Added --bad and save analysis info in --setup_second
Added --bad and save analysis info in --setup_second

Subjects can be removed from second-level analysis with --bad and
information about the analysis is saved to info.txt in setup_second.

KuperbergLab/MRI_scripts,KuperbergLab/MRI_scripts,KuperbergLab/MRI_scripts,KuperbergLab/MRI_scripts