Deep Learning-Based Diffusion MRI Tractography: Integrating Spatial and Anatomical Information

Diffusion MRI tractography technique enables non-invasive visualization of the white matter pathways in the brain. It plays a crucial role in neuroscience and clinical fields by facilitating the study of brain connectivity and neurological disorders. However, the accuracy of reconstructed tractograms has been a longstanding challenge. Recently, deep learning methods have been applied to improve tractograms for better white matter coverage, but often comes at the expense of generating excessive false-positive connections. This is largely due to their reliance on local information to predict long range streamlines. To improve the accuracy of streamline propagation predictions, we introduce a novel deep learning framework that integrates image-domain spatial information and anatomical information along tracts, with the former extracted through convolutional layers and the later modeled via a Transformer-decoder. Additionally, we employ a weighted loss function to address fiber class imbalance encountered during training. We evaluate the proposed method on the simulated ISMRM 2015 Tractography Challenge dataset, achieving a valid streamline rate of 66.2%, white matter coverage of 63.8%, and successfully reconstructing 24 out of 25 bundles. Furthermore, on the multi-site Tractoinferno dataset, the proposed method demonstrates its ability to handle various diffusion MRI acquisition schemes, achieving a 5.7% increase in white matter coverage and a 4.1% decrease in overreach compared to RNN-based methods.

Reliable Deep Diffusion Tensor Estimation: Rethinking the Power of Data-Driven Optimization Routine

Diffusion tensor imaging (DTI) holds significant importance in clinical diagnosis and neuroscience research. However, conventional model-based fitting methods often suffer from sensitivity to noise, leading to decreased accuracy in estimating DTI parameters. While traditional data-driven deep learning methods have shown potential in terms of accuracy and efficiency, their limited generalization to out-of-training-distribution data impedes their broader application due to the diverse scan protocols used across centers, scanners, and studies. This work aims to tackle these challenges and promote the use of DTI by introducing a data-driven optimization-based method termed DoDTI. DoDTI combines the weighted linear least squares fitting algorithm and regularization by denoising technique. The former fits DW images from diverse acquisition settings into diffusion tensor field, while the latter applies a deep learning-based denoiser to regularize the diffusion tensor field instead of the DW images, which is free from the limitation of fixed-channel assignment of the network. The optimization object is solved using the alternating direction method of multipliers and then unrolled to construct a deep neural network, leveraging a data-driven strategy to learn network parameters. Extensive validation experiments are conducted utilizing both internally simulated datasets and externally obtained in-vivo datasets. The results, encompassing both qualitative and quantitative analyses, showcase that the proposed method attains state-of-the-art performance in DTI parameter estimation. Notably, it demonstrates superior generalization, accuracy, and efficiency, rendering it highly reliable for widespread application in the field.

3D-EPI Blip-Up/Down Acquisition with CAIPI and Joint Hankel Structured Low-Rank Reconstruction for Rapid Distortion-Free High-Resolution T2* Mapping

Purpose: This work aims to develop a novel distortion-free 3D-EPI acquisition and image reconstruction technique for fast and robust, high-resolution, whole-brain imaging as well as quantitative T2* mapping. Methods: 3D-Blip-Up and -Down Acquisition (3D-BUDA) sequence is designed for both single- and multi-echo 3D GRE-EPI imaging using multiple shots with blip-up and -down readouts to encode B0 field map information. Complementary k-space coverage is achieved using controlled aliasing in parallel imaging (CAIPI) sampling across the shots. For image reconstruction, an iterative hard-thresholding algorithm is employed to minimize the cost function that combines field map information informed parallel imaging with the structured low-rank constraint for multi-shot 3D-BUDA data. Extending 3D-BUDA to multi-echo imaging permits T2* mapping. For this, we propose constructing a joint Hankel matrix along both echo and shot dimensions to improve the reconstruction. Results: Experimental results on in vivo multi-echo data demonstrate that, by performing joint reconstruction along with both echo and shot dimensions, reconstruction accuracy is improved compared to standard 3D-BUDA reconstruction. CAIPI sampling is further shown to enhance the image quality. For T2* mapping, T2* values from 3D-Joint-CAIPI-BUDA and reference multi-echo GRE are within limits of agreement as quantified by Bland-Altman analysis. Conclusions: The proposed technique enables rapid 3D distortion-free high-resolution imaging and T2* mapping. Specifically, 3D-BUDA enables 1-mm isotropic whole-brain imaging in 22 s at 3 T and 9 s on a 7 T scanner. The combination of multi-echo 3D-BUDA with CAIPI acquisition and joint reconstruction enables distortion-free whole-brain T2* mapping in 47 s at 1.1x1.1x1.0 mm3 resolution.