Changes for page Widget 3D Head

Last modified by paulapopa on 2025/05/30 15:03
From version 29.1
edited by paulapopa
on 2025/05/30 14:55
Change comment: There is no comment for this version
To version 10.1
edited by paulapopa
on 2022/04/12 13:27
Change comment: There is no comment for this version

Summary

Details

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Title
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1 -Widget 3D Head
1 +Widget 3D
Content
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1 -Source code: [[https:~~/~~/github.com/the-virtual-brain/tvb-widgets>>https://github.com/the-virtual-brain/tvb-widgets]]
1 +TODO - Not yet released!
2 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 7  == Purpose ==
8 8  
9 -It is a Jupyter widget intended for visualization of the 3D Head data available for a patient:
5 +It is a Jupyter widget intended for visualization of the 3D data available for a patient:
10 10  
11 11  * surfaces of different types (cortex, face, skull, etc)
12 -* connectivity region centers and edges
8 +* connectivity region centers
13 13  * sensors locations (SEEG, MEG, EEG)
14 14  
15 -On cortical surfaces, it can also display region parcellation. 
16 -
17 17  == Inputs ==
18 18  
19 19  It supports the above data in the form of their corresponding TVB datatypes:
20 20  
21 21  * Surface (CorticalSurface, FaceSurface, etc)
22 -* Parcellation (RegionMapping)
23 23  * Connectivity
24 24  * Sensors (SensorsInternal, SensorsMEG, SensorsEEG)
25 25  
... ... @@ -34,77 +34,77 @@
34 34  
35 35  We need to first import the widget __API from tvbwidgets__// //package, together with the __TVB API __and the __display__ function:
36 36  
37 -{{code language="python" layout="LINENUMBERS"}}
30 +(% class="box" %)
31 +(((
38 38  import tvbwidgets.api as api
33 +
39 39  from tvb.simulator.lab import *
40 -from IPython.core.display_functions import display 
41 -{{/code}}
42 42  
43 -Then, there are 2 options to work with the widget:
36 +from IPython.core.display_functions import display
37 +)))
44 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
39 +Then, we instantiate the **SurfaceWidget** 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:
47 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:
41 +(% class="box" %)
42 +(((
43 +widget = api.SurfaceWidget()
49 49  
50 -{{code language="python" layout="LINENUMBERS"}}
51 -widget = api.HeadBrowser()
52 -display(widget)
53 -{{/code}}
45 +face = surfaces.FaceSurface().from_file()
54 54  
47 +face.configure()
55 55  
56 -For the second option, the API is described below:
49 +widget.add_datatype(face)
50 +display(widget)
51 +)))
57 57  
58 -In a cell, we load the data using the TVB API:
53 +{{html}}
54 +<iframe src="https://drive.google.com/file/d/1Egp9Lk-HGMATc9em6Kw_jSHmybTD2vzM/preview" width="840" height="480" allow="autoplay"></iframe>
55 +{{/html}}
59 59  
60 -{{code language="python" layout="LINENUMBERS"}}
61 -surface = surfaces.Surface.from_file()
62 -surface.configure()
57 +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.
63 63  
64 -face = surfaces.Surface.from_file('face_8614.zip')
65 -face.configure()
59 +The **Config** object can be used to tweak the display options for each datatype.
66 66  
67 -reg_map = region_mapping.RegionMapping.from_file()
61 +In the code below, we add a **Connectivity** and SEEG **Sensors:**
68 68  
69 -conn = connectivity.Connectivity.from_file()
63 +(% class="box" %)
64 +(((
65 +conn = connectivity.Connectivity().from_file()
66 +
70 70  conn.configure()
71 71  
72 -seeg = sensors.SensorsInternal.from_file()
73 -seeg.configure()
74 -{{/code}}
69 +widget.add_datatype(conn)
75 75  
76 -Then we prepare the **HeadWidget** for display:
77 77  
78 -{{code language="python" layout="LINENUMBERS"}}
79 -widget = api.HeadWidget([face, conn, seeg])
80 -display(widget)
81 -{{/code}}
72 +seeg = sensors.SensorsInternal().from_file()
82 82  
83 -[[image:head.png]]
74 +seeg.configure()
84 84  
85 -Next, we can continue adding other datatypes to this widget, by calling //**add_datatype**// multiple times.
76 +widget.add_datatype(seeg, api.SurfaceWidgetConfig(name='SEEG'))
77 +)))
86 86  
87 -In the code below, we add the **CorticalSurface** with a **RegionMapping** as parcellation**:**
79 +{{html}}
80 +<iframe src="https://drive.google.com/file/d/1vFqqzXle8VGcHaLB-OdE-6BdetK9aJ1T/preview" width="840" height="480" allow="autoplay"></iframe>
81 +{{/html}}
88 88  
89 -{{code language="python" layout="LINENUMBERS"}}
90 -widget.add_datatype(surface, reg_map)
91 -{{/code}}
83 +We can also provide a **RegionMapping** to be used as colormap for a surface:
92 92  
93 -[[image:cort.png]]
85 +(% class="box" %)
86 +(((
87 +reg_map = region_mapping.RegionMapping.from_file()
94 94  
89 +config = api.SurfaceWidgetConfig(name='Cortex')
95 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:
91 +config.add_region_mapping_as_cmap(reg_map)
97 97  
98 98  
94 +cortex = surfaces.CorticalSurface().from_file()
99 99  
100 -I can rotate the surface and zoom in/out:
96 +cortex.configure()
101 101  
102 -[[image:parcel.png]]
98 +widget.add_datatype(cortex, config)
99 +)))
103 103  
104 -I could also make it transparent to visualize the connectivity centers and their edges:
105 -
106 -[[image:conncenters.png]]
107 -
108 -Also, I can hide the connectivity and display only the SEEG sensors:
109 -
110 -[[image:seeg.png]]
101 +{{html}}
102 +<iframe src="https://drive.google.com/file/d/1z2yEuQWUT2Poxh63adYbBdhKPcWGskex/preview" width="840" height="480" allow="autoplay"></iframe>
103 +{{/html}}
conncenters.png
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head.png
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parcel.png
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Public

TVB Widgets