Check for open issues, or report new ones on GitHub.
Fixed in 0.38.3, Windows only (#52): due to unexpected data loss in
multiprocessing.sharedctypes.RawArrayfor large arrays, permutation tests on large datasets using multiprocessing could return spurious results in which p-values for all clusters were reported as exactly 0.
New in 0.37
gui.select_components()): Sort noisy epochs by dominant components - makes it easier to find components that capture specific artifacts.
load.fiff.events()now loads events from all stim-channels. To use a subset, use the
plot.styles_for_twoway()to quickly generate different color and line-style combinations.
MneExperiment.plot_evoked(): plot sensor data with corresponding source estimates
API: By default, events are now loaded from all stim-channels. To only use a subset of stim-channels, use the new
New in 0.36
New in 0.35
In the source time-course window, display the range of the data before and after cleaning in real-time.
New keyboard shortcut:
alt + arrowkeys to go to the beginning/end.
New context-menu commands: find top component for an epoch.
NDVar.dot()generalized to multiple dimensions.
New in 0.34
plot.Scatterwith some parameter changes for improved functionality.
boosting(): Option to store TRFs for the different test partitions (
unitparameter to represent time in units other than seconds.
reportsubmodule with shortcuts for data summary and visualization.
load.convert_pickle_protocol()for compatibility with older Python version.
New in 0.33
New in 0.32
Requires at least Python 3.7
When using a
basis, the function now considers the effect of the basis when normalizing predictors. This change leads to slightly different results, so TRFs should not be compared between this and previous versions. To facilitate keeping track of this change, it corresponds to a change in the
tstopfor different predictors (contributed by Joshua Kulasingham)
Cross-validation of model fit (
decimparameter now also have
More control over Events
New in 0.31
delimparameter renamed to
testndAPI: For permutation tests, the
samplesparameter now defaults to 10,000 (previously 0)
byparameter is deprecated, use
NDVar.smooth()with a window with an even number of samples, and
boosting()with a basis with an even number of samples: the time axis is now consistent with
scipy.signal.convolve()(was previously shifted by half a sample)
testnd.LMGroup.coefficients_dataset()now returns a wide form table by default
plot.BarplotHorizontal: Horizontal bar-plot
SubParc: Simplified subset parcellation
New in 0.30
Support for vector data (with many contributions from Proloy Das):
ICA-GUI: tool to find high amplitude signals
Documentation: New Examples section
New in 0.29
API: Better default parameters for
Predictor-specific stopping for
General layout parameters for plot size relative to screen size
Better plots for masked statistic maps
New in 0.28
Transition to Python 3.6
matchparameter is now determined automatically and does not need to be specified anymore in most cases.
Previously capitalized argument and attribute names
Xaxare now lowercase.
Topomap-plot argument order changed to provide consistency between different plots.
Independent measures t-test
New in 0.27
To change the parcellation of an
NDVarwith source-space data, use the new function
SourceSpace.set_parc()method has been removed because dimension objects should be treated as immutable, as they can be shared between different
NDVar.smooth(): window-based smoothing now uses a symmetric window, which can lead to slightly different results.
NDVar.ols(): regress on a dimension.
plot.brain.SequencePlotterto plot multiple anatomical images on one figure.
New functions and objects:
New in 0.26
ANOVAs now support mixed models with between- and within-subjects factors (see examples at
load.fiff: when generating epochs from raw data, a new
tstopargument allows specifying the time interval exclusive of the last sample.
New in 0.25
When using iPython 5 or later, GUI start and stop is now automatic. It is possible to revert to the old behavior with
There are new hotkeys for most plots (see the individual plots’ help for details).
Plots automatically rescale when the window is resized.
defaults['experiment'], with support for multiple sessions in one experiment (see Setting up the file structure).
sel_epochhas been removed, use
raw='clm'has been renamed to
Custom preprocessing pipelines (see
modelparameter for ANOVA tests is now optional (see
New in 0.24
MneExperiment: For data from the NYU New York system converted with
mne< 0.13, the
MneExperiment.meg_systemattribute needs to be set to
"KIT-157"to distinguish it from data collected with the KIT UMD system.
masked_parameter_map()method of cluster-based test results: use of
pmin=Noneis deprecated, use
MneExperiment.make_report_rois()includes corrected p-values in reports for tests in more than one ROI
MneExperiment.make_rej()now has a
decimparameter to improve display performance.
MneExperiment: BEM-solution files are now created dynamically with
mneand are not cached any more. This can lead to small changes in results due to improved numerical precision. Delete old files to free up space with
MneExperiment: analysis parameter connectivity
Shift-Tfor a large topo-map with sensor names.
New in 0.23
New in 0.22
Epoch Rejection GUI:
New “Tools” menu.
New “Info” tool to show summary info on the rejection.
New “Find Bad Channels” tool to automatically find bad channels.
Set marked channels by clicking on topo-map.
Faster page redraw.
MneExperiment: new method
plot.configure(): option to revert to wxPython backend for
New in 0.21
New epoch parameters:
vardefparameter to load variables from a test definition.
Log files stored in the root directory.
MneExperiment.parcs) based on combinations can also include split commands.
.sort_idxmethods renamed to
New in 0.20
MneExperiment: new analysis parameter
select_clusters='all'to keep all clusters in cluster tests (see select_clusters (cluster selection criteria)).
testnd.configure()to limit the number of CPUs that are used in permutation cluster tests.
New in 0.19
Two-stage tests (see
Safer cache-handling. See note at Analysis.
The default format for plots in reports is now SVG since they are displayed correctly in Safari 9.0. Use
plot.configure()to change the default format.
plot.ColorListhas a new argument called labels.
Rejection-GUI: The option to plot the data range only has been removed.
New in 0.18
API: The first argument for
MneExperiment.plot_annot()is now parc.
combine()has been deprecated and replaced with a new parameter called
API: Several plotting functions have a new
xticklabelsparameter to suppress x-axis tick labels (e.g.
choose()to combine data in different
NDVarson a case by case basis.
gui.select_epochs()): Press Shift-i when hovering over an epoch to enter channels for interpolation manually.
MneExperiment.show_file_status()now shows the last modification date of each file.
Under OS X 10.8 and newer running code under a notifier statement now automatically prevents the computer from going to sleep.
New in 0.17
MneExperiment.brain_plot_defaultscan be used to customize PySurfer plots in movies and reports.
MneExperiment.trigger_shiftcan now also be a dictionary mapping subject name to shift value.
The rejection GUI now allows selecting individual channels for interpolation using the ‘i’ key.
Parcellations based on combinations of existing labels, as well as parcellations based on regions around points specified in MNI coordinates can now be defined in
NDVarcan be indexed with lists of region names, e.g.,
plot.brain.bin_table()function signature changed slightly (more parameters, new
hemiparameter inserted to match other functions’ argument order).
Var.as_factor()mapped unspecified values to
str(value). Now they are mapped to
''. This also applies to
MneExperiment.variablesentries with unspecified values.
New in 0.16
New function for plotting a legend for annot-files:
plot.brain.annot_legend()(automatically used in reports).
Epoch definitions in
MneExperiment.epochscan now include a
'base'parameter, which will copy the given “base” epoch and modify it with the current definition.
MneExperiment.make_mov_ga_dspm()are fixed but require PySurfer 0.6.
plot.brainfunction signatures changed slightly to accommodate more layout-related arguments.
New in 0.15
The Eelbrain package on the PYPI is now compiled with Anaconda. This means that the package can now be installed into an Anaconda distribution with
easy_installhas to be used for the Canopy distribution.
gui.select_epochs(): Set marked channels through menu (View > Mark Channels)
Datasets can be saved as tables in RTF format (
plot.Timeplot: the default spread indicator changed to SEM, and there is a new argument for timelabels.
test.anovais now a function with a slightly changed signature. The old class has been renamed to
test.onewaywas removed. Use
API: the default value of the
plot.Timeplotparameter bottom changed from 0 to None (determined by the data).
Plotting: New option for the figure legend
'draggable'(drag the legend with the mouse pointer).
New in 0.14
plot.Topomapargument sensors changed to sensorlabels.
GUI: The python/Quit Eelbrain menu command now closes all windows to ensure that unsaved documents are handled properly. In order to yield to the terminal without closing windows, use the Go/Yield to Terminal command (Command-Alt-Q).
testnd.TContrastRelated: support for unary operation abs.
New in 0.13
gui.select_epochs()GUI can now also be used to set bad channels.
MneExperimentsubclasses will combine bad channel information from rejection files with bad channel information from bad channel files. Note that while bad channel files set bad channels for a given raw file globally, rejection files set bad channels only for the given epoch.
Factorobjects can now remember a custom cell order which determines the order in tables and plots.
Var.as_factor()method can now assign all unmentioned codes to a default value.
API: Subclasses should remove the
MneExperimentcan now be imported directly from
MneExperiment._defaultsattribute should be renamed to
A draft for a guide at The MneExperiment Pipeline.
Cached files are now saved in a separate folder at
root/eelbrain-cache. The cache can be cleared using
MneExperiment.clear_cache(). To preserve cached test results, move the
root/testfolder into the
New in 0.12
Datasetconstruction changed, allows setting the number of cases in the Dataset.
plot.SensorMap2dwas renamed to
API: The default number of samples for reports is now 10’000.
New epoch parameter
'n_cases': raise an error if an epoch definition does not yield expected number of trials.
A custom baseline period for epochs can now be specified as a parameter in the epoch definition (e.g.,
'baseline': (-0.2, -0.1)). When loading data, specifying
baseline=Trueuses the epoch’s custom baseline.
New in 0.11
Change in the way the covariance matrix is defined: The epoch for the covariance matrix should be specified in
MneExperiment.epochs['cov']. The regularization is no longer part of
set_inv(), but is instead set with
cov='bestreg'automatically selects the regularization parameter for each subejct.
Var.as_factor()allows more efficient labeling when multiple values share the same label.
New in 0.10
New in 0.9
FactorAPI change: The
repargument was renamed to
T-values for regression coefficients through
MneExperiment: subject name patterns and eog_sns are now handled automatically.
Barplotplots can use pooled error for variability estimates (on by default for related measures designs, can be turned off using the
API: for consistency, the argument to specify the kind of error to plot changed to
errorin both plots.
New in 0.8
New in 0.6
New recipes (outdated).
New in 0.5
eelbrain.eellabmodules are deprecated. Everything can now me imported from
New in 0.4
New in 0.3
Optimized clustering for cluster permutation tests.
New in 0.2
gui.SelectEpochsEpoch rejection GIU has a new “GA” button to plot the grand average of all accepted trials
Cluster permutation tests in
testnduse multiple cores; To disable multiprocessing set
eelbrain._stats.testnd.multiprocessing = False.
New in 0.1.7
New in 0.1.5
plot.topo.TopoButterflyplot: new keyboard commands (