Improving diffusion MRI using simultaneous multi-slice echo planar imaging

Design and rationale of "Antecedents and correlates of well-being in young adults with congenital heart disease in the Boston Circulatory Arrest Study (BCAS-Adult)"

OBJECTIVES

Neurodevelopmental challenges are common among children and adolescents with congenital heart disease (CHD), affecting up to 50% of patients, and recent data suggests they are also present in adulthood. Longitudinal predictors of these challenges in adults have not been studied. The goal of this study was to assess well-being in adults with d-transposition of the great arteries (d-TGA) who had been enrolled in the Boston Circulatory Arrest Study (BCAS) where developmental follow-up was reported throughout childhood and adolescence with brain MRI imaging correlation in adolescence. Well-being was defined through neuropsychological, behavioral and mental health outcomes, quality of life, and social and educational attainment. Brain MRI metrics were also collected.

DESIGN AND ENROLLMENT

Study participants were age 26-33 years and recruited from the BCAS cohort (n= 171 in neonatal cohort, n=139 age 16 years). We assessed neuropsychological, psychiatric, and lifestyle outcomes, and brain MRI features. In this paper, we detail the BCAS-Adult protocols for the study assessments and data collected, approaches, and challenges encountered. Key analyses proposed from this study and its outcomes are outlined including comparisons to local controls or national norms and longitudinal outcome predictors.

CONCLUSIONS

The results from this study will elucidate neuropsychological performance, mental health status, and brain MRI patterns of the BCAS cohort in young adulthood, as well as the predictors and trajectory of these outcomes beginning in early infancy. Study results can inform screening and assessment, anticipatory guidance, and interventions to give children with CHD the best chance to maximize success in adulthood.

Noise reduction in magnitude diffusion-weighted images using spatial similarity and diffusion redundancy

PURPOSE

Diffusion-weighted imaging (DWI) has significant value in clinical application, which however suffers from a serious low signal-to-noise ratio (SNR) problem, especially at high spatial resolution and/or high diffusion sensitivity factor.

METHODS

Here, we propose a denoising method for magnitude DWI. The method consists of two modules: pre-denoising and post-filtering, the former mines the diffusion redundancy by local kernel principal component analysis, and the latter fully mines the non-local self-similarity using patch-based non-local mean.

RESULTS

Validated by simulation and in vivo datasets, the experiment results show that the proposed method is capable of improving the SNR of the whole brain, thus enhancing the performance for diffusion metrics estimation, crossing fiber discrimination, and human brain fiber tractography tracking compared with the different three state-of-the-art comparison methods. More importantly, the proposed method consistently exhibits superior performance to comparison methods when used for denoising diffusion data acquired with sensitivity encoding (SENSE).

CONCLUSION

The proposed denoising method is expected to show significant practicability in acquiring high-quality whole-brain diffusion data, which is crucial for many neuroscience studies.

Connectome harmonic decomposition tracks the presence of disconnected consciousness during ketamine-induced unresponsiveness

BACKGROUND

Ketamine, in doses suitable to induce anaesthesia in humans, gives rise to a unique state of unresponsiveness accompanied by vivid experiences and sensations, making it possible to disentangle the correlated but distinct concepts of conscious awareness and behavioural responsiveness. This distinction is often overlooked in the study of consciousness.

METHODS

The mathematical framework of connectome harmonic decomposition (CHD) was used to view functional magnetic resonance imaging (fMRI) signals during ketamine-induced unresponsiveness as distributed patterns across spatial scales. The connectome harmonic signature of this particular state was mapped onto signatures of other states of consciousness for comparison.

RESULTS

An increased prevalence of fine-grained connectome harmonics was found in fMRI signals obtained during ketamine-induced unresponsiveness, indicating higher granularity. After statistical assessment, the ketamine sedation harmonic signature showed alignment with signatures of LSD-induced (fixed effect =0.0113 [0.0099, 0.0127], P<0.001) or ketamine-induced (fixed effect =0.0087 [0.0071, 0.0103], P<0.001) psychedelic states, and misalignment with signatures seen in unconscious individuals owing to propofol sedation (fixed effect =-0.0213 [-0.0245, -0.0181], P<0.001) or brain injury (fixed effect =-0.0205 [-0.0234, -0.0178], P<0.001).

CONCLUSIONS

The CHD framework, which only requires resting-state fMRI data and can be applied retrospectively, has the ability to track alterations in conscious awareness in the absence of behavioural responsiveness on a group level. This is possible because of ketamine's unique property of decoupling these two facets, and is important for consciousness and anaesthesia research.

Effects of Aging, Estimated Fitness, and Cerebrovascular Status on White Matter Microstructural Health

White matter (WM) microstructural health declines with increasing age, with evidence suggesting that improved cardiorespiratory fitness (CRF) may mitigate this decline. Specifically, higher fit older adults tend to show preserved WM microstructural integrity compared to their lower fit counterparts. However, the extent to which fitness and aging independently impact WM integrity across the adult lifespan is still an open question, as is the extent to which cerebrovascular health mediates these relationships. In a large sample (N = 125, aged 25-72), we assessed the impact of age and estimated cardiorespiratory fitness on fractional anisotropy (FA, derived using diffusion weighted imaging, dwMRI) and probed the mediating role of cerebrovascular health (derived using diffuse optical tomography of the cerebral arterial pulse, pulse-DOT) in these relationships. After orthogonalizing age and estimated fitness and computing a PCA on whole brain WM regions, we found several WM regions impacted by age that were independent from the regions impacted by estimated fitness (hindbrain areas, including brainstem and cerebellar tracts), whereas other areas showed interactive effects of age and estimated fitness (midline areas, including fornix and corpus callosum). Critically, cerebrovascular health mediated both relationships suggesting that vascular health plays a linking role between age, fitness, and brain health. Secondarily, we assessed potential sex differences in these relationships and found that, although females and males generally showed the same age-related FA declines, males exhibited somewhat steeper declines than females. Together, these results suggest that age and fitness impact specific WM regions and highlight the mediating role of cerebrovascular health in maintaining WM health across adulthood.

Apparent Diffusion Coefficient fMRI shines light on white matter resting-state connectivity compared to BOLD

Resting-state functional magnetic resonance imaging (fMRI) is used to derive functional connectivity (FC) between brain regions. Typically, blood oxygen level-dependent (BOLD) contrast is used. However, BOLD's reliance on neurovascular coupling poses challenges in reflecting brain activity accurately, leading to reduced sensitivity in white matter (WM). WM BOLD signals have long been considered physiological noise, although recent evidence shows that both stimulus-evoked and resting-state WM BOLD signals resemble those in gray matter (GM), albeit smaller in amplitude. We introduce apparent diffusion coefficient fMRI (ADC-fMRI) as a promising functional contrast for GM and WM FC, capturing activity-driven neuromorphological fluctuations. Our study compares BOLD-fMRI and ADC-fMRI FC in GM and WM, showing that ADC-fMRI mirrors BOLD-fMRI connectivity in GM, while capturing more robust FC in WM. ADC-fMRI displays higher average clustering and average node strength in WM, and higher inter-subject similarity, compared to BOLD. Taken together, this suggests that ADC-fMRI is a reliable tool for exploring FC that incorporates gray and white matter nodes in a novel way.

Real-time fMRI using multi-band echo-volumar imaging with millimeter spatial resolution and sub-second temporal resolution at 3 tesla

Purpose

In this study we develop undersampled echo-volumar imaging (EVI) using multi-band/simultaneous multi-slab encoding in conjunction with multi-shot slab-segmentation to accelerate 3D encoding and to reduce the duration of EVI encoding within slabs. This approach combines the sampling efficiency of single-shot 3D encoding with the sensitivity advantage of multi-echo acquisition. We describe the pulse sequence development and characterize the spatial-temporal resolution limits and BOLD sensitivity of this approach for high-speed task-based and resting-state fMRI at 3 T. We study the feasibility of further acceleration using compressed sensing (CS) and assess compatibility with NORDIC denoising.

Methods

Multi-band echo volumar imaging (MB-EVI) combines multi-band encoding of up to 6 slabs with CAIPI shifting, accelerated EVI encoding within slabs using up to 4-fold GRAPPA accelerations, 2-shot kz-segmentation and partial Fourier acquisitions along the two phase-encoding dimensions. Task-based and resting-state fMRI at 3 Tesla was performed across a range of voxel sizes (between 1 and 3 mm isotropic), repetition times (118-650 ms), and number of slabs (up to 12). MB-EVI was compared with multi-slab EVI (MS-EVI) and multi-band-EPI (MB-EPI).

Results

Image quality and temporal SNR of MB-EVI was comparable to MS-EVI when using 2-3 mm spatial resolution. High sensitivity for mapping task-based activation and resting-state connectivity at short TR was measured. Online deconvolution of T2* signal decay markedly reduced spatial blurring and improved image contrast. The high temporal resolution of MB-EVI enabled sensitive mapping of high-frequency resting-state connectivity above 0.3 Hz with 3 mm isotropic voxel size (TR: 163 ms). Detection of task-based activation with 1 mm isotropic voxel size was feasible in scan times as short as 1 min 13 s. Compressed sensing with up to 2.4-fold retrospective undersampling showed negligible loss in image quality and moderate region-specific losses in BOLD sensitivity. NORDIC denoising significantly enhanced fMRI sensitivity without introducing image blurring.

Conclusion

Combining MS-EVI with multi-band encoding enables high overall acceleration factors and provides flexibility for maximizing spatial-temporal resolution and volume coverage. The high BOLD sensitivity of this hybrid MB-EVI approach and its compatibility with online image reconstruction enables high spatial-temporal resolution real-time task-based and resting state fMRI.

Structural connectome construction using constrained spherical deconvolution in multi-shell diffusion-weighted magnetic resonance imaging

Connectional neuroanatomical maps can be generated in vivo by using diffusion-weighted magnetic resonance imaging (dMRI) data, and their representation as structural connectome (SC) atlases adopts network-based brain analysis methods. We explain the generation of high-quality SCs of brain connectivity by using recent advances for reconstructing long-range white matter connections such as local fiber orientation estimation on multi-shell dMRI data with constrained spherical deconvolution, which yields both increased sensitivity to detecting crossing fibers compared with competing methods and the ability to separate signal contributions from different macroscopic tissues, and improvements to streamline tractography such as anatomically constrained tractography and spherical-deconvolution informed filtering of tractograms, which have increased the biological accuracy of SC creation. Here, we provide step-by-step instructions to creating SCs by using these methods. In addition, intermediate steps of our procedure can be adapted for related analyses, including region of interest-based tractography and quantification of local white matter properties. The associated software MRtrix3 implements the relevant tools for easy application of the protocol, with specific processing tasks deferred to components of the FSL software. The protocol is suitable for users with expertise in dMRI and neuroscience and requires between 2 h and 13 h to complete, depending on the available computational system.

Data- and Physics-Driven Deep Learning Based Reconstruction for Fast MRI: Fundamentals and Methodologies

Magnetic Resonance Imaging (MRI) is a pivotal clinical diagnostic tool, yet its extended scanning times often compromise patient comfort and image quality, especially in volumetric, temporal and quantitative scans. This review elucidates recent advances in MRI acceleration via data and physics-driven models, leveraging techniques from algorithm unrolling models, enhancement-based methods, and plug-and-play models to the emerging full spectrum of generative model-based methods. We also explore the synergistic integration of data models with physics-based insights, encompassing the advancements in multi-coil hardware accelerations like parallel imaging and simultaneous multi-slice imaging, and the optimization of sampling patterns. We then focus on domain-specific challenges and opportunities, including image redundancy exploitation, image integrity, evaluation metrics, data heterogeneity, and model generalization. This work also discusses potential solutions and future research directions, with an emphasis on the role of data harmonization and federated learning for further improving the general applicability and performance of these methods in MRI reconstruction.

Evidence of supratentorial white matter injury prior to treatment in children with posterior fossa tumors using diffusion MRI

Background

Pediatric brain tumor survivors can have neurocognitive deficits that negatively impact their quality of life, but it is unclear if deficits are primarily caused by treatments, such as radiotherapy, or manifest earlier due to the tumor and related complications. The aim of this work is to characterize white matter injury caused by brain tumors, unrelated to treatment effects, and explore heterogeneity in these white matter abnormalities between individual patients.

Methods

We used diffusion tensor imaging and neurite orientation dispersion diffusion imaging to assess white matter injury in 8 posterior fossa tumor patients. A novel one-against-many approach was used by comparing an individual patient to 20 age- and sex-matched healthy controls to assess variability in white matter abnormalities between the posterior fossa tumor patients. White matter was analyzed at presentation (prior to treatment), postsurgery (24-72 hours after surgery), and at follow-up (3-18 months after surgery).

Results

We demonstrate white matter abnormalities in 5 posterior fossa tumor patients before treatment, likely related to tumor-induced hydrocephalus, which persisted after treatment. White matter changes were complex and patient-specific, and group-based comparisons with control subjects may fail to detect these individual abnormalities.

Conclusions

Identifying pretreatment white matter injury in posterior fossa tumor patients highlights the importance of personalized assessment of brain microstructure, which should be considered in minimizing neurocognitive deficits to improve patient quality of life.

Time-division multiplexing (TDM) sequence removes bias in T2 estimation and relaxation-diffusion measurements

PURPOSE

To compare the performance of multi-echo (ME) and time-division multiplexing (TDM) sequences for accelerated relaxation-diffusion MRI (rdMRI) acquisition and to examine their reliability in estimating accurate rdMRI microstructure measures.

METHOD

The ME, TDM, and the reference single-echo (SE) sequences with six TEs were implemented using Pulseq with single-band (SB) and multi-band 2 (MB2) acceleration factors. On a diffusion phantom, the image intensities of the three sequences were compared, and the differences were quantified using the normalized RMS error (NRMSE). Shinnar-Le Roux (SLR) pulses were implemented for the SB-ME and SB-SE sequences to investigate the impact of slice profiles on ME sequences. For the in-vivo brain scan, besides the image intensity comparison and T2-estimates, different methods were used to assess sequence-related effects on microstructure estimation, including the relaxation diffusion imaging moment (REDIM) and the maximum-entropy relaxation diffusion distribution (MaxEnt-RDD).

RESULTS

TDM performance was similar to the gold standard SE acquisition, whereas ME showed greater biases (3-4× larger NRMSEs for phantom, 2× for in-vivo). T2 values obtained from TDM closely matched SE, whereas ME sequences underestimated the T2 relaxation time. TDM provided similar diffusion and relaxation parameters as SE using REDIM, whereas SB-ME exhibited a 60% larger bias in the  map and on average 3.5× larger bias in the covariance between relaxation-diffusion coefficients.

CONCLUSION

Our analysis demonstrates that TDM provides a more accurate estimation of relaxation-diffusion measurements while accelerating the acquisitions by a factor of 2 to 3.

White matter differences between younger and older adults revealed by fixel-based analysis

The process of healthy aging involves complex alterations in neural structures, with white matter (WM) changes significantly impacting cognitive and motor functions. Conventional methods such as diffusion tensor imaging provide valuable insights, but their limitations in capturing complex WM geometry advocate for more advanced approaches. In this study involving 120 healthy volunteers, we investigated whole-brain WM differences between young and old individuals using a novel technique called fixel-based analysis (FBA). This approach revealed that older adults exhibited reduced FBA-derived metrics in several WM tracts, with frontal areas particularly affected. Surprisingly, age-related differences in FBA-derived measures showed no significant correlation with risk factors such as alcohol consumption, exercise frequency, or pulse pressure but predicted cognitive performance. These findings emphasize FBA's potential in characterizing complex WM changes and the link between cognitive abilities and WM alterations in healthy aging. Overall, this study advances our understanding of age-related neurodegeneration, highlighting the importance of comprehensive assessments that integrate advanced neuroimaging techniques, cognitive evaluation, and demographic factors to gain insights into healthy aging.

Improving MR axon radius estimation in human white matter using spiral acquisition and field monitoring

PURPOSE

To compare MR axon radius estimation in human white matter using a multiband spiral sequence combined with field monitoring to the current state-of-the-art echo-planar imaging (EPI)-based approach.

METHODS

A custom multiband spiral sequence was used for diffusion-weighted imaging at ultra-highb $$ b $$ -values. Field monitoring and higher order image reconstruction were employed to greatly reduce artifacts in spiral images. Diffusion weighting parameters were chosen to match a state-of-the art EPI-based axon radius mapping protocol. The spiral approach was compared to the EPI approach by comparing the image signal-to-noise ratio (SNR) and performing a test-retest study to assess the respective variability and repeatability of axon radius mapping. Effective axon radius estimates were compared over white matter voxels and along the left corticospinal tract.

RESULTS

Increased SNR and reduced artifacts in spiral images led to reduced variability in resulting axon radius maps, especially in low-SNR regions. Test-retest variability was reduced by a factor of approximately 1.5 using the spiral approach. Reduced repeatability due to significant bias was found for some subjects in both spiral and EPI approaches, and attributed to scanner instability, pointing to a previously unknown limitation of the state-of-the-art approach.

CONCLUSION

Combining spiral readouts with field monitoring improved mapping of the effective axon radius compared to the conventional EPI approach.

Transdiagnostic Symptom Domains are Associated with Head Motion During Multimodal Imaging in Children

Background

Head motion is a challenge for neuroimaging research in developmental populations. However, it is unclear how transdiagnostic symptom domains including attention, disruptive behavior (e.g., externalizing behavior), and internalizing problems are linked to scanner motion in children, particularly across structural and functional MRI. The current study examined whether transdiagnostic domains of attention, disruptive behavior, and internalizing symptoms are associated with scanner motion in children during multimodal imaging.

Methods

In a sample of 9,045 children aged 9-10 years in the Adolescent Brain Cognitive Development (ABCD) Study, logistic regression and linear mixed-effects models were used to examine associations between motion and behavior. Motion was indexed using ABCD Study quality control metrics and mean framewise displacement for the following: T1-weighted structural, resting-state fMRI, diffusion MRI, Stop-Signal Task, Monetary Incentive Delay task, and Emotional n-Back task. The Child Behavior Checklist was used as a continuous measure of symptom severity.

Results

Greater attention and disruptive behavior problem severity was associated with a lower likelihood of passing motion quality control across several imaging modalities. In contrast, increased internalizing severity was associated with a higher likelihood of passing motion quality control. Increased attention and disruptive behavior problem severity was also associated with increased mean motion, whereas increased internalizing problem severity was associated with decreased mean motion.

Conclusion

Transdiagnostic domains emerged as predictors of motion in youths. These findings have implications for advancing development of generalizable and robust brain-based biomarkers, computational approaches for mitigating motion effects, and enhancing accessibility of imaging protocols for children with varying symptom severities.

Comparison of T1-weighted landmark placement and ROI transfer onto diffusion-weighted EPI sequences for targeted tractography tasks in the optic nerve

Diffusion-based tractography in the optic nerve requires sampling strategies assisted by anatomical landmark information (regions of interest [ROIs]). We aimed to investigate the feasibility of expert-placed, high-resolution T1-weighted ROI-data transfer onto lower spatial resolution diffusion-weighted images. Slab volumes from 20 volunteers were acquired and preprocessed including distortion bias correction and artifact reduction. Constrained spherical deconvolution was used to generate a directional diffusion information grid (fibre orientation distribution-model [FOD]). Three neuroradiologists marked landmarks on both diffusion imaging variants and structural datasets. Structural ROI information (volumetric interpolated breath-hold sequence [VIBE]) was respectively registered (linear with 6/12 degrees of freedom [DOF]) onto single-shot EPI (ss-EPI) and readout-segmented EPI (rs-EPI) volumes, respectively. All eight ROI/FOD-combinations were compared in a targeted tractography task of the optic nerve pathway. Inter-rater reliability for placed ROIs among experts was highest in VIBE images (lower confidence interval 0.84 to 0.97, mean 0.91) and lower in both ss-EPI (0.61 to 0.95, mean 0.79) and rs-EPI (0.59 to 0.86, mean 0.70). Tractography success rate based on streamline selection performance was highest in VIBE-drawn ROIs registered (6-DOF) onto rs-EPI FOD (70.0% over 5%-threshold, capped to failed ratio 39/16) followed by both 12-DOF-registered (67.5%; 41/16) and nonregistered VIBE (67.5%; 40/23). On ss-EPI FOD, VIBE-ROI-datasets obtained fewer streamlines overall with each at 55.0% above 5%-threshold and with lower capped to failed ratio (6-DOF: 35/36; 12-DOF: 34/34, nonregistered 33/36). The combination of VIBE-placed ROIs (highest inter-rater reliability) with 6-DOF registration onto rs-EPI targets (best streamline selection performance) is most suitable for white matter template generation required in group studies.

Simultaneous multislice echo-planar diffusion-weighted imaging (DWI) in patients with focal liver lesions: a comparative study with conventional DWI

Background

Simultaneous multislice (SMS) technology improves acquisition efficiency of diffusion-weighted imaging (DWI). This study aimed to evaluate the performance of SMS-DWI in image quality and apparent diffusion coefficient (ADC) measurements for focal liver lesions (FLLs) as compared with that of conventional DWI (CON-DWI).

Methods

The institutional ethics committee of West China Hospital, Sichuan University approved this single-center, prospective study conducted from February 2021 to March 2022. Free-breathing SMS-DWI and CON-DWI examinations were acquired on a 3-T scanner with b-values of 50, 400, and 800 s/mm2. Qualitative image quality and quantitative measurements of signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR), and ADC were compared between SMS-DWI and CON-DWI. The ADC values for FLLs were further compared between SMS-DWI and CON-DWI in different patient subgroups. The intra- and interreader agreements were assessed. Significance was set at P<0.05.

Results

This study included 116 patients (96 males, 20 females; mean age 52.0±10.7 years) with 119 FLLs. No significant differences were observed between SMS-DWI and CON-DWI regarding overall image quality in any b-value DWIs, and there were also no differences observed between SMS-DWI and CON-DWI (b=800 s/mm2) for either SNR or CNR (both P values >0.05). ADC values obtained from CON-DWI were higher than those from SMS-DWI in all FLLs [(1.31±0.47)×10-3 vs. (1.26±0.46)×10-3 mm2/s; P=0.004], and similar findings were observed across the different patient subgroups. The consistency analysis showed intrareader intraclass correlation coefficient (ICC) values of 0.792-0.944 and interreader ICC values of 0.758-0.861 for quantitative measurements (SNR, CNR, and ADC) and kappa values of 0.609-0.878 for qualitative image quality.

Conclusions

SMS-DWI achieved a 37% reduction in scan time compared to CON-DWI while maintaining comparable overall image quality. Notably, the ADC values for FLLs were observed to be quantitatively lower with SMS-DWI.

Effects of Aging, Fitness, and Cerebrovascular Status on White Matter Microstructural Health

White matter (WM) microstructural health declines with increasing age, with evidence suggesting that improved cardiorespiratory fitness (CRF) may mitigate this decline. Specifically, higher fit older adults tend to show preserved WM microstructural integrity compared to their lower fit counterparts. However, the extent to which fitness and aging independently impact WM integrity across the adult lifespan is still an open question, as is the extent to which cerebrovascular health mediates these relationships. In a large sample (N = 125, aged 25-72), we assessed the impact of age and fitness on fractional anisotropy (FA, derived using diffusion weighted imaging, DWI) and probed the mediating role of cerebrovascular health (derived using diffuse optical tomography of the cerebral arterial pulse, pulse-DOT) in these relationships. After orthogonalizing age and fitness and computing a PCA on whole brain WM regions, we found several WM regions impacted by age that were independent from the regions impacted by fitness (hindbrain areas, including brainstem and cerebellar tracts), whereas other areas showed interactive effects of age and fitness (midline areas, including fornix and corpus callosum). Critically, cerebrovascular health mediated both relationships suggesting that vascular health plays a linking role between age, fitness, and brain health. Secondarily, we assessed potential sex differences in these relationships and found that, although females and males generally showed the same age-related FA declines, males exhibited somewhat steeper declines than females. Together, these results suggest that age and fitness impact specific WM regions and highlight the mediating role of cerebrovascular health in maintaining WM health across adulthood.

Evaluating the effect of denoising submillimeter auditory fMRI data with NORDIC

Functional magnetic resonance imaging (fMRI) has emerged as an essential tool for exploring human brain function. Submillimeter fMRI, in particular, has emerged as a tool to study mesoscopic computations. The inherently low signal-to-noise ratio (SNR) at submillimeter resolutions warrants the use of denoising approaches tailored at reducing thermal noise-the dominant contributing noise component in high-resolution fMRI. NOise Reduction with DIstribution Corrected Principal Component Analysis (NORDIC PCA) is one of such approaches, and has been benchmarked against other approaches in several applications. Here, we investigate the effects that two versions of NORDIC denoising have on auditory submillimeter data. While investigating auditory functional responses poses unique challenges, we anticipated NORDIC to have a positive impact on the data on the basis of previous applications. Our results show that NORDIC denoising improves the detection sensitivity and the reliability of estimates in submillimeter auditory fMRI data. These effects can be explained by the reduction of the noise-induced signal variability. However, we did observe a reduction in the average response amplitude (percent signal change) within regions of interest, which may suggest that a portion of the signal of interest, which could not be distinguished from general i.i.d. noise, was also removed. We conclude that, while evaluating the effects of the signal reduction induced by NORDIC may be necessary for each application, using NORDIC in high-resolution auditory fMRI studies may be advantageous because of the large reduction in variability of the estimated responses.

Deep Learning-based Image Enhancement Techniques for Fast MRI in Neuroimaging

Despite its superior soft tissue contrast and non-invasive nature, MRI requires long scan times due to its intrinsic signal acquisition principles, a main drawback which technological advancements in MRI have been focused on. In particular, scan time reduction is a natural requirement in neuroimaging due to detailed structures requiring high resolution imaging and often volumetric (3D) acquisitions, and numerous studies have recently attempted to harness deep learning (DL) technology in enabling scan time reduction and image quality improvement. Various DL-based image reconstruction products allow for additional scan time reduction on top of existing accelerated acquisition methods without compromising the image quality.

Time-division multiplexing (TDM) sequence removes bias in T2 estimation and relaxation-diffusion measurements

Purpose

To compare the performance of multi-echo (ME) and time-division multiplexing (TDM) sequences for accelerated relaxation-diffusion MRI (rdMRI) acquisition and to examine their reliability in estimating accurate rdMRI microstructure measures.

Method

The ME, TDM, and the reference single-echo (SE) sequences with six echo times (TE) were implemented using Pulseq with single-band (SB-) and multi-band 2 (MB2-) acceleration factors. On a diffusion phantom, the image intensities of the three sequences were compared, and the differences were quantified using the normalized root mean squared error (NRMSE). For the in-vivo brain scan, besides the image intensity comparison and T2-estimates, different methods were used to assess sequence-related effects on microstructure estimation, including the relaxation diffusion imaging moment (REDIM) and the maximum-entropy relaxation diffusion distribution (MaxEnt-RDD).

Results

TDM performance was similar to the gold standard SE acquisition, whereas ME showed greater biases (3-4× larger NRMSEs for phantom, 2× for in-vivo). T2 values obtained from TDM closely matched SE, whereas ME sequences underestimated the T2 relaxation time. TDM provided similar diffusion and relaxation parameters as SE using REDIM, whereas SB-ME exhibited a 60% larger bias in the map and on average 3.5× larger bias in the covariance between relaxation-diffusion coefficients.

Conclusion

Our analysis demonstrates that TDM provides a more accurate estimation of relaxation-diffusion measurements while accelerating the acquisitions by a factor of 2 to 3.

Referenceless Nyquist ghost correction outperforms standard navigator-based method and improves efficiency of in vivo diffusion tensor cardiovascular magnetic resonance

PURPOSE

The study aims to assess the potential of referenceless methods of EPI ghost correction to accelerate the acquisition of in vivo diffusion tensor cardiovascular magnetic resonance (DT-CMR) data using both computational simulations and data from in vivo experiments.

METHODS

Three referenceless EPI ghost correction methods were evaluated on mid-ventricular short axis DT-CMR spin echo and STEAM datasets from 20 healthy subjects at 3T. The reduced field of view excitation technique was used to automatically quantify the Nyquist ghosts, and DT-CMR images were fit to a linear ghost model for correction.

RESULTS

Numerical simulation showed the singular value decomposition (SVD) method is the least sensitive to noise, followed by Ghost/Object method and entropy-based method. In vivo experiments showed significant ghost reduction for all correction methods, with referenceless methods outperforming navigator methods for both spin echo and STEAM sequences at b = 32, 150, 450, and 600  smm - 2 $$ {\mathrm{smm}}^{-2} $$ . It is worth noting that as the strength of the diffusion encoding increases, the performance gap between the referenceless method and the navigator-based method diminishes.

CONCLUSION

Referenceless ghost correction effectively reduces Nyquist ghost in DT-CMR data, showing promise for enhancing the accuracy and efficiency of measurements in clinical practice without the need for any additional reference scans.

Distinct alterations in white matter properties and organization related to maternal treatment initiation in neonates exposed to HIV but uninfected

HIV exposed-uninfected (HEU) infants and children are at risk of developmental delays as compared to HIV uninfected unexposed (HUU) populations. The effects of exposure to in utero HIV and ART regimens on the HEU the developing brain are not well understood. In a cohort of 2-week-old newborns, we used diffusion tensor imaging (DTI) tractography and graph theory to examine the influence of HIV and ART exposure in utero on neonate white matter integrity and organisation. The cohort included HEU infants born to mothers who started ART before conception (HEUpre) and after conception (HEUpost), as well as HUU infants from the same community. We investigated HIV exposure and ART duration group differences in DTI metrics (fractional anisotropy (FA) and mean diffusivity (MD)) and graph measures across white matter. We found increased MD in white matter connections involving the thalamus and limbic system in the HEUpre group compared to HUU. We further identified reduced nodal efficiency in the basal ganglia. Within the HEUpost group, we observed reduced FA in cortical-subcortical and cerebellar connections as well as decreased transitivity in the hindbrain area compared to HUU. Overall, our analysis demonstrated distinct alterations in white matter integrity related to the timing of maternal ART initiation that influence regional brain network properties.

Diffusion weighted imaging with reverse encoding distortion correction: Improvement of image quality and distortion for accurate ADC evaluation in in vitro and in vivo studies

PURPOSE

The purpose of this in vivo study was to determine the effect of reverse encoding direction (RDC) on apparent diffusion coefficient (ADC) measurements and its efficacy for improving image quality and diagnostic performance for differentiating malignant from benign tumors on head and neck diffusion-weighted imaging (DWI).

METHODS

Forty-eight patients with head and neck tumors underwent DWI with and without RDC and pathological examinations. Their tumors were then divided into two groups: malignant (n = 21) and benign (n = 27). To determine the utility of RDC for DWI, the difference in the deformation ratio (DR) between DWI and T2-weighted images of each tumor was determined for each tumor area. To compare ADC measurement accuracy of DWIs with and without RDC for each patient, ADC values for tumors and spinal cord were determined by using ROI measurements. To compare DR and ADC between two methods, Student's t-tests were performed. Then, ADC values were compared between malignant and benign tumors by Student's t-test on each DWI. Finally, sensitivity, specificity and accuracy were compared by means of McNemar's test.

RESULTS

DR of DWI with RDC was significantly smaller than that without RDC (p < 0.0001). There were significant differences in ADC between malignant and benign lesions on each DWI (p < 0.05). However, there were no significant difference of diagnostic accuracy between the two DWIs (p > 0.05).

CONCLUSION

RDC can improve image quality and distortion of DWI and may have potential for more accurate ADC evaluation and differentiation of malignant from benign head and neck tumors.

Evaluating the effect of denoising submillimeter auditory fMRI data with NORDIC

Functional magnetic resonance imaging (fMRI) has emerged as an essential tool for exploring human brain function. Submillimeter fMRI, in particular, has emerged as a tool to study mesoscopic computations. The inherently low signal-to-noise ratio (SNR) at submillimeter resolutions warrants the use of denoising approaches tailored at reducing thermal noise - the dominant contributing noise component in high resolution fMRI. NORDIC PCA is one of such approaches, and has been benchmarked against other approaches in several applications. Here, we investigate the effects that two versions of NORDIC denoising have on auditory submillimeter data. As investigating auditory functional responses poses unique challenges, we anticipated that the benefit of this technique would be especially pronounced. Our results show that NORDIC denoising improves the detection sensitivity and the reliability of estimates in submillimeter auditory fMRI data. These effects can be explained by the reduction of the noise-induced signal variability. However, we also observed a reduction in the average response amplitude (percent signal), which may suggest that a small amount of signal was also removed. We conclude that, while evaluating the effects of the signal reduction induced by NORDIC may be necessary for each application, using NORDIC in high resolution auditory fMRI studies may be advantageous because of the large reduction in variability of the estimated responses.

Neuroinflammatory imaging markers in white matter: insights into the cerebral consequences of post-acute sequelae of COVID-19 (PASC)

Symptoms of coronavirus disease 2019 (COVID-19) can persist for months or years after infection, a condition called Post-Acute Sequelae of COVID-19 (PASC). Whole-brain white matter and cortical gray matter health were assessed using multi-shell diffusion tensor imaging. Correlational tractography was utilized to dissect the nature and extent of white matter changes. In this study of 42 male essential workers, the most common symptoms of Neurological PASC (n = 24) included fatigue (n = 19) and headache (n = 17). Participants with neurological PASC demonstrated alterations to whole-brain white matter health when compared to controls made up of uninfected, asymptomatic, or mildly infected controls (n = 18). Large differences were evident between PASC and controls in measures of fractional anisotropy (Cohen's D=-0.54, P = 0.001) and cortical isotropic diffusion (Cohen's D = 0.50, P = 0.002). Symptoms were associated with white matter fractional anisotropy (fatigue: rho = -0.62, P< 0.001; headache: rho = -0.66, P < 0.001), as well as nine other measures of white and gray matter health. Brain fog was associated with improved cerebral functioning including improved white matter isotropic diffusion and quantitative anisotropy. This study identified changes across measures of white and gray matter connectivity, neuroinflammation, and cerebral atrophy that were interrelated and associated with differences in symptoms of PASC. These results provide insights into the long-term cerebral implications of COVID-19.

Distinct alterations in white matter properties and organization related to maternal treatment initiation in neonates exposed to HIV but uninfected

HIV exposed-uninfected (HEU) infants and children are at risk of developmental delays as compared to uninfected unexposed (HUU) populations. The effects of exposure to in utero HIV and ART regimens on the HEU the developing brain are not well understood. In a cohort of 2-week-old newborns, we used diffusion tensor imaging (DTI) tractography and graph theory to examine the influence of HIV and ART exposure in utero on neonate white matter integrity and organisation. The cohort included HEU infants born to mothers who started ART before conception (HEUpre) and after conception (HEUpost), as well as HUU infants from the same community. We investigated HIV exposure and ART duration group differences in DTI metrics (fractional anisotropy (FA) and mean diffusivity (MD)) and graph measures across white matter. We found increased MD in white matter connections involving the thalamus and limbic system in the HEUpre group compared to HUU. We further identified reduced nodal efficiency in the basal ganglia. Within the HEUpost group, we observed reduced FA in cortical-subcortical and cerebellar connections as well as decreased transitivity in the hindbrain area compared to HUU. Overall, our analysis demonstrated distinct alterations in white matter integrity related to the timing of maternal ART initiation that influence regional brain network properties.

The Brain Connectome for Clinical Neuroscience

In this chapter, we introduce the topic of the brain connectome, consisting of the complete set of both the structural and functional connections of the brain. Connectomic information and the large-scale network architecture of the brain provide an improved understanding of the organization and functional relevance of human cortical and subcortical anatomy. We discuss various analytical methods to both identify and interpret structural and functional connectivity data. In turn, we discuss how these data provide significant clinical promise for neurosurgery, neurology, and psychiatry in that more informed decisions can be made based on connectomic information. These data can provide safer and more informed network-based neurosurgery for brain tumor patients and even offer the possibility to modulate the brain connectome.

Arachidonic and docosahexaenoic acid supplementation and brain maturation in preterm infants; a double blind RCT

BACKGROUND

Arachidonic acid (ARA) and docosahexaenoic acid (DHA) are important structural components of neural cellular membranes and possess anti-inflammatory properties. Very preterm infants are deprived of the enhanced placental supply of these fatty acids, but the benefit of postnatal supplementation on brain development is uncertain. The aim of this study was to test the hypothesis that early enteral supplementation with ARA and DHA in preterm infants improves white matter (WM) microstructure assessed by diffusion-weighted MRI at term equivalent age.

METHODS

In this double-blind, randomized controlled trial, infants born before 29 weeks gestational age were allocated to either 100 mg/kg ARA and 50 mg/kg DHA (ARA:DHA group) or medium chain triglycerides (control). Supplements were started on the second day of life and provided until 36 weeks postmenstrual age. The primary outcome was brain maturation assessed by diffusion tensor imaging (DTI) using Tract-Based Spatial Statistics (TBSS) analysis.

RESULTS

We included 120 infants (60 per group) in the trial; mean (range) gestational age was 26+3 (22+6 - 28+6) weeks and postmenstrual age at scan was 41+3 (39+1 - 47+0) weeks. Ninety-two infants underwent MRI imaging, and of these, 90 had successful T1/T2 weighted MR images and 74 had DTI data of acceptable quality. TBSS did not show significant differences in mean or axial diffusivity between the groups, but demonstrated significantly higher fractional anisotropy in several large WM tracts in the ARA:DHA group, including corpus callosum, the anterior and posterior limb of the internal capsula, inferior occipitofrontal fasciculus, uncinate fasciculus, and the inferior longitudinal fasciculus. Radial diffusivity was also significantly lower in several of the same WM tracts in the ARA:DHA group.

CONCLUSION

This study suggests that supplementation with ARA and DHA at doses matching estimated fetal accretion rates improves WM maturation compared to control treatment, but further studies are needed to ascertain any functional benefit.

CLINICAL TRIAL REGISTRATION

www.

CLINICALTRIALS

gov; ID:NCT03555019.

Cerebellar growth, volume and diffusivity in children cooled for neonatal encephalopathy without cerebral palsy

Children cooled for HIE and who did not develop cerebral palsy (CP) still underperform at early school age in motor and cognitive domains and have altered supra-tentorial brain volumes and white matter connectivity. We obtained T1-weighted and diffusion-weighted MRI, motor (MABC-2) and cognitive (WISC-IV) scores from children aged 6-8 years who were cooled for HIE secondary to perinatal asphyxia without CP (cases), and controls matched for age, sex, and socioeconomic status. In 35 case children, we measured cerebellar growth from infancy (age 4-15 days after birth) to childhood. In childhood, cerebellar volumes were measured in 26 cases and 23 controls. Diffusion properties (mean diffusivity, MD and fractional anisotropy, FA) were calculated in 24 cases and 19 controls, in 9 cerebellar regions. Cases with FSIQ ≤ 85 had reduced growth of cerebellar width compared to those with FSIQ > 85 (p = 0.0005). Regional cerebellar volumes were smaller in cases compared to controls (p < 0.05); these differences were not significant when normalised to total brain volume. There were no case-control differences in MD or FA. Interposed nucleus volume was more strongly associated with IQ in cases than in controls (p = 0.0196). Other associations with developmental outcome did not differ between cases and controls.

Three-dimensional diffusion MRI using simultaneous multislab with blipped-CAIPI in a 4D k-space framework

PURPOSE

To develop an efficient simultaneous multislab imaging method with blipped-controlled aliasing in parallel imaging (blipped-SMSlab) in a 4D k-space framework, and to demonstrate its efficacy in high-resolution diffusion MRI (dMRI).

THEORY AND METHODS

First, the SMSlab 4D k-space signal expression is formulated, and the phase interferences from intraslab and interslab encodings on the same physical z-axis are analyzed. Then, the blipped-SMSlab dMRI sequence is designed, with blipped-controlled aliasing in parallel imaging (blipped-CAIPI) gradients for interslab encoding, and a 2D multiband accelerated navigator for inter-kz-shot phase correction. Third, strategies are developed to remove the phase interferences, by RF phase modulation and/or phase correction during reconstruction, thus decoupling intraslab and interslab encodings that are otherwise entangled. In vivo experiments are performed to validate the blipped-SMSlab method and preliminarily evaluate its performance in high-resolution dMRI compared with traditional 2D imaging.

RESULTS

In the 4D k-space framework, interslab and intraslab phase interferences of blipped-SMSlab are successfully removed using the proposed strategies. Compared with non-CAIPI sampling, the blipped-SMSlab acquisition reduces the g-factor and g-factor-related SNR penalty by about 12%. In addition, in vivo experiments show the SNR advantage of blipped-SMSlab dMRI over traditional 2D dMRI for 1.3-mm and 1.0-mm isotropic resolution imaging with matched acquisition time.

CONCLUSION

Removing interslab and intraslab phase interferences enables SMSlab dMRI with blipped-CAIPI in a 4D k-space framework. The proposed blipped-SMSlab dMRI is demonstrated to be more SNR-efficient than 2D dMRI and thus capable of high-quality, high-resolution fiber orientation detection.

Effect of Temporal Sampling Rate on Estimates of the Perfusion Parameters for Patients with Moyamoya Disease Assessed with Simultaneous Multislice Dynamic Susceptibility Contrast-enhanced MR Imaging

PURPOSE

The effect of temporal sampling rate (TSR) on perfusion parameters has not been fully investigated in Moyamoya disease (MMD); therefore, this study evaluated the influence of different TSRs on perfusion parameters quantitatively and qualitatively by applying simultaneous multi-slice (SMS) dynamic susceptibility contrast-enhanced MR imaging (DSC-MRI).

METHODS

DSC-MRI datasets were acquired from 28 patients with MMD with a TSR of 0.5 s. Cerebral blood flow (CBF), cerebral blood volume (CBV), mean transit time (MTT), time to peak (TTP), and time to maximum tissue residue function (Tmax) were calculated for eight TSRs ranging from 0.5 to 4.0 s in 0.5-s increments that were subsampled from a TSR of 0.5 s datasets. Perfusion measurements and volume for chronic ischemic (Tmax ≥ 2 s) and non-ischemic (Tmax < 2 s) areas for each TSR were compared to measurements with a TSR of 0.5 s, as was visual perfusion map analysis.

RESULTS

CBF, CBV, and Tmax values tended to be underestimated, whereas MTT and TTP values were less influenced, with a longer TSR. Although Tmax values were overestimated in the TSR of 1.0 s in non-ischemic areas, differences in perfusion measurements between the TSRs of 0.5 and 1.0 s were generally minimal. The volumes of the chronic ischemic areas with a TSR ≥ 3.0 s were significantly underestimated. In CBF and CBV maps, no significant deterioration was noted in image quality up to 3.0 and 2.5 s, respectively. The image quality of MTT, TTP, and Tmax maps for the TSR of 1.0 s was similar to that for the TSR of 0.5 s but was significantly deteriorated for the TSRs of ≥ 1.5 s.

CONCLUSION

In the assessment of MMD by SMS DSC-MRI, application of TSRs of ≥ 1.5 s may lead to deterioration of the perfusion measurements; however, that was less influenced in TSRs of ≤ 1.0 s.

Whole-body diffusion magnetic resonance imaging with simultaneous multi-slice excitation in children and adolescents

BACKGROUND

Whole-body magnetic resonance imaging (WB-MRI) is an increasingly used guideline-based imaging modality for oncological and non-oncological pathologies during childhood and adolescence. While diffusion-weighted imaging (DWI), a part of WB-MRI, enhances image interpretation and improves sensitivity, it also requires the longest acquisition time during a typical WB-MRI scan protocol. Interleaved short tau inversion recovery (STIR) DWI with simultaneous multi-slice (SMS) acquisition is an effective way to speed up examinations.

OBJECTIVE

In this study of children and adolescents, we compared the acquisition time, image quality, signal-to-noise ratio (SNR) and apparent diffusion coefficient (ADC) values of an interleaved STIR SMS-DWI sequence with a standard non-accelerated DWI sequence for WB-MRI.

MATERIALS AND METHODS

Twenty children and adolescents (mean age: 13.9 years) who received two WB-MRI scans at a maximum interval of 18 months, consisting of either standard DWI or SMS-DWI MRI, respectively, were included. For quantitative evaluation, the signal-to-noise ratio (SNR) was determined for b800 images and ADC maps of seven anatomical regions. Image quality evaluation was independently performed by two experienced paediatric radiologists using a 5-point Likert scale. The measurement time per slice stack, pause between measurements including shim and total measurement time of DWI for standard DWI and SMS-DWI were extracted directly from the scan data.

RESULTS

When including the shim duration, the acquisition time for SMS-DWI was 43% faster than for standard DWI. Qualitatively, the scores of SMS-DWI were higher in six locations in the b800 images and four locations in the ADC maps. There was substantial agreement between both readers, with a Cohen's kappa of 0.75. Quantitatively, the SNR in the b800 images and the ADC maps did not differ significantly from one another.

CONCLUSION

Whole body-MRI with SMS-DWI provided equivalent image quality and reduced the acquisition time almost by half compared to the standard WB-DWI protocol.

Functional Magnetic Resonance Imaging and Diffusion Tensor Imaging for Language Mapping in Brain Tumor Surgery: Validation With Direct Cortical Stimulation and Cortico-Cortical Evoked Potential

OBJECTIVE

Functional magnetic resonance imaging (fMRI) and diffusion tensor imaging-derived tractography (DTI-t) contribute to the localization of language areas, but their accuracy remains controversial. This study aimed to investigate the diagnostic performance of preoperative fMRI and DTI-t obtained with a simultaneous multi-slice technique using intraoperative direct cortical stimulation (DCS) or corticocortical evoked potential (CCEP) as reference standards.

MATERIALS AND METHODS

This prospective study included 26 patients (23-74 years; male:female, 13:13) with tumors in the vicinity of Broca's area who underwent preoperative fMRI and DTI-t. A site-by-site comparison between preoperative (fMRI and DTI-t) and intraoperative language mapping (DCS or CCEP) was performed for 226 cortical sites to calculate the sensitivity and specificity of fMRI and DTI-t for mapping Broca's areas. For sites with positive signals on fMRI or DTI-t, the true-positive rate (TPR) was calculated based on the concordance and discordance between fMRI and DTI-t.

RESULTS

Among 226 cortical sites, DCS was performed in 100 sites and CCEP was performed in 166 sites. The specificities of fMRI and DTI-t ranged from 72.4% (63/87) to 96.8% (122/126), respectively. The sensitivities of fMRI (except for verb generation) and DTI-t were 69.2% (9/13) to 92.3% (12/13) with DCS as the reference standard, and 40.0% (16/40) or lower with CCEP as the reference standard. For sites with preoperative fMRI or DTI-t positivity (n = 82), the TPR was high when fMRI and DTI-t were concordant (81.2% and 100% using DCS and CCEP, respectively, as the reference standards) and low when fMRI and DTI-t were discordant (≤ 24.2%).

CONCLUSION

fMRI and DTI-t are sensitive and specific for mapping Broca's area compared with DCS and specific but insensitive compared with CCEP. A site with a positive signal on both fMRI and DTI-t represents a high probability of being an essential language area.

Mammillary body abnormalities and cognitive outcomes in children cooled for neonatal encephalopathy

AIM

To evaluate mammillary body abnormalities in school-age children without cerebral palsy treated with therapeutic hypothermia for neonatal hypoxic-ischaemic encephalopathy (cases) and matched controls, and associations with cognitive outcome, hippocampal volume, and diffusivity in the mammillothalamic tract (MTT) and fornix.

METHOD

Mammillary body abnormalities were scored from T1-weighted magnetic resonance imaging (MRI) in 32 cases and 35 controls (median age [interquartile range] 7 years [6 years 7 months-7 years 7 months] and 7 years 4 months [6 years 7 months-7 years 7 months] respectively). Cognition was assessed using the Wechsler Intelligence Scale for Children, Fourth Edition. Hippocampal volume (normalized by total brain volume) was measured from T1-weighted MRI. Radial diffusivity and fractional anisotropy were measured in the MTT and fornix, from diffusion-weighted MRI using deterministic tractography.

RESULTS

More cases than controls had mammillary body abnormalities (34% vs 0%; p < 0.001). Cases with abnormal mammillary bodies had lower processing speed (p = 0.016) and full-scale IQ (p = 0.028) than cases without abnormal mammillary bodies, and lower scores than controls in all cognitive domains (p < 0.05). Cases with abnormal mammillary bodies had smaller hippocampi (left p = 0.016; right p = 0.004) and increased radial diffusivity in the right MTT (p = 0.004) compared with cases without mammillary body abnormalities.

INTERPRETATION

Cooled children with mammillary body abnormalities at school-age have reduced cognitive scores, smaller hippocampi, and altered MTT microstructure compared with those without mammillary body abnormalities, and matched controls.

WHAT THIS PAPER ADDS

Cooled children are at higher risk of mammillary body abnormalities than controls. Abnormal mammillary bodies are associated with reduced cognitive scores and smaller hippocampi. Abnormal mammillary bodies are associated with altered mammillothalamic tract diffusivity.

Targeted Modulation of Human Brain Interregional Effective Connectivity With Spike-Timing Dependent Plasticity

OBJECTIVE

The ability to selectively up- or downregulate interregional brain connectivity would be useful for research and clinical purposes. Toward this aim, cortico-cortical paired associative stimulation (ccPAS) protocols have been developed in which two areas are repeatedly stimulated with a millisecond-level asynchrony. However, ccPAS results in humans using bifocal transcranial magnetic stimulation (TMS) have been variable, and the mechanisms remain unproven. In this study, our goal was to test whether ccPAS mechanism is spike-timing-dependent plasticity (STDP).

MATERIALS AND METHODS

Eleven healthy participants received ccPAS to the left primary motor cortex (M1) → right M1 with three different asynchronies (5 milliseconds shorter, equal to, or 5 milliseconds longer than the 9-millisecond transcallosal conduction delay) in separate sessions. To observe the neurophysiological effects, single-pulse TMS was delivered to the left M1 before and after ccPAS while cortico-cortical evoked responses were extracted from the contralateral M1 using source-resolved electroencephalography.

RESULTS

Consistent with STDP mechanisms, the effects on synaptic strengths flipped depending on the asynchrony. Further implicating STDP, control experiments suggested that the effects were unidirectional and selective to the targeted connection.

CONCLUSION

The results support the idea that ccPAS induces STDP and may selectively up- or downregulate effective connectivity between targeted regions in the human brain.

Evaluation of simultaneous multi-slice readout-segmented diffusion-weighted MRI acquisition in human optic nerve measurements

Diffusion-weighted magnetic resonance imaging (dMRI) is the only available method to measure the tissue properties of white matter tracts in living human brains and has opened avenues for neuroscientific and clinical studies on human white matter. However, dMRI using conventional simultaneous multi-slice (SMS) single-shot echo planar imaging (ssEPI) still presents challenges in the analyses of some specific white matter tracts, such as the optic nerve, which are heavily affected by susceptibility-induced artifacts. In this study, we evaluated dMRI data acquired by using SMS readout-segmented EPI (rsEPI), which aims to reduce susceptibility-induced artifacts by dividing the acquisition space into multiple segments along the readout direction to reduce echo spacing. To this end, we acquired dMRI data from 11 healthy volunteers by using SMS ssEPI and SMS rsEPI, and then compared the dMRI data of the human optic nerve between the SMS ssEPI and SMS rsEPI datasets by visual inspection of the datasets and statistical comparisons of fractional anisotropy (FA) values. In comparison with the SMS ssEPI data, the SMS rsEPI data showed smaller susceptibility-induced distortion and exhibited a significantly higher FA along the optic nerve. In summary, this study demonstrates that despite its prolonged acquisition time, SMS rsEPI is a promising approach for measuring the tissue properties of the optic nerve in living humans and will be useful for future neuroscientific and clinical investigations of this pathway.

Diffusion MRI data analysis assisted by deep learning synthesized anatomical images (DeepAnat)

Diffusion MRI is a useful neuroimaging tool for non-invasive mapping of human brain microstructure and structural connections. The analysis of diffusion MRI data often requires brain segmentation, including volumetric segmentation and cerebral cortical surfaces, from additional high-resolution T1-weighted (T1w) anatomical MRI data, which may be unacquired, corrupted by subject motion or hardware failure, or cannot be accurately co-registered to the diffusion data that are not corrected for susceptibility-induced geometric distortion. To address these challenges, this study proposes to synthesize high-quality T1w anatomical images directly from diffusion data using convolutional neural networks (CNNs) (entitled "DeepAnat"), including a U-Net and a hybrid generative adversarial network (GAN), and perform brain segmentation on synthesized T1w images or assist the co-registration using synthesized T1w images. The quantitative and systematic evaluations using data of 60 young subjects provided by the Human Connectome Project (HCP) show that the synthesized T1w images and results for brain segmentation and comprehensive diffusion analysis tasks are highly similar to those from native T1w data. The brain segmentation accuracy is slightly higher for the U-Net than the GAN. The efficacy of DeepAnat is further validated on a larger dataset of 300 more elderly subjects provided by the UK Biobank. Moreover, the U-Nets trained and validated on the HCP and UK Biobank data are shown to be highly generalizable to the diffusion data from Massachusetts General Hospital Connectome Diffusion Microstructure Dataset (MGH CDMD) acquired with different hardware systems and imaging protocols and therefore can be used directly without retraining or with fine-tuning for further improved performance. Finally, it is quantitatively demonstrated that the alignment between native T1w images and diffusion images uncorrected for geometric distortion assisted by synthesized T1w images substantially improves upon that by directly co-registering the diffusion and T1w images using the data of 20 subjects from MGH CDMD. In summary, our study demonstrates the benefits and practical feasibility of DeepAnat for assisting various diffusion MRI data analyses and supports its use in neuroscientific applications.

SLfRank: Shinnar-Le-Roux Pulse Design With Reduced Energy and Accurate Phase Profiles Using Rank Factorization

The Shinnar-Le-Roux (SLR) algorithm is widely used to design frequency selective pulses with large flip angles. We improve its design process to generate pulses with lower energy (by as much as 26%) and more accurate phase profiles. Concretely, the SLR algorithm consists of two steps: (1) an invertible transform between frequency selective pulses and polynomial pairs that represent Cayley-Klein (CK) parameters and (2) the design of the CK polynomial pair to match the desired magnetization profiles. Because the CK polynomial pair is bi-linearly coupled, the original algorithm sequentially solves for each polynomial instead of jointly. This results in sub-optimal pulses. Instead, we leverage a convex relaxation technique, commonly used for low rank matrix recovery, to address the bi-linearity. Our numerical experiments show that the resulting pulses are almost always globally optimal in practice. For slice excitation, the proposed algorithm results in more accurate linear phase profiles. And in general the improved pulses have lower energy than the original SLR pulses.

Simultaneous Multislice Accelerated TSE for Improved Spatiotemporal Resolution and Diagnostic Accuracy in Magnetic Resonance Neurography: A Feasibility Study

OBJECTIVES

This study aims to evaluate the utility of simultaneous multislice (SMS) acceleration for routine magnetic resonance neurography (MRN) at 3 T.

MATERIALS AND METHODS

Patients with multiple sclerosis underwent MRN of the sciatic nerve consisting of a standard fat-saturated T2-weighted turbo spin echo (TSE) sequence using integrated parallel acquisition technique (PAT2) acceleration and 2 T2 TSE sequences using a combination of PAT-SMS acceleration (1) to reduce scan time (PAT2-SMS2; SMS-TSE FAST ) and (2) for time neutral increase of in-plane resolution (PAT1-SMS2; SMS-TSE HR ). Acquisition times were 5:29 minutes for the standard T2 TSE, 3:12 minutes for the SMS-TSE FAST , and 5:24 minutes for the SMS-TSE HR . Six qualitative imaging parameters were analyzed by 2 blinded readers using a 5-point Likert scale and T2 nerve lesions were quantified, respectively. Qualitative and quantitative image parameters were compared, and both interrater and intrarater reproducibility were statistically assessed. In addition, signal-to-noise ratio/contrast-to-noise ratio (CNR) was obtained in healthy controls using the exact same imaging protocol.

RESULTS

A total of 15 patients with MS (mean age ± standard deviation, 38.1 ± 11 years) and 10 healthy controls (mean age, 29.1 ± 7 years) were enrolled in this study. CNR analysis was highly reliable (intraclass correlation coefficient, 0.755-0.948) and revealed a significant CNR decrease for the sciatic nerve for both SMS protocols compared with standard T2 TSE (SMS-TSE FAST /SMS-TSE HR , -39%/-55%; P ≤ 0.01). Intrarater and interrater reliability of qualitative image review was good to excellent (κ: 0.672-0.971/0.617-0.883). Compared with the standard T2 TSE sequence, both SMS methods were shown to be superior in reducing pulsatile flow artifacts ( P < 0.01). Ratings for muscle border sharpness, detailed muscle structures, nerve border sharpness, and nerve fascicular structure did not differ significantly between the standard T2 TSE and the SMS-TSE FAST ( P > 0.05) and were significantly better for the SMS-TSE HR than for standard T2 TSE ( P < 0.001). Muscle signal homogeneity was mildly inferior for both SMS-TSE FAST ( P > 0.05) and SMS-TSE HR ( P < 0.001). A significantly higher number of T2 nerve lesions were detected by SMS-TSE HR ( P ≤ 0.01) compared with the standard T2 TSE and SMS-TSE FAST , whereas no significant difference was observed between the standard T2 TSE and SMS-TSE FAST .

CONCLUSIONS

Implementation of SMS offers either to substantially reduce acquisition time by over 40% without significantly impeding image quality compared with the standard T2 TSE or to increase in-plane resolution for a high-resolution approach and improved depiction of T2 nerve lesions while keeping acquisition times constant. This addresses the specific needs of MRN by providing different imaging approaches for 2D clinical MRN.

Functional and Structural Properties of Interhemispheric Interaction between Bilateral Precentral Hand Motor Regions in a Top Wheelchair Racing Paralympian

Long-term motor training can cause functional and structural changes in the human brain. Assessing how the training of specific movements affects specific parts of the neural circuitry is essential to understand better the underlying mechanisms of motor training-induced plasticity in the human brain. We report a single-case neuroimaging study that investigated functional and structural properties in a professional athlete of wheelchair racing. As wheelchair racing requires bilateral synchronization of upper limb movements, we hypothesized that functional and structural properties of interhemispheric interactions in the central motor system might differ between the professional athlete and controls. Functional and diffusion magnetic resonance imaging (fMRI and dMRI) data were obtained from a top Paralympian (P1) in wheelchair racing. With 23 years of wheelchair racing training starting at age eight, she holds an exceptional competitive record. Furthermore, fMRI and dMRI data were collected from three other paraplegic participants (P2-P4) with long-term wheelchair sports training other than wheelchair racing and 37 able-bodied control volunteers. Based on the fMRI data analyses, P1 showed activation in the bilateral precentral hand sections and greater functional connectivity between these sections during a right-hand unimanual task. In contrast, other paraplegic participants and controls showed activation in the contralateral hemisphere and deactivation in the ipsilateral hemisphere. Moreover, dMRI data analysis revealed that P1 exhibited significantly lower mean diffusivity along the transcallosal pathway connecting the bilateral precentral motor regions than control participants, which was not observed in the other paraplegic participants. These results suggest that long-term training with bilaterally synchronized upper-limb movements may promote bilateral recruitment of the precentral hand sections. Such recruitment may affect the structural circuitry involved in the interhemispheric interaction between the bilateral precentral regions. This study provides valuable evidence of the extreme adaptability of the human brain.

Simultaneous multislice diffusion-weighted imaging versus standard diffusion-weighted imaging in whole-body PET/MRI

OBJECTIVE

To compare standard (STD-DWI) single-shot echo-planar imaging DWI and simultaneous multislice (SMS) DWI during whole-body positron emission tomography (PET)/MRI regarding acquisition time, image quality, and lesion detection.

METHODS

Eighty-three adults (47 females, 57%), median age of 64 years (IQR 52-71), were prospectively enrolled from August 2018 to March 2020. Inclusion criteria were (a) abdominal or pelvic tumors and (b) PET/MRI referral from a clinician. Patients were excluded if whole-body acquisition of STD-DWI and SMS-DWI sequences was not completed. The evaluated sequences were axial STD-DWI at b-values 50-400-800 s/mm2 and the apparent diffusion coefficient (ADC), and axial SMS-DWI at b-values 50-300-800 s/mm2 and ADC, acquired with a 3-T PET/MRI scanner. Three radiologists rated each sequence's quality on a five-point scale. Lesion detection was quantified using the anatomic MRI sequences and PET as the reference standard. Regression models were constructed to quantify the association between all imaging outcomes/scores and sequence type.

RESULTS

The median whole-body STD-DWI acquisition time was 14.8 min (IQR 14.1-16.0) versus 7.0 min (IQR 6.7-7.2) for whole-body SMS-DWI, p < 0.001. SMS-DWI image quality scores were higher than STD-DWI in the abdomen (OR 5.31, 95% CI 2.76-10.22, p < 0.001), but lower in the cervicothoracic junction (OR 0.21, 95% CI 0.10-0.43, p < 0.001). There was no significant difference in the chest, mediastinum, pelvis, and rectum. STD-DWI detected 276/352 (78%) lesions while SMS-DWI located 296/352 (84%, OR 1.46, 95% CI 1.02-2.07, p = 0.038).

CONCLUSIONS

In cancer staging and restaging, SMS-DWI abbreviates acquisition while maintaining or improving the diagnostic yield in most anatomic regions.

KEY POINTS

• Simultaneous multislice diffusion-weighted imaging enables faster whole-body image acquisition. • Simultaneous multislice diffusion-weighted imaging maintains or improves image quality when compared to single-shot echo-planar diffusion-weighted imaging in most anatomical regions. • Simultaneous multislice diffusion-weighted imaging leads to superior lesion detection.

Technical Advancements in Abdominal Diffusion-weighted Imaging

Since its first observation in the 18th century, the diffusion phenomenon has been actively studied by many researchers. Diffusion-weighted imaging (DWI) is a technique to probe the diffusion of water molecules and create a MR image with contrast based on the local diffusion properties. The DWI pixel intensity is modulated by the hindrance the diffusing water molecules experience. This hindrance is caused by structures in the tissue and reflects the state of the tissue. This characteristic makes DWI a unique and effective tool to gain more insight into the tissue's pathophysiological condition. In the past decades, DWI has made dramatic technical progress, leading to greater acceptance in clinical practice. In the abdominal region, however, acquiring DWI with good quality is challenging because of several reasons, such as large imaging volume, respiratory and other types of motion, and difficulty in achieving homogeneous fat suppression. In this review, we discuss technical advancements from the past decades that help mitigate these problems common in abdominal imaging. We describe the use of scan acceleration techniques such as parallel imaging and compressed sensing to reduce image distortion in echo planar imaging. Then we compare techniques developed to mitigate issues due to respiratory motion, such as free-breathing, respiratory-triggering, and navigator-based approaches. Commonly used fat suppression techniques are also introduced, and their effectiveness is discussed. Additionally, the influence of the abovementioned techniques on image quality is demonstrated. Finally, we discuss the current and future clinical applications of abdominal DWI, such as whole-body DWI, simultaneous multiple-slice excitation, intravoxel incoherent motion, and the use of artificial intelligence. Abdominal DWI has the potential to develop further in the future, thanks to scan acceleration and image quality improvement driven by technological advancements. The accumulation of clinical proof will further drive clinical acceptance.

Alteration of brain function and systemic inflammatory tone in older adults by decreasing the dietary palmitic acid intake

Prior studies in younger adults showed that reducing the normally high intake of the saturated fatty acid, palmitic acid (PA), in the North American diet by replacing it with the monounsaturated fatty acid, oleic acid (OA), decreased blood concentrations and secretion by peripheral blood mononuclear cells (PBMCs) of interleukin (IL)-1β and IL-6 and changed brain activation in regions of the working memory network. We examined the effects of these fatty acid manipulations in the diet of older adults. Ten subjects, aged 65-75 years, participated in a randomized, cross-over trial comparing 1-week high PA versus low PA/high OA diets. We evaluated functional magnetic resonance imaging (fMRI) using an N-back test of working memory and a resting state scan, cytokine secretion by lipopolysaccharide (LPS)-stimulated PBMCs, and plasma cytokine concentrations. During the low PA compared to the high PA diet, we observed increased activation for the 2-back minus 0-back conditions in the right dorsolateral prefrontal cortex (Broadman Area (BA) 9; p < 0.005), but the effect of diet on working memory performance was not significant (p = 0.09). We observed increased connectivity between anterior regions of the salience network during the low PA/high OA diet (p < 0.001). The concentrations of IL-1β (p = 0.026), IL-8 (p = 0.013), and IL-6 (p = 0.009) in conditioned media from LPS-stimulated PBMCs were lower during the low PA/high OA diet. This study suggests that lowering the dietary intake of PA down-regulated pro-inflammatory cytokine secretion and altered working memory, task-based activation and resting state functional connectivity in older adults.

Reverse encoding distortion correction for diffusion-weighted MRI: Efficacy for improving image quality and ADC evaluation for differentiating malignant from benign areas in suspected prostatic cancer patients

PURPOSE

The purpose of this study was to determine the influenceof reverse encoding distortion correction (RDC) on ADC measurement and its efficacy for improving image quality and diagnostic performance for differentiating malignant from benign prostatic areas on prostatic DWI.

METHODS

Forty suspected prostatic cancer patients underwent DWI with or without RDC (i.e. RDC DWI or DWI) using a 3 T MR system as well as pathological examinations. The pathological examination results indicated 86 areas were malignant while 86 out of 394 areas were computationally selected as benign. SNR for benign areas and muscle and ADCs for malignant and benign areas were determined by ROI measurements on each DWI. Moreover, overall image quality was assessed with a 5-point visual scoring system on each DWI. Paired t-test or Wilcoxon's signed rank test was performed to compare SNR and overall image quality for DWIs. ROC analysis was then used to compare the diagnostic performance, and sensitivity (SE), specificity (SP) and accuracy (AC) of ADC were compared between two DWI by means of McNemar's test.

RESULTS

SNR and overall image quality of RDC DWI showed significant improvements when compared with those of DWI (p < 0.05). Areas under the curve (AUC), SP and AC of DWI RDC DWI (AUC: 0.85, SP: 72.1%, AC: 79.1%) were significantly better than those of DWI (AUC: 0.79, p = 0.008; SP: 64%, p = 0.02; AC: 74.4%, p = 0.008).

CONCLUSION

RDC technique has the potential to improve image quality and ability to differentiate malignant from benign prostatic areas on DWIs of suspected prostatic cancer patients.

Linear multi-scale modeling of diffusion MRI data: A framework for characterization of oriented structures across length scales

Diffusion-weighted magnetic resonance imaging (DW-MRI) has evolved to provide increasingly sophisticated investigations of the human brain's structural connectome in vivo. Restriction spectrum imaging (RSI) is a method that reconstructs the orientation distribution of diffusion within tissues over a range of length scales. In its original formulation, RSI represented the signal as consisting of a spectrum of Gaussian diffusion response functions. Recent technological advances have enabled the use of ultra-high b-values on human MRI scanners, providing higher sensitivity to intracellular water diffusion in the living human brain. To capture the complex diffusion time dependence of the signal within restricted water compartments, we expand upon the RSI approach to represent restricted water compartments with non-Gaussian response functions, in an extended analysis framework called linear multi-scale modeling (LMM). The LMM approach is designed to resolve length scale and orientation-specific information with greater specificity to tissue microstructure in the restricted and hindered compartments, while retaining the advantages of the RSI approach in its implementation as a linear inverse problem. Using multi-shell, multi-diffusion time DW-MRI data acquired with a state-of-the-art 3 T MRI scanner equipped with 300 mT/m gradients, we demonstrate the ability of the LMM approach to distinguish different anatomical structures in the human brain and the potential to advance mapping of the human connectome through joint estimation of the fiber orientation distributions and compartment size characteristics.

Factors associated with MRI success in children cooled for neonatal encephalopathy and controls

OBJECTIVE

To investigate if an association exists between motion artefacts on brain MRI and comprehension, co-ordination, or hyperactivity scores in children aged 6-8 years, cooled for neonatal encephalopathy (cases) and controls.

METHODS

Case children (n = 50) without cerebral palsy were matched with 43 controls for age, sex, and socioeconomic status. Children underwent T1-weighted (T1w), diffusion-weighted image (DWI) brain MRI and cognitive, behavioural, and motor skills assessment. Stepwise multivariable logistic regression assessed associations between unsuccessful MRI and comprehension (including Weschler Intelligence Scale for Children (WISC-IV) verbal comprehension, working memory, processing speed and full-scale IQ), co-ordination (including Movement Assessment Battery for Children (MABC-2) balance, manual dexterity, aiming and catching, and total scores) and hyperactivity (including Strengths and Difficulties Questionnaire (SDQ) hyperactivity and total difficulties scores).

RESULTS

Cases had lower odds of completing both T1w and DWIs (OR: 0.31, 95% CI 0.11-0.89). After adjusting for case-status and sex, lower MABC-2 balance score predicted unsuccessful T1w MRI (OR: 0.81, 95% CI 0.67-0.97, p = 0.022). Processing speed was negatively correlated with relative motion on DWI (r = -0.25, p = 0.026) and SDQ total difficulties score was lower for children with successful MRIs (p = 0.049).

CONCLUSIONS

Motion artefacts on brain MRI in early school-age children are related to the developmental profile.

IMPACT

Children who had moderate/severe neonatal encephalopathy are less likely to have successful MRI scans than matched controls. Motion artefact on MRI is associated with lower MABC-2 balance scores in both children who received therapeutic hypothermia for neonatal encephalopathy and matched controls, after controlling for case-status and sex. Exclusion of children with motion artefacts on brain MRI can introduce sampling bias, which impacts the utility of neuroimaging to understand the brain-behaviour relationship in children with functional impairments.

Cerebral blood volume sensitive layer-fMRI in the human auditory cortex at 7T: Challenges and capabilities

The development of ultra high field fMRI signal readout strategies and contrasts has led to the possibility of imaging the human brain in vivo and non-invasively at increasingly higher spatial resolutions of cortical layers and columns. One emergent layer-fMRI acquisition method with increasing popularity is the cerebral blood volume sensitive sequence named vascular space occupancy (VASO). This approach has been shown to be mostly sensitive to locally-specific changes of laminar microvasculature, without unwanted biases of trans-laminar draining veins. Until now, however, VASO has not been applied in the technically challenging cortical area of the auditory cortex. Here, we describe the main challenges we encountered when developing a VASO protocol for auditory neuroscientific applications and the solutions we have adopted. With the resulting protocol, we present preliminary results of laminar responses to sounds and as a proof of concept for future investigations, we map the topographic representation of frequency preference (tonotopy) in the auditory cortex.

Multi-band multi-shot diffusion MRI reconstruction with joint usage of structured low-rank constraints and explicit phase mapping

PURPOSE

To develop a joint reconstruction method for multi-band multi-shot diffusion MRI.

THEORY AND METHODS

Multi-band multi-shot EPI acquisition is an effective approach for high-resolution diffusion MRI, but requires specific algorithms to correct the inter-shot phase variations. The phase correction can be done by first estimating the explicit phase map and then feeding it into the k-space signal formulation model. Alternatively, the phase information can be used indirectly as structured low-rank constraints in k-space. The 2 methods differ in reconstruction accuracy and efficiency. We aim to combine the 2 different approaches for improved image quality and reconstruction efficiency simultaneously, termed "joint usage of structured low-rank constraints and explicit phase mapping" (JULEP). The proposed JULEP reconstruction is tested on both single-band and multi-band, multi-shot diffusion data, with different resolutions and b values. The results of JULEP are compared with conventional methods with explicit phase mapping (i.e., multiplexed sensitivity-encoding [MUSE]) and structured low-rank constraints (i.e., MUSSELS), and another joint reconstruction method (i.e., network estimated artifacts for tempered reconstruction [NEATR]).

RESULTS

JULEP improves the quality of the navigator and subsequently facilitates the reconstruction of final diffusion images. Compared with all 3 other methods (MUSE, MUSSELS, and NEATR), JULEP mitigates residual structural bias and improves temporal SNRs in the final diffusion image, particularly at high multi-band factors. Compared with MUSSELS, JULEP also improves computational efficiency.

CONCLUSION

The proposed JULEP method significantly improves the image quality and reconstruction efficiency of multi-band multi-shot diffusion MRI, which can promote a broader application of high-resolution diffusion MRI.

Calibration of concomitant field offsets using phase contrast MRI for asymmetric gradient coils

PURPOSE

Asymmetric gradient coils introduce zeroth- and first-order concomitant field terms, in addition to higher-order terms common to both asymmetric and symmetric gradients. Salient to compensation strategies is the accurate calibration of the concomitant field spatial offset parameters for asymmetric coils. A method that allows for one-time calibration of the offset parameters is described.

THEORY AND METHODS

A modified phase contrast pulse sequence with single-sided bipolar flow encoding is proposed to calibrate the offsets for asymmetric, transverse gradient coils. By fitting the measured phase offsets to different gradient amplitudes, the spatial offsets were calculated by fitting the phase variation. This was used for calibrating real-time pre-emphasis compensation of the zeroth- and first-order concomitant fields.

RESULTS

Image quality improvement with the proposed corrections was demonstrated in phantom and healthy volunteers with non-Cartesian and Cartesian trajectory acquisitions. Concomitant field compensation using the calibrated offsets resulted in a residual phase error <3% at the highest gradient amplitude and demonstrated substantial reduction of image blur and slice position/selection artifacts.

CONCLUSIONS

The proposed implementation provides an accurate method for calibrating spatial offsets that can be used for real-time concomitant field compensation of zeroth and first-order terms, substantially reducing artifacts without retrospective correction or sequence specific waveform modifications.

Automated detection of axonal damage along white matter tracts in acute severe traumatic brain injury

New techniques for individualized assessment of white matter integrity are needed to detect traumatic axonal injury (TAI) and predict outcomes in critically ill patients with acute severe traumatic brain injury (TBI). Diffusion MRI tractography has the potential to quantify white matter microstructure in vivo and has been used to characterize tract-specific changes following TBI. However, tractography is not routinely used in the clinical setting to assess the extent of TAI, in part because focal lesions reduce the robustness of automated methods. Here, we propose a pipeline that combines automated tractography reconstructions of 40 white matter tracts with multivariate analysis of along-tract diffusion metrics to assess the presence of TAI in individual patients with acute severe TBI. We used the Mahalanobis distance to identify abnormal white matter tracts in each of 18 patients with acute severe TBI as compared to 33 healthy subjects. In all patients for which a FreeSurfer anatomical segmentation could be obtained (17 of 18 patients), including 13 with focal lesions, the automated pipeline successfully reconstructed a mean of 37.5 ± 2.1 white matter tracts without the need for manual intervention. A mean of 2.5 ± 2.1 tracts resulted in partial or failed reconstructions and needed to be reinitialized upon visual inspection. The pipeline detected at least one abnormal tract in all patients (mean: 9.1 ± 7.9) and accurately discriminated between patients and controls (AUC: 0.91). The number and neuroanatomic location of abnormal tracts varied across patients and levels of consciousness. The premotor, temporal, and parietal sections of the corpus callosum were the most commonly damaged tracts (in 10, 9, and 8 patients, respectively), consistent with prior histopathological studies of TAI. TAI measures were not associated with concurrent behavioral measures of consciousness. In summary, we provide proof-of-principle evidence that an automated tractography pipeline has translational potential to detect and quantify TAI in individual patients with acute severe TBI.