Mapping histology to metabolism: coregistration of stained whole-brain sections to premortem PET in Alzheimer's disease

Tensor image registration library: Deformable registration of stand-alone histology images to whole-brain post-mortem MRI data

BACKGROUND

Accurate registration between microscopy and MRI data is necessary for validating imaging biomarkers against neuropathology, and to disentangle complex signal dependencies in microstructural MRI. Existing registration methods often rely on serial histological sampling or significant manual input, providing limited scope to work with a large number of stand-alone histology sections. Here we present a customisable pipeline to assist the registration of stand-alone histology sections to whole-brain MRI data.

METHODS

Our pipeline registers stained histology sections to whole-brain post-mortem MRI in 4 stages, with the help of two photographic intermediaries: a block face image (to undistort histology sections) and coronal brain slab photographs (to insert them into MRI space). Each registration stage is implemented as a configurable stand-alone Python script using our novel platform, Tensor Image Registration Library (TIRL), which provides flexibility for wider adaptation. We report our experience of registering 87 PLP-stained histology sections from 14 subjects and perform various experiments to assess the accuracy and robustness of each stage of the pipeline.

RESULTS

All 87 histology sections were successfully registered to MRI. Histology-to-block registration (Stage 1) achieved 0.2-0.4 mm accuracy, better than commonly used existing methods. Block-to-slice matching (Stage 2) showed great robustness in automatically identifying and inserting small tissue blocks into whole brain slices with 0.2 mm accuracy. Simulations demonstrated sub-voxel level accuracy (0.13 mm) of the slice-to-volume registration (Stage 3) algorithm, which was observed in over 200 actual brain slice registrations, compensating 3D slice deformations up to 6.5 mm. Stage 4 combined the previous stages and generated refined pixelwise aligned multi-modal histology-MRI stacks.

CONCLUSIONS

Our open-source pipeline provides robust automation tools for registering stand-alone histology sections to MRI data with sub-voxel level precision, and the underlying framework makes it readily adaptable to a diverse range of microscopy-MRI studies.

Inflammation: major denominator of obesity, Type 2 diabetes and Alzheimer's disease-like pathology?

Adipose tissue is an active metabolic organ that contributes to processes such as energy storage and utilization and to the production of a number of metabolic agents, such as adipokines, which play a role in inflammation. In this review, we try to elucidate the connections between peripheral inflammation at obesity and Type 2 diabetes and the central inflammatory process. Multiple lines of evidence highlight the importance of peripheral inflammation and its link to neuroinflammation, which can lead to neurodegenerative diseases such as dementia, Alzheimer's disease (AD) and Parkinson's disease. In addition to the accumulation of misfolded amyloid beta (Aβ) peptide and the formation of the neurofibrillary tangles of hyperphosphorylated tau protein in the brain, activated microglia and reactive astrocytes are the main indicators of AD progression. They were found close to Aβ plaques in the brains of both AD patients and rodent models of Alzheimer's disease-like pathology. Cytokines are key players in pro- and anti-inflammatory processes and are also produced by microglia and astrocytes. The interplay of seemingly unrelated pathways between the periphery and the brain could, in fact, have a common denominator, with inflammation in general being a key factor affecting neuronal processes in the brain. An increased amount of white adipose tissue throughout the body seems to be an important player in pro-inflammatory processes. Nevertheless, other important factors should be studied to elucidate the pathological processes of and the relationship among obesity, Type 2 diabetes and neurodegenerative diseases.

Rhesus Macaque Brain Atlas Regions Aligned to an MRI Template

To aid in the analysis of rhesus macaque brain images, we aligned digitized anatomical regions from the widely used atlas of Paxinos et al. to a published magnetic resonance imaging (MRI) template based on a large number of subjects. Digitally labelled atlas images were aligned to the template in 2D and then in 3D. The resulting grey matter regions appear qualitatively to be well registered to the template. To quantitatively validate the procedure, MR brain images of 20 rhesus macaques were aligned to the template along with regions drawn by hand in striatal and cortical areas in each subject's MRI. There was good geometric overlap between the hand drawn regions and the template regions. Positron emission tomography (PET) images of the same subjects showing uptake of a dopamine D₂ receptor ligand were aligned to the template space, and good agreement was found between tracer binding measures calculated using the hand drawn and template regions. In conclusion, an anatomically defined set of rhesus macaque brain regions has been aligned to an MRI template and has been validated for analysis of PET imaging in a subset of striatal and cortical areas. The entire set of over 200 regions is publicly available at https://www.nitrc.org/ . Graphical Abstract ᅟ.

Dissecting the pathobiology of altered MRI signal in amyotrophic lateral sclerosis: A post mortem whole brain sampling strategy for the integration of ultra-high-field MRI and quantitative neuropathology

BACKGROUND

Amyotrophic lateral sclerosis (ALS) is a clinically and histopathologically heterogeneous neurodegenerative disorder, in which therapy is hindered by the rapid progression of disease and lack of biomarkers. Magnetic resonance imaging (MRI) has demonstrated its potential for detecting the pathological signature and tracking disease progression in ALS. However, the microstructural and molecular pathological substrate is poorly understood and generally defined histologically. One route to understanding and validating the pathophysiological correlates of MRI signal changes in ALS is to directly compare MRI to histology in post mortem human brains.

RESULTS

The article delineates a universal whole brain sampling strategy of pathologically relevant grey matter (cortical and subcortical) and white matter tracts of interest suitable for histological evaluation and direct correlation with MRI. A standardised systematic sampling strategy that was compatible with co-registration of images across modalities was established for regions representing phosphorylated 43-kDa TAR DNA-binding protein (pTDP-43) patterns that were topographically recognisable with defined neuroanatomical landmarks. Moreover, tractography-guided sampling facilitated accurate delineation of white matter tracts of interest. A digital photography pipeline at various stages of sampling and histological processing was established to account for structural deformations that might impact alignment and registration of histological images to MRI volumes. Combined with quantitative digital histology image analysis, the proposed sampling strategy is suitable for routine implementation in a high-throughput manner for acquisition of large-scale histology datasets. Proof of concept was determined in the spinal cord of an ALS patient where multiple MRI modalities (T1, T2, FA and MD) demonstrated sensitivity to axonal degeneration and associated heightened inflammatory changes in the lateral corticospinal tract. Furthermore, qualitative comparison of R2* and susceptibility maps in the motor cortex of 2 ALS patients demonstrated varying degrees of hyperintense signal changes compared to a control. Upon histological evaluation of the same region, intensity of signal changes in both modalities appeared to correspond primarily to the degree of microglial activation.

CONCLUSION

The proposed post mortem whole brain sampling methodology enables the accurate intraindividual study of pathological propagation and comparison with quantitative MRI data, to more fully understand the relationship of imaging signal changes with underlying pathophysiology in ALS.

Transformation diffusion reconstruction of three-dimensional histology volumes from two-dimensional image stacks

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A method for 3D reconstruction of serial 2D histology image stacks is proposed.

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Pre-alignment to an external pre-cut reference (blockface) prevents shape artifacts.

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Formulated as diffusion of transformations from each slice to its neighbors.

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Registrations replaced by much faster transformation operations.

Traditional histology is the gold standard for tissue studies, but it is intrinsically reliant on two-dimensional (2D) images. Study of volumetric tissue samples such as whole hearts produces a stack of misaligned and distorted 2D images that need to be reconstructed to recover a congruent volume with the original sample's shape. In this paper, we develop a mathematical framework called Transformation Diffusion (TD) for stack alignment refinement as a solution to the heat diffusion equation. This general framework does not require contour segmentation, is independent of the registration method used, and is trivially parallelizable. After the first stack sweep, we also replace registration operations by operations in the space of transformations, several orders of magnitude faster and less memory-consuming. Implementing TD with operations in the space of transformations produces our Transformation Diffusion Reconstruction (TDR) algorithm, applicable to general transformations that are closed under inversion and composition. In particular, we provide formulas for translation and affine transformations. We also propose an Approximated TDR (ATDR) algorithm that extends the same principles to tensor-product B-spline transformations. Using TDR and ATDR, we reconstruct a full mouse heart at pixel size 0.92 µm × 0.92 µm, cut 10 µm thick, spaced 20 µm (84G). Our algorithms employ only local information from transformations between neighboring slices, but the TD framework allows theoretical analysis of the refinement as applying a global Gaussian low-pass filter to the unknown stack misalignments. We also show that reconstruction without an external reference produces large shape artifacts in a cardiac specimen while still optimizing slice-to-slice alignment. To overcome this problem, we use a pre-cutting blockface imaging process previously developed by our group that takes advantage of Brewster's angle and a polarizer to capture the outline of only the topmost layer of wax in the block containing embedded tissue for histological sectioning.

Extending two-dimensional histology into the third dimension through conventional micro computed tomography

Histological examination achieves sub-micrometer resolution laterally. In the third dimension, however, resolution is limited to section thickness. In addition, histological sectioning and mounting sections on glass slides introduce tissue-dependent stress and strain. In contrast, state-of-the-art hard X-ray micro computed tomography (μCT) systems provide isotropic sub-micrometer resolution and avoid sectioning artefacts. The drawback of μCT in the absorption contrast mode for visualising physically soft tissue is a low attenuation difference between anatomical features. In this communication, we demonstrate that formalin-fixed paraffin-embedded human cerebellum yields appropriate absorption contrast in laboratory-based μCT data, comparable to conventional histological sections. Purkinje cells, for example, are readily visible. In order to investigate the pros and cons of complementary approaches, two- and three-dimensional data were manually and automatically registered. The joint histogram of histology and the related μCT slice allows for a detailed discussion on how to integrate two-dimensional information from histology into a three-dimensional tomography dataset. This methodology is not only rewarding for the analysis of the human cerebellum, but it also has relevance for investigations of tissue biopsies and post-mortem applications. Our data indicate that laboratory-based μCT as a modality can fill the gap between synchrotron radiation-based μCT and histology for a variety of tissues. As the information from haematoxylin and eosin (H&E) stained sections and μCT data is related, one can colourise local X-ray absorption values according to the H&E stain. Hence, μCT data can correlate and virtually extend two-dimensional (2D) histology data into the third dimension.

A method for accurate spatial registration of PET images and histopathology slices

BACKGROUND

Accurate alignment between histopathology slices and positron emission tomography (PET) images is important for radiopharmaceutical validation studies. Limited data is available on the registration accuracy that can be achieved between PET and histopathology slices acquired under routine pathology conditions where slices may be non-parallel, non-contiguously cut and of standard block size. The purpose of this study was to demonstrate a method for aligning PET images and histopathology slices acquired from patients with laryngeal cancer and to assess the registration accuracy obtained under these conditions.

METHODS

Six subjects with laryngeal cancer underwent a (64)Cu-copper-II-diacetyl-bis(N4-methylthiosemicarbazone) ((64)Cu-ATSM) PET computed tomography (CT) scan prior to total laryngectomy. Sea urchin spines were inserted into the pathology specimen to act as fiducial markers. The specimen was fixed in formalin, as per standard histopathology operating procedures, and was then CT scanned and cut into millimetre-thick tissue slices. A subset of the tissue slices that included both tumour and fiducial markers was taken and embedded in paraffin blocks. Subsequently, microtome sectioning and haematoxylin and eosin staining were performed to produce 5-μm-thick tissue sections for microscopic digitisation. A series of rigid registration procedures was performed between the different imaging modalities (PET; in vivo CT-i.e. the CT component of the PET-CT; ex vivo CT; histology slices) with the ex vivo CT serving as the reference image. In vivo and ex vivo CTs were registered using landmark-based registration. Histopathology and ex vivo CT images were aligned using the sea urchin spines with additional anatomical landmarks where available. Registration errors were estimated using a leave-one-out strategy for in vivo to ex vivo CT and were estimated from the RMS landmark accuracy for histopathology to ex vivo CT.

RESULTS

The mean ± SD accuracy for registration of the in vivo to ex vivo CT images was 2.66 ± 0.66 mm, and the accuracy for registration of histopathology to ex vivo CT was 0.86 ± 0.41 mm. Estimating the PET to in vivo CT registration accuracy to equal the PET-CT alignment accuracy of 1 mm resulted in an overall average registration error between PET and histopathology slices of 3.0 ± 0.7 mm.

CONCLUSIONS

We have developed a registration method to align PET images and histopathology slices with an accuracy comparable to the spatial resolution of the PET images.

Patch-Based Nonlinear Image Registration for Gigapixel Whole Slide Images

OBJECTIVE

Image registration of whole slide histology images allows the fusion of fine-grained information-like different immunohistochemical stains-from neighboring tissue slides. Traditionally, pathologists fuse this information by looking subsequently at one slide at a time. If the slides are digitized and accurately aligned at cell level, automatic analysis can be used to ease the pathologist's work. However, the size of those images exceeds the memory capacity of regular computers.

METHODS

We address the challenge to combine a global motion model that takes the physical cutting process of the tissue into account with image data that is not simultaneously globally available. Typical approaches either reduce the amount of data to be processed or partition the data into smaller chunks to be processed separately. Our novel method first registers the complete images on a low resolution with a nonlinear deformation model and later refines this result on patches by using a second nonlinear registration on each patch. Finally, the deformations computed on all patches are combined by interpolation to form one globally smooth nonlinear deformation. The NGF distance measure is used to handle multistain images.

RESULTS

The method is applied to ten whole slide image pairs of human lung cancer data. The alignment of 85 corresponding structures is measured by comparing manual segmentations from neighboring slides. Their offset improves significantly, by at least 15%, compared to the low-resolution nonlinear registration.

CONCLUSION/SIGNIFICANCE

The proposed method significantly improves the accuracy of multistain registration which allows us to compare different antibodies at cell level.

Autopsy as Gold Standard in FDG-PET Studies in Dementia

Positron emission tomography (PET) imaging with F18-fluorodeoxyglucose (FDG) is increasingly used as an adjunct to clinical evaluation in the diagnosis of dementia. Considering that most FDG-PET studies in dementia use clinical diagnosis as gold standard and that clinical diagnosis is approximately 80% sensitive or accurate, we aim to review the evidence-based data on the diagnostic accuracy of brain FDG-PET in dementia when cerebral autopsy is used as gold standard. We searched the PubMed and Medline databases for dementia-related articles that correlate histopathological diagnosis at autopsy with FDG-PET imaging and found 47 articles among which there were only 5 studies of 20 patients or more. We were able to conclude that sensitivity and specificity of FDG-PET for Alzheimer's disease are good, but more studies using histopathological diagnosis at autopsy as gold standard are needed in order to evaluate what FDG-PET truly adds to premortem diagnostic accuracy in dementia.

3D reconstruction of 2D fluorescence histology images and registration with in vivo MR images: application in a rodent stroke model

To validate and add value to non-invasive imaging techniques, the corresponding histology is required to establish biological correlates. We present an efficient, semi-automated image-processing pipeline that uses immunohistochemically stained sections to reconstruct a 3D brain volume from 2D histological images before registering these with the corresponding 3D in vivo magnetic resonance images (MRI). A multistep registration procedure that first aligns the "global" volume by using the centre of mass and then applies a rigid and affine alignment based on signal intensities is described. This technique was applied to a training set of three rat brain volumes before being validated on three normal brains. Application of the approach to register "abnormal" images from a rat model of stroke allowed the neurobiological correlates of the variations in the hyper-intense MRI signal intensity caused by infarction to be investigated. For evaluation, the corresponding anatomical landmarks in MR and histology were defined to measure the registration accuracy. A registration error of 0.249 mm (approximately one in-plane voxel dimension) was evident in healthy rat brains and of 0.323 mm in a rodent model of stroke. The proposed reconstruction and registration pipeline allowed for the precise analysis of non-invasive MRI and corresponding microstructural histological features in 3D. We were thus able to interrogate histology to deduce the cause of MRI signal variations in the lesion cavity and the peri-infarct area.

Recent advances in imaging Alzheimer's disease

Advances in brain imaging technology in the past five years have contributed greatly to the understanding of Alzheimer's disease (AD). Here, we review recent research related to amyloid imaging, new methods for magnetic resonance imaging analyses, and statistical methods. We also review research that evaluates AD risk factors and brain imaging, in the context of AD prediction and progression. We selected a variety of illustrative studies, describing how they advanced the field and are leading AD research in promising new directions.

Combined MR, fluorescence and histology imaging strategy in a human breast tumor xenograft model

Applications of molecular imaging in cancer and other diseases frequently require the combination of in vivo imaging modalities, such as MR and optical imaging, with ex vivo optical, fluorescence, histology and immunohistochemical imaging to investigate and relate molecular and biological processes to imaging parameters within the same region of interest. We have developed a multimodal image reconstruction and fusion framework that accurately combines in vivo MRI and MRSI, ex vivo brightfield and fluorescence microscopic imaging and ex vivo histology imaging. Ex vivo brightfield microscopic imaging was used as an intermediate modality to facilitate the ultimate link between ex vivo histology and in vivo MRI/MRSI. Tissue sectioning necessary for optical and histology imaging required the generation of a three-dimensional reconstruction module for two-dimensional ex vivo optical and histology imaging data. We developed an external fiducial marker-based three-dimensional reconstruction method, which was able to fuse optical brightfield and fluorescence with histology imaging data. The registration of the three-dimensional tumor shape was pursued to combine in vivo MRI/MRSI and ex vivo optical brightfield and fluorescence imaging data. This registration strategy was applied to in vivo MRI/MRSI, ex vivo optical brightfield/fluorescence and histology imaging datasets obtained from human breast tumor models. Three-dimensional human breast tumor datasets were successfully reconstructed and fused with this platform.

Pathologic lesions in neurodegenerative diseases

This chapter will discuss two of the most widely used approaches to assessing brain structure: neuroimaging and neuropathology. Whereas neuropathologic approaches to studying the central nervous system have been utilized for many decades and have provided insights into morphologic correlates of dementia for over 100 years, accurate structural imaging techniques "blossomed" with the development and refinement of computerized tomographic scanning and magnetic resonance imaging (MRI), beginning in the late 1970s. As Alzheimer disease progresses over time, there is progressive atrophy of the hippocampus and neocortex--this can be quantified and regional accentuation of the atrophy can be evaluated using quantitative MRI scanning. Furthermore, ligands for amyloid proteins have recently been developed--these can be used in positron emission tomography studies to localize amyloid proteins, and (in theory) study the dynamics of their deposition (and clearance) within the brain over time. Neuropathologic studies of the brain, using highly specific antibodies, can demonstrate synapse loss and the deposition of proteins important in AD progression--specifically ABeta and phosphor-tau. Finally, neuropathologic assessment of (autopsy) brain specimens can provide important correlation with sophisticated neuroimaging techniques.

Staging Alzheimer's disease progression with multimodality neuroimaging

Rapid developments in medical neuroimaging have made it possible to reconstruct the trajectory of Alzheimer's disease (AD) as it spreads through the living brain. The current review focuses on the progressive signature of brain changes throughout the different stages of AD. We integrate recent findings on changes in cortical gray matter volume, white matter fiber tracts, neuropathological alterations, and brain metabolism assessed with molecular positron emission tomography (PET). Neurofibrillary tangles accumulate first in transentorhinal and cholinergic brain areas, and 4-D maps of cortical volume changes show early progressive temporo-parietal cortical thinning. Findings from diffusion tensor imaging (DTI) for assessment fiber tract integrity show cortical disconnection in corresponding brain networks. Importantly, the developmental trajectory of brain changes is not uniform and may be modulated by several factors such as onset of disease mechanisms, risk-associated and protective genes, converging comorbidity, and individual brain reserve. There is a general agreement between in vivo brain maps of cortical atrophy and amyloid pathology assessed through PET, reminiscent of post mortem histopathology studies that paved the way in the staging of AD. The association between in vivo and post mortem findings will clarify the temporal dynamics of pathophysiological alterations in the development of preclinical AD. This will be important in designing effective treatments that target specific underlying disease AD mechanisms.

Association between executive dysfunction and hippocampal volume in Alzheimer's disease

BACKGROUND

Some previous research has hypothesized that executive dysfunction in patients with early Alzheimer's disease (AD) occurs as a result of a disconnection between different cerebral areas. The aim of the present study was to evaluate how the hippocampal volume influences executive function as a non-memory cognitive function.

METHODS

From 157 consecutive patients with AD or amnestic mild cognitive impairment (A-MCI), we recruited 107 subjects who had a global Clinical Dementia Rating (CDR) of 0.5 or 1.0 and whose degree of hippocampal atrophy had been measured using magnetic resonance imaging (MRI); the severity of atrophy was assessed using the voxel-based specific regional analysis for Alzheimer's disease (VSRAD) system. We divided the subjects into three groups: mild atrophy, 0 < Z-score < 1.0 (N = 21); moderate atrophy, 1.0 ≤ Z-score < 2.0 (N = 46); or severe atrophy, 2.0 ≤ Z-score < 4.0 (N = 40) according to the Z-score and compared the Frontal Assessment Battery (FAB) and its subtest scores between each atrophy group.

RESULTS

The results demonstrated that age, sex ratio, duration of illness, education years, MMSE score, Behave-AD score, and proportion of atrophy area in total brain (%) were not significantly different among the three groups. Only the go/no-go score among the six subtests was significantly lower for increasing atrophy severity (P < 0.05). Furthermore, hippocampal atrophy significantly influenced the go/no-go score independently of interactions from whether the diagnosis was early AD or A-MCI (P < 0.05).

CONCLUSION

These results support a significant association between hippocampal atrophy and executive dysfunction as a non-memory cognitive impairment in patients with early AD and A-MCI.

Semi-automatic deformable registration of prostate MR images to pathological slices

PURPOSE

To present a semi-automatic deformable registration algorithm for co-registering T2-weighted (T2w) images of the prostate with whole-mount pathological sections of prostatectomy specimens.

MATERIALS AND METHODS

Twenty-four patients underwent 1.5 Tesla (T) endorectal MR imaging before radical prostatectomy with whole-mount step-section pathologic analysis of surgical specimens. For each patient, the T2w imaging containing the largest area of tumor was manually matched with the corresponding pathologic slice. The prostate was co-registered using a free-form deformation (FFD) algorithm based on B-splines. Registration quality was assessed through differences between prostate diameters measured in right-left (RL) and anteroposterior (AP) directions on T2w images and pathologic slices and calculation of the Dice similarity coefficient, D, for the whole prostate (WP), the peripheral zone (PZ) and the transition zone (TZ).

RESULTS

The mean differences in diameters measured on pathology and MR imaging in the RL direction and the AP direction were 0.49 cm and -0.63 cm, respectively, before registration and 0.10 cm and -0.11 cm, respectively, after registration. The mean D values for the WP, PZ and TZ, were 0.76, 0.65, and 0.77, respectively, before registration and increased to 0.91, 0.76, and 0.85, respectively, after registration. The improvements in D were significant for all three tissues (P < 0.001 for all).

CONCLUSION

The proposed semi-automatic method enabled successful co-registration of anatomical prostate MR images to pathologic slices.

Smoothness-guided 3-D reconstruction of 2-D histological images

This paper tackles two problems: (1) the reconstruction of 3-D volumes from 2-D post-mortem slices (e.g., histology, autoradiography, immunohistochemistry) in the absence of external reference, and (2) the quantitative evaluation of the 3-D reconstruction. We note that the quality of a reconstructed volume is usually assessed by considering the smoothness of some reconstructed structures of interest (e.g., the gray-white matter surfaces in brain images). Here we propose to use smoothness as a means to drive the reconstruction process itself. From a pair-wise rigid reconstruction of the 2-D slices, we first extract the boundaries of structures of interest. Those are then smoothed with a min-max curvature flow confined to the 2-D planes in which the slices lie. Finally, for each slice, we estimate a linear or flexible transformation from the sparse displacement field computed from the flow, which we apply to the original 2-D slices to obtain a smooth volume. In addition, we present a co-occurrence matrix-based technique to quantify the smoothness of reconstructed volumes. We discuss and validate the application of both our reconstruction approach and the smoothness measure on synthetic examples as well as real histological data.

Deformable registration of histological sections to brain MR images using a hybrid boundary-based slice-to-volume approach

Registration of histology to three-dimensional (3D) magnetic resonance (MR) images is often required for the analysis of brain structure and investigation of brain pathologies. A novel algorithm for deformable registration of an individual histological section to a brain MR image is described. The cost function uses a novel hybrid intensity- and boundary surface-based measure that reflects the contrast of histological slice intensities across the boundary of the pial and inner cortical surface. The algorithm relies on implicit representation of cortical surfaces reconstructed from an anatomical MR image, and computes the cost function in a level set framework. The algorithm is evaluated on cross-modality registration of myelin-stained histological sections to a high-resolution MR image of the human brain.

Slice-to-Volume Nonrigid Registration of Histological Sections to MR Images of the Human Brain

Registration of histological images to three-dimensional imaging modalities is an important step in quantitative analysis of brain structure, in architectonic mapping of the brain, and in investigation of the pathology of a brain disease. Reconstruction of histology volume from serial sections is a well-established procedure, but it does not address registration of individual slices from sparse sections, which is the aim of the slice-to-volume approach. This study presents a flexible framework for intensity-based slice-to-volume nonrigid registration algorithms with a geometric transformation deformation field parametrized by various classes of spline functions: thin-plate splines (TPS), Gaussian elastic body splines (GEBS), or cubic B-splines. Algorithms are applied to cross-modality registration of histological and magnetic resonance images of the human brain. Registration performance is evaluated across a range of optimization algorithms and intensity-based cost functions. For a particular case of histological data, best results are obtained with a TPS three-dimensional (3D) warp, a new unconstrained optimization algorithm (NEWUOA), and a correlation-coefficient-based cost function.

Characterization of 7- and 19-month-old Tg2576 mice using multimodal in vivo imaging: limitations as a translatable model of Alzheimer's disease

With 90% of neuroscience clinical trials failing to see efficacy, there is a clear need for the development of disease biomarkers that can improve the ability to predict human Alzheimer's disease (AD) trial outcomes from animal studies. Several lines of evidence, including genetic susceptibility and disease studies, suggest the utility of fluorodeoxyglucose positron emission tomography (FDG-PET) as a potential biomarker with congruency between humans and animal models. For example, early in AD, patients present with decreased glucose metabolism in the entorhinal cortex and several regions of the brain associated with disease pathology and cognitive decline. While several of the commonly used AD mouse models fail to show all the hallmarks of the disease or the limbic to cortical trajectory, there has not been a systematic evaluation of imaging-derived biomarkers across animal models of AD, contrary to what has been achieved in recent years in the Alzheimer's Disease Neuroimaging Initiative (ADNI) (Miller, 2009). If animal AD models were found to mimic endpoints that correlate with the disease onset, progression, and relapse, then the identification of such markers in animal models could afford the field a translational tool to help bridge the preclinical-clinical gap. Using a combination of FDG-PET and functional magnetic resonance imaging (fMRI), we examined the Tg2576 mouse for global and regional measures of brain glucose metabolism at 7 and 19 months of age. In experiment 1 we observed that at younger ages, when some plaque burden and cognitive deficits have been reported, Tg2576 mice showed hypermetabolism as assessed with FDG-PET. This hypermetabolism decreased with age to levels similar to wild type (WT) counterparts such that the 19-month-old transgenic (Tg) mice did not differ from age matched WTs. In experiment 2, using cerebral blood volume (CBV) fMRI, we demonstrated that the hypermetabolism observed in Tg mice at 7 months could not be explained by changes in hemodynamic parameters as no differences were observed when compared with WTs. Taken together, these data identify brain hypermetabolism in Tg2576 mice which cannot be accounted for by changes in vascular compliance. Instead, the hypermetabolism may reflect a neuronal compensatory mechanism. Our data are discussed in the context of disease biomarker identification and target validation, suggesting little or no utility for translational based studies using Tg2576 mice.

Large Deformation Diffeomorphic Metric Mapping Registration of Reconstructed 3D Histological Section Images and in vivo MR Images

Our current understanding of neuroanatomical abnormalities in neuropsychiatric diseases is based largely on magnetic resonance imaging (MRI) and post mortem histological analyses of the brain. Further advances in elucidating altered brain structure in these human conditions might emerge from combining MRI and histological methods. We propose a multistage method for registering 3D volumes reconstructed from histological sections to corresponding in vivo MRI volumes from the same subjects: (1) manual segmentation of white matter (WM), gray matter (GM) and cerebrospinal fluid (CSF) compartments in histological sections, (2) alignment of consecutive histological sections using 2D rigid transformation to construct a 3D histological image volume from the aligned sections, (3) registration of reconstructed 3D histological volumes to the corresponding 3D MRI volumes using 3D affine transformation, (4) intensity normalization of images via histogram matching, and (5) registration of the volumes via intensity based large deformation diffeomorphic metric (LDDMM) image matching algorithm. Here we demonstrate the utility of our method in the transfer of cytoarchitectonic information from histological sections to identify regions of interest in MRI scans of nine adult macaque brains for morphometric analyses. LDDMM improved the accuracy of the registration via decreased distances between GM/CSF surfaces after LDDMM (0.39 ± 0.13 mm) compared to distances after affine registration (0.76 ± 0.41 mm). Similarly, WM/GM distances decreased to 0.28 ± 0.16 mm after LDDMM compared to 0.54 ± 0.39 mm after affine registration. The multistage registration method may find broad application for mapping histologically based information, for example, receptor distributions, gene expression, onto MRI volumes.

Ways toward an early diagnosis in Alzheimer's disease: the Alzheimer's Disease Neuroimaging Initiative (ADNI)

With the increasing life expectancy in developed countries, the incidence of Alzheimer's disease (AD) and thus its socioeconomic impact are growing. Increasing knowledge over the last years about the pathomechanisms involved in AD allow for the development of specific treatment strategies aimed at slowing down or even preventing neuronal death in AD. However, this requires also that (1) AD can be diagnosed with high accuracy, because non-AD dementias would not benefit from an AD-specific treatment; (2) AD can be diagnosed in very early stages when any intervention would be most effective; and (3) treatment efficacy can be reliably and meaningfully monitored. Although there currently is no ideal biomarker that would fulfill all these requirements, there is increasing evidence that a combination of currently existing neuroimaging and cerebrospinal fluid (CSF) and blood biomarkers can provide important complementary information and thus contribute to a more accurate and earlier diagnosis of AD. The Alzheimer's Disease Neuroimaging Initiative (ADNI) is exploring which combinations of these biomarkers are the most powerful for diagnosis of AD and monitoring of treatment effects.

Longitudinal multimodal imaging in mild to moderate Alzheimer disease: a pilot study with memantine

OBJECTIVE

To study the feasibility of multimodal neuroimaging in mild to moderate Alzheimer disease (AD) and to estimate the size of possible treatment effects of memantine on potential functional, structural and metabolic biomarkers of disease progression.

METHODS

In this randomised, double-blind, placebo-controlled pilot study, 36 patients with moderate AD received 52 weeks of memantine (20 mg/day) or placebo. Patients were re-evaluated after 26 and 52 weeks to measure the change from baseline in several outcome measures including global and regional glucose metabolism, total brain and hippocampal volumes, as well as chemical shift imaging-derived global and regional N-acetylaspartate and myoinositol concentrations.

RESULTS

In the total population, global glucose metabolism decreased by 2.3% (p<0.01), total brain volume by 2.1% (p<0.001) and hippocampal volume by 2.7% (p<0.01) after 52 weeks. Chemical shift imaging (CSI) spectra were severely affected by patient-induced artefacts and highly variable. Patients receiving memantine showed less decline in glucose metabolism in all brain areas than patients on placebo. Their loss of hippocampal volume was substantially smaller (2.4% vs 4.0%). No between-group differences were seen for changes in total brain volume.

CONCLUSIONS

The results support the use of multimodal imaging including MRI and positron emission tomography (PET) to monitor the progression of moderate AD. CSI yielded unreliable longitudinal results. The data suggest that memantine has potentially protective effects in AD and they can be used for planning larger confirmatory studies on the cerebral effects of memantine.

Three-dimensional reconstruction of stained histological slices and 3D non-linear registration with in-vivo MRI for whole baboon brain

The correlation between post-mortem data and in-vivo brain images is of high interest for studying neurodegenerative diseases. This paper describes a protocol that matches a series of stained histological slices of a baboon brain with an anatomical MRI scan of the same subject using an intermediate 3D-consistent volume of "blockface" photographs taken during the sectioning process. Each stained histological section of the baboon brain was first registered to its corresponding blockface photograph using a novel "hemi-rigid" transformation. This piecewise rigid 2D transformation was specifically adapted to the registration of slices which contained both hemispheres. Subsenquently, to correct the global 3D deformations of the brain caused by histological preparation and fixation, a 3D elastic transformation was estimated between the blockface volume and the MRI data. This 3D elastic transformation was then applied to the histological volume previously aligned using the hemi-rigid method to complete the registration of the series of stained histological slices with the MRI data. We assessed the efficacy of our method by evaluating the quality of matching of anatomical features as well as the difference of volume measurements between the MRI and the histological images. Two complete baboon brains (with the exception of cerebellum) were successfully processed using our protocol.

Towards multimodal atlases of the human brain

Atlases of the human brain have an important impact on neuroscience. The emergence of ever more sophisticated imaging techniques, brain mapping methods and analytical strategies has the potential to revolutionize the concept of the brain atlas. Atlases can now combine data describing multiple aspects of brain structure or function at different scales from different subjects, yielding a truly integrative and comprehensive description of this organ. These integrative approaches have provided significant impetus for the human brain mapping initiatives, and have important applications in health and disease.

A low temperature embedding and section registration strategy for 3D image reconstruction of the rat brain from autoradiographic sections

In studies on animal models of human brain pathologies, three-dimensional reconstruction from histological sections is particularly useful when assessing the morphologic, functional and biochemical changes induced by pathology. It allows assessing lesion heterogeneity in planes different from the cutting plane and allows correlating the histology with images obtained in vivo, such as by means of magnetic resonance imaging. To create a 3D volume from autoradiographic sections with minimal distortion, both cryosectioning as well as section registration need to be optimal. This paper describes a strategy whereby four external fiducial markers are positioned outside the rat brain with the use of a low temperature brain embedding procedure. The fiducial markers proposed here can be rapidly added to any frozen tissue block with no impact on the subsequent histological operations. Since embedding is performed at a low temperature, no tissue degradation occurs due to sample heating. The markers enable robust and almost error free registration, even in the presence of missing sections and poor image quality. Furthermore, the markers may be used to partially correct for global distortions.

A three-dimensional, histological and deformable atlas of the human basal ganglia. I. Atlas construction based on immunohistochemical and MRI data

This paper describes the construction of an atlas of the human basal ganglia. The successive steps of the construction were as follows. First a postmortem specimen was subjected to a MRI acquisition prior to extraction of the brain from the skull. The brain was then cryosectioned (70 microm thickness). One section out of ten (80 sections) was Nissl-stained with cresyl violet, another series of 80 sections was immunostained for the calcium binding protein calbindin. Contours of basal ganglia nuclei including their calbindin-stained functional subdivisions, fiber bundles and ventricles (n=80 structures) were traced from histological sections and digitized. A novelty of this atlas is the MRI acquisition, which represents the core data element of the study. MRI was used for the coregistration of the atlas data and permitted, through multimodal (Nissl, calbindin, images of cryosectioning, T1 and T2 MRI) and 3D optimization, the production of anatomically and geometrically consistent 3D surfaces, which can be sliced through any desired orientation. The atlas MRI is also used for its deformation to provide accurate conformation to the MRI of living patients, thus adding information at the histological level to the patient's MRI volume. This latter aspect will be presented in a forthcoming paper.

Validation of PET imaging by alignment to histology slices

The aim of this project is to verify the accuracy of positron emission tomography (PET) in identifying the tumour boundary and eventually to enable PET-guided resection with removal of significantly smaller margins. We present a novel use of an image-guided surgery system to enable alignment of preoperative PET images to postoperative histology. The oral cancer patients must have a high resolution CT scan as well as undergoing PET imaging. Registration of these images to the patient during surgery is achieved using a device that attaches to the patient's upper or lower teeth. During the procedure markers are placed around the lesion within tissue that is to be resected. These are marked along with any convenient anatomical landmarks using the image guidance system, providing the location of the points in the preoperative images. After the sample has been resected, slices through at least 3 of these points are made and photographed. Registration should be possible using these landmarks, but the accuracy of alignment is much improved by marking the bone surface in the histology image and registering to preoperative CT.

3D volume reconstruction of a mouse brain from histological sections using warp filtering

Sectioning tissues for optical microscopy often introduces upon the resulting sections distortions that make 3D reconstruction difficult. Here we present an automatic method for producing a smooth 3D volume from distorted 2D sections in the absence of any undistorted references. The method is based on pairwise elastic image warps between successive tissue sections, which can be computed by 2D image registration. Using a Gaussian filter, an average warp is computed for each section from the pairwise warps in a group of its neighboring sections. The average warps deform each section to match its neighboring sections, thus creating a smooth volume where corresponding features on successive sections lie close to each other. The proposed method can be used with any existing 2D image registration method for 3D reconstruction. In particular, we present a novel image warping algorithm based on dynamic programming that extends Dynamic Time Warping in 1D speech recognition to compute pairwise warps between high-resolution 2D images. The warping algorithm efficiently computes a restricted class of 2D local deformations that are characteristic between successive tissue sections. Finally, a validation framework is proposed and applied to evaluate the quality of reconstruction using both real sections and a synthetic volume.

The creation of a brain atlas for image guided neurosurgery using serial histological data

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.

Computational biology for visualization of brain structure

The complexity and variability of human brain (as well as other species) across subjects is so great that reliance on maps and atlases is essential to effectively manipulate, analyze and interpret brain data. Central to these tasks is the construction of averages, templates and models to describe how the brain and its component parts are organized. Design of appropriate reference systems and visualization strategies for human brain data presents considerable challenges, since these systems must capture how brain structure and function vary in large populations, across age and gender, in different disease states, across imaging modalities and even across species. This paper will describe the application of brain maps to a variety of questions and problems in health and disease. It includes a brief survey of different types of maps, including those that capture dynamic patterns of brain change over time.

Correcting spatial distortion in histological images

We described an interactive method for correcting spatial distortion in histology samples, applied them to a large set of image data, and quantitatively evaluated the quality of the corrections. We demonstrated registration of histology samples to photographs of macroscopic tissue samples and to MR images. We first described methods for obtaining corresponding fiducial and anatomical points, including a new technique for determining boundary correspondence points. We then describe experimental methods for tissue preparation, including a technique for adding color-coded internal and boundary ink marks that are used to validate the method by measuring the registration error. We applied four different transformations with internal and boundary correspondence points, and measured the distance error between other internal ink fiducials. A large number of boundary points, typically 20-30, and at least two internal points were required for accurate warping registration. Interior errors with the transformation methods were ordered: thin plate spline (TPS) approximately non-warping<<triangle warping<polynomial warping. Although non-warping surprisingly gave the lowest interior distance error (0.5+/-0.3mm), TPS was more robust, gave an insignificantly greater error (0.6+/-0.3mm) and much better results near boundaries where distortion was more evident, and allowed us to correct torn histology samples, a common problem. Using the method to evaluate RF thermal ablation, we found good zonal correlation between MR images and corrected histology samples. The method can be practically applied to this and other emerging applications such as in vivo molecular imaging.

Neuroimaging biomarkers for clinical trials of disease-modifying therapies in Alzheimer's disease

The pathophysiologic process leading to neurodegeneration in Alzheimer's disease (AD) is thought to begin long before clinical symptoms develop. Existing therapeutics for AD improve symptoms, but increasing efforts are being directed toward the development of therapies to impede the pathologic progression of the disease. Although these medications must ultimately demonstrate efficacy in slowing clinical decline, there is a critical need for biomarkers that will indicate whether a candidate disease-modifying therapeutic agent is actually altering the underlying degenerative process. A number of in vivo neuroimaging techniques, which can reliably and noninvasively assess aspects of neuroanatomy, chemistry, physiology, and pathology, hold promise as biomarkers. These neuroimaging measures appear to relate closely to neuropathological and clinical data, such as rate of cognitive decline and risk of future decline. As this work has matured, it has become clear that neuroimaging measures may serve a variety of potential roles in clinical trials of candidate neurotherapeutic agents for AD, depending in part on the question of interest and phase of drug development. In this article, we review data related to the range of neuroimaging biomarkers of Alzheimer's disease and consider potential applications of these techniques to clinical trials, particularly with respect to the monitoring of disease progression in trials of disease-modifying therapies.

Three-Dimensional Registration of Magnetic Resonance Image Data to Histological Sections with Model-Based Evaluation

We developed a three-dimensional (3D) registration method to align medical scanner data with histological sections. After acquiring 3D medical scanner images, we sliced and photographed the tissue using, a custom apparatus, to obtain a volume of tissue section images. Histological samples from the sections were digitized using a video microscopy system. We aligned the histology and medical images to the reference tissue images using our 3D registration method. We applied the method to correlate in vivo magnetic resonance (MR) and histological measurements for radio-frequency thermal ablation lesions in rabbit thighs. For registration evaluation, we used an ellipsoid model to describe the lesion surfaces. The model surface closely fit the inner (M1) and outer (M2) boundaries of the hyperintense region in MR lesion images, and the boundary of necrosis (H1) in registered histology images. We used the distance between the model surfaces to indicate the 3D registration error. For four experiments, we measured a registration accuracy of 0.96+/- 0.13 mm (mean+/-SD) from the absolute distance between the M2 and H1 model surfaces, which compares favorably to the 0.70 mm in-plane MR voxel dimension. This suggests that our registration method provides sufficient spatial correspondence to correlate 3D medical scanner and histology data.

Discovery and integrative neuroscience

Hypothesis driven research has been shown to be an excellent model for pursuing investigations in neuroscience. The Human Genome Project demonstrated the added value of discovery research, especially in areas where large amounts of data are produced. Neuroscience has become a data rich field, and one that would be enhanced by incorporating the discovery approach. Databases, as well as analytical, modeling and simulation tools, will have to be developed, and they will need to be interoperable and federated. This paper presents an overview of the development of the field of neuroscience databases and associate tools: Neuroinformatics. The primary focus is on the impact of NIH funding of this process. The important issues of data sharing, as viewed from the perspective of the scientist and private and public funding organizations, are discussed. Neuroinformatics will provide more than just a sophisticated array of information technologies to help scientists understand and integrate nervous system data. It will make available powerful models of neural functions and facilitate discovery, hypothesis formulation and electronic collaboration.

A standardized method for brain-cutting suitable for both stereology and MRI-brain co-registration

We have developed an agar-embedding method for brain-slicing that minimizes the geometrical distortions which arise from handling and slicing the fixed postmortem brain. To facilitate postmortem brain-magnetic resonance imaging (MRI) co-registration, each hemisphere is processed separately. We embed the fixed brain hemisphere with reference markers in agar. The block containing the brain and markers is sliced at a fixed interval using a rotary slicer. Each slice is photographed with a high-resolution digital camera. The digital images are realigned as a 3-dimensional volume via a control point-based registration method for multi-slice registration. The realigned multiple slices of the reconstructed postmortem hemisphere are then co-registered to corresponding slices of an in vivo reference MRI-volume. We illustrate these postmortem MRI-brain co-registration methods to correlate in vivo T2-weighted MRI hyperintensities in gray and white matter with underlying pathology. For design-based stereology, the volume of interest (VOI) is defined using reproducible anatomical boundaries. This method is suitable for stereologic measures of structures ranging from defined nuclei to whole brain.

Global and local gray matter loss in mild cognitive impairment and Alzheimer's disease

PURPOSE

Mild cognitive impairment (MCI) is thought to be the prodromal phase to Alzheimer's disease (AD). We analyzed patterns of gray matter (GM) loss to examine what characterizes MCI and what determines the difference with AD.

MATERIALS AND METHODS

Thirty-three subjects with AD, 14 normal elderly controls (NCLR), and 22 amnestic MCI subjects were included and underwent brain MR imaging. Global GM volume was assessed using segmentation and local GM volume was assessed using voxel-based morphometry (VBM); VBM was optimized for template mismatch and statistical mass.

RESULTS

AD subjects had significantly (12.3%) lower mean global GM volume when compared to controls (517 +/- 58 vs. 590 +/- 52 ml; P < 0.001). Global GM volume in the MCI group (552 +/- 52) was intermediate between these two: 6.2% lower than AD and 6.5% higher than the controls but not significantly different from either group. VBM showed that subjects with MCI had significant local reductions in gray matter in the medial temporal lobe (MTL), the insula, and thalamus compared to NCLR subjects. By contrast, when compared to subjects with AD, MCI subjects had more GM in the parietal association areas and the anterior and the posterior cingulate.

CONCLUSION

GM loss in the MTL characterizes MCI, while GM loss in the parietal and cingulate cortices might be a feature of AD.

Hemispheric asymmetries of hypometabolism associated with semantic memory impairment in Alzheimer's disease: a study using positron emission tomography with fluorodeoxyglucose-F18

Considerable disagreement exists about the neuroanatomical basis of conceptual-semantic impairments observed in a subgroup of patients with Alzheimer's disease (AD) at mild to moderate stages of the disease. Several studies of groups of patients have shown correlations between focal hypometabolism or hypoperfusion in left hemispheric areas and measures of verbal semantic memory impairment in AD patients. The question remains, however, whether left hemispheric hypometabolism is sufficient to produce such impairment in the single case and whether nonverbal semantic knowledge is also affected. We used positron emission tomography (PET) with fluorodeoxyglucose-F18 (FDG), statistical parametric mapping (SPM), and tests of verbal and nonverbal semantic memory in 11 AD patients with a mean score on the Mini-Mental State Examination of 22.6 (+/-2.8). Naming impairment was significantly associated with left hemispheric asymmetry of hypometabolism on a single-case basis. Our correlation analysis showed that metabolism in left anterior temporal, posterior inferior temporal, inferior parietal and medial occipital areas (Brodmann areas: 21/38, 37, 40 and 19) correlated with both verbal and nonverbal semantic performance. We conclude that left hemispheric synaptic dysfunction, as measured by regional glucose hypometabolism, was sufficient to produce semantic impairments in our patients. The majority of areas affected in our patients with semantic impairments were involved in multimodal or supramodal (verbal and nonverbal) semantic knowledge.

Fusion of autoradiographs with an MR volume using 2-D and 3-D linear transformations

In the past years, the development of 3-D medical imaging has enabled the 3-D imaging of in vivo tissues, from an anatomical (MR, CT) or even functional (fMRI, PET, SPECT) point of view. However, despite immense technological progress, the resolution of these images is still short of the level of anatomical or functional details that in vitro imaging (e.g., histology, autoradiography) permits. The motivation of this work is to compare fMRI activations to activations observed in autoradiographic images from the same animals. We aim to fuse post-mortem autoradiographic data with a pre-mortem anatomical MR image. We first reconstruct a 3-D volume from the 2-D autoradiographic sections, coherent both in geometry and intensity. Then, this volume is fused with the MR image. This way, we ensure that the reconstructed 3-D volume can be superimposed onto the MR image that represents the reference anatomy. We demonstrate that this fusion can be achieved by using only simple global transformations (rigid and/or affine, 2-D and 3-D), while yielding very satisfactory results.

Imaging is superior to cognitive testing for early diagnosis of Alzheimer’s disease

Alzheimer's disease (AD) starts at a molecular level possibly decades earlier than could be detected by neuropsychological tests (NPTs). Neuropathological and neuroimaging data suggest that amyloid accumulation precedes the clinical onset of AD. Disease-modifying agents would have to be used early to alter the course of AD. Therefore, preclinical diagnosis is necessary. Structural and functional neuroimaging are superior for detection of the earliest stages of AD. Magnetic resonance imaging (MRI) and positron emission tomography (PET) techniques, including amyloid visualization, will have therapeutic importance for prevention as well as intervention as further refinements of current imaging techniques and biochemical markers occur. Neuropsychological tests measure the effect of pathology for an individual based upon norms obtained from an artificial population-often white and relatively highly educated. Unless serial NPTs are performed, the individual is compared to a population to which they may not conform. Neuroimaging can provide objective measures of preclinical disease state and, when measured serially, rate of change. Such information can be used in prevention trials.

Imaging Alzheimer's disease: clinical applications

Extensive PET imaging research on AD has been conducted since PET scanners became available in the early 1980s. PET imaging using FDG, now commercially available, can detect early metabolic changes in AD and differential metabolic features of various dementing disorders. Image analysis techniques have also advanced in the field of functional brain imaging and permit accurate and consistent scan interpretation. PET studies that involve autopsy-confirmed cases suggest that the PET diagnosis of AD is no worse or may even be better than clinical diagnosis. Limited prospective studies demonstrated the effects of PET imaging in dementia management, which precludes the approval of FDG PET for more widespread, reimbursable use. Further evidence for the efficacy of PET imaging through well-organized clinical studies, as well as continuing efforts in technologic development and basic research to characterize functional alterations in dementing disorders in living patients, are equally important to achieve the goal of better dementia care.

The LONI Pipeline Processing Environment

The analysis of raw data in neuroimaging has become a computationally entrenched process with many intricate steps run on increasingly larger datasets. Many software packages exist that provide either complete analyses or specific steps in an analysis. These packages often possess diverse input and output requirements, utilize different file formats, run in particular environments, and have limited abilities with certain types of data. The combination of these packages to achieve more sensitive and accurate results has become a common tactic in brain mapping studies but requires much work to ensure valid interoperation between programs. The handling, organization, and storage of intermediate data can prove difficult as well. The LONI Pipeline Processing Environment is a simple, efficient, and distributed computing solution to these problems enabling software inclusion from different laboratories in different environments. It is used here to derive a T1-weighted MRI atlas of the human brain from 452 normal young adult subjects with fully automated processing. The LONI Pipeline Processing Environment's parallel processing efficiency using an integrated client/server dataflow model was 80.9% when running the atlas generation pipeline from a PC client (Acer TravelMate 340T) on 48 dedicated server processors (Silicon Graphics Inc. Origin 3000). The environment was 97.5% efficient when the same analysis was run on eight dedicated processors.

Neuroimaging in dementia with Lewy bodies: metabolism, neurochemistry, and morphology

Dementia with Lewy bodies (DLB) is recognized as one of the most common forms of neurodegenerative dementia. Neuroimaging contributes to a better understanding of the pathophysiology of DLB by examining alterations in brain metabolism, neurochemisty, and morphology in living patients. Neuroimaging can provide objective and quantifiable antemortem markers for the presence of and the progression of DLB and permits differentiation from other dementias. This article reviews current neuroimaging findings in DLB with particular attention to occipital hypometabolism, dopaminergic and cholinergic deficits, and medial temporal lobe atrophy as measured by positron emission tomography, single-photon emission computed tomography, and magnetic resonance imaging.

Dynamics of gray matter loss in Alzheimer's disease

We detected and mapped a dynamically spreading wave of gray matter loss in the brains of patients with Alzheimer's disease (AD). The loss pattern was visualized in four dimensions as it spread over time from temporal and limbic cortices into frontal and occipital brain regions, sparing sensorimotor cortices. The shifting deficits were asymmetric (left hemisphere > right hemisphere) and correlated with progressively declining cognitive status (p < 0.0006). Novel brain mapping methods allowed us to visualize dynamic patterns of atrophy in 52 high-resolution magnetic resonance image scans of 12 patients with AD (age 68.4 +/- 1.9 years) and 14 elderly matched controls (age 71.4 +/- 0.9 years) scanned longitudinally (two scans; interscan interval 2.1 +/- 0.4 years). A cortical pattern matching technique encoded changes in brain shape and tissue distribution across subjects and time. Cortical atrophy occurred in a well defined sequence as the disease progressed, mirroring the sequence of neurofibrillary tangle accumulation observed in cross sections at autopsy. Advancing deficits were visualized as dynamic maps that change over time. Frontal regions, spared early in the disease, showed pervasive deficits later (>15% loss). The maps distinguished different phases of AD and differentiated AD from normal aging. Local gray matter loss rates (5.3 +/- 2.3% per year in AD v 0.9 +/- 0.9% per year in controls) were faster in the left hemisphere (p < 0.029) than the right. Transient barriers to disease progression appeared at limbic/frontal boundaries. This degenerative sequence, observed in vivo as it developed, provides the first quantitative, dynamic visualization of cortical atrophic rates in normal elderly populations and in those with dementia.