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plotmri.m
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plotmri.m
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% plotmri() - Overlay activation on MNI normalized brain and vizualize it.
%
% Usage:
% >> mri = plotmri( mri, act, 'key', val, ... );
%
% Inputs:
% mri - mri structure normalized to MNI brain. Supposed to contain
% a field anatomy and a field transform. 4-D array with color
% from 0 to 1.
% act - activation value, one per voxel.
%
% optional inputs:
% 'mrigamma' - [float] mri gamma factor (alter contrast). 1 does not
% change contrast. < 1 increases contrast; > 1 decreases
% contrast.
% 'actgamma' - [float] activity gamma factor (alter contrast). 1 does not
% change contrast. < 1 increases contrast; > 1 decreases
% contrast.
% 'cmap' - [hot] colormap for activity
% 'plot' - [X Y Z] plot one MRI slices at MNI coordinate [X Y Z].
% 'scroll' - ['on'|'off'] GUI for selecting slices. Default is 'on'.
%
%
% Example: see loreta_importcomp()
%
% Author: Arnaud Delorme, SCCN, INC, UCSD, 2005
% Copyright (C) Arnaud Delorme, SCCN, INC, UCSD, 2005 [email protected]
%
% 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 mri = plotmri( mri, activations, varargin)
if nargin < 1
help plotmri;
return;
end;
if ~isstr(mri)
g = finputcheck(varargin, { ...
'actgamma' 'real' [0 Inf] 1;
'mrigamma' 'real' [0 Inf] 1;
'actfactor' 'real' [0 Inf] 0.4;
'transform' 'real' [] eye(4);
'colchan' 'integer' [0 Inf] 1;
'cmap' 'integer' [0 Inf] hot;
'plot' 'real' [] [];
'scroll' 'string' { 'on' 'off' } 'on' });
if isstr(g), error(g); end;
disp('Slice number in MNI coordinates (mm)');
% find point with highest activation value
% ----------------------------------------
if isempty(g.plot)
[tmp ind] = max(activations(:));
activations(ind) = 2;
[i j] = find( activations == 2 );
activations(ind) = tmp;
[sx sy sz] = size(activations);
g.plot(1) = i;
g.plot(2) = mod(j-1,sy)+1;
g.plot(3) = (j-g.plot(2))/sy+1;
plotinmricoord = g.plot;
g.plot = g.transform*[g.plot+1 1]';
g.plot = g.plot(1:3)';
disp('Finding maximum of activity');
end;
% set the activation to true color
% --------------------------------
g.act = activations;
tmpact = g.act.^g.actgamma;
ncolors = size(g.cmap,1);
tmpact = round(tmpact/max(tmpact(:))*(ncolors-1))+1; % -> range: colors 1:ncolors
newprob3d = zeros(size(tmpact,1), size(tmpact,2), size(tmpact,3), 3);
for ix = 1:size(newprob3d,1) % could somehow use matrix ops here???
for iy = 1:size(newprob3d,2)
for iz = 1:size(newprob3d,3)
newprob3d(ix, iy, iz, :) = g.cmap(tmpact(ix, iy, iz),:);
end;
end;
end;
% compute MRI after gamma factor etc...
% -------------------------------------
g.invtransf = pinv(g.transform);
g.mri = mri;
try
g.curmri = g.mri.^g.mrigamma;
catch,
g.curmri = g.mri.anatomy.^g.mrigamma;
end;
% make true color if necessary
% ----------------------------
if ndims(g.curmri) == 3
g.curmri(:,:,:,2) = g.curmri(:,:,:,1);
g.curmri(:,:,:,3) = g.curmri(:,:,:,1);
end;
% normalize
% ---------
newprob3d = newprob3d / max(newprob3d(:));
g.curmri = g.curmri / max(g.curmri(:));
g.curmri = 0.5*g.curmri + 0.5*newprob3d;
g.curmri(plotinmricoord(1), plotinmricoord(2), plotinmricoord(3), :) = 0;
% make scrolling buttons
% ----------------------
g.fid = figure( 'position', [60 705 1010 335]);
set(g.fid, 'userdata', g);
[sx sy sz tmp] = size(g.mri);
h1 = axes('unit', 'pixel', 'position', [58 57 290 270], 'tag', 'view1');
h2 = axes('unit', 'pixel', 'position', [358 57 290 270], 'tag', 'view2');
h3 = axes('unit', 'pixel', 'position', [658 57 290 270], 'tag', 'view3');
makescroll(h1, g.plot(3), 'view1', 2, g.scroll);
makescroll(h2, g.plot(2), 'view2', 2, g.scroll);
makescroll(h3, g.plot(1), 'view3', 2, g.scroll);
set(gcf, 'color', 'k');
plotmri('redraw', 'all');
return;
else
g = get(gcf, 'userdata');
options = { 'FaceColor','texturemap', 'EdgeColor','none', 'CDataMapping', ...
'direct','tag','img', 'facelighting', 'none' };
coord(3) = str2num(get(findobj(g.fid, 'tag', 'textview1'), 'string'));
coord(2) = str2num(get(findobj(g.fid, 'tag', 'textview2'), 'string'));
coord(1) = str2num(get(findobj(g.fid, 'tag', 'textview3'), 'string'));
slice = round(g.invtransf*[ coord 1]')';
% string command (for now just redraw)
% ------------------------------------
if strcmpi(activations, 'all') | strcmpi(activations, 'view1'), redraw(1, slice, g); end;
if strcmpi(activations, 'all') | strcmpi(activations, 'view2'), redraw(2, slice, g); end;
if strcmpi(activations, 'all') | strcmpi(activations, 'view3'), redraw(3, slice, g); end;
end;
% redraw different slices
% -----------------------
function redraw(viewnb, slicenb, g);
options = { 'FaceColor','texturemap', 'EdgeColor','none', 'CDataMapping', ...
'scaled','tag','img', 'facelighting', 'none' };
[sx sy sz tmp] = size(g.curmri);
maxs = max([ sx sy sz ]);
switch viewnb
case 1, img1 = squeeze(g.curmri(:,:,slicenb(3),:));
axes(findobj(g.fid, 'tag', 'view1'));
delete(findobj(g.fid, 'tag', 'surfview1'));
surface([0 0; sx sx], [0 sy; 0 sy], [0 0; 0 0], img1, options{:}, 'tag', 'surfview1');
xlim([0 maxs]); ylim([0 maxs]); zlim([0 maxs]);
axis off; axis equal;
view( [0 0 1] );
case 2, img2 = squeeze(g.curmri(:,slicenb(2),:,:));
axes(findobj(g.fid, 'tag', 'view2'));
delete(findobj(g.fid, 'tag', 'surfview2'));
surface([0 0; sx sx], [0 0; 0 0], [0 sz; 0 sz], img2, options{:}, 'tag', 'surfview2');
xlim([0 maxs]); ylim([0 maxs]); zlim([0 maxs]);
axis off; axis equal;
view( [0 1 0] );
case 3, img3 = squeeze(g.curmri(slicenb(1),:,:,:));
axes(findobj(g.fid, 'tag', 'view3'));
delete(findobj(g.fid, 'tag', 'surfview3'));
surface([0 0; 0 0], [0 0; sy sy], [0 sz; 0 sz], img3, options{:}, 'tag', 'surfview3');
xlim([0 maxs]); ylim([0 maxs]); zlim([0 maxs]);
axis off; axis equal;
view( [1 0 0] );
end;
return;
% make GUI for each plot
% ----------------------
function makescroll(fid, curcoords, tag, coordinc, visible)
set(fid, 'unit', 'normalized');
pos = get(fid, 'position');
set(fid, 'tag', tag);
s = [pos(1) pos(2) 0 0]+[0.04 0 0 0];
q = [pos(3) pos(4) pos(3) pos(4)];
ht = 0.05;
wd = 0.03;
coordminus = [0.03 -0.05 wd ht]+s;
coordtext = [0.08 -0.05 0.04 ht]+s;
coordcom = [0.11 -0.05 wd ht]+s;
coordplus = [0.15 -0.05 wd ht]+s;
cb_minus = [ 'tmpobj = findobj(gcbf, ''tag'', ''text' tag ''');' ...
'tmpval = str2num(get(tmpobj,''string'')) - ' num2str(coordinc) ';' ...
'set(tmpobj, ''string'', num2str(tmpval));' ...
'clear tmpval, tmpobj;' ...
'plotmri(''update'', ''' tag ''');' ];
cb_plus = [ 'tmpobj = findobj(gcbf, ''tag'', ''text' tag ''');' ...
'tmpval = str2num(get(tmpobj,''string'')) + ' num2str(coordinc) ';' ...
'set(tmpobj, ''string'', num2str(tmpval));' ...
'clear tmpval, tmpobj;' ...
'plotmri(''update'', ''' tag ''');' ];
% make buttons
% ------------
h(1) = uicontrol( 'unit', 'normalized', 'style', 'edit', 'tag', [ 'text' tag], 'position', ...
coordtext, 'string', num2str(curcoords), 'callback', ['plotmri(''update'', ''' tag ''');' ]);
h(2) = uicontrol( 'unit', 'normalized', 'style', 'text', 'position', ...
coordcom, 'string', 'mm', 'backgroundcolor', 'k', 'foregroundcolor', 'w' );
h(3) = uicontrol( 'unit', 'normalized', 'style', 'pushbutton', 'position', ...
coordminus, 'string', '-', 'callback', cb_minus);
h(4) = uicontrol( 'unit', 'normalized', 'style', 'pushbutton', 'position', ...
coordplus, 'string', '+', 'callback', cb_plus);
set(h, 'visible', visible);