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

sgiavasis commented 9 months ago

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 commented 9 months ago

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

shnizzedy commented 9 months ago

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)

FCP-INDI / C-PAC