A simple and objective method for reproducible resting state network (RSN) detection in fMRI

Spatial Independent Component Analysis (ICA) decomposes the time by space functional MRI (fMRI) matrix into a set of 1-D basis time courses and their associated 3-D spatial maps that are optimized for mutual independence. When applied to resting state fMRI (rsfMRI), ICA produces several spatial independent components (ICs) that seem to have biological relevance - the so-called resting state networks (RSNs). The ICA problem is well posed when the true data generating process follows a linear mixture of ICs model in terms of the identifiability of the mixing matrix. However, the contrast function used for promoting mutual independence in ICA is dependent on the finite amount of observed data and is potentially non-convex with multiple local minima. Hence, each run of ICA could produce potentially different IC estimates even for the same data. One technique to deal with this run-to-run variability of ICA was proposed by Yang et al. (2008) in their algorithm RAICAR which allows for the selection of only those ICs that have a high run-to-run reproducibility. We propose an enhancement to the original RAICAR algorithm that enables us to assign reproducibility p-values to each IC and allows for an objective assessment of both within subject and across subjects reproducibility. We call the resulting algorithm RAICAR-N (N stands for null hypothesis test), and we have applied it to publicly available human rsfMRI data (http://www.nitrc.org). Our reproducibility analyses indicated that many of the published RSNs in rsfMRI literature are highly reproducible. However, we found several other RSNs that are highly reproducible but not frequently listed in the literature.Comment: 54 pages, 13 figure

A Scale-Space Medialness Transform Based on Boundary Concordance Voting

The Concordance-based Medial Axis Transform (CMAT) presented in this paper is a multiscale medial axis (MMA) algorithm that computes the medial response from grey-level boundary measures. This non-linear operator responds only to symmetric structures, overcoming the limitations of linear medial operators which create “side-lobe” responses for symmetric structures and respond to edge structures. In addition, the spatial localisation of the medial axis and the identification of object width is improved in the CMAT algorithm compared with linear algorithms. The robustness of linear medial operators to noise is preserved in our algorithm. The effectiveness of the CMAT is accredited to the concordance property described in this paper. We demonstrate the performance of this method with test figures used by other authors and medical images that are relatively complex in structure. In these complex images the benefit of the improved response of our non-linear operator is clearly visible

Outlier Detection in Heterogeneous Datasets using Automatic Tuple Expansion

Rapidly developing areas of information technology are generating massive amounts of data. Human errors, sensor failures, and other unforeseen circumstances unfortunately tend to undermine the quality and consistency of these datasets by introducing outliers -- data points that exhibit surprising behavior when compared to the rest of the data. Characterizing, locating, and in some cases eliminating these outliers offers interesting insight about the data under scrutiny and reinforces the confidence that one may have in conclusions drawn from otherwise noisy datasets. In this paper, we describe a tuple expansion procedure which reconstructs rich information from semantically poor SQL data types such as strings, integers, and floating point numbers. We then use this procedure as the foundation of a new user-guided outlier detection framework, dBoost, which relies on inference and statistical modeling of heterogeneous data to flag suspicious fields in database tuples. We show that this novel approach achieves good classification performance, both in traditional numerical datasets and in highly non-numerical contexts such as mostly textual datasets. Our implementation is publicly available, under version 3 of the GNU General Public License

Computerized Analysis of Magnetic Resonance Images to Study Cerebral Anatomy in Developing Neonates

The study of cerebral anatomy in developing neonates is of great importance for the understanding of brain development during the early period of life. This dissertation therefore focuses on three challenges in the modelling of cerebral anatomy in neonates during brain development. The methods that have been developed all use Magnetic Resonance Images (MRI) as source data. To facilitate study of vascular development in the neonatal period, a set of image analysis algorithms are developed to automatically extract and model cerebral vessel trees. The whole process consists of cerebral vessel tracking from automatically placed seed points, vessel tree generation, and vasculature registration and matching. These algorithms have been tested on clinical Time-of- Flight (TOF) MR angiographic datasets. To facilitate study of the neonatal cortex a complete cerebral cortex segmentation and reconstruction pipeline has been developed. Segmentation of the neonatal cortex is not effectively done by existing algorithms designed for the adult brain because the contrast between grey and white matter is reversed. This causes pixels containing tissue mixtures to be incorrectly labelled by conventional methods. The neonatal cortical segmentation method that has been developed is based on a novel expectation-maximization (EM) method with explicit correction for mislabelled partial volume voxels. Based on the resulting cortical segmentation, an implicit surface evolution technique is adopted for the reconstruction of the cortex in neonates. The performance of the method is investigated by performing a detailed landmark study. To facilitate study of cortical development, a cortical surface registration algorithm for aligning the cortical surface is developed. The method first inflates extracted cortical surfaces and then performs a non-rigid surface registration using free-form deformations (FFDs) to remove residual alignment. Validation experiments using data labelled by an expert observer demonstrate that the method can capture local changes and follow the growth of specific sulcus

Spatial-temporal data mining procedure: LASR

This paper is concerned with the statistical development of our spatial-temporal data mining procedure, LASR (pronounced ``laser''). LASR is the abbreviation for Longitudinal Analysis with Self-Registration of large-$p$-small-$n$ data. It was motivated by a study of ``Neuromuscular Electrical Stimulation'' experiments, where the data are noisy and heterogeneous, might not align from one session to another, and involve a large number of multiple comparisons. The three main components of LASR are: (1) data segmentation for separating heterogeneous data and for distinguishing outliers, (2) automatic approaches for spatial and temporal data registration, and (3) statistical smoothing mapping for identifying ``activated'' regions based on false-discovery-rate controlled $p$-maps and movies. Each of the components is of interest in its own right. As a statistical ensemble, the idea of LASR is applicable to other types of spatial-temporal data sets beyond those from the NMES experiments.Comment: Published at http://dx.doi.org/10.1214/074921706000000707 in the IMS Lecture Notes--Monograph Series (http://www.imstat.org/publications/lecnotes.htm) by the Institute of Mathematical Statistics (http://www.imstat.org