Cine short-axis imaging

Cine short-axis CMR is the CardiacNexus backbone for ventricular structure, ventricular function, myocardial mass/wall thickness, and short-axis mechanics.

Modality
Cine short-axis CMR
UKB source
Data Field 20209
Pipeline step
Short-axis ventricular segmentation, ED/ES timing, volume/mass/function extraction, and SAX strain/torsion analysis
Outputs
ventricular_volume.csv, strain_sax.csv, timeseries/ventricle.npz, timeseries/strain_sax.npz, ventricular and strain QC plots
Maturity
Source-audited modality page

Current pipeline role

The ventricular-volume route reads sa.nii.gz and seg_sa.nii.gz, requires short-axis QC, defines ED as frame 0 for retrospectively gated bSSFP, and defines ES as the minimum LV volume frame. It writes LV/RV volumes, myocardial mass, stroke volume, ejection fraction, cardiac output/index, BSA-indexed rows, selected diameters, sphericity indices, filling-rate rows, and timeseries/ventricle.npz.

The short-axis strain route reads SAX strain inputs and ventricular timing, writes strain_sax.csv, stores timeseries/strain_sax.npz, and generates circumferential/radial strain, strain-rate, timing, diastolic index, torsion, and recoil outputs when the required contours and peak detection are available.

Current outputs

Output familyCurrent rowsSource pathNotes
Ventricular structureEDV/ESV, indexed volumes, LV diameters, sphericity rowssrc/feature_extraction/Short_Axis_20209/eval_ventricular_volume.pyED frame is fixed at 0; ES is minimum LV volume
Ventricular functionstroke volume, EF, cardiac output, cardiac index, filling-rate rowseval_ventricular_volume.pyfilling-rate rows depend on volume-curve peak detection
Myocardial mass and wall thicknessmyocardial mass, mass index, M/V, wall thickness/thickening and related rowseval_ventricular_volume.pysegmentation and geometry-sensitive
SAX mechanicscircumferential/radial strain, strain-rate, timing, diastolic index, torsion, recoilsrc/feature_extraction/Short_Axis_20209/eval_strain_sax.pydeformation-sensitive; requires backend/QC caveats
Time series and QCtimeseries/ventricle.npz, timeseries/strain_sax.npz, ED/ES overlays, strain plotsimplementation sources aboveused by downstream LAX, flow, and combined features

QC and interpretation caveats

Short-axis rows depend on segmentation quality, basal/apical slice handling, voxel geometry, ED/ES frame selection, BSA availability, ECG overlays when used, and derivative peak detection. Volume and mass rows are more mature than deformation-sensitive strain/torsion rows.

Short-axis timing is reused by other modality routes. If timeseries/ventricle.npz is missing or inconsistent, long-axis strain, phase-contrast timing cross-checks, and combined cross-chamber rows may fail or be skipped.

Source audit

  • Ventricular ED/ES definitions, output families, BSA/indexing behavior, time-series keys, and QC plots were checked against eval_ventricular_volume.py.
  • SAX strain, strain-rate, timing, torsion, recoil, and QC plot families were checked against eval_strain_sax.py.
  • docs/data/output_column_inventory.yml records the ventricular_volume and strain_sax artifact contracts.
  • Textbook context boundary: broad clinical textbook context is not surfaced here because implementation and linked phenotype pages are sufficient for draft rollout.
Short-axis myocardial segment context from the CardiacNexus manuscript image cache
Short-axis segment schematic from the manuscript image cache, cited there to Voigt et al. 2015, shown to orient ventricular volume, mass, wall-thickness, and strain routes that depend on the cine short-axis stack. CardiacNexus emits the page-specific output rows described in the linked phenotype pages, not every segment shown in the source schematic.Source: manuscript image cache citing Voigt et al. 2015; permission and exact source-panel review pending for draft use.
  • Displayed figure provenance is recorded in docs/data/figure_provenance.yml; permission and exact reuse wording remain pending for public release.