neurodesk

A flexible, scalable, and easy to use data analysis environment for reproducible neuroimaging

For inquiries, please click on the "Discussions" tab above. Alternatively, you may contact Steffen Bollmann (https://github.com/stebo85), Oren Civier (https://github.com/civier) or Aswin Narayanan (https://github.com/aswinnarayanan).

Run Desktop with neurodesk installed in a Docker container

Quickstart: https://github.com/NeuroDesk/vnm/

Linux

Requirements:

• python (https://docs.conda.io/en/latest/miniconda.html#linux-installers)
• singularity (https://sylabs.io/guides/3.5/user-guide/quick_start.html)
• lmod (https://lmod.readthedocs.io/en/latest/)

Inital install

command line mode - For non-desktop experience (e.g. running on an HPC)

If running on cli only ...

• Load singularity and for best performance it should be 3.x e.g. module load singularity/3.5.0
• Run git clone https://github.com/NeuroDesk/neurodesk.git 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 neurodesk to change into the directory
• Run bash build.sh --cli to install in cli mode
• Run bash containers.sh for installing indiviual containers or bash containers.sh --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.
• 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

For Lxde desktops

If running on an lxde desktop... Run bash build.sh --lxde --edit

For Mate desktops

Run bash build.sh --init (or bash build.sh --lxde --edit)
lxde/mate: Mate
installdir: Where all the neurodesk files will be stored (Default: ./local)
appmenu: The linux menu xml file. (Usually /etc/xdg/menus/****-applications.menu)
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 install.sh to install
Creates symlinks to menu files in installation dir

sudo bash uninstall.sh to uninstall
Removes symlinks

To update

Run git pull
Run bash build.sh
install.sh does not need to be run again

To download all containers

Run bash containers.sh --all

Windows

WSL (w/ Ubuntu + LXDE)

For more information on WSL: https://docs.microsoft.com/en-us/windows/wsl/

Setting up

1. Setup WSL2 using the following instructions (Ubuntu 18.04 recommended)
   https://docs.microsoft.com/en-us/windows/wsl/install-win10
   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

Running

1. sudo service xrdp start to start xrdp server
2. Open Microsoft Remote Desktop Connection in Windows host
3. Connect to localhost:3390
   An LXDE desktop should as a Microsoft Remote Desktop
4. Follow Linux guide from here on

Acknowledgments