ENH: write template output such that things sort together

[cookpa]

A few fixes

• Replaced all the "let" statements and other traps that prevent running with bash -e, and turned that on.

• Fixed error checking in pairwise registration stage

• Attempted to make output more readable by prefixing input indices, rather than adding them at the end. Trying to make things easier to list and review, especially with multiple modalities

[cookpa]

Editing bash is always scary but I have run both the faces and the brain slices example successfully

[gdevenyi]

If you're willing to go through some painful testing, this is the gold standard,
http://redsymbol.net/articles/unofficial-bash-strict-mode/

And even more painful, getting to pass, https://github.com/koalaman/shellcheck

[cookpa]

Thanks @gdevenyi