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Overview of systems
Listed below are some of the different systems that will be useful to understand and use for neuroimaging analysis. The descriptions of the platform's capabilities are written specifically for FRONTIER neuroimaging projects.
1. XNAT
XNAT is an imaging-based platform that is currently used to archive and store raw scans. All original MRI sequences (T1, DWI, fMRI, etc.) are stored in XNAT as a DICOM and NIfTI format. XNAT is used for storing raw scans, viewing scans, and downloading scans in preparation for pre-processing.
User guide: XNAT user guide
Access: You can log in to XNAT, here, using your unikey. Please contact Sophie, James or Ramon for access to the Frontier project if you can’t see it in XNAT.
2. Research data store (RDS)
The RDS is where you should store all project information and data. All information in the RDS is backed up and securely stored. However, no heavy processing/analysis can be conducted on the RDS.
User guide: RDS user guide
Registration: Contact supervisor to create a dashr project.
Access: You can access RDS via terminal or by mapping a network drive. See here for more information.
3. Artemis
Artemis is a high-performance computing (HPC) cluster that is used for advanced computing tasks, such as modelling, batch data processing and analysis. All neuroimaging processing and analysis must be conducted on Artemis on the /scratch/project folder. However, you should not store data here in the long term, as this space is only for active processing and is not safely secured/backed up. Therefore, after the processing and analysis of a project is completed, this data should be moved into the RDS and deleted from scratch.
User guide: Artemis user guide
Registration: Contact supervisor to create a dashr project.
Access: You can access Artemis via terminal, ssh clients or graphical login nodes.
Artemis training calendar: https://www.sydney.edu.au/research/facilities/sydney-informatics-hub/workshops-and-training/training-calendar.html
Artemis training recorded: https://sydney-informatics-hub.github.io/training.artemis.introhpc/
Data transfer training: https://sydney-informatics-hub.github.io/training.artemis.rds/
4. ARGUS
ARGUS is a GPU-powered Linux virtual research desktop. In simpler terms, you can treat ARGUS as a normal point and click computer that is connected to the University network. You can use ARGUS to run programs that have a graphical aspect (e.g. fsleyes, mrview). Window users can also use this as a method to access Artemis via the ARGUS terminal (mac users can already access Artemis using the terminal on their own computer).
Frontier maintains a shared desktop that everyone within Frontier can use. Multiple people can access the shared desktop at the same time.
Each supervisor (Fiona, Muireann and Ramon) also maintains a private desktop. Each private desktop can only hold one user at any one time. To gain access to these desktops, please contact the relevant supervisor.
User guide: ARGUS user guide
Registration: Contact the relevant supervisor to gain access to their desktop.
User access: uniconnect.cloud.com
Admin access: citrix.cloud.com
To understand how all of these systems are relevant to the general neuroimaging process, click here.