XNAT installation

Create a user xnat and add him to the docker group. Do the following as xnat using its home as a core of the environment.

Follow dockerizet XNAT instructions. Checkout the configuration directory and copy default environment.

From the setup directory, link xnat-data and postgres-data out from the configuration and into the storage area - to split configuration in home from storage in data.

sudo mkdir /data/xnat-data
sudo mkdir /data/postgres-data
sudo su xnat
cd ~/xnat-docker-compose
ln -s /data/xnat-data
ln -s /data/postgres-data

Some modifications might be necessary in docker-compose.yaml. For example, for XNAT to report on port 8090, lines 56 and 57 of the original should be changed to:

56 ports:
57      "8090:80"

and the port number should be added to proxy_redirect in nginx/nginx.conf, line 52 and 53

52     proxy_redirect                      http://xnat-web:8080 $scheme://localhost:8090;
53      proxy_set_header Host               $http_host;

However, should you want to use the default port, no modification should be required.

Update XNAT configuration

• When loging in as admin to XNAT, make sure you update the SMTP settings. In my case, I had to switch to port 587, and turn identification and SSL tunneling to ON.

• In Administration->Site administration->DICOM SCP Receivers set AET name of the PACS to the desired value. In my case I used RUBENS as the AET name.

• Still testing the best option to merge series. Right now, I've set Prevent Cross-modality Session Merger to disabled (the text says merging is allowed) under Miscallaneous.

• Edit Project Routing. Normally XNAT looks at a set of predefined fields to match data and project. I basically want all data to go into a single project, and a cludge to do so is putting (0010,0020):^([0-9]+)/[0-9]+$:1 t:^(.*)$ r:IRAEMM into Site Administration -> Session Upload & Anonymization -> Project Routing (Site Wide) configuration window. This routes anything that matches N/M where N and M are (multi-digit) numbers to IRAEMM project.

XNAT-OHIF

Install yarn:

curl -sS https://dl.yarnpkg.com/debian/pubkey.gpg | sudo apt-key add -
echo "deb https://dl.yarnpkg.com/debian/ stable main" | sudo tee /etc/apt/sources.list.d/yarn.list
sudo apt update
sudo apt install yarn

Get OHIF XNAT and compile

git clone --recurse-submodules https://bitbucket.org/icrimaginginformatics/ohif-viewer-xnat-plugin.git
cd ohif-viewer-xnat-plugin
git submodule update --init --recursive
build_plugin.sh