Tim Coalson

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...

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...

> This PR is back to being impossible to follow for me. You may have lost the "hide whitespace" setting (or turned it off for a different diff/PR). Click the...

This looks like debian has gone in a similar direction with the cmake scripts: https://packages.debian.org/sid/amd64/libquazip1-qt5-dev/filelist The debian build logs say it is using the in-source version of quazip at the...

You seem to have deleted `ICAFIX/scripts/melodicicasso.m` with the comment that it was superfluous, which seems to be the only copy of it that was in your branch. What was the...

That log snippet doesn't appear to have tested the ICASSO mode. That relies on matlab, so I'm guessing that is currently a problem for you to run testing.

Set `--ica-method=ICASSO` on hcp_fix_multi_run and see what happens. I imagine your testing dataset isn't large, so the default of using all physical cores will probably be fine, but if it...

The single vs double quotes in the `opts_Add*` section has (had anyway, in the template) a purpose, somewhat: double quotes on the description means you can expand variables, and use...

> I reviewed the code and have nothing new to add. Tim and Matt already marked everything that sticks out. > > Do you want me to run any tests...

Ah, I see, specifically `FSL_FIX_MCR`. We may not have tested compiled mode after that change. The other variables are defined by the script, so they shouldn't trip `set -u` (even...