Quantitative Ex Vivo MRI Changes due to Progressive Formalin Fixation in Whole Human Brain Specimens: Longitudinal Characterization of Diffusion, Relaxometry, and Myelin Water Fraction Measurements at 3T

Myelin water imaging of in vivo and ex vivo human brains using multi-echo gradient echo at 3 T and 7 T

PURPOSE

To compare the myelin water fraction (MWF) measurements between 3 T and 7 T and between in vivo and ex vivo human brains, and to investigate the relationship between multi-echo gradient-echo (mGRE)-based 3D MWF and myelin content using histological staining, which has not been validated in the human brain.

METHODS

In this study, we performed 3D mGRE-based MWF measurements on five ex vivo human brain hemispheres and five healthy volunteers at 3 T and 7 T with 1 mm isotropic resolution. The data were fitted with theT 2 * $$ {\mathrm{T}}_2^{\ast } $$ based on a three compartment complex-valued model to estimate MWF. We obtained myelin basic protein (MBP) staining from two tissue blocks and co-registered the MWF map and histology image for voxel-wise correlation between the two.

RESULTS

The MWF values measured from 7 T were overall higher than 7 T, but data between the two field strength demonstrated high correlations both in vivo (r = 0.88) and ex vivo (r = 0.83) across 19 white matter regions. Moreover, the MWF measurements showed a good agreement between in vivo and ex vivo assessments at 3 T (r = 0.61) and 7 T (r = 0.54). Based on MBP staining, the MWF values exhibited strong positive correlations with myelin content on both 3 T (r = 0.68 and r = 0.78 for the two tissue blocks) and 7 T (r = 0.64 and r = 0.82 for the two tissue blocks).

CONCLUSION

The findings demonstrated that the mGRE-based MWF mapping can be used to quantify myelin content in the human brain, despite the field-strength dependency of the measurements.

Comparative analysis of in situ and ex situ postmortem brain MRI: Evaluating volumetry, DTI, and relaxometry

PURPOSE

To compare postmortem in situ with ex situ MRI parameters, including volumetry, diffusion tensor imaging (DTI), and relaxometry for assessing methodology-induced alterations, which is a crucial prerequisite when performing MRI biomarker validation.

METHODS

MRI whole-brain scans of five deceased patients with amyotrophic lateral sclerosis were performed at 3 T. In situ scans were conducted within 32 h after death (SD 18 h), and ex situ scans after brain extraction and 3 months of formalin fixation. The imaging protocol included MP2RAGE, DTI, and multi-contrast spin-echo and multi-echo gradient-echo sequences. Volumetry, fractional anisotropy, mean diffusivity, T1, T2, andT 2 * $$ {T}_2^{\ast } $$ have been assessed for specific brain regions.

RESULTS

When comparing ex situ to in situ values, the following results were obtained. Deep gray matter as well as the thalamus and the hippocampus showed a reduced volume. Fractional anisotropy was reduced in the cortex and the whole brain. Mean diffusivity was decreased in white matter and deep gray matter. T1 and T2 were reduced in all investigated structures, whereasT 2 * $$ {T}_2^{\ast } $$ was increased in the cortex.

CONCLUSION

The results of this study show that the volumes and MRI parameters of several brain regions are potentially affected by tissue extraction and subsequent formalin fixation, suggesting that methodological alterations are present in ex situ MRI. To avoid overlap of indistinguishable methodological and disease-related changes, we recommend performing in situ postmortem MRI as an additional intermediate step for in vivo MRI biomarker validation.

Differential effects of prolonged post-fixation on immunohistochemical and histochemical staining for postmortem human brains

Purpose

Immunohistochemical (IHC) and histochemical (HC) staining techniques are widely used on human brains that are post-fixed in formalin and stored in brain banks worldwide for varying durations, from months to decades. Understanding the effects of prolonged post-fixation, postmortem interval (PMI), and age on these staining procedures is important for accurately interpreting their outcomes, thereby improving the diagnosis and research of brain disorders afflicting millions of people worldwide.

Methods

In this study, we conducted both IHC and HC staining on the prefrontal cortex of postmortem human brains post-fixed for 1, 5, 10, 15, and 20 years. For IHC staining, we used two antibodies for each marker: the neuron marker neuronal nuclear antigen (NeuN), the astrocyte marker glial fibrillary acidic protein (GFAP), and the microglia marker ionized calcium-binding adaptor molecule 1 (Iba1). For HC staining, we conducted hematoxylin and eosin Y (H&E), cresyl violet (CV), and Luxol fast blue (LFB) stains to examine neuropils, neurons, and myelin, respectively.

Results

We observed that the intensity of NeuN, Iba1, CV, or LFB staining was negatively correlated with post-fixation durations. Conversely, we detected a positive correlation between the intensity of GFAP and H&E staining and post-fixation durations. Moreover, there was no correlation between the intensity of NeuN, GFAP, Iba1, H&E, CV, and LFB staining and PMI. Additionally, no correlation was found between these staining intensities and age, except for the intensity of GFAP immunostained by one antiserum, which was negatively correlated with age.

Conclusion

Taken together, these findings suggest that prolonged post-fixation has both positive and negative effects, while age and PMI exert limited influence on these IHC and HC parameters. Therefore, it is essential to consider these differential changes when interpreting results derived from tissues with extended post-fixation durations. Furthermore, if feasible, we recommend conducting IHC and HC staining on human brains with the same post-fixation time spans and using the most optimal antibodies to mitigate the impact on subsequent analyses.

Yet more evidence that non-aqueous myelin lipids can be directly imaged with ultrashort echo time (UTE) MRI on a clinical 3T scanner: a lyophilized red blood cell membrane lipid study

Direct imaging of semi-solid lipids, such as myelin, is of great interest as a noninvasive biomarker of neurodegenerative diseases. Yet, the short T2 relaxation times of semi-solid lipid protons hamper direct detection through conventional magnetic resonance imaging (MRI) pulse sequences. In this study, we examined whether a three-dimensional ultrashort echo time (3D UTE) sequence can directly acquire signals from membrane lipids. Membrane lipids from red blood cells (RBC) were collected from commercially available blood as a general model of the myelin lipid bilayer and subjected to D2O exchange and freeze-drying for complete water removal. Sufficiently high MR signals were detected with the 3D UTE sequence, which showed an ultrashort T2* of ∼77-271 µs and a short T1 of ∼189 ms for semi-solid RBC membrane lipids. These measurements can guide designing UTE-based sequences for direct in vivo imaging of membrane lipids.

The myelin water imaging transcriptome: myelin water fraction regionally varies with oligodendrocyte-specific gene expression

Identifying sensitive and specific measures that can quantify myelin are instrumental in characterizing microstructural changes in neurological conditions. Neuroimaging transcriptomics is emerging as a valuable technique in this regard, offering insights into the molecular basis of promising candidates for myelin quantification, such as myelin water fraction (MWF). We aimed to demonstrate the utility of neuroimaging transcriptomics by validating MWF as a myelin measure. We utilized data from a normative MWF brain atlas, comprised of 50 healthy subjects (mean age = 25 years, range = 17-42 years) scanned at 3 Tesla. Magnetic resonance imaging data included myelin water imaging to extract MWF and T1 anatomical scans for image registration and segmentation. We investigated the inter-regional distributions of gene expression data from the Allen Human Brain Atlas in conjunction with inter-regional MWF distribution patterns. Pearson correlations were used to identify genes with expression profiles mirroring MWF. The Single Cell Type Atlas from the Human Protein Atlas was leveraged to classify genes into gene sets with high cell type specificity, and a control gene set with low cell type specificity. Then, we compared the Pearson correlation coefficients for each gene set to determine if cell type-specific gene expression signatures correlate with MWF. Pearson correlation coefficients between MWF and gene expression for oligodendrocytes and adipocytes were significantly higher than for the control gene set, whereas correlations between MWF and inhibitory/excitatory neurons were significantly lower. Our approach in integrating transcriptomics with neuroimaging measures supports an emerging technique for understanding and validating MRI-derived markers such as MWF.

Toward an optimal cadaveric brain model for neurosurgical education: assessment of preservation, parenchyma, vascular injection, and imaging

OBJECTIVE

We assessed types of cadaveric head and brain tissue specimen preparations that are used in a high throughput neurosurgical research laboratory to determine optimal preparation methods for neurosurgical anatomical research, education, and training.

METHODS

Cadaveric specimens (N = 112) prepared using different preservation and vascular injection methods were imaged, dissected, and graded by 11 neurosurgeons using a 21-point scale. We assessed the quality of tissue and preservation in both the anterior and posterior circulations. Tissue quality was evaluated using a 9-point magnetic resonance imaging (MRI) scale.

RESULTS

Formalin-fixed specimens yielded the highest scores for assessment (mean ± SD [17.0 ± 2.8]) vs. formalin-flushed (17.0 ± 3.6) and MRI (6.9 ± 2.0). Cadaver assessment and MRI scores were positively correlated (P < 0.001, R2 0.60). Analysis showed significant associations between cadaver assessment scores and specific variables: nonformalin fixation (β = -3.3), preservation within ≤72 h of death (β = 1.8), and MRI quality score (β = 0.7). Formalin-fixed specimens exhibited greater hardness than formalin-flushed and nonformalin-fixed specimens (P ≤ 0.006). Neurosurgeons preferred formalin-flushed specimens injected with colored latex.

CONCLUSION

For better-quality specimens for neurosurgical education and training, formalin preservation within ≤72 h of death was preferable, as was injection with colored latex. Formalin-flushed specimens more closely resembled live brain parenchyma. Assessment scores were lower for preparation techniques performed > 72 h postmortem and for nonformalin preservation solutions. The positive correlation between cadaver assessment scores and our novel MRI score indicates that donation organizations and institutional buyers should incorporate MRI as a screening tool for the selection of high-quality specimens.

A toolkit for stroke infarct volume estimation in rodents

Stroke volume is a key determinant of infarct severity and an important metric for evaluating treatments. However, accurate estimation of stroke volume can be challenging, due to the often confined 2-dimensional nature of available data. Here, we introduce a comprehensive semi-automated toolkit to reliably estimate stroke volumes based on (1) whole brains ex-vivo magnetic resonance imaging (MRI) and (2) brain sections that underwent immunofluorescence staining. We located and quantified infarct areas from MRI three days (acute) and 28 days (chronic) after photothrombotic stroke induction in whole mouse brains. MRI results were compared with measures obtained from immunofluorescent histologic sections of the same brains. We found that infarct volume determined by post-mortem MRI was highly correlated with a deviation of only 6.6 % (acute) and 4.9 % (chronic) to the measurements as determined in the histological brain sections indicating that both methods are capable of accurately assessing brain tissue damage (Pearson r > 0.9, p < 0.001). The Dice similarity coefficient (DC) showed a high degree of coherence (DC > 0.8) between MRI-delineated regions of interest (ROIs) and ROIs obtained from histologic sections at four to six pre-defined landmarks, with histology-based delineation demonstrating higher inter-operator similarity compared to MR images. We further investigated stroke-related scarring and post-ischemic angiogenesis in cortical peri‑infarct regions and described a negative correlation between GFAP+fluorescence intensity and MRI-obtained lesion size.

Analyzing the cortical fine structure as revealed by ex-vivo anatomical MRI

The human cortex has a rich fiber structure as revealed by myelin-staining of histological slices. Myelin also contributes to the image contrast in Magnetic Resonance Imaging (MRI). Recent advances in Magnetic Resonance (MR) scanner and imaging technology allowed the acquisition of an ex-vivo data set at an isotropic resolution of 100 µm. This study focused on a computational analysis of this data set with the aim of bridging between histological knowledge and MRI-based results. This work highlights: (1) the design and implementation of a processing chain that extracts intracortical features from a high-resolution MR image; (2) a demonstration of the correspondence between MRI-based cortical intensity profiles and the myelo-architectonic layering of the cortex; (3) the characterization and classification of four basic myelo-architectonic profile types; (4) the distinction of cortical regions based on myelo-architectonic features; and (5) the segmentation of cortical modules in the entorhinal cortex.

Empirical relationship between TEM-derived myelin volume fraction and MRI-R2 values in aging ex vivo rat corpus callosum

Ex vivo ratiometric measurements of short- and long-T2 components using the multiple spin echo sequence of MRI are often employed to evaluate alterations in myelin content in the white matter (WM) of the brain. However, the relationship between absolute MRI-T2 values (long-T2 component) and myelin volumetric information in aged ex vivo rodent WM appears to be influenced by factors such as animal species, field strength, and fixation durations/washing. Here, multiple spin echo sequence-based MRI-R2 (the reciprocal of T2) values were measured in the corpus callosum (CC) region in the post-mortem rat brains (n = 9) of different age groups with common fixation techniques without washing at 7 T. Transmission electron microscopy (TEM)-based quantification of myelin volume fraction (MVF) and corresponding Monte-Carlo simulation to estimate relaxation rates (R2,IE) due to diffusion in the presence of inhomogeneous magnetic field perturbation in intra- and extra-cellular (IE) spaces were respectively performed. To determine whether the short-T2 components originating from myelin water were mixed with long-T2 components from IE water or were undetectable, the MVF values obtained from TEM results were respectively compared with MRI-R2 and R2,IE values. A significant correlation (Pearson's correlation coefficient r = 0.8763; p < 0.01) of average MRI-R2 and MVF values was observed. Estimated R2,IE values from Monte-Carlo simulations in IE water signals were also positively correlated (r = 0.8281; p < 0.01) with MVF values. However, the magnitudes of R2,IE values were much smaller than those observed for MRI-R2 values, indicating that changes in R2 related MVF are likely dominated by myelin water components. Such comparisons between independent parameters from MRI, TEM, and simulations support the suggestion that myelin water signals were indistinguishably mixed to exhibit mono-exponential T2 relaxation, and multiple spin echo sequence-based MRI-R2 values in aging ex vivo rat CC without prolonged washing still reflect the volumetric information of myelin, likely due to enhanced water exchange across the myelin.

Developmental and regional dependence of macromolecular proton fraction and fractional anisotropy in fixed brain tissue

An important advantage of imaging fixed tissue is a gain in signal-to-noise ratio and in resolution due to unlimited scan time. However, the fidelity of quantitative MRI parameters in fixed brain tissue, particularly in developmental settings, requires validation. Macromolecular proton fraction (MPF) and fractional anisotropy (FA) indices are quantitative markers of myelination and axonal integrity relevant to preclinical and clinical research. The goal of this study was to assert the correspondence of MR-derived markers of brain development MPF and FA between in vivo and fixed tissue measures. MPF and FA were compared in several white and gray matter structures of the normal mouse brain at 2, 4, and 12 weeks of age. At each developmental stage, in vivo imaging was performed, followed by paraformaldehyde fixation and a second imaging session. MPF maps were acquired from three source images (magnetization transfer weighted, proton density weighted, and T1 weighted), and FA was obtained from diffusion tensor imaging. The MPF and FA values, measured in the cortex, striatum, and major fiber tracts, were compared before and after fixation using Bland-Altman plots, regression analysis, and analysis of variance. MPF values of the fixed tissue were consistently greater than those from in vivo measurements. Importantly, this bias varied significantly with brain region and the developmental stage of the tissue. At the same time, FA values were preserved after fixation, across tissue types and developmental stages. The results of this study suggest that MPF and FA in fixed brain tissue can be used as a proxy for in vivo measurements, but additional considerations should be made to correct for the bias in MPF.

Ultra-high-field MRI of postmortem human fetal wrist joints: initial experience

BACKGROUND

This study aimed to assess the feasibility of postmortem ultra-high-field magnetic resonance imaging (UHF-MRI) to study fetal musculoskeletal anatomy and explore the contribution of variation in iodine and formaldehyde (paraformaldehyde, PFA) treatment of tissue.

METHODS

Seven upper extremities from human fetuses with gestational ages of 19 to 24 weeks were included in this experimental study, approved by the Medical Research Ethics Committee. The specimens were treated with various storage (0.2-4% PFA) and staining (Lugol's solution) protocols and the wrist joint was subsequently imaged with 7.0 T UHF-MRI. Soft-tissue contrast was quantified by determining regions of interest within a chondrified carpal bone (CCB) from the proximal row, the triangular fibrocartilage (TFC), and the pronator quadratus muscle (PQM) and calculating the contrast ratios (CRs) between mean signal intensities of CCB to TFC and CCB to PQM.

RESULTS

UHF-MRI showed excellent soft-tissue contrast in different musculoskeletal tissues. Increasing storage time in 4% PFA, CRs decreased, resulting in a shift from relatively hyperintense to hypointense identification of the CCB. Storage in 0.2% PFA barely influenced the CRs over time. Lugol's solution caused an increase in CRs and might have even contributed to the inversion of the CRs.

CONCLUSIONS

UHF-MRI is a feasible technique to image musculoskeletal structures in fetal upper extremities and most successful after short storage in 4% PFA or prolonged storage in 0.2% PFA. The use of Lugol's solution is not detrimental on soft-tissue MRI contrast and therefore enables effectively combining UHF-MRI with contrast-enhanced micro-computed tomography using a single preparation of the specimen.

RELEVANCE STATEMENT

UHF-MRI can be performed after CE-micro-CT to take advantage of both techniques.

KEY POINTS

• UHF-MRI is feasible to study human fetal cartilaginous and ligamentous anatomy. • Storage in low PFA concentrations (i.e., 0.2%) improves soft-tissue contrast in UHF-MRI. • Limited preservation time in high concentrations of PFA improves soft-tissue contrast in UHF-MRI. • Prior staining with Lugol's solution does not reduce soft-tissue contrast in UHF-MRI.

Acquisition and Analysis of Excised Neocortex from Pediatric Patients with Focal Cortical Dysplasia Using Mesoscale Diffusion MRI

Non-invasive classification of focal cortical dysplasia (FCD) subtypes remains challenging from a radiology perspective. Quantitative imaging biomarkers (QIBs) have the potential to distinguish subtypes that lack pathognomonic features and might help in defining the extent of abnormal connectivity associated with each FCD subtype. A key motivation of diagnostic imaging is to improve the localization of a "lesion" that can guide the surgical resection of affected tissue, which is thought to cause seizures. Conversely, surgical resections to eliminate or reduce seizures provided unique opportunities to develop magnetic resonance imaging (MRI)-based QIBs by affording long scan times to evaluate multiple contrast mechanisms at the mesoscale (0.5 mm isotropic voxel dimensions). Using ex vivo hybrid diffusion tensor imaging on a 9.4 T MRI scanner, the grey to white matter ratio of scalar indices was lower in the resected middle temporal gyrus (MTG) of two neuropathologically confirmed cases of FCD compared to non-diseased control postmortem fixed temporal lobes. In contrast, fractional anisotropy was increased within FCD and also adjacent white matter tracts. Connectivity (streamlines/mm3) in the MTG was higher in FCD, suggesting that an altered connectivity at the lesion locus can potentially provide a tangible QIB to distinguish and characterize FCD abnormalities. However, as illustrated here, a major challenge for a robust tractographical comparison lies in the considerable differences in the ex vivo processing of bioptic and postmortem samples. Mesoscale diffusion MRI has the potential to better define and characterize epileptic tissues obtained from surgical resection to advance our understanding of disease etiology and treatment.

Microstructural Neurodegeneration of the Entorhinal-Hippocampus Pathway along the Alzheimer's Disease Continuum

BACKGROUND

Conventional neuroimaging biomarkers for the neurodegeneration of Alzheimer's disease (AD) are not sensitive enough to detect neurodegenerative alterations during the preclinical stage of AD individuals.

OBJECTIVE

We examined whether neurodegeneration of the entorhinal-hippocampal pathway could be detected along the AD continuum using ultra-high-field diffusion tensor imaging and tractography for ex vivo brain tissues.

METHODS

Postmortem brain specimens from a cognitively unimpaired individual without AD pathological changes (non-AD), a cognitively unimpaired individual with AD pathological changes (preclinical AD), and a demented individual with AD pathological changes (AD dementia) were scanned with an 11.7T diffusion magnetic resonance imaging. Fractional anisotropy (FA) values of the entorhinal layer II and number of perforant path fibers counted by tractography were compared among the AD continuum. Following the imaging analyses, the status of myelinated fibers and neuronal cells were verified by subsequent serial histological examinations.

RESULTS

At 250μm (zipped to 125μm) isotropic resolution, the entorhinal layer II islands and the perforant path fibers could be identified in non-AD and preclinical AD, but not in AD dementia, followed by histological verification. The FA value of the entorhinal layer II was the highest among the entorhinal laminae in non-AD and preclinical AD, whereas the FA values in the entorhinal laminae were homogeneously low in AD dementia. The FA values and number of perforant path fibers decreased along the AD continuum (non-AD>preclinical AD > AD dementia).

CONCLUSION

We successfully detected neurodegenerative alterations of the entorhinal-hippocampal pathway at the preclinical stage of the AD continuum.

Effective R2 relaxation rate, derived from dual-contrast fast-spin-echo MRI, enables detection of hemisphere differences in iron level and dopamine function in Parkinson's disease and healthy individuals

BACKGROUND

Clinical estimates of brain iron concentration are achievable with quantitative transverse relaxation rate R₂, via time-consuming multiple spin-echo (SE) sequences. The objective of this study was to investigate whether quantitative iron-sensitive information may be derived from 3.0 T dual-contrast fast-spin-echo (FSE) sequences (typically employed in anatomical non-quantitative evaluations), as a routinely-collected alternative to evaluate iron levels in healthy (HC) and Parkinson's disease (PD) brains.

NEW METHOD

MRI 3.0 T FSE data from the Parkinson's Progression Markers Initiative (PPMI) (12 PD, 12 age- and gender-matched HC subjects) were cross-sectionally and longitudinally evaluated. A new measure, 'effective R₂', was calculated for bilateral subcortical grey matter (caudate nucleus, putamen, globus pallidus, red nucleus, substantia nigra). Linear regression analysis was performed to correlate 'effective R₂' with models of age-dependent brain iron concentration and striatal dopamine transporter (DaT) receptor binding ratio.

RESULTS

Effective R₂ was strongly correlated with estimated brain iron concentration. In PD, putaminal effective R₂ difference was observed between the hemispheres contra-/ipsi-lateral to the predominantly symptomatic side at onset. This hemispheric difference was correlated with the putaminal DaT binding ratios in PD.

COMPARISON WITH EXISTING METHOD(S)

Effective R₂, derived from rapid dual-contrast FSE sequences, showed viability as an alternative to R₂ from SE sequences. Linear correlation of effective R₂ with estimated iron concentration was comparable to documented iron-dependent R₂. The effective R₂ correlation coefficient was consistent with theoretical R₂ iron-dependence at 3.0 T.

CONCLUSIONS

Effective R₂ has clinical potential as a fast quantitative method, as an alternative to R₂, to aid evaluation of brain iron levels and DaT function.

Cortical myelin profile variations in healthy aging brain: A T1w/T2w ratio study

Demyelination is observed in both healthy aging and age-related neurodegenerative disorders. While the significance of myelin within the cortex is well acknowledged, studies focused on intracortical demyelination and depth-specific structural alterations in normal aging are lacking. Using the recently available Human Connectome Project Aging dataset, we investigated intracortical myelin in a normal aging population using the T1w/T2w ratio. To capture the fine changes across cortical depths, we employed a surface-based approach by constructing cortical profiles traveling perpendicularly through the cortical ribbon and sampling T1w/T2w values. The curvatures of T1w/T2w cortical profiles may be influenced by differences in local myeloarchitecture and other tissue properties, which are known to vary across cortical regions. To quantify the shape of these profiles, we parametrized the level of curvature using a nonlinearity index (NLI) that measures the deviation of the profile from a straight line. We showed that NLI exhibited a steep decline in aging that was independent of local cortical thinning. Further examination of the profiles revealed that lower T1w/T2w near the gray-white matter boundary and superficial cortical depths were major contributors to the apparent NLI variations with age. These findings suggest that demyelination and changes in other T1w/T2w related tissue properties in normal aging may be depth-specific and highlight the potential of NLI as a unique marker of microstructural alterations within the cerebral cortex.

Alterations of brain microstructures in a mouse model of prenatal opioid exposure detected by diffusion MRI

Growing opioid use among pregnant women is fueling a crisis of infants born with prenatal opioid exposure. A large body of research has been devoted to studying the management of opioid withdrawal during the neonatal period in these infants, but less substantive work has explored the long-term impact of prenatal opioid exposure on neurodevelopment. Using a translationally relevant mouse model of prenatal methadone exposure (PME), the aim of the study is to investigate the cerebral microstructural differences between the mice with PME and prenatal saline exposure (PSE). The brains of eight-week-old male offspring with either PME (n = 15) or PSE (n = 15) were imaged using high resolution in-vivo diffusion magnetic resonance imaging on a 9.4 Tesla small animal scanner. Brain microstructure was characterized using diffusion tensor imaging (DTI) and Bingham neurite orientation dispersion and density imaging (Bingham-NODDI). Voxel-based analysis (VBA) was performed using the calculated microstructural parametric maps. The VBA showed significant (p < 0.05) bilateral alterations in fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (AD), radial diffusivity (RD), orientation dispersion index (ODI) and dispersion anisotropy index (DAI) across several cortical and subcortical regions, compared to PSE. Particularly, in PME offspring, FA, MD and AD were significantly higher in the hippocampus, dorsal amygdala, thalamus, septal nuclei, dorsal striatum and nucleus accumbens. These DTI-based results suggest widespread bilateral microstructural alterations across cortical and subcortical regions in PME offspring. Consistent with the observations in DTI, Bingham-NODDI derived ODI exhibited significant reduction in PME offspring within the hippocampus, dorsal striatum and cortex. NODDI-based results further suggest reduction in dendritic arborization in PME offspring across multiple cortical and subcortical regions. To our best knowledge, this is the first study of prenatal opioid exposure to examine microstructural organization in vivo. Our findings demonstrate perturbed microstructural complexity in cortical and subcortical regions persisting into early adulthood which could interfere with critical neurodevelopmental processes in individuals with prenatal opioid exposure.

Empirical transmit field bias correction of T1w/T2w myelin maps

T1-weighted divided by T2-weighted (T1w/T2w) myelin maps were initially developed for neuroanatomical analyses such as identifying cortical areas, but they are increasingly used in statistical comparisons across individuals and groups with other variables of interest. Existing T1w/T2w myelin maps contain radiofrequency transmit field (B1+) biases, which may be correlated with these variables of interest, leading to potentially spurious results. Here we propose two empirical methods for correcting these transmit field biases using either explicit measures of the transmit field or alternatively a 'pseudo-transmit' approach that is highly correlated with the transmit field at 3T. We find that the resulting corrected T1w/T2w myelin maps are both better neuroanatomical measures (e.g., for use in cross-species comparisons), and more appropriate for statistical comparisons of relative T1w/T2w differences across individuals and groups (e.g., sex, age, or body-mass-index) within a consistently acquired study at 3T. We recommend that investigators who use the T1w/T2w approach for mapping cortical myelin use these B1+ transmit field corrected myelin maps going forward.

Ultra-high field (10.5T) diffusion-weighted MRI of the macaque brain

Diffu0sion-weighted magnetic resonance imaging (dMRI) is a non-invasive imaging technique that provides information about the barriers to the diffusion of water molecules in tissue. In the brain, this information can be used in several important ways, including to examine tissue abnormalities associated with brain disorders and to infer anatomical connectivity and the organization of white matter bundles through the use of tractography algorithms. However, dMRI also presents certain challenges. For example, historically, the biological validation of tractography models has shown only moderate correlations with anatomical connectivity as determined through invasive tract-tracing studies. Some of the factors contributing to such issues are low spatial resolution, low signal-to-noise ratios, and long scan times required for high-quality data, along with modeling challenges like complex fiber crossing patterns. Leveraging the capabilities provided by an ultra-high field scanner combined with denoising, we have acquired whole-brain, 0.58 mm isotropic resolution dMRI with a 2D-single shot echo planar imaging sequence on a 10.5 Tesla scanner in anesthetized macaques. These data produced high-quality tractograms and maps of scalar diffusion metrics in white matter. This work demonstrates the feasibility and motivation for in-vivo dMRI studies seeking to benefit from ultra-high fields.

Resolution and b value dependent Structural Connectome in ex vivo Mouse Brain

Diffusion magnetic resonance imaging has been widely used in both clinical and preclinical studies to characterize tissue microstructure and structural connectivity. The diffusion MRI protocol for the Human Connectome Project (HCP) has been developed and optimized to obtain high-quality, high-resolution diffusion MRI (dMRI) datasets. However, such efforts have not been fully explored in preclinical studies, especially for rodents. In this study, high quality dMRI datasets of mouse brains were acquired at 9.4T system from two vendors. In particular, we acquired a high-spatial resolution dMRI dataset (25 μm isotropic with 126 diffusion encoding directions), which we believe to be the highest spatial resolution yet obtained; and a high-angular resolution dMRI dataset (50 μm isotropic with 384 diffusion encoding directions), which we believe to be the highest angular resolution compared to the dMRI datasets at the microscopic resolution. We systematically investigated the effects of three important parameters that affect the final outcome of the connectome: b value (1000s/mm² to 8000 s/mm²), angular resolution (10 to 126), and spatial resolution (25 μm to 200 μm). The stability of tractography and connectome increase with the angular resolution, where more than 50 angles is necessary to achieve consistent results. The connectome and quantitative parameters derived from graph theory exhibit a linear relationship to the b value (R² > 0.99); a single-shell acquisition with b value of 3000 s/mm² shows comparable results to the multi-shell high angular resolution dataset. The dice coefficient decreases and both false positive rate and false negative rate gradually increase with coarser spatial resolution. Our study provides guidelines and foundations for exploration of tradeoffs among acquisition parameters for the structural connectome in ex vivo mouse brain.

Imaging white matter microstructure with gradient-echo phase imaging: Is ex vivo imaging with formalin-fixed tissue a good approximation of the in vivo brain?

Purpose

Ex vivo imaging is a commonly used approach to investigate the biophysical mechanism of orientation‐dependent signal phase evolution in white matter. Yet, how phase measurements are influenced by the structural alteration in the tissue after formalin fixation is not fully understood. Here, we study the effects on magnetic susceptibility, microstructural compartmentalization, and chemical exchange measurement with a postmortem formalin‐fixed whole‐brain human tissue.

Methods

A formalin‐fixed, postmortem human brain specimen was scanned with multiple orientations to the main magnetic field direction for robust bulk magnetic susceptibility measurement with conventional quantitative susceptibility imaging models. White matter samples were subsequently excised from the whole‐brain specimen and scanned in multiple rotations on an MRI scanner to measure the anisotropic magnetic susceptibility and microstructure‐related contributions in the signal phase and to validate the findings of the whole‐brain data.

Results

The bulk isotropic magnetic susceptibility of ex vivo whole‐brain imaging is comparable to in vivo imaging, with noticeable enhanced nonsusceptibility contributions. The excised specimen experiment reveals that anisotropic magnetic susceptibility and compartmentalization phase effect were considerably reduced in the formalin‐fixed white matter specimens.

Conclusions

Formalin‐fixed postmortem white matter exhibits comparable isotropic magnetic susceptibility to previous in vivo imaging findings. However, the measured phase and magnitude data of the fixed white matter tissue shows a significantly weaker orientation dependency and compartmentalization effect. Alternatives to formalin fixation are needed to better reproduce the in vivo microstructural effects in postmortem samples.

Quantitative susceptibility mapping and R1 measurement: Determination of the myelin volume fraction in the aging ex vivo rat corpus callosum

In studies of the white matter (WM) in aging brains, both quantitative susceptibility mapping (QSM) and direct R₁ measurement offer potentially useful ex vivo MRI tools that allow volumetric characterization of myelin content changes. Despite the technical importance of such MRI methods in numerous age-related diseases, the supposed linear relationship between the estimates of either the QSM or R₁ method and age-affected myelin contents has not been validated. In this study, the absolute myelin volume fraction (MVF) was determined by transmission electron microscopy (TEM) as a gold standard measure for comparison with the values obtained by the aforementioned MR methods. To theoretically evaluate and understand the MR signal characteristics, QSM simulations were performed using the finite perturber method (FPM). Specifically, the simulation geometry modeling was based on TEM-derived structures aligned orthogonally to the main magnetic field, the construct of which was used to estimate the magnetic field shift (ΔB) changes arising from the conjectured myelin structures. Experimentally, ex vivo corpus callosum (CC) samples from rat brains obtained at 6 weeks (n = 3), 4 months (n = 3), and 20 months (n = 3) after birth were used to establish the relationship between changes quantified by either QSM or R₁ with the absolute MVF by TEM. From the ex vivo brain samples, the scatterplot of mean MVF versus R₁ was fitted to a linear equation, where R_1mean  = 0.7948 × MVF_mean  + 0.8118 (Pearson's correlation coefficient r = 0.9138; p < 0.01), while the scatterplot of mean MVF versus MRI-derived magnetic susceptibility (χ) was also fitted to a line where χ_{measured,mean}  = -0.1218 × MVF_mean  - 0.006345 (r = -0.8435; p < 0.01). As a result of the FPM-based QSM simulations, a linearly proportional relationship between the simulated magnetic susceptibility, χ_{simulated,mean} , and MVF (r = -0.9648; p < 0.01) was established. Such a statistically significant linear correlation between MRI-derived values by the QSM (or R₁ ) method and MVF demonstrated that variable myelin contents in the WM (i.e., CC) can be quantified across multiple stages of aging. These findings further support that both techniques based on QSM and R₁ provide an efficient means of studying the brain-aging process with accurate volumetric quantification of the myelin content in WM.

A time-course study of actively stained mouse brains: Diffusion tensor imaging parameters and connectomic stability over 1 year

While the application of diffusion tensor imaging (DTI), tractography, and connectomics to fixed tissue is a common practice today, there have been limited studies examining the effects of fixation on brain microstructure over extended periods. This mouse model time-course study reports the changes of regional brain volumes and diffusion scalar parameters, such as fractional anisotropy, across 12 representative brain regions as measures of brain structural stability. The scalar DTI parameters and regional volumes were highly variable over the first 2 weeks after fixation. The same parameters were consistent over a 2-8-week window after fixation, which means confounds from tissue stability over that scanning window were minimal. Quantitative connectomes were analyzed over the same time with extension out to 1 year. While there was some change in the scalar metrics at 1 year after fixation, these changes were sufficiently small, particularly in white matter, to support reproducible connectomes over a period ranging from 2-weeks to 1-year post-fixation. These findings delineate a scanning period, during which brain volumes, diffusion scalar metrics, and connectomes are remarkably consistent.

Developing formalin-based fixative agents for post mortem brain MRI at 9.4 T

PURPOSE

To develop fixative agents for high-field MRI with suitable dielectric properties and measure MR properties in immersion-fixed brain tissue.

METHODS

Dielectric properties of formalin-based agents were assessed (100 MHz-4.5 GHz), and four candidate fixatives with/without polyvinylpyrrolidone (PVP) and different salt concentrations were formulated. B₁ field and MR properties (T₁ , R 2 ∗ , R₂ , R 2 ' , and magnetic susceptibility [QSM]) were observed in white and gray matter of pig brain samples during 0.5-35 days of immersion fixation. The kinetics were fitted using exponential functions. The immersion time required to reach maximum R 2 ∗ values at different tissue depths was used to estimate the Medawar coefficient for fixative penetration. The effect of replacing the fixatives with Fluoroinert and phosphate-buffered saline as embedding media was also evaluated.

RESULTS

The dielectric properties of formalin were nonlinearly modified by increasing amounts of additives. With 5% PVP and 0.04% NaCl, the dielectric properties and B₁ field reflected in vivo conditions. The highest B₁ values were found in white matter with PVP and varied significantly with tissue depth and embedding media, but not with immersion time. The MR properties depended on PVP yielding lower T₁ , higher R 2 ∗ , more paramagnetic QSM values, and a lower Medawar coefficient (0.9 mm / h ; without PVP: 1.5). Regardless of fixative, switching to phosphate-buffered saline as embedder caused a paramagnetic shift in QSM and decreased R 2 ∗ that progressed during 1 month of storage, whereas no differences were found with Fluorinert.

CONCLUSION

In vivo-like B₁ fields can be achieved in formalin fixatives using PVP and a low salt concentration, yielding lower T₁ , higher R 2 ∗ , and more paramagnetic QSM than without additives. The kinetics of R 2 ∗ allowed estimation of fixative tissue penetration.

Mapping the human lateral geniculate nucleus and its cytoarchitectonic subdivisions using quantitative MRI

The human lateral geniculate nucleus (LGN) of the visual thalamus is a key subcortical processing site for visual information analysis. Due to its small size and deep location within the brain, a non-invasive characterization of the LGN and its microstructurally distinct magnocellular (M) and parvocellular (P) subdivisions in humans is challenging. Here, we investigated whether structural quantitative MRI (qMRI) methods that are sensitive to underlying microstructural tissue features enable MR-based mapping of human LGN M and P subdivisions. We employed high-resolution 7 Tesla in-vivo qMRI in N = 27 participants and ultra-high resolution 7 Tesla qMRI of a post-mortem human LGN specimen. We found that a quantitative assessment of the LGN and its subdivisions is possible based on microstructure-informed qMRI contrast alone. In both the in-vivo and post-mortem qMRI data, we identified two components of shorter and longer longitudinal relaxation time (T₁) within the LGN that coincided with the known anatomical locations of a dorsal P and a ventral M subdivision, respectively. Through ground-truth histological validation, we further showed that the microstructural MRI contrast within the LGN pertains to cyto- and myeloarchitectonic tissue differences between its subdivisions. These differences were based on cell and myelin density, but not on iron content. Our qMRI-based mapping strategy paves the way for an in-depth understanding of LGN function and microstructure in humans. It further enables investigations into the selective contributions of LGN subdivisions to human behavior in health and disease.

Changes in magnetic resonance imaging relaxation time on postmortem magnetic resonance imaging of formalin-fixed human normal heart tissue

Background

Postmortem magnetic resonance imaging (MRI) has been used to investigate the cause of death, but due to time constraints, it is not widely applied to the heart. Therefore, MRI analysis of the heart after formalin fixation was previously performed. However, the changes in MRI signal values based on the fixation time of formalin were not investigated. The objective was to investigate changes over time in the T1- and T2-values of MRI signals in normal areas of hearts removed during autopsy, hearts subsequently fixed in formalin, and heart specimens sliced for the preparation of pathological specimens.

Methods

The study subjects were 21 autopsy cases in our hospital between May 26, 2019 and February 16, 2020 whose hearts were removed and scanned by MRI. The male:female ratio was 14:7, and their ages at death ranged from 9 to 92 years (mean age 65.0 ± 19.7 years). Postmortem (PM)-MRI was conducted with a 0.3-Tesla (0.3-T) scanner containing a permanent magnet. A 4-channel QD head coil was used as the receiver coil. Scans were performed immediately after removal, post-formalin fixation, and after slicing; 7 cases were scanned at all three time points.

Results

The T1- and T2-values were calculated from the MRI signals of each sample organ at each scanning stage. Specimens were sliced from removed organs after formalin fixation, and the changes in T1- and T2-values over time were graphed to obtain an approximate curve. The median T1-values at each measurement time point tended to decrease from immediately after removal. The T2-values showed the same tendency to decrease, but this tendency was more pronounced for the T1-values.

Conclusion

MRI signal changes in images of heart specimens were investigated. Formalin fixation shortened both T1- and T2-values over time, and approximation formulae were derived to show these decreases over time. The shortening of T1- and T2-values can be understood as commensurate with the reduction in the water content (water molecules) of the formalin-fixed heart.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12880-021-00666-5.

Investigation of the magnetic susceptibility properties of fresh and fixed mouse heart, liver, skeletal muscle and brain tissue

PURPOSE

Several magnetic resonance imaging (MRI) techniques exploit the difference in magnetic susceptibilities between tissues, but systematic measurements of tissue susceptibility are lacking. Furthermore, there is the question as to whether chemical fixation that is used for ex vivo MRI studies, affects the magnetic properties of the tissue. Here, we determined the magnetic susceptibility and water content of fresh and chemically fixed mouse tissue.

METHODS

Mass susceptibility of brain, heart, liver and skeletal muscle samples were determined on a vibrating sample magnetometer at room temperature. Measurements at 50, 125, 200 and 295 K were performed to assess the temperature dependence of susceptibility. Moreover, we measured water content of fresh and fixed samples.

RESULTS

All samples show mass susceptibilities between -0.068 and -1.929 × 10^-8 m³/kg, compared to -9.338 × 10^-9 m³/kg of double distilled water. Heart tissue has a more diamagnetic susceptibility than the other tissues. Compared to fresh tissue, fixed tissue has a less diamagnetic susceptibility. Fixed tissue was not different in water content to fresh tissue and showed no consistent dependence of susceptibility with temperature, whereas fresh tissue shows a decrease to at least 125 K, indicative of a paramagnetic component.

CONCLUSIONS

Biological tissues are diamagnetic in comparison to water, where the heart is more diamagnetic than the other tissues, with paramagnetic contributions. Fixation rendered tissue less diamagnetic compared to fresh tissue. Our measurements revealed differences in tissue susceptibility between VSM and QSM, inviting more research to compare susceptibility-based MRI methods with physical measurements of tissue susceptibility.

A 48-channel receive array coil for mesoscopic diffusion-weighted MRI of ex vivo human brain on the 3 T connectome scanner

In vivo diffusion-weighted magnetic resonance imaging is limited in signal-to-noise-ratio (SNR) and acquisition time, which constrains spatial resolution to the macroscale regime. Ex vivo imaging, which allows for arbitrarily long scan times, is critical for exploring human brain structure in the mesoscale regime without loss of SNR. Standard head array coils designed for patients are sub-optimal for imaging ex vivo whole brain specimens. The goal of this work was to design and construct a 48-channel ex vivo whole brain array coil for high-resolution and high b-value diffusion-weighted imaging on a 3T Connectome scanner. The coil was validated with bench measurements and characterized by imaging metrics on an agar brain phantom and an ex vivo human brain sample. The two-segment coil former was constructed for a close fit to a whole human brain, with small receive elements distributed over the entire brain. Imaging tests including SNR and G-factor maps were compared to a 64-channel head coil designed for in vivo use. There was a 2.9-fold increase in SNR in the peripheral cortex and a 1.3-fold gain in the center when compared to the 64-channel head coil. The 48-channel ex vivo whole brain coil also decreases noise amplification in highly parallel imaging, allowing acceleration factors of approximately one unit higher for a given noise amplification level. The acquired diffusion-weighted images in a whole ex vivo brain specimen demonstrate the applicability and advantage of the developed coil for high-resolution and high b-value diffusion-weighted ex vivo brain MRI studies.

Sensitivity of fiber orientation dependent R 2 ∗ to temperature and post mortem interval

PURPOSE

R 2 ∗ imaging of brain white matter is well known for being sensitive to the orientation of nerve fibers with respect to the B₀ field of the MRI scanner. The goal of this study was to evaluate whether and to which extent fiber orientation dependent R 2 ∗ differs between in vivo and post mortem in situ examinations, and to investigate the influence of varying temperatures and post mortem intervals (PMI).

METHODS

Post mortem in situ and in vivo MRI scans were conducted at 3T. R 2 ∗ was acquired with a multi-echo gradient-echo sequence, and the orientation of white matter fibers was computed using diffusion tensor imaging (DTI). Fitting of the measured fiber orientation dependent R 2 ∗ was performed using three different formulations of a previously proposed model.

RESULTS

R 2 ∗ increased with increasing fiber angle for in vivo and post mortem in situ examinations, whereby the orientation dependency was lower post mortem. The different formulations of the fiber orientation model resulted in an identical fit, but showed large variations of the estimated parameters. The higher order orientation dependent R 2 ∗ components significantly decreased with decreasing temperature, while the orientation independent R 2 ∗ components showed no significant correlation with either temperature or PMI.

CONCLUSION

Although the mean diffusivity is strongly reduced post mortem, we could successfully estimate the fiber angle using DTI. Due to the strong correlation of the higher order orientation dependent R 2 ∗ components with temperature, the decreased R 2 ∗ fiber orientation dependency post mortem in situ might primarily be attributed to the lower brain temperature.

Evaluation of early microstructural changes in the R6/1 mouse model of Huntington's disease by ultra-high field diffusion MR imaging

Diffusion MRI (dMRI) has been able to detect early structural changes related to neurological symptoms present in Huntington's disease (HD). However, there is still a knowledge gap to interpret the biological significance at early neuropathological stages. The purpose of this study is two-fold: (i) establish if the combination of Ultra-High Field Diffusion MRI (UHFD-MRI) techniques can add a more comprehensive analysis of the early microstructural changes observed in HD, and (ii) evaluate if early changes in dMRI microstructural parameters can be linked to cellular biomarkers of neuroinflammation. Ultra-high field magnet (16.7T), diffusion tensor imaging (DTI), and neurite orientation dispersion and density imaging (NODDI) techniques were applied to fixed ex-vivo brains of a preclinical model of HD (R6/1 mice). Fractional anisotropy (FA) was decreased in deep and superficial grey matter (GM) as well as white matter (WM) brain regions with well-known early HD microstructure and connectivity pathology. NODDI parameters associated with the intracellular and extracellular compartment, such as intracellular ventricular fraction (ICVF), orientation dispersion index (ODI), and isotropic volume fractions (IsoVF) were altered in R6/1 mice GM. Further, histological studies in these areas showed that glia cell markers associated with neuroinflammation (GFAP & Iba1) were consistent with the dMRI findings. dMRI can be used to extract non-invasive information of neuropathological events present in the early stages of HD. The combination of multiple imaging techniques represents a better approach to understand the neuropathological process allowing the early diagnosis and neuromonitoring of patients affected by HD.

Diffusion Tensor Imaging Reveals Whole-Brain Microstructural Changes in the P301L Mouse Model of Tauopathy

INTRODUCTION

Increased expression of hyperphosphorylated tau and the formation of neurofibrillary tangles are associated with neuronal loss and white matter damage. Using high-resolution ex vivo diffusion tensor imaging (DTI), we investigated microstructural changes in the white and grey matter in the P301L mouse model of human tauopathy at 8.5 months of age. For unbiased computational analysis, we implemented a pipeline for voxel-based analysis (VBA) and atlas-based analysis (ABA) of DTI mouse brain data.

METHODS

Hemizygous and homozygous transgenic P301L mice and non-transgenic littermates were used. DTI data were acquired for generation of fractional anisotropy (FA), mean diffusivity (MD), radial diffusivity (RD), and axial diffusivity (AD) maps. VBA on the entire brain was performed using SPM8 and the SPM Mouse toolbox. Initially, all DTI maps were coregistered with the Allen mouse brain atlas to bring them to one common coordinate space. In VBA, coregistered DTI maps were normalized and smoothed in order to perform two-sample and unpaired t tests with false discovery rate correction to compare hemizygotes with non-transgenic littermates, homozygotes with non-transgenic littermates, and hemizygotes with homozygotes on each DTI parameter map. In ABA, the average values for selected regions of interests were computed with coregistered DTI maps and labels in Allen mouse brain atlas. Afterwards, a Kruskal-Wallis one-way ANOVA on ranks with a Tukey post hoc test was executed on the estimated average values.

RESULTS

With VBA, we found pronounced and brain-wide spread changes when comparing homozygous, P301L mice with non-transgenic littermates, which were not seen when comparing hemizygous P301L with non-transgenic animals. Statistical comparison of DTI metrics in selected brain regions by ABA corroborated findings from VBA. FA was found to be decreased in most brain regions, while MD, RD, and AD were increased in homozygotes compared to hemizygotes and non-transgenic littermates.

DISCUSSION/CONCLUSION

High-resolution ex vivo DTI demonstrated brain-wide microstructural and gene-dose-dependent changes in the P301L mouse model of human tauopathy. The DTI analysis pipeline may serve for the phenotyping of models of tauopathy and other brain diseases.

Decoding the microstructural properties of white matter using realistic models

Multi-echo gradient echo (ME-GRE) magnetic resonance signal evolution in white matter has a strong dependence on the orientation of myelinated axons with respect to the main static field. Although analytical solutions have been able to predict some of the white matter (WM) signal behaviour of the hollow cylinder model, it has been shown that realistic models of WM offer a better description of the signal behaviour observed. In this work, we present a pipeline to (i) generate realistic 2D WM models with their microstructure based on real axon morphology with adjustable fiber volume fraction (FVF) and g-ratio. We (ii) simulate their interaction with the static magnetic field to be able to simulate their MR signal. For the first time, we (iii) demonstrate that realistic 2D WM models can be used to simulate a MR signal that provides a good approximation of the signal obtained from a real 3D WM model derived from electron microscopy. We then (iv) demonstrate in silico that 2D WM models can be used to predict microstructural parameters in a robust way if ME-GRE multi-orientation data is available and the main fiber orientation in each pixel is known using DTI. A deep learning network was trained and characterized in its ability to recover the desired microstructural parameters such as FVF, g-ratio, free and bound water transverse relaxation and magnetic susceptibility. Finally, the network was trained to recover these micro-structural parameters from an ex vivo dataset acquired in 9 orientations with respect to the magnetic field and 12 echo times. We demonstrate that this is an overdetermined problem and that as few as 3 orientations can already provide comparable results for some of the decoded metrics.

Temperature dependence and histological correlation of inhomogeneous magnetization transfer and myelin water imaging in ex vivo brain

PURPOSE

The promise of inhomogeneous magnetization transfer (ihMT) as a new myelin imaging method was studied in ex vivo human brain tissue and in relation to myelin water fraction (MWF). The temperature dependence of both methods was characterized, as well as their correspondence with a histological measure of myelin content. Unfiltered and filtered ihMT protocols were studied by adjusting the saturation scheme to preserve or attenuate signal from tissue with short dipolar relaxation time T_1D.

METHODS

ihMT ratio (ihMTR) and MWF maps were acquired at 7 T from formalin-fixed human brain samples at 22.5 °C, 30 °C and 37 °C. The impact of temperature on unfiltered ihMTR, filtered ihMTR and MWF was investigated and compared to myelin basic protein staining.

RESULTS

Unfiltered ihMTR exhibited no temperature dependence, whereas filtered ihMTR increased with increasing temperature. MWF decreased at higher temperature, with an increasing prevalence of areas where the myelin water signal was unreliably determined, likely related to a reduction in T₂ peak separability at higher temperatures ex vivo. MWF and ihMTR showed similar per-sample correlation with myelin staining at room temperature. At 37 ^°C, filtered ihMTR was more strongly correlated with myelin staining and had increased dynamic range compared to unfiltered ihMTR.

CONCLUSIONS

Given the temperature dependence of filtered ihMT, increased dynamic range, and strong myelin specificity that persists at higher temperatures, we recommend carefully controlled temperatures close to 37 °C for filtered ihMT acquisitions. Unfiltered ihMT may also be useful, due to its independence from temperature, higher amplitude values, and sensitivity to short T_1D components. Ex vivo myelin water imaging should be performed at room temperature, to avoid fitting issues found at higher temperatures.

Can MRI measure myelin? Systematic review, qualitative assessment, and meta-analysis of studies validating microstructural imaging with myelin histology

Recent years have seen an increased understanding of the importance of myelination in healthy brain function and neuropsychiatric diseases. Non-invasive microstructural magnetic resonance imaging (MRI) holds the potential to expand and translate these insights to basic and clinical human research, but the sensitivity and specificity of different MR markers to myelination is a subject of debate. To consolidate current knowledge on the topic, we perform a systematic review and meta-analysis of studies that validate microstructural imaging by combining it with myelin histology. We find meta-analytic evidence for correlations between various myelin histology metrics and markers from different MRI modalities, including fractional anisotropy, radial diffusivity, macromolecular pool, magnetization transfer ratio, susceptibility and longitudinal relaxation rate, but not mean diffusivity. Meta-analytic correlation effect sizes range widely, between R2 = 0.26 and R2 = 0.82. However, formal comparisons between MRI-based myelin markers are limited by methodological variability, inconsistent reporting and potential for publication bias, thus preventing the establishment of a single most sensitive strategy to measure myelin with MRI. To facilitate further progress, we provide a detailed characterisation of the evaluated studies as an online resource. We also share a set of 12 recommendations for future studies validating putative MR-based myelin markers and deploying them in vivo in humans.

Non-negative least squares computation for in vivo myelin mapping using simulated multi-echo spin-echo T2 decay data

Multi-compartment T₂ mapping has gained particular relevance for the study of myelin water in the brain. As a facilitator of rapid saltatory axonal signal transmission, myelin is a cornerstone indicator of white matter development and function. Regularized non-negative least squares fitting of multi-echo T₂ data has been widely employed for the computation of the myelin water fraction (MWF), and the obtained MWF maps have been histopathologically validated. MWF measurements depend upon the quality of the data acquisition, B₁⁺ homogeneity and a range of fitting parameters. In this special issue article, we discuss the relevance of these factors for the accurate computation of multi-compartment T₂ and MWF maps. We generated multi-echo spin-echo T₂ decay curves following the Carr-Purcell-Meiboom-Gill approach for various myelin concentrations and myelin T₂ scenarios by simulating the evolution of the magnetization vector between echoes based on the Bloch equations. We demonstrated that noise and imperfect refocusing flip angles yield systematic underestimations in MWF and intra-/extracellular water geometric mean T₂ (gmT₂ ). MWF estimates were more stable than myelin water gmT₂ time across different settings of the T₂ analysis. We observed that the lower limit of the T₂ distribution grid should be slightly shorter than TE₁ . Both TE₁ and the acquisition echo spacing also have to be sufficiently short to capture the rapidly decaying myelin water T₂ signal. Among all parameters of interest, the estimated MWF and intra-/extracellular water gmT₂ differed by approximately 0.13-4 percentage points and 3-4 ms, respectively, from the true values, with larger deviations observed in the presence of greater B₁⁺ inhomogeneities and at lower signal-to-noise ratio. Tailoring acquisition strategies may allow us to better characterize the T₂ distribution, including the myelin water, in vivo.

Evaluation of the diffusion MRI white matter tract integrity model using myelin histology and Monte-Carlo simulations

Quantitative evaluation of brain myelination has drawn considerable attention. Conventional diffusion-based magnetic resonance imaging models, including diffusion tensor imaging and diffusion kurtosis imaging (DKI),¹ have been used to infer the microstructure and its changes in neurological diseases. White matter tract integrity (WMTI) was proposed as a biophysical model to relate the DKI-derived metrics to the underlying microstructure. Although the model has been validated on ex vivo animal brains, it was not well evaluated with ex vivo human brains. In this study, histological samples (namely corpus callosum) from postmortem human brains have been investigated based on WMTI analyses on a clinical 3T scanner and comparisons with gold standard myelin staining in proteolipid protein and Luxol fast blue. In addition, Monte Carlo simulations were conducted to link changes from ex vivo to in vivo conditions based on the microscale parameters of water diffusivity and permeability. The results show that WMTI metrics, including axonal water fraction AWF, radial extra-axonal diffusivity D_e^⊥, and intra-axonal diffusivity D_awere needed to characterize myelin content alterations. Thus, WMTI model metrics are shown to be promising candidates as sensitive biomarkers of demyelination.

Improved MR fingerprinting for relaxation measurement in the presence of semisolid magnetization transfer

PURPOSE

To characterize and minimize the magnetization transfer (MT) effect in MR fingerprinting (MRF) relaxation measurements with a 2-pool (2P) MT model of multiple tissue types.

THEORY AND METHODS

Semisolid MT effect in MRF was modeled using 2P Bloch-McConnell equations. The combinations of MT parameters of multiple tissues (white [WM] and gray matter [GM]) were used to build the MRF dictionary. Both 1-pool (1P) and 2P models were simulated to characterize the dependence on MT. Relaxations measured using MRF with spin-echo saturation-recovery (SR) or inversion-recovery preparations were compared with conventional SR-prepared T1 and multiple spin-echo T2 measurements. The simulations results were validated with phantoms and brain tissue samples.

RESULTS

The MRF signal was different from the 1P and 2P models. 1P MRF produced significantly (P < .05) underestimated T1 in WM (20-30%) and GM (7-10%), while 2P MRF measured consistent T1 and T2 in both WM and GM with conventional measurements (pairwise test P > .1; correlated P < .05). Simulations showed that SR-prepared MRF measuring T1 had much less errors against the variation of the macromolecular fraction. Compared with inversion-recovery preparation, SR-prepared MRF produced higher relaxation correlations (R > 0.9) with conventional measurements in both WM and GM across samples, suggesting that SR-prepared MRF was less sensitive to the compositive effect of multiple MT parameters variations.

CONCLUSIONS

2P MRF using a combination of MT parameters for multiple tissue types can measure consistent relaxations with conventional methods. With the 2P models, SR-prepared MRF would provide an option for robust relaxation measurement under heterogeneous MT.

Longitudinal assessment of tissue properties and cardiac diffusion metrics of the ex vivo porcine heart at 7 T: Impact of continuous tissue fixation using formalin

In this study we aimed to assess the effects of continuous formalin fixation on diffusion and relaxation metrics of the ex vivo porcine heart at 7 T. Magnetic resonance imaging was performed on eight piglet hearts using a 7 T whole body system. Hearts were measured fresh within 3 hours of cardiac arrest followed by immersion in 10% neutral buffered formalin. T₂^* and T₂ were assessed using a gradient multi-echo and multi-echo spin echo sequence, respectively. A spin echo and a custom stimulated echo sequence were employed to assess diffusion time-dependent changes in metrics of cardiac diffusion tensor imaging. SNR was determined for b = 0 images. Scans were performed for 5 mm thick apical, midcavity and basal slices (in-plane resolution: 1 mm) and repeated 7, 15, 50, 100 and 200 days postfixation. Eigenvalues of the apparent diffusion coefficient (ADC) and fractional anisotropy (FA) decreased significantly (P < 0.05) following fixation. Relative to fresh hearts, FA values 7 and 200 days postfixation were 90% and 80%, while respective relative ADC values at those fixation stages were 78% and 92%. Statistical helix and sheetlet angle distributions as well as respective mean and median values showed no systematic influence of continuous formalin fixation. Similar to changes in the ADC, values for T₂ , T₂^* and SNR dropped initially postfixation. Respective relative values compared with fresh hearts at day 7 were 64%, 79% and 68%, whereas continuous fixation restored T₂ , T₂^* and SNR leading to relative values of 74%, 100%, and 81% at day 200, respectively. Relaxation parameters and diffusion metrics are significantly altered by continuous formalin fixation. The preservation of microstructure metrics following prolonged fixation is a key finding that may enable future studies of ventricular remodeling in cardiac pathologies.

Advanced Multicompartment Diffusion MRI Models and Their Application in Multiple Sclerosis

Conventional MR imaging techniques are sensitive to pathologic changes of the brain and spinal cord seen in MS, but they lack specificity for underlying axonal and myelin integrity. By isolating the signal contribution from different tissue compartments, newly developed advanced multicompartment diffusion MR imaging models have the potential to detect specific tissue subtypes and associated injuries with increased pathologic specificity. These models include neurite orientation dispersion and density imaging, diffusion basis spectrum imaging, multicompartment microscopic diffusion MR imaging with the spherical mean technique, and models enabled through high-gradient diffusion MR imaging. In this review, we provide an appraisal of the current literature on the physics principles, histopathologic validation, and clinical applications of each of these techniques in both brains and spinal cords of patients with MS. We discuss limitations of each of the methods and directions that future research could take to provide additional validation of their roles as biomarkers of axonal and myelin injury in MS.

Histopathology of diffusion-weighted imaging-positive lesions in cerebral amyloid angiopathy

Small subclinical hyperintense lesions are frequently encountered on brain diffusion-weighted imaging (DWI) scans of patients with cerebral amyloid angiopathy (CAA). Interpretation of these DWI+ lesions, however, has been limited by absence of histopathological examination. We aimed to determine whether DWI+ lesions represent acute microinfarcts on histopathology in brains with advanced CAA, using a combined in vivo MRI-ex vivo MRI-histopathology approach. We first investigated the histopathology of a punctate cortical DWI+ lesion observed on clinical in vivo MRI 7 days prior to death in a CAA case. Subsequently, we assessed the use of ex vivo DWI to identify similar punctate cortical lesions post-mortem. Intact formalin-fixed hemispheres of 12 consecutive cases with CAA and three non-CAA controls were subjected to high-resolution 3 T ex vivo DWI and T2 imaging. Small cortical lesions were classified as either DWI+/T2+ or DWI-/T2+. A representative subset of lesions from three CAA cases was selected for detailed histopathological examination. The DWI+ lesion observed on in vivo MRI could be matched to an area with evidence of recent ischemia on histopathology. Ex vivo MRI of the intact hemispheres revealed a total of 130 DWI+/T2+ lesions in 10/12 CAA cases, but none in controls (p = 0.022). DWI+/T2+ lesions examined histopathologically proved to be acute microinfarcts (classification accuracy 100%), characterized by presence of eosinophilic neurons on hematoxylin and eosin and absence of reactive astrocytes on glial fibrillary acidic protein-stained sections. In conclusion, we suggest that small DWI+ lesions in CAA represent acute microinfarcts. Furthermore, our findings support the use of ex vivo DWI as a method to detect acute microinfarcts post-mortem, which may benefit future histopathological investigations on the etiology of microinfarcts.

Higher-order diffusion MRI characterization of mesorectal lymph nodes in rectal cancer

PURPOSE

Mesorectal lymph node staging plays an important role in treatment decision making. Here, we explore the benefit of higher-order diffusion MRI models accounting for non-Gaussian diffusion effects to classify mesorectal lymph nodes both 1) ex vivo at ultrahigh field correlated with histology and 2) in vivo in a clinical scanner upon patient staging.

METHODS

The preclinical investigation included 54 mesorectal lymph nodes, which were scanned at 16.4 T with an extensive diffusion MRI acquisition. Eight diffusion models were compared in terms of goodness of fit, lymph node classification ability, and histology correlation. In the clinical part of this study, 10 rectal cancer patients were scanned with diffusion MRI at 1.5 T, and 72 lymph nodes were analyzed with Apparent Diffusion Coefficient (ADC), Intravoxel Incoherent Motion (IVIM), Kurtosis, and IVIM-Kurtosis.

RESULTS

Compartment models including restricted and anisotropic diffusion improved the preclinical data fit, as well as the lymph node classification, compared to standard ADC. The comparison with histology revealed only moderate correlations, and the highest values were observed between diffusion anisotropy metrics and cell area fraction. In the clinical study, the diffusivity from IVIM-Kurtosis was the only metric showing significant differences between benign (0.80 ± 0.30 μm² /ms) and malignant (1.02 ± 0.41 μm² /ms, P = .03) nodes. IVIM-Kurtosis also yielded the largest area under the receiver operating characteristic curve (0.73) and significantly improved the node differentiation when added to the standard visual analysis by experts based on T₂ -weighted imaging.

CONCLUSION

Higher-order diffusion MRI models perform better than standard ADC and may be of added value for mesorectal lymph node classification in rectal cancer patients.

Influence of water based embedding media composition on the relaxation properties of fixed tissue

BACKGROUND

In MRI of formalin-fixed tissue one of the problems is the dependence of tissue relaxation properties on formalin composition and composition of embedding medium (EM) used for scanning. In this study, we investigated molecular mechanisms by which the EM composition affects T2 relaxation directly and T1 relaxation indirectly.

OBJECTIVE

To identify principal components of formaldehyde based EM and the mechanism by which they affect relaxation properties of fixed tissue.

METHODS

We recorded high resolution ¹H NMR spectra of common formalin fixatives at temperatures in the range of 5 °C to 45 °C. We also measured T1 and T2 relaxation times of various organs of formalin fixed (FF) zebrafish at 7 T at 21 °C and 31 °C in several EM with and without fixative or gadolinium contrast agents.

RESULTS

We showed that the major source of T2 variability is chemical exchange between protons from EM hydroxyls and water, mediated by the presence of phosphate ions. The exchange rate increases with temperature, formaldehyde concentration in EM and phosphate concentration in EM. Depending on which side of the coalescence the system resides, the temperature increase can lead to either shortening or prolongation of T2, or to no noticeable change at all when very close to the coalescence. Chemical exchange can be minimized by washing out from EM the fixative, the phosphate or both.

CONCLUSION

The dependence of T2 in fixed tissue on the fixative origin and composition described in prior literature could be attributed to the phosphate buffer accelerated chemical exchange among the fixative hydroxyls and the tissue water. More consistent results in the relaxation measurements could be obtained by stricter control of the fixative composition or by scanning fixed tissue in PBS without fixative.

Matching ex vivo MRI With Iron Histology: Pearls and Pitfalls

Iron levels in the brain can be estimated using newly developed specific magnetic resonance imaging (MRI) sequences. This technique has several applications, especially in neurodegenerative disorders like Alzheimer's disease or Parkinson's disease. Coupling ex vivo MRI with histology allows neuroscientists to better understand what they see in the images. Iron is one of the most extensively studied elements, both by MRI and using histological or physical techniques. Researchers were initially only able to make visual comparisons between MRI images and different types of iron staining, but the emergence of specific MRI sequences like R2* or quantitative susceptibility mapping meant that quantification became possible, requiring correlations with physical techniques. Today, with advances in MRI and image post-processing, it is possible to look for MRI/histology correlations by matching the two sorts of images. For the result to be acceptable, the choice of methodology is crucial, as there are hidden pitfalls every step of the way. In order to review the advantages and limitations of ex vivo MRI correlation with iron-based histology, we reviewed all the relevant articles dealing with the topic in humans. We provide separate assessments of qualitative and quantitative studies, and after summarizing the significant results, we emphasize all the pitfalls that may be encountered.

Formalin tissue fixation biases myelin-sensitive MRI

PURPOSE

Chemical fixatives such as formalin form cross-links between proteins and affect the relaxation times and diffusion properties of tissue. These fixation-induced changes likely also affect myelin density measurements produced by quantitative magnetization transfer and myelin water imaging. In this work, we evaluate these myelin-sensitive MRI methods for fixation-induced biases.

METHODS

We perform quantitative magnetization transfer, myelin water imaging, and deuterium oxide-exchanged zero TE imaging on unfixed human spinal cord tissue at 9.4 Tesla and repeat these measurements after 1 day and 31 days of formalin fixation.

RESULTS

The quantitative magnetization-transfer bound pool fraction increased by 30.7% ± 21.1% after 1 day of fixation and by 42.6% ± 33.9% after 31 days of fixation. Myelin water fraction increased by 39.7% ± 15.5% and 37.0% ± 15.9% at these same time points, and mean T₂ of the myelin water pool nearly doubled. Reference-normalized deuterium oxide-exchanged zero TE signal intensity increased by 8.17% ± 6.03% after 31 days of fixation but did not change significantly after 1 day of fixation. After fixation, specimen cross-sectional area decreased by approximately 5%; after correction for shrinkage, changes in deuterium oxide-exchanged zero TE intensity were nearly eliminated.

CONCLUSION

Bound pool fraction and myelin water fraction are significantly increased by formalin fixation, whereas deuterium oxide-exchanged zero TE intensity is minimally affected. Changes in quantitative magnetization transfer and myelin water imaging may be due in part to delamination and formation of vacuoles in the myelin sheath. Deuterium oxide-exchanged signal intensity may be altered by fixation-induced changes in myelin lipid solid-state ¹ H T₁ . We urge caution in the comparison of these measurements across subjects or specimens in different states, especially unfixed versus fixed tissue.

Post-Mortem MRI and Histopathology in Neurologic Disease: A Translational Approach

In this review, combined post-mortem brain magnetic resonance imaging (MRI) and histology studies are highlighted, illustrating the relevance of translational approaches to define novel MRI signatures of neuropathological lesions in neuroinflammatory and neurodegenerative disorders. Initial studies combining post-mortem MRI and histology have validated various MRI sequences, assessing their sensitivity and specificity as diagnostic biomarkers in neurologic disease. More recent studies have focused on defining new radiological (bio)markers and implementing them in the clinical (research) setting. By combining neurological and neuroanatomical expertise with radiological development and pathological validation, a cycle emerges that allows for the discovery of novel MRI biomarkers to be implemented in vivo. Examples of this cycle are presented for multiple sclerosis, Alzheimer's disease, Parkinson's disease, and traumatic brain injury. Some applications have been shown to be successful, while others require further validation. In conclusion, there is much to explore with post-mortem MRI and histology studies, which can eventually be of high relevance for clinical practice.

MR Imaging Properties of ex vivo Common Marmoset Brain after Formaldehyde Fixation

Purpose:

Ex vivo brains have different MRI properties than in vivo brains because of chemical changes caused by fixative solutions, which change the signal intensity and/or tissue contrast on MR images. In this study, we investigated and compared the MRI properties of in vivo and ex vivo brains.

Methods:

Using a Bruker 9.4T experimental scanner unit for animals (Biospin GmbH, Ettlingen, Germany), we performed this study on the common marmoset. We measured the relaxation and diffusion values in the white matter and cortex of common marmosets and compared these values between in vivo brains (n = 20) and ex vivo brains (n = 20). Additionally, we observed the relationship between the tissue fixation duration and MRI properties by imaging a brain that underwent long-term fixation in a preliminary examination (n = 1).

Results:

The T₁ values of ex vivo brains were decreased compared with those of in vivo brains; however, there were no significant difference in the T₂ and T2* values of in vivo and ex vivo brains. Axial, radial, and mean diffusivity values of ex vivo brains decreased to approximately 65% and 52% of those of in vivo brains in the cortex and white matter, respectively. Conversely, fractional anisotropy values were not significantly different between in vivo and ex vivo brains.

Conclusion:

The T₁ values and diffusion coefficient values of the ex vivo brains were strikingly different than those of the in vivo brains. Conversely, there were no significant changes in the T₂, T2* or fractional anisotropy values. Altogether, the dehydration caused by tissue fixation and the reduction in brain temperature were involved in changing the relaxation and diffusion coefficient values. Here, it was difficult to specify all factors causing these changes. Further detailed study is needed to examine changes in MRI properties.

The choice of embedding media affects image quality, tissue R2 * , and susceptibility behaviors in post-mortem brain MR microscopy at 7.0T

PURPOSE

The quality and precision of post-mortem MRI microscopy may vary depending on the embedding medium used. To investigate this, our study evaluated the impact of 5 widely used media on: (1) image quality, (2) contrast of high spatial resolution gradient-echo (T₁ and T₂ ^* -weighted) MR images, (3) effective transverse relaxation rate (R₂ ^* ), and (4) quantitative susceptibility measurements (QSM) of post-mortem brain specimens.

METHODS

Five formaldehyde-fixed brain slices were scanned using 7.0T MRI in: (1) formaldehyde solution (formalin), (2) phosphate-buffered saline (PBS), (3) deuterium oxide (D₂ O), (4) perfluoropolyether (Galden), and (5) agarose gel. SNR and contrast-to-noise ratii (SNR/CNR) were calculated for cortex/white matter (WM) and basal ganglia/WM regions. In addition, median R₂ ^* and QSM values were extracted from caudate nucleus, putamen, globus pallidus, WM, and cortical regions.

RESULTS

PBS, Galden, and agarose returned higher SNR/CNR compared to formalin and D₂ O. Formalin fixation, and its use as embedding medium for scanning, increased tissue R₂ ^* . Imaging with agarose, D₂ O, and Galden returned lower R₂ ^* values than PBS (and formalin). No major QSM offsets were observed, although spatial variance was increased (with respect to R₂ ^* behaviors) for formalin and agarose.

CONCLUSIONS

Embedding media affect gradient-echo image quality, R₂ ^* , and QSM in differing ways. In this study, PBS embedding was identified as the most stable experimental setup, although by a small margin. Agarose and Galden were preferred to formalin or D₂ O embedding. Formalin significantly increased R₂ ^* causing noisier data and increased QSM variance.