beps.yml

# template
# - number:
#   title:
#   leads:
#     - name:
#   update:
#   blocking:

- number: "004"
  title: Susceptibility Weighted Imaging (SWI)
  leads:
  update: Looking for a new leader.
  content:
    - raw
  blocking: Looking for a new leader.
  google_doc_created: 2017-04
  pull_request_created:
  pull_request_merged:

- number: "011"
  title: Structural preprocessing derivatives
  leads:
    - name: Viviana Siless
  update: |
    Opened [pull request](https://github.com/bids-standard/bids-specification/pull/518){:target:"_blank"}.

    Features:
    - surfaces,
    - scalar maps on surfaces
    - morphometrics.

    Need to conform with final Common Derivatives and gather community feedback.
  content:
    - derivative
  blocking: |
    Blocked by BIDS-validator extending and PyBIDS implementation for common
    derivatives
  google_doc_created: 2017-08
  pull_request_created: 2020-06
  pull_request_merged:

- number: "012"
  title: Functional preprocessing derivatives
  leads:
    - name: Chris Markiewicz
  update: |
    Opened the [pull request](https://github.com/bids-standard/bids-specification/pull/519){:target:"_blank"}.

    Features:
    - Derivative images (mean, ALFF, ReHo, etc.),
    - Time series (confounds, decompositions, etc.)
  content:
    - derivative
  blocking: Blocked by BIDS-validator extending and PyBIDS implementation
  google_doc_created: 2018-10
  pull_request_created: 2020-06
  pull_request_merged:

- number: "014"
  title: Affine transformations and nonlinear field warps
  leads:
    - name: Oscar Esteban
  update: |
    - Creating file format (X5) to store spatial transforms.

    - [There is a software prototype - NiTransforms](https://osf.io/8aq7b/){:target:"_blank"} demonstrates implementation of this BEP.
    NiTransforms has been tested and integrated to work within fMRIPrep
  content:
    - derivative
  blocking: In progress.
  google_doc_created: 2017-08
  pull_request_created:
  pull_request_merged:

- number: "016"
  title: Diffusion weighted imaging derivatives
  leads:
    - name: Franco Pestilli
    - name: Oscar Esteban
  update: |
    - Being discussed [here](https://github.com/bids-standard/bids-bep016){:target:"_blank"}.
    - Coordinating with BEP017.
    - Diffusion-weighted model description merged, but must comply to [this](https://github.com/bids-standard/bids-bep016/issues/7){:target:"_blank"}.
    - Upcoming integration across DWI, Tractography, Tractometry, and Connectivity (from fMRI and DWI)
  content:
    - derivative
  blocking: None
  google_doc_created:
  pull_request_created:
  pull_request_merged:

- number: "017"
  title: Generic BIDS connectivity data schema
  leads:
    - name: Eugene Duff
  update: |
    - [Current state](https://bids.neuroimaging.io/bep017){:target:"_blank}.
    - Intended as a meeting point for minimal harmonisation of connectivity-based formats across modalities.
    - Seeking use cases spanning modalities and input defining connectivity based formats
  content:
    - derivative
  blocking: None
  google_doc_created: 2017-05
  pull_request_created:
  pull_request_merged:

- number: "020"
  title: Eye Tracking including Gaze Position and Pupil Size
  leads:
    - name: Dejan Draschkow
  update: |
    - BEP close to PR submission, examples and validator under development.
    - Seeking additional BEP lead to help incorporate into standard contact [dejan](mailto:dejan.draschow@psy.ox.ac.uk) to get involved.
  content:
    - raw
  blocking: None
  google_doc_created: 2018-04
  pull_request_created: 2022-06
  pull_request_merged:

- number: "021"
  title: Common Electrophysiological Derivatives
  leads:
    - name: Arnaud Delorme
    - name: Dora Hermes
    - name: Mainak Jas
    - name: Guiomar Niso
    - name: Robert Oostenveld
    - name: Cyril Pernet
  update: |
    - Discussion [here](https://github.com/bids-standard/bep021){:target:"_blank"} UCSD to include head models with BIDS EEG data.
    - Developments of BIDS M/EEG pipelines will trigger discussion on storing derived data.
  content:
    - derivative
  blocking: Mostly on hold.
  google_doc_created: 2018-05
  pull_request_created:
  pull_request_merged:

- number: "022"
  title: Magnetic Resonance Spectroscopy (MRS)
  leads:
    - name:  Mark Mikkelsen
    - name: William Clarke
    - name: Martin Wilson
  update: |
    - Group discussions [here](https://forum.mrshub.org/t/bids-for-spectroscopy/83){:target:"_blank"}
    and [here](https://forum.mrshub.org/t/nifti-mrs-discussion-thread/443){:target:"_blank"}.
    - Developed NifTI standard for MRS data - presented abstract at ISMRM; manuscript in preparation.
  content:
    - raw
  blocking: None
  google_doc_created: 2018-05
  pull_request_created: 2023-06
  pull_request_merged:

- number: "023"
  title: PET Preprocessing derivatives
  leads:
    - name: Martin Noergaard
    - name: Graham Searle
    - name: Melanie Ganz
  update: |
    - Work in progress following BEP009 incorporation into spec.
    - Coord. kickoff scheduled Sept. 2021 to capture various experimental designs
      and needs for preprocessing and pharmacokinetic modeling.
    - Focused on staying aligned with derivatives for MRI (structural, functional, ASL, diffusion)
  content:
    - derivative
  blocking: Progressing and soliciting input from senior PET experts.
  google_doc_created: 2018-08
  pull_request_created:
  pull_request_merged:

- number: "024"
  title: Computed Tomography scan (CT)
  leads:
    - name: Hugo Boniface
  update: Lead seeking more contributors and experts.
  content:
    - raw
  blocking: None
  google_doc_created: 2018-11
  pull_request_created:
  pull_request_merged:

- number: "026"
  title: Microelectrode Recordings
  leads:
    - name:
  update: BEP is open to new leadership, see also [BEP032 (animal electrophys)](https://bids.neuroimaging.io/bep032){:target:"_blank"}
  content:
    - raw
  blocking: Searching for a new leader.
  google_doc_created: 2018-04
  pull_request_created:
  pull_request_merged:

- number: "028"
  title:  Provenance
  leads:
    - name: Satra Ghosh
    - name: Camille Maumet
  update: |
    - BEP aims to provide a description of data manipulation
      and transformations steps related to a BIDS data element via BIDS structured sidecar JSON-LD files.
    - Can be used to describe provenance at different levels of granularity.
    - Discussions held in [this repository](https://github.com/bids-standard/BEP028_BIDSprov){:target:"_blank"}.
    - A set of [examples](https://github.com/bids-standard/BEP028_BIDSprov/tree/master/examples){:target:"_blank"}
    and [user stories](https://github.com/bids-standard/BEP028_BIDSprov/issues/48){:target:"_blank"} are being refined.
  content:
    - metadata
  blocking: None
  google_doc_created: 2018-08
  pull_request_created:
  pull_request_merged:

- number: "032"
  title:  Animal electrophysiology
  leads:
    - name: Sylvain Takerkart
    - name: Julia Sprenger
  update: |
    - New BEP, collecting comments and community feedback which may be submitted
    [here](https://github.com/INCF/neuroscience-data-structure/issues),
    directly to [Sylvain](mailto:sylvain.takerkart@univ-amu.fr) &
    [Julia](mailto:julia.sprenger@univ-amu.fr), or
    [here](https://www.incf.org/sig/incf-working-group-standardized-data){:target:"_blank"} during the ~monthly meeting.
    - Example datasets [here](https://gin.g-node.org/NeuralEnsemble/BEP032-examples){:target:"_blank"}.
    - Supporting early stage interaction with: [ProbeInterface & SpikeInterface](https://github.com/SpikeInterface){:target:"_blank"},
    [AnDO](https://github.com/INT-NIT/AnDO){:target:"_blank"},
    interoperability with NWB and NIX data/metadata formats.
  content:
    - raw
  blocking: None
  google_doc_created: 2020-12
  pull_request_created: 2022-11
  pull_request_merged:

- number: "033"
  title: Advanced Diffusion Weighted Imaging (aDWI)
  leads:
    - name: James Gholam
    - name: Leandro Beltrachini
    - name: Filip Szczepankiewicz
  update: |
    - New BEP, seeking contributors and collecting community feedback relating to:
    priority sequences to support, best supported binary structured formats
    (e.g. CBOR? HDF5? MsgPack?).
    - Comments may be submitted directly on the document.
    - Generating example datasets [here](https://github.com/JAgho/MISP_plot/tree/main){:target:"_blank"}
    and determining best practice w/ vendors to record data in-sequence
  content:
    - raw
  blocking: None
  google_doc_created: 2021-04
  pull_request_created:
  pull_request_merged:

- number: "034"
  title: Computational modeling
  leads:
    - name: Michael Schirner
    - name: Petra Ritter
  update: |
    BEP Computational Models: PR open for review and discussion
    [here](https://github.com/bids-standard/bids-specification/pull/850)
  content:
    - derivative
    - metadata
  blocking: None
  google_doc_created: 2021-02
  pull_request_created: 2021-08
  pull_request_merged:

- number: "035"
  title: Modular extensions for individual participant data mega-analyses with non-compliant derivatives
  leads:
    - name: Giuseppe Gallitto
    - name: Balint Kincses
    - name: Tamas Spisak
  update: |
    - BEP revised: now collecting further comments and community feedback.
    - Collaborators with mega-analysis experience or with actual example use-cases
      (planned/ongoing/finished mega analyses) welcome!
  content:
    - derivative
  blocking: None
  google_doc_created: 2021-12
  pull_request_created:
  pull_request_merged:

- number: "036"
  title:  Phenotypic Data Guidelines
  leads:
    - name: "[Eric Earl](mailto:eric.earl@nih.gov)"
    - name: "[Samuel Guay](mailto:samuel.guay@umontreal.ca)"
  update: |
    - BEP drafted.
    - Poster presentation at OHBM 2022.
    - Now collecting community comments and feedback.
    - All collaborators are welcome.
  content:
    - raw
  blocking: More reviews and discussions are necessary.
  google_doc_created: 2021-10
  pull_request_created:
  pull_request_merged:

- number: "037"
  title: Non-Invasive Brain Stimulation (NIBS)
  leads:
    - name: "[Giacomo Bertazzoli](mailto:giacomo.bertazzoli@unitn.it)"
    - name: "[Vittorio Iacovella](mailto:vittorio.iacovella@unitn.it)"
    - name: "[Carlo Miniussi](mailto:carlo.miniussi@unitn.it)"
    - name: "[Marta Bortoletto](mailto:marta.bortoletto@cognitiveneuroscience.it)"
  update: New BEP, collecting community comments and feedback. All collaborators are welcome.
  content:
    - raw
  blocking: None
  google_doc_created: 2022-09
  pull_request_created:
  pull_request_merged:

- number: "038"
  title: Atlases
  leads:
    - name: "[James Kent](mailto:jamesdkent21@gmail.com)"
    - name: "[Peer Herholz](mailto:herholz.peer@gmail.com)"
    - name: "[Eugene Duff](mailto:eugene.duff@paediatrics.ox.ac.uk)"
    - name: "[Anthony Galassi](mailto:anthony.galassi@nih.gov)"
  update: New BEP, collecting community comments and feedback. All collaborators are welcome.
  content:
    - raw
  blocking: None
  google_doc_created: 2022-09
  pull_request_created:
  pull_request_merged:

- number: "039"
  title: Dimensionality reduction-based networks
  leads:
    - name: "[Arianna Sala](mailto:arianna.sala@uliege.be)"
    - name: "[Anibal Heinsfeld](mailto:anibalsolon@utexas.edu)"
    - name: "[Cyrus Eierud](mailto:ceierud@gsu.edu)"
    - name: "[Franco Pestilli](mailto:pestilli@utexas.edu)"
    - name: "[Peer Herholz](mailto:herholz.peer@gmail.com)"
  update: New BEP, collecting community comments and feedback. All collaborators are welcome.
  content:
    - raw
  blocking: None
  google_doc_created: 2021-10
  pull_request_created:
  pull_request_merged:

- number: "040"
  title: Functional Ultrasound (fUS)
  leads:
    - name: "[Jean-Charles Mariani](mailto:jean-charles.mariani@cri-paris.org)"
    - name: "[Samuel Diebolt](mailto:samuel.diebolt@iconeus.com)"
    - name: "[Thomas Deffieux](mailto:thomas.deffieux@inserm.fr)"
  update: New BEP, collecting community comments and feedback. All collaborators are welcome.
  content:
    - raw
  blocking: None
  google_doc_created: 2023-03
  pull_request_created:
  pull_request_merged:

- number: "041"
  title: Statistical Model Derivatives
  leads:
    - name: "[Taylor Salo](mailto:salot@pennmedicine.upenn.edu)"
  update: New BEP, collecting community comments and feedback. All collaborators are welcome.
  content:
    - derivative
  blocking: None
  google_doc_created: 2022-08
  pull_request_created:
  pull_request_merged:

- number: "042"
  title: Electromyography (EMG)
  leads:
    - name: "[Seyed Yahya Shirazi](mailto:shirazi@ieee.org)"
  update: New BEP, collecting community comments and feedback. All collaborators are welcome.
  content:
    - raw
  blocking: None
  google_doc_created: 2023-01
  pull_request_created:
  pull_request_merged:

- number: "043"
  title: BIDS Term Mapping
  leads:
    - name: "[Chris Markiewicz](mailto:markiewicz@stanford.edu)"
    - name: "[Eric Earl](mailto:eric.earl@nih.gov)"
  update: For being able to map non-BIDS data as BIDS-compatible. Now collecting community comments and feedback. All collaborators are welcome.
  content:
    - metadata
  blocking: None
  google_doc_created: 2024-03
  pull_request_created:
  pull_request_merged:

- number: "044"
  title: Stimuli
  leads:
    - name: "[Seyed Yahya Shirazi](mailto:shirazi@ieee.org)"
    - name: Dora Hermes
    - name: Yaroslav O. Halchenko
    - name: Kay Robbins
    - name: Scott Makeig
  update: |
    - 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: None
  google_doc_created: 2023-09-12
  pull_request_created:
  pull_request_merged: