erppcatoolkit-support — support list

Re: [Erppcatoolkit-support] initial errors - unsure what to do..?

[Andrew H. <and...@uc...>]

hi Joseph,

sure - i tried with .set files that were saved by EEGLab both as one  
file and as a separate .dat and .set.
both had the headerformat error, and i've put a (41mb) archive of  
files you can reproduce with, here:
http://zaidellab.org/stage/data/Andrew/setfiles.zip

thanks,
andrew


On Aug 27, 2009, at 5:31 AM, Joseph Dien wrote:

> How odd...
>
> I'll need you to send me a copy of your file.  Could be something  
> funky about the conversion from .cnt to .set.  Use yousendit.com to  
> send it to jd...@ma....
>
> Cheers!
>
> Joe
>
> On Aug 27, 2009, at 12:57 AM, Andrew Hill wrote:
>
>> hello,
>>
>> i've just begun exploring EP toolkit, to work with a bunch of .set
>> files that were created from neuroscan .cnt files, imported and
>> epoched by event type in EEGLab.   in trying to begin the
>> "Preprocess", i'm just getting errors, using .set as an input type,
>> 1:750 and 1:150 as points and baseline (3 second epochs) and  
>> selecting
>> an individual subject .set file (epochs of one trial type):
>>
>> ??? Attempt to reference field of non-structure array.
>>
>> Error in ==> ep_stripAdds at 59
>>    if ~isempty(find(strcmp('RAW',EPdata.subTypes), 1))
>>
>> Error in ==> ep_artifactCorrection at 543
>> [data]=ep_stripAdds(data);
>>
>> Error in ==> ep at 727
>>        ep_artifactCorrection(inArg);
>>
>> ??? Error while evaluating uicontrol Callback
>>
>>
>> abandoning the Preprocess, i instead tried to create an  
>> (unartifacted)
>> "Average" from similar .set files, but after the prompt for the save-
>> as file type, i get:
>>
>> ??? Error using ==> read_header at 747
>> unsupported header format
>>
>> Error in ==> read_data at 282
>>  hdr = read_header(filename, 'headerformat', headerformat);
>>
>> Error in ==> ep_readData at 554
>>        [theData]=read_data(fileName,'dataformat',fileFormat,
>> 'headerformat',fileFormat);
>>
>> Error in ==> ep_averageData at 118
>> inputData=ep_readData(thisReadArg);
>>
>> Error in ==> ep at 911
>>
>> averagedData
>> =
>> ep_averageData
>> (sessionFiles
>> ,importFormat
>> ,fileType,averagingMethod,EPmain.preferences.average.trimLevel);
>> ??? Error while evaluating uicontrol Callback
>>
>>
>> this is on Mac OS X 10.5.x, Matlab R2009a, with 4gb of RAM, and dual
>> 2.8 Core2Duos...
>>
>> what am I doing wrong?
>> or is something else going on that needs to be addressed?
>>
>> thanks,
>> andrew
>>
>>
>> ------------------------------------------------------------------------------
>> Let Crystal Reports handle the reporting - Free Crystal Reports  
>> 2008 30-Day
>> trial. Simplify your report design, integration and deployment -  
>> and focus on
>> what you do best, core application coding. Discover what's new with
>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>> _______________________________________________
>> Erppcatoolkit-support mailing list
>> Erp...@li...
>> https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support
>
>
> --------------------------------------------------------------------------------
>
> Joseph Dien,
> Senior Research Scientist
> Center for Advanced Study of Language
> University of Maryland , Box 25
> College Park , MD 20742-0025
>
> E-mail: jd...@ma...
> Phone: 301-226-8848
> Fax: 301-226-8811
> http://homepage.mac.com/jdien07/
>
>
>
>
>
>
>

Re: [Erppcatoolkit-support] initial errors - unsure what to do..?

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

How odd...

I'll need you to send me a copy of your file.  Could be something  
funky about the conversion from .cnt to .set.  Use yousendit.com to  
send it to jd...@ma....

Cheers!

Joe

On Aug 27, 2009, at 12:57 AM, Andrew Hill wrote:

> hello,
>
> i've just begun exploring EP toolkit, to work with a bunch of .set
> files that were created from neuroscan .cnt files, imported and
> epoched by event type in EEGLab.   in trying to begin the
> "Preprocess", i'm just getting errors, using .set as an input type,
> 1:750 and 1:150 as points and baseline (3 second epochs) and selecting
> an individual subject .set file (epochs of one trial type):
>
> ??? Attempt to reference field of non-structure array.
>
> Error in ==> ep_stripAdds at 59
>     if ~isempty(find(strcmp('RAW',EPdata.subTypes), 1))
>
> Error in ==> ep_artifactCorrection at 543
> [data]=ep_stripAdds(data);
>
> Error in ==> ep at 727
>         ep_artifactCorrection(inArg);
>
> ??? Error while evaluating uicontrol Callback
>
>
> abandoning the Preprocess, i instead tried to create an (unartifacted)
> "Average" from similar .set files, but after the prompt for the save-
> as file type, i get:
>
> ??? Error using ==> read_header at 747
> unsupported header format
>
> Error in ==> read_data at 282
>   hdr = read_header(filename, 'headerformat', headerformat);
>
> Error in ==> ep_readData at 554
>         [theData]=read_data(fileName,'dataformat',fileFormat,
> 'headerformat',fileFormat);
>
> Error in ==> ep_averageData at 118
> inputData=ep_readData(thisReadArg);
>
> Error in ==> ep at 911
>
> averagedData
> =
> ep_averageData
> (sessionFiles
> ,importFormat
> ,fileType,averagingMethod,EPmain.preferences.average.trimLevel);
> ??? Error while evaluating uicontrol Callback
>
>
> this is on Mac OS X 10.5.x, Matlab R2009a, with 4gb of RAM, and dual
> 2.8 Core2Duos...
>
> what am I doing wrong?
> or is something else going on that needs to be addressed?
>
> thanks,
> andrew
>
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008  
> 30-Day
> trial. Simplify your report design, integration and deployment - and  
> focus on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> Erppcatoolkit-support mailing list
> Erp...@li...
> https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support


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

Joseph Dien,
Senior Research Scientist
Center for Advanced Study of Language
University of Maryland , Box 25
College Park , MD 20742-0025

E-mail: jd...@ma...
Phone: 301-226-8848
Fax: 301-226-8811
http://homepage.mac.com/jdien07/

[Erppcatoolkit-support] initial errors - unsure what to do..?

[Andrew H. <and...@uc...>]

hello,

i've just begun exploring EP toolkit, to work with a bunch of .set  
files that were created from neuroscan .cnt files, imported and  
epoched by event type in EEGLab.   in trying to begin the  
"Preprocess", i'm just getting errors, using .set as an input type,  
1:750 and 1:150 as points and baseline (3 second epochs) and selecting  
an individual subject .set file (epochs of one trial type):

??? Attempt to reference field of non-structure array.

Error in ==> ep_stripAdds at 59
     if ~isempty(find(strcmp('RAW',EPdata.subTypes), 1))

Error in ==> ep_artifactCorrection at 543
[data]=ep_stripAdds(data);

Error in ==> ep at 727
         ep_artifactCorrection(inArg);

??? Error while evaluating uicontrol Callback


abandoning the Preprocess, i instead tried to create an (unartifacted)  
"Average" from similar .set files, but after the prompt for the save- 
as file type, i get:

??? Error using ==> read_header at 747
unsupported header format

Error in ==> read_data at 282
   hdr = read_header(filename, 'headerformat', headerformat);

Error in ==> ep_readData at 554
         [theData]=read_data(fileName,'dataformat',fileFormat,  
'headerformat',fileFormat);

Error in ==> ep_averageData at 118
inputData=ep_readData(thisReadArg);

Error in ==> ep at 911
          
averagedData 
= 
ep_averageData 
(sessionFiles 
,importFormat 
,fileType,averagingMethod,EPmain.preferences.average.trimLevel);
??? Error while evaluating uicontrol Callback


this is on Mac OS X 10.5.x, Matlab R2009a, with 4gb of RAM, and dual  
2.8 Core2Duos...

what am I doing wrong?
or is something else going on that needs to be addressed?

thanks,
andrew

[Erppcatoolkit-support] ERP PCA Toolkit 1.3 release

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

I've just posted version 1.35 of the EP Toolkit.  Aside from the usual  
bug fixes and improvements to error handling, I've enhanced the  
artifact correction routines.  The PCA process has been further  
streamlined.  The documentation has been updated and expanded.  I've  
also overhauled the file system to provide the foundation for further  
improvements, especially better support of non EGI file formats.  I'm  
also moving the package towards the implementation of a graphical user  
interface, with the help of Abbie Kressner and Paul Yoder.  A full  
list of changes is provided below.

You can download the Toolkit at:

https://sourceforge.net/projects/erppcatoolkit/


If you wish to be informed of new releases, please be sure to sign up  
for the mailing list:

https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support


Let me know if you have any questions.

Cheers!

Joe
1) Fixed spatial PCA crashing doPCA. 2) blinkCorrection can now accept  
data files with multiple events per trial as long as there is one and  
only one at stimulus onset. 3) Fixed reversal of cell and subject  
fields when using readData for non-EGIS file formats. 4) Increased  
scaling of blinkCorrection plots so that blinks are more visible. 5)  
Added artifact detection and correction routines to blinkCorrection  
function, including bad channel interpolation. 6) Added automatic  
generation of cell combinations for the PCAtoEGISscript stage. 7)  
Added automatic statistical evaluation of factor results, using robust  
statistics. 8) More information added to the data and PCA output  
structured variables. 9) Eliminated need for separate PCAtoEGISscripts  
for one and two-stage PCAs. 10) Robust statistics prints to file with  
html format, allowing for formatting. 11) Updated EGIS session file  
utilities to have endian support. 12) Missing data number for  
parametric PCA changed to -999. 13) Increased range of files that can  
be read by readData and the number of options for it. 14) Added  
mergeEPfiles function so that data from Neuroscan can be analyzed. 15)  
Added writeData function so full range of supported output files is  
supported across the Toolkit functions. 16) Added editCells function  
for editing cells and making difference waves. 17) Batch selection of  
files in blinkCorrection file requester added.
--------------------------------------------------------------------------------

Joseph Dien, Ph.D.
Birth Defects Center
Davidson Hall, Room 314A
Belknap Campus
University of Louisville
Louisville, KY 40292

Office: Davidson Hall 314d (Belknap)
E-mail: jd...@ma...
Phone: 502-852-2512
Fax: 502-852-2408
http://homepage.mac.com/jdien07/

[Erppcatoolkit-support] ERP PCA Toolkit 1.3 release

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

I've just posted a new update to the ERP PCA Toolkit (version 1.3).   
It contains a number of improvements.  For users of NetStation, it now  
automatically sets the file type and montage for EGIS files so ResFool  
and QuickType are no longer needed.  I've also brought my eyeblink  
correction tool and robust statistics tools up to date and have folded  
them into the Toolkit.  I should be publishing a formal treatment of  
the eyeblink correction tool soon.  I've been using both of these  
tools for some time and have been quite satisfied with them.

You can download the Toolkit at: https://sourceforge.net/projects/erppcatoolkit/

Let me know if you have any questions.

Cheers!

Joe

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

Joseph Dien, Ph.D.
Birth Defects Center
Davidson Hall, Room 314A
Belknap Campus
University of Louisville
Louisville, KY 40292

Office: Davidson Hall 314d (Belknap)
E-mail: jd...@ma...
Phone: 502-852-2512
Fax: 502-852-4702
http://homepage.mac.com/jdien07/

[Erppcatoolkit-support] minor update

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

I just posted a minor update (version 1.23) of the EP Toolkit.  Among  
other things, it includes a fix to parametric PCA maps, a fix to  
unique variance calculations, better support for file formats other  
than EGIS, and addition of some useful EGIS file utilities.

Cheers!

Joe



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

Joseph Dien
Assistant Professor of Psychology
Department of Psychology
419 Fraser Hall (by the coke machine)
1415 Jayhawk Blvd
University of Kansas
Lawrence, KS 66045-7556
E-mail: jd...@ma...
Office: 785-864-9822 (note: no voicemail)
Fax: 785-864-5696
http://people.ku.edu/~jdien/Dien.html

[Erppcatoolkit-support] minor update

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

I just posted a minor update (version 1.22) of the EP Toolkit.   
Rotations will be a bit slower because it follows a recommendation to  
run them multiple times with random starting places to avoid getting  
stuck in a local minimum.  I also changed the recommendation for  
temporal PCA back to Promax from Oblimin since my latest testing  
indicates Promax still has an edge, although they are pretty close so  
there is no need to rerun any analyses that have been done with Oblimin.

Cheers!

Joe



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

Joseph Dien
Assistant Professor of Psychology
Department of Psychology
419 Fraser Hall (by the coke machine)
1415 Jayhawk Blvd
University of Kansas
Lawrence, KS 66045-7556
E-mail: jd...@ma...
Office: 785-864-9822 (note: no voicemail)
Fax: 785-864-5696
http://people.ku.edu/~jdien/Dien.html

Re: [Erppcatoolkit-support] decomposed individual ERP waves do not resemble to the original inidudual ERP waves?

[Hongying Z. <hy...@ee...>]

Dear Joe,

Yes. The results are perfectly fit my expectation and the same case
applies to the output of 'Amount of variance (communality) accounted'.
In the previous version, it confused me for a long time, for this
variance output is not equals to calculation by scree value.
It's all right now.

Many thanks.

Best Regards,
H.Y.Zheng

On Fri, Feb 22, 2008 at 10:58 AM, Joseph Dien <jd...@ma...> wrote:
> Good catch!  There was a bug in the subjects option for the PCAtoEGIS
>  function, which I haven't been using.
>  I've put a fix in the 1.21 version which I just released.  I'm
>  attaching an updated version of your test file (nice job with it!) so
>  you can check it out.
>
>  Cheers!
>
>  Joe
>
>
>
>
>
>
>
>
>  --------------------------------------------------------------------------------
>
>  Joseph Dien
>  Assistant Professor of Psychology
>  Department of Psychology
>  419 Fraser Hall (by the coke machine)
>  1415 Jayhawk Blvd
>  University of Kansas
>  Lawrence, KS 66045-7556
>  E-mail: jd...@ma...
>  Office: 785-864-9822 (note: no voicemail)
>  Fax: 785-864-5696
>  http://people.ku.edu/~jdien/Dien.html
>
>
>
>
>
>



-- 
==========================================
Ms. Zheng Hongying
Ph.D (Post-candidacy)
Room 310, Ho Sin-Hang Engineering Building
Department of Electronic Engineering
The Chinese University of Hong Kong
Shatin, Hong Kong, China
Tel:   +852 2609 8250
Email: hy...@ee...
Lab:   www.ee.cuhk.edu.hk/~lel/
==========================================

[Erppcatoolkit-support] ERP PCA Toolkit 1.21 release

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

I've just posted a new update to the ERP PCA Toolkit (version 1.21).   
It has a number of improvements.  One notable improvement is that  
output is now packaged in a structured variable which makes it easier  
to organize results.  This has also enabled me to simplify the user  
interface.  A second improvement is that I've added a number of new  
rotations, including Oblimin that I am now recommending over Promax  
for temporal PCA based on some simulation results that I am now  
writing up for publication.  I continue to recommend Infomax for  
spatial PCA.  A third improvement is the ability to specify the kappa  
for Promax and for Oblimin.  There has also been a fix to the subjects  
mode of the PCAtoEGIS function.  The tutorial file has been expanded  
to provide guidance on these and other issues.

You can download the Toolkit at: https://sourceforge.net/projects/erppcatoolkit/

Let me know if you have any questions.

Cheers!

Joe



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

Joseph Dien
Assistant Professor of Psychology
Department of Psychology
419 Fraser Hall (by the coke machine)
1415 Jayhawk Blvd
University of Kansas
Lawrence, KS 66045-7556
E-mail: jd...@ku...
Office: 785-864-9822 (note: no voicemail)
Fax: 785-864-5696
http://people.ku.edu/~jdien/Dien.html

Re: [Erppcatoolkit-support] decomposed individual ERP waves do not resemble to the original inidudual ERP waves?

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

Good catch!  There was a bug in the subjects option for the PCAtoEGIS  
function, which I haven't been using.
I've put a fix in the 1.21 version which I just released.  I'm  
attaching an updated version of your test file (nice job with it!) so  
you can check it out.

Cheers!

Joe

[Erppcatoolkit-support] ERP PCA Toolkit 1.21 release

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

I've just posted a new update to the ERP PCA Toolkit (version 1.21).   
It has a number of improvements.  One notable improvement is that  
output is now packaged in a structured variable which makes it easier  
to organize results.  This has also enabled me to simplify the user  
interface.  A second improvement is that I've added a number of new  
rotations, including Oblimin that I am now recommending over Promax  
for temporal PCA based on some simulation results that I am now  
writing up for publication.  I continue to recommend Infomax for  
spatial PCA.  A third improvement is the ability to specify the kappa  
for Promax and for Oblimin.  There has also been a fix to the subjects  
mode of the PCAtoEGIS function.  The tutorial file has been expanded  
to provide guidance on these and other issues.

You can download the Toolkit at: https://sourceforge.net/projects/erppcatoolkit/

Let me know if you have any questions.

Cheers!

Joe



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

Joseph Dien
Assistant Professor of Psychology
Department of Psychology
419 Fraser Hall (by the coke machine)
1415 Jayhawk Blvd
University of Kansas
Lawrence, KS 66045-7556
E-mail: jd...@ku...
Office: 785-864-9822 (note: no voicemail)
Fax: 785-864-5696
http://people.ku.edu/~jdien/Dien.html

Re: [Erppcatoolkit-support] decomposed individual ERP waves do not resemble to the original inidudual ERP waves?

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

Good catch!  There was a bug in the subjects option for the PCAtoEGIS  
function, which I haven't been using.
I've put a fix in the 1.21 version which I just released.  I'm  
attaching an updated version of your test file (nice job with it!) so  
you can check it out.

Cheers!

Joe

[Erppcatoolkit-support] decomposed individual ERP waves do not resemble to the original inidudual ERP waves?

[Hongying Z. <hy...@ee...>]

Dear ERP PCA tookkit users,

I'm confused about the output, when I applied the toolkit (temporal
PCA) to the sample dataset (introduced in Dien, J., & Frishkoff, G. A.
(2005). Principal components analysis of ERP data. In T. C. Handy
(Ed.), Event related potentials: A methods handbook (pp. 189-208).
Cambridge,Massachusetts; London,England: The MIT Press.)

Since the first 2 factors explained the 100% variance of dataset,2
factors are retained only. After the analysis, I obtained decomposed
factor waves for each subject (the "facWaves" output from PCAtoEGIS
function). But the wave pattern for decomposed factor waves are
different from original individual waves. (Although the grand average
pattern is the same for these two conditions).  Is it reasonable, why?

Here I attached the matlab file for generating the figure (figure 6.
for original individual ERP waves and figure 7. for decomposed
individual factor waves).

Best Regards,
H.Y.Zheng

-- 
==========================================
Ms. Zheng Hongying
Ph.D (Post-candidacy)
Room 310, Ho Sin-Hang Engineering Building
Department of Electronic Engineering
The Chinese University of Hong Kong
Shatin, Hong Kong, China
Tel: +852 2609 8250
Email: hy...@ee...
Lab: www.ee.cuhk.edu.hk/~lel/
==========================================