Reducing variability in along-tract analysis with diffusion profile realignment

Diffusion weighted MRI (dMRI) provides a non invasive virtual reconstruction of the brain's white matter structures through tractography. Analyzing dMRI measures along the trajectory of white matter bundles can provide a more specific investigation than considering a region of interest or tract-averaged measurements. However, performing group analyses with this along-tract strategy requires correspondence between points of tract pathways across subjects. This is usually achieved by creating a new common space where the representative streamlines from every subject are resampled to the same number of points. If the underlying anatomy of some subjects was altered due to, e.g. disease or developmental changes, such information might be lost by resampling to a fixed number of points. In this work, we propose to address the issue of possible misalignment, which might be present even after resampling, by realigning the representative streamline of each subject in this 1D space with a new method, coined diffusion profile realignment (DPR). Experiments on synthetic datasets show that DPR reduces the coefficient of variation for the mean diffusivity, fractional anisotropy and apparent fiber density when compared to the unaligned case. Using 100 in vivo datasets from the HCP, we simulated changes in mean diffusivity, fractional anisotropy and apparent fiber density. Pairwise Student's t-tests between these altered subjects and the original subjects indicate that regional changes are identified after realignment with the DPR algorithm, while preserving differences previously detected in the unaligned case. This new correction strategy contributes to revealing effects of interest which might be hidden by misalignment and has the potential to improve the specificity in longitudinal population studies beyond the traditional region of interest based analysis and along-tract analysis workflows.Comment: v4: peer-reviewed round 2 v3 : deleted some old text from before peer-review which was mistakenly included v2 : peer-reviewed version v1: preprint as submitted to journal NeuroImag

Investigation on the optimization approaches of diffusion weighted imaging

The corticospinal tract is important in the guidance of neurosurgery. Therefore precise tractography in the pre-operative plan is necessary. However, the inherent drawback of DWI in image acquisition makes it easy to be affected by bulk motion and pulsatile motion and also to produce image distortions because of EPI acquisitions. Therefore, optimized approaches aimed at reducing or eliminating these artifacts and improve image quality have been investigated. Pulsatile motion occurs during the cardiac systolic period and has been reported to produce motion artifacts in the brain stem and basal ganglia, which might affect the corticospinal tract. Up to now, there is no consensus on the real effect of pulsatile motion on the diffusion properties, diffusion tensor parameters and fiber tractography, and the role of cardiac gating to overcome these effects is also not very clear. So in part 1 of the current study, we analyzed the influence of pulsatile motion and the contribution of cardiac-gating in the improvement of the quality of DWI, DTI and tractography. We found obvious signal attenuation in the brain stem and cerebellum. Pulsatile motion led to an over-estimation of FA and under-estimation of MD along the CST. Cardiac-gating could help to reduce the bias of the diffusion tensor parameters. Although pulsatile motion resulted in motion artifacts, bias of the diffusion tensor parameters and deviation of the principal eigenvector direction, it did not influence tract volume and location when a deterministic algorithm was applied for the reconstruction of the tract. Therefore, in this part we knew that cardiac-gating could help to avoid the motion artifacts and bias of the diffusion tensor parameters. But for the tractography of CST, the current image acquisition methods with high angular resolution or averaging seemed already able to overcome the effects of pulsatile motion, and cardiac-gating can’t make significant contribution. In part 2 of this study, we focused on another approach for improving the DWI image quality, the denoising algorithm POAS (Position-orientation adaptive smoothing). The DWI suffers more easily from artifacts during acquisition and always has a low SNR, which might lead to erroneous decisions in the determination of the diffusion metrics and fiber tractography in clinics. Although plenty of denoising methods have been proposed up to now, POAS came into consideration because POAS reduces image noise in the whole brain with edge-preserving properties and avoids blurring. In this study, we found that POAS reduced noise directly on DWIs and improved SNR dramatically, and consequently, POAS also reduced the bias and variation of the diffusion tensor quantities, such as FA. In tractography, after processing with POAS, a greater fiber volume of the CST was reconstructed compared to the original datasets. At the same time, reconstruction of the CST in POAS-processed datasets gained more stability and less variability which could compensate for the effect of a high angular resolution in some degree. In the future, the application of POAS in pathological cases should be conducted to verify its practical value in the clinics. In neuroscience, the image quality of DWI and the precision of the diffusion tensor parameters are essential. Both of the above approaches could be applied to optimize the analysis. During neurosurgical operations, the accuracy of tract reconstruction, or space occupation, has more importance. So POAS could be considered to improve tractography while cardiac-gating did not have significant effects. More advanced approaches should be further investigated

Analyse et reconstruction de faisceaux de la matière blanche

L'imagerie par résonance magnétique de diffusion (IRMd) est une modalité d'acquisition permettant de sonder les tissus biologiques et d'en extraire une variété d'informations sur le mouvement microscopique des molécules d'eau. Plus spécifiquement à l'imagerie médicale, l'IRMd permet l'investigation des structures fibreuses de nombreux organes et facilite la compréhension des processus cognitifs ou au diagnostic. Dans le domaine des neurosciences, l'IRMd est cruciale à l'exploration de la connectivité structurelle de la matière blanche. Cette thèse s'intéresse plus particulièrement à la reconstruction de faisceaux de la matière blanche ainsi qu'à leur analyse. Toute la complexité du traitement des données commençant au scanneur jusqu'à la création d'un tractogramme est extrêmement importante. Par contre, l'application spécifique de reconstruction des faisceaux anatomiques plausibles est ultimement le véritable défi de l'IRMd. L'optimisation des paramètres de la tractographie, le processus de segmentation manuelle ou automatique ainsi que l'interprétation des résultats liée à ces faisceaux sont toutes des étapes du processus avec leurs lots de difficultés

Diffusion and Perfusion MRI in Paediatric Posterior Fossa Tumours

Brain tumours in children frequently occur in the posterior fossa. Most undergo surgical resection, after which up to 25% develop cerebellar mutism syndrome (CMS), characterised by mutism, emotional lability and cerebellar motor signs; these typically improve over several months. This thesis examines the application of diffusion (dMRI) and arterial spin labelling (ASL) perfusion MRI in children with posterior fossa tumours. dMRI enables non-invasive in vivo investigation of brain microstructure and connectivity by a computational process known as tractography. The results of a unique survey of British neurosurgeons’ attitudes towards tractography are presented, demonstrating its widespread adoption and numerous limitations. State-of-the-art modelling of dMRI data combined with tractography is used to probe the anatomy of cerebellofrontal tracts in healthy children, revealing the first evidence of a topographic organization of projections to the frontal cortex at the superior cerebellar peduncle. Retrospective review of a large institutional series shows that CMS remains the most common complication of posterior fossa tumour resection, and that surgical approach does not influence surgical morbidity in this cohort. A prospective case-control study of children with posterior fossa tumours treated at Great Ormond Street Hospital is reported, in which children underwent longitudinal MR imaging at three timepoints. A region-of-interest based approach did not reveal any differences in dMRI metrics with respect to CMS status. However, the candidate also conducted an analysis of a separate retrospective cohort of medulloblastoma patients at Stanford University using an automated tractography pipeline. This demonstrated, in unprecedented spatiotemporal detail, a fine-grained evolution of changes in cerebellar white matter tracts in children with CMS. ASL studies in the prospective cohort showed that following tumour resection, increases in cortical cerebral blood flow were seen alongside reductions in blood arrival time, and these effects were modulated by clinical features of hydrocephalus and CMS. The results contained in this thesis are discussed in the context of the current understanding of CMS, and the novel anatomical insights presented provide a foundation for future research into the condition