documentation - use MATLAB instead of Matlab in the documentation

git-svn-id: svn+ssh://svn.fcdonders.nl/home/svnroot/fieldtrip/trunk@9226 0cf7c7f0-3615-4144-b4e6-68da3bce3cd0

@config/config.m

@@ -18,7 +18,7 @@
 % to each field are being counted.
 %
 % The config object can be used throughout your FieldTrip function
-% as if it were a plain Matlab structure. At the end of your FieldTrip
+% as if it were a plain MATLAB structure. At the end of your FieldTrip
 % function you can report the fields that were
 %   - not used (references=0)
 %   - locally assigned as compared to assigned by the end user (assignments>0)

@config/struct.m

@@ -23,7 +23,7 @@
 % $Id$
 
 if nargin==1
-  % convert the config object into a regular Matlab structure
+  % convert the config object into a regular MATLAB structure
   for i=1:numel(x)
     y(i) = struct(x(i).value);
   end
@@ -39,7 +39,7 @@
     end
   end
 else
-  % mimic the behaviour of the builtin Matlab struct function
+  % mimic the behaviour of the builtin MATLAB struct function
   if mod(nargin,2)
     error('Incorrect number of input arguments (should be key-value pairs)')
   end

@config/struct2cell.m

@@ -1,7 +1,7 @@
 function c = struct2cell(s)
 
 % STRUCT2CELL Convert structure array to cell array by first converting
-% the config objection into a struct and then using standard Matlab call.
+% the config objection into a struct and then using standard MATLAB call.
 
 % Copyright (C) 2008, Robert Oostenveld
 %

Contents.m

@@ -1,7 +1,7 @@
 % FieldTrip
 % Version unknown fieldtriptoolbox.org DD-MM-YYYY
 %
-% FieldTrip is the Matlab toolbox for MEG and EEG analysis that is being developed at
+% FieldTrip is the MATLAB toolbox for MEG and EEG analysis that is being developed at
 % the Centre for Cognitive Neuroimaging of the Donders Institute for Brain, Cognition
 % and Behaviour together with collaborating institutes. The FieldTrip software is
 % released as open source under the GNU general public license.
@@ -12,7 +12,7 @@
 % supports the data formats of all major MEG systems (CTF, Neuromag, BTi) and of the
 % most popular EEG systems, and new formats can be added easily. FieldTrip contains
 % high-level functions that you can use to construct your own analysis protocol in
-% Matlab. Furthermore, it easily allows developers to incorporate low-level algorithms
+% MATLAB. Furthermore, it easily allows developers to incorporate low-level algorithms
 % for new EEG/MEG analysis methods.
 %
 % The FieldTrip software is free but copyrighted software, distributed under the terms
@@ -58,7 +58,7 @@
 % the GPL is not allowed!
 %
 % Below is an overview of the most important FieldTrip functions, sorted by category.
-% You can get more details on a function by typing "help functionname" in Matlab.
+% You can get more details on a function by typing "help functionname" in MATLAB.
 %
 % Preprocessing and reading data
 %   ft_definetrial

besa2fieldtrip.m

@@ -7,7 +7,7 @@
 % Use as
 %   [data] = besa2fieldtrip(filename)
 % where the filename should point to a BESA datafile (or data that
-% is exported by BESA). The output is a Matlab structure that is
+% is exported by BESA). The output is a MATLAB structure that is
 % compatible with FieldTrip.
 %
 % The format of the output structure depends on the type of datafile:
@@ -19,7 +19,7 @@
 %   *.dat combined with a *.gen or *.generic is converted to a structure similar to the output of PREPROCESSING
 %
 % Note (*): If the BESA toolbox by Karsten Hochstatter is found on your
-% Matlab path, the readBESAxxx functions will be used (where xxx=tfc/swf),
+% MATLAB path, the readBESAxxx functions will be used (where xxx=tfc/swf),
 % alternatively the private functions from FieldTrip will be used.
 %
 % See also EEGLAB2FIELDTRIP

fieldtrip2fiff.m

@@ -188,7 +188,7 @@ function fieldtrip2fiff(filename, data)
 
 % otherwise reconstruct it
 fprintf('Reconstructing channel locations, it might be inaccurate\n')
-FIFF = fiff_define_constants; % some constants are not defined in the Matlab function
+FIFF = fiff_define_constants; % some constants are not defined in the MATLAB function
 
 if isfield(data, 'grad')
   hasgrad = true;

fileio/ft_create_buffer.m

@@ -1,7 +1,7 @@
 function ft_create_buffer(port)
 
 % FT_CREATE_BUFFER starts the thread with the TCP server attached to the local
-% Matlab instance. The TCP server will listen to the specified network
+% MATLAB instance. The TCP server will listen to the specified network
 % port, and accept incoming read and write requests.
 %
 % Use as

fileio/ft_destroy_buffer.m

@@ -1,7 +1,7 @@
 function ft_destroy_buffer
 
 % FT_DESTROY_BUFFER stops the thread with the TCP server attached to
-% the local Matlab instance and removes all data from memory.
+% the local MATLAB instance and removes all data from memory.
 %
 % Use as
 %   ft_destroy_buffer

fileio/ft_filetype.m

@@ -1082,8 +1082,8 @@
   content = 'electrophysiological data';
 elseif filetype_check_extension(filename, '.mat') && filetype_check_header(filename, 'MATLAB')
   type = 'matlab';
-  manufacturer = 'Matlab';
-  content = 'Matlab binary data';
+  manufacturer = 'MATLAB';
+  content = 'MATLAB binary data';
 elseif filetype_check_header(filename, 'RIFF', 0) && filetype_check_header(filename, 'WAVE', 8)
   type = 'riff_wave';
   manufacturer = 'Microsoft';

fileio/ft_read_data.m

@@ -750,7 +750,7 @@
     ft_hastoolbox('egi_mff', 1);
     % ensure that the JVM is running and the jar file is on the path
       %%%%%%%%%%%%%%%%%%%%%%
-      %workaround for Matlab bug resulting in global variables being cleared
+      %workaround for MATLAB bug resulting in global variables being cleared
       globalTemp=cell(0);
       globalList=whos('global');
       varList=whos;
@@ -763,7 +763,7 @@
       mff_setup;
 
       %%%%%%%%%%%%%%%%%%%%%%
-      %workaround for Matlab bug resulting in global variables being cleared
+      %workaround for MATLAB bug resulting in global variables being cleared
       varNames={varList.name};
       for i=1:length(globalList)
           eval([globalList(i).name '=globalTemp{i};']);

fileio/ft_read_event.m

@@ -993,7 +993,7 @@
     % this is multiplexed data in a *.bin file, accompanied by a matlab file containing the header and event
     [path, file, ext] = fileparts(filename);
     filename = fullfile(path, [file '.mat']);
-    % read the events from the Matlab file
+    % read the events from the MATLAB file
     tmp   = load(filename, 'event');
     event = tmp.event;
 
@@ -1107,7 +1107,7 @@
     end
 
   case 'matlab'
-    % read the events from a normal Matlab file
+    % read the events from a normal MATLAB file
     tmp   = load(filename, 'event');
     event = tmp.event;
 

fileio/ft_read_header.m

@@ -983,7 +983,7 @@
     % ensure that the JVM is running and the jar file is on the path
 
     %%%%%%%%%%%%%%%%%%%%%%
-    %workaround for Matlab bug resulting in global variables being cleared
+    %workaround for MATLAB bug resulting in global variables being cleared
     globalTemp=cell(0);
     globalList=whos('global');
     varList=whos;
@@ -996,7 +996,7 @@
     mff_setup;
 
     %%%%%%%%%%%%%%%%%%%%%%
-    %workaround for Matlab bug resulting in global variables being cleared
+    %workaround for MATLAB bug resulting in global variables being cleared
     varNames={varList.name};
     for i=1:length(globalList)
       eval(['global ' globalList(i).name ';']);
@@ -1045,7 +1045,7 @@
     hdr.nTrials     = 1;  % since continuous
     hdr.orig        = []; % this will contain the chunks (if present)
 
-    % add the contents of attached FIF_header chunk after decoding to Matlab structure
+    % add the contents of attached FIF_header chunk after decoding to MATLAB structure
     if isfield(orig, 'neuromag_header')
       if isempty(cachechunk)
         % this only needs to be decoded once
@@ -1074,7 +1074,7 @@
       hdr.orig = cachechunk;
     end
 
-    % add the contents of attached RES4 chunk after decoding to Matlab structure
+    % add the contents of attached RES4 chunk after decoding to MATLAB structure
     if isfield(orig, 'ctf_res4')
       if isempty(cachechunk)
         % this only needs to be decoded once
@@ -1100,14 +1100,14 @@
       hdr.orig.ctf_res4 = orig.ctf_res4;
     end
 
-    % add the contents of attached NIFTI-1 chunk after decoding to Matlab structure
+    % add the contents of attached NIFTI-1 chunk after decoding to MATLAB structure
     if isfield(orig, 'nifti_1')
       hdr.nifti_1 = decode_nifti1(orig.nifti_1);
       % add the raw chunk as well
       hdr.orig.nifti_1 = orig.nifti_1;
     end
 
-    % add the contents of attached SiemensAP chunk after decoding to Matlab structure
+    % add the contents of attached SiemensAP chunk after decoding to MATLAB structure
     if isfield(orig, 'siemensap') && exist('sap2matlab')==3 % only run this if MEX file is present
       hdr.siemensap = sap2matlab(orig.siemensap);
       % add the raw chunk as well

ft_analysispipeline.m

@@ -42,7 +42,7 @@
 % This function uses the nested cfg and cfg.previous that are present in
 % the data structure. It will use the configuration and the nested previous
 % configurations to climb all the way back into the tree. This funtction
-% will print a complete Matlab script to screen (and optionally to file).
+% will print a complete MATLAB script to screen (and optionally to file).
 % Furthermore, it will show an interactive graphical flowchart
 % representation of the steps taken during the pipeline(i). In the flowchart
 % you can click on one of the steps to see the configuration details of

ft_analysisprotocol.m

@@ -2,7 +2,7 @@
 
 % FT_ANALYSISPROTOCOL tries to reconstruct the complete analysis protocol that
 % was used to create an arbitrary FieldTrip data structure. It will create
-% a Matlab script (as text file) and a flowchart with a graphical
+% a MATLAB script (as text file) and a flowchart with a graphical
 % representation.
 %
 % Use as
@@ -43,7 +43,7 @@
 % This function uses the nested cfg and cfg.previous that are present in
 % the data structure. It will use the configuration and the nested previous
 % configurations to climb all the way back into the tree. This funtction
-% will print a complete Matlab script to screen (and optionally to file).
+% will print a complete MATLAB script to screen (and optionally to file).
 % Furthermore, it will show an interactive graphical flowchart
 % representation of the steps taken during the analysis. In the flowchart
 % you can click on one of the steps to see the configuration details of
@@ -175,7 +175,7 @@
 try
   thisname = getsubfield(datacfg, 'version.name');
   if isstruct(thisname)
-    % I think that this was needed for Matlab 6.5
+    % I think that this was needed for MATLAB 6.5
     thisname = thisname.name;
   end
   [p, f] = fileparts(thisname);

ft_compile_mex.m

@@ -20,7 +20,7 @@ function ft_compile_mex(force)
 % procedure for setting up the MEX environment.
 %
 % The logic in this script is to first build a list of files that actually
-% need compilation for the particular platform that Matlab is running on,
+% need compilation for the particular platform that MATLAB is running on,
 % and then to go through that list. Functions are added to the list by
 % giving their destination directory and (relative to that) the name of the
 % source file (without the .c). Optionally, you can specify a list of

ft_defaults.m

@@ -126,7 +126,7 @@
   end
 
   try
-    % this directory contains various functions that were obtained from elsewere, e.g. Matlab file exchange
+    % this directory contains various functions that were obtained from elsewere, e.g. MATLAB file exchange
     ft_hastoolbox('fileexchange', 3, 1); % not required
   end
 

ft_definetrial.m

@@ -18,7 +18,7 @@
 % A call to FT_DEFINETRIAL results in the trial definition "trl" being
 % added to the output configuration structure. The trials are defined
 % according to the triggers, trials or other events in the data, or
-% from a user-specified Matlab function (subsequently referred to as
+% from a user-specified MATLAB function (subsequently referred to as
 % the trial function) which returns "trl". The user can specify the
 % name of his/her custom trial function that is tailored to the
 % experimental paradigm, or use the default trial function
@@ -154,7 +154,7 @@
 
   % determine the number of outpout arguments of the user-supplied trial function
   try
-    % the nargout function in Matlab 6.5 and older does not work on function handles
+    % the nargout function in MATLAB 6.5 and older does not work on function handles
     num = nargout(cfg.trialfun);
   catch
     num = 1;

ft_documentationindex.m

@@ -152,7 +152,7 @@
 currletter = char(96);
 fprintf(fid, '====== Index of configuration options ======\n\n');
 fprintf(fid, 'A detailed description of each function is available in the [[:reference|reference documentation]].\n\n');
-fprintf(fid, 'This index to the reference documentation is automatically generated from the Matlab code every day. Therefore you should not edit this page manually, since your changes would be overwritten automatically. If you want to suggest corrections to the documentation, please send them by email to the mailing list or to one of the main developers (see [[:contact]]).\n\n');
+fprintf(fid, 'This index to the reference documentation is automatically generated from the MATLAB code every day. Therefore you should not edit this page manually, since your changes would be overwritten automatically. If you want to suggest corrections to the documentation, please send them by email to the mailing list or to one of the main developers (see [[:contact]]).\n\n');
 for i=1:size(index,1)
   fprintf('%s -- %s -- %s\n', index{i,2}, index{i,3}, index{i,1});
   if isempty(index{i,1})

ft_documentationreference.m

@@ -116,7 +116,7 @@ function ft_documentationreference(outdir)
 
   fid = fopen(filename, 'wt');
   fprintf(fid, '=====  %s =====\n\n', upper(funname{i}));
-  fprintf(fid, 'Note that this reference documentation is identical to the help that is displayed in Matlab when you type "help %s".\n\n', funname{i});
+  fprintf(fid, 'Note that this reference documentation is identical to the help that is displayed in MATLAB when you type "help %s".\n\n', funname{i});
   fprintf(fid, '<html><pre>\n');   % required for docuwiki > use html preformatted style
   fprintf(fid, '%s', str);
   fprintf(fid, '</pre></html>\n'); % required for docuwiki

ft_freqanalysis.m

@@ -453,6 +453,7 @@
 
 ft_progress('init', cfg.feedback, 'processing trials');
 for itrial = 1:ntrials
+
   %disp(['processing trial ' num2str(itrial) ': ' num2str(size(data.trial{itrial},2)) ' samples']);
   fbopt.i = itrial;
   fbopt.n = ntrials;

ft_freqstatistics.m

@@ -27,7 +27,7 @@
 %   cfg.method       = different methods for calculating the significance probability and/or critical value
 %                    'montecarlo'    get Monte-Carlo estimates of the significance probabilities and/or critical values from the permutation distribution,
 %                    'analytic'      get significance probabilities and/or critical values from the analytic reference distribution (typically, the sampling distribution under the null hypothesis),
-%                    'stats'         use a parametric test from the Matlab statistics toolbox,
+%                    'stats'         use a parametric test from the MATLAB statistics toolbox,
 %                    'crossvalidate' use crossvalidation to compute predictive performance
 %
 %   cfg.design       = Nxnumobservations: design matrix (for examples/advice, please see the Fieldtrip wiki,
@@ -330,7 +330,7 @@
   statfield = fieldnames(stat);
 else
   % only the probability was returned as a single matrix, reformat into a structure
-  dum = stat; stat = []; % this prevents a Matlab warning that appears from release 7.0.4 onwards
+  dum = stat; stat = []; % this prevents a MATLAB warning that appears from release 7.0.4 onwards
   stat.prob = dum;
   statfield = fieldnames(stat);
 end

ft_mvaranalysis.m

@@ -480,6 +480,6 @@
 %------------------------------------------------------
 %---subfunction to ensure that the first two input arguments are of double
 % precision this prevents an instability (bug) in the computation of the
-% tapers for Matlab 6.5 and 7.0
+% tapers for MATLAB 6.5 and 7.0
 function [tap] = double_dpss(a, b, varargin)
 tap = dpss(double(a), double(b), varargin{:});

ft_sliceinterp.m

@@ -361,7 +361,7 @@
 % merge anatomy, functional data and mask
 fprintf('constructing overlay...');
 if ischar(cfg.colormap)
-  % replace string by colormap using standard Matlab function
+  % replace string by colormap using standard MATLAB function
   cfg.colormap = colormap(cfg.colormap);
 end
 cmap = cfg.colormap;

ft_sourceplot.m

@@ -1031,7 +1031,7 @@
 
   if strcmp(cfg.colorbar,  'yes'),
     if hasfun
-      % use a normal Matlab colorbar
+      % use a normal MATLAB colorbar
       hc = colorbar;
       set(hc, 'YLim', [fcolmin fcolmax]);
     else
@@ -1128,7 +1128,7 @@
   axis off
   if strcmp(cfg.colorbar,  'yes'),
     if hasfun
-      % use a normal Matlab coorbar
+      % use a normal MATLAB coorbar
       hc = colorbar;
       set(hc, 'YLim', [fcolmin fcolmax]);
     else
@@ -1212,7 +1212,7 @@ function plot2D(vols2D, scales, doimage)
 hasfun = length(vols2D)>1 && ~isempty(vols2D{2});
 hasmsk = length(vols2D)>2 && ~isempty(vols2D{3});
 
-% the transpose is needed for displaying the matrix using the Matlab image() function
+% the transpose is needed for displaying the matrix using the MATLAB image() function
 if hasana; ana = vols2D{1}'; end;
 if hasfun && ~doimage; fun = vols2D{2}'; end;
 if hasfun && doimage;  fun = permute(vols2D{2},[2 1 3]); end;
@@ -1443,7 +1443,7 @@ function cb_redraw(h, eventdata)
   if opt.hasfun
     % vectorcolorbar = linspace(fscolmin, fcolmax,length(cfg.funcolormap));
     % imagesc(vectorcolorbar,1,vectorcolorbar);colormap(cfg.funcolormap);
-    % use a normal Matlab colorbar, attach it to the invisible 4th subplot
+    % use a normal MATLAB colorbar, attach it to the invisible 4th subplot
     try
       caxis([opt.fcolmin opt.fcolmax]);
     end