EEG-Clean-Tools

Contains tools for the PREP pipeline for standardized preprocessing of EEG. You can find user documention at: http://vislab.github.io/EEG-Clean-Tools/

Note: For convenience, EEGLABPlugin directory contains the latest released version of the PREP that can be unzipped into your EEGLAB plugins directory.

Citing the PREP pipeline

The PREP pipeline is freely available under the GNU General Public License. Please cite the following publication if using:

Bigdely-Shamlo N, Mullen T, Kothe C, Su K-M and Robbins KA (2015)
The PREP pipeline: standardized preprocessing for large-scale EEG analysis
Front. Neuroinform. 9:16. doi: 10.3389/fninf.2015.00016

People

The PREP pipeline incorporates many algorithms that were developed at USCS SCCN over many years by Nima Bigdely-Shamlo, Tim Mullen and Christian Kothe. Kyung Min Su performed most of the machine learning evaluation of PREP. Cassidy Matousek and Jeremy Cockfield worked on the interfaces for the EEGLAB plugin as well as associated visualization tools. Kay Robbins of UTSA is the lead developer and maintainer of PREP.

Support:

This research was sponsored by the Army Research Laboratory and was accomplished under Cooperative Agreement Number W911NF-10-2-0022. The views and conclusions contained in this document/software are those of the authors and should not be interpreted as representing the official policies, either expressed or implied, of the Army Research Laboratory or the U.S. Government. The U.S. Government is authorized to reproduce and distribute reprints for Government purposes notwithstanding any copyright notation herein.

Releases

Version 0.56.0 Released 8/01/2021

• Corrected parfor failure when channel number not consecutive
• Fixed missing badChannelsFromDropout in updateBadChannels issue#28

Version 0.55.4 Released 7/26/2020

• Correctly restored EEGLAB options after execution
• Added functions to output errors from etc.noiseDetection
• Corrected findpeaks naming conflict in Chronux
• Post process does not execute if Prep had errors

Version 0.55.3 Released 10/19/2017

• Fixed issue with interpolated channels when interpolation order is pre-process
• Fixed issue with correct removal of interpolated channels during post-processing
• Reordered preprocessing and report buttons on master GUI

Version 0.55.2 Released 08/18/2017

• Fixed undefined reference to referenceOut in prepPipeline post process

Version 0.55.1 Released 06/03/2017

• Wrote printListCompressed to display channels more compactly
• Put in a MATLAB version check because legend titles not supported in 2014b
• Fixed spacing on output of interpolated channel numbers

Version 0.55.0 Released 05/29/2017

• Changed the EEG.etc.noiseDetection structure to contain removed channels and interpolated channels for easier access
• Fixed reporting to work when bad channels have been removed
• Added original channel labels to EEG.etc.noiseDetection for ease in reporting
• Added Blasst as an unsupported line noise removal option
• Moved legend of spectrum to right, put in checks for removed channels
• Corrected bug in smoothing in cleanline
• Corrected several reporting issues
• Default behavior now outputs errors to command line in addition to logging
• Renamed several functions to make naming scheme consistent
• Started supporting changelog in versions
• Fixed bug in struct2str and improved com return on pop_prepPipeline

Version 0.52 Released

• Modified code to handle EEG structures with empty EEG.error.
• Performed additional minor cleanup.

Version 0.51 Not released

• Developing bad window visualization plugin for EEGLAB

Version 0.50 Released

• Made several cleanup modifications to ready for release.

Version 0.48 (Not released -- version 0.47 with EEGLAB integration)

• Integrated EEGLAB plugin

• Changed the default structure value field name from defaults.default to default.value and propagated the change

• Changed default names of line noise and global trend to linenoise and globaltrend

• Modified the resampling step to allow an option low pass filter to remove downsampling artifacts just below Nyquist frequency.

  Version 0.47 (Not released -- version 0.46 with additional changes)

• Minor refactoring of performReference to avoid 1 extra filtering operation --- should not reflect results.

• Also added average and specific referencing methods -- not tested as yet.

Version 0.46 (Not released - version 0.45 with additional changes)

• Fixed remapping of bad evaluation channels into original channel numbers (relevant when there are none EEG channels interspersed in the channel locations.
• Passed detrend information in reference structure to allow detrending with other than the defaults
• Corrected several channel mapping issues in the reporting.

Version 0.45 (Not released - version 0.44 with additional changes)

• Refactored report to allow statistics to be gathered from noisy structures

Version 0.44 (Not released - version 0.43 with additional changes)

• Corrected a minor issue with reporting -- difference between robust and ordinary reference had axes reversed.
• Updated to run with plotting compatible with MATLAB 2014b
• Added box on to cummulative plots.

Version 0.43 (Not released - version 0.42 with additional changes)

• Corrected a minor issue with reporting -- mean scalp correlation map for beforeInterpolation was plotting the Original data rather than the beforeInterpolation data.

Version 0.42 (Not released - version 0.41 with additional changes)

• Added default line frequencies as multiples of 60 up to half nyquist.

Version 0.41 (Not released - version 0.40 with additional changes)

• Replaced default method with channel forgetting and median initialization
• Converted EEG to double at the beginning of the pipeline
• Added a noisyStatisticsForInterpolation field to the reference reporting structure.

Version 0.40 (Not yet released - major change in strategy)

• Changed the name from StandardLevel2 to PrepPipeline
• Implemented the HP filter-free strategy
• Added a keepFiltered version -- if false (the default) the data in the repository is not high pass filtered
• Added an option for removing global trend
• Incorporated the different reference schemes into a single performReference

Version 0.28 (Not yet released)

• Changed the name of the noisyParameter structure in EEG.etc to noiseDetection. This is a major change with corresponding change in ESS.
• Added a specificReferenceChannels field to reference structure
• Changed the averageReference field name to referenceSignal in reference structure
• Included a referenceType field in the reference structure (this can be 'robust', 'average', or 'specific')
• Eliminated the don't interpolateHFChannels flag.
• Added routines to do specificReference (mastoid or average)
• Modified showSpectrum to return the spectra of all of the channels.
• Detrending at 0.2 Hz has replaced FIR filtering as default trend removal.

Version 0.27 Released 1/7/2015

• Correct version of bug fix in cleanLineNoise -- watch that single precision conversion!

Version 0.26 Released 1/7/2015

• Release to fix bug in cleanLineNoise --- channels that are not lineNoiseChannels were set to zero rather than being carried forward.

  Version 0.25 Released 1/5/2015 (major)

• Removed saving of temporary file after line noise removal

• Fixed report of relative reference

• Modified findNoisyChannels to exclude NaN and constant channels from noisyChannel thresholding, but to designate them as bad channels

• Moved resampling step before high pass filter

• Assigned return values in a separate step

• Put error check in ShowSpectrum when invalid data is invalid

• Correct minor issues with PlotScalpMap

• Added extractReferenceStatistics -- which extracts summary statistics for an entire archive.

• Added iterations on the remove robust reference

• Added a summary reporting scheme for spotting problematic datasets.

Version 0.24 Released 12/7/2104 (major)

• Fixed channel selection bug in showSpectrum
• Added error handling for failures in standardLevel2Pipeline
• Added error reporting for failures
• Corrected time scale on visualization of difference between robust and mean reference
• Added channel labels as well as numbers to spectrum visualization
• Fixed major bug in robustReference so that original signal is rereferenced
• Revised and expanded the reporting

Version 0.23 Released 11/13/2014

• Removed the channel locations and channel information from noisyOut because it is already in the reference structure at top level.
• Added reporting of average fraction of channels bad in windows.
• Added first version of hdf5support -- rewrites the noisyParameters to an HDF5 file.

Version 0.22 Released 11/9/2014

• Revised the method of computing the windowed channel deviations
• Added summary reporting functions
• Added a check to only perform ransac when sufficiently good channels are available
• Added check to only perform ransac when channel locations are available
• Fixed the input parameter structure on findNoisyChannels
• Added the infrastructure for the summary of all datasets

Version 0.21 Released 10/30/2104

• Removed any reference to chanlocs in highPassFilter
• Full integration with ESS Study Level 2 code
• Preliminary version of Standard Level 2 Report finalized (gives pdf)

Version 0.20 Released 10/18/2014

• Converted standardLevel2Pipeline to a function
• Moved the computationTimes structure to standardLevel2Pipeline so that it is returned.

Version 0.19 Released 10/16/2014

• Refactored name is also included in the params structure.
• Renamed rereferencedChannels as channelsToBeReferenced to agree with ESS.

Version 0.18 Released 10/15/2014

• Refactored so that all input to the pipeline is in a single params structure.
• Fixed the HF noise reporting windows and several minor bugs
• Added visualizations to show number of bad channels in each window