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 new file mode 100755 index 0000000..32acafd --- /dev/null +++ b/code/eeg_timing_test/date-2024-09-06_arrow-alert_v1-2-timing-test_stim-timing.vmrk @@ -0,0 +1,1617 @@ +BrainVision Data Exchange Marker File Version 1.0 + +[Common Infos] +Codepage=UTF-8 +DataFile=date-2024-09-06_arrow-alert_v1-2-timing-test_stim-timing.eeg + +[Marker Infos] +; Each entry: Mk=,,, +; , +; Fields are delimited by commas, some fields might be omitted (empty). +; Commas in type or description text are coded as "\1". +Mk1=New Segment,,1,1,0,20240906151728008041 +Mk2=Stimulus,S 54,9369,1,0 +Mk3=Stimulus,S128,9382,1,0 +Mk4=Stimulus,S 53,11294,1,0 +Mk5=Stimulus,S128,11303,1,0 +Mk6=Stimulus,S 51,12922,1,0 +Mk7=Stimulus,S128,12934,1,0 +Mk8=Stimulus,S 54,14560,1,0 +Mk9=Stimulus,S128,14572,1,0 +Mk10=Stimulus,S 54,16095,1,0 +Mk11=Stimulus,S128,16105,1,0 +Mk12=Stimulus,S 54,17907,1,0 +Mk13=Stimulus,S128,17920,1,0 +Mk14=Stimulus,S 52,19934,1,0 +Mk15=Stimulus,S128,19946,1,0 +Mk16=Stimulus,S 54,21506,1,0 +Mk17=Stimulus,S128,21515,1,0 +Mk18=Stimulus,S 52,23351,1,0 +Mk19=Stimulus,S128,23361,1,0 +Mk20=Stimulus,S 51,25170,1,0 +Mk21=Stimulus,S128,25179,1,0 +Mk22=Stimulus,S 52,27000,1,0 +Mk23=Stimulus,S128,27010,1,0 +Mk24=Stimulus,S 53,28709,1,0 +Mk25=Stimulus,S128,28721,1,0 +Mk26=Stimulus,S 53,30329,1,0 +Mk27=Stimulus,S128,30339,1,0 +Mk28=Stimulus,S 53,32335,1,0 +Mk29=Stimulus,S128,32348,1,0 +Mk30=Stimulus,S 53,34064,1,0 +Mk31=Stimulus,S128,34076,1,0 +Mk32=Stimulus,S 53,35871,1,0 +Mk33=Stimulus,S128,35884,1,0 +Mk34=Stimulus,S 52,37746,1,0 +Mk35=Stimulus,S128,37756,1,0 +Mk36=Stimulus,S 51,39747,1,0 +Mk37=Stimulus,S128,39758,1,0 +Mk38=Stimulus,S 52,41760,1,0 +Mk39=Stimulus,S128,41772,1,0 +Mk40=Stimulus,S 54,43393,1,0 +Mk41=Stimulus,S128,43402,1,0 +Mk42=Stimulus,S 54,45071,1,0 +Mk43=Stimulus,S128,45083,1,0 +Mk44=Stimulus,S 52,46873,1,0 +Mk45=Stimulus,S128,46883,1,0 +Mk46=Stimulus,S 51,48735,1,0 +Mk47=Stimulus,S128,48747,1,0 +Mk48=Stimulus,S 52,50422,1,0 +Mk49=Stimulus,S128,50435,1,0 +Mk50=Stimulus,S 53,52341,1,0 +Mk51=Stimulus,S128,52353,1,0 +Mk52=Stimulus,S 51,54319,1,0 +Mk53=Stimulus,S128,54331,1,0 +Mk54=Stimulus,S 51,56291,1,0 +Mk55=Stimulus,S128,56301,1,0 +Mk56=Stimulus,S 54,57921,1,0 +Mk57=Stimulus,S128,57933,1,0 +Mk58=Stimulus,S 54,59620,1,0 +Mk59=Stimulus,S128,59632,1,0 +Mk60=Stimulus,S 52,61155,1,0 +Mk61=Stimulus,S128,61164,1,0 +Mk62=Stimulus,S 54,62803,1,0 +Mk63=Stimulus,S128,62812,1,0 +Mk64=Stimulus,S 52,64417,1,0 +Mk65=Stimulus,S128,64427,1,0 +Mk66=Stimulus,S 51,66084,1,0 +Mk67=Stimulus,S128,66096,1,0 +Mk68=Stimulus,S 51,67874,1,0 +Mk69=Stimulus,S128,67885,1,0 +Mk70=Stimulus,S 51,69748,1,0 +Mk71=Stimulus,S128,69760,1,0 +Mk72=Stimulus,S 52,71513,1,0 +Mk73=Stimulus,S128,71525,1,0 +Mk74=Stimulus,S 53,73327,1,0 +Mk75=Stimulus,S128,73339,1,0 +Mk76=Stimulus,S 53,75044,1,0 +Mk77=Stimulus,S128,75055,1,0 +Mk78=Stimulus,S 51,76778,1,0 +Mk79=Stimulus,S128,76791,1,0 +Mk80=Stimulus,S 53,78484,1,0 +Mk81=Stimulus,S128,78494,1,0 +Mk82=Stimulus,S 54,84591,1,0 +Mk83=Stimulus,S128,84600,1,0 +Mk84=Stimulus,S 51,86493,1,0 +Mk85=Stimulus,S128,86503,1,0 +Mk86=Stimulus,S 51,88087,1,0 +Mk87=Stimulus,S128,88100,1,0 +Mk88=Stimulus,S 53,89932,1,0 +Mk89=Stimulus,S128,89944,1,0 +Mk90=Stimulus,S 54,91904,1,0 +Mk91=Stimulus,S128,91912,1,0 +Mk92=Stimulus,S 51,93564,1,0 +Mk93=Stimulus,S128,93575,1,0 +Mk94=Stimulus,S 53,95329,1,0 +Mk95=Stimulus,S128,95341,1,0 +Mk96=Stimulus,S 54,97320,1,0 +Mk97=Stimulus,S128,97332,1,0 +Mk98=Stimulus,S 52,98876,1,0 +Mk99=Stimulus,S128,98887,1,0 +Mk100=Stimulus,S 54,100629,1,0 +Mk101=Stimulus,S128,100639,1,0 +Mk102=Stimulus,S 52,102642,1,0 +Mk103=Stimulus,S128,102653,1,0 +Mk104=Stimulus,S 51,104433,1,0 +Mk105=Stimulus,S128,104443,1,0 +Mk106=Stimulus,S 53,106185,1,0 +Mk107=Stimulus,S128,106197,1,0 +Mk108=Stimulus,S 53,107945,1,0 +Mk109=Stimulus,S128,107958,1,0 +Mk110=Stimulus,S 51,109657,1,0 +Mk111=Stimulus,S128,109670,1,0 +Mk112=Stimulus,S 54,111552,1,0 +Mk113=Stimulus,S128,111564,1,0 +Mk114=Stimulus,S 53,113160,1,0 +Mk115=Stimulus,S128,113170,1,0 +Mk116=Stimulus,S 54,114936,1,0 +Mk117=Stimulus,S128,114948,1,0 +Mk118=Stimulus,S 52,116647,1,0 +Mk119=Stimulus,S128,116659,1,0 +Mk120=Stimulus,S 53,118334,1,0 +Mk121=Stimulus,S128,118347,1,0 +Mk122=Stimulus,S 52,120271,1,0 +Mk123=Stimulus,S128,120280,1,0 +Mk124=Stimulus,S 53,121834,1,0 +Mk125=Stimulus,S128,121843,1,0 +Mk126=Stimulus,S 52,123857,1,0 +Mk127=Stimulus,S128,123867,1,0 +Mk128=Stimulus,S 51,125551,1,0 +Mk129=Stimulus,S128,125563,1,0 +Mk130=Stimulus,S 54,127414,1,0 +Mk131=Stimulus,S128,127426,1,0 +Mk132=Stimulus,S 54,129435,1,0 +Mk133=Stimulus,S128,129445,1,0 +Mk134=Stimulus,S 54,131393,1,0 +Mk135=Stimulus,S128,131405,1,0 +Mk136=Stimulus,S 53,133038,1,0 +Mk137=Stimulus,S128,133049,1,0 +Mk138=Stimulus,S 51,134979,1,0 +Mk139=Stimulus,S128,134991,1,0 +Mk140=Stimulus,S 52,137012,1,0 +Mk141=Stimulus,S128,137021,1,0 +Mk142=Stimulus,S 51,138781,1,0 +Mk143=Stimulus,S128,138793,1,0 +Mk144=Stimulus,S 53,140330,1,0 +Mk145=Stimulus,S128,140339,1,0 +Mk146=Stimulus,S 51,141905,1,0 +Mk147=Stimulus,S128,141916,1,0 +Mk148=Stimulus,S 51,143597,1,0 +Mk149=Stimulus,S128,143608,1,0 +Mk150=Stimulus,S 52,145477,1,0 +Mk151=Stimulus,S128,145488,1,0 +Mk152=Stimulus,S 52,147163,1,0 +Mk153=Stimulus,S128,147176,1,0 +Mk154=Stimulus,S 53,149191,1,0 +Mk155=Stimulus,S128,149204,1,0 +Mk156=Stimulus,S 52,151218,1,0 +Mk157=Stimulus,S128,151229,1,0 +Mk158=Stimulus,S 54,153220,1,0 +Mk159=Stimulus,S128,153232,1,0 +Mk160=Stimulus,S 52,154792,1,0 +Mk161=Stimulus,S128,154801,1,0 +Mk162=Stimulus,S 53,161117,1,0 +Mk163=Stimulus,S128,161128,1,0 +Mk164=Stimulus,S 54,162778,1,0 +Mk165=Stimulus,S128,162789,1,0 +Mk166=Stimulus,S 54,164330,1,0 +Mk167=Stimulus,S128,164342,1,0 +Mk168=Stimulus,S 52,166198,1,0 +Mk169=Stimulus,S128,166209,1,0 +Mk170=Stimulus,S 51,168000,1,0 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+"S128,1494030" +"S 43,1495772" +"S128,1495781" +"S 44,1497546" +"S128,1497558" +"S 41,1499378" +"S128,1499390" +"S 43,1501289" +"S128,1501299" +"S 44,1503162" +"S128,1503173" +"S 41,1505164" +"S128,1505175" +"S 41,1507140" +"S128,1507153" +"S 41,1508815" +"S128,1508828" +"S 41,1510837" +"S128,1510845" +"S127,1514406" +"S255,1514692" +"S127,1514703" diff --git a/code/eeg_timing_test/thrive_stim_timing_test.R b/code/eeg_timing_test/thrive_stim_timing_test.R index c7c30b9..76c83d9 100755 --- a/code/eeg_timing_test/thrive_stim_timing_test.R +++ b/code/eeg_timing_test/thrive_stim_timing_test.R @@ -5,15 +5,18 @@ # 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. + +# Last update: Sep. 9th, 2024 + # 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. +# Change the address below to where you have stored vmrk filesz. path <- ("/Users/kihossei/Documents/GitHub/thrive-dataset/code/eeg_timing_test") - -mrkTxt <- readLines(paste(path, "/thrive_sys1_timingTest_stim.vmrk", sep = "")) # load the .vmrk file into the workspace. +# Change the address below to name of the vmrk file name. +mrkTxt <- readLines(paste(path, "/date-2024-09-06_arrow-alert_v1-2-timing-test_stim-timing.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. @@ -42,80 +45,91 @@ 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)) +# add a piece of code to count the number of stimuli. The actual number should be 800 trials. Any deviation from this 800 +# should be flagged. -practice_dat <- setNames(data.frame(matrix(ncol = 1)), c("timeDiff")) # creating an empty data frame that will be filled with time difference values! + +######################################################################################################################## +########## RUN THE CODE BELOW If YOU WANT RUN TIMING TEST USING The SOCIAL and NON-SOCIAL Conditions.################### +######################################################################################################################## + +flanker_dat <- 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$colC[i-1], "S 4")){ + if ( str_detect(newDat$colC[i-1], "S 41") || str_detect(newDat$colC[i-1], "S 42") || str_detect(newDat$colC[i-1], "S 43") || str_detect(newDat$colC[i-1], "S 44")){ secondVal <- str2num(gsub(".*S128,", "", newDat$colC[i])) firstVal <- str2num(gsub(".*,", "", newDat$colC[i-1])) diffVal <- secondVal - firstVal dVal[1,] <- diffVal - practice_dat <- rbind(practice_dat, dVal) - } - } - } else { - next - } -} - - -practice_dat <- na.omit(practice_dat, na.action = "omit") -mean(practice_dat$timeDiff) -sd(practice_dat$timeDiff) + flanker_dat <- rbind(flanker_dat, dVal) - -nonSocial_dat <- setNames(data.frame(matrix(ncol = 1)), c("timeDiff")) # creating an empty data frame that will be filled with time difference values! -dVal <- setNames(data.frame(matrix(ncol = 1)), c("timeDiff")) - -# If you wana perform the flanker timing test for stimulus presentation run the code below! -for (i in 1:nrow(newDat)) { - if (str_detect(newDat$colC[i], "S128")) { - if (i != 1){ - if ( str_detect(newDat$colC[i-1], "S 41") || str_detect(newDat$colC[i-1], "S 42") || str_detect(newDat$colC[i-1], "S 43") || str_detect(newDat$colC[i-1], "S 44")){ + } else if (str_detect(newDat$colC[i-1], "S 51") || str_detect(newDat$colC[i-1], "S 52") || str_detect(newDat$colC[i-1], "S 53") || str_detect(newDat$colC[i-1], "S 54")){ secondVal <- str2num(gsub(".*S128,", "", newDat$colC[i])) firstVal <- str2num(gsub(".*,", "", newDat$colC[i-1])) diffVal <- secondVal - firstVal dVal[1,] <- diffVal - nonSocial_dat <- rbind(nonSocial_dat, dVal) + flanker_dat <- rbind(flanker_dat, dVal) } } } else { next } } -nonSocial_dat <- na.omit(nonSocial_dat, na.action = "omit") -mean(nonSocial_dat$timeDiff) -sd(nonSocial_dat$timeDiff) +flanker_dat <- na.omit(flanker_dat, na.action = "omit") +# THE AVERAGE of Stimulus TIME OFFSET +time_offset_avg <- mean(flanker_dat$timeDiff) +### Printing output +print(paste("The average time offset is ", time_offset_avg)) +#### end of printing output +# THE SD of Stimulus TIME OFFSET +time_offset_sd <- sd(flanker_dat$timeDiff) +print(paste("The Standard Deviation (SD) of time offset is ", time_offset_sd)) + +# The following line tells you the number of flanker trials. +# It should be 800. If it is different (especially, low), it means there is sth wrong and need to +# be examined. +print(paste("Number of flanker task markers are", nrow(flanker_dat))) + +######################################### END of SOCIAL AND NONSOCIAL TIMING TEST ###################################### +######################################################################################################################## +######################################################################################################################## +########## RUN THE CODE BELOW If YOU WANT RUN TIMING TEST USING ONLY PRACTICE TRIALS.################################### +######################################################################################################################## -social_dat <- setNames(data.frame(matrix(ncol = 1)), c("timeDiff")) # creating an empty data frame that will be filled with time difference values! +practice_dat <- 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 51") || str_detect(newDat$colC[i-1], "S 52") || str_detect(newDat$colC[i-1], "S 53") || str_detect(newDat$colC[i-1], "S 54")){ + if ( str_detect(newDat$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$colC[i-1])) diffVal <- secondVal - firstVal dVal[1,] <- diffVal - social_dat <- rbind(social_dat, dVal) + practice_dat <- rbind(practice_dat, dVal) } } } else { next } } -social_dat <- na.omit(social_dat, na.action = "omit") -mean(social_dat$timeDiff) -sd(social_dat$timeDiff) + + +practice_dat <- na.omit(practice_dat, na.action = "omit") +mean(practice_dat$timeDiff) +sd(practice_dat$timeDiff) + +################################################ END of PRACTICE TIMING TEST ########################################### +######################################################################################################################## ######## 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