This is a web based interactive tool to register MRI volumes to the Marmoset Atlas.

Users can load and visualize their MRI volumes (NIfTI-1 format), interactively reorient them (to allow correct registration), then submit for registration & transformation, and finally retrieve their image volume transformed in the Atlas space.

It is implemented following a multi-container architecture, since actual registration process are intended to run remotely, but it can also be used in "Desktop" mode where all components run on the same machine.

• For linux Users:
  git and docker

• For macOS Users:
  git and Docker Desktop

• For Windows Users:
  wsl2 and Docker Desktop

Important note:

Be sure that you and your organization comply with the licensing terms of Docker, especially if you are intending to use Docker Desktop.

see:

• https://www.docker.com/pricing/faq/#subscriptionandlicensing
• https://www.docker.com/legal/docker-subscription-service-agreement/

AbART is run under WSL (Windows Subsystem for Linux), allowing to use the same commands as the Linux and macOS ones (described in next section).
Therefore, a few extra steps are necessary to properly setup wsl and Docker Desktop, as follow:

• Install wsl (see https://docs.microsoft.com/en-us/windows/wsl/install), then set default version to 2 (wsl --set-default-version 2).

• Then install a linux distro from Microsoft store (https://aka.ms/wslstore). Note: Since Docker WSL integration relies on glibc, we recommend to use Ubuntu 22.04LTS over the lighter Alpine distro that won't work by default for our purpose.

• Set the linux distro including glibc as the default one (e.g. wsl --set-default Ubuntu-22.04), and ensure that Docker integration WSL with default distro is enabled (see https://docs.docker.com/desktop/windows/wsl/#enabling-docker-support-in-wsl-2-distros).

• Note: Several reboots might be necessary after installation of the different components.

• Start a new terminal running the default distro (shortcut [Windows]+R, then type wsl),

• ( Depending on the distro used, git needs to be installed if not shipped by default. )

• Execute the following commands in at the wsl terminal prompt.

1. clone this repo to get the scripts :

#shallow clone this repo
git clone --depth 1 https://github.com/cau-riken/abart.git

# pull published images before starting 
sudo docker pull rikencau/abart-worker:latest
sudo docker pull rikencau/abart-manager:latest
sudo docker pull rikencau/abart-ui:latest

2. Start the Docker stack :

#go to the cloned repo directory
cd abart
./start.sh

Notes :

• the UI should automatically open in your web-browser, at this url: http://localhost:9090/index.html
• The containers can be stopped by pressing [Ctrl]+[C] key in the terminal window.
• Manager process will produce logs on the terminal console while it is running.

Tested configurations:

• Linux Ubuntu 22.04lts, Docker Engine v20.10.8 / Firefox 100 & Chromium 101.
• macOs Big Sur 11.6.6, Docker Desktop v4.8.2 (Docker Engine v20.10.14) / Firefox 91.9.1esr & Chrome 101 & Safari 15.5, but for performance reasons, the use of Safari is not recommended.
• Windows 10.0 (build 19043), Docker Desktop v4.9.0 (WSL2) / Firefox v101.0.1 & Edge v102.0.1245.39