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Questions

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about The Cancer Imaging Archive (TCIA) Website:

1. Do you have a User's Guide?

A detailed TCIA user's guide can be obtained by clicking on on TCIA User User’s Guide.

2. How do I contact TCIA Help Desk?

The TCIA Help Desk can be reached in one of two ways:

  1. By email: help@cancerimagingarchive.net
  2. By phone: +1 314-747-4254

3. What are the hours of operation for TCIA Help Desk?

The hours of operation are 7:00am 00 am to 5:00pm 00 pm CST, MMonday-F.  Although Friday. Although the Help Desk is closed weekends and holidays, you can submit a request can be submitted at any time.  Holiday hours Holidayhours and further information may be found found here.

4. What if I have questions on navigating TCIA website?

The The TCIA User Guide should  should provide all the direction you need.  If you have additional questions please contact TCIA Help Desk. Simply call ( Please contact TCIA’s Help Desk with additional questions by calling +1 314-747-4254) or send sending an email to help@cancerimagingarchive.net to the TCIA Help Desk .

5. What if I am unable to connect to TCIA website?

Please contact TCIA TCIA’s Help Desk . Simply call (+1 314-747-4254 ) or send us an email (help@cancerimagingarchive.net to the TCIA Help Desk).  

6. How do I submit feedback to TCIA website?

We welcome and appreciate your comments.   Feedback maybe submitted via feedback@cancerimagingarchive.net

7. What if I am being prompted to enter a verification code, but

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there is no verification code available and

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no place to type it?

A security warning prompt displays and asks "Do you want to view only the webpage content that was delivered securely". Answer Answer NO to  to the prompt in order to see the captcha information that is used for verification.

If you answer YES, the captcha information will NOT display.

Questions

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about User Accounts:

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1. When I try to register

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after entering the

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captcha phrase, I get

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a PMW 5033 error or an error message stating, "The PWM configuration is invalid or corrupt. Please correct the error, or remove the configuration file."

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How do I proceed?

Assuming you are using Internet Explorer, change your browser's language to English by following these steps:

1. From the menu bar, select Tools.
2. Select Internet Options.
3. Click on General > Language and set to English (US).

2. How do I obtain a TCIA user ID and password?

From TCIA From TCIA’s login page, click on the the Register Now link link.   

3. What if I have issues pertaining to my TCIA user ID or password?

Assuming that you already have an account, from TCIA from TCIA’s login page, click on the I cannot access my account link link.

Questions

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about Accessing Collections:

1. How do I find

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additional information about a specific collection?

You can reference the corresponding wiki pages for any particular collection when you are logged into TCIA. From the search page, in the Collection collection area, mouse over and click on the “question mark” which will return question mark symbol for information on each collection. If there is a wiki available for the collection, click on it.

OR

You can find additional information pertaining to image data from the TCIA home page > : http://www.cancerimagingarchive.net/

In the middle of the page, under For Researchers, click on the link titled The Image Collections, which will direct you to our Public Wikipublic wiki. This wiki pages is organized into purpose-built Collections.

A collection of studies typically includes studies from several subjects (patients). In some collections, there may be only one study per subject. In other collections, subjects may have been followed over time, in which case there will be multiple studies per subject. The subjects typically have in common a particular disease in common and/or disease at a particular anatomical site (prostate, lung, brain, etc.).

The wiki table on the wiki of contents contains a list of collections available on The Cancer Imaging ArchiveTCIA. Each link in the table of contents contains information concerning the scientific value of a collection , as well as additional meta-data where when available from the data providers.

Under the Completed and Ongoing Collections table, you can sort any of the columns. For example if you are looking for MRI images of the Prostate, you could , for magnetic resonance images (MRIs) of the prostate, sort by Anatomical Sites, which will bring all MRIs of the Prostate prostate to the top of the list.

2. How do I request access to a restricted collection?

Access to To access a restricted collection requires prior approval. Simply call (, you can gain approval by calling the Help Desk at +1 314-747-4254) or , or send an email email to help@cancerimagingarchive.net to the TCIA Help Desk. Please indicate the name of the restricted collection.

3. How do I determine the status of a collection that has been submitted?

Please contact TCIA Help Desk . Simply call (+1 314-747-4254 ) or send an email (help@cancerimagingarchive.net to the TCIA Help Desk. Please ) and indicate the name of the collection.

4. Is

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a listing

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of all of the modality abbreviations available?

Yesthey are listed here.

Questions

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about Searching for Images:

1. How do I search and download images as well as find out information about a specific collection?

Let's begin by using the the modality of MR Using MRI images of the prostate as an example to download MRI images of the Prostate, follow the steps below to download images from a specific collection:1.

  1. Log into TCIA.

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  1. Click on the Search Images link.

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  1. To download all the MRI prostate images

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  1. , select MR under Image Modality(ies)

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  1. , select prostate under Anatomical

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  1. Site,

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  1. and click on Submit.

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  1. Click on the

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  1. Check All button to select

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  1. all.

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  1. Selecting the series

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  1. you wish to download and

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  1. clicking the

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  1. Add To Basket

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  1. button

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  1. puts

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  1. them all into the basket.

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  1. To determine the collection that the images go to

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  1. , the collection ID will show up along with the subject ID when the system does the search.

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  1. Select "View My Basket".

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  1. On the next page, you

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  1. need not

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  1. check any boxes unless you wish to remove a series from your basket. In that case, you would select the box and then click on the

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  1. Remove Selected Items

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  1. button at the top.

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  1. Click on the Download Manager link

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You can reference the corresponding wiki pages for any particular collection when you are logged into TCIA. From the search page, in the Collection area, mouse over and click on the “question mark” which will return information on each collection. If there is a wiki available for the collection, click on it.

OR You can find additional information pertaining to image data from the TCIA home page > http://www.cancerimagingarchive.net/

You do not need to be logged into TCIA to view this information. In the middle of the page, under For Researchers, click on the link titled The Image Collections which will direct you to our Public Wiki. This wiki pages is organized into purpose-built Collections.

A collection of studies typically includes studies from several subjects (patients). In some collections, there may be only one study per subject. In other collections, subjects may have been followed over time, in which case there will be multiple studies per subject. The subjects typically have in common a particular disease and/or particular anatomical site (prostate, lung, brain, etc.)

The table on the wiki contains a list of collections available on The Cancer Imaging Archive. Each link in the table contains information concerning the scientific value of a collection, as well as additional meta-data where available from the data providers.

Under the Completed and Ongoing Collections table, you can sort any of the columns. For example if you are looking for MRI images of the Prostate, you could sort by Anatomical Sites which will bring all MRIs of the Prostate to the top of the list.

  1. and see question #1 in the previous section.

2. How do I search images?

The National Biomedical Imaging Archive (NBIA) software enables you to search searching for images in The Cancer Imaging Archive's local in TCIA’s local in vivo image repository.  See See Chapter 2 of the TCIA User's Guide for  for more detailed instructions.

3. What if my image search comes up empty?

You must use caution not to create such a restrictive query that the search returns no results.  Our recommendation is you start If your query is too restrictive, the search will return no results. Try starting with one criterion and add more additional criteria one at a time to refine your search.

4. How do I manage and view images in my 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.  See  See Chapter 3 of the TCIA User's Guide for  for detailed instructions.

5. What if I have a question

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about my query history or saving queries?

After you launch a search, the Search Criteria page displays the search criteria summary for your review. It , and allows you to save the query for future use.  See  See Chapter 2 of the TCIA User's Guide for  for more information.

6. What if I have a question pertaining to creating, editing, or searching a shared list?

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.   See See Chapter 3 of the TCIA User's Guide for  for more information.

7. How do I search for images showing a particular disease?

The collection Collection descriptions provide the best source of information about what disease was studied.  On the search-images  On the Search Images page, scroll down to the Collections collections block , and click on the question - mark to the left of the collection name.  Click  Click to see a brief description of the collection, ; it will usually with have pointers to a site where more detailed information about the collection is available. 

Questions

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about Downloading Images:

1. How do I download images in JPEG, TIFF, or BMP rather than DICOM format?

The Download Manager permits only the downloading of DICOM images only.
If you want to To capture a large number of images, you should download them in DICOM and then reference the websites below for assistance with utilities that will convert DICOM images to other formats.

  1. http://www.idoimaging.com
  2. http://pixelmed.com

If you wish to only download To download only a single image (or a handful of images - one at a time): (1)

  1. In the NBIA application, choose a study and series, then Show Images;

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  1. Right-click over the image and Save Picture As

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  1. .(jpeg).

2. How do I download annotated image files?

The .XML files are in the series folder since they are related to the images in that series.  You  You can best find the annotated files by viewing the list of files in a given folder.   

3. What Java version is required for Download Manager?

Java version 6 or higher of the Java Runtime Environment (JRE) must be installed to be able to open the Download Manager. See See Chapter 3 of the TCIA User's Guide for  for more information.

On some systems, notably later versions of the Mac OS X, the system may not recognize the Certificate Authority that The Cancer Imaging Archive uses to protect content from the web site transmitted via the https protocol and to sign Java Web Start applications, such as the Download Managers.  In these cases, Java may give a certificate warning, asking if you really trust this site enough to run the program.  In all cases, newer versions of Java will also ask the user if they really want to launch a program that has access to their files.  (Obviously, Download Manager needs such access in order to store downloaded files.) The user must answer in the affirmative (i.e. 'yes, I trust this site' or 'yes, I trust this program' in order for Download Manager to start.  One can avoid the warnings by either putting the cancerimagingarchive.net into "exceptions" list (i.e. trusted sites list) on the security tab in Java's control panel (only available in later versions of Java 7), or lowering the Java security level temporarily to "Medium" (not recommended).

Does Download Manager work with any browser?

Theoretically, yes.  However, we principally test with Firefox, Chrome, and Internet Explorer.  We also test with Safari (the default browser on most Macs), and it did work up to version delivered on Mac OS X version 10.8.3 (Mountain Lion).  After 10.8.3, Safari will silently download the JNLP file used to launch the Download Manager, but will not automatically start the Download Manager program.  Safari does not give the user any warning, so to the casual user it appears that the Download Manager link is broken.  One has to go to the Downloads folder, find the JNLP file just downloaded, and then command | control | right click the JNLP file and select "Run" from the pop-up context menu to start the Download Manager.

Are there operating system requirements for Download Manager?

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4

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What if I receive an error message from Download Manager or Download Manager hangs?

The number of series that can be downloaded using Download Manager is dependent on several factors. Average : average image size, RAM on your computer, and Java limitations all factor into how much you can download. If you experience issues or errors associated with the download you will need to , reduce the number of series in your basket and try again.

5. I am behind a proxy server, will Download Manager work?

Accessing The Cancer Imaging Archive's TCIA’s Download Manager directly through a proxy server is currently not supported. If your only access to the Internet is through a proxy server, then our current recommendation is to ask your IT Department to allow your workstation to bypass the proxy server for direct access to to https://public.cancerimagingarchive.net/ncia.

Java may be configured to utilize proxy settings; however, the developers of NBIA have not tested whether Download Manager correctly handles such settings.

6. What if I am unable to download images through

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Download Manager and receive an error message in the status bar?

In order for our Our support team needs the following information to perform additional troubleshooting, the following information is needed:
1. A screen capture of the error message.
2. A screen capture of the Java console (you may need to enable viewing the Java console using the Control Panel > Java Control Panel > Advanced > Settings: Java Console > Show Console).
3. Operating system and version.

  • Windows XP: Start > Control Panel > System > General tab.
  • Windows 7: Start > Control Panel > System and Security > System. 

4. Browser and version.

  • Internet Explorer: From the menu bar, select Help > About Internet Explorer.

7. How many series can Download Manager download from a single shopping cart?

Although theoretically there is no The maximum number of series that the download manager can manage from Java allows Download Manager to hold in a single shopping cart , we recommend limiting a shopping cart to no more than 3500 series. To determine how many series are in your basket at a given time, on the left nav at the top (is around 3500. The number of series in your basket will display on the left navigator at the top under My Data Basket > View Contents) the number of series in a basket will display.

Image Removed 

Questions about the TCGA-related imaging data:

How do I find

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additional information about brain tumors?

Please refer to the The Cancer Genome Atlas-Glioblastoma Multiforme (TCGA-GBM (Glioblastoma multiforme ) collection as a for well-documented collection of of brain-tumor images as described inhere: https://wiki.cancerimagingarchive.net/display/Public/TCGA-GBM. (This wiki page also links to the wiki pages describing the related research activities and related resources). On this page, in .)

In the Related Data section, there is a link to a blank GBM Case Quality Control Form that details the kinds and descriptions of clinical data collected. The data are freely available from the TCGA Data Portal: https://tcga-data.nci.nih.gov/tcga.

Once herethere, the you would click on the link to the Glioblastoma multiforme [ GBM ] data. Since TCIA does not host the TCGA Data Portal, we do not offer guidance for browsing the Data Portal.

The TCGA-LGG (Low Lower Grade Glioma (LGG) collectionis collection is another set of brain - tumor images:   TCGA-LGG.

Questions

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about Tumors:

Do the exams in TCIA show both malignant and benign tumors?

All patients that who are part of TCIA at this time are cancer-positive by definition. We don’t have any no collections of non-malignant tumors or healthy patients, so in general the tumors would be malignant. The only exception could would be patients with multiple tumors who might have a benign tumor in addition to a malignant tumor, but at least one tumor should always will be malignant in each patient.