This the multi-page printable view of this section. Click here to print.

Return to the regular view of this page.


For more advanced users who prefer a command-line interface

Neurocommand requires a Linux host machine, virtual machine or WSL for Windows.

1 - Getting Started

Select your operating system to get started with neurocommand.

1.1 - Linux

Install neurocommand on Linux

Ways of using Neurocommand in Linux:

  1. You can use Neurocontainers directly via CVMFS:
  2. or you can install Neurocommand as described here:




command line mode (e.g. running on an HPC or CVL)

  • Load singularity and for best performance it should be 3.x e.g. module load singularity/3.5.0
  • Load or install aria2 to optimize the download performance of our containers e.g. module load aria2c
  • Run git clone to clone the repository - make sure to clone this to a directory with enough storage, write permissions and NOT a symbolic link (to be sure run cd `pwd -P`)!
  • Run cd neurocommand to change into the directory
  • Run pip3 install -r neurodesk/requirements.txt --user to install pre-requisite python packages
  • Run bash --cli to install in cli mode
  • Run bash for installing indiviual containers or bash --all for installing all containers
  • Run module use $PWD/local/containers/modules/ to add the containers to your module search path. Add this to your .bashrc if working. When adding to your .bashrc you will need to replace $PWD to point to the correct path, i.e. module use ~/neurocommand/local/containers/modules/.
  • Run ml avail to see the installed containers at the top of the list (neurodesk containers will take preference over system modules with the same name). - If a container is not yet there run ml --ignore_cache avail
  • Every time you start a new shell you will need to run conda activate neurocommand. Unless you added it to your .bashrc, you will also need to run module use PathToYourContainers.

For Lxde desktops

If running on an lxde desktop… Run bash --lxde --edit

For Mate desktops

Run bash --init (or bash --lxde --edit)
lxde/mate: Mate
installdir: Where all the neurocommand files will be stored (Default: ./local)
appmenu: The linux menu xml file. (Usually /etc/xdg/menus/****
appdir: Location for the .desktop files for this linux desktop (Usually /usr/share/applications)
deskdir: Location for the .directory files for this linux desktop (Typically /usr/share/desktop-directories)

For desktop menus:

sudo bash to install
Creates symlinks to menu files in installation dir

sudo bash to uninstall
Removes symlinks

To update

Run git pull
Run bash # this updates the neurocommand but not the modules does not need to be run again to update containers go into the neurodesktop directory and run bash Choose the module you want to update for example you want to update mrtrix3/3.0.2 module with the eddy_cuda fix: ~/neurocommand/local/ mrtrix3 3.0.2 20221108 mrview $@

To download all containers

Run bash --all

1.2 - Windows

Install neurocommand on Windows

WSL (w/ Ubuntu + LXDE)

For more information on WSL:

Setting up

  1. Setup WSL2 using the following instructions (Ubuntu 18.04 recommended) Proceed until a Ubuntu bash shell is available from the Windows Host
    Run the remaining commands in the Bash shell
  2. sudo apt-get install lxde to install LXDE desktop in WSL
  3. Reboot
  4. sudo apt-get install xrdp to install XRDP in WSL
  5. Open /etc/xrdp/xrdp.ini Change port=3389 to port=3390 and save
  6. Run echo startlxde > ~/.xsession


  1. sudo service xrdp start to start xrdp server
  2. Open Microsoft Remote Desktop Connection in Windows host
  3. Connect to localhost:3390
  4. In the next login page, leave Session as Xorg. Enter your WSL username and password and click OK
  5. This should open an LXDE Linux Desktop environment. Follow Linux guide from here on