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Executive Summary

Excerpt

This guide provides an overview of The Cancer Imaging Archive (TCIA)

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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 The Cancer Imaging Archive 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 The Cancer Imaging Archive 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 The Cancer Imaging Archive TCIA database searches.


Questions about the use of this guide should be sent to The Cancer Imaging Archive TCIA's 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 (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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Chapter 1 – Getting Started

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1.1 Introduction to The Cancer Imaging Archive


The Cancer Imaging Archive TCIA 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 that support these functions:

  • 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 improve the use of imaging in today's cancer research and practice by increasing the increases the efficiency and reproducibility of imaging cancer detection and diagnosis, leveraging imaging to provide providing 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 TCIA using the CTP ( Clinical Trial Processing (CTP) software software. Any potential user may then access The Cancer Imaging Archive TCIA to search for and download images and associated annotation files. Images are stored in DICOM, 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 forthetc. For more information about DICOM, see http://medical.nema.org.
The Cancer Imaging Archive

TCIA 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 TCIA 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 ArchiveTCIA.
  • Log into The Cancer Imaging ArchiveTCIA.



                                Figure 1.1 Welcome Page

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To register a new user in The Cancer Imaging ArchiveTCIA, 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.

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Once you have submitted your entry form, a message will be conveyed to The Cancer Imaging Archive 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.

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If you have any questions in the mean time , 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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When you enter http://cancerimagingarchive.net to access The Cancer Imaging ArchiveTCIA, the welcome page displays. Click LOG ON TO THE CANCER IMAGING ARCHIVE to bring up the login page.


                                                  Figure 1.3 Login Page

If you have already registered with The Cancer Imaging ArchiveTCIA, perform the following steps to login:

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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 The Cancer Imaging Archive site TCIA's site URL. If you fail to do that, the login failure message may not appear.

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2. If you have persistent difficulty logging in, click I cannot access my account on The Cancer Imaging Archive login 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 The Cancer Imaging Archive Help TCIA's 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 TCIA's home page displays several panels and menu bars.


                                            Figure 1.4 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 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 The Cancer Imaging Archive TCIA 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 ArchiveTCIA.

 



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 ArchiveTCIA.

N/A

Privacy Notice

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

N/A

Disclaimer

Displays The Cancer Imaging Archive 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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1.5 Application Support

For any general information about TCIA, support questions, or to report a bug, contact The Cancer Imaging Archive User 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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1.6 Using

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TCIA's Online Help

The online help has been written to help you master the NBIA software. To access online help in The Cancer Imaging ArchiveTCIA, 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 ArchiveTCIA.

  • 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 ( ) 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 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 of Help by entering query text in the search text box.

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The NBIA software enables you to search for images in The Cancer Imaging ArchiveTCIA's local in vivo image repository.   NBIA also supports a Remote Search remote search function to search in other NBIA servers connected to caGrid; however, 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 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 has annotation files (indicated by Yes in the Contains Annotations column), they are automatically downloaded as well. 

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

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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 or 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.

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2.2 Performing a Simple Search

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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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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)

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                                          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 3 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 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.

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.

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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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2.3 Performing an Advanced Search

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

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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. 

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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)

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                                    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 you leave both options unselected, the results will be the same--as though you had selected oth 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 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 3 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 groups 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 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 the search will return.
 
Note: This number also defines the number of thumbnail images that will display in the Search Results (Images for Series).

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                   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.

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                              Figure 2.6 DICOM Search Criteria

Criteria

Description

Series Description

Enter your description of the Seriesseries. 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 , 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

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 from the second drop-down list and specify the maximum peak distribution.

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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 TCIA's database at image series level, follow these steps:

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

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    a. Select an option in the first drop-down list. Options include The Cancer Imaging Archive entitiesTCIA 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 number of Results results that will display per page. Default is set at 10.

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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.

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).

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             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.

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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.

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2.6 Working with Saved Search Queries

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                                   Figure 2.9 Save Query option

Note: If you launched launch 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.

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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.

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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 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.

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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:

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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 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:

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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

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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).

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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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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 items—the entire patient, a study, or a series----to 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.

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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.

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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.

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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, save a query, 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).

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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 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).

            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) 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.

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.

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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.

  • 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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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 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.

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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

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.

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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.

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 When the viewer opens (Figure 3.4), click the play forward button . The Cancer Imaging Archive TCIA 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.

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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 ArchiveTCIA, 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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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

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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

The location of the image.

 "Local" represents The CANCER IMAGING ARCHIVE  archive that you are currently logged into.

HTML Comment

Other locations are remote sites selected with the Remote Search option. For more information about the Remote Search option, see Specifying Remote Search Sites.

                                                    Table 3.5 My Data Basket field

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

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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

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The Edit My Shared List page that opens displays a list of Shared Lists 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.

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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

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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.

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3.7.4 Exporting a Shared List

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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

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Once you are satisfied with your selections, click Download *Manager *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.

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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.

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 Java Webstart ( JNLP ) applications.

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.

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Note that files downloaded this way are not zipped. The downloaded file(s) are stored in a file structure such as Collection collection name/patient id/study instance UID/ series instance UID/image SOP instance UID under the destination folder.

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3.8.1. Download Errors

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 Windowwindow: "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 re-tries 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 Cancer Imaging Archive the TCIA team.