From ad81ddb844b2ebafcc79d57cbc62c50671734556 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sat, 19 Oct 2024 13:17:58 +0200
Subject: [PATCH 1/3] [REF] split entities table - relates to #473

---
 docs/extensions/general-guidelines.md | 43 ++++++++++++++++-----------
 1 file changed, 25 insertions(+), 18 deletions(-)

diff --git a/docs/extensions/general-guidelines.md b/docs/extensions/general-guidelines.md
index 4a95ca9f..c9d38d22 100644
--- a/docs/extensions/general-guidelines.md
+++ b/docs/extensions/general-guidelines.md
@@ -143,24 +143,31 @@ Try not to deviate from BIDS conventions in your extension.
 
 A common dictionary (BIDS keys) is what makes BIDS successful,
 it is thus essential to not create many new entities.
-Many of the current BEPs have developed useful terms that we recommend here:
-
-| Entity                                               | BEP(s)                                                                                   | Description                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
-|------------------------------------------------------|------------------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| desc-<label>                                         | BEP003 (merged)                                                                          | Alphanumeric label, for any use, up to pipelines to determine what are valuable, for example,  Common desc acronyms: lp30: low pass filtered at 30 Hz hp05: high-pass filtered at 0.5 Hz reref: re-references to another electrodemc: motion corrected sm: smoothed pvc: partial volume corrected McPvc: motion and partial volume corrected  Note: concatenation of the above is possible, preferable in the order in which they were applied when applicable: like McPvc, RerefLp30. PascalCase is recommended when concatenating descriptions |
-| space-<label>                                        | BEP003 (merged)                                                                          | Name of space file is aligned to (standard or non-standard)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
-| res-<label>                                          | BEP003 (merged)                                                                          | Identifier for spatial resolution (details in sidecar)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
-| den-<label>                                          | BEP003 (merged)                                                                          | Identifier for mesh density (details in sidecar)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
-| label-<label>                                        | BEP003 (merged)                                                                          | Label of ROI described by mask file                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              |
-| hemi-{L\|R}                                          | BEP011                                                                                   | File describes left or right hemibrain                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
-| model-<label>                                        | BEP016, BEP039                                                                           | Name of model generating derivative file                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         |
-| param-<label>                                        | BEP016, BEP039                                                                           | Name of parameter represented by file                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            |
-| seg-<label> (equivalent of the current atlas entity) | Changing the current derivatives                                                         | As per current atlas definition a label the user MAY use to distinguish a different segmentations, like `atlas/atlas-DKT_space-FSaverage.nii` `sub-01/sub-01_space-T1_seg-DKT_dseg.nii` (are there current uses of the `atlas` key that would be broken changing to `seg`?)                                                                                                                                                                                                                                                                      |
-| atlas-<label> (as new entity)                        | BEP003, BEP038                                                                           | Atlas is defined as per Merrian-Webster, a bound collection of maps (i.e. labeled brain regions) and metadata (tables, or textual matter) like `atlas-x_space-MNI305_ext` or `atlas-DKT_ext`                                                                                                                                                                                                                                                                                                                                                     |
-| group-<label>                                        | BEP039                                                                                   | Name of group combining over subjects                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            |
-| node-<label>                                         | No BEP (BEP-002 working implementation)                                                  | Name of processing node generating derivative file                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               |
-| stat-<label>                                         | BEP016 (contemplated but not currently present in proposal), also useful for atlas BEP38 | The theory was that one could like computing the mean value across all values in a time series, or within a DWI shell, or the like. The particular aggregate statistic may not be an adequate descriptor; you could also need eg. the axis along which the aggregate was applied, which elements were or were not included in the aggregate... So it might be too much complexity to hand to a single entity?                                                                                                                                    |
-| meas-<label>                                         | BEP017,BEP23                                                                             | Description of the quantity described by the file when the suffix is insufficient (eg. binding value, relaxation time)                                                                                                                                                                                                                                                                                                                                                                                                                           |
+Many of the current BEPs have developed useful terms that we recommend here.
+
+#### Existing entities
+
+| Entity        | BEP(s)          | Description                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
+|---------------|-----------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| desc-<label>  | BEP003 (merged) | Alphanumeric label, for any use, up to pipelines to determine what are valuable, for example,  Common desc acronyms: lp30: low pass filtered at 30 Hz hp05: high-pass filtered at 0.5 Hz reref: re-references to another electrodemc: motion corrected sm: smoothed pvc: partial volume corrected McPvc: motion and partial volume corrected  Note: concatenation of the above is possible, preferable in the order in which they were applied when applicable: like McPvc, RerefLp30. PascalCase is recommended when concatenating descriptions |
+| space-<label> | BEP003 (merged) | Name of space file is aligned to (standard or non-standard)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
+| res-<label>   | BEP003 (merged) | Identifier for spatial resolution (details in sidecar)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
+| den-<label>   | BEP003 (merged) | Identifier for mesh density (details in sidecar)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
+| label-<label> | BEP003 (merged) | Label of ROI described by mask file                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              |
+| hemi-{L\|R}   | BEP011          | File describes left or right hemibrain                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
+| seg-<label>   |                 | As per current atlas definition a label the user MAY use to distinguish a different segmentations, like `atlas/atlas-DKT_space-FSaverage.nii` `sub-01/sub-01_space-T1_seg-DKT_dseg.nii` (are there current uses of the `atlas` key that would be broken changing to `seg`?)                                                                                                                                                                                                                                                                      |
+
+#### Proposed entities
+
+| Entity        | BEP(s)                                                                                   | Description                                                                                                                                                                                                                                                                                                                                                                                                   |
+|---------------|------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            |
+| model-<label> | BEP016, BEP039                                                                           | Name of model generating derivative file                                                                                                                                                                                                                                                                                                                                                                      |
+| param-<label> | BEP016, BEP039                                                                           | Name of parameter represented by file                                                                                                                                                                                                                                                                                                                                                                         |
+| atlas-<label> | BEP003, BEP038                                                                           | Atlas is defined as per Merrian-Webster, a bound collection of maps (i.e. labeled brain regions) and metadata (tables, or textual matter) like `atlas-x_space-MNI305_ext` or `atlas-DKT_ext`                                                                                                                                                                                                                  |
+| group-<label> | BEP039                                                                                   | Name of group combining over subjects                                                                                                                                                                                                                                                                                                                                                                         |
+| node-<label>  | No BEP (BEP-002 working implementation)                                                  | Name of processing node generating derivative file                                                                                                                                                                                                                                                                                                                                                            |
+| stat-<label>  | BEP016 (contemplated but not currently present in proposal), also useful for atlas BEP38 | The theory was that one could like computing the mean value across all values in a time series, or within a DWI shell, or the like. The particular aggregate statistic may not be an adequate descriptor; you could also need eg. the axis along which the aggregate was applied, which elements were or were not included in the aggregate... So it might be too much complexity to hand to a single entity? |
+| meas-<label>  | BEP017,BEP23                                                                             | Description of the quantity described by the file when the suffix is insufficient (eg. binding value, relaxation time)                                                                                                                                                                                                                                                                                        |
 
 ### Derivatives BEP and provenance
 

From 7aa9dc4aab79e23fcc3cef0e9625e3c75907d20f Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sat, 19 Oct 2024 14:40:53 +0200
Subject: [PATCH 2/3] add templates (#541)

---
 docs/extensions/beps.md                       |   4 +
 docs/getting_started/templates/index.md       |  24 +++
 docs/impact/index.md                          |  20 +++
 makefile                                      |   1 +
 mkdocs.yml                                    |   3 +
 templates/README.md                           | 152 ++++++++++++++++++
 templates/dataset_description.json            |  28 ++++
 ...d => yyyy-mm-dd-steering-group-minutes.md} |  11 +-
 tools/README.md                               |   4 +
 9 files changed, 240 insertions(+), 7 deletions(-)
 create mode 100644 docs/getting_started/templates/index.md
 create mode 100644 templates/README.md
 create mode 100644 templates/dataset_description.json
 rename templates/{YYYY-MM-DD-Steering-Group-minutes.md => yyyy-mm-dd-steering-group-minutes.md} (70%)

diff --git a/docs/extensions/beps.md b/docs/extensions/beps.md
index 26ccd92b..4a17c5b8 100644
--- a/docs/extensions/beps.md
+++ b/docs/extensions/beps.md
@@ -17,6 +17,10 @@ Below is a table of BEPs that have been merged.
 The references of the final publication for those BEPS
 can be found in the BIDS [specification](https://bids-specification.readthedocs.io/en/latest/01-introduction.html#datatype-specific-publications).
 
+<!-- use snippet to include a file
+https://facelessuser.github.io/pymdown-extensions/extensions/snippets/#snippets-notation
+-->
+
 --8<-- "tmp/bids_timeline.html"
 
 {{ MACROS___generate_beps_table(file="beps_completed.yml", type="completed") }}
diff --git a/docs/getting_started/templates/index.md b/docs/getting_started/templates/index.md
new file mode 100644
index 00000000..69bdb630
--- /dev/null
+++ b/docs/getting_started/templates/index.md
@@ -0,0 +1,24 @@
+# Templates
+
+This section contains templates of different files you can find in a BIDS dataset,
+so tou can copy-paste-modity them into your own dataset.
+
+## README.md
+
+<!-- use snippet to include a file
+https://facelessuser.github.io/pymdown-extensions/extensions/snippets/#snippets-notation
+-->
+
+```markdown
+--8<-- "templates/README.md"
+```
+
+## dataset_description.json
+
+<!-- use snippet to include a file
+https://facelessuser.github.io/pymdown-extensions/extensions/snippets/#snippets-notation
+-->
+
+```json
+--8<-- "templates/dataset_description.json"
+```
diff --git a/docs/impact/index.md b/docs/impact/index.md
index f7a9e940..f3efe5c1 100644
--- a/docs/impact/index.md
+++ b/docs/impact/index.md
@@ -43,6 +43,10 @@ A listing of the previous grants can be found [here](../collaboration/acknowledg
 
 ### Datasets
 
+<!-- use snippet to include a file
+https://facelessuser.github.io/pymdown-extensions/extensions/snippets/#snippets-notation
+-->
+
 --8<-- "tmp/openneuro_data_growth.html"
 
 ### Citation Count
@@ -51,6 +55,10 @@ BIDS references are  centralized in a [zotero group](https://www.zotero.org/grou
 
 You can also find them [in the specification](https://bids-specification.readthedocs.io/en/latest/introduction.html#citing-bids)
 
+<!-- use snippet to include a file
+https://facelessuser.github.io/pymdown-extensions/extensions/snippets/#snippets-notation
+-->
+
 --8<-- "tmp/citation_per_year.html"
 
 ### GitHub stars
@@ -99,12 +107,24 @@ we have over 300 credited contributors.
 
 Guessed with [gender-guesser](https://pypi.org/project/gender-guesser/)
 
+<!-- use snippet to include a file
+https://facelessuser.github.io/pymdown-extensions/extensions/snippets/#snippets-notation
+-->
+
 --8<-- "data/people/gender.md"
 
 #### Contributors affiliations
 
+<!-- use snippet to include a file
+https://facelessuser.github.io/pymdown-extensions/extensions/snippets/#snippets-notation
+-->
+
 --8<-- "data/people/affiliations.md"
 
+<!-- use snippet to include a file
+https://facelessuser.github.io/pymdown-extensions/extensions/snippets/#snippets-notation
+-->
+
 --8<-- "tmp/affiliations.html"
 
 ### GitHub dependents
diff --git a/makefile b/makefile
index f5823def..d36f6d39 100644
--- a/makefile
+++ b/makefile
@@ -54,5 +54,6 @@ lint: remark
 remark: package.json
 	npx remark \
 		./docs \
+		./templates \
 		--frail \
 		--rc-path .remarkrc
diff --git a/mkdocs.yml b/mkdocs.yml
index 517cf54b..7ce62a12 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -131,6 +131,8 @@ nav:
             -   getting_started/tutorials/conversion/pet.md
     -   How to:
         -   getting_started/how_to/index.md
+    -   Templates:
+        -   getting_started/templates/index.md
 -   Tools:
     -   tools/index.md
     -   tools/validator.md
@@ -177,6 +179,7 @@ theme:
   features:
     - announce.dismiss
     - content.action.edit
+    - content.code.copy
     - content.tooltips
     - footnotes
     - header.autohide
diff --git a/templates/README.md b/templates/README.md
new file mode 100644
index 00000000..1a4de270
--- /dev/null
+++ b/templates/README.md
@@ -0,0 +1,152 @@
+# README
+
+The README is usually the starting point for researchers using your data
+and serves as a guidepost for users of your data. A clear and informative
+README makes your data much more usable.
+
+In general you can include information in the README that is not captured by some other
+files in the BIDS dataset (dataset_description.json, events.tsv, ...).
+
+It can also be useful to also include information that might already be
+present in another file of the dataset but might be important for users to be aware of
+before preprocessing or analysing the data.
+
+If the README gets too long you have the possibility to create a `/doc` folder
+and add it to the `.bidsignore` file to make sure it is ignored by the BIDS validator.
+
+## Details related to access to the data
+
+-   [ ] Data user agreement
+
+If the dataset requires a data user agreement, link to the relevant information.
+
+-   [ ] Contact person
+
+Indicate the name and contact details (email and ORCID) of the person responsible for additional information.
+
+-   [ ] Practical information to access the data
+
+If there is any special information related to access rights or
+how to download the data make sure to include it.
+For example, if the dataset was curated using datalad,
+make sure to include the relevant section
+from the [datalad handbook](http://handbook.datalad.org/en/latest/basics/101-180-FAQ.html#how-can-i-help-others-get-started-with-a-shared-dataset)
+
+## Overview
+
+-   [ ] Project name (if relevant)
+-   [ ] Year(s) that the project ran
+
+If no `scans.tsv` is included, this could at least cover when the data acquisition
+starter and ended. Local time of day is particularly relevant to subject state.
+
+-   [ ] Brief overview of the tasks in the experiment
+
+A paragraph giving an overview of the experiment. This should include the
+goals or purpose and a discussion about how the experiment tries to achieve
+these goals.
+
+-   [ ] Description of the contents of the dataset
+
+An easy thing to add is the output of the bids-validator that describes what type of
+data and the number of subject one can expect to find in the dataset.
+
+-   [ ] Independent variables
+
+A brief discussion of condition variables (sometimes called contrasts
+or independent variables) that were varied across the experiment.
+
+-   [ ] Dependent variables
+
+A brief discussion of the response variables (sometimes called the
+dependent variables) that were measured and or calculated to assess
+the effects of varying the condition variables. This might also include
+questionnaires administered to assess behavioral aspects of the experiment.
+
+-   [ ] Control variables
+
+A brief discussion of the control variables --- that is what aspects
+were explicitly controlled in this experiment. The control variables might
+include subject pool, environmental conditions, set up, or other things
+that were explicitly controlled.
+
+-   [ ] Quality assessment of the data
+
+Provide a short summary of the quality of the data ideally with descriptive statistics if relevant
+and with a link to more comprehensive description (like with MRIQC) if possible.
+
+## Methods
+
+### Subjects
+
+A brief sentence about the subject pool in this experiment.
+
+Remember that `Control` or `Patient` status should be defined in the `participants.tsv`
+using a group column.
+
+-   [ ] Information about the recruitment procedure
+-   [ ] Subject inclusion criteria (if relevant)
+-   [ ] Subject exclusion criteria (if relevant)
+
+### Apparatus
+
+A summary of the equipment and environment setup for the
+experiment. For example, was the experiment performed in a shielded room
+with the subject seated in a fixed position.
+
+### Initial setup
+
+A summary of what setup was performed when a subject arrived.
+
+### Task organization
+
+How the tasks were organized for a session.
+This is particularly important because BIDS datasets usually have task data
+separated into different files.
+
+-   [ ] Was task order counter-balanced?
+-   [ ] What other activities were interspersed between tasks?
+-   [ ] In what order were the tasks and other activities performed?
+
+### Task details
+
+As much detail as possible about the task and the events that were recorded.
+
+### Additional data acquired
+
+A brief indication of data other than the
+imaging data that was acquired as part of this experiment. In addition
+to data from other modalities and behavioral data, this might include
+questionnaires and surveys, swabs, and clinical information. Indicate
+the availability of this data.
+
+This is especially relevant if the data are not included
+in a [`phenotype` folder](https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#phenotypic-and-assessment-data).
+
+### Experimental location
+
+This should include any additional information regarding the
+the geographical location and facility that cannot be included
+in the relevant json files.
+
+### Missing data
+
+Mention something if some participants are missing some aspects of the data.
+This can take the form of a processing log and/or abnormalities about the dataset.
+
+Some examples:
+
+-   A brain lesion or defect only present in one participant
+
+-   Some experimental conditions missing on a given run for a participant because
+    of some technical issue.
+
+-   Any noticeable feature of the data for certain participants
+
+-   Differences (even slight) in protocol for certain participants.
+
+### Notes
+
+Any additional information or pointers to information that
+might be helpful to users of the dataset. Include qualitative information
+related to how the data acquisition went.
diff --git a/templates/dataset_description.json b/templates/dataset_description.json
new file mode 100644
index 00000000..e21decba
--- /dev/null
+++ b/templates/dataset_description.json
@@ -0,0 +1,28 @@
+{
+    "Name": "",
+    "BIDSVersion": "1.10.0",
+    "HEDVersion": "8.2.0",
+    "DatasetType": "raw",
+    "License": "",
+    "Authors": [
+        "",
+        "",
+        ""
+    ],
+    "Acknowledgements": "",
+    "HowToAcknowledge": "",
+    "Funding": [
+        "",
+        "",
+        ""
+    ],
+    "EthicsApprovals": [
+        ""
+    ],
+    "ReferencesAndLinks": [
+        "",
+        "",
+        ""
+    ],
+    "DatasetDOI": "doi:"
+}
diff --git a/templates/YYYY-MM-DD-Steering-Group-minutes.md b/templates/yyyy-mm-dd-steering-group-minutes.md
similarity index 70%
rename from templates/YYYY-MM-DD-Steering-Group-minutes.md
rename to templates/yyyy-mm-dd-steering-group-minutes.md
index 000460e4..a15cfa48 100644
--- a/templates/YYYY-MM-DD-Steering-Group-minutes.md
+++ b/templates/yyyy-mm-dd-steering-group-minutes.md
@@ -3,7 +3,7 @@ slug: Steering Group executive summary, action items, and minutes
 date:
 author:
 categories:
-  - steering group minutes
+-   steering group minutes
 ---
 
 # Steering Group minutes
@@ -12,15 +12,12 @@ Date:
 
 <!--more-->
 
-### Executive Summary
+## Executive Summary
 
-### Action items
+## Action items
 
 | Action item |
 | ----------- |
 |             |
 
-### Minutes
-
--
--
+## Minutes
diff --git a/tools/README.md b/tools/README.md
index 2d1197dc..7ec538df 100644
--- a/tools/README.md
+++ b/tools/README.md
@@ -59,6 +59,10 @@ The resulting citation count is then visualized using [Plotly](https://plotly.co
 - HTML figures and other content that can be updated is "stored" in external files
   that are injected into markdown files using [snippets](https://facelessuser.github.io/pymdown-extensions/extensions/snippets/)
 
+<!-- use snippet to include a file
+https://facelessuser.github.io/pymdown-extensions/extensions/snippets/#snippets-notation
+-->
+
 ```text
 --8<-- "tmp/bids_timeline.html"
 ```

From a17924e2acd2bc92bd4d2946bdb3fce7f3feeed9 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sat, 19 Oct 2024 14:47:01 +0200
Subject: [PATCH 3/3] [FIX] fix dead links (#542)

* [FIX] fix dead links

* fix

* update config

* update links
---
 .../2023-05-25-steering-group-minutes.md      |  3 +-
 docs/blog/posts/bids-news-september-2024.md   |  2 +-
 docs/getting_started/resources/talks.md       | 28 +++++++++----------
 docs/getting_started/tutorials/annotation.md  |  4 +--
 md_link_check_config.json                     |  4 ++-
 5 files changed, 21 insertions(+), 20 deletions(-)

diff --git a/docs/blog/posts/2023-05-25-steering-group-minutes.md b/docs/blog/posts/2023-05-25-steering-group-minutes.md
index 1729ab4d..6e14a970 100644
--- a/docs/blog/posts/2023-05-25-steering-group-minutes.md
+++ b/docs/blog/posts/2023-05-25-steering-group-minutes.md
@@ -135,8 +135,7 @@ Add a list of BIDS ignore files:
 Should we reach out to the new **Imaging Neuroscience** journal while
 they are still developing their platform?
 
-Potentially reach out to someone on their [[editorial
-board]](https://janeway.imaging-neuroscience.org/editorialteam/)
+Potentially reach out to someone on their [editorial board](https://direct.mit.edu/imag/pages/editorial-info)
 
 -   possible Thomas Yeo, Damian Fair
 
diff --git a/docs/blog/posts/bids-news-september-2024.md b/docs/blog/posts/bids-news-september-2024.md
index a4281ade..6c22394a 100644
--- a/docs/blog/posts/bids-news-september-2024.md
+++ b/docs/blog/posts/bids-news-september-2024.md
@@ -47,7 +47,7 @@ You can find more [about BIDS governance](https://bids-website.readthedocs.io/en
 
 ## Recent venues BIDS presented
 
-BIDS continues to be featured in different venues. Our very own maintainer extraordinaire, Rémi Gau, was recently featured in a yet-to-be-released podcast. The BIDS Town Hall was featured at OHBM again this year in June. For a full recount refer to [this blog post](https://bids-website.readthedocs.io/en/latest/blog/2024/07/01/BIDS%20Town%20Hall%202024%3A%20summary.html).
+BIDS continues to be featured in different venues. Our very own maintainer extraordinaire, Rémi Gau, was recently featured in a yet-to-be-released podcast. The BIDS Town Hall was featured at OHBM again this year in June. For a full recount refer to [this blog post](./town-hall-2024-debrief.md).
 
 ## BIDS Extension Proposals (BEPs)
 
diff --git a/docs/getting_started/resources/talks.md b/docs/getting_started/resources/talks.md
index fc617a11..a3840332 100644
--- a/docs/getting_started/resources/talks.md
+++ b/docs/getting_started/resources/talks.md
@@ -20,20 +20,20 @@ Two great resources for curated lists of talks and slides are:
 
 ## Other Slideshows and talk
 
-| Title                                                                            | Speaker                             | Year | Occasion                                                                                                                                              | Location                             | Video                                                                                        | Slides                                                                                                                       |
-| -------------------------------------------------------------------------------- | ----------------------------------- | ---- | ----------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------ | -------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------- |
-| BIDS: underlying data management principles                                      | Remi Gau                            | 2022 | [Open Research at the Wellcome Centre for Integrative Neuroimaging (WIN)](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/) | Online                               | [link](https://vimeo.com/showcase/7645853/video/668642973)                                   | [link](https://osf.io/h6gsr/)                                                                                                |
-| BIDS: a recipe for success                                                       | Patricia Clement                    | 2021 | [GlimR](https://glimr.eu/) BIDS workshop                                                                                                              |                                      | [link](https://www.youtube.com/watch?v=ukgiAP2Hn3E)                                          | [link](https://osf.io/nu24a)                                                                                                 |
-| BIDS conversion                                                                  | Remi Gau & Guiomar Niso             | 2021 | ACCS & OHBM Webinar and Workshop Series                                                                                                               | online                               | [link](https://www.youtube.com/watch?v=m7vEHGpqQIw)                                          | [link](https://remi-gau.github.io/bids_cookbook/)                                                                            |
-| The BIDS Ecosystem                                                               | Chris Markiewicz                    | 2020 | Neuro Data Science School                                                                                                                             | Online                               | n/a                                                                                          | [link](https://effigies.github.io/bids-ecosystem/)                                                                           |
-| BIDS Applications and Derivatives                                                | Chris Markiewicz                    | 2019 | BIDS Computational Models Workshop                                                                                                                    | Princeton USA                        | n/a                                                                                          | [link](https://effigies.github.io/bids-derivatives/)                                                                         |
-| BIDS Apps Metadata                                                               | Chris Markiewicz                    | 2019 | Making Open Neuroscience Infrastructure Interoperable (MONII 2.0)                                                                                     | Montreal, Canada                     | n/a                                                                                          | [link](https://effigies.github.io/bids-metadata/)                                                                            |
-| BIDS - Open Science Working Group                                                | A Shephard                          | 2018 | n/a                                                                                                                                                   | Aston University, Birmingham England | n/a                                                                                          | [link](https://github.com/bids-standard/bids-starter-kit/files/2068336/Brain.Imaging.Data.Structure.-.OSWG.pptx)             |
-| FAIR Data - BIDS datasets                                                        | Maryann Martone & Jeffrey Grethe    | 2018 | OHBM                                                                                                                                                  | Singapore                            | [link](https://www.pathlms.com/ohbm/courses/8246/sections/12542/video_presentations/115883#) | n/a                                                                                                                          |
-| ReproIn: automatic, shareable, version-controlled BIDS datasets from MR scanners | Matteo Visconti di Oleggio Castello | 2018 | OHBM                                                                                                                                                  | Singapore                            | n/a                                                                                          | [link](https://www.pathlms.com/ohbm/courses/8246/sections/12541/video_presentations/115999#)                                 |
-| OpenNeuro presentation                                                           | Krzysztof Gorgolewski               | 2017 | OHBM                                                                                                                                                  | Vancouver, Canada                    | [link](https://www.pathlms.com/ohbm/courses/5158/sections/7806/video_presentations/76062#)   | [link](https://www.slideshare.net/chrisfilo1/openneuro-a-free-online-platform-for-sharing-and-analysis-of-neuroimaging-data) |
-| fMRIprep                                                                         | Krzysztof Gorgolewski               | 2017 | n/a                                                                                                                                                   | Stanford University, Stanford USA    | n/a                                                                                          | [link](https://www.slideshare.net/chrisfilo1/fmriprep-robust-and-easy-to-use-fmri-preprocessing-pipeline)                    |
-| BIDS                                                                             | Krzysztof Gorgolewski               | 2016 | OHBM                                                                                                                                                  | Geneva, Switzerland                  | n/a                                                                                          | [link](https://www.slideshare.net/chrisfilo1/the-brain-imaging-data-structure-ohbm-2016)                                     |
+| Title                                                                            | Speaker                             | Year | Occasion                                                                | Location                             | Video                                                                                        | Slides                                                                                                                       |
+| -------------------------------------------------------------------------------- | ----------------------------------- | ---- | ------------------------------------------------------------------------| ------------------------------------ | -------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------- |
+| BIDS: underlying data management principles                                      | Remi Gau                            | 2022 | Open Research at the Wellcome Centre for Integrative Neuroimaging (WIN) | Online                               | [link](https://vimeo.com/showcase/7645853/video/668642973)                                   | [link](https://osf.io/h6gsr/)                                                                                                |
+| BIDS: a recipe for success                                                       | Patricia Clement                    | 2021 | [GlimR](https://glimr.eu/) BIDS workshop                                |                                      | [link](https://www.youtube.com/watch?v=ukgiAP2Hn3E)                                          | [link](https://osf.io/nu24a)                                                                                                 |
+| BIDS conversion                                                                  | Remi Gau & Guiomar Niso             | 2021 | ACCS & OHBM Webinar and Workshop Series                                 | online                               | [link](https://www.youtube.com/watch?v=m7vEHGpqQIw)                                          | [link](https://remi-gau.github.io/bids_cookbook/)                                                                            |
+| The BIDS Ecosystem                                                               | Chris Markiewicz                    | 2020 | Neuro Data Science School                                               | Online                               | n/a                                                                                          | [link](https://effigies.github.io/bids-ecosystem/)                                                                           |
+| BIDS Applications and Derivatives                                                | Chris Markiewicz                    | 2019 | BIDS Computational Models Workshop                                      | Princeton USA                        | n/a                                                                                          | [link](https://effigies.github.io/bids-derivatives/)                                                                         |
+| BIDS Apps Metadata                                                               | Chris Markiewicz                    | 2019 | Making Open Neuroscience Infrastructure Interoperable (MONII 2.0)       | Montreal, Canada                     | n/a                                                                                          | [link](https://effigies.github.io/bids-metadata/)                                                                            |
+| BIDS - Open Science Working Group                                                | A Shephard                          | 2018 | n/a                                                                     | Aston University, Birmingham England | n/a                                                                                          | [link](https://github.com/bids-standard/bids-starter-kit/files/2068336/Brain.Imaging.Data.Structure.-.OSWG.pptx)             |
+| FAIR Data - BIDS datasets                                                        | Maryann Martone & Jeffrey Grethe    | 2018 | OHBM                                                                    | Singapore                            | [link](https://www.pathlms.com/ohbm/courses/8246/sections/12542/video_presentations/115883#) | n/a                                                                                                                          |
+| ReproIn: automatic, shareable, version-controlled BIDS datasets from MR scanners | Matteo Visconti di Oleggio Castello | 2018 | OHBM                                                                    | Singapore                            | n/a                                                                                          | [link](https://www.pathlms.com/ohbm/courses/8246/sections/12541/video_presentations/115999#)                                 |
+| OpenNeuro presentation                                                           | Krzysztof Gorgolewski               | 2017 | OHBM                                                                    | Vancouver, Canada                    | [link](https://www.pathlms.com/ohbm/courses/5158/sections/7806/video_presentations/76062#)   | [link](https://www.slideshare.net/chrisfilo1/openneuro-a-free-online-platform-for-sharing-and-analysis-of-neuroimaging-data) |
+| fMRIprep                                                                         | Krzysztof Gorgolewski               | 2017 | n/a                                                                     | Stanford University, Stanford USA    | n/a                                                                                          | [link](https://www.slideshare.net/chrisfilo1/fmriprep-robust-and-easy-to-use-fmri-preprocessing-pipeline)                    |
+| BIDS                                                                             | Krzysztof Gorgolewski               | 2016 | OHBM                                                                    | Geneva, Switzerland                  | n/a                                                                                          | [link](https://www.slideshare.net/chrisfilo1/the-brain-imaging-data-structure-ohbm-2016)                                     |
 
 <!-- TEMPLATE -->
 <!-- | Title    | Speaker  | Year | Occasion    | Location     | [link](video) | [link](slides)    |  -->
diff --git a/docs/getting_started/tutorials/annotation.md b/docs/getting_started/tutorials/annotation.md
index 57b90a40..720a9bc0 100644
--- a/docs/getting_started/tutorials/annotation.md
+++ b/docs/getting_started/tutorials/annotation.md
@@ -26,13 +26,13 @@ Annotations in BIDS can be done at several levels, including the dataset, subjec
 funding, and citation information.
 This file does not provide any actual description of the data.
 
-> You can fill in this blank [dataset description template](https://raw.githubusercontent.com/bids-standard/bids-starter-kit/main/templates/dataset_description.json) or use it as a guide.
+> You can fill in this blank [dataset description template](../templates/index.md#dataset_descriptionjson) or use it as a guide.
 
 ### Dataset description (`README`)
 `README` file is a top-level text file that gives the actual overview of the dataset.
 A comprehensive `README` is essential for users of your data.
 
-> You can edit the [README template](https://raw.githubusercontent.com/bids-standard/bids-starter-kit/main/templates/README.MD) with the vital information needed for others to analyze your dataset.
+> You can edit the [README template](../templates/index.md#readmemd) with the vital information needed for others to analyze your dataset.
 
 ## Subject annotations
 Annotations at the subject level can be done in the `participants.tsv` file,
diff --git a/md_link_check_config.json b/md_link_check_config.json
index 187cf690..c41ec222 100644
--- a/md_link_check_config.json
+++ b/md_link_check_config.json
@@ -14,8 +14,10 @@
     },
     {
       "pattern": "^https://www.instagram.com/bidsstandard.*"
+    },
+    {
+      "pattern": "^https://direct.mit.edu/imag/pages/editorial-info"
     }
-
   ],
   "timeout": "20s",
   "retryOn429": true