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https://wiki.xnat.org/documentation/how-to-use-xnat
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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.
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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).
If you are interested in retrieving a specific subset of data, it can be easier to use filtering rather than the search functionYou should select what data you want to see in your search, you will likely want detailed MR Sessions data as shown below:
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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.
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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.
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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. Then you select option 2 from the final menu “3. Download Data” and submit to download a ZIP file of your selectionsWhen 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.
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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”.
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You then have a number of filtering options to choose from, for this example you would need to select “LIKE”.
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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”.
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Finally, you select how you would like the data downloaded (you will likely just want a ZIP file) and then press “Submit” at the bottom of the screen. Your file will be downloaded with separate folders for each sessionWhen 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.