Deep learning-assisted preclinical MR fingerprinting for sub-millimeter T1 and T2 mapping of entire macaque brain.

PURPOSE: Preclinical MR fingerprinting (MRF) suffers from long acquisition time for organ-level coverage due to demanding image resolution and limited undersampling capacity. This study aims to develop a deep learning-assisted fast MRF framework for sub-millimeter T1 and T2 mapping of entire macaque brain on a preclinical 9.4 T MR system. METHODS: Three dimensional MRF images were reconstructed by singular value decomposition (SVD) compressed reconstruction. T1 and T2 mapping for each axial slice exploited a self-attention assisted residual U-Net to suppress aliasing-induced quantification errors, and the transmit-field (B1 + ) measurements for robustness against B1 + inhomogeneity. Supervised network training used MRF images simulated via virtual parametric maps and a desired undersampling scheme. This strategy bypassed the difficulties of acquiring fully sampled preclinical MRF data to guide network training. The proposed fast MRF framework was tested on experimental data acquired from ex vivo and in vivo macaque brains. RESULTS: The trained network showed reasonable adaptability to experimental MRF images, enabling robust delineation of various T1 and T2 distributions in the brain tissues. Further, the proposed MRF framework outperformed several existing fast MRF methods in handling the aliasing artifacts and capturing detailed cerebral structures in the mapping results. Parametric mapping of entire macaque brain at nominal resolution of 0.35 × $$ \times $$ 0.35 × $$ \times $$ 1 mm3 can be realized via a 20-min 3D MRF scan, which was sixfold faster than the baseline protocol. CONCLUSION: Introducing deep learning to MRF framework paves the way for efficient organ-level high-resolution quantitative MRI in preclinical applications.

DeepSTI: Towards tensor reconstruction using fewer orientations in susceptibility tensor imaging.

Susceptibility tensor imaging (STI) is an emerging magnetic resonance imaging technique that characterizes the anisotropic tissue magnetic susceptibility with a second-order tensor model. STI has the potential to provide information for both the reconstruction of white matter fiber pathways and detection of myelin changes in the brain at mm resolution or less, which would be of great value for understanding brain structure and function in healthy and diseased brain. However, the application of STI in vivo has been hindered by its cumbersome and time-consuming acquisition requirement of measuring susceptibility induced MR phase changes at multiple head orientations. Usually, sampling at more than six orientations is required to obtain sufficient information for the ill-posed STI dipole inversion. This complexity is enhanced by the limitation in head rotation angles due to physical constraints of the head coil. As a result, STI has not yet been widely applied in human studies in vivo. In this work, we tackle these issues by proposing an image reconstruction algorithm for STI that leverages data-driven priors. Our method, called DeepSTI, learns the data prior implicitly via a deep neural network that approximates the proximal operator of a regularizer function for STI. The dipole inversion problem is then solved iteratively using the learned proximal network. Experimental results using both simulation and in vivo human data demonstrate great improvement over state-of-the-art algorithms in terms of the reconstructed tensor image, principal eigenvector maps and tractography results, while allowing for tensor reconstruction with MR phase measured at much less than six different orientations. Notably, promising reconstruction results are achieved by our method from only one orientation in human in vivo, and we demonstrate a potential application of this technique for estimating lesion susceptibility anisotropy in patients with multiple sclerosis.

Automatic brain extraction from 3D fetal MR image with deep learning-based multi-step framework.

Brain extraction is a fundamental prerequisite step in neuroimage analysis for fetus. Due to surrounding maternal tissues and unpredictable movement, brain extraction from fetal Magnetic Resonance (MR) images is a challenging task. In this paper, we propose a novel deep learning-based multi-step framework for brain extraction from 3D fetal MR images. In the first step, a global localization network is applied to estimate probability maps for brain candidates. Connected-component labeling algorithm is applied to eliminate small erroneous components and accurately locate the candidate brain area. In the second step, a local refinement network is implemented in the brain candidate area to obtain fine-grained probability maps. Final extraction results are derived by a fusion network with the two cascaded probability maps obtained from previous two steps. Experimental results demonstrate that our proposed method has superior performance compared with existing deep learning-based methods.

Harmonized neonatal brain MR image segmentation model for cross-site datasets.

Accurate segmentation of white matter, gray matter and cerebrospinal fluid from neonatal brain MR images is of great importance in characterizing early brain development. Deep-learning-based methods have been successfully applied to neonatal brain MRIs with superior performance if testing subjects were acquired with the same imaging protocols/scanners as training subjects. However, for the testing subjects acquired with different imaging protocols/scanners, they cannot achieve accurate segmentation results due to large appearance/pattern differences between the testing and training subjects. Besides, imaging artifacts, like head motion, which are inevitable during the imaging acquisition process, also pose a challenge for the segmentation methods. To address these issues, in this paper, we propose a harmonized neonatal brain MR image segmentation model that harmonizes testing images acquired by different protocols/scanners into the domain of training images through a cycle-consistent generative adversarial network (CycleGAN). Meanwhile, the artifacts can be largely alleviated during the harmonization. Then, a densely-connected U-Net based segmentation model trained in the domain of training images can be applied robustly for segmenting the harmonized testing images. Comparisons with existing methods illustrate the better performance of the proposed method on neonatal brain MR images from cross-sites, a grand segmentation challenge, as well as images with artifacts.

Using Artificial Intelligence to Detect COVID-19 and Community-acquired Pneumonia Based on Pulmonary CT: Evaluation of the Diagnostic Accuracy.

Background Coronavirus disease 2019 (COVID-19) has widely spread all over the world since the beginning of 2020. It is desirable to develop automatic and accurate detection of COVID-19 using chest CT. Purpose To develop a fully automatic framework to detect COVID-19 using chest CT and evaluate its performance. Materials and Methods In this retrospective and multicenter study, a deep learning model, the COVID-19 detection neural network (COVNet), was developed to extract visual features from volumetric chest CT scans for the detection of COVID-19. CT scans of community-acquired pneumonia (CAP) and other non-pneumonia abnormalities were included to test the robustness of the model. The datasets were collected from six hospitals between August 2016 and February 2020. Diagnostic performance was assessed with the area under the receiver operating characteristic curve, sensitivity, and specificity. Results The collected dataset consisted of 4352 chest CT scans from 3322 patients. The average patient age (±standard deviation) was 49 years ± 15, and there were slightly more men than women (1838 vs 1484, respectively; P = .29). The per-scan sensitivity and specificity for detecting COVID-19 in the independent test set was 90% (95% confidence interval [CI]: 83%, 94%; 114 of 127 scans) and 96% (95% CI: 93%, 98%; 294 of 307 scans), respectively, with an area under the receiver operating characteristic curve of 0.96 (P < .001). The per-scan sensitivity and specificity for detecting CAP in the independent test set was 87% (152 of 175 scans) and 92% (239 of 259 scans), respectively, with an area under the receiver operating characteristic curve of 0.95 (95% CI: 0.93, 0.97). Conclusion A deep learning model can accurately detect coronavirus 2019 and differentiate it from community-acquired pneumonia and other lung conditions. © RSNA, 2020 Online supplemental material is available for this article.

Submillimeter MR fingerprinting using deep learning-based tissue quantification.

PURPOSE: To develop a rapid 2D MR fingerprinting technique with a submillimeter in-plane resolution using a deep learning-based tissue quantification approach. METHODS: A rapid and high-resolution MR fingerprinting technique was developed for brain T1 and T2 quantification. The 2D acquisition was performed using a FISP-based MR fingerprinting sequence and a spiral trajectory with 0.8-mm in-plane resolution. A deep learning-based method was used to replace the standard template matching method for improved tissue characterization. A novel network architecture (i.e., residual channel attention U-Net) was proposed to improve high-resolution details in the estimated tissue maps. Quantitative brain imaging was performed with 5 adults and 2 pediatric subjects, and the performance of the proposed approach was compared with several existing methods in the literature. RESULTS: In vivo measurements with both adult and pediatric subjects show that high-quality T1 and T2 mapping with 0.8-mm in-plane resolution can be achieved in 7.5 seconds per slice. The proposed deep learning method outperformed existing algorithms in tissue quantification with improved accuracy. Compared with the standard U-Net, high-resolution details in brain tissues were better preserved by the proposed residual channel attention U-Net. Experiments on pediatric subjects further demonstrated the potential of the proposed technique for fast pediatric neuroimaging. Alongside reduced data acquisition time, a 5-fold acceleration in tissue property mapping was also achieved with the proposed method. CONCLUSION: A rapid and high-resolution MR fingerprinting technique was developed, which enables high-quality T1 and T2 quantification with 0.8-mm in-plane resolution in 7.5 seconds per slice.

High-resolution 3D MR Fingerprinting using parallel imaging and deep learning.

MR Fingerprinting (MRF) is a relatively new imaging framework capable of providing accurate and simultaneous quantification of multiple tissue properties for improved tissue characterization and disease diagnosis. While 2D MRF has been widely available, extending the method to 3D MRF has been an actively pursued area of research as a 3D approach can provide a higher spatial resolution and better tissue characterization with an inherently higher signal-to-noise ratio. However, 3D MRF with a high spatial resolution requires lengthy acquisition times, especially for a large volume, making it impractical for most clinical applications. In this study, a high-resolution 3D MR Fingerprinting technique, combining parallel imaging and deep learning, was developed for rapid and simultaneous quantification of T1 and T2 relaxation times. Parallel imaging was first applied along the partition-encoding direction to reduce the amount of acquired data. An advanced convolutional neural network was then integrated with the MRF framework to extract features from the MRF signal evolution for improved tissue characterization and accelerated mapping. A modified 3D-MRF sequence was also developed in the study to acquire data to train the deep learning model that can be directly applied to prospectively accelerate 3D MRF scans. Our results of quantitative T1 and T2 maps demonstrate that improved tissue characterization can be achieved using the proposed method as compared to prior methods. With the integration of parallel imaging and deep learning techniques, whole-brain (26 × 26 × 18 cm3) quantitative T1 and T2 mapping with 1-mm isotropic resolution were achieved in ~7 min. In addition, a ~7-fold improvement in processing time to extract tissue properties was also accomplished with the deep learning approach as compared to the standard template matching method. All of these improvements make high-resolution whole-brain quantitative MR imaging feasible for clinical applications.

Errata: Erratum to "Deep Learning for Fast and Spatially Constrained Tissue Quantification From Highly Accelerated Data in Magnetic Resonance Fingerprinting".

[This corrects the article PMC6692257.].

Deep Learning for Fast and Spatially Constrained Tissue Quantification From Highly Accelerated Data in Magnetic Resonance Fingerprinting.

Magnetic resonance fingerprinting (MRF) is a quantitative imaging technique that can simultaneously measure multiple important tissue properties of human body. Although MRF has demonstrated improved scan efficiency as compared to conventional techniques, further acceleration is still desired for translation into routine clinical practice. The purpose of this paper is to accelerate MRF acquisition by developing a new tissue quantification method for MRF that allows accurate quantification with fewer sampling data. Most of the existing approaches use the MRF signal evolution at each individual pixel to estimate tissue properties, without considering the spatial association among neighboring pixels. In this paper, we propose a spatially constrained quantification method that uses the signals at multiple neighboring pixels to better estimate tissue properties at the central pixel. Specifically, we design a unique two-step deep learning model that learns the mapping from the observed signals to the desired properties for tissue quantification, i.e.: 1) with a feature extraction module for reducing the dimension of signals by extracting a low-dimensional feature vector from the high-dimensional signal evolution and 2) a spatially constrained quantification module for exploiting the spatial information from the extracted feature maps to generate the final tissue property map. A corresponding two-step training strategy is developed for network training. The proposed method is tested on highly undersampled MRF data acquired from human brains. Experimental results demonstrate that our method can achieve accurate quantification for T1 and T2 relaxation times by using only 1/4 time points of the original sequence (i.e., four times of acceleration for MRF acquisition).

RCA-U-Net: Residual Channel Attention U-Net for Fast Tissue Quantification in Magnetic Resonance Fingerprinting.

Magnetic resonance fingerprinting (MRF) is a relatively new imaging framework which allows rapid and simultaneous quantification of multiple tissue properties, such as T1 and T2 relaxation times, in one acquisition. To accelerate the data sampling in MRF, a variety of methods have been proposed to extract tissue properties from highly accelerated MRF signals. While these methods have demonstrated promising results, further improvement in the accuracy, especially for T2 quantification, is needed. In this paper, we present a novel deep learning approach, namely residual channel attention U-Net (RCA-U-Net), to perform the tissue quantification task in MRF. The RCA-U-Net combines the U-Net structure with residual channel attention blocks, to make the network focus on more informative features and produce better quantification results. In addition, we improved the preprocessing of MRF data by masking out the noisy signals in the background for improved quantification at tissue boundaries. Our experimental results on two in vivo brain datasets with different spatial resolutions demonstrate that the proposed method improves the accuracy of T2 quantification with MRF under high acceleration rates (i.e., 8 and 16) as compared to the state-of-the-art methods.

Deep Learning for Fast and Spatially-Constrained Tissue Quantification from Highly-Undersampled Data in Magnetic Resonance Fingerprinting (MRF).

Magnetic resonance fingerprinting (MRF) is a novel quantitative imaging technique that allows simultaneous measurements of multiple important tissue properties in human body, e.g., T1 and T2 relaxation times. While MRF has demonstrated better scan efficiency as compared to conventional quantitative imaging techniques, further acceleration is desired, especially for certain subjects such as infants and young children. However, the conventional MRF framework only uses a simple template matching algorithm to quantify tissue properties, without considering the underlying spatial association among pixels in MRF signals. In this work, we aim to accelerate MRF acquisition by developing a new post-processing method that allows accurate quantification of tissue properties with fewer sampling data. Moreover, to improve the accuracy in quantification, the MRF signals from multiple surrounding pixels are used together to better estimate tissue properties at the central target pixel, which was simply done with the signal only from the target pixel in the original template matching method. In particular, a deep learning model, i.e., U-Net, is used to learn the mapping from the MRF signal evolutions to the tissue property map. To further reduce the network size of U-Net, principal component analysis (PCA) is used to reduce the dimensionality of the input signals. Based on in vivo brain data, our method can achieve accurate quantification for both T1 and T2 by using only 25% time points, which are four times of acceleration in data acquisition compared to the original template matching method.

Quantification of relaxation times in MR Fingerprinting using deep learning.

MRF is a new quantitative MR imaging technique, which can provide rapid and simultaneous measurement of multiple tissue properties. Compared to the fast speed for data acquisition, the post-processing to extract tissue properties with MRF is relatively slow and often requires a large memory for the storage of both image dataset and MRF dictionary. In this study, a convolutional neural network was developed, which can provide rapid estimation of multiple tissue properties in 0.1 sec. The T1 and T2 values obtained in white matter and gray matter are also in a good agreement with the results from pattern matching.