Matching of digitised brain atlas to magnetic resonance images

Multimodal 7T Imaging of Thalamic Nuclei for Preclinical Deep Brain Stimulation Applications

Precise neurosurgical targeting of electrode arrays within the brain is essential to the successful treatment of a range of brain disorders with deep brain stimulation (DBS) therapy. Here, we describe a set of computational tools to generate in vivo, subject-specific atlases of individual thalamic nuclei thus improving the ability to visualize thalamic targets for preclinical DBS applications on a subject-specific basis. A sequential nonlinear atlas warping technique and a Bayesian estimation technique for probabilistic crossing fiber tractography were applied to high field (7T) susceptibility-weighted and diffusion-weighted imaging, respectively, in seven rhesus macaques. Image contrast, including contrast within thalamus from the susceptibility-weighted images, informed the atlas warping process and guided the seed point placement for fiber tractography. The susceptibility-weighted imaging resulted in relative hyperintensity of the intralaminar nuclei and relative hypointensity in the medial dorsal nucleus, pulvinar, and the medial/ventral border of the ventral posterior nuclei, providing context to demarcate borders of the ventral nuclei of thalamus, which are often targeted for DBS applications. Additionally, ascending fiber tractography of the medial lemniscus, superior cerebellar peduncle, and pallidofugal pathways into thalamus provided structural demarcation of the ventral nuclei of thalamus. The thalamic substructure boundaries were validated through in vivo electrophysiological recordings and post-mortem blockface tissue sectioning. Together, these imaging tools for visualizing and segmenting thalamus have the potential to improve the neurosurgical targeting of DBS implants and enhance the selection of stimulation settings through more accurate computational models of DBS.

Comparison of atlas- and magnetic resonance imaging-based stereotactic targeting of the globus pallidus internus in the performance of deep brain stimulation for treatment of dystonia

OBJECT

To assess the validity of relying on atlases during stereotactic neurosurgery, the authors compared target coordinates in the globus pallidus internus (GPi) obtained using magnetic resonance (MR) imaging with those determined using an atlas. The targets were used in deep brain stimulation (DBS) for the treatment of generalized dystonia.

METHODS

Thirty-five patients, who were treated using bilateral DBS of the GPi, were included in this study. The target was selected on three-dimensional MR images by direct visual recognition of the GPi. The coordinates were automatically recorded using dedicated software. They were translated into the anterior commissure-posterior commissure (AC-PC) coordinate system by using a matrix transformation process. The same GPi target was defined, based on the locations of brain structures shown in the atlases of Schaltenbrand and Talairach. Magnetic resonance imaging-based GPi target coordinates were statistically compared with the corresponding atlas-based coordinates by applying the Student t-test. A significant difference (p < 0.001) was demonstrated in x, y, and z directions between MR imaging-based and Schaltenbrand atlas-derived target coordinates. The comparison with normalized Talairach atlas coordinates demonstrated a significant difference (p < 0.01) in the y and z directions, although not in the x direction (p = 0.12). No significant correlation existed between MR imaging-based target coordinates and patient age (p > 0.1). No significant correlation was observed between MR imaging-based target coordinates and patient sex in the y and z directions (p > 0.9), although it was significant in the x direction (p < 0.05). A significant variation in coordinates and the length of the AC-PC line was revealed only in the y direction (p < 0.005).

CONCLUSIONS

A significant difference was found between target coordinates obtained by direct visual targeting on MR images (validated by postoperative clinical results) and those obtained by indirect targeting based on atlases.

Landmark-based morphometrics of the normal adult brain using MRI

We describe the application of statistical shape analysis to homologous landmarks on the cortical surface of the adult human brain. Statistical shape analysis has a sound theoretical basis. Landmarks are identified on the surface of a 3-D reconstruction of the segmented cortical surface from magnetic resonance image (MRI) data. Using publicly available software (morphologika) the location and size dependence of the landmarks are removed and the differences in landmark distribution across subjects are analysed using principal component analysis. These differences, representing shape differences between subjects, can be visually assessed using wireframe models and transformation grids. The MRI data of 58 adult brains (27 female and 15 left handed) were examined. Shape differences in the whole brain are described which concern the relative orientation of frontal lobe sulci. Analysis of all 116 hemispheres revealed a statistically significant difference (P < 0.001) between left and right hemispheres. This finding was significant for right- but not left-handed subjects alone. No other significant age, gender, handedness, or brain-size correlations with shape differences were found.

The Morel stereotactic atlas of the human thalamus: atlas-to-MR registration of internally consistent canonical model

In 1997, Morel, Magnin, and Jeanmonod presented a microscopic stereotactic atlas of the human thalamus. Parcellations of thalamic nuclei did not only use cyto- and myeloarchitectonic criteria, but were additionally corroborated by staining for calcium-binding proteins, which bears functional significance. The atlas complies with the Anglosaxon nomenclature elaborated by Jones and the data were sampled in three orthogonal planes in the AC-PC reference space. We report on the generation of three-dimensional digital models of the thalamus based on the three sets of sections (sagittal, horizontal, and frontal). Spatial differences between the three anatomical specimens were evaluated using the centers of gravity of 13 selected nuclei as landmarks. Subsequent linear regression analysis yielded equations, which were used to normalize the frontal and horizontal digital models to the sagittal one. The outcome is an internally consistent Canonical Model of Morel's atlas, which minimizes the linear component of the variability between the three sectioned anatomical specimens. In addition, we demonstrate the feasibility of the atlas-to-MRI registration in conjunction with on-line visualization of the trajectory in the digital models.

Lesion segmentation and manual warping to a reference brain: intra- and interobserver reliability

The study of subjects with acquired brain damage has been an invaluable tool for exploring human brain function, and the description of lesion locations within and across subjects is an important component of this method. Such descriptions usually involve the separation of lesioned from nonlesioned tissue (lesion segmentation) and the description of the lesion location in terms of a standard anatomical reference space (lesion warping). The objectives of this study were to determine the sources and magnitude of variability involved in lesion segmentation and warping using the MAP-3 approach. Each of two observers segmented the lesion volume in ten brain-damaged subjects twice, so as to permit pairwise comparisons of both intra- and interobserver agreement. The segmented volumes were then warped to a reference brain using both a manual (MAP-3) and an automated (AIR-3) technique. Observer agreement between segmented and warped volumes was analyzed using four measures: volume size, distance between the volume surfaces, percentage of nonoverlapping voxels, and percentage of highly discrepant voxels. The techniques for segmentation and warping produced high agreement within and between observers. For example, in most instances, the warped volume surfaces created by different observers were separated by less than 3 mm. The performance of the automated warping technique compared favorably to the manual technique in most subjects, although important exceptions were found. Overall, these results establish benchmark parameters for expert and automated lesion transfer, and indicate that a high degree of confidence can be placed in the detailed anatomical interpretation of focal brain damage based upon the MAP-3 technique.

Registration and warping of magnetic resonance images to histological sections

We present a method for coregistration and warping of magnetic resonance images (MRI) to histological sections for comparison purposes. This methodology consists of a modified head and hat surface-based registration algorithm followed by a new automated warping approach using nonlinear thin plate splines to compensate for distortions between the data sets. To test the methodology, 15 male Wistar rats were subjected to focal cerebral ischemia via permanent occlusion of the middle cerebral artery. The MRI images were acquired in separate groups of animals at 16-24 h (n = 9) and 48-168 h (n = 6) postocclusion. After imaging, animals were immediately sacrificed and hematoxylin- and eosin-stained brain sections were obtained for histological analysis. The MRI was coregistered and warped to histological sections. The MRI lesion areas were defined using the Eigenimage (EI) filter technique. The EI is a linear filter that maximizes the projection of a desired tissue (ischemic tissue) while it minimizes the projection of undesired tissues (nonischemic tissue) onto a composite image called an EI. When using coregistration without warping the MRI lesion area demonstrated poor correlation (r = 0.55, p > 0.01) with a percent difference between the two lesion areas of 22.5% +/- 10.8%. After warping, the MRI and histology had significant correlation (r = 0.97, p < 0.01) and a decreased percent difference of 5.56% +/- 4.31%. This methodology is simple and robust for coregistration and warping of MRI to histological sections and can be utilized in many applications for comparison of MRI to histological data.

A brainstem stereotactic atlas in a three-dimensional magnetic resonance imaging navigation system: first experiences with atlas-to-patient registration

OBJECT

The authors describe a computer-resident digital representation of a stereotactic atlas of the human brainstem, its semiautomated registration to sagittal fast low-angle shot three-dimensional (3-D) magnetic resonance (MR) imaging data sets in 27 healthy volunteers and 24 neurosurgical patients, and an analysis of the subsequent transforms needed to refine the initial registration.

METHODS

Contour drawings from the atlas, which offer the 70th percentile of variation of anatomical structures, were interpolated into an isotropic 3-D representation. Initial atlas-to-patient registration was based on the fastigium/ventricular floor plane reference system. The quality of the fit was evaluated using superimposition of the atlas and MR images. If necessary, the atlas was tailored to the individual anatomy by using additional transforms. On average, the atlas had to be stretched by 2 to 6% in the three directions of space. Scale factors varied over a broad range from -8 to +19% and the benefit of visual interactive control of the atlas-to-patient registration was evident. Analysis of distances within the pons measured in the midsagittal MR imaging slices and the required scale factors revealed significant correlations that may be used to reduce the amount of user interaction in the coregistration substantially. In 70.6% of the cases, the atlas had to be shifted in a cranial direction along the brainstem axis (in 25.5% of cases 3-4 mm, in 45.1% of cases 1-2 mm). This was due to a more caudal position of the fastigium cerebelli on the MR images compared with the atlas.

CONCLUSIONS

This observation, in conjunction with the variability of the height of the fourth ventricle in our MR imaging data (range 6.1-15.2 mm, mean 10.1 mm, standard deviation 1.8 mm) calls into question the role of the fastigium cerebelli as an anatomical landmark for localization within the brainstem.