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://escholarship.org/content/qt00d4q8cp/qt00d4q8cp.pdf?t=odeb86 (potenially useful)

MRIQC DATABASE - Current Working Report-**

Sep/14/2020
Days since last subject in report: 91
Number of participants in this report: 46
Incoming Pitt: 16
Incoming Kansas: 16
Incoming Kansas: 14

Pending MRIQC: 10689, 10721

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).

Current Report- Kansas

MPRAGE

SubID Site Date_MR2 cnr fwhm_avg snr_total snrd_total
20170 Kansas 06/15/20 1.884900 4.108496 11.25097 66.95278
20330 Kansas 07/08/20 1.668712 4.127651 10.51618 60.74235
20323 Kansas 07/10/20 1.747889 4.064607 10.98687 61.68946
20274 Kansas 07/13/20 1.544535 4.014781 10.20957 57.67526
20258 Kansas 07/15/20 1.450917 4.232798 10.68856 66.78965
20037 Kansas 07/16/20 1.503661 4.137749 10.94723 77.47226
20327 Kansas 07/20/20 1.285592 4.131850 10.25772 61.29801
20331 Kansas 07/24/20 1.635432 3.833671 11.06725 54.24456
20343 Kansas 07/27/20 1.591479 4.217649 11.20122 77.12056
20348 Kansas 08/05/20 1.483717 4.330540 10.91285 68.06976
20340 Kansas 08/06/20 1.785190 4.321075 10.20623 56.74300
20345 Kansas 08/17/20 1.613922 4.083148 11.03539 77.65933
20347 Kansas 08/20/20 1.449830 3.923960 10.59585 72.29890
20300 Kansas 08/24/20 1.923907 3.988701 10.92428 53.37801
20358 Kansas 08/27/20 1.314777 4.045575 10.03317 72.18032
20310 Kansas 08/31/20 1.787870 3.924387 11.02097 56.08918

NBACK

SubID Site Task Date_MR2 dvars_nstd fwhm_avg fd_mean gcor snr tsnr
20170 Kansas nback 06/15/20 34.84533 2.297131 0.1793773 0.01276570 1.778672 44.04737
20330 Kansas nback 07/08/20 59.52388 2.403809 0.4150245 0.01006100 1.841101 26.76669
20323 Kansas nback 07/10/20 38.13373 2.387157 0.2445120 0.01089700 2.546522 37.14779
20274 Kansas nback 07/13/20 59.55621 2.430977 0.4534187 0.00736002 2.216727 32.97443
20258 Kansas nback 07/15/20 49.53731 2.371285 0.2736694 0.01428340 2.082178 25.43520
20037 Kansas nback 07/16/20 59.88981 2.410841 0.3482434 0.00200454 1.789889 28.09171
20327 Kansas nback 07/20/20 47.63272 2.343887 0.2792766 0.00819645 1.980867 35.09879
20331 Kansas nback 07/24/20 54.66126 2.314600 0.4935140 0.00569531 2.864666 28.12425
20343 Kansas nback 07/27/20 33.02264 2.307669 0.1578657 0.01172360 1.954248 41.29494
20348 Kansas nback 08/05/20 49.57399 2.354495 0.3565393 0.00994865 2.124355 24.79946
20340 Kansas nback 08/06/20 123.01203 2.464527 0.6204804 0.01633880 1.960302 23.14562
20345 Kansas nback 08/17/20 54.24810 2.221967 0.2572760 0.00869047 2.027474 29.40172
20347 Kansas nback 08/20/20 40.56621 2.467927 0.1328122 0.01370450 2.213198 28.81335
20300 Kansas nback 08/24/20 51.87829 2.370468 0.2130984 0.01380050 2.073485 32.56287
20358 Kansas nback 08/27/20 44.44637 2.398323 0.2472936 0.00918155 2.393842 41.01569
20310 Kansas nback 08/31/20 61.87581 2.441877 0.5611313 0.00824503 1.953316 21.22079

Resting State

SubID Site Task Date_MR2 dvars_nstd fwhm_avg fd_mean gcor snr tsnr
20170 Kansas rest 06/15/20 32.64384 2.463177 0.1182065 0.01087370 1.999372 41.34343
20330 Kansas rest 07/08/20 44.06226 2.522441 0.3251245 0.00373217 2.098747 34.86936
20323 Kansas rest 07/10/20 30.69738 2.589236 0.1707013 0.00654751 2.754794 34.64736
20274 Kansas rest 07/13/20 42.96489 2.654448 0.2949879 0.00742794 2.495128 29.77706
20258 Kansas rest 07/15/20 35.93182 2.524587 0.1324498 0.00270533 2.312988 39.47795
20037 Kansas rest 07/16/20 38.85638 2.685179 0.2668994 0.00781471 2.044437 19.92033
20327 Kansas rest 07/20/20 43.44047 2.520568 0.3100773 0.00326652 2.268222 35.03562
20331 Kansas rest 07/24/20 38.88410 2.458204 0.2023441 0.00635786 3.167152 32.92430
20343 Kansas rest 07/27/20 28.21129 2.493808 0.1367992 0.00567244 2.200881 36.71963
20348 Kansas rest 08/05/20 35.21463 2.528777 0.1465126 0.01081640 2.417979 33.21704
20340 Kansas rest 08/06/20 70.96924 2.704427 0.6192957 0.01497430 2.175625 23.04009
20345 Kansas rest 08/17/20 34.21947 2.396264 0.1396122 0.02474550 2.289901 34.83775
20347 Kansas rest 08/20/20 35.76970 2.763845 0.2532986 0.01742480 2.246721 24.59678
20300 Kansas rest 08/24/20 43.68423 2.542181 0.2646913 0.01957730 2.287419 35.36897
20358 Kansas rest 08/27/20 34.88426 2.565355 0.2288611 0.00543178 2.526552 37.79082
20310 Kansas rest 08/31/20 38.00573 2.573367 0.2631254 0.00665264 2.234252 25.83931

RISE Encoding

SubID Site Task Date_MR2 dvars_nstd fwhm_avg fd_mean gcor snr tsnr
20170 Kansas riseenc 06/15/20 35.11880 2.471317 0.1559670 0.01061760 2.005385 35.89806
20330 Kansas riseenc 07/08/20 45.88415 2.541600 0.3580594 0.00268348 2.086139 32.69686
20323 Kansas riseenc 07/10/20 34.20941 2.571051 0.1964752 0.00753491 2.749181 34.30915
20274 Kansas riseenc 07/13/20 43.06869 2.638099 0.2798462 0.00595185 2.504734 29.92072
20258 Kansas riseenc 07/15/20 51.87351 2.619892 0.4133127 0.00332319 2.341130 23.30942
20037 Kansas riseenc 07/16/20 49.03542 2.622685 0.3704850 0.00426242 2.008237 26.58851
20327 Kansas riseenc 07/20/20 47.95311 2.576908 0.3593180 0.00422952 2.262398 28.09762
20331 Kansas riseenc 07/24/20 55.67667 2.548540 0.5889087 0.00394644 3.149156 22.94835
20343 Kansas riseenc 07/27/20 30.81109 2.495821 0.1661911 0.00664736 2.187687 35.34461
20348 Kansas riseenc 08/05/20 42.08816 2.571977 0.3520539 0.01275680 2.409312 26.61238
20340 Kansas riseenc 08/06/20 66.82896 2.654711 0.5498940 0.00594469 2.172042 29.36524
20345 Kansas riseenc 08/17/20 45.66823 2.451029 0.3038751 0.00621673 2.263049 24.80238
20347 Kansas riseenc 08/20/20 41.25181 2.755263 0.3113347 0.00573839 2.279455 26.17400
20300 Kansas riseenc 08/24/20 53.39835 2.598572 0.3948066 0.01553060 2.310401 25.79485
20358 Kansas riseenc 08/27/20 37.67276 2.585223 0.2331977 0.00676081 2.555501 34.98655
20310 Kansas riseenc 08/31/20 47.52026 2.623048 0.4131675 0.00648574 2.186992 20.93177

RISE Recognition

SubID Site Task Date_MR2 dvars_nstd fwhm_avg fd_mean gcor snr tsnr
20170 Kansas riserec 06/15/20 33.16094 2.474932 0.1258654 0.01406690 2.002817 35.33727
20330 Kansas riserec 07/08/20 43.82366 2.625400 0.3492882 0.01450020 2.074925 21.59289
20323 Kansas riserec 07/10/20 31.41425 2.582299 0.1617228 0.00428146 2.713099 36.42266
20274 Kansas riserec 07/13/20 43.43836 2.687239 0.2915260 0.01212190 2.461439 23.68615
20258 Kansas riserec 07/15/20 39.44489 2.594261 0.1786178 0.00663622 2.322808 28.02868
20037 Kansas riserec 07/16/20 45.73497 2.794836 0.3319522 0.01130230 1.972630 16.58714
20327 Kansas riserec 07/20/20 43.30749 2.557319 0.3036224 0.00373352 2.287695 31.66143
20331 Kansas riserec 07/24/20 45.00759 2.542867 0.2930052 0.01687860 3.118886 24.37406
20343 Kansas riserec 07/27/20 29.88802 2.524529 0.1488456 0.00936236 2.192921 28.89966
20348 Kansas riserec 08/05/20 38.06568 2.559675 0.2080486 0.00840109 2.397043 27.14784
20340 Kansas riserec 08/06/20 69.82175 2.670700 0.6123261 0.00600892 2.134866 27.95917
20345 Kansas riserec 08/17/20 42.44913 2.406037 0.2286408 0.01253580 2.276061 29.35390
20347 Kansas riserec 08/20/20 42.65967 2.625727 0.2844215 0.01191340 2.414012 31.01672
20300 Kansas riserec 08/24/20 60.46817 2.687667 0.5431605 0.05495220 2.377599 14.37808
20358 Kansas riserec 08/27/20 37.58895 2.609660 0.2649152 0.00528563 2.529349 34.01580
20310 Kansas riserec 08/31/20 44.63542 2.603779 0.3850162 0.01520930 2.187887 21.20323

DTI

SubID Site Date_MR2 meanFA meanRELrms_b1500 tsnr_b1500 outmean_b1500 meanRELrms_b3000 tsnr_b3000 outmean_b3000
20170 Kansas 06/15/20 0.325725 0.379205 6.285238 289.312 0.557982 4.289071 408.219
20330 Kansas 07/08/20 0.262814 0.224805 6.822529 142.641 0.480469 4.667186 288.641
20323 Kansas 07/10/20 0.280344 0.312042 6.645499 195.938 0.529130 4.397756 330.609
20274 Kansas 07/13/20 0.272786 0.526391 5.969359 159.516 0.784177 4.192993 330.156
20258 Kansas 07/15/20 0.283293 0.253419 6.035906 240.578 0.378376 4.436716 348.406
20037 Kansas 07/16/20 0.292011 0.299274 6.109456 268.219 0.440236 4.264305 417.484
20327 Kansas 07/20/20 0.277611 0.339432 6.090276 167.375 0.545792 4.291758 380.203
20331 Kansas 07/24/20 0.291398 0.347151 6.091831 152.797 0.588648 4.151163 317.562
20343 Kansas 07/27/20 0.281549 0.253723 6.699424 134.625 0.431558 4.713018 285.625
20348 Kansas 08/05/20 0.281920 0.289484 6.172408 172.938 0.510555 4.276680 389.641
20340 Kansas 08/06/20 0.239187 0.417368 5.864719 207.812 0.511246 4.358064 404.266
20345 Kansas 08/17/20 0.304792 0.217032 6.305823 145.844 0.440748 4.316167 325.828
20347 Kansas 08/20/20 0.281696 0.312182 6.370015 208.828 0.476357 4.308933 381.172
20300 Kansas 08/24/20 0.260481 0.319680 6.078897 200.688 0.398190 4.311953 347.953
20358 Kansas 08/27/20 0.303476 0.314006 6.643829 144.641 0.460927 4.356806 291.422
20310 Kansas 08/31/20 0.289105 0.431961 6.365740 173.672 0.605582 4.501634 341.609

T2 Flair

SubID Site Date_MR2 Session snr
20170 Kansas 06/15/20 MR2 2.4883
20330 Kansas 07/08/20 MR2 2.6630
20323 Kansas 07/10/20 MR2 2.7109
20274 Kansas 07/13/20 MR2 2.7601
20258 Kansas 07/15/20 MR2 2.5434
20037 Kansas 07/16/20 MR2 2.8211
20327 Kansas 07/20/20 MR2 2.6994
20331 Kansas 07/24/20 MR2 2.8296
20343 Kansas 07/27/20 MR2 2.6176
20348 Kansas 08/05/20 MR2 2.6973
20340 Kansas 08/06/20 MR2 2.3298
20345 Kansas 08/17/20 MR2 2.7824
20347 Kansas 08/20/20 MR2 2.8043
20300 Kansas 08/24/20 MR2 2.5587
20358 Kansas 08/27/20 MR2 2.8251
20310 Kansas 08/31/20 MR2 2.6222

pCASL

SubID Site Date_MR2 Session tsnr outmean
20170 Kansas 06/15/20 MR2 0.924683 5778.70
20330 Kansas 07/08/20 MR2 0.954541 6721.70
20323 Kansas 07/10/20 MR2 1.147524 5343.85
20274 Kansas 07/13/20 MR2 0.956348 5492.25
20258 Kansas 07/15/20 MR2 1.081632 5770.05
20037 Kansas 07/16/20 MR2 0.905851 6303.20
20327 Kansas 07/20/20 MR2 1.064488 6216.35
20331 Kansas 07/24/20 MR2 1.237460 5467.75
20343 Kansas 07/27/20 MR2 0.790739 5077.25
20348 Kansas 08/05/20 MR2 0.808656 5481.50
20340 Kansas 08/06/20 MR2 0.762597 5929.15
20345 Kansas 08/17/20 MR2 1.318926 6335.30
20347 Kansas 08/20/20 MR2 0.712278 5408.95
20300 Kansas 08/24/20 MR2 1.130867 5213.30
20358 Kansas 08/27/20 MR2 2.389446 5821.40
20310 Kansas 08/31/20 MR2 0.717666 4896.15

 

 

Current Report- University of Pittsburgh

MPRAGE

SubID Site Date_MR2 cnr fwhm_avg snr_total snrd_total
10757 UPitt 07/27/20 1.436567 4.313853 9.662195 45.14086
10582 UPitt 07/28/20 1.332279 4.099986 9.211300 47.50731
10697 UPitt 08/06/20 1.809272 4.189113 10.512477 75.36305
10568 UPitt 08/08/20 1.530401 4.249166 10.494056 58.77056
10792 UPitt 08/10/20 1.848172 4.265896 10.186254 80.07552
10776 UPitt 08/15/20 1.722118 4.278121 10.158347 58.42526
10796 UPitt 08/17/20 1.675504 4.144321 10.123645 56.84206
10807 UPitt 08/20/20 1.722610 3.991088 10.189027 55.04274
10593 UPitt 08/22/20 1.833468 4.269636 10.273674 48.78436
10561 UPitt 08/25/20 2.090759 4.242416 10.890854 53.57542
10833 UPitt 08/25/20 1.776787 4.116928 9.765266 59.67859
10711 UPitt 08/29/20 1.697676 4.652728 8.802191 34.70430
10741 UPitt 09/03/20 1.925764 4.082974 10.284516 84.95687
10831 UPitt 09/08/20 1.824611 4.121065 10.171786 64.06875
10689 UPitt 09/12/20 NA NA NA NA
10721 UPitt 09/14/20 NA NA NA NA

NBACK

SubID Site Task Date_MR2 dvars_nstd fwhm_avg fd_mean gcor snr tsnr
10757 UPitt nback 07/27/20 60.48437 2.404979 0.3294422 0.01232900 1.870073 24.98520
10582 UPitt nback 07/28/20 81.66100 2.383245 0.4907551 0.01283210 1.959747 25.01064
10697 UPitt nback 08/06/20 59.98200 2.696204 0.3233925 0.01034600 1.398284 22.24083
10568 UPitt nback 08/08/20 46.94473 2.457653 0.2534071 0.00824144 1.804746 35.59747
10792 UPitt nback 08/10/20 38.90757 2.458484 0.1855390 0.01008110 1.617850 36.26836
10776 UPitt nback 08/15/20 41.91314 2.474813 0.2393778 0.00986353 1.720182 47.46822
10796 UPitt nback 08/17/20 53.30343 2.441155 0.3003302 0.00587815 1.887437 25.64059
10807 UPitt nback 08/20/20 43.84630 2.272251 0.1645546 0.00548139 1.996627 40.23836
10593 UPitt nback 08/22/20 76.07655 2.375595 0.5615033 0.01568820 2.041628 22.06007
10561 UPitt nback 08/25/20 50.38902 2.387032 0.2396760 0.01700790 1.981375 42.72220
10833 UPitt nback 08/25/20 54.65998 2.417981 0.3797663 0.00652884 2.230737 35.75117
10711 UPitt nback 08/29/20 47.63996 2.462381 0.2505152 0.00274086 1.789862 37.53840
10741 UPitt nback 09/03/20 68.06339 2.488861 0.3096904 0.00965121 1.403432 28.57906
10831 UPitt nback 09/08/20 56.46185 2.447355 0.3401714 0.00884926 1.781677 30.73614

Resting State

SubID Site Task Date_MR2 dvars_nstd fwhm_avg fd_mean gcor snr tsnr
10757 UPitt rest 07/27/20 43.66714 2.569041 0.34090266 0.01749150 2.055874 27.28202
10582 UPitt rest 07/28/20 51.87031 2.598743 0.39207805 0.00600898 2.141295 23.48130
10697 UPitt rest 08/06/20 32.90921 2.799121 0.09670884 0.00647886 1.576694 35.30286
10568 UPitt rest 08/08/20 30.13907 2.596337 0.14878291 0.01302380 1.981147 42.40559
10792 UPitt rest 08/10/20 36.80039 2.584683 0.19288870 0.01233750 1.798428 37.56530
10776 UPitt rest 08/15/20 30.77635 2.676801 0.14563017 0.00509109 1.886821 31.91524
10796 UPitt rest 08/17/20 53.88895 2.549995 0.37554313 0.00550773 2.092677 32.80464
10807 UPitt rest 08/20/20 34.40084 2.472149 0.15055266 0.00864897 2.234009 32.24890
10593 UPitt rest 08/22/20 42.24847 2.541473 0.27892780 0.01600180 2.239254 27.25356
10561 UPitt rest 08/25/20 46.35741 2.594503 0.25425445 0.00847026 2.145750 37.50250
10833 UPitt rest 08/25/20 48.56234 2.600684 0.35016522 0.00670837 2.436343 30.10893
10711 UPitt rest 08/29/20 50.36416 2.617980 0.38606167 0.00709994 2.006670 30.81661
10741 UPitt rest 09/03/20 38.64944 2.659804 0.16650925 0.00704371 1.544806 30.19953
10831 UPitt rest 09/08/20 41.50496 2.663964 0.20423898 0.00744655 1.963426 26.62877

RISE Encoding

SubID Site Task Date_MR2 dvars_nstd fwhm_avg fd_mean gcor snr tsnr
10757 UPitt riseenc 07/27/20 51.56200 2.560101 0.3924616 0.01995230 2.072552 25.41077
10582 UPitt riseenc 07/28/20 65.91734 2.643807 0.5895850 0.00637540 2.147377 19.08770
10697 UPitt riseenc 08/06/20 48.77057 2.884619 0.2995150 0.00901752 1.563959 22.35551
10568 UPitt riseenc 08/08/20 36.97228 2.681331 0.2306669 0.00566513 1.962565 29.59605
10792 UPitt riseenc 08/10/20 34.74948 2.590309 0.1654299 0.00970065 1.808745 38.02615
10776 UPitt riseenc 08/15/20 35.84437 2.638732 0.1882195 0.00814593 1.894379 37.66327
10796 UPitt riseenc 08/17/20 53.28458 2.614463 0.3861438 0.01339690 2.107869 25.06097
10807 UPitt riseenc 08/20/20 39.34091 2.461861 0.2057262 0.00615610 2.231497 32.98536
10593 UPitt riseenc 08/22/20 46.47127 2.566385 0.3603944 0.00679937 2.242494 24.78056
10561 UPitt riseenc 08/25/20 49.45549 2.601147 0.2653549 0.01008170 2.142371 33.50156
10833 UPitt riseenc 08/25/20 48.88925 2.633020 0.3769142 0.01063540 2.424542 26.76085
10711 UPitt riseenc 08/29/20 44.24801 2.622037 0.2793373 0.00321498 1.989544 33.11755
10741 UPitt riseenc 09/03/20 57.36295 2.672228 0.3532436 0.01815870 1.549067 22.78842
10831 UPitt riseenc 09/08/20 42.29585 2.659128 0.2199218 0.00395494 1.978218 26.78306

RISE Recognition

SubID Site Task Date_MR2 dvars_nstd fwhm_avg fd_mean gcor snr tsnr
10757 UPitt riserec 07/27/20 52.82349 2.575887 0.3972374 0.02038090 2.104004 21.29503
10582 UPitt riserec 07/28/20 53.21976 2.574460 0.4010414 0.00380077 2.130765 25.15993
10697 UPitt riserec 08/06/20 40.34733 2.849231 0.2196678 0.01384900 1.556904 25.41018
10568 UPitt riserec 08/08/20 32.10622 2.637723 0.1703485 0.00663834 1.958052 35.61686
10792 UPitt riserec 08/10/20 37.31518 2.601937 0.1874465 0.01467960 1.815410 30.68972
10776 UPitt riserec 08/15/20 33.84091 2.656547 0.2098469 0.00271039 1.891188 36.81128
10796 UPitt riserec 08/17/20 54.38550 2.637097 0.4100342 0.00419715 2.094362 23.78827
10807 UPitt riserec 08/20/20 40.89938 2.504891 0.2140533 0.00350272 2.199435 30.88942
10593 UPitt riserec 08/22/20 49.89581 2.604791 0.4360869 0.00898871 2.255510 22.26905
10561 UPitt riserec 08/25/20 47.21128 2.628759 0.2576336 0.00912185 2.153980 31.08812
10833 UPitt riserec 08/25/20 47.14044 2.618172 0.3612042 0.00453368 2.441765 27.61428
10711 UPitt riserec 08/29/20 46.90642 2.639604 0.2994993 0.00577838 1.978251 30.37532
10741 UPitt riserec 09/03/20 50.46134 2.663823 0.2951789 0.00559562 1.615781 21.59912
10831 UPitt riserec 09/08/20 44.02487 2.732027 0.2448011 0.00570997 1.963949 20.38404

DTI

SubID Site Date_MR2 meanFA meanRELrms_b1500 tsnr_b1500 outmean_b1500 meanRELrms_b3000 tsnr_b3000 outmean_b3000
10757 UPitt 07/27/20 0.275487 0.219651 6.698467 315.062 0.462552 5.307718 501.750
10582 UPitt 07/28/20 0.256412 0.241906 7.577419 159.031 0.429043 5.483058 330.734
10697 UPitt 08/06/20 0.303895 0.223833 7.288034 178.312 0.371718 5.341231 368.953
10568 UPitt 08/08/20 0.300605 0.307825 7.160814 182.422 0.426380 5.233388 360.297
10792 UPitt 08/10/20 0.255724 0.201665 7.168672 200.656 0.349414 5.479376 405.953
10776 UPitt 08/15/20 0.271148 0.247063 7.390846 144.938 0.422050 5.397699 331.156
10796 UPitt 08/17/20 0.269446 0.229514 7.034108 184.750 0.400390 5.322574 351.219
10807 UPitt 08/20/20 0.273601 0.166346 7.157634 201.891 0.382463 5.391168 392.984
10593 UPitt 08/22/20 0.254611 0.384841 6.689379 283.031 0.564060 5.146265 456.688
10561 UPitt 08/25/20 0.303956 0.232250 7.503021 157.094 0.407508 5.435843 317.641
10833 UPitt 08/25/20 0.294873 0.282285 7.080975 220.094 0.415479 5.242953 451.359
10711 UPitt 08/29/20 0.251387 0.364792 6.653299 265.859 0.482341 5.429846 468.656
10741 UPitt 09/03/20 0.310437 0.249057 6.956609 181.391 0.417907 5.085960 392.859
10831 UPitt 09/08/20 0.284300 0.281403 6.853806 218.484 0.423560 5.302399 436.594

T2 Flair

SubID Site Date_MR2 Session snr
10757 UPitt 07/27/20 MR2 2.4163
10582 UPitt 07/28/20 MR2 2.4918
10697 UPitt 08/06/20 MR2 2.4412
10792 UPitt 08/10/20 MR2 2.1703
10776 UPitt 08/15/20 MR2 2.2647
10796 UPitt 08/17/20 MR2 1.8809
10807 UPitt 08/20/20 MR2 2.1719
10593 UPitt 08/22/20 MR2 2.5920
10561 UPitt 08/25/20 MR2 2.3442
10833 UPitt 08/25/20 MR2 2.4733
10711 UPitt 08/29/20 MR2 1.9128
10741 UPitt 09/03/20 MR2 2.3617
10831 UPitt 09/08/20 MR2 2.4740

pCASL

SubID Site Date_MR2 Session tsnr outmean
10757 UPitt 07/27/20 MR2 0.667253 8004.15
10582 UPitt 07/28/20 MR2 1.013378 5298.40
10697 UPitt 08/06/20 MR2 1.124747 5702.15
10792 UPitt 08/10/20 MR2 1.310424 6789.60
10776 UPitt 08/15/20 MR2 0.815638 5210.15
10796 UPitt 08/17/20 MR2 0.915385 5270.75
10807 UPitt 08/20/20 MR2 1.150751 6201.15
10593 UPitt 08/22/20 MR2 1.270342 6591.15
10561 UPitt 08/25/20 MR2 1.093998 5383.05
10833 UPitt 08/25/20 MR2 1.742166 7324.55
10711 UPitt 08/29/20 MR2 1.093324 7289.80
10741 UPitt 09/03/20 MR2 1.189407 6667.60
10831 UPitt 09/08/20 MR2 1.239375 6629.55

 

 

Current Report- University of Northeastern

MPRAGE

SubID Site Date_MR2 cnr fwhm_avg snr_total snrd_total
30556 Northeastern 08/11/20 1.703964 4.412626 9.851323 56.64858
30428 Northeastern 08/17/20 1.739622 3.998439 10.396463 56.10329
30547 Northeastern 08/17/20 1.722748 3.881557 10.055623 47.55263
30585 Northeastern 08/19/20 1.832231 4.174253 10.278784 47.35275
30542 Northeastern 08/19/20 2.224089 4.086323 11.459064 54.14856
30438 Northeastern 08/21/20 1.689838 4.284662 10.071411 73.96128
30589 Northeastern 08/24/20 1.861222 4.052216 10.423235 62.66303
30554 Northeastern 08/26/20 1.793031 4.107038 10.147395 62.82607
30550 Northeastern 08/27/20 1.772576 4.207365 10.126005 51.78335
30649 Northeastern 08/31/20 1.831014 4.280189 9.878582 52.05166
30666 Northeastern 09/01/20 1.823158 4.130286 9.797319 62.15384
30526 Northeastern 09/03/20 2.164768 4.074274 10.942922 53.39972
30624 Northeastern 09/08/20 1.929459 4.048554 10.969003 70.00986
30574 Northeastern 09/09/20 1.742605 4.115643 9.397338 59.45575

NBACK

SubID Site Date_MR2 dvars_nstd fwhm_avg fd_mean gcor snr tsnr
30556 Northeastern 08/11/20 43.22496 2.370540 0.2304815 0.01155120 2.188173 32.72476
30428 Northeastern 08/17/20 35.18058 2.356140 0.1325404 0.00581660 2.011204 33.00288
30547 Northeastern 08/17/20 59.18847 2.418015 0.4656024 0.00807211 2.011320 25.33565
30585 Northeastern 08/19/20 56.81553 2.270004 0.4427349 0.00499001 2.378348 32.52813
30542 Northeastern 08/19/20 60.87319 2.336481 0.3357140 0.00437256 1.921762 27.58009
30438 Northeastern 08/21/20 35.01421 2.495669 0.1886067 0.00533819 1.644725 44.35849
30589 Northeastern 08/24/20 54.37629 2.422285 0.2190052 0.01051840 1.726148 44.17758
30554 Northeastern 08/26/20 53.16349 2.533265 0.2964901 0.00633224 1.569651 27.41463
30550 Northeastern 08/27/20 67.10823 2.306104 0.3381805 0.00825295 2.400304 23.26671
30649 Northeastern 08/31/20 61.09134 2.338419 0.4117060 0.00860644 2.045084 38.34180
30666 Northeastern 09/01/20 59.51915 2.325997 0.2937309 0.00774067 1.776496 31.60639
30526 Northeastern 09/03/20 57.03751 2.284543 0.4339301 0.00570247 2.138296 35.31617
30624 Northeastern 09/08/20 32.84663 2.352368 0.1453724 0.00530096 1.718177 41.86347
30574 Northeastern 09/09/20 76.38851 2.399341 0.5681411 0.01256970 1.794803 20.36464

Resting State

SubID Site Date_MR2 dvars_nstd fwhm_avg fd_mean gcor snr tsnr
30556 Northeastern 08/11/20 43.78147 2.588744 0.2270915 0.01140520 2.417126 27.51789
30428 Northeastern 08/17/20 36.90346 2.535660 0.2497877 0.00359692 2.270518 33.04697
30547 Northeastern 08/17/20 41.42359 2.603321 0.2528262 0.01279690 2.196929 22.79950
30585 Northeastern 08/19/20 45.77306 2.469956 0.2850300 0.00942359 2.591611 29.22804
30542 Northeastern 08/19/20 44.26925 2.483915 0.3570472 0.00271595 2.180014 30.17480
30438 Northeastern 08/21/20 37.71149 2.749192 0.2515508 0.00877981 1.820114 25.57794
30589 Northeastern 08/24/20 44.99626 2.597209 0.2738870 0.01084840 1.936250 36.04660
30554 Northeastern 08/26/20 32.01937 2.606911 0.1541554 0.00515798 1.798742 39.03378
30550 Northeastern 08/27/20 58.50068 2.435351 0.5386426 0.00820431 2.614584 34.19207
30649 Northeastern 08/31/20 48.00047 2.525809 0.3817079 0.00242035 2.240652 33.95995
30666 Northeastern 09/01/20 38.20702 2.496872 0.2222972 0.00944649 1.964644 32.66449
30526 Northeastern 09/03/20 36.14759 2.442093 0.2726352 0.00650963 2.367222 40.11944
30624 Northeastern 09/08/20 35.40354 2.526683 0.2024224 0.00659468 1.929386 38.73706
30574 Northeastern 09/09/20 51.39379 2.620377 0.4108957 0.00511281 1.970860 21.80918

RISE Encoding

SubID Site Date_MR2 dvars_nstd fwhm_avg fd_mean gcor snr tsnr
30556 Northeastern 08/11/20 41.92883 2.595617 0.1890847 0.00669700 2.377165 29.39766
30428 Northeastern 08/17/20 54.24351 2.625041 0.4829197 0.00716846 2.236592 22.76351
30547 Northeastern 08/17/20 45.19250 2.558089 0.3003325 0.00968033 2.198237 29.04947
30585 Northeastern 08/19/20 53.21368 2.492789 0.5337373 0.00473892 2.648051 26.87404
30542 Northeastern 08/19/20 47.30994 2.503152 0.3858264 0.02150350 2.210938 25.48333
30438 Northeastern 08/21/20 39.95984 2.740280 0.3195999 0.00614703 1.832830 28.43999
30589 Northeastern 08/24/20 46.38244 2.609547 0.2851915 0.01039810 1.927892 37.21531
30554 Northeastern 08/26/20 42.52641 2.682933 0.2420147 0.00992251 1.783429 28.17387
30550 Northeastern 08/27/20 62.66452 2.528085 0.5959481 0.01096830 2.644316 23.01927
30649 Northeastern 08/31/20 46.35049 2.525620 0.3636455 0.00780651 2.232230 33.69349
30666 Northeastern 09/01/20 55.52520 2.570723 0.4259954 0.01071940 1.983468 23.38644
30526 Northeastern 09/03/20 37.94397 2.450408 0.2868614 0.00414723 2.362063 36.23666
30624 Northeastern 09/08/20 32.92643 2.628372 0.2351991 0.00192698 1.928435 25.28976
30574 Northeastern 09/09/20 63.97481 2.611524 0.5670265 0.01049140 1.996106 20.77844

RISE Recognition

SubID Site Date_MR2 dvars_nstd fwhm_avg fd_mean gcor snr tsnr
30556 Northeastern 08/11/20 40.82757 2.594073 0.1530700 0.00571177 2.376034 28.25480
30428 Northeastern 08/17/20 38.07779 2.580528 0.2635642 0.01061530 2.236834 27.61291
30547 Northeastern 08/17/20 44.66759 2.571577 0.3176784 0.00993537 2.264510 23.22917
30585 Northeastern 08/19/20 45.65252 2.496392 0.3569665 0.00697599 2.669423 25.60670
30542 Northeastern 08/19/20 49.28384 2.496051 0.4025276 0.00352014 2.199630 26.49872
30438 Northeastern 08/21/20 31.57747 2.725116 0.1935923 0.00376075 1.810628 30.45838
30589 Northeastern 08/24/20 44.25340 2.606092 0.2674573 0.00783699 1.928698 36.80125
30554 Northeastern 08/26/20 41.53925 2.665235 0.2534323 0.00590320 1.776969 30.26834
30550 Northeastern 08/27/20 62.72304 2.494712 0.5843393 0.00974855 2.629624 26.63286
30649 Northeastern 08/31/20 46.89190 2.532800 0.3546163 0.00652313 2.228078 31.56189
30666 Northeastern 09/01/20 42.86211 2.559141 0.2740897 0.00940638 1.968121 25.62945
30526 Northeastern 09/03/20 37.17751 2.451855 0.2892838 0.00394591 2.360385 37.39183
30624 Northeastern 09/08/20 31.61140 2.620831 0.1705327 0.00440630 1.910097 24.10885
30574 Northeastern 09/09/20 71.86844 2.609103 0.6857692 0.01757450 2.032013 19.65086

DTI

SubID Site Date_MR2 meanFA meanRELrms_b1500 tsnr_b1500 outmean_b1500 meanRELrms_b3000 tsnr_b3000 outmean_b3000
30556 Northeastern 08/11/20 0.266298 0.219347 7.304699 212.719 0.356089 5.516371 430.109
30428 Northeastern 08/17/20 0.269715 0.176630 7.597799 172.938 0.420985 5.565000 330.047
30547 Northeastern 08/17/20 0.264250 0.389762 7.202325 182.531 0.597447 5.453587 425.500
30585 Northeastern 08/19/20 0.257714 0.404621 7.249927 164.156 0.501257 5.113839 611.547
30542 Northeastern 08/19/20 0.311690 0.257966 7.054725 234.891 0.424864 5.490257 380.953
30438 Northeastern 08/21/20 0.271058 0.302717 7.058566 284.594 0.493170 5.592477 438.047
30589 Northeastern 08/24/20 0.282046 0.166541 7.190368 230.062 0.307111 5.742332 485.797
30554 Northeastern 08/26/20 0.243530 0.222684 7.355388 176.719 0.383843 5.789012 347.984
30550 Northeastern 08/27/20 0.307103 0.273224 6.791347 331.594 0.399092 5.358034 410.453
30649 Northeastern 08/31/20 0.259451 0.258563 7.374113 231.234 0.433556 5.785075 465.516
30666 Northeastern 09/01/20 0.307452 0.257861 6.588570 675.812 0.422448 5.432947 557.469
30526 Northeastern 09/03/20 0.276533 0.321795 7.204895 158.203 0.381512 5.576710 366.219
30624 Northeastern 09/08/20 0.276233 0.248281 7.411839 136.062 0.457763 5.436253 309.094
30574 Northeastern 09/09/20 0.259928 0.455343 6.487860 308.625 0.636341 5.234456 461.234

T2 Flair

SubID Site Date_MR2 Session snr
30556 Northeastern 08/11/20 MR2 2.5853
30428 Northeastern 08/17/20 MR2 2.6321
30547 Northeastern 08/17/20 MR2 2.4731
30585 Northeastern 08/19/20 MR2 2.3567
30542 Northeastern 08/19/20 MR2 2.4218
30438 Northeastern 08/21/20 MR2 2.3874
30589 Northeastern 08/24/20 MR2 2.3441
30554 Northeastern 08/26/20 MR2 2.3547
30550 Northeastern 08/27/20 MR2 2.3777
30649 Northeastern 08/31/20 MR2 2.1693
30666 Northeastern 09/01/20 MR2 2.4496
30526 Northeastern 09/03/20 MR2 2.2442
30624 Northeastern 09/08/20 MR2 2.4713
30574 Northeastern 09/09/20 MR2 2.2481

pCASL

SubID Site Date_MR2 Session tsnr outmean
30556 Northeastern 08/11/20 MR2 1.526874 6317.00
30428 Northeastern 08/17/20 MR2 1.333662 5256.05
30547 Northeastern 08/17/20 MR2 1.786179 6640.00
30585 Northeastern 08/19/20 MR2 2.183538 6352.95
30542 Northeastern 08/19/20 MR2 1.386072 4807.05
30438 Northeastern 08/21/20 MR2 1.191580 6549.20
30589 Northeastern 08/24/20 MR2 1.180270 6401.80
30554 Northeastern 08/26/20 MR2 1.289971 5833.05
30550 Northeastern 08/27/20 MR2 1.879487 6010.85
30649 Northeastern 08/31/20 MR2 1.279982 5692.40
30666 Northeastern 09/01/20 MR2 1.072492 6035.85
30526 Northeastern 09/03/20 MR2 1.449602 5532.10
30624 Northeastern 09/08/20 MR2 1.237035 5346.70
30574 Northeastern 09/09/20 MR2 1.005330 6231.65

 

 

 

 

ANOVA Database: MPRAGE Report

Recent Scans:

ANOVA Database: N-Back Report

University of Pittsburgh
n meanFD > 0.5mm: 9
Particpants: 10030, 10064, 10182, 10253, 10238, 10266, 10329, 10341, 10593

University of Kansas
n meanFD > 0.5mm: 10
Particpants: 20021, 20027, 20087, 20088, 20120, 20146, 20162, 20271, 20310, 20340

Northeastern University
n meanFD > 0.5mm: 2
Particpants: 30163, 30574

Monthly N-Back Report: New Scans
Upcoming QC: 10689, 10721

ANOVA Database: REST Report

University of Pittsburgh
n meanFD > 0.5mm:8
Particpants: 10026, 10030, 10043, 10059, 10110, 10203, 10238, 10266

University of Kansas
n meanFD > 0.5mm:9
Particpants: 20087, 20101, 20146, 20135, 20246, 20284, 20271, 20311, 20340

Northeastern University
n meanFD > 0.5mm:4
Particpants: 30136, 30173, 30146, 30550

Missing:
--Participants: 10689, 10721

Monthly REST Report: New Scans Missing: 0
--Participants:

 

ANOVA Database: RISE Encoding Report

University of Pittsburgh
n meanFD > 0.5mm:14
Particpants: 10026, 10043, 10059, 10064, 10066, 10110, 10182, 10238, 10266, 10329, 10297, 10341, 10399, 10582

University of Kansas
n meanFD > 0.5mm:15
Particpants: 20027, 20018, 20045, 20077, 20087, 20088, 20146, 20118, 20145, 20162, 20135, 20221, 20271, 20331, 20340

Northeastern University
n meanFD > 0.5mm: 5
Particpants: 30035, 30146, 30585, 30550, 30574

Missing Rise Encoding Data:
--Participants 10689, 10721

Monthly Rise1 Report: New Scans
Missing Rise 1 Data: 0
--Participants

 

 

ANOVA Database: RISE Recognition Report

University of Pittsburgh
n meanFD > 0.5mm: 13
Particpants: 10026, 10043, 10059, 10064, 10066, 10182, 10214, 10238, 10266, 10329, 10297, 10341, 10399

University of Kansas
n meanFD > 0.5mm: 11
Particpants: 20077, 20087, 20120, 20110, 20146, 20162, 20212, 20221, 20271, 20313, 20340

Northeastern University
n meanFD > 0.5mm: 3
Particpants: 30146, 30550, 30574

Missing Rise Recognition Data:
--Participants 10689, 10721, 20181, 30235

Monthly Rise 2 Report: New Scans
--Participants 10689, 10721

 

ANOVA Database: DTI Report

##   [1]  445.219  342.562  739.781  457.266  319.578  338.234  403.469  344.219
##   [9]  414.062  340.344  620.188  373.844  422.375  359.484  727.125  564.750
##  [17]  345.906  291.531  692.766  341.828  357.531  347.594  421.031  455.625
##  [25]  367.922  353.797  853.688  459.391  374.000  363.906  437.547  385.875
##  [33]  620.203  369.812  425.156  310.484  429.125  371.703  628.531  322.344
##  [41]  338.141  359.969  410.312  357.812  365.609  513.453  324.344  361.984
##  [49]  480.672  280.609  789.094  351.891  381.250  338.453  301.312  297.578
##  [57]  454.719  372.953  371.422  578.438  361.438  474.047  446.141  335.000
##  [65]  392.688  382.469  384.578  342.203  444.125  376.250  424.797  345.562
##  [73]  459.609  318.422  468.188  317.641  468.656  456.688  368.953  330.734
##  [81]  501.750  405.953  331.156  392.859  351.219  451.359  392.984  436.594
##  [89]  382.328  327.312  338.234  525.281  404.906  411.609  471.328  375.969
##  [97]  276.656  353.891  328.578  347.562  319.094  239.234  362.750  362.203
## [105]  350.438  307.047  370.141  408.719  331.484  295.953  587.469  274.938
## [113]  343.703  321.500  547.406  421.438  418.406  395.141  448.375  767.188
## [121]  405.516  369.594  334.453  479.172  595.016  521.000  346.031  489.281
## [129]  325.969  222.859  521.438  439.031  341.375  340.984  388.828  293.844
## [137]  365.641  340.547  288.766  521.312  321.172  250.391  340.328  330.062
## [145]  282.172  338.109  329.750  442.406  268.375  255.953  388.797  318.250
## [153]  240.891  254.391 1081.880  301.594  308.625  211.281  261.672  303.922
## [161]  330.156  372.703  348.406  375.234  420.828  268.719  315.172  423.484
## [169]  259.375  347.953  321.875  309.750  409.781  408.219  288.625  389.562
## [177]  452.141  388.703  492.562  417.484  446.531  341.609  330.609  288.641
## [185]  317.562  380.203  325.828  285.625  389.641  404.266  381.172  291.422
## [193]  418.266  388.031  286.203  737.219  382.016  518.719  438.594  411.766
## [201]  336.953  358.219  397.250  323.234  342.547  474.594  365.047  485.547
## [209]  286.234  347.781  340.547  253.516  446.266  435.438  394.750  468.672
## [217]  362.438  401.344  571.844  421.109  437.328  431.219  385.891  285.516
## [225]  341.891  437.656  373.969  356.281  330.047  347.984  366.219  485.797
## [233]  611.547  425.500  380.953  410.453  430.109  465.516  438.047  309.094
## [241]  557.469  461.234

Missing DTI: 5
--Subjects: 10568, 10689, 10721, 20181, 30163

Monthly DTI Report: New Scans Missing DTI: 0
--Subjects:

 

ANOVA Database: pCASL Report

Missing pCASL: 5
--Subjects: 10568 , 20084, 20181, 30059, 30163

Monthly pCASL Report: New Scans
Missing pCASL: 0
--Subjects:

 

ANOVA Database: T2 Flair Report

Missing T2 Flair: 3
--Subjects: 10568 , 20181, 30163

Monthly T2 Flair Report: New Scans
Missing Flair: 0
--Subjects:

 

 

Quarterly Visualizations

T1 MPRAGE

library(tidyverse)
library(lubridate)
library(reshape2)
library(ggExtra)
library(plotly)
library(ggplotlyExtra)
library(scales) # to access breaks/formatting functions
library(ggpubr)
library(ggthemes)
library(ggplot2)

MRIQC_Admin.df$SubID<-as.character(MRIQC_Admin.df$SubID)
POST_MPRAGE.IQMs.df$SubID<-as.character(POST_MPRAGE.IQMs.df$SubID)
POST_MPRAGE_QC04<-left_join(MRIQC_Admin.df, POST_MPRAGE.IQMs.df)
POST_MPRAGE_QC04<-POST_MPRAGE_QC04[complete.cases(POST_MPRAGE_QC04$cnr),]
POST_MPRAGE_QC04<-POST_MPRAGE_QC04[!(duplicated(POST_MPRAGE_QC04$SubID)),]
DATA<-  POST_MPRAGE_QC04
#IGNITE Imaging QC Across Time
DATA$Date_MR2<-as.Date(DATA$Date_MR2, format = "%Y-%m-%d")
DATA<-arrange( DATA,DATA$Date_MR2)
DATA$Date_MR2<-as.Date(DATA$Date_MR2)
DATA<-DATA[complete.cases(DATA$Date_MR2),]
DATA$THREE_MO<-lubridate::floor_date(DATA$Date_MR2, "3 months")
DATA$Quarters <- format(as.Date(DATA$THREE_MO), "%b/%y")
DATA$MONTH<-lubridate::floor_date(DATA$Date_MR2, "1 month")
DATA$Months<- format(as.Date(DATA$MONTH), "%b/%y")
DATA$Site<-as.factor(DATA$Site)
DATA<-DATA %>%
  select(SubID,Site,Quarters,cnr,fwhm_avg,snr_total, snrd_total)
DATA$Quarters<-factor(DATA$Quarters, levels=c("Jan/18", "Oct/18 ", "Jan/19", "Apr/19", "Jul/19", "Oct/19","Jan/20" ,"Apr/20" ,"Jul/20" ))
DATA<-arrange( DATA,DATA$Quarters)
DATA$Site<-as.factor(DATA$Site)




scaled_data <- DATA %>%
                  dplyr::group_by(Site, Quarters, add=TRUE) %>%
                  mutate(cnrZ = scale(cnr),
                         fwhm_avgZ=scale(fwhm_avg),
                         snrZ = scale(snr_total),
                         snrdZ = scale(snrd_total))


scaled_data <- scaled_data %>% select(SubID, Site, Quarters ,ends_with("Z"))
scaled_data<-as.data.frame(scaled_data)
dfmelt<-melt(scaled_data, id.vars = c("SubID","Site","Quarters"), measure.vars =c("cnrZ","fwhm_avgZ","snrZ","snrdZ" ))
dfmelt$value<-as.numeric(dfmelt$value)
dfmelt$Outlier_FLAG<-ifelse((dfmelt$value <= (-2) |dfmelt$value >= (2)) , "Outlier", "NotOutlier")
p <- ggplot2::ggplot(dfmelt, aes(x=Quarters, y=value,fill=variable))+
    geom_boxplot()+
    theme(legend.position = "none")+
    facet_grid(variable~., scales  = "free_y")+
 geom_point(data=dfmelt %>% group_by(Quarters, add=TRUE ) %>%  filter(Outlier_FLAG=="Outlier"),aes(label=SubID))
plotly::ggplotly(p)

BOLD N-Back

BOLD Resting State

BOLD Rise Encoding

BOLD Rise Recognition