-
Notifications
You must be signed in to change notification settings - Fork 0
/
m11_Coherence.m
305 lines (280 loc) · 11.1 KB
/
m11_Coherence.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
301
302
303
304
305
clear all
tic
disp('Initializing Files')
filepath = 'C:\Users\ipzach\Documents\MATLAB';
cd(filepath)
load('SpkInfo.mat')
Fs = 1250; % Sampling Frequency; needed for filtering and plotting
% Theta/Delta state to analyze
TD = 2; %High 1, Low 2, Full 3
%%%%%%%%%%%%%%%%%%%%%%%%%
% Group, Band, LR, Animal, Layer/layer
Co = zeros(6,4,2,12,4,4);
%% Stroke group to analyze
% 1:4 6 ref Spk Info
for group = [1:4 6]
%% 1.Load the right and left side signals
%load H/L TD indexes
count = 0;
for animal = 1: length(SpkInfo{group,2})
REM = ['C:\Users\ipzach\Documents\MATLAB\Data' filesep SpkInfo{group,1} '_' num2str(animal) filesep 'cREM.mat'];
try
load(REM);
catch
disp('Missing REM File')
continue
end
if isempty(cREM.R.start) || isempty(cREM.R.end)
disp('Missing REM Start or End Times for Right Side')
cd ..
continue
end
if isempty(cREM.L.start) || isempty(cREM.L.end)
disp('Missing REM Start or End Times for Left Side')
cd ..
continue
end
if isempty(SpkInfo{group,2}(animal).L_chn{3}) || isempty(SpkInfo{group,2}(animal).R_chn{3})
disp('Missing SpkInfo')
continue
end
activefilepath = ['C:\Users\ipzach\Documents\MATLAB\Data' filesep SpkInfo{group,1} '_' num2str(animal) filesep 'concatenatedLFP.mat'];
load(activefilepath);
disp(['Loaded ' SpkInfo{group,1} '_' num2str(animal)])
% mkdir(['C:\Users\ipzach\Documents\MATLAB\Comodulograms' filesep SpkInfo{group,1} '_' num2str(animal)])
% % % % % % % % % % % % %
count = count +1;
for layer = 1:6
switch layer
case 1
A = 1;
B = 2;
compare = 'Cortex-SLM';
case 2
A = 1;
B = 3;
compare = 'Cortex-Pyr';
case 3
A = 1;
B = 4;
compare = 'Cortex-Oriens';
case 4
A = 2;
B = 3;
compare = 'SLM-Pyr';
case 5
A = 2;
B = 4;
compare = 'SLM-Oriens';
case 6
A = 3;
B = 4;
compare = 'Pyr-Oriens';
end
disp(compare)
AL_LFP = cLFP(:, SpkInfo{group,2}(animal).L_chn{A}(1));
AR_LFP = cLFP(:, SpkInfo{group,2}(animal).R_chn{A}(1));
BL_LFP = cLFP(:, SpkInfo{group,2}(animal).L_chn{B}(1));
BR_LFP = cLFP(:, SpkInfo{group,2}(animal).R_chn{B}(1));
for iBand = 1:5
switch iBand
case 1
range = linspace(0.1,3,20);
case 2
range = linspace(4,7,20);
case 3
range = linspace(30,58,20);
case 4
range = linspace(62,200,20);
case 5
range = linspace(0,200,50);
end % switch iBand
% Loading Right Side LFPs
TDIdx = []; % Array for relevant data points indices
% disp('grabbing indices')
switch TD
case 1
% Get indices of High Theta/Delta
for iRem = 1:length(cREM.R.start)
TDIdx = [TDIdx (round(cREM.R.start(iRem)*Fs)):(round(cREM.R.end(iRem)*Fs))];
end
REMtitle = 'H';
% Get indices of Low Theta/Delta
case 2
LowRightStart = cREM.R.end(1:end-1);
LowRightEnd = cREM.R.start(2:end);
for iRem = 1:length(LowRightStart)
TDIdx = [TDIdx (round(LowRightStart(iRem)*Fs)):(round(LowRightEnd(iRem)*Fs))];
end
REMtitle = 'L';
% For entire reading
case 3
TDIdx = 1 : length(cLFP);
REMtitle = 'F';
end
ARH_LFP = AR_LFP(TDIdx);
BRH_LFP = BR_LFP(TDIdx);
% 'Loading left side LFPs'
TDIdx = []; % Array for relevant data points indices
switch TD
case 1
%Get indices of High Theta/Delta
for iRem = 1:length(cREM.L.start)
TDIdx = [TDIdx (round(cREM.L.start(iRem)*Fs)):(round(cREM.L.end(iRem)*Fs))];
end
case 2
% Get indices of Low Theta/Delta
LowLeftStart = cREM.L.end(1:end-1);
LowLeftEnd = cREM.L.start(2:end);
for iRem = 1:length(LowLeftStart)
TDIdx = [TDIdx (round(LowLeftStart(iRem)*Fs)+1):(round(LowLeftEnd(iRem)*Fs))];
end
case 3
%For entire reading
TDIdx = 1 : length(cLFP);
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Creat an array of the relevant data points
ALH_LFP = AL_LFP(TDIdx);
BLH_LFP = BL_LFP(TDIdx);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
try
Co(group,iBand,1,count,A,B) = mean(mscohere(ALH_LFP,BLH_LFP,hamming(12500),[],range,1250));
catch
disp(['Coherence for ' SpkInfo{group,1} num2str(animal) ' Left not calculated'])
end
try
Co(group,iBand,2,count,A,B) = mean(mscohere(ARH_LFP,BRH_LFP,hamming(12500),[],range,1250));
catch
disp(['Coherence for ' SpkInfo{group,1} num2str(animal) ' Right not calculated'])
end
end % band
end % layer
end % animal
end % group
%
%% Coherence
Co(Co == 0) = NaN;
count = 0;
lab1 = {'Ctx','SLM','Pyr'};
lab2 = {'SLM','Pyr','Oriens'};
for i = [1:4 6]
switch i
case 1
treatName = 'Control';
case 2
treatName = 'EES';
case 3
treatName = '1MS';
case 4
treatName = '2WS';
case 6
treatName = 'EES';
end
for j = 1:5
switch j
case 1
groupName = 'Delta';
case 2
groupName = 'Theta';
case 3
groupName = 'Gamma';
case 4
groupName = 'HGamma';
case 5
groupName = 'Full';
end
count = count +1;
combineRec = squeeze(nanmean(Co,3));
% Group, Band, Animal, Layer, layer
combineAnimal = squeeze(nanmean(combineRec,3));
% group, band, layer, layer
subplot(5,5,count)
h = heatmap(squeeze(combineAnimal(i,j,1:3,2:4)));
h.ColorbarVisible = 'off';
set(gca,'xData',lab2,'yData',lab1);
caxis([0 1]);
if i ==1
title(groupName)
end
if j ==1
ylabel(treatName)
end
end
end
%% stats
for band = 1:5
for layComb = 1:6
% First we want to grab individual values, create 2-way labels for
% them, then concatenate everything together
switch layComb
case 1
ctr = squeeze(combineRec(1, band, :, 1, 2));
EEC = squeeze(combineRec(2, band, :, 1, 2));
MS1 = squeeze(combineRec(3, band, :, 1, 2));
WS2 = squeeze(combineRec(4, band, :, 1, 2));
EES = squeeze(combineRec(6, band, :, 1, 2));
case 2
ctr = squeeze(combineRec(1, band, :, 1, 3));
EEC = squeeze(combineRec(2, band, :, 1, 3));
MS1 = squeeze(combineRec(3, band, :, 1, 3));
WS2 = squeeze(combineRec(4, band, :, 1, 3));
EES = squeeze(combineRec(6, band, :, 1, 3));
case 3
ctr = squeeze(combineRec(1, band, :, 1, 4));
EEC = squeeze(combineRec(2, band, :, 1, 4));
MS1 = squeeze(combineRec(3, band, :, 1, 4));
WS2 = squeeze(combineRec(4, band, :, 1, 4));
EES = squeeze(combineRec(6, band, :, 1, 4));
case 4
ctr = squeeze(combineRec(1, band, :, 2, 3));
EEC = squeeze(combineRec(2, band, :, 2, 3));
MS1 = squeeze(combineRec(3, band, :, 2, 3));
WS2 = squeeze(combineRec(4, band, :, 2, 3));
EES = squeeze(combineRec(6, band, :, 2, 3));
case 5
ctr = squeeze(combineRec(1, band, :, 2, 4));
EEC = squeeze(combineRec(2, band, :, 2, 4));
MS1 = squeeze(combineRec(3, band, :, 2, 4));
WS2 = squeeze(combineRec(4, band, :, 2, 4));
EES = squeeze(combineRec(6, band, :, 2, 4));
case 5
ctr = squeeze(combineRec(1, band, :, 3, 4));
EEC = squeeze(combineRec(2, band, :, 3, 4));
MS1 = squeeze(combineRec(3, band, :, 3, 4));
WS2 = squeeze(combineRec(4, band, :, 3, 4));
EES = squeeze(combineRec(6, band, :, 3, 4));
end % switch layComb
ctr(isnan(ctr)) = [];
EEC(isnan(EEC)) = [];
MS1(isnan(MS1)) = [];
WS2(isnan(WS2)) = [];
CtrAgeLab = cell(length(ctr),1);
CtrAgeLab(:) = {'Ctr'};
CtrtreatLab = cell(length(ctr),1);
CtrtreatLab(:) = {'Std'};
EECAgeLab = cell(length(EEC),1);
EECAgeLab(:) = {'Ctr'};
EECtreatLab = cell(length(EEC),1);
EECtreatLab(:) = {'EE'};
MS1AgeLab = cell(length(MS1),1);
MS1AgeLab(:) = {'1MS'};
MS1treatLab = cell(length(MS1),1);
MS1treatLab(:) = {'Std'};
WS2AgeLab = cell(length(WS2),1);
WS2AgeLab(:) = {'2WS'};
WS2treatLab = cell(length(WS2),1);
WS2treatLab(:) = {'Std'};
EESAgeLab = cell(length(WS2),1);
EESAgeLab(:) = {'1MS'};
EEStreatLab = cell(length(WS2),1);
EEStreatLab(:) = {'EE'};
vals = [ctr; EEC; MS1; EES];
ageLabs = [CtrAgeLab; EECAgeLab; MS1AgeLab; EESAgeLab];
dbLabs = [CtrtreatLab; EECtreatLab; MS1treatLab; EEStreatLab];
[~,~,stats] = anovan(vals,{ageLabs,dbLabs},'model','interaction');
drawnnow
pause(0.1)
% [C,M] = multcompare(stats,'Dimension',[1 2],'CType','bonferroni');
end % for layComb
end% for band