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MEG file formats

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

Value Description
ctf CTF (directory with .ds extension)
fif Neuromag / Elekta / MEGIN and BabyMEG (file with extension .fif)
4d BTi / 4D Neuroimaging (directory 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 directory 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 directory.

[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 (for example, .meg4, .res4). 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: https://www.fieldtriptoolbox.org/getting_started/ctf

Neuromag/Elekta/MEGIN

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

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

Cross-talk and fine-calibration files

In case internal active shielding (IAS) was used during acquisition, raw FIFF files need to be processed using Maxwell filtering (signal-space separation, SSS) to make the data usable. To this end, two specific files are needed: The cross-talk file, and the fine-calibration file, both of which are produced by the MaxFilter software and the work of the Neuromag/Elekta/MEGIN engineers during maintenance of the MEG acquisition system. Both files are thus specific to the site of recording and may change in the process of regular system maintenance.

In BIDS, the cross-talk and fine-calibration files are shared unmodified, including their original extensions (.fif for cross-talk and .dat for fine-calibration), but with BIDS file naming convention and by using the acq entity.

  • cross-talk file template: sub-<label>[_ses-<label>]_acq-crosstalk_meg.fif
  • fine-calibration file template: sub-<label>[_ses-<label>]_acq-calibration_meg.dat

Note that cross-talk files MUST be denoted using acq-crosstalk and fine-calibration files MUST be denoted using acq-calibration.

The cross-talk and fine-calibration data MUST be stored in the subject-level meg directory, which may be nested inside a ses-<label> directory, as shown in the following examples.

Example with single session (omitted session directory)

├─ sub-01/
│  └─ meg/
│     ├─ sub-01_coordsystem.json 
│     ├─ sub-01_task-rest_meg.fif 
│     ├─ sub-01_task-rest_meg.json 
│     ├─ sub-01_task-rest_channels.tsv 
│     ├─ sub-01_acq-crosstalk_meg.fif 
│     └─ sub-01_acq-calibration_meg.dat 
└─ sub-02/
   └─ meg/
      ├─ sub-02_coordsystem.json 
      ├─ sub-02_task-rest_meg.fif 
      ├─ sub-02_task-rest_meg.json 
      ├─ sub-02_task-rest_channels.tsv 
      ├─ sub-02_acq-crosstalk_meg.fif 
      └─ sub-02_acq-calibration_meg.dat 

Example with multiple sessions

└─ sub-01/
   ├─ ses-01/
   │  ├─ sub-01_ses-01_scans.tsv 
   │  └─ meg/
   │     ├─ sub-01_ses-01_coordsystem.json 
   │     ├─ sub-01_ses-01_task-rest_run-01_meg.fif 
   │     ├─ sub-01_ses-01_task-rest_run-01_meg.json 
   │     ├─ sub-01_ses-01_task-rest_run-01_channels.tsv 
   │     ├─ sub-01_ses-01_acq-crosstalk_meg.fif 
   │     └─ sub-01_ses-01_acq-calibration_meg.dat 
   └─ ses-02/
      ├─ sub-01_ses-02_scans.tsv 
      └─ meg/
         ├─ sub-01_ses-02_coordsystem.json 
         ├─ sub-01_ses-02_task-rest_run-01_meg.fif 
         ├─ sub-01_ses-02_task-rest_run-01_meg.json 
         ├─ sub-01_ses-02_task-rest_run-01_channels.tsv 
         ├─ sub-01_ses-02_acq-crosstalk_meg.fif 
         └─ sub-01_ses-02_acq-calibration_meg.dat 

Sharing FIFF data after signal-space separation (SSS)

After applying SSS (for example, by using the MaxFilter software), files SHOULD be renamed with the corresponding label (for example, proc-sss) and placed in a derivatives subdirectory.

Example:

└─ sub-control01/
   └─ ses-001/
      └─ meg/
         ├─ sub-control01_ses-001_task-rest_run-01_proc-sss_meg.fif 
         └─ sub-control01_ses-001_task-rest_run-01_proc-sss_meg.json 

Split files

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 filenames, but also the internal file pointers will be updated.

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

If there are multiple parts of a recording and the optional scans.tsv is provided, remember to list all files separately in scans.tsv and that the entries for the acq_time column in scans.tsv MUST all be identical, as described in Scans file.

Example:

└─ sub-control01/
   └─ ses-001/
      └─ meg/
         ├─ 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:

Recording dates in .fif files

It is important to note that recording dates in .fif files are represented as int32 format seconds since (or before) the Epoch (1970-01-01T00:00:00.000000 UTC). Integers in int32 format can encode values from -2,147,483,647 to +2,147,483,647. Due to this representation, the Neuromag/Elekta/MEGIN file format for MEG (.fif) does not support recording dates earlier than 1901-12-13T08:45:53.000000 UTC or later than 2038-01-19T03:14:07.000000 UTC.

BTi/4D neuroimaging

Each experimental run on a 4D neuroimaging/BTi system results in a directory 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 parent run-specific directory and keep the original files for each run inside (for example, 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: https://www.fieldtriptoolbox.org/getting_started/bti

KIT/Yokogawa/Ricoh

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:

└─ 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> 

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> entity and no more that two marker files may be associated with one raw data file. While the acquisition entity 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: https://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 directory: 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 (for example, sensor position relative to subject’s head, head markers, stimulus information).

Example:

└─ sub-control01/
   └─ ses-001/
      └─ 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.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.