On the impact of B0 shimming algorithms on single-voxel MR spectroscopy.

PURPOSE: To assess the impact of different B0 shimming algorithms on MRS. METHODS: B0 field maps and single-voxel MR spectroscopy were acquired in the prefrontal cortex of five volunteers at 3 T using five different B0 shimming approaches. B0 shimming was achieved using Siemens' proprietary shim algorithm, in addition to the Pseudo-Inverse (PI), Quadratic Programming (QuadProg), Least Squares (LSq), and Gradient optimization (Grad) algorithms. The standard deviation of the shimmed B0 field, as well as the SNR and FWHM of the measured metabolites, was used to evaluate the performance of each B0 shimming algorithm. RESULTS: Compared to Siemens's shim, significant reductions (p < 0.01) in the standard deviation of the B0 field distribution within the MRS voxel were observed for the PI, QuadProg, and Grad algorithms (3.8 Hz, 7.3 Hz, and 3.9 Hz respectively, compared to 11.5 Hz for Siemens), but not for the LSq (12.9 Hz) algorithm. Moreover, significantly increased SNR and reduced FWHM for the N-acetylaspartate metabolite were consistent with the improvement in B0 homogeneity for the aforementioned shimming algorithms. CONCLUSION: Here, we demonstrate that the choice of B0 shimming algorithm can have a significant impact on the quality of MR spectra and that significant improvements in spectrum quality could be achieved by using alternatives to the default vendor approach.

RF shimming in the cervical spinal cord at 7 T.

PURPOSE: Advancing the development of 7 T MRI for spinal cord imaging is crucial for the enhanced diagnosis and monitoring of various neurodegenerative diseases and traumas. However, a significant challenge at this field strength is the transmit field inhomogeneity. Such inhomogeneity is particularly problematic for imaging the small, deep anatomical structures of the cervical spinal cord, as it can cause uneven signal intensity and elevate the local specific absorption ratio, compromising image quality. This multisite study explores several RF shimming techniques in the cervical spinal cord. METHODS: Data were collected from 5 participants between two 7 T sites with a custom 8Tx/20Rx parallel transmission coil. We explored two radiofrequency (RF) shimming approaches from an MRI vendor and four from an open-source toolbox, showcasing their ability to enhance transmit field and signal homogeneity along the cervical spinal cord. RESULTS: The circularly polarized (CP), coefficient of variation (CoV), and specific absorption rate (SAR) efficiency shim modes showed the highest B1 + efficiency, and the vendor-based "patient" and "volume" modes showed the lowest B1 + efficiency. The coefficient of variation method produced the highest CSF/spinal cord contrast on T2*-weighted scans (ratio of 1.27 ± 0.03), and the lowest variation of that contrast along the superior-inferior axis. CONCLUSION: The study's findings highlight the potential of RF shimming to advance 7 T MRI's clinical utility for central nervous system imaging by enabling more homogenous and efficient spinal cord imaging. Additionally, the research incorporates a reproducible Jupyter Notebook, enhancing the study's transparency and facilitating peer verification.

Body size interacts with the structure of the central nervous system: A multi-center in vivo neuroimaging study.

Clinical research emphasizes the implementation of rigorous and reproducible study designs that rely on between-group matching or controlling for sources of biological variation such as subject's sex and age. However, corrections for body size (i.e. height and weight) are mostly lacking in clinical neuroimaging designs. This study investigates the importance of body size parameters in their relationship with spinal cord (SC) and brain magnetic resonance imaging (MRI) metrics. Data were derived from a cosmopolitan population of 267 healthy human adults (age 30.1±6.6 years old, 125 females). We show that body height correlated strongly or moderately with brain gray matter (GM) volume, cortical GM volume, total cerebellar volume, brainstem volume, and cross-sectional area (CSA) of cervical SC white matter (CSA-WM; 0.44≤r≤0.62). In comparison, age correlated weakly with cortical GM volume, precentral GM volume, and cortical thickness (-0.21≥r≥-0.27). Body weight correlated weakly with magnetization transfer ratio in the SC WM, dorsal columns, and lateral corticospinal tracts (-0.20≥r≥-0.23). Body weight further correlated weakly with the mean diffusivity derived from diffusion tensor imaging (DTI) in SC WM (r=-0.20) and dorsal columns (-0.21), but only in males. CSA-WM correlated strongly or moderately with brain volumes (0.39≤r≤0.64), and weakly with precentral gyrus thickness and DTI-based fractional anisotropy in SC dorsal columns and SC lateral corticospinal tracts (-0.22≥r≥-0.25). Linear mixture of sex and age explained 26±10% of data variance in brain volumetry and SC CSA. The amount of explained variance increased at 33±11% when body height was added into the mixture model. Age itself explained only 2±2% of such variance. In conclusion, body size is a significant biological variable. Along with sex and age, body size should therefore be included as a mandatory variable in the design of clinical neuroimaging studies examining SC and brain structure.

Calibration-free parallel transmission of the cervical, thoracic, and lumbar spinal cord at 7T.

PURPOSE: To address the limitations of spinal cord imaging at ultra-high field (UHF) due to time-consuming parallel transmit (pTx) adjustments. This study introduces calibration-free offline computed universal shim modes that can be applied seamlessly for different pTx RF coils and spinal cord target regions, substantially enhancing spinal cord imaging efficiency at UHF. METHODS: A library of channel-wise relative B 1 + $$ {B}_1^{+} $$ maps for the cervical spinal cord (six datasets) and thoracic and lumbar spinal cord (nine datasets) was constructed to optimize transmit homogeneity and efficiency for these regions. A tailored B0 shim was optimized for the cervical spine to enhance spatial magnetic field homogeneity further. The performance of the universal shims was validated using absolute saturation based B 1 + $$ {B}_1^{+} $$ mapping and high-resolution 2D and 3D multi-echo gradient-recalled echo (GRE) data to assess the image quality. RESULTS: The proposed universal shims demonstrated a 50% improvement in B 1 + $$ {B}_1^{+} $$ efficiency compared to the default (zero phase) shim mode. B 1 + $$ {B}_1^{+} $$ homogeneity was also improved by 20%. The optimized universal shims achieved performance comparable to subject-specific pTx adjustments, while eliminating the need for lengthy pTx calibration times, saving about 10 min per experiment. CONCLUSION: The development of universal shims represents a significant advance by eliminating time-consuming subject-specific pTx adjustments. This approach is expected to make UHF spinal cord imaging more accessible and user-friendly, particularly for non-pTx experts.

Shimming toolbox: An open-source software toolbox for B0 and B1 shimming in MRI.

PURPOSE: Introduce Shimming Toolbox ( https://shimming-toolbox.org), an open-source software package for prototyping new methods and performing static, dynamic, and real-time B0 shimming as well as B1 shimming experiments. METHODS: Shimming Toolbox features various field mapping techniques, manual and automatic masking for the brain and spinal cord, B0 and B1 shimming capabilities accessible through a user-friendly graphical user interface. Validation of Shimming Toolbox was demonstrated in three scenarios: (i) B0 dynamic shimming in the brain at 7T using custom AC/DC coils, (ii) B0 real-time shimming in the spinal cord at 3T, and (iii) B1 static shimming in the spinal cord at 7T. RESULTS: The B0 dynamic shimming of the brain at 7T took about 10 min to perform. It showed a 47% reduction in the standard deviation of the B0 field, associated with noticeable improvements in geometric distortions in EPI images. Real-time dynamic xyz-shimming in the spinal cord took about 5 min and showed a 30% reduction in the standard deviation of the signal distribution. B1 static shimming experiments in the spinal cord took about 10 min to perform and showed a 40% reduction in the coefficient of variation of the B1 field. CONCLUSION: Shimming Toolbox provides an open-source platform where researchers can collaborate, prototype and conveniently test B0 and B1 shimming experiments. Future versions will include additional field map preprocessing techniques, optimization algorithms, and compatibility across multiple MRI manufacturers.

Comparison of multicenter MRI protocols for visualizing the spinal cord gray matter.

PURPOSE: Spinal cord gray-matter imaging is valuable for a number of applications, but remains challenging. The purpose of this work was to compare various MRI protocols at 1.5 T, 3 T, and 7 T for visualizing the gray matter. METHODS: In vivo data of the cervical spinal cord were collected from nine different imaging centers. Data processing consisted of automatically segmenting the spinal cord and its gray matter and co-registering back-to-back scans. We computed the SNR using two methods (SNR_single using a single scan and SNR_diff using the difference between back-to-back scans) and the white/gray matter contrast-to-noise ratio per unit time. Synthetic phantom data were generated to evaluate the metrics performance. Experienced radiologists qualitatively scored the images. We ran the same processing on an open-access multicenter data set of the spinal cord MRI (N = 267 participants). RESULTS: Qualitative assessments indicated comparable image quality for 3T and 7T scans. Spatial resolution was higher at higher field strength, and image quality at 1.5 T was found to be moderate to low. The proposed quantitative metrics were found to be robust to underlying changes to the SNR and contrast; however, the SNR_single method lacked accuracy when there were excessive partial-volume effects. CONCLUSION: We propose quality assessment criteria and metrics for gray-matter visualization and apply them to different protocols. The proposed criteria and metrics, the analyzed protocols, and our open-source code can serve as a benchmark for future optimization of spinal cord gray-matter imaging protocols.

Open-access quantitative MRI data of the spinal cord and reproducibility across participants, sites and manufacturers.

In a companion paper by Cohen-Adad et al. we introduce the spine generic quantitative MRI protocol that provides valuable metrics for assessing spinal cord macrostructural and microstructural integrity. This protocol was used to acquire a single subject dataset across 19 centers and a multi-subject dataset across 42 centers (for a total of 260 participants), spanning the three main MRI manufacturers: GE, Philips and Siemens. Both datasets are publicly available via git-annex. Data were analysed using the Spinal Cord Toolbox to produce normative values as well as inter/intra-site and inter/intra-manufacturer statistics. Reproducibility for the spine generic protocol was high across sites and manufacturers, with an average inter-site coefficient of variation of less than 5% for all the metrics. Full documentation and results can be found at https://spine-generic.rtfd.io/ . The datasets and analysis pipeline will help pave the way towards accessible and reproducible quantitative MRI in the spinal cord.

Generic acquisition protocol for quantitative MRI of the spinal cord.

Quantitative spinal cord (SC) magnetic resonance imaging (MRI) presents many challenges, including a lack of standardized imaging protocols. Here we present a prospectively harmonized quantitative MRI protocol, which we refer to as the spine generic protocol, for users of 3T MRI systems from the three main manufacturers: GE, Philips and Siemens. The protocol provides guidance for assessing SC macrostructural and microstructural integrity: T1-weighted and T2-weighted imaging for SC cross-sectional area computation, multi-echo gradient echo for gray matter cross-sectional area, and magnetization transfer and diffusion weighted imaging for assessing white matter microstructure. In a companion paper from the same authors, the spine generic protocol was used to acquire data across 42 centers in 260 healthy subjects. The key details of the spine generic protocol are also available in an open-access document that can be found at https://github.com/spine-generic/protocols . The protocol will serve as a starting point for researchers and clinicians implementing new SC imaging initiatives so that, in the future, inclusion of the SC in neuroimaging protocols will be more common. The protocol could be implemented by any trained MR technician or by a researcher/clinician familiar with MRI acquisition.

Centering inclusivity in the design of online conferences-An OHBM-Open Science perspective.

As the global health crisis unfolded, many academic conferences moved online in 2020. This move has been hailed as a positive step towards inclusivity in its attenuation of economic, physical, and legal barriers and effectively enabled many individuals from groups that have traditionally been underrepresented to join and participate. A number of studies have outlined how moving online made it possible to gather a more global community and has increased opportunities for individuals with various constraints, e.g., caregiving responsibilities. Yet, the mere existence of online conferences is no guarantee that everyone can attend and participate meaningfully. In fact, many elements of an online conference are still significant barriers to truly diverse participation: the tools used can be inaccessible for some individuals; the scheduling choices can favour some geographical locations; the set-up of the conference can provide more visibility to well-established researchers and reduce opportunities for early-career researchers. While acknowledging the benefits of an online setting, especially for individuals who have traditionally been underrepresented or excluded, we recognize that fostering social justice requires inclusivity to actively be centered in every aspect of online conference design. Here, we draw from the literature and from our own experiences to identify practices that purposefully encourage a diverse community to attend, participate in, and lead online conferences. Reflecting on how to design more inclusive online events is especially important as multiple scientific organizations have announced that they will continue offering an online version of their event when in-person conferences can resume.

Impact of magnetic susceptibility anisotropy at 3 T and 7 T on T2*-based myelin water fraction imaging.

PURPOSE: Myelin Water Fraction (MWF) mapping can be achieved by fitting multi-gradient recalled echo (MGRE) magnitude images with a three-component model or a pseudo-continuous T2∗ distribution. Recent findings of compartment-specific orientation-dependent magnetic susceptibility shifts have spurred the inclusion of frequency offset (Δf) terms in the fitting models. In this work, we performed simulations to assess the impact of Δf's on the MWF, derived from three different fitting models, at two field strengths. THEORY AND METHODS: White matter MGRE signals were simulated using the Hollow Cylinder Fiber Model at 3 and 7 T, for a range of fiber orientations (θ), and analyzed using: 1) a multi-component T2∗ signal magnitude model (MCMT2∗); 2) a three-component T2∗ signal magnitude model (3CMT2∗); and, 3) a three-component complex T2∗ signal model (3CCT2∗). RESULTS: At 3 T, MCMT2∗ & 3CMT2∗ yielded accurate MWFs: (11.9±1.1)% and (11.7±1.0)% (mean± standard deviation across 1000 simulations, true MWF = 12%), respectively. 3CCT2∗ MWFs were less accurate and had the largest variability: (9.2±5.0)%. At 7 T, MCMT2∗ and 3CMT2∗ MWFs became less accurate as θ increased. This was remedied by 3CCT2∗, at the expense of accuracy for small θ. CONCLUSION: This work suggests that if no information regarding Δf is sought, MCMT2∗ and 3CMT2∗ are preferable at 3 T. At 7 T, Δf cannot be overlooked.

Multi-gradient-echo myelin water fraction imaging: Comparison to the multi-echo-spin-echo technique.

PURPOSE: Myelin water fraction (MWF) mapping based on multi-gradient recalled-echo (MGRE) imaging has been proposed as an alternative to the conventional multi-echo-spin-echo (MESE) approach. In this work, we performed a comparative study of MESE and MGRE-derived MWFs in the same subject group. METHODS: MESE and MGRE data were acquired in 12 healthy volunteers at 3T. T2* decay curves were corrected for the effects of field inhomogeneities and multicomponent analysis of T2  and T2* signals was performed using non-negative least-squares fitting. RESULTS: When comparing MGRE and MESE-MWFs across volunteers, no significant differences were observed between average values in WM, deep GM (dGM), and cortical GM (cGM) that were (14 ± 3%), (6 ± 2%), and (8 ± 2%) for MGRE, and (13 ± 2%), (6 ± 1%), and (7 ± 1%), respectively, for MESE. The MGRE and MESE-MWFs showed a strong correlation (r2 = 0.84) and Bland-Altman analysis revealed a small positive bias of (0.8 ± 1.6%) (absolute difference) for the MGRE-MWF. CONCLUSION: Overall, we observed excellent agreement between the two techniques. The small positive bias of the MGRE-MWF is thought to be a consequence of its potentially reduced sensitivity to water exchange effects, compared to the MESE-MWF. This work suggests that with careful correction for the effects of field inhomogeneities, MGRE-MWF imaging is a promising alternative to the MESE approach. Magn Reson Med 79:1439-1446, 2018. © 2017 International Society for Magnetic Resonance in Medicine.

Field inhomogeneity correction for gradient echo myelin water fraction imaging.

PURPOSE: Recently, the multi-echo gradient echo (MGRE) sequence has been proposed for multicomponent T2* (MC T2*) based myelin water fraction (MWF) mapping. This approach has appeal because it can provide fast whole-brain coverage, has low specific absorption rate, and short echo spacing. However, the MGRE signal requires correction for accurate MWF mapping, because of its sensitivity to magnetic field inhomogeneities (ΔB0 ). We propose a ΔB0 correction method for 2D MGRE data obtained for MWF mapping. THEORY AND METHODS: Latter-echo MGRE data were fit to estimate B0 gradients in the slice-select direction ( Gz). The decay signal was corrected for the effects of Gz, and MC T2* analysis was performed using nonnegative least-squares fitting. The method was evaluated using simulations and its performance demonstrated in healthy volunteers. RESULTS: Simulations showed that MWFs are significantly biased in the presence of Gz and that our correction method leads to accurate MWF estimates. In vivo MWF maps obtained from corrected data showed recovery of MWF estimates in areas of high ΔB0, and overall good agreement with literature values obtained with the reference MC T2-based method. CONCLUSION: A new algorithm was presented for ΔB0 correction of 2D MGRE echo data acquired for MWF imaging. Simulations and in vivo data showed an improvement in MWF estimates. Magn Reson Med 78:49-57, 2017. © 2016 International Society for Magnetic Resonance in Medicine.

MRI-based myelin water imaging: A technical review.

Multiexponential T2 relaxation time measurement in the central nervous system shows a component that originates from water trapped between the lipid bilayers of myelin. This myelin water component is of significant interest as it provides a myelin-specific MRI signal of value in assessing myelin changes in cerebral white matter in vivo. In this article, the various acquisition and analysis strategies proposed to date for myelin water imaging are reviewed and research conducted into their validity and clinical applicability is presented. Comparisons between the imaging methods are made with a discussion regarding potential difficulties and model limitations.