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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 flavor of DXJupyterlab.

FreeSurfer License Registration

To use FreeSurfer on the DNAnexus Platform, you need a valid FreeSurfer license. You can register for the FreeSurfer license here.

Using the FreeSurfer License on DNAnexus

To use the FreeSurfer license complete the following steps:
  1. 1.
    Upload the license text file to your project on the DNAnexus platform.
  2. 2.
    Launch the DXJupyterlab app using the IMAGE_PROCESSING feature.
  3. 3.
    Once the DXJUpyterlab is running, open your existing notebook (or a new notebook) and download the license file into the FREESURFER_HOME directory, like so:
Python kernel:
!dx download license.txt -o $FREESURFER_HOME
Bash kernel:
dx download license.txt -o $FREESURFER_HOME