/
ea_calc_vatstats.m
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ea_calc_vatstats.m
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function [PL]=ea_calc_vatstats(resultfig,options,hmchanged)
% Calculate VAT stats (atlas intersection and volume)
% Stimulation information w.r.t the VTA will also be stored in stats.
% __________________________________________________________________________________
% Copyright (C) 2014 Charite University Medicine Berlin, Movement Disorders Unit
% Andreas Horn
set(0,'CurrentFigure',resultfig)
ea_dispt('Visualizing VTA...');
hold on
% get app data
stimparams=getappdata(resultfig,'stimparams');
S=getappdata(resultfig,'curS');
for side=1:length(stimparams)
VAT{side}=stimparams(side).VAT;
end
if ~exist('hmchanged','var')
hmchanged=1;
end
stimDir = [options.subj.stimDir, filesep, ea_nt(options), S.label];
fileBasePath = [stimDir, filesep, 'sub-', options.subj.subjId, '_sim-'];
% clean downstreamfiles if necessary
if hmchanged
ea_delete([fileBasePath, 'binary_model-*_hemi-R_hemidesc-FlippedFromLeft.nii']);
ea_delete([fileBasePath, 'binary_model-*_hemi-L_hemidesc-FlippedFromRight.nii']);
ea_delete([fileBasePath, 'efield_model-*_hemi-R_hemidesc-FlippedFromLeft.nii']);
ea_delete([fileBasePath, 'efield_model-*_hemi-L_hemidesc-FlippedFromRight.nii']);
ea_delete([fileBasePath, 'efieldgauss_model-*_hemi-R_hemidesc-FlippedFromLeft.nii']);
ea_delete([fileBasePath, 'efieldgauss_model-*_hemi-L_hemidesc-FlippedFromRight.nii']);
ea_delete([fileBasePath, 'binary_model-*_seed-dMRI.nii']);
ea_delete([fileBasePath, 'binary_model-*_seed-dMRI_hemi-L.nii']);
ea_delete([fileBasePath, 'binary_model-*_seed-dMRI_hemi-R.nii']);
ea_delete([fileBasePath, 'binary_model-*_seed-fMRI.nii']);
ea_delete([fileBasePath, 'binary_model-*_seed-fMRI_hemi-L.nii']);
ea_delete([fileBasePath, 'binary_model-*_seed-fMRI_hemi-R.nii']);
end
%prepare statvat exports once if needed.
if options.expstatvat.do % export statvat nifti images.
tV=spm_vol([ea_space(options),'bb.nii']);
tnii=spm_read_vols(tV);
tnii(:)=0;
%generate mesh of hires MNI
[x,y,z]=ind2sub(size(tnii),1:numel(tnii));
templatecoords=[x;y;z;ones(1,length(x))]; clear x y z
templatecoords=tV.mat*templatecoords;
templatecoords=templatecoords(1:3,:)';
end
togglenames={'vaton','quivon'};
for but=1:length(togglenames)
eval([togglenames{but},'=getappdata(resultfig,''',togglenames{but},''');']);
expand=1;
if isempty(eval(togglenames{but}))
%eval([togglenames{but},'=repmat(1,expand,length(options.sides));']);
%changed to max, as to include for sure the array as large as the maximum side used,
%as this code was intended for the bilateral cases
%maybe will have to change it to minimum have two elements, to always include at least R and L sides
%For example, before if the side was only Left, the multiplier would have been only 1
eval([togglenames{but},'=repmat(1,expand,max(options.sides));']);
end
setappdata(resultfig,togglenames{but},eval(togglenames{but}));
end
clear expand
% assign the place where to write stim stats into struct
if isfield(options,'groupmode')
if options.groupmode
S.label=['gs_',options.groupid]; % hard reset label to group stim label
end
end
try
load(options.subj.stats, 'ea_stats');
catch
ea_stats = struct;
end
[ea_stats, thisstim] = ea_assignstimcnt(ea_stats,S);
if (isfield(VAT{1},'VAT') && isstruct(VAT{1}.VAT)) || ((length(VAT)>1) && isfield(VAT{2},'VAT') && isstruct(VAT{2}.VAT)) % e.g. simbio model used
vat=1;
for iside=1:length(options.sides)
side=options.sides(iside);
try
nVAT{side}.VAT{vat}=VAT{side}.VAT.vertices;
K(side).K{vat}=VAT{side}.VAT.faces;
catch
nVAT{side}.VAT{vat}=[];
K(side).K{vat}=[];
end
end
VAT=nVAT;
end
for iside=1:length(options.sides)
side=options.sides(iside);
switch side
case 1
sidec='R';
case 2
sidec='L';
end
for vat=1:length(VAT{side}.VAT)
if ~exist('K','var') % e.g. maedler model used
try
K(side).K{vat}=convhulln(VAT{side}.VAT{vat}+randn(size(VAT{side}.VAT{vat}))*0.000001); % create triangulation.
catch
keyboard
if isnan(VAT{side}.VAT) % empty VTA
continue
end
end
else % still maedler model used
try
K(side).K{vat}; % not defined
catch
K(side).K{vat}=convhulln(VAT{side}.VAT{vat}+randn(size(VAT{side}.VAT{vat}))*0.000001); % create triangulation.
end
end
% show vat
if ~isempty(K(side).K{vat})
PL.vatsurfs(side,vat)=trisurf(K(side).K{vat},VAT{side}.VAT{vat}(:,1),VAT{side}.VAT{vat}(:,2),VAT{side}.VAT{vat}(:,3),...
abs(repmat(60,length(VAT{side}.VAT{vat}),1)...
+randn(length(VAT{side}.VAT{vat}),1)*2)');
% the following is some code required for
% Web/JSON/BrainBrowser-Export.
PL.vatfv(side,vat).vertices=[VAT{side}.VAT{vat}(:,1),VAT{side}.VAT{vat}(:,2),VAT{side}.VAT{vat}(:,3)];
PL.vatfv(side,vat).faces=K(side).K{vat};
PL.vatfv(side,vat).normals=get(PL.vatsurfs(side,vat),'Vertexnormals');
PL.vatfv(side,vat).colors=repmat([1,0,0,0.7],size(PL.vatfv(side,vat).vertices,1),1);
ea_spec_atlas(PL.vatsurfs(side,vat),'vat',jet,1);
vatgrad=getappdata(resultfig,'vatgrad');
if ~isempty(vatgrad)
try % only one hemisphere could be defined.
if stimparams(side).volume
reduc=ceil(length(vatgrad(side).x)/100000);
PL.quiv(side)=quiver3(vatgrad(side).x(1:reduc:end),vatgrad(side).y(1:reduc:end),vatgrad(side).z(1:reduc:end),vatgrad(side).qx(1:reduc:end),vatgrad(side).qy(1:reduc:end),vatgrad(side).qz(1:reduc:end),0,'w-','LineWidth',1);
end
end
end
if options.writeoutstats
ea_dispt('Writing out stats...');
ea_stats.stimulation(thisstim).label=S.label;
ea_stats.stimulation(thisstim).vat(side,vat).amp=S.amplitude{side};
ea_stats.stimulation(thisstim).vat(side,vat).label=S.label;
ea_stats.stimulation(thisstim).vat(side,vat).contact=vat;
ea_stats.stimulation(thisstim).vat(side,vat).side=side;
modelLabel = ea_simModel2Label(S.model);
% VTA volume and efield volume
ea_stats.stimulation(thisstim).vat(side,vat).volume=stimparams(1,side).volume(vat);
if isfile([fileBasePath, 'efield_model-', modelLabel, '_hemi-', sidec, '.nii'])
vefieldfile = [fileBasePath, 'efield_model-', modelLabel, '_hemi-', sidec, '.nii'];
end
atlasName = options.atlasset;
if ~strcmp(atlasName, 'Use none')
load([ea_space(options,'atlases'),atlasName,filesep,'atlas_index.mat']);
for atlas=1:length(atlases.names)
if any(S.amplitude{side}) % stimulation on
switch atlases.types(atlas)
case 1 % right hemispheric atlas.
atlasfile = [ea_space([],'atlases'),options.atlasset,filesep,'rh',filesep,atlases.names{atlas}];
case 2 % left hemispheric atlas.
atlasfile = [ea_space([],'atlases'),options.atlasset,filesep,'lh',filesep,atlases.names{atlas}];
case 3 % both-sides atlas composed of 2 files.
switch sidec
case {'right', 'R'}
atlasfile = [ea_space([],'atlases'),options.atlasset,filesep,'rh',filesep,atlases.names{atlas}];
case {'left', 'L'}
atlasfile = [ea_space([],'atlases'),options.atlasset,filesep,'lh',filesep,atlases.names{atlas}];
end
case 4 % mixed atlas (one file with one cluster on each hemisphere).
atlasfile = [ea_space([],'atlases'),options.atlasset,filesep,'mixed',filesep,atlases.names{atlas}];
case 5 % midline atlas (one file with one cluster in total).
atlasfile = [ea_space([],'atlases'),options.atlasset,filesep,'midline',filesep,atlases.names{atlas}];
end
if endsWith(atlasfile, {'.nii','.nii.gz'})
atlasfile = ea_niigz(atlasfile);
else % Skip fiber atlas
ea_stats.stimulation(thisstim).vat(side,vat).AtlasIntersection(atlas)=0;
ea_stats.stimulation(thisstim).vat(side,vat).nAtlasIntersection(atlas)=0;
ea_stats.stimulation(thisstim).vat(side,vat).nWithinAtlasIntersection(atlas)=0;
ea_stats.stimulation(thisstim).vat(side,vat).AtlasVolume(atlas)=nan;%if nothing is computed, the atlas volume is not estimated
continue;
end
vatfile = [fileBasePath, 'binary_model-', modelLabel, '_hemi-', sidec, '.nii'];
[~, mm_overlap, normVTAOverlap, normAtlasOverlap, mm_vta, mm_atlas] = ea_vta_overlap(vatfile, atlasfile, sidec);
% Overriding the volume of the vat with the one
% computed from the nifti image, for consistency
% with the atlas/overlap volume estimation
stimparams(1,side).volume(vat) = mm_vta;
ea_stats.stimulation(thisstim).vat(side,vat).AtlasVolume(atlas) = mm_atlas;
ea_stats.stimulation(thisstim).vat(side,vat).AtlasIntersection(atlas) = mm_overlap;
ea_stats.stimulation(thisstim).vat(side,vat).nAtlasIntersection(atlas) = normVTAOverlap; % Overlap in respect of VAT (ratio [0-1]);
ea_stats.stimulation(thisstim).vat(side,vat).nWithinAtlasIntersection(atlas) = normAtlasOverlap; % Overlap in respect of atlas (ratio [0-1])
% now also add efield overlap:
if exist('vefieldfile','var')
[overlap, normOverlap, efieldSum] = ea_efield_overlap(vefieldfile,atlasfile,sidec);
ea_stats.stimulation(thisstim).efield(side,vat).volume = efieldSum;
ea_stats.stimulation(thisstim).efield(side,vat).AtlasIntersection(atlas) = overlap;
ea_stats.stimulation(thisstim).efield(side,vat).nAtlasIntersection(atlas) = normOverlap;
end
else % no stimulation, simply set vi to zero.
ea_stats.stimulation(thisstim).vat(side,vat).AtlasIntersection(atlas)=0;
ea_stats.stimulation(thisstim).vat(side,vat).nAtlasIntersection(atlas)=0;
ea_stats.stimulation(thisstim).vat(side,vat).nWithinAtlasIntersection(atlas)=0;
ea_stats.stimulation(thisstim).vat(side,vat).AtlasVolume(atlas)=nan;%if nothing is computed, the atlas volume is not estimated
end
end
end
save(options.subj.stats, 'ea_stats', '-v7.3');
end
end
end
try
if stimparams(side).volume
if ~isfield(PL, 'ht')
PL.ht=uitoolbar(resultfig);
end
vatbutton(side)=uitoggletool(PL.ht,'CData',ea_get_icn('vat'),'TooltipString','Volume of activated tissue','OnCallback',{@objvisible,PL.vatsurfs(side,:),resultfig,'vaton',[],side,1},'OffCallback',{@objvisible,PL.vatsurfs(side,:),resultfig,'vaton',[],side,0},'State',getstate(vaton(side)));
quivbutton(side)=uitoggletool(PL.ht,'CData',ea_get_icn('quiver'),'TooltipString','E-field','OnCallback',{@objvisible,PL.quiv(side),resultfig,'quivon',[],side,1},'OffCallback',{@objvisible,PL.quiv(side),resultfig,'quivon',[],side,0},'State',getstate(quivon(side)));
end
end
end
% correct togglestates
for iside=1:length(options.sides)
side=options.sides(iside);
if ~vaton(side)
try
objvisible([],[],PL.vatsurfs(side,:),resultfig,'vaton',[],side,0)
end
end
if ~quivon(side)
try
objvisible([],[],PL.quiv(side),resultfig,'quivon',[],side,0)
end
end
end
setappdata(resultfig,'PL',PL);
ea_dispt('');
function objvisible(hobj,ev,atls,resultfig,what,la,side,onoff)
% set visibility
try
set(atls, 'Visible', getstate(onoff));
catch
keyboard
end
% log visibility
tvalue=getappdata(resultfig,what);
if isempty(la)
tvalue(side)=onoff;
else
tvalue(la,side)=onoff;
end
setappdata(resultfig,what,tvalue);
function str=getstate(val)
switch val
case 1
str='on';
case 0
str='off';
end