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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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How to convert fmri brain volumes to brain graph [closed]

I am working with fMRI data of Alzheimer's Disease (AD) patients. I want to convert brain volumes to brain graph and then using different graph metrics, I want to classify the brain volumes in AD and ...
prashant mishra's user avatar
2 votes
0 answers
142 views

Oblique EPI in afni

It is my very first time with afni and I am having problems with the creation of the afni dataset from dicom images. I runned: ...
Marta's user avatar
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2 votes
1 answer
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"st" global variable in SPM8

I have some legacy preprocessing code that is designed to use SPM8. In the alignment function, it refers to a global variable st, which as far as I can tell is not ...
Dan's user avatar
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4 votes
1 answer
512 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 ...
user15099's user avatar
1 vote
1 answer
70 views

How to fix a nii or rec file with partial volume

The problem I have is that the MRI scan is stopped manually, before the exam card is completed. Thus data anaylsis programs read the header and expect a certain number of volumes but it has less, and ...
Josh Albert's user avatar
4 votes
0 answers
87 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 ...
chainhomelow's user avatar
3 votes
1 answer
76 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 ...
Marta's user avatar
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5 votes
2 answers
3k 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, ...
z8080's user avatar
  • 919
4 votes
1 answer
137 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 ...
Anoop Alex's user avatar
4 votes
1 answer
515 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 ...
AlphaOmega's user avatar
5 votes
1 answer
278 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 ...
Natalie's user avatar
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3 votes
0 answers
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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 ...
conjectures's user avatar
1 vote
2 answers
34 views

Generate fMRI from neurotransmitter consumption

As mentioned in this answer, it's possible to generate an fMRI BOLD signal from neurotransmitter consumption. What equation would be appropriate for this use?
Seanny123's user avatar
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3 votes
0 answers
65 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 ...
Seanny123's user avatar
  • 8,853
5 votes
1 answer
403 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 ...
Louis Thibault's user avatar
1 vote
0 answers
50 views

What does O- mean in a NIFTI file name of an MRI?

I am exploring brain MRI scans. Using MRIConvert, I converted dcm files to NIFTI. Some of the outputted NIFTI files have O- in their filenames and I could not figure out what does it mean. Example ...
gruangly's user avatar
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7 votes
2 answers
281 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 ...
grmccreath's user avatar
1 vote
0 answers
29 views

How to display Talairach Image in AFNI correctly?

I am using AFNI to display Talairach image, that is anat+tlrc.BRIK & anat+tlrc.HEAD . But the AFNI only shows part of the image. It looks like this: AFNI is ...
Shawn's user avatar
  • 161
3 votes
1 answer
69 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?
Seanny123's user avatar
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6 votes
1 answer
3k 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 ...
Louis Thibault's user avatar
1 vote
0 answers
95 views

How to convert .tlrc file to .orig file? [closed]

I have files: left_fg+tlrc.BRIK and left_fg+tlrc.HEAD. I want to know how to convert the files to ...
Shawn's user avatar
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4 votes
1 answer
141 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 ...
Shawn's user avatar
  • 161
3 votes
0 answers
66 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 ...
overwhelmed's user avatar
5 votes
1 answer
532 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 ...
machinery's user avatar
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1 vote
0 answers
55 views

reliability of fmri and pet [closed]

While I admit that pet/frmri scanning is possibly reliable when measuring physical aspects of the body, I would like to know how reliable it is when measuring cognitive aspects e.g. emotion. How ...
Anoop Alex's user avatar
2 votes
0 answers
73 views

(Co)Registration in the preprocessing pipeline

I have a general question about registration and coregistration in the preprocessing pipeline of fMRI images. For me it is not clear what this is. So, motion correction, slice time correction, ...
machinery's user avatar
  • 325
3 votes
1 answer
149 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.
machinery's user avatar
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3 votes
1 answer
92 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 ...
JoHKa's user avatar
  • 131
6 votes
1 answer
234 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 ...
user avatar
4 votes
1 answer
115 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 ...
Seanny123's user avatar
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5 votes
1 answer
129 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 ...
Seanny123's user avatar
  • 8,853
9 votes
1 answer
672 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 ...
Malz's user avatar
  • 91
5 votes
1 answer
302 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 ...
Louis Thibault's user avatar
6 votes
1 answer
95 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 ...
fast tooth's user avatar
6 votes
1 answer
581 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?
Fraïssé's user avatar
  • 359
3 votes
1 answer
94 views

Have the effects of MRIs and other electromagnetic devices on human psychology been studied?

What are the effects of MRIs and other electromagnetic devices on the human brain? Naturally they could move metals to or through the brain cell's membrane. I can also see the experience of being in a ...
user avatar
3 votes
1 answer
81 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 ...
Revious's user avatar
  • 1,429
3 votes
1 answer
69 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 ...
Louis Thibault's user avatar
7 votes
1 answer
274 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 ...
z8080's user avatar
  • 919
4 votes
2 answers
3k 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-...
14Gpc's user avatar
  • 45
11 votes
4 answers
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 ...
student's user avatar
  • 111
3 votes
1 answer
539 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 ...
without_direction's user avatar
7 votes
1 answer
136 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 ...
Alex Stone's user avatar
  • 9,390
5 votes
1 answer
56 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, ...
manuela sellitto's user avatar
10 votes
2 answers
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 ...
nrz's user avatar
  • 315
12 votes
2 answers
951 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 ...
Ruben's user avatar
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