This page contains documentation for the latest HOMER2 release v2.1.
This section is in the process of being updated.
If you have a matlab license:
1. Download latest homer2_*.zip zip file from the NITRC website and unzip. This package contains all the matlab scripts for Homer2_UI and AtlasViewerGUI.
2. In matlab, cd to the root homer2 folder in your file system and add paths for all folder under the homer2 root folder.
>> cd C:\…\homer2
>> p = genpath(pwd); addpath(p,’-end’);
3. Start AtlasViewerGUI – it should automatically find the default Colin atlas folder and the Monte Carlo executable, tMCimg.exe.
If you do not have a matlab license:
1. Download the latest AtlasViewerGUI_*.exe file from the NITRC website.
2. Download and install the 64-bit MATLAB Runtime installer, R2014b, for the latest Homer2 release v2.1. ( For release v2.0, download and install the 32-bit MATLAB Runtime installer, R2012b from the same mathworks website. )
3. Create Desktop shortcut to AtlasViewerGUI.exe or drag the AtlasViewerGUI.exe file directly to the Desktop.
4. Download the zip files, Colin.zip and tMCimg.zip (see links below), unzip and move the unzipped Colin and tMCimg folders to C:\Users\Public.
** NOTE : When extracting these zip files, check to make sure the Colin and tMCimg root folders are C:\Users\Public\Colin and C:\Users\Public\tMCimg respectivly and not a layer below that in C:\Users\Public\Colin\Colin and C:\Users\Public\tMCimg\tMCimg. Otherwise AtlasViewerGUI will not find them in the default location and will prompt the user to locate them at startup.
( For release v2.0, move the unzipped Colin and tMCimg folders to the desktop. )
5. Start AtlasViewerGUI.exe by double-clicking on the AtlasViewerGUI shortcut. It should automatically find the default Colin atlas folder and the Monte Carlo executable, tMCimg.exe.
On Linux and MacOS:
2. Follow the instructions in the section above, “If you have a matlab license”, since currently we do not provide the AtlasViewerGUI executable for Linux or MAC.
Download sample data sets here:
The documentation on usage can be found in the HOMER2 User’s Guide.
This section is in the process of being updated.
Basic training on using HOMER2 from the online training session from March 4, 2013. The training session is 60 min long.
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
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.
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.
A short tutorial showing the waterfall plot feature, selecting multiple channels of data to display, and fixing the plot range.
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.
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.
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.
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.