Markov Chain Monte Carlo Random Effects Modeling in Magnetic Resonance Image Processing Using the BRugs Interface to WinBUGS

A common feature of many magnetic resonance image (MRI) data processing methods is the voxel-by-voxel (a voxel is a volume element) manner in which the processing is performed. In general, however, MRI data are expected to exhibit some level of spatial correlation, rendering an independent-voxels treatment inefficient in its use of the data. Bayesian random effect models are expected to be more efficient owing to their information-borrowing behaviour. To illustrate the Bayesian random effects approach, this paper outlines a Markov chain Monte Carlo (MCMC) analysis of a perfusion MRI dataset, implemented in R using the BRugs package. BRugs provides an interface to WinBUGS and its GeoBUGS add-on. WinBUGS is a widely used programme for performing MCMC analyses, with a focus on Bayesian random effect models. A simultaneous modeling of both voxels (restricted to a region of interest) and multiple subjects is demonstrated. Despite the low signal-to-noise ratio in the magnetic resonance signal intensity data, useful model signal intensity profiles are obtained. The merits of random effects modeling are discussed in comparison with the alternative approaches based on region-of-interest averaging and repeated independent voxels analysis. This paper focuses on perfusion MRI for the purpose of illustration, the main proposition being that random effects modeling is expected to be beneficial in many other MRI applications in which the signal-to-noise ratio is a limiting factor

Low-field thermal mixing in [1-13C] pyruvic acid for brute-force hyperpolarization

We detail the process of low-field thermal mixing (LFTM) between 1H and 13C nuclei in neat [1-13C] pyruvic acid at cryogenic temperatures (4–15 K). Using fast-field-cycling NMR, 1H nuclei in the molecule were polarized at modest high field (2 T) and then equilibrated with 13C nuclei by fast cycling (∼300–400 ms) to a low field (0–300 G) that activates thermal mixing. The 13C NMR spectrum was recorded after fast cycling back to 2 T. The 13C signal derives from 1H polarization via LFTM, in which the polarized (‘cold’) proton bath contacts the unpolarised (‘hot’) 13C bath at a field so low that Zeeman and dipolar interactions are similar-sized and fluctuations in the latter drive 1H–13C equilibration. By varying mixing time (tmix) and field (Bmix), we determined field-dependent rates of polarization transfer (1/τ) and decay (1/T1m) during mixing. This defines conditions for effective mixing, as utilized in ‘brute-force’ hyperpolarization of low-γ nuclei like 13C using Boltzmann polarization from nearby protons. For neat pyruvic acid, near-optimum mixing occurs for tmix ∼ 100–300 ms and Bmix ∼ 30–60 G. Three forms of frozen neat pyruvic acid were tested: two glassy samples, (one well-deoxygenated, the other O2-exposed) and one sample pre-treated by annealing (also well-deoxygenated). Both annealing and the presence of O2 are known to dramatically alter high-field longitudinal relaxation (T1) of 1H and 13C (up to 102–103-fold effects). Here, we found smaller, but still critical factors of ∼(2–5)× on both τ and T1m. Annealed, well-deoxygenated samples exhibit the longest time constants, e.g., τ ∼ 30–70 ms and T1m ∼ 1–20 s, each growing vs. Bmix. Mixing ‘turns off’ for Bmix > ∼100 G. That T1m ≫ τ is consistent with earlier success with polarization transfer from 1H to 13C by LFTM

Volume reduction of caudate nucleus is associated with movement coordination deficits in patients with hippocampal atrophy due to perinatal hypoxia-ischaemia

Acute sentinel hypoxia-ischaemia in neonates can target the hippocampus, mammillary bodies, thalamus, and the basal ganglia. Our previous work with paediatric patients with a history of hypoxia-ischaemia has revealed hippocampal and diencephalic damage that impacts cognitive memory. However, the structural and functional status of other brain regions vulnerable to hypoxia-ischaemia, such as the basal ganglia, has not been investigated in these patients. Furthermore, it is not known whether there are any behavioural sequelae of such damage, especially in patients with no diagnosis of neurological disorder. Based on the established role of the basal ganglia and the thalamus in movement coordination, we studied manual motor function in 20 participants exposed to neonatal hypoxia-ischaemia, and a group of 17 healthy controls of comparable age. The patients’ handwriting speed and accuracy was within the normal range (Detailed Assessment of Speed of Handwriting), and their movement adaptation learning (Rotary Pursuit task) was comparable to the control group’s performance. However, as a group, patients showed an impairment in the Grooved Pegboard task and a trend for impairment in speed of movement while performing the Rotary Pursuit task, suggesting that some patients have subtle deficits in fine, complex hand movements. Voxel-based morphometry and volumetry showed bilateral reduction in grey matter volume of the thalamus and caudate nucleus. Reduced volumes in the caudate nucleus correlated across patients with performance on the Grooved Pegboard task. In summary, the fine movement coordination deficit affecting the hand and the wrist in patients exposed to early hypoxic-ischaemic brain injury may be related to reduced volumes of the caudate nucleus, and consistent with anecdotal parental reports of clumsiness and coordination difficulties in this cohort

Quantification of Prostate Cancer Metabolism Using 3D Multiecho bSSFP and Hyperpolarized [1-13 C] Pyruvate: Metabolism Differs Between Tumors of the Same Gleason Grade

BACKGROUND: Three-dimensional (3D) multiecho balanced steady-state free precession (ME-bSSFP) has previously been demonstrated in preclinical hyperpolarized (HP) 13 C-MRI in vivo experiments, and it may be suitable for clinical metabolic imaging of prostate cancer (PCa). PURPOSE: To validate a signal simulation framework for the use of sequence parameter optimization. To demonstrate the feasibility of ME-bSSFP for HP 13 C-MRI in patients. To evaluate the metabolism in PCa measured by ME-bSSFP. STUDY TYPE: Retrospective single-center cohort study. PHANTOMS/POPULATION: Phantoms containing aqueous solutions of [1-13 C] lactate (2.3 M) and [13 C] urea (8 M). Eight patients (mean age 67 ± 6 years) with biopsy-confirmed Gleason 3 + 4 (n = 7) and 4 + 3 (n = 1) PCa. FIELD STRENGTH/SEQUENCES: 1 H MRI at 3 T with T2 -weighted turbo spin-echo sequence used for spatial localization and spoiled dual gradient-echo sequence used for B0 -field measurement. ME-bSSFP sequence for 13 C MR spectroscopic imaging with retrospective multipoint IDEAL metabolite separation. ASSESSMENT: The primary endpoint was the analysis of pyruvate-to-lactate conversion in PCa and healthy prostate regions of interest (ROIs) using model-free area under the curve (AUC) ratios and a one-directional kinetic model (kP ). The secondary objectives were to investigate the correlation between simulated and experimental ME-bSSFP metabolite signals for HP 13 C-MRI parameter optimization. STATISTICAL TESTS: Pearson correlation coefficients with 95% confidence intervals and paired t-tests. The level of statistical significance was set at P  0.96). Therefore, the simulation framework was used for sequence optimization. Whole prostate metabolic HP 13 C-MRI, observing the conversion of pyruvate into lactate, with a temporal resolution of 6 seconds was demonstrated using ME-bSSFP. Both assessed metrics resulted in significant differences between PCa (mean ± SD) (AUC = 0.33 ± 012, kP  = 0.038 ± 0.014) and healthy (AUC = 0.15 ± 0.10, kP  = 0.011 ± 0.007) ROIs. DATA CONCLUSION: Metabolic HP 13 C-MRI in the prostate using ME-bSSFP allows for differentiation between aggressive PCa and healthy tissue. EVIDENCE LEVEL: 2 TECHNICAL EFFICACY: Stage 1

Mutations in thyroid hormone receptor α1 cause premature neurogenesis and progenitor cell depletion in human cortical development.

Mutations in the thyroid hormone receptor α 1 gene (THRA) have recently been identified as a cause of intellectual deficit in humans. Patients present with structural abnormalities including microencephaly, reduced cerebellar volume and decreased axonal density. Here, we show that directed differentiation of THRA mutant patient-derived induced pluripotent stem cells to forebrain neural progenitors is markedly reduced, but mutant progenitor cells can generate deep and upper cortical layer neurons and form functional neuronal networks. Quantitative lineage tracing shows that THRA mutation-containing progenitor cells exit the cell cycle prematurely, resulting in reduced clonal output. Using a micropatterned chip assay, we find that spatial self-organization of mutation-containing progenitor cells in vitro is impaired, consistent with down-regulated expression of cell-cell adhesion genes. These results reveal that thyroid hormone receptor α1 is required for normal neural progenitor cell proliferation in human cerebral cortical development. They also exemplify quantitative approaches for studying neurodevelopmental disorders using patient-derived cells in vitro.NIHR Cambridge Biomedical Centr

The effect of residual Nyquist ghost in quantitative echo-planar diffusion imaging

Single‐shot diffusion‐weighted echo‐planar imaging (EPI) is typically used for most clinical diffusion studies due to its low sensitivity to patient motion. Although the Nyquist ghost artifact in EPI can be substantially reduced, there is frequently a residual ghost with low signal intensity. As reported in this study, this residual ghost can produce severe artifacts when maps of the apparent diffusion coefficient (ADC) are calculated from single‐shot echo‐planar images. The artifacts presented in this paper appear as regions of apparently low ADC which simulate regions of reduced diffusion, but are in fact generated by b‐value dependent Nyquist ghosts of the orbits. Data acquired in vivo were used to demonstrate that these artifacts can be avoided by including standard methods of spatial presaturation or fluid‐suppression in the diffusion‐weighted EPI protocol. In addition, phantom studies were used to illustrate how phase and amplitude variations in the ghost generate the artifacts and theoretical expressions, derived elsewhere, were used to provide a detailed understanding of the artifacts observed in vivo. The level of Nyquist ghost reported for the current generation of commercial scanners suggests that this is a general phenomenon which should be a consideration in all EPI‐based diffusion studies

Hippocampal damage and memory impairment in congenital cyanotic heart disease

Neonatal hypoxia can lead to hippocampal atrophy, which can lead, in turn, to memory impairment. To test the generalizability of this causal sequence, we examined a cohort of 41 children aged 8-16, who, having received the arterial switch operation to correct for transposition of the great arteries, had sustained significant neonatal cyanosis but were otherwise neurodevelopmentally normal. As predicted, the cohort had significant bilateral reduction of hippocampal volumes relative to the volumes of 64 normal controls. They also had significant, yet selective, impairment of episodic memory as measured by standard tests of memory, despite relatively normal levels of intelligence, academic attainment, and verbal fluency. Across the cohort, degree of memory impairment was correlated with degree of hippocampal atrophy suggesting that even as early as neonatal life no other structure can fully compensate for hippocampal injury and its special role in serving episodic long term memory