RMSim: Controlled Respiratory Motion Simulation on Static Patient Scans

This work aims to generate realistic anatomical deformations from static patient scans. Specifically, we present a method to generate these deformations/augmentations via deep learning driven respiratory motion simulation that provides the ground truth for validating deformable image registration (DIR) algorithms and driving more accurate deep learning based DIR. We present a novel 3D Seq2Seq deep learning respiratory motion simulator (RMSim) that learns from 4D-CT images and predicts future breathing phases given a static CT image. The predicted respiratory patterns, represented by time-varying displacement vector fields (DVFs) at different breathing phases, are modulated through auxiliary inputs of 1D breathing traces so that a larger amplitude in the trace results in more significant predicted deformation. Stacked 3D-ConvLSTMs are used to capture the spatial-temporal respiration patterns. Training loss includes a smoothness loss in the DVF and mean-squared error between the predicted and ground truth phase images. A spatial transformer deforms the static CT with the predicted DVF to generate the predicted phase image. 10-phase 4D-CTs of 140 internal patients were used to train and test RMSim. The trained RMSim was then used to augment a public DIR challenge dataset for training VoxelMorph to show the effectiveness of RMSim-generated deformation augmentation. We validated our RMSim output with both private and public benchmark datasets (healthy and cancer patients). The proposed approach can be used for validating DIR algorithms as well as for patient-specific augmentations to improve deep learning DIR algorithms. The code, pretrained models, and augmented DIR validation datasets will be released at https://github.com/nadeemlab/SeqX2Y.

Deformation Driven Seq2Seq Longitudinal Tumor and Organs-at-Risk Prediction for Radiotherapy

Purpose: Radiotherapy presents unique challenges and clinical requirements for longitudinal tumor and organ-at-risk (OAR) prediction during treatment. The challenges include tumor inflammation/edema and radiation-induced changes in organ geometry, whereas the clinical requirements demand flexibility in input/output sequence timepoints to update the predictions on rolling basis and the grounding of all predictions in relationship to the pre-treatment imaging information for response and toxicity assessment in adaptive radiotherapy. Methods: To deal with the aforementioned challenges and to comply with the clinical requirements, we present a novel 3D sequence-to-sequence model based on Convolution Long Short Term Memory (ConvLSTM) that makes use of series of deformation vector fields (DVF) between individual timepoints and reference pre-treatment/planning CTs to predict future anatomical deformations and changes in gross tumor volume as well as critical OARs. High-quality DVF training data is created by employing hyper-parameter optimization on the subset of the training data with DICE coefficient and mutual information metric. We validated our model on two radiotherapy datasets: a publicly available head-and-neck dataset (28 patients with manually contoured pre-, mid-, and post-treatment CTs), and an internal non-small cell lung cancer dataset (63 patients with manually contoured planning CT and 6 weekly CBCTs). Results: The use of DVF representation and skip connections overcomes the blurring issue of ConvLSTM prediction with the traditional image representation. The mean and standard deviation of DICE for predictions of lung GTV at week 4, 5, and 6 were 0.83$\pm$0.09, 0.82$\pm$0.08, and 0.81$\pm$0.10, respectively, and for post-treatment ipsilateral and contralateral parotids, were 0.81$\pm$0.06 and 0.85$\pm$0.02.

Cross-modality (CT-MRI) prior augmented deep learning for robust lung tumor segmentation from small MR datasets

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.