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

Brainstem Surgery: Functional Surgical Anatomy with the Use of an Advanced Modern Intraoperative Neurophysiological Procedure

Intraoperative neurophysiology (ION) in brainstem surgery evolved as brainstem surgery advanced.The original idea of brainstem mapping (BSM) is a neurophysiological procedure to locate cranial nerve motor nuclei (CNMN) on the floor of the fourth ventricle. With the introduction of various skull base approaches to the brainstem, BSM is carried out on any surface of the brainstem to expose the safe entry zone to the intrinsic brainstem lesion. It is the modern concept of BSM, a broader definition of BSM. BSM enables to avoid direct damage to the CNMN when approaching the brainstem through the negative mapping region.The corticobulbar tract (CBT) motor evoked potential (MEP) is another ION procedure in brainstem surgery. It enables monitoring of the functional integrity of the whole cranial motor pathway without interrupting surgical procedures. Combined application of both BSM and CBT-MEP monitoring is indispensable for the functional preservation of the CNMN and their supranuclear innervation during the brainstem surgery.In this paper, the neurophysiological aspect of BSM and the CBT-MEP was fully described. Normal anatomical background of the floor of the fourth ventricle and the detail of the CBT anatomy were demonstrated to better understand their clinical usefulness, limitations, and surgical implications derived from ION procedures. Finally, a future perspective in the role of ION procedures in brainstem surgery was presented. The latest magnetic resonance imaging (MRI) technology can allow surgeons to find an "on the image" safe entry zone to the brainstem. However, the role of BSM and the CBT-MEP monitoring in terms of safe brainstem surgery stays unshakable. Special attention was paid for the recent trend of management in diffuse intrinsic pontine gliomas. A new role of BSM during a stereotactic biopsy was discussed.It is the authors' expectation that the paper enhances the clinical application of a contemporary standard of the ION in brainstem surgery and supports safer brainstem surgery more than ever and in the future.

Direct In Vivo MRI Discrimination of Brain Stem Nuclei and Pathways

BACKGROUND AND PURPOSE

The brain stem is a complex configuration of small nuclei and pathways for motor, sensory, and autonomic control that are essential for life, yet internal brain stem anatomy is difficult to characterize in living subjects. We hypothesized that the 3D fast gray matter acquisition T1 inversion recovery sequence, which uses a short inversion time to suppress signal from white matter, could improve contrast resolution of brain stem pathways and nuclei with 3T MR imaging.

MATERIALS AND METHODS

After preliminary optimization for contrast resolution, the fast gray matter acquisition T1 inversion recovery sequence was performed in 10 healthy subjects (5 women; mean age, 28.8 ± 4.8 years) with the following parameters: TR/TE/TI = 3000/2.55/410 ms, flip angle = 4°, isotropic resolution = 0.8 mm, with 4 averages (acquired separately and averaged outside k-space to reduce motion; total scan time = 58 minutes). One subject returned for an additional 5-average study that was combined with a previous session to create a highest quality atlas for anatomic assignments. A 1-mm isotropic resolution, 12-minute version, proved successful in a patient with a prior infarct.

RESULTS

The fast gray matter acquisition T1 inversion recovery sequence generated excellent contrast resolution of small brain stem pathways in all 3 planes for all 10 subjects. Several nuclei could be resolved directly by image contrast alone or indirectly located due to bordering visualized structures (eg, locus coeruleus and pedunculopontine nucleus).

CONCLUSIONS

The fast gray matter acquisition T1 inversion recovery sequence has the potential to provide imaging correlates to clinical conditions that affect the brain stem, improve neurosurgical navigation, validate diffusion tractography of the brain stem, and generate a 3D atlas for automatic parcellation of specific brain stem structures.

Dorsal extensions of the fastigium cerebelli: an anatomical study using magnetic resonance imaging

BACKGROUND AND PURPOSE

The fastigium cerebelli is an important topographical landmark for neurosurgeons and radiologists. However, few studies have characterized the morphology of the fastigium cerebelli. We aimed to investigate the fastigium cerebelli using postmortem specimens and magnetic resonance imaging (MRI) in vivo.

MATERIALS AND METHODS

Three cadaveric brains were midsagittally sectioned for observing the fastigium cerebelli. Additionally, 66 outpatients underwent MRI, including sagittal T1-weighted imaging, axial T2-weighted imaging, and coronal constructive interference in steady-state (CISS) sequence.

RESULTS

In the cadaveric specimens, the fastigium cerebelli was observed as a beak-like dorsal protrusion of the fourth ventricle. Its inner surface was observed as a small fovea. On serial CISS images, the fastigium cerebelli consistently possessed a pair of triangular-shaped, dorsal extensions lying parasagittally along the nodule. These extensions were classified as symmetrical, right-side dominant, or left-side dominant. The symmetrical type was the most predominant and comprised 60.6% of the extensions, while the right-side dominant and left-side dominant types comprised 13.6 and 25.8%, respectively. In 91% of the 66 patients, the number of slices covering the entirety of the dorsal extensions were the same on both sides. The fastigial angle (θ) formed by lines tangent to the superior and inferior medullary velums varied widely.

CONCLUSIONS

The fastigium cerebelli has a pair of dorsal extensions lying parasagittally along the nodule. Coronal CISS sequence is useful in delineating the fastigium cerebelli in vivo.

Correlating Function and Imaging Measures of the Medial Longitudinal Fasciculus

Objective

To test the validity of diffusion tensor imaging (DTI) measures of tissue injury by examining such measures in a white matter structure with well-defined function, the medial longitudinal fasciculus (MLF). Injury to the MLF underlies internuclear ophthalmoparesis (INO).

Methods

40 MS patients with chronic INO and 15 healthy controls were examined under an IRB-approved protocol. Tissue integrity of the MLF was characterized by DTI parameters: longitudinal diffusivity (LD), transverse diffusivity (TD), mean diffusivity (MD) and fractional anisotropy (FA). Severity of INO was quantified by infrared oculography to measure versional disconjugacy index (VDI).

Results

LD was significantly lower in patients than in controls in the medulla-pons region of the MLF (p < 0.03). FA was also lower in patients in the same region (p < 0.0004). LD of the medulla-pons region correlated with VDI (R = -0.28, p < 0.05) as did FA in the midbrain section (R = 0.31, p < 0.02).

Conclusions

This study demonstrates that DTI measures of brain tissue injury can detect injury to a functionally relevant white matter pathway, and that such measures correlate with clinically accepted evaluation indices for INO. The results validate DTI as a useful imaging measure of tissue integrity.

Feasibility of creating a high-resolution 3D diffusion tensor imaging based atlas of the human brainstem: a case study at 11.7 T

A three-dimensional stereotaxic atlas of the human brainstem based on high resolution ex vivo diffusion tensor imaging (DTI) is introduced. The atlas consists of high resolution (125-255 μm isotropic) three-dimensional DT images of the formalin-fixed brainstem acquired at 11.7 T. The DTI data revealed microscopic neuroanatomical details, allowing three-dimensional visualization and reconstruction of fiber pathways including the decussation of the pyramidal tract fibers, and interdigitating fascicles of the corticospinal and transverse pontine fibers. Additionally, strong gray-white matter contrasts in the apparent diffusion coefficient (ADC) maps enabled precise delineation of gray matter nuclei in the brainstem, including the cranial nerve and the inferior olivary nuclei. Comparison with myelin-stained histology shows that at the level of resolution achieved in this study, the structural details resolved with DTI contrasts in the brainstem were comparable to anatomical delineation obtained with histological sectioning. Major neural structures delineated from DTI contrasts in the brainstem are segmented and three-dimensionally reconstructed. Further, the ex vivo DTI data are nonlinearly mapped to a widely-used in vivo human brain atlas, to construct a high-resolution atlas of the brainstem in the Montreal Neurological Institute (MNI) stereotaxic coordinate space. The results demonstrate the feasibility of developing a 3D DTI based atlas for detailed characterization of brainstem neuroanatomy with high resolution and contrasts, which will be a useful resource for research and clinical applications.

Morphology of the adult midsagittal brainstem in relation to the reference systems MRI-based variability study

RATIONALE AND OBJECTIVES

Anterior/posterior commissure reference system (AC/PC reference system) and the fastigium/ventricular floor plane reference system (FFL/VFL reference system) are two reference systems used in the stereotactic localization of the invisible nuclei of the brainstem in magnetic resonance (MR) images. This study investigated the variation of the midsagittal brainstem in relation to the AC/PC and VFL/FFL reference systems with respect to age and gender.

MATERIALS AND METHODS

High-resolution T1-weighted structural MR images were acquired from 64 adults (age range 21-60 years, 32 males and 32 females). The AC/PC and VFL/FFL reference systems were identified automatically. A set of landmarks of the midsagittal brainstem were defined and localized interactively.

RESULTS

Results illustrated that there was significant difference between the variance of the anteroposterior coordinate of the landmarks in relation to the AC/PC reference system and that in relation to the FFL/VFL reference system (P < .05), the former is larger than the latter. The positions of the landmarks in the females are more anterior than those in the males in relation to the AC/PC reference (P < .05); the difference in relation to the FFL/VFL reference system was not found.

CONCLUSION

Either the FFL/VFL reference system or the AC/PC reference system has its own advantage in the stereotactic localization of the structure in the brainstem.

Stereotactic localization of the human pedunculopontine nucleus: atlas-based coordinates and validation of a magnetic resonance imaging protocol for direct localization

The pedunculopontine nucleus (PPN) is a promising new target for deep brain stimulation (DBS) in parkinsonian patients with gait disturbance and postural instability refractory to other treatment modalities. This region of the brain is unfamiliar territory to most functional neurosurgeons. This paper reviews the anatomy of the human PPN and describes novel, clinically relevant methods for the atlas-based and MRI-based localization of the nucleus. These two methods of PPN localization are evaluated and compared on stereotactic MRI data acquired from a diverse group of 12 patients undergoing implantation of deep brain electrodes at sites other than the PPN. Atlas-based coordinates of the rostral and caudal PPN poles in relation to fourth ventricular landmarks were established by amalgamating information sourced from two published human brain atlases. These landmarks were identified on acquired T1 images and atlas-derived coordinates used to plot the predicted PPN location on all 24 sides. Images acquired using a specifically modified, proton-density MRI protocol were available for each patient and were spatially fused to the T1 images. This widely available and rapid protocol provided excellent definition between gray and white matter within the region of interest. Together with an understanding of the regional anatomy, direct localization of the PPN was possible on all 24 sides. The coordinates for each directly localized nucleus were measured in relation to third and fourth ventricular landmarks. The mean (SD) of the directly localized PPN midpoints was 6.4 mm (0.5) lateral, 3.5 mm (1.0) posterior and 11.4 mm (1.2) caudal to the posterior commissure in the anterior commissure-posterior commissure plane. For the directly localized nucleus, there was similar concordance for the rostral pole of the PPN in relation to third and fourth ventricular landmarks (P>0.05). For the caudal PPN pole, fourth ventricular landmarks provided greater concordance with reference to the anteroposterior coordinate (P<0.001). There was a significant difference between localization of the PPN poles as predicted by atlas-based coordinates and direct MRI localization. This difference affected mainly the rostrocaudal coordinates; the mean lateral and anteroposterior coordinates of the directly localized PPN poles were within 0.5 mm of the atlas-based predicted values. Our findings provide simple, rapid and precise methods that are of clinical relevance to the atlas-based and direct stereotactic localization of the human PPN. Direct MRI localization may allow greater individual accuracy than that afforded by atlas-based coordinates when localizing the human PPN and may be relevant to groups evaluating the clinical role of PPN DBS.

A deformable digital brain atlas system according to Talairach and Tournoux

Brain atlases are valuable tools which assist neurosurgeons during the planning of an intervention. Since a printed atlas book has several disadvantages-among them the difficulty to map the information onto a patient's individual anatomy-we have developed a digital version of the well-established stereotaxic brain atlas of Talairach and Tournoux. Our atlas system is mainly dedicated to assist neurosurgical planning, and its benefits are: (i) a three-dimensional (3D) representation of most brain structures contained in the Talairach atlas; (ii) a nonrigid matching capability which warps the standard atlas anatomy to an individual brain magnetic resonance imaging (MRI) dataset in a few minutes and which is able to take deformations due to tumors into account; (iii) the integration of several sources of neuroanatomical knowledge; (iv) an interface to a navigation system which allows utilization of atlas information intraoperatively. In this paper we outline the algorithm we have developed to achieve 3D surface models of the brain structures. Moreover, we describe the nonrigid matching method which consists of two tasks: firstly, point correspondences between the atlas and the patient are established in an automatic fashion, and secondly these displacement vectors are interpolated using a radial basis function approach to form a continuous transformation function. To generate appropriate target structures for the first of these tasks, we implemented a quick segmentation tool which is capable to segment the cortex and ventricles in less than 5 min. An evaluation shows that our nonrigid approach is more precise than the conventional piecewise linear matching, though it should be further improved for the region around the deep grey nuclei. Summarizing, we developed a Win32 program which permits the convenient and fast application of standardized anatomy to individual brains which potentially contain tumors.

An algorithm for rapid calculation of a probabilistic functional atlas of subcortical structures from electrophysiological data collected during functional neurosurgery procedures

The paper introduces an optimal algorithm for rapid calculation of a probabilistic functional atlas (PFA) of subcortical structures from data collected during functional neurosurgery procedures. The PFA is calculated based on combined intraoperative electrophysiology, pre- and intraoperative neuroimaging, and postoperative neurological verification. The algorithm converts the coordinates of the neurologically most effective contacts into probabilistic functional maps taking into account the geometry of a stimulating electrode. The PFA calculation comprises the reconstruction of the contact coordinates from two orthogonal projections, normalizing (warping) the contacts modeled as cylinders, voxelizing the contact models, calculating the atlas, and computing probability. In addition, an analytical representation of the PFA is formulated based on Gaussian modeling. The initial PFA has been calculated from the data collected during the treatment of 274 Parkinson's disease patients, most of them operated bilaterally (487 operated hemispheres). It contains the most popular stereotactic targets, the subthalamic nucleus, globus pallidus internus, and ventral intermedius nucleus. The key application of the algorithm is targeting in stereotactic and functional neurosurgery, and it also can be employed in human and animal brain research.

A review of medical imaging informatics

This review of medical imaging informatics is a survey of current developments in an exciting field. The focus is on informatics issues rather than traditional data processing and information systems, such as picture archiving and communications systems (PACS) and image processing and analysis systems. In this review, we address imaging informatics issues within the requirements of an informatics system defined by the American Medical Informatics Association. With these requirements as a framework, we review, in four sections: (1) Methods to present imaging and associated data without causing an overload, including image study summarization, content-based medical image retrieval, and natural language processing of text data. (2) Data modeling techniques to represent clinical data with focus on an image data model, including general-purpose time-based multimedia data models, health-care-specific data models, knowledge models, and problem-centric data models. (3) Methods to integrate medical data information from heterogeneous clinical data sources. Advances in centralized databases and mediated architectures are reviewed along with a discussion on our efforts at data integration based on peer-to-peer networking and shared file systems. (4) Visualization schemas to present imaging and clinical data: the large volume of medical data presents a daunting challenge for an efficient visualization paradigm. In this section we review current multimedia visualization methods including temporal modeling, problem-specific data organization, including our problem-centric, context and user-specific visualization interface.

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, 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.

Image content extraction: application to MR images of the brain

A system for automatically extracting image content features was developed that combines registration to a labeled atlas with natural language processing of free-text radiology reports. The system was then tested with T1-weighted, spoiled gradient-echo magnetic resonance (MR) imaging studies of the brain performed in nine patients. The locations of 599 structures were visually assessed by an experienced radiologist and compared with the locations indicated by automated output. The in-plane accuracy of the contours was subjectively evaluated as either good, moderate, or poor. The criterion for classifying a structure as correctly located was that 90% or more of all the images containing the structure had to be correctly identified. For 98% of the structures, the images identified by the automated algorithm agreed with those identified by the radiologist, and in 83% of cases, image contours showed a good in-plane overlap. The results of this validation study demonstrate that this combination of registration and natural language processing is accurate in identifying relevant images from brain MR imaging studies. However, the range of applicability of this technique has yet to be determined by applying the technique to a large number of studies.

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.

Magnetic resonance imaging stereotactic target localization for deep brain stimulation in dystonic children

OBJECT

The actual distortion present in a given series of magnetic resonance (MR) images is difficult to establish. The purpose of this study was to validate an MR imaging-based methodology for stereotactic targeting of the internal globus pallidus during electrode implantation in children in whom general anesthesia had been induced.

METHODS

Twelve children (mean follow up 1 year) suffering from generalized dystonia were treated with deep brain stimulation by using a head frame and MR imaging. To analyze the influence of distortions at every step of the procedure, the geometrical characteristics of the frame were first controlled using the localizer as a phantom. Then pre- and postoperative coordinates of fixed anatomical landmarks and electrode positions, both determined with the head frame in place, were statistically compared. No significant difference was observed between theoretical and measured dimensions of the localizer (Student's t-test, ¿t¿ > 2.2 for 12 patients) in the x, y, and z directions. No significant differences were observed (Wilcoxon paired-sample test) between the following: 1) pre- and postoperative coordinates of the anterior commissure (AC) (deltax = 0.3+/-0.29 mm and deltay = 0.34+/-0.32 mm) and posterior commissure (PC) (deltax = 0.15+/-0.18 mm and deltay = 0.34+/-0.25 mm); 2) pre- and postoperative AC-PC distance (deltaL = 0.33+/-0.22 mm); and 3) preoperative target and final electrode position coordinates (deltax = 0.24+/-0.22 mm; deltay = 0.19+/-0.16 mm).

CONCLUSIONS

In the authors' center, MR imaging distortions did not induce detectable errors during stereotactic surgery in dystonic children. Target localization and electrode implantation could be achieved using MR imaging alone after induction of general anesthesia. The remarkable postoperative improvement in these patients confirmed the accuracy of the procedure (Burke-Marsden-Fahn Dystonia Rating Scale score delta = -83.8%).