Review: Noise and artifact reduction for MRI using deep learning

Review: Noise and artifact reduction for MRI using deep learning

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[lines=3,lhang=0.3,nindent=0em] For several years, numerous attempts have been made to reduce noise and artifacts in MRI. Although there have been many successful methods to address these problems, practical implementation for clinical images is still challenging because of its complicated mechanism. Recently, deep learning received considerable attention, emerging as a machine learning approach in delivering robust MR image processing. The purpose here is therefore to explore further and review noise and artifact reduction using deep learning for MRI.

Introduction

MRI suffers from various kinds of noise and artifacts because of the nature of the NMR signal detection and spatial encoding scheme1. There are several reasons that MRI is sensitive to these undesirable errors compared to other modalities. For instance, hardware-induced errors often stem from a complicated acquisition scheme that depends on a reliable spectrometer, RF coils, and magnetic fields. In addition, a long acquisition time is also an essential reason. Body motion, including respiratory and cardiac motion and B0 drift during the scan, can degrade the image quality as well. Notwithstanding the intense dedication of MR vendors to improve these fundamental problems, noise and artifact are still non-negligible degradations to MR images.

Generally, thermal noise is derived from the human body and MRI system itself, such as RF coils, transmission lines, receiver circuits, and so on. Moreover, external RF noise can be a source of the noise. To make matters worse, some sequences such as diffusion-weighted imaging suffer from low signal-to-noise ratio (SNR) because of their weak signal intensity. To improve the SNR of MR images, the signal averaging approach is widely used, although it requires a longer scan time as the number of excitation (NEX) increases. To address these hitches, many advanced filtering methods have been developed using the underlying assumption of MR images such as noise distribution and structures 2. However, the violation of the assumption often induces the undesirable change of texture. In addition to this, some algorithms utilize iterative reconstruction, which yield long computation time.

Artifacts in MRI are caused by various reasons such as external errors and inappropriate spatial encoding. For example, it is widely known that undersampling in Cartesian imaging results in aliasing artifacts. In this case, compressed sensing (CS) reconstruction is generally used to remove such artifacts. Streak artifact is caused by undersampling, motion, and temporal intensity change owing to contrast agent in radial sampling. Advanced imaging techniques, combined with golden angle trajectory and CS reconstruction, have shown excellent performance against these problems3-7. Lack of high-frequency signal leads to Gibbs artifact, which is also called truncation, or ringing artifact. Simple k-space domain filtering is often used although it may cause blurring. Body imaging suffers from motion artifacts that arise from respiratory and cardiac motion. Respiratory triggering8, fast acquisition9, and radial sampling3 are clinically available to suppress artifacts.

Further, retrospective correction10 approaches have been proposed, although it is still in the research stage. Inhomogeneous B0 field or off-resonance effect results in banding artifacts, which are often seen in balanced steady-state free precession. The development of robust and practical methods is still challenging despite the aforementioned efforts to remove artifacts.

Recently, a deep learning approach, which enables feature extraction and complicated nonlinear image processing, is gaining traction to reduce noise and artifacts in MRI11. Deep learning (DL) is a successful machine learning technique based on the neural network used for segmentation, lesion detection, and reconstruction for MRI. In this study, we review the deep learning techniques and applications for reducing noise and artifacts in MRI. First, we discuss the deep learning architecture used for noise and artifact reduction. The following section describes state-of-the-art applications.

Figure 1: Example of a single-scale CNN structure consisting of multiple convolution layers. Each convolution layer has a set of filters, which is followed by activation function such as ReLU, to extract features of input images. The residual learning approach is usually adopted for noise and artifact reduction. Noise or artifact reduced images are calculated by subtracting the output of the network from input images.

1 Deep Learning Architecture

Many DL networks have been proposed for noise and artifact reduction. Convolutional neural networks (CNN), which has a small receptive field, is widely used for noise reduction because Gaussian noise is incoherent and position-independent. However, only the networks with a larger receptive field are often adopted to improve artifacts because most of the artifacts are distributed globally. In this section, we provide an overview of deep learning architecture commonly used for noise and artifact reduction.

Single-scale CNN (SCNN), which is widely used in the various fields shown in Fig. 1, is efficient in improving noisy images12, 13. SCNN consists of more than one convolution layer without a down- or up-sampling structure, such as pooling and stride. In most cases, residual components such as noise or artifact images are used as the output because it is well-known that the manifold of the residual components has a simpler structure compared to that of the clean image components14, resulting in faster conversion and better generalization of the network. Denoising convolutional neural networks (DnCNN) is also a thriving network used for image denoising through a process of learning residual components of images, which is noise. Besides these, batch normalization is used to improve training time for the network. ResNet is commonly used to achieve a complex and deeper structure of the network to overcome the vanishing gradient problem. ResNet is also used for artifact reduction because it has a large receptive field that covers whole input images owing to a large number of layers 15.

Autoencoders can extract clean features from noisy images, similar to the principal component analysis procedure, which is used to extract significant information from high-dimensional datasets 16. Given that Gondara first developed an autoencoder-based denoising filter for X-ray images17, many studies have been proposed for CT, MRI, and others, recently18, 19. Autoencoder, which has a different mechanism compared to SCNN, compresses the entire image information into a low-dimensional structure to effectively learn underlying manifold. Unfortunately, autoencoders may lose important information such as edge or fine structure, if the input image is not a redundant representation.

U-net, often used for image segmentation, has a large receptive field by utilizing multi-scale features20. This network has asymmetric up- and down-sampling structures with a skip connection, which concatenates each layer, as shown in Fig. 2. The skip connection contributes to capturing localized features such as the fine structure of images. For the artifact reduction, U-net is the most popular network because the large receptive field is generally required to extract the artifact that is commonly observed globally. The study by Lee et al. implied that U-net gave a better de-aliasing performance as compared to SCNN14, although a relatively large number of trainable parameters is required for U-net.

Figure 2: Overview of U-net, which has up- and down-sampling structure - the same as autoencoder - used for noise and artifact reduction. Skip connections by copying features from earlier layers into later layers are used to preserve high-frequency information, which is often lost in the down-sampling step. This network is commonly used for removing artifact reduction, and requires a larger receptive field compared to noise reduction.

Generative adversarial networks (GAN) approach is a promising learning technique for removing noise and artifacts21. GAN consists of two separate networks: generator and discriminator. Generator is the network that creates the output images, noise- or artifact-free images, whereas discriminator acts as a classifier to determine whether the generated output is real or fake. Feedback from the discriminator contributes to updating the network of the generator to create convincing fake images to fool the discriminator. U-net is widely used for the generator.

2 Applications

Figure 3: Specimen images of denoising brain DWI using DnCNN, the Noise2Noise approach. This network includes 17 convolution layers with batch normalization and ReLU. Multi-shot DWI images (a) acquired with NEX of 1 were denoised using the network. PSNR analysis between the denoised and high-NEX images indicated that the network successfully reduced the noise component.

Many applications have been proposed using the above successful DL networks for noise and artifact reduction. Although most parts of them are still research stage, promising results were demonstrated with a limited size of datasets. In this section, we introduce state-of-art applications shown in Tab. 1.

Some DL networks focus on denoising for brain MR imaging. Bermudez et al. proposed an autoencoder with skip connections for T1-weighted (T1w) imaging of the brain19. The developed network, trained with 528 T1w images, significantly improved the image quality based on PSNR analysis. DnCNN is also widely used for denoising of brain MR images22, 23. Denoising using DL is used not only for the improvement of image quality but also for reducing scan time. Currently, MR images with higher resolutions are required to achieve better diagnostic performance. However, improvement of patient experience, particularly scan time, in the MR scanner is also an urgent priority. To overcome these conflicting problems, many DL-based denoising approaches have been developed. Kawamura et al. proposed the DnCNN-based approach for denoising multi-shot diffusion-weighted imaging for the brain. The study showed that highly swift DWI could be achieved by reducing the number of excitations (NEX), as shown in Fig. 3. Kidoh et al. proposed the SCNN network, which can be used for multiple sequences such as T1w, T2w, FLAIR, and MPRAGE24. The proposed network utilizes a discrete cosine transform (DCT) layer to separate zero and high-frequency components. The separated high-frequency components go through 22 convolution layers, whereas the zero-frequency component is connected to the last layer. This structure may contribute to robust denoising performance because it doesn’t use contrast information of images. Imaging can be achieved at a pace of more than twofold by using the proposed method.

Moreover, Arterial spin labeling (ASL) perfusion imaging, which generally suffers from low SNR, with DL denoising is also a promising application25, 26. Xie et al. developed the DL denoising approach for ASL using a wide interface network (WIN)25. The WIN is a residual learning CNN with a large size of convolution kernel and filters. Quantitative analysis based on SNR suggested that the proposed method can reduce the scan time for ASL by reducing NEX. Kim et al. proposed a network consisting of two separate pathways for extracting multi-scale features26. The pathway with convolution kernel, batch normalization, and ReLU is used for the local structure of images. Meanwhile, the other pathway uses a dilated pathway to increase the receptive field in order to extract large-scale information. Evaluation by a radiologist implied that the ASL images with low NEX were significantly improved by using this proposed CNN method.

Further, Streak artifact reduction is one of the most successful applications using DL27. There are many studies for reducing streak artifact for computed tomography (CT) images because streak artifact on CT is a very common undesirable image degradation28-30. Recently, radial sampling for abdominal MR imaging is getting attention because of its robustness against respiratory induced motion3, 5, 6. In the case of radial sampling, streak artifact can be observed in MR images as well as CT. Han et al. developed U-net to remove streak artifacts for the brain and abdominal MR images; a network adopted residual learning with pre-training using CT and MRI datasets. This study indicated that the DL-based method could be superior to conventional compressed sensing algorithms.

Several studies of retrospective and blinded motion artifact correction techniques for the brain31-33, c-spine34, liver35, 36, upper abdomen37, and cardiac38 imaging have been proposed. Pawar et al. proposed the motion artifact reduction technique using the U-net for MPRAGE images of the brain. Evaluation based on naturalness image quality evaluator (NIQE)39, which is reference-free image quality metrics, revealed the proposed method improved the motion artifact. Tamada et al. also proposed a motion artifact reduction for DCE-MRI of the liver using DnCNN-based network with multi-channel input and output. A training dataset was generated by simulating the respiratory motion. The results indicated the DL approach possessed the ability to remove artifacts, as show in Fig. 4. It is a challenge to acquire artifact-free images under the influence of cardiac motion. Oksuz et al. proposed the reconstruction technique for cardiac imaging by combining the 3D CNN and the recurrent convolutional neural network (RCNN)40 used for 2D spatiotemporal imaging. The 3D CNN is adopted to detect the corrupted k-space lines by the motion whereas RCNN removes the motion artifact coming from the corrupted lines.

Besides, some applications are used for removing aliasing artifact alternatives to CS reconstruction41-43. CS reconstruction, which is a fast MRI technique using random undersampling and redundancy of MR images, generally requires long computation time. DL approaches can contribute to the reduction of computation cost for the undersampled datasets. A de-aliasing method using the U-net for undersampled k-space was proposed to achieve efficient reconstruction by Hyun et al. 41. Yang et al. proposed a GAN-based reconstruction method for undersampled images42. Recently, a model-based DL network, which has unrolled architecture, was proposed to reduce trainable parameters of the network43.

The DL-based approach is also useful in solving other complicated problems such as removing Gibbs44-47, metal48-50, and banding artifact51. Zhang et al. proposed the CNN-based Gibbs artifact, which can be an alternative to conventional k-space domain filtering methods45. The results indicated that the proposed method removed artifacts without additional blurring, which is often observed in traditional methods. Kwon proposed metal artifact reduction using the U-net and bipolar readout imaging to improve blurring and distortion caused by a strong off-resonance effect48. Seo et al. developed the CNN to correct metal artifact of MR images acquired using slice encoding for metal artifact correction49.

Figure 4: Sample depictions of aliasing reduction of the liver using multi-channel DnCNN, which have seven layers of convolution layers. Multi-contrast images obtained from DCE-MRI were used for the input of the network. MR images with respiratory artifact and blurring were significantly improved by via this network. The acquisition was implemented using the multi-phase 3D T1-weighted spoiled gradient-echo sequence with a dual-echo bipolar readout.

3 Discussion

In this paper, we summarized DL networks and its applications used for noise and artifact reduction. Typical networks including SCNN, U-net, autoencoder, GAN architectures, which have characteristics of structure different from each other, were explained. Further, we reviewed applications using these networks. The studies reviewed here demonstrate the excellent performance of noise and artifact reduction for MRI. These results revealed that DL-base approaches can be used to remove complicated artifacts such as aliasing, streaking, and so on, which are still challenging problems using conventional methods.

Although many promising techniques have been proposed, challenges of removing noise and artifact using DL exist. To begin with, it is challenging to prepare training datasets for some cases. For noise reduction, images with a large number of NEX are often used as clean datasets. However, motions, such as respiratory, cardiac, and CSF pulsation, during a scan can lead to blurring and undesirable image degradation. Noise2Noise approach could be one of the practical solutions for noise reduction52. Nonetheless, datasets generated by simulation are generally used for artifact reduction. In this case, the discrepancy between the simulated and acquired datasets leads to poor filtering performance.

Furthermore, it is difficult to conduct appropriate image quality evaluation for noise and artifact reduction. MSE, PSNR, and SSIM are widely used to evaluate the image quality, particularly for noise reduction networks. Conversely, there is difficulty in using these conventional metrics for artifact reduction because it is challenging to prepare ground truth datasets that have no artifact images. To evaluate the image quality without ground truth, reference-free metrics such as Blind/Referenceless Image Spatial Quality Evaluator53 and NIQE39 are a reasonable alternative to conventional metrics. However, clinical evaluation is essential for practical use because these metrics offer excellent performance for natural images. It is essential to pay attention to the contrast, texture, and fine structure after DL-based filtering because inappropriate training, such as the use of a small number of datasets and wrong noise or artifact modeling, could lead to a critical change of contexture of images.

4 Conclusion and Outlook

In this study, we reviewed DL-based methods to reduce noise and artifact for MR images. Because of the recent advancement of deep learning technology, a wide variety of techniques are proposed to serve these purposes. However, even though DL-based methods are getting popular in the MR community owing to its excellent performance and low computational cost, there are still issues to be solved for practical use. Nevertheless, some applications are overcoming these setbacks and are about to come onto the clinical site as products from MR vendors. The DL-based method will therefore be widely used in a range of MR applications shortly.

5 References

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Purpose Authors Network
Denoising for T1-weighted brain images Camilo Bermudez, et al19 Autoencoder with skip connections
Denoising for brain MRI Dongsheng Jiang, et al22 Multi-channel DnCNN
Denoising for ASL Ki Hwan Kim et al26 Parallel two CNN with different scale of resolution
Denoising for ASL Danfeng Xie, et al25 Wide Inference Network
Denoising for T1-, T2-weighted, and FLAIR brain images Masafumi Kidoh, et al24 Single-scale CNN with DCT
Denoising for multi-shot DWI of the brain Motohide Kawamura, et al54 DnCNN with Noise2Noise approach
Streak artifact reduction for radial MRI Yoseob Han, et al27 U-net
Motion artifact reduction for brain MRI Patricia Johnson, et al33 Single-scale CNN
Motion artifact reduction for DCE-MRI of the liver Daiki Tamada, et al35 Multi-channel DnCNN
Motion artifact reduction for abdomen MRI Wenhao Jiang, et al37 GAN using U-net as generator network
Motion artifact reduction for cardiac MRI Ilkay Oksuz, et al38 3DCNN and RCNN
Motion artifact reduction for brain MRI Ben A Duffy, et al32 GAN using HighRes3dNet as a generator
Motion artifact reduction for cervical spine MRI Hongpyo Lee, et al34 U-net
Aliasing artifact reduction for undersampled MRI Chang Min Hyun, et al41 U-net
Aliasing artifact reduction for undersampled MRI Guang Yang, et al42 GAN using U-net as generator network
Aliasing artifact reduction for undersampled MRI Hemant Kumar Aggarwal, et al43 Model-based DL
Gibbs artifact reduction Qianqian Zhang, et al45 Single-scale CNN
Gibbs artifact reduction Xiaole Zhao, et al47 Enhanced Deep Super-Resolution Network
Metal artifact reduction Kinam Kwon, et al U-net
Metal artifact reduction Jee Won Kim, et al50 U-net
Metal artifact reduction for SEMAC Sunghun Seo, et al49 U-net
Banding artifact reduction for bSSFP Ki Hwan Kim, et al51 Multilayer perceptron
Table 1: Overview of DL studies for noise and artifact reduction
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