Add dockerfiles and latest analysis script

[K-Meech]

Closes #2

This adds the docker setup files + the latest analysis script
Main changes from the old setup:

• Added installation of zip to the dockerfile
• Updated FSL to the latest version (6.0.7.13)
• Updated distancemap commands for latest FSL version (fixes suggested by Hamied)
• Made sure t1size is an array (otherwise causes errors as t1size[1] etc is empty)
• Minor changes to docker / analysis script to satisfy the linters. I also removed many of the commented out sections in the analysis script + lines mentioning dates/times when code was added
• I modified the linting setup slightly. Both shellcheck and hadolint now use a warning threshold, otherwise they were failing for many minor style issues (flagged as info). I still had to exclude some rules for both that didn't have easy fixes. Happy to change this if you think there's a better solution!

[p-j-smith]

Thanks Kimberly for getting this in, it looks great! A couple of small suggestions but nothing blocking

I'll open an issue to switch to using conda to install FSL

[p-j-smith]

we could create an empty code directory with a .gitkeep file in it and commit it to this repo just so users don't need to create it themselves

[K-Meech]

Good point! Although I'm wondering if we should move away from recommending creating the code/data dirs directly inside the github repo dir anyway? As we're setting each as explicit volumes here: docker run -v "$(pwd)":/home -v "$(pwd)"/code:/code -v "$(pwd)"/data:/data fsl_test >> docker_log.txt 2>&1, it should work with a directory in any location. This would also mean we could use the same setup instructions for pulling the image from dockerhub, where we won't have the github repo locally.

[p-j-smith]

ooo that's a much better idea! Shall we leave it as is for now then and update it once the image is on dockerhub?

[K-Meech]

Sounds good to me!

[K-Meech]

Also (side note) - I'm not sure we need all three volumes? /home is probably sufficient by itself, as long as the code and data dirs are always nested inside?

[p-j-smith]

not for this PR, but as you mentioned offline, let's think about using installing only conda to install only the necessary FSL packages, perhaps using miniforge as a base image

[p-j-smith]

yeah I think this makes sense here - the base image only has one tag anyway and that's latest