Hi, I've just recently started using batch scripts to run my SPM analyses instead of the GUI, and I've come across a problem. I found that when running the second level analysis on exactly the same first level files and with identical parameters, the scripted analysis results in much smoother activations and larger resels, altering the cluster sizes reported. I'm not sure how this has come about, or where I can amend this setting in either the script or in the GUI batch interface. Is there some default that I have failed to specify in my script?
Thanks for your help,