init commit

scsnl · Jan 19, 2022 · 80f7112 · 80f7112
1 parent a68dbad
commit 80f7112
Show file tree

Hide file tree

Showing 3,137 changed files with 1,035,120 additions and 0 deletions.
diff --git a/LME_Analysis/.DS_Store b/LME_Analysis/.DS_Store
diff --git a/LME_Analysis/.Rapp.history b/LME_Analysis/.Rapp.history
diff --git a/LME_Analysis/ieeg_lmer_boxcox.R b/LME_Analysis/ieeg_lmer_boxcox.R
@@ -0,0 +1,26 @@
+# install packages if missing
+# install.packages("lmerTest") 
+
+# other related packages if needed
+# install.packages("readxl")
+# install.packages("lme4")
+# install.packages("nlme")
+# library(readxl)
+# library(nlme)
+
+# load libraries
+library(lmerTest)
+library(bestNormalize)
+
+# Read Data
+Brain.df <- read.csv("C:/Users/ANUP/Desktop/DMN_Final_Submission/LME_Analysis/CorrIncorr_PTE_DMN_HIPP_Encode_Recall.csv", fileEncoding="UTF-8-BOM")
+x = as.numeric(Brain.df$PTE)
+xx = bestNormalize(x)
+xxt = xx[["x.t"]]
+Brain.df$PTE = xxt
+# Run Model with subjects as random effects
+ieegmodel = lmer(PTE ~ Condition + (1|Subject), data=Brain.df)
+
+# Stats
+anova(ieegmodel)
+
diff --git a/scripts_rest/.DS_Store b/scripts_rest/.DS_Store
diff --git a/scripts_rest/BN_Atlas_246_2mm.nii b/scripts_rest/BN_Atlas_246_2mm.nii
diff --git a/scripts_rest/ChIDBipolar.mat b/scripts_rest/ChIDBipolar.mat
diff --git a/scripts_rest/ChIDBipolarArtifactRemove.mat b/scripts_rest/ChIDBipolarArtifactRemove.mat
diff --git a/scripts_rest/ChannelIDBipolar.m b/scripts_rest/ChannelIDBipolar.m
@@ -0,0 +1,39 @@
+%Anup Das
+%26 September, 2018
+%This program finds the channel indices in the pairs.json files
+
+close all;
+clear all;
+clc;
+
+load('FileListBipolar.mat');
+Njson = size(FileList,1);
+ChID = cell(Njson,1);
+
+for i=1:Njson
+
+    d = dir(FileList(i).folder);
+    B = jsondecode(fileread(strcat(FileList(i).folder,'\',d(4).name)));
+    dynamicPath = {char(fieldnames(B)) 'pairs'};
+    D = getfield(B, dynamicPath{:});
+    Nelec = size(fieldnames(D),1);
+    E = fieldnames(D);
+    ChIDTemp = zeros(Nelec,2);
+
+    for j=1:Nelec
+
+        dynamicPath1 = {char(E{j}) 'channel_1'};
+        dynamicPath2 = {char(E{j}) 'channel_2'};       
+        ChIDTemp(j,1) = getfield(D, dynamicPath1{:});
+        ChIDTemp(j,2) = getfield(D, dynamicPath2{:});
+
+    end
+
+    ChID{i,1} = ChIDTemp;
+
+end
+
+save('ChIDBipolar.mat','ChID');
+
+
+
diff --git a/scripts_rest/ChannelIDBipolarArtifactRemove.m b/scripts_rest/ChannelIDBipolarArtifactRemove.m
@@ -0,0 +1,59 @@
+%Anup Das
+%13 June, 2019
+%This program finds the channel indices in the pairs.json files excluding the artifactual channels
+
+close all;
+clear all;
+clc;
+
+Str = '/oak/stanford/groups/menon/projects/a1das/2018_ECoG_DMN_Project/scripts/Release_20171012_scripts/scripts_rest/Release_Metadata_20171010/electrode_categories/';
+
+load('FileListBipolarSherlock.mat');
+Njson = size(FileList,1);
+ChID = cell(Njson,1);
+
+for i=1:Njson
+
+    d = dir(FileList(i).folder);
+    Folder = FileList(i).folder;
+
+    elec_categ_data = upper(importdata(strcat(Str,Folder(114:119),'_electrode_categories.txt')));
+    elec_categ_data = strrep(elec_categ_data,' ','');
+    elec_categ_data = strrep(elec_categ_data,'-','_');
+
+    B = jsondecode(fileread(strcat(FileList(i).folder,'/',d(4).name)));
+    dynamicPath = {char(fieldnames(B)) 'pairs'};
+    D = getfield(B, dynamicPath{:});
+    Nelec = size(fieldnames(D),1);
+    E = fieldnames(D);
+    ChIDTemp = zeros(Nelec,2);
+
+    for j=1:Nelec
+
+        dynamicPath1 = {char(E{j}) 'channel_1'};
+        dynamicPath2 = {char(E{j}) 'channel_2'};
+
+        dynamicPath3 = {char(E{j}) 'code'};
+        newStr = upper(split(getfield(D, dynamicPath3{:}),'-'));
+
+        if (isempty(find(ismember(elec_categ_data,newStr{1,1})))==1 && isempty(find(ismember(elec_categ_data,newStr{2,1})))==1)
+
+            ChIDTemp(j,1) = getfield(D, dynamicPath1{:});
+            ChIDTemp(j,2) = getfield(D, dynamicPath2{:});
+
+        else
+
+            ChIDTemp(j,1) = 0;
+            ChIDTemp(j,2) = 0;
+
+        end
+
+    end
+
+    ChID{i,1} = ChIDTemp;
+
+end
+
+save('ChIDBipolarArtifactRemove.mat','ChID');
+
+
diff --git a/scripts_rest/DMN_Electrodes_1229.mat b/scripts_rest/DMN_Electrodes_1229.mat
diff --git a/scripts_rest/Distance_Results/.DS_Store b/scripts_rest/Distance_Results/.DS_Store
diff --git a/scripts_rest/Distance_Results/Yeo_atlas/.DS_Store b/scripts_rest/Distance_Results/Yeo_atlas/.DS_Store
diff --git a/...las/Inter_7/DistanceVals_interDMN_1_Yeo2011_Brainnetome_HIPP_Corrected_ArtifactRemove.mat b/...las/Inter_7/DistanceVals_interDMN_1_Yeo2011_Brainnetome_HIPP_Corrected_ArtifactRemove.mat
diff --git a/...las/Inter_7/DistanceVals_interDMN_2_Yeo2011_Brainnetome_HIPP_Corrected_ArtifactRemove.mat b/...las/Inter_7/DistanceVals_interDMN_2_Yeo2011_Brainnetome_HIPP_Corrected_ArtifactRemove.mat
diff --git a/...las/Inter_7/DistanceVals_interDMN_3_Yeo2011_Brainnetome_HIPP_Corrected_ArtifactRemove.mat b/...las/Inter_7/DistanceVals_interDMN_3_Yeo2011_Brainnetome_HIPP_Corrected_ArtifactRemove.mat
diff --git a/...las/Inter_7/DistanceVals_interDMN_4_Yeo2011_Brainnetome_HIPP_Corrected_ArtifactRemove.mat b/...las/Inter_7/DistanceVals_interDMN_4_Yeo2011_Brainnetome_HIPP_Corrected_ArtifactRemove.mat
diff --git a/...las/Inter_7/DistanceVals_interDMN_5_Yeo2011_Brainnetome_HIPP_Corrected_ArtifactRemove.mat b/...las/Inter_7/DistanceVals_interDMN_5_Yeo2011_Brainnetome_HIPP_Corrected_ArtifactRemove.mat
diff --git a/...las/Inter_7/DistanceVals_interDMN_6_Yeo2011_Brainnetome_HIPP_Corrected_ArtifactRemove.mat b/...las/Inter_7/DistanceVals_interDMN_6_Yeo2011_Brainnetome_HIPP_Corrected_ArtifactRemove.mat
diff --git a/...atlas/Intra_7/DistanceVals_intraDMN_Yeo2011_Brainnetome_HIPP_Corrected_ArtifactRemove.mat b/...atlas/Intra_7/DistanceVals_intraDMN_Yeo2011_Brainnetome_HIPP_Corrected_ArtifactRemove.mat
diff --git a/...ance_Results/Yeo_atlas/Intra_7/DistanceVals_intraDMN_Yeo2011_Corrected_ArtifactRemove.mat b/...ance_Results/Yeo_atlas/Intra_7/DistanceVals_intraDMN_Yeo2011_Corrected_ArtifactRemove.mat