Unsupervised time course analysis of functional magnetic resonance imaging (fMRI) using self-organizing maps (SOMs)

Stephan G. Erberich; Matthias Fellenberg; Timo Krings; Stefan Kemeny; Wolfgang Reith; Klaus Willmes; Walter Oberschelp

doi:10.1117/12.349596

20 May 1999 Unsupervised time course analysis of functional magnetic resonance imaging (fMRI) using self-organizing maps (SOMs)

Stephan G. Erberich, Matthias Fellenberg, Timo Krings, Stefan Kemeny, Wolfgang Reith, Klaus Willmes, Walter Oberschelp

Author Affiliations +

Proceedings Volume 3660, Medical Imaging 1999: Physiology and Function from Multidimensional Images; (1999) https://doi.org/10.1117/12.349596
Event: Medical Imaging '99, 1999, San Diego, CA, United States

Abstract

Functional Magnetic Resonance Imaging (fMRI) data of the brain includes activated parenchymal voxels, corresponding to the paradigm performed, non-activated parenchymal voxels and background voxels. Statistical tests, e.g. using the general linear model approach of SPM or the Kolmogorov-Smirnov (KS) non-parametric statistic, are common 'supervised' techniques to look for activation in functional brain MRI. Selection of voxel type by comparing the voxel time course with a model of the expected hemodynamic response function (HRF) from the task paradigm has proven to be difficult due to individual and spatial variance of the measured HRF. For the functional differentiation of brain voxels we introduce a method separating brain voxels based on their features in the time domain using a self-organizing map (SOM) neural network technique without modeling the HRF. Since activation measured by fMRI is related to magnetic susceptibility changes in venous blood which represents only 2 - 5% of brain matter, preprocessing is required to remove the majority of non- activated voxels which dominate learning instead of real activation patterns. Using the auto-correlation function one can select voxels which are candidates of being activated. Features of the time course of the selected voxels can be learned with the SOM. In the first step the SOM is trained by the voxels time course, fitting its neurons to the input. After learning, the neurons have adapted to the intrinsic features space of the voxel time courses. Using the trained SOM, voxel time courses are presented again, now labeled by the neuron having the smallest Euclidean distance to the presented voxel time course. The result of the labeling and the learned feature time course vectors are compared visually with the p-value map of the KS statistic. With the SOM map one can visually separate the voxels based on their features in the time domain into different functional task related classes.

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Stephan G. Erberich, Matthias Fellenberg, Timo Krings, Stefan Kemeny, Wolfgang Reith, Klaus Willmes, and Walter Oberschelp "Unsupervised time course analysis of functional magnetic resonance imaging (fMRI) using self-organizing maps (SOMs)", Proc. SPIE 3660, Medical Imaging 1999: Physiology and Function from Multidimensional Images, (20 May 1999); https://doi.org/10.1117/12.349596

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