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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How to find difference between data recorded for 1431 variables for X subjects, across 3 time points?

I am doing research using magnetoencephalography (MEG). I'm performing coherence analysis which, briefly, is a measure of neuronal synchronicity and functional connectivity. For each subject scanned ...
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13 views

Mediation model of time series data

I'm quite new to mediation analysis so hopefully I can clearly explain my problem. I wish to conduct a mediation model with a single mediating variable. The independent variable is a time series EEG ...
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regression analysis assessing the relationship between brain volume and behavioural score, main effect but what to do with the moderating variable?

I am conducting a regression analysis to look at the relationship between a behavioural score and brain volume. My sample is made of 2 patient groups: A and B. The model includes the following ...
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26 views

One sample T-test with covariates lmer? [duplicate]

I have 139 subjects (ID), with measurements taken at two time points (Time1, Time2), at 148 brain regions, a dependent measure called volume, and a covariate called thickness. Each subject has 148 ...
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34 views

For EEG analysis, why is it more efficient to use the raw data than images of the data?

Data Science publications for EEG analysis like EEGNet: A Compact Convolutional Network for EEG-based Brain-Computer Interfaces use the raw EEG data (see: github vlawhern/arl-eegmodels ) rather than ...
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How can I evaluate with R the interaction between a within-subject effect and a continuous variable at the subject level?

Scenario: 62 subjects did a selection task composed of 128 items, that can be divided into four conditions, because each item has a cue and a target (also other options but thats not of interest in ...
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26 views

Developing novel association measure with t-SNE

I am an MSc. student in computing and I am currently writing my thesis on radiogenomics (imaging genomics) for brain cancer research. I NEED YOUR HELP. My supervisor and I are thinking about ...
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204 views

Correction for multiple comparisons with multiple region of interest analyses

I'm having an issue with deciding how to correct for multiple comparisons with my structural MRI region of interest analyses. I have two groups, Group A and Group B, and am looking at cortical ...
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39 views

What type of analysis should i perform on my data

I have two groups of clinical subjects i.e healthy (25 subjects) and patient group (25 subjects) ,for each subject i have volumetric data for several regions of brain (15 regions ). I would like to ...
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328 views

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 ...
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1answer
48 views

Machine Learning application to neuroscientific data

I have the following question, and it is (for me) an open research question. I really don't have a feeling if it is a difficult question or a trivial one, getting a better feeling for approaches I ...
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210 views

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 ...
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78 views

when is linear svm with incremental / decremental learning a good idea?

The data that I want to classify are large 3D medical images (the input vectors are the pixels, order of 1M coefficients). It has been argued that a linear SVM is a good classifier for these data ...
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423 views

What's the meaning of the expansion coefficient of the AR model?

I am trying to understand the meaning of the phi parameter of the AR modeling. A bit of background: I am digging into statistical parametric mapping (SPM) and the prewhitening method, used to get rid ...
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7k views

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 ...
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493 views

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. ...
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489 views

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 ...
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487 views

How to do dimensionality reduction on a huge data set?

I am working with fMRI data of ~1000 subject. Each subject has a feature vector of ~150 million dimension. So I can only keep the feature vectors of ~10 subjects in memory. What are some algorithms ...
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666 views

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 ...
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3answers
2k views

Can you perform an ANOVA on r-values (correlation values)?

I am doing neuroimaging research yielding what is essentially a correlational analysis wherein my output is a brain's-worth of r-values (so like 15000 voxels worth of r-values). In this particular ...
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3answers
1k views

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 ...
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39 views

Map of activated brain regions for special feature extraction method

I have read the following paper: "Feature Extraction for fMRI-Based Human Brain Activity Recognition". The most useful point for me is the new method of extracting features from fMRI images. It ...
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34 views

Request for literature on applications of manifold-valued random variables in medical imaging

I'd appreciate some references/literature on the applications of manifold-valued random variables, i.e., random variables $X:\Omega\to M$, where M is a manifold (could be even infinite dimensional), ...
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81 views

Dealing with overlapping control/patient groups in SPM

Seeing as this question combines statistics, neuroimaging and programming I wasn't sure where to ask it, I apologize if it needs to be moved. I have data from a study where subjects were asked to ...
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2answers
14k views

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 ...
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3k views

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 (...
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432 views

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 ...
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1k views

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/...
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432 views

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 ...
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2answers
912 views

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'...
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1answer
5k views

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 ...