Changes to how masks are initialized + various small option group changes.

1. initializeInputFiles now takes an optional mask directory as an argument. If the directory is specified, there are three options:
   a. If one mask is in the directory, file handlers are initialized with the same mask for all brains.
   b. If multiple masks are in the directory, they are matched with the appropriate brain according to their name. (Names must be similar.)
   c. If the number of masks in the directory does not match the number of brains, the program exits with an error message in the log file.
This masking logic was removed where replicated in registration_chain and pairwise_nlin.

2. Various changes to option groups:
   a. Created a new option group: General registration options, which includes pipeline-name, registration-method and mask-directory
   b. Moved init-model to MBM option group.

3. Fixed tabbing error in getXfms function that was causing registration chains to crash.