REF: generalised anat references 2.0 #477
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mgxd
reviewed
May 7, 2025
| 'data': subject_data[modality], | ||
| 'n': len(subject_data[modality]), | ||
| 'precomputed': f'{modality}_preproc' in precomputed, | ||
| 'role': 'reference' if modality.capitalize() == reference_anat else 'aux', |
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can this just be a bool, since if not we will treat as auxillary
Suggested change
| 'role': 'reference' if modality.capitalize() == reference_anat else 'aux', | |
| 'is_ref': modality.capitalize() == reference_anat, |
| anat_inputs = { | ||
| modality: { | ||
| 'data': subject_data[modality], | ||
| 'n': len(subject_data[modality]), |
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wdyt about
Suggested change
| 'n': len(subject_data[modality]), | |
| 'count': len(subject_data[modality]), |
| 'role': 'reference' if modality.capitalize() == reference_anat else 'aux', | ||
| } | ||
| for modality in ['t1w', 't2w', 'flair'] | ||
| if modality in subject_data.keys() |
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since i believe all keys are in subject_data, this will check if the list is not empty
Suggested change
| if modality in subject_data.keys() | |
| if subject_data.get(modality) |
| @@ -80,8 +82,7 @@ def test_init_anat_preproc_wf( | |||
| hires=False, | |||
| longitudinal=False, | |||
| msm_sulc=False, | |||
| t1w=[str(bids_root / 'sub-01' / 'anat' / 'sub-01_T1w.nii.gz')], | |||
| t2w=[str(bids_root / 'sub-01' / 'anat' / 'sub-01_T2w.nii.gz')], | |||
| anat=collect_anat(collect_data(bids_root, '01')[0], {}, 'T1w'), | |||
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this is pretty noisy and has a lot going on for one line
Comment on lines
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| anat_inputs[reference_anat.lower()].update( | ||
| { | ||
| f'have_{preproc}': f'{reference_anat.lower()}_{preproc}' in precomputed | ||
| for preproc in ['mask', 'tpms', 'dseg'] | ||
| } | ||
| ) |
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looking at this, i wonder if this precomputed parsing would be better suited for a separate function
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After pushing #475 , @mgxd suggested to move the logic to its own workflow.
As a result, we have a new function,
collect_anatwhich will assign a modality as either 'reference' or 'aux'. At the moment, 'reference' is hard-coded to be T1w but this provides an opportunity for command line overrides or alternative pipelines for nirodents/nibabies