🐛 FSL-BET `-m` flag (`mask_boolean`) should not be accessible to users

[sgiavasis]

Describe the bug

The -m toggle should always be On, but furthermore, there is no need for this option to be open as a switch to users. This step should always produce the binary brain mask instead of the already-skullstripped brain, due to C-PAC's dedicated brain extraction block.

Because the possible complication: using a config (such as the fmriprep-options preconfig which has -m set to Off for some reason) and then modifying it to use FSL-BET will lead to no mask being generated, and the skull-stripped brain being passed downstream as a mask.

To reproduce

No response

Preconfig

• [ ] default
• [ ] abcd-options
• [ ] anat-only
• [ ] blank
• [ ] ccs-options
• [ ] fmriprep-options
• [ ] fx-options
• [ ] monkey
• [ ] monkey-ABCD
• [ ] ndmg
• [ ] nhp-macaque
• [ ] preproc
• [ ] rbc-options
• [ ] rodent

Custom pipeline configuration

No response

Run command

No response

Expected behavior

This should just need to be inaccessible as an option, with the -m flag hard-coded to On.

Acceptance criteria

• [ ] Hard-code the -m flag in the FSL BET block.
• [ ] Make sure the mask_boolean keys in all of the configs are removed.

Screenshots

No response

C-PAC version

No response

Container platform

No response

Docker and/or Singularity version(s)

No response

Additional context

No response

[birajstha]

@sgiavasis This branch has been updated. Should I PR to develop yet or should I wait?

[shnizzedy]

Should I PR to develop yet or should I wait?

Please do open a PR to develop! The sooner the PR is up, the more chance we all have to review it

(sometimes I open a PR before I even have any commits in my feature branch, just so I can write out what I'm doing and get eyes on the design)