Thread: [Erppcatoolkit-support] ERP PCA Toolkit 2.21b release
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From: Joseph D. <jd...@ma...> - 2011-01-28 13:50:39
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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...> - 2012-09-10 01:08:28
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New mostly bugfix release. Note especially #13, which fixed a bug that caused data corruption for continuous (unsegmented) data files when performing spectral analysis. Also, if you're interested in learning more about PCA and how to use the ERP PCA Toolkit, I'm holding an all-day workshop on the topic at the Society for Psychophysiological Research conference in New Orleans in October. 1) Average function can now merge together files with different sets of cells. 2) Added option to combine cells in Edit function weighted by number of trials in each average. 3) In windowing function, fixed bad channel handling referring only to first channel in channel area. 4) Fixed missing data numbers being transformed to psd and dB for frequency data. 5) Allow continuous files that have been frequency transformed to be averaged. 6) Fixed overwriting existing file with Transform function if the output file format differed from the input file format. 7) For the Edit function, fixed crash when examining std table of the QC subpane for frequency data. 8) Fixed edit's add cells trial weighting option not working correctly when the cells are not a consecutive series starting with the first. 9) For topo plots, fixed minimum voltage scaling being set to -1000 whenever minimum voltages are below 1000. 10) Fixed crash when trying to add subject ANOVA waveform after computing robust ANOVA and subjects have been trimmed. 11) Fixed crash when trying to add subject ANOVA waveform after computing robust ANOVA and data is not from PCA output. 12) Fixed crash when loading older EP format files with factor data. 13) Fixed selecting incorrect time points when running spectral analysis on continuous data files (data corruption bug!!!!). 14) Improved ability to figure out the cell names of EEGlab files. 15) Fixed crash when combining multiple session files into one average file. 16) Fixed blink templates being saved as text files. 17) For windowing, fixed channel numbers appearing black on black background on windows computers. -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jd...@ma... Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com// |
From: Joseph D. <jd...@ma...> - 2013-02-04 00:36:54
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New release of EP Toolkit. Major feature additions include addition of filtering options, support for manual editing of bad channels and trials, and support for ERPlab file format. Continuing improvements in support of spectral data and ongoing bug fixes and refinements to existing features. Cheers! Joe 1) Added option to set last row to be imported in text files. 2) Fixed crash when changing the sampling rate in the Samples subpane of the Edit function. 3) Fixed subNames, subTypes, cellNames, cellTypes, facNames, and facType fields generated by single file mode and by PCA output and by Transform data not necessarily being column vectors, resulting in crashes in other parts of the Toolkit. 4) Fixed crash when invoking 2D plots in Topos view. 5) Fixed crash when using combining cells or chans for spatial PCA data. 6) Fixed Transform not updating reference type when rereferencing data. 7) Fixed missing markers in Wave plots when data range is less than one. 8) Fixed crash under certain circumstances when windowing data with multiple channels in a channel group. 9) Added option to do internal calculations of frequency data in either amplitude or power form. 10) Fixed erroneous error message and crash when trying to PCA average file where bad channels were dropped rather than replaced. 11) Fixed error message when expanding channel for waveform plot for which the data are no longer available. 12) Fixed not changing prestimulus period in Transform function when reference set to "none." 13) Added frequency filtering (low pass, high pass, bandpass, bandstop, notch) to Transform function. 14) Fixed subNames and subTypes field not being a column vector when averaging multiple files, resulting in no average file being saved. 15) Detects when PCA yields complex numbers due to rounding errors causing relationship matrix to be unsymmetric and makes the relationship matrix symmetric. 16) Since eigenvalue decomposition during PCA is not always in ascending order, sort them first. 17) Handles situation where FFT data has negative values (e.g., due to imprecision in PCA results) and transforming to dB would result in complex numbers, by taking absolute value first. 18) Events assigned to wrong subject (off by one) when reading in average files. 19) Added support for reading .set files generated by Widmann's pop_grandaverage function. 20) Added support for reading .erp files generated by ERPlab. 21) Fixed erroneous "labels" error message when trying to load .study file. 22) Fixed error message when applying PCA to data with only one cell. 23) Fixed problem that loading EP files with frequency PCA data results in damaged data file and error messages. 24) Fixed problem where information for expanding channels in waveform plot is lost under some circumstances. 25) Added option to contextual menu in Topos view to rescale figures according to selected topo map. 26) Fixed bug in reconstruction of PCA data from frequency-domain PCAs. 27) Added markers and expanding window to waveform figures in Topos. 28) Added manual scanning for bad channels and trials. 29) If baseline correction chosen, will occur even if blink correction not performed and it will be applied prior to global bad channel and trial detection. Detrending now performed prior to global bad channel and trial correction and baseline correction. 30) Fixed crash when trimming low end Hz of spectral data using Edit function. 31) Fixed identifying all EGIS files as Hydrocel-128P under OS X 10.8 when using Satimage osx. 32) Added frequency-domain peak measures to windowing function. 33) Fixed crash when combining channels for factor data under certain circumstances (presence of facData due to adds). 34) When saving a dataset, name of dataset changes if new name is chosen for saved dataset. 35) Fixed a variety of issues with the automatic scaling in the topomap figures, especially for spectral data. 36) Fixed error message when generating PCA data from a single subject average. 37) Fixed crash in View pane under when changing a dataset under certain circumstances. 38) Marker fields in View pane no longer reset to blank whenever a change is made in the settings. 39) Clearing volt, hz, and sample parameters in View pane no longer crashes. If value is manually set, will not change until a new dataset is chosen or until the value is cleared (in which case it will be replaced with automatic value). 40) Added writing ERPlab format files. -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jd...@ma... Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com// |
From: Joseph D. <jd...@ma...> - 2013-02-26 23:19:01
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Bugfix release. Nothing major unless you ran into one of them. 1) Fixed error when setting file format preferences to ERPlab files. 2) Fixed failure to save preferences when save preferences button clicked. 3) Changed ms window information provided in header of windowing text files so it ranges from onset of sample to offset of sample rather than onset to onset (e.g., 0-4 ms rather than 0-0 ms for first sample). 4) Fixed ms window information on Window pane so that it ranges from onset of sample to offset of sample rather than offset to offset (e.g., 4-4 ms rather than 0-0 ms for first sample) after changes to the windowing settings. 5) Fixed running baseline correction even on frequency domain data even though baseline fields are grayed out. 6) Fixed time names not being calculated correctly when sampling rate changed using Edit function. 7) Fixed crash in View waves or when setting channel groups in Window function when all channels are along midline or center line. 8) Fixed crashes after Edit function used to trim the range of frequencies due to not applying trimming to std or FacVecF fields. 9) Allow View Scan function to operate on average files. 10) Now checking installation configuration only when EP first started. 11) Fixed peak channels not being identified correctly in Topos view. 12) In Edit function, fixed %age of blink, saccade, move, and bad trials in QC subpane being computed incorrectly for average data. 13) Fixed power field not being included in merged files, such as from Single File Mode, causing crashes elsewhere. 14) Fixed crash when loading in .study average file where the .set files have no prestimulus period. 15) In Topos view, fixed crash when displaying data with a regional channel. 16) Fixed crash when data file has no event information. 17) Fixed crash in Topos view when displaying frequency data in dB scaling and the maximum value is negative. -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jd...@ma... Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com// |
From: Joseph D. <jd...@ma...> - 2013-02-27 00:36:52
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Just realized it's pretty easy to have the EP Toolkit automatically check for updates whenever it is started so just added this functionality. -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jd...@ma... Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com// |
From: Joseph D. <jd...@ma...> - 2013-04-06 02:35:35
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New release of EP Toolkit. Mostly bug fixes and refinements. Note especially fix to calculation of difference and combination waves. Enhancement to Topos view of non-PCA files is helpful for looking for effects. Cheers! Joe 1) In Topos function, fixed peak samples of ERP data being identified by amplitude rather than absolute amplitude. 2) In Topos function, added display of topos at every 50 ms for ERP and TFT data and every Hz for FFT data for non-factor data. 3) Fixed Topos not allowing two datasets to be shown in parallel when they have different regional channels. 4) Fixed Topos crashing when trying to display factor and non-factor data side by side. 5) In Edit function, fixed combining of subjects and chans not correct when weights not the same (as in difference wave). 6) In Edit function, fixed weighting of difference waves for cells and chans and subjects incorrect (waves too small). 7) In Window function, fixed windowed files being labeled as being in dB even when voltage data. 8) In Channels subfunction of the Window Data function, fixed crash when applying factor loadings and there is more than one PCA dataset in the working set. 9) Wave plots can now accommodate datasets with different sets of channels. 10) In Scan function of View pane, fixed crash when using secondary datasets with differing fields, such as PCA and not. 11) In Scan function of View pane, fixed crash when right shifting the cell and a secondary dataset is already at the maximum cell. 12) Improved the controls for the Windowing pane. 13) Improved handling of channel groups in the Channels function of the Windowing pane. 14) In Topos function, added peak point/Hz line to expanded waveform windows. 15) Markers in waveform plots can be set at zero ms. 16) For saved files in ERPlab format, fixed fields ERP.ntrials.rejected and ERP.ntrials.invalid to be vectors of zeros rather than empty set (due Joseph Orr). 17) Accommodated change in Matlab 2013a’s userpath function that, at least on a Mac, can cause it to lose track of the existing EPwork directory. -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jd...@ma... Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com// |
From: Joseph D. <jd...@ma...> - 2013-05-15 23:24:17
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New release of EP Toolkit. Mostly improvements to reading data files, especially simple binary files (including important bug fixes to handling of average files). Also enhancements to windowing with peak measures and to manual editing of bad channels in the Scan function. Cheers! Joe 1) Scaling of topos now obeys the values on the View pane. Also, fixed manual changes to plotting range no longer working. 2) Fixed Simple Binary average files being scrambled when read! EP Toolkit now accommodates loose Simple Binary file format specification rather than make assumptions about its internal structure (there is no formal documentation on it). 3) Better handles ced files where there are channel types other than EEG, FID, and REF. 4) Fixed choosing "auto" as Edit Mode setting in Preprocessing pane resulting in error message. 5) Added option to average together samples around a peak to minpeak and maxpeak measures. 6) Implemented Luck (2005) suggestion to only count as a dip/peak a sample where both neighboring samples are higher/lower. 7) When there is missing data (more likely now with new peak measure code), the NaNs are converted to missing data code specified in preferences setting. 8) Fixed Read function where if baseline was zero ms then instead it was being reported as being 4 ms. 9) Fixed detrend button in Preprocess Data pane not working. 10) Fixed warning when trying to read in Neuroscan files with two physically linked explicit reference sites. 11) Added option to the Trials subpane of the Edit function to load a text file to rename the cell names of all the trials. 12) Added support for reading EGI's epoch-marked simple binary format for session files. 13) Added table to Scan function which lists %age of bad channels and allows channels to be marked globally good or bad. 14) Fixed Scan crashing if the scaling is from zero to zero, as with a bad trial. 15) Fixed automatic global bad channel detection being performed even when editMode set to Manual. -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jd...@ma... Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com// |
From: Joseph D. <jd...@ma...> - 2013-05-31 04:49:08
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New release of EP Toolkit. Mostly bug fixes for better supporting Neuroscan files and for a number of crashing bugs in the Windowing function. Note especially fix for windowing temporal PCA data as it would result in the measures being for the wrong channel! I'm not sure how that one got past me so apologies for any trouble it may have caused. Spatial and temporo-spatial (and spatio-temporal) PCAs are unaffected. Cheers! Joe 1) Fixed Single File Mode in Preprocessing pane crashing when values entered. 2) Fixed Single File Mode in Preprocessing pane crashing. 3) Fixed crashing when merging fixed channel files (like Neuroscan) where there are channels in the data that are not in the CED file. 4) Fixed single file mode single-trial data files not being merged successfully. 5) Added option to eliminate unwanted channels, as in a GFP channel, when reading in the data by marking the channel type as BAD in the CED file. 6) When merging files, as in Single File Mode, channels not present in the initial file simply dropped from succeeding files rather than aborting the run. 7) Single-Trial Files from multiple subjects can now be selected using the Read pane's Single File Mode and read in as separate files. 8) Fixed crash when loading in a channel group file for the Window function and there currently isn't any channel group defined. 9) Fixed crash when going into channel group subpane, cancel out without defining a channel group, and then return to the subpane. 10) Fixed crash when windowing using the minpeak or maxpeak measures with the adjoining samples option and the peak latency was at the upper end of the window. 11) Fixed crash when windowing and there are multiple channels in the area of a channel group. 12) Fixed crash during windowing when factors were used to define the areas of a channel group. 13) During windowing, fixed minpeak and maxpeak measures yielding missing data numbers when the window size was less than three samples, as in the autoPCA mode. 14) Fixed Export button on Edit’s Factors subpane not working. 15) When reading in text data files, multiple delimiters between values (as in space-space) now treated as a single delimiter. 16) Fixed output of windowing being for channel 1 rather than the intended channel for non-spatial PCAs (spatial and temporo-spatial PCAs not affected). -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jd...@ma... Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com// |
From: Joseph D. <jd...@ma...> - 2013-06-19 01:28:33
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New release of EP Toolkit due to serious bug affecting two-step PCA since 2.30. It shouldn't affect ANOVA results but will affect topographic maps or waveforms depending on whether the second step was spatial or temporal respectively, amplitudes of effects (but not statistical significance), and source analyses. My apologies. Thanks to Hiroshi Nittono for reporting the problem. Joe 1) Fixed bug introduced in 2.30 wherein variable standard deviations for two-step PCAs are applied incorrectly, resulting in inaccurate PCA reconstructions. ANOVA results should be fine but topographic maps and source analyses for PCAs where spatial was the second step will be affected, as will waveform plots when the second step was temporal. Thanks to Hiroshi Nittono for reporting this problem. 2) Fixed windowing pane crashing when Herz bins changed. -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jd...@ma... Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com// |
From: Joseph D. <jd...@ma...> - 2013-10-21 20:15:51
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New release of EP Toolkit. Mostly a maintenance release. It fixes a number of bugs, especially in the Channel Group function for performing windowing. Note especially the fix for the feature of using PCA results to choose channels for windowing. It also expands support for EEGlab, ERPlab, BDF, and MFF file formats. The MFF file format is still a work in progress and I am working with EGI and FieldTrip folks to get full support working in Matlab. There was also a lot of work on plumbing behind the scenes to get ready for upcoming features. Please be sure to let me know if any of these revisions has broken a function or if you have any feature requests. Cheers! Joe 1) Fixed dipole analysis in Topos function crashing due to changes in FieldTrip. 2) Fixed crash in Read pane when segmented simple binary session file is incorrectly specified to be an average file by the user. 3) Fixed combining channels into Regional Channel in Edit function or from windowing results in flat waveform. 4) Fixed View crashing if none of the data have electrode coordinates available. 5) Fixed Change Work Directory menu function not working. 6) Initializes mff file support at startup so that it doesn’t crash the toolkit down the line as workaround for Matlab bug. 7) Modified so panes fit on screens with less than 700 vertical pixels. 8) Fixed overview subpane of Edit function graying out number of factors. 9) Fixed not making factor data available for setting channel groups in windowing function when first in analysis set had different number of channels. 10) Fixed not asking for channel group name in windowing function when creating a new one via factor loadings and is currently the initial blank one. 11) Fixed not updating the display of the area names when using factor loadings to define the channel groups in the windowing function. 12) Fixed when using factor loadings to define channel groups in the windowing function, area names not reflecting factors defining them. 13) Fixed when using factor loadings to define channel groups, wrong channels could be chosen. 14) Worked around crash when reading mff files under Matlab 2013b by using alternative mff file format function. 15) When reading file, fixed incorrect inference of reference scheme when a single ref channel is designated. 16) When reading a file, fixed channel type not changed from REF to EEG for flexible channel order file formats. 17) Fixed REF channels assumed to be last for fixed order channel file formats. 18) For reading files, better support for MEG and ANS chan types, and BAD CED code. 19) Added support for mff files with recording stops and with segments. 20) Added support for boundary events (for continuous data where recording was stopped and then restarted). 21) Workaround for EEGlab issue where if a CED file has just the label and the type filled out, the type info migrates over to the theta column for some reason. 22) Changed event sample to count from start of epoch rather than FieldTrip convention of start of recording. 23) Improved detection of Simple Binary files with scrambled cells. 24) Fixed preprocessing function not finding files past the first when batched and they are not in the active directory. 25) Fixed PCA of continuous data generating error message. 26) Full support for ECG channel type. 27) Fixed Read function rejecting files if sampling rate and time names different past three decimals due to rounding errors. 28) Fixed crash when reading EEGlab file if cell names are a mix of numbers and strings. 29) Fixed crash when reading file if type field from CED file contains numbers for some reason. 30) Added recTime field to keep track of recording time of an epoch with respect to the start of the recording session. 31) No longer rearranging single trial data to group by cell. 32) Eliminated offset field from events structure. 33) Fixed topoplot not showing the correct peak channel for non-factor data. 34) Better updating of history field. 35) Added display of trial specs to Scan function. 36) Fixed one-second epochs displayed with View function one sample longer than intended for continuous data. 37) Made a number of fixes to exporting of single-trial data in EEGlab format as it wasn’t working. 38) When reading EEGlab single-trial data, rejected channel and trial information is included. 39) When reading and writing ERPlab files, nTrials information is supported. 40) When reading ERPlab files, channel location information is supported. 41) Ensure that power field comes after analysis field to avoid crash in functions like scan when looking at multiple EP data files. I’ve also committed changes to the FieldTrip I/O to fix problems with trying to load simple binary files (unsegmented files being treated as segmented, crash when simple binary file has no event track, and crash when there are event tracks but no events marked) and mff files (Matlab bug causes global variables to be erased crashing the toolkit and not computing event times correctly and not registering multiple segments correctly and not including events only within period of the epoch and not separating the trials of segmented data and adding better support for segmented files) so the FieldTrip copy should be updated to 10/15/13 or later. Currently, mff average files cannot yet be read. I’ve also reported a bug in EEGlab (still present as of 12_0_2b5) that has been affecting CED files. CED files created with pop_editChans, as described in the tutorial, are defective (the columns are scrambled). If you use this function to create a CED file, check the resulting file using a program like Excel to make sure that the columns are in the right place with respect to the headers. If they do not match up, then move the columns so that they do. The order of the column headers is correct so do not move the column headers, just everything below the headers. -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jd...@ma... Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com// |
From: Joseph D. <jd...@ma...> - 2014-03-23 22:19:06
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Mostly bugfixes to squash bugs caused by recent changes to the internal plumbing of the Toolkit and further refinements of existing features. Also, improved support for reading MFF files, initial support for reading and writing FIFF files, new trimData function to graph and delete unwanted portions of continuous data prior to segmentation, new option to overplot all the trials or all the subject averages using the View Waves function, and new option to plot all the trials or all the subject averages using erpimages. 1) In Scan function, fixed showing bad channel markings for first cell regardless of the currently displayed cell. 2) Fixed crash in saccade correction when there is more than one bad channel. 3) Fixed crash when reading mff file with more than one subject field. 4) Added workaround for Matlab bug which has been causing screen size to periodically register as being zero. 5) Fixed crash when stripping off single factors from combination factors, as in the Save function. 6) Fixed crash when trying to topoplot data where electrode coordinate information is present but all coordinates are missing. 7) Added option in Edit function’s Overview subpane to load in new electrode coordinates. 8) When reading in boundary events in mff files, duration field contains the length of the recording pause. 9) Added Trim Data option to the Segment Data function. 10) Fixed crash when non-Mac user tries to open mff files by selecting a directory that does not contain any mff files or selects the mff file itself. 11) Fixed crash when running a two-step PCA on a PCA file generated prior to version 2.40. 12) Fixed aborting PCA when factor loadings slightly over 1 due to rounding errors. 13) Fixed crash when reading ced file with REF channel type indicated. 14) Fixed crash when using View with TFT data. 15) Fixed crash when trying to plot frequency data in Topos with dB scaling where the power equals zero. 16) Added View function option to plot or erpimage all trials and all subjects. 17) pca no longer optional field for EP file format. No fields are optional. 18) EP file fields now have standardized ordering to fix crash in Scan function when looking at files with different orderings. 19) Fixed crash, as in scree plot, when a file has different types of adds in a category (e.g., GAV and AVG in subjects) 20) Fixed PCA not correctly recognizing that a file has already undergone two-step PCA. 21) Fixed subjects subpane of Edit function specifying average subject type as being AVE rather than AVG. 22) Fix for not properly adding new blinks to the template for single trial data. 23) Fixed REF channel type not being changed to EEG for files with one reference channel, resulting in some continuous files not being made available for forming blink templates. 24) Fixed crash for EGIS average files with custom cell header lengths. 25) Fixed when using single file mode to read in single-trial files, all the resulting files are identical to the very first subject. 26) Handling decimal sampling rates more gracefully. 27) Changed MEG channel type to MGA (axial gradiometer) and MGP (planar gradiometer) and MGM (magnetometer). MEG support still not ready. 28) Fixed crash when reading mff file with subject field where the field was left blank. 29) ced label for electrode coordinates provided by file (e.g., eeglab, MFF, FIFF formats) is "internal”. 30) Added support for reading FIFF files. It's a pretty complex file format so this is only a first-pass implementation. 31) Eliminated file type check for EGIS files since NetStation generates average EGIS headers that are incorrectly marked as being session files. 32) Uses internal electrode coordinates provided by MFF and FIFF files and added preferences to automatically rotate such electrode coordinates to face upwards if needed. 33) Improved saving data in text format so will check for overwriting and for FFT data will save as freq by chan. 34) Added support for writing Neuromag FIFF file format. It's a pretty complex file format so this is only a first-pass implementation. 35) Changed uses of "temp" as a variable name to "tempVar" due to other Matlab programmers often using it as a function name, resulting in collisions. 36) Fixed crash when using "all" channels option in Windowing function and no channel groups have been defined yet. 37) Added ability to window single-trial data. 38) Fixed crash when editing cells using the Edit function. 38) For PCA files, fixed recTime field not including space for the 'all' cell, resulting in crashes when edited. 39) Combining of factors in Edit function now done as simple addition rather than as averaging. 40) Fixed error if adding a factor combination to a PCA file with no combined factors. 41) Windowing outputs cells in actual order rather than alphabetical order. 42) Eliminated noTable option for old versions of Matlab. 43) Fixed crash when segmenting or previewing. 44) Fixed segmenting table + button mirroring the first line of the table rather than the current settings above the table. 45) Fixed segmenting table - button deleting all but second to last line rather than just the last line. 46) The events 'SESS','CELL','TRSP','bgin' are not excluded from being displayed for continuous files in the Display and the Scan functions when the evt option is checked, only for single-trial and average files. 47) Fixed crash when appending channels in the Edit function. 48) Fixed all but one channel is flat for grand average combined factors, as in the "all" factor from PCAs. 49) Fixed all but one channel is flat for combined cells if one already has a combined factor, as when one uses the Edit function to combined cells on a factor cell containing an "all" cell. 50) Fixed waveforms added during ANOVAs to correspond to trimmed cell means being all flat. 51) Average numbers, trial specs, and events carried over to the PCA file. I’ve also committed changes to the FieldTrip I/O to fix mff files generated by NetStation 4.5.4 as they have nanosecond timing rather than microsecond timing and to fix a crash when there are no events in the user markup track. I’ve also made a fix to FieldTrip to fix a crash when loading in an EEGlab .set file with no events, so those wishing to read mff or EEGlab .set files should update to 1/31/14 or later. -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jd...@ma... Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com// |
From: Joseph D. <jd...@ma...> - 2014-03-30 06:27:06
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Some stragglers that missed the 2.42 release. I’m about to make some substantial feature additions and wanted to get these in before I start making more changes to the internal architecture of the Toolkit. Cheers! Joe 1) Adds mne toolbox to the path to avoid crashes when reading or writing FIFF format files. 2) Fixed crash when loading file type that has internal channel names (like Neuroscan) and the only mismatch between it and the ced file is a single implicit REF channel or there is no mismatch and there is a single explicit REF channel. 3) Added .cov field to hold the channel covariance matrix generated during averaging for later inspection regarding channel quality. 4) Fixed when loading in a new file that had the same name as multiple existing files, appending dashed number to prior dashed number instead of replacing it (e.g., "name-1-2”). 5) Fixed crash when running an ANOVA on a PCA dataset results in trimmed cell means being added to it. 6) Fixed crash when selecting time points and there are empty event cells. 7) When the dataset name has been changed on the Overview page, Edit will ask if the unedited dataset should be kept in addition to the edited version when Done is pressed. 8) Further improvements to writing out FIFF format files. -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jd...@ma... Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com// ------------------------------------------------------------------------------ Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech _______________________________________________ Erppcatoolkit-support mailing list Erp...@li... https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support |
From: Joseph D. <jd...@ma...> - 2014-08-13 02:27:20
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New release of EP Toolkit. Some highlights are: upgrades to the filtering functionality, support for BrainVision EEG files, sample-by-sample analysis, latency-locked and jitter-correction averaging, improved EEGlab .set file format support, improved mff file format support, added option to explore rereferencing effects in Topos view, added PARE-corrected average referencing to Transform function. 1) Fixed crash when performing combination of subjects with file containing .cov information. 2) Added -all- and -erpimage- options to the Factors list in View. 3) Fixed keys field of events not being added when missing, resulting in EP files created by older versions of Toolkit not being readable. 4) Fixed crash when there are multiple global and trialwise bad channels. Apparently Mathworks changed something again in recent versions of Matlab. 5) Fixed crash when running artifact correction on an average file with multiple subjects. 6) Fixed problem where under some circumstances the files after the first of a batch could not be found by the Transform function. 7) Fixed not putting factor variance information in correct location when loading PCA .ept files, resulting in "There are 0 factors that meet the minimum variance criterion" error messages when trying to autoPCA them. 8) Fixed AutoPCA generating nothing but missing data values when maxcentroid and mincentroid measures chosen. 9) Fixed crash in View when overplotting two sets of data where one has regional channels not present in the other. 10) -all- and -erpimage- options in View leave out adds if lower levels are present (e.g., for subjects, leaves out grand averages if individual subjects are present). 11) Fixed weighting not correct when computing difference waves that do not sum to zero (not sure why anyone might do this but fixed just in case). 12) Fixed calculation of the SubNum field (number of subjects going into averages) when combining cells. 13) Based on additional information from the MNE community, made some corrections to how the covariance matrix and the effective sample size are calculated, for when generating FIFF files. 14) in Topos function, for finding peak channels and points and Hz, uses only the first dataset as the index for this. 15) Fixed crash when replacing bad channels in an average file and a cell is bad. 16) Allows choosing either Hanning or multi-taper methods for spectral measures. 17) Eliminated upper bound to smoothing in multi-taper frequency measures as no longer seems to apply. 18) Fixed 'all' option for Window Data leaving out last channel. 19) Repair referencing after performing artifact correction to support performing analyses on unreferenced data, as in spectral analyses. 20) Added conversion of REF channel type to EEG for older EP files, which can otherwise result in various reference channel problems. 21) Added ability to perform PCA on datasets with bad data. 22) FacScr observations are now always arranged with permutations in order of the seven data dimensions. PCA files made prior to 2.44 cannot be used for two-step PCA. The first step will need to be rerun. 23) Fixed minimum and maximum values for spectral PCA datasets not being calculated corrected when using View functions. 24) Fixed not able to load in EP files with frequency PCA data. 25) Fixed crash when changing pages in Topos view with frequency data. 26) Fixed 2D expanded head plots for Topos view for frequency data. 27) Fixed jack-knife test possibly conducted on wrong factor or just crashing in Topos view. 28) Fixed rescale option for frequency data in Topos view. 29) Fixed when spectral range changed in View function and dB or psd options are on, the values are immediately further transformed. 30) Fixed crash on last page of topos for frequency PCA data. 31) Fixed crash when saving edits in Scan function. 32) In the Scan function, fixed all subjects shown as having a bad cell if the first subject in an average dataset has a bad cell. 33) Fixed peak latency of factors expressed as one sample too late in the Edit function. 34) Added legend to wave plots. 35) When using factors to set channel areas in the Window function, can now specify whether to use largest absolute, negative, or positive loadings. 36) Will no longer keep resetting the factor loading threshold back to the original number in the Window function. 37) Fixed crash when running an ANOVA on a windowed text file generated by autoPCA and the adds option is on. 38) Fixed minimum and maximum voltages in View pane not reflecting correct values for single trial data. 39) Added support for reading BrainVision EEG files. 40) Fixed crash in blink template function when frequency or factor files are present by excluding them entirely. 41) Fixed blink template waveform plot not adjusting to new length when switching datasets. 42) For blink template function, fixed marker for blink and saccade not placed at correct latency after switching between datasets with the same number of samples but different baselines. 43) Fixed crash when loading an ept file with no theta values for the electrode coordinates. 44) Fixed crash when there is more than one bad channel and the reference is mean mastoid. 45) Fixed crash in saccade correction due to bug introduced in last version. 46) Fixed crash when the ced file has no type field. 47) Fixed crash in topoplots when there are electrodes without coordinates. 48) Allow for manual windowing of PCA files rather than just autoPCA. 49) Fixed list of trials for single-trial data in View pane not correct. 50) Added simple averaging of trials in Edit function's cell subpane for single-trial data. 51) In preprocessing, if current reference not specified, default to original reference. 52) Fixed blink and saccade correction in Preprocessing function could issue false error that template had wrong number of electrodes. 53) Fixed crash in Preprocessing function when correcting blink or saccade in continuous file. 54) Fixed crash in Preprocessing when there are multiple chunks and some have blink factors and some do not. 55) Fixed crash in Preprocessing function when replacing bad channels in continuous data. 56) Transforms can be applied to non-EEG channel types and which data mode can be specified. 57) Fixed crash when filtering continuous data and there are no boundary events present. 58) Fixed blank keys event fields being created without a .key after the keys level. 59) Added "starts", "ends", "contains", and "follows" keywords to Segment function. 60) Fixed Edit function reordering cells in single-trial data when anything clicked or changed in the Cells table and they were not already in alphabetical order. 61) Added support for sample-by-sample, CWT, and Woody Filter PCA comparisons using both non-parametric t-tests and jack-knife tests (including addition of STS chanType). 62) In Edit function, fixed deleting wrong cell of single-trial data when cells were not in alphabetical order. 63) Added support for SMI eye-tracking data to be merged with EEG data. 64) Added latency-locked and jitter-correction averaging options. 65) Fixed cov.Nq field (used for FIFF file format support) not being formed correctly when combining subjects, resulting in crashes later on. 66) Fixed subject selection not being applied to .cov.Nq field (used for FIFF file format support), resulting in crashes down the line for combined subject average files. 67) Added fix for crash when trying to read mff files that erroneously label their COM channel as being a reference channel. 68) Fixed crash when saving file with an empty .keys field in EEGlab .set format. 69) Added additional filtering options, including one-pass causal filters and order settings. Also providing graphs of effects of filtering on the data in the frequency and temporal domains. 70) Simplified event keys field structure. 71) Fixed labels for REG channels being blank when saving EEGlab .set format files. 72) For single_trial data, the event latency values now conform to "for epoched datasets the event latencies are also encoded in sample points with respect to the beginning of the data (as if the data were continuous)". http://sccn.ucsd.edu/wiki/Chapter_03:_Event_Processing rather than being in terms of the beginning of the original continuous data. 73) Fixed adding 'trigger' events if they are already present. 74) Fixed epoch event field in saved .set files referring to trial number from complete dataset rather than in terms of the EEG file (the one condition). 75) Fixed urevent event field in saved .set files reflecting event numbering of full dataset rather than just the one condition in the EEG file. 76) Fixed sometimes adding too many epoch entries when exporting single_trial .set files, resulting in aborted export process. 77) Handles better situation where a field of an event is empty. 78) Fixed bug where windowing of spatial PCAs of ERPs and temporal and spatial PCAs of spectral data started with first sample of the epoch rather than the sample specified. 79) Fixed crash under some conditions when selecting points from a continuous file, as when using the trimData function. 80) Fixed only first event sample being updated when points selected from continuous data, as in trimming data. 81) Fixed boundary events falling on edge of selected time range not being deleted. 82) Fixed edits in trimData function not being saved when clicking on "keep". 83) Fixed crash in blink Template function when the dataset contains a boundary event. 84) Further improved mff file format support. 85) Adds, like blink and saccade channels, are stripped out of preprocessed data if the output file format is not ept. 86) Fixed crash in Edit function when reordering subjects. 87) Fixed .cov.Nq not being updated when stripping off subject adds, resulting in error messages. 88) Fixed CSD option of Transform crashing. 89) Fixed crash when median averaging frequency-domain data. 90) Fixed Topos function not displaying frequency-domain data. 91) Added option to explore effects of rereferencing to View Topos function. 92) In transform function, setting std field to empty rather than trying to rereference. 93) Added PARE-corrected average reference option to the Transform function. Cheers! Joe -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jd...@ma... Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com// |