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2014


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Dynamical source analysis of hippocampal sharp-wave ripple episodes

Ramirez-Villegas, J. F., Logothetis, N. K., Besserve, M.

Bernstein Conference, 2014 (poster)

ei

DOI [BibTex]

2014


DOI [BibTex]


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FID-guided retrospective motion correction based on autofocusing

Babayeva, M., Loktyushin, A., Kober, T., Granziera, C., Nickisch, H., Gruetter, R., Krueger, G.

Joint Annual Meeting ISMRM-ESMRMB, Milano, Italy, 2014 (poster)

ei

[BibTex]

[BibTex]


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Cluster analysis of sharp-wave ripple field potential signatures in the macaque hippocampus

Ramirez-Villegas, J. F., Logothetis, N. K., Besserve, M.

Computational and Systems Neuroscience Meeting (COSYNE), 2014 (poster)

ei

[BibTex]

[BibTex]


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oxel level [18]F-FDG PET/MRI unsupervised segmentation of the tumor microenvironment

Katiyar, P., Divine, M. R., Pichler, B. J., Disselhorst, J. A.

World Molecular Imaging Conference, 2014 (poster)

ei

[BibTex]

[BibTex]

2011


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Spatiotemporal mapping of rhythmic activity in the inferior convexity of the macaque prefrontal cortex

Panagiotaropoulos, T., Besserve, M., Crocker, B., Kapoor, V., Tolias, A., Panzeri, S., Logothetis, N.

41(239.15), 41st Annual Meeting of the Society for Neuroscience (Neuroscience), November 2011 (poster)

Abstract
The inferior convexity of the macaque prefrontal cortex (icPFC) is known to be involved in higher order processing of sensory information mediating stimulus selection, attention and working memory. Until now, the vast majority of electrophysiological investigations of the icPFC employed single electrode recordings. As a result, relatively little is known about the spatiotemporal structure of neuronal activity in this cortical area. Here we study in detail the spatiotemporal properties of local field potentials (LFP's) in the icPFC using multi electrode recordings during anesthesia. We computed the LFP-LFP coherence as a function of frequency for thousands of pairs of simultaneously recorded sites anterior to the arcuate and inferior to the principal sulcus. We observed two distinct peaks of coherent oscillatory activity between approximately 4-10 and 15-25 Hz. We then quantified the instantaneous phase of these frequency bands using the Hilbert transform and found robust phase gradients across recording sites. The dependency of the phase on the spatial location reflects the existence of traveling waves of electrical activity in the icPFC. The dominant axis of these traveling waves roughly followed the ventral-dorsal plane. Preliminary results show that repeated visual stimulation with a 10s movie had no dramatic effect on the spatial structure of the traveling waves. Traveling waves of electrical activity in the icPFC could reflect highly organized cortical processing in this area of prefrontal cortex.

ei

Web [BibTex]

2011


Web [BibTex]


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Evaluation and Optimization of MR-Based Attenuation Correction Methods in Combined Brain PET/MR

Mantlik, F., Hofmann, M., Bezrukov, I., Schmidt, H., Kolb, A., Beyer, T., Reimold, M., Schölkopf, B., Pichler, B.

2011(MIC18.M-96), 2011 IEEE Nuclear Science Symposium, Medical Imaging Conference (NSS-MIC), October 2011 (poster)

Abstract
Combined PET/MR provides simultaneous molecular and functional information in an anatomical context with unique soft tissue contrast. However, PET/MR does not support direct derivation of attenuation maps of objects and tissues within the measured PET field-of-view. Valid attenuation maps are required for quantitative PET imaging, specifically for scientific brain studies. Therefore, several methods have been proposed for MR-based attenuation correction (MR-AC). Last year, we performed an evaluation of different MR-AC methods, including simple MR thresholding, atlas- and machine learning-based MR-AC. CT-based AC served as gold standard reference. RoIs from 2 anatomic brain atlases with different levels of detail were used for evaluation of correction accuracy. We now extend our evaluation of different MR-AC methods by using an enlarged dataset of 23 patients from the integrated BrainPET/MR (Siemens Healthcare). Further, we analyze options for improving the MR-AC performance in terms of speed and accuracy. Finally, we assess the impact of ignoring BrainPET positioning aids during the course of MR-AC. This extended study confirms the overall prediction accuracy evaluation results of the first evaluation in a larger patient population. Removing datasets affected by metal artifacts from the Atlas-Patch database helped to improve prediction accuracy, although the size of the database was reduced by one half. Significant improvement in prediction speed can be gained at a cost of only slightly reduced accuracy, while further optimizations are still possible.

ei

Web [BibTex]

Web [BibTex]


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Atlas- and Pattern Recognition Based Attenuation Correction on Simultaneous Whole-Body PET/MR

Bezrukov, I., Schmidt, H., Mantlik, F., Schwenzer, N., Hofmann, M., Schölkopf, B., Pichler, B.

2011(MIC18.M-116), 2011 IEEE Nuclear Science Symposium, Medical Imaging Conference (NSS-MIC), October 2011 (poster)

Abstract
With the recent availability of clinical whole-body PET/MRI it is possible to evaluate and further develop MR-based attenuation correction methods using simultaneously acquired PET/MR data. We present first results for MRAC on patient data acquired on a fully integrated whole-body PET/MRI (Biograph mMR, Siemens) using our method that applies atlas registration and pattern recognition (ATPR) and compare them to the segmentation-based (SEG) method provided by the manufacturer. The ATPR method makes use of a database of previously aligned pairs of MR-CT volumes to predict attenuation values on a continuous scale. The robustness of the method in presence of MR artifacts was improved by location and size based detection. Lesion to liver and lesion to blood ratios (LLR and LBR) were compared for both methods on 29 iso-contour ROIs in 4 patients. ATPR showed >20% higher LBR and LLR for ROIs in and >7% near osseous tissue. For ROIs in soft tissue, both methods yielded similar ratios with max. differences <6% . For ROIs located within metal artifacts in the MR image, ATPR showed >190% higher LLR and LBR than SEG, where ratios <0.1 occured. For lesions in the neighborhood of artifacts, both ratios were >15% higher for ATPR. If artifacts in MR volumes caused by metal implants are not accounted for in the computation of attenuation maps, they can lead to a strong decrease of lesion to background ratios, even to disappearance of hot spots. Metal implants are likely to occur in the patient collective receiving combined PET/MR scans, of our first 10 patients, 3 had metal implants. Our method is currently able to account for artifacts in the pelvis caused by prostheses. The ability of the ATPR method to account for bone leads to a significant increase of LLR and LBR in osseous tissue, which supports our previous evaluations with combined PET/CT and PET/MR data. For lesions within soft tissue, lesion to background ratios of ATPR and SEG were comparable.

ei

Web [BibTex]

Web [BibTex]


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Retrospective blind motion correction of MR images

Loktyushin, A., Nickisch, H., Pohmann, R.

Magnetic Resonance Materials in Physics, Biology and Medicine, 24(Supplement 1):498, 28th Annual Scientific Meeting ESMRMB, October 2011 (poster)

Abstract
We present a retrospective method, which significantly reduces ghosting and blurring artifacts due to subject motion. No modifications to the sequence (as in [2, 3]), or the use of additional equipment (as in [1]) are required. Our method iteratively searches for the transformation, that applied to the lines in k-space -- yields the sparsest Laplacian filter output in the spatial domain.

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Model based reconstruction for GRE EPI

Blecher, W., Pohmann, R., Schölkopf, B., Seeger, M.

Magnetic Resonance Materials in Physics, Biology and Medicine, 24(Supplement 1):493-494, 28th Annual Scientific Meeting ESMRMB, October 2011 (poster)

Abstract
Model based nonlinear image reconstruction methods for MRI [3] are at the heart of modern reconstruction techniques (e.g.compressed sensing [6]). In general, models are expressed as a matrix equation where y and u are column vectors of k-space and image data, X model matrix and e independent noise. However, solving the corresponding linear system is not tractable. Therefore fast nonlinear algorithms that minimize a function wrt.the unknown image are the method of choice: In this work a model for gradient echo EPI, is proposed that incorporates N/2 Ghost correction and correction for field inhomogeneities. In addition to reconstruction from full data, the model allows for sparse reconstruction, joint estimation of image, field-, and relaxation-map (like [5,8] for spiral imaging), and improved N/2 ghost correction.

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Simultaneous multimodal imaging of patients with bronchial carcinoma in a whole body MR/PET system

Brendle, C., Sauter, A., Schmidt, H., Schraml, C., Bezrukov, I., Martirosian, P., Hetzel, J., Müller, M., Claussen, C., Schwenzer, N., Pfannenberg, C.

Magnetic Resonance Materials in Physics, Biology and Medicine, 24(Supplement 1):141, 28th annual scientific meeting of the European Society for Magnetic Resonance in Medicine and Biology (ESMRB), October 2011 (poster)

Abstract
Purpose/Introduction: Lung cancer is among the most frequent cancers (1). Exact determination of tumour extent and viability is crucial for adequate therapy guidance. [18F]-FDG-PET allows accurate staging and the evaluation of therapy response based on glucose metabolism. Diffusion weighted MRI (DWI) is another promising tool for the evaluation of tumour viability (2,3). The aim of the study was the simultaneous PET-MR acquisition in lung cancer patients and correlation of PET and MR data. Subjects and Methods: Seven patients (age 38-73 years, mean 61 years) with highly suspected or known bronchial carcinoma were examined. First, a [18F]-FDG-PET/CT was performed (injected dose: 332-380 MBq). Subsequently, patients were examined at the whole-body MR/PET (Siemens Biograph mMR). The MRI is a modified 3T Verio whole body system with a magnet bore of 60 cm (max. amplitude gradients 45 mT/m, max. slew rate 200 T/m/s). Concerning the PET, the whole-body MR/PET system comprises 56 detector cassettes with a 59.4 cm transaxial and 25.8 cm axial FoV. The following parameters for PET acquisition were applied: 2 bed positions, 6 min/bed with an average uptake time of 124 min after injection (range: 110-143 min). The attenuation correction of PET data was conducted with a segmentation-based method provided by the manufacturer. Acquired PET data were reconstructed with an iterative 3D OSEM algorithm using 3 iterations and 21 subsets, Gaussian filter of 3 mm. DWI MR images were recorded simultaneously for each bed using two b-values (0/800 s/mm2). SUVmax and ADCmin were assessed in a ROI analysis. The following ratios were calculated: SUVmax(tumor)/SUVmean(liver) and ADCmin(tumor)/ADCmean(muscle). Correlation between SUV and ADC was analyzed (Pearson’s correlation). Results: Diagnostic scans could be obtained in all patients with good tumour delineation. The spatial matching of PET and DWI data was very exact. Most tumours showed a pronounced FDG-uptake in combination with decreased ADC values. Significant correlation was found between SUV and ADC ratios (r = -0.87, p = 0.0118). Discussion/Conclusion: Simultaneous MR/PET imaging of lung cancer is feasible. The whole-body MR/PET system can provide complementary information regarding tumour viability and cellularity which could facilitate a more profound tumour characterization. Further studies have to be done to evaluate the importance of these parameters for therapy decisions and monitoring

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Support Vector Machines for finding deletions and short insertions using paired-end short reads

Grimm, D., Hagmann, J., König, D., Weigel, D., Borgwardt, KM.

International Conference on Intelligent Systems for Molecular Biology (ISMB), 2011 (poster)

ei

Web [BibTex]

Web [BibTex]


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Statistical estimation for optimization problems on graphs

Langovoy, M., Sra, S.

Empirical Inference Symposium, 2011 (poster)

ei

[BibTex]


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Transfer Learning with Copulas

Lopez-Paz, D., Hernandez-Lobato, J.

Neural Information Processing Systems (NIPS), 2011 (poster)

ei

PDF [BibTex]

PDF [BibTex]

2001


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Perception of Planar Shapes in Depth

Wichmann, F., Willems, B., Rosas, P., Wagemans, J.

Journal of Vision, 1(3):176, First Annual Meeting of the Vision Sciences Society (VSS), December 2001 (poster)

Abstract
We investigated the influence of the perceived 3D-orientation of planar elliptical shapes on the perception of the shapes themselves. Ellipses were projected onto the surface of a sphere and subjects were asked to indicate if the projected shapes looked as if they were a circle on the surface of the sphere. The image of the sphere was obtained from a real, (near) perfect sphere using a highly accurate digital camera (real sphere diameter 40 cm; camera-to-sphere distance 320 cm; for details see Willems et al., Perception 29, S96, 2000; Photometrics SenSys 400 digital camera with Rodenstock lens, 12-bit linear luminance resolution). Stimuli were presented monocularly on a carefully linearized Sony GDM-F500 monitor keeping the scene geometry as in the real case (sphere diameter on screen 8.2 cm; viewing distance 66 cm). Experiments were run in a darkened room using a viewing tube to minimize, as far as possible, extraneous monocular cues to depth. Three different methods were used to obtain subjects' estimates of 3D-shape: the method of adjustment, temporal 2-alternative forced choice (2AFC) and yes/no. Several results are noteworthy. First, mismatch between perceived and objective slant tended to decrease with increasing objective slant. Second, the variability of the settings, too, decreased with increasing objective slant. Finally, we comment on the results obtained using different psychophysical methods and compare our results to those obtained using a real sphere and binocular vision (Willems et al.).

ei

Web DOI [BibTex]

2001


Web DOI [BibTex]


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Plaid maskers revisited: asymmetric plaids

Wichmann, F.

pages: 57, 4. T{\"u}binger Wahrnehmungskonferenz (TWK), March 2001 (poster)

Abstract
A large number of psychophysical and physiological experiments suggest that luminance patterns are independently analysed in channels responding to different bands of spatial frequency. There are, however, interactions among stimuli falling well outside the usual estimates of channels' bandwidths. Derrington & Henning (1989) first reported that, in 2-AFC sinusoidal-grating detection, plaid maskers, whose components are oriented symmetrically about the signal orientation, cause a substantially larger threshold elevation than would be predicted from their sinusoidal constituents alone. Wichmann & Tollin (1997a,b) and Wichmann & Henning (1998) confirmed and extended the original findings, measuring masking as a function of presentation time and plaid mask contrast. Here I investigate masking using plaid patterns whose components are asymmetrically positioned about the signal orientation. Standard temporal 2-AFC pattern discrimination experiments were conducted using plaid patterns and oblique sinusoidal gratings as maskers, and horizontally orientated sinusoidal gratings as signals. Signal and maskers were always interleaved on the display (refresh rate 152 Hz). As in the case of the symmetrical plaid maskers, substantial masking was observed for many of the asymmetrical plaids. Masking is neither a straightforward function of the plaid's constituent sinusoidal components nor of the periodicity of the luminance beats between components. These results cause problems for the notion that, even for simple stimuli, detection and discrimination are based on the outputs of channels tuned to limited ranges of spatial frequency and orientation, even if a limited set of nonlinear interactions between these channels is allowed.

ei

Web [BibTex]

Web [BibTex]


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The pedestal effect with a pulse train and its constituent sinusoids

Henning, G., Wichmann, F., Bird, C.

Twenty-Sixth Annual Interdisciplinary Conference, 2001 (poster)

Abstract
Curves showing "threshold" contrast for detecting a signal grating as a function of the contrast of a masking grating of the same orientation, spatial frequency, and phase show a characteristic improvement in performance at masker contrasts near the contrast threshold of the unmasked signal. Depending on the percentage of correct responses used to define the threshold, the best performance can be as much as a factor of three better than the unmasked threshold obtained in the absence of any masking grating. The result is called the pedestal effect (sometimes, the dipper function). We used a 2AFC procedure to measure the effect with harmonically related sinusoids ranging from 2 to 16 c/deg - all with maskers of the same orientation, spatial frequency and phase - and with masker contrasts ranging from 0 to 50%. The curves for different spatial frequencies are identical if both the vertical axis (showing the threshold signal contrast) and the horizontal axis (showing the masker contrast) are scaled by the threshold contrast of the signal obtained with no masker. Further, a pulse train with a fundamental frequency of 2 c/deg produces a curve that is indistinguishable from that of a 2-c/deg sinusoid despite the fact that at higher masker contrasts, the pulse train contains at least 8 components all of them equally detectable. The effect of adding 1-D spatial noise is also discussed.

ei

[BibTex]

[BibTex]


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Modeling the Dynamics of Individual Neurons of the Stomatogastric Networks with Support Vector Machines

Frontzek, T., Gutzen, C., Lal, TN., Heinzel, H-G., Eckmiller, R., Böhm, H.

Abstract Proceedings of the 6th International Congress of Neuroethology (ICN'2001) Bonn, abstract 404, 2001 (poster)

Abstract
In small rhythmic active networks timing of individual neurons is crucial for generating different spatial-temporal motor patterns. Switching of one neuron between different rhythms can cause transition between behavioral modes. In order to understand the dynamics of rhythmically active neurons we analyzed the oscillatory membranpotential of a pacemaker neuron and used different neural network models to predict dynamics of its time series. In a first step we have trained conventional RBF networks and Support Vector Machines (SVMs) using gaussian kernels with intracellulary recordings of the pyloric dilatator neuron in the Australian crayfish, Cherax destructor albidus. As a rule SVMs were able to learn the nonlinear dynamics of pyloric neurons faster (e.g. 15s) than RBF networks (e.g. 309s) under the same hardware conditions. After training SVMs performed a better iterated one-step-ahead prediction of time series in the pyloric dilatator neuron with regard to test error and error sum. The test error decreased with increasing number of support vectors. The best SVM used 196 support vectors and produced a test error of 0.04622 as opposed to the best RBF with 0.07295 using 26 RBF-neurons. In pacemaker neuron PD the timepoint at which the membranpotential will cross threshold for generation of its oscillatory peak is most important for determination of the test error. Interestingly SVMs are especially better in predicting this important part of the membranpotential which is superimposed by various synaptic inputs, which drive the membranpotential to its threshold.

ei

[BibTex]

[BibTex]