Merge pull request #203 from tsalo/new-beps

[ENH] Add computational models and mega-analysis BEPs
bids-standard · Sep 20, 2021 · a8657b9 · a8657b9
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diff --git a/README.md b/README.md
@@ -20,4 +20,4 @@ The specification is hosted on [https://bids-specification.readthedocs.io](https
 
 ## Asking questions about BIDS
 
-If you have questions how to apply BIDS to your dataset, how to use a shared BIDS dataset, or about tools to convert and/or handle BIDS datasets, please see the [getting started](https://bids.neuroimaging.io/getting_started.html) page.
+If you have questions how to apply BIDS to your dataset, how to use a shared BIDS dataset, or about tools to convert and/or handle BIDS datasets, please see the [getting started](https://bids.neuroimaging.io/get_started.html) page.
diff --git a/_bep_collection/bep034.md b/_bep_collection/bep034.md
@@ -0,0 +1,4 @@
+---
+redirect_to:
+  - https://docs.google.com/document/d/1NT1ERdL41oz3NibIFRyVQ2iR8xH-dKY-lRCB4eyVeRo/edit
+---
diff --git a/_bep_collection/bep035.md b/_bep_collection/bep035.md
@@ -0,0 +1,4 @@
+---
+redirect_to:
+  - https://docs.google.com/document/d/10RpFFsG_ESj0orGIqJ0yK4DTpeoyrmd4RjX2ER-P31k/edit
+---
diff --git a/_pages/get_involved.md b/_pages/get_involved.md
@@ -57,7 +57,7 @@ will have to wait for BIDS 2.0 are listed
 [here](https://docs.google.com/document/d/1LEgsMiisGDe1Gv-hBp1EcLmoz7AlKj6VYULUgDD3Zdw){:target="_blank"}.
 
 | Extension label                                                 | Title                                                                                                      | Moderators/ leads                                                | Summary                                                                                                                                                                                                                                   | Blocking point(s)                                                                      |
-| --------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------- |
+| --------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------- |
 | [BEP002](https://bids.neuroimaging.io/bep002){:target:"_blank"} | The BIDS Models Specification                                                                              | Tal Yarkoni , Chris Markiewcz                                    | Reworked structure - list of steps is now a directed,graph, [Model zoo](https://github.com/bids-standard/model-zoo){:target:"_blank"}, Abstracted transformations, to ease interoperability of implementations                         | Stat Models released v1.0.0-rc1 in June 2021 - Please review! |
 | [BEP004](https://bids.neuroimaging.io/bep004){:target:"_blank"} | Susceptibility Weighted Imaging (SWI)                                                                      | Available                                                        | Looking for a new leader.                                                                                                                                                                                                              | Searching for a new leader.                                                            |
 | [BEP011](https://bids.neuroimaging.io/bep011){:target:"_blank"} | The structural preprocessing derivatives                                                                   | Viviana Siless                                                   | Features Surfaces, Scalar maps on Surfaces, and Morphometrics. Opened [pull request](https://github.com/bids-standard/bids-specification/pull/518){:target:"_blank"}. Need to conform with final Common Derivatives and gather community feedback. | Blocked by BIDS-validator extending and PyBIDS implementation for common derivatives |
@@ -73,14 +73,16 @@ will have to wait for BIDS 2.0 are listed
 | [BEP023](https://bids.neuroimaging.io/bep023){:target:"_blank"} | PET Preprocessing derivatives                                                                              | Martin Noergaard, Graham Searle, Melanie Ganz                    | 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) | Progressing and soliciting input from senior PET experts. |
 | [BEP024](https://bids.neuroimaging.io/bep024){:target:"_blank"} | Computed Tomography scan (CT)                                                                              | Hugo Boniface                                                    | Lead seeking more contributors and experts.                                                                                                                                                                    | None.                                                                                  |
 | [BEP025](https://bids.neuroimaging.io/bep025){:target:"_blank"} | Medical Imaging Data structure (MIDS)                                                                      | Jose Manuel Saborit Torres, Maria de la Iglesia Vayá             | Enhancing [BEP025 preprint](https://arxiv.org/abs/2010.00434){:target:"_blank"}. Provided [automated tool](https://github.com/BIMCV-CSUSP/MIDS){:target:"_blank"} to convert projects uploaded to XNAT platforms to BIDS/MIDS. Example datasets: [Massive Image Data Anatomy Spine](https://bimcv.cipf.es/bimcv-projects/project-midas/){:target:"_blank"}, [BIMCV-COVID19+](https://bimcv.cipf.es/bimcv-projects/bimcv-covid19/){:target:"_blank"}, and [BIMCV-COVID19-](https://bimcv.cipf.es/bimcv-projects/bimcv-covid19/#1590859488150-148be708-c3f3){:target:"_blank"}. Included Kaggle Challenge [SIIM-FISABIO-RSNA COVID-19 Detection](https://www.kaggle.com/c/siim-covid19-detection/overview){:target:"_blank"} | None.
-| [BEP026](https://bids.neuroimaging.io/bep026){:target:"_blank"} | Microelectrode Recordings                                                                                  |                                                                  | BEP is open to new leadership, see also [BEP032 (animal electrophys)](https://bids.neuroimaging.io/bep032){:target:"_blank"} | Searching for a new leader. | 
+| [BEP026](https://bids.neuroimaging.io/bep026){:target:"_blank"} | Microelectrode Recordings                                                                                  |                                                                  | BEP is open to new leadership, see also [BEP032 (animal electrophys)](https://bids.neuroimaging.io/bep032){:target:"_blank"} | Searching for a new leader. |
 | [BEP027](https://bids.neuroimaging.io/bep027){:target:"_blank"} | BIDS Applications 2.0                                                                                      | Chris Markiewicz and Greg Kiar                                   | Focusing on: command-line conventions, I/O interface descriptors, and common behavior (e.g., exit codes for failure modes); relies upon the Boutiques standard. Re-conception of BIDS Apps| None.                                                                           |
 | [BEP028](https://bids.neuroimaging.io/bep028){:target:"_blank"} | Provenance                                                                                                 | Satra Ghosh and Camille Maumet                                   | 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. Dicussions 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. | None.                                                                                  |
 | [BEP029](https://bids.neuroimaging.io/bep029){:target:"_blank"} | Virtual and physical motion data                                                                           | Sein Jeung and Julius Welzel                                     | BEP is developing and starting to finalize as discussions concerning example datasets are completed.  | None. |
 | [BEP030](https://bids.neuroimaging.io/bep030){:target:"_blank"} | Near Infrared Spectroscopy (NIRS)                                                                          | Robert Luke and Luca Pollonini                                   | BEP presented at the society for fNIRS conference. Have developed SNRIF data format. Opened as [pull request](https://forum.mrshub.org/t/nifti-mrs-discussion-thread/443){:target:"_blank"}. Primarily for continuous wave NIRS (CW-NIRS), but want to ensure not to preclude future extensions. Examples and validator efforts in progress. Inviting colleagues from time- and frequency-domain fNIRS to review proposal.| None.                                                                                  |
 | [BEP031](https://bids.neuroimaging.io/bep031){:target:"_blank"} | Microscopy                                                                                                 | Marie-Hélène Bourget and Julien Cohen-Adad                       | BEP is finalizing proposal and community review, preparing to submit to specification in Fall 2021. Metadata related pull requests for [sample entity and samples.tsv](https://github.com/bids-standard/bids-specification/pull/812){:target:"_blank"} and [participants.tsv](https://github.com/bids-standard/bids-specification/pull/816){:target:"_blank"}. | None.                                                                                  |
 | [BEP032](https://bids.neuroimaging.io/bep032){:target:"_blank"} | Animal electrophysiology                                                                                   | Sylvain Takerkart and Julia Sprenger                             | New BEP, collecting comments and community feedback which may be submitted [here](https://github.com/INCF/neuroscience-data-structure/issues), directly to [Sylvain](mailto:[email protected]) & [Julia](mailto:[email protected]), 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.                                                                                                                    | None.                                           |
 | [BEP033](https://bids.neuroimaging.io/bep033){:target:"_blank"} | Advanced Diffusion Weighted Imaging (aDWI)                                                                 | James Gholam, Leandro Beltrachini and Filip Szczepankiewicz      | 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 | None.                                           |
+| [BEP034](https://bids.neuroimaging.io/bep034){:target:"_blank"} | Computational modeling                                                                                     | Michael Schirner and Petra Ritter                                | BEP Computational Models: PR open for review and discussion [here](https://github.com/bids-standard/bids-specification/pull/850). | None.                                           |
+| [BEP035](https://bids.neuroimaging.io/bep035){:target:"_blank"} | Extended derivatives structure for individual-level meta-analyses based on non-BIDS compliant datasets     | Giuseppe Gallitto and Tamas Spisak                               | New BEP, collecting comments and community feedback, especially on handling "conditions-of-interests". Collaborators with mega-analysis experience or with actual example use-cases (planned/ongoing/finished mega analyses) welcome! | None.                                           |
 
 
 ### Completed BEPs
Original file line number	Diff line number	Diff line change
Expand Up		@@ -20,4 +20,4 @@ The specification is hosted on [https://bids-specification.readthedocs.io](https

		## Asking questions about BIDS

		If you have questions how to apply BIDS to your dataset, how to use a shared BIDS dataset, or about tools to convert and/or handle BIDS datasets, please see the [getting started](https://bids.neuroimaging.io/getting_started.html) page.
		If you have questions how to apply BIDS to your dataset, how to use a shared BIDS dataset, or about tools to convert and/or handle BIDS datasets, please see the [getting started](https://bids.neuroimaging.io/get_started.html) page.