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_bad_channels(ch_names[, descriptions, …])	Update which channels are marked as “bad” 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)	Get the group min and max number of daysback necessary for BIDS specs.
print_dir_tree(folder[, max_depth, return_str])	Recursively print a directory tree.
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)	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.

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. Writing modified files with MNE-BIDS mne_bids.write_raw_bids