FreeSurfer in JupyterLab

Learn how to use FreeSurfer in JupyterLab.

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 for more information.

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.

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.

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