Slicer
This is not a complete article: This is a draft, a work in progress that is intended to be published into an article, which may or may not be ready for inclusion in the main wiki. It should not necessarily be considered factual or authoritative.
3D Slicer is an open source software platform for medical image informatics, image processing, and three-dimensional visualization. Built over two decades through support from the National Institutes of Health and a worldwide developer community, Slicer brings free, powerful cross-platform processing tools to physicians, researchers, and the general public.
IMPORTANT
Never make intense use of Slicer on the login nodes! Submit jobs using the command line whenever possible and if you must visualize your data using the GUI, please do so on an interactive node. Using parallel rendering on the shared login nodes will result in the termination of your session.
Loading Slicer
[name@server ~]$ module load slicer/4.10.1
Using the GUI
Using the Slicer GUI requires X11 forwarding, which you should make sure is enabled.
You can find information on how to connect with MobaXTerm and use X11 fowarding on the Connecting_with_MobaXTerm page.
extension "MIT-SHM" missing
Windows users might encounter an error message similar to this:
Xlib: extension "MIT-SHM" missing on display "localhost:86.0".
It can be fixed by disabling the extension on the cluster:
[name@server ~]$ export XLIB_NO_SHM=1
Use an interactive node
Runtime is limited on the login nodes, so you will need to request a testing job to have more time for exploring and visualizing your data. Additionally, by doing so, you will have access to the 40 cores of each of the nodes requested.
request an interactive job, ie.
[name@server ~]$ salloc --time=1:0:0 --ntasks=2 --x11 --account=def-someuser
this will connect you to a node. Note the --x11 argument, which will enable X11 forwarding on the interactive node.
You can then load Slicer and run it on the interactive node.
[name@server ~]$ module load slicer
[name@server ~]$ Slicer
Once you are done and have closed Slicer, you can terminate the allocation
[name@server ~]$ exit