extensions.yaml

---
# This file describes valid file extensions in the specification.
.*:
  name: Any Extension
  description: |
    Any extension is allowed.
.ave:
  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:
  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:
  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:
  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](../99-appendices/08-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:
  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 folder 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:
  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:
  name: MEG Fine-Calibration Format
  description: |
    A fine-calibration file used for Neuromag/Elekta/MEGIN MEG recording hardware.
.ds/:
  name: CTF MEG Dataset Folder
  description: |
    A folder for MEG data, typically containing a `.meg4` file for the data and a `.res4` file for the resources.
.edf:
  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:
  name: BrainVision Binary Data
  description: |
    A binary data file in the
    [BrainVision Core Data Format](https://www.brainproducts.com/productdetails.php?id=21&tab=5).
    These files come in three-file sets, including a `.vhdr`, a `.vmrk`, and a `.eeg` file.
.fdt:
  name: EEGLAB FDT
  description: |
    An [EEGLAB](https://sccn.ucsd.edu/eeglab) file.

    The format used by the MATLAB toolbox [EEGLAB](https://sccn.ucsd.edu/eeglab).
    Each recording consists of a `.set` file with an optional `.fdt` file.
.fif:
  name: Functional Imaging File Format
  description: |
    An MEG file format used by Neuromag, Elekta, and MEGIN.
.jpg:
  name: Joint Photographic Experts Group Format
  description: |
    A JPEG image file.
.json:
  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:
  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 folder 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`).
.md:
  name: Markdown
  description: |
    A Markdown file.
.mefd/:
  name: Multiscale Electrophysiology File Format Version 3.0
  description: |
    A folder in the [MEF3](https://osf.io/e3sf9/) format.

    Each recording consists of a `.mefd` directory.
.mhd:
  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:
  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.
.nii:
  name: NIfTI
  description: |
    A Neuroimaging Informatics Technology Initiative (NIfTI) data file.
.nii.gz:
  name: Compressed NIfTI
  description: |
    A compressed Neuroimaging Informatics Technology Initiative (NIfTI) data file.
.nwb:
  name: Neurodata Without Borders Format
  description: |
    A [Neurodata Without Borders](https://nwb-schema.readthedocs.io) file.

    Each recording consists of a single `.nwb` file.
.ome.btf:
  name: Open Microscopy Environment BigTIFF
  description: |
    A [BigTIFF](https://www.awaresystems.be/imaging/tiff/bigtiff.html) image file, for very large images.
.ome.tif:
  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:
  name: Portable Network Graphics
  description: |
    A [Portable Network Graphics](http://www.libpng.org/pub/png/) file.
.pos:
  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:
  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:
  name: reStructuredText
  description: |
    A [reStructuredText](https://docutils.sourceforge.io/rst.html) file.
.set:
  name: EEGLAB SET
  description: |
    An [EEGLAB](https://sccn.ucsd.edu/eeglab) file.

    The format used by the MATLAB toolbox [EEGLAB](https://sccn.ucsd.edu/eeglab).
    Each recording consists of a `.set` file with an optional `.fdt` file.
.sqd:
  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:
  name: Tag Image File Format
  description: |
    A [Tag Image File Format](https://en.wikipedia.org/wiki/TIFF) file.
.trg:
  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 folder 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:
  name: Tab-Delimited
  description: |
    A tab-delimited file.
.tsv.gz:
  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:
  name: Text
  description: |
    A free-form text file.

    Tab-delimited files should have the `.tsv` extension rather than a `.txt` extension.
.vhdr:
  name: BrainVision Text Header
  description: |
    A text header file in the
    [BrainVision Core Data Format](https://www.brainproducts.com/productdetails.php?id=21&tab=5).
    These files come in three-file sets, including a `.vhdr`, a `.vmrk`, and a `.eeg` file.
.vmrk:
  name: BrainVision Marker
  description: |
    A text marker file in the
    [BrainVision Core Data Format](https://www.brainproducts.com/productdetails.php?id=21&tab=5).
    These files come in three-file sets, including a `.vhdr`, a `.vmrk`, and a `.eeg` file.
/:
  name: Folder
  description: |
    A folder with no extension.
    Corresponds to BTi/4D data.
None:
  name: No extension
  description: |
    A file with no extension.