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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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 ...
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8 views

How to read ROI location from .nii file?

NIFTI file formats (.nii) are used to store MRI/fMRI data in. I have a NIFTI file that is supposed to contain the locations of 375 brain regions. I am having trouble working with the file (it was ...
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1answer
4 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?
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18 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 ...
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13 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 ...
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17 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 ...
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14 views

Independent Component Analysis (ICA) in FSL vs fastICA: Why do they vary?

I was doing ICA in FSL via Melodic gui and fastICA in R on Auditory data from SPM http://www.fil.ion.ucl.ac.uk/spm/data/auditory/. No matter whether I keep the default settings in Melodic gui or ...
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1answer
34 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 ...
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18 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 ...
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1answer
53 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
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1answer
191 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 ...
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31 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 ...
3
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1answer
35 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 ...
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33 views

Brain extraction and save images as .img file

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 ...
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15 views

Descriptions of functions of brain areas listed in the Harvard Oxford Atlas

I am interested in finding a resource describing the functions of the areas listed in the Harvard Oxford Atlas of the human brain. It would be considered a bonus if it were machine readable (e.g. ...
4
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1answer
63 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 ...
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38 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 ...
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0answers
22 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, ...
2
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1answer
36 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
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1answer
27 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 ...
5
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1answer
71 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 ...
3
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1answer
65 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 ...
5
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1answer
86 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 ...
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1answer
225 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 ...
5
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1answer
71 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
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1answer
42 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 ...
5
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1answer
167 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?
3
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1answer
64 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 ...
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1answer
43 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 ...
7
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1answer
56 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 ...
4
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1answer
331 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-...
7
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3answers
567 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 ...
3
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1answer
287 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 ...
6
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1answer
87 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 ...
5
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1answer
47 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, ...
9
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2answers
787 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 ...
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2answers
492 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 ...