Mimics software

The right lung lobe, airway, and lesions from anonymous patient chest CT images were manually segmented using Mimics software (Materialise Inc., Louvain, Belgium). The obtained chest areas were exported to the 3-matic software (Materialise Inc., Leuven, Belgium) for post-processing. The various well-known shapes and sizes of lung diseases including ground glass opacity (GGO) and solid nodules were artificially modeled and inserted in the images. Each phantom was designed and manufactured by one type of material and printer without need of assembly. Based on the HU measurements in Figures 2 and 3, abnormality lesions including GGO and solid nodules was set with 80 and 100 percent infill ratios, respectively. The lesions were set with appropriate infill ratios using the Ultimaker Cura. The final model file was converted into an STL file format for printing using the FDM printers.

The three V. rhodanica fossils were initially imaged using µCT at the AST-RX platform at the MNHN and then using PPC-SRµCT at the European Synchrotron Radiation Facility Synchrotron (ESRF, ID 19 beamline, Grenoble, France). PPC-SRµCT data have a voxel size of 12.64 µm (MHNH.B.74247, MHNH.B.74243 and MHNH.B.74244); AST-RX platform µCT data have a voxel size of 88.60 µm (MHNH.B.74244). Specimens of V. infernalis were analysed using µCT at the Microscopy and Imaging Facility of the American Museum of Natural History (New York, USA). The voxel size for each specimen analysed was 38.40 µm for AMNH IZC 361496, and 18.25 µm for YPM IZ 018297.GP. See Supplementary material for microtomography details.
Final CT data were reduced in size using ImageJ software (cropping and size reduction by binning 2 × 2 × 2), and then segmented using Mimics software (Materialise NV, Belgium, Version 21.0). The contrasting densities of the mineralized soft tissues were utilized to identify anatomical features for segmentation. Morphological reconstructions were carried out for the three V. rhodanica specimens incorporating all possible internal and external soft tissues. A full reconstruction of V. infernalis was carried out on AMNH IZC 361496. Some suckers in YPM IZ 018297.GP had more clearly defined boundaries and these were integrated into the analysis to augment the data gathered from AMNH IZC 361496.

During the awake baseline low‐radiation‐dose CT with CFD, patients were placed in a supine position and were asked to hold their breath at the end of a normal inspiration. Based on the scanned areas starting at the nasopharynx down to the larynx, 3D computer‐aided design models were reconstructed using Mimics software (Materialise, Leuven, Belgium). These models were subsequently transferred into a computational grid by FluidDa NV (Kontich, Belgium). The upper airway volume was determined and expressed as the effective upper airway volume in which air flows through, excluding leakage into the mouth. The total volume and the volume of the three individual sections of the pharynx were measured: velopharynx, oropharynx, and hypopharynx. Additional anatomical parameters, such as the minimal cross‐sectional area and the upper airway resistance were calculated.

A three-dimensional (3D) T₁-weighted sagittal volumetric interpolated breath-hold examination (VIBE) of the study knee and a 3D T₁-coronal lower-limb scan were undertaken prior to biomechanical assessment using a 3 Tesla MRI machine (Siemens Medical Systems, Erlangen, Germany). The 3D images of the lower limb bones and tibiofemoral joint cartilage were then segmented using Mimics software (Materialise, Leuven, Belgium). These segmentations were used to inform subject-specific anatomical geometry during modelling.