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Author

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1		-XWiki.paulapopa
	1	+XWiki.reginafilange

Content

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1	1	Source code: [[https:~~/~~/github.com/the-virtual-brain/tvb-widgets>>https://github.com/the-virtual-brain/tvb-widgets]]
2	2
3		-Immediate testing: [[https:~~/~~/lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/TVB%20Widgets/REPO/tvb-widgets/notebooks/HeadWidget.ipynb>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/TVB%20Widgets/REPO/tvb-widgets/notebooks/HeadWidget.ipynb]]
	3	+This is part of a Pypi release: [[https:~~/~~/pypi.org/project/tvb-widgets/>>https://pypi.org/project/tvb-widgets/]]
4	4
	5	+//**tvb-widgets**// is also already installed in the official image released for EBRAINS lab, where you can test it directly.
	6	+
5	5	== Purpose ==
6	6
7	7	It is a Jupyter widget intended for visualization of the 3D Head data available for a patient:
8	8
9	9	* surfaces of different types (cortex, face, skull, etc)
10		-* connectivity region centers
	12	+* connectivity region centers and edges
11	11	* sensors locations (SEEG, MEG, EEG)
12	12
	15	+On cortical surfaces, it can also display region parcellation.
	16	+
13	13	== Inputs ==
14	14
15	15	It supports the above data in the form of their corresponding TVB datatypes:
16	16
17	17	* Surface (CorticalSurface, FaceSurface, etc)
	22	+* Parcellation (RegionMapping)
18	18	* Connectivity
19	19	* Sensors (SensorsInternal, SensorsMEG, SensorsEEG)
20	20
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43	43	1. Use a file browser to load the data and automatically display it
44	44	1. Use directly the API to load the data and display it
45	45
46		-
47	47	For the first option, you have to run the following 2 lines of code in a notebook cell and then just use the UI controls:
48	48
49	49	(% class="box" %)
...	...	@@ -52,7 +52,11 @@
52	52	display(widget)
53	53	)))
54	54
	59	+{{html}}
	60	+<iframe width="840" height="480" src="https://www.youtube.com/embed/BCCh-wdcnVo" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
	61	+{{/html}}
55	55
	63	+
56	56	For the second option, the API is described below:
57	57
58	58	In a new cell, we instantiate the **HeadWidget** and a **FaceSurface** datatype that we want to visualize. Using the //**add_datatype**// method we add the surface to our widget and __display__ the widget:
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70	70	)))
71	71
72	72	{{html}}
73		-<iframe src="https://drive.google.com/file/d/1Egp9Lk-HGMATc9em6Kw_jSHmybTD2vzM/preview" width="840" height="480" allow="autoplay"></iframe>
	81	+<iframe width="840" height="480" src="https://www.youtube.com/embed/8bmjKp3BYFA" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
74	74	{{/html}}
75	75
76		-Next, we can continue adding other datatypes to this widget, by calling //**add_datatype**// multiple times. A maximum of 10 datatypes are supported by this widget.
	84	+Next, we can continue adding other datatypes to this widget, by calling //**add_datatype**// multiple times.
77	77
78		-The **Config** object can be used to tweak the display options for each datatype.
79		-
80	80	In the code below, we add a **Connectivity** and SEEG **Sensors:**
81	81
82	82	(% class="box" %)
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92	92
93	93	seeg.configure()
94	94
95		-widget.add_datatype(seeg, api.HeadWidgetConfig(name='SEEG'))
	101	+widget.add_datatype(seeg)
96	96	)))
97	97
98	98	{{html}}
99		-<iframe src="https://drive.google.com/file/d/1RLwts75Hh31LoPdWLK7QOM61KIsOabF1/preview" width="840" height="480" allow="autoplay"></iframe>
	105	+<iframe width="840" height="480" src="https://www.youtube.com/embed/6UQhL9gd1HM" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
100	100	{{/html}}
101	101
102		-We can also provide a **RegionMapping** to be used as colormap for a surface:
	108	+We can also provide a **RegionMapping** to be used as parcellation for a surface:
103	103
104	104	(% class="box" %)
105	105	(((
106	106	reg_map = region_mapping.RegionMapping.from_file()
107	107
108		-config = api.HeadWidgetConfig(name='Cortex')
109	109
110		-config.add_region_mapping_as_cmap(reg_map)
111		-
112		-
113	113	cortex = surfaces.CorticalSurface().from_file()
114	114
115	115	cortex.configure()
116	116
117	117
118		-widget = api.HeadWidget()
	120	+widget.add_datatype(cortex, reg_map)
119	119
120		-widget.add_datatype(cortex, config)
121		-
122	122	display(widget)
123	123	)))
124	124
125	125	{{html}}
126		-<iframe src="https://drive.google.com/file/d/1zrbjdb8Y4V5rqg7Y7LDGlHHMS0RH8luz/preview" width="840" height="480" allow="autoplay"></iframe>
	126	+<iframe width="840" height="480" src="https://www.youtube.com/embed/aDC2TJm2NxM" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
127	127	{{/html}}