Assessment of Calcaneal Spongy Bone Magnetic Resonance Characteristics in Women: A Comparison between Measures Obtained at 0.3 T, 1.5 T, and 3.0 T.

BACKGROUND: There is a growing interest in bone tissue MRI and an even greater interest in using low-cost MR scanners. However, the characteristics of bone MRI remain to be fully defined, especially at low field strength. This study aimed to characterize the signal-to-noise ratio (SNR), T2, and T2* in spongy bone at 0.3 T, 1.5 T, and 3.0 T. Furthermore, relaxation times were characterized as a function of bone-marrow lipid/water ratio content and trabecular bone density. METHODS: Thirty-two women in total underwent an MR-imaging investigation of the calcaneus at 0.3 T, 1.5 T, and 3.0 T. MR-spectroscopy was performed at 3.0 T to assess the fat/water ratio. SNR, T2, and T2* were quantified in distinct calcaneal regions (ST, TC, and CC). ANOVA and Pearson correlation statistics were used. RESULTS: SNR increase depends on the magnetic field strength, acquisition sequence, and calcaneal location. T2* was different at 3.0 T and 1.5 T in ST, TC, and CC. Relaxation times decrease as much as the magnetic field strength increases. The significant linear correlation between relaxation times and fat/water found in healthy young is lost in osteoporotic subjects. CONCLUSION: The results have implications for the possible use of relaxation vs. lipid/water marrow content for bone quality assessment and the development of quantitative MRI diagnostics at low field strength.

MP2RAGE vs. MPRAGE surface-based morphometry in focal epilepsy.

In drug-resistant focal epilepsy, detecting epileptogenic lesions using MRI poses a critical diagnostic challenge. Here, we assessed the utility of MP2RAGE-a T1-weighted sequence with self-bias correcting properties commonly utilized in ultra-high field MRI-for the detection of epileptogenic lesions using a surface-based morphometry pipeline based on FreeSurfer, and compared it to the common approach using T1w MPRAGE, both at 3T. We included data from 32 patients with focal epilepsy (5 MRI-positive, 27 MRI-negative with lobar seizure onset hypotheses) and 94 healthy controls from two epilepsy centres. Surface-based morphological measures and intensities were extracted and evaluated in univariate GLM analyses as well as multivariate unsupervised 'novelty detection' machine learning procedures. The resulting prediction maps were analyzed over a range of possible thresholds using alternative free-response receiver operating characteristic (AFROC) methodology with respect to the concordance with predefined lesion labels or hypotheses on epileptogenic zone location. We found that MP2RAGE performs at least comparable to MPRAGE and that especially analysis of MP2RAGE image intensities may provide additional diagnostic information. Secondly, we demonstrate that unsupervised novelty-detection machine learning approaches may be useful for the detection of epileptogenic lesions (maximum AFROC AUC 0.58) when there is only a limited lesional training set available. Third, we propose a statistical method of assessing lesion localization performance in MRI-negative patients with lobar hypotheses of the epileptogenic zone based on simulation of a random guessing process as null hypothesis. Based on our findings, it appears worthwhile to study similar surface-based morphometry approaches in ultra-high field MRI (≥ 7 T).

A predictor-corrector phase unwrapping algorithm for temporally undersampled gradient-echo MRI.

PURPOSE: To develop a method for unwrapping temporally undersampled and nonlinear gradient recalled echo (GRE) phase. THEORY AND METHODS: Temporal unwrapping is performed as a sequential one step prediction of the echo phase, followed by a correction to the nearest integer wrap-count. A spatio-temporal extension of the 1D predictor corrector unwrapping (PCU) algorithm improves the prediction accuracy, and thereby maintains spatial continuity. The proposed method is evaluated using numerical phantom, physical phantom, and in vivo brain data at both 3 T and 9.4 T. The unwrapping performance is compared with the state-of-the-art temporal and spatial unwrapping algorithms, and the spatio-temporal iterative virtual-echo based Nyquist sampled (iVENyS) algorithm. RESULTS: Simulation results showed significant reduction in unwrapping errors at higher echoes compared with the state-of-the-art algorithms. Similar to the iVENyS algorithm, the PCU algorithm was able to generate spatially smooth phase images for in vivo data acquired at 3 T and 9.4 T, bypassing the use of additional spatial unwrapping step. A key advantage over iVENyS algorithm is the superior performance of PCU algorithm at higher echoes. CONCLUSION: PCU algorithm serves as a robust phase unwrapping method for temporally undersampled and nonlinear GRE phase, particularly in the presence of high field gradients.

Distribution of corpora amylacea in the human midbrain: using synchrotron radiation phase-contrast microtomography, high-field magnetic resonance imaging, and histology.

Corpora amylacea (CA) are polyglucosan aggregated granules that accumulate in the human body throughout aging. In the cerebrum, CA have been found in proximity to ventricular walls, pial surfaces, and blood vessels. However, studies showing their three-dimensional spatial distribution are sparse. In this study, volumetric images of four human brain stems were obtained with MRI and phase-contrast X-ray microtomography, followed up by Periodic acid Schiff stain for validation. CA appeared as hyperintense spheroid structures with diameters up to 30 µm. An automatic pipeline was developed to segment the CA, and the spatial distribution of over 200,000 individual corpora amylacea could be investigated. A threefold-or higher-density of CA was detected in the dorsomedial column of the periaqueductal gray (860-4,200 CA count/mm3) than in the superior colliculus (150-340 CA count/mm3). We estimated that about 2% of the CA were located in the immediate vicinity of the vessels or in the peri-vascular space. While CA in the ependymal lining of the cerebral aqueduct was rare, the sub-pial tissue of the anterior and posterior midbrain contained several CA. In the sample with the highest CA density, quantitative maps obtained with MRI revealed high R2* values and a diamagnetic shift in a region which spatially coincided with the CA dense region.

Simulated and experimental phantom data for multi-center quality assurance of quantitative susceptibility maps at 3 T, 7 T and 9.4 T.

PURPOSE: To develop methods for quality assurance of quantitative susceptibility mapping (QSM) using MRI at different magnetic field strengths, and scanners, using different MR-sequence protocols, and post-processing pipelines. METHODS: We built a custom phantom based on iron in two forms: homogeneous susceptibility ('free iron') and with fine-scaled variations in susceptibility ('clustered iron') at different iron concentrations. The phantom was measured at 3.0 T (two scanners), 7.0 T and 9.4 T using multi-echo, gradient echo acquisition sequences. A digital phantom analogue to the iron-phantom, tailored to obtain similar results as in experimentation was developed, with similar geometry and susceptibility values. Morphology enabled dipole inversion was applied to the phase images to obtain QSM for experimental and simulated data using the MEDI + 0 approach for background regularization. RESULTS: Across all scanners, QSM-values showed a linear increase with iron concentrations. The QSM-relaxivity was 0.231 ± 0.047 ppm/mM for free and 0.054 ± 0.013 ppm/mM for clustered iron, with adjusted determination coefficients (DoC) ≥ 0.87. Similarly, the simulations yielded linear increases (DoC ≥ 0.99). In both the experimental and digital phantoms, the estimated molar susceptibility was lower with clustered iron, because clustering led to highly localized field effects. CONCLUSION: Our iron phantom can be used to evaluate the capability of QSM to detect local variations in susceptibility across different field strengths, when using different MR-sequence protocols. The devised simulation method captures the effect of iron clustering in QSM as seen experimentally and could be used in the future to optimize QSM processing pipelines and achieve higher accuracy for local field effects, as also seen in Alzheimer's beta-amyloid plaques.

Clinical Significance of Diffusion Tensor Imaging in Metachromatic Leukodystrophy.

BACKGROUND: Metachromatic leukodystrophy (MLD) is a lysosomal enzyme deficiency disorder leading to progressive demyelination and, consecutively, to cognitive and motor decline. Brain magnetic resonance imaging (MRI) can detect affected white matter as T2 hyperintense areas but cannot quantify the gradual microstructural process of demyelination more accurately. Our study aimed to investigate the value of routine MR diffusion tensor imaging in assessing disease progression. METHODS: MR diffusion parameters (apparent diffusion coefficient [ADC] and fractional anisotropy [FA]) were in the frontal white matter, central region (CR), and posterior limb of the internal capsule in 111 MR datasets from a natural history study of 83 patients (age: 0.5-39.9 years; 35 late-infantile, 45 juvenile, 3 adult, with clinical diffusion sequences of different scanner manufacturers) as well as 120 controls. Results were correlated with clinical parameters reflecting motor and cognitive function. RESULTS: ADC values increase and FA values decrease depending on disease stage/severity. They show region-specific correlations with clinical parameters of motor and cognitive symptoms, respectively. Higher ADC levels in CR at diagnosis predicted a disease course with more rapid motor deterioration in juvenile MLD patients. In highly organized tissues such as the corticospinal tract, in particular, diffusion MR parameters were highly sensitive to MLD-associated changes and did not correlate with the visual quantification of T2 hyperintensities. CONCLUSION: Our results show that diffusion MRI can deliver valuable, robust, clinically meaningful, and easily obtainable/accessible/available parameters in the assessment of prognosis and progression of MLD. Therefore, it provides additional quantifiable information to established methods such as T2 hyperintensity.

Prediction of motion induced magnetic fields for human brain MRI at 3 T.

OBJECTIVE: Maps of B0 field inhomogeneities are often used to improve MRI image quality, even in a retrospective fashion. These field inhomogeneities depend on the exact head position within the static field but acquiring field maps (FM) at every position is time consuming. Here we propose a forward simulation strategy to obtain B0 predictions at different head-positions. METHODS: FM were predicted by combining (1) a multi-class tissue model for estimation of tissue-induced fields, (2) a linear k-space model for capturing gradient imperfections, (3) a dipole estimation for quantifying lower-body perturbing fields (4) and a position-dependent tissue mask to model FM alterations caused by large motion effects. The performance of the combined simulation strategy was compared with an approach based on a rigid body transformation of the FM measured in the reference position to the new position. RESULTS: The transformed FM provided inconsistent results for large head movements (> 5° rotation, approximately), while the simulation strategy had a superior prediction accuracy for all positions. The simulated FM was used to optimize B0 shims with up to 22.2% improvement with respect to the transformed FM approach. CONCLUSION: The proposed simulation strategy is able to predict movement-induced B0 field inhomogeneities yielding more precise estimates of the ground truth field homogeneity than the transformed FM.

Characterization of the blood oxygen level dependent hemodynamic response function in human subcortical regions with high spatiotemporal resolution.

Subcortical brain regions are absolutely essential for normal human function. These phylogenetically early brain regions play critical roles in human behaviors such as the orientation of attention, arousal, and the modulation of sensory signals to cerebral cortex. Despite the critical health importance of subcortical brain regions, there has been a dearth of research on their neurovascular responses. Blood oxygen level dependent (BOLD) functional MRI (fMRI) experiments can help fill this gap in our understanding. The BOLD hemodynamic response function (HRF) evoked by brief (<4 s) neural activation is crucial for the interpretation of fMRI results because linear analysis between neural activity and the BOLD response relies on the HRF. Moreover, the HRF is a consequence of underlying local blood flow and oxygen metabolism, so characterization of the HRF enables understanding of neurovascular and neurometabolic coupling. We measured the subcortical HRF at 9.4T and 3T with high spatiotemporal resolution using protocols that enabled reliable delineation of HRFs in individual subjects. These results were compared with the HRF in visual cortex. The HRF was faster in subcortical regions than cortical regions at both field strengths. There was no significant undershoot in subcortical areas while there was a significant post-stimulus undershoot that was tightly coupled with its peak amplitude in cortex. The different BOLD temporal dynamics indicate different vascular dynamics and neurometabolic responses between cortex and subcortical nuclei.

Microvascular imaging of the unstained human superior colliculus using synchrotron-radiation phase-contrast microtomography.

Characterizing the microvasculature of the human brain is critical to advance understanding of brain vascular function. Most methods rely on tissue staining and microscopy in two-dimensions, which pose several challenges to visualize the three-dimensional structure of microvessels. In this study, we used an edge-based segmentation method to extract the 3D vasculature from synchrotron radiation phase-contrast microtomography (PC-µCT) of two unstained, paraffin-embedded midbrain region of the human brain stem. Vascular structures identified in PC-µCT were validated with histology of the same specimen. Using the Deriche-Canny edge detector that was sensitive to the boundary between tissue and vascular space, we could segment the vessels independent of signal variations in PC-µCT images. From the segmented volumetric vasculature, we calculated vessel diameter, vessel length and volume fraction of the vasculature in the superior colliculi. From high resolution images, we found the most frequent vessel diameter to be between 8.6-10.2 µm. Our findings are consistent with the known anatomy showing two types of vessels with distinctive morphology: peripheral collicular vessels and central collicular vessels. The proposed method opens up new possibilities for vascular research of the central nervous system using synchrotron radiation PC-µCT of unstained human tissue.

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

PURPOSE: To develop improved tissue masks for QSM. METHODS: Masks including voxels at the brain surface were automatically generated from the magnitude alone (MM) or combined with test functions from the first (PG) or second (PB) derivative of the sign of the wrapped phase. Phase images at 3T and 9.4T were simulated at different TEs and used to generate a mask, PItoh , with between-voxel phase differences less than π. MM, PG, and PB were compared with PItoh . QSM were generated from 3D multi-echo gradient-echo data acquired at 9.4T (21 subjects aged: 20-56y), and from the QSM2016 challenge 3T data using different masks, unwrapping, background removal, and dipole inversion algorithms. QSM contrast was quantified using age-based iron concentrations. RESULTS: Close to air cavities, phase wraps became denser with increasing field and echo time, yielding increased values of the test functions. Compared with PItoh , PB had the highest Dice coefficient, while PG had the lowest and MM the highest percentage of voxels outside PItoh. Artifacts observed in QSM at 9.4T with MM were mitigated by stronger background filters but yielded a reduced QSM contrast. With PB, QSM contrast was greater and artifacts diminished. Similar results were obtained with challenge data, evidencing larger effects of mask close to air cavities. CONCLUSION: Automatic, phase-based masking founded on the second derivative of the sign of the wrapped phase, including cortical voxels at the brain surface, was able to mitigate artifacts and restore QSM contrast across cortical and subcortical brain regions.

Perception is associated with the brain's metabolic response to sensory stimulation.

Processing of incoming sensory stimulation triggers an increase of cerebral perfusion and blood oxygenation (neurovascular response) as well as an alteration of the metabolic neurochemical profile (neurometabolic response). Here, we show in human primary visual cortex (V1) that perceived and unperceived isoluminant chromatic flickering stimuli designed to have similar neurovascular responses as measured by blood oxygenation level-dependent functional magnetic resonance imaging (BOLD-fMRI) have markedly different neurometabolic responses as measured by proton functional magnetic resonance spectroscopy (1H-fMRS). In particular, a significant regional buildup of lactate, an index of aerobic glycolysis, and glutamate, an index of malate-aspartate shuttle, occurred in V1 only when the flickering was perceived, without any relation with other behavioral or physiological variables. Whereas the BOLD-fMRI signal in V1, a proxy for input to V1, was insensitive to flickering perception by design, the BOLD-fMRI signal in secondary visual areas was larger during perceived than unperceived flickering, indicating increased output from V1. These results demonstrate that the upregulation of energy metabolism induced by visual stimulation depends on the type of information processing taking place in V1, and that 1H-fMRS provides unique information about local input/output balance that is not measured by BOLD-fMRI.

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 , R2∗ , R2 , R2' , 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 R2∗ 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 R2∗ , 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 R2∗ 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 R2∗ , and more paramagnetic QSM than without additives. The kinetics of R2∗ allowed estimation of fixative tissue penetration.

Quantitative Susceptibility Mapping of the Basal Ganglia and Thalamus at 9.4 Tesla.

The thalamus (Th) and basal ganglia (BG) are central subcortical connectivity hubs of the human brain, whose functional anatomy is still under intense investigation. Nevertheless, both substructures contain a robust and reproducible functional anatomy. The quantitative susceptibility mapping (QSM) at ultra-high field may facilitate an improved characterization of the underlying functional anatomy in vivo. We acquired high-resolution QSM data at 9.4 Tesla in 21 subjects, and analyzed the thalamic and BG by using a prior defined functional parcellation. We found a more substantial contribution of paramagnetic susceptibility sources such as iron in the pallidum in contrast to the caudate, putamen, and Th in descending order. The diamagnetic susceptibility sources such as myelin and calcium revealed significant contributions in the Th parcels compared with the BG. This study presents a detailed nuclei-specific delineation of QSM-provided diamagnetic and paramagnetic susceptibility sources pronounced in the BG and the Th. We also found a reasonable interindividual variability as well as slight hemispheric differences. The results presented here contribute to the microstructural knowledge of the Th and the BG. In specific, the study illustrates QSM values (myelin, calcium, and iron) in functionally similar subregions of the Th and the BG.

Multi-echo gradient-recalled-echo phase unwrapping using a Nyquist sampled virtual echo train in the presence of high-field gradients.

PURPOSE: To develop a spatio-temporal approach to accurately unwrap multi-echo gradient-recalled echo phase in the presence of high-field gradients. THEORY AND METHODS: Using the virtual echo-based Nyquist sampled (VENyS) algorithm, the temporal unwrapping procedure is modified by introduction of one or more virtual echoes between the first lower and the immediate higher echo, so as to reinstate the Nyquist condition at locations with high-field gradients. An iterative extension of the VENyS algorithm maintains spatial continuity by adjusting the phase rotations to make the neighborhood phase differences less than π. The algorithm is evaluated using simulated data, Gadolinium contrast-doped phantom, and in vivo brain, abdomen, and chest data sets acquired at 3 T and 9.4 T. The unwrapping performance is compared with the standard temporal unwrapping algorithm used in the morphology-enabled dipole inversion-QSM pipeline as a benchmark for validation. RESULTS: Quantitative evaluation using numerical phantom showed significant reduction in unwrapping errors in regions of large field gradients, and the unwrapped phase revealed an exact match with the linear concentration profile of vials in a gadolinium contrast-doped phantom data acquired at 9.4 T. Without the need for additional spatial unwrapping, the iterative VENyS algorithm was able to generate spatially continuous phase images. Application to in vivo data resulted in better unwrapping performance, especially in regions with large susceptibility changes such as the air/tissue interface. CONCLUSION: The iterative VENyS algorithm serves as a robust unwrapping method for multi-echo gradient-recalled echo phase in the presence of high-field gradients.

Disturbed Balance of Inhibitory Signaling Links Hearing Loss and Cognition.

Neuronal hyperexcitability in the central auditory pathway linked to reduced inhibitory activity is associated with numerous forms of hearing loss, including noise damage, age-dependent hearing loss, and deafness, as well as tinnitus or auditory processing deficits in autism spectrum disorder (ASD). In most cases, the reduced central inhibitory activity and the accompanying hyperexcitability are interpreted as an active compensatory response to the absence of synaptic activity, linked to increased central neural gain control (increased output activity relative to reduced input). We here suggest that hyperexcitability also could be related to an immaturity or impairment of tonic inhibitory strength that typically develops in an activity-dependent process in the ascending auditory pathway with auditory experience. In these cases, high-SR auditory nerve fibers, which are critical for the shortest latencies and lowest sound thresholds, may have either not matured (possibly in congenital deafness or autism) or are dysfunctional (possibly after sudden, stressful auditory trauma or age-dependent hearing loss linked with cognitive decline). Fast auditory processing deficits can occur despite maintained basal hearing. In that case, tonic inhibitory strength is reduced in ascending auditory nuclei, and fast inhibitory parvalbumin positive interneuron (PV-IN) dendrites are diminished in auditory and frontal brain regions. This leads to deficits in central neural gain control linked to hippocampal LTP/LTD deficiencies, cognitive deficits, and unbalanced extra-hypothalamic stress control. Under these conditions, a diminished inhibitory strength may weaken local neuronal coupling to homeostatic vascular responses required for the metabolic support of auditory adjustment processes. We emphasize the need to distinguish these two states of excitatory/inhibitory imbalance in hearing disorders: (i) Under conditions of preserved fast auditory processing and sustained tonic inhibitory strength, an excitatory/inhibitory imbalance following auditory deprivation can maintain precise hearing through a memory linked, transient disinhibition that leads to enhanced spiking fidelity (central neural gain⇑) (ii) Under conditions of critically diminished fast auditory processing and reduced tonic inhibitory strength, hyperexcitability can be part of an increased synchronization over a broader frequency range, linked to reduced spiking reliability (central neural gain⇓). This latter stage mutually reinforces diminished metabolic support for auditory adjustment processes, increasing the risks for canonical dementia syndromes.

T2-Pseudonormalization and Microstructural Characterization in Advanced Stages of Late-infantile Metachromatic Leukodystrophy.

PURPOSE: T2-weighted signal hyperintensities in white matter (WM) are a diagnostic finding in brain magnetic resonance imaging (MRI) of patients with metachromatic leukodystrophy (MLD). In our systematic investigation of the evolution of T2-hyperintensities in patients with the late-infantile form, we describe and characterize T2-pseudonormalization in the advanced stage of the natural disease course. METHODS: The volume of T2-hyperintensities was quantified in 34 MRIs of 27 children with late-infantile MLD (median age 2.25 years, range 0.5-5.2 years). In three children with the most advanced clinical course (age >4 years) and for whom the T2-pseudonormalization was the most pronounced, WM microstructure was investigated using a multimodal MRI protocol, including diffusion-weighted imaging, MR spectroscopy (MRS), myelin water fraction (MWF), magnetization transfer ratio (MTR), T1-mapping and quantitative susceptibility mapping. RESULTS: T2-hyperintensities in cerebral WM returned to normal in large areas of 3 patients in the advanced disease stage. Multimodal assessment of WM microstructure in areas with T2-pseudonormalization revealed highly decreased values for NAA, neurite density, isotropic water, mean and radial kurtosis, MWF and MTR, as well as increased radial diffusivity. CONCLUSION: In late-infantile MLD patients, we found T2-pseudonormalization in WM tissue with highly abnormal microstructure characterizing the most advanced disease stage. Pathological hallmarks might be a loss of myelin, but also neuronal loss as well as increased tissue density due to gliosis and accumulated storage material. These results suggest that a multimodal MRI protocol using more specific microstructural parameters than T2-weighted sequences should be used when evaluating the effect of treatment trials in MLD.

Depth relationships and measures of tissue thickness in dorsal midbrain.

Dorsal human midbrain contains two nuclei with clear laminar organization, the superior and inferior colliculi. These nuclei extend in depth between the superficial dorsal surface of midbrain and a deep midbrain nucleus, the periaqueductal gray matter (PAG). The PAG, in turn, surrounds the cerebral aqueduct (CA). This study examined the use of two depth metrics to characterize depth and thickness relationships within dorsal midbrain using the superficial surface of midbrain and CA as references. The first utilized nearest-neighbor Euclidean distance from one reference surface, while the second used a level-set approach that combines signed distances from both reference surfaces. Both depth methods provided similar functional depth profiles generated by saccadic eye movements in a functional MRI task, confirming their efficacy for delineating depth for superficial functional activity. Next, the boundaries of the PAG were estimated using Euclidean distance together with elliptical fitting, indicating that the PAG can be readily characterized by a smooth surface surrounding PAG. Finally, we used the level-set approach to measure tissue depth between the superficial surface and the PAG, thus characterizing the variable thickness of the colliculi. Overall, this study demonstrates depth-mapping schemes for human midbrain that enables accurate segmentation of the PAG and consistent depth and thickness estimates of the superior and inferior colliculi.