FreeSurfer in DXJupyterLab

Learn how to use FreeSurfer in DXJupyterLab.

DXJupyterLab is accessible to all users of the UK Biobank Research Analysis Platform and the Our Future Health Trusted Research Environment.

A license is required to access DXJupyterLab 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 and IMAGE_ML features of DXJupyterLab. The IMAGE_ML feature provides additional AI/ML capabilities through the MONAI frameworks alongside FreeSurfer.

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 DXJupyterLab app and specify either the IMAGE_PROCESSING feature (for image processing only) or the IMAGE_ML feature (for image processing with additional AI/ML capabilities).

3. Once DXJupyterLab 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