I am working with a group of students through analyzing the Stroop data on openneuro.org. While I can use flirt from the gui in one step to coregister the functional to anatomical data for any one participant, some students only ever get the mat file. I’m having them use the command line flirt to then apply the transformation matrix file. However, there is not documentation that explains why someone would only get a transformation matrix while others get the matrix and the transformed functional data. I have a slightly older version of FSL (5.0.10), could that be a factor?