Questions 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 TCIA User’s Guide.
2. How do I contact TCIA Help Desk?
The TCIA Help Desk can be reached in one of two ways:
- By email: email@example.com
- By phone: +1 314-747-4254
3. What are the hours of operation for TCIA Help Desk?
The hours of operation are 7:00 am to 5:00 pm CST, Monday-Friday. Although the Help Desk is closed weekends and holidays, a request can be submitted at any time. Holidayhours and further information may be found here.
4. What if I have questions on navigating TCIA website?
The TCIA User Guide should provide all the direction you need. Please contact TCIA’s Help Desk with additional questions by calling +1 314-747-4254 or sending an email to firstname.lastname@example.org .
5. What if I am unable to connect to TCIA website?
Please contact TCIA’s Help Desk (+1 314-747-4254 ) or send us an email (email@example.com).
6. How do I submit feedback to TCIA website?
We welcome and appreciate your comments. Feedback maybe submitted via firstname.lastname@example.org
7. What if I am being prompted to enter a verification code, but there is no verification code available and 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 NO 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 about User Accounts
1. When I try to register after entering the captcha phrase, I get 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." 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’s login page, click on the Register Now link.
3. What if I have issues pertaining to my TCIA user ID or password?
Assuming that you already have an account, from TCIA’s login page, click on the I cannot access my account link.
Questions about Accessing Collections
1. How do I find 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 area, mouse over and click on the question mark symbol for information on each collection. If there is a wiki available for the collection, click on it.
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 wiki. This wiki is organized into purpose-built Collections.
A collection of studies typically includes 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 a particular disease in common and/or disease at a particular anatomical site (prostate, lung, brain, etc.).
The wiki table of contents contains a list of collections available on TCIA. Each link in the table of contents contains information concerning the scientific value of a collection as well as additional meta-data when available from the data providers.
Under the Completed and Ongoing Collections table, you can sort columns. For example, for magnetic resonance images (MRIs) of the prostate, sort by Anatomical Sites, which will bring all MRIs of the prostate to the top of the list.
2. How do I request access to a restricted collection?
To access a restricted collection, you can gain approval by calling the Help Desk at +1 314-747-4254, or send an email to email@example.com. 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 (+1 314-747-4254 ) or send an email (firstname.lastname@example.org) and indicate the name of the collection.
4. Is a listing of all of the modality abbreviations available?
Yes, they are listed here.
Questions about Searching for Images
1. How do I search and download images as well as find out information about a specific collection?
Using MRI images of the prostate as an example, follow the steps below to download images from a specific collection:
- Log into TCIA.
- Click on the Search Images link.
- To download all the MRI prostate images, select MR under Image Modality(ies), select prostate under Anatomical Site, and click on Submit.
- Click on the Check All button to select all. Selecting the series you wish to download and clicking the Add To Basket button puts them all into the basket. To determine the collection that the images go to, the collection ID will show up along with the subject ID when the system does the search.
- Select "View My Basket".
- On the next page, you need not 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 Remove Selected Items button at the top.
- Click on the Download Manager link and see question #1 in the previous section.
2. How do I search images?
The National Biomedical Imaging Archive (NBIA) software enables searching for images in TCIA’s local in vivo image repository. See Chapter 2 of the TCIA User's Guide for more detailed instructions.
3. What if my image search comes up empty?
If your query is too restrictive, the search will return no results. Try starting with one criterion and add 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 TCIA, you can add items at any level to your data basket for subsequent download. See Chapter 3 of the TCIA User's Guide for detailed instructions.
5. What if I have a question about my query history or saving queries?
After you launch a search, the Search Criteria page displays the search criteria summary for your review, and allows you to save the query for future use. See Chapter 2 of the TCIA User's Guide 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, record the exact name of the shared list to distribute to others who may want to use it. See Chapter 3 of the TCIA User's Guide for more information.
7. How do I search for images showing a particular disease?
Collection descriptions provide information about what disease was studied. On the Search Images page, scroll down to the collections block and click on the question mark to the left of the collection name. Click to see a brief description of the collection; it will usually have pointers to a site where more detailed information about the collection is available.
8. How do I search for images if I know the patient (subject) ID?
The NBIA software enables you to search for images in TCIA's image repository in a variety of ways. Although searching for a particular collection is the most common you can also search for the images belonging to one or more subjects. Simply start on the Search page and enter one or more subject ID strings, separated by commas.
Questions about Downloading Images
1. How do I download images in JPEG, TIFF, or BMP rather than DICOM format?
The Download Manager permits downloading of DICOM images only. To capture a large number of images, download them in DICOM and then reference the websites below for assistance with utilities that will convert DICOM images to other formats.
To download only a single image (or a handful of images one at a time):
- In the NBIA application, choose a study and series, then Show Images;
- Right-click over the image and Save Picture As .(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 can 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 Chapter 3 of the TCIA User's Guide for more information.
4. 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 image size, RAM on your computer, and Java limitations. If you experience issues or errors associated with the download, reduce the number of series in your basket and try again.
5. I am behind a proxy server, will Download Manager work?
Accessing 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, our current recommendation is to ask your IT Department to allow your workstation to bypass the proxy server for direct access 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. 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.
7. Are there operating system requirements for Download Manager?
In theory, the Download Manager, being Java based, will work on any operating system. However, the Mac OS X operating system has been imposing additional security requirements on Java Web Start programs, such as the Download Manager, which make it difficult to run them without having administrative access to the Mac. In particular, the Gatekeeper function in 10.8.4 (Mountain Lion) and later versions of Mac OS X by default blocks starting third party programs that have not been either obtained from the Apple App store, or that have not been signed with an Apple Developer ID. This includes, naturally, Java Web Start programs such as the Download Manager. To get around this restriction, one can either change the default Gatekeeper setting, found in the Security tab of Apple System Preferences, to allow the running of 3rd party applications, or download the JNLP file used to launch the Download Manager, and then command | control | right click the JNLP file and select "Run" from the pop-up context menu. Note that either method requires either having administrative access to the Mac OS, or knowing the username/password of an administrator account, since the Mac will prompt for this information.
8. What if I am unable to download images through Download Manager and receive an error message in the status bar?
Our support team needs the following information to perform additional troubleshooting:
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.
9. How many series can Download Manager download from a single shopping cart?
The maximum number of series that Java allows Download Manager to hold in a single shopping cart 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.
10. Using the Download Manager default location for downloading files?
When downloading images to the default destination, make sure all folders in that destination path are visible and writeable. If you unable to see them and/or they are not writeable, please consult with your system administrator OR change the default to a destination you know to be visible and writeable.
Questions about the TCGA-related imaging data
How do I find additional information about brain tumors?
Please refer to The Cancer Genome Atlas-Glioblastoma Multiforme (TCGA-GBM) collection for well-documented brain-tumor images as described here: https://wiki.cancerimagingarchive.net/display/Public/TCGA-GBM. (This wiki page also links to pages describing related research activities and related resources.)
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 there, click on the link to GBM data. Since TCIA does not host the TCGA Data Portal, we do not offer guidance for browsing the Data Portal.
The TCGA-Lower Grade Glioma (LGG) collection is another set of brain tumor images: TCGA-LGG.
Questions about Tumors
Do the exams in TCIA show both malignant and benign tumors?
All patients who are part of TCIA at this time are cancer-positive by definition. We have no collections of non-malignant tumors or healthy patients. The only exception would be patients with multiple tumors who might have a benign tumor in addition to a malignant tumor, but at least one tumor will be malignant in each patient.
MRI Basic Science and Abbreviations
Study materials for physicists and other clinical scientists learning the basics of magnetic resonance imaging (MRI): http://www.revisemri.com. Abbreviations only: http://www.revisemri.com/questions/misc/mri_abbrev