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 conserve the original file extension (e.g., .meg4
, .res4
,
etc.). The renaming of CTF datasets SHOULD be done using the CTF newDs
command-line application.
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 specific specifications for cross-talk and fine-calibration matrix files in the present MEG-BIDS version.
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 data runs exceeding 2Gb, the data is stored in two separate files:
sub-control01_ses-001_task-rest_run-01_meg.fif
sub-control01_ses-001_task-rest_run-01_meg-1.fif
Each of these two files has a pointer to the next file. In some software applications, like MNE, one can simply specify the name of the first file, and data will be read in both files via this pointer. For this reason, it is RECOMMENDED to rename and write back the file once read, to avoid the persistence of a pointer associated with the old file name.
Naming convention:
sub-control01_ses-001_task-rest_run-01_part-01_meg.fif
sub-control01_ses-001_task-rest_run-01_part-02_meg.fif
More about the Neuromag/Elekta/MEGIN data organization at: http://www.fieldtriptoolbox.org/getting_started/neuromag And BabyMEG : http://www.fieldtriptoolbox.org/getting_started/babysquid
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 (.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. One SHOULD
rename/create a father run specific directory and keep the original files for
each run inside.
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
Where:
sub-control01_ses-001_task-rest_run-01_meg/
sub-control01_ses-001_task-rest_run-01_markers.<mrk,sqd>
sub-control01_ses-001_task-rest_run-01_meg.<con,sqd>
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
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
Where:
sub-control01_ses-001_task-rest_run-01_meg/
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
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). One should rename/create a father run specific directory and keep
the original files for each run inside.
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
Where:
sub-control01_ses-001_task-rest_run-01_meg/
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 in
section 5.2. 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.