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 scan acquisition with stimulus presentation. Is synchronization between the scanner and the stimulus presentation necessary for every trial or is it enough if the scanner and the presentation are synchronized for the first trial?

This question is asked assuming that trials are jittered.


I have a Matlab script to present my stimuli and I've decided on the acquisition parameters (see below). I'll have to start the stimulus presentation with Matlab over a button press after a few dummy scans, as the scanner is not equipped with a synchronization box that tracks the scanner pulses and conveys them to my stimulus delivery computer. So, my presentation is only synchronized with the first scanner impulse.

The stimuli will be presented according to the following parameters and in the following order:

  1. Fixation cross for 600-800ms (length randomly varying in 25 ms steps)
  2. Video for 3 seconds (length not varied, but video type (natural or computer-generated) is randomized)
  3. Blank screen for 3-5 seconds (length randomly varying in 250 ms steps)

Acquisition parameters

  • TR = 1.7s, TE = 30ms
  • Whole brain acquisition
  • Voxel size 3x3 mm, slice thickness = 3.9mm
  • $\begingroup$ I'm not an fMRI expert, but it's far from optimal without synchronization so try to address the hardware limitation. It seems strange to me that the MRI is not ready for research - tried talking to your supervisor? There could be delays in the stimulus presentation. These delays could accumulate over time. One way to check these delays is using an external timer for the entire session and then compute the total time that your stimulus presentation resulted in (i.e. the sum of the durations of all time windows in MATLAB). $\endgroup$
    – noumenal
    Feb 14, 2018 at 14:52
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    $\begingroup$ Thank you noumenal for your opinion @noumenal. I totally agree with you about the hardware limitation. The scanner is generally used for clinical MRIs, which is why it it is not equipped for research purposes. We will just use it "on loan". Unfortunately I will have to deal with it as I already discussed this with my supervisor several times and he is not willing to invest in the hardware. I appreciate the idea with the external timer, I will implement this! With this information and the matlab trial protocoll I hopefully will have a slight idea of possible timing/delay effects. $\endgroup$
    – Hanna
    Feb 16, 2018 at 7:12
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    $\begingroup$ My professor-friend agrees with @noumenal. $\endgroup$
    – Seanny123
    Feb 16, 2018 at 18:10
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    $\begingroup$ @Seanny123 and professor-friend: Thank you very much for your input! I'm close now to get a synchronization box on loan, so hopefully I will be able to synchronize the scanner properly. $\endgroup$
    – Hanna
    Feb 19, 2018 at 9:43


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