Working with Metadata

Working with Metadata#

Querying for Metadata Files#

You can query specific files by using specific suffix parameters. This allows you to access important BIDS metadata files such as events.tsv, channels.tsv, or scans.tsv, which contain valuable information about your recordings, channels, or scanning sessions.

Common suffixes in MEG data:

  • events: search for event files, which contains time_stamps and event markers.

  • coordystem: search for the file specifying the coordinate system used in the recording.

  • channels: search for the file which specifies channel names and types.

  • scans: search for the files documenting the different scan sequences that were run.

Here are some examples of how to query for your event files with the suffix events:

all_events = layout.get(suffix='events',return_type='filename')
print(all_events)

#Output
#['./ancp-bids/tests/data/ds003483/sub-009/ses-1/meg/sub-009_ses-1_task-deduction_run-1_events.tsv',
#'./ancp-bids/tests/data/ds003483/sub-009/ses-1/meg/sub-009_ses-1_task-induction_run-1_events.tsv',
#...
#'./ancp-bids/tests/data/ds003483/sub-031/ses-1/meg/sub-031_ses-1_task-deduction_run-1_events.tsv',
#'./ancp-bids/tests/data/ds003483/sub-031/ses-1/meg/sub-031_ses-1_task-induction_run-1_events.tsv']

all_events = layout.get(suffix='events', return_type='filename')
print(all_events)

#Output: It will give you all the events, both .tsv and .json files for every participant. It's a very long output.

The get() function allows you to combine multiple parameters to narrow down your search based on your specific needs. For example, you can specify if you want to search for your event files in .json or .tsv format with the parameter extension.

events_sub009_deduc = layout.get(suffix='events', subject='009', extension='.tsv', task='deduction', returntype='filename')
print(events_sub009_deduc)

#Output
#The tsv file of the deduction task of the ninth subject: 
#['./ancp-bids/test/data/ds003483/sub-009/ses-1/meg/sub-009_ses-1_task-deduction_run-1_events.tsv']

events_sub08 = layout.get(suffix='events', sub='08', run='02', extension='.tsv', return_type='filename')
print(events_sub08)

#Output
#The tsv file of the 2nd run of the eigth subject: 
#['/home/abaxman/.ancp-bids/datasets/ds005/sub-08/func/sub-08_task-mixedgamblestask_run-02_events.tsv']

Extracting Metadata from Sidecars#

Metadata stored in JSON files can be queried using layout.get_metadata along the directory path. This will return a dictionary with keys and values.

metadata = layout.get_metadata(layout.get(task='induction', suffix='meg',return_type='filename')[3])

print("metadata: ", list(metadata.keys()))
print("Value of Dewar position: ", metadata['DewarPosition'])

#Output:
#metadata:  ['AssociatedEmptyRoom', 'CapManufacturer',
#'CapManufacturersModelName', 'ContinuousHeadLocalization',
#'DeviceSerialNumber', 'DewarPosition', 'DigitizedHeadPoints',
#'DigitizedLandmarks', 'ECGChannelCount', 'ECOGChannelCount',
#'EEGChannelCount', 'EEGPlacementScheme', 'EEGReference',
#'EMGChannelCount', 'EOGChannelCount', 'EpochLength',
#'HeadCoilFrequency', 'InstitutionAddress', 'InstitutionName',
#'InstitutionalDepartmentName', 'Instructions', 'MEGChannelCount',
#'MEGREFChannelCount', 'Manufacturer', 'ManufacturersModelName',
#'MiscChannelCount', 'PowerLineFrequency', 'RecordingDuration',
#'RecordingType', 'SEEGChannelCount', 'SamplingFrequency',
#'SoftwareFilters', 'SoftwareVersions', 'SubjectArtefactDescription',
#'TaskDescription', 'TaskName', 'TriggerChannelCount', 'Description',
#'RawSources', 'Authors', 'BaselineCorrection', 'BaselineCorrectionMethod',
#'BaselinePeriod']
#Value of Dewar position: 'upright'

metadata = layout.get_metadata(layout.get(task='mixedgamblestask', suffix='bold',return_type='filename')[3])

print("metadata: ", list(metadata.keys()))
print("Value of RepetitionTime: ", metadata['RepetitionTime'])

#Output:
#metadata:  ['RepetitionTime', 'TaskName', 'SliceTiming']
#Value of RepetitionTime:  2.0

Next Section#

In the next section we will cover how to write derivatives ensuring BIDS-compliant naming and structure.

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