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5 votes
Accepted

What do NaNs represent in an SPM β-map?

Apparently, this can happen when your ROI is near the edge of the brain as reported here. The thread is pretty old though so this might have been fixed by today and there is another reason in your ...
awakenting's user avatar
5 votes
Accepted

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

I can see one case in which you still might analyze the data. This only works under three conditions: your paradigm has no variable durations of either stimulus presentations or breaks or others (or ...
awakenting's user avatar
5 votes

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

From meta-analyses that include musical emotion inductions, there is not much evidence that we can reliably distinguish between emotions in the brain, independent of the emotion induction procedure or ...
mrt's user avatar
  • 4,388
3 votes

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

See https://www.reddit.com/r/neuro/comments/5y4pta/does_anyone_know_where_i_can_find_a_repository_of/ for a similar question. Websites that were posted there include http://www.humanconnectome.org/...
honi's user avatar
  • 1,875
3 votes
Accepted

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

The coefficient is the measure of how strongly the given factor predicts the dependent variable, or in other words how much of the variance in the dependent variable can be explained by that factor. ...
Henry Brice's user avatar
3 votes

Activation of brain reasoning areas during dreaming

I cannot answer from fMRI's, but this theory conflicts with other anecdotal evidence from medicine. In sensory deprivation, or under psychotomimetic substances, you can be awake and unimpaired ...
jobermark's user avatar
  • 139
3 votes
Accepted

How was fMRI performed before EPI became available?

Short answer Older image collection techniques like GRASS and FLASH are slower than EPI, but still fast enough to operate within the time span of the neurovascular delay. Background The speed of ...
AliceD's user avatar
  • 20.7k
3 votes
Accepted

Does only the time-series data of fMRI matter or does spatial distribution of the signal values also matter?

Usually, but not always, fMRI timeseries are used to compute functional connectivity by calculating Pearson correlations among voxels or ROIs. The equation for the Pearson correlation can be written ...
Bryan Krause's user avatar
  • 7,436
2 votes

Generate fMRI from neurotransmitter consumption

It is not clear what neurotransmitter you are interested in, but one model that relates the PET ligand affinity to the cerebral blood volume (CBV) from fMRI looks like this: Source: Neurovascular ...
noumenal's user avatar
  • 628
2 votes
Accepted

Generate fMRI from neurotransmitter consumption

The simplest equation for getting a BOLD signal from neurotransmitter that I could find was in "Tracing Problem Solving in Real Time: fMRI Analysis of the Subject-paced Tower of Hanoi", which itself ...
Seanny123's user avatar
  • 8,853
2 votes

Open access 7T resting-state fMRI dataset

The Nighres project has released some 7T MRI datasets and tools to run them. You can read the paper on the tools here, and download the datasets from NITRC here.
Scott Edmunds's user avatar
2 votes

fMRI images: In-plane resolution, slice thickness

The information you seek is contained in the header of the image file. Matlab has open source tools for reading the header information. e.g., http://www.mathworks.com/matlabcentral/fileexchange/29344-...
sometimes_sci's user avatar
2 votes

MRI images upside-down in FSLVIEW

Simply fslreorient2std will orient the images as you would expect. From https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Orientation%20Explained: fslreorient2std - this ...
Jonathan's user avatar
  • 121
2 votes

Open fMRI data?

There was recently an issue about repositories for neuroimaging data. I just copied the table listing all of them from this paper. (Feel free to add links, I will do so when I have more time.) Title, ...
2 votes

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

Short answer Pleasant and unpleasant music activate other areas of the cortex, potentially allowing for differentiation of music-related emotions based on fMRI scans alone. Background An fMRI study ...
AliceD's user avatar
  • 20.7k
2 votes

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

I must say I am not an expert, but the following sources look helpful: Gao et al. (2013) write The voxel value in the resulting dataset represents the number of streamline samples passing ...
AliceD's user avatar
  • 20.7k
2 votes

"st" global variable in SPM8

it seems that it is a struct variable that is central to how images are visualized in spm. I found a description in the spm source code in this github repository (I linked to the exact line where it ...
awakenting's user avatar
2 votes

What does fMRI data look like after pre-processing?

The MRI signal is a small electrical current induced in the receiver coil by the precession of magnetization during resonance, i.e., a manifestation of Faraday's Law of Induction, wherein a changing ...
AliceD's user avatar
  • 20.7k
2 votes

EEG in fMRI: High frequency "deltas" in EEG after gradient artifact removal

These seem to be simply gradient artifact remnants- Brain products analyzer didn't fully clean them. Looking over the spectrogram of another EEG before the gradient artifact removal- it seems as if ...
user2522941's user avatar
2 votes
Accepted

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

Short answer The mean diffusivity (MD) in diffusion tensor imaging is a sensitive, yet a rather non-specific measure. Changes in MD tell you that water movement is altered, yet why and how will have ...
AliceD's user avatar
  • 20.7k
2 votes

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

Note. I initially scan read the question, I have rewritten my answer as a consequence, and due to the comments given. As highlighted by others here Multi-voxel pattern analysis (MVPA) is an ...
Comte's user avatar
  • 1,196
2 votes
Accepted

Temporally truncate BOLD data

It looks like fslroi is the tool I'm looking for. To temporally truncate a scan the usage would be ...
G Warner's user avatar
  • 141
2 votes
Accepted

View fMRI results with AAL3 atlas

I think to use the MRIcorn is the easiest way, You can put the AAL3v1.nii.gz and AAL3v1.nii.txt into the mricron-templates folder. by the way which software you use to do fMRI meta-analysis? best, ...
Hui Zheng's user avatar
2 votes
Accepted

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

Interestingly enough, I myself have been reading papers like these for some weeks. Although I think your question does not have a correct answer (since it is a little bit open) I can try to give my ...
JFR's user avatar
  • 76
2 votes

Both using a strong magnetic field, why does TMS affect the brain but not MRI?

Relevant for the reaction of a physical system to an excitation is most of all the frequency spectrum of the signal. Most signals have a center frequency and a bandwidth, i.e. you can specify ...
oliver's user avatar
  • 121
1 vote
Accepted

How to fix a nii or rec file with partial volume

I found the solution using the python package nibabel. The code is rather simple. If filename is your nii, or rec file use: ...
Josh Albert's user avatar
1 vote

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

The biology underlying the BOLD response is much slower than typical TRs, so I would say on one hand it doesn't really matter because the TR interval is not the time scale that matters. On the other ...
Bryan Krause's user avatar
  • 7,436
1 vote
Accepted

What type of data can we get from fMRI to calculate correlations?

The BOLD response is used in fMRI to provide a quantified measure of activation: https://en.wikipedia.org/wiki/Haemodynamic_response. It is based on the ratio of oxygenated vs. non-oxygenated blood, ...
Cameron Brick's user avatar
1 vote
Accepted

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

This is not a circular question. In fact, using fMRI to create targets is useful to determine TMS targets outside of the motor cortex or visual cortex. See the study here that used fMRI during a task ...
velvetshelter's user avatar

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