function hdr = read_ctf_res4(fname)

% READ_CTF_RES4 reads the header in RES4 format from a CTF dataset
%
% Use as
%   [hdr] = read_ctf_res4(filename)
%
% See also READ_CTF_MEG4

% "VSM MedTech Ltd. authorizes the release into public domain under the
% GPL licence of the Matlab source code files "read_ctf_res4.m" and
% "read_ctf_meg4.m" by the authors of said files from the F.C. Donders
% Centre, Nijmegen, The Netherlands."

% Author(s): Jim McKay November 1999
% Last revision: Jim McKay
% Copyright (c) 1999-2000 CTF Systems Inc. All Rights Reserved.
%
% modifications Copyright (C) 2002, Ole Jensen
% modifications Copyright (C) 2003, Robert Oostenveld
%
% $Log: read_ctf_res4.m,v $
% Revision 1.14  2007/03/07 08:58:46  roboos
% Do not determine the MEG, REF and EEG channels based on the first character of the channel label, removed rowMEG etc from the header. The relevant information is contained in hdr.sensType.
%
% Revision 1.13  2006/03/06 09:41:23  roboos
% changed some |s into ||s
%
% Revision 1.12  2005/07/28 15:12:27  roboos
% fixed bug in hdr.timeVec (thanks to Sanja Kovacevic)
%
% Revision 1.11  2005/05/26 09:58:08  roboos
% removed the construction of grad, that is now done in a separate fieldtrip function (ctf2grad)
%
% Revision 1.10  2005/05/24 07:34:37  roboos
% added sensType to the output header
%
% Revision 1.9  2005/05/23 11:20:17  roboos
% fixed bug for run description which is longer than 256 characters, improved reading of filter information (thanks to Durk Talsma)
%
% Revision 1.8  2005/04/27 06:18:21  roboos
% added support for MEG42RS format, which seems to work (only tested on a single dataset from MIND Institute in Albuquerque, NM, USA)
%
% Revision 1.7  2005/02/18 13:16:58  roboos
% VSM MedTech Ltd. authorised the release of this code in the public domain
% updated the copyrights, updated the help
%
% Revision 1.6  2004/07/02 11:43:32  roboos
% typographic change in comment
%
% Revision 1.5  2004/06/28 07:34:41  roberto
% added some extra low-level output fields to header, added cm units
%
% Revision 1.4  2003/04/01 07:51:53  roberto
% fixed bug in gradiometer channel labels
%
% Revision 1.3  2003/03/28 17:27:27  roberto
% renamed output gradiometer from gradHC to grad
%
% Revision 1.2  2003/03/24 12:34:33  roberto
% minor changes
%
% Revision 1.1  2003/03/13 14:27:09  roberto
% separated read_ctf_ds into res4-header part and data part
% restructured the res4 part, using (incorrect) CTF documentation
%

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% read header information
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

fid = fopen(fname,'r','ieee-be');

% Check if header file exist
if fid == -1
    errMsg = strcat('Could not open header file:',fname);
    error(errMsg);
end

% First 8 bytes contain filetype, check is fileformat is correct.
% This function was written for MEG41RS, but also seems to work for MEG42RS.
r_head=setstr(fread(fid,8,'uint8'))';
if ~strcmp(r_head(1,1:7),'MEG41RS') & ~strcmp(r_head(1,1:7),'MEG42RS')
  fclose(fid)
  errMsg = sprintf('Resource file format (%s) is not supported for file %s', r_head(1,1:7), fname);
  error(errMsg);
end %if

% Read the initial parameters
appName       = setstr(fread(fid,256,'uint8'))' ;
dataOrigin    = setstr(fread(fid,256,'uint8'))' ;
dataDescrip   = setstr(fread(fid,256,'uint8'))' ;
no_trial_avgd = fread(fid,1,'int16')          ;
data_time     = setstr(fread(fid,255,'uint8'))';
data_date     = setstr(fread(fid,255,'uint8'))';

fseek(fid,1288,'bof');
% Read the general recording parameters
no_samples  = fread(fid,1,'int32');
no_channels = fread(fid,1,'int16');
fseek(fid,2,'cof');			% hole of 2 bytes due to improper alignment
sample_rate = fread(fid,1,'double');
epoch       = fread(fid,1,'double');
no_trials   = fread(fid,1,'int16');
fseek(fid,2,'cof');			% hole of 2 bytes due to improper alignment
preTrigpts=fread(fid,1,'int32');

fseek(fid,1360,'bof');
% read in the meg4Filesetup structure
run_name     = setstr(fread(fid,32,'uint8')');
run_title    = setstr(fread(fid,256,'uint8')');
instruments  = setstr(fread(fid,32,'uint8')');
coll_desc    = setstr(fread(fid,32,'uint8')');
subj_id      = setstr(fread(fid,32,'uint8')');
operator     = setstr(fread(fid,32,'uint8')') ;
sensFilename = setstr(fread(fid,60,'uint8')') ;

% not nececssary to seek, the file pointer is already at the desired location
% fseek(fid,1836,'bof');

% Read in the run description length
rd_len=fread(fid,1,'uint32');
% Go to the run description and read it in
fseek(fid,1844,'bof');
run_desc=setstr(fread(fid,rd_len,'uint8')');

% read in the filter information
num_filt=fread(fid,1,'uint16');
for fi=0:(num_filt-1),
  %filt_info=fread(fid,18,'uint8');
  filt_freq =fread(fid,1, 'double');
  filt_class=fread(fid,1, 'uint32');
  filt_type =fread(fid,1, 'uint32');
  num_fparm=fread(fid, 1, 'uint16');
  %num_fparm=filt_info(18);
  if num_fparm ~= 0,
    filt_parm=fread(fid,8*num_fparm,'uint8');
  end % if
end % for fi

% Read in the channel names
for i=1:no_channels,
    temp=fread(fid,32,'uint8')';
    temp(find(temp<32 )) = ' ';		% remove non-printable characters
    temp(find(temp>126)) = ' ';		% remove non-printable characters
    endstr = findstr(temp, '-'); temp(endstr:end) = ' ';	% cut off at '-'
    endstr = findstr(temp, ' '); temp(endstr:end) = ' ';	% cut off at ' '
    chan_name(i,:) = char(temp);		% as char array
    chan_label{i}  = deblank(char(temp));	% as cell array
end %for

% pre-allocate some memory space
sensGain = zeros([no_channels,1]);
qGain    = zeros([no_channels,1]);
ioGain   = zeros([no_channels,1]);
sensType = zeros([no_channels,1]);

% Read in the sensor information
fp = ftell(fid);
for chan=1:no_channels,
    fread(fid,1,'uint8');			% Read and ignore 1 byte from enum
    sensType(chan)=fread(fid,1,'uint8');	% Read sensor type
    fread(fid,2,'uint8');			% Read and ignore originalRunNum
    fread(fid,4,'uint8');			% Read and ignore coilShape
    sensGain(chan)=fread(fid,1,'double');	% Read sensor gain in Phi0/Tesla
    qGain(chan)=fread(fid,1,'double');		% Read qxx gain (usually 2^20 for Q20)
    ioGain(chan)=fread(fid,1,'double');		% Read i/o gain of special sensors (usually 1.0)
    ioOffset(chan)=fread(fid,1,'double');
    numCoils(chan)=fread(fid,1,'int16');
    grad_order_no(chan)=fread(fid,1,'int16');
    fread(fid,4,'uint8');

    % read the coil positions and orientations
    for i=1:8
      Chan(chan).coil(i).pos = fread(fid,3,'double')';	
      fread(fid,1,'double');
      Chan(chan).coil(i).ori = fread(fid,3,'double')';
      fread(fid,3,'double');
    end

    % read the coil positions and orientations in head coordinates(?)
    for i=1:8
      Chan(chan).coilHC(i).pos = fread(fid,3,'double')';	
      fread(fid,1,'double');
      Chan(chan).coilHC(i).ori = fread(fid,3,'double')';
      fread(fid,3,'double');
    end

    % jump to the next sensor info record
    fseek(fid, fp+chan*1328, 'bof');
end % for chan

% close the header file
fclose(fid);

% according to Tom Holroyd, the sensor types are
%
% meg channels are 5, refmag 0, refgrad 1, adcs 18.
% UPPT001 is 11
% UTRG001 is 11
% SCLK01 is 17
% STIM is 11
% SCLK01 is 17
% EEG057 is 9
% ADC06 is 18
% ADC07 is 18
% ADC16 is 18
% V0 is 15

% assign all the variables that should be outputted as header information
hdr.Fs          = sample_rate;
hdr.nChans      = no_channels;
hdr.nSamples    = no_samples;
hdr.nSamplesPre = preTrigpts;
hdr.timeVec     = (1:no_samples)/sample_rate - preTrigpts/sample_rate - 1/sample_rate;
hdr.nTrials     = no_trials;
hdr.gainV       = ioGain./(qGain.*sensGain);
hdr.ioGain      = ioGain;
hdr.qGain       = qGain;
hdr.sensGain    = sensGain;
hdr.sensType    = sensType;

hdr.label       = chan_label(:);
hdr.nameALL     = chan_name;
hdr.Chan        = Chan;
% hdr.rowMEG      = rowMEG;
% hdr.rowEEG      = rowEEG;
% hdr.rowTRIG     = rowTRIG;
% hdr.rowREF      = rowREF;
% hdr.nameEEG     = [];
% hdr.nameMEG     = [];
% hdr.nameEOG     = [];
% hdr.trigV       = [];
% hdr.SwapData    = [];



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The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.