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Human brain atlases have been evolving tremendously, propelled recently by brain big projects, and driven by sophisticated imaging techniques, advanced brain mapping methods, vast data, analytical strategies, and powerful computing. We overview here this evolution in four categories: content, applications, functionality, and availability, in contrast to other works limited mostly to content. Four atlas generations are distinguished: early cortical maps, print stereotactic atlases, early digital atlases, and advanced brain atlas platforms, and 5 avenues in electronic atlases spanning the last two generations. Content-wise, new electronic atlases are categorized into eight groups considering their scope, parcellation, modality, plurality, scale, ethnicity, abnormality, and a mixture of them. Atlas content developments in these groups are heading in 23 various directions. Application-wise, we overview atlases in neuroeducation, research, and clinics, including stereotactic and functional neurosurgery, neuroradiology, neurology, and stroke. Functionality-wise, tools and functionalities are addressed for atlas creation, navigation, individualization, enabling operations, and application-specific. Availability is discussed in media and platforms, ranging from mobile solutions to leading-edge supercomputers, with three accessibility levels. The major application-wise shift has been from research to clinical practice, particularly in stereotactic and functional neurosurgery, although clinical applications are still lagging behind the atlas content progress. Atlas functionality also has been relatively neglected until recently, as the management of brain data explosion requires powerful tools. We suggest that the future human brain atlas-related research and development activities shall be founded on and benefit from a standard framework containing the core virtual brain model cum the brain atlas platform general architecture.

The knowledge of cerebrovascular variants is essential in education, training, diagnosis and treatment. The current way of presentation of vasculature and, particularly, vascular variants is insufficient. Our purpose is to construct a three-dimensional (3D) interactive atlas of cerebral arterial variants along with exploration tools allowing the investigator just with a few clicks to better and faster understand the variants and their spatial relationships. A 3D model of the cerebral arterial system created earlier, fully labeled with names and diameters, is used as a reference. As the vast material about vascular variability is incomplete and not fully documented, our approach synthesizes variants in 3D based on existing knowledge. The variants are created from literature using a dedicated vascular editor and embedded into the reference model. Sixty 3D variants and branching patterns are created including the internal carotid, middle cerebral, anterior cerebral, posterior cerebral, vertebral and basilar arteries, and circle of Willis. Their prevalence rates are given. The atlas is developed to explore the variants individually or embedded into the reference vasculature. Real-time interactive manipulation of variants and reference vasculature (rotate/zoom/pan/view) is provided. This atlas facilitates the investigator to easily get familiarized with the variants and rapidly explore them. It aids in presentation of vascular variants and understanding their spatial relationships either individually or embedded into the surrounding reference cerebrovasculature. It is useful for medical students, educators to prepare teaching materials, and clinicians for scan interpretation. It is easily extensible with additional variant instances, new variants, branching patterns, and supporting textual materials.

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.

Background: This work quantifies and visualises 3D inconsistencies of the ventrointermediate nucleus (VIM) of the thalamus, including the VIM externum (VIMe) and VIM internum (VIMi), in the Schaltenbrand-Wahren (SW) brain atlas., Method: For each VIM, VIMe, VIMi the 3D models, 3D-A, 3D-C and 3D-S were reconstructed from the SW axial, coronal and sagittal microseries, respectively, by applying a shape-based method. All 3D models, placed in the SW coordinate system, were compared quantitatively in terms of location (centroids), size (volumes), shape (normalised eigen values), orientation (eigen vectors), and mutual spatial relationships (overlaps and inclusions)., Findings: The reconstructed 3D models differ significantly in location, size, shape, and inclusion rate. The centroid of 3D-A/VIM differs considerably from those of 3D-C/VIM and 3D-S/VIM. The difference between the centroids of 3D-C/VIM and 3D-S/VIM is in laterality only: that of 3D-C/VIM is located more medially (11.85 mm) than that of 3D-S/VIM (14.62 mm). 3D-A/VIM has the smallest volume (69.00 mm(3)); 3D-C/VIM is 3.71 and 3D-S/VIM 3.89 times larger. The overlap is also highly variable: 104.88 mm(3) for 3D-C/VIM with 3D-S/VIM, and very low (3.22 and 7.45 mm(3)) when 3D-A/VIM is involved. The highest inclusion rate is for 3D-C/VIM with 3D-S/VIM (39.10 and 40.97%) and the lowest for 3D-A/VIM with 3D-C/VIM (1.26 and 4.66%). The centroid of 3D-A/VIMe differs noticeably from those of 3D-C/VIMe and 3D-S/VIMe. The difference between the centroids of 3D-C/VIMe and 3D-S/VIMe is mainly in laterality: that of 3D-C/VIMe is located more medially (12.91 mm) than that of 3D-S/VIMe (16.65 mm). 3D-A/VIMe has the smallest volume (49.87 mm(3)); 3D-S/VIMe is 3.24 and 3D-C/VIMe 3.36 times larger. The overlap sizes are low: 32.72 mm(3) for 3D-C/VIMe with 3D-S/VIMe, and very low (1.32 and 2.01 mm(3)) when 3D-A/VIMe is involved. The inclusion rates are also low: the highest is for 3D-C/VIMe with 3D-S/VIMe (19.53 and 20.29%) and the lowest for 3D-A/VIMe with 3D-C/VIMe (1.19 and 4.01%). Lateral scaling of the coronal microseries by 1.2897 to match the 3D-C/VIMe and 3D-S/VIMe centroids increases the inclusion rates for the sagittal microseries by more than twice. The volume of scaled 3D-C enlarges to 216.24 mm(3) which is 1.34 bigger than that of 3D-S. There are substantial differences among the centroids of 3D-A/VIMi, 3D-C/VIMi and 3D-S/VIMi. The centroid of 3D-A/VIMi is located more anteriorly (-1.92 mm) than that of 3D-C/VIMi (-5.02 mm). The centroid of 3D-A/VIMi is located more ventrally (2.88 mm) than those of 3D-C/VIMi and 3D-S/VIMi (each at 5.34 mm). 3D-A/VIMi has the smallest volume (19.75 mm(3)); 3D-S/VIMi is 3.23 and 3D-C/VIMi 4.30 times larger. 3D-A/VIMi practically does not overlap with 3D-C/VIMi and 3D-S/VIMi. The inclusion rates for 3D-C/VIMi with 3D-S/VIMi are medium (32.63 and 43.43%)., Conclusion: Each VIM, VIMe, VIMi as reconstructed from the SW atlas has a significant 3D inaccuracy within each orientation and across them. Therefore, absolute and direct reliance on the original SW atlas is unreliable and unsafe, and this atlas has to be used with great care and understanding of its strengths and limitations.

Background: The role of the brain atlas is changing in many aspects with the advancements in stereotactic and functional neurosurgery. Therefore, there is a critical need to construct a new atlas. This paper addresses the definition and construction of an atlas, ideal (in our opinion) for stereotactic and functional neurosurgery. The essence of the new atlas is not only its population-based structural and functional content, but also its continuous "self-updatability" with the new clinical results obtained., Method: The ideal atlas defined here contains four major components: brain models, knowledge database, tools, and clinical results. Towards its creation, a multi-atlas is proposed. The construction of the initial version of the multi-atlas is detailed with the probabilistic functional atlas (PFA), interpolated Talairach-Tournoux atlas, and enhanced Schaltenbrand-Wahren atlas. These atlases are put in a spatial register by matching their AC-PC distances and heights of the thalamus; the Schaltenbrand coronal and sagittal microseries are scaled laterally to match the target structure centroids with the locations of the best targets of the PFA., Findings: Construction of an initial version of the ideal stereotactic atlas is feasible at present from the available resources. To achieve that, our three atlases (PFA, Talairach and Schaltenbrand) are enhanced and combined together. A single lateral scaling factor per target structure is feasible to co-register the Schaltenbrand atlas with PFA in four situations (compensated against the third ventricle, non-compensated, bilateral, and non-bilateral). The STN has to be stretched by 18% more than the VIM on the Schaltenbrand coronal microseries, and the VIM has to be compressed by 13% less than the STN on the Schaltenbrand sagittal microseries., Conclusion: The new multi-atlas can potentially be more useful than the currently employed atlases and will facilitate further development of the ideal atlas for stereotactic and functional neurosurgery.

The Schaltenbrand-Wahren (SW) brain atlas has many limitations: the major two are three-dimensional (3D) inconsistency and spatial sparseness. In this work, we quantify and visualize the 3D inconsistency of the subthalamic nucleus (STN). The STN 3D models, 3D-A, 3D-C and 3D-S, are reconstructed from the SW axial, coronal, and sagittal microseries, respectively, by using a shape-based (NURBS) approach. All three models are placed in the SW coordinate system and compared quantitatively in terms of location (centroids), size (volumes), shape (normalized eigenvalues), orientation (eigenvectors), and mutual spatial relationships (overlaps and inclusions). Analysis is done in 3D within each orientation and across them. A dedicated tool is developed for quantitative validation of 3D modeling. The average error achieved is 0.088 mm, which is at the resolution limit of the digital SW atlas. The reconstructed 3D STN models differ in location, size, shape, orientation, overlap size, and inclusion rate. The 3D-S volume is 1.27 times larger than that of 3D-A and 1.38 times larger than that of 3D-C. The highest overlap size is found between 3D-A and 3D-S. The highest inclusion rates of 52.5 and 66.6% are for 3D-A and 3D-S. 3D-C has the lowest overlap size and results in the lowest inclusion rates (around 20-30%), meaning that 3D-C is substantially displaced in comparison to 3D-A and 3D-S. The lateral centroid coordinate of 3D-C is 9.18 mm while that of 3D-S is 12.17 mm. Each of the 3D models has some limitation: 3D-A in orientation, 3D-C in location, and 3D-S in shape realism. The STN in comparison to the actual almond is smaller, and relatively (i.e. normalized to the same height) 2.2-2.4 times wider and 3.7-5.5 times longer. 3D-C becomes more similar to 3D-S by scaling the SW coronal microseries laterally by 1.3257. Then the lateral coordinates of their centroids coincide, the difference between them in orientation is 0.11 mm, and 3D-S is only 1.06 times larger than the scaled 3D-C. This operation substantially improves registration of the SW atlas with the probabilistic functional atlas. However, 3D visualization shows that both 3D-S and scaled 3D-C models are heavily interwoven resulting in low inclusion rates of about 60%. The STN in the SW atlas shows severe 3D inaccuracy within each orientation and across them, and it has to be employed with great care and understanding of its limitations., (2006 S. Karger AG, Basel)

The Talairach-Tournoux (TT) atlas is probably the most often used brain atlas. We overview briefly the activities in developments of electronic versions of the TT atlas and focus on our more than 10-yr efforts in its continuous enhancement resulting in three main versions: TT-1997, TT-2000, and TT-2004. The recent TT-2004 version is substantially improved over the digitized print original with a higher structure parcellation, better quality and resolution of individual structures, and improved three-dimensional (3D) spatial consistency. It is also much more suitable for developing atlas-based applications owing to pure color-coding (for automatic structure labeling), contour representation (to avoid scan blocking by the overlaid atlas), and color cross-atlas consistency (for the simultaneous use of multiple atlases). We also provide a procedure for 3D spatial consistency improvement and illustrate its use. Finally, we present some of our latest atlas-assisted applications for fast and automatic interpretation of morphological, stroke, and molecular images, and discuss the future steps in TT atlas enhancement.

This paper introduces a method for generation and validation of a probabilistic functional brain atlas of subcortical structures from electrophysiological and neuroimaging data. The method contains three major steps: (1) acquisition of pre, intra, and postoperative multimodal data; (2) selection of an accurate data set for atlas generation; and (3) generation of the atlas from the selected data set. The method is applied to construct the probabilistic functional atlas of the human subthalamic nucleus (STN). The STN atlas has been built from data collected during surgical treatment of 184 patients with Parkinson's disease. It is based on preoperative X-ray ventriculography imaging, intraoperative electrophysiological measurements and X-ray imaging, and postoperative neurological assessment. The atlas features a high resolution of 0.25 mm(3) and a high accuracy of 0.25 mm. It is dynamic and can be rapidly recalculated for arbitrary resolution and extended by adding new patient data. The atlas can easily be reformatted and warped to match patient-specific data. Its applications include planning of subthalamic stimulations and neuroscience research to study functional properties of the STN. The presented method is general and can be applied for constructing human and animal probabilistic brain atlases.

Objective: The Schaltenbrand-Wahren atlas (SWA) is anatomical, sparse and inconsistent in three dimensions. A high-resolution, electrophysiology-based atlas derived from numerous specimens overcomes these limitations. A combined anatomy-physiology atlas leverages the strengths and complementarity of both, which is studied here., Method: An electronic version of the SWA was constructed. A probabilistic functional atlas (PFA) was developed from electrophysiological and neuroimaging data with 0.25 mm3 resolution. A combined atlas is constructed by co-registering the PFA with the SWA by applying linear scaling along the intercommissural distance and the height of the thalamus., Results: An anatomy-physiology atlas is superior to its component atlases. When in register, the anatomical and functional atlases are displayed together and used simultaneously. A structure of interest from the PFA can be displayed with high resolution, compensating for its sparseness in the SWA, while its surrounding structures are obtained from the SWA. The best anatomical and functional targets can be compared: for the subthalamic nucleus, the horizontal and lateral coordinates of the SWA-based and PFA- based targets are approximately the same, while the latter is located 1.3-1.5 mm more anteriorly., Conclusion: An anatomy-physiology atlas may enhance the accuracy of targeting and increase the neurosurgeon's confidence. It also opens new research avenues to serve as a reference for: (1) constructing an extendable atlas by adding new electrophysiological data, (2) comparing anatomical and functional targets, (3) studying and comparing various symptoms, and (4) comparing image-based targets obtained from various modalities., (2004 S. Karger AG, Basel.)

Object: Functional imaging is an established neurosurgical modality for studying the brain in health and disease. Identifying numerous activation loci on many functional images and reading their underlying cortical and subcortical anatomy, coordinates, and anatomical and functional values is a tedious, time-consuming, and error-prone task. In this study the authors propose a novel approach to this problem by using an electronic brain atlas in conjunction with a locus-driven mechanism., Methods: The Brain Atlas for Functional Imaging containing an enhanced and extended electronic version of the Talairach-Tournoux brain atlas was used for analysis. It enables loading of anatomical and functional data, correlation of these data, identification of activation loci, and their labeling with Brodmann areas, gyri, and subcortical structures by means of the atlas. The Talairach proportional grid system transformation is used to register the anatomical and functional data with the atlas. The availability of numerous tools supports this process. A locus-driven mechanism for analysis of activation loci is implemented. Locus placement within the activation region is supported by thresholding, and its location can be further edited in three dimensions on any orthogonal plane. Once all loci are identified and edited, their labels, coordinates, and anatomical/functional values are read automatically and saved in an external file. This mechanism enables the analysis to be performed in an automated, rapid, explicit, three-dimensionally consistent, and user-friendly way., Conclusions: The electronic brain atlas with locus-driven mechanism is a useful tool for localization analysis of functional images.

Objective: This paper describes an Internet portal for stereotactic and functional neurosurgery with a probabilistic functional atlas (PFA) calculated from electrophysiological and neuroimaging data. This portal enables (1) data sharing among neurosurgeons; (2) the calculation of probabilistic functional maps of stereotactic target structures from a neurosurgeon's own data, optionally combined with data from other neurosurgeons, and (3) the construction and development of a PFA of the human brain by the neurosurgical community via the Internet., Method: The overall approach is done in three steps: (1) development and validation of the algorithm for PFA generation; (2) design and development of the portal for stereotactic and functional neurosurgery with tools for the rapid calculation, presentation, and use of the PFA, and (3) portal testing with the initial data acquired for 274 Parkinson's disease patients, 487 hemispheres, and 500 best contacts. This paper covers step 2 and some results from step 3., Results: The Internet portal has been developed in Java and tested with the available data. Functions have been developed for: (1) data input, transfer, and editing; (2) data selection for PFA generation; (3) PFA generation; (4) PFA display and interactive manipulation, and (5) target planning. The portal has been put on the Internet for public use and so far more than 100 users downloaded it., Conclusion: The Internet portal for stereotactic and functional neurosurgery with a PFA potentially increases both the accuracy of targeting and the neurosurgeon's confidence. The portal may be useful for both experienced functional neurosurgeons who have studied numerous cases and novices in the field. The use of the PFA through this portal, and sharing and expanding its content by neurosurgeons represents a paradigm shift from manufacturer centric to community centric., (Copyright 2002 S. Karger AG, Basel)

Objective: This paper introduces a method for localization analysis of functional images assisted by a brain atlas. The usefulness of the system developed, based on this method, is analyzed for human brain mapping and neuroradiology., Materials and Methods: We use an enhanced and extended electronic Talairach-Tournoux brain atlas, containing segmented and labeled subcortical structures, Brodmann's areas, and gyri. The brain atlas serves as a tool for anatomy referencing, segmentation, labeling, registration, and providing 3D anatomical relationships. The process of localization analysis is decomposed into five steps: data loading, feature extraction, data normalization, identification and editing of loci, and getting labels and values. This analysis is supported by near real-time data-to-atlas warping based on the Talairach transformation. Metanalysis is enabled by merging the current and external lists of activation loci., Results: We have designed, developed, tested, and deployed a commercial system for atlas-assisted localization analysis of functional images. This is the first system where an electronic version of the Talairach-Tournoux brain atlas is used interactively for analysis of functional images. This system runs on personal computers and provides functions for a rapid normalization of anatomical and functional volumetric data, data segmentation and labeling, readout of Talairach coordinates, and data display. It also is empowered with several unique features including: interactive warping facilitating fine tuning of the data-to-atlas fit, a backtracking mechanism to compensate for missing landmarks and enhancing the outcome of the overall process of data analysis, navigation on the triplanar formed by the data and the atlas, multiple-images-in-one display with atlas-anatomy-function blending, a fast locus-controlled generation of results, editing of loci, multiple label display, and saving and reading of loci. The system normalizes a single image in near real-time (0.7 s), so analysis of anatomical and functional datasets can be done on-the-fly regardless of the number of slices. The same task performed by the state-of-the-art non-linear registration methods may require up to several days., Conclusions: The system is a useful tool for atlas-assisted localization analysis and a helpful adjunct to function/location metanalysis in human brain mapping research. It is also a step forward in bringing the atlas and the clinical data together within a practical and powerful solution that is fast and flexible, yet low-cost and affordable.

This paper presents a novel approach for the use of the Atlas for Stereotaxy of the Human Brain by Schaltenbrand and Wahren [Stuttgart, Thieme, 1977] for anatomical targeting in functional neurosurgery. We propose to use simultaneously all three electronic axial, coronal and sagittal mutually coregistered Schaltenbrand-Wahren brain atlas microseries. The printed atlas microseries are digitized, extended to cover both hemispheres, contoured, labeled, organized into atlas volumes, and mutually coregistered. The electronic atlas is interactively registered with the data by using the three-dimensional Talairach proportional grid system transformation, followed up by local warping in the region of interest based on any clearly visible landmarks. The detailed targeting steps for pallidotomy, thalamotomy and subthalamotomy are formulated. The potential of this approach is to increase the accuracy of target definition, to decrease the time of the procedure by reducing the number of microelectrode tracts, and to give an extra degree of confidence to the neurosurgeon. The advantages of the approach and the limitations of the Schaltenbrand-Wahren atlas are discussed.

The Electronic Clinical Brain Atlas is a CD-ROM containing several classic brain atlases and a real-time yet simple registration function that deforms the atlases to match them with specific patient studies. This article presents the use of this registration function for functional neurosurgery planning. We first propose the CD-ROM assisted planning procedure, then illustrate it with two cases: a pallidal stimulation and a thalamic stimulation. The Schaltenbrand-Wahren atlas is registered and scaled to conform with an actual patient's data by means of two-dimensional (2-D) local deformations performed in multiple orientations. First a rectangular region of interest (ROI), which is set between any clearly visible landmarks chosen by the neurosurgeon, is measured on the film or scanner console. The corresponding atlas plate with the target is then deformed in real time for the same landmarks, such that the dimensions of this ROI are the same on the film and on the deformed atlas plate. Next the target is set on the deformed (individualized) atlas plate and its coordinates are read. The individualized atlas plate can also be printed on transparent foil and superimposed on the film or, alternatively, this superimposition can be done electronically. The planning steps can be repeated for all available orientations. The proposed atlas-assisted planning procedure extends the traditional use of printed stereotactic atlases by individualizing them to specific patients. The preliminary results show that this procedure may improve the definition of the target and may have several advantages over other approaches, such as indirect measurements based on the AC-PC line or 1-D (intercommissural distance based) scaling. It provides the neurosurgeon with a convenient and immediate means of accessing ancillary data that is usually only available in the printed form.