* What is the difference between the Project Directory and a Session?

In FSFAST the Project directory is were you run all of the FSFAST commands from. A session is the folder where all the data from a given visit of a given subject are stored. All the sessions will be located in the Project directory.

* What gets stored in a Run directory?

When you first set up the data for FSFAST processing, the raw data (eg, f.nii.gz) get stored in the Run directory as well as the paradigm files (ie, stimulus timing). The output of pre-processing will also be stored in the Run directory. The directory structure is set up as: Project/Session/FSD/Run. The Run directory is always a 3-digit, zero-padded number (eg, 003).