ARTDock

ArtDock is a Docker image containing Babak Ardekani's Automatic Registration Toolbox for cross-compatibility and ease-of-usage.

Docker Installation

The first step is actually installing Docker. One can easily download and install this from the Docker Desktop page by following instructions for respective platforms.

Building ARTDock

1. Using terminal, change directory with

cd [clone directory]

2. Then, build the dockerfile with

docker build -t artdock .

Until this repo is made availble on DockerHub, this is the only way to build this Docker image.

Running ARTDock

Running with GUI

ARTDock can be called with a GUI using X11 window forwarding. Windows users can use Xming X Server for X11 forwarding, while Mac users can use XQuartz

The remaning portion of this section will show the steps to run art GUI on a Mac, using instructions posted on the page How to show X11 windows with Docker on Mac.

1. Install XQuartz with Homebrew

   brew cask install xquartz
   

2. Open XQuartz with open -a XQuartz, then enable ‘Allow connections from network clients’ in XQuartz's preferences [Mac menu bar > XQuartz > Preferences > Security].

3. Quit and restart XQuartz for these settings to take effect.

4. Allow localhost for X11 forwarding:

   xhost + 127.0.0.1
   

5. Run ARTDock with the -e DISPLAY flag:

   docker run -it --rm \
   -e DISPLAY=host.docker.internal:0  \
   artdock art2  
   

Alternatively, you may execute the bash file with art2gui to run this command on Mac.

Running w/o GUI

While ARTDock is in experimental stages, one can run ARTdock with the following syntax:

docker run -it --rm -v [folder to mount]:[mount point] artdock

This command will activate the container with contents of /[folder to mount] in /[mount point]. The three primary commands included in this Docker images are: 3dwarper, applywarp3d, and acpcdetect.

Example:

One can run automated non-linear registration with the following command:

3dwarper -v -o [mount point]/output/transformed_img.nii -sub /[mount point]/input/subject.nii -trg /[mount point]/input/target.nii

A real transformation commad from activation to transformation is:

docker run -it --rm -v /Users/sid/Downloads/Mouse/data:/data artdock

3dwarper -v -acpc \
-o /data/out/w1t2m8.nii \
-sub /data/same_mice_T1_2/w1t2m8/rrdki_0.nii \
-trg /data/same_mice_T1_2/w1t1m8/rrdki_0.nii