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Automated quantification of data acquired as part of an MRI exam requires identification of the specific acquisition of relevance to a particular analysis. This motivates the development of methods capable of reliably classifying MRI acquisitions according to their nominal contrast type, e.g., T1 weighted, T1 post-contrast, T2 weighted, T2-weighted FLAIR, proton-density weighted. Prior studies have investigated using imaging-based methods and DICOM metadata-based methods with success on cohorts of patients acquired as part of a clinical trial. This study compares the performance of these methods on heterogeneous clinical datasets acquired with many different scanners from many institutions. RF and CNN models were trained on metadata and pixel data, respectively. A combined RF model incorporated CNN logits from the pixel-based model together with metadata. Four cohorts were used for model development and evaluation: MS research (n = 11,106 series), MS clinical (n = 3244 series), glioma research (n = 612 series, test/validation only), and ADNI PTSD (n = 477 series, training only). Together, these cohorts represent a broad range of acquisition contexts (scanners, sequences, institutions) and subject pathologies. Pixel-based CNN and combined models achieved accuracies between 97 and 98% on the clinical MS cohort. Validation/test accuracies with the glioma cohort were 99.7% (metadata only) and 98.4 (CNN). Accurate and generalizable classification of MRI acquisition contrast types was demonstrated. Such methods are important for enabling automated data selection in high-throughput and big-data image analysis applications.

BackgroundDiagnostic classification of diffuse gliomas now requires an assessment of molecular features, often including IDH-mutation and 1p19q-codeletion status. Because genetic testing requires an invasive process, an alternative noninvasive approach is attractive, particularly if resection is not recommended. The goal of this study was to evaluate the effects of training strategy and incorporation of biologically relevant images on predicting genetic subtypes with deep learning.MethodsOur dataset consisted of 384 patients with newly diagnosed gliomas who underwent preoperative MRI with standard anatomical and diffusion-weighted imaging, and 147 patients from an external cohort with anatomical imaging. Using tissue samples acquired during surgery, each glioma was classified into IDH-wildtype (IDHwt), IDH-mutant/1p19q-noncodeleted (IDHmut-intact), and IDH-mutant/1p19q-codeleted (IDHmut-codel) subgroups. After optimizing training parameters, top performing convolutional neural network (CNN) classifiers were trained, validated, and tested using combinations of anatomical and diffusion MRI with either a 3-class or tiered structure. Generalization to an external cohort was assessed using anatomical imaging models.ResultsThe best model used a 3-class CNN containing diffusion-weighted imaging as an input, achieving 85.7% (95% CI: [77.1, 100]) overall test accuracy and correctly classifying 95.2%, 88.9%, 60.0% of the IDHwt, IDHmut-intact, and IDHmut-codel tumors. In general, 3-class models outperformed tiered approaches by 13.5%-17.5%, and models that included diffusion-weighted imaging were 5%-8.8% more accurate than those that used only anatomical imaging.ConclusionTraining a classifier to predict both IDH-mutation and 1p19q-codeletion status outperformed a tiered structure that first predicted IDH-mutation, then 1p19q-codeletion. Including apparent diffusion coefficient (ADC), a surrogate marker of cellularity, more accurately captured differences between subgroups.

Although fully automated volumetric approaches for monitoring brain tumor response have many advantages, most available deep learning models are optimized for highly curated, multi-contrast MRI from newly diagnosed gliomas, which are not representative of post-treatment cases in the clinic. Improving segmentation for treated patients is critical to accurately tracking changes in response to therapy. We investigated mixing data from newly diagnosed (n = 208) and treated (n = 221) gliomas in training, applying transfer learning (TL) from pre- to post-treatment imaging domains, and incorporating spatial regularization for T2-lesion segmentation using only T2 FLAIR images as input to improve generalization post-treatment. These approaches were evaluated on 24 patients suspected of progression who had received prior treatment. Including 26% of treated patients in training improved performance by 13.9%, and including more treated and untreated patients resulted in minimal changes. Fine-tuning with treated glioma improved sensitivity compared to data mixing by 2.5% (p < 0.05), and spatial regularization further improved performance when used with TL by 95th HD, Dice, and sensitivity (6.8%, 0.8%, 2.2%; p < 0.05). While training with ≥60 treated patients yielded the majority of performance gain, TL and spatial regularization further improved T2-lesion segmentation to treated gliomas using a single MR contrast and minimal processing, demonstrating clinical utility in response assessment. [ABSTRACT FROM AUTHOR]

Purpose: To explore the contributions of fundus autofluorescence (FAF) topographic imaging features to the performance of convolutional neural network-based deep learning (DL) algorithms in predicting geographic atrophy (GA) growth rate., Methods: Retrospective study with data from study eyes from three clinical trials (NCT02247479, NCT02247531, NCT02479386) in GA. The algorithm was initially trained with full FAF images, and its performance was considered benchmark. Ablation experiments investigated the contribution of imaging features to the performance of the algorithms. Three FAF image regions were defined relative to GA: Lesion, Rim, and Background. For No Lesion, No Rim, and No Background datasets, a single region of interest was removed at a time. For Lesion, Rim, and Background Shuffled datasets, individual region pixels were randomly shuffled. For Lesion, Rim, and Background Mask datasets, masks of the regions were used. A Convex Hull dataset was generated to evaluate the importance of lesion size. Squared Pearson correlation (r2) was used to compare the predictive performance of ablated datasets relative to the benchmark., Results: The Rim region influenced r2 more than the other two regions in all experiments, indicating the most relevant contribution of this region to the performance of the algorithms. In addition, similar performance was observed for all regions when pixels were shuffled or only a mask was used, indicating intensity information was not independently informative without textural context., Conclusions: These ablation experiments enabled topographic clinical insights on FAF images from a DL-based GA progression prediction algorithm., Translational Relevance: Results from this study may lead to new insights on GA progression prediction.

Objective: To develop deep learning models for annualized geographic atrophy (GA) growth rate prediction using fundus autofluorescence (FAF) images and spectral-domain OCT volumes from baseline visits, which can be used for prognostic covariate adjustment to increase power of clinical trials., Design: This retrospective analysis estimated GA growth rate as the slope of a linear fit on all available measurements of lesion area over a 2-year period. Three multitask deep learning models-FAF-only, OCT-only, and multimodal (FAF and OCT)-were developed to predict concurrent GA area and annualized growth rate., Participants: Patients were from prospective and observational lampalizumab clinical trials., Methods: The 3 models were trained on the development data set, tested on the holdout set, and further evaluated on the independent test sets. Baseline FAF images and OCT volumes from study eyes of patients with bilateral GA (NCT02247479; NCT02247531; and NCT02479386) were split into development (1279 patients/eyes) and holdout (443 patients/eyes) sets. Baseline FAF images from study eyes of NCT01229215 (106 patients/eyes) and NCT02399072 (169 patients/eyes) were used as independent test sets., Main Outcome Measures: Model performance was evaluated using squared Pearson correlation coefficient (r 2 ) between observed and predicted lesion areas/growth rates. Confidence intervals were calculated by bootstrap resampling (B = 10 000)., Results: On the holdout data set, r 2 (95% confidence interval) of the FAF-only, OCT-only, and multimodal models for GA lesion area prediction was 0.96 (0.95-0.97), 0.91 (0.87-0.95), and 0.94 (0.92-0.96), respectively, and for GA growth rate prediction was 0.48 (0.41-0.55), 0.36 (0.29-0.43), and 0.47 (0.40-0.54), respectively. On the 2 independent test sets, r 2 of the FAF-only model for GA lesion area was 0.98 (0.97-0.99) and 0.95 (0.93-0.96), and for GA growth rate was 0.65 (0.52-0.75) and 0.47 (0.34-0.60)., Conclusions: We show the feasibility of using baseline FAF images and OCT volumes to predict individual GA area and growth rates using a multitask deep learning approach. The deep learning-based growth rate predictions could be used for covariate adjustment to increase power of clinical trials., Financial Disclosure(s): Proprietary or commercial disclosure may be found after the references., (Copyright © 2022 American Academy of Ophthalmology. Published by Elsevier Inc. All rights reserved.)