From 9a0c46e8bc800d61d9e90d1cfd7781d776515baf Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Mon, 19 Jun 2023 11:00:33 +0200 Subject: [PATCH] [ENH] Add steering minutes 2023 (#310) * add notes 2023 * try fixing link * ignore failing link --- .codespellrc | 2 +- .gitignore | 2 + _config.yml | 1 + _posts/2022-01-27-Steering-Group-minutes.md | 2 +- _posts/2022-11-17-Steering-Group-minutes.md | 14 +- _posts/2022-12-08-Steering-Group-minutes.md | 4 +- _posts/2023-01-19-Steering-Group-minutes.md | 412 ++++++++++++++++++++ _posts/2023-02-09-Steering-Group-minutes.md | 319 +++++++++++++++ _posts/2023-03-02-Steering-Group-minutes.md | 111 ++++++ _posts/2023-03-23-Steering-Group-minutes.md | 165 ++++++++ _posts/2023-04-13-Steering-Group-minutes.md | 219 +++++++++++ _posts/2023-05-04-Steering-Group-minutes.md | 193 +++++++++ md_link_check_config.json | 3 + tools/convert_to_md.py | 2 +- tools/convert_to_md.sh | 2 +- 15 files changed, 1438 insertions(+), 13 deletions(-) create mode 100644 _posts/2023-01-19-Steering-Group-minutes.md create mode 100644 _posts/2023-02-09-Steering-Group-minutes.md create mode 100644 _posts/2023-03-02-Steering-Group-minutes.md create mode 100644 _posts/2023-03-23-Steering-Group-minutes.md create mode 100644 _posts/2023-04-13-Steering-Group-minutes.md create mode 100644 _posts/2023-05-04-Steering-Group-minutes.md diff --git a/.codespellrc b/.codespellrc index d499a573..d558690a 100644 --- a/.codespellrc +++ b/.codespellrc @@ -1,4 +1,4 @@ [codespell] -skip = .git,Gemfile.lock,_sass,_site +skip = .git,Gemfile.lock,_sass,_site,tools/convert_to_md.py ignore-words-list = foo,bar,baz builtin = clear,rare,en-GB_to_en-US diff --git a/.gitignore b/.gitignore index 36e8fc31..64bf13d8 100644 --- a/.gitignore +++ b/.gitignore @@ -4,3 +4,5 @@ Gemfile.lock _site/* .DS_Store .sass-cache +tools/inputs +tools/*.html diff --git a/_config.yml b/_config.yml index b918b502..0268ce8d 100644 --- a/_config.yml +++ b/_config.yml @@ -51,3 +51,4 @@ exclude: - README.md - Gemfile* - vendor + - tools diff --git a/_posts/2022-01-27-Steering-Group-minutes.md b/_posts/2022-01-27-Steering-Group-minutes.md index 84d24154..906cc7cd 100644 --- a/_posts/2022-01-27-Steering-Group-minutes.md +++ b/_posts/2022-01-27-Steering-Group-minutes.md @@ -308,4 +308,4 @@ Date: Thursday, January 27, 2022 Franco: -[[https://github.com/bids-standard/bids-specification/pull/487]{.underline}](https://github.com/bids-standard/bids-specification/pull/487) +[https://github.com/bids-standard/bids-specification/pull/487](https://github.com/bids-standard/bids-specification/pull/487) diff --git a/_posts/2022-11-17-Steering-Group-minutes.md b/_posts/2022-11-17-Steering-Group-minutes.md index 969d8167..fe5a70c4 100644 --- a/_posts/2022-11-17-Steering-Group-minutes.md +++ b/_posts/2022-11-17-Steering-Group-minutes.md @@ -282,27 +282,27 @@ Date: Thursday, November 17th, 2022 Extension leads/moderators: - Giacomo Bertazzoli - > \<[[giacomo.bertazzoli\@unitn.it]{.underline}](mailto:giacomo.bertazzoli@unitn.it)\>, + > \<[giacomo.bertazzoli\@unitn.it](mailto:giacomo.bertazzoli@unitn.it)\>, - Vittorio Iacovella - > \<[[vittorio.iacovella\@unitn.it]{.underline}](mailto:vittorio.iacovella@unitn.it)\>, + > \<[vittorio.iacovella\@unitn.it](mailto:vittorio.iacovella@unitn.it)\>, - Carlo Miniussi - > \<[[carlo.miniussi\@unitn.it]{.underline}](mailto:carlo.miniussi@unitn.it)\>, + > \<[carlo.miniussi\@unitn.it](mailto:carlo.miniussi@unitn.it)\>, - Marta Bortoletto - > \<[[marta.bortoletto\@cognitiveneuroscience.it]{.underline}](mailto:marta.bortoletto@cognitiveneuroscience.it)\>. + > \<[marta.bortoletto\@cognitiveneuroscience.it](mailto:marta.bortoletto@cognitiveneuroscience.it)\>. Extension co-moderators: - Martina Bulgari - > \<[[martina.bulgari\@cognitiveneuroscience.it]{.underline}](mailto:martina.bulgari@cognitiveneuroscience.it)\>, + > \<[martina.bulgari\@cognitiveneuroscience.it](mailto:martina.bulgari@cognitiveneuroscience.it)\>, - Eleonora Marcantoni - > \<[[eleonoramarcantoni\@gmail.com]{.underline}](mailto:eleonoramarcantoni@gmail.com)\>, + > \<[eleonoramarcantoni\@gmail.com](mailto:eleonoramarcantoni@gmail.com)\>, - Giacomo Guidali - > \<[[giacomo.guidali\@cognitiveneuroscience.it]{.underline}](mailto:giacomo.guidali@cognitiveneuroscience.it)\>. + > \<[giacomo.guidali\@cognitiveneuroscience.it](mailto:giacomo.guidali@cognitiveneuroscience.it)\>. Next week visitors: TBD on slack - we will meet 15 minutes early diff --git a/_posts/2022-12-08-Steering-Group-minutes.md b/_posts/2022-12-08-Steering-Group-minutes.md index a07b432a..053ada25 100644 --- a/_posts/2022-12-08-Steering-Group-minutes.md +++ b/_posts/2022-12-08-Steering-Group-minutes.md @@ -358,6 +358,6 @@ Date: Thursday, December 8th, 2022 -**Guest:** Martin Szinte, lead for [[BEP020: Eye tracking including gaze +**Guest:** Martin Szinte, lead for [BEP020: Eye tracking including gaze position and pupil -size]{.underline}](https://docs.google.com/document/d/1eggzTCzSHG3AEKhtnEDbcdk-2avXN6I94X8aUPEBVsw/edit?usp=sharing) +size](https://docs.google.com/document/d/1eggzTCzSHG3AEKhtnEDbcdk-2avXN6I94X8aUPEBVsw/edit?usp=sharing) diff --git a/_posts/2023-01-19-Steering-Group-minutes.md b/_posts/2023-01-19-Steering-Group-minutes.md new file mode 100644 index 00000000..40c355c1 --- /dev/null +++ b/_posts/2023-01-19-Steering-Group-minutes.md @@ -0,0 +1,412 @@ +--- +title: Steering Group minutes +author: +display: true +--- + +# Steering Group minutes 2023/01/19 + +Date: Thursday, January 19th, 2023 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + Topic + + + + Relevant Links + +
+ Chris Rorden + +

+ + + https://github.com/bids-standard/bids-specification/issues/1350 + + +

+

+ Updating + + + https://bids.neuroimaging.io/bep_guide.html + + + → + + + https://github.com/bids-standard/bids-website/issues/269 + + +

+
+

+ Recognizing BIDS validated datasets +

+
+

+ Unique badges? +

+

+ Action: make list of places where these could be advertised +

+
+ 		+

+ BIDS is not yet required in journals, we could reach out to journals for this. +

+

+ OpenNeuro is typically where BIDS datasets are shared. +

+

+ Action: add journal level policy for BIDS validation, start at aperture and then extend to others +

+
+

+ Community projects board +

+
    +
  • +
    +

    + Under ‘get involved’ on homepage +

    +
    +
    • +
+ 		+ Deferred to next meeting due to unclear “Topic” +
+

+ Writing up BIDS usage survey into blog post +

+

+ (Franklin) —> Kim +

+ 		+

+ Some of the analysis code: +

+

+ + + https://github.com/bids-standard/usage_survey + + +

+

+ Add info from MRIQC: +

+

+ June 2022: QC metrics from ~375K unique BOLD scans and ~280K T1 scans +

+
+

+ Task definition: +

+
    +
  • +
    +

    + Task addition for all other modalities besides fMRI +

    +
    +
    • +
  • +
    +

    + Clarification of tasks in appendix +

    +
    +
    • +
+ 		+

+ Task addition PRs: +

+

+ Anat: + + + https://github.com/bids-standard/bids-specification/pull/1185 + + + - merged +

+

+ PET: + + + https://github.com/bids-standard/bids-specification/pull/1196 + + + - merged +

+

+ Task clarification: +

+

+ + + https://github.com/bids-standard/bids-specification/issues/1314 + + + - merged +

+
+

+ BIDS derivatives meeting +

+
    +
  • +
    +

    + organized by OpenNeuroPET project +

    +
    +
    • +
  • +
    +

    + end of march PET BIDS derivatives +

    +
    +
    • +
  • +
    +

    + General BIDS derivatives - 3rd week of June in Copenhangen - invites to follow for all BEP leads + maintainers (‘we’ openneuro PET have some budget for this ; applying for more) +

    +
    +
    • +
+ 		+
+ Yes or No (maybe just a question for Kim): Can we continue adding Steering Group meeting notes to the BIDS website? + +

+ + + https://bids.neuroimaging.io/news.html + + +

+

+ Kim can start doing this again - +

+
+

+ (Added by Eric) Sell BIDS merchandise on TeePublic.com? +

+
    +
  • +
    +

    + Easy sign-up +

    +
    +
    • +
  • +
    +

    + Proceeds could to go to Wikimedia Foundation +

    +
    +
    • +
  • +
    +

    + Can I skip adding the “(c) 2019 BIDS Contributors” to the image? +

    +
    +
    • +
+ 		+

+ + + https://www.teepublic.com/designer-signup + + +

+

+ + + https://github.com/bids-standard/bids-specification/tree/master/BIDS_logo + + +

+

+ + + https://github.com/bids-standard/bids-specification/blob/master/LICENSE + + +

+

+ Committee appears to be agreeable with all of this +

+
+

+ Update governance (added by Rémi): +

+

+ Rémi and Eric met to talk about several things. +

+
    +
  • +
    +

    + Ask “Does the Governance website and documentation state how it itself should be amended?” +

    +
    +
    • +
  • +
    +

    + Propose governance for an Advisory Group members’ (lead of merged BEP) commitment: +

    +
    +
      +
    • +
      +

      + Cannot ask them to commit for life +

      +
      +
      • +
    • +
      +

      + maybe 2 year minimum plus designating a successor, or some such thing +

      +
      +
      • +
    +
    • +
  • +
    +

    + Draft email for consent of completed BEP leads for them to be part of the Advisory group or to nominate someone(s) else +

    +
    +
    • +
+ 		+ + + https://bids.neuroimaging.io/governance.html + + +
+ + +## Notes + +**Present:** Robert Oostenveld, Guiomar Niso, Eric Earl (visiting +maintainer), Yaroslav Halchenko, Kim Ray + +**Guest: invite Chris Rorden** + +**NOTES from Chris Rorden:** + +BEPs are done by experts, but implementations are not done by experts + +BEPs document examples, but are not clear enough in implementation +details (to entry level users).\ +Shows unit testing for converting/translating metadata, requires test +datasets and correct outputs + +Terminology differs e.g. between Siemens and Philips + +- PET example where dicom standards were not used for BIDS + +- [http://www.oneukrainian.com/tmp/DICOMfields.txt](http://www.oneukrainian.com/tmp/DICOMfields.txt) + has rough grep for descriptions of DICOMs fields matching. Some + match some not. + +Suggests possibly reaching out to the tool experts/manufacturers to +better implement BEPs from start to end. + +- Liaisons have been responsive on neurostars (Phillip Clinical + Scientists UK Matthew Clemence \[github drmclem\] Mayo Sandeep + Ganji \[github sandeepganji\]) + +We have a statement to align BIDS with current standards and +vocabularies + +- Yarik could not locate it... + +SOLUTION: + +We cannot assume dcm2nii will fix all of our data conversions. + +Reach out to developers for more input on BEPs before they are approved + +Provide empty header files for examples of data + +- Would be great to have example datasets with sourcedata/ and code/ + and README.md provided to describe HOW data was + converted/translated + +Additional expectations for BEPS before they are approved + +- advise each BEP to reach out to manufacturers to make them aware of + the standardization ongoing, see the BEP, possibly provide + feedback and even may be align metadata/terminology + +Consider/formalize a common principle to choose DICOM fields naming in +favor of adding new names. + +[Ariels's PR](https://github.com/bids-standard/usage\_survey/blob/main/2021/BIDS\_usage\_survey\_results.md) + +Guio : Lets plan for BIDS Townhall in OpenScience Room - OHBM diff --git a/_posts/2023-02-09-Steering-Group-minutes.md b/_posts/2023-02-09-Steering-Group-minutes.md new file mode 100644 index 00000000..2b1dbfa9 --- /dev/null +++ b/_posts/2023-02-09-Steering-Group-minutes.md @@ -0,0 +1,319 @@ +--- +title: Steering Group minutes +author: +display: true +--- + +# Steering Group minutes 2023/02/09 + +Date: Thursday, February 9th, 2023 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + Topic + + + + Relevant Links + +
+

+ Community projects board +

+
    +
  • +
    +

    + Under ‘get involved’ on homepage +

    +
    +
    • +
+ 		+
+

+ Task definition: +

+
    +
  • +
    +

    + Task addition for all other modalities besides fMRI +

    +
    +
    • +
  • +
    +

    + Clarification of tasks in appendix +

    +
    +
    • +
+ 		+

+ Task addition PRs: +

+

+ + + Anat + + + - merged +

+

+ + + PET + + + - merged +

+

+

+

+ + + Task clarification + + + - merged +

+
+

+ BIDS derivatives meeting +

+
    +
  • +
    +

    + organized by OpenNeuroPET project +

    +
    +
    • +
  • +
    +

    + end of march PET BIDS derivatives +

    +
    +
    • +
  • +
    +

    + General BIDS derivatives - 3rd week of June in Copenhagen - invites to follow for all BEP leads + maintainers (‘we’ openneuro PET have some budget for this ; applying for more) +

    +
    +
    • +
+ 		+
+

+ Update governance (added by Rémi): +

+

+ Rémi and Eric met to talk about several things. +

+
    +
  • +
    +

    + Ask “Does the Governance website and documentation state how it itself should be amended?” +

    +
    +
    • +
  • +
    +

    + Propose governance for an Advisory Group members’ (lead of merged BEP) commitment: +

    +
    +
      +
    • +
      +

      + Cannot ask them to commit for life +

      +
      +
      • +
    • +
      +

      + maybe 2 year minimum plus designating a successor, or some such thing +

      +
      +
      • +
    +
    • +
  • +
    +

    + Draft email for consent of completed BEP leads for them to be part of the Advisory group or to nominate someone(s) else +

    +
    +
    • +
+ 		+

+ + + https://bids.neuroimaging.io/governance.html + + +

+

+ + + https://docs.google.com/document/d/18PpfSgcHckqejTZsRZlEDlJ_yD3JiwSQ8kCjVXorg6U/edit + + +

+
+ Chris Rorden also got in touch with the DICOM working groups recently to bring up similar issues he raised in the last Steering Committee Meeting. (KIM RAY) + +

+ + + https://docs.google.com/document/d/1cxv1o4FVALb9sZPX7Jr2XIAyvP6zBd5xQV5BzISFZ7Q/edit?usp=sharing + + +

+

+ Copy of email chain from Chris with DICOM working groups. +

+
+ +## Notes + +Suggestion to add make the [decision making +rules](https://github.com/bids-standard/bids-specification/blob/master/DECISION-MAKING.md) +more visible + +Is this a suggestion to make the team more visible or funding, including +for example BEP funding like +[https://www.nature.com/articles/sdata2018110\#Ack1](https://www.nature.com/articles/sdata2018110#Ack1)? +The team, and BEP leaders, as well as funding and who is supported by +the funding + +Guio: we need to revisit the BIDS funding landing page, and update the +figures. Suggested to prioritize these updates during a brain hack? + +Stefan: The Maintainers team does not have capacity to redesign the +website. + +ACTION: Yaroslav will submit a pull request/issue (done: +[https://github.com/bids-standard/bids-website/pull/279](https://github.com/bids-standard/bids-website/pull/279) +for starters) with table to github to add funding and a link to the +contributor/funders page and Stefan will follow up + +Task definitions (Cyril): task was specific to fMRI, however it has now +been added to PET, and MRI anat, see +[pull](https://github.com/bids-standard/bids-specification/pull/1392). +However it still needs to be implemented in the BIDS validator and +examples. See issues below: + +Outstanding, but WIP: +- [https://github.com/bids-standard/bids-validator/pull/1578](https://github.com/bids-standard/bids-validator/pull/1578) +- [https://github.com/bids-standard/bids-validator/issues/1564](https://github.com/bids-standard/bids-validator/issues/1564) + +BIDS derivatives meeting : next week the first round of invites will be +extended, looking for more funding to support travel. Aiming for 20-30 +attendees. Currently some people will have some, limited, or no +financial support for travel to the meeting. + +Considerations: What is the plan for the Program ? Will there be a +hybrid option? + +Current suggestions (Cyril), have people come with data and complete +examples to improve BEPS + +Stefan: + +- Amendment 1 - every BEP lead will join the BIDS advisory group +forever (not ideal), proposed to allow individuals to leave the +advisory group after 2 years and asked to suggest a replacement. +- Amendment 2 - we don\'t currently have a process to change the BIDS +governance, some solutions have been put forth: +[https://docs.google.com/document/d/18PpfSgcHckqejTZsRZlEDlJ\_yD3JiwSQ8kCjVXorg6U/edit](https://docs.google.com/document/d/18PpfSgcHckqejTZsRZlEDlJ_yD3JiwSQ8kCjVXorg6U/edit) +- Amendment 3 - BIDS contributors - governance states that all +contributors are equal, but this needs to be amended because many +contributors at some point are no longer active and this creates issues +when minimum % of votes are required for certain elections. WIP for +current and new wording - maintainers are working on this and the +steering group can comment and give feedback. + +GUIO: Suggestion to include a list of Advisory Group members. + +Robert: What is the order of amendments to be approved? + +Stefan - suggests all amendments to be at once. This has been done +before, there is precedence. + +Yaroslav: recommends new language to define active & inactive advisory +group members. + +Chris Rorden also got in touch with the DICOM working groups - its a +good idea, however its possibly beyond the expertise of individuals in +the steering group and beyond the time constraints of the BIDS steering +group. + +Alignment with BIDS and DICOM should be encouraged, but time is the +obstacle for working with DICOMs. Maybe DICOM working group 16 may be +worthwhile to interact with to inform/influence their decision making to +align with BIDS. + +Can Chris facilitate this with working group 16? Perhaps Yarik can voice +steering group issues with guidance from Chris (who is likely most +familiar with issues between DICOM and BIDS). + +**ACTION**: email DICOM and present BIDS to them with support form Chris. + +DICOM meeting notes - https://www.dicomstandard.org/activity/wgs + +Cyril: discussed with aperture on submitting data papers (including a +logo to indicate the dataset is BIDS compliant). data must be BIDS +validated, it must include a sharing statement, if its not on openneuro +then there must be a way to ensure it is BIDS validated. Cyril will make +progress on this to be approved by aperture. + +Ariel: what is the status of BIDS being included in COBIDAS? + +Future Guests? None identified yet. + +Non-invasive stimulation - making good progress + +Two Atlas BEPS +https://github.com/bids-standard/bids-specification/issues/1379 diff --git a/_posts/2023-03-02-Steering-Group-minutes.md b/_posts/2023-03-02-Steering-Group-minutes.md new file mode 100644 index 00000000..244a0a7d --- /dev/null +++ b/_posts/2023-03-02-Steering-Group-minutes.md @@ -0,0 +1,111 @@ +--- +title: Steering Group minutes +author: +display: true +--- + +# Steering Group minutes 2023/03/02 + +Date: Thursday, March 2nd, 2023 + + + + + + + + + + + + + + + + + +
+ + Topic + + + + Relevant Links + +
+ Peer Herholtz Guest: Discussing two Atlas BEPs + + + + https://github.com/bids-standard/bids-specification/issues/1379 + + +
+ +## NOTES + +**Present:** Robert Oostenveld, Guiomar Niso, Cyril Pernet, Ariel Rokem, +Chris Markiewicz (Maintainer guest), Yaroslav Halchenko, Kim Ray +(Secretariat) + +**Guest: Peer Herholtz** + +Peer Herholtz - Atlas BEPs + +September 2022 BIDS Connectivity Project started an Atlas BEP (led by +Peer) + +Jan 2023 another community started an Atlas BEP +([flyxiaye](https://github.com/flyxiaye)) + +Feb 2023 both BEP leads met, Talo Salo was in attendance, to determine +how the teams should move forward + +Conclusion: + +- Peer's BEP focuses on storing utilizing writing analyses +- [flyxiaye](https://github.com/flyxiaye): focuses on + how atlases should be characterized, described, and what meta-data is + needed to navigate an atlas. (Taylor Salo mentioned this BEP doesn't + follow the typical BEP flow, similar to template flow) +- the two BEPs appear complementary yet distinct. The teams will move + forward and collaborate where possible. + +Comments: + +How much are atlas BEPs tools or extensions? If they are tools, then +perhaps they should be BIDSapps. + +- The goal of Peer's Atlas BEP is to provide a way to include + atlas/ROI/template information in derivatives for connectivity + analyses + +Inside the specification - where does the Atlas BEP fit? + +- Could be part of BEP 17 connectivity matrices, or statistical + models, as well as others + +- Should align with other BEPs (e.g. provenance BEP) + +- It's been proposed to have an atlas directory by Peer's working + group, but agrees that the atlas can be applicable in different + way + +- RAW is defined by something that is provided by 'hardware', + Derivatives is data that's been derived from raw - thus atlases + should be in derivatives? + +- Peer's Atlas BEP currently suggests storing atlases in derivatives + or in subject level + +- Could atlas be considered as a separate subject?(Guio) + +- Example: MEG has unique file formats, EEG has many caps, but does + this need to be stored in BIDS + +- BIDS defines standard templates at: + [https://bids-specification.readthedocs.io/en/stable/appendices/coordinate-systems.html\#standard-template-identifiers](https://bids-specification.readthedocs.io/en/stable/appendices/coordinate-systems.html#standard-template-identifiers) + +- These things (altases, ROIs) are well defined. They should be + formalized in BIDS, but clearly it\'s not yet agreed upon how or + where. diff --git a/_posts/2023-03-23-Steering-Group-minutes.md b/_posts/2023-03-23-Steering-Group-minutes.md new file mode 100644 index 00000000..0cb3963a --- /dev/null +++ b/_posts/2023-03-23-Steering-Group-minutes.md @@ -0,0 +1,165 @@ +--- +title: Steering Group minutes +author: +display: true +--- + +# Steering Group minutes 2023/03/23 + +Date: Thursday, March 23rd, 2023 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + Topic + + + + Relevant Links + +
+ “Model” / “Resultset” directory proposal + + + + https://github.com/bids-standard/bids-specification/pull/1280 + + +
+ BIDS Derivatives retreat June 21st - 23rd + + + + https://openneuropet.github.io/bidsderivativemeeting/ + + +
+ Summary of the PET-BIDS derivatives meeting + + + + BIDS Extension Proposal 23 (BEP023): PET Preprocessing Derivatives + + +
+ Meeting with the DICOM team + + Yaroslav sent a follow up email offering to join DICOM committee meeting +
+

+ Stefan: Here are three issues that could benefit from steering input (in particular those familiar with ephys experience) +

+
    +
  • +
    +

    + https://github.com/bids-standard/bids-specification/pull/1441 +

    +
    +
    +

    + https://github.com/bids-standard/bids-specification/issues/1436 +

    +
    +
    +

    + https://github.com/bids-standard/bids-specification/issues/1446 +

    +
    +
    • +
+ 		+
+ +## Notes + +"Model" / "Resultset" directory proposal derivatives [pull +request](https://github.com/bids-standard/bids-specification/pull/1280) + +New proposal of models (e.g. dti models) where derivatives may be +created from this model thus creating parameters and derivatives of a +model that have overlapping meta-data. + +Proposed Solution: + +- add a 'results' directory that contains the files of the model with + metadata describing those files. Is it okay to add an additional + nested directory like this? + +- MFP (model fit parameter) and MDP (model derived parameter) suffixes + +Concern: + +- this appears to be very dwi specific, should the suffixes be dwi + specific? +- Why is datatype not under model label in the [pull + request](https://github.com/bids-standard/bids-specification/pull/1280) + example? +- Is the proposed organization of data aligned with user community? - + should we request input from community to determine where these + results should be stored +- [https://github.com/bids-standard/bids-specification/issues/751\#issuecomment-820800800](https://github.com/bids-standard/bids-specification/issues/751#issuecomment-820800800) +- How does this apply to more general data modalities? Like mEEG, + SPECT - more use cases beyond dMRI would be helpful +- "BIDS-like derivatives in other modalities: + [https://data.donders.ru.nl/collections/di/dccn/DSC\_3031000.00\_191?0](https://data.donders.ru.nl/collections/di/dccn/DSC_3031000.00_191?0), see also + [https://github.com/Donders-Institute/infant-cluster-effectsize](https://github.com/Donders-Institute/infant-cluster-effectsize) + (for the scripts that generate the result) +- Other ideas: tarballs instead of directories, HDF5 files instead of + directories. + + +BIDS Derivatives Retreat + +- For general derivatives group (not just pet) +- See link for more information + +Summary of the PET-BIDS derivatives meeting + +- Meeting happened 2 weeks ago (March 10th) +- Mostly an onboarding meeting for the importance and relevance of + PET-BIDS derivatives +- Raw PET data is now part of BIDS, now the second half of the white + paper will address the derivatives aspect of PET +- The PET users are more clinically oriented, more diverse user + groups, less agreement within the community in data standards +- The community is between two ideas: a more restrictive approach with + data types allowed, or free datatypes with detailed provenance + +Meeting with the DICOM team + +- We need to formalize our current state of affairs, see which terms + align/ dont align +- We need to follow up on email from Kim on Feb 14 asking to present + at a dicom committee meeting. diff --git a/_posts/2023-04-13-Steering-Group-minutes.md b/_posts/2023-04-13-Steering-Group-minutes.md new file mode 100644 index 00000000..17401522 --- /dev/null +++ b/_posts/2023-04-13-Steering-Group-minutes.md @@ -0,0 +1,219 @@ +--- +title: Steering Group minutes +author: +display: true +--- + +# Steering Group minutes 2023/04/13 + +Date: Thursday, April 13th, 2023 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + Topic + + + + Relevant Links + +
+

+ Stefan: Here are three issues that could benefit from steering input (in particular those familiar with ephys experience) +

+ + 		+

+ Cyril: (1) in + + + https://bids-specification.readthedocs.io/en/latest/modality-specific-files/task-events.html + + + sample is not defined, ie custom column, not sure I follow the why in issue 1441 (2) +

+

+ Issue 1436 -- yes let’s do that, robert also agreed on that (3) seems like there is a consensus +

+
+

+ + Remi Gau + +

+

+ Discussed at the maintainers meeting: a PR that "standardizes" contributors info. +

+

+ This PR does several things: one of them is that it would start adding the list of our contributors (as 'authors') to the zenodo release of the BIDS specification that we get our DOI from. +

+

+ The problem is that there has not yet been an agreement on how authors/ contributors should be listed in those zenodo releases: see this old issue +

+

+ + + [DISCUSSION] acknowledge contributors in DOIed specs on Zenodo · Issue #66 · bids-standard/bids-specification · GitHub + + +

+

+ This aspect of the PR can put on hold for now but "we" (the maintainers) felt that it would be good if the steering group took a decision on this old issue (that may actually need rethinking given how much time has passed and that we have had so many new modalities and contributions since it was opened). +

+ 		+

+ + bids-specification 1115 + +

+

+ + bids-specification 66 + +

+
+ Discussion with DICOM - where are we at? + + Discuss next meeting +
+ Discussion with journals - where are we at? (badges for BIDS datasets) + +

+ Aperture is fine with this, but they are in the middle of updating their website +

+

+ Should we push ahead with scientific data? (their staff are familiar with BIDS and may be a good next journal to approach) +

+
+ OHBM best practice? + + Cyril: John Pyles has circulated the OHBM BIDS 2 doc - reviewing of the proposal? +
+ + +## NOTES + +Github pull request - [bids-specification 1441](https://github.com/bids-standard/bids-specification/pull/1441) +and [bids-specification 1457](https://github.com/bids-standard/bids-specification/pull/1457) +- The requesters want to change from number to integer, it was likely + in a previous version but not in the current. +- The sample is not defined, this could be defined in the json - +- This should be fine then + +Github pull request: Formalize how channel types are shared between +modalities that use channels.tsv files. [bids-specification 436](https://github.com/bids-standard/bids-specification/issues/1436) + +Github pull request: ENH: Array data in .tsv cells - [bids-specification 1446](https://github.com/bids-standard/bids-specification/issues/1446) +- We might need an example of nesting +- 80/20 rules may need to apply here where we define rules for + examples that occur 80% of the time. +- Why not just repeat the rows for each channel? Example: the onset + time for multiple channels could be listed across multiple rows + instead of condescending them into a single row/entry (Ariel will + suggest this in the pull request) + +Github pull request: [DISCUSSION] acknowledge contributors in DOIed +specs on Zenodo - [bids-specification 66](https://github.com/bids-standard/bids-specification/issues/66) +- What rule should be used for author order on zenodo DOI? +- Proposal: use a random number generator for each new push of authors + to keep order 'fair' for all, possibly include an alphabetical + list on the BIDS website for ease of author identification +- **Final decision: alphabetical is simple and standard, order does + not imply importance, PR is fine.** +- Clarify it explicitly in the text + +Journals including badges to indicate BIDS compliant dataset: +- Aperture is agreeable, their website is under development +- Suggestions: next journal to approach could be **scientific data** + given their familiarity with BIDS. +- Action: email the Scientific Data editor in chief from the BIDS + Steering Committee +- Question standardization of implementation across journals? + - Guio will provide and example draft +- Question: who/what will identify BIDS compliant datasets? + - BIDS validator can, however users can include many \#BIDS IGNORE + files + - Either the validator will need to output bidsignore info or + reviewers/editors will need to check the bidsignore files + themselves. + +OHBM best practice committee +- Cyril: John Pyles has circulated the OHBM doc of BIDS 2- reviewing + of the proposal? + - This will be reviewed by individuals external from BIDS + - There will be multiple versions , not all versions need to be + reviewed +- 'What is BIDS' should be presented to the community, who should lead + this presentation? + - Experts from each field? + +Was there a podcast ([OHBM Neurosalience](https://www.youtube.com/playlist?list=PLg2e4R8SdhpdIMG7Tb9WAEZA6HRnx8Vsb)) +where Peter Bandettini suggested someone talk about BIDS? +- Originated in October 2022, sounds like a good opportunity for more + exposure, Cyril will reply to the email thread + +Next Meeting Guest: +- possibly JB Poline regarding a new tool (could be posted as an issue + on github?) +- Maintainers met with the functional ultrasound group but they are + likely too premature for this meeting. + +Cyril: the BIDS retreat is looking for additional funding to increase +the support for the meeting. Who should be additionally invited? + +MRTRIX team, BIDS connectivity group, diff --git a/_posts/2023-05-04-Steering-Group-minutes.md b/_posts/2023-05-04-Steering-Group-minutes.md new file mode 100644 index 00000000..c690989e --- /dev/null +++ b/_posts/2023-05-04-Steering-Group-minutes.md @@ -0,0 +1,193 @@ +--- +title: Steering Group minutes +author: +display: true +--- + +# Steering Group minutes 2023/05/04 + +Date: Thursday, May 4th, 2023 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + Topic + + + + Relevant Links + +
+ Discussion with DICOM - where are we at? + + No new updates, Yaroslav is sending another email reminder . Outstanding PR: + + + bids-specification/pull/1450 + + +
+ OHBM best practice updates? + +
+ + + OHBM Neurosalience + + + podcast opportunity to talk about BIDS + +
+ OHBM townhall status; BEP updates + +
+ BIDS derivatives meeting + +
+ BIDS 2.0 getting the ball rolling? + + + + Issues · bids-standard/bids-2-devel · GitHub + + +
+ +## NOTES + +**Present:** Robert Oostenveld, Cyril Pernet, Guiomar Niso, Ariel Rokem, +Yaroslav Halchenko, Chris Markiewicz + +**Guest:** Guy Jones (unable to attend, will invite for next meeting) + +### Discussion with DICOM group + +Yaroslav sent a follow up email to the DICOM committees during the +previous meeting, we heard a brief email acknowledgment in response but +no progress in identifying a committee to meet with. + +Yaroslav will send another email reminder. + +Related PR link the relevant links: Add explicit wording on DICOM terms +correspondence + +Yaroslav schema: +[2022-tx-big-neuroscience.html](http://datasets.datalad.org/centerforopenneuroscience/talks/2022-tx-big-neuroscience.html#/3/2/1) +- being proposed improved as +[bids-starter-kit/pull/294](https://github.com/bids-standard/bids-starter-kit/pull/294) + +Cyril\'s dicom2bids in pet: +[dicom2bids.json](https://github.com/openneuropet/PET2BIDS/blob/main/metadata/dicom2bids.json) + +### OHBM Best Practices Updates + +April 12, John Piles says things are in progress - chairs JB Poline and +other co-chair is organizing it. + +### OHBM Neurosalience Podcast + +Peter agreed but we need to +find a times for this, and we need to identify who would be the +appropriate representative. + +Topic Suggestion: discuss what's new in BIDS and a high-level overview of +BIDS. + +Related Discussion: **BIDS news** +(https://bids.neuroimaging.io/news.html) - this could be an additional +avenue for sharing BIDS updates + +We should use multiple avenues for sharing BIDS updates/news: podcast, +website, publication (Russ is working on a 'history' of BIDS +publication), twitter (let maintains and steering committee each take a +month rotations for responsibility). + +Suggestion - to make the BIDS landing page more active and include news +updates. + +### OHBM townhall status + +BIDS and BEP updates should be reported (used to be Franklin, +maintainers can take this role) + +Peer Herholtz will have updates on BIDS \'connectivity' related BEPS + +Due to changes in the OS-SIG Scheduling, the typical OHBM BIDS +townhall may need to be a bit different than usual. + +Franklin used to write the organizers requesting for an hour townhall, +the steering committee (Cyril will work on finding a time for a BIDS +townhall) + +Suggestions: Submit a BIDS proposal for a townhall or symposium for +next OHBM. (Kim will add a reminder in November to discuss and plan +this.) + +### BIDS derivatives meeting + +Invitations have/are going out. Website is being developed. About 25 +attendees. + +Cyril would like to send out an email with meeting goals and vision to +help with structuring the meeting. + +Possible a larger vision for how derivatives will be used + +Ask for attendees to bring data examples to help with derivative +development. + +A current delay for derivatives is developing a validator. + +Robert and Ariel: suggest reaching out to people in other fields for +future direction for derivatives (how they use their data derivatives - +astronomy, and possibly geosciences?) + +### BIDS 2.0 getting the ball rolling + +This needs to happen - What should be included in BIDS 2.0 ? + +There are currently many existing updates, can a group of people meet +and discuss which points should be prioritized. + +Address: what are the technical barriers with BIDS 1 and 1.2 to allow +them to coexist, and we need to make sure that BIDS 2.0 will not break +previous BIDS. + +We need to establish how prior BIDSapps will handle BIDS2 data. + +[https://semver.org/](https://semver.org/) diff --git a/md_link_check_config.json b/md_link_check_config.json index 1ec51c73..6379ed48 100644 --- a/md_link_check_config.json +++ b/md_link_check_config.json @@ -23,6 +23,9 @@ }, { "pattern": "^https://web.archive.org/web/20170813183704/http://wiki.incf.org/mediawiki/index.php/Neuroimaging_Task_Force" + }, + { + "pattern": "^https://data.donders.ru.nl/collections" } ], "timeout": "20s", diff --git a/tools/convert_to_md.py b/tools/convert_to_md.py index 65c1bea8..010b563c 100644 --- a/tools/convert_to_md.py +++ b/tools/convert_to_md.py @@ -54,7 +54,7 @@ def rename_files(input_folder): month, day = line.split(" ")[2:] - day = day.replace("th", "") + day = day.replace("th", "").replace("rd", "").replace("nd", "").replace("st", "") if month in MONTH_MAPPING: month = MONTH_MAPPING[month] diff --git a/tools/convert_to_md.sh b/tools/convert_to_md.sh index bdab447c..560d9385 100644 --- a/tools/convert_to_md.sh +++ b/tools/convert_to_md.sh @@ -5,7 +5,7 @@ # # from https://github.com/llbbl/scripts/blob/main/util/convert_all_word_files.sh -YEAR="2022" +YEAR="2023" # save current working directory to variable cwd=$(pwd)/inputs/${YEAR}