I am running VBM to compare three groups (two patient, one control). 

My groups are unequal sizes so I am using a subset of two groups to match the smallest group. I want to add the additional subjects back in for the fslvbm_3_proc command. 

So, I have added the additional scans to the directory and ran flvbm_1_bet on them. I have created the design matrix and contrast files with all subjects included. 

When I run fslvbm_3_proc, a list of all subjects appears in the terminal but, only the subjects included in the template are actually included the GM_mod_merg* files. 

Have I missed a step? Could someone help me understand why my steps are not letting the command know that I have added subjects so I can run randomise?

Thank you very much in advance!

Chiara