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Sample records for 3d brain pet

  1. Structured light 3D tracking system for measuring motions in PET brain imaging

    NASA Astrophysics Data System (ADS)

    Olesen, Oline V.; Jørgensen, Morten R.; Paulsen, Rasmus R.; Højgaard, Liselotte; Roed, Bjarne; Larsen, Rasmus

    2010-02-01

    Patient motion during scanning deteriorates image quality, especially for high resolution PET scanners. A new proposal for a 3D head tracking system for motion correction in high resolution PET brain imaging is set up and demonstrated. A prototype tracking system based on structured light with a DLP projector and a CCD camera is set up on a model of the High Resolution Research Tomograph (HRRT). Methods to reconstruct 3D point clouds of simple surfaces based on phase-shifting interferometry (PSI) are demonstrated. The projector and camera are calibrated using a simple stereo vision procedure where the projector is treated as a camera. Additionally, the surface reconstructions are corrected for the non-linear projector output prior to image capture. The results are convincing and a first step toward a fully automated tracking system for measuring head motions in PET imaging.

  2. Optimization of PET activation studies based on the SNR measured in the 3-D Hoffman brain phantom.

    PubMed

    Li, H H; Votaw, J R

    1998-08-01

    This work investigates the noise properties of O-15 water PET images in an attempt to increase the sensitivity of activation studies. A method for computing the amount of noise within a region of interest (ROI) from the uncertainty in the raw data was implemented for three-dimensional (3-D) positron emission tomography (PET). The method was used to study the signal-to-noise ratio (SNR) of regions-of-interest (ROI's) inside a 3-D Hoffman brain phantom. Saturation occurs at an activity concentration of 2.2 mCi/l which corresponds to a 75-mCi O-15 water injection into a normal person of average weight. This establishes the upper limit for injections for human brain studies using 3-D PET on the Siemens ECAT 921 EXACT scanner. Data from human brain activation studies on four normal volunteers using two-dimensional (2-D) PET were analyzed. The biological variation was found to be 5% in 1-ml ROI's. The variance for a complete activation study was calculated, for a variety of protocols, by combining the Poisson noise propagated from the raw data in the phantom experiments with the biological variation. A protocol that is predicted to maximize the SNR in dual-condition activation experiments while remaining below the radiation safety limit is: ten scans with 45 mCi per injection. The data should not be corrected for random or scatter events since they do not help in the identification of activation sites while they do add noise to the image. Due to the lower noise level of 3-D PET, the threshold for detecting a true change in activity concentration is 10%-20% lower than 2-D PET. Because of this, a 3-D activation experiment using the Siemens 921 scanner requires fewer subjects for equal statistical power.

  3. Real-time 3D motion tracking for small animal brain PET

    NASA Astrophysics Data System (ADS)

    Kyme, A. Z.; Zhou, V. W.; Meikle, S. R.; Fulton, R. R.

    2008-05-01

    High-resolution positron emission tomography (PET) imaging of conscious, unrestrained laboratory animals presents many challenges. Some form of motion correction will normally be necessary to avoid motion artefacts in the reconstruction. The aim of the current work was to develop and evaluate a motion tracking system potentially suitable for use in small animal PET. This system is based on the commercially available stereo-optical MicronTracker S60 which we have integrated with a Siemens Focus-220 microPET scanner. We present measured performance limits of the tracker and the technical details of our implementation, including calibration and synchronization of the system. A phantom study demonstrating motion tracking and correction was also performed. The system can be calibrated with sub-millimetre accuracy, and small lightweight markers can be constructed to provide accurate 3D motion data. A marked reduction in motion artefacts was demonstrated in the phantom study. The techniques and results described here represent a step towards a practical method for rigid-body motion correction in small animal PET. There is scope to achieve further improvements in the accuracy of synchronization and pose measurements in future work.

  4. Development of a High Precision Axial 3-D PET for Brain Imaging

    NASA Astrophysics Data System (ADS)

    Bolle, E.; Braem, A.; Casella, C.; Chesi, E.; Clinthorne, N.; Cochran, E.; De Leo, R.; Dissertori, G.; Djambazov, L.; Honscheid, K.; Huh, S.; Johnson, I.; Joram, C.; Kagan, H.; Lacasta, C.; Lustermann, W.; Meddi, F.; Nappi, E.; Nessi-Tedaldi, F.; Oliver, J. F.; Pauss, F.; Rafecas, M.; Renker, D.; Rudge, A.; Schinzel, D.; Schneider, T.; Séguinot, J.; Smith, S.; Solevi, P.; Stapnes, S.; Vilardi, I.; Weilhammer, P.

    2009-12-01

    We describe a PET device based on a novel method to extract the coordinates of the interaction point of the 511keV γ rays from 100 mm long and thin LYSO (Lutetium Yttrium OxyorthoSilicate) scintillator bars, positioned axially in the tomograph. The coordinate along the hit crystal is measured by using a hodoscope of Wave Length Shifting (WLS) plastic strips mounted perpendicularly to each plane of scintillators. As photodetectors, new Geiger mode Avalanche PhotoDetectors (G-APDs) with integrated electronics are being used to detect both the hit crystal in a block (x and y coordinates) and the interaction point in the crystal (z coordinate) through the light escaping from the crystal and transmitted to the WLS strips. In this way, the γ interaction point can be determined with a spatial resolution of few cubic millimeters down to a minimum deposited energy of about 50 keV, resulting in a volumetric precision very close to the limits imposed by the physics of the positron annihilation. The method allows to increase the detection efficiency without affecting the spatial resolution by adding scintillator planes in the radial direction. A demonstrator scanner, based on two matrices of 8 × 6 LYS crystals and 312 WLS strips, slotted in between the crystals, is under construction. Preliminary results from the feasibility studies of the various components will be presented.

  5. Evaluation of the ECAT EXACT HR{sup +} 3D PET scanner in {sup 15}O-water brain activation studies

    SciTech Connect

    Moreno-Cantu, J.J.; Thompson, C.J.; Zatorre, R.J.

    1996-12-31

    We evaluated the performance of the ECAT EXACT HR{sup +} 3D whole body PET scanner when employed to measure brain function using {sup 15}O-water-bolus activation protocols in single data acquisition sessions. Using vibrotactile and auditory stimuli as independent activation tasks, we studied the scanner`s performance under different imaging conditions in four healthy volunteers. Cerebral blood flow images were acquired from each volunteer using {sup 15}O-water-bolus injections of activity varying from 5 to 20mCi. Performance characteristics. The scanner`s dead time grew linearly with injected dose from 10% to 25%. Random events varied from 30% to 50% of the detected events. Scattered events were efficiently corrected at all doses. Noise-effective-count curves plateau at about 15mCi. One-session 12-injection bolus PET activation protocol. Using an acquisition protocol that accounts for the scanner`s performance and the practical aspects of imaging volunteers and patients in one session, we assessed the correlation between the statistical significance of activation foci and the dose per injection used The one-session protocol employs 12 bolus injections per subject. We present evidence suggesting that 15-20mCi is the optimal dose per injection to be used routinely in one-time scanning sessions.

  6. Segmentation of 3D microPET images of the rat brain via the hybrid gaussian mixture method with kernel density estimation.

    PubMed

    Chen, Tai-Been; Chen, Jyh-Cheng; Lu, Henry Horng-Shing

    2012-01-01

    Segmentation of positron emission tomography (PET) is typically achieved using the K-Means method or other approaches. In preclinical and clinical applications, the K-Means method needs a prior estimation of parameters such as the number of clusters and appropriate initialized values. This work segments microPET images using a hybrid method combining the Gaussian mixture model (GMM) with kernel density estimation. Segmentation is crucial to registration of disordered 2-deoxy-2-fluoro-D-glucose (FDG) accumulation locations with functional diagnosis and to estimate standardized uptake values (SUVs) of region of interests (ROIs) in PET images. Therefore, simulation studies are conducted to apply spherical targets to evaluate segmentation accuracy based on Tanimoto's definition of similarity. The proposed method generates a higher degree of similarity than the K-Means method. The PET images of a rat brain are used to compare the segmented shape and area of the cerebral cortex by the K-Means method and the proposed method by volume rendering. The proposed method provides clearer and more detailed activity structures of an FDG accumulation location in the cerebral cortex than those by the K-Means method.

  7. Brain PET scan

    MedlinePlus

    ... Tell the difference between Parkinson disease and other movement disorders Several PET scans may be taken to determine ... identify where the seizures start in your brain Movement disorders (such as Parkinson disease )

  8. Spatial resolution limits for the isotropic-3D PET detector X’tal cube

    NASA Astrophysics Data System (ADS)

    Yoshida, Eiji; Tashima, Hideaki; Hirano, Yoshiyuki; Inadama, Naoko; Nishikido, Fumihiko; Murayama, Hideo; Yamaya, Taiga

    2013-11-01

    Positron emission tomography (PET) has become a popular imaging method in metabolism, neuroscience, and molecular imaging. For dedicated human brain and small animal PET scanners, high spatial resolution is needed to visualize small objects. To improve the spatial resolution, we are developing the X’tal cube, which is our new PET detector to achieve isotropic 3D positioning detectability. We have shown that the X’tal cube can achieve 1 mm3 uniform crystal identification performance with the Anger-type calculation even at the block edges. We plan to develop the X’tal cube with even smaller 3D grids for sub-millimeter crystal identification. In this work, we investigate spatial resolution of a PET scanner based on the X’tal cube using Monte Carlo simulations for predicting resolution performance in smaller 3D grids. For spatial resolution evaluation, a point source emitting 511 keV photons was simulated by GATE for all physical processes involved in emission and interaction of positrons. We simulated two types of animal PET scanners. The first PET scanner had a detector ring 14.6 cm in diameter composed of 18 detectors. The second PET scanner had a detector ring 7.8 cm in diameter composed of 12 detectors. After the GATE simulations, we converted the interacting 3D position information to digitalized positions for realistic segmented crystals. We simulated several X’tal cubes with cubic crystals from (0.5 mm)3 to (2 mm)3 in size. Also, for evaluating the effect of DOI resolution, we simulated several X’tal cubes with crystal thickness from (0.5 mm)3 to (9 mm)3. We showed that sub-millimeter spatial resolution was possible using cubic crystals smaller than (1.0 mm)3 even with the assumed physical processes. Also, the weighted average spatial resolutions of both PET scanners with (0.5 mm)3 cubic crystals were 0.53 mm (14.6 cm ring diameter) and 0.48 mm (7.8 cm ring diameter). For the 7.8 cm ring diameter, spatial resolution with 0.5×0.5×1.0 mm3 crystals

  9. Evaluation of the ECAT EXACT HR+ 3-D PET scanner in H2(15)O brain activation studies: dose fractionation strategies for rCBF and signal enhancing protocols.

    PubMed

    Moreno-Cantú, J J; Thompson, C J; Zatorre, R J

    1998-12-01

    We evaluated the performance of the ECAT EXACT HR+ 3-D whole-body positron emission tomography (PET) scanner when employed to measure brain function using H2(15)O bolus activation protocols that are completed in single same-day data acquisition sessions. Using vibrotactile and auditory stimuli as independent activation tasks, we studied the scanner performance under different imaging conditions in five healthy volunteers. Cerebral blood flow images were acquired from each volunteer using H2(15)O bolus injections of activity varying from 5-20 mCi. One-session dose-fractionation strategies were analyzed for rCBF, standard activity-concentration, switched, and cold-bolus/switched protocols. Performance characteristics. The scanner dead time grew linearly with injected dose from 10% to 25%. Random events varied from 30% to 50% of the detected events. Random and scattered events were corrected adequately at all doses. Estimated noise-effective-count curves plateau at about 10 mCi. One-session 12-injection bolus PET activation protocols. Using an acquisition protocol that accounts for the scanner performance and the practical aspects of imaging volunteers and neurological patients in a single same-day session, we assessed the correlation between the significance of activation foci and the dose/injection used. The one-session protocol employs 12 bolus injections/subject. We present evidence suggesting that when an rCBF protocol is used, image noise is reduced significantly when the activity injected increases from 5 to 10 mCi. Increasing the dose from 10 to 15 or 20 mCi yielded further but smaller reductions. Our observations also suggest that image noise will be strongly reduced if a 20-mCi dose/injection is used when data are collected using protocols that employ long acquisition times such as a switched or a cold-bolus/switched protocol.

  10. Comparison of bootstrap resampling methods for 3-D PET imaging.

    PubMed

    Lartizien, C; Aubin, J-B; Buvat, I

    2010-07-01

    Two groups of bootstrap methods have been proposed to estimate the statistical properties of positron emission tomography (PET) images by generating multiple statistically equivalent data sets from few data samples. The first group generates resampled data based on a parametric approach assuming that data from which resampling is performed follows a Poisson distribution while the second group consists of nonparametric approaches. These methods either require a unique original sample or a series of statistically equivalent data that can be list-mode files or sinograms. Previous reports regarding these bootstrap approaches suggest different results. This work compares the accuracy of three of these bootstrap methods for 3-D PET imaging based on simulated data. Two methods are based on a unique file, namely a list-mode based nonparametric (LMNP) method and a sinogram based parametric (SP) method. The third method is a sinogram-based nonparametric (SNP) method. Another original method (extended LMNP) was also investigated, which is an extension of the LMNP methods based on deriving a resampled list-mode file by drawings events from multiple original list-mode files. Our comparison is based on the analysis of the statistical moments estimated on the repeated and resampled data. This includes the probability density function and the moments of order 1 and 2. Results show that the two methods based on multiple original data (SNP and extended LMNP) are the only methods that correctly estimate the statistical parameters. Performances of the LMNP and SP methods are variable. Simulated data used in this study were characterized by a high noise level. Differences among the tested strategies might be reduced with clinical data sets with lower noise.

  11. OpenPET: a novel open-type PET system for 3D dose verification in particle therapy

    NASA Astrophysics Data System (ADS)

    Yamaya, T.

    2017-01-01

    The OpenPET is the world’s first open-type 3D PET scanner for PET image-guided particle therapy such as in situ dose verification and direct tumour tracking. Even with a full-ring geometry, the OpenPET has an open gap between its two detector rings through which the treatment beam passes. Following the initial proposal of the dual-ring OpenPET (DROP), the single-ring OpenPET (SROP) was also proposed as a more efficient geometry than DROP in terms of manufacturing cost and sensitivity. A small SROP prototype was developed and feasibility of visualizing a 3D distribution of beam stopping positions inside a phantom was shown with the help of radioisotope particle beams, used as primary beams. Following these results, a full-size whole-body SROP prototype was developed.

  12. Streamlined, Inexpensive 3D Printing of the Brain and Skull

    PubMed Central

    Cash, Sydney S.

    2015-01-01

    Neuroimaging technologies such as Magnetic Resonance Imaging (MRI) and Computed Tomography (CT) collect three-dimensional data (3D) that is typically viewed on two-dimensional (2D) screens. Actual 3D models, however, allow interaction with real objects such as implantable electrode grids, potentially improving patient specific neurosurgical planning and personalized clinical education. Desktop 3D printers can now produce relatively inexpensive, good quality prints. We describe our process for reliably generating life-sized 3D brain prints from MRIs and 3D skull prints from CTs. We have integrated a standardized, primarily open-source process for 3D printing brains and skulls. We describe how to convert clinical neuroimaging Digital Imaging and Communications in Medicine (DICOM) images to stereolithography (STL) files, a common 3D object file format that can be sent to 3D printing services. We additionally share how to convert these STL files to machine instruction gcode files, for reliable in-house printing on desktop, open-source 3D printers. We have successfully printed over 19 patient brain hemispheres from 7 patients on two different open-source desktop 3D printers. Each brain hemisphere costs approximately $3–4 in consumable plastic filament as described, and the total process takes 14–17 hours, almost all of which is unsupervised (preprocessing = 4–6 hr; printing = 9–11 hr, post-processing = <30 min). Printing a matching portion of a skull costs $1–5 in consumable plastic filament and takes less than 14 hr, in total. We have developed a streamlined, cost-effective process for 3D printing brain and skull models. We surveyed healthcare providers and patients who confirmed that rapid-prototype patient specific 3D models may help interdisciplinary surgical planning and patient education. The methods we describe can be applied for other clinical, research, and educational purposes. PMID:26295459

  13. Streamlined, Inexpensive 3D Printing of the Brain and Skull.

    PubMed

    Naftulin, Jason S; Kimchi, Eyal Y; Cash, Sydney S

    2015-01-01

    Neuroimaging technologies such as Magnetic Resonance Imaging (MRI) and Computed Tomography (CT) collect three-dimensional data (3D) that is typically viewed on two-dimensional (2D) screens. Actual 3D models, however, allow interaction with real objects such as implantable electrode grids, potentially improving patient specific neurosurgical planning and personalized clinical education. Desktop 3D printers can now produce relatively inexpensive, good quality prints. We describe our process for reliably generating life-sized 3D brain prints from MRIs and 3D skull prints from CTs. We have integrated a standardized, primarily open-source process for 3D printing brains and skulls. We describe how to convert clinical neuroimaging Digital Imaging and Communications in Medicine (DICOM) images to stereolithography (STL) files, a common 3D object file format that can be sent to 3D printing services. We additionally share how to convert these STL files to machine instruction gcode files, for reliable in-house printing on desktop, open-source 3D printers. We have successfully printed over 19 patient brain hemispheres from 7 patients on two different open-source desktop 3D printers. Each brain hemisphere costs approximately $3-4 in consumable plastic filament as described, and the total process takes 14-17 hours, almost all of which is unsupervised (preprocessing = 4-6 hr; printing = 9-11 hr, post-processing = <30 min). Printing a matching portion of a skull costs $1-5 in consumable plastic filament and takes less than 14 hr, in total. We have developed a streamlined, cost-effective process for 3D printing brain and skull models. We surveyed healthcare providers and patients who confirmed that rapid-prototype patient specific 3D models may help interdisciplinary surgical planning and patient education. The methods we describe can be applied for other clinical, research, and educational purposes.

  14. Fourier-wavelet restoration in PET/CT brain studies

    NASA Astrophysics Data System (ADS)

    Knešaurek, Karin

    2012-10-01

    Our goal is to improve brain PET imaging through the application of a novel, hybrid Fourier-wavelet (WFT) restoration technique. The major limitation of PET studies is a relatively poor resolution in comparison with MRI and CT imaging and there is a need for improved PET imaging. A GE DLS PET/CT 16 slice system was used to acquire the studies. In order to create restoration filters the point source study was performed. The 6-fillable spheres and 3D Hoffman brain phantom studies were acquired and used to test and optimize the restoration approach. The patient data used in the study were acquired in a 3D PET mode, using the standard clinical protocol. Here, we have implemented Fourier-wavelet regularized restoration. In the Fourier domain, the inverse of modulation transfer function was multiplied by a Butterworth low-pass filter, order n=6 and cut-off frequency f=0.35 cycles/pixel. In addition, wavelet (Daubechies, order 2) noise suppression was applied by “hard threshold”. Hot spheres and 3D Hoffman brain studies showed that the restoration process not only improves resolution and contrast but also improves quantification in 3D PET/CT imaging. The average contrast increase was 19% and the quantification improved in the range 8-20% depending on sphere size. In the restored images, there was no significant increase in noise when compared with the original images. The clinical studies followed brain phantom findings, i.e., the restored images had better contrast and resolution properties, when compared with the original images. The results of the study demonstrate that the quality and quantification of 3D brain 18F FDG PET images can be significantly improved by Fourier-wavelet (WFT) restoration filtering.

  15. Multimodal 3D PET/CT system for bronchoscopic procedure planning

    NASA Astrophysics Data System (ADS)

    Cheirsilp, Ronnarit; Higgins, William E.

    2013-02-01

    Integrated positron emission tomography (PET) / computed-tomography (CT) scanners give 3D multimodal data sets of the chest. Such data sets offer the potential for more complete and specific identification of suspect lesions and lymph nodes for lung-cancer assessment. This in turn enables better planning of staging bronchoscopies. The richness of the data, however, makes the visualization and planning process difficult. We present an integrated multimodal 3D PET/CT system that enables efficient region identification and bronchoscopic procedure planning. The system first invokes a series of automated 3D image-processing methods that construct a 3D chest model. Next, the user interacts with a set of interactive multimodal graphical tools that facilitate procedure planning for specific regions of interest (ROIs): 1) an interactive region candidate list that enables efficient ROI viewing in all tools; 2) a virtual PET-CT bronchoscopy rendering with SUV quantitative visualization to give a "fly through" endoluminal view of prospective ROIs; 3) transverse, sagittal, coronal multi-planar reformatted (MPR) views of the raw CT, PET, and fused CT-PET data; and 4) interactive multimodal volume/surface rendering to give a 3D perspective of the anatomy and candidate ROIs. In addition the ROI selection process is driven by a semi-automatic multimodal method for region identification. In this way, the system provides both global and local information to facilitate more specific ROI identification and procedure planning. We present results to illustrate the system's function and performance.

  16. Respiratory motion correction in 3-D PET data with advanced optical flow algorithms.

    PubMed

    Dawood, Mohammad; Buther, Florian; Jiang, Xiaoyi; Schafers, Klaus P

    2008-08-01

    The problem of motion is well known in positron emission tomography (PET) studies. The PET images are formed over an elongated period of time. As the patients cannot hold breath during the PET acquisition, spatial blurring and motion artifacts are the natural result. These may lead to wrong quantification of the radioactive uptake. We present a solution to this problem by respiratory-gating the PET data and correcting the PET images for motion with optical flow algorithms. The algorithm is based on the combined local and global optical flow algorithm with modifications to allow for discontinuity preservation across organ boundaries and for application to 3-D volume sets. The superiority of the algorithm over previous work is demonstrated on software phantom and real patient data.

  17. Algorithms for calculating detector efficiency normalization coefficients for true coincidences in 3D PET

    NASA Astrophysics Data System (ADS)

    Badawi, R. D.; Lodge, M. A.; Marsden, P. K.

    1998-01-01

    Accurate normalization of lines of response in 3D PET is a prerequisite for quantitative reconstruction. Most current methods are component based, calculating a series of geometric and intrinsic detector efficiency factors. We have reviewed the theory behind several existing algorithms for calculating detector efficiency factors in 2D and 3D PET, and have extended them to create a range of new algorithms. Three of the algorithms described are `fully 3D' in that they make use of data from all detector rings for the calculation of the efficiencies of any one line of response. We have assessed the performance of the new and existing methods using simulated and real data, and have demonstrated that the fully 3D algorithms allow the rapid acquisition of crystal efficiency normalization data using low-activity sources. Such methods enable the use of scatter-free scanning line sources or the use of very short acquisitions of cylindrical sources for routine normalization.

  18. Fully-3D PET image reconstruction using scanner-independent, adaptive projection data and highly rotation-symmetric voxel assemblies.

    PubMed

    Scheins, J J; Herzog, H; Shah, N J

    2011-03-01

    For iterative, fully 3D positron emission tomography (PET) image reconstruction intrinsic symmetries can be used to significantly reduce the size of the system matrix. The precalculation and beneficial memory-resident storage of all nonzero system matrix elements is possible where sufficient compression exists. Thus, reconstruction times can be minimized independently of the used projector and more elaborate weighting schemes, e.g., volume-of-intersection (VOI), are applicable. A novel organization of scanner-independent, adaptive 3D projection data is presented which can be advantageously combined with highly rotation-symmetric voxel assemblies. In this way, significant system matrix compression is achieved. Applications taking into account all physical lines-of-response (LORs) with individual VOI projectors are presented for the Siemens ECAT HR+ whole-body scanner and the Siemens BrainPET, the PET component of a novel hybrid-MR/PET imaging system. Measured and simulated data were reconstructed using the new method with ordered-subset-expectation-maximization (OSEM). Results are compared to those obtained by the sinogram-based OSEM reconstruction provided by the manufacturer. The higher computational effort due to the more accurate image space sampling provides significantly improved images in terms of resolution and noise.

  19. Thoracic cavity definition for 3D PET/CT analysis and visualization.

    PubMed

    Cheirsilp, Ronnarit; Bascom, Rebecca; Allen, Thomas W; Higgins, William E

    2015-07-01

    X-ray computed tomography (CT) and positron emission tomography (PET) serve as the standard imaging modalities for lung-cancer management. CT gives anatomical details on diagnostic regions of interest (ROIs), while PET gives highly specific functional information. During the lung-cancer management process, a patient receives a co-registered whole-body PET/CT scan pair and a dedicated high-resolution chest CT scan. With these data, multimodal PET/CT ROI information can be gleaned to facilitate disease management. Effective image segmentation of the thoracic cavity, however, is needed to focus attention on the central chest. We present an automatic method for thoracic cavity segmentation from 3D CT scans. We then demonstrate how the method facilitates 3D ROI localization and visualization in patient multimodal imaging studies. Our segmentation method draws upon digital topological and morphological operations, active-contour analysis, and key organ landmarks. Using a large patient database, the method showed high agreement to ground-truth regions, with a mean coverage=99.2% and leakage=0.52%. Furthermore, it enabled extremely fast computation. For PET/CT lesion analysis, the segmentation method reduced ROI search space by 97.7% for a whole-body scan, or nearly 3 times greater than that achieved by a lung mask. Despite this reduction, we achieved 100% true-positive ROI detection, while also reducing the false-positive (FP) detection rate by >5 times over that achieved with a lung mask. Finally, the method greatly improved PET/CT visualization by eliminating false PET-avid obscurations arising from the heart, bones, and liver. In particular, PET MIP views and fused PET/CT renderings depicted unprecedented clarity of the lesions and neighboring anatomical structures truly relevant to lung-cancer assessment.

  20. Thoracic Cavity Definition for 3D PET/CT Analysis and Visualization

    PubMed Central

    Cheirsilp, Ronnarit; Bascom, Rebecca; Allen, Thomas W.; Higgins, William E.

    2015-01-01

    X-ray computed tomography (CT) and positron emission tomography (PET) serve as the standard imaging modalities for lung-cancer management. CT gives anatomical detail on diagnostic regions of interest (ROIs), while PET gives highly specific functional information. During the lung-cancer management process, a patient receives a co-registered whole-body PET/CT scan pair and a dedicated high-resolution chest CT scan. With these data, multimodal PET/CT ROI information can be gleaned to facilitate disease management. Effective image segmentation of the thoracic cavity, however, is needed to focus attention on the central chest. We present an automatic method for thoracic cavity segmentation from 3D CT scans. We then demonstrate how the method facilitates 3D ROI localization and visualization in patient multimodal imaging studies. Our segmentation method draws upon digital topological and morphological operations, active-contour analysis, and key organ landmarks. Using a large patient database, the method showed high agreement to ground-truth regions, with a mean coverage = 99.2% and leakage = 0.52%. Furthermore, it enabled extremely fast computation. For PET/CT lesion analysis, the segmentation method reduced ROI search space by 97.7% for a whole-body scan, or nearly 3 times greater than that achieved by a lung mask. Despite this reduction, we achieved 100% true-positive ROI detection, while also reducing the false-positive (FP) detection rate by >5 times over that achieved with a lung mask. Finally, the method greatly improved PET/CT visualization by eliminating false PET-avid obscurations arising from the heart, bones, and liver. In particular, PET MIP views and fused PET/CT renderings depicted unprecedented clarity of the lesions and neighboring anatomical structures truly relevant to lung-cancer assessment. PMID:25957746

  1. Brain tumor locating in 3D MR volume using symmetry

    NASA Astrophysics Data System (ADS)

    Dvorak, Pavel; Bartusek, Karel

    2014-03-01

    This work deals with the automatic determination of a brain tumor location in 3D magnetic resonance volumes. The aim of this work is not the precise segmentation of the tumor and its parts but only the detection of its location. This work is the first step in the tumor segmentation process, an important topic in neuro-image processing. The algorithm expects 3D magnetic resonance volumes of brain containing a tumor. The detection is based on locating the area that breaks the left-right symmetry of the brain. This is done by multi-resolution comparing of corresponding regions in left and right hemisphere. The output of the computation is the probabilistic map of the tumor location. The created algorithm was tested on 80 volumes from publicly available BRATS databases containing 3D brain volumes afflicted by a brain tumor. These pathological structures had various sizes and shapes and were located in various parts of the brain. The locating performance of the algorithm was 85% for T1-weighted volumes, 91% for T1-weighted contrast enhanced volumes, 96% for FLAIR and T2-wieghted volumes and 95% for their combinations.

  2. 3D quantitative analysis of brain SPECT images

    NASA Astrophysics Data System (ADS)

    Loncaric, Sven; Ceskovic, Ivan; Petrovic, Ratimir; Loncaric, Srecko

    2001-07-01

    The main purpose of this work is to develop a computer-based technique for quantitative analysis of 3-D brain images obtained by single photon emission computed tomography (SPECT). In particular, the volume and location of ischemic lesion and penumbra is important for early diagnosis and treatment of infracted regions of the brain. SPECT imaging is typically used as diagnostic tool to assess the size and location of the ischemic lesion. The segmentation method presented in this paper utilizes a 3-D deformable model in order to determine size and location of the regions of interest. The evolution of the model is computed using a level-set implementation of the algorithm. In addition to 3-D deformable model the method utilizes edge detection and region growing for realization of a pre-processing. Initial experimental results have shown that the method is useful for SPECT image analysis.

  3. Prediction of standard-dose brain PET image by using MRI and low-dose brain [{sup 18}F]FDG PET images

    SciTech Connect

    Kang, Jiayin; Gao, Yaozong; Shi, Feng; Lalush, David S.; Lin, Weili; Shen, Dinggang

    2015-09-15

    Purpose: Positron emission tomography (PET) is a nuclear medical imaging technology that produces 3D images reflecting tissue metabolic activity in human body. PET has been widely used in various clinical applications, such as in diagnosis of brain disorders. High-quality PET images play an essential role in diagnosing brain diseases/disorders. In practice, in order to obtain high-quality PET images, a standard-dose radionuclide (tracer) needs to be used and injected into a living body. As a result, it will inevitably increase the patient’s exposure to radiation. One solution to solve this problem is predicting standard-dose PET images using low-dose PET images. As yet, no previous studies with this approach have been reported. Accordingly, in this paper, the authors propose a regression forest based framework for predicting a standard-dose brain [{sup 18}F]FDG PET image by using a low-dose brain [{sup 18}F]FDG PET image and its corresponding magnetic resonance imaging (MRI) image. Methods: The authors employ a regression forest for predicting the standard-dose brain [{sup 18}F]FDG PET image by low-dose brain [{sup 18}F]FDG PET and MRI images. Specifically, the proposed method consists of two main steps. First, based on the segmented brain tissues (i.e., cerebrospinal fluid, gray matter, and white matter) in the MRI image, the authors extract features for each patch in the brain image from both low-dose PET and MRI images to build tissue-specific models that can be used to initially predict standard-dose brain [{sup 18}F]FDG PET images. Second, an iterative refinement strategy, via estimating the predicted image difference, is used to further improve the prediction accuracy. Results: The authors evaluated their algorithm on a brain dataset, consisting of 11 subjects with MRI, low-dose PET, and standard-dose PET images, using leave-one-out cross-validations. The proposed algorithm gives promising results with well-estimated standard-dose brain [{sup 18}F]FDG PET

  4. Benchmarking PET for geoscientific applications: 3D quantitative diffusion coefficient determination in clay rock

    NASA Astrophysics Data System (ADS)

    Lippmann-Pipke, J.; Gerasch, R.; Schikora, J.; Kulenkampff, J.

    2017-04-01

    The 3D diagonal anisotropic effective diffusion coefficient of Na+, Deff=(Dxx, Dyy, Dzz), was quantified in a clay material in one single experiment/simulation. That is possible due to the combination of the non-invasive observation of Na+ diffusion in Opalinus clay by means of GeoPET method (PET: positron emission tomography) followed by quantitative 3D+t data evaluation by means of the finite element numerical modelling (FEM). The extracted anisotropic effective diffusion coefficient parallel (||) and normal (⊥) to the bedding of the clay rock, Deff=(D||, D⊥, D||) are comparable to those obtained on earlier experimental studies in the same clay material but with different methods. We consider this study as benchmark for the long-standing development of our GeoPET method, that explicitly includes a resolute and physics based attenuation and Compton scatter correction algorithm (Kulenkampff, J., M. Gründig, A. Zakhnini and J. Lippmann-Pipke (2016). "Geoscientific process monitoring with positron emission tomography (GeoPET)." Solid Earth 7: 1217-1231). We suggest GeoPET based fluid flow transport visualization combined with computer based process simulation henceforth as a qualified way for the quantification of three-dimensional, effective transport parameters in geosciences.

  5. A 3D digital map of rat brain.

    PubMed

    Toga, A W; Santori, E M; Hazani, R; Ambach, K

    1995-01-01

    A three dimensional (3D) computerized map of rat brain anatomy created with digital imaging techniques is described. Six male Sprague-Dawley rats, weighing 270-320 g, were used in the generation of this atlas. Their heads were frozen, and closely spaced cryosectional images were digitally captured. Each serial data set was organized into a digital volume, reoriented into a flat skull position, and brought into register with each other. A volume representative of the group following registration was chosen based on its anatomic correspondence with the other specimens as measured by image correlation coefficients and landmark matching. Mean positions of lambda, bregma, and the interaural plane of the group within the common coordinate system were used to transform the representative volume into a 3D map of rat neuroanatomy. images reconstructed from this 3D map are available to the public via Internet with an anonymous file transfer protocol (FTP) and World Wide Web. A complete description of the digital map is provided in a comprehensive set of sagittal planes (up to 0.031 mm spacing) containing stereotaxic reference grids. Sets of coronal and horizontal planes, resampled at the same increment, also are included. Specific anatomic features are identified in a second collection of images. Stylized anatomic boundaries and structural labels were incorporated into selected orthogonal planes. Electronic sharing and interactive use are benefits afforded by a digital format, but the foremost advantage of this 3D map is its whole brain integrated representation of rat in situ neuroanatomy.

  6. Internet2-based 3D PET image reconstruction using a PC cluster

    NASA Astrophysics Data System (ADS)

    Shattuck, D. W.; Rapela, J.; Asma, E.; Chatzioannou, A.; Qi, J.; Leahy, R. M.

    2002-08-01

    We describe an approach to fast iterative reconstruction from fully three-dimensional (3D) PET data using a network of PentiumIII PCs configured as a Beowulf cluster. To facilitate the use of this system, we have developed a browser-based interface using Java. The system compresses PET data on the user's machine, sends these data over a network, and instructs the PC cluster to reconstruct the image. The cluster implements a parallelized version of our preconditioned conjugate gradient method for fully 3D MAP image reconstruction. We report on the speed-up factors using the Beowulf approach and the impacts of communication latencies in the local cluster network and the network connection between the user's machine and our PC cluster.

  7. Internet2-based 3D PET image reconstruction using a PC cluster.

    PubMed

    Shattuck, D W; Rapela, J; Asma, E; Chatzioannou, A; Qi, J; Leahy, R M

    2002-08-07

    We describe an approach to fast iterative reconstruction from fully three-dimensional (3D) PET data using a network of PentiumIII PCs configured as a Beowulf cluster. To facilitate the use of this system, we have developed a browser-based interface using Java. The system compresses PET data on the user's machine, sends these data over a network, and instructs the PC cluster to reconstruct the image. The cluster implements a parallelized version of our preconditioned conjugate gradient method for fully 3D MAP image reconstruction. We report on the speed-up factors using the Beowulf approach and the impacts of communication latencies in the local cluster network and the network connection between the user's machine and our PC cluster.

  8. Energy-based scatter correction for 3-D PET scanners using NaI(T1) detectors.

    PubMed

    Adam, L E; Karp, J S; Freifelder, R

    2000-05-01

    Earlier investigations with BGO positron emission tomography (PET) scanners showed that the scatter correction technique based on multiple acquisitions with different energy windows are problematic to implement because of the poor energy resolution of BGO (22%), particularly for whole-body studies. We believe that these methods are likely to work better with NaI(TI) because of the better energy resolution achievable with NaI(TI) detectors (10%). Therefore, we investigate two different choices for the energy window, a low-energy window (LEW) on the Compton spectrum at 400-450 keV, and a high-energy window (HEW) within the photopeak (lower threshold above 511 keV). The results obtained for our three-dimensional (3-D) (septa-less) whole-body scanners [axial field of view (FOV) of 12.8 cm and 25.6 cm] as well as for our 3-D brain scanner (axial FOV of 25.6 cm) show an accurate prediction of the scatter distribution for the estimation of trues method (ETM) using a HEW, leading to a significant reduction of the scatter contamination. The dual-energy window (DEW) technique using a LEW is shown to be intrinsically wrong; in particular, it fails for line source and bar phantom measurements. However, the method is able to produce good results for homogeneous activity distributions. Both methods are easy to implement, are fast, have a low noise propagation, and will be applicable to other PET scanners with good energy resolution and stability, such as hybrid NaI(TI) PET/SPECT dual-head cameras and future PET cameras with GSO or LSO scintillators.

  9. Fourier-based reconstruction for fully 3-D PET: optimization of interpolation parameters.

    PubMed

    Matej, Samuel; Kazantsev, Ivan G

    2006-07-01

    Fourier-based approaches for three-dimensional (3-D) reconstruction are based on the relationship between the 3-D Fourier transform (FT) of the volume and the two-dimensional (2-D) FT of a parallel-ray projection of the volume. The critical step in the Fourier-based methods is the estimation of the samples of the 3-D transform of the image from the samples of the 2-D transforms of the projections on the planes through the origin of Fourier space, and vice versa for forward-projection (reprojection). The Fourier-based approaches have the potential for very fast reconstruction, but their straightforward implementation might lead to unsatisfactory results if careful attention is not paid to interpolation and weighting functions. In our previous work, we have investigated optimal interpolation parameters for the Fourier-based forward and back-projectors for iterative image reconstruction. The optimized interpolation kernels were shown to provide excellent quality comparable to the ideal sinc interpolator. This work presents an optimization of interpolation parameters of the 3-D direct Fourier method with Fourier reprojection (3D-FRP) for fully 3-D positron emission tomography (PET) data with incomplete oblique projections. The reprojection step is needed for the estimation (from an initial image) of the missing portions of the oblique data. In the 3D-FRP implementation, we use the gridding interpolation strategy, combined with proper weighting approaches in the transform and image domains. We have found that while the 3-D reprojection step requires similar optimal interpolation parameters as found in our previous studies on Fourier-based iterative approaches, the optimal interpolation parameters for the main 3D-FRP reconstruction stage are quite different. Our experimental results confirm that for the optimal interpolation parameters a very good image accuracy can be achieved even without any extra spectral oversampling, which is a common practice to decrease errors

  10. 3D image reconstruction for PET by multi-slice rebinning and axial filtering. [Positron Emission Tomography (PET)

    SciTech Connect

    Lewitt, R.M. Pennsylvania Univ., Philadelphia, PA . Dept. of Radiology); Muehllehner, G. ); Karp, J.S. . Dept. of Radiology)

    1991-01-01

    Two different approaches are used at present to reconstruct from 3D coincidence data in PET. We refer to these approaches as the single-slice rebinning approach and the fully-3D approach. The single-slice rebinning approach involves geometrical approximations, but it requires the least possible amount of computation. Fully-3D reconstruction algorithms, both iterative and non-iterative, do not make such approximations, but require much more computation. Multi-slice rebinning with axial filtering is a new approach which attempts to achieve the geometrical accuracy of the fully-3D approach with the simplicity and modest amount of computation of the single-slice rebinning approach. The first step (multi-slice rebinning) involves rebinning of coincidence lines into a stack of 2D sinograms, where multiple sinograms are incremented for each oblique coincidence line. This operation is followed by an axial filtering operation, either before or after slice-by-slice reconstruction, to reduce the blurring in the axial direction. Tests with simulated and experimental data indicate that the new method has better geometrical accuracy than single-slice rebinning, at the cost of only a modest increase in computation. 11 refs.

  11. Parameterization of 3D brain structures for statistical shape analysis

    NASA Astrophysics Data System (ADS)

    Zhu, Litao; Jiang, Tianzi

    2004-05-01

    Statistical Shape Analysis (SSA) is a powerful tool for noninvasive studies of pathophysiology and diagnosis of brain diseases. It also provides a shape constraint for the segmentation of brain structures. There are two key problems in SSA: the representation of shapes and their alignments. The widely used parameterized representations are obtained by preserving angles or areas and the alignments of shapes are achieved by rotating parameter net. However, representations preserving angles or areas do not really guarantee the anatomical correspondence of brain structures. In this paper, we incorporate shape-based landmarks into parameterization of banana-like 3D brain structures to address this problem. Firstly, we get the triangulated surface of the object and extract two landmarks from the mesh, i.e. the ends of the banana-like object. Then the surface is parameterized by creating a continuous and bijective mapping from the surface to a spherical surface based on a heat conduction model. The correspondence of shapes is achieved by mapping the two landmarks to the north and south poles of the sphere and using an extracted origin orientation to select the dateline during parameterization. We apply our approach to the parameterization of lateral ventricle and a multi-resolution shape representation is obtained by using the Discrete Fourier Transform.

  12. 3D image reconstruction for PET by multi-slice rebinning and axial filtering

    SciTech Connect

    Lewitt, R.M. |; Muehllehner, G.; Karp, J.S.

    1991-12-01

    Two different approaches are used at present to reconstruct from 3D coincidence data in PET. We refer to these approaches as the single-slice rebinning approach and the fully-3D approach. The single-slice rebinning approach involves geometrical approximations, but it requires the least possible amount of computation. Fully-3D reconstruction algorithms, both iterative and non-iterative, do not make such approximations, but require much more computation. Multi-slice rebinning with axial filtering is a new approach which attempts to achieve the geometrical accuracy of the fully-3D approach with the simplicity and modest amount of computation of the single-slice rebinning approach. The first step (multi-slice rebinning) involves rebinning of coincidence lines into a stack of 2D sinograms, where multiple sinograms are incremented for each oblique coincidence line. This operation is followed by an axial filtering operation, either before or after slice-by-slice reconstruction, to reduce the blurring in the axial direction. Tests with simulated and experimental data indicate that the new method has better geometrical accuracy than single-slice rebinning, at the cost of only a modest increase in computation. 11 refs.

  13. Fast 3D fluid registration of brain magnetic resonance images

    NASA Astrophysics Data System (ADS)

    Leporé, Natasha; Chou, Yi-Yu; Lopez, Oscar L.; Aizenstein, Howard J.; Becker, James T.; Toga, Arthur W.; Thompson, Paul M.

    2008-03-01

    Fluid registration is widely used in medical imaging to track anatomical changes, to correct image distortions, and to integrate multi-modality data. Fluid mappings guarantee that the template image deforms smoothly into the target, without tearing or folding, even when large deformations are required for accurate matching. Here we implemented an intensity-based fluid registration algorithm, accelerated by using a filter designed by Bro-Nielsen and Gramkow. We validated the algorithm on 2D and 3D geometric phantoms using the mean square difference between the final registered image and target as a measure of the accuracy of the registration. In tests on phantom images with different levels of overlap, varying amounts of Gaussian noise, and different intensity gradients, the fluid method outperformed a more commonly used elastic registration method, both in terms of accuracy and in avoiding topological errors during deformation. We also studied the effect of varying the viscosity coefficients in the viscous fluid equation, to optimize registration accuracy. Finally, we applied the fluid registration algorithm to a dataset of 2D binary corpus callosum images and 3D volumetric brain MRIs from 14 healthy individuals to assess its accuracy and robustness.

  14. Unsupervised fuzzy segmentation of 3D magnetic resonance brain images

    NASA Astrophysics Data System (ADS)

    Velthuizen, Robert P.; Hall, Lawrence O.; Clarke, Laurence P.; Bensaid, Amine M.; Arrington, J. A.; Silbiger, Martin L.

    1993-07-01

    Unsupervised fuzzy methods are proposed for segmentation of 3D Magnetic Resonance images of the brain. Fuzzy c-means (FCM) has shown promising results for segmentation of single slices. FCM has been investigated for volume segmentations, both by combining results of single slices and by segmenting the full volume. Different strategies and initializations have been tried. In particular, two approaches have been used: (1) a method by which, iteratively, the furthest sample is split off to form a new cluster center, and (2) the traditional FCM in which the membership grade matrix is initialized in some way. Results have been compared with volume segmentations by k-means and with two supervised methods, k-nearest neighbors and region growing. Results of individual segmentations are presented as well as comparisons on the application of the different methods to a number of tumor patient data sets.

  15. Assessment of a fully 3D Monte Carlo reconstruction method for preclinical PET with iodine-124

    NASA Astrophysics Data System (ADS)

    Moreau, M.; Buvat, I.; Ammour, L.; Chouin, N.; Kraeber-Bodéré, F.; Chérel, M.; Carlier, T.

    2015-03-01

    Iodine-124 is a radionuclide well suited to the labeling of intact monoclonal antibodies. Yet, accurate quantification in preclinical imaging with I-124 is challenging due to the large positron range and a complex decay scheme including high-energy gammas. The aim of this work was to assess the quantitative performance of a fully 3D Monte Carlo (MC) reconstruction for preclinical I-124 PET. The high-resolution small animal PET Inveon (Siemens) was simulated using GATE 6.1. Three system matrices (SM) of different complexity were calculated in addition to a Siddon-based ray tracing approach for comparison purpose. Each system matrix accounted for a more or less complete description of the physics processes both in the scanned object and in the PET scanner. One homogeneous water phantom and three heterogeneous phantoms including water, lungs and bones were simulated, where hot and cold regions were used to assess activity recovery as well as the trade-off between contrast recovery and noise in different regions. The benefit of accounting for scatter, attenuation, positron range and spurious coincidences occurring in the object when calculating the system matrix used to reconstruct I-124 PET images was highlighted. We found that the use of an MC SM including a thorough modelling of the detector response and physical effects in a uniform water-equivalent phantom was efficient to get reasonable quantitative accuracy in homogeneous and heterogeneous phantoms. Modelling the phantom heterogeneities in the SM did not necessarily yield the most accurate estimate of the activity distribution, due to the high variance affecting many SM elements in the most sophisticated SM.

  16. Assessment of a fully 3D Monte Carlo reconstruction method for preclinical PET with iodine-124.

    PubMed

    Moreau, M; Buvat, I; Ammour, L; Chouin, N; Kraeber-Bodéré, F; Chérel, M; Carlier, T

    2015-03-21

    Iodine-124 is a radionuclide well suited to the labeling of intact monoclonal antibodies. Yet, accurate quantification in preclinical imaging with I-124 is challenging due to the large positron range and a complex decay scheme including high-energy gammas. The aim of this work was to assess the quantitative performance of a fully 3D Monte Carlo (MC) reconstruction for preclinical I-124 PET. The high-resolution small animal PET Inveon (Siemens) was simulated using GATE 6.1. Three system matrices (SM) of different complexity were calculated in addition to a Siddon-based ray tracing approach for comparison purpose. Each system matrix accounted for a more or less complete description of the physics processes both in the scanned object and in the PET scanner. One homogeneous water phantom and three heterogeneous phantoms including water, lungs and bones were simulated, where hot and cold regions were used to assess activity recovery as well as the trade-off between contrast recovery and noise in different regions. The benefit of accounting for scatter, attenuation, positron range and spurious coincidences occurring in the object when calculating the system matrix used to reconstruct I-124 PET images was highlighted. We found that the use of an MC SM including a thorough modelling of the detector response and physical effects in a uniform water-equivalent phantom was efficient to get reasonable quantitative accuracy in homogeneous and heterogeneous phantoms. Modelling the phantom heterogeneities in the SM did not necessarily yield the most accurate estimate of the activity distribution, due to the high variance affecting many SM elements in the most sophisticated SM.

  17. Evaluation of simulation-based scatter correction for 3-D PET cardiac imaging

    SciTech Connect

    Watson, C.C.; Newport, D.; Casey, M.E.; Kemp, R.A. de; Beanlands, R.S.; Schmand, M. |

    1997-02-01

    Quantitative imaging of the human thorax poses one of the most difficult challenges for three-dimensional (3-D) (septaless) positron emission tomography (PET), due to the strong attenuation of the annihilation radiation and the large contribution of scattered photons to the data. In [{sup 18}F] fluorodeoxyglucose (FDG) studies of the heart with the patient`s arms in the field of view, the contribution of scattered events can exceed 50% of the total detected coincidences. Accurate correction for this scatter component is necessary for meaningful quantitative image analysis and tracer kinetic modeling. For this reason, the authors have implemented a single-scatter simulation technique for scatter correction in positron volume imaging. In this paper they describe this algorithm and present scatter correction results from human and chest phantom studies.

  18. High accuracy multiple scatter modelling for 3D whole body PET.

    PubMed

    Markiewicz, P J; Tamal, M; Julyan, P J; Hastings, D L; Reader, A J

    2007-02-07

    A new technique for modelling multiple-order Compton scatter which uses the absolute probabilities relating the image space to the projection space in 3D whole body PET is presented. The details considered in this work give a valuable insight into the scatter problem, particularly for multiple scatter. Such modelling is advantageous for large attenuating media where scatter is a dominant component of the measured data, and where multiple scatter may dominate the total scatter depending on the energy threshold and object size. The model offers distinct features setting it apart from previous research: (1) specification of the scatter distribution for each voxel based on the transmission data, the physics of Compton scattering and the specification of a given PET system; (2) independence from the true activity distribution; (3) in principle no scaling or iterative process is required to find the distribution; (4) explicit multiple scatter modelling; (5) no scatter subtraction or addition to the forward model when included in the system matrix used with statistical image reconstruction methods; (6) adaptability to many different scatter compensation methods from simple and fast to more sophisticated and therefore slower methods; (7) accuracy equivalent to that of a Monte Carlo model. The scatter model has been validated using Monte Carlo simulation (SimSET).

  19. Acquisition and automated 3-D segmentation of respiratory/cardiac-gated PET transmission images

    SciTech Connect

    Reutter, B.W.; Klein, G.J.; Brennan, K.M.; Huesman, R.H. |

    1996-12-31

    To evaluate the impact of respiratory motion on attenuation correction of cardiac PET data, we acquired and automatically segmented gated transmission data for a dog breathing on its own under gas anesthesia. Data were acquired for 20 min on a CTI/Siemens ECAT EXACT HR (47-slice) scanner configured for 12 gates in a static study, Two respiratory gates were obtained using data from a pneumatic bellows placed around the dog`s chest, in conjunction with 6 cardiac gates from standard EKG gating. Both signals were directed to a LabVIEW-controlled Macintosh, which translated them into one of 12 gate addresses. The respiratory gating threshold was placed near end-expiration to acquire 6 cardiac-gated datasets at end-expiration and 6 cardiac-gated datasets during breaths. Breaths occurred about once every 10 sec and lasted about 1-1.5 sec. For each respiratory gate, data were summed over cardiac gates and torso and lung surfaces were segmented automatically using a differential 3-D edge detection algorithm. Three-dimensional visualizations showed that lung surfaces adjacent to the heart translated 9 mm inferiorly during breaths. Our results suggest that respiration-compensated attenuation correction is feasible with a modest amount of gated transmission data and is necessary for accurate quantitation of high-resolution gated cardiac PET data.

  20. Study of a high-resolution, 3D positioning cadmium zinc telluride detector for PET

    NASA Astrophysics Data System (ADS)

    Gu, Y.; Matteson, J. L.; Skelton, R. T.; Deal, A. C.; Stephan, E. A.; Duttweiler, F.; Gasaway, T. M.; Levin, C. S.

    2011-03-01

    This paper investigates the performance of 1 mm resolution cadmium zinc telluride (CZT) detectors for positron emission tomography (PET) capable of positioning the 3D coordinates of individual 511 keV photon interactions. The detectors comprise 40 mm × 40 mm × 5 mm monolithic CZT crystals that employ a novel cross-strip readout with interspersed steering electrodes to obtain high spatial and energy resolution. The study found a single anode FWHM energy resolution of 3.06 ± 0.39% at 511 keV throughout most of the detector volume. Improved resolution is expected with properly shielded front-end electronics. Measurements made using a collimated beam established the efficacy of the steering electrodes in facilitating enhanced charge collection across anodes, as well as a spatial resolution of 0.44 ± 0.07 mm in the direction orthogonal to the electrode planes. Finally, measurements based on coincidence electronic collimation yielded a point spread function with 0.78 ± 0.10 mm FWHM, demonstrating 1 mm spatial resolution capability transverse to the anodes—as expected from the 1 mm anode pitch. These findings indicate that the CZT-based detector concept has excellent performance and shows great promise for a high-resolution PET system.

  1. Study of a high-resolution, 3D positioning cadmium zinc telluride detector for PET.

    PubMed

    Gu, Y; Matteson, J L; Skelton, R T; Deal, A C; Stephan, E A; Duttweiler, F; Gasaway, T M; Levin, C S

    2011-03-21

    This paper investigates the performance of 1 mm resolution cadmium zinc telluride (CZT) detectors for positron emission tomography (PET) capable of positioning the 3D coordinates of individual 511 keV photon interactions. The detectors comprise 40 mm × 40 mm × 5 mm monolithic CZT crystals that employ a novel cross-strip readout with interspersed steering electrodes to obtain high spatial and energy resolution. The study found a single anode FWHM energy resolution of 3.06 ± 0.39% at 511 keV throughout most of the detector volume. Improved resolution is expected with properly shielded front-end electronics. Measurements made using a collimated beam established the efficacy of the steering electrodes in facilitating enhanced charge collection across anodes, as well as a spatial resolution of 0.44 ± 0.07 mm in the direction orthogonal to the electrode planes. Finally, measurements based on coincidence electronic collimation yielded a point spread function with 0.78 ± 0.10 mm FWHM, demonstrating 1 mm spatial resolution capability transverse to the anodes-as expected from the 1 mm anode pitch. These findings indicate that the CZT-based detector concept has excellent performance and shows great promise for a high-resolution PET system.

  2. Study of a high-resolution, 3-D positioning cadmium zinc telluride detector for PET

    PubMed Central

    Gu, Y; Matteson, J L; Skelton, R T; Deal, A C; Stephan, E A; Duttweiler, F; Gasaway, T M; Levin, C S

    2011-01-01

    This paper investigates the performance of 1 mm resolution Cadmium Zinc Telluride (CZT) detectors for positron emission tomography (PET) capable of positioning the 3-D coordinates of individual 511 keV photon interactions. The detectors comprise 40 mm × 40 mm × 5 mm monolithic CZT crystals that employ a novel cross-strip readout with interspersed steering electrodes to obtain high spatial and energy resolution. The study found a single anode FWHM energy resolution of 3.06±0.39% at 511 keV throughout most the detector volume. Improved resolution is expected with properly shielded front-end electronics. Measurements made using a collimated beam established the efficacy of the steering electrodes in facilitating enhanced charge collection across anodes, as well as a spatial resolution of 0.44±0.07 mm in the direction orthogonal to the electrode planes. Finally, measurements based on coincidence electronic collimation yielded a point spread function with 0.78±0.10 mm FWHM, demonstrating 1 mm spatial resolution capability transverse to the anodes – as expected from the 1 mm anode pitch. These findings indicate that the CZT-based detector concept has excellent performance and shows great promise for a high-resolution PET system. PMID:21335649

  3. The effect of activity outside the field-of-view on image signal-to-noise ratio for 3D PET with 15O

    NASA Astrophysics Data System (ADS)

    Ibaraki, Masanobu; Sugawara, Shigeki; Nakamura, Kazuhiro; Kinoshita, Fumiko; Kinoshita, Toshibumi

    2011-05-01

    Activity outside the field-of-view (FOV) degrades the count rate performance of 3D PET and consequently reduces signal-to-noise ratios (SNRs) of reconstructed images. The aim of this study was to evaluate a neck-shield installed in a 3D PET scanner for reducing the effect of the outside FOV activity. Specifically, we compared brain PET scans (15O2 and H215O) with and without the use of the neck-shield. Image SNRs were directly estimated by a sinogram bootstrap method. The bootstrap analysis showed that the use of the neck-shield improved the SNR by 8% and 19% for H215O and 15O2, respectively. The SNR improvements were predominantly due to the reduction of the random count rates. Noise equivalent count rate (NECR) analysis provided SNR estimates that were very similar with the bootstrap-based results for H215O, but not for 15O2. This discrepancy may be due to the fundamental difference between the two methods: the bootstrap method directly calculates the local SNR of reconstructed images, whereas the NECR calculation is based on the whole-gantry count rates, indicating a limitation of the conventional NECR-based method as a tool for assessing the image SNR. Although quantitative parameters, e.g. cerebral blood flow, did not differ when examined with and without the neck-shield, the use of the shield for brain 15O study is recommended in terms of the image SNR.

  4. 3D registration of micro PET-CT for measurable correlates of dyspeptic symptoms in mice

    NASA Astrophysics Data System (ADS)

    Camp, Jon; Simpson, Kathryn; Bardsley, Michael R.; Popko, Laura N.; Young, David L.; Kemp, Bradley J.; Lowe, Val; Ordog, Tamas; Robb, Richard

    2009-02-01

    Patients with chronic calorie insufficiency commonly suffer from upper gastrointestinal dysfunction and consequent dyspeptic symptoms, which may interfere with their nutritional rehabilitation. To investigate the relationship between gastric dysfunction and feeding behavior, we exposed mice to chronic caloric restriction and demonstrated gastric motor abnormalities in them. Gastric dysmotility is typically associated with dyspeptic symptoms but sensations cannot be directly assessed in animal models. Therefore, as an initial step toward establishing measurable correlates of postprandial symptoms in small animals, we have attempted to characterize central responses to food intake by positron emission tomography-computerized microtomography (PET-CT) in normal and calorically restricted mice. Animals consumed a standard test meal after an overnight fast before receiving 2-deoxy-2[18F]fluoro-D-glucose tracer. The same mice were also scanned in the fasting state on a separate day. We were able to bring the fed and fasting PET volume images into spatial registration with each other and with an MR-derived atlas of the mouse brain, so that the differences in uptake between the two states could be mapped quantitatively against the neuroanatomic regions of the atlas. Our approach is suitable for studying the effects of gastric dysmotilities on central responses to feeding.

  5. Evaluation of a 3D point spread function (PSF) model derived from Monte Carlo simulation for a small animal PET scanner

    NASA Astrophysics Data System (ADS)

    Yao, Rutao; Ramachandra, Ranjith M.; Panse, Ashish; Balla, Deepika; Yan, Jianhua; Carson, Richard E.

    2010-04-01

    We previously designed a component based 3-D PSF model to obtain a compact yet accurate system matrix for a dedicated human brain PET scanner. In this work, we adapted the model to a small animal PET scanner. Based on the model, we derived the system matrix for back-to-back gamma source in air, fluorine-18 and iodine-124 source in water by Monte Carlo simulation. The characteristics of the PSF model were evaluated and the performance of the newly derived system matrix was assessed by comparing its reconstructed images with the established reconstruction program provided on the animal PET scanner. The new system matrix showed strong PSF dependency on the line-of-response (LOR) incident angle and LOR depth. This confirmed the validity of the two components selected for the model. The effect of positron range on the system matrix was observed by comparing the PSFs of different isotopes. A simulated and an experimental hot-rod phantom study showed that the reconstruction with the proposed system matrix achieved better resolution recovery as compared to the algorithm provided by the manufacturer. Quantitative evaluation also showed better convergence to the expected contrast value at similar noise level. In conclusion, it has been shown that the system matrix derivation method is applicable to the animal PET system studied, suggesting that the method may be used for other PET systems and different isotope applications.

  6. Quantitative PET imaging with the 3T MR-BrainPET

    NASA Astrophysics Data System (ADS)

    Weirich, C.; Scheins, J.; Lohmann, P.; Tellmann, L.; Byars, L.; Michel, C.; Rota Kops, E.; Brenner, D.; Herzog, H.; Shah, N. J.

    2013-02-01

    The new hybrid imaging technology of MR-PET allows for simultaneous acquisition of versatile MRI contrasts and the quantitative metabolic imaging with PET. In order to achieve the quantification of PET images with minimal residual error the application of several corrections is crucial. In this work we present our results on quantification with the 3T MR BrainPET scanner.

  7. Confocal laser scanning microscopy and 3-D reconstructions of neuronal structures in human brain cortex.

    PubMed

    Belichenko, P V; Dahlström, A

    1995-09-01

    Human brain material was studied with Lucifer yellow (LY) microinjections, indirect Texas red immunofluorescence, and confocal laser scanning microscopy (CLSM). The scanned images were transferred to a Silicon Graphics (SG) IRIS computer equipped with software for reconstructing the 3-D architecture of cells. By employing dual channel CLSM (Bio-Rad MRC 600), LY-injected cells and Texas red immunofluorescence could be studied simultaneously. Autopsy material with 2- to 48-h postmortem delays (6 control and 2 Rett's syndrome cases) as well as biopsy material (14 cases with therapy-resistant partial epilepsy--TRPE--undergoing neurosurgery) were used. In each specimen, 100-200 pyramidal and nonpyramidal neurons were visualized by LY microinjection. Single neurons were imaged and 2-D reconstructions of each neuron were made using z-projections of serial optical images; 3-D reconstructions and rotations were computed using the SG workstation, with VoxelView software from Vital Images (UK), and stored in a "neuronal library" on laser or magnetic optical disks. In Ret's syndrome cases and in patients with TRPE various abnormalities in the dendritic geometry of pyramidal and nonpyramidal cells have been found. The combination of LY injections with immunofluorescence allows the investigation of transmitter-related substances around the LY-injected cells. Using antibodies to synaptic vesicle proteins, presynaptic elements docking onto individual spines have been demonstrated. This approach may contribute to the understanding of different neurological and psychiatric disorders and may be useful in the Mapping of the Human Brain project. It may also be integrated with functional imaging by PET scan and with the human genome project.

  8. A Registration Method Based on Contour Point Cloud for 3D Whole-Body PET and CT Images

    PubMed Central

    Yang, Qiyao; Wang, Zhiguo; Zhang, Guoxu

    2017-01-01

    The PET and CT fusion image, combining the anatomical and functional information, has important clinical meaning. An effective registration of PET and CT images is the basis of image fusion. This paper presents a multithread registration method based on contour point cloud for 3D whole-body PET and CT images. Firstly, a geometric feature-based segmentation (GFS) method and a dynamic threshold denoising (DTD) method are creatively proposed to preprocess CT and PET images, respectively. Next, a new automated trunk slices extraction method is presented for extracting feature point clouds. Finally, the multithread Iterative Closet Point is adopted to drive an affine transform. We compare our method with a multiresolution registration method based on Mattes Mutual Information on 13 pairs (246~286 slices per pair) of 3D whole-body PET and CT data. Experimental results demonstrate the registration effectiveness of our method with lower negative normalization correlation (NC = −0.933) on feature images and less Euclidean distance error (ED = 2.826) on landmark points, outperforming the source data (NC = −0.496, ED = 25.847) and the compared method (NC = −0.614, ED = 16.085). Moreover, our method is about ten times faster than the compared one. PMID:28316979

  9. Using 3-D OFEM for movement correction and quantitative evaluation in dynamic cardiac NH3 PET images

    NASA Astrophysics Data System (ADS)

    Lin, Hong-Dun; Yang, Bang-Hung; Chen, Chih-Hao; Wu, Liang-Chih; Liu, Ren-Shyan; Chung, Being-Tau; Lin, Kang-Ping

    2005-04-01

    Various forms of cardiac pathology, such as myocardial ischemia and infarction, can be characterized with 13NH3-PET images. In clinical situation, polar map (bullseye image), which derived by combining images from multiple planes (designated by the circle around the myocardium in the above images), so that information of the entire myocardium can be displayed in a single image for diagnosis. However, image artifact problem always arises from body movement or breathing motion in image acquisition period and results in indefinite myocardium disorder region shown in bullseye image. In this study, a 3-D motion and movement correction method is developed to solve the image artifact problem to improve the accuracy of diagnostic bullseye image. The proposed method is based on 3-D optical flow estimation method (OFEM) and cooperates with the particular dynamic imaging protocol, which snaps serial PET images (5 frames) in later half imaging period. The 3-D OFEM assigns to each image point in the visual 3-D flow velocity field, which associates with the non-rigid motion of the time-varying brightness of a sequence of images. It presents vectors of corresponding images position between frames for motion correction. To validate the performance of proposed method, 10 normal and 20 abnormal whole-body dynamic PET imaging studies were applied, and the results show that the bullseye images, which generated by corrected images, present clear and definite tissue region for clinical diagnosis.

  10. Nanofabricated Neural Probes for Dense 3-D Recordings of Brain Activity

    PubMed Central

    2016-01-01

    Computations in brain circuits involve the coordinated activation of large populations of neurons distributed across brain areas. However, monitoring neuronal activity in the brain of intact animals with high temporal and spatial resolution has remained a technological challenge. Here we address this challenge by developing dense, three-dimensional (3-D) electrode arrays for electrophysiology. The 3-D arrays constitute the front-end of a modular and configurable system architecture that enables monitoring neuronal activity with unprecedented scale and resolution. PMID:27766885

  11. A 3D MR-acquisition scheme for nonrigid bulk motion correction in simultaneous PET-MR

    SciTech Connect

    Kolbitsch, Christoph Prieto, Claudia; Schaeffter, Tobias; Tsoumpas, Charalampos

    2014-08-15

    Purpose: Positron emission tomography (PET) is a highly sensitive medical imaging technique commonly used to detect and assess tumor lesions. Magnetic resonance imaging (MRI) provides high resolution anatomical images with different contrasts and a range of additional information important for cancer diagnosis. Recently, simultaneous PET-MR systems have been released with the promise to provide complementary information from both modalities in a single examination. Due to long scan times, subject nonrigid bulk motion, i.e., changes of the patient's position on the scanner table leading to nonrigid changes of the patient's anatomy, during data acquisition can negatively impair image quality and tracer uptake quantification. A 3D MR-acquisition scheme is proposed to detect and correct for nonrigid bulk motion in simultaneously acquired PET-MR data. Methods: A respiratory navigated three dimensional (3D) MR-acquisition with Radial Phase Encoding (RPE) is used to obtain T1- and T2-weighted data with an isotropic resolution of 1.5 mm. Healthy volunteers are asked to move the abdomen two to three times during data acquisition resulting in overall 19 movements at arbitrary time points. The acquisition scheme is used to retrospectively reconstruct dynamic 3D MR images with different temporal resolutions. Nonrigid bulk motion is detected and corrected in this image data. A simultaneous PET acquisition is simulated and the effect of motion correction is assessed on image quality and standardized uptake values (SUV) for lesions with different diameters. Results: Six respiratory gated 3D data sets with T1- and T2-weighted contrast have been obtained in healthy volunteers. All bulk motion shifts have successfully been detected and motion fields describing the transformation between the different motion states could be obtained with an accuracy of 1.71 ± 0.29 mm. The PET simulation showed errors of up to 67% in measured SUV due to bulk motion which could be reduced to less than

  12. Brain morphology imaging by 3D microscopy and fluorescent Nissl staining.

    PubMed

    Lazutkin, A A; Komissarova, N V; Toptunov, D M; Anokhin, K V

    2013-07-01

    Modern optical methods (multiphoton and light-sheet fluorescent microscopy) allow 3D imaging of large specimens of the brain with cell resolution. It is therefore essential to refer the resultant 3D pictures of expression of transgene, protein, and other markers in the brain to the corresponding structures in the atlas. This implies counterstaining of specimens with morphological dyes. However, there are no methods for contrasting large samples of the brain without their preliminary slicing. We have developed a method for fluorescent Nissl staining of whole brain samples. 3D reconstructions of specimens of the hippocampus, olfactory bulbs, and cortex were created. The method can be used for morphological control and evaluation of the effects of various factors on the brain using 3D microscopy technique.

  13. Wakefield Simulation of CLIC PETS Structure Using Parallel 3D Finite Element Time-Domain Solver T3P

    SciTech Connect

    Candel, A.; Kabel, A.; Lee, L.; Li, Z.; Ng, C.; Schussman, G.; Ko, K.; Syratchev, I.; /CERN

    2009-06-19

    In recent years, SLAC's Advanced Computations Department (ACD) has developed the parallel 3D Finite Element electromagnetic time-domain code T3P. Higher-order Finite Element methods on conformal unstructured meshes and massively parallel processing allow unprecedented simulation accuracy for wakefield computations and simulations of transient effects in realistic accelerator structures. Applications include simulation of wakefield damping in the Compact Linear Collider (CLIC) power extraction and transfer structure (PETS).

  14. Brain PET in the Diagnosis of Alzheimer’s Disease

    PubMed Central

    Marcus, Charles; Mena, Esther; Subramaniam, Rathan M.

    2015-01-01

    Objectives The aim of this article was to review the current role of brain PET in the diagnosis of Alzheimer dementia. The characteristic patterns of glucose metabolism on brain FDG-PET can help in differentiating Alzheimer’s disease from other causes of dementia such as frontotemporal dementia and dementia of Lewy body. Amyloid brain PET may exclude significant amyloid deposition and thus Alzheimer’s disease in appropriate clinical setting. Conclusions FDG-PET and amyloid PET imaging are valuable in the assessment of patients with Alzheimer’s disease. PMID:25199063

  15. 3-D brain MRI tissue classification on FPGAs.

    PubMed

    Koo, Jahyun J; Evans, Alan C; Gross, Warren J

    2009-12-01

    Many automatic algorithms have been proposed for analyzing magnetic resonance imaging (MRI) data sets. With the increasingly large data sets being used in brain mapping, there has been a significant rise in the need for accelerating these algorithms. Partial volume estimation (PVE), a brain tissue classification algorithm for MRI, was implemented on a field-programmable gate array (FPGA)-based high performance reconfigurable computer using the Mitrion-C high-level language (HLL). This work develops on prior work in which we conducted initial studies on accelerating the prior information estimation algorithm. In this paper, we extend the work to include probability density estimation and present new results and additional analysis. We used several simulated and real human brain MR images to evaluate the accuracy and performance improvement of the proposed algorithm. The FPGA-based probability density estimation and prior information estimation implementation achieved an average speedup over an Itanium 2 CPU of 2.5 x and 9.4 x , respectively. The overall performance improvement of the FPGA-based PVE algorithm was 5.1 x with four FPGAs.

  16. Lanthanum halide scintillators for time-of-flight 3-D pet

    DOEpatents

    Karp, Joel S.; Surti, Suleman

    2008-06-03

    A Lanthanum Halide scintillator (for example LaCl.sub.3 and LaBr.sub.3) with fast decay time and good timing resolution, as well as high light output and good energy resolution, is used in the design of a PET scanner. The PET scanner includes a cavity for accepting a patient and a plurality of PET detector modules arranged in an approximately cylindrical configuration about the cavity. Each PET detector includes a Lanthanum Halide scintillator having a plurality of Lanthanum Halide crystals, a light guide, and a plurality of photomultiplier tubes arranged respectively peripherally around the cavity. The good timing resolution enables a time-of-flight (TOF) PET scanner to be developed that exhibits a reduction in noise propagation during image reconstruction and a gain in the signal-to-noise ratio. Such a PET scanner includes a time stamp circuit that records the time of receipt of gamma rays by respective PET detectors and provides timing data outputs that are provided to a processor that, in turn, calculates time-of-flight (TOF) of gamma rays through a patient in the cavity and uses the TOF of gamma rays in the reconstruction of images of the patient.

  17. Combining a wavelet transform with a channelized Hotelling observer for tumor detection in 3D PET oncology imaging

    NASA Astrophysics Data System (ADS)

    Lartizien, Carole; Tomei, Sandrine; Maxim, Voichita; Odet, Christophe

    2007-03-01

    This study evaluates new observer models for 3D whole-body Positron Emission Tomography (PET) imaging based on a wavelet sub-band decomposition and compares them with the classical constant-Q CHO model. Our final goal is to develop an original method that performs guided detection of abnormal activity foci in PET oncology imaging based on these new observer models. This computer-aided diagnostic method would highly benefit to clinicians for diagnostic purpose and to biologists for massive screening of rodents populations in molecular imaging. Method: We have previously shown good correlation of the channelized Hotelling observer (CHO) using a constant-Q model with human observer performance for 3D PET oncology imaging. We propose an alternate method based on combining a CHO observer with a wavelet sub-band decomposition of the image and we compare it to the standard CHO implementation. This method performs an undecimated transform using a biorthogonal B-spline 4/4 wavelet basis to extract the features set for input to the Hotelling observer. This work is based on simulated 3D PET images of an extended MCAT phantom with randomly located lesions. We compare three evaluation criteria: classification performance using the signal-to-noise ratio (SNR), computation efficiency and visual quality of the derived 3D maps of the decision variable λ. The SNR is estimated on a series of test images for a variable number of training images for both observers. Results: Results show that the maximum SNR is higher with the constant-Q CHO observer, especially for targets located in the liver, and that it is reached with a smaller number of training images. However, preliminary analysis indicates that the visual quality of the 3D maps of the decision variable λ is higher with the wavelet-based CHO and the computation time to derive a 3D λ-map is about 350 times shorter than for the standard CHO. This suggests that the wavelet-CHO observer is a good candidate for use in our guided

  18. Comparison of 2D and 3D qualitative whole body positron emission tomography (PET) without attenuation or scatter correction

    SciTech Connect

    Kohlmyer, S.G.; Mankoff, D.A.; Lewellen, T.K.; Kaplan, M.S.

    1996-12-31

    The increased sensitivity of 3D PET reduces image noise but can also result in a loss of contrast due to higher scatter fractions. Phantom studies were performed to compare tumor detectability in 2D and 3D qualitative whole body PET without scatter or attenuation correction. Lesion detectability was defined as: detectability = contrast/noise = (-) / {sigma}liver, where and are the average of lesion and liver regions of interest (ROIs), respectively. Liver, heart, and soft tissue sections of a Data Spectrum torso phantom containing a Teflon spine insert were filled with F-18 to match relative concentrations found in clinical FDG studies. Spherical lesions of 1.2 and 2.2 cm diameter were placed in the liver with a lesion to liver activity concentration ratio of 2 : 1. Resulting 2D and 3D images were compared for equivalent whole body acquisition times. Circular ROIs, half the diameter of the lesions, were placed on the tumors and the surrounding background. Background ROIs were normalized to account for the spatially variant bias caused by the absence of the scatter and attenuation corrections. Detectability was greater in the 3D images over the range of count densities and lesion sizes studied, although the difference in detectability between 2D and 3D decreases with decreasing lesion size. These results suggest that 3D imaging is preferable to 2D imaging for clinical qualitative whole body scanning without scatter or attenuation correction. Further studies representing a larger range of clinical applications are required.

  19. Experimental validation of improved 3D SBP positioning algorithm in PET applications using UW Phase II Board

    NASA Astrophysics Data System (ADS)

    Jorge, L. S.; Bonifacio, D. A. B.; DeWitt, Don; Miyaoka, R. S.

    2016-12-01

    Continuous scintillator-based detectors have been considered as a competitive and cheaper approach than highly pixelated discrete crystal positron emission tomography (PET) detectors, despite the need for algorithms to estimate 3D gamma interaction position. In this work, we report on the implementation of a positioning algorithm to estimate the 3D interaction position in a continuous crystal PET detector using a Field Programmable Gate Array (FPGA). The evaluated method is the Statistics-Based Processing (SBP) technique that requires light response function and event position characterization. An algorithm has been implemented using the Verilog language and evaluated using a data acquisition board that contains an Altera Stratix III FPGA. The 3D SBP algorithm was previously successfully implemented on a Stratix II FPGA using simulated data and a different module design. In this work, improvements were made to the FPGA coding of the 3D positioning algorithm, reducing the total memory usage to around 34%. Further the algorithm was evaluated using experimental data from a continuous miniature crystal element (cMiCE) detector module. Using our new implementation, average FWHM (Full Width at Half Maximum) for the whole block is 1.71±0.01 mm, 1.70±0.01 mm and 1.632±0.005 mm for x, y and z directions, respectively. Using a pipelined architecture, the FPGA is able to process 245,000 events per second for interactions inside of the central area of the detector that represents 64% of the total block area. The weighted average of the event rate by regional area (corner, border and central regions) is about 198,000 events per second. This event rate is greater than the maximum expected coincidence rate for any given detector module in future PET systems using the cMiCE detector design.

  20. Midsagittal plane extraction from brain images based on 3D SIFT

    NASA Astrophysics Data System (ADS)

    Wu, Huisi; Wang, Defeng; Shi, Lin; Wen, Zhenkun; Ming, Zhong

    2014-03-01

    Midsagittal plane (MSP) extraction from 3D brain images is considered as a promising technique for human brain symmetry analysis. In this paper, we present a fast and robust MSP extraction method based on 3D scale-invariant feature transform (SIFT). Unlike the existing brain MSP extraction methods, which mainly rely on the gray similarity, 3D edge registration or parameterized surface matching to determine the fissure plane, our proposed method is based on distinctive 3D SIFT features, in which the fissure plane is determined by parallel 3D SIFT matching and iterative least-median of squares plane regression. By considering the relative scales, orientations and flipped descriptors between two 3D SIFT features, we propose a novel metric to measure the symmetry magnitude for 3D SIFT features. By clustering and indexing the extracted SIFT features using a k-dimensional tree (KD-tree) implemented on graphics processing units, we can match multiple pairs of 3D SIFT features in parallel and solve the optimal MSP on-the-fly. The proposed method is evaluated by synthetic and in vivo datasets, of normal and pathological cases, and validated by comparisons with the state-of-the-art methods. Experimental results demonstrated that our method has achieved a real-time performance with better accuracy yielding an average yaw angle error below 0.91° and an average roll angle error no more than 0.89°.

  1. Optimization of PET instrumentation for brain activation studies

    SciTech Connect

    Dahlbom, M.; Cherry, S.R.; Hoffman, E.J. . Dept. of Radiological Science); Eriksson, L. . Dept. of Clinical Neurophysiology); Wienhard, K. )

    1993-08-01

    By performing cerebral blood flow studies with positron emission tomography (PET), and comparing blood flow images of different states of activation, functional mapping of the brain is possible. The ability of current commercial instruments to perform such studies is investigated in this work, based on a comparison of noise equivalent count (NEC) rates. Differences in the NEC performance of the different scanners in conjunction with scanner design parameters, provide insights into the importance of block design (size, dead time, crystal thickness) and overall scanner design (sensitivity and scatter fraction) for optimizing data from activation studies. The newer scanners with removable septa, operating with 3-D acquisition, have much higher sensitivity, but require new methodology for optimized operation. Only by administering multiple low doses (fractionation) of the flow tracer can the high sensitivity be utilized.

  2. A volume of intersection approach for on-the-fly system matrix calculation in 3D PET image reconstruction

    NASA Astrophysics Data System (ADS)

    Lougovski, A.; Hofheinz, F.; Maus, J.; Schramm, G.; Will, E.; van den Hoff, J.

    2014-02-01

    The aim of this study is the evaluation of on-the-fly volume of intersection computation for system’s geometry modelling in 3D PET image reconstruction. For this purpose we propose a simple geometrical model in which the cubic image voxels on the given Cartesian grid are approximated with spheres and the rectangular tubes of response (ToRs) are approximated with cylinders. The model was integrated into a fully 3D list-mode PET reconstruction for performance evaluation. In our model the volume of intersection between a voxel and the ToR is only a function of the impact parameter (the distance between voxel centre to ToR axis) but is independent of the relative orientation of voxel and ToR. This substantially reduces the computational complexity of the system matrix calculation. Based on phantom measurements it was determined that adjusting the diameters of the spherical voxel size and the ToR in such a way that the actual voxel and ToR volumes are conserved leads to the best compromise between high spatial resolution, low noise, and suppression of Gibbs artefacts in the reconstructed images. Phantom as well as clinical datasets from two different PET systems (Siemens ECAT HR+ and Philips Ingenuity-TF PET/MR) were processed using the developed and the respective vendor-provided (line of intersection related) reconstruction algorithms. A comparison of the reconstructed images demonstrated very good performance of the new approach. The evaluation showed the respective vendor-provided reconstruction algorithms to possess 34-41% lower resolution compared to the developed one while exhibiting comparable noise levels. Contrary to explicit point spread function modelling our model has a simple straight-forward implementation and it should be easy to integrate into existing reconstruction software, making it competitive to other existing resolution recovery techniques.

  3. Evaluation of 3D cognitive fatigue using heart-brain synchronization.

    PubMed

    Park, Sangin; Won, Myoung Ju; Lee, Eui Chul; Mun, Sungchul; Park, Min-Chul; Whang, Mincheol

    2015-08-01

    The purpose of this study was to identify an evaluation method for 3D cognitive fatigue based on a heart-brain synchronization phenomenon known as the heartbeat evoked potential (HEP). Thirty undergraduate students (15 females) watched a video in both 2D and 3D for an hour. Because visual fatigue is related to cognitive load, the HEP was used as an indicator of communication between the heart and the brain and therefore of cognitive function; responses were compared after 2D and 3D viewing. At the standard EEG sites F3 and F4, the alpha activity of the first and second HEP components was significantly increased after 3D video viewing relative to 2D. This increase likely indicates that sensory input from 3D video requires heavy computation by the brain, stimulating heart activity. The conclusion is that the first and second HEP components are significant parameters that can quantitatively evaluate 3D visual fatigue. Further work is needed to uncover the cause of 3D visual fatigue.

  4. Hybrid atlas-based and image-based approach for segmenting 3D brain MRIs

    NASA Astrophysics Data System (ADS)

    Bueno, Gloria; Musse, Olivier; Heitz, Fabrice; Armspach, Jean-Paul

    2001-07-01

    This work is a contribution to the problem of localizing key cerebral structures in 3D MRIs and its quantitative evaluation. In pursuing it, the cooperation between an image-based segmentation method and a hierarchical deformable registration approach has been considered. The segmentation relies on two main processes: homotopy modification and contour decision. The first one is achieved by a marker extraction stage where homogeneous 3D regions of an image, I(s), from the data set are identified. These regions, M(I), are obtained combining information from deformable atlas, achieved by the warping of eight previous labeled maps on I(s). Then, the goal of the decision stage is to precisely locate the contours of the 3D regions set by the markers. This contour decision is performed by a 3D extension of the watershed transform. The anatomical structures taken into consideration and embedded into the atlas are brain, ventricles, corpus callosum, cerebellum, right and left hippocampus, medulla and midbrain. The hybrid method operates fully automatically and in 3D, successfully providing segmented brain structures. The quality of the segmentation has been studied in terms of the detected volume ratio by using kappa statistic and ROC analysis. Results of the method are shown and validated on a 3D MRI phantom. This study forms part of an on-going long term research aiming at the creation of a 3D probabilistic multi-purpose anatomical brain atlas.

  5. Toward the automatic quantification of in utero brain development in 3D structural MRI: A review.

    PubMed

    Benkarim, Oualid M; Sanroma, Gerard; Zimmer, Veronika A; Muñoz-Moreno, Emma; Hahner, Nadine; Eixarch, Elisenda; Camara, Oscar; González Ballester, Miguel Angel; Piella, Gemma

    2017-02-14

    Investigating the human brain in utero is important for researchers and clinicians seeking to understand early neurodevelopmental processes. With the advent of fast magnetic resonance imaging (MRI) techniques and the development of motion correction algorithms to obtain high-quality 3D images of the fetal brain, it is now possible to gain more insight into the ongoing maturational processes in the brain. In this article, we present a review of the major building blocks of the pipeline toward performing quantitative analysis of in vivo MRI of the developing brain and its potential applications in clinical settings. The review focuses on T1- and T2-weighted modalities, and covers state of the art methodologies involved in each step of the pipeline, in particular, 3D volume reconstruction, spatio-temporal modeling of the developing brain, segmentation, quantification techniques, and clinical applications. Hum Brain Mapp, 2017. © 2017 Wiley Periodicals, Inc.

  6. Wearable 3-D Photoacoustic Tomography for Functional Brain Imaging in Behaving Rats

    PubMed Central

    Tang, Jianbo; Coleman, Jason E.; Dai, Xianjin; Jiang, Huabei

    2016-01-01

    Understanding the relationship between brain function and behavior remains a major challenge in neuroscience. Photoacoustic tomography (PAT) is an emerging technique that allows for noninvasive in vivo brain imaging at micrometer-millisecond spatiotemporal resolution. In this article, a novel, miniaturized 3D wearable PAT (3D-wPAT) technique is described for brain imaging in behaving rats. 3D-wPAT has three layers of fully functional acoustic transducer arrays. Phantom imaging experiments revealed that the in-plane X-Y spatial resolutions were ~200 μm for each acoustic detection layer. The functional imaging capacity of 3D-wPAT was demonstrated by mapping the cerebral oxygen saturation via multi-wavelength irradiation in behaving hyperoxic rats. In addition, we demonstrated that 3D-wPAT could be used for monitoring sensory stimulus-evoked responses in behaving rats by measuring hemodynamic responses in the primary visual cortex during visual stimulation. Together, these results show the potential of 3D-wPAT for brain study in behaving rodents. PMID:27146026

  7. Wearable 3-D Photoacoustic Tomography for Functional Brain Imaging in Behaving Rats.

    PubMed

    Tang, Jianbo; Coleman, Jason E; Dai, Xianjin; Jiang, Huabei

    2016-05-05

    Understanding the relationship between brain function and behavior remains a major challenge in neuroscience. Photoacoustic tomography (PAT) is an emerging technique that allows for noninvasive in vivo brain imaging at micrometer-millisecond spatiotemporal resolution. In this article, a novel, miniaturized 3D wearable PAT (3D-wPAT) technique is described for brain imaging in behaving rats. 3D-wPAT has three layers of fully functional acoustic transducer arrays. Phantom imaging experiments revealed that the in-plane X-Y spatial resolutions were ~200 μm for each acoustic detection layer. The functional imaging capacity of 3D-wPAT was demonstrated by mapping the cerebral oxygen saturation via multi-wavelength irradiation in behaving hyperoxic rats. In addition, we demonstrated that 3D-wPAT could be used for monitoring sensory stimulus-evoked responses in behaving rats by measuring hemodynamic responses in the primary visual cortex during visual stimulation. Together, these results show the potential of 3D-wPAT for brain study in behaving rodents.

  8. Exact and approximate Fourier rebinning algorithms for the solution of the data truncation problem in 3-D PET.

    PubMed

    Bouallègue, Fayçal Ben; Crouzet, Jean-François; Comtat, Claude; Fourcade, Marjolaine; Mohammadi, Bijan; Mariano-Goulart, Denis

    2007-07-01

    This paper presents an extended 3-D exact rebinning formula in the Fourier space that leads to an iterative reprojection algorithm (iterative FOREPROJ), which enables the estimation of unmeasured oblique projection data on the basis of the whole set of measured data. In first approximation, this analytical formula also leads to an extended Fourier rebinning equation that is the basis for an approximate reprojection algorithm (extended FORE). These algorithms were evaluated on numerically simulated 3-D positron emission tomography (PET) data for the solution of the truncation problem, i.e., the estimation of the missing portions in the oblique projection data, before the application of algorithms that require complete projection data such as some rebinning methods (FOREX) or 3-D reconstruction algorithms (3DRP or direct Fourier methods). By taking advantage of all the 3-D data statistics, the iterative FOREPROJ reprojection provides a reliable alternative to the classical FOREPROJ method, which only exploits the low-statistics nonoblique data. It significantly improves the quality of the external reconstructed slices without loss of spatial resolution. As for the approximate extended FORE algorithm, it clearly exhibits limitations due to axial interpolations, but will require clinical studies with more realistic measured data in order to decide on its pertinence.

  9. Trans3D: a free tool for dynamical visualization of EEG activity transmission in the brain.

    PubMed

    Blinowski, Grzegorz; Kamiński, Maciej; Wawer, Dariusz

    2014-08-01

    The problem of functional connectivity in the brain is in the focus of attention nowadays, since it is crucial for understanding information processing in the brain. A large repertoire of measures of connectivity have been devised, some of them being capable of estimating time-varying directed connectivity. Hence, there is a need for a dedicated software tool for visualizing the propagation of electrical activity in the brain. To this aim, the Trans3D application was developed. It is an open access tool based on widely available libraries and supporting both Windows XP/Vista/7(™), Linux and Mac environments. Trans3D can create animations of activity propagation between electrodes/sensors, which can be placed by the user on the scalp/cortex of a 3D model of the head. Various interactive graphic functions for manipulating and visualizing components of the 3D model and input data are available. An application of the Trans3D tool has helped to elucidate the dynamics of the phenomena of information processing in motor and cognitive tasks, which otherwise would have been very difficult to observe. Trans3D is available at: http://www.eeg.pl/.

  10. Development of PET/MRI with insertable PET for simultaneous PET and MR imaging of human brain

    SciTech Connect

    Jung, Jin Ho; Choi, Yong Jung, Jiwoong; Kim, Sangsu; Lim, Hyun Keong; Im, Ki Chun; Oh, Chang Hyun; Park, Hyun-wook; Kim, Kyung Min; Kim, Jong Guk

    2015-05-15

    Purpose: The purpose of this study was to develop a dual-modality positron emission tomography (PET)/magnetic resonance imaging (MRI) with insertable PET for simultaneous PET and MR imaging of the human brain. Methods: The PET detector block was composed of a 4 × 4 matrix of detector modules, each consisting of a 4 × 4 array LYSO coupled to a 4 × 4 Geiger-mode avalanche photodiode (GAPD) array. The PET insert consisted of 18 detector blocks, circularly mounted on a custom-made plastic base to form a ring with an inner diameter of 390 mm and axial length of 60 mm. The PET gantry was shielded with gold-plated conductive fabric tapes with a thickness of 0.1 mm. The charge signals of PET detector transferred via 4 m long flat cables were fed into the position decoder circuit. The flat cables were shielded with a mesh-type aluminum sheet with a thickness of 0.24 mm. The position decoder circuit and field programmable gate array-embedded DAQ modules were enclosed in an aluminum box with a thickness of 10 mm and located at the rear of the MR bore inside the MRI room. A 3-T human MRI system with a Larmor frequency of 123.7 MHz and inner bore diameter of 60 cm was used as the PET/MRI hybrid system. A custom-made radio frequency (RF) coil with an inner diameter of 25 cm was fabricated. The PET was positioned between gradient and the RF coils. PET performance was measured outside and inside the MRI scanner using echo planar imaging, spin echo, turbo spin echo, and gradient echo sequences. MRI performance was also evaluated with and without the PET insert. The stability of the newly developed PET insert was evaluated and simultaneous PET and MR images of a brain phantom were acquired. Results: No significant degradation of the PET performance caused by MR was observed when the PET was operated using various MR imaging sequences. The signal-to-noise ratio of MR images was slightly degraded due to the PET insert installed inside the MR bore while the homogeneity was

  11. Is 3D printing safe? Analysis of the thermal treatment of thermoplastics: ABS, PLA, PET, and nylon.

    PubMed

    Wojtyła, Szymon; Klama, Piotr; Baran, Tomasz

    2017-02-06

    The fast development of low-cost desktop three-dimensional (3D) printers has made those devices widely accessible for goods manufacturing at home. However, is it safe? Users may belittle the effects or influences of pollutants (organic compounds and ultrafine particles) generated by the devices in question. Within the scope of this study, the authors attempt to investigate thermal decomposition of the following commonly used, commercially available thermoplastic filaments: acrylonitrile-butadiene-styrene (ABS), polylactic acid (PLA), polyethylene terephthalate (PET), and nylon. Thermogravimetric analysis has shown the detailed thermal patterns of their behavior upon increasing temperature in neutral atmosphere, while GC analysis of organic vapors emitted during the process of heating thermoplastics have made it possible to obtain crucial pieces of information about the toxicity of 3D printing process. The conducted study has shown that ABS is significantly more toxic than PLA. The emission of volatile organic compounds (VOC) has been in the range of 0.50 μmol/h. Styrene has accounted for more than 30% of total VOC emitted from ABS, while for PLA, methyl methacrylate has been detected as the predominant compound (44% of total VOCs emission). Moreover, the authors have summarized available or applicable methods that can eliminate formed pollutants and protect the users of 3D printers. This paper summarizes theoretical knowledge on thermal degradation of polymers used for 3D printers and shows results of authors' investigation, as well as presents forward-looking solutions that may increase the safety of utilization of 3D printers.

  12. Metabolic brain PET pattern underlying hyperkinetic seizures.

    PubMed

    Guedj, Eric; McGonigal, Aileen; Vaugier, Lisa; Mundler, Olivier; Bartolomei, Fabrice

    2012-09-01

    This study aims to contribute to the identification of selective brain regions involved in hyperkinetic behaviors. We studied the whole-brain voxel-based interictal metabolic 18FDG-PET pattern of 23 patients with hyperkinetic seizures, in comparison with both 15 healthy subjects similar for age and gender, and 23 patients without hyperkinetic seizures. Patients were in particular similar for the localization of the epileptogenic zone, this having been defined using stereoelectroencephalography (SEEG) when clinically indicated (15/23 patients with hyperkinetic seizures and 13/23 patients without hyperkinetic seizures). Using conjunction voxel-based analysis, patients with hyperkinetic seizures exhibited significant hypometabolism within bilateral midbrain and the right caudate head, in comparison both to healthy subjects (p<0.05, FDR-corrected for the voxel) and to patients without hyperkinetic seizures (p<0.0167, uncorrected for the voxel). Findings were secondarily confirmed separately in each subgroup of patients with frontal, temporal or posterior epilepsy. These findings argue for a specific subcortical metabolic impairment in patients with hyperkinetic seizures, within brain structures supposed to be involved in the generation of primitive motor programs.

  13. Automatic Segmentation of Lung Carcinoma Using 3D Texture Features in 18-FDG PET/CT.

    PubMed

    Markel, Daniel; Caldwell, Curtis; Alasti, Hamideh; Soliman, Hany; Ung, Yee; Lee, Justin; Sun, Alexander

    2013-01-01

    Target definition is the largest source of geometric uncertainty in radiation therapy. This is partly due to a lack of contrast between tumor and healthy soft tissue for computed tomography (CT) and due to blurriness, lower spatial resolution, and lack of a truly quantitative unit for positron emission tomography (PET). First-, second-, and higher-order statistics, Tamura, and structural features were characterized for PET and CT images of lung carcinoma and organs of the thorax. A combined decision tree (DT) with K-nearest neighbours (KNN) classifiers as nodes containing combinations of 3 features were trained and used for segmentation of the gross tumor volume. This approach was validated for 31 patients from two separate institutions and scanners. The results were compared with thresholding approaches, the fuzzy clustering method, the 3-level fuzzy locally adaptive Bayesian algorithm, the multivalued level set algorithm, and a single KNN using Hounsfield units and standard uptake value. The results showed the DTKNN classifier had the highest sensitivity of 73.9%, second highest average Dice coefficient of 0.607, and a specificity of 99.2% for classifying voxels when using a probabilistic ground truth provided by simultaneous truth and performance level estimation using contours drawn by 3 trained physicians.

  14. Automatic Segmentation of Lung Carcinoma Using 3D Texture Features in 18-FDG PET/CT

    PubMed Central

    Markel, Daniel; Caldwell, Curtis; Alasti, Hamideh; Soliman, Hany; Ung, Yee; Lee, Justin; Sun, Alexander

    2013-01-01

    Target definition is the largest source of geometric uncertainty in radiation therapy. This is partly due to a lack of contrast between tumor and healthy soft tissue for computed tomography (CT) and due to blurriness, lower spatial resolution, and lack of a truly quantitative unit for positron emission tomography (PET). First-, second-, and higher-order statistics, Tamura, and structural features were characterized for PET and CT images of lung carcinoma and organs of the thorax. A combined decision tree (DT) with K-nearest neighbours (KNN) classifiers as nodes containing combinations of 3 features were trained and used for segmentation of the gross tumor volume. This approach was validated for 31 patients from two separate institutions and scanners. The results were compared with thresholding approaches, the fuzzy clustering method, the 3-level fuzzy locally adaptive Bayesian algorithm, the multivalued level set algorithm, and a single KNN using Hounsfield units and standard uptake value. The results showed the DTKNN classifier had the highest sensitivity of 73.9%, second highest average Dice coefficient of 0.607, and a specificity of 99.2% for classifying voxels when using a probabilistic ground truth provided by simultaneous truth and performance level estimation using contours drawn by 3 trained physicians. PMID:23533750

  15. 3D printing of layered brain-like structures using peptide modified gellan gum substrates.

    PubMed

    Lozano, Rodrigo; Stevens, Leo; Thompson, Brianna C; Gilmore, Kerry J; Gorkin, Robert; Stewart, Elise M; in het Panhuis, Marc; Romero-Ortega, Mario; Wallace, Gordon G

    2015-10-01

    The brain is an enormously complex organ structured into various regions of layered tissue. Researchers have attempted to study the brain by modeling the architecture using two dimensional (2D) in vitro cell culturing methods. While those platforms attempt to mimic the in vivo environment, they do not truly resemble the three dimensional (3D) microstructure of neuronal tissues. Development of an accurate in vitro model of the brain remains a significant obstacle to our understanding of the functioning of the brain at the tissue or organ level. To address these obstacles, we demonstrate a new method to bioprint 3D brain-like structures consisting of discrete layers of primary neural cells encapsulated in hydrogels. Brain-like structures were constructed using a bio-ink consisting of a novel peptide-modified biopolymer, gellan gum-RGD (RGD-GG), combined with primary cortical neurons. The ink was optimized for a modified reactive printing process and developed for use in traditional cell culturing facilities without the need for extensive bioprinting equipment. Furthermore the peptide modification of the gellan gum hydrogel was found to have a profound positive effect on primary cell proliferation and network formation. The neural cell viability combined with the support of neural network formation demonstrated the cell supportive nature of the matrix. The facile ability to form discrete cell-containing layers validates the application of this novel printing technique to form complex, layered and viable 3D cell structures. These brain-like structures offer the opportunity to reproduce more accurate 3D in vitro microstructures with applications ranging from cell behavior studies to improving our understanding of brain injuries and neurodegenerative diseases.

  16. WE-AB-204-03: A Novel 3D Printed Phantom for 4D PET/CT Imaging and SIB Radiotherapy Verification

    SciTech Connect

    Soultan, D; Murphy, J; Moiseenko, V; Cervino, L; Gill, B

    2015-06-15

    Purpose: To construct and test a 3D printed phantom designed to mimic variable PET tracer uptake seen in lung tumor volumes. To assess segmentation accuracy of sub-volumes of the phantom following 4D PET/CT scanning with ideal and patient-specific respiratory motion. To plan, deliver and verify delivery of PET-driven, gated, simultaneous integrated boost (SIB) radiotherapy plans. Methods: A set of phantoms and inserts were designed and manufactured for a realistic representation of lung cancer gated radiotherapy steps from 4D PET/CT scanning to dose delivery. A cylindrical phantom (40x 120 mm) holds inserts for PET/CT scanning. The novel 3D printed insert dedicated to 4D PET/CT mimics high PET tracer uptake in the core and lower uptake in the periphery. This insert is a variable density porous cylinder (22.12×70 mm), ABS-P430 thermoplastic, 3D printed by uPrint SE Plus with inner void volume (5.5×42 mm). The square pores (1.8×1.8 mm2 each) fill 50% of outer volume, resulting in a 2:1 SUV ratio of PET-tracer in the void volume with respect to porous volume. A matching in size cylindrical phantom is dedicated to validate gated radiotherapy. It contains eight peripheral holes matching the location of the porous part of the 3D printed insert, and one central hole. These holes accommodate adaptors for Farmer-type ion chamber and cells vials. Results: End-to-end test were performed from 4D PET/CT scanning to transferring data to the planning system and target volume delineation. 4D PET/CT scans were acquired of the phantom with different respiratory motion patterns and gating windows. A measured 2:1 18F-FDG SUV ratio between inner void and outer volume matched the 3D printed design. Conclusion: The novel 3D printed phantom mimics variable PET tracer uptake typical of tumors. Obtained 4D PET/CT scans are suitable for segmentation, treatment planning and delivery in SIB gated treatments of NSCLC.

  17. TU-F-12A-05: Sensitivity of Textural Features to 3D Vs. 4D FDG-PET/CT Imaging in NSCLC Patients

    SciTech Connect

    Yang, F; Nyflot, M; Bowen, S; Kinahan, P; Sandison, G

    2014-06-15

    Purpose: Neighborhood Gray-level difference matrices (NGLDM) based texture parameters extracted from conventional (3D) 18F-FDG PET scans in patients with NSCLC have been previously shown to associate with response to chemoradiation and poorer patient outcome. However, the change in these parameters when utilizing respiratory-correlated (4D) FDG-PET scans has not yet been characterized for NSCLC. The Objectives: of this study was to assess the extent to which NGLDM-based texture parameters on 4D PET images vary with reference to values derived from 3D scans in NSCLC. Methods: Eight patients with newly diagnosed NSCLC treated with concomitant chemoradiotherapy were included in this study. 4D PET scans were reconstructed with OSEM-IR in 5 respiratory phase-binned images and corresponding CT data of each phase were employed for attenuation correction. NGLDM-based texture features, consisting of coarseness, contrast, busyness, complexity and strength, were evaluated for gross tumor volumes defined on 3D/4D PET scans by radiation oncologists. Variation of the obtained texture parameters over the respiratory cycle were examined with respect to values extracted from 3D scans. Results: Differences between texture parameters derived from 4D scans at different respiratory phases and those extracted from 3D scans ranged from −30% to 13% for coarseness, −12% to 40% for contrast, −5% to 50% for busyness, −7% to 38% for complexity, and −43% to 20% for strength. Furthermore, no evident correlations were observed between respiratory phase and 4D scan texture parameters. Conclusion: Results of the current study showed that NGLDM-based texture parameters varied considerably based on choice of 3D PET and 4D PET reconstruction of NSCLC patient images, indicating that standardized image acquisition and analysis protocols need to be established for clinical studies, especially multicenter clinical trials, intending to validate prognostic values of texture features for NSCLC.

  18. 3D brain MR angiography displayed by a multi-autostereoscopic screen

    NASA Astrophysics Data System (ADS)

    Magalhães, Daniel S. F.; Ribeiro, Fádua H.; Lima, Fabrício O.; Serra, Rolando L.; Moreno, Alfredo B.; Li, Li M.

    2012-02-01

    The magnetic resonance angiography (MRA) can be used to examine blood vessels in key areas of the body, including the brain. In the MRA, a powerful magnetic field, radio waves and a computer produce the detailed images. Physicians use the procedure in brain images mainly to detect atherosclerosis disease in the carotid artery of the neck, which may limit blood flow to the brain and cause a stroke and identify a small aneurysm or arteriovenous malformation inside the brain. Multi-autostereoscopic displays provide multiple views of the same scene, rather than just two, as in autostereoscopic systems. Each view is visible from a different range of positions in front of the display. This allows the viewer to move left-right in front of the display and see the correct view from any position. The use of 3D imaging in the medical field has proven to be a benefit to doctors when diagnosing patients. For different medical domains a stereoscopic display could be advantageous in terms of a better spatial understanding of anatomical structures, better perception of ambiguous anatomical structures, better performance of tasks that require high level of dexterity, increased learning performance, and improved communication with patients or between doctors. In this work we describe a multi-autostereoscopic system and how to produce 3D MRA images to be displayed with it. We show results of brain MR angiography images discussing, how a 3D visualization can help physicians to a better diagnosis.

  19. Custom Fit 3D-Printed Brain Holders for Comparison of Histology with MRI in Marmosets

    PubMed Central

    Guy, Joseph R.; Sati, Pascal; Leibovitch, Emily; Jacobson, Steven; Silva, Afonso C.; Reich, Daniel S.

    2015-01-01

    Background MRI has the advantage of sampling large areas of tissue and locating areas of interest in 3D space in both living and ex vivo systems, whereas histology has the ability to examine thin slices of ex vivo tissue with high detail and specificity. Although both are valuable tools, it is currently difficult to make high-precision comparisons between MRI and histology due to large differences inherent to the techniques. A method combining the advantages would be an asset to understanding the pathological correlates of MRI. New Method 3D-printed brain holders were used to maintain marmoset brains in the same orientation during acquisition of ex vivo MRI and pathologic cutting of the tissue. Results The results of maintaining this same orientation show that sub-millimeter, discrete neuropathological features in marmoset brain consistently share size, shape, and location between histology and ex vivo MRI, which facilitates comparison with serial imaging acquired in vivo. Comparison with Existing Methods Existing methods use computational approaches sensitive to data input in order to warp histologic images to match large-scale features on MRI, but the new method requires no warping of images, due to a preregistration accomplished in the technique, and is insensitive to data formatting and artifacts in both MRI and histology. Conclusions The simple method of using 3D-printed brain holders to match brain orientation during pathologic sectioning and MRI acquisition enables rapid and precise comparison of small features seen on MRI to their underlying histology. PMID:26365332

  20. REGULARIZED 3D FUNCTIONAL REGRESSION FOR BRAIN IMAGE DATA VIA HAAR WAVELETS.

    PubMed

    Wang, Xuejing; Nan, Bin; Zhu, Ji; Koeppe, Robert

    2014-06-01

    The primary motivation and application in this article come from brain imaging studies on cognitive impairment in elderly subjects with brain disorders. We propose a regularized Haar wavelet-based approach for the analysis of three-dimensional brain image data in the framework of functional data analysis, which automatically takes into account the spatial information among neighboring voxels. We conduct extensive simulation studies to evaluate the prediction performance of the proposed approach and its ability to identify related regions to the outcome of interest, with the underlying assumption that only few relatively small subregions are truly predictive of the outcome of interest. We then apply the proposed approach to searching for brain subregions that are associated with cognition using PET images of patients with Alzheimer's disease, patients with mild cognitive impairment, and normal controls.

  1. Optimization of transmission and emission scan duration in 3D whole-body PET

    SciTech Connect

    Beyer, T.; Kinahan, P.E.; Townsend, D.W.

    1996-12-31

    Whole-body PET imaging is being increasingly used to identify and localize malignant disease remote from the site of the primary tumor. Patients are typically scanned at multiple contiguous bed positions over an axial length of 75-100 cm. For oncology patients, the total scan duration should not exceed about an hour and therefore only 5-10 minutes of imaging can be performed at each bed position. To minimize the total scan duration, the transmission scan is often omitted and the emission scan reconstructed without attenuation correction. However, whole-body scans reconstructed without attenuation correction can lead to incorrect diagnosis, particularly for tumors located deep within the body. We have performed a series of torso phantom measurements to investigate the optimal partition of scan time between the emission and transmission scans for a fixed total scan duration. We find that a transmission fraction of about 0.4 is optimal for a 5 min and 10 min total acquisition time per bed position. The optimal partition depends on the way the attenuation correction factors are calculated and on the reconstruction algorithm.

  2. Correlation of preoperative MRI and intraoperative 3D ultrasound to measure brain tissue shift

    NASA Astrophysics Data System (ADS)

    Gobbi, David G.; Lee, Belinda K. H.; Peters, Terence M.

    2001-05-01

    B-Mode ultrasound is often used during neurosurgery to provide intra-operative images of the brain though a craniotomy, but the use of 3D ultrasound during surgery is still in its infancy. We have developed a system that provides real-time freehand 3D ultrasound reconstruction at a reduced resolution. The reconstruction proceeds incrementally and the 3D image is overlayed, via a computer, on a pre-operative 3D MRI scan. This provides the operator with the necessary feedback to maintain a constant freehand sweep-rate, and also ensures that the sweep covers the desired anatomical volume. All of the ultrasound video frames are buffered, and a full-resolution, compounded reconstruction proceeds once the manual sweep is complete. We have also developed tools for manual tagging of homologous landmarks in the 3D MRI and 3D ultrasound volumes that use a piecewise cubic approximation of thin-plate spline interpolation to achieve interactive nonlinear registration and warping of the MRI volume to the ultrasound volume: Each time a homologous point-pair is identified by the use, the image of the warped MRI is updated on the computer screen after less than 0.5 s.

  3. Effects of multiple-interaction photon events in a high-resolution PET system that uses 3-D positioning detectors

    PubMed Central

    Gu, Yi; Pratx, Guillem; Lau, Frances W. Y.; Levin, Craig S.

    2010-01-01

    Purpose: The authors’ laboratory is developing a dual-panel, breast-dedicated PET system. The detector panels are built from dual-LSO-position-sensitive avalanche photodiode (PSAPD) modules—units holding two 8×8 arrays of 1 mm3 LSO crystals, where each array is coupled to a PSAPD. When stacked to form an imaging volume, these modules are capable of recording the 3-D coordinates of individual interactions of a multiple-interaction photon event (MIPE). The small size of the scintillation crystal elements used increases the likelihood of photon scattering between crystal arrays. In this article, the authors investigate how MIPEs impact the system photon sensitivity, the data acquisition scheme, and the quality and quantitative accuracy of reconstructed PET images. Methods: A Monte Carlo simulated PET scan using the dual-panel system was performed on a uniformly radioactive phantom for the photon sensitivity study. To establish the impact of MIPEs on a proposed PSAPD multiplexing scheme, experimental data were collected from a dual-LSO-PSAPD module edge-irradiated with a 22Na point source, the data were compared against simulation data based on an identical setup. To assess the impact of MIPEs on the dual-panel PET images, a simulated PET of a phantom comprising a matrix of hot spherical radiation sources of varying diameters immersed in a warm background was performed. The list-mode output data were used for image reconstruction, where various methods were used for estimating the location of the first photon interaction in MIPEs for more accurate line of response positioning. The contrast recovery coefficient (CRC), contrast to noise ratio (CNR), and the full width at half maximum spatial resolution of the spheres in the reconstructed images were used as figures of merit to facilitate comparison. Results: Compared to image reconstruction employing only events with interactions confined to one LSO array, a potential single photon sensitivity gain of >46.9% (>115

  4. Fractality in the neuron axonal topography of the human brain based on 3-D diffusion MRI

    NASA Astrophysics Data System (ADS)

    Katsaloulis, P.; Ghosh, A.; Philippe, A. C.; Provata, A.; Deriche, R.

    2012-05-01

    In this work the fractal architecture of the neuron axonal topography of the human brain is evaluated, as derived from 3-D diffusion MRI (dMRI) acquisitions. This is a 3D extension of work performed previously in 2D regions of interest (ROIs), where the fractal dimension of the neuron axonal topography was computed from dMRI data. A group study with 18 subjects is here conducted and the fractal dimensions D f of the entire 3-D volume of the brains is estimated via the box counting, the correlation dimension and the fractal mass dimension methods. The neuron axon data is obtained using tractography algorithms on diffusion tensor imaging of the brain. We find that all three calculations of D f give consistent results across subjects, namely, they demonstrate fractal characteristics in the short and medium length scales: different fractal exponents prevail at different length scales, an indication of multifractality. We surmise that this complexity stems as a collective property emerging when many local brain units, performing different functional tasks and having different local topologies, are recorded together.

  5. Implementation of a fully 3D system model for brain SPECT with fan- beam-collimator OSEM reconstruction with 3D total variation regularization

    NASA Astrophysics Data System (ADS)

    Ye, Hongwei; Krol, Andrzej; Lipson, Edward D.; Lu, Yao; Xu, Yuesheng; Lee, Wei; Feiglin, David H.

    2007-03-01

    In order to improve tomographically reconstructed image quality, we have implemented a fully 3D reconstruction, using an ordered subsets expectation maximization (OSEM) algorithm for fan-beam collimator (FBC) SPECT, along with a volumetric system model-fan-volume system model (FVSM), a modified attenuation compensation, a 3D depth- and angle-dependent resolution and sensitivity correction, and a 3D total variation (TV) regularization. SPECT data were acquired in a 128x64 matrix, in 120 views with a circular orbit. The numerical Zubal brain phantom was used to simulate a FBC HMPAO Tc-99m brain SPECT scan, and a low noise and scatter-free projection dataset was obtained using the SimSET Monte Carlo package. A SPECT scan for a mini-Defrise phantom and brain HMPAO SPECT scans for five patients were acquired with a triple-head gamma camera (Triad 88) equipped with a low-energy high-resolution (LEHR) FBC. The reconstructed images, obtained using clinical filtered back projection (FBP), OSEM with a line-length system model (LLSM) and 3D TV regularization, and OSEM with FVSM and 3D TV regularization were quantitatively studied. Overall improvement in the image quality has been observed, including better axial and transaxial resolution, better integral uniformity, higher contrast-to-noise ration between the gray matter and the white matter, and better accuracy and lower bias in OSEM-FVSM, compared with OSEM-LLSM and clinical FBP.

  6. Evaluation of the combined effects of target size, respiratory motion and background activity on 3D and 4D PET/CT images

    NASA Astrophysics Data System (ADS)

    Park, Sang-June; Ionascu, Dan; Killoran, Joseph; Mamede, Marcelo; Gerbaudo, Victor H.; Chin, Lee; Berbeco, Ross

    2008-07-01

    Gated (4D) PET/CT has the potential to greatly improve the accuracy of radiotherapy at treatment sites where internal organ motion is significant. However, the best methodology for applying 4D-PET/CT to target definition is not currently well established. With the goal of better understanding how to best apply 4D information to radiotherapy, initial studies were performed to investigate the effect of target size, respiratory motion and target-to-background activity concentration ratio (TBR) on 3D (ungated) and 4D PET images. Using a PET/CT scanner with 4D or gating capability, a full 3D-PET scan corrected with a 3D attenuation map from 3D-CT scan and a respiratory gated (4D) PET scan corrected with corresponding attenuation maps from 4D-CT were performed by imaging spherical targets (0.5-26.5 mL) filled with 18F-FDG in a dynamic thorax phantom and NEMA IEC body phantom at different TBRs (infinite, 8 and 4). To simulate respiratory motion, the phantoms were driven sinusoidally in the superior-inferior direction with amplitudes of 0, 1 and 2 cm and a period of 4.5 s. Recovery coefficients were determined on PET images. In addition, gating methods using different numbers of gating bins (1-20 bins) were evaluated with image noise and temporal resolution. For evaluation, volume recovery coefficient, signal-to-noise ratio and contrast-to-noise ratio were calculated as a function of the number of gating bins. Moreover, the optimum thresholds which give accurate moving target volumes were obtained for 3D and 4D images. The partial volume effect and signal loss in the 3D-PET images due to the limited PET resolution and the respiratory motion, respectively were measured. The results show that signal loss depends on both the amplitude and pattern of respiratory motion. However, the 4D-PET successfully recovers most of the loss induced by the respiratory motion. The 5-bin gating method gives the best temporal resolution with acceptable image noise. The results based on the 4D

  7. Interactive 3D visualization of structural changes in the brain of a person with corticobasal syndrome.

    PubMed

    Hänel, Claudia; Pieperhoff, Peter; Hentschel, Bernd; Amunts, Katrin; Kuhlen, Torsten

    2014-01-01

    The visualization of the progression of brain tissue loss in neurodegenerative diseases like corticobasal syndrome (CBS) can provide not only information about the localization and distribution of the volume loss, but also helps to understand the course and the causes of this neurodegenerative disorder. The visualization of such medical imaging data is often based on 2D sections, because they show both internal and external structures in one image. Spatial information, however, is lost. 3D visualization of imaging data is capable to solve this problem, but it faces the difficulty that more internally located structures may be occluded by structures near the surface. Here, we present an application with two designs for the 3D visualization of the human brain to address these challenges. In the first design, brain anatomy is displayed semi-transparently; it is supplemented by an anatomical section and cortical areas for spatial orientation, and the volumetric data of volume loss. The second design is guided by the principle of importance-driven volume rendering: A direct line-of-sight to the relevant structures in the deeper parts of the brain is provided by cutting out a frustum-like piece of brain tissue. The application was developed to run in both, standard desktop environments and in immersive virtual reality environments with stereoscopic viewing for improving the depth perception. We conclude, that the presented application facilitates the perception of the extent of brain degeneration with respect to its localization and affected regions.

  8. Comparative brain morphology of Neotropical parrots (Aves, Psittaciformes) inferred from virtual 3D endocasts.

    PubMed

    Carril, Julieta; Tambussi, Claudia Patricia; Degrange, Federico Javier; Benitez Saldivar, María Juliana; Picasso, Mariana Beatriz Julieta

    2016-08-01

    Psittaciformes are a very diverse group of non-passerine birds, with advanced cognitive abilities and highly developed locomotor and feeding behaviours. Using computed tomography and three-dimensional (3D) visualization software, the endocasts of 14 extant Neotropical parrots were reconstructed, with the aim of analysing, comparing and exploring the morphology of the brain within the clade. A 3D geomorphometric analysis was performed, and the encephalization quotient (EQ) was calculated. Brain morphology character states were traced onto a Psittaciformes tree in order to facilitate interpretation of morphological traits in a phylogenetic context. Our results indicate that: (i) there are two conspicuously distinct brain morphologies, one considered walnut type (quadrangular and wider than long) and the other rounded (narrower and rostrally tapered); (ii) Psittaciformes possess a noticeable notch between hemisphaeria that divides the bulbus olfactorius; (iii) the plesiomorphic and most frequently observed characteristics of Neotropical parrots are a rostrally tapered telencephalon in dorsal view, distinctly enlarged dorsal expansion of the eminentia sagittalis and conspicuous fissura mediana; (iv) there is a positive correlation between body mass and brain volume; (v) psittacids are characterized by high EQ values that suggest high brain volumes in relation to their body masses; and (vi) the endocranial morphology of the Psittaciformes as a whole is distinctive relative to other birds. This new knowledge of brain morphology offers much potential for further insight in paleoneurological, phylogenetic and evolutionary studies.

  9. Reconstruction of a 3D stereotactic brain atlas and its contour-to-contour elastic deformation

    NASA Astrophysics Data System (ADS)

    Kimura, Masahiko; Otsuki, Taisuke

    1993-06-01

    We describe a refined method for estimating the 3-D geometry of cerebral structures of a patient's brain from magnetic resonance (MR) images by adapting a 3-D atlas to the images. The 3-D atlas represents the figures of anatomical subdivisions of deep cerebral structures as series of contours reconstructed from a stereotactic printed atlas. The method correlates corresponding points and curve segments that are recognizable in both the atlas and the image, by elastically deforming the atlas two-dimensionally, while maintaining the point-to-point and contour-to-contour correspondence, until equilibrium is reached. We have used the method experimentally for a patient with Parkinson's disease, and successfully estimated the substructures of the thalamus to be treated.

  10. 3D texture-based classification applied on brain white matter lesions on MR images

    NASA Astrophysics Data System (ADS)

    Leite, Mariana; Gobbi, David; Salluzi, Marina; Frayne, Richard; Lotufo, Roberto; Rittner, Letícia

    2016-03-01

    Lesions in the brain white matter are among the most frequently observed incidental findings on MR images. This paper presents a 3D texture-based classification to distinguish normal appearing white matter from white matter containing lesions, and compares it with the 2D approach. Texture analysis were based on 55 texture attributes extracted from gray-level histogram, gray-level co-occurrence matrix, run-length matrix and gradient. The results show that the 3D approach achieves an accuracy rate of 99.28%, against 97.41% of the 2D approach by using a support vector machine classifier. Furthermore, the most discriminating texture attributes on both 2D and 3D cases were obtained from the image histogram and co-occurrence matrix.

  11. A novel 3D graph cut based co-segmentation of lung tumor on PET-CT images with Gaussian mixture models

    NASA Astrophysics Data System (ADS)

    Yu, Kai; Chen, Xinjian; Shi, Fei; Zhu, Weifang; Zhang, Bin; Xiang, Dehui

    2016-03-01

    Positron Emission Tomography (PET) and Computed Tomography (CT) have been widely used in clinical practice for radiation therapy. Most existing methods only used one image modality, either PET or CT, which suffers from the low spatial resolution in PET or low contrast in CT. In this paper, a novel 3D graph cut method is proposed, which integrated Gaussian Mixture Models (GMMs) into the graph cut method. We also employed the random walk method as an initialization step to provide object seeds for the improvement of the graph cut based segmentation on PET and CT images. The constructed graph consists of two sub-graphs and a special link between the sub-graphs which penalize the difference segmentation between the two modalities. Finally, the segmentation problem is solved by the max-flow/min-cut method. The proposed method was tested on 20 patients' PET-CT images, and the experimental results demonstrated the accuracy and efficiency of the proposed algorithm.

  12. Interactive algorithms for the segmentation and quantitation of 3-D MRI brain scans.

    PubMed

    Freeborough, P A; Fox, N C; Kitney, R I

    1997-05-01

    Interactive algorithms are an attractive approach to the accurate segmentation of 3D brain scans as they potentially improve the reliability of fully automated segmentation while avoiding the labour intensiveness and inaccuracies of manual segmentation. We present a 3D image analysis package (MIDAS) with a novel architecture enabling highly interactive segmentation algorithms to be implemented as add on modules. Interactive methods based on intensity thresholding, region growing and the constrained application of morphological operators are also presented. The methods involve the application of constraints and freedoms on the algorithms coupled with real time visualisation of the effect. This methodology has been applied to the segmentation, visualisation and measurement of the whole brain and a small irregular neuroanatomical structure, the hippocampus. We demonstrate reproducible and anatomically accurate segmentations of these structures. The efficacy of one method in measuring volume loss (atrophy) of the hippocampus in Alzheimer's disease is shown and is compared to conventional methods.

  13. Analysis and 3D visualization of structures of animal brains obtained from histological sections

    NASA Astrophysics Data System (ADS)

    Forero-Vargas, Manuel G.; Fuentes, Veronica; Lopez, D.; Moscoso, A.; Merchan, Miguel A.

    2002-11-01

    This paper presents a new application for the analysis of histological sections and their 3D visualization. The process is performed in few steps. First, a manual process is necessary to determine the regions of interest, including image digitalization, drawing of borders and alignment between all images. Then, a reconstruction process is made. After sampling the contour, the structure of interest is displayed. The application is experimentally validated and some results on histological sections of a rodent's brain (hamster and rat) are shown.

  14. 3D Brain Segmentation Using Dual-Front Active Contours with Optional User Interaction

    PubMed Central

    Yezzi, Anthony; Cohen, Laurent D.

    2006-01-01

    Important attributes of 3D brain cortex segmentation algorithms include robustness, accuracy, computational efficiency, and facilitation of user interaction, yet few algorithms incorporate all of these traits. Manual segmentation is highly accurate but tedious and laborious. Most automatic techniques, while less demanding on the user, are much less accurate. It would be useful to employ a fast automatic segmentation procedure to do most of the work but still allow an expert user to interactively guide the segmentation to ensure an accurate final result. We propose a novel 3D brain cortex segmentation procedure utilizing dual-front active contours which minimize image-based energies in a manner that yields flexibly global minimizers based on active regions. Region-based information and boundary-based information may be combined flexibly in the evolution potentials for accurate segmentation results. The resulting scheme is not only more robust but much faster and allows the user to guide the final segmentation through simple mouse clicks which add extra seed points. Due to the flexibly global nature of the dual-front evolution model, single mouse clicks yield corrections to the segmentation that extend far beyond their initial locations, thus minimizing the user effort. Results on 15 simulated and 20 real 3D brain images demonstrate the robustness, accuracy, and speed of our scheme compared with other methods. PMID:23165037

  15. Robust automatic rodent brain extraction using 3-D pulse-coupled neural networks (PCNN).

    PubMed

    Chou, Nigel; Wu, Jiarong; Bai Bingren, Jordan; Qiu, Anqi; Chuang, Kai-Hsiang

    2011-09-01

    Brain extraction is an important preprocessing step for further processing (e.g., registration and morphometric analysis) of brain MRI data. Due to the operator-dependent and time-consuming nature of manual extraction, automated or semi-automated methods are essential for large-scale studies. Automatic methods are widely available for human brain imaging, but they are not optimized for rodent brains and hence may not perform well. To date, little work has been done on rodent brain extraction. We present an extended pulse-coupled neural network algorithm that operates in 3-D on the entire image volume. We evaluated its performance under varying SNR and resolution and tested this method against the brain-surface extractor (BSE) and a level-set algorithm proposed for mouse brain. The results show that this method outperforms existing methods and is robust under low SNR and with partial volume effects at lower resolutions. Together with the advantage of minimal user intervention, this method will facilitate automatic processing of large-scale rodent brain studies.

  16. Automatic procedure for realistic 3D finite element modelling of human brain for bioelectromagnetic computations

    NASA Astrophysics Data System (ADS)

    Aristovich, K. Y.; Khan, S. H.

    2010-07-01

    Realistic computer modelling of biological objects requires building of very accurate and realistic computer models based on geometric and material data, type, and accuracy of numerical analyses. This paper presents some of the automatic tools and algorithms that were used to build accurate and realistic 3D finite element (FE) model of whole-brain. These models were used to solve the forward problem in magnetic field tomography (MFT) based on Magnetoencephalography (MEG). The forward problem involves modelling and computation of magnetic fields produced by human brain during cognitive processing. The geometric parameters of the model were obtained from accurate Magnetic Resonance Imaging (MRI) data and the material properties - from those obtained from Diffusion Tensor MRI (DTMRI). The 3D FE models of the brain built using this approach has been shown to be very accurate in terms of both geometric and material properties. The model is stored on the computer in Computer-Aided Parametrical Design (CAD) format. This allows the model to be used in a wide a range of methods of analysis, such as finite element method (FEM), Boundary Element Method (BEM), Monte-Carlo Simulations, etc. The generic model building approach presented here could be used for accurate and realistic modelling of human brain and many other biological objects.

  17. 3D-segmentation of the 18F-choline PET signal for target volume definition in radiation therapy of the prostate.

    PubMed

    Ciernik, I Frank; Brown, Derek W; Schmid, Daniel; Hany, Thomas; Egli, Peter; Davis, J Bernard

    2007-02-01

    Volumetric assessment of PET signals becomes increasingly relevant for radiotherapy (RT) planning. Here, we investigate the utility of 18F-choline PET signals to serve as a structure for semi-automatic segmentation for forward treatment planning of prostate cancer. 18F-choline PET and CT scans of ten patients with histologically proven prostate cancer without extracapsular growth were acquired using a combined PET/CT scanner. Target volumes were manually delineated on CT images using standard software. Volumes were also obtained from 18F-choline PET images using an asymmetrical segmentation algorithm. PTVs were derived from CT 18F-choline PET based clinical target volumes (CTVs) by automatic expansion and comparative planning was performed. As a read-out for dose given to non-target structures, dose to the rectal wall was assessed. Planning target volumes (PTVs) derived from CT and 18F-choline PET yielded comparable results. Optimal matching of CT and 18F-choline PET derived volumes in the lateral and cranial-caudal directions was obtained using a background-subtracted signal thresholds of 23.0+/-2.6%. In antero-posterior direction, where adaptation compensating for rectal signal overflow was required, optimal matching was achieved with a threshold of 49.5+/-4.6%. 3D-conformal planning with CT or 18F-choline PET resulted in comparable doses to the rectal wall. Choline PET signals of the prostate provide adequate spatial information amendable to standardized asymmetrical region growing algorithms for PET-based target volume definition for external beam RT.

  18. Sparse Bayesian framework applied to 3D super-resolution reconstruction in fetal brain MRI

    NASA Astrophysics Data System (ADS)

    Becerra, Laura C.; Velasco Toledo, Nelson; Romero Castro, Eduardo

    2015-01-01

    Fetal Magnetic Resonance (FMR) is an imaging technique that is becoming increasingly important as allows assessing brain development and thus make an early diagnostic of congenital abnormalities, spatial resolution is limited by the short acquisition time and the unpredictable fetus movements, in consequence the resulting images are characterized by non-parallel projection planes composed by anisotropic voxels. The sparse Bayesian representation is a flexible strategy which is able to model complex relationships. The Super-resolution is approached as a regression problem, the main advantage is the capability to learn data relations from observations. Quantitative performance evaluation was carried out using synthetic images, the proposed method demonstrates a better reconstruction quality compared with standard interpolation approach. The presented method is a promising approach to improve the information quality related with the 3-D fetal brain structure. It is important because allows assessing brain development and thus make an early diagnostic of congenital abnormalities.

  19. Segmentation of Brain MRI Using SOM-FCM-Based Method and 3D Statistical Descriptors

    PubMed Central

    Ortiz, Andrés; Palacio, Antonio A.; Górriz, Juan M.; Ramírez, Javier; Salas-González, Diego

    2013-01-01

    Current medical imaging systems provide excellent spatial resolution, high tissue contrast, and up to 65535 intensity levels. Thus, image processing techniques which aim to exploit the information contained in the images are necessary for using these images in computer-aided diagnosis (CAD) systems. Image segmentation may be defined as the process of parcelling the image to delimit different neuroanatomical tissues present on the brain. In this paper we propose a segmentation technique using 3D statistical features extracted from the volume image. In addition, the presented method is based on unsupervised vector quantization and fuzzy clustering techniques and does not use any a priori information. The resulting fuzzy segmentation method addresses the problem of partial volume effect (PVE) and has been assessed using real brain images from the Internet Brain Image Repository (IBSR). PMID:23762192

  20. Fast 3D Chemical Exchange Saturation Transfer (CEST) Imaging of the Human Brain

    PubMed Central

    Zhu, He; Jones, Craig K.; van Zijl, Peter C. M.; Barker, Peter B.; Zhou, Jinyuan

    2010-01-01

    Chemical exchange saturation transfer (CEST) MRI can detect low-concentration compounds with exchangeable protons through saturation transfer to water. CEST imaging is generally slow, as it requires acquisition of saturation images at multiple frequencies. In addition, multi-slice imaging is complicated by saturation effects differing from slice to slice because of relaxation losses. In this study, a fast three-dimensional (3D) CEST imaging sequence is presented that allows whole-brain coverage for a frequency-dependent saturation spectrum (z-spectrum, 26 frequencies) in less than 10 min. The approach employs a 3D gradient- and spin-echo (GRASE) readout using a prototype 32-channel phased-array coil, combined with two-dimensional SENSE accelerations. Results from a homogenous protein-containing phantom at 3T show that the sequence produced a uniform contrast across all slices. To show translational feasibility, scans were also performed on five healthy human subjects. Results for CEST images at 3.5ppm downfield of the water resonance, so-called amide proton transfer (APT) images, show that lipid signals are sufficiently suppressed and artifacts caused by B0 inhomogeneity can be removed in post-processing. The scan time and image quality of these in vivo results show that 3D CEST MRI using GRASE acquisition is feasible for whole-brain CEST studies at 3T in a clinical time frame. PMID:20632402

  1. 3D pattern of brain atrophy in HIV/AIDS visualized using tensor-based morphometry

    PubMed Central

    Chiang, Ming-Chang; Dutton, Rebecca A.; Hayashi, Kiralee M.; Lopez, Oscar L.; Aizenstein, Howard J.; Toga, Arthur W.; Becker, James T.; Thompson, Paul M.

    2011-01-01

    35% of HIV-infected patients have cognitive impairment, but the profile of HIV-induced brain damage is still not well understood. Here we used tensor-based morphometry (TBM) to visualize brain deficits and clinical/anatomical correlations in HIV/AIDS. To perform TBM, we developed a new MRI-based analysis technique that uses fluid image warping, and a new α-entropy-based information-theoretic measure of image correspondence, called the Jensen–Rényi divergence (JRD). Methods 3D T1-weighted brain MRIs of 26 AIDS patients (CDC stage C and/or 3 without HIV-associated dementia; 47.2 ± 9.8 years; 25M/1F; CD4+ T-cell count: 299.5 ± 175.7/µl; log10 plasma viral load: 2.57 ± 1.28 RNA copies/ml) and 14 HIV-seronegative controls (37.6 ± 12.2 years; 8M/6F) were fluidly registered by applying forces throughout each deforming image to maximize the JRD between it and a target image (from a control subject). The 3D fluid registration was regularized using the linearized Cauchy–Navier operator. Fine-scale volumetric differences between diagnostic groups were mapped. Regions were identified where brain atrophy correlated with clinical measures. Results Severe atrophy (~15–20% deficit) was detected bilaterally in the primary and association sensorimotor areas. Atrophy of these regions, particularly in the white matter, correlated with cognitive impairment (P=0.033) and CD4+ T-lymphocyte depletion (P=0.005). Conclusion TBM facilitates 3D visualization of AIDS neuropathology in living patients scanned with MRI. Severe atrophy in frontoparietal and striatal areas may underlie early cognitive dysfunction in AIDS patients, and may signal the imminent onset of AIDS dementia complex. PMID:17035049

  2. Computation of a high-resolution MRI 3D stereotaxic atlas of the sheep brain.

    PubMed

    Ella, Arsène; Delgadillo, José A; Chemineau, Philippe; Keller, Matthieu

    2017-02-15

    The sheep model was first used in the fields of animal reproduction and veterinary sciences and then was utilized in fundamental and preclinical studies. For more than a decade, magnetic resonance (MR) studies performed on this model have been increasingly reported, especially in the field of neuroscience. To contribute to MR translational neuroscience research, a brain template and an atlas are necessary. We have recently generated the first complete T1-weighted (T1W) and T2W MR population average images (or templates) of in vivo sheep brains. In this study, we 1) defined a 3D stereotaxic coordinate system for previously established in vivo population average templates; 2) used deformation fields obtained during optimized nonlinear registrations to compute nonlinear tissues or prior probability maps (nlTPMs) of cerebrospinal fluid (CSF), gray matter (GM), and white matter (WM) tissues; 3) delineated 25 external and 28 internal sheep brain structures by segmenting both templates and nlTPMs; and 4) annotated and labeled these structures using an existing histological atlas. We built a quality high-resolution 3D atlas of average in vivo sheep brains linked to a reference stereotaxic space. The atlas and nlTPMs, associated with previously computed T1W and T2W in vivo sheep brain templates and nlTPMs, provide a complete set of imaging space that are able to be imported into other imaging software programs and could be used as standardized tools for neuroimaging studies or other neuroscience methods, such as image registration, image segmentation, identification of brain structures, implementation of recording devices, or neuronavigation. J. Comp. Neurol. 525:676-692, 2017. © 2016 Wiley Periodicals, Inc.

  3. PET radiopharmaceuticals for probing enzymes in the brain

    PubMed Central

    Holland, Jason P; Cumming, Paul; Vasdev, Neil

    2013-01-01

    Biologically important processes in normal brain function and brain disease involve the action of various protein-based receptors, ion channels, transporters and enzymes. The ability to interrogate the location, abundance and activity of these entities in vivo using non-invasive molecular imaging can provide unprecedented information about the spatio-temporal dynamics of brain function. Indeed, positron emission tomography (PET) imaging is transforming our understanding of the central nervous system and brain disease. Great emphasis has historically been placed on developing radioligands for the non-invasive detection of neuroreceptors. In contrast, relatively few enzymes have been amenable to examination by PET imaging procedures based upon trapping or accumulation of enzymatic products, because only a subset of enzymes have sufficient catalytic rate to produce measureable accumulation within the practical time-limit of PET recordings. However, high affinity inhibitors are now serving as tracers for enzymes, particularly for measuring the abundance of enzymes mediating intracellular signal transduction in the brain, which offer a rich diversity of potential targets for drug discovery. The purpose of this review is to summarize well-known radiotracers for brain enzymes, and draw attention to recent developments in PET radiotracers for imaging signal transduction pathways in the brain. The review is organized by target class and focuses on structural chemistry of the best-established radiotracers identified in each class. PMID:23638333

  4. Coculture system with an organotypic brain slice and 3D spheroid of carcinoma cells.

    PubMed

    Chuang, Han-Ning; Lohaus, Raphaela; Hanisch, Uwe-Karsten; Binder, Claudia; Dehghani, Faramarz; Pukrop, Tobias

    2013-10-09

    Patients with cerebral metastasis of carcinomas have a poor prognosis. However, the process at the metastatic site has barely been investigated, in particular the role of the resident (stromal) cells. Studies in primary carcinomas demonstrate the influence of the microenvironment on metastasis, even on prognosis(1,2). Especially the tumor associated macrophages (TAM) support migration, invasion and proliferation(3). Interestingly, the major target sites of metastasis possess tissue-specific macrophages, such as Kupffer cells in the liver or microglia in the CNS. Moreover, the metastatic sites also possess other tissue-specific cells, like astrocytes. Recently, astrocytes were demonstrated to foster proliferation and persistence of cancer cells(4,5). Therefore, functions of these tissue-specific cell types seem to be very important in the process of brain metastasis(6,7). Despite these observations, however, up to now there is no suitable in vivo/in vitro model available to directly visualize glial reactions during cerebral metastasis formation, in particular by bright field microscopy. Recent in vivo live imaging of carcinoma cells demonstrated their cerebral colonization behavior(8). However, this method is very laborious, costly and technically complex. In addition, these kinds of animal experiments are restricted to small series and come with a substantial stress for the animals (by implantation of the glass plate, injection of tumor cells, repetitive anaesthesia and long-term fixation). Furthermore, in vivo imaging is thus far limited to the visualization of the carcinoma cells, whereas interactions with resident cells have not yet been illustrated. Finally, investigations of human carcinoma cells within immunocompetent animals are impossible(8). For these reasons, we established a coculture system consisting of an organotypic mouse brain slice and epithelial cells embedded in matrigel (3D cell sphere). The 3D carcinoma cell spheres were placed directly next to

  5. Biological Interpretation of Quantitative PET Brain Data

    NASA Astrophysics Data System (ADS)

    Sossi, Vesna

    2002-11-01

    The variety of available positron emission tomography (PET) radiotracers and the ability of providing quantitative estimates of radiotracer concentrations make PET an invaluable tool in the in-vivo investigation of biological processes. Mathematical descriptions of the processes under investigation are used to extract relevant kinetic parameters from the time course of radioactivity concentrations. Such kinetic parameters can provide a quantitative description of both, the characteristics of a particular process, and its changes due to various disease states.

  6. 3D mapping of neuronal migration in the embryonic mouse brain with magnetic resonance microimaging.

    PubMed

    Deans, Abby E; Wadghiri, Youssef Zaim; Aristizábal, Orlando; Turnbull, Daniel H

    2015-07-01

    A prominent feature of the developing mammalian brain is the widespread migration of neural progenitor (NP) cells during embryogenesis. A striking example is provided by NP cells born in the ventral forebrain of mid-gestation stage mice, which subsequently migrate long distances to their final positions in the cortex and olfactory bulb. Previous studies have used two-dimensional histological methods, making it difficult to analyze three-dimensional (3D) migration patterns. Unlike histology, magnetic resonance microimaging (micro-MRI) is a non-destructive, quantitative and inherently 3D imaging method for analyzing mouse embryos. To allow mapping of migrating NP cells with micro-MRI, cells were labeled in situ in the medial (MGE) and lateral (LGE) ganglionic eminences, using targeted in utero ultrasound-guided injection of micron-sized particles of iron-oxide (MPIO). Ex vivo micro-MRI and histology were then performed 5-6days after injection, demonstrating that the MPIO had magnetically labeled the migrating NP populations, which enabled 3D visualization and automated segmentation of the labeled cells. This approach was used to analyze the distinct patterns of migration from the MGE and LGE, and to construct rostral-caudal migration maps from each progenitor region. Furthermore, abnormal migratory phenotypes were observed in Nkx2.1(-/-) embryos, most notably a significant increase in cortical neurons derived from the Nkx2.1(-/-) LGE. Taken together, these results demonstrate that MPIO labeling and micro-MRI provide an efficient and powerful approach for analyzing 3D cell migration patterns in the normal and mutant mouse embryonic brain.

  7. Respiratory motion compensation for simultaneous PET/MR based on a 3D-2D registration of strongly undersampled radial MR data: a simulation study

    NASA Astrophysics Data System (ADS)

    Rank, Christopher M.; Heußer, Thorsten; Flach, Barbara; Brehm, Marcus; Kachelrieß, Marc

    2015-03-01

    We propose a new method for PET/MR respiratory motion compensation, which is based on a 3D-2D registration of strongly undersampled MR data and a) runs in parallel with the PET acquisition, b) can be interlaced with clinical MR sequences, and c) requires less than one minute of the total MR acquisition time per bed position. In our simulation study, we applied a 3D encoded radial stack-of-stars sampling scheme with 160 radial spokes per slice and an acquisition time of 38 s. Gated 4D MR images were reconstructed using a 4D iterative reconstruction algorithm. Based on these images, motion vector fields were estimated using our newly-developed 3D-2D registration framework. A 4D PET volume of a patient with eight hot lesions in the lungs and upper abdomen was simulated and MoCo 4D PET images were reconstructed based on the motion vector fields derived from MR. For evaluation, average SUVmean values of the artificial lesions were determined for a 3D, a gated 4D, a MoCo 4D and a reference (with ten-fold measurement time) gated 4D reconstruction. Compared to the reference, 3D reconstructions yielded an underestimation of SUVmean values due to motion blurring. In contrast, gated 4D reconstructions showed the highest variation of SUVmean due to low statistics. MoCo 4D reconstructions were only slightly affected by these two sources of uncertainty resulting in a significant visual and quantitative improvement in terms of SUVmean values. Whereas temporal resolution was comparable to the gated 4D images, signal-to-noise ratio and contrast-to-noise ratio were close to the 3D reconstructions.

  8. Generation and transplantation of reprogrammed human neurons in the brain using 3D microtopographic scaffolds

    PubMed Central

    Carlson, Aaron L.; Bennett, Neal K.; Francis, Nicola L.; Halikere, Apoorva; Clarke, Stephen; Moore, Jennifer C.; Hart, Ronald P.; Paradiso, Kenneth; Wernig, Marius; Kohn, Joachim; Pang, Zhiping P.; Moghe, Prabhas V.

    2016-01-01

    Cell replacement therapy with human pluripotent stem cell-derived neurons has the potential to ameliorate neurodegenerative dysfunction and central nervous system injuries, but reprogrammed neurons are dissociated and spatially disorganized during transplantation, rendering poor cell survival, functionality and engraftment in vivo. Here, we present the design of three-dimensional (3D) microtopographic scaffolds, using tunable electrospun microfibrous polymeric substrates that promote in situ stem cell neuronal reprogramming, neural network establishment and support neuronal engraftment into the brain. Scaffold-supported, reprogrammed neuronal networks were successfully grafted into organotypic hippocampal brain slices, showing an ∼3.5-fold improvement in neurite outgrowth and increased action potential firing relative to injected isolated cells. Transplantation of scaffold-supported neuronal networks into mouse brain striatum improved survival ∼38-fold at the injection site relative to injected isolated cells, and allowed delivery of multiple neuronal subtypes. Thus, 3D microscale biomaterials represent a promising platform for the transplantation of therapeutic human neurons with broad neuro-regenerative relevance. PMID:26983594

  9. [The advantages and limitations of brain function analyses by PET].

    PubMed

    Kato, M; Taniwaki, T; Kuwabara, Y

    2000-12-01

    PET has been proved to be a powerful tool for exploring the brain function. We discussed the advantages and limitations of PET for analyzing the brain function on the basis of our clinical and experimental experiences of functional imaging. A multimodality PET study measuring cerebral energy metabolism (CMRO2 and CMRglc), cerebral blood flow (CBF), oxygen extraction fraction (OEF) and neurotransmitter function (presynaptic and postsynaptic) opens up a closer insight into a precise pathophysiology of the brain dysfunction: In cerebral infarction, it reveals a state of "misery perfusion" in the acute stage, "luxury perfusion" in the intermediate stage, and proportionately decreased CBF and CMRO2 in the chronic stage. Neurotransmitter function may identify specifically a neuronal subgroup of dysfunction. Owing to the low temporal resolution of PET, a neuronal activity may propagate transsynaptically to remote areas during the period of scanning, resulting in an obscured primary site of the neuronal activity. Uncoupling between neuronal activities and cerebral energy metabolism/CBF may occur under a certain state of brain pathology, particularly after an acute destructive lesion, according to our experimental studies. Neurotransmitter function may reveal the effect of drugs on the brain function, and may be useful for developing a new method of drug therapy for brain diseases in the future.

  10. A Novel Multiparametric Approach to 3D Quantitative MRI of the Brain.

    PubMed

    Palma, Giuseppe; Tedeschi, Enrico; Borrelli, Pasquale; Cocozza, Sirio; Russo, Carmela; Liu, Saifeng; Ye, Yongquan; Comerci, Marco; Alfano, Bruno; Salvatore, Marco; Haacke, E Mark; Mancini, Marcello

    2015-01-01

    Magnetic Resonance properties of tissues can be quantified in several respects: relaxation processes, density of imaged nuclei, magnetism of environmental molecules, etc. In this paper, we propose a new comprehensive approach to obtain 3D high resolution quantitative maps of arbitrary body districts, mainly focusing on the brain. The theory presented makes it possible to map longitudinal (R1), pure transverse (R2) and free induction decay ([Formula: see text]) rates, along with proton density (PD) and magnetic susceptibility (χ), from a set of fast acquisition sequences in steady-state that are highly insensitive to flow phenomena. A novel denoising scheme is described and applied to the acquired datasets to enhance the signal to noise ratio of the derived maps and an information theory approach compensates for biases from radio frequency (RF) inhomogeneities, if no direct measure of the RF field is available. Finally, the results obtained on sample brain scans of healthy controls and multiple sclerosis patients are presented and discussed.

  11. Fast 3D visualization of endogenous brain signals with high-sensitivity laser scanning photothermal microscopy

    PubMed Central

    Miyazaki, Jun; Iida, Tadatsune; Tanaka, Shinji; Hayashi-Takagi, Akiko; Kasai, Haruo; Okabe, Shigeo; Kobayashi, Takayoshi

    2016-01-01

    A fast, high-sensitivity photothermal microscope was developed by implementing a spatially segmented balanced detection scheme into a laser scanning microscope. We confirmed a 4.9 times improvement in signal-to-noise ratio in the spatially segmented balanced detection compared with that of conventional detection. The system demonstrated simultaneous bi-modal photothermal and confocal fluorescence imaging of transgenic mouse brain tissue with a pixel dwell time of 20 μs. The fluorescence image visualized neurons expressing yellow fluorescence proteins, while the photothermal signal detected endogenous chromophores in the mouse brain, allowing 3D visualization of the distribution of various features such as blood cells and fine structures probably due to lipids. This imaging modality was constructed using compact and cost-effective laser diodes, and will thus be widely useful in the life and medical sciences. PMID:27231615

  12. The influence of familiarity on brain activation during haptic exploration of 3-D facemasks.

    PubMed

    James, Thomas W; Servos, Philip; Kilgour, Andrea R; Huh, Eunji; Lederman, Susan

    2006-04-24

    Little is known about the neural substrates that underlie difficult haptic discrimination of 3-D within-class object stimuli. Recent work [A.R. Kilgour, R. Kitada, P. Servos, T.W. James, S.J. Lederman, Haptic face identification activates ventral occipital and temporal areas: an fMRI study, Brain Cogn. (in press)] suggests that the left fusiform gyrus may contribute to the identification of facemasks that are haptically explored in the absence of vision. Here, we extend this line of research to investigate the influence of familiarity. Subjects were trained extensively to individuate a set of facemasks in the absence of vision using only haptic exploration. Brain activation was then measured using fMRI while subjects performed a haptic face recognition task on familiar and unfamiliar facemasks. A group analysis contrasting familiar and unfamiliar facemasks found that the left fusiform gyrus produced greater activation with familiar facemasks.

  13. PET evaluation of the dopamine system of the human brain

    SciTech Connect

    Volkow, N.D.; Fowler, J.S.; Gatley, S. |

    1996-07-01

    Dopamine plays a pivotal role in the regulation and control of movement, motivation and cognition. It also is closely linked to reward, reinforcement and addiction. Abnormalities in brain dopamine are associated with many neurological and psychiatric disorders including Parkinson`s disease, schizophrenia and substance abuse. This close association between dopamine and neurological and psychiatric diseases and with substance abuse make it an important topic in research in the neurosciences and an important molecular target in drug development. PET enables the direct measurement of components of the dopamine system in the living human brain. It relies on radiotracers which label dopamine receptors, dopamine transporters, precursors of dopamine or compounds which have specificity for the enzymes which degrade dopamine. Additionally, by using tracers that provide information on regional brain metabolism or blood flow as well as neurochemically specific pharmacological interventions, PET can be used to assess the functional consequences of change in brain dopamine activity. PET dopamine measurements have been used to investigate the normal human brain and its involvement in psychiatric and neurological diseases. It has also been used in psychopharmacological research to investigate dopamine drugs used in the treatment of Parkinson`s disease and of schizophrenia as well as to investigate the effects of drugs of abuse on the dopamine system. Since various functional and neurochemical parameters can be studied in the same subject, PET enables investigation of the functional integrity of the dopamine system in the human brain and investigation of the interactions of dopamine with other neurotransmitters. This paper summarizes the different tracers and experimental strategies developed to evaluate the various elements of the dopamine system in the human brain with PET and their applications to clinical research. 254 refs., 7 figs., 3 tabs.

  14. 3D geometric split-merge segmentation of brain MRI datasets.

    PubMed

    Marras, Ioannis; Nikolaidis, Nikolaos; Pitas, Ioannis

    2014-05-01

    In this paper, a novel method for MRI volume segmentation based on region adaptive splitting and merging is proposed. The method, called Adaptive Geometric Split Merge (AGSM) segmentation, aims at finding complex geometrical shapes that consist of homogeneous geometrical 3D regions. In each volume splitting step, several splitting strategies are examined and the most appropriate is activated. A way to find the maximal homogeneity axis of the volume is also introduced. Along this axis, the volume splitting technique divides the entire volume in a number of large homogeneous 3D regions, while at the same time, it defines more clearly small homogeneous regions within the volume in such a way that they have greater probabilities of survival at the subsequent merging step. Region merging criteria are proposed to this end. The presented segmentation method has been applied to brain MRI medical datasets to provide segmentation results when each voxel is composed of one tissue type (hard segmentation). The volume splitting procedure does not require training data, while it demonstrates improved segmentation performance in noisy brain MRI datasets, when compared to the state of the art methods.

  15. Visualization and mapping of neurosurgical functional brain data onto a 3-D MR-based model of the brain surface.

    PubMed

    Modayur, B R; Prothero, J; Rosse, C; Jakobovits, R; Brinkley, J F

    1996-01-01

    The Human Brain Project was initiated with the goal of developing methods for managing and sharing information about the brain. As a prototype Human Brain Project application we are developing a system for organizing, visualizing, integrating and sharing information about human language function. The goal of the brain mapping component of our work, described in this article, is to generate the 3D location and extent of cortical language sites with respect to a uniform, 3D patient coordinate system. The language sites of individual patients can then be combined with or related to other patient data in terms of a Talairach, surface-based, or other deformable coordinate systems. Language site mapping is done by visually comparing an intraoperative photograph with the rendered image (from MRI data). The techniques outlined in this article have been utilized to map cortical language sites of six patients. Preliminary results point to the adequacy of our volume visualizations for language mapping. The strength of the visualization scheme lies in the combination of interactive segmentation with volume and surface visualization. We are now in the process of acquiring more patient data to further validate the usefulness of our method.

  16. 3D variational brain tumor segmentation on a clustered feature set

    NASA Astrophysics Data System (ADS)

    Popuri, Karteek; Cobzas, Dana; Jagersand, Martin; Shah, Sirish L.; Murtha, Albert

    2009-02-01

    Tumor segmentation from MRI data is a particularly challenging and time consuming task. Tumors have a large diversity in shape and appearance with intensities overlapping the normal brain tissues. In addition, an expanding tumor can also deflect and deform nearby tissue. Our work addresses these last two difficult problems. We use the available MRI modalities (T1, T1c, T2) and their texture characteristics to construct a multi-dimensional feature set. Further, we extract clusters which provide a compact representation of the essential information in these features. The main idea in this paper is to incorporate these clustered features into the 3D variational segmentation framework. In contrast to the previous variational approaches, we propose a segmentation method that evolves the contour in a supervised fashion. The segmentation boundary is driven by the learned inside and outside region voxel probabilities in the cluster space. We incorporate prior knowledge about the normal brain tissue appearance, during the estimation of these region statistics. In particular, we use a Dirichlet prior that discourages the clusters in the ventricles to be in the tumor and hence better disambiguate the tumor from brain tissue. We show the performance of our method on real MRI scans. The experimental dataset includes MRI scans, from patients with difficult instances, with tumors that are inhomogeneous in appearance, small in size and in proximity to the major structures in the brain. Our method shows good results on these test cases.

  17. Utilizing 3D Printing Technology to Merge MRI with Histology: A Protocol for Brain Sectioning

    PubMed Central

    Luciano, Nicholas J; Sati, Pascal; Nair, Govind; Guy, Joseph R; Ha, Seung-Kwon; Absinta, Martina; Chiang, Wen-Yang; Leibovitch, Emily C; Jacobson, Steven; Silva, Afonso C; Reich, Daniel S.

    2016-01-01

    Magnetic resonance imaging (MRI) allows for the delineation between normal and abnormal tissue on a macroscopic scale, sampling an entire tissue volume three-dimensionally. While MRI is an extremely sensitive tool for detecting tissue abnormalities, association of signal changes with an underlying pathological process is usually not straightforward. In the central nervous system, for example, inflammation, demyelination, axonal damage, gliosis, and neuronal death may all induce similar findings on MRI. As such, interpretation of MRI scans depends on the context, and radiological-histopathological correlation is therefore of the utmost importance. Unfortunately, traditional pathological sectioning of brain tissue is often imprecise and inconsistent, thus complicating the comparison between histology sections and MRI. This article presents novel methodology for accurately sectioning primate brain tissues and thus allowing precise matching between histology and MRI. The detailed protocol described in this article will assist investigators in applying this method, which relies on the creation of 3D printed brain slicers. Slightly modified, it can be easily implemented for brains of other species, including humans. PMID:28060281

  18. Utilizing 3D Printing Technology to Merge MRI with Histology: A Protocol for Brain Sectioning.

    PubMed

    Luciano, Nicholas J; Sati, Pascal; Nair, Govind; Guy, Joseph R; Ha, Seung-Kwon; Absinta, Martina; Chiang, Wen-Yang; Leibovitch, Emily C; Jacobson, Steven; Silva, Afonso C; Reich, Daniel S

    2016-12-06

    Magnetic resonance imaging (MRI) allows for the delineation between normal and abnormal tissue on a macroscopic scale, sampling an entire tissue volume three-dimensionally. While MRI is an extremely sensitive tool for detecting tissue abnormalities, association of signal changes with an underlying pathological process is usually not straightforward. In the central nervous system, for example, inflammation, demyelination, axonal damage, gliosis, and neuronal death may all induce similar findings on MRI. As such, interpretation of MRI scans depends on the context, and radiological-histopathological correlation is therefore of the utmost importance. Unfortunately, traditional pathological sectioning of brain tissue is often imprecise and inconsistent, thus complicating the comparison between histology sections and MRI. This article presents novel methodology for accurately sectioning primate brain tissues and thus allowing precise matching between histology and MRI. The detailed protocol described in this article will assist investigators in applying this method, which relies on the creation of 3D printed brain slicers. Slightly modified, it can be easily implemented for brains of other species, including humans.

  19. Deformable templates guided discriminative models for robust 3D brain MRI segmentation.

    PubMed

    Liu, Cheng-Yi; Iglesias, Juan Eugenio; Tu, Zhuowen

    2013-10-01

    Automatically segmenting anatomical structures from 3D brain MRI images is an important task in neuroimaging. One major challenge is to design and learn effective image models accounting for the large variability in anatomy and data acquisition protocols. A deformable template is a type of generative model that attempts to explicitly match an input image with a template (atlas), and thus, they are robust against global intensity changes. On the other hand, discriminative models combine local image features to capture complex image patterns. In this paper, we propose a robust brain image segmentation algorithm that fuses together deformable templates and informative features. It takes advantage of the adaptation capability of the generative model and the classification power of the discriminative models. The proposed algorithm achieves both robustness and efficiency, and can be used to segment brain MRI images with large anatomical variations. We perform an extensive experimental study on four datasets of T1-weighted brain MRI data from different sources (1,082 MRI scans in total) and observe consistent improvement over the state-of-the-art systems.

  20. Comparison of 3D Maximum A Posteriori and Filtered Backprojection algorithms for high resolution animal imaging in microPET

    SciTech Connect

    Chatziioannou, A.; Qi, J.; Moore, A.; Annala, A.; Nguyen, K.; Leahy, R.M.; Cherry, S.R.

    2000-01-01

    We have evaluated the performance of two three dimensional reconstruction algorithms with data acquired from microPET, a high resolution tomograph dedicated to small animal imaging. The first was a linear filtered-backprojection algorithm (FBP) with reprojection of the missing data and the second was a statistical maximum-aposteriori probability algorithm (MAP). The two algorithms were evaluated in terms of their resolution performance, both in phantoms and in vivo. Sixty independent realizations of a phantom simulating the brain of a baby monkey were acquired, each containing 3 million counts. Each of these realizations was reconstructed independently with both algorithms. The ensemble of the sixty reconstructed realizations was used to estimate the standard deviation as a measure of the noise for each reconstruction algorithm. More detail was recovered in the MAP reconstruction without an increase in noise relative to FBP. Studies in a simple cylindrical compartment phantom demonstrated improved recovery of known activity ratios with MAP. Finally in vivo studies also demonstrated a clear improvement in spatial resolution using the MAP algorithm. The quantitative accuracy of the MAP reconstruction was also evaluated by comparison with autoradiography and direct well counting of tissue samples and was shown to be superior.

  1. Compact and mobile high resolution PET brain imager

    DOEpatents

    Majewski, Stanislaw [Yorktown, VA; Proffitt, James [Newport News, VA

    2011-02-08

    A brain imager includes a compact ring-like static PET imager mounted in a helmet-like structure. When attached to a patient's head, the helmet-like brain imager maintains the relative head-to-imager geometry fixed through the whole imaging procedure. The brain imaging helmet contains radiation sensors and minimal front-end electronics. A flexible mechanical suspension/harness system supports the weight of the helmet thereby allowing for patient to have limited movements of the head during imaging scans. The compact ring-like PET imager enables very high resolution imaging of neurological brain functions, cancer, and effects of trauma using a rather simple mobile scanner with limited space needs for use and storage.

  2. Effects of magnetic fields of up to 9.4 T on resolution and contrast of PET images as measured with an MR-BrainPET.

    PubMed

    Shah, N Jon; Herzog, Hans; Weirich, Christoph; Tellmann, Lutz; Kaffanke, Joachim; Caldeira, Liliana; Kops, Elena Rota; Qaim, Syed M; Coenen, Heinz H; Iida, Hidehiro

    2014-01-01

    Simultaneous, hybrid MR-PET is expected to improve PET image resolution in the plane perpendicular to the static magnetic field of the scanner. Previous papers have reported this either by simulation or experiment with simple sources and detector arrangements. Here, we extend those studies using a realistic brain phantom in a recently installed MR-PET system comprising a 9.4 T MRI-scanner and an APD-based BrainPET insert in the magnet bore. Point and line sources and a 3D brain phantom were filled with 18F (low-energy positron emitter), 68Ga (medium energy positron emitter) or 120I, a non-standard positron emitter (high positron energies of up to 4.6 MeV). Using the BrainPET insert, emission scans of the phantoms were recorded at different positions inside and outside the magnet bore such that the magnetic field was 0 T, 3 T, 7 T or 9.4 T. Brain phantom images, with the 'grey matter' compartment filled with 18F, showed no obvious resolution improvement with increasing field. This is confirmed by practically unchanged transaxial FWHM and 'grey/white matter' ratio values between at 0T and 9.4T. Field-dependent improvements in the resolution and contrast of transaxial PET images were clearly evident when the brain phantom was filled with 68Ga or 120I. The grey/white matter ratio increased by 7.3% and 16.3%, respectively. The greater reduction of the FWTM compared to FWHM in 68Ga or 120I line-spread images was in agreement with the improved contrast of 68Ga or 120I images. Notwithstanding elongations seen in the z-direction of 68Ga or 120I point source images acquired in foam, brain phantom images show no comparable extension. Our experimental study confirms that integrated MR-PET delivers improved PET image resolution and contrast for medium- and high-energy positron emitters even though the positron range is reduced only in directions perpendicular to the magnetic field.

  3. Effects of Magnetic Fields of up to 9.4 T on Resolution and Contrast of PET Images as Measured with an MR-BrainPET

    PubMed Central

    Shah, N. Jon; Herzog, Hans; Weirich, Christoph; Tellmann, Lutz; Kaffanke, Joachim; Caldeira, Liliana; Kops, Elena Rota; Qaim, Syed M.; Coenen, Heinz H.; Iida, Hidehiro

    2014-01-01

    Simultaneous, hybrid MR-PET is expected to improve PET image resolution in the plane perpendicular to the static magnetic field of the scanner. Previous papers have reported this either by simulation or experiment with simple sources and detector arrangements. Here, we extend those studies using a realistic brain phantom in a recently installed MR-PET system comprising a 9.4 T MRI-scanner and an APD-based BrainPET insert in the magnet bore. Point and line sources and a 3D brain phantom were filled with 18F (low-energy positron emitter), 68Ga (medium energy positron emitter) or 120I, a non-standard positron emitter (high positron energies of up to 4.6 MeV). Using the BrainPET insert, emission scans of the phantoms were recorded at different positions inside and outside the magnet bore such that the magnetic field was 0 T, 3 T, 7 T or 9.4 T. Brain phantom images, with the ‘grey matter’ compartment filled with 18F, showed no obvious resolution improvement with increasing field. This is confirmed by practically unchanged transaxial FWHM and ‘grey/white matter’ ratio values between at 0T and 9.4T. Field-dependent improvements in the resolution and contrast of transaxial PET images were clearly evident when the brain phantom was filled with 68Ga or 120I. The grey/white matter ratio increased by 7.3% and 16.3%, respectively. The greater reduction of the FWTM compared to FWHM in 68Ga or 120I line-spread images was in agreement with the improved contrast of 68Ga or 120I images. Notwithstanding elongations seen in the z-direction of 68Ga or 120I point source images acquired in foam, brain phantom images show no comparable extension. Our experimental study confirms that integrated MR-PET delivers improved PET image resolution and contrast for medium- and high-energy positron emitters even though the positron range is reduced only in directions perpendicular to the magnetic field. PMID:24755872

  4. Stereotactic PET atlas of the human brain: Aid for visual interpretation of functional brain images

    SciTech Connect

    Minoshima, S.; Koeppe, R.A.; Frey, A.; Ishihara, M.; Kuhl, D.E.

    1994-06-01

    In the routine analysis of functional brain images obtained by PET, subjective visual interpretation is often used for anatomic localization. To enhance the accuracy and consistency of the anatomic interpretation, a PET stereotactic atlas and localization approach was designed for functional brain images. The PET atlas was constructed from a high-resolution [{sup 18}F]fluorodeoxyglucose (FDG) image set of a normal volunteer (a 41-yr-ld woman). The image set was reoriented stereotactically, according to the intercommissural (anterior and posterior commissures) line and transformed to the standard stereotactic atlas coordinates. Cerebral structures were annotated on the transaxial planes using a proportional grid system and surface-rendered images. The stereotactic localization technique was applied to image sets from patients with Alzheimer`s disease, and areas of functional alteration were localized visually by referring to the PET atlas. Major brain structures were identified on both transaxial planes and surface-rendered images. In the stereotactic system, anatomic correspondence between the PET atlas and stereotactically reoriented individual image sets of patients with Alzheimer`s disease facilitated both indirect and direct localization of the cerebral structures. Because rapid stereotactic alignment methods for PET images are now available for routine use, the PET atlas will serve as an aid for visual interpretation of functional brain images in the stereotactic system. Widespread application of stereotactic localization may be used in functional brain images, not only in the research setting, but also in routine clinical situations. 41 refs., 3 figs.

  5. Evaluation of MRI and cannabinoid type 1 receptor PET templates constructed using DARTEL for spatial normalization of rat brains

    SciTech Connect

    Kronfeld, Andrea; Müller-Forell, Wibke; Buchholz, Hans-Georg; Maus, Stephan; Reuss, Stefan; Schreckenberger, Mathias; Miederer, Isabelle; Lutz, Beat

    2015-12-15

    Purpose: Image registration is one prerequisite for the analysis of brain regions in magnetic-resonance-imaging (MRI) or positron-emission-tomography (PET) studies. Diffeomorphic anatomical registration through exponentiated Lie algebra (DARTEL) is a nonlinear, diffeomorphic algorithm for image registration and construction of image templates. The goal of this small animal study was (1) the evaluation of a MRI and calculation of several cannabinoid type 1 (CB1) receptor PET templates constructed using DARTEL and (2) the analysis of the image registration accuracy of MR and PET images to their DARTEL templates with reference to analytical and iterative PET reconstruction algorithms. Methods: Five male Sprague Dawley rats were investigated for template construction using MRI and [{sup 18}F]MK-9470 PET for CB1 receptor representation. PET images were reconstructed using the algorithms filtered back-projection, ordered subset expectation maximization in 2D, and maximum a posteriori in 3D. Landmarks were defined on each MR image, and templates were constructed under different settings, i.e., based on different tissue class images [gray matter (GM), white matter (WM), and GM + WM] and regularization forms (“linear elastic energy,” “membrane energy,” and “bending energy”). Registration accuracy for MRI and PET templates was evaluated by means of the distance between landmark coordinates. Results: The best MRI template was constructed based on gray and white matter images and the regularization form linear elastic energy. In this case, most distances between landmark coordinates were <1 mm. Accordingly, MRI-based spatial normalization was most accurate, but results of the PET-based spatial normalization were quite comparable. Conclusions: Image registration using DARTEL provides a standardized and automatic framework for small animal brain data analysis. The authors were able to show that this method works with high reliability and validity. Using DARTEL

  6. MRI-based elastic-mapping method for inter-subject comparison of brain FDG-PET images

    SciTech Connect

    Yang, J.; Huang, S.C.; Lin, K.P.; Small, G.; Phelps, M.E.

    1996-12-31

    Inter-subject anatomic differences prohibits direct image-wise statistical evaluation of brain FDG-PET images of Alzheimer`s disease (AD) patients. In this study, we propose a MRI-based elastic-mapping method which enables image-wise evaluation. The method involves intra-subject MR-PET registration, 3-D elastic mapping of two set of MR images, and elastically transforming the co-registered PET images. The MR-PET registration used simulated PET images, which were based on segmentation of MR images. In the 3-D elastic mapping stage, first a global linear scaling was applied to compensate for brain size difference, then a deformation field was obtained by minimizing the regional sum of squared difference between the two sets of MR images. Two groups (AD patient and normal control), each with three subjects, were included in the current study. After processing, images from all subjects have similar shapes. Averaging the images across all subjects (either within the individual group or for both groups) give images indistinguishable from original single subject FDG images (i.e. without much spatial resolution loss), except with lower image noise level. The method is expected to allow statistical image-wise analysis to be performed across different subjects.

  7. Adaptive Image Enhancement for Tracing 3D Morphologies of Neurons and Brain Vasculatures.

    PubMed

    Zhou, Zhi; Sorensen, Staci; Zeng, Hongkui; Hawrylycz, Michael; Peng, Hanchuan

    2015-04-01

    It is important to digitally reconstruct the 3D morphology of neurons and brain vasculatures. A number of previous methods have been proposed to automate the reconstruction process. However, in many cases, noise and low signal contrast with respect to the image background still hamper our ability to use automation methods directly. Here, we propose an adaptive image enhancement method specifically designed to improve the signal-to-noise ratio of several types of individual neurons and brain vasculature images. Our method is based on detecting the salient features of fibrous structures, e.g. the axon and dendrites combined with adaptive estimation of the optimal context windows where such saliency would be detected. We tested this method for a range of brain image datasets and imaging modalities, including bright-field, confocal and multiphoton fluorescent images of neurons, and magnetic resonance angiograms. Applying our adaptive enhancement to these datasets led to improved accuracy and speed in automated tracing of complicated morphology of neurons and vasculatures.

  8. Whole-brain 3D mapping of human neural transplant innervation

    PubMed Central

    Doerr, Jonas; Schwarz, Martin Karl; Wiedermann, Dirk; Leinhaas, Anke; Jakobs, Alina; Schloen, Florian; Schwarz, Inna; Diedenhofen, Michael; Braun, Nils Christian; Koch, Philipp; Peterson, Daniel A.; Kubitscheck, Ulrich; Hoehn, Mathias; Brüstle, Oliver

    2017-01-01

    While transplantation represents a key tool for assessing in vivo functionality of neural stem cells and their suitability for neural repair, little is known about the integration of grafted neurons into the host brain circuitry. Rabies virus-based retrograde tracing has developed into a powerful approach for visualizing synaptically connected neurons. Here, we combine this technique with light sheet fluorescence microscopy (LSFM) to visualize transplanted cells and connected host neurons in whole-mouse brain preparations. Combined with co-registration of high-precision three-dimensional magnetic resonance imaging (3D MRI) reference data sets, this approach enables precise anatomical allocation of the host input neurons. Our data show that the same neural donor cell population grafted into different brain regions receives highly orthotopic input. These findings indicate that transplant connectivity is largely dictated by the circuitry of the target region and depict rabies-based transsynaptic tracing and LSFM as efficient tools for comprehensive assessment of host–donor cell innervation. PMID:28102196

  9. Fast Bayesian whole-brain fMRI analysis with spatial 3D priors.

    PubMed

    Sidén, Per; Eklund, Anders; Bolin, David; Villani, Mattias

    2017-02-01

    Spatial whole-brain Bayesian modeling of task-related functional magnetic resonance imaging (fMRI) is a great computational challenge. Most of the currently proposed methods therefore do inference in subregions of the brain separately or do approximate inference without comparison to the true posterior distribution. A popular such method, which is now the standard method for Bayesian single subject analysis in the SPM software, is introduced in Penny et al. (2005b). The method processes the data slice-by-slice and uses an approximate variational Bayes (VB) estimation algorithm that enforces posterior independence between activity coefficients in different voxels. We introduce a fast and practical Markov chain Monte Carlo (MCMC) scheme for exact inference in the same model, both slice-wise and for the whole brain using a 3D prior on activity coefficients. The algorithm exploits sparsity and uses modern techniques for efficient sampling from high-dimensional Gaussian distributions, leading to speed-ups without which MCMC would not be a practical option. Using MCMC, we are for the first time able to evaluate the approximate VB posterior against the exact MCMC posterior, and show that VB can lead to spurious activation. In addition, we develop an improved VB method that drops the assumption of independent voxels a posteriori. This algorithm is shown to be much faster than both MCMC and the original VB for large datasets, with negligible error compared to the MCMC posterior.

  10. Whole-brain 3D mapping of human neural transplant innervation.

    PubMed

    Doerr, Jonas; Schwarz, Martin Karl; Wiedermann, Dirk; Leinhaas, Anke; Jakobs, Alina; Schloen, Florian; Schwarz, Inna; Diedenhofen, Michael; Braun, Nils Christian; Koch, Philipp; Peterson, Daniel A; Kubitscheck, Ulrich; Hoehn, Mathias; Brüstle, Oliver

    2017-01-19

    While transplantation represents a key tool for assessing in vivo functionality of neural stem cells and their suitability for neural repair, little is known about the integration of grafted neurons into the host brain circuitry. Rabies virus-based retrograde tracing has developed into a powerful approach for visualizing synaptically connected neurons. Here, we combine this technique with light sheet fluorescence microscopy (LSFM) to visualize transplanted cells and connected host neurons in whole-mouse brain preparations. Combined with co-registration of high-precision three-dimensional magnetic resonance imaging (3D MRI) reference data sets, this approach enables precise anatomical allocation of the host input neurons. Our data show that the same neural donor cell population grafted into different brain regions receives highly orthotopic input. These findings indicate that transplant connectivity is largely dictated by the circuitry of the target region and depict rabies-based transsynaptic tracing and LSFM as efficient tools for comprehensive assessment of host-donor cell innervation.

  11. A brain-computer interface method combined with eye tracking for 3D interaction.

    PubMed

    Lee, Eui Chul; Woo, Jin Cheol; Kim, Jong Hwa; Whang, Mincheol; Park, Kang Ryoung

    2010-07-15

    With the recent increase in the number of three-dimensional (3D) applications, the need for interfaces to these applications has increased. Although the eye tracking method has been widely used as an interaction interface for hand-disabled persons, this approach cannot be used for depth directional navigation. To solve this problem, we propose a new brain computer interface (BCI) method in which the BCI and eye tracking are combined to analyze depth navigation, including selection and two-dimensional (2D) gaze direction, respectively. The proposed method is novel in the following five ways compared to previous works. First, a device to measure both the gaze direction and an electroencephalogram (EEG) pattern is proposed with the sensors needed to measure the EEG attached to a head-mounted eye tracking device. Second, the reliability of the BCI interface is verified by demonstrating that there is no difference between the real and the imaginary movements for the same work in terms of the EEG power spectrum. Third, depth control for the 3D interaction interface is implemented by an imaginary arm reaching movement. Fourth, a selection method is implemented by an imaginary hand grabbing movement. Finally, for the independent operation of gazing and the BCI, a mode selection method is proposed that measures a user's concentration by analyzing the pupil accommodation speed, which is not affected by the operation of gazing and the BCI. According to experimental results, we confirmed the feasibility of the proposed 3D interaction method using eye tracking and a BCI.

  12. TBIdoc: 3D content-based CT image retrieval system for traumatic brain injury

    NASA Astrophysics Data System (ADS)

    Li, Shimiao; Gong, Tianxia; Wang, Jie; Liu, Ruizhe; Tan, Chew Lim; Leong, Tze Yun; Pang, Boon Chuan; Lim, C. C. Tchoyoson; Lee, Cheng Kiang; Tian, Qi; Zhang, Zhuo

    2010-03-01

    Traumatic brain injury (TBI) is a major cause of death and disability. Computed Tomography (CT) scan is widely used in the diagnosis of TBI. Nowadays, large amount of TBI CT data is stacked in the hospital radiology department. Such data and the associated patient information contain valuable information for clinical diagnosis and outcome prediction. However, current hospital database system does not provide an efficient and intuitive tool for doctors to search out cases relevant to the current study case. In this paper, we present the TBIdoc system: a content-based image retrieval (CBIR) system which works on the TBI CT images. In this web-based system, user can query by uploading CT image slices from one study, retrieval result is a list of TBI cases ranked according to their 3D visual similarity to the query case. Specifically, cases of TBI CT images often present diffuse or focal lesions. In TBIdoc system, these pathological image features are represented as bin-based binary feature vectors. We use the Jaccard-Needham measure as the similarity measurement. Based on these, we propose a 3D similarity measure for computing the similarity score between two series of CT slices. nDCG is used to evaluate the system performance, which shows the system produces satisfactory retrieval results. The system is expected to improve the current hospital data management in TBI and to give better support for the clinical decision-making process. It may also contribute to the computer-aided education in TBI.

  13. Using 3-D shape models to guide segmentation of MR brain images.

    PubMed Central

    Hinshaw, K. P.; Brinkley, J. F.

    1997-01-01

    Accurate segmentation of medical images poses one of the major challenges in computer vision. Approaches that rely solely on intensity information frequently fail because similar intensity values appear in multiple structures. This paper presents a method for using shape knowledge to guide the segmentation process, applying it to the task of finding the surface of the brain. A 3-D model that includes local shape constraints is fitted to an MR volume dataset. The resulting low-resolution surface is used to mask out regions far from the cortical surface, enabling an isosurface extraction algorithm to isolate a more detailed surface boundary. The surfaces generated by this technique are comparable to those achieved by other methods, without requiring user adjustment of a large number of ad hoc parameters. Images Figure 1 Figure 2 Figure 3 Figure 4 PMID:9357670

  14. Initialisation of 3D level set for hippocampus segmentation from volumetric brain MR images

    NASA Astrophysics Data System (ADS)

    Hajiesmaeili, Maryam; Dehmeshki, Jamshid; Bagheri Nakhjavanlo, Bashir; Ellis, Tim

    2014-04-01

    Shrinkage of the hippocampus is a primary biomarker for Alzheimer's disease and can be measured through accurate segmentation of brain MR images. The paper will describe the problem of initialisation of a 3D level set algorithm for hippocampus segmentation that must cope with the some challenging characteristics, such as small size, wide range of intensities, narrow width, and shape variation. In addition, MR images require bias correction, to account for additional inhomogeneity associated with the scanner technology. Due to these inhomogeneities, using a single initialisation seed region inside the hippocampus is prone to failure. Alternative initialisation strategies are explored, such as using multiple initialisations in different sections (such as the head, body and tail) of the hippocampus. The Dice metric is used to validate our segmentation results with respect to ground truth for a dataset of 25 MR images. Experimental results indicate significant improvement in segmentation performance using the multiple initialisations techniques, yielding more accurate segmentation results for the hippocampus.

  15. Brain tumor segmentation in 3D MRIs using an improved Markov random field model

    NASA Astrophysics Data System (ADS)

    Yousefi, Sahar; Azmi, Reza; Zahedi, Morteza

    2011-10-01

    Markov Random Field (MRF) models have been recently suggested for MRI brain segmentation by a large number of researchers. By employing Markovianity, which represents the local property, MRF models are able to solve a global optimization problem locally. But they still have a heavy computation burden, especially when they use stochastic relaxation schemes such as Simulated Annealing (SA). In this paper, a new 3D-MRF model is put forward to raise the speed of the convergence. Although, search procedure of SA is fairly localized and prevents from exploring the same diversity of solutions, it suffers from several limitations. In comparison, Genetic Algorithm (GA) has a good capability of global researching but it is weak in hill climbing. Our proposed algorithm combines SA and an improved GA (IGA) to optimize the solution which speeds up the computation time. What is more, this proposed algorithm outperforms the traditional 2D-MRF in quality of the solution.

  16. Hybrid PET/MR Imaging and Brain Connectivity

    PubMed Central

    Aiello, Marco; Cavaliere, Carlo; Salvatore, Marco

    2016-01-01

    In recent years, brain connectivity is gaining ever-increasing interest from the interdisciplinary research community. The study of brain connectivity is characterized by a multifaceted approach providing both structural and functional evidence of the relationship between cerebral regions at different scales. Although magnetic resonance (MR) is the most established imaging modality for investigating connectivity in vivo, the recent advent of hybrid positron emission tomography (PET)/MR scanners paved the way for more comprehensive investigation of brain organization and physiology. Due to the high sensitivity and biochemical specificity of radiotracers, combining MR with PET imaging may enrich our ability to investigate connectivity by introducing the concept of metabolic connectivity and cometomics and promoting new insights on the physiological and molecular bases underlying high-level neural organization. This review aims to describe and summarize the main methods of analysis of brain connectivity employed in MR imaging and nuclear medicine. Moreover, it will discuss practical aspects and state-of-the-art techniques for exploiting hybrid PET/MR imaging to investigate the relationship of physiological processes and brain connectivity. PMID:26973446

  17. Growth trajectories of the human fetal brain tissues estimated from 3D reconstructed in utero MRI

    PubMed Central

    Scott, Julia A.; Habas, Piotr A.; Kim, Kio; Rajagopalan, Vidya; Hamzelou, Kia S.; Corbett-Detig, James M.; Barkovich, A. James; Glenn, Orit A.; Studholme, Colin

    2012-01-01

    In the latter half of gestation (20 to 40 gestational weeks), human brain growth accelerates in conjunction with cortical folding and the deceleration of ventricular zone progenitor cell proliferation. These processes are reflected in changes in the volume of respective fetal tissue zones. Thus far, growth trajectories of the fetal tissue zones have been extracted primarily from 2D measurements on histological sections and magnetic resonance imaging (MRI). In this study, the volumes of major fetal zones—cortical plate (CP), subplate and intermediate zone (SP+IZ), germinal matrix (GMAT), deep gray nuclei (DG), and ventricles (VENT)—are calculated from automatic segmentation of motion-corrected, 3D reconstructed MRI. We analyzed 48 T2-weighted MRI scans from 39 normally developing fetuses in utero between 20.57 and 31.14 gestational weeks (GW). The supratentorial volume (STV) increased linearly at a rate of 15.22% per week. The SP+IZ (14.75% per week) and DG (15.56% per week) volumes increased at similar rates. The CP increased at a greater relative rate (18.00% per week), while the VENT (9.18% per week) changed more slowly. Therefore, CP increased as a fraction of STV and the VENT fraction declined. The total GMAT volume slightly increased then decreased after 25 GW. We did not detect volumetric sexual dimorphisms or total hemispheric volume asymmetries, which may emerge later in gestation. Further application of the automated fetal brain segmentation to later gestational ages will bridge the gap between volumetric studies of premature brain development and normal brain development in utero. PMID:21530634

  18. Growth trajectories of the human fetal brain tissues estimated from 3D reconstructed in utero MRI.

    PubMed

    Scott, Julia A; Habas, Piotr A; Kim, Kio; Rajagopalan, Vidya; Hamzelou, Kia S; Corbett-Detig, James M; Barkovich, A James; Glenn, Orit A; Studholme, Colin

    2011-08-01

    In the latter half of gestation (20-40 gestational weeks), human brain growth accelerates in conjunction with cortical folding and the deceleration of ventricular zone progenitor cell proliferation. These processes are reflected in changes in the volume of respective fetal tissue zones. Thus far, growth trajectories of the fetal tissue zones have been extracted primarily from 2D measurements on histological sections and magnetic resonance imaging (MRI). In this study, the volumes of major fetal zones-cortical plate (CP), subplate and intermediate zone (SP+IZ), germinal matrix (GMAT), deep gray nuclei (DG), and ventricles (VENT)--are calculated from automatic segmentation of motion-corrected, 3D reconstructed MRI. We analyzed 48 T2-weighted MRI scans from 39 normally developing fetuses in utero between 20.57 and 31.14 gestational weeks (GW). The supratentorial volume (STV) increased linearly at a rate of 15.22% per week. The SP+IZ (14.75% per week) and DG (15.56% per week) volumes increased at similar rates. The CP increased at a greater relative rate (18.00% per week), while the VENT (9.18% per week) changed more slowly. Therefore, CP increased as a fraction of STV and the VENT fraction declined. The total GMAT volume slightly increased then decreased after 25 GW. We did not detect volumetric sexual dimorphisms or total hemispheric volume asymmetries, which may emerge later in gestation. Further application of the automated fetal brain segmentation to later gestational ages will bridge the gap between volumetric studies of premature brain development and normal brain development in utero.

  19. 3D perfused brain phantom for interstitial ultrasound thermal therapy and imaging: design, construction and characterization

    NASA Astrophysics Data System (ADS)

    Martínez, José M.; Jarosz, Boguslaw J.

    2015-03-01

    Thermal therapy has emerged as an independent modality of treating some tumors. In many clinics the hyperthermia, one of the thermal therapy modalities, has been used adjuvant to radio- or chemotherapy to substantially improve the clinical treatment outcomes. In this work, a methodology for building a realistic brain phantom for interstitial ultrasound low dose-rate thermal therapy of the brain is proposed. A 3D brain phantom made of the tissue mimicking material (TMM) had the acoustic and thermal properties in the 20-32 °C range, which is similar to that of a brain at 37 °C. The phantom had 10-11% by mass of bovine gelatin powder dissolved in ethylene glycol. The TMM sonicated at 1 MHz, 1.6 MHz and 2.5 MHz yielded the amplitude attenuation coefficients of 62  ±  1 dB m-1, 115  ±  4 dB m-1 and 175  ±  9 dB m-1, respectively. The density and acoustic speed determination at room temperature (~24 °C) gave 1040  ±  40 kg m-3 and 1545  ±  44 m s-1, respectively. The average thermal conductivity was 0.532 W m-1 K-1. The T1 and T2 values of the TMM were 207  ±  4 and 36.2  ±  0.4 ms, respectively. We envisage the use of our phantom for treatment planning and for quality assurance in MRI based temperature determination. Our phantom preparation methodology may be readily extended to other thermal therapy technologies.

  20. 3D perfused brain phantom for interstitial ultrasound thermal therapy and imaging: design, construction and characterization.

    PubMed

    Martínez, José M; Jarosz, Boguslaw J

    2015-03-07

    Thermal therapy has emerged as an independent modality of treating some tumors. In many clinics the hyperthermia, one of the thermal therapy modalities, has been used adjuvant to radio- or chemotherapy to substantially improve the clinical treatment outcomes. In this work, a methodology for building a realistic brain phantom for interstitial ultrasound low dose-rate thermal therapy of the brain is proposed. A 3D brain phantom made of the tissue mimicking material (TMM) had the acoustic and thermal properties in the 20-32 °C range, which is similar to that of a brain at 37 °C. The phantom had 10-11% by mass of bovine gelatin powder dissolved in ethylene glycol. The TMM sonicated at 1 MHz, 1.6 MHz and 2.5 MHz yielded the amplitude attenuation coefficients of 62  ±  1 dB m(-1), 115  ±  4 dB m(-1) and 175  ±  9 dB m(-1), respectively. The density and acoustic speed determination at room temperature (~24 °C) gave 1040  ±  40 kg m(-3) and 1545  ±  44 m s(-1), respectively. The average thermal conductivity was 0.532 W m(-1) K(-1). The T1 and T2 values of the TMM were 207  ±  4 and 36.2  ±  0.4 ms, respectively. We envisage the use of our phantom for treatment planning and for quality assurance in MRI based temperature determination. Our phantom preparation methodology may be readily extended to other thermal therapy technologies.

  1. 3D inpatient dose reconstruction from the PET-CT imaging of {sup 90}Y microspheres for metastatic cancer to the liver: Feasibility study

    SciTech Connect

    Fourkal, E.; Veltchev, I.; Lin, M.; Meyer, J.; Koren, S.; Doss, M.; Yu, J. Q.

    2013-08-15

    Purpose: The introduction of radioembolization with microspheres represents a significant step forward in the treatment of patients with metastatic disease to the liver. This technique uses semiempirical formulae based on body surface area or liver and target volumes to calculate the required total activity for a given patient. However, this treatment modality lacks extremely important information, which is the three-dimensional (3D) dose delivered by microspheres to different organs after their administration. The absence of this information dramatically limits the clinical efficacy of this modality, specifically the predictive power of the treatment. Therefore, the aim of this study is to develop a 3D dose calculation technique that is based on the PET imaging of the infused microspheres.Methods: The Fluka Monte Carlo code was used to calculate the voxel dose kernel for {sup 90}Y source with voxel size equal to that of the PET scan. The measured PET activity distribution was converted to total activity distribution for the subsequent convolution with the voxel dose kernel to obtain the 3D dose distribution. In addition, dose-volume histograms were generated to analyze the dose to the tumor and critical structures.Results: The 3D inpatient dose distribution can be reconstructed from the PET data of a patient scanned after the infusion of microspheres. A total of seven patients have been analyzed so far using the proposed reconstruction method. Four patients underwent treatment with SIR-Spheres for liver metastases from colorectal cancer and three patients were treated with Therasphere for hepatocellular cancer. A total of 14 target tumors were contoured on post-treatment PET-CT scans for dosimetric evaluation. Mean prescription activity was 1.7 GBq (range: 0.58–3.8 GBq). The resulting mean maximum measured dose to targets was 167 Gy (range: 71–311 Gy). Mean minimum dose to 70% of target (D70) was 68 Gy (range: 25–155 Gy). Mean minimum dose to 90% of target

  2. Monte Carlo simulations of GeoPET experiments: 3D images of tracer distributions (18F, 124I and 58Co) in Opalinus clay, anhydrite and quartz

    NASA Astrophysics Data System (ADS)

    Zakhnini, Abdelhamid; Kulenkampff, Johannes; Sauerzapf, Sophie; Pietrzyk, Uwe; Lippmann-Pipke, Johanna

    2013-08-01

    Understanding conservative fluid flow and reactive tracer transport in soils and rock formations requires quantitative transport visualization methods in 3D+t. After a decade of research and development we established the GeoPET as a non-destructive method with unrivalled sensitivity and selectivity, with due spatial and temporal resolution by applying Positron Emission Tomography (PET), a nuclear medicine imaging method, to dense rock material. Requirements for reaching the physical limit of image resolution of nearly 1 mm are (a) a high-resolution PET-camera, like our ClearPET scanner (Raytest), and (b) appropriate correction methods for scatter and attenuation of 511 keV—photons in the dense geological material. The latter are by far more significant in dense geological material than in human and small animal body tissue (water). Here we present data from Monte Carlo simulations (MCS) reflecting selected GeoPET experiments. The MCS consider all involved nuclear physical processes of the measurement with the ClearPET-system and allow us to quantify the sensitivity of the method and the scatter fractions in geological media as function of material (quartz, Opalinus clay and anhydrite compared to water), PET isotope (18F, 58Co and 124I), and geometric system parameters. The synthetic data sets obtained by MCS are the basis for detailed performance assessment studies allowing for image quality improvements. A scatter correction method is applied exemplarily by subtracting projections of simulated scattered coincidences from experimental data sets prior to image reconstruction with an iterative reconstruction process.

  3. Dosimetry in brain tumor phantom at 15 MV 3D conformal radiation therapy

    PubMed Central

    2013-01-01

    Glioblastoma multiforme (GBM) is the most common, aggressive, highly malignant and infiltrative of all brain tumors with low rate of control. The main goal of this work was to evaluate the spatial dose distribution into a GBM simulator inside a head phantom exposed to a 15 MV 3D conformal radiation therapy in order to validate internal doses. A head and neck phantom developed by the Ionizing Radiation Research Group (NRI) was used on the experiments. Such phantom holds the following synthetic structures: brain and spinal cord, skull, cervical and thoracic vertebrae, jaw, hyoid bone, laryngeal cartilages, head and neck muscles and skin. Computer tomography (CT) of the simulator was taken, capturing a set of contrasted references. Therapy Radiation planning (TPS) was performed based on those CT images, satisfying a 200 cGy prescribed dose split in three irradiation fields. The TPS assumed 97% of prescribed dose cover the prescribed treatment volume (PTV). Radiochromic films in a solid water phantom provided dose response as a function of optical density. Spatial dosimetric distribution was generated by radiochromic film samples at coronal, sagittal-anterior and sagittal-posterior positions, inserted into tumor simulator and brain. The spatial dose profiles held 70 to 120% of the prescribed dose. In spite of the stratified profile, as opposed to the smooth dose profile from TPS, the tumor internal doses were within a 5% deviation from 214.4 cGy evaluated by TPS. 83.2% of the points with a gamma value of less than 1 (3%/3mm) for TPS and experimental values, respectively. At the tumor, measured at coronal section, a few dark spots in the film caused the appearance of outlier points in 13-15% of dose deviation percentage. And, as final conclusion, such dosimeter choice and the physical anthropomorphic and anthropometric phantom provided an efficient method for validating radiotherapy protocols. PMID:23829593

  4. Simultaneous MRI and PET imaging of a rat brain

    NASA Astrophysics Data System (ADS)

    Raylman, Raymond R.; Majewski, Stan; Lemieux, Susan K.; Sendhil Velan, S.; Kross, Brian; Popov, Vladimir; Smith, Mark F.; Weisenberger, Andrew G.; Zorn, Carl; Marano, Gary D.

    2006-12-01

    Multi-modality imaging is rapidly becoming a valuable tool in the diagnosis of disease and in the development of new drugs. Functional images produced with PET fused with anatomical structure images created by MRI will allow the correlation of form with function. Our group is developing a system to acquire MRI and PET images contemporaneously. The prototype device consists of two opposed detector heads, operating in coincidence mode. Each MRI-PET detector module consists of an array of LSO detector elements coupled through a long fibre optic light guide to a single Hamamatsu flat panel position-sensitive photomultiplier tube (PSPMT). The use of light guides allows the PSPMTs to be positioned outside the bore of a 3T MRI scanner where the magnetic field is relatively small. To test the device, simultaneous MRI and PET images of the brain of a male Sprague Dawley rat injected with FDG were successfully obtained. The images revealed no noticeable artefacts in either image set. Future work includes the construction of a full ring PET scanner, improved light guides and construction of a specialized MRI coil to permit higher quality MRI imaging.

  5. 2D-3D registration for brain radiation therapy using a 3D CBCT and a single limited field-of-view 2D kV radiograph

    NASA Astrophysics Data System (ADS)

    Munbodh, R.; Moseley, D. J.

    2014-03-01

    We report results of an intensity-based 2D-3D rigid registration framework for patient positioning and monitoring during brain radiotherapy. We evaluated two intensity-based similarity measures, the Pearson Correlation Coefficient (ICC) and Maximum Likelihood with Gaussian noise (MLG) derived from the statistics of transmission images. A useful image frequency band was identified from the bone-to-no-bone ratio. Validation was performed on gold-standard data consisting of 3D kV CBCT scans and 2D kV radiographs of an anthropomorphic head phantom acquired at 23 different poses with parameter variations along six degrees of freedom. At each pose, a single limited field of view kV radiograph was registered to the reference CBCT. The ground truth was determined from markers affixed to the phantom and visible in the CBCT images. The mean (and standard deviation) of the absolute errors in recovering each of the six transformation parameters along the x, y and z axes for ICC were varphix: 0.08(0.04)°, varphiy: 0.10(0.09)°, varphiz: 0.03(0.03)°, tx: 0.13(0.11) mm, ty: 0.08(0.06) mm and tz: 0.44(0.23) mm. For MLG, the corresponding results were varphix: 0.10(0.04)°, varphiy: 0.10(0.09)°, varphiz: 0.05(0.07)°, tx: 0.11(0.13) mm, ty: 0.05(0.05) mm and tz: 0.44(0.31) mm. It is feasible to accurately estimate all six transformation parameters from a 3D CBCT of the head and a single 2D kV radiograph within an intensity-based registration framework that incorporates the physics of transmission images.

  6. SU-D-201-07: Exploring the Utility of 4D FDG-PET/CT Scans in Design of Radiation Therapy Planning Compared with 3D PET/CT: A Prospective Study

    SciTech Connect

    Ma, C; Yin, Y

    2015-06-15

    Purpose: A method using four-dimensional(4D) PET/CT in design of radiation treatment planning was proposed and the target volume and radiation dose distribution changes relative to standard three-dimensional (3D) PET/CT were examined. Methods: A target deformable registration method was used by which the whole patient’s respiration process was considered and the effect of respiration motion was minimized when designing radiotherapy planning. The gross tumor volume of a non-small-cell lung cancer was contoured on the 4D FDG-PET/CT and 3D PET/CT scans by use of two different techniques: manual contouring by an experienced radiation oncologist using a predetermined protocol; another technique using a constant threshold of standardized uptake value (SUV) greater than 2.5. The target volume and radiotherapy dose distribution between VOL3D and VOL4D were analyzed. Results: For all phases, the average automatic and manually GTV volume was 18.61 cm3 (range, 16.39–22.03 cm3) and 31.29 cm3 (range, 30.11–35.55 cm3), respectively. The automatic and manually volume of merged IGTV were 27.82 cm3 and 49.37 cm3, respectively. For the manual contour, compared to 3D plan the mean dose for the left, right, and total lung of 4D plan have an average decrease 21.55%, 15.17% and 15.86%, respectively. The maximum dose of spinal cord has an average decrease 2.35%. For the automatic contour, the mean dose for the left, right, and total lung have an average decrease 23.48%, 16.84% and 17.44%, respectively. The maximum dose of spinal cord has an average decrease 1.68%. Conclusion: In comparison to 3D PET/CT, 4D PET/CT may better define the extent of moving tumors and reduce the contouring tumor volume thereby optimize radiation treatment planning for lung tumors.

  7. Correlation of pre-operative MRI and intra-operative 3D ultrasound to measure brain tissue shift

    NASA Astrophysics Data System (ADS)

    Gobbi, David G.; Comeau, Roch M.; Lee, Belinda K. H.; Peters, Terence M.

    2000-04-01

    The usefulness of stereotactic neurosurgery performed via a craniotomy is limited because the craniotomy leads to a brain tissue shift of 10 mm on average. We have recently completed an examination of 2D intra-operative ultrasound as a means of visualization and measurement of brain shift. A commercial 3D tracking system was used for real-time registration of the ultrasound video to pre-operative MR images, and annotation of the images was used to measure the shift. More than 15 surgical cases have been performed thus far with the 2D system. We are now undertaking phantom studies with tracked 3D ultrasound, and have developed sophisticated tools for real- time overlay of ultrasound and MRI volumes. These tools include a virtual-reality view of the ultrasound probe with live ultrasound video superimposed over a 3D -rendered MRI of the brain, as well as 3D ultrasound/MRI transparency overlay views. Algorithms to automatically extract landmarks from MRI and 3D ultrasound images are under development. We aim to use these landmarks to automatically generate nonlinear warp transformations to correct the pre-operative MRI as well as surgical target coordinates for brain shift. Portions of the C++ code developed for this project have been contributed to the open-source Visualization Toolkit (VTK).

  8. MO-G-17A-03: MR-Based Cortical Bone Segmentation for PET Attenuation Correction with a Non-UTE 3D Fast GRE Sequence

    SciTech Connect

    Ai, H; Pan, T; Hwang, K

    2014-06-15

    Purpose: To determine the feasibility of identifying cortical bone on MR images with a short-TE 3D fast-GRE sequence for attenuation correction of PET data in PET/MR. Methods: A water-fat-bone phantom was constructed with two pieces of beef shank. MR scans were performed on a 3T MR scanner (GE Discovery™ MR750). A 3D GRE sequence was first employed to measure the level of residual signal in cortical bone (TE{sub 1}/TE{sub 2}/TE{sub 3}=2.2/4.4/6.6ms, TR=20ms, flip angle=25°). For cortical bone segmentation, a 3D fast-GRE sequence (TE/TR=0.7/1.9ms, acquisition voxel size=2.5×2.5×3mm{sup 3}) was implemented along with a 3D Dixon sequence (TE{sub 1}/TE{sub 2}/TR=1.2/2.3/4.0ms, acquisition voxel size=1.25×1.25×3mm{sup 3}) for water/fat imaging. Flip angle (10°), acquisition bandwidth (250kHz), FOV (480×480×144mm{sup 3}) and reconstructed voxel size (0.94×0.94×1.5mm{sup 3}) were kept the same for both sequences. Soft tissue and fat tissue were first segmented on the reconstructed water/fat image. A tissue mask was created by combining the segmented water/fat masks, which was then applied on the fast-GRE image (MRFGRE). A second mask was created to remove the Gibbs artifacts present in regions in close vicinity to the phantom. MRFGRE data was smoothed with a 3D anisotropic diffusion filter for noise reduction, after which cortical bone and air was separated using a threshold determined from the histogram. Results: There is signal in the cortical bone region in the 3D GRE images, indicating the possibility of separating cortical bone and air based on signal intensity from short-TE MR image. The acquisition time for the 3D fast-GRE sequence was 17s, which can be reduced to less than 10s with parallel imaging. The attenuation image created from water-fat-bone segmentation is visually similar compared to reference CT. Conclusion: Cortical bone and air can be separated based on intensity in MR image with a short-TE 3D fast-GRE sequence. Further research is required

  9. The Ultrasound Brain Helmet: Simultaneous Multi-transducer 3D Transcranial Ultrasound Imaging

    NASA Astrophysics Data System (ADS)

    Lindsey, Brooks D.

    In this work, I examine the problem of rapid imaging of stroke and present ultrasound-based approaches for addressing it. Specifically, this dissertation discusses aberration and attenuation due to the skull as sources of image degradation and presents a prototype system for simultaneous 3D bilateral imaging via both temporal acoustic windows. This system uses custom sparse array transducers built on flexible multilayer circuits that can be positioned for simultaneous imaging via both temporal acoustic windows, allowing for registration and fusion of multiple real-time 3D scans of cerebral vasculature. I examine hardware considerations for new matrix arrays—transducer design and interconnects—in this application. Specifically, it is proposed that signal-to-noise ratio (SNR) may be increased by reducing the length of probe cables. This claim is evaluated as part of the presented system through simulation, experimental data, and in vivo imaging. Ultimately, gains in SNR of 7 dB are realized by replacing a standard probe cable with a much shorter flex interconnect; higher gains may be possible using ribbon-based probe cables. In vivo images are presented depicting cerebral arteries with and without the use of microbubble contrast agent that have been registered and fused using a search algorithm which maximizes normalized cross-correlation. The scanning geometry of a brain helmet-type system is also utilized to allow each matrix array to serve as a correction source for the opposing array. Aberration is estimated using cross-correlation of RF channel signals followed by least mean squares solution of the resulting overdetermined system. Delay maps are updated and real-time 3D scanning resumes. A first attempt is made at using multiple arrival time maps to correct multiple unique aberrators within a single transcranial imaging volume, i.e. several isoplanatic patches. This adaptive imaging technique, which uses steered unfocused waves transmitted by the opposing or

  10. Intensity-based 2D 3D registration for lead localization in robot guided deep brain stimulation.

    PubMed

    Hunsche, Stefan; Sauner, Dieter; Majdoub, Faycal El; Neudorfer, Clemens; Poggenborg, Jörg; Goßmann, Axel; Maarouf, Mohammad

    2017-03-21

    Intraoperative assessment of lead localization has become a standard procedure during deep brain stimulation surgery in many centers, allowing immediate verification of targeting accuracy and, if necessary, adjustment of the trajectory. The most suitable imaging modality to determine lead positioning, however, remains controversially discussed. Current approaches entail the implementation of computed tomography and magnetic resonance imaging. In the present study, we adopted the technique of intensity-based 2D 3D registration that is commonly employed in stereotactic radiotherapy and spinal surgery. For this purpose, intraoperatively acquired 2D x-ray images were fused with preoperative 3D computed tomography (CT) data to verify lead placement during stereotactic robot assisted surgery. Accuracy of lead localization determined from 2D 3D registration was compared to conventional 3D 3D registration in a subsequent patient study. The mean Euclidian distance of lead coordinates estimated from intensity-based 2D 3D registration versus flat-panel detector CT 3D 3D registration was 0.7 mm  ±  0.2 mm. Maximum values of these distances amounted to 1.2 mm. To further investigate 2D 3D registration a simulation study was conducted, challenging two observers to visually assess artificially generated 2D 3D registration errors. 95% of deviation simulations, which were visually assessed as sufficient, had a registration error below 0.7 mm. In conclusion, 2D 3D intensity-based registration revealed high accuracy and reliability during robot guided stereotactic neurosurgery and holds great potential as a low dose, cost effective means for intraoperative lead localization.

  11. Intensity-based 2D 3D registration for lead localization in robot guided deep brain stimulation

    NASA Astrophysics Data System (ADS)

    Hunsche, Stefan; Sauner, Dieter; El Majdoub, Faycal; Neudorfer, Clemens; Poggenborg, Jörg; Goßmann, Axel; Maarouf, Mohammad

    2017-03-01

    Intraoperative assessment of lead localization has become a standard procedure during deep brain stimulation surgery in many centers, allowing immediate verification of targeting accuracy and, if necessary, adjustment of the trajectory. The most suitable imaging modality to determine lead positioning, however, remains controversially discussed. Current approaches entail the implementation of computed tomography and magnetic resonance imaging. In the present study, we adopted the technique of intensity-based 2D 3D registration that is commonly employed in stereotactic radiotherapy and spinal surgery. For this purpose, intraoperatively acquired 2D x-ray images were fused with preoperative 3D computed tomography (CT) data to verify lead placement during stereotactic robot assisted surgery. Accuracy of lead localization determined from 2D 3D registration was compared to conventional 3D 3D registration in a subsequent patient study. The mean Euclidian distance of lead coordinates estimated from intensity-based 2D 3D registration versus flat-panel detector CT 3D 3D registration was 0.7 mm  ±  0.2 mm. Maximum values of these distances amounted to 1.2 mm. To further investigate 2D 3D registration a simulation study was conducted, challenging two observers to visually assess artificially generated 2D 3D registration errors. 95% of deviation simulations, which were visually assessed as sufficient, had a registration error below 0.7 mm. In conclusion, 2D 3D intensity-based registration revealed high accuracy and reliability during robot guided stereotactic neurosurgery and holds great potential as a low dose, cost effective means for intraoperative lead localization.

  12. 4D Magnetic Resonance Velocimetry in a 3D printed brain aneurysm

    NASA Astrophysics Data System (ADS)

    Amili, Omid; Schiavazzi, Daniele; Coletti, Filippo

    2016-11-01

    Cerebral aneurysms are of great clinical importance. It is believed that hemodynamics play a critical role in the development, growth, and rupture of brain arteries with such condition. The flow structure in the aneurysm sac is complex, unsteady, and three-dimensional. Therefore the time-resolved measurement of the three-dimensional three-component velocity field is crucial to predict the clinical outcome. In this study magnetic resonance velocimetry is used to assess the fluid dynamics inside a 3D printed model of a giant intracranial aneurysm. We reach sub-millimeter resolution while resolving sixteen instances within the cardiac cycle. The physiological flow waveform is imposed using an in-house built pump in a flow circuit where the cardiovascular impedance is matched. The flow evolution over time is reconstructed in detail. The complex flow structure is characterized by vortical and helical motions that reside in the aneurysm for most part of the cycle. The 4D pressured distribution is also reconstructed from the velocity field. The present case study was used in a previous CFD challenge, therefore these results may provide useful experimental comparison for simulations performed by other research groups.

  13. 3D quantification of brain microvessels exposed to heavy particle radiation

    NASA Astrophysics Data System (ADS)

    Hintermüller, C.; Coats, J. S.; Obenaus, A.; Nelson, G.; Krucker, T.; Stampanoni, M.

    2009-09-01

    Space radiation with high energy particles and cosmic rays presents a significant hazard to spaceflight crews. Recent reviews of the health risk to astronauts from ionizing radiation concluded to establish a level of risk which may indicate the possible performance decrements and decreased latency of late dysfunction syndromes (LDS) of the brain. A hierarchical imaging approach developed at ETH Zürich and PSI, which relies on synchrotron based X-ray Tomographic Microscopy (SRXTM), was used to visualize and analyze 3D vascular structures down to the capillary level in their precise anatomical context. Various morphological parameters, such as overall vessel volume, vessel thickness and spacing, are extracted to characterize the vascular structure within a region of interest. For a first quantification of the effect of high energy particles on the vasculature we scanned a set of 6 animals, all of same age. The animals were irradiated with 1 Gy, 2 Gy and 4 Gy of 600MeV 56Fe heavy particles simulating the space radiation environment. We found that with increasing dose the diameter of vessels and the overall vessel volume are decreased whereas the vessel spacing is increased. As these parameters reflect blood flow in three-dimensional space they can be used as indicators for the degree of vascular efficiency which can have an impact on the function and development of lung tissue or tumors.

  14. Measured count-rate performance of the Discovery STE PET/CT scanner in 2D, 3D and partial collimation acquisition modes.

    PubMed

    Macdonald, L R; Schmitz, R E; Alessio, A M; Wollenweber, S D; Stearns, C W; Ganin, A; Harrison, R L; Lewellen, T K; Kinahan, P E

    2008-07-21

    We measured count rates and scatter fraction on the Discovery STE PET/CT scanner in conventional 2D and 3D acquisition modes, and in a partial collimation mode between 2D and 3D. As part of the evaluation of using partial collimation, we estimated global count rates using a scanner model that combined computer simulations with an empirical live-time function. Our measurements followed the NEMA NU2 count rate and scatter-fraction protocol to obtain true, scattered and random coincidence events, from which noise equivalent count (NEC) rates were calculated. The effect of patient size was considered by using 27 cm and 35 cm diameter phantoms, in addition to the standard 20 cm diameter cylindrical count-rate phantom. Using the scanner model, we evaluated two partial collimation cases: removing half of the septa (2.5D) and removing two-thirds of the septa (2.7D). Based on predictions of the model, a 2.7D collimator was constructed. Count rates and scatter fractions were then measured in 2D, 2.7D and 3D. The scanner model predicted relative NEC variation with activity, as confirmed by measurements. The measured 2.7D NEC was equal or greater than 3D NEC for all activity levels in the 27 cm and 35 cm phantoms. In the 20 cm phantom, 3D NEC was somewhat higher ( approximately 15%) than 2.7D NEC at 100 MBq. For all higher activity concentrations, 2.7D NEC was greater and peaked 26% above the 3D peak NEC. The peak NEC in 2.7D mode occurred at approximately 425 MBq, and was 26-50% greater than the peak 3D NEC, depending on object size. NEC in 2D was considerably lower, except at relatively high activity concentrations. Partial collimation shows promise for improved noise equivalent count rates in clinical imaging without altering other detector parameters.

  15. Performance modeling of a wearable brain PET (BET) camera

    NASA Astrophysics Data System (ADS)

    Schmidtlein, C. R.; Turner, J. N.; Thompson, M. O.; Mandal, K. C.; Häggström, I.; Zhang, J.; Humm, J. L.; Feiglin, D. H.; Krol, A.

    2016-03-01

    Purpose: To explore, by means of analytical and Monte Carlo modeling, performance of a novel lightweight and low-cost wearable helmet-shaped Brain PET (BET) camera based on thin-film digital Geiger Avalanche Photo Diode (dGAPD) with LSO and LaBr3 scintillators for imaging in vivo human brain processes for freely moving and acting subjects responding to various stimuli in any environment. Methods: We performed analytical and Monte Carlo modeling PET performance of a spherical cap BET device and cylindrical brain PET (CYL) device, both with 25 cm diameter and the same total mass of LSO scintillator. Total mass of LSO in both the BET and CYL systems is about 32 kg for a 25 mm thick scintillator, and 13 kg for 10 mm thick scintillator (assuming an LSO density of 7.3 g/ml). We also investigated a similar system using an LaBr3 scintillator corresponding to 22 kg and 9 kg for the 25 mm and 10 mm thick systems (assuming an LaBr3 density of 5.08 g/ml). In addition, we considered a clinical whole body (WB) LSO PET/CT scanner with 82 cm ring diameter and 15.8 cm axial length to represent a reference system. BET consisted of distributed Autonomous Detector Arrays (ADAs) integrated into Intelligent Autonomous Detector Blocks (IADBs). The ADA comprised of an array of small LYSO scintillator volumes (voxels with base a×a: 1.0 <= a <= 2.0 mm and length c: 3.0 <= c <= 6.0 mm) with 5-65 μm thick reflective layers on its five sides and sixth side optically coupled to the matching array of dGAPDs and processing electronics with total thickness of 50 μm. Simulated energy resolution was 10.8% and 3.3% for LSO and LaBr3 respectively and the coincidence window was set at 2 ns. The brain was simulated as a sphere of uniform F-18 activity with diameter of 10 cm embedded in a center of water sphere with diameter of 10 cm. Results: Analytical and Monte Carlo models showed similar results for lower energy window values (458 keV versus 445 keV for LSO, and 492 keV versus 485 keV for LaBr3

  16. Use of the FLUKA Monte Carlo code for 3D patient-specific dosimetry on PET-CT and SPECT-CT images.

    PubMed

    Botta, F; Mairani, A; Hobbs, R F; Vergara Gil, A; Pacilio, M; Parodi, K; Cremonesi, M; Coca Pérez, M A; Di Dia, A; Ferrari, M; Guerriero, F; Battistoni, G; Pedroli, G; Paganelli, G; Torres Aroche, L A; Sgouros, G

    2013-11-21

    Patient-specific absorbed dose calculation for nuclear medicine therapy is a topic of increasing interest. 3D dosimetry at the voxel level is one of the major improvements for the development of more accurate calculation techniques, as compared to the standard dosimetry at the organ level. This study aims to use the FLUKA Monte Carlo code to perform patient-specific 3D dosimetry through direct Monte Carlo simulation on PET-CT and SPECT-CT images. To this aim, dedicated routines were developed in the FLUKA environment. Two sets of simulations were performed on model and phantom images. Firstly, the correct handling of PET and SPECT images was tested under the assumption of homogeneous water medium by comparing FLUKA results with those obtained with the voxel kernel convolution method and with other Monte Carlo-based tools developed to the same purpose (the EGS-based 3D-RD software and the MCNP5-based MCID). Afterwards, the correct integration of the PET/SPECT and CT information was tested, performing direct simulations on PET/CT images for both homogeneous (water) and non-homogeneous (water with air, lung and bone inserts) phantoms. Comparison was performed with the other Monte Carlo tools performing direct simulation as well. The absorbed dose maps were compared at the voxel level. In the case of homogeneous water, by simulating 10(8) primary particles a 2% average difference with respect to the kernel convolution method was achieved; such difference was lower than the statistical uncertainty affecting the FLUKA results. The agreement with the other tools was within 3–4%, partially ascribable to the differences among the simulation algorithms. Including the CT-based density map, the average difference was always within 4% irrespective of the medium (water, air, bone), except for a maximum 6% value when comparing FLUKA and 3D-RD in air. The results confirmed that the routines were properly developed, opening the way for the use of FLUKA for patient-specific, image

  17. Use of the FLUKA Monte Carlo code for 3D patient-specific dosimetry on PET-CT and SPECT-CT images*

    PubMed Central

    Botta, F; Mairani, A; Hobbs, R F; Vergara Gil, A; Pacilio, M; Parodi, K; Cremonesi, M; Coca Pérez, M A; Di Dia, A; Ferrari, M; Guerriero, F; Battistoni, G; Pedroli, G; Paganelli, G; Torres Aroche, L A; Sgouros, G

    2014-01-01

    Patient-specific absorbed dose calculation for nuclear medicine therapy is a topic of increasing interest. 3D dosimetry at the voxel level is one of the major improvements for the development of more accurate calculation techniques, as compared to the standard dosimetry at the organ level. This study aims to use the FLUKA Monte Carlo code to perform patient-specific 3D dosimetry through direct Monte Carlo simulation on PET-CT and SPECT-CT images. To this aim, dedicated routines were developed in the FLUKA environment. Two sets of simulations were performed on model and phantom images. Firstly, the correct handling of PET and SPECT images was tested under the assumption of homogeneous water medium by comparing FLUKA results with those obtained with the voxel kernel convolution method and with other Monte Carlo-based tools developed to the same purpose (the EGS-based 3D-RD software and the MCNP5-based MCID). Afterwards, the correct integration of the PET/SPECT and CT information was tested, performing direct simulations on PET/CT images for both homogeneous (water) and non-homogeneous (water with air, lung and bone inserts) phantoms. Comparison was performed with the other Monte Carlo tools performing direct simulation as well. The absorbed dose maps were compared at the voxel level. In the case of homogeneous water, by simulating 108 primary particles a 2% average difference with respect to the kernel convolution method was achieved; such difference was lower than the statistical uncertainty affecting the FLUKA results. The agreement with the other tools was within 3–4%, partially ascribable to the differences among the simulation algorithms. Including the CT-based density map, the average difference was always within 4% irrespective of the medium (water, air, bone), except for a maximum 6% value when comparing FLUKA and 3D-RD in air. The results confirmed that the routines were properly developed, opening the way for the use of FLUKA for patient-specific, image

  18. Use of the FLUKA Monte Carlo code for 3D patient-specific dosimetry on PET-CT and SPECT-CT images

    NASA Astrophysics Data System (ADS)

    Botta, F.; Mairani, A.; Hobbs, R. F.; Vergara Gil, A.; Pacilio, M.; Parodi, K.; Cremonesi, M.; Coca Pérez, M. A.; Di Dia, A.; Ferrari, M.; Guerriero, F.; Battistoni, G.; Pedroli, G.; Paganelli, G.; Torres Aroche, L. A.; Sgouros, G.

    2013-11-01

    Patient-specific absorbed dose calculation for nuclear medicine therapy is a topic of increasing interest. 3D dosimetry at the voxel level is one of the major improvements for the development of more accurate calculation techniques, as compared to the standard dosimetry at the organ level. This study aims to use the FLUKA Monte Carlo code to perform patient-specific 3D dosimetry through direct Monte Carlo simulation on PET-CT and SPECT-CT images. To this aim, dedicated routines were developed in the FLUKA environment. Two sets of simulations were performed on model and phantom images. Firstly, the correct handling of PET and SPECT images was tested under the assumption of homogeneous water medium by comparing FLUKA results with those obtained with the voxel kernel convolution method and with other Monte Carlo-based tools developed to the same purpose (the EGS-based 3D-RD software and the MCNP5-based MCID). Afterwards, the correct integration of the PET/SPECT and CT information was tested, performing direct simulations on PET/CT images for both homogeneous (water) and non-homogeneous (water with air, lung and bone inserts) phantoms. Comparison was performed with the other Monte Carlo tools performing direct simulation as well. The absorbed dose maps were compared at the voxel level. In the case of homogeneous water, by simulating 108 primary particles a 2% average difference with respect to the kernel convolution method was achieved; such difference was lower than the statistical uncertainty affecting the FLUKA results. The agreement with the other tools was within 3-4%, partially ascribable to the differences among the simulation algorithms. Including the CT-based density map, the average difference was always within 4% irrespective of the medium (water, air, bone), except for a maximum 6% value when comparing FLUKA and 3D-RD in air. The results confirmed that the routines were properly developed, opening the way for the use of FLUKA for patient-specific, image

  19. Transvaginal 3-d power Doppler ultrasound evaluation of the fetal brain at 10-13 weeks' gestation.

    PubMed

    Hata, Toshiyuki; Tanaka, Hirokazu; Noguchi, Junko

    2012-03-01

    The objective of this study was to measure the fetal brain volume (FBV) and vascularization and blood flow using transvaginal 3-D power Doppler (3DPD) ultrasound late in the first trimester of pregnancy. 3DPD ultrasound examinations with the VOCAL imaging analysis program were performed on 36 normal fetuses from 10-13 weeks' gestation. FBV and 3DPD indices related to the fetal brain vascularization (vascularization index [VI], flow index [FI] and vascularization flow index [VFI]) were calculated in each fetus. Intra- and interclass correlation coefficients and intra- and interobserver agreements of measurements were assessed. FBV was curvilinearly correlated well with the gestational age (R2 = 0.861, p < 0.0001). All 3-D power Doppler indices (VI, FI and VFI) showed no change at 10-13 weeks' gestation. FBV and all 3-D power Doppler indices (VI, FI and VFI) showed a correlation > 0.82, with good intra- and interobserver agreement. Our findings suggest that 3-D ultrasound is a superior means of evaluating the FBV in utero, and that 3-D power Doppler ultrasound histogram analysis may provide new information on the assessment of fetal brain perfusion.

  20. A fully automatic, threshold-based segmentation method for the estimation of the Metabolic Tumor Volume from PET images: validation on 3D printed anthropomorphic oncological lesions

    NASA Astrophysics Data System (ADS)

    Gallivanone, F.; Interlenghi, M.; Canervari, C.; Castiglioni, I.

    2016-01-01

    18F-Fluorodeoxyglucose (18F-FDG) Positron Emission Tomography (PET) is a standard functional diagnostic technique to in vivo image cancer. Different quantitative paramters can be extracted from PET images and used as in vivo cancer biomarkers. Between PET biomarkers Metabolic Tumor Volume (MTV) has gained an important role in particular considering the development of patient-personalized radiotherapy treatment for non-homogeneous dose delivery. Different imaging processing methods have been developed to define MTV. The different proposed PET segmentation strategies were validated in ideal condition (e.g. in spherical objects with uniform radioactivity concentration), while the majority of cancer lesions doesn't fulfill these requirements. In this context, this work has a twofold objective: 1) to implement and optimize a fully automatic, threshold-based segmentation method for the estimation of MTV, feasible in clinical practice 2) to develop a strategy to obtain anthropomorphic phantoms, including non-spherical and non-uniform objects, miming realistic oncological patient conditions. The developed PET segmentation algorithm combines an automatic threshold-based algorithm for the definition of MTV and a k-means clustering algorithm for the estimation of the background. The method is based on parameters always available in clinical studies and was calibrated using NEMA IQ Phantom. Validation of the method was performed both in ideal (e.g. in spherical objects with uniform radioactivity concentration) and non-ideal (e.g. in non-spherical objects with a non-uniform radioactivity concentration) conditions. The strategy to obtain a phantom with synthetic realistic lesions (e.g. with irregular shape and a non-homogeneous uptake) consisted into the combined use of standard anthropomorphic phantoms commercially and irregular molds generated using 3D printer technology and filled with a radioactive chromatic alginate. The proposed segmentation algorithm was feasible in a

  1. 3D BrainCV: simultaneous visualization and analysis of cells and capillaries in a whole mouse brain with one-micron voxel resolution.

    PubMed

    Wu, Jingpeng; He, Yong; Yang, Zhongqin; Guo, Congdi; Luo, Qingming; Zhou, Wei; Chen, Shangbin; Li, Anan; Xiong, Benyi; Jiang, Tao; Gong, Hui

    2014-02-15

    Systematic cellular and vascular configurations are essential for understanding fundamental brain anatomy and metabolism. We demonstrated a 3D brainwide cellular and vascular (called 3D BrainCV) visualization and quantitative protocol for a whole mouse brain. We developed a modified Nissl staining method that quickly labeled the cells and blood vessels simultaneously in an entire mouse brain. Terabytes 3D datasets of the whole mouse brains, with unprecedented details of both individual cells and blood vessels, including capillaries, were simultaneously imaged at 1-μm voxel resolution using micro-optical sectioning tomography (MOST). For quantitative analysis, we proposed an automatic image-processing pipeline to perform brainwide vectorization and analysis of cells and blood vessels. Six representative brain regions from the cortex to the deep, including FrA, M1, PMBSF, V1, striatum, and amygdala, and six parameters, including cell number density, vascular length density, fractional vascular volume, distance from the cells to the nearest microvessel, microvascular length density, and fractional microvascular volume, had been quantitatively analyzed. The results showed that the proximity of cells to blood vessels was linearly correlated with vascular length density, rather than the cell number density. The 3D BrainCV made overall snapshots of the detailed picture of the whole brain architecture, which could be beneficial for the state comparison of the developing and diseased brain.

  2. Analysis and correction of count rate reduction during simultaneous MR-PET measurements with the BrainPET scanner.

    PubMed

    Weirich, Christoph; Brenner, Daniel; Scheins, Jürgen; Besancon, Etienne; Tellmann, Lutz; Herzog, Hans; Shah, N Jon

    2012-07-01

    In hybrid magnetic resonance-positron emission tomography (MR-PET) studies with the Siemens 3T MR-BrainPET scanner an instantaneous reduction of the PET sensitivity was observed during execution of certain MR sequences. This interference was investigated in detail with custom-made as well as standard clinical MR sequences. The radio-frequency pulses, the switched gradient fields and the constant magnetic field were examined as the relevant parameters of the magnetic resonance imaging (MRI) system as well as the air temperature within the PET detectors. Our investigation comprised the analysis of the analog PET signals, the total count rates, the geometric distribution of the count rate reduction within the BrainPET detector as well as reconstructed images. The fast switching magnetic field gradients were identified to distort the analog PET detector signals. The measured count rate reduction was found to be less than 3%, but only up to 2% in the case of echo planar imaging sequences, as applied in functional MRI. For clinical sequences routinely used in hybrid MR-BrainPET measurements, a correction method has been designed, implemented, and evaluated .

  3. The ultrasound brain helmet: early human feasibility study of multiple simultaneous 3D scans of cerebral vasculature

    NASA Astrophysics Data System (ADS)

    Lindsey, Brooks D.; Ivancevich, Nikolas M.; Whitman, John; Light, Edward; Fronheiser, Matthew; Nicoletto, Heather A.; Laskowitz, Daniel T.; Smith, Stephen W.

    2009-02-01

    We describe early stage experiments to test the feasibility of an ultrasound brain helmet to produce multiple simultaneous real-time 3D scans of the cerebral vasculature from temporal and suboccipital acoustic windows of the skull. The transducer hardware and software of the Volumetrics Medical Imaging real-time 3D scanner were modified to support dual 2.5 MHz matrix arrays of 256 transmit elements and 128 receive elements which produce two simultaneous 64° pyramidal scans. The real-time display format consists of two coronal B-mode images merged into a 128° sector, two simultaneous parasagittal images merged into a 128° × 64° C-mode plane, and a simultaneous 64° axial image. Real-time 3D color Doppler images acquired in initial clinical studies after contrast injection demonstrate flow in several representative blood vessels. An offline Doppler rendering of data from two transducers simultaneously scanning via the temporal windows provides an early visualization of the flow in vessels on both sides of the brain. The long-term goal is to produce real-time 3D ultrasound images of the cerebral vasculature from a portable unit capable of internet transmission, thus enabling interactive 3D imaging, remote diagnosis and earlier therapeutic intervention. We are motivated by the urgency for rapid diagnosis of stroke due to the short time window of effective therapeutic intervention.

  4. Use of High Resolution 3D Diffusion Tensor Imaging to Study Brain White Matter Development in Live Neonatal Rats

    PubMed Central

    Cai, Yu; McMurray, Matthew S.; Oguz, Ipek; Yuan, Hong; Styner, Martin A.; Lin, Weili; Johns, Josephine M.; An, Hongyu

    2011-01-01

    High resolution diffusion tensor imaging (DTI) can provide important information on brain development, yet it is challenging in live neonatal rats due to the small size of neonatal brain and motion-sensitive nature of DTI. Imaging in live neonatal rats has clear advantages over fixed brain scans, as longitudinal and functional studies would be feasible to understand neuro-developmental abnormalities. In this study, we developed imaging strategies that can be used to obtain high resolution 3D DTI images in live neonatal rats at postnatal day 5 (PND5) and PND14, using only 3 h of imaging acquisition time. An optimized 3D DTI pulse sequence and appropriate animal setup to minimize physiological motion artifacts are the keys to successful high resolution 3D DTI imaging. Thus, a 3D rapid acquisition relaxation enhancement DTI sequence with twin navigator echoes was implemented to accelerate imaging acquisition time and minimize motion artifacts. It has been suggested that neonatal mammals possess a unique ability to tolerate mild-to-moderate hypothermia and hypoxia without long term impact. Thus, we additionally utilized this ability to minimize motion artifacts in magnetic resonance images by carefully suppressing the respiratory rate to around 15/min for PND5 and 30/min for PND14 using mild-to-moderate hypothermia. These imaging strategies have been successfully implemented to study how the effect of cocaine exposure in dams might affect brain development in their rat pups. Image quality resulting from this in vivo DTI study was comparable to ex vivo scans. fractional anisotropy values were also similar between the live and fixed brain scans. The capability of acquiring high quality in vivo DTI imaging offers a valuable opportunity to study many neurological disorders in brain development in an authentic living environment. PMID:22013426

  5. Optimising rigid motion compensation for small animal brain PET imaging

    NASA Astrophysics Data System (ADS)

    Spangler-Bickell, Matthew G.; Zhou, Lin; Kyme, Andre Z.; De Laat, Bart; Fulton, Roger R.; Nuyts, Johan

    2016-10-01

    Motion compensation (MC) in PET brain imaging of awake small animals is attracting increased attention in preclinical studies since it avoids the confounding effects of anaesthesia and enables behavioural tests during the scan. A popular MC technique is to use multiple external cameras to track the motion of the animal’s head, which is assumed to be represented by the motion of a marker attached to its forehead. In this study we have explored several methods to improve the experimental setup and the reconstruction procedures of this method: optimising the camera-marker separation; improving the temporal synchronisation between the motion tracker measurements and the list-mode stream; post-acquisition smoothing and interpolation of the motion data; and list-mode reconstruction with appropriately selected subsets. These techniques have been tested and verified on measurements of a moving resolution phantom and brain scans of an awake rat. The proposed techniques improved the reconstructed spatial resolution of the phantom by 27% and of the rat brain by 14%. We suggest a set of optimal parameter values to use for awake animal PET studies and discuss the relative significance of each parameter choice.

  6. A multiscale approach for the reconstruction of the fiber architecture of the human brain based on 3D-PLI

    PubMed Central

    Reckfort, Julia; Wiese, Hendrik; Pietrzyk, Uwe; Zilles, Karl; Amunts, Katrin; Axer, Markus

    2015-01-01

    Structural connectivity of the brain can be conceptionalized as a multiscale organization. The present study is built on 3D-Polarized Light Imaging (3D-PLI), a neuroimaging technique targeting the reconstruction of nerve fiber orientations and therefore contributing to the analysis of brain connectivity. Spatial orientations of the fibers are derived from birefringence measurements of unstained histological sections that are interpreted by means of a voxel-based analysis. This implies that a single fiber orientation vector is obtained for each voxel, which reflects the net effect of all comprised fibers. We have utilized two polarimetric setups providing an object space resolution of 1.3 μm/px (microscopic setup) and 64 μm/px (macroscopic setup) to carry out 3D-PLI and retrieve fiber orientations of the same tissue samples, but at complementary voxel sizes (i.e., scales). The present study identifies the main sources which cause a discrepancy of the measured fiber orientations observed when measuring the same sample with the two polarimetric systems. As such sources the differing optical resolutions and diverging retardances of the implemented waveplates were identified. A methodology was implemented that enables the compensation of measured different systems' responses to the same birefringent sample. This opens up new ways to conduct multiscale analysis in brains by means of 3D-PLI and to provide a reliable basis for the transition between different scales of the nerve fiber architecture. PMID:26388744

  7. Intersection Based Motion Correction of Multi-Slice MRI for 3D in utero Fetal Brain Image Formation

    PubMed Central

    Kim, Kio; Habas, Piotr A.; Rousseau, Francois; Glenn, Orit A.; Barkovich, Anthony J.; Studholme, Colin

    2012-01-01

    In recent years post-processing of fast multi-slice MR imaging to correct fetal motion has provided the first true 3D MR images of the developing human brain in utero. Early approaches have used reconstruction based algorithms, employing a two step iterative process, where slices from the acquired data are re-aligned to an approximate 3D reconstruction of the fetal brain, which is then refined further using the improved slice alignment. This two step slice-to-volume process, although powerful, is computationally expensive in needing a 3D reconstruction, and is limited in its ability to recover sub-voxel alignment. Here, we describe an alternative approach which we term slice intersection motion correction (SIMC), that seeks to directly co-align multiple slice stacks by considering the matching structure along all intersecting slice pairs in all orthogonally planned slices that are acquired in clinical imaging studies. A collective update scheme for all slices is then derived, to simultaneously drive slices into a consistent match along their lines of intersection. We then describe a 3D reconstruction algorithm that, using the final motion corrected slice locations, suppresses through-plane partial volume effects to provide a single high isotropic resolution 3D image. The method is tested on simulated data with known motions and is applied to retrospectively reconstruct 3D images from a range of clinically acquired imaging studies. The quantitative evaluation of the registration accuracy for the simulated data sets demonstrated a significant improvement over previous approaches. An initial application of the technique to studying clinical pathology is included, where the proposed method recovered up to 15 mm of translation and 30 degrees of rotation for individual slices, and produced full 3D reconstructions containing clinically useful additional information not visible in the original 2D slices. PMID:19744911

  8. Effects of image noise, respiratory motion, and motion compensation on 3D activity quantification in count-limited PET images

    NASA Astrophysics Data System (ADS)

    Siman, W.; Mawlawi, O. R.; Mikell, J. K.; Mourtada, F.; Kappadath, S. C.

    2017-01-01

    The aims of this study were to evaluate the effects of noise, motion blur, and motion compensation using quiescent-period gating (QPG) on the activity concentration (AC) distribution—quantified using the cumulative AC volume histogram (ACVH)—in count-limited studies such as 90Y-PET/CT. An International Electrotechnical Commission phantom filled with low 18F activity was used to simulate clinical 90Y-PET images. PET data were acquired using a GE-D690 when the phantom was static and subject to 1-4 cm periodic 1D motion. The static data were down-sampled into shorter durations to determine the effect of noise on ACVH. Motion-degraded PET data were sorted into multiple gates to assess the effect of motion and QPG on ACVH. Errors in ACVH at AC90 (minimum AC that covers 90% of the volume of interest (VOI)), AC80, and ACmean (average AC in the VOI) were characterized as a function of noise and amplitude before and after QPG. Scan-time reduction increased the apparent non-uniformity of sphere doses and the dispersion of ACVH. These effects were more pronounced in smaller spheres. Noise-related errors in ACVH at AC20 to AC70 were smaller (<15%) compared to the errors between AC80 to AC90 (>15%). The accuracy of ACmean was largely independent of the total count. Motion decreased the observed AC and skewed the ACVH toward lower values; the severity of this effect depended on motion amplitude and tumor diameter. The errors in AC20 to AC80 for the 17 mm sphere were  -25% and  -55% for motion amplitudes of 2 cm and 4 cm, respectively. With QPG, the errors in AC20 to AC80 of the 17 mm sphere were reduced to  -15% for motion amplitudes  <4 cm. For spheres with motion amplitude to diameter ratio  >0.5, QPG was effective at reducing errors in ACVH despite increases in image non-uniformity due to increased noise. ACVH is believed to be more relevant than mean or maximum AC to calculate tumor control and normal tissue complication probability

  9. High-resolution imaging of the large non-human primate brain using microPET: a feasibility study

    NASA Astrophysics Data System (ADS)

    Naidoo-Variawa, S.; Hey-Cunningham, A. J.; Lehnert, W.; Kench, P. L.; Kassiou, M.; Banati, R.; Meikle, S. R.

    2007-11-01

    The neuroanatomy and physiology of the baboon brain closely resembles that of the human brain and is well suited for evaluating promising new radioligands in non-human primates by PET and SPECT prior to their use in humans. These studies are commonly performed on clinical scanners with 5 mm spatial resolution at best, resulting in sub-optimal images for quantitative analysis. This study assessed the feasibility of using a microPET animal scanner to image the brains of large non-human primates, i.e. papio hamadryas (baboon) at high resolution. Factors affecting image accuracy, including scatter, attenuation and spatial resolution, were measured under conditions approximating a baboon brain and using different reconstruction strategies. Scatter fraction measured 32% at the centre of a 10 cm diameter phantom. Scatter correction increased image contrast by up to 21% but reduced the signal-to-noise ratio. Volume resolution was superior and more uniform using maximum a posteriori (MAP) reconstructed images (3.2-3.6 mm3 FWHM from centre to 4 cm offset) compared to both 3D ordered subsets expectation maximization (OSEM) (5.6-8.3 mm3) and 3D reprojection (3DRP) (5.9-9.1 mm3). A pilot 18F-2-fluoro-2-deoxy-d-glucose ([18F]FDG) scan was performed on a healthy female adult baboon. The pilot study demonstrated the ability to adequately resolve cortical and sub-cortical grey matter structures in the baboon brain and improved contrast when images were corrected for attenuation and scatter and reconstructed by MAP. We conclude that high resolution imaging of the baboon brain with microPET is feasible with appropriate choices of reconstruction strategy and corrections for degrading physical effects. Further work to develop suitable correction algorithms for high-resolution large primate imaging is warranted.

  10. Intrinsic spatial resolution evaluation of the X'tal cube PET detector based on a 3D crystal block segmented by laser processing.

    PubMed

    Yoshida, Eiji; Tashima, Hideaki; Inadama, Naoko; Nishikido, Fumihiko; Moriya, Takahiro; Omura, Tomohide; Watanabe, Mitsuo; Murayama, Hideo; Yamaya, Taiga

    2013-01-01

    The X'tal cube is a depth-of-interaction (DOI)-PET detector which is aimed at obtaining isotropic resolution by effective readout of scintillation photons from the six sides of a crystal block. The X'tal cube is composed of the 3D crystal block with isotropic resolution and arrays of multi-pixel photon counters (MPPCs). In this study, to fabricate the 3D crystal block efficiently and precisely, we applied a sub-surface laser engraving (SSLE) technique to a monolithic crystal block instead of gluing segmented small crystals. The SSLE technique provided micro-crack walls which carve a groove into a monolithic scintillator block. Using the fabricated X'tal cube, we evaluated its intrinsic spatial resolution to show a proof of concept of isotropic resolution. The 3D grids of 2 mm pitch were fabricated into an 18 × 18 × 18 mm(3) monolithic lutetium yttrium orthosilicate (LYSO) crystal by the SSLE technique. 4 × 4 MPPCs were optically coupled to each surface of the crystal block. The X'tal cube was uniformly irradiated by (22)Na gamma rays, and all of the 3D grids on the 3D position histogram were separated clearly by an Anger-type calculation from the 96-channel MPPC signals. Response functions of the X'tal cube were measured by scanning with a (22)Na point source. The gamma-ray beam with a 1.0 mm slit was scanned in 0.25 mm steps by positioning of the X'tal cube at vertical and 45° incident angles. The average FWHM resolution at both incident angles was 2.1 mm. Therefore, we confirmed the isotropic spatial resolution performance of the X'tal cube.

  11. Weight Gain following Pallidal Deep Brain Stimulation: A PET Study.

    PubMed

    Sauleau, Paul; Drapier, Sophie; Duprez, Joan; Houvenaghel, Jean-François; Dondaine, Thibaut; Haegelen, Claire; Drapier, Dominique; Jannin, Pierre; Robert, Gabriel; Le Jeune, Florence; Vérin, Marc

    2016-01-01

    The mechanisms behind weight gain following deep brain stimulation (DBS) surgery seem to be multifactorial and suspected depending on the target, either the subthalamic nucleus (STN) or the globus pallidus internus (GPi). Decreased energy expenditure following motor improvement and behavioral and/or metabolic changes are possible explanations. Focusing on GPi target, our objective was to analyze correlations between changes in brain metabolism (measured with PET) and weight gain following GPi-DBS in patients with Parkinson's disease (PD). Body mass index was calculated and brain activity prospectively measured using 2-deoxy-2[18F]fluoro-D-glucose PET four months before and four months after the start of GPi-DBS in 19 PD patients. Dopaminergic medication was included in the analysis to control for its possible influence on brain metabolism. Body mass index increased significantly by 0.66 ± 1.3 kg/m2 (p = 0.040). There were correlations between weight gain and changes in brain metabolism in premotor areas, including the left and right superior gyri (Brodmann area, BA 6), left superior gyrus (BA 8), the dorsolateral prefrontal cortex (right middle gyrus, BAs 9 and 46), and the left and right somatosensory association cortices (BA 7). However, we found no correlation between weight gain and metabolic changes in limbic and associative areas. Additionally, there was a trend toward a correlation between reduced dyskinesia and weight gain (r = 0.428, p = 0.067). These findings suggest that, unlike STN-DBS, motor improvement is the major contributing factor for weight gain following GPi-DBS PD, confirming the motor selectivity of this target.

  12. Weight Gain following Pallidal Deep Brain Stimulation: A PET Study

    PubMed Central

    Sauleau, Paul; Drapier, Sophie; Duprez, Joan; Houvenaghel, Jean-François; Dondaine, Thibaut; Haegelen, Claire; Drapier, Dominique; Jannin, Pierre; Robert, Gabriel; Le Jeune, Florence; Vérin, Marc

    2016-01-01

    The mechanisms behind weight gain following deep brain stimulation (DBS) surgery seem to be multifactorial and suspected depending on the target, either the subthalamic nucleus (STN) or the globus pallidus internus (GPi). Decreased energy expenditure following motor improvement and behavioral and/or metabolic changes are possible explanations. Focusing on GPi target, our objective was to analyze correlations between changes in brain metabolism (measured with PET) and weight gain following GPi-DBS in patients with Parkinson’s disease (PD). Body mass index was calculated and brain activity prospectively measured using 2-deoxy-2[18F]fluoro-D-glucose PET four months before and four months after the start of GPi-DBS in 19 PD patients. Dopaminergic medication was included in the analysis to control for its possible influence on brain metabolism. Body mass index increased significantly by 0.66 ± 1.3 kg/m2 (p = 0.040). There were correlations between weight gain and changes in brain metabolism in premotor areas, including the left and right superior gyri (Brodmann area, BA 6), left superior gyrus (BA 8), the dorsolateral prefrontal cortex (right middle gyrus, BAs 9 and 46), and the left and right somatosensory association cortices (BA 7). However, we found no correlation between weight gain and metabolic changes in limbic and associative areas. Additionally, there was a trend toward a correlation between reduced dyskinesia and weight gain (r = 0.428, p = 0.067). These findings suggest that, unlike STN-DBS, motor improvement is the major contributing factor for weight gain following GPi-DBS PD, confirming the motor selectivity of this target. PMID:27070317

  13. Technical Note: Immunohistochemical evaluation of mouse brain irradiation targeting accuracy with 3D-printed immobilization device

    SciTech Connect

    Zarghami, Niloufar Jensen, Michael D.; Talluri, Srikanth; Dick, Frederick A.; Foster, Paula J.; Chambers, Ann F.; Wong, Eugene

    2015-11-15

    Purpose: Small animal immobilization devices facilitate positioning of animals for reproducible imaging and accurate focal radiation therapy. In this study, the authors demonstrate the use of three-dimensional (3D) printing technology to fabricate a custom-designed mouse head restraint. The authors evaluate the accuracy of this device for the purpose of mouse brain irradiation. Methods: A mouse head holder was designed for a microCT couch using CAD software and printed in an acrylic based material. Ten mice received half-brain radiation while positioned in the 3D-printed head holder. Animal placement was achieved using on-board image guidance and computerized asymmetric collimators. To evaluate the precision of beam localization for half-brain irradiation, mice were sacrificed approximately 30 min after treatment and brain sections were stained for γ-H2AX, a marker for DNA breaks. The distance and angle of the γ-H2AX radiation beam border to longitudinal fissure were measured on histological samples. Animals were monitored for any possible trauma from the device. Results: Visualization of the radiation beam on ex vivo brain sections with γ-H2AX immunohistochemical staining showed a sharp radiation field within the tissue. Measurements showed a mean irradiation targeting error of 0.14 ± 0.09 mm (standard deviation). Rotation between the beam axis and mouse head was 1.2° ± 1.0° (standard deviation). The immobilization device was easily adjusted to accommodate different sizes of mice. No signs of trauma to the mice were observed from the use of tooth block and ear bars. Conclusions: The authors designed and built a novel 3D-printed mouse head holder with many desired features for accurate and reproducible radiation targeting. The 3D printing technology was found to be practical and economical for producing a small animal imaging and radiation restraint device and allows for customization for study specific needs.

  14. Correction technique for cascade gammas in I-124 imaging on a fully-3D, Time-of-Flight PET Scanner.

    PubMed

    Surti, Suleman; Scheuermann, Ryan; Karp, Joel S

    2009-06-01

    It has been shown that I-124 PET imaging can be used for accurate dose estimation in radio-immunotherapy techniques. However, I-124 is not a pure positron emitter, leading to two types of coincidence events not typically encountered: increased random coincidences due to non-annihilation cascade photons, and true coincidences between an annihilation photon and primarily a coincident 602 keV cascade gamma (true coincidence gamma-ray background). The increased random coincidences are accurately estimated by the delayed window technique. Here we evaluate the radial and time distributions of the true coincidence gamma-ray background in order to correct and accurately estimate lesion uptake for I-124 imaging in a time-of-flight (TOF) PET scanner. We performed measurements using a line source of activity placed in air and a water-filled cylinder, using F-18 and I-124 radio-isotopes. Our results show that the true coincidence gamma-ray backgrounds in I-124 have a uniform radial distribution, while the time distribution is similar to the scattered annihilation coincidences. As a result, we implemented a TOF-extended single scatter simulation algorithm with a uniform radial offset in the tail-fitting procedure for accurate correction of TOF data in I-124 imaging. Imaging results show that the contrast recovery for large spheres in a uniform activity background is similar in F-18 and I-124 imaging. There is some degradation in contrast recovery for small spheres in I-124, which is explained by the increased positron range, and reduced spatial resolution, of I-124 compared to F-18. Our results show that it is possible to perform accurate TOF based corrections for I-124 imaging.

  15. Time efficiency and diagnostic agreement of 2-D versus 3-D ultrasound acquisition of the neonatal brain.

    PubMed

    Romero, Javier M; Madan, Neil; Betancur, Ilda; Ciobanu, Adrian; Murphy, Erin; McCullough, Danielle; Grant, P Ellen

    2014-08-01

    The purpose of this study was to compare acquisition time efficiency and diagnostic agreement of neonatal brain ultrasound (US) scans obtained with a 3-D volume US acquisition protocol and the conventional 2-D acquisition protocol. Ninety-one consecutive premature neonatal brain ultrasound scans were prospectively performed on 59 neonates with the conventional 2-D acquisition protocol. Immediately after the 2-D study, a coronal 3-D ultrasound volume was acquired and later reconstructed into axial and sagittal planes. All 59 neonates were imaged in the neonatal intensive care unit to rule out intracranial hemorrhage. Total time for 2-D and 3-D acquisition protocols was recorded, and a two-tailed t-test was used to determine if study durations differed significantly. One pediatric neuroradiologist reviewed the reformatted 3-D images, tomographic ultrasound images. Results were compared with the clinical interpretation of the 2-D conventional study. The mean scanning time for the 2-D US acquisition protocol was 10.56 min (standard deviation [SD] = 7.11), and that for the 3-D volume US acquisition protocol was 1.48 min (SD = 0.59) (p ≤ 0.001). Inter-observer agreement revealed k values of 0.84 for hydrocephalus, 0.80 for germinal matrix hemorrhage/intraventricular hemorrhage, 0.74 for periventricular leukomalacia and 0.91 for subdural collection, hence near-perfect to substantial agreement between imaging protocols. There was a significant decrease in acquisition time for the 3-D volume ultrasound acquisition protocol compared with the conventional 2-D US protocol (p = <0.001), without compromising the diagnostic quality compared with a conventional 2-D US imaging protocol.

  16. 3D watershed-based segmentation of internal structures within MR brain images

    NASA Astrophysics Data System (ADS)

    Bueno, Gloria; Musse, Olivier; Heitz, Fabrice; Armspach, Jean-Paul

    2000-06-01

    In this paper an image-based method founded on mathematical morphology is presented in order to facilitate the segmentation of cerebral structures on 3D magnetic resonance images (MRIs). The segmentation is described as an immersion simulation, applied to the modified gradient image, modeled by a generated 3D region adjacency graph (RAG). The segmentation relies on two main processes: homotopy modification and contour decision. The first one is achieved by a marker extraction stage where homogeneous 3D regions are identified in order to attribute an influence zone only to relevant minima of the image. This stage uses contrasted regions from morphological reconstruction and labeled flat regions constrained by the RAG. The goal of the decision stage is to precisely locate the contours of regions detected by the marker extraction. This decision is performed by a 3D extension of the watershed transform. Upon completion of the segmentation, the outcome of the preceding process is presented to the user for manual selection of the structures of interest (SOI). Results of this approach are described and illustrated with examples of segmented 3D MRIs of the human head.

  17. Measuring dopamine release in the human brain with PET

    SciTech Connect

    Volkow, N.D. |; Fowler, J.S.; Logan, J.; Wang, G.J.

    1995-12-01

    The dopamine system is involved in the regulation of brain regions that subserve motor, cognitive and motivational behaviors. Disruptions of dopamine (DA) function have ben implicated in neurological and psychiatric illnesses including substance abuse as well as on some of the deficits associated with aging of the human brain. This has made the DA system an important topic in research in the neurosciences and neuroimaging as well as an important molecular target for drug development. Positron Emission Tomography (PET), was the first technology that enabled direct measurement of components of the DA system in the living human brain. Imaging studies of DA in the living brain have been indirect, relying on the development of radiotracers to label DA receptors, DA transporters, compounds which have specificity for the enzymes which degrade synaptic DA. Additionally, through the use of tracers that provide information on regional brain activity (ie brain glucose metabolism and cerebral blood flow) and of appropriate pharmacological interventions, it has been possible to assess the functional consequences of changes in brain DA activity. DA specific ligands have been useful in the evaluation of patients with neuropsychiatric illnesses as well as to investigate receptor blockade by antipsychotic drugs. A limitation of strategies that rely on the use of DA specific ligands is that the measures do not necessarily reflect the functional state of the dopaminergic system and that there use to study the effects of drugs is limited to the investigation of receptor or transporter occupancy. Newer strategies have been developed in an attempt to provide with information on dopamine release and on the functional responsivity of the DA system in the human brain. This in turn allows to investigate the effects of pharmacological agent in an analogous way to what is done with microdialysis techniques.

  18. 3D ultrasound in assessment of growth and development of frontal lobes in children with perinatal brain injury.

    PubMed

    Liu, Yunfeng; Zhou, Congle; Wang, Hongmei; Tang, Zezhong; Ding, Haiyan

    2009-01-01

    To investigate the functions of cranial 3D ultrasound in the assessment of growth and development of the volume of frontal lobes in children with perinatal brain injury, 226 neonates of different gestational ages and 86 full term with perinatal brain injury were selected as subjects. The volume of frontal lobe of neonate increased with gestational age within 7 days after birth (r=0.676, P<0.05). The volume of frontal lobe in the 33 children with serious brain injury was lower than that in the control group at 1 month and the difference was significant at 3 and 6 months (P<0.01). There was a correlation between the long-term nervous system dysplasia and the slow increase of frontal lobe volume. The volume of frontal lobe increases with gestational age. The brain injury during the perinatal period affects the development of frontal lobe and is related with neural dysplasia. 3D ultrasound is useful for evaluating the normal and abnormal brain development.

  19. 3D high spectral and spatial resolution imaging of ex vivo mouse brain

    SciTech Connect

    Foxley, Sean Karczmar, Gregory S.; Domowicz, Miriam; Schwartz, Nancy

    2015-03-15

    Purpose: Widely used MRI methods show brain morphology both in vivo and ex vivo at very high resolution. Many of these methods (e.g., T{sub 2}{sup *}-weighted imaging, phase-sensitive imaging, or susceptibility-weighted imaging) are sensitive to local magnetic susceptibility gradients produced by subtle variations in tissue composition. However, the spectral resolution of commonly used methods is limited to maintain reasonable run-time combined with very high spatial resolution. Here, the authors report on data acquisition at increased spectral resolution, with 3-dimensional high spectral and spatial resolution MRI, in order to analyze subtle variations in water proton resonance frequency and lineshape that reflect local anatomy. The resulting information compliments previous studies based on T{sub 2}{sup *} and resonance frequency. Methods: The proton free induction decay was sampled at high resolution and Fourier transformed to produce a high-resolution water spectrum for each image voxel in a 3D volume. Data were acquired using a multigradient echo pulse sequence (i.e., echo-planar spectroscopic imaging) with a spatial resolution of 50 × 50 × 70 μm{sup 3} and spectral resolution of 3.5 Hz. Data were analyzed in the spectral domain, and images were produced from the various Fourier components of the water resonance. This allowed precise measurement of local variations in water resonance frequency and lineshape, at the expense of significantly increased run time (16–24 h). Results: High contrast T{sub 2}{sup *}-weighted images were produced from the peak of the water resonance (peak height image), revealing a high degree of anatomical detail, specifically in the hippocampus and cerebellum. In images produced from Fourier components of the water resonance at −7.0 Hz from the peak, the contrast between deep white matter tracts and the surrounding tissue is the reverse of the contrast in water peak height images. This indicates the presence of a shoulder in

  20. Comparing 3D Gyrification Index and area-independent curvature-based measures in quantifying neonatal brain folding

    NASA Astrophysics Data System (ADS)

    Rodriguez-Carranza, Claudia E.; Mukherjee, P.; Vigneron, Daniel; Barkovich, James; Studholme, Colin

    2007-03-01

    In this work we compare 3D Gyrification Index and our recently proposed area-independent curvature-based surface measures [26] for the in-vivo quantification of brain surface folding in clinically acquired neonatal MR image data. A meaningful comparison of gyrification across brains of different sizes and their subregions will only be possible through the quantification of folding with measures that are independent of the area of the region of analysis. This work uses a 3D implementation of the classical Gyrification Index, a 2D measure that quantifies folding based on the ratio of the inner and outer contours of the brain and which has been used to study gyral patterns in adults with schizophrenia, among other conditions. The new surface curvature-based measures and the 3D Gyrification Index were calculated on twelve premature infants (age 28-37 weeks) from which surfaces of cerebrospinal fluid/gray matter (CSF/GM) interface and gray matter/white matter (GM/WM) interface were extracted. Experimental results show that our measures better quantify folding on the CSF/GM interface than Gyrification Index, and perform similarly on the GM/WM interface.

  1. In vivo MEMRI characterization of brain metastases using a 3D Look-Locker T1-mapping sequence

    PubMed Central

    Castets, Charles R.; Koonjoo, Néha; Hertanu, Andreea; Voisin, Pierre; Franconi, Jean-Michel; Miraux, Sylvain; Ribot, Emeline J.

    2016-01-01

    Although MEMRI (Manganese Enhanced MRI) informations were obtained on primary tumors in small animals, MEMRI data on metastases are lacking. Thus, our goal was to determine if 3D Look-Locker T1 mapping was an efficient method to evaluate Mn ions transport in brain metastases in vivo. The high spatial resolution in 3D (156 × 156 × 218 μm) of the sequence enabled to detect metastases of 0.3 mm3. In parallel, the T1 quantitation enabled to distinguish three populations of MDA-MB-231 derived brain metastases after MnCl2 intravenous injection: one with a healthy blood-tumor barrier that did not internalize Mn2+ ions, and two others, which T1 shortened drastically by 54.2% or 24%. Subsequent scans of the mice, enabled by the fast acquisition (23 min), demonstrated that these T1 reached back their pre-injection values in 24 h. Contrarily to metastases, the T1 of U87-MG glioma remained 26.2% shorter for one week. In vitro results supported the involvement of the Transient Receptor Potential channels and the Calcium-Sensing Receptor in the uptake and efflux of Mn2+ ions, respectively. This study highlights the ability of the 3D Look-Locker T1 mapping sequence to study heterogeneities (i) amongst brain metastases and (ii) between metastases and glioma regarding Mn transport. PMID:27995976

  2. Clinical applications of choline PET/CT in brain tumors.

    PubMed

    Giovannini, Elisabetta; Lazzeri, Patrizia; Milano, Amalia; Gaeta, Maria Chiara; Ciarmiello, Andrea

    2015-01-01

    Malignant gliomas and metastatic tumors are the most common forms of brain tumors. From a clinical perspective, neuroimaging plays a significant role, in diagnosis, treatment planning, and follow-up. To date MRI is considered the current clinical gold standard for imaging, however, despite providing superior structural detail it features poor specificity in identifying viable tumors in brain treated with surgery, radiation, or chemotherapy. In the last years functional neuroimaging has become largely widespread thanks to the use of molecular tracers employed in cellular metabolism which has significantly improved the management of patients with brain tumors, especially in the post-treatment phase. Despite the considerable progress of molecular imaging in oncology its use in the diagnosis of brain tumors is still limited by a few wellknown technical problems. Because 18F-FDG, the most common radiotracer used in oncology, is avidly accumulated by normal cortex, the low tumor/background signal ratio makes it difficult to distinguish the tumor from normal surrounding tissues. By contrast, radiotracers with higher specificity for the tumor are labeled with a short half-life isotopes which restricts their use to those centers equipped with a cyclotron and radiopharmacy facility. 11C-choline has been reported as a suitable tracer for neuroimaging application. The recent availability of choline labeled with a long half-life radioisotope as 18F increases the possibility of studying this tracer's potential role in the staging of brain tumors. The present review focuses on the possible clinical applications of PET/CT with choline tracers in malignant brain tumors and brain metastases, with a special focus on malignant gliomas.

  3. Characterization of a sub-assembly of 3D position sensitive cadmium zinc telluride detectors and electronics from a sub-millimeter resolution PET system

    NASA Astrophysics Data System (ADS)

    Abbaszadeh, Shiva; Gu, Yi; Reynolds, Paul D.; Levin, Craig S.

    2016-09-01

    Cadmium zinc telluride (CZT) offers key advantages for small animal positron emission tomography (PET), including high spatial and energy resolution and simple metal deposition for fabrication of very small pixel arrays. Previous studies have investigated the intrinsic spatial, energy, and timing resolution of an individual sub-millimeter resolution CZT detector. In this work we present the first characterization results of a system of these detectors. The 3D position sensitive dual-CZT detector module and readout electronics developed in our lab was scaled up to complete a significant portion of the final PET system. This sub-system was configured as two opposing detection panels containing a total of twelve 40~\\text{mm}× 40~\\text{mm}× 5 mm monolithic CZT crystals for proof of concept. System-level characterization studies, including optimizing the trigger threshold of each channel’s comparators, were performed. 68Ge and 137Cs radioactive isotopes were used to characterize the energy resolution of all 468 anode channels in the sub-system. The mean measured global 511 keV photopeak energy resolution over all anodes was found to be 7.35+/- 1.75 % FWHM after correction for photon interaction depth-dependent signal variation. The measured global time resolution was 37 ns FWHM, a parameter to be further optimized, and the intrinsic spatial resolution was 0.76 mm FWHM.

  4. Markerless rat head motion tracking using structured light for brain PET imaging of unrestrained awake small animals

    NASA Astrophysics Data System (ADS)

    Miranda, Alan; Staelens, Steven; Stroobants, Sigrid; Verhaeghe, Jeroen

    2017-03-01

    Preclinical positron emission tomography (PET) imaging in small animals is generally performed under anesthesia to immobilize the animal during scanning. More recently, for rat brain PET studies, methods to perform scans of unrestrained awake rats are being developed in order to avoid the unwanted effects of anesthesia on the brain response. Here, we investigate the use of a projected structure stereo camera to track the motion of the rat head during the PET scan. The motion information is then used to correct the PET data. The stereo camera calculates a 3D point cloud representation of the scene and the tracking is performed by point cloud matching using the iterative closest point algorithm. The main advantage of the proposed motion tracking is that no intervention, e.g. for marker attachment, is needed. A manually moved microDerenzo phantom experiment and 3 awake rat [18F]FDG experiments were performed to evaluate the proposed tracking method. The tracking accuracy was 0.33 mm rms. After motion correction image reconstruction, the microDerenzo phantom was recovered albeit with some loss of resolution. The reconstructed FWHM of the 2.5 and 3 mm rods increased with 0.94 and 0.51 mm respectively in comparison with the motion-free case. In the rat experiments, the average tracking success rate was 64.7%. The correlation of relative brain regional [18F]FDG uptake between the anesthesia and awake scan reconstructions was increased from on average 0.291 (not significant) before correction to 0.909 (p  <  0.0001) after motion correction. Markerless motion tracking using structured light can be successfully used for tracking of the rat head for motion correction in awake rat PET scans.

  5. Brain PET metabolic abnormalities in a case of varicella-zoster virus encephalitis.

    PubMed

    Coiffard, Benjamin; Guedj, Eric; Daumas, Aurélie; Leveque, Pierre; Villani, Patrick

    2014-09-01

    The role of brain 18F-FDG PET in the diagnostic evaluation of encephalitis has been recently suggested, especially in limbic encephalitis, but descriptions are mainly limited to small case reports. However, the evaluation of cerebral metabolism by 18F-FDG PET has never been described for varicella-zoster virus encephalitis. We report the first case of varicella-zoster virus encephalitis in which 18F-FDG PET revealed brain metabolic abnormalities. Brain metabolic PET imaging was analyzed by comparing the patient's brain 18F-FDG PET scans to that of 12 healthy subjects. Compared with healthy subjects, significant hypometabolism and hypermetabolism were found and evolved over time with treatment.

  6. Brain tissue segmentation in PET-CT images using probabilistic atlas and variational Bayes inference.

    PubMed

    Xia, Yong; Wang, Jiabin; Eberl, Stefan; Fulham, Michael; Feng, David Dagan

    2011-01-01

    PET-CT provides aligned anatomical (CT) and functional (PET) images in a single scan, and has the potential to improve brain PET image segmentation, which can in turn improve quantitative clinical analyses. We propose a statistical segmentation algorithm that incorporates the prior anatomical knowledge represented by probabilistic brain atlas into the variational Bayes inference to delineate gray matter (GM), white matter (WM) and cerebrospinal fluid (CSF) in brain PET-CT images. Our approach adds an additional novel aspect by allowing voxels to have variable and adaptive prior probabilities of belonging to each class. We compared our algorithm to the segmentation approaches implemented in the expectation maximization segmentation (EMS) and statistical parametric mapping (SPM8) packages in 26 clinical cases. The results show that our algorithm improves the accuracy of brain PET-CT image segmentation.

  7. Brain shaving: adaptive detection for brain PET data

    NASA Astrophysics Data System (ADS)

    Grecchi, Elisabetta; Doyle, Orla M.; Bertoldo, Alessandra; Pavese, Nicola; Turkheimer, Federico E.

    2014-05-01

    The intricacy of brain biology is such that the variation of imaging end-points in health and disease exhibits an unpredictable range of spatial distributions from the extremely localized to the very diffuse. This represents a challenge for the two standard approaches to analysis, the mass univariate and the multivariate that exhibit either strong specificity but not as good sensitivity (the former) or poor specificity and comparatively better sensitivity (the latter). In this work, we develop an analytical methodology for positron emission tomography that operates an extraction (‘shaving’) of coherent patterns of signal variation while maintaining control of the type I error. The methodology operates two rotations on the image data, one local using the wavelet transform and one global using the singular value decomposition. The control of specificity is obtained by using the gap statistic that selects, within each eigenvector, a subset of significantly coherent elements. Face-validity of the algorithm is demonstrated using a paradigmatic data-set with two radiotracers, [11C]-raclopride and [11C]-(R)-PK11195, measured on the same Huntington's disease patients, a disorder with a genetic based diagnosis. The algorithm is able to detect the two well-known separate but connected processes of dopamine neuronal loss (localized in the basal ganglia) and neuroinflammation (diffusive around the whole brain). These processes are at the two extremes of the distributional envelope, one being very sparse and the latter being perfectly Gaussian and they are not adequately detected by the univariate and the multivariate approaches.

  8. 3D volume reconstruction of a mouse brain histological sections using warp filtering

    SciTech Connect

    Ju, Tao; Warren, Joe; Carson, James P.; Bello, Musodiq; Kakadiaris, Ioannis; Chiu, Wah; Thaller, Christina; Eichele, Gregor

    2006-09-30

    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.

  9. 3D volume reconstruction of a mouse brain from histological sections using warp filtering.

    PubMed

    Ju, Tao; Warren, Joe; Carson, James; Bello, Musodiq; Kakadiaris, Ioannis; Chiu, Wah; Thaller, Christina; Eichele, Gregor

    2006-09-30

    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.

  10. Perceptual integration for qualitatively different 3-D cues in the human brain.

    PubMed

    Dövencioğlu, Dicle; Ban, Hiroshi; Schofield, Andrew J; Welchman, Andrew E

    2013-09-01

    The visual system's flexibility in estimating depth is remarkable: We readily perceive 3-D structure under diverse conditions from the seemingly random dots of a "magic eye" stereogram to the aesthetically beautiful, but obviously flat, canvasses of the Old Masters. Yet, 3-D perception is often enhanced when different cues specify the same depth. This perceptual process is understood as Bayesian inference that improves sensory estimates. Despite considerable behavioral support for this theory, insights into the cortical circuits involved are limited. Moreover, extant work tested quantitatively similar cues, reducing some of the challenges associated with integrating computationally and qualitatively different signals. Here we address this challenge by measuring fMRI responses to depth structures defined by shading, binocular disparity, and their combination. We quantified information about depth configurations (convex "bumps" vs. concave "dimples") in different visual cortical areas using pattern classification analysis. We found that fMRI responses in dorsal visual area V3B/KO were more discriminable when disparity and shading concurrently signaled depth, in line with the predictions of cue integration. Importantly, by relating fMRI and psychophysical tests of integration, we observed a close association between depth judgments and activity in this area. Finally, using a cross-cue transfer test, we found that fMRI responses evoked by one cue afford classification of responses evoked by the other. This reveals a generalized depth representation in dorsal visual cortex that combines qualitatively different information in line with 3-D perception.

  11. Characterization of a high resolution and high sensitivity pre-clinical PET scanner with 3D event reconstruction

    NASA Astrophysics Data System (ADS)

    Rissi, M.; Bolle, E.; Völgyes, D.; Bjaalie, J. G.; Dorholt, O.; Hines, K. E.; Røhne, O.; Skretting, A.; Stapnes, S.

    2012-12-01

    COMPET is a preclinical PET scanner aiming towards a high sensitivity, a high resolution and MRI compatibility by implementing a novel detector geometry. In this approach, long scintillating LYSO crystals are used to absorb the γ-rays. To determine the point of interaction (POI) between γ-ray and crystal, the light exiting the crystals on one of the long sides is collected with wavelength shifters (WLS) perpendicularly arranged to the crystals. This concept has two main advantages: (1) The parallax error is reduced to a minimum and is equal for the whole field of view (FOV). (2) The POI and its energy deposit is known in all three dimension with a high resolution, allowing for the reconstruction of Compton scattered γ-rays. Point (1) leads to a uniform point source resolution (PSR) distribution over the whole FOV, and also allows to place the detector close to the object being imaged. Both points (1) and (2) lead to an increased sensitivity and allow for both high resolution and sensitivity at the same time, while keeping a low number of readout channels. In total, COMPET incorporates 1080 readout channels (600 crystals, 480 WLS). It has an axial FOV of 80 mm and adjustable bore opening between 30 mm and 80 mm. It consists of four modules with five layers each. Simulations show a PSR of below 1 mm in the transaxial plane and a sensitivity of up to 16% in the center of the FOV. The readout is based on time over threshold signals, sampled with an FPGA, which allows for the measurement of high event rates at the order of mega-counts per seconds. Its compact design and compatibility to high magnetic fields will allow to use it as an insert for an already existing MRI scanner. A first semi-layer with 12 WLS and 10 LYSO crystal was built and connected to the COMPET readout system. Coincidence data between this module and a tagger crystal using a small Ge-68 and a 60 MBq F-18 source was taken.

  12. Evaluation of a novel PDE10A PET radioligand, [(11) C]T-773, in nonhuman primates: brain and whole body PET and brain autoradiography.

    PubMed

    Takano, Akihiro; Stepanov, Vladimir; Gulyás, Balázs; Nakao, Ryuji; Amini, Nahid; Miura, Shotaro; Kimura, Haruhide; Taniguchi, Takahiko; Halldin, Christer

    2015-07-01

    Phosphodiesterase 10A (PDE10A) is considered to be a key target for the treatment of several neuropsychiatric diseases. The characteristics of [(11) C]T-773, a novel positron emission tomography (PET) radioligand with high binding affinity and selectivity for PDE10A, were evaluated in autoradiography and in nonhuman primate (NHP) PET. Brain PET measurements were performed under baseline conditions and after administration of a selective PDE10A inhibitor, MP-10. Total distribution volume (VT ) and binding potential (BPND ) were calculated using various kinetic models. Whole body PET measurements were performed to calculate the effective dose of [(11) C]T-773. Autoradiography studies in postmortem human and monkey brain sections showed high accumulation of [(11) C]T-773 in the striatum and substantia nigra which was blocked by MP-10. Brain PET showed high accumulation of [(11) C]T-773 in the striatum, and the data could be fitted using a two tissue compartment model. BPND was approximately 1.8 in the putamen when the cerebellum was used as the reference region. Approximately 70% of PDE10A binding was occupied by 1.8 mg/kg of MP-10. Whole body PET showed high accumulation of [(11) C]T-773 in the liver, kidney, heart, and brain in the initial phase. The radioligand was partly excreted via bile and the gastrointestinal tract, and partly excreted through the urinary tract. The calculated effective dose was 0.007 mSv/MBq. In conclusion, [(11) C]T-773 was demonstrated to be a promising PET radioligand for PDE10A with favorable brain kinetics. Dosimetry results support multiple PET measurements per person in human studies. Further research is required with [(11) C]T-773 in order to test the radioligand's potential clinical applications.

  13. Multi-atlas attenuation correction supports full quantification of static and dynamic brain PET data in PET-MR.

    PubMed

    Merida, Ines; Reilhac, Anthonin; Redoute, Jerome; Heckemann, Rolf; Costes, Nicolas; Hammers, Alexander

    2017-02-09

    Introduction In simultaneous PET-MR, attenuation maps are not directly available. Essential for absolute radioactivity quantification, they need to be derived from MR or PET data to correct for gamma photon attenuation by the imaged object. We evaluate a multi-atlas attenuation correction method for brain imaging (MaxProb) on static [18F]FDG PET and, for the first time, on dynamic PET, using the serotoninergic tracer [18F]MPPF. Methods A database of 40 MR/CT image pairs (atlases) was used. The MaxProb method synthesises subject-specific pseudo-CTs by registering each atlas to the target subject space. Atlas CT intensities are then fused via label propagation and majority voting. Here, we compared these pseudo-CTs with the real CTs in a leave-one-out design, contrasting the MaxProb approach with a simplified single-atlas method (SingleAtlas). We evaluated the impact of pseudo-CT accuracy on reconstructed PET images, compared to PET data reconstructed with real CT, at the regional and voxel levels for the following: radioactivity images; time-activity curves; and kinetic parameters (non-displaceable binding potential, BPND). Results On static [18F]FDG, the mean bias for MaxProb ranged between 0 and 1% for 73 out of 84 regions assessed, and exceptionally peaked at 2.5% for only one region. Statistical parametric map analysis of MaxProb-corrected PET data showed significant differences in less than 0.02% of the brain volume, whereas SingleAtlas-corrected data showed significant differences in 20% of the brain volume. On dynamic [18F]MPPF, most regional errors on BPND ranged from -1 to +3% (maximum bias 5%) for the MaxProb method. With SingleAtlas, errors were larger and had higher variability in most regions. PET quantification bias increased over the duration of the dynamic scan for SingleAtlas, but not for MaxProb. We show that this effect is due to the interaction of the spatial tracer-distribution heterogeneity variation over time with the degree of accuracy of the

  14. Multi-atlas attenuation correction supports full quantification of static and dynamic brain PET data in PET-MR

    NASA Astrophysics Data System (ADS)

    Mérida, Inés; Reilhac, Anthonin; Redouté, Jérôme; Heckemann, Rolf A.; Costes, Nicolas; Hammers, Alexander

    2017-04-01

    In simultaneous PET-MR, attenuation maps are not directly available. Essential for absolute radioactivity quantification, they need to be derived from MR or PET data to correct for gamma photon attenuation by the imaged object. We evaluate a multi-atlas attenuation correction method for brain imaging (MaxProb) on static [18F]FDG PET and, for the first time, on dynamic PET, using the serotoninergic tracer [18F]MPPF. A database of 40 MR/CT image pairs (atlases) was used. The MaxProb method synthesises subject-specific pseudo-CTs by registering each atlas to the target subject space. Atlas CT intensities are then fused via label propagation and majority voting. Here, we compared these pseudo-CTs with the real CTs in a leave-one-out design, contrasting the MaxProb approach with a simplified single-atlas method (SingleAtlas). We evaluated the impact of pseudo-CT accuracy on reconstructed PET images, compared to PET data reconstructed with real CT, at the regional and voxel levels for the following: radioactivity images; time-activity curves; and kinetic parameters (non-displaceable binding potential, BPND). On static [18F]FDG, the mean bias for MaxProb ranged between 0 and 1% for 73 out of 84 regions assessed, and exceptionally peaked at 2.5% for only one region. Statistical parametric map analysis of MaxProb-corrected PET data showed significant differences in less than 0.02% of the brain volume, whereas SingleAtlas-corrected data showed significant differences in 20% of the brain volume. On dynamic [18F]MPPF, most regional errors on BPND ranged from -1 to  +3% (maximum bias 5%) for the MaxProb method. With SingleAtlas, errors were larger and had higher variability in most regions. PET quantification bias increased over the duration of the dynamic scan for SingleAtlas, but not for MaxProb. We show that this effect is due to the interaction of the spatial tracer-distribution heterogeneity variation over time with the degree of accuracy of the attenuation maps. This

  15. Culturing thick brain slices: an interstitial 3D microperfusion system for enhanced viability.

    PubMed

    Rambani, Komal; Vukasinovic, Jelena; Glezer, Ari; Potter, Steve M

    2009-06-15

    Brain slice preparations are well-established models for a wide spectrum of in vitro investigations in the neuroscience discipline. However, these investigations are limited to acute preparations or thin organotypic culture preparations due to the lack of a successful method that allows culturing of thick organotypic brain slices. Thick brain slice cultures suffer necrosis due to ischemia deep in the tissue resulting from a destroyed circulatory system and subsequent diffusion-limited supply of nutrients and oxygen. Although thin organotypic brain slice cultures can be successfully cultured using a well-established roller-tube method (a monolayer organotypic culture) (Gahwiler B H. Organotypic monolayer cultures of nervous tissue. J Neurosci Methods. 1981; 4: 329-342) or a membrane-insert method (up to 1-4 cell layers, <150 microm) (Stoppini L, Buchs PA, Muller D. A simple method for organotypic cultures of neural tissue. J Neurosci Methods 1991; 37: 173-182), these methods fail to support thick tissue preparations. A few perfusion methods (using submerged or interface/microfluidic chambers) have been reported to enhance the longevity (up to few hours) of acute slice preparations (up to 600 microm thick) (Hass HL, Schaerer B, Vosmansky M. A simple perfusion chamber for study of nervous tissue slices in vitro. J Neurosci Methods 1979; 1: 323-325; Nicoll RA, Alger BE. A simple chamber for recording from submerged brain slices. J Neurosci Methods 1981; 4: 153-156; Passeraub PA, Almeida AC, Thakor NV. Design, microfabrication and characterization of a microfluidic chamber for the perfusion of brain tissue slices. J Biomed Dev 2003; 5: 147-155). Here, we report a unique interstitial microfluidic perfusion technique to culture thick (700 microm) organotypic brain slices. The design of the custom-made microperfusion chamber facilitates laminar, interstitial perfusion of oxygenated nutrient medium throughout the tissue thickness with concomitant removal of depleted medium

  16. Segmentation of brain blood vessels using projections in 3-D CT angiography images.

    PubMed

    Babin, Danilo; Vansteenkiste, Ewout; Pizurica, Aleksandra; Philips, Wilfried

    2011-01-01

    Segmenting cerebral blood vessels is of great importance in diagnostic and clinical applications, especially in quantitative diagnostics and surgery on aneurysms and arteriovenous malformations (AVM). Segmentation of CT angiography images requires algorithms robust to high intensity noise, while being able to segment low-contrast vessels. Because of this, most of the existing methods require user intervention. In this work we propose an automatic algorithm for efficient segmentation of 3-D CT angiography images of cerebral blood vessels. Our method is robust to high intensity noise and is able to accurately segment blood vessels with high range of luminance values, as well as low-contrast vessels.

  17. Scalable fluidic injector arrays for viral targeting of intact 3-D brain circuits.

    PubMed

    Chan, Stephanie; Bernstein, Jacob; Boyden, Edward

    2010-01-21

    Our understanding of neural circuits--how they mediate the computations that subserve sensation, thought, emotion, and action, and how they are corrupted in neurological and psychiatric disorders--would be greatly facilitated by a technology for rapidly targeting genes to complex 3-dimensional neural circuits, enabling fast creation of "circuit-level transgenics." We have recently developed methods in which viruses encoding for light-sensitive proteins can sensitize specific cell types to millisecond-timescale activation and silencing in the intact brain. We here present the design and implementation of an injector array capable of delivering viruses (or other fluids) to dozens of defined points within the 3-dimensional structure of the brain (Figure. 1A, 1B). The injector array comprises one or more displacement pumps that each drive a set of syringes, each of which feeds into a polyimide/fused-silica capillary via a high-pressure-tolerant connector. The capillaries are sized, and then inserted into, desired locations specified by custom-milling a stereotactic positioning board, thus allowing viruses or other reagents to be delivered to the desired set of brain regions. To use the device, the surgeon first fills the fluidic subsystem entirely with oil, backfills the capillaries with the virus, inserts the device into the brain, and infuses reagents slowly (<0.1 microliters/min). The parallel nature of the injector array facilitates rapid, accurate, and robust labeling of entire neural circuits with viral payloads such as optical sensitizers to enable light-activation and silencing of defined brain circuits. Along with other technologies, such as optical fiber arrays for light delivery to desired sets of brain regions, we hope to create a toolbox that enables the systematic probing of causal neural functions in the intact brain. This technology may not only open up such systematic approaches to circuit-focused neuroscience in mammals, and facilitate labeling of

  18. Segmentation and quantitative evaluation of brain MRI data with a multiphase 3D implicit deformable model

    NASA Astrophysics Data System (ADS)

    Angelini, Elsa D.; Song, Ting; Mensh, Brett D.; Laine, Andrew

    2004-05-01

    Segmentation of three-dimensional anatomical brain images into tissue classes has applications in both clinical and research settings. This paper presents the implementation and quantitative evaluation of a four-phase three-dimensional active contour implemented with a level set framework for automated segmentation of brain MRIs. The segmentation algorithm performs an optimal partitioning of three-dimensional data based on homogeneity measures that naturally evolves to the extraction of different tissue types in the brain. Random seed initialization was used to speed up numerical computation and avoid the need for a priori information. This random initialization ensures robustness of the method to variation of user expertise, biased a priori information and errors in input information that could be influenced by variations in image quality. Experimentation on three MRI brain data sets showed that an optimal partitioning successfully labeled regions that accurately identified white matter, gray matter and cerebrospinal fluid in the ventricles. Quantitative evaluation of the segmentation was performed with comparison to manually labeled data and computed false positive and false negative assignments of voxels for the three organs. We report high accuracy for the two comparison cases. These results demonstrate the efficiency and flexibility of this segmentation framework to perform the challenging task of automatically extracting brain tissue volume contours.

  19. A biofidelic 3D culture model to study the development of brain cellular systems.

    PubMed

    Ren, M; Du, C; Herrero Acero, E; Tang-Schomer, M D; Özkucur, N

    2016-04-26

    Little is known about how cells assemble as systems during corticogenesis to generate collective functions. We built a neurobiology platform that consists of fetal rat cerebral cortical cells grown within 3D silk scaffolds (SF). Ivermectin (Ivm), a glycine receptor (GLR) agonist, was used to modulate cell resting membrane potential (Vmem) according to methods described in a previous work that implicated Ivm in the arrangement and connectivity of cortical cell assemblies. The cells developed into distinct populations of neuroglial stem/progenitor cells, mature neurons or epithelial-mesenchymal cells. Importantly, the synchronized electrical activity in the newly developed cortical assemblies could be recorded as local field potential (LFP) measurements. This study therefore describes the first example of the development of a biologically relevant cortical plate assembly outside of the body. This model provides i) a preclinical basis for engineering cerebral cortex tissue autografts and ii) a biofidelic 3D culture model for investigating biologically relevant processes during the functional development of cerebral cortical cellular systems.

  20. A biofidelic 3D culture model to study the development of brain cellular systems

    PubMed Central

    Ren, M.; Du, C.; Herrero Acero, E.; Tang-Schomer, M. D.; Özkucur, N.

    2016-01-01

    Little is known about how cells assemble as systems during corticogenesis to generate collective functions. We built a neurobiology platform that consists of fetal rat cerebral cortical cells grown within 3D silk scaffolds (SF). Ivermectin (Ivm), a glycine receptor (GLR) agonist, was used to modulate cell resting membrane potential (Vmem) according to methods described in a previous work that implicated Ivm in the arrangement and connectivity of cortical cell assemblies. The cells developed into distinct populations of neuroglial stem/progenitor cells, mature neurons or epithelial-mesenchymal cells. Importantly, the synchronized electrical activity in the newly developed cortical assemblies could be recorded as local field potential (LFP) measurements. This study therefore describes the first example of the development of a biologically relevant cortical plate assembly outside of the body. This model provides i) a preclinical basis for engineering cerebral cortex tissue autografts and ii) a biofidelic 3D culture model for investigating biologically relevant processes during the functional development of cerebral cortical cellular systems. PMID:27112667

  1. Culturing thick brain slices: An interstitial 3D microperfusion system for enhanced viability

    PubMed Central

    Rambani, Komal; Vukasinovic, Jelena; Glezer, Ari; Potter, Steve M.

    2009-01-01

    Brain slice preparations are well-established models for a wide spectrum of in vitro investigations in the neuroscience discipline. However, these investigations are limited to acute preparations or thin organotypic culture preparations due to the lack of a successful method that allows culturing of thick organotypic brain slices. Thick brain slice cultures suffer necrosis due to ischemia deep in the tissue resulting from a destroyed circulatory system and subsequent diffusion-limited supply of nutrients and oxygen. Although thin organotypic brain slice cultures can be successfully cultured using a well established roller tube method (a monolayer organotypic culture) (Gahwiler B H, 1981) or a membrane insert method (up to 1–4 cell layers, <150μm)(Stoppini L et al., 1991), these methods fail to support thick tissue preparations. A few perfusion methods (using submerged or interface/microfluidic chambers) have been reported to enhance the longevity (up to few hours) of acute slice preparations (up to 600μm thick) (Hass H L et al., 1979; Nicoll R A and Alger B E, 1981; Passeraub P A et al., 2003). Here, we report a unique interstitial microfluidic perfusion technique to culture thick (700μm) organotypic brain slices. The design of the custom-made micro-perfusion chamber facilitates laminar, interstitial perfusion of oxygenated nutrient medium throughout the tissue thickness with concomitant removal of depleted medium and catabolites. We examined the utility of this perfusion method to enhance the viability of the thick organotypic brain slice cultures after 2 days and 5 days in vitro (DIV). We investigated the range of amenable flow rates that enhance the viability of 700μm thick organotypic brain slices compared to the unperfused control cultures. Our perfusion method allows up to 84.6% viability (P<0.01) and up to 700μm thickness, even after 5 DIV. Our results also confirm that these cultures are functionally active and have their in vivo cytoarchitecture

  2. 3D shape analysis of the brain's third ventricle using a midplane encoded symmetric template model

    PubMed Central

    Kim, Jaeil; Valdés Hernández, Maria del C.; Royle, Natalie A.; Maniega, Susana Muñoz; Aribisala, Benjamin S.; Gow, Alan J.; Bastin, Mark E.; Deary, Ian J.; Wardlaw, Joanna M.; Park, Jinah

    2016-01-01

    Background Structural changes of the brain's third ventricle have been acknowledged as an indicative measure of the brain atrophy progression in neurodegenerative and endocrinal diseases. To investigate the ventricular enlargement in relation to the atrophy of the surrounding structures, shape analysis is a promising approach. However, there are hurdles in modeling the third ventricle shape. First, it has topological variations across individuals due to the inter-thalamic adhesion. In addition, as an interhemispheric structure, it needs to be aligned to the midsagittal plane to assess its asymmetric and regional deformation. Method To address these issues, we propose a model-based shape assessment. Our template model of the third ventricle consists of a midplane and a symmetric mesh of generic shape. By mapping the template's midplane to the individuals’ brain midsagittal plane, we align the symmetric mesh on the midline of the brain before quantifying the third ventricle shape. To build the vertex-wise correspondence between the individual third ventricle and the template mesh, we employ a minimal-distortion surface deformation framework. In addition, to account for topological variations, we implement geometric constraints guiding the template mesh to have zero width where the inter-thalamic adhesion passes through, preventing vertices crossing between left and right walls of the third ventricle. The individual shapes are compared using a vertex-wise deformity from the symmetric template. Results Experiments on imaging and demographic data from a study of aging showed that our model was sensitive in assessing morphological differences between individuals in relation to brain volume (i.e. proxy for general brain atrophy), gender and the fluid intelligence at age 72. It also revealed that the proposed method can detect the regional and asymmetrical deformation unlike the conventional measures: volume (median 1.95 ml, IQR 0.96 ml) and width of the third

  3. Impact of metal artefacts due to EEG electrodes in brain PET/CT imaging

    NASA Astrophysics Data System (ADS)

    Lemmens, Catherine; Montandon, Marie-Louise; Nuyts, Johan; Ratib, Osman; Dupont, Patrick; Zaidi, Habib

    2008-08-01

    The goal of this study is to investigate the impact of electroencephalogram (EEG) electrodes on the visual quality and quantification of 18F-FDG PET images in neurological PET/CT examinations. For this purpose, the scans of 20 epilepsy patients with EEG monitoring were used. The CT data were reconstructed with filtered backprojection (FBP) and with a metal artefact reduction (MAR) algorithm. Both data sets were used for CT-based attenuation correction (AC) of the PET data. Also, a calculated AC (CALC) technique was considered. A volume of interest (VOI)-based analysis and a voxel-based quantitative analysis were performed to compare the different AC methods. Images were also evaluated visually by two observers. It was shown with simulations and phantom measurements that from the considered AC methods, the MAR-AC can be used as the reference in this setting. The visual assessment of PET images showed local hot spots outside the brain corresponding to the locations of the electrodes when using FBP-AC. In the brain, no abnormalities were observed. The quantitative analysis showed a very good correlation between PET-FBP-AC and PET-MAR-AC, with a statistically significant positive bias in the PET-FBP-AC images of about 5-7% in most brain voxels. There was also good correlation between PET-CALC-AC and PET-MAR-AC, but in the PET-CALC-AC images, regions with both a significant positive and negative bias were observed. EEG electrodes give rise to local hot spots outside the brain and a positive quantification bias in the brain. However, when diagnosis is made by mere visual assessment, the presence of EEG electrodes does not seem to alter the diagnosis. When quantification is performed, the bias becomes an issue especially when comparing brain images with and without EEG monitoring.

  4. SU-E-J-141: Activity-Equivalent Path Length Approach for the 3D PET-Based Dose Reconstruction in Proton Therapy

    SciTech Connect

    Attili, A; Vignati, A; Giordanengo, S; Kraan, A; Dalmasso, F; Battistoni, G

    2015-06-15

    Purpose: Ion beam therapy is sensitive to uncertainties from treatment planning and dose delivery. PET imaging of induced positron emitter distributions is a practical approach for in vivo, in situ verification of ion beam treatments. Treatment verification is usually done by comparing measured activity distributions with reference distributions, evaluated in nominal conditions. Although such comparisons give valuable information on treatment quality, a proper clinical evaluation of the treatment ultimately relies on the knowledge of the actual delivered dose. Analytical deconvolution methods relating activity and dose have been studied in this context, but were not clinically applied. In this work we present a feasibility study of an alternative approach for dose reconstruction from activity data, which is based on relating variations in accumulated activity to tissue density variations. Methods: First, reference distributions of dose and activity were calculated from the treatment plan and CT data. Then, the actual measured activity data were cumulatively matched with the reference activity distributions to obtain a set of activity-equivalent path lengths (AEPLs) along the rays of the pencil beams. Finally, these AEPLs were used to deform the original dose distribution, yielding the actual delivered dose. The method was tested by simulating a proton therapy treatment plan delivering 2 Gy on a homogeneous water phantom (the reference), which was compared with the same plan delivered on a phantom containing inhomogeneities. Activity and dose distributions were were calculated by means of the FLUKA Monte Carlo toolkit. Results: The main features of the observed dose distribution in the inhomogeneous situation were reproduced using the AEPL approach. Variations in particle range were reproduced and the positions, where these deviations originated, were properly identified. Conclusions: For a simple inhomogeneous phantom the 3D dose reconstruction from PET

  5. Toward a 3D model of human brain development for studying gene/environment interactions.

    PubMed

    Hogberg, Helena T; Bressler, Joseph; Christian, Kimberly M; Harris, Georgina; Makri, Georgia; O'Driscoll, Cliona; Pamies, David; Smirnova, Lena; Wen, Zhexing; Hartung, Thomas

    2013-01-01

    This project aims to establish and characterize an in vitro model of the developing human brain for the purpose of testing drugs and chemicals. To accurately assess risk, a model needs to recapitulate the complex interactions between different types of glial cells and neurons in a three-dimensional platform. Moreover, human cells are preferred over cells from rodents to eliminate cross-species differences in sensitivity to chemicals. Previously, we established conditions to culture rat primary cells as three-dimensional aggregates, which will be humanized and evaluated here with induced pluripotent stem cells (iPSCs). The use of iPSCs allows us to address gene/environment interactions as well as the potential of chemicals to interfere with epigenetic mechanisms. Additionally, iPSCs afford us the opportunity to study the effect of chemicals during very early stages of brain development. It is well recognized that assays for testing toxicity in the developing brain must consider differences in sensitivity and susceptibility that arise depending on the time of exposure. This model will reflect critical developmental processes such as proliferation, differentiation, lineage specification, migration, axonal growth, dendritic arborization and synaptogenesis, which will probably display differences in sensitivity to different types of chemicals. Functional endpoints will evaluate the complex cell-to-cell interactions that are affected in neurodevelopment through chemical perturbation, and the efficacy of drug intervention to prevent or reverse phenotypes. The model described is designed to assess developmental neurotoxicity effects on unique processes occurring during human brain development by leveraging human iPSCs from diverse genetic backgrounds, which can be differentiated into different cell types of the central nervous system. Our goal is to demonstrate the feasibility of the personalized model using iPSCs derived from individuals with neurodevelopmental disorders

  6. Towards Implementing an MR-based PET Attenuation Correction Method for Neurological Studies on the MR-PET Brain Prototype

    PubMed Central

    Catana, Ciprian; van der Kouwe, Andre; Benner, Thomas; Michel, Christian J.; Hamm, Michael; Fenchel, Matthias; Fischl, Bruce; Rosen, Bruce; Schmand, Matthias; Sorensen, A. Gregory

    2013-01-01

    A number of factors have to be considered for implementing an accurate attenuation correction (AC) in a combined MR-PET scanner. In this work, some of these challenges were investigated and an AC method based entirely on the MR data obtained with a single dedicated sequence was developed and used for neurological studies performed with the MR-PET human brain scanner prototype. Methods The focus was on the bone/air segmentation problem, the bone linear attenuation coefficient selection and the RF coil positioning. The impact of these factors on the PET data quantification was studied in simulations and experimental measurements performed on the combined MR-PET scanner. A novel dual-echo ultra-short echo time (DUTE) MR sequence was proposed for head imaging. Simultaneous MR-PET data were acquired and the PET images reconstructed using the proposed MR-DUTE-based AC method were compared with the PET images reconstructed using a CT-based AC. Results Our data suggest that incorrectly accounting for the bone tissue attenuation can lead to large underestimations (>20%) of the radiotracer concentration in the cortex. Assigning a linear attenuation coefficient of 0.143 or 0.151 cm−1 to bone tissue appears to give the best trade-off between bias and variability in the resulting images. Not identifying the internal air cavities introduces large overestimations (>20%) in adjacent structures. Based on these results, the segmented CT AC method was established as the “silver standard” for the segmented MR-based AC method. Particular to an integrated MR-PET scanner, ignoring the RF coil attenuation can cause large underestimations (i.e. up to 50%) in the reconstructed images. Furthermore, the coil location in the PET field of view has to be accurately known. Good quality bone/air segmentation can be performed using the DUTE data. The PET images obtained using the MR-DUTE- and CT-based AC methods compare favorably in most of the brain structures. Conclusion An MR-DUTE-based AC

  7. Simultaneous fMRI-PET of the opioidergic pain system in human brain.

    PubMed

    Wey, Hsiao-Ying; Catana, Ciprian; Hooker, Jacob M; Dougherty, Darin D; Knudsen, Gitte M; Wang, Danny J J; Chonde, Daniel B; Rosen, Bruce R; Gollub, Randy L; Kong, Jian

    2014-11-15

    MRI and PET provide complementary information for studying brain function. While the potential use of simultaneous MRI/PET for clinical diagnostic and disease staging has been demonstrated recently; the biological relevance of concurrent functional MRI-PET brain imaging to dissect neurochemically distinct components of the blood oxygenation level dependent (BOLD) fMRI signal has not yet been shown. We obtained sixteen fMRI-PET data sets from eight healthy volunteers. Each subject participated in randomized order in a pain scan and a control (nonpainful pressure) scan on the same day. Dynamic PET data were acquired with an opioid radioligand, [(11)C]diprenorphine, to detect endogenous opioid releases in response to pain. BOLD fMRI data were collected at the same time to capture hemodynamic responses. In this simultaneous human fMRI-PET imaging study, we show co-localized responses in thalamus and striatum related to pain processing, while modality specific brain networks were also found. Co-localized fMRI and PET signal changes in the thalamus were positively correlated suggesting that pain-induced changes in opioid neurotransmission contribute a significant component of the fMRI signal change in this region. Simultaneous fMRI-PET provides unique opportunities allowing us to relate specific neurochemical events to functional hemodynamic activation and to investigate the impacts of neurotransmission on neurovascular coupling of the human brain in vivo.

  8. High-throughput, high-frequency 3-D ultrasound for in utero analysis of embryonic mouse brain development.

    PubMed

    Aristizábal, Orlando; Mamou, Jonathan; Ketterling, Jeffrey A; Turnbull, Daniel H

    2013-12-01

    With the emergence of the mouse as the predominant model system for studying mammalian brain development, in utero imaging methods are urgently required to analyze the dynamics of brain growth and patterning in mouse embryos. To address this need, we combined synthetic focusing with a high-frequency (38-MHz) annular-array ultrasound imaging system for extended depth-of-field, coded excitation for improved penetration and respiratory-gated transmit/receive. This combination allowed non-invasive in utero acquisition of motion-free 3-D data from individual embryos in approximately 2 min, and data from four or more embryos in a pregnant mouse in less than 30 min. Data were acquired from 148 embryos spanning 5 d of early to mid-gestational stages of brain development. The results indicated that brain anatomy and cerebral vasculature can be imaged with this system and that quantitative analyses of segmented cerebral ventricles can be used to characterize volumetric changes associated with mouse brain development.

  9. The effect of activity outside the field of view on image quality for a 3D LSO-based whole body PET/CT scanner.

    PubMed

    Matheoud, R; Secco, C; Della Monica, P; Leva, L; Sacchetti, G; Inglese, E; Brambilla, M

    2009-10-07

    The purpose of this study was to quantify the influence of outside field of view (FOV) activity concentration (A(c)(,out)) on the noise equivalent count rate (NECR), scatter fraction (SF) and image quality of a 3D LSO whole-body PET/CT scanner. The contrast-to-noise ratio (CNR) was the figure of merit used to characterize the image quality of PET scans. A modified International Electrotechnical Commission (IEC) phantom was used to obtain SF and counting rates similar to those found in average patients. A scatter phantom was positioned at the end of the modified IEC phantom to simulate an activity that extends beyond the scanner. The modified IEC phantom was filled with (18)F (11 kBq mL(-1)) and the spherical targets, with internal diameter (ID) ranging from 10 to 37 mm, had a target-to-background ratio of 10. PET images were acquired with background activity concentrations into the FOV (A(c)(,bkg)) about 11, 9.2, 6.6, 5.2 and 3.5 kBq mL(-1). The emission scan duration (ESD) was set to 1, 2, 3 and 4 min. The tube inside the scatter phantom was filled with activities to provide A(c)(,out) in the whole scatter phantom of zero, half, unity, twofold and fourfold the one of the modified IEC phantom. Plots of CNR versus the various parameters are provided. Multiple linear regression was employed to study the effects of A(c)(,out) on CNR, adjusted for the presence of variables (sphere ID, A(c)(,bkg) and ESD) related to CNR. The presence of outside FOV activity at the same concentration as the one inside the FOV reduces peak NECR of 30%. The increase in SF is marginal (1.2%). CNR diminishes significantly with increasing outside FOV activity, in the range explored. ESD and A(c)(,out) have a similar weight in accounting for CNR variance. Thus, an experimental law that adjusts the scan duration to the outside FOV activity can be devised. Recovery of CNR loss due to an elevated A(c)(,out) activity seems feasible by modulating the ESD in individual bed positions according to A(c)(,out).

  10. Optimization of 3-D MP-RAGE sequences for structural brain imaging.

    PubMed

    Deichmann, R; Good, C D; Josephs, O; Ashburner, J; Turner, R

    2000-07-01

    An optimized MR sequence for structural three-dimensional brain scans is presented, giving good T(1) contrast and excellent white matter/gray matter segmentation. Modification of the usual linear phase encoding order to centric phase encoding restores the contrast loss, which usually occurs after magnetization preparation during the acquisition process when large volumes are imaged. The deleterious effects on the point-spread function are compensated by means of an appropriate k-space filter. RF coil inhomogeneities are corrected by means of shaped excitation pulses. High contrast-to-noise images of the entire brain with 1 mm isotropic resolution can be obtained in 12 min. The contrast-to-noise-ratio is about 100% higher than for sequences based on linear phase encoding.

  11. Fast, Accurate and Precise Mid-Sagittal Plane Location in 3D MR Images of the Brain

    NASA Astrophysics Data System (ADS)

    Bergo, Felipe P. G.; Falcão, Alexandre X.; Yasuda, Clarissa L.; Ruppert, Guilherme C. S.

    Extraction of the mid-sagittal plane (MSP) is a key step for brain image registration and asymmetry analysis. We present a fast MSP extraction method for 3D MR images, based on automatic segmentation of the brain and on heuristic maximization of the cerebro-spinal fluid within the MSP. The method is robust to severe anatomical asymmetries between the hemispheres, caused by surgical procedures and lesions. The method is also accurate with respect to MSP delineations done by a specialist. The method was evaluated on 64 MR images (36 pathological, 20 healthy, 8 synthetic), and it found a precise and accurate approximation of the MSP in all of them with a mean time of 60.0 seconds per image, mean angular variation within a same image (precision) of 1.26o and mean angular difference from specialist delineations (accuracy) of 1.64o.

  12. 3D active shape models of human brain structures: application to patient-specific mesh generation

    NASA Astrophysics Data System (ADS)

    Ravikumar, Nishant; Castro-Mateos, Isaac; Pozo, Jose M.; Frangi, Alejandro F.; Taylor, Zeike A.

    2015-03-01

    The use of biomechanics-based numerical simulations has attracted growing interest in recent years for computer-aided diagnosis and treatment planning. With this in mind, a method for automatic mesh generation of brain structures of interest, using statistical models of shape (SSM) and appearance (SAM), for personalised computational modelling is presented. SSMs are constructed as point distribution models (PDMs) while SAMs are trained using intensity profiles sampled from a training set of T1-weighted magnetic resonance images. The brain structures of interest are, the cortical surface (cerebrum, cerebellum & brainstem), lateral ventricles and falx-cerebri membrane. Two methods for establishing correspondences across the training set of shapes are investigated and compared (based on SSM quality): the Coherent Point Drift (CPD) point-set registration method and B-spline mesh-to-mesh registration method. The MNI-305 (Montreal Neurological Institute) average brain atlas is used to generate the template mesh, which is deformed and registered to each training case, to establish correspondence over the training set of shapes. 18 healthy patients' T1-weightedMRimages form the training set used to generate the SSM and SAM. Both model-training and model-fitting are performed over multiple brain structures simultaneously. Compactness and generalisation errors of the BSpline-SSM and CPD-SSM are evaluated and used to quantitatively compare the SSMs. Leave-one-out cross validation is used to evaluate SSM quality in terms of these measures. The mesh-based SSM is found to generalise better and is more compact, relative to the CPD-based SSM. Quality of the best-fit model instance from the trained SSMs, to test cases are evaluated using the Hausdorff distance (HD) and mean absolute surface distance (MASD) metrics.

  13. Lossless 3-D reconstruction and registration of semi-quantitative gene expression data in the mouse brain

    PubMed Central

    Enlow, Matthew A.; Ju, Tao; Kakadiaris, Ioannis A.; Carson, James P.

    2012-01-01

    As imaging, computing, and data storage technologies improve, there is an increasing opportunity for multiscale analysis of three-dimensional datasets (3-D). Such analysis enables, for example, microscale elements of multiple macroscale specimens to be compared throughout the entire macroscale specimen. Spatial comparisons require bringing datasets into co-alignment. One approach for co-alignment involves elastic deformations of data in addition to rigid alignments. The elastic deformations distort space, and if not accounted for, can distort the information at the microscale. The algorithms developed in this work address this issue by allowing multiple data points to be encoded into a single image pixel, appropriately tracking each data point to ensure lossless data mapping during elastic spatial deformation. This approach was developed and implemented for both 2-D and 3-D registration of images. Lossless reconstruction and registration was applied to semi-quantitative cellular gene expression data in the mouse brain, enabling comparison of multiple spatially registered 3-D datasets without any augmentation of the cellular data. Standard reconstruction and registration without the lossless approach resulted in errors in cellular quantities of ~ 8%. PMID:22256218

  14. Lossless 3-D reconstruction and registration of semi-quantitative gene expression data in the mouse brain.

    PubMed

    Enlow, Matthew A; Ju, Tao; Kakadiaris, Ioannis A; Carson, James P

    2011-01-01

    As imaging, computing, and data storage technologies improve, there is an increasing opportunity for multiscale analysis of three-dimensional datasets (3-D). Such analysis enables, for example, microscale elements of multiple macroscale specimens to be compared throughout the entire macroscale specimen. Spatial comparisons require bringing datasets into co-alignment. One approach for co-alignment involves elastic deformations of data in addition to rigid alignments. The elastic deformations distort space, and if not accounted for, can distort the information at the microscale. The algorithms developed in this work address this issue by allowing multiple data points to be encoded into a single image pixel, appropriately tracking each data point to ensure lossless data mapping during elastic spatial deformation. This approach was developed and implemented for both 2-D and 3D registration of images. Lossless reconstruction and registration was applied to semi-quantitative cellular gene expression data in the mouse brain, enabling comparison of multiple spatially registered 3-D datasets without any augmentation of the cellular data. Standard reconstruction and registration without the lossless approach resulted in errors in cellular quantities of ∼ 8%.

  15. Global brain atrophy and corticospinal tract alterations in ALS, as investigated by voxel-based morphometry of 3-D MRI.

    PubMed

    Kassubek, Jan; Unrath, Alexander; Huppertz, Hans-Jürgen; Lulé, Dorothée; Ethofer, Thomas; Sperfeld, Anne-Dorte; Ludolph, Albert C

    2005-12-01

    In ALS, advanced magnetic resonance imaging (MRI) techniques are increasingly used to investigate the underlying pathology. In this study, the technique of voxel-based morphometry (VBM) was applied to 3-D MRI data in ALS patients to localize regional grey and white matter changes. Twenty-two ALS patients (mean age 58+/-9 years) with clinically definite ALS by revised El Escorial criteria were studied. None of the patients had any signs of associated frontotemporal dementia. High-resolution 3-D MRI data sets of the whole brain, collected on a 1.5 T scanner, were analysed by statistical parametric mapping (SPM) and VBM in comparison to an age-matched normal data base consisting of 22 healthy volunteers (mean age 59+/-11 years), for grey matter and white matter segments separately. Global brain atrophy was assessed by calculation of brain parenchymal fractions (BPF). In ALS patients, BPF were significantly reduced compared to controls (p = 0.0003), indicating global brain atrophy. Regional decreases of grey matter density were found in the ALS patients at corrected p<0.01 in the right-hemispheric primary motor cortex (area of the highest Z-score) and in the left medial frontal gyrus. Furthermore, regional white matter alterations were observed along the corticospinal tracts bilaterally and in multiple smaller areas including corpus callosum, cerebellum, frontal and occipital subcortical regions. Besides considerable global atrophy in ALS, the topography of ALS-associated cerebral morphological changes could be mapped using VBM, in particular white matter signal changes along the bilateral corticospinal tracts, but also in extra-motor areas. VBM might be a potential tool to visualize disease progression in future longitudinal studies.

  16. Framework for the construction of a Monte Carlo simulated brain PET-MR image database

    NASA Astrophysics Data System (ADS)

    Thomas, B. A.; Erlandsson, K.; Drobnjak, I.; Pedemonte, S.; Vunckx, K.; Bousse, A.; Reilhac-Laborde, A.; Ourselin, S.; Hutton, B. F.

    2014-01-01

    Simultaneous PET-MR acquisition reduces the possibility of registration mismatch between the two modalities. This facilitates the application of techniques, either during reconstruction or post-reconstruction, that aim to improve the PET resolution by utilising structural information provided by MR. However, in order to validate such methods for brain PET-MR studies it is desirable to evaluate the performance using data where the ground truth is known. In this work, we present a framework for the production of datasets where simulations of both the PET and MR, based on real data, are generated such that reconstruction and post-reconstruction approaches can be fairly compared.

  17. A Real-Time Magnetoencephalography Brain-Computer Interface Using Interactive 3D Visualization and the Hadoop Ecosystem.

    PubMed

    McClay, Wilbert A; Yadav, Nancy; Ozbek, Yusuf; Haas, Andy; Attias, Hagaii T; Nagarajan, Srikantan S

    2015-09-30

    Ecumenically, the fastest growing segment of Big Data is human biology-related data and the annual data creation is on the order of zetabytes. The implications are global across industries, of which the treatment of brain related illnesses and trauma could see the most significant and immediate effects. The next generation of health care IT and sensory devices are acquiring and storing massive amounts of patient related data. An innovative Brain-Computer Interface (BCI) for interactive 3D visualization is presented utilizing the Hadoop Ecosystem for data analysis and storage. The BCI is an implementation of Bayesian factor analysis algorithms that can distinguish distinct thought actions using magneto encephalographic (MEG) brain signals. We have collected data on five subjects yielding 90% positive performance in MEG mid- and post-movement activity. We describe a driver that substitutes the actions of the BCI as mouse button presses for real-time use in visual simulations. This process has been added into a flight visualization demonstration. By thinking left or right, the user experiences the aircraft turning in the chosen direction. The driver components of the BCI can be compiled into any software and substitute a user's intent for specific keyboard strikes or mouse button presses. The BCI's data analytics OPEN ACCESS Brain. Sci. 2015, 5 420 of a subject's MEG brainwaves and flight visualization performance are stored and analyzed using the Hadoop Ecosystem as a quick retrieval data warehouse.

  18. Volumetric and surface-based 3D MRI analyses of fetal isolated mild ventriculomegaly: brain morphometry in ventriculomegaly.

    PubMed

    Scott, Julia A; Habas, Piotr A; Rajagopalan, Vidya; Kim, Kio; Barkovich, A James; Glenn, Orit A; Studholme, Colin

    2013-05-01

    Diagnosis of fetal isolated mild ventriculomegaly (IMVM) is the most common brain abnormality on prenatal ultrasound. We have set to identify potential alterations in brain development specific to IMVM in tissue volume and cortical and ventricular local surface curvature derived from in utero magnetic resonance imaging (MRI). Multislice 2D T2-weighted MRI were acquired from 32 fetuses (16 IMVM, 16 controls) between 22 and 25.5 gestational weeks. The images were motion-corrected and reconstructed into 3D volumes for volumetric and curvature analyses. The brain images were automatically segmented into cortical plate, cerebral mantle, deep gray nuclei, and ventricles. Volumes were compared between IMVM and control subjects. Surfaces were extracted from the segmentations for local mean surface curvature measurement on the inner cortical plate and the ventricles. Linear models were estimated for age-related and ventricular volume-associated changes in local curvature in both the inner cortical plate and ventricles. While ventricular volume was enlarged in IMVM, all other tissue volumes were not different from the control group. Ventricles increased in curvature with age along the atrium and anterior body. Increasing ventricular volume was associated with reduced curvature over most of the ventricular surface. The cortical plate changed in curvature with age at multiple sites of primary sulcal formation. Reduced cortical folding was detected near the parieto-occipital sulcus in IMVM subjects. While tissue volume appears to be preserved in brains with IMVM, cortical folding may be affected in regions where ventricles are dilated.

  19. Efficient fully 3D list-mode TOF PET image reconstruction using a factorized system matrix with an image domain resolution model

    PubMed Central

    Zhou, Jian; Qi, Jinyi

    2014-01-01

    A factorized system matrix utilizing an image domain resolution model is attractive in fully 3D TOF PET image reconstruction using list-mode data. In this paper, we study a factored model based on sparse matrix factorization that is comprised primarily of a simplified geometrical projection matrix and an image blurring matrix. Beside the commonly-used Siddon's raytracer, we propose another more simplified geometrical projector based on the Bresenham's raytracer which further reduces the computational cost. We discuss in general how to obtain an image blurring matrix associated with a geometrical projector, and provide theoretical analysis that can be used to inspect the efficiency in model factorization. In simulation studies, we investigate the performance of the proposed sparse factorization model in terms of spatial resolution, noise properties and computational cost. The quantitative results reveal that the factorization model can be as efficient as a nonfactored model such as the analytical model while its computational cost can be much lower. In addition we conduct Monte Carlo simulations to identify the conditions under which the image resolution model can become more efficient in terms of image contrast recovery. We verify our observations using the provided theoretical analysis. The result offers a general guide to achieve optimal reconstruction performance based on a sparse factorization model with an only image domain resolution model. PMID:24434568

  20. Efficient fully 3D list-mode TOF PET image reconstruction using a factorized system matrix with an image domain resolution model.

    PubMed

    Zhou, Jian; Qi, Jinyi

    2014-02-07

    A factorized system matrix utilizing an image domain resolution model is attractive in fully 3D time-of-flight PET image reconstruction using list-mode data. In this paper, we study a factored model based on sparse matrix factorization that is comprised primarily of a simplified geometrical projection matrix and an image blurring matrix. Beside the commonly-used Siddon's ray-tracer, we propose another more simplified geometrical projector based on the Bresenham's ray-tracer which further reduces the computational cost. We discuss in general how to obtain an image blurring matrix associated with a geometrical projector, and provide theoretical analysis that can be used to inspect the efficiency in model factorization. In simulation studies, we investigate the performance of the proposed sparse factorization model in terms of spatial resolution, noise properties and computational cost. The quantitative results reveal that the factorization model can be as efficient as a non-factored model, while its computational cost can be much lower. In addition we conduct Monte Carlo simulations to identify the conditions under which the image resolution model can become more efficient in terms of image contrast recovery. We verify our observations using the provided theoretical analysis. The result offers a general guide to achieve the optimal reconstruction performance based on a sparse factorization model with an image domain resolution model.

  1. Non-spin-echo 3D transverse hadamard encoded proton spectroscopic imaging in the human brain.

    PubMed

    Cohen, Ouri; Tal, Assaf; Goelman, Gadi; Gonen, Oded

    2013-07-01

    A non-spin-echo multivoxel proton MR localization method based on three-dimensional transverse Hadamard spectroscopic imaging is introduced and demonstrated in a phantom and the human brain. Spatial encoding is achieved with three selective 90° radiofrequency pulses along perpendicular axes: The first two create a longitudinal ±M(Z) Hadamard order in the volume of interest. The third pulse spatially Hadamard-encodes the ±M(Z)s in the volume of interest in the third direction while bringing them to the transverse plane to be acquired immediately. The approaching-ideal point spread function of Hadamard encoding and very short acquisition delay yield signal-to-noise-ratios of 20 ± 8, 23 ± 9, and 31 ± 10 for choline, creatine, and N-acetylaspartate in the human brain at 1.5 T from 1 cm(3) voxels in 21 min. The advantages of transverse Hadamard spectroscopic imaging are that unlike gradient (Fourier) phase-encoding: (i) the volume of interest does not need to be smaller than the field of view to prevent aliasing; (ii) the number of partitions in each direction can be small, 8, 4, or even 2 at no cost in point spread function; (iii) the volume of interest does not have to be contiguous; and (iv) the voxel profile depends on the available B1 and pulse synthesis paradigm and can, therefore, at least theoretically, approach "ideal" "1" inside and "0" elsewhere.

  2. Classification of mathematics deficiency using shape and scale analysis of 3D brain structures

    NASA Astrophysics Data System (ADS)

    Kurtek, Sebastian; Klassen, Eric; Gore, John C.; Ding, Zhaohua; Srivastava, Anuj

    2011-03-01

    We investigate the use of a recent technique for shape analysis of brain substructures in identifying learning disabilities in third-grade children. This Riemannian technique provides a quantification of differences in shapes of parameterized surfaces, using a distance that is invariant to rigid motions and re-parameterizations. Additionally, it provides an optimal registration across surfaces for improved matching and comparisons. We utilize an efficient gradient based method to obtain the optimal re-parameterizations of surfaces. In this study we consider 20 different substructures in the human brain and correlate the differences in their shapes with abnormalities manifested in deficiency of mathematical skills in 106 subjects. The selection of these structures is motivated in part by the past links between their shapes and cognitive skills, albeit in broader contexts. We have studied the use of both individual substructures and multiple structures jointly for disease classification. Using a leave-one-out nearest neighbor classifier, we obtained a 62.3% classification rate based on the shape of the left hippocampus. The use of multiple structures resulted in an improved classification rate of 71.4%.

  3. DLP technology application: 3D head tracking and motion correction in medical brain imaging

    NASA Astrophysics Data System (ADS)

    Olesen, Oline V.; Wilm, Jakob; Paulsen, Rasmus R.; Højgaard, Liselotte; Larsen, Rasmus

    2014-03-01

    In this paper we present a novel sensing system, robust Near-infrared Structured Light Scanning (NIRSL) for three-dimensional human model scanning application. Human model scanning due to its nature of various hair and dress appearance and body motion has long been a challenging task. Previous structured light scanning methods typically emitted visible coded light patterns onto static and opaque objects to establish correspondence between a projector and a camera for triangulation. In the success of these methods rely on scanning objects with proper reflective surface for visible light, such as plaster, light colored cloth. Whereas for human model scanning application, conventional methods suffer from low signal to noise ratio caused by low contrast of visible light over the human body. The proposed robust NIRSL, as implemented with the near infrared light, is capable of recovering those dark surfaces, such as hair, dark jeans and black shoes under visible illumination. Moreover, successful structured light scan relies on the assumption that the subject is static during scanning. Due to the nature of body motion, it is very time sensitive to keep this assumption in the case of human model scan. The proposed sensing system, by utilizing the new near-infrared capable high speed LightCrafter DLP projector, is robust to motion, provides accurate and high resolution three-dimensional point cloud, making our system more efficient and robust for human model reconstruction. Experimental results demonstrate that our system is effective and efficient to scan real human models with various dark hair, jeans and shoes, robust to human body motion and produces accurate and high resolution 3D point cloud.

  4. Evaluation and validation methods for intersubject nonrigid 3D image registration of the human brain

    NASA Astrophysics Data System (ADS)

    Guo, Ting; Starreveld, Yves P.; Peters, Terry M.

    2005-04-01

    This work presents methodologies for assessing the accuracy of non-rigid intersubject registration algorithms from both qualitative and quantitative perspectives. The first method was based on a set of 43 anatomical landmarks. MRI brain images of 12 subjects were non-rigidly registered to the standard MRI dataset. The "gold-standard" coordinates of the 43 landmarks in the target were estimated by averaging their coordinates after 6 tagging sessions. The Euclidean distance between each landmark of a subject after warping to the reference space and the homologous "gold-standard" landmark on the reference image was considered as the registration error. Another method based on visual inspection software displaying the spatial change of colour-coded spheres, before and after warping, was also developed to evaluate the performance of the non-rigid warping algorithms within the homogeneous regions in the deep-brain. Our methods were exemplified by assessing and comparing the accuracy of two intersubject non-rigid registration approaches, AtamaiWarp and ANIMAL algorithms. From the first method, the average registration error was 1.04mm +/- 0.65mm for AtamaiWarp, and 1.59mm +/- 1.47mm for ANIMAL. With maximum registration errors of 2.78mm and 3.90mm respectively, AtamaiWarp and ANIMAL located 58% and 35% landmarks respectively with registration errors less than 1mm. A paired t-test showed that the differences in registration error between AtamaiWarp and ANIMAL were significant (P < 0.002) demonstrating that AtamaiWarp, in addition to being over 60 times faster than ANIMAL, also provides more accurate results. From the second method, both algorithms treated the interior of homogeneous regions in an appropriate manner.

  5. 3D-Reconstructions and Virtual 4D-Visualization to Study Metamorphic Brain Development in the Sphinx Moth Manduca Sexta.

    PubMed

    Huetteroth, Wolf; El Jundi, Basil; El Jundi, Sirri; Schachtner, Joachim

    2010-01-01

    DURING METAMORPHOSIS, THE TRANSITION FROM THE LARVA TO THE ADULT, THE INSECT BRAIN UNDERGOES CONSIDERABLE REMODELING: new neurons are integrated while larval neurons are remodeled or eliminated. One well acknowledged model to study metamorphic brain development is the sphinx moth Manduca sexta. To further understand mechanisms involved in the metamorphic transition of the brain we generated a 3D standard brain based on selected brain areas of adult females and 3D reconstructed the same areas during defined stages of pupal development. Selected brain areas include for example mushroom bodies, central complex, antennal- and optic lobes. With this approach we eventually want to quantify developmental changes in neuropilar architecture, but also quantify changes in the neuronal complement and monitor the development of selected neuronal populations. Furthermore, we used a modeling software (Cinema 4D) to create a virtual 4D brain, morphing through its developmental stages. Thus the didactical advantages of 3D visualization are expanded to better comprehend complex processes of neuropil formation and remodeling during development. To obtain datasets of the M. sexta brain areas, we stained whole brains with an antiserum against the synaptic vesicle protein synapsin. Such labeled brains were then scanned with a confocal laser scanning microscope and selected neuropils were reconstructed with the 3D software AMIRA 4.1.

  6. Superfast elastic registration of histologic images of a whole rat brain for 3D reconstruction

    NASA Astrophysics Data System (ADS)

    Wirtz, Stefan; Fischer, Bernd; Modersitzki, Jan; Schmitt, Oliver

    2004-05-01

    We present a super-fast and parameter-free algorithm for non-rigid elastic registration of images of a serially sectioned whole rat brain. The purpose is to produce a three-dimensional high-resolution reconstruction. The registration is modelled as a minimization problem of a functional consisting of a distance measure and a regularizer based on the elastic potential of the displacement field. The minimization of the functional leads to a system of non-linear partial differential equations, the so-called Navier-Lame equations (NLE). Discretization of the NLE and a fixed point type iteration method lead to a linear system of equations, which has to be solved at each iteration step. We not only present a super-fast solution technique for this system, but also come up with sound strategies for accelerating the outer iteration. This does include a multi-scale approach based on a Gaussian pyramid as well as a clever estimation of the material constants for the elastic potential. The results of the registration process were controlled by an expert who was able to recognize histological details like laminations which was not possible before. Therefore, it is essential to apply elastic registration to this kind of imaging problem. Finally, the visually pleasing results were quantified by a distance measure leading to an improvement of about 79% after just 35 iteration steps.

  7. CT and MRI Assessment and Characterization Using Segmentation and 3D Modeling Techniques: Applications to Muscle, Bone and Brain.

    PubMed

    Gargiulo, Paolo; Helgason, Thordur; Ramon, Ceon; Jr, Halldór Jónsson; Carraro, Ugo

    2014-03-31

    This paper reviews the novel use of CT and MRI data and image processing tools to segment and reconstruct tissue images in 3D to determine characteristics of muscle, bone and brain. This to study and simulate the structural changes occurring in healthy and pathological conditions as well as in response to clinical treatments. Here we report the application of this methodology to evaluate and quantify: 1. progression of atrophy in human muscle subsequent to permanent lower motor neuron (LMN) denervation, 2. muscle recovery as induced by functional electrical stimulation (FES), 3. bone quality in patients undergoing total hip replacement and 4. to model the electrical activity of the brain. Study 1: CT data and segmentation techniques were used to quantify changes in muscle density and composition by associating the Hounsfield unit values of muscle, adipose and fibrous connective tissue with different colors. This method was employed to monitor patients who have permanent muscle LMN denervation in the lower extremities under two different conditions: permanent LMN denervated not electrically stimulated and stimulated. Study 2: CT data and segmentation techniques were employed, however, in this work we assessed bone and muscle conditions in the pre-operative CT scans of patients scheduled to undergo total hip replacement. In this work, the overall anatomical structure, the bone mineral density (BMD) and compactness of quadriceps muscles and proximal femoral was computed to provide a more complete view for surgeons when deciding which implant technology to use. Further, a Finite element analysis provided a map of the strains around the proximal femur socket when solicited by typical stresses caused by an implant press fitting. Study 3 describes a method to model the electrical behavior of human brain using segmented MR images. The aim of the work is to use these models to predict the electrical activity of the human brain under normal and pathological conditions by

  8. A Real-Time Magnetoencephalography Brain-Computer Interface Using Interactive 3D Visualization and the Hadoop Ecosystem

    PubMed Central

    McClay, Wilbert A.; Yadav, Nancy; Ozbek, Yusuf; Haas, Andy; Attias, Hagaii T.; Nagarajan, Srikantan S.

    2015-01-01

    Ecumenically, the fastest growing segment of Big Data is human biology-related data and the annual data creation is on the order of zetabytes. The implications are global across industries, of which the treatment of brain related illnesses and trauma could see the most significant and immediate effects. The next generation of health care IT and sensory devices are acquiring and storing massive amounts of patient related data. An innovative Brain-Computer Interface (BCI) for interactive 3D visualization is presented utilizing the Hadoop Ecosystem for data analysis and storage. The BCI is an implementation of Bayesian factor analysis algorithms that can distinguish distinct thought actions using magneto encephalographic (MEG) brain signals. We have collected data on five subjects yielding 90% positive performance in MEG mid- and post-movement activity. We describe a driver that substitutes the actions of the BCI as mouse button presses for real-time use in visual simulations. This process has been added into a flight visualization demonstration. By thinking left or right, the user experiences the aircraft turning in the chosen direction. The driver components of the BCI can be compiled into any software and substitute a user’s intent for specific keyboard strikes or mouse button presses. The BCI’s data analytics of a subject’s MEG brainwaves and flight visualization performance are stored and analyzed using the Hadoop Ecosystem as a quick retrieval data warehouse. PMID:26437432

  9. Comprehensive 3D Model of Shock Wave-Brain Interactions in Blast-Induced Traumatic Brain Injuries

    DTIC Science & Technology

    2009-10-01

    waves can cause brain damage by other mechanisms including excess pressure (leading to contusions), excess strain (leading to subdural ... hematomas and/or diffuse axonal injuries), and, in particular, cavitation effects (leading to subcellular damage). This project aims at the development of a

  10. MR-Based PET Motion Correction Procedure for Simultaneous MR-PET Neuroimaging of Human Brain

    PubMed Central

    Weirich, Christoph; Rota Kops, Elena; Celik, Abdullah; Tellmann, Lutz; Stöcker, Tony; Herzog, Hans; Shah, Nadim Jon

    2012-01-01

    Positron Emission Tomography (PET) images are prone to motion artefacts due to the long acquisition time of PET measurements. Recently, simultaneous magnetic resonance imaging (MRI) and PET have become available in the first generation of Hybrid MR-PET scanners. In this work, the elimination of artefacts due to head motion in PET neuroimages is achieved by a new approach utilising MR-based motion tracking in combination with PET list mode data motion correction for simultaneous MR-PET acquisitions. The method comprises accurate MR-based motion measurements, an intra-frame motion minimising and reconstruction time reducing temporal framing algorithm, and a list mode based PET reconstruction which utilises the Ordinary Poisson Algorithm and avoids axial and transaxial compression. Compared to images uncorrected for motion, an increased image quality is shown in phantom as well as in vivo images. In vivo motion corrected images show an evident increase of contrast at the basal ganglia and a good visibility of uptake in tiny structures such as superior colliculi. PMID:23189127

  11. MR-based PET motion correction procedure for simultaneous MR-PET neuroimaging of human brain.

    PubMed

    Ullisch, Marcus Görge; Scheins, Jürgen Johann; Weirich, Christoph; Rota Kops, Elena; Celik, Abdullah; Tellmann, Lutz; Stöcker, Tony; Herzog, Hans; Shah, Nadim Jon

    2012-01-01

    Positron Emission Tomography (PET) images are prone to motion artefacts due to the long acquisition time of PET measurements. Recently, simultaneous magnetic resonance imaging (MRI) and PET have become available in the first generation of Hybrid MR-PET scanners. In this work, the elimination of artefacts due to head motion in PET neuroimages is achieved by a new approach utilising MR-based motion tracking in combination with PET list mode data motion correction for simultaneous MR-PET acquisitions. The method comprises accurate MR-based motion measurements, an intra-frame motion minimising and reconstruction time reducing temporal framing algorithm, and a list mode based PET reconstruction which utilises the Ordinary Poisson Algorithm and avoids axial and transaxial compression. Compared to images uncorrected for motion, an increased image quality is shown in phantom as well as in vivo images. In vivo motion corrected images show an evident increase of contrast at the basal ganglia and a good visibility of uptake in tiny structures such as superior colliculi.

  12. Postmortem 3-D brain hemisphere cortical tau and amyloid-β pathology mapping and quantification as a validation method of neuropathology imaging.

    PubMed

    Smid, Lojze M; Kepe, Vladimir; Vinters, Harry V; Bresjanac, Mara; Toyokuni, Tatsushi; Satyamurthy, Nagichettiar; Wong, Koon-Pong; Huang, Sung-Cheng; Silverman, Daniel H S; Miller, Karen; Small, Gary W; Barrio, Jorge R

    2013-01-01

    This work is aimed at correlating pre-mortem [18F]FDDNP positron emission tomography (PET) scan results in a patient with dementia with Lewy bodies (DLB), with cortical neuropathology distribution determined postmortem in three physical dimensions in whole brain coronal sections. Analysis of total amyloid-β (Aβ) distribution in frontal cortex and posterior cingulate gyrus confirmed its statistically significant correlation with cortical [18F]FDDNP PET binding values (distribution volume ratios, DVR) (p < 0.001, R = 0.97, R2 = 0.94). Neurofibrillary tangle (NFT) distribution correlated significantly with cortical [18F]FDDNP PET DVR in the temporal lobe (p < 0.001, R = 0.87, R2 = 0.76). Linear combination of Aβ and NFT densities was highly predictive of [18F]FDDNP PET DVR through all analyzed regions of interest (p < 0.0001, R = 0.92, R2 = 0.85), and both densities contributed significantly to the model. Lewy bodies were present at a much lower level than either Aβ or NFTs and did not significantly contribute to the in vivo signal. [18F]FDG PET scan results in this patient were consistent with the distinctive DLB pattern of hypometabolism. This work offers a mapping brain model applicable to all imaging probes for verification of imaging results with Aβ and/or tau neuropathology brain distribution using immunohistochemistry, fluorescence microscopy, and autoradiography.

  13. Ultra-low-cost 3D gaze estimation: an intuitive high information throughput compliment to direct brain-machine interfaces

    NASA Astrophysics Data System (ADS)

    Abbott, W. W.; Faisal, A. A.

    2012-08-01

    Eye movements are highly correlated with motor intentions and are often retained by patients with serious motor deficiencies. Despite this, eye tracking is not widely used as control interface for movement in impaired patients due to poor signal interpretation and lack of control flexibility. We propose that tracking the gaze position in 3D rather than 2D provides a considerably richer signal for human machine interfaces by allowing direct interaction with the environment rather than via computer displays. We demonstrate here that by using mass-produced video-game hardware, it is possible to produce an ultra-low-cost binocular eye-tracker with comparable performance to commercial systems, yet 800 times cheaper. Our head-mounted system has 30 USD material costs and operates at over 120 Hz sampling rate with a 0.5-1 degree of visual angle resolution. We perform 2D and 3D gaze estimation, controlling a real-time volumetric cursor essential for driving complex user interfaces. Our approach yields an information throughput of 43 bits s-1, more than ten times that of invasive and semi-invasive brain-machine interfaces (BMIs) that are vastly more expensive. Unlike many BMIs our system yields effective real-time closed loop control of devices (10 ms latency), after just ten minutes of training, which we demonstrate through a novel BMI benchmark—the control of the video arcade game ‘Pong’.

  14. Ultra-low-cost 3D gaze estimation: an intuitive high information throughput compliment to direct brain-machine interfaces.

    PubMed

    Abbott, W W; Faisal, A A

    2012-08-01

    Eye movements are highly correlated with motor intentions and are often retained by patients with serious motor deficiencies. Despite this, eye tracking is not widely used as control interface for movement in impaired patients due to poor signal interpretation and lack of control flexibility. We propose that tracking the gaze position in 3D rather than 2D provides a considerably richer signal for human machine interfaces by allowing direct interaction with the environment rather than via computer displays. We demonstrate here that by using mass-produced video-game hardware, it is possible to produce an ultra-low-cost binocular eye-tracker with comparable performance to commercial systems, yet 800 times cheaper. Our head-mounted system has 30 USD material costs and operates at over 120 Hz sampling rate with a 0.5-1 degree of visual angle resolution. We perform 2D and 3D gaze estimation, controlling a real-time volumetric cursor essential for driving complex user interfaces. Our approach yields an information throughput of 43 bits s(-1), more than ten times that of invasive and semi-invasive brain-machine interfaces (BMIs) that are vastly more expensive. Unlike many BMIs our system yields effective real-time closed loop control of devices (10 ms latency), after just ten minutes of training, which we demonstrate through a novel BMI benchmark--the control of the video arcade game 'Pong'.

  15. Steady-State VEP-Based Brain-Computer Interface Control in an Immersive 3D Gaming Environment

    NASA Astrophysics Data System (ADS)

    Lalor, E. C.; Kelly, S. P.; Finucane, C.; Burke, R.; Smith, R.; Reilly, R. B.; McDarby, G.

    2005-12-01

    This paper presents the application of an effective EEG-based brain-computer interface design for binary control in a visually elaborate immersive 3D game. The BCI uses the steady-state visual evoked potential (SSVEP) generated in response to phase-reversing checkerboard patterns. Two power-spectrum estimation methods were employed for feature extraction in a series of offline classification tests. Both methods were also implemented during real-time game play. The performance of the BCI was found to be robust to distracting visual stimulation in the game and relatively consistent across six subjects, with 41 of 48 games successfully completed. For the best performing feature extraction method, the average real-time control accuracy across subjects was 89%. The feasibility of obtaining reliable control in such a visually rich environment using SSVEPs is thus demonstrated and the impact of this result is discussed.

  16. Evaluation of a video-based head motion tracking system for dedicated brain PET

    NASA Astrophysics Data System (ADS)

    Anishchenko, S.; Beylin, D.; Stepanov, P.; Stepanov, A.; Weinberg, I. N.; Schaeffer, S.; Zavarzin, V.; Shaposhnikov, D.; Smith, M. F.

    2015-03-01

    Unintentional head motion during Positron Emission Tomography (PET) data acquisition can degrade PET image quality and lead to artifacts. Poor patient compliance, head tremor, and coughing are examples of movement sources. Head motion due to patient non-compliance can be an issue with the rise of amyloid brain PET in dementia patients. To preserve PET image resolution and quantitative accuracy, head motion can be tracked and corrected in the image reconstruction algorithm. While fiducial markers can be used, a contactless approach is preferable. A video-based head motion tracking system for a dedicated portable brain PET scanner was developed. Four wide-angle cameras organized in two stereo pairs are used for capturing video of the patient's head during the PET data acquisition. Facial points are automatically tracked and used to determine the six degree of freedom head pose as a function of time. The presented work evaluated the newly designed tracking system using a head phantom and a moving American College of Radiology (ACR) phantom. The mean video-tracking error was 0.99±0.90 mm relative to the magnetic tracking device used as ground truth. Qualitative evaluation with the ACR phantom shows the advantage of the motion tracking application. The developed system is able to perform tracking with accuracy close to millimeter and can help to preserve resolution of brain PET images in presence of movements.

  17. SU-E-J-123: Assessing Segmentation Accuracy of Internal Volumes and Sub-Volumes in 4D PET/CT of Lung Tumors Using a Novel 3D Printed Phantom

    SciTech Connect

    Soultan, D; Murphy, J; James, C; Hoh, C; Moiseenko, V; Cervino, L; Gill, B

    2015-06-15

    Purpose: To assess the accuracy of internal target volume (ITV) segmentation of lung tumors for treatment planning of simultaneous integrated boost (SIB) radiotherapy as seen in 4D PET/CT images, using a novel 3D-printed phantom. Methods: The insert mimics high PET tracer uptake in the core and 50% uptake in the periphery, by using a porous design at the periphery. A lung phantom with the insert was placed on a programmable moving platform. Seven breathing waveforms of ideal and patient-specific respiratory motion patterns were fed to the platform, and 4D PET/CT scans were acquired of each of them. CT images were binned into 10 phases, and PET images were binned into 5 phases following the clinical protocol. Two scenarios were investigated for segmentation: a gate 30–70 window, and no gating. The radiation oncologist contoured the outer ITV of the porous insert with on CT images, while the internal void volume with 100% uptake was contoured on PET images for being indistinguishable from the outer volume in CT images. Segmented ITVs were compared to the expected volumes based on known target size and motion. Results: 3 ideal breathing patterns, 2 regular-breathing patient waveforms, and 2 irregular-breathing patient waveforms were used for this study. 18F-FDG was used as the PET tracer. The segmented ITVs from CT closely matched the expected motion for both no gating and gate 30–70 window, with disagreement of contoured ITV with respect to the expected volume not exceeding 13%. PET contours were seen to overestimate volumes in all the cases, up to more than 40%. Conclusion: 4DPET images of a novel 3D printed phantom designed to mimic different uptake values were obtained. 4DPET contours overestimated ITV volumes in all cases, while 4DCT contours matched expected ITV volume values. Investigation of the cause and effects of the discrepancies is undergoing.

  18. A SiPM-based isotropic-3D PET detector X'tal cube with a three-dimensional array of 1 mm(3) crystals.

    PubMed

    Yamaya, Taiga; Mitsuhashi, Takayuki; Matsumoto, Takahiro; Inadama, Naoko; Nishikido, Fumihiko; Yoshida, Eiji; Murayama, Hideo; Kawai, Hideyuki; Suga, Mikio; Watanabe, Mitsuo

    2011-11-07

    We are developing a novel, general purpose isotropic-3D PET detector X'tal cube which has high spatial resolution in all three dimensions. The research challenge for this detector is implementing effective detection of scintillation photons by covering six faces of a segmented crystal block with silicon photomultipliers (SiPMs). In this paper, we developed the second prototype of the X'tal cube for a proof-of-concept. We aimed at realizing an ultimate detector with 1.0 mm(3) cubic crystals, in contrast to our previous development using 3.0 mm(3) cubic crystals. The crystal block was composed of a 16 × 16 × 16 array of lutetium gadolinium oxyorthosilicate (LGSO) crystals 0.993 × 0.993 × 0.993 mm(3) in size. The crystals were optically glued together without inserting any reflector inside and 96 multi-pixel photon counters (MPPCs, S10931-50P, i.e. six faces each with a 4 × 4 array of MPPCs), each having a sensitive area of 3.0 × 3.0 mm(2), were optically coupled to the surfaces of the crystal block. Almost all 4096 crystals were identified through Anger-type calculation due to the finely adjusted reflector sheets inserted between the crystal block and light guides. The reflector sheets, which formed a belt of 0.5 mm width, were placed to cover half of the crystals of the second rows from the edges in order to improve identification performance of the crystals near the edges. Energy resolution of 12.7% was obtained at 511 keV with almost uniform light output for all crystal segments thanks to the effective detection of the scintillation photons.

  19. Kinetic measurements are necessary for description of brain receptors with PET

    SciTech Connect

    Ma, M.; Me, R.

    1984-01-01

    Following injection of radiolabeled spiperone a brain PET image demonstrates a distribution of tracer similar to the known distribution of dopamine receptors. However, the usefulness of a single PET image to quantitate receptor density can be limited by the effect of local blood flow (CBF), brain permeability (P), forward receptor rate constant (k1), and the reverse receptor rate constant (k-1). Using a 3-compartment model that the authors have described and successfully employed to interpret brain receptor kinetics with PET, the authors have simulated the effect of changes in the above variables on the image contrast (IC) between receptor-containing tissue (T), and receptor-free tissue like cerebellum (C), expressing this contrast as (T-C)/C. The blood activity curve and initial values for the variables were taken from their in vivo PET work in baboons using 18-F-spiperone. The model shows IC increases directly with time, not reaching 90% of maximum until over 3 hours. Thus, the timing of a single PET scan is critical for reproducible results. While the effect of changes in CBF are very small, changes in P, k1 and k-1 at 60 minutes, and k1 and k-1 at 120 minutes result in substantial changes in the observed IC. Until more is known about the behavior of these variables reliable description of brain receptors requires dynamic PET data from sequential images, analyzed by an appropriate mathematical model.

  20. Dynamic functional imaging of brain glucose utilization using fPET-FDG

    SciTech Connect

    Villien, Marjorie; Wey, Hsiao-Ying; Mandeville, Joseph B.; Catana, Ciprian; Polimeni, Jonathan R.; Sander, Christin Y.; Zürcher, Nicole R.; Chonde, Daniel B.; Fowler, Joanna S.; Rosen, Bruce R.; Hooker, Jacob M.

    2014-06-14

    We report that glucose is the principal source of energy for the brain and yet the dynamic response of glucose utilization to changes in brain activity is still not fully understood. Positron emission tomography (PET) allows quantitative measurement of glucose metabolism using 2-[18F]-fluorodeoxyglucose (FDG). However, FDG PET in its current form provides an integral (or average) of glucose consumption over tens of minutes and lacks the temporal information to capture physiological alterations associated with changes in brain activity induced by tasks or drug challenges. Traditionally, changes in glucose utilization are inferred by comparing two separate scans, which significantly limits the utility of the method. We report a novel method to track changes in FDG metabolism dynamically, with higher temporal resolution than exists to date and within a single session. Using a constant infusion of FDG, we demonstrate that our technique (termed fPET-FDG) can be used in an analysis pipeline similar to fMRI to define within-session differential metabolic responses. We use visual stimulation to demonstrate the feasibility of this method. Ultimately, this new method has a great potential to be used in research protocols and clinical settings since fPET-FDG imaging can be performed with most PET scanners and data acquisition and analysis are straightforward. fPET-FDG is a highly complementary technique to MRI and provides a rich new way to observe functional changes in brain metabolism.

  1. Dynamic functional imaging of brain glucose utilization using fPET-FDG

    DOE PAGES

    Villien, Marjorie; Wey, Hsiao-Ying; Mandeville, Joseph B.; ...

    2014-06-14

    We report that glucose is the principal source of energy for the brain and yet the dynamic response of glucose utilization to changes in brain activity is still not fully understood. Positron emission tomography (PET) allows quantitative measurement of glucose metabolism using 2-[18F]-fluorodeoxyglucose (FDG). However, FDG PET in its current form provides an integral (or average) of glucose consumption over tens of minutes and lacks the temporal information to capture physiological alterations associated with changes in brain activity induced by tasks or drug challenges. Traditionally, changes in glucose utilization are inferred by comparing two separate scans, which significantly limits themore » utility of the method. We report a novel method to track changes in FDG metabolism dynamically, with higher temporal resolution than exists to date and within a single session. Using a constant infusion of FDG, we demonstrate that our technique (termed fPET-FDG) can be used in an analysis pipeline similar to fMRI to define within-session differential metabolic responses. We use visual stimulation to demonstrate the feasibility of this method. Ultimately, this new method has a great potential to be used in research protocols and clinical settings since fPET-FDG imaging can be performed with most PET scanners and data acquisition and analysis are straightforward. fPET-FDG is a highly complementary technique to MRI and provides a rich new way to observe functional changes in brain metabolism.« less

  2. Dynamic Functional Imaging of Brain Glucose Utilization using fPET-FDG

    PubMed Central

    Villien, Marjorie; Wey, Hsiao-Ying; Mandeville, Joseph B.; Catana, Ciprian; Polimeni, Jonathan R.; Sander, Christin Y.; Zürcher, Nicole R.; Chonde, Daniel B.; Fowler, Joanna S.; Rosen, Bruce R.; Hooker, Jacob M.

    2014-01-01

    Glucose is the principal source of energy for the brain and yet the dynamic response of glucose utilization to changes in brain activity is still not fully understood. Positron emission tomography (PET) allows quantitative measurement of glucose metabolism using 2-[18F]-fluorodeoxyglucose (FDG). However, FDG PET in its current form provides an integral (or average) of glucose consumption over tens of minutes and lacks the temporal information to capture physiological alterations associated with changes in brain activity induced by tasks or drug challenges. Traditionally, changes in glucose utilization are inferred by comparing two separate scans, which significantly limits the utility of the method. We report a novel method to track changes in FDG metabolism dynamically, with higher temporal resolution than exists to date and within a single session. Using a constant infusion of FDG, we demonstrate that our technique (termed fPET-FDG) can be used in an analysis pipeline similar to fMRI to define within-session differential metabolic responses. We use visual stimulation to demonstrate the feasibility of this method. This new method has a great potential to be used in research protocols and clinical settings since fPET-FDG imaging can be performed with most PET scanners and data acquisition and analysis is straightforward. fPET-FDG is a highly complementary technique to MRI and provides a rich new way to observe functional changes in brain metabolism. PMID:24936683

  3. Dynamic functional imaging of brain glucose utilization using fPET-FDG.

    PubMed

    Villien, Marjorie; Wey, Hsiao-Ying; Mandeville, Joseph B; Catana, Ciprian; Polimeni, Jonathan R; Sander, Christin Y; Zürcher, Nicole R; Chonde, Daniel B; Fowler, Joanna S; Rosen, Bruce R; Hooker, Jacob M

    2014-10-15

    Glucose is the principal source of energy for the brain and yet the dynamic response of glucose utilization to changes in brain activity is still not fully understood. Positron emission tomography (PET) allows quantitative measurement of glucose metabolism using 2-[(18)F]-fluorodeoxyglucose (FDG). However, FDG PET in its current form provides an integral (or average) of glucose consumption over tens of minutes and lacks the temporal information to capture physiological alterations associated with changes in brain activity induced by tasks or drug challenges. Traditionally, changes in glucose utilization are inferred by comparing two separate scans, which significantly limits the utility of the method. We report a novel method to track changes in FDG metabolism dynamically, with higher temporal resolution than exists to date and within a single session. Using a constant infusion of FDG, we demonstrate that our technique (termed fPET-FDG) can be used in an analysis pipeline similar to fMRI to define within-session differential metabolic responses. We use visual stimulation to demonstrate the feasibility of this method. This new method has a great potential to be used in research protocols and clinical settings since fPET-FDG imaging can be performed with most PET scanners and data acquisition and analysis are straightforward. fPET-FDG is a highly complementary technique to MRI and provides a rich new way to observe functional changes in brain metabolism.

  4. Evaluation of sub-voxel registration accuracy between MRI and 3D MR spectroscopy of the brain

    NASA Astrophysics Data System (ADS)

    Rousseau, Francois; Maudsley, Andrew; Ebel, Andreas; Darkazanli, Ammar; Weber, Patrice; Sivasankaran, Krishnakumar; Yu, Yingjian; Studholme, Colin

    2005-04-01

    The implementation of Magnetic Resonance Spectroscopic Imaging (MRSI) for diagnostic imaging benefits from close integration of the lower-spatial resolution MRSI information with information from high-resolution structural MRI. Since patients can commonly move between acquisitions, it is necessary to account for possible mis-registration between the datasets arising from differences in patient positioning. In this paper we evaluate the use of 4 common multi-modality registration criteria to recover alignment between high resolution structural MRI and 3D MRSI data of the brain with sub-voxel accuracy. We explore the use of alternative MRSI water reference images to provide different types of structural information for the alignment process. The alignment accuracy was evaluated using both synthetically created MRSI and MRI data and a set of carefully collected subject image data with known ground truth spatial transformation between image volumes. The final accuracy and precision of estimates were assessed using multiple random starts of the registration algorithm. Sub voxel accuracy was found by all four similarity criteria with normalized mutual information providing the lowest target registration error for the 7 subject images. This effort supports the ongoing development of a database of brain metabolite distributions in normal subjects, which will be used in the evaluation of metabolic changes in neurological diseases.

  5. 3D Deep Learning for Multi-modal Imaging-Guided Survival Time Prediction of Brain Tumor Patients

    PubMed Central

    Nie, Dong; Zhang, Han; Adeli, Ehsan; Liu, Luyan

    2016-01-01

    High-grade glioma is the most aggressive and severe brain tumor that leads to death of almost 50% patients in 1–2 years. Thus, accurate prognosis for glioma patients would provide essential guidelines for their treatment planning. Conventional survival prediction generally utilizes clinical information and limited handcrafted features from magnetic resonance images (MRI), which is often time consuming, laborious and subjective. In this paper, we propose using deep learning frameworks to automatically extract features from multi-modal preoperative brain images (i.e., T1 MRI, fMRI and DTI) of high-grade glioma patients. Specifically, we adopt 3D convolutional neural networks (CNNs) and also propose a new network architecture for using multi-channel data and learning supervised features. Along with the pivotal clinical features, we finally train a support vector machine to predict if the patient has a long or short overall survival (OS) time. Experimental results demonstrate that our methods can achieve an accuracy as high as 89.9% We also find that the learned features from fMRI and DTI play more important roles in accurately predicting the OS time, which provides valuable insights into functional neuro-oncological applications. PMID:28149967

  6. 3D Deep Learning for Multi-modal Imaging-Guided Survival Time Prediction of Brain Tumor Patients.

    PubMed

    Nie, Dong; Zhang, Han; Adeli, Ehsan; Liu, Luyan; Shen, Dinggang

    2016-10-01

    High-grade glioma is the most aggressive and severe brain tumor that leads to death of almost 50% patients in 1-2 years. Thus, accurate prognosis for glioma patients would provide essential guidelines for their treatment planning. Conventional survival prediction generally utilizes clinical information and limited handcrafted features from magnetic resonance images (MRI), which is often time consuming, laborious and subjective. In this paper, we propose using deep learning frameworks to automatically extract features from multi-modal preoperative brain images (i.e., T1 MRI, fMRI and DTI) of high-grade glioma patients. Specifically, we adopt 3D convolutional neural networks (CNNs) and also propose a new network architecture for using multi-channel data and learning supervised features. Along with the pivotal clinical features, we finally train a support vector machine to predict if the patient has a long or short overall survival (OS) time. Experimental results demonstrate that our methods can achieve an accuracy as high as 89.9% We also find that the learned features from fMRI and DTI play more important roles in accurately predicting the OS time, which provides valuable insights into functional neuro-oncological applications.

  7. Postmortem examination of patient H.M.’s brain based on histological sectioning and digital 3D reconstruction

    NASA Astrophysics Data System (ADS)

    Annese, Jacopo; Schenker-Ahmed, Natalie M.; Bartsch, Hauke; Maechler, Paul; Sheh, Colleen; Thomas, Natasha; Kayano, Junya; Ghatan, Alexander; Bresler, Noah; Frosch, Matthew P.; Klaming, Ruth; Corkin, Suzanne

    2014-01-01

    Modern scientific knowledge of how memory functions are organized in the human brain originated from the case of Henry G. Molaison (H.M.), an epileptic patient whose amnesia ensued unexpectedly following a bilateral surgical ablation of medial temporal lobe structures, including the hippocampus. The neuroanatomical extent of the 1953 operation could not be assessed definitively during H.M.’s life. Here we describe the results of a procedure designed to reconstruct a microscopic anatomical model of the whole brain and conduct detailed 3D measurements in the medial temporal lobe region. This approach, combined with cellular-level imaging of stained histological slices, demonstrates a significant amount of residual hippocampal tissue with distinctive cytoarchitecture. Our study also reveals diffuse pathology in the deep white matter and a small, circumscribed lesion in the left orbitofrontal cortex. The findings constitute new evidence that may help elucidate the consequences of H.M.’s operation in the context of the brain’s overall pathology.

  8. Postmortem examination of patient H.M.’s brain based on histological sectioning and digital 3D reconstruction

    PubMed Central

    Annese, Jacopo; Schenker-Ahmed, Natalie M.; Bartsch, Hauke; Maechler, Paul; Sheh, Colleen; Thomas, Natasha; Kayano, Junya; Ghatan, Alexander; Bresler, Noah; Frosch, Matthew P.; Klaming, Ruth; Corkin, Suzanne

    2014-01-01

    Modern scientific knowledge of how memory functions are organized in the human brain originated from the case of Henry G. Molaison (H.M.), an epileptic patient whose amnesia ensued unexpectedly following a bilateral surgical ablation of medial temporal lobe structures, including the hippocampus. The neuroanatomical extent of the 1953 operation could not be assessed definitively during H.M.’s life. Here we describe the results of a procedure designed to reconstruct a microscopic anatomical model of the whole brain and conduct detailed 3D measurements in the medial temporal lobe region. This approach, combined with cellular-level imaging of stained histological slices, demonstrates a significant amount of residual hippocampal tissue with distinctive cytoarchitecture. Our study also reveals diffuse pathology in the deep white matter and a small, circumscribed lesion in the left orbitofrontal cortex. The findings constitute new evidence that may help elucidate the consequences of H.M.’s operation in the context of the brain’s overall pathology. PMID:24473151

  9. Changes in topological organization of functional PET brain network with normal aging.

    PubMed

    Liu, Zhiliang; Ke, Lining; Liu, Huafeng; Huang, Wenhua; Hu, Zhenghui

    2014-01-01

    Recent studies about brain network have suggested that normal aging is associated with alterations in coordinated patterns of the large-scale brain functional and structural systems. However, age-related changes in functional networks constructed via positron emission tomography (PET) data are still barely understood. Here, we constructed functional brain networks composed of 90 regions in younger (mean age 36.5 years) and older (mean age 56.3 years) age groups with PET data. 113 younger and 110 older healthy individuals were separately selected for two age groups, from a physical examination database. Corresponding brain functional networks of the two groups were constructed by thresholding average cerebral glucose metabolism correlation matrices of 90 regions and analysed using graph theoretical approaches. Although both groups showed normal small-world architecture in the PET networks, increased clustering and decreased efficiency were found in older subjects, implying a degeneration process that brain system shifts from a small-world network to regular one along with normal aging. Moreover, normal senescence was related to changed nodal centralities predominantly in association and paralimbic cortex regions, e.g. increasing in orbitofrontal cortex (middle) and decreasing in left hippocampus. Additionally, the older networks were about equally as robust to random failures as younger counterpart, but more vulnerable against targeted attacks. Finally, methods in the construction of the PET networks revealed reasonable robustness. Our findings enhanced the understanding about the topological principles of PET networks and changes related to normal aging.

  10. Changes in Topological Organization of Functional PET Brain Network with Normal Aging

    PubMed Central

    Liu, Huafeng; Huang, Wenhua; Hu, Zhenghui

    2014-01-01

    Recent studies about brain network have suggested that normal aging is associated with alterations in coordinated patterns of the large-scale brain functional and structural systems. However, age-related changes in functional networks constructed via positron emission tomography (PET) data are still barely understood. Here, we constructed functional brain networks composed of regions in younger (mean age years) and older (mean age years) age groups with PET data. younger and older healthy individuals were separately selected for two age groups, from a physical examination database. Corresponding brain functional networks of the two groups were constructed by thresholding average cerebral glucose metabolism correlation matrices of regions and analysed using graph theoretical approaches. Although both groups showed normal small-world architecture in the PET networks, increased clustering and decreased efficiency were found in older subjects, implying a degeneration process that brain system shifts from a small-world network to regular one along with normal aging. Moreover, normal senescence was related to changed nodal centralities predominantly in association and paralimbic cortex regions, e.g. increasing in orbitofrontal cortex (middle) and decreasing in left hippocampus. Additionally, the older networks were about equally as robust to random failures as younger counterpart, but more vulnerable against targeted attacks. Finally, methods in the construction of the PET networks revealed reasonable robustness. Our findings enhanced the understanding about the topological principles of PET networks and changes related to normal aging. PMID:24586370

  11. Anatomy-guided brain PET imaging incorporating a joint prior model

    NASA Astrophysics Data System (ADS)

    Lu, Lijun; Ma, Jianhua; Feng, Qianjin; Chen, Wufan; Rahmim, Arman

    2015-03-01

    We proposed a maximum a posterior (MAP) framework for incorporating information from co-registered anatomical images into PET image reconstruction through a novel anato-functional joint prior. The characteristic of the utilized hyperbolic potential function is determinate by the voxel intensity differences within the anatomical image, while the penalization is computed based on voxel intensity differences in reconstructed PET images. Using realistic simulated 18FDG PET scan data, we optimized the performance of the proposed MAP reconstruction with the joint prior (JP-MAP) and compared its performance with conventional 3D MLEM and 3D MAP reconstructions. The proposed JP-MAP reconstruction algorithm resulted in quantitatively enhanced reconstructed images, as demonstrated in extensive FDG PET simulation study. The proposed method was also tested on a 20 min Florbetapir patient study performed on the high-resolution research tomograph. It was shown to outperform conventional methods in visual as well as quantitative accuracy assessment (in terms of regional noise versus activity value performance). The JP-MAP method was also compared with another MR-guided MAP reconstruction method, utilizing the Bowsher prior and was seen to result in some quantitative enhancements, especially in the case of MR-PET mis-registrations, and a definitive improvement in computational performance.

  12. Global cerebral glucose utilization is independent of brain size: a PET Study

    SciTech Connect

    Hatazawa, J.; Brooks, R.A.; Di Chiro, G.; Campbell, G.

    1987-07-01

    Cerebral glucose metabolic rates were measured in 80 normal volunteers by studying the uptake of (/sup 18/F)deoxyglucose with positron emission tomography (PET), using three PET scanners. A brain size index was determined from the PET images using either length-width or area measurements of the brain at a standard level. There was a significant negative correlation between glucose metabolism per unit volume and brain size that was well described by an inverse functional relationship, implying that the total glucose consumption of the brain is approximately constant. Analyses of men versus women revealed no sex differences in total brain glucose consumption, although there were differences in brain size and in glucose metabolism per unit volume. Similarly there was no significant correlation of total brain glucose consumption with age. The variation with brain size accounted for 46% of the logarithmic intersubject metabolic variance. When comparing global metabolic rates in different subjects, multiplying the rates by a brain size index has the dual advantage of correcting for differences related to brain size and correcting for differences in cerebrospinal fluid volume.

  13. Effect of Cyclosporin A on the Uptake of D3-Selective PET Radiotracers in Rat Brain

    PubMed Central

    Tu, Zhude; Li, Shihong; Xu, Jinbin; Chu, Wenhua; Jones, Lynne A.; Luedtke, Robert R.; Mach, Robert H.

    2011-01-01

    Introduction Four benzamide analogs having a high affinity and selectivity for D3 versus D2 receptors were radiolabeled with 11C or 18F for in vivo evaluation. Methods Precursors were synthesized and the four D3 selective benzamide analogs were radiolabeled. The tissue distribution and brain uptake of the four compounds were evaluated in control rats and rats pretreated with cyclosporin A, a modulator of P-glycoprotein and an inhibitor of other ABC efflux transporters that contribute to the blood brain barrier. MicroPET imaging was carried out for [11C]6 in a control and a cyclosporin A pre-treated rat. Results All four compounds showed low brain uptake in control rats at 5 and 30 min post-injection; despite recently reported rat behavioral studies conducted on analogs 6 (WC-10) and 7 (WC-44). Following administration of cyclosporin A, increased brain uptake was observed with all four PET radiotracers at both 5 and 30 min post-i.v. injection. An increase in brain uptake following modulation/inhibition of the ABC transporters was also observed in the microPET study. Conclusions These data suggest that D3 selective conformationally-flexible benzamide analogs which contain a N-2-methoxyphenylpiperazine moiety are substrates for P-glycoprotein or other ABC transporters expressed at the blood-brain barrier, and that PET radiotracers containing this pharmacophore may display low brain uptake in rodents due to the action of these efflux transporters. PMID:21718948

  14. A unified approach to diffusion direction sensitive slice registration and 3-D DTI reconstruction from moving fetal brain anatomy.

    PubMed

    Fogtmann, Mads; Seshamani, Sharmishtaa; Kroenke, Christopher; Xi Cheng; Chapman, Teresa; Wilm, Jakob; Rousseau, Francois; Studholme, Colin

    2014-02-01

    This paper presents an approach to 3-D diffusion tensor image (DTI) reconstruction from multi-slice diffusion weighted (DW) magnetic resonance imaging acquisitions of the moving fetal brain. Motion scatters the slice measurements in the spatial and spherical diffusion domain with respect to the underlying anatomy. Previous image registration techniques have been described to estimate the between slice fetal head motion, allowing the reconstruction of 3D a diffusion estimate on a regular grid using interpolation. We propose Approach to Unified Diffusion Sensitive Slice Alignment and Reconstruction (AUDiSSAR) that explicitly formulates a process for diffusion direction sensitive DW-slice-to-DTI-volume alignment. This also incorporates image resolution modeling to iteratively deconvolve the effects of the imaging point spread function using the multiple views provided by thick slices acquired in different anatomical planes. The algorithm is implemented using a multi-resolution iterative scheme and multiple real and synthetic data are used to evaluate the performance of the technique. An accuracy experiment using synthetically created motion data of an adult head and an experiment using synthetic motion added to sedated fetal monkey dataset show a significant improvement in motion-trajectory estimation compared to current state-of-the-art approaches. The performance of the method is then evaluated on challenging but clinically typical in utero fetal scans of four different human cases, showing improved rendition of cortical anatomy and extraction of white matter tracts. While the experimental work focuses on DTI reconstruction (second-order tensor model), the proposed reconstruction framework can employ any 5-D diffusion volume model that can be represented by the spatial parameterizations of an orientation distribution function.

  15. A Unified Approach to Diffusion Direction Sensitive Slice Registration and 3-D DTI Reconstruction From Moving Fetal Brain Anatomy

    PubMed Central

    Fogtmann, Mads; Seshamani, Sharmishtaa; Kroenke, Christopher; Cheng, Xi; Chapman, Teresa; Wilm, Jakob; Rousseau, François

    2014-01-01

    This paper presents an approach to 3-D diffusion tensor image (DTI) reconstruction from multi-slice diffusion weighted (DW) magnetic resonance imaging acquisitions of the moving fetal brain. Motion scatters the slice measurements in the spatial and spherical diffusion domain with respect to the underlying anatomy. Previous image registration techniques have been described to estimate the between slice fetal head motion, allowing the reconstruction of 3-D a diffusion estimate on a regular grid using interpolation. We propose Approach to Unified Diffusion Sensitive Slice Alignment and Reconstruction (AUDiSSAR) that explicitly formulates a process for diffusion direction sensitive DW-slice-to-DTI-volume alignment. This also incorporates image resolution modeling to iteratively deconvolve the effects of the imaging point spread function using the multiple views provided by thick slices acquired in different anatomical planes. The algorithm is implemented using a multi-resolution iterative scheme and multiple real and synthetic data are used to evaluate the performance of the technique. An accuracy experiment using synthetically created motion data of an adult head and a experiment using synthetic motion added to sedated fetal monkey dataset show a significant improvement in motion-trajectory estimation compared to a state-of-the-art approaches. The performance of the method is then evaluated on challenging but clinically typical in utero fetal scans of four different human cases, showing improved rendition of cortical anatomy and extraction of white matter tracts. While the experimental work focuses on DTI reconstruction (second-order tensor model), the proposed reconstruction framework can employ any 5-D diffusion volume model that can be represented by the spatial parameterizations of an orientation distribution function. PMID:24108711

  16. Image derived input functions for dynamic High Resolution Research Tomograph PET brain studies.

    PubMed

    Mourik, Jurgen E M; van Velden, Floris H P; Lubberink, Mark; Kloet, Reina W; van Berckel, Bart N M; Lammertsma, Adriaan A; Boellaard, Ronald

    2008-12-01

    The High Resolution Research Tomograph (HRRT) is a dedicated human brain positron emission tomography (PET) scanner. The aim of the present study was to validate the use of image derived input functions (IDIF) as an alternative for arterial sampling for HRRT human brain studies. To this end, IDIFs were extracted from 3D ordinary Poisson ordered subsets expectation maximization (OP-OSEM) and reconstruction based partial volume corrected (PVC) OP-OSEM images. IDIFs, either derived directly from regions of interest or further calibrated using manual samples taken during scans, were evaluated for dynamic [(11)C]flumazenil data (n=6). Results obtained with IDIFs were compared with those obtained using blood sampler input functions (BSIF). These comparisons included areas under the curve (AUC) for peak (0-3.3 min) and tail (3.3-55.0 min). In addition, slope, intercept and Pearson's correlation coefficient of tracer kinetic analysis results based on IDIF and BSIF were calculated for each subject. Good peak AUC ratios (0.83+/-0.21) between IDIF and BSIF were found for calibrated IDIFs extracted from OP-OSEM images. This combination of IDIFs and images also provided good slope values (1.07+/-0.11). Improved resolution, as obtained with PVC OP-OSEM, changed AUC ratios to 1.14+/-0.35 and, for tracer kinetic analysis, slopes changed to 0.95+/-0.13. For all reconstructions, non-calibrated IDIFs gave poorer results (>61+/-34% higher slopes) compared with calibrated IDIFs. The results of this study indicate that the use of IDIFs, extracted from OP-OSEM or PVC OP-OSEM images, is feasible for dynamic HRRT data, thereby obviating the need for online arterial sampling.

  17. Simultaneous PET-MRI reveals brain function in activated and resting state on metabolic, hemodynamic and multiple temporal scales.

    PubMed

    Wehrl, Hans F; Hossain, Mosaddek; Lankes, Konrad; Liu, Chih-Chieh; Bezrukov, Ilja; Martirosian, Petros; Schick, Fritz; Reischl, Gerald; Pichler, Bernd J

    2013-09-01

    Combined positron emission tomography (PET) and magnetic resonance imaging (MRI) is a new tool to study functional processes in the brain. Here we study brain function in response to a barrel-field stimulus simultaneously using PET, which traces changes in glucose metabolism on a slow time scale, and functional MRI (fMRI), which assesses fast vascular and oxygenation changes during activation. We found spatial and quantitative discrepancies between the PET and the fMRI activation data. The functional connectivity of the rat brain was assessed by both modalities: the fMRI approach determined a total of nine known neural networks, whereas the PET method identified seven glucose metabolism-related networks. These results demonstrate the feasibility of combined PET-MRI for the simultaneous study of the brain at activation and rest, revealing comprehensive and complementary information to further decode brain function and brain networks.

  18. F18 EF5 PET/CT Imaging in Patients with Brain Metastases from Breast Cancer

    DTIC Science & Technology

    2013-07-01

    with Brain Metastases from Breast Cancer PRINCIPAL INVESTIGATOR: Lilie Lin, MD CONTRACTING ORGANIZATION: University of Pennsylvania...Annual 3. DATES COVERED 01 July 2012 to 30 June 2013 4. TITLE AND SUBTITLE F18 EF5 PET/CT Imaging in Patients with Brain Metastases from Breast 5a...SUPPLEMENTARY NOTES 14. ABSTRACT The aim of this study is to estimate the degree of residual hypoxia after whole brain radiation therapy in patients

  19. A System for True and False Memory Prediction Based on 2D and 3D Educational Contents and EEG Brain Signals

    PubMed Central

    2016-01-01

    We studied the impact of 2D and 3D educational contents on learning and memory recall using electroencephalography (EEG) brain signals. For this purpose, we adopted a classification approach that predicts true and false memories in case of both short term memory (STM) and long term memory (LTM) and helps to decide whether there is a difference between the impact of 2D and 3D educational contents. In this approach, EEG brain signals are converted into topomaps and then discriminative features are extracted from them and finally support vector machine (SVM) which is employed to predict brain states. For data collection, half of sixty-eight healthy individuals watched the learning material in 2D format whereas the rest watched the same material in 3D format. After learning task, memory recall tasks were performed after 30 minutes (STM) and two months (LTM), and EEG signals were recorded. In case of STM, 97.5% prediction accuracy was achieved for 3D and 96.6% for 2D and, in case of LTM, it was 100% for both 2D and 3D. The statistical analysis of the results suggested that for learning and memory recall both 2D and 3D materials do not have much difference in case of STM and LTM. PMID:26819593

  20. A System for True and False Memory Prediction Based on 2D and 3D Educational Contents and EEG Brain Signals.

    PubMed

    Bamatraf, Saeed; Hussain, Muhammad; Aboalsamh, Hatim; Qazi, Emad-Ul-Haq; Malik, Amir Saeed; Amin, Hafeez Ullah; Mathkour, Hassan; Muhammad, Ghulam; Imran, Hafiz Muhammad

    2016-01-01

    We studied the impact of 2D and 3D educational contents on learning and memory recall using electroencephalography (EEG) brain signals. For this purpose, we adopted a classification approach that predicts true and false memories in case of both short term memory (STM) and long term memory (LTM) and helps to decide whether there is a difference between the impact of 2D and 3D educational contents. In this approach, EEG brain signals are converted into topomaps and then discriminative features are extracted from them and finally support vector machine (SVM) which is employed to predict brain states. For data collection, half of sixty-eight healthy individuals watched the learning material in 2D format whereas the rest watched the same material in 3D format. After learning task, memory recall tasks were performed after 30 minutes (STM) and two months (LTM), and EEG signals were recorded. In case of STM, 97.5% prediction accuracy was achieved for 3D and 96.6% for 2D and, in case of LTM, it was 100% for both 2D and 3D. The statistical analysis of the results suggested that for learning and memory recall both 2D and 3D materials do not have much difference in case of STM and LTM.

  1. A discriminative model-constrained EM approach to 3D MRI brain tissue classification and intensity non-uniformity correction

    NASA Astrophysics Data System (ADS)

    Wels, Michael; Zheng, Yefeng; Huber, Martin; Hornegger, Joachim; Comaniciu, Dorin

    2011-06-01

    We describe a fully automated method for tissue classification, which is the segmentation into cerebral gray matter (GM), cerebral white matter (WM), and cerebral spinal fluid (CSF), and intensity non-uniformity (INU) correction in brain magnetic resonance imaging (MRI) volumes. It combines supervised MRI modality-specific discriminative modeling and unsupervised statistical expectation maximization (EM) segmentation into an integrated Bayesian framework. While both the parametric observation models and the non-parametrically modeled INUs are estimated via EM during segmentation itself, a Markov random field (MRF) prior model regularizes segmentation and parameter estimation. Firstly, the regularization takes into account knowledge about spatial and appearance-related homogeneity of segments in terms of pairwise clique potentials of adjacent voxels. Secondly and more importantly, patient-specific knowledge about the global spatial distribution of brain tissue is incorporated into the segmentation process via unary clique potentials. They are based on a strong discriminative model provided by a probabilistic boosting tree (PBT) for classifying image voxels. It relies on the surrounding context and alignment-based features derived from a probabilistic anatomical atlas. The context considered is encoded by 3D Haar-like features of reduced INU sensitivity. Alignment is carried out fully automatically by means of an affine registration algorithm minimizing cross-correlation. Both types of features do not immediately use the observed intensities provided by the MRI modality but instead rely on specifically transformed features, which are less sensitive to MRI artifacts. Detailed quantitative evaluations on standard phantom scans and standard real-world data show the accuracy and robustness of the proposed method. They also demonstrate relative superiority in comparison to other state-of-the-art approaches to this kind of computational task: our method achieves average

  2. 5-HT Radioligands for Human Brain Imaging With PET and SPECT

    PubMed Central

    Paterson, Louise M.; Kornum, Birgitte R.; Nutt, David J.; Pike, Victor W.; Knudsen, Gitte M.

    2014-01-01

    The serotonergic system plays a key modulatory role in the brain and is the target for many drug treatments for brain disorders either through reuptake blockade or via interactions at the 14 subtypes of 5-HT receptors. This review provides the history and current status of radioligands used for positron emission tomography (PET) and single photon emission computerized tomography (SPECT) imaging of human brain serotonin (5-HT) receptors, the 5-HT transporter (SERT), and 5-HT synthesis rate. Currently available radioligands for in vivo brain imaging of the 5-HT system in humans include antagonists for the 5-HT1A, 5-HT1B, 5-HT2A, and 5-HT4 receptors, and for SERT. Here we describe the evolution of these radioligands, along with the attempts made to develop radioligands for additional serotonergic targets. We describe the properties needed for a radioligand to become successful and the main caveats. The success of a PET or SPECT radioligand can ultimately be assessed by its frequency of use, its utility in humans, and the number of research sites using it relative to its invention date, and so these aspects are also covered. In conclusion, the development of PET and SPECT radioligands to image serotonergic targets is of high interest, and successful evaluation in humans is leading to invaluable insight into normal and abnormal brain function, emphasizing the need for continued development of both SPECT and PET radioligands for human brain imaging. PMID:21674551

  3. MRI-guided brain PET image filtering and partial volume correction.

    PubMed

    Yan, Jianhua; Lim, Jason Chu-Shern; Townsend, David W

    2015-02-07

    Positron emission tomography (PET) image quantification is a challenging problem due to limited spatial resolution of acquired data and the resulting partial volume effects (PVE), which depend on the size of the structure studied in relation to the spatial resolution and which may lead to over or underestimation of the true tissue tracer concentration. In addition, it is usually necessary to perform image smoothing either during image reconstruction or afterwards to achieve a reasonable signal-to-noise ratio. Typically, an isotropic Gaussian filtering (GF) is used for this purpose. However, the noise suppression is at the cost of deteriorating spatial resolution. As hybrid imaging devices such as PET/MRI have become available, the complementary information derived from high definition morphologic images could be used to improve the quality of PET images. In this study, first of all, we propose an MRI-guided PET filtering method by adapting a recently proposed local linear model and then incorporate PVE into the model to get a new partial volume correction (PVC) method without parcellation of MRI. In addition, both the new filtering and PVC are voxel-wise non-iterative methods. The performance of the proposed methods were investigated with simulated dynamic FDG brain dataset and (18)F-FDG brain data of a cervical cancer patient acquired with a simultaneous hybrid PET/MR scanner. The initial simulation results demonstrated that MRI-guided PET image filtering can produce less noisy images than traditional GF and bias and coefficient of variation can be further reduced by MRI-guided PET PVC. Moreover, structures can be much better delineated in MRI-guided PET PVC for real brain data.

  4. MRI-guided brain PET image filtering and partial volume correction

    NASA Astrophysics Data System (ADS)

    Yan, Jianhua; Chu-Shern Lim, Jason; Townsend, David W.

    2015-02-01

    Positron emission tomography (PET) image quantification is a challenging problem due to limited spatial resolution of acquired data and the resulting partial volume effects (PVE), which depend on the size of the structure studied in relation to the spatial resolution and which may lead to over or underestimation of the true tissue tracer concentration. In addition, it is usually necessary to perform image smoothing either during image reconstruction or afterwards to achieve a reasonable signal-to-noise ratio. Typically, an isotropic Gaussian filtering (GF) is used for this purpose. However, the noise suppression is at the cost of deteriorating spatial resolution. As hybrid imaging devices such as PET/MRI have become available, the complementary information derived from high definition morphologic images could be used to improve the quality of PET images. In this study, first of all, we propose an MRI-guided PET filtering method by adapting a recently proposed local linear model and then incorporate PVE into the model to get a new partial volume correction (PVC) method without parcellation of MRI. In addition, both the new filtering and PVC are voxel-wise non-iterative methods. The performance of the proposed methods were investigated with simulated dynamic FDG brain dataset and 18F-FDG brain data of a cervical cancer patient acquired with a simultaneous hybrid PET/MR scanner. The initial simulation results demonstrated that MRI-guided PET image filtering can produce less noisy images than traditional GF and bias and coefficient of variation can be further reduced by MRI-guided PET PVC. Moreover, structures can be much better delineated in MRI-guided PET PVC for real brain data.

  5. Quantitative Evaluation of Atlas-based Attenuation Correction for Brain PET in an Integrated Time-of-Flight PET/MR Imaging System.

    PubMed

    Yang, Jaewon; Jian, Yiqiang; Jenkins, Nathaniel; Behr, Spencer C; Hope, Thomas A; Larson, Peder E Z; Vigneron, Daniel; Seo, Youngho

    2017-02-23

    Purpose To assess the patient-dependent accuracy of atlas-based attenuation correction (ATAC) for brain positron emission tomography (PET) in an integrated time-of-flight (TOF) PET/magnetic resonance (MR) imaging system. Materials and Methods Thirty recruited patients provided informed consent in this institutional review board-approved study. All patients underwent whole-body fluorodeoxyglucose PET/computed tomography (CT) followed by TOF PET/MR imaging. With use of TOF PET data, PET images were reconstructed with four different attenuation correction (AC) methods: PET with patient CT-based AC (CTAC), PET with ATAC (air and bone from an atlas), PET with ATACpatientBone (air and tissue from the atlas with patient bone), and PET with ATACboneless (air and tissue from the atlas without bone). For quantitative evaluation, PET mean activity concentration values were measured in 14 1-mL volumes of interest (VOIs) distributed throughout the brain and statistical significance was tested with a paired t test. Results The mean overall difference (±standard deviation) of PET with ATAC compared with PET with CTAC was -0.69 kBq/mL ± 0.60 (-4.0% ± 3.2) (P < .001). The results were patient dependent (range, -9.3% to 0.57%) and VOI dependent (range, -5.9 to -2.2). In addition, when bone was not included for AC, the overall difference of PET with ATACboneless (-9.4% ± 3.7) was significantly worse than that of PET with ATAC (-4.0% ± 3.2) (P < .001). Finally, when patient bone was used for AC instead of atlas bone, the overall difference of PET with ATACpatientBone (-1.5% ± 1.5) improved over that of PET with ATAC (-4.0% ± 3.2) (P < .001). Conclusion ATAC in PET/MR imaging achieves similar quantification accuracy to that from CTAC by means of atlas-based bone compensation. However, patient-specific anatomic differences from the atlas causes bone attenuation differences and misclassified sinuses, which result in patient-dependent performance variation of ATAC. (©) RSNA, 2017

  6. Proposed helmet PET geometries with add-on detectors for high sensitivity brain imaging.

    PubMed

    Tashima, Hideaki; Yamaya, Taiga

    2016-10-07

    For dedicated brain PET, we can significantly improve sensitivity for the cerebrum region by arranging detectors in a compact hemisphere. The geometrical sensitivity for the top region of the hemisphere is increased compared with conventional cylindrical PET consisting of the same number of detectors. However, the geometrical sensitivity at the center region of the hemisphere is still low because the bottom edge of the field-of-view is open, the same as for the cylindrical PET. In this paper, we proposed a helmet PET with add-on detectors for high sensitivity brain PET imaging for both center and top regions. The key point is the add-on detectors covering some portion of the spherical surface in addition to the hemisphere. As the location of the add-on detectors, we proposed three choices: a chin detector, ear detectors, and a neck detector. For example, the geometrical sensitivity for the region-of-interest at the center was increased by 200% by adding the chin detector which increased the size by 12% of the size of the hemisphere detector. The other add-on detectors gave almost the same increased sensitivity effect as the chin detector did. Compared with standard whole-body-cylindrical PET, the proposed geometries can achieve 2.6 times higher sensitivity for brain region even with less than 1/4 detectors. In addition, we conducted imaging simulations for geometries with a diameter of 250 mm and with high resolution depth-of-interaction detectors. The simulation results showed that the proposed geometries increased image quality, and all of the add-on detectors were equivalently effective. In conclusion, the proposed geometries have high potential for widespread applications in high-sensitivity, high-resolution, and low-cost brain PET imaging.

  7. Proposed helmet PET geometries with add-on detectors for high sensitivity brain imaging

    NASA Astrophysics Data System (ADS)

    Tashima, Hideaki; Yamaya, Taiga

    2016-10-01

    For dedicated brain PET, we can significantly improve sensitivity for the cerebrum region by arranging detectors in a compact hemisphere. The geometrical sensitivity for the top region of the hemisphere is increased compared with conventional cylindrical PET consisting of the same number of detectors. However, the geometrical sensitivity at the center region of the hemisphere is still low because the bottom edge of the field-of-view is open, the same as for the cylindrical PET. In this paper, we proposed a helmet PET with add-on detectors for high sensitivity brain PET imaging for both center and top regions. The key point is the add-on detectors covering some portion of the spherical surface in addition to the hemisphere. As the location of the add-on detectors, we proposed three choices: a chin detector, ear detectors, and a neck detector. For example, the geometrical sensitivity for the region-of-interest at the center was increased by 200% by adding the chin detector which increased the size by 12% of the size of the hemisphere detector. The other add-on detectors gave almost the same increased sensitivity effect as the chin detector did. Compared with standard whole-body-cylindrical PET, the proposed geometries can achieve 2.6 times higher sensitivity for brain region even with less than 1/4 detectors. In addition, we conducted imaging simulations for geometries with a diameter of 250 mm and with high resolution depth-of-interaction detectors. The simulation results showed that the proposed geometries increased image quality, and all of the add-on detectors were equivalently effective. In conclusion, the proposed geometries have high potential for widespread applications in high-sensitivity, high-resolution, and low-cost brain PET imaging.

  8. Strain and rate-dependent neuronal injury in a 3D in vitro compression model of traumatic brain injury.

    PubMed

    Bar-Kochba, Eyal; Scimone, Mark T; Estrada, Jonathan B; Franck, Christian

    2016-08-02

    In the United States over 1.7 million cases of traumatic brain injury are reported yearly, but predictive correlation of cellular injury to impact tissue strain is still lacking, particularly for neuronal injury resulting from compression. Given the prevalence of compressive deformations in most blunt head trauma, this information is critically important for the development of future mitigation and diagnosis strategies. Using a 3D in vitro neuronal compression model, we investigated the role of impact strain and strain rate on neuronal lifetime, viability, and pathomorphology. We find that strain magnitude and rate have profound, yet distinctively different effects on the injury pathology. While strain magnitude affects the time of neuronal death, strain rate influences the pathomorphology and extent of population injury. Cellular injury is not initiated through localized deformation of the cytoskeleton but rather driven by excess strain on the entire cell. Furthermore we find that, mechanoporation, one of the key pathological trigger mechanisms in stretch and shear neuronal injuries, was not observed under compression.

  9. Strain and rate-dependent neuronal injury in a 3D in vitro compression model of traumatic brain injury

    NASA Astrophysics Data System (ADS)

    Bar-Kochba, Eyal; Scimone, Mark T.; Estrada, Jonathan B.; Franck, Christian

    2016-08-01

    In the United States over 1.7 million cases of traumatic brain injury are reported yearly, but predictive correlation of cellular injury to impact tissue strain is still lacking, particularly for neuronal injury resulting from compression. Given the prevalence of compressive deformations in most blunt head trauma, this information is critically important for the development of future mitigation and diagnosis strategies. Using a 3D in vitro neuronal compression model, we investigated the role of impact strain and strain rate on neuronal lifetime, viability, and pathomorphology. We find that strain magnitude and rate have profound, yet distinctively different effects on the injury pathology. While strain magnitude affects the time of neuronal death, strain rate influences the pathomorphology and extent of population injury. Cellular injury is not initiated through localized deformation of the cytoskeleton but rather driven by excess strain on the entire cell. Furthermore we find that, mechanoporation, one of the key pathological trigger mechanisms in stretch and shear neuronal injuries, was not observed under compression.

  10. Strain and rate-dependent neuronal injury in a 3D in vitro compression model of traumatic brain injury

    PubMed Central

    Bar-Kochba, Eyal; Scimone, Mark T.; Estrada, Jonathan B.; Franck, Christian

    2016-01-01

    In the United States over 1.7 million cases of traumatic brain injury are reported yearly, but predictive correlation of cellular injury to impact tissue strain is still lacking, particularly for neuronal injury resulting from compression. Given the prevalence of compressive deformations in most blunt head trauma, this information is critically important for the development of future mitigation and diagnosis strategies. Using a 3D in vitro neuronal compression model, we investigated the role of impact strain and strain rate on neuronal lifetime, viability, and pathomorphology. We find that strain magnitude and rate have profound, yet distinctively different effects on the injury pathology. While strain magnitude affects the time of neuronal death, strain rate influences the pathomorphology and extent of population injury. Cellular injury is not initiated through localized deformation of the cytoskeleton but rather driven by excess strain on the entire cell. Furthermore we find that, mechanoporation, one of the key pathological trigger mechanisms in stretch and shear neuronal injuries, was not observed under compression. PMID:27480807

  11. PET Radiotracers: crossing the blood-brain barrier and surviving metabolism

    PubMed Central

    Pike, Victor W.

    2009-01-01

    Radiotracers for imaging protein targets in living human brain with positron emission tomography (PET) are increasingly useful in clinical research and in drug development. Such radiotracers must fulfill many criteria, among which an ability to enter brain adequately and reversibly without contamination by troublesome radiometabolites is desirable for accurate measurement of the density of a target protein (e.g., neuroreceptor, transporter, enzyme or plaque). Candidate radiotracers may fail as a result of poor passive brain entry, rejection from brain by efflux transporters or undesirable metabolism. These issues are reviewed. Emerging PET radiotracers for measuring efflux transporter function, and new strategies for ameliorating radiotracer metabolism are discussed. A growing understanding of the molecular features affecting the brain penetration, metabolism and efflux transporter sensitivity of prospective radiotracers should ultimately lead to their more rational and efficient design, and also to their greater efficacy. PMID:19616318

  12. Segmentation of brain PET-CT images based on adaptive use of complementary information

    NASA Astrophysics Data System (ADS)

    Xia, Yong; Wen, Lingfeng; Eberl, Stefan; Fulham, Michael; Feng, Dagan

    2009-02-01

    Dual modality PET-CT imaging provides aligned anatomical (CT) and functional (PET) images in a single scanning session, which can potentially be used to improve image segmentation of PET-CT data. The ability to distinguish structures for segmentation is a function of structure and modality and varies across voxels. Thus optimal contribution of a particular modality to segmentation is spatially variant. Existing segmentation algorithms, however, seldom account for this characteristic of PET-CT data and the results using these algorithms are not optimal. In this study, we propose a relative discrimination index (RDI) to characterize the relative abilities of PET and CT to correctly classify each voxel into the correct structure for segmentation. The definition of RDI is based on the information entropy of the probability distribution of the voxel's class label. If the class label derived from CT data for a particular voxel has more certainty than that derived from PET data, the corresponding RDI will have a higher value. We applied the RDI matrix to balance adaptively the contributions of PET and CT data to segmentation of brain PET-CT images on a voxel-by-voxel basis, with the aim to give the modality with higher discriminatory power a larger weight. The resultant segmentation approach is distinguished from traditional approaches by its innovative and adaptive use of the dual-modality information. We compared our approach to the non-RDI version and two commonly used PET-only based segmentation algorithms for simulation and clinical data. Our results show that the RDI matrix markedly improved PET-CT image segmentation.

  13. Comparison of 3D-OP-OSEM and 3D-FBP reconstruction algorithms for High-Resolution Research Tomograph studies: effects of randoms estimation methods

    NASA Astrophysics Data System (ADS)

    van Velden, Floris H. P.; Kloet, Reina W.; van Berckel, Bart N. M.; Wolfensberger, Saskia P. A.; Lammertsma, Adriaan A.; Boellaard, Ronald

    2008-06-01

    The High-Resolution Research Tomograph (HRRT) is a dedicated human brain positron emission tomography (PET) scanner. Recently, a 3D filtered backprojection (3D-FBP) reconstruction method has been implemented to reduce bias in short duration frames, currently observed in 3D ordinary Poisson OSEM (3D-OP-OSEM) reconstructions. Further improvements might be expected using a new method of variance reduction on randoms (VRR) based on coincidence histograms instead of using the delayed window technique (DW) to estimate randoms. The goal of this study was to evaluate VRR in combination with 3D-OP-OSEM and 3D-FBP reconstruction techniques. To this end, several phantom studies and a human brain study were performed. For most phantom studies, 3D-OP-OSEM showed higher accuracy of observed activity concentrations with VRR than with DW. However, both positive and negative deviations in reconstructed activity concentrations and large biases of grey to white matter contrast ratio (up to 88%) were still observed as a function of scan statistics. Moreover 3D-OP-OSEM+VRR also showed bias up to 64% in clinical data, i.e. in some pharmacokinetic parameters as compared with those obtained with 3D-FBP+VRR. In the case of 3D-FBP, VRR showed similar results as DW for both phantom and clinical data, except that VRR showed a better standard deviation of 6-10%. Therefore, VRR should be used to correct for randoms in HRRT PET studies.

  14. Repurposing the Microsoft Kinect for Windows v2 for external head motion tracking for brain PET

    NASA Astrophysics Data System (ADS)

    Noonan, P. J.; Howard, J.; Hallett, W. A.; Gunn, R. N.

    2015-11-01

    Medical imaging systems such as those used in positron emission tomography (PET) are capable of spatial resolutions that enable the imaging of small, functionally important brain structures. However, the quality of data from PET brain studies is often limited by subject motion during acquisition. This is particularly challenging for patients with neurological disorders or with dynamic research studies that can last 90 min or more. Restraining head movement during the scan does not eliminate motion entirely and can be unpleasant for the subject. Head motion can be detected and measured using a variety of techniques that either use the PET data itself or an external tracking system. Advances in computer vision arising from the video gaming industry could offer significant benefits when re-purposed for medical applications. A method for measuring rigid body type head motion using the Microsoft Kinect v2 is described with results presenting  ⩽0.5 mm spatial accuracy. Motion data is measured in real-time at 30 Hz using the KinectFusion algorithm. Non-rigid motion is detected using the residual alignment energy data of the KinectFusion algorithm allowing for unreliable motion to be discarded. Motion data is aligned to PET listmode data using injected pulse sequences into the PET/CT gantry allowing for correction of rigid body motion. Pilot data from a clinical dynamic PET/CT examination is shown.

  15. Advances in PET imaging of P-glycoprotein function at the blood-brain barrier.

    PubMed

    Syvänen, Stina; Eriksson, Jonas

    2013-02-20

    Efflux transporter P-glycoprotein (P-gp) at the blood-brain barrier (BBB) restricts substrate compounds from entering the brain and may thus contribute to pharmacoresistance observed in patient groups with refractory epilepsy and HIV. Altered P-gp function has also been implicated in neurodegenerative diseases such as Alzheimer's and Parkinson's disease. Positron emission tomography (PET), a molecular imaging modality, has become a promising method to study the role of P-gp at the BBB. The first PET study of P-gp function was conducted in 1998, and during the past 15 years two main categories of P-gp PET tracers have been investigated: tracers that are substrates of P-gp efflux and tracers that are inhibitors of P-gp function. PET, as a noninvasive imaging technique, allows translational research. Examples of this are preclinical investigations of P-gp function before and after administering P-gp modulating drugs, investigations in various animal and disease models, and clinical investigations regarding disease and aging. The objective of the present review is to give an overview of available PET radiotracers for studies of P-gp and to discuss how such studies can be designed. Further, the review summarizes results from PET studies of P-gp function in different central nervous system disorders.

  16. Repurposing the Microsoft Kinect for Windows v2 for external head motion tracking for brain PET.

    PubMed

    Noonan, P J; Howard, J; Hallett, W A; Gunn, R N

    2015-11-21

    Medical imaging systems such as those used in positron emission tomography (PET) are capable of spatial resolutions that enable the imaging of small, functionally important brain structures. However, the quality of data from PET brain studies is often limited by subject motion during acquisition. This is particularly challenging for patients with neurological disorders or with dynamic research studies that can last 90 min or more. Restraining head movement during the scan does not eliminate motion entirely and can be unpleasant for the subject. Head motion can be detected and measured using a variety of techniques that either use the PET data itself or an external tracking system. Advances in computer vision arising from the video gaming industry could offer significant benefits when re-purposed for medical applications. A method for measuring rigid body type head motion using the Microsoft Kinect v2 is described with results presenting  ⩽0.5 mm spatial accuracy. Motion data is measured in real-time at 30 Hz using the KinectFusion algorithm. Non-rigid motion is detected using the residual alignment energy data of the KinectFusion algorithm allowing for unreliable motion to be discarded. Motion data is aligned to PET listmode data using injected pulse sequences into the PET/CT gantry allowing for correction of rigid body motion. Pilot data from a clinical dynamic PET/CT examination is shown.

  17. PET Imaging of Tau Deposition in the Aging Human Brain

    PubMed Central

    Schonhaut, Daniel R.; O’Neil, James P.; Janabi, Mustafa; Ossenkoppele, Rik; Baker, Suzanne L.; Vogel, Jacob W.; Faria, Jamie; Schwimmer, Henry D.; Rabinovici, Gil D.; Jagust, William J.

    2016-01-01

    SUMMARY Tau pathology is a hallmark of Alzheimer’s disease (AD) but also occurs in normal cognitive aging. Using the tau PET agent 18F-AV-1451, we examined retention patterns in cognitively normal older people in relation to young controls and AD patients. Age and β-amyloid (measured using PiB PET) were differentially associated with tau tracer retention in healthy aging. Older age was related to increased tracer retention in regions of the medial temporal lobe, which predicted worse episodic memory performance. PET detection of tau in other isocortical regions required the presence of cortical β-amyloid, and was associated with decline in global cognition. Furthermore, patterns of tracer retention corresponded well with Braak staging of neurofibrillary tau pathology. The present study defined patterns of tau tracer retention in normal aging in relation to age, cognition, and β-amyloid deposition. PMID:26938442

  18. Five-year experience of quality control for a 3D LSO-based whole-body PET scanner: results and considerations.

    PubMed

    Matheoud, R; Goertzen, A L; Vigna, L; Ducharme, J; Sacchetti, G; Brambilla, M

    2012-07-01

    PET scanners require routine monitoring and quality control (QC) to ensure proper scanner performance. QC helps to ensure that PET equipment performs as specified by the manufacturer and that there have not been significant changes in the system response since acceptance. In this work we describe the maintenance history and we report on the results obtained from the PET system QC testing program over 5 years at two centers, both utilizing a Siemens Biograph 16 HiRez PET/CT system. QC testing programs were based on international standards and included the manufacturer's daily QC, monthly uniformity and sensitivity, quarterly cross-calibration and annual resolution and image quality. For the Winnipeg and Novara sites, two and one PET detector blocks have been replaced, respectively. Neither system has had other significant PET system related hardware replacements. The manufacturer's suggested daily QC was sensitive to detecting problems in the function of PET detector elements. The same test was not sensitive for detecting long term drifts in the systems: the Novara system observed a significant deterioration over five years of testing in the sensitivity which exhibited a decrease of 16% as compared to its initial value measured at system installation. The measure of the energy spectrum, showed that the 511 keV photopeak had shifted to a position of 468 keV. This shift was corrected by having service personnel perform a complete system calibration and detector block setup. We recommend including tests of system energy response and of sensitivity as part of a QC program since they can provide useful information on the actual performance of the scanner. A modification of the daily QC test by the manufacturer is suggested to monitor the long term stability of the system. Image quality and spatial resolution tests have proven to be of limited value for monitoring the system over time.

  19. ACR-ASNR Practice Parameter for Brain PET/CT Imaging Dementia.

    PubMed

    Frey, Kirk A; Lodge, Martin A; Meltzer, Carolyn Cidis; Peller, Patrick J; Wong, Terence Z; Hess, Christopher P; Petrella, Jeffrey R; Sair, Haris I; Subramaniam, Rathan M

    2016-02-01

    This practice parameter is for both FDG and amyloid brain PET or PET/computed tomography (CT) for patients with cognitive decline, and has been developed collaboratively by the American College of Radiology (ACR) and the American Society for Neuroradiology (ASNR). It is estimated that the number of people with dementia, 36.5 million worldwide in 2010, will increase to 65.7 million in 2030 and to 115 million in 2050. Four primary neurodegenerative etiologies of dementia have been defined: Alzheimer disease (AD), vascular dementia, frontotemporal dementia (FTD), and dementia with Lewy bodies (DLB). Alzheimer disease is the most common form of dementia, accounting for approximately 60%-80% of all cases. Indications for FDG and amyloid brain PET and qualifications for personnel are discussed in this practice parameter.

  20. Mapping human brain fatty acid amide hydrolase activity with PET

    PubMed Central

    Rusjan, Pablo M; Wilson, Alan A; Mizrahi, Romina; Boileau, Isabelle; Chavez, Sofia E; Lobaugh, Nancy J; Kish, Stephen J; Houle, Sylvain; Tong, Junchao

    2013-01-01

    Endocannabinoid tone has recently been implicated in a number of prevalent neuropsychiatric conditions. [11C]CURB is the first available positron emission tomography (PET) radiotracer for imaging fatty acid amide hydrolase (FAAH), the enzyme which metabolizes the prominent endocannabinoid anandamide. Here, we sought to determine the most suitable kinetic modeling approach for quantifying [11C]CURB that binds selectively to FAAH. Six healthy volunteers were scanned with arterial blood sampling for 90 minutes. Kinetic parameters were estimated regionally using a one-tissue compartment model (TCM), a 2-TCM with and without irreversible trapping, and an irreversible 3-TCM. The 2-TCM with irreversible trapping provided the best identifiability of PET outcome measures among the approaches studied (coefficient of variation (COV) of the net influx constant Ki and the composite parameter λk3 (λ=K1/k2) <5%, and COV(k3)<10%). Reducing scan time to 60 minutes did not compromise the identifiability of rate constants. Arterial spin labeling measures of regional cerebral blood flow were only slightly correlated with Ki, but not with k3 or λk3. Our data suggest that λk3 is sensitive to changes in FAAH activity, therefore, optimal for PET quantification of FAAH activities with [11C]CURB. Simulations showed that [11C]CURB binding in healthy subjects is far from a flow-limited uptake. PMID:23211960

  1. Individual 3D region-of-interest atlas of the human brain: automatic training point extraction for neural-network-based classification of brain tissue types

    NASA Astrophysics Data System (ADS)

    Wagenknecht, Gudrun; Kaiser, Hans-Juergen; Obladen, Thorsten; Sabri, Osama; Buell, Udalrich

    2000-04-01

    Individual region-of-interest atlas extraction consists of two main parts: T1-weighted MRI grayscale images are classified into brain tissues types (gray matter (GM), white matter (WM), cerebrospinal fluid (CSF), scalp/bone (SB), background (BG)), followed by class image analysis to define automatically meaningful ROIs (e.g., cerebellum, cerebral lobes, etc.). The purpose of this algorithm is the automatic detection of training points for neural network-based classification of brain tissue types. One transaxial slice of the patient data set is analyzed. Background separation is done by simple region growing. A random generator extracts spatially uniformly distributed training points of class BG from that region. For WM training point extraction (TPE), the homogeneity operator is the most important. The most homogeneous voxels define the region for WM TPE. They are extracted by analyzing the cumulative histogram of the homogeneity operator response. Assuming a Gaussian gray value distribution in WM, a random number is used as a probabilistic threshold for TPE. Similarly, non-white matter and non-background regions are analyzed for GM and CSF training points. For SB TPE, the distance from the BG region is an additional feature. Simulated and real 3D MRI images are analyzed and error rates for TPE and classification calculated.

  2. Validation of true low-dose (18)F-FDG PET of the brain.

    PubMed

    Fällmar, David; Lilja, Johan; Kilander, Lena; Danfors, Torsten; Lubberink, Mark; Larsson, Elna-Marie; Sörensen, Jens

    2016-01-01

    The dosage of (18)F-FDG must be sufficient to ensure adequate PET image quality. For younger patients and research controls, the lowest possible radiation dose should be used. The purpose of this study was to find a protocol for FDG-PET of the brain with reduced radiation dose and preserved quantitative characteristics. Eight patients with neurodegenerative disorders and nine controls (n=17) underwent FDG-PET/CT twice on separate occasions, first with normal-dose (3 MBq/kg), and second with low-dose (0.75 MBq/kg, 25% of the original). Five additional controls (total n=22) underwent FDG-PET twice, using normal-dose and ultra-low-dose (0.3 MBq/kg, 10% of original). All subjects underwent MRI. Ten-minute summation images were spatially normalized and intensity normalized. Regional standard uptake value ratios (SUV-r) were calculated using an automated atlas. SUV-r values from the normal- and low-dose images were compared pairwise. No clinically significant bias was found in any of the three groups. The mean absolute difference in regional SUV-r values was 0.015 (1.32%) in controls and 0.019 (1.67%) in patients. The ultra-low-dose protocol produced a slightly higher mean difference of 0.023 (2.10%). The main conclusion is that 0.75 MBq/kg (56 MBq for a 75-kg subject) is a sufficient FDG dose for evaluating regional SUV-ratios in brain PET scans in adults with or without neurodegenerative disease, resulting in a reduction of total PET/CT effective dose from 4.54 to 1.15 mSv. The ultra-low-dose (0.5 mSv) could be useful in research studies requiring serial PET in healthy controls or children.

  3. The MINDView brain PET detector, feasibility study based on SiPM arrays

    NASA Astrophysics Data System (ADS)

    González, Antonio J.; Majewski, Stan; Sánchez, Filomeno; Aussenhofer, Sebastian; Aguilar, Albert; Conde, Pablo; Hernández, Liczandro; Vidal, Luis F.; Pani, Roberto; Bettiol, Marco; Fabbri, Andrea; Bert, Julien; Visvikis, Dimitris; Jackson, Carl; Murphy, John; O'Neill, Kevin; Benlloch, Jose M.

    2016-05-01

    The Multimodal Imaging of Neurological Disorders (MINDView) project aims to develop a dedicated brain Positron Emission Tomography (PET) scanner with sufficient resolution and sensitivity to visualize neurotransmitter pathways and their disruptions in mental disorders for diagnosis and follow-up treatment. The PET system should be compact and fully compatible with a Magnetic Resonance Imaging (MRI) device in order to allow its operation as a PET brain insert in a hybrid imaging setup with most MRI scanners. The proposed design will enable the currently-installed MRI base to be easily upgraded to PET/MRI systems. The current design for the PET insert consists of a 3-ring configuration with 20 modules per ring and an axial field of view of ~15 cm and a geometrical aperture of ~33 cm in diameter. When coupled to the new head Radio Frequency (RF) coil, the inner usable diameter of the complete PET-RF coil insert is reduced to 26 cm. Two scintillator configurations have been tested, namely a 3-layer staggered array of LYSO with 1.5 mm pixel size, with 35×35 elements (6 mm thickness each) and a black-painted monolithic LYSO block also covering about 50×50 mm2 active area with 20 mm thickness. Laboratory test results associated with the current MINDView PET module concept are presented in terms of key parameters' optimization, such as spatial and energy resolution, sensitivity and Depth of Interaction (DOI) capability. It was possible to resolve all pixel elements from the three scintillator layers with energy resolutions as good as 10%. The monolithic scintillator showed average detector resolutions varying from 3.5 mm in the entrance layer to better than 1.5 mm near the photosensor, with average energy resolutions of about 17%.

  4. Validation of true low-dose 18F-FDG PET of the brain

    PubMed Central

    Fällmar, David; Lilja, Johan; Kilander, Lena; Danfors, Torsten; Lubberink, Mark; Larsson, Elna-Marie; Sörensen, Jens

    2016-01-01

    The dosage of 18F-FDG must be sufficient to ensure adequate PET image quality. For younger patients and research controls, the lowest possible radiation dose should be used. The purpose of this study was to find a protocol for FDG-PET of the brain with reduced radiation dose and preserved quantitative characteristics. Eight patients with neurodegenerative disorders and nine controls (n=17) underwent FDG-PET/CT twice on separate occasions, first with normal-dose (3 MBq/kg), and second with low-dose (0.75 MBq/kg, 25% of the original). Five additional controls (total n=22) underwent FDG-PET twice, using normal-dose and ultra-low-dose (0.3 MBq/kg, 10% of original). All subjects underwent MRI. Ten-minute summation images were spatially normalized and intensity normalized. Regional standard uptake value ratios (SUV-r) were calculated using an automated atlas. SUV-r values from the normal- and low-dose images were compared pairwise. No clinically significant bias was found in any of the three groups. The mean absolute difference in regional SUV-r values was 0.015 (1.32%) in controls and 0.019 (1.67%) in patients. The ultra-low-dose protocol produced a slightly higher mean difference of 0.023 (2.10%). The main conclusion is that 0.75 MBq/kg (56 MBq for a 75-kg subject) is a sufficient FDG dose for evaluating regional SUV-ratios in brain PET scans in adults with or without neurodegenerative disease, resulting in a reduction of total PET/CT effective dose from 4.54 to 1.15 mSv. The ultra-low-dose (0.5 mSv) could be useful in research studies requiring serial PET in healthy controls or children. PMID:27766185

  5. Bioengineered 3D brain tumor model to elucidate the effects of matrix stiffness on glioblastoma cell behavior using PEG-based hydrogels.

    PubMed

    Wang, Christine; Tong, Xinming; Yang, Fan

    2014-07-07

    Glioblastoma (GBM) is the most common and aggressive form of primary brain tumor with a median survival of 12-15 months, and the mechanisms underlying GBM tumor progression remain largely elusive. Given the importance of tumor niche signaling in driving GBM progression, there is a strong need to develop in vitro models to facilitate analysis of brain tumor cell-niche interactions in a physiologically relevant and controllable manner. Here we report the development of a bioengineered 3D brain tumor model to help elucidate the effects of matrix stiffness on GBM cell fate using poly(ethylene-glycol) (PEG)-based hydrogels with brain-mimicking biochemical and mechanical properties. We have chosen PEG given its bioinert nature and tunable physical property, and the resulting hydrogels allow tunable matrix stiffness without changing the biochemical contents. To facilitate cell proliferation and migration, CRGDS and a MMP-cleavable peptide were chemically incorporated. Hyaluronic acid (HA) was also incorporated to mimic the concentration in the brain extracellular matrix. Using U87 cells as a model GBM cell line, we demonstrate that such biomimetic hydrogels support U87 cell growth, spreading, and migration in 3D over the course of 3 weeks in culture. Gene expression analyses showed U87 cells actively deposited extracellular matrix and continued to upregulate matrix remodeling genes. To examine the effects of matrix stiffness on GBM cell fate in 3D, we encapsulated U87 cells in soft (1 kPa) or stiff (26 kPa) hydrogels, which respectively mimics the matrix stiffness of normal brain or GBM tumor tissues. Our results suggest that changes in matrix stiffness induce differential GBM cell proliferation, morphology, and migration modes in 3D. Increasing matrix stiffness led to delayed U87 cell proliferation inside hydrogels, but cells formed denser spheroids with extended cell protrusions. Cells cultured in stiff hydrogels also showed upregulation of HA synthase 1 and matrix

  6. Scatter correction for large non-human primate brain imaging using microPET

    NASA Astrophysics Data System (ADS)

    Naidoo-Variawa, S.; Lehnert, W.; Banati, R. B.; Meikle, S. R.

    2011-04-01

    The baboon is well suited to pre-clinical evaluation of novel radioligands for positron emission tomography (PET). We have previously demonstrated the feasibility of using a high resolution animal PET scanner for this application in the baboon brain. However, the non-homogenous distribution of tissue density within the head may give rise to photon scattering effects that reduce contrast and compromise quantitative accuracy. In this study, we investigated the magnitude and distribution of scatter contributing to the final reconstructed image and its variability throughout the baboon brain using phantoms and Monte Carlo simulated data. The scatter fraction is measured up to 36% at the centre of the brain for a wide energy window (350-650 keV) and 19% for a narrow (450-650 keV) window. We observed less than 3% variation in the scatter fraction throughout the brain and found that scattered events arising from radioactivity outside the field of view contribute less than 1% of measured coincidences. In a contrast phantom, scatter and attenuation correction improved contrast recovery compared with attenuation correction on its own and reduced bias to less than 10% at the expense of the reduced signal-to-noise ratio. We conclude that scatter correction is a necessary step for ensuring high quality measurements of the radiotracer distribution in the baboon brain with a microPET scanner, while it is not necessary to model out of field of view scatter or a spatially variant scatter function.

  7. Short-Term Practice Effects and Brain Hypometabolism: Preliminary Data from an FDG PET Study.

    PubMed

    Duff, Kevin; Horn, Kevin P; Foster, Norman L; Hoffman, John M

    2015-05-01

    Practice effects are improvements in cognitive test scores due to repeated exposure to the same tests. Typically viewed as error, short-term practice effects have been shown to provide valuable clinical information about diagnosis, prognosis, and treatment outcomes in older patients with mild cognitive impairments. This study examined short-term practice effects across one week and brain hypometabolism on fluoro-2-deoxyglucose (FDG) positron emission tomography (PET) in 25 older adults (15 intact, 10 Mild Cognitive Impairment). Averaged cerebral brain metabolism on FDG PET was correlated with multiple cognitive scores at baseline in those with Mild Cognitive Impairment, and short-term practice effects accounted for additional variance in these same subjects. The relationship between brain metabolism and cognition (either at baseline or practice effects) was minimal in the intact individuals. Although needing replication in larger samples, short-term practice effects on tests of executive functioning and memory may provide valuable information about biomarkers of Alzheimer's disease.

  8. 3D Reconstructed Cyto-, Muscarinic M2 Receptor, and Fiber Architecture of the Rat Brain Registered to the Waxholm Space Atlas

    PubMed Central

    Schubert, Nicole; Axer, Markus; Schober, Martin; Huynh, Anh-Minh; Huysegoms, Marcel; Palomero-Gallagher, Nicola; Bjaalie, Jan G.; Leergaard, Trygve B.; Kirlangic, Mehmet E.; Amunts, Katrin; Zilles, Karl

    2016-01-01

    High-resolution multiscale and multimodal 3D models of the brain are essential tools to understand its complex structural and functional organization. Neuroimaging techniques addressing different aspects of brain organization should be integrated in a reference space to enable topographically correct alignment and subsequent analysis of the various datasets and their modalities. The Waxholm Space (http://software.incf.org/software/waxholm-space) is a publicly available 3D coordinate-based standard reference space for the mapping and registration of neuroanatomical data in rodent brains. This paper provides a newly developed pipeline combining imaging and reconstruction steps with a novel registration strategy to integrate new neuroimaging modalities into the Waxholm Space atlas. As a proof of principle, we incorporated large scale high-resolution cyto-, muscarinic M2 receptor, and fiber architectonic images of rat brains into the 3D digital MRI based atlas of the Sprague Dawley rat in Waxholm Space. We describe the whole workflow, from image acquisition to reconstruction and registration of these three modalities into the Waxholm Space rat atlas. The registration of the brain sections into the atlas is performed by using both linear and non-linear transformations. The validity of the procedure is qualitatively demonstrated by visual inspection, and a quantitative evaluation is performed by measurement of the concordance between representative atlas-delineated regions and the same regions based on receptor or fiber architectonic data. This novel approach enables for the first time the generation of 3D reconstructed volumes of nerve fibers and fiber tracts, or of muscarinic M2 receptor density distributions, in an entire rat brain. Additionally, our pipeline facilitates the inclusion of further neuroimaging datasets, e.g., 3D reconstructed volumes of histochemical stainings or of the regional distributions of multiple other receptor types, into the Waxholm Space

  9. 3D Reconstructed Cyto-, Muscarinic M2 Receptor, and Fiber Architecture of the Rat Brain Registered to the Waxholm Space Atlas.

    PubMed

    Schubert, Nicole; Axer, Markus; Schober, Martin; Huynh, Anh-Minh; Huysegoms, Marcel; Palomero-Gallagher, Nicola; Bjaalie, Jan G; Leergaard, Trygve B; Kirlangic, Mehmet E; Amunts, Katrin; Zilles, Karl

    2016-01-01

    High-resolution multiscale and multimodal 3D models of the brain are essential tools to understand its complex structural and functional organization. Neuroimaging techniques addressing different aspects of brain organization should be integrated in a reference space to enable topographically correct alignment and subsequent analysis of the various datasets and their modalities. The Waxholm Space (http://software.incf.org/software/waxholm-space) is a publicly available 3D coordinate-based standard reference space for the mapping and registration of neuroanatomical data in rodent brains. This paper provides a newly developed pipeline combining imaging and reconstruction steps with a novel registration strategy to integrate new neuroimaging modalities into the Waxholm Space atlas. As a proof of principle, we incorporated large scale high-resolution cyto-, muscarinic M2 receptor, and fiber architectonic images of rat brains into the 3D digital MRI based atlas of the Sprague Dawley rat in Waxholm Space. We describe the whole workflow, from image acquisition to reconstruction and registration of these three modalities into the Waxholm Space rat atlas. The registration of the brain sections into the atlas is performed by using both linear and non-linear transformations. The validity of the procedure is qualitatively demonstrated by visual inspection, and a quantitative evaluation is performed by measurement of the concordance between representative atlas-delineated regions and the same regions based on receptor or fiber architectonic data. This novel approach enables for the first time the generation of 3D reconstructed volumes of nerve fibers and fiber tracts, or of muscarinic M2 receptor density distributions, in an entire rat brain. Additionally, our pipeline facilitates the inclusion of further neuroimaging datasets, e.g., 3D reconstructed volumes of histochemical stainings or of the regional distributions of multiple other receptor types, into the Waxholm Space

  10. Response to Deep Brain Stimulation in Three Brain Targets with Implications in Mental Disorders: A PET Study in Rats

    PubMed Central

    Casquero-Veiga, Marta; Hadar, Ravit; Pascau, Javier; Winter, Christine; Desco, Manuel; Soto-Montenegro, María Luisa

    2016-01-01

    Objective To investigate metabolic changes in brain networks by deep brain stimulation (DBS) of the medial prefrontal cortex (mPFC), nucleus accumbens (NAcc) and dorsomedial thalamus (DM) using positron emission tomography (PET) in naïve rats. Methods 43 male Wistar rats underwent stereotactic surgery and concentric bipolar platinum-iridium electrodes were bilaterally implanted into one of the three brain sites. [18F]-fluoro-2-deoxy-glucose-PET (18FDG-PET) and computed tomography (CT) scans were performed at the 7th (without DBS) and 9th day (with DBS) after surgery. Stimulation period matched tracer uptake period. Images were acquired with a small-animal PET-CT scanner. Differences in glucose uptake between groups were assessed with Statistical Parametric Mapping. Results DBS induced site-specific metabolic changes, although a common increased metabolic activity in the piriform cortex was found for the three brain targets. mPFC-DBS increased metabolic activity in the striatum, temporal and amygdala, and reduced it in the cerebellum, brainstem (BS) and periaqueductal gray matter (PAG). NAcc-DBS increased metabolic activity in the subiculum and olfactory bulb, and decreased it in the BS, PAG, septum and hypothalamus. DM-DBS increased metabolic activity in the striatum, NAcc and thalamus and decreased it in the temporal and cingulate cortex. Conclusions DBS induced significant changes in 18FDG uptake in brain regions associated with the basal ganglia-thalamo-cortical circuitry. Stimulation of mPFC, NAcc and DM induced different patterns of 18FDG uptake despite interacting with the same circuitries. This may have important implications to DBS research suggesting individualized target selection according to specific neural modulatory requirements. PMID:28033356

  11. Errors in MR-based attenuation correction for brain imaging with PET/MR scanners

    NASA Astrophysics Data System (ADS)

    Rota Kops, Elena; Herzog, Hans

    2013-02-01

    AimAttenuation correction of PET data acquired by hybrid MR/PET scanners remains a challenge, even if several methods for brain and whole-body measurements have been developed recently. A template-based attenuation correction for brain imaging proposed by our group is easy to handle and delivers reliable attenuation maps in a short time. However, some potential error sources are analyzed in this study. We investigated the choice of template reference head among all the available data (error A), and possible skull anomalies of the specific patient, such as discontinuities due to surgery (error B). Materials and methodsAn anatomical MR measurement and a 2-bed-position transmission scan covering the whole head and neck region were performed in eight normal subjects (4 females, 4 males). Error A: Taking alternatively one of the eight heads as reference, eight different templates were created by nonlinearly registering the images to the reference and calculating the average. Eight patients (4 females, 4 males; 4 with brain lesions, 4 w/o brain lesions) were measured in the Siemens BrainPET/MR scanner. The eight templates were used to generate the patients' attenuation maps required for reconstruction. ROI and VOI atlas-based comparisons were performed employing all the reconstructed images. Error B: CT-based attenuation maps of two volunteers were manipulated by manually inserting several skull lesions and filling a nasal cavity. The corresponding attenuation coefficients were substituted with the water's coefficient (0.096/cm). ResultsError A: The mean SUVs over the eight templates pairs for all eight patients and all VOIs did not differ significantly one from each other. Standard deviations up to 1.24% were found. Error B: After reconstruction of the volunteers' BrainPET data with the CT-based attenuation maps without and with skull anomalies, a VOI-atlas analysis was performed revealing very little influence of the skull lesions (less than 3%), while the filled nasal

  12. Quantification of F-18 FDG PET images in temporal lobe epilepsy patients using probabilistic brain atlas.

    PubMed

    Kang, K W; Lee, D S; Cho, J H; Lee, J S; Yeo, J S; Lee, S K; Chung, J K; Lee, M C

    2001-07-01

    A probabilistic atlas of the human brain (Statistical Probabilistic Anatomical Maps: SPAM) was developed by the international consortium for brain mapping (ICBM). It is a good frame for calculating volume of interest (VOI) in many fields of brain images. After calculating the counts in VOI using the product of probability of SPAM images and counts in FDG images, asymmetric indices (AI) were calculated and used for finding epileptogenic zones in mesial temporal lobe epilepsy (mTLE). FDG PET images from 18 surgically confirmed mTLE patients and 22 age-matched controls were spatially normalized to the average brain MRI template of ICBM. Counts from normalized PET images were multiplied with the probability of 12 VOIs from SPAM images in both temporal lobes. Finally AI were calculated on each pair of VOIs, and compared with visual assessment. If AI of mTLE patients were not within 2.9 standard deviation from those of normal control group (P < 0.008; Bonferroni correction for P < 0.05), epileptogenic zones were considered to be found successfully. The counts of VOIs in the normal control group were symmetric (AI < 4.3%, paired t test P > 0.05) except for those of the inferior temporal gyrus (P < 0.001). By AIs in six pairs of VOIs, PET in mTLE had deficit on one side (P < 0.05). Lateralization was correct in only 14/18 of patients by AI, but 17/18 were consistent with visual inspection. In three patients with normal AI, PET images were symmetric on visual inspection. The asymmetric indices obtained by taking the product of the statistical probability anatomical map and FDG PET, correlated well with visual assessment in mTLE patients. SPAM is useful for the quantification of VOIs in functional images.

  13. Assessment of C-phycocyanin effect on astrocytes-mediated neuroprotection against oxidative brain injury using 2D and 3D astrocyte tissue model

    PubMed Central

    Min, Seul Ki; Park, Jun Sang; Luo, Lidan; Kwon, Yeo Seon; Lee, Hoo Cheol; Jung Shim, Hyun; Kim, Il-Doo; Lee, Ja-Kyeong; Shin, Hwa Sung

    2015-01-01

    Drugs are currently being developed to attenuate oxidative stress as a treatment for brain injuries. C-phycocyanin (C-Pc) is an antioxidant protein of green microalgae known to exert neuroprotective effects against oxidative brain injury. Astrocytes, which compose many portions of the brain, exert various functions to overcome oxidative stress; however, little is known about how C-Pc mediates the antioxidative effects of astrocytes. In this study, we revealed that C-Pc intranasal administration to the middle cerebral artery occlusion (MCAO) rats ensures neuroprotection of ischemic brain by reducing infarct size and improving behavioral deficits. C-Pc also enhanced viability and proliferation but attenuated apoptosis and reactive oxygen species (ROS) of oxidized astrocytes, without cytotoxicity to normal astrocytes and neurons. To elucidate how C-Pc leads astrocytes to enhance neuroprotection and repair of ischemia brain, we firstly developed 3D oxidized astrocyte model. C-Pc had astrocytes upregulate antioxidant enzymes such as SOD and catalase and neurotrophic factors BDNF and NGF, while alleviating inflammatory factors IL-6 and IL-1β and glial scar. Additionally, C-Pc improved viability of 3D oxidized neurons. In summary, C-Pc was concluded to activate oxidized astrocytes to protect and repair the ischemic brain with the combinatorial effects of improved antioxidative, neurotrophic, and anti-inflammatory mechanisms. PMID:26399322

  14. Assessment of C-phycocyanin effect on astrocytes-mediated neuroprotection against oxidative brain injury using 2D and 3D astrocyte tissue model.

    PubMed

    Min, Seul Ki; Park, Jun Sang; Luo, Lidan; Kwon, Yeo Seon; Lee, Hoo Cheol; Shim, Hyun Jung; Kim, Il-Doo; Lee, Ja-Kyeong; Shin, Hwa Sung

    2015-09-24

    Drugs are currently being developed to attenuate oxidative stress as a treatment for brain injuries. C-phycocyanin (C-Pc) is an antioxidant protein of green microalgae known to exert neuroprotective effects against oxidative brain injury. Astrocytes, which compose many portions of the brain, exert various functions to overcome oxidative stress; however, little is known about how C-Pc mediates the antioxidative effects of astrocytes. In this study, we revealed that C-Pc intranasal administration to the middle cerebral artery occlusion (MCAO) rats ensures neuroprotection of ischemic brain by reducing infarct size and improving behavioral deficits. C-Pc also enhanced viability and proliferation but attenuated apoptosis and reactive oxygen species (ROS) of oxidized astrocytes, without cytotoxicity to normal astrocytes and neurons. To elucidate how C-Pc leads astrocytes to enhance neuroprotection and repair of ischemia brain, we firstly developed 3D oxidized astrocyte model. C-Pc had astrocytes upregulate antioxidant enzymes such as SOD and catalase and neurotrophic factors BDNF and NGF, while alleviating inflammatory factors IL-6 and IL-1β and glial scar. Additionally, C-Pc improved viability of 3D oxidized neurons. In summary, C-Pc was concluded to activate oxidized astrocytes to protect and repair the ischemic brain with the combinatorial effects of improved antioxidative, neurotrophic, and anti-inflammatory mechanisms.

  15. Localization of Metal Electrodes in the Intact Rat Brain Using Registration of 3D Microcomputed Tomography Images to a Magnetic Resonance Histology Atlas1,2,3

    PubMed Central

    Borg, Jana Schaich; Vu, Mai-Anh; Badea, Cristian; Badea, Alexandra; Johnson, G. Allan

    2015-01-01

    Abstract Simultaneous neural recordings taken from multiple areas of the rodent brain are garnering growing interest because of the insight they can provide about spatially distributed neural circuitry. The promise of such recordings has inspired great progress in methods for surgically implanting large numbers of metal electrodes into intact rodent brains. However, methods for localizing the precise location of these electrodes have remained severely lacking. Traditional histological techniques that require slicing and staining of physical brain tissue are cumbersome and become increasingly impractical as the number of implanted electrodes increases. Here we solve these problems by describing a method that registers 3D computed tomography (CT) images of intact rat brains implanted with metal electrode bundles to a magnetic resonance imaging histology (MRH) atlas. Our method allows accurate visualization of each electrode bundle’s trajectory and location without removing the electrodes from the brain or surgically implanting external markers. In addition, unlike physical brain slices, once the 3D images of the electrode bundles and the MRH atlas are registered, it is possible to verify electrode placements from many angles by “reslicing” the images along different planes of view. Furthermore, our method can be fully automated and easily scaled to applications with large numbers of specimens. Our digital imaging approach to efficiently localizing metal electrodes offers a substantial addition to currently available methods, which, in turn, may help accelerate the rate at which insights are gleaned from rodent network neuroscience. PMID:26322331

  16. Continuous Scintillator Detector Blocks for Simultaneous Pet-Mr Imaging of the Human Brain

    NASA Astrophysics Data System (ADS)

    Rato Mendes, Pedro

    2010-04-01

    Continuous scintillator detector blocks have several advantages over pixelated designs, presenting a larger active volume and a lower cost with comparable or better energy and spatial resolutions. In this paper we describe the operation of continuous detector blocks for positron emission tomography (PET) and their suitability for multimodality imaging operating inside a magnetic resonance (MR) scanner. This detector technology is being used on a full-scale clinical scanner for human brain PET studies presently under development at Ciemat. Results will be presented on the laboratory characterization of monolithic scintillators coupled to APD matrices with ASIC readout, including images of point sources from a prototype dual-head demonstrator illustrating the potential of continuous scintillator detector blocks for high-resolution PET-MR imaging.

  17. PET study of 11C-acetoacetate kinetics in rat brain during dietary treatments affecting ketosis.

    PubMed

    Bentourkia, M'hamed; Tremblay, Sébastien; Pifferi, Fabien; Rousseau, Jacques; Lecomte, Roger; Cunnane, Stephen

    2009-04-01

    Normally, the brain's fuel is glucose, but during fasting it increasingly relies on ketones (beta-hydroxybutyrate, acetoacetate, and acetone) produced in liver mitochondria from fatty acid beta-oxidation. Although moderately raised blood ketones produced on a very high fat ketogenic diet have important clinical effects on the brain, including reducing seizures, ketone metabolism by the brain is still poorly understood. The aim of the present work was to assess brain uptake of carbon-11-labeled acetoacetate (11C-acetoacetate) by positron emission tomography (PET) imaging in the intact, living rat. To vary plasma ketones, we used three dietary conditions: high carbohydrate control diet (low plasma ketones), fat-rich ketogenic diet (raised plasma ketones), and 48-h fasting (raised plasma ketones). 11C-acetoacetate metabolism was measured in the brain, heart, and tissue in the mouth area. Using 11C-acetoacetate and small animal PET imaging, we have noninvasively quantified an approximately seven- to eightfold enhanced brain uptake of ketones on a ketogenic diet or during fasting. This opens up an opportunity to study brain ketone metabolism in humans.

  18. FDG-PET imaging in mild traumatic brain injury: a critical review.

    PubMed

    Byrnes, Kimberly R; Wilson, Colin M; Brabazon, Fiona; von Leden, Ramona; Jurgens, Jennifer S; Oakes, Terrence R; Selwyn, Reed G

    2014-01-09

    Traumatic brain injury (TBI) affects an estimated 1.7 million people in the United States and is a contributing factor to one third of all injury related deaths annually. According to the CDC, approximately 75% of all reported TBIs are concussions or considered mild in form, although the number of unreported mild TBIs (mTBI) and patients not seeking medical attention is unknown. Currently, classification of mTBI or concussion is a clinical assessment since diagnostic imaging is typically inconclusive due to subtle, obscure, or absent changes in anatomical or physiological parameters measured using standard magnetic resonance (MR) or computed tomography (CT) imaging protocols. Molecular imaging techniques that examine functional processes within the brain, such as measurement of glucose uptake and metabolism using [(18)F]fluorodeoxyglucose and positron emission tomography (FDG-PET), have the ability to detect changes after mTBI. Recent technological improvements in the resolution of PET systems, the integration of PET with magnetic resonance imaging (MRI), and the availability of normal healthy human databases and commercial image analysis software contribute to the growing use of molecular imaging in basic science research and advances in clinical imaging. This review will discuss the technological considerations and limitations of FDG-PET, including differentiation between glucose uptake and glucose metabolism and the significance of these measurements. In addition, the current state of FDG-PET imaging in assessing mTBI in clinical and preclinical research will be considered. Finally, this review will provide insight into potential critical data elements and recommended standardization to improve the application of FDG-PET to mTBI research and clinical practice.

  19. FDG-PET imaging in mild traumatic brain injury: a critical review

    PubMed Central

    Byrnes, Kimberly R.; Wilson, Colin M.; Brabazon, Fiona; von Leden, Ramona; Jurgens, Jennifer S.; Oakes, Terrence R.; Selwyn, Reed G.

    2013-01-01

    Traumatic brain injury (TBI) affects an estimated 1.7 million people in the United States and is a contributing factor to one third of all injury related deaths annually. According to the CDC, approximately 75% of all reported TBIs are concussions or considered mild in form, although the number of unreported mild TBIs (mTBI) and patients not seeking medical attention is unknown. Currently, classification of mTBI or concussion is a clinical assessment since diagnostic imaging is typically inconclusive due to subtle, obscure, or absent changes in anatomical or physiological parameters measured using standard magnetic resonance (MR) or computed tomography (CT) imaging protocols. Molecular imaging techniques that examine functional processes within the brain, such as measurement of glucose uptake and metabolism using [18F]fluorodeoxyglucose and positron emission tomography (FDG-PET), have the ability to detect changes after mTBI. Recent technological improvements in the resolution of PET systems, the integration of PET with magnetic resonance imaging (MRI), and the availability of normal healthy human databases and commercial image analysis software contribute to the growing use of molecular imaging in basic science research and advances in clinical imaging. This review will discuss the technological considerations and limitations of FDG-PET, including differentiation between glucose uptake and glucose metabolism and the significance of these measurements. In addition, the current state of FDG-PET imaging in assessing mTBI in clinical and preclinical research will be considered. Finally, this review will provide insight into potential critical data elements and recommended standardization to improve the application of FDG-PET to mTBI research and clinical practice. PMID:24409143

  20. Development and use of a kinetic FDG-PET dataset simulated from the MNI standard brain

    NASA Astrophysics Data System (ADS)

    Schottlander, David; Guimond, Alexandre; Pan, Xiao-Bo; Brady, Michael; Declerck, Jérôme; Collins, Louis; Evans, Alan C.; Reilhac, Anthonin

    2006-03-01

    Simulated data is an important tool for evaluation of reconstruction and image processing algorithms in the frequent absence of ground truth, in-vivo data from living subjects. This is especially true in the case of dynamic PET studies, in which counting statistics of the volume can vary widely over the time-course of the acquisition. Realistic simulated data-sets which model anatomy and physiology, and make explicit the spatial and temporal image acquisition characteristics, facilitate experimentation with a wide range of the conditions anticipated in practice, and which can severely challenge algorithm performance and reliability. As a first example, we have developed a realistic dynamic FDG-PET data-set using the PET-SORTEO Monte Carlo simulation code and the MNI digital brain phantom. The phantom is a three-dimensional data-set that defines the spatial distribution of different tissues. Time activity curves were calculated using an impulse response function specified by generally accepted rate constants, convolved with an input function obtained by blood sampling, and assigned to grey and white matter tissue regions. We created a dynamic PET study using PET-SORTEO configured to simulate an ECAT Exact HR+. The resulting sinograms were reconstructed with all corrections, using variations of FBP and OSEM. Having constructed the dynamic PET data-sets, we used them to evaluate the performance of intensity-based registration as part of a tool for quantifying hyper/hypo perfusion with particular application to analysis of brain dementia scans, and a study of the stability of kinetic parameter estimation.

  1. Would gestational age and presence of brain anomalies affect interobserver reliability of fetal head biometry? Using off-line analysis of 3-D dataset.

    PubMed

    Salman, Mona S M; Mousa, Hatem A; Twining, Peter; Jones, Nia W; James, David; Momtaz, Mohamed; Aboulghar, Mona; El-Sheikhah, Ahmad; Bugg, George

    2012-01-01

    The objective was to assess interobserver reliability of fetal head biometry using archived three-dimensional (3-D) volumes and the impact of gestational age and presence of brain anomalies on examiners' performance. Seventy nine 3-D volume datasets of fetal head were examined: 27 were normal and 52 had brain abnormalities. Off-line analysis was done by three fetal medicine experts (E1, E2 and E2), all were blinded to history and patient details. Measurements of the biparietal diameter (BPD), head circumference (HC), lateral ventricle (Vp) and transcerebellar diameter (TCD) were compared between examiners and to two-dimensional (2-D) measurements. Comparisons were made at two gestational age groups (≤22 and >22 weeks) and in presence and absence of brain anomalies. The intraclass coefficient showed a significantly high level of measurement agreement between 3-D examiners and 2-D, with values >0.9 throughout (p < 0.001). Bias was evident between 3-D examiners. E2 produced smaller measurements. The mean percentage difference between this examiner and the other two in BPD, HC, Vp and TCD measurements was significant, of 1.6%, 1%, 4.9% and 1.8%, respectively. E1 measured statistically larger for HC and TCD. E3 measured significantly larger for only BPD. The presence of anomalies was of no influence on the 3-D examiners' performance except for E3 who showed bias in BPD measurements only in cases with brain anomalies. Unlike other examiners, bias of E2 was only seen at gestational age group ≤22 weeks. Limits of agreement in measurements between observers were narrow for all parameters but were widest for the Vp measurements, being ±23% of the mean difference. Despite the above bias, the actual mean difference between examiners was small and unlikely to be of any clinical significance. Off-line measurement of fetal head biometry using 3-D volumes is reliable. In our study, presence of brain anomalies was unlikely to influence the reproducibility of measurements

  2. Generation of attenuation map for MR-based attenuation correction of PET data in the head area employing 3D short echo time MR imaging

    NASA Astrophysics Data System (ADS)

    Khateri, Parisa; Salighe Rad, Hamidreza; Fathi, Anahita; Ay, Mohammad Reza

    2013-02-01

    Attenuation correction is a crucial step to get accurate quantification of Positron Emission Tomography (PET) data. An attenuation map to provide attenuation coefficients at 511 keV can be generated using Magnetic Resonance Images (MRI). One of the main steps involved in MR-based attenuation correction (MRAC) of PET data is to separate bone from air. Low signal intensity of bone in conventional MRI makes it difficult to separate bone from air in the head area, while their attenuation coefficients are very different. In literature, several groups proposed ultrashort echo-time (UTE) sequences to differentiate bone from air [4,5,7], because these sequences are capable of imaging tissues with short T2* relaxation time, such as cortical bone; however, they are difficult to use, expensive and time-consuming. Employing short echo-time (STE) MRI in combination with long echo-time (LTE) MRI, and along with high performance image processing algorithms is a good substitute for UTE-based PET attenuation correction; they are widely available, easy to use, inexpensive and much faster than UTE pulse sequences. In this work, we propose the use of STE sequences along with LTE ones, as well as a dedicated image processing method to differentiate bone from air cavities in the head area by creating contrast between the tissues. Attenuation coefficients at 511 kev, relying on literature [5], will then be assigned to the voxels. Acquisition was performed on a clinical 3T Tim Trio scanner (Siemens Medical Solution, Erlangen, Germany), employing a dual echo sequence. To achieve an optimized protocol with the best result for discrimination of bone and air, two types of acquisitions were performed, with and without fat suppression; the acquisition parameters were as follows: TE=1.21/5 ms, TR=5/17, FA=30, and TE=1.12/3.16 ms, TR=5/5, FA=12 for non-fat-suppressed and fat-suppressed protocol, respectively. Contrast enhancement and tissue segmentation were applied as processing steps, to

  3. Integrated modeling of PET and DTI information based on conformal brain mapping

    NASA Astrophysics Data System (ADS)

    Zou, Guangyu; Xi, Yongjian; Heckenburg, Greg; Duan, Ye; Hua, Jing; Gu, Xiangfeng

    2006-03-01

    Recent advances in imaging technologies, such as Magnetic Resonance Imaging (MRI), Positron Emission Tomography (PET) and Diffusion Tensor Imaging (DTI) have accelerated brain research in many aspects. In order to better understand the synergy of the many processes involved in normal brain function, integrated modeling and analysis of MRI, PET, and DTI is highly desirable. Unfortunately, the current state-of-art computational tools fall short in offering a comprehensive computational framework that is accurate and mathematically rigorous. In this paper we present a framework which is based on conformal parameterization of a brain from high-resolution structural MRI data to a canonical spherical domain. This model allows natural integration of information from co-registered PET as well as DTI data and lays the foundation for a quantitative analysis of the relationship between diverse data sets. Consequently, the system can be designed to provide a software environment able to facilitate statistical detection of abnormal functional brain patterns in patients with a large number of neurological disorders.

  4. In vivo characterization of chronic traumatic encephalopathy using [F-18]FDDNP PET brain imaging.

    PubMed

    Barrio, Jorge R; Small, Gary W; Wong, Koon-Pong; Huang, Sung-Cheng; Liu, Jie; Merrill, David A; Giza, Christopher C; Fitzsimmons, Robert P; Omalu, Bennet; Bailes, Julian; Kepe, Vladimir

    2015-04-21

    Chronic traumatic encephalopathy (CTE) is an acquired primary tauopathy with a variety of cognitive, behavioral, and motor symptoms linked to cumulative brain damage sustained from single, episodic, or repetitive traumatic brain injury (TBI). No definitive clinical diagnosis for this condition exists. In this work, we used [F-18]FDDNP PET to detect brain patterns of neuropathology distribution in retired professional American football players with suspected CTE (n = 14) and compared results with those of cognitively intact controls (n = 28) and patients with Alzheimer's dementia (AD) (n = 24), a disease that has been cognitively associated with CTE. [F-18]FDDNP PET imaging results in the retired players suggested the presence of neuropathological patterns consistent with models of concussion wherein brainstem white matter tracts undergo early axonal damage and cumulative axonal injuries along subcortical, limbic, and cortical brain circuitries supporting mood, emotions, and behavior. This deposition pattern is distinctively different from the progressive pattern of neuropathology [paired helical filament (PHF)-tau and amyloid-β] in AD, which typically begins in the medial temporal lobe progressing along the cortical default mode network, with no or minimal involvement of subcortical structures. This particular [F-18]FDDNP PET imaging pattern in cases of suspected CTE also is primarily consistent with PHF-tau distribution observed at autopsy in subjects with a history of mild TBI and autopsy-confirmed diagnosis of CTE.

  5. In vivo characterization of chronic traumatic encephalopathy using [F-18]FDDNP PET brain imaging

    PubMed Central

    Barrio, Jorge R.; Small, Gary W.; Wong, Koon-Pong; Huang, Sung-Cheng; Liu, Jie; Merrill, David A.; Giza, Christopher C.; Fitzsimmons, Robert P.; Omalu, Bennet; Bailes, Julian; Kepe, Vladimir

    2015-01-01

    Chronic traumatic encephalopathy (CTE) is an acquired primary tauopathy with a variety of cognitive, behavioral, and motor symptoms linked to cumulative brain damage sustained from single, episodic, or repetitive traumatic brain injury (TBI). No definitive clinical diagnosis for this condition exists. In this work, we used [F-18]FDDNP PET to detect brain patterns of neuropathology distribution in retired professional American football players with suspected CTE (n = 14) and compared results with those of cognitively intact controls (n = 28) and patients with Alzheimer’s dementia (AD) (n = 24), a disease that has been cognitively associated with CTE. [F-18]FDDNP PET imaging results in the retired players suggested the presence of neuropathological patterns consistent with models of concussion wherein brainstem white matter tracts undergo early axonal damage and cumulative axonal injuries along subcortical, limbic, and cortical brain circuitries supporting mood, emotions, and behavior. This deposition pattern is distinctively different from the progressive pattern of neuropathology [paired helical filament (PHF)-tau and amyloid-β] in AD, which typically begins in the medial temporal lobe progressing along the cortical default mode network, with no or minimal involvement of subcortical structures. This particular [F-18]FDDNP PET imaging pattern in cases of suspected CTE also is primarily consistent with PHF-tau distribution observed at autopsy in subjects with a history of mild TBI and autopsy-confirmed diagnosis of CTE. PMID:25848027

  6. Iodine-122-labeled amphetamine derivative with potential for PET brain blood-flow studies

    SciTech Connect

    Mathis, C.A.; Sargent, T. 3d.; Shulgin, A.T.

    1985-11-01

    The positron emitter SSI (t1/2 3.6 min) was collected from a xenon- SS/iodine- SS ( SSXe/ SSI) generator and incorporated into an amphetamine analog, 2,4-dimethoxy-N,N-dimethyl-5-( SSI)iodophenylisopropylamine (5-( SSI)-2,4-DNNA). The remote synthesis was achieved in 3 min with a 50% radioincorporation yield and a product radiopurity of greater than 98%. 5-( SSI)-2,4-DNNA was injected into a beagle dog and a brain section imaged with positron emission tomography (PET). The uptake and retention of 5-( SSI)-2,4-DNNA was compared to that of YSRb in the same animal. Dynamic PET activity data were obtained 0-20 min postinjection of 5-( SSI)-2,4-DNNA and showed rapid uptake by brain and good cerebral/extracerebral tissue distinction. A whole-body scan of a dog was also obtained with 5-123I-2,4-DNNA showing uptake in brain, lung, and other body organs. The feasibility of incorporating SSI into an extracted brain perfusion agent for use with PET is demonstrated.

  7. Evoked Potentials and Neuropsychological Tests Validate Positron Emission Topography (PET) Brain Metabolism in Cognitively Impaired Patients

    PubMed Central

    Braverman, Eric R.; Blum, Kenneth; Damle, Uma J.; Kerner, Mallory; Dushaj, Kristina; Oscar-Berman, Marlene

    2013-01-01

    Fluorodeoxyglucose (FDG) Positron Emission Topography (PET) brain hypometabolism (HM) correlates with diminished cognitive capacity and risk of developing dementia. However, because clinical utility of PET is limited by cost, we sought to determine whether a less costly electrophysiological measure, the P300 evoked potential, in combination with neuropsychological test performance, would validate PET HM in neuropsychiatric patients. We found that patients with amnestic and non-amnestic cognitive impairment and HM (n = 43) evidenced significantly reduced P300 amplitudes, delayed latencies, and neuropsychological deficits, compared to patients with normal brain metabolism (NM; n = 187). Data from patients with missing cognitive test scores (n = 57) were removed from the final sample, and logistic regression modeling was performed on the modified sample (n = 173, p = .000004). The logistic regression modeling, based on P300 and neuropsychological measures, was used to validate membership in the HM vs. NM groups. It showed classification validation in 13/25 HM subjects (52.0%) and in 125/148 NM subjects (84.5%), correlating with total classification accuracy of 79.8%. In this paper, abnormal P300 evoked potentials coupled with cognitive test impairment validates brain metabolism and mild/moderate cognitive impairment (MCI). To this end, we cautiously propose incorporating electrophysiological and neuropsychological assessments as cost-effective brain metabolism and MCI indicators in primary care. Final interpretation of these results must await required additional studies confirming these interesting results. PMID:23526928

  8. Distinct Contributions of Astrocytes and Pericytes to Neuroinflammation Identified in a 3D Human Blood-Brain Barrier on a Chip.

    PubMed

    Herland, Anna; van der Meer, Andries D; FitzGerald, Edward A; Park, Tae-Eun; Sleeboom, Jelle J F; Ingber, Donald E

    2016-01-01

    Neurovascular inflammation is a major contributor to many neurological disorders, but modeling these processes in vitro has proven to be difficult. Here, we microengineered a three-dimensional (3D) model of the human blood-brain barrier (BBB) within a microfluidic chip by creating a cylindrical collagen gel containing a central hollow lumen inside a microchannel, culturing primary human brain microvascular endothelial cells on the gel's inner surface, and flowing medium through the lumen. Studies were carried out with the engineered microvessel containing endothelium in the presence or absence of either primary human brain pericytes beneath the endothelium or primary human brain astrocytes within the surrounding collagen gel to explore the ability of this simplified model to identify distinct contributions of these supporting cells to the neuroinflammatory response. This human 3D BBB-on-a-chip exhibited barrier permeability similar to that observed in other in vitro BBB models created with non-human cells, and when stimulated with the inflammatory trigger, tumor necrosis factor-alpha (TNF-α), different secretion profiles for granulocyte colony-stimulating factor (G-CSF) and interleukin-6 (IL-6) were observed depending on the presence of astrocytes or pericytes. Importantly, the levels of these responses detected in the 3D BBB chip were significantly greater than when the same cells were co-cultured in static Transwell plates. Thus, as G-CSF and IL-6 have been reported to play important roles in neuroprotection and neuroactivation in vivo, this 3D BBB chip potentially offers a new method to study human neurovascular function and inflammation in vitro, and to identify physiological contributions of individual cell types.

  9. Distinct Contributions of Astrocytes and Pericytes to Neuroinflammation Identified in a 3D Human Blood-Brain Barrier on a Chip

    PubMed Central

    FitzGerald, Edward A.; Park, Tae-Eun; Sleeboom, Jelle J. F.; Ingber, Donald E.

    2016-01-01

    Neurovascular inflammation is a major contributor to many neurological disorders, but modeling these processes in vitro has proven to be difficult. Here, we microengineered a three-dimensional (3D) model of the human blood-brain barrier (BBB) within a microfluidic chip by creating a cylindrical collagen gel containing a central hollow lumen inside a microchannel, culturing primary human brain microvascular endothelial cells on the gel’s inner surface, and flowing medium through the lumen. Studies were carried out with the engineered microvessel containing endothelium in the presence or absence of either primary human brain pericytes beneath the endothelium or primary human brain astrocytes within the surrounding collagen gel to explore the ability of this simplified model to identify distinct contributions of these supporting cells to the neuroinflammatory response. This human 3D BBB-on-a-chip exhibited barrier permeability similar to that observed in other in vitro BBB models created with non-human cells, and when stimulated with the inflammatory trigger, tumor necrosis factor-alpha (TNF-α), different secretion profiles for granulocyte colony-stimulating factor (G-CSF) and interleukin-6 (IL-6) were observed depending on the presence of astrocytes or pericytes. Importantly, the levels of these responses detected in the 3D BBB chip were significantly greater than when the same cells were co-cultured in static Transwell plates. Thus, as G-CSF and IL-6 have been reported to play important roles in neuroprotection and neuroactivation in vivo, this 3D BBB chip potentially offers a new method to study human neurovascular function and inflammation in vitro, and to identify physiological contributions of individual cell types. PMID:26930059

  10. A Factor-Image Framework to Quantification of Brain Receptor Dynamic PET Studies

    PubMed Central

    Wang, Z. Jane; Szabo, Zsolt; Lei, Peng; Varga, József; Liu, K. J. Ray

    2007-01-01

    The positron emission tomography (PET) imaging technique enables the measurement of receptor distribution or neurotransmitter release in the living brain and the changes of the distribution with time and thus allows quantification of binding sites as well as the affinity of a radioligand. However, quantification of receptor binding studies obtained with PET is complicated by tissue heterogeneity in the sampling image elements (i.e., voxels, pixels). This effect is caused by a limited spatial resolution of the PET scanner. Spatial heterogeneity is often essential in understanding the underlying receptor binding process. Tracer kinetic modeling also often requires an intrusive collection of arterial blood samples. In this paper, we propose a likelihood-based framework in the voxel domain for quantitative imaging with or without the blood sampling of the input function. Radioligand kinetic parameters are estimated together with the input function. The parameters are initialized by a subspace-based algorithm and further refined by an iterative likelihood-based estimation procedure. The performance of the proposed scheme is examined by simulations. The results show that the proposed scheme provides reliable estimation of factor time-activity curves (TACs) and the underlying parametric images. A good match is noted between the result of the proposed approach and that of the Logan plot. Real brain PET data are also examined, and good performance is observed in determining the TACs and the underlying factor images. PMID:18769527

  11. PET imaging of neurogenic activity in the adult brain: Toward in vivo imaging of human neurogenesis.

    PubMed

    Tamura, Yasuhisa; Kataoka, Yosky

    2017-01-01

    Neural stem cells are present in 2 neurogenic regions, the subventricular zone (SVZ) and the subgranular zone (SGZ) of the hippocampal dentate gyrus (DG), and continue to generate new neurons throughout life. Adult hippocampal neurogenesis is linked to a variety of psychiatric disorders such as depression and anxiety, and to the therapeutic effects of antidepressants, as well as learning and memory. In vivo imaging for hippocampal neurogenic activity may be used to diagnose psychiatric disorders and evaluate the therapeutic efficacy of antidepressants. However, these imaging techniques remain to be established until now. Recently, we established a quantitative positron emission tomography (PET) imaging technique for neurogenic activity in the adult brain with 3'-deoxy-3'-[(18)F]fluoro-L-thymidine ([(18)F]FLT) and probenecid, a drug transporter inhibitor in blood-brain barrier. Moreover, we showed that this PET imaging technique can monitor alterations in neurogenic activity in the hippocampus of adult rats with depression and following treatment with an antidepressant. This PET imaging method may assist in diagnosing depression and in monitoring the therapeutic efficacy of antidepressants. In this commentary, we discuss the possibility of in vivo PET imaging for neurogenic activity in adult non-human primates and humans.

  12. Pharmacologic perturbation as a potential tool to increase the sensitivity of FDG-PET in the evaluation of brain tumors

    SciTech Connect

    Wong, F.C.L.; Kim, E.E.; Yung, W.K.A.

    1994-05-01

    The usefulness of F-18 FDG PET in the study of brain tumors is limited by the high baseline cortical uptake which decreases the contrast of the tumor. Two alternatives to increase the tumor/background contrast have been reported: barbiturate-induced coma and postprandial state. This project evaluates the effects of sedation with diazepam or of oral glucose intake on the brain tumor/background contrast during F-18 FDG PET studies.

  13. Evaluation of MLACF based calculated attenuation brain PET imaging for FDG patient studies

    NASA Astrophysics Data System (ADS)

    Bal, Harshali; Panin, Vladimir Y.; Platsch, Guenther; Defrise, Michel; Hayden, Charles; Hutton, Chloe; Serrano, Benjamin; Paulmier, Benoit; Casey, Michael E.

    2017-04-01

    Calculating attenuation correction for brain PET imaging rather than using CT presents opportunities for low radiation dose applications such as pediatric imaging and serial scans to monitor disease progression. Our goal is to evaluate the iterative time-of-flight based maximum-likelihood activity and attenuation correction factors estimation (MLACF) method for clinical FDG brain PET imaging. FDG PET/CT brain studies were performed in 57 patients using the Biograph mCT (Siemens) four-ring scanner. The time-of-flight PET sinograms were acquired using the standard clinical protocol consisting of a CT scan followed by 10 min of single-bed PET acquisition. Images were reconstructed using CT-based attenuation correction (CTAC) and used as a gold standard for comparison. Two methods were compared with respect to CTAC: a calculated brain attenuation correction (CBAC) and MLACF based PET reconstruction. Plane-by-plane scaling was performed for MLACF images in order to fix the variable axial scaling observed. The noise structure of the MLACF images was different compared to those obtained using CTAC and the reconstruction required a higher number of iterations to obtain comparable image quality. To analyze the pooled data, each dataset was registered to a standard template and standard regions of interest were extracted. An SUVr analysis of the brain regions of interest showed that CBAC and MLACF were each well correlated with CTAC SUVrs. A plane-by-plane error analysis indicated that there were local differences for both CBAC and MLACF images with respect to CTAC. Mean relative error in the standard regions of interest was less than 5% for both methods and the mean absolute relative errors for both methods were similar (3.4%  ±  3.1% for CBAC and 3.5%  ±  3.1% for MLACF). However, the MLACF method recovered activity adjoining the frontal sinus regions more accurately than CBAC method. The use of plane-by-plane scaling of MLACF images was found to be a

  14. Dual-modality brain PET-CT image segmentation based on adaptive use of functional and anatomical information.

    PubMed

    Xia, Yong; Eberl, Stefan; Wen, Lingfeng; Fulham, Michael; Feng, David Dagan

    2012-01-01

    Dual medical imaging modalities, such as PET-CT, are now a routine component of clinical practice. Medical image segmentation methods, however, have generally only been applied to single modality images. In this paper, we propose the dual-modality image segmentation model to segment brain PET-CT images into gray matter, white matter and cerebrospinal fluid. This model converts PET-CT image segmentation into an optimization process controlled simultaneously by PET and CT voxel values and spatial constraints. It is innovative in the creation and application of the modality discriminatory power (MDP) coefficient as a weighting scheme to adaptively combine the functional (PET) and anatomical (CT) information on a voxel-by-voxel basis. Our approach relies upon allowing the modality with higher discriminatory power to play a more important role in the segmentation process. We compared the proposed approach to three other image segmentation strategies, including PET-only based segmentation, combination of the results of independent PET image segmentation and CT image segmentation, and simultaneous segmentation of joint PET and CT images without an adaptive weighting scheme. Our results in 21 clinical studies showed that our approach provides the most accurate and reliable segmentation for brain PET-CT images.

  15. The Relationship of 3D Human Skull Motion to Brain Tissue Deformation in Magnetic Resonance Elastography Studies.

    PubMed

    Badachhape, Andrew A; Okamoto, Ruth J; Durham, Ramona S; Efron, Brent D; Nadell, Sam J; Johnson, Curtis L; Bayly, Philip V

    2017-03-07

    In traumatic brain injury (TBI), membranes such as the dura mater, arachnoid mater, and pia mater play a vital role in transmitting motion from the skull to brain tissue. Magnetic Resonance Elastography (MRE) is an imaging technique developed for non-invasive estimation of soft tissue material parameters. In MRE, dynamic deformation of brain tissue is induced by skull vibrations; however skull motion and its mode of transmission to the brain remain largely uncharacterized. In this study, displacements of points in the skull, reconstructed using data from an array of MRI-safe accelerometers, were compared to displacements of neighboring material points in brain tissue, estimated from MRE measurements. Comparison of the relative amplitudes, directions, and temporal phases of harmonic motion in the skulls and brains of six human subjects shows that the skull-brain interface significantly attenuates and delays transmission of motion from skull to brain. In contrast, in a cylindrical gelatin "phantom", displacements of the rigid case (reconstructed from accelerometer data) were transmitted to the gelatin inside (estimated from MRE data) with little attenuation or phase lag. This quantitative characterization of the skull-brain interface will be valuable in the parameterization and validation of computer models of TBI.

  16. Non-planar interconnects in double-sided flexible Cu-PET substrates using a laser-assisted maskless microdeposition process: 3D finite element modeling and experimental analysis

    NASA Astrophysics Data System (ADS)

    Jabari, Elahe; Tong, Steven; Azhari, Amir; Toyserkani, Ehsan

    2014-03-01

    Non-planar (3D) interconnects have an important role in the electronic packaging industry these days. These unconventional interconnects allow manufacturers to save materials and space while connecting circuit components on flexible and non-planar substrates. Among a variety of flexible boards, double-sided flexible substrates have attracted the electronic industry to effectively and compactly develop miniaturized flexible devices such as sensors-on-chips. This study reports our developmental procedure for the creation of non-planar silver interconnects on the edge of double-sided copper substrates separated by a layer of polyethylene terephthalate (PET) using laser-assisted maskless microdeposition (LAMM). The article consists of the characterization of the LAMM process to effectively deposit Ag nanoparticles for production of conductive interconnects. Several parameters, including the deposition and laser processing parameters, are optimized to achieve interconnects free of pores, cracks and delamination. For investigating the topography and microstructure of interconnects, various analytical tools, such as SEM, XRD, Profilometery, and EDS were used. Furthermore, a 3D finite element numerical model was developed to predict the laser processing of silver nanoparticles on the substrate. The model includes a coupled thermal and structural governing physics to derive the temperature history throughout the simulation as well as strain/displacement within the substrate, which is identified the major source of cark formation in Ag tracks. The SEM micrographs of the laser processed nanoparticles suggest that a minimum of 1.24 W laser power was needed for an effective nanoparticles sintering to obtain conductive 3D interconnects with minimum amount of cracks whereas a 1.7 W laser power caused PET to decompose.

  17. Guidelines to PET measurements of the target occupancy in the brain for drug development.

    PubMed

    Takano, Akihiro; Varrone, Andrea; Gulyás, Balázs; Salvadori, Piero; Gee, Antony; Windhorst, Albert; Vercouillie, Johnny; Bormans, Guy; Lammertsma, Adriaan A; Halldin, Christer

    2016-11-01

    This guideline summarizes the current view of the European Association of Nuclear Medicine Drug Development Committee. The purpose of this guideline is to guarantee a high standard of PET studies that are aimed at measuring target occupancy in the brain within the framework of development programs of drugs that act within the central nervous system (CNS drugs). This guideline is intended to present information specifically adapted to European practice. The information provided should be applied within the context of local conditions and regulations.

  18. Real-time motion- and B0-correction for LASER-localized spiral-accelerated 3D-MRSI of the brain at 3T.

    PubMed

    Bogner, Wolfgang; Hess, Aaron T; Gagoski, Borjan; Tisdall, M Dylan; van der Kouwe, Andre J W; Trattnig, Siegfried; Rosen, Bruce; Andronesi, Ovidiu C

    2014-03-01

    The full potential of magnetic resonance spectroscopic imaging (MRSI) is often limited by localization artifacts, motion-related artifacts, scanner instabilities, and long measurement times. Localized adiabatic selective refocusing (LASER) provides accurate B1-insensitive spatial excitation even at high magnetic fields. Spiral encoding accelerates MRSI acquisition, and thus, enables 3D-coverage without compromising spatial resolution. Real-time position- and shim/frequency-tracking using MR navigators correct motion- and scanner instability-related artifacts. Each of these three advanced MRI techniques provides superior MRSI data compared to commonly used methods. In this work, we integrated in a single pulse sequence these three promising approaches. Real-time correction of motion, shim, and frequency-drifts using volumetric dual-contrast echo planar imaging-based navigators were implemented in an MRSI sequence that uses low-power gradient modulated short-echo time LASER localization and time efficient spiral readouts, in order to provide fast and robust 3D-MRSI in the human brain at 3T. The proposed sequence was demonstrated to be insensitive to motion- and scanner drift-related degradations of MRSI data in both phantoms and volunteers. Motion and scanner drift artifacts were eliminated and excellent spectral quality was recovered in the presence of strong movement. Our results confirm the expected benefits of combining a spiral 3D-LASER-MRSI sequence with real-time correction. The new sequence provides accurate, fast, and robust 3D metabolic imaging of the human brain at 3T. This will further facilitate the use of 3D-MRSI for neuroscience and clinical applications.

  19. (18)F-FET PET Uptake Characteristics in Patients with Newly Diagnosed and Untreated Brain Metastasis.

    PubMed

    Unterrainer, Marcus; Galldiks, Norbert; Suchorska, Bogdana; Kowalew, Lara-Caroline; Wenter, Vera; Schmid-Tannwald, Christine; Niyazi, Maximilian; Bartenstein, Peter; Langen, Karl-Josef; Albert, Nathalie L

    2017-04-01

    In patients with brain metastasis, PET using labeled amino acids has gained clinical importance, mainly regarding the differentiation of viable tumor tissue from treatment-related effects. However, there is still limited knowledge concerning the uptake characteristics in patients with newly diagnosed and untreated brain metastases. Hence, we evaluated the uptake characteristics in these patients using dynamic O-(2-(18)F-fluoroethyl)-l-tyrosine ((18)F-FET) PET. Methods: Patients with newly diagnosed brain metastases without prior local therapy and (18)F-FET PET scanning were retrospectively identified in 2 centers. Static and dynamic PET parameters (maximal/mean tumor-to-brain-ratio [TBRmax/TBRmean], biologic tumor volume [BTV], and time-activity curves with minimal time to peak [TTPmin]) were evaluated and correlated with MRI parameters (maximal lesion diameter, volume of contrast enhancement) and originating primary tumor. Results: Forty-five brain metastases in 30 patients were included. Forty of 45 metastases (89%) had a TBRmax ≥ 1.6 and were classified as (18)F-FET-positive (median TBRmax, 2.53 [range, 1.64-9.47]; TBRmean, 1.86 [range, 1.63-5.48]; and BTV, 3.59 mL [range, 0.04-23.98 mL], respectively). In 39 of 45 brain metastases eligible for dynamic analysis, a wide range of TTPmin was observed (median, 22.5 min; range, 4.5-47.5 min). All (18)F-FET-negative metastases had a diameter of ≤ 1.0 cm, whereas metastases with a > 1.0 cm diameter all showed pathologic (18)F-FET uptake, which did not correlate with lesion size. The highest variability of uptake intensity was observed within the group of melanoma metastases. Conclusion: Untreated metastases predominantly show increased (18)F-FET uptake, and only a third of metastases < 1.0 cm were (18)F-FET-negative, most likely because of scanner resolution and partial-volume effects. In metastases > 1.0 cm, (18)F-FET uptake intensity was highly variable and independent of tumor size (even intraindividually). (18

  20. PET imaging of brain inflammation during early epileptogenesis in a rat model of temporal lobe epilepsy

    PubMed Central

    2012-01-01

    Background Recently, inflammatory cascades have been suggested as a target for epilepsy therapy. Positron emission tomography (PET) imaging offers the unique possibility to evaluate brain inflammation longitudinally in a non-invasive translational manner. This study investigated brain inflammation during early epileptogenesis in the post-kainic acid-induced status epilepticus (KASE) model with post-mortem histology and in vivo with [18F]-PBR111 PET. Methods Status epilepticus (SE) was induced (N = 13) by low-dose injections of KA, while controls (N = 9) received saline. Translocator protein (TSPO) expression and microglia activation were assessed with [125I]-CLINDE autoradiography and OX-42 immunohistochemistry, respectively, 7 days post-SE. In a subgroup of rats, [18F]-PBR111 PET imaging with metabolite-corrected input function was performed before post-mortem evaluation. [18F]-PBR111 volume of distribution (Vt) in volume of interests (VOIs) was quantified by means of kinetic modelling and a VOI/metabolite-corrected plasma activity ratio. Results Animals with substantial SE showed huge overexpression of TSPO in vitro in relevant brain regions such as the hippocampus and amygdala (P < 0.001), while animals with mild symptoms displayed a smaller increase in TSPO in amygdala only (P < 0.001). TSPO expression was associated with OX-42 signal but without obvious cell loss. Similar in vivo [18F]-PBR111 increases in Vt and the simplified ratio were found in key regions such as the hippocampus (P < 0.05) and amygdala (P < 0.01). Conclusion Both post-mortem and in vivo methods substantiate that the brain regions important in seizure generation display significant brain inflammation during epileptogenesis in the KASE model. This work enables future longitudinal investigation of the role of brain inflammation during epileptogenesis and evaluation of anti-inflammatory treatments. PMID:23136853

  1. Attenuation correction for the large non-human primate brain imaging using microPET

    NASA Astrophysics Data System (ADS)

    Naidoo-Variawa, S.; Lehnert, W.; Kassiou, M.; Banati, R.; Meikle, S. R.

    2010-04-01

    Assessment of the biodistribution and pharmacokinetics of radiopharmaceuticals in vivo is often performed on animal models of human disease prior to their use in humans. The baboon brain is physiologically and neuro-anatomically similar to the human brain and is therefore a suitable model for evaluating novel CNS radioligands. We previously demonstrated the feasibility of performing baboon brain imaging on a dedicated small animal PET scanner provided that the data are accurately corrected for degrading physical effects such as photon attenuation in the body. In this study, we investigated factors affecting the accuracy and reliability of alternative attenuation correction strategies when imaging the brain of a large non-human primate (papio hamadryas) using the microPET Focus 220 animal scanner. For measured attenuation correction, the best bias versus noise performance was achieved using a 57Co transmission point source with a 4% energy window. The optimal energy window for a 68Ge transmission source operating in singles acquisition mode was 20%, independent of the source strength, providing bias-noise performance almost as good as for 57Co. For both transmission sources, doubling the acquisition time had minimal impact on the bias-noise trade-off for corrected emission images, despite observable improvements in reconstructed attenuation values. In a [18F]FDG brain scan of a female baboon, both measured attenuation correction strategies achieved good results and similar SNR, while segmented attenuation correction (based on uncorrected emission images) resulted in appreciable regional bias in deep grey matter structures and the skull. We conclude that measured attenuation correction using a single pass 57Co (4% energy window) or 68Ge (20% window) transmission scan achieves an excellent trade-off between bias and propagation of noise when imaging the large non-human primate brain with a microPET scanner.

  2. Investigation of partial volume correction methods for brain FDG PET studies

    SciTech Connect

    Yang, J.; Huang, S.C.; Mega, M.; Toga, A.W.; Small, G.W.; Phelps, M.E.; Lin, K.P.

    1996-12-01

    The use of positron emission tomography (PET) in quantitative fluorodeoxyglucose (FDG) studies of aging and dementia has been limited by partial volume effects. A general method for correction of partial volume effects (PVE) in PET involves the following common procedures; segmentation of MRI brain images into gray matter (GM), white matter (WM), cerebral spinal fluid (CSF), and muscle (MS) components; MRI PET registration; and generation of simulated PET images. Afterward, two different approaches can be taken. The first approach derives first a pixel-by-pixel correction map as the ratio of the measured image to the simulated image [with realistic full-width at half-maximum (FWHM)]. The correction map was applied to the MRI segmentation image. Regions of interest (ROI`s) can then be applied to give results free of partial volume effects. The second approach uses the ROI values of the simulated ``pure`` image (with negligible FWHM) and those of the simulated and the measured PET images to correct for the PVE effect. By varying the ratio of radiotracer concentrations for different tissue components, the in-plane FWHM`s of a three-dimensional point spread function, and the ROI size, the authors evaluated the performance of these two approaches in terms of their accuracy and sensitivity to different simulation configurations. The results showed that both approaches are more robust than the approach developed by Muller-Gartner et al., and the second approach is more accurate and more robust than the first. In conclusion, the authors recommend that the second approach should be used on FDG PET images to correct for partial volume effects and to determine whether an apparent change in GM radiotracer concentration is truly due to metabolic changes.

  3. Predicting Alzheimer's disease by classifying 3D-Brain MRI images using SVM and other well-defined classifiers

    NASA Astrophysics Data System (ADS)

    Matoug, S.; Abdel-Dayem, A.; Passi, K.; Gross, W.; Alqarni, M.

    2012-02-01

    Alzheimer's disease (AD) is the most common form of dementia affecting seniors age 65 and over. When AD is suspected, the diagnosis is usually confirmed with behavioural assessments and cognitive tests, often followed by a brain scan. Advanced medical imaging and pattern recognition techniques are good tools to create a learning database in the first step and to predict the class label of incoming data in order to assess the development of the disease, i.e., the conversion from prodromal stages (mild cognitive impairment) to Alzheimer's disease, which is the most critical brain disease for the senior population. Advanced medical imaging such as the volumetric MRI can detect changes in the size of brain regions due to the loss of the brain tissues. Measuring regions that atrophy during the progress of Alzheimer's disease can help neurologists in detecting and staging the disease. In the present investigation, we present a pseudo-automatic scheme that reads volumetric MRI, extracts the middle slices of the brain region, performs segmentation in order to detect the region of brain's ventricle, generates a feature vector that characterizes this region, creates an SQL database that contains the generated data, and finally classifies the images based on the extracted features. For our results, we have used the MRI data sets from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database.

  4. Concurrent Low Brain and High Liver Uptake on FDG PET Are Associated with Cardiovascular Risk Factors

    PubMed Central

    Nam, Hyun-Yeol; Jun, Sungmin; Pak, Kyoungjune

    2017-01-01

    Objective Concurrent low brain and high liver uptake are sometimes observed on fluorine-18-labeled fluoro-2-deoxy-D-glucose (FDG) positron emission tomography (PET). We investigated the potential clinical significance of this uptake pattern related to metabolic syndrome (MS). Materials and Methods We retrospectively reviewed data from 264 consecutive males who had undergone general health check-ups, including FDG PET/CT scans. After an overnight fast, the men had their peripheral blood drawn and the levels of various laboratory parameters measured; an FDG PET/CT scan was performed on the same day. We measured the maximum standardized uptake values of the brain and liver from regions of interest manually placed over the frontal cortex at the level of the centrum semiovale and the right lobe of the liver parenchyma, respectively. Results Fasting blood glucose (FBG; odds ratio [OR] = 1.063, p < 0.001) and glycated hemoglobin (HbA1c; OR = 3.634, p = 0.010) were the strongest predictive factors for low brain FDG uptake, whereas waist circumference (OR = 1.200, p < 0.001) and γ-glutamyl transpeptidase (OR = 1.012, p = 0.001) were the strongest predictive factors for high liver uptake. Eleven subjects (4.2%) showed concurrent low brain and high liver FDG uptake, and all but one of these subjects (90.9%) had MS. Systolic blood pressure, waist circumference, FBG, triglyceride, alanine aminotransferase, insulin resistance (measured by homeostasis model assessment), insulin, HbA1c, and body mass index were higher in subjects with this FDG uptake pattern than in those without (all, p < 0.001). Conclusion Concurrent low brain and high liver FDG uptake were closely associated with MS. Moreover, subjects with this pattern had higher values for various cardiovascular risk factors than did those without. PMID:28246520

  5. Cardiac-induced physiological noise in 3D gradient echo brain imaging: Effect of k -space sampling scheme

    NASA Astrophysics Data System (ADS)

    Kristoffersen, Anders; Goa, Pål Erik

    2011-09-01

    The physiological noise in 3D image acquisition is shown to depend strongly on the sampling scheme. Five sampling schemes are considered: Linear, Centric, Segmented, Random and Tuned. Tuned acquisition means that data acquisition at k-space positions k and - k are separated with a specific time interval. We model physiological noise as a periodic temporal oscillation with arbitrary spatial amplitude in the physical object and develop a general framework to describe how this is rendered in the reconstructed image. Reconstructed noise can be decomposed in one component that is in phase with the signal (parallel) and one that is 90° out of phase (orthogonal). Only the former has a significant influence on the magnitude of the signal. The study focuses on fMRI using 3D EPI. Each k-space plane is acquired in a single shot in a time much shorter than the period of the physiological noise. The above mentioned sampling schemes are applied in the slow k-space direction and noise propagates almost exclusively in this direction. The problem then, is effectively one-dimensional. Numerical simulations and analytical expressions are presented. 3D noise measurements and 2D measurements with high temporal resolution are conducted. The measurements are performed under breath-hold to isolate the effect of cardiac-induced pulsatile motion. We compare the time-course stability of the sampling schemes and the extent to which noise propagates from a localized source into other parts of the imaging volume. Tuned and Linear acquisitions perform better than Centric, Segmented and Random.

  6. Histograms of Oriented 3D Gradients for Fully Automated Fetal Brain Localization and Robust Motion Correction in 3 T Magnetic Resonance Images

    PubMed Central

    Macnaught, Gillian; Denison, Fiona C.; Reynolds, Rebecca M.; Semple, Scott I.; Boardman, James P.

    2017-01-01

    Fetal brain magnetic resonance imaging (MRI) is a rapidly emerging diagnostic imaging tool. However, automated fetal brain localization is one of the biggest obstacles in expediting and fully automating large-scale fetal MRI processing. We propose a method for automatic localization of fetal brain in 3 T MRI when the images are acquired as a stack of 2D slices that are misaligned due to fetal motion. First, the Histogram of Oriented Gradients (HOG) feature descriptor is extended from 2D to 3D images. Then, a sliding window is used to assign a score to all possible windows in an image, depending on the likelihood of it containing a brain, and the window with the highest score is selected. In our evaluation experiments using a leave-one-out cross-validation strategy, we achieved 96% of complete brain localization using a database of 104 MRI scans at gestational ages between 34 and 38 weeks. We carried out comparisons against template matching and random forest based regression methods and the proposed method showed superior performance. We also showed the application of the proposed method in the optimization of fetal motion correction and how it is essential for the reconstruction process. The method is robust and does not rely on any prior knowledge of fetal brain development. PMID:28251155

  7. 3D spatially encoded and accelerated TE-averaged echo planar spectroscopic imaging in healthy human brain.

    PubMed

    Iqbal, Zohaib; Wilson, Neil E; Thomas, M Albert

    2016-03-01

    Several different pathologies, including many neurodegenerative disorders, affect the energy metabolism of the brain. Glutamate, a neurotransmitter in the brain, can be used as a biomarker to monitor these metabolic processes. One method that is capable of quantifying glutamate concentration reliably in several regions of the brain is TE-averaged (1) H spectroscopic imaging. However, this type of method requires the acquisition of multiple TE lines, resulting in long scan durations. The goal of this experiment was to use non-uniform sampling, compressed sensing reconstruction and an echo planar readout gradient to reduce the scan time by a factor of eight to acquire TE-averaged spectra in three spatial dimensions. Simulation of glutamate and glutamine showed that the 2.2-2.4 ppm spectral region contained 95% glutamate signal using the TE-averaged method. Peak integration of this spectral range and home-developed, prior-knowledge-based fitting were used for quantitation. Gray matter brain phantom measurements were acquired on a Siemens 3 T Trio scanner. Non-uniform sampling was applied retrospectively to these phantom measurements and quantitative results of glutamate with respect to creatine 3.0 (Glu/Cr) ratios showed a coefficient of variance of 16% for peak integration and 9% for peak fitting using eight-fold acceleration. In vivo scans of the human brain were acquired as well and five different brain regions were quantified using the prior-knowledge-based algorithm. Glu/Cr ratios from these regions agreed with previously reported results in the literature. The method described here, called accelerated TE-averaged echo planar spectroscopic imaging (TEA-EPSI), is a significant methodological advancement and may be a useful tool for categorizing glutamate changes in pathologies where affected brain regions are not known a priori. Copyright © 2016 John Wiley & Sons, Ltd.

  8. Assessment of rodent brain activity using combined [(15)O]H2O-PET and BOLD-fMRI.

    PubMed

    Wehrl, Hans F; Martirosian, Petros; Schick, Fritz; Reischl, Gerald; Pichler, Bernd J

    2014-04-01

    The study of brain activation in small animals is of high interest for neurological research. In this study, we proposed a protocol to monitor brain activation in rats following whisker stimulation using the short half-life PET tracer [(15)O]H2O as a marker for cerebral blood flow. This technique enables the study of baseline and activation conditions in fast succession within the same scanning session. Furthermore, we compared the results obtained from PET imaging with additional BOLD-fMRI data acquired in the same animals within the same anesthetic session in immediate succession. Although the maximum relative signal changes during brain activity observed with PET were substantially higher compared to the BOLD-fMRI results, statistical analyses showed that the number of activated voxels in PET was lower compared to the fMRI measurements. Furthermore, there was a difference in the activation centers in both the shape and location between PET and fMRI. The discrepancy in the number of activated voxels could be attributed to a lower overall contrast-to-noise ratio of the PET images compared to BOLD-fMRI, whereas the difference in the spatial location indicates a more fundamental process, involving the different physiological origins of the PET and BOLD-fMRI response. This study clearly demonstrates that [(15)O]H2O-PET activation studies may be performed in small laboratory animals, and shows the complementary nature of studying brain activation using [(15)O]H2O-PET and fMRI.

  9. A robust framework for soft tissue simulations with application to modeling brain tumor mass effect in 3D MR images

    NASA Astrophysics Data System (ADS)

    Hogea, Cosmina; Biros, George; Abraham, Feby; Davatzikos, Christos

    2007-12-01

    We present a framework for black-box and flexible simulation of soft tissue deformation for medical imaging and surgical planning applications. Our main motivation in the present work is to develop robust algorithms that allow batch processing for registration of brains with tumors to statistical atlases of normal brains and construction of brain tumor atlases. We describe a fully Eulerian formulation able to handle large deformations effortlessly, with a level-set-based approach for evolving fronts. We use a regular grid—fictitious domain method approach, in which we approximate coefficient discontinuities, distributed forces and boundary conditions. This approach circumvents the need for unstructured mesh generation, which is often a bottleneck in the modeling and simulation pipeline. Our framework employs penalty approaches to impose boundary conditions and uses a matrix-free implementation coupled with a multigrid-accelerated Krylov solver. The overall scheme results in a scalable method with minimal storage requirements and optimal algorithmic complexity. We illustrate the potential of our framework to simulate realistic brain tumor mass effects at reduced computational cost, for aiding the registration process towards the construction of brain tumor atlases.

  10. Alpha shape theory for 3D visualization and volumetric measurement of brain tumor progression using magnetic resonance images.

    PubMed

    Hamoud Al-Tamimi, Mohammed Sabbih; Sulong, Ghazali; Shuaib, Ibrahim Lutfi

    2015-07-01

    Resection of brain tumors is a tricky task in surgery due to its direct influence on the patients' survival rate. Determining the tumor resection extent for its complete information via-à-vis volume and dimensions in pre- and post-operative Magnetic Resonance Images (MRI) requires accurate estimation and comparison. The active contour segmentation technique is used to segment brain tumors on pre-operative MR images using self-developed software. Tumor volume is acquired from its contours via alpha shape theory. The graphical user interface is developed for rendering, visualizing and estimating the volume of a brain tumor. Internet Brain Segmentation Repository dataset (IBSR) is employed to analyze and determine the repeatability and reproducibility of tumor volume. Accuracy of the method is validated by comparing the estimated volume using the proposed method with that of gold-standard. Segmentation by active contour technique is found to be capable of detecting the brain tumor boundaries. Furthermore, the volume description and visualization enable an interactive examination of tumor tissue and its surrounding. Admirable features of our results demonstrate that alpha shape theory in comparison to other existing standard methods is superior for precise volumetric measurement of tumor.

  11. The ultrasound brain helmet: new transducers and volume registration for in vivo simultaneous multi-transducer 3-D transcranial imaging.

    PubMed

    Lindsey, Brooks D; Light, Edward D; Nicoletto, Heather A; Bennett, Ellen R; Laskowitz, Daniel T; Smith, Stephen W

    2011-06-01

    Because stroke remains an important and time-sensitive health concern in developed nations, we present a system capable of fusing 3-D transcranial ultrasound volumes acquired from two sides of the head. This system uses custom sparse array transducers built on flexible multilayer circuits that can be positioned for simultaneous imaging through both temporal acoustic windows, allowing for potential registration of multiple real-time 3-D scans of cerebral vasculature. We examine hardware considerations for new matrix arrays-transducer design and interconnects-in this application. Specifically, it is proposed that SNR may be increased by reducing the length of probe cables. This claim is evaluated as part of the presented system through simulation, experimental data, and in vivo imaging. Ultimately, gains in SNR of 7 dB are realized by replacing a standard probe cable with a much shorter flex interconnect; higher gains may be possible using ribbon-based probe cables. In vivo images are presented, showing cerebral arteries with and without the use of microbubble contrast agent; they have been registered and fused using a simple algorithm which maximizes normalized cross-correlation.

  12. Positron Emission Tomography (PET) Quantification of GABAA Receptors in the Brain of Fragile X Patients.

    PubMed

    D'Hulst, Charlotte; Heulens, Inge; Van der Aa, Nathalie; Goffin, Karolien; Koole, Michel; Porke, Kathleen; Van De Velde, Marc; Rooms, Liesbeth; Van Paesschen, Wim; Van Esch, Hilde; Van Laere, Koen; Kooy, R Frank

    2015-01-01

    Over the last several years, evidence has accumulated that the GABAA receptor is compromised in animal models for fragile X syndrome (FXS), a common hereditary form of intellectual disability. In mouse and fly models, agonists of the GABAA receptor were able to rescue specific consequences of the fragile X mutation. Here, we imaged and quantified GABAA receptors in vivo in brain of fragile X patients using Positron Emission Topography (PET) and [11C]flumazenil, a known high-affinity and specific ligand for the benzodiazepine site of GABAA receptors. We measured regional GABAA receptor availability in 10 fragile X patients and 10 control subjects. We found a significant reduction of on average 10% in GABAA receptor binding potential throughout the brain in fragile X patients. In the thalamus, the brain region showing the largest difference, the GABAA receptor availability was even reduced with 17%. This is one of the first reports of a PET study of human fragile X brain and directly demonstrates that the GABAA receptor availability is reduced in fragile X patients. The study reinforces previous hypotheses that the GABAA receptor is a potential target for rational pharmacological treatment of fragile X syndrome.

  13. Quantitative estimation of 3-D fiber course in gross histological sections of the human brain using polarized light.

    PubMed

    Axer, H; Axer, M; Krings, T; Keyserlingk, D G

    2001-02-15

    Series of polarized light images can be used to achieve quantitative estimates of the angles of inclination (z-direction) and direction (in xy-plane) of central nervous fibers in histological sections of the human brain. (1) The corpus callosum of a formalin-fixed human brain was sectioned at different angles of inclination of nerve fibers and at different thicknesses of the samples. The minimum, and maximum intensities, and their differences revealed a linear relationship to the angle of inclination of fibers. It was demonstrated that sections with a thickness of 80--120 microm are best suited for estimating the angle of inclination. (2) Afterwards the optic tracts of eight formalin-fixed human brains were sliced at different angles of fiber inclination at 100 microm. Measurements of intensity in 30 pixels in each section were used to calculate a linear function of calibration. The maximum intensities and the differences between maximum and minimum values measured with two polars only were best suited for estimation of fiber inclination. (3) Gross histological brain slices of formalin-fixed human brains were digitized under azimuths from 0 to 80 degrees using two polars only. These sequences were used to estimate the inclination of fibers (in z-direction). The same slices were digitized under azimuths from 0 to 160 degrees in steps of 20 degrees using a quarter wave plate additionally. These sequences were used to estimate the direction of the fibers in xy-direction. The method can be used to produce maps of fiber orientation in gross histological sections of the human brain similar to the fiber orientation maps derived by diffusion weighted magnetic resonance imaging.

  14. Brain FDG-PET metabolic abnormalities in Macrophagic Myofasciitis: Are They Stable?

    PubMed

    Blanc-Durand, Paul; Van Der Gucht, Axel; Aoun Sebaiti, Mehdi; Abulizi, Mukedaisi; Authier, Francois-Jérome; Itti, Emmanuel

    2017-03-16

    We address this letter in addition to our recent published study (1). The aim is to add some insight to the evolution of the brain abnormalities that are observed with macrophagic myofasciitis (MMF). MMF is a chronic disease whom evolution is slow and symptoms first may occurs from months to year after a vaccination containing aluminium hydroxid adjuvants (2). Nevertheless, its evolution is not fully understood or known. MMF associated cognitive dysfunction (MACD) is based on a tripod combining dysexecutive syndrom, visual memory impairment and interhemispheric disconnection. One pilot study suggest that MACD appears clinically stable over time (3). One recent study evaluating a support vector machine classifier also suggest that the abnormalities observed with 18-fluorodeoxyglose positron emission tomography ((18)F-FDG PET) may be sensitive and could be used to monitor patients. The study population comes from cohort followed in our Reference Center for Rare Neuromuscular Diseases and data were collected retrospectively. Among those patients, 15 had two consecutives (18)F-FDG PET brain acquisitions (median age 42.1 [range 20.9 to 63.5]) following the same brain protocol acquisition as previously described (1). Median time duration between the two examinations was 2.3 years (range 0.5 to 4]. Using analysis of covariance and negative or positive contrast in SPM12, a t-test mask was generated from the comparison between the two means of the first cerebral (18)F-FDG PET images and between the mean of the second acquisition. Results of the comparison were collected at a P-value < 0.005 at the voxel level, for clusters k ≥ 200 voxels (corrected for cluster volume) with adjustment for age. Brain abnormalities maps didn't show any statistical difference between the two examinations confirming the idea that MMF is a slowly or not progressive disease and it is in concordance with the fact that neurological symptoms even if fluctuate do not worsen over time (nor ameliorate).

  15. Atlas construction for dynamic (4D) PET using diffeomorphic transformations.

    PubMed

    Bieth, Marie; Lombaert, Hervé; Reader, Andrew J; Siddiqi, Kaleem

    2013-01-01

    A novel dynamic (4D) PET to PET image registration procedure is proposed and applied to multiple PET scans acquired with the high resolution research tomograph (HRRT), the highest resolution human brain PET scanner available in the world. By extending the recent diffeomorphic log-demons (DLD) method and applying it to multiple dynamic [11C]raclopride scans from the HRRT, an important step towards construction of a PET atlas of unprecedented quality for [11C]raclopride imaging of the human brain has been achieved. Accounting for the temporal dimension in PET data improves registration accuracy when compared to registration of 3D to 3D time-averaged PET images. The DLD approach was chosen for its ease in providing both an intensity and shape template, through iterative sequential pair-wise registrations with fast convergence. The proposed method is applicable to any PET radiotracer, providing 4D atlases with useful applications in high accuracy PET data simulations and automated PET image analysis.

  16. Microcomputer-based technique for 3-D reconstruction and volume measurement of computed tomographic images. Part 2: Anaplastic primary brain tumors.

    PubMed

    Albright, R E; Fram, E K

    1988-12-01

    Serial computed tomography (CT) plays an integral part in monitoring effects of therapy for primary anaplastic brain tumors. Despite advances in CT technology, clinicians often cannot obtain accurate quantitative volume information to complement the qualitative assessment of tumor change. This paper presents a microcomputer-based method that provides both quantitative volume measurements and 3-D reconstructions of primary anaplastic brain tumors based on their hard copy CT or magnetic resonance imaging studies. The findings of this study demonstrate that planimetry is feasible for routine clinical use and is superior in accuracy to the spherical geometric model, which is shown to significantly overestimate tumor volume. The findings of 62 quantitative tumor studies (17 patients) showed a direct relationship between the total tumor volume and the volume of the hypodense intratumor core. There was no evidence of a relationship between the total tumor volume and the amount of peritumor low density (edema).

  17. Semi-automated 3D segmentation of major tracts in the rat brain: comparing DTI with standard histological methods.

    PubMed

    Gyengesi, Erika; Calabrese, Evan; Sherrier, Matthew C; Johnson, G Allan; Paxinos, George; Watson, Charles

    2014-03-01

    Researchers working with rodent models of neurological disease often require an accurate map of the anatomical organization of the white matter of the rodent brain. With the increasing popularity of small animal MRI techniques, including diffusion tensor imaging (DTI), there is considerable interest in rapid segmentation methods of neurological structures for quantitative comparisons. DTI-derived tractography allows simple and rapid segmentation of major white matter tracts, but the anatomic accuracy of these computer-generated fibers is open to question and has not been rigorously evaluated in the rat brain. In this study, we examine the anatomic accuracy of tractography-based segmentation in the adult rat brain. We analysed 12 major white matter pathways using semi-automated tractography-based segmentation alongside manual segmentation of Gallyas silver-stained histology sections. We applied four fiber-tracking algorithms to the DTI data-two integration methods and two deflection methods. In many cases, tractography-based segmentation closely matched histology-based segmentation; however different tractography algorithms produced dramatically different results. Results suggest that certain white matter pathways are more amenable to tractography-based segmentation than others. We believe that these data will help researchers decide whether it is appropriate to use tractography-based segmentation of white matter structures for quantitative DTI-based analysis of neurologic disease models.

  18. FDG PET brain scan demonstrated glucose hypometabolism of bilateral caudate nuclei and putamina in a patient with chorea-acanthocytosis.

    PubMed

    Cui, Ruixue; You, Hui; Niu, Na; Li, Fang

    2015-12-01

    Chorea-acanthocytosis is 1 type of neuroacanthocytosis that is a group of rare, hereditary neurodegenerative disorders. We presented a brain FDG PET finding of a 31-year-old woman with chorea-acanthocytosis. The images demonstrated significant hypometabolism in bilateral caudate nuclei and putamina. The finding of FDG PET is more prominent than that of MRI. Another interesting observation is the mildly increased FDG uptake in pituitary gland, although its relationship with the disease is unclear.

  19. Short-Term Practice Effects and Brain Hypometabolism: Preliminary Data from an FDG PET Study

    PubMed Central

    Duff, Kevin; Horn, Kevin P.; Foster, Norman L.; Hoffman, John M.

    2015-01-01

    Practice effects are improvements in cognitive test scores due to repeated exposure to the same tests. Typically viewed as error, short-term practice effects have been shown to provide valuable clinical information about diagnosis, prognosis, and treatment outcomes in older patients with mild cognitive impairments. This study examined short-term practice effects across one week and brain hypometabolism on fluoro-2-deoxyglucose (FDG) positron emission tomography (PET) in 25 older adults (15 intact, 10 Mild Cognitive Impairment). Averaged cerebral brain metabolism on FDG PET was correlated with multiple cognitive scores at baseline in those with Mild Cognitive Impairment, and short-term practice effects accounted for additional variance in these same subjects. The relationship between brain metabolism and cognition (either at baseline or practice effects) was minimal in the intact individuals. Although needing replication in larger samples, short-term practice effects on tests of executive functioning and memory may provide valuable information about biomarkers of Alzheimer’s disease. PMID:25908614

  20. Preserved pontine glucose metabolism in Alzheimer disease: A reference region for functional brain image (PET) analysis

    SciTech Connect

    Minoshima, Satoshi; Frey, K.A.; Foster, N.L.; Kuhl, D.W.

    1995-07-01

    Our goal was to examine regional preservation of energy metabolism in Alzheimer disease (AD) and to evaluate effects of PET data normalization to reference regions. Regional metabolic rates in the pons, thalamus, putamen, sensorimotor cortex, visual cortex, and cerebellum (reference regions) were determined stereotaxically and examined in 37 patients with probable AD and 22 normal controls based on quantitative {sup 18}FDG-PET measurements. Following normalization of metabolic rates of the parietotemporal association cortex and whole brain to each reference region, distinctions of the two groups were assessed. The pons showed the best preservation of glucose metabolism in AD. Other reference regions showed relatively preserved metabolism compared with the parietotemporal association cortex and whole brain, but had significant metabolic reduction. Data normalization to the pons not only enhanced statistical significance of metabolic reduction in the parietotemporal association cortex, but also preserved the presence of global cerebral metabolic reduction indicated in analysis of the quantitative data. Energy metabolism in the pons in probable AD is well preserved. The pons is a reliable reference for data normalization and will enhance diagnostic accuracy and efficiency of quantitative and nonquantitative functional brain imaging. 39 refs., 2 figs., 3 tabs.

  1. Striatofrontal Deafferentiation in MSA-P: Evaluation with [18F]FDG Brain PET

    PubMed Central

    Kim, Hae Won; Oh, Minyoung; Oh, Jungsu S.; Oh, Seung Jun; Lee, Sang Ju; Chung, Sun Ju; Kim, Jae Seung

    2017-01-01

    Background Although cognitive impairment is not a consistent feature of multiple system atrophy (MSA), increasing evidence suggests that cognitive impairment is common in MSA with predominant parkinsonism (MSA-P). It is assumed that the cognitive impairment in MSA-P is caused by the striatal dysfunction and disruption of striatofrontal connections. The aim of this study was to evaluate the relationship between regional glucose metabolism in the frontal cortex and striatum in patients with MSA-P using [18F]FDG brain PET. Methods Twenty-nine patients with MSA-P and 28 healthy controls underwent [18F]FDG brain PET scan. The [18F]FDG brain PET images were semiquantitatively analyzed on the basis of a template in standard space. The regional glucose metabolism of the cerebral cortex and striatum were compared between MSA-P and healthy control groups. The correlations between age, symptom duration, H&Y stage, UPDRS III score, MMSE score, and glucose metabolism in the cerebellum and striatum to glucose metabolism in the frontal cortex were evaluated by multivariate analysis. Results The glucose metabolism in the frontal cortex and striatum in MSA-P patients were significantly lower than those in healthy controls. Glucose metabolism in the striatum was the most powerful determinant of glucose metabolism in the frontal cortex in MSA-P. Only age and glucose metabolism in the cerebellum were independent variables affecting the glucose metabolism in the frontal cortex in healthy controls. Conclusion The decrease in frontal glucose metabolism in MSA-P is related to the decrease in striatal glucose metabolism. This result provided evidence of striatofrontal deafferentiation in patients with MSA-P. PMID:28085923

  2. [(11)C]MADAM, a new serotonin transporter radioligand characterized in the monkey brain by PET.

    PubMed

    Halldin, Christer; Lundberg, Johan; Sóvágó, Judit; Gulyás, Balázs; Guilloteau, Denis; Vercouillie, Johnny; Emond, Patrick; Chalon, Sylvie; Tarkiainen, Jari; Hiltunen, Jukka; Farde, Lars

    2005-12-01

    The aim of this study was to explore the potential of a new selective serotonin transporter (5-HTT) inhibitor, N,N-dimethyl-2-(2-amino-4-methylphenylthio)benzylamine (MADAM, K(i)=1.65 nM), as a PET radioligand for examination of 5-HTT in the nonhuman primate brain. MADAM was radiolabeled by an N-methylation reaction using [(11)C]methyl triflate and the binding was characterized by PET in four cynomolgus monkeys. Metabolite levels in plasma were measured by gradient high-performance liquid chromatography (HPLC). The radiochemical incorporation yield of [(11)C]MADAM was 75-80% and the specific radioactivity at the time of administration was 34-652 GBq/micromol (n=8). The highest uptake of radioactivity was observed in striatum, thalamus, mesencephalon, and the lower brainstem. Lower binding was detected in neocortex and the lowest radioactive uptake was found in the cerebellum. This distribution is in accordance with the known expression of 5-HTT in vitro. The fraction of the total radioactivity in monkey plasma representing unchanged [(11)C]MADAM was 20% at 45 min after injection, as measured by gradient HPLC. Pretreatment measurements, using unlabeled citalopram, GBR 12909, and maprotiline, as well as a displacement measurement, using unlabeled MADAM, confirmed that [(11)C]MADAM binds selectively and reversibly to 5-HTT, and support the use of the cerebellum as reference region. The present characterization of binding in the monkey brain suggests that [(11)C]MADAM is a potential PET radioligand for quantitative studies of 5-HTT binding in the human brain.

  3. Brain (18)F-FDG PET Metabolic Abnormalities in Patients with Long-Lasting Macrophagic Myofascitis.

    PubMed

    Van Der Gucht, Axel; Aoun Sebaiti, Mehdi; Guedj, Eric; Aouizerate, Jessie; Yara, Sabrina; Gherardi, Romain K; Evangelista, Eva; Chalaye, Julia; Cottereau, Anne-Ségolène; Verger, Antoine; Bachoud-Levi, Anne-Catherine; Abulizi, Mukedaisi; Itti, Emmanuel; Authier, François-Jérôme

    2017-03-01

    The aim of this study was to characterize brain metabolic abnormalities in patients with macrophagic myofascitis (MMF) and the relationship with cognitive dysfunction through the use of PET with (18)F-FDG. Methods:(18)F-FDG PET brain imaging and a comprehensive battery of neuropsychological tests were performed in 100 consecutive MMF patients (age [mean ± SD], 45.9 ± 12 y; 74% women). Images were analyzed with statistical parametric mapping (SPM12). Through the use of analysis of covariance, all (18)F-FDG PET brain images of MMF patients were compared with those of a reference population of 44 healthy subjects similar in age (45.4 ± 16 y; P = 0.87) and sex (73% women; P = 0.88). The neuropsychological assessment identified 4 categories of patients: those with no significant cognitive impairment (n = 42), those with frontal subcortical (FSC) dysfunction (n = 29), those with Papez circuit dysfunction (n = 22), and those with callosal disconnection (n = 7). Results: In comparison with healthy subjects, the whole population of patients with MMF exhibited a spatial pattern of cerebral glucose hypometabolism (P < 0.001) involving the occipital lobes, temporal lobes, limbic system, cerebellum, and frontoparietal cortices, as shown by analysis of covariance. The subgroup of patients with FSC dysfunction exhibited a larger extent of involved areas (35,223 voxels vs. 13,680 voxels in the subgroup with Papez circuit dysfunction and 5,453 voxels in patients without cognitive impairment). Nonsignificant results were obtained for the last subgroup because of its small population size. Conclusion: Our study identified a peculiar spatial pattern of cerebral glucose hypometabolism that was most marked in MMF patients with FSC dysfunction. Further studies are needed to determine whether this pattern could represent a diagnostic biomarker of MMF in patients with chronic fatigue syndrome and cognitive dysfunction.

  4. Region specific optimization of continuous linear attenuation coefficients based on UTE (RESOLUTE): application to PET/MR brain imaging.

    PubMed

    Ladefoged, Claes N; Benoit, Didier; Law, Ian; Holm, Søren; Kjær, Andreas; Højgaard, Liselotte; Hansen, Adam E; Andersen, Flemming L

    2015-10-21

    The reconstruction of PET brain data in a PET/MR hybrid scanner is challenging in the absence of transmission sources, where MR images are used for MR-based attenuation correction (MR-AC). The main challenge of MR-AC is to separate bone and air, as neither have a signal in traditional MR images, and to assign the correct linear attenuation coefficient to bone. The ultra-short echo time (UTE) MR sequence was proposed as a basis for MR-AC as this sequence shows a small signal in bone. The purpose of this study was to develop a new clinically feasible MR-AC method with patient specific continuous-valued linear attenuation coefficients in bone that provides accurate reconstructed PET image data. A total of 164 [(18)F]FDG PET/MR patients were included in this study, of which 10 were used for training. MR-AC was based on either standard CT (reference), UTE or our method (RESOLUTE). The reconstructed PET images were evaluated in the whole brain, as well as regionally in the brain using a ROI-based analysis. Our method segments air, brain, cerebral spinal fluid, and soft tissue voxels on the unprocessed UTE TE images, and uses a mapping of R(*)2 values to CT Hounsfield Units (HU) to measure the density in bone voxels. The average error of our method in the brain was 0.1% and less than 1.2% in any region of the brain. On average 95% of the brain was within  ±10% of PETCT, compared to 72% when using UTE. The proposed method is clinically feasible, reducing both the global and local errors on the reconstructed PET images, as well as limiting the number and extent of the outliers.

  5. Region specific optimization of continuous linear attenuation coefficients based on UTE (RESOLUTE): application to PET/MR brain imaging

    NASA Astrophysics Data System (ADS)

    Ladefoged, Claes N.; Benoit, Didier; Law, Ian; Holm, Søren; Kjær, Andreas; Højgaard, Liselotte; Hansen, Adam E.; Andersen, Flemming L.

    2015-10-01

    The reconstruction of PET brain data in a PET/MR hybrid scanner is challenging in the absence of transmission sources, where MR images are used for MR-based attenuation correction (MR-AC). The main challenge of MR-AC is to separate bone and air, as neither have a signal in traditional MR images, and to assign the correct linear attenuation coefficient to bone. The ultra-short echo time (UTE) MR sequence was proposed as a basis for MR-AC as this sequence shows a small signal in bone. The purpose of this study was to develop a new clinically feasible MR-AC method with patient specific continuous-valued linear attenuation coefficients in bone that provides accurate reconstructed PET image data. A total of 164 [18F]FDG PET/MR patients were included in this study, of which 10 were used for training. MR-AC was based on either standard CT (reference), UTE or our method (RESOLUTE). The reconstructed PET images were evaluated in the whole brain, as well as regionally in the brain using a ROI-based analysis. Our method segments air, brain, cerebral spinal fluid, and soft tissue voxels on the unprocessed UTE TE images, and uses a mapping of R2* values to CT Hounsfield Units (HU) to measure the density in bone voxels. The average error of our method in the brain was 0.1% and less than 1.2% in any region of the brain. On average 95% of the brain was within  ±10% of PETCT, compared to 72% when using UTE. The proposed method is clinically feasible, reducing both the global and local errors on the reconstructed PET images, as well as limiting the number and extent of the outliers.

  6. Spatial variability and reproducibility of GABA-edited MEGA-LASER 3D-MRSI in the brain at 3 T.

    PubMed

    Hnilicová, Petra; Považan, Michal; Strasser, Bernhard; Andronesi, Ovidiu C; Gajdošík, Martin; Dydak, Ulrike; Ukropec, Jozef; Dobrota, Dušan; Trattnig, Siegfried; Bogner, Wolfgang

    2016-11-01

    The reproducibility of gamma-aminobutyric acid (GABA) quantification results, obtained with MRSI, was determined on a 3 T MR scanner in healthy adults. In this study, a spiral-encoded, GABA-edited, MEGA-LASER MRSI sequence with real-time motion-scanner-instability corrections was applied for robust 3D mapping of neurotransmitters in the brain. In particular, the GABA(+) (i.e. GABA plus macromolecule contamination) and Glx (i.e. glutamate plus glutamine contamination) signal was measured. This sequence enables 3D-MRSI with about 3 cm(3) nominal resolution in about 20 min. Since reliable quantification of GABA is challenging, the spatial distribution of the inter-subject and intra-subject variability of GABA(+) and Glx levels was studied via test-retest assessment in 14 healthy volunteers (seven men-seven women). For both inter-subject and intra-subject repeated measurement sessions a low coefficient of variation (CV) and a high intraclass correlation coefficient (ICC) were found for GABA(+) and Glx ratios across all evaluated voxels (intra-/inter-subject: GABA(+) ratios, CV ~ 8%-ICC > 0.75; Glx ratios, CV ~ 6%-ICC > 0.70). The same was found in selected brain regions for Glx ratios versus GABA(+) ratios (CV varied from about 5% versus about 8% in occipital and parietal regions, to about 8% versus about 10% in the frontal area, thalamus, and basal ganglia). These results provide evidence that 3D mapping of GABA(+) and Glx using the described methodology provides high reproducibility for application in clinical and neuroscientific studies.

  7. 18F-labeled FECNT: a selective radioligand for PET imaging of brain dopamine transporters.

    PubMed

    Goodman, M M; Kilts, C D; Keil, R; Shi, B; Martarello, L; Xing, D; Votaw, J; Ely, T D; Lambert, P; Owens, M J; Camp, V M; Malveaux, E; Hoffman, J M

    2000-01-01

    Fluorine-18 labeled 2beta-carbomethoxy-3beta-(4-chlorophenyl)-8-(2-fluoroethyl)nort ropane (FECNT) was synthesized in the development of a dopamine transporter (DAT) imaging ligand for positron emission tomography (PET). The methods of radiolabeling and ligand synthesis of FECNT, and the results of the in vitro characterization and in vivo tissue distribution in rats and in vivo PET imaging in rhesus monkeys of [18F]FECNT are described. Fluorine-18 was introduced into 2beta-carbomethoxy-3beta-(4-chlorophenyl)-8-(2-fluoroethyl)nort ropane (4) by preparation of 1-[18F]fluoro-2-tosyloxyethane (2) followed by alkylation of 2beta-carbomethoxy-3beta-(4-chlorophenyl)nortropane (3) in 21% radiochemical yield (decay corrected to end of bombardment [EOB]). Competition binding in cells stably expressing the transfected human DAT serotonin transporter (SERT) and norepinephrine transporter (NET) labeled by [3H]WIN 35428, [3H]citalopram, and [3H]nisoxetine, respectively, indicated the following order of DAT affinity: GBR 12909 > CIT > 2beta-carbomethoxy-3beta-(4-chlorophenyl)-8-(3-fluoropropyl) nortropane (FPCT) > FECNT. The affinity of FECNT for SERT and NET was 25- and 156-fold lower, respectively, than for DAT. Blocking studies were performed in rats with a series of transporter-specific agents and demonstrated that the brain uptake of [18F]FECNT was selective and specific for DAT-rich regions. PET brain imaging studies in monkeys demonstrated high [18F]FECNT uptake in the caudate and putamen that resulted in caudate-to-cerebellum and putamen-to-cerebellum ratios of 10.5 at 60 min. [18F]FECNT uptake in the caudate/putamen peaked in less than 75 min and exhibited higher caudate- and putamen-to-cerebellum ratios at transient equilibrium than reported for 11C-WIN 35,428, [11C]CIT/RTI-55, or [18F]beta-CIT-FP. Analysis of monkey arterial plasma samples using high performance liquid chromatography determined that there was no detectable formation of lipophilic radiolabeled

  8. Radionuclide labeling and evaluation of candidate radioligands for PET imaging of histone deacetylase in the brain.

    PubMed

    Seo, Young Jun; Muench, Lisa; Reid, Alicia; Chen, Jinzhu; Kang, Yeona; Hooker, Jacob M; Volkow, Nora D; Fowler, Joanna S; Kim, Sung Won

    2013-12-15

    Histone deacetylases (HDACs) regulate gene expression by inducing conformational changes in chromatin. Ever since the discovery of a naturally occurring HDAC inhibitor, trichostatin A (TSA) stimulated the recent development of suberoylanilide (SAHA, Zolinza®), HDAC has become an important molecular target for drug development. This has created the need to develop specific in vivo radioligands to study epigenetic regulation and HDAC engagement for drug development for diseases including cancer and psychiatric disorders. 6-([(18)F]Fluoroacetamido)-1-hexanoicanilide ([(18)F]FAHA) was recently developed as a HDAC substrate and shows moderate blood-brain barrier (BBB) permeability and specific signal (by metabolic trapping/or deacetylation) but rapid metabolism. Here, we report the radiosynthesis of two carbon-11 labeled candidate radiotracers (substrate- and inhibitor-based radioligand) for HDAC and their evaluation in non-human primate brain. PET studies showed very low brain uptake and rapid metabolism of both labeled compounds but revealed a surprising enhancement of brain penetration by F for H substitution when comparing one of these to [(18)F]FAHA. Further structural refinement is needed for the development of brain-penetrant, metabolically stable HDAC radiotracers and to understand the role of fluorine substitution on brain penetration.

  9. Weight gain following subthalamic nucleus deep brain stimulation: a PET study.

    PubMed

    Sauleau, Paul; Le Jeune, Florence; Drapier, Sophie; Houvenaghel, Jean-François; Dondaine, Thibaut; Haegelen, Claire; Lalys, Florent; Robert, Gabriel; Drapier, Dominique; Vérin, Marc

    2014-12-01

    Several hypotheses have been put forward to explain weight gain after deep brain stimulation (DBS), but none provides a fully satisfactory account of this adverse effect. We analyzed the correlation between changes in brain metabolism (using positron emission tomography [PET] imaging) and weight gain after bilateral subthalamic nucleus DBS in patients with Parkinson's disease. Body mass index was calculated and brain activity prospectively measured using 2-deoxy-2[18F]fluoro-D-glucose 3 months before and 4 months after the start of subthalamic nucleus deep brain stimulation in 23 patients with Parkinson's disease. Motor complications (United Parkinson's Disease Rating Scale [UPDRS]-IV scores) and dopaminergic medication were included in the analysis to control for their possible influence on brain metabolism. Mean ± standard deviation (SD) body mass index increased significantly by 0.8 ± 1.5 kg/m(2) (P = 0.03). Correlations were found between weight gain and changes in brain metabolism in limbic and associative areas, including the orbitofrontal cortex (Brodmann areas [BAs] 10 and 11), lateral and medial parts of the temporal lobe (BAs 20, 21, 22,39 and 42), anterior cingulate cortex (BA 32), and retrosplenial cortex (BA 30). However, we found no correlation between weight gain and metabolic changes in sensorimotor areas. These findings suggest that changes in associative and limbic processes contribute to weight gain after subthalamic nucleus DBS in Parkinson's disease.

  10. Designing a compact high performance brain PET scanner—simulation study

    NASA Astrophysics Data System (ADS)

    Gong, Kuang; Majewski, Stan; Kinahan, Paul E.; Harrison, Robert L.; Elston, Brian F.; Manjeshwar, Ravindra; Dolinsky, Sergei; Stolin, Alexander V.; Brefczynski-Lewis, Julie A.; Qi, Jinyi

    2016-05-01

    The desire to understand normal and disordered human brain function of upright, moving persons in natural environments motivates the development of the ambulatory micro-dose brain PET imager (AMPET). An ideal system would be light weight but with high sensitivity and spatial resolution, although these requirements are often in conflict with each other. One potential approach to meet the design goals is a compact brain-only imaging device with a head-sized aperture. However, a compact geometry increases parallax error in peripheral lines of response, which increases bias and variance in region of interest (ROI) quantification. Therefore, we performed simulation studies to search for the optimal system configuration and to evaluate the potential improvement in quantification performance over existing scanners. We used the Cramér-Rao variance bound to compare the performance for ROI quantification using different scanner geometries. The results show that while a smaller ring diameter can increase photon detection sensitivity and hence reduce the variance at the center of the field of view, it can also result in higher variance in peripheral regions when the length of detector crystal is 15 mm or more. This variance can be substantially reduced by adding depth-of-interaction (DOI) measurement capability to the detector modules. Our simulation study also shows that the relative performance depends on the size of the ROI, and a large ROI favors a compact geometry even without DOI information. Based on these results, we propose a compact ‘helmet’ design using detectors with DOI capability. Monte Carlo simulations show the helmet design can achieve four-fold higher sensitivity and resolve smaller features than existing cylindrical brain PET scanners. The simulations also suggest that improving TOF timing resolution from 400 ps to 200 ps also results in noticeable improvement in image quality, indicating better timing resolution is desirable for brain imaging.

  11. Motion correction of PET brain images through deconvolution: II. Practical implementation and algorithm optimization

    NASA Astrophysics Data System (ADS)

    Raghunath, N.; Faber, T. L.; Suryanarayanan, S.; Votaw, J. R.

    2009-02-01

    Image quality is significantly degraded even by small amounts of patient motion in very high-resolution PET scanners. When patient motion is known, deconvolution methods can be used to correct the reconstructed image and reduce motion blur. This paper describes the implementation and optimization of an iterative deconvolution method that uses an ordered subset approach to make it practical and clinically viable. We performed ten separate FDG PET scans using the Hoffman brain phantom and simultaneously measured its motion using the Polaris Vicra tracking system (Northern Digital Inc., Ontario, Canada). The feasibility and effectiveness of the technique was studied by performing scans with different motion and deconvolution parameters. Deconvolution resulted in visually better images and significant improvement as quantified by the Universal Quality Index (UQI) and contrast measures. Finally, the technique was applied to human studies to demonstrate marked improvement. Thus, the deconvolution technique presented here appears promising as a valid alternative to existing motion correction methods for PET. It has the potential for deblurring an image from any modality if the causative motion is known and its effect can be represented in a system matrix.

  12. Ligands for SPECT and PET imaging of muscarinic-cholinergic receptors of the heart and brain

    SciTech Connect

    Knapp, F.F. Jr.; McPherson, D.W.; Luo, H.

    1995-06-01

    Interest in the potential use of cerebral SPECT and PET imaging for determination of the density and activity of muscarinic-cholinergic receptors (mAChR) has been stimulated by the changes in these receptors which occur in many neurological diseases. In addition, the important involvement of mAChR in modulating negative inotropic cardiac activity suggests that such receptor ligands may have important applications in evaluation of changes which may occur in cardiac disease. In this paper, the properties of several key muscarinic receptor ligands being developed or which have been used for clinical SPECT and PET are discussed. In addition, the ORNL development of the new iodinated IQNP ligand based on QNB and the results of in vivo biodistribution studies in rats, in vitro competitive binding studies and ex vivo autoradiographic experiments are described. The use of radioiodinated IQNP may offer several advantages in comparison to IQNB because of its easy and high yield preparation and high brain uptake and the potential usefulness of the {open_quotes}partial{close_quotes} subtype selective IONP isomers. We also describe the development of new IQNP-type analogues which offer the opportunity for radiolabeling with positron-emitting radioisotopes (carbon-11, fluorine-18 and bromine-76) for potential use with PET.

  13. Imaging of sigma1 receptors in the human brain using PET and [11C]SA4503.

    PubMed

    Toyohara, Jun; Sakata, Muneyuki; Ishiwata, Kiichi

    2009-09-01

    Sigma(1) receptors were imaged in living human brain by positron emission tomography (PET) using [(11)C] SA4503. A dynamic 90-min scan and kinetic analysis enabled quantification of receptor density in the brain. The sigma(1) receptors were distributed throughout the brain in normal subjects, but decreased in the frontal, temporal, and occipital lobes, cerebellum and thalamus in patients with early Alzheimer's disease and in the putamen in patients with Parkinson's disease. In addition, rates of receptor occupancy by the neuroleptic haloperidol and the selective serotonin reuptake inhibitor fluvoxamine were evaluated by [(11)C]SA4503-PET and found to be high. [(11)C]SA4503-PET is useful for studying the pathophysiology of neurological and psychiatric disorders such as schizophrenia and for evaluation of the pharmacodynamics of psychiatric drugs.

  14. A Dual Tracer PET-MRI Protocol for the Quantitative Measure of Regional Brain Energy Substrates Uptake in the Rat

    PubMed Central

    Roy, Maggie; Nugent, Scott; Tremblay, Sébastien; Descoteaux, Maxime; Beaudoin, Jean-François; Tremblay, Luc; Lecomte, Roger; Cunnane, Stephen C

    2013-01-01

    We present a method for comparing the uptake of the brain's two key energy substrates: glucose and ketones (acetoacetate [AcAc] in this case) in the rat. The developed method is a small-animal positron emission tomography (PET) protocol, in which 11C-AcAc and 18F-fluorodeoxyglucose (18F-FDG) are injected sequentially in each animal. This dual tracer PET acquisition is possible because of the short half-life of 11C (20.4 min). The rats also undergo a magnetic resonance imaging (MRI) acquisition seven days before the PET protocol. Prior to image analysis, PET and MRI images are coregistered to allow the measurement of regional cerebral uptake (cortex, hippocampus, striatum, and cerebellum). A quantitative measure of 11C-AcAc and 18F-FDG brain uptake (cerebral metabolic rate; μmol/100 g/min) is determined by kinetic modeling using the image-derived input function (IDIF) method. Our new dual tracer PET protocol is robust and flexible; the two tracers used can be replaced by different radiotracers to evaluate other processes in the brain. Moreover, our protocol is applicable to the study of brain fuel supply in multiple conditions such as normal aging and neurodegenerative pathologies such as Alzheimer's and Parkinson's diseases. PMID:24430432

  15. Optimized MLAA for quantitative non-TOF PET/MR of the brain

    NASA Astrophysics Data System (ADS)

    Benoit, Didier; Ladefoged, Claes N.; Rezaei, Ahmadreza; Keller, Sune H.; Andersen, Flemming L.; Højgaard, Liselotte; Hansen, Adam E.; Holm, Søren; Nuyts, Johan

    2016-12-01

    For quantitative tracer distribution in positron emission tomography, attenuation correction is essential. In a hybrid PET/CT system the CT images serve as a basis for generation of the attenuation map, but in PET/MR, the MR images do not have a similarly simple relationship with the attenuation map. Hence attenuation correction in PET/MR systems is more challenging. Typically either of two MR sequences are used: the Dixon or the ultra-short time echo (UTE) techniques. However these sequences have some well-known limitations. In this study, a reconstruction technique based on a modified and optimized non-TOF MLAA is proposed for PET/MR brain imaging. The idea is to tune the parameters of the MLTR applying some information from an attenuation image computed from the UTE sequences and a T1w MR image. In this MLTR algorithm, an {αj} parameter is introduced and optimized in order to drive the algorithm to a final attenuation map most consistent with the emission data. Because the non-TOF MLAA is used, a technique to reduce the cross-talk effect is proposed. In this study, the proposed algorithm is compared to the common reconstruction methods such as OSEM using a CT attenuation map, considered as the reference, and OSEM using the Dixon and UTE attenuation maps. To show the robustness and the reproducibility of the proposed algorithm, a set of 204 [18F]FDG patients, 35 [11C]PiB patients and 1 [18F]FET patient are used. The results show that by choosing an optimized value of {αj} in MLTR, the proposed algorithm improves the results compared to the standard MR-based attenuation correction methods (i.e. OSEM using the Dixon or the UTE attenuation maps), and the cross-talk and the scale problem are limited.

  16. Methods for the correction of vascular artifacts in PET O-15 water brain-mapping studies

    SciTech Connect

    Chen, K.; Reiman, E.M. |; Lawson, M.; Yun, L.S.; Bandy, D.

    1996-12-01

    While positron emission tomographic (PET) measurements of regional cerebral blood flow (rCBF) can be used to map brain regions that are involved in normal and pathological human behaviors, measurements in the anteromedial temporal lobe can be confounded by the combined effects of radiotracer activity in neighboring arteries and partial-volume averaging. The authors now describe two simple methods to address this vascular artifact. One method utilizes the early frames of a dynamic PET study, while the other method utilizes a coregistered magnetic resonance image (MRI) to characterize the vascular region of interest (VROI). Both methods subsequently assign a common value to each pixel in the VROI for the control scan and the activation scan. To study the vascular artifact and to demonstrate the ability of the proposed methods correcting the vascular artifact, four dynamic PET scans were performed in a single subject during the same behavioral state. For each of the four scans, a vascular scan containing vascular activity was computed as the summation of the images acquired 0--60 s after radiotracer administrations, and a control scan containing minimal vascular activity was computed as the summation of the images acquired 20--80 s after radiotracer administration. t-score maps calculated from the four pairs of vascular and control scans were used to characterize regional blood flow differences related to vascular activity before and after the applications of each vascular artifact correction method. Both methods eliminated the observed differences in vascular activity, as well as the vascular artifact observed in the anteromedial temporal lobes. Using PET data from a study of normal human emotion, these methods permitted us to identify rCBF increases in the anteromedial temporal lobe free from the potentially confounding, combined effects of vascular activity and partial-volume averaging.

  17. Image-derived input function obtained in a 3TMR-brainPET

    NASA Astrophysics Data System (ADS)

    da Silva, N. A.; Herzog, H.; Weirich, C.; Tellmann, L.; Rota Kops, E.; Hautzel, H.; Almeida, P.

    2013-02-01

    Aim: The combination of a high-resolution MR-compatible BrainPET insert operated within a 3 T MAGNETOM Trio MR scanner is an excellent tool for obtaining an image derived input function (IDIF), due to simultaneous imaging. In this work, we explore the possibility of obtaining an IDIF from volumes of interest (VOI) defined over the carotid arteries (CAs) using the MR data. Material and methods: FDG data from three patients without brain disorders were included. VOIs were drawn bilaterally over the CAs on a MPRAGE image using a 50% isocontour (MR50VOI). CA PET/MR co-registration was examined based on an individual and combined CA co-registration. After that, to estimate the IDIF, the MR50VOI average (IDIF-A), four hottest pixels per plane (IDIF-4H) and four hottest pixels in VOI (IDIF-4V) were considered. A model-based correction for residual partial volume effects involving venous blood samples was applied, from which partial volume (PV) and spillover (SP) coefficients were estimated. Additionally, a theoretical PV coefficient (PVt) was calculated based on MR50VOI. Results: The results show an excellent co-registration between the MR and PET, with an area under the curve ratio between both co-registration methods of 1.00±0.04. A good agreement between PV and PVt was found for IDIF-A, with PV of 0.39±0.06 and PVt 0.40±0.03, and for IDIF-4H, with PV of 0.47±0.05 and PVt 0.47±0.03. The SPs were 0.20±0.03 and 0.21±0.03 for IDIF-A and IDIF-4H, respectively. Conclusion: The integration of a high resolution BrainPET in an MR scanner allows to obtain an IDIF from an MR-based VOI. This must be corrected for a residual partial volume effect.

  18. Application of single- and dual-energy CT brain tissue segmentation to PET monitoring of proton therapy

    NASA Astrophysics Data System (ADS)

    Berndt, Bianca; Landry, Guillaume; Schwarz, Florian; Tessonnier, Thomas; Kamp, Florian; Dedes, George; Thieke, Christian; Würl, Matthias; Kurz, Christopher; Ganswindt, Ute; Verhaegen, Frank; Debus, Jürgen; Belka, Claus; Sommer, Wieland; Reiser, Maximilian; Bauer, Julia; Parodi, Katia

    2017-03-01

    The purpose of this work was to evaluate the ability of single and dual energy computed tomography (SECT, DECT) to estimate tissue composition and density for usage in Monte Carlo (MC) simulations of irradiation induced β + activity distributions. This was done to assess the impact on positron emission tomography (PET) range verification in proton therapy. A DECT-based brain tissue segmentation method was developed for white matter (WM), grey matter (GM) and cerebrospinal fluid (CSF). The elemental composition of reference tissues was assigned to closest CT numbers in DECT space (DECTdist). The method was also applied to SECT data (SECTdist). In a validation experiment, the proton irradiation induced PET activity of three brain equivalent solutions (BES) was compared to simulations based on different tissue segmentations. Five patients scanned with a dual source DECT scanner were analyzed to compare the different segmentation methods. A single magnetic resonance (MR) scan was used for comparison with an established segmentation toolkit. Additionally, one patient with SECT and post-treatment PET scans was investigated. For BES, DECTdist and SECTdist reduced differences to the reference simulation by up to 62% when compared to the conventional stoichiometric segmentation (SECTSchneider). In comparison to MR brain segmentation, Dice similarity coefficients for WM, GM and CSF were 0.61, 0.67 and 0.66 for DECTdist and 0.54, 0.41 and 0.66 for SECTdist. MC simulations of PET treatment verification in patients showed important differences between DECTdist/SECTdist and SECTSchneider for patients with large CSF areas within the treatment field but not in WM and GM. Differences could be misinterpreted as PET derived range shifts of up to 4 mm. DECTdist and SECTdist yielded comparable activity distributions, and comparison of SECTdist to a measured patient PET scan showed improved agreement when compared to SECTSchneider. The agreement between predicted and measured PET

  19. [The brain mechanism of error detection: the P.E.T. study].

    PubMed

    Kireev, M V; Korotkov, A D; Poliakov, Iu I; Anichkov, A D; Medvedev, S V

    2011-10-01

    In present research, the brain maintenance of the error detection mechanism was studied in resting condition and while subjects consciously implemented incorrect actions (i.e. deception). Assessment of the regional cerebral blood flow revealed involvement of anterior cingulated cortex in deception. The obtained data indicate that it is impossible to consciously control the activity of the error detection mechanism. PET study of patients with obsessive compulsive disorder in resting condition revealed a decrease of brain glucose metabolism in the anterior cingulated cortex in comparison with healthy subjects. These data pointed to malfunctioning of the error detection mechanism. The findings support the formerly proposed hypothesis about the impact of the error detection mechanism in formation and support of obsessive compulsive disorder.

  20. Joint factor and kinetic analysis of dynamic FDOPA PET scans of brain cancer patients.

    PubMed

    Dowson, N; Bourgeat, P; Rose, S; Daglish, M; Smith, J; Fay, M; Coulthard, A; Winter, C; MacFarlane, D; Thomas, P; Crozier, S; Salvado, O

    2010-01-01

    Kinetic analysis is an essential tool of Positron Emission Tomography image analysis. However it requires a pure tissue time activity curve (TAC) in order to calculate the system parameters. Pure tissue TACs are particularly difficult to obtain in the brain as the low resolution of PET means almost all voxels are a mixture of tissues. Factor analysis explicitly accounts for mixing but is an underdetermined problem that can give arbitrary results. A joint factor and kinetic analysis is proposed whereby factor analysis explicitly accounts for mixing of tissues. Hence, more meaningful parameters are obtained by the kinetic models, which also ensure a less ambiguous solution to the factor analysis. The method was tested using a cylindrical phantom and the 18F-DOPA data of a brain cancer patient.

  1. MO-F-CAMPUS-J-03: Development of a Human Brain PET for On-Line Proton Beam-Range Verification

    SciTech Connect

    Shao, Yiping

    2015-06-15

    Purpose: To develop a prototype PET for verifying proton beam-range before each fractionated therapy that will enable on-line re-planning proton therapy. Methods: Latest “edge-less” silicon photomultiplier arrays and customized ASIC readout electronics were used to develop PET detectors with depth-of-interaction (DOI) measurement capability. Each detector consists of one LYSO array with each end coupled to a SiPM array. Multiple detectors can be seamlessly tiled together to form a large detector panel. Detectors with 1.5×1.5 and 2.0×2.0 mm crystals at 20 or 30 mm lengths were studied. Readout of individual SiPM or signal multiplexing was used to transfer 3D interaction position-coded analog signals through flexible-print-circuit cables or PCB board to dedicated ASIC front-end electronics to output digital timing pulses that encode interaction information. These digital pulses can be transferred to, through standard LVDS cables, and decoded by a FPGA-based data acquisition of coincidence events and data transfer. The modular detector and scalable electronics/data acquisition will enable flexible PET system configuration for different imaging geometry. Results: Initial detector performance measurement shows excellent crystal identification even with 30 mm long crystals, ∼18% and 2.8 ns energy and timing resolutions, and around 2–3 mm DOI resolution. A small prototype PET scanner with one detector ring has been built and evaluated, validating the technology and design. A large size detector panel has been fabricated by scaling up from modular detectors. Different designs of resistor and capacitor based signal multiplexing boards were tested and selected based on optimal crystal identification and timing performance. Stackable readout electronics boards and FPGA-based data acquisition boards were developed and tested. A brain PET is under construction. Conclusion: Technology of large-size DOI detector based on SiPM array and advanced readout has been

  2. Preclinical Properties of 18F-AV-45: A PET Agent for Aβ Plaques in the Brain

    PubMed Central

    Choi, Seok Rye; Golding, Geoff; Zhuang, Zhiping; Zhang, Wei; Lim, Nathaniel; Hefti, Franz; Benedum, Tyler E.; Kilbourn, Michael R.; Skovronsky, Daniel; Kung, Hank F.

    2011-01-01

    β-amyloid plaques (Aβ plaques) in the brain, containing predominantly fibrillary Aβ peptide aggregates, represent a defining pathologic feature of Alzheimer disease (AD). Imaging agents targeting the Aβ plaques in the living human brain are potentially valuable as biomarkers of pathogenesis processes in AD. (E)-4-(2-(6-(2-(2-(2-18F-fluoroethoxy)ethoxy)ethoxy)pyridin-3-yl)vinyl)-N-methyl benzenamine (18F-AV-45) is such as an agent currently in phase III clinical studies for PET of Aβ plaques in the brain. Methods In vitro binding of 18F-AV-45 to Aβ plaques in the postmortem AD brain tissue was evaluated by in vitro binding assay and autoradiography. In vivo biodistribution of 18F-AV-45 in mice and ex vivo autoradiography of AD transgenic mice (APPswe/PSEN1) with Aβ aggregates in the brain were performed. Small-animal PET of a monkey brain after an intravenous injection of 18F-AV-45 was evaluated. Results 18F-AV-45 displayed a high binding affinity and specificity to Aβ plaques (Kd, 3.72 ± 0.30 nM). In vitro autoradiography of postmortem human brain sections showed substantial plaque labeling in AD brains and not in the control brains. Initial high brain uptake and rapid washout from the brain of healthy mice and monkey were observed. Metabolites produced in the blood of healthy mice after an intravenous injection were identified. 18F-AV-45 displayed excellent binding affinity to Aβ plaques in the AD brain by ex vivo autoradiography in transgenic AD model mice. The results lend support that 18F-AV-45 may be a useful PET agent for detecting Aβ plaques in the living human brain. PMID:19837759

  3. Brain metabolic changes in Hodgkin disease patients following diagnosis and during the disease course: An 18F-FDG PET/CT study

    PubMed Central

    CHIARAVALLOTI, AGOSTINO; PAGANI, MARCO; CANTONETTI, MARIA; DI PIETRO, BARBARA; TAVOLOZZA, MARIO; TRAVASCIO, LAURA; DI BIAGIO, DANIELE; DANIELI, ROBERTA; SCHILLACI, ORAZIO

    2015-01-01

    The aim of the present study was to investigate brain glucose metabolism in patients with Hodgkin disease (HD) after diagnosis and during chemotherapy treatment. Following the administration of first-line doxorubicin, bleomycin, vinblastine and dacarbazine (ABVD) chemotherapy, 74 HD patients underwent 18F-fluoro-2-deoxy-D-glucose (18F-FDG) positron emission tomography (PET)/computed tomography brain scans, both baseline (PET0) and interim (PET2) at the Department of Biomedicine and Prevention, University of Rome Tor Vergata (Rome, Italy). Fifty-seven patients were further evaluated 15±6 days after four additional cycles (PET6). Furthermore, a control group (CG) of 40 chemotherapy-naïve subjects was enrolled. Differences in brain 18F-FDG uptake between the CG, PET0, PET2 and PET6 scans were analyzed using statistical parametric mapping. Compared with the PET0 and CG scans, the PET2 scan demonstrated a higher metabolic activity in Brodmann area (BA) 39, and a metabolic reduction in BA 11 bilaterally and in left BA 32. All of these changes disappeared at PET6. The results of the present study indicate that ABVD chemotherapy has a limited impact on brain metabolism. PMID:25621038

  4. Plasma based markers of [11C] PiB-PET brain amyloid burden.

    PubMed

    Kiddle, Steven John; Thambisetty, Madhav; Simmons, Andrew; Riddoch-Contreras, Joanna; Hye, Abdul; Westman, Eric; Pike, Ian; Ward, Malcolm; Johnston, Caroline; Lupton, Michelle Katharine; Lunnon, Katie; Soininen, Hilkka; Kloszewska, Iwona; Tsolaki, Magda; Vellas, Bruno; Mecocci, Patrizia; Lovestone, Simon; Newhouse, Stephen; Dobson, Richard

    2012-01-01

    Changes in brain amyloid burden have been shown to relate to Alzheimer's disease pathology, and are believed to precede the development of cognitive decline. There is thus a need for inexpensive and non-invasive screening methods that are able to accurately estimate brain amyloid burden as a marker of Alzheimer's disease. One potential method would involve using demographic information and measurements on plasma samples to establish biomarkers of brain amyloid burden; in this study data from the Alzheimer's Disease Neuroimaging Initiative was used to explore this possibility. Sixteen of the analytes on the Rules Based Medicine Human Discovery Multi-Analyte Profile 1.0 panel were found to associate with [(11)C]-PiB PET measurements. Some of these markers of brain amyloid burden were also found to associate with other AD related phenotypes. Thirteen of these markers of brain amyloid burden--c-peptide, fibrinogen, alpha-1-antitrypsin, pancreatic polypeptide, complement C3, vitronectin, cortisol, AXL receptor kinase, interleukin-3, interleukin-13, matrix metalloproteinase-9 total, apolipoprotein E and immunoglobulin E--were used along with co-variates in multiple linear regression, and were shown by cross-validation to explain >30% of the variance of brain amyloid burden. When a threshold was used to classify subjects as PiB positive, the regression model was found to predict actual PiB positive individuals with a sensitivity of 0.918 and a specificity of 0.545. The number of APOE [Symbol: see text] 4 alleles and plasma apolipoprotein E level were found to contribute most to this model, and the relationship between these variables and brain amyloid burden was explored.

  5. Long-term effects of 'ecstasy' abuse on the human brain studied by FDG PET.

    PubMed

    Buchert, R; Obrocki, J; Thomasius, R; Väterlein, O; Petersen, K; Jenicke, L; Bohuslavizki, K H; Clausen, M

    2001-08-01

    The popular recreational drug, 'ecstasy', mainly contains 3,4-methylenedioxymethamphetamine (MDMA) as the psychotropic agent. MDMA is suspected of causing neurotoxic lesions to the serotonergic system as demonstrated by animal studies, examinations of human cerebrospinal fluid, and the first positron emission tomography (PET) studies using the serotonin transporter ligand [11C]-McN5652. Damage of serotonergic afferents might mediate long-lasting alterations of cerebral glucose metabolism as a secondary effect. To study a relationship between ecstasy use and long-lasting alterations, PET using 2-[18F]-fluoro-2-deoxy-d-glucose (FDG) was performed in 93 ecstasy users and 27 subjects without any known history of illicit-drug abuse. As an index of glucose metabolism, mean normalized FDG uptake was determined in both groups using a computerized brain atlas, and was compared for a selected number of brain regions. FDG uptake was normalized in each individual by dividing local FDG uptake by the maximum FDG uptake in the individual's brain. Within the group of ecstasy users we examined the relationship between FDG uptake and cumulative ecstasy dose, time since last ecstasy ingestion at the time of PET scanning, and age at first ecstasy use, respectively. Normalized FDG uptake was reduced within the striatum and amygdala of ecstasy users when compared to controls. No statistically significant correlation of the FDG uptake and the cumulative dose of ecstasy was detected. A positive correlation was found in the cingulate between FDG uptake and the time since last ecstasy ingestion. As compared to the control group, normalized FDG uptake in the cingulate was reduced in ecstasy users who took ecstasy during the last 6 months, while it was elevated in former ecstasy users who did not consume ecstasy for more than 1 year. FDG uptake was significantly more affected in ecstasy users who started to consume ecstasy before the age of 18 years. In conclusion, ecstasy abuse causes long

  6. Specification and estimation of sources of bias affecting neurological studies in PET/MR with an anatomical brain phantom

    NASA Astrophysics Data System (ADS)

    Teuho, J.; Johansson, J.; Linden, J.; Saunavaara, V.; Tolvanen, T.; Teräs, M.

    2014-01-01

    Selection of reconstruction parameters has an effect on the image quantification in PET, with an additional contribution from a scanner-specific attenuation correction method. For achieving comparable results in inter- and intra-center comparisons, any existing quantitative differences should be identified and compensated for. In this study, a comparison between PET, PET/CT and PET/MR is performed by using an anatomical brain phantom, to identify and measure the amount of bias caused due to differences in reconstruction and attenuation correction methods especially in PET/MR. Differences were estimated by using visual, qualitative and quantitative analysis. The qualitative analysis consisted of a line profile analysis for measuring the reproduction of anatomical structures and the contribution of the amount of iterations to image contrast. The quantitative analysis consisted of measurement and comparison of 10 anatomical VOIs, where the HRRT was considered as the reference. All scanners reproduced the main anatomical structures of the phantom adequately, although the image contrast on the PET/MR was inferior when using a default clinical brain protocol. Image contrast was improved by increasing the amount of iterations from 2 to 5 while using 33 subsets. Furthermore, a PET/MR-specific bias was detected, which resulted in underestimation of the activity values in anatomical structures closest to the skull, due to the MR-derived attenuation map that ignores the bone. Thus, further improvements for the PET/MR reconstruction and attenuation correction could be achieved by optimization of RAMLA-specific reconstruction parameters and implementation of bone to the attenuation template.

  7. Radionecrosis versus disease progression in brain metastasis. Value of (18)F-DOPA PET/CT/MRI.

    PubMed

    Hernández Pinzón, J; Mena, D; Aguilar, M; Biafore, F; Recondo, G; Bastianello, M

    2016-01-01

    The use of (18)F-DOPA PET/CT with magnetic resonance imaging fusion and the use of visual methods and quantitative analysis helps to differentiate between changes post-radiosurgery vs. suspicion of disease progression in a patient with brain metastases from melanoma, thus facilitating taking early surgical action.

  8. Quantitative imaging of protein targets in the human brain with PET

    NASA Astrophysics Data System (ADS)

    Gunn, Roger N.; Slifstein, Mark; Searle, Graham E.; Price, Julie C.

    2015-11-01

    PET imaging of proteins in the human brain with high affinity radiolabelled molecules has a history stretching back over 30 years. During this period the portfolio of protein targets that can be imaged has increased significantly through successes in radioligand discovery and development. This portfolio now spans six major categories of proteins; G-protein coupled receptors, membrane transporters, ligand gated ion channels, enzymes, misfolded proteins and tryptophan-rich sensory proteins. In parallel to these achievements in radiochemical sciences there have also been significant advances in the quantitative analysis and interpretation of the imaging data including the development of methods for image registration, image segmentation, tracer compartmental modeling, reference tissue kinetic analysis and partial volume correction. In this review, we analyze the activity of the field around each of the protein targets in order to give a perspective on the historical focus and the possible future trajectory of the field. The important neurobiology and pharmacology is introduced for each of the six protein classes and we present established radioligands for each that have successfully transitioned to quantitative imaging in humans. We present a standard quantitative analysis workflow for these radioligands which takes the dynamic PET data, associated blood and anatomical MRI data as the inputs to a series of image processing and bio-mathematical modeling steps before outputting the outcome measure of interest on either a regional or parametric image basis. The quantitative outcome measures are then used in a range of different imaging studies including tracer discovery and development studies, cross sectional studies, classification studies, intervention studies and longitudinal studies. Finally we consider some of the confounds, challenges and subtleties that arise in practice when trying to quantify and interpret PET neuroimaging data including motion artifacts

  9. Modification of a Colliculo-thalamocortical Mouse Brain Slice, Incorporating 3-D printing of Chamber Components and Multi-scale Optical Imaging.

    PubMed

    Slater, Bernard J; Fan, Anthony Y; Stebbings, Kevin A; Saif, M Taher A; Llano, Daniel A

    2015-09-18

    The ability of the brain to process sensory information relies on both ascending and descending sets of projections. Until recently, the only way to study these two systems and how they interact has been with the use of in vivo preparations. Major advances have been made with acute brain slices containing the thalamocortical and cortico-thalamic pathways in the somatosensory, visual, and auditory systems. With key refinements to our recent modification of the auditory thalamocortical slice(1), we are able to more reliably capture the projections between most of the major auditory midbrain and forebrain structures: the inferior colliculus (IC), medial geniculate body (MGB), thalamic reticular nucleus (TRN), and the auditory cortex (AC). With portions of all these connections retained, we are able to answer detailed questions that complement the questions that can be answered with in vivo preparations. The use of flavoprotein autofluorescence imaging enables us to rapidly assess connectivity in any given slice and guide the ensuing experiment. Using this slice in conjunction with recording and imaging techniques, we are now better equipped to understand how information processing occurs at each point in the auditory forebrain as information ascends to the cortex, and the impact of descending cortical modulation. 3-D printing to build slice chamber components permits double-sided perfusion and broad access to networks within the slice and maintains the widespread connections key to fully utilizing this preparation.

  10. Imaging Epigenetic Regulation by Histone Deacetylases in the Brain using PET/MRI with 18F-FAHA

    PubMed Central

    Yeh, Hsien-Hsien; Tian, Mei; Hinz, Rainer; Young, Daniel; Shavrin, Alexander; Mukhapadhyay, Uday; Flores, Leo G.; Balatoni, Julius; Soghomonyan, Suren; Jeong, Hwan J.; Pal, Ashutosh; Uthamanthil, Rajesh; Jackson, James N.; Nishii, Ryuichi; Mizuma, Hiroshi; Onoe, Hirotaka; Kagawa, Shinya; Higashi, Tatsuya; Fukumitsu, Nobuyoshi; Alauddin, Mian; Tong, William; Herholz, Karl; Gelovani, Juri G.

    2012-01-01

    Epigenetic modifications mediated by histone deacetylases (HDACs) play important roles in the mechanisms of different neurologic diseases and HDAC inhibitors (HDACIs) have shown promise in therapy. However, pharmacodynamic profiles of many HDACIs in the brain remain largely unknown due to the lack of validated methods for noninvasive imaging of HDACs expression-activity. In this study, dynamic PET/CT imaging was performed in 4 rhesus macaques using [18F]FAHA, a novel HDAC substrate, and [18F]fluoroacetate, the major radio-metabolite of [18F]FAHA, and fused with corresponding MR images of the brain. Quantification of [18F]FAHA accumulation in the brain was performed using a customized dual-tracer pharmacokinetic model. Immunohistochemical analyses of brain tissue revealed the heterogeneity of expression of individual HDACs in different brain structures and cell types and confirmed that PET/CT/MRI with [18F]FAHA reflects the level of expression-activity of HDAC class IIa enzymes. Furthermore, PET/CT/MRI with [18F]FAHA enabled non-invasive, quantitative assessment of pharmacodynamics of HDACs inhibitor SAHA in the brain. PMID:22995777

  11. On the accuracy of a mutual information algorithm for PET-MR image registration

    NASA Astrophysics Data System (ADS)

    Karaiskos, P.; Malamitsi, J.; Andreou, J.; Prassopoulos, V.; Valotassiou, V.; Laspas, F.; Sandilos, P.; Torrens, M.

    2009-07-01

    Image registration has been increasingly used in radiation diagnosis and treatment planning as a means of information integration from different imaging modalities (e.g. MRI, PET, CT). Especially for brain lesions, accurate 3D registration and fusion of MR and PET images can provide comprehensive information about the patient under study by relating functional information from PET images to the detailed anatomical information available in MR images. However, direct PET-MR image fusion in soft tissue is complicated mainly due to the lack of conspicuous anatomical features in PET images. This study describes the implementation and validation of a mutual information registration algorithm for this purpose. Ten patients with brain lesions underwent MR and PET/CT scanning. MR-PET registration was performed a) based on the well validated MR-CT registration technique and copying the transformation to the PET images derived from the PET/CT scan (MR/PET/CT registration method) and b) directly from the MR and PET images without taking into account the CT images (MR/PET registration method). In order to check the registration accuracy of the MR/PET method, the lesion (target) was contoured in the PET images and it was transferred to the MR images using both the above methods. The MR/PET/CT method served as the gold standard for target contouring. Target contours derived by the MR/PET method were compared with the gold standard target contours for each patient and the deviation between the two contours was used to estimate the accuracy of the PET-MR registration method. This deviation was less than 3 mm (i.e. comparable to the imaging voxel of the PET/CT scanning) for 9/10 of the cases studied. Results show that the mutual information algorithm used is able to perform the PET-MR registration reliably and accurately.

  12. Including anatomical and functional information in MC simulation of PET and SPECT brain studies. Brain-VISET: a voxel-based iterative method.

    PubMed

    Marti-Fuster, Berta; Esteban, Oscar; Thielemans, Kris; Setoain, Xavier; Santos, Andres; Ros, Domenec; Pavia, Javier

    2014-10-01

    Monte Carlo (MC) simulation provides a flexible and robust framework to efficiently evaluate and optimize image processing methods in emission tomography. In this work we present Brain-VISET (Voxel-based Iterative Simulation for Emission Tomography), a method that aims to simulate realistic [ (99m) Tc]-SPECT and [ (18) F]-PET brain databases by including anatomical and functional information. To this end, activity and attenuation maps generated using high-resolution anatomical images from patients were used as input maps in a MC projector to simulate SPECT or PET sinograms. The reconstructed images were compared with the corresponding real SPECT or PET studies in an iterative process where the activity inputs maps were being modified at each iteration. Datasets of 30 refractory epileptic patients were used to assess the new method. Each set consisted of structural images (MRI and CT) and functional studies (SPECT and PET), thereby allowing the inclusion of anatomical and functional variability in the simulation input models. SPECT and PET sinograms were obtained using the SimSET package and were reconstructed with the same protocols as those employed for the clinical studies. The convergence of Brain-VISET was evaluated by studying the behavior throughout iterations of the correlation coefficient, the quotient image histogram and a ROI analysis comparing simulated with real studies. The realism of generated maps was also evaluated. Our findings show that Brain-VISET is able to generate realistic SPECT and PET studies and that four iterations is a suitable number of iterations to guarantee a good agreement between simulated and real studies.

  13. Positron emission tomography (PET) studies of dopaminergic/cholinergic interactions in the baboon brain

    SciTech Connect

    Dewey, S.L.; Brodie, J.D.; Fowler, J.S.; MacGregor, R.R.; Schlyer, D.J.; King, P.T.; Alexoff, D.L.; Volkow, N.D.; Shiue, C.Y.; Wolf, A.P. )

    1990-01-01

    Interactions between the dopaminergic D2 receptor system and the muscarinic cholinergic system in the corpus striatum of adult female baboons (Papio anubis) were examined using positron emission tomography (PET) combined with (18F)N-methylspiroperidol (( 18F)NMSP) (to probe D2 receptor availability) and (N-11C-methyl)benztropine (to probe muscarinic cholinergic receptor availability). Pretreatment with benztropine, a long-lasting anticholinergic drug, bilaterally reduced the incorporation of radioactivity in the corpus striatum but did not alter that observed in the cerebellum or the rate of metabolism of (18F)NMSP in plasma. Pretreatment with unlabelled NMSP, a potent dopaminergic antagonist, reduced the incorporation of (N-11C-methyl)benztropine in all brain regions, with the greatest effect being in the corpus striatum greater than cortex greater than thalamus greater than cerebellum, but did not alter the rate of metabolism of the labelled benztropine in the plasma. These reductions in the incorporation of either (18F)NMSP or (N-11C-methyl)benztropine exceeded the normal variation in tracer incorporation in repeated studies in the same animal. This study demonstrates that PET can be used as a tool for investigating interactions between neurochemically different yet functionally linked neurotransmitters systems in vivo and provides insight into the consequences of multiple pharmacologic administration.

  14. Marker-less multi-frame motion tracking and compensation in PET-brain imaging

    NASA Astrophysics Data System (ADS)

    Lindsay, C.; Mukherjee, J. M.; Johnson, K.; Olivier, P.; Song, X.; Shao, L.; King, M. A.

    2015-03-01

    In PET brain imaging, patient motion can contribute significantly to the degradation of image quality potentially leading to diagnostic and therapeutic problems. To mitigate the image artifacts resulting from patient motion, motion must be detected and tracked then provided to a motion correction algorithm. Existing techniques to track patient motion fall into one of two categories: 1) image-derived approaches and 2) external motion tracking (EMT). Typical EMT requires patients to have markers in a known pattern on a rigid too attached to their head, which are then tracked by expensive and bulky motion tracking camera systems or stereo cameras. This has made marker-based EMT unattractive for routine clinical application. Our main contributions are the development of a marker-less motion tracking system that uses lowcost, small depth-sensing cameras which can be installed in the bore of the imaging system. Our motion tracking system does not require anything to be attached to the patient and can track the rigid transformation (6-degrees of freedom) of the patient's head at a rate 60 Hz. We show that our method can not only be used in with Multi-frame Acquisition (MAF) PET motion correction, but precise timing can be employed to determine only the necessary frames needed for correction. This can speeds up reconstruction by eliminating the unnecessary subdivision of frames.

  15. Construction and Evaluation of Quantitative Small-Animal PET Probabilistic Atlases for [18F]FDG and [18F]FECT Functional Mapping of the Mouse Brain

    PubMed Central

    Casteels, Cindy; Vunckx, Kathleen; Aelvoet, Sarah-Ann; Baekelandt, Veerle; Bormans, Guy; Van Laere, Koen; Koole, Michel

    2013-01-01

    Automated voxel-based or pre-defined volume-of-interest (VOI) analysis of small-animal PET data in mice is necessary for optimal information usage as the number of available resolution elements is limited. We have mapped metabolic ([18F]FDG) and dopamine transporter ([18F]FECT) small-animal PET data onto a 3D Magnetic Resonance Microscopy (MRM) mouse brain template and aligned them in space to the Paxinos co-ordinate system. In this way, ligand-specific templates for sensitive analysis and accurate anatomical localization were created. Next, using a pre-defined VOI approach, test-retest and intersubject variability of various quantification methods were evaluated. Also, the feasibility of mouse brain statistical parametric mapping (SPM) was explored for [18F]FDG and [18F]FECT imaging of 6-hydroxydopamine-lesioned (6-OHDA) mice. Methods Twenty-three adult C57BL6 mice were scanned with [18F]FDG and [18F]FECT. Registrations and affine spatial normalizations were performed using SPM8. [18F]FDG data were quantified using (1) an image-derived-input function obtained from the liver (cMRglc), using (2) standardized uptake values (SUVglc) corrected for blood glucose levels and by (3) normalizing counts to the whole-brain uptake. Parametric [18F]FECT binding images were constructed by reference to the cerebellum. Registration accuracy was determined using random simulated misalignments and vectorial mismatch determination. Results Registration accuracy was between 0.21–1.11 mm. Regional intersubject variabilities of cMRglc ranged from 15.4% to 19.2%, while test-retest values were between 5.0% and 13.0%. For [18F]FECT uptake in the caudate-putamen, these values were 13.0% and 10.3%, respectively. Regional values of cMRglc positively correlated to SUVglc measured within the 45–60 min time frame (spearman r = 0.71). Next, SPM analysis of 6-OHDA-lesioned mice showed hypometabolism in the bilateral caudate-putamen and cerebellum, and an unilateral striatal decrease in DAT

  16. Organization of Endothelial Cells, Pericytes, and Astrocytes into a 3D Microfluidic in Vitro Model of the Blood-Brain Barrier.

    PubMed

    Wang, Jack D; Khafagy, El-Sayed; Khanafer, Khalil; Takayama, Shuichi; ElSayed, Mohamed E H

    2016-03-07

    The endothelial cells lining the capillaries supplying the brain with oxygen and nutrients form a formidable barrier known as the blood-brain barrier (BBB), which exhibits selective permeability to small drug molecules and virtually impermeable to macromolecular therapeutics. Current in vitro BBB models fail to replicate this restrictive behavior due to poor integration of the endothelial cells with supporting cells (pericytes and astrocytes) following the correct anatomical organization observed in vivo. We report the coculture of mouse brain microvascular endothelial cells (b.End3), pericytes, with/without C8-D1A astrocytes in layered microfluidic channels forming three-dimensional (3D) bi- and triculture models of the BBB. The live/dead assay indicated high viability of all cultured cells up to 21 days. Trans-endothelial electrical resistance (TEER) values confirmed the formation of intact monolayers after 3 days in culture and showed statistically higher values for the triculture model compared to the single and biculture models. Screening the permeability of [(14)C]-mannitol and [(14)C]-urea showed the ability of bi- and triculture models to discriminate between different markers based on their size. Further, permeability of [(14)C]-mannitol across the triculture model after 18 days in culture matched its reported permeability across the BBB in vivo. Mathematical calculations also showed that the radius of the tight junctions pores (R) in the triculture model is similar to the reported diameter of the BBB in vivo. Finally, both the bi- and triculture models exhibited functional expression of the P-glycoprotein efflux pump, which increased with the increase in the number of days in culture. These results collectively indicate that the triculture model is a robust in vitro model of the BBB.

  17. Evaluation of brain perfusion in specific Brodmann areas in Frontotemporal dementia and Alzheimer disease using automated 3-D voxel based analysis

    NASA Astrophysics Data System (ADS)

    Valotassiou, V.; Papatriantafyllou, J.; Sifakis, N.; Karageorgiou, C.; Tsougos, I.; Tzavara, C.; Zerva, C.; Georgoulias, P.

    2009-05-01

    Introduction. Brain perfusion studies with single-photon emission computed tomography (SPECT) have been applied in demented patients to provide better discrimination between frontotemporal dementia (FTD) and Alzheimer's disease (AD). Aim. To assess the perfusion of specific Brodmann (Br) areas of the brain cortex in FTD and AD patients, using NeuroGam processing program to provide 3D voxel-by-voxel cerebral SPECT analysis. Material and methods. We studied 34 consecutive patients. We used the established criteria for the diagnosis of dementia and the specific established criteria for the diagnosis of FTD and AD. All the patients had a neuropsychological evaluation with a battery of tests including the mini-mental state examination (MMSE).Twenty-six patients (16 males, 10 females, mean age 68.76±6.51 years, education 11.81±4.25 years, MMSE 16.69±9.89) received the diagnosis of FTD and 8 patients (all females, mean age 71.25±10.48 years, education 10±4.6 years, MMSE 12.5±3.89) the diagnosis of AD. All the patients underwent a brain SPECT. We applied the NeuroGam Software for the evaluation of brain perfusion in specific Br areas in the left (L) and right (R) hemispheres. Results. Statistically significant hypoperfusion in FTD compared to AD patients, was found in the following Br areas: 11L (p<0.0001), 11R, 20L, 20R, 32L, 38L, 38R, 44L (p<0.001), 32R, 36L, 36R, 45L, 45R, 47R (p<0.01), 9L, 21L, 39R, 44R, 46R, 47L (p<0.05). On the contrary, AD patients presented significant (p<0.05) hypoperfusion in 7R and 39R Br areas. Conclusion. NeuroGam processing program of brain perfusion SPECT could result in enhanced accuracy for the differential diagnosis between AD and FTD patients.

  18. Validating novel tau PET tracer [F-18]-AV-1451 (T807) on postmortem brain tissue

    PubMed Central

    Marquie, Marta; Normandin, Marc D.; Vanderburg, Charles R.; Costantino, Isabel; Bien, Elizabeth A.; Rycyna, Lisa G.; Klunk, William E.; Mathis, Chester A.; Ikonomovic, Milos D.; Debnath, Manik L.; Vasdev, Neil; Dickerson, Bradford C.; Gomperts, Stephen N.; Growdon, John H.; Johnson, Keith A.; Frosch, Matthew P.; Hyman, Bradley T.; Gomez-Isla, Teresa

    2016-01-01

    Objective To examine region and substrate-specific autoradiographic and in vitro binding patterns of PET tracer [F-18]-AV-1451 (previously known as T807), tailored to allow in vivo detection of paired helical filament tau-containing lesions, and to determine whether there is off-target binding to other amyloid/non-amyloid proteins. Methods We applied [F-18]-AV-1451 phosphor screen autoradiography, [F-18]-AV-1451 nuclear emulsion autoradiography and [H-3]-AV-1451 in vitro binding assays to the study of postmortem samples from patients with a definite pathological diagnosis of Alzheimer’s disease, frontotemporal lobar degeneration-tau, frontotemporal lobar degeneration-TDP-43, progressive supranuclear palsy, corticobasal degeneration, dementia with Lewy bodies, multiple system atrophy, cerebral amyloid angiopathy and elderly controls free of pathology. Results Our data suggest that AV-1451 strongly binds to tau lesions primarily made of paired helical filaments in Alzheimer’s brains e.g. intra and extraneuronal tangles and dystrophic neurites, but does not seem to bind to a significant extent to neuronal and glial inclusions mainly composed of straight tau filaments in non-Alzheimer tauopathy brains or to β-amyloid, α-synuclein or TDP-43-containing lesions. AV-1451 off-target binding to neuromelanin- and melanin-containing cells and, to a lesser extent, to brain hemorrhagic lesions was identified. Interpretation Our data suggest that AV-1451 holds promise as surrogate marker for the detection of brain tau pathology in the form of tangles and paired helical filament-tau-containing neurites in Alzheimer’s brains but also point to its relatively lower affinity for lesions primarily made of straight tau filaments in non-Alzheimer tauopathy cases and to the existence of some AV-1451 off-target binding. These findings provide important insights for interpreting in vivo patterns of [F-18]-AV-1451 retention. PMID:26344059

  19. PET imaging of ischemia-induced impairment of mitochondrial complex I function in monkey brain

    PubMed Central

    Tsukada, Hideo; Ohba, Hiroyuki; Nishiyama, Shingo; Kanazawa, Masakatsu; Kakiuchi, Takeharu; Harada, Norihiro

    2014-01-01

    To assess the capability of 18F-2-tert-butyl-4-chloro-5-{6-[2-(2-fluoroethoxy)-ethoxy]-pyridin-3-ylmethoxy}-2H-pyridazin-3-one (18F-BCPP-EF), a novel positron emission tomography (PET) probe for mitochondrial complex I (MC-I) activity, as a specific marker of ischemia-induced neuronal death without being disturbed by inflammation, translational research was conducted using an animal PET in ischemic brains of Cynomolgus monkeys (Macaca fascicularis). Focal ischemia was induced by the right middle cerebral artery occlusion for 3 hours, then PET scans were conducted at Day-7 with 15O-gases for regional cerebral blood flow (rCBF) and regional cerebral metabolism of oxygen (rCMRO2), and 18F-BCPP-EF for MC-I with arterial blood sampling. On Day-8, the additional PET scans conducted with 11C-flumazenil (11C-FMZ) for central-type benzodiazepine receptors, 11C-PBR28 for translocator protein, and 18F-fluoro-2-deoxy-D-glucose (18F-FDG) for regional cerebral metabolic rate of glucose (rCMRglc). The total distribution volume (VT) values of 18F-BCPP-EF showed the significant reduction in MC-I activity in the damaged area at Day-7. When correlated with rCBF and rCMRO2, the VT values of 18F-BCPP-EF provided better correlation with rCMRO2 than with rCBF. In the inflammatory regions (region of interest, ROIPBR) of the ischemic hemisphere detected with 11C-PBR28, higher 18F-FDG uptake and lower VT of 18F-BCPP-EF, 11C-FMZ, and rCMRO2 than those in normal contralateral hemisphere were observed. These results strongly suggested that 18F-BCPP-EF could discriminate the neuronal damaged areas with neuroinflammation, where 18F-FDG could not owing to its high uptake into the activated microglia. PMID:24447952

  20. SU-E-QI-03: Compartment Modeling of Dynamic Brain PET - The Effect of Scatter and Random Corrections On Parameter Errors

    SciTech Connect

    Häggström, I; Karlsson, M; Larsson, A; Schmidtlein, C

    2014-06-15

    Purpose: To investigate the effects of corrections for random and scattered coincidences on kinetic parameters in brain tumors, by using ten Monte Carlo (MC) simulated dynamic FLT-PET brain scans. Methods: The GATE MC software was used to simulate ten repetitions of a 1 hour dynamic FLT-PET scan of a voxelized head phantom. The phantom comprised six normal head tissues, plus inserted regions for blood and tumor tissue. Different time-activity-curves (TACs) for all eight tissue types were used in the simulation and were generated in Matlab using a 2-tissue model with preset parameter values (K1,k2,k3,k4,Va,Ki). The PET data was reconstructed into 28 frames by both ordered-subset expectation maximization (OSEM) and 3D filtered back-projection (3DFBP). Five image sets were reconstructed, all with normalization and different additional corrections C (A=attenuation, R=random, S=scatter): Trues (AC), trues+randoms (ARC), trues+scatters (ASC), total counts (ARSC) and total counts (AC). Corrections for randoms and scatters were based on real random and scatter sinograms that were back-projected, blurred and then forward projected and scaled to match the real counts. Weighted non-linearleast- squares fitting of TACs from the blood and tumor regions was used to obtain parameter estimates. Results: The bias was not significantly different for trues (AC), trues+randoms (ARC), trues+scatters (ASC) and total counts (ARSC) for either 3DFBP or OSEM (p<0.05). Total counts with only AC stood out however, with an up to 160% larger bias. In general, there was no difference in bias found between 3DFBP and OSEM, except in parameter Va and Ki. Conclusion: According to our results, the methodology of correcting the PET data for randoms and scatters performed well for the dynamic images where frames have much lower counts compared to static images. Generally, no bias was introduced by the corrections and their importance was emphasized since omitting them increased bias extensively.

  1. [(18)F]FDG-PET Combined with MRI Elucidates the Pathophysiology of Traumatic Brain Injury in Rats.

    PubMed

    Brabazon, Fiona; Wilson, Colin M; Shukla, Dinesh K; Mathur, Sanjeev; Jaiswal, Shalini; Bermudez, Sara; Byrnes, Kimberly R; Selwyn, Reed

    2017-03-01

    Non-invasive measurements of brain metabolism using (18)F-fluorodeoxyglucose (FDG) with positron emission tomography (PET) may provide important information about injury severity following traumatic brain injury (TBI). There is growing interest in the potential of combining functional PET imaging with anatomical and functional magnetic resonance imaging (MRI). This study aimed to investigate the effectiveness of combining clinically available FDG-PET with T2 and diffusion MR imaging, with a particular focus on inflammation and the influence of glial alterations after injury. Adult male Sprague Dawley rats underwent a moderate controlled cortical impact (CCI) injury followed by FDG-PET, MRI, and histological evaluation. FDG uptake showed significant alterations in the corpus callosum, hippocampus, and amygdala after TBI, demonstrating that a relatively "focal" CCI injury can result in global alterations. Analysis of MRI T2 intensity and apparent diffusion coefficient (ADC) also showed significant alterations in these regions to include cytotoxic and vasogenic edema. Histology showed increased glial activation in the corpus callosum and hippocampus that was associated with increased FDG uptake at sub-acute time-points. Glial activation was not detected in the amygdala but neuronal damage was evident, as the amygdala was the only region to show a reduction in both FDG uptake and ADC at sub-acute time-points. Overall, FDG-PET detected glial activation but was confounded by the presence of cell damage, whereas MRI consistently detected cell damage but was confounded by glial activation. These results demonstrate that FDG-PET and MRI can be used together to improve our understanding of the complex alterations in the brain after TBI.

  2. NEMA and clinical evaluation of a novel brain PET-CT scanner

    PubMed Central

    Grogg, Kira S.; Toole, Terrence; Ouyang, Jinsong; Zhu, Xuping; Normandin, Marc; Johnson, Keith; Alpert, Nathaniel M.; Fakhri, Georges El

    2016-01-01

    The aim of this study was to determine the performance of a novel mobile human brain/small animal PET-CT system, developed by Photo Diagnostic Systems Inc. The scanner has a 35.7-cm diameter bore and a 22-cm axial extent. The detector ring has 7 modules each with 3×4 cerium-doped lutetium yttrium orthosilicate crystal blocks, each consisting of 22×22 outer layer and 21×21 inner layer crystals, each layer 1 cm thick. Light is collected by 12×12 SiPMs. The integrated CT can be used for attenuation correction and anatomical localization. The scanner was designed as a low-cost device that nevertheless produces high-quality PET images with the unique capability of battery-powered propulsion, enabling use in many settings. Methods Spatial resolution, sensitivity and noise-equivalent count rate (NECR) were measured based on the National Electrical Manufacturers Association NU2-2012 procedures. Reconstruction was done with tight energy and timing cuts: 400-650 keV and 7ns, and loose cuts: 350-700 keV and 10ns. Additional image quality measurements were made from phantoms, human, and animal studies. Performance was compared to a reference scanner (ECAT Exact HR+) with comparable imaging properties. Results The full-width half-max transverse resolution at 1 cm (10 cm) radius is 3.2 mm (5.2 mm radial, 3.1 mm tangential) and the axial resolution is 3.5 mm (4.0 mm). For tight (loose) cuts, a sensitivity of 7.5 (11.7) kcps/MBq at the center increases to 8.8 (13.9) kcps/MBq at a 10 cm radial offset. The maximum NECR of 19.5 (22.7) kcps was achieved for an activity concentration of 2.9 kBq/ml. Contrast recovery for 4:1 hot cylinder to warm background was 76% for the 25 mm diameter cylinder, but decreased with decreasing cylinder size. The quantitation agrees within 2% of the known activity distribution and concentration. Brain phantom and human scans have shown agreement in SUV values and image quality with the HR+. Conclusion We have characterized the performance of the NeuroPET

  3. Parkinson's disease-related perfusion and glucose metabolic brain patterns identified with PCASL-MRI and FDG-PET imaging

    PubMed Central

    Teune, Laura K.; Renken, Remco J.; de Jong, Bauke M.; Willemsen, Antoon T.; van Osch, Matthias J.; Roerdink, Jos B.T.M.; Dierckx, Rudi A.; Leenders, Klaus L.

    2014-01-01

    Introduction Under normal conditions, the spatial distribution of resting cerebral blood flow and cerebral metabolic rate of glucose are closely related. A relatively new magnetic resonance (MR) technique, pseudo-continuous arterial spin labeling (PCASL), can be used to measure regional brain perfusion. We identified a Parkinson's disease (PD)-related perfusion and metabolic covariance pattern in the same patients using PCASL and FDG-PET imaging and assessed (dis)similarities in the disease-related pattern between perfusion and metabolism in PD patients. Methods Nineteen PD patients and seventeen healthy controls underwent [18F]-fluorodeoxyglucose positron emission tomography (FDG-PET) imaging. Of 14 PD patients and all healthy controls PCASL-MRI could be obtained. Data were analyzed using scaled subprofile model/principal component analysis (SSM/PCA). Results Unique Parkinson's disease-related perfusion and metabolic covariance patterns were identified using PCASL and FDG-PET in the same patients. The PD-related metabolic covariance brain pattern is in high accordance with previously reports. Also our disease-related perfusion pattern is comparable to the earlier described perfusion pattern. The most marked difference between our perfusion and metabolic patterns is the larger perfusion decrease in cortical regions including the insula. Conclusion We identified PD-related perfusion and metabolic brain patterns using PCASL and FDG-PET in the same patients which were comparable with results of existing research. In this respect, PCASL appears to be a promising addition in the early diagnosis of individual parkinsonian patients. PMID:25068113

  4. 18F-FDG PET/CT Brain Imaging on a Patient With Paraneoplastic Opsoclonus-Myoclonus Syndrome Arising out of a Mature Cystic Teratoma.

    PubMed

    Na, Chang Ju; Jeong, Young Jin; Lim, Seok Tae; Sohn, Myung-Hee; Jeong, Hwan-Jeong

    2016-02-01

    Opsoclonus-myoclonus syndrome (OMS) is an involuntary multidirectional eye movement accompanied by myoclonic jerks and a subtype of paraneoplastic neurological syndromes. Clinical features of OMS include opsoclonus with myoclonic jerks and cerebellar ataxia. Although there have been a few studies on brain FDG PET in paraneoplastic neurological syndrome associated with some kinds of malignancies such as lung and gastric cancer, brain FDG PET of patients with OMS caused by a mature cystic teratoma has not been reported. Here, we described a case of brain FDG PET/CT studies performed in a woman with OMS provoked from a mature cystic teratoma.

  5. Epileptic Activity Increases Cerebral Amino Acid Transport Assessed by 18F-Fluoroethyl-l-Tyrosine Amino Acid PET: A Potential Brain Tumor Mimic.

    PubMed

    Hutterer, Markus; Ebner, Yvonne; Riemenschneider, Markus J; Willuweit, Antje; McCoy, Mark; Egger, Barbara; Schröder, Michael; Wendl, Christina; Hellwig, Dirk; Grosse, Jirka; Menhart, Karin; Proescholdt, Martin; Fritsch, Brita; Urbach, Horst; Stockhammer, Guenther; Roelcke, Ulrich; Galldiks, Norbert; Meyer, Philipp T; Langen, Karl-Josef; Hau, Peter; Trinka, Eugen

    2017-01-01

    O-(2-(18)F-fluoroethyl)-l-tyrosine ((18)F-FET) PET is a well-established method increasingly used for diagnosis, treatment planning, and monitoring in gliomas. Epileptic activity, frequently occurring in glioma patients, can influence MRI findings. Whether seizures also affect (18)F-FET PET imaging is currently unknown. The aim of this retrospective analysis was to investigate the brain amino acid metabolism during epileptic seizures by (18)F-FET PET and to elucidate the pathophysiologic background.

  6. Evaluation of the dependence of the exposure dose on the attenuation correction in brain PET/CT scans using 18F-FDG

    NASA Astrophysics Data System (ADS)

    Choi, Eun-Jin; Jeong, Moon-Taeg; Jang, Seong-Joo; Choi, Nam-Gil; Han, Jae-Bok; Yang, Nam-Hee; Dong, Kyung-Rae; Chung, Woon-Kwan; Lee, Yun-Jong; Ryu, Young-Hwan; Choi, Sung-Hyun; Seong, Kyeong-Jeong

    2014-01-01

    This study examined whether scanning could be performed with minimum dose and minimum exposure to the patient after an attenuation correction. A Hoffman 3D Brain Phantom was used in BIO_40 and D_690 PET/CT scanners, and the CT dose for the equipment was classified as a low dose (minimum dose), medium dose (general dose for scanning) and high dose (dose with use of contrast medium) before obtaining the image at a fixed kilo-voltage-peak (kVp) and milliampere (mA) that were adjusted gradually in 17-20 stages. A PET image was then obtained to perform an attenuation correction based on an attenuation map before analyzing the dose difference. Depending on tube current in the range of 33-190 milliampere-second (mAs) when BIO_40 was used, a significant difference in the effective dose was observed between the minimum and the maximum mAs (p < 0.05). According to a Scheffe post-hoc test, the ratio of the minimum to the maximum of the effective dose was increased by approximately 5.26-fold. Depending on the change in the tube current in the range of 10-200 mA when D_690 was used, a significant difference in the effective dose was observed between the minimum and the maximum of mA (p < 0.05). The Scheffe posthoc test revealed a 20.5-fold difference. In conclusion, because effective exposure dose increases with increasing operating current, it is possible to reduce the exposure limit in a brain scan can be reduced if the CT dose can be minimized for a transmission scan.

  7. Digimouse: a 3D whole body mouse atlas from CT and cryosection data

    NASA Astrophysics Data System (ADS)

    Dogdas, Belma; Stout, David; Chatziioannou, Arion F.; Leahy, Richard M.

    2007-02-01

    We have constructed a three-dimensional (3D) whole body mouse atlas from coregistered x-ray CT and cryosection data of a normal nude male mouse. High quality PET, x-ray CT and cryosection images were acquired post mortem from a single mouse placed in a stereotactic frame with fiducial markers visible in all three modalities. The image data were coregistered to a common coordinate system using the fiducials and resampled to an isotropic 0.1 mm voxel size. Using interactive editing tools we segmented and labelled whole brain, cerebrum, cerebellum, olfactory bulbs, striatum, medulla, masseter muscles, eyes, lachrymal glands, heart, lungs, liver, stomach, spleen, pancreas, adrenal glands, kidneys, testes, bladder, skeleton and skin surface. The final atlas consists of the 3D volume, in which the voxels are labelled to define the anatomical structures listed above, with coregistered PET, x-ray CT and cryosection images. To illustrate use of the atlas we include simulations of 3D bioluminescence and PET image reconstruction. Optical scatter and absorption values are assigned to each organ to simulate realistic photon transport within the animal for bioluminescence imaging. Similarly, 511 keV photon attenuation values are assigned to each structure in the atlas to simulate realistic photon attenuation in PET. The Digimouse atlas and data are available at http://neuroimage.usc.edu/Digimouse.html.

  8. Factors affecting bilateral temporal lobe hypometabolism on 18F-FDG PET brain scan in unilateral medial temporal lobe epilepsy.

    PubMed

    Tepmongkol, Supatporn; Srikijvilaikul, Teeradej; Vasavid, Pataramon

    2013-11-01

    Bilateral temporal lobe hypometabolism (BTH) on (18)F-FDG PET brain scan is frequently seen in unilateral medial temporal lobe epilepsy (mTLE). This study aimed to identify the factors that influence BTH in patients with mTLE in order to minimize the significant factor(s) prior to performing a FDG-PET brain scan. Forty patients with unilateral mTLE who underwent (18)F-FDG PET scan for presurgical epilepsy workup were included. Bilateral temporal lobe hypometabolism of the anterior and medial parts of the temporal lobe was identified by a semiquantitative visual scale. Lateralization of TLE was identified by either intracranial EEG (22/40 cases) and/or improvement of seizure 2 years after temporal lobectomy (37/40 cases). The factors analyzed included basic demographic characteristics (age, sex, occupation, years of education, and handedness), history related to seizure (age at epilepsy onset and epilepsy duration, history of febrile seizure and head injury, frequency of seizure with impaired cognition in the last 3 months, presence of secondarily generalized tonic-clonic seizure, automatism side, presence of postictal confusion, and side of MRI temporal abnormality), information during video-EEG monitoring (clinical lateralization, interictal scalp EEG lateralization (interictal epileptiform discharge), and ictal scalp EEG lateralization), and information during the FDG-PET study (duration from the last seizure (≤2 days or >2 days), last seizure type, and the presence of slow waves or sharp waves during the FDG uptake period). Significant factors related to BTH were analyzed using multivariate analysis. Only the ≤2-day duration from the last seizure to the PET scan shows a significant effect (p=0.021) on BTH finding with 15 times greater incidence compared to a duration >2 days. Bilateral temporal lobe hypometabolism, which causes conflict in lateralizing the epileptogenic zone in temporal lobe epilepsy, can be avoided by performing PET scan more than 2 days

  9. Unexpected detection of melanoma brain metastasis by PET with iodine-124 betaCIT.

    PubMed

    Cascini, Giuseppe Lucio; Ciarmiello, Andrea; Labate, Angelo; Tamburrini, Stefania; Quattrone, Aldo

    2009-10-01

    To study the potential impact of iodine-124-beta-carbomethoxy-3beta(4-iodophenyl)tropane (I-124 betaCIT) in Parkinson disease, a I-124 betaCIT-PET scan was performed in 30-year-old man with suspected early Parkinson disease. The scan showed normal striatum uptake together with a focal spot in the left parietal cortex. The subsequent magnetic resonance imaging of the brain revealed a corresponding nodular lesion, presumably representing a metastasis. After clinical and diagnostic evaluation, a malignant metastatic melanoma was discovered. betaCIT is a cocaine derivative with a high affinity for dopamine and serotonin transporters mainly used to image the density of the dopamine reuptake transporter. In fact the role of I-123 betaCIT is typically represented by Parkinsonian syndromes of uncertain classification. The iodine-124 betaCIT uptake is a marker of dopamine transporters density, and the presence of focal uptake corresponding to a lesion on magnetic resonance images suggests a specific binding in this case of melanoma brain metastasis.

  10. Application of single- and dual-energy CT brain tissue segmentation to PET monitoring of proton therapy.

    PubMed

    Berndt, Bianca; Landry, Guillaume; Schwarz, Florian; Tessonnier, Thomas; Kamp, Florian; Dedes, Georgios; Thieke, Christian; Wuerl, Matthias; Kurz, Christopher; Ganswindt, Ute; Verhaegen, Frank; Debus, Juergen; Belka, Claus; Sommer, Wieland; Reiser, Maximilian; Bauer, Julia; Parodi, Katia

    2017-02-09

    The purpose of this work was to evaluate the ability of single and dual energy computed tomography (SECT, DECT) to estimate tissue composition and density for usage in Monte Carlo (MC) simulations of irradiation induced β+ activity distributions. This was done to assess the impact on positron emission tomography (PET) range verification in proton therapy. A DECT-based brain tissue segmentation method was developed for white matter (WM), grey matter (GM) and cerebrospinal fluid (CSF). The elemental composition of reference tissues was assigned to closest CT numbers in DECT space (DECTdist). The method was also applied to SECT data (SECTdist). In a validation experiment, the proton irradiation induced PET activity of three brain equivalent solutions (BES) was compared to simulations based on different tissue segmentations. Five patients scanned with a dual source DECT scanner were analyzed to compare the different segmentation methods. A single magnetic resonance (MR) scan was used for comparison with an established segmentation toolkit. Additionally, one patient with SECT and post-treatment PET scans was investigated. For BES, DECTdist and SECTdist reduced differences to the reference simulation by up to 62% when compared to the conventional stoichiometric segmentation (SECTSchneider). In comparison to MR brain segmentation, Dice similarity coefficients for WM, GM and CSF were 0.61, 0.67 and 0.66 for DECTdist and 0.54, 0.41 and 0.66 for SECTdist. MC simulations of PET treatment verification in patients showed important differences between DECTdist/SECTdist and SECTSchneider for patients with large CSF areas within the treatment field but not in WM and GM. Differences could be misinterpreted as PET derived range shifts of up to 4 mm. DECTdist and SECTdist yielded comparable activity distributions, and comparison of SECT

  11. Europeana and 3D

    NASA Astrophysics Data System (ADS)

    Pletinckx, D.

    2011-09-01

    The current 3D hype creates a lot of interest in 3D. People go to 3D movies, but are we ready to use 3D in our homes, in our offices, in our communication? Are we ready to deliver real 3D to a general public and use interactive 3D in a meaningful way to enjoy, learn, communicate? The CARARE project is realising this for the moment in the domain of monuments and archaeology, so that real 3D of archaeological sites and European monuments will be available to the general public by 2012. There are several aspects to this endeavour. First of all is the technical aspect of flawlessly delivering 3D content over all platforms and operating systems, without installing software. We have currently a working solution in PDF, but HTML5 will probably be the future. Secondly, there is still little knowledge on how to create 3D learning objects, 3D tourist information or 3D scholarly communication. We are still in a prototype phase when it comes to integrate 3D objects in physical or virtual museums. Nevertheless, Europeana has a tremendous potential as a multi-facetted virtual museum. Finally, 3D has a large potential to act as a hub of information, linking to related 2D imagery, texts, video, sound. We describe how to create such rich, explorable 3D objects that can be used intuitively by the generic Europeana user and what metadata is needed to support the semantic linking.

  12. Neurobehavioural dysfunction following mild traumatic brain injury in childhood: a case report with positive findings on positron emission tomography (PET).

    PubMed

    Roberts, M A; Manshadi, F F; Bushnell, D L; Hines, M E

    1995-07-01

    The present case study describes the neurobehavioural, neurodiagnostic, and positron emission tomography (PET) scan findings in a child who sustained a whiplash-type injury in a motor vehicle accident. Although neck and back pain were reported immediately, neurobehavioural symptoms, such as staring spells, gradually increased in frequency over a 2-year period following the accident. At 4 years after the accident the patient's symptoms persisted, as reported by teachers and parents, and more extensive diagnostic work-up was initiated. Standard EEG was normal while two ambulatory EEGs were abnormal and interpreted as epileptiform. A PET scan showed evidence of marked hypometabolism in both temporal lobes. Neuropsychological findings were consistent with PET findings and reflected verbal and visual memory deficits in the context of high average intelligence. Treatment with carbamazepine, verapamil, and fluoxetine greatly improved the patient's symptoms. The present case illustrates an example of a poor outcome in a paediatric case of mild traumatic brain injury, the importance of PET in demonstrating definitive evidence of brain dysfunction, and the child's positive response to anticonvulsant medication.

  13. Free-running ADC- and FPGA-based signal processing method for brain PET using GAPD arrays

    NASA Astrophysics Data System (ADS)

    Hu, Wei; Choi, Yong; Hong, Key Jo; Kang, Jihoon; Jung, Jin Ho; Huh, Youn Suk; Lim, Hyun Keong; Kim, Sang Su; Kim, Byung-Tae; Chung, Yonghyun

    2012-02-01

    Currently, for most photomultiplier tube (PMT)-based PET systems, constant fraction discriminators (CFD) and time to digital converters (TDC) have been employed to detect gamma ray signal arrival time, whereas anger logic circuits and peak detection analog-to-digital converters (ADCs) have been implemented to acquire position and energy information of detected events. As compared to PMT the Geiger-mode avalanche photodiodes (GAPDs) have a variety of advantages, such as compactness, low bias voltage requirement and MRI compatibility. Furthermore, the individual read-out method using a GAPD array coupled 1:1 with an array scintillator can provide better image uniformity than can be achieved using PMT and anger logic circuits. Recently, a brain PET using 72 GAPD arrays (4×4 array, pixel size: 3 mm×3 mm) coupled 1:1 with LYSO scintillators (4×4 array, pixel size: 3 mm×3 mm×20 mm) has been developed for simultaneous PET/MRI imaging in our laboratory. Eighteen 64:1 position decoder circuits (PDCs) were used to reduce GAPD channel number and three off-the-shelf free-running ADC and field programmable gate array (FPGA) combined data acquisition (DAQ) cards were used for data acquisition and processing. In this study, a free-running ADC- and FPGA-based signal processing method was developed for the detection of gamma ray signal arrival time, energy and position information all together for each GAPD channel. For the method developed herein, three DAQ cards continuously acquired 18 channels of pre-amplified analog gamma ray signals and 108-bit digital addresses from 18 PDCs. In the FPGA, the digitized gamma ray pulses and digital addresses were processed to generate data packages containing pulse arrival time, baseline value, energy value and GAPD channel ID. Finally, these data packages were saved to a 128 Mbyte on-board synchronous dynamic random access memory (SDRAM) and then transferred to a host computer for coincidence sorting and image reconstruction. In order to

  14. PET quantification of the norepinephrine transporter in human brain with (S,S)-18F-FMeNER-D2.

    PubMed

    Moriguchi, Sho; Kimura, Yasuyuki; Ichise, Masanori; Arakawa, Ryosuke; Takano, Harumasa; Seki, Chie; Ikoma, Yoko; Takahata, Keisuke; Nagashima, Tomohisa; Yamada, Makiko; Mimura, Masaru; Suhara, Tetsuya

    2016-12-15

    Norepinephrine transporter (NET) in the brain plays important roles in human cognition and the pathophysiology of psychiatric disorders. Two radioligands, (S,S)-(11)C-MRB and (S,S)-(18)F-FMeNER-D2, have been used for imaging NETs in the thalamus and midbrain (including locus coeruleus) using positron emission topography (PET) in humans. However, NET density in the equally important cerebral cortex has not been well quantified because of unfavorable kinetics with (S,S)-(11)C-MRB and defluorination with (S,S)-(18)F-FMeNER-D2, which can complicate NET quantification in the cerebral cortex adjacent to the skull containing defluorinated (18)F radioactivity. In this study, we have established analysis methods of quantification of NET density in the brain including cerebral cortex using (S,S)-(18)F-FMeNER-D2 PET.

  15. Can brain thallium 201 SPECT substitute for F-18-FDG PET in detecting recurrent brain tumor in the presence of radiation necrosis; correlation with biopsy/surgery results

    SciTech Connect

    Antar, M.A.; Barnett, G.H.; McIntyre, W.J.

    1994-05-01

    F-18-FDG PET man has been largely successful in differentiating between radiation necrosis and recurrent brain tumors. Because of the expense and unavailability of PET scanners in most clinical centers, Tl-201 SPECT scan may offer an alternative. Therefore, we have evaluated both techniques in 18 patients (13 men and 5 women) whose ages range from 28 to 74 year old. Eleven patients had glioblastoma multiformi and 4 patients high grade astrocytoma and 3 patient meningiosarcoma. All patients received radiation therapy (5500-6000 Rad) and 13 patients received also chemotherapy. PET scan was performed 40-60 min. after 5-10 mCi of F-18 FDG (i.v.) and SPECT 30 min. after 4.6 mCi of Tl-201 chloride (i.v.). Severe FDG hypometabolism was evident in the irradiated regions, in all patients. Evidence of tumor recurrence was seen in 15 patients by both FDG PET and Thallium 201 SPECT. The ratio of peak pixel uptake of suspected tumor to that of normal cortex for FDG ranged from 0.67 to 1.5 with a mean of 1.02. The ratio of peak pixel uptake of thallium 201 in the suspected lesion to that of the contralateral scalp area ranges from 0.8 to 1.9 with mean of 1.1. There was concordance between the findings of PET and SPECT in 16/18 patients. However, the volume of involvement differs in these patients; most likely secondary to different mechanisms of uptake and both studies may complement each other. Subsequent biopsy/surgery in 11 patients confirmed tumor recurrence in 10 out of 11 patients. The findings suggest that thallium 201 brain SPECT scan can provide similar (but not identical) information regarding brain tumor recurrence in these patients.

  16. Evaluation of the Dopamine Hypothesis of ADHD with PET Brain Imaging

    SciTech Connect

    Swanson, James

    2010-04-28

    The Dopamine (DA) Hypothesis of ADHD (Wender, 1971; Levy, 1990) suggests that abnormalities in the synaptic mechanisms of DA transmission may be disrupted, and specific abnormalities in DA receptors and DA transporters (DAT) have been proposed (see Swanson et al, 1998). Early studies with small samples (e.g., n = 6, Dougherty et al, 1999) used single photon emission tomography (SPECT) and the radioligand (123I Altropane) to test a theory that ADHD may be caused by an over expression of DAT and reported 'a 70% increase in age-corrected dopamine transporter density in patients with attention deficit hyperactivity disorder compared with healthy controls' and suggested that treatment with stimulant medication decreased DAT density in ADHD patients and corrected an underlying abnormality (Krause et al, 2000). The potential importance of these findings was noted by Swanson (1999): 'If true, this is a major finding and points the way for new investigations of the primary pharmacological treatment for ADHD (with the stimulant drugs - e.g., methylphenidate), for which the dopamine transporter is the primary site of action. The potential importance of this finding demands special scrutiny'. This has been provided over the past decade using Positron Emission Tomography (PET). Brain imaging studies were conducted at Brookhaven National Laboratory (BNL) in a relatively large sample of stimulant-naive adults assessed for DAT (11C cocaine) density and DA receptors (11C raclopride) availability. These studies (Volkow et al, 2007; Volkow et al, 2009) do not confirm the hypothesis of increased DAT density and suggest the opposite (i.e., decreased rather than increased DAT density), and follow-up after treatment (Wang et al, 2010) does not confirm the hypothesis that therapeutic doses of methylphenidate decrease DAT density and suggests the opposite (i.e., increased rather than decreased DAT density). The brain regions implicated by these PET imaging studies also suggest that a

  17. Evaluation of the Dopamine Hypothesis of ADHD with PET Brain Imaging

    ScienceCinema

    Swanson, James [University of California, Irvine, California, United States

    2016-07-12

    The Dopamine (DA) Hypothesis of ADHD (Wender, 1971; Levy, 1990) suggests that abnormalities in the synaptic mechanisms of DA transmission may be disrupted, and specific abnormalities in DA receptors and DA transporters (DAT) have been proposed (see Swanson et al, 1998). Early studies with small samples (e.g., n = 6, Dougherty et al, 1999) used single photon emission tomography (SPECT) and the radioligand (123I Altropane) to test a theory that ADHD may be caused by an over expression of DAT and reported 'a 70% increase in age-corrected dopamine transporter density in patients with attention deficit hyperactivity disorder compared with healthy controls' and suggested that treatment with stimulant medication decreased DAT density in ADHD patients and corrected an underlying abnormality (Krause et al, 2000). The potential importance of these findings was noted by Swanson (1999): 'If true, this is a major finding and points the way for new investigations of the primary pharmacological treatment for ADHD (with the stimulant drugs - e.g., methylphenidate), for which the dopamine transporter is the primary site of action. The potential importance of this finding demands special scrutiny'. This has been provided over the past decade using Positron Emission Tomography (PET). Brain imaging studies were conducted at Brookhaven National Laboratory (BNL) in a relatively large sample of stimulant-naive adults assessed for DAT (11C cocaine) density and DA receptors (11C raclopride) availability. These studies (Volkow et al, 2007; Volkow et al, 2009) do not confirm the hypothesis of increased DAT density and suggest the opposite (i.e., decreased rather than increased DAT density), and follow-up after treatment (Wang et al, 2010) does not confirm the hypothesis that therapeutic doses of methylphenidate decrease DAT density and suggests the opposite (i.e., increased rather than decreased DAT density). The brain regions implicated by these PET imaging studies also suggest that a

  18. Impact of target-to-background ratio, target size, emission scan duration, and activity on physical figures of merit for a 3D LSO-based whole body PET/CT scanner.

    PubMed

    Brambilla, M; Matheoud, R; Secco, C; Sacchetti, G; Comi, S; Rudoni, M; Carriero, A; Inglese, E

    2007-10-01

    The aim of our work is to describe the way in which physical figures of merit such as contrast-to-noise ratio (CNR) behave when varying acquisition parameters such as emission scan duration (ESD) or activity at the start of acquisition (A(acq)) that in clinical practice can be selected by the user, or object properties such as target dimensions or target-to-background (T/B) ratio, which depend uniquely on the intrinsic characteristics of the object being imaged. Figures of merit, used to characterize image quality and quantitative accuracy for a 3D-LSO based PET/CT scanner, were studied as a function of ESD and A(acq) for different target sizes and T/B ratios using a multivariate approach in a wide range of conditions approaching the ones that can be encountered in clinical practice. An annular ring of water bags of 3 cm thickness was fitted over an IEC phantom in order to obtain counting rates similar to those found in average patients. The average scatter fraction (SF) of the modified IEC phantom was similar to the mean SF measured on patients with a similar scanner. A supplemental set of micro-hollow spheres was positioned inside the phantom. The NEMA NU 2-2001 scatter phantom was positioned at the end of the IEC phantom to approximate the clinical situation of having activity that extends beyond the scanner. The phantoms were filled with a solution of water and 18F (12 kBq/mL) and the spheres with various T/B ratios of 22.5, 10.3, and 3.6. Sequential imaging was performed to acquire PET images with varying background activity concentrations of about 12, 9, 6.4, 5.3, and 3.1 kBq/mL, positioned on the linear portion of the phantom's NECR curve, well below peak NECR of 61.2 kcps that is reached at 31.8 kBq/mL. The ESD was set to 1, 2, 3, and 4 min/bed. With T/B ratios of 3.6, 10.3, and 22.5, the 13.0, 8.1, and 6.5 mm spheres were detectable for the whole ranges of background activity concentration and ESD, respectively. The ESD resulted as the most significant

  19. Impact of target-to-background ratio, target size, emission scan duration, and activity on physical figures of merit for a 3D LSO-based whole body PET/CT scanner

    SciTech Connect

    Brambilla, M.; Matheoud, R.; Secco, C.; Sacchetti, G.; Comi, S.; Rudoni, M.; Carriero, A.; Inglese, E.

    2007-10-15

    The aim of our work is to describe the way in which physical figures of merit such as contrast-to-noise ratio (CNR) behave when varying acquisition parameters such as emission scan duration (ESD) or activity at the start of acquisition (A{sub acq}) that in clinical practice can be selected by the user, or object properties such as target dimensions or target-to-background (T/B) ratio, which depend uniquely on the intrinsic characteristics of the object being imaged. Figures of merit, used to characterize image quality and quantitative accuracy for a 3D-LSO based PET/CT scanner, were studied as a function of ESD and A{sub acq} for different target sizes and T/B ratios using a multivariate approach in a wide range of conditions approaching the ones that can be encountered in clinical practice. An annular ring of water bags of 3 cm thickness was fitted over an IEC phantom in order to obtain counting rates similar to those found in average patients. The average scatter fraction (SF) of the modified IEC phantom was similar to the mean SF measured on patients with a similar scanner. A supplemental set of micro-hollow spheres was positioned inside the phantom. The NEMA NU 2-2001 scatter phantom was positioned at the end of the IEC phantom to approximate the clinical situation of having activity that extends beyond the scanner. The phantoms were filled with a solution of water and {sup 18}F (12 kBq/mL) and the spheres with various T/B ratios of 22.5, 10.3, and 3.6. Sequential imaging was performed to acquire PET images with varying background activity concentrations of about 12, 9, 6.4, 5.3, and 3.1 kBq/mL, positioned on the linear portion of the phantom's NECR curve, well below peak NECR of 61.2 kcps that is reached at 31.8 kBq/mL. The ESD was set to 1, 2, 3, and 4 min/bed. With T/B ratios of 3.6, 10.3, and 22.5, the 13.0, 8.1, and 6.5 mm spheres were detectable for the whole ranges of background activity concentration and ESD, respectively. The ESD resulted as the most

  20. Classification of Parkinsonian Syndromes from FDG-PET Brain Data Using Decision Trees with SSM/PCA Features

    PubMed Central

    Mudali, D.; Teune, L. K.; Renken, R. J.; Leenders, K. L.; Roerdink, J. B. T. M.

    2015-01-01

    Medical imaging techniques like fluorodeoxyglucose positron emission tomography (FDG-PET) have been used to aid in the differential diagnosis of neurodegenerative brain diseases. In this study, the objective is to classify FDG-PET brain scans of subjects with Parkinsonian syndromes (Parkinson's disease, multiple system atrophy, and progressive supranuclear palsy) compared to healthy controls. The scaled subprofile model/principal component analysis (SSM/PCA) method was applied to FDG-PET brain image data to obtain covariance patterns and corresponding subject scores. The latter were used as features for supervised classification by the C4.5 decision tree method. Leave-one-out cross validation was applied to determine classifier performance. We carried out a comparison with other types of classifiers. The big advantage of decision tree classification is that the results are easy to understand by humans. A visual representation of decision trees strongly supports the interpretation process, which is very important in the context of medical diagnosis. Further improvements are suggested based on enlarging the number of the training data, enhancing the decision tree method by bagging, and adding additional features based on (f)MRI data. PMID:25918550

  1. Automated reference region extraction and population-based input function for brain [11C]TMSX PET image analyses

    PubMed Central

    Rissanen, Eero; Tuisku, Jouni; Luoto, Pauliina; Arponen, Eveliina; Johansson, Jarkko; Oikonen, Vesa; Parkkola, Riitta; Airas, Laura; Rinne, Juha O

    2015-01-01

    [11C]TMSX ([7-N-methyl-11C]-(E)-8-(3,4,5-trimethoxystyryl)-1,3,7-trimethylxanthine) is a selective adenosine A2A receptor (A2AR) radioligand. In the central nervous system (CNS), A2AR are linked to dopamine D2 receptor function in striatum, but they are also important modulators of inflammation. The golden standard for kinetic modeling of brain [11C]TMSX positron emission tomography (PET) is to obtain arterial input function via arterial blood sampling. However, this method is laborious, prone to errors and unpleasant for study subjects. The aim of this work was to evaluate alternative input function acquisition methods for brain [11C]TMSX PET imaging. First, a noninvasive, automated method for the extraction of gray matter reference region using supervised clustering (SCgm) was developed. Second, a method for obtaining a population-based arterial input function (PBIF) was implemented. These methods were created using data from 28 study subjects (7 healthy controls, 12 multiple sclerosis patients, and 9 patients with Parkinson's disease). The results with PBIF correlated well with original plasma input, and the SCgm yielded similar results compared with cerebellum as a reference region. The clustering method for extracting reference region and the population-based approach for acquiring input for dynamic [11C]TMSX brain PET image analyses appear to be feasible and robust methods, that can be applied in patients with CNS pathology. PMID:25370856

  2. Automated reference region extraction and population-based input function for brain [(11)C]TMSX PET image analyses.

    PubMed

    Rissanen, Eero; Tuisku, Jouni; Luoto, Pauliina; Arponen, Eveliina; Johansson, Jarkko; Oikonen, Vesa; Parkkola, Riitta; Airas, Laura; Rinne, Juha O

    2015-01-01

    [(11)C]TMSX ([7-N-methyl-(11)C]-(E)-8-(3,4,5-trimethoxystyryl)-1,3,7-trimethylxanthine) is a selective adenosine A2A receptor (A2AR) radioligand. In the central nervous system (CNS), A2AR are linked to dopamine D2 receptor function in striatum, but they are also important modulators of inflammation. The golden standard for kinetic modeling of brain [(11)C]TMSX positron emission tomography (PET) is to obtain arterial input function via arterial blood sampling. However, this method is laborious, prone to errors and unpleasant for study subjects. The aim of this work was to evaluate alternative input function acquisition methods for brain [(11)C]TMSX PET imaging. First, a noninvasive, automated method for the extraction of gray matter reference region using supervised clustering (SCgm) was developed. Second, a method for obtaining a population-based arterial input function (PBIF) was implemented. These methods were created using data from 28 study subjects (7 healthy controls, 12 multiple sclerosis patients, and 9 patients with Parkinson's disease). The results with PBIF correlated well with original plasma input, and the SCgm yielded similar results compared with cerebellum as a reference region. The clustering method for extracting reference region and the population-based approach for acquiring input for dynamic [(11)C]TMSX brain PET image analyses appear to be feasible and robust methods, that can be applied in patients with CNS pathology.

  3. FDG-PET in the Evaluation of Brain Metabolic Changes Induced by Cognitive Stimulation in aMCI Subjects.

    PubMed

    Ciarmiello, Andrea; Gaeta, Maria Chiara; Benso, Francesco; Del Sette, Massimo

    2015-01-01

    Cognitive training has reported to improve cognitive performance in Mild Cognitive Impairment (MCI) as well as in older healthy subjects. 18F-FDG-PET is widely used in the diagnoses of dementia for its ability to identify early metabolic changes. This study was aimed to assess the effect of cognitive stimulation on brain metabolic network and clinical cognitive performance. Thirty aMCI subjects were enrolled in the study and allocated in two groups matched for cognitive profile, sex and schooling and then randomly assigned to the training arm or to the placebo arm. All subjects underwent neuropsychological assessment and PET imaging before and after intervention. We found significant association between brain metabolism and cognitive stimulation in treated aMCI subjects. Brain metabolic changes included Brodmann areas reported to be involved in working memory and attentive processes as well as executive functions. Our study shows that metabolic changes occur earlier than possible clinical changes related to the intervention. 18F-FDG-PET could provide a useful biomarker of response to identify a population of aMCI suitable to respond to treatment, according to most recent data on default network mode and its adaptivity to external stimuli.

  4. 3d-3d correspondence revisited

    DOE PAGES

    Chung, Hee -Joong; Dimofte, Tudor; Gukov, Sergei; ...

    2016-04-21

    In fivebrane compactifications on 3-manifolds, we point out the importance of all flat connections in the proper definition of the effective 3d N = 2 theory. The Lagrangians of some theories with the desired properties can be constructed with the help of homological knot invariants that categorify colored Jones polynomials. Higgsing the full 3d theories constructed this way recovers theories found previously by Dimofte-Gaiotto-Gukov. As a result, we also consider the cutting and gluing of 3-manifolds along smooth boundaries and the role played by all flat connections in this operation.

  5. Brain metastases detectability of routine whole body (18)F-FDG PET and low dose CT scanning in 2502 asymptomatic patients with solid extracranial tumors.

    PubMed

    Bochev, Pavel; Klisarova, Aneliya; Kaprelyan, Ara; Chaushev, Borislav; Dancheva, Zhivka

    2012-01-01

    As fluorine-18-fluorodesoxyglucose positron emission tomography/computed tomography ( (18)F-FDG PET/CT) is gaining wider availability, more and more patients with malignancies undergo whole body PET/CT, mostly to assess tumor spread in the rest of the body, but not in the brain. Brain is a common site of metastatic spread in patients with solid extracranial tumors. Gold standard in the diagnosis of brain metastases remains magnetic resonance imaging (MRI). However MRI is not routinely indicated and is not available for all cancer patients. Fluorine-18-FDG PET is considered as having poor sensitivity in detecting brain metastases, but this may not be true for PET/CT. The aim of our study was to assess the value of (18)F-FDG PET/CT in the detection of brain metastases found by whole body scan including the brain, in patients with solid extracranial neoplasms. A total of 2502 patients with solid extracranial neoplasms were studied. All patients underwent a routine whole body (18)F-FDG PET/CT scan with the whole brain included in the scanned field. Patients with known or suspected brain metastases were preliminary excluded from the study. Hypermetabolic and ring-like brain lesions on the PET scan were considered as metastases. Lesions with CT characteristics of brain metastases were regarded as such irrespective of their metabolic pattern. Lesions in doubt were verified by MRI during first testing or on follow-up or by operation. Our results showed that brain lesions, indicative of and verified to be metastases were detected in 25 out of the 2502 patients (1%), with lung cancer being the most common primary. Twenty three out of these 25 patients had no neurological symptoms by the time of the scan. The detection rate of brain metastases was relatively low, but information was obtained with a minimum increase of radiation burden. In conclusion, whole body (18)F-FDG PET/CT detected brain metastases in 1% of the patients if brain was included in the scanned field. Brain

  6. Development of a New Radiofluorinated Quinoline Analog for PET Imaging of Phosphodiesterase 5 (PDE5) in Brain

    PubMed Central

    Liu, Jianrong; Wenzel, Barbara; Dukic-Stefanovic, Sladjana; Teodoro, Rodrigo; Ludwig, Friedrich-Alexander; Deuther-Conrad, Winnie; Schröder, Susann; Chezal, Jean-Michel; Moreau, Emmanuel; Brust, Peter; Maisonial-Besset, Aurélie

    2016-01-01

    Phosphodiesterases (PDEs) are enzymes that play a major role in cell signalling by hydrolysing the secondary messengers cyclic adenosine monophosphate (cAMP) and/or cyclic guanosine monophosphate (cGMP) throughout the body and brain. Altered cyclic nucleotide-mediated signalling has been associated with a wide array of disorders, including neurodegenerative disorders. Recently, PDE5 has been shown to be involved in neurodegenerative disorders such as Alzheimer’s disease, but its precise role has not been elucidated yet. To visualize and quantify the expression of this enzyme in brain, we developed a radiotracer for specific PET imaging of PDE5. A quinoline-based lead compound has been structurally modified resulting in the fluoroethoxymethyl derivative ICF24027 with high inhibitory activity towards PDE5 (IC50 = 1.86 nM). Radiolabelling with fluorine-18 was performed by a one-step nucleophilic substitution reaction using a tosylate precursor (RCY(EOB) = 12.9% ± 1.8%; RCP > 99%; SA(EOS) = 70–126 GBq/μmol). In vitro autoradiographic studies of [18F]ICF24027 on different mouse tissue as well as on porcine brain slices demonstrated a moderate specific binding to PDE5. In vivo studies in mice revealed that [18F]ICF24027 was metabolized under formation of brain penetrable radiometabolites making the radiotracer unsuitable for PET imaging of PDE5 in brain. PMID:27110797

  7. Performance Enhancement of the RatCAP Awake Rate Brain PET System

    SciTech Connect

    Vaska, P.; Vaska, P.; Woody, C.; Schlyer, D.; Radeka, V.; O'Connor, P.; Park, S.-J.; Pratte, J.-F.; Junnarkar, M.; Purschke, S.; Southekal, S.; Stoll, S.; Schiffer, W.; Neill, J.; Wharton, D.; Myers, N.; Wiley, S.; Kandasamy, A.; Fried, J.; Krishnamoorthy, S. Kriplani, A.; Maramraju, S.; Lecomte, R.; Fontaine, R.

    2011-03-01

    The first full prototype of the RatCAP PET system, designed to image the brain of a rat while conscious, has been completed. Initial results demonstrated excellent spatial resolution, 1.8 mm FWHM with filtered backprojection and <1.5 mm FWHM with a Monte Carlo based MLEM method. However, noise equivalent countrate studies indicated the need for better timing to mitigate the effect of randoms. Thus, the front-end ASIC has been redesigned to minimize time walk, an accurate coincidence time alignment method has been implemented, and a variance reduction technique for the randoms is being developed. To maximize the quantitative capabilities required for neuroscience, corrections are being implemented and validated for positron range and photon noncollinearity, scatter (including outside the field of view), attenuation, randoms, and detector efficiency (deadtime is negligible). In addition, a more robust and compact PCI-based optical data acquisition system has been built to replace the original VME-based system while retaining the linux-based data processing and image reconstruction codes. Finally, a number of new animal imaging experiments have been carried out to demonstrate the performance of the RatCAP in real imaging situations, including an F-18 fluoride bone scan, a C-11 raclopride scan, and a dynamic C-11 methamphetamine scan.

  8. Improved attenuation correction for freely moving animal brain PET studies using a virtual scanner geometry

    NASA Astrophysics Data System (ADS)

    Angelis, Georgios I.; Ryder, William J.; Kyme, Andre Z.; Fulton, Roger R.; Meikle, Steven R.

    2014-03-01

    Attenuation correction in positron emission tomography brain imaging of freely moving animals can be very challenging since the body of the animal is often within the field of view and introduces a non negligible atten- uating factor that can degrade the quantitative accuracy of the reconstructed images. An attractive approach that avoids the need for a transmission scan involves the generation of the convex hull of the animal's head based on the reconstructed emission images. However, this approach ignores the potential attenuation introduced by the animal's body. In this work, we propose a virtual scanner geometry, which moves in synchrony with the animal's head and discriminates between those events that traverse only the animal's head (and therefore can be accurately compensated for attenuation) and those that might have also traversed the animal's body. For each pose a new virtual scanner geometry was defined and therefore a new system matrix was calculated leading to a time-varying system matrix. This new approach was evaluated on phantom data acquired on the microPET Focus 220 scanner using a custom-made rat phantom. Results showed that when the animal's body is within the FOV and not accounted for during attenuation correction it can lead to bias of up to 10%. On the contrary, at- tenuation correction was more accurate when the virtual scanner was employed leading to improved quantitative estimates (bias <2%), without the need to account for the animal's body.

  9. Motion correction of PET brain images through deconvolution: I. Theoretical development and analysis in software simulations

    NASA Astrophysics Data System (ADS)

    Faber, T. L.; Raghunath, N.; Tudorascu, D.; Votaw, J. R.

    2009-02-01

    Image quality is significantly degraded even by small amounts of patient motion in very high-resolution PET scanners. Existing correction methods that use known patient motion obtained from tracking devices either require multi-frame acquisitions, detailed knowledge of the scanner, or specialized reconstruction algorithms. A deconvolution algorithm has been developed that alleviates these drawbacks by using the reconstructed image to estimate the original non-blurred image using maximum likelihood estimation maximization (MLEM) techniques. A high-resolution digital phantom was created by shape-based interpolation of the digital Hoffman brain phantom. Three different sets of 20 movements were applied to the phantom. For each frame of the motion, sinograms with attenuation and three levels of noise were simulated and then reconstructed using filtered backprojection. The average of the 20 frames was considered the motion blurred image, which was restored with the deconvolution algorithm. After correction, contrast increased from a mean of 2.0, 1.8 and 1.4 in the motion blurred images, for the three increasing amounts of movement, to a mean of 2.5, 2.4 and 2.2. Mean error was reduced by an average of 55% with motion correction. In conclusion, deconvolution can be used for correction of motion blur when subject motion is known.

  10. [In vivo visualization of neurotransmitter function in the human brain by PET].

    PubMed

    Itoh, M; Yanai, K; Yamaguchi, S; Fujiwara, T; Nagasawa, H; Yokoyama, H; Iinuma, K; Ido, T

    1995-03-01

    Measurement of cerebral blood flow and energy metabolism using PET with 15O and 18F labeled tracers allows quantitative evaluation of cerebral metabolism that can be perturbed in pathological states. Neurotransmission is a new target that is visualized by labeling of substrates of enzymes that are involved in neurotransmitter synthesis or degradation. Neuronal receptors are mapped by introducing the labeled ligands that are specifically bound to the receptors in question. We developed unique tracers that label dopamine D2 or histamine H1 receptors. With other available ligands for the muscarinic cholinergic receptors and [18F] fluorodopa, we started clinical investigations to document the state of neurotransmission in patients with epilepsy, Parkinson's disease and dementia. Using [11C] doxepin we observed an increase of H1 receptors in the epileptic foci that showed decreased glucose metabolic rate at the interictal phase. This phenomenon is compatible with reported increase of mu opiate receptors in the brains of epileptic patients. Brain uptake of FDOPA (Ki), calculated by the graphical plot was found relatively stable with age both in the normal population and dementia patients. However, the striatal Ki of FDOPA of severely demented patients significantly reduced, compared with the normal aged subjects. The correlation analysis between FDOPA Ki and severity of dementia as assessed by mini-mental state examination revealed a significant reduction of Ki associated with the disease progression. Increase in D2 receptor density as assessed by the uptake of YM 09151-2 was observed in cases with reduced FDOPA uptake, which may correspond to the state of supersensitivity of the D2 receptors.

  11. Cerebral 5-HT release correlates with [(11)C]Cimbi36 PET measures of 5-HT2A receptor occupancy in the pig brain.

    PubMed

    Jørgensen, Louise M; Weikop, Pia; Villadsen, Jonas; Visnapuu, Tanel; Ettrup, Anders; Hansen, Hanne D; Baandrup, Anders O; Andersen, Flemming L; Bjarkam, Carsten R; Thomsen, Carsten; Jespersen, Bo; Knudsen, Gitte M

    2017-02-01

    Positron emission tomography (PET) can, when used with appropriate radioligands, non-invasively generate temporal and spatial information about acute changes in brain neurotransmitter systems. We for the first time evaluate the novel 5-HT2A receptor agonist PET radioligand, [(11)C]Cimbi-36, for its sensitivity to detect changes in endogenous cerebral 5-HT levels, as induced by different pharmacological challenges. To enable a direct translation of PET imaging data to changes in brain 5-HT levels, we calibrated the [(11)C]Cimbi-36 PET signal in the pig brain by simultaneous measurements of extracellular 5-HT levels with microdialysis and [(11)C]Cimbi-36 PET after various acute interventions (saline, citalopram, citalopram + pindolol, fenfluramine). In a subset of pigs, para-chlorophenylalanine pretreatment was given to deplete cerebral 5-HT. The interventions increased the cerebral extracellular 5-HT levels to 2-11 times baseline, with fenfluramine being the most potent pharmacological enhancer of 5-HT release, and induced a varying degree of decline in [(11)C]Cimbi-36 binding in the brain, consistent with the occupancy competition model. The observed correlation between changes in the extracellular 5-HT level in the pig brain and the 5-HT2A receptor occupancy indicates that [(11)C]Cimbi-36 binding is sensitive to changes in endogenous 5-HT levels, although only detectable with PET when the 5-HT release is sufficiently high.

  12. One-step preparation of [(18)F]FPBM for PET imaging of serotonin transporter (SERT) in the brain.

    PubMed

    Qiao, Hongwen; Zhang, Yan; Wu, Zehui; Zhu, Lin; Choi, Seok Rye; Ploessl, Karl; Kung, Hank F

    2016-08-01

    Serotonin transporters (SERT) in the brain play an important role in normal brain function. Selective serotonin reuptake inhibitors such as fluoxetine, sertraline, paroxetine, escitalopram, etc., specifically target SERT binding in the brain. Development of SERT imaging agents may be useful for studying the function of SERT by in vivo imaging. A one-step preparation of [(18)F]FPBM, 2-(2'-(dimethylamino)methyl)-4'-(3-([(18)F]fluoropropoxy)phenylthio)benzenamine, for positron emission tomography (PET) imaging of SERT binding in the brain was achieved. An active OTs intermediate, 9, was reacted with [(18)F]F(-)/K222 to produce [(18)F]FPBM in one step and in high radiochemical yield. This labeling reaction was evaluated and optimized under different temperatures, bases, solvents, and varying amounts of precursor 9. The radiolabeling reaction led to the desired [(18)F]FPBM in one step and the crude product was purified by HPLC purification to give no-carrier-added [(18)F]FPBM (radiochemical yield, 24-33%, decay corrected; radiochemical purity >99%). PET imaging studies in normal monkeys (n=4) showed fast, pronounced uptakes in the midbrain and thalamus, regions known to be rich in SERT binding sites. A displacement experiment with escitalopram (5mg/kg iv injection at 30min after [(18)F]FPBM injection) showed a rapid and complete reversal of SERT binding, suggesting that binding by [(18)F]FPBM was highly specific and reversible. A one-step radiolabeling method coupled with HPLC purification for preparation of [(18)F]FPBM was developed. Imaging studies suggest that it is feasible to use this method to prepare [(18)F]FPBM for in vivo PET imaging of SERT binding in the brain.

  13. 3D and Education

    NASA Astrophysics Data System (ADS)

    Meulien Ohlmann, Odile

    2013-02-01

    Today the industry offers a chain of 3D products. Learning to "read" and to "create in 3D" becomes an issue of education of primary importance. 25 years professional experience in France, the United States and Germany, Odile Meulien set up a personal method of initiation to 3D creation that entails the spatial/temporal experience of the holographic visual. She will present some different tools and techniques used for this learning, their advantages and disadvantages, programs and issues of educational policies, constraints and expectations related to the development of new techniques for 3D imaging. Although the creation of display holograms is very much reduced compared to the creation of the 90ies, the holographic concept is spreading in all scientific, social, and artistic activities of our present time. She will also raise many questions: What means 3D? Is it communication? Is it perception? How the seeing and none seeing is interferes? What else has to be taken in consideration to communicate in 3D? How to handle the non visible rela