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 |
|---|---|---|---|---|
| phys[protocol_id].mat | phys | .study_id | link to study in database | |
| .name | name | |||
| .start_time | date-time: precise start time of recording
| |||
| .num_channels | ||||
| .channel{1:N} | cell array of channels | |||
| .name | channel name | |||
| .type | "rec" (recorded) or "calc" (calculated) | |||
| .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 | |||
| .offset | time offset from phys.start_time | |||
| .calc_sourcechans | for calculated channels; cell array of "rec" channel names used to calculate "calc" channel | |||
| .descr | description (optional) | |||
| .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. | |||
| .time | time in seconds |
CSPM functions that read/write in this format
phys_format_whh.m: converts raw WHH data