Getting started with Artinis NIRS data
Artinis Medical Systems BV is a Dutch company that develops and produces systems for functional NIRS. Artinis has multiple hardware designs, which all work with the same Oxysoft acquisition and analysis software.
The data that is recorded with Oxysoft is organized in various files: all data recorded during a measurement is contained in binary .oxy3 or .oxy4 files. The information about the transmitter and receiver optodes is represented in an optode template, which is an XML file. After data acquisition some processing can be done using OxySoft, the results of this are stored in a project file, which again is an XML file.
The oxy3/oxy4 file contains the optical data and data from the ADC-channels. The file will also contain any triggers recorded during the measurement, which allow for synchronization with a stimulus presentation computer. In FieldTrip we can use ft_read_header and ft_read_data to read the content, but usually we prefer to use the higher level ft_preprocessing
The optode template contains the layouts of the transmitting and receiving optodes. This file contains different groups of layouts, also called optode templates or montages. Each indiviudal layout has an unique ID, which is stored with the measurement. It can be read in using ft_prepare_layout and used for plotting. See also the /tutorial/layout and /tutorial/plotting tutorial.
The project file can contain data that was added after the measurement, e.g. events extracted from the trigger channel, or events that were manually added after the measurement. This makes the project file relevant in ft_definetrial and Artinis provides a custom trial function to parse this file and use it for segmenting the continuous data in trials. Furthermore the project file can contain spatial 3D MNI-coordinates of the optodes. Note that the project file can refer to multiple recordings, but also that one oxy3/oxy4 file can be included in multiple project files. This means that there is no guaranteed unique mapping between oxy3/oxy4 files and project files.