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TSV lookup tables for segmentation do not allow extra columns #1993

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Remi-Gau opened this issue Nov 28, 2024 · 3 comments · May be fixed by #2054
Open

TSV lookup tables for segmentation do not allow extra columns #1993

Remi-Gau opened this issue Nov 28, 2024 · 3 comments · May be fixed by #2054

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@Remi-Gau
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See here:

https://bids-specification.readthedocs.io/en/latest/derivatives/imaging.html#common-image-derived-labels

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bids-specification/src/schema/rules/tabular_data/derivatives/common_derivatives.yaml

Line 2 in 6a40161

SegmentationLookup:

Is there a reason for this?

For context I am trying to use this to help standardize the atlases in nilearn and adding some extra columns would be handy.
@Remi-Gau
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@effigies forgot to ask you about this one yesterday?

@effigies
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effigies commented Dec 13, 2024 •
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I doubt it:

bids-specification/src/schema/rules/tabular_data/derivatives/common_derivatives.yaml

Lines 2 to 13 in 00917e6

SegmentationLookup:
selectors:
- dataset.dataset_description.DatasetType == "derivative"
- intersects([suffix], ["dseg", "probseg"])
columns:
index: required
name__segmentations: required
abbreviation: optional
color: optional
mapping: optional
index_columns: [index]

We have no additional_columns field, so it's presumably defaulting to not allowed. IMO we should probably default to allowed, and in any event I don't see any reason not to allow (or at least "allowed_if_defined") this one.

cc @rwblair for thoughts.

@effigies effigies linked a pull request Feb 13, 2025 that will close this issue
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@effigies
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@Remi-Gau Opened #2054.

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[ENH] Allow additional columns if defined for various TSV files effigies/bids-specification
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@effigies @Remi-Gau