Creation of Computerized 3D MRI-Integrated Atlases of the Human Basal Ganglia and Thalamus

Functional brain imaging and neurosurgery in subcortical areas often requires visualization of brain nuclei beyond the resolution of current magnetic resonance imaging (MRI) methods. We present techniques used to create: (1) a lower resolution 3D atlas, based on the Schaltenbrand and Wahren print atlas, which was integrated into a stereotactic neurosurgery planning and visualization platform (VIPER); and (2) a higher resolution 3D atlas derived from a single set of manually segmented histological slices containing nuclei of the basal ganglia, thalamus, basal forebrain, and medial temporal lobe. Both atlases were integrated to a canonical MRI (Colin27) from a young male participant by manually identifying homologous landmarks. The lower resolution atlas was then warped to fit the MRI based on the identified landmarks. A pseudo-MRI representation of the high-resolution atlas was created, and a non-linear transformation was calculated in order to match the atlas to the template MRI. The atlas can then be warped to match the anatomy of Parkinson's disease surgical candidates by using 3D automated non-linear deformation methods. By way of functional validation of the atlas, the location of the sensory thalamus was correlated with stereotactic intraoperative physiological data. The position of subthalamic electrode positions in patients with Parkinson's disease was also evaluated in the atlas-integrated MRI space. Finally, probabilistic maps of subthalamic stimulation electrodes were developed, in order to allow group analysis of the location of contacts associated with the best motor outcomes. We have therefore developed, and are continuing to validate, a high-resolution computerized MRI-integrated 3D histological atlas, which is useful in functional neurosurgery, and for functional and anatomical studies of the human basal ganglia, thalamus, and basal forebrain

A Multi-Path Approach to Histology Volume Reconstruction

This paper presents a method for correcting erratic pairwise registrations when reconstructing a volume from 2D histology slices. Due to complex and unpredictable alterations of the content of histology images, a pairwise rigid registration between two adjacent slices may fail systematically. Conversely, a neighbouring registration, which potentially involves one of these two slices, will work. This grounds our approach: using correct spatial correspondences established through neighbouring registrations to account for direct failures. We propose to search the best alignment of every couple of adjacent slices from a finite set of transformations that involve neighbouring slices in a transitive fashion. Using the proposed method, we obtained reconstructed volumes with increased coherence compared to the classical pairwise approach, both in synthetic and real data

A New Approach for Deep Gray Matter Analysis Using Partial-Volume Estimation.

INTRODUCTION: The existence of partial volume effects in brain MR images makes it challenging to understand physio-pathological alterations underlying signal changes due to pathology across groups of healthy subjects and patients. In this study, we implement a new approach to disentangle gray and white matter alterations in the thalamus and the basal ganglia. The proposed method was applied to a cohort of early multiple sclerosis (MS) patients and healthy subjects to evaluate tissue-specific alterations related to diffuse inflammatory or neurodegenerative processes. METHOD: Forty-three relapsing-remitting MS patients and nineteen healthy controls underwent 3T MRI including: (i) fluid-attenuated inversion recovery, double inversion recovery, magnetization-prepared gradient echo for lesion count, and (ii) T1 relaxometry. We applied a partial volume estimation algorithm to T1 relaxometry maps to gray and white matter local concentrations as well as T1 values characteristic of gray and white matter in the thalamus and the basal ganglia. Statistical tests were performed to compare groups in terms of both global T1 values, tissue characteristic T1 values, and tissue concentrations. RESULTS: Significant increases in global T1 values were observed in the thalamus (p = 0.038) and the putamen (p = 0.026) in RRMS patients compared to HC. In the Thalamus, the T1 increase was associated with a significant increase in gray matter characteristic T1 (p = 0.0016) with no significant effect in white matter. CONCLUSION: The presented methodology provides additional information to standard MR signal averaging approaches that holds promise to identify the presence and nature of diffuse pathology in neuro-inflammatory and neurodegenerative diseases

Ultra-High Field Magnetic Resonance Imaging for Stereotactic Neurosurgery

Stereotactic neurosurgery is a subspecialty within neurosurgery concerned with accurate targeting of brain structures. Deep brain stimulation (DBS) is a specific type of stereotaxy in which electrodes are implanted in deep brain structures. It has proven therapeutic efficacy in Parkinson’s disease and Essential Tremor, but with an expanding number of indications under evaluation including Alzheimer’s disease, depression, epilepsy, and obesity, many more Canadians with chronic health conditions may benefit. Accurate surgical targeting is crucial with millimeter deviations resulting in unwanted side effects including muscle contractions, or worse, vessel injury. Lack of adequate visualization of surgical targets with conventional lower field strengths (1.5/3 Tesla) has meant that standard-of-care surgical treatment has relied on indirect targeting using standardized landmarks to find a correspondence with a histological ``template\u27\u27 of the brain. For this reason, these procedures routinely require awake testing and microelectrode recording, which increases operating room time, patient discomfort, and risk of complications. Advances in ultra-high field (\u3e= 7 Tesla or 7T) imaging have important potential implications for targeting structures enabling better visualization as a result of its increased (sub-millimeter) spatial resolution, tissue contrast, and signal-to-noise ratio. The work in this thesis explores ways in which ultra-high field magnetic resonance imaging can be integrated into the practice of stereotactic neurosurgery. In Chapter 2, an ultra-high field MRI template is integrated into the surgical workflow to assist with planning for deep brain stimulation surgery cases. Chapter 3 describes a novel anatomical fiducial placement protocol that is developed, validated, and used prospectively to quantify the limits of template-assisted surgical planning. In Chapter 4, geometric distortions at 7T that may impede the ability to perform accurate surgical targeting are characterized in participant data, and generally noted to be away from areas of interest for stereotactic targeting. Finally, Chapter 5 discusses a number of important stereotactic targets that are directly visualized and described for the first time in vivo, paving the way for patient-specific surgical planning using ultra-high field MRI

Digital Atlasing and Standardization in the Mouse Brain

Computer Systems, Imagery and Medi

Registration of 3D fetal neurosonography and MRI.

We propose a method for registration of 3D fetal brain ultrasound with a reconstructed magnetic resonance fetal brain volume. This method, for the first time, allows the alignment of models of the fetal brain built from magnetic resonance images with 3D fetal brain ultrasound, opening possibilities to develop new, prior information based image analysis methods for 3D fetal neurosonography. The reconstructed magnetic resonance volume is first segmented using a probabilistic atlas and a pseudo ultrasound image volume is simulated from the segmentation. This pseudo ultrasound image is then affinely aligned with clinical ultrasound fetal brain volumes using a robust block-matching approach that can deal with intensity artefacts and missing features in the ultrasound images. A qualitative and quantitative evaluation demonstrates good performance of the method for our application, in comparison with other tested approaches. The intensity average of 27 ultrasound images co-aligned with the pseudo ultrasound template shows good correlation with anatomy of the fetal brain as seen in the reconstructed magnetic resonance image

The Connectivity of the Human Pulvinar: A Diffusion Tensor Imaging Tractography Study

Previous studies in nonhuman primates and cats have shown that the pulvinar receives input from various cortical and subcortical areas involved in vision. Although the contribution of the pulvinar to human vision remains to be established, anatomical tracer and electrophysiological animal studies on cortico-pulvinar circuits suggest an important role of this structure in visual spatial attention, visual integration, and higher-order visual processing. Because methodological constraints limit investigations of the human pulvinar's function, its role could, up to now, only be inferred from animal studies. In the present study, we used an innovative imaging technique, Diffusion Tensor Imaging (DTI) tractography, to determine cortical and subcortical connections of the human pulvinar. We were able to reconstruct pulvinar fiber tracts and compare variability across subjects in vivo. Here we demonstrate that the human pulvinar is interconnected with subcortical structures (superior colliculus, thalamus, and caudate nucleus) as well as with cortical regions (primary visual areas (area 17), secondary visual areas (area 18, 19), visual inferotemporal areas (area 20), posterior parietal association areas (area 7), frontal eye fields and prefrontal areas). These results are consistent with the connectivity reported in animal anatomical studies