Before using XFSL, you need to organize(or maybe re-organize) your data first.
In XFSL philosophy, each project has a unique folder(where the $PROJECTROOT redirects to in the code), under which are folders for each individual subjects, folder for group analysis, and folders for other files, such as behavioral data etc. Detailed in the attached picture.
Under each subject's folder, there should be two folders: data and analysis. Please save all NIFTI raw data into the data folder, such as structural MRI data (MNPRAGE/3D, DTI) and functional data.