🐛 Repair Freesurfer FSL `ccs-options` brain mask workflow

[sgiavasis]

Describe the bug

1. The FSL BET node should output the binary brain mask, not the skull-stripped brain.

   • This should be:
   • wf.connect(skullstrip, 'mask_file',
   • instead of wf.connect(skullstrip, 'out_file',

2. The final result is just a field of "snow" and not a correct binary mask. The final node is the problem.

   • Replace the "brain mask to native" node entirely (or remove it).

PENDING: More details to come, issue in progress.

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

• The BET path of this workflow should produce a binary mask.
• The final result should also be a binary mask.

Acceptance criteria

• Workflow produces a high-quality binary brain mask that continues downstream to the rest of the pipeline and can be used interchangeably as part of the forkable masking options.

Screenshots

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C-PAC version

v1.8.7

Container platform

No response

Docker and/or Singularity version(s)

No response

Additional context

No response