-
Notifications
You must be signed in to change notification settings - Fork 98
/
ea_calc_vatstats.m
300 lines (254 loc) · 13.1 KB
/
ea_calc_vatstats.m
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
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