[Neuroimaging] [ANN] MNE-Python 0.24
Richard Höchenberger
richard.hoechenberger at gmail.com
Thu Nov 4 08:28:49 EDT 2021
Hello everyone,
We are very pleased to announce the new v0.24 release of MNE-Python! [image:
:balloon:][image: :balloon:][image: :balloon:]
This release is the culmination of more than 6 months of work by 45
contributors, 13 of whom contributed for the very first time – meaning
almost one third of contributors were first-timers! Thanks so much to all
of you! [image: :pray:]
We are extremely excited to share all the amazing things we’ve been working
on.
<https://mne.discourse.group/#google-summer-of-code-1>Google Summer of Code
The MNE-Python team supervised three students in this year’s Google Summer
of Code (GSoC) <https://summerofcode.withgoogle.com/>. We are thrilled to
announce that all of our students successfully finished their projects, greatly
enhancing the MNE-Python user experience:
- Adam Li <https://adam2392.github.io/> produced the MNE-Connectivity
<https://mne.tools/mne-connectivity/stable/index.html> package for
advanced connectivity analysis with MNE-Python.
- Alex Rockhill <https://github.com/alexrockhill> created a new GUI for
the localization of intracranial electrodes on CT and MRI scans, available
via mne.gui.locate_ieeg()
<https://mne.tools/stable/auto_tutorials/clinical/10_ieeg_localize.html#marking-the-location-of-each-electrode-contact>
.
- Martin Schulz <https://github.com/marsipu> reimagined the time-series
data browser and created the mne-qt-browser
<https://github.com/mne-tools/mne-qt-browser>package that will redefine
your experience of visual data inspection: faster, smoother, better.
Adam, Alex, and Martin: We had a blast working with you! Thank you for your
effort, endurance, and persistence!
<https://mne.discourse.group/#summary-of-the-most-notable-changes-2>Summary
of the most notable changes
- The coregistration GUI has been rebuilt from the ground up using a
state-of-the-art technology stack. It was tedious and difficult work,
believe us, but it was worth it! What changes for you? The GUI should be
more responsive, easier to use, and work more reliably on all
platforms! [image:
:raised_hands:]
- Working with intracranial recordings? A new GUI, mne.gui.locate_ieeg(),
helps to localize intracranial electrodes with CT and MR scans! [image:
:brain:]
- Ever heard of MNE reports? These single-file HTML documents can help
you track an entire analysis from beginning to end, and share the results
with your coworkers. With this release, reports are easier to use
and looking
better than ever
<https://mne.tools/stable/auto_tutorials/intro/70_report.html#sphx-glr-auto-tutorials-intro-70-report-py>
! [image: :star_struck:]
- Often find yourself creating separate evokeds for the different event
types in your epochs? Well, we just made your life a bit easier!
Epochs.average() now has a by_event_type parameter to automatically
produce evokeds for each event type – no need to write a loop
anymore! [image:
:relieved:]
- A new, modern, good-looking and fast way to visualize time-series data
has been added by Martin Schulz via the new (optional) mne-qt-browser
<https://github.com/mne-tools/mne-qt-browser> package. We are certain it
will redefine your experience of visual data inspection in MNE-Python!
<https://mne.discourse.group/#our-selection-of-highlights-3>Our selection
of highlights
<https://mne.discourse.group/#preprocessing-epochs-and-evokeds-4>Preprocessing,
epochs, and evokeds
- Acquired some data with breaks [image: :coffee:] between experimental
blocks, but the recording kept on running? These breaks can now be
automatically annotated via mne.preprocessing.annotate_break().
- The figures produced by ICA.plot_sources() for evoked data now use
different colors and line styles to make it easier to tell components apart.
[image: :bar_chart:]
- We have added cortical signal suppression (CSS) via
mne.preprocessing.cortical_signal_suppression(). [image: :no_bell:]
- Epochs.average() now has a by_event_type parameter to generate evokeds
for each event type. [image: :sunglasses:]
- We know you missed it: Evoked objects now have a get_data() method,
just like Raw and Epochs! You’re welcome. [image: :pray:]
<https://mne.discourse.group/#source-estimation-5>Source estimation
- The coregistration GUI has been rebuilt from the ground up and no
longer requires Mayavi. [image: :hammer_and_wrench:]
- We’ve added a new function, mne.bem.make_scalp_surfaces(), to compute
the scalp surfaces required for coregistration. Previously, this could only
be done on the command line. [image: :skull:]
- mne.inverse_sparse.mixed_norm now supports the SURE method to automate
setting of the regularization parameter. [image:
:chart_with_upwards_trend:]
<https://mne.discourse.group/#ieeg-6>iEEG
- There is a new GUI, mne.gui.locate_ieeg(), to locate intracranial
electrode contacts from a CT and anatomical MRI scans. This is described in
a new tutorial
<https://mne.tools/stable/auto_tutorials/clinical/10_ieeg_localize.html>.
[image: :brain:]
<https://mne.discourse.group/#fnirs-7>fNIRS
- Oxy- and deoxyhemoglobin data types can now be interpolated. [image:
:drop_of_blood:]
- NIRSport, NIRSport2, and data acquired with NIRx devices using Aurora
software version 2021.9 can now be read. [image: :open_book:]
<https://mne.discourse.group/#reports-8>Reports
- We completely revamped the report experience: new HTML layout, many
new methods, more flexibility! The functionality is demonstrated in
the respective
tutorial <https://mne.tools/stable/auto_tutorials/intro/70_report.html>.
[image:
:closed_book:]
<https://mne.discourse.group/#file-io-9>File I/O
- We’ve added support for exporting evoked MFF and raw EDF+ files. [image:
:articulated_lorry:]
- All functions for reading and writing files should now automatically
handle ~ (the tilde character) and expand it to the user’s home
directory. Saves you Linux and macOS folks some typing! [image:
:keyboard:]
<https://mne.discourse.group/#dependencies-10>Dependencies
- pooch <https://www.fatiando.org/pooch/latest/> is now required to
download the included datasets. [image: :open_file_folder:]
<https://mne.discourse.group/#api-enhancements-changes-and-deprecations-11>API
enhancements, changes, and deprecations
- All get_data() methods now have tmin and tmax parameters to specify
which time period to get. No more manual fiddling with those pesky indices!
[image: :stopwatch:]
- You should not modify the Info object manually as this can have
unexpected consequences. We’re now starting to enforce this and produce
warnings if you don’t follow our advice 🥸 And in a future release of
MNE-Python, these warnings will change into exceptions. So please pay
attention to them! And do let us know if you need help avoiding them.
- We will remove Mayavi and PySurfer 3D plotting backends in the next
version. [image: :wastebasket:]
- The mne kit2fiff GUI has been split off into the separate mne-kit-gui
<https://github.com/mne-tools/mne-kit-gui> package. [image: :package:]
- The mne.gui.fiducials() GUI has been deprecated, use mne coreg or
mne_kit_gui.fiducials() to set MRI fiducials instead. [image:
:wastebasket:]
<https://mne.discourse.group/#full-changelog-12>Full changelog
For a full list of improvements and API changes, see the changelog
<https://mne.tools/stable/whats_new.html#version-0-24>.
<https://mne.discourse.group/#installing-the-new-release-13>Installing the
new release
Since quite a few things – including dependencies – have changed, we
recommend creating a new environment with a “fresh” installation. Please
follow the installation instructions
<https://mne.tools/stable/install/mne_python.html> on our website.
<https://mne.discourse.group/#feedback-14>Feedback
As usual, we welcome your bug reports, feature requests, critiques, and
contributions. Development takes place on GitHub. If you would like to
contribute, star ⭐ the project, or just take a peek at the code, visit
mne-tools/mne-python <https://github.com/mne-tools/mne-python>.
<https://mne.discourse.group/#staying-up-to-date-15>Staying up to date
You may follow us on Twitter at @mne_news <https://twitter.com/mne_news>
<https://mne.discourse.group/#getting-help-16>Getting help
The MNE-Python forum <https://mne.discourse.group/> is an excellent way to
ask your questions and to share your knowledge with others. We also
announce our bi-weekly online office hours there.
And of course, we provide a large body of documentation, tutorials, and
examples on our website, mne.tools.
<https://mne.discourse.group/#closing-remarks-17>Closing remarks
We hope you will enjoy the new features and the many, many small
improvements we have added, and are looking forward to receiving your
feedback.
We will also start highlighting and demonstrating some of the new
functionality in brief tutorials and video clips shortly, so be sure to follow
us <https://twitter.com/mne_news>on Twitter to not miss any of those!
Stay safe and take care!
The MNE-Python developers
<https://mne.discourse.group/#contributors-18>Contributors
MNE-Python is a community-driven project. We are always very happy to
welcome new contributors of code and documentation! 45 people contributed
to this release, and 13 of them (29%) contributed for the very first time –
thank you so much for your time and effort, we truly appreciate it!
This is the list of contributors, in alphabetical order.
<https://mne.discourse.group/#first-time-contributors-19>First-time
contributors
- Darin Erat Sleiter
- Dominique Makowski
- Evgeny Goldstein
- Jan Sosulski
- John Samuelsson
- Joshua Teves
- Marian Dovgialo
- Mathieu Scheltienne
- Pierre-Antoine Bannier
- Reza Shoorangiz
- Romain Derollepot
- Timothy Gates
- Xiaokai Xia
<https://mne.discourse.group/#all-other-contributors-20>All other
contributors
- Adam Li
- Alex Rockhill
- Alexandre Gramfort
- Britta Westner
- Clemens Brunner
- Daniel McCloy
- David Julien
- Denis A. Engemann
- Eric Larson
- Erica Peterson
- Evan Hathaway
- Fede Raimondo
- Gansheng Tan
- Guillaume Favelier
- Hubert Banville
- Jean-Remi King
- Jeff Stout
- Johann Benerradi
- Josh Koen
- Lukas Hecker
- Luke Bloy
- Marijn van Vliet
- Martin Schulz
- Mikołaj Magnuski
- Richard Höchenberger
- Riessarius Stargardsky
- Robert Luke
- Ross Maddox
- Ryan Law
- Stefan Appelhoff
- Steve Matindi
- Valerii Chirkov
[image: :heart:] [image: :heart:] [image: :heart:]
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