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[FIX] Clarify continuous recording metadata fields #167

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May 7, 2019
Merged

[FIX] Clarify continuous recording metadata fields #167

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9ef1adb
[FIX] Clarify continuous recording metadata fields
effigies Mar 6, 2019
f06b555
Merge remote-tracking branch 'upstream/master' into enh/timeseries_me…
effigies Apr 15, 2019
165347e
ENH: Make StartTime definition modality-neutral
effigies Apr 16, 2019
e5b6da5
ENH: Explicitly allow per-column metadata in physio files
effigies Apr 18, 2019
0b7a530
Update src/04-modality-specific-files/06-physiological-and-other-cont…
sappelhoff Apr 23, 2019
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26 changes: 15 additions & 11 deletions src/04-modality-specific-files/06-physiological-and-other-continous-recordings.md
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Expand Up @@ -22,17 +22,21 @@ directory. For example:`task-movie_stim.tsv.gz`
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
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line) and a JSON for storing start time, sampling frequency, and name of the
columns from the TSV. Please note that in contrast to other TSV files this one
does not include a header line. Instead the name of columns are specified in the
JSON file. This is to improve compatibility with existing software (FSL PNM) as
well as make support for other file formats possible in the future. Start time
should be expressed in seconds in relation to the time of start of acquisition
of the first volume in the corresponding imaging file (negative values are
allowed). Sampling frequency should be expressed in Hz. Recordings with
different sampling frequencies and/or starting times should be stored in
separate files. The following naming conventions should be used for column
names:
line) and a JSON for storing the following metadata fields:

| Field name | Definition |
| :---------------- | :----------------------------------------------------------------------------------------------------------------------------------------------------------- |
| SamplingFrequency | REQUIRED. Sampling frequency in Hz of all columns in the file. |
| StartTime | REQUIRED. Start time in seconds in relation to the start of acquisition of the first volume in the corresponding imaging file (negative values are allowed). |
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This sounds like it only applies to MRI data

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Agree- what about "Start time in seconds in relation to the first data sample in the corresponding neural dataset (negative values are allowed)"

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I'm assuming "start of acquisition of the first volume" is an attempt to precisely define the onset of the first data sample. What about: "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)."

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Hmm. I'm noticing that this appears in func/. Is that going to cause problems with MEG/EEG/iEEG? Or would this be similar to a simultaneous fMRI/EEG?

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What do you mean by

I'm noticing that this appears in func/

?

+1 on changing to: "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)." as @effigies suggests

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@sappelhoff I mean that on line 7, we specify that these files occur in the func/ subdirectory. Should this be expanded to include other directory names?

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Ah I see, yes it could be made more general, for example with a <modality> placeholder? The text below would have to be adjusted so that the <matches> placeholder does not only refer to MRI data 👍

| Columns | REQUIRED. Names of columns in file. |

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it is probably good to add units as optional

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I agree

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I was moving to add this, but we should probably consider how to make this as conformant as possible with https://bids-specification.readthedocs.io/en/stable/02-common-principles.html#tabular-files.

For example, we could then allow the same metadata for each column (LongName, Description, Levels, Units, TermURL). So something like:

{
  "SamplingFrequency": 10,
  "StartTime": 0.0,
  "Columns": ["cardiac"],
  "cardiac": {
    "LongName": "continuous pulse measurement",
    "Units": "mV",
    "TermURL": "..."
  }
}

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+1, looks like a good reuse of existing structure

Please note that in contrast to other TSV files this one does not include a
header line. Instead the name of columns are specified in the JSON file.
This is to improve compatibility with existing software (FSL PNM) as
well as make support for other file formats possible in the future.
Recordings with different sampling frequencies and/or starting times should be
stored in separate files.
The following naming conventions should be used for column names:

| Column name | Definition |
| :---------- | :--------------------------------------------------- |
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