neurodesk

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

To post an inquiry, please select the "Discussions" tab above (https://github.com/NeuroDesk/neurodesk/discussions), and press the "New Discussion" button. Alternatively, you may contact Steffen Bollmann (https://github.com/stebo85), Oren Civier (https://anif.org.au/team/oren-civier/) or Aswin Narayanan (https://github.com/aswinnarayanan).

2-minutes tutorial video from OHBM 2021: https://www.youtube.com/watch?v=JLv_5fycugw

Neurodesk website: https://neurodesk.github.io/

Run Desktop with neurodesk installed in a Docker container

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

Linux

Requirements:

python3.6+
- Recommend using Miniconda (https://docs.conda.io/en/latest/miniconda.html#linux-installers)
- With virtual conda environments (https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html)
singularity (https://sylabs.io/guides/3.5/user-guide/quick_start.html)
lmod (https://lmod.readthedocs.io/en/latest/)
git

Initial install

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 pip3 install -r neurodesk/requirements.txt to install pre-requisite python packages

[Option 1] 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 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

[Option 2] For Lxde desktops

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

[Option 3] 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

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
sudo apt-get install lxde to install LXDE desktop in WSL
Reboot
sudo apt-get install xrdp to install XRDP in WSL
Open /etc/xrdp/xrdp.ini Change port=3389 to port=3390 and save
Run echo startlxde > ~/.xsession

Running

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

Funding

Thank you to Oracle for Research for providing Oracle Cloud credits and related resources to support this project.

This project is supported by an Australian Research Data Commons (ARDC) Platform project “Australian Electrophysiology Data Analytics PlaTform (AEDAPT)”.

sybernix/neurodesk