-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathget_movement.R
73 lines (65 loc) · 9.26 KB
/
get_movement.R
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
library(dplyr)
rm(list=ls())
subject <- c(3003, 3004, 3005, 3006, 3009, 3011, 3013, 3016, 3017, 3018, 3021, 3022, 3023, 3024, 3025, 3026, 3027, 3029, 3030, 3031, 3032, 3034, 3036, 3037, 3039, 3040, 3041, 3042, 3043, 3044, 3045, 3046, 3050, 3051, 3052, 3055, 3056, 3057, 3058, 3059, 3060, 3061, 3062, 3063, 3066, 3067, 3068, 3069, 3070, 3071, 3072, 3073, 3074, 3075, 3076, 3077, 3078, 3079, 3080, 3081, 3082, 3083, 3084, 3085, 3086, 3087, 3089, 3091, 3093, 3094, 3095, 3096, 3097, 3098, 3099, 3100, 3101, 3102, 3103, 3104, 3106, 3107, 3108, 3110, 3111, 3112, 3113, 3114, 3116, 3117, 3118, 3120, 3123, 3125, 3126, 3127, 3128, 3129, 3130, 3132, 3133, 3134, 3136, 3137, 3138, 3139, 3140, 3141, 3142, 3144, 3145, 3148, 3149, 3150, 3151, 3152, 3153, 3155, 3157, 3158, 3160, 3161, 3163, 3164, 3165, 3166, 3167, 3168, 3169, 3171, 3172, 3173, 3175, 3176, 3177, 3181, 3182, 3183, 3184, 3185, 3186, 3187, 3188, 3189, 3192, 3193, 3195, 3197, 3198, 3199, 3200, 3201, 3202, 3203, 3204, 3205, 3206, 3207, 3208, 3209, 4101, 5000, 5001, 5002, 5003, 5004, 5006, 5007, 5008, 5009, 5010, 5011, 5012, 5014, 5015, 5016, 5017, 5018, 5020, 5022, 5024, 5025, 5026, 5027, 5028, 5029, 5030, 5031, 5032, 5034, 5035, 5036, 5037, 5038, 5039, 5040, 5041, 5043, 5044, 5047, 5048, 5050, 5051, 5052, 5054, 5055, 5059, 5061, 5062, 5064, 5065, 5066, 5067, 5068, 5069, 5070, 5072, 5073, 5074, 5075, 5076)
session <- c(60844114, 60642114, 60730114, 61218714, 60946214, 60913814, 61230414, 61319014, 61449114, 61434514, 61032114, 61145414, 61432614, 61722814, 61549914, 61521914, 61535914, 61620714, 61750814, 61721914, 61708114, 61822714, 61763914, 63926214, 62369814, 64069714, 64182514, 64184914, 64125314, 64272114, 64066514, 64243014, 64559714, 64444714, 64442614, 64342014, 64558514, 64459014, 64744514, 64977014, 64645914, 64572314, 64747014, 65047514, 64975114, 64990514, 64932914, 65147714, 65060914, 65076014, 60223115, 65062714, 60641315, 65248914, 60093215, 60527515, 60498815, 60628415, 60483615, 60512015, 60597115, 60595615, 60526115, 60700715, 60540315, 60585615, 60926915, 61045415, 60801315, 60712915, 60743615, 60900715, 60930815, 61027015, 61031615, 61348315, 60988915, 61032515, 61231215, 61290115, 61017415, 61333815, 61230315, 61491515, 61001215, 61346915, 61636915, 61388015, 61435015, 61535415, 61635515, 61620715, 61705915, 61693915, 61895515, 61835415, 61822415, 61907115, 62137915, 63764115, 63551315, 63937815, 63954715, 63853815, 63739515, 63710315, 63940415, 64040415, 63825815, 63969115, 64012615, 64128115, 64153315, 64154215, 64415115, 63868015, 64069515, 64024015, 64356315, 64416115, 64573115, 64743515, 64457015, 64917015, 64632215, 64470115, 64875115, 65050315, 64859015, 64948715, 64731715, 64861115, 65061515, 60511116, 60585716, 60667716, 60527716, 60683216, 60727216, 60815816, 60700916, 60900316, 60898816, 61029516, 61101116, 61304416, 61636716, 61680116, 61507016, 61491816, 61835516, 61632616, 61693416, 61722516, 61708616, 61823616, 61837616, 61924316, 61936216, 61807916, 64874513, 63969514, 64024314, 64157414, 64427014, 64343414, 64670814, 64557614, 64657514, 64544814, 64672514, 64746014, 64628814, 64661014, 64686414, 64974114, 65074914, 60439215, 60643215, 60842315, 61331615, 61144615, 61101215, 60885915, 61102415, 61044415, 60927915, 61216515, 61303315, 61447415, 61518315, 61736215, 61723415, 61807915, 63537915, 61851815, 63750515, 61794415, 63939515, 64053115, 64227215, 64357315, 64443515, 64340315, 64224815, 65059715, 64617215, 64831215, 64659615, 64934915, 64958315, 60094116, 60423316, 60830516, 61190016, 61014516, 61088816, 61204616, 61405416, 61319516, 61780216)
#############################################################################################################################
############################################################ MID ############################################################
#############################################################################################################################
for (i in 1:length(subject)) {
confound1 <- read.table(file = paste0("/Shared/oleary/functional/UICL/BIDS/derivatives/fmriprep/mid/fmriprep/sub-",subject[i],"/ses-",session[i],"/func/sub-",subject[i],"_ses-",session[i],"_task-mid_run-1_bold_confounds.tsv"), header = T, stringsAsFactors = F) %>% select(X, Y, Z, RotX, RotY, RotZ)
confound2 <- read.table(file = paste0("/Shared/oleary/functional/UICL/BIDS/derivatives/fmriprep/mid/fmriprep/sub-",subject[i],"/ses-",session[i],"/func/sub-",subject[i],"_ses-",session[i],"_task-mid_run-2_bold_confounds.tsv"), header = T, stringsAsFactors = F) %>% select(X, Y, Z, RotX, RotY, RotZ)
confound3 <- read.table(file = paste0("/Shared/oleary/functional/UICL/BIDS/derivatives/fmriprep/mid/fmriprep/sub-",subject[i],"/ses-",session[i],"/func/sub-",subject[i],"_ses-",session[i],"_task-mid_run-3_bold_confounds.tsv"), header = T, stringsAsFactors = F) %>% select(X, Y, Z, RotX, RotY, RotZ)
cal <- function(dataframe) {
for (j in c('dX', 'dY', 'dZ', 'dRotX', 'dRotY', 'dRotZ', 'excess')) {dataframe[j] <- NA}
for (k in 2:nrow(dataframe)) {dataframe[k, "dX"] <- abs(dataframe[k, "X"] - dataframe[k-1, "X"])}
for (k in 2:nrow(dataframe)) {dataframe[k, "dY"] <- abs(dataframe[k, "Y"] - dataframe[k-1, "Y"])}
for (k in 2:nrow(dataframe)) {dataframe[k, "dZ"] <- abs(dataframe[k, "Z"] - dataframe[k-1, "Z"])}
for (k in 2:nrow(dataframe)) {dataframe[k, "dRotX"] <- abs(dataframe[k, "RotX"] - dataframe[k-1, "RotX"])}
for (k in 2:nrow(dataframe)) {dataframe[k, "dRotY"] <- abs(dataframe[k, "RotY"] - dataframe[k-1, "RotY"])}
for (k in 2:nrow(dataframe)) {dataframe[k, "dRotZ"] <- abs(dataframe[k, "RotZ"] - dataframe[k-1, "RotZ"])}
for (k in 2:nrow(dataframe)) {ifelse(dataframe[k, "dX"] > 3 | dataframe[k, "dY"] > 3 | dataframe[k, "dZ"] > 3 |
dataframe[k, "dRotX"] > 3 | dataframe[k, "dRotY"] > 3 | dataframe[k, "dRotZ"] > 3,
dataframe[k, "excess"] <- 1, dataframe[k, "excess"] <- 0)}
return(dataframe)}
confound1 <- cal(confound1)
confound2 <- cal(confound2)
confound3 <- cal(confound3)
excess1 <- sum(confound1$excess, na.rm = T)
excess2 <- sum(confound2$excess, na.rm = T)
excess3 <- sum(confound3$excess, na.rm = T)
excess.sum <- sum(excess1, excess2, excess3)
id <- subject[i]
df <- data.frame(id, excess1, excess2, excess3, excess.sum)
write.table(df, file =
paste0("/Shared/oleary/functional/UICL/BIDS/derivatives/fmriprep/mid/fmriprep/excess_mid.txt"),
sep = '\t', row.names = F, col.names =! file.exists("/Shared/oleary/functional/UICL/BIDS/derivatives/fmriprep/mid/fmriprep/excess_mid.txt"), quote = F, append = T)
}
#############################################################################################################################
###################################################### STOP SIGNAL TASK######################################################
#############################################################################################################################
for (i in 1:length(subject)) {
confound1 <- read.table(file = paste0("/Shared/oleary/functional/UICL/BIDS/derivatives/fmriprep/stopsignal/fmriprep/sub-",subject[i],"/ses-",session[i],"/func/sub-",subject[i],"_ses-",session[i],"_task-stopsignal_run-1_bold_confounds.tsv"), header = T, stringsAsFactors = F) %>% select(X, Y, Z, RotX, RotY, RotZ)
confound2 <- read.table(file = paste0("/Shared/oleary/functional/UICL/BIDS/derivatives/fmriprep/stopsignal/fmriprep/sub-",subject[i],"/ses-",session[i],"/func/sub-",subject[i],"_ses-",session[i],"_task-stopsignal_run-2_bold_confounds.tsv"), header = T, stringsAsFactors = F) %>% select(X, Y, Z, RotX, RotY, RotZ)
cal <- function(dataframe) {
for (j in c('dX', 'dY', 'dZ', 'dRotX', 'dRotY', 'dRotZ', 'excess')) {dataframe[j] <- NA}
for (k in 2:nrow(dataframe)) {dataframe[k, "dX"] <- abs(dataframe[k, "X"] - dataframe[k-1, "X"])}
for (k in 2:nrow(dataframe)) {dataframe[k, "dY"] <- abs(dataframe[k, "Y"] - dataframe[k-1, "Y"])}
for (k in 2:nrow(dataframe)) {dataframe[k, "dZ"] <- abs(dataframe[k, "Z"] - dataframe[k-1, "Z"])}
for (k in 2:nrow(dataframe)) {dataframe[k, "dRotX"] <- abs(dataframe[k, "RotX"] - dataframe[k-1, "RotX"])}
for (k in 2:nrow(dataframe)) {dataframe[k, "dRotY"] <- abs(dataframe[k, "RotY"] - dataframe[k-1, "RotY"])}
for (k in 2:nrow(dataframe)) {dataframe[k, "dRotZ"] <- abs(dataframe[k, "RotZ"] - dataframe[k-1, "RotZ"])}
for (k in 2:nrow(dataframe)) {ifelse(dataframe[k, "dX"] > 3 | dataframe[k, "dY"] > 3 | dataframe[k, "dZ"] > 3 |
dataframe[k, "dRotX"] > 3 | dataframe[k, "dRotY"] > 3 | dataframe[k, "dRotZ"] > 3,
dataframe[k, "excess"] <- 1, dataframe[k, "excess"] <- 0)}
return(dataframe)}
confound1 <- cal(confound1)
confound2 <- cal(confound2)
excess1 <- sum(confound1$excess, na.rm = T)
excess2 <- sum(confound2$excess, na.rm = T)
excess.sum <- sum(excess1, excess2)
id <- subject[i]
df <- data.frame(id, excess1, excess2, excess.sum)
write.table(df, file =
paste0("/Shared/oleary/functional/UICL/BIDS/derivatives/fmriprep/stopsignal/fmriprep/excess_sst.txt"),
sep = '\t', row.names = F, col.names =! file.exists("/Shared/oleary/functional/UICL/BIDS/derivatives/fmriprep/stopsignal/fmriprep/excess_sst.txt"), quote = F, append = T)
}