Neurodesk Singularity Containers

Our docker containers are converted to singularity containers and stored on Object storage.

Download Singularity Containers

First get an overview of which containers are available as Singularity containers:

curl -s

assign the container name to a variable:

export container=itksnap_3.8.0_20201208

Then download the containers. An easy way is to use CURL (e.g. downloading from the US location):

curl -X GET${container}.simg -O

or from australia

curl -X GET${container}.simg -O

or from europe

curl -X GET${container}.simg -O

A faster way is pulling from multiple storage locations at once using aria2:


Singularity Containers and GPUs

Some of our containers contain GPU-accelerated applications. Here is an example that tests the GPU accelerated program eddy in FSL:

curl -X GET -O
git clone
singularity shell --nv fsl_6.0.5.1_20221016.simg
cd gpu_test/etest/

Transparent Singularity

The singularity containers can be also be used in combination with our Transparent Singularity Tool, which wraps the executables inside a container to make them easily available for pipelines. More information can be found here:

one example to do this is:

curl -s
export container=itksnap_3.8.0_20201208
git clone ${container}
cd ${container}
./ ${container}
Last modified September 25, 2023: update to new version 2023-09-20 (088e1f8)