Appendix VI: MEG file formats

Each MEG system brand has specific file organization and data formats. RECOMMENDED values for manufacturer_specific_extensions:

Value	Definition
`ctf`	CTF (folder with `.ds` extension)
`fif`	Neuromag / Elekta / MEGIN and BabyMEG (file with extension `.fif`)
`4d`	BTi / 4D Neuroimaging (folder containing multiple files without extensions)
`kit`	KIT / Yokogawa / Ricoh (file with extension `.sqd`, `.con`, `.raw`, `.ave` or `.mrk`)
`kdf`	KRISS (file with extension `.kdf`)
`itab`	Chieti system (file with extension `.raw` and `.mhd`)

Below are specifications for each system brand.

CTF

Each experimental run with a CTF system yields a folder with a .ds extension, containing several files. The OPTIONAL digitized positions of the head points are usually stored in a separate .pos file, not necessarily within the .ds folder.

[sub-<label>[_ses-<label>]_headshape.pos]
sub-<label>[_ses-<label>]_task-<label>[_run-<index>]_meg.ds>

CTF's data storage is therefore via directories containing multiple files. The files contained within a .ds directory are named such that they match the parent directory, but preserve the original file extension (e.g., .meg4, .res4, etc.). The renaming of CTF datasets SHOULD be done with a specialized software such as the CTF newDs command-line application or MNE-BIDS.

Example:

sub-control01/
    ses-001/
        sub-control01_ses-001_scans.tsv
        meg/
            sub-control01_ses-001_coordsystem.json
            sub-control01_ses-001_headshape.pos
            sub-control01_ses-001_task-rest_run-01_meg.ds
            sub-control01_ses-001_task-rest_run-01_meg.json
            sub-control01_ses-001_task-rest_run-01_channels.tsv

To learn more about CTF’s data organization: http://www.fieldtriptoolbox.org/getting_started/ctf

Neuromag/Elekta/MEGIN

Neuromag/Elekta/MEGIN data and Tristan Technologies BabyMEG data is stored with file extension .fif. The digitized positions of the head points are saved inside the fif file along with the MEG data, with typically no _headshape file.

sub-<label>[_ses-<label>]_task-<label>[_run-<index>]_meg.fif

Note that we do not provide specifications for cross-talk and fine-calibration matrix files in the current version of BIDS.

Example:

sub-control01/
    ses-001/
        sub-control01_ses-001_scans.tsv
        meg/
            sub-control01_ses-001_coordsystem.json
            sub-control01_ses-001_task-rest_run-01_meg.fif
            sub-control01_ses-001_task-rest_run-01_meg.json
            sub-control01_ses-001_task-rest_run-01_channels.tsv

After applying the MaxFilter pre-processing tool, files should be renamed with the corresponding label (e.g., proc-sss) and placed into a derivatives subfolder.

Example:

sub-control01_ses-001_task-rest_run-01_proc-sss_meg.fif
sub-control01_ses-001_task-rest_run-01_proc-sss_meg.json

In the case of long data recordings that exceed a file size of 2Gb, the .fif files are conventionally split into multiple parts. For example:

some_file.fif
some_file-1.fif

Each of these files has an internal pointer to the next file. This is important when renaming these split recordings to the BIDS convention. Instead of a simple renaming, files should be read in and saved under their new names with dedicated tools like MNE, which will ensure that not only the file names, but also the internal file pointers will be updated.

It is RECOMMENDED that .fif files with multiple parts use the split-<index> entity to indicate each part.

Example:

sub-control01_ses-001_task-rest_run-01_split-01_meg.fif
sub-control01_ses-001_task-rest_run-01_split-02_meg.fif

More information can be found under the following links:

BTi/4D neuroimaging

Each experimental run on a 4D neuroimaging/BTi system results in a folder containing multiple files without extensions.

[sub-<label>[_ses-<label>]_headshape.pos]
sub-<label>[_ses-<label>]_task-<label>[_run-<index>]_meg>

One SHOULD rename/create a father run specific directory and keep the original files for each run inside (e.g., c,rfhp0.1Hz, config and hs_file).

Example:

sub-control01/
    ses-001/
        sub-control01_ses-001_scans.tsv
        meg/
            sub-control01_ses-001_coordsystem.json
            sub-control01_ses-001_headshape.pos
            sub-control01_ses-001_task-rest_run-01_meg
            sub-control01_ses-001_task-rest_run-01_meg.json
            sub-control01_ses-001_task-rest_run-01_channels.tsv

Where:

sub-control01_ses-001_task-rest_run-01_meg/
    config
    hs_file
    e,rfhp1.0Hz.COH
    c,rfDC

More about the 4D neuroimaging/BTi data organization at: http://www.fieldtriptoolbox.org/getting_started/bti

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.

Example:

sub-control01/
    ses-001/
        sub-control01_ses-001_scans.tsv
        meg/
            sub-control01_ses-001_coordsystem.json
            sub-control01_ses-001_headshape.txt
            sub-control01_ses-001_task-rest_run-01_meg
            sub-control01_ses-001_task-rest_run-01_meg.json
            sub-control01_ses-001_task-rest_run-01_channels.tsv
            sub-control01_ses-001_task-rest[_acq-<label>]_run-01_markers.<mrk,sqd>
            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 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 the two marker measurements occur before and after the raw data acquisition, pre and post are used to differentiate the two situations.

More about the KIT/Yokogawa/Ricoh data organization at: http://www.fieldtriptoolbox.org/getting_started/yokogawa

KRISS

Each experimental run on the KRISS system produces a file with extension .kdf. Additional files can be available in the same folder: the digitized positions of the head points (\_digitizer.txt), the position of the center of the MEG coils (.chn) and the event markers (.trg).

[sub-<label>[_ses-<label>]_headshape.txt]
sub-<label>[_ses-<label>]_task-<label>[_run-<index>]_meg.kdf
sub-<label>[_ses-<label>]_task-<label>[_run-<index>]_meg.chn
sub-<label>[_ses-<label>]_task-<label>[_run-<index>]_meg.trg
sub-<label>[_ses-<label>]_task-<label>[_acq-<label>]_digitizer.txt

Example:

sub-control01/
    ses-001/
        sub-control01_ses-001_scans.tsv
        meg/
            sub-control01_ses-001_coordsystem.json
            sub-control01_ses-001_headshape.txt
            sub-control01_ses-001_task-rest_run-01_meg
            sub-control01_ses-001_task-rest_run-01_meg.json
            sub-control01_ses-001_task-rest_run-01_channels.tsv
            sub-control01_ses-001_task-rest_run-01_meg.chn
            sub-control01_ses-001_task-rest_run-01_meg.kdf
            sub-control01_ses-001_task-rest_run-01_meg.trg
            sub-control01_ses-001_task-rest_digitizer.txt

ITAB

Each experimental run on a ITAB-ARGOS153 system yields a raw (.raw) data file plus an associated binary header file (.mhd). The raw data file has an ASCII header that contains detailed information about the data acquisition system, followed by binary data. The associated binary header file contains part of the information from the ASCII header, specifically the one needed to process data, plus other information on offline preprocessing performed after data acquisition (e.g., sensor position relative to subject’s head, head markers, stimulus information).

Example:

sub-control01/
    ses-001/
        sub-control01_ses-001_coordsystem.json
        sub-control01_ses-001_headshape.txt
        sub-control01_ses-001_task-rest_run-01_meg
        sub-control01_ses-001_task-rest_run-01_meg.json
        sub-control01_ses-001_task-rest_run-01_channels.tsv
        sub-control01_ses-001_task-rest_run-01_meg.raw
        sub-control01_ses-001_task-rest_run-01_meg.raw.mhd

Aalto MEG–MRI

For stand-alone MEG data, the Aalto hybrid device uses the standard .fif data format and follows the conventions of Elekta/Neuromag as described above. The .fif files may contain unreconstructed MRI data. The inclusion of MRI data and information for accurate reconstruction will be fully standardized at a later stage.