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🚚 Give templates BIDS names #4

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shnizzedy opened this issue Oct 15, 2021 · 1 comment
Open
2 tasks

🚚 Give templates BIDS names #4

shnizzedy opened this issue Oct 15, 2021 · 1 comment
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BIDS https://bids-specification.readthedocs.io/ enhancement New feature or request help wanted Extra attention is needed

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@shnizzedy
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Related problem

The filenames are currently not following any consistent pattern (the macaque files are nearly in BIDS):

atlases/label
β”œβ”€β”€ Human
β”‚Β Β  β”œβ”€β”€ aal_mask_pad.nii.gz
β”‚Β Β  β”œβ”€β”€ CC200.nii.gz
β”‚Β Β  β”œβ”€β”€ CC400.nii.gz
β”‚Β Β  β”œβ”€β”€ csf_mask_xtedit.nii.gz
β”‚Β Β  β”œβ”€β”€ ez_mask_pad.nii.gz
β”‚Β Β  β”œβ”€β”€ ho_mask_pad.nii.gz
β”‚Β Β  β”œβ”€β”€ Mask_ABIDE_85Percent_GM.nii.gz
β”‚Β Β  β”œβ”€β”€ PNAS_Smith09_rsn10.nii.gz
β”‚Β Β  β”œβ”€β”€ rois_3mm.nii.gz
β”‚Β Β  └── tt_mask_pad.nii.gz
└── Macaque
    β”œβ”€β”€ MacaqueYerkes19_T1w_0.5mm_brain_mask.nii.gz
    β”œβ”€β”€ MacaqueYerkes19_T1w_0.5mm_brain.nii.gz
    β”œβ”€β”€ MacaqueYerkes19_T1w_0.5mm.nii.gz
    β”œβ”€β”€ MacaqueYerkes19_T1w_1.0mm_brain_mask.nii.gz
    β”œβ”€β”€ MacaqueYerkes19_T1w_1.0mm_brain.nii.gz
    β”œβ”€β”€ MacaqueYerkes19_T1w_1.0mm.nii.gz
    β”œβ”€β”€ MacaqueYerkes19_T1w_2mm_brain_mask.nii.gz
    β”œβ”€β”€ MacaqueYerkes19_T1w_2mm_brain.nii.gz
    └── MacaqueYerkes19_T1w_2mm.nii.gz

Proposed feature

Rename all these images following the BIDS specification

Acceptance criteria

Alternatives

No response

Additional context

  1. I think it would be great to also include sidecars like in Neuroparc's specification, but I think that's a follow-up to this, not necessary to resolve this issue.
  2. For the renaming acceptance criterion, I think it would be useful to make a CSV (or some other format) file that handles the mappings, so it's both machine- and human-readable without a lot of digging.
@shnizzedy shnizzedy added enhancement New feature or request BIDS https://bids-specification.readthedocs.io/ labels Oct 15, 2021
@shnizzedy
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Is it safe to assume that these are all space-MNI152NLin6?

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Labels
BIDS https://bids-specification.readthedocs.io/ enhancement New feature or request help wanted Extra attention is needed
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