--fix-only option for hcp_fix_multi_run

[demsarjure]

This feature implements a new parameter (--fix-only) for hcp_fix_multi_run. This parameter can be used when to speed up ICAFix optimizations by skipping melodic and proceed with FIX on a previously computed ICA solution.

[glasserm]

For some reason this diff is really hard to interpret. Any idea why it is a sea of red and green even though I assume the changes were pretty minor?

[glasserm]

Also, it looks like there are conflicts that need to be resolved.

[coalsont]

Indentation. In the gear button on the "files changed" page, check "hide whitespace".

Github says no conflicts for squash, but there are some changes from -volume-math/-volume-merge to fslmaths/fslmerge, which I am unsure of the purpose of. If they weren't intentional, something may have been done something with the branch history that could cause a regression (for instance, copying an old version of a file, making edits, and then committing it to the current branch state after a reset).

[sivcek]

I have committed the version with the changes requested:

• adding the functionality to the latest master to avoid reverting existing code
• changing --fix-only to --skip-ica
• using opts_StringToBool to process the input string
• adding a log message reporting that an old fix solution was found and backed up

[coalsont]

The unresolved items as I see it are:

• @glasserm suggested the backup saving should be a separate option, and I suggested having the name of the backup be passed into the script, which is more predictable than being generated from the date/time at which it reached that line in the script.
• @mharms seconded (I think?) my --reuse-existing-ica suggestion for the flag name