erppcatoolkit-support — support list

[Erppcatoolkit-support] EP Toolkit 2.89 released

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

EP Toolkit version 2.89 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

Okay, I'm an idiot. Actually 2.86 and 2.87 were fine. I just forgot I had done some convoluted programming to try to reduce memory usage. So my attempted fix for a non-problem in 2.88 was the actual bug. This is all now fixed with 2.89. I'm adding some additional checks to my test script to preclude this sort of thing in the future.

Otherwise, I made some minor improvements in the factor score computation routines and added a mains noise correction option to the Preprocessing function (incorporating the one made available through the PREP Pipeline).

I’m making continued improvements to the Preprocessing Function in support of a methods paper I’m writing.

Stay healthy everyone!

Joe

1) Made further improvements to PTB file format support. 
2) Fixed crash in Average function when task names used in segmentation. 
3) Fixed sometimes crashing when trying to generate the legend in View Waves figure. 
4) Fixed assumption that channel names derived from hdr.labels is a column-vector, resulting in failure to read when they are not. 
5) Added mains noise correction to preprocessing function. 
6) Fixed crash when combining subjects into a grand average and there are task specs. 
7) Modified auto-alignment of electrode coordinates to work with EGI montages even when the fiducial locations are missing. 
8) Improved the factor score computation for PCA and ICA rotations. 
9) Fixed minor factor score computation bug added in 2.88.

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

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 2.88 released

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

EP Toolkit version 2.88 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

This release has an important bugfix for the PCA function.  I just realized I made a subtle error with the doPCA.m code as of version 2.86.  In the PCA process, there are three points at which one might mean-correct the data.  The first is the computation of the relationship matrix (covariance normally).  The second is the computation of the factor scores (whether the data multiplied by the factor scoring coefficients are mean-corrected).  The third is the resulting factor scores themselves.  The same goes for ICA, except that whereas there is no relationships matrix in the first step, the data itself can be mean corrected prior to the rotation.  Prior to 2.86, the first and third steps were mean-corrected but not the second.  In 2.86 and 2.87 the second step was also inadvertently mean-corrected.

Not mean-correcting the data prior to computing factor scores has the effect of allocating the mean offsets of the variables to the various factors just as the variance was allocated.  If it is mean-corrected, then the mean offsets don’t show up in the factor scores.  Doing it this way is the normal procedure for both PCA and ICA.  It won’t have a major effect on temporal analyses if the data are average referenced since they then have a mean of zero by definition; likewise, spatial analyses will not be much affected if they are detrended (continuous) or baseline corrected (single-trial).  

More problematic and additional to the mean-correction issue is that if the correlation matrix option was chosen (normally not recommended for EEG data), then the data were also variance-corrected prior to computing the factor scores, which would also affect results by equalizing the extent to which each variable contributed to the factor scores.

So in sum, the PCA results of version 2.86 and 2.87 are problematic (non-standard at the least) and blink correction in version 2.87 was also affected.  The effects on the results will generally be subtle (which is how it got past me) but rerunning the analyses is advisable.  Apologies for any trouble caused by this oversight. 

On the plus side, I’ve also added the option to have up to eight colors plotted in waveform figures and the colors can now be set as desired.

1) Fixed BV header fix option no longer appearing in Save function. 
2) Fixed View pane min and max voltage values not updating correctly when there are colors that have been set to "none.” 
3) Added support for up to eight colors in waveform figures. 
4) Added preference settings to control the colors of the waveforms. 
5) Added preference buttons to panes. 
6) Added AMICA rotation. 
7) In doPCA function, fixed data being mean-corrected prior to being multiplied by factor scoring coefficients/activation weights and being variance-corrected if the COR option was chosen.

Stay healthy everyone!

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 2.87 released

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

EP Toolkit version 2.87 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

This release has an important bugfix for the Edit function treating negative weights as positive when generating difference waves.  Other than that, there are a variety of bugfixes. There is also a new addition of the Extended-Infomax, FastICA, JADE, and SOBI ICA rotations for both the PCA function and the blink correction routine.

1) Fixed crash when using alpha correction, saccade, and EMG correction options in Preprocessing function. 
2) Fixed crash in Average function when Drop Events option not selected. 
3) SampleTest applies test to all channels, not just EEG channels. 
4) Added JADE, SOBI, and fastICA rotations to PCA. 
5) Turned off binICA since it seems to be slower than matlab code even for linux now. 
6) Bad observations are output from PCA and blink correction as NaN rather than zeros. 
7) Added preferences setting to set rotation type for blink correction. 
8) Parallelized channel interpolation when Matlab Distributed Computing Toolbox is installed. 
9) Fixed error when using Alpha correction option in preprocessing and there is a bad EOG channel. 
10) Fixed crash when adding subjects, as in appending. 
11) Fixed crash for PCA of frequency data, including alpha correction option of preprocessing. 
12) Automatically regenerates corrupted EPdataset files. 
13) Fixed when reading mff files, fiducial information not being formatted correctly in the implicit field, resulting in crashes down the line. 
14) Fixed negative weights being treated as positive when adding data together using the Edit function. 
15) Fixed Average function only grand averaging trial specs of last cell of subject average files. 
16) Fixed issues with reinitializing EPeeg RAM cache rather than updating it when updating an existing dataset in the working set. 
17) Fixed crash with COR option of PCA function. 
18) Fixed crash when loading EEGlab .study dataset. 
19) Fixed crash when reading EGI data in .set format due to issues with reading unicode text files. 
20) Made epsilon setting of Geomin rotation controllable via RotOpt input parameter (thanks to Andreas Widmann).

Stay healthy everyone!

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 2.86 released

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

EP Toolkit version 2.86 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

Aside from the usual bugfixes, this release has the following enhancements: 1) BOSC and eBOSC options in the Transform function.  2) ReSync option in the Average function.  3) NIPALS option for decomposition in the PCA function.  4) Automatic electrode coordinate assignment and enhanced ability to edit them.  5) Support for Psychophysiology Toolbox and FieldTrip data files.  Also a major fix for reading edf format files.

The EP Toolkit has gotten to be quite complex so it’s hard for me to test for all possible bugs.  My next priority is to add functionality for logging and scripting so I can automate testing.  As ever, I am happy to respond to bug reports, within my time constraints.

Stay healthy everyone!

Joe
1) Fixed spike potential step of preprocessing function not correcting single-trial data correctly. 

2) Improved auto spike potential correction with the use of a grand average template since it seems to be pretty consistent across subjects. 

3) Fixed crash in View Topos when using -all- option and one of the datasets has less items. 

4) Fixed spike potential step of preprocessing function not rereferencing data to Pz when using manual template. 

5) Fixed not saving very large EPdataset caches. 

6) Fixed crash when deleting dataset in working set that is cached in EPeeg. 

7) Overview subpane of Edit function now accommodates files with unknown reference. 

8) Overview subpane of Edit function change ced button now properly accomodates channels that have no coordinates or are not EEG data. 

9) Artifact correction function now remaps blink and saccade file templates if they are for a different electrode montage. 

10) Canonical templates for blinks and saccades and saccade spike potentials are provided in the new templates directory. 

11) Fixed ced reader defaulting to "EEG" for all empty fields rather than just for the type field. 

12) Fixed ced reader sometimes reading CED fields as unicode rather than numbers. 

13) When reading a file and there is no eloc information, automatically add canonical coordinates based on channel names, including EOG channels. 

14) 3D heads and source analyses now uses improved method for co-registering eloc coordinates, based on Oostenveld's Standard-10-5-Cap385.sfp file. 

15) Added new options to the Channels subpane of the Edit function for setting the electrode coordinates of channels and displaying them on a 3D head to assess accuracy. 

16) The CED button of the Edit function (on both the Overview and the Channels subpanes) has the option to obtain default electode locations for canonical 10-05 channels if no ced file is chosen (with non-matches left blank). If that too is declined, then there is the option to simply delete the electrode information. If that too is declined then the action is cancelled. 

17) Fixed crash when loading old ept file without reference field. 

18) Fixed crash in sample test pane when one of the datasets has electrode coordinates with missing values. 

19) Fixed under some conditions mff files will be read in as single precision, resulting in crashes. 

20) Fixed crash in saccade correction of Preprocessing function when using a file template and there are bad channels. 

21) Added support for BOSC and eBOSC analysis option to Transform, View, and Window functions. 

22) NaN values no longer included in means and medians, resulting in NaN, when using Average function. 

23) NaN values now ignored when computing adds in the Edit function. 

24) Bad Channels figures now computed more correctly when computing adds in the Edit function. 

25) Fixed crash when combining channels using the Edit function. 

26) Fixed averaging not working when there are multiple sessions per subject. 

27) Fixed problems with selecting and averaging and deleting cells of single-trial data using the Edit function's Cell pane. 

28) Fixed adding redundant copies to the stims entries when selecting subsets of the data. 

29) Fixed crash when rereferencing data and there are no good reference channels in a given epoch. 

30) Improved support for reading edf files with varying sampling rates. 

31) Fixed crash in some situations when deleting member of EPeeg cache from working set. 

32) Fixed crash in Edit Samples when halving sampling rate and the data includes standard deviations and covariances. 

33) Fixed weights in Subjects pane of Edit function not reflecting changes in Sessions pane. 

34) Added mffmatlabio to external directory since FieldTrip does not have the latest version. 

35) Added support for reading fieldtrip and PTB files. 

36) Added support for writing FieldTrip files. 

37) Made fixes to the FIFF file format saving option. 

38) Added NIPALS decomposition option for PCA function. 

39) Correlation matrix type now allowed for ICA in PCA function. 

40) Fixed not weighting levels correctly in 'combined' cells and factors and grand averages in PCA output. 

41) Restored support for fiducial coordinates for mff files. 

42) Fixed crashes when reading EGIS average files and simple binary files.

43) Fixed not segmenting based on information in the value field of events. 

44) Fixed crash in autoPCA with frequency PCA data.

45) Fixed crash when Loading an example ANOVA file in ANOVA function that has only one session.

46) Fixed crash when switching to EGIS data in sampleTest.




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

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 mailing list
Erp...@li... <mailto:Erp...@li...>
https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support
_______________________________________________
Erppcatoolkit-support mailing list
Erp...@li...
https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support

[Erppcatoolkit-support] EP Toolkit 2.85 released

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

EP Toolkit version 2.85 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

This is a bugfix release for things that got past my QE testing.  For the next release, I’m planning an enhancement that will facilitate automated testing.

Joe
1) Fixed crash in Read function when using Single File Mode. 

2) Fixed crash when adding a combined factor to a dataset with no combined factors yet. 

3) If text file has an extra delimiter at the start of each row, ignore it. 

4) Fixed crash when reading in text files. 

4.5) Fixed crash when merging data that are not averages. 

5) Fixed single file mode putting frequency bands into different trials for single-trial data. 

6) Fixed crash when reordering subject and there are no session numbers. 

7) Fixed failure to read mff combined subject average files. 

8) Fixed error check unnecessarily resetting EPeeg cache. 8) Fixed scree of random data for three-step PCA. 

9) Fixed crash when choosing "SD and covariances" option and there are non-EEG channels with NaN values. 

10) Fixed crash in blink artifact correction when 'saccadeET','fixationET' events occur during a blink period. 

11) Fixed crash when reading in frequency data with single file mode.

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

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 mailing list
Erp...@li...
https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support

[Erppcatoolkit-support] EP Toolkit 2.84 released

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

EP Toolkit version 2.84 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

Thanks in part to the kind support of two researchers, this release includes enhanced support for multiple-session data and tracking of standard deviation information.  I’ve also spent a lot of effort on the plumbing, making it faster and more efficient.  I also went through the entire tutorial to ensure all the steps are still working and fixed a lot of bugs and glitches.  Finally, I got tired of the continual problems from Matlab’s incomplete support for the many variations (especially unicode) of .txt files, as when editing .ced or ANOVA files, so I wrote a function that should prevent any further issues.

Joe
1) In the Edit function, clicking a Select checkbox also changes the weight. 

 2) Fixed crash when updating the EPwork cache. 

 3) Added support for multiple sessions with the same subject. 

 4) Added option in SampleTest to compare between different sessions. 

 5) Fixed crash in ANOVA function when performing pairwise followups on significant effects with more than two between group levels. 

 5) Fixed crash in Window function when leaving the pane, changing the cellnames in the chosen dataset, and then returning to the Window pane. 

 6) Fixed crash in Cells subpane of Edit function when changing name of a trial of single-trial data to a novel name in the Trial subpane and then switching to the Cells subpane. 

 7) Enabled reading of text files with a greater range of variations in character encoding, end-of-line markers, and field separation markers, including Unicode16. Also accommodating .csv suffix. 

 8) Now allowing NaN in EEG channels. I imagine it'll break some things but better than treating them as zeros I think. 

 9) Now ignores bad channels during rereferencing and marks as a bad trial/average if all the reference channes are bad. 

 10) Noise estimates are now always a simple mean regardless of the averaging method chosen. Also, grand average noise is now the subject-wise mean of noise estimates from the first level of averaging. 

11) Cousineau-Morey confidence intervals now based on number of waves from the same subject being used in the figures. Original implementation was not correct. 

 12) Fixed outputting an extra column of NaNs in the cell mean tables for ANOVAs with no within factors. 

 13) Added ability to keep track of correct standard deviation scores after rereferencing or adding data together with Edit. 

 14) Added ability to window standard deviation scores. 

 15) Added option to keep track of trialwise standard deviations, which is quite computationally and memory demanding so by default it is turned off. 

 16) May now drop noise information to reduce memory and time requirements. 

17) When importing data, fixed implicit mastoid channel a mirror of the wrong channel for case where it is mean mastoid reference with one explicit and one implicit channel and the order of the channels has bee changed by the CED file. 

18) subjectwise standard deviation and confidence intervals are now computed on the fly so no longer need to store them, saving time and memory. 

 19) Added support for session information and session ANOVA factors and ICC reliability output. 

 20) Fixed crash in ANOVA when between group level names have more than one character. 

 21) Fixed waveforms not being displayed in expanded channels when chosen colors are non-consecutive (e.g., just blue and green). 

 22) Fixed crash in View Topos when sampling rate of voltage data is not an even multiple of 1000 (e.g., 512). 

 23) When loading E-Prime spec files, stopped assigning EPoffset to .onsetdelay field as the delay is likely present in the stimulus appearance time as well. 

 24) Fixed crash when applying Transform to a file with channel adds, as in preprocessed data. 

 25) Fixed crash in View Waves when displaying data with ERPimages. 

 26) Fixed crash in Preprocessing function with fMRIb fMRI correction option and there are TR markers with decimal sample numbers. 

 27) Fixed losing all events with decimal samples when using Trim function. 

 28) Fixed crash in View Scan when there are no events in the present waveform. 

29) Fixed crash in View Scan when zooming in or out. 

 30) Fixed View Scan not showing single event lines at the correct latency. 

 31) Fixed View Scan not displaying event line if the initial epoch did not have an event or leaving it unchanged if changing from an epoch with an event to one without. 

 32) Fixed crash when using low-pass filter with sampleTest. 

 33) Fixed labels of scale graph for View Waves. 

 34) Fixed combined factors from PCA output too large (not divided by number of factors going into waveform). 

 35) Fixed generation of names of between group adds from the ANOVA function. 

 36) Fixed crash when running CSD in Transform.

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

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 2.83 released

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

EP Toolkit version 2.83 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

This is mostly a bugfix release.  I am prioritizing work that supports the projects of two researchers who are providing consulting fees, so there has especially been work on the segmentation function (you may need to adjust existing segmentation tables) and mff file importing.

1) Fixed crash in View>Scan due to rounding error when the sampling rate is high (e.g., 1024). 
2) Will no longer keep asking for ced file in single file mode if user chooses cancel to first request. 
3) Fixed cannot undo grand function in subjects subpane of Edit function. 
4) Fixed crash in Transform function when filter parameters result in unstable filter coefficients. 
5) Added append button to sample subpane of Edit function. 
6) Fixed Save button grayed out when the working set is empty. 
7) Fixed BAD CED option not working for batch files in the Transform function. 
8) Updated reading of event info from mff continuous files to work with the new mffmatlabio routine. 
9) Fixed crash in Window function with maxPeaks option when the epoch is only one sample long, as in temporal PCA data. 
10) Fixed crash when applying autoPCA in Window function to single-trial PCA data. 
11) Fixed crash when trying to read BrainVision .seg and .dat files. 
12) Fixed crash in blink correction and saccade potential correction when the events structure is empty. 
13) Fixed Segment function criteria not working when .value or .type fields of the events structure are numeric rather than strings. 
14) Fixed crash in ANOVA function when performing pairwise followups on significant effects with more than two levels and there were also between group factors. 
15) Added -rangesamps- option to the Segment function. 
16) in Segment function, eventlock field is now always only based on the .type field, with additional specs needed to utilize the .value field. 
17) Fixed crash in Segment function when segmenting continuous data with at least one recording interruption (a boundary event). 
18) Fixed Segment function to correctly compute number of samples when sample sizes are not integers. 
19) Fixed crash in saccade potential correction step of Preporcessing function when there are bad channels.

In my capacity as a FieldTrip developer, I have submitted a revision to the BrainVision I/O code so that if there is no marker file, it will not crash the program. I do not know yet when it will be incorporated into the FieldTrip release. It will likely be a part of whatever release follows 20191025.
--------------------------------------------------------------------------------

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 mailing list
Erp...@li... <mailto:Erp...@li...>
https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support

Re: [Erppcatoolkit-support] error with AutoPCA

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

please type ver at the command line and send me the output.

Joe

> On Oct 14, 2019, at 00:49, Cellier, Dillan E <dil...@ui...> wrote:
> 
> Hello,
> 
> I am attempting to run autoPCA on some temporal-spatial PCA data, and I am encountering an error related to the conditions specified.
> 
> The error is: 
> 
> Subscripted assignment dimension mismatch.
> 
> Error in ep (line 6027)
>                     inputcells{find(strcmp(EPmain.window.outCells(iCell),outCellNames))}(end+1)=theCell;
>  
> I've also tried creating a new cell ("avg1") by averaging over all epochs, just to test this, but when I do so it says that "avg1" is not in the dataset. 
> 
> I would greatly appreciate any help you might have for me! Thank you.
> 
> Best wishes,
> 
> Dillan Cellier, B.A.
> Post-baccalaureate Fellow & Lab Manager
> Hwang Lab for Neurocognitive Dynamics
> Dept. of Psychological and Brain Sciences @ University of Iowa
> _______________________________________________
> Erppcatoolkit-support mailing list
> Erp...@li... <mailto:Erp...@li...>
> https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support <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
E-mail: jd...@ma...
Cell Phone: 202-297-8117
http://joedien.com

[Erppcatoolkit-support] error with AutoPCA

[Cellier, D. E <dil...@ui...>]

Hello,

I am attempting to run autoPCA on some temporal-spatial PCA data, and I am encountering an error related to the conditions specified.

The error is:

Subscripted assignment dimension mismatch.

Error in ep (line 6027)
                    inputcells{find(strcmp(EPmain.window.outCells(iCell),outCellNames))}(end+1)=theCell;

I've also tried creating a new cell ("avg1") by averaging over all epochs, just to test this, but when I do so it says that "avg1" is not in the dataset.

I would greatly appreciate any help you might have for me! Thank you.

Best wishes,

Dillan Cellier, B.A.
Post-baccalaureate Fellow & Lab Manager
Hwang Lab for Neurocognitive Dynamics
Dept. of Psychological and Brain Sciences @ University of Iowa

[Erppcatoolkit-support] EP Toolkit 2.82 released

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

EP Toolkit version 2.82 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

This is a bugfix release.  Trying to get them all stomped out before moving on to new enhancements.

1) Fixed error message during startup that EPmain.preferences.view.lineSize was in error and resetting preferences to default values. 
2) Fixed crash in View Topos when mixing -all- and single choices, as with factors. 
3) Fixed View Topos showing real rather than imaginary data in the imaginary lines when not using -all- option for subjects, trials, or factors. 
4) Fixed View not defaulting to correct subject for colors other than blue when changing datasets. 
5) Fixed View defaults for factors and subjects when switching dataset types to a factor dataset. 
6) Fixed crash for 3D heads due to changes in EEGlab2019. 
7) Fixed crash when viewing continuous data with View Topos. 
8) Fixed Segment function crashing upon entering pane. 
9) Fixed Template function crashing upon entering pane.

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

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 mailing list
Erp...@li...
https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support

[Erppcatoolkit-support] EP Toolkit 2.81 released

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

EP Toolkit version 2.81 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

More bug fixes.  Also added an option to generate p-value maps and to control the line width and channel label size of the View figures for preparing manuscripts.

Also, Peter Molfese is hosting, and EGI is sponsoring, an EP Toolkit workshop by myself at NIH (Bethesda campus) on Tue Sept 24th 2019 just prior to the SPR conference in Washington DC.  The workshop is open to the public and is free.  For more information: https://bit.ly/2m7qpkp <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbit.ly%2F2m7qpkp&data=02%7C01%7C%7C3d3e15d4e1de4053d78d08d738a8b615%7C1a407a2d76754d178692b3ac285306e4%7C0%7C0%7C637040169575228918&sdata=mNeFZk6PoSJiyEMBgoroUIJ%2FQrta0mJ3OA7PBYdrahU%3D&reserved=0>

Joe

1) Fixed reset button not working properly for PCA function. 
2) Fixed Edit function not combining factors correctly. 
3) Fixed Edit function dropping all combined factors when deleting any factors. 
4) Fixed not displaying RT lines in waveform figures. 
5) Fixed crash in Edit function when sorting single-trial data on the cells subpane. 
6) Fixed export trials including the selection column. 
7) Fixed no longer marking unsaved changes to data in active set with an asterisk. 
8) Added t-map option to the sampleTest function. 
9) Fixed crash for 3D heads in View Topos. 
10) Added preferences for waveform figure linewidth and channel font size. 
11) Fixed crash in View Scans because Scan button was enabled while -all- setting chosen for the main dataset. 
12) Fixed crash when adding cells of subjects via Edit function where the .cov field is present but empty. 
13) Fixed crash in saccade correction of artifact correction function when there are non-EEG channels. 
14) Fixed detrending option of artifact correction function detrending non-EEG channels too. 
15) Fixed crash in View Scan with continuous data when toggling off edit mode and there are no bad data visible.  
16) Fixed crash in saccade potential correction routine of artifact correction function when there is a global bad channel. 
17) Fixed crash when using preview mode in Segment function with specs table. 
18) In Segment function, example specs table is now linked to the example data so if the latter is changed then the former is cleared but otherwise it will be used in preview mode. 
19) Fixed crash in Artifact Correction function when selecting alpha option. 
20) Fixed View Topos function not correctly labeling cells at top of columns for single-trial data. 
21) Fixed crash in View when color other than blue had -all- selected for cells or subjects and the data had events and then a dataset was changed.

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

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 2.80 released

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

EP Toolkit version 2.80 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

A slew of bug fixes.  Also made further fixes to the disappearing button problem on OS X (ep.m file had grown too large).

Joe

1) Fixed crash in View pane when changing datasets and there was no RT data in the prior dataset. 
2) In Edit function, added column names to the output of export QC info. 
3) Fixed crash in Averaging function when either min RT or max RT fields are empty. 
4) Fixed crash in Transform function. 
5) ANOVA function now ignores extra carriage returns at end of windowed data files. 
6) Fixed not reading ANOVA text files properly if using Linux or OS X end-of-line convention (e.g., linefeeds). 
7) Fixed crash when running PCA. 
8) Fixed crash when running Window function on a non-PCA dataset after having run it on a PCA dataset without using AutoPCA. 
9) Fixed crash when using the same Window settings on an ANOVA file with more columns. 
10) Fixed crash in ANOVA function when Bonferroni field left empty. 
11) Fixed crash in ANOVA function when applied to non-factor data and adds option is being used. 
12) Fixed manually changing voltage settings in View function not working. 
13) Fixed existing adds being deleted by Window adds option when Windowing defines new output cell names.

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

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 2.79 released

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

EP Toolkit version 2.79 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

Aside from the usual bug fixes, have added some improvements to the View Topos mode and its controls.  Also improved speed of functions somewhat by caching EEG data in RAM for those with computers with enough memory.  Also added a status button that indicates when the Toolkit is processing and can abort functions and reset its status when pressed.  The compiled mex code for the robust ANOVAs was unintentionally turned off in recent releases and has been turned back on for six-fold improvement in speed.  Also it now uses a pseudo-inverse for calculations, which allows it to better handle singularity.

Joe

1) Fixed crash when the -all- option is used and then the dataset is changed and is then viewed with View Topos. 
2) Fix EPheader option can also fix missing EP headers. 
3) Fixed crash in View Topos when using fixed min and max voltages. 
4) Fixed crash in View Waves when plotting sampleTest results without waveforms. 
5) Added popupmenu to View Topos to change range to symmetrical numbers. 
6) Changed View Topo’s time mode so that every sample is displayed rather than just every 50 ms. 
7) Updated dipole analysis so it continues to work with current versions of FieldTrip. 
8) Fixed crash in Edit function after adding combined cell and then deleting cells. 
9) Topos page controls now labeled by row label rather than page number. 
10) Fixed crash when conducting second or third step PCA on PCA data from prior to version 2.76. 
11) Added EP reset button to upper right corner. 
12) Fixed case where a previous error leaves behind a copy of the temporary CED file, resulting in errors when trying to read a new CED file. 
13) Fixed case where user does not have write permission for Matlab active directory, resulting in failure to read the CED file. 
14) Fixed crash in saccade correction step of Preprocessing function when data have no events. 
15) No longer maintains noise and std information when combining subjects in factor data as not really needed and requires substantial memory space. 
16) Finally figured out why Matlab was sometimes leaving out GUI controls even with the drawnow command. 
17) Now maintains a copy of the most recent datasets from the active set in RAM to minimize disk access time. 
18) Fixed Greek letter mu garbled in some figure labels. 
19) Fixed crash when conducting sample test and there are cells listed after sample test cells. 
20) Fixed case in movement correction module of Preprocessing function where channel has sporadic high amplitude bad data, derailing mean correction. 
21) Accelerates artifact correction by adding option to keep chunks in RAM. 
22) Added subplots for global bad channels to Preprocessing function summary plots. 
23) In preprocessing function, global bad channel detection now based on baselined/detrended copy of data. 
24) Fixed not using trial specs when resegmenting single-trial data. 
25) Restored compiled functions for robust ANOVAs, which was turned off in version 2.72 (oops). 
26) Improved default setting behavior of the View controls. 
27) Changed, in robust ANOVA code, inv calls to pinv to better handle singular and near-singular data. 
28) Fixed crash when saving averaged data in text format. 
29) Fixed crash when chunking single-trial or averaged data.


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

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 2.78 released

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

EP Toolkit version 2.78 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

Mostly bugfixes.  Added Microvolt-scaled Factor Pattern subpane to Edit>PCA suitable for generating summary figures of the factor loadings for publications.

Joe

1) Added option to convert mode of Save function to fix truncated EP header in continuous BrainVision files. 
2) Fixed crash when loading spec table in Segment function and there are no continuous data in the working set. 
3) Fixed crash when selecting subjects from a dataset with no task specs. 
4) Fixed crash in View Topos and Preprocess Template for 3D heads due to changes in Matlab 2019a. 
5) Fixed dropping adds such as the grand average from an existing dataset in active set when adding ANOVAadds. 
6) Fixed crash when displaying continuous data in View Topos under Matlab 2016a. 
7) Fixed crash when performing three-step PCA. 
8) Added support for three-step PCA to PCA pane of Edit function. 
9) Added scaled FacPat subpanes to PCA pane of Edit function.

In my capacity as a FieldTrip developer, I have revised the BrainVision I/O code so that if one has renamed the files, it can still find the new names of the .vhdr and .vmrk files as long as they match that of the .eeg file. This will be part of FieldTrip after the 20190419 release.

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

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 mailing list
Erp...@li... <mailto:Erp...@li...>
https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support <https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support>

[Erppcatoolkit-support] EP Toolkit 2.77 released

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

EP Toolkit version 2.77 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

Just bugfixes, especially for a crash on startup for versions of Matlab prior to 2018a.

Joe

1) Fixed crash and incorrect bad channel and bad trial info in View>Scan for single-trial data where a trial has been deleted via the Edit function. 
2) Fixed setting weights in Subjects subpane changing them for the Cells subpane instead. 
3) Fixed crash on startup on Matlab earlier than 2018a. 
4) Fixed crash when merging files. 
5) Implemented workaround for limitations in reading averaged mff files.

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

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 mailing list
Erp...@li... <mailto:Erp...@li...>
https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support

[Erppcatoolkit-support] EP Toolkit 2.76 released

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

EP Toolkit version 2.76 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

Aside from the usual bug fixes, I’ve made some enhancements to the Edit function and added support for Signal Detection Theory measures.

Also, I have not been able to obtain grant funding to support development of the EP Toolkit. I am therefore instituting a support program. While I will happily continue to answer simple questions, fix bugs, and consider feature requests, this kind of support will only be available as time permits. Expedited bug fixes, extended explanations, and simple feature additions, are available for a $1000 annual consulting honorarium. I would also be happy to provide an onsite 1-2 day workshop on the EP Toolkit and ERP methods in general in return for a $1000 honorarium plus travel and lodging.

Joe

1) Fixed .fiff data not being scaled correctly whenever the eloc data were not initially provided. 
2) Fixed bug wherein ANOVA or Window adds waveforms not calculated correctly when grand average data is listed prior to any of the subject average data or combined cells before any of the single cells. 
3) Fixed crash in Read function when using Single File Mode with averaged non-EP file format data. 
4) Fixed crash when merging average type files, as in reading files. 
5) Fixed crash when sorting data by subject and there are no subject specs. 
6) Fixed Read function not identifying cell names in mff single-trial data correctly, although using a heuristic that may not work for all files. 
7) Fixed crash in Preprocessing function when applying "mark" option to bad channels and data are chunked. 
8) In Segment function, fixed -follows- and -precedes- options not working as expected. 
9) Fixed Segment function user interface including a blank when populating lists of potential spec names for datasets with no keys. 
10) Fixed crash in View>Scan when zooming in (+) or zooming out (-) segmented data that has no events. 
11) Fixed crash when using noFigure option for preprocessing. 
12) Fixed crash when selecting an event in the Events subpane of the Edit function. 
13) Added delete button and select and order columns to the Trials subpane. 
14) Fixed Segment Preview using contents of specs table even when from a different file. Instead, user must now choose the text file when running Preview. 
15) Now takes takes DisplayScaleFactor setting into account when determining font size (for Linux on HiDPI). 
16) When appending subjects and renaming duplicate subject names, now uses original name as the stem. 
17) Fixed crash in View Topos for continuous files with events. 
18) When editing data using the Edit function, select and weight values are updated appropriately on all the subpanes. Also a variety of glitches were fixed. 
19) For Edit function, when reordering data, added handling of case where there are duplicate entries in the sort order. 
20) Fixed crash when combining data with no time points, as in generating frequency PCA data. 
21) Fixed crash when a file has fewer trial specs than the other files in a batch averaging run. 
22) In Average function, when timeout dropping is turned off, no longer drops zero RT trials for being less than minimum RT criterion. 
23) Fixed crash in Window function when adding regional Adds to the dataset. 
24) Added specification of tasks during segmentation to enable generation of signal detection measures D-Prime and c during averaging, which can then be output for analysis during Windowing.

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

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 mailing list
Erp...@li...
https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support

[Erppcatoolkit-support] EP Toolkit 2.75 released

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

EP Toolkit version 2.75 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

A few more bug fixes and refinements focusing on the Edit and View functions.

Happy New Year!

Joe

1) Fixed not adding adds to waveforms when using ANOVA function to perform between-subject analyses. Also, now only provides waveform for the ANOVA channel. The group waveform is added as a generic 'autopca' entry to accommodate factors having differing peak channels and latencies. 
2) Fixed not handling reordering of CMB factors correctly. 
3) Now allows CMB and SGL factors to be intermixed. 
4) Added sort button to Factors subpane of the Edit function. 
5) Now treats CMB factors like SGL factors on the Factors subpane of the Edit function. 
6) FacVar and FacVarQ now include CMB factors. 
7) Various fixes to the Factors subpane of the Edit function. 
8) workaround for Fieldtrip bug that can cause FFT transform to fail. 
9) Fixed crash when TFT applied to data segments less than 500 ms long. 
10) Improved default auto-scaling for View Waves and View Topos. 
11) Fixed not adding cell in case where only one cell is to be added, as in Windowing Adds. 
12) Fixes to handling of coherence data in View Waves and View Topos. 
13) Fixed Preprocessing function not taking previously edited bad trials into account when identifying channels bad due to being flat. 
14) Fixed not identifying Cz channel correctly for saccade potential correction in Preprocessing function. 
15) Fixed problem that could keep average .fiff file from being read. 
16) Fixed crash in View when the dataset only has REG channels. 
17) Fixed crash in View Scan when there is only one channel in the dataset. 
18) Added Grand button to the Subjects and Cells subpanes of the Edit function. 
19) Added limited support for writing out data in mff file format.

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

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 mailing list
Erp...@li... <mailto:Erp...@li...>
https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support <https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support>
_______________________________________________
Erppcatoolkit-support mailing list
Erp...@li... <mailto:Erp...@li...>
https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support <https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support>
_______________________________________________
Erppcatoolkit-support mailing list
Erp...@li... <mailto:Erp...@li...>
https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support

[Erppcatoolkit-support] EP Toolkit 2.74 released

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

EP Toolkit version 2.74 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

A few more bug fixes.

Happy Holidays!

Joe

1) Fixed crash when starting up the EP Toolkit for the first time on a computer. 
2) Fixed not treating mff files as a file rather than a directory on non-Mac systems. 
3) Handles multi-subject average mff files under new v3 mff code by making some assumptions. 
4) Fixed crash when starting EP Toolkit with newer FieldTrip versions due to change in mff code. 
5) Made fontsize smaller on linux.

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

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 mailing list
Erp...@li... <mailto:Erp...@li...>
https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support <https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support>
_______________________________________________
Erppcatoolkit-support mailing list
Erp...@li... <mailto:Erp...@li...>
https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support
_______________________________________________
Erppcatoolkit-support mailing list
Erp...@li...
https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support

[Erppcatoolkit-support] EP Toolkit 2.73 released

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

EP Toolkit version 2.73 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

Trying to finish out the year with a clean slate.  Just a few bug fixes but they are show-stoppers for folks affected.

Happy Holidays!

Joe

1) Fixed error message in Preprocessing function when clicking on Run and Single File mode not checked.  
2) Fixed crash when adding cells or trials with trial specs to an existing file that already has trial specs, as in averaging.  
3) Fixed displaying event lines in waveform figures even when events set to -none- when there are events in the data but no RT information.  
4) Shifted mff import procedure to FieldTrip's v3 for improved mff import support.

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

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 mailing list
Erp...@li... <mailto:Erp...@li...>
https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support <https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support>
_______________________________________________
Erppcatoolkit-support mailing list
Erp...@li...
https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support

[Erppcatoolkit-support] EP Toolkit 2.72 released

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

EP Toolkit version 2.72 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

Mostly bugfixes and improvements to support for text file data format.  Two very important fixes to the new compiled robust ANOVA code included in version 2.70.  Be sure to check this out if you are using the robust ANOVA statistics.  Apologies for any problems this may have caused.

1) Fixed crash when replacing bad channels in Preprocessing function and Edit Mode is set to Manual. 
2) Fixed good epochs in average files being treated as bad (and being zeroed) erroneously while bad epochs not zeroed.  
3) Fixed good channels in average files being treated as bad (and being replaced) erroneously while bad channels not replaced.  
4) Fixed Preprocessing function not preserving Average Reference notation and therefore rereferencing such data to the original reference site.  
5) Fixed View Topos sometimes crashing with -all- cells or -all- subjects.  
6) In View Topos, added Electrodes option to contextual menu to see electrode locations on a 2D map.  
7) Fixed expanded waveform figures from View Topos showing wrong channel.  
8) Added line indicating latency of topos to expanded waveform figures from View Topos.  
9) Fixed crash when displaying data using -all- factors option and the leftmost dataset is not PCA data.  
10) Fixed not reordering impedance values when reordering channels using Edit function.  
11) Fixed not using third exclusion criteria for specs text file in the Segment function.  
12) Increased maximum number of channel areas to 15 in the Channels pane of the Window function.  
13) In Segment function, fixed e-prime specs not being merged into data in case where more than one code is used as the time-lock event (e.g., where the event label codes the experimental condition).  
14) In Preprocessing function, fixed bad EOG channels that were temporarily interpolated not being fixed by the replace or mark bad channel option.  
15) In Preprocessing function, fixed crash for single-trial data where a blink occurs at the end of an epoch.  
16) Fixed .sample field for blink_start and blink_end events.  
17) Added support for specifying sample rate for text data.  
18) No longer resets all the preference settings to default when a new preference field is added by an EP version.  
18) Fixed crash when reading an events text file and there is a problem with it.  19) Fixed crash in trials tab of Edit function.  
20) Fixed crash when reordering by cells data with no trial specs.  
21) Fixed not reading subject specs when present as secondary file.  
22) Fixed event spec files so that when text files are read using single file mode, the events information is matched up correctly.  
23) Fixed robust ANOVA results incorrect when there is missing data.  
24) Fixed robust ANOVA results incorrect when means are trimmed (e.g., if trimming is set at .05 and the sample size is 20 or larger so smallest and largest sample is being dropped in each cell).  
25) Fixed Append subjects in Edit function only adding the last selected file rather than all of them.  
26) Added third exclusion option to Segment function specs pane.


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

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 mailing list
Erp...@li... <mailto:Erp...@li...>
https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support

[Erppcatoolkit-support] EP Toolkit 2.71 released

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

EP Toolkit version 2.71 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

Mostly bugfixes.

1) Added support for EEGlab derived Cartesian coordinates from standard-10-5-cap385.ced and using EEGlab's more precise transform for cartesian coordinates from .sfp file. 
2) Fixed crash in Preprocessing function when chunking and there are no trial specs.  
3) Fixed crash in Preprocessing function when blink correcting multi-subject files.  
4) Fixed not having actually fixed EEGlab bug in 2.70 for reading ced files with fields in scrambled order.  
5) Fixed crash if there are impedances listed for a BrainVision file but no reference.  
6) Fixed crash when plotting waveforms with the positive down option chosen in preferences.  
7) Fixed file type control in the Average function not working properly.  
8) Fixed crash when using Subject Type in Average function.   
9) Fixed crash when generating a grand average from multiple combined-subject average files.  
10) Fixed readlocs taking contents of next column when Type column in a CED file is left empty; now defaults to EEG.  
11) Fixed crash when adding a dataset to the active set where there are no "EEG" channels.

Updated the BrainVision I/O code in FieldTrip to be able to extract the impedance values from more versions of .vhdr files (including an older version of PyCorder which produced double-spaced text and a current version of BrainVision Recorder that uses a different format).  This should show up in FieldTrip distributions as of 11/25/18.
--------------------------------------------------------------------------------

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 mailing list
Erp...@li...
https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support

[Erppcatoolkit-support] EP Toolkit 2.70 released

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

EP Toolkit version 2.70 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

Mostly improvements to the ANOVA function, including MEX files to greatly speed it up.  Also support for importing E-Prime trial specifics.  RIDE has been added to average function options.

1) ANOVA function now includes MSE and standard error in the output.  
2) Added RIDE option to the Averaging function.  
3) Fixed latencies of event lines in View Waves function.  
4) Fixed crash in ANOVA when there are missing spec values for between group factors.  
5) Fixed sometimes skipping follow-up statistics in ANOVAs, perhaps due to a change in Matlab?  
6) Added mex files to speed up ANOVAs.  
7) Added item-averaging option.  
8) Turned off the effect size output as current implementation too limited to be useful, pending further research by Lisa Lix.  
9) Added support for reading E-Prime text output to add trial spec information during segmentation.  
10) Fixed not being able to batch run ANOVAs from an autoPCA when the peak channels changed from factor to factor.  
11) Fixed windowing function crashing with single-trial data.  
12) Fixed crash in SampleTest function when a dataset in the active set lacks electrode coordinates.  
13) Fixed crash for follow-up pairwise contrasts for significant effects when the factor has more than two levels.  
14) Made EP Toolkit robust to variations in the order of the .ced fields as EEGlab will generate ced files with different field orders under some circumstances and this would previously result in scrambling of the electrode coordinate information.  
15) No longer necessary to edit the icadefs file if not running linux.  
16) Changed "TS-EPoffset" to "EPoffset”.  
17) Can now segment using a single segmentation table even when there are multiple continuous files with different conditions for a given subject without causing problems during averaging.

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

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 2.69 released

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

EP Toolkit version 2.69 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

Mostly fixes to FIFF file format support and frequency-domain user interface bugs.  Also sped up View-Scan and PCA functions, which had gotten too sluggish.  Also made a number of improvements to the ANOVA function.

1) Fixed crash when saving data with a regional channel in fiff format.  
2) Fixed filenames malformed when saving a multi-subject file in fiff format.  
3) When reading fiff files, fixed covNum and avgNum fields being set to cell arrays, resulting in crashes later on.  
4) Improved support for writing fiff files in numerous ways.  
5) When reading fiff files, now detects average reference projection and applies average reference to the channels.  
6) Fixed bug in calculation of .covNum field (for fiff files).  
7) Corrected calculation of covNum field (for fiff files) when using trial weighting option with combination of cell averages.  
7) In View Topos mode, now taking absolute value for calculating peak channel and timepoint, which can make a big difference for non average reference data.  
8) Fixed recTime values generated by Segment function not correct (no effect of bug on EP Toolkit functions).  
9) Fixed BadChan QC of Edit function including regional channels in its computation.  
10) Fixed crash when running contrast with the ANOVA function and there is no between group variable.  
11) For ANOVA function, added follow-up pairwise contrasts for significant effects when the factor has more than two levels.  
12) Modified so that sample test function also works with combined (CMB) cells.  
13) Fixed PCA Woody and template Woody options of SampleTest function crashing.  
14) Fixed crash when using Edit function to generate a grand average of frequency-domain data.  
15) Fixed crash in View function for frequency-domain data.  
16) Fixed crash when windowing frequency-domain data.  
17) Fixed crash in View Waves function when the maximum amplitude is negative.  
18) Fixed missing Factor popupmenus for TFT factor data in View function.  
19) Changed in PCA function name of "all" factors and cells to "combined" to reduce confusion with '-all-' option in View function.  
20) In View topos function, improved auto-scaling for dB scaled frequency-domain data.  
21) In View Topos, fixed dipole and jack-knife right-click options not available for frequency-domain data.  
22) Optimized stdCM field calculation so PCAs wouldn't take so darn long.  
23) Fixed TFT so it does not result in NaN at the ends of the resulting output when the sampling rate of segmented data is an even multiple of 250Hz.  
24) Added additional information to beginning of ANOVA output files.  
25) Sped up speed of scans after addition of event marking slowed it down unacceptably.  26) Modified Cousineau-Morey standard error computation to be specific to two-cell contrasts since that is the EP Toolkit's intended use of this figure.  Confidence intervals for waveforms plotted using View may be too narrow if the grand average was computed with an earlier version of EP Toolkit.  No statistical analyses are affected by this issue.

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

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 2.68 released

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

EP Toolkit version 2.68 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

Aside from the usual bug fixes, the functionality for displaying event marks in waveform figures has been enhanced, including reaction time.

1) Fixed crash in View Scan when the data has channels without electrode coordinates.  
2) Fixed crash in View Scan when clicking for plot point without first advancing the plotting window.  
3) Fixed crash sometimes when starting Window Data pane.  
4) Fixed failing to perform PCA scree test when noise field consists of zeros.  
5) Added preference option to turn off BV header encoding.  
6) Sorts batch files by name prior to running ANOVAs, averages, and preprocessing.  
7) Fixed not adding new cells as adds (if enabled) if new cell names specified during windowing.  
8) Fixed crash during ANOVA if a cell name is specified that is not present in the original data if adds are enabled.  
9) Fixed crash in Save function when clicking on table rather than using Convert mode.  
10) Don't remove star for unsaved data when save is cancelled for whatever reason.  
11) Fixed Average function not handling case where some files to be averaged have impedance information and some do not, resulting in later crashes.  
12) Added option to add marks for RT and selected events to View figures.  
13) Added sort popupmenu for subjects, cells, and trials subpanes to Edit function.  
14) Fixed crash when editing contents of trials subpane of Edit function.  
15) Fixed Segment function using next available TRSP when a TRSP is missing instead of just dropping the trial when using BV header encoding option.  
16) Added Synch checkbox to Topos view so that when the channel or the time point is changed for one row, it is changed for all of them.

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

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 2.67 released

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

EP Toolkit version 2.67 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

Aside from the usual bug fixes, support has been added for computing RT and accuracy for each cell (if available in the EEG data files) during averaging and then outputting them into text files for ANOVAs.  The View Topos function has increased flexibility for what dimension of the data files can be listed as the rows. The Windowing function now provides more control over how the cells are output.

1) function unable to batch multiple files when the ced.   
2) Fixed unable to use eloc information from a batch of .ept files when they originally used different ced files.  
3) Fixed in Preprocessing function EMG correction not creating EMG channel when saccade correction performed and crashing when not performed.  
4) Fixed in Views function cells popupmenu listing all trials rather than just one of each name.  
5) Added option to double sampling rate in the Samples subpane of the Edit function.  
6) Read files now handles situation where one of the directories has a space after its name.  
7) Fixed Average function giving errors when there are more subjects than channels.  
8) Segmentation now handles situation where the recording was aborted before the last trial spec was recorded whereas before it was eliminating all trial specs.  
9) Fixed crash when reading .ept file that has event with empty key.  
10) Fixed adding erroneous sph field to the eloc structure when making certain types of edits to the channels using the Edit function.  
11) Fixed crash when adding a channel and there are impedance values.  
12) Fixed crash when performing scree on second step of a two-step PCA.  
13) Added calculation of RT and accuracy summary scores during averaging.  
14) Fixed preprocessing turning data to NaN when detrend option chosen and no baseline set and data are not continuous.  
15) Fixed preprocessing function not outputing to log correct mean number of detected global bad channels for average files.  
16) Preprocessing now only only interpolating bad EOG channels if blink or saccade correction options selected.  
17) Fixed crashes when running preprocessing function on combined subject average files.    
18) Consolidated summary figure for average files so no longer one per subject.  
19) Fixed bug when combining subjects with trial specs where they are all the same string value across the subjects, resulting in failure to combine.  
20) Added listing of RT and accuracy numbers in the Cells view of the Edit function for averaged data.  
21) Added support for outputting behavioral data in the Window function.  
22) Fixed crash when expanding Topos figure of factor waveforms.  
23) Fixed sometimes one too many pages when displaying factors, resulting in a crash when one visits the erroneous one.  
24) Fixed color bar missing in Topos view.  
25) Fixed crash in saccade procedure of the Artifact Correction function when there are bad channels present.  
26) If trying to save a data file in EP format and preferences are set to v6 or v7 and it is over 2GB, then instead of not saving it will now save in v7.3 format.  
27) Fixed crash in Edit function when reordering cells of PCA data.  
28) Added support for View Topos listing all trials or cells or subjects.  
29) Cell box for Window Data function now allows blanks so may edit freely to change order or to drop cells.  'none' no longer recognized as a keyword.  
30) Cell box for Window Data function no longer sorting cell names alphabetically for average files.  
31) Window Data pane settings no longer resetting every time one leaves the pane.  
32) Segmentation function no longer misses events when the .value field is a number rather than a string.

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

Joseph Dien, PhD
Senior Research Scientist
Human Development and Quantitative Methodology Department
University of Maryland, College Park
http://joedien.com <http://joedien.com/>
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org <http://slashdot.org/>! http://sdm.link/slashdot_______________________________________________ <http://sdm.link/slashdot_______________________________________________>
Erppcatoolkit-support mailing list
Erp...@li... <mailto:Erp...@li...>
https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support <https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support>