Diffusion tensor estimation with transformer neural networks

A hybrid approach based on multipath Swin transformer and ConvMixer for white blood cells classification

White blood cells (WBC) play an effective role in the body's defense against parasites, viruses, and bacteria in the human body. Also, WBCs are categorized based on their morphological structures into various subgroups. The number of these WBC types in the blood of non-diseased and diseased people is different. Thus, the study of WBC classification is quite significant for medical diagnosis. Due to the widespread use of deep learning in medical image analysis in recent years, it has also been used in WBC classification. Moreover, the ConvMixer and Swin transformer models, recently introduced, have garnered significant success by attaining efficient long contextual characteristics. Based on this, a new multipath hybrid network is proposed for WBC classification by using ConvMixer and Swin transformer. This proposed model is called Swin Transformer and ConvMixer based Multipath mixer (SC-MP-Mixer). In the SC-MP-Mixer model, firstly, features with strong spatial details are extracted with the ConvMixer. Then Swin transformer effectively handle these features with self-attention mechanism. In addition, the ConvMixer and Swin transformer blocks consist of a multipath structure to obtain better patch representations in the SC-MP-Mixer. To test the performance of the SC-MP-Mixer, experiments were performed on three WBC datasets with 4 (BCCD), 8 (PBC) and 5 (Raabin) classes. The experimental studies resulted in an accuracy of 99.65% for PBC, 98.68% for Raabin, and 95.66% for BCCD. When compared with the studies in the literature and the state-of-the-art models, it was seen that the SC-MP-Mixer had more effective classification results.

NVAM-Net: deep learning networks for reconstructing high-quality fiber orientation distributions

PURPOSE

Diffusion magnetic resonance imaging (dMRI) is a widely used non-invasive method for investigating brain anatomical structures. Conventional techniques for estimating fiber orientation distribution (FOD) from dMRI data often neglect voxel-level spatial relationships, leading to ambiguous associations between target voxels and their neighbors, which, in turn, adversely impacts FOD accuracy. This study aims to address this issue by introducing a novel neural network, the neighboring voxel attention mechanism network (NVAM-Net), designed to reconstruct high-quality FOD images.

METHODS

The NVAM-Net leverages a Transformer architecture and incorporates two innovative attention mechanisms: voxel attention and surface attention. These mechanisms are specifically designed to capture overlooked features among neighboring voxels. The processed features are subsequently passed through two fully connected layers, further enhancing FOD estimation accuracy by separately estimating spherical harmonics (SH) coefficients of varying orders.

RESULTS

The experimental findings, based on the Human Connectome Project (HCP) dataset, reveal that the reconstructed super-resolution FOD images achieve results comparable to those obtained through more advanced dMRI acquisition protocols. These results underscore the NVAM-Net's robust performance in reconstructing multi-shell multi-tissue constrained spherical deconvolution (MSMT-CSD).

CONCLUSION

In summary, this research underscores the NVAM-Net's advantages and practical feasibility in reconstructing high-quality FOD images. It provides a reliable reference point for clinical applications in the field of diffusion magnetic resonance imaging.

Gauge equivariant convolutional neural networks for diffusion mri

Diffusion MRI (dMRI) is an imaging technique widely used in neuroimaging research, where the signal carries directional information of underlying neuronal fibres based on the diffusivity of water molecules. One of the shortcomings of dMRI is that numerous images, sampled at gradient directions on a sphere, must be acquired to achieve a reliable angular resolution for model-fitting, which translates to longer scan times, higher costs, and barriers to clinical adoption. In this work we introduce gauge equivariant convolutional neural network (gCNN) layers for dMRI that overcome the challenges associated with the signal being acquired on a sphere with antipodal points identified. This is done by noting that the domain is equivalent to the real projective plane, ℝ P 2 , which is a non-euclidean and a non-orientable manifold. This is in stark contrast to a rectangular grid which typical convolutional neural networks (CNNs) are designed for. We apply our method to upsample angular resolution for predicting diffusion tensor imaging (DTI) parameters from just six diffusion gradient directions. The symmetries introduced allow gCNNs the ability to train with fewer subjects as compared to a baseline model that involves only 3D convolutions.

Deep learning-based diffusion tensor cardiac magnetic resonance reconstruction: a comparison study

In vivo cardiac diffusion tensor imaging (cDTI) is a promising Magnetic Resonance Imaging (MRI) technique for evaluating the microstructure of myocardial tissue in living hearts, providing insights into cardiac function and enabling the development of innovative therapeutic strategies. However, the integration of cDTI into routine clinical practice poses challenging due to the technical obstacles involved in the acquisition, such as low signal-to-noise ratio and prolonged scanning times. In this study, we investigated and implemented three different types of deep learning-based MRI reconstruction models for cDTI reconstruction. We evaluated the performance of these models based on the reconstruction quality assessment, the diffusion tensor parameter assessment as well as the computational cost assessment. Our results indicate that the models discussed in this study can be applied for clinical use at an acceleration factor (AF) of × 2 and × 4 , with the D5C5 model showing superior fidelity for reconstruction and the SwinMR model providing higher perceptual scores. There is no statistical difference from the reference for all diffusion tensor parameters at AF × 2 or most DT parameters at AF × 4 , and the quality of most diffusion tensor parameter maps is visually acceptable. SwinMR is recommended as the optimal approach for reconstruction at AF × 2 and AF × 4 . However, we believe that the models discussed in this study are not yet ready for clinical use at a higher AF. At AF × 8 , the performance of all models discussed remains limited, with only half of the diffusion tensor parameters being recovered to a level with no statistical difference from the reference. Some diffusion tensor parameter maps even provide wrong and misleading information.

Review on deep learning fetal brain segmentation from Magnetic Resonance images

Brain segmentation is often the first and most critical step in quantitative analysis of the brain for many clinical applications, including fetal imaging. Different aspects challenge the segmentation of the fetal brain in magnetic resonance imaging (MRI), such as the non-standard position of the fetus owing to his/her movements during the examination, rapid brain development, and the limited availability of imaging data. In recent years, several segmentation methods have been proposed for automatically partitioning the fetal brain from MR images. These algorithms aim to define regions of interest with different shapes and intensities, encompassing the entire brain, or isolating specific structures. Deep learning techniques, particularly convolutional neural networks (CNNs), have become a state-of-the-art approach in the field because they can provide reliable segmentation results over heterogeneous datasets. Here, we review the deep learning algorithms developed in the field of fetal brain segmentation and categorize them according to their target structures. Finally, we discuss the perceived research gaps in the literature of the fetal domain, suggesting possible future research directions that could impact the management of fetal MR images.

Artificial intelligence for diffusion MRI-based tissue microstructure estimation in the human brain: an overview

Artificial intelligence (AI) has made significant advances in the field of diffusion magnetic resonance imaging (dMRI) and other neuroimaging modalities. These techniques have been applied to various areas such as image reconstruction, denoising, detecting and removing artifacts, segmentation, tissue microstructure modeling, brain connectivity analysis, and diagnosis support. State-of-the-art AI algorithms have the potential to leverage optimization techniques in dMRI to advance sensitivity and inference through biophysical models. While the use of AI in brain microstructures has the potential to revolutionize the way we study the brain and understand brain disorders, we need to be aware of the pitfalls and emerging best practices that can further advance this field. Additionally, since dMRI scans rely on sampling of the q-space geometry, it leaves room for creativity in data engineering in such a way that it maximizes the prior inference. Utilization of the inherent geometry has been shown to improve general inference quality and might be more reliable in identifying pathological differences. We acknowledge and classify AI-based approaches for dMRI using these unifying characteristics. This article also highlighted and reviewed general practices and pitfalls involving tissue microstructure estimation through data-driven techniques and provided directions for building on them.