Skip to end of metadata
Go to start of metadata

ALERT

This is outdated documentation describing an older version of TCIA's software stack. Please refer to the Cancer Imaging Archive User's Guide for current documentation.

This chapter describes how to review results of TCIA database searches.

Topics in this chapter include:

Search Results Overview

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

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

A Simple Search, Text Search, and Advanced Search each orders search results by Subject ID on the Search Results (by Subject) page. Clicking that Subject ID displays the studies and image series matching the search criteria for that subject. For more information, see Search Results (Studies for Subject).

You can view images associated with studies for the selected subject in various ways, including:

  • viewing all study images in a DICOM web viewer,
  • viewing thumbnails of all study images on the Search Results (Images for Series) page
  • viewing selected images in your desktop DICOM viewer,
  • viewing all study images in an animated cine loop,
  • or viewing the DICOM header of the first image in the series.

Retrieving objects for download

At any point in the process of reviewing results, you can add items - all data pertaining to a patient, study, or an image series - to your data basket. When items are in your data basket, you must take a subsequent step to download them.

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

Return to top of page

Search Results (Studies for Subject)

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

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

Field

Description

Series

Series identification number

Description

Description of the Series

Modality

Image modality

Manufacturer

Name of the manufacturer of the image series

Images

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

Thumbnails

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

Cine Mode

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

DICOM

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

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

Add to Basket


 

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

For more information, see Managing the Data Basket.

Add a Study series to Basket

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

Return to top of page

Search Results (Images for Series)

Clicking the icon in the Search Results (by Subject) page opens thumbnails of all images in the selected series. In this documentation, this page is called Search Results (Images for Series).

Click View Image under any thumbnail to save the image as a file or open it in the DICOM viewer.

Return to top of page

Viewing Image Animation

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

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

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

Animation Controls

Action

Reset start and end button

Reset start and end.

Yellow bar

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

Fast backward

Click to return to the first image in the set.

Back arrow

Click to play animation backward through the series.

Minus

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

Arrow slider on a line

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

Plus sign

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

Forward arrow

Click to play animation forward through the series.

Fast forward double arrow

Click to progress to the last image in the set.

Cycle arrow

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


Tip

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

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

Return to top of page

Obtaining DICOM Viewers

Most image data and some associated data within The Cancer Imaging Archive (TCIA) is stored in DICOM format.  There are a variety of both open source and commercial DICOM tools that could be used to manipulate and view these files. While TCIA does not endorse nor recommend any particular tool, here is a list of tools that we or our partners have used in our daily work. More information about DICOM is available.

Select Tools > List of DICOM Tools to open a page of selected links to freeware DICOM image viewers. This list is provided for your convenience. Many other DICOM viewers are available on the internet. This is not an endorsement of the listed viewers.

Before using the viewers

The images in this image repository need to be downloaded before you can view them using the viewers.

Return to top of page

Downloading TCIA Images

Unable to render {include} The included page could not be found.

Return to top of page

Using the TCIA Download Manager

Unable to render {include} The included page could not be found.

Return to top of page

Working with the Data Basket

As you search TCIA, you can add any data items to your data basket to download later. The items in your data basket remain there only for the current work session.

Adding Items to Your Basket

Unable to render {include} The included page could not be found.

Return to top of page

Managing the Data Basket

Unable to render {include} The included page could not be found.

Return to top of page

Downloading the Data Basket

Unable to render {include} The included page could not be found.

Return to top of page

Working With Shared Lists

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

Creating a Shared List

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

Who can create a shared list?

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

To create a shared list

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

Data Basket

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

Access to your list

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

Menu Option:

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


Return to top of page

Editing a Shared List

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

Shared List

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

To edit a shared list

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

To delete a shared list

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

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

Return to top of page

Searching a Shared List

Any user can search for a shared list.

To search for a shared list

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

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

Return to top of page

Exporting a Shared List

Once you have created a shared list, you can export it as a .csv file.

To export a shared list

  1. Above the data table, click Shared List > Export Series ID.
    The shared list opens in the data basket.
    Data basket displaying export shared list options
    The export begins immediately. A dialog box appears, prompting you to open (in Excel) or save the file.
  2. Select to open or save the file.

Return to top of page

Managing a Shared List

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

Permissions

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

 To delete a shared list, follow these steps:

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

Return to top of page

  • No labels