Welcome to the NITRC Image Repository, or NITRC-IR for short.
Here you can find curated, community generated neuroimaging data sets that might help in
your research.
You may find this front end familiar, as NITRC-IR leverages XNAT's popular data storage platform.
In the lower middle section, Projects box, you'll see a list of all the data sets that
you may access.
Unlike NITRC where you do not have to register to download its tools and resources, you DO
have to be a NITRC registered user and a member of the NITRC tool or resource that owns the
data set to download most of the data on NITRC-IR.
If you are not already registered with NITRC, it's free and easy.
From the NITRC home page, click the Register link.
Fill in the required information, and click the Register button at the bottom of the form.
Your registration is automatically approved.
Simply click on the link in the e-mail you receive to verify your e-mail address and
establish your account.
If you lose the confirmation e-mail or forget your password, you can always access this
information from the Member Login page.
Click here [Lost your password?] to reset your password, and click here [Resend confirmation
email to a pending account] to resend the confirmation e-mail to establish your account.
Let's log in as a registered NITRC user and go back to the Image Repository.
Click Image Repository under Tools & Resources to get back to the IR Home page.
This user is not a member of any NITRC tool or resource and only has access to the unprotected
public data sets.
But, there is a secret door to finding the other data sets that you may wish to use in
your research.
We can see a list of those protected data sets by clicking Other Projects in the navigation
tree on the left side of the page.
So, ABIDE and ADHD-200 are protected data, and we know that because there are locks in
the Access column.
You must be a member of the tool/resource that owns a protected data set in order to
access it, so you need to join the 1000 Functional Connectomes Project on NITRC to access ABIDE
and ADHD-200 data.
We can do that from NITRC-IR.
Click on the title or ID for ABIDE.
The message you see indicates that this user does not have access to the ABIDE data.
Click "request access here."
Add a comment if you like, and click the Submit Request button.
You will need to wait for an administrator to approve your request.
When your membership is approved, all data sets owned by 1000 FCP will be listed on your
IR home page.
Let's log out and log back in as a member of 1000 FCP to demonstrate this.
[Logging in as a member of 1000 Function Connectomes Project.]
Now, we see ABIDE and ADHD-200 listed in the Projects box since both data sets are owned
by 1000 FCP and this user is a member of that resource.
Now that we have access to all this data, let's see how we can find images that would
be meaningful for our research.
Click the Advanced Search link at the top right of the page.
In step 1, we are picking the starting point for the data we want returned.
Leave Pivot Data Type as MR Sessions to start with this data.
In step 2, we are selecting addition data that we want to show in our results.
Brief and detailed are pre-defined column sets for the data type.
Let's included Subjects.
We have to select Brief because a detailed column set is not defined for Subjects.
Let's also select the Detailed column set for MR Sessions to bring back all the data
we can for the image sessions.
Click the Next button to continue.
In step 3, we enter our Search Criteria to refine the results to our specific needs.
On the MR Sessions tab, let's select male for Gender, enter 10-20 for Age, 3 for Field
Strength, and 2000 milliseconds for Resting TR.
Click the Submit button to see the results.
We have found a subset of 541 MR Sessions that meet our criteria.
This list includes the detailed image session data and brief subject data that we requested.
You may choose to look at a specific image session by clicking on the link in the Label
column.
If you click on a scan type you will see its details.
You may download all the session data in XML format by clicking Download XML under Download
in the Action box.
You may also download specific images for this session by clicking Download Images instead.
Here, we'll select the file type that we want, check the images that we want to download,
and click the Download button.
Now, you can save the images to a file on your computer to use in your research.
What if you wanted to download ALL the images from the search you performed.
Let's go back to our result set.
To the right above the results under Options, select Download.
For step 1, we want to select the MR sessions that we want to include in the download.
All are checked by default.
For step 2, check the image data to include in the download.
You have to select at least one.
Let's select 'rest' scans.
For step 3, we select the download format.
We'll just leave the direct download with the project and subject in the path.
For step 4, we submit the requested download.
You must have Java installed in order to use the download applet.
You may get a security warning the first time you use this, but you must run the Java applet
in order to continue with the download.
If the applet is running, you will see this page, where you enter or select a folder in
which to save your images.
Click the Start button to begin the download.
This will obviously take some time if you're downloading a lot of images.
The progress bar will show your progress, and the message above will indicate how much
data you've downloaded until the download is complete.
You now have the data stored on your computer for you to use in your research.
So, when you go to publish, please don't forget to acknowledge the NITRC Image Repository
so others can benefit from this useful tool!