Diffusion imaging of whole, post-mortem human brains on a clinical MRI scanner

Abstract

Diffusion imaging of post mortem brains has great potential both as a reference for brain specimens that undergo sectioning, and as a link between in vivo diffusion studies and “gold standard” histology/dissection. While there is a relatively mature literature on post mortem diffusion imaging of animals, human brains have proven more challenging due to their incompatibility with high-performance scanners. This study presents a method for post mortem diffusion imaging of whole, human brains using a clinical 3-Tesla scanner with a 3D segmented EPI spin-echo sequence. Results in eleven brains at 0.94 × 0.94 × 0.94 mm resolution are presented, and in a single brain at 0.73 × 0.73 × 0.73 mm resolution. Region-of-interest analysis of diffusion tensor parameters indicate that these properties are altered compared to in vivo (reduced diffusivity and anisotropy), with significant dependence on post mortem interval (time from death to fixation). Despite these alterations, diffusion tractography of several major tracts is successfully demonstrated at both resolutions. We also report novel findings of cortical anisotropy and partial volume effects.

Deep Into the Fibers! Postmortem Diffusion Tensor Imaging in Forensic Radiology

“…[31][32][33][34][35][36] Imaging of a formalinfixed specimen results in signal alteration of the ex situ brain tissue and therefore may also alter PMDTI. If the brain is not fixed with formalin, continuing decomposition potentially impairs PMDTI, and frozen tissue as an alternative to fixation may interfere with anisotropy.…”

Collaborative patch-based super-resolution for diffusion-weighted images

“…Such HR and UHR D W i m a g e s w i t h h i g h S N R c o u l d p r o v i d e a b e t t e r s e n s i t i v i t y f o r the study of brain microstructure (Mori and van Zijl, 2002;Mukherjee et al, 2008;Zeineh et al, 2012). Moreover, these images could play an important role in fiber tractography to enable tracking of finer bundles or to better handle the fiber crossing problem (Dyrby et al, 2011;Miller et al, 2011;Raffelt et al, 2012). However, the acquisition of such HR or UHR images remains a challenging problem in clinical conditions since improvement in resolution is obtained at the cost of either lower SNR, longer acquisition time or both.…”

“…Therefore, such approaches are limited in clinical applications. For instance, five days of scanning followed by the averaging of five acquisitions were required in (Miller et al, 2011) t o o b t a i n post-mortem UHR D W i m a g e s w i t h h i g h S N R at 0.73x0.73x0.73mm 3 . To limit acquisition time, less efficient approaches can be used to obtain UHR DW images such as zero padding in k-space.…”

Cross-Subject Comparison of Local Diffusion MRI Parameters

“…We use very highresolution data in order to be able to view what we consider the underlying "ground truth" structures, while also downsampling the raw data in order to simulate how these structures would appear in more "normal" resolution data. The data is a complete ex vivo human brain, acquired at 0.7 Â 0.7 Â 0.7 mm resolution, using a 3D segmented spin echo sequence on a 3 T Siemens Tim Trio over 99 hours (Miller et al, 2011). In Figure 10.13a we see a cortical ROI of the FA image derived from the original data.…”