Automated extraction and variability analysis of sulcal neuroanatomy

Systematic mapping of the variability in cortical sulcal anatomy is an area of increasing interest which presents numerous methodological challenges. To address these issues, we have implemented sulcal extraction and assisted labeling (SEAL) to automatically extract the two-dimensional (2-D) surface ribbons that represent the median axis of cerebral sulci and to neuroanatomically label these entities. To encode the extracted three-dimensional (3-D) cortical sulcal schematic topography (CSST) we define a relational graph structure composed of two main features: vertices (representing sulci) and arcs (representing the relationships between sulci). Vertices contain a parametric representation of the surface ribbon buried within the sulcus. Points on this surface are expressed in stereotaxic coordinates (i.e., with respect to a standardized brain coordinate system). For each of these vertices, we store length, depth, and orientation as well as anatomical attributes (e.g., hemisphere, lobe, sulcus type, etc.). Each arc stores the 3-D location of the junction between sulci as well as a list of its connecting sulci. Sulcal labeling is performed semiautomatically by selecting a sulcal entity in the CSST and selecting from a menu of candidate sulcus names. In order to help the user in the labeling task, the menu is restricted to the most likely candidates by using priors for the expected sulcal spatial distribution. These priors, i.e., sulcal probabilistic maps, were created from the spatial distribution of 34 sulci traced manually on 36 different subjects. Given these spatial probability maps, the user is provided with the likelihood that the selected entity belongs to a particular sulcus. The cortical structure representation obtained by SEAL is suitable to extract statistical information about both the spatial and the structural composition of the cerebral cortical topography. This methodology allows for the iterative construction of a successively more complete statistical models of the cerebral topography containing spatial distributions of the most important structures, their morphometrics, and their structural components.

Allelotype analysis of uterine leiomyoma: localization of a potential tumor suppressor gene to a 4-cM region of chromosome 7q

Uterine leiomyoma is a benign smooth muscle tumor of the myometrium and is the most commonly encountered neoplasm in women of reproductive age. As for most benign tumors, the pathogenesis of leiomyoma remains obscure, especially at the molecular genetic level. The purpose of this study was to perform a genome-wide allelotype analysis to identify potential sites of tumor suppressor gene inactivation. Fifty-two cases of uterine leiomyoma were subjected to allelotype analysis by using matched pairs of tumor and blood DNA. Loss of heterozygosity (LOH) was assessed at 61 microsatellite markers distributed throughout the genome and representing all 41 chromosome arms. In general, LOH was very rare except on chromosome 7q, where LOH was observed in 34% of all informative tumors. Fine-deletion mapping with 25 microsatellite markers from the 7q22 region revealed a minimal deletion unit of approximately 4 cM, bounded by the markers D7S2453 proximally and D7S496 distally, that probably harbors a novel tumor suppressor gene involved in the etiology of this tumor.

Human brain function during odor encoding and recognition. A PET activation study

In previous positron emission tomography (PET) studies we have shown significant regional cerebral blood flow (rCBF) increases during olfactory stimulation: unilaterally in the right orbitofrontal cortex, and bilaterally in the inferior frontal and temporal lobes (piriform cortex). In the present study we investigated brain function during different stages of olfactory memory processing. Subjects were scanned during four tasks: odor encoding, long-term odor recognition, short-term odor recognition and a no-odor sensorimotor control task. Subjects were 12 right-handed healthy volunteers (6 men, 6 women). Each subject underwent a training session four days prior to their PET scan to learn the six odors required for the long-term memory scan. PET scans were obtained with a Siemens Exact ECAT HR+ 3D system using H2(15)O methodology and 60-sec scanning intervals. PET images were coregistered with each subject's magnetic resonance imaging scan, averaged, and transformed into standard stereotaxic space. Paired image subtractions were analyzed for rCBF changes. Preliminary analyses have revealed significant activation of the right orbitofrontal region and bilateral piriform cortices during the long-term odor recognition task compared with the control task. Activation of the right piriform cortex was present during the short-term recognition task. Brain activity during encoding and retrieval tasks also involved prefrontal cortices. PET activation studies of memory in other modalities have led to hypotheses of a hemispheric encoding/retrieval asymmetry in frontal cortex; the generalizability of this theory to olfactory memory will be discussed.

Cerebellar contributions to motor timing: a PET study of auditory and visual rhythm reproduction

The perception and production of temporal patterns, or rhythms, is important for both music and speech. However, the way in which the human brain achieves accurate timing of perceptual input and motor output is as yet little understood. Central control of both motor timing and perceptual timing across modalities has been linked to both the cerebellum and the basal ganglia (BG). The present study was designed to test the hypothesized central control of temporal processing and to examine the roles of the cerebellum, BG, and sensory association areas. In this positron emission tomography (PET) activation paradigm, subjects reproduced rhythms of increasing temporal complexity that were presented separately in the auditory and visual modalities. The results provide support for a supramodal contribution of the lateral cerebellar cortex and cerebellar vermis to the production of a timed motor response, particularly when it is complex and/or novel. The results also give partial support to the involvement of BG structures in motor timing, although this may be more directly related to implementation of the motor response than to timing per se. Finally, sensory association areas and the ventrolateral frontal cortex were found to be involved in modality-specific encoding and retrieval of the temporal stimuli. Taken together, these results point to the participation of a number of neural structures in the production of a timed motor response from an external stimulus. The role of the cerebellum in timing is conceptualized not as a clock or counter but simply as the structure that provides the necessary circuitry for the sensory system to extract temporal information and for the motor system to learn to produce a precisely timed response.

Automated atlas integration and interactive three-dimensional visualization tools for planning and guidance in functional neurosurgery

Many critical functionally distinct subcortical structures are not distinguishable on anatomical magnetic resonance imaging (MRI) scans. In order to provide the neurosurgeon with this missing information, a deformable volumetric atlas of the basal ganglia and thalamus has been created from the Schaltenbrand and Wahren atlas of cryogenic slices. The volumetric atlas can be automatically deformed to an individual patient's MRI. To facilitate the clinical use of the atlas, a visualization platform has been developed for preoperative and intraoperative use which permits manipulation of the merged atlas and MRI data sets in two- and three-dimensional views. The platform includes graphical tools which allow the visualization of projections of a leukotome and other surgical tools with respect to the atlas data, as well as preregistered images from any other imaging modality. In addition, a graphical interface has been designed to create custom virtual lesions using computer models of neurosurgical tools for intraoperative planning. To date this system has been employed as an adjunct to over 30 functional neurosurgical cases including surgery for movement disorders.

Increased oxygen consumption in human visual cortex: response to visual stimulation

To test whether a sufficiently complex visual stimulus causes the consumption of oxygen to rise in the human visual cortex, we used positron emission tomography (PET) to measure the cerebral metabolic rate of oxygen (CMRO2) during visual stimulation in 6 healthy normal volunteers. A yellow-blue checkerboard, reversing its contrast at a frequency of 8 Hz, was presented for a period of 7 min, beginning 4 min before the onset of a 3-min scan. In the baseline condition, subjects fixated a cross-hair from 30 s before until the end of the 3-min scan. The CMRO2 was calculated with the two-compartment weighted integration method (1). The checkerboard minus baseline subtraction yielded statistically significant increases in CMRO2 in the primary (V1) and higher order visual cortices (V4 and V5). The significant CMRO2 increases were detected in these regions in both the group average and in each individual subject.

Current status of food-borne parasitic zoonoses in South Africa and Namibia

Epidemiological data on food-borne parasitic zoonoses in countries of southern Africa are sporadic. In a study of toxoplasmosis in South Africa, there was an overall prevalence of 21% (2, 147/10,228). Prevalences vary between the different cultural groups and from one geographical region to another. The prevalence rate for the San (Bushmen) people of Namibia and Botswana was 9% (65/725) compared to the 30% (190/635) found in the Indian and Black communities of Kwazulu-Natal province, South Africa. These variations are probably linked to the dietary habits of the different cultural communities. Cysticercosis appears to be most prevalent in the Eastern Cape Province (former Transkei), where pigs roam freely and sanitation facilities are inadequate or non-existent. Segments of tapeworms often feature as an ingredient of concoctions prepared by traditional healers and are suspected sources of many of the cases of cysticercosis in South Africa. Trichinella nelsoni has been identified in wild game in South Africa: so far no cases of infection in humans have been recorded. Cases of Sarcocystis have been identified in some instances but infection is probably underdiagnosed in the country.

Improved correlation between scores on the expanded disability status scale and cerebral lesion load in relapsing-remitting multiple sclerosis. Results of the application of new imaging methods

We hypothesized that a better correlation between MRI and clinical measures of neurological disability using the expanded disability status scale (EDSS) in multiple sclerosis could be obtained by assessing lesion load only in and around the corticospinal tracts, since the EDSS is weighted towards motor and ambulatory deficits. Multiple sclerosis lesions in cerebral MRIs from 39 patients with relapsing-remitting multiple sclerosis were manually painted using a three-dimensional computer display tool and mapped into a standardized three-dimensional coordinate space. Total lesion load was then measured. A mask to expose only the corticospinal tract was extracted from an MRI atlas and used to measure lesion load in the corticospinal tract. To account for the residual anatomical variability among the different MRI volumes after stereotaxic transformation, the corticospinal tract mask was dilated to various degrees and the lesion load remeasured. Spearman's rank correlation coefficient was used to calculate the correlation between the EDSS and total lesion load and corticospinal tract lesion load and between the EDSS subscores and total lesion load and corticospinal tract lesion load. Spearman's rank correlation coefficient between the EDSS and total lesion load was 0.6, probably reflecting the rather broad EDSS range represented in the study. The highest correlation of 0.67 was between the EDSS and corticospinal tract lesion load, dilated with a blurring kernel of 8-10 mm. The pyramidal subscore alone showed a weaker correlation with total lesion load, and with corticospinal tract lesion load, than did the overall EDSS, possibly reflecting the narrow range of disability in these subscores in patients with EDSS scores of 1-6.5. The imperfect correlation between the EDSS and corticospinal tract lesion load suggests that factors other than cerebral T2-weighted lesion volume are important determinants of disability.

A role for the hippocampal formation in implicit memory: a 3-D PET study

The apparent preservation of word priming effects in amnesia has been interpreted as supporting the view that implicit memory depends on brain systems that are independent of mesial temporal lobe structures which are in part responsible for explicit memory disorders. Nevertheless, a number of studies have demonstrated word priming deficits in amnesic patients relatively to normal subjects, suggesting that such structures may also be involved in implicit memory. To determine whether one such structure, the hippocampal formation, is a component of the brain system subserving word priming, a 3-D PET study was carried out in 13 normal individuals. Encoding was carried out using the brief multiple presentation technique, a procedure that allows one to effectively circumvent contamination of implicit memory tasks by explicit memory strategies. Results revealed that word priming was indeed associated with an activation of the right hippocampal formation. This finding of an hippocampal involvement in word priming calls into question the notion of absolute dissociability between the brain systems underlying performance on various explicit and implicit memory tasks.

Design and construction of a realistic digital brain phantom

After conception and implementation of any new medical image processing algorithm, validation is an important step to ensure that the procedure fulfills all requirements set forth at the initial design stage. Although the algorithm must be evaluated on real data, a comprehensive validation requires the additional use of simulated data since it is impossible to establish ground truth with in vivo data. Experiments with simulated data permit controlled evaluation over a wide range of conditions (e.g., different levels of noise, contrast, intensity artefacts, or geometric distortion). Such considerations have become increasingly important with the rapid growth of neuroimaging, i.e., computational analysis of brain structure and function using brain scanning methods such as positron emission tomography and magnetic resonance imaging. Since simple objects such as ellipsoids or parallelepipedes do not reflect the complexity of natural brain anatomy, we present the design and creation of a realistic, high-resolution, digital, volumetric phantom of the human brain. This three-dimensional digital brain phantom is made up of ten volumetric data sets that define the spatial distribution for different tissues (e.g., grey matter, white matter, muscle, skin, etc.), where voxel intensity is proportional to the fraction of tissue within the voxel. The digital brain phantom can be used to simulate tomographic images of the head. Since the contribution of each tissue type to each voxel in the brain phantom is known, it can be used as the gold standard to test analysis algorithms such as classification procedures which seek to identify the tissue "type" of each image voxel. Furthermore, since the same anatomical phantom may be used to drive simulators for different modalities, it is the ideal tool to test intermodality registration algorithms. The brain phantom and simulated MR images have been made publicly available on the Internet (http://www.bic.mni.mcgill.ca/brainweb).

Abnormal basal ganglia outflow in Parkinson's disease identified with PET. Implications for higher cortical functions

In this study we examined the effects of striatal dopamine depletion on cortical and subcortical blood flow changes during two tasks known to involve frontostriatal circuitry. Regional cerebral blood flow was measured in six patients with moderate Parkinson's disease and in six age-matched control subjects while they performed easy and difficult versions of a modified Tower of London planning task and a mnemonic variant of this task that required short-term retention and reproduction of problem solutions, as well as a control condition that involved identical visual stimuli and motor responses. Relative to control conditions, the planning task was associated with an increase in cerebral blood flow centred on the internal segment of the right globus pallidus in the age-matched control subjects, and a decrease in the same region in the patients with Parkinson's disease. A similar inverse relationship between the task-specific blood flow change observed in the control group and that observed in the Parkinson's disease patients was not found in any other subcortical or cortical area examined, including regions of the dorsolateral frontal cortex known to be involved in this task. When blood flow in the spatial working memory task was examined, a similarly specific dissociation between the two groups of subjects was observed at similar coordinates in the right pallidum. We conclude that striatal dopamine depletion disrupts the normal pattern of basal ganglia outflow in Parkinson's disease and consequently, affects the expression of frontal-lobe functions by interrupting normal transmission of information through frontostriatal circuitry.

Correction for partial volume effects in PET: principle and validation

The accuracy of PET for measuring regional radiotracer concentrations in the human brain is limited by the finite resolution capability of the scanner and the resulting partial volume effects (PVEs). We designed a new algorithm to correct for PVEs by characterizing the geometric interaction between the PET system and the brain activity distribution.

METHODS

The partial volume correction (PVC) algorithm uses high-resolution volumetric MR images correlated with the PET volume. We used a PET simulator to calculate recovery and cross-contamination factors of identified tissue components in the brain model. These geometry-dependent transfer coefficients form a matrix representing the fraction of true activity from each distinct brain region observed in any given set of regions of interest. This matrix can be inverted to correct for PVEs, independent of the tracer concentrations in each tissue component. A sphere phantom was used to validate the simulated point-spread function of the PET scanner. Accuracy and precision of the PVC method were assessed using a human basal ganglia phantom. A constant contrast experiment was performed to explore the recovery capability and statistic error propagation of PVC in various noise conditions. In addition, a dual-isotope experiment was used to evaluate the ability of the PVC algorithm to recover activity concentrations in small structures surrounded by background activity with a different radioactive half-life. This models the time-variable contrast between regions that is often seen in neuroreceptor studies.

RESULTS

Data from the three-dimensional brain phantom demonstrated a full recovery capability of PVC with less than 10% root mean-square error in terms of absolute values, which decreased to less than 2% when results from four PET slices were averaged. Inaccuracy in the estimation of 18F tracer half-life in the presence of 11C background activity was in the range of 25%-50% before PVC and 0%-6% after PVC, for resolution varying from 6 to 14 mm FWHM. In terms of noise propagation, the degradation of the coefficient of variation after PVC was found to be easily predictable and typically on the order of 25%.

CONCLUSION

The PVC algorithm allows the correction for PVEs simultaneously in all identified brain regions, independent of tracer levels.

Functional anatomy of musical processing in listeners with absolute pitch and relative pitch

We used both structural and functional brain imaging techniques to investigate the neural basis of absolute pitch (AP), a specialized skill present in some musicians. By using positron emission tomography, we measured cerebral blood flow during the presentation of musical tones to AP possessors and to control musicians without AP. Listening to musical tones resulted in similar patterns of increased cerebral blood flow in auditory cortical areas in both groups, as expected. The AP group also demonstrated activation of the left posterior dorsolateral frontal cortex, an area thought to be related to learning conditional associations. However, a similar pattern of left dorsolateral frontal activity was also observed in non-AP subjects when they made relative pitch judgments of intervals, such as minor or major. Conversely, activity within the right inferior frontal cortex was observed in control but not in AP subjects during the interval-judgment task, suggesting that AP possessors need not access working memory mechanisms in this task. MRI measures of cortical volume indicated a larger left planum temporale in the AP group, which correlated with performance on an pitch-naming task. Our findings suggest that AP may not be associated with a unique pattern of cerebral activity but rather may depend on the recruitment of a specialized network involved in the retrieval and manipulation of verbal-tonal associations.

Enhancement of MR images using registration for signal averaging

PURPOSE

With the advent of noninvasive neuroimaging, a plethora of digital human neuroanatomical atlases has been developed. The accuracy of these atlases is constrained by the resolution and signal-gathering powers of available imaging equipment. In an attempt to circumvent these limitations and to produce a high resolution in vivo human neuroanatomy, we investigated the usefulness of intrasubject registration for post hoc MR signal averaging.

METHOD

Twenty-seven high resolution (7 x 0.78 and 20 x 1.0 mm3) T1-weighted volumes were acquired from a single subject, along with 12 double echo T2/proton density-weighted volumes. These volumes were automatically registered to a common stereotaxic space in which they were subsampled and intensity averaged. The resulting images were examined for anatomical quality and usefulness for other analytical techniques.

RESULTS

The quality of the resulting image from the combination of as few as five T1 volumes was visibly enhanced. The signal-to-noise ratio was expected to increase as the root of the number of contributing scans to 5.2, n = 27. The improvement in the n = 27 average was great enough that fine anatomical details, such as thalamic subnuclei and the gray bridges between the caudate and putamen, became crisply defined. The gray/white matter boundaries were also enhanced, as was the visibility of any finer structure that was surrounded by tissue of varying T1 intensity. The T2 and proton density average images were also of higher quality than single scans, but the improvement was not as dramatic as that of the T1 volumes.

CONCLUSION

Overall, the enhanced signal in the averaged images resulted in higher quality anatomical images, and the data lent themselves to several postprocessing techniques. The high quality of the enhanced images permits novel uses of the data and extends the possibilities for in vivo human neuroanatomy.

A nonparametric method for automatic correction of intensity nonuniformity in MRI data

A novel approach to correcting for intensity nonuniformity in magnetic resonance (MR) data is described that achieves high performance without requiring a model of the tissue classes present. The method has the advantage that it can be applied at an early stage in an automated data analysis, before a tissue model is available. Described as nonparametric nonuniform intensity normalization (N3), the method is independent of pulse sequence and insensitive to pathological data that might otherwise violate model assumptions. To eliminate the dependence of the field estimate on anatomy, an iterative approach is employed to estimate both the multiplicative bias field and the distribution of the true tissue intensities. The performance of this method is evaluated using both real and simulated MR data.

Dose-dependent reduction of cerebral blood flow during rapid-rate transcranial magnetic stimulation of the human sensorimotor cortex

Rapid-rate transcranial magnetic stimulation (rTMS) was used to stimulate the primary sensorimotor cortex in six healthy volunteers while regional changes in cerebral blood flow (CBF) were simultaneously measured by means of positron emission tomography. A figure-eight TMS coil (Cadwell Corticoil) was positioned, using frameless stereotaxy, over the probabilistic location of the left primary sensorimotor cortex, and a series of brief 10-Hz trains of TMS was delivered at subthreshold intensity during each of six 60-s scans. The scans differed in the number of trains delivered, namely 5, 10, 15, 20, 25, and 30 trains/scan, respectively. In the left primary sensorimotor cortex, CBF covaried significantly and negatively with the number of stimulus trains. These CBF decreases may reflect TMS-induced activation of local inhibitory mechanisms known to play a role in TMS-related phenomena, such as the electromyographic silent period.

Flavor processing: more than the sum of its parts

We used positron emission tomography to evaluate differential processing of olfactory, gustatory and combined olfactory and gustatory (flavor) stimuli as indicated by comparison of evoked cerebral blood flow (CBF) changes during these conditions. We found significant CBF decreases in primary gustatory and secondary gustatory and olfactory cortices during simultaneous presentation compared with independent presentations of identical stimuli, suggesting that flavor processing is not represented by a simple convergence of its component senses. Additionally, CBF increases in the amygdala and basal forebrain were observed in a mismatched flavor condition versus a matched flavor condition, suggesting a role for these structures in processing novel or unpleasant stimuli.

Characterizing the response of PET and fMRI data using multivariate linear models

This paper presents a new method for characterizing brain responses in both PET and fMRI data. The aim is to capture the correlations between the scans of an experiment and a set of external predictor variables that are thought to affect the scans, such as type, intensity, or shape of stimulus response. Its main feature is a Canonical Variates Analysis (CVA) of the estimated effects of the predictors from a multivariate linear model (MLM). The advantage of this over current methods is that temporal correlations can be incorporated into the model, making the MLM method suitable for fMRI as well as PET data. Moreover, tests for the presence of any correlation, and inference about the number of canonical variates needed to capture that correlation, can be based on standard multivariate statistics, rather than simulations. When applied to an fMRI data set previously analyzed by another CVA method, the MLM method reveals a pattern of responses that is closer to that detected in an earlier non-CVA analysis.

Obligatory role of the LIFG in synonym generation: evidence from PET and cortical stimulation

We report results from a patient in whom we obtained converging evidence from positron emission tomography (PET) and intraoperative stimulation mapping to support a one-way dissociation between the functional areas involved in word repetition and synonym generation. Intraoperative stimulation mapping interfered with synonym generation but did not disturb word repetition at the same left inferior frontal site at which a cerebral blood flow (CBF) increase had been observed for a synonym generation task. The results for this single subject suggest that the functional areas involved in different aspects of linguistic processing are dissociable and that specific disruption under conditions of cortical stimulation can be correlated with the brain regions identified via PET as the most active during performance of a specific task.