🧹 Harmonize T1-mask pipeline config keys

[Florian Rupprecht]

Related problem

There are many keys in the pipeline config that let users specify T1-masks:

1. registration_workflows.anatomical_registration.registration.FSL-FNIRT.ref_mask_res-2

   C-PAC/CPAC/resources/configs/pipeline_config_abcd-options.yml

   Line 99 in 2a9750c

    ref_mask_res-2: /opt/dcan-tools/pipeline/global/templates/MNI152_T1_2mm_brain_mask_dil.nii.gz 

2. registration_workflows.anatomical_registration.T1w_brain_template_mask

   C-PAC/CPAC/resources/configs/pipeline_config_abcd-options.yml

   Line 185 in 2a9750c

    T1w_brain_template_mask: /opt/dcan-tools/pipeline/global/templates/MNI152_T1_${resolution_for_anat}_brain_mask.nii.gz 

3. registration_workflows.functional_registration.func_registration_to_template.target_template.T1_template.T1w_brain_template_mask_funcreg

   C-PAC/CPAC/resources/configs/pipeline_config_abcd-options.yml

   Line 256 in 2a9750c

    T1w_brain_template_mask_funcreg: /usr/share/data/fsl-mni152-templates/MNI152_T1_${func_resolution}_brain_mask.nii.gz 

4. anatomical_preproc.brain_extraction.FreeSurfer-BET.T1w_brain_template_mask_ccs

   C-PAC/CPAC/resources/configs/pipeline_config_blank.yml

   Line 269 in 2a9750c

    T1w_brain_template_mask_ccs: /ccs_template/MNI152_T1_1mm_first_brain_mask.nii.gz 

Proposed feature

Investigate and collapse redundancies across pipelines and maybe move the new key(s) under functional_preproc.func_masking to be more easy to find

Acceptance criteria

• Investigated and collapsed redundancies across pipelines
• (If sensible) moved new key(s) under functional_preproc.func_masking
• Add documentation about what steps are affected by the T1 masks

Alternatives

No response

Additional context

No response

[Jon Clucas]

Related: #1738

[Steve Giavasis]

Also related: #2047