nitrc:Future User Guide - Tool/Resource Feature: Image Repository
From NITRC Wiki
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NITRC Image Repository offers a cloud-based federated neuroimaging data storage system for resource sharing of neuroimaging data in DlCOM and NIFTI formats. You may access the image repository by clicking "Image Repository" in the main menu under "Tools & Resources" or by clicking on the "Image Repository" tool/resource menu item for any tool/resource that has elected to use the image repository (see Note below). Through the image repository you may search for stored images based on demographics, imaging parameters, and fMRI descriptors. From the search results you may select and download images. NITRC's image repository is an implementation of XNAT, Extensible Neuroimaging Archive Toolkit. For more information on using XNAT, please refer to the online XNAT 1.5 Documentation.
| Note: Currently, NITRC only offers this beta functionality for 1000 Functional Connectomes. In the future other NITRC tools/resources may have the ability to make their datasets available to the NITRC community through the Image Repository. |
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User Access
Any NITRC tool/resource with an Image Repository link has a corresponding XNAT project. If the XNAT project is public, then all NITRC users, including guests who are not logged in, may view and download data in the project. If the XNAT project is private or protected, then only members of the project may view and download data in the project. For all XNAT projects only NITRC tool/resource administrators may add or modify data associated with their project. NITRC runs a script every 10 minutes to update the members of the XNAT project based on the membership of the corresponding NITRC tool/resource.
| Project Accessibility | User Type | User Access |
|---|---|---|
| Public | All | Read Only |
| Private/Protected | Non-members | No Access |
| Private/Protected | Member | Read Only |
| All | Administrator | Full (Read & Write) |
Navigating the Image Repository
The Image Repository Home page lists all public XNAT projects and the private XNAT projects for which you are a member. Simply click on the project name (for example, fcon_1000) in the list to access the project report page and the data available for that project.
| Note: The number of projects, subjects, and imaging sessions is displayed under the "Search" label. These numbers represent all projects (public and private) in the Image Repository. You will only be able to access data for public projects and the private projects for which you are a member. |
When you are on project or imaging session pages, click the "Image Repository Home" link at the top of the page to return home.
You may also use the menu in the box on the left side of your screen to navigate the Image Repository. The menu is broken into three main sections: Projects, Stored Searches, and Data. You may expand and collapse the sections for easy access to data important to you.
- Projects: Any recent projects that you have looked at will be listed under Recent, and any projects that you have added to your favorites will be listed under Favorite. (You may need to refresh the browser screen to display a newly accessed project or favorite.) Click on a project name to access data for that project. Click on My projects to list all public projects and projects for which you are a member. Click on Other projects to see public projects for which you are not a member.
- Stored Searches: Any search that you have previous saved will be listed here. (You may need to refresh the browser screen to display a newly saved search.) Click on the search name to display the search results for that search.
- Data: Click on Subjects to list all accessible subjects. Click on MR Sessions to list all accessible MR sessions.
Searching the Image Repository
You may search the Image Repository from the home page. Click on the tab corresponding to the information you are looking for: Projects, Subjects, MR (sessions), PET (sessions), or CT (sessions). Enter your search criteria and click the "Submit" button to see your search results.
Search Criteria: The search engine allows for multiple criteria formats. The possible formats are dictated by the data type of the corresponding search field.
- Numeric search
- Search criteria must be separated by a comma, which acts as an OR. Thus, 8,10,15 would return results where the field is equal to 8, 10, or 15.
- Negative numbers must be enclosed in parenthesis (-5).
- Possible criteria types are <=,>=,<,> or using a range 10-19. If no comparison type is specified the default is = (equal to). Thus, 5-10,15,>=20 would return results that are between 5 and 10, equal to 15, or greater than or equal to 20.
- String search
- If the value is in single quotes, like 'brown', then the search will return the results which match exactly. Otherwise, the search will return results which contain the text (case independent). Thus, brown returns brownster, brown, or BROWN records.
- Search criteria may be separated by a comma or an empty space, which acts as an OR. Thus, brown, 'richard' pete would return results where the field is like brown, equal to richard, or like pete.
- % or * can be used as a wildcard value.
Saving Search Results: When you get your search results, you may save the data for use in a spreadsheet. Click the "Options" box above the search results and select "Spreadsheet." A .csv file will be downloaded, so you can import the data into a spreadsheet using your favorite spreadsheet software.
Storing Searches: When you get your search results, you may store the search criteria to run again in the future. Click the "Options" box above the search results and select "Save Search." Give the search a name (brief description) and click the "Submit" button. Your saved search will appear in the navigation box on the left side of the screen under "Stored Searches." (You will need to refresh the browser screen to display a newly saved search.)
Downloading Images
You can download images for an individual session or do a batch download for several sessions.
Individual Download: In order to download images for an individual session, you must first access the session. From any of the reporting pages or search results listings, you can access a subject and/or an imaging session by clicking on its name in the list.
When you select a subject, you must then select the imaging session from the list of experiments on the subject details page . For example, on the AnnArbor_sub00306 subject details page, you must click the MR Session link in the list of experiments. This opens the AnnArbor_sub00306 MR session details page.
When you select an imaging session, you go right to the imaging session details page (for example, AnnArbor_sub00306).
From the imaging session details page, click "Download Images" under "Download" in the "Actions" box. This opens a screen where you may choose the specific images to download. Select the file type for the download, make sure the box is checked for each image you want to download, and click the "Download" button. The image files are downloaded to your local default file download location.
Batch Download: XNAT includes a download applet for downloading files from multiple imaging sessions. The download applet is available from the project report page (for example, fcon_1000) by clicking "Download Images" in the "Actions" box. The download applet is also available from the search results listing for MR, PET, and CT searches or from an imaging session report page (for example, MR sessions) by clicking the "Options" box and selecting "Download" from the list. Either of these links will take you to the Image Data Download page.
Follow the steps on the Image Data Download page to download the images you want.
- Confirm sessions for download: Make sure the box is checked for each session you want to include in your download.
- Select image data to download: Make sure the box is a checked each type of data you want to include in your download.
- Select download format: Select either direct download or XML catalog. Make sure the boxes are checked appropriately if you want to include the projects and/or subjects in the file paths.
- Submit data request: Click the "Submit" button to initiate the download.
This opens a screen that allows you to select your download location and start the download. (You need to have Java installed on your computer and allow it to run in your browser for the applet to work.) Your batch download may take some time to complete. This screen shows the status of the download.
