Quantitative assessment of the susceptibility artefact and its interaction with motion in diffusion MRI

Evaluation of microstructural changes in the brain in transfusion dependent thalassemia patients with advanced magnetic resonance imaging techniques

PURPOSE

Transfusion-dependent thalassemia (TDT) is associated with iron accumulation in the body and an increased tendency for thrombosis. With the increased life expectancy in these patients, the detection of neurocognitive complications has gained importance. This study investigates the microstructural changes in TDT patients using advanced diffusion MRI techniques and their relationship with laboratory parameters.

METHODS

The study included 14 TDT patients and 14 control subjects. Tract-based spatial statistics (TBSS) were used to examine differences in DTI parameters such as fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (AD), and radial diffusivity (RD) in thalassemia patients using multi-shell DWI images. The mean kurtosis (MK) difference was investigated using diffusion kurtosis imaging. Fiber density (FD), fiber cross-section (FC), and fiber density and cross-section (FDC) differences were examined using fixel-based analysis. In the patient group, correlative tractography was used to investigate the relationship between DTI parameters and platelet (PLT) and ferritin levels.

RESULTS

Increase in RD and MD was observed, particularly in the white matter tracts of the corona radiata in patient group. Additionally, an increase in AD was detected in a limited area. Correlative tractography in thalasemia patients showed a positive correlation between increases in RD, MD, and AD with PLT and ferritin. Fixel-based analysis demonstrated a dispersed distribution in white matter fibers, with a more pronounced decrease in FD, FC, and FDC in the internal capsule.

CONCLUSION

There is widespread involvement in the white matter and fiber tracts in thalassemia patients, which is highly correlated with thrombotic parameters.

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.

Cortical Macro- and Microstructural Changes in Parkinson's Disease with Probable Rapid Eye Movement Sleep Behavior Disorder

BACKGROUND

Evidence regarding cortical atrophy patterns in Parkinson's disease (PD) with probable rapid eye movement sleep behavior disorder (RBD) (PD-pRBD) remains scarce. Cortical mean diffusivity (cMD), as a novel imaging biomarker highly sensitive to detecting cortical microstructural changes in different neurodegenerative diseases, has not been investigated in PD-pRBD yet.

OBJECTIVES

The aim was to investigate cMD as a sensitive measure to identify subtle cortical microstructural changes in PD-pRBD and its relationship with cortical thickness (CTh).

METHODS

Twenty-two PD-pRBD, 31 PD without probable RBD (PD-nonpRBD), and 28 healthy controls (HC) were assessed using 3D T1-weighted and diffusion-weighted magnetic resonance imaging on a 3-T scanner and neuropsychological testing. Measures of cortical brain changes were obtained through cMD and CTh. Two-class group comparisons of a general linear model were performed (P < 0.05). Cohen's d effect size for both approaches was computed.

RESULTS

PD-pRBD patients showed higher cMD than PD-nonpRBD patients in the left superior temporal, superior frontal, and precentral gyri, precuneus cortex, as well as in the right middle frontal and postcentral gyri and paracentral lobule (d > 0.8), whereas CTh did not detect significant differences. PD-pRBD patients also showed increased bilateral posterior cMD in comparison with HCs (d > 0.8). These results partially overlapped with CTh results (0.5 < d < 0.8). PD-nonpRBD patients showed no differences in cMD when compared with HCs but showed cortical thinning in the left fusiform gyrus and lateral occipital cortex bilaterally (d > 0.5).

CONCLUSIONS

cMD may be more sensitive than CTh displaying significant cortico-structural differences between PD subgroups, indicating this imaging biomarker's utility in studying early cortical changes in PD. © 2024 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.

Assessing interstitial fluid dynamics in type 2 diabetes mellitus and prediabetes cases through diffusion tensor imaging analysis along the perivascular space

Background and purpose

Glymphatic system in type 2 diabetes mellitus (T2DM) but not in the prodrome, prediabetes (Pre-DM) was investigated using diffusion tensor image analysis along the perivascular space (DTI-ALPS). Association between glymphatic system and insulin resistance of prominent characteristic in T2DM and Pre-DM between is yet elucidated. Therefore, this study delves into the interstitial fluid dynamics using the DTI-ALPS in both Pre-DM and T2DM and association with insulin resistance.

Materials and methods

In our cross-sectional study, we assessed 70 elderly individuals from the Bunkyo Health Study, which included 22 with Pre-DM, 18 with T2DM, and 33 healthy controls with normal glucose metabolism (NGM). We utilized the general linear model (GLM) to evaluate the ALPS index based on DTI-ALPS across these groups, considering variables like sex, age, intracranial volume, years of education, anamnesis of hypertension and hyperlipidemia, and the total Fazekas scale. Furthermore, we have explored the relationship between the ALPS index and insulin resistance, as measured by the homeostasis model assessment of insulin resistance (HOMA-IR) using GLM and the same set of covariates.

Results

In the T2DM group, the ALPS index demonstrated a reduction compared with the NGM group [family-wise error (FWE)-corrected p < 0.001; Cohen's d = -1.32]. Similarly, the Pre-DM group had a lower ALPS index than the NGM group (FWE-corrected p < 0.001; Cohen's d = -1.04). However, there was no significant disparity between the T2DM and Pre-DM groups (FWE-corrected p = 1.00; Cohen's d = -0.63). A negative correlation was observed between the ALPS index and HOMA-IR in the combined T2DM and Pre-DM groups (partial correlation coefficient r = -0.35, p < 0.005).

Conclusion

The ALPS index significantly decreased in both the pre-DM and T2DM groups and showed a correlated with insulin resistance. This indicated that changes in interstitial fluid dynamics are associated with insulin resistance.

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.

Divergence time estimates for the hypoxia-inducible factor-1 alpha (HIF1α) reveal an ancient emergence of animals in low-oxygen environments

Unveiling the tempo and mode of animal evolution is necessary to understand the links between environmental changes and biological innovation. Although the earliest unambiguous metazoan fossils date to the late Ediacaran period, molecular clock estimates agree that the last common ancestor (LCA) of all extant animals emerged ~850 Ma, in the Tonian period, before the oldest evidence for widespread ocean oxygenation at ~635-560 Ma in the Ediacaran period. Metazoans are aerobic organisms, that is, they are dependent on oxygen to survive. In low-oxygen conditions, most animals have an evolutionarily conserved pathway for maintaining oxygen homeostasis that triggers physiological changes in gene expression via the hypoxia-inducible factor (HIFa). However, here we confirm the absence of the characteristic HIFa protein domain responsible for the oxygen sensing of HIFa in sponges and ctenophores, indicating the LCA of metazoans lacked the functional protein domain as well, and so could have maintained their transcription levels unaltered under the very low-oxygen concentrations of their environments. Using Bayesian relaxed molecular clock dating, we inferred that the ancestral gene lineage responsible for HIFa arose in the Mesoproterozoic Era, ~1273 Ma (Credibility Interval 957-1621 Ma), consistent with the idea that important genetic machinery associated with animals evolved much earlier than the LCA of animals. Our data suggest at least two duplication events in the evolutionary history of HIFa, which generated three vertebrate paralogs, products of the two successive whole-genome duplications that occurred in the vertebrate LCA. Overall, our results support the hypothesis of a pre-Tonian emergence of metazoans under low-oxygen conditions, and an increase in oxygen response elements during animal evolution.

Exercise habits and mental health: Exploring the significance of multimodal imaging markers

Engaging in regular physical activity and establishing exercise habits is known to have multifaceted benefits extending beyond physical health to cognitive and mental well-being. This study explores the intricate relationship between exercise habits, brain imaging markers, and mental health outcomes. While extensive evidence supports the positive impact of exercise on cognitive functions and mental health, recent advancements in multimodal imaging techniques provide a new dimension to this exploration. By using a cross-sectional multimodal brain-behavior statistic in participants with different exercise habits, we aim to unveil the intricate mechanisms underlying exercise's influence on cognition and mental health, including the status of depression, anxiety, and quality of life. This integration of exercise science and imaging promises to substantiate cognitive benefits on mental health and uncover functional and structural changes underpinning these effects. This study embarks on a journey to explore the significance of multimodal imaging metrics (i.e., structural and functional metrics) in deciphering the intricate interplay between exercise habits and mental health, enhancing the comprehension of how exercise profoundly shapes psychological well-being. Our analysis of group comparisons uncovered a strong association between regular exercise habits and improved mental well-being, encompassing factors such as depression, anxiety levels, and overall life satisfaction. Additionally, individuals who engaged in exercise displayed enhanced brain metrics across different modalities. These metrics encompassed greater gray matter volume within the left frontal regions and hippocampus, improved white matter integrity in the frontal-occipital fasciculus, as well as more robust functional network configurations in the anterior segments of the default mode network. The interplay between exercise habits, brain adaptations, and mental health outcomes underscores the pivotal role of an active lifestyle in nurturing a resilient and high-functioning brain, thus paving the way for tailored interventions and improved well-being.

Framewise multi-echo distortion correction for superior functional MRI

Functional MRI (fMRI) data are severely distorted by magnetic field (B0) inhomogeneities which currently must be corrected using separately acquired field map data. However, changes in the head position of a scanning participant across fMRI frames can cause changes in the B0 field, preventing accurate correction of geometric distortions. Additionally, field maps can be corrupted by movement during their acquisition, preventing distortion correction altogether. In this study, we use phase information from multi-echo (ME) fMRI data to dynamically sample distortion due to fluctuating B0 field inhomogeneity across frames by acquiring multiple echoes during a single EPI readout. Our distortion correction approach, MEDIC (Multi-Echo DIstortion Correction), accurately estimates B0 related distortions for each frame of multi-echo fMRI data. Here, we demonstrate that MEDIC's framewise distortion correction produces improved alignment to anatomy and decreases the impact of head motion on resting-state functional connectivity (RSFC) maps, in higher motion data, when compared to the prior gold standard approach (i.e., TOPUP). Enhanced framewise distortion correction with MEDIC, without the requirement for field map collection, furthers the advantage of multi-echo over single-echo fMRI.

Glymphatic system impairment in corticobasal syndrome: diffusion tensor image analysis along the perivascular space (DTI-ALPS)

PURPOSE

This study aimed to evaluate the along the perivascular space (ALPS) index based on the diffusion tensor image ALPS (DTI-ALPS) in corticobasal degeneration with corticobasal syndrome (CBD-CBS) and investigate its correlation with motor and cognitive functions.

MATERIALS AND METHODS

The data of 21 patients with CBD-CBS and 17 healthy controls (HCs) were obtained from the 4-Repeat Tauopathy Neuroimaging Initiative and the Frontotemporal Lobar Degeneration Neuroimaging Initiative databases. Diffusion magnetic resonance imaging was performed using a 3-Tesla MRI scanner. The ALPS index based on DTI-ALPS was automatically calculated after preprocessing. The ALPS index was compared between the CBD-CBS and HC groups via a general linear model analysis, with covariates such as age, sex, years of education, and intracranial volume (ICV). Furthermore, to confirm the relation between the ALPS index and the motor and cognitive score in CBD-CBS, the partial Spearman's rank correlation coefficient was calculated with covariates such as age, sex, years of education, and ICV. A p value of < 0.05 was considered as statistically significant in all statistical analyses.

RESULTS

The ALPS index of CBD-CBS was significantly lower than that of HC (Cohen's d =  - 1.53, p < 0.005). Moreover, the ALPS index had a significant positive correlation with the mini mental state evaluation score (rs = 0.65, p < 0.005) and a significant negative correlation with the unified Parkinson's Disease Rating Scale III score (rs =  - 0.75, p < 0.001).

CONCLUSION

The ALPS index of patients with CBD-CBS, which is significantly lower than that of HCs, is significantly associated with motor and cognitive functions.

Improved dynamic distortion correction for fMRI using single-echo EPI and a readout-reversed first image (REFILL)

The boundaries between tissues with different magnetic susceptibilities generate inhomogeneities in the main magnetic field which change over time due to motion, respiration and system instabilities. The dynamically changing field can be measured from the phase of the fMRI data and corrected. However, methods for doing so need multi-echo data, time-consuming reference scans and/or involve error-prone processing steps, such as phase unwrapping, which are difficult to implement robustly on the MRI host. The improved dynamic distortion correction method we propose is based on the phase of the single-echo EPI data acquired for fMRI, phase offsets calculated from a triple-echo, bipolar reference scan of circa 3-10 s duration using a method which avoids the need for phase unwrapping and an additional correction derived from one EPI volume in which the readout direction is reversed. This Reverse-Encoded First Image and Low resoLution reference scan (REFILL) approach is shown to accurately measure B0 as it changes due to shim, motion and respiration, even with large dynamic changes to the field at 7 T, where it led to a > 20% increase in time-series signal to noise ratio compared to data corrected with the classic static approach. fMRI results from REFILL-corrected data were free of stimulus-correlated distortion artefacts seen when data were corrected with static field mapping. The method is insensitive to shim changes and eddy current differences between the reference scan and the fMRI time series, and employs calculation steps that are simple and robust, allowing most data processing to be performed in real time on the scanner image reconstruction computer. These improvements make it feasible to routinely perform dynamic distortion correction in fMRI.

Multisite harmonization of diffusion tensor image analysis along the perivascular space using the COMBined Association Test

PURPOSE

This multisite study aimed to use the COMBined Association Test (COMBAT), a harmonization technique that uses regression of covariates with an empirical Bayesian framework, to harmonize diffusion tensor image analysis along the perivascular space (DTI-ALPS) variations caused by scanner, site, and protocol differences.

MATERIALS AND METHODS

This study included multisite diffusion magnetic resonance imaging (dMRI) data of 45 patients with Alzheimer's disease (AD) and 82 cognitively normal (CN) participants from the AD neuroimaging initiative database. The dMRI data were obtained with two b values (0 and 1000 s/mm2) from 27 institutions and three different 3-Tesla MRI scanners (two vendors). The ALPS index was calculated from multisite dMRI data, and COMBAT was used to harmonize the factors causing site variations. Welch's t test was used, Cohen's d was calculated to compare the difference in the ALPS index between AD and CN before and after harmonization, and Pearson's correlation coefficient was calculated to assess the relationships between the ALPS index and the cognitive score, [18F] fluorodeoxyglucose (FDG)-positron emission tomography (PET), and [18F] florbetapir (AV45)-PET standardized uptake value ratios (SUVRs).

RESULTS

COMBAT harmonized scanner differences and increased Cohen's d of the left and right ALPS indexes between AD and CN from 0.288 to 0.438 and 0.328 to 0.480, respectively. The ALPS indexes were significantly different between AD and CN after harmonization (P < 0.05) but not before it. Moreover, Pearson's correlation coefficients between the ALPS index and cognitive score, FDG-PET, and AV45-PET SUVRs were higher after harmonization than before it.

CONCLUSION

This study demonstrates the application of COMBAT harmonization to eliminate between-scanner, site, and protocol variations in the ALPS index calculated from DTI-ALPS using dMRI and possibly facilitate the use of the ALPS index in multi-center studies.

Reproducibility of automated calculation technique for diffusion tensor image analysis along the perivascular space

PURPOSE

The method of diffusion tensor image analysis along the perivascular space (DTI-ALPS) was gathering attention to evaluate the brain's glymphatic function or interstitial fluid dynamics. However, to the best knowledge, no study was conducted on the reproducibility of these automated methods for ALPS index values. Therefore, the current study evaluated the ALPS index reproducibility based on DTI-ALPS using two major automated calculation techniques in scan and rescan of the same subject on the same day.

MATERIALS AND METHODS

This study included 23 participants, including 2 with Alzheimer's disease, 15 with mild cognitive impairment, and 6 with cognitive normals. Scan and rescan data of diffusion magnetic resonance images were obtained, as well as automatically index for ALPS (ALPS index) and ALPS index maintaining tensor vector orientation information (vALPS index) with region of interest on the template fractional anisotropy map calculated by FSL software.These ALPS indices were compared in terms of scan and rescan reproducibility.

RESULTS

The absolute difference in ALPS-index values between scan and rescan was larger in the ALPS index than in the vALPS index by approximately 0.6% as the relative difference. Cohen's d for the left and right ALPS indices between methods were 0.121 and 0.159, respectively.

CONCLUSION

The vALPS index based on DTI-ALPS maintaining tensor vector orientation information has higher reproducibility than the ALPS index. This result encourages a multisite study on the ALPS index with a large sample size and helps detect a subtle pathological change in the ALPS index.

Impact of susceptibility-induced distortion correction on perfusion imaging by pCASL with a segmented 3D GRASE readout

PURPOSE

The consensus for the clinical implementation of arterial spin labeling (ASL) perfusion imaging recommends a segmented 3D Gradient and Spin-Echo (GRASE) readout for optimal signal-to-noise-ratio(SNR). The correction of the associated susceptibility-induced geometric distortions has been shown to improve diagnostic precision, but its impact on ASL data has not been systematically assessed and it is not consistently part of pre-processing pipelines. Here, we investigate the effects of susceptibility-induced distortion correction on perfusion imaging by pseudo-continuous ASL (pCASL) with a segmented 3D GRASE readout.

METHODS

Data acquired from 28 women using pCASL with 3D GRASE at 3T was analyzed using three pre-processing options: without distortion correction, with distortion correction, and with spatial smoothing (without distortion correction) matched to control for blurring effects induced by distortion correction. Maps of temporal SNR (tSNR) and relative perfusion were analyzed in eight regions-of-interest (ROIs) across the brain.

RESULTS

Distortion correction significantly affected tSNR and relative perfusion across the brain. Increases in tSNR were like those produced by matched spatial smoothing in most ROIs, indicating that they were likely due to blurring effects. However, that was not the case in the frontal and temporal lobes, where we also found increased relative perfusion with distortion correction even compared with matched spatial smoothing. These effects were found in both controls and patients, with no interactions with the participant group.

CONCLUSION

Correction of Susceptibility-induced distortions significantly impacts ASL perfusion imaging using a segmented 3D GRASE readout, and this step should therefore be considered in ASL pre-processing pipelines. This is of special importance in clinical studies, reporting perfusion across ROIs defined on relatively undistorted images and when conducting group analyses requiring the alignment of images across different subjects.

Using synthetic MR images for distortion correction

Functional MRI (fMRI) data acquired using echo-planar imaging (EPI) are highly distorted by magnetic field inhomogeneities. Distortion and differences in image contrast between EPI and T1-weighted and T2-weighted (T1w/T2w) images makes their alignment a challenge. Typically, field map data are used to correct EPI distortions. Alignments achieved with field maps can vary greatly and depends on the quality of field map data. However, many public datasets lack field map data entirely. Additionally, reliable field map data is often difficult to acquire in high-motion pediatric or developmental cohorts. To address this, we developed Synth, a software package for distortion correction and cross-modal image registration that does not require field map data. Synth combines information from T1w and T2w anatomical images to construct an idealized undistorted synthetic image with similar contrast properties to EPI data. This synthetic image acts as an effective reference for individual-specific distortion correction. Using pediatric (ABCD: Adolescent Brain Cognitive Development) and adult (MSC: Midnight Scan Club; HCP: Human Connectome Project) data, we demonstrate that Synth performs comparably to field map distortion correction approaches, and often outperforms them. Field map-less distortion correction with Synth allows accurate and precise registration of fMRI data with missing or corrupted field map information.

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.

Connectomic Basis for Tremor Control in Stereotactic Radiosurgical Thalamotomy

BACKGROUND AND PURPOSE

Given the increased use of stereotactic radiosurgical thalamotomy and other ablative therapies for tremor, new biomarkers are needed to improve outcomes. Using resting-state fMRI and MR tractography, we hypothesized that a "connectome fingerprint" can predict tremor outcomes and potentially serve as a targeting biomarker for stereotactic radiosurgical thalamotomy.

MATERIALS AND METHODS

We evaluated 27 patients who underwent unilateral stereotactic radiosurgical thalamotomy for essential tremor or tremor-predominant Parkinson disease. Percentage postoperative improvement in the contralateral limb Fahn-Tolosa-Marin Clinical Tremor Rating Scale (TRS) was the primary end point. Connectome-style resting-state fMRI and MR tractography were performed before stereotactic radiosurgery. Using the final lesion volume as a seed, "connectivity fingerprints" representing ideal connectivity maps were generated as whole-brain R-maps using a voxelwise nonparametric Spearman correlation. A leave-one-out cross-validation was performed using the generated R-maps.

RESULTS

The mean improvement in the contralateral tremor score was 55.1% (SD, 38.9%) at a mean follow-up of 10.0 (SD, 5.0) months. Structural connectivity correlated with contralateral TRS improvement (r = 0.52; P  = .006) and explained 27.0% of the variance in outcome. Functional connectivity correlated with contralateral TRS improvement (r = 0.50; P  = .008) and explained 25.0% of the variance in outcome. Nodes most correlated with tremor improvement corresponded to areas of known network dysfunction in tremor, including the cerebello-thalamo-cortical pathway and the primary and extrastriate visual cortices.

CONCLUSIONS

Stereotactic radiosurgical targets with a distinct connectivity profile predict improvement in tremor after treatment. Such connectomic fingerprints show promise for developing patient-specific biomarkers to guide therapy with stereotactic radiosurgical thalamotomy.

SEMAC + VAT for Suppression of Artifacts Induced by Dental-Implant-Supported Restorations in Magnetic Resonance Imaging

The purpose of this study was to assess the feasibility of SEMAC + VAT to reduce artifacts induced by dental implant-supported restorations, such as its impact on the image quality. Dental-implant supported restorations were installed in a dry mandible. Magnetic resonance scans were acquired on a 3-Tesla MRI system. Artifact suppression (SEMAC + VAT) was applied with different intensity modes (weak, moderate, strong). Artifacts assessment was performed by measuring the mandible volume increase in MRI images prior (reference dataset) and after installation of dental implant-supported prosthesis. Image quality was assessed by two examiners using a five-point scale. Inter-examiner concordance and correlation analysis was performed with Cronbach's alpha and Spearman's test with a significance level at p = 0.05. Mandible volume increased by 60.23% when no artifact suppression method was used. By applying SEMAC + VAT, the volume increase ranged from 17.13% (strong mode) to 32.77% (weak mode). Visualization of mandibular bone was positively correlated with SEMAC intensity degree. SEMAC + VAT reduced MRI artifacts caused by dental-implant supported restorations. A stronger suppression mode improved visualization of mandibular bone in detriment of the scanning time.

BundleWarp, streamline-based nonlinear registration of white matter tracts

Nonlinear registration plays a central role in most neuroimage analysis methods and pipelines, such as in tractography-based individual and group-level analysis methods. However, nonlinear registration is a non-trivial task, especially when dealing with tractography data that digitally represent the underlying anatomy of the brain's white matter. Furthermore, such process often changes the structure of the data, causing artifacts that can suppress the underlying anatomical and structural details. In this paper, we introduce BundleWarp, a novel and robust streamline-based nonlinear registration method for the registration of white matter tracts. BundleWarp intelligently warps two bundles while preserving the bundles' crucial topological features. BundleWarp has two main steps. The first step involves the solution of an assignment problem that matches corresponding streamlines from the two bundles (iterLAP step). The second step introduces streamline-specific point-based deformations while keeping the topology of the bundle intact (mlCPD step). We provide comparisons against streamline-based linear registration and image-based nonlinear registration methods. BundleWarp quantitatively and qualitatively outperforms both, and we show that BundleWarp can deform and, at the same time, preserve important characteristics of the original anatomical shape of the bundles. Results are shown on 1,728 pairs of bundle registrations across 27 different bundle types. In addition, we present an application of BundleWarp for quantifying bundle shape differences using the generated deformation fields.

Automatic bundle-specific white matter fiber tracking tool using diffusion tensor imaging data: A pilot trial in the application of language-related glioma resection

Cerebral neoplasms like gliomas may cause intracranial pressure increasing, neural tract deviation, infiltration, or destruction in peritumoral areas, leading to neuro-functional deficits. Novel tracking technology, such as DTI, can objectively reveal and visualize three-dimensional white matter trajectories; in combination with intraoperative navigation, it can help achieve maximum resection whilst minimizing neurological deficit. Since the reconstruction of DTI raw data largely relies on the technical engineering and anatomical experience of the operator; it is time-consuming and prone to operator-induced bias. Here, we develop new user-friendly software to automatically segment and reconstruct functionally active areas to facilitate precise surgery. In this pilot trial, we used an in-house developed software (DiffusionGo) specially designed for neurosurgeons, which integrated a reliable diffusion-weighted image (DWI) preprocessing pipeline that embedded several functionalities from software packages of FSL, MRtrix3, and ANTs. The preprocessing pipeline is as follows: 1. DWI denoising, 2. Gibbs-ringing removing, 3. Susceptibility distortion correction (process if opposite polarity data were acquired), 4. Eddy current and motion correction, and 5. Bias correction. Then, this fully automatic multiple assigned criteria algorithms for fiber tracking were used to achieve easy modeling and assist precision surgery. We demonstrated the application with three language-related cases in three different centers, including a left frontal, a left temporal, and a left frontal-temporal glioma, to achieve a favorable surgical outcome with language function preservation or recovery. The DTI tracking result using DiffusionGo showed robust consistency with direct cortical stimulation (DCS) finding. We believe that this fully automatic processing pipeline provides the neurosurgeon with a solution that may reduce time costs and operating errors and improve care quality and surgical procedure quality across different neurosurgical centers.

Visualization of human optic nerve by diffusion tensor mapping and degree of neuropathy

Diffusion-weighted magnetic resonance imaging of the human optic nerve and tract is technically difficult because of its small size, the inherent strong signal generated by the surrounding fat and the cerebrospinal fluid, and due to eddy current-induced distortions and subject movement artifacts. The effects of the bone canal through which the optic nerve passes, and the proximity of blood vessels, muscles and tendons are generally unknown. Also, the limited technical capabilities of the scanners and the minimization of acquisition times result in poor quality diffusion-weighted images. It is challenging for current tractography methods to accurately track optic pathway fibers that correspond to known anatomy. Despite these technical limitations and low image resolution, here we show how to visualize the optic nerve and tract and quantify nerve atrophy. Our visualization method based on the analysis of the diffusion tensor shows marked differences between a healthy male subject and a male subject with progressive optic nerve neuropathy. These differences coincide with diffusion scalar metrics and are not visible on standard morphological images. A quantification of the degree of optic nerve atrophy in a systematic way is provided and it is tested on 9 subjects from the Human Connectome Project.

Estimation of undistorted images in brain echo-planar images with distortions using the conjugate gradient method with anatomical regularization

PURPOSE

Although echo-planar imaging (EPI) is widely used for diffusion magnetic resonance (MR) imaging, EPI images suffer from susceptibility-induced geometric distortions. We herein propose a new estimation method for undistorted EPI images using anatomical T₁ -weighted images (T₁ WIs) based on the physics of MR imaging.

METHODS

Our proposed method estimates the undistorted EPI image in the image domain while estimating the magnetic field inhomogeneity map using the conjugate gradient method with anatomical regularization. Our method synthesizes the distorted image to match the measured EPI image containing geometric distortions by alternately updating the undistorted EPI image and the magnetic field inhomogeneity map. We evaluated our proposed method and compared it with a nonrigid registration-based distortion correction method using simulated data and using real data. In the evaluation of the estimation of the magnetic field inhomogeneity map, we used the normalized root-mean-squared error (NRMSE) between the estimated results and the ground truth. In the evaluation of the estimation of undistorted images, we used mutual information (MI) between the undistorted EPI image and the anatomical T₁ WI.

RESULTS

Using the simulated data, the means and standard deviations of the NRMSE values in the nonrigid registration-based method and proposed method were 1.29 ± 0.63 and 0.64 ± 0.30, respectively. The MI values in the proposed method were larger than those in the nonrigid registration-based method in all evaluated slices. For the real data, the proposed method improved the distortion, and the MI values in the proposed method were larger than those in the nonrigid registration-based method. In the estimation of the magnetic field inhomogeneity map, the NRMSE values in our method were smaller than those in the nonrigid registration-based method.

CONCLUSIONS

We demonstrated that our proposed method can estimate the regions with compressed distortions that are not well represented by the nonrigid registration-based methods. The results suggest that the proposed method could be useful in analyses combining EPI images with T₁ WIs.

Altered development of structural MRI connectome hubs at near-term age in very and moderately preterm infants

Preterm infants may exhibit altered developmental patterns of the brain structural network by endogenous and exogenous stimuli, which are quantifiable through hub and modular network topologies that develop in the third trimester. Although preterm brain networks can compensate for white matter microstructural abnormalities of core connections, less is known about how the network developmental characteristics of preterm infants differ from those of full-term infants. We identified 13 hubs and 4 modules and revealed subtle differences in edgewise connectivity and local network properties between 134 preterm and 76 full-term infants, identifying specific developmental patterns of the brain structural network in preterm infants. The modules of preterm infants showed an imbalanced composition. The edgewise connectivity in preterm infants showed significantly decreased long- and short-range connections and local network properties in the dorsal superior frontal gyrus. In contrast, the fusiform gyrus and several nonhub regions showed significantly increased wiring of short-range connections and local network properties. Our results suggested that decreased local network in the frontal lobe and excessive development in the occipital lobe may contribute to the understanding of brain developmental deviances in preterm infants.

NeoRS: A Neonatal Resting State fMRI Data Preprocessing Pipeline

Resting state functional MRI (rsfMRI) has been shown to be a promising tool to study intrinsic brain functional connectivity and assess its integrity in cerebral development. In neonates, where functional MRI is limited to very few paradigms, rsfMRI was shown to be a relevant tool to explore regional interactions of brain networks. However, to identify the resting state networks, data needs to be carefully processed to reduce artifacts compromising the interpretation of results. Because of the non-collaborative nature of the neonates, the differences in brain size and the reversed contrast compared to adults due to myelination, neonates can’t be processed with the existing adult pipelines, as they are not adapted. Therefore, we developed NeoRS, a rsfMRI pipeline for neonates. The pipeline relies on popular neuroimaging tools (FSL, AFNI, and SPM) and is optimized for the neonatal brain. The main processing steps include image registration to an atlas, skull stripping, tissue segmentation, slice timing and head motion correction and regression of confounds which compromise functional data interpretation. To address the specificity of neonatal brain imaging, particular attention was given to registration including neonatal atlas type and parameters, such as brain size variations, and contrast differences compared to adults. Furthermore, head motion was scrutinized, and motion management optimized, as it is a major issue when processing neonatal rsfMRI data. The pipeline includes quality control using visual assessment checkpoints. To assess the effectiveness of NeoRS processing steps we used the neonatal data from the Baby Connectome Project dataset including a total of 10 neonates. NeoRS was designed to work on both multi-band and single-band acquisitions and is applicable on smaller datasets. NeoRS also includes popular functional connectivity analysis features such as seed-to-seed or seed-to-voxel correlations. Language, default mode, dorsal attention, visual, ventral attention, motor and fronto-parietal networks were evaluated. Topology found the different analyzed networks were in agreement with previously published studies in the neonate. NeoRS is coded in Matlab and allows parallel computing to reduce computational times; it is open-source and available on GitHub (https://github.com/venguix/NeoRS). NeoRS allows robust image processing of the neonatal rsfMRI data that can be readily customized to different datasets.

Unsupervised Deep Learning for FOD-Based Susceptibility Distortion Correction in Diffusion MRI

Susceptibility induced distortion is a major artifact that affects the diffusion MRI (dMRI) data analysis. In the Human Connectome Project (HCP), the state-of-the-art method adopted to correct this kind of distortion is to exploit the displacement field from the B0 image in the reversed phase encoding images. However, both the traditional and learning-based approaches have limitations in achieving high correction accuracy in certain brain regions, such as brainstem. By utilizing the fiber orientation distribution (FOD) computed from the dMRI, we propose a novel deep learning framework named DistoRtion Correction Net (DrC-Net), which consists of the U-Net to capture the latent information from the 4D FOD images and the spatial transformer network to propagate the displacement field and back propagate the losses between the deformed FOD images. The experiments are performed on two datasets acquired with different phase encoding (PE) directions including the HCP and the Human Connectome Low Vision (HCLV) dataset. Compared to two traditional methods topup and FODReg and two deep learning methods S-Net and flow-net, the proposed method achieves significant improvements in terms of the mean squared difference (MSD) of fractional anisotropy (FA) images and minimum angular difference between two PEs in white matter and also brainstem regions. In the meantime, the proposed DrC-Net takes only several seconds to predict a displacement field, which is much faster than the FODReg method.

A high-resolution multi-shell 3T diffusion magnetic resonance imaging dataset as part of the Amsterdam Ultra-high field adult lifespan database (AHEAD)

In order to further our understanding of brain function and the underlying networks, more advanced diffusion weighted magnetic resonance imaging (DWI MRI) data are essential. Here we present freely available high-resolution multi-shell multi-directional 3 Tesla (T) DWI MRI data as part of the ‘Amsterdam Ultra-high field adult lifespan database’ (AHEAD). The 3T DWI AHEAD dataset include 1.28mm isotropic whole brain DWI data of 49 healthy adult participants between 18 and 90 years old. The acquired data include DWIs at three non-zero b-values (48 directions, b-value 700 s/mm²; 56 directions, b-value 1000 s/mm²; 64 directions, b-value 1600 s/mm²) including a total of twelve volumes with a b-value of 0 s/mm² (b0 volumes). In addition, eight b0 volumes with a reversed phase encoding direction were acquired to correct for distortions. To facilitate future use, the DWI data have been denoised, corrected for eddy currents, susceptibility-induced off-resonance field distortions, bias fields, and are skull stripped.

The Effects of Nicotine and Cannabis Co-Use During Late Adolescence on White Matter Fiber Tract Microstructure

OBJECTIVE

Co-use of cannabis and nicotine and tobacco products (NTPs) in adolescence/young adulthood is common and associated with worse outcomes than the use of either substance in isolation. Despite this, little is known about the unique contributions of co-use to neurostructural microstructure during this neurodevelopmentally important period. This study sought to investigate the interactive effects of nicotine and cannabis co-use on white matter fiber tract microstructure in emerging adulthood.

METHOD

A total of 111 late adolescent (16-22 years old) nicotine (NTP; n = 55, all past-year cannabis users) and non-nicotine users (non-NTP; n = 56, 61% reporting cannabis use in the past year) completed demographic and clinical interviews and a neuroimaging session comprising anatomical and diffusion-weighted imaging scans. Group connectometry analysis identified white matter tracts significantly associated with the interaction between nicotine group and past-year cannabis use according to generalized fractional anisotropy (GFA).

RESULTS

Nicotine Group × Cannabis Use interactions were observed in the right and left cingulum and left fornix tracts (false discovery rate = 0.053), where greater cannabis use was associated with increased GFA in the cingulum and left fornix, but only when co-used with nicotine.

CONCLUSIONS

This report represents the first group connectometry analysis in late adolescent/young adult cannabis and/or NTP users. Results suggest that co-use of cannabis and NTPs results in a structurally distinct white matter phenotype as compared with cannabis use only, although to what extent this may change over time with more chronic nicotine and cannabis use remains to be examined in future work.

The Effects of Nicotine and Cannabis Co-Use During Late Adolescence on White Matter Fiber Tract Microstructure

OBJECTIVE

Co-use of cannabis and nicotine and tobacco products (NTPs) in adolescence/young adulthood is common and associated with worse outcomes than the use of either substance in isolation. Despite this, little is known about the unique contributions of co-use to neurostructural microstructure during this neurodevelopmentally important period. This study sought to investigate the interactive effects of nicotine and cannabis co-use on white matter fiber tract microstructure in emerging adulthood.

METHOD

A total of 111 late adolescent (16-22 years old) nicotine (NTP; n = 55, all past-year cannabis users) and non-nicotine users (non-NTP; n = 56, 61% reporting cannabis use in the past year) completed demographic and clinical interviews and a neuroimaging session comprising anatomical and diffusion-weighted imaging scans. Group connectometry analysis identified white matter tracts significantly associated with the interaction between nicotine group and past-year cannabis use according to generalized fractional anisotropy (GFA).

RESULTS

Nicotine Group × Cannabis Use interactions were observed in the right and left cingulum and left fornix tracts (false discovery rate = 0.053), where greater cannabis use was associated with increased GFA in the cingulum and left fornix, but only when co-used with nicotine.

CONCLUSIONS

This report represents the first group connectometry analysis in late adolescent/young adult cannabis and/or NTP users. Results suggest that co-use of cannabis and NTPs results in a structurally distinct white matter phenotype as compared with cannabis use only, although to what extent this may change over time with more chronic nicotine and cannabis use remains to be examined in future work.

Manifold-based respiratory phase estimation enables motion and distortion correction of free-breathing cardiac diffusion tensor MRI

PURPOSE

For in vivo cardiac DTI, breathing motion and B₀ field inhomogeneities produce misalignment and geometric distortion in diffusion-weighted (DW) images acquired with conventional single-shot EPI. We propose using a dimensionality reduction method to retrospectively estimate the respiratory phase of DW images and facilitate both distortion correction (DisCo) and motion compensation.

METHODS

Free-breathing electrocardiogram-triggered whole left-ventricular cardiac DTI using a second-order motion-compensated spin echo EPI sequence and alternating directionality of phase encoding blips was performed on 11 healthy volunteers. The respiratory phase of each DW image was estimated after projecting the DW images into a 2D space with Laplacian eigenmaps. DisCo and motion compensation were applied to the respiratory sorted DW images. The results were compared against conventional breath-held T₂ half-Fourier single shot turbo spin echo. Cardiac DTI parameters including fractional anisotropy, mean diffusivity, and helix angle transmurality were compared with and without DisCo.

RESULTS

The left-ventricular geometries after DisCo and motion compensation resulted in significantly improved alignment of DW images with T₂ reference. DisCo reduced the distance between the left-ventricular contours by 13.2% ± 19.2%, P < .05 (2.0 ± 0.4 for DisCo and 2.4 ± 0.5 mm for uncorrected). DisCo DTI parameter maps yielded no significant differences (mean diffusivity: 1.55 ± 0.13 × 10^-3 mm² /s and 1.53 ± 0.13 × 10^-3 mm² /s, P = .09; fractional anisotropy: 0.375 ± 0.041 and 0.379 ± 0.045, P = .11; helix angle transmurality: 1.00% ± 0.10°/% and 0.99% ± 0.12°/%, P = .44), although the orientation of individual tensors differed.

CONCLUSION

Retrospective respiratory phase estimation with LE-based DisCo and motion compensation in free-breathing cardiac DTI resulting in significantly reduced geometric distortion and improved alignment within and across slices.

What's New and What's Next in Diffusion MRI Preprocessing

Diffusion MRI (dMRI) provides invaluable information for the study of tissue microstructure and brain connectivity, but suffers from a range of imaging artifacts that greatly challenge the analysis of results and their interpretability if not appropriately accounted for. This review will cover dMRI artifacts and preprocessing steps, some of which have not typically been considered in existing pipelines or reviews, or have only gained attention in recent years: brain/skull extraction, B-matrix incompatibilities w.r.t the imaging data, signal drift, Gibbs ringing, noise distribution bias, denoising, between- and within-volumes motion, eddy currents, outliers, susceptibility distortions, EPI Nyquist ghosts, gradient deviations, B₁ bias fields, and spatial normalization. The focus will be on “what’s new” since the notable advances prior to and brought by the Human Connectome Project (HCP), as presented in the predecessing issue on “Mapping the Connectome” in 2013. In addition to the development of novel strategies for dMRI preprocessing, exciting progress has been made in the availability of open source tools and reproducible pipelines, databases and simulation tools for the evaluation of preprocessing steps, and automated quality control frameworks, amongst others. Finally, this review will consider practical considerations and our view on “what’s next” in dMRI preprocessing.

Slab boundary artifact correction in multislab imaging using convolutional-neural-network-enabled inversion for slab profile encoding

PURPOSE

This study aims to propose a novel algorithm for slab boundary artifact correction in both single-band multislab imaging and simultaneous multislab (SMSlab) imaging.

THEORY AND METHODS

In image domain, the formation of slab boundary artifacts can be regarded as modulating the artifact-free images using the slab profiles and introducing aliasing along the slice direction. Slab boundary artifact correction is the inverse problem of this process. An iterative algorithm based on convolutional neural networks (CNNs) is proposed to solve the problem, termed CNN-enabled inversion for slab profile encoding (CPEN). Diffusion-weighted SMSlab images and reference images without slab boundary artifacts were acquired in 7 healthy subjects for training. Images of 5 healthy subjects were acquired for testing, including single-band multislab and SMSlab images with 1.3-mm or 1-mm isotropic resolution. CNN-enabled inversion for slab profile encoding was compared with a previously reported method (i.e., nonlinear inversion for slab profile encoding [NPEN]).

RESULTS

CNN-enabled inversion for slab profile encoding reduces the slab boundary artifacts in both single-band multislab and SMSlab images. It also suppresses the slab boundary artifacts in the diffusion metric maps. Compared with NPEN, CPEN shows fewer residual artifacts in different acquisition protocols and more significant improvements in quantitative assessment, and it also accelerates the computation by more than 35 times.

CONCLUSION

CNN-enabled inversion for slab profile encoding can reduce the slab boundary artifacts in multislab acquisitions. It shows better slab boundary artifact correction capacity, higher robustness, and computation efficiency when compared with NPEN. It has the potential to improve the accuracy of multislab acquisitions in high-resolution DWI and functional MRI.

Exploring Peritumoral Neural Tracts by Using Neurite Orientation Dispersion and Density Imaging

Diffusion Tensor Imaging (DTI) tractography has been widely used in brain tumor surgery to ensure thorough resection and minimize functional damage. However, due to enhanced anisotropic uncertainty in the area with peritumoral edema, diffusion tractography is generally not practicable leading to high false-negative results in neural tracking. In this study, we evaluated the usefulness of the neurite orientation dispersion and density imaging (NODDI) derived tractography for investigating structural heterogeneity of the brain in patients with brain tumor. A total of 24 patients with brain tumors, characterized by peritumoral edema, and 10 healthy counterparts were recruited from 2014 to 2021. All participants underwent magnetic resonance imaging. Moreover, we used the images obtained from the healthy participants for calibrating the orientation dispersion threshold for NODDI-derived corticospinal tract (CST) reconstruction. Compared to DTI, NODDI-derived tractography has a great potential to improve the reconstruction of fiber tracking through regions of vasogenic edema. The regions with edematous CST in NODDI-derived tractography demonstrated a significant decrease in the intracellular volume fraction (VF_ic, p < 0.000) and an increase in the isotropic volume fraction (VF_iso, p < 0.014). Notably, the percentage of the involved volume of the concealed CST and lesion-to-tract distance could reflect the motor function of the patients. After the tumor resection, four patients with 1–5 years follow-up were showed subsidence of the vasogenic edema and normal CST on DTI tractography. NODDI-derived tractography revealed tracts within the edematous area and could assist neurosurgeons to locate the neural tracts that are otherwise not visualized by conventional DTI tractography.

Magnetic Resonance Simulation in Education: Quantitative Evaluation of an Actual Classroom Experience

Magnetic resonance is an imaging modality that implies a high complexity for radiographers. Despite some simulators having been developed for training purposes, we are not aware of any attempt to quantitatively measure their educational performance. The present study gives an answer to the question: Does an MRI simulator built on specific functional and non-functional requirements help radiographers learn MRI theoretical and practical concepts better than traditional educational method based on lectures? Our study was carried out in a single day by a total of 60 students of a main hospital in Madrid, Spain. The experiment followed a randomized pre-test post-test design with a control group that used a traditional educational method, and an experimental group that used our simulator. Knowledge level was assessed by means of an instrument with evidence of validity in its format and content, while its reliability was analyzed after the experiment. Statistical differences between both groups were measured. Significant statistical differences were found in favor of the participants who used the simulator for both the post-test score and the gain (difference between post-test and pre-test scores). The effect size turned out to be significant as well. In this work we evaluated a magnetic resonance simulation paradigm as a tool to help in the training of radiographers. The study shows that a simulator built on specific design requirements is a valuable complement to traditional education procedures, backed up with significant quantitative results.

Directed stimulation of the dentato-rubro-thalamic tract for deep brain stimulation in essential tremor: a blinded clinical trial

OBJECTIVE

Observational studies utilising diffusion tractography have suggested a common mechanism for tremor alleviation in deep brain stimulation for essential tremor: the decussating portion of the dentato-rubro-thalamic tract. We hypothesised that directional stimulation of the dentato-rubro-thalamic tract would result in greater tremor improvement compared to sham programming, as well as comparable improvement as more tedious standard-of-care programming.

METHODS

A prospective, blinded crossover trial was performed to assess the feasibility, safety and outcomes of programming based solely on dentato-rubro-thalamic tract anatomy. Using magnetic resonance imaging diffusion-tractography, the dentato-rubro-thalamic tract was identified and a connectivity-based treatment setting was derived by modelling a volume of tissue activated using directional current steering oriented towards the dentato-rubro-thalamic tract centre. A sham setting was created at approximately 180° opposite the connectivity-based treatment. Standard-of-care programming at 3 months was compared to connectivity-based treatment and sham settings that were blinded to the programmer. The primary outcome measure was percentage improvement in the Fahn-Tolosa-Marín tremor rating score compared to the preoperative baseline.

RESULTS

Among the six patients, tremor rating scores differed significantly among the three experimental conditions (P=0.030). The mean tremor rating score improvement was greater with the connectivity-based treatment settings (64.6% ± 14.3%) than with sham (44.8% ± 18.6%; P=0.031) and standard-of-care programming (50.7% ± 19.2%; P=0.062). The distance between the centre of the dentato-rubro-thalamic tract and the volume of tissue activated inversely correlated with the percentage improvement in the tremor rating score (R²=0.24; P=0.04). No significant adverse events were encountered.

CONCLUSIONS

Using a blinded, crossover trial design, we have shown the technical feasibility, safety and potential efficacy of connectivity-based stimulation settings in deep brain stimulation for treatment of essential tremor.

Minimal specifications for non-human primate MRI: Challenges in standardizing and harmonizing data collection

Recent methodological advances in MRI have enabled substantial growth in neuroimaging studies of non-human primates (NHPs), while open data-sharing through the PRIME-DE initiative has increased the availability of NHP MRI data and the need for robust multi-subject multi-center analyses. Streamlined acquisition and analysis protocols would accelerate and improve these efforts. However, consensus on minimal standards for data acquisition protocols and analysis pipelines for NHP imaging remains to be established, particularly for multi-center studies. Here, we draw parallels between NHP and human neuroimaging and provide minimal guidelines for harmonizing and standardizing data acquisition. We advocate robust translation of widely used open-access toolkits that are well established for analyzing human data. We also encourage the use of validated, automated pre-processing tools for analyzing NHP data sets. These guidelines aim to refine methodological and analytical strategies for small and large-scale NHP neuroimaging data. This will improve reproducibility of results, and accelerate the convergence between NHP and human neuroimaging strategies which will ultimately benefit fundamental and translational brain science.

The impact of susceptibility correction on diffusion metrics in adolescents

BACKGROUND

Diffusion tensor imaging is a widely used imaging method of brain white matter, but it is prone to imaging artifacts. The data corrections can affect the measured values.

OBJECTIVE

To explore the impact of susceptibility correction on diffusion metrics.

MATERIALS AND METHODS

A cohort of 27 healthy adolescents (18 boys, 9 girls, mean age 12.7 years) underwent 3-T MRI, and we collected two diffusion data sets (anterior-posterior). The data were processed both with and without susceptibility artifact correction. We derived fractional anisotropy, mean diffusivity and histogram data of fiber length distribution from both the corrected and uncorrected data, which were collected from the corpus callosum, corticospinal tract and cingulum bilaterally.

RESULTS

Fractional anisotropy and mean diffusivity values significantly differed when comparing the pathways in all measured tracts. The fractional anisotropy values were lower and the mean diffusivity values higher in the susceptibility-corrected data than in the uncorrected data. We found a significant difference in total tract length in the corpus callosum and the corticospinal tract.

CONCLUSION

This study indicates that susceptibility correction has a significant effect on measured fractional anisotropy, and on mean diffusivity values and tract lengths. To receive reliable and comparable results, the correction should be used systematically.

Bundle-Specific Axon Diameter Index as a New Contrast to Differentiate White Matter Tracts

In the central nervous system of primates, several pathways are characterized by different spectra of axon diameters. In vivo methods, based on diffusion-weighted magnetic resonance imaging, can provide axon diameter index estimates non-invasively. However, such methods report voxel-wise estimates, which vary from voxel-to-voxel for the same white matter bundle due to partial volume contributions from other pathways having different microstructure properties. Here, we propose a novel microstructure-informed tractography approach, COMMITAxSize, to resolve axon diameter index estimates at the streamline level, thus making the estimates invariant along trajectories. Compared to previously proposed voxel-wise methods, our formulation allows the estimation of a distinct axon diameter index value for each streamline, directly, furnishing a complementary measure to the existing calculation of the mean value along the bundle. We demonstrate the favourable performance of our approach comparing our estimates with existing histologically-derived measurements performed in the corpus callosum and the posterior limb of the internal capsule. Overall, our method provides a more robust estimation of the axon diameter index of pathways by jointly estimating the microstructure properties of the tissue and the macroscopic organisation of the white matter connectivity.

Age-Related Alterations in DTI Metrics in the Human Brain-Consequences for Age Correction

Background: Over the life span, the diffusion metrics in brain MRI show different, partly nonlinear changes. These age-dependent changes also seem to exhibit regional differences with respect to the brain anatomy. The age correction of a study cohort's diffusion metrics might thus require consideration of age-related factors. Methods: Diffusion tensor imaging data sets were acquired from 219 healthy participants at ages between 19 and 81 years. Fractional anisotropy (FA), mean diffusivity (MD), and axial and radial diffusivity (AD and RD, respectively) maps were analyzed by a tract of interest-based fiber tracking approach. To describe diffusion metrics as a function of the participant age, linear splines were used to perform curve fitting in 21 specific tract systems covering different functional areas and diffusion directions. Results: In the majority of tracts, an interpolation with a change of alteration rate during adult life described the diffusion properties more accurately than a linear model. Consequently, the diffusion properties remained relatively stable until a decrease (of FA) or increase (of MD, AD, and RD) started at a region-specific time point, whereas a uniform change of diffusion properties was observed only in a few tracts. Single tracts, e.g., located in the cerebellum, remained nearly unaltered throughout the ages between 19 and 81 years. Conclusions: Age corrections of diffusion properties should not be applied to all white matter regions and all age spans in the same way. Therefore, we propose three different approaches for age correction based on fiber tracking techniques, i.e., no correction for areas that do not experience age-related changes and two variants of an age correction depending on the age range of the cohort and the tracts considered.

Improving distortion correction for isotropic high-resolution 3D diffusion MRI by optimizing Jacobian modulation

PURPOSE

To improve distortion correction for isotropic high-resolution whole-brain 3D diffusion MRI when in a time-saving acquisition scenario.

THEORY AND METHODS

Data were acquired using simultaneous multi-slab (SMSlab) acquisitions, with a b = 0 image pair encoded by reversed polarity gradients (RPG) for phase encoding (PE) and diffusion weighted images encoded by a single PE direction. Eddy current-induced distortions were corrected first. During the following susceptibility distortion correction, image deformation was first corrected by the field map estimated from the b = 0 image pair. Intensity variation was subsequently corrected by Jacobian modulation. Two Jacobian modulation methods were compared. They calculated the Jacobian modulation map from the field map, or from the deformation corrected b = 0 image pair, termed as J_Field and J_RPG , respectively. A modified version of the J_RPG method, with proper smoothing, was further proposed for improved correction performance, termed as J_RPG-smooth .

RESULTS

Compared to J_Field modulation, less remaining distortions are observed when using the J_RPG and J_RPG-smooth methods, especially in areas with large B0 field inhomogeneity. The original J_RPG method causes signal-to-noise ratio (SNR) deficiency problem, which manifests as degraded SNR of the diffusion weighted images, while the J_RPG-smooth method maintains the original image SNR. Less estimation errors of diffusion metrics are observed when using the J_RPG-smooth method.

CONCLUSION

This study improves the distortion correction for isotropic high-resolution whole-brain 3D diffusion MRI by optimizing Jacobian modulation. The optimized method outperforms the conventional J_Field method regarding intensity variation correction and accuracy of diffusion metrics estimation, and outperforms the original J_RPG method regarding SNR performance.

Tracking white-matter brain modifications in chronic non-bothersome acoustic trauma tinnitus

•

Tractography was compared between two groups of tinnitus and control participants.

•

Diffusion was modeled with ss3t-CSD allowing apparent fiber density (AFD) calculation.

•

27 bundles of interest were chosen for their link to the auditory and limbic systems.

•

AFD was significantly increased in the tinnitus group in the right frontal isthmus.

•

AFD in the acoustic radiations was not significantly different between the groups.

Subjective tinnitus is a symptom characterized by the perception of sound with no external acoustic source, most often accompanied by co-morbidities. To date, the specific role of white matter abnormalities related to tinnitus reaches no consensus in the literature. The goal of this study was to explore the structural connectivity related to tinnitus percept per se, thus focusing on a specific population presenting chronic non-bothersome tinnitus of similar etiology (noise induced) without co-morbidities. We acquired diffusion-weighted images with high angular resolution in a homogeneous group of mildly impacted tinnitus participants (n = 19) and their matched controls (n = 19). We focused the study on two subsets of fiber bundles of interest: on one hand, we extracted the acoustic radiation and further included any intersecting fiber bundles; on the other hand, we explored the tracts related to the limbic system. We modeled the diffusion signal using constrained spherical deconvolution. We conducted a deep-learning based tractography segmentation and mapped Apparent Fiber Density (AFD) on the bundles of interest. C, as well as Fractional Anisotropy (FA) and FOD peak amplitude for comparison. Between group statistical comparison was performed along the 27 tracts of interest controlling for confounding hearing loss, tinnitus severity, and duration since onset. We tested a potential correlation with hearing loss, tinnitus duration and tinnitus handicap score along these tracts. In the tinnitus group, we observed increased AFD related to chronic tinnitus percept after acoustic trauma in two main white matter regions. First, in the right hemisphere, in the isthmus between inferior temporal and inferior frontal cortices, in the uncinate fasciculus (UF), and in the inferior fronto-occipital bundle (IFO). Second, in the left hemisphere, underneath the superior parietal region in the thalamo parietal tract and parieto-occipital pontine tract. Between-group differences in the acoustic radiations were not significant with AFD but were with FA. Furthermore, significant correlations with hearing loss were found in the left hemisphere in the inferior longitudinal fasciculus and in the fronto-pontine tract. No additional correlation was found with tinnitus duration nor with tinnitus handicap, as reflected by THI scores. The regions that displayed tinnitus related increased AFD also displayed increased FA. The isthmus of the UF and IFO in the right hemisphere appear to be involved with a number of neuropsychiatric and traumatic disorders confirming the involvement of the limbic system even in chronic non-bothersome tinnitus subjects, potentially suggesting a common pathway between these pathologies. White matter changes underneath the superior parietal cortex found here in tinnitus participants supports the implication of an auditory-somatosensory pathway in tinnitus perception.

Modified Diffusion Tensor Image Processing Pipeline for Archived Studies of Patients With Leukoencephalopathy

BACKGROUND

In archived diffusion tensor imaging (DTI) studies, a reversed-phase encoding (PE) scan required to correct the distortion in single-shot echo-planar imaging (EPI) may not have been acquired. Furthermore, DTI tractography is adversely affected by incorrect white matter segmentation due to leukoencephalopathy (LE). All these issues need to be addressed.

PURPOSE

To propose and evaluate a modified DTI processing pipeline with DIstortion COrrection using pseudo T₂ -weighted images (DICOT) to overcome limitations in existing acquisition protocols.

STUDY TYPE

Retrospective feasibility.

SUBJECTS

DICOT was assessed in simulated data and 84 acute lymphoblastic leukemia (ALL) patients with reversed PE acquired. The pipeline was then tested in 522 scans from 261 ALL patients without a reversed PE acquired.

FIELD STRENGTH/SEQUENCE

A 3 T; diffusion-weighted EPI; 3D magnetization prepared rapid acquisition gradient echo (MPRAGE).

STATISTICAL TESTS

Repeated measures analysis of variance and Tukey post hoc tests were performed to compare fractional anisotropy (FA) values obtained by different methods.

ASSESSMENT

FA and corresponding absolute error maps were obtained using TOPUP, DICOT, INVERSION (Inverse contrast Normalization for VERy Simple registratION) and NO CORR (no correction). Each method was assessed by comparing to TOPUP. The pipeline in the ALL patients was evaluated based on the failure rate of the distortion correction using the global correlation values.

RESULTS

Using DICOT reduced the mean absolute errors by an average of 32% in FA in simulation datasets. In 84 patients, the error reductions were approximately 15% in FA with DICOT, while it was 5% with INVERSION. No significant differences between the TOPUP and DICOT were observed in FA with P = 0.090/0.894(AP/PA). Only 15 of 516 examinations requiring any additional manual intervention.

CONCLUSION

This modified pipeline produced better results than the INVERSION. Furthermore, robust performance was demonstrated in archived patient scans acquired without an inverse PE necessary for TOPUP correction.

EVIDENCE LEVEL

3 TECHNICAL EFFICACY: Stage 2.

Multiband diffusion tensor imaging for presurgical mapping of motor and language pathways in patients with brain tumors

BACKGROUND AND PURPOSE

Assessment of the essential white matter fibers of arcuate fasciculus and corticospinal tract (CST), required for preoperative planning in brain tumor patients, relies on the reliability of diffusion tensor imaging (DTI). The recent development of multiband DTI (mb-DTI) based on simultaneous multislice excitation could maintain the overall quality of tractography while not exceeding standard clinical care time. To address this potential, we performed quantitative analyses to evaluate tractography results of arcuate fasciculus and CST acquired by mb-DTI in brain tumor patients.

METHODS

We retrospectively analyzed 44 patients with brain lesions who underwent presurgical single-shot DTI (s-DTI) and mb-DTI. We measured DTI parameters: fractional anisotropy (FA) and mean diffusivity (MD [mm² s^-1 ]) in whole brain and tumor regions; and the tractography parameters: fiber FA, MD (mm² s^-1 ), volume (mm³ ), and length (mm) in the whole brain, arcuate fasciculus, and CST. Additionally, three neuroradiologists performed a blinded visual assessment comparing s-DTI with mb-DTI.

RESULTS

The mb-DTI showed higher mean FA and lower MD (r > .95, p < .002) in whole brain and tumor regions of interest; slightly higher fiber FA, volume, and length; and slightly lower fiber MD in whole brain, arcuate fasciculus, and CST than in s-DTI. These differences were significant for fiber FA in all tracts; length (mm) in arcuate fasciculus; and fiber MD (mm² s^-1 ) and volume (mm³ ) in all patients with tumor involved in the arcuate fasciculus, CST, and whole brain tracts (p = .001). Visual assessment demonstrated that both techniques produced visually similar tracts.

CONCLUSIONS

This study demonstrated the clinical potential and significant advantages of preoperative mb-DTI in brain tumor patients.

Quantitative Assessment of the Impact of Geometric Distortions and Their Correction on fMRI Data Analyses

Functional magnetic resonance imaging (fMRI) data is typically collected with gradient-echo echo-planar imaging (GE-EPI) sequences, which are particularly prone to the susceptibility artifact as a result of B₀ field inhomogeneity. The component derived from in-plane spin dephasing induces pixel intensity variations and, more critically, geometric distortions. Despite the physical mechanisms underlying the susceptibility artifact being well established, a systematic investigation on the impact of the associated geometric distortions, and the direct comparison of different approaches to tackle them, on fMRI data analyses is missing. Here, we compared two different distortion correction approaches, by acquiring additional: (1) EPI data with reversed phase encoding direction (TOPUP), and (2) standard (and undistorted) GE data at two different echo times (GRE). We first characterized the geometric distortions and the correction approaches based on the estimated ΔB₀ field offset and voxel shift maps, and then conducted three types of analyses on the distorted and corrected fMRI data: (1) registration into structural data, (2) identification of resting-state networks (RSNs), and (3) mapping of task-related brain regions of interest. GRE estimated the largest voxel shifts and more positively impacted the quality of the analyses, in terms of the (significantly lower) cost function of the registration, the (higher) spatial overlap between the RSNs and appropriate templates, and the (significantly higher) sensitivity of the task-related mapping based on the Z-score values of the associated activation maps, although also evident when considering TOPUP. fMRI data should thus be corrected for geometric distortions, with the choice of the approach having a modest, albeit positive, impact on the fMRI analyses.

The effects of nicotine and cannabis co-use during adolescence and young adulthood on white matter cerebral blood flow estimates

RATIONALE

Co-use of cannabis and nicotine is common among adolescents/young adults and is associated with poorer psychological and physical outcomes, compared with single substance use. Little is known about the impact of co-use on the developing brain.

OBJECTIVES

Preliminary investigation of the effects of nicotine on white matter (WM) cerebral blood flow (CBF) in adolescents/young adults and its potential moderation by cannabis use.

METHODS

Adolescent/young adult (16-22 years old) nicotine and tobacco product users (NTP; N = 37) and non-nicotine users (non-NTP; N = 26) underwent a neuroimaging session comprised of anatomical, optimized pseudo-continuous arterial spin labeling, and diffusion tensor imaging scans. Groups were compared on whole-brain WM CBF estimates and their relation to past-year cannabis use. Follow-up analyses assessed correlations between identified CBF clusters and corresponding fractional anisotropy (FA) values.

RESULTS

Group by cannabis effects were observed in five clusters (voxel-wise alpha < 0.001, cluster-wise alpha < 0.05; ≥ 11 contiguous voxels): non-NTP exhibited positive correlations between CBF and cannabis use in all clusters, whereas no significant relationships were observed for NTP. Greater CBF extracted from one cluster (including portions of right superior longitudinal fasciculus) was associated with reduced FA for non-NTP group only.

CONCLUSIONS

This is the first investigation of WM health as indexed by CBF, and its association with FA, in adolescents/young adults with nicotine and/or cannabis use. Results suggest that cannabis use by itself may be related to increased CBF in WM fiber tracts demonstrating poorer structural intergrity, yet the occurrence of even infrequent NTP use (greater than once per month) appears to diminish this relationship.

Deconvolution-based distortion correction of EPI using analytic single-voxel point-spread functions

PURPOSE

To develop a postprocessing algorithm that corrects geometric distortions due to spatial variations of the static magnetic field amplitude, B₀ , and effects from relaxation during signal acquisition in EPI.

THEORY AND METHODS

An analytic, complex point-spread function is deduced for k-space trajectories of EPI variants and applied to corresponding acquisitions in a resolution phantom and in human volunteers at 3 T. With the analytic point-spread function and experimental maps of B₀ (and, optionally, the effective transverse relaxation time, T 2 * ) as input, a point-spread function matrix operator is devised for distortion correction by a Thikonov-regularized deconvolution in image space. The point-spread function operator provides additional information for an appropriate correction of the signal intensity distribution. A previous image combination algorithm for acquisitions with opposite phase blip polarities is adapted to the proposed method to recover destructively interfering signal contributions.

RESULTS

Applications of the proposed deconvolution-based distortion correction ("DecoDisCo") algorithm demonstrate excellent distortion corrections and superior performance regarding the recovery of an undistorted intensity distribution in comparison to a multifrequency reconstruction. Examples include full and partial Fourier standard EPI scans as well as double-shot center-out trajectories. Compared with other distortion-correction approaches, DecoDisCo permits additional deblurring to obtain sharper images in cases of significant T 2 * effects.

CONCLUSION

Robust distortion corrections in EPI acquisitions are feasible with high quality by regularized deconvolution with an analytic point-spread function. The general algorithm, which is publicly released on GitHub, can be straightforwardly adapted for specific EPI variants or other acquisition schemes.

Anxiety and the Neurobiology of Temporally Uncertain Threat Anticipation

When extreme, anxiety-a state of distress and arousal prototypically evoked by uncertain danger-can be debilitating. Uncertain anticipation is a shared feature of situations that elicit signs and symptoms of anxiety across psychiatric disorders, species, and assays. Despite the profound significance of anxiety for human health and wellbeing, the neurobiology of uncertain-threat anticipation remains unsettled. Leveraging a paradigm adapted from animal research and optimized for fMRI signal decomposition, we examined the neural circuits engaged during the anticipation of temporally uncertain and certain threat in 99 men and women. Results revealed that the neural systems recruited by uncertain and certain threat anticipation are anatomically colocalized in frontocortical regions, extended amygdala, and periaqueductal gray. Comparison of the threat conditions demonstrated that this circuitry can be fractionated, with frontocortical regions showing relatively stronger engagement during the anticipation of uncertain threat, and the extended amygdala showing the reverse pattern. Although there is widespread agreement that the bed nucleus of the stria terminalis and dorsal amygdala-the two major subdivisions of the extended amygdala-play a critical role in orchestrating adaptive responses to potential danger, their precise contributions to human anxiety have remained contentious. Follow-up analyses demonstrated that these regions show statistically indistinguishable responses to temporally uncertain and certain threat anticipation. These observations provide a framework for conceptualizing anxiety and fear, for understanding the functional neuroanatomy of threat anticipation in humans, and for accelerating the development of more effective intervention strategies for pathological anxiety.SIGNIFICANCE STATEMENT Anxiety-an emotion prototypically associated with the anticipation of uncertain harm-has profound significance for public health, yet the underlying neurobiology remains unclear. Leveraging a novel neuroimaging paradigm in a relatively large sample, we identify a core circuit responsive to both uncertain and certain threat anticipation, and show that this circuitry can be fractionated into subdivisions with a bias for one kind of threat or the other. The extended amygdala occupies center stage in neuropsychiatric models of anxiety, but its functional architecture has remained contentious. Here we demonstrate that its major subdivisions show statistically indistinguishable responses to temporally uncertain and certain threat. Collectively, these observations indicate the need to revise how we think about the neurobiology of anxiety and fear.

Integration of an intelligent tutoring system in a magnetic resonance simulator for education: Technical feasibility and user experience

BACKGROUND AND OBJECTIVE

In this paper we propose to include an intelligent tutoring system (ITS) within a magnetic resonance (MR) simulator that has been developed in house. With this, we intend to measure the impact, in terms of user experience, of including an ITS in our simulator.

METHODS

We thoroughly describe the integration procedure and we have tested the benefits of this integration by means of two actual educational experiences, with one of them using the simulator as a standalone tool, and the other with the joint use of simulator+ITS. The experiences have consisted of two online courses with a number of students around 180 in both of them, where measurements of usability, perceived utility and likelihood to recommend were collected.

RESULTS

We have observed that the three measurements improved noticeably in the second course with respect to the first one; specifically, overall usability improved by 22.3%, perceived utility by an average of 55.1% and likelihood to recommend by 13.7%. In addition, quantitative measurements are complemented with comments in free text format directly provided by the students. Results show evidence on the benefits of integrating an ITS in terms of quantitative user experience, as well as qualitative comparative comments directly by students of both courses.

CONCLUSIONS

This is the first time that an ITS is used within the scope of MR simulation for training purposes. Benefits of integrating an ITS within an MR simulator have been evaluated in terms of user experience, with satisfactory comparative results.

Distortion correction of diffusion weighted MRI without reverse phase-encoding scans or field-maps

Diffusion magnetic resonance images may suffer from geometric distortions due to susceptibility induced off resonance fields, which cause geometric mismatch with anatomical images and ultimately affect subsequent quantification of microstructural or connectivity indices. State-of-the art diffusion distortion correction methods typically require data acquired with reverse phase encoding directions, resulting in varying magnitudes and orientations of distortion, which allow estimation of an undistorted volume. Alternatively, additional field maps acquisitions can be used along with sequence information to determine warping fields. However, not all imaging protocols include these additional scans and cannot take advantage of state-of-the art distortion correction. To avoid additional acquisitions, structural MRI (undistorted scans) can be used as registration targets for intensity driven correction. In this study, we aim to (1) enable susceptibility distortion correction with historical and/or limited diffusion datasets that do not include specific sequences for distortion correction and (2) avoid the computationally intensive registration procedure typically required for distortion correction using structural scans. To achieve these aims, we use deep learning (3D U-nets) to synthesize an undistorted b0 image that matches geometry of structural T1w images and intensity contrasts from diffusion images. Importantly, the training dataset is heterogenous, consisting of varying acquisitions of both structural and diffusion. We apply our approach to a withheld test set and show that distortions are successfully corrected after processing. We quantitatively evaluate the proposed distortion correction and intensity-based registration against state-of-the-art distortion correction (FSL topup). The results illustrate that the proposed pipeline results in b0 images that are geometrically similar to non-distorted structural images, and more closely match state-of-the-art correction with additional acquisitions. In addition, we show generalizability of the proposed approach to datasets that were not in the original training / validation / testing datasets. These datasets included varying populations, contrasts, resolutions, and magnitudes and orientations of distortion and show efficacious distortion correction. The method is available as a Singularity container, source code, and an executable trained model to facilitate evaluation.

White Matter Abnormalities in Retired Professional Rugby League Players with a History of Concussion

The topic of potential long-term neurological consequences from having multiple concussions during a career in collision sports is controversial. We sought to investigate white matter microstructure using diffusion tensor imaging (DTI) in retired professional Australian National Rugby League (NRL) players (n = 11) with a history of multiple self-reported concussions compared with age- and education-matched controls (n = 13) who have had no history of brain trauma. Diffusion-weighted images were acquired with a Siemens 3T scanner. All participants completed a clinical interview. There were no significant differences between groups on measures of depression, anxiety, stress, or post-concussion symptoms; however, NRL players scored significantly higher on the alcohol use disorder identification test (AUDIT). Voxelwise analyses of DTI measures were performed using tract-based spatial statistics (TBSS) with age and AUDIT scores included as covariates. TBSS revealed significantly reduced fractional anisotropy (FA), and increased radial diffusivity (RD), axial diffusivity (AD), and trace (TR) in white matter regions of recently retired NRL players compared with controls. FA was significantly reduced in the right superior longitudinal fasciculus and right corticospinal tract while TR, RD, and AD were increased in these regions, as well as the corpus callosum, forceps major, right uncinate fasciculus, and left corticospinal tract. In summary, DTI in a small cohort of recently retired professional NRL players with a history of multiple concussions showed differences in white matter microstructure compared with age- and education-matched controls with no history of brain trauma.

Deep flow-net for EPI distortion estimation

INTRODUCTION

Geometric distortions along the phase encoding direction caused by off-resonant spins are a major issue in EPI based functional and diffusion imaging. The widely used blip up/down approach estimates the underlying distortion field from a pair of images with inverted phase encoding direction. Typically, iterative methods are used to find a solution to the ill-posed problem of finding the displacement field that maps up/down acquisitions onto each other. Here, we explore the use of a deep convolutional network to estimate the displacement map from a pair of input images.

METHODS

We trained a deep convolutional U-net architecture that was previously used to estimate optic flow between moving images to learn to predict the distortion map from an input pair of distorted EPI acquisitions. During the training step, the network minimizes a loss function (similarity metric) that is calculated from corrected input image pairs. This approach does not require the explicit knowledge of the ground truth distortion map, which is difficult to get for real life data.

RESULTS

We used data from a total of N_train ​= ​22 healthy subjects to train our network. A separate dataset of N_test ​= ​12 patients including some with abnormal findings and unseen acquisition modes, e.g. LR-encoding, coronal orientation) was reserved for testing and evaluation purposes. We compared our results to FSL's topup function with default parameters that served as the gold standard. We found that our approach results in a correction accuracy that is virtually identical to the optimum found by an iterative search, but with reduced computational time.

CONCLUSION

By using a deep convolutional network, we can reduce the processing time to a few seconds per volume, which is significantly faster than iterative approaches like FSL's topup which takes around 10min on the same machine (but using only 1 CPU). This facilitates the use of a blip up/down scheme for all diffusion-weighted acquisitions and potential real-time EPI distortion correction without sacrificing accuracy.

Evaluation of Six Phase Encoding Based Susceptibility Distortion Correction Methods for Diffusion MRI

Purpose: Susceptibility distortions impact diffusion MRI data analysis and is typically corrected during preprocessing. Correction strategies involve three classes of methods: registration to a structural image, the use of a fieldmap, or the use of images acquired with opposing phase encoding directions. It has been demonstrated that phase encoding based methods outperform the other two classes, but unfortunately, the choice of which phase encoding based method to use is still an open question due to the absence of any systematic comparisons.

Methods: In this paper we quantitatively evaluated six popular phase encoding based methods for correcting susceptibility distortions in diffusion MRI data. We employed a framework that allows for the simulation of realistic diffusion MRI data with susceptibility distortions. We evaluated the ability for methods to correct distortions by comparing the corrected data with the ground truth. Four diffusion tensor metrics (FA, MD, eigenvalues and eigenvectors) were calculated from the corrected data and compared with the ground truth. We also validated two popular indirect metrics using both simulated data and real data. The two indirect metrics are the difference between the corrected LR and AP data, and the FA standard deviation over the corrected LR, RL, AP, and PA data.

Results: We found that DR-BUDDI and TOPUP offered the most accurate and robust correction compared to the other four methods using both direct and indirect evaluation metrics. EPIC and HySCO performed well in correcting b₀ images but produced poor corrections for diffusion weighted volumes, and also they produced large errors for the four diffusion tensor metrics. We also demonstrate that the indirect metric (the difference between corrected LR and AP data) gives a different ordering of correction quality than the direct metric.

Conclusion: We suggest researchers to use DR-BUDDI or TOPUP for susceptibility distortion correction. The two indirect metrics (the difference between corrected LR and AP data, and the FA standard deviation) should be interpreted together as a measure of distortion correction quality. The performance ranking of the various tools inferred from direct and indirect metrics differs slightly. However, across all tools, the results of direct and indirect metrics are highly correlated indicating that the analysis of indirect metrics may provide a good proxy of the performance of a correction tool if assessment using direct metrics is not feasible.