Wiki source code of Widget 3D Head

Last modified by paulapopa on 2025/05/30 15:03
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1 Source code: [[https:~~/~~/github.com/the-virtual-brain/tvb-widgets>>https://github.com/the-virtual-brain/tvb-widgets]]
2
3 This is part of a Pypi release: [[https:~~/~~/pypi.org/project/tvb-widgets/>>https://pypi.org/project/tvb-widgets/]]
4
5 //**tvb-widgets**// is also already installed in the official image released for EBRAINS lab, where you can test it directly.
6
7 == Purpose ==
8
9 It is a Jupyter widget intended for visualization of the 3D Head data available for a patient:
10
11 * surfaces of different types (cortex, face, skull, etc)
12 * connectivity region centers and edges
13 * sensors locations (SEEG, MEG, EEG)
14
15 On cortical surfaces, it can also display region parcellation. 
16
17 == Inputs ==
18
19 It supports the above data in the form of their corresponding TVB datatypes:
20
21 * Surface (CorticalSurface, FaceSurface, etc)
22 * Parcellation (RegionMapping)
23 * Connectivity
24 * Sensors (SensorsInternal, SensorsMEG, SensorsEEG)
25
26 == Installation ==
27
28 (% class="box" %)
29 (((
30 pip install tvb-widgets
31 )))
32
33 == API usage ==
34
35 We need to first import the widget __API from tvbwidgets__// //package, together with the __TVB API __and the __display__ function:
36
37 {{code language="python" layout="LINENUMBERS"}}
38 import tvbwidgets.api as api
39 from tvb.simulator.lab import *
40 from IPython.core.display_functions import display 
41 {{/code}}
42
43 Then, there are 2 options to work with the widget:
44
45 1. Use a file browser to load the data and automatically display it
46 1. Use directly the API to load the data and display it
47
48 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:
49
50 {{code language="python" layout="LINENUMBERS"}}
51 widget = api.HeadBrowser()
52 display(widget)
53 {{/code}}
54
55
56 For the second option, the API is described below:
57
58 In a cell, we load the data using the TVB API:
59
60 {{code language="python" layout="LINENUMBERS"}}
61 surface = surfaces.Surface.from_file()
62 surface.configure()
63
64 face = surfaces.Surface.from_file('face_8614.zip')
65 face.configure()
66
67 reg_map = region_mapping.RegionMapping.from_file()
68
69 conn = connectivity.Connectivity.from_file()
70 conn.configure()
71
72 seeg = sensors.SensorsInternal.from_file()
73 seeg.configure()
74 {{/code}}
75
76 Then we prepare the **HeadWidget** for display:
77
78 {{code language="python" layout="LINENUMBERS"}}
79 widget = api.HeadWidget([face, conn, seeg])
80 display(widget)
81 {{/code}}
82
83 [[image:head.png]]
84
85 Next, we can continue adding other datatypes to this widget, by calling //**add_datatype**// multiple times.
86
87 In the code below, we add the **CorticalSurface** with a **RegionMapping** as parcellation**:**
88
89 {{code language="python" layout="LINENUMBERS"}}
90 widget.add_datatype(surface, reg_map)
91 {{/code}}
92
93 [[image:cort.png]]
94
95
96 In the upper-right corner, a menu is displayed. This will allow us to control what we want to visualize. For example, I can hide the head in order to get a better view of the cortical surface:
97
98
99
100 I can rotate the surface and zoom in/out:
101
102 [[image:parcel.png]]
103
104 I could also make it transparent to visualize the connectivity centers and their edges, by moving the slider highlighted in red:
105
106 [[image:transp.png]]
107
108 Or, I can hide the connectivity and display only the SEEG sensors:
109
110 [[image:seeg.png]]
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TVB Widgets