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FreeSurfer License File to Run a FreeSurfer or fMRIPrep Gear


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.

There are 3 ways to include a FreeSurfer License when running fMRIPrep in Flywheel:

  1. Input file
  2. Configuration option
  3. Project context

Instruction Steps

Input File

Upload license.txt 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.


Configuration Option

In recent gears you can copy the text from the license.txt file and paste it into configuration as shown here for BIDS fMRIPrep. After choosing which gear to run, click on "Configuration":

Screen_Shot_2019-12-18_at_3.39.57_PM.png then scroll down to find "FREESURFER_LICENSE" (here the configuration option is called "gear-FREESURFER_LICENSE"), and paste in the text as shown:


You can select and copy all of the text from the license.txt file at once and when you paste it, it will be space separated. Then set other configuration options, inputs, etc., and run the gear.

Project Context

Neither of the above options are used to provide the FreeSurfer license, the gear will look for it in the project "info" metadata. To include a FreeSurfer license this way, click on the project's "Information" tab and then on the + to add "Custom Information":


Select "String" to add a key-value pair where the value is a string:

Screen_Shot_2019-12-18_at_3.17.49_PM.png then:

  1. type exactly, "FREESURFER_LICENSE" in all caps and with an underscore between the words in the "key" field and
  2. copy the text from your license.txt file and paste it into the "value" field:


Like this:


Finally, press "Save".

Note that if license information is provided in more than one of the ways described above, the gear will choose the license in this order:

  1. Input file
  2. Configuration option
  3. Project context