Dan Wu

Kelly Payette, Hongwei Li, Priscille de Dumast et al.

In-utero fetal MRI is emerging as an important tool in the diagnosis and analysis of the developing human brain. Automatic segmentation of the developing fetal brain is a vital step in the quantitative analysis of prenatal neurodevelopment both in the research and clinical context. However, manual segmentation of cerebral structures is time-consuming and prone to error and inter-observer variability. Therefore, we organized the Fetal Tissue Annotation (FeTA) Challenge in 2021 in order to encourage the development of automatic segmentation algorithms on an international level. The challenge utilized FeTA Dataset, an open dataset of fetal brain MRI reconstructions segmented into seven different tissues (external cerebrospinal fluid, grey matter, white matter, ventricles, cerebellum, brainstem, deep grey matter). 20 international teams participated in this challenge, submitting a total of 21 algorithms for evaluation. In this paper, we provide a detailed analysis of the results from both a technical and clinical perspective. All participants relied on deep learning methods, mainly U-Nets, with some variability present in the network architecture, optimization, and image pre- and post-processing. The majority of teams used existing medical imaging deep learning frameworks. The main differences between the submissions were the fine tuning done during training, and the specific pre- and post-processing steps performed. The challenge results showed that almost all submissions performed similarly. Four of the top five teams used ensemble learning methods. However, one team's algorithm performed significantly superior to the other submissions, and consisted of an asymmetrical U-Net network architecture. This paper provides a first of its kind benchmark for future automatic multi-tissue segmentation algorithms for the developing human brain in utero.

Tianshu Zheng, Cong Sun, Weihao Zheng et al.

Diffusion magnetic resonance imaging (dMRI) is an important tool in characterizing tissue microstructure based on biophysical models, which are complex and highly non-linear. Resolving microstructures with optimization techniques is prone to estimation errors and requires dense sampling in the q-space. Deep learning based approaches have been proposed to overcome these limitations. Motivated by the superior performance of the Transformer, in this work, we present a learning-based framework based on Transformer, namely, a Microstructure Estimation Transformer with Sparse Coding (METSC) for dMRI-based microstructure estimation with downsampled q-space data. To take advantage of the Transformer while addressing its limitation in large training data requirements, we explicitly introduce an inductive bias - model bias into the Transformer using a sparse coding technique to facilitate the training process. Thus, the METSC is composed with three stages, an embedding stage, a sparse representation stage, and a mapping stage. The embedding stage is a Transformer-based structure that encodes the signal to ensure the voxel is represented effectively. In the sparse representation stage, a dictionary is constructed by solving a sparse reconstruction problem that unfolds the Iterative Hard Thresholding (IHT) process. The mapping stage is essentially a decoder that computes the microstructural parameters from the output of the second stage, based on the weighted sum of normalized dictionary coefficients where the weights are also learned. We tested our framework on two dMRI models with downsampled q-space data, including the intravoxel incoherent motion (IVIM) model and the neurite orientation dispersion and density imaging (NODDI) model. The proposed method achieved up to 11.25 folds of acceleration in scan time and outperformed the other state-of-the-art learning-based methods.