Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userDeep cross-modality (MR-CT) educed distillation learning for cone beam CT lung tumor segmentation
98
0
0.0
(
0
)
Ask ChatGPT about the research
No Arabic abstract
Despite the widespread availability of in-treatment room cone beam computed tomography (CBCT) imaging, due to the lack of reliable segmentation methods, CBCT is only used for gross set up corrections in lung radiotherapies. Accurate and reliable auto-segmentation tools could potentiate volumetric response assessment and geometry-guided adaptive radiation therapies. Therefore, we developed a new deep learning CBCT lung tumor segmentation method. Methods: The key idea of our approach called cross modality educed distillation (CMEDL) is to use magnetic resonance imaging (MRI) to guide a CBCT segmentation network training to extract more informative features during training. We accomplish this by training an end-to-end network comprised of unpaired domain adaptation (UDA) and cross-domain segmentation distillation networks (SDN) using unpaired CBCT and MRI datasets. Feature distillation regularizes the student network to extract CBCT features that match the statistical distribution of MRI features extracted by the teacher network and obtain better differentiation of tumor from background.} We also compared against an alternative framework that used UDA with MR segmentation network, whereby segmentation was done on the synthesized pseudo MRI representation. All networks were trained with 216 weekly CBCTs and 82 T2-weighted turbo spin echo MRI acquired from different patient cohorts. Validation was done on 20 weekly CBCTs from patients not used in training. Independent testing was done on 38 weekly CBCTs from patients not used in training or validation. Segmentation accuracy was measured using surface Dice similarity coefficient (SDSC) and Hausdroff distance at 95th percentile (HD95) metrics.
rate research
Read More
Accurate and robust segmentation of lung cancers from CTs is needed to more accurately plan and deliver radiotherapy and to measure treatment response. This is particularly difficult for tumors located close to mediastium, due to low soft-tissue contrast. Therefore, we developed a new cross-modality educed distillation (CMEDL) approach, using unpaired CT and MRI scans, whereby a teacher MRI network guides a student CT network to extract features that signal the difference between foreground and background. Our contribution eliminates two requirements of distillation methods: (i) paired image sets by using an image to image (I2I) translation and (ii) pre-training of the teacher network with a large training set by using concurrent training of all networks. Our framework uses an end-to-end trained unpaired I2I translation, teacher, and student segmentation networks. Our framework can be combined with any I2I and segmentation network. We demonstrate our frameworks feasibility using 3 segmentation and 2 I2I methods. All networks were trained with 377 CT and 82 T2w MRI from different sets of patients. Ablation tests and different strategies for incorporating MRI information into CT were performed. Accuracy was measured using Dice similarity (DSC), surface Dice (sDSC), and Hausdorff distance at the 95$^{th}$ percentile (HD95). The CMEDL approach was significantly (p $<$ 0.001) more accurate than non-CMEDL methods, quantitatively and visually. It produced the highest segmentation accuracy (sDSC of 0.83 $pm$ 0.16 and HD95 of 5.20 $pm$ 6.86mm). CMEDL was also more accurate than using either pMRIs or the combination of CTs with pMRIs for segmentation.
Lung tumors, especially those located close to or surrounded by soft tissues like the mediastinum, are difficult to segment due to the low soft tissue contrast on computed tomography images. Magnetic resonance images contain superior soft-tissue contrast information that can be leveraged if both modalities were available for training. Therefore, we developed a cross-modality educed learning approach where MR information that is educed from CT is used to hallucinate MRI and improve CT segmentation. Our approach, called cross-modality educed deep learning segmentation (CMEDL) combines CT and pseudo MR produced from CT by aligning their features to obtain segmentation on CT. Features computed in the last two layers of parallelly trained CT and MR segmentation networks are aligned. We implemented this approach on U-net and dense fully convolutional networks (dense-FCN). Our networks were trained on unrelated cohorts from open-source the Cancer Imaging Archive CT images (N=377), an internal archive T2-weighted MR (N=81), and evaluated using separate validation (N=304) and testing (N=333) CT-delineated tumors. Our approach using both networks were significantly more accurate (U-net $P <0.001$; denseFCN $P <0.001$) than CT-only networks and achieved an accuracy (Dice similarity coefficient) of 0.71$pm$0.15 (U-net), 0.74$pm$0.12 (denseFCN) on validation and 0.72$pm$0.14 (U-net), 0.73$pm$0.12 (denseFCN) on the testing sets. Our novel approach demonstrated that educing cross-modality information through learned priors enhances CT segmentation performance
Lack of large expert annotated MR datasets makes training deep learning models difficult. Therefore, a cross-modality (MR-CT) deep learning segmentation approach that augments training data using pseudo MR images produced by transforming expert-segmented CT images was developed. Eighty-One T2-weighted MRI scans from 28 patients with non-small cell lung cancers were analyzed. Cross-modality prior encoding the transformation of CT to pseudo MR images resembling T2w MRI was learned as a generative adversarial deep learning model. This model augmented training data arising from 6 expert-segmented T2w MR patient scans with 377 pseudo MRI from non-small cell lung cancer CT patient scans with obtained from the Cancer Imaging Archive. A two-dimensional Unet implemented with batch normalization was trained to segment the tumors from T2w MRI. This method was benchmarked against (a) standard data augmentation and two state-of-the art cross-modality pseudo MR-based augmentation and (b) two segmentation networks. Segmentation accuracy was computed using Dice similarity coefficient (DSC), Hausdroff distance metrics, and volume ratio. The proposed approach produced the lowest statistical variability in the intensity distribution between pseudo and T2w MR images measured as Kullback-Leibler divergence of 0.069. This method produced the highest segmentation accuracy with a DSC of 0.75 and the lowest Hausdroff distance on the test dataset. This approach produced highly similar estimations of tumor growth as an expert (P = 0.37). A novel deep learning MR segmentation was developed that overcomes the limitation of learning robust models from small datasets by leveraging learned cross-modality priors to augment training. The results show the feasibility of the approach and the corresponding improvement over the state-of-the-art methods.
Multimodal positron emission tomography-computed tomography (PET-CT) is used routinely in the assessment of cancer. PET-CT combines the high sensitivity for tumor detection with PET and anatomical information from CT. Tumor segmentation is a critical element of PET-CT but at present, there is not an accurate automated segmentation method. Segmentation tends to be done manually by different imaging experts and it is labor-intensive and prone to errors and inconsistency. Previous automated segmentation methods largely focused on fusing information that is extracted separately from the PET and CT modalities, with the underlying assumption that each modality contains complementary information. However, these methods do not fully exploit the high PET tumor sensitivity that can guide the segmentation. We introduce a multimodal spatial attention module (MSAM) that automatically learns to emphasize regions (spatial areas) related to tumors and suppress normal regions with physiologic high-uptake. The resulting spatial attention maps are subsequently employed to target a convolutional neural network (CNN) for segmentation of areas with higher tumor likelihood. Our MSAM can be applied to common backbone architectures and trained end-to-end. Our experimental results on two clinical PET-CT datasets of non-small cell lung cancer (NSCLC) and soft tissue sarcoma (STS) validate the effectiveness of the MSAM in these different cancer types. We show that our MSAM, with a conventional U-Net backbone, surpasses the state-of-the-art lung tumor segmentation approach by a margin of 7.6% in Dice similarity coefficient (DSC).
Creating large scale high-quality annotations is a known challenge in medical imaging. In this work, based on the CycleGAN algorithm, we propose leveraging annotations from one modality to be useful in other modalities. More specifically, the proposed algorithm creates highly realistic synthetic CT images (SynCT) from prostate MR images using unpaired data sets. By using SynCT images (without segmentation labels) and MR images (with segmentation labels available), we have trained a deep segmentation network for precise delineation of prostate from real CT scans. For the generator in our CycleGAN, the cycle consistency term is used to guarantee that SynCT shares the identical manually-drawn, high-quality masks originally delineated on MR images. Further, we introduce a cost function based on structural similarity index (SSIM) to improve the anatomical similarity between real and synthetic images. For segmentation followed by the SynCT generation from CycleGAN, automatic delineation is achieved through a 2.5D Residual U-Net. Quantitative evaluation demonstrates comparable segmentation results between our SynCT and radiologist drawn masks for real CT images, solving an important problem in medical image segmentation field when ground truth annotations are not available for the modality of interest.
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
