Questions tagged [fmri]

For questions about methodology and tools related to functional magnetic resonance imaging. For general questions about brain-structure use neurobiology, and for general imaging questions use neuroimaging.

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12
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2answers
862 views

What are different ways to determine centroids of fMRI activation, their drawbacks and perks?

I'm reading an older article on bilingualism (Kim, Relkin, Lee, & Hirsch, 1997) for a seminar. They were interested in the spatial separation of two languages in early and late bilinguals. They ...
11
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4answers
2k views

Open fMRI data?

Are there any open fMRI datasets available on the internet? Experimental design doesn't matter much, since I would be working towards a new data analysis method. If the distributed data has been ...
10
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2answers
1k views

Plotting publication-quality ball-and-stick models of brain connectivity in 3D

I'm working on brain imaging (fMRI) and I'm looking for a way to plot brain effective connectivity (dynamic causal modeling) parameters between different brain regions in a 3D plot. The plotting ...
9
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1answer
590 views

How does glial cell activity influence fMRI, EEG signals?

Glial cells comprise about 80% of the cells in the human brain. But physiological models of EEG and fMRI often relate only to neuronal activity. How do glial cells affect large-scale imaging ...
8
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1answer
707 views

In fMRI analyses, what is the t-test actually comparing?

In a 1st-level fMRI analysis, it is unclear to me what the t-test performed for each voxel is actually comparing. I've seen this being described in one of two different ways: The t-test estimates how ...
7
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2answers
243 views

Open access 7T resting-state fMRI dataset

I'm looking for an open access dataset of 7-tesla resting state fMRI images of human subjects. I've been able to find one so far (http://www.nature.com/articles/sdata201454). However, I need images ...
7
votes
1answer
121 views

Is there any fMRI evidence for different "states of mind"?

If you've seen a snickers commercial, it goes something like "you are a different person when you are hungry". I'm interested if the person's brain actually looks different when observed through fMRI ...
7
votes
1answer
230 views

Why "fractional" anisotropy?

Why is Fractional Anisotropy (FA), a measure in diffusion tensor imaging, called "fractional"? I'd have thought "local", i.e. voxel-wise, would have been the correct way to qualify the anisotropy that ...
6
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1answer
497 views

What does fMRI measure exactly

It is true that blood flows to wherever the brain is most activated and does fMRI measure the blood flow inside of the brain through oxygen content?
6
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1answer
168 views

Are there any studies (fMRI scans, etc) showing why some people (supposedly) are more open to hypnotism?

In this article published in Harper's magazine back in 1996, journalist David Foster Wallace described his experience with hypnotist Nigel Ellery (see the last section of the article, titled "THE ...
6
votes
1answer
80 views

Reference request for creator of heuristic for processing fMRI data (T.Nichols)

I am using nilearn and nipy package for python processing FMRI data. When computing mask, it says: Compute and write the mask of an image based on the grey level This is based on an heuristic ...
6
votes
1answer
2k views

Why is my SPM batch job printing a warning repeatedly?

I'm aware of the ambivalence of cogsci.stacexchange with regards to asking questions about code, but this question really is about SPM, specifically, so I think that the domain-specific nature of my ...
5
votes
1answer
184 views

How to analyze event-related fMRI data with missing fMRI trigger in logfile?

I have the following problem: we conducted an event-related fMRI experiment using Presentation software to display the experiment. Usually each fMRI pulse/scan is logged in the presentation log file ...
5
votes
1answer
240 views

What do NaNs represent in an SPM β-map?

I've estimated a model for an fMRI dataset, so I now have a beta_*.nii file for each regressor in my model. In a seperate step, I've defined ROIs using marsbar and ...
5
votes
1answer
295 views

Is there a good entry-level tutorial for SPM?

The title pretty much says it all. I need to do some fMRI data analysis and I can't find any entry-level tutorials for Statistical Parameter Mapping (SPM). I've looked at some of the videos on the ...
5
votes
2answers
2k views

Difference between reverse inference and decoding (e.g. MVPA) in fMRI

Reverse inference, i.e. the use of brain activation (fMRI) data to infer the engagement of a certain mental function, is heavily criticised (e.g., Poldrack 2011, Neuron). At the same time, decoding, ...
5
votes
1answer
117 views

Neurophysiological indications of focus and motivation

Is there any way to detect a subject being focused or highly motivated (assuming that these two states are essentially the same) using any sort of external detection, such as fMRI or EEG? How would ...
5
votes
1answer
53 views

Is it reasonable to have a factor with only two levels in a carry-over design for an fMRI study?

I'm planning a carry-over design for an fMRI study. To save time, since it seems that I'll need a huge number of trials for my purpose, I'm wondering if it's reasonable to have a matrix 2x3x3, ...
5
votes
1answer
457 views

How can I visualize DTI tractography streamlines generated from FSL's probtrackX in 3D?

I currently have track files of diffusion tensor imaging (DTI) data generated from FSL's probtrackX tractography tool. What is the best software to visualize the streamlines from FSL in 3D?
5
votes
1answer
411 views

fMRI images: In-plane resolution, slice thickness

I have a set of fMRI images (.nii.gz). Now I want to infer the in-plane resolution and the slice thickness. Can this information and perhaps additional information be retrieved with FSL or Matlab? And ...
4
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1answer
123 views

How to get anatomical masks?

I recently read a paper called "An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions". I want to use the ...
4
votes
1answer
107 views

Can fMRI and EEG signals be generated from NEF models?

The basic function of the NEF is to map the outside world onto neurons, using the firing rates of the neurons. It also supports various neuron models. Have these firing rates been used to create EEG ...
4
votes
2answers
2k views

MRI images upside-down in FSLVIEW

I'm visualizing structural data in FSLVIEW, but the sagittal and coronal planes are both upside-down / not in the conventional orientation, i.e. rotated by 90º and 180º. I understand that this upside-...
4
votes
1answer
480 views

where can i find preprocessed fmri data set for alzheimer's disease

I want to work on identification of Alzheimer's patients based on given fMRI data.Basically, I want to implement the following paper https://www.ncbi.nlm.nih.gov/pubmed/25907414. Where can I get ...
4
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1answer
112 views

Activation of brain reasoning areas during dreaming

I would say that dreaming is like any conscious experience, except that objective reasoning is turned off. Do fMRI imaging studies indicate that the reasoning centers of the brain are inactive during ...
4
votes
1answer
407 views

What does 'Mean Diffusivity' tell me about the connectivity of cortical areas?

I am reading an article about changes in thalamic volume and connections in relation to age and I understand that thalamic volume decreases with age. The authors find that mean diffusivity (MD) in ...
4
votes
1answer
384 views

What is meant by "degrees of freedom" in fMRI?

I am reading the paper "Classical and Bayesian Inference in Neuroimaging" by Friston. In the introduction he says: "[...] a trivially small activation can be declared significant if there are ...
4
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0answers
19 views

Do I report all anatomical regions in a large significant cluster identified in functional connectivity seed-to-voxel analysis?

I am conducting a resting-state functional connectivity seed-to-voxel analysis on the 25 participants from the NYC test-retest dataset using the CONN toolbox with the Posterior Cingulate Cortex of the ...
4
votes
0answers
33 views

Timing accuracy in presentation of videos with different frame rates (with COGENT)

For our fMRI study we want to present videos of 3 seconds duration. The videos have different frame rates: 48 videos were recorded with 50 fps 16 videos were recorded with 25fps 64 videos were ...
4
votes
0answers
76 views

Good Resources for Learning Modeling of fMRI Data [closed]

As a neuroscience student who works with fMRI I'm competent at the standard univariate analyses and resting state analysis techniques in AFNI and MATLAB/SPM. However, I want to learn how to use models ...
3
votes
1answer
65 views

Can memory access be detected via fMRI?

Can the use of memory, in it's various forms (working memory, procedural, semantic), be detected and distinguished from one another via fMRI?
3
votes
1answer
72 views

How was fMRI performed before EPI became available?

How did fMRI work before Echo-planar imaging (EPI) became available? EPI allows fast imaging and high temporal resolution, but it became commercial in the second half of the '90s. How was it possible ...
3
votes
1answer
113 views

Slices and aquisition of fMRI

Is a slice obtained with functional MRI (fMRI) always 3-dimensional, i.e., x-y-z? I thought that a typical fMRI scan's total imaged volume would be 4D, i.e., made up of 3D slices plus time.
3
votes
1answer
76 views

Finding consciousness through EEG

I've read an article about the consciousness in vegetative patients. Adrian Owen is one of the neuroscientist making research on this field. The article published on "Le scienze" was about the usage ...
3
votes
1answer
41 views

Excluding psychometry and interview methods, is there any physical or molecular method that can confirm mild autism?

ASD is a set of very much heterogeneous symptoms with some common characteristics like lack of eye contact, lack of social guesswork, difficulty in learning unwritten social norms or conventions, ...
3
votes
1answer
597 views

What does fMRI data look like after pre-processing?

I wish to know what fMRI data looks like after preprocessing. My Understanding My understanding is that fMRI is MRI in time dimension that is we have repeated scans of brain volume. A voxel is a ...
3
votes
1answer
85 views

Why superimposing PET data on MRI scan images instead of doing fMRI scans?

I'm currently reading this paper: Savic & Lindström (2008). PET and MRI show differences in cerebral asymmetry and functional connectivity between homo- and heterosexual subjects. It certainly ...
3
votes
1answer
61 views

Are there any fMRI decoding papers examining the relationship between attentional cueing and activity in V1?

I'm interested in reading on the influence of exogenous attention on cortical representations in early visual areas, but so far my google-fu seems to be failing me. There seems to be some literature ...
3
votes
1answer
531 views

What are new and exciting research areas or applications in systems neuroscience? [closed]

Like the title says, what are new and exciting research areas or applications in systems neuroscience? I know the question is a broad one, so let me narrow it down a bit: I will get my master's ...
3
votes
0answers
21 views

On performing threshold-free-cluster-enhancement permutation tests--in combination with SPM--and then displaying the results on an MNI template

I'm trying out numerous comparison correction methods on my fMRI dataset and I've encountered multiple papers which used threshold free cluster enhancement, which I'd like to incorporate, but I'm ...
3
votes
0answers
20 views

slice spaing in rsFMRI

I have a rsFMRI sequence that includes slice spacing. I have not seen that before. Why anybody would add slice spacing between 2 measured slices? Is it a mistake or there is a rationale behind, eg ...
3
votes
0answers
43 views

What can combined EEG-fMRI tell us about the brain activity that two separate EEG and fMRI experiments cannot?

I am trying to get my head around what questions I can expect to have answered about brain activity that cannot be answered by doing two separate EEG and fMRI experiments. I am aware that fMRI ...
3
votes
0answers
23 views

How to identify the Default Mode Network in fMRI images?

I am relatively new to the realm of fMRI modality and the project that I am working on requires me to find the number of clusters in healthy and schizophrenic fMRI images by generating the Default ...
3
votes
0answers
26 views

Is it an issue to use a model for stimulus selection, when the same model is later tested against fMRI data based on those stimuli?

I am planning an fMRI experiment which looks at similarity of human brain activation when prompted with known words. The goal of the experiment is to compare the similarity of activation with ...
3
votes
0answers
36 views

Task-based fMRI dataset with very simple task (e.g. view stripes)

For my Bachelor thesis I need an fMRI dataset in order to look for causal relationships. I want to be able to confirm my work, so the causal relationships should already be known. Therefore, ideally ...
3
votes
0answers
58 views

How do different emotional intensity ratings within a condition influence the comparison across different conditions in an event-related fMRI task?

I'm planning an event-related fMRI-experiment to investigate the difference in processing natural and computer-generated expressions. For this, we recorded videos of 4 different actors posing fearful ...
3
votes
0answers
43 views

What is the effect of Gibbs artifact on multi voxel pattern analysis?

I have collected a EPI BOLD sequence data using Siemens skyra 3T. The voxel size is 3x3x3 mm^3. TR = 2s. I am seeing Gibbs artifact similar to the image: People have suggested to smooth the data to ...
3
votes
0answers
17 views

Convention for selection of summary slices in fMRI

Looking at papers, I often see an fMRI volume summarised by taking a single axial, sagittal and coronal slice (typically in MNI152 space). For an example see Figure 1 in de Bie et al, 2011 [1]. The ...
3
votes
0answers
61 views

How are abstract relations represented neurally?

It is known that concepts with similar attributes (color, shape... Etc.) are represented in a similar manner in the brain. However, is there any evidence of abstract relations, such as the as causal ...
3
votes
0answers
59 views

Brain extraction and save images as .img file [closed]

I have been working on Auditory data (from FIL) to read the .img files as numeric numbers of intensity of each voxels over time in array/matrix format using AnalyzeFMRI package in R. It gives me ...