Statistical Analysis Stack Exchange
Statistical Analysis Stack Exchange

Questions tagged [neuroimaging]

Various techniques to create a visual representation of the activity of nervous systems, such as fMRI, EEG, MEG, PET, etc.

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40,000 neuroscience papers might be wrong

I saw this article in the Economist about a seemingly devastating paper [1] casting doubt on "something like 40,000 published [fMRI] studies." The error, they say, is because of "erroneous statistical assumptions." I read the paper and see it's…
R Greg Stacey
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How to interpret PCA on time-series data?

I am trying to understand the use of PCA in a recent journal article titled "Mapping brain activity at scale with cluster computing" Freeman et al., 2014 (free pdf available on the lab website). They use PCA on time series data, and use the PCA…
statHacker
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A paper mentions a "Monte Carlo simulation to determine the number of principal components"; how does it work?

I'm doing a Matlab analysis on MRI data where I have performed PCA on a matrix sized 10304x236 where 10304 is the number of voxels (think of them as pixels) and 236 is the number of timepoints. The PCA gives me 236 Eigenvalues and their related…
chainhomelow
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The best way for clustering an adjacency matrix

I've had a hard time interpreting resulting clusters of an adjacency matrix. I have 200 relatively big matrices representing subjects that contains partial correlations (z scores) of time series (neural data). The goal is to cluster those 210…
Fahd
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Large number of correlations with MRI region of interest (ROI) variables: What adjustment should I perform?

In our group, we have measured grey matter volumes of about 20 regions of interest (ROI) and frequency of cannabis use. Now, we would like find out whether cannabis use is associated with grey matter volumes of any of the measured brain regions.…
zarat
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What is Bartlett's theory?

This neuroimaging paper has been cited thousands of times. In it, a method is proposed for computing the correlations among several seed regions and all other brain voxels. Part of this method involves z-scoring Fisher z values: To combine…
user28511
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5-way interaction

I am running a mixed factors ANOVA for a brain imaging study on language processing. The design includes four within-subject factors: complexity: simple/complex; agreement: correct/number violation/gender violation; hemisphere: left/right; region:…
José Alemán Bañón
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What does the number of independent components produced by ICA depend on?

I'm a student working on my bachelor thesis performing independent component analysis (ICA) on some fMRI data using MELODIC FSL. I would like to ask some questions regarding the results of ICA. Usually I obtain about 50 components per subject but…
Laura Palacio
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Visualization of a nondirected graph with nodes in specific positions

I have a variety of brain regions and information about how they're connected. (Not FMRI in this case, but the diffusion information about the white matter tracts connecting gray matter regions.) I'd like to graph this information sensibly to…
Thomas
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Is Fisher's z transformation necessary when comparing the variances of correlation coefficients?

I am working on functional connectivity between brain regions, where functional connectivity is represented by the Pearson correlation coefficient between the time series (fMRI) of brain regions. I am interested in the dynamics of functional…
Samira
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Removing nuisance PCA components from the fMRI data

So in attempting to replicate analysis pipeline from Tambini & Davachi, PNAS 2013, Persistence of hippocampal multivoxel patterns into postencoding rest is related to memory I'm hoping to use PCA as a noise reduction technique in MATLAB but I have…
chainhomelow
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Comparing Functional Connectivity as measured by fMRI

This question has been giving me a headache for a while so I'll define the problem before asking the question. fMRI is a measure of Blood Oxygenation Level Dependent signal. Higher the blood oxygenation, higher the signal. Of course, there is noise…
user84405
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Recommendation for books/notes for linear mixed effect models for longitudinal data?

I'm a beginner in data analysis who needs to learn (say in a period of 2 to 3 weeks or so) the key ideas and techniques in the linear mixed effect models for longitudinal data. I'll apply them in computational neuroscience, for shape analysis. I'd…
Mathmath
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What is a null conjunction analysis in an fMRI study?

I'm reading an article, The commonality of neural networks for verbal and visual short-term memory (Majerus et al., J Cogn Neurosci 2010 22(11): 2570), about brain imaging in which the results are analysed with multiple analyses. One of them is a…
Mien
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I have p >> n and no overfitting, why?

I try to classify a brainstate (binary problem) on fMRI-data using a SVM (scikit-learn, which wrapps libsvm). Also I use clusters arround local maxima in group-level TMaps as mask for the subject scanns, leading to roughly p=1500 features. Given…
Uzaku
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