High-resolution QSM for functional and structural depiction of subthalamic nuclei in DBS presurgical mapping

Three-dimensional EPI with shot-selective CAIPIRIHANA for rapid high-resolution quantitative susceptibility mapping at 3 T

PURPOSE

QSM provides insight into healthy brain aging and neuropathologies such as multiple sclerosis (MS), traumatic brain injuries, brain tumors, and neurodegenerative diseases. Phase data for QSM are usually acquired from 3D gradient-echo (3D GRE) scans with long acquisition times that are detrimental to patient comfort and susceptible to patient motion. This is particularly true for scans requiring whole-brain coverage and submillimeter resolutions. In this work, we use a multishot 3D echo plannar imaging (3D EPI) sequence with shot-selective 2D CAIPIRIHANA to acquire high-resolution, whole-brain data for QSM with minimal distortion and blurring.

METHODS

To test clinical viability, the 3D EPI sequence was used to image a cohort of MS patients at 1-mm isotropic resolution at 3 T. Additionally, 3D EPI data of healthy subjects were acquired at 1-mm, 0.78-mm, and 0.65-mm isotropic resolution with varying echo train lengths (ETLs) and compared with a reference 3D GRE acquisition.

RESULTS

The appearance of the susceptibility maps and the susceptibility values for segmented regions of interest were comparable between 3D EPI and 3D GRE acquisitions for both healthy and MS participants. Additionally, all lesions visible in the MS patients on the 3D GRE susceptibility maps were also visible on the 3D EPI susceptibility maps. The interplay among acquisition time, resolution, echo train length, and the effect of distortion on the calculated susceptibility maps was investigated.

CONCLUSION

We demonstrate that the 3D EPI sequence is capable of rapidly acquiring submillimeter resolutions and providing high-quality, clinically relevant susceptibility maps.

Value of Quantitative Susceptibility Mapping in Clinical Neuroradiology

Quantitative susceptibility mapping (QSM) is a unique technique for providing quantitative information on tissue magnetic susceptibility using phase image data. QSM can provide valuable information regarding physiological and pathological processes such as iron deposition, hemorrhage, calcification, and myelin. QSM has been considered for use as an imaging biomarker to investigate physiological status and pathological changes. Although various studies have investigated the clinical applications of QSM, particularly regarding the use of QSM in clinical practice, have not been examined well. This review provides on an overview of the basics of QSM and its clinical applications in neuroradiology. LEVEL OF EVIDENCE: 2 TECHNICAL EFFICACY: Stage 2.

Recommended implementation of quantitative susceptibility mapping for clinical research in the brain: A consensus of the ISMRM electro-magnetic tissue properties study group

This article provides recommendations for implementing QSM for clinical brain research. It is a consensus of the International Society of Magnetic Resonance in Medicine, Electro-Magnetic Tissue Properties Study Group. While QSM technical development continues to advance rapidly, the current QSM methods have been demonstrated to be repeatable and reproducible for generating quantitative tissue magnetic susceptibility maps in the brain. However, the many QSM approaches available have generated a need in the neuroimaging community for guidelines on implementation. This article outlines considerations and implementation recommendations for QSM data acquisition, processing, analysis, and publication. We recommend that data be acquired using a monopolar 3D multi-echo gradient echo (GRE) sequence and that phase images be saved and exported in Digital Imaging and Communications in Medicine (DICOM) format and unwrapped using an exact unwrapping approach. Multi-echo images should be combined before background field removal, and a brain mask created using a brain extraction tool with the incorporation of phase-quality-based masking. Background fields within the brain mask should be removed using a technique based on SHARP or PDF, and the optimization approach to dipole inversion should be employed with a sparsity-based regularization. Susceptibility values should be measured relative to a specified reference, including the common reference region of the whole brain as a region of interest in the analysis. The minimum acquisition and processing details required when reporting QSM results are also provided. These recommendations should facilitate clinical QSM research and promote harmonized data acquisition, analysis, and reporting.

Thin slab quantitative susceptibility mapping

PURPOSE

Susceptibility maps reconstructed from thin slabs may suffer underestimation due to background-field removal imperfections near slab boundaries and the increased difficulty of solving a 3D-inversion problem with reduced support, particularly in the direction of the main magnetic field. Reliable QSM reconstruction from thin slabs would enable focal acquisitions in a much-reduced scan time.

METHODS

This work proposes using additional rapid low-resolution data of extended spatial coverage to improve background-field estimation and regularize the inversion-to-susceptibility process for high resolution, thin slab data. The new method was tested using simulated and in-vivo brain data of high resolution (0.33 × 0.33 × 0.33 mm3 and 0.54 × 0.54 × 0.65 mm3 , respectively) at 3T, and compared to the standard large volume approach.

RESULTS

Using the proposed method, in-vivo high-resolution QSM at 3T was obtained from slabs of width as small as 10.4 mm, aided by a lower-resolution dataset of 24 times coarser voxels. Simulations showed that the proposed method produced more consistent measurements from slabs of at least eight slices. Reducing the mean ROI error to 5% required the low-resolution data to cover ˜60 mm in the direction of the main field, have at least 2-mm isotropic resolution that is not coarser than the high-resolution data by more than four-fold in any direction.

CONCLUSION

Applying the proposed method enabled focal QSM acquisitions at sub-millimeter resolution within reasonable acquisition time.

Direct localization and delineation of human pedunculopontine nucleus based on a self-supervised magnetic resonance image super-resolution method

The pedunculopontine nucleus (PPN) is a small brainstem structure and has attracted attention as a potentially effective deep brain stimulation (DBS) target for the treatment of Parkinson's disease (PD). However, the in vivo location of PPN remains poorly described and barely visible on conventional structural magnetic resonance (MR) images due to a lack of high spatial resolution and tissue contrast. This study aims to delineate the PPN on a high-resolution (HR) atlas and investigate the visibility of the PPN in individual quantitative susceptibility mapping (QSM) images. We combine a recently constructed Montreal Neurological Institute (MNI) space unbiased QSM atlas (MuSus-100), with an implicit representation-based self-supervised image super-resolution (SR) technique to achieve an atlas with improved spatial resolution. Then guided by a myelin staining histology human brain atlas, we localize and delineate PPN on the atlas with improved resolution. Furthermore, we examine the feasibility of directly identifying the approximate PPN location on the 3.0-T individual QSM MR images. The proposed SR network produces atlas images with four times the higher spatial resolution (from 1 to 0.25 mm isotropic) without a training dataset. The SR process also reduces artifacts and keeps superb image contrast for further delineating small deep brain nuclei, such as PPN. Using the myelin staining histological atlas as guidance, we first identify and annotate the location of PPN on the T1-weighted (T1w)-QSM hybrid MR atlas with improved resolution in the MNI space. Then, we relocate and validate that the optimal targeting site for PPN-DBS is at the middle-to-caudal part of PPN on our atlas. Furthermore, we confirm that the PPN region can be identified in a set of individual QSM images of 10 patients with PD and 10 healthy young adults. The contrast ratios of the PPN to its adjacent structure, namely the medial lemniscus, on images of different modalities indicate that QSM substantially improves the visibility of the PPN both in the atlas and individual images. Our findings indicate that the proposed SR network is an efficient tool for small-size brain nucleus identification. HR QSM is promising for improving the visibility of the PPN. The PPN can be directly identified on the individual QSM images acquired at the 3.0-T MR scanners, facilitating a direct targeting of PPN for DBS surgery.

Automated Segmentation of Midbrain Structures in High-Resolution Susceptibility Maps Based on Convolutional Neural Network and Transfer Learning

Background

Accurate delineation of the midbrain nuclei, the red nucleus (RN), substantia nigra (SN) and subthalamic nucleus (STN), is important in neuroimaging studies of neurodegenerative and other diseases. This study aims to segment midbrain structures in high-resolution susceptibility maps using a method based on a convolutional neural network (CNN).

Methods

The susceptibility maps of 75 subjects were acquired with a voxel size of 0.83 × 0.83 × 0.80 mm³ on a 3T MRI system to distinguish the RN, SN, and STN. A deeply supervised attention U-net was pre-trained with a dataset of 100 subjects containing susceptibility maps with a voxel size of 0.63 × 0.63 × 2.00 mm³ to provide initial weights for the target network. Five-fold cross-validation over the training cohort was used for all the models’ training and selection. The same test cohort was used for the final evaluation of all the models. Dice coefficients were used to assess spatial overlap agreement between manual delineations (ground truth) and automated segmentation. Volume and magnetic susceptibility values in the nuclei extracted with automated CNN delineation were compared to those extracted by manual tracing. Consistencies of volume and magnetic susceptibility values by different extraction strategies were assessed by Pearson correlation coefficients and Bland-Altman analyses.

Results

The automated CNN segmentation method achieved mean Dice scores of 0.903, 0.864, and 0.777 for the RN, SN, and STN, respectively. There were no significant differences between the achieved Dice scores and the inter-rater Dice scores (p > 0.05 for each nucleus). The overall volume and magnetic susceptibility values of the nuclei extracted by the automatic CNN method were significantly correlated with those by manual delineation (p < 0.01).

Conclusion

Midbrain structures can be precisely segmented in high-resolution susceptibility maps using a CNN-based method.

Automatic detection of neuromelanin and iron in the midbrain nuclei using a magnetic resonance imaging ‐based brain template

Parkinson disease (PD) is a chronic progressive neurodegenerative disorder characterized pathologically by early loss of neuromelanin (NM) in the substantia nigra pars compacta (SNpc) and increased iron deposition in the substantia nigra (SN). Degeneration of the SN presents as a 50 to 70% loss of pigmented neurons in the ventral lateral tier of the SNpc at the onset of symptoms. Also, using magnetic resonance imaging (MRI), iron deposition and volume changes of the red nucleus (RN), and subthalamic nucleus (STN) have been reported to be associated with disease status and rate of progression. Further, the STN serves as an important target for deep brain stimulation treatment in advanced PD patients. Therefore, an accurate in‐vivo delineation of the SN, its subregions and other midbrain structures such as the RN and STN could be useful to better study iron and NM changes in PD. Our goal was to use an MRI template to create an automatic midbrain deep gray matter nuclei segmentation approach based on iron and NM contrast derived from a single, multiecho magnetization transfer contrast gradient echo (MTC‐GRE) imaging sequence. The short echo TE = 7.5 ms data from a 3D MTC‐GRE sequence was used to find the NM‐rich region, while the second echo TE = 15 ms was used to calculate the quantitative susceptibility map for 87 healthy subjects (mean age ± SD: 63.4 ± 6.2 years old, range: 45–81 years). From these data, we created both NM and iron templates and calculated the boundaries of each midbrain nucleus in template space, mapped these boundaries back to the original space and then fine‐tuned the boundaries in the original space using a dynamic programming algorithm to match the details of each individual's NM and iron features. A dual mapping approach was used to improve the performance of the morphological mapping of the midbrain of any given individual to the template space. A threshold approach was used in the NM‐rich region and susceptibility maps to optimize the DICE similarity coefficients and the volume ratios. The results for the NM of the SN as well as the iron containing SN, STN, and RN all indicate a strong agreement with manually drawn structures. The DICE similarity coefficients and volume ratios for these structures were 0.85, 0.87, 0.75, and 0.92 and 0.93, 0.95, 0.89, 1.05, respectively, before applying any threshold on the data. Using this fully automatic template‐based deep gray matter mapping approach, it is possible to accurately measure the tissue properties such as volumes, iron content, and NM content of the midbrain nuclei.

[Deep brain stimulation of the subthalamic nucleus for parkinson's disease: awake vs asleep]

BACKGROUND

Deep brain stimulation (DBS) of the subthalamic nucleus (STN) is known to be an effective and safe neurosurgical procedure for Parkinson's disease (PD). Traditionally, awake implantation of stimulation system is carried out using microelectrode registration and intraoperative stimulation. Development of neuroimaging technologies enables direct STN imaging. Therefore, asleep surgery without additional intraoperative verification is possible. This approach reduces surgery time and can potentially decrease the incidence of hemorrhagic and infectious complications. The advantages of one method or another are being discussed.

OBJECTIVE

To assess the benefits and limitations of various methods for DBS system implantation for bilateral STN stimulation, to study the issues of stereotaxic accuracy, efficiency and safety of asleep and awake electrode implantation into STN.

MATERIAL AND METHODS

We reviewed the articles published in the PubMed database. Searching algorithm included the following keywords: «asleep DBS», «Parkinson's disease», «subthalamic nucleus», «3T MRI», «SWI», «SWAN».

RESULTS

There were 31 articles devoted to asleep DBS of STN including 4 meta-analyses, 3 prospective controlled studies, 13 retrospective controlled studies and 11 studies without a control group.

CONCLUSION

Asleep implantation of electrodes for DBS of STN can be performed only after a clear imaging of STN boundaries with high-quality MRI.

Visualization of iron-rich subcortical structures in non-human primates in vivo by quantitative susceptibility mapping at 3T MRI

Magnetic resonance imaging (MRI) is now an essential tool in the field of neuroscience involving non-human primates (NHP). Structural MRI scanning using T1-weighted (T1w) or T2-weighted (T2w) images provides anatomical information, particularly for experiments involving deep structures such as the basal ganglia and cerebellum. However, for certain subcortical structures, T1w and T2w image contrasts are insufficient for their detection of important anatomical details. To better visualize such structures in the macaque brain, we applied a relatively new method called quantitative susceptibility mapping (QSM), which enhances tissue contrast based on the local tissue magnetic susceptibility. The QSM significantly improved the visualization of important structures, including the ventral pallidum (VP), globus pallidus external and internal segments (GPe and GPi), substantia nigra (SN), subthalamic nucleus (STN) in the basal ganglia and the dentate nucleus (DN) in the cerebellum. We quantified this the contrast enhancement by systematically comparing of contrast-to-noise ratios (CNRs) of QSM images relative to the corresponding T1w and T2w images. In addition, QSM values of some structures were correlated to the age of the macaque subjects. These results identify the QSM method as a straightforward and useful tool for clearly visualizing details of subcortical structures that are invisible with more traditional scanning sequences.

Direct Targeting of the Anterior Nucleus of the Thalamus via 3 T Quantitative Susceptibility Mapping

Objective: Deep brain stimulation (DBS) of the anterior nucleus of the thalamus (ANT) is a potentially effective, minimally invasive, and reversible method for treating epilepsy. The goal of this study was to explore whether 3 T quantitative susceptibility mapping (QSM) could delineate the ANT from surrounding structures, which is important for the direct targeting of DBS surgery.

Methods: We obtained 3 T QSM, T1-weighted (T1w), and T2-weighted (T2w) images from 11 patients with Parkinson’s disease or dystonia who received subthalamic nucleus (STN) or globus pallidus interna (GPi) DBS surgery in our center. The ANT and its surrounding white matter structures on QSM were compared with available atlases. The contrast-to-noise ratios (CNRs) of ANT relative to the external medullary lamina (eml) were compared across the three imaging modalities. Additionally, the morphology and location of the ANT were depicted in the anterior commissure (AC)-posterior commissure (PC)-based system.

Results: ANT can be clearly distinguished from the surrounding white matter laminas and appeared hyperintense on QSM. The CNRs of the ANT-eml on QSM, T1w, and T2w images were 10.20 ± 4.23, 1.71 ± 1.03, and 1.35 ± 0.70, respectively. One-way analysis of variance (ANOVA) indicated significant differences in CNRs among QSM, T1w, and T2w imaging modalities [F(2) = 85.28, p < 0.0001]. In addition, both the morphology and location of the ANT were highly variable between patients in the AC–PC-based system.

Conclusion: The potential utility of QSM for the visualization of ANTs in clinical imaging is promising and may be suitable for targeting the ANT for DBS to treat epilepsy.

Motoric impairment versus iron deposition gradient in the subthalamic nucleus in Parkinson's disease

OBJECTIVE

The objective of this study was to investigate the correlation between the quantitative susceptibility mapping (QSM) signal gradient of the subthalamic nucleus (STN) and motor impairment in patients with Parkinson's disease (PD).

METHODS

All PD patients who had undergone QSM MRI for presurgical deep brain stimulation (DBS) planning were eligible for inclusion in this study. The entire STN and its three functional subdivisions, as well as the adjacent white matter (WM), were segmented and measured. The QSM value difference between the entire STN and adjacent WM (STN-WM), between the limbic and associative regions of the STN (L-A), and between the associative and motor regions of the STN (A-M) were obtained as measures of gradient and were input into an unsupervised k-means clustering algorithm to automatically categorize the overall boundary distinctness between the STN and adjacent WM and between STN subdivisions (gradient blur [GB] and gradient sharp [GS] groups). Statistical tests were performed to compare clinical and image measurements for discrimination between GB and GS groups.

RESULTS

Of the 39 study patients, 19 were categorized into the GB group and 20 into the GS group, based on quantitative cluster analysis. The GB group had a significantly higher presurgical off-medication Unified Parkinson's Disease Rating Scale Part III score (51.289 ± 20.741) than the GS group (38.5 ± 16.028; p = 0.037). The GB group had significantly higher QSM values for the STN and its three subdivisions and adjacent WM than those for the GS group (p < 0.01). The GB group also demonstrated a significantly higher STN-WM gradient in the right STN (p = 0.01). The GB group demonstrated a significantly lower L-A gradient in both the left and the right STN (p < 0.02).

CONCLUSIONS

Advancing PD with more severe motor impairment leads to more iron deposition in the STN and adjacent WM, as shown in the QSM signal. Loss of the STN inner QSM signal gradient should be considered as an image marker for more severe motor impairment in PD patients.

Multiecho complex total field inversion method (mcTFI) for improved signal modeling in quantitative susceptibility mapping

PURPOSE

Typical quantitative susceptibility mapping (QSM) reconstruction steps consist of first estimating the magnetization field from the gradient-echo images, and then reconstructing the susceptibility map from the estimated field. The errors from the field-estimation steps may propagate into the final QSM map, and the noise in the estimated field map may no longer be zero-mean Gaussian noise, thus, causing streaking artifacts in the resulting QSM. A multiecho complex total field inversion (mcTFI) method was developed to compute the susceptibility map directly from the multiecho gradient echo images using an improved signal model that retains the Gaussian noise property in the complex domain. It showed improvements in QSM reconstruction over the conventional field-to-source inversion.

METHODS

The proposed mcTFI method was compared with the nonlinear total field inversion (nTFI) method in a numerical brain with hemorrhage and calcification, the numerical brains provided by the QSM Challenge 2.0, 18 brains with intracerebral hemorrhage scanned at 3T, and 6 healthy brains scanned at 7T.

RESULTS

Compared with nTFI, the proposed mcTFI showed more accurate QSM reconstruction around the lesions in the numerical simulations. The mcTFI reconstructed QSM also showed the best image quality with the least artifacts in the brains with intracerebral hemorrhage scanned at 3T and healthy brains scanned at 7T.

CONCLUSION

The proposed multiecho complex total field inversion improved QSM reconstruction over traditional field-to-source inversion through better signal modeling.

Direct visualization of deep brain stimulation targets in patients with Parkinson's disease via 3-T quantitative susceptibility mapping

BACKGROUND

The direct visualization of brain nuclei on magnetic resonance (MR) images is important for target localization during deep brain stimulation (DBS) in patients with Parkinson's disease (PD). We demonstrated the superiority of 3-T high-resolution submillimeter voxel size quantitative susceptibility mapping (QSM) for delineating the subthalamic nucleus (STN) and the globus pallidus internus (GPi).

METHODS

Preoperative 3-T QSM and T2 weighted (T2w) images were obtained from ten patients with PD. Qualitative visualization scores were analyzed by two neurosurgeons on both images using a 4-point and 5-point scale, respectively. Images were also compared with regard to contrast-to-noise ratios (CNRs) and edge detection power for the STN and GPi. The Wilcoxon rank-sum test and the signed-rank test were used to compare measurements between the two images.

RESULTS

Visualization scores for the STN and GPi, the mean CNR of the STN relative to the zona incerta (ZI) and the substantia nigra, and the mean CNR of the GPi relative to the internal capsule (IC) and the globus pallidum externum, were significantly higher on QSM images than on T2w images (P < 0.01). The edge detection powers of the STN-ZI and GPi-IC on QSM were significantly larger (by 2.6- and 3.8-fold, respectively) than those on T2w images (P < 0.01). QSM detected asymmetry of the STN in two patients.

CONCLUSIONS

QSM images provided improved delineation ability for the STN and GPi when compared to T2w images. Our findings are important for patients with PD who undergo DBS surgery, particularly those with asymmetric bilateral nuclei.

Iron-sensitive magnetic resonance imaging in Parkinson's disease: a systematic review and meta-analysis

OBJECTIVE

To evaluate the diagnostic performance of iron-sensitive sequences targeting the substantia nigra for distinguishing patients with Parkinson's disease from control participants and to identify factors causing heterogeneity.

METHODS

A systematic literature search in the Ovid-MEDLINE and EMBASE databases was performed for studies reporting the relevant topic before March 6, 2020. The pooled sensitivity and specificity values with their 95% confidence intervals were calculated using bivariate random-effects modeling. Subgroup and meta-regression analyses were also performed to determine factors influencing heterogeneity affecting the diagnostic performance among the clinical, MRI, and analytic characteristics.

RESULTS

A total of 22 articles including 1126 patients with Parkinson's disease and 933 control participants were enrolled in this systematic review and meta-analysis. Of those, 12 studies used objective analyses of quantitative susceptibility measurements, and 10 visually assessed the nigrosome-1 in subjective analyses. Iron-sensitive nigral magnetic resonance imaging showed a pooled sensitivity of 92% (95% confidence interval 88-95%) and a pooled specificity of 90% (95% confidence interval 81-95%). According to subgroup and meta-regression analyses, a longer mean disease duration in patients with Parkinson's disease (≥ 5 years), subjective analysis, a smaller size of pixel (< 0.6 mm²), a larger flip angle (> 15°), a smaller slice thickness (≤ 1 mm), and specific targeting of the substantia nigra pars compacta improved the diagnostic performance.

CONCLUSION

Iron-sensitive nigral magnetic resonance imaging had a favorable diagnostic performance in discriminating patients with Parkinson's disease from control participants. Subjective analytic methods remain superior to objective approaches. Further improvements of the spatial resolution and contrast-to-noise ratio to specifically target the nigrosome-1 with objective analytic methods will be needed.

QSM is an imaging biomarker for chronic glial activation in multiple sclerosis lesions

BACKGROUND

Inflammation in chronic active lesions occurs behind a closed blood-brain barrier and cannot be detected with MRI. Activated microglia are highly enriched for iron and can be visualized with quantitative susceptibility mapping (QSM), an MRI technique used to delineate iron.

OBJECTIVE

To characterize the histopathological correlates of different QSM hyperintensity patterns in MS lesions.

METHODS

MS brain slabs were imaged with MRI and QSM, and processed for histology. Immunolabeled cells were quantified in the lesion rim, center, and adjacent normal-appearing white matter (NAWM). Iron⁺ myeloid cell densities at the rims were correlated with susceptibilities. Human-induced pluripotent stem cell (iPSC)-derived microglia were used to determine the effect of iron on the production of reactive oxygen species (ROS) and pro-inflammatory cytokines.

RESULTS

QSM hyperintensity at the lesion perimeter correlated with activated iron⁺ myeloid cells in the rim and NAWM. Lesions with high punctate or homogenous QSM signal contained no or minimally activated iron^- myeloid cells. In vitro, iron accumulation was highest in M1-polarized human iPSC-derived microglia, but it did not enhance ROS or cytokine production.

CONCLUSION

A high QSM signal outlining the lesion rim but not punctate signal in the center is a biomarker for chronic inflammation in white matter lesions.

Precise targeting of the globus pallidus internus with quantitative susceptibility mapping for deep brain stimulation surgery

OBJECTIVE

The goal of this study was to demonstrate the use of quantitative susceptibility mapping (QSM)-based images to precisely localize the globus pallidus internus (GPi) for deep brain stimulation (DBS) planning and to enhance postsurgical visualization of the DBS lead positions.

METHODS

Presurgical T1-weighted (T1w), T2-weighted (T2w), and QSM images as well as postsurgical CT images were obtained in 29 patients with Parkinson's disease. To enhance the contrast within the GP, a hybrid contrast was created by linearly combining T1w and QSM images. Contrast-to-noise ratios (CNRs) of the GPi on T1w, T2w, QSM, and hybrid images were compared. The CNR differences were tested using the 1-way ANOVA method. The visualization of the DBS lead position was demonstrated by merging the postsurgical CT with presurgical MR images.

RESULTS

The hybrid images yield the best CNRs for GPi depiction and the visualization of the postsurgical DBS lead position was significantly improved.

CONCLUSIONS

QSM-based images allow for confident localization of borders of the GPi that is superior to T1w and T2w images. High-contrast hybrid images can be used for precisely directed DBS targeting, e.g., GPi DBS for the treatment of advanced Parkinson's disease.