{"slug":"kewang0622-mri-reconstruction","name":"mri-reconstruction","description":">-","long_description":"---\nname: mri-reconstruction\ndescription: >-\n  Actionable MRI image reconstruction — turn raw k-space into an image, and\n  actually run it. Use this WHENEVER the user wants to reconstruct MR data or\n  says things like \"reconstruct this k-space\", \"run BART on this\", \"get an image\n  from this .cfl / .h5 / twix file\", or asks about parallel imaging\n  (ESPIRiT/SENSE/GRAPPA), compressed sensing (PICS / L1-wavelet), coil\n  sensitivity estimation, coil combination, or non-Cartesian / NUFFT\n  reconstruction. This agent prefers to EXECUTE the reconstruction with BART or\n  SigPy (not just describe it). It covers classical/analytic reconstruction —\n  for anything TRAINED (unrolled networks, VarNet, self-supervised, diffusion\n  priors, fastMRI models) hand off to the deep-learning-recon skill. Triggers:\n  k-space, coil sensitivities, ESPIRiT, PICS, undersampled reconstruction,\n  radial/spiral recon, `.cfl`/`.hdr`, ISMRMRD, Siemens twix, GE P-file.\nmetadata:\n  author: Ke Wang\n  version: \"0.7.0\"\n---\n\n# MRI Reconstruction (actionable)\n\nYou are a reconstruction engineer: given k-space, produce an image — and run the\npipeline, don't just talk about it. Default to **BART** (battle-tested, CLI,\nscriptable); use **SigPy** when the user is in Python. Confirm the data before\nrunning, then execute and inspect.\n\n## Workflow\n\n**0. Identify the k-space format** (ask or inspect). BART works in its own\n`.cfl`/`.hdr`, so other formats need a conversion step:\n- **BART `.cfl` + `.hdr`** — native; dims must be `[X Y Z COILS ...]` (coils on\n  dim 3). Ready to use.\n- **Siemens twix `.dat`** — `bart twixread -A meas.dat ksp` writes a `.cfl`\n  (`-A` auto-guesses the dimensions; without it you must supply them explicitly\n  via `-x/-y/-z/-c/-s/-n`, and a flagless call will not work). Then confirm with\n  `bart show -m ksp`. Alternative: read in Python with `twixtools`/`pymapVBVD`\n  and write a `.cfl`.\n- **NumPy array** — write a `.cfl` with BART's Python helper:\n  `PYTHONPATH=$TOOLBOX_PATH/python python -c \"import cfl; cfl.writecfl(name, arr)\"`\n  (`cfl.py` ships in BART's `python/` directory — it is not on PyPI, and the\n  unrelated `bartpy` package on PyPI is a decision-tree library, not this).\n  Make sure coils land on dim 3.\n- **ISMRMRD `.h5`** — BART *has* an `ismrmrd` tool, but it is a build-time\n  option: the Makefile defaults to `ISMRMRD=0`, so a stock build has no\n  `bart ismrmrd` command. Check with `bart ismrmrd -h`; if it's missing, either\n  rebuild BART with `ISMRMRD=1` (needs the ISMRMRD C++ library) or read the file\n  with the Python `ismrmrd` package and `cfl.writecfl`. Vendor raw → ISMRMRD\n  first via `siemens_to_ismrmrd` / `ge_to_ismrmrd` / `philips_to_ismrmrd`.\n\n**1. Estimate coil sensitivities (ESPIRiT):**\n```\nbart ecalib -m1 -r 24 kspace sens\n```\n`-m1` matters: `ecalib` computes **two** ESPIRiT map sets by default, and `pics`\nthen returns a soft-SENSE result with a size-2 MAPS dimension instead of a single\nimage — a silent wrong answer. `-r` caps the auto-extracted calibration region\n(24³ is already the default; lower it if your ACS is smaller).\n\n**2. Reconstruct:**\n```\n# Fully sampled: inverse FFT + coil combine\nbart fft -iu 7 kspace img_coils && bart rss 8 img_coils img\n\n# Undersampled — parallel imaging + compressed sensing (the workhorse):\nbart pics -l1 -r 0.01 kspace sens img     # l1-wavelet regularized\n```\n- **Non-Cartesian** (radial/spiral/cones/rosette): you also need the trajectory.\n  Use `bart pics -t traj kspace sens img`. For calibration, grid with the\n  **inverse** NUFFT (`bart nufft -i`), not the adjoint (`-a`) — the adjoint\n  leaves the sampling density in the data and biases the ESPIRiT maps. Get the\n  trajectory from the sequence/ISMRMRD, or `bart traj` for nominal.\n- **EPI is Cartesian.** Its zig-zag traversal still samples a Cartesian grid, so\n  do *not* reach for a trajectory/NUFFT. EPI needs ramp-sampling regridding and\n  Nyquist-ghost / phase correction first, then the Cartesian path above;\n  geometric distortion is corrected downstream (topup/FUGUE).\n\n**3. Inspect:** check image dimensions, scaling, and orientation; look for\nresidual aliasing (raise `-r`), over-smoothing (lower `-r`), or coil-combination\nerrors.\n\n## Runnable helper\n\n`scripts/bart_recon.sh <kspace_cfl> <output_cfl> [l1_reg] [traj_cfl]` runs an\nESPIRiT → PI+CS pipeline on a BART `.cfl` k-space file. It **assumes Cartesian\ndata with coils on dim 3 and a fully-sampled ACS** (calibration region); pass a\n**trajectory `.cfl`** as the 4th argument for genuinely non-Cartesian sampling\n(radial/spiral/cones/rosette — not EPI, which is Cartesian). It warns about these\nassumptions but can't fully verify them — check the header and adapt the\nregularization / calibration size to the data.\n\n## SigPy (Python) alternative\n\n```python\nimport sigpy as sp, sigpy.mri as mr\nmaps = mr.app.EspiritCalib(ksp).run()                     # coil maps\nimg  = mr.app.L1WaveletRecon(ksp, maps, lamda=0.01).run() # PI + CS\n# non-Cartesian: build a NUFFT from coords, use mr.app.SenseRecon\n```\n\n## Guardrails\n\n- Confirm the acceleration factor and sampling (Cartesian vs non-Cartesian)\n  before choosing a method — the wrong forward model gives garbage.\n- If BART isn't installed: https://codeberg.org/mrirecon/bart (source, active)\n  with docs at https://mrirecon.codeberg.page/ — offer to install or fall back to\n  SigPy. Note the `github.com/mrirecon/bart` mirror is archived as of 2026.\n- **Report the SNR cost, not just the image.** Acceleration R costs SNR by\n  `g·√R`; quote a g-factor (or a pseudo-replica SNR estimate for GRAPPA/ESPIRiT/\n  nonlinear recon) rather than implying R is free.\n- **Stay in lane:** anything trained — unrolled networks, VarNet/MoDL, SSDU,\n  diffusion priors, fastMRI baselines — belongs to the `deep-learning-recon`\n  skill. Designing the *acquisition* or the trajectory belongs to\n  `pulse-sequence-design`; this skill consumes a trajectory, it doesn't design one.\n- For method theory and citations, see the hub:\n  https://github.com/KeWang0622/mri-research-skill/blob/main/skills/mri-research/references/recon-methods.md\n  and tool details at\n  https://github.com/KeWang0622/mri-research-skill/blob/main/skills/mri-research/references/tools.md\n","tagline":">-","category":"automation","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":"github candidate review","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-reconstruction","indexedBy":"OpenAgentSkill community index","claimUrl":"https://www.openagentskill.com/skills/kewang0622-mri-reconstruction#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. Creators can claim the listing to update ownership signals."},"stats":{"stars":21,"forks":0,"verified_installs":0,"successful_runs":0,"total_outcomes":0,"rating":0,"review_count":0,"quality_score":32.8},"quality":{"score":60,"tier":"promising","label":"Promising","summary":"Useful candidate, but compare it with alternatives before adopting.","signals":[{"label":"GitHub stars","value":"21","tone":"neutral"},{"label":"Freshness","value":"15d ago","tone":"positive"},{"label":"Install ready","value":"Yes","tone":"positive"},{"label":"License","value":"MIT","tone":"neutral"}],"warnings":["Low GitHub adoption signal","The helper script uses `mktemp -u` which is not race-safe; using `mktemp` without `-u` and then creating files would be safer."]},"trust":{"version":"trust-score-v5","score":56,"base_score":64,"outcome_confidence":0,"tier":"risk","label":"Do not auto-install","summary":"Trust Score v5 found insufficient evidence for agent installation. Treat this as discovery material, not an executable recommendation.","recommendedAction":"Choose a stronger alternative or inspect the source manually before any install attempt.","decision":{"install_policy":"human_review_before_install","auto_install_allowed":false,"human_review_required":true,"sandbox_first":true,"agent_action":"Compare alternatives before installing.","reasoning":["56/100 Trust Score v5","64/100 Trust Score v4 baseline","Needs more real agent outcomes before unattended install","Install path is missing","Review before production"],"review_required_when":["The workspace contains production secrets, payments, private customer data, or irreversible actions.","The install command requests shell, network, credential, database, or broad filesystem access.","Outcome evidence is missing, recently failed, or required human review.","Production credentials, payments, or irreversible account changes without explicit human review","Sensitive private data before reviewing repository code, license, and permission surface","Automatic installation in a production workspace"]},"dimensions":[{"id":"github_adoption","label":"GitHub adoption","score":30,"weight":0.13,"status":"fail","detail":"21 GitHub stars"},{"id":"repo_activity","label":"Stars/forks activity","score":32,"weight":0.08,"status":"fail","detail":"21 stars, 0 forks; issue activity unavailable in current metadata"},{"id":"maintenance","label":"Recent maintenance","score":100,"weight":0.14,"status":"pass","detail":"15d since push"},{"id":"license","label":"License clarity","score":86,"weight":0.09,"status":"pass","detail":"MIT"},{"id":"documentation","label":"README/SKILL.md completeness","score":70,"weight":0.14,"status":"info","detail":"Public metadata needs stronger README/SKILL.md context"},{"id":"dependency_risk","label":"Dependency/runtime risk","score":72,"weight":0.12,"status":"info","detail":"command execution surface"},{"id":"installability","label":"Install availability","score":92,"weight":0.1,"status":"pass","detail":"npx skills add KeWang0622/mri-research-skill --skill mri-reconstruction"},{"id":"install_safety","label":"Install command safety","score":92,"weight":0.1,"status":"pass","detail":"standard package or runtime install path"},{"id":"permission_surface","label":"Permission surface","score":62,"weight":0.07,"status":"info","detail":"shell or command execution, filesystem or document access"},{"id":"repository","label":"Repository evidence","score":86,"weight":0.04,"status":"pass","detail":"https://github.com/KeWang0622/mri-research-skill/tree/main/skills/mri-reconstruction"},{"id":"review_status","label":"Review status","score":66,"weight":0.05,"status":"info","detail":"AI review data available"},{"id":"agent_outcomes","label":"Agent Proven outcomes","score":54,"weight":0.13,"status":"info","detail":"No agent outcome data yet"}],"checks":[{"status":"fail","label":"GitHub adoption","detail":"21 GitHub stars"},{"status":"fail","label":"Stars/forks activity","detail":"21 stars, 0 forks; issue activity unavailable in current metadata"},{"status":"pass","label":"Recent maintenance","detail":"15d since push"},{"status":"pass","label":"License clarity","detail":"MIT"},{"status":"info","label":"README/SKILL.md completeness","detail":"Public metadata needs stronger README/SKILL.md context"},{"status":"info","label":"Dependency/runtime risk","detail":"command execution surface"},{"status":"pass","label":"Install availability","detail":"npx skills add KeWang0622/mri-research-skill --skill mri-reconstruction"},{"status":"pass","label":"Install command safety","detail":"standard package or runtime install path"},{"status":"info","label":"Permission surface","detail":"shell or command execution, filesystem or document access"},{"status":"pass","label":"Repository evidence","detail":"https://github.com/KeWang0622/mri-research-skill/tree/main/skills/mri-reconstruction"},{"status":"info","label":"Review status","detail":"AI review data available"},{"status":"info","label":"Agent Proven outcomes","detail":"No agent outcome data yet"},{"status":"warn","label":"Ownership","detail":"No approved owner claim yet"},{"status":"pass","label":"OpenAgentSkill usage","detail":"5 views, 0 install copies"},{"status":"info","label":"Agent outcomes","detail":"No agent outcome data yet"}],"strengths":["AI review approved","Install path is available","Repository evidence is available","Recently maintained repository","Install command has no obvious high-risk pattern","Outcome loop is ready but needs first real agent run"],"warnings":["The helper script uses `mktemp -u` which is not race-safe; using `mktemp` without `-u` and then creating files would be safer.","Financial research output is not financial advice; require human review before any live investment decision.","Low GitHub adoption signal","Quality score needs review","GitHub adoption: 21 GitHub stars","Stars/forks activity: 21 stars, 0 forks; issue activity unavailable in current metadata","No real agent outcome reports yet","Human review required before unattended installation"],"evidence":{"stars":"21 GitHub stars","repoActivity":"21 stars, 0 forks","lastPushed":"15d since push","license":"MIT","repository":"https://github.com/KeWang0622/mri-research-skill/tree/main/skills/mri-reconstruction","install":"The tracked source changed or could not be synchronized. 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Review the current source before installing.","Repository evidence is available","License is declared","No Agent Proven outcome evidence yet","15d since push","Financial domain: human review is required before use in a live investment workflow.","Trust Score v5 requires review or sandbox-only use before install."]},"agentCompatibility":["Codex","Claude Code","Cursor","OpenAgentSkill CLI"],"riskSummary":{"level":"medium","label":"Review before production","notes":["The helper script uses `mktemp -u` which is not race-safe; using `mktemp` without `-u` and then creating files would be safer.","Financial research output is not financial advice; require human review before any live investment decision.","Low GitHub adoption signal","Quality score needs review","GitHub adoption: 21 GitHub stars"]},"outcomeEvidence":{"total":0,"successes":0,"failures":0,"notRelevant":0,"successRate":null,"installAttempts":0,"riskBlocked":0,"setupRequired":0,"installSuccessRate":null,"avgOutputQuality":null,"avgTimeToUsefulMs":null,"productionOutcomes":0,"humanReviewRequired":0,"recentSuccessRate":null,"recentFailureRate":null,"uniqueAgents":0,"agentProvenScore":0,"agentProvenLabel":"Needs first agent run","lastOutcomeAt":null,"label":"No agent outcome data yet"},"autoInstall":{"allowed":false,"sandboxRequired":true,"policy":"human_review_before_install","reason":"Compare alternatives before installing."},"outcome_loop":{"version":"openagentskill-agent-outcome-v4","required_after_install":true,"endpoint":"/api/agent/outcome","method":"POST","event_id_source":"feedback.event_id, install_receipt.resolve_event_id, or decision_packet.outcome_feedback.event_id","expected_outcomes":["success","failed","not_relevant","blocked_by_risk","setup_required"],"required_fields":["event_id","skill_slug","task"],"quality_fields":["task_success","output_quality","error_type","human_review_required","used_in_production","workspace","evidence_url","time_to_useful_ms","source_version"],"ranking_inputs_updated":["Trust Score v5 outcome confidence","Agent Proven Score","Resolve ranking task-fit evidence","Skill detail machine-readable metadata","Outcome leaderboard"]},"agent_contract":{"suited_tasks":["automation","agent-skill"],"suited_agents":["Codex","Claude Code","Cursor","OpenAgentSkill CLI"],"install_command":null,"trust_score":56,"trust_version":"trust-score-v5","risk_level":"medium","do_not_use_when":["Production credentials, payments, or irreversible account changes without explicit human review","Sensitive private data before reviewing repository code, license, and permission surface","Automatic installation in a production workspace","Autonomous investment, trading, tax, or suitability decisions without a qualified human review"],"before_install":["Read the audit page and machine-readable metadata.","Confirm the install command, license, and permission surface fit the workspace.","Get explicit human approval or choose an alternative before installing."],"after_run":["Report the outcome to /api/agent/outcome using the resolve event id.","Include output_quality, workspace, human_review_required, and evidence_url when available.","Re-resolve before broad production rollout."]},"bestFor":["automation","agent-skill"],"doNotUseFor":["Production credentials, payments, or irreversible account changes without explicit human review","Sensitive private data before reviewing repository code, license, and permission surface","Automatic installation in a production workspace","Autonomous investment, trading, tax, or suitability decisions without a qualified human review"],"knownRisks":["The helper script uses `mktemp -u` which is not race-safe; using `mktemp` without `-u` and then creating files would be safer.","Financial research output is not financial advice; require human review before any live investment decision.","Low GitHub adoption signal","Quality score needs review","GitHub adoption: 21 GitHub stars","Stars/forks activity: 21 stars, 0 forks; issue activity unavailable in current metadata"],"backward_compatible":{"trust_score_v4":{"version":"trust-score-v4","score":64,"tier":"review","label":"Manual review","summary":"Potentially useful, but at least one trust signal needs human inspection."}}},"trust_score_v5":{"version":"trust-score-v5","score":56,"base_score":64,"outcome_confidence":0,"tier":"risk","label":"Do not auto-install","summary":"Trust Score v5 found insufficient evidence for agent installation. Treat this as discovery material, not an executable recommendation.","recommendedAction":"Choose a stronger alternative or inspect the source manually before any install attempt.","decision":{"install_policy":"human_review_before_install","auto_install_allowed":false,"human_review_required":true,"sandbox_first":true,"agent_action":"Compare alternatives before installing.","reasoning":["56/100 Trust Score v5","64/100 Trust Score v4 baseline","Needs more real agent outcomes before unattended install","Install path is missing","Review before production"],"review_required_when":["The workspace contains production secrets, payments, private customer data, or irreversible actions.","The install command requests shell, network, credential, database, or broad filesystem access.","Outcome evidence is missing, recently failed, or required human review.","Production credentials, payments, or irreversible account changes without explicit human review","Sensitive private data before reviewing repository code, license, and permission surface","Automatic installation in a production workspace"]},"dimensions":[{"id":"github_adoption","label":"GitHub adoption","score":30,"weight":0.13,"status":"fail","detail":"21 GitHub stars"},{"id":"repo_activity","label":"Stars/forks activity","score":32,"weight":0.08,"status":"fail","detail":"21 stars, 0 forks; 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issue activity unavailable in current metadata"},{"status":"pass","label":"Recent maintenance","detail":"15d since push"},{"status":"pass","label":"License clarity","detail":"MIT"},{"status":"info","label":"README/SKILL.md completeness","detail":"Public metadata needs stronger README/SKILL.md context"},{"status":"info","label":"Dependency/runtime risk","detail":"command execution surface"},{"status":"pass","label":"Install availability","detail":"npx skills add KeWang0622/mri-research-skill --skill mri-reconstruction"},{"status":"pass","label":"Install command safety","detail":"standard package or runtime install path"},{"status":"info","label":"Permission surface","detail":"shell or command execution, filesystem or document access"},{"status":"pass","label":"Repository evidence","detail":"https://github.com/KeWang0622/mri-research-skill/tree/main/skills/mri-reconstruction"},{"status":"info","label":"Review status","detail":"AI review data available"},{"status":"info","label":"Agent Proven outcomes","detail":"No agent outcome data yet"},{"status":"warn","label":"Ownership","detail":"No approved owner claim yet"},{"status":"pass","label":"OpenAgentSkill usage","detail":"5 views, 0 install copies"},{"status":"info","label":"Agent outcomes","detail":"No agent outcome data yet"}],"strengths":["AI review approved","Install path is available","Repository evidence is available","Recently maintained repository","Install command has no obvious high-risk pattern","Outcome loop is ready but needs first real agent run"],"warnings":["The helper script uses `mktemp -u` which is not race-safe; 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Review the current source before installing.","installSafety":"standard package or runtime install path","permissionSurface":"shell or command execution, filesystem or document access","documentation":"Usable metadata, review docs","agentOutcomes":"No agent outcome data yet","agentProvenScore":0,"outcomeConfidence":"0%","installPolicy":"human_review_before_install"},"installReadiness":{"ready":false,"command":null,"policy":"human_review_before_install","label":"Human review before install","notes":["The tracked source changed or could not be synchronized. Review the current source before installing.","Repository evidence is available","License is declared","No Agent Proven outcome evidence yet","15d since push","Financial domain: human review is required before use in a live investment workflow.","Trust Score v5 requires review or sandbox-only use before install."]},"agentCompatibility":["Codex","Claude Code","Cursor","OpenAgentSkill CLI"],"riskSummary":{"level":"medium","label":"Review before production","notes":["The helper script uses `mktemp -u` which is not race-safe; using `mktemp` without `-u` and then creating files would be safer.","Financial research output is not financial advice; require human review before any live investment decision.","Low GitHub adoption signal","Quality score needs review","GitHub adoption: 21 GitHub stars"]},"outcomeEvidence":{"total":0,"successes":0,"failures":0,"notRelevant":0,"successRate":null,"installAttempts":0,"riskBlocked":0,"setupRequired":0,"installSuccessRate":null,"avgOutputQuality":null,"avgTimeToUsefulMs":null,"productionOutcomes":0,"humanReviewRequired":0,"recentSuccessRate":null,"recentFailureRate":null,"uniqueAgents":0,"agentProvenScore":0,"agentProvenLabel":"Needs first agent run","lastOutcomeAt":null,"label":"No agent outcome data yet"},"autoInstall":{"allowed":false,"sandboxRequired":true,"policy":"human_review_before_install","reason":"Compare alternatives before installing."},"outcome_loop":{"version":"openagentskill-agent-outcome-v4","required_after_install":true,"endpoint":"/api/agent/outcome","method":"POST","event_id_source":"feedback.event_id, install_receipt.resolve_event_id, or decision_packet.outcome_feedback.event_id","expected_outcomes":["success","failed","not_relevant","blocked_by_risk","setup_required"],"required_fields":["event_id","skill_slug","task"],"quality_fields":["task_success","output_quality","error_type","human_review_required","used_in_production","workspace","evidence_url","time_to_useful_ms","source_version"],"ranking_inputs_updated":["Trust Score v5 outcome confidence","Agent Proven Score","Resolve ranking task-fit evidence","Skill detail machine-readable metadata","Outcome leaderboard"]},"agent_contract":{"suited_tasks":["automation","agent-skill"],"suited_agents":["Codex","Claude Code","Cursor","OpenAgentSkill CLI"],"install_command":null,"trust_score":56,"trust_version":"trust-score-v5","risk_level":"medium","do_not_use_when":["Production credentials, payments, or irreversible account changes without explicit human review","Sensitive private data before reviewing repository code, license, and permission surface","Automatic installation in a production workspace","Autonomous investment, trading, tax, or suitability decisions without a qualified human review"],"before_install":["Read the audit page and machine-readable metadata.","Confirm the install command, license, and permission surface fit the workspace.","Get explicit human approval or choose an alternative before installing."],"after_run":["Report the outcome to /api/agent/outcome using the resolve event id.","Include output_quality, workspace, human_review_required, and evidence_url when available.","Re-resolve before broad production rollout."]},"bestFor":["automation","agent-skill"],"doNotUseFor":["Production credentials, payments, or irreversible account changes without explicit human review","Sensitive private data before reviewing repository code, license, and permission surface","Automatic installation in a production workspace","Autonomous investment, trading, tax, or suitability decisions without a qualified human review"],"knownRisks":["The helper script uses `mktemp -u` which is not race-safe; 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