Preface: You have to log into the Pitt network via Pulse Secure first, and then either use the terminal to access Zeus or a remote desktop program. You will need to mount 2 file-server dirs before running this script (/IGNITE_Imaging & /IGNITE_Admin). Use the go tab in the apple toolbar as you normally would to mount both directories on REHA.

Links:
* https://neurostars.org/t/mriqc-users-excluding-bold-data/4560
* https://cran.r-project.org/web/packages/ERSA/vignettes/ERSA.html
* https://nhsrcommunity.com/blog/animating-a-graph-over-time-in-shiny/
* https://indrajeetpatil.github.io/groupedstats/
* https://cran.rstudio.com/web/packages/kableExtra/vignettes/awesome_table_in_html.html
* https://escholarship.org/content/qt00d4q8cp/qt00d4q8cp.pdf?t=odeb86 (potenially useful)

Imported Data

Neuroimaging Calendar Google

library(gcalendr)
#calendar_auth("alysha.gilmore.92@gmail.com")
calendar_ids <- calendar_list()
my_cal_id <- "4iukca7nkso9cqqsnmqcaqvtr4@group.calendar.google.com"
BACH.Neuroimaging.Cal <- calendar_events(my_cal_id, days_in_past = 0, days_in_future = 7)
PET_CAL<-BACH.Neuroimaging.Cal[stringr::str_detect(BACH.Neuroimaging.Cal$summary, pattern="PET")==TRUE, ]
MRI_CAL<-BACH.Neuroimaging.Cal[stringr::str_detect(BACH.Neuroimaging.Cal$summary, pattern="MRI")==TRUE, ]
EBACH_MRI_CAL<-MRI_CAL[stringr::str_detect(MRI_CAL$summary, pattern="#E1")==TRUE, ]
COGx_MRI_CAL<-MRI_CAL[stringr::str_detect(MRI_CAL$summary, pattern="CogEx")==TRUE, ]
#`r    Blue`

Upcoming MRI Sessions:
Upcoming PET Sessions:
#_

IGNITE MRIQC Database (IGNITE_QC_Database.xlsx)
IGNITE Data Entry
ANOVA Databases (IGNITE_ANOVA_Database_MASTER.xlsx)

-

MRIQC Pipeline (/IGNITE_Admin/QC_04/.)
## [1] "SubID"         "Session"       "snr"           "session_entry"
RedCap Database (All, no dates)
MASTER Spreadsheets (/IGNITE_Admin/WeeklyReport/.)

_
# Merge

Visualization Factors / ExPanDaR App

RedCap Data Entry from last report

No Pending Data Entry

Currently pending data entry

TBH

Pending MRIQC Initiation..

Baseline Scans: No New Baseline MRIs
Follow-Up Scans: 30739MR2

Pending MRIQC04_Step04 Initiation..

Pending Addition to Master Spreadsheets..

PRE MPRAGE: Baseline MASTER Spreadsheets up to date
PRE DTI: Baseline MASTER DTI Spreadsheets up to date

 

Pending Addition to ANOVA Daubtabase..

30350MR2, 10525MR2, 10527MR2, 20370MR2, 30351MR2, 30446MR2, 20208MR2, 10881MR2, 10907MR2, 30739MR2

_

Current Working Report-

Nov/10/2020
Number of participants in this report: 10
First scan date in current report: Oct/29/2020
Last scan date in current report: Nov/09/2020
Days since last subject in report: 11

New Scans / Running Totals:

Kansas University 2 / 301

New Baseline: 0
New Follow-Up: 2

University of Pittsburgh 4 / 304

New Baseline: 0
New Follow-Up:4

Northeastern University 4 / 209

New Baseline:0
New Follow-Up:4

KEY:
Blue meanFD > 0.5mm.
Yellow value is greater/less than 2 standard deviations from ANOVA spreadsheet site mean.
Red value is greater/less than 3 standard deviations from ANOVA spreadsheet site mean.
Formatter only values on poor quality (i.e. high FD / low snr).

_

University of Pittsburgh

New Scans / Total Scans: 4 / 304 New Baseline: 0
-Withdrew/Excluded after baseline MRI:
- 8
- 2
New Follow-Up:4
- Completed MR2: 189
- Lost to Follow-Up: 11
- Upcoming Follow-Up Assesments: 0

MPRAGE

Pending QC: 10525, 10527, 10881, 10907

SubID Session Date cnr fwhm_avg snr_total snrd_total

NBACK

SubID Site task_id Date dvars_nstd fwhm_avg fd_mean gcor snr tsnr
10525 UPitt nback 2020-11-02 50.97860 2.442801 0.2765201 0.01286160 2.282109 36.95706
10527 UPitt nback 2020-11-02 71.67916 2.307492 0.3963867 0.00964894 1.731730 33.14484
10881 UPitt nback 2020-11-06 46.68880 2.334273 0.2067844 0.01634350 1.905129 30.83784
10907 UPitt nback 2020-11-09 83.37973 2.344169 0.3828051 0.00709511 1.958038 25.89179

Resting State

SubID Site task_id Date dvars_nstd fwhm_avg fd_mean gcor snr tsnr
10525 UPitt rest 2020-11-02 43.42475 2.633828 0.1957918 0.00975158 2.417174 35.02382
10527 UPitt rest 2020-11-02 47.61794 2.462831 0.2927003 0.00562625 1.913282 37.80247
10881 UPitt rest 2020-11-06 47.02678 2.510437 0.3145864 0.00785112 2.032107 34.23534
10907 UPitt rest 2020-11-09 68.75346 2.570164 0.5980894 0.00722871 2.135160 25.02091

RISE Encoding

SubID task_id Date dvars_nstd fwhm_avg fd_mean gcor snr tsnr
10525 riseenc 2020-11-02 44.37800 2.647875 0.2167234 0.00520580 2.395900 33.13267
10527 riseenc 2020-11-02 50.79932 2.475575 0.3302052 0.00539323 1.920546 33.15372
10881 riseenc 2020-11-06 49.58960 2.535963 0.3505161 0.00822708 2.056646 28.67291
10907 riseenc 2020-11-09 74.45629 2.616661 0.6540006 0.00838588 2.126902 20.79921

RISE Recognition

SubID task_id Date dvars_nstd fwhm_avg fd_mean gcor snr tsnr
10525 riserec 2020-11-02 42.85278 2.663693 0.2039061 0.00441241 2.372482 32.07430
10527 riserec 2020-11-02 50.08968 2.463805 0.3262183 0.00564003 1.930655 34.91496
10881 riserec 2020-11-06 46.40946 2.526287 0.3310918 0.00886594 2.067920 31.37144
10907 riserec 2020-11-09 77.62390 2.600525 0.6728749 0.01150210 2.136856 21.88182

DTI

10525, 10527, 10881, 10907

Site SubID Session Date ScanNotes QC3 QC4 meanFA meanRELrms_b1500 tsnr_b1500 outmean_b1500 meanRELrms_b3000 tsnr_b3000 outmean_b3000

T2 Flair

Site SubID Session Date ScanNotes QC3 QC4 snr

pCASL

r pitt.MISSING.Monthly.pCASL

Site SubID Session Date ScanNotes QC3 QC4 tsnr outmean

_

Kansas University 2 / 301

New Baseline: 0 -No Baseline MRI: 2
-Withdrew/Excluded after baseline MRI: 3
New Follow-Up: 2 - Completed MR2: 182 - Upcoming Follow-Up Assesments: 0

MPRAGE

Pending QC: 20370, 20208
Withheld: 20032MR1, 20174MR1, 20014MR2, 20025MR2, 20022MR2, 20027MR2, 20033MR2, 20021MR2, 20028MR2, 20034MR2, 20035MR2, 20057MR2, 20041MR2, 20062MR2, 20018MR2, 20070MR2, 20058MR2, 20084MR2, 20075MR2, 20045MR2, 20050MR2, 20065MR2, 20080MR2, 20087MR2, 20093MR2, 20082MR2, 20089MR2, 20077MR2, 20096MR2, 20099MR2, 20120MR2, 20091MR2, 20088MR2, 20133MR2, 20104MR2, 20108MR2, 20121MR2, 20110MR2, 20118MR2, 20161MR2, 20146MR2, 20101MR2, 20142MR2, 20145MR2, 20085MR2, 20122MR2, 20116MR2, 20140MR2, 20132MR2, 20188MR2, 20165MR2, 20171MR2, 20123MR2, 20428MR1, 20175MR2, 20181MR2, 20138MR2, 20162MR2, 20217MR2, 20200MR2, 20158MR2, 20209MR2, 20153MR2, 20195MR2, 20203MR2, 20185MR2, 20135MR2, 20212MR2, 20210MR2, 20221MR2, 20225MR2, 20218MR2, 20224MR2, 20214MR2, 20230MR2, 20253MR2, 20284MR2, 20277MR2, 20291MR2, 20281MR2, 20304MR2, 20271MR2, 20285MR2, 20275MR2, 20246MR2, 20311MR2, 20247MR2, 20170MR2, 20308MR2, 20313MR2, 20307MR2, 20317MR2, 20241MR2, 20330MR2, 20323MR2, 20274MR2, 20258MR2, 20037MR2, 20327MR2, 20331MR2, 20343MR2, 20348MR2, 20340MR2, 20345MR2, 20347MR2, 20300MR2, 20358MR2, 20310MR2, 20349MR2, 20243MR2, 20363MR2, 20368MR2, 20353MR2, 20367MR2, 20369MR2, 20322MR2, 20374MR2, 20377MR2, 20378MR2, 20379MR2, 20370MR2, 20208MR2

SubID Session Date cnr fwhm_avg snr_total snrd_total

NBACK

SubID Session task_id Date dvars_nstd fwhm_avg fd_mean gcor snr tsnr
20370 MR2 nback 2020-11-02 62.23698 2.341533 0.3935115 0.0253112 2.002558 27.17298
20208 MR2 nback 2020-11-05 40.86874 2.310137 0.1673367 0.0247099 2.065768 51.28577

Resting State

SubID task_id Date dvars_nstd fwhm_avg fd_mean gcor snr tsnr
20370 rest 2020-11-02 37.90827 2.584271 0.2971192 0.00449981 2.213509 28.82017
20208 rest 2020-11-05 33.74118 2.514100 0.1911363 0.00389608 2.322858 38.17902

RISE Encoding

SubID task_id Date dvars_nstd fwhm_avg fd_mean gcor snr tsnr
20370 riseenc 2020-11-02 40.65204 2.588220 0.3396614 0.00576842 2.230378 27.02083
20208 riseenc 2020-11-05 36.02584 2.488327 0.1968181 0.00738280 2.310691 40.78728

RISE Recognition

SubID task_id Date dvars_nstd fwhm_avg fd_mean gcor snr tsnr
20370 riserec 2020-11-02 70.47554 2.683673 0.6724141 0.0351928 2.230728 15.68174
20208 riserec 2020-11-05 38.45514 2.557809 0.2546659 0.0110227 2.290773 28.01402

DTI

Pending QC/Missing Sequence: 20370, 20208

Site SubID Session Date ScanNotes QC3 QC4 meanFA meanRELrms_b1500 tsnr_b1500 outmean_b1500 meanRELrms_b3000 tsnr_b3000 outmean_b3000

T2 Flair

SubID Session Date snr

pCASL

SubID Session Date tsnr outmean

20370, 20208

 

 

 

 

_

Northeastern University 4 / 209

New Baseline:0
New Follow-Up:4 Completed MR2: 70 Upcoming Follow-Up Assesments: 74

### MPRAGE
Pending QC: 30350, 30351, 30446, 30739

SubID Session Date cnr fwhm_avg snr_total snrd_total
30350 MR2 2020-10-29 NA NA NA NA
30351 MR2 2020-11-03 NA NA NA NA
30446 MR2 2020-11-04 NA NA NA NA
30739 MR2 2020-11-09 NA NA NA NA

NBACK

SubID Session task_id Date dvars_nstd fwhm_avg fd_mean gcor snr tsnr
30350 MR2 nback 2020-10-29 34.84884 2.416516 0.1310497 0.00905379 1.993055 35.0591

Resting State

SubID task_id Date dvars_nstd fwhm_avg fd_mean gcor snr tsnr
30350 rest 2020-10-29 34.5066 2.549336 0.1943078 0.012124 2.145448 36.85815

RISE Encoding

SubID task_id Date dvars_nstd fwhm_avg fd_mean gcor snr tsnr
30350 riseenc 2020-10-29 39.22825 2.576721 0.2670452 0.00474984 2.140223 35.05923

RISE Recognition

SubID task_id Date dvars_nstd fwhm_avg fd_mean gcor snr tsnr
30350 riserec 2020-10-29 35.37551 2.590483 0.2068415 0.00742661 2.180388 32.35938

DTI

30350, 30351, 30446, 30739

Site SubID Session Date ScanNotes QC3 QC4 meanFA meanRELrms_b1500 tsnr_b1500 outmean_b1500 meanRELrms_b3000 tsnr_b3000 outmean_b3000

T2 Flair

Site SubID Session Date ScanNotes QC3 QC4 subject_id snr

pCASL

Site SubID Session Date ScanNotes QC3 QC4 subject_id tsnr outmean

# _

Visualization

T1 MPRAGE

DTI

T2 Flair & pCASL

BOLD N-Back

BOLD Resting State

BOLD Rise Encoding

BOLD Rise Recognition

_

_
# Mean Comparisons

Structural

MPRAGE

library(DT)


ADMIN.MASTER.STRUCT$PPE_1<-as.factor(ADMIN.MASTER.STRUCT$PPE_1)
MPRAGE_cnr.compar<-ggpubr::compare_means(snr_total ~ Scanner , ADMIN.MASTER.STRUCT)
DT::datatable(MPRAGE_cnr.compar, rownames = FALSE)

MPRAGE_fwhm_avg.compar<-ggpubr::compare_means(fwhm_avg ~ Scanner , ADMIN.MASTER.STRUCT)
DT::datatable(MPRAGE_fwhm_avg.compar, rownames = FALSE)

SNR.compar<-ggpubr::compare_means(snr_total ~ Scanner , ADMIN.MASTER.STRUCT)
DT::datatable(SNR.compar, rownames = FALSE)

MPRAGE_snrd_total.compar<-ggpubr::compare_means(snrd_total ~ Scanner, ADMIN.MASTER.STRUCT)
DT::datatable(MPRAGE_snrd_total.compar, rownames = FALSE)

DTI

meanFA.compar<-ggpubr::compare_means(meanFA ~ Scanner , ADMIN.MASTER.STRUCT)
DT::datatable(meanFA.compar, rownames = FALSE)

meanRELrms_b1500.compar<-ggpubr::compare_means(meanRELrms_b1500 ~ Scanner , ADMIN.MASTER.STRUCT)
DT::datatable(meanRELrms_b1500.compar, rownames = FALSE)

tsnr_b1500compar<-ggpubr::compare_means(tsnr_b1500 ~ Scanner , ADMIN.MASTER.STRUCT)
DT::datatable(tsnr_b1500compar, rownames = FALSE)

outmean_b1500.compar<-ggpubr::compare_means(outmean_b1500 ~ Scanner , ADMIN.MASTER.STRUCT)
DT::datatable(outmean_b1500.compar, rownames = FALSE)

ADMIN.MASTER.STRUCT$meanRELrms_b3000
meanRELrms_b3000.compar<-ggpubr::compare_means(meanRELrms_b3000 ~ Scanner , ADMIN.MASTER.STRUCT)
DT::datatable(meanRELrms_b3000.compar, rownames = FALSE)

tsnr_b3000compar<-ggpubr::compare_means(tsnr_b3000 ~ Scanner , ADMIN.MASTER.STRUCT)
DT::datatable(tsnr_b3000compar, rownames = FALSE)

outmean_b3000.compar<-ggpubr::compare_means(outmean_b3000 ~ Scanner , ADMIN.MASTER.STRUCT)
DT::datatable(outmean_b3000.compar, rownames = FALSE)


ab<-((lm(meanFA ~ tsnr_b1500*Scanner, ADMIN.MASTER.STRUCT)))
visreg::visreg(ab, "Scanner", by="tsnr_b1500", overlay=TRUE )

dc<-(lm(meanFA ~ tsnr_b3000+Scanner, ADMIN.MASTER.STRUCT))
visreg::visreg(dc, "Scanner", by="tsnr_b3000", overlay=TRUE )

T2 Flair

FLAIR_snr.compar<-ggpubr::compare_means(snr ~ Scanner , ADMIN.MASTER.STRUCT)
DT::datatable(FLAIR_snr.compar, rownames = FALSE)

pCASL

pCASL_outmean.compar<-ggpubr::compare_means(outmean ~ Scanner , ADMIN.MASTER.STRUCT)
DT::datatable(pCASL_outmean.compar, rownames = FALSE)

pCASL_tsnr.compar<-ggpubr::compare_means(tsnr ~ Scanner , ADMIN.MASTER.STRUCT)
DT::datatable(pCASL_tsnr.compar, rownames = FALSE)

 

 

Functional

N-Back

MASTER<-ADMIN.MASTER.BOLD %>% filter(task_id=="nback") 

dvars_nstd.compar<-ggpubr::compare_means(dvars_nstd ~ Scanner , MASTER)
DT::datatable(dvars_nstd.compar, rownames = FALSE)
fd_mean.compar<-ggpubr::compare_means(fd_mean ~ Scanner , MASTER)
DT::datatable(fd_mean.compar, rownames = FALSE)
fwhm_avg.compar<-ggpubr::compare_means(fwhm_avg ~ Scanner , MASTER)
DT::datatable(fwhm_avg.compar, rownames = FALSE)
gcor.compar<-ggpubr::compare_means(gcor ~ Scanner , MASTER)
DT::datatable(gcor.compar, rownames = FALSE)
snr.compar<-ggpubr::compare_means(snr ~ Scanner , MASTER)
DT::datatable(snr.compar, rownames = FALSE)
tsnr.compar<-ggpubr::compare_means(tsnr ~ Scanner   , MASTER)
DT::datatable(tsnr.compar, rownames = FALSE)

Rest

MASTER<-ADMIN.MASTER.BOLD %>% filter(task_id=="rest") 
dvars_nstd.compar<-ggpubr::compare_means(dvars_nstd ~ Scanner , MASTER)
DT::datatable(dvars_nstd.compar, rownames = FALSE)
fd_mean.compar<-ggpubr::compare_means(fd_mean ~ Scanner , MASTER)
DT::datatable(fd_mean.compar, rownames = FALSE)
fwhm_avg.compar<-ggpubr::compare_means(fwhm_avg ~ Scanner , MASTER)
DT::datatable(fwhm_avg.compar, rownames = FALSE)
gcor.compar<-ggpubr::compare_means(gcor ~ Scanner , MASTER)
DT::datatable(gcor.compar, rownames = FALSE)
snr.compar<-ggpubr::compare_means(snr ~ Scanner , MASTER)
DT::datatable(snr.compar, rownames = FALSE)
tsnr.compar<-ggpubr::compare_means(tsnr ~ Scanner , MASTER)
DT::datatable(tsnr.compar, rownames = FALSE)

RISE1

MASTER<-ADMIN.MASTER.BOLD %>% filter(task_id=="riseenc") 
dvars_nstd.compar<-ggpubr::compare_means(dvars_nstd ~ Scanner , MASTER)
DT::datatable(dvars_nstd.compar, rownames = FALSE)
fd_mean.compar<-ggpubr::compare_means(fd_mean ~ Scanner , MASTER)
DT::datatable(fd_mean.compar, rownames = FALSE)
fwhm_avg.compar<-ggpubr::compare_means(fwhm_avg ~ Scanner , MASTER)
DT::datatable(fwhm_avg.compar, rownames = FALSE)
gcor.compar<-ggpubr::compare_means(gcor ~ Scanner , MASTER)
DT::datatable(gcor.compar, rownames = FALSE)
snr.compar<-ggpubr::compare_means(snr ~ Scanner , MASTER)
DT::datatable(snr.compar, rownames = FALSE)
tsnr.compar<-ggpubr::compare_means(tsnr ~ Scanner , MASTER)
DT::datatable(tsnr.compar, rownames = FALSE)

### RISE2

MASTER<-ADMIN.MASTER.BOLD %>% filter(task_id=="riserec") 
dvars_nstd.compar<-ggpubr::compare_means(dvars_nstd ~ Scanner , MASTER)
DT::datatable(dvars_nstd.compar, rownames = FALSE)
fd_mean.compar<-ggpubr::compare_means(fd_mean ~ Scanner , MASTER)
DT::datatable(fd_mean.compar, rownames = FALSE)
fwhm_avg.compar<-ggpubr::compare_means(fwhm_avg ~ Scanner , MASTER)
DT::datatable(fwhm_avg.compar, rownames = FALSE)
gcor.compar<-ggpubr::compare_means(gcor ~ Scanner , MASTER)
DT::datatable(gcor.compar, rownames = FALSE)
snr.compar<-ggpubr::compare_means(snr ~ Scanner , MASTER)
DT::datatable(snr.compar, rownames = FALSE)
tsnr.compar<-ggpubr::compare_means(tsnr ~ Scanner , MASTER)
DT::datatable(tsnr.compar, rownames = FALSE)

LMER

 

 

 

 

_

Current Report Analyses-

UPitt

Indivdual differences vs. Scanner-

** Issue with DTI preceed recent issues.

pCASL <- ADMIN.MASTER.STRUCT %>% select(SubID,Site,Session, Scanner, WeeklyReport, tsnr, outmean)
pCASL$Scanner<-as.factor(pCASL$Scanner)

mod<-(lm(tsnr~ WeeklyReport-1, pCASL))
mod.mean<-emmeans(mod, "WeeklyReport")
pairs(mod.mean)

mod<-(lm(tsnr~ Scanner-1, pCASL))
mod.mean<-emmeans(mod, "Scanner")
pairs(mod.mean)

mod<-(lm(tsnr~ WeeklyReport*Scanner, pCASL))
mod.mean<-emmeans(mod, "Scanner", by="WeeklyReport")
pairs(mod.mean)

mod<-(lm(tsnr~ WeeklyReport*Scanner, pCASL))
mod.mean<-emmeans(mod, "WeeklyReport", by="Scanner")
pairs(mod.mean)

PITT<-FLAIR %>%  filter(Site=="UPitt") %>%  select(SubID,Site ,Scanner, WeeklyReport,snr )
PITT$Scanner<-as.factor(PITT$Scanner)
PITT$WeeklyReport<-as.factor(PITT$WeeklyReport)

mod<-(lm(snr~ WeeklyReport, PITT))
mod.mean<-emmeans(mod, "WeeklyReport")
pairs(mod.mean)

mod<-(lm(snr~ Scanner, PITT))
mod.mean<-emmeans(mod, "Scanner")
pairs(mod.mean)

mod<-(lm(snr~ Scanner*WeeklyReport, PITT))
mod.mean<-emmeans(mod, "WeeklyReport", by="Scanner")
pairs(mod.mean)

mod<-(lm(snr~ Scanner*WeeklyReport, PITT))
mod.mean<-emmeans(mod, "Scanner", by="WeeklyReport")
pairs(mod.mean)

 

 

SCRAP !

Pending/Missing Data

T1 MPRAGE

Pending or Excluded: 10036MR1, 10057MR2, 20032MR1, 10239MR1, 10299MR1, 10185MR1, 10383MR1, 10004MR2, 10013MR2, 20174MR1, 10012MR2, 10023MR2, 10019MR2, 10017MR2, 10026MR2, 10030MR2, 10044MR2, 10043MR2, 10055MR2, 30001MR2, 10041MR2, 30012MR2, 10053MR2, 30014MR2, 10083MR2, 10064MR2, 30017MR2, 10059MR2, 10062MR2, 30035MR2, 30037MR2, 10079MR2, 10066MR2, 10082MR2, 30059MR2, 10541MR1, 10088MR2, 10622MR1, 20014MR2, 20025MR2, 20022MR2, 10085MR2, 20027MR2, 10113MR2, 20033MR2, 10107MR2, 30080MR2, 10623MR1, 20021MR2, 20028MR2, 30071MR2, 20034MR2, 30031MR2, 20035MR2, 10136MR2, 30093MR2, 30042MR2, 10110MR2, 30072MR2, 30040MR2, 10141MR2, 10168MR2, 20057MR2, 20041MR2, 10149MR2, 30043MR2, 10123MR2, 20062MR2, 10151MR2, 30117MR2, 20018MR2, 10789MR1, 10135MR2, 10098MR2, 20070MR2, 10203MR2, 10190MR2, 30123MR2, 30136MR2, 20058MR2, 20084MR2, 10182MR2, 20075MR2, 20045MR2, 10214MR2, 10257MR2, 20050MR2, 20065MR2, 30127MR2, 10253MR2, 30148MR2, 30152MR2, 10227MR2, 10150MR2, 20080MR2, 10218MR2, 10238MR2, 10226MR2, 20087MR2, 30161MR2, 10266MR2, 20093MR2, 20082MR2, 20089MR2, 30163MR2, 10273MR2, 20077MR2, 20096MR2, 20099MR2, 20120MR2, 10302MR2, 20091MR2, 20088MR2, 10125MR2, 10319MR2, 30173MR2, 20133MR2, 10339MR2, 20104MR2, 30177MR2, 30146MR2, 10297MR2, 10322MR2, 20108MR2, 20121MR2, 10272MR2, 20110MR2, 10329MR2, 10356MR2, 20118MR2, 20161MR2, 20146MR2, 10325MR2, 20101MR2, 20142MR2, 20145MR2, 10375MR2, 20085MR2, 20122MR2, 20116MR2, 20140MR2, 30235MR2, 10334MR2, 20132MR2, 30222MR2, 10372MR2, 30223MR2, 10392MR2, 20188MR2, 30250MR2, 20165MR2, 20171MR2, 20123MR2, 10384MR2, 20428MR1, 10341MR2, 20175MR2, 20181MR2, 20138MR2, 10401MR2, 20162MR2, 20217MR2, 20200MR2, 20158MR2, 10399MR2, 10404MR2, 10402MR2, 20209MR2, 10436MR2, 20153MR2, 20195MR2, 10396MR2, 20203MR2, 10418MR2, 30249MR2, 30283MR2, 20185MR2, 10417MR2, 20135MR2, 30321MR2, 10470MR2, 30236MR2, 20212MR2, 20210MR2, 20221MR2, 20225MR2, 20218MR2, 30338MR2, 20224MR2, 30341MR2, 20214MR2, 30349MR2, 10475MR2, 10477MR2, 20230MR2, 10476MR2, 20253MR2, 20284MR2, 20277MR2, 20291MR2, 20281MR2, 20304MR2, 20271MR2, 20285MR2, 20275MR2, 20246MR2, 20311MR2, 20247MR2, 20170MR2, 20308MR2, 20313MR2, 20307MR2, 20317MR2, 20241MR2, 20330MR2, 20323MR2, 20274MR2, 20258MR2, 20037MR2, 20327MR2, 20331MR2, 10757MR2, 20343MR2, 10582MR2, 20348MR2, 10697MR2, 20340MR2, 10568MR2, 10792MR2, 30556MR2, 10776MR2, 10796MR2, 20345MR2, 30428MR2, 30547MR2, 30585MR2, 30542MR2, 10807MR2, 20347MR2, 30438MR2, 10593MR2, 20300MR2, 30589MR2, 10561MR2, 10833MR2, 30554MR2, 20358MR2, 30550MR2, 10711MR2, 20310MR2, 30649MR2, 30666MR2, 10741MR2, 30526MR2, 10831MR2, 30624MR2, 30574MR2, 10689MR2, 20349MR2, 30709MR2, 10466MR2, 20243MR2, 20363MR2, 10721MR2, 30764MR2, 10554MR2, 10815MR2, 30404MR2, 30681MR2, 30583MR2, 10861MR2, 20368MR2, 30449MR2, 10599MR2, 10528MR2, 20353MR2, 30725MR2, 10449MR2, 30701MR2, 20367MR2, 30711MR2, 10848MR2, 10565MR2, 20369MR2, 30553MR2, 10727MR2, 20322MR2, 10499MR2, 10410MR2, 20374MR2, 30369MR2, 10851MR2, 20377MR2, 30795MR2, 10909MR2, 10896MR2, 20378MR2, 30284MR2, 30397MR2, 10515MR2, 20379MR2, 30350MR2, 30448MR2, 10512MR2, 10525MR2, 10527MR2, 20370MR2, 30351MR2, 30446MR2, 20208MR2, 10881MR2, 10919MR2, 10907MR2, 30739MR2

DTI

Excluded from Report: 10036MR1, 10057MR2, 30059MR1, 20032MR1, 10239MR1, 10299MR1, 10185MR1, 10383MR1, 10004MR2, 10013MR2, 20174MR1, 10012MR2, 10023MR2, 10019MR2, 10017MR2, 10026MR2, 10030MR2, 10044MR2, 10043MR2, 10055MR2, 30001MR2, 10041MR2, 10515MR1, 30012MR2, 10053MR2, 30014MR2, 10083MR2, 10064MR2, 30017MR2, 10059MR2, 10062MR2, 30035MR2, 30037MR2, 10079MR2, 10066MR2, 10082MR2, 30059MR2, 10541MR1, 10088MR2, 10622MR1, 20014MR2, 20025MR2, 20022MR2, 10085MR2, 20027MR2, 10113MR2, 20033MR2, 10107MR2, 30080MR2, 10623MR1, 20021MR2, 20028MR2, 30071MR2, 20034MR2, 30031MR2, 20035MR2, 30405MR1, 10642MR1, 10136MR2, 30093MR2, 30042MR2, 10110MR2, 30072MR2, 30040MR2, 10141MR2, 10168MR2, 20057MR2, 20041MR2, 10149MR2, 30043MR2, 10123MR2, 20062MR2, 10151MR2, 30117MR2, 20018MR2, 10789MR1, 10135MR2, 10098MR2, 20070MR2, 10203MR2, 10190MR2, 30123MR2, 30136MR2, 20058MR2, 20084MR2, 10182MR2, 20075MR2, 20045MR2, 10214MR2, 10257MR2, 20050MR2, 20065MR2, 30127MR2, 10253MR2, 30148MR2, 30152MR2, 10227MR2, 10150MR2, 20080MR2, 10218MR2, 10238MR2, 10226MR2, 20087MR2, 30161MR2, 10266MR2, 20093MR2, 20082MR2, 20089MR2, 30163MR2, 10273MR2, 20077MR2, 20096MR2, 20099MR2, 20120MR2, 10302MR2, 20091MR2, 20088MR2, 10125MR2, 10319MR2, 30173MR2, 20133MR2, 10339MR2, 20104MR2, 30177MR2, 30146MR2, 10297MR2, 10322MR2, 20108MR2, 20121MR2, 10272MR2, 20110MR2, 10329MR2, 10356MR2, 20118MR2, 20161MR2, 20146MR2, 10325MR2, 20101MR2, 20142MR2, 20145MR2, 10375MR2, 20085MR2, 20122MR2, 20116MR2, 20140MR2, 30235MR2, 10334MR2, 20132MR2, 30222MR2, 10372MR2, 30223MR2, 10392MR2, 20188MR2, 30250MR2, 20165MR2, 20171MR2, 20123MR2, 10384MR2, 20428MR1, 10341MR2, 20175MR2, 20181MR2, 20138MR2, 10401MR2, 20162MR2, 20217MR2, 20200MR2, 20158MR2, 10399MR2, 10404MR2, 10402MR2, 20209MR2, 10436MR2, 20153MR2, 20195MR2, 10396MR2, 20203MR2, 10418MR2, 30249MR2, 30283MR2, 20185MR2, 10417MR2, 20135MR2, 30321MR2, 10470MR2, 30236MR2, 20212MR2, 20210MR2, 20221MR2, 20225MR2, 20218MR2, 30338MR2, 20224MR2, 30341MR2, 20214MR2, 30349MR2, 10475MR2, 10477MR2, 20230MR2, 10476MR2, 20253MR2, 20284MR2, 20277MR2, 20291MR2, 20281MR2, 20304MR2, 20271MR2, 20285MR2, 20275MR2, 20246MR2, 20311MR2, 20247MR2, 20170MR2, 20308MR2, 20313MR2, 20307MR2, 20317MR2, 20241MR2, 20330MR2, 20323MR2, 20274MR2, 20258MR2, 20037MR2, 20327MR2, 20331MR2, 10757MR2, 20343MR2, 10582MR2, 20348MR2, 10697MR2, 20340MR2, 10568MR2, 10792MR2, 30556MR2, 10776MR2, 10796MR2, 20345MR2, 30428MR2, 30547MR2, 30585MR2, 30542MR2, 10807MR2, 20347MR2, 30438MR2, 10593MR2, 20300MR2, 30589MR2, 10561MR2, 10833MR2, 30554MR2, 20358MR2, 30550MR2, 10711MR2, 20310MR2, 30649MR2, 30666MR2, 10741MR2, 30526MR2, 10831MR2, 30624MR2, 30574MR2, 10689MR2, 20349MR2, 30709MR2, 10466MR2, 20243MR2, 20363MR2, 10721MR2, 30764MR2, 10554MR2, 10815MR2, 30404MR2, 30681MR2, 30583MR2, 10861MR2, 20368MR2, 30449MR2, 10599MR2, 10528MR2, 20353MR2, 30725MR2, 10449MR2, 30701MR2, 20367MR2, 30711MR2, 10848MR2, 10565MR2, 20369MR2, 30553MR2, 10727MR2, 20322MR2, 10499MR2, 10410MR2, 20374MR2, 30369MR2, 10851MR2, 20377MR2, 30795MR2, 10909MR2, 10896MR2, 20378MR2, 30284MR2, 30397MR2, 10515MR2, 20379MR2, 30350MR2, 30448MR2, 10512MR2, 10525MR2, 10527MR2, 20370MR2, 30351MR2, 30446MR2, 20208MR2, 10881MR2, 10919MR2, 10907MR2, 30739MR2

T2 Flair

Excluded from Report: 10036MR1, 10057MR2, 10064MR1, 30059MR1, 20032MR1, 10239MR1, 10299MR1, 10185MR1, 10383MR1, 30235MR1, 10004MR2, 10013MR2, 20174MR1, 10012MR2, 10023MR2, 10019MR2, 10017MR2, 10026MR2, 10030MR2, 10044MR2, 10043MR2, 10055MR2, 30001MR2, 10041MR2, 10515MR1, 30012MR2, 10053MR2, 30014MR2, 10083MR2, 10064MR2, 30017MR2, 10059MR2, 10062MR2, 30035MR2, 30037MR2, 10079MR2, 10066MR2, 10082MR2, 30059MR2, 10541MR1, 10088MR2, 10622MR1, 20014MR2, 20025MR2, 20022MR2, 10085MR2, 20027MR2, 10113MR2, 20033MR2, 10107MR2, 30080MR2, 10623MR1, 20021MR2, 20028MR2, 30071MR2, 20034MR2, 30031MR2, 20035MR2, 30405MR1, 10642MR1, 10136MR2, 30093MR2, 30042MR2, 10110MR2, 30072MR2, 30040MR2, 10141MR2, 10168MR2, 20057MR2, 20041MR2, 10149MR2, 30043MR2, 10123MR2, 20062MR2, 10151MR2, 30117MR2, 20018MR2, 10789MR1, 10135MR2, 10098MR2, 10741MR1, 20070MR2, 10203MR2, 10190MR2, 30123MR2, 30136MR2, 20058MR2, 20084MR2, 10182MR2, 20075MR2, 20045MR2, 10214MR2, 10257MR2, 20050MR2, 20065MR2, 30127MR2, 10253MR2, 30148MR2, 30152MR2, 10227MR2, 10150MR2, 20080MR2, 10218MR2, 10238MR2, 10226MR2, 20087MR2, 30161MR2, 10266MR2, 20093MR2, 20082MR2, 20089MR2, 30163MR2, 10273MR2, 20077MR2, 10909MR1, 20096MR2, 20099MR2, 20120MR2, 10302MR2, 20091MR2, 20088MR2, 10125MR2, 10319MR2, 30173MR2, 20133MR2, 10339MR2, 20104MR2, 30177MR2, 30146MR2, 10297MR2, 10322MR2, 20108MR2, 20121MR2, 10272MR2, 20110MR2, 10329MR2, 10356MR2, 20118MR2, 20161MR2, 20146MR2, 10325MR2, 20101MR2, 20142MR2, 20145MR2, 10375MR2, 30927MR1, 20085MR2, 20122MR2, 20116MR2, 20140MR2, 30235MR2, 10334MR2, 20132MR2, 30222MR2, 10372MR2, 30223MR2, 10392MR2, 20188MR2, 30250MR2, 20165MR2, 20171MR2, 20123MR2, 10384MR2, 20428MR1, 10341MR2, 20175MR2, 20181MR2, 20138MR2, 10401MR2, 20162MR2, 20217MR2, 20200MR2, 20158MR2, 10399MR2, 10404MR2, 10402MR2, 20209MR2, 10436MR2, 20153MR2, 20195MR2, 10396MR2, 20203MR2, 10418MR2, 30249MR2, 30283MR2, 20185MR2, 10417MR2, 20135MR2, 30321MR2, 10470MR2, 30236MR2, 20212MR2, 20210MR2, 20221MR2, 20225MR2, 20218MR2, 30338MR2, 20224MR2, 30341MR2, 20214MR2, 30349MR2, 10475MR2, 10477MR2, 20230MR2, 10476MR2, 20253MR2, 20284MR2, 20277MR2, 20291MR2, 20281MR2, 20304MR2, 20271MR2, 20285MR2, 20275MR2, 20246MR2, 20311MR2, 20247MR2, 20170MR2, 20308MR2, 20313MR2, 20307MR2, 20317MR2, 20241MR2, 20330MR2, 20323MR2, 20274MR2, 20258MR2, 20037MR2, 20327MR2, 20331MR2, 10757MR2, 20343MR2, 10582MR2, 20348MR2, 10697MR2, 20340MR2, 10568MR2, 10792MR2, 30556MR2, 10776MR2, 10796MR2, 20345MR2, 30428MR2, 30547MR2, 30585MR2, 30542MR2, 10807MR2, 20347MR2, 30438MR2, 10593MR2, 20300MR2, 30589MR2, 10561MR2, 10833MR2, 30554MR2, 20358MR2, 30550MR2, 10711MR2, 20310MR2, 30649MR2, 30666MR2, 10741MR2, 30526MR2, 10831MR2, 30624MR2, 30574MR2, 10689MR2, 20349MR2, 30709MR2, 10466MR2, 20243MR2, 20363MR2, 10721MR2, 30764MR2, 10554MR2, 10815MR2, 30404MR2, 30681MR2, 30583MR2, 10861MR2, 20368MR2, 30449MR2, 10599MR2, 10528MR2, 20353MR2, 30725MR2, 10449MR2, 30701MR2, 20367MR2, 30711MR2, 10848MR2, 10565MR2, 20369MR2, 30553MR2, 10727MR2, 20322MR2, 10499MR2, 10410MR2, 20374MR2, 30369MR2, 10851MR2, 20377MR2, 30795MR2, 10909MR2, 10896MR2, 20378MR2, 30284MR2, 30397MR2, 10515MR2, 20379MR2, 30350MR2, 30448MR2, 10512MR2, 10525MR2, 10527MR2, 20370MR2, 30351MR2, 30446MR2, 20208MR2, 10881MR2, 10919MR2, 10907MR2, 30739MR2

pCASL

Excluded from Report: 10012MR1, 10036MR1, 10041MR1, 10057MR2, 10064MR1, 30059MR1, 20032MR1, 10238MR1, 10239MR1, 10273MR1, 10266MR1, 10299MR1, 10185MR1, 10341MR1, 10383MR1, 30235MR1, 10004MR2, 10013MR2, 20174MR1, 10012MR2, 10023MR2, 10019MR2, 10017MR2, 10026MR2, 10030MR2, 10044MR2, 10043MR2, 10055MR2, 30001MR2, 10041MR2, 10515MR1, 30012MR2, 10053MR2, 30014MR2, 10083MR2, 10064MR2, 30017MR2, 10059MR2, 10062MR2, 30035MR2, 30037MR2, 10079MR2, 10066MR2, 10082MR2, 30059MR2, 10541MR1, 10088MR2, 10622MR1, 20014MR2, 20025MR2, 20022MR2, 10085MR2, 20027MR2, 10113MR2, 20033MR2, 10107MR2, 30080MR2, 10623MR1, 20021MR2, 20028MR2, 30071MR2, 20034MR2, 30031MR2, 20035MR2, 30405MR1, 10642MR1, 10136MR2, 30093MR2, 30042MR2, 10110MR2, 30072MR2, 30040MR2, 10141MR2, 10168MR2, 20057MR2, 20041MR2, 10149MR2, 30043MR2, 10123MR2, 20062MR2, 10151MR2, 30117MR2, 20018MR2, 10789MR1, 10135MR2, 10098MR2, 10741MR1, 20070MR2, 10815MR1, 10203MR2, 10190MR2, 30123MR2, 30136MR2, 20058MR2, 20084MR2, 10182MR2, 20075MR2, 20045MR2, 10214MR2, 10257MR2, 20050MR2, 20065MR2, 30127MR2, 10253MR2, 30148MR2, 30152MR2, 10227MR2, 10150MR2, 10840MR1, 20080MR2, 10218MR2, 10238MR2, 10226MR2, 20087MR2, 30161MR2, 10266MR2, 20093MR2, 20082MR2, 20089MR2, 30163MR2, 10273MR2, 20077MR2, 10909MR1, 20096MR2, 20099MR2, 20120MR2, 10302MR2, 20091MR2, 20088MR2, 10125MR2, 10319MR2, 30173MR2, 20133MR2, 10339MR2, 20104MR2, 30177MR2, 30146MR2, 10297MR2, 10322MR2, 20108MR2, 20121MR2, 10272MR2, 20110MR2, 10329MR2, 10356MR2, 20118MR2, 20161MR2, 20146MR2, 10325MR2, 20101MR2, 20142MR2, 20145MR2, 10375MR2, 30927MR1, 20085MR2, 20122MR2, 20116MR2, 20140MR2, 30235MR2, 10334MR2, 20132MR2, 30222MR2, 10372MR2, 30223MR2, 10392MR2, 20188MR2, 30250MR2, 20165MR2, 20171MR2, 20123MR2, 10384MR2, 20428MR1, 10341MR2, 20175MR2, 20181MR2, 20138MR2, 10401MR2, 20162MR2, 20217MR2, 20200MR2, 20158MR2, 10399MR2, 10404MR2, 10402MR2, 20209MR2, 10436MR2, 20153MR2, 20195MR2, 10396MR2, 20203MR2, 10418MR2, 30249MR2, 30283MR2, 20185MR2, 10417MR2, 20135MR2, 30321MR2, 10470MR2, 30236MR2, 31069MR1, 20212MR2, 20210MR2, 20221MR2, 20225MR2, 20218MR2, 30338MR2, 20224MR2, 30341MR2, 20214MR2, 30349MR2, 10475MR2, 10477MR2, 20230MR2, 10476MR2, 20253MR2, 20284MR2, 20277MR2, 20291MR2, 20281MR2, 20304MR2, 20271MR2, 20285MR2, 20275MR2, 20246MR2, 20311MR2, 20247MR2, 20170MR2, 20308MR2, 20313MR2, 20307MR2, 20317MR2, 20241MR2, 20330MR2, 20323MR2, 20274MR2, 20258MR2, 20037MR2, 20327MR2, 20331MR2, 10757MR2, 20343MR2, 10582MR2, 20348MR2, 10697MR2, 20340MR2, 10568MR2, 10792MR2, 30556MR2, 10776MR2, 10796MR2, 20345MR2, 30428MR2, 30547MR2, 30585MR2, 30542MR2, 10807MR2, 20347MR2, 30438MR2, 10593MR2, 20300MR2, 30589MR2, 10561MR2, 10833MR2, 30554MR2, 20358MR2, 30550MR2, 10711MR2, 20310MR2, 30649MR2, 30666MR2, 10741MR2, 30526MR2, 10831MR2, 30624MR2, 30574MR2, 10689MR2, 20349MR2, 30709MR2, 10466MR2, 20243MR2, 20363MR2, 10721MR2, 30764MR2, 10554MR2, 10815MR2, 30404MR2, 30681MR2, 30583MR2, 10861MR2, 20368MR2, 30449MR2, 10599MR2, 10528MR2, 20353MR2, 30725MR2, 10449MR2, 30701MR2, 20367MR2, 30711MR2, 10848MR2, 10565MR2, 20369MR2, 30553MR2, 10727MR2, 20322MR2, 10499MR2, 10410MR2, 20374MR2, 30369MR2, 10851MR2, 20377MR2, 30795MR2, 10909MR2, 10896MR2, 20378MR2, 30284MR2, 30397MR2, 10515MR2, 20379MR2, 30350MR2, 30448MR2, 10512MR2, 10525MR2, 10527MR2, 20370MR2, 30351MR2, 30446MR2, 20208MR2, 10881MR2, 10919MR2, 10907MR2, 30739MR2

Excluded from BOLD Report

*IGNITE Baseline MRI Report
library(stringr)
library(dplyr)
source("/Volumes/IGNITE_Imaging/QC_Output/R_IGNITE/RedCap/PRE/Data/IGNITEDatabase-IGNITEBaselineMRIRep_R_2020-10-08_1259.r")

PRE_MRI<-data
PRE_MRI$mri_sum_scan_time<-as.character(PRE_MRI$mri_sum_scan_time)
rm(data)
#table(PRE_MRI$mri_sum_scan_time %in% RedCap$mri_sum_scan_time)
RedCap_PRE<-full_join(RedCap, PRE_MRI, by="mri_sum_scan_time")
RedCap_PRE<-RedCap_PRE[complete.cases(RedCap_PRE$mri_sum_scan_time),]
RedCap_PRE<-RedCap_PRE[!(RedCap_PRE$mri_sum_scan_time==""),]
RedCap_PRE$mri_sum_scan_time<-as.POSIXct(RedCap_PRE$mri_sum_scan_time,tz=Sys.timezone())
*IGNITE Post MRI Report
library(stringr)
library(dplyr)
source("/Volumes/IGNITE_Imaging/QC_Output/R_IGNITE/RedCap/POST/Data/IGNITEDatabase-IGNITEPostMRIReport_R_2020-10-08_1317.r")
POST_MRI<-data

POST_MRI$mri_sum_scan_time <- as.character(POST_MRI$mri_sum_scan_time)
#table(POST_MRI$mri_sum_scan_time %in% RedCap$mri_sum_scan_time)
RedCap_PRE<-RedCap_PRE[!(RedCap_PRE$mri_sum_scan_time==""),]

rm(data)
RedCap_POST<-full_join(RedCap_PRE, POST_MRI, by="mri_sum_scan_time")
RedCap_PRE<-RedCap_PRE[!(RedCap_PRE$mri_sum_scan_time==""),]
*Task Performance by site (RedCap)
RedCap %>% select(SubID,Session, mri_, vo2_age,mri_sum_1back_rt, mri_sum_1back_acc, mri_sum_2back_rt ,mri_sum_2back_acc  )

df<-c("SubID","mri_site", 
       "mri_sum_1back_rt", "mri_sum_1back_acc", "mri_sum_2back_rt" ,"mri_sum_2back_acc" )
DATA_M1<-RedCap[df]
DATA_M1<-melt(DATA_M1, id.vars =c("SubID", "Site", "Sex"), measure.vars = c( "mri_sum_1back_acc"))
DATA_M1$Site<-as.factor(DATA_M1$Site)
DATA_M1$Sex<-as.factor(DATA_M1$Sex)

ggstatsplot::grouped_ggbetweenstats(
  data = DATA_M1,
  x = Site,
  y = value,
grouping.var  = Sex,
   nboot = 10,
  effsize.type = "biased", # type of effect size
  pairwise.comparisons = TRUE,
  outlier.coef = 3,
  messages = FALSE,
  outlier.tagging = TRUE,
  outlier.label = SubID,
  mean.plotting = TRUE,
  p.adjust.method = "bonferroni",
ylab = "value",
title.prefix = "1-Back ACC")