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removingArt_AwakeIso_pipe.m
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removingArt_AwakeIso_pipe.m
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%% To perform spectral analysis on all data
%% entering in data
genDir = '/synology/adeeti/ecog/iso_awake_VEPs/';
cd(genDir)
allDir = [dir('*GL1'); dir('*GL10'); dir('*GL3')];
ident1 = '2019*';
ident2 = '2020*';
stimIndex = [0, Inf];
START_AT = 1;
driveLocation = '/home/adeeti/Dropbox/';
%%
for d = 1:length(allDir)
cd([genDir, allDir(d).name])
mouseID = allDir(d).name;
mouseECoGFolder = '/synology/adeeti/ecog/iso_awake_VEPs/';
genPicsDir = ['/synology/adeeti/ecog/images/Iso_Awake_VEPs/', mouseID, '/'];
dirIn = [mouseECoGFolder, mouseID, '/'];
disp(['Analyzing mouse ', mouseID])
allData = dir(ident1);
identifier = ident1;
if isempty(allData)
allData = dir(ident2);
identifier = ident2;
end
%% artifact removal and preprocessing
dirPic = [genPicsDir, 'preprocessing/'];
dirOut = dirIn;
MAXSTIM = 1;
ADD_MAN_NOISE_CHANNELS = 0;
ANALYZE_IND = 0;
REMOVE_STIM_ARTIFACT = 1;
PicByTrialType = 0;
PicByAnesType = 1;
PicByAnesAndTrial = 0;
removingArtifactAndInterpolating
%% finding latency
clearvars -except d genDir allDir ident1 ident2 dirIn identifier START_AT stimIndex genPicsDir mouseID driveLocation stimIndex
findLatency
%% Wavelets and making average spec pictures
clearvars -except d genDir allDir ident1 ident2 dirIn identifier START_AT stimIndex genPicsDir mouseID
close all
dirPic1 = [genPicsDir, 'AverageSpec/'];
dirWAVE = [dirIn, 'Wavelets/'];
USE_SNIPPITS = 1;
waveletAnalysis
%% Filter Data at gamma and delta
clearvars -except d genDir allDir ident1 ident2 dirIn identifier START_AT stimIndex dirWAVE genPicsDir mouseID
close all
dirWAVE = [dirIn, 'Wavelets/'];
dirFILT = [dirIn, 'FiltData/'];
lowBound = 4;
highBound = 12;
filterDataandHilbertSavingAll
lowBound = 20;
highBound = 80;
filterDataandHilbertSavingAll
%% ITPC
clearvars -except d genDir allDir ident1 ident2 dirIn identifier START_AT stimIndex dirWAVE dirFILT genPicsDir mouseID
close all
dirPicITPC = [genPicsDir, 'localITPC/'];
useStimIndex = 0;
useNumStim = 1;
lowestLatVariable = 'lowLat';
stimIndex = [0, Inf]; %if want all, stimIndex = matStimIndex; % if want
%all uniStimIndexes/multiStimIndexes, use [uniStimIndex, multiStimIndex] =
%findUniMutliStimIndex(matStimIndex), [stimIndex, ~] = findUniMutliStimIndex(matStimIndex)
numStim = 1;
ITPC_for_all_exp
%% delta coherence movies
clc
clearvars -except d genDir allDir ident1 ident2 dirIn identifier START_AT stimIndex dirWAVE dirFILT genPicsDir mouseID
close all
dirCoh35Movies = [genPicsDir, 'coher5MoviesOutlines/'];
dropboxLocation = '/home/adeeti/Dropbox/ProektLab_code/Adeeti_code/'; %'C:\Users\adeeti\Dropbox\KelzLab\';
fr = 5;
moviesCoherenceSinglesOnly
%% gamma coherence movies
clc
clearvars -except d genDir allDir ident1 ident2 dirIn identifier START_AT stimIndex dirWAVE dirFILT genPicsDir mouseID
close all
dirCoh35Movies = [genPicsDir, 'coher5MoviesOutlines/'];
dropboxLocation = '/home/adeeti/Dropbox/ProektLab_code/Adeeti_code/'; %'C:\Users\adeeti\Dropbox\KelzLab\';
fr = 35;
moviesCoherenceSinglesOnly
end