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Changes for page Widget 3D Head

Last modified by paulapopa on 2025/05/30 15:03
From version 23.1
edited by paulapopa
on 2023/03/23 13:16
Change comment: There is no comment for this version
To version 28.1
edited by paulapopa
on 2025/05/30 14:46
Change comment: There is no comment for this version

Summary

Details

Page properties
Content
... ... @@ -9,14 +9,17 @@
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
12 +* connectivity region centers and edges
13 13  * sensors locations (SEEG, MEG, EEG)
14 14  
15 +On cortical surfaces, it can also display region parcellation. 
16 +
15 15  == Inputs ==
16 16  
17 17  It supports the above data in the form of their corresponding TVB datatypes:
18 18  
19 19  * Surface (CorticalSurface, FaceSurface, etc)
22 +* Parcellation (RegionMapping)
20 20  * Connectivity
21 21  * Sensors (SensorsInternal, SensorsMEG, SensorsEEG)
22 22  
... ... @@ -31,15 +31,12 @@
31 31  
32 32  We need to first import the widget __API from tvbwidgets__// //package, together with the __TVB API __and the __display__ function:
33 33  
34 -(% class="box" %)
35 -(((
37 +{{code language="python" layout="LINENUMBERS"}}
36 36  import tvbwidgets.api as api
37 -
38 38  from tvb.simulator.lab import *
40 +from IPython.core.display_functions import display 
41 +{{/code}}
39 39  
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
... ... @@ -47,85 +47,47 @@
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 -(% class="box" %)
51 -(((
50 +{{code language="python" layout="LINENUMBERS"}}
52 52  widget = api.HeadBrowser()
53 53  display(widget)
54 -)))
53 +{{/code}}
55 55  
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>{{/html}}
58 58  
59 -
60 60  For the second option, the API is described below:
61 61  
62 -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:
58 +In a cell, we load the data using the TVB API:
63 63  
64 -(% class="box" %)
65 -(((
66 -widget = api.HeadWidget()
60 +{{code language="python" layout="LINENUMBERS"}}
61 +surface = surfaces.Surface.from_file()
62 +surface.configure()
67 67  
68 -face = surfaces.FaceSurface().from_file()
69 -
64 +face = surfaces.Surface.from_file('face_8614.zip')
70 70  face.configure()
71 71  
72 -widget.add_datatype(face)
73 -display(widget)
74 -)))
67 +reg_map = region_mapping.RegionMapping.from_file()
75 75  
76 -{{html}}
77 -<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>
78 -{{/html}}
79 -
80 -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.
81 -
82 -The **Config** object can be used to tweak the display options for each datatype.
83 -
84 -In the code below, we add a **Connectivity** and SEEG **Sensors:**
85 -
86 -(% class="box" %)
87 -(((
88 -conn = connectivity.Connectivity().from_file()
89 -
69 +conn = connectivity.Connectivity.from_file()
90 90  conn.configure()
91 91  
92 -widget.add_datatype(conn)
93 -
94 -
95 -seeg = sensors.SensorsInternal().from_file()
96 -
72 +seeg = sensors.SensorsInternal.from_file()
97 97  seeg.configure()
74 +{{/code}}
98 98  
99 -widget.add_datatype(seeg, api.HeadWidgetConfig(name='SEEG'))
100 -)))
76 +Then we prepare the **HeadWidget** for display:
101 101  
102 -{{html}}
103 -<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>
104 -{{/html}}
78 +{{code language="python" layout="LINENUMBERS"}}
79 +widget = api.HeadWidget([face, conn, seeg])
80 +display(widget)
81 +{{/code}}
105 105  
106 -We can also provide a **RegionMapping** to be used as colormap for a surface:
83 +[[image:head.png]]
107 107  
108 -(% class="box" %)
109 -(((
110 -reg_map = region_mapping.RegionMapping.from_file()
85 +Next, we can continue adding other datatypes to this widget, by calling //**add_datatype**// multiple times.
111 111  
112 -config = api.HeadWidgetConfig(name='Cortex')
87 +In the code below, we add the **CorticalSurface** with a **RegionMapping** as parcellation**:**
113 113  
114 -config.add_region_mapping_as_cmap(reg_map)
89 +{{code language="python" layout="LINENUMBERS"}}
90 +widget.add_datatype(surface, reg_map)
91 +{{/code}}
115 115  
116 -
117 -cortex = surfaces.CorticalSurface().from_file()
118 -
119 -cortex.configure()
120 -
121 -
122 -widget = api.HeadWidget()
123 -
124 -widget.add_datatype(cortex, config)
125 -
126 -display(widget)
127 -)))
128 -
129 -{{html}}
130 -<iframe src="https://drive.google.com/file/d/1zrbjdb8Y4V5rqg7Y7LDGlHHMS0RH8luz/preview" width="840" height="480" allow="autoplay"></iframe>
131 -{{/html}}
93 +[[image:cort.png]]
conncenters.png
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1 +XWiki.paulapopa
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cort.png
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head.png
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1 +XWiki.reginafilange
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menu.png
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seeg.png
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Public

TVB Widgets