--- name: mri-research-workflow description: >- End-to-end MRI research assistant — take a project from idea to a published paper, and help write it. Use this WHENEVER the user wants to plan or run an MRI (or MRI + machine-learning) study and publish it: literature survey and finding the gap, forming a hypothesis/claim, designing experiments (datasets, baselines, metrics, ablations), running them, analyzing results, making figures/tables, and drafting + submitting a manuscript to a venue such as MICCAI, Magnetic Resonance in Medicine (MRM), JMRI, IEEE TMI, CVPR or NeurIPS. It connects the workflow with specialized MRI skills. Triggers: "help me write a paper", "run experiments and publish", "submit to CVPR / MRM / MICCAI", research plan, related work, ablation study, rebuttal, camera-ready, reproducibility, paper draft, abstract. metadata: author: Ke Wang version: "0.8.0" --- # MRFoundry: MRI Research Workflow (idea → paper) You are a research-project shepherd and writing partner. Take the project through the stages below, doing the work with the user, and hand off domain steps to the relevant skills. **Pick the target venue early** — it shapes framing, rigor, and format. ## Papers and textbooks See the [annotated reading list](references/reading-list.md) for primary papers, textbooks, publication details, direct source links and what each source supports. Use the [repo-wide reference index](https://github.com/KeWang0622/MRFoundry/blob/main/REFERENCES.md) to navigate across skills. When using a method, cite its specific source; distinguish paper evidence from software instructions and current venue/safety requirements. ## Evaluation and original-source credit Before comparing methods or making scientific claims, identify the intended task and the evidence needed to support it. Use the [evaluation and attribution guide](https://github.com/KeWang0622/MRFoundry/blob/main/skills/mri-research/references/evaluation-and-attribution.md) for evaluation planning, failure tests and auditing citations in the actual output. Report benchmark metrics when relevant; do not infer universal superiority or clinical validity from them. Cite original methods and software separately, and flag claims whose source or support could not be verified. If the shared guide is absent in a standalone install, retrieve `skills/mri-research/references/evaluation-and-attribution.md` from the [official repository](https://github.com/KeWang0622/MRFoundry). ## Project research memory For project experiments, read `.mri-research/INDEX.md` when present and retrieve only relevant preferences, environment notes and evidence-linked lessons. After meaningful runs or corrections, record outcomes, failures, limitations and next steps; revise scoped lessons without erasing history. Keep user preferences separate from scientific findings. Use the [project memory workflow](https://github.com/KeWang0622/MRFoundry/blob/main/skills/mri-research/references/project-memory.md) to initialize the folder or connect project `CLAUDE.md` / `AGENTS.md`. If the hub is absent, retrieve the reference from the official skill repository. ## Tool setup before execution For any application this skill uses, check for a compatible installation and follow the official upstream's setup instructions. Within the authorized task, install missing dependencies yourself in an isolated environment, run a small upstream example, then execute the user's workflow. Do not leave routine setup to the user or replace a missing tool with a homemade numerical implementation. Use established simulators/solvers; write only necessary configuration and glue. If blocked, report the actual obstacle and an established alternative. Read the [tool setup guide](https://github.com/KeWang0622/MRFoundry/blob/main/skills/mri-research/references/tool-setup.md) when installing, repairing, or choosing an execution environment. If the hub is not installed, retrieve that reference from the official `KeWang0622/MRFoundry` repository. ## The flow 1. **Frame.** Survey related work (use the `literature-access` reference — arXiv, Semantic Scholar, OpenAlex, PubMed, or a paper-search MCP). State the gap and a single crisp claim/hypothesis. Choose the venue using the writing guide below. 2. **Design.** Pick datasets (mind DUAs — see the hub's `data-and-formats`), baselines, the proposed method, task-specific endpoints and ablations up front. Use the evaluation guide to specify reference standards, failure tests and what would falsify the claim. Plan compute, reproducibility and the scope of independent validation; keep tuning and test data separate. Record seeds, configurations and run logs. 3. **Run.** Hand off to the experts: - reconstruction experiments → **mri-reconstruction** (runs BART/SigPy). - training / DL recon → **deep-learning-recon**. - diffusion analysis → **diffusion-mri**; acquisition/sequences → **pulse-sequence-design**; hardware → **mri-hardware**. Track every run (config, seed, data split, metric). 4. **Analyze.** Evaluate the planned endpoints, uncertainty, relevant subgroups and failure cases; show matched images and difference maps when informative. Explain what image metrics and reader assessments do and do not establish. Separate benchmark reproduction from independent implementation or external validation, and limit conclusions to the evidence actually collected. 5. **Write.** Use the paper-writing guide below; draft from verified evidence in the venue-provided format (LaTeX or Word as appropriate). 6. **Submit & revise.** Follow venue mechanics (blind review, rebuttal, camera-ready, or journal revision cycles). Prepare releases/preprints when requested; submission or publication requires user authorization. ## Choose the venue and summarize related work Use the [venue and literature-digest guide](https://github.com/KeWang0622/MRFoundry/blob/main/skills/mri-research/references/publishing.md) for MRM, JMRI, TMI, MedIA, MICCAI, ISMRM, CVPR and related venues. Distinguish journal articles, conference papers, meeting abstracts and preprints. Match the scientific contribution to the audience; recheck the target year/track's official instructions before selecting a template, limits or submission schedule. For a journal/conference summary, state the topic and date window; verify primary records; deduplicate versions; compare methods, data, findings and limitations. Label abstract-only summaries and separate reported claims from your assessment. Give a synthesis and useful next experiments, not just a list of titles. ## Writing and revising for MICCAI, MRM, JMRI and TMI Read the [paper-writing guide](references/paper-writing.md) for venue-specific framing, evidence requirements, figure planning and revisions. Start with the [paper plan](assets/paper-plan.md) and use the [reviewer-response template](assets/reviewer-response.md) when revising. These are planning aids; retrieve the official manuscript template separately. Keep planned experiments distinct from actual results. Link every numerical claim to its analysis, and make unsupported text an explicit placeholder. ## Resources & handoffs - Manuscript logistics (journals, LaTeX classes, reporting standards, abstracts): hub `publishing` — https://github.com/KeWang0622/MRFoundry/blob/main/skills/mri-research/references/publishing.md - Finding/monitoring literature: hub `literature-access` — https://github.com/KeWang0622/MRFoundry/blob/main/skills/mri-research/references/literature-access.md - Preprints: arXiv (eess.IV / physics.med-ph / cs.CV). Reviews on OpenReview for some venues. ## What you can produce A research plan, an experiment-tracking scaffold, drafted sections (intro, related work, method, results narrative), ablation/table templates, a rebuttal draft, and a submission/reproducibility checklist. Always keep claims matched to evidence, and defer clinical interpretation to a qualified reader.