| Literature DB >> 35082346 |
Liyue Shen1, Jimmy Zheng2, Edward H Lee1, Katie Shpanskaya3, Emily S McKenna3, Mahesh G Atluri3, Dinko Plasto4, Courtney Mitchell4, Lillian M Lai5, Carolina V Guimaraes3, Hisham Dahmoush3, Jane Chueh6, Safwan S Halabi3, John M Pauly1, Lei Xing7, Quin Lu8, Ozgur Oztekin9, Beth M Kline-Fath10, Kristen W Yeom11.
Abstract
Magnetic resonance imaging offers unrivaled visualization of the fetal brain, forming the basis for establishing age-specific morphologic milestones. However, gauging age-appropriate neural development remains a difficult task due to the constantly changing appearance of the fetal brain, variable image quality, and frequent motion artifacts. Here we present an end-to-end, attention-guided deep learning model that predicts gestational age with R2 score of 0.945, mean absolute error of 6.7 days, and concordance correlation coefficient of 0.970. The convolutional neural network was trained on a heterogeneous dataset of 741 developmentally normal fetal brain images ranging from 19 to 39 weeks in gestational age. We also demonstrate model performance and generalizability using independent datasets from four academic institutions across the U.S. and Turkey with R2 scores of 0.81-0.90 after minimal fine-tuning. The proposed regression algorithm provides an automated machine-enabled tool with the potential to better characterize in utero neurodevelopment and guide real-time gestational age estimation after the first trimester.Entities:
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Year: 2022 PMID: 35082346 PMCID: PMC8791965 DOI: 10.1038/s41598-022-05468-5
Source DB: PubMed Journal: Sci Rep ISSN: 2045-2322 Impact factor: 4.379
R2 score and mean absolute error performance across model architectures.
R2 scores and corresponding MAE (days) are shown for each model architecture. ResNet-50 was used as the backbone. The Basic Network analyzes the entire image as input without attention masking. For each column, the best performance based on R2 score and mean absolute error is colored in blue. The highest performing architecture across all tested permutations is in red.
Figure 1Regression performance of an attention-guided multi-plane ResNet-50 model. Model performance of the highest-scoring architecture visualized above. (a) Correlation between predicted brain age and ground truth (R2 = 0.945) is represented by the line of best fit (blue). The dashed line is the ideal regression, where prediction equals true age. (b) Differences between predictions and ground truth are shown on the modified Bland–Altman plot. Corresponding 5%, 10th, 25th, 50th, 75th, 90th, and 95th quantile curves based on local piecewise regression analysis are drawn.
External validation of attention-guided, multi-plane, 1-slice and 3-slice models.
R2 scores and corresponding MAE (days) are shown before and after fine-tuning on data from other institutions. This external validation uses the highest-scoring model architecture (attention-guided multi-plane) based on the Stanford dataset. 20% of each external dataset was used for fine-tuning and the other 80% for testing model performance and generalizability. The largest improvements in R2 and MAE are shown in blue for each dataset. The most generalizable architecture for each dataset is in red.
MRI datasets and acquisition parameters by institution.
| Institution | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Stanford | CHLA | CCHMC | SJH | TTRH | |||||
| No. of subjects | 741 | 156 | 64 | 25 | 189 | ||||
| Median GA (range), wks | 30.6 (19–39) | 30.6 (20–40) | 24.6 (16–39) | 28.7 (19–36) | 26.1 (18–40) | ||||
| Field strength | 1.5 T, 3 T | 1.5 T, 3 T | 1.5 T | 1.5 T, 3 T | 1.5 T | ||||
| Manufacturer and Scanner | GE Discovery 750 W, Optima 450 W, Signa HDxt & Excite | Philips Ingenia & Achieva | GE Signa HDxt Philips Ingenia | GE Signa HDxt & Excite | Siemens Magnetom Aero & Avanto | ||||
| Sequence | ssFSE | ssTSE | ssFSE, ssTSE, bTFE, FIESTA | ssFSE, FIESTA | HASTE, TRUFI | ||||
| Repetition time, ms | 600–6,000 | 750–2625 | 12,500–15,000 | 3–5 | 4000 | 4.6–4.9 | 1,300–2,300 | 3.6–5.0 | 1200–1700 |
| Echo time, ms | 67–420 | 70–120 | 90–120 | 1.5–2.3 | 80–120 | 1.9–2.1 | 78–93 | 1.4–2.0 | 104–198 |
| Flip angle | 90° | 90° | 75°–110° | 75°, 90° | 62°–180° | ||||
| Field of view, mm | 180 × 180–440 × 440 | 160 × 160–450 × 450 | 240 × 240–380 × 380 | 240 × 240–340 × 340 | 129 × 187–380 × 380 | ||||
| In-plane resolution | 0.35 × 0.35–1.57 × 1.57 | 0.48 × 0.48–1.28 × 1.28 | 0.55 × 0.55–1.37 × 1.37 | 0.46 × 0.46–0.67 × 0.67 | 0.37 × 0.37–1.66 × 1.66 | ||||
| Median no. of slices (range) | 23 (7–48) | 44 (20–100) | 20 (5–53) | 22 (14–47) | 26 (10–84) | ||||
| Median slice thickness (range), mm | 4 (2–5) | 3 (2.5–5.5) | 4 (3–6) | 4 (4–5) | 4 (3–5) | ||||
ssFSE single-shot fast spin-echo, ssTSE single-shot turbo spin-echo, bTFE balanced turbo field echo, FIESTA fast imaging employing steady state acquisition, HASTE half-Fourier acquisition single-shot turbo spin-echo, TRUFI true fast imaging with steady-state free precession.
Figure 2ResNet-50 architecture for brain age regression with attention-guided mask inference. A single sagittal image with dimensions 224 × 224 is shown as an input to the global branch. Architectures incorporating multiple slices and planes are not displayed. The input of the local branch is a weighted image isolating the region of interest automatically generated from attention-guided mask inference. Global and local branches contain five convolutional layers (conv1 to conv5), each consisting of 3–6 building blocks (boxes) with a convolution, batch normalization, and rectified linear unit (ReLU), streamlined by shortcut connections (gray dotted arrows). Output sizes are denoted by k × k. Feature maps from both branches enter a max pooling layer and are subsequently fed to a fully connected layer (fc). The MSE for each branch and the total loss are minimized via gradient descent (black dotted arrows), simultaneously tuning model weights for both local and global branches via backpropagation. Age predictions (GA) are generated from each branch and averaged to produce the final age estimation.
Figure 3Examples of heatmap generation and region of interest mask inference. Top: Global input images show the entire view of a maternal womb captured on MRI in all three planes. Middle: Corresponding heatmaps derived from the last convolutional layer identify high-value areas for attention-based learning. Increasing activation values correspond to the color spectrum from violet to yellow. Bottom: Application of a 2D Gaussian mask generates a re-weighted heatmap highlighting the region of interest.