What's new and what's next in diffusion MRI preprocessing

Sex-related variability of white matter tracts in the whole HCP cohort

Behavioral differences between men and women have been studied extensively, as have differences in brain anatomy. However, most studies have focused on differences in gray matter, while white matter has been much less studied. We conducted a comprehensive study of 77 deep white matter tracts to analyze their volumetric and microstructural variability between men and women in the full Human Connectome Project (HCP) cohort of 1065 healthy individuals aged 22-35 years. We found a significant difference in total brain volume between men and women (+ 12.6% in men), consistent with the literature. 16 tracts showed significant volumetric differences between men and women, one of which stood out due to a larger effect size: the corpus callosum genu, which was larger in women (+ 7.3% in women, p = 5.76 × 10-19). In addition, we found several differences in microstructural parameters between men and women, both using standard Diffusion Tensor Imaging (DTI) parameters and more complex microstructural parameters from the Neurite Orientation Dispersion and Density Imaging (NODDI) model, with the tracts showing the greatest differences belonging to motor (cortico-spinal tracts, cortico-cerebellar tracts) or limbic (cingulum, fornix, thalamo-temporal radiations) systems. These microstructural differences may be related to known behavioral differences between the sexes in timed motor performance, aggressiveness/impulsivity, and social cognition.

Diffusion MRI in prostate cancer with ultra-strong whole-body gradients

Diffusion-weighted MRI (dMRI) is universally recommended for the detection and classification of prostate cancer (PCa), with PI-RADS recommendations to acquire b-values of ≥1.4 ms/μm2. However, clinical dMRI suffers from a low signal-to-noise ratio (SNR) as the consequence of prolonged echo times (TEs) attributable to the limited gradient power in the range of 40-80 mT/m. To overcome this, MRI systems with strong gradients have been designed but so far have mainly been applied in the brain. The aim of this work was to assess the feasibility, data quality, SNR and contrast-to-noise ratio (CNR) of measurements in PCa with a 300 mT/m whole-body system. A cohort of men without and with diagnosed PCa were imaged on a research-only 3T Connectom Siemens MRI system equipped with a gradient amplitude of 300 mT/m. dMRI at high b-values were acquired using high gradient amplitudes and compared with gradient capabilities mimicking clinical systems. Data artefacts typically amplified with stronger gradients were assessed and their correction evaluated. The SNR gains and lesion-to-healthy tissue CNR were statistically tested investigating the effect of protocol and b-value. The diagnostic quality of the images for different dMRI protocols was assessed by an experienced radiologist using a 5-point Likert scale and an adapted PI-QUAL scoring system. The strong gradients for prostate dMRI allowed a significant gain in SNR per unit time compared with clinical gradients. Furthermore, a 1.6-2.1-fold increase in CNR was observed. Despite the more pronounced artefacts typically associated with strong gradients, a satisfactory correction could be achieved. Smoother and less biased parameter maps were obtained with protocols at shorter TEs. The results of this study show that dMRI in PCa with a whole-body 300-mT/m scanner is feasible without a report of physiological effects, SNR and CNR can be improved compared with lower gradient strengths, and artefacts do not negate the benefits of strong gradients and can be ameliorated. This assessment provides the first essential step towards unveiling the full potential of cutting-edge scanners, now increasingly becoming available, to advance early detection and diagnostic precision.

What has brain diffusion magnetic resonance imaging taught us about chronic primary pain: a narrative review

ABSTRACT

Chronic pain is a pervasive and debilitating condition with increasing implications for public health, affecting millions of individuals worldwide. Despite its high prevalence, the underlying neural mechanisms and pathophysiology remain only partly understood. Since its introduction 35 years ago, brain diffusion magnetic resonance imaging (MRI) has emerged as a powerful tool to investigate changes in white matter microstructure and connectivity associated with chronic pain. This review synthesizes findings from 58 articles that constitute the current research landscape, covering methods and key discoveries. We discuss the evidence supporting the role of altered white matter microstructure and connectivity in chronic primary pain conditions, highlighting the importance of studying multiple chronic pain syndromes to identify common neurobiological pathways. We also explore the prospective clinical utility of diffusion MRI, such as its role in identifying diagnostic, prognostic, and therapeutic biomarkers. Furthermore, we address shortcomings and challenges associated with brain diffusion MRI in chronic primary pain studies, emphasizing the need for the harmonization of data acquisition and analysis methods. We conclude by highlighting emerging approaches and prospective avenues in the field that may provide new insights into the pathophysiology of chronic pain and potential new therapeutic targets. Because of the limited current body of research and unidentified targeted therapeutic strategies, we are forced to conclude that further research is required. However, we believe that brain diffusion MRI presents a promising opportunity for enhancing our understanding of chronic pain and improving clinical outcomes.

Methodological considerations on diffusion MRI tractography in infants aged 0-2 years: a scoping review

Diffusion MRI (dMRI) enables studying the complex architectural organization of the brain's white matter (WM) through virtual reconstruction of WM fiber tracts (tractography). Despite the anticipated clinical importance of applying tractography to study structural connectivity and tract development during the critical period of rapid infant brain maturation, detailed descriptions on how to approach tractography in young infants are limited. Over the past two decades, tractography from infant dMRI has mainly been applied in research settings and focused on diffusion tensor imaging (DTI). Only few studies used techniques superior to DTI in terms of disentangling information on the brain's organizational complexity, including crossing fibers. While more advanced techniques may enhance our understanding of the intricate processes of normal and abnormal brain development and extensive knowledge has been gained from application on adult scans, their applicability in infants has remained underexplored. This may partially be due to the higher technical requirements versus the need to limit scan time in young infants. We review various previously described methodological practices for tractography in the infant brain (0-2 years-of-age) and provide recommendations to optimize advanced tractography approaches to enable more accurate reconstructions of the brain WM's complexity. IMPACT: Diffusion tensor imaging is the technique most frequently used for fiber tracking in the developing infant brain but is limited in capability to disentangle the complex white matter organization. Advanced tractography techniques allow for reconstruction of crossing fiber bundles to better reflect the brain's complex organization. Yet, they pose practical and technical challenges in the fast developing young infant's brain. Methods on how to approach advanced tractography in the young infant's brain have hardly been described. Based on a literature review, recommendations are provided to optimize tractography for the developing infant brain, aiming to advance early diagnosis and neuroprotective strategies.

Signal drift in diffusion MRI of the brain: effects on intravoxel incoherent motion parameter estimates

OBJECTIVES

Signal drift has been put forward as one of the fundamental confounding factors in diffusion MRI (dMRI) of the brain. This study characterizes signal drift in dMRI of the brain, evaluates correction methods, and exemplifies its impact on parameter estimation for three intravoxel incoherent motion (IVIM) protocols.

MATERIALS AND METHODS

dMRI of the brain was acquired in ten healthy subjects using protocols designed to enable retrospective characterization and correction of signal drift. All scans were acquired twice for repeatability analysis. Three temporal polynomial correction methods were evaluated: (1) global, (2) voxelwise, and (3) spatiotemporal. Effects of acquisition order were simulated using estimated drift fields.

RESULTS

Signal drift was around 2% per 5 min in the brain as a whole, but reached above 5% per 5 min in the frontal regions. Only correction methods taking spatially varying signal drift into account could achieve effective corrections. Altered acquisition order introduced both systematic changes and differences in repeatability in the presence of signal drift.

DISCUSSION

Signal drift in dMRI of the brain was found to be spatially varying, calling for correction methods taking this into account. Without proper corrections, choice of protocol can affect dMRI parameter estimates and their repeatability.

Feasibility study to unveil the potential: considerations of constrained spherical deconvolution tractography with unsedated neonatal diffusion brain MRI data

Purpose

The study aimed to (1) assess the feasibility constrained spherical deconvolution (CSD) tractography to reconstruct crossing fiber bundles with unsedated neonatal diffusion MRI (dMRI), and (2) demonstrate the impact of spatial and angular resolution and processing settings on tractography and derived quantitative measures.

Methods

For the purpose of this study, the term-equivalent dMRIs (single-shell b800, and b2000, both 5 b0, and 45 gradient directions) of two moderate-late preterm infants (with and without motion artifacts) from a local cohort [Brain Imaging in Moderate-late Preterm infants (BIMP) study; Calgary, Canada] and one infant from the developing human connectome project with high-quality dMRI (using the b2600 shell, comprising 20 b0 and 128 gradient directions, from the multi-shell dataset) were selected. Diffusion tensor imaging (DTI) and CSD tractography were compared on b800 and b2000 dMRI. Varying image resolution modifications, (pre-)processing and tractography settings were tested to assess their impact on tractography. Each experiment involved visualizing local modeling and tractography for the corpus callosum and corticospinal tracts, and assessment of morphological and diffusion measures.

Results

Contrary to DTI, CSD enabled reconstruction of crossing fibers. Tractography was susceptible to image resolution, (pre-) processing and tractography settings. In addition to visual variations, settings were found to affect streamline count, length, and diffusion measures (fractional anisotropy and mean diffusivity). Diffusion measures exhibited variations of up to 23%.

Conclusion

Reconstruction of crossing fiber bundles using CSD tractography with unsedated neonatal dMRI data is feasible. Tractography settings affected streamline reconstruction, warranting careful documentation of methods for reproducibility and comparison of cohorts.

The Advanced BRain Imaging on ageing and Memory (ABRIM) data collection: Study design, data processing, and rationale

To understand the neurocognitive mechanisms that underlie heterogeneity in cognitive ageing, recent scientific efforts have led to a growing public availability of imaging cohort data. The Advanced BRain Imaging on ageing and Memory (ABRIM) project aims to add to these existing datasets by taking an adult lifespan approach to provide a cross-sectional, normative database with a particular focus on connectivity, myelinization and iron content of the brain in concurrence with cognitive functioning, mechanisms of reserve, and sleep-wake rhythms. ABRIM freely shares MRI and behavioural data from 295 participants between 18-80 years, stratified by age decade and sex (median age 52, IQR 36-66, 53.20% females). The ABRIM MRI collection consists of both the raw and pre-processed structural and functional MRI data to facilitate data usage among both expert and non-expert users. The ABRIM behavioural collection includes measures of cognitive functioning (i.e., global cognition, processing speed, executive functions, and memory), proxy measures of cognitive reserve (e.g., educational attainment, verbal intelligence, and occupational complexity), and various self-reported questionnaires (e.g., on depressive symptoms, pain, and the use of memory strategies in daily life and during a memory task). In a sub-sample (n = 120), we recorded sleep-wake rhythms using an actigraphy device (Actiwatch 2, Philips Respironics) for a period of 7 consecutive days. Here, we provide an in-depth description of our study protocol, pre-processing pipelines, and data availability. ABRIM provides a cross-sectional database on healthy participants throughout the adult lifespan, including numerous parameters relevant to improve our understanding of cognitive ageing. Therefore, ABRIM enables researchers to model the advanced imaging parameters and cognitive topologies as a function of age, identify the normal range of values of such parameters, and to further investigate the diverse mechanisms of reserve and resilience.

Diffusion Model-based FOD Restoration from High Distortion in dMRI

Fiber orientation distributions (FODs) is a popular model to represent the diffusion MRI (dMRI) data. However, imaging artifacts such as susceptibility-induced distortion in dMRI can cause signal loss and lead to the corrupted reconstruction of FODs, which prohibits successful fiber tracking and connectivity analysis in affected brain regions such as the brain stem. Generative models, such as the diffusion models, have been successfully applied in various image restoration tasks. However, their application on FOD images poses unique challenges since FODs are 4-dimensional data represented by spherical harmonics (SPHARM) with the 4-th dimension exhibiting order-related dependency. In this paper, we propose a novel diffusion model for FOD restoration that can recover the signal loss caused by distortion artifacts. We use volume-order encoding to enhance the ability of the diffusion model to generate individual FOD volumes at all SPHARM orders. Moreover, we add cross-attention features extracted across all SPHARM orders in generating every individual FOD volume to capture the order-related dependency across FOD volumes. We also condition the diffusion model with low-distortion FODs surrounding high-distortion areas to maintain the geometric coherence of the generated FODs. We trained and tested our model using data from the UK Biobank (n = 1315). On a test set with ground truth (n = 43), we demonstrate the high accuracy of the generated FODs in terms of root mean square errors of FOD volumes and angular errors of FOD peaks. We also apply our method to a test set with large distortion in the brain stem area (n = 1172) and demonstrate the efficacy of our method in restoring the FOD integrity and, hence, greatly improving tractography performance in affected brain regions.

PyHySCO: GPU-enabled susceptibility artifact distortion correction in seconds

Over the past decade, reversed gradient polarity (RGP) methods have become a popular approach for correcting susceptibility artifacts in echo-planar imaging (EPI). Although several post-processing tools for RGP are available, their implementations do not fully leverage recent hardware, algorithmic, and computational advances, leading to correction times of several minutes per image volume. To enable 3D RGP correction in seconds, we introduce PyTorch Hyperelastic Susceptibility Correction (PyHySCO), a user-friendly EPI distortion correction tool implemented in PyTorch that enables multi-threading and efficient use of graphics processing units (GPUs). PyHySCO uses a time-tested physical distortion model and mathematical formulation and is, therefore, reliable without training. An algorithmic improvement in PyHySCO is its use of the one-dimensional distortion correction method by Chang and Fitzpatrick to initialize the non-linear optimization. PyHySCO is published under the GNU public license and can be used from the command line or its Python interface. Our extensive numerical validation using 3T and 7T data from the Human Connectome Project suggests that PyHySCO can achieve accuracy comparable to that of leading RGP tools at a fraction of the cost. We also validate the new initialization scheme, compare different optimization algorithms, and test the algorithm on different hardware and arithmetic precisions.

Optimisation of quantitative brain diffusion-relaxation MRI acquisition protocols with physics-informed machine learning

Diffusion-relaxation MRI aims to extract quantitative measures that characterise microstructural tissue properties such as orientation, size, and shape, but long acquisition times are typically required. This work proposes a physics-informed learning framework to extract an optimal subset of diffusion-relaxation MRI measurements for enabling shorter acquisition times, predict non-measured signals, and estimate quantitative parameters. In vivo and synthetic brain 5D-Diffusion-T1-T2∗-weighted MRI data obtained from five healthy subjects were used for training and validation, and from a sixth participant for testing. One fully data-driven and two physics-informed machine learning methods were implemented and compared to two manual selection procedures and Cramér-Rao lower bound optimisation. The physics-informed approaches could identify measurement-subsets that yielded more consistently accurate parameter estimates in simulations than other approaches, with similar signal prediction error. Five-fold shorter protocols yielded error distributions of estimated quantitative parameters with very small effect sizes compared to estimates from the full protocol. Selected subsets commonly included a denser sampling of the shortest and longest inversion time, lowest echo time, and high b-value. The proposed framework combining machine learning and MRI physics offers a promising approach to develop shorter imaging protocols without compromising the quality of parameter estimates and signal predictions.

Exploring the Potential of Machine Learning Algorithms to Improve Diffusion Nuclear Magnetic Resonance Imaging Models Analysis

Purpose

This paper explores different machine learning (ML) algorithms for analyzing diffusion nuclear magnetic resonance imaging (dMRI) models when analytical fitting shows restrictions. It reviews various ML techniques for dMRI analysis and evaluates their performance on different b-values range datasets, comparing them with analytical methods.

Materials and Methods

After standard fitting for reference, four sets of diffusion-weighted nuclear magnetic resonance images were used to train/test various ML algorithms for prediction of diffusion coefficient (D), pseudo-diffusion coefficient (D*), perfusion fraction (f), and kurtosis (K). ML classification algorithms, including extra-tree classifier (ETC), logistic regression, C-support vector, extra-gradient boost, and multilayer perceptron (MLP), were used to determine the existence of diffusion parameters (D, D*, f, and K) within single voxels. Regression algorithms, including linear regression, polynomial regression, ridge, lasso, random forest (RF), elastic-net, and support-vector machines, were used to estimate the value of the diffusion parameters. Performance was evaluated using accuracy (ACC), area under the curve (AUC) tests, and cross-validation root mean square error (RMSECV). Computational timing was also assessed.

Results

ETC and MLP were the best classifiers, with 94.1% and 91.7%, respectively, for the ACC test and 98.7% and 96.3% for the AUC test. For parameter estimation, RF algorithm yielded the most accurate results The RMSECV percentages were: 8.39% for D, 3.57% for D*, 4.52% for f, and 3.53% for K. After the training phase, the ML methods demonstrated a substantial decrease in computational time, being approximately 232 times faster than the conventional methods.

Conclusions

The findings suggest that ML algorithms can enhance the efficiency of dMRI model analysis and offer new perspectives on the microstructural and functional organization of biological tissues. This paper also discusses the limitations and future directions of ML-based dMRI analysis.

A multimodal submillimeter MRI atlas of the human cerebellum

The human cerebellum is engaged in a broad array of tasks related to motor coordination, cognition, language, attention, memory, and emotional regulation. A detailed cerebellar atlas can facilitate the investigation of the structural and functional organization of the cerebellum. However, existing cerebellar atlases are typically limited to a single imaging modality with insufficient characterization of tissue properties. Here, we introduce a multifaceted cerebellar atlas based on high-resolution multimodal MRI, facilitating the understanding of the neurodevelopment and neurodegeneration of the cerebellum based on cortical morphology, tissue microstructure, and intra-cerebellar and cerebello-cerebral connectivity.

Comparison of distortion correction preprocessing pipelines for DTI in the upper limb

PURPOSE

DTI characterizes tissue microstructure and provides proxy measures of nerve health. Echo-planar imaging is a popular method of acquiring DTI but is susceptible to various artifacts (e.g., susceptibility, motion, and eddy currents), which may be ameliorated via preprocessing. There are many pipelines available but limited data comparing their performance, which provides the rationale for this study.

METHODS

DTI was acquired from the upper limb of heathy volunteers at 3T in blip-up and blip-down directions. Data were independently corrected using (i) FSL's TOPUP & eddy, (ii) FSL's TOPUP, (iii) DSI Studio, and (iv) TORTOISE. DTI metrics were extracted from the median, radial, and ulnar nerves and compared (between pipelines) using mixed-effects linear regression. The geometric similarity of corrected b = 0 images and the slice matched T1-weighted (T1w) images were computed using the Sörenson-Dice coefficient.

RESULTS

Without preprocessing, the similarity coefficient of the blip-up and blip-down datasets to the T1w was 0·80 and 0·79, respectively. Preprocessing improved the geometric similarity by 1% with no difference between pipelines. Compared to TOPUP & eddy, DSI Studio and TORTOISE generated 2% and 6% lower estimates of fractional anisotropy, and 6% and 13% higher estimates of radial diffusivity, respectively. Estimates of anisotropy from TOPUP & eddy versus TOPUP were not different but TOPUP reduced radial diffusivity by 3%. The agreement of DTI metrics between pipelines was poor.

CONCLUSIONS

Preprocessing DTI from the upper limb improves geometric similarity but the choice of the pipeline introduces clinically important variability in diffusion parameter estimates from peripheral nerves.

Assessment of Subject Head Motion in Diffusion MRI

Subject head motion during the acquisition of diffusion-weighted imaging (DWI) of the brain induces artifacts and affects image quality. Information about the frequency and extent of motion could reveal which aspects of motion correction are most necessary. Therefore, we investigate the extent of translation and rotation among participants, and how the motion changes during the scan acquisition. We analyze 5,380 DWI scans from 1,034 participants. We measure the rotations and translations in the sagittal, coronal and transverse planes needed to align the volumes to the first and previous volumes, as well as the displacement. The different types of motion are compared with each other and compared over time. The largest rotation (per minute) is around the right - left axis (median 0.378 °/min, range 0.000 - 11.466°) and the largest translation (per minute) is along the anterior - posterior axis (median 1.867 mm/min, range 0.000 - 10.944 mm). We additionally observe that spikes in movement occur at the beginning of the scan, particularly in anterior - posterior translation. The results show that all scans are affected by subtle head motion, which may impact subsequent image analysis.

Ultrafast diffusion tensor imaging based on deep learning and multi-slice information sharing

Objective. Diffusion tensor imaging (DTI) is excellent for non-invasively quantifying tissue microstructure. Theoretically DTI can be achieved with six different diffusion weighted images and one reference image, but the tensor estimation accuracy is poor in this case. Increasing the number of diffusion directions has benefits for the tensor estimation accuracy, which results in long scan time and makes DTI sensitive to motion. It would be beneficial to decrease the scan time of DTI by using fewer diffusion-weighted images without compromising reconstruction quality.Approach. A novel DTI scan scheme was proposed to achieve fast DTI, where only three diffusion directions per slice was required under a specific direction switching manner, and a deep-learning based reconstruction method was utilized using multi-slice information sharing and correspondingT1-weighted image for high-quality DTI reconstruction. A network with two encoders developed from U-Net was implemented for better utilizing the diffusion data redundancy between neighboring slices. The method performed direct nonlinear mapping from diffusion-weighted images to diffusion tensor.Main results. The performance of the proposed method was verified on the Human Connectome Project public data and clinical patient data. High-quality mean diffusivity, fractional anisotropy, and directionally encoded colormap can be achieved with only three diffusion directions per slice.Significance. High-quality DTI-derived maps can be achieved in less than one minute of scan time. The great reduction of scan time will help push the wider application of DTI in clinical practice.

Anti-seizure medication response and the glymphatic system in patients with focal epilepsy

BACKGROUND AND PURPOSE

We aimed to evaluate (i) glymphatic system function in patients with focal epilepsy in comparison with healthy controls, and (ii) the association between anti-seizure medication (ASM) response and glymphatic system function by using diffusion tensor image analysis along the perivascular space (DTI-ALPS).

METHODS

We retrospectively enrolled 100 patients with focal epilepsy who had normal brain magnetic resonance imaging (MRI) findings, and classified them as "poor" or "good" ASM responders according to their seizure control at the time of brain MRI. We also included 79 age- and sex-matched healthy controls. All patients and healthy controls underwent conventional brain MRI and diffusion tensor imaging. The DTI-ALPS index was calculated using the DSI studio program.

RESULTS

Of the 100 patients with focal epilepsy, 38 and 62 were poor and good ASM responders, respectively. The DTI-ALPS index differed significantly between patients with focal epilepsy and healthy controls and was significantly lower in patients with focal epilepsy (1.55 vs. 1.70; p < 0.001). The DTI-ALPS index also differed significantly according to ASM response and was lower in poor ASM responders (1.48 vs. 1.59; p = 0.047). Furthermore, the DTI-ALPS index was negatively correlated with age (r = -0.234, p = 0.019) and duration of epilepsy (r = -0.240, p = 0.016) in patients with focal epilepsy.

CONCLUSION

Our study is the first to identify, in focal epilepsy patients, a greater reduction in glymphatic system function among poor ASM responders compared to good responders. To confirm our results, further prospective multicenter studies with large sample sizes are needed.

FD-Net: An unsupervised deep forward-distortion model for susceptibility artifact correction in EPI

PURPOSE

To introduce an unsupervised deep-learning method for fast and effective correction of susceptibility artifacts in reversed phase-encode (PE) image pairs acquired with echo planar imaging (EPI).

METHODS

Recent learning-based correction approaches in EPI estimate a displacement field, unwarp the reversed-PE image pair with the estimated field, and average the unwarped pair to yield a corrected image. Unsupervised learning in these unwarping-based methods is commonly attained via a similarity constraint between the unwarped images in reversed-PE directions, neglecting consistency to the acquired EPI images. This work introduces a novel unsupervised deep Forward-Distortion Network (FD-Net) that predicts both the susceptibility-induced displacement field and the underlying anatomically correct image. Unlike previous methods, FD-Net enforces the forward-distortions of the correct image in both PE directions to be consistent with the acquired reversed-PE image pair. FD-Net further leverages a multiresolution architecture to maintain high local and global performance.

RESULTS

FD-Net performs competitively with a gold-standard reference method (TOPUP) in image quality, while enabling a leap in computational efficiency. Furthermore, FD-Net outperforms recent unwarping-based methods for unsupervised correction in terms of both image and field quality.

CONCLUSION

The unsupervised FD-Net method introduces a deep forward-distortion approach to enable fast, high-fidelity correction of susceptibility artifacts in EPI by maintaining consistency to measured data. Therefore, it holds great promise for improving the anatomical accuracy of EPI imaging.

Whole Brain and Corpus Callosum Fractional Anisotropy Differences in Patients with Cognitive Impairment

Diffusion tensor imaging (DTI) is an MRI analysis method that could help assess cognitive impairment (CI) in the ageing population more accurately. In this research, we evaluated fractional anisotropy (FA) of whole brain (WB) and corpus callosum (CC) in patients with normal cognition (NC), mild cognitive impairment (MCI), and moderate/severe cognitive impairment (SCI). In total, 41 participants were included in a cross-sectional study and divided into groups based on Montreal Cognitive Assessment (MoCA) scores (NC group, nine participants, MCI group, sixteen participants, and SCI group, sixteen participants). All participants underwent an MRI examination that included a DTI sequence. FA values between the groups were assessed by analysing FA value and age normative percentile. We did not find statistically significant differences between the groups when analysing CC FA values. Both approaches showed statistically significant differences in WB FA values between the MCI-SCI and MCI-NC groups, where the MCI group participants showed the highest mean FA and highest mean FA normative percentile results in WB.

Advanced Diffusion-Weighted MRI for Cancer Microstructure Assessment in Body Imaging, and Its Relationship With Histology

Diffusion-weighted magnetic resonance imaging (DW-MRI) aims to disentangle multiple biological signal sources in each imaging voxel, enabling the computation of innovative maps of tissue microstructure. DW-MRI model development has been dominated by brain applications. More recently, advanced methods with high fidelity to histology are gaining momentum in other contexts, for example, in oncological applications of body imaging, where new biomarkers are urgently needed. The objective of this article is to review the state-of-the-art of DW-MRI in body imaging (ie, not including the nervous system) in oncology, and to analyze its value as compared to reference colocalized histology measurements, given that demonstrating the histological validity of any new DW-MRI method is essential. In this article, we review the current landscape of DW-MRI techniques that extend standard apparent diffusion coefficient (ADC), describing their acquisition protocols, signal models, fitting settings, microstructural parameters, and relationship with histology. Preclinical, clinical, and in/ex vivo studies were included. The most used techniques were intravoxel incoherent motion (IVIM; 36.3% of used techniques), diffusion kurtosis imaging (DKI; 16.7%), vascular, extracellular, and restricted diffusion for cytometry in tumors (VERDICT; 13.3%), and imaging microstructural parameters using limited spectrally edited diffusion (IMPULSED; 11.7%). Another notable category of techniques relates to innovative b-tensor diffusion encoding or joint diffusion-relaxometry. The reviewed approaches provide histologically meaningful indices of cancer microstructure (eg, vascularization/cellularity) which, while not necessarily accurate numerically, may still provide useful sensitivity to microscopic pathological processes. Future work of the community should focus on improving the inter-/intra-scanner robustness, and on assessing histological validity in broader contexts. LEVEL OF EVIDENCE: NA TECHNICAL EFFICACY: Stage 2.

DENOISING DIFFUSION MRI: CONSIDERATIONS AND IMPLICATIONS FOR ANALYSIS

Development of diffusion MRI (dMRI) denoising approaches has experienced considerable growth over the last years. As noise can inherently reduce accuracy and precision in measurements, its effects have been well characterised both in terms of uncertainty increase in dMRI-derived features and in terms of biases caused by the noise floor, the smallest measurable signal given the noise level. However, gaps in our knowledge still exist in objectively characterising dMRI denoising approaches in terms of both of these effects and assessing their efficacy. In this work, we reconsider what a denoising method should and should not do and we accordingly define criteria to characterise the performance. We propose a comprehensive set of evaluations, including i) benefits in improving signal quality and reducing noise variance, ii) gains in reducing biases and the noise floor and improving, iii) preservation of spatial resolution, iv) agreement of denoised data against a gold standard, v) gains in downstream parameter estimation (precision and accuracy), vi) efficacy in enabling noise-prone applications, such as ultra-high-resolution imaging. We further provide newly acquired complex datasets (magnitude and phase) with multiple repeats that sample different SNR regimes to highlight performance differences under different scenarios. Without loss of generality, we subsequently apply a number of exemplar patch-based denoising algorithms to these datasets, including Non-Local Means, Marchenko-Pastur PCA (MPPCA) in the magnitude and complex domain and NORDIC, and compare them with respect to the above criteria and against a gold standard complex average of multiple repeats. We demonstrate that all tested denoising approaches reduce noise-related variance, but not always biases from the elevated noise floor. They all induce a spatial resolution penalty, but its extent can vary depending on the method and the implementation. Some denoising approaches agree with the gold standard more than others and we demonstrate challenges in even defining such a standard. Overall, we show that dMRI denoising performed in the complex domain is advantageous to magnitude domain denoising with respect to all the above criteria.

Singular vectors of sums of rectangular random matrices and optimal estimation of high-rank signals: The extensive spike model

Across many disciplines spanning from neuroscience and genomics to machine learning, atmospheric science, and finance, the problems of denoising large data matrices to recover hidden signals obscured by noise, and of estimating the structure of these signals, is of fundamental importance. A key to solving these problems lies in understanding how the singular value structure of a signal is deformed by noise. This question has been thoroughly studied in the well-known spiked matrix model, in which data matrices originate from low-rank signal matrices perturbed by additive noise matrices, in an asymptotic limit where matrix size tends to infinity but the signal rank remains finite. We first show, strikingly, that the singular value structure of large finite matrices (of size ∼1000) with even moderate-rank signals, as low as 10, is not accurately predicted by the finite-rank theory, thereby limiting the application of this theory to real data. To address these deficiencies, we analytically compute how the singular values and vectors of an arbitrary high-rank signal matrix are deformed by additive noise. We focus on an asymptotic limit corresponding to an extensive spike model, in which both the signal rank and the size of the data matrix tend to infinity at a constant ratio. We map out the phase diagram of the singular value structure of the extensive spike model as a joint function of signal strength and rank. We further exploit these analytics to derive optimal rotationally invariant denoisers to recover the hidden high-rank signal from the data, as well as optimal invariant estimators of the signal covariance structure. Our extensive-rank results yield several conceptual differences compared to the finite-rank case: (1) as signal strength increases, the singular value spectrum does not directly transition from a unimodal bulk phase to a disconnected phase, but instead there is a bimodal connected regime separating them; (2) the signal singular vectors can be partially estimated even in the unimodal bulk regime, and thus the transitions in the data singular value spectrum do not coincide with a detectability threshold for the signal singular vectors, unlike in the finite-rank theory; (3) signal singular values interact nontrivially to generate data singular values in the extensive-rank model, whereas they are noninteracting in the finite-rank theory; and (4) as a result, the more sophisticated data denoisers and signal covariance estimators we derive, which take into account these nontrivial extensive-rank interactions, significantly outperform their simpler, noninteracting, finite-rank counterparts, even on data matrices of only moderate rank. Overall, our results provide fundamental theory governing how high-dimensional signals are deformed by additive noise, together with practical formulas for optimal denoising and covariance estimation.

Automated motion artifact detection in early pediatric diffusion MRI using a convolutional neural network

Diffusion MRI (dMRI) is a widely used method to investigate the microstructure of the brain. Quality control (QC) of dMRI data is an important processing step that is performed prior to analysis using models such as diffusion tensor imaging (DTI) or neurite orientation dispersion and density imaging (NODDI). When processing dMRI data from infants and young children, where intra-scan motion is common, the identification and removal of motion artifacts is of the utmost importance. Manual QC of dMRI data is (1) time-consuming due to the large number of diffusion directions, (2) expensive, and (3) prone to subjective errors and observer variability. Prior techniques for automated dMRI QC have mostly been limited to adults or school-age children. Here, we propose a deep learning-based motion artifact detection tool for dMRI data acquired from infants and toddlers. The proposed framework uses a simple three-dimensional convolutional neural network (3DCNN) trained and tested on an early pediatric dataset of 2,276 dMRI volumes from 121 exams acquired at 1 month and 24 months of age. An average classification accuracy of 95% was achieved following four-fold cross-validation. A second dataset with different acquisition parameters and ages ranging from 2-36 months (consisting of 2,349 dMRI volumes from 26 exams) was used to test network generalizability, achieving 98% classification accuracy. Finally, to demonstrate the importance of motion artifact volume removal in a dMRI processing pipeline, the dMRI data were fit to the DTI and NODDI models and the parameter maps were compared with and without motion artifact removal.

In vivo disentanglement of diffusion frequency-dependence, tensor shape, and relaxation using multidimensional MRI

Diffusion MRI with free gradient waveforms, combined with simultaneous relaxation encoding, referred to as multidimensional MRI (MD-MRI), offers microstructural specificity in complex biological tissue. This approach delivers intravoxel information about the microstructure, local chemical composition, and importantly, how these properties are coupled within heterogeneous tissue containing multiple microenvironments. Recent theoretical advances incorporated diffusion time dependency and integrated MD-MRI with concepts from oscillating gradients. This framework probes the diffusion frequency, ω , in addition to the diffusion tensor, D , and relaxation, R 1 , R 2 , correlations. A D ( ω ) - R 1 - R 2 clinical imaging protocol was then introduced, with limited brain coverage and 3 mm3 voxel size, which hinder brain segmentation and future cohort studies. In this study, we introduce an efficient, sparse in vivo MD-MRI acquisition protocol providing whole brain coverage at 2 mm3 voxel size. We demonstrate its feasibility and robustness using a well-defined phantom and repeated scans of five healthy individuals. Additionally, we test different denoising strategies to address the sparse nature of this protocol, and show that efficient MD-MRI encoding design demands a nuanced denoising approach. The MD-MRI framework provides rich information that allows resolving the diffusion frequency dependence into intravoxel components based on their D ( ω ) - R 1 - R 2 distribution, enabling the creation of microstructure-specific maps in the human brain. Our results encourage the broader adoption and use of this new imaging approach for characterizing healthy and pathological tissues.

White matter alterations in Attention-Deficit/Hyperactivity Disorder (ADHD): a systematic review of 129 diffusion imaging studies with meta-analysis

Aberrant anatomical brain connections in attention-deficit/hyperactivity disorder (ADHD) are reported inconsistently across diffusion weighted imaging (DWI) studies. Based on a pre-registered protocol (Prospero: CRD42021259192), we searched PubMed, Ovid, and Web of Knowledge until 26/03/2022 to conduct a systematic review of DWI studies. We performed a quality assessment based on imaging acquisition, preprocessing, and analysis. Using signed differential mapping, we meta-analyzed a subset of the retrieved studies amenable to quantitative evidence synthesis, i.e., tract-based spatial statistics (TBSS) studies, in individuals of any age and, separately, in children, adults, and high-quality datasets. Finally, we conducted meta-regressions to test the effect of age, sex, and medication-naïvety. We included 129 studies (6739 ADHD participants and 6476 controls), of which 25 TBSS studies provided peak coordinates for case-control differences in fractional anisotropy (FA)(32 datasets) and 18 in mean diffusivity (MD)(23 datasets). The systematic review highlighted white matter alterations (especially reduced FA) in projection, commissural and association pathways of individuals with ADHD, which were associated with symptom severity and cognitive deficits. The meta-analysis showed a consistent reduced FA in the splenium and body of the corpus callosum, extending to the cingulum. Lower FA was related to older age, and case-control differences did not survive in the pediatric meta-analysis. About 68% of studies were of low quality, mainly due to acquisitions with non-isotropic voxels or lack of motion correction; and the sensitivity analysis in high-quality datasets yielded no significant results. Findings suggest prominent alterations in posterior interhemispheric connections subserving cognitive and motor functions affected in ADHD, although these might be influenced by non-optimal acquisition parameters/preprocessing. Absence of findings in children may be related to the late development of callosal fibers, which may enhance case-control differences in adulthood. Clinicodemographic and methodological differences were major barriers to consistency and comparability among studies, and should be addressed in future investigations.

The Challenge of Diffusion Magnetic Resonance Imaging in Cerebral Palsy: A Proposed Method to Identify White Matter Pathways

Cerebral palsy (CP), a neuromotor disorder characterized by prenatal brain lesions, leads to white matter alterations and sensorimotor deficits. However, the CP-related diffusion neuroimaging literature lacks rigorous and consensual methodology for preprocessing and analyzing data due to methodological challenges caused by the lesion extent. Advanced methods are available to reconstruct diffusion signals and can update current advances in CP. Our study demonstrates the feasibility of analyzing diffusion CP data using a standardized and open-source pipeline. Eight children with CP (8-12 years old) underwent a single diffusion magnetic resonance imaging (MRI) session on a 3T scanner (Achieva 3.0T (TX), Philips Healthcare Medical Systems, Best, The Netherlands). Exclusion criteria were contraindication to MRI and claustrophobia. Anatomical and diffusion images were acquired. Data were corrected and analyzed using Tractoflow 2.3.0 version, an open-source and robust tool. The tracts were extracted with customized procedures based on existing atlases and freely accessed standardized libraries (ANTs, Scilpy). DTI, CSD, and NODDI metrics were computed for each tract. Despite lesion heterogeneity and size, we successfully reconstructed major pathways, except for a participant with a larger lesion. Our results highlight the feasibility of identifying and quantifying subtle white matter pathways. Ultimately, this will increase our understanding of the clinical symptoms to provide precision medicine and optimize rehabilitation.

versaFlow: a versatile pipeline for resolution adapted diffusion MRI processing and its application to studying the variability of the PRIME-DE database

The lack of "gold standards" in Diffusion Weighted Imaging (DWI) makes validation cumbersome. To tackle this task, studies use translational analysis where results in humans are benchmarked against findings in other species. Non-Human Primates (NHP) are particularly interesting for this, as their cytoarchitecture is closely related to humans. However, tools used for processing and analysis must be adapted and finely tuned to work well on NHP images. Here, we propose versaFlow, a modular pipeline implemented in Nextflow, designed for robustness and scalability. The pipeline is tailored to in vivo NHP DWI at any spatial resolution; it allows for maintainability and customization. Processes and workflows are implemented using cutting-edge and state-of-the-art Magnetic Resonance Imaging (MRI) processing technologies and diffusion modeling algorithms, namely Diffusion Tensor Imaging (DTI), Constrained Spherical Deconvolution (CSD), and DIstribution of Anisotropic MicrOstructural eNvironments in Diffusion-compartment imaging (DIAMOND). Using versaFlow, we provide an in-depth study of the variability of diffusion metrics computed on 32 subjects from 3 sites of the Primate Data Exchange (PRIME-DE), which contains anatomical T1-weighted (T1w) and T2-weighted (T2w) images, functional MRI (fMRI), and DWI of NHP brains. This dataset includes images acquired over a range of resolutions, using single and multi-shell gradient samplings, on multiple scanner vendors. We perform a reproducibility study of the processing of versaFlow using the Aix-Marseilles site's data, to ensure that our implementation has minimal impact on the variability observed in subsequent analyses. We report very high reproducibility for the majority of metrics; only gamma distribution parameters of DIAMOND display less reproducible behaviors, due to the absence of a mechanism to enforce a random number seed in the software we used. This should be taken into consideration when future applications are performed. We show that the PRIME-DE diffusion data exhibits a great level of variability, similar or greater than results obtained in human studies. Its usage should be done carefully to prevent instilling uncertainty in statistical analyses. This hints at a need for sufficient harmonization in acquisition protocols and for the development of robust algorithms capable of managing the variability induced in imaging due to differences in scanner models and/or vendors.

Evaluation of motion artefact reduction depending on the artefacts' directions in head MRI using conditional generative adversarial networks

Motion artefacts caused by the patient's body movements affect magnetic resonance imaging (MRI) accuracy. This study aimed to compare and evaluate the accuracy of motion artefacts correction using a conditional generative adversarial network (CGAN) with an autoencoder and U-net models. The training dataset consisted of motion artefacts generated through simulations. Motion artefacts occur in the phase encoding direction, which is set to either the horizontal or vertical direction of the image. To create T2-weighted axial images with simulated motion artefacts, 5500 head images were used in each direction. Of these data, 90% were used for training, while the remainder were used for the evaluation of image quality. Moreover, the validation data used in the model training consisted of 10% of the training dataset. The training data were divided into horizontal and vertical directions of motion artefact appearance, and the effect of combining this data with the training dataset was verified. The resulting corrected images were evaluated using structural image similarity (SSIM) and peak signal-to-noise ratio (PSNR), and the metrics were compared with the images without motion artefacts. The best improvements in the SSIM and PSNR were observed in the consistent condition in the direction of the occurrence of motion artefacts in the training and evaluation datasets. However, SSIM > 0.9 and PSNR > 29 dB were accomplished for the learning model with both image directions. The latter model exhibited the highest robustness for actual patient motion in head MRI images. Moreover, the image quality of the corrected image with the CGAN was the closest to that of the original image, while the improvement rates for SSIM and PSNR were approximately 26% and 7.7%, respectively. The CGAN model demonstrated a high image reproducibility, and the most significant model was the consistent condition of the learning model and the direction of the appearance of motion artefacts.

Reproducible Tract Profiles 2 (RTP2) suite, from diffusion MRI acquisition to clinical practice and research

Diffusion MRI is a complex technique, where new discoveries and implementations occur at a fast pace. The expertise needed for data analyses and accurate and reproducible results is increasingly demanding and requires multidisciplinary collaborations. In the present work we introduce Reproducible Tract Profiles 2 (RTP2), a set of flexible and automated methods to analyze anatomical MRI and diffusion weighted imaging (DWI) data for reproducible tractography. RTP2 reads structural MRI data and processes them through a succession of serialized containerized analyses. We describe the DWI algorithms used to identify white-matter tracts and their summary metrics, the flexible architecture of the platform, and the tools to programmatically access and control the computations. The combination of these three components provides an easy-to-use automatized tool developed and tested over 20 years, to obtain usable and reliable state-of-the-art diffusion metrics at the individual and group levels for basic research and clinical practice.

Integrated diffusion image operator (iDIO): A pipeline for automated configuration and processing of diffusion MRI data

The preprocessing of diffusion magnetic resonance imaging (dMRI) data involve numerous steps, including the corrections for head motion, susceptibility distortion, low signal-to-noise ratio, and signal drifting. Researchers or clinical practitioners often need to configure different preprocessing steps depending on disparate image acquisition schemes, which increases the technical threshold for dMRI analysis for nonexpert users. This could cause disparities in data processing approaches and thus hinder the comparability between studies. To make the dMRI data processing steps transparent and adapt to various dMRI acquisition schemes for researchers, we propose a semi-automated pipeline tool for dMRI named integrated diffusion image operator or iDIO. This pipeline integrates features from a wide range of advanced dMRI software tools and targets at providing a one-click solution for dMRI data analysis, via adaptive configuration for a set of suggested processing steps based on the image header of the input data. Additionally, the pipeline provides options for post-processing, such as estimation of diffusion tensor metrics and whole-brain tractography-based connectomes reconstruction using common brain atlases. The iDIO pipeline also outputs an easy-to-interpret quality control report to facilitate users to assess the data quality. To keep the transparency of data processing, the execution log and all the intermediate images produced in the iDIO's workflow are accessible. The goal of iDIO is to reduce the barriers for clinical or nonspecialist users to adopt the state-of-art dMRI processing steps.

Exercise as therapy for neurodevelopmental and cognitive dysfunction in people with a Fontan circulation: A narrative review

People with a Fontan circulation are at risk of neurodevelopmental delay and disability, and cognitive dysfunction, that has significant implications for academic and occupational attainment, psychosocial functioning, and overall quality of life. Interventions for improving these outcomes are lacking. This review article discusses current intervention practices and explores the evidence supporting exercise as a potential intervention for improving cognitive functioning in people living with a Fontan circulation. Proposed pathophysiological mechanisms underpinning these associations are discussed in the context of Fontan physiology and avenues for future research are recommended.

Advanced spinal cord MRI in multiple sclerosis: Current techniques and future directions

Spinal cord magnetic resonance imaging (MRI) has a central role in multiple sclerosis (MS) clinical practice for diagnosis and disease monitoring. Advanced MRI sequences capable of visualizing and quantifying tissue macro- and microstructure and reflecting different pathological disease processes have been used in MS research; however, the spinal cord remains under-explored, partly due to technical obstacles inherent to imaging this structure. We propose that the study of the spinal cord merits equal ambition in overcoming technical challenges, and that there is much information to be exploited to make valuable contributions to our understanding of MS. We present a narrative review on the latest progress in advanced spinal cord MRI in MS, covering in the first part structural, functional, metabolic and vascular imaging methods. We focus on recent studies of MS and those making significant technical steps, noting the challenges that remain to be addressed and what stands to be gained from such advances. Throughout we also refer to other works that presend more in-depth review on specific themes. In the second part, we present several topics that, in our view, hold particular potential. The need for better imaging of gray matter is discussed. We stress the importance of developing imaging beyond the cervical spinal cord, and explore the use of ultra-high field MRI. Finally, some recommendations are given for future research, from study design to newer developments in analysis, and the need for harmonization of sequences and methods within the field. This review is aimed at researchers and clinicians with an interest in gaining an overview of the current state of advanced MRI research in this field and what is primed to be the future of spinal cord imaging in MS research.

Diffusion tensor imaging pipeline measures of cerebral white matter integrity: An overview of recent advances and prospects

Cerebral small vessel disease (CSVD) is a leading cause of age-related microvascular cognitive decline, resulting in significant morbidity and decreased quality of life. Despite a progress on its key pathophysiological bases and general acceptance of key terms from neuroimaging findings as observed on the magnetic resonance imaging (MRI), key questions on CSVD remain elusive. Enhanced relationships and reliable lesion studies, such as white matter tractography using diffusion-based MRI (dMRI) are necessary in order to improve the assessment of white matter architecture and connectivity in CSVD. Diffusion tensor imaging (DTI) and tractography is an application of dMRI that provides data that can be used to non-invasively appraise the brain white matter connections via fiber tracking and enable visualization of individual patient-specific white matter fiber tracts to reflect the extent of CSVD-associated white matter damage. However, due to a lack of standardization on various sets of software or image pipeline processing utilized in this technique that driven mostly from research setting, interpreting the findings remain contentious, especially to inform an improved diagnosis and/or prognosis of CSVD for routine clinical use. In this minireview, we highlight the advances in DTI pipeline processing and the prospect of this DTI metrics as potential imaging biomarker for CSVD, even for subclinical CSVD in at-risk individuals.

Nonparametric 5D D-R2 distribution imaging with single-shot EPI at 21.1 T: Initial results for in vivo rat brain

In vivo human diffusion MRI is by default performed using single-shot EPI with greater than 50-ms echo times and associated signal loss from transverse relaxation. The individual benefits of the current trends of increasing B0 to boost SNR and employing more advanced signal preparation schemes to improve the specificity for selected microstructural properties eventually may be cancelled by increased relaxation rates at high B0 and echo times with advanced encoding. Here, initial attempts to translate state-of-the-art diffusion-relaxation correlation methods from 3 T to 21.1 T are made to identify hurdles that need to be overcome to fulfill the promises of both high SNR and readily interpretable microstructural information.

Mapping the human connectome using diffusion MRI at 300 mT/m gradient strength: Methodological advances and scientific impact

Tremendous efforts have been made in the last decade to advance cutting-edge MRI technology in pursuit of mapping structural connectivity in the living human brain with unprecedented sensitivity and speed. The first Connectom 3T MRI scanner equipped with a 300 mT/m whole-body gradient system was installed at the Massachusetts General Hospital in 2011 and was specifically constructed as part of the Human Connectome Project. Since that time, numerous technological advances have been made to enable the broader use of the Connectom high gradient system for diffusion tractography and tissue microstructure studies and leverage its unique advantages and sensitivity to resolving macroscopic and microscopic structural information in neural tissue for clinical and neuroscientific studies. The goal of this review article is to summarize the technical developments that have emerged in the last decade to support and promote large-scale and scientific studies of the human brain using the Connectom scanner. We provide a brief historical perspective on the development of Connectom gradient technology and the efforts that led to the installation of three other Connectom 3T MRI scanners worldwide - one in the United Kingdom in Cardiff, Wales, another in continental Europe in Leipzig, Germany, and the latest in Asia in Shanghai, China. We summarize the key developments in gradient hardware and image acquisition technology that have formed the backbone of Connectom-related research efforts, including the rich array of high-sensitivity receiver coils, pulse sequences, image artifact correction strategies and data preprocessing methods needed to optimize the quality of high-gradient strength diffusion MRI data for subsequent analyses. Finally, we review the scientific impact of the Connectom MRI scanner, including advances in diffusion tractography, tissue microstructural imaging, ex vivo validation, and clinical investigations that have been enabled by Connectom technology. We conclude with brief insights into the unique value of strong gradients for diffusion MRI and where the field is headed in the coming years.

Diffusion Kurtosis Imaging of Neonatal Spinal Cord in Clinical Routine

Diffusion kurtosis imaging (DKI) has undisputed advantages over the more classical diffusion magnetic resonance imaging (dMRI) as witnessed by the fast-increasing number of clinical applications and software packages widely adopted in brain imaging. However, in the neonatal setting, DKI is still largely underutilized, in particular in spinal cord (SC) imaging, because of its inherently demanding technological requirements. Due to its extreme sensitivity to non-Gaussian diffusion, DKI proves particularly suitable for detecting complex, subtle, fast microstructural changes occurring in this area at this early and critical stage of development, which are not identifiable with only DTI. Given the multiplicity of congenital anomalies of the spinal canal, their crucial effect on later developmental outcome, and the close interconnection between the SC region and the brain above, managing to apply such a method to the neonatal cohort becomes of utmost importance. This study will (i) mention current methodological challenges associated with the application of advanced dMRI methods, like DKI, in early infancy, (ii) illustrate the first semi-automated pipeline built on Spinal Cord Toolbox for handling the DKI data of neonatal SC, from acquisition setting to estimation of diffusion measures, through accurate adjustment of processing algorithms customized for adult SC, and (iii) present results of its application in a pilot clinical case study. With the proposed pipeline, we preliminarily show that DKI is more sensitive than DTI-related measures to alterations caused by brain white matter injuries in the underlying cervical SC.