Publications by Year: 2021

Björn Lampinen, Jimmy Lätt, Johan Wasselius, Danielle van Westen, and Markus Nilsson. 8/2021. “Time Dependence in Diffusion MRI Predicts Tissue Outcome in Ischemic Stroke Patients.” Magn Reson Med, 86, 2, Pp. 754-64.Abstract
PURPOSE: Reperfusion therapy enables effective treatment of ischemic stroke presenting within 4-6 hours. However, tissue progression from ischemia to infarction is variable, and some patients benefit from treatment up until 24 hours. Improved imaging techniques are needed to identify these patients. Here, it was hypothesized that time dependence in diffusion MRI may predict tissue outcome in ischemic stroke. METHODS: Diffusion MRI data were acquired with multiple diffusion times in five non-reperfused patients at 2, 9, and 100 days after stroke onset. Maps of "rate of kurtosis change" (k), mean kurtosis, ADC, and fractional anisotropy were derived. The ADC maps defined lesions, normal-appearing tissue, and the lesion tissue that would either be infarcted or remain viable by day 100. Diffusion parameters were compared (1) between lesions and normal-appearing tissue, and (2) between lesion tissue that would be infarcted or remain viable. RESULTS: Positive values of k were observed within stroke lesions on day 2 (P = .001) and on day 9 (P = .023), indicating diffusional exchange. On day 100, high ADC values indicated infarction of 50 ± 20% of the lesion volumes. Tissue infarction was predicted by high k values both on day 2 (P = .026) and on day 9 (P = .046), by low mean kurtosis values on day 2 (P = .043), and by low fractional anisotropy values on day 9 (P = .029), but not by low ADC values. CONCLUSIONS: Diffusion time dependence predicted tissue outcome in ischemic stroke more accurately than the ADC, and may be useful for predicting reperfusion benefit.
Alireza Sedghi, Lauren J O'Donnell, Tina Kapur, Erik Learned-Miller, Parvin Mousavi, and William M Wells. 4/2021. “Image Registration: Maximum Likelihood, Minimum Entropy and Deep Learning.” Med Image Anal, 69, Pp. 101939.Abstract
In this work, we propose a theoretical framework based on maximum profile likelihood for pairwise and groupwise registration. By an asymptotic analysis, we demonstrate that maximum profile likelihood registration minimizes an upper bound on the joint entropy of the distribution that generates the joint image data. Further, we derive the congealing method for groupwise registration by optimizing the profile likelihood in closed form, and using coordinate ascent, or iterative model refinement. We also describe a method for feature based registration in the same framework and demonstrate it on groupwise tractographic registration. In the second part of the article, we propose an approach to deep metric registration that implements maximum likelihood registration using deep discriminative classifiers. We show further that this approach can be used for maximum profile likelihood registration to discharge the need for well-registered training data, using iterative model refinement. We demonstrate that the method succeeds on a challenging registration problem where the standard mutual information approach does not perform well.
Filip Szczepankiewicz, Jens Sjölund, Erica Dall'Armellina, Sven Plein, Jürgen E Schneider, Irvin Teh, and Carl-Fredrik Westin. 4/2021. “Motion-Compensated Gradient Waveforms for Tensor-Valued Diffusion Encoding by Constrained Numerical Optimization.” Magn Reson Med, 85, 4, Pp. 2117-26.Abstract
PURPOSE: Diffusion-weighted MRI is sensitive to incoherent tissue motion, which may confound the measured signal and subsequent analysis. We propose a "motion-compensated" gradient waveform design for tensor-valued diffusion encoding that negates the effects bulk motion and incoherent motion in the ballistic regime. METHODS: Motion compensation was achieved by constraining the magnitude of gradient waveform moment vectors. The constraint was incorporated into a numerical optimization framework, along with existing constraints that account for b-tensor shape, hardware restrictions, and concomitant field gradients. We evaluated the efficacy of encoding and motion compensation in simulations, and we demonstrated the approach by linear and planar b-tensor encoding in a healthy heart in vivo. RESULTS: The optimization framework produced asymmetric motion-compensated waveforms that yielded b-tensors of arbitrary shape with improved efficiency compared with previous designs for tensor-valued encoding, and equivalent efficiency to previous designs for linear (conventional) encoding. Technical feasibility was demonstrated in the heart in vivo, showing vastly improved data quality when using motion compensation. The optimization framework is available online in open source. CONCLUSION: Our gradient waveform design is both more flexible and efficient than previous methods, facilitating tensor-valued diffusion encoding in tissues in which motion would otherwise confound the signal. The proposed design exploits asymmetric encoding times, a single refocusing pulse or multiple refocusing pulses, and integrates compensation for concomitant gradient effects throughout the imaging volume.
Angel Torrado-Carvajal, Nicola Toschi, Daniel S Albrecht, Ken Chang, Oluwaseun Akeju, Minhae Kim, Robert R Edwards, Yi Zhang, Jacob M Hooker, Andrea Duggento, Jayashree Kalpathy-Cramer, Vitaly Napadow, and Marco L Loggia. 4/2021. “Thalamic Neuroinflammation as a Reproducible and Discriminating Signature for Chronic Low Back Pain.” Pain, 162, 4, Pp. 1241-49.Abstract
Using positron emission tomography, we recently demonstrated elevated brain levels of the 18kDa translocator protein (TSPO), a glial activation marker, in chronic low back pain (cLBP) patients, compared to healthy controls (HC). Here, we first sought to replicate the original findings in an independent cohort (15 cLBP, 37.8±12.5 y/o; 18 HC, 48.2±12.8 y/o). We then trained random forest (RF) machine learning algorithms based on TSPO imaging features combining discovery and replication cohorts (totaling 25 cLBP, 42.4±13.2 y/o; 27 HC, 48.9±12.6 y/o), in order to explore whether image features other than the mean contain meaningful information that might contribute to the discrimination of cLBP patients and HC. Feature importance was ranked usind SHapley Additive exPlanations (SHAP) values, and the classification performance (in terms of AUC values) of classifiers containing only the mean, other features, or all features was compared using the DeLong test. Both region-of-interest (ROI) and voxelwise analyses replicated the original observation of thalamic TSPO signal elevations in cLBP patients compared to HC (p's<0.05). The RF-based analyses revealed that while the mean is a discriminating feature, other features demonstrate similar level of importance, including the maximum, kurtosis and entropy.Our observations suggest that thalamic neuroinflammatory signal is a reproducible and discriminating feature for cLBP, further supporting a role for glial activation in human chronic low back pain, and the exploration of neuroinflammation as a therapeutic target for chronic pain. This work further shows that TSPO signal contains a richness of information that the simple mean might fail to capture completely.
Lipeng Ning, Filip Szczepankiewicz, Markus Nilsson, Yogesh Rathi, and Carl-Fredrik Westin. 1/2021. “Probing Tissue Microstructure by Diffusion Skewness Tensor Imaging.” Sci Rep, 11, 1, Pp. 135.Abstract
Probing the cellular structure of in vivo biological tissue is a fundamental problem in biomedical imaging and medical science. This work introduces an approach for analyzing diffusion magnetic resonance imaging data acquired by the novel tensor-valued encoding technique for characterizing tissue microstructure. Our approach first uses a signal model to estimate the variance and skewness of the distribution of apparent diffusion tensors modeling the underlying tissue. Then several novel imaging indices, such as weighted microscopic anisotropy and microscopic skewness, are derived to characterize different ensembles of diffusion processes that are indistinguishable by existing techniques. The contributions of this work also include a theoretical proof that shows that, to estimate the skewness of a diffusion tensor distribution, the encoding protocol needs to include full-rank tensor diffusion encoding. This proof provides a guideline for the application of this technique. The properties of the proposed indices are illustrated using both synthetic data and in vivo data acquired from a human brain.
Fan Zhang, Anna Breger, Kang Ik Kevin Cho, Lipeng Ning, Carl-Fredrik Westin, Lauren J O'Donnell, and Ofer Pasternak. 6/2021. “Deep Learning Based Segmentation of Brain Tissue from Diffusion MRI.” Neuroimage, 233, Pp. 117934.Abstract
Segmentation of brain tissue types from diffusion MRI (dMRI) is an important task, required for quantification of brain microstructure and for improving tractography. Current dMRI segmentation is mostly based on anatomical MRI (e.g., T1- and T2-weighted) segmentation that is registered to the dMRI space. However, such inter-modality registration is challenging due to more image distortions and lower image resolution in dMRI as compared with anatomical MRI. In this study, we present a deep learning method for diffusion MRI segmentation, which we refer to as DDSeg. Our proposed method learns tissue segmentation from high-quality imaging data from the Human Connectome Project (HCP), where registration of anatomical MRI to dMRI is more precise. The method is then able to predict a tissue segmentation directly from new dMRI data, including data collected with different acquisition protocols, without requiring anatomical data and inter-modality registration. We train a convolutional neural network (CNN) to learn a tissue segmentation model using a novel augmented target loss function designed to improve accuracy in regions of tissue boundary. To further improve accuracy, our method adds diffusion kurtosis imaging (DKI) parameters that characterize non-Gaussian water molecule diffusion to the conventional diffusion tensor imaging parameters. The DKI parameters are calculated from the recently proposed mean-kurtosis-curve method that corrects implausible DKI parameter values and provides additional features that discriminate between tissue types. We demonstrate high tissue segmentation accuracy on HCP data, and also when applying the HCP-trained model on dMRI data from other acquisitions with lower resolution and fewer gradient directions.
Maria Paula Maziero, Johanna Seitz-Holland, Kang Ik K Cho, Joshua E Goldenberg, Taís W Tanamatis, Juliana B Diniz, Carolina Cappi, Maria Alice de Mathis, Maria CG Otaduy, Maria da Graça Morais Martin, Renata de Melo Felipe da Silva, Roseli G Shavitt, Marcelo C Batistuzzo, Antonio C Lopes, Eurípedes C Miguel, Ofer Pasternak, and Marcelo Q Hoexter. 4/2021. “Cellular and extracellular white matter abnormalities in Obsessive-Compulsive Disorder: A Diffusion MRI Study.” Biol Psychiatry Cogn Neurosci Neuroimaging.Abstract
BACKGROUND: While previous studies have implicated white matter (WM) as a core pathology of Obsessive-Compulsive Disorder (OCD), the underlying neurobiological processes remain elusive. This study utilizes free-water imaging derived from diffusion MRI to identify cellular and extracellular WM abnormalities in patients with OCD compared to controls (Cs). Next, we investigate the association between diffusion measures, and clinical variables in patients. METHODS: We collected diffusion-weighted MRI and clinical data from eighty-three patients with OCD (56 females/27 males, age=37.7 ± 10.6) and 52 Cs (27 females/25 males, age=32.8 ± 11.5). Fractional anisotropy (FA), fractional anisotropy of cellular tissue (FAT), and extracellular free-water (FW) maps were extracted and compared between patients and Cs using tract-based spatial statistics, and voxel-wise comparison in FSL's Randomise. Next, we correlated these WM measures with clinical variables (age-of-onset and symptom severity) and compared them between patients with and without comorbidities and patients with and without psychiatric medication. RESULTS: Patients with OCD demonstrated lower FA (43.4% of the WM skeleton), FAт (31% of the WM skeleton), and higher FW (22.5% of the WM skeleton) compared to Cs. We did not observe significant correlations between diffusion measures and clinical variables. Comorbidities and medication status did not influence diffusion measures. CONCLUSIONS: Our findings of widespread FA, FAт, and FW abnormalities suggest that OCD is associated with both microstructural cellular and extracellular abnormalities beyond the cortico-striato-thalamo-cortical circuits. Future multimodal longitudinal studies are needed to understand better the influence of essential clinical variables across the illness trajectory.
Gabriel Ramos-Llordén, Gonzalo Vegas-Sánchez-Ferrero, Congyu Liao, Carl-Fredrik Westin, Kawin Setsompop, and Yogesh Rathi. 4/2021. “SNR-Enhanced Diffusion MRI With Structure-Preserving Low-Rank Denoising in Reproducing Kernel Hilbert Spaces.” Magn Reson Med.Abstract
PURPOSE: To introduce, develop, and evaluate a novel denoising technique for diffusion MRI that leverages nonlinear redundancy in the data to boost the SNR while preserving signal information. METHODS: We exploit nonlinear redundancy of the dMRI data by means of kernel principal component analysis (KPCA), a nonlinear generalization of PCA to reproducing kernel Hilbert spaces. By mapping the signal to a high-dimensional space, a higher level of redundant information is exploited, thereby enabling better denoising than linear PCA. We implement KPCA with a Gaussian kernel, with parameters automatically selected from knowledge of the noise statistics, and validate it on realistic Monte Carlo simulations as well as with in vivo human brain submillimeter and low-resolution dMRI data. We also demonstrate KPCA denoising on multi-coil dMRI data. RESULTS: SNR improvements up to 2.7 were obtained in real in vivo datasets denoised with KPCA, in comparison to SNR gains of up to 1.8 using a linear PCA denoising technique called Marchenko-Pastur PCA (MPPCA). Compared to gold-standard dataset references created from averaged data, we showed that lower normalized root mean squared error was achieved with KPCA compared to MPPCA. Statistical analysis of residuals shows that anatomical information is preserved and only noise is removed. Improvements in the estimation of diffusion model parameters such as fractional anisotropy, mean diffusivity, and fiber orientation distribution functions were also demonstrated. CONCLUSION: Nonlinear redundancy of the dMRI signal can be exploited with KPCA, which allows superior noise reduction/SNR improvements than the MPPCA method, without loss of signal information.
Jennifer Nitsch, Jordan Sack, Michael W Halle, Jan H Moltz, April Wall, Anna E Rutherford, Ron Kikinis, and Hans Meine. 3/2021. “MRI-Based Radiomic Feature Analysis of End-Stage Liver Disease for Severity Stratification.” Int J Comput Assist Radiol Surg, 16, 3, Pp. 457-66.Abstract
PURPOSE: We aimed to develop a predictive model of disease severity for cirrhosis using MRI-derived radiomic features of the liver and spleen and compared it to the existing disease severity metrics of MELD score and clinical decompensation. The MELD score is compiled solely by blood parameters, and so far, it was not investigated if extracted image-based features have the potential to reflect severity to potentially complement the calculated score. METHODS: This was a retrospective study of eligible patients with cirrhosis ([Formula: see text]) who underwent a contrast-enhanced MR screening protocol for hepatocellular carcinoma (HCC) screening at a tertiary academic center from 2015 to 2018. Radiomic feature analyses were used to train four prediction models for assessing the patient's condition at time of scan: MELD score, MELD score [Formula: see text] 9 (median score of the cohort), MELD score [Formula: see text] 15 (the inflection between the risk and benefit of transplant), and clinical decompensation. Liver and spleen segmentations were used for feature extraction, followed by cross-validated random forest classification. RESULTS: Radiomic features of the liver and spleen were most predictive of clinical decompensation (AUC 0.84), which the MELD score could predict with an AUC of 0.78. Using liver or spleen features alone had slightly lower discrimination ability (AUC of 0.82 for liver and AUC of 0.78 for spleen features only), although this was not statistically significant on our cohort. When radiomic prediction models were trained to predict continuous MELD scores, there was poor correlation. When stratifying risk by splitting our cohort at the median MELD 9 or at MELD 15, our models achieved AUCs of 0.78 or 0.66, respectively. CONCLUSIONS: We demonstrated that MRI-based radiomic features of the liver and spleen have the potential to predict the severity of liver cirrhosis, using decompensation or MELD status as imperfect surrogate measures for disease severity.
Fan Zhang, Kang Ik Kevin Cho, Yingying Tang, Tianhong Zhang, Sinead Kelly, Maria Di Biase, Lihua Xu, Huijun Li, Keshevan Matcheri, Susan Whitfield-Gabrieli, Margaret Niznikiewicz, William S Stone, Jijun Wang, Martha E Shenton, and Ofer Pasternak. 2/2021. “MK-Curve Improves Sensitivity to Identify White Matter Alterations in Clinical High Risk for Psychosis.” Neuroimage, 226, Pp. 117564.Abstract
Diffusion kurtosis imaging (DKI) is a diffusion MRI approach that enables the measurement of brain microstructural properties, reflecting molecular restrictions and tissue heterogeneity. DKI parameters such as mean kurtosis (MK) provide additional subtle information to that provided by popular diffusion tensor imaging (DTI) parameters, and thus have been considered useful to detect white matter abnormalities, especially in populations that are not expected to show severe brain pathologies. However, DKI parameters often yield artifactual output values that are outside of the biologically plausible range, which diminish sensitivity to identify true microstructural changes. Recently we have proposed the mean-kurtosis-curve (MK-Curve) method to correct voxels with implausible DKI parameters, and demonstrated its improved performance against other approaches that correct artifacts in DKI. In this work, we aimed to evaluate the utility of the MK-Curve method to improve the identification of white matter abnormalities in group comparisons. To do so, we compared group differences, with and without the MK-Curve correction, between 115 individuals at clinical high risk for psychosis (CHR) and 93 healthy controls (HCs). We also compared the correlation of the corrected and uncorrected DKI parameters with clinical characteristics. Following the MK-curve correction, the group differences had larger effect sizes and higher statistical significance (i.e., lower p-values), demonstrating increased sensitivity to detect group differences, in particular in MK. Furthermore, the MK-curve-corrected DKI parameters displayed stronger correlations with clinical variables in CHR individuals, demonstrating the clinical relevance of the corrected parameters. Overall, following the MK-curve correction our analyses found widespread lower MK in CHR that overlapped with lower fractional anisotropy (FA), and both measures were significantly correlated with a decline in functioning and with more severe symptoms. These observations further characterize white matter alterations in the CHR stage, demonstrating that MK and FA abnormalities are widespread, and mostly overlap. The improvement in group differences and stronger correlation with clinical variables suggest that applying MK-curve would be beneficial for the detection and characterization of subtle group differences in other experiments as well.
Andrew Beers, James Brown, Ken Chang, Katharina Hoebel, Jay Patel, Ina K Ly, Sara M Tolaney, Priscilla Brastianos, Bruce Rosen, Elizabeth R Gerstner, and Jayashree Kalpathy-Cramer. 1/2021. “DeepNeuro: An Open-Source Deep Learning Toolbox for Neuroimaging.” Neuroinformatics, 19, 1, Pp. 127-40.Abstract
Translating deep learning research from theory into clinical practice has unique challenges, specifically in the field of neuroimaging. In this paper, we present DeepNeuro, a Python-based deep learning framework that puts deep neural networks for neuroimaging into practical usage with a minimum of friction during implementation. We show how this framework can be used to design deep learning pipelines that can load and preprocess data, design and train various neural network architectures, and evaluate and visualize the results of trained networks on evaluation data. We present a way of reproducibly packaging data pre- and postprocessing functions common in the neuroimaging community, which facilitates consistent performance of networks across variable users, institutions, and scanners. We show how deep learning pipelines created with DeepNeuro can be concisely packaged into shareable Docker and Singularity containers with user-friendly command-line interfaces.
Filip Szczepankiewicz, Carl-Fredrik Westin, and Markus Nilsson. 1/2021. “Gradient Waveform Design for Tensor-valued Encoding in Diffusion MRI.” J Neurosci Methods, 348, Pp. 109007.Abstract
Diffusion encoding along multiple spatial directions per signal acquisition can be described in terms of a b-tensor. The benefit of tensor-valued diffusion encoding is that it unlocks the 'shape of the b-tensor' as a new encoding dimension. By modulating the b-tensor shape, we can control the sensitivity to microscopic diffusion anisotropy which can be used as a contrast mechanism; a feature that is inaccessible by conventional diffusion encoding. Since imaging methods based on tensor-valued diffusion encoding are finding an increasing number of applications we are prompted to highlight the challenge of designing the optimal gradient waveforms for any given application. In this review, we first establish the basic design objectives in creating field gradient waveforms for tensor-valued diffusion MRI. We also survey additional design considerations related to limitations imposed by hardware and physiology, potential confounding effects that cannot be captured by the b-tensor, and artifacts related to the diffusion encoding waveform. Throughout, we discuss the expected compromises and tradeoffs with an aim to establish a more complete understanding of gradient waveform design and its impact on accurate measurements and interpretations of data.