Skip to content

Physiological and other continuous recordings

Example datasets with physiological data have been formatted using this specification and can be used for practical guidance when curating a new dataset:

Template:

sub-<label>/[ses-<label>/]
    <datatype>/
        <matches>[_recording-<label>]_physio.tsv.gz
        <matches>[_recording-<label>]_physio.json
        <matches>[_recording-<label>]_stim.tsv.gz
        <matches>[_recording-<label>]_stim.json

Optional: Yes

For the template directory name, <datatype> can correspond to any data recording modality, for example func, anat, dwi, meg, eeg, ieeg, or beh.

In the template filenames, the <matches> part corresponds to task filename before the suffix. For example for the file sub-control01_task-nback_run-1_bold.nii.gz, <matches> would correspond to sub-control01_task-nback_run-1.

The recording-<label> entity can be used to distinguish between several recording files. For example sub-01_task-bart_recording-eyetracking_physio.tsv.gz to contain the eyetracking data in a certain sampling frequency, and sub-01_task-bart_recording-breathing_physio.tsv.gz to contain respiratory measurements in a different sampling frequency.

Physiological recordings (including eyetracking) SHOULD use the _physio suffix, and signals related to the stimulus SHOULD use _stim suffix.

Physiological recordings such as cardiac and respiratory signals and other continuous measures (such as parameters of a film or audio stimuli) can be specified using two files: a gzip compressed TSV file with data (without header line) and a JSON file for storing the following metadata fields.

Note that when supplying a *_<physio|stim>.tsv.gz file, an accompanying *_<physio|stim>.json MUST be supplied as well.

Key name Requirement Level Data type Description
Columns REQUIRED array of strings Names of columns in file.
SamplingFrequency REQUIRED number Sampling frequency (in Hz) of all the data in the recording, regardless of their type (for example, 2400).
StartTime REQUIRED number Start time in seconds in relation to the start of acquisition of the first data sample in the corresponding neural dataset (negative values are allowed).

Additional metadata may be included as in any TSV file to specify, for example, the units of the recorded time series. Please note that, in contrast to other TSV files in BIDS, the TSV files specified for phsyiological and other continuous recordings do not include a header line. Instead the name of columns are specified in the JSON file. This is to improve compatibility with existing software (for example, FSL, PNM) as well as to make support for other file formats possible in the future.

Example *_physio.tsv.gz:

└─ sub-control01/
   └─ func/
      └─ sub-control01_task-nback_physio.tsv.gz 

(after decompression)

34    110    0
44    112    0
23    100    1

Example *_physio.json:

└─ sub-control01/
   └─ func/
      └─ sub-control01_task-nback_physio.json 
{
   "SamplingFrequency": 100.0,
   "StartTime": -22.345,
   "Columns": ["cardiac", "respiratory", "trigger"],
   "cardiac": {
       "Units": "mV"
   }
}

Recommendations for specific use cases

To store pulse or breathing measurements, or the scanner trigger signal, the following naming conventions SHOULD be used for the column names:

Column name Requirement Level Data type Description
cardiac OPTIONAL number continuous pulse measurement
respiratory OPTIONAL number continuous breathing measurement
trigger OPTIONAL number continuous measurement of the scanner trigger signal

For any other data to be specified in columns, the column names can be chosen as deemed appropriate by the researcher.

Recordings with different sampling frequencies or starting times should be stored in separate files.

If the same continuous recording has been used for all subjects (for example in the case where they all watched the same movie), one file MAY be used and placed in the root directory. For example, task-movie_stim.tsv.gz

For motion parameters acquired from MRI scanner side motion correction, the _physio suffix SHOULD be used.

For multi-echo data, a given physio.tsv file is applicable to all echos of a particular run. For example:

└─ sub-01/
   └─ func/
      ├─ sub-01_task-cuedSGT_run-1_physio.tsv.gz 
      ├─ sub-01_task-cuedSGT_run-1_echo-1_bold.nii.gz 
      ├─ sub-01_task-cuedSGT_run-1_echo-2_bold.nii.gz 
      └─ sub-01_task-cuedSGT_run-1_echo-3_bold.nii.gz 

The following RECOMMENDED metadata can also be added in the side-car JSON files of any *_<physio>.tsv.gz file.

Key name Requirement Level Data type Description
DeviceSerialNumber RECOMMENDED string The serial number of the equipment that produced the measurements. A pseudonym can also be used to prevent the equipment from being identifiable, so long as each pseudonym is unique within the dataset.
Manufacturer RECOMMENDED string Manufacturer of the equipment that produced the measurements.
ManufacturersModelName RECOMMENDED string Manufacturer's model name of the equipment that produced the measurements.
SoftwareVersions RECOMMENDED string Manufacturer's designation of software version of the equipment that produced the measurements.