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# readmarkerfile_ctf

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

### Function Synopsis

    [marker_names,n_samples ,trial_time] = readmarkerfile_ctf(DS_FOLDER);

### Help Text

    READMARKERFILE_CTF - Read marker information from CTF MarkerFile.mrk
     function [marker_names,n_samples ,trial_time] = readmarkerfile_ctf(DS_FOLDER);
     Read the CTF markerfile MarkerFile.mrk located in DS_FOLDER
     (a valid .ds CTF data set folder).
     Outputs:
     marker_names is a cell array of strings containing the name of the markers
     n_samples a corresponding cell array; each cell containing the number of events per marker
     trial_time, a cell array - The content of each cell, trial_time{i}, is a N x 2 matrix related to the occurences of marker i
     trial_time{i}(:,1) contains the trial numbers where marker i occured
     trial_time{i}(:,2) contains the corresponding time from sync point in the corresponding trial
     /---Script Author-------------------------------------\
     |                                                      |
     |  *** Sylvain Baillet, Ph.D.                          |
     |  Cognitive Neuroscience & Brain Imaging Laboratory   |
     |  CNRS UPR640 - LENA                                  |
     |  Hopital de la Salpetriere, Paris, France            |
     |  sylvain.baillet@chups.jussieu.fr                    |
     |                                                      |
     \------------------------------------------------------/

     Script History ---------------------------------------------------------

     Script Creation : March 2001 (bst_readmarkerfilectf.m).
     SB  28-Jul-2002 : Renamed to currenty mfilename
     ............... : Updated help header and file description

### Cross-Reference Information

This function is called by

    extract_ctf_markers                C:\BrainStorm_2001\Toolbox\extract_ctf_markers.m
    importdata                         C:\BrainStorm_2001\Toolbox\importdata.m
    sourceimaging                      C:\BrainStorm_2001\Toolbox\sourceimaging.m

### Listing of function C:\BrainStorm_2001\Toolbox\readmarkerfile_ctf.m

    function [marker_names,n_samples ,trial_time] = readmarkerfile_ctf(DS_FOLDER);
    %READMARKERFILE_CTF - Read marker information from CTF MarkerFile.mrk
    % function [marker_names,n_samples ,trial_time] = readmarkerfile_ctf(DS_FOLDER);
    % Read the CTF markerfile MarkerFile.mrk located in DS_FOLDER
    % (a valid .ds CTF data set folder).
    % Outputs:
    % marker_names is a cell array of strings containing the name of the markers
    % n_samples a corresponding cell array; each cell containing the number of events per marker
    % trial_time, a cell array - The content of each cell, trial_time{i}, is a N x 2 matrix related to the occurences of marker i
    % trial_time{i}(:,1) contains the trial numbers where marker i occured
    % trial_time{i}(:,2) contains the corresponding time from sync point in the corresponding trial
    % /---Script Author-------------------------------------\
    % |                                                      |
    % |  *** Sylvain Baillet, Ph.D.                          |
    % |  Cognitive Neuroscience & Brain Imaging Laboratory   |
    % |  CNRS UPR640 - LENA                                  |
    % |  Hopital de la Salpetriere, Paris, France            |
    % |  sylvain.baillet@chups.jussieu.fr                    |
    % |                                                      |
    % \------------------------------------------------------/
    %
    % Script History ---------------------------------------------------------
    %
    % Script Creation : March 2001 (bst_readmarkerfilectf.m).
    % SB  28-Jul-2002 : Renamed to currenty mfilename
    % ............... : Updated help header and file description

    %<autobegin> ---------------------- 09-Jul-2004 22:17:15 -----------------------
    % --------- Automatically Generated Comments Block Using AUTO_COMMENTS ---------
    %
    % CATEGORY: Data Processing
    %
    % At Check-in: $Author: Mosher $  $Revision: 13 $  $Date: 7/09/04 8:42p $
    %
    % This software is part of BrainStorm Toolbox Version 2.0 (Alpha) 09-Jul-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> ------------------------ 09-Jul-2004 22:17:15 -----------------------

    if ~exist(fullfile(DS_FOLDER,'MarkerFile.mrk'),'file'); % No marker file available in current data set
        %error(['MarkerFile MarkerFile.mrk does not exist in directory ',DS_FOLDER]);
        marker_names =[];
        n_samples = [] ; trial_time =[];
        return
    end

    mrkr =  textread(fullfile(DS_FOLDER,'MarkerFile.mrk'),'%s','delimiter','\n'); % Store everything in a cell array of string

    id = find(strcmp(mrkr,'NUMBER OF MARKERS:'));
    n_markers  = str2num(mrkr{id+1});

    id = find(strcmp(mrkr,'NAME:'));
    marker_names = mrkr(id+1);

    id = find(strcmp(mrkr,'NUMBER OF SAMPLES:'));
    n_samples  = str2num(char(mrkr(id+1)));

    mrkr_info = strmatch('TRIAL NUMBER',mrkr)+1; % Lines  where the marker times/trial info start

    for i = 1:n_markers
        trial_time{i} = str2num(char(mrkr(mrkr_info(i):mrkr_info(i)+n_samples(i))));
        if ~isempty(trial_time{i})
            trial_time{i}(:,1) = trial_time{i}(:,1) + 1;
        end
    end

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