Hi Kristen,
If you want the warped anatomy to have a certain resolution,
you can achieve that via either of those same '-master' or
'-mast_dxyz' options.
I'm not sure why you are getting those "Choleski factorization"
errors in 2dImReg. What 2dImReg/3dvolreg commands did you run,
and what error did 3dvolreg display?
Note that 3dAllineate is doing volume registration already. It
may not make sense to also run 3dvolreg, unless you are using
3dAllineate to compute just a single transformation to apply to
all of the registered EPI data.
- rick