API Documentation¶

mne_bids¶

mne_bids:

MNE software for easily interacting with BIDS compatible datasets.

`write_raw_bids`(raw, bids_path[, ...])	Save raw data to a BIDS-compliant folder structure.
`read_raw_bids`(bids_path[, extra_params, verbose])	Read BIDS compatible data.
`write_meg_calibration`(calibration, bids_path)	Write the Elekta/Neuromag/MEGIN fine-calibration matrix to disk.
`write_meg_crosstalk`(fname, bids_path[, verbose])	Write the Elekta/Neuromag/MEGIN crosstalk information to disk.
`BIDSPath`([subject, session, task, ...])	A BIDS path object.
`make_dataset_description`(path, name[, ...])	Create json for a dataset description.
`make_report`(root[, session, verbose])	Create a methods paragraph string from BIDS dataset.
`write_anat`(image, bids_path[, landmarks, ...])	Put anatomical MRI data into a BIDS format.
`mark_channels`(bids_path, *, ch_names, status)	Update status and description of channels in an existing BIDS dataset.
`get_anat_landmarks`(image, info, trans, ...)	Get anatomical landmarks in MRI voxel coordinates.
`update_anat_landmarks`(bids_path, landmarks)	Update the anatomical landmark coordinates of an MRI scan.
`get_head_mri_trans`(bids_path[, ...])	Produce transformation matrix from MEG and MRI landmark points.
`get_anonymization_daysback`(raws[, verbose])	Get the group min and max number of daysback necessary for BIDS specs.
`search_folder_for_text`(entry, folder[, ...])	Find any particular string entry in the text files of a folder.
`print_dir_tree`(folder[, max_depth, return_str])	Recursively print a directory tree.
`get_bids_path_from_fname`(fname[, check, verbose])	Retrieve a BIDSPath object from a filename.
`get_entities_from_fname`(fname[, on_error, ...])	Retrieve a dictionary of BIDS entities from a filename.
`get_entity_vals`(root, entity_key, *[, ...])	Get list of values associated with an entity_key in a BIDS dataset.
`get_datatypes`(root[, verbose])	Get list of data types ("modalities") present in a BIDS dataset.
`inspect_dataset`(bids_path[, find_flat, ...])	Inspect and annotate BIDS raw data.
`update_sidecar_json`(bids_path, entries[, ...])	Update sidecar files using a dictionary or JSON file.
`anonymize_dataset`(bids_root_in, bids_root_out)	Anonymize a BIDS dataset.

mne_bids.stats¶

mne_bids.stats:

Some functions to extract stats from a BIDS dataset.

count_events(root_or_path[, datatype])

Count events present in dataset.

mne_bids.copyfiles¶

mne_bids.copyfiles:

Utility functions to copy raw data files.

When writing BIDS datasets, we often move and/or rename raw data files. several original data formats have properties that restrict such operations. That is, moving/renaming raw data files naively might lead to broken files, for example due to internal pointers that are not being updated.

`copyfile_brainvision`(vhdr_src, vhdr_dest[, ...])	Copy a BrainVision file triplet to a new location and repair links.
`copyfile_edf`(src, dest[, anonymize])	Copy an EDF, EDF+, or BDF file to a new location, optionally anonymize.
`copyfile_eeglab`(src, dest)	Copy a EEGLAB files to a new location and adjust pointer to '.fdt' file.
`copyfile_ctf`(src, dest)	Copy and rename CTF files to a new location.
`copyfile_bti`(raw, dest)	Copy BTi data.
`copyfile_kit`(src, dest, subject_id, ...)	Copy and rename KIT files to a new location.

13. Anonymizing a BIDS dataset

mne_bids.write_raw_bids