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Bump the npm group with 5 updates (#711)
Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Remi Gau <[email protected]> Co-authored-by: Christopher J. Markiewicz <[email protected]>
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.remarkrc

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"preset-lint-recommended",
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"remark-gfm",
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["lint-no-duplicate-headings", false],
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["lint-list-item-indent", "tab-size"],
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["lint-list-item-indent", "tab"],
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["lint-emphasis-marker", "consistent"],
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["lint-maximum-line-length", 500],
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["lint-maximum-heading-length", false],

docs/blog/posts/2023-03-23-steering-group-minutes.md

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Concern:
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- this appears to be very dwi specific, should the suffixes be dwi
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specific?
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- Why is datatype not under model label in the [pull request](https://github.com/bids-standard/bids-specification/pull/1280)
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example?
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- this appears to be very dwi specific, should the suffixes be dwi specific?
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- Why is datatype not under model label in the [pull request](https://github.com/bids-standard/bids-specification/pull/1280) example?
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- Is the proposed organization of data aligned with user community? -
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should we request input from community to determine where these
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results should be stored
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- [https://github.com/bids-standard/bids-specification/issues/751\#issuecomment-820800800](https://github.com/bids-standard/bids-specification/issues/751#issuecomment-820800800)
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- How does this apply to more general data modalities? Like mEEG,
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SPECT - more use cases beyond dMRI would be helpful
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should we request input from community to determine where these
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results should be stored
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[https://github.com/bids-standard/bids-specification/issues/751\#issuecomment-820800800](https://github.com/bids-standard/bids-specification/issues/751#issuecomment-820800800)
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- How does this apply to more general data modalities? Like mEEG, SPECT - more use cases beyond dMRI would be helpful
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- "BIDS-like derivatives in other modalities:
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[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
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[https://github.com/Donders-Institute/infant-cluster-effectsize](https://github.com/Donders-Institute/infant-cluster-effectsize)
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(for the scripts that generate the result)
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- Other ideas: tarballs instead of directories, HDF5 files instead of
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directories.
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[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
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[https://github.com/Donders-Institute/infant-cluster-effectsize](https://github.com/Donders-Institute/infant-cluster-effectsize)
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(for the scripts that generate the result)
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- Other ideas: tarballs instead of directories, HDF5 files instead of directories.
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BIDS Derivatives Retreat
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Summary of the PET-BIDS derivatives meeting
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- Meeting happened 2 weeks ago (March 10th)
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- Mostly an onboarding meeting for the importance and relevance of
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PET-BIDS derivatives
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- Raw PET data is now part of BIDS, now the second half of the white
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paper will address the derivatives aspect of PET
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- The PET users are more clinically oriented, more diverse user
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groups, less agreement within the community in data standards
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- The community is between two ideas: a more restrictive approach with
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data types allowed, or free datatypes with detailed provenance
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- Mostly an onboarding meeting for the importance and relevance of PET-BIDS derivatives
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- Raw PET data is now part of BIDS, now the second half of the white paper will address
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the derivatives aspect of PET
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- The PET users are more clinically oriented, more diverse user groups,
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less agreement within the community in data standards
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- The community is between two ideas: a more restrictive approach
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with data types allowed, or free datatypes with detailed provenance
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Meeting with the DICOM team
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- We need to formalize our current state of affairs, see which terms
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align/ dont align
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- We need to follow up on email from Kim on Feb 14 asking to present
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at a dicom committee meeting.
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- We need to formalize our current state of affairs, see which terms align/ dont align
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- We need to follow up on email from Kim on Feb 14 asking to present at a dicom committee meeting.

docs/blog/posts/2023-04-13-steering-group-minutes.md

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Github pull request - [bids-specification 1441](https://github.com/bids-standard/bids-specification/pull/1441)
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and [bids-specification 1457](https://github.com/bids-standard/bids-specification/pull/1457)
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- The requesters want to change from number to integer, it was likely
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in a previous version but not in the current.
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- The requesters want to change from number to integer, it was likely in a previous version but not in the current.
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- The sample is not defined, this could be defined in the json -
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- This should be fine then
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Github pull request: ENH: Array data in .tsv cells - [bids-specification 1446](https://github.com/bids-standard/bids-specification/issues/1446)
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- We might need an example of nesting
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- 80/20 rules may need to apply here where we define rules for
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examples that occur 80% of the time.
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- 80/20 rules may need to apply here where we define rules for examples that occur 80% of the time.
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- Why not just repeat the rows for each channel? Example: the onset
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time for multiple channels could be listed across multiple rows
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instead of condescending them into a single row/entry (Ariel will
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suggest this in the pull request)
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time for multiple channels could be listed across multiple rows
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instead of condescending them into a single row/entry (Ariel will
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suggest this in the pull request)
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Github pull request: [DISCUSSION] acknowledge contributors in DOIed
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specs on Zenodo - [bids-specification 66](https://github.com/bids-standard/bids-specification/issues/66)
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- What rule should be used for author order on zenodo DOI?
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- Proposal: use a random number generator for each new push of authors
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to keep order 'fair' for all, possibly include an alphabetical
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list on the BIDS website for ease of author identification
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to keep order 'fair' for all, possibly include an alphabetical
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list on the BIDS website for ease of author identification
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- **Final decision: alphabetical is simple and standard, order does
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not imply importance, PR is fine.**
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not imply importance, PR is fine.**
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- Clarify it explicitly in the text
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Journals including badges to indicate BIDS compliant dataset:
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- Aperture is agreeable, their website is under development
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- Suggestions: next journal to approach could be **scientific data**
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given their familiarity with BIDS.
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- Action: email the Scientific Data editor in chief from the BIDS
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Steering Committee
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- Suggestions: next journal to approach could be **scientific data** given their familiarity with BIDS.
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- Action: email the Scientific Data editor in chief from the BIDS Steering Committee
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- Question standardization of implementation across journals?
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- Guio will provide and example draft
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- Question: who/what will identify BIDS compliant datasets?
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- BIDS validator can, however users can include many \#BIDS IGNORE
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files
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- Either the validator will need to output bidsignore info or
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reviewers/editors will need to check the bidsignore files
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themselves.
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- BIDS validator can, however users can include many BIDS IGNORE files
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- Either the validator will need to output bidsignore info or reviewers/editors will need to check the bidsignore files themselves.
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OHBM best practice committee
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- Cyril: John Pyles has circulated the OHBM doc of BIDS 2- reviewing
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of the proposal?
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- Cyril: John Pyles has circulated the OHBM doc of BIDS 2- reviewing of the proposal?
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- This will be reviewed by individuals external from BIDS
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- There will be multiple versions , not all versions need to be
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reviewed
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- 'What is BIDS' should be presented to the community, who should lead
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this presentation?
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- There will be multiple versions , not all versions need to be reviewed
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- 'What is BIDS' should be presented to the community, who should lead this presentation?
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- Experts from each field?
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Was there a podcast ([OHBM Neurosalience](https://www.youtube.com/playlist?list=PLg2e4R8SdhpdIMG7Tb9WAEZA6HRnx8Vsb))
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where Peter Bandettini suggested someone talk about BIDS?
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- Originated in October 2022, sounds like a good opportunity for more
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exposure, Cyril will reply to the email thread
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- Originated in October 2022, sounds like a good opportunity for more exposure, Cyril will reply to the email thread
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Next Meeting Guest:
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- possibly JB Poline regarding a new tool (could be posted as an issue
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on github?)
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- Maintainers met with the functional ultrasound group but they are
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likely too premature for this meeting.
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- possibly JB Poline regarding a new tool (could be posted as an issue on github?)
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- Maintainers met with the functional ultrasound group but they are likely too premature for this meeting.
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Cyril: the BIDS retreat is looking for additional funding to increase
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the support for the meeting. Who should be additionally invited?

docs/blog/posts/2023-05-25-steering-group-minutes.md

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## NOTES
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**Guest Guy Jones: discuss adding badges to the BIDS compliant datasets
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on Scientific Data Journal website.**
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### Guest Guy Jones: discuss adding badges to the BIDS compliant datasets on Scientific Data Journal website
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Guy's Feedback:
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docs/blog/posts/2024-09-19-steering-group-minutes.md

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### Q&A
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> Ariel: to move ahead with discussions we started about BIDS governance structure
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(that is around foundation, non-profit, 501(c)3...), I've asked Chris Holdgraf to come and chat with us at an upcoming meeting.
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Chris directs [2i2c](https://2i2c.org/), and has a unique perspective on these issues.
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He's also a BIDS contributor, having worked extensively on the iEEG BEP and related.
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> (that is around foundation, non-profit, 501(c)3...), I've asked Chris Holdgraf to come and chat with us at an upcoming meeting.
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> Chris directs [2i2c](https://2i2c.org/), and has a unique perspective on these issues.
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> He's also a BIDS contributor, having worked extensively on the iEEG BEP and related.
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- **Q:** What was the funding model that worked best for 2i2c?
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docs/collaboration/reports/google_summer/2024-gsod.md

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## Summary
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| **# Tech Writers** | **TW Project Hours** | **Budget** | **% Project Completed** |
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|:------------------:|:--------------------:|:----------:|:-----------------------:|
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| 1 | 150 | $6,500 USD | 100% |
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| ------------------ | -------------------- | ---------- | ----------------------- |
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| 1 | 150 | $6,500 USD | 100% |
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This project was trying to improve the BIDS Online Presence, which consists primarily of its informational websites and the BIDS specification.
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We were able to migrate away from a multitude of websites and condense down to mainly the one “New” BIDS Website.
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### Budget
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| | |
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| -------------------------------------------------------------------------------------------------------------| -------------------------------------------------------------------------------------------- |
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| How much money did you ask for? | 6500$ USD |
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| How did you come up with this estimate? | Writer stipend: 5000$ <br> Mentor stipend: 500$ * 3 mentors <br> (following GSOC practice) |
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| How many hours of work did you budget for the project? | Writer: 4 h / wk <br> Mentors: 1 h / wk * 4 mentors = 4 h / wk |
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| How many hours of work were actually needed for the project? | Writer: 5 h / wk <br> Mentors: 1.5 h / week * 4 mentors = 6 h / wk |
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| What other expenses did you include in your budget? | None |
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| Did you run into any budget surprises during the project (for example mis-estimates)? If so, please explain. | Mentor time underestimated. Would allocate more for additional mentors or more mentor time. |
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| | |
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| ------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------- |
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| How much money did you ask for? | 6500$ USD |
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| How did you come up with this zestimate? | Writer stipend: 5000$ <br> Mentor stipend: 500$ * 3 mentors <br> (following GSOC practice) |
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| How many hours of work did you budget for the project? | Writer: 4 h / wk <br> Mentors: 1 h / wk * 4 mentors = 4 h / wk |
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| How many hours of work were actually needed for the project? | Writer: 5 h / wk <br> Mentors: 1.5 h / week * 4 mentors = 6 h / wk |
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| What other expenses did you include in your budget? | None |
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| Did you run into any budget surprises during the project (for example mis-estimates)? If so, please explain. | Mentor time underestimated. Would allocate more for additional mentors or more mentor time. |
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### Technical Writer Recruitment
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#### Planned Deliverables
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| Deliverable | % Complete | Relevant Links | Notes |
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| Deliverable | % Complete | Relevant Links | Notes |
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| ----------------------------------------------------------------------- | ---------- | -------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------- |
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| Consolidate into one website | 100% | [new BIDS website](https://bids-website.readthedocs.io/) | Dev site - Planning launch in Q1 2025 to replace the old BIDS website at <https://bids.neuroimaging.io/> |
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| Implement a more friendly main website structure and improve navigation | 100% | [mkdocs TOC configuration](https://github.com/bids-standard/bids-website/blob/main/mkdocs.yml#L88) | User feedback indicates this created significant improvement ( See: [Metrics](#metrics)) |

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