FreeSurfer in DXJupyterLab
Learn how to use FreeSurfer in DXJupyterLab.
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 at the FreeSurfer registration page.
Using the FreeSurfer License on DNAnexus
To use the FreeSurfer license complete the following steps:
Upload the license text file to your project on the DNAnexus Platform.
Launch the DXJupyterLab app using the
IMAGE_PROCESSING
feature.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
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