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From: Joseph D. <jd...@ma...> - 2011-02-03 03:10:08
|
The download problem was indeed due to the Sourceforge folks shutting down file uploads in the wake of a hacker attack. They have informed me that my account has been reactivated and I have verified that it is working properly again now. So anyway, the newest EP Toolkit release is now truly available. My apologies for any inconvenience. ------------------------ I just posted version 2.21. A big bug fix release mostly, plus the usual improvements to error handling and to the user interface. Some highlights are that the EPwork directory and the EPprefs file are now placed inside the default user directory so it should work better with Windows systems. The preprocessing can now be used with continuous files. Also, implemented (experimentally) procedure for removing saccades in the same manner as blinks. Needs to be formally evaluated however. Hopefully can get back to adding new features now. Cheers! Joe 1) In artifact correction routine, fixed badChans and badTrials fields of data files not being recorded for all but last chunk when data are being processed as multiple chunks. 2) For continuous files, data now divided into one second epochs and can be artifact rejected in an epochwise fashion in same fashion as segmented data. 3) Added support for saccade correction to be done in the same fashion as blink correction as opposed to simple rejection of the trial. 4) Now accepts upper case file suffixes (e.g., .EGIS). 5) Now handles mismatch in artifact correction where file template or data has implicit reference and the other one has explicit reference. 6) When reading in EGIS session files with implicit reference channel, adds it in explicitly, thus avoiding crash in eyeblink correction routine. 7) Fixed crash in Window function after switching to a dataset with fewer cells. 8) Fixed crash in ANOVA function when performing ANOVA with no between group factors under Matlab 2008b. 9) No longer aborts blink correction when number of electrode coordinates in blink file and in data match (including implicits). 10) Fixed bottom of Topos window being cut off on laptop screens. 11) Fixed crash in ANOVA function when used prior to data being loaded into the work set yet (due to badly initialized variable). 12) Now putting preferences file and work directory at default user directory if old one cannot be found in order to work better on Windows computers. 13) Type grayed out of Preprocess, Average, Postprocess, and Read functions when set to .ept files since the type is specified by the file. 14) "Done" buttons renamed to "Main" to reduce confusion (thanks to Tim Curran). 15) Fixed channels not being unstandardized correctly in jack-knife function of Topos, resulting in some inaccuracy in dipole results and potentially a crash. 16) Fixed crash when trying to display Topos where some channels are missing electrode coordinates. 17) Wave window title now more descriptive (thanks to Arild Hestvik). 18) View function now defaults to selecting the newest dataset rather than the first dataset (thanks to Arild Hestvik). 19) When adding combinations of cells or subjects, the name of the new addition describes what went into it. 20) Bumped default size for preprocessing chunks up to 200000. 21) Added support for selecting timepoints in preprocessing (previous implementation was non-functional). 22) Fixed View ANOVA function not matching up ANOVA levels with data columns correctly when a subset of the columns are selected. 23) In Contrast function of the ANOVA pane, fixed levels of ANOVA factors being listed in the wrong order when there are more than one ANOVA factor. 24) In Contrast function of the ANOVA pane, fixed crash when no between factor specified. 25) Fixed error message incorrectly rejecting between or within contrast specified as being "1", which should mean no contrast of that type. 26) Added option to manually specify EOG channels for preprocessing for cases where automatic EOG channel selection does not work. 27) Fixed channel controls for Window Pane not working on Matlab versions prior to 7.8. 28) Fixed some channel controls for Window Pane going off screen on a laptop screen. |
From: Joseph D. <jd...@ma...> - 2011-02-01 02:40:37
|
I've been unable to successfully upload the new release to SourceForge. It keeps getting corrupted somehow. I'm thinking it might be related to a recent hacking attack on Sourceforge. They say they've shut down some services while they check their systems and make sure everything is secure. I'll keep you posted. In the meantime, if you have an urgent need for something in the new release, feel free to contact me directly and I'll get it to you by some other method. Sorry for any inconvenience! Joe |
From: Joseph D. <jd...@ma...> - 2011-01-28 13:50:39
|
I just posted version 2.21b. Sourceforge just changed its file management system and somehow it resulted in a problem with my original upload. The file was defective and wouldn't unzip. The new upload is working fine. Sorry for any inconvenience! Joe |
From: Joseph D. <jd...@ma...> - 2011-01-27 03:23:44
|
I just posted version 2.21. A big bug fix release mostly, plus the usual improvements to error handling and to the user interface. Some highlights are that the EPwork directory and the EPprefs file are now placed inside the default user directory so it should work better with Windows systems. The preprocessing can now be used with continuous files. Also, implemented (experimentally) procedure for removing saccades in the same manner as blinks. Needs to be formally evaluated however. Hopefully can get back to adding new features now. Cheers! Joe 1) In artifact correction routine, fixed badChans and badTrials fields of data files not being recorded for all but last chunk when data are being processed as multiple chunks. 2) For continuous files, data now divided into one second epochs and can be artifact rejected in an epochwise fashion in same fashion as segmented data. 3) Added support for saccade correction to be done in the same fashion as blink correction as opposed to simple rejection of the trial. 4) Now accepts upper case file suffixes (e.g., .EGIS). 5) Now handles mismatch in artifact correction where file template or data has implicit reference and the other one has explicit reference. 6) When reading in EGIS session files with implicit reference channel, adds it in explicitly, thus avoiding crash in eyeblink correction routine. 7) Fixed crash in Window function after switching to a dataset with fewer cells. 8) Fixed crash in ANOVA function when performing ANOVA with no between group factors under Matlab 2008b. 9) No longer aborts blink correction when number of electrode coordinates in blink file and in data match (including implicits). 10) Fixed bottom of Topos window being cut off on laptop screens. 11) Fixed crash in ANOVA function when used prior to data being loaded into the work set yet (due to badly initialized variable). 12) Now putting preferences file and work directory at default user directory if old one cannot be found in order to work better on Windows computers. 13) Type grayed out of Preprocess, Average, Postprocess, and Read functions when set to .ept files since the type is specified by the file. 14) "Done" buttons renamed to "Main" to reduce confusion (thanks to Tim Curran). 15) Fixed channels not being unstandardized correctly in jack-knife function of Topos, resulting in some inaccuracy in dipole results and potentially a crash. 16) Fixed crash when trying to display Topos where some channels are missing electrode coordinates. 17) Wave window title now more descriptive (thanks to Arild Hestvik). 18) View function now defaults to selecting the newest dataset rather than the first dataset (thanks to Arild Hestvik). 19) When adding combinations of cells or subjects, the name of the new addition describes what went into it. 20) Bumped default size for preprocessing chunks up to 200000. 21) Added support for selecting timepoints in preprocessing (previous implementation was non-functional). 22) Fixed View ANOVA function not matching up ANOVA levels with data columns correctly when a subset of the columns are selected. 23) In Contrast function of the ANOVA pane, fixed levels of ANOVA factors being listed in the wrong order when there are more than one ANOVA factor. 24) In Contrast function of the ANOVA pane, fixed crash when no between factor specified. 25) Fixed error message incorrectly rejecting between or within contrast specified as being "1", which should mean no contrast of that type. 26) Added option to manually specify EOG channels for preprocessing for cases where automatic EOG channel selection does not work. 27) Fixed channel controls for Window Pane not working on Matlab versions prior to 7.8. 28) Fixed some channel controls for Window Pane going off screen on a laptop screen. |
From: Joseph D. <jd...@ma...> - 2011-01-06 16:25:24
|
Hello Li Ya, sorry to hear you're having some difficulties using the Toolkit. Could you give us a little more information? When you say "However, the EP TOOLKIT and MATLAB cannot response after then." what do you mean? Are you saying the scree test is not happening? Or are you saying that you are unable to take the step after that? If the latter, it would help to tell us exactly what you tried to do and what the Toolkit did. Was there an error message? Did you click on the data set name and nothing happened? etc. etc. Also, it's always helpful to indicate the operating system (Windows 7, OS X 10.5, etc.) and the version of Matlab and the version of the Toolkit. Best way to do it is to type ver in the command window and then paste the results, as in: >> ver ------------------------------------------------------------------------------------- MATLAB Version 7.11.0.584 (R2010b) MATLAB License Number: 521547 Operating System: Mac OS X Version: 10.6.5 Build: 10H574 Java VM Version: Java 1.6.0_22-b04-307-10M3261 with Apple Inc. Java HotSpot(TM) 64-Bit Server VM mixed mode ------------------------------------------------------------------------------------- MATLAB Version 7.11 (R2010b) ERP PCA Toolbox Version 2.21 FastICA for Matlab 7.x and 6.x Version 2.5, October 19 MATLAB Compiler Version 4.14 (R2010b) Statistical Parametric Mapping Version 3684 (SPM8) Symbolic Math Toolbox Version 5.5 (R2010b) Cheers! Joe On Jan 6, 2011, at 12:53 AM, LiYa wrote: > Dear ALL, > > I am new to PCA analyses and I have some question regarding this area. If anyone could please help me I will be more than grateful! > > I intend to do a spatial-temporal PCA. The data is recorded by Brain vision Record and analyzed by Brain Vision Analyzer 2.0. Then the average ERPs for each participate and each condition is export respectivelyto Matlab files’s .mat, followed by saved as EEGLab’s .set by EEGLab. > > After then, I intend to get the input to the PCA consisted of 1500 observations (3 conditions *500 data points per epoch) for each participant and electrode. To achieve this, I read all average data for each participant and each condition at first, and then I choose spatial mode and infomax rotation and place the #factors 0 to do the scree test. However, the EP TOOLKIT and MATLAB cannot response after then. > > What's wrong with my operation? How can I place the input to the PCA consisted of all observations for each participant, each condition, each electrode and each timepoint rightly? > > Many thanks, > > Li Ya > ------------------------------------------------------------------------------ > Learn how Oracle Real Application Clusters (RAC) One Node allows customers > to consolidate database storage, standardize their database environment, and, > should the need arise, upgrade to a full multi-node Oracle RAC database > without downtime or disruption > http://p.sf.net/sfu/oracle-sfdevnl > _______________________________________________ > Erppcatoolkit-support mailing list > Erp...@li... > https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support |
From: LiYa <liy...@ho...> - 2011-01-06 05:53:30
|
Dear ALL, I am new to PCA analyses and I have some question regarding this area. If anyone could please help me I will be more than grateful! I intend to do a spatial-temporal PCA. The data is recorded by Brain vision Record and analyzed by Brain Vision Analyzer 2.0. Then the average ERPs for each participate and each condition is export respectivelyto Matlab files’s .mat, followed by saved as EEGLab’s .set by EEGLab. After then, I intend to get the input to the PCA consisted of 1500 observations (3 conditions *500 data points per epoch) for each participant and electrode. To achieve this, I read all average data for each participant and each condition at first, and then I choose spatial mode and infomax rotation and place the #factors 0 to do the scree test. However, the EP TOOLKIT and MATLAB cannot response after then. What's wrong with my operation? How can I place the input to the PCA consisted of all observations for each participant, each condition, each electrode and each timepoint rightly? Many thanks, Li Ya |
From: Joseph D. <jd...@ma...> - 2010-10-12 03:39:58
|
I just posted version 2.20b. The sole difference from 2.20 is that the Documentation folder is now called "Documentation" rather than "***Documentation***". Strangely enough, it seems that putting the asterisks around the name was causing it to be missing when unzipped on a Windows XP computer. Let me know if you run into any other issues! Cheers! Joe -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist 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...> - 2010-10-11 01:15:41
|
I just posted version 2.20. Just a bug fix release (mostly for the append function), plus the usual improvements to error handling. Hopefully can get back to adding new features now. Please keep up the bug reports! 1) Fixed unable to output result of averaging function in EGIS format. 2) In Edit function, fixed append cells and append subjects and append chans crashing when averaged data (typically ept files) contain noise or std information from having run the averaging with the Toolkit and the new file is not a factor file. 3) In Edit function, fixed append cells and append subjects and append chans not adding std and noise information from the new file. 4) In Edit function, fixed append cells failing if the files contained trial specs, as in EGIS files. 5) Fixed not allowing subject rows to be changeable even when exceeding limits of subject subpane when using a Matlab version predating 2008. 6) Fixed bug when reading data files such that events in the final sample of a segment were being assigned to the succeeding segment and causing a crash if the segment was already the last one. 7) Fixed crash when the montage keyword was followed by a blank, as when preprocessing a batch of non-EGIS files containing more than one data file. 8) Eliminated warning message associated with the Fileparts function starting with Matlab 2010b. 9) Now assumes that all the session files going into an average is using the same montage so doesn't keep asking for it. 10) Standardized error messages. 11) Fixed Edit function not able to append subjects or cells to data with same names by generating new name. 12) Fixed crash in Edit function when appending cells to non-single trial data. 13) Fixed crash in Edit function when appending subjects to a file with more than one subject or appendings cells to a file with more than one cell. 14) Fixed centroid measures in Window function too large due to addition of the left side of the window (e.g., +200 ms for a window of 200-300 ms). Cheers! Joe -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist 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...> - 2010-08-26 01:50:18
|
I just posted version 2.19. Mostly a bug fix release, except for adding support for writing out EGI unsegmented simple binary files. 1) Fixed crash when reading a file if using "trial" events to determine name of cells and the .value field is empty. 2) Fixed crash on start-up when EP Toolkit folder name has been changed. 3) Fixed Single File mode aborting when reading files in conjunction with a .ced file due to "has different channels" error. 4) Fixed errors when importing .study files where the group or the session fields were left blank. 5) Now supports writing out unsegmented simple binary files. 6) Fixed append cells and append subjects functions not working due to fallacious error messages. Cheers! Joe -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist 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...> - 2010-07-28 01:57:20
|
I just posted version 2.18. This is a pure bug fix release. No new features. 1) Fixed when no within factors for ANOVAs, pane indicated needed one within cell rather than zero wthin cells. 2) Fixed freeze after requestor for information (like name of spec being added to a file using the Edit function or the name of a new merged file when using the Single File Mode of the Read function) due to Matlab bug on Windows computers. 3) Now requires use of 20100720 version of FieldTrip so that it makes use of fixed EGI simple binary code. This fix prevents the Toolkit from getting confused by the inclusion of DIN events, resulting in inability to assign trials to the appropriate cells. These newer versions of FieldTrip also no longer have the R13 and R14 files in the compat folder that were destabilizing Matlab. 4) Fixed view pane listing all the trial names of the dataset rather than just those for a specific cell, resulting in crashes when they were selected. 5) Fixed crash in PCAwhen there are variables which are flat (zero standard deviation). 6) Fixed crash in View Topos when doing dipole or 3D function and ced is either empty or "none". 7) For View Topos, fixed 3D, dipole, and jackknife results incorrect for topos not on the first page (when there are multiple pages of topos). 8) Fixed crash when viewing Waves and data are all zero. 9) Fixed grand averages, which are added when computing ANOVAs with between factors, as they were being computed incorrectly when the between factor column was not sorted alphabetically (only affected waveforms, not the ANOVA results). 10) Fixed min and max of factors sometimes not being calculated correctly, resulting in View Waves plots sometimes not having the voltage range set correctly. Cheers! Joe -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist 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...> - 2010-06-20 03:08:22
|
I just posted version 2.17. Aside from the usual bug fixes and improved error handling, the major feature addition is jack-knife PCA analysis. Whenever a PCA is run, the Toolkit will run a series of additional PCAs, one for each subject, where each subject in turn is left out of the sample (thus a twenty subject sample will have twenty PCAs run each with nineteen subjects). The factor loadings from the exercise are then stored for later use. This does have the effect of causing the PCAs to take a little longer than before (the command line window will provide a running count of which jack-knife sample it is working on). Currently, the jack-knife results are only used in the Topos function. If you right-click on a factor and then choose "jack-knife" it will use the results of the jack-knife to compute the source analyses for all the jack-knife samples and then display their locations. The resulting spread gives a sense of how stable the PCA solution was to variations in the subject sample. The jack-knife provides more useful results than doing a separate one for each subject, which would largely just result in a random cloud as the noise level would generally be too high for both PCA and source analysis. The jack-knife source solutions are also used to compute a t-test for which hemispheric dipole is stronger (using the Miller et al, 1998 jack-knife t-test). There are also a couple user interface changes of note: 1) the file suffix for EP file format files is now .ept rather than .mat, to help avoid confusion. Existing files can just be renamed from .mat to .ept. Note that both OS X and Windows can hide the suffix so you may need to make sure it is being displayed so that you can change it, otherwise you could end up with a file that looks like name.ept but is actually name.ept.mat. 2) The Toolkit now puts an asterisk in front of the name of data in the active set that have been changed to remind you to save them if you want to keep them. 1) Fixed crash when rereferencing and there are no implicit channels. 2) Fixed crash when postprocessing (bug introduced in 2.16). 3) Fixed not keeping FID channels in implicit channel info for fixed channel order file formats (e.g., EGIS, text). 4) Fixed electrode information not matching the data for second file onwards when reading files in single cell file mode. 5) For single cell file mode, no longer need to access ced file for every file. 6) Fixed not successfully merging average files together when reading in data using single cell file mode. 7) Fixed cell labels and sub labels not being applied when reading EP file formats, as when using single cell file mode. 8) Fixed baseline control on Samples subpane failing to change baseline value. 9) When importing data via single cell file mode, only adds trial names for single trial data files. 10) View function no longer crashes when average file erroneously has non-empty trial names field. 11) Fixed crash when reading file formats with fixed-order channels when ced file has wrong number of channels. 12) Fixed files sometimes not being recognized as being selected when names are in uppercase. 13) Fixed not ignoring extra tab at end of line of text files, resulting in "not-a-number" errors. 14) Fixed crash in Topos function when trying to display 3D plot or dipole source using .ced file generated from a .elp file. 15) Fixed average files not being generated with .dataName field, which could result in crashes down the line. 16) Added dipole analysis of jack-knifed PCA results to the Topos function of the View Pane. 17) Added name of first session file to the name of the artifact correction log file if just one file or the number of files if more. 18) In listings of files, puts a star in front of files that have unsaved changes. 19) PCA output no longer adds grand average to subjects dimension if the data type is continuous to avoid resulting crashes. 20) Fixed crash when retaining only one factor for an Infomax rotation. 21) Changed the suffix of EP files to ".ept". 22) Fixed crash when loading EP or .set file with name of original ced file in addition to eloc information. 23) Fixed losing the electrode coordinate information (eloc and and ced) when loading in a .study file. 24) Fixed crash when windowing adds regional channel and there is no electrode coordinate information (eloc). 25) Fixed crash when conducting robust ANOVA and there are no spec columns in the ANOVA data file. Thanks to Noriko Tanigawa for reporting a series of bugs and Matt Mollison for making suggestions on how to improve the Toolkit. Cheers! Joe -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist 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...> - 2010-05-26 03:42:11
|
I just posted version 2.16. Aside from the usual bug fixes and improved error handling, the chief new feature is support for EEGlab's .study file format (both reading and writing). Support isn't complete due to some fundamental differences between EEGlab and the EP Toolkit in their file formats and their underlying analysis philosophies. Note also that there was a bug fixed that was causing cells of averages generated by the EP Toolkit to be labeled incorrectly. If you've been using that function be sure to recheck the data! Apologies for letting that one slip by me. Thanks to Kate Bailey for alerting me to this one. 1) Fixed location of the variance accounted for table for old versions of Matlab for two-step PCAs in the Summary subpane of the PCA pane of the Edit function. 2) Fixed crash when reordering cells using the Edit function. 3) Fixed crash when a two-step PCA fails due to an error. 4) In PCA pane, number of factors and title of PCA no longer being changed to blank when changing other PCA settings. 5) Fixed crash when importing .set file or EP file with unavailable or invalid ced file named in ced field. 6) In readData function, fixed channel selection not operating on channel coordinates eloc field (not accessible from GUI). 7) Fixed assumption in Edit function that appended files will be in EGIS format. 8) Fixed crash when merging average files. 9) Added support for reading and writing EEGlab .study files. 10) When saving EEGlab file formats, cells are now saved as separate .set files. 11) When using single file mode to combine data files, fixed subtle bug where a cell or subject names that are supersets of a shorter one (as in "sub010" and "sub01") could be treated as being the same. 12) Fixed cell names being associated with wrong cells after averaging data (thanks to Kate Bailey). Cheers! Joe -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist 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...> - 2010-05-17 04:52:03
|
I just posted version 2.15. Aside from the usual bug fixes and improved error handling, the chief new features involve enhancements to the new topos function. It is now possible to get 2D plots, 3D plots, and simple dipole analyses done by right-clicking on the scalp topography maps (thanks to EEGlab and FieldTrip functions). I've also added a summary page to the PCA pane of the Edit function that provides the basic parameters for a PCA file, as well as providing the "variance accounted for" information that is usually needed for results sections of manuscripts. This information is no longer printed out to the command line as it was getting confusing. 1) Fixed crash when reading data using single file mode with .set files which contain the .eloc information. 2) Fixed crash when reading single_trial data using single file mode. 3) Fixed crash when reading data file that was originally in .set format and then was saved in EP file format. 4) Fixed crash when generating grand average from files with more than one cell by using either mean or median methods. 5) Fixed crash when in Window Data pane using noTable mode (older versions of Matlab) and there are less than five subject specs. 6) Fixed table of cells and table of specs not changing when dataset is changed, when in Window Data pane using noTable mode (older versions of Matlab). 7) Fixed crash when using Topo button of View EEG pane and not all four colors are being used. 8) For Topos of View Pane, fixed can only change channel and latency settings for number of rows equal to number of pages of factors. 9) Fixed Topos of View Pane sometimes crashes when first color is set to none. 10) In Topos of View Pane, added white marker to topos for electrode corresponding to the waveform figures. 11) When reading data,for files with ced set to "eeglab", change to either name in chaninfo.filename field if present, else "none". 12) Added ced to cache contents. 13) In Topos of View Pane, small black dots indicate electrode locations in topographical plots. 14) In Topos of View Pane, may click on electrode dots to move the waveform plot channel. 15) In Topos of View Pane, may right-click on topographical plot to obtain expanded 2D plot. 16) In Topos of View Pane, may right-click on topographical plot to obtain expanded 3D plot. 17) Made blink correction routine more memory efficient by reducing resolution of the blink plots to no more than 10000 points regardless of size of data. 18) For eyeblink correction, fixed when data is mean mastoid, not setting second reference channel to be inverse of the first reference channel. 19) For eyeblink correction, fixed crashes when explicit reference channel is present and identified as being a reference channel. 20) Changed the way the electrodes are highlighted on the Channel Grouping page to get around a bug in older versions of Matlab. May cause compatibility issues though, as I don't have a copy of every Matlab version so I'm not sure which versions of Matlab are affected. Let me know if you run into problems with this. 21) Added summary page to the PCA subpane of the Edit function, including the total variance accounted for information. 22) In Topos of View Pane, may right-click on topographical plot to obtain basic dipole analysis. 23) In Topos of View Pane, electrode names no longer provided alphabetical order in popup menus. 24) Added option to use unrotated solution for PCAs. Cheers! Joe -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist 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...> - 2010-04-27 02:58:51
|
I just posted version 2.14. Aside from the usual bug fixes and improved error handling, I was able to start moving ahead with adding new features. Just added is a facility for displaying scalp topographies (via EEGlab's topoplot) in a format helpful for efficient screening of factor results (topos button on the View pane). Also, thanks to Scott Miller for his extensive edits of the tutorial documentation. 1) When displaying waveforms, fixed zero voltage bar not appearing in expanded waveform figures. 2) When displaying waveforms, fixed stimulus onset bar not appearing in waveforms figures. 3) When displaying waveforms, fixed baseline bar and stimulus onset bar not appearing in expanded waveform figures when click lands on a waveform. 4) When displaying waveforms, fixed real reason waveform figures using much more memory than needed. 5) Fixed wrong peak chans and time points for AutoPCA when not two-step PCA. 6) Scale of waveforms no longer constrained to be at least +/- 1 microvolt when plotting waveforms. 7) Fixed CMB factors not dropped from data when present in .data rather than .facData (which was resulting in error messages about missing factors when, for example, an EGIS factor file was read in and then one switched to the Window pane). 8) Added Topo button to View pane for displaying scalp topographies and screening factors efficiently. 9) Fixed wrong number of channel names when reading fixed order file formats (like EGIS) and the reference channel is implicit. Cheers! Joe -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist 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...> - 2010-03-29 02:36:32
|
I just posted version 2.13. This release mostly consists of improving support for non EGI file formats, including the addition of EEGlab .set file format as an option for saving data files. 1) When generating a PCA dataset, ensure that the summary factor, subject, and cell names are not already taken. If so, add a unique suffix to the name. 2) When reading in data, if .type field is missing from eloc information (due to use of defective .ced file), then add it rather than crashing (assume channels are "EEG"). 3) Support for EDF file format was broken due to dropping of Biosig from FieldTrip (which is used to provide file format support). An attempt has been made to reinstate it but the one sample .edf file that I have yielded defective output. In order to fix this, I would need someone with access to .edf files to work with me to help track down the problem. 4) Fixed crash when viewing waveforms of data with no implicit channels. 5) Fixed crash when reading in .txt file format data (apparently introduced by a recent release). 6) Fixed crash when reading in data where event information is empty. 7) Fixed crash when viewing data with no electrode coordinate information. 8) Fixed text files treating all channels as being implicit when used with ced files with channel names different than the default channel names. 9) When reading data, for file formats with fixed channel orders (such as EGI files and text files), use channel names from ced file if available. 10) Added ability to save data using .set file format (thanks to Grega Repovs for his help). 11) Reduced memory required to display waveforms. Cheers! Joe -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist 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...> - 2010-03-11 03:20:01
|
I just posted version 2.12. It's looking like the bugs are mostly squashed at this point, although some are still trickling in. Should be able to start adding new features soon. Also, due to report of incompatibility of some word processors with the .rtf files I've been using for documentation, I've switched to pdf files. 1) One dimensional cell array fields in the EP internal data file format are now standardized to be column vectors. Some file formats were causing crashes in the Edit function because some of these fields were coming out as row vectors. 2) Fixed crash in doPCA when using grand average option (only useable from command line). 3) When running ANOVAs with between subject factors, fixed having only the first between group waveform being added to the datafile. 4) Fixed bad trials field misnamed and hence horizontal eyebelink detection not having any effect. 5) Fixed lack of splitting of analysis fields (bad channels etc.) when preprocessing resulting in incorrect analysis fields or crash when rejoining the chunks. Cheers! Joe -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist 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...> - 2010-03-01 03:46:25
|
I just posted version 2.11. Aside from the usual bug fixes and minor enhancements, I went through the tutorial file and gave it some updating and polishing. The exercise also turned up a number of bugs which I squashed. A notable addition is relevant to NetStation users. When opening EGIS files (only), NetStation is able to make use of montage information that is added to the file. There are some incompatibilities in the montages between NetStation 4.3 and earlier versions for Hydrocel nets, with 4.3 unable to open montages from earlier versions and vice versa. Because of this problem, I've added an option under the Files preferences to not add the montage to EGIS files (montage information is not used for other types of files). In this case, NetStation will present you with a set of options the first time you open the files and add the information itself. 1) Fixed crash due to changes in 2.10 when loading factor file with CED information with Read function. 2) Fixed loss of some factor information (factor types and combined factor waveforms) when loading EP format factor file using Read function. 3) Fixed bug in code for follow-up ANOVAs that could cause crashes or the wrong factors to be used (but still correctly labeled). 4) Changed bad channel field to negative numbers for uncorrected bad channels to distinguish them from corrected bad channels. 5) Added "repChan" to QC information in the Edit Pane so that one can examine the proportion of replaced bad channels separately from the proportion of uncorrected bad channels. 6) Modified averaging function to accommodate uncorrected bad channels. 7) Counts of total blink trials and movement trials for averaged waveforms now computed by averaging function include only good trials. 8) Averaging function now handles possibility of no good trials for an average. 9) When importing data using the Read function, epochs that are entirely flat across all channels are marked as bad. 10) AvgNum and SubNum fields now calculated when computing grand averages. 11) Fixed crash in Read function when there are two REF channels (as in M1-M2 mean mastoid channels). 12) Can now handle displaying waves from multiple datasets where some of the channels are implicit in one but not the other dataset (as in Neuroscan missing channels). 13) BadChans numbers of QC subpane will now use number of subjects to calculate proportion for grand averages. 14) Fixed bug where during preprocessing, neighboring channels for determing whether a channel is not correlating with its neighbors was sometimes not chosen correctly, which could lead to too many channels being dubbed globally bad. 15) No longer treating shorted channels as being bad channels as this was proving too conservative a criterion. Instead it now just provides a warning message. 16) Preprocessing can now be applied to subject average files with multiple subjects. 17) Analysis fields no longer optional parts of EP file format. 18) In preprocessing, turning off bad channel preferences affects only the relevant bad channel criteria rather than turning off all bad channel detection. 19) Now has option to use file's default reference channels (as indicated by the CED file) in the preprocess pane. 20) Fixed crash when loading in an EP file with ced information. 21) Fixed crash when loading in a .set file that does not have ced information included in its header. 22) Fixed crash when subject adds are being stripped from data with no subject specs (as in Neuroscan files). 23) Fixed crash when adding subject spec via Edit Pane. 24) When importing EP file format data, correctly checks for data type even for "factors" and "grand_average". 25) When running ANOVAs with between subject factors, fixed the addition of grand averages corresponding to the levels of the factors to the dataset. 26) Eliminated chantype field. 27) If there are two reference channels (as in mean mastoids), then no longer require that they have a -1 correlation as one may just be bad. 28) If there are two reference channels (as in mean mastoids), then they are still marked as bad channels if they are flat. 29) When writing out EGIS files, cell names and experiment names are terminated so that they are not padded out with spaces when read by some programs. 30) Fixed error message when reading factor data with combined (CMB) factor in EGIS format. 31) Now reads the nsweeps field of Neuroscan AVG files to fill in the avgNum and subNum fields. 32) Export file dialogs in Edit function now correctly indicate that the file with be of type .txt. 33) Made autoPCA option of Window function more memory efficient so it wouldn't run out of memory. 34) Fixed crash in ANOVA function when level names of between group factors were of different lengths. 35) Now zero-padding factor names (e.g., "003") to maximum number of digits so that they sort properly. 36) Close files after running batch of ANOVAs to avoid "too many files open" error. 37) When running ANOVAs with between subject factors using the output of the autoPCA option, fixed the addition of grand averages corresponding to the levels of the factors to the dataset. 38) Corrected the peak channel and peak time point identification of factors made by the autoPCA option of the window function. 39) Fixed bug that prevented one from fully deleting the contents of edit fields, such as "baseline" on the preprocessing pane. 40) Fixed bug that prevented one from changing the contents of the edit fields on the postprocessing pane. 41) Workaround for Matlab bug that appears to prevent buttons from being colored when pressed on Macs using version 2009b applied to windowing function's PCA guided channel group option too. 42) Fixed crash when viewing data with regional channels. 43) Eliminated updating of baseline field when baseline correction during postprocessing. The part of the segment used for baseline correction may not necessarily correspond to the prestimulus period. 44) Fixed crash when using Edit function's Factor subpane to examine factors that include a combined factor add. 45) Fixed inability to set minimum variance setting for autoPCA preference to anything other than zero. 46) Implicit reference channels will no longer be marked as bad when reading them in. 47) Added option to turn off adding montage information to EGIS file format files due to incompatibility issues with some versions of NetStation. 48) Fixed crash when saving EGIS file format file with a "sex" subject spec field. Cheers! Joe -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist 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...> - 2010-02-01 00:47:45
|
I just posted version 2.10. Aside from the usual updates to the documentation, it makes the following fixes and enhancements (minor bugs and enhanced support for other file formats and continuous files): 1) Can now leave out subject and cell fields when reading files in single file mode (will use default values instead and will assume all the subjects/cells are the same) 2) Fixed crash when reading files using single file mode and operation is aborted due to problem with files 3) In order to accommodate file formats like Neuroscan AVG where bad channels may be dropped from the data file, when reading in file formats that label the channels, they will be reordered to match the order of the ced file. Then, if any channels are missing from the data file then they will be added as bad channels. Conversely, if any channels are in the data but not in the ced file, they will now be properly handled as locationless channels. 4) The type field in the .ced files is now used since the EEGlab bug was apparently fixed and it is now functional. The type field must now be present in the .ced file and assumptions will no longer be made about which ones are REF or FID types. 5) Sped up the View function's waveform displays, requiring some additions to the dataset cache. 6) Fixed contents of analysis fields (which keep track of bad channels etc.) being not arranged correctly when merging files, as in the single file mode. 7) Fixed crash when examining QC data on bad channels and trials via the Edit function. 8) Added support for Neuroscan .eeg and .cnt files. 9) Added ability to plot data from continuous data files in the View function by showing only one second at a time. 10) Epoch ms times now displayed as from beginning of first sample to end of last sample. 11) Fixed bug introduced in 2.07 where checkboxes and subject and cell fields on Read and Preprocess panes impossible to deselect. 12) Fixed bug not updating baseline field when using Postprocess function to baseline correct data. 13) Fixed incorrect subject ID being extracted from EGIS session headers. 14) Refreshes Edit pane when Done button is pressed so when Data Name is changed, the name in the list of datasets is updated. 15) Fixed crash when adding a cell in the edit pane whose type is 'SGL'. 16) Fixed an error message when all the SGL cells have been deleted, leaving only the CMB cells, and one clicks on the Factors subpane of the Edit pane. 17) Fixed crash when reading a file due to events with empty value fields (now uses type field instead if value field is empty). 18) Fixed crash while reading files due to empty type fields in eloc information by assuming they are EEG channels. 19) Fixed not saving event data to single_trial EGI simple binary files. 20) Fixed putting events at the very first sample for EGI simple binary files. In addition, Robert Oostenveld kindly fixed a bug in FieldTrip's support for the .set file format and I just fixed a couple bugs in FieldTrip's support for the EGI Simple Binary format (all having to do with event timing). Be sure to update your copy of FieldTrip (to that of 2/1/2010 or later) if you are using either file format. Make sure to delete the stale copy of FieldTrip in EEGlab. Thanks to Grega Repov for his detailed bug reports. Cheers! Joe -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist 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...> - 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/ |
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 |
From: Joseph D. <jd...@ma...> - 2009-12-10 02:32:59
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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/ |
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 |
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/ |
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 |