Typical processing streams

Homer3 enables you to create your own processing stream files in the Process Stream GUI. This document provides typical processing streams that are used to analyze fNIRS dataset in Homer3 toolbox.

Basic configuration file

The basic processing streams typically include four functions:
a) hmrR_Intensity2OD: converts raw data to optical density;
b) hmrR_BandpassFilt: performs a band-pass filter on optical density data;
c) hmrR_OD2Conc: converts the filtered optical density to hemoglobin concentration;
d) hmrR_BlockAvg: and finally calculates the average hemodynamic response function (HRF).

GLM

You can also estimate the HRF using GLM analysis by incorporating the GLM function in the basic stream. The following processing stream provide a typical processing and parameters for short-separation regression using GLM approach, typically including four functions:
a) hmrR_Intensity2OD: converts raw data to optical density;
b) hmrR_BandpassFilt: performs a band-pass filter on optical density data;
c) hmrR_OD2Conc: converts the filtered optical density to hemoglobin concentration;
d) hmrR_GLM: and finally estimates the HRF using GLM analysis.



Here, these parameter settings build a design matrix with Gaussian basis functions, 3 drift regressors AND with a short separation regressor based on the nearest SS channel.