From f840b3b4463db6621d17b8c9c7c847e259225e1f Mon Sep 17 00:00:00 2001 From: Claude Date: Fri, 9 Oct 2026 09:01:26 +0000 Subject: [PATCH 1/3] Annex 12 pics/ files that were committed as git-annex pointer files They were committed through git's clean filter (plain `git add`), so the tree had small "/annex/objects/KEY" pointer files (unlocked) instead of the symlinks (locked) used everywhere else in this dataset. tools/build_preview.py fetches content only for broken symlinks and copies regular files verbatim, so the PR preview served the pointer text instead of the image, e.g. pics/BIDS-minder.svg rendered blank. `git annex lock` turns them into symlinks; keys are unchanged, and the content of all 12 is on datasets.datalad.org. Co-Authored-By: Claude Opus 5.5 Claude-Session: https://claude.ai/code/session_01LioXKDkasSKTUKxXyXn5N1 --- pics/0000-zoom-background-qrcode.png | 2 +- pics/2016-openfmri-dataset-datalad-howto.png | 2 +- pics/2026-ca-origami-retreat-aicoding-qrcode.png | 2 +- pics/2026-repronim-YODA-BIDS-webinar-qrcode.png | 2 +- pics/2026-usrse-con-talk-qrcode.png | 2 +- pics/202x-mvc-stack-qrcode.png | 2 +- pics/BIDS-minder.svg | 2 +- pics/borrowed/arjlover-webshot.png | 2 +- pics/con-tinuous-term-dandi-cli.png | 2 +- pics/con_logo_square_with_fuzzybackground.png | 2 +- pics/datalad-animated.gif | 2 +- pics/datalad-handbook-basics.svg | 2 +- 12 files changed, 12 insertions(+), 12 deletions(-) mode change 100644 => 120000 pics/0000-zoom-background-qrcode.png mode change 100644 => 120000 pics/2016-openfmri-dataset-datalad-howto.png mode change 100644 => 120000 pics/2026-ca-origami-retreat-aicoding-qrcode.png mode change 100644 => 120000 pics/2026-repronim-YODA-BIDS-webinar-qrcode.png mode change 100644 => 120000 pics/2026-usrse-con-talk-qrcode.png mode change 100644 => 120000 pics/202x-mvc-stack-qrcode.png mode change 100644 => 120000 pics/BIDS-minder.svg mode change 100644 => 120000 pics/borrowed/arjlover-webshot.png mode change 100644 => 120000 pics/con-tinuous-term-dandi-cli.png mode change 100644 => 120000 pics/con_logo_square_with_fuzzybackground.png mode change 100644 => 120000 pics/datalad-animated.gif mode change 100644 => 120000 pics/datalad-handbook-basics.svg diff --git a/pics/0000-zoom-background-qrcode.png b/pics/0000-zoom-background-qrcode.png deleted file mode 100644 index aef37079..00000000 --- a/pics/0000-zoom-background-qrcode.png +++ /dev/null @@ -1 +0,0 @@ -/annex/objects/MD5E-s22796--9fce6bbdb87da9f9a6021c382baf82f8.png diff --git a/pics/0000-zoom-background-qrcode.png b/pics/0000-zoom-background-qrcode.png new file mode 120000 index 00000000..72aea2d7 --- /dev/null +++ b/pics/0000-zoom-background-qrcode.png @@ -0,0 +1 @@ +../.git/annex/objects/WM/pJ/MD5E-s22796--9fce6bbdb87da9f9a6021c382baf82f8.png/MD5E-s22796--9fce6bbdb87da9f9a6021c382baf82f8.png \ No newline at end of file diff --git a/pics/2016-openfmri-dataset-datalad-howto.png b/pics/2016-openfmri-dataset-datalad-howto.png deleted file mode 100644 index 1b1c16ae..00000000 --- a/pics/2016-openfmri-dataset-datalad-howto.png +++ /dev/null @@ -1 +0,0 @@ -/annex/objects/MD5E-s745811--4385a108781c44b220c453ac8b631f61.png diff --git a/pics/2016-openfmri-dataset-datalad-howto.png b/pics/2016-openfmri-dataset-datalad-howto.png new file mode 120000 index 00000000..d2f265e4 --- /dev/null +++ b/pics/2016-openfmri-dataset-datalad-howto.png @@ -0,0 +1 @@ +../.git/annex/objects/08/M4/MD5E-s745811--4385a108781c44b220c453ac8b631f61.png/MD5E-s745811--4385a108781c44b220c453ac8b631f61.png \ No newline at end of file diff --git a/pics/2026-ca-origami-retreat-aicoding-qrcode.png b/pics/2026-ca-origami-retreat-aicoding-qrcode.png deleted file mode 100644 index 365caa5b..00000000 --- a/pics/2026-ca-origami-retreat-aicoding-qrcode.png +++ /dev/null @@ -1 +0,0 @@ -/annex/objects/MD5E-s1156--41a7188d7848f733514076b9a04a9552.png diff --git a/pics/2026-ca-origami-retreat-aicoding-qrcode.png b/pics/2026-ca-origami-retreat-aicoding-qrcode.png new file mode 120000 index 00000000..96c658bf --- /dev/null +++ b/pics/2026-ca-origami-retreat-aicoding-qrcode.png @@ -0,0 +1 @@ +../.git/annex/objects/j6/Kg/MD5E-s1156--41a7188d7848f733514076b9a04a9552.png/MD5E-s1156--41a7188d7848f733514076b9a04a9552.png \ No newline at end of file diff --git a/pics/2026-repronim-YODA-BIDS-webinar-qrcode.png b/pics/2026-repronim-YODA-BIDS-webinar-qrcode.png deleted file mode 100644 index eaf6c772..00000000 --- a/pics/2026-repronim-YODA-BIDS-webinar-qrcode.png +++ /dev/null @@ -1 +0,0 @@ -/annex/objects/MD5E-s860--b7d485c308479377b875439655c6ee24.png diff --git a/pics/2026-repronim-YODA-BIDS-webinar-qrcode.png b/pics/2026-repronim-YODA-BIDS-webinar-qrcode.png new file mode 120000 index 00000000..9f5153de --- /dev/null +++ b/pics/2026-repronim-YODA-BIDS-webinar-qrcode.png @@ -0,0 +1 @@ +../.git/annex/objects/p3/vJ/MD5E-s860--b7d485c308479377b875439655c6ee24.png/MD5E-s860--b7d485c308479377b875439655c6ee24.png \ No newline at end of file diff --git a/pics/2026-usrse-con-talk-qrcode.png b/pics/2026-usrse-con-talk-qrcode.png deleted file mode 100644 index 91b38683..00000000 --- a/pics/2026-usrse-con-talk-qrcode.png +++ /dev/null @@ -1 +0,0 @@ -/annex/objects/MD5E-s1142--804c0917a4833b8aef6d163841f9c20a.png diff --git a/pics/2026-usrse-con-talk-qrcode.png b/pics/2026-usrse-con-talk-qrcode.png new file mode 120000 index 00000000..d57d7e38 --- /dev/null +++ b/pics/2026-usrse-con-talk-qrcode.png @@ -0,0 +1 @@ +../.git/annex/objects/Q5/gw/MD5E-s1142--804c0917a4833b8aef6d163841f9c20a.png/MD5E-s1142--804c0917a4833b8aef6d163841f9c20a.png \ No newline at end of file diff --git a/pics/202x-mvc-stack-qrcode.png b/pics/202x-mvc-stack-qrcode.png deleted file mode 100644 index 6331779a..00000000 --- a/pics/202x-mvc-stack-qrcode.png +++ /dev/null @@ -1 +0,0 @@ -/annex/objects/MD5E-s960--489515732e513e190a205cba3baee12f.png diff --git a/pics/202x-mvc-stack-qrcode.png b/pics/202x-mvc-stack-qrcode.png new file mode 120000 index 00000000..96525864 --- /dev/null +++ b/pics/202x-mvc-stack-qrcode.png @@ -0,0 +1 @@ +../.git/annex/objects/Fv/Pp/MD5E-s960--489515732e513e190a205cba3baee12f.png/MD5E-s960--489515732e513e190a205cba3baee12f.png \ No newline at end of file diff --git a/pics/BIDS-minder.svg b/pics/BIDS-minder.svg deleted file mode 100644 index 69ed1eba..00000000 --- a/pics/BIDS-minder.svg +++ /dev/null @@ -1 +0,0 @@ -/annex/objects/MD5E-s158781--043b0a4cfdbc0a1562c04be00ad5fe23.svg diff --git a/pics/BIDS-minder.svg b/pics/BIDS-minder.svg new file mode 120000 index 00000000..eb54c3c0 --- /dev/null +++ b/pics/BIDS-minder.svg @@ -0,0 +1 @@ +../.git/annex/objects/zX/FG/MD5E-s158781--043b0a4cfdbc0a1562c04be00ad5fe23.svg/MD5E-s158781--043b0a4cfdbc0a1562c04be00ad5fe23.svg \ No newline at end of file diff --git a/pics/borrowed/arjlover-webshot.png b/pics/borrowed/arjlover-webshot.png deleted file mode 100644 index 289ef176..00000000 --- a/pics/borrowed/arjlover-webshot.png +++ /dev/null @@ -1 +0,0 @@ -/annex/objects/MD5E-s232650--a60cb414e2fd6c9b33c8b682a0fcc4de.png diff --git a/pics/borrowed/arjlover-webshot.png b/pics/borrowed/arjlover-webshot.png new file mode 120000 index 00000000..28b7d513 --- /dev/null +++ b/pics/borrowed/arjlover-webshot.png @@ -0,0 +1 @@ +../../.git/annex/objects/Gx/7j/MD5E-s232650--a60cb414e2fd6c9b33c8b682a0fcc4de.png/MD5E-s232650--a60cb414e2fd6c9b33c8b682a0fcc4de.png \ No newline at end of file diff --git a/pics/con-tinuous-term-dandi-cli.png b/pics/con-tinuous-term-dandi-cli.png deleted file mode 100644 index a1dc636a..00000000 --- a/pics/con-tinuous-term-dandi-cli.png +++ /dev/null @@ -1 +0,0 @@ -/annex/objects/MD5E-s72761--54f9720cfa647f76d8c79cf732b723b8.png diff --git a/pics/con-tinuous-term-dandi-cli.png b/pics/con-tinuous-term-dandi-cli.png new file mode 120000 index 00000000..b5eb743d --- /dev/null +++ b/pics/con-tinuous-term-dandi-cli.png @@ -0,0 +1 @@ +../.git/annex/objects/w4/4q/MD5E-s72761--54f9720cfa647f76d8c79cf732b723b8.png/MD5E-s72761--54f9720cfa647f76d8c79cf732b723b8.png \ No newline at end of file diff --git a/pics/con_logo_square_with_fuzzybackground.png b/pics/con_logo_square_with_fuzzybackground.png deleted file mode 100644 index 807aea16..00000000 --- a/pics/con_logo_square_with_fuzzybackground.png +++ /dev/null @@ -1 +0,0 @@ -/annex/objects/MD5E-s20600--f67f49ca4bac25ac758ffaa7acc1d8fb.png diff --git a/pics/con_logo_square_with_fuzzybackground.png b/pics/con_logo_square_with_fuzzybackground.png new file mode 120000 index 00000000..e4f3c4ac --- /dev/null +++ b/pics/con_logo_square_with_fuzzybackground.png @@ -0,0 +1 @@ +../.git/annex/objects/6f/pP/MD5E-s20600--f67f49ca4bac25ac758ffaa7acc1d8fb.png/MD5E-s20600--f67f49ca4bac25ac758ffaa7acc1d8fb.png \ No newline at end of file diff --git a/pics/datalad-animated.gif b/pics/datalad-animated.gif deleted file mode 100644 index 842e1d27..00000000 --- a/pics/datalad-animated.gif +++ /dev/null @@ -1 +0,0 @@ -/annex/objects/MD5E-s189740--60be69aa34d07ebd791ca94676c2f1c1.gif diff --git a/pics/datalad-animated.gif b/pics/datalad-animated.gif new file mode 120000 index 00000000..40608b58 --- /dev/null +++ b/pics/datalad-animated.gif @@ -0,0 +1 @@ +../.git/annex/objects/3X/p9/MD5E-s189740--60be69aa34d07ebd791ca94676c2f1c1.gif/MD5E-s189740--60be69aa34d07ebd791ca94676c2f1c1.gif \ No newline at end of file diff --git a/pics/datalad-handbook-basics.svg b/pics/datalad-handbook-basics.svg deleted file mode 100644 index bc647662..00000000 --- a/pics/datalad-handbook-basics.svg +++ /dev/null @@ -1 +0,0 @@ -/annex/objects/MD5E-s127134--6a6f00168510c933adcd8e1c24c84da5.svg diff --git a/pics/datalad-handbook-basics.svg b/pics/datalad-handbook-basics.svg new file mode 120000 index 00000000..bf7f5b70 --- /dev/null +++ b/pics/datalad-handbook-basics.svg @@ -0,0 +1 @@ +../.git/annex/objects/x0/Vp/MD5E-s127134--6a6f00168510c933adcd8e1c24c84da5.svg/MD5E-s127134--6a6f00168510c933adcd8e1c24c84da5.svg \ No newline at end of file From b31824124d28bfd194f7de3fbc975d87ed2909ae Mon Sep 17 00:00:00 2001 From: Claude Date: Fri, 9 Oct 2026 09:01:26 +0000 Subject: [PATCH 2/3] 2023-bids-dicom: use local copies of externally hosted figures - BIDS-minder slide loaded bids-standard.github.io/bids-starter-kit/ _images/BIDS-minder.svg, which 404s since the starter kit moved to the BIDS website (bids-standard/bids-starter-kit#414). Use our pics/BIDS-minder.svg instead (same mind map, plus a "Zarr" leaf), sized to fit the slide. - "DICOMs in BIDS" slide loaded dbic-flow.png and dbic-conversions.png from ReproNim/reproin master. Annex copies as pics/dbic-flow.png and pics/dbic-conversions.png, added from URLs pinned to the reproin commit that introduced them (unchanged since). To make their content available (CI's git-annex check, and the datasets.datalad.org mirror): git annex registerurl MD5E-s149431--29e378a46a7294f2f7b040a48136c9bf.png \ https://raw.githubusercontent.com/ReproNim/reproin/fe5488b59c607ead1384da0e3efcbe57770c34e8/docs/source/images/dbic-flow.png git annex registerurl MD5E-s293267--d7a4fa9b78b172ed35d73251763a045f.png \ https://raw.githubusercontent.com/ReproNim/reproin/fe5488b59c607ead1384da0e3efcbe57770c34e8/docs/source/images/dbic-conversions.png git annex get pics/dbic-flow.png pics/dbic-conversions.png git annex copy --to datasets.datalad.org pics/dbic-flow.png pics/dbic-conversions.png git push origin git-annex INDEX.md updated accordingly. Closes #30 Co-Authored-By: Claude Opus 5.5 Claude-Session: https://claude.ai/code/session_01LioXKDkasSKTUKxXyXn5N1 --- 2023-bids-dicom.html | 6 +++--- INDEX.md | 9 +++++---- pics/dbic-conversions.png | 1 + pics/dbic-flow.png | 1 + 4 files changed, 10 insertions(+), 7 deletions(-) create mode 120000 pics/dbic-conversions.png create mode 120000 pics/dbic-flow.png diff --git a/2023-bids-dicom.html b/2023-bids-dicom.html index 09982e56..077efcf3 100644 --- a/2023-bids-dicom.html +++ b/2023-bids-dicom.html @@ -241,7 +241,7 @@

BIDS ...

style="position:absolute; left:10%; top:0%; width:80%; opacity: 90%"/> --> - + @@ -300,8 +300,8 @@

We have two widely used standards,
which can benefit from cooperation

DICOMs in BIDS: the recommended source

- - + +
diff --git a/INDEX.md b/INDEX.md index db2d4035..fa489382 100644 --- a/INDEX.md +++ b/INDEX.md @@ -238,13 +238,13 @@ Cross-references in the per-topic lookup point at the shelved path citation (canonical citation slide). - "BIDS ..." features bullets, including "you've seen one BIDS dataset you've seen them all". - - BIDS-minder upstream-images slide - (`bids-standard.github.io/.../BIDS-minder.svg`). + - BIDS-minder slide (`pics/BIDS-minder.svg`). - DICOM ↔ BIDS chronology (1982 DICOM → 2014 BIDS). - Clunie MICCAI 2017 5-image fragments (data is in `pics/2017-Clunie-*.png`). - **"All standards are 'Bad', but some are used"** — recurring rhetorical slide. - - DICOMs in BIDS workflow (sourcedata, .json sidecars, BEP019, PR#1450). + - DICOMs in BIDS workflow (ReproIn `pics/dbic-flow.png` + + `pics/dbic-conversions.png`; sourcedata, .json sidecars, BEP019, PR#1450). ### `2023-brain-dandi-imgdatasrc.html` — short DANDI talk - Tiny deck (86 lines), title-only template; safe to ignore as source. @@ -365,7 +365,8 @@ ReproNim-containers / con/duct / ReproMan) - *Asset*: `pics/webshot-repronim-containers.png`, `pics/repronim-containers-{workflow,show,yoda-lower}.png`, `pics/webshot-con-duct.png`, `pics/screenshot-duct-*.png`, - `pics/duct-mriqc-cerebra.png`, `pics/borrowed/reproin-logo.jpg`. + `pics/duct-mriqc-cerebra.png`, `pics/borrowed/reproin-logo.jpg`, + `pics/dbic-flow.png`, `pics/dbic-conversions.png` (+ `-p1`/`-p2` crops). ### Extend / standards work / BIDS BEPs / BIDS 2.0 - `2026-nih-bids2.0.html` — **best BIDS 2.0 walkthrough**: deprecations diff --git a/pics/dbic-conversions.png b/pics/dbic-conversions.png new file mode 120000 index 00000000..dec1d6c7 --- /dev/null +++ b/pics/dbic-conversions.png @@ -0,0 +1 @@ +../.git/annex/objects/81/7x/MD5E-s293267--d7a4fa9b78b172ed35d73251763a045f.png/MD5E-s293267--d7a4fa9b78b172ed35d73251763a045f.png \ No newline at end of file diff --git a/pics/dbic-flow.png b/pics/dbic-flow.png new file mode 120000 index 00000000..2db3b63b --- /dev/null +++ b/pics/dbic-flow.png @@ -0,0 +1 @@ +../.git/annex/objects/JX/9M/MD5E-s149431--29e378a46a7294f2f7b040a48136c9bf.png/MD5E-s149431--29e378a46a7294f2f7b040a48136c9bf.png \ No newline at end of file From 93ed4b9b000cd6eb16250506048f313a02e78393 Mon Sep 17 00:00:00 2001 From: Claude Date: Wed, 21 Oct 2026 17:36:56 +0000 Subject: [PATCH 3/3] Annex 20 more files that were committed as git-annex pointer files Same as the earlier lock of 12 pics/ files: these came in after that fix, again via plain `git add` (some replaced symlinks, e.g. pics/borrowed/2026-ai-intensifies.png in 8e37efd), so the tree had unlocked "/annex/objects/KEY" pointer files that tools/build_preview.py copies verbatim. `git annex lock`; keys are unchanged, and the content of all 20 is on datasets.datalad.org. 2026-usrse/duct-poster-assets/logos/con_logo_blue_big_tight.svg 2026-usrse/duct-poster-assets/logos/duct_logo.svg pics/20261019-con-website-people-webshot.png pics/20261019-devcon-website-people-webshot.png pics/borrowed/2026-ai-intensifies.png pics/borrowed/aws-mark.png pics/borrowed/dbic-logo.png pics/borrowed/incf-mark.png pics/borrowed/powered-by-aws.png pics/ccn-logo.svg pics/con-projects/bids_logo.png pics/con-projects/dandi_logo.png pics/con-projects/datalad_logo.png pics/con-projects/ember_logo.png pics/con-projects/hcp_logo.png pics/con-projects/incf_logo.png pics/con-projects/nwb_logo.png pics/con-projects/psychopy_logo.png pics/con-projects/scikit-learn_logo.png pics/dartmouth-logo.svg Co-Authored-By: Claude Opus 5.5 Claude-Session: https://claude.ai/code/session_01LioXKDkasSKTUKxXyXn5N1 --- 2026-usrse/duct-poster-assets/logos/con_logo_blue_big_tight.svg | 2 +- 2026-usrse/duct-poster-assets/logos/duct_logo.svg | 2 +- pics/20261019-con-website-people-webshot.png | 2 +- pics/20261019-devcon-website-people-webshot.png | 2 +- pics/borrowed/2026-ai-intensifies.png | 2 +- pics/borrowed/aws-mark.png | 2 +- pics/borrowed/dbic-logo.png | 2 +- pics/borrowed/incf-mark.png | 2 +- pics/borrowed/powered-by-aws.png | 2 +- pics/ccn-logo.svg | 2 +- pics/con-projects/bids_logo.png | 2 +- pics/con-projects/dandi_logo.png | 2 +- pics/con-projects/datalad_logo.png | 2 +- pics/con-projects/ember_logo.png | 2 +- pics/con-projects/hcp_logo.png | 2 +- pics/con-projects/incf_logo.png | 2 +- pics/con-projects/nwb_logo.png | 2 +- pics/con-projects/psychopy_logo.png | 2 +- pics/con-projects/scikit-learn_logo.png | 2 +- pics/dartmouth-logo.svg | 2 +- 20 files changed, 20 insertions(+), 20 deletions(-) mode change 100644 => 120000 2026-usrse/duct-poster-assets/logos/con_logo_blue_big_tight.svg mode change 100644 => 120000 2026-usrse/duct-poster-assets/logos/duct_logo.svg mode change 100644 => 120000 pics/20261019-con-website-people-webshot.png mode change 100644 => 120000 pics/20261019-devcon-website-people-webshot.png mode change 100644 => 120000 pics/borrowed/2026-ai-intensifies.png mode change 100644 => 120000 pics/borrowed/aws-mark.png 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