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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Seminal Books of fMRI

I would like to know what books about fMRI do people consider as key or seminal. I am very familiar with a great amonut of MRI techniques, but I am sort of looking for a book in fMRI that really ...
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Does only the time-series data of fMRI matter or does spatial distribution of the signal values also matter?

I was denoising fMRI data using GLM and had a question regarding the “data” of fMRI in general. (For reference you can look at the “GLM” part of https://fmriprep.org/en/stable/outputs.html or https://...
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Both using a strong magnetic field, why does TMS affect the brain but not MRI?

Both TMS and MRI have strong magnetic field. Why we often assume MRI being very safe because it does not affect the brain while TMS is used to influence the brain?
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4 votes
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67 views

BOLD->functional connectivity->spectral graph theory (e.g. Atasoy 2016) vs BOLD->Fourier Analysis

My read of "Human brain networks function in connectome-specific harmonic waves" (Atasoy 2016) seems to be that you can model brain activity in terms of standing waves of the connectome (...
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3 votes
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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 ...
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Mapping FreeSurfer region numbers to GIFNiftyNet numbers

I'm trying to measure the DICE coefficient of brain segmentations by a highresnet model. For my ground truth, I'm using FreeSurfer segmentations. There is some overlap between the regions used by ...
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Has anyone tried using functional near-infrared spectropathy to quantitively measure sodium concentrations in the brain?

Functional near-infrared spectropathy "fNIRS", is a biophysics/medical technique that uses the near-infrared part of the electromagnetic spectrum (around 680nm to 810nm in wavelength) to ...
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1 vote
1 answer
174 views

View fMRI results with AAL3 atlas

I have an fMRI overlay that was output from meta-analysis software, so I only have the .nii results file, no raw data. I would like to view this file in conjuction with the AAL3 atlas. I usually use ...
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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 ...
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3 votes
0 answers
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 ...
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2 votes
1 answer
51 views

Temporally truncate BOLD data

I'm analyzing some resting-state data and some of the scans are 10 min while others are 7 min. I need to cut the last 3 min off of those with 10 min scans so everyone has 7 min of resting-state data. ...
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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, ...
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PLotting multiple z-scored images in Nilearn

I have 7 z-scored images correlated to the 7 components from cerebellar cerebellar derived ICA resting state components. Using nilearn or any other plotting packages for that matter I would like to ...
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2 votes
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225 views

Noise ceiling estimate is lower than model prediction in RSA?

I am using representational similarity analyses (RSA) to compare models to some fMRI data. As part of this analysis I have computed noise ceilings for each of my regions of interest (ROIs). What's ...
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1 vote
2 answers
101 views

Does the duration of the epoch of interest in fMRI need to be a multiple of TR?

I am designing an fMRI experiment whereby, for each trial, subjects need to listen to an auditory stimulus (of arbitrary duration), and subsequently give a rating for each stimulus. I intend to ...
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Reproducible Dynamic Causal Modeling/ model based effective connectivity analysis for fMRI

I am doing a Masters degree in Cognitive Neuroscience and was thinking on doing my master thesis on effective connectivity in Theory of Mind. I like the model-based approach of Dynamic Causal Modeling ...
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543 views

How to generate functional connectivity matrices after first-level analysis in CONN toolbox?

I have a single subject data(T1w and rs-fMRI BOLD). I am wanting to generate functional connecitivty matrix after preprocessing the raw fMRI. I already used CONN toolbox to do the entire preprocessing....
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What type of data can we get from fMRI to calculate correlations?

Lets say we want to compare the correlation between the activation one part of the brain and rise in value of other variable. The design would be within subjects. What is the data that we can receive ...
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1 vote
1 answer
31 views

task-fMRI to determine TMS site (online stimulation with that same task)?

I am planning an experiment whereby rTMS would be administered to subjects while they perform a language task, with the hopes of improving performance on this task as compared to sham stimulation. ...
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1 answer
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fMRI repetition time (TR) and stimulus duration

I realized that in many neuroscientific experiments, the duration of the stimulus (say the duration of a grating stimuli displayed to subjects) is considerably shorter than the "TR" (roughly speaking ...
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3 votes
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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 ...
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How to generate Structural connectivity(SC) and Functional connectivity(FC) matrices from raw fMRI data?

I am working with The Virtual Brain (TVB) software and require SC and FC matrices as inputs. I have raw rs-fMRI data (T1-w and DTI). Can someone please suggest an end-to-end pipeline for pre-...
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1 vote
1 answer
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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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2 votes
1 answer
476 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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50 views

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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1 vote
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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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3 votes
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25 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 ...
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3 votes
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29 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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4 votes
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35 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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8 votes
1 answer
973 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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3 votes
1 answer
671 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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51 views

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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69 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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2 votes
0 answers
256 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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3 votes
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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 ...
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1 vote
1 answer
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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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2 votes
0 answers
74 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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60 views

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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3 votes
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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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3 votes
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(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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4 votes
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434 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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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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1 vote
2 answers
98 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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5 votes
1 answer
495 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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3 votes
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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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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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Cognitive impairment in fibromyalgia

People suffering from Fibromyalgia (FM) and Chronic Fatigue Syndrome (CFS) often have memory and cognitive complaints. (Glass, 2006) In FM as in CFS, some abnormalities of cerebral blood flow have ...
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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 ...
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2 votes
0 answers
103 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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