Hi Roger,

The size(B)=[1,0] error indicates that you have no ROIs defined (or left after the preprocessing step) for the first-level analysis of some subject (but curiously not for the first subject, otherwise the program would skip that portion of the code). While I am not exactly sure how this could happen, I would probably suggest to re-run the Setup/Preprocessing/FirstLevel steps making sure to overwrite any already-analyzed subjects/seeds (select the proceed for all subjects/seeds option when prompted). This is just to make sure all of the subjects have been processed using the same combination of ROIs. Also I would probably suggest checking whether in the Preprocessing step you are perhaps entering all of the ROIs into the confounds list (this could be one possible reason why you could have no remaining ROIs to analyze); typically the proper selection in the confounds list is to add to this list only the White/CSF ROIs, as well as the realignment parameters and potentially task-related effects. 

Please let me know if this helps. I might be missing something obvious so if none of this helps please send me your conn_*.mat file so that I can have a quick look at it to see if I can figure out what might be going on. 

Best
Alfonso
Originally posted by Roger Beaty: