Help for simulation of task paradigm

[leotozzi88]

Dear Experts,

My situation is as follows: I have some fMRI data recorded during a task paradigm. My task is a block design and I have reason to believe that it will activate a specific set of brain regions. I would like to run a simulation using parameters corresponding to my task design and then compare the results of the simulation to the real data I have.

I have some questions on how to build an event vector that I can feed to the simulation, similarly to what you have shown in your paper.

First of all, does it make sense to model the stimulus as a "on-off" vectors of 0s and 1s?

This is how I did it so far:

# Set up stimulus
import neurolib.utils.stimulus as stim

task_duration = 148*1000  #duration of task
block_duration = 16.74*1000  #duration of a block
dt = 0.1

block1 = stim.StepInput(
    step_size=1, start=25.86*1000, end=25.86*1000+block_duration, n=1
)

block2 = stim.StepInput(
    step_size=1, start=67.96*1000, end=67.96*1000+block_duration, n=1
)

block3 = stim.StepInput(
    step_size=1, start=109.86*1000, end=109.86*1000+block_duration, n=1
)

stimvec=block1+block2+block3
no_input=stim.ZeroInput(n=1)

plt.plot(stimvec.as_array(task_duration, dt).T)

The result is this plot:

Then I created my model using a duration matching my task and using the parameters you used in the paper:

aln = ALNModel(Cmat = Cmat, Dmat = Dmat )
aln.params['duration'] = 148*1000
aln.params["mue_ext_mean"] = 2.56
aln.params["mui_ext_mean"] = 3.52
aln.params["b"] = 4.67
aln.params["tauA"] = 1522.68
aln.params["sigma_ou"] = 0.40

# Here I add the stimulus to the model
stimvec_mdl=stimvec.to_model(aln)
stimvec_mdl[non_stim_areas, :] = 0 # Here non_stim_areas are the indeces of the areas that I expect not to be activated by the stimulus and I set them to 0 (an alternative would be to set them to "no_input" defined above)

# Here I set the stimulus as current
aln.params["ext_exc_current"] = stimvec_mdl

First of all, does the above make sense?

Second, in your paper you multiplied the stimulus by a certain value before assigning it to "ext_exc_current". What does this value represent and what is a good value?