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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.

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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

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Chapter 1 – Getting Started

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1.1 Introduction to The Cancer Imaging Archive


The 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:

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  • 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

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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.

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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.

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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

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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.

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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.

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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 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


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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.


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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:

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  • 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.

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Chapter 2 – SEARCHING FOR IMAGES

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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: 

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3. Text fields. Enter the information requested.

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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.

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

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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.

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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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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:

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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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2.5 Specifying Remote Search Sites

A remote search site is an image database residing outside of the local Cancer Imaging Archive imaging archive. 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.

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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.

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2.6 Working with Saved Search Queries

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).

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

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2.6.1 Saving a Search Query.

To save a search query, perform the following steps:

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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.

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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).

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

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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.

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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.

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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.

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

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Chapter 3 - VIEWING SEARCH RESULTS

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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.

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

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3.2 Search Results (by Subject)

Wiki Markup
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.

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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

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="92b56d3a913c3d11-4ed956e2-4ec14314-8580b91a-37883ea5facd740f4ab8ba18"><ac:plain-text-body><![CDATA[

[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.

]]></ac:plain-text-body></ac:structured-macro>

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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

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  • 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).
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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.

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  • Click View My Basket to display the items in your data basket (see Managing the Data Basket).
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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.

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

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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.

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3.6.1 Adding Items to Your Basket

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

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

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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).

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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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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.

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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.

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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.

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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.

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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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3.7.3 Searching a Shared List

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

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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.

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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.

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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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3.8 Downloading the Data Basket

In the data basket, select the items you want to download.

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