[Erppcatoolkit-support] ERP PCA Toolkit 2.42 release

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

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.

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Joseph Dien,
Senior Research Scientist
University of Maryland 

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