erppcatoolkit-support Mailing List for ERP PCA Toolkit (Page 7)
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From: Joseph D. <jd...@ma...> - 2010-01-18 03:35:31
|
I finally got around to getting the EP Toolkit officially written up. When publishing a paper using it, please be sure to use the following citation as it may help me get support for maintaining and improving it: Dien, J. (in press). The ERP PCA Toolkit: An Open Source Program For Advanced Statistical Analysis of Event Related Potential Data. Journal of Neuroscience Methods. Also, I just posted version 2.09. Aside from the usual updates to the documentation, it makes the following fixes and enhancements: 1) Fixed crash when viewing Window pane for a dataset with less than four cells under Matlab versions prior to 2008. 2) Workaround for Matlab bug that appears to prevent buttons from being colored when pressed in the Channel Group window on Macs using version 2009b under at least some conditions. 3) Fixed crash in ANOVA pane when entering between group name that is not three letters long. 4) Fixed error when changing ced field in overview subpane of edit pane. 5) When reading in an EGIS format file, if none of the EGI montages are chosen, then it will allow for a .ced file to be chosen. 6) Fixed failure due to Matlab bug to redraw View pane when changing the dataset for one of the colors. 7) Fixed crash when examining a file in the View pane with less than four cells. 8) Rounds off ms labels in the scale graph of the Wave Window. 9) Added support to the ANOVA module for non-ERP data with the addition of the "behavioral" keyword. See the tutorial file. There seems to be some issues related to reading .set files created by EEGlab due to what appears to be bugs in the FieldTrip code that is used by the EP Toolkit. I'm in the process of getting this sorted out and will post an update once finished. This will likely require fixes to FieldTrip itself (to which I am a contributor). Make sure to periodically update your copy of FieldTrip and EEGlab to take advantage of such fixes (and to delete the stale copy of FieldTrip in EEGlab and vice versa). I'm also planning on adding the ability to save .set files and to broaden support to EEGlab study structures. Cheers! Joe -------------------------------------------------------------------------------- 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/ |
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From: Joseph D. <jd...@ma...> - 2009-12-11 03:49:43
|
okay, I found the problem. I'll add it to the next update. Meanwhile, just replace the existing ep.m file with the attached one. It fixes the following problem: Fixed crash when viewing Window pane for a dataset with less than four cells under Matlab versions prior to 2008. Cheers! Joe |
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From: Joseph D. <jd...@ma...> - 2009-12-10 02:32:59
|
Hi Jia, I just tried out the function on my computer and it worked fine. It must be some kind of interaction with your file. Please send me a copy via yousendit.com so I can troubleshoot. Cheers! Joe On Dec 9, 2009, at 4:21 PM, Jia Wu wrote: > Hi, > An error occurred when I clicked the "Window" button; and the Window panel didn't seem to be complete. > I attached a picture with the error. > > my system: > Mac 10.5.6 > ERP PCA Toolbox 2.08 Copyright (C) 1999-2009 Joseph Dien > /Applications/MATLAB74/toolbox/fieldtrip-20091103/fileio/read_header.m > /Applications/MATLAB74/toolbox/eeglab7_2_9_18b/functions/sigprocfunc/runica.m > > Thanks! > Jia > <window_error.jpg>------------------------------------------------------------------------------ > Return on Information: > Google Enterprise Search pays you back > Get the facts. > http://p.sf.net/sfu/google-dev2dev > _______________________________________________ > 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 7005 52nd Avenue College Park, MD 20742-0025 E-mail: jd...@ma... Phone: 301-226-8848 Fax: 301-226-8811 http://homepage.mac.com/jdien07/ |
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From: Jia Wu <ji...@ya...> - 2009-12-09 21:21:49
|
Hi, An error occurred when I clicked the "Window" button; and the Window panel didn't seem to be complete. I attached a picture with the error. my system: Mac 10.5.6 ERP PCA Toolbox 2.08 Copyright (C) 1999-2009 Joseph Dien /Applications/MATLAB74/toolbox/fieldtrip-20091103/fileio/read_header.m /Applications/MATLAB74/toolbox/eeglab7_2_9_18b/functions/sigprocfunc/runica.m Thanks! Jia |
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From: Joseph D. <jd...@ma...> - 2009-12-09 05:33:54
|
I just posted version 2.08. It makes two fixes: 1) Fixed faulty bad channel interpolation (x and y coordinates were swapped) for both preprocessing data and when manually constructing a blink template. I'm not sure how this got past me. My apologies for any problems this may have caused folks. 2) Fixed crash in Mark option of preprocessing (thanks to Alex Lamey). An additional note is that I just got alerted that a fix I made to FieldTrip's support for the EEGlab file format a couple months back apparently got lost. FieldTrip was switching over to the Subversion system from CVS (developer software) at the time and there were some glitches. Anyway, the symptom is that .set files using the .set/.fdt dual file format got imported with the channels and time points transposed. If you've run into this, just download a fresh copy of FieldTrip and it should work fine. Cheers! Joe -------------------------------------------------------------------------------- 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/ |
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From: Joseph D. <jd...@ma...> - 2009-12-05 07:26:30
|
I just posted version 2.07. It fixes a bevy of mostly minor issues, including an irritating sporadic bug that made the menus disappear: 1) When reading simple binary files, if the cell names cannot be deduced, put all of the segments into the same single cell rather than just aborting. 2) When importing a text file, ignore tabs at the end of the line. 3) Drops CELL and TRSP events for all simple binary files since NetStation loses the associated information when exporting simple binary files. 4) Replaced "union" statements with "unique" statements because, under certain conditions, they would cause Matlab 2007 to crash when doing preprocessing. 5) Added workaround for sporadic Matlab menu bug that was causing menu to disappear or crash when menu item that is selected is same as before. 6) Fixed crash when loading in blink template for a file or pathname with a space in it. 7) In preprocessing, avoid performing trialwise bad channel detection entirely unless both minmax and maxneighbor parameters are inactive. 8) Fix for bug in trialwise bad channel detection where channel 1 would be marked as bad in too many trials if there was only one globally bad channel. 9) Additional check in preprocessing and PCA functions for ICA failure (denoted by imaginary numbers for weights). 10) In preprocessing, detects non-reference channels that are perfectly correlated and identifies them as bad channels as they must be shorted together. 11) In preprocessing, fixed bug where test of correlation with reference only detecting +1 correlation, not -1 correlation. 12) In preprocessing, fixed bug where if there is an explicit reference channel and it is flat, then all reference channels marked bad and real bad channels are no longer marked bad. 13) In preprocessing, don't apply correlated neighbors test to explicit reference channels as distant reference channels will always be labeled bad. 14) In preprocessing, fixed crash when more than one bad channel under some conditions. 15) Now only asks for montage once when doing a preprocessing batch. Cheers! Joe -------------------------------------------------------------------------------- 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/ |
|
From: Yang, C. <ya...@hk...> - 2009-11-18 06:34:16
|
Dear Joseph: How are you? This is ChinLung Yang. Many thanks for your PCA toolkit. I list my publication with application of the toolkit below: Yang, C. –L., Perfetti, C. A., & Schmalhofer, F. (2007). ERP indicators of text integration across sentence boundaries. Journal of Experimental Psychology: Learning, Memory and Cognition, 33, 55-89. Yang, C. –L., & Perfetti, C. A. (2006). Contextual constraints on the comprehension of relative clause sentences in Chinese: ERPs evidence. The special issue of Brain and Language in Language and Linguistics, 7 (3), 697-730. Yang, C. –L., Perfetti, C. A., & Schmalhofer, F. (2005). Less skilled comprehenders’ ERPs show sluggish word-to-text integration processes. The special issue of Literacy Processes and Literacy Development in Written Language & Literacy, 8(2), 157-181. Also, I would like to ask for reprint of the paper you mentioned below when it is published. Good luck to your submission. regards. ChinLung Quoting Joseph Dien <jd...@ma...>: > Hi everyone, > I'm getting ready to submit a short methodology paper describing the EP > Toolkit and I'd like to include a list of some of the papers that have been > published using it. If you've published such a paper and would like a little > free publicity, could you send me the citation? > > Cheers! > > Joe > > -------------------------------------------------------------------------------- > > Joseph Dien, > Senior Research Scientist > Center for Advanced Study of Language > University of Maryland > 7005 52nd Avenue > College Park, MD 20742-0025 > > E-mail: jd...@ma... > Phone: 301-226-8848 > Fax: 301-226-8811 > http://homepage.mac.com/jdien07/ > > > > > > > > -- ChinLung Yang, Ph.D. Research Assistant Professor State Key Laboratory of Brain and Cognitive Sciences University of Hong Kong (852) 2241-5871 |
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From: Joseph D. <jd...@ma...> - 2009-11-18 04:42:26
|
Hi everyone,
I'm getting ready to submit a short methodology paper describing the EP Toolkit and I'd like to include a list of some of the papers that have been published using it. If you've published such a paper and would like a little free publicity, could you send me the citation?
Cheers!
Joe
--------------------------------------------------------------------------------
Joseph Dien,
Senior Research Scientist
Center for Advanced Study of Language
University of Maryland
7005 52nd Avenue
College Park, MD 20742-0025
E-mail: jd...@ma...
Phone: 301-226-8848
Fax: 301-226-8811
http://homepage.mac.com/jdien07/
|
|
From: Joseph D. <jd...@ma...> - 2009-11-16 21:00:06
|
yes, that's right. The PCA routine generates summary cells, subjects, and factors for you and adds them to the dataset. See the tutorial. Cheers! Joe -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist Center for Advanced Study of Language University of Maryland 7005 52nd Avenue College Park, MD 20742-0025 E-mail: jd...@ma... Phone: 301-226-8848 Fax: 301-226-8811 http://homepage.mac.com/jdien07/ On Monday, November 16, 2009, at 03:48PM, "Jia Wu" <ji...@ya...> wrote: >My data file has 3 events and 20 subjects. It was read by the toolkit as >3 cells and 20 subjects. After I did PCA, the resulted file had 4 cells >and 21 subjects. It also gave me 6 factors even though I specified it as >5. I'm not sure whether I did something wrong or the extra ones had some >special meanings. >Thanks, >Jia > >------------------------------------------------------------------------------ >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 > > |
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From: Jia Wu <ji...@ya...> - 2009-11-16 20:49:15
|
My data file has 3 events and 20 subjects. It was read by the toolkit as 3 cells and 20 subjects. After I did PCA, the resulted file had 4 cells and 21 subjects. It also gave me 6 factors even though I specified it as 5. I'm not sure whether I did something wrong or the extra ones had some special meanings. Thanks, Jia |
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From: Joseph D. <jd...@ma...> - 2009-11-13 03:05:27
|
I just posted version 2.06. It fixes a bug that was unlikely to corrupt data but caused erratic, unpredictable glitches in the Toolkit user interface. 1) Fixed bug where Toolkit was saving all variables into EPwork cache, not just EPdataset, resulting in erratic problems when old values for variables were loaded back into the workspace. Cheers! Joe -------------------------------------------------------------------------------- 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/ |
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From: Joseph D. <jd...@ma...> - 2009-11-12 17:36:26
|
I just posted version 2.05: 1) For preprocessing, when there are multiple chunks, fixed crash when there is an odd number of trials. 2) For preprocessing, when detecting bad channels via perfect correlation, .9999 is now sufficient. Cheers! Joe -------------------------------------------------------------------------------- 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/ |
|
From: Joseph D. <jd...@ma...> - 2009-11-12 03:38:44
|
I tried it out and had no problem. My guess, based on the earlier error message that you sent to me, is that this is again due to some problem with updating to the new version. One tip that may help is that you should always restart Matlab after updating to a new version of the Toolkit (I'll add this to the standard instructions). The reason is that I've noticed that sometimes changes to the code do not register if you are already running it. I'm not sure exactly why this happens. Some kind of Matlab bug I'm thinking. The way Matlab works is that it loads in the .m file, compiles the text into machine language and then runs the machine language and keeps this compiled version in its active memory. Sometimes, it seems, if you make a change to the .m file (like updating the version) Matlab may not update the compiled version that it is actually using and so nothing changes in what it is doing. The only way to be sure that things have been truly updated is to quit out of Matlab and restart it. That way all the compiled code that it has generated gets thrown out so it has to start afresh. Let me know if this doesn't work. Cheers! Joe On Nov 10, 2009, at 12:51 PM, Jia Wu wrote: > Hi, > I intalled 2.04 today and decided to start the analysis from the > beginning. Then I encountered an error when i tried to ready combined > average file in the egis format: > > ************************************************************** > Number of subjects (20) does not divide evenly into the number of > epochs > (3). > ************************************************************** > > I have 20 subjects and 3 conditions. The file used to be able to > read by > eptoolkit. Is there anything I did wrong? > > Thanks, > Jia > > ------------------------------------------------------------------------------ > 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 7005 52nd Avenue College Park, MD 20742-0025 E-mail: jd...@ma... Phone: 301-226-8848 Fax: 301-226-8811 http://homepage.mac.com/jdien07/ |
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From: Joseph D. <jd...@ma...> - 2009-11-10 18:32:34
|
argh.... sorry about this. Send me the file via yousendit.com and I'll get it fixed ASAP. Joe -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist Center for Advanced Study of Language University of Maryland 7005 52nd Avenue College Park, MD 20742-0025 E-mail: jd...@ma... Phone: 301-226-8848 Fax: 301-226-8811 http://homepage.mac.com/jdien07/ On Tuesday, November 10, 2009, at 12:51PM, "Jia Wu" <ji...@ya...> wrote: >Hi, >I intalled 2.04 today and decided to start the analysis from the >beginning. Then I encountered an error when i tried to ready combined >average file in the egis format: > >************************************************************** >Number of subjects (20) does not divide evenly into the number of epochs >(3). >************************************************************** > >I have 20 subjects and 3 conditions. The file used to be able to read by >eptoolkit. Is there anything I did wrong? > >Thanks, >Jia > >------------------------------------------------------------------------------ >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 > > |
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From: Jia Wu <ji...@ya...> - 2009-11-10 17:51:16
|
Hi, I intalled 2.04 today and decided to start the analysis from the beginning. Then I encountered an error when i tried to ready combined average file in the egis format: ************************************************************** Number of subjects (20) does not divide evenly into the number of epochs (3). ************************************************************** I have 20 subjects and 3 conditions. The file used to be able to read by eptoolkit. Is there anything I did wrong? Thanks, Jia |
|
From: Joseph D. <jd...@ma...> - 2009-11-10 04:41:09
|
I just posted version 2.04: 1) Crash when importing continuous simple binary files with events. 2) Crash when exporting data from QC and PCA subpanes when using a Matlab version predating 2008. Cheers! Joe -------------------------------------------------------------------------------- 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/ |
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From: Joseph D. <jd...@ma...> - 2009-11-10 04:05:50
|
Fixed! Am releasing version 4.04 with the fix. Thanks for the report!
Joe
On Nov 9, 2009, at 11:27 AM, Jia Wu wrote:
> Hi,
> When I click the export button on the PCA panel in Edit of the
> spatial-temporal pca result data, the following error occurred:
>
> ??? Reference to non-existent field 'hTable'.
>
> Error in ==> ep_editData at 3608
> tableData=get(EPoverview.handles.PCA.hTable,'Data');
>
> ??? Error using ==> ep_editData('exportPCA');
> Reference to non-existent field 'hTable'.
>
> ??? Error while evaluating uicontrol Callback
>
> Please help!
> Thanks,
> Jia
>
> ------------------------------------------------------------------------------
> 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
7005 52nd Avenue
College Park, MD 20742-0025
E-mail: jd...@ma...
Phone: 301-226-8848
Fax: 301-226-8811
http://homepage.mac.com/jdien07/
|
|
From: Jia Wu <ji...@ya...> - 2009-11-09 16:27:18
|
Hi,
When I click the export button on the PCA panel in Edit of the
spatial-temporal pca result data, the following error occurred:
??? Reference to non-existent field 'hTable'.
Error in ==> ep_editData at 3608
tableData=get(EPoverview.handles.PCA.hTable,'Data');
??? Error using ==> ep_editData('exportPCA');
Reference to non-existent field 'hTable'.
??? Error while evaluating uicontrol Callback
Please help!
Thanks,
Jia
|
|
From: Joseph D. <jd...@ma...> - 2009-11-07 05:15:44
|
I just posted version 2.03: 1) Binica file removed from external folder. 2) Edit window shortened to fit on smaller monitors. 3) Crash during PCA when file was not averaged in EP Toolkit. 4) Crash when saving simple binary format files and the data file was not originally an EGIS format file. 5) Crash when saving single trial simple binary format file and there are more than one events per trial. 6) Single trial simple binary files being saved as ".bin.bin". 7) Fixes to formatting of ANOVA outputs. Cheers! Joe -------------------------------------------------------------------------------- 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/ |
|
From: Jia Wu <ji...@ya...> - 2009-11-05 02:07:58
|
I'm using a macbook with the highest resolution 1280x800. It looks like I couldn't get use Edit function because I could only see the bottom half of the "cancel" button. I tried to move the dock to the right side but it didn't change anything. Is there any way around it? Jia |
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From: Jia Wu <ji...@ya...> - 2009-11-04 20:31:48
|
Hi,
I tried to run temporal-spatial PCA, and an error occurred during the
spatial PCA if I assigned the number of factors.
??? Undefined function or variable "noiseResults".
Error in ==> ep>pickPCAdata at 4145
if isempty(noiseResults)
??? Error while evaluating uicontrol Callback
I went back to the code and saw that "noiseResults" was marked by matlab
saying "the variable can apparently be used before it is defined".
My configurations:
OS 10.5.6
matlab 7.4.0.287 (R2007a)
EP_toolkit 2.0
eeglab7_1_7_18b
fieldtrip-20091103
Best,
Jia
|
|
From: Joseph D. <jd...@ma...> - 2009-11-03 05:38:16
|
I just posted version 2.02. The third bug was a potentially serious one: 1) Fixes crash when using single trial mode with Read data function. 2) Fixes crash in preprocessing for non-continuous data files that do not contain analysis fields when there is more than one chunk. 3) Fixes bug in preprocessing where when there are multiple chunks, the last two are miscalculated such that they include data from earlier chunks (thanks to Siri Kamp). Cheers! Joe -------------------------------------------------------------------------------- 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/ |
|
From: Joseph D. <jd...@ma...> - 2009-11-01 17:05:50
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After some extended testing and bug fixing, I think the ERP PCA Toolkit 2 is ready to move out of beta (thanks to Tim Curran, Grega Repovs, Sebastian Korb, Andrew Hill, Aminda O'Hare, Eric Brian, and others). I can't claim it won't have any more bugs but it should be good enough at this point. The EP Toolkit is intended for ERP researchers as an adjunct to EEGlab. The main development is that I've added a graphical user interface to make it easier to use. I've also added features to further three goals: 1) Facilitating analysis of noisy ERP data, such as developmental or clinical, by the application of automated artifact correction and robust statistics at both the averaging stage and the inferential statistics stage. 2) Facilitating multivariate decomposition of ERP data, preferably using a combination of EEGlab's ICA rotation for the spatial mode and the Promax PCA rotation for the temporal mode. 3) Facilitating inferential data analysis of ERP data using robust statistics not previously available with a user interface. The tutorial provides in-depth guidance on how to use the Toolkit and has been extensively revised. You can download it from: https://sourceforge.net/projects/erppcatoolkit/ To get notices of future releases, join the mailing list: https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support This version of the EP Toolkit is more computationally demanding so it requires Matlab 2006 or more recent. It also needs at least 2GB of RAM and preferably 4GB or more. In general, the faster the computer, the better. It has been extensively tested on OS X and is currently undergoing testing on Windows XP. It can read text, EEGlab .set, EGI simple binary and EGIS, Biosig EDF, and Neuroscan AVG files. I'd be happy to implement support for other file formats if a user is willing to help test them. The EGI format files it saves can in turn be read by programs like EEGLab and BESA. Make sure to download the very latest version of EEGlab and Fieldtrip to use this (as described in the tutorial file). For example, I just today committed a fix to FieldTrip for a bug (reported by Grega Repovs) that causes EEGlab .set files to be scrambled when using the dual file .set/.fdt format (like EEGlab, the EP Toolkit uses FieldTrip's I/O functions to read in other file formats, although this bug didn't affect EEGlab since it doesn't use FieldTrip for its own files). If you find any bugs, please let me know ASAP so I can fix them. If making a bug report, make sure to provide full information, including the error message (if any), the version of the operating system and of Matlab, and a copy of the data file you were trying to analyze. Suggestions and general feedback are also welcome. Note, though, that I don't have grant support for this work so I'm not as free to respond as folks who have full-time funding to support software development. Cheers! Joe -------------------------------------------------------------------------------- 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/ |
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From: Joseph D. <jd...@ma...> - 2009-09-06 22:13:34
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Due to the generous support of Dennis Molfese, I've been able to make a significant upgrade to the EP Toolkit, which is intended for ERP researchers as an adjunct to EEGlab. The main development is that I've added a graphical user interface to make it easier to use. I've also added features to further three goals: 1) Facilitating analysis of noisy ERP data, such as developmental or clinical, by the application of automated artifact correction and robust statistics at both the averaging stage and the inferential statistics stage. 2) Facilitating multivariate decomposition of ERP data, preferably using a combination of EEGlab's ICA rotation for the spatial mode and the Promax PCA rotation for the temporal mode. 3) Facilitating inferential data analysis of ERP data using robust statistics not previously available with a user interface. The tutorial provides in-depth guidance on how to use the Toolkit. This release is currently in beta (meaning no known bugs but it is still undergoing testing and there are likely further bugs lurking). If you are interested in trying it out, you can download it from the usual location: https://sourceforge.net/projects/erppcatoolkit/ This version of the EP Toolkit is more computationally demanding so it requires Matlab 2006 or more recent. It also needs at least 2GB of RAM and preferably 4GB or more. In general, the faster the computer, the better. It has been extensively tested on OS X and is currently undergoing testing on Windows XP. It can read text, EEGlab .set, EGI simple binary and EGIS, Biosig EDF, and Neuroscan AVG files. I'd be happy to implement support for other file formats if a user is willing to help test them. The EGI format files it saves can in turn be read by programs like EEGLab and BESA. In order to use Repov's new OS X compiled runICA code, the attached binica.m file would need to be used to address a bug that otherwise can crash the session. Likewise, to use .set files produced by EEGlab after importing the files from other formats, the following attached popfileio.m file would need to be used so that the .set files are correctly formed and thus readable by the EP Toolkit. The changes have been submitted to Arno and hopefully (if they meet with his approval) will be incorporated into a future EEGlab release (not yet incorporated as of eeglab7_1_4_15b). If you find any bugs, please let me know ASAP so I can fix them. If making a bug report, make sure to provide full information, including the error message (if any), the version of the operating system and of Matlab, and a copy of the data file you were trying to analyze. Suggestions and general feedback are also welcome. Note, though, that I don't have grant support for this work so I'm not as free to respond as folks who have full-time funding to support software development. Cheers! Joe -------------------------------------------------------------------------------- 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/ |
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From: Joseph D. <jd...@ma...> - 2009-08-29 05:50:04
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I couldn't reproduce your error. For the two file set you sent me, the names of the .dat file and of the .set file are different so they appear to be from two different data files. They need to be from the same data file (i.e., have the same name). For the one file version, it worked fine. I just made some fixes to the file I/O code though, which may account for it working okay. I'll be posting a new version of the EP Toolkit later tomorrow. I also just made a fix to FieldTrip's .set file I/O code and posted it to FieldTrip. Download the new FieldTrip build tomorrow as well (since the EP Toolkit uses FieldTrip's file I/O functions to import .set files). If you're still experiencing the error I'll dig into it further. Note that there are also some bugs in the file I/O code of EEGlab as well. If the files were originally imported into EEGlab from another source and then subsequently saved as .set files, they may be defective, accounting for the errors. I just submitted a series of bug fixes to Arno so hopefully they will be included in the next EEGlab build. I'm attaching a copy of the fixed EEGlab file in case you want to use it. Cheers! Joe |
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