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[FIX] Remove mentions of sourcedata in the datatype specific pages #1737

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12 changes: 8 additions & 4 deletions src/common-principles.md
Original file line number Diff line number Diff line change
Expand Up @@ -238,10 +238,14 @@ distinguish partial results from the raw data and share the latter.
See [Storage of derived datasets](#storage-of-derived-datasets) for more on
organizing derivatives.

Similar rules apply to source data, which is defined as data before
harmonization, reconstruction, and/or file format conversion (for example, E-Prime event logs or DICOM files).
Storing actual source files with the data is preferred over links to
external source repositories to maximize long term preservation,
Similar rules apply to source data, which is defined as data
before harmonization, reconstruction, and/or file format conversion
(for example, E-Prime event logs or DICOM files).
Retaining the source data is especially valuable
in a case when conversion fails to preserve crucial metadata
unique to specific acquisition setup.
Storing actual source files with the data is preferred over links
to external source repositories to maximize long term preservation,
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which would suffer if an external repository would not be available anymore.
This specification currently does not go into the details of
recommending a particular naming scheme for including different types of
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12 changes: 4 additions & 8 deletions src/modality-specific-files/electroencephalography.md
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Expand Up @@ -42,14 +42,10 @@ It is RECOMMENDED to use the European data format, or the BrainVision data
format. It is furthermore discouraged to use the other accepted formats over
these RECOMMENDED formats, particularly because there are conversion scripts
available in most commonly used programming languages to convert data into the
RECOMMENDED formats. The data in their original format, if different from the
supported formats, can be stored in the [`/sourcedata` directory](../common-principles.md#source-vs-raw-vs-derived-data).

The original data format is especially valuable in case conversion elicits the
loss of crucial metadata specific to manufacturers and specific EEG systems. We
also encourage users to provide additional meta information extracted from the
manufacturer specific data files in the sidecar JSON file. Other relevant files
MAY be included alongside the original EEG data in `/sourcedata`.
RECOMMENDED formats.

We encourage users to provide additional metadata extracted from the
manufacturer-specific data files in the sidecar JSON file.

Note the `RecordingType`, which depends on whether the data stream on disk
is interrupted or not.
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Expand Up @@ -53,12 +53,8 @@ packages. Other formats that may be considered in the future should have a clear
added advantage over the existing formats and should have wide adoption in the
BIDS community.

The data format in which the data was originally stored is especially valuable
in case conversion elicits the loss of crucial metadata specific to
manufacturers and specific iEEG systems. We also encourage users to provide
additional meta information extracted from the manufacturer-specific data files
in the sidecar JSON file. Other relevant files MAY be included alongside the
original iEEG data in the [`/sourcedata` directory](../common-principles.md#source-vs-raw-vs-derived-data).
We encourage users to provide additional metadata extracted from the
manufacturer-specific data files in the sidecar JSON file.

Note the RecordingType, which depends on whether the data stream on disk is interrupted or not.
Continuous data is by definition 1 segment without interruption.
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3 changes: 0 additions & 3 deletions src/modality-specific-files/microscopy.md
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Expand Up @@ -59,9 +59,6 @@ Microscopy raw data MUST be stored in one of the following formats:

- [OME-ZARR/NGFF](https://ngff.openmicroscopy.org/latest/) (`.ome.zarr` directories)

If different from PNG, TIFF, OME-TIFF, or OME-ZARR, the original unprocessed data in the native format MAY be
stored in the [`/sourcedata` directory](../common-principles.md#source-vs-raw-vs-derived-data).

### Modality suffixes
Microscopy data currently support the following imaging modalities:

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4 changes: 0 additions & 4 deletions src/modality-specific-files/motion.md
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Expand Up @@ -50,10 +50,6 @@ The number of columns in `_motion.tsv` files MUST equal the number of rows
in the associated `_channels.tsv` file.
All relevant metadata about a tracking systems is stored in accompanying sidecar `*_tracksys-<label>_motion.json` file.

The source data from each tracking system in their original format, if different from `.tsv`,
can be stored in the [`/sourcedata` directory](../common-principles.md#source-vs-raw-vs-derived-data).
The original data format MAY hold more metadata than currently specified in the `*_motion.json` file.

When multiple tracking systems are used to record motion or motion capture is used alongside the recording of other BIDS modalities and recordings should be interpreted together,
it is advised to provide a possibility to synchronize recordings.
The preferred way to do so is to use the acquisition time of the first data point of recordings and
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9 changes: 0 additions & 9 deletions src/modality-specific-files/near-infrared-spectroscopy.md
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Expand Up @@ -36,15 +36,6 @@ replicated in the BIDS specification. This redundancy allows the data to be
easily parsed by humans and machines that do not have a SNIRF reader at hand,
which improves findability and tooling development.

Raw NIRS data in the native format, if different from SNIRF, can also
be stored in the [`/sourcedata`](../common-principles.md#source-vs-raw-vs-derived-data)
directory along with code to convert the data to
SNIRF in the [`/code`](../common-principles.md#storage-of-derived-datasets) directory.
The unprocessed raw data should be stored in
the manufacturer's format before any additional processing or conversion is applied.
Retaining the native file format is especially valuable in a case when conversion elicits the
loss of crucial metadata unique to specific manufacturers and NIRS systems.

### Terminology

For proper documentation of NIRS recording metadata, it is important
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