EEProbe release info version 3.3

June 2005 - Release version 3.3

• cntscd (surface current density - laplacian transformation on continuous data)

[TODO] scaling factor to correct for too small values.



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EEProbe databrowser

• added support for Mac OS X ...
  
• ... related code changes for Darwin compatibility, correct key-bindings (shortcut keys)
  
• added alternative editor (can be used with Shift key, while double-click or Enter on file(s))
• new dialogs provide interface to Hilbert transform (cnthilbert), and Laplacian (cntcsd)
• Tools -> Trigger tools -> changed trigger recoding to allow true search and replace of only one trigger (leave empty the 2nd trigger)
  
• added some 'plugin' scripts (available in /opt/eep/share/eep/scripts):

• default average-process template/script
• burstdetection (based on rejection criteria in e.g. an EMG channel)
• trials2bin2cnt (creation of an epoched cnt file, possible to review EOG corrected trials)
• per-channel-process (script to perform rejection/averaging per channel, at the end combined in one AVR file)
• TMSreject (rejection of stimulus artefacts - based on a trigger code, a small part of the signal is omitted in the resulting cnt file; the original triggers are again inserted at each discontinuity)
• average-to-ascii *) (template/script allows continuous scanning, on-the-fly conversion of avr to ascii)
• ps-to-pdf *) (template/script allows continuous scanning, on-the-fly conversion of ps to pdf - requires ImageMagick)

• *) added possibility to run scripts in separate shell (terminal)
  
• new defaults for exports in settings file
• new defaults for correct significance values (0.05, 0.01, 0.001) in xavr*.cfg files
• a new "Scripts" menu, now arranged by type (e.g., templates, shell scripts, awk scripts). The sub-menu for the templates (Run, Edit) is deleted in this version. The templates now always start in the "Edit" mode; the "Run" mode is enabled from the template dialog.
• holding <Shift> with <Double-click> (or <Enter>) on a CNT file, will always start the alternate continuous viewer - an easy switch between qcnt and xcnt, allowing both to be the default setting (Tools -> Databrowser Settings)
  
• bug fixes

• avrstats
• added option to write t-scores (previously only p-values available)
• cntview
• added support for listing of "recording info"
• cntcsd
• NEW program creates Laplacian transformed CNT data
• avrstrip
• always creates AVR file in 'old' format, without history information

Viewers

EEProbe release info version 3.2

February 2004 - Release version 3.2-4

New in this release are Beta (test) versions of the following programs:
• cntspectrum (Fourier transformation - single trial FFT averaging)
• bdf2cnt (BDF data import)
• the new cnthilbert is still in Beta

This release contains some updated functionality in - and related to - the EEProbe databrowser:

• avrview, cntview: license removed
• support for the STANDARD Rejection keyword (cntaverage, cntspectrum)
• a progress indicator for Grand Averaging, Amplitude Retrieval, Peak Detection
• a minor bug fix for the Channel Selection dialogs (sometimes not showing the "Datafile" labels)
• AvrRetrieve: further support for the avrretrieve options --avr and --err.
• AvrRetrieve (amplitude extraction / peak detection): fixed output generation when boundary warnings occurred.
• extended version information available under Help -> About EEProbe... (version of databrowser synchronised to main EEProbe version).

Other Changes are:

• The qcnt viewer as well as the trged program (Trigger/response validation) have been updated to support "classified trigger files" (as created using the xeog).
• The bv2cnt converter now also reads DOS-style *.vhdr files.
• The avrprocess program now supports "compromised" grand averaging mode. In this mode the grand average can be build using all channels from the input files (normally restricted to common channels).

January 2004 - Release version 3.2-2

Release 3.2-2 is only a minor update from Release 3.2-0. This release incorporates a Beta (test) version of the new cnthilbert program (also supported in the databrowser):
• cnthilbert (Hilbert transformation - envelope calculation)

Other fixes are only related to small installation problems.

December 2003 - Release version 3.2-0

This version of the EEP programs is partly a bug-fix release from version 3.1, and incorporates the combined code of MPI and ANT Software.

Some new features have been added:

• license
• cntcheck
• trged (support for time restriction - e.g., for response time validation)
• xavr (support for components display - peak scoring)
• sigv2cnt
• trials2v
• trials2asc
• trials2bin
• bv2cnt
• bin2cnt
• edf2cnt (EDF import and export now supports EVENTS channel)
• egi2cnt
• avr file history
• avrstrip
• mex functions for Matlab 6.0
• a new Qt-based continuous data viewer
Notice that the file formats are not fully compatible to the previous version 3.1 of the EEP package. Of course, the programs of version 3.2 are able to read and process version 3.1 files. But it is not advisable to process version 3.2 files with version 3.1 programs!

The DOS versions of some EEP 3.1 programs are no longer maintained.
The EEP tools for Octave and the program cntfilter_mp are currently not available.
The converter programs

bti2riff and refa2cnt

have not been recompiled.

The following changes/fixes have been made to the programs listed:

General

• license
  The exclusive right to distribute the EEP software is with ANT Software B.V.. Therefore, it is necessary to generate a license key for each MPI PC/workstation intended to run the EEP programs. The keys are stored in the central license file /usr/local/share/eep/license/license.rc on the MPI application server. The user must export the environment variable EEP_LICENSE pointing to that file. (If you are using the bash shell, add the line

  export EEP_LICENSE=/usr/local/share/eep/license/license.rc

  to your .profile or .bashrc in your home directory.)

• revised memory allocation routines
• fixes in decompression routines
• fixes in trigger handling routines --> using trigger codes of up to 8 characters is safe now
• changed scaling limits: allow 32 bit sample range (riff-cnt resolution; previously 22 bit)
• adapted to handle SCAN 4.1 NeuroScan SynAmps format (16 bit channel multiplexed)

• other minor changes

File Formats

• cnt files
  revised file history; use cntview to show the history

• average files
  An ASCII file history was added to the .avr files with the intention to ease the identification of average files and the reproduction of experimental results. The history contains information about the exact processing chain. Use avrview to show the history. But do not rely on the file history for documenting the processing steps. Keep on saving and archiving the protocol ouput generated by the EEP programs and make a log of additional information if necessary.

  Compatibility issues

  Although the file history was introduced compatible to the avr format of version 3.1, the EEP 3.1 programs are broken since they do not access the binary data via the file offsets saved in the header but do falsely rely on a fixed header size. Thus, if you want to exchange your average files with a colleague who is using version 3.1 of the EEP tools or who is using a version prior to 3.1-9 of the commercial version (EEProbe) you must discard the history from your ".avr" files. Use avrstrip to get rid of the file history, in that case. But act with caution and avoid ending up with incomplete history entries in your average files.

  The programs from the Perl Utility Collection aren't broken, as far as I can see. Currently, they simply ignore a present history. Full history support will be implemented later.

Converters

• cnt2asc
  • added channel selection (via command line or configuration file)
    Note the changed syntax of the configuration file with respect to a previously released version!

• ns2riff
  • modified to convert SCAN 4.1 SynAmps files into the riff-raw3 format
    ns2riff_NT obsolete
    Note the differences in the DC correction / DC-reset trigger shift between SCAN 3.x and SCAN 4.1 cnts!
• raw2cnt
  • fix for 32-bit cnt data format

Signal processing

• avraverage
  force max. 2-char condition labels and max. 4-char channel labels
  (abort with an errormsg if the labels are too long)

• avrprocess
  • fix in "-l" mode (user patch for condition label)

• avrretrieve
  • updated version of data output function:
    if an extremum is found at a window boundary (--min / --max mode), log these values and print a warning

• cntaverage
  • baseline rejection search introduced (cfg section "Bsl Rejection")
    You may now define two independent rejection search windows, one of them locked to the condition trigger, as usual, the other locked to the reference trigger. This is of advantage especially in the case of reference displacement.
  • print a warning if baseline and/or averaging window exceed the rejection windows
  • fixed buffer overrun in output filename build

• cntdown
  • fixes in type errors and trigger handling

• cntreject
  • added cfg option "DC-Reset interval"
    The specified time window with respect to each DC-reset trigger is marked rejected.
    cntreject_NT obsolete

• cnttrials
  • bug fix in classification: BLINK/MOVE confusion resolved

Viewers

• xavr
  • fixed buffer overruns
  • added file history stuff (revision of history entries still under process)
  • added components/peaks stuff

• xeog
  • bug fix: BLINK/MOVE confusion resolved

• xcnt
  • channel selection dialog now accepts a list separated by commas and/or whitespaces
    (still accepts regular expressions)
  • fixed scaling limit: 32 bit range (previously 22 bit)
  • added support for changing trace colors interactively (via Legend: use the mouse to click on the channel label)
  • updated time scaling behaviour: e.g., change the page width in the 'Window, Length(sec)' field
  • now provides correct default names when saving .trg .rej files
• qcnt
  This viewer has been developed after the xcnt viewer, but has been totally re-written using the graphics library Qt, instead of Motif.

  User documentation is not ready at this time, however a brief summary is provided here:

  • General usage information:
    • The command line usage is almost identical to xcnt
    • Not implemented yet: filtering
    • Automatically finds qcnt.cfg channels.cfg in ./, ./cfg, ../cfg, ../../cfg
      (qcnt.cfg identical to xcnt.cfg - except for [options] section, is not supported)
      (channels.cfg identical as for xcnt -G option)
    • Automatically creates/uses options in ~/.eep/qcnt.resources
  • New features in this viewer:
    • Open files from menu, shows brief file info, and .trg .rej .cfg file location
    • Screen calibration (Edit menu, Preferences)
    • Time resolution in sec/cm or mm/sec (Edit menu, Preferences)
    • Toolbar includes Amplitude scaling, Time resolution
    • Vertical scrolling of channels:
      increase channel separation for high-density EEG (via toolbar button)
    • Automatic scrolling
    • Signal values listing for all channels at the same time
      (Right-click menu in Channel Legend)

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March 2003 - EEProbe release info version 3.1a (release 3.1-9)

Updates for viewers, new converter programs, small updates in signal processing programs.


New installation procedure:

• Installation support for "rpm", "tgz"
• Standard installation includes the EEProbe Databrowser
• Not using architecture dependent directories anymore (/opt/eep/bin/Linux is now /opt/eep/bin)
• Installation update of user environment:
  • automatic through shell-inclusion of /etc/profile.d/eep.sh, or
  • using a single statement "source /opt/eep/scripts/setEnv.sh" in the user's .bashrc


Updated PDF versions of manuals (see Pdf sub-directory):

• EEProbe Reference manual (same as HTML on-line help)
• Completely revised EEProbe "Getting Started" manual (EEProbe & EEProbe Databrowser)
  • contains: contents (bookmarks), clickable hyperlinks (e.g., contents, references, page numbers)
  • all screenshots in png format available on installation CD

Scripts

Standard interpreter locations:

• /bin/bash
• /usr/bin/perl
• /usr/bin/awk

Please see the on-line documentation for details on:

• trgcount, trgisi, trgvalid, trgselect
• cntextract

New available in the /opt/eep/scripts directory:

• generate3Dpos.awk, ev2trg.awk

Small fixes in the perl scripts:

• asa2avr, asc2avr, avg2avr, avr2asa, avr2avg

Converters

The following converters have been added or updated:

edf2cnt, cnt2edf	implementation of the standard European Data Format includes EVENT channel as input/output
bv2cnt	BrainVision importer
dig2cnt	DIG importer - University of California San Diego
pegasus2cnt	updated to convert also the patient information to .info.txt

cnt2asc

• allow output file specification (if not specified, data is written to stdout - as in previous version)

avr2asc

• allow output file specification (if not specified, data is written to stdout - as in previous version)
• new option "--msec" writes a first column of time values (useful when loading in spreadsheet program)

Signal processing

cntcat

• new version allows to create internal triggers based on external trg input

cntfilter

• added "-x" exclude channels switch
• modified command line switches to be identical to cntsetup, avrinterpol ("-c" still works, identical to "-i")
• added option "-d" to remove large DC offsets

Viewers

xcnt

• Interactively change the screen color of a signal trace via the Channel Legend dialog
• The names of trg, cfg, rej files loaded are now automatically available in the File, Save.. dialogs

xavr

• new "Scaling" dialog for amplitude (maps, diagrams), time manipulation (diagrams only)
• re-implementation of "Signal Values" dialog: can be accessed always, not only through Vector Browser
• new implementation of "Components": perform peak scoring in Signal Inspector, display peaks in main screen
  (requires a [components] section in the xavr display configurations - see the on-line help)
• updates in installation file 3.1-9b (final release):
  • command-line loading of .avr now allows 200 files (previously only 20)
  • "Scaling" dialog: improved behaviour of amplitude, time scale adjustment

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Nov/Dec 2002 - EEProbe release info version 3.1a (release 3.1-8)

ANT Internal test release - released only for a few customers.

Used for new installations on complete Linux acquisition/analysis systems delivered by ANT.

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Feb 2002 - EEProbe release info version 3.1a (release 3.1-7)

Minor changes, includes all previous updates.

Converters

avr2asa

• version 3.3 only writes basename on 'Values' line (in header file .msr)

Licensing

binaries in /opt/eep/bin/Linux/*

• fixed bug in external key-lock library

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November 2001 - EEProbe release info version 3.1a

This release is linked again with GLIBC 2.1.3 and fixes related problems and includes all previous updates.

Converters

egiraw2cnt

• version 1.3 included in standard installation file.

Signal processing

cntreject

• Fixed bug related to channel names uppercase/lowercase. In general, for processing names are *not* case sensitive.

Viewers

xcnt

• separate license possible for acquisition stations

xeog

• '-a' option works again (had problems in release update 5 - Aug 2001)

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August 2001 - EEProbe release info version 3.1a

This is mainly an update for the installation file.

Scripts

avr2asa, asa2avr, avr2avg, avg2avr, pasteavr, xtrctavr, trgmod

• These scripts are now installed together with the other EEProbe tools. Type any of the above commands to see the usage information.
• The scripts expect the 'awk' and 'perl' programs in the following locations: /bin/awk and /usr/local/bin/perl respectively. If needed, make a symbolic link for the perl program by typing the following command (as 'root'): ln -s /usr/bin/perl /usr/local/bin/perl.

Viewers

xavr

• more that 4 configuration files allowed (max 25)

Converters

avr2asc, cnt2asc, eep2riff, raw2cnt, riff2eep, sig2cnt, wasc2cnt, wg2cnt

• removed license check.

ns2riff

• small but significant modification to convert correctly SCAN 4.0 NS SynAmps cnts

Licensing

licinf

• support for external key-lock (serial port)

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January 2001 - EEProbe release info version 3.1a

This version of the EEProbe programs is mainly a bug-fix release from version 3.1.

The following changes/fixes have been made to the programs listed:

Converters

cnt2asc

• added channel selection from channel file

ns2riff

• modified to convert SCAN 4.1 NS SynAmps-Files to RIFF-raw3 format
• DC-reset trigger shifted by 70ms with SCAN 3.x
• by 80ms with SCAN 4.1

raw2cnt

• fix for 32-bit cnt data format

Signal processing

avrretrieve

• updated version of data output function:
• if an extremum is found at a window boundary (--min / --max mode),
• log these values and give a warning

cntaverage

• (fix in parameter printing)
• updated version of baseline rejection search
• (needed in case of reference displacement)
• updated function check_reject_window_settings
• (logs a warning if baseline and/or averaging window exceed the rejection windows)

cntdown

• minor update: small fixes in type errors

cntreject

• adapted for handling NeuroScan 4.1 cnt files
• added cfg option DC_Reset interval

cnttrials

• bug fix in classification code = {"u", "m", "b", "r"} -> {"u", "b", "m", "r"};
• - log baseline rejection-search window
• - log baseline reference triggers
• This becomes important when using reference displacement in average calculations.

Viewers

xavr

• minor fix channellabel display (previously restricted to 15 chars)

xeog

• bug fix: BLINK/MOVE confusion resolved

xcnt

• Channel selection now accepts a comma-separated (or white space) list
• - still accepts regular expressions

General

• revised memory allocation routines
• revised version of compression routines
• changed scaling limits:
• - don't restrict to 22 bit sample range
• - allow 32 bit sample range (cnt-riff resolution!)
• adapted to handle SCAN 4.1 NeuroScan SynAmps format (16 bit channel multiplexed)

• other minor changes

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EEP 3.2 - Maarten van de Velde (eeprobe@ant-neuro.com), last update: 19/02/2004
Copyright © 2000-2004