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pop_dipfit_settings.m
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% pop_dipfit_settings() - select global settings for dipole fitting through a pop up window
%
% Usage:
% >> OUTEEG = pop_dipfit_settings ( INEEG ); % pop up window
% >> OUTEEG = pop_dipfit_settings ( INEEG, 'key1', 'val1', 'key2', 'val2' ... )
%
% Inputs:
% INEEG input dataset
%
% Optional inputs:
% 'hdmfile' - [string] file containing a head model compatible with
% the Fieldtrip dipolefitting() function ("vol" entry)
% 'mrifile' - [string] file containing an anatomical MR head image.
% The MRI must be normalized to the MNI brain. See the .mat
% files used by the sphere and boundary element models
% (For instance, select the sphere model and study 'EEG.dipfit').
% If SPM2 software is installed, dipfit will be able to read
% most MRI file formats for plotting purposes (.mnc files, etc...).
% To plot dipoles in a subject MRI, first normalize the MRI
% to the MNI brain using SPM2.
% 'coordformat' - ['MNI'|'Spherical'] Coordinates returned by the selected
% head model. May be MNI coordinates or spherical coordinates.
% (For spherical coordinates, the head radius is assumed to be 85 mm.
% 'chanfile' - [string] template channel locations file. (This function will
% check whether your channel locations file is compatible with
% your selected head model).
% 'chansel' - [integer vector] indices of channels to use for dipole fitting.
% {default: all}
% 'chanomit' - [integer vector] indices of channels to omit {default: none}
% 'electrodes' - [integer array] indices of channels to include
% in the dipole model. {default: all}
% 'model' - ['standardBEM'|'standardBESA'] use one of the standard
% models. {default: all}
% 'coord_transform' - [float array or string] Talairach transformation matrix for
% aligning the dataset channel locations to the selected
% head model. You may also use the string
% 'warpfiducials' to warp the head model and current
% data fiducials.
% 'alignfiducuals' to align fiducial (rigid transformation)
% % This should be used with caution as
% the alignment often needs manual fine tuning.
% 'plotalignment' - ['on'|'off'] plot electrode alignment with head model
% mesh.
%
% Outputs:
% OUTEEG output dataset
%
% Author: Arnaud Delorme, SCCN, La Jolla 2003-
% Robert Oostenveld, SMI/FCDC, Nijmegen 2003
% MEG flag:
% 'gradfile' - [string] file containing gradiometer locations
% ("gradfile" parameter in Fieldtrip dipolefitting() function)
% SMI, University Aalborg, Denmark http://www.smi.auc.dk/
% FC Donders Centre, University Nijmegen, the Netherlands http://www.fcdonders.kun.nl
% Copyright (C) 2003 arno@salk.edu, Arnaud Delorme, SCCN, La Jolla 2003-2005
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [OUTEEG, com] = pop_dipfit_settings ( EEG, varargin )
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if nargin < 1
help pop_dipfit_settings;
return;
end
if ~plugin_askinstall('Fieldtrip-lite', 'ft_dipolefitting'), return; end
OUTEEG = EEG(1);
com = '';
% get the default values and filenames
dipfitdefs;
% check channel file
if isstruct(EEG) && isfield(EEG(1).chaninfo, 'filename')
originalChanfile = lower(EEG(1).chaninfo.filename);
[filePathTmp,fileNameTmp, extTmp] = fileparts( originalChanfile );
if contains(extTmp, 'lay') || contains(filePathTmp, 'layout') || contains(fileNameTmp, 'layout')
error( [ 'You are using a layout channel coordinate file.' 10 'You may not use these coordinates for source localization.' 10 'They are made for 2-D plotting only.' ])
end
else
originalChanfile = '';
end
if nargin < 2
if ischar(EEG)
userdat = get(gcf, 'userdata');
current = userdat.current_model;
templates = userdat.template_models;
chanfile = userdat.chanfile;
valmodel = get(findobj(gcf, 'tag', 'listmodels'), 'value');
if isequal(EEG, 'setmodel') % redraw
[hdmEnable, hdmString ] = checkStructure(current.hdmfile);
[mriEnable, mriString ] = checkStructure(current.mrifile);
[chanEnable, chanString] = checkStructure(current.chanfile);
coordformat = current.coordformat;
set(findobj(gcf, 'tag', 'hdmfile' ), 'string', hdmString, 'enable', hdmEnable);
set(findobj(gcf, 'tag', 'mri' ), 'string', mriString, 'enable', mriEnable);
set(findobj(gcf, 'tag', 'chans' ), 'string', chanString, 'enable', chanEnable);
set(findobj(gcf, 'tag', 'coord'), 'value' , fastif(strcmpi(current.coordformat,'MNI'),2, ...
fastif(strcmpi(current.coordformat,'Spherical'),1,3)));
set(findobj(gcf, 'tag', 'modelBrowse' ), 'enable', hdmEnable);
set(findobj(gcf, 'tag', 'mriBrowse' ), 'enable', mriEnable);
set(findobj(gcf, 'tag', 'chansBrowse' ), 'enable', chanEnable);
if isfield(current, 'allkeywordstrue') && current.allkeywordstrue && isempty(current.coord_transform)
set(findobj(gcf, 'tag', 'coregcheckbox'), 'value', 1);
set(findobj(gcf, 'tag', 'coregtext'), 'string', '');
else
set(findobj(gcf, 'tag', 'coregcheckbox'), 'value', 0);
if ~isempty(current.coord_transform)
set(findobj(gcf, 'tag', 'coregtext'), 'string', char(vararg2str({ current.coord_transform })));
else
set(findobj(gcf, 'tag', 'coregtext'), 'string', '');
end
end
elseif isequal(EEG, 'changemodel') % redraw
userdat.current_model = userdat.template_models(valmodel);
[userdat.current_model.allkeywordstrue, userdat.current_model.coord_transform] = lookupchantemplate(chanfile, templates(valmodel).coord_transform);
set(gcf, 'userdata', userdat);
pop_dipfit_settings('setmodel');
elseif isequal(EEG, 'coregister') % redraw
coregObj = findobj(gcbf, 'tag', 'coregtext');
tmptransf = get( coregObj, 'string');
[~, tmptransf] = coregister(userdat.chanlocs, current.chanfile, 'mesh', current.hdmfile, ...
'transform', str2num(tmptransf), 'chaninfo1', userdat.chaninfo, 'helpmsg', 'on');
if ~isempty(tmptransf)
set( coregObj, 'string', num2str(tmptransf));
end
end
return;
end
% detect DIPFIT1.0x structure
% ---------------------------
if isfield(EEG(1).dipfit, 'vol')
str = [ 'Dipole information structure from DIPFIT v1.02 detected.' ...
'Keep or erase the old dipole information including dipole locations? ' ...
'In either case, a new dipole model can be constructed.' ];
tmpButtonName=questdlg2( strmultiline(str, 60), 'Old DIPFIT structure', 'Keep', 'Erase', 'Keep');
if strcmpi(tmpButtonName, 'Keep'), return; end
end
% determine default model
% -----------------------
dipfitdefs; % contains template_model
valmodel = 2; % default model now MNI
userdata = [];
if isfield(EEG(1).dipfit, 'hdmfile') && ~isempty(EEG(1).dipfit.hdmfile)
OUTEEG.dipfit = EEG(1).dipfit;
if isequal(EEG(1).dipfit.hdmfile, template_models(1).hdmfile)
valmodel = 1;
elseif isequal(EEG(1).dipfit.hdmfile, template_models(2).hdmfile)
valmodel = 2;
else
valmodel = 3;
end
nocoreg = false;
else
if isfield(EEG(1).chaninfo, 'filename')
if ~isempty(findstr(lower(EEG(1).chaninfo.filename), 'standard-10-5-cap385')), valmodel = 1; end
if ~isempty(findstr(lower(EEG(1).chaninfo.filename), 'standard_1005')), valmodel = 2; end
end
OUTEEG.dipfit.hdmfile = template_models(valmodel).hdmfile;
OUTEEG.dipfit.mrifile = template_models(valmodel).mrifile;
OUTEEG.dipfit.chanfile = template_models(valmodel).chanfile;
OUTEEG.dipfit.coordformat = template_models(valmodel).coordformat;
OUTEEG.dipfit.coord_transform = [];
nocoreg = ~template_models(valmodel).coregval;
end
% coordinate format
if isequal(OUTEEG.dipfit.coordformat, 'spherical')
valcoord = 1;
elseif isequal(OUTEEG.dipfit.coordformat, 'MNI')
valcoord = 2;
else
valcoord = 3;
end
geomvert = [1 1 1 1 1 1 1 1];
geomhorz = {
[1 2]
[0.2 1 1.3 0.5 0.5 ]
[0.2 1 1.3 0.9 0.1 ]
[0.2 1 1.3 0.5 0.5 ]
[0.2 1 1.3 0.5 0.5 ]
[1]
[1 1 0.5 0.5 ]
[1 1 0.5 0.5 ]
};
% define each individual graphical user element
comhelp1 = [ 'warndlg2(strvcat(''The two default head models are in standard_BEM and standard_BESA'',' ...
''' sub-folders in the DIPFIT2 plugin folder, and may be modified there.''), ''Model type'');' ];
comhelp3 = [ 'warndlg2(strvcat(''Any MR image normalized to the MNI brain model may be used for plotting'',' ...
'''(see the DIPFIT 2.0 tutorial for more information)''), ''Model type'');' ];
comhelp2 = [ 'warndlg2(strvcat(''The template location file associated with the head model'',' ...
'''you are using must be entered (see tutorial).''), ''Template location file'');' ];
commandload1 = [ '[filename, filepath] = uigetfile(''*'', ''Select a text file'');' ...
'if filename ~=0,' ...
' set(findobj(''parent'', gcbf, ''tag'', ''hdmfile''), ''string'', [ filepath filename ]);' ...
'end;' ...
'clear filename filepath tagtest;' ];
commandload2 = [ '[filename, filepath] = uigetfile(''*'', ''Select a text file'');' ...
'if filename ~=0,' ...
' set(findobj(''parent'', gcbf, ''tag'', ''chans''), ''string'', [ filepath filename ]);' ...
'end;' ...
'clear filename filepath tagtest;' ];
commandload3 = [ '[filename, filepath] = uigetfile(''*'', ''Select a text file'');' ...
'if filename ~=0,' ...
' set(findobj(''parent'', gcbf, ''tag'', ''mri''), ''string'', [ filepath filename ]);' ...
'end;' ...
'clear filename filepath tagtest;' ];
cb_selectcoreg = 'pop_dipfit_settings(''coregister'');';
cb_selectelectrodes = 'tmplocs = EEG(1).chanlocs; set(findobj(gcbf, ''tag'', ''elec''), ''string'', int2str(pop_chansel({tmplocs.labels}))); clear tmplocs;';
changemodel = 'pop_dipfit_settings(''changemodel'');';
templatenames = { template_models.name };
coordformatlist = { 'spherical (head radius 85 mm)' 'MNI' 'Neuromag (MEG only)' 'Custom'};
coordformatshort = { 'Spherical' 'MNI' 'Custom'};
elements = { ...
{ 'style' 'text' 'string' 'Select a head model' 'fontweight' 'bold' } ...
{ 'style' 'popupmenu' 'string' strvcat(templatenames{:}) ...
'callback' changemodel 'value' valmodel 'tag' 'listmodels' } ...
{ } { 'style' 'text' 'string' 'Output coordinates' } ...
{ 'style' 'popupmenu' 'string' coordformatlist 'tag' 'coord' ...
'value' valcoord 'userdata' 'editable' 'enable' 'on'} { } { } ...
{ } { 'style' 'text' 'string' 'Head model file' 'tag' 'headstr' } ...
{ 'style' 'edit' 'string' '_______' 'tag' 'hdmfile' 'horizontalalignment' 'right' 'userdata' 'editable' 'enable' 'on'} ...
{ 'style' 'pushbutton' 'string' 'Browse' 'tag' 'modelBrowse' 'callback' commandload1 'userdata' 'editable' 'enable' 'off' } ...
{ 'style' 'pushbutton' 'string' 'Help' 'callback' comhelp1 } ...
{ } { 'style' 'text' 'string' 'Associated MRI file for plotting' 'tag' 'mristr' } ...
{ 'style' 'edit' 'string' '_______' 'tag' 'mri' 'horizontalalignment' 'right' 'enable' 'on' } ...
{ 'style' 'pushbutton' 'string' 'Browse' 'tag' 'mriBrowse' 'callback' commandload3 } ...
{ 'style' 'pushbutton' 'string' 'Help' 'callback' comhelp3 } ...
{ } { 'style' 'text' 'string' 'Associated coord. landmarks if any', 'tag', 'chanstr' } ...
{ 'style' 'edit' 'string' '_______' 'tag' 'chans' 'horizontalalignment' 'right' 'userdata' 'editable' 'enable' 'on'} ...
{ 'style' 'pushbutton' 'string' 'Browse' 'tag' 'chansBrowse' 'callback' commandload2 'userdata' 'editable' 'enable' 'on'} ...
{ 'style' 'pushbutton' 'string' 'Help' 'callback' comhelp2 } ...
{ } ...
{ 'style' 'text' 'string' 'Matrix to align chan. locs. with head model' 'userdata' 'coreg' } ...
{ 'style' 'edit' 'string' '' 'tag' 'coregtext' 'userdata' 'coreg' } ...
{ 'style' 'pushbutton' 'string' 'Co-register' 'fontweight' 'bold' 'tag' 'manualcoreg' 'callback' cb_selectcoreg } ...
{ 'style' 'checkbox' 'string' 'No Co-Reg.' 'tag' 'coregcheckbox' 'value' nocoreg 'userdata' 'coreg' } ...
{ 'style' 'text' 'string' 'Channels to omit from dipole fitting' } ...
{ 'style' 'edit' 'string' '' 'tag' 'elec' } ...
{ 'style' 'pushbutton' 'string' '...' 'callback' cb_selectelectrodes } { } ...
};
% plot GUI and protect parameters
% -------------------------------
userdata.template_models = template_models;
userdata.current_model = OUTEEG.dipfit;
userdata.chanlocs = EEG(1).chanlocs;
userdata.chaninfo = EEG(1).chaninfo;
userdata.chanfile = originalChanfile;
optiongui = { 'geometry', geomhorz, 'uilist', elements, 'helpcom', 'pophelp(''pop_dipfit_settings'')', ...
'title', 'Dipole fit settings - pop_dipfit_settings()', ...
'userdata', userdata, 'geomvert', geomvert 'eval' 'pop_dipfit_settings(''setmodel'');' };
[result, ~, ~, restag] = inputgui( optiongui{:});
if isempty(result), return; end
if test_wrong_parameters(restag)
return;
end
% decode GUI inputs
% -----------------
options = {};
if ~strcmpi(restag.hdmfile, 'Matlab structure')
options = { options{:} 'hdmfile' restag.hdmfile };
end
if ~strcmpi( restag.mri, 'Matlab structure')
options = { options{:} 'mrifile' restag.mri };
end
if ~strcmpi( restag.chans, 'Matlab structure')
options = { options{:} 'chanfile' restag.chans };
end
if restag.coord < 3
options = { options{:} 'coordformat' coordformatshort{restag.coord} };
else
if isfield(EEG.dipfit, 'coordformat') && ~isempty(EEG.dipfit.coordformat)
options = { options{:} 'coordformat' EEG.dipfit.coordformat };
else
options = { options{:} 'coordformat' 'other' };
end
end
if ~restag.coregcheckbox
options = { options{:} 'coord_transform' str2num(restag.coregtext) };
end
if ~isempty(restag.elec)
options = { options{:} 'chanomit' str2num(restag.elec) };
end
else
options = varargin;
end
% process multiple datasets
% -------------------------
if length(EEG) > 1
if nargin < 2
[ OUTEEG, com ] = eeg_eval( 'pop_dipfit_settings', EEG, 'warning', 'on', 'params', options );
else
[ OUTEEG, com ] = eeg_eval( 'pop_dipfit_settings', EEG, 'params', options );
end
return;
end
g = finputcheck(options, { 'hdmfile' 'string' [] '';
'mrifile' '' [] '';
'chanfile' '' [] '';
'chanomit' '' [] '';
'chansel' 'integer' [] 1:EEG.nbchan;
'electrodes' 'integer' [] [];
'coord_transform' '' [] ''; % this does nothing while [] set to empty
'plotalignment' 'string' {'on' 'off'} 'off';
'model' 'string' {'standardBEM' 'standardBESA' ''} '';
'coordformat' 'string' { } '' });
if isstr(g), error(g); end
dipfitdefs;
OUTEEG.dipfit = EEG.dipfit;
if ~isempty(g.hdmfile)
OUTEEG.dipfit.hdmfile = g.hdmfile;
end
if ~isempty(g.mrifile)
OUTEEG.dipfit.mrifile = g.mrifile;
end
if ~isempty(g.chanfile)
OUTEEG.dipfit.chanfile = g.chanfile;
end
if ~isempty(g.coordformat)
OUTEEG.dipfit.coordformat = g.coordformat;
end
if strcmpi(g.model, 'standardBESA')
OUTEEG.dipfit.hdmfile = template_models(1).hdmfile;
OUTEEG.dipfit.mrifile = template_models(1).mrifile;
OUTEEG.dipfit.chanfile = template_models(1).chanfile;
OUTEEG.dipfit.coordformat = template_models(1).coordformat;
[~, OUTEEG.dipfit.coord_transform] = lookupchantemplate(originalChanfile, template_models(1).coord_transform);
elseif strcmpi(g.model, 'standardBEM')
OUTEEG.dipfit.hdmfile = template_models(2).hdmfile;
OUTEEG.dipfit.mrifile = template_models(2).mrifile;
OUTEEG.dipfit.chanfile = template_models(2).chanfile;
OUTEEG.dipfit.coordformat = template_models(2).coordformat;
[~, OUTEEG.dipfit.coord_transform] = lookupchantemplate(originalChanfile, template_models(2).coord_transform);
end
if ~isempty(g.chanomit)
OUTEEG.dipfit.chansel = setdiff(1:EEG.nbchan, g.chanomit);
else
OUTEEG.dipfit.chansel = g.chansel;
end
if ischar(g.coord_transform)
if isequal(g.coord_transform, 'warpfiducials')
[~,coord_transform] = coregister(EEG.chaninfo.nodatchans, OUTEEG.dipfit.chanfile, 'warp', 'auto', 'manual', 'off');
OUTEEG.dipfit.coord_transform = coord_transform;
elseif isequal(g.coord_transform, 'alignfiducials')
[~,coord_transform] = coregister(EEG.chaninfo.nodatchans, OUTEEG.dipfit.chanfile, 'warp', 'auto', 'warpmethod', 'globalrescale', 'manual', 'off');
OUTEEG.dipfit.coord_transform = coord_transform;
elseif ~isempty(g.coord_transform)
error('Unknown parameter for coord_transform')
end
else
OUTEEG.dipfit.coord_transform = g.coord_transform;
end
if ~isempty(g.electrodes), OUTEEG.dipfit.chansel = g.electrodes; end
% removing channels with no coordinates
% -------------------------------------
[~, ~, ~, ~, indices] = readlocs(EEG.chanlocs);
if length(indices) < length(EEG.chanlocs)
OUTEEG.dipfit.chansel = intersect( OUTEEG.dipfit.chansel, indices);
fprintf('Warning: %d channels without coordinates removed from dipole fitting\n', OUTEEG.nbchan-length(OUTEEG.dipfit.chansel));
end
if isfield(OUTEEG.chanlocs, 'type') && ~isempty(strfind(OUTEEG.chanlocs(1).type, 'meg'))
if ischar(OUTEEG.dipfit.hdmfile) && ~isempty(strfind(OUTEEG.dipfit.hdmfile, 'dipfit')) && ~isempty(strfind(OUTEEG.dipfit.hdmfile, 'standard_vol'))
if ~isempty(OUTEEG.dipfit.coord_transform)
error('You are using the standard volume but have not specified the model and sensor alignment');
end
end
% read head model and MRI as they need to be aligned with sensors
if ~isstruct(OUTEEG.dipfit.mrifile)
OUTEEG.dipfit.mrifile = ft_read_mri(OUTEEG.dipfit.mrifile);
end
if ~isstruct(OUTEEG.dipfit.hdmfile)
OUTEEG.dipfit.hdmfile = ft_read_headmodel(OUTEEG.dipfit.hdmfile);
end
% check head model
if length(OUTEEG.dipfit.hdmfile.bnd) > 1
disp('Standard EEG head model detected, converting it to single shell MEG')
cfg = [];
cfg.method='singleshell';
OUTEEG.dipfit.hdmfile = ft_prepare_headmodel(cfg, OUTEEG.dipfit.hdmfile.bnd(3)); % use brain surface only
end
% Standard head model
comp = eeglab2fieldtrip(OUTEEG, 'componentanalysis', 'dipfit');
if ~isempty(OUTEEG.dipfit.coord_transform)
% Rational: we change the MRI transformation matrix to match
% the final sensor space based on the provided transformation
% matrix (usually computed using fiducials)
transform_mat = OUTEEG.dipfit.coord_transform;
if isfield(OUTEEG.chaninfo, 'originalnosedir')
if strcmpi(OUTEEG.chaninfo.originalnosedir, '+Y')
transform_mat(6) = transform_mat(6)+pi/2;
OUTEEG.dipfit.coord_transform = [0 0 0 0 0 0 1 1 1];
OUTEEG.dipfit.coord_transform(6) = OUTEEG.dipfit.coord_transform(6)-pi/2;
end
end
tra = traditionaldipfit( transform_mat );
tra = pinv(tra);
% change MRI coordinate system
mri = OUTEEG.dipfit.mrifile;
mri.transform = tra * mri.transform;
mri.coordsys = comp.grad.coordsys; % target coordinate system
mri.unit = comp.grad.unit;
OUTEEG.dipfit.mrifile = mri;
% change head model coordinate system
hdm = OUTEEG.dipfit.hdmfile;
hdm.bnd(end).pos = tra * [ hdm.bnd(end).pos ones(length(hdm.bnd(end).pos),1)]';
hdm.bnd(end).pos = hdm.bnd(end).pos(1:3,:)';
hdm.unit = comp.grad.unit;
% fiduacial coordinate system
elec = readlocs(OUTEEG.dipfit.chanfile);
for iChan = 1:length(elec)
elecTmp = tra * [elec(iChan).X elec(iChan).Y elec(iChan).Z 1]';
[elec(iChan).X, elec(iChan).Y, elec(iChan).Z] = deal(elecTmp(1),elecTmp(2),elecTmp(3));
end
OUTEEG.dipfit.chanfile = elec;
OUTEEG.dipfit.hdmfile = hdm;
else
if 0
% Rational: we perform automated coordinate transformation
% based on the MRI and MEG coordinate space coordinates
% This solution return mostly aligned but quite off solution
% and has been disabled
mri = ft_read_mri(OUTEEG.dipfit.mrifile);
mri.coordsys = 'acpc';
OUTEEG.dipfit.mrifile = ft_convert_coordsys(mri, comp.grad.coordsys); % better to use the fiducials above
hdm = ft_read_headmodel(OUTEEG.dipfit.hdmfile);
hdm.coordsys = 'acpc';
OUTEEG.dipfit.hdmfile = ft_convert_coordsys(hdm, comp.grad.coordsys); % better to use the fiducials above
end
fprintf(2, 'Warning: No transformation specified for MEG sensor coregistration.')
fprintf(2, 'This assumes the head model and MRI given as input are already aligned to your')
fprintf(2, 'sensor space (which is only the case if you did this manually in Fieldtrip).')
end
% ft_convert_coordsys assumes the same units
if isequal(comp.grad.unit, 'cm') && isequal(OUTEEG.dipfit.mrifile.unit, 'mm')
OUTEEG.dipfit.mrifile.transform = traditionaldipfit([0 0 0 0 0 0 1/10 1/10 1/10])*OUTEEG.dipfit.mrifile.transform;
OUTEEG.dipfit.mrifile.unit = 'cm';
OUTEEG.dipfit.hdmfile.bnd.pos = OUTEEG.dipfit.hdmfile.bnd.pos/10;
OUTEEG.dipfit.hdmfile.unit = 'cm';
end
% check alignment
if strcmpi(g.plotalignment, 'on')
if ischar(OUTEEG.dipfit.hdmfile)
hdm = ft_read_headmodel(OUTEEG.dipfit.hdmfile);
else
hdm = OUTEEG.dipfit.hdmfile;
end
if isequal(hdm.unit, 'cm') && isequal(comp.grad.unit, 'mm')
hdm.bnd.pos = hdm.bnd.pos*10;
elseif isequal(hdm.unit, 'mm') && isequal(comp.grad.unit, 'cm')
hdm.bnd.pos = hdm.bnd.pos/10;
elseif ~isequal(hdm.unit, comp.grad.unit)
error('Unknown unit conversion')
end
figure; ft_plot_mesh(comp.grad.chanpos(1:2:end,:), 'vertexindex', true);
ft_plot_mesh(hdm.bnd(1), 'facealpha', 0.5)
end
else
% check alignment
if strcmpi(g.plotalignment, 'on')
if ischar(OUTEEG.dipfit.hdmfile)
hdm = ft_read_headmodel(OUTEEG.dipfit.hdmfile);
else
hdm = OUTEEG.dipfit.hdmfile;
end
figure;
ft_plot_mesh(comp.elec.chanpos(1:2:end,:), 'vertexindex', true);
ft_plot_mesh(hdm.bnd(1), 'facealpha', 0.5)
end
end
% checking electrode configuration
% --------------------------------
if 0
disp('Checking the electrode configuration');
tmpchan = readlocs(OUTEEG.dipfit.chanfile);
[tmp1 ind1 ind2] = intersect( lower({ tmpchan.labels }), lower({ OUTEEG.chanlocs.labels }));
if isempty(tmp1)
disp('No channel labels in common found between template and dataset channels');
if ~isempty(findstr(OUTEEG.dipfit.hdmfile, 'BESA'))
disp('Use the channel editor to fit a head sphere to your channel locations.');
disp('Check for inconsistency in dipole info.');
else
disp('Results using standard BEM model are INACCURATE when the channel locations are not on the head surface!');
end
else % common channels: performing best transformation
TMP = OUTEEG;
elec1 = eeglab2fieldtrip(TMP, 'elec');
elec1 = elec1.elec;
TMP.chanlocs = tmpchan;
elec2 = eeglab2fieldtrip(TMP, 'elec');
elec2 = elec2.elec;
cfg.elec = elec1;
cfg.template = elec2;
cfg.method = 'warp';
elec3 = electrodenormalize(cfg);
% convert back to EEGLAB format
OUTEEG.chanlocs = struct( 'labels', elec3.label, ...
'X' , mat2cell(elec3.elecpos(:,1)'), ...
'Y' , mat2cell(elec3.elecpos(:,2)'), ...
'Z' , mat2cell(elec3.elecpos(:,3)') );
OUTEEG.chanlocs = convertlocs(OUTEEG.chanlocs, 'cart2all');
end
end
com = sprintf('EEG = pop_dipfit_settings( EEG, %s);', vararg2str(options));
% test for structure
% ------------------
function [enableFlag, str] = checkStructure(file)
if isstruct(file)
str = 'Matlab structure';
enableFlag = 'off';
else
str = file;
enableFlag = 'on';
end
% test for wrong parameters
% -------------------------
function bool = test_wrong_parameters(result)
coreg1 = result.coregtext;
coreg2 = result.coregcheckbox;
meg = result.coord;
bool = 0;
if meg == 3, return; end
if coreg2 == 0 && isempty(coreg1)
bool = 1; warndlg2(strvcat('INCORRECT SETTINGS - SELECT THIS MENU AGAIN', ...
'You must co-register your channel locations', ...
'with the head model (Press button, "Co-register".', ...
'and follow instructions); To bypass co-registration,', ...
'check the checkbox " No Co-Reg".'), 'Error');
end