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Quantitative analysis of craniofacial morphology is of interest to scholars working in a wide variety of disciplines, such as anthropology, developmental biology, and medicine. T1-weighted (anatomical) magnetic resonance images (MRI) provide excellent contrast between soft tissues. Given its three-dimensional nature, MRI represents an ideal imaging modality for the analysis of craniofacial structure in living individuals. Here we describe how T1-weighted MR images, acquired to examine brain anatomy, can also be used to analyze facial features. Using a sample of typically developing adolescents from the Saguenay Youth Study (N = 597; 292 male, 305 female, ages: 12 to 18 years), we quantified inter-individual variations in craniofacial structure in two ways. First, we adapted existing nonlinear registration-based morphological techniques to generate iteratively a group-wise population average of craniofacial features. The nonlinear transformations were used to map the craniofacial structure of each individual to the population average. Using voxel-wise measures of expansion and contraction, we then examined the effects of sex and age on inter-individual variations in facial features. Second, we employed a landmark-based approach to quantify variations in face surfaces. This approach involves: (a) placing 56 landmarks (forehead, nose, lips, jaw-line, cheekbones, and eyes) on a surface representation of the MRI-based group average; (b) warping the landmarks to the individual faces using the inverse nonlinear transformation estimated for each person; and (3) using a principal components analysis (PCA) of the warped landmarks to identify facial features (i.e. clusters of landmarks) that vary in our sample in a correlated fashion. As with the voxel-wise analysis of the deformation fields, we examined the effects of sex and age on the PCA-derived spatial relationships between facial features. Both methods demonstrated significant sexual dimorphism in craniofacial structure in areas such as the chin, mandible, lips, and nose.

Cerebral white matter lesions (WMLs) are believed to play an important role in a subset of major depression (MD). We aimed to describe the impact of WMLs on white matter pathways in MD using diffusion tensor imaging (DTI) and magnetization transfer imaging. As a novel approach, we used DTI tractography to assess pathways intersected by WMLs. We examined 22 patients with late-onset MD and 22 age- and gender-matched controls. Parametric maps of fractional anisotropy (FA), apparent diffusion coefficient (ADC), and magnetization transfer ratio (MTR) were obtained to describe tissue integrity. The association between depression severity and the tract-specific localization of WMLs was analyzed on a voxel-by-voxel basis. We showed a significant positive association between depression severity and fiber tracts intersected by WMLs in the left superior longitudinal fasciculus and the right uncinate fasciculus. In both groups, WMLs had significantly lower FA and MTR, and higher ADC than both the tracts they intersected and the normal-appearing white matter (NAWM). In turn, the tracts intersected by WMLs had significantly lower FA and higher ADC than the NAWM. In conclusion, depression severity correlates with the tract-specific localization of WMLs. WMLs have a pronounced effect on white matter integrity in the pathways they intersect., (Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.)

Context: The basal ganglia and thalamus together connect in parallel closed-loop circuits with the cortex. Previous imaging studies have shown modifications of the basal ganglia and cortical targets in individuals with Tourette syndrome (TS), but less is known regarding the role of the thalamus in TS pathogenesis., Objective: To study the morphological features of the thalamus in children and adults with TS., Design: A cross-sectional, case-control study using anatomical magnetic resonance imaging., Setting: University research center., Participants: The 283 participants included 149 with TS and 134 normal control individuals aged 6 to 63 years., Main Outcome Measures: Conventional volumes and measures of surface morphology of the thalamus., Results: Analyses of conventional volumes and surface morphology were consistent in demonstrating an enlargement in TS-affected thalami. Overall volumes were 5% larger in the group composed of children and adults with TS. Statistical maps of surface contour demonstrated enlargement over the lateral thalamus. Post hoc testing indicated that differences in IQ, comorbid illnesses, and medication use did not account for these findings., Conclusions: Morphological abnormalities in the thalamus, together with the disturbances reported in the sensorimotor cortex, striatum, and globus pallidus, support the hypothesis of a circuitwide disorder within motor pathways in TS. The connectivity and function of the numerous and diverse thalamic nuclei within cortical-subcortical circuits constitute an anatomical crossroad wherein enlargement of motor nuclei may represent activity-dependent hypertrophy within this component of cortical-subcortical motor circuits, or an adaptive response within a larger putative compensatory system that could thereby directly modulate activity in motor circuits to attenuate the severity of tics.

Background: Several studies suggest that patients with late-onset major depression (MD) have an increased load of cerebral white-matter lesions (WMLs) compared with age-matched controls. Vascular risk factors such as hypertension and smoking may confound such findings. Our aim was to investigate the association between the localization and load of WMLs in late-onset MD with respect to vascular risk factors., Method: We examined 22 consecutive patients with late-onset first-episode MD and 22 age- and gender-matched controls using whole-brain magnetic resonance imaging (MRI). The localization, number and volume of WMLs were compared between patients and controls, while testing the effect of vascular risk factors., Results: Among subjects with one or more WMLs, patients displayed a significantly higher WML density in two white-matter tracts: the left superior longitudinal fasciculus and the right frontal projections of the corpus callosum. These tracts are part of circuitries essential for cognitive and emotional functions. Analyses revealed no significant difference in the total number and volume of WMLs between groups. Patients and controls showed no difference in vascular risk factors, except for smoking. Lesion load was highly correlated with smoking., Conclusions: Our results indicate that lesion localization rather than lesion load differs between patients with late-onset MD and controls. Increased lesion density in regions associated with cognitive and emotional functions may be crucial in late-onset MD, and vascular risk factors such as smoking may play an important role in the pathophysiology of late-onset MD, consistent with the vascular depression hypothesis.

Objective: The role of the thalamus in the genesis of attention deficit hyperactivity disorder (ADHD) remains poorly understood. The authors used anatomical MRI to examine the morphology of the thalamus in youths with ADHD and healthy comparison youths., Method: The authors examined 46 youths with ADHD and 59 comparison youths 8-18 years of age in a cross-sectional case-control study. Conventional volumes and measures of surface morphology of the thalamus served as the main outcome measures., Results: A mixed-effects model comparing whole thalamic volumes revealed no significant differences between groups. Maps of the thalamic surface revealed significantly smaller regional volumes bilaterally in the pulvinar in youths with ADHD relative to comparison subjects. Post hoc analyses showed that ADHD patients who received stimulants (N=31) had larger conventional thalamic volumes than untreated youths with ADHD, and maps of the thalamic surface showed enlargement over the pulvinar in those receiving stimulants. Smaller regional volumes in the right lateral and left posterior thalamic surfaces were associated with more severe hyperactivity symptoms, whereas larger regional volumes in the right medial thalamic surfaces were associated with more severe symptoms of inattention., Conclusion: These findings demonstrate reduced pulvinar volumes in youths with ADHD and indicate that this same area is relatively enlarged in patients treated with stimulants compared to those untreated. Associations of hyperactivity scores with smaller regional volumes on the lateral thalamic surface and inattention scores with larger regional volumes on the medial thalamic surface suggest the differential involvement of thalamic subcircuits in the pathogenesis of differing ADHD symptoms.

The purpose of our study was to investigate the ability to process achromatic and short-wavelength-sensitive cone (S-cone)-isolating (blue-yellow) stimuli in the blind visual field of hemispherectomized subjects and to demonstrate that blindsight is mediated by a collicular pathway that is independent of S-cone inputs. Blindsight has been described as the ability to respond to visual stimuli in the blind visual field without conscious awareness [Weiskrantz, L., Warrington, E. K., Sanders, M. D., & Marshall, J. Visual capacity in the hemianopic field following a restricted occipital ablation. Brain, 97, 709-728, 1974]. The roles of the subcortical neural structures in blindsight, such as the pulvinar and the superior colliculus, have been debated and an underlying neural correlate has yet to be confirmed. Using fMRI, we tested the ability to process visual stimuli that isolated the achromatic and short-wavelength-sensitive (S-)-cone pathways in three subjects: one control subject, one hemispherectomized subject with blindsight, and one hemispherectomized subject without blindsight. We demonstrated that (1) achromatic and S-cone-isolating stimuli presented to the normal visual hemifield of hemispherectomized subjects and to both visual hemifields of the control subject activated contralateral visual areas (V1/V2), as expected; (2) achromatic stimulus presentation but not S-cone-isolating stimulus presentation to the blind hemifield of the subject with blindsight activated visual areas FEF/V5; (3) whereas the cortical activation of the control subject was enhanced by an additional stimulus (achromatic and S-cone isolating) presented in the contralateral visual field, activation pattern of the subject with blindsight was enhanced by achromatic stimuli only. We conclude that the human superior colliculus is blind to the S-cone-isolating stimuli, and blindsight is mediated by an S-cone-independent collicular pathway.

Although cytoarchitectonic organization of the mammalian cortex into different lamina has been well-studied, identifying the architectural differences that distinguish cortical areas from one another is more challenging. Localization of large anatomical structures is possible using magnetic resonance imaging or invasive techniques (such as anterograde or retrograde tracing), but identifying patterns in gene expression architecture is limited as gene products do not necessarily identify an immediate functional consequence of a specialized area. Expression of specific genes in the mouse and human cortex is most often identified across entire lamina, and areal patterning of expression (when it exists) is most easily differentiated on a layer-by-layer basis. Since cortical organization is defined by the expression of large sets of genes, the task of identifying individual (or groups of structures) cannot be done using individual areal markers. In this manuscript we describe a methodology for clustering gene expression correlation profiles in the C57Bl/6J mouse cortex to identify large-scale genetic relationships between layers and areas. By using the Anatomic Gene Expression Atlas (http://mouse.brain-map.org/agea/) derived from in situ hybridization data in the Allen Brain Atlas, we show that a consistent expression based organization of areal patterning in the mouse cortex exists when clustered on a laminar basis. Surface-based mapping and visualization techniques are used as a representation to clarify these relationships., (Copyright 2009 Elsevier Inc. All rights reserved.)

Background and Purpose: Previous volumetric magnetic resonance imaging (MRI) studies of Parkinson's disease (PD) utilized primarily voxel-based morphometry (VBM), and investigated mostly patients with moderate- to late-stage disease. We now use deformation-based morphometry (DBM), a method purported to be more sensitive than VBM, to test for atrophy in patients with early-stage PD., Methods: T1-weighted MRI images from 24 early-stage PD patients and 26 age-matched normal control subjects were compared using DBM. Two separate studies were conducted, where two minimally-biased nonlinear intensity-average were created; one for all subjects and another for just the PD patients. The DBM technique creates an average population-based MRI-average in an iterative hierarchical fashion. The nonlinear transformations estimated to match each subject to the MRI-average were then analysed., Results: The DBM comparison between patients and controls revealed significant contraction in the left cerebellum, and non-significant trends towards frontal, temporal and cingulate sulcal expansions with frontal and temporal white matter contractions. Within the patient group, the unified PD rating scores were highly correlated with local expansions in or near sulci bordering on frontal and temporal cortex., Conclusion: Our results suggest that DBM could be a sensitive method for detecting morphological changes in early-stage PD.

The Allen Brain Atlas (ABA, www.brain-map.org) is a genome wide, spatially registered collection of cellular resolution in situ hybridization gene expression image data of the C57Bl/6J mouse brain. Derived from the ABA, the Anatomic Gene Expression Atlas (AGEA, http://mouse.brain-map.org/agea) has demonstrated both laminar and areal spatial gene expression correlations in the mouse cortex. While the mouse cortex is lissencephalic, its curvature and substantial bending in boundary areas renders it difficult to visualize and analyze laminar versus areal effects in a rectilinear coordinate framework. In context of human and non-human primate cortex, surface-based representation has proven useful for understanding relative locations of laminar, columnar, and areal features. In this paper, we describe a methodology for constructing surface-based flatmaps of the mouse cortex that enables mapping of gene expression data from individual genes in the ABA, or probabilistic expression maps from the AGEA, to identify and visualize genetic relationships between layers and areas., (Copyright 2009 Elsevier Inc. All rights reserved.)

The intercommissural line joining the anterior and posterior commissures defines stereotactic coordinate systems used in functional neurosurgical procedures. Such coordinate systems are generally accepted in humans and nonhuman primate experimental settings and provide high stereotactic precision and reproducibility. The ethical concern surrounding the use of nonhuman primates has motivated and helped popularize the use of the Göttingen minipig as an alternative experimental model for experimental functional neurosurgery. We investigated the position and variability of the intercommissural line in the minipig brain using in vivo MRI. From these data, standard coordinates for the minipig basal ganglia were estimated. We found the variability of the intercommissural line to be small in the Göttingen minipig and the variability of the basal ganglia structures to the mid-commissural point to be minor.

Due to its unique sensitivity to tissue microstructure, diffusion-weighted magnetic resonance imaging (MRI) has found many applications in clinical and fundamental science. With few exceptions, a more precise correspondence between physiological or biophysical properties and the obtained diffusion parameters remain uncertain due to lack of specificity. In this work, we address this problem by comparing diffusion parameters of a recently introduced model for water diffusion in brain matter to light microscopy and quantitative electron microscopy. Specifically, we compare diffusion model predictions of neurite density in rats to optical myelin staining intensity and stereological estimation of neurite volume fraction using electron microscopy. We find that the diffusion model describes data better and that its parameters show stronger correlation with optical and electron microscopy, and thus reflect myelinated neurite density better than the more frequently used diffusion tensor imaging (DTI) and cumulant expansion methods. Furthermore, the estimated neurite orientations capture dendritic architecture more faithfully than DTI diffusion ellipsoids.

Advanced and exclusive software solutions are offered to reduce susceptibility artefacts on MRI echo-planar sequences. We present a straightforward surgical technique to reduce the cortical distortion and signal loss that normally occur using diffusion tensor imaging (DTI) of the Göttingen minipig brain. Pronounced pneumatisation of the minipig cranium causes considerable susceptibility artefacts at the air/tissue interface around the frontal sinuses. Five Göttingen minipigs had burr holes drilled through the outer lamina of the skull bilaterally at the level of bregma. The underlying frontal sinuses were filled with a suspension of an MRI-compatible alginate. DTI was obtained before and after placing the medium in the sinus, quantifying the change using mutual information and Wilcoxon's rank-sum test. Fibertracking algorithms were applied to visualize the effect of treatment. We showed that the susceptibility artefacts were reduced at the air, bone and brain interfaces and that major cortical fiberbundles could be reliably visualized. This study demonstrated that DTI fibertracking of cortical bundles in experimental animals with extensive skull pneumatisation is feasible even when advanced software is unavailable.

Digital atlases are commonly used in pre-operative planning in functional neurosurgical procedures performed to minimize the symptoms of Parkinson's disease. These atlases can be customized to fit an individual patient's anatomy through atlas-to-patient warping procedures. Once fitted to pre-operative magnetic resonance imaging (MRI) data, the customized atlas can be used to plan and navigate surgical procedures. Linear, piece-wise linear and nonlinear registration methods have been used to customize different digital atlases with varying accuracies. Our goal was to evaluate eight different registration methods for atlas-to-patient customization of a new digital atlas of the basal ganglia and thalamus to demonstrate the value of nonlinear registration for automated atlas-based subcortical target identification in functional neurosurgery. In this work, we evaluate the accuracy of two automated linear techniques, two piece-wise linear techniques (requiring the identification of manually placed anatomical landmarks), and four different automated nonlinear atlas-to-patient warping techniques (where two of the four nonlinear techniques are variants of the ANIMAL algorithm). Since a gold standard of the subcortical anatomy is not available, manual segmentations of the striatum, globus pallidus, and thalamus are used to derive a silver standard for evaluation. Four different metrics, including the kappa statistic, the mean distance between the surfaces, the maximum distance between surfaces, and the total structure volume are used to compare the warping techniques. The results show that nonlinear techniques perform statistically better than linear and piece-wise linear techniques. In addition, the results demonstrate statistically significant differences between the nonlinear techniques, with the ANIMAL algorithm yielding better results.

Vibrotactile stimulation has been used successfully to activate the human somatosensory pathway in functional magnetic resonance imaging (fMRI) experiments. The design and characterization of these devices are of particular interest in frequency discrimination tasks and investigations of the somatopic organization of sensory areas. However, few have investigated the utility of vibrotactile stimulation in a clinical context. We have previously demonstrated that vibrotactile stimulation can provide robust activations in areas targeted in stereotactic functional neurosurgical procedures used for tumour resection (i.e.: primary and secondary somatosensory areas) and subcortical targets for thalamic pain and movement disorders (i.e.: sensory thalamus). The main contribution of this manuscript is the presentation of the design, materials, construction, and validation of a novel vibrotactile stimulator intended for clinical use. The thalamic activations are also compared to a digital atlas in order to evaluate anatomical localization. The proposed stimulator was constructed entirely from non-ferromagnetic parts, uses compressed air to deliver stimulation using computer control, and stimulates the entirety of the hand and fingers to ensure robust somatosensory activations. In addition, this stimulator is constructed entirely from "off-the-shelf" parts and would be easily replicated due to the simplicity of design and the relatively small expense of the parts required. The device was tested by stimulating the right hand of 10 normal controls (5 females, 5 males, all right handed; age range: 25-42 years, mean: 30.9 years, standard deviation: 5.2 years) during an fMRI experiment. The results demonstrate significant single subject activations of primary and secondary somatosensory cortices and of the sensory thalamus.

Morphologic measures have long been used to determine the patho-anatomical signature of different neurologic disorders. However, these measures can also be used to determine effects of specific learning tasks and quantifiable human abilities on cerebral structure. Musicians provide interesting opportunities for this type of analysis as their various skills, such as rhythmic ability and pitch and harmony discrimination (acquired through years of practicing and playing) can be quantified and compared using distinct morphologic analyses. Here, we review magnetic resonance imaging-based morphologic analyses in the music and neuroscience literature and provide some results from our own analysis of rhythmic ability in a cohort of musicians.

Functional magnetic resonance imaging (fMRI) is often used to enhance visualization and provide target localization during the planning phase of neurosurgical procedures. Although parametric maps have been used to identify areas of eloquent cortex such as the primary (S1) and secondary (S2) somatosensory areas for tumor surgery, to date, few fMRI methods exist to localize subcortical targets for surgical interventions used to treat movement disorders. The scanning time required to obtain statistically significant functional signals must be balanced against the possibility of movement artifacts and patient discomfort. We propose a vibrotactile stimulation technique to activate the somatosensory pathway for neurosurgical planning and perform a sensitivity analysis to determine the amount of time required to achieve significant activations of S1, S2, and sensory thalamus in individual subjects. Bilateral stimulation experiments were carried out on two MRI scanners (n = 13 at 1.5 T; n = 5 at 3.0 T). The analysis demonstrates that statistically significant functional activations can be achieved in clinically acceptable times: 16 min at 1.5 T (26/26 experiments) and 6 min at 3.0 T (10/10) for S1 activations; 24 min at 1.5 T (22/26) and 18 min at 3.0 T for S2 activations (9/10); and 32 min at 1.5 T (15/26) and 18 min at 3.0 T (10/10) for activation of thalamic nuclei. These results demonstrate that S1 and S2 activations are robust at 1.5 and 3.0 T, and that robust thalamic activations in individual subjects are possible at 3.0 T. These techniques demonstrate that this technique can be used for preoperative planning for surgical candidates., (2008 Wiley-Liss, Inc.)

Pre-operative magnetic resonance (MRI) and computed tomography (CT) image volumes are often used for planning and guidance during functional neurosurgical procedures. These operations can include the creation of lesions in the thalamus (thalamotomy) or the globus pallidus (pallidotomy), or the insertion of deep brain stimulation (DBS) electrodes in the subcortical nuclei. These subcortical targets are often difficult to localize in pre-operative imaging data due to the limited resolution and contrast available in standard MRI or CT techniques. To address this problem, digital atlases of subcortical nuclei are often used to accurately identify surgical targets since they can be warped to fit each patient's unique anatomy. Targeting accuracy thus depends on the quality of the atlas-to-patient warp. In this paper, three atlas-to-patient warping techniques are compared. Two methods rely on an MRI template as an intermediary to estimate a nonlinear atlas-to-patient transformation. The third is novel, and uses a pseudo-MRI derived from an atlas of the basal ganglia and thalamus to estimate the nonlinear atlas-to-patient transformation directly. The methods are compared using (1) manual segmentations of subcortical nuclei and (2) functional data from intra-operative thalamic stimulation. The results demonstrate that the template-based atlas-to-patient warping technique is the best of the three for customizing the atlas onto patient data.

Quantitative analysis of digitized IHC-stained tissue sections is increasingly used in research studies and clinical practice. Accurate quantification of IHC staining, however, is often complicated by conventional tissue counterstains caused by the color convolution of the IHC chromogen and the counterstain. To overcome this issue, we implemented a new counterstain, Acid Blue 129, which provides homogeneous tissue background staining. Furthermore, we combined this counterstaining technique with a simple, robust, fully automated image segmentation algorithm, which takes advantage of the high degree of color separation between the 3-amino-9-ethyl-carbazole (AEC) chromogen and the Acid Blue 129 counterstain. Rigorous validation of the automated technique against manual segmentation data, using Ki-67 IHC sections from rat C6 glioma and beta-amyloid IHC sections from transgenic mice with amyloid precursor protein (APP) mutations, has shown the automated method to produce highly accurate results compared with ground truth estimates based on the manually segmented images. The synergistic combination of the novel tissue counterstaining and image segmentation techniques described in this study will allow for accurate, reproducible, and efficient quantitative IHC studies for a wide range of antibodies and tissues.

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.

Anatomical studies in animals have described multiple striatal circuits and suggested that sub-components of the striatum, although functionally related, project to distinct cortical areas. To date, anatomical investigations in humans have been limited by methodological constraints such that most of our knowledge of fronto-striatal networks relies on nonhuman primate studies. To better identify the fronto-striatal pathways in the human brain, we used Diffusion Tensor Imaging (DTI) tractography to reconstruct neural connections between the frontal cortex and the caudate nucleus and putamen in vivo. We demonstrate that the human caudate nucleus is interconnected with the prefrontal cortex, inferior and middle temporal gyrus, frontal eye fields, cerebellum and thalamus; the putamen is interconnected with the prefrontal cortex, primary motor area, primary somatosensory cortex, supplementary motor area, premotor area, cerebellum and thalamus. A connectivity-based seed classification analysis identified connections between the dorsolateral prefrontal areas (DLPFC) and the dorsal-posterior caudate nucleus and between the ventrolateral prefrontal areas (VLPFC) and the ventral-anterior caudate nucleus. For the putamen, connections exist between the supplementary motor area (SMA) and dorsal-posterior putamen while the premotor area projects to medial putamen, and the primary motor area to the lateral putamen. Identifying the anatomical organization of the fronto-striatal network has important implications for understanding basal ganglia function and associated disease processes., Competing Interests: Statement: The authors declare that they have no competing financial interests.

Digital and print brain atlases have been used with success to help in the planning of neurosurgical interventions. In this paper, a technique presented for the creation of a brain atlas of the basal ganglia and the thalamus derived from serial histological data. Photographs of coronal histological sections were digitized and anatomical structures were manually segmented. A slice-to-slice nonlinear registration technique was used to correct for spatial distortions introduced into the histological data set at the time of acquisition. Since the histological data were acquired without any anatomical reference (e.g., block-face imaging, post-mortem MRI), this registration technique was optimized to use an error metric which calculates a nonlinear transformation minimizing the mean distance between the segmented contours between adjacent pairs of slices in the data set. A voxel-by-voxel intensity correction field was also estimated for each slice to correct for lighting and staining inhomogeneity. The reconstructed three-dimensional (3D) histological volume can be viewed in transverse and sagittal directions in addition to the original coronal. Nonlinear transformations used to correct for spatial distortions of the histological data were applied to the segmented structure contours. These contours were then tessellated to create three-dimensional geometric objects representing the different anatomic regions in register with the histological volumes. This yields two alternate representations (one histological and one geometric) of the atlas. To register the atlas to a standard reference MR volume created from the average of 27 T1-weighted MR volumes, a pseudo-MRI was created by setting the intensity of each anatomical region defined in the geometric atlas to match the intensity of the corresponding region of the reference MR volume. This allowed the estimation of a 3D nonlinear transformation using a correlation based registration scheme to fit the atlas to the reference MRI. The result of this procedure is a contiguous 3D histological volume, a set of 3D objects defining the basal ganglia and thalamus, both of which are registered to a standard MRI data set, for use for neurosurgical planning.

Digital brain atlases can be used in conjuction with magnetic resonance imaging (MRI) and computed tomography (CT) for planning and guidance during neurosurgery. Digital atlases are advantageous since they can be warped nonlinearly to fit each patient's unique anatomy. Functional neurosurgery with implantation of deep brain stimulating (DBS) electrodes requires accurate targeting, and has become a popular surgical technique in Parkinsonian patients. In this paper, we present a method for integrating postoperative data from subthalamic (STN) DBS implantation into an antomical atlas of the basal ganglia and thalamus. The method estimates electrode position from post-operative magnetic resonance imaging (MRI) data. These electrodes are then warped back into the atlas space and are modelled in three dimensions. The average of these models is then taken to show the region where the majority of STN DBS electrodes were implanted. The group with more favorable post-operative results was separated from the group which responded to the STN DBS implantation procedure less favourably to create a probablisitic distribution of DBS in the STN electrodes.

Digital brain atlases can be used in conjunction with magnetic resonance imaging (MRI) and computed tomography (CT) for planning and guidance during neurosurgery. Digital atlases are advantageous, since they can be warped nonlinearly to fit each patient's unique anatomy. Two atlas-to-patient warping techniques are compared in this paper. The first technique uses an MRI template as an intermediary to estimate a nonlinear atlas-to-patient transformation. The second, is novel, and uses a pseudo-MRI volume, derived from the voxel-label-atlas, to estimate the atlas-to-patient transformation directly. Manual segmentations and functional data are used to validate the two methods.