3D Slicer is a multi-platform, free open source software (FOSS) for visualization and image computing.

3D Slicer is available on the TCHPC clusters (lonsdale, parsons and iitac).

Loading the module

To enable Slicer in your path, run the following:

module load apps Slicer

Submitting a Slicer job

Slicer is an interactive GUI tool, so you must submit an interactive job to the queue.

For example, if you're connect from a Linux desktop, use the following to get a SLURM allocation on the interactive 'application' queue for 2 hours, where TCD_XX_YYYYY is your TCHPC project id:

salloc -N 1 -p application -t 2:00:00 -U TCD_XX_YYYYY

Now ssh to the allocated node:

ssh -Y $SLURM_NODELIST

Load the module, and run Slicer:

[paddy@lonsdale-n144 ~]$ 
[paddy@lonsdale-n144 ~]$ module load apps Slicer
[paddy@lonsdale-n144 ~]$ Slicer3