erppcatoolkit-support — support list

[Erppcatoolkit-support] EP Toolkit 2.9974 released

[Joseph D. <jd...@ma...>]

EP Toolkit version 2.9974 has been released:
https://sourceforge.net/projects/erppcatoolkit/

Mostly bug fixes to get things fully stable before moving on to the 3.00 
release.  Note that Matlab 2025a has broken the method for coloring 
items in popup menus, so they will appear with html code visible 
instead.  I am seeking a solution.  I also fixed the reset button not 
working with 2025a. There may be other glitches with 2025a that I 
haven't encountered yet.

1) Added EP version and time to statistics header output.
2) Sample-by-sample results can be rendered as highlighted region as 
long as the adjoining colors are normal waves, not just for case with 
one sample-by-sample color and two normal waves.
3) Fixed sampleTest dataset popupmenu sometimes not appearing if the 
working set includes datasets with which it cannot be used.
4) Fixed crash when running sampleTest on virtual cells.
5) Fixed crash in View Topos when skipping colors.
6) Fixed crash in View Topos for PCA datasets that are only single-step.
7) Fixed dataset popupmenu in SampleTest function not allowing dataset 
to be changed.
8) Fixed crash when combining cells, as in Edit or SampleTest.
9) Fixed reset button not working on Matlab 2025a.
10) Fixed crash at start if EPdataset does not have lastChange field yet 
and dataset does not have .time field.
11) Added Apple Silicon mex file for the robust statistics computations.
12) Fixed crash when saving datasets with virtual cells or subjects in 
formats other than .ept.
13) Fixed crash when saving dataset in .egia/BESA .raw format where the 
age field is numeric.

Joe
--------------------------------------------------------------------------------

Joseph Dien, PhD
Senior Research Scientist
Human Development and Quantitative Methodology Department
University of Maryland, College Park
http://joedien.com

[Erppcatoolkit-support] EP Toolkit 2.9973 released

[Joseph D. <jd...@ma...>]

EP Toolkit version 2.9973 has been released:
https://sourceforge.net/projects/erppcatoolkit/

More bug fixes.

1) Fixed confidence intervals for pairwise within contrasts.
2) Fixed crash when updating ept files with 2.997 form of virtual subjects.
3) Fixed crash when reading a spatial PCA file that has impedance values.
4) Fixed crash in View Topos when a regional channel is not at the end 
of the channels.
5) Fixed bug when creating virtual cells in Edit, resulting in later 
crashes.
6) Fixed crash on startup of EP Toolkit under some conditions.

Joe
--------------------------------------------------------------------------------

Joseph Dien, PhD
Senior Research Scientist
Human Development and Quantitative Methodology Department
University of Maryland, College Park
http://joedien.com

[Erppcatoolkit-support] EP Toolkit 2.9972 released

[Joseph D. <jd...@ma...>]

EP Toolkit version 2.9972 has been released:
https://sourceforge.net/projects/erppcatoolkit/

More bug fixes, with the goal of eradicating any bugs before moving on 
to a major update.  The only new feature is a preference setting to 
control how the electrodes are marked in View Topos.

1) Fixed crash when abort button hit for the Edit function and Edit 
window was not yet open.
2) Fixed abort button while using Edit function returning user to the 
Edit pane instead of the Edit window, resulting in an unstable user 
interface state.
3) Fixed crash when abort button hit in certain situations.
4) Fixed EP version not updated in preferences, resulting in History 
record not being accurate.
5) In Views pane, fixed Trials popup menu disappearing when data 
settings changed to one where the current option (e.g., -CI-) is not 
applicable.
6) Fixed output of certain aborted procedures not empty, resulting in 
unpredictable behavior.
7) Fixed being unable to read in .ept files that have no virtual 
subjects or cells.
8) Fixed crash when combining channels using Edit function.
9) Fixed crash in Show Waves when fontsize preference set at NaN or zero.
10) Added preference for electrode markings in topo maps.
11) Fixed 2D contextual menu map not exactly corresponding to topomap in 
View>Topos.

Joe
--------------------------------------------------------------------------------

Joseph Dien, PhD
Senior Research Scientist
Human Development and Quantitative Methodology Department
University of Maryland, College Park
http://joedien.com

[Erppcatoolkit-support] EP Toolkit 2.9971 released

[Joseph D. <jd...@ma...>]

EP Toolkit version 2.9971 has been released:
https://sourceforge.net/projects/erppcatoolkit/

Very minor release.  It fixes a crash that can occur in the Edit 
function under a very specific situation. More importantly, it turned 
out that crashes in the Edit function could leave the EP Toolkit in a 
state where it would start producing a lot of mysterious and frustrating 
error messages.  The Edit function has been upgraded to handle crashes 
more gracefully. You'd still need to contact me to fix the crash bug itself.

Joe
--------------------------------------------------------------------------------

Joseph Dien, PhD
Senior Research Scientist
Human Development and Quantitative Methodology Department
University of Maryland, College Park
http://joedien.com

[Erppcatoolkit-support] EP Toolkit 2.997 released

[Joseph D. <jd...@ma...>]

EP Toolkit version 2.997 has been released:
https://sourceforge.net/projects/erppcatoolkit/

This release focused on overhauling the tutorial by using a new N400 
dataset that should provide a better example and that focuses on what a 
standard analysis stream should look like. From a tutorial point of 
view, the most relevant paragraphs have been highlighted in blue font. 
While updating the text, I made a lot of bug fixes and long-deferred 
updates.  A prominent change is the addition of virtual grand average 
subjects and cells that are internally generated when needed.  This 
means changes to the constituents, such as dropping a bad subject, is 
automatically reflected in the virtual grant averages. Aside from being 
handy, this allows the EP Toolkit to properly provide the trimmed 
average waveforms corresponding to the trimmed means of the robust 
statistics. This release is intended to provide a stable version upon 
which to build the 3.0 release.

1) Added option to save channel coordinate files in .sfp format to Save 
CED button in Channels pane of Edit function.
2) Add Channels in Edit function can now add an empty channel if none 
are selected to combine.
3) Can now change a normal channel to a fiducial or vice-versa using the 
Channels pane of the Edit function.
4) Fixed Cousineau-Morey CI calculation including the full eight color 
list even when only four colors are visible.
5) Modified Cousineau-Morey CI calculation so that it excludes CMB 
cells, as in difference waves.
6) Now uses more attractive round topo maps for 2D expanded figures in 
View>Topos function.
7) Fixed incorrect timeName labels when data appended via timepoint 
dimension.
8) Added support to View>Scan for video.
9) Added to View>Scan popupmenu controls for selecting the content of 
the topomaps, which can now be any of the displayed datasets.
10) Added support to View>Scan for files having individualized electrode 
coordinates.
11) In View>Scan, the first dataset is no longer treated specially. The 
current dataset for editing and events is now set by a popupmenu.
12) Various fixes to View>Scan controls.
13) Improved movie function in View>Scan.
13) Added support for EyeLink 1000 eye-tracker data.
14) Added manual controls for time marker in View>Scan.
15) Added BESA .raw file format as option for saving files.
16)  Fixed crash when reading sfp file.
17) Added types for sfp info, assumes first three rows are FID, and 
removed "Fid" from start of their names if present.
18) Added support for reading in supplemental .asf video file.
19) Added support for reading in supplemental .edf EyeLink eye-tracker 
file.
20) Added support for reading in supplemental .sfp file.
21) Added context-menu to add legend to expanded waveform figures.
22) Added lineStyle control for the waveform line preferences.
23) Improved the scree window user interface and it now automatically 
calculates the number of factors to retain.
24) In View>Topos, factor names are now grayed out if they are smaller 
than the minimum factor variance criterion.
25) Fixed crash when making changes in the Edit function and then going 
to the History tab.
26) Fixed sampTest cell names.
27) Fixed crash in View>Waves when plotting sampTest results and colors 
are non-consecutive.
28) Added color picker to View color preferences.
29) Fixed crash when switching Save function to convert mode.
30) Popup menus of spec values in Segment function are now 
alphabetically sorted.
31) No longer presenting abort dialog for each figure during 
preprocessing runs.
32) In Edit function, may now select subjects via QC and Specs panes.
33) Now handles subject specs in same way as trial specs, plus also 
generating summary string for gender/sex.
34) Fixed crash in View>Waves when colors are non-consecutive.
35) In View>Waves, font-size setting now controls scale graph labels as 
well.
36) In View>Waves, fixed bands options not working for averaged data 
when anything like noise or SD were dropped during averaging.
37) In View>Topos, fixed rereference context menu option not marking 
zero voltage line correctly.
38) In View>Topos, fixed 2-Chans contextual menu option crashing for 
t-test results.
39) Fixed View functions not displaying events other than RTs.
40) Fixed crash when making deleting subject in Edit mode and then going 
to the Events tab.
41) Fixed no events for grand average waveforms in View>Waves.
42) Fixed sampTest crash with average file when grand averages are not 
at the end of the list.
43) Fixed crash in View>Waves with an expanded channel when sampleTest 
results are displayed in isolation without waveforms.
44) For ANOVA outputs, fixed outlier plots for between group effects 
displaying same cell for all levels.
45) Fixed regional channels computation not handling NaN data points 
correctly, sometimes resulting in blank waveforms.
46) Fixed ANOVA adds not computing which subjects to include correctly.
47) Fixed ANOVA adds not generating trimmed average waveforms if no 
between group factors.
48) Fixed list of subjects going into a grand average’s variance not 
being updated when reordering the list of subjects.
49) Fixed grand averaging sometimes not correctly computing averaged 
subject specs correctly.
50) Fixed grand averaging sometimes not computing averaged task specs.
51) Fixed crash in combining cells or subjects when non-consecutive.
52) Fixed Save not including sample-by-sample waveform results.
53) Fixed crash when deleting subject spec and it was the last one.
54) Fixed crash when combining cells or subjects and some are bad.
55) Fixed Grand popup menu not handling interspersed grand averages 
properly.
56) Improved Grand popupmenu of Cells pane of Edit function.
57) Added virtual grand averages.
58) Fixed WindowAdds addition of channels to PCA files.
59) Fixed crash when running ANOVAs with a between factor and a within 
electrode factor.
60) Fixed spatial PCA channels not being combined correctly for regional 
channels.
61) Added support for Version 3 ANOVA text files, to ensure ANOVAadds 
are matched to the correct cells.
62) Added final pairwise contrasts between all cells when a within-group 
interaction is significant.
63) In the View Topos function, the topos in the first row can now be 
averaged over a time points and/or Hz window.
64) Fixed various things in the user interface not restricting 
themselves to just the displayed colors, causing problems like crashing.
65) Updated jack-knife function in View Topos to handle frequency data.
66) Improved determination of display range for dB unit FFT data in View 
Topos.
67) Fixed crash when displaying FFT data in View Waves with no events.
68) Restored black electrode dots in main display of View Topos.
69) Made various fixes to buggy View Scan single-trial interface.
70) Fixed sample test results in View Waves rendered in red if just a 
single sample.
71) Fixed crash when combining subjects in certain cases.
72) Fixed crash when using Contrast function of ANOVA pane.
73) Fixed crash in Transform with frequency transformation when all 
channels in a trial are bad.
74) Fixed crash when using View Waves with frequency data.
75) When View Waves with a single timepoint of TFT data, will display 
the FFT wave for that timepoint.
76) Fixed various crashing bugs with coherence data.
77) Added Swap button to the Channels subpane of the Edit function.
78) Fixed crash when saving PCA files.
79) Fixed unable to close Edit pane when there is only one dataset in 
the working set.
80)  Now uses Fisher’s Z transform with coherence data when computing 
grand averages and combined cells as they are essentially correlations.
81) Fixed View Topos bug in display of TFT coherence data.
82) Fixed crash in View Topos dipole function due to change in EEGlab 2025.
83) Fixed not actually temporarily correcting bad EOG channels at start 
of artfact correction routine, resulting in failure to blink and saccade 
correct when there are bad EOG channels.

Joe
--------------------------------------------------------------------------------

Joseph Dien, PhD
Senior Research Scientist
Human Development and Quantitative Methodology Department
University of Maryland, College Park
http://joedien.com

[Erppcatoolkit-support] EP Toolkit 2.996 released

[Joseph D. <jd...@ma...>]

EP Toolkit version 2.996 has been released:
https://sourceforge.net/projects/erppcatoolkit/

The main update was fixing a new bug that was keeping many .ept files 
from being read. Also a crash when generating ANOVAs.  A minor but 
useful enhancement is that in View Topos, the channels popup menus now 
have the peak positive and peak negative channels highlighted so it will 
be easy to switch between the two.  So, for example, P300 factors often 
start with the negative channel since channels around the face tend to 
have high amplitudes (due to the optic channel being low impedance path 
to the brain) and can have higher absolute amplitude than the positive 
channels.

1) Fixed incorrect check of covAVE field against number of subjects 
(2.995 fix was in error).
2) Fixed crash in Window pane when the selected dataset has no history 
field.
3) Fixed crash in some cases due to bug in new improved scaling of ANOVA 
bar plots.
4) Fixed problem with .std to .covAVE backward compatibility conversion 
that was preventing old .ept files from loading.
5) Fixed RT and ACC trial specs being set to NaN for cells and subjects 
combined via the Edit function.
6) Now color codes the channel menus in View Topos with blue for the 
minimum voltage and red for the maximum voltage so both peak channels 
can be readily found.

Joe
--------------------------------------------------------------------------------

Joseph Dien, PhD
Senior Research Scientist
Human Development and Quantitative Methodology Department
University of Maryland, College Park
http://joedien.com

[Erppcatoolkit-support] EP Toolkit 2.995 released

[Joseph D. <jd...@ma...>]

EP Toolkit version 2.995 has been released:
https://sourceforge.net/projects/erppcatoolkit/

The usual set of bug fixes and GUI improvements. Notably, the error bars 
in the new ANOVA bar graphs were too large.  Also the y-axis 
auto-scaling of the bar graphs is now optimized for presentation.

1) Fixed crash in ANOVA function when doing vector scaling test with 
collapsed cells.
2) Fixed not updating "have" value after using the Load ANOVAtable button.
3) Tweaked bad channel detection algorithm so less sensitive to solitary 
bad channels with high amplitude.
4) Median correct displayed data in Template function so more robust 
with non-baseline corrected segmented data when forming manual templates.
5) Fixed crash in some cases when doing followup within contrasts.
6) Fixed incorrect check of covAVE field against number of subjects, 
potentially preventing reading of older ept files.
7) Fixed crash when opening up older files with Edit function that have 
empty History fields.
8) Fixed crash when opening up older PCA files with Edit function that 
do not have Algorithm fields.
9) Fixed error bars in ANOVA figures too large.
10) Fixed Edit window going into infinite loop when appearing in a 
secondary window shorter than the primary one.
11) Fixed Edit window immediately opening after Done when just a single 
file in active set.
12) Disabled minimum size for Edit window to accommodate smaller monitors.
13) Fixed montage submenu not updating when import file format changed 
on Segment pane.
14) May now specify suffix for output segmented files via Preferences 
setting and eliminated SMI suffix preference.
15) Improved scaling of ANOVA bar plots.

Joe
--------------------------------------------------------------------------------

Joseph Dien, PhD
Senior Research Scientist
Human Development and Quantitative Methodology Department
University of Maryland, College Park
http://joedien.com

[Erppcatoolkit-support] EP Toolkit 2.994 released

[Joseph D. <jd...@ma...>]

EP Toolkit version 2.994 has been released:
https://sourceforge.net/projects/erppcatoolkit/

Aside from the usual bug fixes and improvements to the working of the 
user interface, there has been substantial upgrades to the output from 
the ANOVA function, including more comprehensive and up-to-date effect 
sizes, confidence intervals, information used for power analyses, and 
graphs of outliers and effects.  The robust statistics are now current 
as of the perspective represented in Wilcox (2022).

1) Fixed auto option not working for multi-factor structures where the 
first letter represents a factor.
2) Fixed crash when saving ANOVA table name.
3) Added buttons for loading and saving the Window cells table.
4) Added checkboxes to Save function to allow for multiple saves.
5) Fixed Winsorized Standard Errors in output cell tables computed 
incorrectly. Test statistics not affected.
6) Fixed crash when using 10-05 column.
7) Fixed p-value sometimes displayed with more than two significant 
digits by ANOVA function.
8) Fixed not clearing out old column names in ANOVA interface when 
loading in a newer dataset with fewer columns.
9) Fixed crash when loading an ANOVA file with more than one spec.
10) Fixed Winsorized Standard Errors in output cell tables computed 
incorrectly. Test statistics not affected.
11) Fixed robust MSE computed incorrectly for designs with multiple 
factors.  Test statistics not affected.
12) Changed vector scaling test to compute scaling within collapsed 
cells rather than original cells.  Test statistics potentially affected.
13) Added parallel computing calls to accelerate robust statistics.
14) Added buttons to ANOVA output html for selecting between cell means 
tables with SD, Cousineau-Moray SE, robust Cousineau-Moray CI, outlier 
plots, or plots with CI error bars.
15) Fixed crash when loading ANOVA table.
16) Added mean R to ANOVA output for use with power calculations.
17) Fixed Save function checkboxes crashing and also further 
streamlining functionality.
18) Removed Loftus-Masson standard error statistic from ANOVA output.
19) Added dR effect sizes and confidence intervals for pairwise 
within-group effects as well, plus effect sizes for between and within 
group effects with more than two levels.
20) Added bold for non-significant effects with confidence interval 
boundaries less than absolute .2.
21) Moved files list of History pane to a popupmenu so that the contents 
can be better inspected.
22) Changed output of trimmed means to be those of collapsed cells 
(e.g., with 5% trimming, two separate cells with n=10 each would not be 
trimmed whereas a collapsed cell with n=20 would be trimmed. Means 
tables and test statistics potentially affected.

Joe
--------------------------------------------------------------------------------

Joseph Dien, PhD
Senior Research Scientist
Human Development and Quantitative Methodology Department
University of Maryland, College Park
http://joedien.com

[Erppcatoolkit-support] EP Toolkit 2.993 released

[Joseph D. <jd...@ma...>]

EP Toolkit version 2.993 has been released:
https://sourceforge.net/projects/erppcatoolkit/

This release was mostly about fixing bugs and minor enhancemnts.

1) Fixed ignoring EGI montage values when preprocessing ept files with 
EGI data, resulting in incorrect identification of Cz and EOG channels 
and thus suboptimal artifact correction.
2) Improved newCED buttons in Edit function to better accommodate 
different use cases.
3) Added Clear and All buttons to the Trials subpane of the Edit function.
4) Fixed crash when using the Delete button in the Trials subpane of the 
Edit function.
5) Added color coding for QC and Specs subpanes.
6) When reading comma-delimited files, drop single quotes bracketing 
strings.
7) General improvements to how the GUI works.
8) Fixed unable to combine cells or subjects, as in Edit function, when 
all the values of a trial spec were missing data.

Joe
--------------------------------------------------------------------------------

Joseph Dien, PhD
Senior Research Scientist
Human Development and Quantitative Methodology Department
University of Maryland, College Park
http://joedien.com

[Erppcatoolkit-support] EP Toolkit 2.992 released

[Joseph D. <jd...@ma...>]

EP Toolkit version 2.992 has been released:
https://sourceforge.net/projects/erppcatoolkit/

This release was mostly about fixing bugs.
1) In View Waves, fixed SampleTest waves not plotting as highlighted 
region when two normal waves and one STS wave.
2) Fixed crash in View>Scan when clicking channel name to denote bad 
channel and channels are zoomed in and scrolled down.
3) Fixed View>Topos with continuous data providing popupmenu with 
timepoints for the entire dataset, causing crash when a timepoint 
outside the specified time window is chosen.
4) In Edit function, fixed crash when clicking New button.
5) Fixed not finding files under some Matlab configurations when 
batching files via Transform function.
6) Fixed detection of blinks via manual templates made less effective by 
bad channels and reference channels that were not the final channel.
7) Fixed crash with View>Topos with Topogrids option when viewing as 
timepoints.
8) When reading in an mff file, will only consider EEG channels when 
assuming the last is the reference.

Joe
--------------------------------------------------------------------------------

Joseph Dien, PhD
Senior Research Scientist
Human Development and Quantitative Methodology Department
University of Maryland, College Park
http://joedien.com

[Erppcatoolkit-support] EP Toolkit 2.991 released

[Joseph D. <jd...@ma...>]

EP Toolkit version 2.991 has been released:
https://sourceforge.net/projects/erppcatoolkit/

This release was mostly about fixing bugs.
1) Fixed crashing when saving using Trim button of Segment function.
2) Fixed no longer recognizing standard EGI channel names as of 2.99 and 
then crashing.
3) Fixed crash when batching files via Transform function.
4) Added ability to fix BV Headers when encoded using both Response and 
Stimulus events rather than just Stimulus events.
5) Fixed grand average CI bands not appearing in View Waves if there is 
missing data present.
6) Fixed band data in View Waves not matching up to data when a color is 
skipped.
7) Fixed Single File Mode of Preprocessing function aborting with a 
"file not found" error.
8) For EGI montages, if not otherwise specified (as in mff files using 
internal electrode information rather than external ced file), assumes 
last channel is the original reference.
9) Fixed crash when combining cells of an average file containing the 
SDs and covariances and all but one of the cells are empty.

Joe
--------------------------------------------------------------------------------

Joseph Dien, PhD
Senior Research Scientist
Human Development and Quantitative Methodology Department
University of Maryland, College Park
http://joedien.com

Re: [Erppcatoolkit-support] EP Toolkit 2.99 released

[Arild H. <he...@ud...>]

Thanks Joe, I think you are exaggerating when you say you have neglected EP
toolkit!
-Arild

On Fri, Jun 23, 2023 at 5:30 PM Joseph Dien via Erppcatoolkit-support <
erp...@li...> wrote:

> EP Toolkit version 2.99 has been released:
> https://sourceforge.net/projects/erppcatoolkit/
>
> This release was mostly about fixing bugs.  I've been neglecting the EP
> Toolkit, but should be getting back to it next year, in time for the 3.00
> release!
>
> 1) Fixed not allowing for smoothing to be adjusted for wavelet
> multiplication and wavelet convolution options for FFT and TFT transforms.
> 2) Fixed not automatically adjusting bad smoothing values for wavelet
> multiplication and wavelet convolution options for FFT and TFT transforms.
> 3) Fixed crash when clicking on topo for 3D image when a new spline file
> has to be generated, as when there are bad channels.
> 4) Fixed crash in View function controls when the data to be displayed are
> not voltage measures or continuous data.
> 5) Fixed crash in PCA pane when Deep Learning Toolbox not installed.
> 6) Fixed subject specs not matching up correctly when there are multiple
> sessions per subject.
> 7) Improved support for fieldtrip .mat files.
> 8) Attempts to accomodate non-standard EGI channel name conventions like
> "chan001" rather than "E1".
> 9) Fixed filter function returning data unchanged when a data segment is
> bad and consists of all NaN.
> 10) Fixed crash in Segment function when sampling rate is not a multiple
> of 500.
>
> Joe
>
> --------------------------------------------------------------------------------
>
> Joseph Dien, PhD
> Senior Research Scientist
> Human Development and Quantitative Methodology Department
> University of Maryland, College Park
> http://joedien.com
>
>
> _______________________________________________
> Erppcatoolkit-support mailing list
> Erp...@li...
> https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support
>

[Erppcatoolkit-support] EP Toolkit 2.99 released

[Joseph D. <jd...@ma...>]

EP Toolkit version 2.99 has been released:
https://sourceforge.net/projects/erppcatoolkit/

This release was mostly about fixing bugs. I've been neglecting the EP 
Toolkit, but should be getting back to it next year, in time for the 
3.00 release!

1) Fixed not allowing for smoothing to be adjusted for wavelet 
multiplication and wavelet convolution options for FFT and TFT transforms.
2) Fixed not automatically adjusting bad smoothing values for wavelet 
multiplication and wavelet convolution options for FFT and TFT transforms.
3) Fixed crash when clicking on topo for 3D image when a new spline file 
has to be generated, as when there are bad channels.
4) Fixed crash in View function controls when the data to be displayed 
are not voltage measures or continuous data.
5) Fixed crash in PCA pane when Deep Learning Toolbox not installed.
6) Fixed subject specs not matching up correctly when there are multiple 
sessions per subject.
7) Improved support for fieldtrip .mat files.
8) Attempts to accomodate non-standard EGI channel name conventions like 
"chan001" rather than "E1".
9) Fixed filter function returning data unchanged when a data segment is 
bad and consists of all NaN.
10) Fixed crash in Segment function when sampling rate is not a multiple 
of 500.

Joe
--------------------------------------------------------------------------------

Joseph Dien, PhD
Senior Research Scientist
Human Development and Quantitative Methodology Department
University of Maryland, College Park
http://joedien.com

[Erppcatoolkit-support] EP Toolkit 2.98 released

[Joseph D. <jd...@ma...>]

EP Toolkit version 2.98 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

This release was mostly about fixing bugs.  The biggest bug fix was the removal of incompletely implemented epsilon values for robust ANOVA results that had accidentally been left in the released version.  Support for reading NeuroElectric .easy files has been added as well.

1) Fixed not updating "have" value after using the Auto button in the ANOVA function. 
2) In ANOVA function, fixed standard errors only going out to two decimals and thus often being zero for accuracy data. 
3) Fixed crash when there are more than one unique unrecognized channel types. 
4) Fixed crash when combining subjects in certain cases. 
5) Deleted erroneous epsilon output in ANOVA function (zero for compiled code and non-zero for Matlab code) accidentally left active from abortive effort to implement epsilon computation for robust statistics. 
6) Fixed changes to bad trials spec in Preprocessing Preferences not being registered. 
7) Fixed crash in Preprocessing function when preprocessing data with NaN values. 
8) Fixed crash when there is no electrode coordinate information. 
9) Fixed not recognizing lowercase versions of recognized channel types. 
10) Fixed crash when merging Matlab .mat files. 
11) Fixed type information in a CED file going into the theta field when coordinates information is empty and then the now empty type field defaulting to "EEG”. 
12) Fixed crash when reading continuous files in single-file mode and the Cell field has been left empty. 
13) Added support for reading Neuroelectrics .easy files. 
14) Fixed crash when batch reading or converting continuous files. 
15) Fixed failing to read EGI data files with error message about needing to match at least three channels. 
16) Fixed crash when starting up EP Toolkit and EPdataset has no dataset field yet.

Joe
--------------------------------------------------------------------------------

Joseph Dien, PhD
Senior Research Scientist
Human Development and Quantitative Methodology Department
University of Maryland, College Park
http://joedien.com <http://joedien.com/>

[Erppcatoolkit-support] EP Toolkit 2.97 released

[Joseph D. <jd...@ma...>]

EP Toolkit version 2.97 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

This release was mostly about fixing bugs and adding various minor refinements.  The EGI CED files have been updated to reflect the current age-specific electrode coordinate .sfp files provided by EGI.

1) Fixed crash when combining subjects, as in a grand average, and the optional standard deviation information is present. 
2) Fixed crash when combining cells and none are good and there are trial specs present. 
3) Fixed crash when reading .ept files where eloc is missing and ced is specified and the file is a spatial PCA file. 
4) Fixed ANOVA function crashing when there are more than two between-group factors. 
5) Fixed crash when there is a BAD channel specified in the CED file. 
6) Fixed regional channels treated as being BAD channels in cases where non .ept file formats are read in. 
7) Fixed crash when merging files, as in Single File Mode, while applying a CED file with BAD channels. 
8) ChanTypes in .fif files are now ignored as they are apparently specified by users rather than being standardized. Instead CED files will need to be used. 
9) Will now accommodate case where .fif file erroneously codes the EOG channels as being fiducial points. 
10) Added .ced file for EGI Hydrocel-33. 
11) Fixed crash in View Waves when there is only one channel with coordinates. 
12) In View Waves, if there is at least one channel with coordinates and there are too many channels with no coordinates to fit on the left side of the figure, will now space them out in columns. 
13) Fixed crash when reading a file and two REF channels are specified in the CED file. 
14) When reading a text file such as a CED file, empty lines are ignored. 
15) Added support for reading sfp files in Overview pane of Edit function. 
16) Fixed crash when combining subjects and there are empty trial spec values, as when generating a PCA file. 
17) Added support for reading writing Matlab .mat files. 
18) Fixed crash when reading file with empty array as trial specs field. 
19) Fixed crash in Edit function when renaming an implicit channel. 
20) Fixed crash in Edit function when plotting electrode positions with the Head button and there is a fiducial with the name of Nz or T9 or T10. 
21) Fixed weights in Edit function not being reinitialized after deleting channels. 
22) Updated code for recognizing alternate names for EGI reference channel so that it is not added when electrode coordinates are being added if under a different name. 
23) When transforming electrodes to canonical coordinates (as in 3D heads and source analyses), now relies on fiducials plus Cz (plus any other channel name matches) for EGI montages and only uses approximate channel matches if they are not available. 
24) Fixed names of fiducial channels not being included when saving a CED file using the Channels Pane of the Edit function. 
25) Updated the EGI Hydrocel CED files to the current versions. 
26) Added ability to load and save ANOVA table settings and auto ANOVA table button. 
27) Fixed crash when reading a _evt.txt file where there is a header but no data. 
28) Added T in front of variable names when writing a file in stacked format. 
29) When reading in data files, fixed not properly matching up CED with data channels when some of the channel names do not match and at least one of them was a BAD channel. 
30) Names that readlocs reserves for fiducials ('nz' 'lpa' 'rpa' 'nasion' 'left' 'right' 'nazion' 'fidnz' 'fidt9' 'fidt10' 'cms' 'drl' 'nas' 'lht' 'rht' 'lhj' 'rhj') may now be used as channel names. 
31) Fixed crash in blink correction step of preprocess function when sampling rate higher than 1000. 
32) Added option to run either SAS or SPSS version of Promax algorithm. 
33) Turning off the figure labels now also turns off the axis labels in the expanded channel figures.

Note that you will need to update your copy of FieldTrip to a 2021 version or later to be able to read EEGlab files created with version 2021.0 onwards. Also remember to click on Set Path when updating the EP Toolkit and use the "Add with Subfolders" button. I've also made a fix to the FieldTrip's I/O code, which the EP Toolkit uses for reading .fif files that can causes crashes under certain conditions, but they haven't gotten around to incorporating it into the codebase. You can download the fixed file from FieldTrip's github site or write me if you need it, but keep in mind that if the EP Toolkit is not crashing when you read your .fif files, you don't need it.

Joe
--------------------------------------------------------------------------------

Joseph Dien, PhD
Senior Research Scientist
Human Development and Quantitative Methodology Department
University of Maryland, College Park
http://joedien.com <http://joedien.com/>

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[Erppcatoolkit-support] EP Toolkit 2.96 released

[Joseph D. <jd...@ma...>]

EP Toolkit version 2.96 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

This release fixes a lot of bugs that had accumulated and also cleans up the tutorial.  Major new features include support for the SME and the ERA data quality measures, standard errors for the ANOVA output, and an enhanced History functionality that allows you to see exactly what settings were used for each analysis step.

1) Added meanSME and meanNoise options to the Window function. 
2) Added code to work around weird Matlab condition that truncates the statistics lines in the html output files. So far I've only seen this with Matlab 2021a under OS X. 
3) Standard errors are now provided along with the cell means for within-subject analyses in the ANOVA outputs. 
4) Fixed typo that caused crash in the ANOVA preferences pane. 
5) Increased default number of bootstrap samples for robust ANOVAs to 499,999 from 49,999. 
6) Upgraded History functionality. There is now a pane in the Edit function that shows the changes that have been made to the dataset, when, and by whom. Clicking on the checkbox brings up a playback of the EP Toolkit settings. The preferences now allow for specification of information like the user and the institution for use in the history record. 
7) Fixed window add for spectral data so that both real and imaginary components generated correctly. 
8) Fixed EMCP not rejecting trials that contained bad channels unless it was the last channel. 
9) Updated MFFMatlabIO to version 4.0. 
10) Added option for writing edf files. 
11) Fixed crash in artifact correction function when a topo in the templates figure was blank, as when no data were corrected. 
12) Fixed crash when merging files with subject specs. 
13) For difference waves produced by the Edit function, RT trial specs now calculated as the average of the specs rather than the difference so that the RT option in the View function works properly (ACC as well, just to be consistent). 
14) Fixed crash after expanding View pane and using the expanded colors and then closing up the expansion and then expanding a channel waveform. 
15) Fixed crash in Segment function pane when there is a single-trial dataset in the working set that has trials with empty events cells. 
16) Fixed crash in ANOVA function when trying to handle no-header file with between-group variables. 
17) Fixed crash in the Segment function when reading tab-text spec files. 
18) Fixed crash in Segment function when using the specs tab and the specs table is empty. 
19) Fixed crash when trial specs include empty cells. Also, they are now treated the same as NaN values when combining them via Edit functions. 
20) Average function now disables the ACC and RT settings if the model has no such trial specs and also the latest dataset is now chosen as the default model rather than the first. 
21) Added meanERA option to Window function. 
22) Fixed crash in Average function when averaging an .ept file with just one subject spec. 
23) Model dataset now needed for Average function to use the ACC and RT specs. 
24) Fixed crash in View Topos when colors are non-sequential. 
25) Fixed crash when loading continuous mff files. 
26) For Average function, changed default data numbers to NaN and fixed crash when the resulting average has no data. 
27) Added Memory subpane to the Edit function. 
28) Fixed crash in Edit function when editing specs in Trials subpane. 
29) In View Scan, for continuous data, fixed mucked up baseline correction when waveforms only showing a subset of the channels. 
30) Fixed crash with hi-pass filter option in Transform. 
31) Fixed not reading text files with space padded numbers correctly. 
32) Fixed crash in ANOVA function when setting a Between Group factor to "none.” 
33) Fixed problems with handling session labels with Read function in Single File Mode. 
34) Added edit fields to the Trials subpane of the Edit function. 
35) Fixed crash in ANOVA function when trying to handle header file with between-group variables. 
36) Restored automatic addition of adds to PCA files. 
37) Fixed View Waves sometimes crashing when mixing factors and non-factor waveforms. 
38) Fixed crash when running a batch of ANOVA files and the adds option is activated. 
39) Fixed ANOVAs not providing separate follow-ups for between-group factor levels.

Joe
--------------------------------------------------------------------------------

Joseph Dien, PhD
Senior Research Scientist
Human Development and Quantitative Methodology Department
University of Maryland, College Park
http://joedien.com <http://joedien.com/>

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[Erppcatoolkit-support] EP Toolkit 2.95 released

[Joseph D. <jd...@ma...>]

EP Toolkit version 2.95 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

Fixed a couple dumb crashing bugs in the user interface plus not including the updated manual and release notes in the documentation folder.  Argh…

Joe
--------------------------------------------------------------------------------

Joseph Dien, PhD
Senior Research Scientist
Human Development and Quantitative Methodology Department
University of Maryland, College Park
http://joedien.com <http://joedien.com/>

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[Erppcatoolkit-support] EP Toolkit 2.94 released

[Joseph D. <jd...@ma...>]

EP Toolkit version 2.94 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

The major upgrade is to how it handles EGI datasets, which pose challenges since their electrodes do not correspond to the 10-20 system (and its extensions).  Rather than try to infer whether it is an EGI dataset from their channel names or the type of file format, it now has a separate popupmenu for specifying it.  Also, there is now a trial specs subpane (for RT data etc) for the Edit function.

Other than that, there are a number of bugfixes small and large.

Stay healthy everyone!

Joe

1) Fixed crash when saving single-trial data in EGIS format and there is trial spec information which are characters not numbers. 
2) Fixed EOG channels preference control not displaying the channel numbers with correct format and hence not able to read them when Done was hit again on a later occasion. 
3) Fixed error message when reading in a data file where the file type has been designated as grand_average. 
4) Fixed Edit function's CED button on the Overview pane not handling case where remapping all the channels to a new montage. 
5) Average function now allows specs for RT and ACC to be directly specified. 
6) ACC codes can now be set in the Average preferences. 
7) Crash when using item option in Average function fixed. 
8) Fixed crash when using item average option in Average function and the stim trial specs are numeric. 
9) In Average function, fixed not computing mean or median average properly when there is only one trial. 
10) Fixed not handling blank fields (consecutive delimiters) when reading comma-delimited text files. 
11) Fixed Import button for Edit function's Subjects pane not working correctly. 
12) Fixed crash when selecting checkbox in Edit function's Cells pane and there are no events in the data. 
13) Fixed event and subject spec files being saved to the wrong location for text, stacked, and simple binary formats. 
14) Fixed crash when using Average function to form grand average and the files do not contain noise data. 
15) Fixed crash when using mains noise correction option in the Transform function on segmented data that is less than one second long. 
16) Fixed crash when using parametric option of PCA function. 
17) Added Specs pane to Edit function. 
18) Average function now retains original order of cells rather than reordering alphabetically. 
19) Fixed grand popupmenu not working properly for Cells pane of Edit function when the level names have the same length but they do not represent a set of fully-crossed one letter-long level names. 
20) Fixed crash in template function when the EOG channels are specified in preferences and some of them are indicated as being missing with a -1. 
21) Fixed confusing message that non-montages were assumed to be EGI montages (no actual effect). 
22) Added expansion button to the Segment pane to allow for a fuller examination of the segmentation table. 
23) Deprecating obsolete SLAY code and montage preference for EGIS files. 
24) Added montage popupmenu to enable specification of montages, especially for EGI data where the electrodes locations do not correspond to 10-20 locations, so EP Toolkit no longer needs to guess whether the data is EGI data even when channel names have been changed. 
25) Added support for canonical 10-05 coordinates in eloc structure. 
26) Fixed not dropping the full byte mark code at the start of UTF-8 unicode text files. 
27) Fixed crash in Template function when there are channels that are not "EEG" type. 
28) Fixed crash in View Topos when viewing single-trial data. 
29) Added tighter checks of channel, cell, subject, and factor types. 
30) Revised how trial-specs like RT and meta-data are combined by Edit and other functions to align better with how the voltage data are being combined. 
31) Changed the montage codes and made them a required field with a specified list of options.

--------------------------------------------------------------------------------

Joseph Dien, PhD
Senior Research Scientist
Human Development and Quantitative Methodology Department
University of Maryland, College Park
http://joedien.com <http://joedien.com/>

[Erppcatoolkit-support] EP Toolkit 2.93 released

[Joseph D. <jd...@ma...>]

EP Toolkit version 2.93 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

This is a minor bugfix release.

Stay healthy everyone!

Joe

1) Fixed resampling option not generating quite the right number of samples. 
2) Fixed crashes because fields are in the wrong order after manual editing with View Scan. 
3) Fixed edit fields not appearing in View Scan until epoch is changed. 
4) Fixed crash when performing a rereference or combining cells on averaged data with trial-level SDs with NaN values involved. 
5) Now handles case where just some channels names are being changed, if the number of channels missing from the CED is equal to the number that are extra. 
6) Prints last two non-zero digits when MSE is less than 1. 
7) Fixed p-values in ANOVA output sometimes only having one significant digit. 
8) Fixed labels for Factor Scores in PCA subpane in wrong order and added labels to Export function of PCA pane. 
9) Fixed crash in blink correction when boundary point is beyond last good point. 
10) For the Average function, fixed misaveraging trial specs or simply crashing when computing a grand average for a set of average files where the set of cells is variable. 
11) Fixed blank topos appearing in template figure of Preprocessing output for saccade correction templates even when not used.

EP Toolkit now requires Matlab version 2018b or later.

--------------------------------------------------------------------------------

Joseph Dien, PhD
Senior Research Scientist
Human Development and Quantitative Methodology Department
University of Maryland, College Park
http://joedien.com <http://joedien.com/>

[Erppcatoolkit-support] scripting

[Eric F. <eri...@bc...>]

 Hi Dr. Dien and others,

I am new to using the ERP PCA toolkit (but not new to ERP analysis more
generally). I am wondering whether there is any documentation or example
scripts for scripting PCA analysis, rather than doing it through the GUI.

Eric

-----
Eric Fields, Ph.D.
Postdoctoral Fellow
Cognitive and Affective Neuroscience Laboratory
<https://www2.bc.edu/elizabeth-kensinger/>, Boston College
Aging, Culture, and Cognition Laboratory <http://www.brandeis.edu/gutchess/>,
Brandeis University
eri...@bc...

Re: [Erppcatoolkit-support] scripting

[Joseph D. <jd...@ma...>]

Welcome!  I don’t have any such scripts myself.  My philosophy is that each step requires visual inspection and decision-making by a human so automation past what is already available via the GUI is not needed, but it may be that others have put together some.  That said, I plan to start adding some logging and scripting features to the EP Toolkit soon, but not sure when they will be finished.  The header of each function file does have complete documentation on the input and output variables.

Cheers!

Joe

> On Apr 8, 2021, at 15:40, Eric Fields <eri...@bc...> wrote:
> 
> Hi Dr. Dien and others,
> 
> I am new to using the ERP PCA toolkit (but not new to ERP analysis more generally). I am wondering whether there is any documentation or example scripts for scripting PCA analysis, rather than doing it through the GUI.
> 
> Eric
> 
> -----
> Eric Fields, Ph.D.
> Postdoctoral Fellow
> Cognitive and Affective Neuroscience Laboratory <https://www2.bc.edu/elizabeth-kensinger/>, Boston College
> Aging, Culture, and Cognition Laboratory <http://www.brandeis.edu/gutchess/>, Brandeis University
> eri...@bc... <mailto:eri...@bc...>_______________________________________________
> Erppcatoolkit-support mailing list
> Erp...@li...
> https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support

--------------------------------------------------------------------------------

Joseph Dien, PhD
Senior Research Scientist
Department of Human Development and Quantitative Methodology
University of Maryland, College Park
Editor-In-Chief of Biological Psychology (along with Thomas Ritz)
E-mail: jd...@ma...
Cell Phone: 202-297-8117
http://joedien.com

[Erppcatoolkit-support] scripting

[Eric F. <eri...@bc...>]

Hi Dr. Dien and others,

I am new to using the ERP PCA toolkit (but not new to ERP analysis more
generally). I am wondering whether there is any documentation or example
scripts for scripting PCA analysis, rather than doing it through the GUI.

Eric

-----
Eric Fields, Ph.D.
Postdoctoral Fellow
Cognitive and Affective Neuroscience Laboratory
<https://www2.bc.edu/elizabeth-kensinger/>, Boston College
Aging, Culture, and Cognition Laboratory <http://www.brandeis.edu/gutchess/>,
Brandeis University
eri...@bc...

[Erppcatoolkit-support] EP Toolkit 2.92 released

[Joseph D. <jd...@ma...>]

EP Toolkit version 2.92 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

This is mostly a bugfix release, with various minor refinements.  The most helpful upgrade is the addition of a “stacked” text file format, which allows the use of just a single data file for text.  Note that Matlab 2018b or later is now required.  There are still some issues with older EGI montages (pre hydrocel) that I’ll need to work out for the next release.  I also plan to start work on upgrading the logging and scripting capabilities.

Stay healthy everyone!

Joe

1) Can omit channel label in waveform figures by setting label size preference setting to zero. 
2) Fixed not having separate preference settings for figure markings and the line widths settings were not having any effect. 
3) Fixed sometimes crashing when trying to read an EGI data file. 
4) Fixed crash when reading in ced file with BAD channels. 
5) Moved option to fix mains noise from Preprocess function to Transform function and added preferences setting. 
6) May now resize the Edit Window. 
7) Fixed error bands not working in View Waves when there are NaN values. 
8) In Average function, fixed covAVE trial-level standard deviation calculation failing to exclude NaN values. 
9) Calculations involving trial-level standard deviation information, like rereference and grand averaging, now correctly excluding NaN values. 
10) May now click on the legend in Show Waves to edit the names. 
11) Added stacked text format to options for reading and writing data files. 
12) Eliminated legacy 'factors' file type from Read function. 
13) PCA data can now be represented without factor vector compression. 
14) Fixed crashing on start up after installation for certain cases. 
15) Actually fixed crash when using the "grand" button of Edit>Subjects subpane and there are missing values in the selected column. 
16) Fixed problems after using all eight colors to display factor results. 
17) Added additional safeguards for initial EPwork setup. 
18) During reading a file, disabled automatic correction of file type to "continuous" from "single-trial" if there is only one trial. 
19) Resamples the data via interpolation if the time points of the data going into an averaged or merged or appended file are not the same rather than just aborting the operation. 
20) Added option to resample data to any arbitrary sampling rate on Samples subpane of Edit function. 
21) In Segment function, for fractional event times, timeshifts the segments via interpolation so that the start of the epoch exactly corresponds to the event time. 
22) Fixed single-trial windowed output sometimes set to zero rather than missing data number for bad data trials.


EP Toolkit now requires Matlab version 2018b or later.

--------------------------------------------------------------------------------

Joseph Dien, PhD
Senior Research Scientist
Human Development and Quantitative Methodology Department
University of Maryland, College Park
http://joedien.com <http://joedien.com/>
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[Erppcatoolkit-support] EP Toolkit 2.91 released

[Joseph D. <jd...@ma...>]

EP Toolkit version 2.91 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

The major feature upgrade is the option to use conventional ANOVA statistics rather than robust.  I still encourage folks to use robust statistics but it’s nice to have the option to use conventional statistics, especially for things that my robust statistics code doesn’t support yet, like covariates and G*POWER compatible effect size measures.  It also makes it easier to compare the two if you’re trying to make up your mind about using it.  Note that the conventional ANOVA statistics relies on Matlab’s Statistics Toolbox so it has to be part of your install.  I’ve confirmed that it seems to produce results identical to that of SAS and SPSS.

The major bug fix is to the option to drop trials during averaging according to behavioral measures, which wasn’t doing so correctly.  Also, the default for retaining trialwise SDs has been turned back to “none” as it was slowing things down during analysis too much.  Incompatibility problems with EGI datasets where channel names have been changed prior to importing into EP Toolkit have also been resolved.

Stay healthy everyone!

Joe

1) Fixed crash when plotting using subject SD option.  
2) Added support for preferences to manually specify screen size and screen position and RAM information.  
3) if new combined cell added via Edit>Cell was meant to be a difference wave and enough cells are bad that the weights no longer balance to zero, then treat as invalid rather than just crash.  
4) Fixed crash when using the "grand" button of Edit>Subjects subpane and there are missing values in the selected column.  
5) Changed automatic default upper VEOG channels to closer to eyes.  
6) Fixed crash in blink correction step of Preprocessing function when multiple boundary events are present in continuous data.  
7) Fixed cannot change settings in ANOVA function when the cells of the currently selected dataset are not listed in alphabetical order.  
8) Moved spike potential file template to separate file.  
9) Disabled autoTemplate option for spike potential correction since it doesn't seem to work. 
10) Improved template function's waveform display for the spike potential artifact.  
11) Fixed movement artifact correction step still not correcting the artifacts when there are NaN values present.  
12) For Window Data function, fixed subject labels always being output in alphabetical order, resulting in mismatch with the voltage data if the labels were not in alphabetical order.  
13) Fixed crash when reading an events text file with key codes.  
14) Fixed in conversion of EP files to EEGlab format, eloc labels were being saved as cells containing the labels, resulting in errors down the line.  
15) Fixed crash when reading in file format with fixed channels (e.g., text) and REF channels are specified in the CED file.  
16) Fixed crash when reading a file using a BV header and the recording was cut short so it ends on an incomplete TRSP.  
17) Fixed collision of findpeaks function in PrepPipeline with Matlab's own findpeaks function by putting it in a Private directory.  
18) Fixed crash when windowing multi-session data.  
19) Fixed crash in Edit function when using the Factors subpane with one-channel data.  
20) For Segment function, if there are no trial specs, will instead offer the key names, if any, of the event lock event for the ACC and RT popup menus.  
21) Resegmenting single-trial data no longer results in zero segments.  
22) Fixed crash in Segment function when there are no trial specs and the Task field is being used.  
23) In Average function, fixed erroneous error message about multiple task codes when there were task fields left empty.  
24) Fixed crash when preprocessing average data.  
25) In Preprocessing function, can still recognize EGI montages even when some of the electrodes have been renamed and the ced field is not a GSN montage name if at least half still start with 'E’.  
26) Changed default for trialwise SD back to "none" as it was causing functions down the line to take too long.  
27) Added cell to the single-file options in the Average function.  
28) Fixed crash when averaging file with no trial specs.  
29) Fixed crash when reading a continuous file with a boundary event that falls in the extra points that are appended to the last epoch.  
30) When reading data files, noInternal preference option now applies to .ept files as well.  
31) Contrast option of ANOVA function no longer crashes when only a subset of the columns were included.  
32) In Edit function, fixed crash if the trial-wise variance information was retained during averaging and there is an attempt to generate a cell difference wave where cells are bad for a subject.  
33) In Average function, fixed trials not being dropped correctly based on RT and ACC settings.  
34) Added option to ANOVA function for using conventional statistics instead of robust.  Includes ability to use covariates for ANCOVAs and effect size output suitable for G*POWER calculations (both conventional statistics only).  
35) Bonferroni post-hoc corrections upgraded to Dunn-Šidák (slightly higher alpha thresholds, around the fourth decimal).  
36) Fixed Transform function's baseline and rereference options not being robust to presence of NaN values.  
37) Fixed crash when changing channel types in Edit function.  
38) In View Topos function, fixed error when trying to produce 3D graph and there are regional EEG channels present.  
39) Fixed error message when appending subjects, as with the Edit function.  
40) No longer adding regional channel add in Window function if only one channel was used.  
41) Functions like Dipole Analysis can still recognize EGI montages even when some channels are missing as long as they are still labeled in the EGI manner (e.g., E11) or also an equivalent (e.g., EEG 11).  Also, can still recognize even if the file was not .mff or .set.  
42) Fixed crash in Save function when in Convert mode.  
43) Fixed crash in std subpane of QC pane of Edit function with some datasets.  
44) Fixed crash when importing data file with no internal electrode coordinates and no CED file has been selected.  
45) Added workaround for OS X Matlab bug where titles are not presented in file requestors.  
46) Fixed when adding channels as via CED files, the default type was SGL rather than EEG.

--------------------------------------------------------------------------------

Joseph Dien, PhD
Senior Research Scientist
Human Development and Quantitative Methodology Department
University of Maryland, College Park
http://joedien.com <http://joedien.com/>
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[Erppcatoolkit-support] EP Toolkit 2.90 released

[Joseph D. <jd...@ma...>]

EP Toolkit version 2.90 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

A lot of changes are included in this release.  Aside from the usual bugfixes, the major effort has been enhancing the artifact correction function.

Stay healthy everyone!

Joe

1) Fixed crash when reading a file and there is no specSuffix or subjectSpecSuffix fields, as in when reading .study files. 
2) Fixed crash when reading a .study file and the session field is empty. 
3) Fixed and updated support for EEGlab .study session, group, and run fields. 
4) Fixed crash when reading .study file with a missing session name when there are session names in the dataset. 
5) Fixed not handling merging session information correctly when reading data such as .study files, resulting in crashes. 
6) Added EMCP option to the preprocessing function. 
7) Added separate checkbox control for SP correction. 
8) Greatly improved support for NaN values in the Preprocessing function. 
9) Fixed only reading in the first file of a list of mff files. 
10) When saving .eeglab or .erplab files, saves channels using labels in chanNames rather than elocs so that they directly correspond to the names visible to the user in EP Toolkit. 
11) Added ICA options for CRD saccade artifact correction. 
12) Fixed saccade potential correction routine not using outFile name when saving EPchunk to disk rather than to RAM. 
13) Fixed crash when converting data with multiple events per cell, such as continuous data, into FieldTrip format, as in filtering function. 
14) In View Waves function, fixed legend mismatching colors with conditions. 
15) Fixed error when adding channels due to bug in covMatrix code, as in SacPot correction option in artifact correction function. 
16) Fixed save function adding new file with "-1" added to name rather than offering to replace an existing file. 
17) When saving files, ERPlab files no longer include subName in name if there is only one subject. 
18) No longer adds -1 suffix when updating an existing entry in the working set. 
19) When changing name of dataset in working set to match that of saved file, no longer including file suffix. 
20) Fixed crash in Preprocessing function when processing a file with no trial specs, as from an .erp file. 
21) Fixed crash when trying to read a file where a field was left blank in a .ced file. 
22) Fixed crash in Edit function when using 10-05 column in Channels subpane to add electrode coordinates and there are no implicit channels. 
23) Fixed crash when reading non .ept file if there is a channel in the data file that is not in the CED file. 
24) Fixed crash when reading a data file with single file mode and it failed for any reason. 
25) Added preference to turn off use of Matlab Distributed Computing Toolbox in EP Toolbox functions. 
26) Added ICA options for spike potential artifact correction. 
27) Added eye artifact control to Preprocessing function to specify EMCP, MAAC, or single-step ICA options. 
28) Fixed crash in Segment function when segmenting data with 512 Hz sampling rate. 
29) Fixed EP Toolkit forgetting data in working set had been saved (and therefore no longer displaying asterisk in file lists). 
30) In Segment function, fixed -precedes- option accepting all values of events as meeting criteria. 
31) Added -responseCorr- and -responseErr- options to Segment function. 
32) Fixed crash when reading .set file with internal eloc information. 
33) Fixed crash when transforming electrode locations in a .set file with internal eloc information. 
34) Fixed error when reading ced file where two labels are the same. 
35) Fixed Save CED button in Edit Channels function using eloc labels rather than channel names. 
36) Fixed in Edit function modifying electrode coordinates instead blanks them. 
37) Fixed Head button in Channels subpane of Edit function displaying eloc labels instead of chanNames for electrode names. 
38) Added estimated upper VEOG channel locations to the canonical 10-05 electrode coordinates list. 
39) Fixed crash in saccades correction option of Preprocess function when using a saccade template file and there is a bad EOG channel or when it is from a different EEG montage. 
40) Removed preference option to rotate electrode coordinates when importing mff or eeglab files that have internal coordinates as no longer needed. 
41) Added control to Segment function to specify the ACC and RT trial specs. 
42) Fixed a bunch of problems with reading event text files involving blank fields. 
43) Fixed View pane not computing max sample correctly when data is continuous and overall length is less than one second. 
44) Fixed View Topos displaying blank data when there is only one timepoint. 
45) Fixed fiducial channels in CED files being dropped when read in. 
46) Fixed error when adding two continuous segments together and the first has a number of points that does not divided evenly into one-second epochs. 
47) Fixed crash when importing data from a data file with no event information. 
48) Now supports reading in .evt text files generated by NetStation 4.1.2 for continuous files. 
49) Fixed crash when appending continuous segment with events to one without events. 
50) No longer drops TRSP events when reading in simple binary files as they can still be useful even though they are empty. 
51) Added option to salvage NS4 continuous files via simple binary files and event text files. 
52) Fixed crash when plotting data including event lines and some colors are not being used. 
53) Checking for time points with voltages outside of good range set by preferences Saturation setting and changing them to NaN is now handled by the bad channel detection step rather than by individual EOG artifact correction steps. Also now rereferenced to Cz duration this check to make it independent of data reference. 
54) Fixed not being able to plot multiple continuous datasets using View Waves. 
55) Added Topo Grid option to contextual menu in View Topos. 
56) Made fixes to event markings of blinks and blink threshold to 150 from 100. Does not affect EEG blink correction. 
57) Fixed error when reading simple binary file with multiple subjects. 
58) Fixed crash when using Edit>Subjects>Append. 
59) Fixed Preprocessing function tagging epochs with NaN values as being bad trials. 
60) Made a number of improvements to marking of blink events. 
61) Fixed View>Scan so it handles NaN values correctly when centering waveforms. 
62) Correlations for manual blink templates now exclude HEOG channels just like for auto blink templates. 
63) Fixed crash in EMG option of Preprocessing function when there are no good time points in a trial. 
64) Changed automatic default HEOG channels to closest to F9 and F10. 
65) Added ability to ANOVA function to read in text files of data without EP ANOVA header, treating them as behavioral data. 
66) Added option to ANOVA function to run all posthocs even if the effect is not significant. 
67) Fixed crash in Trim function when scrolling along the time axis and there are no events marked on screen. 
68) Fixed crash in Preprocessing function when chunking single-trial data. 
69) Improved blink correction performance in Preprocessing function when an EOG channel was bad and had to be temporarily interpolated. 
70) Fixed EPeeg cache being corrupted after deleting a file from it, resulting in it needing to be reinitialized. 
71) Fixed SOBI factor scoring coefficients not being computed correctly (didn't affect anything important). 
72) Fixed crash when conducting spatial PCA on continuous data and there are bad epochs. 
73) Fixed crash when chunking continuous data. 
74) In ANOVA function, NaN values now treated as missing data and MISSING set to Inf if unspecified. 
75) Changed defaults for Trial SD in the Average function and chunk size, EMG option, blinks Template, and Saccades template in the Preprocess function. 
76) Fixed crash when reading a .set average file. 
77) Added labels to the factor score table in the PCA subpane of the Edit function. 
78) Fixed "grand" button of Edit>Subjects subpane not working. 
79) Fixed crash when reading a file that has a mix of numeric and string values. 
80) In Preprocessing function, when using "vector" method for SP option and original reference is unknown, now provides alert that the data are now in Cz reference and updates the file's reference information accordingly.

--------------------------------------------------------------------------------

Joseph Dien, PhD
Senior Research Scientist
Human Development and Quantitative Methodology Department
University of Maryland, College Park
http://joedien.com <http://joedien.com/>
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