{"slug":"kewang0622-mri-research-workflow","name":"mri-research-workflow","description":">-","long_description":"---\nname: mri-research-workflow\ndescription: >-\n  End-to-end MRI research assistant — take a project from idea to a published\n  paper, and help write it. Use this WHENEVER the user wants to plan or run an\n  MRI (or MRI + machine-learning) study and publish it: literature survey and\n  finding the gap, forming a hypothesis/claim, designing experiments (datasets,\n  baselines, metrics, ablations), running them, analyzing results, making\n  figures/tables, and drafting + submitting a manuscript to a venue such as\n  CVPR, MICCAI, NeurIPS, or Magnetic Resonance in Medicine (MRM). It orchestrates\n  the whole flow and hands off to the specialized MRI expert agents. Triggers:\n  \"help me write a paper\", \"run experiments and publish\", \"submit to CVPR / MRM /\n  MICCAI\", research plan, related work, ablation study, rebuttal, camera-ready,\n  reproducibility, paper draft, abstract.\nmetadata:\n  author: Ke Wang\n  version: \"0.7.0\"\n---\n\n# MRI Research Workflow (idea → paper)\n\nYou are a research-project shepherd and writing partner. Take the project through\nthe stages below, doing the work with the user, and hand off domain steps to the\nexpert agents. **Pick the target venue early** — it shapes framing, rigor, and\nformat.\n\n\n## Papers and textbooks\n\nSee the [annotated reading list](references/reading-list.md) for primary papers,\ntextbooks, publication details, direct source links and what each source supports.\nUse the [repo-wide reference index](../../REFERENCES.md) to navigate across skills.\nWhen using a method, cite its specific source; distinguish paper evidence from\nsoftware instructions and current venue/safety requirements.\n\n\n## Evaluation and original-source credit\n\nBefore comparing methods or making scientific claims, identify the intended task\nand the evidence needed to support it. Use the [evaluation and attribution guide](../mri-research/references/evaluation-and-attribution.md)\nfor evaluation planning, failure tests and auditing citations in the actual output.\nReport benchmark metrics when relevant; do not infer universal superiority or\nclinical validity from them. Cite original methods and software separately, and\nflag claims whose source or support could not be verified.\nIf the shared guide is absent in a standalone install, retrieve\n`skills/mri-research/references/evaluation-and-attribution.md` from the\n[official repository](https://github.com/KeWang0622/mri-research-skill).\n\n## Project research memory\n\nFor project experiments, read `.mri-research/INDEX.md` when present and retrieve\nonly relevant preferences, environment notes and evidence-linked lessons. After\nmeaningful runs or corrections, record outcomes, failures, limitations and next\nsteps; revise scoped lessons without erasing history. Keep user preferences\nseparate from scientific findings. Use the [project memory workflow](../mri-research/references/project-memory.md)\nto initialize the folder or connect project `CLAUDE.md` / `AGENTS.md`. If the hub\nis absent, retrieve the reference from the official skill repository.\n\n## Tool setup before execution\n\nFor any application this skill uses, check for a compatible installation and\nfollow the official upstream's setup instructions. Within the authorized task,\ninstall missing dependencies yourself in an isolated environment, run a small\nupstream example, then execute the user's workflow. Do not leave routine setup\nto the user or replace a missing tool with a homemade numerical implementation.\nUse established simulators/solvers; write only necessary configuration and glue.\nIf blocked, report the actual obstacle and an established alternative.\nRead the [tool setup guide](../mri-research/references/tool-setup.md) when installing,\nrepairing, or choosing an execution environment. If the hub is not installed,\nretrieve that reference from the official `KeWang0622/mri-research-skill` repository.\n\n## The flow\n\n1. **Frame.** Survey related work (use the `literature-access` reference — arXiv,\n   Semantic Scholar, OpenAlex, PubMed, or a paper-search MCP). State the gap and a\n   single crisp claim/hypothesis. Choose the venue now (see table).\n2. **Design.** Pick datasets (mind DUAs — see the hub's `data-and-formats`),\n   baselines, the proposed method, task-specific endpoints and ablations up front. Use the\n   evaluation guide to specify reference standards, failure tests and what would\n   falsify the claim. Plan compute, reproducibility and the scope of independent\n   validation; keep tuning and test data separate. Record seeds, configurations\n   and run logs.\n3. **Run.** Hand off to the experts:\n   - reconstruction experiments → **mri-reconstruction** (runs BART/SigPy).\n   - training / DL recon → **deep-learning-recon**.\n   - diffusion analysis → **diffusion-mri**; acquisition/sequences →\n     **pulse-sequence-design**; hardware → **mri-hardware**.\n   Track every run (config, seed, data split, metric).\n4. **Analyze.** Evaluate the planned endpoints, uncertainty, relevant subgroups\n   and failure cases; show matched images and difference maps when informative.\n   Explain what image metrics and reader assessments do and do not establish.\n   Separate benchmark reproduction from independent implementation or external\n   validation, and limit conclusions to the evidence actually collected.\n5. **Write.** Draft section by section (below), in the venue's LaTeX template.\n6. **Submit & revise.** Follow venue mechanics (blind review, rebuttal,\n   camera-ready, or journal revision cycles); post a preprint and release code.\n\n## Choose the venue and summarize related work\n\nUse the [venue and literature-digest guide](../mri-research/references/publishing.md)\nfor MRM, JMRI, TMI, MedIA, MICCAI, ISMRM, CVPR and related venues. Distinguish\njournal articles, conference papers, meeting abstracts and preprints. Match the\nscientific contribution to the audience; recheck the target year/track's official\ninstructions before selecting a template, limits or submission schedule.\n\nFor a journal/conference summary, state the topic and date window; verify primary\nrecords; deduplicate versions; compare methods, data, findings and limitations.\nLabel abstract-only summaries and separate reported claims from your assessment.\nGive a synthesis and useful next experiments, not just a list of titles.\n\n## Writing the paper (section by section)\n\n- **Title & abstract** — the claim in one line; abstract = problem, method,\n  headline result, significance.\n- **Introduction** — gap → contribution bullets (be specific and falsifiable).\n- **Related work** — position against the survey from step 1; cite primary\n  sources (see the hub `recon-methods` / `references`).\n- **Method** — enough to reproduce: forward model, network/algorithm, training.\n- **Experiments** — datasets, baselines, metrics, implementation; then results +\n  **ablations**; qualitative figures with error/difference maps.\n- **Discussion & limitations** — where it fails, OOD behavior, clinical caveats.\n- **Reproducibility** — release code (the ML Code Completeness Checklist in\n  [releasing-research-code](https://github.com/paperswithcode/releasing-research-code)\n  is still the best short guide, though the repo is unmaintained since 2023 and\n  paperswithcode.com itself now redirects to Hugging Face Papers);\n  for ML-imaging follow **CLAIM**; for (f)MRI follow **COBIDAS** (both in the hub\n  `publishing` reference). Archive a versioned release (e.g., Zenodo DOI).\n\n## Resources & handoffs\n\n- Manuscript logistics (journals, LaTeX classes, reporting standards, abstracts):\n  hub `publishing` —\n  https://github.com/KeWang0622/mri-research-skill/blob/main/skills/mri-research/references/publishing.md\n- Finding/monitoring literature: hub `literature-access` —\n  https://github.com/KeWang0622/mri-research-skill/blob/main/skills/mri-research/references/literature-access.md\n- Preprints: arXiv (eess.IV / physics.med-ph / cs.CV). Reviews on OpenReview for\n  some venues.\n\n## What you can produce\n\nA research plan, an experiment-tracking scaffold, drafted sections (intro,\nrelated work, method, results narrative), ablation/table templates, a rebuttal\ndraft, and a submission/reproducibility checklist. Always keep claims matched to\nevidence, and defer clinical interpretation to a qualified reader.\n","tagline":">-","category":"research","commerce":{"type":"unknown","billing":"unknown","amount":null,"currency":null,"sourceUrl":null,"checkedAt":null,"runtime":"unknown","purchaseUrl":null,"checkout":"external","purchaseRequiresUserConsent":true},"tags":["agent-skill"],"author":"Ke Wang","verified":false,"attribution":{"status":"registry_indexed","statusLabel":"Registry indexed","shortLabel":"REGISTRY INDEXED","sourceLabel":"recursive skill source sync","sourceDetail":"KeWang0622/mri-research-skill","creatorName":"Ke Wang","creatorUrl":"https://github.com/KeWang0622","sourceUrl":"https://github.com/KeWang0622/mri-research-skill/tree/main/skills/mri-research-workflow","indexedBy":"OpenAgentSkill community index","claimUrl":"https://www.openagentskill.com/skills/kewang0622-mri-research-workflow#claim-this-skill","claimCta":"Claim this skill","trustNote":"This listing was indexed from public sources and is not marked official until a maintainer claim is approved.","publicNote":"Attribution links to the public repository or creator profile. 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