New input handing and file outputs

[dowdlelt]

This pull request has:

• several small formatting changes to reduce MatLab complaints (not complete).
• A method to drop volumes at the end of the timeseries (for example to run without nosie volumes, or to easily compare truncated time series performance)
• A new flag to save out the abs(complexResiduals) as a nii file, with the g-factor reapplied to the data
• Adding header information when saving out g-factor map, so its easy to load and compare to original data
• Other small formatting and space changes