Brainstorm/implement command-line parameters

[gdevenyi]

Need to start making script flexible brainstorming list

• run up until specific stage
• run specific stage only (with warning)
• override atlas/template/subject detected resolution
• forcing highmem
• specify registration command
• specify resample command
• specify voting command
• turn on/off morpho
• dryrun mode
• proper status mode (count all the possibilities for outputs)
• run for specific subject
• run basic preprocessing

Probably implement with getopts http://tuxtweaks.com/2014/05/bash-getopts/

Stages should be changed to functions to allow for cleaner looking stage-control logic

[gdevenyi]

Waiting on kvz/bash3boilerplate#23 for some of these

[egarza]

With my .45 x .45 x 1 mm data I already had a walltime problem. So, modifying walltime would be a nice feature out-of-the-box.

[gdevenyi]

As per comment above, modification is waiting on long-form option parsing. In the meantime, you can edit the walltimes manually in stages.sh. See #20 for benchmarking of walltime/memory for single antsRegistration runs.