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[FIX] add paragraph on MEG specific "markers" suffix in MEG spec #653

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45 changes: 27 additions & 18 deletions src/04-modality-specific-files/02-magnetoencephalography.md
Original file line number Diff line number Diff line change
Expand Up @@ -36,27 +36,36 @@ without the need to parse files in proprietary data format. Other relevant files
MAY be included alongside the MEG data; examples are provided below.

This template is for MEG data of any kind, including but not limited to
task-based, resting-state, and noise recordings. If multiple Tasks were
performed within a single Run, the task description can be set to
`task-multitask`. The \_meg.json SHOULD contain details on the Tasks.
task-based, resting-state, and noise recordings.
If multiple *Tasks* were performed within a single *Run*,
the task description can be set to `task-multitask`.
The `*_meg.json` file SHOULD contain details on the *Tasks*.

Some manufacturers' data storage conventions use folders which contain data
files of various nature: for example, CTF's `.ds` format, or BTi/4D.
files of various nature: for example, CTF's `.ds` format, or BTi/4D's data folder.
Yet other manufacturers split their files once they exceed a certain size
limit. For example Neuromag/Elekta/Megin, which can produce several files
for a single recording. Both `some_file.fif` and `some_file-1.fif` would
belong to a single recording. In BIDS, the [`split`](../99-appendices/09-entities.md#split) entity is RECOMMENDED to
deal with split files.
Please refer to [Appendix VI](../99-appendices/06-meg-file-formats.md) for
general information on how to deal with such manufacturer specifics and to see
more examples.

The [`proc-<label>`](../99-appendices/09-entities.md#proc) entity is analogous to [`rec-<label>`](../99-appendices/09-entities.md#proc) for MR and denotes a variant of a file
that was a result of particular processing performed on the device. This is
useful for files produced in particular by Elekta’s MaxFilter (for example, sss, tsss,
trans, quat, mc), which some installations impose to be run on raw data
because of active shielding software corrections before the MEG data can
actually be exploited.
limit.
For example Neuromag/Elekta/Megin, which can produce several files
for a single recording.
Both `some_file.fif` and `some_file-1.fif` would belong to a single recording.
In BIDS, the [`split`](../99-appendices/09-entities.md#split) entity is RECOMMENDED to deal with split files.

Another manufacturer-specific detail pertains to the KIT/Yokogawa/Ricoh sytem,
which saves the MEG sensor coil positions in a separate file with two possible filename extensions (`.sqd`, `.mrk`).
For these files, the `markers` suffix MUST be used.
For example: `sub-01_task-nback_markers.sqd`

Please refer to [Appendix VI](../99-appendices/06-meg-file-formats.md)
for general information on how to deal with such manufacturer specifics and to see more examples.

The [`proc-<label>`](../99-appendices/09-entities.md#proc) entity is analogous to the
[`rec-<label>`](../99-appendices/09-entities.md#rec) entity for MRI,
and denotes a variant of a file that was a result of particular processing performed on the device.
This is useful for files produced in particular by Elekta's MaxFilter
(for example, sss, tsss, trans, quat, mc),
which some installations impose to be run on raw data prior to analysis.
Such processing steps are needed for example because of active shielding software corrections
that have to be performed to before the MEG data can actually be exploited.

### Recording EEG simultaneously with MEG

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23 changes: 17 additions & 6 deletions src/99-appendices/06-meg-file-formats.md
Original file line number Diff line number Diff line change
Expand Up @@ -231,11 +231,11 @@ More about the 4D neuroimaging/BTi data organization at:

## KIT/Yokogawa/Ricoh

Each experimental run on a KIT/Yokogawa/Ricoh system yields a raw
(`.sqd`, `.con`) file with its associated marker coil file(s) (`.sqd`, `.mrk`),
which contains coil positions in the acquisition system’s native space.
Head points and marker points in head space are acquired using third-party
hardware.
Each experimental run on a KIT/Yokogawa/Ricoh system yields a raw file with either
`.sqd` or `.con` extension,
and with its associated marker coil file(s) with either `.sqd` or `.mrk` extension.
The marker coil file(s) contain coil positions in the *acquisition system's native space*.
Head points and marker points in *head space* are acquired using third-party hardware.

Example:

Expand All @@ -253,7 +253,18 @@ sub-control01/
sub-control01_ses-001_task-rest_run-01_meg.<con,sqd>
```

If there are files with multiple marker coils, the marker files must have the
To understand why both `.sqd` and `.con`, as well as both `.sqd` and `.mrk` are valid
extensions, we provide a brief historical perspective on the evolution of the data format:
The original extension for KIT/Yokogawa/Ricoh continuous data was `.sqd`.
This was later modernized to `.con` (to denote "continuous").
However, to preserve backwards compatibility, `.sqd` is still a valid extension for the raw, continuous data file.
The original extension for KIT/Yokogawa/Ricoh marker files was `.sqd` as well.
That lead to the ambiguous situation where both the raw data and the marker file(s) could end on `.sqd`.
To distinguish between continuous data and marker file(s), the internal header of the files needed to be read first.
For this reason, the marker file extension was later modernized to `.mrk` to better disambiguate files.
However again, to preserve backwards compatibility, `.sqd` is still a valid extension for the marker file(s).

If there are multiple files with marker coils, the marker files must have the
`acq-<label>` parameter and no more that two marker files may be associated with
one raw data file.
While the acquisition parameter can take any value, it is RECOMMENDED that if
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