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Executive Summary

This guide provides an overview of the Cancer Imaging Archive hosted by Washington University in St. Louis. It explains how to use the National Biomedical Imaging Archive (NBIA) software to search for and downloading 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, Center for Biomedical Informatics and Information Technology.

The intended audience for this guide are researchers including pathologists and radiologists at cancer centers, CAD developers, academia, and industry that access the Cancer Imaging Archive through commonly available web browser software.

The guide discusses the following topics:
Chapter 1 Getting Started provides an introduction to the Cancer Imaging Archive and describes how to access the Cancer Imaging Archive.
Chapter 2 Searching for Images describes how to search the local and any selected remote image databases.
Chapter 3 Viewing Search Results describes how to review results from the Cancer Imaging Archive database searches


Questions about the use of this guide should be sent to the Cancer Imaging Archive User Support Center at help@cancerimagingarchive.net


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
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

Chapter 1 – Getting Started


1.1 Introduction to the Cancer Imaging Archive


Cancer Imaging Archive provides the cancer research and medical community, industry, and academia access to imaging archives that can be used for many purposes, including the potential to assist in the development and validation of analytical software tools supporting these functions:

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

The archive provides access to imaging resources that improve the use of imaging in today's cancer research and practice by increasing the efficiency and reproducibility of imaging cancer detection and diagnosis, leveraging imaging to provide an objective assessment of therapeutic response, and ultimately enabling the development of imaging resources that will lead to improved clinical decision support.


Clinical trials, physicians and other researchers submit images to the Cancer Imaging Archive using the CTP (Clinical Trial Processing) software. Any potential user may then access the Cancer Imaging Archive to search for and download images and associated annotation files.
Images are stored in the medical image standard, Digital Imaging and Communications in Medicine (DICOM). A DICOM file stores the digital image along with a series of tags that contain metadata about the image such as patient ID, study ID, patient weight, anatomic site, and so forth. For more information about DICOM, see http://medical.nema.org.


The Cancer Imaging Archive is accessible at http://cancerimagingarchive.net. In the welcome page that opens, you can perform the following tasks:

  • Learn the basics about the Cancer Imaging Archive by accessing the information links on the welcome page.
  • Open Quick Links to web sites relevant to the goals and tasks of the Cancer Imaging Archive.
  • Log into the Cancer Imaging Archive.



                                Figure 1.1 Welcome Page

1.2 Registering a New User

To register a new user in the Cancer Imaging Archive, from the Cancer Imaging Archive welcome page click LOG ON TO THE CANCER IMAGING ARCHIVE and follow these steps:
1. Click the Register Now hypertext link under User Login.


                                         Figure 1.2 Login Page

2. Review the Legal Rules of the Road page and indicate your agreement, then click the blue Clicking Here link to continue.

3. In the registration form that opens enter the required information for the new user. Items with an asterisk are required fields.


                  Figure 1.3 User Registration Page

4. 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 the Cancer Imaging Archive User Support Center who will create the new user account.

1.3 Logging into the Cancer Imaging Archive

When you enter http://cancerimaging.archive.net to access the Cancer Imaging Archive, the welcome page displays. Click LOG ON TO THE CANCER IMAGING ARCHIVE to bring up the login page.


                                                  Figure 1.4 Login Page

If you have already registered with the Cancer Imaging Archive, 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 opens, informing you of a failure to login and its possible reasons. In your browser, you should enable a popup blocker exception for the Cancer Imaging Archive 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 the Cancer Imaging Archive 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 the Cancer Imaging Archive Help Account page. Note that you can contact User Support using the contact information on that page.

1.4 Using the Cancer Imaging Archive Home Page

The Cancer Imaging Archive home page that opens after login displays several panels and menu bars.


                                            Figure 1.5 Home Page

Home Page Menu Bar
The top menu bar on the home page consists of the following options.

Option

Description

See for More Information

Home

Returns you to the Cancer Imaging Archive 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 Cancer Imaging Archive and returns you to the login page

N/A


Home Page Left Sidebar
The left sidebar of the home page consists of the following options.

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 the Cancer Imaging Archive.

 



Home Page Bottom Menu Bar
The bottom menu bar consists of the following options.

Option

Description

See for More Information

Feedback

Displays an email addressed to feedback@cancerimagingarchive.net so you can email comments or suggestions about the Cancer Imaging Archive.

N/A

Privacy Notice

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

N/A

Disclaimer

Displays the Cancer Imaging Archive 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


1.5 Application Support

For any general information about the application, application support or to report a bug, contact the Cancer Imaging Archive 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.


1.6 Using the Cancer Imaging Archive Online Help

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

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

Note: You can access online help without being logged into the Cancer Imaging Archive.

  • 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 TOC button ( ) 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 table of contents 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 of Help by entering query text in the search text box.

Chapter 2 – SEARCHING FOR IMAGES

2.1 Performing Searches

The NBIA software enables you to search for images in the local Cancer Imaging Archive in vivo image repository, and if available, to use the Remote Search function to search in remote imaging archives. The NBIA software is designed to perform the following tasks: 

  • Search for images in simple or advanced search mode
  • Combine search criteria defined in those searches 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 have annotation files (indicated by Yes in the Contains Annotations column), they are automatically downloaded as well. 

The Cancer Imaging Archive 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


The NBIA software provides three search modes:

  • 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 click Remove All to remove all items.

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

3. Text fields. Enter the information requested.

2.2 Performing a Simple Search

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. The Nodes to Search section at the top of the page lists the remote databases you can identify to be searched outside the local (Cancer Imaging Archive) imaging archive (Figure 2.1). (See Specifying Remote Search Sites)

 
                                          Figure 2.1 Simple Search page (top)

The remainder of the Simple Search page displays the search criteria (Figure 2.2).

 
                            Figure 2.2 Simple Search criteria

2. Choose the search criteria described in Table 2.1.

Simple Search
Criteria


Description

Image Modality(ies)

Select from the available image classifications and move them to the Selected panel. If none are selected, then the search returns data for all modalities.

Regarding the text options:

  • 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, or if you select both options, the results will be the same as though you had selected both options.

Anatomical Site

Select from the available anatomical sites. If none are selected, then the search returns data for all anatomical sites.

Note: The value NOT SPECIFIED means that the field has no value, is empty or is not given a value as supplied by the source. If you select NOT SPECIFIED, then all images are found where anatomical sites are not specified.

Image Slice
Thickness

Select Image Slice Thickness to allow you to select a thickness range or number. Use the first set of drop-down boxes only to select one thickness by using (=), greater than (>) or greater than or equal to (>=) to a selected thickness. For example, for a thickness greater than 5mm, select the > symbol followed by 5 mm. Leave the text box after "and" blank:



Use both sets of drop-down boxes to select a range of numbers. For example, for a range between 3mm and 7 mm, select > symbol then enter 5 mm. After "and" select the < symbol, then enter 7mm.


If you do not select this, then the search returns data for all image slice thicknesses.

                                     Table 2.1 Simple Search criteria

Simple Search
Criteria


Description

Collection(s)

Collections are NCI-defined groupings of image data sets. Select from the collections to which you have been assigned accessibility. If none are selected, then the search returns data for all collections.
 
Click the (?) icon 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.

Available on CANCER IMAGING ARCHIVE (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.

Results per Page

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

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

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.

2.3 Performing an Advanced Search

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 the Cancer Imaging Archive 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.

3. At the top of the Advanced Search page, the Nodes to Search section lists the remote databases you can identify to be searched outside the local Cancer Imaging Archive imaging archive (Figure 2.1). (See Specifying Remote Search Sites)


                                    Figure 2.3 Advanced Search Page

The remainder of the Advanced Search page displays the search criteria (Figure 2.4).


                          Figure 2.4 Advanced Search page

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

Advanced Search
Criteria


Description

Image Modality(ies)

Select from the available image classifications and move them to the Selected panel. If none are selected, then the search returns data for all modalities.

Regarding the text options:

  • 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, or if you select both options, the results will be the same--as though you had selected oth options.

Anatomical Site

Select from the available anatomical sites. If none are selected, then the search returns data for all anatomical sites.

Note: The value NOT SPECIFIED means that the field has no value, is empty or is not given a value as supplied by the source. If you select NOT SPECIFIED, then all images are found where anatomical sites are not specified.

Image Slice
Thickness

Select I would like to filter by Image Slice Thickness to allow you to select a thickness range or number. Use the first set of drop-down boxes only to select one thickness by using (=), greater than (>) or greater than or equal to (>=) to a selected thickness. For example, for a thickness greater than
5mm, select > 5mm and leave the second text box blank:


Use both sets of drop-down boxes to select a range of numbers. For example, for a range between 3mm and 7 mm, select > 5 mm and < 7mm:


If you do not select this, then the search returns data for all image slice thicknesses.

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.

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



Advanced Search
Criteria


Description

Collection(s)

Collections are groupings of image data sets defined by a system administrator. Select from the available collections. Select from the available collections. If none are selected, then the search returns data for all collections.
Click the (?) icon 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.

Available on CANCER IMAGING ARCHIVE (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 the search will return.
Note: This number also defines the number of thumbnail images that will display in the Search Results (Images for Series) on page 41.

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.

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/.

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. Convolution kernel is a label describing the convolution kernel or algorithm 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

Criteria

Description

Kilovoltage Peak
Distribution

Kilovoltage Peak Distribution is the kilo voltage output of the x-ray generator used by a modality. The DICOM tag group number is 0018 and the element number is 0060. The DICOM attribute name is KVP.
Use the first set of drop-down boxes only (before the AND) to select a peak distribution by using (=), greater than (>) or greater than or equal to (=>).
Use both sets of drop-down boxes to select a range of numbers. From the first drop-down box, select greater than (>) or greater than and equal to (=>) and specify a peak distribution. Then, select less than (<) or less than and equal to (=<) form the second drop-down list and specify the maximum 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 on page xx).
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.

2.4 Performing a Dynamic Search

A dynamic search allows you to build search criteria based on data values or ranges.
To launch a dynamic search in the Cancer Imaging Archive database at image series level, follow these steps:
1. Either before or after logging in, click the Search Images link in the Welcome panel of the Cancer Imaging Archive 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).

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 the Cancer Imaging Archive 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 ( ) for each set of criteria you define.
5. As you add criteria, they display in a table above the criteria fields on the page.
To remove criteria you have added, click the Remove icon ( ).
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 Application.

2.5 Specifying Remote Search Sites


A remote search site is an image database residing outside of the local Cancer Imaging Archive imaging archive. (Note: The local node for the Cancer Imaging Archive is 'Mallinckrodt Institute of Radiology). When you select a remote image database, Simple, Advanced, and Annotation Keyword Search pages display search results for the local Cancer Imaging Archive imaging archive AND any selected remote sites.
To select remote search sites, follow these steps:
1. Initiate the search by following one of these options:

  • Click Search Images on the menu bar.


  • Proceed with a Simple Search in the search form that opens, as described in Performing a Simple Search.


OR

  • Click Advanced Search, as described in Performing an Advanced Search.


At the top of either page that opens, the NBIA software displays a Nodes to Search section
(Figure 2.8).



Figure 2.8 You can interact with remote sites by selecting remote nodes on the Search page.
2. The Available panel shows the name of the remote node. The name used is the research center display name from the service metadata (acquired from the grid index service). As you mouse over the available sites, a popup displays where the site resides, for example "local" or a URL to the service. Select the remote site(s) that you want to search.


Note: By default, if you make no node selection, only the local node is searched.
3. Click the Lookup Search Terms link
The search criteria: modality, anatomic site, convolution kernel, collection, and equipment are populated based upon what actually exists in the searchable nodes. These criteria do not distinguish which comes from where (in the main UI) but Lookup Search Terms breaks this down so you will avoid searching for modality X that isn't available on node Y.
4. Continue defining search criteria as described in Performing a Simple Search
or Performing an Advanced Search.

Note: Once retrieved, you can download remote node data using the Download Manager and the Download All button in the data basket. For more information, see Managing the Data Basket.

2.6 Working with Saved Search Queries


!worddava519a6dbff98bafe94058eeaf4a92642.png|height=2866,width=10214!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).










Figure 2.9 Save Query option
Note: If you launched the search from a previously saved query, then the text field and Save
Query buttons do not display.

2.6.1 Saving a Search Query.

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 and displays a message that indicates the success or failure and suggests any additional actions that are required.

2.6.2 Managing Saved Queries.

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

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 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 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 Search page displaying 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.

2.6.3 Editing Saved Queries

Note: You cannot edit the name of a saved query. You can, however, re‐run 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.

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 and displays a message which indicates the success or failure and performs any additional actions that are required.

2.6.4 Viewing a Query History

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.

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 on page 35).

Table 2.6 Query History
Click the Saved Queries tab to display the Saved Queries page (see Managing Saved
Queries).

Chapter 3 --VIEWING SEARCH RESULTS

3.1 Search Results Overview


In reviewing search results, it is important to review the hierarchy of submissions in the Cancer Imaging Archive.

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

Search results display first as Search Results (by Subject). As you click on Show Studies links in those results, the NBIA software drills down to Search Results (Studies for Subject) where more details for studies display. From these results, when you click Show Images links, the Search Results (Images for Series) display, revealing thumbnail images within a series.
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.

3.2 Search Results (by Subject)

The Search Results (by Subject [patient]) page displays search results categorized by each host site you searched, 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 (<span style="color: #212187"><em>Figure</em></span> <span style="color: #212187"><em>3.1</em></span>) 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.

Figure 3.1 Search Results by Subject
<span style="color: #212187"><em>Table</em></span> <span style="color: #212187"><em>3.1</em></span> 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

Table 3.1 Search Results (by Subject)



Search Result

Description

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="0bb861f5-6e83-417e-a407-349c70ed1c33"><ac:plain-text-body><![CDATA[

[Basket] Check
]]></ac:plain-text-body></ac:structured-macro>
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) (Continued)
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 save a query when you have access to a collection, and then 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 bread crumbs 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).

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

Number of images for that series which can be displayed by clicking the Show Images link. This number includes both visible images that meet the criteria and those that do not. For example, where "3/4" displays, there are 4 studies total for the patient, and 3 of those 4 have images that met the search criteria.
Note: If you select a series with more than two images, you can view an animation of the image collection. For more information, see Search Results (Images for Series) on page 41 and Viewing Image Animation.

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.

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

Search Result

Description

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: <span style="color: #0000ff"></span><span style="color: #0000ff"><a href="https://gforge.nci.nih.gov/frs/?group_id=312">https://gforge.nci.nih.gov/frs/?group_id=312+</a></span>. 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. CANCER IMAGING ARCHIVE 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, CANCER IMAGING ARCHIVE 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.

  • Click the Check All or Uncheck All buttons to select or deselect all items on the search results page or click the check boxes individually.


  • 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).

3.4 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 display on the page. The number of images that displays corresponds to the results per page that you defined when you set the search criteria. .

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

Table 3.3 Images for Series Search Result fields



Search Result

Description

Contains Annota- tions

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

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

Table 3.3 Images for Series Search Result fields (Continued)
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.

  • Click View My Basket to display the items in your data basket (see Managing 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.
You can also launch the animation of an image series from the Data Basket. In the
View column of the Data Basket, click the magnifying glass symbol, (
corresponding to the series you want to view. On the View Series Images page, click the View Series in Cine Mode link.

.

Figure 3.4 Image animation viewer
When the viewer opens (Figure 3.4), click the play forward button (. The Cancer Imaging Archive proceeds to display the images sequentially in a "movie".
The following table describes the action of each of the animation controls.













 


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




 


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

a. .

b. .

a. Click to return to the first image in the series.
b. Click to progress to the last image in the series.


a.


b.

a. Click to play animation backwards through the series
b. Click to play animation forward through the series



a.



b.

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


c.

 

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.

3.6 Working with the Data Basket


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

3.6.1 Adding Items to Your Basket

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.

3.6.2 Managing the Data Basket

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).

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.

Table 3.5 My Data Basket field

Data Basket Field

Description

Location

The location of the image


"Local" represents the CANCER IMAGING ARCHIVE imaging archive that you are currently logged into. Other locations are remote sites selected with the Remote Search option. For more information about the Remote Search option, see Specifying Remote Search Sites on page 31.

Table 3.5 My Data Basket field (Continued)
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.

3.7 Working With Shared Lists

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 Cancer Imaging Archive users.

3.7.1 Creating a Shared List

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 who may want to use the list. 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.

3.7.2 Editing a Shared List

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.

3.7.3 Searching a Shared List

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 that opens, enter the exact name of an existing shared list. To retrieve the list, you must know the exact name given to the shared list.
3. Click Submit to launch the search or Reset to clear the field and start again.

If the search is successful, the NBIA software adds the image series in the shared list to the data basket. If the shared list includes series for which you do not have visibility rights, the NBIA software informs you that the displayed shared list is not complete.

3.7.4 Exporting a 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.

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.

3.8 Downloading the Data Basket

In the data basket, select the items you want to download.
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.
Once you are satisfied with your selections, click Download at the top left of the results table.

Note: The Download Manager initially lists everything in your Data Basket. After you open the Download Manager, however, you can remove from the Download Manager the items you do not want to download.
To download objects using the Download Manager, follow these steps:
1. Click the Download Manager button. This opens the Download Manager
(Figure 3.7).

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.
 If JRE is installed but the version is older than version 6, the browser automatically attempts to upgrade the JRE to version 6o.
If the JRE is not installed, when you click the Download Manager button, the browser prompts you for what it should do with the JNLP file. The Data Basket page includes a link to a page where you can download the JRE: {+}http://www.java.com/en/download+.

The Download Manager lists series items you selected in the data basket. You can mouse over the Patient ID, Study Instance and Series Instance columns to reveal the complete corresponding IDs or you can resize the column by grabbing the header.
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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