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Changes for page Widget 3D Head

Last modified by paulapopa on 2025/05/30 15:03
From version 27.1
edited by paulapopa
on 2025/05/30 14:45
Change comment: There is no comment for this version
To version 24.1
edited by paulapopa
on 2023/03/24 07:58
Change comment: There is no comment for this version

Summary

Details

Page properties
Content
... ... @@ -9,17 +9,14 @@
9 9  It is a Jupyter widget intended for visualization of the 3D Head data available for a patient:
10 10  
11 11  * surfaces of different types (cortex, face, skull, etc)
12 -* connectivity region centers and edges
12 +* 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  
... ... @@ -34,12 +34,15 @@
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"}}
34 +(% class="box" %)
35 +(((
38 38  import tvbwidgets.api as api
37 +
39 39  from tvb.simulator.lab import *
40 -from IPython.core.display_functions import display 
41 -{{/code}}
42 42  
40 +from IPython.core.display_functions import display
41 +)))
42 +
43 43  Then, there are 2 options to work with the widget:
44 44  
45 45  1. Use a file browser to load the data and automatically display it
... ... @@ -47,49 +47,86 @@
47 47  
48 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 49  
50 -{{code language="python" layout="LINENUMBERS"}}
50 +(% class="box" %)
51 +(((
51 51  widget = api.HeadBrowser()
52 52  display(widget)
53 -{{/code}}
54 +)))
54 54  
56 +{{html}}
57 +<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>
58 +{{/html}}
55 55  
60 +
56 56  For the second option, the API is described below:
57 57  
58 -In a cell, we load the data using the TVB API:
63 +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:
59 59  
60 -{{code language="python" layout="LINENUMBERS"}}
61 -surface = surfaces.Surface.from_file()
62 -surface.configure()
65 +(% class="box" %)
66 +(((
67 +widget = api.HeadWidget()
63 63  
64 -face = surfaces.Surface.from_file('face_8614.zip')
69 +face = surfaces.FaceSurface().from_file()
70 +
65 65  face.configure()
66 66  
67 -reg_map = region_mapping.RegionMapping.from_file()
73 +widget.add_datatype(face)
74 +display(widget)
75 +)))
68 68  
69 -conn = connectivity.Connectivity.from_file()
77 +{{html}}
78 +<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>
79 +{{/html}}
80 +
81 +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.
82 +
83 +The **Config** object can be used to tweak the display options for each datatype.
84 +
85 +In the code below, we add a **Connectivity** and SEEG **Sensors:**
86 +
87 +(% class="box" %)
88 +(((
89 +conn = connectivity.Connectivity().from_file()
90 +
70 70  conn.configure()
71 71  
72 -seeg = sensors.SensorsInternal.from_file()
93 +widget.add_datatype(conn)
94 +
95 +
96 +seeg = sensors.SensorsInternal().from_file()
97 +
73 73  seeg.configure()
74 -{{/code}}
75 75  
76 -Then we prepare the **HeadWidget** for display:
100 +widget.add_datatype(seeg, api.HeadWidgetConfig(name='SEEG'))
101 +)))
77 77  
78 -{{code language="python" layout="LINENUMBERS"}}
79 -widget = api.HeadWidget([face, conn, seeg])
80 -display(widget)
81 -{{/code}}
103 +{{html}}
104 +<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>
105 +{{/html}}
82 82  
83 -[[image:head.png]]
107 +We can also provide a **RegionMapping** to be used as colormap for a surface:
84 84  
85 -Next, we can continue adding other datatypes to this widget, by calling //**add_datatype**// multiple times.
109 +(% class="box" %)
110 +(((
111 +reg_map = region_mapping.RegionMapping.from_file()
86 86  
87 -In the code below, we add the **CorticalSurface** with a **RegionMapping** as parcellation**:**
113 +config = api.HeadWidgetConfig(name='Cortex')
88 88  
89 -{{code language="python" layout="LINENUMBERS"}}
90 -widget.add_datatype(surface, reg_map)
91 -{{/code}}
115 +config.add_region_mapping_as_cmap(reg_map)
92 92  
117 +
118 +cortex = surfaces.CorticalSurface().from_file()
119 +
120 +cortex.configure()
121 +
122 +
123 +widget = api.HeadWidget()
124 +
125 +widget.add_datatype(cortex, config)
126 +
127 +display(widget)
128 +)))
129 +
93 93  {{html}}
94 94  <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>
95 95  {{/html}}
conncenters.png
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cort.png
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head.png
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menu.png
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parcel.png
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seeg.png
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Public

TVB Widgets