erppcatoolkit-support — support list

[Erppcatoolkit-support] EP Toolkit 2.66 released

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

EP Toolkit version 2.66 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

I made further improvements to the confidence interval calculations (see tutorial for details) and fixed some bugs.

1) Changed std field of combined subjects (as via the Edit function) to be std of the newly generated grand average data rather than a combination of their std values.  
2) Changed noise field of combined subjects (as via the Edit function) to be noise of the newly generated grand average data rather than a combination of their noise values.  
3) In the View Waves function, implemented Cousineau-Morey confidence interval bands for grand average data.  
4) When combining std values, now sets to zero.  
5) Fixed crash in artifact correction function when detrend option checked.  
6) Fixed crash when expanding waveform in View Topos.  
7) Fixed lack of support for -all- and -erpimage- options for factors in expanded channel windows.  
8) Fixed crash in View Waves when only erpimages are being presented.  
9) Added -all- and -erpimage- options for cells in View Waves function.

I updated import of impedance values from BrainVision files to handle out-of-range and disconnected channels as of FieldTrip20180225.

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 2.65 released

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

EP Toolkit version 2.65 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

This was mostly a bugfix release focusing on preprocessing and the view functions.  An experimental alpha correction option has been added to preprocessing, although it is a memory hog and can crash the computer.  global field power and error band options have been added to the View function.

1) Fixed part of file name after a period when writing out non-EGIS files.
2) Fixed crash in blink correction when chunking and there are events.
3) Fixed crash when preprocessing data containing impedance values.
4) Fixed crash when preprocessing multi-subject average files.
5) Fixed crash when input file has impedances field and channels are being added but none are being added to the impedances field.
6) Fixed crash when averaging data containing impedance values.
7) Fixed boundary events not being handled correctly in BrainVision eeg files.
8) Fixed odd behavior in Read files and Average functions due to Matlab bug in which str2num executes word strings which are function names like "web”.  
9) Fixed saccade potential preprocessing crashing when channels marked as being missing in preprocessing preferences with a -1.
10) Fixed crash in blink correction when 1000 is not evenly divisible by the sampling rate.
11) Fixed crash in preprocessing function when there is an event with an empty .value field.
12) Fixed crash when combining cells and the data is frequency-domain, as when conducting PCA on frequency-domain data.
13) Fixed bugs causing saccade potential to not work as effectively for single-trial data.
14) EMG correction rereferences to Cz to standardize procedure and then restores original reference afterwards.
15) EMG correction  adds an EMG channel to record mean absolute EMG activity removed by the procedure.
16) Fixed crash in blink correction when sample length (e.g., 4ms for 250Hz) did not divide evenly into 100 ms.
17) Fixed crash in saccade correction when no good samples in an epoch.
18) Added an experimental alpha correction option to preprocessing function.  
19) Fixed crash in preprocessing when chunking single-trial data.
20) Added global field power and error band options to the View Waves function.
21) Fixed crash when displaying -all- trials in View Waves function.

To read BrainVision impedances, need at least FieldTrip20171207.

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 2.64 released

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

EP Toolkit version 2.64 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

The most serious bugfix was for the PCA cross-validation option (which I’m renaming "cross-verification" to avoid confusion with a common method for determining number of factors to retain).  It was not producing correct results.
In general, there has been continued improvements to the artifact correction routine, including addition of De Vos's BSS-CCA EMG correction algorithm.  Support for BrainVision files has also been improved, including an option for encoding subject and trial info in the trigger channel.

1) Fixed crash that could occur in the artifact correction function when there are bad time points that exceed the saturation threshold and the dataset is single-trial.  
2) Artifact correction median corrects data prior to saturation check to ensure channels with merely high offsets are not treated as bad data.  
3) Fixed autotemplate missing blinks when sampling rate not 250Hz.  
4) Loosened blink autotemplate slope criteria to better recognize slow blinks.  
5) Artifact correction interpolates bad EOG channels instead of aborting when too many are bad.  
6) Added EMG correction option to Preprocessing function using Maartens De Vos's BSS-CCA code by his kind permission.  
7) Saccade Potential correction works with sampling rates other than 250 Hz.  
8) Fixed crash when trying to save artifact correction summary figure due to Matlab changing their graphics objects AGAIN in 2017b.  
9) Segment function user interface now providing correct default sample range for sampling rates other than 250 Hz.  
10) Segment function user interface now provides only unique set of values for integer trials specs.  
11) Fixed crash when averaging files that have different trial specs.  
12) For artifact correction in general, detrend and baseline correct are now applied per trial for single-trial and average data rather than applied as if it were a continuous dataset (blink correction routine already treated baseline correction this way).  
13) In preprocessing function, eliminated x tick labels to address problem with subplots in summary artifact figure getting squeezed by formatting problem on PCs.  
14) Adding rank check prior to ICA in blink correction.  
15) When reading a file, if none of the channel names match but there are the same number of non-ref EEG channels, will not only use the CED channel names, will assume the ref channels are implicit and add them.  
16) Eliminated restrictions on location of CED files when reading a data file.  
17) Added support for impedance info in BrainVision files.  
18) Added -precedes- crit to the Segment function.  
19) In Segment function, fixed crash when changing value of a -precedes- or -follows- crit to an event name that has no keys.  
20) In Segment function, made fixes to -follows- function for relations other than = and ~= 
21) In Segment function, added support for TS-EPoffset field, which adjusts the epoch time points according to the contents of the field.  
22) Fixed crash when conducting PCA on data where there are trial spec fields that are identical across all the trials/cells and are characters.  
23) Fixed PCA cross-validation option giving wrong results!  
24) Added support for reading EP header information encoded in BrainVision's trigger channel.  
25) Fixed not recognizing ECG channels in mff files.

Joe


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

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

Re: [Erppcatoolkit-support] Cross validation

[Andreas W. <wi...@un...>]

Dear Joe,

> There was indeed a serious bug in this function that I will be fixing immediately.  Thanks for your report!
Good that we found this problem. Sorry for the trouble. I’m relieved that confusion is resolved. Thank you for fixing!

Thanks a lot for your detailed comment on single trial analysis! This is very helpful!

Best regards,
Andreas

> Regarding your more general question about applying the PCA results of the averaged data to the single-trial data, after some further thought I would discourage doing so.  It is important to understand that this procedure is not intended to allow one to apply a factor solution to entirely different datasets per se.  A factor solution is specific to a dataset.  For example, factor scoring coefficients reflect not just what is needed to measure a latent variable (e.g., ERP component) but also what is needed to disentangle it from other overlapping latent variables.  So if both datasets had exactly the same P300 but only the first also had an N400, then applying the PCA results to the second dataset would be invalid.  In the present case, it is likely that the single-trial data has features (e.g., alpha waves and artifacts) that were averaged out.  It would only be valid to apply the factor scoring coefficients from the PCA of one dataset to another dataset if the second dataset had exactly the same latent variables (e.g., same ERP components with exactly the same time course for a temporal PCA, differing only in amplitudes) and the same inter-factor correlations.  This can rarely be said to be the case.  The sole intent is to allow one to compare two different factor solutions on the same dataset to quantitatively determine how similar they are (correlate the two sets of factor scores).  I had chosen to call this procedure “cross-validation" to emphasize this point, although I should probably change the name to something like “cross-verification” to avoid confusion with more common applications of the procedure.
> 
> Thanks again!
> 
> Joe
> 
> 
>> On Nov 19, 2017, at 01:19, Joseph Dien <jd...@ma...> wrote:
>> 
>> Hi Andreas,
>>    1) yes, that is correct.
>> 
>>    2) I haven’t tried doing anything like this.  when you say you tried the former, what you did was take all the single trials from all the subjects and combined them into a single dataset and then applied the cross-validation to this combined dataset?
>> 
>>    3) it should be the same.  Send me your data file along with the settings you used and I’ll take a look at it.
>> 
>> Joe
>> 
>>> On Nov 14, 2017, at 10:01, Andreas Widmann <wi...@un...> wrote:
>>> 
>>> Dear Joe,
>>> 
>>> may I ask three (hopefully not too stupid) questions with respect to cross-validation?
>>> 
>>> (1) I successfully computed a temporal PCA for an ERP dataset (consisting of 4 conditions and 24 subjects each averaged over the individual trials). Now a reviewer wants us to perform a single trial analysis. My initial idea was to somehow "apply" the PCA pattern resulting from the grand-average PCA to the single trials (as we sometimes do "apply" ICA weights to other datasets filtered differently). My naive understanding is that this is what cross-validation does. Is this correct?
>>> 
>>> (2) In case yes, I’m not sure how standardization of factor scores should be performed. Should standardization (as in line 812 of ep_doPCA.m) be done including all trials from all subjects and conditions? Or should standardization be done per subject? I tried the former. The resulting factor scores were (averaged across trials per subject and condition) about factor 4 smaller than the factor scores from the grand-average PCA. Is this expected/plausible?
>>> 
>>> (3) Finally, I tried cross-validation of the same dataset the PCA originally was computed from. The resulting factor scores were similar but not identical. Is this expected/plausible?
>>> 
>>> Thanks a lot for your help! Best,
>>> Andreas
> 
> --------------------------------------------------------------------------------
> 
> Joseph Dien, PhD
> Senior Research Scientist
> Department of Human Development and Quantitative Methodology
> University of Maryland, College Park
> http://joedien.com

Re: [Erppcatoolkit-support] Cross validation

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

There was indeed a serious bug in this function that I will be fixing immediately.  Thanks for your report!

Regarding your more general question about applying the PCA results of the averaged data to the single-trial data, after some further thought I would discourage doing so.  It is important to understand that this procedure is not intended to allow one to apply a factor solution to entirely different datasets per se.  A factor solution is specific to a dataset.  For example, factor scoring coefficients reflect not just what is needed to measure a latent variable (e.g., ERP component) but also what is needed to disentangle it from other overlapping latent variables.  So if both datasets had exactly the same P300 but only the first also had an N400, then applying the PCA results to the second dataset would be invalid.  In the present case, it is likely that the single-trial data has features (e.g., alpha waves and artifacts) that were averaged out.  It would only be valid to apply the factor scoring coefficients from the PCA of one dataset to another dataset if the second dataset had exactly the same latent variables (e.g., same ERP components with exactly the same time course for a temporal PCA, differing only in amplitudes) and the same inter-factor correlations.  This can rarely be said to be the case.  The sole intent is to allow one to compare two different factor solutions on the same dataset to quantitatively determine how similar they are (correlate the two sets of factor scores).  I had chosen to call this procedure “cross-validation" to emphasize this point, although I should probably change the name to something like “cross-verification” to avoid confusion with more common applications of the procedure.

Thanks again!

Joe


> On Nov 19, 2017, at 01:19, Joseph Dien <jd...@ma...> wrote:
> 
> Hi Andreas,
>    1) yes, that is correct.
> 
>    2) I haven’t tried doing anything like this.  when you say you tried the former, what you did was take all the single trials from all the subjects and combined them into a single dataset and then applied the cross-validation to this combined dataset?
> 
>    3) it should be the same.  Send me your data file along with the settings you used and I’ll take a look at it.
> 
> Joe
> 
>> On Nov 14, 2017, at 10:01, Andreas Widmann <wi...@un... <mailto:wi...@un...>> wrote:
>> 
>> Dear Joe,
>> 
>> may I ask three (hopefully not too stupid) questions with respect to cross-validation?
>> 
>> (1) I successfully computed a temporal PCA for an ERP dataset (consisting of 4 conditions and 24 subjects each averaged over the individual trials). Now a reviewer wants us to perform a single trial analysis. My initial idea was to somehow "apply" the PCA pattern resulting from the grand-average PCA to the single trials (as we sometimes do "apply" ICA weights to other datasets filtered differently). My naive understanding is that this is what cross-validation does. Is this correct?
>> 
>> (2) In case yes, I’m not sure how standardization of factor scores should be performed. Should standardization (as in line 812 of ep_doPCA.m) be done including all trials from all subjects and conditions? Or should standardization be done per subject? I tried the former. The resulting factor scores were (averaged across trials per subject and condition) about factor 4 smaller than the factor scores from the grand-average PCA. Is this expected/plausible?
>> 
>> (3) Finally, I tried cross-validation of the same dataset the PCA originally was computed from. The resulting factor scores were similar but not identical. Is this expected/plausible?
>> 
>> Thanks a lot for your help! Best,
>> Andreas

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

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

Re: [Erppcatoolkit-support] Cross validation

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

Hi Andreas,
   1) yes, that is correct.

   2) I haven’t tried doing anything like this.  when you say you tried the former, what you did was take all the single trials from all the subjects and combined them into a single dataset and then applied the cross-validation to this combined dataset?

   3) it should be the same.  Send me your data file along with the settings you used and I’ll take a look at it.

Joe

> On Nov 14, 2017, at 10:01, Andreas Widmann <wi...@un...> wrote:
> 
> Dear Joe,
> 
> may I ask three (hopefully not too stupid) questions with respect to cross-validation?
> 
> (1) I successfully computed a temporal PCA for an ERP dataset (consisting of 4 conditions and 24 subjects each averaged over the individual trials). Now a reviewer wants us to perform a single trial analysis. My initial idea was to somehow "apply" the PCA pattern resulting from the grand-average PCA to the single trials (as we sometimes do "apply" ICA weights to other datasets filtered differently). My naive understanding is that this is what cross-validation does. Is this correct?
> 
> (2) In case yes, I’m not sure how standardization of factor scores should be performed. Should standardization (as in line 812 of ep_doPCA.m) be done including all trials from all subjects and conditions? Or should standardization be done per subject? I tried the former. The resulting factor scores were (averaged across trials per subject and condition) about factor 4 smaller than the factor scores from the grand-average PCA. Is this expected/plausible?
> 
> (3) Finally, I tried cross-validation of the same dataset the PCA originally was computed from. The resulting factor scores were similar but not identical. Is this expected/plausible?
> 
> Thanks a lot for your help! Best,
> Andreas
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Erppcatoolkit-support mailing list
> Erp...@li...
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--------------------------------------------------------------------------------

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] Cross validation

[Andreas W. <wi...@un...>]

Dear Joe,

may I ask three (hopefully not too stupid) questions with respect to cross-validation?

(1) I successfully computed a temporal PCA for an ERP dataset (consisting of 4 conditions and 24 subjects each averaged over the individual trials). Now a reviewer wants us to perform a single trial analysis. My initial idea was to somehow "apply" the PCA pattern resulting from the grand-average PCA to the single trials (as we sometimes do "apply" ICA weights to other datasets filtered differently). My naive understanding is that this is what cross-validation does. Is this correct?

(2) In case yes, I’m not sure how standardization of factor scores should be performed. Should standardization (as in line 812 of ep_doPCA.m) be done including all trials from all subjects and conditions? Or should standardization be done per subject? I tried the former. The resulting factor scores were (averaged across trials per subject and condition) about factor 4 smaller than the factor scores from the grand-average PCA. Is this expected/plausible?

(3) Finally, I tried cross-validation of the same dataset the PCA originally was computed from. The resulting factor scores were similar but not identical. Is this expected/plausible?

Thanks a lot for your help! Best,
Andreas

[Erppcatoolkit-support] EP Toolkit 2.63 released

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

EP Toolkit version 2.63 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

The only change is a bugfix for spatial PCAs, which got broken by the update to how frequency data is handled internally.  This version is intended to provide a stable base for future releases.

Joe


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

Joseph Dien, PhD
Senior Research Scientist
Maryland Neuroimaging Center
University of Maryland, College Park
http://joedien.com <http://joedien.com/>

[Erppcatoolkit-support] EP Toolkit 2.62 released

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

EP Toolkit version 2.62 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

This is mostly a bugfix release focusing on frequency domain analyses, along with a number of small improvements.  The most consequential change is that when combining frequency domain data in all dimensions except channels, the internal representation is converted to absolute amplitude first.  This is discussed further in the tutorial documentation.

Release Notes:

1) Fixed crash when performing time-frequency transform on single-trial data files.  
2) Contrast button of ANOVA pane only presents the between contrast controls if there are more than one between levels.  
3) When performing time-frequency transform on continuous data files, lops off data at ends in increments of one second to that edit epochs still align properly.  
4) Previously would either crash or the edit epochs would end up misaligned by half of the T-F window (which was .5 seconds by default).  
5) Also, since the T-F transform reaches into the adjoining epochs, if they were bad data then the current epoch is also marked as being bad (both for trial and for channels).  
6) Bad data edits passed on to segmented files in segmentation function.  
7) Flexible segments implemented in segmentation function.  
8) Added option to clear working set to File menu.  
8) Fixed crash when segmenting time-frequency data.  
9) Fixed trial names not being correctly numbered when appending trials to a single-trial file using the Edit function, usually resulting in error messages.  
10) Fixed crash when using contrast function.  
11) Added support for averaging multi-file subjects.  
12) Fixed crash when expanding channel of TFT data in View Waves function and not all four colors are being used.  
13) Fixed displaying separate imaginary component of spectral data when the FFT units are not set for complex units.  
14) For TFT data, when View set to display only one Hz bin, switches to waveform display rather than erpimage display.  
15) Supports display of flexible segments.  
16) Fixed View Topos displaying imaginary component of FFT data even if FFT units not specified as being complex.  
17) Improved View Topos auto scaling for dB unit FFT data.  
18) In Show Waves, only EEG chans are subjected to FFT unit conversions.  
19) PCA now drops non-EEG channels and regional EEG channels.  
20) Added support for sample tests for TFT data.  
21) Fixed Window pane crashing when first dataset in working set is not an average file.  
22) Fixed crash when windowing frequency-domain data.  
23) Fixed Window function saves both imaginary and real files for spectral data even when units are not set as complex.  
24) Fixed single-sample duration sampleTest results not displaying in View Waves.  
25) Fixed Window function text file headers not mentioning dB scaling for spectral data.  
26) Scaling input boxes in View pane now allow up to four decimals to better accommodate power units for spectral data.  
27) Fixed not combining trial specs correctly over subjects, resulting in crashes down the line in ANOVA function.  
28) Fixed spectral density conversion incorrectly applied to View pane controls for complex and amplitude scaling, resulting in the numbers being changed from what was input.  
29) Fixed robust ANOVA apparently providing effect size for within contasts of more than two levels when should have been disabled.  
30) Fixed View function's conversion to spectral density dividing by bin width rather than sqrt(bin width).  
31) Fixed View Topos sometimes crashing when frequency band is just one Hz.  
32) Now allows just one sample of TFT data to be chosen for display using the View function.  
33) Improved default auto-scaling for View Waves and View Topos.  
34) When adding together freq data other than channels, switch to amplitude scaling for internal representation.  
35) Fixed crashes in Average function when using median or trimmed means options.  
36) Allow baseline correction to be applied to TFT data.  
37) Improved presentation of TFT erpimages.  
38) Presence of NaN in EEG channels no longer zeroed as bad data if original file was an .ept file (as fix for zeroing out phase-lock transform when there is a flat reference channel).  
39) Improved dragging of red lines in Template Creation pane.  
40) Added Compare Channels option to the View Topos pop-up menu.  
41) Fixed crash in Transform function when filtering continuous data.  
42) Fixed crash that can happen when segmenting continuous data.

Joe


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

Joseph Dien, PhD
Senior Research Scientist
Maryland Neuroimaging Center
University of Maryland, College Park
http://joedien.com <http://joedien.com/>

[Erppcatoolkit-support] EP Toolkit 2.61 released

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

EP Toolkit version 2.61 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

This is mostly a bugfix release to deal with file reading issues.

Release Notes:

1) Fixed crash when performing two-step PCA where first step was created in a prior version of the EP Toolkit.  2) Fixed crash when merging multiple subjects with single cell mode in Read function and .study files.  3) When reading continuous mff files, now recognizes reference channel type correctly.  4) Added option to flip the electrode locations for .mff and .fiff.  5) Fixed crash when rotating electrode coordinates 180 or 270 degrees for .mff and .fiff files.  6) Fixed cannot delete FID channels using the Edit function.  7) Fixed crash in Segmentation function when resegmenting single-trial data.  8) When importing an average file with multiple cells with the same name, modifies the names to be unique rather than assuming single-file type.

Joe


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

Joseph Dien, PhD
Senior Research Scientist
Maryland Neuroimaging Center
University of Maryland, College Park
http://joedien.com <http://joedien.com/>

[Erppcatoolkit-support] EP Toolkit 2.60 released

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

EP Toolkit version 2.60 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

I’ve bumped up the release number from the last one (2.54) to reflect the extensive changes that have been made.  Aside from numerous bug fixes, there have been substantial improvements made to the robust statistics (discussed in Dien, 2017), Scan Continuous Data, and Preprocessing functions.  The changes to the latter (that is now termed the Multiple Algorithm Artifact Correction or MAAC procedure) are the subject of a manuscript that will be submitted soon.

Release Notes:

1) Fixed New button in Edit function inactive.  2) 2D maps in Scan function now leave out bad channels.  3) For preprocessing function, when combining chunks from continuous data, keep events that were added during the preprocessing process to chunks other than the first one.  4) For preprocessing function, added automatic detection and correction of saccade potentials.  5) Fixed crash in template function when clicking for 3D head and there are bad channels present.  6) Fixed crash when using average function and the active set is empty.  7) During preprocessing, detects channels that went flat partway through a session (more than 10%) and labels them as global bad channels.  8) Append subjects in the Edit function can now select multiple files for appending.  9) Fixed crash when changing the Trial Spec Model ofthe Latency-Lock procedure of the Average function.  10) Fixed error when averaging and a cell has no good trials.  11) Reworked the latency-lock and the jitter-correct averaging algorithm to operate in a more straightforward manner.  12) Improved saccade correction by treating as eye position artifact rather than saccade related.  13) Fixed channels with large offsets being erroneously tagged as being bad channels during preprocessing.  14) During bad channel detection in preprocessing, check for difference from inverse of all other channels too since channels in sparser arrays can end up being the only opposite polarity waveform.  15) During bad channel detection in preprocessing, baseline correct with first sample for each epoch when applying maxneighbor criterion so simple offset does not trigger it.  16) In preprocessing function, fixed blink detection algorithm was adding lower VEOG channels rather than subtracting them (making it a little less sensitive than it should have been).  17) Blink correction function now adds blink_start and blink_end events.  18) In Scan function, added temporally arranged event list for navigating to individual events.  19) In Scan function, event lists for setting boundaries of Redisplay are now alphabetic order.  20) In Scan function, global bad channels marked with faded line rather than red zone.  21) Fixed error when generating a grand average with the Average function and there are trial specs.  22) Added saccade potential to set of artifact templates.  23) In template function, can click and drag time point marker in waveform windows.  24) Fixed crash in template function after performing a Clear Template for data with non-EEG channels.  25) For preprocessing function, added template summary figure to saved files.  26) In preprocessing routine, implemented improved saccade correction routines, dropping blink points from saccade potential and saccade corrections and treating saccades as continuous eye position artifact rather than as an episodic motion-related artifact.  27) Changed runica call in PCA and blink correction functions so that they are always initialized with same seed so that ICA results are fully replicable.  28) In Scan function, fixed bad channels being displayed as still bad.  29) Added support for boundary events to blink and saccade correction routines in Preprocessing function.  30) Scaling of non-EEG channels in Scan continuous data function adjusted so variations are visible.  31) NaN values no longer set to zero and bad data flags set.  32) Fixed crash when performing time-frequency transform with dpss multi-taper on continuous data or segments longer than .5 seconds and default smoothing of one second.  33) Fixed time-frequency transform being applied only to first one second of continuous data.  34) Fixed FFT data on amplitude scaling not converted to real numbers in Show Waves and Show Topos functions.  35) Time-frequency transform no longer drops non-EEG/MEG channels.  36) Can view continuous TFT data in the Scan function.  37) Event times now updated to new sample times when performing TFT with Transform Data funcion.  38) Fixed crash when applying filtering to averaged data.  39) Added support for template Woody and for continuous data to Sample Test function.  40) Upgraded controls in View Scan Continuous Data for navigating and examining events.  41) Upgraded eye-position figures in View Scan Continuous Data.  42) Added support for writing out subject spec text files.  43) No longer assumes different data files have the same subject specs when combining them (causing error when not the case).  44) Fixed crash in segment function after changing line after -follows- to 'none'.  45) Fixed segmentation ignoring the 6th criterion.  46) Fixed segmentation section crit "<" and ">" relations being interpreted as the reverse direction.  47) Added eye-tracker plot to template function.  48) In template function, fixed waveform plots not updating when changing segment via popupmenu.  49) Fixed crash when saving edits in View>Scan for continuous data.  50) Added eyeTracker option to blink and saccade correction routines.  51) Improved movement correction routine by excluding EOG channels from the detection algorithm.  52) Reversed + and - buttons to comply with norms for such buttons.  53) Accommodated the datasets in View-Scan function having differing channels.  54) Temporarily mean-center data prior to filtering to minimize filter edge artifact (undone afterwards).  55) Fixed error when generating a grand average with the average function.  56) Fixed crash when switching to jitter-correct in Average Pane and there are no single-trial datasets in the working set.  57) Wrong channels being marked when clicking on channels using Edit mode for cells beyond the first in single-trial data in the Scan function.  58) Fixed error when batch segmenting multiple subject files and there are more than one row of criteria for the same cell name.  59) Added support for New Segment events in brainvision files.  60) Time points with extreme values (as specified by the saturation preference) now excluded from bad channel detection, saccade correction, and blink correction procedures in the Preprocessing function.  Saturation default value changed to 1000.  61) When quitting, Clear Option now leaves the EPwork directory and the preference file intact, so it is no longer necessary to redo the preference settings.  62) Enabled saccade correction in the Preprocessing function even when one or both HEOG channels are bad.  63) Added toggle to edit mode for Scan function of View of continuous data.  64) Improved blink autotemplate procedure.  65) Improved bad channel detection in Preprocessing function.  66) Adjusted "too many bad chans" criterion in Preprocessing function so not based on rounded off number (10% of 33 channels makes the criterion be need more than 3.3 bad channels rather than 3) and also based on total EEG channels rather than all channels.  67) In the Eye Artifact Template Creation window, various fixes to the behavior of the dataset and trial number controls.  68) Made template undo specific to last change.  69) Improved determination of horizontal saccade direction in the Template function so a exemplar is not erroneously reversed when added to the cumulative template.  70) Fixed crash when setting the Mark fields in the View function.

Joe


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

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Senior Research Scientist
Maryland Neuroimaging Center
University of Maryland, College Park
http://joedien.com <http://joedien.com/>
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[Erppcatoolkit-support] EP Toolkit 2.53 released

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

EP Toolkit version 2.54 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

This is just a bugfix release.

Release Notes:

1) Fixed crash when using jitter-correct option in Average and there are bad channels in the jitter-correct channel.
2) Fixed replaced bad channels still being treated as bad by jitter-correct option in Average.
3) Fixed crash when generating a grand average with the Average function.
4) PCA Woody option of SampleTest function not saving latencies and amplitudes to the correct trials.
5) Fixed PCA Woody option of SampleTest function crashing with spatial PCA templates.
6) Fixed crash in blink correction routine when correcting single-trial data.
7) Fixed crash in blink correction routine when no blinks were detected.
8) Fixed crash in template function when scrolling through continuous data and there is an event with an empty .value field.

Joe


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

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Senior Research Scientist
Maryland Neuroimaging Center
University of Maryland, College Park
http://joedien.com <http://joedien.com/>
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[Erppcatoolkit-support] EP Toolkit 2.53 released

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

EP Toolkit version 2.53 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

Aside from the usual bug fixes, I’ve been focusing on further improving support for spectral analyses and an improved Scan function for examining and editing continuous data files.

I would like to note that while a recent methodology paper (Clayson, Baldwin, & Larson, 2013) reported that my centroid latency measure (an option in the Window function) is "biased", the authors generously allowed me to examine the script that ran their simulation analyses and I found that contrary to their methods description they had not randomized the phase of the background sine waves (simulated noise), resulting in a confound.  So in fact the "bias” in the centroid measure was actually due to it to being more sensitive (correctly) to the presence of the confounded noise than the competing methods (which explains why this "bias" was stronger the larger the noise-to-signal ratio).  The authors have accepted this critique and responded that they plan to submit an erratum to their paper.

I would also like to note that I am currently in a soft-money position so if you have found the EP Toolkit to be useful for your research or think that I could otherwise contribute to your studies, I welcome opportunities for collaboration either as a co-author or as a consultant to help support the continued development of the EP Toolkit.

Release Notes:

1) Fixed crash when using Add button in Edit function to add a single cell.
2) Fixed crash in View Waves function when minimum voltage equals the maximum voltage.  
3) Fixed when clicking on Views channels, can only get expanded channel window if one clicks along the very top edge for FFT data.
4) Fixed upper and lower amplitude/power being changed immediately after new values manually entered into the View panel for FFT data.
5) Fixed min and max values displayed in Views pane divided by Hz bin width rather than sqrt(Hz bin width) when set to amplitudes.
6) Now allows power scaled data to be displayed as amplitudes.
7) Amplitude FFT data are represented in complex form.
8) Consolidated spectral unit controls so just four options (cm, am, pw, dB).
9) Fixed power-scaled data in View Waves function divided by square root of Hz bin width rather than Hz bin width.
10) Now allows power scaled FFT data to be output as amplitudes.
11) Fixed Matlab crash in View function when only FFT erpimages are being displayed.  
12) Fixed erpimages of FFT data displaying as blank.
13) If minimum value in View pane is zero, in dB scaling will scale to -2 instead of –inf to maintain useful range.
14) Eliminated option to transform data in power rather than amplitude form to avoid potential confusion.
15) Fixed crash when performing frequency transform on continuous data files.
16) Now doubles amplitude of spectral data when halving the bin size via the Edit function to correct for what it would have been and to ensure that subsequent spectral density scaling will be correct.
17) Fixed crash in View Waves when unable to generate unique labels for the four datasets.
18) Fixed no support for frequency PCA of continuous data in min and max values for View pane.
19) Added improved Scan pane for viewing and editing continuous data.
20) Disabled check to see if subtracting blink factors increased overall variance since semi-singularity correction seems to be controlling the noise problem.
21) Improved event marking of blink peaks.
22) Blink artifact channel now difference between upper and lower EOG channels.
23) Fixed couldn't read text files if in preference settings lastrow equals zero and firstrow is larger than 1.
24) Fixed jack-knife not calculated for first step of PCAs.
25) Fixed computation of peak pos and neg channels and peak channel polarity in Factors subpane of Edit function.
26) Fixed error when saving text files.
27) Fix to semi-singularity check for blinks, which was dropping too many channels.  
28) Dropped .power field.  Spectral data is now always maintained in amplitude scaling internally.

Joe


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

Joseph Dien, PhD
Senior Research Scientist
Maryland Neuroimaging Center
University of Maryland, College Park
E-mail: jd...@ma... <mailto:jd...@ma...>
Cell Phone: 202-297-8117
http://joedien.com <http://joedien.com/>
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[Erppcatoolkit-support] EP Toolkit 2.52 released

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

EP Toolkit version 2.52 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

This is a bug fix release.  The most important, other than fixes for crashes, is that per new information from Dr. Lix the effect size output of the robust ANOVA function has been disabled for within-group contrasts.

1) Fixed crash when preprocessing continuous data.  
2) Fixed crash when performing two-step PCA other than cross-validation.  
3) Fixed crash when performing second step of two-step PCA on older PCA datasets without a numRels field.  
4) Preprocessing function allows EEG files with different numbers of non-EEG channels to be batched together.  
5) Changes to undocumented SMI option.  
6) Preserves order of factors when cross-validating. 
7) Fixed crash in Segment function when the criterion string is longer than the stimulus string for the “starts” and “ends” relationships.  
8) Fixed crash in Transform function when segmented data’s time-lock event occurs after the end of the segment.  
9) Per new information from Lisa Lix, effect size output disabled for within-group contrasts.

Joe


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

Joseph Dien, PhD
Senior Research Scientist
Maryland Neuroimaging Center
University of Maryland, College Park
E-mail: jd...@ma...
Cell Phone: 202-297-8117
http://joedien.com

[Erppcatoolkit-support] EP Toolkit 2.51 released

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

EP Toolkit version 2.51 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

Notable changes include further improvements to EEGLab and mff file format support, addition of a cross-validation option for PCAs, and improvements and corrections for the robust ANOVA implementation.  Note that the EGI CED files have been modified to adopt a uniform labeling system for the vertex channel.  This may result in incompatibilities with files using the original EG CED files but can be addressed by changing the name of the vertex channel as needed.
1) When none of the CED channel names match the data but there are the same number of EEG channels, it will be assumed that they are the same channels and in the same order.  A warning message is provided.  

2) Fixed crash when mff average file has only one subject.  

3) Fixed crash in Edit function’s cells tab for single subject average files with no trial specs.  

4) Fixed crash when appending an average file with trial specs usiong the Edit function.  

5) Fixed aborting averaging when generating a combined subject average file wherein one of the files after the first has more trial specs than the first average file.  

6) Standardized electrode labeling (e.g., E10) when reading mff average files.  

7) Standardized EGI vertex electrode naming (e.g., E129 rather than Cz or REF or VREF) in EP Toolkit code as well as bundled CED files.  

8) On the assumption that EGI users have largely migrated from GSN200 to Hydrocel nets, the default right mastoid channel has been changed from 101 to 100.  

9) Fixed crash when continuous set file has a single eventHdr event and it has an NaN or numeric .value.  

10) Handles the NaN values that EEGlab seems to set channels to when it automatically edits them to being bad data (in contrast to EEGlab’s manual channel rejection which operates via flags in the reject.manual field).  

11) Fixed crash in Edit function when combining cells or subjects and there are trial specs with numbers.  

12) Cells no longer sorted alphabetically when data files are saved in EGIS format.  

13) Fixed crash when appending to a data file with an empty trialspecs field.  

14) Robust ANOVA routine drops ill-conditioned runs from the bootstrapping computations.  

15) Handles case where the entire bootstrap sample is drawn from the same observation and treats as an F of inf.  

16) Edit function’s Factors subpane now provides both negative and positive peak chans.  

17) Fixed crash in Edit function when changing order of cells.  

18) Fixed crash when reading in EEGlab .study datasets.  

19) Fixed crash when merging files (as when using single file mode or reading EEGlab study datasets) that do not have subject specs.  

20) Fixed crash when windowing with the "measure then collapse" option.  

21) Corrected erroneous error message that degrees of freedom of robust ANOVA is calculated per multivariate rather than univariate approach.  

22) Added cross-validation option to PCA.  

23) Fixed NaN effect sizes when PER is set to zero.  

24) Now runs robust ANOVAs 11 times with 4999 sims (by default) and then reports median p-value and whether twice the standard deviation of the p-value exceeds the alpha threshold, in which case the results include the notation that the p-value was “(not confirmed)”. 

25) If effect size d* is made positive, confidence interval signs also flipped.  

26) Includes warning summary of %age of bootstrapping simulation runs with singular and nearly singular matrices in the ANOVA output files.

 



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

Joseph Dien, PhD
Senior Research Scientist
Maryland Neuroimaging Center
University of Maryland, College Park
E-mail: jd...@ma...
Cell Phone: 202-297-8117
http://joedien.com



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

Joseph Dien, PhD
Senior Research Scientist
Maryland Neuroimaging Center
University of Maryland, College Park
E-mail: jd...@ma...
Cell Phone: 202-297-8117
http://joedien.com

Re: [Erppcatoolkit-support] Problem merging .set files

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

Sorry to hear about the problem!  It doesn’t sound like you’re using the Single Cell Files Mode correctly.  The files are supposed to be named in a way that can tell apart the subjects and cells (e.g., TEST01T).  In this case the first four characters indicate the name of the experiment and are ignored.  The next two characters indicate the subject number.  The final character indicates the condition name.  one would write in 5:6 for the subject and 7 for the condition.  Take another look at the instructions in the Tutorial file.
Nonetheless, it shouldn’t be crashing.  At worst it should give you an error message.
Could you send me the names of your files so I can figure out why it is crashing?

Cheers!

Joe


> On Dec 10, 2015, at 09:45, Ines Bramao <ine...@ps...> wrote:
> 
> Hello,
> 
> First of all thank you very much for the nice toolkit! I just started to use it to do PCA analysis.
> 
> I am trying to load eeglab .set files. I have 26 different files, corresponding to the averages of 26 different participants for one condition. As far as I understood the tutorial, for the PCA analysis, the files need to be merged into a single file. In order to do that, I:
> 1) click in the single cell files option; and
> 2) write 1:26 on the subject and 1:26 on the cell box;
> 
> This doesn't work and I get the following error message:
> 
> Index exceeds matrix dimensions.
> Error in ep>readFiles (line 9913)
>             theSubs{theFile}=sessionFiles{theFile}(subPos);
> Error in ep (line 3090)
>         readFiles(theHandles,importFormat,dataType);
> Error while evaluating uicontrol Callback
> 
> However, if I try to load the data of just 10 participants (whatever 10 files I select) it does work out...
> Am I doing something wrong?
> 
> Thank you very much in advance!
> Ines
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Senior Research Scientist
Maryland Neuroimaging Center
University of Maryland, College Park
E-mail: jd...@ma...
Cell Phone: 202-297-8117
http://joedien.com

[Erppcatoolkit-support] Problem merging .set files

[Ines B. <ine...@ps...>]

Hello,

First of all thank you very much for the nice toolkit! I just started to use it to do PCA analysis.

I am trying to load eeglab .set files. I have 26 different files, corresponding to the averages of 26 different participants for one condition. As far as I understood the tutorial, for the PCA analysis, the files need to be merged into a single file. In order to do that, I:
1) click in the single cell files option; and
2) write 1:26 on the subject and 1:26 on the cell box;

This doesn't work and I get the following error message:

Index exceeds matrix dimensions.
Error in ep>readFiles (line 9913)
            theSubs{theFile}=sessionFiles{theFile}(subPos);
Error in ep (line 3090)
        readFiles(theHandles,importFormat,dataType);
Error while evaluating uicontrol Callback

However, if I try to load the data of just 10 participants (whatever 10 files I select) it does work out...
Am I doing something wrong?

Thank you very much in advance!
Ines

[Erppcatoolkit-support] EP Toolkit 2.50 released

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

EP Toolkit version 2.50 has been released:
https://sourceforge.net/projects/erppcatoolkit/ <https://sourceforge.net/projects/erppcatoolkit/>

Notable changes are some fixes to how the units for spectral measures that should be noted by anyone using the EP Toolkit for spectral analyses.  Also, continued improvements to the Segment function, making it possible to first segment the trials, preprocess, and then reassign the trials to different conditions as needed.  It’s no longer necessary to rerun the preprocessing each time one changes the cell criteria.  Also effect sizes have been implemented for the robust ANOVAs.  In order to fully implement Lisa Lix’s new SAS/IML effect size code, I had to make some additions to her d* algorithm (documented in the tutorial).  I’m pretty confident of the additions but she hasn’t had time yet to validate them so they should be understood in this light.

1) Added support for reading edf files with channels of varying sampling rates.  

2) Fixed crash in Segment Pane and in Scan function when continuous dataset has no events.  

3) Fixed navigating around one-second epochs of continuous data in Scan function not working properly.  

4) Changed min and max scale of TopoPlots to be set by plotted data unless overriden.  

5) Fixed crash when using rereference function to change the displayed referencing.  

6) Fixed crash when selecting less than a second of data, as in the Edit function.  

7) Fixed crash when plotting two datasets with different numbers of electrodes and the larger one is the first one.  

8) Performs average reference prior to performing PARE correction via Transform function.  

9) Fixed crash when reading data with an event prior to first sample of data.  

10) Added effect size and confidence intervals to the robust ANOVA output.  

11) For Scan function, fixed centering of continuous data being based on entire dataset rather than just the one-second epoch being viewed, rendering it sometimes not useful.  

12) Fixed unable to save artifact correction summary figure starting with Matlab 2014b.  

13) For Segment function, fixed criterion comparisons not being evaluated correctly for < and >.  Comparisons are now evaluated numerically for numbers, otherwise alphabetically.  

14) Added ability to resegment (and thus reassign cells of) single-trial data.  

15) Fixed choosing Cancel after pressing Edit>Overview>Channel Coordinates automatically erased channel coordinates.  

16) Added feature to Edit function that when electrode coordinates are replaced with new ones, the EEG channels can be remapped via interpolation.  

17) Segmentation function now adds next TRSP event after segmentation event without regard to whether the TRSP event fell within the segmentation period.  

18) Fixed sometimes crashing in eye artifact template creation function when loading a template file and there are datasets with a different number of channels.  

19) In eye artifact template creation function, fixed number of trials in saccade templates not being reset when Clear button used.  

20) In segmentation function, the trial spec sectionTrial and sectionNumbers changed to start with 1 rather than 0.  

21) Fixed crash when running horizontal saccade correction but not vertical saccade correction.  

22) Fixed crash when accessing a dataset in the working set with a different number of fields than that of the current EP format.  

23) Fixed amplitude spectral density calculated as divided by Hz rather than by square root of Hz.  

24) Fixed dB of amplitude data not converted to power first.  

25) Fixed dB units should be labeled as dBV since it is a ratio and therefore has no units.  

26) Changed the frequency bins so that the first one starts at the frequency resolution (e.g., 2hz if the bins are 2Hz wide) rather than always at 1.  

27) Fixed crash in transform function when signal processing toolbox is installed and using multi-taper method for time-frequency transform.  

28) Fixed Window button on main pane not becoming active for single-trial data being present in the active set.  

29) Fixed crash when working set newly initialized and running an ANOVA on behavioral data with adds option activated.  

30) Fixed crash when ANOVA conducted on data with characters instead of numbers.  Now treated as missing data.  

31) When single-trial data is averaged, the contents of trial specs (such as RT) will in the retained trials will also be averaged and these averaged trial specs can be accessed via the Edit function.  

32) In Edit function, fixed channel weight sum not updating when weights changed.  

33) Added capability to specify OR criteria for a condition by just giving them the same name.  

34) Trial spec names no longer continue to have TS- prefix when segmented data saved, which also resulted in trial specs not being recognize during segmentation.  

35) Columns of most tables rearrangeable for greater convenience.  Doing so does not change the data in any manner.  

36) Fixed crash when preferences set to rotate mff/eeglab electrode coordinates 180 or 270 degrees.  

37) Changed default head rotation for electrode coordinates of mff and fiff files to 90 degrees.  

38) Fixed transform function not applying mff/fiff electrode coordinate rotation and text file preference settings.

I’ve also committed changes to the FieldTrip I/O to allow for choosing which channels to read in edf files with heterogenous sampling rates and to fix a bug when reading an mff file with a PC and the file is on a server that has not been mapped to a drive letter.  If these changes are needed, FieldTrip should be updated to at least Sept 24th.  There seems to be a bug affecting reading some mff files generated by NS5 and EGI is working on it.

 



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

Joseph Dien, PhD
Research Associate
Cognitive Neurology
The Johns Hopkins University School of Medicine


 


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Re: [Erppcatoolkit-support] Using PARE correction for EEG data

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

Thanks for the link!  Agreed that the page is a bit confusing.  I looked around some more and found this very lucid explanation of the Biosemi system’s approach:

http://sccn.ucsd.edu/pipermail/eeglablist/2005/000933.html

Given that the CMS is essentially the equivalent of the ground electrode of a conventional system, I agree that it should not be included in the final montage.

Also, after some further thought, I changed my mind about dropping channels with no coordinate information.  The PARE computed without the missing electrodes would in some sense be inconsistent with them but practically the PARE would still provide a best estimate for them.

Thanks for the clarification!

Joe

> On Jul 6, 2015, at 06:25, Andreas Widmann <wi...@un...> wrote:
> 
> Dear Maria and Joe,
> 
>> 1) You really have another electrode so you might not want to discard it.  CMS (in the Biosemi system) is your recording reference electrode.  As I understand it from the online documentation, Biosemi terms this initial data “unreferenced” which is really misleading.  The data necessarily has a reference (you can’t have voltage data that doesn’t have a reference) and the reference site is CMS.  This site is, by definition, a flat line with zero voltage.  To save disk space Biosemi is not including this flat line with the rest of the data but it’s there.  This is relevant since it stops being flat and boring if you rereference.  You should put it back into your dataset one way or another prior to rereferencing.
> The Biosemi system does not apply common mode rejection online but expects CMR to be performed offline by re-referencing. Re-referencing is, thus, mandatory for Biosemi data and, to my understanding, the CMS channel must not be added back to the data and particularly not be included into the average reference or used for interpolation as it contains the noise.
> 
> There is some, also slightly confusing, documentation on the Biosemi website:
> http://www.biosemi.com/faq/cms&drl.htm
> 
> Best,
> Andreas

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

Joseph Dien, PhD
Research Associate
Cognitive Neurology/Neuropsychology
The Johns Hopkins University School of Medicine

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Fax: 410-955-0188
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Re: [Erppcatoolkit-support] Using PARE correction for EEG data

[Andreas W. <wi...@un...>]

Dear Maria and Joe,

> 1) You really have another electrode so you might not want to discard it.  CMS (in the Biosemi system) is your recording reference electrode.  As I understand it from the online documentation, Biosemi terms this initial data “unreferenced” which is really misleading.  The data necessarily has a reference (you can’t have voltage data that doesn’t have a reference) and the reference site is CMS.  This site is, by definition, a flat line with zero voltage.  To save disk space Biosemi is not including this flat line with the rest of the data but it’s there.  This is relevant since it stops being flat and boring if you rereference.  You should put it back into your dataset one way or another prior to rereferencing.
The Biosemi system does not apply common mode rejection online but expects CMR to be performed offline by re-referencing. Re-referencing is, thus, mandatory for Biosemi data and, to my understanding, the CMS channel must not be added back to the data and particularly not be included into the average reference or used for interpolation as it contains the noise.

There is some, also slightly confusing, documentation on the Biosemi website:
http://www.biosemi.com/faq/cms&drl.htm

Best,
Andreas

Re: [Erppcatoolkit-support] Using PARE correction for EEG data

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

Okay, got a sense of it now!  Your question has a lot of interesting angles to it:

1) You really have another electrode so you might not want to discard it.  CMS (in the Biosemi system) is your recording reference electrode.  As I understand it from the online documentation, Biosemi terms this initial data “unreferenced” which is really misleading.  The data necessarily has a reference (you can’t have voltage data that doesn’t have a reference) and the reference site is CMS.  This site is, by definition, a flat line with zero voltage.  To save disk space Biosemi is not including this flat line with the rest of the data but it’s there.  This is relevant since it stops being flat and boring if you rereference.  You should put it back into your dataset one way or another prior to rereferencing.

2) It looks like you used the .ced file that comes with the EP Toolkit, which in turn is a modified version of the one that Biosemi provides.  An issue you are running into is that the electrode positions for EXG1-8 are not available in this CED file and neither is CMS.  This is a problem for PARE since it needs the electrode locations in order to interpolate the head between the electrode positions.  You should see if you can estimate the electrode positions and add them into the ced file.

3) If you want to contrast nose-reference and average reference, you need to be using the same set of electrodes to obtain comparable results.  So when you compute the average reference you need to include the nose reference: EEG = pop_reref(EEG, [1:64 69], 'keepref','on’).  Note also that the EP Toolkit ced file has EXG1-8 marked as BAD, which is an EP Toolkit notation (not meaningful for EEGlab) which tells EP Toolkit to drop those channels.  When you rereferenced to nose, the nose channel was changed from BAD to REF, which meant it was no longer dropped (as indicated in the command window output when the .set file is imported).  So the nose reference file ends up with a nose channel whereas the average reference file does not.  So again a problem since the two files are no longer comparable.

4) The EEGlab rereferencing directions (http://sccn.ucsd.edu/wiki/Chapter_04:_Preprocessing_Tools) has an odd comment about leaving out the reference channels when calculating average reference.  No idea what they are talking about.  

5) I fixed a couple bugs in the Topos view that was causing it to crash when working with your data.

6) I’m not seeing what you said about the nose-reference-PARE not making much difference compared to the average-reference-PARE and that would indeed be very odd.  

7) However, I do see what you mean about getting different results depending on which you started with.  Thinking about it, it makes sense that the PARE corrected average reference would be dependent on the initial reference scheme.  With regular rereferencing, rereferencing between different electrodes is arithmetically interchangeable.  With PARE correction you’re now including all the interpolated space in between the electrodes and there is no guarantee that they will yield equivalent solutions.  One way of putting it is that whereas in an average reference the electrodes all have the same weight, in PARE some electrodes (notably the ones on the periphery) have much more weight since they have the greatest influence on the interpolated underside of the head.  Junghofer et al did not address this issue.  You can play around with this by using the rereference option (right-click menu) in the Topos View pane.

8) So I’m going to change my implementation of the procedure so that average reference is always computed prior to PARE correction so at least it’ll provide the same result regardless of the initial reference scheme.  Also, your dataset reminded me that a PARE-corrected dataset will necessarily need to drop all the electrodes for which coordinates are not available.

I’ll send you a beta version with these changes implemented for testing and will include them in the next release.

Cheers!

Joe

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

Joseph Dien, PhD
Research Associate
Cognitive Neurology
The Johns Hopkins University School of Medicine

On Jul 4, 2015, at 7:32 AM, Maria Teresa Wijaya <mtwijaya@u.nus.edu> wrote:

> Hi Joe,
> 
> Yes I used EXG5 as the nose electrode. In addition to the 64 scalp electrodes, I used 8 external ones as follows: 
> 
> 65 - EXG1 - above left eye
> 66 - EXG2 - below left eye
> 67 - EXG3 - left mastoid
> 68 - EXG4 - beside right eye
> 69 - EXG5 - nose
> 70 - EXG6 - right mastoid
> 71 - EXG7 - left arm 
> 72 - EXG8 - right arm
> 
> Here's my processing pipeline up to the point where I generate the files I sent to you. Everything is done in EEGLAB 10 (Matlab 2010b).
> 
> Nose-referenced files:
> 1. Import from bdf, referenced to EXG5, high pass filtered at 0.1 Hz, low pass filtered at 20 Hz. The command that I used for the referencing is EEG = pop_reref(EEG, [69],'keepref','on')
> 2. Manual rejection of non-typical artifacts
> 3. Removal of bad channels
> 4. ICA (runica) and removal of eye blinks and heart rate components
> 5. Interpolation of bad channels
> 
> Average-referenced files:
> 1-3. same as above
> 4. Interpolation of bad channels
> 5. Re-reference to the average of 64 electrodes. The command that I used is EEG = pop_reref(EEG, [1:64], 'keepref','on')
> 6. ICA (runica) and removal of eye blinks and heart rate components
> 
> Thank you. 
> 
> Regards,
> Maria
> From: Joseph Dien <jd...@ma...>
> Sent: Saturday, July 4, 2015 1:09 PM
> To: Maria Teresa Wijaya
> Cc: erp...@li...
> Subject: Re: [Erppcatoolkit-support] Using PARE correction for EEG data
>  
> I think I see.  You used one of your external channels (EXG5) as a nose channel and then rereferenced to it?  I need to know what EXG1-8 were used as in your dataset and what steps you took after data collection with respect to the reference to generate the two files (as in what software and what settings did you use).
> 
> Thanks!
> 
> Joe
> --------------------------------------------------------------------------------
> 
> Joseph Dien, PhD
> Research Associate
> Cognitive Neurology
> The Johns Hopkins University School of Medicine
> 
> On Jul 3, 2015, at 9:31 PM, Joseph Dien <jd...@ma...> wrote:
> 
>> Before I can address the PARE question, I’m having some trouble with your .set files.  There is an aspect of them which is crashing my code.  Could you tell me how the rereferencing was accomplished?  To both nose and average reference?  In particular, EXG5 is identified as being the reference electrode for the nose referenced dataset rather than CMS.
>> 
>> Joe
>> --------------------------------------------------------------------------------
>> 
>> Joseph Dien, PhD
>> Research Associate
>> Cognitive Neurology
>> The Johns Hopkins University School of Medicine
>> 
>> 
>> On Jun 28, 2015, at 10:16 PM, Maria Teresa Wijaya <mtwijaya@u.nus.edu> wrote:
>> 
>>> Yes, I did, sorry, I forgot about that. I've uploaded the files with the correct names in the folder: https://www.dropbox.com/sh/k2fpxx99kt6u0vg/AACpdOaLICsFdDBpLjollVWma?dl=0
>>> 
>>> Thank you.
>>> 
>>> Maria
>>> 
>>> 
>>> From: Joseph Dien <jd...@ma...>
>>> Sent: Monday, June 29, 2015 3:31 AM
>>> To: Maria Teresa Wijaya
>>> Cc: erp...@li...
>>> Subject: Re: [Erppcatoolkit-support] Using PARE correction for EEG data
>>>  
>>> I’m sorry, I can’t read the .set files you uploaded.  It looks like you renamed the files?  .set files don't let you do that.  Could you send me the files with the original names?
>>> 
>>> Joe
>>> 
>>>> On Jun 26, 2015, at 05:58, Maria Teresa Wijaya <mtwijaya@u.nus.edu> wrote:
>>>> 
>>>> Hi Joe,
>>>> 
>>>> I have uploaded the files to dropbox: https://www.dropbox.com/sh/k2fpxx99kt6u0vg/AACpdOaLICsFdDBpLjollVWma?dl=0
>>>> 
>>>> In my computer I could not load the ones with the event information so I removed the event information and stored them in the .csv file; these can be found in the "no event" folder. The files in the "with event" folder are from the same data set only with the event information intact.
>>>> 
>>>> Thank you!
>>>> 
>>>> Maria
>>>> 
>>>> 
>>>> From: Joseph Dien <jd...@ma...>
>>>> Sent: Thursday, June 25, 2015 8:55 AM
>>>> To: Maria Teresa Wijaya
>>>> Cc: erp...@li...
>>>> Subject: Re: [Erppcatoolkit-support] Using PARE correction for EEG data
>>>>  
>>>> How odd!  Could you send me the nose-referenced and averaged-referenced data files so I can look into this?
>>>> 
>>>> Joe
>>>> 
>>>>> On Jun 23, 2015, at 08:08, Maria Teresa Wijaya <mtwijaya@u.nus.edu> wrote:
>>>>> 
>>>>> Dear Joe, 
>>>>> 
>>>>> Thank you for your quick reply. I have actually tried applying the PARE referencing to both nose-referenced and average-referenced data. In the former, it barely made any noticeable difference while in the latter it did change the grand average waveform. I am not sure why it did not work on the nose-referenced data. Is it actually okay to apply PARE referencing to a data set that has already been referenced to the average of the scalp electrodes?
>>>>> 
>>>>> Thank you.
>>>>> 
>>>>> Regards,
>>>>> Maria
>>>>> 
>>>>> 
>>>>> From: Joseph Dien <jd...@ma...>
>>>>> Sent: Friday, June 19, 2015 9:27 PM
>>>>> To: Maria Teresa Wijaya
>>>>> Cc: erp...@li...
>>>>> Subject: Re: [Erppcatoolkit-support] Using PARE correction for EEG data
>>>>>  
>>>>> Thanks!  You do not need to re-reference first.  The PARE option is just a modified average-reference procedure (referenced to the average of the full interpolated head rather than just the average of the electrode locations).  Use the “re-reference” option in the Topomaps view to get a sense of what it is doing.
>>>>> 
>>>>> Cheers!
>>>>> 
>>>>> Joe
>>>>> --------------------------------------------------------------------------------
>>>>> 
>>>>> Joseph Dien, PhD
>>>>> Research Associate
>>>>> Cognitive Neurology/Neuropsychology
>>>>> The Johns Hopkins University School of Medicine
>>>>> 
>>>>> 
>>>>>> On Jun 19, 2015, at 01:18, Maria Teresa Wijaya <mtwijaya@u.nus.edu> wrote:
>>>>>> 
>>>>>> Hello,
>>>>>> 
>>>>>> First of all, thank you for the amazing EP toolkit. I am currently trying to make use of the PARE correction feature. My data were recorded in Biosemi (64 channels) and have been filtered and re-referenced to nose in EEGLAB.
>>>>>> 
>>>>>> My question is, do I have to first re-reference my data to average before using the PARE correction? 
>>>>>> 
>>>>>> Thank you and apologize if this question is too basic.
>>>>>> 
>>>>>> Regards,
>>>>>> 
>>>>>> Maria
>>>>>> ------------------------------------------------------------------------------
>>>>>> _______________________________________________
>>>>>> Erppcatoolkit-support mailing list
>>>>>> Erp...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support
>>>>> 
>>>> 
>>>> --------------------------------------------------------------------------------
>>>> 
>>>> Joseph Dien, PhD
>>>> Research Associate
>>>> Cognitive Neurology/Neuropsychology
>>>> The Johns Hopkins University School of Medicine
>>>> 
>>>> 
>>> 
>>> --------------------------------------------------------------------------------
>>> 
>>> Joseph Dien, PhD
>>> Research Associate
>>> Cognitive Neurology/Neuropsychology
>>> The Johns Hopkins University School of Medicine
>>> 
>> 
>> ------------------------------------------------------------------------------
>> Don't Limit Your Business. Reach for the Cloud.
>> GigeNET's Cloud Solutions provide you with the tools and support that
>> you need to offload your IT needs and focus on growing your business.
>> Configured For All Businesses. Start Your Cloud Today.
>> https://www.gigenetcloud.com/_______________________________________________
>> Erppcatoolkit-support mailing list
>> Erp...@li...
>> https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support

Re: [Erppcatoolkit-support] Using PARE correction for EEG data

[Maria T. W. <mtwijaya@u.nus.edu>]

Hi Joe,


Yes I used EXG5 as the nose electrode. In addition to the 64 scalp electrodes, I used 8 external ones as follows:


65 - EXG1 - above left eye

66 - EXG2 - below left eye

67 - EXG3 - left mastoid

68 - EXG4 - beside right eye

69 - EXG5 - nose

70 - EXG6 - right mastoid

71 - EXG7 - left arm

72 - EXG8 - right arm

Here's my processing pipeline up to the point where I generate the files I sent to you. Everything is done in EEGLAB 10 (Matlab 2010b).

Nose-referenced files:
1. Import from bdf, referenced to EXG5, high pass filtered at 0.1 Hz, low pass filtered at 20 Hz. The command that I used for the referencing is EEG = pop_reref(EEG, [69],'keepref','on')
2. Manual rejection of non-typical artifacts
3. Removal of bad channels
4. ICA (runica) and removal of eye blinks and heart rate components
5. Interpolation of bad channels

Average-referenced files:
1-3. same as above
4. Interpolation of bad channels
5. Re-reference to the average of 64 electrodes. The command that I used is EEG = pop_reref(EEG, [1:64], 'keepref','on')
6. ICA (runica) and removal of eye blinks and heart rate components

Thank you.

Regards,
Maria
________________________________
From: Joseph Dien <jd...@ma...>
Sent: Saturday, July 4, 2015 1:09 PM
To: Maria Teresa Wijaya
Cc: erp...@li...
Subject: Re: [Erppcatoolkit-support] Using PARE correction for EEG data

I think I see.  You used one of your external channels (EXG5) as a nose channel and then rereferenced to it?  I need to know what EXG1-8 were used as in your dataset and what steps you took after data collection with respect to the reference to generate the two files (as in what software and what settings did you use).

Thanks!

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

Joseph Dien, PhD
Research Associate
Cognitive Neurology
The Johns Hopkins University School of Medicine

On Jul 3, 2015, at 9:31 PM, Joseph Dien <jd...@ma...<mailto:jd...@ma...>> wrote:

Before I can address the PARE question, I’m having some trouble with your .set files.  There is an aspect of them which is crashing my code.  Could you tell me how the rereferencing was accomplished?  To both nose and average reference?  In particular, EXG5 is identified as being the reference electrode for the nose referenced dataset rather than CMS.

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

Joseph Dien, PhD
Research Associate
Cognitive Neurology
The Johns Hopkins University School of Medicine


On Jun 28, 2015, at 10:16 PM, Maria Teresa Wijaya <mtwijaya@u.nus.edu<mailto:mtwijaya@u.nus.edu>> wrote:

Yes, I did, sorry, I forgot about that. I've uploaded the files with the correct names in the folder: https://www.dropbox.com/sh/k2fpxx99kt6u0vg/AACpdOaLICsFdDBpLjollVWma?dl=0

Thank you.

Maria


________________________________
From: Joseph Dien <jd...@ma...<mailto:jd...@ma...>>
Sent: Monday, June 29, 2015 3:31 AM
To: Maria Teresa Wijaya
Cc: erp...@li...<mailto:erp...@li...>
Subject: Re: [Erppcatoolkit-support] Using PARE correction for EEG data

I’m sorry, I can’t read the .set files you uploaded.  It looks like you renamed the files?  .set files don't let you do that.  Could you send me the files with the original names?

Joe

On Jun 26, 2015, at 05:58, Maria Teresa Wijaya <mtwijaya@u.nus.edu<mailto:mtwijaya@u.nus.edu>> wrote:

Hi Joe,

I have uploaded the files to dropbox: https://www.dropbox.com/sh/k2fpxx99kt6u0vg/AACpdOaLICsFdDBpLjollVWma?dl=0

In my computer I could not load the ones with the event information so I removed the event information and stored them in the .csv file; these can be found in the "no event" folder. The files in the "with event" folder are from the same data set only with the event information intact.

Thank you!

Maria


________________________________
From: Joseph Dien <jd...@ma...<mailto:jd...@ma...>>
Sent: Thursday, June 25, 2015 8:55 AM
To: Maria Teresa Wijaya
Cc: erp...@li...<mailto:erp...@li...>
Subject: Re: [Erppcatoolkit-support] Using PARE correction for EEG data

How odd!  Could you send me the nose-referenced and averaged-referenced data files so I can look into this?

Joe

On Jun 23, 2015, at 08:08, Maria Teresa Wijaya <mtwijaya@u.nus.edu<mailto:mtwijaya@u.nus.edu>> wrote:

Dear Joe,

Thank you for your quick reply. I have actually tried applying the PARE referencing to both nose-referenced and average-referenced data. In the former, it barely made any noticeable difference while in the latter it did change the grand average waveform. I am not sure why it did not work on the nose-referenced data. Is it actually okay to apply PARE referencing to a data set that has already been referenced to the average of the scalp electrodes?

Thank you.

Regards,
Maria


________________________________
From: Joseph Dien <jd...@ma...<mailto:jd...@ma...>>
Sent: Friday, June 19, 2015 9:27 PM
To: Maria Teresa Wijaya
Cc: erp...@li...<mailto:erp...@li...>
Subject: Re: [Erppcatoolkit-support] Using PARE correction for EEG data

Thanks!  You do not need to re-reference first.  The PARE option is just a modified average-reference procedure (referenced to the average of the full interpolated head rather than just the average of the electrode locations).  Use the “re-reference” option in the Topomaps view to get a sense of what it is doing.

Cheers!

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

Joseph Dien, PhD
Research Associate
Cognitive Neurology/Neuropsychology
The Johns Hopkins University School of Medicine


On Jun 19, 2015, at 01:18, Maria Teresa Wijaya <mtwijaya@u.nus.edu<mailto:mtwijaya@u.nus.edu>> wrote:

Hello,

First of all, thank you for the amazing EP toolkit. I am currently trying to make use of the PARE correction feature. My data were recorded in Biosemi (64 channels) and have been filtered and re-referenced to nose in EEGLAB.

My question is, do I have to first re-reference my data to average before using the PARE correction?

Thank you and apologize if this question is too basic.

Regards,

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


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

Joseph Dien, PhD
Research Associate
Cognitive Neurology/Neuropsychology
The Johns Hopkins University School of Medicine



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

Joseph Dien, PhD
Research Associate
Cognitive Neurology/Neuropsychology
The Johns Hopkins University School of Medicine


------------------------------------------------------------------------------
Don't Limit Your Business. Reach for the Cloud.
GigeNET's Cloud Solutions provide you with the tools and support that
you need to offload your IT needs and focus on growing your business.
Configured For All Businesses. Start Your Cloud Today.
https://www.gigenetcloud.com/_______________________________________________
Erppcatoolkit-support mailing list
Erp...@li...<mailto:Erp...@li...>
https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support

Re: [Erppcatoolkit-support] Using PARE correction for EEG data

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

I think I see.  You used one of your external channels (EXG5) as a nose channel and then rereferenced to it?  I need to know what EXG1-8 were used as in your dataset and what steps you took after data collection with respect to the reference to generate the two files (as in what software and what settings did you use).

Thanks!

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

Joseph Dien, PhD
Research Associate
Cognitive Neurology
The Johns Hopkins University School of Medicine

On Jul 3, 2015, at 9:31 PM, Joseph Dien <jd...@ma...> wrote:

> Before I can address the PARE question, I’m having some trouble with your .set files.  There is an aspect of them which is crashing my code.  Could you tell me how the rereferencing was accomplished?  To both nose and average reference?  In particular, EXG5 is identified as being the reference electrode for the nose referenced dataset rather than CMS.
> 
> Joe
> --------------------------------------------------------------------------------
> 
> Joseph Dien, PhD
> Research Associate
> Cognitive Neurology
> The Johns Hopkins University School of Medicine
> 
> 
> On Jun 28, 2015, at 10:16 PM, Maria Teresa Wijaya <mtwijaya@u.nus.edu> wrote:
> 
>> Yes, I did, sorry, I forgot about that. I've uploaded the files with the correct names in the folder: https://www.dropbox.com/sh/k2fpxx99kt6u0vg/AACpdOaLICsFdDBpLjollVWma?dl=0
>> 
>> Thank you.
>> 
>> Maria
>> 
>> 
>> From: Joseph Dien <jd...@ma...>
>> Sent: Monday, June 29, 2015 3:31 AM
>> To: Maria Teresa Wijaya
>> Cc: erp...@li...
>> Subject: Re: [Erppcatoolkit-support] Using PARE correction for EEG data
>>  
>> I’m sorry, I can’t read the .set files you uploaded.  It looks like you renamed the files?  .set files don't let you do that.  Could you send me the files with the original names?
>> 
>> Joe
>> 
>>> On Jun 26, 2015, at 05:58, Maria Teresa Wijaya <mtwijaya@u.nus.edu> wrote:
>>> 
>>> Hi Joe,
>>> 
>>> I have uploaded the files to dropbox: https://www.dropbox.com/sh/k2fpxx99kt6u0vg/AACpdOaLICsFdDBpLjollVWma?dl=0
>>> 
>>> In my computer I could not load the ones with the event information so I removed the event information and stored them in the .csv file; these can be found in the "no event" folder. The files in the "with event" folder are from the same data set only with the event information intact.
>>> 
>>> Thank you!
>>> 
>>> Maria
>>> 
>>> 
>>> From: Joseph Dien <jd...@ma...>
>>> Sent: Thursday, June 25, 2015 8:55 AM
>>> To: Maria Teresa Wijaya
>>> Cc: erp...@li...
>>> Subject: Re: [Erppcatoolkit-support] Using PARE correction for EEG data
>>>  
>>> How odd!  Could you send me the nose-referenced and averaged-referenced data files so I can look into this?
>>> 
>>> Joe
>>> 
>>>> On Jun 23, 2015, at 08:08, Maria Teresa Wijaya <mtwijaya@u.nus.edu> wrote:
>>>> 
>>>> Dear Joe, 
>>>> 
>>>> Thank you for your quick reply. I have actually tried applying the PARE referencing to both nose-referenced and average-referenced data. In the former, it barely made any noticeable difference while in the latter it did change the grand average waveform. I am not sure why it did not work on the nose-referenced data. Is it actually okay to apply PARE referencing to a data set that has already been referenced to the average of the scalp electrodes?
>>>> 
>>>> Thank you.
>>>> 
>>>> Regards,
>>>> Maria
>>>> 
>>>> 
>>>> From: Joseph Dien <jd...@ma...>
>>>> Sent: Friday, June 19, 2015 9:27 PM
>>>> To: Maria Teresa Wijaya
>>>> Cc: erp...@li...
>>>> Subject: Re: [Erppcatoolkit-support] Using PARE correction for EEG data
>>>>  
>>>> Thanks!  You do not need to re-reference first.  The PARE option is just a modified average-reference procedure (referenced to the average of the full interpolated head rather than just the average of the electrode locations).  Use the “re-reference” option in the Topomaps view to get a sense of what it is doing.
>>>> 
>>>> Cheers!
>>>> 
>>>> Joe
>>>> --------------------------------------------------------------------------------
>>>> 
>>>> Joseph Dien, PhD
>>>> Research Associate
>>>> Cognitive Neurology/Neuropsychology
>>>> The Johns Hopkins University School of Medicine
>>>> 
>>>> 
>>>>> On Jun 19, 2015, at 01:18, Maria Teresa Wijaya <mtwijaya@u.nus.edu> wrote:
>>>>> 
>>>>> Hello,
>>>>> 
>>>>> First of all, thank you for the amazing EP toolkit. I am currently trying to make use of the PARE correction feature. My data were recorded in Biosemi (64 channels) and have been filtered and re-referenced to nose in EEGLAB.
>>>>> 
>>>>> My question is, do I have to first re-reference my data to average before using the PARE correction? 
>>>>> 
>>>>> Thank you and apologize if this question is too basic.
>>>>> 
>>>>> Regards,
>>>>> 
>>>>> Maria
>>>>> ------------------------------------------------------------------------------
>>>>> _______________________________________________
>>>>> Erppcatoolkit-support mailing list
>>>>> Erp...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support
>>>> 
>>> 
>>> --------------------------------------------------------------------------------
>>> 
>>> Joseph Dien, PhD
>>> Research Associate
>>> Cognitive Neurology/Neuropsychology
>>> The Johns Hopkins University School of Medicine
>>> 
>>> 
>> 
>> --------------------------------------------------------------------------------
>> 
>> Joseph Dien, PhD
>> Research Associate
>> Cognitive Neurology/Neuropsychology
>> The Johns Hopkins University School of Medicine
>> 
> 
> ------------------------------------------------------------------------------
> Don't Limit Your Business. Reach for the Cloud.
> GigeNET's Cloud Solutions provide you with the tools and support that
> you need to offload your IT needs and focus on growing your business.
> Configured For All Businesses. Start Your Cloud Today.
> https://www.gigenetcloud.com/_______________________________________________
> Erppcatoolkit-support mailing list
> Erp...@li...
> https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support

Re: [Erppcatoolkit-support] Using PARE correction for EEG data

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

Before I can address the PARE question, I’m having some trouble with your .set files.  There is an aspect of them which is crashing my code.  Could you tell me how the rereferencing was accomplished?  To both nose and average reference?  In particular, EXG5 is identified as being the reference electrode for the nose referenced dataset rather than CMS.

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

Joseph Dien, PhD
Research Associate
Cognitive Neurology
The Johns Hopkins University School of Medicine


On Jun 28, 2015, at 10:16 PM, Maria Teresa Wijaya <mtwijaya@u.nus.edu> wrote:

> Yes, I did, sorry, I forgot about that. I've uploaded the files with the correct names in the folder: https://www.dropbox.com/sh/k2fpxx99kt6u0vg/AACpdOaLICsFdDBpLjollVWma?dl=0
> 
> Thank you.
> 
> Maria
> 
> 
> From: Joseph Dien <jd...@ma...>
> Sent: Monday, June 29, 2015 3:31 AM
> To: Maria Teresa Wijaya
> Cc: erp...@li...
> Subject: Re: [Erppcatoolkit-support] Using PARE correction for EEG data
>  
> I’m sorry, I can’t read the .set files you uploaded.  It looks like you renamed the files?  .set files don't let you do that.  Could you send me the files with the original names?
> 
> Joe
> 
>> On Jun 26, 2015, at 05:58, Maria Teresa Wijaya <mtwijaya@u.nus.edu> wrote:
>> 
>> Hi Joe,
>> 
>> I have uploaded the files to dropbox: https://www.dropbox.com/sh/k2fpxx99kt6u0vg/AACpdOaLICsFdDBpLjollVWma?dl=0
>> 
>> In my computer I could not load the ones with the event information so I removed the event information and stored them in the .csv file; these can be found in the "no event" folder. The files in the "with event" folder are from the same data set only with the event information intact.
>> 
>> Thank you!
>> 
>> Maria
>> 
>> 
>> From: Joseph Dien <jd...@ma...>
>> Sent: Thursday, June 25, 2015 8:55 AM
>> To: Maria Teresa Wijaya
>> Cc: erp...@li...
>> Subject: Re: [Erppcatoolkit-support] Using PARE correction for EEG data
>>  
>> How odd!  Could you send me the nose-referenced and averaged-referenced data files so I can look into this?
>> 
>> Joe
>> 
>>> On Jun 23, 2015, at 08:08, Maria Teresa Wijaya <mtwijaya@u.nus.edu> wrote:
>>> 
>>> Dear Joe, 
>>> 
>>> Thank you for your quick reply. I have actually tried applying the PARE referencing to both nose-referenced and average-referenced data. In the former, it barely made any noticeable difference while in the latter it did change the grand average waveform. I am not sure why it did not work on the nose-referenced data. Is it actually okay to apply PARE referencing to a data set that has already been referenced to the average of the scalp electrodes?
>>> 
>>> Thank you.
>>> 
>>> Regards,
>>> Maria
>>> 
>>> 
>>> From: Joseph Dien <jd...@ma...>
>>> Sent: Friday, June 19, 2015 9:27 PM
>>> To: Maria Teresa Wijaya
>>> Cc: erp...@li...
>>> Subject: Re: [Erppcatoolkit-support] Using PARE correction for EEG data
>>>  
>>> Thanks!  You do not need to re-reference first.  The PARE option is just a modified average-reference procedure (referenced to the average of the full interpolated head rather than just the average of the electrode locations).  Use the “re-reference” option in the Topomaps view to get a sense of what it is doing.
>>> 
>>> Cheers!
>>> 
>>> Joe
>>> --------------------------------------------------------------------------------
>>> 
>>> Joseph Dien, PhD
>>> Research Associate
>>> Cognitive Neurology/Neuropsychology
>>> The Johns Hopkins University School of Medicine
>>> 
>>> 
>>>> On Jun 19, 2015, at 01:18, Maria Teresa Wijaya <mtwijaya@u.nus.edu> wrote:
>>>> 
>>>> Hello,
>>>> 
>>>> First of all, thank you for the amazing EP toolkit. I am currently trying to make use of the PARE correction feature. My data were recorded in Biosemi (64 channels) and have been filtered and re-referenced to nose in EEGLAB.
>>>> 
>>>> My question is, do I have to first re-reference my data to average before using the PARE correction? 
>>>> 
>>>> Thank you and apologize if this question is too basic.
>>>> 
>>>> Regards,
>>>> 
>>>> Maria
>>>> ------------------------------------------------------------------------------
>>>> _______________________________________________
>>>> Erppcatoolkit-support mailing list
>>>> Erp...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support
>>> 
>> 
>> --------------------------------------------------------------------------------
>> 
>> Joseph Dien, PhD
>> Research Associate
>> Cognitive Neurology/Neuropsychology
>> The Johns Hopkins University School of Medicine
>> 
>> 
> 
> --------------------------------------------------------------------------------
> 
> Joseph Dien, PhD
> Research Associate
> Cognitive Neurology/Neuropsychology
> The Johns Hopkins University School of Medicine
> 

Re: [Erppcatoolkit-support] Using PARE correction for EEG data

[Maria T. W. <mtwijaya@u.nus.edu>]

Yes, I did, sorry, I forgot about that. I've uploaded the files with the correct names in the folder: https://www.dropbox.com/sh/k2fpxx99kt6u0vg/AACpdOaLICsFdDBpLjollVWma?dl=0

Thank you.


Maria


________________________________
From: Joseph Dien <jd...@ma...>
Sent: Monday, June 29, 2015 3:31 AM
To: Maria Teresa Wijaya
Cc: erp...@li...
Subject: Re: [Erppcatoolkit-support] Using PARE correction for EEG data

I’m sorry, I can’t read the .set files you uploaded.  It looks like you renamed the files?  .set files don't let you do that.  Could you send me the files with the original names?

Joe

On Jun 26, 2015, at 05:58, Maria Teresa Wijaya <mtwijaya@u.nus.edu<mailto:mtwijaya@u.nus.edu>> wrote:


Hi Joe,


I have uploaded the files to dropbox: https://www.dropbox.com/sh/k2fpxx99kt6u0vg/AACpdOaLICsFdDBpLjollVWma?dl=0


In my computer I could not load the ones with the event information so I removed the event information and stored them in the .csv file; these can be found in the "no event" folder. The files in the "with event" folder are from the same data set only with the event information intact.


Thank you!


Maria



________________________________
From: Joseph Dien <jd...@ma...<mailto:jd...@ma...>>
Sent: Thursday, June 25, 2015 8:55 AM
To: Maria Teresa Wijaya
Cc: erp...@li...<mailto:erp...@li...>
Subject: Re: [Erppcatoolkit-support] Using PARE correction for EEG data

How odd!  Could you send me the nose-referenced and averaged-referenced data files so I can look into this?

Joe

On Jun 23, 2015, at 08:08, Maria Teresa Wijaya <mtwijaya@u.nus.edu<mailto:mtwijaya@u.nus.edu>> wrote:


Dear Joe,


Thank you for your quick reply. I have actually tried applying the PARE referencing to both nose-referenced and average-referenced data. In the former, it barely made any noticeable difference while in the latter it did change the grand average waveform. I am not sure why it did not work on the nose-referenced data. Is it actually okay to apply PARE referencing to a data set that has already been referenced to the average of the scalp electrodes?


Thank you.


Regards,

Maria


________________________________
From: Joseph Dien <jd...@ma...<mailto:jd...@ma...>>
Sent: Friday, June 19, 2015 9:27 PM
To: Maria Teresa Wijaya
Cc: erp...@li...<mailto:erp...@li...>
Subject: Re: [Erppcatoolkit-support] Using PARE correction for EEG data

Thanks!  You do not need to re-reference first.  The PARE option is just a modified average-reference procedure (referenced to the average of the full interpolated head rather than just the average of the electrode locations).  Use the “re-reference” option in the Topomaps view to get a sense of what it is doing.

Cheers!

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

Joseph Dien, PhD
Research Associate
Cognitive Neurology/Neuropsychology
The Johns Hopkins University School of Medicine


On Jun 19, 2015, at 01:18, Maria Teresa Wijaya <mtwijaya@u.nus.edu<mailto:mtwijaya@u.nus.edu>> wrote:

Hello,

First of all, thank you for the amazing EP toolkit. I am currently trying to make use of the PARE correction feature. My data were recorded in Biosemi (64 channels) and have been filtered and re-referenced to nose in EEGLAB.

My question is, do I have to first re-reference my data to average before using the PARE correction?

Thank you and apologize if this question is too basic.

Regards,

Maria
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--------------------------------------------------------------------------------

Joseph Dien, PhD
Research Associate
Cognitive Neurology/Neuropsychology
The Johns Hopkins University School of Medicine



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

Joseph Dien, PhD
Research Associate
Cognitive Neurology/Neuropsychology
The Johns Hopkins University School of Medicine

Lab E-mail: jd...@jh...<mailto:jd...@jh...>
Private E-mail: jd...@ma...<mailto:jd...@ma...>
Office Phone: 410-614-3115
Cell Phone: 202-297-8117
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http://joedien.com