wehub-resource-sync
638 lines
23 KiB
YAML
638 lines
23 KiB
YAML
---
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# template
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# - number:
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# title:
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# display:
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# google_doc:
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# pull_request:
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# html_preview:
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# leads:
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# # MUST match given-names and family-names from the bids specification citation.cff
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# - given-names: ' '
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# family-names: ' '
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# bids_maintainers:
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# - given-names: ' '
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# family-names: ' '
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# status:
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# blocking:
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# communication_channel:
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# pull_request_created:
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# pull_request_merged:
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- number: '004'
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title: Susceptibility Weighted Imaging
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google_doc: https://docs.google.com/document/d/1kyw9mGgacNqeMbp4xZet3RnDhcMmf4_BmRgKaOkO2Sc/
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content:
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- raw
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leads:
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- given-names: ' '
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family-names: ' '
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bids_maintainers:
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status:
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blocking:
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- Looking for a new leader.
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google_doc_created: 2017-04
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pull_request_created:
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pull_request_merged:
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- number: '011'
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title: Structural preprocessing derivatives
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google_doc: https://docs.google.com/document/d/1YG2g4UkEio4t_STIBOqYOwneLEs1emHIXbGKynx7V0Y/
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pull_request: https://github.com/bids-standard/bids-specification/pull/518
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html_preview: https://bids-specification--518.org.readthedocs.build/en/518/05-derivatives/04-structural-derivatives.html
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content:
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- derivative
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leads:
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- given-names: Viviana
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family-names: Siless
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bids_maintainers:
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- given-names: Christopher J.
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family-names: Markiewicz
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status:
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- Stability! (We haven't touched it in a bit.)
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blocking:
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- Staleness! (We haven't touched it in a bit.)
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- Mostly just need to regroup with other BEPs and make sure we're being consistent.
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google_doc_created: 2017-08
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pull_request_created: 2020-06
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pull_request_merged:
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- number: '012'
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title: Functional preprocessing derivatives
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google_doc:
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pull_request: https://github.com/bids-standard/bids-specification/pull/519
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html_preview: https://bids-specification--519.org.readthedocs.build/en/519/derivatives/functional-derivatives.html
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content:
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- derivative
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leads:
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- given-names: Christopher J.
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family-names: Markiewicz
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bids_maintainers:
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- given-names: Christopher J.
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family-names: Markiewicz
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status:
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- Moderate reworking, post-BEP23 meeting. "boldmap" suffix.
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- Schema implemented; waiting on full schema validation to merge.
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blocking:
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- Overlap with BEP 39 (decompositions).
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- Probably just needs dropping from BEP 12, but need to make sure BEP 39 meets the needs served there.
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google_doc_created: 2018-10
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pull_request_created: 2020-06
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pull_request_merged:
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- number: '014'
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title: Affine transformations and nonlinear field warps
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google_doc: https://docs.google.com/document/d/11gCzXOPUbYyuQx8fErtMO9tnOKC3kTWiL9axWkkILNE/
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content:
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- derivative
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leads:
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- given-names: Oscar
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family-names: Esteban
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bids_maintainers:
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- given-names: Christopher J.
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family-names: Markiewicz
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status:
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- After the kick-off meeting (2019), progress locked on developing a prototype of a new HDF5-based format (X5)
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- Minor bug fixes and features to support more transforms
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- 'Perspectives: The current draft seems sufficient for storing transforms'
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- 'Perspectives: X5 has high promises to enable effortless spatial transforms'
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blocking:
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- Bandwidth to finalize development
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- 'Current blockers: surface transforms & X5 storing'
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google_doc_created: 2017-08
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pull_request_created:
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pull_request_merged:
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- number: '016'
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title: Diffusion weighted imaging derivatives
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pull_request: https://github.com/bids-standard/bids-specification/pull/2211
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content:
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- derivative
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leads:
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- given-names: Franco
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family-names: Pestilli
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- given-names: Oscar
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family-names: Esteban
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bids_maintainers:
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status:
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- adapted general spatial derivatives proposal, meaning using <modality>map, like `dwimap`
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- decided on using `params-` to denote different file types, for example `param-md` or `param-fa`
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- updated meta-data
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blocking:
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google_doc_created:
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pull_request_created:
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pull_request_merged:
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- number: '017'
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title: Generic BIDS connectivity data schema
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display: Connectivity schema
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google_doc: https://docs.google.com/document/d/1ugBdUF6dhElXdj3u9vw0iWjE6f_Bibsro3ah7sRV0GA/
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content:
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- derivative
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leads:
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- given-names: Eugene P.
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family-names: Duff
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bids_maintainers:
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status:
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- specified different formats for dense and sparse matrices
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- 'proposed arrays in h5 or zarr to cover multi-dimensional matrices (for example: dynamic connectivity)'
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blocking:
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google_doc_created: 2017-05
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pull_request_created:
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pull_request_merged:
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- number: '021'
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title: Common Electrophysiological Derivatives
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google_doc: https://docs.google.com/document/d/1PmcVs7vg7Th-cGC-UrX8rAhKUHIzOI-uIOh69_mvdlw/
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content:
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- derivative
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leads:
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- given-names: Arnaud
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family-names: Delorme
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- given-names: Dora
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family-names: Hermes
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- given-names: Mainak
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family-names: Jas
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- given-names: Guiomar
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family-names: Niso
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- given-names: Robert
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family-names: Oostenveld
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- given-names: Cyril
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family-names: Pernet
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- given-names: Christine
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family-names: Rogers
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status:
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- 'Focus on raw-ish data: channels by time: epoching, filtering, interpolation...'
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- 'All provenance tracking: outsourced to BEP028 (“provenance”)'
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- Reusing existing (raw) data formats where applicable
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- 'No additional entities or suffixes: focus on “desc” entity'
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- Create new “descriptions.tsv” file to accompany and document the “desc” entity
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- Working on examples on GitHub
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- 'Perspectives: Derivatives beyond channels by time data will be discussed at a later point'
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blocking:
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google_doc_created: 2018-05
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pull_request_created:
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pull_request_merged:
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- number: '023'
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title: PET Preprocessing derivatives
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google_doc: https://docs.google.com/document/d/1yzsd1J9GT-aA0DWhdlgNr5LCu6_gvbjLyfvYq2FuxlY/
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content:
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- derivative
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leads:
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- given-names: Martin
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family-names: Noergaard
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- given-names: Graham
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family-names: Searle
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- given-names: Melanie
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family-names: Ganz-Benjaminsen
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bids_maintainers:
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- given-names: Anthony
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family-names: Galassi
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status:
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- Defined all the necessary components to be included in the specification
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- Alignment with other modalities obtained at Copenhagen BIDS derivatives meeting
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- Example PET derivatives datasets available on github
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- 'Perspectives: 3rd joint meeting between all PET collaborators in August 2023'
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- 'Perspectives: Aim is to finish the specification during the fall of 2023'
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blocking:
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- Need more example datasets (fore example different tracers) with different preprocessing choices to capture as most of the PET community as possible
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- Need to finish alignment with other modalities
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- Still need to agree on the level of information going into corresponding json files
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google_doc_created: 2018-08
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pull_request_created:
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pull_request_merged:
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- number: '024'
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title: Computed Tomography scan
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google_doc: https://docs.google.com/document/d/1fqnJZ18x5LJC8jiJ8yvPHUGFzNBZ6gW2kywYrUKWtuo/
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content:
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- raw
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leads:
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- given-names: Hugo
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family-names: Boniface
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bids_maintainers:
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status:
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- Lead seeking more contributors and experts.
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blocking:
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google_doc_created: 2018-11
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pull_request_created:
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pull_request_merged:
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- number: '026'
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title: Microelectrode Recordings
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google_doc: https://docs.google.com/document/d/14KC1d5-Lx-7ZSMtwS7pVAAvz-2WR_uoo5FvsNirzqJw/
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content:
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- raw
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leads:
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- given-names: ' '
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family-names: ' '
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bids_maintainers:
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status:
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- BEP is open to new leadership, see also [BEP032 (animal electrophys)](https://docs.google.com/document/d/1oG-C8T-dWPqfVzL2W8HO3elWK8NIh2cOCPssRGv23n0/)
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blocking:
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- Searching for a new leader.
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google_doc_created: 2018-04
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pull_request_created:
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pull_request_merged:
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- number: '028'
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title: Provenance
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google_doc: https://docs.google.com/document/d/1vw3VNDof5cecv2PkFp7Lw_pNUTUo8-m8V4SIdtGJVKs/
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content:
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- metadata
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leads:
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- given-names: Satrajit S.
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family-names: Ghosh
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- given-names: Camille
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family-names: Maumet
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- given-names: Yaroslav O.
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family-names: Halchenko
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bids_maintainers:
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status:
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- '[Specification](https://bids.neuroimaging.io/bep028)'
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- '[Set of examples](https://github.com/bids-standard/BEP028_BIDSprov)'
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- 'Perspectives: Opening up to BIDS community for feedback'
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- 'Perspectives: Engaging with software developers (in progress w/ SPM, AFNI)'
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blocking:
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google_doc_created: 2018-08
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pull_request: https://github.com/bids-standard/bids-specification/pull/2099
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pull_request_created: 2025-04
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pull_request_merged:
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- number: '032'
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title: Microelectrode electrophysiology
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google_doc: https://docs.google.com/document/d/1oG-C8T-dWPqfVzL2W8HO3elWK8NIh2cOCPssRGv23n0/
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pull_request: https://github.com/bids-standard/bids-specification/pull/2307
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html_preview: https://bids-specification--2307.org.readthedocs.build/en/2307/modality-specific-files/microelectrode-electrophysiology.html
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content:
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- raw
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leads:
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- given-names: Sylvain
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family-names: Takerkart
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- given-names: Benjamin
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family-names: Dichter
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- given-names: Yaroslav O.
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family-names: Halchenko
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- given-names: Lyuba
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family-names: Zehl
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- given-names: Andrew
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family-names: Davison
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bids_maintainers:
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- given-names: Rémi
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family-names: Gau
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status:
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- Decided on the new name (not just "Animal" but "Microelectrode"), modalities, datatypes
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- Nearly finalized added metadata
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- PR compiles green, preview is available
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- 'Target: finalize & merge PR into the BIDS specs in 2025'
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blocking:
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- Need to prepare example datasets
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- Need to start thinking about derived data (spike sorted)
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google_doc_created: 2020-12
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pull_request_created: 2022-11
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pull_request_merged:
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- number: '033'
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title: Advanced Diffusion Weighted Imaging
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google_doc: https://docs.google.com/document/d/1en4ByORlPqwDfZwNOOBTj0GwpYBcS0_2peqreTOvwDU/
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content:
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- raw
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leads:
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- given-names: James
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family-names: Gholam
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- given-names: Leandro
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family-names: Beltrachini
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- given-names: Filip
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family-names: Szczepankiewicz
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bids_maintainers:
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status:
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- 'New BEP, seeking contributors and collecting community feedback relating to: priority sequences to support, best supported binary structured formats
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(e.g. CBOR? HDF5? MsgPack?).'
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- Comments may be submitted directly on the document.
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- Generating example datasets [here](https://github.com/JAgho/MISP_plot/tree/main) and determining best practice with vendors to record data in-sequence
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blocking:
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google_doc_created: 2021-04
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pull_request_created:
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pull_request_merged:
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- number: '034'
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title: Computational modeling
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pull_request: https://github.com/bids-standard/bids-specification/pull/967
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html_preview: https://bids-specification--967.org.readthedocs.build/en/967/modality-specific-files/computational-models.html
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content:
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- derivative
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- metadata
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leads:
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- given-names: Michael
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family-names: Schirner
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- given-names: Petra
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family-names: Ritter
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bids_maintainers:
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status:
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- sim2bids app created
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- easier to bring neural simulation data (especially in The Virtual Brain format) into the proposed BIDS Comp Model format
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- 'Perspectives: A roadmap that coordinates efforts across BEPs would be appreciated.'
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blocking:
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- BEPs have overlapping concerns (Comp Models, Spaces and mappings, Generic BIDS connectivity schema, time series, Provenance, Atlases)
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- need to separate concerns & provide a roadmap for each BEP
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google_doc_created: 2021-02
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pull_request_created: 2021-08
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pull_request_merged:
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- number: '035'
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title: Modular extensions for individual participant data mega-analyses with non-compliant derivatives
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display: Mega-analyses
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google_doc: https://docs.google.com/document/d/1tFRNumQyIgjXBNC3brFDLO9FaikjL84noxK6Om-Ctik/
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content:
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- derivative
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leads:
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- given-names: Giuseppe
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family-names: Gallitto
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- given-names: Balint
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family-names: Kincses
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- given-names: Tamas
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family-names: Spisak
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bids_maintainers:
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- given-names: Rémi
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family-names: Gau
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status:
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- Meta-data harmonization with a term-mapper goes to BEP043
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- 'Persperctive: Repeated community review of the simplified proposal'
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blocking:
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- Term-mapping is a general feature => complex, modular proposal
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google_doc_created: 2021-12
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pull_request_created:
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pull_request_merged:
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- number: '036'
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title: Phenotypic Data Guidelines
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google_doc: https://docs.google.com/document/d/1WTkfES8L0vItZVyyR68fc-9cO03jS-kCnMnw6602pbc/
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content:
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- raw
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leads:
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- given-names: Eric
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family-names: Earl
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- given-names: Samuel
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family-names: Guay
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- given-names: Sebastian
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family-names: Urchs
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- given-names: Arshitha
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family-names: Basavaraj
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bids_maintainers:
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- given-names: Chris
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family-names: Markiewicz
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- given-names: Ross
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family-names: Blair
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status:
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- BEP entering community review period shortly.
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- BIDS specification PR 2123.
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- BIDS examples PR 465.
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blocking:
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- A successful community review.
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google_doc_created: 2021-10
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pull_request_created: 2025-05
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pull_request_merged:
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- number: '037'
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title: Non-Invasive Brain Stimulation
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google_doc: https://docs.google.com/document/d/1drYd7kaNbHTcYPR3T_CRDsPcEbFSV7JbJUmhMPeWMqY/
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current_repository: https://github.com/nigelrogasch/nibs-bids/tree/master/nibs-bids-v6/
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current_preprint_editable: https://docs.google.com/document/d/1xfetyFkXh8kqObfCViUvku69pk4ZZw8BC5GL8_Cq9TI/edit?tab=t.0
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current_preprint:
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author_list: https://docs.google.com/spreadsheets/d/1oMImk-HXsyLZtTj3yIa1uY9LX3hVpsCiAGZP3oSV0Eo/edit?gid=0#gid=0
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content:
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- raw
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leads:
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- given-names: Giacomo
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family-names: Bertazzoli
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- given-names: Vittorio
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family-names: Iacovella
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- given-names: Peter J.
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family-names: Fried
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- given-names: Marta
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family-names: Bortoletto
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- given-names: Nigel
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family-names: Rogasch
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past leads (inactive):
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- given-names: Carlo
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family-names: Miniussi
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bids_maintainers:
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- given-names: Rémi
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family-names: Gau
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status:
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- v1.0 2020-11-09 Initial work on specification with vittorio.iacovella@unitn.it carlo.miniussi@unitn.it marta.bortoletto@cognitiveneuroscience.it
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- v1.0 2021-04 First example of a NIBS-BIDS dataset https://gin.g-node.org/CIMeC/TMS-EEG_brain_connectivity_BIDS
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- V1.0 2021-11 Brainhack @Donosti with eleonora.marcantoni@cognitiveneuroscience.it martinabulgari3@gmail.com and g.guidali@campus.unimib.it
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- V1.0 2022-02 First international NIBS-BIDS meeting
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- V1.0 2022-11 First update of the BEP
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- V2.0 2023-08 BEP 2.0 available with the new NIBS-BIDS logic for describing NIBS experiments
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- V3.0 2024-07 BEP 3.0 available with a draft of the final BIDS structure.
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- V4.0 2024-11 BEP 4.0 updated with a new, more comprehensive structure. Added int files for offline stimulation. Harmonized parameters with SimNIBS.
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Use of events and scans files for online stimulation.
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- V4.1 2024-12 BEP 4.1 Comments form December 9th, 2024 5th general meeting implemented, added FAQ section. Met with the BIDS maintenance team in
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January 2025. Agreed on closing the open discussions, lock the google doc and start the PR.
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- V6.2 2026-03 BEP 6.2 Comments form December 12th, 2025 6th general meeting implemented. Met with the BIDS steering team in March 2026. Agreed on
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NSF FAIROS application on NIBS-BIDS implementation https://www.nsf.gov/funding/opportunities/fairos-findable-accessible-interoperable-reusable-open-science.
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Agreed on creating a preprint version of the BEP037 (to bi cited as a work-in-progress).
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blocking:
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google_doc_created: 2022-09
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pull_request_created:
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pull_request_merged:
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- number: '039'
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title: Dimensionality reduction-based networks
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google_doc: https://docs.google.com/document/d/1GTWsj0MFQedXjOaNk6H0or6IDVFyMAysrJ9I4Zmpz2E/
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content:
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- raw
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leads:
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- given-names: Arianna
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family-names: Sala
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- given-names: Anibal
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family-names: Sólon
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- given-names: Cyrus
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family-names: Eierud
|
|
- given-names: Franco
|
|
family-names: Pestilli
|
|
- given-names: Peer
|
|
family-names: Herholz
|
|
bids_maintainers:
|
|
status:
|
|
- adapted general spatial derivatives proposal, meaning using `<modality>map`, for example `eegmap` and `boldmap` for spatial components
|
|
- decided on `model-` and `items-` as keys to denote the utilized model and component number, if files are 3D, respectively
|
|
- updated meta-data and examples
|
|
blocking:
|
|
google_doc_created: 2021-10
|
|
pull_request_created:
|
|
pull_request_merged:
|
|
|
|
- number: '040'
|
|
title: Functional Ultrasound
|
|
google_doc: https://docs.google.com/document/d/1W3z01mf1E8cfg_OY7ZGqeUeOKv659jCHQBXavtmT-T8/
|
|
content:
|
|
- raw
|
|
leads:
|
|
- given-names: Jean-Charles
|
|
family-names: Mariani
|
|
- given-names: Samuel
|
|
family-names: Le Meur-Diebolt
|
|
- given-names: Thomas
|
|
family-names: Deffieux
|
|
bids_maintainers:
|
|
- given-names: Rémi
|
|
family-names: Gau
|
|
status:
|
|
- All issues raised on the original BEP have been resolved.
|
|
- Regular meetings with contributors scheduled.
|
|
- Scanner coordinate system has been proposed to harmonize affine transformations with moving probes.
|
|
- 'Perspectives: Starting to bidsify existing datasets to stress test the BEP.'
|
|
- 'Perspectives: timing metadata has been copied from the fMRI-BIDS specification, but evolutions could be discussed to handle non-stable sampling
|
|
frequencies.'
|
|
blocking:
|
|
google_doc_created: 2023-03
|
|
pull_request_created:
|
|
pull_request_merged:
|
|
|
|
- number: '041'
|
|
title: Statistical Model Derivatives
|
|
google_doc: https://docs.google.com/document/d/1KHzp-yk8KXvkUIhtN71WU0m4P4kKT9C1yvI-i9_kNeY/
|
|
content:
|
|
- derivative
|
|
leads:
|
|
- given-names: Taylor
|
|
family-names: Salo
|
|
bids_maintainers:
|
|
- given-names: Taylor
|
|
family-names: Salo
|
|
status:
|
|
- New BEP, collecting community comments and feedback.
|
|
- All collaborators are welcome.
|
|
blocking:
|
|
google_doc_created: 2022-08
|
|
pull_request_created:
|
|
pull_request_merged:
|
|
|
|
- number: '043'
|
|
title: BIDS Term Mapping
|
|
google_doc: https://docs.google.com/document/d/1LACjc5hFXDpa2l_QddBPR41Vce_gglGv9WeuBB7LsBU/
|
|
content:
|
|
- metadata
|
|
leads:
|
|
- given-names: Christopher J.
|
|
family-names: Markiewicz
|
|
- given-names: Eric A.
|
|
family-names: Earl
|
|
bids_maintainers:
|
|
- given-names: Christopher J.
|
|
family-names: Markiewicz
|
|
- given-names: Eric A.
|
|
family-names: Earl
|
|
status:
|
|
- For being able to map non-BIDS data as BIDS-compatible.
|
|
- Now collecting community comments and feedback.
|
|
- All collaborators are welcome.
|
|
blocking:
|
|
google_doc_created: 2024-03
|
|
pull_request_created:
|
|
pull_request_merged:
|
|
|
|
- number: '044'
|
|
title: Stimuli
|
|
pull_request: https://github.com/bids-standard/bids-specification/pull/2022
|
|
html_preview: https://bids-specification--2022.org.readthedocs.build/en/2022/modality-specific-files/stimuli.html
|
|
leads:
|
|
- given-names: Seyed Yahya
|
|
family-names: Shirazi
|
|
- given-names: Dora
|
|
family-names: Hermes
|
|
- given-names: Yaroslav O.
|
|
family-names: Halchenko
|
|
- given-names: Kay
|
|
family-names: Robbins
|
|
- given-names: Scott
|
|
family-names: Makeig
|
|
bids_maintainers:
|
|
- given-names: Rémi
|
|
family-names: Gau
|
|
status:
|
|
- Community comments and feedback are being collected (January 2025)
|
|
- To harmonize and make more reusable stimuli content under stimuli/
|
|
- Collecting community comments and feedback. All collaborators are welcome.
|
|
- 'Original issue: [#153](https://github.com/bids-standard/bids-specification/issues/153)'
|
|
content:
|
|
- raw
|
|
blocking:
|
|
google_doc_created: 2023-09
|
|
pull_request_created: 2024-12
|
|
pull_request_merged:
|
|
|
|
- number: '045'
|
|
title: Peripheral Physiological Recordings
|
|
display: Physio
|
|
pull_request: https://github.com/bids-standard/bids-specification/pull/2267
|
|
html_preview: https://bids-specification--2267.org.readthedocs.build/en/2267/modality-specific-files/physiological-recordings.html
|
|
google_doc: https://docs.google.com/document/d/1oTfjzY5ZnLIYd0kPPWhR81sBmMuy_jC5YYIaqj6OhSA/edit
|
|
leads:
|
|
- given-names: Mary
|
|
family-names: Miedema
|
|
- given-names: Stefano
|
|
family-names: Moia
|
|
- given-names: Sourav
|
|
family-names: Kulkarni
|
|
bids_maintainers:
|
|
- given-names: Seyed Yahya
|
|
family-names: Shirazi
|
|
status:
|
|
- No longer developed in google doc, moved to <https://github.com/physiopy/bids-specification-physio>.
|
|
- To update standards for physiological data for improved clarity and a broader range of use cases.
|
|
- Now collecting community comments and feedback. All collaborators are welcome.
|
|
- 'Original issue: [#1675](https://github.com/bids-standard/bids-specification/issues/1675).'
|
|
content:
|
|
- raw
|
|
blocking:
|
|
google_doc_created: 2024-08
|
|
pull_request_created: 2025-11
|
|
pull_request_merged:
|
|
|
|
- number: '046'
|
|
title: Diffusion Tractography
|
|
display: Tractography
|
|
google_doc: https://docs.google.com/document/d/1ubDQ2RhgjnfGqoeukzEkPV9YEHhfYMERrj7-3b0c2HI/edit
|
|
leads:
|
|
- given-names: Robert E.
|
|
family-names: Smith
|
|
- given-names: Ariel
|
|
family-names: Rokem
|
|
- given-names: Franco
|
|
family-names: Pestilli
|
|
status:
|
|
- Porting comprehensive description of streamline tractography mechanisms into specification - 10.1016/B978-0-12-817057-1.00023-8
|
|
- Determine appropriate resolution with TRX development - https://tee-ar-ex.github.io/trx-python/
|
|
- Decide on scope of BEP; e.g. whether to include tractometry, complex tract delineation
|
|
content:
|
|
- derivative
|
|
blocking:
|
|
google_doc_created: 2022-02
|
|
pull_request_created:
|
|
pull_request_merged:
|
|
|
|
- number: '047'
|
|
title: Audio/video recordings for behavioral experiments
|
|
display: Behavioral audio/video recordings
|
|
pull_request: https://github.com/bids-standard/bids-specification/pull/2231
|
|
html_preview: https://bids-specification--2231.org.readthedocs.build/en/2231/modality-specific-files/behavioral-experiments.html
|
|
content:
|
|
- raw
|
|
leads:
|
|
- given-names: Benjamin
|
|
family-names: Dichter
|
|
bids_maintainers:
|
|
- given-names: Seyed Yahya
|
|
family-names: Shirazi
|
|
status:
|
|
- Adds support for storing audio and video behavioral recordings (new `_audio` and `_video` suffixes) in the `beh/` directory.
|
|
blocking:
|
|
google_doc_created:
|
|
pull_request_created: 2025-10
|
|
pull_request_merged:
|