A. Thirunavuukarasuu

Atlas-assisted localization analysis of functional images

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, Brodmanns 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.

Quantification and visualization of the three- dimensional inconsistency of the subthalamic nucleus in the Schaltenbrand-Wahren brain atlas

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.

A Probabilistic Functional Atlas of the VIM Nucleus Constructed from Pre-, Intra- and Postoperative Electrophysiological and Neuroimaging Data Acquired during the Surgical Treatment of Parkinson’s Disease Patients

We have previously introduced a concept of a probabilistic functional atlas (PFA) to overcome limitations of the current electronic stereotactic brain atlases: anatomical nature, spatial sparseness, inconsistency and lack of population information. The PFA for the STN has already been developed. This work addresses construction of the PFA for the ventrointermediate nucleus (PFA-VIM). The PFA-VIM is constructed from pre-, intra- and postoperative electrophysiological and neuroimaging data acquired during the surgical treatment of Parkinson’s disease patients. The data contain the positions of the chronically implanted electrodes and their best contacts. For each patient, the intercommissural distance, height of the thalamus and width of the third ventricle were measured. An algorithm was developed to convert these data into the PFA-VIM, and to present them on axial, coronal and sagittal planes and in 3-D. The PFA-VIM gives a spatial distribution of the best contacts, and its probability is proportional to best contact concentration in a given location. The region with the highest probability corresponds to the best target. The PFA-VIM is calculated with 0.25-mm3 resolution from 107 best contacts in two situations: with and without lateral compensation against the width of the third ventricle. For the PFA-VIM compensated laterally, the anterior, lateral and dorsal coordinates of the mean value are (in mm) 6.24, 13.83, 1.68 for the left VIM and 6.54, –13.84, 2.10 for the right VIM. The coordinates of the mean value of the highest probability region along with the highest number of the best contacts (P) are: 6.25, 14.25, 1.75, P = 16, for the left VIM, and 6.0, –14.0, 1.00, P = 18, for the right VIM. The coordinate system origin is at the posterior commissure. For the PFA-VIM not compensated laterally, the coordinates of the mean value are 6.24, 13.99, 1.68 for the left VIM and 6.53, –14.13, 2.10 for the right VIM. The coordinates of the mean value of the highest probability region along with the highest number of the best contacts are 5.58, 13.67, 1.33, P = 14, for the left VIM, and 6.36, –14.03, 1.11, P = 17, for the right VIM. The PFA-VIM atlas overcomes several limitations of the current anatomical atlases and can improve targeting of thalamotomies and thalamic stimulations. It is dynamic and can easily be extended with new cases.

Automatic testing and assessment of neuroanatomy using a digital brain atlas: method and development of computer- and mobile-based applications.

Preparation of tests and students assessment by the instructor are time consuming. We address these two tasks in neuroanatomy education by employing a digital media application with a three‐dimensional (3D), interactive, fully segmented, and labeled brain atlas. The anatomical and vascular models in the atlas are linked to Terminologia Anatomica. Because the cerebral models are fully segmented and labeled, our approach enables automatic and random atlas‐derived generation of questions to test location and naming of cerebral structures. This is done in four steps: test individualization by the instructor, test taking by the students at their convenience, automatic student assessment by the application, and communication of the individual assessment to the instructor. A computer‐based application with an interactive 3D atlas and a preliminary mobile‐based application were developed to realize this approach. The application works in two test modes: instructor and student. In the instructor mode, the instructor customizes the test by setting the scope of testing and student performance criteria, which takes a few seconds. In the student mode, the student is tested and automatically assessed. Self‐testing is also feasible at any time and pace. Our approach is automatic both with respect to test generation and student assessment. It is also objective, rapid, and customizable. We believe that this approach is novel from computer‐based, mobile‐based, and atlas‐assisted standpoints. Anat Sci Educ 2:244–252, 2009.

A Three-Dimensional Interactive Atlas of Cerebral Arterial Variants

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.

A new presentation and exploration of human cerebral vasculature correlated with surface and sectional neuroanatomy.

The increasing complexity of human body models enabled by advances in diagnostic imaging, computing, and growing knowledge calls for the development of a new generation of systems for intelligent exploration of these models. Here, we introduce a novel paradigm for the exploration of digital body models illustrating cerebral vasculature. It enables dynamic scene compositing, real‐time interaction combined with animation, correlation of 3D models with sectional images, quantification as well as 3D manipulation‐independent labeling and knowledge‐related meta labeling (with name, diameter, description, variants, and references). This novel exploration is incorporated into a 3D atlas of cerebral vasculature with arteries and veins along with the surrounding surface and sectional neuroanatomy derived from 3.0 Tesla scans. This exploration paradigm is useful in medical education, training, research, and clinical applications. It enables development of new generation systems for rapid and intelligent exploration of complicated digital body models in real time with dynamic scene compositing from highly parcellated 3D models, continuous navigation, and manipulation‐independent labeling with multiple features. Anat Sci Ed 2:24–33, 2009.

Correlation between the Anatomical and Functional Human Subthalamic Nucleus

This work addresses the spatial correlation between the anatomical and functional human subthalamic nucleus (STN). The anatomical STN (A-STN), derived from the Schaltenbrand-Wahren brain atlas, is histology based. The functional STN (F-STN) is probabilistic, constructed from neuroelectrophysiological and neuroimaging data of 184 Parkinson’s disease patients. The A-STN and F-STN are placed in the same space and compared in terms of mutual relative overlapping of anatomy with function. The F-STN and A-STN correlate well for medium and high probabilities of the F-STN. For probability p ≧ 0.3, >95% of F-STN is inside the A-STN, and for p ≧ 0.5, the complete F-STN is inside the A-STN for each left and right STN. Therefore, the F-STN for p = 0.5 can potentially be used for identification of the STN in neuroimages.

Microelectrode‐guided functional neurosurgery assisted by Electronic Clinical Brain Atlas CD‐ROM

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 patients 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.

Quantification and visualization of three-dimensional inconsistency of the ventrointermediate nucleus of the thalamus in the Schaltenbrand-Wahren brain atlas

SummaryBackground. 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 mm3); 3D-C/VIM is 3.71 and 3D-S/VIM 3.89 times larger. The overlap is also highly variable: 104.88 mm3 for 3D-C/VIM with 3D-S/VIM, and very low (3.22 and 7.45 mm3) 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 mm3); 3D-S/VIMe is 3.24 and 3D-C/VIMe 3.36 times larger. The overlap sizes are low: 32.72 mm3 for 3D-C/VIMe with 3D-S/VIMe, and very low (1.32 and 2.01 mm3) 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 mm3 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 mm3); 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.

Quantification of spatial consistency in the Talairach and Tournoux Stereotactic Atlas

BackgroundThe 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.MethodThe 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.FindingsThe 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.ConclusionThis 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.