-
Notifications
You must be signed in to change notification settings - Fork 2
/
MNI_ecosystem.html
1029 lines (882 loc) · 44.5 KB
/
MNI_ecosystem.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
<!doctype html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>MNI Ecosytem - McGill Centre for Integrative Neuroscience</title>
<!-- The important Javascript libraries -->
<link rel="stylesheet" href="css/reveal.css">
<link rel="stylesheet" href="css/theme/black.css" id="theme">
<!-- Code syntax highlighting -->
<link rel="stylesheet" href="lib/css/zenburn.css">
<!-- Printing and PDF exports -->
<script>
var link = document.createElement( 'link' );
link.rel = 'stylesheet';
link.type = 'text/css';
link.href = window.location.search.match( /print-pdf/gi ) ? 'css/print/pdf.css' : 'css/print/paper.css';
document.getElementsByTagName( 'head' )[0].appendChild( link );
</script>
<!--[if lt IE 9]>
<script src="lib/js/html5shiv.js"></script>
<![endif]-->
</head>
<body>
<div class="reveal">
<!-- Any section element inside of this container is displayed as a slide -->
<div class="slides">
<section>
<!-- FIRST OPTION FIRST PAGE -->
<section>
<h1>THE MNI Ecosystem</h1>
<h4 style="padding-bottom:0px; margin-bottom:0px;" align="center"><font color="f27c30">Database management and processing ecosystem for data-sharing initiatives</font></h4>
<!--ENTER DATE OF PRESENTATION HERE-->
<p><small>NOVEMBER 2017</small></p>
<p><small>Samir Das<br>Director of Technology</small></p>
<p><small><font color="12a3d8"><b>McGill Centre for Integrative Neuroscience</b></font><br><font color="12a3d8"><b>Montreal Neurological Institute</b></font></small></p>
<table class="reveal">
<tr>
<td width="40%" style="vertical-align: middle">
<a href="https://mcin-cnim.ca/" target="_blank"><img src="images/MCIN.png" style="border: 0"></a>
</td>
<td width="15%" style="vertical-align: middle">
<a href="http://www.mcgill.ca/neuro/" target="_blank"><img src="images/Neuro.png" style="border: 0"></a>
</td>
<td width="35%" style="vertical-align: middle">
<a href="http://ludmercentre.ca/" target="_blank"><img src="images/ludmer-new-white.png" style="border: 0"></a>
</td>
</tr>
</table>
</section>
<!-- SECOND OPTION FIRST PAGE -->
<section data-background="images/IBIS_image.png">
<h1 style="text-shadow:-1px -1px 0 #000,1px -1px 0 #000,-1px 1px 0 #000,1px 1px 0 #000;">THE MNI Ecosystem</h1>
<h4 style="padding-bottom:0px; margin-bottom:0px;text-shadow:-1px -1px 0 #000,1px -1px 0 #000,-1px 1px 0 #000,1px 1px 0 #000;" align="center">Database management and processing ecosystem for data-sharing initiatives</h4>
<!--ENTER DATE OF PRESENTATION HERE-->
<p style="text-shadow:-1px -1px 0 #000,1px -1px 0 #000,-1px 1px 0 #000,1px 1px 0 #000;"><small>NOVEMBER 2017</small></p>
<p style="text-shadow:-1px -1px 0 #000,1px -1px 0 #000,-1px 1px 0 #000,1px 1px 0 #000;"><small>Samir Das<br>Director of Technology</small></p>
<p style="text-shadow:-1px -1px 0 #000,1px -1px 0 #000,-1px 1px 0 #000,1px 1px 0 #000;"><small><b>McGill Centre for Integrative Neuroscience</b><br><b>Montreal Neurological Institute</b></small></p>
<table class="reveal">
<tr>
<td width="40%" style="vertical-align: middle">
<a href="https://mcin-cnim.ca/" target="_blank"><img src="images/MCIN.png" style="border: 0"></a>
</td>
<td width="15%" style="vertical-align: middle">
<a href="http://www.mcgill.ca/neuro/" target="_blank"><img src="images/Neuro.png" style="border: 0"></a>
</td>
<td width="35%" style="vertical-align: middle">
<a href="http://ludmercentre.ca/" target="_blank"><img src="images/ludmer-new-white.png" style="border: 0"></a>
</td>
</tr>
</table>
</section>
<!-- THIRD OPTION FOR FIRST PAGE -->
<section data-background="images/brain-background.png">
<h1 style="text-shadow:-1px -1px 0 #000,1px -1px 0 #000,-1px 1px 0 #000,1px 1px 0 #000;">THE MNI Ecosystem</h1>
<h4 style="padding-bottom:0px; margin-bottom:0px; text-shadow:-1px -1px 0 #000, 1px -1px 0 #000,-1px 1px 0 #000,1px 1px 0 #000;" align="center">Database management and processing ecosystem for data-sharing initiatives</h4>
<!--ENTER DATE OF PRESENTATION HERE-->
<p style="text-shadow:-1px -1px 0 #000,1px -1px 0 #000,-1px 1px 0 #000,1px 1px 0 #000;"align="center"><small>NOVEMBER 2017</small></p>
<p style="text-shadow:-1px -1px 0 #000,1px -1px 0 #000,-1px 1px 0 #000,1px 1px 0 #000;" align="center"><small>Samir Das<br>Director of Technology</small></p>
<p style="text-shadow:-1px -1px 0 #000,1px -1px 0 #000,-1px 1px 0 #000,1px 1px 0 #000;" align="center"><small><b>McGill Centre for Integrative Neuroscience</b><br><b>Montreal Neurological Institute</b></small></p>
<table class="reveal">
<tr>
<td width="40%" style="vertical-align: middle">
<a href="https://mcin-cnim.ca/" target="_blank"><img src="images/MCIN.png" style="border: 0"></a>
</td>
<td width="15%" style="vertical-align: middle">
<a href="http://www.mcgill.ca/neuro/" target="_blank"><img src="images/Neuro.png" style="border: 0"></a>
</td>
<td width="35%" style="vertical-align: middle">
<a href="http://ludmercentre.ca/" target="_blank"><img src="images/ludmer-new-white.png" style="border: 0"></a>
</td>
</tr>
</table>
</section>
</section>
<!-- MNI ecosystem menu/summary-->
<section>
<section data-background="images/mni_eco_info_5.jpg" data-background-size="100%">
</section>
<!-- MNI PAPER -->
<section data-transition="fade">
<a href="https://www.researchgate.net/publication/281780543_The_MNI_data-sharing_and_processing_ecosystem" target="_blank"><img src="images/MNI_ecosystem_paper.png" width="90%"></a>
</section>
<!-- WHAT'S INVOLVED? -->
<section id="fragments">
<h2><font color="12a3d8">What’s involved?</font></h2>
<p>
<span class="fragment">Longitudinal Acquisition, Storage and Curation, <font color="f27c30">Interoperability, Reproducibility</font>, Transfer, Anonymization, Security, Privacy, Ethics, APIs, Validation, Quality Control, Protocol Checking, Preprocessing, Analysis, HPC,</span>
<span class="fragment">Provenance, Ontological Standarization,<br><font color="f27c30">Data Harmonization</font>, Upgrades, Maintenance, Bug Fixes, User Interface, Javascript, Bootstrap, Tracking, <font color="f27c30">Extensibility</font>, Data Management, Summary Statistics, Workflows,</span><br>
<span class="fragment">Development, Tool Integration, <font color="f27c30">Data Sharing</font>, Download, Multi-Modal Linking, <font color="f27c30">Querying</font>, Image Processing, Visualization, Networking, System Administration, Partnerships, Funding, HR</span>
<span class="fragment"><font color="f27c30">...No big deal!</font></span>
</p>
</section>
<section>
<h2><font color="12a3d8">LORIS-CBRAIN INTEGRATION</font></h2>
<img src="images/Data_flow.jpg">
</section>
</section>
<!-- WHAT IS LORIS? -->
<section>
<section>
<a href="LORIS_indepth.html#/2" target="_blank"><h2>WHAT IS LORIS?</h2></a>
<table class="reveal">
<tr>
<td width="50%" style="vertical-align: middle">
<a href="http://loris.ca/" target="_blank"><img src="images/loris-new-white.png"></a>
<p><small> “..is a modular and <font color="f27c30">extensible</font> web-based data and project management software that integrates all aspects of a <font color="f27c30">multi-center</font> neuroimaging research study. It is an <font color="f27c30">OPEN SOURCE</font> framework and database suitable for managing <font color="f27c30">large datasets</font>.”</small></p>
</td>
<td>
<a href="https://www.frontiersin.org/articles/10.3389/fninf.2011.00037/full" target="_blank"><img src="images/LORIS_paper.png"></a>
</td>
</tr>
</table>
</section>
<section>
<h2>What is LORIS?</h2>
<br><table class = "reveal" style="padding:0; margin:0" width="50%">
<tr>
<td width="30%" style="vertical-align:middle">
<h4 align="center"><font color="f27c30">Heterogenous data acquisition</font></h4>
</td>
<td width = "30%" style = "vertical-align:middle">
<center><img width="50%" src="images/right-arrow.png" style="background-color:#222222; border:0;"></center>
</td>
<td width = "30%" style="vertical-align:middle">
<h4 align="center"><font color="f27c30">Storage, processing & dissemination</font></h4>
</td>
</tr>
</table>
<img src="images/loris_versatility.png" align="center" style="border:0; margin-top:80px;">
</section>
<section data-background="images/LORIS_global_2.jpg">
<h1 style="margin: 275px 0px 0px 0px;"><font color ="0d4983">LORIS Globally</font></h1>
</section>
<!-- WHAT DOES LORIS DO? -->
<section>
<h2>What does LORIS do?</h2>
<img src="images/LORIS_functionality.png">
</section>
<!-- PERFERRED SLIDE WHAT DOES LORIS DO -->
<section>
<h2>What does LORIS do?</h2>
<img src="images/loris_purpose.jpg" style="border:0" width="75%">
</section>
<!-- LORIS Key features -->
<section data-background="images/loris_features.jpg">
</section>
<section>
<h2>Extensible and modular design</h2>
<table class="reveal" style="margin:-20px 0px -20px 0px;">
<tr>
<td width="50%" style="vertical-align: top">
<img src="images/Dashboard.png">
</td>
<td width="50%" style="vertical-align: middle">
<img src="images/BrainBrowser_VolumeViewer.png">
</td>
</tr>
</table>
<img src="images/Imaging_scans.png" width="57%">
</section>
<!-- WHAT DOES LORIS ACTUALLY DO -->
<section>
<h2>What does LORIS actually do?</font></h2>
<table class="reveal">
<tr>
<td width="40%" style="vertical-align:middle">
<h4 align="center"><font color="f27c30">DATA ENTRY<br>DATA MANAGEMENT<br>DATA VISUALISATION<br>DATA QUERYING<br></font></h4>
<span class="fragment"><h3 align="center"><a href="https://demo.loris.ca" target="_blank">TRY ME!</a></h3></span>
</td>
<td width="60%" style="vertical-align:middle">
<img src="images/loris_arch.png" style="padding:0; margin:0;">
</td>
</tr>
</table>
</section>
<!-- HETEROGENOUS DATA-->
<section data-background="images/Statistics_behavioural.png">
<h2 style="margin: -90px 0px 120px 0px;"><font color="222222">Heterogenous Data</font></h2>
<span class="fragment"><div style="background-color:white; border-radius: 10px;">
<p style="margin:100px 0px 0px 0px;"><font color="f27c30">Candidate Profile, Instrument Builder, Feedback Module, Double Data Entry, Conflict Resolver</font></p>
</div></span>
</section>
<!-- IMAGING DATA -->
<section data-background="images/Imaging_scans_lego.png">
<h2 style="margin:-55px 0px 70px 0px;"><font color="222222">Imaging Data</font></h2>
<span class="fragment"><div style="background-color:white; border-radius:10px;">
<p align="center" style="margin:0; padding: 0px 0px 0px 0px;"><font color="f27c30">1. Acquisition & Storage</font></p>
<p align="center" style="margin:0; padding:0;"><font color="f27c30">2. Visualisation: <font color="12a3d8">Imaging Browser, BrainBrowser</font></font></p>
<p align="center" style="margin:0; padding:0px 0px 5px 0px;"><font color="f27c30">3. Quality Control:<font color="12a3d8"> Radiological Review Module, DCC MRI</font></font></p>
</div></span>
</section
<!-- DQT & Sharing -->
<section data-background="images/Statistics_imaging_new.png" data-background-size="100%">
<h2 style="margin:-150px 0px 200px 0px;"><font color="222222">Data Querying</font></h2>
<span class="fragment"><div align="left" style="margin:0px 200px 0px -50px; padding:0;">
<ul><font color="f27c30">
<p align="center" style="margin:0; padding: 20px 0px 0px 0px;"><li>Imaging Statistiscs</li></p>
<p align="center" style="margin-bottom:-40px; padding: 0px 0px 20px 0px;"><li>Data Querying Tool <font color="12a3d8">(DQT)</font></li></p></font></ul></div>
</span>
</section>
<section data-background="images/DQT_Define_new.png" data-background-size="100%">
<h2><font color="0f4078">Cross-Modal Querying</font></h2>
</section>
<section data-background="images/DQT_Results_new.png" data-background-size="100%">
<h2><font color="0f4078">Real-Time Query Results</font></h2>
</section>
<section data-background="images/DQT_Stats_new.png" data-background-size="100%">
<h2><font color="0f4078">Statistical Analysis</font></h2>
</section>
<section data-background="images/Genomics_CNV.png" data-background-size="100%">
<h2 style="margin: -125px 0px 0px 0px;"><font color="0f4078">Genomics Browser</font></h2>
</section>
<!--WORKFLOW OF Methylation DATA-->
<section data-background="images/methylation_data.png" data-background-size="65%">
</section>
</section>
<!--CBRAIN-->
<section>
<section>
<a href="CBRAIN_indepth.html#/2" target="_blank"><h2>WHAT IS CBRAIN?</h2></a>
<table class="reveal">
<tr>
<td width="50%" style="vertical-align: middle;">
<a href="https://mcin-cnim.ca/technology/cbrain/" target="_blank"><img align="center" src="images/cbrain-blue.png" style="border:0; border-radius:30px;" width="90%"></a>
<p><small><br>“..is an <font color="12a3d8">OPEN SOURCE</font> web-based collaborative <font color="12a3d8">High-Performance Computing (HPC)</font> platform for <font color="12a3d8">neuroimaging research</font>, connecting researchers to the <font color="12a3d8">tools</font> required to handle <font color="12a3d8">large datasets</font>.”</small></p>
</td>
<td width="50%" style="vertical-align: middle">
<a href="https://www.frontiersin.org/articles/10.3389/fninf.2014.00054/full" target="_blank"><img src="images/CBRAIN_paper.png" width="90%"></a>
</td>
</tr>
</table>
</section>
<!-- What does CBRAIN do? -->
<section data-background="images/distributed_execution_2.jpg">
<h2 style="background-color:white;border-radius:15px;margin:-70px 100px 50px 100px"><font color="12a3d8">What does CBRAIN do?</font></h2>
<span class="fragment"><p style="background-color:white; margin: 0px 30px -1000px 30px; border-radius:15px;"><b><font color="f27c30">..enables distributed execution of software pipelines</font></b></p></span>
</section>
<section data-background="images/cbrain_uniview.png">
<p style="background-color:white; padding:0; border-radius:15px;margin:-20px -50px 0px -50px;"><b><font color="12a3d8">..aggregates multiple distributed file systems into uniform view</font></b></p>
</section>
<!--CBRAIN SCHEMA-->
<section data-background="images/CBRAIN_arch.png" data-background-size="65%">
</section>
<!-- WHO USES CBRAIN?-->
<section data-background="images/CBRAIN_distribution.png" data-background-size="65%">
<span class="fragment"><h2><font color="12a3d8">NOW</font></h2></span>
<p><font color="0d4983"><span class="fragment">611 users (199 international)<br>191 sites<br>29 countries</span>
</font></p>
</section>
<!--CBRAIN Computing Resources-->
<section data-background="images/CBRAIN_hours.png" data-background-size="75%">
<span class="fragment"><h2 style="margin-top:-120px;"><font color="222222">CBRAIN Computing Resources</font></h2></span>
<p align="center" style="margin: 260px 350px 0px 0px;"><font color="12a3d8"><span class="fragment">51 tools, 1M+ files<br>6 Compute Canada clusters<br>24M CPU core hours</span></font></p>
</section>
<!--CBRAIN portal-->
<section data-transition="convex">
<h2>CBRAIN portal</h2>
<a href="https://portal.cbrain.mcgill.ca/login" target="_blank"><img src="images/CBRAIN_mainpage.png"></a>
<a href="https://portal.cbrain.mcgill.ca/login" target="_blank"><h4><font color="12a3d8">TRY ME!</font></h4></a>
</section>
<!-- CBRAIN TASKS-->
<section data-background="images/CBRAIN_tasks.png" data-background-size="85%">
</section>
<!-- CIVET (and NIAK?) -->
<section data-background="images/CIVET_processing_steps.png" data-background-size="70%">
<a href="http://www.bic.mni.mcgill.ca/ServicesSoftware/CIVET" target="_blank"><img src="images/CIVET_logo.png" align="right" width="15%"></a>
</section>
<section data-background="images/Boutiques_web.png" data-background-size="80%">
</section>
<section>
<h2>CARMIN</h2>
<p>Common API for Research Medical Imaging Network</p>
<p><small>A common web API for remote pipeline execution</small></p>
</section>
<section data-background="images/NIAK.jpg">
<h2 style="margin: -380px 0px 200px 0px "><font color="222222">NIAK</font></h2>
<a href="http://niak.simexp-lab.org/" target="_blank"><p style="margin:135px 0px 0px 0px;">http://niak.simexp-lab.org/</p></a>
</section>
</section>
<!--Visualization-->
<section data-transition="convex">
<section>
<h2>From Data</h2>
<h2>To</h2>
<h1>Visualization</h1>
</section>
</section>
<!--BrainBrowser-->
<section data-transition="convex">
<section>
<a href = "Brain_browser.html" target="_blank"><h2>BrainBrowser</h2></a>
<p>..a set of web-based <font color="f27c30"><b>3D visualization tools</b></font> primarily used for viewing <font color="12a3d8">neurological data</font> i.e. <font color="12a3d8">MRI scans</font>.</p>
<p><small>It allows for real-time <font color="f27c30">manipulation</font> and <font color="f27c30">analysis</font> of 3D neuroimaging data through any modern web browser. <a href = "https://brainbrowser.cbrain.mcgill.ca/" target="_blank">TRY ME!</a></small></p>
<!--<table class = "reveal">
<tr>
<td width="40%" vertical-align:middle">
<img src="images/BrainBrowser_VolumeViewer.png">
</td>
<td width="60%" vertical-align:middle">
<img src="images/BrainBrowser_SurfaceViewer.png">
</td>
</tr>
</table>-->
<img src="images/Brain_browser_sample.png">
</section>
<!--Surface Viewer-->
<section data-background="images/surface_viewer.png" data-background-size="100%">
</section>
<!-- MACACC Dataset -->
<section data-background="images/MACACC_dataset.png" data-background-size="100%">
</section>
<!--Volume Viewer-->
<section data-background="images/volume_viewer_2.png" data-background-size="100%">
</section>
<section data-background="images/BrainBrowser_VolumeViewer.png" data-background-size="80%">
<h3 style="margin:-270px 0px 0px 0px;"><font color="white">Volume Viewer on LORIS</font></h3>
</section>
</section>
<!-- BIG BRAIN -->
<section data-transition="convex">
<section>
<table class="reveal">
<a href="Big_brain.html#/2" target="_blank"><h2><font color="2bfcf8">BigBrain</h2></font></a>
<tr>
<td width="50%" style="vertical-align: middle">
<p align="center"><small>The <font color="2bfcf8">BigBrain</font> is the digitized reconstruction of <font color="f27c30">7404 hi-res</font> coronal histological sections (20 microns isotropic).</small></p>
<p align="center"><small>It is the brain of a <font color="2bfcf8">65 year-old man</font> with <font color="f27c30">no neurological or psychiatric diseases</font> in clinical records at time of death.</small></p>
<div align="center"><img src="images/BigBrain.png" width="73%" style="border:0;"></div>
</td>
<td width="50%" style="vertical-align: middle">
<a href="http://science.sciencemag.org/content/340/6139/1472" target="_blank"><img src="images/BigBrain_paper.png"></a>
</td>
</tr>
</table>
</section>
<section data-background-video="images/Bigbrain_low.mp4" data-background-color="#000000">
<p class="fragment current-visible"><font size="9" color="blue">BigBrain - high resolution reference brain</font></p>
<p class="fragment current-visible"><font size="9" color="blue">Multimodal integration into an anatomically realistic standard space</font></p>
<p class="fragment current-visible"><font size="9" color="blue">Years of development</font></p>
<p class="fragment current-visible"><font size="9" color="blue">20 micron resolution</font></p>
<p class="fragment current-visible"><font size="9" color="blue">7404 histological slices</font></p>
<p class="fragment current-visible"><font size="9" color="blue">1 Terabyte dataset</font></p>
<p class="fragment current-visible"><font size="9" color="blue"><a href="https://bigbrain.humanbrainproject.org/#!{'layers':{' grey value: ':{'type':'image'_'source':'precomputed://https://neuroglancer.humanbrainproject.org/precomputed/BigBrainRelease.2015/8bit'_'transform':[[1_0_0_-70666600]_[0_1_0_-70000000]_[0_0_1_-58777700]_[0_0_0_1]]}_' tissue type: ':{'type':'segmentation'_'source':'precomputed://https://neuroglancer.humanbrainproject.org/precomputed/BigBrainRelease.2015/classif'_'selectedAlpha':0_'segments':['0'_'100']_'transform':[[1_0_0_-70666600]_[0_1_0_-72910000]_[0_0_1_-58777700]_[0_0_0_1]]}}_'navigation':{'pose':{'position':{'voxelSize':[21166.666015625_20000_21166.666015625]_'voxelCoordinates':[-3338.57958984375_856.3231811523438_-853.1627807617188]}}_'zoomFactor':1400706.647149517}_'perspectiveOrientation':[0.3140767216682434_-0.7418519854545593_0.4988985061645508_-0.3195493221282959]_'perspectiveZoom':1922235.5293810747}" target="_blank"><font color="f27c30"><small>Click to launch the Neuroglancer Viewer!</small></font></a></font></p>
</section>
<section>
<h2>What is BigBrain?</h2>
<p>The <font color="12a3d8">BigBrain dataset</font> is the result of a collaborative effort between the teams of Dr. Katrin Amunts and Dr. Karl Zilles <font color="f27c30">(Forschungszentrum Jülich)</font>, and Dr. Alan Evans <font color="12a3d8">(Montreal Neurological Institute)</font></p>
<p class="fragment"><font size="9" color="12a3d8">Available freely at <a href="https://bigbrain.loris.ca/main.php" target="_blank"><font color="f27c30">https://bigbrain.loris.ca</font></a></font></p>
</section>
<section>
<h2>Visualization with Atelier 3D</h2>
<iframe width="640" height="360" data-src="https://www.youtube.com/embed/W2bmnhLV6R8" frameborder="0" gesture="media" allow="encrypted-media" allowfullscreen></iframe>
</section>
</section>
<!--PIVT-->
<section data-transition="convex">
<section>
<h2>PIVT (New)</h2>
<span class="fragment"><p>Display</p>
<p>Moving Neurogimaging to the web</p>
<p>Easy integration into <font color="12a3d8">CBRAIN</font> and <font color="f27c30">LORIS</font></p>
<p>Pixpipe</p>
<p>Big Brain and Neuroglancer</p>
<p>Feedback</p></span>
</section>
<section>
<img src="images/PIVT_1.png" width="65%" style="border:0">
</section>
</section>
<!-- STUDIES -->
<section>
<section data-transition="convex">
<a href="https://pediatricmri.nih.gov/nihpd/info/publications.html" target="_blank"><img src="images/NIHPD_logo.jpg"></a>
<table class="reveal">
<tr>
<td width="45%" style="vertical-align: middle">
<a href="http://www.sciencedirect.com/science/article/pii/S105381190500710X?via%3Dihub" target="_blank"><img src="images/NIHPD_paper.png"></a>
</td>
<td width="30%" style="vertical-align: middle">
<img src="images/MRI_images_several.jpg">
</td>
<td width="30%" style="vertical-align: middle">
<p><small>
<ul>
<li>8 year study</li>
<li>Longitudinal data</li>
<li>532 subjects</li>
<li>8000 distinct variables</li>
<li>37000 individual assessments</li>
<li>T1, T2, PD, DTI</li>
<li>Spectroscopy</li>
<li>∼3TB of imaging data</li>
<li>2000 MRI acquisitions</li>
</ul>
</small></p>
</td>
</tr>
</table>
</section>
<section data-transition="convex">
<a href="http://www.ibis-network.org/" target="_blank"><img src="images/IBIS.png"></a>
<table class="reveal">
<tr>
<td width="45%" style="vertical-align: middle">
<a href="https://ajp.psychiatryonline.org/doi/abs/10.1176/appi.ajp.2011.11091447?url_ver=Z39.88-2003&rfr_id=ori%3Arid%3Acrossref.org&rfr_dat=cr_pub%3Dpubmed" target="_blank"><img src="images/IBIS_paper.png"></a>
</td>
<td width="30%" style="vertical-align: middle">
<img src="images/IBIS_image.png">
</td>
<td width="30%" style="vertical-align: middle">
<p><small>
<ul>
<li>Infant brain development in autism</li>
<li>3000+ scans</li>
<li>700+ subjects</li>
<li>7000 distinct variables</li>
<li>150,000+ individual assessments</li>
<li>T1, T2, DTI, BOLD</li>
<li>∼5 TBs of imaging data</li>
<li>Genetic/biospecimen data</li>
</ul>
</small></p>
</td>
</tr></table>
</section>
<!--CCNA-->
<section data-transition="convex">
<a href="http://ccna-ccnv.ca/en/" target="_blank"><img src="images/CCNA.png" width="85%"></a>
</section>
<!-- QPN -->
<section data-transition="convex">
<h2>Quebec Parkinson Network</h2>
<a href="http://rpq-qpn.ca/en/" target="_blank"><img src="images/QPN.png" width="90%"></a>
</section>
<!-- OMEGA - small pilot, interest has spiked -->
<section data-transition="convex">
<table class="reveal">
<h2><a href="https://omega.bic.mni.mcgill.ca">OMEGA</a></h2>
<tr>
<td width="65%" style="vertical-align: middle">
<a href="http://www.sciencedirect.com/science/article/pii/S1053811915003183" target="_blank"><img src="images/OMEGA.png"></a>
</td>
<td width="35%" style="vertical-align: middle">
<p><small>
<ul>
<li><a href="https://www.mcgill.ca/bic/resources/omega" target="_blank">Open MEG Archive</a></li><br>
<li>First open MEG repository</li><br>
<li>180 user accounts created</li><br>
<li>Associated structural data</li><br>
<li>500+ reads on academia.edu</li><br>
</ul>
</small></p>
</td>
</tr>
</table>
</section>
<!-- ADNI -->
<section data-transition="zoom">
<h2>ADNI</h2>
<table class="reveal">
<tr>
<td style="vertical-align: middle">
<img src="images/ADNI_paper.png">
</td>
<td style="vertical-align: top">
<p>
<ul>
<li>Cited 343 times</li><br>
<li>Data-use agreements</li><br>
<li>Used for countless analyses</li><br>
<li>Restrictive</li><br>
</ul>
</p>
</td>
</tr>
</table>
</section>
<!-- ABIDE -->
<section data-transition="convex">
<a href="http://preprocessed-connectomes-project.org/abide/" target="_blank"><img src="images/ABIDE_preprocessed.png"></a>
</section>
<!-- Human Brain Project-->
<section data-transition="zoom">
<a href="https://www.humanbrainproject.eu/en/" target="_blank"><img src="images/HBP.png" width="90%"></a>
</section>
</section>
<!-- HEALTHY BRAINS FOR HEALTHY LIVES HBHL -->
<section>
<section>
<a href="HBHL.html" target="_blank"><h2>Healthy Brains for Healthy Lives (HBHL)</h2></a>
<p><small>An interdisciplinary program at McGill University leveraging <font color="#87CEEB">neuroinformatic technologies</font> to <font color="#87CEEB">transform terminal or life-long afflications</font> to treatable or even curable conditions</font></small></p>
<a href="http://www.mcgill.ca/hbhl/home"><img src = "images/HBHL.png"></a>
</section>
<!-- Big Data Curve-->
<section data-transition="zoom">
<img src="images/Big_data.png">
</section>
<!-- Types of data-->
<section data-transition="zoom">
<img src="images/Neuroinformatics_scope.jpg" width="75%">
</section>
<!-- Cross Modal Data-->
<section data-transition="zoom">
<img src="images/Cross_modal.png" width="90%">
</section>
</section>
<!--DATA SHARING-->
<section>
<!--Data sharing including data publishing-->
<section data-background="images/Data_sharing_cartoon.png">
<a href="Data_sharing.html" target="_blank"><h2><font color="black">What is Data Sharing?</font></h2></a>
<p class="fragment roll-in"><font color="purple">Exchange of information</font></p>
<p class="fragment roll-in"><font color="black">Datasets</font></p>
<p class="fragment roll-in"><font color="black">Tools</font></p>
<p class="fragment roll-in"><font color="black">Standardization</font></p>
<p class="fragment roll-in"><font color="black">Databases</font></p>
<p class="fragment roll-in"><font color="black">Collaborations</font></p>
<p class="fragment roll-in"><font color="black">Conferences, Hackathons</font></p>
<p class="fragment roll-in"><font color="black">Facebook, Google, Twitter, etc.</font></p>
<br>
<p><font size="1" color="black">Image source: http://blog.veritythink.com/post/87880448269/creative-data-sharing-and-open-humanitarianism</font></p>
</section>
<!-- Why is Data Sharing Important? -->
<section data-transition="concave">
<h2>Data Sharing Issues</h2>
<table>
<thead>
<tr>
<th><font color="yellow">Benefits </font></th>
<th><font color="yellow">Hurdles </font></th>
</tr>
</thead>
<tbody>
<tr>
<td>More citations</td>
<td>Fear</td>
</tr>
<tr>
<td>Reduces waste/duplication</td>
<td>Technical challenges</td>
</tr>
<tr>
<td>Increased exposure</td>
<td>Privacy concerns</td>
</tr>
<tr>
<td>Access to larger datasets</td>
<td>Data Harmonization</td>
</tr>
<tr>
<td>Access to rare data</td>
<td>Interoperability</td>
</tr>
<tr>
<td>Less attrition</td>
<td>Reproducibility</td>
</tr>
<tr>
<td>Increased validation</td>
<td>Obtaining ethics</td>
</tr>
<tr>
<td>Saving Tax $$/more funding</td>
<td>Public dataset not identical</td>
</tr>
</tbody>
</table>
</section>
<!--Global Data Sharing Initiatives-->
<section data-transition="convex">
<h2>Global Data Sharing Initiatives</h2>
<table class="reveal">
<tr>
<td style="vertical-align:middle">
<small style="margin:0; padding:0;"><a href="http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=1" target="_blank">Committee on Best Practices in Data Analysis and Sharing (COBIDAS)</a></small>
</td>
<td width="20%" style="vertical-align:middle">
<img src="images/nature_neuro.jpg" style="border:0; margin:0; padding:0;">
</td>
</tr>
</table>
<table class="reveal">
<tr>
<td width="52%" style="vertical-align:middle">
<a href="http://www.humanbrainmapping.org/files/2016/COBIDASreport.pdf" target="_blank"><img src="images/COBIDAS.png"></a>
</td>
<td width="48%" style="vertical-align:middle">
<a href="https://www.nature.com/articles/nn.4500" target="_blank"><img src="images/COBIDAS_Nature.png"></a>
</td>
</tr>
</table>
</section>
<!--Interoperability-->
<section data-background="images/Interoperability.jpg" data-background-size="65%">
<!--<h2>Interoperability</h2>
<img src="images/Interoperability.jpg" width="80%" style="border:0;">-->
</section>
<!--Collaboration with other groups -->
<section data-transition="slide">
<h2>Collaboration with global data sharing groups</h2>
<p>
<span class="fragment"><a href="https://www.incf.org" target="_blank">INCF, </a></span>
<span class="fragment"><a href="https://osf.io" target="_blank">Open Science Framework, </a></span>
<span class="fragment"><a href="https://www.nitrc.org" target="_blank">NITRC, </a></span>
<span class="fragment"><a href="http://alleninstitute.org" target="_blank">Allen Institute, </a></span>
<span class="fragment"><a href="https://ndar.nih.gov" target="_blank">NDAR, </a></span>
<span class="fragment"><a href="https://openfmri.org" target="_blank">HAWG (Atlas Building Group), </a></span>
<span class="fragment"><a href="http://www.humanbrainmapping.org" target="_blank">Organization Human Brain Mapping, </a></span>
<span class="fragment"><a href="https://www.humanbrainproject.eu" target="_blank">Human Brain Project, </a></span>
<span class="fragment"><a href="https://www.computecanada.ca" target="_blank">Compute Canada, </a></span>
<span class="fragment"><a href="https://www.maelstrom-research.org" target="_blank">Maelstrom, </a></span>
<span class="fragment"><a href="" target="_blank">Edinburgh BRAINS ImageBank, </a></span>
<span class="fragment"><a href="http://coins.mrn.org" target="_blank">COINS, </a></span>
<span class="fragment"><a href="http://www.xnat.org" target="_blank">XNAT, </a></span>
<span class="fragment"><a href="http://www.creatis.insa-lyon.fr/vip/" target="_blank">VIP, </a></span>
<span class="fragment"><a href="https://www.braincode.ca" target="_blank">BrainCode, </a></span>
<span class="fragment"><a href="http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/" target="_blank">BIDS, </a></span>
<span class="fragment"><a href="http://www.cima-q.ca" target="_blank">NIDM, </a></span>
<span class="fragment"><a href="http://www.neurodevnet.ca" target="_blank">NeuroDevNet, </a></span>
<span class="fragment"><a href="http://gusto.sg/v2/index.php" target="_blank">GUSTO, </a></span>
<span class="fragment"><a href="http://rpq-qpn.ca/en/" target="_blank">QPN, </a></span>
<span class="fragment"><a href="http://www.neurobureau.org" target="_blank">Boutiques, </a></span>
<span class="fragment"><a href="http://www.neurobureau.org" target="_blank">VIP </a></span>
</p>
</section>
<!-- Hackathons -->
<section data-transition="fade">
<table class="reveal">
<h2>Hackathons</h2>
<tr>
<td width="75%" style="vertical-align: middle">
<img src="images/C-BASE.png">
</td>
<td width="25%" style="vertical-align: middle">
<p> Important value of hackathons to data sharing initiatives</p>
<a href="http://www.brainhack.org/" target="_blank"><img src="images/Brainhack.png"></a>
</td>
</tr>
</table>
</section>
<!-- HACKATHON ACCOMPLISHMENTS
<section>
<h2>Hackathon Accomplishments</h2>
<ul>
<li>Automated <font color="f27c30">PET recognition</font> module</li>
<li>Enhanced <font color="12a3d8">DICOM</font> <font color="f27c30">anonymization</font> - making use of PYDICOM</li>
<li>Installed one and half instances of <font color="12a3d8">LORIS</font></li>
<li>Built bridges between various development groups</li>
<li>I got smarter</li>
</ul>
</section> -->
</section>
<!--Open Science-->
<section>
<section data-transition="convex">
<a href="Open_Science.html#/openscience-destination" target="_blank"><h2>Open Science</h2></a>
<table class="reveal">
<tr>
<td width="50%" style="vertical-align: middle">
<a href="http://www.sciencemag.org/news/2016/01/montreal-institute-going-open-accelerate-science" target="_blank"><img src="images/Open_science.png"></a>
</td>
<td width = "50%" style="vertical-align:middle">
<img width="85%" src="images/Nature_open_science.png">
</td>
</tr>
</table>
</section>
<section>
<img src="images/TOSI.png">
</section>
<section>
<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5216036/" target="_blank"><img src="images/Open_science_paper.png"></a>
</section>
<!--Cyberinfrastructure & Cybersecurity -->
<section>
<h2>Cyberinfrastructure</h2>
<img src="images/Cyberinfrastructure.png">
</section>
<section>
<h2>Cybersecurity</h2>
<img src="images/Cybersecurity.png" width="80%">
</section>
<section data-transition="concave">
<h2>Open Science Functionality</h2>
<table>
<thead>
<tr>
<th><font color="yellow">Acquisition & Storage</font></th>
<th><font color="yellow">Dissemination & Analysis</font></th>
</tr>
</thead>
<tbody>
<tr>
<td><small>Organized/Accessible data</small></td>
<td><small>Centralized repository</small></td>
</tr>
<tr>
<td><small>Long term storage</small></td>
<td><small>Provenance Capture</small></td>
</tr>
<tr>
<td><small>Quality Control mechanisms</small></td>
<td><small>API for interoperability</small></td>
</tr>
<tr>
<td><small>Web visualization</small></td>
<td><small>Consent is factored in</small></td>
</tr>
<tr>
<td><small>Tablet/Mobile Friendly</small></td>
<td><small>User account access control</small></td>
</tr>
<tr>
<td><small>Anonymized automatically</small></td>
<td><small>Completely de-identified</small></td>
</tr>
<tr>
<td><small>Cross-modal linking</small></td>
<td><small>Cross-study correlation</small></td>
</tr>
<tr>
<td><small>Online Data Querying</small></td>
<td><small>Access to high performance computing</small></td>
</tr>
</tbody>
</table>
</section>
<section data-transition="concave">
<h2><a href="https://biobank.bic.mni.mcgill.ca" target="_blank">LORIS Biobank instance</a></h2>
<img src="images/Biobank_LORIS.png">
</section>
<section data-transition="concave">
<h2><a href="https://imaging.bic.mni.mcgill.ca" target="_blank">LORIS Imaging instance</a></h2>
<img src="images/BIC_LORIS.png">
</section>
<!--Functionality that the Open Science initiative will provide-->
<section data-transition="concave">
<h2>Benefits of Open Science</h2>
<table>
<tbody>
<tr>
<td><small>Organized/Accessible data</small></td>
<td><small>Greater exposure</small></td>
</tr>
<tr>
<td><small>More collaborations</small></td>
<td><small>Data validation</small></td>
</tr>
<tr>
<td><small>Access to Quality Control results</small></td>
<td><small>Access to larger datasets</small></td>
</tr>
<tr>
<td><small>More citations</small></td>
<td><small>Greater funding</small></td>
</tr>
<tr>
<td><small>Cross-modal linking</small></td>
<td><small>Cross-study correlation</small></td>
</tr>
<tr>
<td><small>More robust findings</small></td>
<td><small>Greater reproducibility</small></td>
</tr>
</tbody>
</table>
</section>
</section>
<!-- RESULTS & HISTORY -->
<section>
<section data-background="images/MRI_images_several.jpg">
<h2 style="margin:-80px 0px 100px 0px"><font color="f27c30">MNI History</font></h2>
<span class="fragment"><p style="background-color:black; border-radius:15px;"><font color="12a3d8">1999: MNI ecosystem implemented for NIH multisite MRI Study of Normal Brain Development</font></p></span>
</section>
<section data-background="images/LORIS_numbers.png">
<h2 style="padding-top:0px; margin-top:0px;"><font color="black">2015</font></h2>
<p><font color="222222">
<span class="fragment"><font color="f27c30">LORIS:</font> 130 sites worldwide, 30,000+ data collection time points, 500+ behavioral instruments, 30+ TBs imaging datasets, 200,000 acquisitions</span>
</font></p>
<p><font color="222222">
<span class="fragment"><font color="12a3d9">CBRAIN:</font> 300+ users, 60 cities, 20 countries,<br>diverse projects: <font color="12a3d8">Prevent AD, K-ADNI, MAVAN, NeuroDevNet, </font>130 virtual sites, 600+ TBs storage grid across 25 servers! </span>
</font></p>
</section>
<!--National Infrastructure-->
<section data-transition="convex">
<h2>National Network</h2>
<table class="reveal">
<tr>
<td width="50%" style="vertical-align: middle">
<img src="images/Networks.png">
</td>
<td>
<img src="images/Open_science_national.png">
</td>
</tr>
</table>
<p>Including "Data Publishing"</p>
</section>
<!--International-->
<section>
<img src="images/International.png">
</section>
</section>
<!-- FUTURE DIRECTION -->
<section>
<h2>Future Direction</h2>
<p><ul>
<span class = "fragment"><li>Phase 2 <font color="f27c30">LORIS</font>/<font color="12a3d8">CBRAIN</font> connectivity</li></span>
<span class = "fragment"><li>Enhanced API</li></span>
<span class = "fragment"><li>Additional modalities (eg. MEG/EEG)</li></span>
<span class = "fragment"><li>Institutional requirements</li></span>
<span class = "fragment"><li>Enhanced visualization</li></span>
<span class = "fragment"><li>Numerous new modules</li></span>
<span class = "fragment"><li><font color="2492bc">Biobanking</font> Tracking</li></span>
<span class = "fragment"><li><font color="12a3d8"><b>Interoperability!</b></font></li></span>
<span class = "fragment"><li>Pipeline reproducibility</li></span>
<span class = "fragment"><li>Cloud technology</li></span>
<span class = "fragment"><li>Flexibility in <b><font color="f27c30">storage</font></b>, </span><span class = "fragment"><b><font color="f27c30">sharing</font></b>, </span><span class = "fragment">and remote <b><font color="f27c30">processing</font></b>!</span></li>
</ul></p>
</section>
<!--Acknowledgements-->
<section>
<section data-transition="slide" data-background="#87CEEB" data-background-transition="zoom">
<table class="reveal">
<tr>
<td width="70%" style="vertical-align: top">
<img src="images/loris_team_2017.jpg" width="85%">
</td>
<td width="30%" style="vertical-align: middle">
<p>Thank you!<small><font color="blue" size="4">Acknowledgements:</font><font color="black" size="2"> Alan Evans, Alex Zijdenbos, Dario Vins, Jonathan Harlap, Matt Charlet, Andrew Corderey, Sebastian Muehlboeck, Reza Adalat, Louis Collins, Vladimir Fonov, Marc Rousseau, Mia Petkova, Rathi Gnanasekaran, David Brownlee, Tarek Sherif, Pierre Rioux, Nic Kassis, Leigh MacIntyre, Claude Lepage, Ilana Leppert, Natasha Beck, Tristan Glatard, Bert Vincent, Lindsay Lewis, Najma Mahani, Elodie Portales-Casamar, Alden Woodward, Sylvain Milot, Jean Francois Malouin, Sylvain Baillet, Daniel Kroetz, Martin Weiss, Mathieu Desrosier, Jason Karamchandani, Amit Bar-Or, Ted Fon, John Brietner, Derek Lo, Patrick Bermudez, Chris Steele, Pamela Patterson and one of my favourites: Pierre Bellec!</font></small></p>
<p><font color="blue" size="4">LORIS team on left</font></p>
</td>
</tr>
</table>
</section>
</section>
</div>
</div>
<script src="lib/js/head.min.js"></script>