8,053 research outputs found
Manifold Learning in MR spectroscopy using nonlinear dimensionality reduction and unsupervised clustering
Purpose To investigate whether nonlinear dimensionality reduction improves unsupervised classification of 1H MRS brain tumor data compared with a linear method. Methods In vivo single-voxel 1H magnetic resonance spectroscopy (55 patients) and 1H magnetic resonance spectroscopy imaging (MRSI) (29 patients) data were acquired from histopathologically diagnosed gliomas. Data reduction using Laplacian eigenmaps (LE) or independent component analysis (ICA) was followed by k-means clustering or agglomerative hierarchical clustering (AHC) for unsupervised learning to assess tumor grade and for tissue type segmentation of MRSI data. Results An accuracy of 93% in classification of glioma grade II and grade IV, with 100% accuracy in distinguishing tumor and normal spectra, was obtained by LE with unsupervised clustering, but not with the combination of k-means and ICA. With 1H MRSI data, LE provided a more linear distribution of data for cluster analysis and better cluster stability than ICA. LE combined with k-means or AHC provided 91% accuracy for classifying tumor grade and 100% accuracy for identifying normal tissue voxels. Color-coded visualization of normal brain, tumor core, and infiltration regions was achieved with LE combined with AHC. Conclusion Purpose To investigate whether nonlinear dimensionality reduction improves unsupervised classification of 1H MRS brain tumor data compared with a linear method. Methods In vivo single-voxel 1H magnetic resonance spectroscopy (55 patients) and 1H magnetic resonance spectroscopy imaging (MRSI) (29 patients) data were acquired from histopathologically diagnosed gliomas. Data reduction using Laplacian eigenmaps (LE) or independent component analysis (ICA) was followed by k-means clustering or agglomerative hierarchical clustering (AHC) for unsupervised learning to assess tumor grade and for tissue type segmentation of MRSI data. Results An accuracy of 93% in classification of glioma grade II and grade IV, with 100% accuracy in distinguishing tumor and normal spectra, was obtained by LE with unsupervised clustering, but not with the combination of k-means and ICA. With 1H MRSI data, LE provided a more linear distribution of data for cluster analysis and better cluster stability than ICA. LE combined with k-means or AHC provided 91% accuracy for classifying tumor grade and 100% accuracy for identifying normal tissue voxels. Color-coded visualization of normal brain, tumor core, and infiltration regions was achieved with LE combined with AHC. Conclusion The LE method is promising for unsupervised clustering to separate brain and tumor tissue with automated color-coding for visualization of 1H MRSI data after cluster analysis
Machine Learning for Neuroimaging with Scikit-Learn
Statistical machine learning methods are increasingly used for neuroimaging
data analysis. Their main virtue is their ability to model high-dimensional
datasets, e.g. multivariate analysis of activation images or resting-state time
series. Supervised learning is typically used in decoding or encoding settings
to relate brain images to behavioral or clinical observations, while
unsupervised learning can uncover hidden structures in sets of images (e.g.
resting state functional MRI) or find sub-populations in large cohorts. By
considering different functional neuroimaging applications, we illustrate how
scikit-learn, a Python machine learning library, can be used to perform some
key analysis steps. Scikit-learn contains a very large set of statistical
learning algorithms, both supervised and unsupervised, and its application to
neuroimaging data provides a versatile tool to study the brain.Comment: Frontiers in neuroscience, Frontiers Research Foundation, 2013, pp.1
Imaging haemodynamic changes related to seizures: comparison of EEG-based general linear model, independent component analysis of fMRI and intracranial EEG
Background: Simultaneous EEG-fMRI can reveal haemodynamic changes associated with epileptic activity which may contribute to understanding seizure onset and propagation.
Methods: Nine of 83 patients with focal epilepsy undergoing pre-surgical evaluation had seizures during EEG-fMRI and analysed using three approaches, two based on the general linear model (GLM) and one using independent component analysis (ICA):
1. EEGs were divided into up to three phases: early ictal EEG change, clinical seizure onset and late ictal EEG change and convolved with a canonical haemodynamic response function (HRF) (canonical GLM analysis).
2. Seizures lasting three scans or longer were additionally modelled using a Fourier basis set across the entire event (Fourier GLM analysis).
3. Independent component analysis (ICA) was applied to the fMRI data to identify ictal BOLD patterns without EEG.
The results were compared with intracranial EEG.
Results:
The canonical GLM analysis revealed significant BOLD signal changes associated with seizures on EEG in 7/9 patients, concordant with the seizure onset zone in 4/7. The Fourier GLM analysis revealed changes in BOLD signal corresponding with the results of the canonical analysis in two patients. ICA revealed components spatially concordant with the seizure onset zone in all patients (8/9 confirmed by intracranial EEG).
Conclusion: Ictal EEG-fMRI visualises plausible seizure related haemodynamic changes. The GLM approach to analysing EEG-fMRI data reveals localised BOLD changes concordant with the ictal onset zone when scalp EEG reflects seizure onset. ICA provides additional information when scalp EEG does not accurately reflect seizures and may give insight into ictal haemodynamics
Modeling sparse connectivity between underlying brain sources for EEG/MEG
We propose a novel technique to assess functional brain connectivity in
EEG/MEG signals. Our method, called Sparsely-Connected Sources Analysis (SCSA),
can overcome the problem of volume conduction by modeling neural data
innovatively with the following ingredients: (a) the EEG is assumed to be a
linear mixture of correlated sources following a multivariate autoregressive
(MVAR) model, (b) the demixing is estimated jointly with the source MVAR
parameters, (c) overfitting is avoided by using the Group Lasso penalty. This
approach allows to extract the appropriate level cross-talk between the
extracted sources and in this manner we obtain a sparse data-driven model of
functional connectivity. We demonstrate the usefulness of SCSA with simulated
data, and compare to a number of existing algorithms with excellent results.Comment: 9 pages, 6 figure
Efficient transfer entropy analysis of non-stationary neural time series
Information theory allows us to investigate information processing in neural
systems in terms of information transfer, storage and modification. Especially
the measure of information transfer, transfer entropy, has seen a dramatic
surge of interest in neuroscience. Estimating transfer entropy from two
processes requires the observation of multiple realizations of these processes
to estimate associated probability density functions. To obtain these
observations, available estimators assume stationarity of processes to allow
pooling of observations over time. This assumption however, is a major obstacle
to the application of these estimators in neuroscience as observed processes
are often non-stationary. As a solution, Gomez-Herrero and colleagues
theoretically showed that the stationarity assumption may be avoided by
estimating transfer entropy from an ensemble of realizations. Such an ensemble
is often readily available in neuroscience experiments in the form of
experimental trials. Thus, in this work we combine the ensemble method with a
recently proposed transfer entropy estimator to make transfer entropy
estimation applicable to non-stationary time series. We present an efficient
implementation of the approach that deals with the increased computational
demand of the ensemble method's practical application. In particular, we use a
massively parallel implementation for a graphics processing unit to handle the
computationally most heavy aspects of the ensemble method. We test the
performance and robustness of our implementation on data from simulated
stochastic processes and demonstrate the method's applicability to
magnetoencephalographic data. While we mainly evaluate the proposed method for
neuroscientific data, we expect it to be applicable in a variety of fields that
are concerned with the analysis of information transfer in complex biological,
social, and artificial systems.Comment: 27 pages, 7 figures, submitted to PLOS ON
Histopathological image analysis : a review
Over the past decade, dramatic increases in computational power and improvement in image analysis algorithms have allowed the development of powerful computer-assisted analytical approaches to radiological data. With the recent advent of whole slide digital scanners, tissue histopathology slides can now be digitized and stored in digital image form. Consequently, digitized tissue histopathology has now become amenable to the application of computerized image analysis and machine learning techniques. Analogous to the role of computer-assisted diagnosis (CAD) algorithms in medical imaging to complement the opinion of a radiologist, CAD algorithms have begun to be developed for disease detection, diagnosis, and prognosis prediction to complement the opinion of the pathologist. In this paper, we review the recent state of the art CAD technology for digitized histopathology. This paper also briefly describes the development and application of novel image analysis technology for a few specific histopathology related problems being pursued in the United States and Europe
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