Towards construction of an ideal stereotactic brain atlas

Corpus callosum area and sectioning: a radioanatomical study correlated with MRI and cadaver morphometry

PURPOSE

The corpus callosum (CC) is the primary interhemispheric connection between the two cerebral hemispheres. Besides their similar morphological characters, there are differences in their measurements. This study aimed to divide the CC into groups using planes based on the anterior commissure (AC) and posterior commissure (PC) and to detect differences in CC magnetic resonance imaging (MRI) and cadaver samples between these groups.

METHODS

The study included 80 patients (40 male and 40 female patients) who underwent normal MRI in the midsagittal plane, and 38 cerebral hemispheres from 40 adult cadaver brains, with each hemisected in the midsagittal plane. The medial surface of the CC was divided vertically into three parts (the anterior, middle, and posterior zones) according to the AC and PC. Areas and parameters were measured in both the cadaveric hemispheres and patient MRI images.

RESULTS

The total CC area and CC areas between, anterior, and posterior to the AC-PC vertical lines were the same in both the MRI and cadaver samples. In addition, morphometric measurements like the CC length, AC-PC length, and CC height at the AC and PC vertical lines, and their correlations were also found to be similar between the MRI and cadaver samples.

CONCLUSION

This study proposes three areas according to AC and PC classification (anterior, middle, and posterior). This new proposed classification is suitable for stereotactic interventions and is useful for obtaining data from MRI images. However, it should be kept in mind that there may be changes and variations.

Towards an Architecture of a Multi-purpose, User-Extendable Reference Human Brain Atlas

Human brain atlas development is predominantly research-oriented and the use of atlases in clinical practice is limited. Here I introduce a new definition of a reference human brain atlas that serves education, research and clinical applications, and is extendable by its user. Subsequently, an architecture of a multi-purpose, user-extendable reference human brain atlas is proposed and its implementation discussed. The human brain atlas is defined as a vehicle to gather, present, use, share, and discover knowledge about the human brain with highly organized content, tools enabling a wide range of its applications, massive and heterogeneous knowledge database, and means for content and knowledge growing by its users. The proposed architecture determines major components of the atlas, their mutual relationships, and functional roles. It contains four functional units, core cerebral models, knowledge database, research and clinical data input and conversion, and toolkit (supporting processing, content extension, atlas individualization, navigation, exploration, and display), all united by a user interface. Each unit is described in terms of its function, component modules and sub-modules, data handling, and implementation aspects. This novel architecture supports brain knowledge gathering, presentation, use, sharing, and discovery and is broadly applicable and useful in student- and educator-oriented neuroeducation for knowledge presentation and communication, research for knowledge acquisition, aggregation and discovery, and clinical applications in decision making support for prevention, diagnosis, treatment, monitoring, and prediction. It establishes a backbone for designing and developing new, multi-purpose and user-extendable brain atlas platforms, serving as a potential standard across labs, hospitals, and medical schools.

Advanced MRI techniques for transcranial high intensity focused ultrasound targeting

Magnetic resonance guided high intensity focused ultrasound is a novel, non-invasive, image-guided procedure that is able to ablate intracranial tissue with submillimetre precision. It is currently FDA approved for essential tremor and tremor dominant Parkinson’s disease. The aim of this update is to review the limitations of current landmark-based targeting techniques of the ventral intermediate nucleus and demonstrate the role of emerging imaging techniques that are relevant for both magnetic resonance guided high intensity focused ultrasound and deep brain stimulation. A significant limitation of standard MRI sequences is that the ventral intermediate nucleus, dentatorubrothalamic tract, and other deep brain nuclei cannot be clearly identified. This paper provides original, annotated images demarcating the ventral intermediate nucleus, dentatorubrothalamic tract, and other deep brain nuclei on advanced MRI sequences such as fast grey matter acquisition T1 inversion recovery, quantitative susceptibility mapping, susceptibility weighted imaging, and diffusion tensor imaging tractography. Additionally, the paper reviews clinical efficacy of targeting with these novel MRI techniques when compared to current established landmark-based targeting techniques. The paper has widespread applicability to both deep brain stimulation and magnetic resonance guided high intensity focused ultrasound.

Microsurgical anatomy of the subthalamic nucleus: correlating fiber dissection results with 3-T magnetic resonance imaging using neuronavigation

OBJECTIVE

Despite the extensive use of the subthalamic nucleus (STN) as a deep brain stimulation (DBS) target, unveiling the extensive functional connectivity of the nucleus, relating its structural connectivity to the stimulation-induced adverse effects, and thus optimizing the STN targeting still remain challenging. Mastering the 3D anatomy of the STN region should be the fundamental goal to achieve ideal surgical results, due to the deep-seated and obscure position of the nucleus, variable shape and relatively small size, oblique orientation, and extensive structural connectivity. In the present study, the authors aimed to delineate the 3D anatomy of the STN and unveil the complex relationship between the anatomical structures within the STN region using fiber dissection technique, 3D reconstructions of high-resolution MRI, and fiber tracking using diffusion tractography utilizing a generalized q-sampling imaging (GQI) model.

METHODS

Fiber dissection was performed in 20 hemispheres and 3 cadaveric heads using the Klingler method. Fiber dissections of the brain were performed from all orientations in a stepwise manner to reveal the 3D anatomy of the STN. In addition, 3 brains were cut into 5-mm coronal, axial, and sagittal slices to show the sectional anatomy. GQI data were also used to elucidate the connections among hubs within the STN region.

RESULTS

The study correlated the results of STN fiber dissection with those of 3D MRI reconstruction and tractography using neuronavigation. A 3D terrain model of the subthalamic area encircling the STN was built to clarify its anatomical relations with the putamen, globus pallidus internus, globus pallidus externus, internal capsule, caudate nucleus laterally, substantia nigra inferiorly, zona incerta superiorly, and red nucleus medially. The authors also describe the relationship of the medial lemniscus, oculomotor nerve fibers, and the medial forebrain bundle with the STN using tractography with a 3D STN model.

CONCLUSIONS

This study examines the complex 3D anatomy of the STN and peri-subthalamic area. In comparison with previous clinical data on STN targeting, the results of this study promise further understanding of the structural connections of the STN, the exact location of the fiber compositions within the region, and clinical applications such as stimulation-induced adverse effects during DBS targeting.

Human brain atlasing: past, present and future

We have recently witnessed an explosion of large-scale initiatives and projects addressing mapping, modeling, simulation and atlasing of the human brain, including the BRAIN Initiative, the Human Brain Project, the Human Connectome Project (HCP), the Big Brain, the Blue Brain Project, the Allen Brain Atlas, the Brainnetome, among others. Besides these large and international initiatives, there are numerous mid-size and small brain atlas-related projects. My contribution to these global efforts has been to create adult human brain atlases in health and disease, and to develop atlas-based applications. For over two decades with my R&D lab I developed 35 brain atlases, licensed to 67 companies and made available in about 100 countries. This paper has two objectives. First, it provides an overview of the state of the art in brain atlasing. Second, as it is already 20 years from the release of our first brain atlas, I summarise my past and present efforts, share my experience in atlas creation, validation and commercialisation, compare with the state of the art, and propose future directions.

From chalkboard, slides, and paper to e-learning: How computing technologies have transformed anatomical sciences education

Until the late-twentieth century, primary anatomical sciences education was relatively unenhanced by advanced technology and dependent on the mainstays of printed textbooks, chalkboard- and photographic projection-based classroom lectures, and cadaver dissection laboratories. But over the past three decades, diffusion of innovations in computer technology transformed the practices of anatomical education and research, along with other aspects of work and daily life. Increasing adoption of first-generation personal computers (PCs) in the 1980s paved the way for the first practical educational applications, and visionary anatomists foresaw the usefulness of computers for teaching. While early computers lacked high-resolution graphics capabilities and interactive user interfaces, applications with video discs demonstrated the practicality of programming digital multimedia linking descriptive text with anatomical imaging. Desktop publishing established that computers could be used for producing enhanced lecture notes, and commercial presentation software made it possible to give lectures using anatomical and medical imaging, as well as animations. Concurrently, computer processing supported the deployment of medical imaging modalities, including computed tomography, magnetic resonance imaging, and ultrasound, that were subsequently integrated into anatomy instruction. Following its public birth in the mid-1990s, the World Wide Web became the ubiquitous multimedia networking technology underlying the conduct of contemporary education and research. Digital video, structural simulations, and mobile devices have been more recently applied to education. Progressive implementation of computer-based learning methods interacted with waves of ongoing curricular change, and such technologies have been deemed crucial for continuing medical education reforms, providing new challenges and opportunities for anatomical sciences educators. Anat Sci Educ 9: 583-602. © 2016 American Association of Anatomists.

MIDA: A Multimodal Imaging-Based Detailed Anatomical Model of the Human Head and Neck

Computational modeling and simulations are increasingly being used to complement experimental testing for analysis of safety and efficacy of medical devices. Multiple voxel- and surface-based whole- and partial-body models have been proposed in the literature, typically with spatial resolution in the range of 1-2 mm and with 10-50 different tissue types resolved. We have developed a multimodal imaging-based detailed anatomical model of the human head and neck, named "MIDA". The model was obtained by integrating three different magnetic resonance imaging (MRI) modalities, the parameters of which were tailored to enhance the signals of specific tissues: i) structural T1- and T2-weighted MRIs; a specific heavily T2-weighted MRI slab with high nerve contrast optimized to enhance the structures of the ear and eye; ii) magnetic resonance angiography (MRA) data to image the vasculature, and iii) diffusion tensor imaging (DTI) to obtain information on anisotropy and fiber orientation. The unique multimodal high-resolution approach allowed resolving 153 structures, including several distinct muscles, bones and skull layers, arteries and veins, nerves, as well as salivary glands. The model offers also a detailed characterization of eyes, ears, and deep brain structures. A special automatic atlas-based segmentation procedure was adopted to include a detailed map of the nuclei of the thalamus and midbrain into the head model. The suitability of the model to simulations involving different numerical methods, discretization approaches, as well as DTI-based tensorial electrical conductivity, was examined in a case-study, in which the electric field was generated by transcranial alternating current stimulation. The voxel- and the surface-based versions of the models are freely available to the scientific community.

A Three-dimensional Deformable Brain Atlas for DBS Targeting. I. Methodology for Atlas Creation and Artifact Reduction

Background:

Targeting in deep brain stimulation (DBS) relies heavily on the ability to accurately localize particular anatomic brain structures. Direct targeting of subcortical structures has been limited by the ability to visualize relevant DBS targets.

Methods and Results:

In this work, we describe the development and implementation, of a methodology utilized to create a three dimensional deformable atlas for DBS surgery. This atlas was designed to correspond to the print version of the Schaltenbrand-Bailey atlas structural contours. We employed a smoothing technique to reduce artifacts inherent in the print version.

Conclusions:

We present the methodology used to create a three dimensional patient specific DBS atlas which may in the future be tested for clinical utility.

Generation of individualized thalamus target maps by using statistical shape models and thalamocortical tractography

BACKGROUND AND PURPOSE

Neurosurgical interventions of the thalamus rely on transferring stereotactic coordinates from an atlas onto the patient's MR brain images. We propose a prototype application for performing thalamus target map individualization by fusing patient-specific thalamus geometric information and diffusion tensor tractography.

MATERIALS AND METHODS

Previously, our workgroup developed a thalamus atlas by fusing anatomic information from 7 histologically processed thalami. Thalamocortical connectivity maps were generated from DTI scans of 40 subjects by using a previously described procedure and were mapped to a standard neuroimaging space. These data were merged into a statistical shape model describing the morphologic variability of the thalamic outline, nuclei, and connectivity landmarks. This model was used to deform the atlas to individual images. Postmortem MR imaging scans were used to quantify the accuracy of nuclei predictions.

RESULTS

Reliable tractography-based markers were located in the ventral lateral thalamus, with the somatosensory connections coinciding with the VPLa and VPLp nuclei; and motor/premotor connections, with the VLpv and VLa nuclei. Prediction accuracy of thalamus outlines was higher with the SSM approach than the ACPC alignment of data (0.56 mm versus 1.24; Dice overlap: 0.87 versus 0.7); for individual nuclei: 0.65 mm, Dice: 0.63 (SSM); 1.24 mm, Dice: 0.4 (ACPC).

CONCLUSIONS

Previous studies have already applied DTI to the thalamus. As a further step in this direction, we demonstrate a hybrid approach by using statistical shape models, which have the potential to cope with intersubject variations in individual thalamus geometry.

A three-dimensional digital segmented and deformable brain atlas of the domestic pig

We used high-magnetic field (4.7 T) magnetic resonance imaging (MRI) to build the first high-resolution (100 microm x 150 microm x 100 microm) three-dimensional (3D) digital atlas in stereotaxic coordinates of the brain of a female domestic pig (Sus scrofa domesticus). This atlas was constructed from one hemisphere which underwent a symmetrical transformation through the midsagittal plane. Concomitant construction of a 3D histological atlas based on the same scheme facilitated control of deep brain structure delimitation and enabled cortical mapping to be achieved. The atlas contains 178 individual cerebral structures including 42 paired and 9 single deep brain structures, 5 ventricular system areas, 6 paired deep cerebellar nuclei, 12 cerebellar lobules and 28 cortical areas per hemisphere. Given the increasing importance of pig brains in medical research, this atlas should be a useful tool for intersubject normalization in anatomical imaging as well as for precisely localizing brain areas in functional MR studies or electrode implantation trials. The atlas can be freely downloaded from our institution's Website.

MR imaging of ventral thalamic nuclei

BACKGROUND AND PURPOSE

The Vim and VPL are important target regions of the thalamus for DBS. Our aim was to clarify the anatomic locations of the ventral thalamic nuclei, including the Vim and VPL, on MR imaging.

MATERIALS AND METHODS

Ten healthy adult volunteers underwent MR imaging by using a 1.5T whole-body scanner. The subjects included 5 men and 5 women, ranging in age from 23 to 38 years, with a mean age of 28 years. The subjects were imaged with STIR sequences (TR/TE/TI = 3200 ms/15 ms/120 ms) and DTI with a single-shot echo-planar imaging technique (TR/TE = 6000 ms/88 ms, b-value = 2000 s/mm(2)). Tractography of the CTC and spinothalamic pathway was used to identify the thalamic nuclei. Tractography of the PT was used as a reference, and the results were superimposed on the STIR image, FA map, and color-coded vector map.

RESULTS

The Vim, VPL, and PT were all in close contact at the level through the ventral thalamus. The Vim was bounded laterally by the PT and medially by the IML. The VPL was bounded anteriorly by the Vim, laterally by the internal capsule, and medially by the IML. The posterior boundary of the VPL was defined by a band of low FA that divided the VPL from the pulvinar.

CONCLUSIONS

The ventral thalamic nuclei can be identified on MR imaging by using reference structures such as the PT and the IML.

Quantification of spatial consistency in the Talairach and Tournoux stereotactic atlas

BACKGROUND

The Talairach-Tournoux (TT) atlas is one of the most prevalent brain atlases. Although its spatial inconsistencies were reported earlier, there has been no systematic quantification of them across the entire atlas, which is addressed here.

METHOD

The consistency of the TT atlas, defined as uniformity of labeling across all three orthogonal atlas orientations, is calculated and presented as maps. It is analyzed in function of discrepancy measuring spatial offset in labeling.

FINDINGS

The TT atlas has 27.4% consistency and 37.7% inconsistency. The most consistent structure is the thalamus (85.7% consistency, 5.4% inconsistency). The consistency of the basal ganglia is good. For 3-mm discrepancy, the inconsistency of major subcortical gray matter structures is very low: 0% (globus pallidus medial and putamen), 0.7% (thalamus), 2.2% (globus pallidus lateral), 4.8% (hippocampus) and 4.9% (caudate nucleus). The inconsistency of all subcortical structures is relatively high (16.8%), caused by a very high inconsistency of white matter tracts. The consistency of stereotactic targets is 69.2% (GPi), 50.0% (STN) and 42.9% (VPL). The overall TT consistency increases by 20% for 1-mm discrepancy, constantly grows by 10% for 2-4-mm discrepancy and slows down to 3% for 5-6-mm discrepancy.

CONCLUSION

This work enhances our understanding of the TT atlas and its variable spatial consistency. It is helpful in using multiple atlas orientations simultaneously. It also may be useful in atlas interpolation and construction of a fully consistent 3D atlas. As the consistency of the main stereotactic targets is medium, the use of the TT atlas in stereotactic procedures requires a great deal of care and understanding of its limitations.

Automated optimization of subcortical cerebral MR imaging-atlas coregistration for improved postoperative electrode localization in deep brain stimulation

BACKGROUND AND PURPOSE

The efficacy of deep brain stimulation in treating movement disorders depends critically on electrode localization, which is conventionally described by using coordinates relative to the midcommissural point. This approach requires manual measurement and lacks spatial normalization of anatomic variances. Normalization is based on intersubject spatial alignment (coregistration) of corresponding brain structures by using different geometric transformations. Here, we have devised and evaluated a scheme for automated subcortical optimization of coregistration (ASOC), which maximizes patient-to-atlas normalization accuracy of postoperative structural MR imaging into the standard Montreal Neurologic Institute (MNI) space for the basal ganglia.

MATERIALS AND METHODS

Postoperative T2-weighted MR imaging data from 39 patients with Parkinson disease and 32 patients with dystonia were globally normalized, representing the standard registration (control). The global transformations were regionally refined by 2 successive linear registration stages (RSs) (ASOC-1 and 2), focusing progressively on the basal ganglia with 2 anatomically selective brain masks, which specify the reference volume (weighted cost function). Accuracy of the RSs was quantified by spatial dispersion of 16 anatomic landmarks and their root-mean-square errors (RMSEs) with respect to predefined MNI-based reference points. The effects of CSF volume, age, and sex on RMSEs were calculated.

RESULTS

Mean RMSEs differed significantly (P < .001) between the global control (4.2 +/- 2.0 mm), ASOC-1 (1.92 +/- 1.02 mm), and ASOC-2 (1.29 +/- 0.78 mm).

CONCLUSIONS

The present method improves the registration accuracy of postoperative structural MR imaging data into MNI space within the basal ganglia, allowing automated normalization with increased precision at stereotactic targets, and enables lead-contact localization in MNI coordinates for quantitative group analysis.

Effect of brain shift on the creation of functional atlases for deep brain stimulation surgery

PURPOSE

In the recent past many groups have tried to build functional atlases of the deep brain using intra-operatively acquired information such as stimulation responses or micro-electrode recordings. An underlying assumption in building such atlases is that anatomical structures do not move between pre-operative imaging and intra-operative recording. In this study, we present evidences that this assumption is not valid. We quantify the effect of brain shift between pre-operative imaging and intra-operative recording on the creation of functional atlases using intra-operative somatotopy recordings and stimulation response data.

METHODS

A total of 73 somatotopy points from 24 bilateral subthalamic nucleus (STN) implantations and 52 eye deviation stimulation response points from 17 bilateral STN implantations were used. These points were spatially normalized on a magnetic resonance imaging (MRI) atlas using a fully automatic non-rigid registration algorithm. Each implantation was categorized as having low, medium or large brain shift based on the amount of pneumocephalus visible on post-operative CT. The locations of somatotopy clusters and stimulation maps were analyzed for each category.

RESULTS

The centroid of the large brain shift cluster of the somatotopy data (posterior, lateral, inferior: 3.06, 11.27, 5.36 mm) was found posterior, medial and inferior to that of the medium cluster (2.90, 13.57, 4.53 mm) which was posterior, medial and inferior to that of the low shift cluster (1.94, 13.92, 3.20 mm). The coordinates are referenced with respect to the mid-commissural point. Euclidean distances between the centroids were 1.68, 2.44 and 3.59 mm, respectively for low-medium, medium-large and low-large shift clusters. We found similar trends for the positions of the stimulation maps. The Euclidian distance between the highest probability locations on the low and medium-large shift maps was 4.06 mm.

CONCLUSION

The effect of brain shift in deep brain stimulation (DBS) surgery has been demonstrated using intra-operative somatotopy recordings as well as stimulation response data. The results not only indicate that considerable brain shift happens before micro-electrode recordings in DBS but also that brain shift affects the creation of accurate functional atlases. Therefore, care must be taken when building and using such atlases of intra-operative data and also when using intra-operative data to validate anatomical atlases.