> For the complete documentation index, see [llms.txt](https://documentation.dnanexus.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://documentation.dnanexus.com/user/jupyter-notebooks/running-dxjupyterlab/freesurfer-in-dxjupyterlab.md).

# FreeSurfer in JupyterLab

{% hint style="info" %}
JupyterLab is accessible to all users of the UK Biobank Research Analysis Platform and Our Future Health Trusted Research Environment.

A license is required to access JupyterLab on the DNAnexus Platform. [Contact DNAnexus Sales](mailto:sales@dnanexus.com) for more information.
{% endhint %}

## About FreeSurfer

​FreeSurfer is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies.

The FreeSurfer package comes pre-installed with the `IMAGE_PROCESSING` [feature of JupyterLab](/user/jupyter-notebooks.md#feature-options).

## FreeSurfer License Registration

To use FreeSurfer on the DNAnexus Platform, you need a valid FreeSurfer license. You can register for the FreeSurfer license at the [FreeSurfer registration page](https://surfer.nmr.mgh.harvard.edu/registration.html).

## Using the FreeSurfer License on DNAnexus

To use the FreeSurfer license, complete the following steps:

1. Upload the license text file to your project on the DNAnexus Platform.
2. Launch the JupyterLab app and specify the `IMAGE_PROCESSING` feature.
3. Once JupyterLab is running, open your existing notebook (or a new notebook) and download the license file into the `FREESURFER_HOME` directory.

The commands to download the license file are as follows:

* Python kernel: `!dx download license.txt -o $FREESURFER_HOME`
* Bash kernel: `dx download license.txt -o $FREESURFER_HOME`


---

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