How do I include a FreeSurfer license when I run fMRIPrep in Flywheel?
In order to run the FreeSurfer gear or the fMRIPrep gear (which uses FreeSurfer in it's pipeline), you will need to obtain a license. Obtaining a license is free on the FreeSurfer website.
The FreeSurfer license comes in the form of a text file typically named `license.txt`. Upload this file as an attachment to your Project page.
After it's been uploaded it will appear in the attachment list as shown.
Now when you want to run the fMRIPrep gear, you will be able to select the license file. On the Run Gear modal, you will be asked to select a freesurfer_license as an input. Click on `Choose Input`.
This will bring you to the file selector. Since we uploaded the license file as a project attachment, we'll need to go up to that level in the hierarchy by clicking on the project name as shown in the screenshot.
You should then see your license file and be able to select it.
Once selected, the file name will show up as the selected input of the gear, and you should be able to start your fMRIPrep job.