FieldTrip is Open Source software and you can use it freely under the GPL license without other restrictions. However, we do appreciate getting acknowledged for the contribution of our project to your research. Please note that your references to FieldTrip also help us to ensure continued funding for the FieldTrip project, code development and support.
Please cite the FieldTrip reference paper when you have used FieldTrip in your study.
Robert Oostenveld, Pascal Fries, Eric Maris, and Jan-Mathijs Schoffelen. FieldTrip: Open Source Software for Advanced Analysis of MEG, EEG, and Invasive Electrophysiological Data. Computational Intelligence and Neuroscience, vol. 2011, Article ID 156869, 9 pages, 2011. doi:10.1155/2011/156869.
Publications that describe (some of) methods that are implemented are listed here.
You can find publications that refer to FieldTrip on Google Scholar.