Physiology Format

From 2015, CSPM uses a new file format for physiology. The old one was "hd2000", which ran separately, but which was very clunky.

Raw data

In the study data folder, the "raw" data is from whatever recording we had: Biopac, IFF-PHYS, instrunet,or WHH. The "phys" folder contains the data in a universal format. (The MRI equivalent is DICOM, PAR/REC, Analyze for the raw, and nifti for the converted.)

phys folder

Each channel is saved as a MATLAB timeseries object, with asynchronous (that is, not necessarily uniformly sampled) time values.

File	Structure	Fields	Subfields	Description
info[protocol_id].mat	P	.study_id		link to study in database
		.start_time		date-time: precise start time of recording Either to nearest second, or to nearest ms - this is relevant for physiology linked to slice times, for example. MySQL needs to be running 5.6.4 or later to record ms: http://dev.mysql.com/doc/refman/5.6/en/fractional-seconds.html
		.num_channels
		.channel{1:N}		cell array of channels
			.name	channel name
			.filename	mat file of timeseries object; variable has channel name. File is located in phys folder). The channels are synchronized such that the time is equivalent (this is critical for events). The time should start at 0. Time is in seconds.
			.sample_rate	empty for asynchronous
		.num_events
		.event{1:N}		Cell array of events; note that these are all events, not only those in the database. For analysis, we will use the database events and select segments of the timeseries. For this reason, the names don't matter too much, as we can select events for analysis and classify them at the same time we incorporate them into the database.
			.name
			.time	time in seconds

CSPM functions that read/write in this format

phys_format_whh.m: converts raw WHH data