High resolution anatomical and quantitative MRI of the entire human occipital lobe ex vivo at 9.4 T

Abstract

Several magnetic resonance imaging (MRI) contrasts are sensitive to myelin content in gray matter in vivo which has ignited ambitions of MRI-based in vivo cortical histology. Ultra-high field (UHF) MRI, at fields of 7 T and beyond, is crucial to provide the resolution and contrast needed to sample contrasts over the depth of the cortex and get closer to layer resolved imaging. Ex vivo MRI of human post mortem samples is an important stepping stone to investigate MRI contrast in the cortex, validate it against histology techniques applied in situ to the same tissue, and investigate the resolutions needed to translate ex vivo findings to in vivo UHF MRI. Here, we investigate key technology to extend such UHF studies to large human brain samples while maintaining high resolution, which allows investigation of the layered architecture of several cortical areas over their entire 3D extent and their complete borders where architecture changes. A 16 channel cylindrical phased array radiofrequency (RF) receive coil was constructed to image a large post mortem occipital lobe sample (~80×80×80 mm3) in a wide-bore 9.4 T human scanner with the aim of achieving high-resolution anatomical and quantitative MR images. Compared with a human head coil at 9.4 T, the maximum Signal-to-Noise ratio (SNR) was increased by a factor of about five in the peripheral cortex. Although the transmit profile with a circularly polarized transmit mode at 9.4 T is relatively inhomogeneous over the large sample, this challenge was successfully resolved with parallel transmit using the kT-points method. Using this setup, we achieved 60μm anatomical images for the entire occipital lobe showing increased spatial definition of cortical details compared to lower resolutions. In addition, we were able to achieve sufficient control over SNR, B0 and B1 homogeneity and multi-contrast sampling to perform quantitative T2* mapping over the same volume at 200 μm. Markov Chain Monte Carlo sampling provided maximum posterior estimates of quantitative T2* and their uncertainty, allowing delineation of the stria of Gennari over the entire length and width of the calcarine sulcus. We discuss how custom RF receive coil arrays built to specific large post mortem sample sizes can provide a platform for UHF cortical layer-specific quantitative MRI over large fields of view.

Ex vivo diffusion MRI of the human brain: Technical challenges and recent advances

“…It is important to realize that high‐quality ex vivo dMRI data do not come easily. Achievable quality depends on the quality and preparation of the sample (its PMI and mode of fixation), pulse sequences tailored to ex vivo imaging, long acquisitions (often days) and sometimes bespoke RF coils or other hardware. This also has the consequence that sample numbers in ex vivo dMRI are often low, something more often seen in classical anatomy studies, which is challenging for the generalization of the results.…”

Role of T1 mapping to evaluate brain aging in a healthy population

“…With conventional MRI methods, cortical thinning, regional atrophy and brain surface morphology can be assessed during aging [6][7][8]. However, conventional MRI has a limited potential to clarify the underlying microstructural tissue processes [9]. On the other hand, quantitative MRI (qMRI) provides the calculation of the T1, T2 and T2* relaxation times, and qMRI is particularly sensitive to the biophysiological processes of aging in GM and WM [10,11].…”

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

“…The most widely used embedding media for imaging human tissue are formaldehyde solutions, 28,29 PBS, 30 and aquaeous gels such as low-melting-point agarose. 11,31 More recently, protonfree agents such as perfluoropolyether compounds (Fomblin or Galden, Solvay, Bruxelles, Belgium and Fluorinert FC-3283, 3M, Delft, Netherlands), 19,[32][33][34][35] a wax-like compound (Paraplast, Sigma-Aldrich, St. Louis, MO), 36 or deuterium oxide (D 2 O) are gaining popularity because of their ability to render dark background on MRI and their overall versatility. D 2 O embedding, for example, has successfully been used to supress water signal for isolating myelin-protons.…”