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end-to-end article, cian yaml update#41

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CMonnin wants to merge 3 commits into
DouglasNeuroInformatics:mainfrom
CMonnin:blog/imaging
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end-to-end article, cian yaml update#41
CMonnin wants to merge 3 commits into
DouglasNeuroInformatics:mainfrom
CMonnin:blog/imaging

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@CMonnin

@CMonnin CMonnin commented Jun 17, 2026

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Summary by CodeRabbit

  • Documentation
    • Published new English and French news/article pages describing an end-to-end workflow to transform disorganized MRI (DICOM/NIfTI) and behavioral data into a finished, reproducible neuroimaging report, including curated dataset deliverables, preprocessing/statistics outputs, and paper-ready figures/tables, plus notes on upcoming automation and reproducibility support.
  • Chores
    • Updated a team member’s profile title and shortened the role description to focus on software development and user support.

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Review Change Stack

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info
⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 3a5c872d-0fc7-46a5-a096-5c075333bcae

📥 Commits

Reviewing files that changed from the base of the PR and between ed0cec7 and 673eca5.

📒 Files selected for processing (2)
  • src/content/news/en/2026-06-17_DICOMS-to-stats.md
  • src/content/news/fr/2026-06-17_DICOMS-to-stats.md
🚧 Files skipped from review as they are similar to previous changes (1)
  • src/content/news/en/2026-06-17_DICOMS-to-stats.md

Walkthrough

Adds two new bilingual (English and French) Markdown articles documenting the Douglas Neuroinformatics Platform's end-to-end service for transforming disorganized MRI data into reproducible brain–behavior analysis, describing deliverables and workflow. Also updates Cian Monnin's team profile from "Junior Developer" to "Scientific Programmer."

Changes

Neuroimaging Platform Narrative Articles (EN/FR)

Layer / File(s) Summary
English platform narrative article
src/content/news/en/2026-06-17_DICOMS-to-stats.md
New article describing the platform's service: converting disorganized MRI scans into finished analysis with clean dataset, preprocessing, statistics aligned to research questions, publication-ready figures/tables, and fully rerunnable scripts. Includes sections on upcoming automation and reproducible research support.
French platform narrative article
src/content/news/fr/2026-06-17_DICOMS-to-stats.md
French counterpart detailing the research data bottleneck (format standardization, quality control, consistent preprocessing), concrete deliverables (curated dataset, full preprocessing, appropriate statistics including multivariate methods, figures/tables, rerunnable analysis), value proposition, upcoming scanner-to-derivatives automation, and reproducible research support with tool references.

Team Profile Update

Layer / File(s) Summary
Cian Monnin profile
src/content/team/cian-monnin.yaml
Position updated from "Junior Developer" to "Scientific Programmer" (EN/FR); description shortened to core responsibilities of software writing/maintenance and user support.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~8 minutes

Possibly related PRs

  • DouglasNeuroInformatics/Website#38: Restructures the team page and adds type-based categorization; this PR updates team member content feeding the same rendering system.

Poem

From dusty DICOMs to a story complete,
Preprocessing transforms the messy to neat.
Statistics and figures, rerunnable scripts too,
The platform lets science shine brightly through.
And Cian, now "Programmer," advances the view! 🧬📊

🚥 Pre-merge checks | ✅ 5
✅ Passed checks (5 passed)
Check name Status Explanation
Description Check ✅ Passed Check skipped - CodeRabbit’s high-level summary is enabled.
Title check ✅ Passed The title directly references both main changes: the end-to-end article (primary) and Cian's YAML update (secondary).
Docstring Coverage ✅ Passed No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Linked Issues check ✅ Passed Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check ✅ Passed Check skipped because no linked issues were found for this pull request.

✏️ Tip: You can configure your own custom pre-merge checks in the settings.

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  • Create PR with unit tests

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Actionable comments posted: 2

🤖 Prompt for all review comments with AI agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Inline comments:
In `@src/content/news/en/2026-06-17_DICOMS-to-stats.md`:
- Around line 36-38: The fenced code block containing the formula "jacobian ~
group + sex + age + behavioural_score" is missing a language identifier. Add the
language specifier "r" immediately after the opening triple backticks to mark
this as an R code block. Change the opening from ``` to ```r to specify the code
language, which enables proper syntax highlighting and satisfies the markdown
linting requirement.

In `@src/content/news/fr/2026-06-17_DICOMS-to-stats.md`:
- Around line 39-41: The fenced code block containing the statistical formula
jacobian ~ group + sex + age + behavioural_score is missing a language
identifier. Add the "r" language specifier immediately after the opening triple
backticks to properly identify this as R code. This will comply with the MD040
markdown linting rule that requires all code blocks to have a language
identifier specified.
🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

  • Push a commit to this branch (recommended)
  • Create a new PR with the fixes

ℹ️ Review info
⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 1b43f31c-59f3-448f-9aa0-cc1b113a314d

📥 Commits

Reviewing files that changed from the base of the PR and between 8b1d8e3 and d297d3b.

📒 Files selected for processing (3)
  • src/content/news/en/2026-06-17_DICOMS-to-stats.md
  • src/content/news/fr/2026-06-17_DICOMS-to-stats.md
  • src/content/team/cian-monnin.yaml

Comment thread src/content/news/en/2026-06-17_DICOMS-to-stats.md Outdated
Comment thread src/content/news/fr/2026-06-17_DICOMS-to-stats.md Outdated
@gdevenyi

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Not quite what I'm looking for here, I'm thinking more about a "marketing" style write up of how we can go from disorganised stale data to a full reproducible neuroimaging report. The fine details here of what software and such aren't needed.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

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🧹 Nitpick comments (2)
src/content/news/fr/2026-06-17_DICOMS-to-stats.md (2)

2-2: 💤 Low value

Simplify YAML title quote escaping.

The title uses doubled single quotes ('D''images') to escape an apostrophe within a single-quoted string. While syntactically valid YAML, this is less readable. Use double quotes instead for cleaner formatting.

🔧 Proposed fix
-title: 'D''images oubliées à un rapport de neuroimagerie complet'
+title: "D'images oubliées à un rapport de neuroimagerie complet"
🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@src/content/news/fr/2026-06-17_DICOMS-to-stats.md` at line 2, The title field
in the YAML frontmatter uses single quotes with doubled single quotes to escape
the apostrophe in "D''images", which reduces readability. Replace the
single-quoted string with double quotes around the entire title value instead.
This allows the apostrophe character to be used directly without requiring
escape sequences, making the YAML frontmatter cleaner and more readable while
maintaining the exact same content.

38-44: 💤 Low value

French style: Consider restructuring for clarity (lines 23, 41, 93 flagged by LanguageTool).

Static analysis flagged three style suggestions in French:

  1. Line 23 — The phrase "un écart entre ce qu'il a et une analyse concrète semble trop grand" could benefit from clearer nominal structure.
  2. Line 41 — "affecter silencieusement" places the adverb before the infinitive; moving it after may flow more naturally.
  3. Line 93 — Starting a sentence with "Et" is stylistically acceptable but could use a comma ("Et le groupe consacre...") to mark a pause.

These are subjective stylistic notes rather than errors. Given the marketing tone and French prose conventions, you may choose to keep the current phrasing. If you wish to refine for polish, these are areas to review.

🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@src/content/news/fr/2026-06-17_DICOMS-to-stats.md` around lines 38 - 44,
Review and apply the three French style refinements flagged by LanguageTool in
the markdown file. First, restructure the phrase on line 23 that reads "un écart
entre ce qu'il a et une analyse concrète semble trop grand" to use a clearer
nominal structure. Second, in the section around line 41 where "affecter
silencieusement" appears, move the adverb after the infinitive so it reads
"affecter silencieusement" becomes the more natural word order. Third, on line
93, add a comma after "Et" at the beginning of the sentence (change "Et le
groupe..." to "Et, le groupe...") to mark a natural pause and improve flow.
These are stylistic refinements to enhance French prose clarity and readability.
🤖 Prompt for all review comments with AI agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Nitpick comments:
In `@src/content/news/fr/2026-06-17_DICOMS-to-stats.md`:
- Line 2: The title field in the YAML frontmatter uses single quotes with
doubled single quotes to escape the apostrophe in "D''images", which reduces
readability. Replace the single-quoted string with double quotes around the
entire title value instead. This allows the apostrophe character to be used
directly without requiring escape sequences, making the YAML frontmatter cleaner
and more readable while maintaining the exact same content.
- Around line 38-44: Review and apply the three French style refinements flagged
by LanguageTool in the markdown file. First, restructure the phrase on line 23
that reads "un écart entre ce qu'il a et une analyse concrète semble trop grand"
to use a clearer nominal structure. Second, in the section around line 41 where
"affecter silencieusement" appears, move the adverb after the infinitive so it
reads "affecter silencieusement" becomes the more natural word order. Third, on
line 93, add a comma after "Et" at the beginning of the sentence (change "Et le
groupe..." to "Et, le groupe...") to mark a natural pause and improve flow.
These are stylistic refinements to enhance French prose clarity and readability.

ℹ️ Review info
⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: f5b932b6-05d0-44ff-8ba2-004fa1d3ab34

📥 Commits

Reviewing files that changed from the base of the PR and between d297d3b and ed0cec7.

📒 Files selected for processing (2)
  • src/content/news/en/2026-06-17_DICOMS-to-stats.md
  • src/content/news/fr/2026-06-17_DICOMS-to-stats.md
✅ Files skipped from review due to trivial changes (1)
  • src/content/news/en/2026-06-17_DICOMS-to-stats.md

@gdevenyi

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Great, lets have some finish up here

  • something about contacting us if you'd like help with developing reproducible research like this
  • advertise that coming soon, we'll have end-to-end services for automating much of this directly from the scanner

@CMonnin

CMonnin commented Jun 19, 2026

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@gdevenyi ok this should be gtg

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2 participants