Segmentation
Segmentation identifies the masks and labels that CardiacNexus feature extraction treats as measurement inputs. Output filenames and label semantics are part of the phenotype contract.
- Modality
- All segmented modalities
- Pipeline step
- Step 2 segmentation
- Outputs
- Segmentation masks, preprocessed LVOT/phase-contrast images, modality-specific QC inputs
- Maturity
- Source-audited method page
Current implementation boundary
step2_segment.py generates visit-specific Slurm scripts and only writes segmentation commands when required source images are present and expected segmentation files are missing, unless overwrite is requested. The step covers aortic scout, long-axis 2ch/4ch and 4chamber segmentation, short-axis segmentation, aortic distensibility segmentation, LVOT preprocessing/segmentation, phase-contrast preprocessing/segmentation, and native T1 segmentation.
Tagged MRI is handled separately during tagged feature extraction; it is not segmented through the same step-2 mask-generation path.
Expected masks by modality
| Modality | Expected mask or prepared output | Downstream pages |
|---|---|---|
| Scout/localizer | seg_aortic_scout.nii.gz | Aortic structure |
| Long-axis cine | seg_la_2ch.nii.gz, seg_la_4ch.nii.gz, seg4_la_4ch.nii.gz | Atrial, cross-chamber, annular, LAX strain |
| Short-axis cine | seg_sa.nii.gz | Ventricular structure/function, mass, wall thickness, SAX strain |
| Aortic distensibility | seg_aortic_dist.nii.gz | Aortic stiffness/distensibility |
| LVOT cine | lvot_processed.nii.gz, seg_lvot.nii.gz | LVOT aortic-root diameters |
| Phase-contrast flow | preprocessed flow files and seg_aortic_flow.nii.gz | Aortic flow and flow displacement |
| Native T1 mapping | seg_shmolli_t1map.nii.gz | Native T1 tissue characterization |
Contract with feature extraction
Changing segmentation filenames, label values, or image-mask geometry without a versioned migration can silently change volumes, areas, strain curves, and aggregate CSV columns. Feature pages therefore document both the current output labels and the segmentation-dependent caveats.
Segmentation-dependent phenotypes
Most CardiacNexus phenotypes are segmentation-dependent measurements. A plausible numeric value can still be unreliable when the upstream mask boundary is wrong.
Source audit
- Segmentation script generation, expected filenames, overwrite behavior, and modality boundaries were checked against
step2_segment.py. - Label semantics and QC caveats were cross-checked against current source-audited modality and phenotype pages.
- Textbook context boundary: broad clinical textbook context is not surfaced here because this is a segmentation implementation boundary page.