Contrast at high field: Relaxation times, magnetization transfer and phase in the rat brain at 16.4 T

Submillimeter Ultra-High Field 9.4 T Brain MR Image Collection and Manual Cortical Segmentations

The UltraCortex repository houses magnetic resonance imaging data of the human brain obtained at an ultra-high field strength of 9.4 T. It contains 86 structural MR images with spatial resolutions ranging from 0.6 to 0.8 mm. Additionally, the repository includes segmentations of 12 brains into gray and white matter compartments. These segmentations have been independently validated by two expert neuroradiologists, thus establishing them as a reliable gold standard. This resource provides researchers with access to high-quality brain imaging data and validated segmentations, facilitating neuroimaging studies and advancing our understanding of brain structure and function. Existing repositories do not accommodate field strengths beyond 7 T, nor do they offer validated segmentations, underscoring the significance of this new resource.

Alpha-180 spin-echo based line-scanning method for high resolution laminar-specific fMRI

Laminar-specific functional magnetic resonance imaging (fMRI) has been widely used to study circuit-specific neuronal activity by mapping spatiotemporal fMRI response patterns across cortical layers. Hemodynamic responses reflect indirect neuronal activity given limit of spatial and temporal resolution. Previous gradient-echo based line-scanning fMRI (GELINE) method was proposed with high temporal (50 ms) and spatial (50 µm) resolution to better characterize the fMRI onset time across cortical layers by employing 2 saturation RF pulses. However, the imperfect RF saturation performance led to poor boundary definition of the reduced region of interest (ROI) and aliasing problems outside of the ROI. Here, we propose α (alpha)-180 spin-echo-based line-scanning fMRI (SELINE) method to resolve this issue by employing a refocusing 180° RF pulse perpendicular to the excitation slice. In contrast to GELINE signals peaked at the superficial layer, we detected varied peaks of laminar-specific BOLD signals across deeper cortical layers with the SELINE method, indicating the well-defined exclusion of the large drain-vein effect with the spin-echo sequence. Furthermore, we applied the SELINE method with 200 ms TR to sample the fast hemodynamic changes across cortical layers with a less draining vein effect. In summary, this SELINE method provides a novel acquisition scheme to identify microvascular-sensitive laminar-specific BOLD responses across cortical depth.

Alternating Look-Locker for quantitative T1 , T1ρ and B1 3D MRI mapping

PURPOSE

To develop a new MRI method, entitled alternating Look-Locker (aLL), for quantitativeT 1 $$ {T}_1 $$ ,T 1 ρ $$ {T}_{1\uprho} $$ , andB 1 $$ {B}_1 $$ 3D mapping.

METHODS

A Look-Locker scheme that alternates magnetization from +Z and -Z axes of the laboratory frame is utilized in combination with a 3D Multi-Band Sweep Imaging with Fourier Transformation (MB-SWIFT) readout. The analytical solution describing the spin evolution during aLL, as well as the correction required for segmented acquisition were derived. The simultaneousB 1 $$ {B}_1 $$ andT 1 $$ {T}_1 $$ mapping are demonstrated on an agar/saline phantom and on an in-vivo rat head.T 1 ρ $$ {T}_{1\uprho} $$ relaxation was achieved by cyclically applying magnetization preparation (MP) modules consisting of two adiabatic pulses.T 1 ρ $$ {T}_{1\uprho} $$ values in the rat brain in-vivo and in a gadobenate dimeglumine (Gd-DTPA) phantom were compared to those obtained with a previously introduced steady-state (SS) method.

RESULTS

The accuracy and precision of the analytical solution was tested by Bloch simulations. With the application of MP modules, the aLL method provides simultaneousT 1 $$ {T}_1 $$ andT 1 ρ $$ {T}_{1\uprho} $$ maps. Conversely, without it, the method can be used for simultaneousT 1 $$ {T}_1 $$ andB 1 $$ {B}_1 $$ mapping.T 1 ρ $$ {T}_{1\uprho} $$ values were similar with both aLL and SS techniques. However, the aLL method resulted in more robust quantitative mapping compared to the SS method. Unlike the SS method, the aLL method does not require additional scans for generatingT 1 $$ {T}_1 $$ maps.

CONCLUSION

The proposed method offers a new flexible tool for quantitative mapping ofT 1 $$ {T}_1 $$ ,T 1 ρ $$ {T}_{1\uprho} $$ , andB 1 $$ {B}_1 $$ . The aLL method can also be used with readout schemes different from MB-SWIFT.

Evaluation of Renal Fibrosis Using Magnetization Transfer Imaging at 1.5T and 3T in a Porcine Model of Renal Artery Stenosis

Renal fibrosis is an important marker in the progression of chronic kidney disease, and renal biopsy is the current reference standard for detecting its presence. Currently, non-invasive methods have only been partially successful in detecting renal fibrosis. Magnetization transfer imaging (MTI) allows estimates of renal fibrosis but may vary with scanning conditions. We hypothesized that MTI-derived renal fibrosis would be reproducible at 1.5T and 3T MRI and over time in fibrotic kidneys. Fifteen pigs with unilateral renal artery stenosis (RAS, n = 9) or age-matched sham controls (n = 6) underwent MTI-MRI at both 1.5T and 3T 6 weeks post-surgery and again 4 weeks later. Magnetization transfer ratio (MTR) measurements of fibrosis in both kidneys were compared between 1.5T and 3T, and the reproducibility of MTI at the two timepoints was evaluated at 1.5T and 3T. MTR at 3T with 600 Hz offset frequency successfully distinguished between normal, stenotic, and contralateral kidneys. There was excellent reproducibility of MTI at 1.5T and 3T over the two timepoints and no significant differences between MTR measurements at 1.5T and 3T. Therefore, MTI is a highly reproducible technique which is sensitive to detect changes in fibrotic compared to normal kidneys in the RAS porcine model at 3T.

Functional mapping of sensorimotor activation in the human thalamus at 9.4 Tesla

Although the thalamus is perceived as a passive relay station for almost all sensory signals, the function of individual thalamic nuclei remains unresolved. In the present study, we aimed to identify the sensorimotor nuclei of the thalamus in humans using task-based fMRI at a field strength of 9.4T by assessing the individual subject-specific sensorimotor BOLD response during a combined active motor (finger-tapping) and passive sensory (tactile-finger) stimulation. We demonstrate that both tasks increase BOLD signal response in the lateral nuclei group (VPL, VA, VLa, and VLp), and in the pulvinar nuclei group (PuA, PuM, and PuL). Finger-tapping stimuli evokes a stronger BOLD response compared to the tactile stimuli, and additionally engages the intralaminar nuclei group (CM and Pf). In addition, our results demonstrate reproducible thalamic nuclei activation during motor and tactile stimuli. This work provides important insight into understanding the function of individual thalamic nuclei in processing various input signals and corroborates the benefits of using ultra-high-field MR scanners for functional imaging of fine-scale deeply located brain structures.

Test-Retest Reproducibility of In Vivo Magnetization Transfer Ratio and Saturation Index in Mice at 9.4 Tesla

BACKGROUND

Magnetization transfer saturation (MTsat) imaging was developed to reduce T1 dependence and improve specificity to myelin, compared to the widely used MT ratio (MTR) approach, while maintaining a feasible scan time. As MTsat imaging is an emerging technique, the reproducibility of MTsat compared to MTR must be evaluated.

PURPOSE

To assess the test-retest reproducibility of MTR and MTsat in the mouse brain at 9.4 T and calculate sample sizes potentially required to detect effect sizes ranging from 6% to 14%.

STUDY TYPE

Prospective.

SUBJECTS

Twelve healthy C57Bl/6 mice.

FIELD STRENGTH/SEQUENCE

9.4 T; magnetization transfer imaging using FLASH-3D Gradient Echo; T2-weighted TurboRARE spin echo.

ASSESSMENT

All mice were scanned at two timepoints (5 days apart). MTR and MTsat maps were analyzed using mean region-of-interest (ROIs: corpus callosum [CC], internal capsule [IC], hippocampus [HC], cortex [CX], and thalamus [TH]), and whole brain voxel-wise analysis.

STATISTICAL TESTS

Bland-Altman plots were used to assess biases between test-retest measurements. Test-retest reproducibility was evaluated via between and within-subject coefficients of variation (bsCV and wsCV, respectively). Sample sizes required were calculated (significance level: 95%; power: 80%), given effect sizes ranging from 6% to 14%, using both between and within-subject approaches. Results were considered statistically significant at P ≤ 0.05.

RESULTS

Bland-Altman plots showed negligible biases between test-retest sessions (MTR: 0.0009; MTsat: 0). ROI-based and voxel-wise CVs revealed high reproducibility for both MTR (ROI-bsCV/wsCV: CC-4.5/2.8%; IC-6.1/5.2%; HC-5.7/4.6%; CX-5.1/2.3%; TH-7.4/4.9%) and MTsat (ROI-bsCV/wsCV: CC-6.3/4.8%; IC-7.3/5.1%; HC-9.5/6.4%; CX-6.7/6.5%; TH-7.2/5.3%). With a sample size of 6, changes on the order of 15% could be detected in MTR and MTsat, both between and within subjects, while smaller changes (6%-8%) required sample sizes of 10-15 for MTR, and 15-20 for MTsat.

DATA CONCLUSION

MTsat exhibited comparable reproducibility to MTR, while providing sensitivity to myelin with less T1 dependence than MTR. EVIDENCE LEVEL: 2 TECHNICAL EFFICACY: Stage 1.

Mapping magnetization transfer saturation (MTsat ) in human brain at 7T: Protocol optimization under specific absorption rate constraints

PURPOSE

To optimize a whole-brain magnetization transfer saturation (MT_sat ) protocol at 7T, focusing on maximizing obtainable MT_sat under the constraints of specific absorption rate (SAR) and transmit field inhomogeneity, while avoiding bias and keeping scan time short.

THEORY AND METHODS

MT_sat is a semi-quantitative metric, obtained by spoiled gradient-echo MRI in the imaging steady-state. Optimization was based on an established 7T dual flip angle protocol, and focused on MT pulse, readout flip angle, repetition time (TR), offset frequency (Δ), and correction of residual effects from transmit field inhomogeneities by separate flip angle mapping.

RESULTS

A 100% SAR level was reached at a 180° MT pulse flip angle, using a compact sinc main lobe (4 ms duration) and minimum TR = 26.5 ms. The use of Δ = +2.0 kHz caused no discernible direct saturation, while Δ = -2.0 kHz resulted in 45% higher MT_sat in white matter (WM) compared to Δ = +2.0 kHz. A 4° readout flip angle eliminated bias while yielding a good signal-to-noise ratio. Increased TR yielded only a little increase in MT_sat , and TR = 26.5 ms (scan time 04:58 min) was thus selected. Post hoc transmit field correction clearly improved homogeneity, especially in WM.

CONCLUSIONS

The range of MT_sat is limited at 7T, and this can partly be overcome by the exploitation of the asymmetry of the macromolecular lineshape through the sign of Δ. To reduce scan time, a compact MT pulse with a sufficiently narrow frequency response should be used. TR and readout flip angle should be kept short/small. Transmit field correction through separate flip angle mapping is required.

High spatiotemporal vessel-specific hemodynamic mapping with multi-echo single-vessel fMRI

High-resolution fMRI enables noninvasive mapping of the hemodynamic responses from individual penetrating vessels in animal brains. Here, a 2D multi-echo single-vessel fMRI (MESV-fMRI) method has been developed to map the fMRI signal from arterioles and venules with a 100 ms sampling rate at multiple echo times (TE, 3-30 ms) and short acquisition windows (<1 ms). The T₂*-weighted signal shows the increased extravascular effect on venule voxels as a function of TE. In contrast, the arteriole voxels show an increased fMRI signal with earlier onset than venules voxels at the short TE (3 ms) with increased blood inflow and volume effects. MESV-fMRI enables vessel-specific T2* mapping and presents T2*-based fMRI time courses with higher contrast-to-noise ratios (CNRs) than the T2*-weighted fMRI signal at a given TE. The vessel-specific T2* mapping also allows semi-quantitative estimation of the oxygen saturation levels (Y) and their changes (ΔY) at a given blood volume fraction upon neuronal activation. The MESV-fMRI method enables vessel-specific T2* measurements with high spatiotemporal resolution for better modeling of the fMRI signal based on the hemodynamic parameters.

A basic MRI anatomy of the rat brain in coronal sections for practical guidance to neuroscientists

Identification of the brain structures in the magnetic resonance imaging (MRI) of the rat is very important for the experimental work of many neuroscientists. Our intention was to recognize most of the structures without overlapping the MRI sections with the histological templates. Three live rats were used for this study who were examined in a micro-MRI apparatus by performing T2-weighted sequences in serial brain sections. Most of the white matter structures were easily identified, e.g. the anterior commissure, corpus callosum with forceps minor and major, cingulum, external and internal capsules, fornix, stria medullaris and terminalis, cranial nerves, mammillothalamic tract, fasciculus retroflexus, medial and lateral lemniscus, posterior commissure, commissures of the superior and inferior colliculi, medial longitudinal fasciculus, and the cerebral peduncle. Large and small gray matter structures were recognized as well, for example, the anterior olfactory structures, nucleus accumbens, caudate putamen, claustrum, bed nucleus of the stria terminalis, pituitary gland, globus pallidus, amygdala, some midline and intralaminar thalamic nuclei, certain hypothalamic nuclei, hippocampal formation, pineal body, periaqueductal gray matter, lateral and medial geniculate bodies, superior and inferior colliculi, and cranial nerves nuclei. All in all, of the total 160 recognized brain structures, 77 were identified without using the corresponding histological atlases. We believe that our labeled MRI pictures could be an important way for quick orientation for evaluating the effects of the experimental work regarding the rat brain.

Determination of optimal parameters for 3D single-point macromolecular proton fraction mapping at 7T in healthy and demyelinated mouse brain

PURPOSE

To determine optimal constrained tissue parameters and off-resonance sequence parameters for single-point macromolecular proton fraction (SP-MPF) mapping based on a comprehensive quantitative magnetization transfer (qMT) protocol in healthy and demyelinated living mice at 7T.

METHODS

Using 3D spoiled gradient echo-based sequences, a comprehensive qMT protocol is performed by sampling the Z-spectrum of mice brains, in vivo. Provided additional T₁ , B 1 + and B₀ maps allow for the estimation of qMT tissue parameters, among which three will be constrained, namely the longitudinal and transverse relaxation characteristics of the free pool (R_1,f T_2,f ), the cross-relaxation rate (R) and the bound pool transverse relaxation time (T_2,r ). Different sets of constrained parameters are investigated to reduce the bias between the SP-MPF and its reference based on the comprehensive protocol.

RESULTS

Based on a whole-brain histogram analysis about the constrained parameters, the optimal experimental parameters that minimize the global bias between reference and SP-MPF maps consist of a 600° and 6 kHz off-resonance irradiation pulse. Following a Bland-Altman analysis over regions of interest, optimal constrained parameters were R_1,f T_2,f  = 0.0129, R = 26.5 s^-1 , and T_2,r  = 9.1 µs, yielding an overall MPF bias of 10^-4 (limits of agreement [-0.0068;0.0070]) and a relative variation of 0.64% ± 5.95% between the reference and the optimal single-point method across all mice.

CONCLUSION

The necessity of estimating animal model- and field-dependent constrained parameters was demonstrated. The single-point MPF method can be reliably applied at 7T, as part of routine preclinical in vivo imaging protocol in mice.

2D multislice MP2RAGE sequence for fast T1 mapping at 7 T: Application to mouse imaging and MR thermometry

PURPOSE

To develop a 2D radial multislice MP2RAGE sequence for fast and reliable T₁ mapping at 7 T in mice and for MR thermometry.

METHODS

The 2D-MP2RAGE sequence was performed with the following parameters: TI₁ -TI₂ -MP2RAGE_TR = 1000-3000-9000 ms. The multiple dead times within the sequence were used for interleaved multislice acquisition, enabling one to acquire six slices in 9 seconds. The excitation pulse shape, inversion selectivity, and interslice gap were optimized. In vitro comparison with the inversion-recovery sequence was performed. The T₁ variations with temperature were measured on tubes with T₁ ranging from 800 ms to 2000 ms. The sequence was used to acquire T₁ maps continuously during 30 minutes on the brain and abdomen of healthy mice.

RESULTS

A three-lobe cardinal sine excitation pulse, combined with an inversion slice thickness and an interslice gap of respectively 150% and 50% of the imaging slice thickness, led to a SD and bias of the T₁ measurements below 1% and 2%, respectively. A linear dependence of T₁ with temperature was measured between 10°C and 60°C. In vivo, less than 1% variation was measured between successive T₁ maps in the mouse brain. In the abdomen, no obvious in-plane motion artifacts were observed but respiratory motion in the slice dimension led to 6% T₁ underestimation.

CONCLUSION

The multislice MP2RAGE sequence could be used for fast whole-body T₁ mapping and MR thermometry. Its reconstruction method would enable on-the-fly reconstruction.

Ultrafast fMRI of the rodent brain using simultaneous multi-slice EPI

Increasing spatial and temporal resolutions of functional MRI (fMRI) measurement has been shown to benefit the study of neural dynamics and functional interaction. However, acceleration of rodent brain fMRI using parallel and simultaneous multi-slice imaging techniques is hampered by the lack of high-density phased-array coils for the small brain. To overcome this limitation, we adapted phase-offset multiplanar and blipped-controlled aliasing echo planar imaging (EPI) to enable simultaneous multi-slice fMRI of the mouse brain using a single loop coil on a 9.4T scanner. Four slice bands of 0.3 × 0.3 × 0.5 mm³ resolution can be simultaneously acquired to cover the whole brain at a temporal resolution of 300 ms or the whole cerebrum in 150 ms. Instead of losing signal-to-noise ratio (SNR), both spatial and temporal SNR can be increased due to the increased k-space sampling compared to a standard single-band EPI. Task fMRI using a visual stimulation shows close to 80% increase of z-score and 4 times increase of activated area in the visual cortex using the multiband EPI due to the highly increased temporal samples. Resting-state fMRI shows reliable detection of bilateral connectivity by both single-band and multiband EPI, but no significant difference was found. Without the need of a dedicated hardware, we have demonstrated a practical method that can enable unparallelly fast whole-brain fMRI for preclinical studies. This technique can be used to increase sensitivity, distinguish transient response or acquire high spatiotemporal resolution fMRI.

Towards microstructure fingerprinting: Estimation of tissue properties from a dictionary of Monte Carlo diffusion MRI simulations

Many closed-form analytical models have been proposed to relate the diffusion-weighted magnetic resonance imaging (DW-MRI) signal to microstructural features of white matter tissues. These models generally make assumptions about the tissue and the diffusion processes which often depart from the biophysical reality, limiting their reliability and interpretability in practice. Monte Carlo simulations of the random walk of water molecules are widely recognized to provide near groundtruth for DW-MRI signals. However, they have mostly been limited to the validation of simpler models rather than used for the estimation of microstructural properties. This work proposes a general framework which leverages Monte Carlo simulations for the estimation of physically interpretable microstructural parameters, both in single and in crossing fascicles of axons. Monte Carlo simulations of DW-MRI signals, or fingerprints, are pre-computed for a large collection of microstructural configurations. At every voxel, the microstructural parameters are estimated by optimizing a sparse combination of these fingerprints. Extensive synthetic experiments showed that our approach achieves accurate and robust estimates in the presence of noise and uncertainties over fixed or input parameters. In an in vivo rat model of spinal cord injury, our approach provided microstructural parameters that showed better correspondence with histology than five closed-form models of the diffusion signal: MMWMD, NODDI, DIAMOND, WMTI and MAPL. On whole-brain in vivo data from the human connectome project (HCP), our method exhibited spatial distributions of apparent axonal radius and axonal density indices in keeping with ex vivo studies. This work paves the way for microstructure fingerprinting with Monte Carlo simulations used directly at the modeling stage and not only as a validation tool.

Two-dimensional magnetization-transfer - CPMG MRI reveals tract-specific signatures in fixed rat spinal cord

Multiexponential T₂ (MET₂) Relaxometry and Magnetization Transfer (MT) are among the most promising MRI-derived techniques for white matter (WM) characterization. Both techniques are shown to have histologically correlated sensitivity to myelin, but these correlations are not fully understood. Furthermore, MET₂ and MT report on different WM features, thus they can be considered specific to different (patho)physiological states. Two-dimensional studies potentially resolving interactions, such as those commonly used in NMR, have been rarely performed in this context. Here, we investigated how off-resonance irradiation affects different MET₂ components in fixed rat spinal cord white matter at 16.4 T. These 2D MT-MET₂ experiments reveal that MT affects both short and long T₂ components in a tract-specific fashion. The spatially distinct signal modulations enhanced contrast between microstructurally-distinct spinal cord tracts. Two hypotheses to explain these findings were proposed: either selective elimination of a short T₂ component through pre-saturation combines with intercompartmental water exchange effects occurring on the irradiation timescale; or, other macromolecular species that exist within the tissue - other than myelin - such as neurofilaments, may be involved in the apparent microstructural segregation of the spinal cord (SC) from MET₂. Though further investigation is required to elucidate the underlying mechanism, this phenomenon adds a new dimension for WM characterization.

Rapid and accurate dictionary-based T2 mapping from multi-echo turbo spin echo data at 7 Tesla

BACKGROUND

Using lower refocusing flip angles in multi-echo turbo spin echo (ME-TSE) sequences at ultra-high magnetic field leads to non-monoexponential signal decay and overestimation of T₂ values due to stimulated and secondary echoes.

PURPOSE

To investigate the feasibility of a fast and accurate reconstruction of quantitative T₂ values using an ME-TSE sequence with reduced refocusing flip angles at 7 Tesla, a dictionary-based reconstruction method was developed and is presented in this work.

STUDY TYPE

Prospective.

SUBJECTS

Phantom measurements with relaxation phantom, four healthy volunteers.

FIELD STRENGTH/SEQUENCE

7 Tesla MRI, multi-echo turbo spin echo (ME-TSE), spin echo (SE), and B₁ mapping.

ASSESSMENT

Based on Bloch simulations and the extended phase graph model, signal decay curves were calculated to account for nonrectangular slice profile, B₁ inhomogeneity, and reduced refocusing flip angles and stored in a dictionary. Data obtained with an ME-TSE sequence at 7 Tesla were matched to this dictionary to obtain T₂ values. To compare the proposed method to reference T₂ values, a spin echo sequence with different echo times was used.

STATISTICAL TESTS

Welch's t-test was used to compare T₂ values in phantom measurements.

RESULTS

T₂ values obtained with the proposed ME-TSE method coincided with the T₂ values from the spin echo experiment in phantom measurements (P = 0.89 for 120° flip angle, P = 0.75 for 180° flip angle). Only for very low B₁ transmit fields, a slight overestimation of T₂ values was observed. In vivo measurements showed lower T₂ values in gray matter (55 ± 2 millisecond) and white matter (39 ± 5 millisecond) compared with literature values of 3 Tesla data.

DATA CONCLUSIONS

The proposed dictionary-based ME-TSE approach provided accurate T₂ values in short measurement time at 7 Tesla with low specific absorption rate burden due to the reduction of refocusing flip angles. Therefore, it can provide new opportunities in clinical high-field MRI to further improve radiographic diagnosis by using quantitative imaging.

LEVEL OF EVIDENCE

1 Technical Efficacy: Stage 1 J. Magn. Reson. Imaging 2019;49:1253-1262.

In-vivo quantitative structural imaging of the human midbrain and the superior colliculus at 9.4T

We explored anatomical details of the superior colliculus (SC) by in vivo magnetic resonance imaging (MRI) at 9.4T. The high signal-to-noise ratio allowed the acquisition of high resolution, multi-modal images with voxel sizes ranging between 176 × 132 × 600 μm and (800)³μm. Quantitative mapping of the longitudinal relaxation rate R1, the effective transverse relaxation rate R2*, and the magnetic susceptibility QSM was performed in 14 healthy volunteers. The images were analyzed in native space as well as after normalization to a common brain space (MNI). The coefficient-of-variation (CoV) across subjects was evaluated in prominent regions of the midbrain, reaching the best reproducibility (CoV of 5%) in the R2* maps of the SC in MNI space, while the CoV in the QSM maps remained high regardless of brain-space. To investigate whether more complex neurobiological architectural features could be detected, depth profiles through the SC layers towards the red nucleus (RN) were evaluated at different levels of the SC along the rostro-caudal axis. This analysis revealed alterations of the quantitative MRI parameters concordant with previous post mortem histology studies of the cyto- and myeloarchitecture of the SC. In general, the R1 maps were hyperintense in areas characterized by the presence of abundant myelinated fibers, and likely enabled detection of the deep white layer VII of the SC adjacent to the periaqueductal gray. While R1 maps failed to reveal finer details, possibly due to the relatively coarse spatial sampling used for this modality, these could be recovered in R2* maps and in QSM. In the central part of the SC along its rostro-caudal axis, increased R2* values and decreased susceptibility values were observed 2 mm below the SC surface, likely reflecting the myelinated fibers in the superficial optic layer (layer III). Towards the deeper layers, a second increase in R2* was paralleled by a paramagnetic shift in QSM suggesting the presence of an iron-rich layer about 3 mm below the surface of the SC, attributed to the intermediate gray layer (IV) composed of multipolar neurons. These results dovetail observations in histological specimens and animal studies and demonstrate that high-resolution multi-modal MRI at 9.4T can reveal several microstructural features of the SC in vivo.

High-resolution three-dimensional macromolecular proton fraction mapping for quantitative neuroanatomical imaging of the rodent brain in ultra-high magnetic fields

A well-known problem in ultra-high-field MRI is generation of high-resolution three-dimensional images for detailed characterization of white and gray matter anatomical structures. T₁-weighted imaging traditionally used for this purpose suffers from the loss of contrast between white and gray matter with an increase of magnetic field strength. Macromolecular proton fraction (MPF) mapping is a new method potentially capable to mitigate this problem due to strong myelin-based contrast and independence of this parameter of field strength. MPF is a key parameter determining the magnetization transfer effect in tissues and defined within the two-pool model as a relative amount of macromolecular protons involved into magnetization exchange with water protons. The objectives of this study were to characterize the two-pool model parameters in brain tissues in ultra-high magnetic fields and introduce fast high-field 3D MPF mapping as both anatomical and quantitative neuroimaging modality for small animal applications. In vivo imaging data were obtained from four adult male rats using an 11.7T animal MRI scanner. Comprehensive comparison of brain tissue contrast was performed for standard R₁ and T₂ maps and reconstructed from Z-spectroscopic images two-pool model parameter maps including MPF, cross-relaxation rate constant, and T₂ of pools. Additionally, high-resolution whole-brain 3D MPF maps were obtained with isotropic 170µm voxel size using the single-point synthetic-reference method. MPF maps showed 3-6-fold increase in contrast between white and gray matter compared to other parameters. MPF measurements by the single-point synthetic reference method were in excellent agreement with the Z-spectroscopic method. MPF values in rat brain structures at 11.7T were similar to those at lower field strengths, thus confirming field independence of MPF. 3D MPF mapping provides a useful tool for neuroimaging in ultra-high magnetic fields enabling both quantitative tissue characterization based on the myelin content and high-resolution neuroanatomical visualization with high contrast between white and gray matter.

In vivo high angular resolution diffusion-weighted imaging of mouse brain at 16.4 Tesla

Magnetic Resonance Imaging (MRI) of the rodent brain at ultra-high magnetic fields (> 9.4 Tesla) offers a higher signal-to-noise ratio that can be exploited to reduce image acquisition time or provide higher spatial resolution. However, significant challenges are presented due to a combination of longer T₁ and shorter T₂/T₂* relaxation times and increased sensitivity to magnetic susceptibility resulting in severe local-field inhomogeneity artefacts from air pockets and bone/brain interfaces. The Stejskal-Tanner spin echo diffusion-weighted imaging (DWI) sequence is often used in high-field rodent brain MRI due to its immunity to these artefacts. To accurately determine diffusion-tensor or fibre-orientation distribution, high angular resolution diffusion imaging (HARDI) with strong diffusion weighting (b >3000 s/mm²) and at least 30 diffusion-encoding directions are required. However, this results in long image acquisition times unsuitable for live animal imaging. In this study, we describe the optimization of HARDI acquisition parameters at 16.4T using a Stejskal-Tanner sequence with echo-planar imaging (EPI) readout. EPI segmentation and partial Fourier encoding acceleration were applied to reduce the echo time (TE), thereby minimizing signal decay and distortion artefacts while maintaining a reasonably short acquisition time. The final HARDI acquisition protocol was achieved with the following parameters: 4 shot EPI, b = 3000 s/mm², 64 diffusion-encoding directions, 125×150 μm² in-plane resolution, 0.6 mm slice thickness, and 2h acquisition time. This protocol was used to image a cohort of adult C57BL/6 male mice, whereby the quality of the acquired data was assessed and diffusion tensor imaging (DTI) derived parameters were measured. High-quality images with high spatial and angular resolution, low distortion and low variability in DTI-derived parameters were obtained, indicating that EPI-DWI is feasible at 16.4T to study animal models of white matter (WM) diseases.

(17)O relaxation times in the rat brain at 16.4 tesla

PURPOSE

Measurement of the cerebral metabolic rate of oxygen (CMRO2 ) by means of direct imaging of the (17) O signal can be a valuable tool in neuroscientific research. However, knowledge of the longitudinal and transverse relaxation times of different brain tissue types is required, which is difficult to obtain because of the low sensitivity of natural abundance H2 (17) O measurements.

METHODS

Using the improved sensitivity at a field strength of 16.4 Tesla, relaxation time measurements in the rat brain were performed in vivo and postmortem with relatively high spatial resolutions, using a chemical shift imaging sequence.

RESULTS

In vivo relaxation times of rat brain were found to be T1 = 6.84 ± 0.67 ms and T2 * = 1.77 ± 0.04 ms. Postmortem H2 (17) O relaxometry at enriched concentrations after inhalation of (17) O2 showed similar T2 * values for gray matter (1.87 ± 0.04 ms) and white matter, significantly longer than muscle (1.27 ± 0.05 ms) and shorter than cerebrospinal fluid (2.30 ± 0.16 ms).

CONCLUSION

Relaxation times of brain H2 (17) O were measured for the first time in vivo in different types of tissues with high spatial resolution. Because the relaxation times of H2 (17) O are expected to be independent of field strength, our results should help in optimizing the acquisition parameters for experiments also at other MRI field strengths.

Signal-to-noise ratio and MR tissue parameters in human brain imaging at 3, 7, and 9.4 tesla using current receive coil arrays

PURPOSE

Relaxation times, transmit homogeneity, signal-to-noise ratio (SNR) and parallel imaging g-factor were determined in the human brain at 3T, 7T, and 9.4T, using standard, tight-fitting coil arrays.

METHODS

The same human subjects were scanned at all three field strengths, using identical sequence parameters and similar 31- or 32-channel receive coil arrays. The SNR of three-dimensional (3D) gradient echo images was determined using a multiple replica approach and corrected with measured flip angle and T2 (*) distributions and the T1 of white matter to obtain the intrinsic SNR. The g-factor maps were derived from 3D gradient echo images with several GRAPPA accelerations.

RESULTS

As expected, T1 values increased, T2 (*) decreased and the B1 -homogeneity deteriorated with increasing field. The SNR showed a distinctly supralinear increase with field strength by a factor of 3.10 ± 0.20 from 3T to 7T, and 1.76 ± 0.13 from 7T to 9.4T over the entire cerebrum. The g-factors did not show the expected decrease, indicating a dominating role of coil design.

CONCLUSION

In standard experimental conditions, SNR increased supralinearly with field strength (SNR ∼ B0 (1.65) ). To take full advantage of this gain, the deteriorating B1 -homogeneity and the decreasing T2 (*) have to be overcome.

Anatomical, functional and molecular biomarker applications of magnetic resonance neuroimaging

ABSTRACT 

MRI and magnetic resonance spectroscopy (MRS) along with computed tomography and PET are the most common imaging modalities used in the clinics to detect structural abnormalities and pathological conditions in the brain. MRI generates superb image resolution/contrast without radiation exposure that is associated with computed tomography and PET; MRS and spectroscopic imaging technologies allow us to measure changes in brain biochemistry. Increasingly, neurobiologists and MRI scientists are collaborating to solve neuroscience problems across sub-cellular through anatomical levels. To achieve successful cross-disciplinary collaborations, neurobiologists must have sufficient knowledge of magnetic resonance principles and applications in order to effectively communicate with their MRI colleagues. This review provides an overview of magnetic resonance techniques and how they can be used to gain insight into the active brain at the anatomical, functional and molecular levels with the goal of encouraging neurobiologists to include MRI/MRS as a research tool in their endeavors.

In vivo proton magnetic resonance spectroscopic imaging of the healthy human brain at 9.4 T: initial experience

OBJECT

In this study, the feasibility of in vivo proton magnetic resonance spectroscopic imaging ((1)H MRSI) of the healthy human brain at a field strength of 9.4 T, using conventional acquisition techniques, is examined and the initial experience is summarized.

MATERIALS AND METHODS

MRSI measurements were performed on a 9.4 T MR scanner (Siemens, Erlangen, Germany) equipped with head-only gradient insert (AC84, Siemens) and custom-developed, 8-channel transmit/24-channel receive, and 16-channel transmit/31-channel receive coils. Spectra were acquired from the superior part of the human brain with a modified STEAM sequence. Spectral quantification was done with LCModel software.

RESULTS

Reasonable quality and signal-to-noise ratio of the acquired spectra allowed reliable quantification of 12 metabolites (Cramer-Rao lower bounds < 20 %), some of which may be difficult to quantify at field strengths below 7 T due to overlapping resonances or low concentrations.

CONCLUSION

While further developments are necessary to minimize chemical shift displacement and homogeneity of the transmit field, it is demonstrated that in vivo (1)H MRSI at a field strength of 9.4 T is possible. However, further studies applying up-to-date techniques to overcome high-field specific problems are needed in order to assess the potential gain in sensitivity that may be offered by MRSI at 9.4 T.

MRI assessment of experimental gliomas using 17.6 T

INTRODUCTION

Using ultra-high-field contrast-enhanced magnetic resonance imaging (MRI), an increase of field strength is associated with a decrease of T 1 relaxivity. Yet, the impact of this effect on signal characteristics and contrast-enhanced pathology remains unclear. Hence, we evaluated the potential of a 17.6-T MRI to assess contrast-enhancing parts of experimentally induced rat gliomas compared to 3 T.

METHODS

A total of eight tumor-bearing rats were used for MRI assessments either at 17.6 T (four rats) or at 3 T (four rats) at 11 days after stereotactic implantation of F98 glioma cells into the right frontal lobe. T 1-weighted sequences were used to investigate signal-to-noise-ratios, contrast-to-noise-ratios, and relative contrast enhancement up to 16 min after double-dose contrast application. In addition, tumor volumes were calculated and compared to histology.

RESULTS

The 17.6-T-derived contrast-enhancing volumes were 31.5 ± 15.4 mm(3) at 4 min, 38.8 ± 12.7 mm(3) at 8 min, 51.1 ± 12.6 mm(3) at 12 min, and 61.5 ± 10.8 mm(3) at 16 min after gadobutrol injection. Corresponding histology-derived volumes were clearly higher (138.8 ± 8.4 mm(3); P < 0.01). At 3 T, contrast-enhancing volumes were 85.2 ± 11.7 mm(3) at 4 min, 107.3 ± 11.0 mm(3) at 8 min, 117.0 ± 10.5 mm(3) at 12 min, and 129.1 ± 10.0 mm(3) at 16 min after contrast agent application. Averaged histology-derived volumes (139.1 ± 13.4 mm(3)) in this group were comparable to the 16-min volume (P ↔16 min = 0.38). Compared to ultra-high-field MRI, all 3-T-derived volumes were significantly higher (P < 0.02).

CONCLUSION

Compared to 3-T-derived images and histology, tumor volumes were underestimated by approximately 50 % at 17.6 T. Hence, contrast-enhanced 17.6-T MRI provided no further benefits in tumor measurement compared to 3 T.

In vivo measurement of transverse relaxation time in the mouse brain at 17.6 T

PURPOSE

To establish regional T1 and T2 values of the healthy mouse brain at ultra-high magnetic field strength of 17.6 T and to follow regional brain T1 and T2 changes with age.

METHODS

In vivo T1 and T2 values in the C57BL/6J mouse brain were followed with age using multislice-multiecho sequence and multiple spin echo saturation recovery with variable repetition time sequence, respectively, at 9.4 and 17.6 T. Gadolinium-tetra-azacyclo-dodecane-tetra-acetic acid phantoms were used to validate in vivo T2 measurements. Student's t-test was used to compare mean relaxation values.

RESULTS

A field-dependent decrease in T2 is shown and validated with phantom measurements. T2 values at 17.6 T typically increased with age in multiple brain regions except in the hypothalamus and the caudate-putamen, where a slight decrease was observed. Furthermore, T1 values in various brain regions of young and old mice are presented at 17.6 T. A large gain in signal-to-noise ratio was observed at 17.6 T.

CONCLUSIONS

This study establishes for the first time the normative T1 and T2 values at 17.6 T over different mouse brain regions with age. The estimates of in vivo T1 and T2 will be useful to optimize pulse sequences for optimal image contrast at 17.6 T and will serve as baseline values against which disease-related relaxation changes can be assessed in mice.