Installation

Quickstart via Neurodesk

QSMxT is available via Neurodesk. Using Neurodesk Play, you can access QSMxT in your browser without any installation.

Once started, QSMxT is available in Neurodesk’s module system and via the applications menu:

Neurodesktop applications menu with QSMxT

Updating QSMxT in Neurodesk

To use the latest version of QSMxT within an older version of Neurodesk, use:

bash /neurocommand/local/fetch_and_run.sh qsmxt 7.2.2 20241029

Docker container

If you prefer to use a Docker container, the following commands will install QSMxT locally:

Windows:

docker run -it -v C:/neurodesktop-storage:/neurodesktop-storage vnmd/qsmxt_7.2.2:20241029

Linux/Mac:

docker run -it -v ~/neurodesktop-storage:/neurodesktop-storage vnmd/qsmxt_7.2.2:20241029

HPC installation

QSMxT can be installed on an HPC or Linux machine using transparent singularity. Transparent singularity installs QSMxT using an Apptainer container and exposes the underlying tools to the host environment, which is necessary for HPCs using PBS Graph or SLURM.

  1. Install or load Singularity or Apptainer on your HPC. Test if it works by executing ‘singularity –version’.
  2. Install the QSMxT container via transparent singularity:
  git clone https://github.com/NeuroDesk/transparent-singularity qsmxt_7.2.2_20241029
cd qsmxt_7.2.2_20241029
./run_transparent_singularity.sh --container qsmxt_7.2.2_20241029.simg
source activate_qsmxt_7.2.2_20241029.simg.sh
  • NOTE: You must have sufficient storage available in $APPTAINER_TMPDIR (by default /tmp), $APPTAINER_CACHEDIR (by default $HOME/.apptainer/cache), and the repository directory to store the QSMxT container.
    1. Check if you have conda installed using ‘which conda’. If it is installed you can skip the first steps of this:
  #Install Miniforge in the current directory. Make sure this directory has enough free space. (skip if conda is already installed)
wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh
bash Miniforge3-Linux-x86_64.sh -b -p ~/miniforge3
source ~/miniforge3/etc/profile.d/conda.sh
export PATH=~/miniforge3/bin/:${PATH}

#create conda environment for qsmxt
conda create -n qsmxt python=3.8
conda activate qsmxt
pip install qsmxt==7.2.2
  1. Run QSMxT commands directly (see using QSMxT). Use the --pbs and --slurm flags with your account string and group to run on an HPCs supporting PBS and SLURM.

Bare metal installation

We recommend the use of software containers for reproducibility and ease of use. However, QSMxT can be installed manually. Please see the detailed instructions for generating the container here.

Older versions and release notes

You can find the software versions and container dates on our Docker page here.

You can find detailed release notes on the GitHub releases page here.