extensions.yaml

---
# This file describes valid file extensions in the specification.
ave:
  value: .ave
  display_name: AVE # not sure what ave stands for
  description: |
    File containing data averaged by segments of interest.

    Used by KIT, Yokogawa, and Ricoh MEG systems.
bdf:
  value: .bdf
  display_name: Biosemi Data Format
  description: |
    A [Biosemi](https://www.biosemi.com/) Data Format file.

    Each recording consists of a single `.bdf` file.
    [`bdf+`](https://www.teuniz.net/edfbrowser/bdfplus%20format%20description.html) files are permitted.
    The capital `.BDF` extension MUST NOT be used.
bval:
  value: .bval
  display_name: FSL-Format Gradient Amplitudes
  description: |
    A space-delimited file containing gradient directions (b-vectors) of diffusion measurement.

    The `bval` file contains the *b*-values (in s/mm<sup>2</sup>) corresponding to the
    volumes in the relevant NIfTI file, with 0 designating *b*=0 volumes.
bvec:
  value: .bvec
  display_name: FSL-Format Gradient Directions
  description: |
    A space-delimited file containing gradient directions (b-vectors) of diffusion measurement.

    This file contains 3 rows with *N* space-delimited floating-point numbers,
    corresponding to the *N* volumes in the corresponding NIfTI file.

    The first row contains the *x* elements, the second row contains the *y* elements and
    the third row contains the *z* elements of a unit vector in the direction of the applied
    diffusion gradient, where the *i*-th elements in each row correspond together to
    the *i*-th volume, with `[0,0,0]` for *non-diffusion-weighted* (also called *b*=0 or *low-b*)
    volumes.

    Following the FSL format for the `bvec` specification, the coordinate system of
    the *b* vectors MUST be defined with respect to the coordinate system defined by
    the header of the corresponding `_dwi` NIfTI file and not the scanner's device
    coordinate system (see [Coordinate systems](SPEC_ROOT/appendices/coordinate-systems.md)).
    The most relevant limitation imposed by this choice is that the gradient information cannot
    be directly stored in this format if the scanner generates *b*-vectors in *scanner coordinates*.
chn:
  value: .chn
  display_name: KRISS CHN
  description: |
    A file generated by KRISS MEG systems containing the position of the center of the MEG coils.

    Each experimental run on the KRISS system produces a file with extension `.kdf`.
    Additional files that may be available in the same directory include
    the digitized positions of the head points (`\_digitizer.txt`),
    the position of the center of the MEG coils (`.chn`),
    and the event markers (`.trg`).
con:
  value: .con
  display_name: KIT/Yokogawa/Ricoh Continuous Data
  description: |
    Raw continuous data from a KIT/Yokogawa/Ricoh MEG system.

    Successor to the `.sqd` extension for raw continuous data.
dat:
  value: .dat
  display_name: MEG Fine-Calibration Format
  description: |
    A fine-calibration file used for Neuromag/Elekta/MEGIN MEG recording hardware.
CTF:
  value: .ds/
  display_name: CTF MEG Dataset Directory
  description: |
    A directory for MEG data, typically containing a `.meg4` file for the data and a `.res4` file for the resources.
dlabelnii:
  value: .dlabel.nii
  display_name: CIFTI-2 Dense Label File
  description: |
    A CIFTI-2 dense label file.

    This extension may only be used in derivative datasets.
edf:
  value: .edf
  display_name: European Data Format
  description: |
    A [European data format](https://www.edfplus.info/) file.

    Each recording consists of a single `.edf`` file.
    [`edf+`](https://www.edfplus.info/specs/edfplus.html) files are permitted.
    The capital `.EDF` extension MUST NOT be used.
eeg:
  value: .eeg
  display_name: BrainVision Binary Data
  description: |
    A binary data file in the
    [BrainVision Core Data Format](https://www.brainproducts.com/support-resources/brainvision-core-data-format-1-0/).
    These files come in three-file sets, including a `.vhdr`, a `.vmrk`, and a `.eeg` file.
fdt:
  value: .fdt
  display_name: EEGLAB FDT
  description: |
    An [EEGLAB](https://sccn.ucsd.edu/eeglab/index.php) file.

    The format used by the MATLAB toolbox [EEGLAB](https://sccn.ucsd.edu/eeglab/index.php).
    Each recording consists of a `.set` file with an optional `.fdt` file.
fif:
  value: .fif
  display_name: Functional Imaging File Format
  description: |
    An MEG file format used by Neuromag, Elekta, and MEGIN.
jpg:
  value: .jpg
  display_name: Joint Photographic Experts Group Format
  description: |
    A JPEG image file.
json:
  value: .json
  display_name: JavaScript Object Notation
  description: |
    A JSON file.

    In the BIDS specification, JSON files are primarily used as "sidecar" files, in which metadata describing "data"
    files are encoded.
    These sidecar files follow the inheritance principle.

    There are also a few special cases of JSON files being first-order data files, such as `genetic_info.json`.
kdf:
  value: .kdf
  display_name: KRISS KDF
  description: |
    A KRISS (file with extension `.kdf`) file.

    Each experimental run on the KRISS system produces a file with extension `.kdf`.
    Additional files that may be available in the same directory include
    the digitized positions of the head points (`\_digitizer.txt`),
    the position of the center of the MEG coils (`.chn`),
    and the event markers (`.trg`).
labelgii:
  value: .label.gii
  display_name: GIFTI label/annotation file
  description: |
    A GIFTI label/annotation file.

    This extension may only be used in derivative datasets.
md:
  value: .md
  display_name: Markdown
  description: |
    A Markdown file.
mefd:
  value: .mefd/
  display_name: Multiscale Electrophysiology File Format Version 3.0
  description: |
    A directory in the [MEF3](https://osf.io/e3sf9/) format.

    Each recording consists of a `.mefd` directory.
mhd:
  value: .mhd
  display_name: ITAB Binary Header
  description: |
    Produced by ITAB-ARGOS153 systems. This file a binary header file, and is generated along with a
    raw data file with the `.raw` extension.
mrk:
  value: .mrk
  display_name: MRK
  description: |
    A file containing MEG sensor coil positions.

    Used by KIT, Yokogawa, and Ricoh MEG systems.
    Successor to the `.sqd` extension for marker files.
OMEZARR:
  value: .ome.zarr/
  display_name: OME Next Generation File Format
  description: |
    An OME-NGFF file.

    OME-NGFF is a [Zarr](https://zarr.readthedocs.io/en/stable/)-based format,
    organizing data arrays in nested directories.
    This format was developed by the Open Microscopy Environment
    to provide data stream access to very large data.
nii:
  value: .nii
  display_name: NIfTI
  description: |
    A Neuroimaging Informatics Technology Initiative (NIfTI) data file.
niigz:
  value: .nii.gz
  display_name: Compressed NIfTI
  description: |
    A compressed Neuroimaging Informatics Technology Initiative (NIfTI) data file.
nix:
  value: .nix
  display_name: Neuroscience Information Exchange Format
  description: |
    A [Neuroscience Information Exchange](https://nixio.readthedocs.io) file.
nwb:
  value: .nwb
  display_name: Neurodata Without Borders Format
  description: |
    A [Neurodata Without Borders](https://nwb-schema.readthedocs.io/en/latest/) file.

    Each recording consists of a single `.nwb` file.
OMEBigTiff:
  value: .ome.btf
  display_name: Open Microscopy Environment BigTIFF
  description: |
    A [BigTIFF](https://www.awaresystems.be/imaging/tiff/bigtiff.html) image file, for very large images.
OMETiff:
  value: .ome.tif
  display_name: Open Microscopy Environment Tag Image File Format
  description: |
    An [OME-TIFF](https://docs.openmicroscopy.org/ome-model/6.1.2/ome-tiff/specification.html#) image file.
png:
  value: .png
  display_name: Portable Network Graphics
  description: |
    A [Portable Network Graphics](http://www.libpng.org/pub/png/) file.
pos:
  value: .pos
  display_name: Head Point Position
  description: |
    File containing digitized positions of the head points.

    This may be produced by a 4D neuroimaging/BTi MEG system or a CTF MEG system.
raw:
  value: .raw
  display_name: RAW
  description: |
    When produced by a KIT / Yokogawa / Ricoh MEG system, this file contains trial-based evoked fields.

    When produced by an ITAB-ARGOS153 system, this file contains raw data and is generated along with
    an associated binary header file  with the `.mhd` extension.
rst:
  value: .rst
  display_name: reStructuredText
  description: |
    A [reStructuredText](https://docutils.sourceforge.io/rst.html) file.
set:
  value: .set
  display_name: EEGLAB SET
  description: |
    An [EEGLAB](https://sccn.ucsd.edu/eeglab/index.php) file.

    The format used by the MATLAB toolbox [EEGLAB](https://sccn.ucsd.edu/eeglab/index.php).
    Each recording consists of a `.set` file with an optional `.fdt` file.
snirf:
  value: .snirf
  display_name: Shared Near Infrared Spectroscopy Format
  description: |
    HDF5 file organized according to the [SNIRF specification](https://github.com/fNIRS/snirf)
sqd:
  value: .sqd
  display_name: SQD
  description: |
    A file containing either raw MEG data or MEG sensor coil positions.
    While this extension is still valid, it has been succeeded by `.con` for raw MEG data and `.mrk` for
    marker information.

    Used by KIT, Yokogawa, and Ricoh MEG systems.
tif:
  value: .tif
  display_name: Tag Image File Format
  description: |
    A [Tag Image File Format](https://en.wikipedia.org/wiki/TIFF) file.
trg:
  value: .trg
  display_name: KRISS TRG
  description: |
    A file generated by KRISS MEG systems containing the event markers.

    Each experimental run on the KRISS system produces a file with extension `.kdf`.
    Additional files that may be available in the same directory include
    the digitized positions of the head points (`\_digitizer.txt`),
    the position of the center of the MEG coils (`.chn`),
    and the event markers (`.trg`).
tsv:
  value: .tsv
  display_name: Tab-Delimited
  description: |
    A tab-delimited file.
tsvgz:
  value: .tsv.gz
  display_name: Compressed Tab-Delimited
  description: |
    A gzipped tab-delimited file.
    This file extension is only used for very large tabular data, such as physiological recordings.
    For smaller data, the unzipped `.tsv` extension is preferred.
txt:
  value: .txt
  display_name: Text
  description: |
    A free-form text file.

    Tab-delimited files should have the `.tsv` extension rather than a `.txt` extension.
vhdr:
  value: .vhdr
  display_name: BrainVision Text Header
  description: |
    A text header file in the
    [BrainVision Core Data Format](https://www.brainproducts.com/support-resources/brainvision-core-data-format-1-0/).
    These files come in three-file sets, including a `.vhdr`, a `.vmrk`, and a `.eeg` file.
vmrk:
  value: .vmrk
  display_name: BrainVision Marker
  description: |
    A text marker file in the
    [BrainVision Core Data Format](https://www.brainproducts.com/support-resources/brainvision-core-data-format-1-0/).
    These files come in three-file sets, including a `.vhdr`, a `.vmrk`, and a `.eeg` file.
Any:
  value: .*
  display_name: Any Extension
  description: |
    Any extension is allowed.
None:
  value: ''
  display_name: No extension
  description: |
    A file with no extension.
Directory:
  value: /
  display_name: Directory
  description: |
    A directory with no extension.
    Corresponds to BTi/4D data.