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.
Steps 1:3 will include importing the excel spreadsheets from each site in our MRIQC database. This database is stored on REHA, in the /IGNITE_Admin directory. Thus, 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.
FULL MPRAGE Report:
| UPitt (N=189) |
Kansas (N=182) |
Northeastern (N=144) |
Overall (N=515) |
|
|---|---|---|---|---|
| MPRAGE_cnr | ||||
| Mean (SD) | 1.69 (0.218) | 1.66 (0.211) | 1.79 (0.255) | 1.71 (0.233) |
| Median [Min, Max] | 1.69 [1.11, 2.77] | 1.63 [1.23, 2.37] | 1.79 [1.21, 2.51] | 1.68 [1.11, 2.77] |
| MPRAGE_fwhm_avg | ||||
| Mean (SD) | 4.15 (0.146) | 4.04 (0.157) | 4.13 (0.235) | 4.11 (0.185) |
| Median [Min, Max] | 4.13 [3.86, 4.59] | 4.03 [3.47, 4.44] | 4.14 [1.82, 4.62] | 4.11 [1.82, 4.62] |
| MPRAGE_snr_total | ||||
| Mean (SD) | 10.1 (0.529) | 10.5 (0.697) | 10.2 (0.961) | 10.3 (0.748) |
| Median [Min, Max] | 10.1 [8.58, 12.3] | 10.5 [7.09, 12.9] | 10.3 [1.82, 12.0] | 10.3 [1.82, 12.9] |
| MPRAGE_snrd_total | ||||
| Mean (SD) | 54.3 (10.4) | 65.0 (9.49) | 56.6 (11.3) | 58.7 (11.4) |
| Median [Min, Max] | 52.9 [24.3, 89.0] | 64.6 [22.5, 94.6] | 56.1 [1.82, 91.4] | 58.6 [1.82, 94.6] |
Monthly MPRAGE Report:
MPRAGE ANOVA Database: https://cran.r-project.org/web/packages/emmeans/vignettes/comparisons.html
# One variable at a time, as we've been doing..
# For example:
# lm <- lm(MPRAGE_cnr ~ Site, data = tmp) #Will give us the model for IQM site means across the entire sample
# #providing one snapshot of our current comparisons between sites...
# #These are often significantly different across diff sites, but what
# information is the providing us over time?
# Next, lets add Site to the model..
#
# lm <- lm(MPRAGE_cnr ~ Site + factor(Quarters), data = tmp)
# lm.s <- emmeans(lm, "Site") # Results are averaged across quarters to provide comparisons between sites
# pairs(lm.s)
# lm.Q <- emmeans(lm, "Quarters") # Results are averaged across sites to provide comparisons between quarters
# pairs(lm.Q)
# lm <- lm(MPRAGE_cnr ~ Site + factor(Quarters) + factor(Quarters), data = tmp)
#pwpm(pigs.emm.s, means = FALSE, flip = TRUE, # args for pwpm()
#reverse = TRUE, # args for pairs()
#side = ">", delta = 0.05, adjust = "none") # args for test()
# Now long version
PRE_MPRAGE_CAT <- PRE_MPRAGE_CAT %>% select(SubID,Site, Quarters, starts_with("MPRAGE_"))
DATA_Q<-melt(PRE_MPRAGE_CAT, id.vars =c("SubID", "Site", "Quarters") )
colnames(DATA_Q)<-c("SubID" , "Site" , "Quarters", "IQMs","value" )
DATA_Q$Site<-as.factor(DATA_Q$Site)
DATA_Q$IQMs<-as.factor(DATA_Q$IQMs)
lm0 <- aov(value ~Site*IQMs, data = DATA_Q)
summary(lm0)## Df Sum Sq Mean Sq F value Pr(>F)
## Site 2 2993 1497 55.45 <2e-16 ***
## IQMs 3 1120284 373428 13835.29 <2e-16 ***
## Site:IQMs 6 8534 1422 52.70 <2e-16 ***
## Residuals 2048 55278 27
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1lm0.site <- emmeans(lm0, "Site", by="IQMs")
pairs(lm0.site)## IQMs = MPRAGE_cnr:
## contrast estimate SE df t.ratio p.value
## UPitt - Kansas 0.0349 0.540 2048 0.065 0.9977
## UPitt - Northeastern -0.1025 0.575 2048 -0.178 0.9826
## Kansas - Northeastern -0.1375 0.579 2048 -0.237 0.9695
##
## IQMs = MPRAGE_fwhm_avg:
## contrast estimate SE df t.ratio p.value
## UPitt - Kansas 0.1038 0.540 2048 0.192 0.9798
## UPitt - Northeastern 0.0127 0.575 2048 0.022 0.9997
## Kansas - Northeastern -0.0911 0.579 2048 -0.157 0.9865
##
## IQMs = MPRAGE_snr_total:
## contrast estimate SE df t.ratio p.value
## UPitt - Kansas -0.3911 0.540 2048 -0.725 0.7487
## UPitt - Northeastern -0.1073 0.575 2048 -0.187 0.9810
## Kansas - Northeastern 0.2838 0.579 2048 0.490 0.8762
##
## IQMs = MPRAGE_snrd_total:
## contrast estimate SE df t.ratio p.value
## UPitt - Kansas -10.7043 0.540 2048 -19.839 <.0001
## UPitt - Northeastern -2.3293 0.575 2048 -4.053 0.0002
## Kansas - Northeastern 8.3750 0.579 2048 14.454 <.0001
##
## P value adjustment: tukey method for comparing a family of 3 estimates####################################################
## AG to add in another model level for QUARTERLY
#tmp %>%
# subset(MPRAGE_cnr, by=="Site")
#scaled_data <- tmp %>%
# group_by(Site) %>%
# mutate(cnrZ = scale(MPRAGE_cnr, center = TRUE),
# fwhmZ = scale(MPRAGE_fwhm_avg, center = TRUE),
# snrZ = scale(MPRAGE_snr_total, center = TRUE),
# snrdZ = scale(MPRAGE_snrd_total, center = TRUE))
#scaled_data <-scaled_data %>%
# select(SubID, ends_with("Z"))FULL N-Back Report:
| UPitt (N=189) |
Kansas (N=182) |
Northeastern (N=144) |
Overall (N=515) |
|
|---|---|---|---|---|
| Nback_dvars_nstd | ||||
| Mean (SD) | 58.8 (17.2) | 51.4 (18.6) | 51.5 (14.7) | 54.2 (17.4) |
| Median [Min, Max] | 55.0 [32.7, 156] | 46.4 [28.1, 135] | 49.0 [30.6, 141] | 50.7 [28.1, 156] |
| Nback_fd_mean | ||||
| Mean (SD) | 0.330 (0.154) | 0.282 (0.150) | 0.286 (0.133) | 0.301 (0.148) |
| Median [Min, Max] | 0.304 [0.0836, 1.12] | 0.240 [0.0883, 0.827] | 0.265 [0.0921, 0.751] | 0.267 [0.0836, 1.12] |
| Nback_fwhm_avg | ||||
| Mean (SD) | 2.40 (0.0782) | 2.39 (0.0821) | 2.39 (0.0902) | 2.39 (0.0833) |
| Median [Min, Max] | 2.40 [2.17, 2.69] | 2.38 [2.18, 2.69] | 2.38 [2.20, 2.70] | 2.39 [2.17, 2.70] |
| Nback_gcor | ||||
| Mean (SD) | 0.0101 (0.00534) | 0.00985 (0.00579) | 0.00960 (0.00520) | 0.00987 (0.00546) |
| Median [Min, Max] | 0.00857 [0.00270, 0.0283] | 0.00854 [0.00166, 0.0535] | 0.00886 [0.00237, 0.0453] | 0.00857 [0.00166, 0.0535] |
| Nback_snr | ||||
| Mean (SD) | 1.97 (0.238) | 2.03 (0.274) | 2.00 (0.282) | 2.00 (0.265) |
| Median [Min, Max] | 1.95 [1.35, 2.86] | 2.02 [1.34, 2.80] | 2.04 [1.38, 2.65] | 2.00 [1.34, 2.86] |
| Nback_tsnr | ||||
| Mean (SD) | 32.1 (7.24) | 35.2 (8.78) | 33.6 (7.16) | 33.6 (7.90) |
| Median [Min, Max] | 31.2 [12.8, 49.1] | 34.7 [13.3, 57.4] | 33.3 [18.2, 49.6] | 33.2 [12.8, 57.4] |
Monthly N-Back Report: New Scans
## [1] "No new baseline NBACK scans"
## Df Sum Sq Mean Sq F value Pr(>F)
## Site 2 530 265 4.513 0.011 *
## IQMs 5 1363379 272676 4645.336 <2e-16 ***
## Site:IQMs 10 6912 691 11.775 <2e-16 ***
## Residuals 3072 180323 59
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## IQMs = Nback_dvars_nstd:
## contrast estimate SE df t.ratio p.value
## UPitt - Kansas 7.393487 0.796 3072 9.292 <.0001
## UPitt - Northeastern 7.375834 0.847 3072 8.703 <.0001
## Kansas - Northeastern -0.017653 0.854 3072 -0.021 0.9998
##
## IQMs = Nback_fd_mean:
## contrast estimate SE df t.ratio p.value
## UPitt - Kansas 0.048228 0.796 3072 0.061 0.9980
## UPitt - Northeastern 0.044371 0.847 3072 0.052 0.9985
## Kansas - Northeastern -0.003857 0.854 3072 -0.005 1.0000
##
## IQMs = Nback_fwhm_avg:
## contrast estimate SE df t.ratio p.value
## UPitt - Kansas 0.015818 0.796 3072 0.020 0.9998
## UPitt - Northeastern 0.013638 0.847 3072 0.016 0.9999
## Kansas - Northeastern -0.002180 0.854 3072 -0.003 1.0000
##
## IQMs = Nback_gcor:
## contrast estimate SE df t.ratio p.value
## UPitt - Kansas 0.000250 0.796 3072 0.000 1.0000
## UPitt - Northeastern 0.000509 0.847 3072 0.001 1.0000
## Kansas - Northeastern 0.000259 0.854 3072 0.000 1.0000
##
## IQMs = Nback_snr:
## contrast estimate SE df t.ratio p.value
## UPitt - Kansas -0.067671 0.796 3072 -0.085 0.9960
## UPitt - Northeastern -0.037607 0.847 3072 -0.044 0.9989
## Kansas - Northeastern 0.030064 0.854 3072 0.035 0.9993
##
## IQMs = Nback_tsnr:
## contrast estimate SE df t.ratio p.value
## UPitt - Kansas -3.141155 0.796 3072 -3.948 0.0002
## UPitt - Northeastern -1.503349 0.847 3072 -1.774 0.1785
## Kansas - Northeastern 1.637806 0.854 3072 1.917 0.1341
##
## P value adjustment: tukey method for comparing a family of 3 estimatesFULL Rest Report:
| UPitt (N=189) |
Kansas (N=182) |
Northeastern (N=144) |
Overall (N=515) |
|
|---|---|---|---|---|
| Rest_dvars_nstd | ||||
| Mean (SD) | 47.1 (9.35) | 41.3 (11.8) | 43.7 (11.4) | 44.1 (11.1) |
| Median [Min, Max] | 45.4 [30.4, 79.0] | 38.3 [24.6, 96.8] | 41.8 [26.8, 108] | 42.1 [24.6, 108] |
| Missing | 0 (0%) | 1 (0.5%) | 0 (0%) | 1 (0.2%) |
| Rest_fd_mean | ||||
| Mean (SD) | 0.304 (0.132) | 0.259 (0.139) | 0.287 (0.158) | 0.284 (0.143) |
| Median [Min, Max] | 0.270 [0.0878, 0.766] | 0.227 [0.0615, 0.812] | 0.249 [0.0882, 1.21] | 0.249 [0.0615, 1.21] |
| Missing | 0 (0%) | 1 (0.5%) | 0 (0%) | 1 (0.2%) |
| Rest_fwhm_avg | ||||
| Mean (SD) | 2.58 (0.0823) | 2.57 (0.0861) | 2.56 (0.0945) | 2.57 (0.0875) |
| Median [Min, Max] | 2.58 [2.33, 2.85] | 2.56 [2.29, 2.94] | 2.55 [2.35, 2.94] | 2.57 [2.29, 2.94] |
| Missing | 0 (0%) | 1 (0.5%) | 0 (0%) | 1 (0.2%) |
| Rest_gcor | ||||
| Mean (SD) | 0.00823 (0.00525) | 0.00893 (0.00527) | 0.00864 (0.00553) | 0.00859 (0.00533) |
| Median [Min, Max] | 0.00715 [0.00131, 0.0422] | 0.00790 [0.00166, 0.0308] | 0.00744 [0.00147, 0.0382] | 0.00740 [0.00131, 0.0422] |
| Missing | 0 (0%) | 1 (0.5%) | 0 (0%) | 1 (0.2%) |
| Rest_snr | ||||
| Mean (SD) | 2.15 (0.239) | 2.27 (0.278) | 2.21 (0.286) | 2.21 (0.271) |
| Median [Min, Max] | 2.14 [1.51, 3.05] | 2.27 [1.47, 3.06] | 2.27 [1.51, 2.79] | 2.23 [1.47, 3.06] |
| Missing | 0 (0%) | 1 (0.5%) | 0 (0%) | 1 (0.2%) |
| Rest_tsnr | ||||
| Mean (SD) | 29.7 (5.02) | 33.1 (6.18) | 31.6 (5.65) | 31.4 (5.80) |
| Median [Min, Max] | 29.3 [17.6, 42.7] | 33.8 [18.7, 49.6] | 31.4 [18.8, 44.1] | 31.3 [17.6, 49.6] |
| Missing | 0 (0%) | 1 (0.5%) | 0 (0%) | 1 (0.2%) |
Monthly Rest Report: New Scans
## [1] "No new baseline Rest scans"## Df Sum Sq Mean Sq F value Pr(>F)
## Site 2 84 42 1.689 0.185
## IQMs 5 955496 191099 7702.881 <2e-16 ***
## Site:IQMs 10 4155 416 16.748 <2e-16 ***
## Residuals 3066 76064 25
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 6 observations deleted due to missingness## IQMs = Rest_dvars_nstd:
## contrast estimate SE df t.ratio p.value
## UPitt - Kansas 5.799730 0.518 3066 11.196 <.0001
## UPitt - Northeastern 3.381948 0.551 3066 6.138 <.0001
## Kansas - Northeastern -2.417782 0.556 3066 -4.347 <.0001
##
## IQMs = Rest_fd_mean:
## contrast estimate SE df t.ratio p.value
## UPitt - Kansas 0.045250 0.518 3066 0.087 0.9958
## UPitt - Northeastern 0.017367 0.551 3066 0.032 0.9995
## Kansas - Northeastern -0.027883 0.556 3066 -0.050 0.9986
##
## IQMs = Rest_fwhm_avg:
## contrast estimate SE df t.ratio p.value
## UPitt - Kansas 0.015096 0.518 3066 0.029 0.9995
## UPitt - Northeastern 0.022729 0.551 3066 0.041 0.9991
## Kansas - Northeastern 0.007634 0.556 3066 0.014 0.9999
##
## IQMs = Rest_gcor:
## contrast estimate SE df t.ratio p.value
## UPitt - Kansas -0.000698 0.518 3066 -0.001 1.0000
## UPitt - Northeastern -0.000415 0.551 3066 -0.001 1.0000
## Kansas - Northeastern 0.000283 0.556 3066 0.001 1.0000
##
## IQMs = Rest_snr:
## contrast estimate SE df t.ratio p.value
## UPitt - Kansas -0.118775 0.518 3066 -0.229 0.9714
## UPitt - Northeastern -0.058281 0.551 3066 -0.106 0.9938
## Kansas - Northeastern 0.060494 0.556 3066 0.109 0.9935
##
## IQMs = Rest_tsnr:
## contrast estimate SE df t.ratio p.value
## UPitt - Kansas -3.436400 0.518 3066 -6.634 <.0001
## UPitt - Northeastern -1.896454 0.551 3066 -3.442 0.0017
## Kansas - Northeastern 1.539946 0.556 3066 2.769 0.0156
##
## P value adjustment: tukey method for comparing a family of 3 estimates
FULL Rise Encoding Report:
| UPitt (N=189) |
Kansas (N=182) |
Northeastern (N=144) |
Overall (N=515) |
|
|---|---|---|---|---|
| RISE_enc_dvars_nstd | ||||
| Mean (SD) | 51.9 (11.7) | 46.0 (15.4) | 47.0 (11.4) | 48.5 (13.3) |
| Median [Min, Max] | 49.6 [33.8, 106] | 42.8 [25.2, 155] | 45.1 [30.6, 95.7] | 46.0 [25.2, 155] |
| Missing | 0 (0%) | 0 (0%) | 2 (1.4%) | 2 (0.4%) |
| RISE_enc_fd_mean | ||||
| Mean (SD) | 0.367 (0.165) | 0.334 (0.239) | 0.326 (0.158) | 0.344 (0.194) |
| Median [Min, Max] | 0.335 [0.130, 1.29] | 0.277 [0.0700, 2.56] | 0.290 [0.103, 0.932] | 0.304 [0.0700, 2.56] |
| Missing | 0 (0%) | 0 (0%) | 2 (1.4%) | 2 (0.4%) |
| RISE_enc_fwhm_avg | ||||
| Mean (SD) | 2.60 (0.0844) | 2.59 (0.0864) | 2.57 (0.0965) | 2.59 (0.0892) |
| Median [Min, Max] | 2.60 [2.35, 2.93] | 2.58 [2.38, 2.96] | 2.56 [2.33, 2.94] | 2.58 [2.33, 2.96] |
| Missing | 0 (0%) | 0 (0%) | 2 (1.4%) | 2 (0.4%) |
| RISE_enc_gcor | ||||
| Mean (SD) | 0.00791 (0.00432) | 0.00865 (0.00722) | 0.00851 (0.00487) | 0.00834 (0.00565) |
| Median [Min, Max] | 0.00653 [0.00149, 0.0215] | 0.00714 [0.00256, 0.0804] | 0.00741 [0.00215, 0.0384] | 0.00704 [0.00149, 0.0804] |
| Missing | 0 (0%) | 0 (0%) | 2 (1.4%) | 2 (0.4%) |
| RISE_enc_snr | ||||
| Mean (SD) | 2.15 (0.237) | 2.27 (0.272) | 2.21 (0.286) | 2.21 (0.268) |
| Median [Min, Max] | 2.14 [1.50, 3.05] | 2.27 [1.47, 3.02] | 2.26 [1.50, 2.78] | 2.21 [1.47, 3.05] |
| Missing | 0 (0%) | 0 (0%) | 2 (1.4%) | 2 (0.4%) |
| RISE_enc_tsnr | ||||
| Mean (SD) | 28.4 (5.47) | 31.1 (7.01) | 30.8 (6.02) | 30.0 (6.32) |
| Median [Min, Max] | 28.0 [14.9, 40.0] | 31.4 [10.6, 49.5] | 30.7 [15.0, 44.7] | 30.0 [10.6, 49.5] |
| Missing | 0 (0%) | 0 (0%) | 2 (1.4%) | 2 (0.4%) |
Monthly RISE1 Report: New Scans
## [1] "No new baseline Rise1 scans"## Df Sum Sq Mean Sq F value Pr(>F)
## Site 2 165 82 2.371 0.0936 .
## IQMs 5 1075718 215144 6200.704 <2e-16 ***
## Site:IQMs 10 4332 433 12.486 <2e-16 ***
## Residuals 3060 106172 35
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 12 observations deleted due to missingness## IQMs = RISE_enc_dvars_nstd:
## contrast estimate SE df t.ratio p.value
## UPitt - Kansas 5.900788 0.612 3060 9.646 <.0001
## UPitt - Northeastern 4.973735 0.654 3060 7.603 <.0001
## Kansas - Northeastern -0.927053 0.660 3060 -1.406 0.3381
##
## IQMs = RISE_enc_fd_mean:
## contrast estimate SE df t.ratio p.value
## UPitt - Kansas 0.032708 0.612 3060 0.053 0.9984
## UPitt - Northeastern 0.041351 0.654 3060 0.063 0.9978
## Kansas - Northeastern 0.008643 0.660 3060 0.013 0.9999
##
## IQMs = RISE_enc_fwhm_avg:
## contrast estimate SE df t.ratio p.value
## UPitt - Kansas 0.011241 0.612 3060 0.018 0.9998
## UPitt - Northeastern 0.029418 0.654 3060 0.045 0.9989
## Kansas - Northeastern 0.018177 0.660 3060 0.028 0.9996
##
## IQMs = RISE_enc_gcor:
## contrast estimate SE df t.ratio p.value
## UPitt - Kansas -0.000745 0.612 3060 -0.001 1.0000
## UPitt - Northeastern -0.000597 0.654 3060 -0.001 1.0000
## Kansas - Northeastern 0.000148 0.660 3060 0.000 1.0000
##
## IQMs = RISE_enc_snr:
## contrast estimate SE df t.ratio p.value
## UPitt - Kansas -0.120160 0.612 3060 -0.196 0.9790
## UPitt - Northeastern -0.062170 0.654 3060 -0.095 0.9950
## Kansas - Northeastern 0.057990 0.660 3060 0.088 0.9957
##
## IQMs = RISE_enc_tsnr:
## contrast estimate SE df t.ratio p.value
## UPitt - Kansas -2.743041 0.612 3060 -4.484 <.0001
## UPitt - Northeastern -2.449590 0.654 3060 -3.745 0.0005
## Kansas - Northeastern 0.293451 0.660 3060 0.445 0.8966
##
## P value adjustment: tukey method for comparing a family of 3 estimates
FULL Rise Recognition Report:
| UPitt (N=189) |
Kansas (N=182) |
Northeastern (N=144) |
Overall (N=515) |
|
|---|---|---|---|---|
| RISE_rec_dvars_nstd | ||||
| Mean (SD) | 51.6 (13.8) | 44.3 (13.2) | 46.1 (10.4) | 47.5 (13.1) |
| Median [Min, Max] | 49.3 [31.5, 154] | 41.6 [25.6, 126] | 45.0 [29.8, 95.6] | 45.1 [25.6, 154] |
| Missing | 0 (0%) | 0 (0%) | 4 (2.8%) | 4 (0.8%) |
| RISE_rec_fd_mean | ||||
| Mean (SD) | 0.360 (0.152) | 0.299 (0.164) | 0.320 (0.148) | 0.327 (0.158) |
| Median [Min, Max] | 0.335 [0.129, 0.921] | 0.257 [0.0938, 1.15] | 0.292 [0.100, 0.981] | 0.299 [0.0938, 1.15] |
| Missing | 0 (0%) | 0 (0%) | 4 (2.8%) | 4 (0.8%) |
| RISE_rec_fwhm_avg | ||||
| Mean (SD) | 2.61 (0.0879) | 2.59 (0.0933) | 2.58 (0.0955) | 2.60 (0.0927) |
| Median [Min, Max] | 2.60 [2.38, 2.95] | 2.59 [2.30, 2.98] | 2.57 [2.36, 2.98] | 2.59 [2.30, 2.98] |
| Missing | 0 (0%) | 0 (0%) | 4 (2.8%) | 4 (0.8%) |
| RISE_rec_gcor | ||||
| Mean (SD) | 0.00826 (0.00563) | 0.00824 (0.00533) | 0.00795 (0.00552) | 0.00817 (0.00548) |
| Median [Min, Max] | 0.00672 [0.00119, 0.0323] | 0.00666 [0.00164, 0.0397] | 0.00652 [0.00146, 0.0405] | 0.00656 [0.00119, 0.0405] |
| Missing | 0 (0%) | 0 (0%) | 4 (2.8%) | 4 (0.8%) |
| RISE_rec_snr | ||||
| Mean (SD) | 2.14 (0.244) | 2.26 (0.278) | 2.21 (0.280) | 2.20 (0.271) |
| Median [Min, Max] | 2.13 [1.32, 3.04] | 2.26 [1.48, 3.09] | 2.26 [1.52, 2.79] | 2.21 [1.32, 3.09] |
| Missing | 0 (0%) | 0 (0%) | 4 (2.8%) | 4 (0.8%) |
| RISE_rec_tsnr | ||||
| Mean (SD) | 26.3 (5.16) | 29.5 (6.38) | 28.3 (5.31) | 28.0 (5.82) |
| Median [Min, Max] | 26.0 [8.26, 41.4] | 29.5 [12.0, 48.2] | 28.3 [17.1, 43.4] | 27.6 [8.26, 48.2] |
| Missing | 0 (0%) | 0 (0%) | 4 (2.8%) | 4 (0.8%) |
Monthly RISE2 Report: New Scans
## [1] "No new baseline RISE2 scans"## Df Sum Sq Mean Sq F value Pr(>F)
## Site 2 300 150 4.642 0.0097 **
## IQMs 5 1006145 201229 6225.267 <2e-16 ***
## Site:IQMs 10 6067 607 18.770 <2e-16 ***
## Residuals 3048 98525 32
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 24 observations deleted due to missingness## IQMs = RISE_rec_dvars_nstd:
## contrast estimate SE df t.ratio p.value
## UPitt - Kansas 7.362031 0.590 3048 12.468 <.0001
## UPitt - Northeastern 5.506835 0.634 3048 8.686 <.0001
## Kansas - Northeastern -1.855197 0.639 3048 -2.903 0.0104
##
## IQMs = RISE_rec_fd_mean:
## contrast estimate SE df t.ratio p.value
## UPitt - Kansas 0.061564 0.590 3048 0.104 0.9940
## UPitt - Northeastern 0.040045 0.634 3048 0.063 0.9978
## Kansas - Northeastern -0.021519 0.639 3048 -0.034 0.9994
##
## IQMs = RISE_rec_fwhm_avg:
## contrast estimate SE df t.ratio p.value
## UPitt - Kansas 0.026102 0.590 3048 0.044 0.9989
## UPitt - Northeastern 0.029424 0.634 3048 0.046 0.9988
## Kansas - Northeastern 0.003323 0.639 3048 0.005 1.0000
##
## IQMs = RISE_rec_gcor:
## contrast estimate SE df t.ratio p.value
## UPitt - Kansas 0.000016 0.590 3048 0.000 1.0000
## UPitt - Northeastern 0.000313 0.634 3048 0.000 1.0000
## Kansas - Northeastern 0.000297 0.639 3048 0.000 1.0000
##
## IQMs = RISE_rec_snr:
## contrast estimate SE df t.ratio p.value
## UPitt - Kansas -0.119238 0.590 3048 -0.202 0.9778
## UPitt - Northeastern -0.072331 0.634 3048 -0.114 0.9928
## Kansas - Northeastern 0.046907 0.639 3048 0.073 0.9970
##
## IQMs = RISE_rec_tsnr:
## contrast estimate SE df t.ratio p.value
## UPitt - Kansas -3.216456 0.590 3048 -5.447 <.0001
## UPitt - Northeastern -1.976862 0.634 3048 -3.118 0.0052
## Kansas - Northeastern 1.239594 0.639 3048 1.939 0.1279
##
## P value adjustment: tukey method for comparing a family of 3 estimates
| UPitt (N=189) |
Kansas (N=182) |
Northeastern (N=144) |
Overall (N=515) |
|
|---|---|---|---|---|
| DTI_meanFA | ||||
| Mean (SD) | 0.285 (0.0171) | 0.277 (0.0233) | 0.276 (0.0172) | 0.280 (0.0199) |
| Median [Min, Max] | 0.285 [0.243, 0.333] | 0.276 [0.241, 0.529] | 0.275 [0.235, 0.322] | 0.279 [0.235, 0.529] |
| Missing | 2 (1.1%) | 0 (0%) | 2 (1.4%) | 4 (0.8%) |
| DTI_meanRELrms_b1500 | ||||
| Mean (SD) | 0.288 (0.0662) | 0.340 (0.140) | 0.243 (0.0748) | 0.294 (0.108) |
| Median [Min, Max] | 0.275 [0.187, 0.604] | 0.313 [0.215, 1.86] | 0.226 [0.137, 0.533] | 0.277 [0.137, 1.86] |
| Missing | 2 (1.1%) | 0 (0%) | 2 (1.4%) | 4 (0.8%) |
| DTI_tsnr_b1500 | ||||
| Mean (SD) | 7.01 (0.381) | 6.25 (0.511) | 7.27 (0.345) | 6.81 (0.602) |
| Median [Min, Max] | 7.07 [5.51, 7.75] | 6.30 [2.20, 7.49] | 7.31 [5.77, 7.95] | 6.88 [2.20, 7.95] |
| Missing | 2 (1.1%) | 0 (0%) | 2 (1.4%) | 4 (0.8%) |
| DTI_outmean_b1500 | ||||
| Mean (SD) | 221 (115) | 209 (205) | 210 (125) | 214 (155) |
| Median [Min, Max] | 196 [108, 1240] | 168 [102, 2200] | 186 [114, 1450] | 183 [102, 2200] |
| Missing | 2 (1.1%) | 0 (0%) | 2 (1.4%) | 4 (0.8%) |
| DTI_meanRELrms_b3000 | ||||
| Mean (SD) | 0.442 (0.0739) | 0.535 (0.183) | 0.394 (0.0748) | 0.462 (0.137) |
| Median [Min, Max] | 0.425 [0.302, 0.737] | 0.504 [0.372, 2.73] | 0.379 [0.258, 0.699] | 0.450 [0.258, 2.73] |
| Missing | 2 (1.1%) | 0 (0%) | 2 (1.4%) | 4 (0.8%) |
| DTI_tsnr_b3000 | ||||
| Mean (SD) | 5.22 (0.283) | 4.41 (0.254) | 5.54 (0.183) | 5.02 (0.536) |
| Median [Min, Max] | 5.26 [3.78, 5.96] | 4.41 [2.13, 4.93] | 5.55 [4.89, 6.21] | 5.17 [2.13, 6.21] |
| Missing | 2 (1.1%) | 0 (0%) | 2 (1.4%) | 4 (0.8%) |
| DTI_outmean_b3000 | ||||
| Mean (SD) | 401 (95.2) | 356 (94.9) | 382 (94.0) | 380 (96.5) |
| Median [Min, Max] | 392 [240, 1130] | 338 [202, 1100] | 366 [255, 1140] | 367 [202, 1140] |
| Missing | 2 (1.1%) | 0 (0%) | 2 (1.4%) | 4 (0.8%) |
Monthly Report: New Scans
## [1] "No new baseline DTI scans"| UPitt (N=189) |
Kansas (N=182) |
Northeastern (N=144) |
Overall (N=515) |
|
|---|---|---|---|---|
| pCASL_tsnr | ||||
| Mean (SD) | 1.20 (0.302) | 0.967 (0.263) | 1.43 (0.377) | 1.18 (0.361) |
| Median [Min, Max] | 1.18 [0.648, 1.96] | 0.914 [0.568, 2.43] | 1.39 [0.767, 3.10] | 1.12 [0.568, 3.10] |
| Missing | 12 (6.3%) | 0 (0%) | 4 (2.8%) | 16 (3.1%) |
| pCASL_outmean | ||||
| Mean (SD) | 5850 (925) | 6130 (1080) | 5880 (807) | 5960 (962) |
| Median [Min, Max] | 5830 [3940, 9710] | 5910 [4500, 11900] | 5910 [3870, 8190] | 5890 [3870, 11900] |
| Missing | 12 (6.3%) | 0 (0%) | 4 (2.8%) | 16 (3.1%) |
Monthly Report: New Scans
## [1] "No new baseline pCASL scans"| UPitt (N=189) |
Kansas (N=182) |
Northeastern (N=144) |
Overall (N=515) |
|
|---|---|---|---|---|
| FLAIR_snr | ||||
| Mean (SD) | 2.42 (0.210) | 2.60 (0.112) | 2.41 (0.156) | 2.48 (0.186) |
| Median [Min, Max] | 2.47 [1.70, 2.80] | 2.59 [2.21, 2.90] | 2.43 [1.89, 2.73] | 2.51 [1.70, 2.90] |
| Missing | 5 (2.6%) | 0 (0%) | 4 (2.8%) | 9 (1.7%) |
Monthly Report: New Scans
## [1] "No new baseline FLAIR scans"PRE_flair_CAT<-PRE_flair_CAT %>% select("SubID", "Site" , "Quarters", "FLAIR_snr")
tmp<-PRE_flair_CAT
DATA_Q<-melt(tmp, id.vars =c("SubID", "Site", "Quarters"))
colnames(DATA_Q)<-c("SubID", "Site" , "Quarters", "FLAIR_snr", "value" )
DATA_Q$Site<-as.factor(DATA_Q$Site)
lm0 <- aov(value ~Site*Quarters, data = DATA_Q)
summary(lm0)## Df Sum Sq Mean Sq F value Pr(>F)
## Site 2 3.794 1.8972 73.338 < 2e-16 ***
## Quarters 10 0.408 0.0408 1.579 0.10967
## Site:Quarters 17 0.993 0.0584 2.259 0.00287 **
## Residuals 476 12.314 0.0259
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 9 observations deleted due to missingnesslm0.site <- emmeans(lm0, "Site", by= "Quarters")
pairs(lm0.site)## Quarters = Apr/13:
## contrast estimate SE df t.ratio p.value
## UPitt - Kansas nonEst NA NA NA NA
## UPitt - Northeastern nonEst NA NA NA NA
## Kansas - Northeastern nonEst NA NA NA NA
##
## Quarters = Apr/18:
## contrast estimate SE df t.ratio p.value
## UPitt - Kansas -0.06488 0.0598 476 -1.086 0.5235
## UPitt - Northeastern -0.04509 0.0638 476 -0.706 0.7599
## Kansas - Northeastern 0.01979 0.0648 476 0.305 0.9499
##
## Quarters = Apr/19:
## contrast estimate SE df t.ratio p.value
## UPitt - Kansas -0.17462 0.0461 476 -3.789 0.0005
## UPitt - Northeastern -0.00755 0.0525 476 -0.144 0.9886
## Kansas - Northeastern 0.16706 0.0491 476 3.400 0.0021
##
## Quarters = Jan/18:
## contrast estimate SE df t.ratio p.value
## UPitt - Kansas -0.11403 0.0758 476 -1.504 0.2900
## UPitt - Northeastern 0.02134 0.0657 476 0.325 0.9435
## Kansas - Northeastern 0.13537 0.0848 476 1.597 0.2480
##
## Quarters = Jan/19:
## contrast estimate SE df t.ratio p.value
## UPitt - Kansas -0.07786 0.0497 476 -1.567 0.2611
## UPitt - Northeastern -0.03839 0.0539 476 -0.713 0.7560
## Kansas - Northeastern 0.03947 0.0549 476 0.718 0.7527
##
## Quarters = Jan/20:
## contrast estimate SE df t.ratio p.value
## UPitt - Kansas -0.21667 0.0609 476 -3.555 0.0012
## UPitt - Northeastern 0.04207 0.0598 476 0.704 0.7613
## Kansas - Northeastern 0.25875 0.0619 476 4.177 0.0001
##
## Quarters = Jul/18:
## contrast estimate SE df t.ratio p.value
## UPitt - Kansas -0.31572 0.0485 476 -6.504 <.0001
## UPitt - Northeastern -0.11685 0.0711 476 -1.643 0.2286
## Kansas - Northeastern 0.19888 0.0685 476 2.904 0.0108
##
## Quarters = Jul/19:
## contrast estimate SE df t.ratio p.value
## UPitt - Kansas -0.25892 0.0536 476 -4.829 <.0001
## UPitt - Northeastern -0.01488 0.0486 476 -0.306 0.9496
## Kansas - Northeastern 0.24404 0.0486 476 5.022 <.0001
##
## Quarters = Oct/17:
## contrast estimate SE df t.ratio p.value
## UPitt - Kansas nonEst NA NA NA NA
## UPitt - Northeastern -0.13539 0.1695 476 -0.799 0.7041
## Kansas - Northeastern nonEst NA NA NA NA
##
## Quarters = Oct/18:
## contrast estimate SE df t.ratio p.value
## UPitt - Kansas -0.14577 0.0460 476 -3.166 0.0047
## UPitt - Northeastern 0.02830 0.0558 476 0.507 0.8679
## Kansas - Northeastern 0.17407 0.0546 476 3.186 0.0044
##
## Quarters = Oct/19:
## contrast estimate SE df t.ratio p.value
## UPitt - Kansas -0.16086 0.0440 476 -3.652 0.0008
## UPitt - Northeastern 0.13474 0.0464 476 2.902 0.0108
## Kansas - Northeastern 0.29560 0.0440 476 6.711 <.0001
##
## P value adjustment: tukey method for comparing a family of 3 estimates