What’s new?

Here we list a changelog of MNE-BIDS.

Version 0.4

Changelog

• Added automatic conversion of FIF to BrainVision format with warning for EEG only data and conversion to FIF for meg non-FIF data, by Alex Rockhill (#237)

• Add possibility to pass raw readers parameters (e.g. allow_maxshield) to read_raw_bids() to allow reading BIDS-formatted data before applying maxfilter, by Sophie Herbst

• New feature in mne_bids.write.write_anat() for shear deface of mri, by Alex Rockhill (#271)

• Added option to anonymize by shifting measurement date with anonymize parameter, in accordance with BIDS specifications, by Alex Rockhill (#280)

• Added mne_bids.get_matched_empty_room() to get empty room filename matching a data file, by Mainak Jas (#290)

• Add ability for mne_bids.get_head_mri_trans() to read fiducial points from fif data without applying maxfilter, by Maximilien Chaumon (#291)

• Added landmark argument to write_anat() to pass landmark location directly for deface, by Alex Rockhill (#292)

• Standardized bids_root and output_path arguments in read_raw_bids(), write_raw_bids(), and make_bids_folder() to just bids_root, by Adam Li (#303)

• Add existence check for write_raw_bids() before make_dataset_description() is called, by Adam Li (#331)

• Update scans.tsv writer to adhere to MNE-Python v0.20+ where meas_date is stored as a datetime object, by Adam Li (#344)

• read_raw_bids() now reads in sidecar json files to set, or estimate Power Line Frequency, by Adam Li (#341)

• Allow FIF files with multiple parts to be read using read_raw_bids(), by Teon Brooks (#346)

• Added handedness to participant files, by Dominik Welke (#354)

• MNE-BIDS can now handle a paths that are pathlib.Path objects (in addition to strings), by Richard Höchenberger (#362)

• The documentation is now available for all MNE-BIDS versions via a dropdown menu, by Stefan Appelhoff (#370)

Bug

• Fixed broken event timing broken by conversion to BV in write_raw_bids(), by Alex Rockhill (#294)

• Support KIT related files .elp and .hsp BIDS conversion in write_raw_bids(), by Fu-Te Wong (#323)

• Enforce that the name arg is a required field for mne_bids.make_dataset_description(), by Teon Brooks and Stefan Appelhoff (#342)

• Fix writing to scans.tsv file when anonymization is turned on, by Adam Li (#352)

• Fix read_raw_bids() to properly read in sidecar json even if a similarly named copy lives inside “derivatives/” sub-folder, by Adam Li (#350)

• Fix read_raw_bids() to properly read in events.tsv sidecar if the ‘trial_type’ description has a “#” character in it by Adam Li (#355)

• Avoid cases in which NumPy would raise a FutureWarning when populating TSV files, by Richard Höchenberger (#372)

• Remove events with an unknown onset, and assume unknown event durations to be zero, when reading BIDS data via read_raw_bids(), by Richard Höchenberger (#375)

Authors

People who contributed to this release (in alphabetical order):

• Adam Li

• Alex Rockhill

• Alexandre Gramfort

• Ariel Rokem

• Dominik Welke

• Fu-Te Wong

• Mainak Jas

• Maximilien Chaumon

• Richard Höchenberger

• Sophie Herbst

• Stefan Appelhoff

• Teon Brooks

Version 0.3

Changelog

• New function mne_bids.utils.get_kinds() for getting data types from a BIDS dataset, by Stefan Appelhoff (#253)

• New function mne_bids.utils.get_entity_vals() allows to get a list of instances of a certain entity in a BIDS directory, by Mainak Jas and Stefan Appelhoff (#252)

• mne_bids.utils.print_dir_tree() now accepts an argument max_depth which can limit the depth until which the directory tree is printed, by Stefan Appelhoff (#245)

• New command line function exposed cp for renaming/copying files including automatic doc generation “CLI”, by Stefan Appelhoff (#225)

• read_raw_bids() now also reads channels.tsv files accompanying a raw BIDS file and sets the channel types accordingly, by Stefan Appelhoff (#219)

• Add example convert_mri_and_trans for using get_head_mri_trans() and write_anat(), by Stefan Appelhoff (#211)

• get_head_mri_trans() allows retrieving a trans object from a BIDS dataset that contains MEG and T1 weighted MRI data, by Stefan Appelhoff (#211)

• write_anat() allows writing T1 weighted MRI scans for subjects and optionally creating a T1w.json sidecar from a supplied trans object, by Stefan Appelhoff (#211)

• read_raw_bids() will return the the raw object with raw.info['bads'] already populated, whenever a channels.tsv file is present, by Stefan Appelhoff (#209)

• read_raw_bids() is now more likely to find event and channel sidecar json files, by Marijn van Vliet (#233)

• Enhanced read_raw_bids() and write_raw_bids() for iEEG coordinates along with example and unit test, by Adam Li (#335)

Bug

• Fixed bug in mne_bids.datasets.fetch_faces_data() where downloading multiple subjects was impossible, by Stefan Appelhoff (#262)

• Fixed bug where read_raw_bids() would throw a ValueError upon encountering strings in the “onset” or “duration” column of events.tsv files, by Stefan Appelhoff (#234)

• Allow raw data from KIT systems to have two marker files specified, by Matt Sanderson (#173)

API

• read_raw_bids() no longer optionally returns events and event_id but returns the raw object with mne.Annotations, whenever an events.tsv file is present, by Stefan Appelhoff (#209)

Authors

People who contributed to this release (in alphabetical order):

• Alexandre Gramfort

• Mainak Jas

• Marijn van Vliet

• Matt Sanderson

• Stefan Appelhoff

• Teon Brooks

Version 0.2

Changelog

• Add a reader for BIDS compatible raw files, by Mainak Jas (#135)

Bug

• Normalize the length of the branches in print_dir_tree() by the length of the root path, leading to more adequate visual display, by Stefan Appelhoff (#192)

• Assert a minimum required MNE-version, by Dominik Welke (#166)

• Add function in mne_bids.utils to copy and rename CTF files mne_bids.utils.copyfile_ctf(), by Romain Quentin (#162)

• Encoding of BrainVision .vhdr/.vmrk files is checked to prevent encoding/decoding errors when modifying, by Dominik Welke (#155)

• The original units present in the raw data will now correctly be written to channels.tsv files for BrainVision, EEGLAB, and EDF, by Stefan Appelhoff (#125)

• Fix logic with inferring unknown channel types for CTF data, by Mainak Jas (#129)

• Fix the file naming for FIF files to only expose the part key-value pair when files are split, by Teon Brooks (#137)

• Allow files with no stim channel, which could be the case for example in resting state data, by Mainak Jas (#167)

• Better handling of unicode strings in TSV files, by Mainak Jas (#172)

• Fix separator in scans.tsv to always be /, by Matt Sanderson (#176)

• Add seeg to mne_bids.utils._handle_kind() when determining the kind of ieeg data, by Ezequiel Mikulan (#180)

• Fix problem in copying CTF files on Network File System due to a bug upstream in Python by Mainak Jas (#174)

• Fix problem in copying BTi files. Now, a utility function ensures that all the related files such as config and headshape are copied correctly, by Mainak Jas (#135)

• Fix name of “sample” and “value” columns on events.tsv files, by Ezequiel Mikulan (#185)

• Update function to copy KIT files to the meg directory, by Matt Sanderson (#187)

API

• make_dataset_description() is now available from mne_bids main namespace, all copyfile functions are available from mne_bids.copyfiles namespace by Stefan Appelhoff (#196)

• Add support for non maxfiltered .fif files, by Maximilien Chaumon (#171)

• Remove support for Neuroscan .cnt data because its support is no longer planned in BIDS, by Stefan Appelhoff (#142)

• Remove support for Python 2 because it is no longer supported in MNE-Python, by Teon Brooks (#141)

• Remove Pandas requirement to reduce number of dependencies, by Matt Sanderson (#122)

• Use more modern API of event_from_annotations in MNE for extracting events in .vhdr and .set files, by Mainak Jas (#167)

Authors

People who contributed to this release (in alphabetical order):

• Alexandre Gramfort

• Chris Holdgraf

• Clemens Brunner

• Dominik Welke

• Ezequiel Mikulan

• Mainak Jas

• Matt Sanderson

• Maximilien Chaumon

• Romain Quentin

• Stefan Appelhoff

• Teon Brooks

Version 0.1

Changelog

• Add example for how to rename BrainVision file triplets: rename_brainvision_files.py by Stefan Appelhoff (#104)

• Add function to fetch BrainVision testing data mne_bids.datasets.fetch_brainvision_testing_data() Stefan Appelhoff (#104)

• Add support for EEG and a corresponding example: make_eeg_bids.py by Stefan Appelhoff (#78)

• Update mne_bids.raw_to_bids() to work for KIT and BTi systems, by Teon Brooks (#16)

• Add support for iEEG and add mne_bids.make_bids_folders() and mne_bids.make_bids_folders(), by Chris Holdgraf (#28 and #37)

• Add command line interface by Teon Brooks (#31)

• Add mne_bids.utils.print_dir_tree() for visualizing directory structures and restructuring package to be more open towards integration of other modalities (iEEG, EEG), by Stefan Appelhoff (#55)

• Automatically generate participants.tsv, by Matt Sanderson (#70)

• Add support for KIT marker files to be exported with raw data, by Matt Sanderson (#114)

Bug

• Correctly handle the case when measurement date is not available, by Mainak Jas (#23)

• Fix counting of miscellaneous channels, by Matt Sanderson (#49)

• The source data is now copied over to the new BIDS directory. Previously this was only true for FIF data, by Stefan Appelhoff (#55)

• Fix ordering of columns in scans.tsv, by Matt Sanderson (#68)

• Fix bug in how artificial trigger channel STI014 is handled in channels.tsv for KIT systems, by Matt Sanderson (#72)

• Fix channel types for KIT system in channels.tsv, by Matt Sanderson (#76)

• Fix the way FIF files are named to satisfy the BIDS part parameters of the filename construction, Teon Brooks (#102)

• Fix how overwriting of data is handled, by Matt Sanderson (#99)

Authors

People who contributed to this release (in alphabetical order):

• Alexandre Gramfort

• Chris Holdgraf

• Kambiz Tavabi

• Mainak Jas

• Matt Sanderson

• Romain Quentin

• Stefan Appelhoff

• Teon Brooks