We use consecutive gaussian basis functions to model the HRF to allow for more flexiblity in the estimated shape of the HRF. This is quite different than using, for instance, a gamma function with specified width and delay parameters and then you estimate the beta which is just the amplitude. In the gamma function case, you get a single beta coefficient for the amplitude that you can do your statistics on. In the gaussian basis functions case, you need to multiple the series of beta coefficients by the basis functions to restore the shape of the HRF. Then you can measure the mean across a chosen time range of that HRF. Then you can look at the statistics of that mean across subjects.

Hello David,

Thank you very much, that makes sense. Can you just explain how to do this on Matlab for someone with very basic calculus background and little matlab skills? 

"you need to multiple the series of beta coefficients by the basis functions to restore the shape of the HRF. Then you can measure the mean across a chosen time range of that HRF. Then you can look at the statistics of that mean across subjects."

Also, if I choose to use the gamma function, do you recommend using the default parameters of [0.1 3.0 10.0 1.8 3.0 10.0]? Sorry I am not very familiar with this function.

I really appreciate your help!!

Hi Bruna,

That multiplication results in HRF, and Homer already outputs HRF with the output name "dcAvg". Please check out the link below. You can also export HRF.

https://github.com/BUNPC/Homer3/wiki/Output-Files

Meryem

Hi @dboas,

I ended up using the gamma function like you had mentioned. 

I was just wondering if there is a better way of exporting the betas in Matlab? I am only able to see them when I go in each subject's .mat file. Is there a way to get all betas for all subjects and conditions?

Thank you!