Documentation

This page contains documentation for HOMER2.

Download sample data sets here:

Tutorials

Training Session 1

Basic training on using HOMER2 from the online training session from March 4, 2013. The training session is 60 min long.

Training Session 2

Recording of the training session from April 16, 2014. This session covered several questions including:

  • excluding channels based on signal level, SNR, and source-detector separation
  • Exporting HRF results
  • Looking at channel cross-correlations
  • Correction motion artifacts on OD rather than intensity
  • A review of the GLM capabilities of Homer
  • Some discussions about AtlasViewer

Displaying Different Channels Of Data in Homer2

This 4-min tutorial demonstrates how to select different channels of data to display. It shows how to select channels from individual sources or detectors, how to display data from multiple sources and detectors, and how to individually hide or deactivate specific channels of data.

Simple Probe

This is the basic introduction to the screen layout of HOMER2, how to view data from different sources and detectors, how to execute a simple processing script to convert from intensity to optical density to concentration, how to bandpass filter the data, and how to block average the response to a stimulus.

Waterfall Plot an Fixed Plot Range

A short tutorial showing the waterfall plot feature, selecting multiple channels of data to display, and fixing the plot range.

Exporting a Data Trace

This tutorial shows how to export data traces from the plot window by right clicking on the line within the plot window. You have the option of saving the single trace, or all traces visible in the plot window. They are saved to a text file where the first column is the time vector and each subsequent channel is the data for one of the channels. The top of each column is labeled to identify the data type and source and detector.

AtlasViewer Digitized Points File

This tutorial shows the basic format of the digits.txt file used by AtlasViewer to register an atlas to the subject. Download this sample data to follow along.

Register Atlas to Subject Digitized Points

This is a tutorial on using AtlasViewer to register the atlas to the 10-20 points (Nz,Iz,A1,A2,Cz) digitized on a subject. If the source and detector positions are digitized and the SD structure is available either from a .SD file or a .nirs file, this tutorial shows that you can also display the measurement list on the registered atlas. Download this sample data to follow along. Note that it is a good idea to save the the viewer state (under the File Menu) before closing AtlasViewer so that when you return, it comes back to the same state. Otherwise you may have to repeat the registration steps.

Register Atlas to Subject Digitized Points and run Monte Carlo Forward Model

This is a tutorial on using AtlasViewer to register the atlas to the 10-20 points (Nz,Iz,A1,A2,Cz) digitized on a subject. If the source and detector positions are also digitized, this tutorial shows you how to run the Monte Carlo photon migration forward model to calculate the sensitivity profile on the cortical surface. Download this sample data to follow along. Note that it is a good idea to save the the viewer state (under the File Menu) before closing AtlasViewer so that when you return, it comes back to the same state. Otherwise you may have to repeat the registration and Monte Carlo steps.

CORRECTION: As shown in this tutorial, you can have only the .SD file and not the .nirs file to provide the SD structure. Also, this tutorial describes the structure of the digpts.txt file.