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Physiological and other continuous recordings

Physiological recordings

Physiological recordings such as cardiac and respiratory signals and other continuous measures (such as parameters of a film or audio stimuli) MAY be specified using a compressed tabular file (TSVGZ file) and a corresponding JSON file for storing metadata fields (see below).

Example datasets

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

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.

TSVGZ headers are specified in metadata files.

TSVGZ files MUST NOT include a header line, as established by the common-principles. As a result, when supplying a *_<physio|stim>.tsv.gz file, an accompanying *_<physio|stim>.json MUST be supplied as well.

The recording-<label> entity MAY 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.

The following tables specify metadata fields for the *_<physio|stim>.json file.

Key name Requirement Level Data type Description
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). This data MAY be specified with sub-second precision using the syntax s[.000000], where s reflects whole seconds, and .000000 reflects OPTIONAL fractional seconds.
Columns REQUIRED array of strings Names of columns in file.

Hardware information

Key name Requirement Level Data type Description
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.
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.

Additional metadata may be included as in any TSV file to specify, for example, the units of the recorded time series.

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"],
    "Manufacturer": "Brain Research Equipment ltd.",
    "cardiac": {
        "Description": "continuous pulse measurement",
        "Units": "mV"
        },
    "respiratory": {
        "Description": "continuous measurements by respiration belt",
        "Units": "mV"
        },
    "trigger": {
        "Description": "continuous measurement of the scanner trigger signal"
        }
}

Note how apart from the general metadata fields like SamplingFrequency, StartTime, Columns, and Manufacturer, each individual column in the TSV file may be documented as its own field in the JSON file (identical to the practice in other TSV+JSON file pairs). Here, only the Description and Units fields are shown, but you may use any other of the defined fields such as TermURL, LongName, and so on. In this example, the "cardiac" and "respiratory" time series are produced by devices from the same manufacturer and follow the same sampling frequency. To specify different sampling frequencies or manufacturers, the time series would have to be split into separate files like *_recording-cardiac_physio.<tsv.gz|json> and *_recording-respiratory_physio.<tsv.gz|json>.

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
Additional Columns OPTIONAL n/a Additional columns are allowed.

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 (and the recording-<label> entity MAY be used to distinguish these 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