Study population
Approval for this retrospective investigation study was obtained from the Institutional review board (approval No. 2020AN0387), and the requirement for informed consent was waived. Between November 2017 to May 2020, 190 MREs were acquired. The inclusion criteria were as follows: (a) age ≥18 years, (b) no known history of liver disease, (c) suspected NAFLD on screening based on ultrasound and laboratory studies, and (d) ≤60 days between MRE and liver biopsy. The exclusion criteria were as follows: (a) history of alcohol consumption; (b) history of chronic liver diseases such as chronic hepatitis B or C infection, autoimmune hepatitis, and primary sclerosing cholangitis; and (c) history of major liver surgery such as liver transplantation and hemihepatectomy. Based on these criteria, 100 consecutive patients were enrolled during the study period (Fig. 1).
Demographic, laboratory, and clinical features, including age, sex, weight, height, and blood test results (alanine aminotransferase [ALT], aspartate aminotransferase [AST], triglyceride, low-density lipoprotein, and platelet count) obtained within one month of MRE were evaluated. The body mass index and aspartate aminotransferase-to-platelet ratio index (APRI) were calculated.
Reference standard for liver fibrosis
Pathologic examination of the liver served as the reference standard for liver fibrosis. All patients underwent percutaneous liver biopsy using an 18-gauge needle with a 20-mm penetration depth targeting segment 5/6. Histology preparations from liver biopsies were retrospectively reviewed by one pathologist (7 years of experience) who was blinded to the clinical data and MRE results. The classification by Kleiner et al. [17] was used to grade and stage NAFLD. Fibrosis was staged between 0 and 4 as follows: F0, absence of fibrosis; F1, perisinusoidal or portal; F2, perisinusoidal and portal/periportal; F3, septal or bridging fibrosis; and F4, cirrhosis. The pathologic hepatic fibrosis stage was classified as mild fibrosis (F0 or F1) or clinically significant fibrosis (F2–F4) [18, 19].
MRI examination
MRI examinations were performed using 3.0-T scanners (Magnetom Skyra; Siemens Healthineers, Erlangen, Germany) with a 30-channel body coil. MRE was performed according to a previously described protocol [20, 21] using commercial hardware and software (Resoundant Inc., Rochester, MN, USA; Syngo MR E11, Siemens Healthineers). In the supine position, the passive acoustic driver was placed on the right chest wall and upper abdominal wall, with its center at the xiphoid process level. An elastic strap was used to secure it to the patient’s body. MRE was performed using a phase-contrast gradient-recalled echo sequence, which applies motion-encoding gradients in synchronization with a 60-Hz external shear wave induced in the abdomen. The total acquisition time was approximately 20 s per slice, and four contiguous slices were obtained for each patient. The acquisition parameters were as follows: axial plane, field of view, 380 mm × 285 mm; acquisition matrix, 128×77; flip angle, 25°; number of excitations, 1; repetition time ms/echo time ms, 50/17; and slice thickness and gap, 5 mm. After the magnitude and phase images were obtained, an inversion algorithm installed in the MRI unit automatically processed raw data images to create several additional images and maps [22].
MRE analysis processing
Three-dimensional (3D) segmentation of MRE images was performed by three radiologists (two abdominal radiologists with 22 years [n = 21] and 10 years [n = 28] of clinical experience, respectively, and a 2-year resident [n = 51]) using a commercial program, AVIEW (version 1.0.32.12, Coreline Soft, Seoul, Korea). As it was a time-consuming task, the three radiologists were randomly assigned patients to perform 3D segmentation. The segmentation was conducted on four contiguous grayscale elastograms with a 95% confidence map (Fig. 2). All radiologists were trained by a software applicator to improve segmentation accuracy before they started the process. After completing the 3D segmentation, the mean and median values of liver fibrosis obtained from AVIEW were organized as 3D ROI values.
Using the grayscale elastogram with a 95% confidence map, two circular ROIs were defined per slice, and up to eight fibrosis values were obtained for each patient (Fig. 3). The ROI area was maintained at approximately 300–350 mm2. ROIs were drawn at two separate sites or at one site while avoiding the edges of the liver [23]. All postprocessing was performed using a commercial workstation by a single abdominal radiologist who had 10 years of experience and was blinded to the clinicopathological data. The obtained liver fibrosis values were organized using mean and median values (2D ROI values). The 2D and 3D ROI values were used for the analysis of radiologic features.
Radiomic feature extraction
Based on MRE data with 3D segmentation applied, several hundreds of radiomic features were analyzed by an artificial intelligence research professor using PyRadiomics (version 3.0, PyRadiomics Community) (Fig. 4) [24]. The features included were related to shape, first-order statistical, second-order statistical (including so-called textural features such as the gray-level co-occurrence matrix, gray-level run-length matrix, gray-level dependence matrix, GLDM, gray level size zone matrix, and neighboring gray-tone difference matrix), and higher-order statistical using wavelet filters.
Data analysis
Feature selection and classification method using machine learning
Although many quantitative features (radiomics, radiologic, and clinical) can be extracted from medical datasets, these may be highly correlated with each other or simply considered as noise. Thus, it is important to reduce features to select a subset of specific features, enhance the performance, and minimize the computational cost. Among radiomics, radiologic, and clinical features, important features for predicting low-grade or clinically significant hepatic fibrosis in patients with NAFLD were selected using a random forest regressor in Python (Python Software Foundation, version 3.6) with the Scikit-learn package (https://github.com/scikit-learn/scikit-learn). A random forest classifier model [25] was trained to use these important features to classify the fibrosis stage. The 20 repeated 10-fold stratified cross-validations verified the stability of the results. We evaluated the area under the receiver operating characteristic curve (AUC) and classifier accuracy. The classifier diagnosed the fibrosis stage based on radiomic, radiologic, or clinical features, or a combination of all features. Statistical differences in the AUC according to each classifier were compared using a machine learning model with Delong’s test. P values <0.05 were considered statistically significant.
Conventional statistical analyses
The demographic and clinical data in the low-grade fibrosis and clinically significant fibrosis groups were compared using the Mann–Whitney U test, chi-squared test, or Fisher's exact test. The liver stiffness determined by the measurements was compared using a paired t-test. All statistical analyses were performed using SPSS Statistics for Windows (version 20.0; IBM Corp., NY, USA). P values <0.05 were considered statistically significant.