FreeSurfer in DXJupyterLab

Learn how to use FreeSurfer in DXJupyterLab.
A license is required to access DXJupyterLab. Contact [email protected] 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