This question is out of scope for this forum.

If you want to automate FSL, contact the FSL jiscmail forum. If you are comfortable with shell scripting, look at the FSL scripting tutorial
 https://open.win.ox.ac.uk/pages/fslcourse/website/#CourseMaterials

If you want to automate using Matlab and SPM, contact the SPM jiscmail forum.

If you want to know how to automate tasks with Python, consider the neurostars forum.