[WIP] ENH: 482 remove fsl dependency

[jbh1091]

Changes proposed in this pull request

Replacement of FSL tools when replacements are available, for example replacing BET with ANTs BrainExtraction. For FSL tools with no viable replacements (mainly FUGUE and PRELUDE) we add a check for FSL environment variables such that containers without FSL can't run them, and those who still want to use FSL are able to. A separate container without FSL will be generated to give users a choice between qsiprep installations with or without FSL installed.

Documentation that should be reviewed

Boilerplate and references require updating to match the removed or replaced FSL functions.

[jbh1091]

Ready for re-review of remaining changes (mostly FAST removal related) when you are @mattcieslak

[mattcieslak]

I noticed that you removed t1_seg from a lot of these workflows. With #553 the t1_seg will be available no matter what, so I'm thinking it would make sense to let the tests fail on this build but keep t1_seg the way it was before in the dwi workflows.

If you revert those, we can merge this into master and then I'll merge it into #553. wdyt?

[jbh1091]

Good point, that works for me! I'll let you know when it's put back in. Ok to still leave out the TPMs or should those be added back as well?

[mattcieslak]

Awesome! The TPMs are never used, so those can stay out

[jbh1091]

Ok, I added all the segmentation node inputs back in. Things to note:
-FAST is still out, meaning the workflows in anatomical.py will fail due to lack of connections since the t1_seg node just isn't there. Any run would fail from a workflow error. Happy to add it back for the brief period in between merging this branch and your refactor
-Removed my addition of T1 atropos in workflows/fieldmap/pepolar.py to return to the original workflow that included seg
-Added back MNI seg nodes as well as t1 seg
-Did not change my removals of FAST options in MRTRIX workflows

Let me know if any other changes are necessary.

[mattcieslak]

It worked?!? If you can run this on a real test dataset and the results look good, I'll go ahead and merge!

[mb3152]

This was from about a week ago with Joey's changes, not your most recent ones and fixing the connections, comparing it to the unstable from about a month ago. Mind merging and we can double check the outputs from the merge?

[mattcieslak]

The most recent version of the master branch is already included here, so if this branch works it will become the master branch when we merge it

looks good

[mb3152]

awesome!! letting Joey hit the final button...