🧹 Harmonize T1-mask pipeline config keys - Githubissues

FCP-INDI / C-PAC

Configurable Pipeline for the Analysis of Connectomes

https://fcp-indi.github.io/

GNU Lesser General Public License v3.0

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🧹 Harmonize T1-mask pipeline config keys #2029

Open nx10 opened 11 months ago

nx10 commented 11 months ago

Related problem

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

registration_workflows.anatomical_registration.registration.FSL-FNIRT.ref_mask_res-2 https://github.com/FCP-INDI/C-PAC/blob/2a9750c1a0075e5ba3f50ef3f54686d9357591b5/CPAC/resources/configs/pipeline_config_abcd-options.yml#L99
registration_workflows.anatomical_registration.T1w_brain_template_mask https://github.com/FCP-INDI/C-PAC/blob/2a9750c1a0075e5ba3f50ef3f54686d9357591b5/CPAC/resources/configs/pipeline_config_abcd-options.yml#L185
registration_workflows.functional_registration.func_registration_to_template.target_template.T1_template.T1w_brain_template_mask_funcreg https://github.com/FCP-INDI/C-PAC/blob/2a9750c1a0075e5ba3f50ef3f54686d9357591b5/CPAC/resources/configs/pipeline_config_abcd-options.yml#L256
anatomical_preproc.brain_extraction.FreeSurfer-BET.T1w_brain_template_mask_ccs https://github.com/FCP-INDI/C-PAC/blob/2a9750c1a0075e5ba3f50ef3f54686d9357591b5/CPAC/resources/configs/pipeline_config_blank.yml#L269

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

shnizzedy commented 11 months ago

Related: https://github.com/FCP-INDI/C-PAC_templates/issues/24

sgiavasis commented 10 months ago

Also related: FCP-INDI/C-PAC#2047