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General Neuroimaging Process

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After understanding the general function of each system, you will need to understand how to use these systems for a neuroimaging project.

*You can skip the first 3 steps if you are comfortable with transferring files from XNAT directly to Artemis using command line.

1. Download files from XNAT to local computer/ARGUS

Raw image files (DICOM and niftii) of FRONTIER scans are currently indexed on XNAT. You will need to search and select the relevant scans and download them into your local computer or ARGUS. If you do download into ARGUS, please delete these scans as soon as they are uploaded to the RDS (step 2).

XNAT guide

 

2. Transfer files from local computer/ARGUS to RDS/Artemis

After downloading the scans onto your local computer or ARGUS, you will need to transfer them to RDS (secure storage). Remember to delete the scans from your local computer/ARGUS once this step has been completed. You can access both the RDS and Artemis scratch folder using the HPC.

Transferring between local computer and HPC.

  • On the HPC, there are two main folder locations to be aware of:

    • /scratch : used for processing/analysis

    • /rds : used for storage

3. Transfer files from RDS to Artemis (/scratch)

Scans need to be copied into /scratch for processing/analysis. Note: Artemis is NOT to be used for long term storage (as it is not secure/backed up).

Transferring data between HPC and RDS using dtq.

  • This method can also be used to transfer files between 2 RDS projects.

4. Run processes on Artemis via job submission

You can submit jobs on Artemis (via terminal) for computing, processing and analysis. Data can also be visualised on Artemis using the graphical login node.

Job submission

Visualising analysis using graphical login node.

 

5. Save data on RDS & delete files off Artemis.

After the project is completed, copy your files onto the RDS for long term storage and delete all files in Artemis to clear up space. You can delete files as you usually do on a computer (e.g. right-click the file and click delete/remove), or you can use the rm command on the command line.

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