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Add changes summary for 0.8 (#845)
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* Add changes summary for 0.8

* Update doc/whats_new.rst

* Update doc/whats_new.rst

* Update release date
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hoechenberger authored Jul 15, 2021
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Expand Up @@ -10,9 +10,35 @@ What's new?
.. currentmodule:: mne_bids
.. _changes_0_8:

Version 0.8 (2021-07-14)
Version 0.8 (2021-07-15)
------------------------

This release brings numerous improvements and fixes based on feedback from our
users, including those working with very large datasets. MNE-BIDS now handles
previously-overlooked edge cases, offers a much more efficient way to
store data on macOS and Linux (using symbolic links), and lays the groundwork
for supporting BIDS derivatives, i.e., storing modified data.

Notable changes
~~~~~~~~~~~~~~~

- You can now write preloaded and potentially modified data with
:func:`mne_bids.write_raw_bids` by passing ``allow_preload=True``. This is
a first step towards supporting derivative files.
- `mne_bids.BIDSPath` now has property getters and setters for all BIDS
entities. What this means is that you can now do things like
``bids_path.subject = '01'`` instead of ``bids_path.update(subject='01')``.
- We now support Deep Brain Stimulation (DBS) data.
- The way we handle anatomical landmarks was greatly revamped to ensure we're
always using the correct coordinate systems. A new function,
`mne_bids.get_anat_landmarks`, helps with extracting fiducial points from
anatomical scans.
- When creating a BIDS dataset from FIFF files on macOS and Linux, MNE-BIDS
can now optionally generate symbolic links to the original files instead of
copies. Simply pass ``symlink=True`` to
:func:`mne_bids.write_raw_bids`. This can massively reduce the storage space
requirements.

Authors
~~~~~~~

Expand All @@ -37,7 +63,7 @@ Detailed list of changes
Enhancements
^^^^^^^^^^^^

- The fields "DigitizedLandmarks" and "DigitizedHeadPoints" in the json sidecar of Neuromag data are now set to True/False depending on whether any landmarks (NAS, RPA, LPA) or extra points are found in raw.info['dig'], by `Eduard Ort`_ (:gh:`772`)
- The fields "DigitizedLandmarks" and "DigitizedHeadPoints" in the json sidecar of Neuromag data are now set to ``true`` or ``false`` depending on whether any landmarks (NAS, RPA, LPA) or extra points are found in ``raw.info['dig']``, by `Eduard Ort`_ (:gh:`772`)
- Updated the "Read BIDS datasets" example to use data from `OpenNeuro <https://openneuro.org>`_, by `Alex Rockhill`_ (:gh:`753`)
- :func:`mne_bids.get_head_mri_trans` is now more lenient when looking for the fiducial points (LPA, RPA, and nasion) in the MRI JSON sidecar file, and accepts a larger variety of landmark names (upper- and lowercase letters; ``'nasion'`` instead of only ``'NAS'``), by `Richard Höchenberger`_ (:gh:`769`)
- :func:`mne_bids.get_head_mri_trans` gained a new keyword argument ``t1_bids_path``, allowing for the MR scan to be stored in a different session or even in a different BIDS dataset than the electrophysiological recording, by `Richard Höchenberger`_ (:gh:`771`)
Expand All @@ -48,7 +74,7 @@ Enhancements
- :func:`mne_bids.write_raw_bids` gained a new parameter ``empty_room`` that allows to specify an associated empty-room recording when writing an MEG data file. This information will be stored in the ``AssociatedEmptyRoom`` field of the MEG JSON sidecar file, by `Richard Höchenberger`_ (:gh:`795`)
- Added support for the new channel type ``'dbs'`` (Deep Brain Stimulation), which was introduced in MNE-Python 0.23, by `Richard Köhler`_ (:gh:`800`)
- :func:`mne_bids.read_raw_bids` now warns in many situations when it encounters a mismatch between the channels in ``*_channels.tsv`` and the raw data, by `Richard Höchenberger`_ (:gh:`823`)
- MNE BIDS now accepts ".mrk" head digitization files used in the KIT/Yokogawa/Ricoh MEG system, by `Jean-Rémi King`_ and `Stefan Appelhoff`_ (:gh:`842`)
- MNE BIDS now accepts ``.mrk`` head digitization files used in the KIT/Yokogawa/Ricoh MEG system, by `Jean-Rémi King`_ and `Stefan Appelhoff`_ (:gh:`842`)

API and behavior changes
^^^^^^^^^^^^^^^^^^^^^^^^
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- :func:`mne_bids.read_raw_bids` crashed when the (optional) ``acq_time`` column was missing in ``*_scans.tsv``, by `Alexandre Gramfort`_ (:gh:`814`)
- :func:`mne_bids.write_raw_bids` doesn't crash anymore if the designated output directory contains the string ``"tsv"``, by `Richard Höchenberger`_ (:gh:`833`)
- :func:`mne_bids.get_head_mri_trans` gave incorrect results when the T1 image was not in LIA format, now all formats function properly, by `Alex Rockhill`_ and `Alexandre Gramfort`_ (:gh:`827`)
- :func:`mne_bids.get_head_mri_trans` and :func:`mne_bids.write_anat` used a T1w image but depended specifically on the freesurfer T1w image. Now the freesurfer subject directory is used, by `Alex Rockhill`_ and `Alexandre Gramfort`_ (:gh:`827`)
- :func:`mne_bids.get_head_mri_trans` and :func:`mne_bids.write_anat` used a T1w image but depended specifically on the freesurfer T1w image. Now the FreeSurfer subjects directory is used, by `Alex Rockhill`_ and `Alexandre Gramfort`_ (:gh:`827`)

:doc:`Find out what was new in previous releases <whats_new_previous_releases>`

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