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 unit if measurement in fMRI because BOLD signal is measured on a typical voxel in different regions of the brain using gradient of the High frequency signal.

For example if we have fMRI scans say of D ADHD patients, V voxels and T time points in a fMRI study then how the fMRI data after pre-processing would be arranged in a matrix form.

If we assume that it is organized in D x V x T then we have a 3D scan of each brain on a time dimension. Since each 3D scan consists of voxels in the brain, and voxels are cubes that have 6 values around them, then where are those 6 values?

If a voxel is a cube, does it have a single value, or 6 potentially different values on each face? I know voxels have coordinates like that in the MNI coordinate system.

  • 1
    $\begingroup$ I am getting confused because in VBM analysis where we have unbalanced dataset on patients and controls . I am not getting how voxel wise comparison is done?.....after not being able to resolve that VMB question I sticked to basic and now want the deeper understanding about the fMRI dataset itself. $\endgroup$
    – Edison
    Commented Apr 24, 2018 at 14:19
  • $\begingroup$ There in VBM i was confused how VBM was being done on the two groups of unequal sizes for example in one study of 30 patients and 50 controls how group wise comparison was made using voxels. That problem triggered in my own brain voxels that I am not understanding the fMRI dataset correctly $\endgroup$
    – Edison
    Commented Apr 24, 2018 at 14:21

1 Answer 1


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 magnetic field induces a voltage in a nearby conductor. The BOLD response often used in fMRI measures the hemodynamic response, i.e., the relative levels of oxyhemoglobin and deoxyhemoglobin that can be detected on the basis of their differential magnetic susceptibility.

As any digital signal, there are limits to the resolution of fMRI, and is dependent on a number of factors (Kashou, 2014), including the field of view (x- and y- directions) and the slice thickness (z-direction). Multiplying the x, y and z sizes results in the total voxel size (Fig. 1). each voxel has 1 value, namely its respective BOLD response signal value.

- Kashou, A Practical Guide to an fMRI Experiment, Intech Open Science (2013)

Fig. 1. Time series of fMRI. source: Principles of fMRI


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