Merge branch 'main' into thrive-changes-review

NDCLab · Sep 17, 2024 · b5746f0 · b5746f0
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diff --git a/code/eeg_timing_test/date-2024-09-06_arrow-alert_v1-2-timing-test_stim-timing.vmrk b/code/eeg_timing_test/date-2024-09-06_arrow-alert_v1-2-timing-test_stim-timing.vmrk
diff --git a/code/eeg_timing_test/mini_mfe_resp_timing_test.R b/code/eeg_timing_test/mini_mfe_resp_timing_test.R
@@ -0,0 +1,112 @@
+
+
+#######  www.ndclab.com   ###########
+# By: Kianoosh Hosseini at NDCLab@FIU  
+# This script reads text files that include triggers sent to the recorder laptop.
+# This script is changed for different timing tests.
+# These files have ".vmrk" extension.
+# install.packages("pracma")
+library(stringr)
+library(pracma)
+library(dplyr)
+
+#setwd("~/Users/kihossei/Desktop") #set working directory to where your text file (the one that you have triggers and their times) is located.
+path <- ("/Users/kihossei/Documents/GitHub/thrive-dataset/code/eeg_timing_test")
+
+mrkTxt <- readLines(paste(path, "/thrive_system2_blockLevel_triggerLoss_prevention_timing_test_resp.vmrk", sep = "")) # load the .vmrk file into the workspace.
+myDat <- setNames(data.frame(matrix(nrow = length(mrkTxt), ncol = 1)), c("colA")) # creates an empty data frame with a single column and row # = length(mrkTxt)
+
+# This for loop creates a dataframe from the loaded text file. 
+for (i in 1:length(mrkTxt)) {
+  myDat[i, 1] <- mrkTxt[i]
+
+}
+
+# Keep rows that have the string "Stimulus"
+newDat <- myDat %>%
+  filter(
+    str_detect(colA, "Stimulus")
+  )
+# Let's delete all the strings to "Stimulus,"
+for (i in 1:nrow(newDat)) {
+  newDat$colB[i] <- gsub(".*Stimulus,", "", newDat$colA[i]) 
+}
+
+# Let's delete all the strings after the ms of the sent marker!
+for (i in 1:nrow(newDat)) {
+  newDat$colC[i] <- gsub(",1,0*.", "", newDat$colB[i]) 
+}
+
+newDat <- subset(newDat, select = -c(colA, colB)) # removing the colA and colB columns.
+proc_fileName <- "resp_timing_output.csv"
+write.csv(newDat,paste(path,proc_fileName, sep = "/", collapse = NULL), row.names=FALSE)
+
+newDat <- read.csv(paste(path,proc_fileName, sep = "/", collapse = NULL))
+
+timeVal <- setNames(data.frame(matrix(ncol = 1)), c("timeDiff")) # creating an empty data frame that will be filled with time difference values!
+dVal <- setNames(data.frame(matrix(ncol = 1)), c("timeDiff"))
+
+# If you wana perform the flanker timing test for responses run the code below!
+# Stim trak markers come first and then resp triggers appear! They may be sent at the same time. In this case, they sum up.
+# For ex., 128 (stim trak marker) adds to 11 or 12 (resp triggers) and become either S139 or S140!
+
+for (i in 1:nrow(newDat)) {
+  if (str_detect(newDat$colC[i], "S139") || str_detect(newDat$colC[i], "S140") ||  str_detect(newDat$colC[i], "S128")) {
+    if (str_detect(newDat$colC[i], "S139") || str_detect(newDat$colC[i], "S140")){
+      if (str_detect(newDat$colC[i-1], "S128")){
+        task_sent_mrk <- str2num(gsub(".*,", "", newDat$colC[i]))
+        stimTrak_mrk <- str2num(gsub(".*,", "", newDat$colC[i-1]))
+        diffVal <- task_sent_mrk - stimTrak_mrk # stim trak trigger came first and then the marker from laptop
+        dVal[1,] <- diffVal
+        timeVal <- rbind(timeVal, dVal)
+      } else if (str_detect(newDat$colC[i-1], "S 11") || str_detect(newDat$colC[i-1], "S 12")){
+        stimTrak_mrk <- str2num(gsub(".*,", "", newDat$colC[i]))
+        task_sent_mrk <- str2num(gsub(".*,", "", newDat$colC[i-1]))
+        diffVal <- task_sent_mrk - stimTrak_mrk # The marker from laptop (task sent trigger) came first and then the stim trak trigger!
+        dVal[1,] <- diffVal
+        timeVal <- rbind(timeVal, dVal)
+      } else {
+        task_sent_mrk <- str2num(gsub(".*,", "", newDat$colC[i]))
+        stimTrak_mrk <- task_sent_mrk
+        diffVal <- task_sent_mrk - stimTrak_mrk # both sent at the same time!
+        dVal[1,] <- diffVal
+        timeVal <- rbind(timeVal, dVal)
+      }
+    } else if (str_detect(newDat$colC[i], "S128")) {
+      if (str_detect(newDat$colC[i-1], "S 11") || str_detect(newDat$colC[i-1], "S 12")){
+        stimTrak_mrk <- str2num(gsub(".*,", "", newDat$colC[i]))
+        task_sent_mrk <- str2num(gsub(".*,", "", newDat$colC[i-1]))
+        diffVal <- task_sent_mrk - stimTrak_mrk # The marker from laptop (task sent trigger) came first and then the stim trak trigger!
+        dVal[1,] <- diffVal
+        timeVal <- rbind(timeVal, dVal)
+      }
+    }
+  }
+}
+
+
+timeVal <- na.omit(timeVal, na.action = "omit")
+mean(timeVal$timeDiff)
+sd(timeVal$timeDiff)
+
+######## Below is the timing test results for the Flanker task of the thrive study task on April 5, 2023- System 2 with block level trigger loss ######
+# response triggers
+# mean(test$value)
+# 0.8303571
+# sd(test$value)
+# 1.754728
+
+######## Below is the timing test results for the Flanker task of the thrive study task on April 5, 2023- System 2 with block level trigger loss ######
+# response triggers
+# mean(test$value)
+# 1.700855
+# sd(test$value)
+# 2.085521
+
+
+
+
+
+
+
+
diff --git a/code/eeg_timing_test/mini_mfe_stim_timing_test.R b/code/eeg_timing_test/mini_mfe_stim_timing_test.R
@@ -0,0 +1,105 @@
+
+
+#######  www.ndclab.com   ###########
+# By: Kianoosh Hosseini at NDCLab@FIU  
+# This script reads text files that include triggers sent to the recorder laptop.
+# This script needed to be changed for different timing tests.
+# These files have ".vmrk" extension.
+# install.packages("pracma")
+library(stringr)
+library(pracma)
+library(dplyr)
+
+#setwd("~/Users/kihossei/Desktop") #set working directory to where your text file (the one that you have triggers and their times) is located.
+path <- ("/Users/kihossei/Documents/GitHub/thrive-dataset/code/eeg_timing_test")
+
+mrkTxt <- readLines(paste(path, "/thrive_system1_blockLevel_triggerLoss_prevention_timing_test_stim.vmrk", sep = "")) # load the .vmrk file into the workspace.
+myDat <- setNames(data.frame(matrix(nrow = length(mrkTxt), ncol = 1)), c("colA")) # creates an empty data frame with a single column and row # = length(mrkTxt)
+
+# This 'for' loop creates a dataframe from the loaded text file. 
+for (i in 1:length(mrkTxt)) {
+  myDat[i, 1] <- mrkTxt[i]
+
+}
+
+# Keep rows that have the string "Stimulus"
+newDat <- myDat %>%
+  filter(
+    str_detect(colA, "Stimulus")
+  )
+# Let's delete all the strings to "Stimulus,"
+for (i in 1:nrow(newDat)) {
+  newDat$colB[i] <- gsub(".*Stimulus,", "", newDat$colA[i]) 
+}
+
+# Let's delete all the strings after the ms of the sent marker!
+for (i in 1:nrow(newDat)) {
+  newDat$colC[i] <- gsub(",1,0*.", "", newDat$colB[i]) 
+}
+
+newDat <- subset(newDat, select = -c(colA, colB)) # removing the colA and colB columns.
+proc_fileName <- "stim_timing_output.csv"
+write.csv(newDat,paste(path,proc_fileName, sep = "/", collapse = NULL), row.names=FALSE)
+
+newDat <- read.csv(paste(path,proc_fileName, sep = "/", collapse = NULL))
+
+timeVal <- setNames(data.frame(matrix(ncol = 1)), c("timeDiff")) # creating an empty data frame that will be filled with time difference values!
+dVal <- setNames(data.frame(matrix(ncol = 1)), c("timeDiff"))
+
+# If you wana perform the flanker timing test for stimulus presentation run the code below!
+for (i in 1:nrow(newDat)) {
+  if (str_detect(newDat$colC[i], "S128")) {
+    if (i != 1){
+      if ( str_detect(newDat$colC[i-1], "S  1")  || str_detect(newDat$colC[i-1], "S  2") || str_detect(newDat$colC[i-1], "S  3") || str_detect(newDat$colC[i-1], "S  4")){
+        secondVal <- str2num(gsub(".*S128,", "", newDat$colC[i]))
+        firstVal <- str2num(gsub(".*,", "", newDat$colC[i-1]))
+        diffVal <- secondVal - firstVal
+        dVal[1,] <- diffVal
+        timeVal <- rbind(timeVal, dVal)
+      }
+    }
+  } else {
+    next
+  }
+}
+
+
+timeVal <- na.omit(timeVal, na.action = "omit")
+mean(timeVal$timeDiff)
+sd(timeVal$timeDiff)
+
+######## Below is the timing test results for the Flanker task of the thrive study task on March 31, 2023- Egret PC with the Old EEG equipment######
+# stimulus triggers
+# mean(test$value)
+# 11.04167
+#  sd(test$value)
+#  1.657151
+
+
+######## Below is the timing test results for the Flanker task of the thrive study task on March 31, 2023- Egret PC with the New EEG equipment######
+# stimulus triggers
+# mean(test$value)
+# 11.475
+#  sd(test$value)
+# 1.534209
+
+
+######## Below is the timing test results for the Flanker task of the thrive study task on April 5, 2023- System 2 with block level trigger loss ######
+# stimulus triggers
+# mean(test$value)
+# 12
+#  sd(test$value)
+# 1.659059
+######## Below is the timing test results for the Flanker task of the thrive study task on April 6, 2023- System 1 with block level trigger loss ######
+# stimulus triggers
+# mean(test$value)
+# 11.46667
+#  sd(test$value)
+# 1.781951
+
+
+
+
+
+
+