Myocardial tissue characterization

Feature summary

Badge legend: Phenotype-family colors group feature types only. Status colors are reserved for evidence tables: muted green means verified, muted amber means method-dependent or schema debt, gray outline means needs verification, and red is reserved for blocked items. Disease badges use neutral navigation styling and are literature-context links only, not diagnoses, classifiers, or validated phenotype-to-ICD associations.

Myocardial tissue characterization phenotypes summarize native T1 relaxation behavior in myocardium and blood pools. This page is source-audited for the current native_T1.csv and native_T1_corrected.csv output names and explicitly separates current native T1 outputs from ECV, which is not emitted by the current pipeline.

Modality
Native T1 mapping
UKB source
Data Field 20214
Pipeline step
ShMOLLI T1 map QC, myocardial/blood-pool T1 extraction, optional cohort-level blood-pool correction
Outputs
native_T1.csv, native_T1_corrected.csv, visualization/ventricle/native_t1.png, visualization/ventricle/native_t1_ivs_fw_blood.png
Maturity
Source-audited phenotype page

Clinical question

Native T1 can help characterize diffuse myocardial tissue changes when interpreted with scanner, field strength, sequence, segmentation, and correction context. CardiacNexus reports quantitative T1 values for cohort phenotyping; it does not diagnose myocarditis, infarction, amyloidosis, Fabry disease, cardiomyopathy, or hypertrophic cardiomyopathy from a single row.

Anatomical and physiological definition

Native T1 is the pre-contrast longitudinal relaxation time. In the current CardiacNexus route, the native T1 map is segmented into myocardium, LV blood pool, and RV blood pool. The myocardium is further summarized globally and split into intraventricular septum (IVS) and free wall (FW) by the helper used in the extraction source.

Blood-pool correction is a derived cohort-level adjustment. The correction script first calculates each subject's mean blood-pool T1 from LV and RV blood-pool values, estimates linear relationships between blood-pool T1 and myocardial T1 across the aggregate, and then adjusts each subject's myocardial T1 using the difference between cohort mean blood R1 and subject blood R1 [5].

Source acquisition and UKB field

Native T1 mapping uses UK Biobank Data Field 20214. The current implementation expects shmolli_t1map.nii.gz and seg_shmolli_t1map.nii.gz. Segmentation labels are 1 for myocardium, 2 for LV blood pool, and 3 for RV blood pool.

What exactly CardiacNexus measures

Native myocardial and blood-pool T1

eval_native_t1.py reads the native T1 map and segmentation, checks ShMOLLI segmentation quality, and calls evaluate_t1_uncorrected. It writes global myocardial T1, IVS T1, FW T1, LV blood-pool T1, and RV blood-pool T1 to native_T1.csv.

Native T1 region measurement panel for myocardium and blood pools
Native T1 region panel from the manuscript image cache, cited there to Puyol-Anton et al. 2020, shown to orient myocardium, septal/free-wall, and LV/RV blood-pool measurement context. CardiacNexus output labels, segmentation labels, and correction behavior are defined in the page text and tables.
Native T1 mapping clinical context from the manuscript image cache
Native T1 mapping context figure from the manuscript image cache, cited there to Barison et al. 2022, shown to orient sequence-level tissue characterization. Scanner, sequence, ShMOLLI, segmentation, and correction caveats remain necessary when interpreting CardiacNexus native T1 rows.Source: manuscript image cache citing Barison et al. 2022; permission and exact source-panel review pending for draft use.

Blood-pool corrected T1

eval_native_t1_corrected.py reads the aggregated native_T1.csv, drops rows missing required native T1 fields, computes each subject's mean blood-pool T1, fits cohort-level linear regressions between blood-pool T1 and each myocardial T1 family, and writes corrected global, IVS, and FW values to native_T1_corrected.csv.

Extracellular volume boundary

ECV requires pre-contrast T1, post-contrast T1, and hematocrit. Those required inputs and output columns are not part of the current native T1 extraction route, so ECV is documented only as clinical context [6].

Extracellular volume context figure from the manuscript image cache
ECV context figure from the manuscript image cache, shown only to document the non-current boundary. CardiacNexus currently promotes native T1 and blood-pool-corrected native T1 rows on this page; ECV is not emitted by the current route.Source: manuscript image cache; permission and exact source-panel review pending for draft use.

Output columns and units

Display familyExact output columnUnitStatusSchema note
Native myocardial T1Native T1: Myocardium-Global [ms]mscurrentuncorrected native T1
Native myocardial T1Native T1: Myocardium-IVS [ms]mscurrentintraventricular septum
Native myocardial T1Native T1: Myocardium-FW [ms]mscurrentfree wall
Native blood-pool T1Native T1: LV Blood Pool [ms]mscurrentLV blood-pool label
Native blood-pool T1Native T1: RV Blood Pool [ms]mscurrentRV blood-pool label
Corrected myocardial T1Native T1-Corrected: Myocardium-Global-corrected [ms]mscurrentcohort-level blood correction
Corrected myocardial T1Native T1-Corrected: Myocardium-IVS-corrected [ms]mscurrentcohort-level blood correction
Corrected myocardial T1Native T1-Corrected: Myocardium-FW-corrected [ms]mscurrentcohort-level blood correction

Output reconciliation

Evidence layerResult
Implementation source5 native T1 rows checked against eval_native_t1.py; 3 corrected rows checked against eval_native_t1_corrected.py
Output inventorydocs/data/output_column_inventory.yml records native_T1 and native_T1_corrected artifact families
Phenotype dictionarydocs/data/phenotype_dictionary.yml links current native and corrected T1 rows to this page
Page output tableall current emitted columns are listed above

Required upstream inputs

  • shmolli_t1map.nii.gz;
  • seg_shmolli_t1map.nii.gz;
  • successful shmolli_pass_quality_control result;
  • aggregated native_T1.csv for corrected outputs;
  • enough non-missing native T1 rows to fit cohort-level correction regressions.

Reference ranges with cohort and method context

FeatureSourceCohortReference valueStatusNote
Native myocardial T1 methodT1 mapping review [1]method reviewnot a normal rangeVerified context sourceDefinitions and scanner/sequence caveats
Automated native T1 quantificationPuyol-Anton et al. [2]UKB-style automated T1 mapping cohortsource-specific valuesVerified context sourceClosest automated-method context; exact row extraction deferred
ShMOLLI normal variationPiechnik et al. [3]healthy 1.5T ShMOLLI cohortsex-specific source valuesVerified context sourceMethod-dependent; do not mix with other sequences
Broad CMR reference updateKawel-Boehm et al. [4]consensus reference updatetissue values are context only hereVerified context sourceUse as broad CMR context, not as a direct CardiacNexus T1 threshold
Blood-pool correctionNickander et al. [5]derivation/validation contextcorrection method contextVerified context sourceSupports correction rationale, not a universal threshold
ECVTissue characterization review [6]reviewnot current outputVerified context sourceECV requires contrast and hematocrit; not emitted here

Source-located registry status: reference_range_sources.yml maps native T1 method context to Taylor 2016, automated native T1 quantification to Puyol-Anton 2020, ShMOLLI normal variation to Piechnik 2013, and blood correction to Nickander 2016. Exact numeric normal rows are not promoted as CardiacNexus thresholds until scanner, field strength, sequence, ROI, correction, and segmentation conventions are source-matched.

Disease interpretation

Native T1 elevation is reported in edema, myocarditis, myocardial infarction, amyloidosis, diffuse fibrosis, hypertrophic cardiomyopathy, dilated cardiomyopathy, and some aortic stenosis/remodeling contexts. Native T1 can be reduced in Fabry disease and iron/lipid-related contexts [1] [6]. These disease badges are navigation/context aids only; method-specific T1 values require scanner, sequence, and correction context.

QC caveats and maturity boundary

Native T1 is highly acquisition-sensitive. Field strength, scanner platform, ShMOLLI implementation, motion, segmentation, partial volume, blood-pool contamination, and correction strategy can change values. Corrected and uncorrected rows should not be pooled without explicit method labels.

The correction route is cohort-dependent because it estimates alpha values from the current aggregate. Changing the cohort, missingness pattern, or aggregate build can change corrected values even when a subject's uncorrected T1 is unchanged.

Implementation provenance

Feature familyFormula or computational routeExact output columnsSource code file and functionUpstream dependenciesConditional behaviorQC artifactsSchema debt
Native myocardial T1segmentation QC, then evaluate_t1_uncorrected summaries for global myocardium, IVS, and FWNative T1: Myocardium-* [ms] rowseval_native_t1.py; evaluate_t1_uncorrectedShMOLLI T1 map, ShMOLLI segmentation, label mapsubject skipped if image, segmentation, QC, or helper failsnative_t1.png, native_t1_ivs_fw_blood.pngvalues written as formatted strings in current CSV
Native blood-pool T1same helper returns LV and RV blood-pool T1 valuesNative T1: LV Blood Pool [ms], Native T1: RV Blood Pool [ms]eval_native_t1.py; evaluate_t1_uncorrectedlabels 2 and 3 in segmentationsubject skipped with native T1 failuresame visualization filesblood-pool rows are correction inputs as well as public outputs
Corrected native T1aggregate-level linear regression on blood-pool T1, then subject correction using blood R1 differencecorrected global, IVS, and FW rowseval_native_t1_corrected.pyaggregated native_T1.csv, non-missing blood-pool and myocardial rowssubject skipped if native T1 row missing; cohort fit depends on available aggregateno new subject-level visualizationcorrected values are cohort-dependent research outputs
ECV boundarynot emitted by the current native T1 routeno current output columnnot applicablepost-contrast T1 and hematocrit would be requiredliterature context onlynonedo not add ECV output rows unless the pipeline emits them

Source audit

  • Current native T1 labels, QC requirements, segmentation labels, and visualization paths were checked against eval_native_t1.py.
  • Current corrected native T1 labels and cohort-level correction behavior were checked against eval_native_t1_corrected.py.
  • docs/data/reference_sources.yml is present and used as the curated reference-source registry for this page.
  • Textbook context boundary: broad Braunwald/Hurst tissue-characterization concepts were not surfaced as a separate section because page-specific T1 mapping, automated native T1, ShMOLLI, blood correction, and tissue-characterization sources are sufficient for draft rollout.
  • Figure provenance is registered in docs/data/figure_provenance.yml for the native T1 region panel; permission and exact source-panel review remain pending for public release, but the figure has complete draft provenance.

References

  1. Taylor AJ, Salerno M, Dharmakumar R, Jerosch-Herold M. T1 Mapping. JACC: Cardiovascular Imaging. 2016;9(1):67-81.
  2. Puyol-Anton E, Ruijsink B, Baumgartner CF, Masci PG, Sinclair M, Konukoglu E, Razavi R, King AP. Automated Quantification of Myocardial Tissue Characteristics from Native T1 Mapping Using Neural Networks with Uncertainty-Based Quality-Control. Journal of Cardiovascular Magnetic Resonance. 2020;22(1):60.
  3. Piechnik SK, Ferreira VM, Lewandowski AJ, Ntusi NA, Banerjee R, Holloway C, Hofman MB, Sado DM, Maestrini V, White SK, Lazdam M, Karamitsos T, Moon JC, Neubauer S, Leeson P, Robson MD. Normal Variation of Magnetic Resonance T1 Relaxation Times in the Human Population at 1.5 T Using ShMOLLI. Journal of Cardiovascular Magnetic Resonance. 2013;15(1):13.
  4. Kawel-Boehm N, Hetzel SJ, Ambale-Venkatesh B, Captur G, Francois CJ, Jerosch-Herold M, Salerno M, Teague SD, Valsangiacomo-Buechel ER, Van Der Geest RJ, Bluemke DA. Reference Ranges for Normal Cardiac Chamber Size and Function Using Cardiovascular Magnetic Resonance. Journal of Cardiovascular Magnetic Resonance. 2020;22(1):87.
  5. Nickander J, Lundin M, Abdula G, Sorensson P, Rosmini S, Moon JC, Kellman P, Sigfridsson A, Ugander M. Blood Correction Reduces Variability and Gender Differences in Native Myocardial T1 Values at 1.5 T Cardiovascular Magnetic Resonance - a Derivation/Validation Approach. Journal of Cardiovascular Magnetic Resonance. 2016;19(1):41.
  6. Barison A, Aimo A, Todiere G, Grigoratos C, Aquaro GD, Emdin M. Cardiovascular Magnetic Resonance for the Diagnosis and Management of Heart Failure with Preserved Ejection Fraction. Heart Failure Reviews. 2022;27(1):191-205.