fMRI: optimize the design of event related fMRI
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. 
You need to have all the files to run these scripts. Please download here.
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
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