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[ENH] Add example dataset for MRI chunk entity #405

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@valosekj valosekj commented Aug 29, 2023

This PR adds an example dataset for the MRI chunk entity.

The "chunk" entity is added to the MRI datatype in bids-standard/bids-specification#1586.

Note that I intentionally did not truncate the data to preserve its nifti header with qforms for different chunks (FOVs). Instead, I created empty masks of the original images --> images are empty, but the nifti header has been preserved.

@effigies
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Please truncate the NIfTI files to headers.

zcat img.nii.gz | head -c 352 | gzip - | sponge img.nii.gz

@valosekj
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Please truncate the NIfTI files to headers.

zcat img.nii.gz | head -c 352 | gzip - | sponge img.nii.gz

Thanks! Done in 6a84c8f

@Remi-Gau
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Could you update the dataset listing?

https://github.com/bids-standard/bids-examples/blob/master/CONTRIBUTING.md#how-to-generate-the-tables-in-the-readme

It is in the root of the repo:
https://github.com/bids-standard/bids-examples/blob/master/dataset_listing.tsv

Ideally it should link to where the "real" data is: may be quite useful in this case

@valosekj
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Could you update the dataset listing?

https://github.com/bids-standard/bids-examples/blob/master/CONTRIBUTING.md#how-to-generate-the-tables-in-the-readme

It is in the root of the repo: https://github.com/bids-standard/bids-examples/blob/master/dataset_listing.tsv

Done in ec44bc3.

Ideally it should link to where the "real" data is: may be quite useful in this case

Unfortunately, the dataset is not publicly available. And I am not aware of any public MRI dataset with "chunks".

@Remi-Gau
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Unfortunately, the dataset is not publicly available. And I am not aware of any public MRI dataset with "chunks".

OK let's keep like that for now but it would be good in the future to be able to point to a real one.

@valosekj
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Since the corresponding PR has been merged, maybe this PR could be merged as well?

@effigies effigies force-pushed the jv/add_mri_chunk_example_dataset branch from ec44bc3 to 43d3a2c Compare November 21, 2023 01:06
@Remi-Gau
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I think this will have to wait for the BIDS validator to be changed to accept this new entity

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3 participants