Denoising arterial spin labeling perfusion MRI with deep machine learning.

PURPOSE Arterial spin labeling (ASL) perfusion MRI is a noninvasive technique for measuring cerebral blood flow (CBF) in a quantitative manner. A technical challenge in ASL MRI is data processing because of the inherently low signal-to-noise-ratio (SNR). Deep learning (DL) is an emerging machine learning technique that can learn a nonlinear transform from acquired data without using any explicit hypothesis. Such a high flexibility may be particularly beneficial for ASL denoising. In this paper, we proposed and validated a DL-based ASL MRI denoising algorithm (DL-ASL). METHODS The DL-ASL network was constructed using convolutional neural networks (CNNs) with dilated convolution and wide activation residual blocks to explicitly take the inter-voxel correlations into account, and preserve spatial resolution of input image during model learning. RESULTS DL-ASL substantially improved the quality of ASL CBF in terms of SNR. Based on retrospective analyses, DL-ASL showed a high potential of reducing 75% of the original acquisition time without sacrificing CBF measurement quality. CONCLUSION DL-ASL achieved improved denoising performance for ASL MRI as compared with current routine methods in terms of higher PSNR, SSIM and Radiologic scores. With the help of DL-ASL, much fewer repetitions may be prescribed in ASL MRI, resulting in a great reduction of the total acquisition time.

[1]  Andrea Vedaldi,et al.  Deep Image Prior , 2017, International Journal of Computer Vision.

[2]  Christophe Zimmer,et al.  Deep learning massively accelerates super-resolution localization microscopy , 2018, Nature Biotechnology.

[3]  Junshen Xu,et al.  200x Low-dose PET Reconstruction using Deep Learning , 2017, ArXiv.

[4]  Yiran Li,et al.  Priors-guided slice-wise adaptive outlier cleaning for arterial spin labeling perfusion MRI , 2018, Journal of Neuroscience Methods.

[5]  Lei Zhang,et al.  Beyond a Gaussian Denoiser: Residual Learning of Deep CNN for Image Denoising , 2016, IEEE Transactions on Image Processing.

[6]  Heung-Il Suk,et al.  Deep Learning in Medical Image Analysis. , 2017, Annual review of biomedical engineering.

[7]  G. Zaharchuk,et al.  Recommended implementation of arterial spin-labeled perfusion MRI for clinical applications: A consensus of the ISMRM perfusion study group and the European consortium for ASL in dementia. , 2015, Magnetic resonance in medicine.

[8]  Thomas T. Liu,et al.  A component based noise correction method (CompCor) for BOLD and perfusion based fMRI , 2007, NeuroImage.

[9]  D. Alsop,et al.  Continuous flow‐driven inversion for arterial spin labeling using pulsed radio frequency and gradient fields , 2008, Magnetic resonance in medicine.

[10]  Yiran Li,et al.  A Two-Stage Multi-loss Super-Resolution Network for Arterial Spin Labeling Magnetic Resonance Imaging , 2019, MICCAI.

[11]  Alan Connelly,et al.  Reduction of errors in ASL cerebral perfusion and arterial transit time maps using image de‐noising , 2010, Magnetic resonance in medicine.

[12]  Vladlen Koltun,et al.  Multi-Scale Context Aggregation by Dilated Convolutions , 2015, ICLR.

[13]  Ning Xu,et al.  Wide Activation for Efficient and Accurate Image Super-Resolution , 2018, ArXiv.

[14]  Konstantinos Kamnitsas,et al.  Efficient multi‐scale 3D CNN with fully connected CRF for accurate brain lesion segmentation , 2016, Medical Image Anal..

[15]  Fei-Fei Li,et al.  Large-Scale Video Classification with Convolutional Neural Networks , 2014, 2014 IEEE Conference on Computer Vision and Pattern Recognition.

[16]  Leslie Ying,et al.  Accelerating magnetic resonance imaging via deep learning , 2016, 2016 IEEE 13th International Symposium on Biomedical Imaging (ISBI).

[17]  J. Detre,et al.  Structural Correlation‐based Outlier Rejection (SCORE) algorithm for arterial spin labeling time series , 2017, Journal of magnetic resonance imaging : JMRI.

[18]  S. Choi,et al.  Improving Arterial Spin Labeling by Using Deep Learning. , 2017, Radiology.

[19]  Enhong Chen,et al.  Image Denoising and Inpainting with Deep Neural Networks , 2012, NIPS.

[20]  Adnan Bibic,et al.  Denoising of arterial spin labeling data: wavelet-domain filtering compared with Gaussian smoothing , 2010, Magnetic Resonance Materials in Physics, Biology and Medicine.

[21]  Demis Hassabis,et al.  Mastering Chess and Shogi by Self-Play with a General Reinforcement Learning Algorithm , 2017, ArXiv.

[22]  Yoshua Bengio,et al.  End-to-end attention-based large vocabulary speech recognition , 2015, 2016 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP).

[23]  Xiaoou Tang,et al.  Learning a Deep Convolutional Network for Image Super-Resolution , 2014, ECCV.

[24]  Yoshua Bengio,et al.  Greedy Layer-Wise Training of Deep Networks , 2006, NIPS.

[25]  John A. Detre,et al.  Arterial spin labeled MRI in prodromal Alzheimer's disease: A multi-site study☆ , 2013, NeuroImage: Clinical.

[26]  J. Detre,et al.  A theoretical and experimental investigation of the tagging efficiency of pseudocontinuous arterial spin labeling , 2007, Magnetic resonance in medicine.

[27]  L. Lin,et al.  A concordance correlation coefficient to evaluate reproducibility. , 1989, Biometrics.

[28]  Xiaoyun Liang,et al.  Voxel-Wise Functional Connectomics Using Arterial Spin Labeling Functional Magnetic Resonance Imaging: The Role of Denoising , 2015, Brain Connect..

[29]  Bram van Ginneken,et al.  A survey on deep learning in medical image analysis , 2017, Medical Image Anal..

[30]  Ze Wang,et al.  Patch-based local learning method for cerebral blood flow quantification with arterial spin-labeling MRI , 2017, Medical & Biological Engineering & Computing.

[31]  Kyoung Mu Lee,et al.  Enhanced Deep Residual Networks for Single Image Super-Resolution , 2017, 2017 IEEE Conference on Computer Vision and Pattern Recognition Workshops (CVPRW).

[32]  Stefan Harmeling,et al.  Image denoising: Can plain neural networks compete with BM3D? , 2012, 2012 IEEE Conference on Computer Vision and Pattern Recognition.

[33]  Geoffrey E. Hinton,et al.  Reducing the Dimensionality of Data with Neural Networks , 2006, Science.

[34]  Thomas Brox,et al.  U-Net: Convolutional Networks for Biomedical Image Segmentation , 2015, MICCAI.

[35]  Demis Hassabis,et al.  Mastering the game of Go with deep neural networks and tree search , 2016, Nature.

[36]  Li Bai,et al.  Deep Learning in Visual Computing and Signal Processing , 2017, Appl. Comput. Intell. Soft Comput..

[37]  Ze Wang,et al.  Arterial spin labeling perfusion MRI signal denoising using robust principal component analysis , 2018, Journal of Neuroscience Methods.

[38]  Yiran Li,et al.  BOLD fMRI-Based Brain Perfusion Prediction Using Deep Dilated Wide Activation Networks , 2019, MLMI@MICCAI.

[39]  Ze Wang,et al.  Improving cerebral blood flow quantification for arterial spin labeled perfusion MRI by removing residual motion artifacts and global signal fluctuations. , 2012, Magnetic resonance imaging.

[40]  Lutz Prechelt,et al.  Early Stopping - But When? , 2012, Neural Networks: Tricks of the Trade.

[41]  Fei-Fei Li,et al.  Deep visual-semantic alignments for generating image descriptions , 2015, CVPR.

[42]  Geoffrey E. Hinton,et al.  Acoustic Modeling Using Deep Belief Networks , 2012, IEEE Transactions on Audio, Speech, and Language Processing.

[43]  Thomas S. Huang,et al.  Balanced Two-Stage Residual Networks for Image Super-Resolution , 2017, 2017 IEEE Conference on Computer Vision and Pattern Recognition Workshops (CVPRW).

[44]  E. C. Wong,et al.  Potential and Pitfalls of Arterial Spin Labeling Based Perfusion Imaging Techniques for MRI , 2000 .

[45]  J. Pauly,et al.  Deep learning enables reduced gadolinium dose for contrast‐enhanced brain MRI , 2018, Journal of magnetic resonance imaging : JMRI.

[46]  Dong Yu,et al.  Deep Learning: Methods and Applications , 2014, Found. Trends Signal Process..

[47]  Jong Chul Ye,et al.  Deep learning with domain adaptation for accelerated projection‐reconstruction MR , 2018, Magnetic resonance in medicine.

[48]  Jimmy Ba,et al.  Adam: A Method for Stochastic Optimization , 2014, ICLR.

[49]  Geoffrey E. Hinton,et al.  Speech recognition with deep recurrent neural networks , 2013, 2013 IEEE International Conference on Acoustics, Speech and Signal Processing.

[50]  Kristian Bredies,et al.  Spatio-temporal TGV denoising for ASL perfusion imaging , 2017, NeuroImage.

[51]  S Warach,et al.  A general kinetic model for quantitative perfusion imaging with arterial spin labeling , 1998, Magnetic resonance in medicine.

[52]  J. Detre,et al.  To smooth or not to smooth? ROC analysis of perfusion fMRI data. , 2005, Magnetic resonance imaging.

[53]  Yun Fu,et al.  Residual Dense Network for Image Super-Resolution , 2018, 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition.

[54]  Cagdas Ulas,et al.  DeepASL: Kinetic Model Incorporated Loss for Denoising Arterial Spin Labeled MRI via Deep Residual Learning , 2018, MICCAI.

[55]  Jian Sun,et al.  Deep Residual Learning for Image Recognition , 2015, 2016 IEEE Conference on Computer Vision and Pattern Recognition (CVPR).

[56]  Yu-Bin Yang,et al.  Image Restoration Using Convolutional Auto-encoders with Symmetric Skip Connections , 2016, ArXiv.

[57]  Ze Wang,et al.  Empirical optimization of ASL data analysis using an ASL data processing toolbox: ASLtbx. , 2008, Magnetic resonance imaging.

[58]  Ze Wang,et al.  Support vector machine learning‐based cerebral blood flow quantification for arterial spin labeling MRI , 2014, Human brain mapping.

[59]  Sergey Ioffe,et al.  Batch Normalization: Accelerating Deep Network Training by Reducing Internal Covariate Shift , 2015, ICML.

[60]  Geoffrey E. Hinton,et al.  Deep Learning , 2015, Nature.

[61]  Chong Wang,et al.  Deep Speech 2 : End-to-End Speech Recognition in English and Mandarin , 2015, ICML.

[62]  Yee Whye Teh,et al.  A Fast Learning Algorithm for Deep Belief Nets , 2006, Neural Computation.

[63]  Christopher Joseph Pal,et al.  Brain tumor segmentation with Deep Neural Networks , 2015, Medical Image Anal..

[64]  Geoffrey E. Hinton,et al.  ImageNet classification with deep convolutional neural networks , 2012, Commun. ACM.

[65]  D. S. Williams,et al.  Magnetic resonance imaging of perfusion using spin inversion of arterial water. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[66]  Thomas S. Huang,et al.  Wide-activated Deep Residual Networks based Restoration for BPG-compressed Images , 2018, CVPR Workshops.

[67]  Kunihiko Fukushima,et al.  Neocognitron: A hierarchical neural network capable of visual pattern recognition , 1988, Neural Networks.

[68]  Andrew Zisserman,et al.  Very Deep Convolutional Networks for Large-Scale Image Recognition , 2014, ICLR.