Dataset Information

Feasibility of deep learning-based tumor segmentation for target delineation and response assessment in grade-4 glioma using multi-parametric MRI.

ABSTRACT:

Background

Tumor burden assessment is essential for radiation therapy (RT), treatment response evaluation, and clinical decision-making. However, manual tumor delineation remains laborious and challenging due to radiological complexity. The objective of this study was to investigate the feasibility of the HD-GLIO tool, an ensemble of pre-trained deep learning models based on the nnUNet-algorithm, for tumor segmentation, response prediction, and its potential for clinical deployment.

Methods

We analyzed the predicted contrast-enhanced (CE) and non-enhancing (NE) HD-GLIO output in 49 multi-parametric MRI examinations from 23 grade-4 glioma patients. The volumes were retrospectively compared to corresponding manual delineations by 2 independent operators, before prospectively testing the feasibility of clinical deployment of HD-GLIO-output to a RT setting.

Results

For CE, median Dice scores were 0.81 (95% CI 0.71-0.83) and 0.82 (95% CI 0.74-0.84) for operator-1 and operator-2, respectively. For NE, median Dice scores were 0.65 (95% CI 0.56-0,69) and 0.63 (95% CI 0.57-0.67), respectively. Comparing volume sizes, we found excellent intra-class correlation coefficients of 0.90 (P < .001) and 0.95 (P < .001), for CE, respectively, and 0.97 (P < .001) and 0.90 (P < .001), for NE, respectively. Moreover, there was a strong correlation between response assessment in Neuro-Oncology volumes and HD-GLIO-volumes (P < .001, Spearman's R² = 0.83). Longitudinal growth relations between CE- and NE-volumes distinguished patients by clinical response: Pearson correlations of CE- and NE-volumes were 0.55 (P = .04) for responders, 0.91 (P > .01) for non-responders, and 0.80 (P = .05) for intermediate/mixed responders.

Conclusions

HD-GLIO was feasible for RT target delineation and MRI tumor volume assessment. CE/NE tumor-compartment growth correlation showed potential to predict clinical response to treatment.

SUBMITTER: Hannisdal MH

PROVIDER: S-EPMC10162115 | biostudies-literature | 2023 Jan-Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Feasibility of deep learning-based tumor segmentation for target delineation and response assessment in grade-4 glioma using multi-parametric MRI.

Hannisdal Marianne H MH Goplen Dorota D Alam Saruar S Haasz Judit J Oltedal Leif L Rahman Mohummad A MA Rygh Cecilie Brekke CB Lie Stein Atle SA Lundervold Arvid A Chekenya Martha M

Neuro-oncology advances 20230101 1

<h4>Background</h4>Tumor burden assessment is essential for radiation therapy (RT), treatment response evaluation, and clinical decision-making. However, manual tumor delineation remains laborious and challenging due to radiological complexity. The objective of this study was to investigate the feasibility of the HD-GLIO tool, an ensemble of pre-trained deep learning models based on the nnUNet-algorithm, for tumor segmentation, response prediction, and its potential for clinical deployment.<h4>M ...[more]

PMID: 37152808

Similar Datasets

Project description:PurposeTo develop a neural ordinary differential equation (ODE) model for visualizing deep neural network behavior during multi-parametric MRI-based glioma segmentation as a method to enhance deep learning explainability.MethodsBy hypothesizing that deep feature extraction can be modeled as a spatiotemporally continuous process, we implemented a novel deep learning model, Neural ODE, in which deep feature extraction was governed by an ODE parameterized by a neural network. The dynamics of (1) MR images after interactions with the deep neural network and (2) segmentation formation can thus be visualized after solving the ODE. An accumulative contribution curve (ACC) was designed to quantitatively evaluate each MR image's utilization by the deep neural network toward the final segmentation results. The proposed Neural ODE model was demonstrated using 369 glioma patients with a 4-modality multi-parametric MRI protocol: T1, contrast-enhanced T1 (T1-Ce), T2, and FLAIR. Three Neural ODE models were trained to segment enhancing tumor (ET), tumor core (TC), and whole tumor (WT), respectively. The key MRI modalities with significant utilization by deep neural networks were identified based on ACC analysis. Segmentation results by deep neural networks using only the key MRI modalities were compared to those using all four MRI modalities in terms of Dice coefficient, accuracy, sensitivity, and specificity.ResultsAll Neural ODE models successfully illustrated image dynamics as expected. ACC analysis identified T1-Ce as the only key modality in ET and TC segmentations, while both FLAIR and T2 were key modalities in WT segmentation. Compared to the U-Net results using all four MRI modalities, the Dice coefficient of ET (0.784→0.775), TC (0.760→0.758), and WT (0.841→0.837) using the key modalities only had minimal differences without significance. Accuracy, sensitivity, and specificity results demonstrated the same patterns.ConclusionThe Neural ODE model offers a new tool for optimizing the deep learning model inputs with enhanced explainability. The presented methodology can be generalized to other medical image-related deep-learning applications.

Project description:BackgroundUncertainty quantification in deep learning is an important research topic. For medical image segmentation, the uncertainty measurements are usually reported as the likelihood that each pixel belongs to the predicted segmentation region. In potential clinical applications, the uncertainty result reflects the algorithm's robustness and supports the confidence and trust of the segmentation result when the ground-truth result is absent. For commonly studied deep learning models, novel methods for quantifying segmentation uncertainty are in demand.PurposeTo develop a U-Net segmentation uncertainty quantification method based on spherical image projection of multi-parametric MRI (MP-MRI) in glioma segmentation.MethodsThe projection of planar MRI data onto a spherical surface is equivalent to a nonlinear image transformation that retains global anatomical information. By incorporating this image transformation process in our proposed spherical projection-based U-Net (SPU-Net) segmentation model design, multiple independent segmentation predictions can be obtained from a single MRI. The final segmentation is the average of all available results, and the variation can be visualized as a pixel-wise uncertainty map. An uncertainty score was introduced to evaluate and compare the performance of uncertainty measurements. The proposed SPU-Net model was implemented on the basis of 369 glioma patients with MP-MRI scans (T1, T1-Ce, T2, and FLAIR). Three SPU-Net models were trained to segment enhancing tumor (ET), tumor core (TC), and whole tumor (WT), respectively. The SPU-Net model was compared with (1) the classic U-Net model with test-time augmentation (TTA) and (2) linear scaling-based U-Net (LSU-Net) segmentation models in terms of both segmentation accuracy (Dice coefficient, sensitivity, specificity, and accuracy) and segmentation uncertainty (uncertainty map and uncertainty score).ResultsThe developed SPU-Net model successfully achieved low uncertainty for correct segmentation predictions (e.g., tumor interior or healthy tissue interior) and high uncertainty for incorrect results (e.g., tumor boundaries). This model could allow the identification of missed tumor targets or segmentation errors in U-Net. Quantitatively, the SPU-Net model achieved the highest uncertainty scores for three segmentation targets (ET/TC/WT): 0.826/0.848/0.936, compared to 0.784/0.643/0.872 using the U-Net with TTA and 0.743/0.702/0.876 with the LSU-Net (scaling factor = 2). The SPU-Net also achieved statistically significantly higher Dice coefficients, underscoring the improved segmentation accuracy.ConclusionThe SPU-Net model offers a powerful tool to quantify glioma segmentation uncertainty while improving segmentation accuracy. The proposed method can be generalized to other medical image-related deep-learning applications for uncertainty evaluation.

Project description:IntroductionThis study aims to develop an imaging model based on multi-parametric MR images for distinguishing between prostate cancer (PCa) and prostate hyperplasia.MethodsA total of 236 subjects were enrolled and divided into training and test sets for model construction. Firstly, a multi-view radiomics modeling strategy was designed in which different combinations of radiomics feature categories (original, LoG, and wavelet) were compared to obtain the optimal input feature sets. Minimum-redundancy maximum-relevance (mRMR) selection and least absolute shrinkage selection operator (LASSO) were used for feature reduction, and the next logistic regression method was used for model construction. Then, a Swin Transformer architecture was designed and trained using transfer learning techniques to construct the deep learning models (DL). Finally, the constructed multi-view radiomics and DL models were combined and compared for model selection and nomogram construction. The prediction accuracy, consistency, and clinical benefit were comprehensively evaluated in the model comparison.ResultsThe optimal input feature set was found when LoG and wavelet features were combined, while 22 and 17 radiomic features in this set were selected to construct the ADC and T2 multi-view radiomic models, respectively. ADC and T2 DL models were built by transferring learning from a large number of natural images to a relatively small sample of prostate images. All individual and combined models showed good predictive accuracy, consistency, and clinical benefit. Compared with using only an ADC-based model, adding a T2-based model to the combined model would reduce the model's predictive performance. The ADCCombinedScore model showed the best predictive performance among all and was transformed into a nomogram for better use in clinics.DiscussionThe constructed models in our study can be used as a predictor in differentiating PCa and BPH, thus helping clinicians make better clinical treatment decisions and reducing unnecessary prostate biopsies.

Dataset Information

Feasibility of deep learning-based tumor segmentation for target delineation and response assessment in grade-4 glioma using multi-parametric MRI.

Background

Methods

Results

Conclusions

Publications

Feasibility of deep learning-based tumor segmentation for target delineation and response assessment in grade-4 glioma using multi-parametric MRI.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets