execute the search, click the Submit button.

For information about search results, see Search Results Overview.

After a search is submitted, search criteria are summarized in a Criteria Selected table. Search results display below the table. For more information about search results, see Initiating Searches from Other Applications.

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After you launch a search, the Search Criteria page displays the search criteria summary for your review. It allows you to save the query for future use. A text field for entering the query name and a Save Query button displays below the search criteria (circled in Figure 2.9).

Image Removed

                                   Figure 2.9 Save Query option

Note: If you launch the search from a previously saved query, then the text field and Save Query buttons do not display.

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To save a search query, perform the following steps:

1. Enter a name for the saved query in the Save Query text field.

2. Click the Save Query button.

The NBIA software attempts to save the query, displays a message that indicates the success or failure, and suggests any additional actions that are required.

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Click the View Saved Queries link in the left sidebar of the viewer to display the Saved Queries page (Figure 2.10).

Image Removed
                   Figure 2.10 Saved Queries page

This page displays a table of all queries that are currently saved for you. Table columns are described in Table 2.5. The 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.

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

New Data Available

An 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 the Resubmit Query button to submit the query using the saved criteria and display the results on the Search Results page. The results contain both old and new data.

Edit Query

Click the Edit Query button to display the criteria that was saved for the query. You can then modify the criteria.

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.

                                                            Table 2.5 Saved Query descriptions and tasks

You can perform the following actions on the Saved Queries page: 

  • Remove Selected Items--Check the box corresponding to any Saved Query line items and click the Remove Selected Items button to delete selected saved queries.

After the NBIA software attempts to delete the queries, it returns you to the Manage Saved Queries page; a message displays that indicates the success or failure and suggests any additional actions that are required.

  • View Query History--Click the Query History tab to display the View Query History page (see Viewing a Query History).
  • Resubmit a Saved Query--If you resubmit a saved query, the name of the saved query displays on the Search Results page with the following message:

                                            These are the results of the {Name} saved query.

If the query is executed for new data only, the following message appears:

                                           These are the results of the {Name} saved query (new data since {Date} only).

{Date} is the last executed date used as part of the criteria of the query to make it only display new results.

...

Note: You cannot edit the name of a saved query. You can, however, rerun the query and save this as a new query with a new name. You can then go back and delete the old query.

Perform the following steps to edit a saved query:

1. Click the Edit Query button from the Saved Queries page (Figure 2.10 Saved Queries page) to display the Search page containing the criteria that was saved for the query. The name of the saved query being edited is shown in the following information message:

                 Saved query {Name} is being edited. After pressing Submit and viewing the results, you will have the option to save the changes.

2. Edit the criteria for the saved query and click Submit.

3. The Search Criteria page (Figure 2.11) displays the criteria and the Search Results page displays the results for the edited criteria.
Image Removed
                     Figure 2.11 Save Edited Query

4. Choose one of the following choices (see Figure 2.11).

     a. Select Update saved query {Query Name} with the new criteria and click Save Query.

     b. Select Save this criteria as a new saved query called, enter a new query name and click Save Query.

     c. If you do not like the results returned by the criteria, navigate back to the Search page to try again.

If you clicked the Save Query button, the system attempts to save the query, displays a message which indicates the success or failure, and performs any additional actions that are required.

...

Click the View Query History link in the left sidebar or the Query History tab from the Saved Queries page to display the Query History page (see Figure 2.12). The Query History page displays a table of the last twenty queries that you executed which includes queries that are not saved and saved queries that are resubmitted.

Image Removed
              Figure 2.12 Query History page

The Query History table contains the data in Table 2.6 

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 (see Initiating Searches from Other Applications).

                                                                                Table 2.6 Query History

Click the Saved Queries tab to display the Saved Queries page (see Managing Saved Queries).

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Note: At any point in the process of reviewing results, you can add items—the entire patient, a study, or a series—to your data basket by selecting the items and clicking the Add to Basket button. This identifies objects to be downloaded.

When you download a series that has annotation files (indicated by Yes in the Contains Annotations column), they are automatically downloaded as well.

...

The Search Results (by Subject [patient]) displays results categorized by each host site, named at the upper left of each set of results. You can collapse each set by clicking the down arrow by the host site.

The results of the search by subject (Figure 3.1) display in table format. Below the table, the numbered sequence of hits in the visible list displays as well as the number of entire hits.
Image Removed
                Figure 3.1 Search Results by Subject

Table 3.1 describes each item in the Search Results (by subject) table.

Search Result

Description

Show Studies

Click this hypertext link to display the studies for this subject.

Collection ID

Collection identifier

Subject ID

Subject identifier

Studies

Contains two numbers: the number of studies that met the criteria /
total number of studies for the subject.

Series

Contains two numbers: the number of series that met the criteria /
total number of series.

[Basket] Check Boxes

Use the check boxes to mark the result for addition to your data basket. Click the Check All/Uncheck All buttons to select or deselect all results, or you can select results individually.

                               Table 3.1 Search Results (by Subject)

1. Click any Show Studies links to display the studies for this subject where more details for studies display. See Search Results (Studies for Subject).

Some search results may display, but results from a disallowed collection are not included.

When you access to a collection, save a query, and resubmit the query later (after your access to the collection has been revoked), the system still has the disallowed collection criteria saved.

2. You can perform the following actions on the Search Results (by Subject) page (Figure 3.1): 

  • Click the down arrow next to a column title to sort the column by that item.
  • Click the Previous (or <<) and Next *(or *>>) buttons at the bottom of the table to display the previous or next set of results. The numbers of the results displayed is shown.
  • Click the page number links to move to a specific page of results.
  • Click the Add to Basket button to add items selected to your data basket (see Adding Items to Your Basket).
  • Click View My Basket to display the items in your data basket (see Managing the Data Basket).

...

3.3 Search Results (Studies for Subject)

When you click a study in the Search Results (by Subject) page, the Search Results (Studies for Subject) page opens, showing Study level in the breadcrumbs, or file path, at the page bottom. This page displays specific information for each study: the Study ID, Date, and Description followed by a table containing the details for each study (Figure 3.2).
Image Removed
            Figure 3.2 Studies for Subject Search Results

Table 3.2 describes each item in the Search Results (for subject) table. 

...

Search Result

...

Description

...

Show Images

...

Click this link to display the images for the series.

...

Series

...

Series ID

...

Images

...

Description

...

Description of the Series.

...

Modality

...

Modality

...

Manufacturer

...

Name of the manufacturer.

...

Contains
Annotations

...

Displays Yes or No, revealing if there are annotation files. Yes becomes a hypertext link if the series has corresponding annotations for which the content type has been identified by curators. Hover over or click the link to display the annotation content type(s). If annotation files are available, but the content type is not known, Yes displays but is not hypertext.

...

Check Box

...

Click the check box to mark the result for addition to your basket. You can click the check box in the header to select all results or you can select results individually.

                                        Table 3.2 Studies for Subject Search ResultsSearch Results for Studies for Subject

To visualize images identified on the search results page, you must have the Cedara I-Response Workstation (IRW) installed on your system.

Note: If you do not have the IRW installed, click this link to the NCICB GForge Download page: https://gforge.nci.nih.gov/frs/?group_id=312https://gforge.nci.nih.gov/frs/?group_id=312+. Toward the top of the page, click the I‐ResponseR.v.[x.zip hypertext link*.* You can download the corresponding user 's guide, accessible from the same site, as well.

1. Start the Cedara IRW on your system.

Note: If the IRW is not executed, you cannot visualize images. NBIA will inform you to install/execute the Cedara first.

2. Click the Visualize Images button to open the IRW window and visualize images in the data basket. For complete instructions on how to use the IRW, refer to the Cedara online help.

Note: If you are not logged in when you click this button, NBIA informs you that you must log in to access this feature.

3. You can perform the following additional actions on the Search Results (Studies for Subject) page.

...

 

3.4 Search Results (Images for Series)

When you click the Show Images link in the Search Results (Studies for Subject) page, this opens the Search Results (Images for Series) page. The bread crumbs at the top and bottom of the page show that you are viewing image thumbnails at the series level.

A table at the top of the page (Figure 3.3) contains information defined for the series, followed by an option to launch an animation of the images (where there are more than two). Thumbnail images for the series you selected are also displayed on the page. The number of images that displays corresponds to the results per page that you defined when you set the search criteria.

Image Removed
   Figure 3.3 Images for Series Search Results

Table 3.3 describes each item in the Search Results (Images for Series) table.

...

Search Result

...

Description

...

Subject ID

...

Subject identification number.

...

Study ID

...

Study identification number.

...

Date

...

Date

...

Modality

...

Modality

...

Manufacturer

...

Name of the manufacturer.

...

Contains Annotations

...

Displays Yes or No, revealing if there are annotation files. Yes becomes a hypertext link if the series has corresponding annotations for which the content type has been identified by curators. Hover over or click the link to display the annotation content type(s). If annotation files are available, but the content type is not known, Yes displays but is not hypertext.

...

Data Location

...

Displays the name of the center housing the data.

...

DICOM

...

                                                                  Table 3.3 Images for Series Search Result fields

You can perform the following actions on the Search Results (Images for Series) page:

  • Launch an animation of the series (where there are more than two thumbnails). Under the table summarizing the series information, click View Movie at the end of the sentence, "To view an animation of the images in this series, ...". For more information, see Viewing Image Animation.
  • To enlarge an image, float your cursor over an image thumbnail (or click it). A larger version of the image displays in the upper right hand corner of the page.
  • Click the Add to Basket button to add the entire series to your data basket (see Adding Items to Your Basket). Images that you add become highlighted on the Images for Series page.

Note: You cannot add images individually to the data basket.

...

 

3.5 Viewing Image Animation

From the Search Results (Images for Series) (DICOM Series) page, you can launch an animation of thumbnails where there are more than two images in the series. Click the View Series in Cine Mode link.

...

 When the viewer opens (Figure 3.4), click the play forward button Image Removed. TCIA proceeds to display the images sequentially in a "movie".

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

...

 

...

 

...

a. Image Removed .

...

b. Image Removed .

...

 

...

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

                                                                          Table 3.4 Image animation controls

Note: If the animation if very sluggish, be sure and note the warning at the bottom of the page.

...

As you review search results in TCIA, you can add items at any level to your data basket for subsequent download.

...

You can add items to your basket at the subject [patient], study, and series levels.

1. To select items, use the Check All and Uncheck All buttons above the search results tables to select or deselect all items on a given search results page or click the corresponding check boxes for items individually.

Note: Check boxes do not exist on the Images for Series page. If you click the Add to Basket button on the page, all of the images in the series are added to the Data Basket.

2. When satisfied, click the Add to Basket button.

The items added to the basket are highlighted on the page from which you initiated this task.

...

Click the View Contents link in the left sidebar, Manage Data Basket from the top menu bar or the View My Basket button from Search Results pages to display the My Data Basket page. This page displays a table of all the items in your data basket (Figure 3.5).

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                               Figure 3.5 My Data Basket page

Table 3.5 describes each item in the Data Basket table

...

Data Basket Field

...

Description

...

Subject ID

...

Subject identification number.

...

Study Instance UID

...

Study identification number.

...

Series ID

...

Series identification number.

...

Number of Images

...

Contains two numbers: Number of Images Selected / Number
Available.

...

Image Size (in MB)

...

Size of the image file in megabytes.

...

Annotation File Size
(in MB)

...

Size of the annotations file in megabytes. This column is N/A if there are no annotations.

...

Select

...

To remove the item from the basket, select the check box and click the Remove Selected Items button.

...

Location

...

                                                    Table 3.5 My Data Basket field

The total size of your data basket and the estimated download time displays at the bottom of the My Data Basket page (Figure 3.5).

To delete an item from your basket, select the check box of an item and click the Remove Selected Items button. You can continue to add items to your data basket from the Search Results pages.

Note: If the series you mark for deletion is part of a Shared List, a message appears alerting you to that fact. The message also includes the name of the shared list and the shared list creator 's email address. This gives you the opportunity to back out of the deletion. For more information see Working With Shared Lists.

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The NBIA software provides a way for you to identify and label a collection of image series for you to use or share with other users.

...

Note: Anyone can create a shared list. Once you do so, you will need to record the exact name of the shared list to distribute to others. That is the only way they can access it.

You can initiate creating a shared list by clicking the Create Shared List link under Tools on the left sidebar or by putting series in the data basket. To create a shared list, follow one of the two following methods:

Left Sidebar Link:
1. Click the Create Shared List link under Tools on the left sidebar.

2. In the Create My Shared List page that opens:

    a. Enter a Name for the list (required).

    b. Add Comments and a Hyperlink where appropriate, which links to relevant or more detailed information about the list (optional).

    c. In the Upload File field, enter the name of a .csv 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.

    d. Click Submit.

Image series from the uploaded file is added to the data basket.

Data Basket
1. Add image series that you want to include in the shared list to the data basket.

2. Click the Create Shared List button.

3. In the Create My Shared List page that opens:

    a. Enter a Name for the list (required).

    b. Add Comments and a Hyperlink, which links to relevant or more detailed information about the list (optional).

    c. Click Submit.

Note: The NBIA software will warn you that not all public users will have access to your list if the list contains any non‐public image series.

...

Note: 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.

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

To edit a shared list, follow these steps:

1. Click the Edit Shared List link under Tools on the left sidebar.

The Edit My Shared List page that opens displays a list of shared lists you have created.

2. Click the name of the shared list you want to edit. The details for the list open on the page.

3. Enter an appropriate comment or hyperlink that provides relevant information about the edited shared list.

4. Browse for the .csv file you want to upload. Doing so replaces the current shared list.

Tip: You cannot delete a shared list.

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 .csv file when you create it. See Exporting a Shared List.

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Any user can search for a shared list. To do so, follow these steps:

1. Click the Search Shared List link under Tools on the left sidebar.

2. In the Search Shared List page, enter the exact name of an existing shared list. To retrieve the list, you must know the exact name given to the shared list.

...

Once you have created a shared list, you can export it as a .csv file. To do so, open the shared list in the data basket. Above the data table, click Shared List and select Export Series ID.

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               Figure 3.6 Data basket displaying export shared list options

The export begins, with a dialog box that opens asking if you want to open (in Excel) or save the file.

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Tip: Disable popup blockers before you download the files. If you do not want to download the annotation files, deselect the Include annotation files in your download check box.

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To download objects using the Download Manager, follow these steps:

1. Click the Download Manager button. (Figure 3.7)

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Figure 3.7 Download Manager showing a download in process in the Progress column

Note: You must have version 6 or higher of the Java Runtime Environment (JRE) installed to be able to open the Download Manager.

If JRE 6 is installed, the Download Manager attempts to start. To run the application, you must click Run in the Warning dialog box indicating the application's digital signature cannot be verified. Before doing so, you can select the More Information... link at the bottom of the dialog to view a more detailed report of any security issues. Then you can evaluate whether you want to run the application.

For some browsers, if JRE is installed but the version is older than version 6, the browser automatically attempts to upgrade the JRE to version 6.x.

If the JRE is not installed, when you click the Download Manager button, the browser prompts you for what it should do with the Java Webstart (JNLP) file.

Note: Depending on one's environment, the browser security settings may need to be configured to allow running JNLP applications.

...

2. Browse for the destination where you want the images/annotations to be downloaded.

Note: If you want to delete items from the Download Manager, select and click the Delete button. The NBIA software does not delete the same item from your data basket when you do so.

3. Click Start to execute the download. You can monitor the download in the Progress column. The Status column indicates when the download for each item is complete.

4. 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 zipped. The downloaded file(s) are stored in a file structure such as collection name/patient id/study instance UID/ series instance UID/image SOP instance UID under the destination folder.

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Errors may occur during the download process (see Figure below).  An "Error" status will appear in the right-hand column, and a message appears at the bottom of the Download Manager window: "An error has occurred. We will keep trying the failed downloads until we either download the data, or you exit the download manager."  The error or even multiple errors will not stop the download process.  The Download Manager will continue on through the download basket; when finished, it then retries those series with Status = Error.  Eventually, all items scheduled for download will download.  To make sure the download is complete and free of errors, scroll up and down through the Download Manager window and make sure the Status for each line (series) is "Complete".  If an error persists for a series, please notify the TCIA team.

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Include Page
NBIA:Cancer Imaging Archive User's Guide
NBIA:Cancer Imaging Archive User's Guide

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