Volumetric evaluation of osteotomy gap following mandibular bilateral sagittal split osteotomy using a novel semi-automated approach: a pilot study.

OBJECTIVES: To establish an analysis pipeline for the volumetric evaluation of the osteotomy site after bilateral sagittal split osteotomy (BSSO). PATIENTS AND METHODS: Cone-beam computed tomography (CBCT) was performed before, directly after BSSO, and 6-12 months after surgery. Image segmentations of each osteotomy gap data set were performed manually by four physicians and were compared to a semi-automatic segmentation approach. RESULTS: Five patients with a total of ten osteotomy gaps were included. The mean interclass correlation coefficient (ICC) of individual patients was 0.782 and the standard deviation 0.080 when using the manual segmentation approach. However, the mean ICC of the evaluation of anatomical sites and time points separately was 0.214, suggesting a large range of deviation within the manual segmentation of each rater. The standard deviation was 0.355, further highlighting the extent of the variation. In contrast, the semi-automatic approach had a mean ICC of 0.491 and a standard deviation of 0.365, which suggests a relatively higher agreement among the operators compared to the manual segmentation approach. Furthermore, the volume of the osteotomy gap in the semi-automatic approach showed the same tendency in every site as the manual segmentation approach, but with less deviation. CONCLUSION: The semi-automatic approach developed in the present study proved to be valid as a standardised method with high repeatability. Such image analysis methods could help to quantify the progression of bone healing after BSSO and beyond, eventually facilitating the earlier identification of patients with retarded healing.

Exploration of Interpretability Techniques for Deep COVID-19 Classification Using Chest X-ray Images.

The outbreak of COVID-19 has shocked the entire world with its fairly rapid spread, and has challenged different sectors. One of the most effective ways to limit its spread is the early and accurate diagnosing of infected patients. Medical imaging, such as X-ray and computed tomography (CT), combined with the potential of artificial intelligence (AI), plays an essential role in supporting medical personnel in the diagnosis process. Thus, in this article, five different deep learning models (ResNet18, ResNet34, InceptionV3, InceptionResNetV2, and DenseNet161) and their ensemble, using majority voting, have been used to classify COVID-19, pneumoniæ and healthy subjects using chest X-ray images. Multilabel classification was performed to predict multiple pathologies for each patient, if present. Firstly, the interpretability of each of the networks was thoroughly studied using local interpretability methods-occlusion, saliency, input X gradient, guided backpropagation, integrated gradients, and DeepLIFT-and using a global technique-neuron activation profiles. The mean micro F1 score of the models for COVID-19 classifications ranged from 0.66 to 0.875, and was 0.89 for the ensemble of the network models. The qualitative results showed that the ResNets were the most interpretable models. This research demonstrates the importance of using interpretability methods to compare different models before making a decision regarding the best performing model.

DS6, Deformation-Aware Semi-Supervised Learning: Application to Small Vessel Segmentation with Noisy Training Data.

Blood vessels of the brain provide the human brain with the required nutrients and oxygen. As a vulnerable part of the cerebral blood supply, pathology of small vessels can cause serious problems such as Cerebral Small Vessel Diseases (CSVD). It has also been shown that CSVD is related to neurodegeneration, such as Alzheimer's disease. With the advancement of 7 Tesla MRI systems, higher spatial image resolution can be achieved, enabling the depiction of very small vessels in the brain. Non-Deep Learning-based approaches for vessel segmentation, e.g., Frangi's vessel enhancement with subsequent thresholding, are capable of segmenting medium to large vessels but often fail to segment small vessels. The sensitivity of these methods to small vessels can be increased by extensive parameter tuning or by manual corrections, albeit making them time-consuming, laborious, and not feasible for larger datasets. This paper proposes a deep learning architecture to automatically segment small vessels in 7 Tesla 3D Time-of-Flight (ToF) Magnetic Resonance Angiography (MRA) data. The algorithm was trained and evaluated on a small imperfect semi-automatically segmented dataset of only 11 subjects; using six for training, two for validation, and three for testing. The deep learning model based on U-Net Multi-Scale Supervision was trained using the training subset and was made equivariant to elastic deformations in a self-supervised manner using deformation-aware learning to improve the generalisation performance. The proposed technique was evaluated quantitatively and qualitatively against the test set and achieved a Dice score of 80.44 ± 0.83. Furthermore, the result of the proposed method was compared against a selected manually segmented region (62.07 resultant Dice) and has shown a considerable improvement (18.98%) with deformation-aware learning.

ReconResNet: Regularised residual learning for MR image reconstruction of Undersampled Cartesian and Radial data.

MRI is an inherently slow process, which leads to long scan time for high-resolution imaging. The speed of acquisition can be increased by ignoring parts of the data (undersampling). Consequently, this leads to the degradation of image quality, such as loss of resolution or introduction of image artefacts. This work aims to reconstruct highly undersampled Cartesian or radial MR acquisitions, with better resolution and with less to no artefact compared to conventional techniques like compressed sensing. In recent times, deep learning has emerged as a very important area of research and has shown immense potential in solving inverse problems, e.g. MR image reconstruction. In this paper, a deep learning based MR image reconstruction framework is proposed, which includes a modified regularised version of ResNet as the network backbone to remove artefacts from the undersampled image, followed by data consistency steps that fusions the network output with the data already available from undersampled k-space in order to further improve reconstruction quality. The performance of this framework for various undersampling patterns has also been tested, and it has been observed that the framework is robust to deal with various sampling patterns, even when mixed together while training, and results in very high quality reconstruction, in terms of high SSIM (highest being 0.990 ± 0.006 for acceleration factor of 3.5), while being compared with the fully sampled reconstruction. It has been shown that the proposed framework can successfully reconstruct even for an acceleration factor of 20 for Cartesian (0.968 ± 0.005) and 17 for radially (0.962 ± 0.012) sampled data. Furthermore, it has been shown that the framework preserves brain pathology during reconstruction while being trained on healthy subjects.

Fine-tuning deep learning model parameters for improved super-resolution of dynamic MRI with prior-knowledge.

Dynamic imaging is a beneficial tool for interventions to assess physiological changes. Nonetheless during dynamic MRI, while achieving a high temporal resolution, the spatial resolution is compromised. To overcome this spatio-temporal trade-off, this research presents a super-resolution (SR) MRI reconstruction with prior knowledge based fine-tuning to maximise spatial information while reducing the required scan-time for dynamic MRIs. A U-Net based network with perceptual loss is trained on a benchmark dataset and fine-tuned using one subject-specific static high resolution MRI as prior knowledge to obtain high resolution dynamic images during the inference stage. 3D dynamic data for three subjects were acquired with different parameters to test the generalisation capabilities of the network. The method was tested for different levels of in-plane undersampling for dynamic MRI. The reconstructed dynamic SR results after fine-tuning showed higher similarity with the high resolution ground-truth, while quantitatively achieving statistically significant improvement. The average SSIM of the lowest resolution experimented during this research (6.25% of the k-space) before and after fine-tuning were 0.939 ± 0.008 and 0.957 ± 0.006 respectively. This could theoretically result in an acceleration factor of 16, which can potentially be acquired in less than half a second. The proposed approach shows that the super-resolution MRI reconstruction with prior-information can alleviate the spatio-temporal trade-off in dynamic MRI, even for high acceleration factors.

Breathing deformation model - application to multi-resolution abdominal MRI.

Dynamic MRI is a technique of acquiring a series of images continuously to follow the physiological changes over time. However, such fast imaging results in low resolution images. In this work, abdominal deformation model computed from dynamic low resolution images have been applied to high resolution image, acquired previously, to generate dynamic high resolution MRI. Dynamic low resolution images were simulated into different breathing phases (inhale and exhale). Then, the image registration between breathing time points was performed using the B-spline SyN deformable model and using cross-correlation as a similarity metric. The deformation model between different breathing phases were estimated from highly undersampled data. This deformation model was then applied to the high resolution images to obtain high resolution images of different breathing phases. The results indicated that the deformation model could be computed from relatively very low resolution images.