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ft_electrodeplacement.m
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ft_electrodeplacement.m
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function [elec] = ft_electrodeplacement(cfg, varargin)
% FT_ELECTRODEPLACEMENT allows manual placement of electrodes on a MRI scan, CT scan
% or on a triangulated surface of the head. This function supports different methods.
%
% VOLUME - Navigate an orthographic display of a volume (e.g. CT or MRI scan), and
% assign an electrode label to the current crosshair location by clicking on a label
% in the eletrode list. You can undo the selection by clicking on the same label
% again. The electrode labels shown in the list can be prespecified using cfg.channel
% when calling ft_electrodeplacement. The zoom slider allows zoomi/ng in at the
% location of the crosshair. The intensity sliders allow thresholding the image's low
% and high values. The magnet feature transports the crosshair to the nearest peak
% intensity voxel, within a certain voxel radius of the selected location. The labels
% feature displays the labels of the selected electrodes within the orthoplot. The
% global feature allows toggling the view between all and near-crosshair
% markers. The scan feature allows toggling between scans when another scan
% is given as input.
%
% HEADSHAPE - Navigate a triangulated scalp (for EEG) or brain (for ECoG) surface,
% and assign an electrode location by clicking on the surface. The electrode is
% placed on the triangulation itself.
%
% 1020 - Starting from a triangulated scalp surface and the nasion, inion, left and
% right pre-auricular points, this automatically constructs and follows contours over
% the surface according to the 5% system. Electrodes are placed at certain relative
% distances along these countours. This is an extension of the 10-20 standard
% electrode placement system and includes the 20%, 10% and 5% locations. See
% "Oostenveld R, Praamstra P. The five percent electrode system for high-resolution
% EEG and ERP measurements. Clin Neurophysiol. 2001 Apr;112(4):713-9" for details.
%
% SHAFT - This is for placing electrodes along a linear sEEG shaft. The tip of the
% shaft, another point along the shaft and the distance between the electrodes should
% be specified. If the shaft is not straight but curved, you should specify multiple
% (at least two) points along the saft, i.e. specify cfg.shaft.along=Nx3 for N
% points. The number of electrodes that is placed is determined from cfg.channel.
%
% GRID - This is for placing electrodes on a regular MxN ECoG grid. Each of the four
% cornerpoints of the grid must be specified, along with the dimensions of the grid.
% Following piecewise linear placement of the electrodes on the grid, you can use
% FT_ELECTRODEREALIGN with cfg.method='project' to project them to the curved brain
% surface.
%
% Use as
% [elec] = ft_electrodeplacement(cfg, ct)
% [elec] = ft_electrodeplacement(cfg, ct, mri, ..)
% where the input mri should be an anatomical CT or MRI volume, or
% [elec] = ft_electrodeplacement(cfg, headshape)
% where the input headshape should be a surface triangulation.
%
% The configuration can contain the following options
% cfg.method = string representing the method for placing the electrodes
% 'volume' interactively locate electrodes on three orthogonal slices of a volumetric MRI or CT scan
% 'headshape' interactively locate electrodes on a head surface
% '1020' automatically locate electrodes on a head surface according to the 10-20 system
% 'shaft' automatically locate electrodes along a linear sEEG shaft
% 'grid' automatically locate electrodes on a MxN ECoG grid
%
% The following options apply to the 'volume' method
% cfg.parameter = string, field in data (default = 'anatomy' if present in data)
% cfg.channel = Nx1 cell-array with selection of channels (default = {'1' '2' ...})
% cfg.elec = struct containing previously placed electrodes (this overwrites cfg.channel)
% cfg.clim = color range of the data (default = [0 1], i.e. the full range)
% cfg.magtype = string representing the 'magnet' type used for placing the electrodes
% 'peakweighted' place electrodes at weighted peak intensity voxel (default)
% 'troughweighted' place electrodes at weighted trough intensity voxel
% 'peak' place electrodes at peak intensity voxel (default)
% 'trough' place electrodes at trough intensity voxel
% 'weighted' place electrodes at center-of-mass
% cfg.magradius = number representing the radius for the cfg.magtype based search (default = 3)
%
% The following options apply to the '1020' method
% cfg.fiducial.nas = 1x3 vector with coordinates
% cfg.fiducial.ini = 1x3 vector with coordinates
% cfg.fiducial.lpa = 1x3 vector with coordinates
% cfg.fiducial.rpa = 1x3 vector with coordinates
% cfg.feedback = string, can be 'yes' or 'no' for detailled feedback (default = 'yes')
%
% The following options apply to the 'shaft' method
% cfg.shaft.tip = 1x3 position of the electrode at the tip of the shaft
% cfg.shaft.along = 1x3 or Nx3 positions along the shaft
% cfg.shaft.distance = scalar, distance between electrodes
%
% The following options apply to the 'grid' method
% cfg.grid.corner1 = 1x3 position of the upper left corner point
% cfg.grid.corner2 = 1x3 position of the upper right corner point
% cfg.grid.corner3 = 1x3 position of the lower left corner point
% cfg.grid.corner4 = 1x3 position of the lower right corner point
%
% In the interactive 'headshape' and 'volume' methods you can click once on an
% already assigned electrode to jump to that electrode position and you can click
% twice to remove the assigned electrode position.
%
% See also FT_ELECTRODEREALIGN, FT_VOLUMEREALIGN, FT_VOLUMESEGMENT, FT_PREPARE_MESH
% Copyright (C) 2015-2019, Arjen Stolk, Sandon Griffin & Robert Oostenveld
%
% This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
% for the documentation and details.
%
% FieldTrip 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 3 of the License, or
% (at your option) any later version.
%
% FieldTrip 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 FieldTrip. If not, see <http://www.gnu.org/licenses/>.
%
% $Id$
% these are used by the ft_preamble/ft_postamble function and scripts
ft_revision = '$Id$';
ft_nargin = nargin;
ft_nargout = nargout;
% do the general setup of the function
ft_defaults
ft_preamble init
ft_preamble debug
ft_preamble loadvar mri
ft_preamble provenance mri
ft_preamble trackconfig
% the ft_abort variable is set to true or false in ft_preamble_init
if ft_abort
return
end
% ensure that old and unsupported options are not being relied on by the end-user's script
% see http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2837
% check if the input cfg is valid for this function
cfg = ft_checkconfig(cfg, 'forbidden', {'channels'}); % prevent accidental typos, see issue 1729
cfg = ft_checkconfig(cfg, 'renamed', {'viewdim', 'axisratio'});
cfg = ft_checkconfig(cfg, 'renamedval', {'method', 'mri', 'volume'});
cfg = ft_checkconfig(cfg, 'renamed', {'newfigure', 'figure'});
% set the defaults
cfg.method = ft_getopt(cfg, 'method'); % volume, headshape, 1020, shaft
cfg.feedback = ft_getopt(cfg, 'feedback', 'yes');
cfg.parameter = ft_getopt(cfg, 'parameter', 'anatomy');
cfg.channel = ft_getopt(cfg, 'channel', []); % default will be determined further down {'1', '2', ...}
cfg.elec = ft_getopt(cfg, 'elec', []); % use previously placed electrodes
cfg.renderer = ft_getopt(cfg, 'renderer', 'opengl');
% view options
cfg.clim = ft_getopt(cfg, 'clim', [0 1]); % initial volume intensity limit voxels
cfg.markerdist = ft_getopt(cfg, 'markerdist', 5); % marker-slice distance view when ~global
% magnet options
cfg.magtype = ft_getopt(cfg, 'magtype', 'peakweighted'); % detect weighted peaks or troughs
cfg.magradius = ft_getopt(cfg, 'magradius', 3); % specify the physical unit radius
cfg.voxelratio = ft_getopt(cfg, 'voxelratio', 'data'); % display size of the voxel, 'data' or 'square'
cfg.axisratio = ft_getopt(cfg, 'axisratio', 'data'); % size of the axes of the three orthoplots, 'square', 'voxel', or 'data'
if isempty(cfg.method) && ~isempty(varargin)
% the default determines on the input data
switch ft_datatype(varargin{1})
case 'volume'
cfg.method = 'volume';
case 'mesh'
cfg.method = 'headshape';
case 'source+mesh'
cfg.method = 'headshape';
end
end
% check if the input data is valid for this function
switch cfg.method
case 'volume'
for v = 1:numel(varargin)
mri{v} = ft_checkdata(varargin{v}, 'datatype', 'volume', 'feedback', 'yes', 'hascoordsys', 'yes', 'hasunit', 'yes');
end
case {'headshape', '1020'}
headshape = fixpos(varargin{1});
headshape = ft_checkdata(headshape, 'hascoordsys', 'yes');
end
% set-up channels labels if possible
chanlabel = {}; chanstring = {};
markerlab = {}; markerpos = {};
if ~isempty(cfg.elec) % re-use previously placed (cfg.elec) electrodes
for e = 1:numel(cfg.elec.label)
chanlabel{end+1,1} = cfg.elec.label{e};
chanstring{end+1} = ['<HTML><FONT color="black">' cfg.elec.label{e} '</FONT></HTML>']; % hmtl'ize
markerlab{end+1,1} = cfg.elec.label{e};
markerpos{end+1,1} = cfg.elec.elecpos(e,:);
end
end
if ~isempty(cfg.channel) % use prespecified (cfg.channel) electrode labels
for c = 1:numel(cfg.channel)
if ~ismember(cfg.channel{c}, chanlabel) % avoid overlap between cfg.channel and elec.label
chanlabel{end+1,1} = cfg.channel{c};
chanstring{end+1} = ['<HTML><FONT color="silver">' cfg.channel{c} '</FONT></HTML>']; % hmtl'ize
markerlab{end+1,1} = {};
markerpos{end+1,1} = zeros(0,3);
end
end
end
if isempty(cfg.elec) && isempty(cfg.channel) % create electrode labels on-the-fly
for c = 1:300
chanlabel{end+1,1} = sprintf('%d', c);
chanstring{end+1} = ['<HTML><FONT color="silver">' sprintf('%d', c) '</FONT></HTML>']; % hmtl'ize
markerlab{end+1,1} = {};
markerpos{end+1,1} = zeros(0,3);
end
end
% this is where the different methods are implemented
switch cfg.method
case 'shaft'
if size(cfg.shaft.along,1)==1
% two points are specified, use a simple linear method
pos = cfg.shaft.tip;
ori = cfg.shaft.along - cfg.shaft.tip;
ori = ori/norm(ori);
elec = [];
elec.label = cfg.channel;
for i=1:numel(elec.label)
elec.elecpos(i,:) = pos + (i-1) * ori * cfg.shaft.distance;
end
else
% more than two points are specified, use a spline
pos = [
cfg.shaft.tip
cfg.shaft.along
];
dist = sqrt(sum(diff(pos,1,1).^2, 2)); % distance between subsequent positions
dist = [0; cumsum(dist)]; % cumulative distance from the tip
cv = csapi(dist', pos'); % spline that goes through all positions
elec = [];
elec.label = cfg.channel;
for i=1:numel(elec.label)
dist = (i-1) * cfg.shaft.distance;
elec.elecpos(i,:) = cfg.shaft.tip + fnval(cv, dist)';
end
end
case 'grid'
% The four cornerpoints specified by the user will not exactly be a rectangle,
% but will have in plane distortion and out-of-plane twist.
% Each cornerpoint with the two edges to its direct neighbours describes a parallellogram.
% We compute the position of each electrode according to this parallellogram
% and then compute the weighted average based on distance to the cornerpoints.
% The cornerpoints are specified like this
%
% 1 2
% 3 4
% parallellogram starting in corner 1
dir12 = cfg.grid.corner2-cfg.grid.corner1; dir12 = dir12/norm(dir12);
dir13 = cfg.grid.corner3-cfg.grid.corner1; dir13 = dir13/norm(dir13);
% parallellogram starting in corner 2
dir21 = cfg.grid.corner1-cfg.grid.corner2; dir21 = dir21/norm(dir21);
dir24 = cfg.grid.corner4-cfg.grid.corner2; dir24 = dir24/norm(dir24);
% parallellogram starting in corner 3
dir31 = cfg.grid.corner1-cfg.grid.corner3; dir31 = dir31/norm(dir31);
dir34 = cfg.grid.corner4-cfg.grid.corner3; dir34 = dir34/norm(dir34);
% parallellogram starting in corner 4
dir42 = cfg.grid.corner2-cfg.grid.corner4; dir42 = dir42/norm(dir42);
dir43 = cfg.grid.corner3-cfg.grid.corner4; dir43 = dir43/norm(dir43);
% assuming a 3x4 grid, the electrodes will be placed like this
%
% 1 2 3 4
% 5 6 7 8
% 9 10 11 12
% specify the number of electrodes in the vertical and horizontal direction
nv = cfg.grid.dim(1);
nh = cfg.grid.dim(2);
% determine the inter-electrode distance in the vertical and horizontal direction
dv = (norm(cfg.grid.corner3-cfg.grid.corner1)/(nv-1) + norm(cfg.grid.corner4-cfg.grid.corner2)/(nv-1))/2;
dh = (norm(cfg.grid.corner2-cfg.grid.corner1)/(nh-1) + norm(cfg.grid.corner4-cfg.grid.corner3)/(nh-1))/2;
ft_notice('electrode spacing along 1st dimension is %f', dv);
ft_notice('electrode spacing along 2nd dimension is %f', dh);
% scale the
dir12 = dir12*dh;
dir13 = dir13*dv;
dir21 = dir21*dh;
dir24 = dir24*dv;
dir31 = dir31*dv;
dir34 = dir34*dh;
dir42 = dir42*dv;
dir43 = dir43*dh;
if isempty(cfg.channel)
ft_notice('using automatic channel labels');
cfg.channel = arrayfun(@num2str, 1:(nh*nv), 'UniformOutput', false);
else
assert(numel(cfg.channel)==nh*nv, 'mismatch between cfg.grid.dim and cfg.channel');
end
pos1 = nan(nh*nv,3);
pos2 = nan(nh*nv,3);
pos3 = nan(nh*nv,3);
pos4 = nan(nh*nv,3);
% determine the position of each electrode according to each parallellogram
k = 1;
for i=1:nv
for j=1:nh
pos1(k,:) = ( i-1)*dir13 + ( j-1)*dir12 + cfg.grid.corner1;
pos2(k,:) = ( i-1)*dir24 + (nh-j)*dir21 + cfg.grid.corner2;
pos3(k,:) = (nv-i)*dir31 + ( j-1)*dir34 + cfg.grid.corner3;
pos4(k,:) = (nv-i)*dir42 + (nh-j)*dir43 + cfg.grid.corner4;
k = k+1;
end % horizontal
end % vertical
d1 = nan(nh*nv,1);
d2 = nan(nh*nv,1);
d3 = nan(nh*nv,1);
d4 = nan(nh*nv,1);
% determine the schematic distance (i.e. counted in steps) to each corner
k = 1;
for i=1:nv
for j=1:nh
d1(k) = norm([( i-1)*dv ( j-1)*dh]);
d2(k) = norm([( i-1)*dv (nh-j)*dh]);
d3(k) = norm([(nv-i)*dv ( j-1)*dh]);
d4(k) = norm([(nv-i)*dv (nh-j)*dh]);
k = k+1;
end % horizontal
end % vertical
% the weight is relative to the range, which is 0.5 times the dimagonal distance
range = sqrt(((nv-1)*dv)^2 + ((nh-1)*dh)^2) / 2;
% compute the weights from the distance
d1 = 10.^(-d1/range);
d2 = 10.^(-d2/range);
d3 = 10.^(-d3/range);
d4 = 10.^(-d4/range);
% normalize the weights
dd = (d1 + d2 + d3 + d4);
d1 = d1 ./ dd;
d2 = d2 ./ dd;
d3 = d3 ./ dd;
d4 = d4 ./ dd;
% compute the weighted position
elec = [];
elec.label = cfg.channel;
elec.elecpos = [d1 d1 d1].*pos1 + [d2 d2 d2].*pos2 + [d3 d3 d3].*pos3 + [d4 d4 d4].*pos4;
case 'headshape'
% start building the figure
h = open_figure(keepfields(cfg, {'figure', 'position', 'visible', 'renderer', 'figurename', 'title'}));
set(h, 'Name', mfilename);
set(h, 'Units', 'normalized');
set(h, 'Color', [1 1 1]);
set(h, 'windowbuttondownfcn', @cb_buttonpress);
set(h, 'windowbuttonupfcn', @cb_buttonrelease);
set(h, 'windowkeypressfcn', @cb_keyboard);
set(h, 'CloseRequestFcn', @cb_quit);
% electrode listbox
h1 = uicontrol('Style', 'listbox', ...
'Parent', h, ...
'Value', [], 'Min', 0, 'Max', numel(chanstring), ...
'Units', 'normalized', ...
'FontSize', 12, ...
'Position', [.8 0.001 .2 .5], ...
'Callback', @cb_eleclistbox, ...
'String', chanstring);
h7 = uicontrol('Style', 'checkbox', ...
'Parent', h, ...
'Value', 1, ...
'String', 'Surface', ...
'Units', 'normalized', ...
'Position', [.8 0.65 .2 .05], ...
'BackgroundColor', [1 1 1], ...
'HandleVisibility', 'on', ...
'Callback', @cb_surfacebutton);
h8 = uicontrol('Style', 'checkbox', ...
'Parent', h, ...
'Value', 0, ...
'String', 'Labels', ...
'Units', 'normalized', ...
'Position', [.8 0.6 .2 .05], ...
'BackgroundColor', [1 1 1], ...
'HandleVisibility', 'on', ...
'Callback', @cb_labelsbutton);
if isfield(headshape, 'color')
h9 = uicontrol('Style', 'checkbox', ...
'Parent', h, ...
'Value', 1, ...
'String', 'Colors', ...
'Units', 'normalized', ...
'Position', [.8 0.55 .2 .05], ...
'BackgroundColor', [1 1 1], ...
'HandleVisibility', 'on', ...
'Callback', @cb_colorsbutton);
end
% give the user instructions
disp('Use the mouse to click on the desired position for the electrode');
disp('Subsequently use the mouse to click on the corresponding electrode label');
disp('Press "v" to update the light position');
disp('Press "q" when you are done');
% create structure to be passed to gui
opt = [];
opt.method = 'headshape'; % this is to use the same functionalities across volume and headshape
opt.headshape = headshape;
opt.label = chanlabel;
opt.axes = [h1 h8];
opt.mainfig = h;
opt.quit = false;
opt.init = true;
opt.pos = [0 0 0]; % middle of the scan, head coordinates (FIXME: this might mess up vertex finding, being an anchor)
opt.showcrosshair = true;
opt.showsurface = true;
opt.showlabels = false;
opt.showcolors = true;
opt.showmarkers = true;
opt.markerlab = markerlab;
opt.markerpos = markerpos;
opt.markerdist = cfg.markerdist; % hidden option
setappdata(h, 'opt', opt);
cb_headshaperedraw(h);
view([90, 0]);
while(opt.quit==0)
uiwait(h);
opt = getappdata(h, 'opt');
end
delete(h);
% collect the results
elec = keepfields(headshape, {'unit', 'coordsys'});
elec.label = {};
elec.elecpos = [];
for i=1:length(opt.markerlab)
if ~isempty(opt.markerlab{i,1})
elec.label = [elec.label; opt.markerlab{i,1}];
elec.elecpos = [elec.elecpos; opt.markerpos{i,1}];
end
end
elec.chanpos = elec.elecpos;
elec.tra = eye(size(elec.elecpos,1));
case 'volume'
% start building the figure
h = open_figure(keepfields(cfg, {'figure', 'position', 'visible', 'renderer', 'figurename', 'title'}));
set(h, 'Name', mfilename);
set(h, 'Units', 'normalized');
set(h, 'Color', [1 1 1]);
set(h, 'MenuBar', 'none');
set(h, 'windowbuttondownfcn', @cb_buttonpress);
set(h, 'windowbuttonupfcn', @cb_buttonrelease);
set(h, 'windowkeypressfcn', @cb_keyboard);
set(h, 'CloseRequestFcn', @cb_quit);
% volume-dependent axis settings
for v = 1:numel(mri)
if strcmp(cfg.axisratio, 'voxel')
% determine the number of voxels to be plotted along each axis
axlen1 = mri{v}.dim(1);
axlen2 = mri{v}.dim(2);
axlen3 = mri{v}.dim(3);
elseif strcmp(cfg.axisratio, 'data')
% determine the length of the edges along each axis
[cp_voxel, cp_head] = cornerpoints(mri{v}.dim, mri{v}.transform);
axlen1 = norm(cp_head(2,:)-cp_head(1,:));
axlen2 = norm(cp_head(4,:)-cp_head(1,:));
axlen3 = norm(cp_head(5,:)-cp_head(1,:));
elseif strcmp(cfg.axisratio, 'square')
% the length of the axes should be equal
axlen1 = 1;
axlen2 = 1;
axlen3 = 1;
end
% this is the size reserved for subplot h1, h2 and h3
h1size(1) = 0.92*axlen1/(axlen1 + axlen2); % x
h1size(2) = 0.92*axlen3/(axlen2 + axlen3); % z
h2size(1) = 0.92*axlen2/(axlen1 + axlen2); % y
h2size(2) = 0.92*axlen3/(axlen2 + axlen3); % z
h3size(1) = 0.92*axlen1/(axlen1 + axlen2); % x
h3size(2) = 0.92*axlen2/(axlen2 + axlen3); % y
% axis handles will hold the anatomical functional if present, along with labels etc.
h1 = axes('position', [0.02 0.02+0.04+h3size(2) h1size(1) h1size(2)]); % x z
h2 = axes('position', [0.02+0.04+h1size(1) 0.02+0.04+h3size(2) h2size(1) h2size(2)]); % y z
h3 = axes('position', [0.02 0.02 h3size(1) h3size(2)]); % x y
set(h1, 'Tag', 'ik', 'Visible', 'off', 'XAxisLocation', 'top'); axis(h1, 'equal');
set(h2, 'Tag', 'jk', 'Visible', 'off', 'YAxisLocation', 'right'); axis(h2, 'equal'); % after rotating in ft_plot_ortho this becomes top
set(h3, 'Tag', 'ij', 'Visible', 'off'); axis(h3, 'equal');
if strcmp(cfg.voxelratio, 'square')
voxlen1 = 1;
voxlen2 = 1;
voxlen3 = 1;
elseif strcmp(cfg.voxelratio, 'data')
% the size of the voxel is scaled with the data
[cp_voxel, cp_head] = cornerpoints(mri{v}.dim, mri{v}.transform);
voxlen1 = norm(cp_head(2,:)-cp_head(1,:))/norm(cp_voxel(2,:)-cp_voxel(1,:));
voxlen2 = norm(cp_head(4,:)-cp_head(1,:))/norm(cp_voxel(4,:)-cp_voxel(1,:));
voxlen3 = norm(cp_head(5,:)-cp_head(1,:))/norm(cp_voxel(5,:)-cp_voxel(1,:));
end
%set(h1, 'DataAspectRatio', 1./[voxlen1 voxlen2 voxlen3]); % FIXME: this no longer works when using mri.transform with ft_plot_ortho (instead of eye(4));
%set(h2, 'DataAspectRatio', 1./[voxlen1 voxlen2 voxlen3]);
%set(h3, 'DataAspectRatio', 1./[voxlen1 voxlen2 voxlen3]);
mri{v}.axes = [h1 h2 h3];
mri{v}.h1size = h1size;
mri{v}.h2size = h2size;
mri{v}.h3size = h3size;
mri{v}.clim = cfg.clim;
mri{v}.slim = [.9 1]; % 90% - maximum
dat = double(mri{v}.(cfg.parameter));
dmin = min(dat(:));
dmax = max(dat(:));
mri{v}.dat = (dat-dmin)./(dmax-dmin); % range between 0 and 1
clear dat dmin dmax
end
% intensity range sliders
h45text = uicontrol('Style', 'text',...
'String', 'Intensity',...
'Units', 'normalized', ...
'Position', [2*mri{1}.h1size(1)-0.02 mri{1}.h3size(2)-0.02 mri{1}.h1size(1)/4 0.04],...
'BackgroundColor', [1 1 1], ...
'HandleVisibility', 'on');
h4 = uicontrol('Style', 'slider', ...
'Parent', h, ...
'Min', 0, 'Max', 1, ...
'Value', cfg.clim(1), ...
'Units', 'normalized', ...
'Position', [2*mri{1}.h1size(1)-0.03 0.10+mri{1}.h3size(2)/3 0.05 mri{1}.h3size(2)/2-0.05], ...
'Callback', @cb_minslider);
h5 = uicontrol('Style', 'slider', ...
'Parent', h, ...
'Min', 0, 'Max', 1, ...
'Value', cfg.clim(2), ...
'Units', 'normalized', ...
'Position', [2*mri{1}.h1size(1)+0.02 0.10+mri{1}.h3size(2)/3 0.05 mri{1}.h3size(2)/2-0.05], ...
'Callback', @cb_maxslider);
% java intensity range slider (dual-knob slider): the java component gives issues when wanting to
% access the opt structure
% [jRangeSlider] = com.jidesoft.swing.RangeSlider(0,1,cfg.clim(1),cfg.clim(2)); % min,max,low,high
% [jRangeSlider, h4] = javacomponent(jRangeSlider, [], h);
% set(h4, 'Units', 'normalized', 'Position', [0.05+h1size(1) 0.07 0.07 h3size(2)], 'Parent', h);
% set(jRangeSlider, 'Orientation', 1, 'PaintTicks', true, 'PaintLabels', true, ...
% 'Background', java.awt.Color.white, 'StateChangedCallback', @cb_intensityslider);
% electrode listbox
h6 = uicontrol('Style', 'listbox', ...
'Parent', h, ...
'Value', [], 'Min', 0, 'Max', numel(chanstring), ...
'Units', 'normalized', ...
'FontSize', 12, ...
'Position', [mri{1}.h1size(1)+0.07 0.02 mri{1}.h2size(1)/2.5 mri{1}.h3size(2)], ...
'Callback', @cb_eleclistbox, ...
'String', chanstring);
% switches / radio buttons
h7text = uicontrol('Style', 'text',...
'String', 'Magnet',...
'Units', 'normalized', ...
'Position', [2*mri{1}.h1size(1)-0.047 0.18 mri{1}.h1size(1)/3 0.04],...
'BackgroundColor', [1 1 1], ...
'HandleVisibility', 'on');
h7 = uicontrol('Style', 'popupmenu',...
'Parent', h, ...
'Value', 4, ... % corresponding to magradius = 3 (see String)
'String', {'0', '1', '2', '3', '4', '5'}, ...
'Units', 'normalized', ...
'Position', [2*mri{1}.h1size(1)-0.103 0.18 mri{1}.h1size(1)/4.25 0.04],...
'BackgroundColor', [1 1 1], ...
'HandleVisibility', 'on', ...
'Callback', @cb_magnetbutton);
radii = get(h7, 'String');
if ~ismember(num2str(cfg.magradius), radii) % add user-specified radius to the list
set(h7, 'String', [radii(:); num2str(cfg.magradius)]);
set(h7, 'Value', numel(radii)+1);
end
h8 = uicontrol('Style', 'checkbox',...
'Parent', h, ...
'Value', 0, ...
'String', 'Labels',...
'Units', 'normalized', ...
'Position', [2*mri{1}.h1size(1)-0.05 0.14 mri{1}.h1size(1)/3 0.04],...
'BackgroundColor', [1 1 1], ...
'HandleVisibility', 'on', ...
'Callback', @cb_labelsbutton);
h9 = uicontrol('Style', 'checkbox',...
'Parent', h, ...
'Value', 0, ...
'String', 'Global',...
'Units', 'normalized', ...
'Position', [2*mri{1}.h1size(1)-0.05 0.10 mri{1}.h1size(1)/3 0.04],...
'BackgroundColor', [1 1 1], ...
'HandleVisibility', 'on', ...
'Callback', @cb_globalbutton);
hscatter = uicontrol('Style', 'checkbox',...
'Parent', h, ...
'Value', 0, ...
'String', 'Scatter',...
'Units', 'normalized', ...
'Position', [2*mri{1}.h1size(1)-0.05 0.06 mri{1}.h1size(1)/3 0.04],...
'BackgroundColor', [1 1 1], ...
'HandleVisibility', 'on', ...
'Callback', @cb_scatterbutton);
hscan = uicontrol('Style', 'checkbox',...
'Parent', h, ...
'Value', 0, ...
'String', 'CT/MRI',...
'Units', 'normalized', ...
'Position', [2*mri{1}.h1size(1)-0.05 0.02 mri{1}.h1size(1)/3 0.04],...
'BackgroundColor', [1 1 1], ...
'HandleVisibility', 'on', ...
'Visible', 'off', ...
'Callback', @cb_scanbutton);
if numel(mri)>1; set(hscan, 'Visible', 'on'); end % only when two scans are given as input
% zoom slider
h10text = uicontrol('Style', 'text',...
'String', 'Zoom',...
'Units', 'normalized', ...
'Position', [1.8*mri{1}.h1size(1)-0.04 mri{1}.h3size(2)-0.02 mri{1}.h1size(1)/4 0.04],...
'BackgroundColor', [1 1 1], ...
'HandleVisibility', 'on');
h10 = uicontrol('Style', 'slider', ...
'Parent', h, ...
'Min', 0, 'Max', 0.9, ...
'Value', 0, ...
'Units', 'normalized', ...
'Position', [1.8*mri{1}.h1size(1)-0.03 0.10+mri{1}.h3size(2)/3 0.05 mri{1}.h3size(2)/2-0.05], ...
'SliderStep', [.1 .1], ...
'Callback', @cb_zoomslider);
% instructions to the user
fprintf(strcat(...
'1. Orthoplot viewing options:\n',...
' a. use the left mouse button to navigate the image, or\n',...
' b. use the arrow keys to increase or decrease the slice number by one\n',...
'2. Orthoplot placement options:\n',...
' a. click an electrode label in the list to assign it to the crosshair location, or\n',...
' b. doubleclick a previously assigned electrode label to remove its marker\n',...
'3. To finalize, close the window or press q on the keyboard\n', ...
'4. See Stolk, Griffin et al. Nature Protocols 2018 for further electrode processing options\n'));
% create structure to be passed to gui
opt = [];
opt.method = 'volume'; % this is to use the same functionalities across volume and headshape
opt.label = chanlabel;
opt.axes = [mri{1}.axes(1) mri{1}.axes(2) mri{1}.axes(3) h4 h5 h6 h7 h8 h9 h10 hscatter hscan];
opt.mainfig = h;
opt.quit = false;
opt.update = [1 1 1];
opt.init = true;
opt.tag = 'ik';
opt.ana = mri{1}.dat; % the plotted anatomy
opt.mri = mri;
opt.currmri = 1;
opt.showcrosshair = true;
opt.pos = [0 0 0]; % middle of the scan, head coordinates
opt.showsurface = true;
opt.showlabels = false;
opt.showcolors = false;
opt.magnet = get(h7, 'Value');
opt.magradius = cfg.magradius;
opt.magtype = cfg.magtype;
opt.showmarkers = true;
opt.global = get(h9, 'Value'); % show all markers in the current slices
opt.scatter = get(hscatter, 'Value'); % additional scatterplot
opt.scan = get(hscan, 'Value'); % switch scans
opt.slim = [.9 1]; % 90% - maximum
opt.markerlab = markerlab;
opt.markerpos = markerpos;
opt.markerdist = cfg.markerdist; % hidden option
opt.clim = cfg.clim;
opt.zoom = 0;
setappdata(h, 'opt', opt);
cb_redraw(h);
while(opt.quit==0)
uiwait(h);
opt = getappdata(h, 'opt');
end
delete(h);
% collect the results
elec = keepfields(mri{1}, {'unit', 'coordsys'});
elec.label = {};
elec.elecpos = [];
for i=1:length(opt.markerlab)
if ~isempty(opt.markerlab{i,1})
elec.label = [elec.label; opt.markerlab{i,1}];
elec.elecpos = [elec.elecpos; opt.markerpos{i,1}];
end
end
elec.chanpos = elec.elecpos;
elec.tra = eye(size(elec.elecpos,1));
case '1020'
% the placement procedure fails if the fiducials coincide with vertices
dist = @(x, y) sqrt(sum(bsxfun(@minus, x, y).^2,2));
tolerance = 0.1 * ft_scalingfactor('mm', headshape.unit); % 0.1 mm
nas = cfg.fiducial.nas;
ini = cfg.fiducial.ini;
lpa = cfg.fiducial.lpa;
rpa = cfg.fiducial.rpa;
if any(dist(headshape.pos, nas)<tolerance)
ft_warning('Nasion coincides with headshape vertex, addding random displacement of about %f %s', tolerance, headshape.unit);
nas = nas + tolerance*randn(1,3);
end
if any(dist(headshape.pos, ini)<tolerance)
ft_warning('Inion coincides with headshape vertex, addding random displacement of about %f %s', tolerance, headshape.unit);
ini = ini + tolerance*randn(1,3);
end
if any(dist(headshape.pos, lpa)<tolerance)
ft_warning('LPA coincides with headshape vertex, addding random displacement of about %f %s', tolerance, headshape.unit);
lpa = lpa + tolerance*randn(1,3);
end
if any(dist(headshape.pos, rpa)<tolerance)
ft_warning('RPA coincides with headshape vertex, addding random displacement of about %f %s', tolerance, headshape.unit);
rpa = rpa + tolerance*randn(1,3);
end
% place the electrodes automatically according to the fiducials
[pos, lab] = elec1020_locate(headshape.pos, headshape.tri, nas, ini, lpa, rpa, istrue(cfg.feedback));
% construct the output
elec = keepfields(headshape, {'unit', 'coordsys'});
elec.elecpos = pos;
elec.label = lab(:);
otherwise
ft_error('unsupported method ''%s''', cfg.method);
end % switch method
% do the general cleanup and bookkeeping at the end of the function
ft_postamble debug
ft_postamble trackconfig
ft_postamble previous mri
ft_postamble provenance elec
ft_postamble history elec
ft_postamble savevar elec
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% SUBFUNCTION
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function cb_redraw(h, eventdata)
h = getparent(h);
opt = getappdata(h, 'opt');
% determine current axes
set(0, 'CurrentFigure', opt.mainfig);
curr_ax = get(h, 'currentaxes');
tag = get(curr_ax, 'tag');
h1 = opt.axes(1);
h2 = opt.axes(2);
h3 = opt.axes(3);
if opt.init
delete(findobj(opt.mainfig, 'Type', 'Surface')); % get rid of old orthos (to facilitate switching scans)
ft_plot_ortho(opt.ana, 'transform', opt.mri{opt.currmri}.transform, 'location', opt.pos, 'style', 'subplot', 'parents', [h1 h2 h3], 'update', opt.update, 'doscale', false, 'clim', opt.clim, 'unit', opt.mri{opt.currmri}.unit);
opt.anahandles = findobj(opt.mainfig, 'Type', 'Surface')';
parenttag = get(opt.anahandles, 'parent');
parenttag{1} = get(parenttag{1}, 'tag');
parenttag{2} = get(parenttag{2}, 'tag');
parenttag{3} = get(parenttag{3}, 'tag');
[i1,i2,i3] = intersect(parenttag, {'ik';'jk';'ij'});
opt.anahandles = opt.anahandles(i3(i2)); % seems like swapping the order
opt.anahandles = opt.anahandles(:)';
set(opt.anahandles, 'tag', 'ana');
% for zooming purposes
opt.axis = zeros(1,6);
opt.axis = [opt.axes(1).XLim opt.axes(1).YLim opt.axes(1).ZLim];
opt.redrawmarkers = true;
opt.reinit = false;
elseif opt.reinit
ft_plot_ortho(opt.ana, 'transform', opt.mri{opt.currmri}.transform, 'location', opt.pos, 'style', 'subplot', 'surfhandle', opt.anahandles, 'update', opt.update, 'doscale', false, 'clim', opt.clim, 'unit', opt.mri{opt.currmri}.unit);
fprintf('==================================================================================\n');
lab = 'crosshair';
switch opt.mri{opt.currmri}.unit
case 'mm'
fprintf('%10s at [%.1f %.1f %.1f] %s\n', lab, opt.pos, opt.mri{opt.currmri}.unit);
case 'cm'
fprintf('%10s at [%.2f %.2f %.2f] %s\n', lab, opt.pos, opt.mri{opt.currmri}.unit);
case 'm'
fprintf('%10s at [%.4f %.4f %.4f] %s\n', lab, opt.pos, opt.mri{opt.currmri}.unit);
otherwise
fprintf('%10s at [%f %f %f] %s\n', lab, opt.pos, opt.mri{opt.currmri}.unit);
end
opt.reinit = false;
end
% zoom
xi = opt.pos(1);
yi = opt.pos(2);
zi = opt.pos(3);
xloadj = ((xi-opt.axis(1))-(xi-opt.axis(1))*opt.zoom);
xhiadj = ((opt.axis(2)-xi)-(opt.axis(2)-xi)*opt.zoom);
yloadj = ((yi-opt.axis(3))-(yi-opt.axis(3))*opt.zoom);
yhiadj = ((opt.axis(4)-yi)-(opt.axis(4)-yi)*opt.zoom);
zloadj = ((zi-opt.axis(5))-(zi-opt.axis(5))*opt.zoom);
zhiadj = ((opt.axis(6)-zi)-(opt.axis(6)-zi)*opt.zoom);
axis(h1, [xi-xloadj xi+xhiadj yi-yloadj yi+yhiadj zi-zloadj zi+zhiadj]);
axis(h2, [xi-xloadj xi+xhiadj yi-yloadj yi+yhiadj zi-zloadj zi+zhiadj]);
axis(h3, [xi-xloadj xi+xhiadj yi-yloadj yi+yhiadj]);
if opt.init
% draw the crosshairs for the first time
delete(findobj(opt.mainfig, 'Type', 'Line')); % get rid of old crosshairs (to facilitate switching scans)
hch1 = ft_plot_crosshair([xi yi-yloadj zi], 'parent', h1, 'color', 'yellow'); % was [xi 1 zi], now corrected for zoom
hch2 = ft_plot_crosshair([xi+xhiadj yi zi], 'parent', h2, 'color', 'yellow'); % was [opt.dim(1) yi zi], now corrected for zoom
hch3 = ft_plot_crosshair([xi yi zi], 'parent', h3, 'color', 'yellow'); % was [xi yi opt.dim(3)], now corrected for zoom
opt.handlescross = [hch1(:)';hch2(:)';hch3(:)'];
else
% update the existing crosshairs, don't change the handles
ft_plot_crosshair([xi yi-yloadj zi], 'handle', opt.handlescross(1, :));
ft_plot_crosshair([xi+xhiadj yi zi], 'handle', opt.handlescross(2, :));
ft_plot_crosshair([xi yi zi], 'handle', opt.handlescross(3, :));
end
if opt.showcrosshair
set(opt.handlescross, 'Visible', 'on');
else
set(opt.handlescross, 'Visible', 'off');
end
% draw markers
if opt.showmarkers && opt.redrawmarkers
delete(findobj(opt.mainfig, 'Type', 'Line', 'Marker', '+')); % remove previous markers
delete(findobj(opt.mainfig, 'Type', 'text')); % remove previous labels
idx = find(~cellfun(@isempty,opt.markerlab)); % non-empty markers
if ~isempty(idx)
for i=1:numel(idx)
markerlab_sel{i,1} = opt.markerlab{idx(i),1};
markerpos_sel(i,:) = opt.markerpos{idx(i),1};
end
tmp1 = markerpos_sel(:,1);
tmp2 = markerpos_sel(:,2);
tmp3 = markerpos_sel(:,3);
subplot(opt.axes(1));
if ~opt.global % filter markers distant to the current slice (N units and further)
posj_idx = find( abs(tmp2 - repmat(yi,size(tmp2))) < opt.markerdist);
posi = tmp1(posj_idx);
posj = tmp2(posj_idx);
posk = tmp3(posj_idx);
else % plot all markers on the current slice
posj_idx = 1:numel(tmp1);
posi = tmp1;
posj = tmp2;
posk = tmp3;
end
if ~isempty(posi)
hold on
plot3(posi, repmat(yi-yloadj,size(posj)), posk, 'marker', '+', 'linestyle', 'none', 'color', 'r'); % [xi yi-yloadj zi]
if opt.showlabels
for i=1:numel(posj_idx)
text(posi(i), yi-yloadj, posk(i), markerlab_sel{posj_idx(i),1}, 'color', [1 .5 0], 'clipping', 'on');
end
end
hold off
end
subplot(opt.axes(2));
if ~opt.global % filter markers distant to the current slice (N units and further)
posi_idx = find( abs(tmp1 - repmat(xi,size(tmp1))) < opt.markerdist);
posi = tmp1(posi_idx);
posj = tmp2(posi_idx);
posk = tmp3(posi_idx);
else % plot all markers on the current slice
posi_idx = 1:numel(tmp1);
posi = tmp1;
posj = tmp2;
posk = tmp3;
end
if ~isempty(posj)
hold on
plot3(repmat(xi+xhiadj,size(posi)), posj, posk, 'marker', '+', 'linestyle', 'none', 'color', 'r'); % [xi+xhiadj yi zi]
if opt.showlabels
for i=1:numel(posi_idx)
text(posi(i)+xhiadj, posj(i), posk(i), markerlab_sel{posi_idx(i),1}, 'color', [1 .5 0], 'clipping', 'on');
end
end
hold off
end
subplot(opt.axes(3));
if ~opt.global % filter markers distant to the current slice (N units and further)
posk_idx = find( abs(tmp3 - repmat(zi,size(tmp3))) < opt.markerdist);
posi = tmp1(posk_idx);
posj = tmp2(posk_idx);
posk = tmp3(posk_idx);
else % plot all markers on the current slice
posk_idx = 1:numel(tmp1);
posi = tmp1;
posj = tmp2;
posk = tmp3;
end
if ~isempty(posk)
hold on
plot3(posi, posj, repmat(zi,size(posk)), 'marker', '+', 'linestyle', 'none', 'color', 'r'); % [xi yi zi]
if opt.showlabels
for i=1:numel(posk_idx)
text(posi(i), posj(i), zi, markerlab_sel{posk_idx(i),1}, 'color', [1 .5 0], 'clipping', 'on');
end
end
hold off
end
clear markerlab_sel markerpos_sel
opt.redrawmarkers = false;
opt.redrawscattermarkers = true;
end % if idx
end % if showmarkers
% also update the scatter appendix
if opt.scatter
cb_scatterredraw(h);
end
% make the last current axes current again
sel = findobj('type', 'axes', 'tag', tag);
if ~isempty(sel)
set(opt.mainfig, 'currentaxes', sel(1));
end
% do not initialize on the next call
opt.init = false;
setappdata(h, 'opt', opt);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% SUBFUNCTION
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function cb_scatterredraw(h, eventdata)
h = getparent(h);
opt = getappdata(h, 'opt');
if ~isfield(opt, 'scatterfig') % initiate in case the figure does not yet exist
opt.scatterfig = figure(...
'Name', [mfilename ' appendix'],...
'Units', 'normalized', ...
'Color', [1 1 1], ...
'Visible', 'on');
set(opt.scatterfig, 'CloseRequestFcn', @cb_scattercleanup);
opt.scatterfig_h1 = axes('position', [0.02 0.02 0.96 0.96]);
set(opt.scatterfig_h1, 'DataAspectRatio', get(opt.axes(1), 'DataAspectRatio'));
axis square; axis tight; axis off; view([90 0]);
xlabel('x'); ylabel('y'); zlabel('z');
% scatter range sliders
opt.scatterfig_h23text = uicontrol('Style', 'text',...
'String', 'Intensity',...
'Units', 'normalized', ...
'Position', [.85+0.03 .26 .1 0.04],...
'BackgroundColor', [1 1 1], ...
'HandleVisibility', 'on');