Dataset Information

A novel fully automated MRI-based deep-learning method for classification of IDH mutation status in brain gliomas.

ABSTRACT:

Background

Isocitrate dehydrogenase (IDH) mutation status has emerged as an important prognostic marker in gliomas. Currently, reliable IDH mutation determination requires invasive surgical procedures. The purpose of this study was to develop a highly accurate, MRI-based, voxelwise deep-learning IDH classification network using T2-weighted (T2w) MR images and compare its performance to a multicontrast network.

Methods

Multiparametric brain MRI data and corresponding genomic information were obtained for 214 subjects (94 IDH-mutated, 120 IDH wild-type) from The Cancer Imaging Archive and The Cancer Genome Atlas. Two separate networks were developed, including a T2w image-only network (T2-net) and a multicontrast (T2w, fluid attenuated inversion recovery, and T1 postcontrast) network (TS-net) to perform IDH classification and simultaneous single label tumor segmentation. The networks were trained using 3D Dense-UNets. Three-fold cross-validation was performed to generalize the networks' performance. Receiver operating characteristic analysis was also performed. Dice scores were computed to determine tumor segmentation accuracy.

Results

T2-net demonstrated a mean cross-validation accuracy of 97.14% ± 0.04 in predicting IDH mutation status, with a sensitivity of 0.97 ± 0.03, specificity of 0.98 ± 0.01, and an area under the curve (AUC) of 0.98 ± 0.01. TS-net achieved a mean cross-validation accuracy of 97.12% ± 0.09, with a sensitivity of 0.98 ± 0.02, specificity of 0.97 ± 0.001, and an AUC of 0.99 ± 0.01. The mean whole tumor segmentation Dice scores were 0.85 ± 0.009 for T2-net and 0.89 ± 0.006 for TS-net.

Conclusion

We demonstrate high IDH classification accuracy using only T2-weighted MR images. This represents an important milestone toward clinical translation.

SUBMITTER: Bangalore Yogananda CG

PROVIDER: S-EPMC7442388 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature

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Publications

A novel fully automated MRI-based deep-learning method for classification of IDH mutation status in brain gliomas.

Bangalore Yogananda Chandan Ganesh CG Shah Bhavya R BR Vejdani-Jahromi Maryam M Nalawade Sahil S SS Murugesan Gowtham K GK Yu Frank F FF Pinho Marco C MC Wagner Benjamin C BC Mickey Bruce B Patel Toral R TR Fei Baowei B Madhuranthakam Ananth J AJ Maldjian Joseph A JA

Neuro-oncology 20200301 3

<h4>Background</h4>Isocitrate dehydrogenase (IDH) mutation status has emerged as an important prognostic marker in gliomas. Currently, reliable IDH mutation determination requires invasive surgical procedures. The purpose of this study was to develop a highly accurate, MRI-based, voxelwise deep-learning IDH classification network using T2-weighted (T2w) MR images and compare its performance to a multicontrast network.<h4>Methods</h4>Multiparametric brain MRI data and corresponding genomic inform ...[more]

PMID: 31637430

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Project description:Background: Deep learning (DL) could predict isocitrate dehydrogenase (IDH) mutation status from MRIs. Yet, previous work focused on CNNs with refined tumor segmentation. To bridge the gap, this study aimed to evaluate the feasibility of developing a Transformer-based network to predict the IDH mutation status free of refined tumor segmentation. Methods: A total of 493 glioma patients were recruited from two independent institutions for model development (TCIA; N = 259) and external test (AHXZ; N = 234). IDH mutation status was predicted directly from T2 images with a Swin Transformer and conventional ResNet. Furthermore, to investigate the necessity of refined tumor segmentation, seven strategies for the model input image were explored: (i) whole tumor slice; (ii-iii) tumor mask and/or not edema; (iv-vii) tumor bounding box of 0.8, 1.0, 1.2, 1.5 times. Performance comparison was made among the networks of different architectures along with different image input strategies, using area under the curve (AUC) and accuracy (ACC). Finally, to further boost the performance, a hybrid model was built by incorporating the images with clinical features. Results: With the seven proposed input strategies, seven Swin Transformer models and seven ResNet models were built, respectively. Based on the seven Swin Transformer models, an averaged AUC of 0.965 (internal test) and 0.842 (external test) were achieved, outperforming 0.922 and 0.805 resulting from the seven ResNet models, respectively. When a bounding box of 1.0 times was used, Swin Transformer (AUC = 0.868, ACC = 80.7%), achieved the best results against the one that used tumor segmentation (Tumor + Edema, AUC = 0.862, ACC = 78.5%). The hybrid model that integrated age and location features into images yielded improved performance (AUC = 0.878, Accuracy = 82.0%) over the model that used images only. Conclusions: Swin Transformer outperforms the CNN-based ResNet in IDH prediction. Using bounding box input images benefits the DL networks in IDH prediction and makes the IDH prediction free of refined glioma segmentation feasible.

Project description:ObjectivesTo employ different automated convolutional neural network (CNN)-based transfer learning (TL) methods for both binary and multiclass classification of Alzheimer's disease (AD) using brain MRI.MethodsHerein, we applied three popular pre-trained CNN models (ResNet101, Xception, and InceptionV3) using a fine-tuned approach of TL on 3D T1-weighted brain MRI from a subset of ADNI dataset (n = 305 subjects). To evaluate power of TL, the aforementioned networks were also trained from scratch for performance comparison. Initially, Unet network segmentedthe MRI scans into characteristic components of gray matter (GM), white matter (WM), and cerebrospinal fluid (CSF). The proposed networks were trained and tested over the pre-processed and augmented segmented and whole images for both binary (NC/AD + progressive mild cognitive impairment (pMCI)+stable MCI (sMCI)) and 4-class (AD/pMCI/sMCI/NC) classification. Also, two independent test sets from the OASIS (n = 30) and AIBL (n = 60) datasets were used to externally assess the performance of the proposed algorithms.ResultsThe proposed TL-based CNN models achieved better performance compared to the training CNN models from scratch. On the ADNI test set, InceptionV3-TL achieved the highest accuracy of 93.75% and AUC of 92.0% for binary classification, as well as the highest accuracy of 93.75% and AUC of 96.0% for multiclass classification of AD on the whole images. On the OASIS test set, InceptionV3-TL outperformed two other models by achieving 93.33% accuracy with 93.0% AUC in binary classification of AD on the whole images. On the AIBL test set, InceptionV3-TL also outperformed two other models in both binary and multiclass classification tasks on the whole MR images and achieved accuracy/AUC of 93.33%/95.0% and 90.0%/93.0%, respectively. The GM segment as input provided the highest performance in both binary and multiclass classification of AD, as compared to the WM and CSF segments.ConclusionThis study demonstrates the potential of applying deep TL approach for automated detection and classification of AD using brain MRI with high accuracy and robustness across internal and external test data, suggesting that these models can possibly be used as a supportive tool to assist clinicians in creating objective opinion and correct diagnosis.Advances in knowledgeWe used CNN-based TL approaches and the augmentation techniques to overcome the insufficient data problem. Our study provides evidence that deep TL algorithms can be used for both binary and multiclass classification of AD with high accuracy.

Dataset Information

A novel fully automated MRI-based deep-learning method for classification of IDH mutation status in brain gliomas.

Background

Methods

Results

Conclusion

Publications

A novel fully automated MRI-based deep-learning method for classification of IDH mutation status in brain gliomas.

Similar Datasets

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