mne_bids.BIDSPath¶

class mne_bids.BIDSPath(subject=None, session=None, task=None, acquisition=None, run=None, processing=None, recording=None, space=None, split=None, root=None, suffix=None, extension=None, datatype=None, check=True)[source]¶

A BIDS path object.

BIDS filename prefixes have one or more pieces of metadata in them. They must follow a particular order, which is followed by this function. This will generate the prefix for a BIDS filename that can be used with many subsequent files, or you may also give a suffix that will then complete the file name.

BIDSPath allows dynamic updating of its entities in place, and operates similar to pathlib.Path. In addition, it can query multiple paths with matching BIDS entities via the match method.

Note that not all parameters are applicable to each suffix of data. For example, electrode location TSV files do not need a “task” field.

Parameters

subjectstr | None: The subject ID. Corresponds to “sub”.
sessionstr | None: The acquisition session. Corresponds to “ses”.
taskstr | None: The experimental task. Corresponds to “task”.
acquisition: str | None: The acquisition parameters. Corresponds to “acq”.
runint | None: The run number. Corresponds to “run”.
processingstr | None: The processing label. Corresponds to “proc”.
recordingstr | None: The recording name. Corresponds to “rec”.
spacestr | None: The coordinate space for anatomical and sensor location files (e.g., *_electrodes.tsv, *_markers.mrk). Corresponds to “space”. Note that valid values for space must come from a list of BIDS keywords as described in the BIDS specification.
splitint | None: The split of the continuous recording file for .fif data. Corresponds to “split”.
suffixstr | None: The filename suffix. This is the entity after the last _ before the extension. E.g., 'channels'. The following filename suffix’s are accepted: ‘meg’, ‘markers’, ‘eeg’, ‘ieeg’, ‘T1w’, ‘participants’, ‘scans’, ‘electrodes’, ‘coordsystem’, ‘channels’, ‘events’, ‘headshape’, ‘digitizer’, ‘beh’, ‘physio’, ‘stim’
extensionstr | None: The extension of the filename. E.g., '.json'.
datatypestr: The BIDS data type, e.g., 'anat', 'func', 'eeg', 'meg', 'ieeg'.
rootpath-like | None: The root directory of the BIDS dataset.
checkbool: If True, enforces BIDS conformity. Defaults to True.

Notes

BIDS entities are generally separated with a "_" character, while entity key/value pairs are separated with a "-" character. There are checks performed to make sure that there are no '-', '_', or '/' characters contained in any entity keys or values.

To represent a filename such as dataset_description.json, one can set check=False, and pass suffix='dataset_description' and extension='.json'.

BIDSPath can also be used to represent file and folder names of data types that are not yet supported through MNE-BIDS, but are recognized by BIDS. For example, one can set datatype to dwi or func and pass check=False to represent diffusion-weighted imaging and functional MRI paths.

Examples

Generate a BIDSPath object and inspect it

>>> bids_path = BIDSPath(subject='test', session='two', task='mytask',
...                      suffix='ieeg', extension='.edf')
>>> print(bids_path.basename)
sub-test_ses-two_task-mytask_ieeg.edf
>>> bids_path
BIDSPath(
root: None
datatype: ieeg
basename: sub-test_ses-two_task-mytask_ieeg.edf)

Copy and update multiple entities at once

>>> new_bids_path = bids_path.copy().update(subject='test2',
...                                         session='one')
>>> print(new_bids_path.basename)
sub-test2_ses-one_task-mytask_ieeg.edf

Printing a BIDSPath will show a relative path when root is not set

>>> print(new_bids_path)
sub-test2/ses-one/ieeg/sub-test2_ses-one_task-mytask_ieeg.edf

Setting suffix without an identifiable datatype will make BIDSPath try to guess the datatype

>>> new_bids_path = new_bids_path.update(suffix='channels',
...                                      extension='.tsv')
>>> print(new_bids_path)
sub-test2/ses-one/ieeg/sub-test2_ses-one_task-mytask_channels.tsv

You can set a new root for the BIDS dataset. Let’s see what the different properties look like for our object:

>>> new_bids_path = new_bids_path.update(root='/bids_dataset')
>>> print(new_bids_path.root.as_posix())
/bids_dataset
>>> print(new_bids_path.basename)
sub-test2_ses-one_task-mytask_channels.tsv
>>> print(new_bids_path)
/bids_dataset/sub-test2/ses-one/ieeg/sub-test2_ses-one_task-mytask_channels.tsv
>>> print(new_bids_path.directory.as_posix())
/bids_dataset/sub-test2/ses-one/ieeg

Attributes

entitiesdict: Return dictionary of the BIDS entities.
datatypestr | None: The BIDS data type, e.g.
basenamestr: Path basename.
rootpathlib.Path: The root directory of the BIDS dataset.
directorypathlib.Path: Get the BIDS parent directory.
fpathpathlib.Path: Full filepath for this BIDS file.
checkbool: Whether to enforce BIDS conformity.

Methods

`copy`()	Copy the instance.
`find_empty_room`([use_sidecar_only, verbose])	Find the corresponding empty-room file of an MEG recording.
`match`([check])	Get a list of all matching paths in the root directory.
`mkdir`([exist_ok])	Create the directory structure of the BIDS path.
`update`(*[, check])	Update inplace BIDS entity key/value pairs in object.

__hash__ = None¶

property acquisition: Optional[str]¶: The acquisition parameters.

property basename¶: Path basename.

copy()[source]¶

Copy the instance.

Returns

bidspathBIDSPath: The copied bidspath.

property datatype: Optional[str]¶: The BIDS data type, e.g. 'anat', 'meg', 'eeg'.

property directory¶

Get the BIDS parent directory.

If subject, session and datatype are set, then they will be used to construct the directory location. For example, if subject='01', session='02' and datatype='ieeg', then the directory would be:

<root>/sub-01/ses-02/ieeg

Returns

data_pathpathlib.Path: The path of the BIDS directory.

property entities¶: Return dictionary of the BIDS entities.

property extension: Optional[str]¶: The extension of the filename, including a leading period.

find_empty_room(use_sidecar_only=False, verbose=None)[source]¶

Find the corresponding empty-room file of an MEG recording.

This will only work if the .root attribute of the mne_bids.BIDSPath instance has been set.

Parameters

use_sidecar_onlybool: Whether to only check the AssociatedEmptyRoom entry in the sidecar JSON file or not. If False, first look for the entry, and if unsuccessful, try to find the best-matching empty-room recording in the dataset based on the measurement date.

Returns

BIDSPath | None: The path corresponding to the best-matching empty-room measurement. Returns None if none was found.
verbosebool | str | int | None: Control verbosity of the logging output. If None, use the default verbosity level. See the logging documentation and mne.verbose() for details. Should only be passed as a keyword argument.

property fpath¶

Full filepath for this BIDS file.

Getting the file path consists of the entities passed in and will get the relative (or full if root is passed) path.

Returns

bids_fpathpathlib.Path: Either the relative, or full path to the dataset.

match(check=False)[source]¶

Get a list of all matching paths in the root directory.

Performs a recursive search, starting in .root (if set), based on BIDSPath.entities object. Ignores .json files.

Parameters

checkbool: If True, only returns paths that conform to BIDS. If False (default), the .check attribute of the returned mne_bids.BIDSPath object will be set to True for paths that do conform to BIDS, and to False for those that don’t.

Returns

bids_pathslist of mne_bids.BIDSPath: The matching paths.

property meg_calibration_fpath¶

Find the matching Elekta/Neuromag/MEGIN fine-calibration file.

This requires that at least root and subject are set, and that datatype is either 'meg' or None.

Returns

pathpathlib.Path | None: The path of the fine-calibration file, or None if it couldn’t be found.

property meg_crosstalk_fpath¶

Find the matching Elekta/Neuromag/MEGIN crosstalk file.

This requires that at least root and subject are set, and that datatype is either 'meg' or None.

Returns

pathpathlib.Path | None: The path of the crosstalk file, or None if it couldn’t be found.

mkdir(exist_ok=True)[source]¶

Create the directory structure of the BIDS path.

Parameters

exist_okbool: If False, raise an exception if the directory already exists. Otherwise, do nothing (default).

Returns

selfBIDSPath: The BIDSPath object.

property processing: Optional[str]¶: The processing label.

property recording: Optional[str]¶: The recording name.

property root: Optional[pathlib.Path]¶: The root directory of the BIDS dataset.

property run: Optional[str]¶: The run number.

property session: Optional[str]¶: The acquisition session.

property space: Optional[str]¶: The coordinate space for an anatomical or sensor position file.

property split: Optional[str]¶: The split of the continuous recording file for .fif data.

property subject: Optional[str]¶: The subject ID.

property suffix: Optional[str]¶: The filename suffix.

property task: Optional[str]¶: The experimental task.

update(*, check=None, **kwargs)[source]¶

Update inplace BIDS entity key/value pairs in object.

run and split are auto-parsed to have two numbers when passed in. For example, if run=1, then it will become run='01'.

Also performs error checks on various entities to adhere to the BIDS specification. Specifically: - datatype should be one of: anat, eeg, ieeg, meg - extension should be one of the accepted file extensions in the file path: .con, .sqd, .fif, .pdf, .ds, .vhdr, .edf, .bdf, .set, .edf, .set, .mef, .nwb - suffix should be one of the acceptable file suffixes in: meg, markers, eeg, ieeg, T1w, participants, scans, electrodes, channels, coordsystem, events, headshape, digitizer, beh, physio, stim - Depending on the modality of the data (EEG, MEG, iEEG), space should be a valid string according to Appendix VIII in the BIDS specification.

Parameters

checkNone | bool: If a boolean, controls whether to enforce BIDS conformity. This will set the .check attribute accordingly. If None, rely on the existing .check attribute instead, which is set upon mne_bids.BIDSPath instantiation. Defaults to None.
**kwargsdict: It can contain updates for valid BIDS path entities: ‘subject’, ‘session’, ‘task’, ‘acquisition’, ‘processing’, ‘run’, ‘recording’, ‘space’, ‘suffix’, ‘split’, ‘extension’, or updates for ‘root’ or ‘datatype’.

Returns

bidspathBIDSPath: The updated instance of BIDSPath.

Examples

If one creates a bids basename using mne_bids.BIDSPath():

>>> bids_path = BIDSPath(subject='test', session='two',
...                      task='mytask', suffix='channels',
...                      extension='.tsv')
>>> print(bids_path.basename)
sub-test_ses-two_task-mytask_channels.tsv
>>> # Then, one can update this `BIDSPath` object in place
>>> bids_path = bids_path.update(acquisition='test', suffix='ieeg',
...                              extension='.vhdr', task=None)
>>> print(bids_path.basename)
sub-test_ses-two_acq-test_ieeg.vhdr

mne_bids.write_meg_crosstalk

mne_bids.make_dataset_description

mne_bids.BIDSPath¶

Examples using mne_bids.BIDSPath¶

Examples using `mne_bids.BIDSPath`¶