Optimised pipeline for high-resolution dMRI of the post-mortem human brainstem

Abstract: Diffusion MRI (dMRI) measures the diffusion of water molecules with the use of magnetic resonance. For dMRI of the brain, diffusivity within white fibre tracts is central to revealing intricate fibre architecture. A decade since the conception of the Human Connectome Project (HCP), the consortium associated with HCP has produced a pipeline, as well as raw dMRI data set that are widely used in the field of brain connectomics today. The achievable spatial resolution achieved with the in-vivo pipeline and resulting dataset developed by HCP however, is limited by the scan time which can be tolerated by human subjects. Much higher spatial resolution requires much longer scan times in the order of several hours or even days, which can be only realized using dMRI on post-mortem human brain. Post-mortem dMRI allows for longer scan time, higher SNR (Signal to Noise ratio) and access to higher gradient strength in pre-clinical scanners that can lead to resolution of complicated white fibre architecture, thereby revealing anatomical structures not seen before. However, there is still a lack of agreement in the dMRI brain imaging field for an established pipeline adapted specifically to accommodate the special needs of post-mortem tissue.

This thesis project aims to address the lack of cohesive workflow by breaking a state-of-the-art workflow into and optimising four major sequential steps.

Pre-Scan: A specialised tissue holder and container were designed to hold the post-mortem human brain and to minimise bulk susceptibility effect. 1% PFA was found, out of four often used solutions, to possess an overall combination of favourably long T2 and highest MD values and therefore is the most optimal solution to immerse the post-mortem tissue during scanning.

Scan: A 3D-dw-SE scan sequence was found to be superior over 2D-dw-SE in that it produced signal that followed a Gaussian distribution, whereby the signals from WM and GM of the brain tissue were distinct, leading to clear contrast between GM and WM. The 3D-dw-SE scan sequence also does not produce temperature fluctuation despite long scan times compared to the widely used EPI sequences.

Post-Scan: Global tractography was favoured over the popular local tractography methods, probabilistic and deterministic tractography, due to the nature of global tractography in considering inter-voxel relationships leading to its ability to withstand noise and artifacts.
Furthermore, global tractography-generated tracts displayed cohesive tracts with a higher density over a spatial area that strongly suggest high fidelity to ground truth of the tract tracked when compared to probabilistic tractography.

Applications: In testing the rigours of the optimised workflow, known decussation and pain tracts from the HCP data set were compared to those from the post-mortem brainstem sample. Anatomically feasible yet novel tracts were observed when using the optimised workflow

Angaben zum Objekt

• Standort: Deutsche Nationalbibliothek Frankfurt am Main
• Umfang: Online-Ressource
• Sprache: Englisch
• Anmerkungen: Universität Freiburg, Dissertation, 2022

Klassifikation und Themen

• Schlagwort: Kernspintomografie ; Diffusionsgewichtete Magnetresonanztomografie

Beteiligte, Orts- und Zeitangaben

• Ereignis: Veröffentlichung
• (wo): Freiburg
• (wer): Universität
• (wann): 2022
• Urheber: Teo, Shi Jia
• Beteiligte Personen und Organisationen: Hennig, Jürgen ; Leibold, Christian ; Rotter, Stefan ; Albert-Ludwigs-Universität Freiburg. Fakultät für Biologie

Weitere Informationen

• DOI: 10.6094/UNIFR/231585
• URN: urn:nbn:de:bsz:25-freidok-2315852
• Rechteinformation: Open Access; Der Zugriff auf das Objekt ist unbeschränkt möglich.
• Letzte Aktualisierung: 15.08.2025, 07:33 MESZ