[Master Index] [Index for Toolbox]

# readme

## (Toolbox/readme.m in BrainStorm 2.0 (Alpha))

### Help Text

    README - What's New in Each Revision of BrainStorm 2.0 (Alpha)

     By it's very nature, Alpha development/revision is not as controlled as later
     versions. Below are approximate comments as to what we are improving in each
     version

     02-Nov-2004

     Fixed bug in the CTF loading routine. Tested the warping of the EEG
     electrod array to the Montreal phantom surface.

     12-Oct-2004

     Summer months spent quietly making numerous improvements and bug fixes.
     Several new additions to the inverse routines. LCMV Beamforming now
     added, with noise significance scaling. The linear MMS ("min norm") now
     also offers noise scaling. EEG loading for Neuroscan and EGI manufacturer
     types added, and the EEG routines tested. "Landmarks" are now treated
     separately from Channels, and both types can now be used to warp a
     surrogate head to the desired head shape. The BEM routines continue
     testing. The primary problem is a "garbage in garbage out" occuring when
     "reducepatch" is used to decimate a dense tesselation, resulting in poor
     surfaces. Better routines are under study.

     20-July-2004

     - Data import:
     For better interchange with BrainVisa software (see
     http://brainvisa.info) :
      -> New MRI format import filters include GIS MR format
      -> New Tessellation format import filters include MESH

     12-July-2004

     - Data import of BESA and Neuroscan average EEG files is now operative:
     Access is through DataManager -> File -> Import Data -> Pick-up a Data
     Format
     Electrode locations can be read from multiple file formats:
          '.elp' simple BESA ASCII format
          '.dat' NeuroScan for BESA electrode format
          '.res' NeuroScan for Curry format
          '.sfp' ZEBRIS ASCII format
     [Thanks to Felix Darvas: SIPI/USC]

     09-July-2004

     - Data averaging within a study is now operative:
     Access is through DataViewer -> Basic Processing -> Average
                       Select data files within current study folder
                       Enter a value in ms for acceptable time-jitter about
                       some time-locked event (default is 0)
                       Selected data files are then averaged, with adaptation
                       of time window if original data don't have same lenght
                       or time limits and stored in a BrainStorm data file
                       within current study folder.
     - Data filtering is now operating again (-> Matlab Signal Processing Toolbox is required):
       Access is through : DataViewer -> Basic Processing -> Filter
                           A new GUI is created and offers the possibility to
                                     - bandpass filter data using a zero-phase filter
                                     - for EEG : move to average-reference potentials, once bad channels were removed
     - Fixed bug when importing from CTF markers: some time clipping may occur
     when requested time window about a marker occurence would end up having
     an edge outisde the trial time limits. A message is now issued within
     DS2BRAINSTORM stating that time clipping has occured and related event
     data files have now a Time variable with proper length
     - Fixed bug in 2D layout measures display: DataViewer -> DataViewing ->
     2D layout
     - EXTRACT_CHANNELS: Fixed bug for CTF computation when first MEG channel containing coef
                     correction information is declared as BAD: store coef
                     information in first good MEG channel and trim number of
                     lines of correction matrix to proper number of good MEG
                     channels only (crucial when running RAP_MUSIC estimation).
     - Minor change to DataViewer GUI layout : direct access to Averager and
     and Filter
     - Moved obsolete code to Archive:
        [filter_win.m and .mat] + [mri_scan_params.fig and .m] + [waves_multi.m and
        .mat]

     08-July-2004

     - Fixed miscellaneous file access issues encountered under Linux (e.g. during data import)

     07-July-2004

     - Fixed uicontext menu bug under Linux in DATA_MANAGER: could not load
       data using right click.
     - Fixed minor SUBJECT_EDITOR bugs:
            .new values for field entries of the
            subject file are now properly displayed at once when user click on 'save'
            button;
            .Date of Modification field is automatically set to current day's date when subject file is updated
            .Anatomy-> Import now properly calls BST_MRIVIEWER (was still calling older MRITool)

     06-July-2004

     - Import raw MRI: Axial/Sagittal/Coronal pulldown menu switch is now
       operative.

     21-June-2004

     - Baillet Release 2 now available in Paris, France. Mom and baby daughter
       doing very well, Dad and older brother very happy.

     - Added locked-view Zoom feature to MRIViewer:
    		.Go to View -> Zoom : extends Matlab's zoom feature in a single
    		view by automatically adjusting axes limits to the other 2
    		orthogonal views.

     - Change of colormap in MRIViewer GUI (bst_mriviewer.fig):
            . Menu -> View -> Change Colormap : calls Matlab's 6.5 Colormap Editor

     - Ensured that all figures by default are set with handle visibility "on"
     - Added routine "find_mfiles", called from the command line that reverse
       engineers the m-files that open a particular figure
     - Added figure names to some of the Data Viewer outputs
     - Added Matlab default file menus to the Time Series and Topography of the MRI
       Viewer, to the Data Time Series of the Data Viewer output.

     16-June-2004

     - Added AVIPLAYER in PublicToolbox (create / save and playback AVI movies directly within BrainStorm's dataViewer)
     - User can alter/load and save custom colormaps using interaction with
     COLORMAPEDITOR (Matlab 6.5 and greater only)
     - Fixed bugs in loading raw data as to the DataType
     - Fixed bug in tesselation tool listing the EEG channel names for alignment
     - Minor alignment of MRI Viewer when reusing
     - Bug when viewing more than seven sources in bst_wavedata_display fixed.

     15-June-2004

     Fixed calls to overlapping-sphere forward modelling (MEG and EEG)

     14-June-2004

     Fixed setting of analysis time window in RAP-MUSIC
        - now properly updates the display time window in Viewer
        - signal subspace statistics automatically update once a new time
          window is defined
     Fixed bug in assignement of empty Anatomy and Tesselation fields in
       subject editor

     Renamed Phantom/SampleRaw data to be of type "Mixed", added how to load text
       file, added brainstormstudy.mat file for convenience, changed "type" button
       to have more explicit directions on whether the sample data are homogeneous
       or of mixed types.

     Added similar how_to_load file to the Phantom/montreal_data folder.

     Updated Matlab bug information on the Forum pages, added info on unzipping.

     11-June-2004

     Added Help menu item for reporting bugs to the Forum
     Fixed bad link in Help menu for Local Web Pages
     Added this What's New feature as readme.m file in the toolbox
     Added categories to the BrainStorm Forum pages

### Cross-Reference Information

This is called by

    bst_static_taskbar                 C:\BrainStorm_2001\Toolbox\bst_static_taskbar.m

### Listing of C:\BrainStorm_2001\Toolbox\readme.m

    %README - What's New in Each Revision of BrainStorm 2.0 (Alpha)
    %
    % By it's very nature, Alpha development/revision is not as controlled as later
    % versions. Below are approximate comments as to what we are improving in each
    % version
    %
    % 02-Nov-2004
    %
    % Fixed bug in the CTF loading routine. Tested the warping of the EEG
    % electrod array to the Montreal phantom surface.
    %
    % 12-Oct-2004
    %
    % Summer months spent quietly making numerous improvements and bug fixes.
    % Several new additions to the inverse routines. LCMV Beamforming now
    % added, with noise significance scaling. The linear MMS ("min norm") now
    % also offers noise scaling. EEG loading for Neuroscan and EGI manufacturer
    % types added, and the EEG routines tested. "Landmarks" are now treated
    % separately from Channels, and both types can now be used to warp a
    % surrogate head to the desired head shape. The BEM routines continue
    % testing. The primary problem is a "garbage in garbage out" occuring when
    % "reducepatch" is used to decimate a dense tesselation, resulting in poor
    % surfaces. Better routines are under study.
    %
    %
    % 20-July-2004
    %
    % - Data import:
    % For better interchange with BrainVisa software (see
    % http://brainvisa.info) :
    %  -> New MRI format import filters include GIS MR format
    %  -> New Tessellation format import filters include MESH
    %
    % 12-July-2004
    %
    % - Data import of BESA and Neuroscan average EEG files is now operative:
    % Access is through DataManager -> File -> Import Data -> Pick-up a Data
    % Format
    % Electrode locations can be read from multiple file formats:
    %      '.elp' simple BESA ASCII format
    %      '.dat' NeuroScan for BESA electrode format
    %      '.res' NeuroScan for Curry format
    %      '.sfp' ZEBRIS ASCII format
    % [Thanks to Felix Darvas: SIPI/USC]
    %
    % 09-July-2004
    %
    % - Data averaging within a study is now operative:
    % Access is through DataViewer -> Basic Processing -> Average
    %                   Select data files within current study folder
    %                   Enter a value in ms for acceptable time-jitter about
    %                   some time-locked event (default is 0)
    %                   Selected data files are then averaged, with adaptation
    %                   of time window if original data don't have same lenght
    %                   or time limits and stored in a BrainStorm data file
    %                   within current study folder.
    % - Data filtering is now operating again (-> Matlab Signal Processing Toolbox is required):
    %   Access is through : DataViewer -> Basic Processing -> Filter
    %                       A new GUI is created and offers the possibility to
    %                                 - bandpass filter data using a zero-phase filter
    %                                 - for EEG : move to average-reference potentials, once bad channels were removed
    % - Fixed bug when importing from CTF markers: some time clipping may occur
    % when requested time window about a marker occurence would end up having
    % an edge outisde the trial time limits. A message is now issued within
    % DS2BRAINSTORM stating that time clipping has occured and related event
    % data files have now a Time variable with proper length
    % - Fixed bug in 2D layout measures display: DataViewer -> DataViewing ->
    % 2D layout
    % - EXTRACT_CHANNELS: Fixed bug for CTF computation when first MEG channel containing coef
    %                 correction information is declared as BAD: store coef
    %                 information in first good MEG channel and trim number of
    %                 lines of correction matrix to proper number of good MEG
    %                 channels only (crucial when running RAP_MUSIC estimation).
    % - Minor change to DataViewer GUI layout : direct access to Averager and
    % and Filter
    % - Moved obsolete code to Archive:
    %    [filter_win.m and .mat] + [mri_scan_params.fig and .m] + [waves_multi.m and
    %    .mat]
    %
    % 08-July-2004
    %
    % - Fixed miscellaneous file access issues encountered under Linux (e.g. during data import)
    %
    % 07-July-2004
    %
    % - Fixed uicontext menu bug under Linux in DATA_MANAGER: could not load
    %   data using right click.
    % - Fixed minor SUBJECT_EDITOR bugs:
    %        .new values for field entries of the
    %        subject file are now properly displayed at once when user click on 'save'
    %        button;
    %        .Date of Modification field is automatically set to current day's date when subject file is updated
    %        .Anatomy-> Import now properly calls BST_MRIVIEWER (was still calling older MRITool)
    %
    % 06-July-2004
    %
    % - Import raw MRI: Axial/Sagittal/Coronal pulldown menu switch is now
    %   operative.
    %
    % 21-June-2004
    %
    % - Baillet Release 2 now available in Paris, France. Mom and baby daughter
    %   doing very well, Dad and older brother very happy.
    %
    % - Added locked-view Zoom feature to MRIViewer:
    %        .Go to View -> Zoom : extends Matlab's zoom feature in a single
    %        view by automatically adjusting axes limits to the other 2
    %        orthogonal views.
    %
    % - Change of colormap in MRIViewer GUI (bst_mriviewer.fig):
    %        . Menu -> View -> Change Colormap : calls Matlab's 6.5 Colormap Editor
    %
    % - Ensured that all figures by default are set with handle visibility "on"
    % - Added routine "find_mfiles", called from the command line that reverse
    %   engineers the m-files that open a particular figure
    % - Added figure names to some of the Data Viewer outputs
    % - Added Matlab default file menus to the Time Series and Topography of the MRI
    %   Viewer, to the Data Time Series of the Data Viewer output.
    %
    % 16-June-2004
    %
    % - Added AVIPLAYER in PublicToolbox (create / save and playback AVI movies directly within BrainStorm's dataViewer)
    % - User can alter/load and save custom colormaps using interaction with
    % COLORMAPEDITOR (Matlab 6.5 and greater only)
    % - Fixed bugs in loading raw data as to the DataType
    % - Fixed bug in tesselation tool listing the EEG channel names for alignment
    % - Minor alignment of MRI Viewer when reusing
    % - Bug when viewing more than seven sources in bst_wavedata_display fixed.
    %
    % 15-June-2004
    %
    % Fixed calls to overlapping-sphere forward modelling (MEG and EEG)
    %
    %
    % 14-June-2004
    %
    % Fixed setting of analysis time window in RAP-MUSIC
    %    - now properly updates the display time window in Viewer
    %    - signal subspace statistics automatically update once a new time
    %      window is defined
    % Fixed bug in assignement of empty Anatomy and Tesselation fields in
    %   subject editor
    %
    % Renamed Phantom/SampleRaw data to be of type "Mixed", added how to load text
    %   file, added brainstormstudy.mat file for convenience, changed "type" button
    %   to have more explicit directions on whether the sample data are homogeneous
    %   or of mixed types.
    %
    % Added similar how_to_load file to the Phantom/montreal_data folder.
    %
    % Updated Matlab bug information on the Forum pages, added info on unzipping.
    %
    % 11-June-2004
    %
    % Added Help menu item for reporting bugs to the Forum
    % Fixed bad link in Help menu for Local Web Pages
    % Added this What's New feature as readme.m file in the toolbox
    % Added categories to the BrainStorm Forum pages

    %<autobegin> ---------------------- 02-Nov-2004 16:16:29 -----------------------
    % --------- Automatically Generated Comments Block Using AUTO_COMMENTS ---------
    %
    % CATEGORY: Help
    %
    % At Check-in: $Author: Mosher $  $Revision: 29 $  $Date: 11/02/04 2:38p $
    %
    % This software is part of BrainStorm Toolbox Version 2.0 (Alpha) 02-Nov-2004
    %
    % Principal Investigators and Developers:
    % ** Richard M. Leahy, PhD, Signal & Image Processing Institute,
    %    University of Southern California, Los Angeles, CA
    % ** John C. Mosher, PhD, Biophysics Group,
    %    Los Alamos National Laboratory, Los Alamos, NM
    % ** Sylvain Baillet, PhD, Cognitive Neuroscience & Brain Imaging Laboratory,
    %    CNRS, Hopital de la Salpetriere, Paris, France
    %
    % See BrainStorm website at http://neuroimage.usc.edu for further information.
    %
    % Copyright (c) 2004 BrainStorm by the University of Southern California
    % This software distributed  under the terms of the GNU General Public License
    % as published by the Free Software Foundation. Further details on the GPL
    % license can be found at http://www.gnu.org/copyleft/gpl.html .
    %
    % FOR RESEARCH PURPOSES ONLY. THE SOFTWARE IS PROVIDED "AS IS," AND THE
    % UNIVERSITY OF SOUTHERN CALIFORNIA AND ITS COLLABORATORS DO NOT MAKE ANY
    % WARRANTY, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES OF
    % MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE, NOR DO THEY ASSUME ANY
    % LIABILITY OR RESPONSIBILITY FOR THE USE OF THIS SOFTWARE.
    %<autoend> ------------------------ 02-Nov-2004 16:16:29 -----------------------

    % ----------------------------- Script History ---------------------------------
    % JCM 11-Jun-2004  Began this file. Just add comments above for BrainStorm
    %                  improvements. Add each new revision to the TOP of the pile,
    %                  so that is what the user first sees in the help window.
    % ----------------------------- Script History ---------------------------------

    % The filename "readme.m" is a special filename in Matlab, accessed by
    % "whatsnew"
    % or "info" commands, but mostly deprecated. We'll simply call it with a helpwin
    % function.

    helpwin(mfilename)

Produced by color_mat2html, a customized BrainStorm 2.0 (Alpha) version of mat2html on Tue Nov 2 16:17:59 2004
Cross-Directory links are: ON