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Downloading your files from XNAT into RDS or Scratch using the XML:
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You can either download your files using the XNAT desktop client (Option 1 below) or by submitting a job to the data transfer que in Artemis (Option 2 below). If you would like to download straight into scratch, you will need to do this through Artemis (Option 2). Using the desktop client may be simpler or more intuitive, however, using Artemis has many upsides. Firstly, you don’t need to be using your computers own resources to download. Secondly, XNAT downloads the scans with an impractical folder structure + naming convention (see below).
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Using Artemis will result in a better naming convention and folder structure (as below).
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Option 1: XNAT Desktop Client (only to RDS).
If you have the RDS mapped to your desktop (you can find out how to do that here if you haven’t already: Research Data Store) you can use the XNAT Desktop Client to download directly into an RDS folder. Once you have downloaded and installed the client (https://download.xnat.org/desktop-client/), you’ll need to open it and enter your XNAT credentials. You can save these so that you only need to enter your password on subsequent logins.
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You can track the progress of the download in “Transfer History”.
Option 2: Submit a job through Artemis.
1. Move the XML file from your local downloads to an Artemis accessible location
The XML file is the file that is downloaded after selecting option 3 on the XNAT download page. This is the option you will need to select to download the data via Artemis. You can easily just drag and drop the file into your RDS folder it if you have it mapped to your local device (Research Data Store). You can also move the XML straight into Artemis from your downloads folder if this is quicker for you.
2. The PBS script
To get Artemis to download scans from XNAT, we can use a tool called xnat-get from a collection of command line tools: XNAT-Utils (Command line client XNAT-Utils (Artemis)). To do so we will need to submit it as a job request with a pbs script. To create the pbs script copy and paste the below into a text editor:
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The first argument is the location and file name of the XML file.
The second argument (after --target) is the location you would like the XNAT files downloaded to.
Apply any options you would like, outlined in the comments of the script. **Please note the --convert_to options are not currently working.
Now your script is ready to go. Make sure to save it with the extension as pbs and that it’s Unix compatible.
3. Submit the Job in Artemis
First, navigate to your login node (the directory you are in when you first log in to Artemis). If you haven’t used xnatutils before, you will need to create an environment for it by doing the following. Please enter each line one at a time:
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