help_data_channel

(Toolbox/help_data_channel.m in BrainStorm 2.0 (Alpha))

Function Synopsis

helptext = help_data_channel;

Help Text

HELP_DATA_CHANNEL - Information on database files of type 'channel'
 function helptext = help_data_channel;

    Landmark : a structure specifying locations of extra points of interests with fields:
              Loc : a 3 x n array of landmark locations in meters coordinate system
             Name : a 1 x n cell array of string used to label the landmarks

     Channel : An array of structures. Each element in the array comprises 
                the following fields
              Loc : 3 x n, one column per coil, location in meters in SCS
           Weight : 1 x n, relative gradiometer weights, e.g. [1 -1] or [1 -2 1]
           Orient : 3 x n, one column per coil, Cartesian orientation in SCS
             Type : String, must be {'MEG', 'EEG', 'MEG REF','EEG REF', 'OTHER'};
             Name : String, short label, usually machine assigned 'MEG 001'
          Comment : See explanation below
 
  The Comment field is somewhat complicated, CBB.
          Comment : Keywords or data. If TYPE is 'EEG' and data are average referenced, 
                    then Comment must be 'AVERAGE REF', and all Loc are a single location.
                    If EEG are data are differential, then two Loc and Weights
                    are used, and Comment is '' (blank). 
                    If EEG data are single ended, then Loc is one location,
                    there can ONLY be one Type of 'EEG REF', Comment is '', and
                    algorithms know to search for the reference channel.
                    If MEG data, and there are reference channels, the
                    reference channels are marked Type 'MEG REF'. Then the
                    FIRST Channel of Type 'MEG' has a Comment field that gives
                    the transformation matrix that builds the higher
                    gradiometers. See notes below for calculation method.

 Obsolete
           System : String    e.g. 'CTF 151', this field apparently not used.

 -- Notes --
 SCS is the patient coordinate system, i.e. the coil location is with respect
    to the subject's origin. See BrainStorm reference on coordinate systems:

    http://neuroimage.usc.edu/brainstorm/GUI_CoordinateSystem.htm

 A "channel" comprises the locations of the array's output, usually the
    result of combining "n" different coil locations.

 The reference channels are used to form "virtual gradiometers." If there are
  151 head channels (Type 'MEG') and 29 reference channels (Type 'MEG REF'),
  then the reference weighting matrix is 151 x 29. The 151 originally recorded
  data channels are modified in the machine or external to BrainStorm as Ffinal
  = Forg - W*Fref; If Gfinal is the gain matrix for the noise-weighted gain
  matrix (151 rows), Ghead is the gain matrix for each channel without noise
  weighting (151 rows),  Gref is the gain matrix for each of the reference
  channels (29 rows), and W is the reference channel weights, then:

   Gfinal = Ghead - W*Gref;

  See help_data_raw for descriptions on how to manually store this information
  and importation. At this time, CTF weighting information is automatically
  handled. 

 See also HELP_DATA_RAW

Listing of function C:\BrainStorm_2001\Toolbox\help_data_channel.m

function helptext = help_data_channel;
%HELP_DATA_CHANNEL - Information on database files of type 'channel'
% function helptext = help_data_channel;
%
%    Landmark : a structure specifying locations of extra points of interests with fields:
%              Loc : a 3 x n array of landmark locations in meters coordinate system
%             Name : a 1 x n cell array of string used to label the landmarks
%
%     Channel : An array of structures. Each element in the array comprises 
%                the following fields
%              Loc : 3 x n, one column per coil, location in meters in SCS
%           Weight : 1 x n, relative gradiometer weights, e.g. [1 -1] or [1 -2 1]
%           Orient : 3 x n, one column per coil, Cartesian orientation in SCS
%             Type : String, must be {'MEG', 'EEG', 'MEG REF','EEG REF', 'OTHER'};
%             Name : String, short label, usually machine assigned 'MEG 001'
%          Comment : See explanation below
% 
%  The Comment field is somewhat complicated, CBB.
%          Comment : Keywords or data. If TYPE is 'EEG' and data are average referenced, 
%                    then Comment must be 'AVERAGE REF', and all Loc are a single location.
%                    If EEG are data are differential, then two Loc and Weights
%                    are used, and Comment is '' (blank). 
%                    If EEG data are single ended, then Loc is one location,
%                    there can ONLY be one Type of 'EEG REF', Comment is '', and
%                    algorithms know to search for the reference channel.
%                    If MEG data, and there are reference channels, the
%                    reference channels are marked Type 'MEG REF'. Then the
%                    FIRST Channel of Type 'MEG' has a Comment field that gives
%                    the transformation matrix that builds the higher
%                    gradiometers. See notes below for calculation method.
%
% Obsolete
%           System : String    e.g. 'CTF 151', this field apparently not used.
%
% -- Notes --
% SCS is the patient coordinate system, i.e. the coil location is with respect
%    to the subject's origin. See BrainStorm reference on coordinate systems:
%
%    http://neuroimage.usc.edu/brainstorm/GUI_CoordinateSystem.htm
%
% A "channel" comprises the locations of the array's output, usually the
%    result of combining "n" different coil locations.
%
% The reference channels are used to form "virtual gradiometers." If there are
%  151 head channels (Type 'MEG') and 29 reference channels (Type 'MEG REF'),
%  then the reference weighting matrix is 151 x 29. The 151 originally recorded
%  data channels are modified in the machine or external to BrainStorm as Ffinal
%  = Forg - W*Fref; If Gfinal is the gain matrix for the noise-weighted gain
%  matrix (151 rows), Ghead is the gain matrix for each channel without noise
%  weighting (151 rows),  Gref is the gain matrix for each of the reference
%  channels (29 rows), and W is the reference channel weights, then:
%
%   Gfinal = Ghead - W*Gref;
%
%  See help_data_raw for descriptions on how to manually store this information
%  and importation. At this time, CTF weighting information is automatically
%  handled. 
%
% See also HELP_DATA_RAW

%<autobegin> ---------------------- 26-May-2004 11:30:25 -----------------------
% --------- Automatically Generated Comments Block Using AUTO_COMMENTS ---------
%
% CATEGORY: Help
%
% At Check-in: $Author: Mosher $  $Revision: 14 $  $Date: 5/26/04 9:59a $
%
% This software is part of BrainStorm Toolbox Version 2.0 (Alpha) 24-May-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> ------------------------ 26-May-2004 11:30:25 -----------------------


% This help file template was generated by 'make_help' on 24-Sep-2003 13:58:32
%
% This help file is callable as "help help_data_channel" (at the command line),
%  "help_data_channel" (in the Matlab help window), or
%  "txt = help_data_channel;" (no display, return only txt).
 
if nargout,
   helptext = help(mfilename); % return help block to output variable
else
   helpwin(mfilename); % no output variable, display in help window
end