Add DCEASY home site for petmri DCE-MRI software suite

[Copilot]

The org had no public-facing landing page to help users discover and navigate the DCE-MRI tools across its repositories.

Changes

• index.html — Single-page GitHub Pages site named DCEASY (Dynamic Contrast-Enhanced Analysis SYstem) with:

  • 5-step pipeline overview mapping workflow stages to specific tools
  • Tool cards for ROCKETSHIP, AutoAIF, AIFArtist, parametric_scripts, gpufit, and DCEPrep — each with language badge, key features, and links to GitHub/wiki/paper
  • Task-to-tool lookup table ("Which tool do I need?")
  • Quick-start code snippets for ROCKETSHIP (MATLAB), AutoAIF (Python), and AIFArtist (Python)
  • Contact/contributing section

• styles.css — Responsive layout (CSS Grid, clamp() typography), color-coded cards; dark Midnight-inspired theme (#151515 background, #63c0f5 cyan accents, dark cards and tables); no external dependencies

• .github/workflows/pr-preview.yml — GitHub Actions workflow using rossjrw/pr-preview-action that deploys a live preview of the site to pr-preview/pr-{number}/ on the gh-pages branch when a PR is opened or updated, and automatically removes it when the PR is closed

Tools covered

Tool	Language	Role
ROCKETSHIP	MATLAB	End-to-end DCE-MRI analysis GUI
AutoAIF (vascular_function)	Python	Preferred: automatic AIF detection via 3D U-Net (MRM 2025)
AIFArtist	Python	Manual multi-rater AIF annotation (BIDS)
parametric_scripts	MATLAB	Pre-contrast T1/T2/ADC map generation
gpufit	CUDA / C++	GPU-accelerated pharmacokinetic curve fitting (Sci Rep 2017)
DCEPrep	Shell / Python	End-to-end preprocessing & Ktrans analysis pipeline (BIDS, Docker)

Original prompt

Build a home site of our org's DCE-MRI software suite (arbitrarily) called DCEASY, with an overview (links and descriptions) of each repo. Anyone interested in DCE processing should be able to easily navigate this site and find a tool they need.

[lsaca05]

@copilot You mind adding a GitHub Actions workflow that deploys a preview of the GitHub Pages deployment when a PR is opened or updated, and deletes it when the PR closes? I want to see what the site looks like with your changes.

[Copilot]

@copilot You mind adding a GitHub Actions workflow that deploys a preview of the GitHub Pages deployment when a PR is opened or updated, and deletes it when the PR closes? I want to see what the site ...

Added .github/workflows/pr-preview.yml (commit Add GitHub Actions workflow for PR preview deployments). It uses rossjrw/pr-preview-action@v1.8.1 and triggers on pull_request events (opened, synchronize, reopened, closed):

• On open/update — deploys the site to https://petmri.github.io/petmri.github.io/pr-preview/pr-{number}/ via the gh-pages branch.
• On close — automatically removes that preview directory.

The gh-pages branch needs to be configured as the GitHub Pages source in the repo settings for the preview URLs to resolve.

[github-actions]

PR Preview Action v1.8.1
🚀 View preview at https://petmri.github.io/pr-preview/pr-1/
Built to branch gh-pages at 2026-06-26 19:58 UTC. Preview will be ready when the GitHub Pages deployment is complete.

[lsaca05]

@copilot Add AutoAIF https://github.com/petmri/vascular_function as the preferred option for AIF detection. Make DCEASY stand for Dynamic Contrast-Enhanced Analysis SYstem. Also add gpufit https://github.com/petmri/gpufit.

[Copilot]

@copilot Add AutoAIF https://github.com/petmri/vascular_function as the preferred option for AIF detection. Make DCEASY stand for Dynamic Contrast-Enhanced Analysis SYstem. Also add gpufit https://git...

Done in commit Add AutoAIF and gpufit; expand DCEASY acronym:

• DCEASY now stands for Dynamic Contrast-Enhanced Analysis SYstem (title, tagline, intro, footer all updated).
• AutoAIF (vascular_function) added as a tool card (3D U-Net, Python/TensorFlow, MRM 2025 paper), marked as the preferred option in the pipeline overview, comparison table, and a new quick-start snippet.
• gpufit added as a tool card (CUDA/C++ Levenberg–Marquardt fitting, MRI pharmacokinetic models, pre-built binaries, Sci Rep 2017 paper) and as a row in the comparison table.

[lsaca05]

@copilot the white background is making my eyes bleed. Consider the Midnight Jekyll theme by GitHub.

[Copilot]

@copilot the white background is making my eyes bleed. Consider the Midnight Jekyll theme by GitHub.

Done in commit Apply dark Midnight-inspired theme to styles.css. The site now uses a dark palette matching Midnight's aesthetic — #151515 page background, #1e1e1e cards/tables, #63c0f5 cyan accents for links, step numbers, section underlines, and primary buttons, with light gray body text throughout. No external dependencies added.

[lsaca05]

@copilot I have just made the DCEPrep repo public. Add that to the site.

[Copilot]

@copilot I have just made the DCEPrep repo public. Add that to the site.

Done in commit Add DCEPrep to DCEASY site. DCEPrep now appears:

• Pipeline overview — step 2 updated to show DCEPrep as the end-to-end option alongside parametric_scripts (standalone).
• Tool card — Shell / Python badge, dark teal header, highlights covering BIDS I/O, VFA T1 mapping, bias field correction, z-axis normalisation, FSL mcflirt motion correction, AutoAIF integration, Ktrans/vp mapping, HTML QC reports, and Docker.
• Comparison table — two new rows: "Full preprocessing pipeline (T1 map, motion correction, AIF, Ktrans)" and "Dockerized end-to-end DCE-MRI preprocessing & analysis".