swinburne_tools

Tools specific to users associated with Swinburne University of Technology

Creating a Nectar VM and connecting to the Ozstar filesystem

Go to https://desktop.rc.nectar.org.au/home/

Select 'Login VIA AAF (Australia)' or 'Australia Access Federation'

Select your organisation

Login (if necessary)

Select 'Neurodesktop' from the 'Desktop Library' (you may have to scroll down to see it)

Click '+Create Desktop'

Keep the 'Default zone' and click 'Create'

...wait....

Click 'Open Desktop'

If you get a pop-up window 'See txt and images copied to the clipboard', click 'Allow'.

Once the VM has started, click on the 'LXTerminal' icon at the bottom left corner of the browser window.

Run the following line in the terminal (use Ctrl-Shift-v to paste), and enter your ozstar username and password when prompted:

curl -Ls https://raw.githubusercontent.com/SwinburneNeuroimaging/swinburne_tools/main/ozstar_setup.sh > /tmp/tmp.sh; bash /tmp/tmp.sh

This only has to be run once when the virtual machine is created.

Sometimes the connection to the ozstar filesystem will be dropped (this will happen if the machine gets 'shelved' for instance). You can run the command

reconnect_ozstar

in a terminal to reconnect to ozstar at any time.

Using the mne coreg utility

1. This first step only needs to be done once on a new virtual machine. Click on the menu button on the bottom left corner of the screen and navigate to the 'mneextended 1.1.0' link.

Clicking on this will open a terminal and a new container will be downloaded. When this has finished, close this terminal.

2. Open a new terminal (see 'LXTerminal' above) and copy and paste the following:

   apptainer  shell --bind /fred,/dagg/public/neuro,/home /cvmfs/neurodesk.ardc.edu.au/containers/mneextended_1.1.0_20220819/mneextended_1.1.0_20220819.simg
   

3. Then copy and paste the following:

   source /opt/miniconda-4.7.12/etc/profile.d/conda.sh
   conda activate mne-extended
   

4. Finally, start the mne coregistration gui with the following, where SUBJECTS_DIR should be something like /fred/ozxxx/freesurfer/subjects

   mne coreg -d SUBJECTS_DIR
   

   You can also do mne coreg --help for other command line options. [Note this can take a long time to start]