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# elpos2bs

## (Toolbox/elpos2bs.m in BrainStorm 2.0 (Alpha))

### Function Synopsis

    [Channel,landmark]=elpos2bs(fnamein,fnameout,type)

### Help Text

    ELPOS2BS - this function converts electrode position files into BrainStorm Channel format
     function [Channel,landmark]=elpos2bs(fnamein,fnameout,type)
     fnamein = input file name
     fnameout = output filename for BrainStorm format. If fnameout=[], no file
     is saved
     type = input data format
          = 'elp' simple BESA ASCII format
          = 'dat' NeuroScan for BESA electrode format
          = 'res' NeuroScan for Curry format
          = 'sfp' ZEBRIS ASCII format
     Channel = returns brainstorm Channel structure
               Channel.Loc = elctrode position. default = [0;0;0];
               Channel.Orient = Channel orientiation. Does not apply for electrodes. default =[1;0;0];
               Channel.Weight = Channel weighting. default=1;
               Channel.Type = Channel type. default='EEG'
               Channel.Comment =Channel comment. default='';
               Channel.Name = Channel name. default='';
               Channel.System = Channel system. default='';
     landmark = the brainstorm landmark structure
                landmark.Loc(1:3,1:n) = landmark locations
                landmark.Name={1:n} list of landmark names

### Cross-Reference Information

This function is called by

    importdata                         C:\BrainStorm_2001\Toolbox\importdata.m

### Listing of function C:\BrainStorm_2001\Toolbox\elpos2bs.m

    function [Channel,landmark]=elpos2bs(fnamein,fnameout,type)
    %ELPOS2BS - this function converts electrode position files into BrainStorm Channel format
    % function [Channel,landmark]=elpos2bs(fnamein,fnameout,type)
    % fnamein = input file name
    % fnameout = output filename for BrainStorm format. If fnameout=[], no file
    % is saved
    % type = input data format
    %      = 'elp' simple BESA ASCII format
    %      = 'dat' NeuroScan for BESA electrode format
    %      = 'res' NeuroScan for Curry format
    %      = 'sfp' ZEBRIS ASCII format
    % Channel = returns brainstorm Channel structure
    %           Channel.Loc = elctrode position. default = [0;0;0];
    %           Channel.Orient = Channel orientiation. Does not apply for electrodes. default =[1;0;0];
    %           Channel.Weight = Channel weighting. default=1;
    %           Channel.Type = Channel type. default='EEG'
    %           Channel.Comment =Channel comment. default='';
    %           Channel.Name = Channel name. default='';
    %           Channel.System = Channel system. default='';
    % landmark = the brainstorm landmark structure
    %            landmark.Loc(1:3,1:n) = landmark locations
    %            landmark.Name={1:n} list of landmark names

    %<autobegin> ---------------------- 12-Oct-2004 11:38:10 -----------------------
    % --------- Automatically Generated Comments Block Using AUTO_COMMENTS ---------
    %
    % CATEGORY: Unknown Category
    %
    % Subfunctions in this file, in order of occurrence in file:
    %   [ix]=scan_reference(Channel) % search for possible reference channel
    %   [Channel,landmark]=elp2bsint(fnamein,unitCorrection)
    %   [Channel,landmark]=dat2bsint(fnamein,unitCorrection)
    %   [Channel,landmark]=res2bsint(fnamein,unitCorrection)
    %   [Channel,landmark]=sfp2bsint(fnamein,unitCorrection)
    %
    % At Check-in: $Author: Mosher $  $Revision: 6 $  $Date: 10/12/04 10:19a $
    %
    % This software is part of BrainStorm Toolbox Version 2.0 (Alpha) 11-Oct-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> ------------------------ 12-Oct-2004 11:38:10 -----------------------

    % ----------------------------- Script History ---------------------------------
    % (c) 2004 Felix Darvas, Ph.D. , SIPI University of Southern California
    % JCM 12-Oct-2004 Header comments
    % ----------------------------- Script History ---------------------------------

    % setting defaults

    %ask for units
    str = {'meters' 'centimeters' 'millimeters'};
    [unit,v] = listdlg('PromptString','Select units of channel file','selectionmode','single','Liststring',str);
    if(unit == 1) %meters
        unitCorrection = 1;
    end
    if(unit == 2) %centimeters
        unitCorrection = 100;
    end
    if(unit == 3) %millimeters
        unitCorrection = 1000;
    end

    Channel=struct('Loc',zeros(3,1),'Orient',[1;0;0],'Weight',1,'Type','EEG','Comment','','Name','','System','');

    if(strcmp(type,'elp'))
        [Channel,landmark]=elp2bsint(fnamein,unitCorrection); % getting channel info in ELP format. It is still not clear, were we place the reference information!
    end

    if(strcmp(type,'dat'))
        [Channel,landmark]=dat2bsint(fnamein,unitCorrection); % getting channel info in DAT format. It is still not clear, were we place the reference information!
    end

    if(strcmp(type,'res'))
         [Channel,landmark]=res2bsint(fnamein,unitCorrection); % getting channel info in DAT format. It is still not clear, were we place the reference information!
    end
    if(strcmp(type,'sfp'))
         [Channel,landmark]=sfp2bsint(fnamein,unitCorrection); % getting channel info in SFP format. It is still not clear, were we place the reference information!
    end

    fusion=[Channel landmark];
    ixlandmark=zeros(1,length(fusion));
    ixlandmark(length(Channel)+1:end)=1;
    ixlm=find(ixlandmark>0);
    ps=sprintf('found %i predefined landmarks',length(landmark));
    [Selection,ok] = listdlg('ListString',{fusion.Name},'InitialValue',ixlm,'PromptString',ps,'Name','Landmark definition');
    landmark=[];
    for i=1:length(Selection)
        landmark.Loc(1:3,i)=fusion(Selection(i)).Loc(1:3,1);
        landmark.Name{i}=fusion(Selection(i)).Name;
    end
    fusion(Selection)=[];
    Channel=fusion;
    ix=scan_reference(Channel); % search for a possible reference electrode;

    if(ix>0)
        % there is a reference electrode candidate
        Channel(ix).Type='EEG REF';
    %     for i=1:length(Channel)
    %         Channel(i).Loc(:,2)=Channel(ix).Loc(:,1); % follow BS convention and set 2nd position in channel to reference position.
    %     end
    else
        % there is no apparent reference. Assume average reference.
        for i=1:length(Channel)
            Channel(i).Comment='AVERAGE REF';
            %Channel(i).Loc(:,2)=Channel(i).Loc(:,1); % dont know what to do with average ref? Assume every channel is reference.
        end
    end
    if(~isempty(fnameout))
        save(fnameout,'Channel');
    end
    return

    function [ix]=scan_reference(Channel) % search for possible reference channel
    ix=-1;
    ref_found=0;
    % look for names like 'ref' first
    for i=1:length(Channel)
        label=Channel(i).Name;
        label=lower(label);
        if(findstr(label,'ref'))
            if(ref_found==0)
                ix=i;
                ref_found==1;
            else
                label2=Channel(ix).Name;
                outs=sprintf('there are ambiguous electrode labels in %s and %s! Will keep %s as reference.',label,label2,label);
                error(outs);
            end
        end
    end
    % check for 'cz'
    if(ref_found==0)
        for i=1:length(Channel)
            label=Channel(i).Name;
            label=lower(label);
            if(strcmp(label,'cz'))
                if(ref_found==0)
                    ix=i;
                    ref_found==1;
                else
                    label2=Channel(ix).Name;
                    outs=sprintf('there are ambiguous electrode labels in %s and %s! Will keep %s as reference.',label,label2,label);
                    error(outs);
                end
            end
        end
    end

    % importing 'elp' format
    function [Channel,landmark]=elp2bsint(fnamein,unitCorrection)
    Channel=struct('Loc',zeros(3,1),'Orient',[1;0;0],'Weight',1,'Type','EEG','Comment','','Name','','System','');
    %landmark=struct('Loc',zeros(3,1),'Orient',[0;0;0],'Weight',1,'Type','EEG','Comment','','Name','','System','')
    landmark=[];
    fpin=fopen(fnamein);
    if(fpin>0)
        k=1;
        while(~feof(fpin))
            label{k}=fscanf(fpin,'%s',1);
            pos{k}=fscanf(fpin,'%e',[1 3]);
            k=k+1;
        end
        fclose(fpin);
    else
        msg=sprintf('File %s does not exist',fnamein);
        error(msg);
        Channel=[];
        return
    end
    Channel=struct('Loc',zeros(3,1),'Orient',[0;0;0],'Weight',1,'Type','EEG','Comment','converted from ELP','Name','EEG 01','System','Neuroscan SynAmp');
    for i=1:k-2;
        Channel(i).Loc(:,1)=pos{i}'/unitCorrection;
        Channel(i).Orient=[0;0;0];
        Channel(i).Weight=1;
        Channel(i).Type='EEG';
        Channel(i).Comment='';
        Channel(i).Name=label{i};
        Channel(i).System='Neuroscan SynAmp';
    end

    % importing 'dat' format
    function [Channel,landmark]=dat2bsint(fnamein,unitCorrection)
    Channel=struct('Loc',zeros(3,1),'Orient',[0;0;0],'Weight',1,'Type','EEG','Comment','','Name','','System','');
    %landmark=struct('Loc',zeros(3,1),'Orient',[0;0;0],'Weight',1,'Type','EEG','Comment','','Name','','System','')
    landmark=[];
    fpin=fopen(fnamein);
    if(fpin>0)
        k=1;
        while(~feof(fpin))
            label{k}=fscanf(fpin,'%s',1);
           hi=fscanf(fpin,'%i',1);
           if(~isempty(hi))
                typ(k)=hi;
            end
            pos{k}=fscanf(fpin,'%e',[1 3]);
            k=k+1;
        end
        fclose(fpin);
    else
        msg=sprintf('File %s does not exist',fnamein);
        error(msg);
        Channel=[];
        return
    end
    ix=find(typ==69 | typ==88);
    Channel=struct('Loc',zeros(3,1),'Orient',[0;0;0],'Weight',1,'Type','EEG','Comment','converted from ELP','Name','EEG 01','System','Neuroscan SynAmp');
    for i=1:length(ix);
        Channel(i).Loc(:,1)=pos{ix(i)}'/unitCorrection;
        Channel(i).Orient=[0;0;0];
        Channel(i).Weight=1;
        Channel(i).Type='EEG';
        Channel(i).Comment='';
        Channel(i).Name=label{ix(i)};
        Channel(i).System='Neuroscan SynAmp';
    end
    ix=find(typ>75 & typ<83);
    for i=1:length(ix);
        landmark(i).Loc(:,1)=pos{ix(i)}'/unitCorrection;
        landmark(i).Orient=[0;0;0];
        landmark(i).Weight=1;
        landmark(i).Type='LANDMARK';
        landmark(i).Comment='';
        landmark(i).Name=label{ix(i)};
        landmark(i).System='Neuroscan SynAmp';
    end

    % importing 'res' format
    function [Channel,landmark]=res2bsint(fnamein,unitCorrection)
    Channel=struct('Loc',zeros(3,1),'Orient',[0;0;0],'Weight',1,'Type','EEG','Comment','','Name','','System','');
    %landmark=struct('Loc',zeros(3,1),'Orient',[0;0;0],'Weight',1,'Type','EEG','Comment','','Name','','System','')
    landmark=[];
    fpin=fopen(fnamein);
    if(fpin>0)
        k=1;
        while(~feof(fpin))
            hi=fscanf(fpin,'%i',1);
           if(~isempty(hi))
                typ(k)=hi;
            end
            pos{k}=fscanf(fpin,'%e',[1 3]);
            dummy=fscanf(fpin,'%i',1);
            label{k}=fscanf(fpin,'%s',1);
            k=k+1;
        end
        fclose(fpin);
    else
        msg=sprintf('File %s does not exist',fnamein);
        error(msg);
        Channel=[];
        return
    end
    Channel=struct('Loc',zeros(3,1),'Orient',[0;0;0],'Weight',1,'Type','EEG','Comment','','Name','','System','Neuroscan SynAmp');
    ix=find(typ==0);
    for i=1:length(ix);
        Channel(i).Loc(:,1)=pos{ix(i)}'/unitCorrection;
        Channel(i).Orient=[0;0;0];
        Channel(i).Weight=1;
        Channel(i).Type='EEG';
        Channel(i).Comment='';
        Channel(i).Name=label{ix(i)};
        Channel(i).System='Neuroscan SynAmp';
    end
    ix=find(typ<0);
    for i=1:length(ix);
        landmark(i).Loc(:,1)=pos{ix(i)}'/unitCorrection;
        landmark(i).Orient=[0;0;0];
        landmark(i).Weight=1;
        landmark(i).Type='LANDMARK';
        landmark(i).Comment='';
        landmark(i).Name=label{ix(i)};
        landmark(i).System='Neuroscan SynAmp';
    end

    function [Channel,landmark]=sfp2bsint(fnamein,unitCorrection)
    Channel=struct('Loc',zeros(3,1),'Orient',[0;0;0],'Weight',1,'Type','EEG','Comment','','Name','','System','');
    %landmark=struct('Loc',zeros(3,1),'Orient',[0;0;0],'Weight',1,'Type','EEG','Comment','','Name','','System','')
    landmark=[];
    fpin=fopen(fnamein);
    if(fpin>0)
        k=1;
        while(~feof(fpin))
            label{k}=fscanf(fpin,'%s',1);
            pos{k}=fscanf(fpin,'%e',[1 3]);
            k=k+1;
        end
        fclose(fpin);
    else
        msg=sprintf('File %s does not exist',fnamein);
        error(msg);
        Channel=[];
        return
    end
    Channel=struct('Loc',zeros(3,1),'Orient',[0;0;0],'Weight',1,'Type','EEG','Comment','','Name','','System','Neuroscan SynAmp');
    ix=1:k-2;
    for i=1:length(ix);
        Channel(i).Loc(:,1)=pos{ix(i)}'/unitCorrection;
        Channel(i).Orient=[0;0;0];
        Channel(i).Weight=1;
        Channel(i).Type='EEG';
        Channel(i).Comment='';
        Channel(i).Name=label{ix(i)};
        Channel(i).System='SFP';
    end

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