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: 10520MR2, 20400MR2

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..

10525MR2, 10527MR2, 20370MR2, 30351MR2, 30446MR2, 20208MR2, 10881MR2, 10919MR2, 10907MR2, 30739MR2, 30718MR2, 30498MR2, 30434MR2, 20383MR2, 30355MR2, 10969MR2, 10520MR2, 30329MR2, 30475MR2, 20400MR2

_

Current Working Report-

Nov/24/2020
Number of participants in this report: 21
First scan date in current report: NA
Last scan date in current report: NA
Days since last subject in report: NA

New Scans / Running Totals:

Kansas University 4 / 0

New Baseline: 0
New Follow-Up: 4

University of Pittsburgh 7 / 0

New Baseline: 0
New Follow-Up:7

Northeastern University 9 / 0

New Baseline:0
New Follow-Up:9

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: 7 / 0 New Baseline: 0
-Withdrew/Excluded after baseline MRI:
- 15
- 2
New Follow-Up:7
- Completed MR2: 189
- Lost to Follow-Up: 11
- Upcoming Follow-Up Assesments: 0

MPRAGE

Pending QC: 10525, 10527, 10881, 10919, 10907, 10969, 10520

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
10919 UPitt nback 2020-11-07 41.21791 2.502971 0.1424920 0.01712840 1.541468 32.64374
10907 UPitt nback 2020-11-09 83.37973 2.344169 0.3828051 0.00709511 1.958038 25.89179
10969 UPitt nback 2020-11-17 109.61513 2.250911 0.5063708 0.00541188 2.063567 30.41105

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
10919 UPitt rest 2020-11-07 44.94023 2.672151 0.2698996 0.01757360 1.696985 29.25439
10907 UPitt rest 2020-11-09 68.75346 2.570164 0.5980894 0.00722871 2.135160 25.02091
10969 UPitt rest 2020-11-17 81.26134 2.502871 0.8527760 0.00519992 2.280501 23.25352

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
10919 riseenc 2020-11-07 45.97954 2.668331 0.2707035 0.01239600 1.673276 34.78518
10907 riseenc 2020-11-09 74.45629 2.616661 0.6540006 0.00838588 2.126902 20.79921
10969 riseenc 2020-11-17 77.76613 2.476353 0.7268124 0.00544970 2.252733 27.80753

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
10919 riserec 2020-11-07 45.54796 2.707516 0.2701547 0.01076490 1.685466 24.70743
10907 riserec 2020-11-09 77.62390 2.600525 0.6728749 0.01150210 2.136856 21.88182
10969 riserec 2020-11-17 77.93743 2.487293 0.7231499 0.00391064 2.268801 25.63895

DTI

10525, 10527, 10881, 10919, 10907, 10969, 10520

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 4 / 0

New Baseline: 0 -No Baseline MRI: 2
-Withdrew/Excluded after baseline MRI: 3
New Follow-Up: 4 - Completed MR2: 182 - Upcoming Follow-Up Assesments: 0

MPRAGE

Pending QC: 20370, 20208, 20383, 20400

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, 20383, 20400

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, 20383, 20400

 

 

 

 

Northeastern University 9 / 0

New Baseline:0
New Follow-Up:9 Completed MR2: 76 Upcoming Follow-Up Assesments: 68

MPRAGE

Pending QC: 30351, 30446, 30739, 30718, 30498, 30434, 30355, 30329, 30475

SubID Session Date cnr fwhm_avg snr_total snrd_total
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
30718 MR2 2020-11-10 NA NA NA NA
30498 MR2 2020-11-12 NA NA NA NA
30434 MR2 2020-11-13 NA NA NA NA
30355 MR2 2020-11-16 NA NA NA NA
30329 MR2 2020-11-18 NA NA NA NA
30475 MR2 2020-11-19 NA NA NA NA

NBACK

SubID Session task_id Date dvars_nstd fwhm_avg fd_mean gcor snr tsnr
30351 MR2 nback 2020-11-03 45.93924 2.423556 0.1835629 0.00605482 1.426994 43.22558
30446 MR2 nback 2020-11-04 41.78706 2.418959 0.1451479 0.02126610 1.577115 44.90837
30739 MR2 nback 2020-11-09 73.29501 2.601017 0.4294743 0.01207900 1.405502 25.00592
30718 MR2 nback 2020-11-10 55.36341 2.410080 0.1827560 0.00817864 1.519147 39.24774
30498 MR2 nback 2020-11-12 60.16004 2.622188 0.3259613 0.01537370 1.435621 21.36928
30434 MR2 nback 2020-11-13 39.09122 2.331392 0.1394662 0.01706240 1.955953 46.15441
30355 MR2 nback 2020-11-16 45.51942 2.492247 0.3117857 0.00564297 1.886057 29.62539
30329 MR2 nback 2020-11-18 69.05111 2.420213 0.3620678 0.01835900 2.240770 22.47489
30475 MR2 nback 2020-11-19 38.40408 2.518192 0.1844216 0.01289790 1.615776 32.93932

Resting State

SubID task_id Date dvars_nstd fwhm_avg fd_mean gcor snr tsnr
30351 rest 2020-11-03 37.92033 2.577245 0.1696815 0.00577609 1.616952 36.30946
30446 rest 2020-11-04 37.84232 2.555185 0.1961283 0.01350020 1.750953 44.66651
30739 rest 2020-11-09 63.93234 2.747229 0.4774687 0.00340832 1.546195 27.42763
30718 rest 2020-11-10 54.23795 2.576197 0.3436962 0.01348150 1.697632 33.89586
30498 rest 2020-11-12 45.61471 2.713361 0.2171764 0.01193880 1.653258 32.29779
30434 rest 2020-11-13 42.25649 2.509251 0.2784587 0.01430930 2.205517 30.26337
30355 rest 2020-11-16 33.35838 2.651921 0.2030312 0.01689950 2.067530 28.35424
30329 rest 2020-11-18 63.54281 2.596251 0.5245754 0.01473460 2.381680 27.85690
30475 rest 2020-11-19 33.71675 2.721157 0.1889249 0.00527649 1.843086 26.28828

RISE Encoding

SubID task_id Date dvars_nstd fwhm_avg fd_mean gcor snr tsnr
30351 riseenc 2020-11-03 40.19787 2.574652 0.1589866 0.00633457 1.603669 39.52031
30446 riseenc 2020-11-04 37.93056 2.559028 0.1493230 0.01508320 1.735262 43.51526
30739 riseenc 2020-11-09 55.45668 2.754512 0.4042982 0.01244400 1.571366 26.60630
30718 riseenc 2020-11-10 52.41200 2.576143 0.3132003 0.00818910 1.685837 37.20770
30498 riseenc 2020-11-12 64.99240 2.849407 0.5072177 0.00821111 1.599845 20.53995
30434 riseenc 2020-11-13 44.19981 2.509048 0.2827076 0.01334130 2.204276 32.57531
30355 riseenc 2020-11-16 49.74328 2.725037 0.6423539 0.02948880 2.118124 17.68168
30329 riseenc 2020-11-18 58.53846 2.597601 0.4080317 0.00371727 2.395968 28.65411
30475 riseenc 2020-11-19 34.64949 2.708312 0.2032994 0.01977170 1.825324 27.78584

RISE Recognition

SubID task_id Date dvars_nstd fwhm_avg fd_mean gcor snr tsnr
30351 riserec 2020-11-03 39.95976 2.559311 0.1561923 0.00492514 1.613090 41.25333
30446 riserec 2020-11-04 39.95373 2.585352 0.1614665 0.02015060 1.726367 33.98261
30739 riserec 2020-11-09 54.65427 2.748697 0.4007980 0.00347551 1.588372 25.95492
30718 riserec 2020-11-10 50.82658 2.592024 0.3090299 0.00569120 1.692576 31.63899
30498 riserec 2020-11-12 51.70850 2.772220 0.3030902 0.00793803 1.584029 27.32238
30434 riserec 2020-11-13 44.67437 2.507613 0.2949730 0.00881390 2.182080 32.40619
30355 riserec 2020-11-16 35.53274 2.671249 0.2231797 0.00703244 2.036502 28.35925
30329 riserec 2020-11-18 62.60931 2.585553 0.4548995 0.00560155 2.417202 30.00567
30475 riserec 2020-11-19 33.41982 2.676889 0.1683018 0.01004070 1.813417 33.69099

DTI

30351, 30446, 30739, 30718, 30498, 30434, 30355, 30329, 30475

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, NA, 10515MR2, 20379MR2, 30350MR2, 30448MR2, 10512MR2, 10525MR2, 10527MR2, 20370MR2, 30351MR2, 30446MR2, 20208MR2, 10881MR2, 10919MR2, 10907MR2, 30739MR2, 30718MR2, 30498MR2, 30434MR2, 20383MR2, 30355MR2, 10969MR2, 10520MR2, 30329MR2, 30475MR2, 20400MR2

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, NA, 10515MR2, 20379MR2, 30350MR2, 30448MR2, 10512MR2, 10525MR2, 10527MR2, 20370MR2, 30351MR2, 30446MR2, 20208MR2, 10881MR2, 10919MR2, 10907MR2, 30739MR2, 30718MR2, 30498MR2, 30434MR2, 20383MR2, 30355MR2, 10969MR2, 10520MR2, 30329MR2, 30475MR2, 20400MR2

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, NA, 10515MR2, 20379MR2, 30350MR2, 30448MR2, 10512MR2, 10525MR2, 10527MR2, 20370MR2, 30351MR2, 30446MR2, 20208MR2, 10881MR2, 10919MR2, 10907MR2, 30739MR2, 30718MR2, 30498MR2, 30434MR2, 20383MR2, 30355MR2, 10969MR2, 10520MR2, 30329MR2, 30475MR2, 20400MR2

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, NA, 10515MR2, 20379MR2, 30350MR2, 30448MR2, 10512MR2, 10525MR2, 10527MR2, 20370MR2, 30351MR2, 30446MR2, 20208MR2, 10881MR2, 10919MR2, 10907MR2, 30739MR2, 30718MR2, 30498MR2, 30434MR2, 20383MR2, 30355MR2, 10969MR2, 10520MR2, 30329MR2, 30475MR2, 20400MR2

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")