FreeSurfer in DXJupyterLab
Learn how to use FreeSurfer in DXJupyterLab.
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.To use FreeSurfer on the DNAnexus Platform, you need a valid FreeSurfer license. You can register for the FreeSurfer license here.
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 using the
IMAGE_PROCESSINGfeature. - 3.Once the DXJUpyterlab is running, open your existing notebook (or a new notebook) and download the license file into the
FREESURFER_HOMEdirectory, like so:
Python kernel:
!dx download license.txt -o $FREESURFER_HOME
Bash kernel:
dx download license.txt -o $FREESURFER_HOME
Last modified 1mo ago