XNAT (Imaging Data Service)

XNAT is an open source imaging informatics platform developed by the Neuroinformatics Research Group at Washington University. It facilitates storing, securing, organization, sharing, viewing and downloading of imaging (and associated) data. XNAT.Sydney (part of the Imaging Data Service) is an XNAT database used to store imaging data at the University of Sydney. The data is organised into projects owned by different investigators. The ForeFront Frontier FTD project (project ID: FRONTIER) holds all of Frontier’s MRI scans.

The following are simple instructions on how to access, find, view and download data from Frontier’s project in XNAT.Sydney. Further information can be found in the Imaging Data Service user guide, and on the XNAT wiki page, linked below.

https://sydneyuni.atlassian.net/wiki/spaces/RC/pages/214073450

https://wiki.xnat.org/documentation/how-to-use-xnat

Logging in:

University of Sydney Staff can log in to XNAT using their UniKey. Just select “USYD_Unikey” from the LOGIN dropdown menu and then put in your details. To gain access to the FRONTIER project in XNAT someone will need to add you as a member or a collaborator. Please email Sophie and Ramon if you require access (sophie.matis@sydney.edu.au & ramon.landin-romero@sydney.edu.au).

You can log in here.

Searching: 

You can quickly search for an individual participant, session or scan by entering the ID into the search bar on the right-hand side of the navigation bar at the top of the page.

Open

You can also search for multiple sessions or participants using the advanced search. Here you can enter multiple session or participant IDs, or you can search for all scans from a specific scanner, or in a specific date range. At this time, you cannot search subject fields (such as age or gender).

You should select what data you want to see in your search, you will likely want detailed MR Sessions data as shown below:

Open

Once you have done a search you can filter the results of the search even further. Please refer to the “Filtering” and “Downloading a filtered data set” sections below.

Viewing:

To view the scans from a particular session you can navigate to the session by entering the session ID into the search bar, selecting it from your search results or browsing. You then select “View Session” or “View Legacy XImgView” from the “Actions” menu to the right of the session details.

Once you have opened the viewer, you select the scan you would like to view, and it will load into the viewer. Please note that currently there are some quality issues when using the Legacy viewer to view NIfTY files.

Downloading scans from a single session:

If you would like to download some or all the scans from the sessions you are viewing, select “Download” -> “Download Images” from the Actions menu to the right of the session details.

You can then specify which scans you would like to download and what type/s of files you want. All options are pre-selected automatically, so if you do not want all the available files, you will need to de-select some. When using data from XNAT, it is important not to store it on your local device, as such we recommend you don’t use option 2 for downloading. Once you know which files you would like to download, please refer to these instructions on how to download: Downloading files from XNAT.

Browsing:

You can browse through subjects by clicking on the browse dropdown from the navigation bar and selecting “My Projects” -> “Frontier”. You can also do this by selecting “Data” -> “Subjects”. You can browse through MR sessions by selecting “Browse” -> “Data” -> “MR Sessions”. In this browsing view you can see the subject ID, date, scans, and scanner and can sort or filter the sessions with any of these headings by clicking on them.

If you are part of more than one project, you will also see MR sessions from any other projects while browsing and can filter them out by filtering with the “Project” column.

Filtering:

As mentioned under the previous heading, while browsing data (“Browse” -> “Data” -> “MR Sessions”) you can filter the sessions to retrieve only a subset of sessions that you are interested in.

For example, if you are interested in seeing all sessions with a Coronal 3d T1 from 2020 you would first want to filter out any sessions that do not include that scan by clicking on the top of the “Scans” column and then selecting filter. If you do not have the scans column, select “Options” → “Edit Columns”, and then add the column called “Aggregated Scan Counts”.

You then have a number of filtering options to choose from, for this example you would need to select “LIKE”. 

Then you can enter the name of the scan you are interested in. In this example “Cor 3d T1”.

*Note: you wouldn’t select “=” for this type of filtering as the whole string of scans for the session is being looked at, rather than the scan names individually.  You can then press submit and your filter will be applied to the sessions.

For our example, you would then want to filter by date to get only scans from 2020. To do this you would select the heading for the “Date” column and select “Filter”.

You can then select “BETWEEN” and enter the dates on either end of the date range you want the scans from. For our example of retrieving only scans from 2020, we would enter the below:

Then press submit to apply the filter. *Note: In XNAT you need to put the month before the day when entering dates (as prompted).

You can filter any other columns in much the same way and can always see the filters that you have applied above the sessions (circled in the image below).

If you would like to filter by a variable that does not appear as one of the columns in the sessions table, you can search for another column to add by selecting “Options” -> “Edit Columns”

If there is an unavailable variable that you would like to use to filter your searches, or that you feel might be helpful for others, please email sophie.matis@sydney.edu.au to see if that variable / column can be added.

Downloading a filtered data set:

Once you have filtered the sessions to find the scans you are interested in, you can then download that set of data. To do so, select the “Options” dropdown on the top left of the sessions and then select “Download”.

You will then be taken to the download page where you can further specify which files you would like to download. Automatically, every option will be selected, so if you would like to further narrow down your data set, you will want to de-select some of the options.

Continuing on with the previous example, if you were only interested in the Cor 3D T1 scans, you could de-select all the scans under “Scan Types” and then select only those, as illustrated below.

The number in the brackets to the left of the scan type tells you how many sessions have this type of scan.

You can also select which file types you would like to download under “Select Image Data” depending on whether you prefer to work with DICOM or NIfTI.

Finally, you select how you would like the data downloaded and then press “Submit” at the bottom of the screen. When using data from XNAT, it is important not to store it on your local device, as such we recommend you don’t use option 2 for downloading. Once you know which files you would like to download, please refer to these instructions on how to download Downloading files from XNAT and select option 1 or 3 accordingly.