CONSeg: Voxelwise Glioma Conformal Segmentation

Background and Purpose: Glioma segmentation is crucial for clinical decisions and treatment planning. Uncertainty quantification methods, including conformal prediction (CP), can enhance segmentation models reliability. This study aims to use CP in glioma segmentation. Methods: We used the UCSF and UPenn glioma datasets, with the UCSF dataset split into training (70%), validation (10%), calibration (10%), and test (10%) sets, and the UPenn dataset divided into external calibration (30%) and external test (70%) sets. A UNet model was trained, and its optimal threshold was set to 0.5 using prediction normalization. To apply CP, the conformal threshold was selected based on the internal/external calibration nonconformity score, and CP was subsequently applied to the internal/external test sets, with coverage reported for all. We defined the uncertainty ratio (UR) and assessed its correlation with the Dice score coefficient (DSC). Additionally, we categorized cases into certain and uncertain groups based on UR and compared their DSC. We also evaluate the correlation between UR and DSC of the BraTS fusion model segmentation (BFMS), and compare DSC in the certain and uncertain subgroups. Results: The base model achieved a DSC of 0.8628 and 0.8257 on the internal and external test sets, respectively. The CP coverage was 0.9982 for the internal test set and 0.9977 for the external test set. Statistical analysis showed a significant negative correlation between UR and DSC for test sets (p<0.001). UR was also linked to significantly lower DSCs in the BFMS (p<0.001). Additionally, certain cases had significantly higher DSCs than uncertain cases in test sets and the BFMS (p<0.001). Conclusion: CP effectively quantifies uncertainty in glioma segmentation. Using CONSeg improves the reliability of segmentation models and enhances human-computer interaction.

Comparative Analysis of 2D and 3D ResNet Architectures for IDH and MGMT Mutation Detection in Glioma Patients

Gliomas are the most common cause of mortality among primary brain tumors. Molecular markers, including Isocitrate Dehydrogenase (IDH) and O[6]-methylguanine-DNA methyltransferase (MGMT) influence treatment responses and prognosis. Deep learning (DL) models may provide a non-invasive method for predicting the status of these molecular markers. To achieve non-invasive determination of gene mutations in glioma patients, we compare 2D and 3D ResNet models to predict IDH and MGMT status, using T1, post-contrast T1, and FLAIR MRI sequences. USCF glioma dataset was used, which contains 495 patients with known IDH and 410 patients with known MGMT status. The dataset was divided into training (60%), tuning (20%), and test (20%) subsets at the patient level. The 2D models take axial, coronal, and sagittal tumor slices as three separate models. To ensemble the 2D predictions the three different views were combined using logistic regression. Various ResNet architectures (ResNet10, 18, 34, 50, 101, 152) were trained. For the 3D approach, we incorporated the entire brain tumor volume in the ResNet10, 18, and 34 models. After optimizing each model, the models with the lowest tuning loss were selected for further evaluation on the separate test sets. The best-performing models in IDH prediction were the 2D ResNet50, achieving a test area under the receiver operating characteristic curve (AUROC) of 0.9096, and the 3D ResNet34, which reached a test AUROC of 0.8999. For MGMT status prediction, the 2D ResNet152 achieved a test AUROC of 0.6168; however, all 3D models yielded AUROCs less than 0.5. Overall, the study indicated that both 2D and 3D models showed high predictive value for IDH prediction, with slightly better performance in 2D models.