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fMRI: optimize the design of event related fMRI

Fa-Hsuan Lin edited this page Nov 2, 2019 · 1 revision

These Matlab scripts will optimize the timing of the stimulus presence based on specified constraints (e.g., the TR of fMRI acquisition, the duration of the experiment, the minimal inter-stimulus-interval allowed, etc). The output can be either a text file or a Matlab data (.mat) file, either one of which can be further exported to other stimulus presentation software, such as Presentation or E-PRIME.

Here is an example of the improvement of the "efficiency" of stimuli onsets in an event-related fMRI design.

Codes

You need to have all the files to run these scripts. Please download here.

Example 1:

This example attempts to optimize the timing of the stimulus presentation using the following parameters: HRF duration: 30 seconds HRF pre-stimulus duration: 6 seconds HRF basis function: canonical HRF basis TR= 2 seconds (fMRI data acquisition repetition time) Time step in optimizing the stimuli: 1 second Experiment duration: 4 min. (240 seconds) Experiment minimal inter-stimulus-interval (ISI): 1 second Total type of total stimuli: 1 Total number of stimuli: 64 Optimizing contrast: condition “1″ alone Optimization iterations: 100

Input code: efficiency_test1.m
Output Matlab mat file: ex1-opt_param_24-Nov-2008.mat
Output Text file: ex1-opt_param_24-Nov-2008.txt

Example 2:

This example attempts to optimize the timing of the stimulus presentation using the following parameters:

HRF duration: 30 seconds HRF pre-stimulus duration: 6 seconds HRF basis function: finite impulse response (FIR) function TR= 0.1 second (fMRI data acquisition repetition time) Time step in optimizing the stimuli: 1 second Experiment duration: 4 min. (240 seconds) Experiment minimal inter-stimulus-interval (ISI): 3 second Total type of total stimuli: 2 Total number of stimuli: 32 Optimizing contrast: between condition “2″ and condition “3″ Optimization iterations: 1000

Input code: efficiency_test2.m
Output Matlab mat file: ex2-opt_param_09-Jan-2017.mat
Output Text file: ex2-opt_param_09-Jan-2017.txt

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