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Getting started with Homer |
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Homer is a set of MATLAB scripts used for analyzing fNIRS data to obtain estimates and maps of brain activation. It has evolved since the early 1990s, first as the Photon Migration Imaging toolbox, then HOMER and Homer2, and development now continues as Homer3
The Homer software is described in the paper HomER: a review of time-series analysis methods for near-infrared spectroscopy of the brain. You can download Homer here on NITRC and you can also find more technical documentation on NITRC, for example on the .nirs file format.
FieldTrip can read data in the .nirs format that has been (pre)processed in Homer. This also offers an opportunity to process NIRS data formats in FieldTrip for which we not (not yet) have import functions: you can read them into Homer (or use one of the conversion scripts to convert the data to Homer format), save it to .nirs and then continue your analysis using the FieldTrip data structures and functions.
The Homer .nirs format is technically a MATLAB file in disguise. It contains multiple variables and structures that you should combine in one top-level nirs structure. You can read it with
nirs = load(filename, '-mat');
By specifying the output variable nirs to the MATLAB load function, all separate variables contained in the file are grouped together in a structure. Subsequently you could update/change that structure and save it back to disk with
save(filename, 'nirs', -struct');
The .nirs files are directly supported by the low-level ft_read_header, ft_read_data and ft_read_event functions. This also means that you can use the high-level ft_definetrial and ft_preprocessing functions for your analysis script, as explained in the tutorials.