Improved test-retest reliability of R 2 * $$ {\mathrm{R}}_2^{\ast } $$ and susceptibility quantification using multishot multi-echo 3D EPI

PURPOSE

This study aimed to evaluate the potential of 3D EPI for improving the reliability ofT 2 * $$ {\mathrm{T}}_2^{\ast } $$ -weighted data and quantification ofR 2 * $$ {\mathrm{R}}_2^{\ast } $$ decay rate and susceptibility (χ) compared with conventional gradient-echo (GRE)-based acquisition.

METHODS

Eight healthy subjects in a wide age range were recruited. Each subject received repeated scans for both GRE and EPI acquisitions with an isotropic 1 mm resolution at 3 T. Maps ofR 2 * $$ {\mathrm{R}}_2^{\ast } $$ and χ were quantified, and their interscan differences were used to evaluate the test-retest reliability. Interprotocol differences ofR 2 * $$ {\mathrm{R}}_2^{\ast } $$ and χ between GRE and EPI were also measured voxel by voxel and in selected regions of interest to test the consistency between the two acquisition methods.

RESULTS

The quantifications ofR 2 * $$ {\mathrm{R}}_2^{\ast } $$ and χ using EPI protocols showed increased test-retest reliability with higher EPI factors up to 5 as performed in the experiment and were consistent with those based on GRE.

CONCLUSION

The result suggests that multishot multi-echo 3D EPI can be a useful alternative acquisition method forT 2 * $$ {\mathrm{T}}_2^{\ast } $$ -weighted MRI and quantification ofR 2 * $$ {\mathrm{R}}_2^{\ast } $$ and χ with reduced scan time, improved test-retest reliability, and similar accuracy compared with commonly used 3D GRE.

Whole brain pattern of iron accumulation in REM sleep behavior disorder

Isolated REM sleep behavior disorder (iRBD) is an early stage of synucleinopathy with most patients progressing to Parkinson's disease (PD) or related conditions. Quantitative susceptibility mapping (QSM) in PD has identified pathological iron accumulation in the substantia nigra (SN) and variably also in basal ganglia and cortex. Analyzing whole-brain QSM across iRBD, PD, and healthy controls (HC) may help to ascertain the extent of neurodegeneration in prodromal synucleinopathy. 70 de novo PD patients, 70 iRBD patients, and 60 HCs underwent 3 T MRI. T1 and susceptibility-weighted images were acquired and processed to space standardized QSM. Voxel-based analyses of grey matter magnetic susceptibility differences comparing all groups were performed on the whole brain and upper brainstem levels with the statistical threshold set at family-wise error-corrected p-values <.05. Whole-brain analysis showed increased susceptibility in the bilateral fronto-parietal cortex of iRBD patients compared to both PD and HC. This was not associated with cortical thinning according to the cortical thickness analysis. Compared to iRBD, PD patients had increased susceptibility in the left amygdala and hippocampal region. Upper brainstem analysis revealed increased susceptibility within the bilateral SN for both PD and iRBD compared to HC; changes were located predominantly in nigrosome 1 in the former and nigrosome 2 in the latter group. In the iRBD group, abnormal dopamine transporter SPECT was associated with increased susceptibility in nigrosome 1. iRBD patients display greater fronto-parietal cortex involvement than incidental early-stage PD cohort indicating more widespread subclinical neuropathology. Dopaminergic degeneration in the substantia nigra is paralleled by susceptibility increase, mainly in nigrosome 1.

Exploiting gradient-echo frequency evolution: Probing white matter microstructure and extracting bulk susceptibility-induced frequency for quantitative susceptibility mapping

PURPOSE

This work is to investigate the microstructure-induced frequency shift in white matter (WM) with crossing fibers and to separate the microstructure-related frequency shift from the bulk susceptibility-induced frequency shift by model fitting the gradient-echo (GRE) frequency evolution for potentially more accurate quantitative susceptibility mapping (QSM).

METHODS

A hollow-cylinder fiber model (HCFM) with two fiber populations was developed to investigate GRE frequency evolutions in WM voxels with microstructural orientation dispersion. The simulated and experimentally measured TE-dependent local frequency shift was then fitted to a simplified frequency evolution model to obtain a microstructure-related frequency difference parameter (∆ f $$ \Delta f $$ ) and a TE-independent bulk susceptibility-induced frequency shift (C f $$ {C}_f $$ ). The obtainedC f $$ {C}_f $$ was then used for QSM reconstruction. Reconstruction performances were evaluated using a numerical head phantom and in vivo data and then compared to other multi-echo combination methods.

RESULTS

GRE frequency evolutions and∆ f $$ \Delta f $$ -based tissue parameters in both parallel and crossing fibers determined from our simulations were comparable to those observed in vivo. The TE-dependent frequency fitting method outperformed other multi-echo combination methods in estimatingC f $$ {C}_f $$ in simulations. The fitted∆ f $$ \Delta f $$ ,C f $$ {C}_f $$ , and QSM could be improved further by navigator-based B0 fluctuation correction.

CONCLUSION

A HCFM with two fiber populations can be used to characterize microstructure-induced frequency shifts in WM regions with crossing fibers. HCFM-based TE-dependent frequency fitting provides tissue contrast related to microstructure (∆ f $$ \Delta f $$ ) and in addition may help improve the quantification accuracy ofC f $$ {C}_f $$ and the corresponding QSM.

Quantifying cerebral microbleeds using quantitative susceptibility mapping from magnetization-prepared rapid gradient-echo

T1-weighted magnetization-prepared rapid gradient-echo (MPRAGE) is commonly included in brain studies for structural imaging using magnitude images; however, its phase images can provide an opportunity to assess microbleed burden using quantitative susceptibility mapping (QSM). This potential application for MPRAGE-based QSM was evaluated using in vivo and simulated measurements. Possible factors affecting image quality were also explored. Detection sensitivity was evaluated against standard multiecho gradient echo (MEGE) QSM using 3-T in vivo data of 15 subjects with a combined total of 108 confirmed microbleeds. The two methods were compared based on the microbleed size and susceptibility measurements. In addition, simulations explored the detection sensitivity of MPRAGE-QSM at different representative magnetic field strengths and echo times using microbleeds of different size, susceptibility, and location. Results showed that in vivo microbleeds appeared to be smaller (× 0.54) and of higher mean susceptibility (× 1.9) on MPRAGE-QSM than on MEGE-QSM, but total susceptibility estimates were in closer agreement (slope: 0.97, r2 : 0.94), and detection sensitivity was comparable. In simulations, QSM at 1.5 T had a low contrast-to-noise ratio that obscured the detection of many microbleeds. Signal-to-noise ratio (SNR) levels at 3 T and above resulted in better contrast and increased detection. The detection rates for microbleeds of minimum one-voxel diameter and 0.4-ppm susceptibility were 0.55, 0.80, and 0.88 at SNR levels of 1.5, 3, and 7 T, respectively. Size and total susceptibility estimates were more consistent than mean susceptibility estimates, which showed size-dependent underestimation. MPRAGE-QSM provides an opportunity to detect and quantify the size and susceptibility of microbleeds of at least one-voxel diameter at B0  of 3 T or higher with no additional time cost, when standard T2 *-weighted images are not available or have inadequate spatial resolution. The total susceptibility measure is more robust against sequence variations and might allow combining data from different protocols.

Quantitative susceptibility mapping for iron monitoring of multiple subcortical nuclei in type 2 diabetes mellitus: a systematic review and meta-analysis

Introduction

Iron accumulation in the brain has been linked to diabetes, but its role in subcortical structures involved in motor and cognitive functions remains unclear. Quantitative susceptibility mapping (QSM) allows the non-invasive quantification of iron deposition in the brain. This systematic review and meta-analysis examined magnetic susceptibility measured by QSM in the subcortical nuclei of patients with type 2 diabetes mellitus (T2DM) compared with controls.

Methods

PubMed, Scopus, and Web of Science databases were systematically searched [following Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines] for studies reporting QSM values in the deep gray matter (DGM) regions of patients with T2DM and controls. Pooled standardized mean differences (SMDs) for susceptibility were calculated using fixed-effects meta-analysis models, and heterogeneity was assessed using I2. Sensitivity analyses were conducted, and publication bias was evaluated using Begg's and Egger's tests.

Results

Six studies including 192 patients with T2DM and 245 controls were included. This study found a significant increase in iron deposition in the subcortical nuclei of patients with T2DM compared to the control group. The study found moderate increases in the putamen (SMD = 0.53, 95% CI 0.33 to 0.72, p = 0.00) and dentate nucleus (SMD = 0.56, 95% CI 0.27 to 0.85, p = 0.00) but weak associations between increased iron levels in the caudate nucleus (SMD = 0.32, 95% CI 0.13 to 0.52, p = 0.00) and red nucleus (SMD = 0.22, 95% CI 0.00 0.44, p = 0.05). No statistical significance was found for iron deposition alterations in the globus pallidus (SMD = 0.19; 95% CI -0.01 to 0.38; p = 0.06) and substantia nigra (SMD = 0.12, 95% CI -0.10, 0.34, p = 0.29). Sensitivity analysis showed that the findings remained unaffected by individual studies, and consistent increases were observed in multiple subcortical areas.

Discussion

QSM revealed an increase in iron in the DGM/subcortical nuclei in T2DM patients versus controls, particularly in the motor and cognitive nuclei, including the putamen, dentate nucleus, caudate nucleus, and red nucleus. Thus, QSM may serve as a potential biomarker for iron accumulation in T2DM patients. However, further research is needed to validate these findings.

Longitudinal Associations of Magnetic Susceptibility with Clinical Severity in Parkinson's Disease

BACKGROUND

Dementia is common in Parkinson's disease (PD), but there is wide variation in its timing. A critical gap in PD research is the lack of quantifiable markers of progression, and methods to identify early stages of dementia. Atrophy-based magnetic resonance imaging (MRI) has limited sensitivity in detecting or tracking changes relating to PD dementia, but quantitative susceptibility mapping (QSM), sensitive to brain tissue iron, shows potential for these purposes.

OBJECTIVE

The objective of the paper is to study, for the first time, the longitudinal relationship between cognition and QSM in PD in detail.

METHODS

We present a longitudinal study of clinical severity in PD using QSM, including 59 PD patients (without dementia at study onset), and 22 controls over 3 years.

RESULTS

In PD, increased baseline susceptibility in the right temporal cortex, nucleus basalis of Meynert, and putamen was associated with greater cognitive severity after 3 years; and increased baseline susceptibility in basal ganglia, substantia nigra, red nucleus, insular cortex, and dentate nucleus was associated with greater motor severity after 3 years. Increased follow-up susceptibility in these regions was associated with increased follow-up cognitive and motor severity, with further involvement of hippocampus relating to cognitive severity. However, there were no consistent increases in susceptibility over 3 years.

CONCLUSIONS

Our study suggests that QSM may predict changes in cognitive severity many months prior to overt cognitive involvement in PD. However, we did not find robust longitudinal changes in QSM over the course of the study. Additional tissue metrics may be required together with QSM for it to monitor progression in clinical practice and therapeutic trials. © 2024 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.

Iron quantification in basal ganglia: quantitative susceptibility mapping as a potential biomarker for Alzheimer's disease - a systematic review and meta-analysis

Introduction

Alzheimer's disease (AD), characterized by distinctive pathologies such as amyloid-β plaques and tau tangles, also involves deregulation of iron homeostasis, which may accelerate neurodegeneration. This meta-analysis evaluated the use of quantitative susceptibility mapping (QSM) to detect iron accumulation in the deep gray matter (DGM) of the basal ganglia in AD, contributing to a better understanding of AD progression, and potentially leading to new diagnostic and therapeutic approaches.

Methods

Using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, we systematically searched the PubMed, Scopus, Web of Sciences, and Google Scholar databases up to October 2023 for studies employing QSM in AD research. Eligibility criteria were based on the PECO framework, and we included studies assessing alterations in magnetic susceptibility indicative of iron accumulation in the DGM of patients with AD. After initial screening and quality assessment using the Newcastle-Ottawa Scale, a meta-analysis was conducted to compare iron levels between patients with AD and healthy controls (HCs) using a random-effects model.

Results

The meta-analysis included nine studies comprising 267 patients with AD and 272 HCs. There were significantly higher QSM values, indicating greater iron deposition, in the putamen (standardized mean difference (SMD) = 1.23; 95% CI: 0.62 to 1.84; p = 0.00), globus pallidus (SMD = 0.79; 95% CI: 0.07 to 1.52; p = 0.03), and caudate nucleus (SMD = 0.72; 95% CI: 0.39 to 1.06; p = 0.00) of AD patients compared to HCs. However, no significant differences were found in the thalamus (SMD = 1.00; 95% CI: -0.42 to 2.43; p = 0.17). The sensitivity analysis indicated that no single study impacted the overall results. Age was identified as a major contributor to heterogeneity across all basal ganglia nuclei in subgroup analysis. Older age (>69 years) and lower male percentage (≤30%) were associated with greater putamen iron increase in patients with AD.

Conclusion

The study suggests that excessive iron deposition is linked to the basal ganglia in AD, especially the putamen. The study underscores the complex nature of AD pathology and the accumulation of iron, influenced by age, sex, and regional differences, necessitating further research for a comprehensive understanding.

Oxygen extraction fraction (OEF) values and applications in neurological diseases

One of the goals of this systematic review is to provide a meta-analysis-derived mean OEF of healthy volunteers. Another aim of this study is to indicate the OEF ranges of various neurological pathologies. Potential clinical applications of OEF metrics are presented. Peer-reviewed studies reporting OEF metrics derived from computed tomography (CT)/positron emission tomography (PET) and/or magnetic resonance imaging (MRI) were considered. Databases utilized included MEDLINE, PubMed, EMBASE, Web of Science, and Google Scholar. The Newcastle-Ottawa scoring system was used for evaluating studies. R Studio was utilized for the meta-analysis calculations when appropriate. The GRADE framework was utilized to assess additional findings. Of 2267 potential studies, 165 met the inclusion criteria. The healthy volunteer meta-analysis included 339 subjects and found a mean OEF value of 38.87 (37.38, 40.36), with a prediction interval of 32.40-45.34. There were no statistical differences in OEF values derived from PET versus MRI. We provided a GRADE A certainty rating for the use of OEF metrics to predict stroke occurrence in patients with symptomatic carotid or cerebral vessel disease. We provided a GRADE B certainty rating for monitoring treatment response in Moyamoya disease. Use of OEF metrics in diagnosing and/or monitoring other conditions had a GRADE C certainty rating or less. OEF might have a role in diagnosing and monitoring patients with symptomatic carotid or cerebral vessel disease and Moyamoya disease. While we found insufficient evidence to support measuring OEF metrics in other patient populations, in many cases, further studies are warranted.

Improving quantitative susceptibility mapping for the identification of traumatic brain injury neurodegeneration at the individual level

BACKGROUND

Emerging evidence suggests that traumatic brain injury (TBI) is a major risk factor for developing neurodegenerative disease later in life. Quantitative susceptibility mapping (QSM) has been used by an increasing number of studies in investigations of pathophysiological changes in TBI. However, generating artefact-free quantitative susceptibility maps in brains with large focal lesions, as in the case of moderate-to-severe TBI (ms-TBI), is particularly challenging. To address this issue, we utilized a novel two-pass masking technique and reconstruction procedure (two-pass QSM) to generate quantitative susceptibility maps (QSMxT; Stewart et al., 2022, Magn Reson Med.) in combination with the recently developed virtual brain grafting (VBG) procedure for brain repair (Radwan et al., 2021, NeuroImage) to improve automated delineation of brain areas. We used QSMxT and VBG to generate personalised QSM profiles of individual patients with reference to a sample of healthy controls.

METHODS

Chronic ms-TBI patients (N = 8) and healthy controls (N = 12) underwent (multi-echo) GRE, and anatomical MRI (MPRAGE) on a 3T Siemens PRISMA scanner. We reconstructed the magnetic susceptibility maps using two-pass QSM from QSMxT. We then extracted values of magnetic susceptibility in grey matter (GM) regions (following brain repair via VBG) across the whole brain and determined if they deviate from a reference healthy control group [Z-score < -3.43 or > 3.43, relative to the control mean], with the aim of obtaining personalised QSM profiles.

RESULTS

Using two-pass QSM, we achieved susceptibility maps with a substantial increase in quality and reduction in artefacts irrespective of the presence of large focal lesions, compared to single-pass QSM. In addition, VBG minimised the loss of GM regions and exclusion of patients due to failures in the region delineation step. Our findings revealed deviations in magnetic susceptibility measures from the HC group that differed across individual TBI patients. These changes included both increases and decreases in magnetic susceptibility values in multiple GM regions across the brain.

CONCLUSIONS

We illustrate how to obtain magnetic susceptibility values at the individual level and to build personalised QSM profiles in ms-TBI patients. Our approach opens the door for QSM investigations in more severely injured patients. Such profiles are also critical to overcome the inherent heterogeneity of clinical populations, such as ms-TBI, and to characterize the underlying mechanisms of neurodegeneration at the individual level more precisely. Moreover, this new personalised QSM profiling could in the future assist clinicians in assessing recovery and formulating a neuroscience-guided integrative rehabilitation program tailored to individual TBI patients.

Glutathione Depletion and Concomitant Elevation of Susceptibility in Patients with Parkinson's Disease: State-of-the-Art MR Spectroscopy and Neuropsychological Study

Parkinson's disease (PD) is characterized by extrapyramidal motor disturbances and nonmotor cognitive impairments which impact activities of daily living. Although the etiology of PD is still obscure, autopsy reports suggest that oxidative stress (OS) is one of the important factors in the pathophysiology of PD. In the current study, we have investigated the impact of OS in PD by measuring the antioxidant glutathione (GSH) levels from the substantia nigra (SN), left hippocampus (LH) and neurotransmitter γ-amino butyric acid (GABA) levels from SN region. Concomitant quantitative susceptibility mapping (QSM) from SN and LH was also acquired from thirty-eight PD patients and 30 age-matched healthy controls (HC). Glutathione levels in the SN region decreased significantly and susceptibility increased significantly in PD compared to HC. Nonsignificant depletion of GABA was observed in the SN region. GSH levels in the LH region were depleted significantly, but LH susceptibility did not alter in the PD cohort compared to HC. Neuropsychological and physical assessment demonstrated significant impairment of cognitive functioning in PD patients compared to HC. GSH depletion was negatively correlated to motor function performance. Multivariate receiver operating characteristic (ROC) curve analysis on the combined effect of GSH, GABA, and susceptibility in the SN region yielded an improved diagnostic accuracy of 86.1% compared to individual diagnostic accuracy based on GSH (65.8%), GABA (57.5%), and susceptibility (69.6%). This is the first comprehensive report in PD demonstrating significant GSH depletion as well as concomitant iron enhancement in the SN region.

Super-resolution QSM in little or no additional time for imaging (NATIve) using 2D EPI imaging in 3 orthogonal planes

Quantitative Susceptibility Mapping has the potential to provide additional insights into neurological diseases but is typically based on a quite long (5-10 min) 3D gradient-echo scan which is highly sensitive to motion. We propose an ultra-fast acquisition based on three orthogonal (sagittal, coronal and axial) 2D simultaneous multi-slice EPI scans with 1 mm in-plane resolution and 3 mm thick slices. Images in each orientation are corrected for susceptibility-related distortions and co-registered with an iterative non-linear Minimum Deformation Averaging (Volgenmodel) approach to generate a high SNR, super-resolution data set with an isotropic resolution of close to 1 mm. The net acquisition time is 3 times the volume acquisition time of EPI or about 12 s, but the three volumes could also replace "dummy scans" in fMRI, making it feasible to acquire QSM in little or No Additional Time for Imaging (NATIve). NATIve QSM values agreed well with reference 3D GRE QSM in the basal ganglia in healthy subjects. In patients with multiple sclerosis, there was also a good agreement between the susceptibility values within lesions and control ROIs and all lesions which could be seen on 3D GRE QSMs could also be visualized on NATIve QSMs. The approach is faster than conventional 3D GRE by a factor of 25-50 and faster than 3D EPI by a factor of 3-5. As a 2D technique, NATIve QSM was shown to be much more robust to motion than the 3D GRE and 3D EPI, opening up the possibility of studying neurological diseases involving iron accumulation and demyelination in patients who find it difficult to lie still for long enough to acquire QSM data with conventional methods.

Prediction of amyloid positron emission tomography positivity using multiple regression analysis of quantitative susceptibility mapping

PURPOSE

To develop a method for predicting amyloid positron emission tomography (PET) positivity based on multiple regression analysis of quantitative susceptibility mapping (QSM).

MATERIALS AND METHODS

This prospective study included 39 patients with suspected dementia from four centers. QSM images were obtained through a 3-T, three-dimensional radiofrequency-spoiled gradient-echo sequence with multiple echoes. The cortical standard uptake value ratio (SUVR) was obtained using amyloid PET with 18F-flutemetamol, and susceptibility in the brain regions was obtained using QSM. A multiple regression model to predict cortical SUVR was constructed based on susceptibilities in multiple brain regions, with the constraint that cortical SUVR and susceptibility were positively correlated. The discrimination performance of the Aβ-positive and Aβ-negative cohorts was evaluated based on the predicted SUVR using the area under the receiver operating characteristic curve (AUC) and Mann-Whitney U test.

RESULTS

The correlation coefficients between true and predicted SUVR were increased by incorporating the constraint, and the AUC to discriminate between the Aβ-positive and Aβ-negative cohorts reached to 0.79 (p < 0.01).

CONCLUSION

These preliminary results suggest that a QSM-based multiple regression model can predict amyloid PET positivity with fair accuracy.

Exploring the antibacterial potential of magnetite/Quince seed mucilage/Ag nanocomposite: Synthesis, characterization, and activity assessment

In this study, we present a novel core-shell antibacterial agent designed for water disinfection purposes. The nanocomposite is synthesized by combining quince seed mucilage (QSM) as the shell material and Fe3O4 as the core material. The integration of antibacterial silver nanoparticles (Ag NPs) onto the QSM shell effectively prevents agglomeration of the Ag NPs, resulting in a larger contact surface area with bacteria and consequently exhibiting enhanced antibacterial activity. The incorporation of magnetic Fe3O4 NPs with a saturation magnetization of 55.2 emu·g-1 as the core allows for easy retrieval of the nanocomposites from the medium using a strong magnetic field, enabling their reusability. The Fe3O4/QSM/Ag nanocomposite is extensively characterized using XRD, FT-IR, VSM, DLS, FE-SEM, and TEM techniques. The characterization results confirm the successful synthesis of the nanocomposites, with an average particle size of 73 nm and no contamination or impurities detected. The nanocomposites exhibit superparamagnetic properties, with a saturated magnetization of 22.69 emu·g-1, ensuring facile separation from water. The antibacterial activity of the synthesized nanocomposite is evaluated using the disk diffusion method against both Gram-positive and Gram-negative bacteria. The results reveal excellent antibacterial efficacy, with minimum inhibition concentrations (MIC) of 0.8 mg·mL-1 against E. coli and S. typhimurium. Furthermore, the measurement of released silver ions in water using ICP-OES indicates a low concentration of remaining silver ions in the medium, highlighting the controlled release of antimicrobial agents. Overall, this study provides valuable insights into the development of advanced antibacterial agents for water disinfection applications, offering potential solutions to combat microbial contamination effectively.

Iron quantification in basal ganglia using quantitative susceptibility mapping in a patient with ALS: a case report and literature review

Background

Quantitative susceptibility mapping (QSM) is a magnetic resonance imaging (MRI) technique that can measure the magnetic susceptibility of tissues, which can reflect their iron content. QSM has been used to detect iron accumulation in cortical and subcortical brain regions. However, its application in subcortical regions such as the basal ganglia, particularly the putamen, is rare in patients with amyotrophic lateral sclerosis (ALS).

Case presentation and literature review

We present the case of a 40-year-old male patient with ALS who underwent an MRI for QSM. We compared his QSM images with those of a control subject and performed a quantitative analysis of the magnetic susceptibility values in the putamen regions. We also reviewed the literature on previous QSM studies in ALS and summarized their methods and findings. Our QSM analysis revealed increased magnetic susceptibility values in the bilateral putamen of the ALS patient compared to controls, indicating iron overload. This finding is consistent with previous studies reporting iron dysregulation in subcortical nuclei in ALS. We also discussed the QSM processing techniques used in our study and in the literature, highlighting their advantages and limitations.

Conclusion

This case report demonstrates the potential of QSM as a sensitive MRI biomarker for evaluating iron levels in subcortical regions of ALS patients. QSM can provide quantitative information on iron deposition patterns in both motor and extra-motor areas of ALS patients, which may help understand the pathophysiology of ALS and monitor disease progression. Further studies with larger samples are needed to validate these results and explore the clinical implications of QSM in ALS.

Quantitative MRI protocol and decision model for a 'one stop shop' early-stage Parkinsonism diagnosis: Study design

Differentiating among early-stage parkinsonisms is a challenge in clinical practice. Quantitative MRI can aid the diagnostic process, but studies with singular MRI techniques have had limited success thus far. Our objective is to develop a multi-modal MRI method for this purpose. In this review we describe existing methods and present a dedicated quantitative MRI protocol, a decision model and a study design to validate our approach ahead of a pilot study. We present example imaging data from patients and a healthy control, which resemble related literature.

Quantitative Susceptibility Mapping MRI in Deep-Brain Nuclei in First-Episode Psychosis

BACKGROUND

Psychosis is related to neurochemical changes in deep-brain nuclei, particularly suggesting dopamine dysfunctions. We used an magnetic resonance imaging-based technique called quantitative susceptibility mapping (QSM) to study these regions in psychosis. QSM quantifies magnetic susceptibility in the brain, which is associated with iron concentrations. Since iron is a cofactor in dopamine pathways and co-localizes with inhibitory neurons, differences in QSM could reflect changes in these processes.

METHODS

We scanned 83 patients with first-episode psychosis and 64 healthy subjects. We reassessed 22 patients and 21 control subjects after 3 months. Mean susceptibility was measured in 6 deep-brain nuclei. Using linear mixed models, we analyzed the effect of case-control differences, region, age, gender, volume, framewise displacement (FD), treatment duration, dose, laterality, session, and psychotic symptoms on QSM.

RESULTS

Patients showed a significant susceptibility reduction in the putamen and globus pallidus externa (GPe). Patients also showed a significant R2* reduction in GPe. Age, gender, FD, session, group, and region are significant predictor variables for QSM. Dose, treatment duration, and volume were not predictor variables of QSM.

CONCLUSIONS

Reduction in QSM and R2* suggests a decreased iron concentration in the GPe of patients. Susceptibility reduction in putamen cannot be associated with iron changes. Since changes observed in putamen and GPe were not associated with symptoms, dose, and treatment duration, we hypothesize that susceptibility may be a trait marker rather than a state marker, but this must be verified with long-term studies.

Robust breast quantitative susceptibility mapping in the presence of silicone

PURPOSE

To (a) develop a preconditioned water-fat-silicone total field inversion (wfsTFI) algorithm that directly estimates the susceptibility map from complex multi-echo data in the breast in the presence of silicone and to (b) evaluate the performance of wfsTFI for breast quantitative susceptibility mapping (QSM) in silico and in vivo in comparison with formerly proposed methods.

METHODS

Numerical simulations and in vivo multi-echo gradient echo breast measurements were performed to compare wfsTFI to a previously proposed field map-based linear total field inversion algorithm (lTFI) with and without the consideration of the chemical shift of silicone in the field map estimation step. Specifically, a simulation based on an in vivo scan and data from five patients were included in the analysis.

RESULTS

In the simulation, wfsTFI is able to significantly decrease the normalized root mean square error from lTFI without (4.46) and with (1.77) the consideration of the chemical shift of silicone to 0.68. Both the in silico and in vivo wfsTFI susceptibility maps show reduced shadowing artifacts in local tissue adjacent to silicone, reduced streaking artifacts and no erroneous single voxels of diamagnetic susceptibility in proximity to silicone.

CONCLUSION

The proposed wfsTFI method can automatically distinguish between subjects with and without silicone. Furthermore wfsTFI accounts for the presence of silicone in the QSM dipole inversion and allows for the robust estimation of susceptibility in proximity to silicone breast implants and hence allows the visualization of structures that would otherwise be dominated by artifacts on susceptibility maps.

Improved test-retest reliability of R2* and susceptibility quantification using multi-shot multi-echo 3D EPI

This study aimed to evaluate the potential of 3D echo-planar imaging (EPI) for improving the reliability of T2*-weighted (T2*w) data and quantification of R2* decay rate and susceptibility (χ) compared to conventional gradient echo (GRE)-based acquisition. Eight healthy subjects in a wide age range were recruited. Each subject received repeated scans for both GRE and EPI acquisitions with an isotropic 1 mm resolution at 3 T. Maps of R2* and χ were quantified and compared using their inter-scan difference to evaluate the test-retest reliability. Inter-protocol differences of R2* and χ between GRE and EPI were also measured voxel by voxel and in selected ROIs to test the consistency between the two acquisition methods. The quantifications of R2* and χ using EPI protocols showed increased test-retest reliability with higher EPI factors up to 5 as performed in the experiment and were consistent with those based on GRE. This result suggested multi-shot multi-echo 3D EPI can be a useful alternative acquisition method for T2*w MRI and quantification of R2* and χ with reduced scan time, improved test-retest reliability and similar accuracy compared to commonly used 3D GRE.

Investigating the performance of susceptibility-weighted images in Fricke gel dosimeter reading and optimizing the related imaging parameters

Fricke gel dosimeters are especially useful in small-field dosimetry and validation of treatment delivery in&#xD;three-dimensional space with features such as tissue equivalence, non-toxicity, high spatial resolution, nondependence&#xD;on energy, and dose rate. The use of basic MRI imaging protocols (T1W and T2W) for reading&#xD;Fricke gel dosimeters has always been considered the dominant method in many studies. However, the&#xD;development and application of advanced MRI techniques for more accurate readings of Fricke gel&#xD;dosimeters can be useful. Considering that in the main structure of Fricke gel, there are conversions of iron&#xD;ions to each other, this study aimed to investigate the performance of susceptibility-based images (SWI and&#xD;QSM) based on magnetic susceptibility in the reading of Fricke gel dosimeters and to optimize the related&#xD;imaging parameters. For this purpose, a Fricke-Xylenol orange-gelatin was made at five concentrations of&#xD;iron ammonium sulfate. To obtain gel dosimeter calibration curves, vials containing gel were subjected to&#xD;irradiation at three different doses by a linear accelerator. The reading of gel dosimeters was performed&#xD;using MRI imaging in three protocols, T1W, T2W, and SWI, and analyzed with a method unique to each&#xD;one. Finally, the results obtained from the three protocols were compared with each other. The comparison&#xD;of calibration curves in three imaging protocols shows that the sensitivity of calibration curves in SWI was&#xD;about three times its value in T2W, and on the other hand, the reported sensitivity in T1W was very small&#xD;compared to the other two protocols. The linearity factor was similar between SWI and T1W protocols and&#xD;higher in T2W. Therefore, it is concluded that in addition to the relaxometry techniques that have been used&#xD;as a conventional method for reading Fricke gel dosimeter, SWI imaging has high sensitivity and specificity&#xD;for reading dosimeter gel based on iron.

Quantitation of Brain and Blood Glutathione and Iron in Healthy Age Groups Using Biophysical and In Vivo MR Spectroscopy: Potential Clinical Application

The antioxidant glutathione (GSH) and pro-oxidant iron levels play a balancing role in the modulation of oxidative stress (OS). There is a significant depletion of GSH in the left hippocampus (LH) in patients with Alzheimer's disease (AD) with concomitant elevation of iron level. However, the correlation of GSH and iron distribution patterns between the brain and the peripheral system (blood) is not yet known. We measured GSH and magnetic susceptibility (e.g., iron) in the LH region along with GSH in plasma and iron in serum across four age groups consisting of healthy volunteers (age range 18-72 y, n = 70). We report non-variability of the mean GSH in the plasma and LH region across mentioned age groups. The mean iron level in the LH region does not change, but the iron level in the serum in the 51-72 y age group increases non-significantly. Regression analysis of our data indicated that GSH and iron levels (both in blood and in brain) are not related to age. This research pave the way for the identification of a risk/susceptibility biomarker for AD and Parkinson's disease from the evaluation of GSH (in plasma) and iron (in serum) levels concomitantly.

Investigating the effect of oblique image acquisition on the accuracy of QSM and a robust tilt correction method

PURPOSE

Quantitative susceptibility mapping (QSM) is used increasingly for clinical research where oblique image acquisition is commonplace, but its effects on QSM accuracy are not well understood.

THEORY AND METHODS

The QSM processing pipeline involves defining the unit magnetic dipole kernel, which requires knowledge of the direction of the main magnetic fieldB ^ 0 $$ {\hat{\boldsymbol{B}}}_{\mathbf{0}} $$ with respect to the acquired image volume axes. The direction ofB ^ 0 $$ {\hat{\boldsymbol{B}}}_{\mathbf{0}} $$ is dependent on the axis and angle of rotation in oblique acquisition. Using both a numerical brain phantom and in vivo acquisitions in 5 healthy volunteers, we analyzed the effects of oblique acquisition on magnetic susceptibility maps. We compared three tilt-correction schemes at each step in the QSM pipeline: phase unwrapping, background field removal and susceptibility calculation, using the RMS error and QSM-tuned structural similarity index.

RESULTS

Rotation of wrapped phase images gave severe artifacts. Background field removal with projection onto dipole fields gave the most accurate susceptibilities when the field map was first rotated into alignment withB ^ 0 $$ {\hat{\boldsymbol{B}}}_{\mathbf{0}} $$ . Laplacian boundary value and variable-kernel sophisticated harmonic artifact reduction for phase data background field removal methods gave accurate results without tilt correction. For susceptibility calculation, thresholded k-space division, iterative Tikhonov regularization, and weighted linear total variation regularization, all performed most accurately when local field maps were rotated into alignment withB ^ 0 $$ {\hat{\boldsymbol{B}}}_{\mathbf{0}} $$ before susceptibility calculation.

CONCLUSION

For accurate QSM, oblique acquisition must be taken into account. Rotation of images into alignment withB ^ 0 $$ {\hat{\boldsymbol{B}}}_{\mathbf{0}} $$ should be carried out after phase unwrapping and before background-field removal. We provide open-source tilt-correction code to incorporate easily into existing pipelines: https://github.com/o-snow/QSM_TiltCorrection.git.

Quantitative Evaluation of Oxygen Extraction Fraction Changes in the Monkey Brain during Acute Stroke by Using Quantitative Susceptibility Mapping

BACKGROUND

The oxygen extraction fraction (OEF) indicates the brain's oxygen consumption and can be estimated by using the quantitative susceptibility mapping (QSM) MRI technique. Recent studies have suggested that OEF alteration following stroke is associated with the viability of at-risk tissue. In the present study, the temporal evolution of OEF in the monkey brain during acute stroke was investigated using QSM.

METHODS

Ischemic stroke was induced in adult rhesus monkeys (n = 8) with permanent middle cerebral artery occlusion (pMCAO) by using an interventional approach. Diffusion-, T2-, and T2*-weighted images were conducted on day 0, day 2, and day 4 post-stroke using a clinical 3T scanner. Progressive changes in magnetic susceptibility and OEF, along with their correlations with the transverse relaxation rates and diffusion indices, were examined.

RESULTS

The magnetic susceptibility and OEF in injured gray matter of the brain significantly increased during the hyperacute phase, and then decreased significantly on day 2 and day 4. Moreover, the temporal changes of OEF in gray matter were moderately correlated with mean diffusivity (MD) (r = 0.52; p = 0.046) from day 0 to day 4. Magnetic susceptibility in white matter progressively increased (from negative values to near zero) during acute stroke, and significant increases were seen on day 2 (p = 0.08) and day 4 (p = 0.003) when white matter was significantly degenerated. However, significant reduction of OEF in white matter was not seen until day 4 post-stroke.

CONCLUSION

The preliminary results demonstrate that QSM-derived OEF is a robust approach to examine the progressive changes of gray matter in the ischemic brain from the hyperacute phase to the subacute phase of stroke. The changes of OEF in gray matter were more prominent than those in white matter following stroke insult. The findings suggest that QSM-derived OEF may provide complementary information for understanding the neuropathology of the brain tissue following stroke and predicting stroke outcomes.

Validation of liver quantitative susceptibility mapping across imaging parameters at 1.5 T and 3.0 T using SQUID susceptometry as reference

PURPOSE

To validate QSM-based biomagnetic liver susceptometry (BLS) to measure liver iron overload at 1.5 T and 3.0 T using superconducting quantum interference devices (SQUID)-based BLS as reference.

METHODS

Subjects with known or suspected iron overload were recruited for QSM-BLS at 1.5 T and 3.0 T using eight different protocols. SQUID-BLS was also obtained in each subject to provide susceptibility reference. A recent QSM method based on data-adaptive regularization was used to obtain susceptibility and R 2 * $$ {\mathrm{R}}_2^{\ast } $$ maps. Measurements of susceptibility and R 2 * $$ {\mathrm{R}}_2^{\ast } $$ were obtained in the right liver lobe. Linear mixed-effects analysis was used to estimate the contribution of specific acquisition parameters to QSM-BLS. Linear regression and Bland-Altman analyses were used to assess the relationship between QSM-BLS and SQUID-BLS/ R 2 * $$ {\mathrm{R}}_2^{\ast } $$ .

RESULTS

Susceptibility maps showed high subjective quality for each acquisition protocol across different iron levels. High linear correlation was observed between QSM-BLS and SQUID-BLS at 1.5 T (r² range, [0.82, 0.84]) and 3.0 T (r² range, [0.77, 0.85]) across different acquisition protocols. QSM-BLS and R 2 * $$ {\mathrm{R}}_2^{\ast } $$ were highly correlated at both field strengths (r² range at 1.5 T, [0.94, 0.99]; 3.0 T, [0.93, 0.99]). High correlation (r²  = 0.99) between 1.5 T and 3.0 T QSM-BLS, with narrow reproducibility coefficients (range, [0.13, 0.21] ppm) were observed for each protocol.

CONCLUSION

This work evaluated the feasibility and performance of liver QSM-BLS across iron levels and acquisition protocols at 1.5 T and 3.0 T. High correlation and reproducibility were observed between QSM-BLS and SQUID-BLS across protocols and field strengths. In summary, QSM-BLS may enable reliable and reproducible quantification of liver iron concentration.

Tilted quantitative susceptibility mapping at oblique MRI (tiltQSM)

OBJECTIVE

If the phase image matrix was acquired from oblique MRI, it is needed to deal with the oblique effect for quantitative susceptibility mapping (QSM), as addressed in this paper.

METHODS

We proposed two methods for QSM reconstruction from slice-tilted MRI phase image (tiltQSM): 1) rotData per anti-tilting phase image rotation back into the B₀-upright system, and 2) rotKernel per pro-tilting dipole kernel rotation into the same oblique setting as defined by the tilted phase image. Both matrix methods were implemented in an additional preprocessing subroutine to ensure that the phase image and the dipole kernel were represented in the same coordinate system (either in B₀-upright system or in B₀-tilted system); thereafter tiltQSM could be completed through a regular QSM procedure. Besides the oblique effect, tiltQSM also suffers from MRI anisotropy. We provided numeric simulations, phantom tests and in vivo brain experiments on tiltQSM with oblique MRI (axial slice tilting at 3T).

RESULTS

The tiltQSM reconstruction could attain a performance corr > 0.90 (spatial correlation conformance) for small tilting angles <10°. The tiltQSM performance could be further degraded by voxel anisotropy due to image matrix rotation (digital geometry error).

CONCLUSIONS

To seek inverse solutions of MRI phase images acquired at oblique MRI (e.g. in axial slice tilting), we proposed tiltQSM to deal with the oblique effect per matrix rotation (either rotData or rotKernel) in a preprocessing subroutine prior to a regular QSM procedure. In practice, it is always recommended to acquire MRI phase images in isotropic matrix at zero obliqueness (or limited to small tilting angles <10°) for maximal (optimal) QSM reconstruction.

Data adaptive regularization with reference tissue constraints for liver quantitative susceptibility mapping

PURPOSE

To improve repeatability and reproducibility across acquisition parameters and reduce bias in quantitative susceptibility mapping (QSM) of the liver, through development of an optimized regularized reconstruction algorithm for abdominal QSM.

METHODS

An optimized approach to estimation of magnetic susceptibility distribution is formulated as a constrained reconstruction problem that incorporates estimates of the input data reliability and anatomical priors available from chemical shift-encoded imaging. The proposed data-adaptive method was evaluated with respect to bias, repeatability, and reproducibility in a patient population with a wide range of liver iron concentration (LIC). The proposed method was compared to the previously proposed and validated approach in liver QSM for two multi-echo spoiled gradient-recalled echo protocols with different acquisition parameters at 3T. Linear regression was used for evaluation of QSM methods against a reference FDA-approved R 2 $$ {R}_2 $$ -based LIC measure and R 2 ∗ $$ {R}_2^{\ast } $$ measurements; repeatability/reproducibility were assessed by Bland-Altman analysis.

RESULTS

The data-adaptive method produced susceptibility maps with higher subjective quality due to reduced shading artifacts. For both acquisition protocols, higher linear correlation with both R 2 $$ {R}_2 $$ - and R 2 ∗ $$ {R}_2^{\ast } $$ -based measurements were observed for the data-adaptive method ( r 2 = 0 . 74 / 0 . 69 $$ {r}^2=0.74/0.69 $$ for R 2 $$ {R}_2 $$ , 0 . 97 / 0 . 95 $$ 0.97/0.95 $$ for R 2 ∗ $$ {R}_2^{\ast } $$ ) than the standard method ( r 2 = 0 . 60 / 0 . 66 $$ {r}^2=0.60/0.66 $$ and 0 . 79 / 0 . 88 $$ 0.79/0.88 $$ ). For both protocols, the data-adaptive method enabled better test-retest repeatability (repeatability coefficients 0.19/0.30 ppm for the data-adaptive method, 0.38/0.47 ppm for the standard method) and reproducibility across protocols (reproducibility coefficient 0.28 vs. 0.53ppm) than the standard method.

CONCLUSIONS

The proposed data-adaptive QSM algorithm may enable quantification of LIC with improved repeatability/reproducibility across different acquisition parameters as 3T.

Irreversible Alterations of Susceptibility in Cushing's Disease: A Longitudinal QSM Study

OBJECTIVES

Chronic exposure to hypercortisolism is associated with accelerated aging and neurodegenerative diseases, while Cushing's disease (CD) is the most common form of endogenous hypercortisolism exposure. This study aimed to assess longitudinal susceptibility changes in CD using quantitative susceptibility mapping (QSM) before and after resolution of hypercortisolism.

METHODS

In this study, twenty-four CD patients and 24 healthy controls underwent magnetic resonance imaging with QSM. All CD patients underwent MRI scans before and after the curative operation.

RESULTS

After resolution of hypercortisolism, irreversibly altered susceptibility values were found in the anterior cingulate cortex, frontal lobe, caudate and red nucleus. These alterations were significantly correlated with the changes in gray matter/white matter volumes and clinical features. Additionally, decrease susceptibility was found in several regions in CD patients.

CONCLUSION

Chronic exposure to hypercortisolism may be related to susceptibility alterations and significantly correlated with altered brain volumes and clinical features. in CD patients. The decrease of susceptibility might suggest the involvement of the calcium deregulation in these alterations.

Multi-echo dipole inversion for magnetic susceptibility mapping

PURPOSE

Reconstructing tissue magnetic susceptibility (QSM) from MRI phase data involves solving multiple consecutive ill-posed inverse problems such as phase unwrapping, background field removal, and field-to-source inversion. Multi-echo acquisitions present an additional challenge, as the magnetization field is typically computed from the multiple phase data prior to reconstructing the susceptibility map. Processing the multiple phase data introduces errors during the field estimation, violating assumptions of the subsequent inverse problems, manifesting as streaking artifacts in the susceptibility map. To address this challenge, we propose a multi-echo field-to-source forward model that forgoes the field estimation step. Moreover, we propose a fully general underestimation correction step to recover susceptibility sources that were regularized away during the field-to-source inversion.

METHODS

The multi-echo forward model and correction step were validated on the QSM Challenge 2.0 datasets and compared to the standard single field-to-source model in in vivo human brains using different types of deconvolution algorithms.

RESULTS

On the QSM Challenge 2.0 datasets the multi-echo forward model and correction step attain state-of-the-art results on all metrics by a wide margin. Experiments in in vivo brains show that the multi-echo model is in agreement with the single field-to-source model and that the proposed forward model and correction step can be used with any available dipole inversion method.

CONCLUSION

A multi-echo field-to-source forward model forgoes the need to fit multi-echo phase data and achieves state-of-the-art results on the QSM Challenge 2.0 data. Underestimated low-frequency susceptibility distributions can be partially recovered using a correction step.

Incomplete spectrum QSM using support information

Introduction

Reconstructing a bounded object from incomplete k-space data is a well posed problem, and it was recently shown that this incomplete spectrum approach can be used to reconstruct undersampled MRI images with similar quality to compressed sensing approaches. Here, we apply this incomplete spectrum approach to the field-to-source inverse problem encountered in quantitative magnetic susceptibility mapping (QSM). The field-to-source problem is an ill-posed problem because of conical regions in frequency space where the dipole kernel is zero or very small, which leads to the kernel's inverse being ill-defined. These "ill-posed" regions typically lead to streaking artifacts in QSM reconstructions. In contrast to compressed sensing, our approach relies on knowledge of the image-space support, more commonly referred to as the mask, of our object as well as the region in k-space with ill-defined values. In the QSM case, this mask is usually available, as it is required for most QSM background field removal and reconstruction methods.

Methods

We tuned the incomplete spectrum method (mask and band-limit) for QSM on a simulated dataset from the most recent QSM challenge and validated the QSM reconstruction results on brain images acquired in five healthy volunteers, comparing incomplete spectrum QSM to current state-of-the art-methods: FANSI, nonlinear dipole inversion, and conventional thresholded k-space division.

Results

Without additional regularization, incomplete spectrum QSM performs slightly better than direct QSM reconstruction methods such as thresholded k-space division (PSNR of 39.9 vs. 39.4 of TKD on a simulated dataset) and provides susceptibility values in key iron-rich regions similar or slightly lower than state-of-the-art algorithms, but did not improve the PSNR in comparison to FANSI or nonlinear dipole inversion. With added (ℓ1-wavelet based) regularization the new approach produces results similar to compressed sensing based reconstructions (at sufficiently high levels of regularization).

Discussion

Incomplete spectrum QSM provides a new approach to handle the "ill-posed" regions in the frequency-space data input to QSM.

Cognition and brain iron deposition in whole grey matter regions and hippocampal subfields

Regional brain iron accumulation is observed in many neurodegenerative diseases, including Alzheimer's disease and Parkinson's disease, and is associated with cognitive decline. We explored associations between age, cognition and iron content in grey matter regions and hippocampal subfields in 380 participants of the Aberdeen children of the 1950s cohort and their first-generation relatives (aged 26-72 years). Participants underwent cognitive assessment at the time of MRI scanning. Quantitative susceptibility mapping of these MRI data was used to assess iron content in grey matter regions and in hippocampal subfields. Principle component analysis was performed on cognitive test scores to create a general cognition score. Spline analysis was used with the Akaike information criterion to determine if order 1, 2 or 3 natural splines were optimal for assessing non-linear relationships between regional iron and age. Multivariate linear models were used to assess associations between regional iron and cognition. Higher iron correlated with older age in the left putamen across all ages and in the right putamen of only participants over 58. Whereas a decrease in iron with older age was observed in the right thalamus and left pallidum across all ages. Right amygdala iron levels were associated with poorer general cognition scores and poorer immediate recall scores. Iron was not associated with any measures of cognitive performance in other regions of interest. Our results suggest that, whilst iron in some regions was associated with cognitive performance, there is an overall lack of association between regional iron content and cognitive ability in cognitively healthy individuals.

Quantitative Susceptibility Mapping: Translating an Investigative Research Tool into High Volume Clinical Diagnostic Imaging

Quantitative susceptibility mapping (QSM) is an MRI-based technique for iron quantification of targeted tissue. QSM provides information relevant to clinicians in a broad range of diagnostic contexts, including sickle cell disease, inflammatory/demyelinating processes, and neoplasms. However, major MRI vendors do not offer QSM post-processing in a form ready for general use. This work describes a vendor-agnostic approach for scaling QSM analysis from a research technique to a routine diagnostic test. We provide the details needed to seamlessly integrate hardware, software, and clinical systems to provide QSM processing for a busy clinical radiology workflow. This approach can be generalized to other advanced MRI acquisitions and analyses with proven diagnostic utility, yet without crucial MR vendor support.

Feasibility of ultrashort echo time quantitative susceptibility mapping with a 3D cones trajectory in the human brain

Purpose

Quantitative susceptibility mapping (QSM) has surfaced as a promising non-invasive quantitative biomarker that provides information about tissue composition and microenvironment. Recently, ultrashort echo time quantitative susceptibility mapping (UTE-QSM) has been investigated to achieve QSM of short T2 tissues. As the feasibility of UTE-QSM has not been demonstrated in the brain, the goal of this study was to develop a UTE-QSM with an efficient 3D cones trajectory and validate it in the human brain.

Materials and methods

An ultrashort echo time (UTE) cones sequence was implemented in a 3T clinical MRI scanner. Six images were acquired within a single acquisition, including UTE and gradient recalled echo (GRE) images. To achieve QSM, a morphology-enabled dipole inversion (MEDI) algorithm was incorporated, which utilizes both magnitude and phase images. Three fresh cadaveric human brains were scanned using the 3D cones trajectory with eight stretching factors (SFs) ranging from 1.0 to 1.7. In addition, five healthy volunteers were recruited and underwent UTE-QSM to demonstrate the feasibility in vivo. The acquired data were processed with the MEDI-QSM pipeline.

Results

The susceptibility maps estimated by UTE-QSM showed reliable tissue contrast. In the ex vivo experiment, high correlations were found between the baseline (SF of 1.0) and SFs from 1.1 to 1.7 with Pearson's correlations of 0.9983, 0.9968, 0.9959, 0.9960, 0.9954, 0.9943, and 0.9879, respectively (all p-values < 0.05). In the in vivo experiment, the measured QSM values in cortical gray matter, juxtacortical white matter, corpus callosum, caudate, and putamen were 25.4 ± 4.0, -21.8 ± 3.2, -22.6 ± 10.0, 77.5 ± 18.8, and 53.8 ± 7.1 ppb, consistent with the values reported in the literature.

Conclusion

Ultrashort echo time quantitative susceptibility mapping enables direct estimation of the magnetic susceptibility in the brain with a dramatically reduced total scan time by use of a stretched 3D cones trajectory. This technique provides a new biomarker for susceptibility mapping in the in vivo brain.

Susceptibility networks reveal independent patterns of brain iron abnormalities in multiple sclerosis

Brain iron homeostasis is necessary for healthy brain function. MRI and histological studies have shown altered brain iron levels in the brains of patients with multiple sclerosis (MS), particularly in the deep gray matter (DGM). Previous studies were able to only partially separate iron-modifying effects because of incomplete knowledge of iron-modifying processes and influencing factors. It is therefore unclear to what extent and at which stages of the disease different processes contribute to brain iron changes. We postulate that spatially covarying magnetic susceptibility networks determined with Independent Component Analysis (ICA) reflect, and allow for the study of, independent processes regulating iron levels. We applied ICA to quantitative susceptibility maps for 170 individuals aged 9-81 years without neurological disease ("Healthy Aging" (HA) cohort), and for a cohort of 120 patients with MS and 120 age- and sex-matched healthy controls (HC; together the "MS/HC" cohort). Two DGM-associated "susceptibility networks" identified in the HA cohort (the Dorsal Striatum and Globus Pallidus Interna Networks) were highly internally reproducible (i.e. "robust") across multiple ICA repetitions on cohort subsets. DGM areas overlapping both robust networks had higher susceptibility levels than DGM areas overlapping only a single robust network, suggesting that these networks were caused by independent processes of increasing iron concentration. Because MS is thought to accelerate brain aging, we hypothesized that associations between age and the two robust DGM-associated networks would be enhanced in patients with MS. However, only one of these networks was altered in patients with MS, and it had a null age association in patients with MS rather than a stronger association. Further analysis of the MS/HC cohort revealed three additional disease-related networks (the Pulvinar, Mesencephalon, and Caudate Networks) that were differentially altered between patients with MS and HCs and between MS subtypes. Exploratory regression analyses of the disease-related networks revealed differential associations with disease duration and T2 lesion volume. Finally, analysis of ROI-based disease effects in the MS/HC cohort revealed an effect of disease status only in the putamen ROI and exploratory regression analysis did not show associations between the caudate and pulvinar ROIs and disease duration or T2 lesion volume, showing the ICA-based approach was more sensitive to disease effects. These results suggest that the ICA network framework increases sensitivity for studying patterns of brain iron change, opening a new avenue for understanding brain iron physiology under normal and disease conditions.

Multisite reproducibility of quantitative susceptibility mapping and effective transverse relaxation rate in deep gray matter at 3 T using locally optimized sequences in 24 traveling heads

Iron concentration in the human brain plays a crucial role in several neurodegenerative diseases and can be monitored noninvasively using quantitative susceptibility mapping (QSM) and effective transverse relaxation rate (R₂ *) mapping from multiecho T₂ *-weighted images. Large population studies enable better understanding of pathologies and can benefit from pooling multisite data. However, reproducibility may be compromised between sites and studies using different hardware and sequence protocols. This work investigates QSM and R₂ * reproducibility at 3 T using locally optimized sequences from three centers and two vendors, and investigates possible reduction of cross-site variability through postprocessing approaches. Twenty-four healthy subjects traveled between three sites and were scanned twice at each site. Scan-rescan measurements from seven deep gray matter regions were used for assessing within-site and cross-site reproducibility using intraclass correlation coefficient (ICC) and within-subject standard deviation (SDw) measures. In addition, multiple QSM and R₂ * postprocessing options were investigated with the aim to minimize cross-site sequence-related variations, including: mask generation approach, echo-timing selection, harmonizing spatial resolution, field map estimation, susceptibility inversion method, and linear field correction for magnitude images. The same-subject cross-site region of interest measurements for QSM and R₂ * were highly correlated (R²  ≥ 0.94) and reproducible (mean ICC of 0.89 and 0.82 for QSM and R₂ *, respectively). The mean cross-site SDw was 4.16 parts per billion (ppb) for QSM and 1.27 s^-1 for R₂ *. For within-site measurements of QSM and R₂ *, the mean ICC was 0.97 and 0.87 and mean SDw was 2.36 ppb and 0.97 s^-1 , respectively. The precision level is regionally dependent and is reduced in the frontal lobe, near brain edges, and in white matter regions. Cross-site QSM variability (mean SDw) was reduced up to 46% through postprocessing approaches, such as masking out less reliable regions, matching available echo timings and spatial resolution, avoiding the use of the nonconsistent magnitude contrast between scans in field estimation, and minimizing streaking artifacts.

Phase-based masking for quantitative susceptibility mapping of the human brain at 9.4T

PURPOSE

To develop improved tissue masks for QSM.

METHODS

Masks including voxels at the brain surface were automatically generated from the magnitude alone (MM) or combined with test functions from the first (PG) or second (PB) derivative of the sign of the wrapped phase. Phase images at 3T and 9.4T were simulated at different TEs and used to generate a mask, PItoh , with between-voxel phase differences less than π. MM, PG, and PB were compared with PItoh . QSM were generated from 3D multi-echo gradient-echo data acquired at 9.4T (21 subjects aged: 20-56y), and from the QSM2016 challenge 3T data using different masks, unwrapping, background removal, and dipole inversion algorithms. QSM contrast was quantified using age-based iron concentrations.

RESULTS

Close to air cavities, phase wraps became denser with increasing field and echo time, yielding increased values of the test functions. Compared with PItoh , PB had the highest Dice coefficient, while PG had the lowest and MM the highest percentage of voxels outside PItoh. Artifacts observed in QSM at 9.4T with MM were mitigated by stronger background filters but yielded a reduced QSM contrast. With PB, QSM contrast was greater and artifacts diminished. Similar results were obtained with challenge data, evidencing larger effects of mask close to air cavities.

CONCLUSION

Automatic, phase-based masking founded on the second derivative of the sign of the wrapped phase, including cortical voxels at the brain surface, was able to mitigate artifacts and restore QSM contrast across cortical and subcortical brain regions.

Developmental trajectory of magnetic susceptibility in the healthy rhesus macaque brain

Quantitative susceptibility mapping (QSM) is used to quantify iron deposition in non-human primates in our study. Although QSM has many applications in detecting iron deposits in the human brain, including the distribution of iron deposits in specific brain regions, the change of iron deposition with aging, and the comparison of iron deposits between diseased groups and healthy controls, few studies have applied QSM to non-human primates, while most animal brain experiments focus on biochemical and anatomical results instead of non-invasive experiments. Additionally, brain imaging in children's research is difficult, but can be substituted using young rhesus monkeys, which are very similar to humans, as research animals. Therefore, understanding the relationship between iron deposition and age in rhesus macaques' brains can offer insights into both the developmental trajectory of magnetic susceptibility in the animal model and the correlated evidence in children's research. Twenty-three healthy rhesus macaque monkeys (23 ± 7.85 years, range 2-29 years) were included in this research. Seven regions of interest (ROIs-globus pallidus, substantia nigra, dentate nucleus, caudate nucleus, putamen, thalamus, red nucleus) have been analyzed in terms of QSM and R₂ * (apparent relaxation rate). Susceptibility in most ROIs correlated significantly with the growth of age, similarly to the results for R₂ *, but showed different trends in the thalamus and red nucleus, which may be caused by the different sensitivities of myelination and iron deposition in R₂ * and QSM analysis. By assessing the correlation between iron content and age in healthy rhesus macaques' brains using QSM, we provide a piece of pilot information on normality for advanced animal disease models. Meanwhile, this study also could serve as the normative basis for further clinical studies using QSM for iron content quantification. Due to the comparison of the susceptibility on the same experimental objects, this research can also provide practical support for future research on characteristics for QSM and R₂ *.

Quantitative susceptibility mapping (QSM) of the cardiovascular system: challenges and perspectives

Quantitative susceptibility mapping (QSM) is a powerful, non-invasive, magnetic resonance imaging (MRI) technique that relies on measurement of magnetic susceptibility. So far, QSM has been employed mostly to study neurological disorders characterized by iron accumulation, such as Parkinson's and Alzheimer's diseases. Nonetheless, QSM allows mapping key indicators of cardiac disease such as blood oxygenation and myocardial iron content. For this reason, the application of QSM offers an unprecedented opportunity to gain a better understanding of the pathophysiological changes associated with cardiovascular disease and to monitor their evolution and response to treatment. Recent studies on cardiovascular QSM have shown the feasibility of a non-invasive assessment of blood oxygenation, myocardial iron content and myocardial fibre orientation, as well as carotid plaque composition. Significant technical challenges remain, the most evident of which are related to cardiac and respiratory motion, blood flow, chemical shift effects and susceptibility artefacts. Significant work is ongoing to overcome these challenges and integrate the QSM technique into clinical practice in the cardiovascular field.

Quantitative susceptibility-weighted imaging in presence of strong susceptibility sources: Application to hemorrhage

PURPOSE

To optimize quantitative susceptibility-weighted imaging also known as true susceptibility-weighted imaging (tSWI) for strong susceptibility sources like hemorrhage and compare to standard susceptibility-weighted imaging (SWI) and quantitative susceptibility mapping (QSM).

METHODS

Ten patients with known intracerebral hemorrhage were scanned using a 3D SWI sequence. The magnitude and phase images were utilized to compute QSM, tSWI and SWI images. tSWI parameters including the upper threshold for creating susceptibility-weighted masks and the multiplication factor were optimized for hemorrhage depiction. Combined tSWI was also computed with independent optimized parameters for both veins and hemorrhagic regions. tSWI results were compared to SWI and QSM utilizing region-of-interest measurements, Pearson's correlation and Kruskal-Wallis test.

RESULTS

Fifteen hemorrhages were found, with mean susceptibility 0.81 ± 0.37 ppm. Unlike SWI which utilizes a phase mask, tSWI uses a mask computed from QSM. In tSWI, the weighted mask required an extended upper threshold far beyond the standard level for more effective visualization of hemorrhage texture. The upper threshold was set to the mean maximum susceptibility in the hemorrhagic region (3.24 ppm) with a multiplication factor of 2. The blooming effect, seen in SWI, was observed to be larger in hemorrhages with higher susceptibility values (r = 0.78, p < 0.001) with reduced blooming on tSWI. On SWI, 4 out of 15 hemorrhages showed phase wrap artifacts in the hemorrhagic region and all patients showed some phase wraps in the air-tissue interface near the auditory and frontal sinuses. These phase wrap artifacts were absent on tSWI. In hemorrhagic region, a higher correlation was observed between the actual susceptibility values and mean gray value for tSWI (r = -0.93, p < 0.001) than SWI (r = -0.87, p < 0.001).

CONCLUSION

In hemorrhage, tSWI minimizes both blooming effects and phase wrap artifacts observed in SWI. However, unlike SWI, tSWI requires an altered upper threshold for best hemorrhage depiction that greatly differs from the standard value. tSWI can be used as a complementary technique for visualizing hemorrhage along with SWI.

Anemia Increases Oxygen Extraction Fraction in Deep Brain Structures but Not in the Cerebral Cortex

Sickle cell disease (SCD) is caused by a single amino acid mutation in hemoglobin, causing chronic anemia and neurovascular complications. However, the effects of chronic anemia on oxygen extraction fraction (OEF), especially in deep brain structures, are less well understood. Conflicting OEF values have been reported in SCD patients, but have largely attributed to different measurement techniques, faulty calibration, and different locations of measurement. Thus, in this study, we investigated the reliability and agreement of two susceptibility-based methods, quantitative susceptibility mapping (QSM) and complex image summation around a spherical or a cylindrical object (CISSCO), for OEF measurements in internal cerebral vein (ICV), reflecting oxygen saturation in deep brain structures. Both methods revealed that SCD patients and non-sickle anemia patients (ACTL) have increased OEF in ICV (42.6% ± 5.6% and 30.5% ± 3.6% in SCD by CISSCO and QSM respectively, 37.0% ± 4.1% and 28.5% ± 2.3% in ACTL) compared with controls (33.0% ± 2.3% and 26.8% ± 1.8%). OEF in ICV varied reciprocally with hematocrit (r ² = 0.92, 0.53) and oxygen content (r ² = 0.86, 0.53) respectively. However, an opposite relationship was observed for OEF measurements in sagittal sinus (SS) with the widely used T₂-based oximetry, T₂-Relaxation-Under-Spin-Tagging (TRUST), in the same cohorts (31.2% ± 6.6% in SCD, 33.3% ± 5.9% in ACTL and 36.8% ± 5.6% in CTL). Importantly, we demonstrated that hemoglobin F and other fast moving hemoglobins decreased OEF by TRUST and explained group differences in sagittal sinus OEF between anemic and control subjects. These data demonstrate that anemia causes deep brain hypoxia in anemia subjects with concomitant preservation of cortical oxygenation, as well as the key interaction of the hemoglobin dissociation curve and cortical oxygen extraction.

Brain Iron and Mental Health Symptoms in Youth with and without Prenatal Alcohol Exposure

Prenatal alcohol exposure (PAE) negatively affects brain development and increases the risk of poor mental health. We investigated if brain volumes or magnetic susceptibility, an indirect measure of brain iron, were associated with internalizing or externalizing symptoms in youth with and without PAE. T1-weighted and quantitative susceptibility mapping (QSM) MRI scans were collected for 19 PAE and 40 unexposed participants aged 7.5–15 years. Magnetic susceptibility and volume of basal ganglia and limbic structures were extracted using FreeSurfer. Internalizing and Externalizing Problems were assessed using the Behavioural Assessment System for Children (BASC-2-PRS). Susceptibility in the nucleus accumbens was negatively associated with Internalizing Problems, while amygdala susceptibility was positively associated with Internalizing Problems across groups. PAE moderated the relationship between thalamus susceptibility and internalizing symptoms as well as the relationship between putamen susceptibility and externalizing symptoms. Brain volume was not related to internalizing or externalizing symptoms. These findings highlight that brain iron is related to internalizing and externalizing symptoms differently in some brain regions for youth with and without PAE. Atypical iron levels (high or low) may indicate mental health issues across individuals, and iron in the thalamus may be particularly important for behavior in individuals with PAE.

Blip up-down acquisition for spin- and gradient-echo imaging (BUDA-SAGE) with self-supervised denoising enables efficient T2 , T2 *, para- and dia-magnetic susceptibility mapping

PURPOSE

To rapidly obtain high resolution T₂ , T₂ *, and quantitative susceptibility mapping (QSM) source separation maps with whole-brain coverage and high geometric fidelity.

METHODS

We propose Blip Up-Down Acquisition for Spin And Gradient Echo imaging (BUDA-SAGE), an efficient EPI sequence for quantitative mapping. The acquisition includes multiple T₂ *-, T₂ '-, and T₂ -weighted contrasts. We alternate the phase-encoding polarities across the interleaved shots in this multi-shot navigator-free acquisition. A field map estimated from interim reconstructions was incorporated into the joint multi-shot EPI reconstruction with a structured low rank constraint to eliminate distortion. A self-supervised neural network (NN), MR-Self2Self (MR-S2S), was used to perform denoising to boost SNR. Using Slider encoding allowed us to reach 1 mm isotropic resolution by performing super-resolution reconstruction on volumes acquired with 2 mm slice thickness. Quantitative T₂ (=1/R₂ ) and T₂ * (=1/R₂ *) maps were obtained using Bloch dictionary matching on the reconstructed echoes. QSM was estimated using nonlinear dipole inversion on the gradient echoes. Starting from the estimated R₂ /R₂ * maps, R₂ ' information was derived and used in source separation QSM reconstruction, which provided additional para- and dia-magnetic susceptibility maps.

RESULTS

In vivo results demonstrate the ability of BUDA-SAGE to provide whole-brain, distortion-free, high-resolution, multi-contrast images and quantitative T₂ /T₂ * maps, as well as yielding para- and dia-magnetic susceptibility maps. Estimated quantitative maps showed comparable values to conventional mapping methods in phantom and in vivo measurements.

CONCLUSION

BUDA-SAGE acquisition with self-supervised denoising and Slider encoding enables rapid, distortion-free, whole-brain T₂ /T₂ * mapping at 1 mm isotropic resolution under 90 s.

Quantitative MRI Harmonization to Maximize Clinical Impact: The RIN-Neuroimaging Network

Neuroimaging studies often lack reproducibility, one of the cardinal features of the scientific method. Multisite collaboration initiatives increase sample size and limit methodological flexibility, therefore providing the foundation for increased statistical power and generalizable results. However, multisite collaborative initiatives are inherently limited by hardware, software, and pulse and sequence design heterogeneities of both clinical and preclinical MRI scanners and the lack of benchmark for acquisition protocols, data analysis, and data sharing. We present the overarching vision that yielded to the constitution of RIN-Neuroimaging Network, a national consortium dedicated to identifying disease and subject-specific in-vivo neuroimaging biomarkers of diverse neurological and neuropsychiatric conditions. This ambitious goal needs efforts toward increasing the diagnostic and prognostic power of advanced MRI data. To this aim, 23 Italian Scientific Institutes of Hospitalization and Care (IRCCS), with technological and clinical specialization in the neurological and neuroimaging field, have gathered together. Each IRCCS is equipped with high- or ultra-high field MRI scanners (i.e., ≥3T) for clinical or preclinical research or has established expertise in MRI data analysis and infrastructure. The actions of this Network were defined across several work packages (WP). A clinical work package (WP1) defined the guidelines for a minimum standard clinical qualitative MRI assessment for the main neurological diseases. Two neuroimaging technical work packages (WP2 and WP3, for clinical and preclinical scanners) established Standard Operative Procedures for quality controls on phantoms as well as advanced harmonized quantitative MRI protocols for studying the brain of healthy human participants and wild type mice. Under FAIR principles, a web-based e-infrastructure to store and share data across sites was also implemented (WP4). Finally, the RIN translated all these efforts into a large-scale multimodal data collection in patients and animal models with dementia (i.e., case study). The RIN-Neuroimaging Network can maximize the impact of public investments in research and clinical practice acquiring data across institutes and pathologies with high-quality and highly-consistent acquisition protocols, optimizing the analysis pipeline and data sharing procedures.

HFP-QSMGAN: QSM from homodyne-filtered phase images

PURPOSE

Homodyne filtering is a standard preprocessing step in the estimation of SWI. Unfortunately, SWI is not quantitative, and QSM cannot be accurately estimated from filtered phase images. Compared with gradient-echo sequences suitable for computing QSM, SWI is more readily available and is often the only susceptibility-sensitive sequence acquired in the clinical setting. In this project, we aimed to quantify susceptibility from the homodyne-filtered phase (HFP), acquired for computing susceptibility-weighted images, using convolutional neural networks to solve the compounded problem of (1) computing the solution to the inverse dipole problem, and (2) compensating for the effects of the homodyne filtering.

METHODS

Two convolutional neural networks, the U-Net and a modified QSMGAN architecture (HFP-QSMGAN), were trained to predict QSM maps at different TEs from HFP images. The QSM maps were quantified from a gradient-echo sequence acquired in the same individuals using total generalized variation (TGV)-QSM. The QSM maps estimated directly from the HFP were also included for comparison. Voxel-wise predictions and, importantly, regional predictions of susceptibility with adjustment to a reference region, were compared.

RESULTS

Our results indicate that the U-Net model provides more accurate voxel-wise predictions of susceptibility compared with HFP-QSMGAN and HFP-QSM. However, regional estimates of susceptibility predicted by HFP-QSMGAN are more strongly correlated with the values from TGV-QSM compared with those of U-Net and HFP-QSM.

CONCLUSION

Accurate prediction of susceptibility can be achieved from filtered SWI phase using convolutional neural networks.

Quantitative susceptibility mapping of the head-and-neck using SMURF fat-water imaging with chemical shift and relaxation rate corrections

PURPOSE

To address the challenges posed by fat-water chemical shift artifacts and relaxation rate discrepancies to quantitative susceptibility mapping (QSM) outside the brain, and to generate accurate susceptibility maps of the head-and-neck at 3 and 7 Tesla.

METHODS

Simultaneous Multiple Resonance Frequency (SMURF) imaging was extended to 7 Tesla and used to acquire head-and-neck gradient echo images at both 3 and 7 Tesla. Separated fat and water images were corrected for Type 1 (displacement) and Type 2 (phase discrepancy) chemical shift artefacts, and for the bias resulting from differences in T1 and T 2 ∗ relaxation rates, recombined and used as the basis for QSM. A novel phase signal-based masking approach was used to generate head-and-neck masks.

RESULTS

SMURF generated well-separated fat and water images of the head-and-neck. Corrections for chemical shift artefacts and relaxation rate differences removed overestimation of the susceptibility values, blurring in the susceptibility maps, and the disproportionate influence of fat in mixed voxels. The resulting susceptibility maps showed high correspondence between the paramagnetic areas and the locations of fatty tissues and the susceptibility estimates were similar to literature values. The proposed masking approach was shown to provide a simple means of generating head-and-neck masks.

CONCLUSION

Corrections for Type 1 and Type 2 chemical shift artefacts and for fat-water relaxation rate differences, mainly in T1 , were shown to be required for accurate susceptibility mapping of fatty-body regions. SMURF made it possible to apply these corrections and generate high-quality susceptibility maps of the entire head-and-neck at both 3 and 7 Tesla.

[Quantitative susceptibility mapping in assessment of inflammation and neurodegeneration in multiple sclerosis]

Quantitative susceptibility mapping (QSM) is a relatively new MRI technique that may potentially help estimate iron concentrations in the brain. It plays a big role in diagnosis of many pathological processes, including multiple sclerosis (MS). Iron metabolism in the brain is a complex and not fully understood process. It is known that the content of iron in the brain increases with age; in addition, its accumulation is often observed in many neurodegenerative diseases, including MS foci, and its amount changes over time. In this regard, the values of magnetic susceptibility obtained using QSM can potentially become a convenient biomarker that reflects the latent activity and progression of MS, which, in turn, can influence the choice of therapy and the tactics of treating patients.

Streaking artifact suppression of quantitative susceptibility mapping reconstructions via L1-norm data fidelity optimization (L1-QSM)

PURPOSE

The presence of dipole-inconsistent data due to substantial noise or artifacts causes streaking artifacts in quantitative susceptibility mapping (QSM) reconstructions. Often used Bayesian approaches rely on regularizers, which in turn yield reduced sharpness. To overcome this problem, we present a novel L1-norm data fidelity approach that is robust with respect to outliers, and therefore prevents streaking artifacts.

METHODS

QSM functionals are solved with linear and nonlinear L1-norm data fidelity terms using functional augmentation, and are compared with equivalent L2-norm methods. Algorithms were tested on synthetic data, with phase inconsistencies added to mimic lesions, QSM Challenge 2.0 data, and in vivo brain images with hemorrhages.

RESULTS

The nonlinear L1-norm-based approach achieved the best overall error metric scores and better streaking artifact suppression. Notably, L1-norm methods could reconstruct QSM images without using a brain mask, with similar regularization weights for different data fidelity weighting or masking setups.

CONCLUSION

The proposed L1-approach provides a robust method to prevent streaking artifacts generated by dipole-inconsistent data, renders brain mask calculation unessential, and opens novel challenging clinical applications such asassessing brain hemorrhages and cortical layers.

Substantia nigra iron affects functional connectivity networks modifying working memory performance in younger adults

Brain iron affects working memory (WM) but the impact of iron content in deep grey matter nuclei on WM networks is unknown. We aimed to test whether deep grey matter nuclei iron concentration can affect resting-state functional connectivity (rsFC) within brain networks modifying WM performance. An N-back WM paradigm was applied in a hundred healthy younger adults. The participants then underwent a resting-state functional magnetic resonance imaging (fMRI) for brain network analysis and quantitative susceptibility mapping (QSM) imaging for assessment of deep grey matter nuclei iron concentration. Higher substantia nigra (SN) iron concentration was associated with lower rsFC between SN and brain regions of the temporal/frontal lobe but with better WM performance after controlling for age, gender and education. A follow-up mediation analysis also indicated that functional connectivity may mediate the link between SN iron and WM performance. Our results suggest that high SN iron concentration may affect communication between the SN and temporal/frontal lobe and is associated with strengthened WM performance in younger adults.

QQ-NET - using deep learning to solve quantitative susceptibility mapping and quantitative blood oxygen level dependent magnitude (QSM+qBOLD or QQ) based oxygen extraction fraction (OEF) mapping

PURPOSE

To improve accuracy and speed of quantitative susceptibility mapping plus quantitative blood oxygen level-dependent magnitude (QSM+qBOLD or QQ) -based oxygen extraction fraction (OEF) mapping using a deep neural network (QQ-NET).

METHODS

The 3D multi-echo gradient echo images were acquired in 34 ischemic stroke patients and 4 healthy subjects. Arterial spin labeling and diffusion weighted imaging (DWI) were also performed in the patients. NET was developed to solve the QQ model inversion problem based on Unet. QQ-based OEF maps were reconstructed with previously introduced temporal clustering, tissue composition, and total variation (CCTV) and NET. The results were compared in simulation, ischemic stroke patients, and healthy subjects using a two-sample Kolmogorov-Smirnov test.

RESULTS

In the simulation, QQ-NET provided more accurate and precise OEF maps than QQ-CCTV with 150 times faster reconstruction speed. In the subacute stroke patients, OEF from QQ-NET had greater contrast-to-noise ratio (CNR) between DWI-defined lesions and their unaffected contralateral normal tissue than with QQ-CCTV: 1.9 ± 1.3 vs 6.6 ± 10.7 (p = 0.03). In healthy subjects, both QQ-CCTV and QQ-NET provided uniform OEF maps.

CONCLUSION

QQ-NET improves the accuracy of QQ-based OEF with faster reconstruction.

Above-ground biomass references for urban trees from terrestrial laser scanning data

BACKGROUND AND AIMS

Within extending urban areas, trees serve a multitude of functions (e.g. carbon storage, suppression of air pollution, mitigation of the 'heat island' effect, oxygen, shade and recreation). Many of these services are positively correlated with tree size and structure. The quantification of above-ground biomass (AGB) is of especial importance to assess its carbon storage potential. However, quantification of AGB is difficult and the allometries applied are often based on forest trees, which are subject to very different growing conditions, competition and form. In this article we highlight the potential of terrestrial laser scanning (TLS) techniques to extract highly detailed information on urban tree structure and AGB.

METHODS

Fifty-five urban trees distributed over seven cities in Switzerland were measured using TLS and traditional forest inventory techniques before they were felled and weighed. Tree structure, volume and AGB from the TLS point clouds were extracted using quantitative structure modelling. TLS-derived AGB estimates were compared with AGB estimates based on forest tree allometries dependent on diameter at breast height only. The correlations of various tree metrics as AGB predictors were assessed.

KEY RESULTS

Estimates of AGB derived by TLS showed good performance when compared with destructively harvested references, with an R2 of 0.954 (RMSE = 556 kg) compared with 0.837 (RMSE = 1159 kg) for allometrically derived AGB estimates. A correlation analysis showed that different TLS-derived wood volume estimates as well as trunk diameters and tree crown metrics show high correlation in describing total wood AGB, outperforming tree height.

CONCLUSIONS

Wood volume estimates based on TLS show high potential to estimate tree AGB independent of tree species, size and form. This allows us to retrieve highly accurate non-destructive AGB estimates that could be used to establish new allometric equations without the need for extensive destructive harvesting.