NeuroTychoWiki - User contributions [en]

LocalGlobal Details

2024-07-06T13:13:16Z

Mkomatsu: /* Sample code for Monkey Ji and Rc */

== Experiment Settings ==
Not that the followings are default settings, and the actual details are in the each paper.

Stimuli: x=800 Hz, Y=1600 Hz, 50 ms duration No raise/fall time

Trial: ISI = 150 ms (thus SOA = 200 ms), ITI = [1.8 2.0] s

Block: 10 types, randomized order

1 block contains 100 trials (20 habituation, 64 standards, and 16 deviants).

Tone Index:

1. xxxxx

2. xxxxY

3. xxxx_

4. YYYYY

5. YYYYx

6. YYYY_

Block Index:

1. xxxxx with deviant xxxxY

2. xxxxx with omission xxxx_

3. xxxxY with deviant xxxxx

4. xxxxY with omission xxxx_

5. pure omission xxxx_

6. YYYYY with deviant YYYYx

7. YYYYY with omission YYYY_

8. YYYYx with deviant YYYYY

9. YYYYx with omission YYYY_

10. pure omission YYYY_

== Data format ==

Data can be download from Brain/MINDS data portal.

One zip file has one date data which consists of a session.

For Monkey Ji and Rc:

‘ECoG_ch**.mat‘ had ECoG data of electrode. ** means number of electrode. Sampling rate was 1 kHz.

‘ECoGTime.mat‘ had time of ECoG data.

‘Event.mat‘ had information of condition.

‘Eye.mat‘ had eye tracking data recorded from right eye.

‘Audio.mat‘ had a audio data.

For Monkey Yo, Ca and Rm:

‘ECoG_ch**.mat‘ had ECoG data of electrode. ** means number of electrode. Sampling rate was 1017.25 Hz.

‘TriG_ch2.mat‘ had information of condition.

‘Aud_ch1.mat‘ had a audio data.

== Sample code for Monkey Ji and Rc ==

clear

addpath(genpath('D:\MATLAB_toolboxes\eeglab14_1_1b'))
cd G:\Local_global_marmoset

Subject='Ji';
% Subject='Rc';

Expt_name=sprintf('%s20*',Subject);
Expt=ls(Expt_name);
Expt_num=size(Expt,1);

FS=1000; %Hz
DS=1;

Channel_num=96;

%%

Data_all=[];
Time=[];
Stim_time=[];
Block_idx=[];
Trial_idx=[];
Expt_idx=[];

Time_offset=0;

for expt=1:Expt_num

cd(Expt(expt,:))
load Event %allBlockIdx allTrialIdx StimOn

fprintf(1,'>> Expt%d/%d: %s (%.1f min)(%d trials)\n',expt, Expt_num,Expt(expt,:),length(EventTime)/1000/60,length(StimOn))

Data=zeros(Channel_num,length([1:DS:length(EventTime)]));

for ch=1:Channel_num
FN=sprintf('ECoG_ch%d',ch);
load(FN)

str=sprintf('Data(ch,:)=ECoGData_ch%d(1:DS:end);',ch);
eval(str)
end

Data_all=[Data_all Data];
Time=[Time EventTime(1:DS:end)/FS+Time_offset];
Stim_time=[Stim_time StimOn/FS+Time_offset];
Block_idx=[Block_idx allBlockIdx];
Trial_idx=[Trial_idx allTrialIdx];
Expt_idx=[Expt_idx ones(1,length(allTrialIdx))*expt];

Time_offset=Time(end)+DS/FS;

clear Data EventTime StimOn

cd ..

end

== Sample code for Monkey Yo, Ca and Rm ==

clear

addpath(genpath('D:\MATLAB_toolboxes\eeglab14_1_1b'))
cd G:\Local_global_marmoset

Subject='Ca';
% Subject='Rm';
% Subject='Yo';

Expt_name=sprintf('%s20*',Subject);
Expt=ls(Expt_name);
Expt_num=size(Expt,1);

FS=1017.25; %Hz
DS=1;

Channel_num=96;

Trial_per_block=100;

%% Block info

Block_type_name{1}='xxxxx with deviant xxxxY';
Block_type_name{2}='xxxxx with omission xxxx_';
Block_type_name{3}='xxxxY with deviant xxxxx';
Block_type_name{4}='xxxxY with omission xxxx_';

Anag_xx=40;
Anag_xY=80;
Anag_xo=120;

%%
Data_all=[];
Block_idx=[];
Trial_idx=[];
Expt_idx=[];
Stim_idx=[];

Idx_offset=0;

for expt=1:Expt_num

cd(Expt(expt,:))

%% Event
load('TriG_ch2.mat')

%trim Trig if longer than wave
load('ECoG_ch1');

if length(Trig)>length(wave)
Trig=Trig(1:length(wave));
end

%downsample
Trig=Trig(1:DS:end);

Onset=find(diff(Trig)>10);
Nope=find(Trig(Onset)>10);
Onset(Nope)=[];

Trial_idx_expt=round(Trig(Onset+10)/40); %1: xxxxx; 2: xxxxY; 3:xxxxo

Block_idx_expt=zeros(1,length(Onset));

%%% Could be only 3 blocks
Block_per_expt=ceil(length(Block_idx_expt)/Trial_per_block);

for block=1:Block_per_expt
if block<Block_per_expt
XX=Trial_idx_expt([1:Trial_per_block]+(block-1)*Trial_per_block);
else % the last block could be short
XX=Trial_idx_expt((1+(block-1)*Trial_per_block):end);
end
Stand=XX(1);
Dev=find(XX~=Stand);
Dev=XX(Dev(1));

if Stand==1 & Dev==2
B_type=1;
elseif Stand==1 & Dev==3
B_type=2;
elseif Stand==2 & Dev==1
B_type=3;
elseif Stand==2 & Dev==3
B_type=4;
else
B_type=-1;
end

if block<Block_per_expt
Block_idx_expt([1:Trial_per_block]+(block-1)*Trial_per_block)=B_type;
else
Block_idx_expt((1+(block-1)*Trial_per_block):end)=B_type;
end

end

Trial_idx=[Trial_idx Trial_idx_expt];
Block_idx=[Block_idx Block_idx_expt];
Expt_idx=[Expt_idx ones(1,length(Onset))*expt];

Stim_idx=[Stim_idx Onset+Idx_offset];

Idx_offset=Idx_offset+length(Trig);

%%
fprintf(1,'>> Expt %d/%d: %s (%d trials)\n',expt, Expt_num,Expt(expt,:),length(Onset))

Data=zeros(Channel_num,length(Trig));
for ch=1:Channel_num
FN=sprintf('ECoG_ch%d',ch);
load(FN)

Data(ch,:)=wave(1:DS:end);
end

Data_all=[Data_all Data];

clear Data wave
cd ..
end
Time=[0:size(Data_all,2)-1]/FS*DS;
Stim_time=Time(Stim_idx);

LocalGlobal Details

2024-07-06T13:12:41Z

Mkomatsu:

== Experiment Settings ==
Not that the followings are default settings, and the actual details are in the each paper.

Stimuli: x=800 Hz, Y=1600 Hz, 50 ms duration No raise/fall time

Trial: ISI = 150 ms (thus SOA = 200 ms), ITI = [1.8 2.0] s

Block: 10 types, randomized order

1 block contains 100 trials (20 habituation, 64 standards, and 16 deviants).

Tone Index:

1. xxxxx

2. xxxxY

3. xxxx_

4. YYYYY

5. YYYYx

6. YYYY_

Block Index:

1. xxxxx with deviant xxxxY

2. xxxxx with omission xxxx_

3. xxxxY with deviant xxxxx

4. xxxxY with omission xxxx_

5. pure omission xxxx_

6. YYYYY with deviant YYYYx

7. YYYYY with omission YYYY_

8. YYYYx with deviant YYYYY

9. YYYYx with omission YYYY_

10. pure omission YYYY_

== Data format ==

Data can be download from Brain/MINDS data portal.

One zip file has one date data which consists of a session.

For Monkey Ji and Rc:

‘ECoG_ch**.mat‘ had ECoG data of electrode. ** means number of electrode. Sampling rate was 1 kHz.

‘ECoGTime.mat‘ had time of ECoG data.

‘Event.mat‘ had information of condition.

‘Eye.mat‘ had eye tracking data recorded from right eye.

‘Audio.mat‘ had a audio data.

For Monkey Yo, Ca and Rm:

‘ECoG_ch**.mat‘ had ECoG data of electrode. ** means number of electrode. Sampling rate was 1017.25 Hz.

‘TriG_ch2.mat‘ had information of condition.

‘Aud_ch1.mat‘ had a audio data.

== Sample code for Monkey Ji and Rc ==

clear

addpath(genpath('D:\MATLAB_toolboxes\eeglab14_1_1b'))
cd G:\Local_global_marmoset

Subject='Ji';
% Subject='Rc';

Expt_name=sprintf('%s20*',Subject);
Expt=ls(Expt_name);
Expt_num=size(Expt,1);

FS=1000; %Hz
DS=1;

Channel_num=96;

%%
Data_all=[];
Time=[];
Stim_time=[];
Block_idx=[];
Trial_idx=[];
Expt_idx=[];

Time_offset=0;

for expt=1:Expt_num

cd(Expt(expt,:))
load Event %allBlockIdx allTrialIdx StimOn

fprintf(1,'>> Expt%d/%d: %s (%.1f min)(%d trials)\n',expt, Expt_num,Expt(expt,:),length(EventTime)/1000/60,length(StimOn))

Data=zeros(Channel_num,length([1:DS:length(EventTime)]));

for ch=1:Channel_num
FN=sprintf('ECoG_ch%d',ch);
load(FN)

str=sprintf('Data(ch,:)=ECoGData_ch%d(1:DS:end);',ch);
eval(str)
end

Data_all=[Data_all Data];
Time=[Time EventTime(1:DS:end)/FS+Time_offset];
Stim_time=[Stim_time StimOn/FS+Time_offset];
Block_idx=[Block_idx allBlockIdx];
Trial_idx=[Trial_idx allTrialIdx];
Expt_idx=[Expt_idx ones(1,length(allTrialIdx))*expt];

Time_offset=Time(end)+DS/FS;

clear Data EventTime StimOn

cd ..

end

== Sample code for Monkey Yo, Ca and Rm ==

clear

addpath(genpath('D:\MATLAB_toolboxes\eeglab14_1_1b'))
cd G:\Local_global_marmoset

Subject='Ca';
% Subject='Rm';
% Subject='Yo';

Expt_name=sprintf('%s20*',Subject);
Expt=ls(Expt_name);
Expt_num=size(Expt,1);

FS=1017.25; %Hz
DS=1;

Channel_num=96;

Trial_per_block=100;

%% Block info

Block_type_name{1}='xxxxx with deviant xxxxY';
Block_type_name{2}='xxxxx with omission xxxx_';
Block_type_name{3}='xxxxY with deviant xxxxx';
Block_type_name{4}='xxxxY with omission xxxx_';

Anag_xx=40;
Anag_xY=80;
Anag_xo=120;

%%
Data_all=[];
Block_idx=[];
Trial_idx=[];
Expt_idx=[];
Stim_idx=[];

Idx_offset=0;

for expt=1:Expt_num

cd(Expt(expt,:))

%% Event
load('TriG_ch2.mat')

%trim Trig if longer than wave
load('ECoG_ch1');

if length(Trig)>length(wave)
Trig=Trig(1:length(wave));
end

%downsample
Trig=Trig(1:DS:end);

Onset=find(diff(Trig)>10);
Nope=find(Trig(Onset)>10);
Onset(Nope)=[];

Trial_idx_expt=round(Trig(Onset+10)/40); %1: xxxxx; 2: xxxxY; 3:xxxxo

Block_idx_expt=zeros(1,length(Onset));

%%% Could be only 3 blocks
Block_per_expt=ceil(length(Block_idx_expt)/Trial_per_block);

for block=1:Block_per_expt
if block<Block_per_expt
XX=Trial_idx_expt([1:Trial_per_block]+(block-1)*Trial_per_block);
else % the last block could be short
XX=Trial_idx_expt((1+(block-1)*Trial_per_block):end);
end
Stand=XX(1);
Dev=find(XX~=Stand);
Dev=XX(Dev(1));

if Stand==1 & Dev==2
B_type=1;
elseif Stand==1 & Dev==3
B_type=2;
elseif Stand==2 & Dev==1
B_type=3;
elseif Stand==2 & Dev==3
B_type=4;
else
B_type=-1;
end

if block<Block_per_expt
Block_idx_expt([1:Trial_per_block]+(block-1)*Trial_per_block)=B_type;
else
Block_idx_expt((1+(block-1)*Trial_per_block):end)=B_type;
end

end

Trial_idx=[Trial_idx Trial_idx_expt];
Block_idx=[Block_idx Block_idx_expt];
Expt_idx=[Expt_idx ones(1,length(Onset))*expt];

Stim_idx=[Stim_idx Onset+Idx_offset];

Idx_offset=Idx_offset+length(Trig);

%%
fprintf(1,'>> Expt %d/%d: %s (%d trials)\n',expt, Expt_num,Expt(expt,:),length(Onset))

Data=zeros(Channel_num,length(Trig));
for ch=1:Channel_num
FN=sprintf('ECoG_ch%d',ch);
load(FN)

Data(ch,:)=wave(1:DS:end);
end

Data_all=[Data_all Data];

clear Data wave
cd ..
end
Time=[0:size(Data_all,2)-1]/FS*DS;
Stim_time=Time(Stim_idx);

LocalGlobal Details

2024-07-06T13:08:44Z

Mkomatsu: /* Sample code for Monkey Ji and Rc */

LocalGlobal Details

2024-07-05T08:05:23Z

Mkomatsu: Created page with "== Experiment Settings == Not that the followings are default settings, and the actual details are in the each paper. Stimuli: x=800 Hz, Y=1600 Hz, 50 ms duration No raise/..."

Main Page

2024-07-05T06:32:05Z

Mkomatsu: /* Menu */

'''Wiki for Neurotycho.org'''

Welcome to Wiki.Neurotycho!

Project Tycho is named after Tycho Brahe. The project aims to share reliable massive neural and behavioral data for understanding brain mechanism. The dataset was recorded and distributed by Laboratory for Adaptive Intelligence, BSI, RIKEN. It is not only for neuroscientists but for everyone who is interested in learning neural mechanism.

[[File:Ss.png]]

== Menu ==
*Manual
** [[Manual|Install Manual for Python and others]]
** [[Manual_jp|Install manual for Python and others in Japanese]]
 
*Web application
**[[Begins]]
**[[Begins_jp]]
 
*Methods
**[[Multi-dimensional Recording]]
***[[ECoG]]
***[[Motion Capture]]
***[[Non-invasive Head Fixture]]
***[[Head Free Eye Tracking]]
***[[Surgical Procedure]]
 
*Preliminary results
**[[EEG-ECoG recording]]
 
*Task details
**[[Visual Grating Task Details]]
**[[Emotional Movie Task Details]]
**[[Anesthesia and Sleep Task Details]]
**[[Auditory Oddball Details]]
**[[LocalGlobal Details]]
**[[Fixation Details]]
**[[Visually Guided Saccade Details]]
**[[Passive viewing Details]]
**[[Memory-guided saccade Details]]

 
*FAQ for each task
**[[Visual Grating Task]]
**[[Sleep Task]]
**[[Social Competition Task]]
**[[Emotional Movie Task]]
**[[Epidural-ECoG Food-Tracking Task]]
**[[Subdural-ECoG Food-Tracking Task]]
**[[Spatial Map of ECoG array]]
**[[MRI Data]]
 
*Sample scripts for each task
**[[Auditory Oddball Scripts]]
 
*Open Lab @ RIKEN BSI
**[[Open Lab|What is Open Lab?]]

----

To the extent possible under law, neurotycho.org has waived all copyright and related or neighboring rights to downloadable dataset in Project Tycho. This work is published from: Japan.

Auditory Oddball Scripts

2023-10-26T07:31:21Z

Mkomatsu: /* Preprocessings and ERP plots */

We assume that we are in the data folder.

== Preprocessings and ERP plots ==

clear; close all;

DataDir=sprintf(['./']);
nCH=numel(dir([DataDir 'ECoG_ch*']));
n=whos('-file',[DataDir 'ECoG_ch1.mat']);
ECoG=zeros(nCH,n.size(2));

% load data
load([DataDir 'repEvent']);
for ch=1:nCH
openfile=sprintf('ECoG_ch%d',ch);
ECoG(ch,:)=struct2array(load([DataDir openfile]));
end
ECoG=0.25*ECoG;

% CMR (Common Median Reference)
mECoG=ECoG-ones(nCH,1)*median(ECoG);

% bandpass filter with digital filter
Fs=1000;
N=100;
Wn=[1 30]/(Fs/2);
fil=fir1(N,Wn,'bandpass');
meth='FIR digital filter';
fdmdata=filtfilt(fil,1,mECoG')';

% align on the stimulus onsets
rtime=(-1100:1000);
for t=1:length(repEvent)
fdmrpt(:,t,:)=fdmdata(:,repEvent(t,6)+503*repEvent(t,5)+rtime);
end

% plot standard and deviant ERPs
figure
for ch=1:nCH
subplot(6,6,ch-36*(ceil(ch/36)-1));

% trial rejection
data=squeeze(fdmrpt(ch,:,:));
[I K]=find(std(data,[],2)>(mean(std(data,[],2))+3*std(std(data,[],2))));
trial=[1:size(data,1)]; trial(I)=[];
data=data(trial,:);

% cut data
STD=data(:,rtime>=-603 & rtime<=-3);
DEV=data(:,rtime>=-100 & rtime<=500);

% base line correction
STD=STD-mean(mean(STD(:,1:100)));
DEV=DEV-mean(mean(DEV(:,1:100)));

plot(-100:500,mean(STD),'b'); hold on
plot(-100:500,mean(DEV),'g');
plot([0 0],[-15 15],'k'); hold off
set(gca,'XLim',[-100 500],'YLim',[-15 15],'YDir','reverse')
ylabel(['ch' num2str(ch)])
end

[[File:Demo.jpg|600px]]

Marmoset Optogenetics Details

2017-09-30T03:31:38Z

Mkomatsu:

== Data format ==

There are two zip files, each contain data collected from a day of each monkey, including three types of MATLAB files:

1. ECoG_chXX.mat: ECoG signals for each electrode with the sampling rate of 1000Hz.

2. Event.mat:

EventTbl(struct) includes the information of each photo stimulation.

StimTbl_Label: {'Ch' 'Output' 'Trial' 'ITI' 'Start' 'End'}

StimTbl: {400x6 double}

-Ch and Output indicate a number of LED and intensity of stimuli, respectively.

3. ElectrodesXX.mat: Information of the ECoG electrode locations

LINE: The outline of the marmoset brain

MRI: The MRI image of the marmoset brain

X: X positions of the electrodes

Y: Y positions of the electrodes

XL: X positions of the LEDs

YL: Y positions of the LEDs

XI: X positions of the injection sites

YI: Y positions of the injection sites

== Reference ==

Komatsu M, Sugano E, Tomita H and Fujii N (2017) A Chronically Implantable Bidirectional Neural Interface for Non-human Primates. Front. Neurosci. 11:514. doi:10.3389/fnins.2017.00514

Marmoset Optogenetics Details

2017-09-30T03:22:10Z

Mkomatsu: Created page with "== Data format == There are two zip files, each contain data collected from a day of each monkey, including three types of MATLAB files: 1. ECoG_ch*.mat: ECoG signals for e..."

== Data format ==

There are two zip files, each contain data collected from a day of each monkey, including three types of MATLAB files:

1. ECoG_ch*.mat: ECoG signals for each electrode with the sampling rate of 1000Hz.

2. Event.mat:

EventTbl includes the information of each photo stimulation.

StimTbl_Label: {'Ch' 'Output' 'Trial' 'ITI' 'Start' 'End'}

StimTbl: {400x6 double}

*Ch and Output indicate a number of LED and intensity of stimuli, respectively.

3. ElectrodesXX.mat: Information of the ECoG electrode locations

LINE: The outline of the marmoset brain

MRI: The MRI image of the marmoset brain

X: X positions of the electrodes

Y: Y positions of the electrodes

XL: X positions of the LEDs

YL: Y positions of the LEDs

XI: X positions of the injection sites

YI: Y positions of the injection sites

== Reference ==

Komatsu M, Sugano E, Tomita H and Fujii N (2017) A Chronically Implantable Bidirectional Neural Interface for Non-human Primates. Front. Neurosci. 11:514. doi: <a href="https://www.frontiersin.org/articles/10.3389/fnins.2017.00514/full">10.3389/fnins.2017.00514</a>

Auditory Oddball Scripts

2016-03-02T07:28:50Z

Mkomatsu:

We assume that we are in the data folder.

== Preprocessings and ERP plots ==

clear; close all;

DataDir=sprintf(['./']);
nCH=numel(dir([DataDir 'ECoG_ch*']));
n=whos('-file',[DataDir 'ECoG_ch1.mat'],'-regexp','ECoGData_ch1');
ECoG=zeros(nCH,n.size(2));

% load data
load([DataDir 'repEvent']);
for ch=1:nCH
openfile=sprintf('ECoG_ch%d',ch);
ECoG(ch,:)=struct2array(load([DataDir openfile]));
end
ECoG=0.25*ECoG;

% CMR (Common Median Reference)
mECoG=ECoG-ones(nCH,1)*median(ECoG);

% bandpass filter with digital filter
Fs=1000;
N=100;
Wn=[1 30]/(Fs/2);
fil=fir1(N,Wn,'bandpass');
meth='FIR digital filter';
fdmdata=filtfilt(fil,1,mECoG')';

% align on the stimulus onsets
rtime=(-1100:1000);
for t=1:length(repEvent)
fdmrpt(:,t,:)=fdmdata(:,repEvent(t,6)+503*repEvent(t,5)+rtime);
end

% plot standard and deviant ERPs
figure
for ch=1:nCH
subplot(6,6,ch-36*(ceil(ch/36)-1));

% trial rejection
data=squeeze(fdmrpt(ch,:,:));
[I K]=find(std(data,[],2)>(mean(std(data,[],2))+3*std(std(data,[],2))));
trial=[1:size(data,1)]; trial(I)=[];
data=data(trial,:);

% cut data
STD=data(:,rtime>=-603 & rtime<=-3);
DEV=data(:,rtime>=-100 & rtime<=500);

% base line correction
STD=STD-mean(mean(STD(:,1:100)));
DEV=DEV-mean(mean(DEV(:,1:100)));

plot(-100:500,mean(STD),'b'); hold on
plot(-100:500,mean(DEV),'g');
plot([0 0],[-15 15],'k'); hold off
set(gca,'XLim',[-100 500],'YLim',[-15 15],'YDir','reverse')
ylabel(['ch' num2str(ch)])
end

[[File:Demo.jpg|600px]]

Auditory Oddball Scripts

2016-03-02T07:26:50Z

Mkomatsu:

== A sample script for ERP plots ==

We assume that we are in the data folder.

clear; close all;

DataDir=sprintf(['./']);
nCH=numel(dir([DataDir 'ECoG_ch*']));
n=whos('-file',[DataDir 'ECoG_ch1.mat'],'-regexp','ECoGData_ch1');
ECoG=zeros(nCH,n.size(2));

% load data
load([DataDir 'repEvent']);
for ch=1:nCH
openfile=sprintf('ECoG_ch%d',ch);
ECoG(ch,:)=struct2array(load([DataDir openfile]));
end
ECoG=0.25*ECoG;

% CMR (Common Median Reference)
mECoG=ECoG-ones(nCH,1)*median(ECoG);

% bandpass filter with digital filter
Fs=1000;
N=100;
Wn=[1 30]/(Fs/2);
fil=fir1(N,Wn,'bandpass');
meth='FIR digital filter';
fdmdata=filtfilt(fil,1,mECoG')';

% align on the stimulus onsets
rtime=(-1100:1000);
for t=1:length(repEvent)
fdmrpt(:,t,:)=fdmdata(:,repEvent(t,6)+503*repEvent(t,5)+rtime);
end

% plot standard and deviant ERPs
figure
for ch=1:nCH
subplot(6,6,ch-36*(ceil(ch/36)-1));

% trial rejection
data=squeeze(fdmrpt(ch,:,:));
[I K]=find(std(data,[],2)>(mean(std(data,[],2))+3*std(std(data,[],2))));
trial=[1:size(data,1)]; trial(I)=[];
data=data(trial,:);

% cut data
STD=data(:,rtime>=-603 & rtime<=-3);
DEV=data(:,rtime>=-100 & rtime<=500);

% base line correction
STD=STD-mean(mean(STD(:,1:100)));
DEV=DEV-mean(mean(DEV(:,1:100)));

plot(-100:500,mean(STD),'b'); hold on
plot(-100:500,mean(DEV),'g');
plot([0 0],[-15 15],'k'); hold off
set(gca,'XLim',[-100 500],'YLim',[-15 15],'YDir','reverse')
ylabel(['ch' num2str(ch)])
end

[[File:Demo.jpg|600px]]

Auditory Oddball Scripts

2016-03-02T07:25:55Z

Mkomatsu: Created page with "== Sample script for ERP plots == We assume that we are in the data folder. clear; close all; DataDir=sprintf(['./']); nCH=numel(dir([DataDir 'ECoG_ch*'])); n=whos..."

== Sample script for ERP plots ==

We assume that we are in the data folder.

clear; close all;

DataDir=sprintf(['./']);
nCH=numel(dir([DataDir 'ECoG_ch*']));
n=whos('-file',[DataDir 'ECoG_ch1.mat'],'-regexp','ECoGData_ch1');
ECoG=zeros(nCH,n.size(2));

% load data
load([DataDir 'repEvent']);
for ch=1:nCH
openfile=sprintf('ECoG_ch%d',ch);
ECoG(ch,:)=struct2array(load([DataDir openfile]));
end
ECoG=0.25*ECoG;

% CMR (Common Median Reference)
mECoG=ECoG-ones(nCH,1)*median(ECoG);

% bandpass filter with digital filter
Fs=1000;
N=100;
Wn=[1 30]/(Fs/2);
fil=fir1(N,Wn,'bandpass');
meth='FIR digital filter';
fdmdata=filtfilt(fil,1,mECoG')';

% align on the stimulus onsets
rtime=(-1100:1000);
for t=1:length(repEvent)
fdmrpt(:,t,:)=fdmdata(:,repEvent(t,6)+503*repEvent(t,5)+rtime);
end

% plot standard and deviant ERPs
figure
for ch=1:nCH
subplot(6,6,ch-36*(ceil(ch/36)-1));

% trial rejection
data=squeeze(fdmrpt(ch,:,:));
[I K]=find(std(data,[],2)>(mean(std(data,[],2))+3*std(std(data,[],2))));
trial=[1:size(data,1)]; trial(I)=[];
data=data(trial,:);

% cut data
STD=data(:,rtime>=-603 & rtime<=-3);
DEV=data(:,rtime>=-100 & rtime<=500);

% base line correction
STD=STD-mean(mean(STD(:,1:100)));
DEV=DEV-mean(mean(DEV(:,1:100)));

plot(-100:500,mean(STD),'b'); hold on
plot(-100:500,mean(DEV),'g');
plot([0 0],[-15 15],'k'); hold off
set(gca,'XLim',[-100 500],'YLim',[-15 15],'YDir','reverse')
ylabel(['ch' num2str(ch)])
end

[[File:Demo.jpg|600px]]

File:Demo.jpg

2016-03-02T07:06:27Z

Mkomatsu:

Main Page

2016-03-02T06:37:02Z

Mkomatsu:

'''Wiki for Neurotycho.org'''

Welcome to Wiki.Neurotycho!

Project Tycho is named after Tycho Brahe. The project aims to share reliable massive neural and behavioral data for understanding brain mechanism. The dataset was recorded and distributed by Laboratory for Adaptive Intelligence, BSI, RIKEN. It is not only for neuroscientists but for everyone who is interested in learning neural mechanism.

[[File:Ss.png]]

== Menu ==
*Manual
** [[Manual|Install Manual for Python and others]]
** [[Manual_jp|Install manual for Python and others in Japanese]]
 
*Web application
**[[Begins]]
**[[Begins_jp]]
 
*Methods
**[[Multi-dimensional Recording]]
***[[ECoG]]
***[[Motion Capture]]
***[[Non-invasive Head Fixture]]
***[[Head Free Eye Tracking]]
***[[Surgical Procedure]]
 
*Preliminary results
**[[EEG-ECoG recording]]
 
*Task details
**[[Visual Grating Task Details]]
**[[Emotional Movie Task Details]]
**[[Anesthesia and Sleep Task Details]]
**[[Auditory Oddball Details]]
**[[Fixation Details]]
**[[Visually Guided Saccade Details]]
**[[Passive viewing Details]]
**[[Memory-guided saccade Details]]

 
*FAQ for each task
**[[Visual Grating Task]]
**[[Sleep Task]]
**[[Social Competition Task]]
**[[Emotional Movie Task]]
**[[Epidural-ECoG Food-Tracking Task]]
**[[Subdural-ECoG Food-Tracking Task]]
**[[Spatial Map of ECoG array]]
**[[MRI Data]]
 
*Sample scripts for each task
**[[Auditory Oddball Scripts]]
 
*Open Lab @ RIKEN BSI
**[[Open Lab|What is Open Lab?]]

----

To the extent possible under law, neurotycho.org has waived all copyright and related or neighboring rights to downloadable dataset in Project Tycho. This work is published from: Japan.

Auditory Oddball Details

2015-10-02T11:02:34Z

Mkomatsu:

== Data format ==

There are three zip files, each contain data collected from a day, including three types of MATLAB files:

1. ECoG_ch*.mat: ECoG signals for each electrode with the sampling rate of 1000Hz.

2. repEvent.mat:

repEvent includes the information of each tone-train (1-6 columns).

Column 1: train number

Column 2: current frequency index

Column 3: next frequency index

Column 4: SOA, repetition number

Column 5: repetition number

Column 6: time stump of train onset

Idx2Freq is a table of frequency index and actual frequency.

3. ElectrodesFr.mat: Information of the ECoG electrode locations

LINE: The outline of the marmoset brain

X: X positions of the electrodes

Y: Y positions of the electrodes

== Reference ==

Komatsu M, Takaura K, Fujii N (2015). “Mismatch negativity in common marmosets: Whole-cortical recordings with multi-channel electrocorticograms.” Scientific Reports (in press).

Auditory Oddball Details

2015-10-02T10:36:29Z

Mkomatsu: Created page with "== Data format == There are three zip files, each contain data collected from a day, including three types of MATLAB files: 1. ECoG_ch*.mat: ECoG signals for each electrode wi..."

Main Page

2015-10-02T10:13:20Z

Mkomatsu:

'''Wiki for Neurotycho.org'''

Welcome to Wiki.Neurotycho!

Project Tycho is named after Tycho Brahe. The project aims to share reliable massive neural and behavioral data for understanding brain mechanism. The dataset was recorded and distributed by Laboratory for Adaptive Intelligence, BSI, RIKEN. It is not only for neuroscientists but for everyone who is interested in learning neural mechanism.

[[File:Ss.png]]

== Menu ==
*Manual
** [[Manual|Install Manual for Python and others]]
** [[Manual_jp|Install manual for Python and others in Japanese]]
 
*Web application
**[[Begins]]
**[[Begins_jp]]
 
*Methods
**[[Multi-dimensional Recording]]
***[[ECoG]]
***[[Motion Capture]]
***[[Non-invasive Head Fixture]]
***[[Head Free Eye Tracking]]
***[[Surgical Procedure]]
 
*Preliminary results
**[[EEG-ECoG recording]]
 
*Task details
**[[Anesthesia and Sleep Task Details]]
**[[Emotional Movie Task Details]]
**[[Auditory Oddball Details]]
 
*FAQ for each Task
**[[Visual Grating Task]]
**[[Sleep Task]]
**[[Social Competition Task]]
**[[Emotional Movie Task]]
**[[Epidural-ECoG Food-Tracking Task]]
**[[Subdural-ECoG Food-Tracking Task]]
**[[Spatial Map of ECoG array]]
**[[MRI Data]]
 
*Open Lab @ RIKEN BSI
**[[Open Lab|What is Open Lab?]]

----

To the extent possible under law, neurotycho.org has waived all copyright and related or neighboring rights to downloadable dataset in Project Tycho. This work is published from: Japan.

Emotional Movie Task Details

2015-09-16T06:50:09Z

Mkomatsu: /* Data format */

== Subjects ==

Subject 1: K2

Subject 2: Chibi

Subject 3: Kin2

== Data format ==

For each subjects (Subjects 1, 2, and 3), there are three zip files, each contain data collected from a day, including three types of MATLAB files:

1. LFP_ch*.mat: ECoG signals for each electrode with the sampling rate of 1000Hz.

2. Task_ino.mat: SessionData.MovieSequence includes the sequence of the video clips (in indices 1 to 6).

Clip 1: CmRf (“cF2_Tama”)

Clip 2: CwRf (“cF2_WallwSnd”)

Clip 3: ChRf (“cF2_Yasuo”)

Clip 4: CmRn (“cN1_Tama”)

Clip 5: CwRn (“cN1_WallwSnd”)

Clip 6: ChRn (“cN1_Yasuo”)

3. Movie_start_time.mat: Indices of movie onsets

4. Electrode_fmri_outline_with_MW.mat: Information of the ECoG electrode locations

I: The image of electrode layout

X: X positions of the electrodes

Y: Y positions of the electrodes

== Reference ==

Chao ZC, Nagasaka Y, Fujii N (2015). “Cortical network architecture for context processing in primate brain.” eLife.

Emotional Movie Task Details

2015-09-16T06:41:16Z

Mkomatsu: Undo revision 86116 by Mkomatsu (talk)

== Subjects ==

Subject 1: K2

Subject 2: Chibi

Subject 3: Kin2

== Data format ==

For each subjects (Subjects 1, 2, and 3), there are three zip files, each contain data collected from a day, including three types of MATLAB files:

1. LFP_ch*.mat: ECoG signals for each electrode with the sampling rate of 1000Hz.

2. Task_ino.mat: SessionData.MovieSequence includes the sequence of the video clips (in indices 1 to 6).

1: CmRf (“cF2_Tama”)

2: CwRf (“cF2_WallwSnd”)

3: ChRf (“cF2_Yasuo”)

4: CmRn (“cN1_Tama”)

5: CwRn (“cN1_WallwSnd”)

6: ChRn (“cN1_Yasuo”)

3. Movie_start_time.mat: Indices of movie onsets

4. Electrode_fmri_outline_with_MW.mat: Information of the ECoG electrode locations

I: The image of electrode layout

X: X positions of the electrodes

Y: Y positions of the electrodes

== Reference ==

Chao ZC, Nagasaka Y, Fujii N (2015). “Cortical network architecture for context processing in primate brain.” eLife.

Emotional Movie Task Details

2015-09-16T06:40:54Z

Mkomatsu:

== Subjects ==

Subject 1: K2

Subject 2: Chibi

Subject 3: Kin2

== Data format ==

For each subjects (Subjects 1, 2, and 3), there are three zip files, each contain data collected from a day, including three types of MATLAB files:

1. LFP_ch*.mat: ECoG signals for each electrode with the sampling rate of 1000Hz.

2. Task_ino.mat: SessionData.MovieSequence includes the sequence of the video clips (in indices 1 to 6).

1: CmRf (“cF2_Tama”)

2: CwRf (“cF2_WallwSnd”)

3: ChRf (“cF2_Yasuo”)

4: CmRn (“cN1_Tama”)

5: CwRn (“cN1_WallwSnd”)

6: ChRn (“cN1_Yasuo”)

3. Movie_start_time.mat: Indices of movie onsets

4. Electrode_fmri_outline_with_MW.mat: Information of the ECoG electrode locations

I: The image of electrode layout

X: X positions of the electrodes

Y: Y positions of the electrodes

== Reference ==

Chao ZC, Nagasaka Y, Fujii N (2015). “Cortical network architecture for context processing in primate brain.” eLife.