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Changes for page Widget 3D Head

Last modified by paulapopa on 2025/05/30 15:03
From version 21.1
edited by paulapopa
on 2023/03/01 17:12
Change comment: There is no comment for this version
To version 25.1
edited by reginafilange
on 2025/05/30 13:47
Change comment: There is no comment for this version

Summary

Details

Page properties
Author
... ... @@ -1,1 +1,1 @@
1 -XWiki.paulapopa
1 +XWiki.reginafilange
Content
... ... @@ -1,20 +1,25 @@
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  
... ... @@ -43,7 +43,6 @@
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" %)
... ... @@ -53,7 +53,7 @@
53 53  )))
54 54  
55 55  {{html}}
56 -<iframe src="https://drive.google.com/file/d/1lY3X5eqJfOLmkmHuBa2iq_Aas8mDPa1e/preview" width="840" height="480" allow="autoplay"></iframe>
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>
57 57  {{/html}}
58 58  
59 59  
... ... @@ -74,13 +74,11 @@
74 74  )))
75 75  
76 76  {{html}}
77 -<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>
78 78  {{/html}}
79 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.
84 +Next, we can continue adding other datatypes to this widget, by calling //**add_datatype**// multiple times.
81 81  
82 -The **Config** object can be used to tweak the display options for each datatype.
83 -
84 84  In the code below, we add a **Connectivity** and SEEG **Sensors:**
85 85  
86 86  (% class="box" %)
... ... @@ -96,36 +96,30 @@
96 96  
97 97  seeg.configure()
98 98  
99 -widget.add_datatype(seeg, api.HeadWidgetConfig(name='SEEG'))
101 +widget.add_datatype(seeg)
100 100  )))
101 101  
102 102  {{html}}
103 -<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>
104 104  {{/html}}
105 105  
106 -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:
107 107  
108 108  (% class="box" %)
109 109  (((
110 110  reg_map = region_mapping.RegionMapping.from_file()
111 111  
112 -config = api.HeadWidgetConfig(name='Cortex')
113 113  
114 -config.add_region_mapping_as_cmap(reg_map)
115 -
116 -
117 117  cortex = surfaces.CorticalSurface().from_file()
118 118  
119 119  cortex.configure()
120 120  
121 121  
122 -widget = api.HeadWidget()
120 +widget.add_datatype(cortex, reg_map)
123 123  
124 -widget.add_datatype(cortex, config)
125 -
126 126  display(widget)
127 127  )))
128 128  
129 129  {{html}}
130 -<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>
131 131  {{/html}}
Public

TVB Widgets