Merge pull request #65 from MaastrichtU-IDS/SeunDev

Add Freesurfer documentation to the dsri website

website/docs/deploy-neurodocker.md

@@ -19,6 +19,39 @@ In this page we will show you how to generate a Docker image with popular Neuros
 
 ::: 
 
+## JupyterLab with FreeSurfer
+
+Start a JupyterLab container with Freesurfer pre-installed providing admin (`sudo`) privileges to install anything you need from the terminal (e.g. pip or apt packages)
+
+When instantiating the template you can provide a few parameters similar to the standard JupyterLab, such as:
+
+* **Password** to access the notebook
+* Optionally you can provide a **git repository** to be automatically cloned in the JupyterLab (if there is a `requirements.txt` packages will be automatically installed with `pip`)
+* **Docker image** to use for the notebook (see below for more details on customizing the docker image) 
+* Your **git username and email** to automatically configure git
+
+The DSRI will automatically create a persistent volume to store data you will put in the `/home/jovyan/work` folder (the folder used by the notebook interface). You can find the persistent volumes in the DSRI web UI, go to the **Administrator** view > **Storage** > **Persistent Volume Claims**
+
+<img src="/img/screenshot-freesurfer.png" alt="Deploy Freesurfer" style={{maxWidth: '100%', maxHeight: '100%'}} />
+
+You can also link your git repository to the project for automatic deployment see [using git in JupyterLab](https://dsri.maastrichtuniversity.nl/docs/deploy-jupyter#-use-git-in-jupyterlab)
+
+This can also be deployed using Helm from the terminal, the steps are:
+
+```bash
+helm repo add dsri https://maastrichtu-ids.github.io/dsri-helm-charts/
+helm repo update
+helm install freesurfer dsri/jupyterlab \
+  --set serviceAccount.name=anyuid \
+  --set openshiftRoute.enabled=true \
+  --set image.repository=ghcr.io/maastrichtu-ids/jupyterlab \
+  --set image.tag=freesurfer \
+  --set storage.mountPath=/root \
+  --set password=changeme
+oc get route --selector app.kubernetes.io/instance=freesurfer --no-headers -o=custom-columns=HOST:.spec.host
+```
+Log in to the corresponding jupyter notebook and start the terminal, then enter `freesurfer` as a command
+
 ## FreeSurfer and FSL
 
 Generate a `Dockerfile` with: