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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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Typical and minimum voxel sizes for various field strength MRI machines?

Hoping somebody can give me some real world numbers on the typical capabilities of 3T and 7T MRI machines in terms of there minimum voxel size (specifically in relation to there use in fMRI studies if ...
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What methods exist for converting channel-wise directed (effective) connectiviy estimates to ROI-wise connectivity estimates?

I am reading up on directed connectivity estimates (e.g. Granger causality, DTF, dDTF) in an attempt to find a method that allows me to appropriately convert channel-wise connectivity estimates into ...
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19 views

What is the difference between an Atlas and a Parcellation?

I come from a computer science background and am just starting out in the area of analyzing brain imaging data (fMRI predominantly) and while going through some of the literature, I am kind of ...
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fMRI datasets for emotion states

Would there be any open fMRI datasets available that specifically analyse a subjects emotional state? The objective is to apply deep learning methods to categorise subjects emotional state based on ...
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23 views

fMRI ROI analysis: independence

In a 2x2 factorial, is it appropriate to look at an interaction at the second-level, group analysis (e.g., using SPM) and define this as an ROI to restrict follow-up main effect contrasts? Or is this ...
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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 ...
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23 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 ...
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26 views

Is subcortical brain possible to investigate with functional resonance imaging (fMRI)?

Signals from Amygdala may be confounded and according to Huettel et al.,2009, "subcortical nuclei such as the caudate, putamen and the thalamus are all sufficiently large to encompass multiple ...
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25 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 ...
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Still-high spatial resolution of (smoothed) fMRI activation clusters!

There appears to be a mismatch between how fMRI results are presented graphically and how we know the analyses are normally done. Say we do a group-level analysis for some contrast of interest, and ...
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1answer
53 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 ...
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1answer
158 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 ...
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Voxel wise comparison (Voxel Based Morphometry or VBM) across subjects in fMRI studies

I am new to fMRI field. In many fMRI studies like This Study a voxel wise comparison is made across subjects and controls . As we know that dataset in fMRI in the form of 3D matrix like Subjects x ...
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64 views

Temporal and frequency analysis of brain network to study autism disorders

I know it has shown in the literature that autism disorder affects brain network connectivity based on rs-fMRI data (Plitt, Barnes, & Martin, 2015). They have local over-...
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53 views

Visualization of ICA (Independent component analysis) results to the brain spatial regions

In Calhoun et al, 2002, on the application of ICA to fMRI on page 4, ICA data is mapped to the different regions in the brain. Brain Activation Maps Question My specific question here is that when ...
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23 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 ...
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1answer
21 views

EEG in fMRI: High frequency “deltas” in EEG after gradient artifact removal

EEG was taken inside an fMRI, including ECG, EXG and eye tracking system. Sampling rate was 5000 Hz. Sync box was used. After running Brain Product Analyzer gradient artifact removal (using markers ...
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48 views

Is synchronization between the MRI scanner and the stimulus presentation necessary for every trial?

I'm planning an event-related fMRI-experiment to investigate the difference in processing natural and computer-generated facial emotion expressions. I've seen a lot of studies that synchronize the ...
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How to implement an incidental processing task without a fMRI-compatible response box?

Background I'm planning an event-related fMRI-experiment to investigate the difference in processing natural and computer-generated facial emotion expressions. My supervisor and I are discussing ...
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48 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 ...
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21 views

(Flavours of) Psychophysiological Interactions

The paper by Fischmeister et al. 2016 (Cortex) analysed fMRI task-related connectivity patterns, for two tasks that relied vs did not rely on recursive reasoning. Namely, they found "increased ...
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1answer
148 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 ...
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29 views

SPM5 - contrast vectors too long when applied to a new SPM.mat file

Background: I am using fMRI individual level analysis data from my supervisor's previous paper. Before I can perform PPI on the data, I need to update the 1st level analysis batch files since they ...
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2answers
79 views

Can we identify specific emotions on the basis of fMRI scans?

I am looking for fMRI studies in which the emotional response of a person listening to music is visible in the fMRI scans, paralleled by a retrospective think aloud report of the person describing his/...
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1answer
154 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?
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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 ...
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86 views

What is Reaction time method? [closed]

I'm having some trouble with understanding Reaction Time (RT) method. I have a hypothesis that M occurs at B where M is a mental activity and B is a location in the brain. To verify it, I want to ...
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48 views

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 ...
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0answers
58 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: ...
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1answer
30 views

“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 ...
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1answer
286 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 ...
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1answer
21 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 ...
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67 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 ...
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1answer
57 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 ...
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2answers
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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, ...
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1answer
100 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 ...
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1answer
236 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 ...
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1answer
99 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 ...
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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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2answers
30 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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57 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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1answer
103 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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0answers
39 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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1answer
169 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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21 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
60 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?
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1answer
1k 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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62 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 ...
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1answer
72 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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0answers
51 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 ...