Tagged: Magnetic resonance

Multiresolution hierarchical blind recovery of biochemical markers of brain cancer in MRSI

We present a multi-resolution hierarchical application of the constrained non-negative matrix factorization (cNMF) algorithm for blindly recovering constituent source spectra in magnetic resonance spectroscopic imaging (MRSI). cNMF is an extension of non-negative matrix factorization (NMF) that includes a positivity constraint on amplitudes of recovered spectra. We apply cNMF hierarchically, with spectral recovery and subspace reduction constraining which observations are used in the next level of processing. The decomposition model recovers physically meaningful spectra which are highly tissue-specific, for example spectra indicative of tumor proliferation, given a processing hierarchy that proceeds coarse-to-fine. We demonstrate the decomposition procedure on /sup 1/H long TE brain MRS data. The results show recovery of markers for normal brain tissue, low proliferative tissue and highly proliferative tissue. The coarse-to-fine hierarchy also makes the algorithm computationally efficient, thus it is potentially well-suited for use in diagnostic work-up.

Nonnegative matrix factorization for rapid recovery of constituent spectra in magnetic resonance chemical shift imaging of the brain

We present an algorithm for blindly recovering constituent source spectra from magnetic resonance (MR) chemical shift imaging (CSI) of the human brain. The algorithm, which we call constrained nonnegative matrix factorization (cNMF), does not enforce independence or sparsity, instead only requiring the source and mixing matrices to be nonnegative. It is based on the nonnegative matrix factorization (NMF) algorithm, extending it to include a constraint on the positivity of the amplitudes of the recovered spectra. This constraint enables recovery of physically meaningful spectra even in the presence of noise that causes a significant number of the observation amplitudes to be negative. We demonstrate and characterize the algorithm’s performance using /sup 31/P volumetric brain data, comparing the results with two different blind source separation methods: Bayesian spectral decomposition (BSD) and nonnegative sparse coding (NNSC). We then incorporate the cNMF algorithm into a hierarchical decomposition framework, showing that it can be used to recover tissue-specific spectra given a processing hierarchy that proceeds coarse-to-fine. We demonstrate the hierarchical procedure on /sup 1/H brain data and conclude that the computational efficiency of the algorithm makes it well-suited for use in diagnostic work-up.

Recovery of metabolomic spectral sources using non-negative matrix factorization

1H magnetic resonance spectra (MRS) of biofluids contain rich biochemical information about the metabolic status of an organism. Through the application of pattern recognition and classification algorithms, such data have been shown to provide information for disease diagnosis as well as the effects of potential therapeutics. In this paper we describe a novel approach, using non-negative matrix factorization (NMF), for rapidly identifying metabolically meaningful spectral patterns in1H MRS. We show that the intensities of these identified spectral patterns can be related to the onset of, and recovery from, toxicity in both a time-related and dose-related fashion. These patterns can be seen as a new type of biomarker for the biological effect under study. We demonstrate, using k-means clustering, that the recovered patterns can be used to characterize the metabolic status of the animal during the experiment.

Multi-resolution hierarchical blind recovery of biochemical markers of brain cancer in MRSI

We present a multi-resolution hierarchical application of the constrained non-negative matrix factorization (cNMF) algorithm for blindly recovering constituent source spectra in magnetic resonance spectroscopic imaging (MRSI). cNMF is an extension of non-negative matrix factorization (NMF) that includes a positivity constraint on amplitudes of recovered spectra. We apply cNMF hierarchically, with spectral recovery and subspace reduction constraining which observations are used in the next level of processing. The decomposition model recovers physically meaningful spectra which are highly tissue-specific, for example spectra indicative of tumor proliferation, given a processing hierarchy that proceeds coarse-to-fine. We demonstrate the decomposition procedure on /sup 1/H long TE brain MRS data. The results show recovery of markers for normal brain tissue, low proliferative tissue and highly proliferative tissue. The coarse-to-fine hierarchy also makes the algorithm computationally efficient, thus it is potentially well-suited for use in diagnostic work-up.