SubCMap: subject and condition specific effect maps

Current methods for statistical analysis of neuroimaging data identify condition related structural alterations in the human brain by detecting group differences. They construct detailed maps showing population-wide changes due to a condition of interest. Although extremely useful, methods do not provide information on the subject-specific structural alterations and they have limited diagnostic value because group assignments for each subject are required for the analysis. In this article, we propose SubCMap, a novel method to detect subject and condition specific structural alterations. SubCMap is designed to work without the group assignment information in order to provide diagnostic value. Unlike outlier detection methods, SubCMap detections are condition-specific and can be used to study the effects of various conditions or for diagnosing diseases. The method combines techniques from classification, generalization error estimation and image restoration to the identify the condition-related alterations. Experimental evaluation is performed on synthetically generated data as well as data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database. Results on synthetic data demonstrate the advantages of SubCMap compared to population-wide techniques and higher detection accuracy compared to outlier detection. Analysis with the ADNI dataset show that SubCMap detections on cortical thickness data well correlate with non-imaging markers of Alzheimer's Disease (AD), the Mini Mental State Examination Score and Cerebrospinal Fluid amyloid-β levels, suggesting the proposed method well captures the inter-subject variation of AD effects

Evaluating of bootstrap procedures for fMRI data

Over the last decade the bootstrap procedure is gaining popularity in the statistical analysis of neuroimaging data. This powerful procedure can be used for example in the non-parametric analysis of neuro-imaging data. As fMRI data are complexly structured with both temporal and spatial dependencies, such bootstrap procedures may indeed offer an elegant solution. However, a thorough investigation on the most appropriate bootstrapping procedure for fMRI data has to our knowledge never been performed. Friman and Westin (2005) showed that a bootstrap procedure based on pre-whitening the temporal structure of fMRI time series is superior to procedures based on wavelets or Fourier decomposition of the signal, especially in the case of blocked fMRI designs. For time-series, several bootstrap schemes can be exploited though (see e.g. Lahiri, 2003). For the re-sampling of residuals from general linear models fitted on fMRI data, we examine more specifically here the differences between 1) bootstrapping pre-whitened residuals which are based on parametric assumptions of the temporal structure, 2) a blocked bootstrapping which avoids making such assumptions (with several variants like the circular bootstrap,. . . ), and 3) a combination of both bootstrap procedures. We furthermore explore whether the bootstrap procedures is best applied before or after smoothing the volume of interest. Based on real data and simulation studies, we discuss the temporal and spatial properties of the bootstrapped volumes for all possible combinations and nd interesting differences

The impact of cognitive training on cerebral white matter in community-dwelling elderly : one-year prospective longitudinal diffusion tensor imaging study

It has been shown that cognitive training (CogTr) is effective and recuperative for older adults, and can be used to fight against cognitive decline. In this study, we investigated whether behavioural gains from CogTr would extend to white matter (WM) microstructure, and whether training-induced changes in WM integrity would be associated with improvements in cognitive function, using diffusion tensor imaging (DTI). 48 healthy community elderly were either assigned to multi-domain or single-domain CogTr groups to receive 24 sessions over 12 weeks, or to a control group. DTI was performed at both baseline and 12-month follow-up. Positive effects of multi-domain CogTr on long-term changes in DTI indices were found in posterior parietal WM. Participants in the multi-domain group showed a trend of long-term decrease in axial diffusivity (AD) without significant change in fractional anisotropy (FA), mean diffusivity (MD) or radial diffusivity (RD), while those in the control group displayed a significant FA decrease, and an increase in MD and RD. In addition, significant relationships between an improvement in processing speed and changes in RD, MD and AD were found in the multi-domain group. These findings support the hypothesis that plasticity of WM can be modified by CogTr, even in late adulthood

Robust Group-Level Inference in Neuroimaging Genetic Studies

International audienceGene-neuroimaging studies involve high-dimensional data that have a complex statistical structure and that are likely to be contaminated with outliers. Robust, outlier-resistant methods are an alternative to prior outliers removal, which is a difficult task under high-dimensional unsupervised settings. In this work, we consider robust regression and its application to neuroimaging through an example gene-neuroimaging study on a large cohort of 300 subjects. We use randomized brain parcellation to sample a set of adapted low-dimensional spatial models to analyse the data. We combine this approach with robust regression in an analysis method that we show is outperforming state-of-the-art neuroimaging analysis methods

Modeling Social Sensory Processing During Social Computerized Cognitive Training for Psychosis Spectrum: The Resting-State Approach

Background: Greater impairments in early sensory processing predict response to auditory computerized cognitive training (CCT) in patients with recent-onset psychosis (ROP). Little is known about neuroimaging predictors of response to social CCT, an experimental treatment that was recently shown to induce cognitive improvements in patients with psychosis. Here, we investigated whether ROP patients show interindividual differences in sensory processing change and whether different patterns of SPC are (1) related to the differential response to treatment, as indexed by gains in social cognitive neuropsychological tests and (2) associated with unique resting-state functional connectivity (rsFC). Methods: Twenty-six ROP patients completed 10 h of CCT over the period of 4–6 weeks. Subject-specific improvement in one CCT exercise targeting early sensory processing—a speeded facial Emotion Matching Task (EMT)—was studied as potential proxy for target engagement. Based on the median split of SPC from the EMT, two patient groups were created. Resting-state activity was collected at baseline, and bold time series were extracted from two major default mode network (DMN) hubs: left medial prefrontal cortex (mPFC) and left posterior cingulate cortex (PCC). Seed rsFC analysis was performed using standardized Pearson correlation matrices, generated between the average time course for each seed and each voxel in the brain. Results: Based on SPC, we distinguished improvers—i.e., participants who showed impaired performance at baseline and reached the EMT psychophysical threshold during CCT—from maintainers—i.e., those who showed intact EMT performance at baseline and sustained the EMT psychophysical threshold throughout CCT. Compared to maintainers, improvers showed an increase of rsFC at rest between PCC and left superior and medial frontal regions and the cerebellum. Compared to improvers, maintainers showed increased rsFC at baseline between PCC and superior temporal and insular regions bilaterally. Conclusions: In ROP patients with an increase of connectivity at rest in the default mode network, social CCT is still able to induce sensory processing changes that however do not translate into social cognitive gains. Future studies should investigate if impairments in short-term synaptic plasticity are responsible for this lack of response and can be remediated by pharmacological augmentation during CCT

New advances in the Clinica software platform for clinical neuroimaging studies

International audienc

BrainStat: A toolbox for brain-wide statistics and multimodal feature associations

Analysis and interpretation of neuroimaging datasets has become a multidisciplinary endeavor, relying not only on statistical methods, but increasingly on associations with respect to other brain-derived features such as gene expression, histological data, and functional as well as cognitive architectures. Here, we introduce BrainStat - a toolbox for (i) univariate and multivariate linear models in volumetric and surface-based brain imaging datasets, and (ii) multidomain feature association of results with respect to spatial maps of post-mortem gene expression and histology, task-based fMRI meta-analysis, as well as resting-state fMRI motifs across several common surface templates. The combination of statistics and feature associations into a turnkey toolbox streamlines analytical processes and accelerates cross-modal research. The toolbox is implemented in both Python and MATLAB, two widely used programming languages in the neuroimaging and neuroinformatics communities. BrainStat is openly available and complemented by an expandable documentation

Multi-aspect testing and ranking inference to quantify dimorphism in the cytoarchitecture of cerebellum of male, female and intersex individuals: a model applied to bovine brains

The dimorphism among male, female and freemartin intersex bovines, focusing on the vermal lobules VIII and IX, was analyzed using a novel data analytics approach to quantify morphometric differences in the cytoarchitecture of digitalized sections of the cerebellum. This methodology consists of multivariate and multi-aspect testing for cytoarchitecture-ranking, based on neuronal cell complexity among populations defined by factors, such as sex, age or pathology. In this context, we computed a set of shape descriptors of the neural cell morphology, categorized them into three domains named size, regularity and density, respectively. The output and results of our methodology are multivariate in nature, allowing an in-depth analysis of the cytoarchitectonic organization and morphology of cells. Interestingly, the Purkinje neurons and the underlying granule cells revealed the same morphological pattern: female possessed larger, denser and more irregular neurons than males. In the Freemartin, Purkinje neurons showed an intermediate setting between males and females, while the granule cells were the largest, most regular and dense. This methodology could be a powerful instrument to carry out morphometric analysis providing robust bases for objective tissue screening, especially in the field of neurodegenerative pathologies

Multi-aspect testing and ranking inference to quantify dimorphism in the cytoarchitecture of cerebellum of male, female and intersex individuals: a model applied to bovine brains.

The dimorphism among male, female and freemartin intersex bovines, focusing on the vermal lobules VIII and IX, was analyzed using a novel data analytics approach to quantify morphometric differences in the cytoarchitecture of digitalized sections of the cerebellum. This methodology consists of multivariate and multi-aspect testing for cytoarchitecture-ranking, based on neuronal cell complexity among populations defined by factors, such as sex, age or pathology. In this context, we computed a set of shape descriptors of the neural cell morphology, categorized them into three domains named size, regularity and density, respectively. The output and results of our methodology are multivariate in nature, allowing an in-depth analysis of the cytoarchitectonic organization and morphology of cells. Interestingly, the Purkinje neurons and the underlying granule cells revealed the same morphological pattern: female possessed larger, denser and more irregular neurons than males. In the Freemartin, Purkinje neurons showed an intermediate setting between males and females, while the granule cells were the largest, most regular and dense. This methodology could be a powerful instrument to carry out morphometric analysis providing robust bases for objective tissue screening, especially in the field of neurodegenerative pathologies

A Comparative Study on Tissue Classification of Brain MR Images Using DIPY, SPM, and FSL Frameworks

Introduction: Complexity metrics have been suggested to characterize treatment plans based on machine parameters such as multileaf collimator (MLC) position. Several complexity metrics have been proposed and related to the Intensity-modulated radiation therapy (IMRT) quality assurance results. This study aims to evaluate aperture-based complexity metrics on MLC openings used in clinicaland establish a correlation between plan complexity and the gamma passing rate (GPR) for the IMRT plans.Material and Methods: We implemented the aperture-based complexity metric on MLC openings of the IMRT treatment plan for breast  and central nervous system (CNS) cases . The modulation complexity score (MCS), the edge area metric (EAM), the converted area metric (CAM), the circumference/area (CPA), and the ratio monitor unit MU/Gy are evaluated in this study. The complexity score was calculated using Matlab. The MatriXX Evolution was used for dose verification. The dose distribution was  analyzed using the OmniPro-I'mRT program  and the gamma index was assessed using two criteria: 3%/3 mm and 3%/2 mm. The correlation between the calculated complexity score and the GPR  is analyzed using SPSS.Results: The complexity score calculated by MCS, EAM, CAM, CPA, and MU/Gy shows breast plan is more complex than the CNS plan. The results of the correlation test of the complexity metric and GPR show that only the EAM metric shows a good correlation with GPR for both cases.Conclusion: EAM strongly correlates with the gamma pass rate. The MCS, CAM, CPA, and MU/Gy have a weak correlation with the GPR