Identification of Precise 3D CT Radiomics for Habitat Computation by Machine Learning in Cancer
To identify precise three-dimensional radiomics features in CT images that enable computation of stable and biologically meaningful habitats with machine learning for cancer heterogeneity assessment.
Materials and Methods
This retrospective study included 2436 liver or lung lesions from 605 CT scans (November 2010–December 2021) in 331 patients with cancer (mean age, 64.5 years ± 10.1 [SD]; 185 male patients). Three-dimensional radiomics were computed from original and perturbed (simulated retest) images with different combinations of feature computation kernel radius and bin size. The lower 95% confidence limit (LCL) of the intraclass correlation coefficient (ICC) was used to measure repeatability and reproducibility. Precise features were identified by combining repeatability and reproducibility results (LCL of ICC ≥ 0.50). Habitats were obtained with Gaussian mixture models in original and perturbed data using precise radiomics features and compared with habitats obtained using all features. The Dice similarity coefficient (DSC) was used to assess habitat stability. Biologic correlates of CT habitats were explored in a case study, with a cohort of 13 patients with CT, multiparametric MRI, and tumor biopsies.
Results
Three-dimensional radiomics showed poor repeatability (LCL of ICC: median [IQR], 0.442 [0.312–0.516]) and poor reproducibility against kernel radius (LCL of ICC: median [IQR], 0.440 [0.33–0.526]) but excellent reproducibility against bin size (LCL of ICC: median [IQR], 0.929 [0.853–0.988]). Twenty-six radiomics features were precise, differing in lung and liver lesions. Habitats obtained with precise features (DSC: median [IQR], 0.601 [0.494–0.712] and 0.651 [0.52–0.784] for lung and liver lesions, respectively) were more stable than those obtained with all features (DSC: median [IQR], 0.532 [0.424–0.637] and 0.587 [0.465–0.703] for lung and liver lesions, respectively; P < .001). In the case study, CT habitats correlated quantitatively and qualitatively with heterogeneity observed in multiparametric MRI habitats and histology.
Conclusion
Precise three-dimensional radiomics features were identified on CT images that enabled tumor heterogeneity assessment through stable tumor habitat computation.
Olivia Prior, MSc, Carlos Macarro, MSc, Víctor Navarro, BSc, Camilo Monreal, MSc, Marta Ligero, MSc, Alonso Garcia-Ruiz, MSc, Garazi Serna, PhD, Sara Simonetti, MD, PhD, Irene Braña, MD, PhD, Maria Vieito, MD, PhD, Manuel Escobar, MD, Jaume Capdevila, MD, Annette T. Byrne, MD, PhD, Rodrigo Dienstmann, MD, Rodrigo Toledo, PhD, Paolo Nuciforo, MD, PhD, Elena Garralda, MD, MSc, Francesco Grussu, PhD, Kinga Bernatowicz, PhD,#* and Raquel Perez-Lopez, MD, PhD
From the Radiomics Group, Vall d'Hebron Institute of Oncology, Carrer de Natzaret 115-117, Barcelona 08035, Spain (O.P., C. Macarro, C. Monreal, M.L., A.G.R., F.G., K.B., R.P.L.); Oncology Data Science Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain (V.N., R.D.); Molecular Pathology Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain (G.S., S.S., P.N.); Department of Medical Oncology, Vall d'Hebron University Hospital, Barcelona, Spain (I.B., M.V., E.G., J.C.); Molecular Therapeutic Research Unit, Vall d'Hebron Institute of Oncology, Barcelona, Spain (I.B., M.V., E.G., J.C.); Department of Radiology, Vall d'Hebron University Hospital, Barcelona, Spain (M.E.); Biomakers and Clonal Dynamics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain (R.T.); Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland (A.T.B.); and National Pre-clinical Imaging Centre, Dublin, Ireland (A.T.B.)
Source: Identification of Precise 3D CT Radiomics for Habitat Computation by Machine Learning in Cancer