FreeSurfer (NeuroImaging)

Overview and Setup  

FreeSurfer is an open source package for the analysis and visualization of structural, functional, and diffusion neuroimaging data from cross-sectional and longitudinal studies.

To access the OOD web portal, please refer to our Getting Started with Open OnDemand documentation page. Once logged into the portal, you can launch FreeSurfer from under the Neuroimaging header.

Configuring FreeSurfer  

To get started, connect to OOD and choose FreeSurfer from the Neuroimaging header.

In the submission form, you can choose the account, partition, the length of your job, the number of nodes, the number of cores per node, memory per core (GB), and the node type. Unless you have a specific reason, we recommend leaving Path to License.txt, Subject Directory, and Command to run as listed in the form.

  Note

• For account, put whatever group account you’re associated with. If you do not have a group account, use free.
• The partition is always ood
• Node type is any

After you click “Launch”, a new session will be queued. Once the session is active your page will appear as follows:

When launching FreeSurfer, you’ll notice two key sliders: compression and image quality. These settings can greatly affect your overall experience. To optimize performance, we suggest cranking up the image quality slider to the highest setting (9). If you’re not satisfied with the result, it’s easy to close the tab, adjust the sliders, and start again. Experimentation is key to finding the perfect balance between performance and visual quality for your environment.

Using FreeSurfer  

Click on “Launch FreeSurfer” to begin using FreeSurfer. Once you have entered your session, you should see the FreeSurfer page below:

This is a typical FreeSurfer interface that should be familiar to frequent users.